+ 186 20.9 0.0 0.0 INTRON_3 1248 1290 (398891) + (TG)n Simple_repeat 2 44 (0) 1
ANNOTATION EVIDENCE:
186 20.93 0.00 0.00 INTRON_3 1248 1290 398891 C (CA)n Simple_repeat 138 180 0 100
INTRON_3 1248 TGTGCATGTGTGTGTGTGTATAAATACGTGCGTGTGTGTGTGT 1290
ii i ivi ii i
C (CA)n#Simple_ 180 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 138
Matrix = Unknown
Transitions / transversions = 8.00 (8 / 1)
Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0)
+ 2363 8.7 0.3 0.0 INTRON_3 3193 3481 (396700) C AluSx4 SINE/Alu (22) 290 1 2
ANNOTATION EVIDENCE:
2234 9.69 0.69 0.00 INTRON_3 3193 3481 396700 C AluSx SINE/Alu 1 291 21 0
INTRON_3 3193 TTTTTTTCTGAGACAGAGTCTTGCTCTGTCACCCAGGCTGGAGTGCAGTG 3242
i i i i
C AluSx#SINE/Al 291 TTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTG 242
INTRON_3 3243 GCACAATCTCGGCTCACTGCAAGCTCCGCCTCCTGGGTTCAAGCGATTCT 3292
i i v i
C AluSx#SINE/Al 241 GCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCT 192
INTRON_3 3293 TCTGCCTCAGCCTCCGGAGTAGCTGGGACCACAGGCAAATGCCACCACAT 3342
i v ii ivii ii
C AluSx#SINE/Al 191 CCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGC 142
INTRON_3 3343 CCGGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATATTGGCC 3392
i i
C AluSx#SINE/Al 141 CCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCC 92
INTRON_3 3393 AGGGTGGTCTCAAACTCCTGACCTT--GTGATCCGCCCACCTCGGCCTCC 3440
v i i-- i
C AluSx#SINE/Al 91 AGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCC 42
INTRON_3 3441 CAGAGTGCTGGGATTAAAGGCGTGAGCCACCGCACCCAGCC 3481
i v i i
C AluSx#SINE/Al 41 CAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 4.60 (23 / 5)
Gap_init rate = 0.00 (1 / 288), avg. gap size = 2.00 (2 / 1)
+ 30 60.0 0.0 0.0 INTRON_3 4774 4803 (395378) + AT_rich Low_complexity 1 30 (0) 3
ANNOTATION EVIDENCE:
30 60.00 0.00 0.00 INTRON_3 4774 4803 395378 + AT_rich Low_complexity 140 169 131 46
INTRON_3 4774 ATTAATTTTTATTATTTATTTATTTAAAAT 4803
vvv v v v vvvv v ???????
AT_rich#Low_c 140 ATTAAAAATAAATAATATAATTTWWWWWWW 169
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 11)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 3319 13.4 1.0 0.0 INTRON_3 4805 5325 (394856) C L1PB3 LINE/L1 (10) 6144 5619 4
ANNOTATION EVIDENCE:
3319 13.44 0.96 0.00 INTRON_3 4805 5325 394856 C L1PB3_3end LINE/L1 366 891 10 17
INTRON_3 4805 TCAACAGCTTTAGGGGTACAAGTGGTTTTTGGTTTTATGGATGAATTGTA 4854
i vi
C L1PB3_3end#LI 891 TCAATAGCTTTAGGGGTACAAGTGGTTTTTGGTTACATGGATGAATTGTA 842
INTRON_3 4855 TAGTGATGAAGTCTGAGTTTTTAGTGCACCCGTCACTTGAGTAGTGTACA 4904
i i v i ii
C L1PB3_3end#LI 841 TAGTGGTGAAGTCTGGGATTTTAGTGCACCCATCACCCGAGTAGTGTACA 792
INTRON_3 4905 TTCTACCCAATATCTAGTTTTTTGTTTTTCTCCTTTCTCCC--CCTTCT- 4951
v vv ii iii v iii -- i i-
C L1PB3_3end#LI 791 TTGTACCCAATAGGTAGTTTTTCATCCCTCACCCCCCTCCCACCCTCCCC 742
INTRON_3 4952 GCTTCTGAGTCTCCAGTGTCCATTATACCACTCTGTATGCCTTTGCAAAC 5001
? i iv
C L1PB3_3end#LI 741 NCTTCTGAGTCTCCAATGTCCATTATACCACTCTGTATGCCTTTGCGTAC 692
INTRON_3 5002 CCATAGCTTAGCTCTCTCTTATAAGTGAGAATATACATTATTTGGTTTTC 5051
i v i i iv
C L1PB3_3end#LI 691 CCATAGCTTAGCTCCCACTTATAAGTGAGAACATGCGGTATTTGGTTTTC 642
INTRON_3 5052 CATTCCTGAGTTACTGCACTTAGAGTAATGGACTCCAGCTCCCTGGAAGT 5101
v ii v i v vv
C L1PB3_3end#LI 641 CATTCCTGAGTTACTTCACTTAGGATAATGGCCTCCAGTTCCATCCAAGT 592
INTRON_3 5102 TGCTGAAAAAGACATCATTTTATTCTTTGTTATGGCTGAGTAGTATTTCA 5151
v i ii v i
C L1PB3_3end#LI 591 TGCTGCAAAAGACATTATTTCGTTCTTTTTTATGGCTGAGTAGTATTCCA 542
INTRON_3 5152 TGGTATATATGTCCCA--TTTTCTTTATCCACTTATTGATTGATGGGCCC 5199
i i v -- i i i v
C L1PB3_3end#LI 541 TGGTGTATATATACCACATTTTCTTTATCCACTCATCGGTTGATGGGCAC 492
INTRON_3 5200 TTAGGGTGGTTCCAAATCTTTACAATTGTAAATTGTGCTGCAATAAACAT 5249
v i v i i i
C L1PB3_3end#LI 491 TTAGGTTGATTCCATATCTTTGCAATTGTGAATTGTGCTGCGATAAACAT 442
INTRON_3 5250 ATATGTGAAGGTGTCTTTTTGATATAGTGGCTTCTTTTCCTTTAGGTAGA 5299
iii v i i i
C L1PB3_3end#LI 441 ACGCGTGCAGGTGTCTTTTTGATATAATGACTTCTTTTCCTTTGGGTAGA 392
INTRON_3 5300 TACCCAGTAGTGAGATTGTTGGATTG 5325
i i i
C L1PB3_3end#LI 391 TACCCAGTAGTGGGATTGCTGGATCG 366
Matrix = 18p37g.matrix
Transitions / transversions = 2.29 (48 / 21)
Gap_init rate = 0.01 (3 / 520), avg. gap size = 1.67 (5 / 3)
+16560 10.3 1.1 0.8 INTRON_3 5355 11796 (388385) C L1PA7 LINE/L1 (21) 6448 1 5
ANNOTATION EVIDENCE:
6943 6.26 0.11 0.11 INTRON_3 5355 6234 393947 C L1PA7_3end LINE/L1 1 880 21 51
INTRON_3 5355 TTAATTTCTGGGGTACATGTGCAGAACATGCAGTTTTGTTACATAGATAT 5404
v i i v i
C L1PA7_3end#LI 880 TTAAGTTCTGGGATACATGTGCAGAACGTGCAGGTTTGTTACATAGGTAT 831
INTRON_3 5405 ACACATGCCATGGCGGCTTGCTCCACCCATCAACCTGTCACCTACATTAG 5454
i i i v i i
C L1PA7_3end#LI 830 ACACGTGCCATGGTGGTTTGCTGCACCCATCAACCCGTCATCTACATTAG 781
INTRON_3 5455 GTATTTCTCCTAATGTTATCCCTCCCCTAGCCCCCCATCGCCCAAAAGGC 5504
i i v i v
C L1PA7_3end#LI 780 GTATTTCTCCTAATGCTATCCCTCCCCTAGCCCCCCACCCCCCGACAGGC 731
INTRON_3 5505 CCTGGTGTGTGATGTTCCCATCCCTATGTCCATGTGTTGTCATTGTTCAA 5554
i v i v
C L1PA7_3end#LI 730 CCCGGTGTGTGATGTTCCCCTCCCTGTGTCCATGTGTTCTCATTGTTCAA 681
INTRON_3 5555 CTCCCACTTATGAGTGAGAACATGCGGTGTTTGGTTTTCTGTTCTTGTGA 5604
i v
C L1PA7_3end#LI 680 CTCCCACTTATGAGTGAGAACATGCGGTGTTTGGTTTTCTGTTCCTGTGT 631
INTRON_3 5605 TAGTTTTCTGAGAATGATGGTTTCCAGCTTCATCCATGTCCCTGCAAAGG 5654
v
C L1PA7_3end#LI 630 TAGTTTGCTGAGAATGATGGTTTCCAGCTTCATCCATGTCCCTGCAAAGG 581
INTRON_3 5655 ACATGAACTCATCCTTTTTTTATGGCTGCATAGTATTCCATGGTGTATAT 5704
-
C L1PA7_3end#LI 580 ACATGAACTCATCCTTTTTT-ATGGCTGCATAGTATTCCATGGTGTATAT 532
INTRON_3 5705 GTGCCACATTTTCTTTATACAGTCTATTATGGATGGACAATTGGGTTGGT 5754
v i v i v
C L1PA7_3end#LI 531 GTGCCACATTTTCTTTATCCAGTCTATCATTGATGGGCATTTGGGTTGGT 482
INTRON_3 5755 TCCAAGTCTTTCCTATTGTAAATAGTGCCACAATAAACATGTGTGTGCAT 5804
v i i ii ii
C L1PA7_3end#LI 481 TCCAAGTCTTTGCTATTGTGAACAGTGCTGCAATAAACATACGTGTGCAT 432
INTRON_3 5805 GTGTCTTTATAGTAGAATGATTTATAATCCTTTGGGTATATACCCAGTAA 5854
C L1PA7_3end#LI 431 GTGTCTTTATAGTAGAATGATTTATAATCCTTTGGGTATATACCCAGTAA 382
INTRON_3 5855 TGGGATTGCTGGGTCAAATGGTGTTTCTGGTTCTAGATCCTTGAGGAATT 5904
i i
C L1PA7_3end#LI 381 TGGGATTGCTGGGTCAAATGGTATTTCTGGTTCTAGATCCTTGAGGAATC 332
INTRON_3 5905 GCCACACTGTCTTCCACAATGGTTGAACTAATTTACACTCCCACCAACAG 5954
C L1PA7_3end#LI 331 GCCACACTGTCTTCCACAATGGTTGAACTAATTTACACTCCCACCAACAG 282
INTRON_3 5955 TGTAAAAGCATTCCTATTTCTCCATATTCTCTCCAGCATTTCTTGTTTCC 6004
i i i i v
C L1PA7_3end#LI 281 TGTAAAAGCGTTCCTATTTCTCCACATCCTCTCCAGCATCTGTTGTTTCC 232
INTRON_3 6005 TGACTTTTCAATGATCACCATTCTAACTGGCGTGAGATGGTATCCCATTG 6054
i i i
C L1PA7_3end#LI 231 TGACTTTTTAATGATCGCCATTCTAACTGGCGTGAGATGGTATCTCATTG 182
INTRON_3 6055 TGGTTTTGATTTGCATTTCTCCAATGACCAGTGATGATGAGCATTTTTTC 6104
i v
C L1PA7_3end#LI 181 TGGTTTTGATTTGCATTTCTCTAATGACCAGTGATGATGAGCTTTTTTTC 132
INTRON_3 6105 ATATGTCTGTTAGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCAT 6154
i i i
C L1PA7_3end#LI 131 ATATGTTTGTTGGCCGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCAT 82
INTRON_3 6155 ATTCTTTGCCTACTTTTTGATGGGGTTGTTTGTTTTTT-CTTGTAAATTT 6203
i i i -
C L1PA7_3end#LI 81 ATCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTT 32
INTRON_3 6204 GTTTAAGTTCTTTGTAGATTCTGGATGTTAG 6234
i i
C L1PA7_3end#LI 31 GTTTAAGTTCCTTGTAGATTCTGGATATTAG 1
Matrix = 20p37g.matrix
Transitions / transversions = 2.67 (40 / 15)
Gap_init rate = 0.00 (2 / 879), avg. gap size = 1.00 (2 / 2)
16560 8.89 0.21 0.13 INTRON_3 6086 8428 391753 C L1P3_orf2 LINE/L1 950 3294 0 52
INTRON_3 6086 TGATGATGAGCATTTTTTCATATGTCTGTTAGCTGCATAAATGTCTTCTT 6135
v v i i i
C L1P3_orf2#LIN 3294 TGATGTTGAGCTTTTTTTCATATGTTTGTTGGCCGCATAAATGTCTTCTT 3245
INTRON_3 6136 TTGAGAAGTGTCTGTTCATATTCTTTGCCTACTTTTTGATGGGGTTGTTT 6185
i i i i
C L1P3_orf2#LIN 3244 TTGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAATGGGGTTGTTT 3195
INTRON_3 6186 GTTTTTT-CTTGTAAATTTGTTTAAGTTCTTTGTAGATTCTGGATGTTAG 6234
- i i
C L1P3_orf2#LIN 3194 GTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAGATTCTGGATATTAG 3145
INTRON_3 6235 CCCTTTGTCAGATGGATAGATTGCAAAAATTTTCTCCCGTTCTGTAGGTT 6284
v i
C L1P3_orf2#LIN 3144 ACCTTTGTCAGATGGATAGATTGCAAAAATTTTCTCCCATTCTGTAGGTT 3095
INTRON_3 6285 GCCTGTTCACTTTGATAATAGTTTCTTTTGCTGTGCAGAAGCTCTTGAGT 6334
i i i v
C L1P3_orf2#LIN 3094 GTCTGTTCACTCTGATGATAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGT 3045
INTRON_3 6335 TTAATTGGATCCCATTTGTCAATTTTGGTTTTTGTTGCCAGTGCTTTTCG 6384
i v i v v v
C L1P3_orf2#LIN 3044 TTAATTAGATCCCATTTGTCAATTTTTGCTTTTGTTGCAATTGCTTTTGG 2995
INTRON_3 6385 TGTTTTAGACATGAAGTCTTTGCCCATGCCTACGTCCTGAATGGTATTGC 6434
i viv i i i
C L1P3_orf2#LIN 2994 CGTTTTCATCATGAAATCTTTGCCCGTGCCTATGTCCTGAATGGTATTGC 2945
INTRON_3 6435 CCAGGTTTTCTTCTAGGATTTTTAAGGTCCCAGGTCTTACATTTAAGTAT 6484
i i i vi iiii i v
C L1P3_orf2#LIN 2944 CTAGATTTTCTTCTAGGGTTTTTATAGTTTTGGGTTTTACATTTAAGTCT 2895
INTRON_3 6485 TTGTTCCATCTTGAGTTGATTTTTGTATAAGGTGTAAGTAAGGGGTCCAG 6534
iv i v
C L1P3_orf2#LIN 2894 TTAATCCATCTTGAGTTAATTTTTGTATAAGGTGTAAGGAAGGGGTCCAG 2845
INTRON_3 6535 TTTCAGTTTTATGCATATGGCTAGCCAGTTTTCCCAACA---TTTATTAA 6581
i v i i ---
C L1P3_orf2#LIN 2844 TTTCAATTTTCTGCATATGGCTAGCCAGTTCTCCCAGCACCATTTATTAA 2795
INTRON_3 6582 ATAGGGAATCTTTTCCCCATTGCTTGTTTGTGTCAGGTTTGTTAAAGATC 6631
i v ii
C L1P3_orf2#LIN 2794 ATAGGGAATCCTTTCCCCATTGCTTGTTTTTGTCAGGTTTGTCGAAGATC 2745
INTRON_3 6632 AGATGGTTGTAGATGTGTGGTGTTATTTCTGAGGCCTCTGTTCTTTTCCA 6681
i v ?i i v
C L1P3_orf2#LIN 2744 AGATGGTTGTAGATGTGCGGTCTTATTTCTGAGNTCTCTATTCTGTTCCA 2695
INTRON_3 6682 TTGGTCTATATATCTGTTTTGGTACCAGTACCATGCTGTTTTGGTTACTG 6731
i i v
C L1P3_orf2#LIN 2694 TTGGTCTATGTGTCTGTTTTTGTACCAGTACCATGCTGTTTTGGTTACTG 2645
INTRON_3 6732 TAGCCTTGTAGTATAATTTGAAGTCAGGTAGCATGATGCCTCCAGCTTTG 6781
i i i
C L1P3_orf2#LIN 2644 TAGCCTTGTAGTATAGTTTGAAGTCGGGTAGCGTGATGCCTCCAGCTTTG 2595
INTRON_3 6782 TTCTTGTTGCTCAGGATTGTCTTAGCCCTGTGGGCTCTTTTTTGGTTTCA 6831
v i i iv ii i
C L1P3_orf2#LIN 2594 TTCTTTTTGCTTAGGATTGTCTTGGCTATACGGGCTCTTTTTTGGTTCCA 2545
INTRON_3 6832 TATGCAGTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGTCAGTGGTA 6881
v v i v i
C L1P3_orf2#LIN 2544 TATGAATTTTAAAGTAGTTTTTTCTAATTCTGTGAAGAATGTCAATGGTA 2495
INTRON_3 6882 GCTTGATGGGGATATAGCATTGAATCTATAAATTACTTTGGGCAGTATGG 6931
i i i --
C L1P3_orf2#LIN 2494 GTTTAATGGGAATA--GCATTGAATCTATAAATTACTTTGGGCAGTATGG 2447
INTRON_3 6932 CCATTTTCACGATATTGATTCTTCCTATCCATAAGCATGGAATGTTTTTC 6981
i
C L1P3_orf2#LIN 2446 CCATTTTCACGATATTGATTCTTCCTATCCATGAGCATGGAATGTTTTTC 2397
INTRON_3 6982 CATTTGTTTGTGTCGTCTTTTATTTCACTGAGCAGTGGTTTGTAGTTCTC 7031
v i v vi
C L1P3_orf2#LIN 2396 CATTTGTTTGTGTCCTCTCTGATTTCCTTGAGCAGTGGTTTGTAGTTCTC 2347
INTRON_3 7032 CTTGAAGAGGTACTTCACATCCCTTGTAAGTTGGACTCCTAGGTATTTTA 7081
v v v i v i
C L1P3_orf2#LIN 2346 CTTGAAGAGGTCCTTCACTTCCCTTGTTAGCTGTATTCCTAGGTATTTTA 2297
INTRON_3 7082 TTCTCTTAGTAGCAATTGTGAATGGGAGTTCATTCATGATTTGGCTCTCT 7131
v
C L1P3_orf2#LIN 2296 TTCTCTTTGTAGCAATTGTGAATGGGAGTTCATTCATGATTTGGCTCTCT 2247
INTRON_3 7132 GTTTGTCTATTATTGGTGTATAGGAATGCTTGTGATTTTTGCACATTGAT 7181
i i i
C L1P3_orf2#LIN 2246 GCTTGTCTGTTGTTGGTGTATAGGAATGCTTGTGATTTTTGCACATTGAT 2197
INTRON_3 7182 TTTGTATCCTGAGACCTTACTGAAGTTGCTTATCAGCTTAAGGAGATTTT 7231
i i i v
C L1P3_orf2#LIN 2196 TTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGAAGCTTTT 2147
INTRON_3 7232 GGGCTGAGAAGATGGGGTTTTCTAAATATACAATCATGTCATCTGCAAAC 7281
v i vi
C L1P3_orf2#LIN 2146 GGGCTGAGACGATGGGGTTTTCTAGATATAGGATCATGTCATCTGCAAAC 2097
INTRON_3 7282 AGAGACAATTTGACTTCCTCTCTTCCTATTTGAATACGCTTTATTTCTTT 7331
v
C L1P3_orf2#LIN 2096 AGAGACAATTTGACTTCCTCTCTTCCTATTTGAATACCCTTTATTTCTTT 2047
INTRON_3 7332 CTTTTGCCTGATTGTCCTAGCCAGAACTTCCAATAGTATGTTGAGTAGGA 7381
i i i v i
C L1P3_orf2#LIN 2046 CTCTTGCCTGATTGCCCTGGCCAGAACTTCCAATACTATGTTGAATAGGA 1997
INTRON_3 7382 GTGGTTAGAGAGGGCTTCCTTGTCTTTCGCTGGTTTTCAAAGGGAATACT 7431
v v vi i i i
C L1P3_orf2#LIN 1996 GTGGTGAGAGAGGGCATCCTTGTCTTGTGCCGGTTTTCAAGGGGAATGCT 1947
INTRON_3 7432 TCTAGTTTTTGCCCATTCAGTATGATATTGGTTGTGGATTTGTCATAAGT 7481
i i i i i
C L1P3_orf2#LIN 1946 TCCAGCTTTTGCCCATTCAGTATGATATTGGCTGTGGGTTTGTCATAAAT 1897
INTRON_3 7482 AGCTCTTATTATTTTGAGATATGTTCCATCAATACCCAGTTTATTGAGAG 7531
i i ? i
C L1P3_orf2#LIN 1896 GGCTCTTATTATTTTGAGGTATGTTCCNTCAATACCTAGTTTATTGAGAG 1847
INTRON_3 7532 ATTTTAGCATGAAGGGGTGTTGAATTTTGTCAAAGGCCTTTTCTGCATCT 7581
v i i i i i
C L1P3_orf2#LIN 1846 TTTTTAACATGAAGGGATGTTGAATTTTATCGAAGGCCTTTTCTGCGTCT 1797
INTRON_3 7582 ATTGAGATAATCATGTGGTTTTTGTGATTGGTTCTGTTCATGTGGTGGAT 7631
vv i i i i
C L1P3_orf2#LIN 1796 ATTGAGATAATCATGTGGTTTTTGTCTTTAGTTCTGTTTATGTGATGAAT 1747
INTRON_3 7632 TACGTTTATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCAGGGATGA 7681
i
C L1P3_orf2#LIN 1746 TACGTTTATTGATTTGCGTATGTTGAACCAGCCTTGCATCCCGGGGATGA 1697
INTRON_3 7682 AGCCGACTTGATCGTGGTGGATAAGCTTTTGGATGTGCTGCTGGATTCGG 7731
v
C L1P3_orf2#LIN 1696 AGCCGACTTGATCGTGGTGGATAAGCTTTTTGATGTGCTGCTGGATTCGG 1647
INTRON_3 7732 TTTGCCAGTATTTTATTGAGGATTTTCGCATCGATGTTCATCAGGGATAT 7781
i
C L1P3_orf2#LIN 1646 TTTGCCAGTATTTTATTGAGGATTTTTGCATCGATGTTCATCAGGGATAT 1597
INTRON_3 7782 TGGCCTGAAATTTTCTTTTTTTGTTGTGTCTCTGCCAGGCTTTGGTATCA 7831
i i i
C L1P3_orf2#LIN 1596 TGGCCTGAAGTTTTCTTTTTTTGTTGTATCTCTGCCAGGTTTTGGTATCA 1547
INTRON_3 7832 GGATGATGCTGGGCTCATAAAATGAGTTAGGGAGGATTCCCTCTTTTTCT 7881
v v i v
C L1P3_orf2#LIN 1546 GGATGATGCTGGCCTCATAAAATGAGTTAGGGAGGAGTCCCTCCTTTTCA 1497
INTRON_3 7882 GTTGTTTGGAGTAGTTTCAGAAGGAATGGTACCTGTTCCTCTTTGTACCT 7931
i i i v i
C L1P3_orf2#LIN 1496 ATTGTTTGGAATAGTTTCAGAAGAAATGGTACCAGCTCCTCTTTGTACCT 1447
INTRON_3 7932 CTGGTAGAATTCGGCTGTGAATCTGTCTGGTCCTCAACGTTTTTTTGGTT 7981
i i i vii -
C L1P3_orf2#LIN 1446 CTGGTAGAATTCAGCTGTAAATCCGTCTGGTCCTGGGC-TTTTTTTGGTT 1398
INTRON_3 7982 GGTAGGCTATTAATTACTGCTTCAATTTCCGAACTTATTATTGGTTTTTT 8031
v i v i i v
C L1P3_orf2#LIN 1397 GGTAGGCTATTTATTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATT 1348
INTRON_3 8032 CAGAGATTCGACTTCTTCCTGGTTTAGACTTGGGAGGGTGTATGTGTCTA 8081
i i i v i
C L1P3_orf2#LIN 1347 CAGGGATTCAACTTCTTCCTGGTTCAGTCTTGGGAGGGTGTATGTGTCCA 1298
INTRON_3 8082 GGAATTTATCCATTTCTTCTAGATTTTCCAGTTTATTTGCGTAGAGGTGT 8131
i i
C L1P3_orf2#LIN 1297 GGAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCATAGAGGTGT 1248
INTRON_3 8132 TTATAATATTCTCTGATGGTAGTTCGTATTTCTGTGGGATCGGTGGTGAT 8181
i v i i i
C L1P3_orf2#LIN 1247 TTATAGTATTCTCTGATGGTTGTTTGTATTTCTGTGGGGTCAGTGGTGAT 1198
INTRON_3 8182 ATCACCTATATCATTTTTTATTGTGCCTATTTGATTCTTCTCTCTTTTTT 8231
v v i i
C L1P3_orf2#LIN 1197 ATCCCCTTTATCATTTTTTATTGTGTCTATTTGATTCTTCTCTCTTTTCT 1148
INTRON_3 8232 TCTGTATTAGCCTGGCTAGTGGTCTATGTATTTTGTTGATGTTTTCAAAA 8281
v i i i v i i v
C L1P3_orf2#LIN 1147 TCTTTATTAGTCTAGCTAGCGGTCTATCTATTTTATTAATTTTTTCAAAA 1098
INTRON_3 8282 AAC-AGCTCCTGGATTCATTGATTTTTTGAAGGGTTTTTCATGTCTCTAT 8330
- i
C L1P3_orf2#LIN 1097 AACCAGCTCCTGGATTCATTGATTTTTTGAAGGGTTTTTCGTGTCTCTAT 1048
INTRON_3 8331 CTCCCTCAGTTCTGCTCTGGTCTTGGTTATTACTTGTCTTCCCTTAAATT 8380
i i i v ivi iv
C L1P3_orf2#LIN 1047 CTCCTTCAGTTCCGCTCTGATCTTGGTTATTTCTTGTCTTCTGCTAGCTT 998
INTRON_3 8381 TTGAATTTGTTTGCTGTTGCTTCTCTAATTCTTTTAATTTTGATGTTA 8428
v ii v v i i v
C L1P3_orf2#LIN 997 TGGGGTTTGTTTGCTCTTGGTTCTCTAGTTCTTTTAGTTGTGATGTTA 950
Matrix = 20p37g.matrix
Transitions / transversions = 2.12 (140 / 66)
Gap_init rate = 0.00 (5 / 2342), avg. gap size = 1.60 (8 / 5)
7876 13.01 1.61 3.12 INTRON_3 7971 9399 390782 C L1P1_orf2 LINE/L1 1 1408 1886 53
INTRON_3 7971 TTTTTTTGGTTGGTAGGCTATTAATTACTGCTTCAATTTCCGAACTTATT 8020
i ii i i iv v i i i
C L1P1_orf2#LIN 1408 TCTTTTTGGTTGGTAAACTATTGATTATTGCCACAATTTCAGAGCCTGTT 1359
INTRON_3 8021 ATTGGTTTTTTCAGAGATTCGACTTCTTCCTGGTTTAGACTTGGGAGGGT 8070
i v i v i
C L1P1_orf2#LIN 1358 ATTGGTCTATTCAGAGATTCAACTTCTTCCTGGTTTAGTCTTGGGAGAGT 1309
INTRON_3 8071 GTATGTGTCTAGGAATTTATCCATTTCTTCTAGATTTTCCAGTTTATTTG 8120
v v i
C L1P1_orf2#LIN 1308 GTATGTGTCGAGGAATGTATCCATTTCTTCTAGATTTTCTAGTTTATTTG 1259
INTRON_3 8121 CGTAGAGGTGTTTATAATATTCTCTGATGGTAGTTCGTATTTCTGTGGGA 8170
i i i
C L1P1_orf2#LIN 1258 CGTAGAGGTGTTTGTAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGA 1209
INTRON_3 8171 TCGGTGGTGATATCACCTATATCATTTTTTATTGTGCCTATTTGATTCTT 8220
v v i
C L1P1_orf2#LIN 1208 TCGGTGGTGATATCCCCTTTATCATTTTTTATTGTGTCTATTTGATTCTT 1159
INTRON_3 8221 CTCTCTTTTTTTCTGTATTAGCCTGGCTAGTGGTCTATGTATTTTGTTGA 8270
v i v i vv
C L1P1_orf2#LIN 1158 CTCTCTTTTTTTCTTTATTAGTCTTGCTAGCGGTCTATCAATTTTGTTGA 1109
INTRON_3 8271 TGTTTTCAAAAAACAGCTCCTGGATTCATTGATT---TTTTGAAGGGTTT 8317
vi vivii iv i--- v --- vi i v
C L1P1_orf2#LIN 1108 TCCTTTCAAAAAACCAGCTCCTGG---ATTCATTGATTTTTTGAAGGGTT 1062
INTRON_3 8318 TTCATGTCTCTATCTCCCTCAGTTCTGCTCTGGTCTTGGTTATTACTTGT 8367
i- v v v ii i--- v i v - i - v i
C L1P1_orf2#LIN 1061 TTT-TGTGTCTCTATTTCC---TTCAGTTCTGCTCT-GATT-TTAGTTAT 1018
INTRON_3 8368 --CTTCCCTTAAATTTTGAATTTGTTTGCTGTTGCTTCTCTAATTCTTTT 8415
-- v -----------i i v v ------- viv
C L1P1_orf2#LIN 1017 TTCTTGCCTT-----------CTGCTAGCTTTTG-------AATGTGTTT 986
INTRON_3 8416 AATTTTGATGTTAAAATTAAAAGAATTAAATATTAAATTAAAAGAATTTA 8465
iv i v v vv i -------i ----- v iv-- vv
C L1P1_orf2#LIN 985 GCTCTTGCTTTTCTAGTT-------CT-----TTTAATTGT--GATGTTA 950
INTRON_3 8466 AATTGTTTTAATTTTTTATCTTTCCTGCTTTCTCTTGTGGGCATTTAGTG 8515
iiv i-- vv i
C L1P1_orf2#LIN 949 GGGTGTC--AATTTTGGATCTTTCCTGCTTTCTCTTGTAGGCATTTAGTG 902
INTRON_3 8516 TTATAAATTTCTCTGTACACACTGCTTTAAATGTGTCCCAGAGATTCTGG 8565
i i v i i
C L1P1_orf2#LIN 901 CTATAAATTTCCCTCTACACACTGCTTTGAATGCGTCCCAGAGATTCTGG 852
INTRON_3 8566 TATGTTGTGTCTTCGTTCTCATTGGTTTCAAAGAATGTCTTTACTTCTGC 8615
v i i ii i
C L1P1_orf2#LIN 851 TATGTGGTGTCTTTGTTCTCGTTGGTTTCAAAGAACATCTTTATTTCTGC 802
INTRON_3 8616 CTTCATTTAGTTATTTACCCAGTAGTCATTCAGGAGCAGGTTGTTTAGTT 8665
v v i
C L1P1_orf2#LIN 801 CTTCATTTCGTTATGTACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTT 752
INTRON_3 8666 TCCATGTAGTTG--------TGAGTGAGTTTCTTAATCCTGAGTTCTAGT 8707
-------- v
C L1P1_orf2#LIN 751 TCCATGTAGTTGAGCGGCTTTGAGTGAGATTCTTAATCCTGAGTTCTAGT 702
INTRON_3 8708 TTGATTGCACTGTGGTCTGAGAGACTGTTTGTTATGATTTCTGTTCTTTT 8757
iv i
C L1P1_orf2#LIN 701 TTGATTGCACTGTGGTCTGAGAGATAGTTTGTTATAATTTCTGTTCTTTT 652
INTRON_3 8758 GCATCTGCTGAGGAGTGTTTTACTTCCAATTATGTGGTCAATTTTAGAAT 8807
i i v i i i
C L1P1_orf2#LIN 651 ACATTTGCTGAGGAGAGCTTTACTTCCAACTATGTGGTCAATTTTGGAAT 602
INTRON_3 8808 AAGTGTGATGTGGTGCTGAGAATGATGTATATTCTGTTGATTTGGGGTGG 8857
i i i vi
C L1P1_orf2#LIN 601 AGGTGTGGTGTGGTGCTGAAAAAAATGTATATTCTGTTGATTTGGGGTGG 552
INTRON_3 8858 AGAGTTCTGGAGATGTCTATTAGGTCTTCTTGGCCCAGAGCTGAATTCAA 8907
v v iv i
C L1P1_orf2#LIN 551 AGAGTTCTGTAGATGTCTATTAGGTCTGCTTGGTGCAGAGCTGAGTTCAA 502
INTRON_3 8908 GTCCTGAATATCTTTGTTAATTTTCTGTCTCATTGATCTGTCTAATATTG 8957
v ii i i i i i
C L1P1_orf2#LIN 501 TTCCTGGGTATCCTTGTTGACTTTCTGTCTCGTTGATCTGTCTAATGTTG 452
INTRON_3 8958 ACAGTGGGGTGTTAAAGTCTCCCGACTGTTATTGTGTGGGAGTCTACATC 9007
- i i v vi
C L1P1_orf2#LIN 451 ACAGTGGGGTGTTAAAGTCTCCC-ATTATTAATGTGTGGGAGTCTAAGTC 403
INTRON_3 9008 TCTTTGTAGGTCTCTAAGAACTTGCT----------GAGTGTTCTTGTAT 9047
v ? i ---------- i i i
C L1P1_orf2#LIN 402 TCTTTGTAGGTCACTWAGGACTTGCTTTATGAATCTGGGTGCTCCTGTAT 353
INTRON_3 9048 TGGGTGCATATATATTTAGGATAGTTAACTCTTCTTGCTGCATTGATCCA 9097
v i i i v v
C L1P1_orf2#LIN 352 TGGGTGCATAAATATTTAGGATAGTTAGCTCCTCTTGTTGAATTGATCCC 303
INTRON_3 9098 TTTACCATTACATAATGCTCTTCCTTGTCTCTTTTGATCTTTGTTGGTTT 9147
ii vi i
C L1P1_orf2#LIN 302 TTTACCATTATGTAATGGCCTTCTTTGTCTCTTTTGATCTTTGTTGGTTT 253
INTRON_3 9148 AAAGTCTGTTTCATCAGAGATTAAGATCGCAACTCCTGTTTTTTTTTGCT 9197
i i i i i ii i
C L1P1_orf2#LIN 252 AAAGTCTGTTTTATCAGAGACTAGGATTGCAACCCCTGCCTTTTTTTGTT 203
INTRON_3 9198 TTCCATTTCCTTGGTAAATATTCCTCCATCCGTTTATTTTGAGACTATGT 9247
vv i v v v
C L1P1_orf2#LIN 202 TTCCATTGGCTTGGTAGATCTTCCTCCATCCTTTTATTTTGAGCCTATGT 153
INTRON_3 9248 GTGTCTTTGCAGGTGGGCTGGGTCTCCTGAATACAGCACACTGATGGATC 9297
i v i v i i
C L1P1_orf2#LIN 152 GTGTCTCTGCACGTGAGATGGGTTTCCTGAATACAGCACACTGATGGGTC 103
INTRON_3 9298 TTGACTCTTTATCCAATTTGCCAGTCTGTGTCTTTTAATTGGGGCATTTA 9347
i vi v
C L1P1_orf2#LIN 102 TTGACTCTTTATCCAACTTGCCAGTCTGTGTCTTTTAATTGCAGAATTTA 53
INTRON_3 9348 GTCTGTTTACATTTAAGGTTAATATTGTTATGTGTGAATTTGATCCTGTC 9397
ii i i
C L1P1_orf2#LIN 52 GTCCATTTATATTTAAAGTTAATATTGTTATGTGTGAATTTGATCCTGTC 3
INTRON_3 9398 AT 9399
C L1P1_orf2#LIN 2 AT 1
Matrix = 20p37g.matrix
Transitions / transversions = 1.56 (109 / 70)
Gap_init rate = 0.01 (16 / 1428), avg. gap size = 4.19 (67 / 16)
10972 11.85 2.08 1.03 INTRON_3 9250 10979 389202 C L1P2_5end LINE/L1 528 2275 0 54
INTRON_3 9250 GTCTTTGCAGGTGGGCTGGGTCTCCTGAATACAGCACACTGATGGATCTT 9299
i v i v i
C L1P2_5end#LIN 2275 GTCTCTGCACGTGAGATGGGTCTCCTGAATACAGCACACTGATGGGTCTT 2226
INTRON_3 9300 GACTCTTTATCCAATTTGCCAGTCTGTGTCTTTTAATTGGGGCATTTAGT 9349
i
C L1P2_5end#LIN 2225 GACTCTTTATCCAATTTGCCAGTCTGTGTCTTTTAATTGGGGCATTTAGC 2176
INTRON_3 9350 CTGTTTACATTTAAGGTTAATATTGTTATGTGTGAATTTGATCCTGTCAT 9399
ii
C L1P2_5end#LIN 2175 CCATTTACATTTAAGGTTAATATTGTTATGTGTGAATTTGATCCTGTCAT 2126
INTRON_3 9400 ---GATGCTAGCTGGTTGTTTTGCCCATTAGTTGATGCAGTTTCTTCATA 9446
--- i i i
C L1P2_5end#LIN 2125 TATGATGTTAGCTGGTTATTTTGCCCGTTAGTTGATGCAGTTTCTTCATA 2076
INTRON_3 9447 GTGTTGATGCTCTT-ACAATTTGGTATGTTTTTGCCGTGGCTGATACCAG 9495
ii i v - i v i i
C L1P2_5end#LIN 2075 GCATCGATGGTCTTTACAATTTGGCATGTTTTTGCAGTGGCTGGTACCGG 2026
INTRON_3 9496 TTGTTCCTTTCCAGATTTAGTGTTTCCTTCAGGAGCTCTTGTAAGGCAAG 9545
vi i i
C L1P2_5end#LIN 2025 TTGTTCCTTTCCATGTTTAGTGCTTCCTTCAGGAGCTCTTGTAAGGCAGG 1976
INTRON_3 9546 CCTGGTGGTGACAAAATCTCTCATCATTTACTTGTCTGTAATGGATTTTA 9595
v i v
C L1P2_5end#LIN 1975 CCTGGTGGTGACAAAATCTCTCAGCATTTGCTTGTCTGTAAAGGATTTTA 1926
INTRON_3 9596 TTTCTCCTTCACTTATGAAACTTAGTTTGGTTGGTTATGAAATTCTGGGT 9645
i i v
C L1P2_5end#LIN 1925 TTTCTCCTTCACTTATGAAGCTTAGTTTGGCTGGATATGAAATTCTGGGT 1876
INTRON_3 9646 TGAAAATTCTTTTCTTTAAGAATGTTGAATATTGGCCCC-ATTCTTTTCT 9694
- i i
C L1P2_5end#LIN 1875 TGAAAATTCTTTTCTTTAAGAATGTTGAATATTGGCCCCCACTCTCTTCT 1826
INTRON_3 9695 GGCTTGTAGGGTTTCTGCAGAGAGATCCACTGTTAGTCTGATGGGCTTCC 9744
v i
C L1P2_5end#LIN 1825 GGCTTGTAGGGTTTCTGCCGAGAGATCCGCTGTTAGTCTGATGGGCTTCC 1776
INTRON_3 9745 CTTTGTGGGTAACCCGAACTTTCTCTCTGGCTGTGCTTAACATTTTTTCC 9794
v iv
C L1P2_5end#LIN 1775 CTTTGTGGGTAACCCGACCTTTCTCTCTGGCTGCCCTTAACATTTTTTCC 1726
INTRON_3 9795 TGCATTTCAACCTTGGTGAATCTGACGATAATGTGTCTTGGGGTTGCTCT 9844
v i v
C L1P2_5end#LIN 1725 TTCATTTCAACCTTGGTGAATCTGACAATTATGTGTCTTGGGGTTGCTCT 1676
INTRON_3 9845 TCTCAAGGAGCATCTTTGTAGTGTTCTCTGCATTTCCTGATTTTGAATGT 9894
i i i i v
C L1P2_5end#LIN 1675 TCTCGAGGAGTATCTTTGTGGTGTTCTCTGTATTTCCTGAATTTGAATGT 1626
INTRON_3 9895 TGTGCTGTCTTGCTAGGTTGGGGAGGTTCTCCTGGATAATATCCCGAAGA 9944
vv i i i
C L1P2_5end#LIN 1625 TGGCCTGCCTTGCTAGGTTGGGGAAGTTCTCCTGGATAATATCCTGAAGA 1576
INTRON_3 9945 GTGTTTTCCAACTTGGCTCCATTCTCCTCATCGCTTTCAGGTACACCAAT 9994
i i i i
C L1P2_5end#LIN 1575 GTGTTTTCCAACTTGGTTCCATTCTCCCCGTCACTTTCAGGTACACCAAT 1526
INTRON_3 9995 TAGATGTAGATTTGGTCTTTTTCACATAGTCCCATATTTCTTGGAGGCTT 10044
i i i -
C L1P2_5end#LIN 1525 CAAACGTAGATTTGGTCTTTT-CACATAGTCCCATATTTCTTGGAGGCTT 1477
INTRON_3 10045 TTTCTGTTCCTTTTTATTCTTTTTTCTCTAATCTTGTCTTCTC----TAT 10090
v ii i i ? ----
C L1P2_5end#LIN 1476 TGTTCGTTTCTTTTTACTCTTTTTTCTCTAANCTTGTCTTCTCGCTTTAT 1427
INTRON_3 10091 TTCATTAAGTTGATCTTCAATTACTGATACCCTTTCTTTCGCTTGATCGA 10140
v i i i
C L1P2_5end#LIN 1426 TTCATTAATTTGATCTTCAATCACTGATACCCTTTCTTCCACTTGATCGA 1377
INTRON_3 10141 TTCAGCTATTGAAACTTGTGTATGCTTCACGAAGTTCTTGTGCTGTGTTT 10190
v i i i v i ii v
C L1P2_5end#LIN 1376 ATCGGCTATTGAAGCTTGTGCATGCGTCACGAAGTTCTCGTGCCATGGTT 1327
INTRON_3 10191 TTCAGCTCCATCAGGTCATTTATGTTCTTTTCTCAGCTGATTATTCTAGT 10240
v v i vvi v
C L1P2_5end#LIN 1326 TTCAGCTCCATCAGGTCATTTAAGGTCTTCTCTACACTGTTTATTCTAGT 1277
INTRON_3 10241 TAGCAATTCGTCTAACCTTTTTTCAAGGTTCTTAGCTTCCTTACATGGGG 10290
v i i ivv
C L1P2_5end#LIN 1276 TAGCCATTCGTCTAACCTTTTTTCAAGGTTTTTAGCTTCCTTGCGATGGG 1227
INTRON_3 10291 TTAGAACATGCTCCTTTAGCTCAGAGGAGTTTGCTGTTACCCACCTTCTG 10340
? i i i i v
C L1P2_5end#LIN 1226 TTNGAACATGCTCCTTTAGCTCGGAGAAGTTTGTTATTACCGACCTTCTG 1177
INTRON_3 10341 AAGCCTACTTCTGTCGATCTGTCAAACTCATTCTCCATCTAGTTTTGTTC 10390
i iii v i i i
C L1P2_5end#LIN 1176 AAGCCTACTTCTGTCAACTCGTCAAAGTCATTCTCCGTCCAGCTTTGTTC 1127
INTRON_3 10391 CCTTGCTGGAGAGGAGTTGTGATCCTTTGGAGGAGAAGCAGCATTCTGGT 10440
v v i i vi ii
C L1P2_5end#LIN 1126 CGTTGCTGGCGAGGAGCTGCGATCCTTTGGAGGAGAAGAGGCGCTCTGGT 1077
INTRON_3 10441 TTTTGGAATTTTCAGCCTTTTTGCACTGGTTTCTCCCCATCTTTGTGGAT 10490
i i i v v
C L1P2_5end#LIN 1076 TTTTAGAATTTTCAGCTTTTCTGCTCTGGTTTCTCCCCATCTTTGTGGTT 1027
INTRON_3 10491 TTATCTACCTTTGGTCTTTGATGTTGGTGACCTTTGGATGGGGTCTTTGA 10540
vii i v v
C L1P2_5end#LIN 1026 TTATCTACCTTTGGTCTTTGATGTTGGTGACCTACAGATGGGGTTTTGGT 977
INTRON_3 10541 GTGGATGT-------------------GCTATTTTTTTCTATTTGTTAGT 10571
------------------- ii i
C L1P2_5end#LIN 976 GTGGATGTCCTTTTTGTTGATGTTGATGCTATTCCTTTCTGTTTGTTAGT 927
INTRON_3 10572 GTTCTTTCTGACAGTCAGGCCCCTCTGCTGCTGGTCTGCTGGAGTTTGCT 10621
v i i i v v i
C L1P2_5end#LIN 926 TTTCCTTCTAACAGTCAGGTCCCTCAGCTGCAGGTCTGTTGGAGTTTGCT 877
INTRON_3 10622 GGAGGCCCACTCCTGACTGTGTTTGCCTGGGTATCACCAGCAGAGGCTGC 10671
i v iv i
C L1P2_5end#LIN 876 GGAGGTCCACTCCAGACCCTGTTTGCCTGGGTATCACCAGCGGAGGCTGC 827
INTRON_3 10672 AGAACAGCAAAGATTGCTGTCTGATCTTTCCT-CTGGAAGCTTCTTCCCA 10720
v v vviiiivvv vi - vvv v i iv
C L1P2_5end#LIN 826 AGAACAGCAAATATTGCAGAACAGCAAATATTGCTGCCTGATCCTTCCTC 777
INTRON_3 10721 GAGGGGAACCTGCCAAATGCCAACCAGAG-----CTCTCCTGTATGAGGT 10765
v--- v v ----- i -- ----- i v
C L1P2_5end#LIN 776 T---GGAAGCTTC-----GTC--CCAGAGGGGCACCCGCCTGTATGAGGT 737
INTRON_3 10766 GTCCGTTAGCCCCTACTGGGAGGTGTCTCCCAGTCAGGATACATAGAGGT 10815
i ii i v ii i
C L1P2_5end#LIN 736 GTCTGTCGGCCCCTACTGGGAGGTGTCTCCCAGTTAGGCTACACGGGGGT 687
INTRON_3 10816 CAGGGACCCACTTGAGGCGGCAGTCTGACCCTTAGCAGAGCTCGAATGCT 10865
v v v vv i i i
C L1P2_5end#LIN 686 CAGGGACCCACTTGAGGAGGCAGTCTGTCCGTTCTCAGAGCTCAAACGCC 637
INTRON_3 10866 GTGCTGGGAGGTCTGCTGCTCTCTTCAGAGCCATCAGGCAGGGACATTTA 10915
iv ii ii i i
C L1P2_5end#LIN 636 GTGCTGGGAGAACCACTGCTCTCTTCAGAGCTGTCAGACAGGGACGTTTA 587
INTRON_3 10916 AGTTTGCGGAAACTGCACCCACAGCTGCCCCTTTCCCCAG--GTGCTCTG 10963
i i ii i----- v i- vii --i i
C L1P2_5end#LIN 586 AGTCTGCAGAAGTTGT-----CTGCTGCCT-TTTGTTCAGCTATGCCCTG 543
INTRON_3 10964 TCCCAGGGAGATGGGG 10979
i vi - i i
C L1P2_5end#LIN 542 CCCCCAG-AGGTGGAG 528
Matrix = 20p37g.matrix
Transitions / transversions = 1.83 (130 / 71)
Gap_init rate = 0.01 (15 / 1729), avg. gap size = 3.60 (54 / 15)
11678 12.15 1.88 0.23 INTRON_3 10098 11796 388385 C L1P3_5end LINE/L1 1 1727 0 55
INTRON_3 10098 AGTTGATCTTCAATTACTGATACCCTTTCTTTCGCTTGATCGATTCAGCT 10147
iv i ii i
C L1P3_5end#LIN 1727 AGTTGATCTTCAATCTCTGATATCCTTTCTTCTGCTTGATCGATTCGGCT 1678
INTRON_3 10148 ATTGAAACTTGTGTATGCTTCACGAAGTTCTTGTGCTGTGTTTTTCAGCT 10197
v ii
C L1P3_5end#LIN 1677 ATTGATACTTGTGTATGCTTCACGAAGTTCTCATGCTGTGTTTTTCAGCT 1628
INTRON_3 10198 CCATCAGGTCATTTATGTTCTTTTCTCAGCTGATTATTCTAGTTAGCAAT 10247
i v i i
C L1P3_5end#LIN 1627 CCATCAGGTCATTTATGTTCTTCTCTAAACTGGTTATTCTAGTTAGCAAT 1578
INTRON_3 10248 TCGTCTAACCTTTTTTCAAGGTTCTTAGCTTCCTTACATGGGGTTAGAAC 10297
v i v
C L1P3_5end#LIN 1577 TCCTCTAACCTTTTTTCAAGGTTCTTAGCTTCCTTGCATTGGGTTAGAAC 1528
INTRON_3 10298 ATGCTCCTTTAGCTCAGAGGAGTTTGCTGTTACCCACCTTCTGAAGCCTA 10347
i i i
C L1P3_5end#LIN 1527 ATGCTCCTTTAGCTCGGAGGAGTTTGTTATTACCCACCTTCTGAAGCCTA 1478
INTRON_3 10348 CTTCTGTCGATCTGTCAAACTCATTCTCCATCTAGTTTTGTTCCCTTGCT 10397
i ii i i
C L1P3_5end#LIN 1477 CTTCTGTCAATTCGTCAAACTCATTCTCCGTCCAGTTTTGTTCCCTTGCT 1428
INTRON_3 10398 GGAGAGGAGTTGTGATCCTTTGGAGGAGAAGCAGCATTCTGGTTTTTGGA 10447
v i vi i
C L1P3_5end#LIN 1427 GGCGAGGAGTTGTGATTCTTTGGAGGAGAAGAGGCGTTCTGGTTTTTGGA 1378
INTRON_3 10448 ATTTTCAGCCTTTTTGCACTGGTTTCTCCCCATCTTTGTGGATTTATCTA 10497
i i i
C L1P3_5end#LIN 1377 ATTTTCAGCCTTTTTGCACTGGTTTTTCCTCATCTTCGTGGATTTATCTA 1328
INTRON_3 10498 CCTTTGGTCTTTGATGTTGGTGACCTTTGGATGGGGTCTTTGAGTGGATG 10547
i i i v i
C L1P3_5end#LIN 1327 CCTTTGGTCTTTGATGTTGGTGACCTTCGGATGGGGTTTCTGTGTGGACG 1278
INTRON_3 10548 T-------------------GCTATTTTTTTCTATTTGTTAGTGTTCTTT 10578
------------------- vi ii v i
C L1P3_5end#LIN 1277 TCCTTTTTGTTGATGTTGATGCTATTGCTTTCCGTTTGTTAGTTTTCCTT 1228
INTRON_3 10579 CTGACAGTCAGGCCCCTCTGCTGCTGGTCTGCTGGAGTTTGCTGGAGGCC 10628
i v i
C L1P3_5end#LIN 1227 CTAACAGTCAGGCCCCTCTGCTGCAGGTCTGCTGGAGTTTGCTGGAGGTC 1178
INTRON_3 10629 CACTCCTGACTGTGTTTGCCTGGGTATCACCAGCAGAGGCTGCAGAACAG 10678
v iv ? i
C L1P3_5end#LIN 1177 CACTCCAGACCCTGTTTGCCTGGRTATCACCAGCGGAGGCTGCAGAACAG 1128
INTRON_3 10679 CAAAGATTGCTGTCTGATCTTTCCTCTGGAAGCTTCTTCCCAGAGGGGAA 10728
i v i v v
C L1P3_5end#LIN 1127 CAAAGATTGCTGCCTGTTCCTTCCTCTGGAAGCTTCGTCCCAGAGGGGCA 1078
INTRON_3 10729 CCTGCCAAATGCCAACCAGAGCTCTCCTGTATGAGGTGTCCGTTAGCCCC 10778
ii i i i i iii ?
C L1P3_5end#LIN 1077 CCCACCAGATGCCAGCCGGAGCTCTCCTGTATGAGGTGTCTGTCGACYCC 1028
INTRON_3 10779 TACTGGGAGGTGTCTCCCAGTCAGGATACATAGAGGTCAGGGACCCACTT 10828
i vi i i
C L1P3_5end#LIN 1027 TGCTGGGAGGTGTCTCCCAGTCAGGAGGCACAGGGGTCAGGGACCCACTT 978
INTRON_3 10829 GAGGCGGCAGTCTGACCCTTAGCAGAGCTCGAATGCTGTGCTGGGAGGTC 10878
v v iii i
C L1P3_5end#LIN 977 GAGGAGGCAGTCTGTCCCTTAGCAGAGCTCGAGCACTGTGCTGGGAGATC 928
INTRON_3 10879 TGCTGCTCTCTTCAGAGCCATCAGGCAGGGACATTTAAGTTTGCGGAAAC 10928
i iiv i i i v i
C L1P3_5end#LIN 927 CGCTGCTCTCTTCAGAGCTGGCAGGCAGGAACGTTTAAGTCTGCTGAAGC 878
INTRON_3 10929 TGCACCCACAGCTGCCCCTTTCCCCAGGTGCTCTGTCCCAGGGAGATGGG 10978
i i i
C L1P3_5end#LIN 877 TGCGCCCACAGCCGCCCCTTCCCCCAGGTGCTCTGTCCCAGGGAGATGGG 828
INTRON_3 10979 GGTTTTATCTATAAGTCCCTGACTGGGGCTGCTGCCTTTTTTTCAGACAT 11028
i i i v
C L1P3_5end#LIN 827 AGTTTTATCTATAAGCCCCTGACTGGGGCTGCTGCCTTTCTTTCAGAGAT 778
INTRON_3 11029 GCCCTGCCCAGAGAAGGGAAATCT-----GGCAGTCTGGCCACAGCAACC 11073
i i i ----- i vi?i
C L1P3_5end#LIN 777 GCCCTGCCCAGAGAGGAGGAATCTAGAGAGGCAGTCTGGCTACAGCCGNT 728
INTRON_3 11074 ATGCTGAGCTGCAGTGGGCTCCGCCCAGTTTGAACTTTTCAGAGGCTTTG 11123
v v ii i iiii v
C L1P3_5end#LIN 727 TTGCGGAGCTGTGGTGGGCTCCGCCCAGTTCGAACTTCCTGGTGGCTTTG 678
INTRON_3 11124 TTTACATTGTGAGCATAAAACCGCCTACTCAAGCTTCAACAATGGTAGAC 11173
i viv i ii ii i
C L1P3_5end#LIN 677 TTTACACTGTGAGGGGAAAACCGCCTACTCAAGCCTCAGTAATGGCGGAT 628
INTRON_3 11174 GCCCCTCACCTCACCAAGCTCATGCATCCCAGGTCAATCTCAGACTGCTG 11223
v i iv i ii
C L1P3_5end#LIN 627 GCCCCTCCCCCCACCAAGCTCGAGCATCCCAGGTCGACTTCAGACTGCTG 578
INTRON_3 11224 GTGTGCTGGCAGTGAGATTTTCAAGCCAGTGGATCTTAGTTTGCTGGGCT 11273
--- i v i
C L1P3_5end#LIN 577 ---TGCTGGCAGCGAGAATTTCAAGCCAGTGGATCTTAGCTTGCTGGGCT 531
INTRON_3 11274 CTGTGGGGGTGGGACCCTCTGAGCCAGACCACTTGGCTCCCTGGCTTCAG 11323
i i v i
C L1P3_5end#LIN 530 CCGTGGGGGTGGGATCCACTGAGCTAGACCACTTGGCTCCCTGGCTTCAG 481
INTRON_3 11324 CACCCCTTTCCAGGGGAGTGAACAGTTCTGTCTCGCTGGCGTTTCAGGCA 11373
- i i i
C L1P3_5end#LIN 480 C-CCCCTTTCCAGGGGAGTGAACAGTTCTGTCTCACTGGCGTTCCAGGCG 432
INTRON_3 11374 CCATTGGGGTATGGAAAAAAATAACTCCTGCACCTAATTCGTTATCTGCC 11423
i i i v v ii v i
C L1P3_5end#LIN 431 CCACTGGGGTACGAAAAAAAAAAACTCCTGCAGCTAGCTCGGTGTCTGCC 382
INTRON_3 11424 CAAATGGCCACCCAGTTTTGTGCTTGAAACTTAGGGCACTGGTGGGGTAG 11473
i ii ii v v
C L1P3_5end#LIN 381 CAAACGGCTGCCCAGTTTTGTGCTTGAAACCCAGGGCCCTGGTGGTGTAG 332
INTRON_3 11474 GGACCGGAGGGAATCTCCTGGTTTGCGGGTGTTGAAAACCGTGGGACAAA 11523
v v i i vvi i i v i
C L1P3_5end#LIN 331 GCACCCGAGGGAATCTCCTGGTCTGTGGGTTGCGAAGACCATGGGAAAAG 282
INTRON_3 11524 TGCAGTGTCTGTGCCTGA-------GTTCCTCA-GGCTCAGTCCCTCACA 11565
iii i v v ------- i- v i
C L1P3_5end#LIN 281 CATAGTATCTGGGCCGGAATGCAYCGTTCCTCGTGGCACAGTCCCTCACG 232
INTRON_3 11566 GCTTCCCTTGGGTGGGGGAGAAAATTCTCTGACCCCTTGTGCTTCCTGGG 11615
v i ii i i i i
C L1P3_5end#LIN 231 GCTTCCCTTGGCTAGGGGAGGGAGTTCCCTGACCCCTTGCGCTTCCCGGG 182
INTRON_3 11616 TGAGGCGACACCCCACCCTCCTTCGTCTTGCTCTCCATGGGCTGCACCTA 11665
i v vv i i i i
C L1P3_5end#LIN 181 TGAGGCGACGCCCCACCCTGCTTCTGCTCGCCCTCCGTGGGCTGCACCCA 132
INTRON_3 11666 CTATCCAACCAGACCCAATGCGATGAACCAGGTACCTCAGTTGGAAATGC 11715
i i v v i i ?
C L1P3_5end#LIN 131 CTGTCTAACCAGTCCCAATGAGATGAGCCGGGTACCTCAGTTGGAAATGN 82
INTRON_3 11716 AGAAATCACCTGCCTTCTGCATCGATCTCGCTGGGAGATGCAGACTGGAG 11765
i i v ii
C L1P3_5end#LIN 81 AGAAATCACCTGCCTTCTGCGTTGATCTCGCTGGGAGCTGCAGACCAGAG 32
INTRON_3 11766 CTTCTCCTATTCGGCCATCTTGCCAGCAATC 11796
vi v i
C L1P3_5end#LIN 31 CTGTTCCTATTCGGCCATCTTGCCAGCCACC 1
Matrix = 20p37g.matrix
Transitions / transversions = 2.74 (148 / 54)
Gap_init rate = 0.00 (6 / 1698), avg. gap size = 6.00 (36 / 6)
+ 3581 10.3 2.6 6.6 INTRON_3 11889 11959 (388222) C L1PB1 LINE/L1 (3) 6864 6800 6
ANNOTATION EVIDENCE:
3581 10.30 2.61 6.61 INTRON_3 11889 11959 388222 C L1PB1_3end LINE/L1 831 895 3 18
INTRON_3 11889 TTTTACTTCAATAG-TTTTTCGGGAACAGGTGGTTTTTGGTTACATGCAT 11937
i - v v v
C L1PB1_3end#LI 895 TTTTATTTCAATAGGTTTTTGGGGAACAGGTGGTGTTTGGTTACATGAAT 846
INTRON_3 11938 AAATTCTTTACTGGTAATTTCT 11959
i v -------
C L1PB1_3end#LI 845 AAGTTCTTTAGTGGT------- 831
Matrix = 18p37g.matrix
Transitions / transversions = 0.50 (2 / 4)
Gap_init rate = 0.03 (2 / 70), avg. gap size = 4.00 (8 / 2)
+ 845 9.4 0.0 1.6 INTRON_3 11960 12089 (388092) + (TTTC)n Simple_repeat 1 128 (0) 7
ANNOTATION EVIDENCE:
845 9.38 0.00 1.56 INTRON_3 11960 12089 388092 C (GAAA)n Simple_repeat 1 128 52 96
INTRON_3 11960 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCTCTCTCTCTCTC 12009
i i i i
C (GAAA)n#Simpl 128 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 79
INTRON_3 12010 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTTTCTTTCTT 12059
i i i i i i i i --
C (GAAA)n#Simpl 78 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT--TTCTTTCTTTCTT 31
INTRON_3 12060 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 12089
C (GAAA)n#Simpl 30 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 1
Matrix = Unknown
Transitions / transversions = 0.0 (12 / 0)
Gap_init rate = 0.01 (1 / 129), avg. gap size = 2.00 (2 / 1)
3581 10.30 2.61 6.61 INTRON_3 12090 12097 388084 C L1PB1_3end LINE/L1 830 830 68 19
INTRON_3 12090 TTCCTTTC 12097
--------
C L1PB1_3end#LI 830 -------- 831
Matrix = 18p37g.matrix
Transitions / transversions = 0.0 (0 / 0)
Gap_init rate = 0.14 (1 / 7), avg. gap size = 8.00 (8 / 1)
+ 2237 14.2 0.0 0.0 INTRON_3 12098 12408 (387773) C AluSq2 SINE/Alu (1) 311 1 8
ANNOTATION EVIDENCE:
2129 14.52 0.00 0.32 INTRON_3 12098 12408 387773 C AluSx SINE/Alu 1 310 2 1
INTRON_3 12098 TTTCTTTCCTTTCTTTCTTTTCTTTTTTAAGACGGAATTTCCCTGTTGTT 12147
i ii i i i i i i v -i i
C AluSx#SINE/Al 310 TTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCT-CTGTC 262
INTRON_3 12148 GCCCAGGCTGGAGTGCAATGGCACAATCTTGGCTCTCTGCAACCTCTGCC 12197
i i i i v i
C AluSx#SINE/Al 261 GCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
INTRON_3 12198 TCCCAGGTTCAAGTGATTCTCTTGCTTCAGCCTCCTGAGTAGCTGGGATT 12247
i i i i i
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATT 162
INTRON_3 12248 ACAAGCATGTGCCACCACATCTGGCTAATTTTTAAATTTTTAGTAGAGAT 12297
i ii i ii i iv i
C AluSx#SINE/Al 161 ACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGAC 112
INTRON_3 12298 GGGGTTTCATCATGTTGGCCAGGCTAGTCTTGAACTCCTGCCCTCAGGTG 12347
i i i v
C AluSx#SINE/Al 111 GGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTG 62
INTRON_3 12348 ATCCTCCTGCCTCGGCCTCCCAAAGTGCTGGGAATACAGACATGAGCCAC 12397
v i v i i
C AluSx#SINE/Al 61 ATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC 12
INTRON_3 12398 TGTACCCGGCC 12408
i ii
C AluSx#SINE/Al 11 CGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 6.50 (39 / 6)
Gap_init rate = 0.00 (1 / 310), avg. gap size = 1.00 (1 / 1)
+ 3581 10.3 2.6 6.6 INTRON_3 12409 12718 (387463) C L1PB1 LINE/L1 (68) 6799 6497 6
ANNOTATION EVIDENCE:
3581 10.30 2.61 6.61 INTRON_3 12409 12718 387463 C L1PB1_3end LINE/L1 528 830 68 20
INTRON_3 12409 TTTAGTTGTGATTTCTGAGATTTTGGTGCACTCATCACCCAAGCAGTGTA 12458
--------- i i
C L1PB1_3end#LI 830 ---------GATTTCTGAGATTTTGGTGCACCCATCACCCGAGCAGTGTA 790
INTRON_3 12459 CACTGTAATCAGTGTGTCATCTTTTATCCCTC-------TCCAACTCT-- 12499
vi i vi ------- v i --
C L1PB1_3end#LI 789 CACTGTACCCAATGTGTAGTCTTTTATCCCTCACCCCCCTCCCACCCTTT 740
INTRON_3 12500 -----GAGTCTCCAAAGTCCATTGTATCATTCTTATGCCTTTGCATCCTC 12544
----- i
C L1PB1_3end#LI 739 CCCCCGAGTCCCCAAAGTCCATTGTATCATTCTTATGCCTTTGCATCCTC 690
INTRON_3 12545 ATAACTTAGTTCCAACTTATGAGTGAGAACATACAATGTTTGGTTTTCCA 12594
i i v i
C L1PB1_3end#LI 689 ATAGCTTAGCTCCCACTTATGAGTGAGAACATACGATGTTTGGTTTTCCA 640
INTRON_3 12595 ATCCCTGAGTTACTTCACTTACAATAATGGTCTCCAGTTCCATCCAAGTT 12644
- i v i i
C L1PB1_3end#LI 639 -TTCCTGAGTTACTTCACTTAGAATAATGGTCTCCAATTCCATCCAGGTT 591
INTRON_3 12645 GCTGCAAATGGTCTTATTTCTTTCCTTTTTATGGCTGAGTAGTATTCCAT 12694
i viv v
C L1PB1_3end#LI 590 GCTGCGAATGCCATTATTTCGTTCCTTTTTATGGCTGAGTAGTATTCCAT 541
INTRON_3 12695 GGTGTGCATGTGTGTTTGTTTCTG 12718
i ii i ii-----------
C L1PB1_3end#LI 540 GGTATATATATAC----------- 528
Matrix = 18p37g.matrix
Transitions / transversions = 2.62 (21 / 8)
Gap_init rate = 0.02 (5 / 309), avg. gap size = 7.00 (35 / 5)
+ 285 12.8 0.0 0.0 INTRON_3 12719 12765 (387416) + (TA)n Simple_repeat 2 48 (0) 9
ANNOTATION EVIDENCE:
285 12.77 0.00 0.00 INTRON_3 12719 12765 387416 C (TA)n Simple_repeat 134 180 0 97
INTRON_3 12719 TATATGTGTATATACATATATATATATACACATATATAAATATATAT 12765
i i i i i v
C (TA)n#Simple_ 180 TATATATATATATATATATATATATATATATATATATATATATATAT 134
Matrix = Unknown
Transitions / transversions = 5.00 (5 / 1)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 3581 10.3 2.6 6.6 INTRON_3 12766 12986 (387195) C L1PB1 LINE/L1 (371) 6496 6275 6
ANNOTATION EVIDENCE:
3581 10.30 2.61 6.61 INTRON_3 12766 12986 387195 C L1PB1_3end LINE/L1 306 527 371 21
INTRON_3 12766 CACATTTTCTTTATCTACTTGTTGGTTGTTGAGCGTTTAGTCTAGTTCTG 12815
i ii i v i i i v i ii
C L1PB1_3end#LI 527 CACATTTTCTTTATCCACTCATTGATTGATGGGCATTTGGGCTGGTTCCA 478
INTRON_3 12816 TATTTTTGCAATTGCAAATTGTGCTGCTATAAA-ATGCATGTGCAAGTGT 12864
i - i i
C L1PB1_3end#LI 477 TATTTTTGCAATTGCGAATTGTGCTGCTATAAACATGCGTGTGCAAGTAT 428
INTRON_3 12865 GTTTTTCAAATAATGACTTCCTTTCCTCTGGGTAGATACCCAATAGTGGG 12914
v iv i i
C L1PB1_3end#LI 427 CTTTTTCGTATAATGACTTCTTTTCCTCTGGGTAGATACCCAGTAGTGGG 378
INTRON_3 12915 ATTGCTGGATCAAATGGTAGTTCTGCTTTTAGTTCTTTAAGGAATCTTCA 12964
v i i
C L1PB1_3end#LI 377 ATTGCTGGATCAAATGGTAGATCTACTTTTAGTTCTTTAAGGAATCTCCA 328
INTRON_3 12965 TACTGTTTTCCATAGTGGTTGT 12986
i
C L1PB1_3end#LI 327 CACTGTTTTCCATAGTGGTTGT 306
Matrix = 18p37g.matrix
Transitions / transversions = 3.80 (19 / 5)
Gap_init rate = 0.00 (1 / 220), avg. gap size = 1.00 (1 / 1)
+ 9600 11.8 1.0 0.8 INTRON_3 12988 13198 (386983) C L1PB1 LINE/L1 (2097) 4765 4557 6
ANNOTATION EVIDENCE:
9600 11.84 0.97 0.78 INTRON_3 12988 13198 386983 C L1PB_orf2 LINE/L1 1732 1940 1354 56
INTRON_3 12988 TTTTCCCTGTTCAGTATGATGTTCACTGTGAGTTTGTCATAGATGGCTTT 13037
ii ? vi i
C L1PB_orf2#LIN 1940 TTTTCCCCATTCAGTATNATGTTGGCTGTGGGTTTGTCATAGATGGCTTT 1891
INTRON_3 13038 TATTACATTGAGGTATGTGCCTTCTATGTTGATTTTGCTGAGGGTGTTTT 13087
i v ? ii --
C L1PB_orf2#LIN 1890 TATTACATTAAGGTATGTCCCTTNTATGCCGATTTTGCTGAGGGT--TTT 1843
INTRON_3 13088 AATCATAAAGGGATGCTGGATTTCCTCAGCTGCTTTTTCTGTATCTATTG 13137
iv iv i
C L1PB_orf2#LIN 1842 AATCATAAAGGGATGCTGGATTTTGTCAAATGCTTTTTCTGCATCTATTG 1793
INTRON_3 13138 AGATGATCATATGATTTTTGTTTTTAATTCTGTTTATGTGATGCATCACA 13187
i i i
C L1PB_orf2#LIN 1792 AGATGATCATGTGATTTTTGTTTTTAATTCTGTTTATGTGGTGTATCACA 1743
INTRON_3 13188 TTTATTGACTT 13198
C L1PB_orf2#LIN 1742 TTTATTGACTT 1732
Matrix = 20p37g.matrix
Transitions / transversions = 3.25 (13 / 4)
Gap_init rate = 0.00 (1 / 210), avg. gap size = 2.00 (2 / 1)
7600 21.89 1.55 2.45 INTRON_3 12988 13198 386983 C L1M2_orf2 LINE/L1 1729 1937 1354 57
INTRON_3 12988 TTTTCCCTGTTCAGTATGATGTTCACTGTGAGTTTGTCATAGATGGCTTT 13037
ii vi i v i
C L1M2_orf2#LIN 1937 TTTTCCCCATTCAGTATGATGTTAGCTGTGGGTTTGTCATATATGGCCTT 1888
INTRON_3 13038 TATTACATTGAGGTATGTGCCTTCTATGTTGATTTTGCTGAGGGTGTTTT 13087
iii i v iiiv v i i v -
C L1M2_orf2#LIN 1887 TATTGTGTTGAGGTACGTTCCTTCTATACCTAATTTGTTGAGAGTTTTT- 1839
INTRON_3 13088 AATCATAAAGGGATGCTGGATTTCCTCAGCTGCTTTTTCTGTATCTATTG 13137
- i i i iv iv i
C L1M2_orf2#LIN 1838 -ATCATGAAGGGATGTTGAATTTTATCAAATGCTTTTTCTGCATCTATTG 1790
INTRON_3 13138 AGATGATCATATGATTTTTGTTTTTAATTCTGTTTATGTGATGCATCACA 13187
i i ii v v i i
C L1M2_orf2#LIN 1789 AAATGATCATATGGTTTTTGTCCTTCATTCTGTTAATGTGATGTATCACG 1740
INTRON_3 13188 TTTATTGACTT 13198
i
C L1M2_orf2#LIN 1739 TTTATTGATTT 1729
Matrix = 20p37g.matrix
Transitions / transversions = 2.70 (27 / 10)
Gap_init rate = 0.00 (1 / 210), avg. gap size = 2.00 (2 / 1)
+ 4338 5.1 0.7 0.4 INTRON_3 13199 13754 (386427) + LTR6B LTR/ERV1 1 558 (0) 10
ANNOTATION EVIDENCE:
4338 5.06 0.72 0.36 INTRON_3 13199 13754 386427 + LTR6B LTR/ERV1 1 558 0 16
INTRON_3 13199 TGTAATGCCCAACCTGGTTTTTACTAACTCTGTTTTTAGACTCTCCCTTT 13248
v i
LTR6B#LTR/ERV 1 TGTAATGCCCAACCTTGTTTTTACTAACCCTGTTTTTAGACTCTCCCTTT 50
INTRON_3 13249 TCCTTTAATCACCTAGCCTTGTTTCCACCTGAATTGACTCTCCCTTAGCT 13298
-
LTR6B#LTR/ERV 51 -CCTTTAATCACCTAGCCTTGTTTCCACCTGAATTGACTCTCCCTTAGCT 99
INTRON_3 13299 AAGAGAGCCAGACAGACTCCATCTTGGCTCTTTCACTGGCAGCCCCTTCC 13348
LTR6B#LTR/ERV 100 AAGAGAGCCAGACAGACTCCATCTTGGCTCTTTCACTGGCAGCCCCTTCC 149
INTRON_3 13349 TCAAGGACTTAACTTGTGCAAGCTGACTCCCAGCACATCCAAGAATGCAA 13398
LTR6B#LTR/ERV 150 TCAAGGACTTAACTTGTGCAAGCTGACTCCCAGCACATCCAAGAATGCAA 199
INTRON_3 13399 TTAGCTGATAAGATACTGTGGCAAGCTATATCCACAGTTTCCAGGAATTT 13448
i i i i i
LTR6B#LTR/ERV 200 TTAACTGATAAGATACTGTGGCGAGCTATATCCGCAGTTCCCAGGAATTC 249
INTRON_3 13449 GTCCGATTGATAACTCCCAAAGCCCCGGGTCTGTCACCTTGTAATAGTCT 13498
v v i
LTR6B#LTR/ERV 250 GTCCGATTGATAACGCCCAAAGCCCCGCGTCTATCACCTTGTAATAGTCT 299
INTRON_3 13499 TAAGGCCCCTGCACCTGGAACTGTTTACTTTCCTGTAACCATTTATCCTT 13548
i
LTR6B#LTR/ERV 300 TAAAGCCCCTGCACCTGGAACTGTTTACTTTCCTGTAACCATTTATCCTT 349
INTRON_3 13549 TTAACTTTTT-GACTACTTTACTTCTGTAAAATTGTTTTAACTAGACGCC 13597
- v -
LTR6B#LTR/ERV 350 TTAACTTTTTTGCCTACTTTACTTCTGTAAAATTGTTTTAACTAGAC-CC 398
INTRON_3 13598 CCCCTCCCCTTCCTAAACCAAGGTATAAAAGTTAATCAAGCCCCTTCCTT 13647
i i vv v i i
LTR6B#LTR/ERV 399 CCCCTCCCCTTTCTAAACCAAAGTATAAAAGAAAATCTAGCCCCTTCTTC 448
INTRON_3 13648 GGGGCCAAGAGAATTTTGAGCGTTAGCCGTCTCTTGGTTGCTGGCTAA-T 13696
i i ii i -
LTR6B#LTR/ERV 449 GGGGCCGAGAGAACTTTGAGCGTTAGCCGTCTCTTGGCCGCCGGCTAAAT 498
INTRON_3 13697 AAA-GGACTCTTAATTCATCTCAAAGTGTGGCCTTTT-TCTAACTTGCTC 13744
- i v - i
LTR6B#LTR/ERV 499 AAACGGACTCTTAATTCGTCTCAAAGTGTGGCGTTTTCTCTAACTCGCTC 548
INTRON_3 13745 AGGTACAACA 13754
i
LTR6B#LTR/ERV 549 GGGTACAACA 558
Matrix = 18p37g.matrix
Transitions / transversions = 2.50 (20 / 8)
Gap_init rate = 0.01 (6 / 555), avg. gap size = 1.00 (6 / 6)
+ 9600 13.7 1.1 1.1 INTRON_3 13755 15388 (384793) C L1PB1 LINE/L1 (2306) 4556 2926 6
ANNOTATION EVIDENCE:
7600 21.89 1.55 2.45 INTRON_3 13755 15388 384793 C L1M2_orf2 LINE/L1 101 1728 1563 59
INTRON_3 13755 ACTTGTGTATGTTAAACCATCTCTGCATCTCTGGTGTGAAACCCACTTGA 13804
---- i i ii i vi v
C L1M2_orf2#LIN 1728 ----GCGTATGTTGAACCATCCTTGCATCCCTGGGATGAATCCCACTTGA 1683
INTRON_3 13805 TCATAGTGTATTATATTTTTGATATGCTGTTGTATTTGGTTAGCTAGTAT 13854
i v v v i i v i v
C L1M2_orf2#LIN 1682 TCATGGTGAATGATCTTTTTAATGTGCTGTTGAATTCGGTTTGCTAGTAT 1633
INTRON_3 13855 TTTTTTTGAGGATTTTTGGATCTATGTTCATCAGGGATATTGGTCTGCAG 13904
v - v i i
C L1M2_orf2#LIN 1632 TTTGTT-GAGGATTTTTGCATCTATGTTCATCAGGGATATTGGCCTGTAG 1584
INTRON_3 13905 TTTTTTGTTTTTGTTATGTCCTTTCTTGGTTTTGGTATGAAGGTGATACT 13954
i v i vii v i i i
C L1M2_orf2#LIN 1583 TTTTCTTTTTTTGTTGTGTCCTTGTCTGGTTTTGGTATCAGGGTAATGCT 1534
INTRON_3 13955 GGCTTCATAGAATGATTAAGGAAGGGAACCTCTTTCTTTA-TCTTGTGGA 14003
i v vv ?ivv iiii i - i v
C L1M2_orf2#LIN 1533 GGCCTCATAGAATGAGTTTGGAAGNATTCCCTCCTCTTCAATTTTTTGGA 1484
INTRON_3 14004 ATAGTGTCAGTAGGATTGCTACCAATTATT---TCAATGTTCAATAGAAT 14050
v v v i v ii i v --- v iii
C L1M2_orf2#LIN 1483 ATAGTTTGAGAAGAATTGGTATTAGTTCTTCTTTAAATGTTTGGTAGAAT 1434
INTRON_3 14051 TCAGCTGAGAATCCATCTTCTCCTGGACTTTTTTTTTTGTTGGCAATTTT 14100
v v v vvv i i -- v v ivi
C L1M2_orf2#LIN 1433 TCAGCAGTGAAGCCATCAGGTCCTGGGCTTTTCTTT--GATGGGAGACTT 1386
INTRON_3 14101 TAAATTACCATTTCAATCTCACTACTTGTTATTGGTCTGTTTAGAGTTTC 14150
vv iiv ?i ii i v
C L1M2_orf2#LIN 1385 TTTATTACTGATTCAATCTCNTTACTCATTATTGGTCTGTTCAGATTTTC 1336
INTRON_3 14151 TGTTTCTTTCTGATTTAATCTAGGAGGGTTGTAGACTTCCAGGAATTTAT 14200
i iv i v vi viiv
C L1M2_orf2#LIN 1335 TATTTCTTCATGATTCAATCTTGGTAGGTTGTATGTGTCCAGGAATTTAT 1286
INTRON_3 14201 CCATGTCCTGTAAATTTTCTAGTTTGTGCACGTAAAGGTGTTCCTGGTAG 14250
v i v ii ? i i vvi i v v v ii
C L1M2_orf2#LIN 1285 CCATTTCTTCTAGGTTNTCCAATTTGTTGGCATATAGTTGTTCATAATAG 1236
INTRON_3 14251 CCTTGAATTATCTTTTGCATTTCTGTGGTATTGGCTGTAATATCTCCCAT 14300
i ivv v i i ii i i iv
C L1M2_orf2#LIN 1235 TCTCTTATGATCCTTTGTATTTCTGTGGTATCAGTTGTAATGTCTCCTTT 1186
INTRON_3 14301 CCCATTTCTAATTGAGCTTATTAGGATCTTCTCTCTTCTTTTCTTGGTTA 14350
ii i i vvii v ii i ii ---
C L1M2_orf2#LIN 1185 TTCATCTCTGATTTTATTTATTTGAGTCTTCTCTCTTTTTTTTCT---TA 1139
INTRON_3 14351 ATCTCACTAATGATGTATCAATTTTGTTTATCTCTTCAAAGAACCAGCTT 14400
i vi v i v i i i i i
C L1M2_orf2#LIN 1138 GTCTAGCTAAAGGTTTGTCAATTTTGTTTATCTTTTCAAAAAACCAACTC 1089
INTRON_3 14401 TTTGTTTCTTTTATCTTTTTT----TTTTTTTGGTTTCAATTTCATGTAA 14446
v v v ---- i i v v v
C L1M2_orf2#LIN 1088 TTTGTTTCGTTGATCTTTTGTATTGTTTTTTTAGTCTCTATTTCATTTAT 1039
INTRON_3 14447 TTCTTCTCTGATCTTGATT---TCTTTTCTTCTGCTTGGTTTGGGTTTGG 14493
v v --- i i viv i
C L1M2_orf2#LIN 1038 TTCTGCTCTGATCTTTATTATTTCTTTCCTTCTACTAATTTTGGGTTTAG 989
INTRON_3 14494 TTTGTTCTTGTTTCTCTAGTTCCTTGAAGTATGATCTTAGATTGTTTATT 14543
i i iii iv i
C L1M2_orf2#LIN 988 TTTGTTCTTGTTTTTCTAGTTCCTTGAGGTGCAACGTTAGGTTGTTTATT 939
INTRON_3 14544 TGTACTCTTTCAGACTTTTTCATGTAGGCATTTGATGCTATGAACTTTCC 14593
viv v?vi v iv i i
C L1M2_orf2#LIN 938 TGAGATCTTTCTNCTTTTTTGATGTAGGCATTTATTGCTATAAACTTCCC 889
INTRON_3 14594 TCTTAGCATTGCTTTAGCTGTATCCCGGAGGTTTTGAGAAGTTGAATCAC 14643
v i v iv iv v vi iv
C L1M2_orf2#LIN 888 TCTTAGAACTGCTTTTGCTGTATCCCATAGGTTTTGGTATGTTGTGTTTC 839
INTRON_3 14644 GGTTATGATTCAGTTCAAAGAATTAAAAAAATTTCCGTCTTGATTTCATT 14693
vi v v iivi ii vvvv - v i i v i
C L1M2_orf2#LIN 838 CATTTTCATTTGTCTCAAGAAATTTTTTAA-TTTCCTTTTTAATTTCTTC 790
INTRON_3 14694 GTTGACCCAAAGATCATTCAAGAGCAGATTATTTAATTTCCATGTATTTG 14743
i vv i ii i vi i
C L1M2_orf2#LIN 789 ATTGACCCATTGGTTGTTCAGGAGCATGTTGTTTAATTTCCATGTATTTG 740
INTRON_3 14744 TATAGTTCTGAGGGTTTCTTTTGGAGTTAATTTCTAGTTTTATTC-ACTG 14792
? iiv ii i ii vvi i ? - i
C L1M2_orf2#LIN 739 TANAGTTTCCAAAGTTCCTCCTGTTATTGATTTCTAGTTTTATNCCATTG 690
INTRON_3 14793 TGTTCTGAGAGGATACTTGATATAATTTCAATTTTTAAAAAATGTATTGA 14842
v v i i i ivv - v i i
C L1M2_orf2#LIN 689 TGGTCAGAAAAGATACTTGATATGATTTCAATTTTCTTAAA-TTTGTTAA 641
INTRON_3 14843 GACTTGTTTTGTGAC---ATATATGGTCTATCTTGGTGCATATTCTATGT 14889
i --- i i i v v i i
C L1M2_orf2#LIN 640 GACTTGTTTTGTGGCCTAACATATGATCTATCCTGGAGAATGTTCCATGT 591
INTRON_3 14890 GCTGATGAAAAGAATGTATATTCTACAGATGTTGAGTAGAATGTTCTGTA 14939
? v i i i v ii i
C L1M2_orf2#LIN 590 GCNGTTGAGAAGAATGTGTATTCTGCAGCTGTTGGATGGAATGTTCTGTA 541
INTRON_3 14940 AATATCTGCTAAGTCCATTTGTTCTAGGTTATAGTTTAAGTCCCTTGTTT 14989
i i i v iv ii vv
C L1M2_orf2#LIN 540 AATGTCTGTTAGGTCCATTTGGTCTAGAGTGCAGTTTAAGTCCGATGTTT 491
INTRON_3 14990 CTTTGTTGTCTTTCTGTATTGATGACCTGTCTAGTGCTGTCAGTGAAATA 15039
vi v v i i v vv iii i
C L1M2_orf2#LIN 490 CTTTGTTGATTTTCTGTCTGGATGATCTGTCCATTGCTGAAAGTGGGGTG 441
INTRON_3 15040 TTGAAGTCCCCCACCATTATTGTGTTGCTGTGTATCTC---------AT- 15079
i i i v v --------- -
C L1M2_orf2#LIN 440 TTGAAGTCCCCTACTATTATTGTATTGCAGTCTATCTCTCCCTTTAGATC 391
INTRON_3 15080 --TTCAT---TGTTTTATAAATTTGGGAGCTCCAGTGTTAGGTTCATATA 15124
-- v --- i v i v i v
C L1M2_orf2#LIN 390 TATTAATATTTGCTTTATATATTTAGGTGCTCCAGTGTTGGGTGCATATA 341
INTRON_3 15125 TATTTAAGATTGTGATATTTTCCTGTTGGACTGATCCTTTTAGCTTTGTG 15174
vi v ii i i i i i i v v i i
C L1M2_orf2#LIN 340 TATTTACAATTGTTATATCCTCTTGCTGAATTGACCCCTTTATCATTATA 291
INTRON_3 15175 TAATGTCCCTCTTTGTCTTTTTAAACTGTTGTTGCTTTTAAGTCTGTTTT 15224
v i i vv v v vi v i
C L1M2_orf2#LIN 290 TAATGACCTTCTTTGTCTCTTTTTACAGTTTTTGACTTAAAGTCTATTTT 241
INTRON_3 15225 TTCCGATATAAGAGTAGCTACTCCTGTTCACTTTTGGTGTCCGTTTGCAT 15274
v i vi i v v i
C L1M2_orf2#LIN 240 ATCTGATATAAGTATAGCTACTCCTGCTCTCTTTTGGTTTCCATTTGCAT 191
INTRON_3 15275 GGGATATCTTTTTTTCACTCTTTTACCTTAAGTTGATGTGAGTTGTTATG 15324
i i- ii i i i v iv v iv ?i
C L1M2_orf2#LIN 190 GGAATATCTTTTTC-CATCCCTTCACTTTCAGTCTATGTGTGTCCTTANA 142
INTRON_3 15325 TGTTAGGTGAGTCTCTTGAAGACAGCAGATACTTGGTTGGTGGATTTTTT 15374
v v i v i v ------- v i i --
C L1M2_orf2#LIN 141 GGTGAAGTGAGTCTCTTGTAGGCAGCATATA-------GTTGGGTCTT-- 101
INTRON_3 15375 TTTAAAAAATGAAA 15388
--------------
C L1M2_orf2#LIN 101 -------------- 102
Matrix = 20p37g.matrix
Transitions / transversions = 1.39 (206 / 148)
Gap_init rate = 0.01 (18 / 1633), avg. gap size = 3.67 (66 / 18)
9600 11.84 0.97 0.78 INTRON_3 13755 15082 385099 C L1PB_orf2 LINE/L1 398 1731 1563 58
INTRON_3 13755 ACTTGTGTATGTTAAACCATCTCTGCATCTCTGGTGTGAAACCCACTTGA 13804
---- i i i i
C L1PB_orf2#LIN 1731 ----GCGTATGTTAAACCATCCCTGCATCCCTGGTATGAAACCCACTTGA 1686
INTRON_3 13805 TCATAGTGTATTATATTTTTGATATGCTGTTGTATTTGGTTAGCTAGTAT 13854
i v v v i
C L1PB_orf2#LIN 1685 TCATGGTGGATTATCTTTTTGATATGCTGTTGGATTCGGTTAGCTAGTAT 1636
INTRON_3 13855 TTTTTTTGAGGATTTTTGGATCTATGTTCATCAGGGATATTGGTCTGCAG 13904
v -i ? v i
C L1PB_orf2#LIN 1635 TTTGTT-AAGGATTTTNGCATCTATGTTCATCAGGGATATTGGTCTGTAG 1587
INTRON_3 13905 TTTTTTGTTTTTGTTATGTCCTTTCTTGGTTTTGGTATGAAGGTGATACT 13954
i v ? i v i
C L1PB_orf2#LIN 1586 TTTTCTTTTTTNGTTATGTCCTTTCCTGGTTTTGGTATTAGGGTGATACT 1537
INTRON_3 13955 GGCTTCATAGAATGATTAAGGAAGGGA-ACCTCTTTCTTTATCTTGTGGA 14003
v i v-v i
C L1PB_orf2#LIN 1536 GGCTTCATAGAATGATTTAGGGAGGGTTCCCTCTTTCTCTATCTTGTGGA 1487
INTRON_3 14004 ATAGTGTCAGTAGGATTGCTACCAATTATT---TCAATGTTCAATAGAAT 14050
i v v --- v iiii
C L1PB_orf2#LIN 1486 ATAGTGTCAATAGGATTGGTACCAATTCTTCTTTGAATGTCTGGTAGAAT 1437
INTRON_3 14051 TCAGCTGAGAATCCATCTTCTCCTGGACTTTTTTTTTTGTTGGCAATTTT 14100
? v i vv -- i
C L1PB_orf2#LIN 1436 TCNGCTGTGAATCCGTCTGGTCCTGGACTTTTTTTT--GTTGGTAATTTT 1389
INTRON_3 14101 TAAATTACCATTTCAATCTCACTACTTGTTATTGGTCTGTTTAGAGTTTC 14150
? i i i i ?
C L1PB_orf2#LIN 1388 TNAATTACCATTTCAATCTCGCTGCTTGTTATTGGTCTGTTCAGGGTNTC 1339
INTRON_3 14151 TGTTTCTTTCTGATTTAATCTAGGAGGGTTGTAGACTTCCAGGAATTTAT 14200
i? i v v?i
C L1PB_orf2#LIN 1338 TANTTCTTCCTGATTTAAGCTAGGAGGGTTGTATNTTTCCAGGAATTTAT 1289
INTRON_3 14201 CCATGTCCTGTAAATTTTCTAGTTTGTGCACGTAAAGGTGTTCCTGGTAG 14250
v v ii i i v i
C L1PB_orf2#LIN 1288 CCATCTCCTCTAGGTTTTCTAGTTTATGCGCGTAAAGGTGTTCATAGTAG 1239
INTRON_3 14251 CCTTGAATTATCTTTTGCATTTCTGTGGTATTGGCTGTAATATCTCCCAT 14300
v i i ii i i
C L1PB_orf2#LIN 1238 CCTTGAATGATCTTTTGTATTTCTGTGGTGTCAGTTGTAATATCTCCCGT 1189
INTRON_3 14301 CCCATTTCTAATTGAGCTTATTAGGATCTTCTCTCTTCTTTTCTTGGTTA 14350
ii i v i
C L1PB_orf2#LIN 1188 TTCGTTTCTAATTGAGCTTATTTGGATTTTCTCTCTTCTTTTCTTGGTTA 1139
INTRON_3 14351 ATCTCACTAATGATGTATCAATTTTGTTTATCTCTTCAAAGAACCAGCTT 14400
ii i v i i
C L1PB_orf2#LIN 1138 ATCTTGCTAATGGTCTATCAATTTTATTTATCTTTTCAAAGAACCAGCTT 1089
INTRON_3 14401 TTTGTTTCTTTTATCTTTTTT-TTTTTTTG---GTTTCAATTTCATGTAA 14446
v v - --- v i
C L1PB_orf2#LIN 1088 TTTGTTTCATTTATCTTTTGTATTTTTTTGTTTGTTTCAATTTCATTTAG 1039
INTRON_3 14447 TTCTTCTCTGATCTTG---ATTTCTTTTCTTCTGCTTGGTTTGGGTTTGG 14493
v --- i v
C L1PB_orf2#LIN 1038 TTCTGCTCTGATCTTGGTTATTTCCTTTCTTCTGCTGGGTTTGGGTTTGG 989
INTRON_3 14494 TTTGTTCTTGTTTCTCTAGTTCCTTGAAGTATGATCTTAGATTGTTTATT 14543
i i i i i
C L1PB_orf2#LIN 988 TTTGTTCTTGTTTCTCTAGTTCCTTGAGGTGTGACCTTAGATTGTCTGTT 939
INTRON_3 14544 TGTACTCTTTCAGACTTTTTCATGTAGGCATTTGATGCTATGAACTTTCC 14593
i v iiv
C L1PB_orf2#LIN 938 TGTGCTCTTTCAGACTTTTTGATGTAGGCATTTAGGGCTATGAACTTTCC 889
INTRON_3 14594 TCTTAGCATTGCTTTAGCTGTATCCCGGAGGTTTTGAGAAGTTGAATCAC 14643
ii i v i v i vi
C L1PB_orf2#LIN 888 TCTTAGCACCGCCTTTGCTGTATCCCAGAGGTTTTGATAGGTTGTGTCAC 839
INTRON_3 14644 GGTTATGATTCAGTTCAAAGAATTAAAAAAATTTCCGTCTTGATTTCATT 14693
vi i vi i vvvv - i
C L1PB_orf2#LIN 838 TATTGTCGTTCAGTTCGAAGAATTTTTTAA-TTTCCATCTTGATTTCATT 790
INTRON_3 14694 GTTGACCCAAAGATCATTCAAGAGCAGATTATTTAATTTCCATGTATTTG 14743
? v i i
C L1PB_orf2#LIN 789 NTTGACCCAATGATCATTCAGGAGCAGGTTATTTAATTTCCATGTATTTG 740
INTRON_3 14744 TATAGTTCTGAGGGTTTCTTTTGGAGTTAATTTCTAGTTTTATTC-ACTG 14792
i i i i i i i -
C L1PB_orf2#LIN 739 CATGGTTTTGAAGGTTCCTTTTGGAGTTGATTTCCAGTTTTATTCCACTG 690
INTRON_3 14793 TGTTCTGAGAGGATACTTGATATAATTTCAATTTTTAAAAAATGTATTGA 14842
v ii i ivv - v
C L1PB_orf2#LIN 689 TGGTCTGAGAGAGTGCTTGATATAATTTCAATTTTCTTAAA-TTTATTGA 641
INTRON_3 14843 GACTTGTTTTGTGACATAT---ATGGTCTATCTTGGTGCATATTCTATGT 14889
i i i v --- v v ?i i
C L1PB_orf2#LIN 640 GGCTCGTTTTGTGGCCTATCATATGGTCTATCTTGGAGAANGTTCCATGT 591
INTRON_3 14890 GCTGATGAAAAGAATGTATATTCTACAGATGTTGAGTAGAATGTTCTGTA 14939
? v i i v i i
C L1PB_orf2#LIN 590 GCTGNTGAATAGAATGTGTATTCTGCAGTTGTTGGGTGGAATGTTCTGTA 541
INTRON_3 14940 AATATCTGCTAAGTCCATTTGTTCTAGGTTATAGTTTAAGTCCCTTGTTT 14989
? i i v i v
C L1PB_orf2#LIN 540 NATATCTGTTAAGTCCATTTGTTCCAGGGTATAGTTTAAATCCATTGTTT 491
INTRON_3 14990 CTTTGTTGTCTTTCTGTATTGATGACCTGTCTAGTGCTGTCAGTGAAATA 15039
v v i i
C L1PB_orf2#LIN 490 CTTTGTTGACTTTCTGTCTTGATGACCTGTCTAGTGCTGTCAGTGGAGTA 441
INTRON_3 15040 TTGAAGTCCCCCACCATTATTGTGTTGCTGTGTATCTCATTTC 15082
i v
C L1PB_orf2#LIN 440 TTGAAGTCCCCCACTATTATTGTGTTGCTGTCTATCTCATTTC 398
Matrix = 20p37g.matrix
Transitions / transversions = 1.75 (96 / 55)
Gap_init rate = 0.01 (12 / 1327), avg. gap size = 2.00 (24 / 12)
+ 4440 9.7 0.3 0.5 INTRON_3 15389 16010 (384171) C L1PA10 LINE/L1 (6) 6162 5542 11
ANNOTATION EVIDENCE:
4440 9.70 0.32 0.48 INTRON_3 15389 16010 384171 C L1PA10_3end LINE/L1 289 909 6 22
INTRON_3 15389 TTAAATTTTATTTTAAGTTCTGGGATACATGTGCAGGATATGAATATTTG 15438
v i i i v vi
C L1PA10_3end#L 909 TTAATTTTTATTTTAAGTTCCGGGGTACATGTGCAGGATGTGCAGGTTTG 860
INTRON_3 15439 TTACATAGGTAAACATGTGCTATGGTGGTTTGCTGCGCCTATCAACCCAT 15488
i i i
C L1PA10_3end#L 859 TTACATAGGTAAACGTGTGCCATGGTGGTTTGCTGCACCTATCAACCCAT 810
INTRON_3 15489 CACCTAGGTATTAAGCCCAGCATGCATTAGCTATTTTTCCTAATGCTTTT 15538
i i
C L1PA10_3end#L 809 CACCTAGGTATTAAGCCCAGCATGCATTAGCTATTTTTCCTAATGCTCTC 760
INTRON_3 15539 CTTCCCCTTGCCAC-ATCCCCCAGCAGGCCCCAGTATGTGTTGTTTCCCT 15587
i iii v - i ii i i
C L1PA10_3end#L 759 CCTCCCCCCACCCCCACCCCCCGACAGGCCCCAGTGTGTGTTGTTCCCCT 710
INTRON_3 15588 CCCTGT-TCCAGGTGTTCTCACTGTTTAGGTCCCACTTATAAGTGAGAAC 15636
- v i i v
C L1PA10_3end#L 709 CCCTGTGTCCATGTGTTCTCATTGTTCAGCTCCCACTTATAAGTGAGAAC 660
INTRON_3 15637 ATATGGTGTTTGGTTTTCTATTCCTTTGTTAGTTTGCTGAGGATAATGGC 15686
ii i vi
C L1PA10_3end#L 659 ATGCGGTGTTTGGTTTTCTGTTCCTGCGTTAGTTTGCTGAGGATAATGGC 610
INTRON_3 15687 TTCCAGGTTCATCCATGTCCCTACAAAGGACATGATCTCATTCCTTTTTA 15736
v i i
C L1PA10_3end#L 609 TTCCAGCTCCATCCATGTCCCTGCAAAGGACATGATCTCATTCCTTTTTA 560
INTRON_3 15737 TGGCTGCATCGTATTCCATGGTGTATCTTCTGTACCACATTTTCTTTATT 15786
v v --- i
C L1PA10_3end#L 559 TGGCTGCATAGTATTCCATGGTGTATAT---GTACCACATTTTCTTTATC 513
INTRON_3 15787 CAGTCTATCATTGATGGGTATTTTGGTTGATTCCATGTCTTTGCTATTGT 15836
i v
C L1PA10_3end#L 512 CAGTCTATCATTGATGGGCATTTGGGTTGATTCCATGTCTTTGCTATTGT 463
INTRON_3 15837 GAATAGTGCTGGAATGAACATATGCATACATATATCTTTGTAATATAATA 15886
v ii i i i i v i
C L1PA10_3end#L 462 GAATAGTGCTGCAATGAACATACACGTGCATGTATCTTTATAATAGAATG 413
INTRON_3 15887 ATTTATATTCCTTTGGGTATATACCCTGTAATGGGATTGTTGAGTCAAAT 15936
v i i
C L1PA10_3end#L 412 ATTTATATTCCTTTGGGTATATACCCAGTAATGGGATTGCTGGGTCAAAT 363
INTRON_3 15937 GGTATTTCTGGTTCTAGGTCTTTAAGGAATTGCCACATCATCTTCCGCTA 15986
i i i iii i v
C L1PA10_3end#L 362 GGTATTTCTGGTTCTAGATCTTTGAGGAATCGCCACACTGTCTTCCACAA 313
INTRON_3 15987 TGGTTGAACTAACTTACATTCCCA 16010
i
C L1PA10_3end#L 312 TGGTTGAACTAATTTACATTCCCA 289
Matrix = 18p37g.matrix
Transitions / transversions = 3.00 (45 / 15)
Gap_init rate = 0.00 (3 / 621), avg. gap size = 1.67 (5 / 3)
+ 9986 17.6 2.1 0.9 INTRON_3 16011 18795 (381386) C L1PB1 LINE/L1 (3934) 2925 1 6
ANNOTATION EVIDENCE:
7600 21.89 1.55 2.45 INTRON_3 16011 16102 384079 C L1M2_orf2 LINE/L1 16 100 3191 60
INTRON_3 16011 GTTTGGTGGATTTTTATCCATTCTGCCATTCTATATCTTTTAAGTGGAGC 16060
------- v i i v v
C L1M2_orf2#LIN 100 GTTT-------TTTTATCCATTCAGCCACTCTATGTCTTTTAATTGGAGA 58
INTRON_3 16061 ATTTAGGCCATTTACATTCAACATTAGTATTGAGATATGAGG 16102
iv vi ? v v vi i
C L1M2_orf2#LIN 57 ATTTAATCCATTTACATTCAAGGTNATTATTGATAGGTAAGG 16
Matrix = 20p37g.matrix
Transitions / transversions = 0.75 (6 / 8)
Gap_init rate = 0.01 (1 / 91), avg. gap size = 7.00 (7 / 1)
3515 25.88 2.37 2.81 INTRON_3 16021 17201 382980 C L1PA15-16_5end LINE/L1 1734 2909 53 61
INTRON_3 16021 TTTTTATCCATTCTGCCATTCTATATCTTTTAAGTGGAGCATTTAGGCCA 16070
vii i i ii i i
C L1PA15-16_5en 2909 TTTTTATCCAACTTGCCACTCTGTGCCTTTTAAGTGGGGCATTTAGACCA 2860
INTRON_3 16071 TTTACATTCAACATTAGTATTGAGATATGAGGTATTG-TTCTGTTCTGTA 16119
vi i v i v - i i iv -
C L1PA15-16_5en 2859 TTTACATTCAAGGTTAATATTGATATGTGAGGTTTTGATCCTATCGTG-A 2811
INTRON_3 16120 TTCTAATTGTTGCCTGAATACCTTGTGTTTTTTTCCCCATTGTGTTATTG 16169
---- i iv iv i i iv i ----- vi
C L1PA15-16_5en 2810 ----AGTTGTTAGCTGGTTGCTTTGTAGTTTCT-----ATTGTGTGGTTG 2770
INTRON_3 16170 TTTTATAGACCCTATGAGATTTATGCTTTAAGGAAGTTCTATTTTGGT-- 16217
i ivi i i v v i i - viv i -- v --
C L1PA15-16_5en 2769 CTTTATAGGGTCTGTGGGCTATGTACTT-AAGTGTGTTTT--TGTGGTAG 2723
INTRON_3 16218 ---GTAT--TTTAAGGTTTTGTTTCAAGATTTAGAACTCCTTTTCGCATT 16262
--- -- i---- i v vi i vv v i
C L1PA15-16_5en 2722 CAGGTATCGTTC----TTTCGTTTCCATGTTTAGAACTCCCTTAAGGATC 2677
INTRON_3 16263 TCTTGTAGTGCTGGCTTGGTAGTGGTGAATTCTCTCAGCATTTG----TC 16308
iv ii i i iii i i ii ----
C L1PA15-16_5en 2676 TCTTGTAAGGCTGGTCTAGTGGTAACGAATTCCCTTAGCGCTTGCTTGTC 2627
INTRON_3 16309 TGAAAAAGACTTTATCTGTCCTTCATTTAAGAAGCTTAGTTTTGTTGGAT 16358
i i i v ii v v iv
C L1PA15-16_5en 2626 TGGAAAAGATTTTATTTCTCCTTCGCTTATGAAGCTTAGTTTGGCGGGAT 2577
INTRON_3 16359 ACAAAATTGTTGGCTGACAATTATTTTGTTTCAGGAGGCTAAAGATAATA 16408
ii v i iv v v v v i v i i ivv
C L1PA15-16_5en 2576 ATGAAATTCTTGGTTGGAATTTCTTTTCTTTAAGAATGCTGAAAATAGGC 2527
INTRON_3 16409 CTCCAATCCCTTCTGGCTTGTAGGGTTTCTGCTGAGAATTC---TGTTAA 16455
i i i i v --- i
C L1PA15-16_5en 2526 CCCCAATCTCTCCTGGCTTGTAAGGTTTCTGCTGAGAAGTCCGCTGTTAG 2477
INTRON_3 16456 TCTTATAGGTTTTTCTGTATAGTTTACCTGATGCTTTTGTCTCACAGGTC 16505
i v i v ii v i vv v i ivi v vi v vii
C L1PA15-16_5en 2476 CCTGATGGGGTTCCCTTTGTACGTGATCTGACCTTTTTCTCTAGCTGCCT 2427
INTRON_3 16506 TTAAGATTCTTTCCTGT-GTCTTGATTATAGATAACTTGATGACTATGTG 16554
i i v - iv iiv i i iii i i
C L1PA15-16_5en 2426 TTAAGATTTTTTTCTTTAGCGTTGACCTTGGACAGTCTGGTGACTATATG 2377
INTRON_3 16555 CCTAGGTGATGATCTTTTTGCAATGAATTCCTCAGATGTTCTTTGAGCTT 16604
v v v i vv v ii v i i iii
C L1PA15-16_5en 2376 CCTTGGTGATGTTCATTTTGTATAGTATCTCGCAGGTGTTCTCTGGATTT 2327
INTRON_3 16605 CTAGTATTTAGTTGTCTAGATCTCTAGCAAGGCCAGGGAAGTTTTCTCCA 16654
v i i v vv iii i iv
C L1PA15-16_5en 2326 CTTGTATCTGGATGTCTACCTCTCTAGCAAGATTAGGGAAATTTTCTTGA 2277
INTRON_3 16655 ATTAGTCCCTCAAATAAGTTTTCCAAACTTTTAGATTTCTCTTCTTC--- 16701
v v iii v viv i i ---
C L1PA15-16_5en 2276 ATTATTCCCTCAAATATGTTTTCCAGGTTGTTTACTTTTTCTCCTTCTCT 2227
INTRON_3 16702 CTTAGGAACACCAGTTATTCTTAGGTTTGTCTGTTTGACATAATTTCAAA 16751
i ii i v v vii i v ii v
C L1PA15-16_5en 2226 CTCAGGAATGCCAATAATTCGTAGGTTTGGTCGCTTTACATAATCCCATA 2177
INTRON_3 16752 TTTCTTGGAAGCTTTGTTCATTTTTCTCAAATTCTTTTTTCTTAGTCTTT 16801
iii ii - v vi i
C L1PA15-16_5en 2176 TTTCTCAAAGACTTTGTTCATTTTT-TAAAATTCTTTTTTCTTTATTTTT 2128
INTRON_3 16802 GTCCGATTGGGTTAATTCGAAAG-CC--TCTTTGAGCTCTGAAGTTCTTT 16848
i i i - -- ii i
C L1PA15-16_5en 2127 GTCTGACTGGGTTAGTTCGAAAGACCGGTCTTCAAGCTCTGAAATTCTTT 2078
INTRON_3 16849 CTTCTACTTGTTCTAGTCGATTGTTGAAACTTTCCAGTGCATTTTGTATT 16898
i v i v v i i v v i v v
C L1PA15-16_5en 2077 CTTCTGCTTGGTCCAGTCTATTGATAAAGCTTTCAATTGTATTTTGAAAT 2028
INTRON_3 16899 TCTCTAAGTGTGTCTTTCATTTCCAGAAGTTGTGATTG-TTTTTCTTTAT 16947
ii v i v i v - i i v
C L1PA15-16_5en 2027 TCCTTAAGTGAGTTTTTCAATTCCAGAAGCTCTGATTGATTTCTTTTTAA 1978
INTRON_3 16948 GATATCTATTTCTCTGAAGCATTTTTAATCCATATTCCATATTGTTCTTT 16997
i i i -------- ii ---- v i iiv --
C L1PA15-16_5en 1977 GATGTTTATCTCT--------TCCTT----CATTTCCTGGATTG--CTTT 1942
INTRON_3 16998 TCA--TTTCTTTAAGTTAGTTCTCTCATTTCTCTGGTATCTCCTTGAGTA 17045
vv -- iv ii i vvvi v v v v iv
C L1PA15-16_5en 1941 AGAAGTTTCTTTGTGTTGATTTTCAACCTTGTCTTGGATCTCATTGAGCT 1892
INTRON_3 17046 GCTTAATAATCAATCCCCTGAATTGCTTATCAGGCAATTCAGAATT--CT 17093
v i vii v v ii vi v v v v i -- v
C L1PA15-16_5en 1891 TCCTTGCAATCCATGCTTTGAATTCTTTATCTGTCATTTCTGAGTTTCCA 1842
INTRON_3 17094 TCTTGGTTTGGATCCATTGCTGGGGAGCTAGTGTGATCTTTTCAGGGTAT 17143
i v iv i i viv i
C L1PA15-16_5en 1841 TTTTGGTTAGGGACCATTGCTGGAGAGCTAGTGTGATCCTTTGGTGGTGT 1792
INTRON_3 17144 TA-TAGAGCCCTGTTTTATCATATTACCAGAATTGTTTTTCTGGTTCCTT 17192
i - v vi vvi - iv i v viv
C L1PA15-16_5en 1791 CACTACATTCAGATTTT-TCATGGTGCCAGAATTCTTGCGCTGGTTCCTT 1743
INTRON_3 17193 CTCATTTGG 17201
i
C L1PA15-16_5en 1742 CTCATCTGG 1734
Matrix = 20p37g.matrix
Transitions / transversions = 1.50 (178 / 119)
Gap_init rate = 0.02 (24 / 1180), avg. gap size = 2.54 (61 / 24)
9986 13.99 2.22 0.55 INTRON_3 16524 18141 382040 C L1PBa_5end LINE/L1 710 2354 617 62
INTRON_3 16524 TCTTGATTATAGATAACTTGATGACTATGTGCCTAGGTGATGATCTTTTT 16573
i v i
C L1PBa_5end#LI 2354 TCTTGACTTTAGATAACCTGATGACTATGTGCCTAGGTGATGATCTTTTT 2305
INTRON_3 16574 GCAATGAATTCCTCAGATGTTCTTTGAGCT---------TCTAGTATTTA 16614
ii i i i --------- v i
C L1PBa_5end#LI 2304 GTGATGAATTTCCCAGGTGTTCTTTGAGCTCTTTGAGCTTCTTGTATTTG 2255
INTRON_3 16615 GTTGTCTAGATCTCTAGCAAGGCCAGGGAAGTTTTCTCCAATTAGTCCCT 16664
v ii ? v
C L1PBa_5end#LI 2254 GATGTCTAGATCTCTAGCAAGGCCAGGGAAGTTTTCCTCRATTATTCCCT 2205
INTRON_3 16665 CAAATAAGTTTTCCAAACTTTTAGATTTCTCTTCTTCCTTAGGAACACCA 16714
v i
C L1PBa_5end#LI 2204 CAAATATGTTTTCCAAACTTTTAGATTTCTCTTCTTCCTCAGGAACACCA 2155
INTRON_3 16715 GTTATTCTTAGGTTTGTCTGTTTGACATAATTTCAAATTTCTTGGAAGCT 16764
i viii i ii i i
C L1PBa_5end#LI 2154 ATTATTCTTAGGTTTGGTCATTTAACATAATCCCAAACTTCTTGGAGGCT 2105
INTRON_3 16765 TTGTTCATTTTTCTCAAATTCTTTTTTCTTAGTCTTTGTCCGATTGGGTT 16814
i v v iv
C L1PBa_5end#LI 2104 TTGTTCATTTTTTTAAAATTCTTTTTTCTTTGTCTTTGTTGGATTGGGTT 2055
INTRON_3 16815 AATTCGAAAGCCT---CTTTGAGCTCTGAAGTTCTTTCTTCTACTTGTTC 16861
? ---
C L1PBa_5end#LI 2054 AATTYGAAAGCCTTGTCTTTGAGCTCTGAAGTTCTTTCTTCTACTTGTTC 2005
INTRON_3 16862 TAGTCGATTGTTGAAACTTTCCAGTGCATTTTGTATTTCTCTAAGTGTGT 16911
v v v i ? i
C L1PBa_5end#LI 2004 GATTCTATTGCTGARACTTTCCAGTGCATTTTGCATTTCTCTAAGTGTGT 1955
INTRON_3 16912 CTTTCATTTCCAGAAGTTGTGATT-----GTTTTTC-TTTATGATATCTA 16955
? ----- i- ?
C L1PBa_5end#LI 1954 CYTTCATTTCCAGAAGTTGTGATTAGTTTGTTTTTTATTTATGNTATCTA 1905
INTRON_3 16956 TTTCTCTGAAGCATTTTTAATCCATATTCCATATTGTTCTTTTCA-TTTC 17004
i vv iv ? i ii ii i i -
C L1PBa_5end#LI 1904 TTTCTCTGGAGATTTTTCCATYCATATCCTGTATCATTTTTTTTAATTTC 1855
INTRON_3 17005 TTTAAGTTAGTTCTCTCATTTCTCTGGTATCTCCTTGAGTAGCTTAATAA 17054
i i v v ii
C L1PBa_5end#LI 1854 TTTAAGTTGGTTTTCACCTTTCTCTGGTGCCTCCTTGAGTAGCTTAATAA 1805
INTRON_3 17055 TCAATCCCCTGAATTGCTTATCAGGCAATTCAGAA--TTCTTCTTGGTTT 17102
i ii vi v v i--
C L1PBa_5end#LI 1804 TCAACCTTCTGAATTCTTTTTCTGGCAATTCAGAGATTTCTTCTTGGTTT 1755
INTRON_3 17103 GGATCCATTGCTGGGGAGCTAGTGTGATCTTTTCAGGGTATTATAGAGCC 17152
v vi i v i
C L1PBa_5end#LI 1754 GGATCCATTGCTGGTGAGCTAGTGTGATCTTTTGGGGGTGTTAAAGAACC 1705
INTRON_3 17153 CTGTTTTATCATATTACCAGAATTGTTTTTCTGGTTCCTTCTCATTTGGG 17202
i i
C L1PBa_5end#LI 1704 TTGTTTTGTCATATTACCAGAATTGTTTTTCTGGTTCCTTCTCATTTGGG 1655
INTRON_3 17203 TAGACTATGTCAGAGGGAAGATCTGGGACTCAAGAGCTGCTGTTCAGTTT 17252
i v
C L1PBa_5end#LI 1654 TAGACTATGTCAGAGGGAAGATCTGGGACTCAAGGGCTGCTGTTCAGATT 1605
INTRON_3 17253 CTTTTGTCCCATGGTGTGATCCCTTCATGTGGTGCTCTTCCCCTTCCCCT 17302
v v v i
C L1PBa_5end#LI 1604 CTTTTGTCCCATGGGGTGCTCCCTTGATGTGGTGCTCTCCCCCTTCCCCT 1555
INTRON_3 17303 AGGGATGGGGCTTTCTGGGAGCCAGACTGCAATGATCATTATTGCCCTTC 17352
i i ? i i ii i
C L1PBa_5end#LI 1554 AGGGATGGGGCTTCCTGAGAGCYAAACTGCAGTGATTGTTATTGCTCTTC 1505
INTRON_3 17353 TGGGTCTCGCTATCAAGTGGGGCTCCCAGGCTCCAAGCTGGTTCTGGGGA 17402
v i i v i v i iii v
C L1PBa_5end#LI 1504 TGGGTCTAGCCACCCAGTGGAGCTACTAGGCTCTGGGCTGGTACTGGGGA 1455
INTRON_3 17403 ATGTCTGCAAAGAGTCCTATGATGTGATCCATCTTCAGGTCTC--AGCCA 17450
i i --
C L1PBa_5end#LI 1454 GTGTCTGCAAAGAGTCCTGTGATGTGATCCATCTTCAGGTCTCTCAGCCA 1405
INTRON_3 17451 TGGATACTAGTGTCTGCTGTGGTGGAGGTGGCAGGGGAGTAAACTAGACT 17500
i iii v i i v i
C L1PBa_5end#LI 1404 TGGATACCAGCACCTGCTCTGGTGGAGGTAGCAGGGGAGTGAAGTGGACT 1355
INTRON_3 17501 GTGTCAGGGTCCTTAGTTGTAGCTATGTTTAGTGTGCTGGCTTTCTTGAA 17550
v v i i v i
C L1PBa_5end#LI 1354 CTGTGAGGGTCCTTGGTTGTAGTTTTGTTTAGTGTGCTGGTTTTCTTGAA 1305
INTRON_3 17551 TGATGGATTATGCTAGCAGTAAAGTTGTCATGTGTAGAGACTCAGAACCT 17600
v - i i v v i
C L1PBa_5end#LI 1304 TGCTGG-TTATGCTAGCAGTGAAGTTGTCACGTGGACAGACTCAGGACCT 1256
INTRON_3 17601 CTGGTTAGCCAGGATGTTGCAGGCAGTAGAATTACCTGTTGTTTCCTTAT 17650
i v i iv
C L1PBa_5end#LI 1255 CTGGTTAGCCAGGATGTTGCAGGCAGTGGAATTAGCTGTTGTTTTCTCCT 1206
INTRON_3 17651 TCTTGGGGGAGCAGGGTTATTCTGTCATGAGTTGTTGTAATGGCCTGAGT 17700
i v -- i i i i
C L1PBa_5end#LI 1205 TCCTTGG--AGCAGGGTTGTTCTGTTATGAGTTGCTGTAATGGCTTGAGT 1158
INTRON_3 17701 TGGTTGACCTCCAGCCAGAAGGTGGCACTTTCAAGAGAGCACCAGCTGCA 17750
i i ? i ii
C L1PBa_5end#LI 1157 TGGTTGGCCTCCAGCCAGGAGGTGGCNCTTTCAAGAGAGCATCAGCTGTG 1108
INTRON_3 17751 ACAGTAGTAAGGAG-ATCTACGCTTGCCATACATTGGCCAGGGTAACTAT 17799
ii - i - vi v v viv vi v i v
C L1PBa_5end#LI 1107 GTAGTA-TAGGGAGGATACAAGCTTGCCCTAGGGTCACCTGGATAAGTAT 1059
INTRON_3 17800 TCTGGTTTCCCAGGCGATGGGTGGGGCCATAAAGCTTGGATGAGCT---G 17846
v i i i ii i ivv v v ---
C L1PBa_5end#LI 1058 TCAGGTTTCTCAGGTGGTGGGCAGGGCCATAGAGCTCCCAAGAGATTATG 1009
INTRON_3 17847 TCTTTTCTGTTCAGCTACTAGGGCAGGTAGTGAAATACCATCAGGTTGGG 17896
? v v ? i i? v v v
C L1PBa_5end#LI 1008 TCYTTTGTCTTCRGCTACCAGGGTRGGTAGAGAAAGACCATCAGGTGGGG 959
INTRON_3 17897 GCAGGGTTAGGTGAGTCTGGGCTCAGACT-----TGGGCAAGGCTTGCTG 17941
i?v i ----- ?i
C L1PBa_5end#LI 958 GCAGGGTTAGGCRTGTCTGAGCTCAGACTCTCCTTGGGCRGGGCTTGCTG 909
INTRON_3 17942 CGGCCACTGTGGGGGATTGGT-TGTGGTTCTCAGGCCAATGGGGTTATAT 17990
i ii v v- i i
C L1PBa_5end#LI 908 TGGCTGCTGTGGGGGATGGGGGTGTGGTTCTCAGGCCAATGGAGTTATGT 859
INTRON_3 17991 TCCAGAGGGGATTATGGCTGCCTCTGCTGT---GTCACATAGTTCACCAG 18037
vii i--- i i v
C L1PBa_5end#LI 858 TCCCAGGGGGATTATGGCTGCCTCTGCTGCTGCGTCATACAGGTCACCAG 809
INTRON_3 18038 GGAAGTGGGGGCATAGCTGGTAGCAAAAGGCCTCACTCAGCTCCCACACA 18087
v - ii i ii v i ii
C L1PBa_5end#LI 808 GGAAGTGGGGGAA-AGCCAGCAGTGACAGGCCTCACCCAGCTCCCATGCA 760
INTRON_3 18088 GTTGGTAAGGCTGGTCTTGTTCCTGCAGTGCCTCACTCAGACCTTGCACC 18137
iii i ii iii ii v i - i - v--
C L1PBa_5end#LI 759 GCCAGCAAGGCCAGTCTCACTCCCACTGTGCCCC-CCCA-ACA--GCACC 714
INTRON_3 18138 AGGT 18141
i
C L1PBa_5end#LI 713 AAGT 710
Matrix = 20p37g.matrix
Transitions / transversions = 2.07 (143 / 69)
Gap_init rate = 0.01 (19 / 1617), avg. gap size = 2.37 (45 / 19)
3674 20.30 1.78 0.44 INTRON_3 18123 18795 381386 C L1PBa_5end LINE/L1 1 682 2289 63
INTRON_3 18123 CTCAGACCTTGCACCAGGTCGTAAGCTTCCCTGCTGAGAAAGCAAGCACA 18172
v v v iiii i i? vi
C L1PBa_5end#LI 682 CTGAGAACTTGCCCCAGGCTACAAGCCTCCCCRCTGAGAAAGCAAGCAGG 633
INTRON_3 18173 GATTTCAGGCCCTGCCCCTCCC-ATCTGCTCACACTGTCATCACCAGCTC 18221
v ?ii -ii i ii v vv i i
C L1PBa_5end#LI 632 GCTTTCAGGCNTCGCCCCTCCCCGCCTGCCCACACCATCAGCTGCGGCTT 583
INTRON_3 18222 CTGTGCTCGTTATCTGCAGCAGTCCCCATTCGCCTCCTGGATTCTGCTCA 18271
? - v i ii i i ?i
C L1PBa_5end#LI 582 CTGTGCTCRT-ATCTGCAGCACTTCCCATTCATCCCCCGGATTCTGYCCA 534
INTRON_3 18272 TGAAAATTCACTCCCAGTCAAAATTATTACAGATTTCAGTTGGAAGCTTC 18321
v ?iv?i ? ? i v i i
C L1PBa_5end#LI 533 GGAAAATTCRTGYTCRGTCRAAATTATTACAAAGTTCAGCTGGAAGTTTC 484
INTRON_3 18322 TTTCACCCTGTAGCCCCTCCCTAATTCTACTTGCTGCCTTCTCTAGGGAC 18371
i v i i ?i i i v v i i i i
C L1PBa_5end#LI 483 CTTCTCCCTGTGGTCYTTCCCCAATTCCACTGGCAGCCCTCCCCAAGGAC 434
INTRON_3 18372 CCTTGAGAGATAA-GTTAGGGATGACTTCCTTGGGCTCGAGCTAAAGACT 18420
i v - i ii i i i iii
C L1PBa_5end#LI 433 CCCTGTGAGATAAAGTCAGAAATGGCTTCCCTGGGCTTGAGCTGGGGACT 384
INTRON_3 18421 AGGAGTGCCTACAAGGCTCTTCCCACTGTTGGTTCTACTTCTGTATTTTG 18470
i i i vv i i ii
C L1PBa_5end#LI 383 GGGAGTGCCTACAGGGCTCTTCCCACTGCTTCTTCTACTTTTATATTTCA 334
INTRON_3 18471 CATGGTTCCCTAAATCCATTTCAACTATAGGTAAGGTTAAATCTTTCTCC 18520
v? i i i i v? i
C L1PBa_5end#LI 333 CTNGGCTCTCTAAATTCATTTCAGCTCYAGGTAAGGTTAAATCCTTCTCC 284
INTRON_3 18521 TGTGATCTGGATTTTCAGATTCCCCATTGGGGATGTGTGTTCAGAGGCA- 18569
i v i -
C L1PBa_5end#LI 283 TGTGATCTGGATTTTCAGGTTCCCCAGTGAGGATGTGTGTTCAGAGGCAG 234
INTRON_3 18570 -------TGTTTTCCCCCTCTCACGCTTTGGGAACTCACAGTTTTTTGCC 18612
-------ivi i v ? v
C L1PBa_5end#LI 233 ACTTTCCCCCTTTCCCCCTCTCACACTTTGGGCACTCACAGTTTTTYGGC 184
INTRON_3 18613 TGTG--ATGGAGAATTTGCAGTGGCATGCCACTTCTTTCAAAGGATCAGT 18660
v-- -- ?i v i v
C L1PBa_5end#LI 183 TGTCTCATGGAG--TTTGCAGYAGCAAGCCACTTCTTTCAAAGGGTCTGT 136
INTRON_3 18661 GAATTCTTTCAGTTTTCCTAGTACGTTCCCATGGTGGTTCTTGGAGCAAA 18710
ii i i ii i
C L1PBa_5end#LI 135 GAATTCTTTTGGTTTTCCTGGTATGTTCCTGTGGTAGTTCTTGGAGCAAA 86
INTRON_3 18711 AGTTCACAGTGTGAATCTCCACATGCTGTTCTGTCCATGCCAGTGGGAAC 18760
ii? i ?? v v i
C L1PBa_5end#LI 85 AGTTCATGRTGTGAGTCTCCACAYRCTGTTCTGTCCATCCAAGTGGGAGC 36
INTRON_3 18761 TGTGTATTAACCCAGTATCCAATCTGCCGTCTTCC 18795
iivi ii v iv v i? i i
C L1PBa_5end#LI 35 TGCAAGTTAGTCCTGCCTCCTATCCRCCATTTTCC 1
Matrix = 20p37g.matrix
Transitions / transversions = 2.61 (86 / 33)
Gap_init rate = 0.01 (6 / 672), avg. gap size = 2.50 (15 / 6)
+ 191 23.2 1.8 7.5 INTRON_3 19158 19213 (380968) C L2b LINE/L2 (4) 3371 3319 12
ANNOTATION EVIDENCE:
191 23.18 1.79 7.55 INTRON_3 19158 19213 380968 C L2b_3end LINE/L2 410 462 4 27
INTRON_3 19158 ATTCAACTTTCAACAG-CATTTGCTGAGTGCTTACTGTATACCACTATCT 19206
--- i- i ii i i i v-ii i
C L2b_3end#LINE 462 ATTCA---TTCAACAAACATTTACTGAGCACCTACTGTGTGCCAG-GCCC 417
INTRON_3 19207 TCTGCTG 19213
v
C L2b_3end#LINE 416 TGTGCTG 410
Matrix = 25p37g.matrix
Transitions / transversions = 5.00 (10 / 2)
Gap_init rate = 0.05 (3 / 55), avg. gap size = 1.67 (5 / 3)
+ 3513 21.4 3.3 2.3 INTRON_3 19279 20742 (379439) + MER52A LTR/ERV1 1 1658 (465) 13
ANNOTATION EVIDENCE:
686 25.11 8.10 7.08 INTRON_3 19279 19488 380693 + MER52A LTR/ERV1 1 212 1543 105
INTRON_3 19279 TGATGGCAGTGGCAGCCCATATGGAGTGGCTGCTGTGAAGATGCCAGCTG 19328
i i i v i iv v i
MER52A#LTR/ER 1 TGATGGCAGCGGCGGCCCGTCTGGAGTGGCCGCTGCCATGATGCCGGCTG 50
INTRON_3 19329 CAGTTTGGGAGGCACAGCCAGGGCTGCACACTCCATGGAGCT-------- 19370
ivv i i i i i i--------
MER52A#LTR/ER 51 CAGCGGGGGAGGCGCGGCCGGGGCTGCGCGCTCCATGGAGCCAGCGGGAG 100
INTRON_3 19371 ---------GGCAGGAGCCCCACTCCATTTTGAGTTGGCACAGTGGGAGC 19411
--------- i i i v ii ---i i
MER52A#LTR/ER 101 CCGGGAACAGGCGGGAGCCCCGCCCCCTTCCGAGTTGG---GGCGGGAGC 147
INTRON_3 19412 CCCATCTTTCCAGACAAAGCTGAAGCTGCCCAGTGATGGCTGCGGACCCA 19461
i ------ i iiiv v i i------vi i
MER52A#LTR/ER 148 TCC------CCGGGTGCAGCTGCAGCCGCCCAA------ACGCAGACCCA 185
INTRON_3 19462 GGGATCTCTGCACTCTCAAATGCCAGG 19488
vv i ii iiiiv i
MER52A#LTR/ER 186 GGCCTCCCTGTGCTCTTGGGGGCCGGG 212
Matrix = 20p37g.matrix
Transitions / transversions = 3.08 (37 / 12)
Gap_init rate = 0.02 (4 / 209), avg. gap size = 8.00 (32 / 4)
3140 25.12 4.75 5.08 INTRON_3 19325 20272 379909 + MER52D LTR/ERV1 503 1447 676 106
INTRON_3 19325 GCTGCAGTTTGGGAGGCACAGCCAGGGCTGCACACTCCATGGAGCTGG-- 19372
i---- ii i --
MER52D#LTR/ER 503 GCTGCAA----GGAGGCACAGCCAGGGCTGCATGCTCCACGGAGCTGGTG 548
INTRON_3 19373 ----------------CAGGAGCCCCACTCCATTTTGAGTTGGCACAGTG 19406
---------------- i i - ?i? ???? vi
MER52D#LTR/ER 549 GGAGCCAGGGAGCAGGCAGGAGCCCCGCCCC-TNCNGNNNNGGCAGGGTG 597
INTRON_3 19407 GGAGCCCCATCTTTCCAGACAAAGCTGAAGCTGCCCAGTGATGGCTGCGG 19456
i ------- iiiv v v iviii i
MER52D#LTR/ER 598 GGAGCTCC-------CAGGTGCAGCTGCAGCTGCCCTGCTGCAGCTGTGG 640
INTRON_3 19457 ACCCAGGGATCTCTGCACTCTCAAATGCCAGGGAAG--CTCCTCTGCCCC 19504
v iiiiv v -- i i i
MER52D#LTR/ER 641 ACCCAGGCATCTCTGCACTCTTGGGGGCCCGGGAAGGCCCCCCCTACCCC 690
INTRON_3 19505 AGCAGGCTCGGAAGTGCCTACTCCTGCTGTCTGGCCTTGCCATGCTTCTG 19554
v ? ?i i i i i iv v i ii
MER52D#LTR/ER 691 TGCAGGCTNGGRGGTGTCTGCTCCCGCTGCCTGGCCTCTCCCTGCTCCCA 740
INTRON_3 19555 GTGCCTGCACCAATTTTGGAGCAAAGTTGAGGCCAAGCCTGGGTACTGTT 19604
ii v ? i i ?? i ? ii i
MER52D#LTR/ER 741 GCACCTGCTCCRATCTCGGAGCARNGTTGGGGCCAAGCCYGGGCGCTGTC 790
INTRON_3 19605 GCAACCTGGCTGGGTTGGCATGTGCTTGGGGCAGTGCTGACACACCAGTC 19654
i i i vv iiii i i i
MER52D#LTR/ER 791 ACAGCCTGGCCGGGTGTGCACACACTCGGGGCAGCGCTGACACACCAGCC 840
INTRON_3 19655 CCCTGCTGCCTTGGCCCCCTCTGGACTTTGGGTGCCAACAAACACAGGAG 19704
ii i ii i? i ii
MER52D#LTR/ER 841 CCCTGCCACCTCGGCCCCCTCCAGACTTTGGGCRCCAACAAGCATGGGAG 890
INTRON_3 19705 GGAGCCTGAGGGAGGGGCTGAGGGTGGCTCAGCACAGGCCTGCAGGCACC 19754
v ii - ii i i? v ii
MER52D#LTR/ER 891 GGAGGCCAAGGG-GGGGCTGAGGGCAGCTCGGTNCTGGCCTGCAGGTGCC 939
INTRON_3 19755 TCTTGGCACTAACAGCCTGGGAGTTGTGGACATGATTAATGGTGGCAGGA 19804
i iv ? ??iii ? ---------
MER52D#LTR/ER 940 CCTTGGCATGARCAGCCTGGGYRCCATGRACA---------GTGGCAGGA 980
INTRON_3 19805 GGCAGACAGGCTTCTGGGCAGAAAGTGGTGGGTATCTGGTGAAGCCCCAC 19854
i ?i i v ? vi ii
MER52D#LTR/ER 981 GGCAGACAGGCTCCTGGGYGGAAGGGGGYGGGTCCCCAGTGAAGCCCCAC 1030
INTRON_3 19855 CTTCAAGCCAGGAATTGCCTGAAGCATGGGGGCCAGGCTGTGAGTTCTGG 19904
i vv v ii iv i i?-
MER52D#LTR/ER 1031 CTTCAAGCCAGGGAGGGCCTGAAGCCTGGGGGCTGGGCTGCCAGTCCCR- 1079
INTRON_3 19905 CTGGAGTCTGAGGACCAGAGTGAGAACTTACGGT-CCTTTTTCCGGGCCC 19953
------- ---i i ii - i i i
MER52D#LTR/ER 1080 -------C---AGACCAGAGTGGGAACTTGTGGTGCCTTTTCCTGGGCCT 1119
INTRON_3 19954 ACCCATAGCCACCCATGGACCAAATCAGTACACACTTTCTCCCTTCTAAG 20003
i i i - i i ii i i i
MER52D#LTR/ER 1120 GCCCATGGCCGCCCATGGACCAA-TCGGCATGCACTTCCTCCCCTCTGAG 1168
INTRON_3 20004 -CCCGTAAAAACCCTGGACTCAGTCAGACT-CAGGCAGAAAT-CA-GGAT 20049
- i i ii i i i-v i i? - -i v
MER52D#LTR/ER 1169 GCCCATAAAAGCCCCAGGCTCAGCCAGACCAGAGACAGAGSTGCACAGAG 1218
INTRON_3 20050 GACCTGCCTGCAGGTA--TGAGCCACCCACTCCAGGTCTCCTCTCCAC-T 20096
i i iv -- vvvi ii vv ----- vvvv v-
MER52D#LTR/ER 1219 GACCTACCCGCAGAGAGATGAGGGCTCTGCTAGAG-----CTGAGGAGAT 1263
INTRON_3 20097 GA--GGA-------CTGCAGAATCAATGGGACAACCTGCCTCAGTGCCCA 20137
-- ------- i- -- ii v ii ii v i i-
MER52D#LTR/ER 1264 GACGGGATGACCAGCTGCAGAG-CA--GGAGCTACCCACTCCAGGGTCT- 1309
INTRON_3 20138 GGCGCAGCCTCAACTTTGCTCTGAA-ATTGGATAGGA-G--CTACCCACT 20183
-- - --i vi vv vv - i v i - -- i ii v
MER52D#LTR/ER 1310 --C-C--TCTCTGCTGAGAGCTGAAGACTTGATGGGATGACCTGCCTGCA 1354
INTRON_3 20184 CCATG----TCCCCTTTTTGCTGAAGGCTGCACAGACGTCAGGACAACCT 20229
vviv ---- v i i i ii v vv i ii v
MER52D#LTR/ER 1355 GAGAGGAGCTACCCTCTCTGCTAAGAGCTGAACACTCATTGGGACACCCT 1404
INTRON_3 20230 GCCTACGGATAGGAGCTACCCACTCTGGGTCTCCTCTCTGCTG 20272
v v i vi? vv
MER52D#LTR/ER 1405 GGCTACGGAGAGGAGCTGCCCACTGCRGGTCTCCTCTGAGCTG 1447
Matrix = 20p37g.matrix
Transitions / transversions = 2.50 (145 / 58)
Gap_init rate = 0.03 (29 / 947), avg. gap size = 3.21 (93 / 29)
3513 19.26 0.32 2.10 INTRON_3 19498 20128 380053 + MER52A LTR/ERV1 376 995 760 107
INTRON_3 19498 CTGCCCCAGCAGGCTCGGAAGTGCCTACTCCTGCTGTCTGGCCTTGCCAT 19547
i i - i i i i iv v
MER52A#LTR/ER 376 CCGCTCC-GCAGGCTCAGAAGTGCCTGCTCCCGCTGCCTGGCCTCTCCCT 424
INTRON_3 19548 GCTTCTGGTGCCTGCACCAATTTTGGAGCAAAGTTGAGGCCAAGCCTGGG 19597
i ? i i v i i ? i i
MER52A#LTR/ER 425 GCTCCYGGCGCCCGCTCCGATTTCGGAGCAAAGTTGYGGCCGAGCCCGGG 474
INTRON_3 19598 TACTGTTGCAACCTGGCTGGGTTGGCATGTGCTTGGGGCAGTGCTGACAC 19647
ii i i i vv iiiii i i
MER52A#LTR/ER 475 CGCTGTCGCAACCCGGCCGGGTGTGTGCACGCTCGGGGCAGCGCTGACAC 524
INTRON_3 19648 ACCAGTCCCCTGCTGCCTTGGCCCCCTCTGGACTTTGGGTGCCAACAAAC 19697
i i i i i i i i i
MER52A#LTR/ER 525 GCCAGCCCCCTGCCGCCTCGGCCCCCTCCGGACTTTGGGCGCCGACGAGC 574
INTRON_3 19698 ACAGGAGGGAGCCTGAGGGAGGGGCTGAGGGTGGCTCAGCACAGGCCTGC 19747
ii v i - ii i i ?
MER52A#LTR/ER 575 ATGGGAGGGAGGCCGAGGG-GGGGCTGAGGGCAGCTCGGCGCKGGCCTGC 623
INTRON_3 19748 AGGCACCTCTTGGCACTAACAGCCTGGGAGTTGTGGACATGATTAATGGT 19797
i i i v --- i--- --- i i
MER52A#LTR/ER 624 AGGCGCCCCTCGGCACGAACAGCCTGGG---TGC---CATGA---ACGGC 664
INTRON_3 19798 GGCAGGAGGCAGACAGGCTTCTGGGCAGAAAGTGGTGGGTATCTGGTGAA 19847
i i v i vi i
MER52A#LTR/ER 665 AGCAGGAGGCAGACAGGCTCCTGGGCAGAAAGGGGCGGGTCCCCGGTGAA 714
INTRON_3 19848 GCCCCACCTTCAAGCCAGGAATTGCCTGAAGCATGGGGGCCAGGCTGTGA 19897
i i iv v i iv
MER52A#LTR/ER 715 ACCCCACCTTCAAGCCAGGGACGGCCTGAAGCCTGGGGGCCGGGCTGCCA 764
INTRON_3 19898 GTTCTGGCTGGAGTCTGAGGACCAGAGTGAGAACTTACGGTCCTTTTTCC 19947
i v i v ? i ?i v i
MER52A#LTR/ER 765 GTTCCGGGTGGAGTCCGCGGMCCGGAGTGAGAACTTRTGGTGCTTTTTCT 814
INTRON_3 19948 GGGCCCACCCATAGCCACCCATGGACCAAATCAGTACACACTTTCTCCCT 19997
i i - i i i i
MER52A#LTR/ER 815 GGGCCCACCCATGGCCGCCCATGGACCAA-TCAGCACGCACTTCCTCCCC 863
INTRON_3 19998 TCT-AAGCCCGTAAAAACCCTGGACTCAGTCAGACTCAGGCAGAAATCAG 20046
- ? i i i ? ? ?i??i
MER52A#LTR/ER 864 TCTGARGCCCATAAAAACCCCGGACTCAGCCAGACTYAGRCAGAYGWYGG 913
INTRON_3 20047 GATGACCTGCCTGCAGGTATGAGCCACCCACTCCAGG-TCTCCTCTCCAC 20095
i v - iv v i i - ii
MER52A#LTR/ER 914 GACGACCAGC-TGCAGAGAGGAGCTACCCACTCCGGGGTCTCCTCTCTGC 962
INTRON_3 20096 TGAGGACTGCAGAATCAATGGGACAACCTGCCT 20128
ii ? i? i?i ii
MER52A#LTR/ER 963 TGAGAGCTGCASAGWCGWCGGGATGACCTGCCT 995
Matrix = 20p37g.matrix
Transitions / transversions = 4.83 (87 / 18)
Gap_init rate = 0.01 (9 / 630), avg. gap size = 1.67 (15 / 9)
1144 18.13 1.03 0.51 INTRON_3 20211 20404 379777 + MER52A LTR/ERV1 903 1097 658 108
INTRON_3 20211 ACAGACGTCAGGACAACCTGCCTACGGATAGGAGCTACCCACTCTGGG-T 20259
? ? ??i i v - i i v i -
MER52A#LTR/ER 903 RCAGAYGWYGGGACGACCAGC-TGCAGAGAGGAGCTACCCACTCCGGGGT 951
INTRON_3 20260 CTCCTCTCTGCTGAGAACTGCACACTCATCAGGATGACTTGTCTGCAGAT 20309
i ? v? i? i i i v
MER52A#LTR/ER 952 CTCCTCTCTGCTGAGAGCTGCASAGWCGWCGGGATGACCTGCCTGCAGAG 1001
INTRON_3 20310 AGGAGCTACCCACTCT-GGGTCTCCTCTCCACTGAGAGCTGCACAATTGT 20358
i- ii v v i
MER52A#LTR/ER 1002 AGGAGCTACCCACTCCAGGGTCTCCTCTCTGCTGAGAGCTGAACACTCGT 1051
INTRON_3 20359 CAGGACGACCTGCCTGTGGATATGAGCTACCCACTGAAGGTCTCCT 20404
i ? ? i ? v vi
MER52A#LTR/ER 1052 CGGGACGMCCTGSCTGCGGARAGGAGCTACCCACTGCGGGTCTCCT 1097
Matrix = 20p37g.matrix
Transitions / transversions = 2.12 (17 / 8)
Gap_init rate = 0.02 (3 / 193), avg. gap size = 1.00 (3 / 3)
1513 23.08 5.39 3.37 INTRON_3 20335 20742 379439 + MER52D LTR/ERV1 1243 1658 465 109
INTRON_3 20335 CTCCACTGAGAGCTGCACAATTGTCAGGACGACCTGCCTGTGGA-TATGA 20383
ii - viv iv v i i v - ii -i v
MER52D#LTR/ER 1243 CTCTGCT-AGAGCTGAGGAGATGACGGGATGACCAGC-TGCAGAGCAGGA 1290
INTRON_3 20384 GCTACCCACTG-AAGGTCTCCTCTTCACTGAGGGCTGCAAACTTGACAGG 20432
v- i iii i v i ii
MER52D#LTR/ER 1291 GCTACCCACTCCAGGGTCTCCTCTCTGCTGAGAGCTGAAGACTTGATGGG 1340
INTRON_3 20433 ATCACTTGCCTGTGACTAGGACTGCTCACTATGGGTCTCCTTGCCACTGA 20482
v i iiivv -- - i------ ii i ---
MER52D#LTR/ER 1341 ATGACCTGCCTGCAGAGAGGA--GCT-ACC------CTCTCTGCTA---A 1378
INTRON_3 20483 CAGCTG--TACTCATCAGAACCACCTGCCTGTAGAAAGGAGCTACCCACC 20530
v --i ii i vv v iii i i i
MER52D#LTR/ER 1379 GAGCTGAACACTCATTGGGACACCCTGGCTACGGAGAGGAGCTGCCCACT 1428
INTRON_3 20531 TTGGATCTCCTGAGAGCTGTATAGTCACTCAATAAAGCAACTCTTTGCCT 20580
vi? i vv vivi ii vv i i
MER52D#LTR/ER 1429 GCRGGTCTCCTCTGAGCTGTTCTATTGCTCAATAAAGCTCCTCTTCGTCT 1478
INTRON_3 20581 TGCTCACCC-CTAGTTTTCCATGTACCTCATTATTCCTGGACACAGGACA 20629
- i v v ii? v ?
MER52D#LTR/ER 1479 TGCTCACCCTCCACTTGTCTGYGTACCTCATTCTTCCTGGACRCAGGACA 1528
INTRON_3 20630 AGAACTC-----------AATGGTGGGACTGAAAGAGCTGTAACACAAAC 20668
----------- i i i i
MER52D#LTR/ER 1529 AGAACTCGGGACCTGCTAAATGGCGAGGCTAAAAGAGCTGTAACACAAAC 1578
INTRON_3 20669 AGTGCTGAAACACGCCCCC-ACTTGCCTTGTTGTGGGCAACAAGAAGGAG 20717
v i i-i vii i ii i
MER52D#LTR/ER 1579 AGGGCTGAAACATGCCCCTTGCTTGCCACATTGCGGGTGACAAGAAGAAG 1628
INTRON_3 20718 AGAAGCGAT-----AAGGAGAGAAGAGCTG 20742
v v-----
MER52D#LTR/ER 1629 AGAAGAGAGGAGAGAAGGAGAGAAGAGCTG 1658
Matrix = 20p37g.matrix
Transitions / transversions = 2.03 (59 / 29)
Gap_init rate = 0.03 (13 / 407), avg. gap size = 2.77 (36 / 13)
1816 21.31 4.90 0.26 INTRON_3 20356 20722 379459 + MER52A LTR/ERV1 908 1291 464 110
INTRON_3 20356 TGTCAGGACGACCTGCCTGTGGATATGAGCTACCCACTG-AAGGTCTCCT 20404
? ??i v - ii v v v-ii
MER52A#LTR/ER 908 YGWYGGGACGACCAGC-TGCAGAGAGGAGCTACCCACTCCGGGGTCTCCT 956
INTRON_3 20405 CTTCACTGAGGGCTGCAAACTTGACAGGATCACTTGCCTGTGACTAGGA- 20453
iii i ? v?i ? i v i iiivv -
MER52A#LTR/ER 957 CTCTGCTGAGAGCTGCASAGWCGWCGGGATGACCTGCCTGCAGAGAGGAG 1006
INTRON_3 20454 CTGCTCACTAT-GGGTCTCCTTGCCACTGACAGCTG--TACTCATCAGAA 20500
i i vi- iv ii v --i i i i
MER52A#LTR/ER 1007 CTACCCACTCCAGGGTCTCCTCTCTGCTGAGAGCTGAACACTCGTCGGGA 1056
INTRON_3 20501 CCACCTGCCTGTAGAAAGGAGCTACCCACCTTGGATCTCCTGAGAGCTGT 20550
v? ? ii ? ivi i
MER52A#LTR/ER 1057 CGMCCTGSCTGCGGARAGGAGCTACCCACTGCGGGTCTCCTGAGAGCTGT 1106
INTRON_3 20551 ATAGTCACTCAATAAAGCAACTCTTTGCCTTGCTCACCC-CTAGTTTTCC 20599
viv i vv i - i v v
MER52A#LTR/ER 1107 TCTGTCGCTCAATAAAGCTCCTCTTCGCCTTGCTCACCCTCCACTTGTCC 1156
INTRON_3 20600 ATGTACCTCATTATTCCTGGACACAGGACAAGAACTC-----------AA 20638
ii v iii -----------
MER52A#LTR/ER 1157 GCGTACCTCATTCTTCCTGGACGTGGGACAAGAACTCGGGACCCACCGAA 1206
INTRON_3 20639 TGGTGGGACTGAAAGAGCTGTAACACAAACAGTGCTGAAACACGCCCCC- 20687
i i v -
MER52A#LTR/ER 1207 TGGCGGGGCTGAAAGAGCTGTAACACAAACAGGGCTGAAACACGCCCCCT 1256
INTRON_3 20688 ACTTGCCTTGTTGTGGGCAACAAGAAGGAGAGAAG 20722
i ii vi i i
MER52A#LTR/ER 1257 GCTCACCACGTTGTGGGCGACGAGAAGGAGAGAAG 1291
Matrix = 20p37g.matrix
Transitions / transversions = 2.14 (47 / 22)
Gap_init rate = 0.02 (8 / 366), avg. gap size = 2.38 (19 / 8)
+ 421 23.9 8.0 1.3 INTRON_3 20809 21058 (379123) C L1M5 LINE/L1 (642) 5482 5210 14
ANNOTATION EVIDENCE:
421 26.27 8.72 0.47 INTRON_3 20809 21003 379178 C L1ME4a_3end LINE/L1 19 229 642 64
INTRON_3 20809 TCTTTTAAAGTTTTTTTCAGTCTAGCAGCTAAAAAAC---ATCTAATTGT 20855
- i vi i i iii v i i--- v
C L1ME4a_3end#L 229 TCTTTTAAA-TCTTTGCCAATTTGATAGGTGAAAAATGGTATCTCATTGT 181
INTRON_3 20856 TG----------CAGTTTTCTGACTATAATTGGGGTTTG-TATATTTTAA 20894
---------- v i i i i? v i vi-i ? v
C L1ME4a_3end#L 180 TGTTTTAATTTGCATTTCTTTGATTACNAGTGAGGTTGAACATNTTTTCA 131
INTRON_3 20895 CCTGTTTATTGGTGATTTGCCTATCCTCTTTGGTGAATTACCTTTTCATA 20944
v iv iv v i v ii v i
C L1ME4a_3end#L 130 CATGTTTATTGGCCATTTGTATTTCTTCTTTTGTGAATTGTCTGTTCATG 81
INTRON_3 20945 TTCTATGCC--TTTTTAAATTGGG-TGTTGATCTTTTTCTTAATAGTTTG 20991
ii v i -- vv - vi ? v ii
C L1ME4a_3end#L 80 TCTTTTGTCCGTTTTTCTATTGGGGTGTTCGTCTTTTTCTNATTGATTTG 31
INTRON_3 20992 TAATTGCTCTTT 21003
vv
C L1ME4a_3end#L 30 TAAGAGCTCTTT 19
Matrix = 20p37g.matrix
Transitions / transversions = 1.40 (28 / 20)
Gap_init rate = 0.03 (6 / 194), avg. gap size = 3.00 (18 / 6)
410 22.73 7.65 1.67 INTRON_3 20889 21058 379123 C L1M5_orf2 LINE/L1 3101 3280 14 65
INTRON_3 20889 TTTTAACCTGTTTATTGGTGATTTGCCTATCCTCTTTGGTGAATTACCTT 20938
v iv iv vv v v i v
C L1M5_orf2#LIN 3280 TTTTCATATGTTTATTGGCCATTTGGATATCCTCTTTTGTGAAGTGCCTG 3231
INTRON_3 20939 TTCATATTCTATGCC--TTTTTAAATTGGGT-GTTGATCTTTTTCTTAAT 20985
vi ii v -- vv - ivi v
C L1M5_orf2#LIN 3230 TTCAAGTCTTTTGCCCATTTTTCTATTGGGTTGTCTGTCTTTTTCTTATT 3181
INTRON_3 20986 AGTTTGTAATTGCTCTTTGTGAAT---AGAAATGTTAATCCTTTGTCA-- 21030
ii ivv i i iv ---i v -- i i --
C L1M5_orf2#LIN 3180 GATTTGTAGGAGTTCTTTATATATTCTGGATATG--AGTTCTTTGTCAGN 3133
INTRON_3 21031 --TATGTATTGCAAACCATTTTT---CACTCTG 21058
-- i- ? i---
C L1M5_orf2#LIN 3132 TATATGTATTGCAAAT-ATNTTCTCCCACTCTG 3101
Matrix = 20p37g.matrix
Transitions / transversions = 1.06 (19 / 18)
Gap_init rate = 0.04 (7 / 169), avg. gap size = 2.29 (16 / 7)
+ 404 29.5 11.7 4.2 INTRON_3 21114 21927 (378254) C L1M5 LINE/L1 (1152) 4994 4095 14
ANNOTATION EVIDENCE:
283 32.87 5.46 4.15 INTRON_3 21114 21351 378830 C L1M5_orf2 LINE/L1 2645 2885 409 66
INTRON_3 21114 CTGGAATTTATGTTTACATGTAGTGTGATGT----GTATAAGTATATAAC 21159
v v iii i i v ---- -i ?v ----
C L1M5_orf2#LIN 2885 CTGGAATTGATTTTTGTGTATGGTGTGAGGTAGGGGT-CAAGNTT----C 2841
INTRON_3 21160 ATTTTCTTCCAAATGACTAGCCAGCTTTGTCTACACTGTTT-TTAAAA-- 21206
i v iv v ii v?vi vi ii - i --
C L1M5_orf2#LIN 2840 ATTTTTTTCCATATGGATATCCAATTGNCCCAGCACCATTTATTGAAAAG 2791
INTRON_3 21207 --CATTTTTTGCC-ACTGTATTGAAATACCATAGATGTTATATATTATAT 21253
--i i v - ? v ? i? ivvv i ? v i - v
C L1M5_orf2#LIN 2790 ACTATTCTTTCCCCACTGNATTGCANTGNCACCTTTGTCANAAATCA-AG 2742
INTRON_3 21254 TATACTCCCACATGTATTTGTACCTATTTCTGAATTCTGTTTTCTGT--C 21301
i?---- i i i v vii i i i v v --
C L1M5_orf2#LIN 2741 TGN----CCATATATGTGTGGGTCTGTTTCTGGACTCTCTATTCTGTTCC 2696
INTRON_3 21302 ATTTTCCTATTC-TTTATTTCTGTGCCAATGGTATACTGTTTTGATTTCT 21350
vvi i- i iii ?i ivi i i i v
C L1M5_orf2#LIN 2695 ATTGGTCTATTTGTCTATCCTTNCGCCAATACCACACTGTCTTAATTACT 2646
INTRON_3 21351 G 21351
C L1M5_orf2#LIN 2645 G 2645
Matrix = 20p37g.matrix
Transitions / transversions = 1.68 (42 / 25)
Gap_init rate = 0.04 (10 / 237), avg. gap size = 2.30 (23 / 10)
404 26.30 10.03 5.23 INTRON_3 21339 21667 378514 C L1M5_orf2 LINE/L1 2287 2630 664 67
INTRON_3 21339 GTTTTGATTTCTGGTAAGGCTTATTAACTACTCT---CTCATTTTTCTTT 21385
i v i? ----- v v i---i ii i
C L1M5_orf2#LIN 2630 GTCTTGATATCTGGTAGNG-----TAAGTCCTCCAACTTTGTTCTTCTTT 2586
INTRON_3 21386 TTAAAGATTTACTTGACTATTC----------------CCATATAATTAC 21419
v vv i ---------------- -- i
C L1M5_orf2#LIN 2585 TTCAAGATTGTCTTGGCTATTCTTGGCCCTTTGCATTTCCATATAA--AT 2538
INTRON_3 21420 TTTTCAAAATGAACTTTTCATTTTCTCCAGTTCAAGAAAATTCATCACTG 21469
-- i v i v v -- --- i iiiiiii--
C L1M5_orf2#LIN 2537 TTT--AGAATCAGCTTGTCAATTTC--CA---CAAAAAAACCTGCTG--G 2497
INTRON_3 21470 GATTCCATTTGGAATTACATTCAAATTATTGTCCAATTTGGGAAGGATTG 21519
ii?v i i v vi v vi i i
C L1M5_orf2#LIN 2496 GATTTTNATTGGGATTGCATTGAATCTATAGATCAATTTGGGGAGAATTG 2447
INTRON_3 21520 ATATTTTT-CAGTATTG--TCTTCCACTTAA-GAAAATAGTATATATCTC 21565
i i - i -- v iv - v i v
C L1M5_orf2#LIN 2446 ACATCTTTACAATATTGAGTCTTCCAATCCATGAACATGGTATATCTCTC 2397
INTRON_3 21566 CATTTGTTCAG---TTATTTTGTGTCACTTGGTAAC--TTGACAATATTT 21610
i i --- v vi v v iii i-- vii i v i
C L1M5_orf2#LIN 2396 CATTTATTTAGGTCTTCTTTAATTTCTCTCAATAATGTTTTGTAGTTTTC 2347
INTRON_3 21611 AGAATTT---TCTT-TCTAT-TCTTATTAAATTTATTTTAAGATATTTTA 21655
? v v?--- - vi - i i iiv i v
C L1M5_orf2#LIN 2346 NGTATANAGGTCTTGTACATNTTTTATTAGATTTATTCCTAGGTATTTGA 2297
INTRON_3 21656 TAGTTTTATTGA 21667
- -
C L1M5_orf2#LIN 2296 T-GTTTT-TTGA 2287
Matrix = 20p37g.matrix
Transitions / transversions = 1.69 (49 / 29)
Gap_init rate = 0.05 (18 / 328), avg. gap size = 2.83 (51 / 18)
389 30.70 10.59 2.92 INTRON_3 21673 21927 378254 C L1M5_orf2 LINE/L1 1986 2259 1035 26
INTRON_3 21673 AATTT--TTTTCCACTTGTAAGTTTTTTTCTGGTGTAAAGAGAAAATGCA 21720
-- v ---- v v i i v --- i
C L1M5_orf2#LIN 2259 AATTTCATTTTCCAATTGT----TTGTTGCTAGTATATAGA---AATACA 2217
INTRON_3 21721 --TACTTTAATTATTTTAAACTTGTATTCATTCCTTTTACCAAATT---T 21765
-- iv vvv v i vi i v vvii i i ---
C L1M5_orf2#LIN 2216 ATTGATTTTTGTATATTGACTTTGTATCCAGTAACCTTGCTAAATTCACT 2167
INTRON_3 21766 TCTTAATTCTAGTAGCTTATTCATAGAGTGTTTTGTGTTTCATAGGTATA 21815
v i ii iii v v vi iv v ?
C L1M5_orf2#LIN 2166 TATTAATTCTAATAATTTATCTGTAGATTCTTTTGGATTTTCTATGTANA 2117
INTRON_3 21816 CAGTCTTATCA----AGGACAA----AGGTATATTTGTCTTTTTTCTAAA 21857
i v i ----v i i ---- v v v - ii i v
C L1M5_orf2#LIN 2116 CAATCATGTCATCTGCGAATAATGACAGTTTTATTTCT-TCCTTTCCAAT 2068
INTRON_3 21858 TTTT-TACCGATTATTTTCCTTT--TAATTTATC---------AAAATCC 21895
ii - vv iii -- ivi i--------- ii iii
C L1M5_orf2#LIN 2067 CCTTATACCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACTT 2018
INTRON_3 21896 CCAAAAGAAGATTGAAAAATAGTGGTGATAGC 21927
iv v vi v iv
C L1M5_orf2#LIN 2017 CCAGTACAATGTTGAATAGAAGTGGTGATAGC 1986
Matrix = Unknown
Transitions / transversions = 1.27 (42 / 33)
Gap_init rate = 0.04 (11 / 254), avg. gap size = 3.18 (35 / 11)
+ 560 30.4 10.9 1.3 INTRON_3 22183 22722 (377459) C L1ME4a LINE/L1 (253) 5931 5338 15
ANNOTATION EVIDENCE:
230 30.69 5.22 3.15 INTRON_3 22183 22431 377750 C L1MB7_3end LINE/L1 425 678 253 68
INTRON_3 22183 ATTTTATATAAATCCAGTAATACAGTATGTG-CCTGTTAT--CTTGTTAC 22229
i vv i v i - v i -- v i v
C L1MB7_3end#LI 678 ATTTCATATAAATGGAATCATACAATATGTGGCCTTTTGTGTCTGGCTTC 629
INTRON_3 22230 ---CACCT----TAAAATTTTGTGGACTTCTTTC-TGTCTATAGCAATAA 22271
--- i ---- vi -i iiv v i - - i - --
C L1MB7_3end#LI 628 TTTCACTTAGCATAATGTTTT-CGAGGTTCATCCATGT-TGTAGCA-T-- 584
INTRON_3 22272 GTAT-AGGATCATATTATTTTTAATGGCTACCTTAGAATTACATTGTATG 22320
- v iivi vi v iivv - iv v
C L1MB7_3end#LI 583 GTATCAGTACTTCATTCCTTTTTATGGCCGAAT-AATATTCCATTGTATG 535
INTRON_3 22321 GATGTATCATAATT-ATTTAATTGATCTTCTGTTGATAGCTCTCATGGTT 22369
i i i v -i viiiv v v i viv ivv
C L1MB7_3end#LI 534 GATATACCACATTTTGTTTATCCATTCATCAGTTGATGGACATTTGGGTT 485
INTRON_3 22370 GTCTCTAATTTTTCATGATTATAAATGATGTCATGATGAACATCATTGTA 22419
i i v viiv i i iiiiv -- i
C L1MB7_3end#LI 484 GTTTCCACTTTTTGGCTATTATGAATAATGCTGCTATGAACAT--TTGTG 437
INTRON_3 22420 GATATATTTTTG 22431
v i vi
C L1MB7_3end#LI 436 TACAAGTTTTTG 425
Matrix = 20p37g.matrix
Transitions / transversions = 1.31 (42 / 32)
Gap_init rate = 0.05 (13 / 248), avg. gap size = 1.62 (21 / 13)
560 24.35 1.30 1.30 INTRON_3 22282 22435 377746 C L1ME4a_3end LINE/L1 422 575 296 69
INTRON_3 22282 ATATTATTTTTAATGGCTACCTTAGAATTACATTGTATGGATGTATCATA 22331
i ? i v - iv v ? i
C L1ME4a_3end#L 575 ACATNATTTTTAATGGCTGCAT-AATATTCCATTNTATGGATGTACCATA 527
INTRON_3 22332 ATT-ATTTAATTGATCTTCTGTTGATAG-CTCTCATGGTTGTCTCTAATT 22379
- iii? ii i v i - vi i - i i
C L1ME4a_3end#L 526 ATTTATTTAACCANTCCCCTATTGTTGGACATTTA-GGTTGTTTCCAATT 478
INTRON_3 22380 TTTCATGATTATAAATGATGTCATGATGAACATCATTGTAGATATATTTT 22429
iiv i iiii v v v i
C L1ME4a_3end#L 477 TTTCGCTATTATAAATAATGCTGCGATGAACATCCTTGTACATAAATCTT 428
INTRON_3 22430 TGCACA 22435
i?
C L1ME4a_3end#L 427 TGTNCA 422
Matrix = 20p37g.matrix
Transitions / transversions = 2.67 (24 / 9)
Gap_init rate = 0.03 (4 / 153), avg. gap size = 1.00 (4 / 4)
336 33.54 9.03 0.64 INTRON_3 22435 22722 377459 C L1ME4a_3end LINE/L1 85 396 475 70
INTRON_3 22435 AATTCCTAGAAGTGTGATTGCT---TC---------CCGCATATTTAAAA 22472
vi i --- ---------v?i v ii
C L1ME4a_3end#L 396 AATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTTTAAGG 347
INTRON_3 22473 TT-TTAATGTAT-TTAGTAAAGGGACTTTTATAAATGTCCTGCCAGTTTA 22520
i - i ii - ivi vv v i ii v v iv i i
C L1ME4a_3end#L 346 CTCTTGATACATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCAATTTA 297
INTRON_3 22521 TACTTATCCCAACACTACACAGGAGAGCTCATAAATCTTGTCTCATATTA 22570
i iviv i v ii iii v i i vvv? ivvv i viiii
C L1ME4a_3end#L 296 CACTCCCACCAGCAGTGTATGAGAGTGCCCGTTTCNCCACACCCTCGCCA 247
INTRON_3 22571 ATCCTGATTATTTTCCATTCTTTTA--TCTTTGTCAGTGTAATAGACAAT 22618
iv ?v v v - -- i i v i iii v
C L1ME4a_3end#L 246 ACACTGNGTATTATCAAT-CTTTTAAATCTTTGCCAATTTGATAGGTGAA 198
INTRON_3 22619 AATTGATATGGCATTGTTGTTTGTAATTT-TATTTCATTGACTGCGAGTG 22667
v i vv - -i v i i ?
C L1ME4a_3end#L 197 AAATGGTATCTCATTGTTGTTT-TAATTTGCATTTCTTTGATTACNAGTG 149
INTRON_3 22668 AAGGTAACTGTCTTTTTACATTCTT------TATTTTTATTTTTTCT--- 22708
i v i vii ? i vi ------i v i ---
C L1ME4a_3end#L 148 AGGTTGAACATNTTTTCACATGTTTATTGGCCATTTGTATTTCTTCTTTT 99
INTRON_3 22709 GGGAATTATCTTTT 22722
v i v
C L1ME4a_3end#L 98 GTGAATTGTCTGTT 85
Matrix = 20p37g.matrix
Transitions / transversions = 1.46 (54 / 37)
Gap_init rate = 0.03 (10 / 287), avg. gap size = 2.80 (28 / 10)
+ 4594 10.6 2.4 0.0 INTRON_3 22779 23455 (376726) C L1PA13 LINE/L1 (3) 6160 5468 16
ANNOTATION EVIDENCE:
4594 10.64 2.36 0.00 INTRON_3 22779 23455 376726 C L1PA13_3end LINE/L1 215 907 3 71
INTRON_3 22779 TTTTATTTAATATATTTTTTAAGTTCAGTGGTACATGTGCAGGTTTGTTA 22828
v iv v v v
C L1PA13_3end#L 907 TTTTTTTTAACTTTTATTTTAAGTTCAGGGGTACATGTGCAGGTTTGTTA 858
INTRON_3 22829 GATAGGTAAATTTGTGTCATGGGGGTTTGTTCTACAGATTATTTGATCAC 22878
v i v v
C L1PA13_3end#L 857 CATAGGTAAACTTGTGTCATGGGGGTTTGTTGTACAGATTATTTCATCAC 808
INTRON_3 22879 CGAGGTATTAAACCTAGTACCCATTAGTTATTTTTCCTGATCCTCTCCCT 22928
v i
C L1PA13_3end#L 807 CCAGGTATTAAGCCTAGTACCCATTAGTTATTTTTCCTGATCCTCTCCCT 758
INTRON_3 22929 CCTCCCACCCTCCACCCTCTGATAGGCCCCAGTATCTGTTGTGCCCCTCT 22978
ii i v v
C L1PA13_3end#L 757 CCTCCCACCCTCCACCCTCCAATAGGCCCCAGTGTGTGTTGTTCCCCTCT 708
INTRON_3 22979 ATGTGTCCATTTGTTTTCATTGTTTAGCTCCCACTTGTAAGTGAGAGCAT 23028
v i ii i i
C L1PA13_3end#L 707 ATGTGTCCATGTGTTCTCATCATTTAGCTCCCACTTATAAGTGAGAACAT 658
INTRON_3 23029 GCAGTATTTGGTTTTCTGCTTCTGTGTTAGTTTGCTAAAGATGATGGCCT 23078
i i i i i i
C L1PA13_3end#L 657 GCGGTATTTGGTTTTCTGTTCCTGCGTTAGTTTGCTAAGGATAATGGCCT 608
INTRON_3 23079 CCAGCTCCATCCATGTCCCTGCAAAGATCATGCTCTTACT---TTTTATG 23125
iv v i i ---
C L1PA13_3end#L 607 CCAGCTCCATCCATGTCCCTGCAAAGGACATGATCTCATTCTTTTTTATG 558
INTRON_3 23126 ACTGCATAGTATTCTGTGGT-----------ACATTTTCTTTATTCTGTC 23164
i ii ----------- i v
C L1PA13_3end#L 557 GCTGCATAGTATTCCATGGTGTATATGTACCACATTTTCTTTATCCAGTC 508
INTRON_3 23165 TACCATTGATGGGCATTTAGGTTGATTTTATGTTTTTGCTATTGTAAATA 23214
i ii i i
C L1PA13_3end#L 507 TATCATTGATGGGCATTTAGGTTGATTCCATGTCTTTGCTATTGTGAATA 458
INTRON_3 23215 GTGCTGCAATGAACATACGCATGTATGTGTCT--GTGATACAATGATTTA 23262
i i i --i i v
C L1PA13_3end#L 457 GTGCTGCAATGAACATATGCGTGCATGTGTCTTTATAATAGAATGATTTA 408
INTRON_3 23263 CATTCTTTTGGGTATATAACCAGTAATGGGATTGCTGGGTTGAATGGTAG 23312
i i v i v
C L1PA13_3end#L 407 TATTCCTTTGGGTATATACCCAGTAATGGGATTGCTGGGTCGAATGGTAT 358
INTRON_3 23313 TTCTGTTTTTAGCTCTTTGAGAAATTACCACACTGTTTTCCTCAATGGTT 23362
i v i ii i v
C L1PA13_3end#L 357 TTCTGTCTTTAGGTCTTTGAGGAATCGCCACACTGTCTTCCACAATGGTT 308
INTRON_3 23363 GAACTAATTTACACTCTCACCCATGGTGTATAAGCATTCCTTTTTCTCTG 23412
i v ii i i
C L1PA13_3end#L 307 GAACTAATTTACACTCCCACCAACAGTGTATAAGCGTTCCTTTTTCTCCG 258
INTRON_3 23413 CATCCTTGCCAGCATCTGTTATGTTTTGACTTTTTAATAAAAG 23455
v i v v
C L1PA13_3end#L 257 CAACCTCGCCAGCATCTGTTATTTTTTGACTTTTTAATAATAG 215
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (48 / 24)
Gap_init rate = 0.00 (3 / 676), avg. gap size = 5.33 (16 / 3)
+ 2253 11.2 0.7 0.0 INTRON_3 23467 23760 (376421) + AluSq2 SINE/Alu 1 296 (16) 17
ANNOTATION EVIDENCE:
2168 11.60 0.68 0.34 INTRON_3 23467 23760 376421 + AluSx SINE/Alu 1 295 17 2
INTRON_3 23467 GGCCGAGCATGGTGGCTCATGCCTGTAATCCCAGAACTTTGAGAGGCTGA 23516
i ii i v i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 23517 GGCAGGTGGATCA--TGAGGTCAAGAGATTGAGACCATCCTGGCCAACAT 23564
i i -- i v i v
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
INTRON_3 23565 GGTGAAACCCTATCTTTACTAAAAATACAAAAATTAGCTGGGCGTGGTGG 23614
ii i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGG 150
INTRON_3 23615 CACATGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGTAGGAGAATCACT 23664
i ii i i i
AluSx#SINE/Al 151 CGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCT 200
INTRON_3 23665 TGAACCTGGGAGGTGGAGGTTGCAGTGAGCCAAGATCGCACGATTGCAGT 23714
i i i i v i v
AluSx#SINE/Al 201 TGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACT 250
INTRON_3 23715 CCAGCCTGGGCAACAAGAGTGAAACTCTGTCTCAAAAAAAAAAAAA 23760
i - i i i
AluSx#SINE/Al 251 CCAGCCTGGGCGACA-GAGCGAGACTCCGTCTCAAAAAAAAAAAAA 295
Matrix = 14p37g.matrix
Transitions / transversions = 5.80 (29 / 5)
Gap_init rate = 0.01 (2 / 293), avg. gap size = 1.50 (3 / 2)
+ 354 12.9 0.0 0.0 INTRON_3 23761 23822 (376359) + L1M1 LINE/L1 5459 5520 (783) 18
ANNOTATION EVIDENCE:
354 12.90 0.00 0.00 INTRON_3 23761 23822 376359 + L1MA4A_3end LINE/L1 206 267 783 72
INTRON_3 23761 TTAGAATGGCTATTATTAAAAAGTCAAAACATAATAGATGCAGGAGAGGA 23810
v v i v v
L1MA4A_3end#L 206 TTAGAATGGCTATTATTAAAAAGACAAAAAATAACAGATGCTGGCGAGGA 255
INTRON_3 23811 TATGGAGAACAG 23822
ii v
L1MA4A_3end#L 256 TGCGGAGAAAAG 267
Matrix = 20p37g.matrix
Transitions / transversions = 0.60 (3 / 5)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0)
+ 8187 9.0 2.5 0.6 INTRON_3 23843 25105 (375076) C L1PA13 LINE/L1 (716) 5452 4175 16
ANNOTATION EVIDENCE:
1226 6.45 6.38 1.01 INTRON_3 23843 24030 376151 C L1PA12_3end LINE/L1 2 199 716 73
INTRON_3 23843 TGAAATGGTATCTTATTGTGGTTTTGATTTGCATTTCTCTAATGATCAGT 23892
i i
C L1PA12_3end#L 199 TGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTAATGATCAGT 150
INTRON_3 23893 GATGTTGAGCTTTTTTTCATAGGATTATTGGCCACATATATGTCTT---T 23939
v ? i i ---
C L1PA12_3end#L 149 GATGTTGAGCTTTTTTTCATATGMTTGTTGGCCACATGTATGTCTTCTTT 100
INTRON_3 23940 CAAAAAGTGTCTTTTCATGTCCTTTGCCCACTTTTTAATGG--------- 23980
ii i v ---------
C L1PA12_3end#L 99 TGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAATGGGGTTGTTTG 50
INTRON_3 23981 TTTTTTTAAATCGTAAATTTGTTTAAGTTCCTTATAGATGCTGGATATTA 24030
v-- i
C L1PA12_3end#L 49 TTTTTTTC--TTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGATATTA 2
Matrix = 20p37g.matrix
Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.02 (3 / 187), avg. gap size = 4.67 (14 / 3)
8187 9.44 1.81 0.57 INTRON_3 23892 25105 375076 C L1PREC2_orf2 LINE/L1 2066 3294 0 74
INTRON_3 23892 TGATGTTGAGCTTTTTTTCATAGGATTATTGGCCACATATATGTCTT--- 23938
i v v i i ---
C L1PREC2_orf2# 3294 TGATATTGAGCTTTTTTTCATATGCTTGTTGGCCACATGTATGTCTTCTT 3245
INTRON_3 23939 TCAAAAAGTGTCTTTTCATGTCCTTTGCCCACTTTTTAATGG-------- 23980
ii v --------
C L1PREC2_orf2# 3244 TTGAAAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAATGGGGTTGTTT 3195
INTRON_3 23981 -TTTTTTTAAATCGTAAATTTGTTTAAGTTCCTTATAGATGCTGGATATT 24029
- v-- i
C L1PREC2_orf2# 3194 GTTTTTTTC--TTGTAAATTTGTTTAAGTTCCTTATAGATGCTGGATATT 3147
INTRON_3 24030 AAACCTTTGTCGGATGCATAGTTTGCAAATATTTTCTTCCATTCTGTAGG 24079
i i i
C L1PREC2_orf2# 3146 AGACCTTTGTCAGATGCATAGTTTGCAAATATTTTCTCCCATTCTGTAGG 3097
INTRON_3 24080 TTGTCTGTTTACTCTGTTAATAGTTTCTTCTGTGGTGCAAAAGCTCTTTA 24129
i i iv i v
C L1PREC2_orf2# 3096 TTGTCTGTTTACTCTGTTGATAGTTTCTTTTGCTGTGCAGAAGCTCTTAA 3047
INTRON_3 24130 GTTTAATTAGATCCTGTTTGCCAATTTTTGCTTTTGTCGTGATTGCTTTT 24179
ii i i ii
C L1PREC2_orf2# 3046 GTTTAATTAGATCCCATTTGTCAATTTTTGCTTTTGTTGCAATTGCTTTT 2997
INTRON_3 24180 GGCGTCTTTGTCATGAAATCTTTGCCTGTTCCTATGTCCAGGATGGTACT 24229
i i i i
C L1PREC2_orf2# 2996 GGCGTCTTCGTCATGAAATCTTTGCCCGTTCCTATGTCCAGAATGGTATT 2947
INTRON_3 24230 GCCTAGGTTATCTTCCAGGGTTTTTA-AGTTTTGTGTTTTACATTTAAAT 24278
i - v i
C L1PREC2_orf2# 2946 GCCTAGGTTGTCTTCCAGGGTTTTTATAGTTTTGGGTTTTACATTTAAGT 2897
INTRON_3 24279 CTTTAATTCATCTTG-GTTGATTTTTGTATATGGTGTAAGGAAGGGGTCC 24327
i -
C L1PREC2_orf2# 2896 CTTTAATCCATCTTGAGTTGATTTTTGTATATGGTGTAAGGAAGGGGTCC 2847
INTRON_3 24328 AGCTTCAATCATCTGCATATGGCTAGCCAGTTAGTCCAGCACCATTTTTT 24377
i v vi v
C L1PREC2_orf2# 2846 AGTTTCAATCTTCTGCATATGGCTAGCCAGTTATCCCAGCACCATTTATT 2797
INTRON_3 24378 GAATAGGAAGTCATTTCCCCATTGCTTGTTTTTGTCAGCTTTGTCAAAGA 24427
i v i
C L1PREC2_orf2# 2796 GAATAGGGAGTCCTTTCCCCATTGCTTGTTTTTGTCAGCTTTGTCGAAGA 2747
INTRON_3 24428 TCAGATGGTTTTAGATGTGCAGCCTTATTTCTGGGCCCGCTATTCTGTTC 24477
v i i i v
C L1PREC2_orf2# 2746 TCAGATGGTTGTAGGTGTGCGGCCTTATTTCTGGGCTCTCTATTCTGTTC 2697
INTRON_3 24478 CATTAGTCTATGTGTCTGTTTTTGTACCAGTGCCATGATGTTTTGGTGAC 24527
i i v v
C L1PREC2_orf2# 2696 CATTGGTCTATGTGTCTGTTTTTGTACCAGTACCATGCTGTTTTGGTTAC 2647
INTRON_3 24528 TGTAGTTCTGTAGCATAGTTTGAAGTCAGGTAGTATGATGTAATGCCTCC 24577
ii i ii ----- i i
C L1PREC2_orf2# 2646 TGTAGCCCTGTAGTATAGTTTGAAGTTGGGTA-----ACGTGATGCCTCC 2602
INTRON_3 24578 AGCTTTGTTCTTTTTGCTTAGGATTGTCTTGGATATTTGGGCTCTTTTTT 24627
i v i
C L1PREC2_orf2# 2601 AGCTTTGTTCTTTTTGCTTAGGATTGCCTTGGCTATTCGGGCTCTTTTTT 2552
INTRON_3 24628 GCTTCCATATGAATATTAAAATAGCTTTTTCTAGTTCTGTGAAGAATGCC 24677
v v i i
C L1PREC2_orf2# 2551 GGTTCCATATGAATTTTAAAATAGTTTTTTCTAGTTCTGTGAAGAATGTC 2502
INTRON_3 24678 ATTGGTAGTTTAA-AGGAATAGTATTGAATCTATAAATTGCTTTGGGCAG 24726
i - i i
C L1PREC2_orf2# 2501 ATTGGTAGTTTGATAGGAATAGCATTGAATCTGTAAATTGCTTTGGGCAG 2452
INTRON_3 24727 TATGACCATTTTAACAAAATTGATTCTTCCTGTCCATGAGCATGTAATGT 24776
i ii v i v
C L1PREC2_orf2# 2451 TATGGCCATTTTAATGATATTGATTCTTCCTATCCATGAGCATGGAATGT 2402
INTRON_3 24777 TTT-CCATTTGATTGCATCATCTTTGATTTCTTTGAGCAGTATTTTGTAG 24825
- v ii i i i
C L1PREC2_orf2# 2401 TTTTCCATTTGTTTGTGTCATCTCTGATTTCTTTGAGCAGTGTTTTGTAA 2352
INTRON_3 24826 TTTTGCTTATAGAGATTTTTTACCTCTCTCATTAGCTGTATTCCTAGGTA 24875
i vv i i i i vi
C L1PREC2_orf2# 2351 TTCTCATTGTAGAGATCTTTCACCTCCCTGGTTAGCTGTATTCCTAGGTA 2302
INTRON_3 24876 TTTTATTCTTTTTGTGGCAGTTGTGAATGGGATTGCATTCCTGATTTAGC 24925
i i i
C L1PREC2_orf2# 2301 TTTTATTCTTTTTGTGGCAATTGTGAATGGGATTGCGTTCCTGATTTGGC 2252
INTRON_3 24926 CCTCAGGTTGACTGTTG-----GTGTAGCAATGCTAGTGATTTTTGTACA 24970
i i v i ----- i v i
C L1PREC2_orf2# 2251 TCTCGGCTTGGCTGTTGTTGGTGTATAGGAATGCTAGTGATTTTTGTACG 2202
INTRON_3 24971 TTGATTTTTTATCTTGAGACTTTGCTGAAGTTATTTATCAGTTTAAGGAG 25020
v i i i i v
C L1PREC2_orf2# 2201 TTGATTTTGTATCCTGAAACTTTGCTGAAGTTGTTTATCAGCTGAAGGAG 2152
INTRON_3 25021 CTTTTAGAT-GAGACTATGGGTTTTTCTAGATACAGAATCATGTCAACTG 25069
i ii- v i iv
C L1PREC2_orf2# 2151 CTTTTGGGCCGAGACTATGGGGTTTTCTAGATATAGAATCATGTCGTCTG 2102
INTRON_3 25070 TAAACAGGTATAGTTTGGCTTCCTCTCTTCCTATTT 25105
i v i
C L1PREC2_orf2# 2101 CAAACAGGGATAGTTTGACTTCCTCTCTTCCTATTT 2066
Matrix = 20p37g.matrix
Transitions / transversions = 2.68 (83 / 31)
Gap_init rate = 0.01 (10 / 1213), avg. gap size = 2.90 (29 / 10)
+ 336 17.5 0.0 0.0 INTRON_3 25116 25178 (375003) + CT-rich Low_complexity 118 180 (0) 19
ANNOTATION EVIDENCE:
336 17.46 0.00 0.00 INTRON_3 25116 25178 375003 C (GA)n Simple_repeat 118 180 0 101
INTRON_3 25116 TCCCTCCCTCCCTCCCTCCCTCCCTCTCTCTCTCTTTCTTTCTCTTTCTT 25165
i i i i i i i i i i
C (GA)n#Simple_ 180 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 131
INTRON_3 25166 TCTTTCTCTCTCT 25178
i
C (GA)n#Simple_ 130 TCTCTCTCTCTCT 118
Matrix = Unknown
Transitions / transversions = 0.0 (11 / 0)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
+ 2803 9.7 0.5 3.8 INTRON_3 25181 25199 (374982) C L1PA13 LINE/L1 (1954) 4192 4175 16
ANNOTATION EVIDENCE:
2803 9.66 0.45 3.75 INTRON_3 25181 25199 374982 C L1PREC2_orf2 LINE/L1 2066 2083 1211 75
INTRON_3 25181 CTTTCTTTCTTTTCTTTTC 25199
i i iiiv -
C L1PREC2_orf2# 2083 CTTCCTCTCTTCCTATTT- 2066
Matrix = 20p37g.matrix
Transitions / transversions = 5.00 (5 / 1)
Gap_init rate = 0.06 (1 / 18), avg. gap size = 1.00 (1 / 1)
+ 2077 14.5 2.6 0.0 INTRON_3 25200 25503 (374678) C AluSx1 SINE/Alu (0) 312 1 20
ANNOTATION EVIDENCE:
1926 14.80 2.63 0.00 INTRON_3 25200 25503 374678 C AluSx SINE/Alu 1 312 0 3
INTRON_3 25200 TTTCTTTCTTTTCCTTTCTTTCTTTCTTTTCA-------TTTTGTTCTGT 25242
i i ii i i i v ------- i i i
C AluSx#SINE/Al 312 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGT 263
INTRON_3 25243 CATCCAGGCTGGAGTGCAGTGGCACACTCTTGGCTCACTTCAACCTCCAC 25292
ii i iv i v i
C AluSx#SINE/Al 262 CGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGC 213
INTRON_3 25293 CTCCCAGGTTCCAGTGAGTCTCCTGCCTCA-TCTCCCAAGTAGCTGGGAA 25341
i v i v -i i v
C AluSx#SINE/Al 212 CTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGAT 163
INTRON_3 25342 TACAGGTGCCTACCACCACGCCCAGCTAATTTTTGTATTTTTCGTAGAGA 25391
i vii i v
C AluSx#SINE/Al 162 TACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGA 113
INTRON_3 25392 CAGGGTTTCATCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAAGT 25441
i i i i
C AluSx#SINE/Al 112 CGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGT 63
INTRON_3 25442 GGTCTGACCACCTCAGCCTCCCAAAGTGCTGAGATTACAGGCGTGAGCCA 25491
i i v i i i
C AluSx#SINE/Al 62 GATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCA 13
INTRON_3 25492 CCACACTCGGCC 25503
i i i
C AluSx#SINE/Al 12 CCGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 4.00 (36 / 9)
Gap_init rate = 0.01 (2 / 303), avg. gap size = 4.00 (8 / 2)
+ 2803 9.7 0.5 3.8 INTRON_3 25504 25696 (374485) C L1PA13 LINE/L1 (1972) 4174 3983 16
ANNOTATION EVIDENCE:
2803 9.66 0.45 3.75 INTRON_3 25504 25696 374485 C L1PREC2_orf2 LINE/L1 1874 2065 1229 76
INTRON_3 25504 CGGGATGCCCTTTATTTCTTTCTCTTGCCTG-TTTCTCTGGCCAGGACTT 25552
-- - v
C L1PREC2_orf2# 2065 --GGATGCCCTTTATTTCTTTCTCTTGCCTGATTGCTCTGGCCAGGACTT 2018
INTRON_3 25553 CCAATACTATATTGAAT-GGAGTGGTGAGAGAGGCTATCCTTGTCTTGTG 25601
i - vi
C L1PREC2_orf2# 2017 CCAATACTATGTTGAATAGGAGTGGTGAGAGAGGGCATCCTTGTCTTGTG 1968
INTRON_3 25602 CTGGTTTTCAAGGGTAGTGCTTCCAGCTTTTGCCCATTCAGTATGATATT 25651
i v i i
C L1PREC2_orf2# 1967 CCGGTTTTCAAGGGGAATGCTTCCAGCTTTTGCCCATTCAGTATGATGTT 1918
INTRON_3 25652 CACTGTGGGTTTGTCATAGATGGCTCTTATTATTTTGAGGTATGG 25696
vi -
C L1PREC2_orf2# 1917 GGCTGTGGGTTTGTCATAGATGGCTCTTATTATTTTGAGGTATG- 1874
Matrix = 20p37g.matrix
Transitions / transversions = 1.50 (6 / 4)
Gap_init rate = 0.02 (4 / 192), avg. gap size = 1.25 (5 / 4)
+ 2447 9.4 0.0 0.0 INTRON_3 25697 25995 (374186) C AluY SINE/Alu (11) 300 2 21
ANNOTATION EVIDENCE:
2412 9.36 0.00 0.00 INTRON_3 25697 25995 374186 C AluY SINE/Alu 2 300 11 4
INTRON_3 25697 TTTTTTTTTTTTTTTTTTGGAGAAGGAGTCTTGCTCTGTTGCTCAGGCTG 25746
v v i i i
C AluY#SINE/Alu 300 TTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTG 251
INTRON_3 25747 GAGTGCAGTGGCGTGATCTCAGCTCACTGCAAACTCTGCCTCCTGGGTTC 25796
i i i i i
C AluY#SINE/Alu 250 GAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTC 201
INTRON_3 25797 ATGCCATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGCGCCT 25846
i i i
C AluY#SINE/Alu 200 ACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCC 151
INTRON_3 25847 GCCAACACACCTGGCTAATTTTTTGTATTTTTAGTAGAGACAGGGTTTCA 25896
v i i i
C AluY#SINE/Alu 150 GCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCA 101
INTRON_3 25897 CCATGTTAGCCAGGATGGTCTCGATCTCCTGACCTTGTGATCCACCCACC 25946
i i i i
C AluY#SINE/Alu 100 CCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCC 51
INTRON_3 25947 TTGGCCTCCCAAAGTGCTGGGATTATAGACGTGAGCTACCACACCCAGC 25995
i i i i i i i
C AluY#SINE/Alu 50 TCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p37g.matrix
Transitions / transversions = 8.33 (25 / 3)
Gap_init rate = 0.00 (0 / 298), avg. gap size = 0.0 (0 / 0)
+ 2803 9.7 0.5 3.8 INTRON_3 25996 26222 (373959) C L1PA13 LINE/L1 (2164) 3982 3766 16 *
ANNOTATION EVIDENCE:
2803 9.66 0.45 3.75 INTRON_3 25996 26222 373959 C L1PREC2_orf2 LINE/L1 1657 1873 1421 77
INTRON_3 25996 TGAGGTAGGTTCTTTCAATACTTAGTTTATTGAGAGTTTTTAACATGAAG 26045
--------- i i
C L1PREC2_orf2# 1873 ---------TTCCTTCAATACCTAGTTTATTGAGAGTTTTTAACATGAAG 1833
INTRON_3 26046 GGGTGTTGAATTTTATGGAAAGCTTTTCCTGCGTCTATTGAGATAATAGT 26095
i vi i i i vi
C L1PREC2_orf2# 1832 GGATGTTGAATTTTATCAAAAGCCTTTTCTGCATCTATTGAGATAATCAT 1783
INTRON_3 26096 GTTTTTTTTTGTCTTTAATTCTGTTTATGTGATGGATCACATCTATTGAT 26145
vv - i i i
C L1PREC2_orf2# 1782 GTGGTTTTT-GTCTTTAGTTCTGTTTATGTGATGAATCACATTTATTGAT 1734
INTRON_3 26146 TTGCATATGTTGAACCAACCTTGCATCCCAGAAATAAAGCTTACTTGATT 26195
i i ii i i
C L1PREC2_orf2# 1733 TTGCGTATGTTGAACCAACCTTGCATCCCGGGGATAAAGCCTACTTGATC 1684
INTRON_3 26196 GTGATGAATAAGCTTTTTGATGTGGTG 26222
i i v v
C L1PREC2_orf2# 1683 GTGGTGGATTAGCTTTTTGATGTGCTG 1657
Matrix = 20p37g.matrix
Transitions / transversions = 3.17 (19 / 6)
Gap_init rate = 0.01 (2 / 226), avg. gap size = 5.00 (10 / 2)
+ 4386 13.0 0.9 3.7 INTRON_3 26205 26980 (373201) C L1PA13 LINE/L1 (2340) 3806 3052 16
ANNOTATION EVIDENCE:
4386 12.98 0.90 3.71 INTRON_3 26205 26980 373201 C L1PREC2_orf2 LINE/L1 943 1697 1597 78
INTRON_3 26205 AAGCTT-TTTGAT-GTGGTGGATAAGATTTTTGATATGCTGCTGGATTCA 26252
i -i - v v i i
C L1PREC2_orf2# 1697 AAGCCTACTTGATCGTGGTGGATTAGCTTTTTGATGTGCTGCTGGATTCG 1648
INTRON_3 26253 GTTTACCAGTATTTTGCTTAGGATTTTTGCATCGATGTTCATCAAGGATA 26302
i v i v
C L1PREC2_orf2# 1647 GTTTGCAAGTATTTTGTTGAGGATTTTTGCATCGATGTTCATCAAGGATA 1598
INTRON_3 26303 TTGGCCTGAATTTTTCTTTTTTTAAATTGTGTCTCTGCTATGTTTTGGCA 26352
v i-- i v i
C L1PREC2_orf2# 1597 TTGGCCTGAAGTTTTCTTTTTTTG--TTGTGTCTCTGCCAGGTTTTGGTA 1550
INTRON_3 26353 TCAGGATGATCCTGGCCTCCTAGAATGAGTTAGGGAAGGGTCCCTCATCC 26402
v v i i i v
C L1PREC2_orf2# 1549 TCAGGATGATGCTGGCCTCATAGAATGAGTTGGGGAGGAGTCCCTCCTCC 1500
INTRON_3 26403 TCAATTTTTTGGAATAGTTTCAGTAGGAACAGTACCAGCTTTTCTTTTTA 26452
ii i v
C L1PREC2_orf2# 1499 TCAATTTTTTGGAATAGTTTCAGTAGGAATGGTACCAGCTCTTCTTTGTA 1450
INTRON_3 26453 TAACTGGTAGAATTCGACTGTGAATCTGTTTGTTCCTGGGCTTTTTTGGG 26502
i v i i i v v
C L1PREC2_orf2# 1449 CATCTGGTAGAATTCGGCTGTGAATCCGTCTGGTCCTGGGCTTTTTTTGG 1400
INTRON_3 26503 GTGTTAGGCTATTTATTACTGTTTCAATTTCAGAGCTCATTATTGGTCTG 26552
v v v i i
C L1PREC2_orf2# 1399 TTGGTAGGCTATTTATTACTGATTCAATTTCGGAGCTCGTTATTGGTCTG 1350
INTRON_3 26553 TTCATGAATTCCATTTCTTACTGGCTCTGTCTTGGGAGGGTGTATGTGTA 26602
v i v v v i v v
C L1PREC2_orf2# 1349 TTCAGGGAATCAATTTCTTCCTGGTTCAGTCTTGGGAGGGTGTATGTGTC 1300
INTRON_3 26603 CAGAAATTTATTCATTTCTTCTGTATTTTCTAGTTTATGTGCATAGAGAT 26652
i i i ivi i i
C L1PREC2_orf2# 1299 CAGGAATTTATCCATCTCTTCTAGGTTTTCTAGTTTGTGTGCATAGAGGT 1250
INTRON_3 26653 GTTTATAATAATTGCTTATGATTATTTATATTTCTGTGGGGTCAGTGGTA 26702
ii i i v v i i
C L1PREC2_orf2# 1249 GTTCGTAGTAGTTTCTGATGGTTATTTGTATTTCTGTGGGGTCAGTGGTA 1200
INTRON_3 26703 ATACCCTCTTTGTTGTTTCTGACGATGTTTATTTGGGTCTTCTCTCTT-- 26750
i i i ii i ivi i --
C L1PREC2_orf2# 1199 ACATCCCCTTTGTCATTTCTAATTGTGTTTATTTGGATCTTCTCTCTTTT 1150
INTRON_3 26751 ---CTTTATTTGTCTAGCTAGAGTTCTATCTATTTTATTAGTTTTTTTTT 26797
--- v v vi i i ---
C L1PREC2_orf2# 1149 CTTCTTTATTAGTCTAGCTAGCGGCCTATCTATCTTATTAATTTTTT--- 1103
INTRON_3 26798 TTTTTTTTTTTTTTTTTTTTTTTCAAAAAAACAACTCTTGGATTTGCTGA 26847
----------------------- v i i i
C L1PREC2_orf2# 1102 -----------------------CAAAAAACCAACTCCTGGATTCGTTGA 1076
INTRON_3 26848 TCTTTTGAATGGTTTTTTATGTCTCAGTCTCCTTTAGTTCAGCTCCGAGT 26897
ii ii i i v
C L1PREC2_orf2# 1075 TCTTTTGAATGGTTTTTCGTGTCTCGATCTCCTTCAGTTCAGCTCTGATT 1026
INTRON_3 26898 TTGGTTATTTCTTGTCTTCTGCTAGCTTTAGAGTTGGTTTTCTCTTGGTT 26947
i i v v
C L1PREC2_orf2# 1025 TTGGTTATTTCTTGTCTTCTGCTAGCTTTGGGGTTGGTTTGCTCTTGCTT 976
INTRON_3 26948 CTCTGGTTCTCTTAGTTGTGATGTGAGGTTTTT 26980
i i i v v
C L1PREC2_orf2# 975 CTCTAGTTCTTTCAGTTGTGATGTTAGGTTGTT 943
Matrix = 20p37g.matrix
Transitions / transversions = 1.77 (62 / 35)
Gap_init rate = 0.01 (5 / 775), avg. gap size = 7.00 (35 / 5)
+ 25 60.0 0.0 0.0 INTRON_3 27014 27038 (373143) + AT_rich Low_complexity 1 25 (0) 22 *
ANNOTATION EVIDENCE:
25 60.00 0.00 0.00 INTRON_3 27014 27038 373143 C AT_rich Low_complexity 140 164 136 47
INTRON_3 27014 GGATTAATTTAATTTATTAATTAAT 27038
?? vvvvv vvvv vv vv
C AT_rich#Low_c 164 SSAAATTATATTATTTATTTTTAAT 140
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 13)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
+ 30 70.0 0.0 0.0 INTRON_3 27016 27045 (373136) + AT_rich Low_complexity 1 30 (0) 23
ANNOTATION EVIDENCE:
30 70.00 0.00 0.00 INTRON_3 27016 27045 373136 + AT_rich Low_complexity 127 156 144 48
INTRON_3 27016 ATTAATTTAATTTATTAATTAATTAATTTA 27045
????????????? vv vvv vvv
AT_rich#Low_c 127 WWWWWWWWWWWWWATTAAAAATAAATAATA 156
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 8)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 203 18.6 2.3 0.0 INTRON_3 27198 27240 (372941) + T-rich Low_complexity 135 178 (0) 24
ANNOTATION EVIDENCE:
203 18.60 2.33 0.00 INTRON_3 27198 27240 372941 C (GAAA)n Simple_repeat 135 178 2 103
INTRON_3 27198 TCTTTCTTTTCGTTTTTCTTT-TCGCTTTCTTTCTTTTTTTGTT 27240
iiv i - iv i v
C (GAAA)n#Simpl 178 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 135
Matrix = Unknown
Transitions / transversions = 1.67 (5 / 3)
Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1)
+ 182 22.9 2.1 0.0 INTRON_3 27641 27688 (372493) C L2a LINE/L2 (253) 3173 3125 25
ANNOTATION EVIDENCE:
182 22.92 2.08 0.00 INTRON_3 27641 27688 372493 C L2a_3end LINE/L2 216 264 253 28
INTRON_3 27641 TTATATATGGCAGTCAGGGAAGGCCTCTCTTAGC-TGTGACTTTTCAAC 27688
v v ii v v v-v v v i
C L2a_3end#LINE 264 TTAAATAGGGTGGTCAGGGAAGGCCTCACTGAGAAGGTGACATTTGAGC 216
Matrix = 25p37g.matrix
Transitions / transversions = 0.38 (3 / 8)
Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1)
+ 370 17.1 5.8 9.3 INTRON_3 28483 28637 (371544) C Charlie10 DNA/hAT-Charlie (143) 2679 2530 26
ANNOTATION EVIDENCE:
370 17.07 5.81 9.33 INTRON_3 28483 28637 371544 C Charlie10 DNA/hAT-Charlie 2530 2679 143 111
INTRON_3 28483 TACCAGCTCAA--TTTTTCATTA---GATTCAACCTTCATAAAATTGTAT 28527
v i -- i --- vvv i
C Charlie10#DNA 2679 TACAAGCCCAAAATTTTTTATTATTAGATTCAACAGACATAAAATTATAT 2630
INTRON_3 28528 TTTATACATATGATCAGAAAAAAACAA-TATG-GGAAAAAGGTTATAATT 28575
--- ------- v v - - ?--- v
C Charlie10#DNA 2629 TTTA---ATA-------AATACAACAAATATGAGGAAAAAN---AGAATT 2593
INTRON_3 28576 ACAAAAACTGTACGTATTGTACAGTAAAAGCATTGCAT-T-GGCAGTTAA 28623
i ii v v i ii - - - i
C Charlie10#DNA 2592 ATAAAAACTGTACACATTGTTCATTGAAAGTGT-GCATATAGGCAATTAA 2544
INTRON_3 28624 TACAGAGAATCACT 28637
i i i?
C Charlie10#DNA 2543 TATAGAAAATTNCT 2530
Matrix = 20p37g.matrix
Transitions / transversions = 1.44 (13 / 9)
Gap_init rate = 0.06 (10 / 154), avg. gap size = 2.30 (23 / 10)
+ 1306 22.0 0.6 5.8 INTRON_3 28644 28784 (371397) + AluJb SINE/Alu 1 133 (179) 27
ANNOTATION EVIDENCE:
1306 22.00 0.61 5.77 INTRON_3 28644 28784 371397 + AluJb SINE/Alu 1 133 179 14
INTRON_3 28644 GGCCAGGTGTAGTGGCTCACTCCTGTAATCCAGATTCTTTGGGAGGCCAA 28693
i i ii v viiiv i
AluJb#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 28694 GATGAGAAAATTGCTTGAAGCCAGGAGTTCAAGAACAGCCTGGGCAACAT 28743
ii i ii ii iv i v
AluJb#SINE/Al 51 GGCGGGAGGATCACTTGAGCCCAGGAGTTCGAGACCAGCCTGGGCAACAT 100
INTRON_3 28744 AGCAAAGCCCTGTCTCTACAAAAAATAAAAAAAAAAAAATT 28784
i ii i i v --------
AluJb#SINE/Al 101 GGTGAAACCCCGTCTCTACAAAAAATACAAAAA-------- 133
Matrix = 14p37g.matrix
Transitions / transversions = 3.67 (22 / 6)
Gap_init rate = 0.01 (1 / 140), avg. gap size = 8.00 (8 / 1)
+ 2574 5.0 0.0 0.7 INTRON_3 28785 29082 (371099) + AluY SINE/Alu 1 296 (15) 28
ANNOTATION EVIDENCE:
2474 5.06 0.00 0.68 INTRON_3 28785 29082 371099 + AluY SINE/Alu 1 296 15 5
INTRON_3 28785 GGCCAAGCGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAA 28834
ii i i i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 28835 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 28884
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
INTRON_3 28885 TGAAACCCCGTCTCTACTAAAAATACCAAAAAATTAGCTGGGTGTGTTGG 28934
- i i v
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATAC-AAAAAATTAGCCGGGCGTGGTGG 149
INTRON_3 28935 CGGGCGCCTGCAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGGG 28984
i i v
AluY#SINE/Alu 150 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 199
INTRON_3 28985 TGAACCCGGGAAGCAAGAGCTTGCAGTGAGCCGAGATGGCGCCACTGCAC 29034
i i- v
AluY#SINE/Alu 200 TGAACCCGGGAGGCG-GAGCTTGCAGTGAGCCGAGATCGCGCCACTGCAC 248
INTRON_3 29035 TCCAGCCTGGGTGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAA 29082
i
AluY#SINE/Alu 249 TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAA 296
Matrix = 14p37g.matrix
Transitions / transversions = 4.00 (12 / 3)
Gap_init rate = 0.01 (2 / 297), avg. gap size = 1.00 (2 / 2)
+ 1306 22.0 0.6 5.8 INTRON_3 29083 29268 (370913) + AluJb SINE/Alu 134 312 (0) 27
ANNOTATION EVIDENCE:
1306 22.00 0.61 5.77 INTRON_3 29083 29268 370913 + AluJb SINE/Alu 134 312 0 15
INTRON_3 29083 CACATTTAGCTGGGCGAGGTGGTGCATGTGTATAGTCCCAGCTTCCCCGT 29132
----- i v i ii iv i v i v v
AluJb#SINE/Al 134 -----TTAGCCGGGCGTGGTGGCGCGCGCCTGTAGTCCCAGCTACTCGGG 178
INTRON_3 29133 TGGCTCAGGCAGGAGGATCCCTTGAAGCTGAGGAGTTGGATGTTAACGGC 29182
v v v iv i - v v v i i- i i
AluJb#SINE/Al 179 AGGCTGAGGCAGGAGGATCGCTTGAGCCCG-GGAGGTCGAGGCTG-CAGT 226
INTRON_3 29183 CAACTATGTTCCTGCCACTGCACTCCAACCTGGGTGACAGAGCAA--CCC 29230
v i ii v vi i i i --
AluJb#SINE/Al 227 GAGCCGTGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACCC 276
INTRON_3 29231 TGTCTCAATAAAACAAAACAAACAAGCAAACAAAAAAA 29268
v v v v -- v
AluJb#SINE/Al 277 TGTCTCAAAAAAAAAAAAAAAAAAA--AAAAAAAAAAA 312
Matrix = 14p37g.matrix
Transitions / transversions = 1.00 (20 / 20)
Gap_init rate = 0.03 (5 / 185), avg. gap size = 2.20 (11 / 5)
+ 2375 8.4 4.0 0.0 INTRON_3 29307 29605 (370576) C AluY SINE/Alu (0) 311 1 29
ANNOTATION EVIDENCE:
2264 8.36 4.01 0.00 INTRON_3 29307 29605 370576 C AluY SINE/Alu 1 311 0 6
INTRON_3 29307 TTCTTCTTCTTCTTTTTTTTTTTTTTTTTTGAGACGGAGTCTC------- 29349
i i i i -------
C AluY#SINE/Alu 311 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGT 262
INTRON_3 29350 -----AGGCTGGAGTGCAGTGGCGCCATCTTGGCTCACTGCAAGCTCTGC 29394
----- v i i
C AluY#SINE/Alu 261 CGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGC 212
INTRON_3 29395 CTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGTAC 29444
v
C AluY#SINE/Alu 211 CTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGAC 162
INTRON_3 29445 CACAGGTGCCTACCACCACGCCCAGCCAATTTTTTGTATTTTTAGTGGAG 29494
i i ii i i i
C AluY#SINE/Alu 161 TACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAG 112
INTRON_3 29495 ACGGGATTTCACCATGTTAGCCAGGATGGTCTCGATGTCCTGACCTCGTG 29544
i i v
C AluY#SINE/Alu 111 ACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTG 62
INTRON_3 29545 ATCCACCCGTCTCAGCCCCCCAAAGTGCTGGGATTACAGGCATGAGCCAC 29594
i i i i i
C AluY#SINE/Alu 61 ATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC 12
INTRON_3 29595 CGCACCCAGCC 29605
i i
C AluY#SINE/Alu 11 CGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 7.33 (22 / 3)
Gap_init rate = 0.00 (1 / 298), avg. gap size = 12.00 (12 / 1)
+ 292 27.8 0.0 0.0 INTRON_3 30157 30228 (369953) + Charlie7 DNA/hAT-Charlie 270 341 (2271) 30 *
ANNOTATION EVIDENCE:
292 27.78 0.00 0.00 INTRON_3 30157 30228 369953 + Charlie7 DNA/hAT-Charlie 270 341 2271 112
INTRON_3 30157 CCTAATTGATTAGTTTATTTCCAGTGTATTTCAACGTGTTGCAGTTCACA 30206
v i vi vi ii i ii v i ii i i
Charlie7#DNA/ 270 CCTCACTCGTTCATTTGCTTTCAGCATATTGCGATATATTGCAGTTTACA 319
INTRON_3 30207 TGTCCCTAGCTAAGTGGACTTA 30228
v i i
Charlie7#DNA/ 320 TGTGCCTAGTTAAGTGGATTTA 341
Matrix = 20p37g.matrix
Transitions / transversions = 3.00 (15 / 5)
Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0)
+ 596 27.2 7.0 4.1 INTRON_3 30210 30393 (369788) + Charlie7 DNA/hAT-Charlie 374 554 (2058) 31
ANNOTATION EVIDENCE:
596 27.18 7.04 4.11 INTRON_3 30210 30393 369788 + Charlie7 DNA/hAT-Charlie 374 554 2058 113
INTRON_3 30210 CCCTAGCTAAGTGGACTTAAAGT-----AAAGGGATTTTTGAAAATAAAT 30254
vi v i --- ----- ii ii v v i
Charlie7#DNA/ 374 CCCTCACAAAATGGAC---AAGTGGCTTAAAAAGATTCCTGCAAAGAAAC 420
INTRON_3 30255 TG--GATTAAATATAGTACTAATAATGTCAGCACATAGGAACAACAAGAA 30302
i -- i v i iv viv
Charlie7#DNA/ 421 CGCGGATTGAAGATAATACTAATAATGCAAGCACAAGCGAACAACAAGAA 470
INTRON_3 30303 AATTGCAAAGCTAATGGTTTGTCTT-TAATATGAACTCTTGGTCAGCCAT 30351
v i i iiv ivi i- i i i v i
Charlie7#DNA/ 471 AATGGCAGAGCTGACACTTCTCCTCCTAGTACGAGCTCTTCGTCAGCCAC 520
INTRON_3 30352 GTAATGAGGTAAAAATAGTCCGAAAAGAAGTTGAGCCAAAAA 30393
i v i i i -- vi ---- iv ii i --
Charlie7#DNA/ 521 ATTACGAGGTAAAAACAAT--GACGA----TCTAATCAGA-- 554
Matrix = 20p37g.matrix
Transitions / transversions = 2.13 (32 / 15)
Gap_init rate = 0.04 (7 / 183), avg. gap size = 2.71 (19 / 7)
+ 345 16.1 1.2 3.7 INTRON_3 30394 30477 (369704) + L1PB4 LINE/L1 6074 6155 (1) 32
ANNOTATION EVIDENCE:
345 16.07 1.19 3.66 INTRON_3 30394 30477 369704 + L1PB4_3end LINE/L1 821 902 1 23
INTRON_3 30394 AAAAACCTAAATTACTTCACTAATACACAGTATATTCATGTAACACAACT 30443
i i i --- i v i i i v
L1PB4_3end#LI 821 AAAAGCCCAGA---CTTCACCACTACGCAATATATCCATGTAACAAAACT 867
INTRON_3 30444 GCACTTGTACCTC-TAATTTTATAAAACTAAAAAA 30477
i - v i v
L1PB4_3end#LI 868 GCACTTGTACCCCCTAAATCTATAAAAATAAAAAA 902
Matrix = 18p37g.matrix
Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.02 (2 / 83), avg. gap size = 2.00 (4 / 2)
+ 596 27.2 7.0 4.1 INTRON_3 30478 30576 (369605) + Charlie7 DNA/hAT-Charlie 555 665 (1947) 31
ANNOTATION EVIDENCE:
596 27.18 7.04 4.11 INTRON_3 30478 30576 369605 + Charlie7 DNA/hAT-Charlie 555 665 1947 114
INTRON_3 30478 TTT--TAAAGAGTTA---AAAAAGTCTG---TTATTAAAAA-ACTATTTG 30518
i --i ii i --- ?i --- i i -
Charlie7#DNA/ 555 TCTGACAAGAAGTCAGCAAAAAAGNTTGAAATTATCAAGAAGACTATTTG 604
INTRON_3 30519 AAACTTGGATTTACATTTGTTAT-ATT--TCATGAATCTTATTGAAAGTT 30565
iv iiii - --iv i iiiivv v
Charlie7#DNA/ 605 AAATATGGATTTACATCCACTATCATTAACGATGAACCTCGCCCTAAGTG 654
INTRON_3 30566 TATATAATGCC 30576
vi
Charlie7#DNA/ 655 TATATTGTGCC 665
Matrix = 20p37g.matrix
Transitions / transversions = 3.33 (20 / 6)
Gap_init rate = 0.06 (6 / 98), avg. gap size = 2.00 (12 / 6)
+ 339 24.9 5.9 4.2 INTRON_3 30588 30843 (369338) + Charlie7 DNA/hAT-Charlie 2351 2610 (2) 33
ANNOTATION EVIDENCE:
339 24.88 5.86 4.23 INTRON_3 30588 30843 369338 + Charlie7 DNA/hAT-Charlie 2351 2610 2 115
INTRON_3 30588 TATTAATACTGTTCTTTAAATG-GAGCAAAATGGTTTTTGAACCATTATC 30636
v iv v v - - - v i vv
Charlie7#DNA/ 2351 TATTAATAGTAATGTTTTAATGAGAGCAAAA-GGTTTT-GTACTATTAAA 2398
INTRON_3 30637 AAAGTAAA-ACAAATT--TTAAAAATATTACTTA----ATTTTCAGCTGA 30679
v v? - ? -- v ii ---- i i v v
Charlie7#DNA/ 2399 TAATNAAATANAAATTATTTTAAAATATTGTTTATTTCATCTTTATCTCA 2448
INTRON_3 30680 TTAATTTAAAATT----CTGTTTG-ATCTGTTTTATAATGTA-ATTATAT 30723
ivv ----? v -i v - v
Charlie7#DNA/ 2449 TCCTTTTAAAATTTCTANTTTTTGTGTATGTTTTATAATGTACATAATAT 2498
INTRON_3 30724 ATTACCGCAGTAGGTGCATATGTAATATACATGTGTGTATATACGTATGT 30773
vii - ---i i - ---i v i v vi i
Charlie7#DNA/ 2499 ATTAGTACA-TAG---TACATGTA-TATA---ATTTATAAATAAATATAT 2540
INTRON_3 30774 ATATATGAATGATATATGTTCAAAAATGTTTTATCAATAAGTATATACAA 30823
viiv i ii i - v iii ii v i i i
Charlie7#DNA/ 2541 ATATATTGGGGGTGCATGCTCAAAA-TTTTTTACTGATGGGGATGTGCGA 2589
INTRON_3 30824 T-AAAAATATTTAGAGACCAC 30843
- vi i
Charlie7#DNA/ 2590 TCAAAAAAGTTTGGAGACCAC 2610
Matrix = 20p37g.matrix
Transitions / transversions = 1.23 (32 / 26)
Gap_init rate = 0.06 (15 / 255), avg. gap size = 1.73 (26 / 15)
+ 388 31.9 0.0 1.8 INTRON_3 30873 30987 (369194) + MIR SINE/MIR 2 114 (148) 34
ANNOTATION EVIDENCE:
388 31.86 0.00 1.77 INTRON_3 30873 30987 369194 + MIR SINE/MIR 2 114 148 29
INTRON_3 30873 CAACATAGAAGAATGGTTATGAGCAGGAACTTTGGGGTTAAACAGACGTA 30922
ii v v i v v i i i ii i v v - i
MIR#SINE/MIR 2 CAGTATAGCATAGTGGTTAAGAGCACGGACTCTGGAGCCAGACTGCC-TG 50
INTRON_3 30923 GGTTTGGATTCTGTATTTACCATGTACTAGTTTTATGGAGCTTGTGCAAA 30972
i i i i vv i i iv i v i - v v i
MIR#SINE/MIR 51 GGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTG-ACCTTGGGCAAG 99
INTRON_3 30973 CTACTTGATCTCACT 30987
i i i v
MIR#SINE/MIR 100 TTACTTAACCTCTCT 114
Matrix = 25p37g.matrix
Transitions / transversions = 1.77 (23 / 13)
Gap_init rate = 0.02 (2 / 114), avg. gap size = 1.00 (2 / 2)
+ 2292 7.0 2.5 0.0 INTRON_3 31650 31776 (368405) + AluY SINE/Alu 1 127 (184) 35
ANNOTATION EVIDENCE:
2292 6.99 2.45 0.00 INTRON_3 31650 31776 368405 + AluY SINE/Alu 1 127 184 7
INTRON_3 31650 GGCCGGGCACGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 31699
i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 31700 GGCAAACGGATCACGAGGTCAGGAGATCAAGACCATCCTGGCTCACATGG 31749
iii i v i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
INTRON_3 31750 TGAAACCCCGTCTCTACTAAAAATACA 31776
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACA 127
Matrix = 14p37g.matrix
Transitions / transversions = 6.00 (6 / 1)
Gap_init rate = 0.00 (0 / 126), avg. gap size = 0.0 (0 / 0)
+ 456 3.5 0.0 0.0 INTRON_3 31777 31834 (368347) + (CAAAA)n Simple_repeat 2 59 (0) 36
ANNOTATION EVIDENCE:
456 3.45 0.00 0.00 INTRON_3 31777 31834 368347 + (CAAAA)n Simple_repeat 2 59 121 98
INTRON_3 31777 AAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACACAAC 31826
v
(CAAAA)n#Simp 2 AAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAAC 51
INTRON_3 31827 AAAAAAAA 31834
v
(CAAAA)n#Simp 52 AAAACAAA 59
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 2)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0)
+ 2292 7.0 2.5 0.0 INTRON_3 31835 31992 (368189) + AluY SINE/Alu 128 292 (19) 35
ANNOTATION EVIDENCE:
2292 6.99 2.45 0.00 INTRON_3 31835 31992 368189 + AluY SINE/Alu 128 292 19 8
INTRON_3 31835 -------GCCGGGCATGGTGGCAGGCGCCTGTAGTCCTAGCTACTCGGGA 31877
------- i i i
AluY#SINE/Alu 128 AAAATTAGCCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGA 177
INTRON_3 31878 GGCTGAGGCAGGAGAATGGTGTGAACCCAGGAGGTGGAGCTTGCAGTGAG 31927
i i i
AluY#SINE/Alu 178 GGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAG 227
INTRON_3 31928 CCAAGATTGTGCCACTGTACTCCAGCCTGGGTGACAGAGCGAGACTCTGT 31977
i i i i i i
AluY#SINE/Alu 228 CCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGT 277
INTRON_3 31978 CTCAAAAAAGAAAAA 31992
i
AluY#SINE/Alu 278 CTCAAAAAAAAAAAA 292
Matrix = 14p37g.matrix
Transitions / transversions = 0.0 (13 / 0)
Gap_init rate = 0.01 (1 / 157), avg. gap size = 7.00 (7 / 1)
+ 199 30.1 24.3 0.0 INTRON_3 32069 32171 (368010) + MIRc SINE/MIR 39 166 (102) 37
ANNOTATION EVIDENCE:
199 30.10 24.27 0.00 INTRON_3 32069 32171 368010 + MIRc SINE/MIR 39 166 102 30
INTRON_3 32069 GAGTTGAGA-GACCTGGATTT------TAGCTTTGCCATTTGCTTCGCAT 32111
iii - i i------ i i i i vvvii
MIRc#SINE/MIR 39 GAGTCAGGAAGACCTGGGTTCGAGTCCTGGCTCTGCCACTTACTAGCTGT 88
INTRON_3 32112 GTATTCTGGGGCAA----C--------------CCTCAGCTTCCTCATTC 32143
ivi v ---- -------------- i ii
MIRc#SINE/MIR 89 GTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 138
INTRON_3 32144 ATAAACTTGGAATTAGAGTATTTGCCTT 32171
i v v i v v i ii i
MIRc#SINE/MIR 139 GTAAAATGGGGATAATAATACCTGCCCT 166
Matrix = 25p37g.matrix
Transitions / transversions = 2.44 (22 / 9)
Gap_init rate = 0.04 (4 / 102), avg. gap size = 6.25 (25 / 4)
+ 441 35.3 5.1 9.3 INTRON_3 32180 32435 (367746) C L2b LINE/L2 (4) 3371 3126 38
ANNOTATION EVIDENCE:
441 35.33 5.08 9.35 INTRON_3 32180 32435 367746 C L2b_3end LINE/L2 217 462 4 31
INTRON_3 32180 ATTCACTCAACCCATATTT---GAGCACCTAGAATGTGCTGGCATGTGCT 32226
i vv i --- ------- --- i
C L2b_3end#LINE 462 ATTCATTCAACAAACATTTACTGAGCACCTA-------CTG---TGTGCC 423
INTRON_3 32227 AG-CACTGTGCTACTCACTAGGGATATGTAGATGA-TAAGACTTGACCCA 32274
- v ivv i i i iivv i -i v- i
C L2b_3end#LINE 422 AGGCCCTGTGCTGGGCGCTGGGGACACAGCGGTGAACAAGACA-GACCCG 374
INTRON_3 32275 ATCCCTGCCCTCACTGAAGTTATACTTCAATATGTACAATATTTAATATT 32324
i v iv i i v i i iv vivi i ---------
C L2b_3end#LINE 373 GTCCCTGCCCTCACGGAGCTCACAGTCCAGTGGGGGAGACA--------- 333
INTRON_3 32325 TGAAATATGTACAAACAATTACAGATCTCTAGCATTGGGGCTATATTGGA 32374
- v i iv? i ? i - i ivv iivii iviv i i
C L2b_3end#LINE 332 -GACATGTAANCAGACAATNATA-ACCCAGAGTGGCAGGGTAGGACTGGG 285
INTRON_3 32375 GGAAT----AGGAG----TCTGAGTTGGCCTAGGGGAATTAAAGGGCTTT 32416
iii---- ----i vii i i- i ii i vvi
C L2b_3end#LINE 284 GGGGCCCAGAGGAGGGCGCCTGACCCGGCCTGGGGGG-TCAGGGAGGGCT 236
INTRON_3 32417 TCATAAAGGAAGTGGTACT 32435
v ii i ii i
C L2b_3end#LINE 235 TCCTGGAGGAGGTGACATT 217
Matrix = 25p37g.matrix
Transitions / transversions = 2.20 (55 / 25)
Gap_init rate = 0.04 (11 / 255), avg. gap size = 3.27 (36 / 11)
+ 482 20.8 2.7 0.0 INTRON_3 32822 32941 (367240) C Arthur1A DNA/hAT-Tip100 (0) 177 90 39
ANNOTATION EVIDENCE:
468 21.67 10.00 0.00 INTRON_3 32822 32941 367240 C Arthur1B DNA/hAT-Tip100 1094 1225 0 117
INTRON_3 32822 CAGAGGTGGGTCCTAATTTTGTGGAGTCTGTAGCTTACAGAATTACAGAG 32871
i i i vii i i v i v v?i i
C Arthur1B#DNA/ 1225 CAGGGGCGGATCCAGGTTTTGTGGGGCCTGAAGCTTATACAATTTKGGGG 1176
INTRON_3 32872 GCTCTCTTTAAGAAAAAGAATACAAAATTATGAAT------TCACTTATA 32915
i i ------ i vv ii
C Arthur1B#DNA/ 1175 GCCCTCTTTAAGAAAAAGAATACAAAATTACGAATACAAAATTAGGTACG 1126
INTRON_3 32916 AAAGTGTATAT------GGAAAGACAAAAGAA 32941
v ------i v v
C Arthur1B#DNA/ 1125 AAAGTGAATATTTATTTAGAATGAGAAAAGAA 1094
Matrix = 20p37g.matrix
Transitions / transversions = 1.78 (16 / 9)
Gap_init rate = 0.02 (2 / 119), avg. gap size = 6.00 (12 / 2)
482 20.45 0.00 0.00 INTRON_3 32822 32909 367272 C Arthur1A DNA/hAT-Tip100 90 177 0 116
INTRON_3 32822 CAGAGGTGGGTCCTAATTTTGTGGAGTCTGTAGCTTACAGAATTACAGAG 32871
i i i vii i i v i v vvi i
C Arthur1A#DNA/ 177 CAGGGGCGGATCCAGGTTTTGTGGGGCCTGAAGCTTATACAATTTGGGGG 128
INTRON_3 32872 GCTCTCTTTAAGAAAAAGAATACAAAATTATGAATTCA 32909
i i v
C Arthur1A#DNA/ 127 GCCCTCTTTAAGAAAAAGAATACAAAATTACGAATACA 90
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (12 / 6)
Gap_init rate = 0.00 (0 / 87), avg. gap size = 0.0 (0 / 0)
+ 1852 16.5 1.2 0.9 INTRON_3 32942 33277 (366904) + L1MC LINE/L1 4670 5006 (1140) 40
ANNOTATION EVIDENCE:
1852 16.52 1.19 0.89 INTRON_3 32942 33277 366904 + L1MC_orf2 LINE/L1 2561 2897 397 79
INTRON_3 32942 CTAGAATAGCCAACACAATACTAAAGAGGAAGAACAAAGTCAGAGGGCTG 32991
i i i ii ii i
L1MC_orf2#LIN 2561 CCAGAATAGCCAACACAATATTGAAGGAGAAGAACAAAGTTGGAGGACTG 2610
INTRON_3 32992 ACAAGTCCCAACT-CAATACTTACTATAAAATGACAATAATCAAGACCAC 33040
vvv i - v iiv i vii
L1MC_orf2#LIN 2611 ACACTACCCGACTTCAAGACTTACTATAAAGCTACAGTAATCAAGACAGT 2660
INTRON_3 33041 GTGGTATTGGTGAAAGAATAGACAAATAGATCAATGGGACAGAATAGAGA 33090
i i
L1MC_orf2#LIN 2661 GTGGTATTGGCGAAAGAATAGACAAATAGATCAATGGAACAGAATAGAGA 2710
INTRON_3 33091 GCGCAGAAATAGACCCCCATATATATAGTAAACTGATCTTTGACAAAGGA 33140
v v v v
L1MC_orf2#LIN 2711 GCCCAGAAATAGACCCACATAAATATAGTCAACTGATCTTTGACAAAGGA 2760
INTRON_3 33141 GGAAGGGTAATTCAATGGAGGAAGGATAGTCTTTTTGACACATGGCACCA 33190
v i i v v i ii v ii ii
L1MC_orf2#LIN 2761 GCAAAGGCAATACAATGGAGCAAAGATAGTCTTTTCAACAAATGGTGCTG 2810
INTRON_3 33191 GAACAACTGGCTATCTAGATACACAAAAAAAATGAGTCTGAAAACAGACT 33240
vi i v i --- i ii v i
L1MC_orf2#LIN 2811 GAACAACTGGACATCCACATGCA---AAAAAATGAATCTAGACACAGACC 2857
INTRON_3 33241 TTATATCTTTCATAAAAATTAACTCA---TGGATCATGGA 33277
i i i i --- ii
L1MC_orf2#LIN 2858 TTACACCCTTCACAAAAATTAACTCAAAATGGATCACAGA 2897
Matrix = 20p37g.matrix
Transitions / transversions = 2.24 (38 / 17)
Gap_init rate = 0.01 (3 / 335), avg. gap size = 2.33 (7 / 3)
+ 516 12.1 0.0 0.0 INTRON_3 33312 33394 (366787) + L1MC LINE/L1 4988 5070 (1076) 40
ANNOTATION EVIDENCE:
516 12.05 0.00 0.00 INTRON_3 33312 33394 366787 + L1MC_orf2 LINE/L1 2879 2961 333 80
INTRON_3 33312 ACTTAAAATGGATCATAGACCTAAGTGTAAAATGATAAACTGTAAAGCTT 33361
i i i vv i i i
L1MC_orf2#LIN 2879 ACTCAAAATGGATCACAGACCTAAATGTAAAATGCAAAACTATAAAACTC 2928
INTRON_3 33362 TTAGAAGATAACATAGGAGAAAATATAGATGAC 33394
i v
L1MC_orf2#LIN 2929 CTAGAAGATAACATAGGAGAAAATCTAGATGAC 2961
Matrix = 20p37g.matrix
Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.00 (0 / 82), avg. gap size = 0.0 (0 / 0)
+ 379 18.2 0.0 0.0 INTRON_3 33387 33463 (366718) + L1MC LINE/L1 5039 5115 (1031) 40 *
ANNOTATION EVIDENCE:
379 18.18 0.00 0.00 INTRON_3 33387 33463 366718 + L1MC_orf2 LINE/L1 2930 3006 288 81
INTRON_3 33387 TAGATGACAACATAGGAGAAAATGTAGATGAACTTGGATCTGTCCATGAG 33436
v i v v i ? v v v
L1MC_orf2#LIN 2930 TAGAAGATAACATAGGAGAAAATCTAGATGACCTTGGGTNTGGCGATGAC 2979
INTRON_3 33437 TCTTTTGATAAAACAACAAAGGCAGGA 33463
i v v v v
L1MC_orf2#LIN 2980 TTTTTAGATACAACACCAAAGGCACGA 3006
Matrix = 20p37g.matrix
Transitions / transversions = 0.30 (3 / 10)
Gap_init rate = 0.00 (0 / 76), avg. gap size = 0.0 (0 / 0)
+ 236 28.7 14.9 1.2 INTRON_3 34962 35035 (365146) C MIRc SINE/MIR (171) 97 14 41
ANNOTATION EVIDENCE:
236 28.72 14.86 1.19 INTRON_3 34962 35035 365146 C MIRc SINE/MIR 14 97 171 32
INTRON_3 34962 CAAGGTCACACAGTTATGTAGGTGG---------GACTAAAATCTAAACT 35002
i - i --------- vi i i iiii
C MIRc#SINE/MIR 97 CAAGGTCACACAGCTA-GTAAGTGGCAGAGCCAGGACTCGAACCCAGGTC 49
INTRON_3 35003 TTG--GATTTTGAGTTCATTGTTCTTCCCATTACA 35035
v-- i iii i v i i i i
C MIRc#SINE/MIR 48 TTCCTGACTCCAAGTCCAGTGCTCTTTCCACTGCA 14
Matrix = 25p37g.matrix
Transitions / transversions = 6.00 (18 / 3)
Gap_init rate = 0.04 (3 / 73), avg. gap size = 4.00 (12 / 3)
+ 229 28.4 13.4 3.2 INTRON_3 35241 35382 (364799) C L2c LINE/L2 (134) 3253 3098 42
ANNOTATION EVIDENCE:
229 28.37 13.38 3.21 INTRON_3 35241 35382 364799 C L2c_3end LINE/L2 189 344 134 33
INTRON_3 35241 ATGACAACACATG--GAGGATAAGTGCTGTACTCTTAGAGATAAGGATAA 35288
v i v --i v i v ---i iii vi i i
C L2c_3end#LINE 344 ATTACAATACAAGTTAATGATAAGTGCTATAAT---GGGAGTATAGACAG 298
INTRON_3 35289 AGTGTTGTGGAA-CTCAGA---------CTA-ACTTGCCT-GGGGAATAG 35326
i i i i - v --------- - v ? - ii vi
C L2c_3end#LINE 297 GGTGCTATGGGAGCACAGAGGAGGGCACCTAGACTAGNCTTGGGGGGTCA 248
INTRON_3 35327 GGAGGGGCTTCACT-----ATGTGGATGTCTTACCTGAGTCTTGAAGGAA 35371
iii - ----- v - ii v v ? v
C L2c_3end#LINE 247 GGGAAGGCTTC-CTGGAGGAGGTG-ACATCTGAGCTGAGNCTTGAAGGAT 200
INTRON_3 35372 GAATATGAATT 35382
i v i
C L2c_3end#LINE 199 GAGTAGGAGTT 189
Matrix = 25p37g.matrix
Transitions / transversions = 1.85 (24 / 13)
Gap_init rate = 0.06 (9 / 141), avg. gap size = 2.67 (24 / 9)
+ 2197 14.3 0.0 0.0 INTRON_3 37068 37368 (362813) + AluSx SINE/Alu 1 301 (11) 43
ANNOTATION EVIDENCE:
2104 14.29 0.00 0.00 INTRON_3 37068 37368 362813 + AluSx SINE/Alu 1 301 11 9
INTRON_3 37068 GGCCAGATGTGGTGGCTCACACCTGTAATCCCAGCACTCTGGGAGGCCAA 37117
i ii i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 37118 GGCGGGTGGATCCCCTGAGGTCAGGAGTTTAAGACCAGCCCAGCCAACAT 37167
i v ii ii
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
INTRON_3 37168 GATGAAACCCCATCTCTACTAAAAATACAAAAATTAACCAGGCATGGTGG 37217
i i i i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGG 150
INTRON_3 37218 TGCACACCTGTAGTCCTAACTACTGGGGAGGCTGAGGCAGGAGAATCGCT 37267
i i i i i i v
AluSx#SINE/Al 151 CGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCT 200
INTRON_3 37268 TGCATCCAGGAGGCAGAGGTTGCAGCGAGCTGAAATCACACCACTGCACT 37317
v i i i i i i i i
AluSx#SINE/Al 201 TGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACT 250
INTRON_3 37318 CCAGCCTGGGTGATAGAGTGAGATGCCATCTCAAAAAACAACAAAAACAA 37367
i i i iv i v v v
AluSx#SINE/Al 251 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 300
INTRON_3 37368 A 37368
AluSx#SINE/Al 301 A 301
Matrix = 14p37g.matrix
Transitions / transversions = 5.14 (36 / 7)
Gap_init rate = 0.00 (0 / 300), avg. gap size = 0.0 (0 / 0)
+ 595 29.1 8.3 0.5 INTRON_3 37388 37591 (362590) + MIRb SINE/MIR 40 259 (9) 44
ANNOTATION EVIDENCE:
595 29.05 8.33 0.45 INTRON_3 37388 37591 362590 + MIRb SINE/MIR 40 259 9 34
INTRON_3 37388 TAGAATGAGTCAG--CAGGACTAGAATGCTAACTTTA--ACTT--TAATA 37431
i i v v -- v ii v v ii i i-- -- iiv
MIRb#SINE/MIR 40 TGGAGTCAGGCAGACCTGGGTTCGAATCCTGGCTCTGCCACTTACTAGCT 89
INTRON_3 37432 GTGAAACTTTGGAAAA------TAACCACTTTAAGCCCCAACTTTATTAG 37475
vi i iv ------ v i i i ii iv i v
MIRb#SINE/MIR 90 GTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCAT 139
INTRON_3 37476 CTATAAA-TGGGGATAATATTATCTACTTCATAAGGTTATTATGAAGATT 37524
i - v i i ii i i i i
MIRb#SINE/MIR 140 CTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATT 189
INTRON_3 37525 AAGT-AGTT--TGTATGTTTAG-GTTTAGCACAGTATCTATCTTATAGTA 37570
i - v -- i vv - i ii iv vi i
MIRb#SINE/MIR 190 AAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACACAGTA 239
INTRON_3 37571 AGCCCTTAGGTAAGTGGCAGC 37591
v i i- i i
MIRb#SINE/MIR 240 AGCGCTCAA-TAAATGGTAGC 259
Matrix = 25p37g.matrix
Transitions / transversions = 2.28 (41 / 18)
Gap_init rate = 0.04 (9 / 203), avg. gap size = 2.00 (18 / 9)
+ 213 6.5 0.0 0.0 INTRON_3 37593 37623 (362558) + (TTA)n Simple_repeat 1 31 (0) 45
ANNOTATION EVIDENCE:
213 6.45 0.00 0.00 INTRON_3 37593 37623 362558 C (TAA)n Simple_repeat 148 178 2 99
INTRON_3 37593 ATTATTAATATTATTATTATTATTATTTTTA 37623
v v
C (TAA)n#Simple 178 ATTATTATTATTATTATTATTATTATTATTA 148
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 2)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)
+ 1046 17.6 7.1 5.2 INTRON_3 37624 37905 (362276) + L1M4 LINE/L1 3724 4010 (2136) 46
ANNOTATION EVIDENCE:
1046 17.59 7.09 5.23 INTRON_3 37624 37905 362276 + L1M4_orf2 LINE/L1 1615 1901 1393 82
INTRON_3 37624 GATACAAAGTTCTTTAATAACTTACTAACAAAGTCAATTCAACAACATGT 37673
i iv i i i vv i viv i i --
L1M4_orf2#LIN 1615 GATGCAAAAATCCTCAACAAAATACTAGCAAACCGAATCCAGCAACAT-- 1662
INTRON_3 37674 AAAACTTATAAAAAAGATTATATATATCATGACCCAGTTGGATTTATTTC 37723
------- i i i-- v v ii
L1M4_orf2#LIN 1663 -------ATAAAAAGGATTATACAC--CATGACCAAGTGGGATTTATCCC 1703
INTRON_3 37724 AGAAATGCAAGATTGTCTTTATATTTGAAAATCAGTAGTGCAATGTA-TA 37772
i i vi v i ?i i ---- -
L1M4_orf2#LIN 1704 AGGAATGCAAGGTTGGTTTAACATMCGAAAATCAAT----CAATGTAATA 1749
INTRON_3 37773 TATCATATTAATAGAATGAAGGACAAAAAT-ACAT---CATCTCAA-AGA 37817
i i i i- --- -
L1M4_orf2#LIN 1750 CACCATATTAATAGAATAAAGGACAAAAACCACATGATCATCTCAATAGA 1799
INTRON_3 37818 TGCAGAAAAAACATTTGATAAAACCCAACA----TTTATAATAAAAATTC 37863
i i i i ---- i i iv
L1M4_orf2#LIN 1800 CGCAGAAAAAGCATTTGACAAAATCCAACACCNTTTCATGATAAAAACAC 1849
INTRON_3 37864 TCAGCAAACTAGAA-------GAAACTTCATT---CTGATAAAGGGCATC 37903
i i ------- i v i---
L1M4_orf2#LIN 1850 TCAACAAACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATC 1899
INTRON_3 37904 TA 37905
L1M4_orf2#LIN 1900 TA 1901
Matrix = 20p37g.matrix
Transitions / transversions = 3.18 (35 / 11)
Gap_init rate = 0.04 (10 / 281), avg. gap size = 3.50 (35 / 10)
+ 3233 22.0 4.6 0.8 INTRON_3 37911 38786 (361395) + L1M4 LINE/L1 4423 5334 (830) 46
ANNOTATION EVIDENCE:
3233 23.40 4.00 0.45 INTRON_3 37911 38760 361421 + L1M4_orf2 LINE/L1 2314 3193 101 83
INTRON_3 37911 AATTTAACAAAAG---TATGATAATTGTACATTGCATTTTATAAACCATT 37957
--- iii ? v i i v vvi? i v
L1M4_orf2#LIN 2314 AATTTAACAAAAGAAGTGCAANACTTATACACTGAAAACKACAAAACATT 2363
INTRON_3 37958 CTTGAAA-----TAAAGAAAATTTAAA---ATAGAGAGACAGCCTATGAT 37999
v ----- i ii --- i i i v i v
L1M4_orf2#LIN 2364 GTTGAAAGAAATTAAAGAAGACCTAAATAAATGGAAAGATATCCCATGTT 2413
INTRON_3 38000 CATGGATTGGAGAACTCAATATTGTTAAGATGACAGTTTTCCTCAAATTA 38049
ii i i i vi i i
L1M4_orf2#LIN 2414 CATGGATTGGAAGACTTAATATTGTTAAGATGGCAATACTCCCCAAATTG 2463
INTRON_3 38050 ATCTGCAGATTTAACACAATCTTTATCAAAATCCCAGTAGGCTTTTGTGT 38099
i i i ii iv v v i
L1M4_orf2#LIN 2464 ATCTACAGATTCAACGCAATCCCTATCAAAATCCCAGCTGCCTTTTTTGC 2513
INTRON_3 38100 AGAAATTGACAGGTTTCTCCTAAAATTTATAAAGAAATGCAAAGGATCTA 38149
i i vv i vi i i i
L1M4_orf2#LIN 2514 AGAAATTGACAAGCTGATCCTAAAATTCATATGGAAATGCAAGGGACCCA 2563
INTRON_3 38150 GAATAACCAAAATAATTTTGAAAAAGGAAGAACAAATTTAGAAAATTTTT 38199
i i i - v i ii i ivi
L1M4_orf2#LIN 2564 GAATAGCCAAAACAATCTTGAAAAAG-AAGAACAAAGTTGGAGGACTCAC 2612
INTRON_3 38200 ACTACTCAATATCAAAACATTTTGTAATACTATAATAATGGAGACAGTGT 38249
v i v v vi ii vi i i vi
L1M4_orf2#LIN 2613 ACTTCCCAATTTCAAAACTTACTACAAAGCTACAGTAATCAAGACAGTGT 2662
INTRON_3 38250 GGTATTTGTATAAAGATAGGTATACAGATAAATGGAACAGAATTAAGAGT 38299
i v i i ii i v i i
L1M4_orf2#LIN 2663 GGTACTGGCATAAGGATAGACATATAGATCAATGGAATAGAATTGAGAGT 2712
INTRON_3 38300 TT-GCAATAATCGC------TTATG--------ATTTTTGACAAAGGTAT 38334
ii- v v v ------ -------- i i ii
L1M4_orf2#LIN 2713 CCAGAAATAAACCCATACATTTATGGTCAATTGATTTTCGACAAGGGTGC 2762
INTRON_3 38335 TAAAACAATATAAGAGTGAAAAGCTAGTCTTTTCAACAAGTAGTACTGGG 38384
i i v vi vi v iiv i i i
L1M4_orf2#LIN 2763 CAAGACCATTCAATGGGGAAAGAATAGTCTTTTCAACAAATGGTGCTGGG 2812
INTRON_3 38385 ACAAGTGGATATTCGGATTAAAAAAAATAAATTTAGATCATTACCTCAGA 38434
v ?i iv vv i i v i i vi v
L1M4_orf2#LIN 2813 ACAACTGGATAKCCACATGCAAAAGAATGAAGTTGGACCCCTACCTCACA 2862
INTRON_3 38435 CCACACACGAAGTTTAGCTCAAAATGGACCATAGACATAA-TGTACCAGG 38483
i i i iv i i ? v - vv v
L1M4_orf2#LIN 2863 CCATATACAAAAATTAACTCAAAATGGATCAWAGACCTAAATGTAAGAGC 2912
INTRON_3 38484 TAAAACTATAAATCTTCTACAATAAAAGATAGGAGAAAGTTCTCATGTTC 38533
v ii v v v ? v i ii i vi
L1M4_orf2#LIN 2913 TAAAACTATAAAACTCTTAGAAGAAAACATAGGNGTAAATCTTCGTGACC 2962
INTRON_3 38534 TTGGTGTGGGCAAAGAGTTCTTAGACATAACCATAACAGCTAGGGC--CA 38581
vv i v iv i i vvi v vvii --
L1M4_orf2#LIN 2963 TTGGGTTAGGCAATGGTTTCTTAGATATGACACCAAAAGCACAAGCAACA 3012
INTRON_3 38582 TGAGAAAAA-T-GATAAATTTAACCTCATTAAAATTAAAAACTTTTGTAC 38629
vi - - vi i i i
L1M4_orf2#LIN 3013 AAAGAAAAAATAGATAAATTGGACTTCATCAAAATTAAAAACTTTTGTGC 3062
INTRON_3 38630 TTCAAAAGACACTATTAAGAAAATAAAAAGACAAGTCACAAGCTGGACAA 38679
i i i i vi iiv i- i
L1M4_orf2#LIN 3063 TTCAAAGGACACTATCAAGAAAGTGAAAAGACAACCCACAGAATGGG-AG 3111
INTRON_3 38680 AAAAT---TGCATATTATATATCTGGTAAAGGTCTTCTATCCAGAATAGA 38726
--- v i i i v v v
L1M4_orf2#LIN 3112 AAAATATTTGCAAATCATATATCTGATAAGGGACTTGTATCCAGAATATA 3161
INTRON_3 38727 AAAAAAAAACTCTTACAACTCGATTATAAAAAAA 38760
v i -- i v i
L1M4_orf2#LIN 3162 TAAAGAA--CTCTTACAACTCAATAATAAAAAGA 3193
Matrix = 20p37g.matrix
Transitions / transversions = 1.76 (123 / 70)
Gap_init rate = 0.02 (14 / 849), avg. gap size = 2.71 (38 / 14)
227 17.31 7.79 2.47 INTRON_3 38710 38786 361395 + L1ME2_3end LINE/L1 1 81 830 85
INTRON_3 38710 CTTCTATCCAGAATAGAAAAAAAAAACTCTTACAACTCGATTATAAAAAA 38759
v v v i -- i i v i
L1ME2_3end#LI 1 CTTGTATCCAGAATATATAAAGAA--CTCCTACAACTCAATAATAAAAAG 48
INTRON_3 38760 A-----AACCCAATTAAAAAG-AGACAGAAAAC 38786
----- i-i i i i
L1ME2_3end#LI 49 ACAAACAACCCAATTAAAAAATGGGCAAAAGAC 81
Matrix = 20p37g.matrix
Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.04 (3 / 76), avg. gap size = 2.67 (8 / 3)
238 11.10 7.69 2.94 INTRON_3 38710 38774 361407 + L1MB7_3end LINE/L1 1 68 863 84
INTRON_3 38710 CTTCTATCCAGAATAGAAAAAAAAAACTCTTACAACTCGATTATAAAAAA 38759
v v v i -- i iv
L1MB7_3end#LI 1 CTTGTATCCAGAATATATAAAGAA--CTCTTACAACTCAACAATAAAAAA 48
INTRON_3 38760 A-----AACCCAATTAAAAA 38774
-----
L1MB7_3end#LI 49 ACAAACAACCCAATTAAAAA 68
Matrix = 20p37g.matrix
Transitions / transversions = 0.75 (3 / 4)
Gap_init rate = 0.03 (2 / 64), avg. gap size = 3.50 (7 / 2)
+ 898 17.9 0.6 0.0 INTRON_3 38787 38965 (361216) + L1M4 LINE/L1 5286 5465 (715) 46
ANNOTATION EVIDENCE:
898 17.88 0.56 0.00 INTRON_3 38787 38965 361216 + L1MB4_3end LINE/L1 33 212 715 86
INTRON_3 38787 ACTCA-CAGAGAAAAAAAAAATAACCTGATTAAAAAATGGGAAAAGGACA 38835
- ivi v ii v v
L1MB4_3end#LI 33 ACTCAACAACAAAAAAACAAATAACCCAATTAAAAAATGGGCAAAGGACT 82
INTRON_3 38836 TGATTAGACATTTTTCCAAAGAAGATATTCAAATGGCTAATAAGCACATG 38885
v i v i
L1MB4_3end#LI 83 TGAATAGACATTTCTCCAAAGAAGATATACAAATGGCCAATAAGCACATG 132
INTRON_3 38886 AAAAGATGCTTAACATCATTAACCAACAGGAAAGTTGAAATTAAAAGCAC 38935
i i ?i vi i i vv i v
L1MB4_3end#LI 133 AAAAGATGCTCAACATCACTANTCATTAGGGAAATGCAAATCAAAACCAC 182
INTRON_3 38936 AATATGATATCAGTGCACATCCACTAGAAT 38965
iv i viv i i
L1MB4_3end#LI 183 AATGAGATACCACCTCACACCCACTAGGAT 212
Matrix = 20p37g.matrix
Transitions / transversions = 1.38 (18 / 13)
Gap_init rate = 0.01 (1 / 178), avg. gap size = 1.00 (1 / 1)
+ 207 28.3 0.0 2.2 INTRON_3 38968 39014 (361167) C L2c LINE/L2 (84) 3303 3258 47
ANNOTATION EVIDENCE:
207 28.27 0.00 2.17 INTRON_3 38968 39014 361167 C L2c_3end LINE/L2 349 394 84 35
INTRON_3 38968 CTCTTGAGAAGATTATAGTCTGGTTGGAAAAGACAGACACATAAATA 39014
i ii i v i i i - ii ?i i
C L2c_3end#LINE 394 CCCTCAAGGAGCTCACAGTCTAGT-GGAGGAGACAGACANGTAAACA 349
Matrix = 25p37g.matrix
Transitions / transversions = 11.00 (11 / 1)
Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1)
+ 6049 4.6 0.0 0.1 INTRON_3 39164 39904 (360277) C L1PA5 LINE/L1 (0) 6154 5415 48
ANNOTATION EVIDENCE:
6049 4.60 0.00 0.14 INTRON_3 39164 39904 360277 C L1PA5_3end LINE/L1 162 901 0 24
INTRON_3 39164 TTTTTTTTTTTTTATTATATTTTAAGTTCTAGGGTACATGTGCACAATAT 39213
? i ii
C L1PA5_3end#LI 901 TTTTTTTTTTSTTATTATACTTTAAGTTCTAGGGTACATGTGCACAACGT 852
INTRON_3 39214 GCAGGTTTGTTACATATGTATACATGTGCCATGTTGGTGTGCTGCACCCA 39263
C L1PA5_3end#LI 851 GCAGGTTTGTTACATATGTATACATGTGCCATGTTGGTGTGCTGCACCCA 802
INTRON_3 39264 TTAACTCGTCATTTACGTTAGTTATATCTCCTAATGCTATCCCTCCCCTC 39313
i v i
C L1PA5_3end#LI 801 TTAACTCGTCATTTACATTAGGTATATCTCCTAATGCTATCCCTCCCCCC 752
INTRON_3 39314 TCCCCCGACCCCACGACAGGCCCCGGTGTGTGATGTTCCCCTTCCTGTGT 39363
v i
C L1PA5_3end#LI 751 TCCCCCCACCCCACAACAGGCCCCGGTGTGTGATGTTCCCCTTCCTGTGT 702
INTRON_3 39364 CCATGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAACATGTGGTG 39413
v i
C L1PA5_3end#LI 701 CCAAGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAACATGCGGTG 652
INTRON_3 39414 TTTGGTTTTTTGTCCTTGCAATAGTTTGCTGAGAATGATGGTTTCCACCT 39463
i v
C L1PA5_3end#LI 651 TTTGGTTTTTTGTCCTTGCGATAGTTTGCTGAGAATGATGGTTTCCAGCT 602
INTRON_3 39464 TCAGCCATGTCCTTACAAAGCACATGAACTCATCCTTTTTTATGGCTGCA 39513
v i v
C L1PA5_3end#LI 601 TCATCCATGTCCCTACAAAGGACATGAACTCATCCTTTTTTATGGCTGCA 552
INTRON_3 39514 TAGTATTCCATGGTGTATATGTGCCATATTTTCTTAATTCAGTCTATCAT 39563
i i
C L1PA5_3end#LI 551 TAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCAT 502
INTRON_3 39564 TGATGGACATTTGGGTTGGTTCCAAGTCTTTGCTGTTGTGAAGAGTGCCG 39613
? i v
C L1PA5_3end#LI 501 TGSTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCCG 452
INTRON_3 39614 CAATAAACAAACATATGCATGTGTCTTTATAGCAGCATGATTTATAATCC 39663
v i i
C L1PA5_3end#LI 451 CAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAATCC 402
INTRON_3 39664 TTTGGGTATATACCCAATAATGGGATGGCTGAGTCAAATGGTATTTCTAG 39713
i i
C L1PA5_3end#LI 401 TTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAG 352
INTRON_3 39714 TTCTAGATTGTTGAGGAATTGCCACACTGTCTTCCACAATGGTTGAACTA 39763
ivi i ?
C L1PA5_3end#LI 351 TTCTAGATCCCTGAGGAATCGCCACACTGSCTTCCACAATGGTTGAACTA 302
INTRON_3 39764 GTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCT 39813
C L1PA5_3end#LI 301 GTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCT 252
INTRON_3 39814 CTCCAGCACCTGCTGTTTCCTGACTTTTTAATGATCACCATTCTAACTGG 39863
i i
C L1PA5_3end#LI 251 CTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATCGCCATTCTAACTGG 202
INTRON_3 39864 TGTGAGATGGTGTCTCATTGTGGTTTTTGATTTGCATTTCT 39904
i -
C L1PA5_3end#LI 201 TGTGAGATGGTATCTCATTGTGGTTTT-GATTTGCATTTCT 162
Matrix = 18p37g.matrix
Transitions / transversions = 2.44 (22 / 9)
Gap_init rate = 0.00 (1 / 740), avg. gap size = 1.00 (1 / 1)
+25177 6.8 0.2 0.0 INTRON_3 39906 45221 (354960) C L1PA5 LINE/L1 (807) 5339 11 48
ANNOTATION EVIDENCE:
25177 5.28 0.25 0.00 INTRON_3 39906 43127 357054 C L1P1_orf2 LINE/L1 1 3230 64 87
INTRON_3 39906 TTCATATCCTTCACCCACTTGTTGATGGGGTTGTTTGTTTTTTTCTTGTA 39955
i i v
C L1P1_orf2#LIN 3230 TTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTA 3181
INTRON_3 39956 AATTTGTTTGAGTTCTTTGTAGAACCTGGATATTAGCCCTTTGCCAGATG 40005
v vi i
C L1P1_orf2#LIN 3180 AATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATG 3131
INTRON_3 40006 AGTAGATTGCAAAATTTTTCTCCCATTCTGTAGGTTGCCTGTTCACTCTG 40055
i i v vi
C L1P1_orf2#LIN 3130 AGTAGGTTGCGAAAATTTTCTCCCATGTTGTAGGTTGCCTGTTCACTCTG 3081
INTRON_3 40056 ATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTGAGTTTAATTAGATCCCA 40105
v
C L1P1_orf2#LIN 3080 ATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCA 3031
INTRON_3 40106 TTTGTCAATTTTGGCTTTTGTTACCATTGCTTTTGGTGTTTTAGACATAA 40155
i i i
C L1P1_orf2#LIN 3030 TTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGGTGTTTTGGACATGA 2981
INTRON_3 40156 AGTCCTTGTCCATGCCTATGTCCTGAATGGTATTGCCTAAGTTTTCTCCT 40205
i i v i i
C L1P1_orf2#LIN 2980 AGTCCTTGCCCACGCCTATGTCCTGAATGGTAATGCCTAGGTTTTCTTCT 2931
INTRON_3 40206 GGGGTTTTTATGGTTTTAGGTCTAACATGTAAGTCTTTAATCCATCTTGA 40255
i i v i
C L1P1_orf2#LIN 2930 AGGGTTTTTATGGTTTTAGGTCTAACGTTTAAATCTTTAATCCATCTTGA 2881
INTRON_3 40256 ATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTGCAGCTTTCTCC 40305
i v v
C L1P1_orf2#LIN 2880 ATTGATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTAC 2831
INTRON_3 40306 ATATGGCTAGCCAGTTTTCCTAGCACCATTGATTAAATAGGGAACCCTTT 40355
i v i
C L1P1_orf2#LIN 2830 ATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTT 2781
INTRON_3 40356 CCCCATTTCTTGTTCTTGTCAGGTTTGTCAATGATCAGATGGTTGTAGAT 40405
v i v v i
C L1P1_orf2#LIN 2780 CCCCATTGCTTGTTTTTCTCAGGTTTGTCAAAGATCAGATAGTTGTAGAT 2731
INTRON_3 40406 GTGTGGTGTTATTTCTGAGGCCTCTGTTCTGTTCCATTGGTCTATATCTC 40455
i i ii v i
C L1P1_orf2#LIN 2730 ATGCGGCATTATTTCTGAGGGCTCTGTTCTGTTCCATTGATCTATATCTC 2681
INTRON_3 40456 TGTTTTGGTACCGGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTAT 40505
i
C L1P1_orf2#LIN 2680 TGTTTTGGTACCAGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTAT 2631
INTRON_3 40506 AGTTTGAAGTCAGGTAGTATGATGCCTCCAGTTTTGTTCTTTTGGCTTAG 40555
i i
C L1P1_orf2#LIN 2630 AGTTTGAAGTCAGGTAGTGTGATGCCTCCAGCTTTGTTCTTTTGGCTTAG 2581
INTRON_3 40556 GATTGTCTTGGCAATGCGGGCTCTCTTTTGGTTCCATATGAACTTTAAAG 40605
v i i
C L1P1_orf2#LIN 2580 GATTGACTTGGCGATGCGGGCTCTTTTTTGGTTCCATATGAACTTTAAAG 2531
INTRON_3 40606 TAGTTTTTTCCAATTCTGCGAAGAAAGTCATTGGTAGCTTGATGGGGATG 40655
i
C L1P1_orf2#LIN 2530 TAGTTTTTTCCAATTCTGTGAAGAAAGTCATTGGTAGCTTGATGGGGATG 2481
INTRON_3 40656 GCATTGAATCTATAAATGACCTTGGGCAGTATGGCCATTTTCACGATATC 40705
i v i
C L1P1_orf2#LIN 2480 GCATTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACGATATT 2431
INTRON_3 40706 GATTCTTCCTACCCATGAGCATGGAATGTTCTTCCATTTGTTTGTATCCT 40755
i
C L1P1_orf2#LIN 2430 GATTCTTCCTACCCATGAGCATGGAATGTTCTTCCATTTGTTTGTGTCCT 2381
INTRON_3 40756 CTTTTATTTCATTGAGCAGTGGTTTGTAGTTCTCCTTGAAGAGGTCCTTC 40805
v
C L1P1_orf2#LIN 2380 CTTTTATTTCCTTGAGCAGTGGTTTGTAGTTCTCCTTGAAGAGGTCCTTC 2331
INTRON_3 40806 ACATCCCTTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAT 40855
C L1P1_orf2#LIN 2330 ACATCCCTTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAAT 2281
INTRON_3 40856 TGTGAATGGGAGTTCACTGATGATGTGGCTCTCTGTTTGTCTGTTATTGG 40905
iv v i
C L1P1_orf2#LIN 2280 TGTGAATGGGAGTTCACCCATGATTTGGCTCTCTGTTTGTCTGTTGTTGG 2231
INTRON_3 40906 TGTATAAGAATGCTTGTGATTTTTGTACATTGATTTTGTATCCTGAGACT 40955
C L1P1_orf2#LIN 2230 TGTATAAGAATGCTTGTGATTTTTGTACATTGATTTTGTATCCTGAGACT 2181
INTRON_3 40956 TTGCTGAAGTTGCTTATCAGCTTAAGGAGATTTTTGGCTGAGACAATGGG 41005
v i
C L1P1_orf2#LIN 2180 TTGCTGAAGTTGCTTATCAGCTTAAGGAGATTTTGGGCTGAGACGATGGG 2131
INTRON_3 41006 GTTTTCTAGATATACAATCATGTCATCTGCAAACAGGGACAATTTGACTT 41055
v i
C L1P1_orf2#LIN 2130 GTTTTCTAGATAAACAATCATGTCGTCTGCAAACAGGGACAATTTGACTT 2081
INTRON_3 41056 CCTCTTTTCCTAATTGAATACCCTTTATTTCCTTCTCCTGCCTAATTGCC 41105
i
C L1P1_orf2#LIN 2080 CCTCTTTTCCTAATTGAATACCCTTTATTTCCTTCTCCTGCCTGATTGCC 2031
INTRON_3 41106 CTGGCCAGAACTTCCAACACTATGTTGACTAGGAGGGGTGAGAAAGGGCA 41155
v v i
C L1P1_orf2#LIN 2030 CTGGCCAGAACTTCCAACACTATGTTGAATAGGAGCGGTGAGAGAGGGCA 1981
INTRON_3 41156 TCCCTGTCTTATGCCGGTTTTCAAAGGGAATGCTTCCAGTTTTTGCCCAT 41205
i i
C L1P1_orf2#LIN 1980 TCCCTGTCTTGTGCCAGTTTTCAAAGGGAATGCTTCCAGTTTTTGCCCAT 1931
INTRON_3 41206 TCAGTATGATATTGGCTGTGGGTTTGTCATAAATAGCTCTTATTATTTTG 41255
i
C L1P1_orf2#LIN 1930 TCAGTATGATATTGGCTGTGGGTTTGTCATAGATAGCTCTTATTATTTTG 1881
INTRON_3 41256 AGATACGTCCCATCAGTACCTAATGTATTGAGAGTTTTTAGCATGAAGGG 41305
i i v
C L1P1_orf2#LIN 1880 AAATACGTCCCATCAATACCTAATTTATTGAGAGTTTTTAGCATGAAGGG 1831
INTRON_3 41306 TTGTTGAATTTTGTCACAGGCCTTTTCTGCATCTGTTGAGATAATCATGT 41355
v i i
C L1P1_orf2#LIN 1830 TTGTTGAATTTTGTCAAAGGCTTTTTCTGCATCTATTGAGATAATCATGT 1781
INTRON_3 41356 GGTTTTTGTCTTTGGTTCTGTTTATATGATGGATTACATTTATTGATTTG 41405
i v
C L1P1_orf2#LIN 1780 GGTTTTTGTCTTTGGCTCTGTTTATATGCTGGATTACATTTATTGATTTG 1731
INTRON_3 41406 CATATGTTGAACCAGCCTTGTATCCCAGGGTTGAAGCCCACTTGATCATG 41455
i i i v
C L1P1_orf2#LIN 1730 CGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGCCCACTTGATCATG 1681
INTRON_3 41456 GTGGGTAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTAT 41505
i
C L1P1_orf2#LIN 1680 GTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTTGCCAGTATTTTAT 1631
INTRON_3 41506 TGAGGATTTTTGCATCGTTGTTCATCAGGGATATTGGTCTAAAATTCTCT 41555
iv i
C L1P1_orf2#LIN 1630 TGAGGATTTTTGCATCAATGTTCATCAAGGATATTGGTCTAAAATTCTCT 1581
INTRON_3 41556 TTTTTTGTTGTGTCTCTGCCAGGCTTTGGTATCAGGATGATGCTGGCGTC 41605
v v i v
C L1P1_orf2#LIN 1580 TTTTTGGTTGTGTCTCTGCCCGGCTTTGGTATCAGAATGATGCTGGCCTC 1531
INTRON_3 41606 ATAAAATGAGTTAGGGAGGATTCCCTCTTTTTCTATTGATTGGAATAGTT 41655
C L1P1_orf2#LIN 1530 ATAAAATGAGTTAGGGAGGATTCCCTCTTTTTCTATTGATTGGAATAGTT 1481
INTRON_3 41656 TCAGAAAGAATGGTACCAGCTCCTCCTTGTACCGCTGGTAGAATTCGGCT 41705
i i v
C L1P1_orf2#LIN 1480 TCAGAAGGAATGGTACCAGTTCCTCCTTGTACCTCTGGTAGAATTCGGCT 1431
INTRON_3 41706 GTGAATCCATCTGGTCCTGGCCTTTTTTTGGTTGGTAGGGTATTAATTAT 41755
v i iiv i
C L1P1_orf2#LIN 1430 GTGAATCCATCTGGTCCTGGACTCTTTTTGGTTGGTAAACTATTGATTAT 1381
INTRON_3 41756 TGCCTCAATTTCAGAGCCTGTTATTGGTCTATTCAGGGATTCAACTTCTT 41805
v i
C L1P1_orf2#LIN 1380 TGCCACAATTTCAGAGCCTGTTATTGGTCTATTCAGAGATTCAACTTCTT 1331
INTRON_3 41806 CCTGGTTTAGTCTTGGGAGGGTGTATGTGTCCAGGAATTTATCCATTTCT 41855
i v v
C L1P1_orf2#LIN 1330 CCTGGTTTAGTCTTGGGAGAGTGTATGTGTCGAGGAATGTATCCATTTCT 1281
INTRON_3 41856 TCTAGATTTTCTCGTTTATTTCCGTAGAGGTGTTTATAGTATTCTCTGAT 41905
v v i
C L1P1_orf2#LIN 1280 TCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTGTAGTATTCTCTGAT 1231
INTRON_3 41906 GGTAGTTTGTATTTCTGTGGGATCGGTGGTGATATCCCCTTTATCATTTT 41955
C L1P1_orf2#LIN 1230 GGTAGTTTGTATTTCTGTGGGATCGGTGGTGATATCCCCTTTATCATTTT 1181
INTRON_3 41956 TTATTGCATCTATTTGATTCTTCTCTCTTTTCTTCTTTATTAGTCTTGCT 42005
ii i
C L1P1_orf2#LIN 1180 TTATTGTGTCTATTTGATTCTTCTCTCTTTTTTTCTTTATTAGTCTTGCT 1131
INTRON_3 42006 AGTGGTCTATCAATTTTGTTGATCTTTTCAAAAAACCAGCTCCTGGATTC 42055
i i
C L1P1_orf2#LIN 1130 AGCGGTCTATCAATTTTGTTGATCCTTTCAAAAAACCAGCTCCTGGATTC 1081
INTRON_3 42056 ATTAATTTTTTGAAGGGTTTTTTGTGTCTCTATTTCCTTTAGTTCTGCTC 42105
i i
C L1P1_orf2#LIN 1080 ATTGATTTTTTGAAGGGTTTTTTGTGTCTCTATTTCCTTCAGTTCTGCTC 1031
INTRON_3 42106 TGATCTTAGTTATTTCTTGCCTTCTGCTAGCTTTTGAATGTGTTTGCTCT 42155
i
C L1P1_orf2#LIN 1030 TGATTTTAGTTATTTCTTGCCTTCTGCTAGCTTTTGAATGTGTTTGCTCT 981
INTRON_3 42156 TGCTTCTCTAGTTCT---AATTGTGATGTTAGGATGTCAATTTTAGATCT 42202
i --- i i
C L1P1_orf2#LIN 980 TGCTTTTCTAGTTCTTTTAATTGTGATGTTAGGGTGTCAATTTTGGATCT 931
INTRON_3 42203 TTCCTGCTTTCTCTTGTGGGCATTTAGTGCTATAAATTTACCTCTACACA 42252
i v
C L1P1_orf2#LIN 930 TTCCTGCTTTCTCTTGTAGGCATTTAGTGCTATAAATTTCCCTCTACACA 881
INTRON_3 42253 CTGCATTAAATGTGTCCCAGAGATTCTGGTATGTTGTGTCTTTGTTCTCA 42302
v i i v i
C L1P1_orf2#LIN 880 CTGCTTTGAATGCGTCCCAGAGATTCTGGTATGTGGTGTCTTTGTTCTCG 831
INTRON_3 42303 TTGGTTTCAAAGAACATCTTCATTTCTGCCTTCTTTTCGTTATGTACCCA 42352
i v
C L1P1_orf2#LIN 830 TTGGTTTCAAAGAACATCTTTATTTCTGCCTTCATTTCGTTATGTACCCA 781
INTRON_3 42353 GTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCATGTAGTTGAGCAGTTTT 42402
i i
C L1P1_orf2#LIN 780 GTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCATGTAGTTGAGCGGCTTT 731
INTRON_3 42403 AAGTGAGTTTCTTAATCCTGAGTCCTAGTTTGATTGCACTGTGGTCTGAG 42452
i v i
C L1P1_orf2#LIN 730 GAGTGAGATTCTTAATCCTGAGTTCTAGTTTGATTGCACTGTGGTCTGAG 681
INTRON_3 42453 AGAGAGTTTGTCATAATTTCTGTTCTTTTACATTTGCTGAGGAGTGCTTT 42502
v i v
C L1P1_orf2#LIN 680 AGATAGTTTGTTATAATTTCTGTTCTTTTACATTTGCTGAGGAGAGCTTT 631
INTRON_3 42503 ACTTCCAACTATGTGGTCAGTTTTGGAATAAGTGAGATGTGGTGCTGAGA 42552
i i v i i
C L1P1_orf2#LIN 630 ACTTCCAACTATGTGGTCAATTTTGGAATAGGTGTGGTGTGGTGCTGAAA 581
INTRON_3 42553 AGAATGTATATTCTGTTGATTTGGGGTGGAGAGTTCTGTAGATGTCTATT 42602
i
C L1P1_orf2#LIN 580 AAAATGTATATTCTGTTGATTTGGGGTGGAGAGTTCTGTAGATGTCTATT 531
INTRON_3 42603 AGGTCCACTTGGTGCAGAGTTGAGTTCAATTCCTGGATATCCTTGTTAAC 42652
ii i i i
C L1P1_orf2#LIN 530 AGGTCTGCTTGGTGCAGAGCTGAGTTCAATTCCTGGGTATCCTTGTTGAC 481
INTRON_3 42653 TT-CTGTCTTGTTGATCT----AATGTTGACAGTGGGGTGTTAAAGTTTC 42697
- i ---- i
C L1P1_orf2#LIN 480 TTTCTGTCTCGTTGATCTGTCTAATGTTGACAGTGGGGTGTTAAAGTCTC 431
INTRON_3 42698 CCATTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGGTCTCTAAGGACT 42747
v v ?
C L1P1_orf2#LIN 430 CCATTATTAATGTGTGGGAGTCTAAGTCTCTTTGTAGGTCACTWAGGACT 381
INTRON_3 42748 TGCTTTGTGAATCTGGGTGCTCCTGTATTGGGTGCATATATATTTAGGAT 42797
i v
C L1P1_orf2#LIN 380 TGCTTTATGAATCTGGGTGCTCCTGTATTGGGTGCATAAATATTTAGGAT 331
INTRON_3 42798 AGTTAGCCCATCTTGTTGAATTGATCCCTTTACCATTATGTAATGTCCTT 42847
i v v
C L1P1_orf2#LIN 330 AGTTAGCTCCTCTTGTTGAATTGATCCCTTTACCATTATGTAATGGCCTT 281
INTRON_3 42848 CTTTGTCTCTTTTGATCTTTGTTGGTTTAAAGTCTGTTTTATGAGAGACT 42897
v
C L1P1_orf2#LIN 280 CTTTGTCTCTTTTGATCTTTGTTGGTTTAAAGTCTGTTTTATCAGAGACT 231
INTRON_3 42898 AGGATTGCAACCCCTGCCTTTTTTTGTTTTCCATTTGCTTGGTAGATCTT 42947
v
C L1P1_orf2#LIN 230 AGGATTGCAACCCCTGCCTTTTTTTGTTTTCCATTGGCTTGGTAGATCTT 181
INTRON_3 42948 CCTCCATCCCTTTATTTTGAGCCTATGTGTGTCTTTGCATGTGAGATGGG 42997
i i i
C L1P1_orf2#LIN 180 CCTCCATCCTTTTATTTTGAGCCTATGTGTGTCTCTGCACGTGAGATGGG 131
INTRON_3 42998 TTTCCTGAATACAGCACACTGATGGGTCTTGACTCTTTATACAGTTTGCC 43047
v ii
C L1P1_orf2#LIN 130 TTTCCTGAATACAGCACACTGATGGGTCTTGACTCTTTATCCAACTTGCC 81
INTRON_3 43048 AGTCTGTGTCTTTTAATTGGAGCATTTAGCCCATTTATATTTAAGGTTAA 43097
v v i i
C L1P1_orf2#LIN 80 AGTCTGTGTCTTTTAATTGCAGAATTTAGTCCATTTATATTTAAAGTTAA 31
INTRON_3 43098 TATTGTAATGTATGAATTTTATCCTGTCAT 43127
v i v
C L1P1_orf2#LIN 30 TATTGTTATGTGTGAATTTGATCCTGTCAT 1
Matrix = 20p37g.matrix
Transitions / transversions = 1.82 (109 / 60)
Gap_init rate = 0.00 (3 / 3221), avg. gap size = 2.67 (8 / 3)
16767 9.00 0.22 0.00 INTRON_3 42978 45221 354960 C L1P1_5end LINE/L1 11 2259 0 88
INTRON_3 42978 GTCTTTGCATGTGAGATGGGTTTCCTGAATACAGCACACTGATGGGTCTT 43027
i i i
C L1P1_5end#LIN 2259 GTCTCTGCACGTGAGATGGGTTTCCTGAATACGGCACACTGATGGGTCTT 2210
INTRON_3 43028 GACTCTTTATACAGTTTGCCAGTCTGTGTCTTTTAATTGGAGCATTTAGC 43077
v i
C L1P1_5end#LIN 2209 GACTCTTTATCCAATTTGCCAGTCTGTGTCTTTTAATTGGAGCATTTAGC 2160
INTRON_3 43078 CCATTTATATTTAAGGTTAATATTGTAATGTATGAATTTTATCCTGTCAT 43127
i i v i v
C L1P1_5end#LIN 2159 CCATTTACATTTAAAGTTAATATTGTTATGTGTGAATTTGATCCTGTCAT 2110
INTRON_3 43128 TATGATGTTAGCTGGTTATTTTGCTCGTTAGTTGATGCAGTTGCTTCCTA 43177
i v
C L1P1_5end#LIN 2109 TATGACGTTAGCTGGTTATTTTGCTCGTTAGTTGATGCAGTTTCTTCCTA 2060
INTRON_3 43178 GCCTCGATGGTCTTTACAATTTGGCATGTTTTTGCAGTGGCTGGTACCGG 43227
i i i
C L1P1_5end#LIN 2059 GCCTTGATGGTCTTTACAATTTGGCATGTTTTTGCAGCGGCTGGTACTGG 2010
INTRON_3 43228 TTGTTCCTTTCCATGTTTAGTGCTTCCTTCAGGAGCTCTTTTAGGGCAGG 43277
i
C L1P1_5end#LIN 2009 TTGTTCCTTTCCATGTTTAGCGCTTCCTTCAGGAGCTCTTTTAGGGCAGG 1960
INTRON_3 43278 CCTGGTGGTGACAAAATC----AGCCTTTGCTTGTGTGTAAAGTATTTTA 43323
---- v v
C L1P1_5end#LIN 1959 CCTGGTGGTGACAAAATCTCTCAGCATTTGCTTGTCTGTAAAGTATTTTA 1910
INTRON_3 43324 TTTCTCCTTCACTTATGAAGCTTAGTTTGGCTGGATATGAAATTCTGGGT 43373
i
C L1P1_5end#LIN 1909 TTTCTCCTTCGCTTATGAAGCTTAGTTTGGCTGGATATGAAATTCTGGGT 1860
INTRON_3 43374 TGAAAATTCTTTTCTTTAAGAATGTTGAATATTGGCCCCTACTCTCTTCT 43423
i i
C L1P1_5end#LIN 1859 CGAAAATTCTTTTCTTTAAGAATGTTGAATATTGGCCCCCACTCTCTTCT 1810
INTRON_3 43424 GGCTTGTAGAGTTTCTGACGAGAGATCTGCTGTTAGTCTGATGGGCTTCC 43473
v v i
C L1P1_5end#LIN 1809 GGCTTGTAGAGTTTCTGCCGAGAGATCAGCCGTTAGTCTGATGGGCTTCC 1760
INTRON_3 43474 CTTTGAGGGTAACCCGACCTTTCTCTCTGGCTGCCCTTAACATTTTTTCC 43523
v
C L1P1_5end#LIN 1759 CTTTGTGGGTAACCCGACCTTTCTCTCTGGCTGCCCTTAACATTTTTTCC 1710
INTRON_3 43524 TTCATTTCAACTTTGGTGAATCTGACAATTATGTGTCTTGGAGTTGCTGT 43573
v
C L1P1_5end#LIN 1709 TTCATTTCAACTTTGGTGAATCTGACAATTATGTGTCTTGGAGTTGCTCT 1660
INTRON_3 43574 TTTTGAGGAGTATCTTTGTGGCGTTATCTGTATTTCCTGAATTTGAATGT 43623
i i v i i
C L1P1_5end#LIN 1659 TCTCGAGGAGTATCTTTGTGGCGTTCTCTGTATTTCCTGAATCTGAACGT 1610
INTRON_3 43624 TGGTCTGCCTTGCTAGATTGGGAAAGTTCTCCTGGCTAATATCCTGCAGA 43673
i i v
C L1P1_5end#LIN 1609 TGGCCTGCCTTGCTAGATTGGGGAAGTTCTCCTGGATAATATCCTGCAGA 1560
INTRON_3 43674 GTGTTTTCCAACTTGGTTCCGTTCTCCCCGTCACTTTCAGGTACACCAGT 43723
i i
C L1P1_5end#LIN 1559 GTGTTTTCCAACTTGGTTCCATTCTCCCCGTCACTTTCAGGTACACCAAT 1510
INTRON_3 43724 CAGATGTAGATTTGGTCTTTTCACATAGTCCCCTATTTCTTGGAGGTTTT 43773
i i v i
C L1P1_5end#LIN 1509 CAGACGCAGATTTGGTCTTTTCACATAGTCCCATATTTCTTGGAGGCTTT 1460
INTRON_3 43774 ATTTGTTTCTTTTTACTCTTTTTTCTCTAAACTTCTCTTCTCACTTCATT 43823
i i i i
C L1P1_5end#LIN 1459 GTTCGTTTCTTTTTATTCTTTTTTCTCTAAACTTCTCTTCTCGCTTCATT 1410
INTRON_3 43824 TCATTCATTTGATCTTCAGTCACTGATACCCTTTCTTCCAGTTGATCGAG 43873
v v vi
C L1P1_5end#LIN 1409 TCATTCATTTCATCTTCCGTCACTGATACCCTTTCTTCCAGTTGATCGCA 1360
INTRON_3 43874 TTGGGTACTGAAGCTTATGTATTTGTCATGTAGTTCTTGTGCCATGGTTT 43923
i v i v i i i i v
C L1P1_5end#LIN 1359 TCGGCTACTGAGGCTTCTGCATTCGTCACGTAGTTCTCGTGCCTTGGTTT 1310
INTRON_3 43924 TTAGCTCCATCAGGTCATTTAAGGACTTCTCTATGCTGGTTATTCTAGTA 43973
i v iiii v
C L1P1_5end#LIN 1309 TCAGCTCCATCAGGTCCTTTAAGGACTTCTCTGCATTGGTTATTCTAGTT 1260
INTRON_3 43974 AGCCATTCATCTAATCTTTTTTCAAGGTTTTTAGCTTCTTTGCGATGGAT 44023
v i i i vi v i
C L1P1_5end#LIN 1259 ATCCATTCATCTAATTTTTTTTCAAAGTTTTTAACTTCTTTGCCGTTGGT 1210
INTRON_3 44024 TCGAACTTCCTTCTTTAGCTCGGAGAAGTTTGATTGTCTGAAGCCTTCTT 44073
i i v v i
C L1P1_5end#LIN 1209 TCGAATTTCCTCCTGTAGCTCGGAGTAGTTTGATCGTCTGAAGCCTTCTT 1160
INTRON_3 44074 CTCTCAACTTGTCAAAGTCATTCTCCACCCAGCTTTGTTCCATTGCTGAC 44123
i iii i ii
C L1P1_5end#LIN 1159 CTCTCAACTCGTCAAAGTCATTCTCTGTCCAGCTTTGTTCCGTTGCTGGT 1110
INTRON_3 44124 AAGGAGCTGCGTTCCTTTGGAGGAGTAGAGGTGCTCTGATTTTTAGAATT 44173
i i v i i
C L1P1_5end#LIN 1109 GAGGAGCTGCGTTCCTTTGGAGAAGGAGAGGCGCTCTGATTTTTAGAGTT 1060
INTRON_3 44174 TTCAGCTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTGCCT 44223
i i i
C L1P1_5end#LIN 1059 TCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACCT 1010
INTRON_3 44224 TTAGTCTTTGATGATGGTGACATACAGATGGGGTTTTGGTGTAAATGTCC 44273
i i v ii
C L1P1_5end#LIN 1009 TTGGTCTTTGATGATGGTGACGTACAGATGGGTTTTTGGTGTGGATGTCC 960
INTRON_3 44274 TTTCTGTTTGTTAGTTTTCATTCTAATAGTCAGGACCCTCAGCTGCAGTT 44323
v i v v
C L1P1_5end#LIN 959 TTTCTGTTTGTTAGTTTTCCTTCTAACAGACAGGACCCTCAGCTGCAGGT 910
INTRON_3 44324 CTGCTGGAGTTTGCTGGAGGTCCACTCCAGACCCTGTTTGCCTGGGTATC 44373
i
C L1P1_5end#LIN 909 CTGTTGGAGTTTGCTGGAGGTCCACTCCAGACCCTGTTTGCCTGGGTATC 860
INTRON_3 44374 AGCAGTGGAGGCTGCAGAACGGTGAATATTGCTGAACAGGAAATGTAGCT 44423
i v i i v v v i iv
C L1P1_5end#LIN 859 AGCAGCGGTGGCTGCAGAACAGTGGATATTGGTGAACCGCAGATGCTGCT 810
INTRON_3 44424 GCCTCATTGTTTCTCTGGAAGCTTCGTCTCAGAGGGATACCCAGCCGTGT 44473
v i i i i ii i
C L1P1_5end#LIN 809 GCCTGATCGTTCCTCTGGAAGTTTTGTCTCAGAGGAGTACCCGGCCGTGT 760
INTRON_3 44474 GAGGTGTCACTCTGCCCCTACTAGGGGGTGCCTCCCAGTTAGGCTACTCG 44523
v i i
C L1P1_5end#LIN 759 GAGGTGTCAGTCCGCCCCTACTGGGGGGTGCCTCCCAGTTAGGCTACTCG 710
INTRON_3 44524 GGGATCAGGGACCCACTTGAGGAGGCAGTCTGTCTGTTCTTAGGTCTCAA 44573
i i i i i v
C L1P1_5end#LIN 709 GGGGTCAGGGACCCACTTGAGGAGGCAGTCTGCCCGTTCTCAGATCTGAA 660
INTRON_3 44574 ACTCTGTGCTTGGAGAACCACTACTCTCTTCAAAGCTGTCAGACAGGGAC 44623
i vi v i
C L1P1_5end#LIN 659 GCTGCGTGCTGGGAGAACCACTGCTCTCTTCAAAGCTGTCAGACAGGGAC 610
INTRON_3 44624 ATTTAAATCTGCAGAGGTTTCTGCTGCCTTTT-GTTCAGCTATGCCCTGC 44672
i v i - iiv i
C L1P1_5end#LIN 609 ATTTAAGTCTGCAGAGGTTACTGCTGTCTTTTTGTTTGTCTGTGCCCTGC 560
INTRON_3 44673 CCCCAGGGTTGGAGCCTACAGAGGCAGGCAGGCTTCCTTTAGCTGTGGTG 44722
i v i v
C L1P1_5end#LIN 559 CCCCAGAGGTGGAGCCTACAGAGGCAGGCAGGCCTCCTTGAGCTGTGGTG 510
INTRON_3 44723 GGTTCCACCCAGTTCAAGCTTCCAGCCTGCTTTGTTTACCTACCCAAGCC 44772
i i v v i vi
C L1P1_5end#LIN 509 GGCTCCACCCAGTTCGAGCTTCCCGGCCGCTTTGTTTACCTAATCAAGCC 460
INTRON_3 44773 TCAGCAATGGCGGTCACCCCTCCCCCAGCCTCGCTGCTGCCTTGCAGTTT 44822
vi v i i
C L1P1_5end#LIN 459 TGGGCAATGGCGGGCGCCCCTCCCCCAGCCTCGCTGCCGCCTTGCAGTTT 410
INTRON_3 44823 GATCTCAGACTACTGTGCTAGCAATGAGCGAGACTCCACGGGCATGGGTC 44872
i i v ii i i v
C L1P1_5end#LIN 409 GATCTCGGACTGCTGTGCTAGCAATCAGCGAGACTCCGTGGGCGTAGGAC 360
INTRON_3 44873 CCTGTGAGCCATGTGCGGGATATAATCTCCTGGTGTGCCATTTGCTAAGA 44922
vi v i i vi v
C L1P1_5end#LIN 359 CCTCCGAGCCAGGTGCGGGATATAATCTCCTGGTGCGCCGTTTTTTAAGC 310
INTRON_3 44923 CTGTTGGAAAAGCGCAGTATTAGAGTGGGAGTGACCTGATTTTCCAGGTG 44972
i i i i i
C L1P1_5end#LIN 309 CCGTCGGAAAAGCGCAGTATTAGGGCGGGAGTGACCCGATTTTCCAGGTG 260
INTRON_3 44973 CCGTCTGTCACAGCTTCCCTTGGCTAGGAAAGGGAATTCCCTGACCCCTT 45022
vv i i i
C L1P1_5end#LIN 259 CCGTCTGTCACCCCTTTCTTTGACTAGGAAAGGGAATTCCCTGACCCCTT 210
INTRON_3 45023 GCACTTGCTGGGTGAGGCGATGCCTCGCGCTGCTTCAGCTCACACTCGGT 45072
i v i v i i v
C L1P1_5end#LIN 209 GCGCTTCCCGGGTGAGGCGATGCCTCGCCCTGCTTCGGCTCACGCACGGT 160
INTRON_3 45073 GGGCTGCACCCACTGTCCTGCACCCACTGTCTGACAAGCCCCAGTGAGAT 45122
v i i vv
C L1P1_5end#LIN 159 GCGCTGCACCCACTGTCCTGCGCCCACTGTCTGGCACTCCCCAGTGAGAT 110
INTRON_3 45123 GAACCCAGTACCTCAGTTGGAAATGCAGAAATCACCCATCTTCTGCATCA 45172
ii i i i
C L1P1_5end#LIN 109 GAACCTGGTACCTCAGTTGGAAATGCAGAAATCACCCGTCTTCTGCGTCG 60
INTRON_3 45173 CTCACGCTGGGAGCTGTAGACTGGAGCTGTTCCTATTTGGCCATCTTGG 45221
i i
C L1P1_5end#LIN 59 CTCACGCTGGGAGCTGTAGACCGGAGCTGTTCCTATTCGGCCATCTTGG 11
Matrix = 20p37g.matrix
Transitions / transversions = 2.16 (138 / 64)
Gap_init rate = 0.00 (2 / 2243), avg. gap size = 2.50 (5 / 2)
+ 1014 20.5 7.0 1.6 INTRON_3 45809 46130 (354051) C MER2 DNA/TcMar-Tigger (0) 345 1 49
ANNOTATION EVIDENCE:
1014 18.32 3.96 0.00 INTRON_3 45809 46010 354171 C MER2 DNA/TcMar-Tigger 136 345 0 118
INTRON_3 45809 CAGTCATCTCTCAGCATTTGTTGGGGATTTATTCCAGGACCCTT-ATTGA 45857
i i i i ii v vi ii-iiv
C MER2#DNA/TcMa 345 CAGTCGTCCCTCGGTATCCGTGGGGGATTGGTTCCAGGACCCCCCGCGGA 296
INTRON_3 45858 TACCAAAATCTGAGGGTGCCCAACTCCTTGATATAAAATGGGTTAATATT 45907
iiv i i v i ? vv i
C MER2#DNA/TcMa 295 TACCAAAATCCACGGATGCTCAAGTCCCTKATATAAAATGGCGTAGTATT 246
INTRON_3 45908 TTCATATAACCTACACACATC------TAGA-TTTACATCATTTCTAGAT 45950
v i ------ v - v i
C MER2#DNA/TcMa 245 TGCATATAACCTACGCACATCCTCCCGTATACTTTAAATCATCTCTAGAT 196
INTRON_3 45951 TACTTTTAATACATAATACAGTGTAAATTCTATGTAAATAGTTGTTTTGC 46000
v v i v v i
C MER2#DNA/TcMa 195 TACTTATAATACCTAATACAATGTAAATGCTATGTAAATAGTTGTTATAC 146
INTRON_3 46001 TGTATTGGTT 46010
v
C MER2#DNA/TcMa 145 TGTATTGTTT 136
Matrix = 20p37g.matrix
Transitions / transversions = 1.40 (21 / 15)
Gap_init rate = 0.01 (3 / 201), avg. gap size = 2.67 (8 / 3)
417 24.26 12.12 4.23 INTRON_3 45933 46130 354051 C MER2 DNA/TcMar-Tigger 1 213 132 119
INTRON_3 45933 TTTACATCATTTCTAGATTACTTTTAATACATAATACAGTGTAAATTCTA 45982
v i v v i v
C MER2#DNA/TcMa 213 TTTAAATCATCTCTAGATTACTTATAATACCTAATACAATGTAAATGCTA 164
INTRON_3 45983 TGTAAATAGTTGTTTTGCTGTATTGGTTTTTAAATTTATATTA------- 46025
v i - vvii v v ivi -------
C MER2#DNA/TcMa 163 TGTAAATAGTTGTTATACTGTATTG-TTTAGGGAATAATGACAAGGAAAA 115
INTRON_3 46026 ---TTTTTAT-TGTT--GTAT---TGTTACTTTTCAGTTATTT------- 46059
--- i v i- -- i---i iv iv i v v -------
C MER2#DNA/TcMa 114 AAGTCTGTACATGTTCAGTACAGACGCAACCATCCATTTTTTTCCCCGAA 65
INTRON_3 46060 -ATTTCCAACACATGGTTGATTGAATTCATGGATTGAAATCTGTGGAACC 46108
- i i iv ii i i i -------- i
C MER2#DNA/TcMa 64 TATTTTCGATCCGCGGTTGGTTGAATCCACGGAT--------GCGGAACC 23
INTRON_3 46109 CATAGATATGTAGGACTAACTG 46130
ii i v i ii
C MER2#DNA/TcMa 22 CACGGATACGGAGGGCCGACTG 1
Matrix = 20p37g.matrix
Transitions / transversions = 1.71 (29 / 17)
Gap_init rate = 0.04 (7 / 197), avg. gap size = 4.71 (33 / 7)
+ 539 31.7 6.0 0.5 INTRON_3 46355 46538 (353643) + MIRc SINE/MIR 45 238 (30) 50
ANNOTATION EVIDENCE:
539 31.68 5.98 0.52 INTRON_3 46355 46538 353643 + MIRc SINE/MIR 45 238 30 36
INTRON_3 46355 GGAAGATCTGGGATTCAGTCCTGGTTCTTCCATTTACTACCAGTTTCATT 46404
i v iv i v i v v v v ii
MIRc#SINE/MIR 45 GGAAGACCTGGGTTCGAGTCCTGGCTCTGCCACTTACTAGCTGTGTGACC 94
INTRON_3 46405 TTGGACATATTATTCAATTTCTGTAAACC-CA-TTGTCTTATCTATAAAA 46452
i vi i i i ii v i i - - vi i i
MIRc#SINE/MIR 95 TTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA 144
INTRON_3 46453 CGAG-ATAAT--------TTCTATCTAGTTCGTAGGATTATAGTTTAGAT 46493
i i - --------ii ii vi ii i i v vvi
MIRc#SINE/MIR 145 TGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGAT 194
INTRON_3 46494 TAAGTGAAATAAGTTACATTAGAAGTACTTTAAAAATTGTAAAAT 46538
i i i vv ii v - ii iv i i
MIRc#SINE/MIR 195 CAAATGAGATAATGTATGTGA-AAGCGCTTTGTAAACTGTAAAGT 238
Matrix = 25p37g.matrix
Transitions / transversions = 2.22 (40 / 18)
Gap_init rate = 0.03 (5 / 183), avg. gap size = 2.40 (12 / 5)
+ 23 50.0 0.0 0.0 INTRON_3 46823 46852 (353329) + AT_rich Low_complexity 1 30 (0) 51
ANNOTATION EVIDENCE:
23 50.00 0.00 0.00 INTRON_3 46823 46852 353329 + AT_rich Low_complexity 132 161 139 49
INTRON_3 46823 ATTAAATACATAAAATTTTTTAATATTATT 46852
????????vv v vvv v
AT_rich#Low_c 132 WWWWWWWWATTAAAAATAAATAATATAATT 161
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 7)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 531 26.2 11.3 0.2 INTRON_3 47752 47916 (352265) + MIR SINE/MIR 86 268 (0) 52
ANNOTATION EVIDENCE:
505 29.14 9.09 2.27 INTRON_3 47752 47916 352265 + MIRb SINE/MIR 93 268 0 37
INTRON_3 47752 TAACTTTGGGAACATTGTTCGACAACCTTGGACCTCAGTTTTCTTATCTC 47801
i i v vi iii ii vv ii ii i i v
MIRb#SINE/MIR 93 TGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG 142
INTRON_3 47802 TAAAATAGGCAACAA-AATGTCTACCCCATAGGATTGTTGTTAGGATTAA 47850
i -i i - ii i ii i v
MIRb#SINE/MIR 143 TAAAATGGG-GATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAA 191
INTRON_3 47851 ATAAG----------TGAAGCACTTAGATAAGTGCCCAGTACATGGTA-- 47888
i ---------- i i vvv ii i ii --
MIRb#SINE/MIR 192 ATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACACAGTAAG 241
INTRON_3 47889 --TTGAATAAATTTAAGTAATACTGTTATT 47916
--i v ---i iiv i
MIRb#SINE/MIR 242 CGCTCAATAAAT---GGTAGCTCTATTATT 268
Matrix = 25p37g.matrix
Transitions / transversions = 3.27 (36 / 11)
Gap_init rate = 0.03 (5 / 164), avg. gap size = 3.80 (19 / 5)
531 25.85 11.56 0.00 INTRON_3 47752 47898 352283 + MIR SINE/MIR 86 249 13 38
INTRON_3 47752 TAACTTTGGGAACATTGTTCGACAACCTTGGACCTCAGTTTTCTTATCTC 47801
i i v vi ii ii vv ii vi i i v
MIR#SINE/MIR 86 TGACCTTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTG 135
INTRON_3 47802 TAAAATAGG--CAACAA-AATGTCTACCCCATAGGATTGTTGTTAGGATT 47848
i --i i - i ii i i v
MIR#SINE/MIR 136 TAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATT 185
INTRON_3 47849 AAATAAGT----------GAAGCACTTAGATAAGTGCCCAGTACATGGTA 47888
i ----------i i vv ii i i
MIR#SINE/MIR 186 AAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTA 235
INTRON_3 47889 ----TTGAATAAAT 47898
----i v
MIR#SINE/MIR 236 AGCGCTCAATAAAT 249
Matrix = 25p37g.matrix
Transitions / transversions = 2.80 (28 / 10)
Gap_init rate = 0.03 (4 / 146), avg. gap size = 4.25 (17 / 4)
+ 316 24.8 7.5 1.2 INTRON_3 47982 48140 (352041) + L1ME4a LINE/L1 5780 5948 (176) 53
ANNOTATION EVIDENCE:
316 24.82 7.55 1.18 INTRON_3 47982 48140 352041 + L1ME4a_3end LINE/L1 527 695 176 89
INTRON_3 47982 TATTGTATAATTATTCAGTGGAATGTTATGCAGCTATTAAAT-TTATAGA 48030
v i vii v? i i i v- ? - v
L1ME4a_3end#L 527 TATGGTACATCCATANAATGGAATATTATGCAGCCATTAAAAATNAT-GT 575
INTRON_3 48031 TTT------ATTTTTAATGAAGAGGAAAAATATTTGTGG-ATAATGTTAA 48073
------ v viv i ii ii i-
L1ME4a_3end#L 576 TTTCGAAGAATATTTAATGACATGGGAAAATGCTCATGATATAATGTTAA 625
INTRON_3 48074 GAGAAAAA--CATG-TACAAAACC-CATCTGCTGAATGATCTCAATTTCG 48119
v -- v - i-i v i v v i i
L1ME4a_3end#L 626 GTGAAAAAAGCAGGNTACAAAACTGTATATACAGTATGATCCCAATTTTG 675
INTRON_3 48120 TTTTGAAAAGGAATATATGAA 48140
v?- vi? i
L1ME4a_3end#L 676 TTAN-AAAATANATATATAAA 695
Matrix = 20p37g.matrix
Transitions / transversions = 1.33 (20 / 15)
Gap_init rate = 0.05 (8 / 158), avg. gap size = 1.75 (14 / 8)
+ 387 30.0 6.3 5.3 INTRON_3 48233 48374 (351807) + L1M5 LINE/L1 2224 2369 (3846) 54
ANNOTATION EVIDENCE:
387 30.02 6.35 5.30 INTRON_3 48233 48374 351807 + L1MC4_5end LINE/L1 2224 2369 186 90
INTRON_3 48233 ATGGTCTTTATGCATCCAGTAAAATAATAG---TTTCAGATTTCAC-CAT 48278
v v iv i i v v v i--- - vi - i
L1MC4_5end#LI 2224 ATGGGCTTAACTCACCTATTAAAAGAAAAAGATTTTCA-ATTTGGCTCAC 2272
INTRON_3 48279 AAGGTAAGACC--ACCGTCCATTGTATACAAGCAAAGAAAGTACTTTAAA 48326
i i -- ii viii --- v -i i v
L1MC4_5end#LI 2273 AAAGCAAGACCCAACTATATGCTGTATACAAG---AGACA-CACCTAAAA 2318
INTRON_3 48327 AT-GCAATTCAGAAGAACTGAAAATAAAAAG-TGTGAAAAG-TATACCAG 48373
v- ii iii i ii - viv -
L1MC4_5end#LI 2319 AAAGTGATTCAGAAAGGCTAAAAATAAAGGGATGGACAAAGATATACCAG 2368
INTRON_3 48374 G 48374
L1MC4_5end#LI 2369 G 2369
Matrix = 20p37g.matrix
Transitions / transversions = 1.85 (24 / 13)
Gap_init rate = 0.06 (9 / 141), avg. gap size = 1.56 (14 / 9)
+ 2391 14.5 8.4 1.4 INTRON_3 48375 48851 (351330) + L1MB8 LINE/L1 5669 6178 (0) 55
ANNOTATION EVIDENCE:
2391 14.46 8.39 1.37 INTRON_3 48375 48851 351330 + L1MB8_3end LINE/L1 416 925 0 25
INTRON_3 48375 ATGTCCACACAAAAACTTGTATACAAATATTTATAACAGCATTAGTCATA 48424
? i i i i i v
L1MB8_3end#LI 416 ANGTCCACACAAAAACTTGTACACGAATGTTCATAGCAGCATTATTCATA 465
INTRON_3 48425 ATTGCTAAAAAGTAGAAATTAC----------------TGATGAATGGAT 48458
v i i iv ----------------
L1MB8_3end#LI 466 ATAGCCAAAAAGTGGAAACAACCCAAATGTCCATCAACTGATGAATGGAT 515
INTRON_3 48459 AAACAAAATGTGATATATCCATACAATGGAATATTACTTAGCAATAAGAA 48508
i ii i i i
L1MB8_3end#LI 516 AAATAAAATGTGGCATATCCATACAATGGAATATTATTCAGCAATAAAAA 565
INTRON_3 48509 GAAATGAAATATTGATACATGCTACAACATGGATGAACCTGGAAAACATT 48558
i i i v
L1MB8_3end#LI 566 GGAATGAAGTACTGATACATGCTACAACATGGATGAACCTTGAAAACATT 615
INTRON_3 48559 GTGCTATG---------CCACTCACAAATGGTTACATTATTGTGTGATTC 48599
ii v --------- v v iii - i
L1MB8_3end#LI 616 ACGCTAAGTGAAAGAAGCCAGTCACAAAAGACCACAT-ATTGTATGATTC 664
INTRON_3 48600 CATTTATATGAGATGTCTGGCATAGTCAAACCTATAGAGACAGAAAGTAG 48649
i ii v v i i
L1MB8_3end#LI 665 CATTTATATGAAATGTCCAGAATAGGCAAATCCATAGAGACAGAAAGTAG 714
INTRON_3 48650 GTTAGTAGTTAACTAGAACTGGAGGCTTTGAAGGAC--ATGGGGAGTGCC 48697
i i iv i ii i ---- iv-- v
L1MB8_3end#LI 715 ATTAGTGGTTGCCTGGGGCTGGGGG----GAAGGGGGAATGGGGAGTGAC 760
INTRON_3 48698 TGCTAATAGC------GTTTCTTTTTGTGGGTGATGAAAATGTTCTAAAA 48741
i v------ v -
L1MB8_3end#LI 761 TGCTAATGGGTACGGGGTTTCTTTTGG-GGGTGATGAAAATGTTCTAAAA 809
INTRON_3 48742 TTGAATGTGGTGATGGTTGCACAACT--ATAAATATACTAAAAACTATTG 48789
- v --i i i
L1MB8_3end#LI 810 T-GATTGTGGTGATGGTTGCACAACTCTGTGAATATACTAAAAACCATTG 858
INTRON_3 48790 AATTCTACAGTTTAAATGGTTGAA--GTATAGCA---GAATTCCATCCCA 48834
v v v -- i i --- vi i
L1MB8_3end#LI 859 AATTGTACACTTTAAATGGGTGAATTGTATGGTATGTGAATTATATCTCA 908
INTRON_3 48835 CTGAAGCTGTTTAAAAA 48851
v i i v
L1MB8_3end#LI 909 ATAAAGCTATTAAAAAA 925
Matrix = 18p37g.matrix
Transitions / transversions = 2.19 (46 / 21)
Gap_init rate = 0.02 (11 / 476), avg. gap size = 4.27 (47 / 11)
+ 387 30.0 6.3 5.3 INTRON_3 48852 49007 (351174) + L1M5 LINE/L1 2370 2525 (3690) 54
ANNOTATION EVIDENCE:
387 30.02 6.35 5.30 INTRON_3 48852 49007 351174 + L1MC4_5end LINE/L1 2370 2525 30 91
INTRON_3 48852 TGTCACCAGGTAAATACAAAAAAG--GAGTCACAATAGAAATATCAGTGA 48899
------ ii ii v ? -- i iii ?vvi vv
L1MC4_5end#LI 2370 ------CAAATGGAAACAANAAAGAAGGGCTGCAATNTTGATATCAGATA 2413
INTRON_3 48900 AAGTGAATGTTAAACTAAAAAGCATTAAATGAGATGAAACTAACTTTACC 48949
i? vv i i i i v ii i-- vvv i-
L1MC4_5end#LI 2414 AAGTANAATTCAAGCCAAAAAGCATTAAACGTGACAAAG--AAGGGTAT- 2460
INTRON_3 48950 ATGCTGAATACTAATAGATACAATATGCAATGA--------TAGTTGTGA 48991
- vi?i ii v vi vii --------i ? i
L1MC4_5end#LI 2461 -TTTNAAACGCTAAAAGCCACAATTCACAATGAAGATATAACANTTATGA 2509
INTRON_3 48992 ATATCTATGTACCAAA 49007
i
L1MC4_5end#LI 2510 ATATCTATGCACCAAA 2525
Matrix = 20p37g.matrix
Transitions / transversions = 1.87 (28 / 15)
Gap_init rate = 0.03 (5 / 155), avg. gap size = 4.00 (20 / 5)
+ 1990 14.9 1.0 1.6 INTRON_3 49023 49331 (350850) C AluJr SINE/Alu (4) 308 2 56
ANNOTATION EVIDENCE:
1781 17.43 0.97 1.63 INTRON_3 49023 49331 350850 C AluJb SINE/Alu 2 308 4 10
INTRON_3 49023 TTCTTTTCTTTTCTTTTTTTTTTCTTCCAAAAGACAAAGTCTCAGGTCTG 49072
i i i i ----i ii - v
C AluJb#SINE/Al 308 TTTTTTTTTTTTTTTTTTTTTTTTTT----GAGACAGGGTCTC-GCTCTG 264
INTRON_3 49073 TTATCCAC-CTAAAGTGCAGTGGTGTAATCATAGCTCACTGCAGCCTTGA 49121
iii v- ii i ii ii i
C AluJb#SINE/Al 263 TCGCCCAGGCTGGAGTGCAGTGGCGCGATCACGGCTCACTGCAGCCTCGA 214
INTRON_3 49122 ACTCCTGGGCTCAGGTGATACTCCTGCCTCAGCCTCCCTA--AGATGGGA 49169
v i i i v v -- v
C AluJb#SINE/Al 213 CCTCCCGGGCTCAAGCGATCCTCCTGCCTCAGCCTCCCGAGTAGCTGGGA 164
INTRON_3 49170 CTACAGGCACACACCACCACACTCAGCTAATTTTTAAATTTTTTGTAGAG 49219
i i i i i i iv
C AluJb#SINE/Al 163 CTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTTGTAGAG 114
INTRON_3 49220 ATGGAGTCTCACTTTGTTGCCCAGGCTGGTTTGGAACTCCTGACCTCAAG 49269
i i i iv i v iv
C AluJb#SINE/Al 113 ACGGGGTTTCACCATGTTGCCCAGGCTGGTCTCGAACTCCTGGGCTCAAG 64
INTRON_3 49270 CGATCCTCCCACCTTGGCCTCCCAAAGTGCTGGGATTATAGGTGTGAGCC 49319
i i i i i
C AluJb#SINE/Al 63 TGATCCTCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCC 14
INTRON_3 49320 ACTGTGACCAGC 49331
i i v i
C AluJb#SINE/Al 13 ACCGCGCCCGGC 2
Matrix = 14p37g.matrix
Transitions / transversions = 3.82 (42 / 11)
Gap_init rate = 0.01 (4 / 308), avg. gap size = 2.00 (8 / 4)
+ 2300 12.8 0.0 0.0 INTRON_3 49382 49693 (350488) + AluSz SINE/Alu 1 312 (0) 57
ANNOTATION EVIDENCE:
2219 13.14 0.00 0.00 INTRON_3 49382 49693 350488 + AluSx SINE/Alu 1 312 0 11
INTRON_3 49382 GGCCTGGTGTGGAGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGA 49431
v i i v i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 49432 GGTGGGCGGACCACTAGAGGTTAGTAGTTTGAGACTAGCCTGGCCAACAC 49481
i i iv i v i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
INTRON_3 49482 GGTGAAACCCTGCCTCTACTAAAAATACAAAAATTAGCCAGGTGTGGTGA 49531
i i i i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGG 150
INTRON_3 49532 CATGTGCCTATAATCTCAGCTACTCCAGAGGCTGAGGCAGGAGAATCGCT 49581
ii i i i vi
AluSx#SINE/Al 151 CGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCT 200
INTRON_3 49582 TGAGCTTGGGAGGTAGAGGTTGCAGAGAGCCAAGATGGCACCACTGCACT 49631
i ii ii v i v i
AluSx#SINE/Al 201 TGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACT 250
INTRON_3 49632 CCAGCCTGGGCCACAGAGAAAGACTCTGTCTCAGAAAAAAAAAAAAAAAA 49681
v vi i i
AluSx#SINE/Al 251 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 300
INTRON_3 49682 AAAAAAAAAAAA 49693
AluSx#SINE/Al 301 AAAAAAAAAAAA 312
Matrix = 14p37g.matrix
Transitions / transversions = 3.56 (32 / 9)
Gap_init rate = 0.00 (0 / 311), avg. gap size = 0.0 (0 / 0)
+ 234 0.0 0.0 0.0 INTRON_3 49697 49722 (350459) + (TA)n Simple_repeat 2 27 (0) 58
ANNOTATION EVIDENCE:
234 0.00 0.00 0.00 INTRON_3 49697 49722 350459 C (TA)n Simple_repeat 154 179 1 102
INTRON_3 49697 ATATATATATATATATATATATATAT 49722
C (TA)n#Simple_ 179 ATATATATATATATATATATATATAT 154
Matrix = Unknown
Transitions / transversions = 0.0 (0 / 0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
+ 239 27.1 6.8 10.6 INTRON_3 49986 50278 (349903) + L1M5 LINE/L1 2873 3155 (3059) 54
ANNOTATION EVIDENCE:
239 27.10 6.83 10.60 INTRON_3 49986 50278 349903 + L1M5_orf2 LINE/L1 696 978 2316 92
INTRON_3 49986 AATAAAGCTAGAAATTAATAACGTGAACGACGAC----AAACCCTGCTCC 50031
v i i-i v ii ---- i i--- v
L1M5_orf2#LIN 696 AATTAAGCTAGAAATCAATAACA-AAAAGATAACTAGAAAATCCC---CA 741
INTRON_3 50032 AATGT--GGAAATTAAAAAACAAAAATAAAAGCCCCCAAACTCTCTTTTA 50079
-- iv i ---- ---------------- i
L1M5_orf2#LIN 742 AATGTTTGGAAATTAAGCAATA----TA----------------CTTCTA 771
INTRON_3 50080 AGTAATTCATGGGTCAAATGGAAAATATAAGCAACTTTAAATTATAAAAT 50129
i ii -- i v v - - vv v
L1M5_orf2#LIN 772 AATAACCCATGGGTCAAA--GAAGAAATCA-CAA-TGGAAATTAGAAAAT 817
INTRON_3 50130 -TTCTG----GAA-AATAATGGTAG--CAAAATATTAGAAACTGTGAAAT 50171
- i ---- -i iv i-- i v i i vi ii
L1M5_orf2#LIN 818 ATTTTGAACTGAATGATAATGAAAATACGACATATCAAAACTTGTGGGAT 867
INTRON_3 50172 AGAGCTAAAACAGTGGTCCTAGGAAAATTTGGAGTCACAGATA-----AT 50216
iv i v ivv i iv i vi i i-----
L1M5_orf2#LIN 868 GCAGCTAAAGCAGTGCTTAGAGGGAAATTTATAGCCTTAAATGCATATAT 917
INTRON_3 50217 TATCAATAAAGAAAGAGTAAAAAAATCAATGTATTGAGCACTTAATTTAA 50266
vv vi iv ? -- vv? i ?iii ?i i
L1M5_orf2#LIN 918 TAGAAAAGAAGAAAGGCTNAAAA--TCAATGATNTAAGCNTCCANCTCAA 965
INTRON_3 50267 AAAGTT-GAAAAA 50278
i i -
L1M5_orf2#LIN 966 GAAGCTAGAAAAA 978
Matrix = 20p37g.matrix
Transitions / transversions = 1.79 (43 / 24)
Gap_init rate = 0.05 (16 / 292), avg. gap size = 3.12 (50 / 16)
+ 1119 25.0 4.6 4.9 INTRON_3 50436 50801 (349380) + MLT1A0 LTR/ERVL-MaLR 1 365 (0) 59
ANNOTATION EVIDENCE:
1119 25.00 4.64 4.93 INTRON_3 50436 50801 349380 + MLT1A0 LTR/ERVL-MaLR 1 365 0 120
INTRON_3 50436 TGCTATAGTTTGAATGTAT-----CCTCCAAAATTCATGTGTTGGAAACT 50480
i i v ----- i i - i
MLT1A0#LTR/ER 1 TGCTATGGTCTGAATGTTTGTGTCCCCCCAAAATTCATATGTTG-AAACC 49
INTRON_3 50481 TAATCCC-GATGCAACAATGTTGGGAAGTGATGCTTAATGGGAGGTGATT 50529
-i ii iii i i i iv i v-
MLT1A0#LTR/ER 50 TAATCCCCAATGTGATGGTATTAGGAGGTGGGGCCTT-TGGGAGGTGATT 98
INTRON_3 50530 AGTTCATGAGAGTTCCATCCTTATGAATGT-ATCAATGCTGCTATAAAAG 50578
v i ivvvii i v- i i ivi
MLT1A0#LTR/ER 99 AGGTCATGAGGGCGGAGCCCTCATGAATGGGATTAGTGCCCTTATAAAAG 148
INTRON_3 50579 TGCTTTTGGGAGTGGGCTCTTGCACTTGACATTCCACCTTCTGCTATGTG 50628
v vii?i--- v i i---- ----- - i i
MLT1A0#LTR/ER 149 AGACCYC---AGAGAGCTCC----CTTG-----CC-CCTTCCGCCATGTG 185
INTRON_3 50629 ATGATGCAGCATGCAAGGCACCATCT-TGGA--AGAAGATGG--CCTCAC 50673
v ii iiv - i i - i -- i i --
MLT1A0#LTR/ER 186 AGGACACAGTGAG-AAGGCGCCGTCTATGAACCAGGAAATGGGCCCTCAC 234
INTRON_3 50674 CAGTTACTGAACCTGCGGGTGCCTCAACCTTAGACTTCTCAACCCCCAGA 50723
vi i v i ii i i i i i
MLT1A0#LTR/ER 235 CAGACACTGAATCTGCCGGCGCCTTGATCTTGGACTTCCCAGCCTCCAGA 284
INTRON_3 50724 ACTACGAGCTACTAAATTTCCCTT---CATAAATTACTCAGTCT--GGTA 50768
ii v- v iv ---i ii i --
MLT1A0#LTR/ER 285 ACTGTGAGA-AATAAATTTCTGTTGTTTATAAGCTACCCAGTCTATGGTA 333
INTRON_3 50769 TTCTGTCATGGGAGTGCAAAACAGTCTCAGACA 50801
i i i v iv i - v v
MLT1A0#LTR/ER 334 TTTTGTTATAGCAGCCCGAA-CAGACTAAGACA 365
Matrix = 20p37g.matrix
Transitions / transversions = 2.74 (63 / 23)
Gap_init rate = 0.05 (17 / 365), avg. gap size = 2.06 (35 / 17)
+ 25 71.9 0.0 0.0 INTRON_3 50843 50874 (349307) + AT_rich Low_complexity 1 32 (0) 60
ANNOTATION EVIDENCE:
25 71.88 0.00 0.00 INTRON_3 50843 50874 349307 + AT_rich Low_complexity 122 153 147 50
INTRON_3 50843 TAAAAATTTATTCAAAATTTTAAATTTATAAA 50874
??????????????????v vv v v
AT_rich#Low_c 122 WWWWWWWWWWWWWWWWWWATTAAAAATAAATA 153
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 5)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 2156 11.4 1.0 0.3 INTRON_3 51001 51289 (348892) C AluSx3 SINE/Alu (21) 291 1 61
ANNOTATION EVIDENCE:
1981 11.84 1.73 0.68 INTRON_3 51001 51289 348892 C AluSx SINE/Alu 1 292 20 12
INTRON_3 51001 TTTTTTTTTTGAAATGGAGCCTTGCTCTGTCACC-AGGCTGGAGGTACAG 51049
i i i i i - - i
C AluSx#SINE/Al 292 TTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAG-TGCAG 244
INTRON_3 51050 TGGCACGATCTCAGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGTGATT 51099
i i i i i
C AluSx#SINE/Al 243 TGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATT 194
INTRON_3 51100 CCCCTGCCTCAGCCTCCCAAGTAGGTGGGACTACAGGCACACACCACCAT 51149
i i v i i i i i
C AluSx#SINE/Al 193 CTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCAC 144
INTRON_3 51150 GCCCGGTTAATTTTTTGTATTTT-AGTAGAGATGCGGTTTCACTATGTTG 51198
i - - i v i
C AluSx#SINE/Al 143 GCCCGGCTAATTTTT-GTATTTTTAGTAGAGACGGGGTTTCACCATGTTG 95
INTRON_3 51199 GCCAGGCTGGTCTCAAACTCCTGACCTT--GTGATCTGCCCACTTCGACC 51246
i i-- i i i i
C AluSx#SINE/Al 94 GCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCC 45
INTRON_3 51247 TCC-AAAGTGCTGTGATTATAGGCGTGAGCCACTGTGCCCAGCC 51289
- v i i i i
C AluSx#SINE/Al 44 TCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 10.33 (31 / 3)
Gap_init rate = 0.02 (6 / 288), avg. gap size = 1.17 (7 / 6)
+ 242 30.1 15.5 4.5 INTRON_3 51445 51625 (348556) C MIRb SINE/MIR (64) 204 5 62
ANNOTATION EVIDENCE:
242 30.08 15.47 4.50 INTRON_3 51445 51625 348556 C MIRb SINE/MIR 5 204 64 39
INTRON_3 51445 TGTGTTGTTTC---TAATTGTTACAACAACTTTGCAAAAATTGGT-GGTG 51490
ii i i --- iv i ii i ----- - i
C MIRb#SINE/MIR 204 TGCATTATCTCATTTAATCCTCACAACAACCCTGCGA-----GGTAGGTA 160
INTRON_3 51491 ATATTATCA--ATTATGTAT-TAAGAAAATGGTGGCTCAGAAAGGCTAAG 51537
v v-- v ii v- i i iv v i i
C MIRb#SINE/MIR 159 TTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAG 110
INTRON_3 51538 GGAC------AAGGCTG----ACT-TTGAATGTTAG-GCT-GGCTTTGAA 51574
v ------ iii----i -v i i vi - i- v i
C MIRb#SINE/MIR 109 TGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCAGGATTCGAA 60
INTRON_3 51575 --------TGTTTTACTCCAAAACTCAGTTAGGCACCTTCCCTCAGACCA 51616
-------- ii v i i - --- v i viiiv
C MIRb#SINE/MIR 59 CCCAGGTCTGCCTGACTCCAAAGCCC-GT---GCTCTTTCCACTGCACCA 14
INTRON_3 51617 TGCTGTACC 51625
i iv
C MIRb#SINE/MIR 13 CGCTGCCCC 5
Matrix = 25p37g.matrix
Transitions / transversions = 2.25 (36 / 16)
Gap_init rate = 0.07 (13 / 180), avg. gap size = 2.85 (37 / 13)
+ 584 26.3 7.1 1.0 INTRON_3 51980 52175 (348006) + MER103C DNA/hAT-Charlie 34 241 (56) 63
ANNOTATION EVIDENCE:
584 26.27 7.14 0.96 INTRON_3 51980 52175 348006 + MER103C DNA/hAT-Charlie 34 241 56 121
INTRON_3 51980 AATTCTGTGGGATTTTATTAGATGTTGTGTGGTGGGAAGAGGTTGCATGG 52029
i i i v v i ii- iviii - v i
MER103C#DNA/h 34 AGTTCCGCGGGATGTTAATAGGTGTTAC-TGAAAAAAAG-GGTTCCGTGG 81
INTRON_3 52030 TTATGCAGGTTTGGGAAATACTGAGTTAAA---------ACAG---TTTT 52067
i vii i ii i --------- --- i
MER103C#DNA/h 82 TCAAATAAGTTTGGGAAACGCTGGGTTAAACAAAGTTAAACAGGTTTCTT 131
INTRON_3 52068 TCCTATAGGACTTATCCAAGCCTTTAATATGCTGATATATAT-GTGAATC 52116
v ii v vi i i ii -
MER103C#DNA/h 132 TACTGCAGGACTTCTCAGAGCCTTTAATATGCTAATGTGCATTGTGAATC 181
INTRON_3 52117 TCAATGAGATGAATATAGAATGTGGTTTTCCCTAATTTTATTTGATCA-G 52165
v v iv i v ii iv i i vi i -
MER103C#DNA/h 182 TCCAAGAGGGGGATATAGTATGCAGCGTTTCCCAAACTTATTTGACCACG 231
INTRON_3 52166 TAACTCTTTT 52175
v i
MER103C#DNA/h 232 GAACCCTTTT 241
Matrix = 20p37g.matrix
Transitions / transversions = 2.40 (36 / 15)
Gap_init rate = 0.03 (6 / 195), avg. gap size = 2.67 (16 / 6)
+ 270 27.3 3.9 0.0 INTRON_3 52798 52874 (347307) + MIRc SINE/MIR 31 110 (158) 64
ANNOTATION EVIDENCE:
270 27.27 3.90 0.00 INTRON_3 52798 52874 347307 + MIRc SINE/MIR 31 110 158 40
INTRON_3 52798 TGGACATAGAGTCTAGA-GACCTGGGTTC-AGCTTTTGCTCTGC-AGGTA 52844
v i vi - - iii v - vv
MIRc#SINE/MIR 31 TGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCTGGCTCTGCCACTTA 80
INTRON_3 52845 CCAACTAAGTGGCTTTGAACAAATAACATA 52874
i i iv i i ii i v v
MIRc#SINE/MIR 81 CTAGCTGTGTGACCTTGGGCAAGTCACTTA 110
Matrix = 25p37g.matrix
Transitions / transversions = 1.62 (13 / 8)
Gap_init rate = 0.04 (3 / 76), avg. gap size = 1.00 (3 / 3)
+ 216 33.8 0.0 3.4 INTRON_3 53310 53401 (346780) C MER5B DNA/hAT-Charlie (0) 178 90 65 *
ANNOTATION EVIDENCE:
216 33.75 0.00 3.37 INTRON_3 53310 53401 346780 C MER5B DNA/hAT-Charlie 90 178 0 41
INTRON_3 53310 CAGTAGTTTTCAAAAGTAAATAAGCATAAGAATTACCTGAGGAACTTATT 53359
i i vvv iiv ivi vi i i i --
C MER5B#DNA/hAT 178 CAGTGGTTCTCAACCTTGGCTGCACATTGGAATCACCTGGGGAGCTT--T 131
INTRON_3 53360 AGAAAAATGAAGATTAATAGGCCGCAACCTCAGAGCTCTTGA 53401
- ivv vvv i i v v i v ii
C MER5B#DNA/hAT 130 A-AAAAATACTGATGCCTGGGTCCCACCCCCAGAGATTCTGA 90
Matrix = 25p37g.matrix
Transitions / transversions = 1.14 (16 / 14)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 242 23.6 0.0 5.9 INTRON_3 53332 53403 (346778) + MER5A DNA/hAT-Charlie 34 101 (88) 66
ANNOTATION EVIDENCE:
242 23.61 0.00 5.88 INTRON_3 53332 53403 346778 + MER5A DNA/hAT-Charlie 34 101 88 42
INTRON_3 53332 AGCATAAGAATTACCTGAGGAACTTATTAGAAAAATGAAGATTAATAGGC 53381
v v i - i -- v i vvii
MER5A#DNA/hAT 34 AGCATCAGCATCACCTG-GGAACTTGTTAGAAA--TGCAAATTCTCGGGC 80
INTRON_3 53382 CGCAACCTCAGAGCTCTTGAGT 53403
v - i v vi i
MER5A#DNA/hAT 81 CCCA-CCCCAGACCTACTGAAT 101
Matrix = 25p37g.matrix
Transitions / transversions = 1.00 (8 / 8)
Gap_init rate = 0.04 (3 / 71), avg. gap size = 1.33 (4 / 3)
+ 227 23.7 4.0 3.0 INTRON_3 53641 53740 (346441) + T-rich Low_complexity 78 178 (0) 67
ANNOTATION EVIDENCE:
227 23.70 4.00 2.97 INTRON_3 53641 53740 346441 C (TAAA)n Simple_repeat 78 178 2 104
INTRON_3 53641 TACTCATTTATTTATTTGTTCAAATATTT-CTCATTTATGCATGTAT--A 53687
i i i i vv -i i vi v --
C (TAAA)n#Simpl 178 TATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTA 129
INTRON_3 53688 CTTAAATTTTATTTAGC-ACTTATTGATTCTTAAATTTATTTATATTTAT 53736
i --- vi- i v iv vv v v v
C (TAAA)n#Simpl 128 TTTA---TTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTT 82
INTRON_3 53737 ATTT 53740
C (TAAA)n#Simpl 81 ATTT 78
Matrix = Unknown
Transitions / transversions = 0.92 (11 / 12)
Gap_init rate = 0.04 (4 / 99), avg. gap size = 1.75 (7 / 4)
+ 366 25.1 25.1 1.0 INTRON_3 53836 54022 (346159) C L2a LINE/L2 (1) 3425 3194 68
ANNOTATION EVIDENCE:
283 30.00 1.23 1.23 INTRON_3 53836 53916 346265 C L2a_3end LINE/L2 436 516 1 43
INTRON_3 53836 TTCCTTCGTTCAGAACATATTTATTGGGGATGGACTATGTACTAGGCACT 53885
v i iv v i viivv i i
C L2a_3end#LINE 516 TTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACT 467
INTRON_3 53886 GTT-TAATTACTGCAGAATATAATAATGACCA 53916
- ivii -i i i ii i v
C L2a_3end#LINE 466 GTTCTAGGCGCTG-GGGATACAGCAGTGAACA 436
Matrix = 25p37g.matrix
Transitions / transversions = 2.00 (16 / 8)
Gap_init rate = 0.03 (2 / 80), avg. gap size = 1.00 (2 / 2)
366 21.48 9.26 0.85 INTRON_3 53915 54022 346159 C L2a_3end LINE/L2 285 401 116 44
INTRON_3 53915 CATTTTAG-AAGAGAAGA--GAAAATAAGC-------TAAACAAAATGTT 53954
i -ii i i -- v i ------- ii i v
C L2a_3end#LINE 401 CATTCTAGTGGGGGGAGACAGACAATAAACAAATAAATAAGTAAAATATA 352
INTRON_3 53955 TATTCTGCTAGATGGTGATGAGTGCTATGGAGAAAAATTACAGCAGGAAA 54004
v v ii i - v iv
C L2a_3end#LINE 351 TAGTATGTCAGATGGTGATAAGTGCTATGGAGAAAAAT-AAAGCAGGGTA 303
INTRON_3 54005 GGGGGGCTAGGGAGTATT 54022
i v i?
C L2a_3end#LINE 302 AGGGGGATAGGGAGTGNT 285
Matrix = 25p37g.matrix
Transitions / transversions = 2.14 (15 / 7)
Gap_init rate = 0.04 (4 / 107), avg. gap size = 2.75 (11 / 4)
+ 8817 8.0 2.4 0.3 INTRON_3 54026 56026 (344155) + L1PB1 LINE/L1 4111 6151 (0) 69
ANNOTATION EVIDENCE:
8817 8.56 1.48 0.46 INTRON_3 54026 55305 344876 + L1PB_orf2 LINE/L1 2002 3294 0 93
INTRON_3 54026 TTCTAAATAGGATACTG--AGTACTAGCCAGAGCAATCAAACAAGAGAAA 54073
v v -- -- v i
L1PB_orf2#LIN 2002 TTCAACATAG--TACTGGAAGTCCTAGCCAGAGCAATCAGACAAGAGAAA 2049
INTRON_3 54074 GAAGTAAAGGGCATCCAGATCAGTAAAGAGGAAGCCCAATTGTCACTGTT 54123
i i i i v i i
L1PB_orf2#LIN 2050 GAAATAAAGGGCATCCAAATCGGTAAAGAGGAAGTCAAACTGTCGCTGTT 2099
INTRON_3 54124 TGCTGATGACATGATTGTATA--TGGAAAACCCTAAAGACTCATCCAAAA 54171
i i ? -- i v i
L1PB_orf2#LIN 2100 TGCTGATGATATGATCGTNTACCTAGAAAACCCTAAAGACTCCTCCAGAA 2149
INTRON_3 54172 AGCTCCTAGA-CTGGTAAATGGATTCAGAAAAGTTTTAGGATACAAAATT 54220
- i ? i v i?
L1PB_orf2#LIN 2150 AGCTCCTAGAACTGATAAANGAATTCAGCAAAGTTTCNGGATACAAAATT 2199
INTRON_3 54221 AATGTATACAAATCAGTAGCCCTGCTATACACCAACAGCAATCAAGCTGA 54270
i i ? i i
L1PB_orf2#LIN 2200 AATGTACACAAATCAGTAGCTCTNCTATACACCAACAGCGACCAAGCTGA 2249
INTRON_3 54271 GAATTAAATCAAGAGCTTAACCCCTTTTACAATAGCTGCAGAAAAA-TAA 54319
i i i i -
L1PB_orf2#LIN 2250 GAATCAAATCAAGAACTCAACCCCTTTTACAATAGCTGCAAAAAAAATAA 2299
INTRON_3 54320 AATACTTAAGAATATACTTAACCAAGGAGGTGAAAGAACTCTACAAGGAA 54369
i i v
L1PB_orf2#LIN 2300 AATACTTAGGAATATACCTAACCAAGGAGGTGAAAGACCTCTACAAGGAA 2349
INTRON_3 54370 AACTATGAAAGACTGCTGAAAGAAATCAGAGATAACACAAACAAATGGAA 54419
ii v v i
L1PB_orf2#LIN 2350 AACTACAAAACACTGCTGAAAGAAATCATAGATGACACAAACAAATGGAA 2399
INTRON_3 54420 ACACATCCCATGCTCATGGATGGGTAGAATCTTTATTGTGAAAATCACCA 54469
vv v
L1PB_orf2#LIN 2400 ACACATCCCATGCTCATGGATGGGTAGAATCAATATTGTGAAAATGACCA 2449
INTRON_3 54470 TACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCTATCAAAATACCA 54519
i
L1PB_orf2#LIN 2450 TACTGCCAAAAGCAATCTACAAATTCAATGCAATTCCCATCAAAATACCA 2499
INTRON_3 54520 CCATCATTCTTCACAGAACTAGAGAAAACAAACCTATAATTCATATGGAG 54569
i v v i
L1PB_orf2#LIN 2500 CCATCATTCTTCACAGAACTAGAAAAAACAATCCTAAAATTCATATGGAA 2549
INTRON_3 54570 CCAAAAAAAAGAGCTCAGATAGCTAAAGCAAGACTAAGCAAAAAGAACAA 54619
-- i iv i
L1PB_orf2#LIN 2550 CCAAAAAA--GAGCCCGCATAGCCAAAGCAAGACTAAGCAAAAAGAACAA 2597
INTRON_3 54620 ACTTGGAGGCATTACATTACCTAGCTTCAAATTATATTTTAAGGCCATAG 54669
ii i iii i i v
L1PB_orf2#LIN 2598 ATCTGGAGGCATCACATTACCTGATTTCAAACTATACTATAAGGCCATAG 2647
INTRON_3 54670 TCACCAAAACAGCACAGTACTGGTATAAAAATAGGCACATAGACCAATGG 54719
ii
L1PB_orf2#LIN 2648 TCACCAAAACAGCATGGTACTGGTATAAAAATAGGCACATAGACCAATGG 2697
INTRON_3 54720 AACAGAATAGAGAACCCAGAAATAAAGCCAAATACTTAACGGCCAACTGA 54769
v - i
L1PB_orf2#LIN 2698 AACAGAATAGAGAACCCAGAAATAAACCCAAATACTTA-CAGCCAACTGA 2746
INTRON_3 54770 TCTTCAACAAAGCAAACAAAAACA--AAGTGGGGATAGGACACCCTGTTC 54817
i -- v i
L1PB_orf2#LIN 2747 TCTTCGACAAAGCAAACAAAAACATAAAGTGGGGAAAGGACACCCTATTC 2796
INTRON_3 54818 AACAAATGGTGCTGTGATAACTGGCAAGCCACATGTAGAAGAATGAAACT 54867
v i ? i
L1PB_orf2#LIN 2797 AACAAATGGTGCTGGGATAATTGGCNAGCCACATGTAGGAGAATGAAACT 2846
INTRON_3 54868 GGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGAATCAAAG 54917
i i
L1PB_orf2#LIN 2847 GGATCCTCATCTCTCACCTTATACAAAAATCAACTCAAGATGGATCAAGG 2896
INTRON_3 54918 GCTTAAATCTAAGACCTGAAACCATAAAGATTCTAGAAGATAACATCGGA 54967
i i i i
L1PB_orf2#LIN 2897 ACTTAAATCTAAGACCTGAAACTATAAAAATTCTAGAAGATAACATTGGA 2946
INTRON_3 54968 AAAACCCTTCTAGACATTGGCTTATGCAAAGAGTTTATGACCAAGAACCC 55017
v i v i
L1PB_orf2#LIN 2947 AAAACCCTTCTAGACATTGGCTTAGGCAAGGATTTCATGACCAAGAACCC 2996
INTRON_3 55018 AAAAGCAAATGCAACCAAAACAAAAATAAATGGATGGGACTTA-TGAAAC 55066
v i i ? - v
L1PB_orf2#LIN 2997 AAAAGCAAATGCAACAAAAACAAAGATAAATAGNTGGGACTTAATTAAAC 3046
INTRON_3 55067 TAAAAAGCATCTGCACAGCAAAAGAAATAATCAGCAGAGTAAACAG---- 55112
i v i i i i ----
L1PB_orf2#LIN 3047 TAAAGAGCTTCTGCACGGCAAAAGGAACAGTCAGCAGAGTAAACAGACAA 3096
INTRON_3 55113 --CATAGAGTGGGAGAAAATCTTTGCAATCTATACATCCAACAGAGGACT 55160
-- i ii ii i
L1PB_orf2#LIN 3097 CCCACAGAGTGGGAGAAAATCTTCACAATCTATACATCTGACAAAGGACT 3146
INTRON_3 55161 AATATCCAGAATCTACAAGGAACTCAAACAAATCAGCAAGGAAAAAAGCA 55210
? i -
L1PB_orf2#LIN 3147 AATATCCAGAATCTACAANGAACTCAAACAAATCAGCAAGAAAAAAA-CA 3195
INTRON_3 55211 AATAATTTCAT-AAAAAGTGGGCTAAGGACATGAATAAGCAATTCTCAAA 55259
i ii - ii
L1PB_orf2#LIN 3196 AACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCTCAAA 3245
INTRON_3 55260 AGAAGATATACAAATGGCCAACAAACATG---AAAAATGTTCAACCTCA 55305
i--- i v
L1PB_orf2#LIN 3246 AGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAACATCA 3294
Matrix = 20p37g.matrix
Transitions / transversions = 3.08 (77 / 25)
Gap_init rate = 0.01 (13 / 1279), avg. gap size = 1.92 (25 / 13)
686 19.39 2.41 0.59 INTRON_3 55160 55325 344856 + L1ME3F_3end LINE/L1 2 170 820 94
INTRON_3 55160 TAATATCCAGAATCTACAAGGAACTCAAACAAATCAGCAAGGAAAAAAGC 55209
i v v i i vv ii i i -
L1ME3F_3end#L 2 TAGTATCAAGAATATATAAAGAACTCCTACAAATCAATAAGAAAAAGA-C 50
INTRON_3 55210 AAATAATTTCATA-AAAAGTGGGCTAAGGACATGAATAAGCAATTCTCAA 55258
i iiiv - i v i i i v v i
L1ME3F_3end#L 51 AAACAACCCAATAGAAAAATGGGCAAAAGACATGAACAGGCATTTCACAG 100
INTRON_3 55259 AAGAAGATATACAAATGGCCAACAAACAT--GAAAA-ATGTTCAACCTCA 55305
i v i i i -- - i
L1ME3F_3end#L 101 AAGAGGAAACACGAATGGCCAATAAACATATGAAAAGATGCTCAACCTCA 150
INTRON_3 55306 TTAATTATCAGGGAAATGCA 55325
i v
L1ME3F_3end#L 151 TTAGTAATCAGGGAAATGCA 170
Matrix = 20p37g.matrix
Transitions / transversions = 2.20 (22 / 10)
Gap_init rate = 0.02 (4 / 165), avg. gap size = 1.25 (5 / 4)
5318 6.71 1.99 0.14 INTRON_3 55325 56026 344155 + L1PB1_3end LINE/L1 184 898 0 95
INTRON_3 55325 ATGTGATACCATCTTACTCCTGCAAGAATGGCCATAATAAAAAAA----- 55369
i i v -----
L1PB1_3end#LI 184 ATGCGATACCACCTTACTCCTGCAAGAATGGCCATAATCAAAAAATNAAA 233
INTRON_3 55370 ----AATAGATGTTGGTGTGGATGTGGTGAAAAGGGAATGCTTTTACACT 55415
---- i ii i
L1PB1_3end#LI 234 AAATAATAGATGTTGGCGTGGATGTGGTGAAAAGGGAACACTTCTACACT 283
INTRON_3 55416 GTTGGTGGGAATGTAAACTAGTACAACCACTACAGAAAACAGTGTGGAGA 55465
i ii
L1PB1_3end#LI 284 GCTGGTGGGAATGTAAACTAGTACAACCACTATGGAAAACAGTGTGGAGA 333
INTRON_3 55466 TTCCTTAAAGAACTAAAAGTAGATCTACCATTTGATCCAGCAATCCCACT 55515
L1PB1_3end#LI 334 TTCCTTAAAGAACTAAAAGTAGATCTACCATTTGATCCAGCAATCCCACT 383
INTRON_3 55516 CCTGGGTATCTACCCAGAGGAAAATAAGTCATTATACGAAAAAGATACTT 55565
v v
L1PB1_3end#LI 384 ACTGGGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAAGATACTT 433
INTRON_3 55566 GCACATGCATGTTTATAGCAGTGCAATTCACAGTTGCAAAAATGTGGAAC 55615
i ii i i i
L1PB1_3end#LI 434 GCACACGCATGTTTATAGCAGCACAATTCGCAATTGCAAAAATATGGAAC 483
INTRON_3 55616 CCGCCCAAATGCCCATCAATCTATGAGTGGTTAAAGAAAATGTGGTATAT 55665
v v v
L1PB1_3end#LI 484 CAGCCCAAATGCCCATCAATCAATGAGTGGATAAAGAAAATGTGGTATAT 533
INTRON_3 55666 ATACACCATAGAATACTACTCAGCCATAAAAAGGAATGAAATAATGGCAA 55715
i i i v
L1PB1_3end#LI 534 ATATACCATGGAATACTACTCAGCCATAAAAAGGAACGAAATAATGGCAT 583
INTRON_3 55716 TTACAGCAACCTGGATGGAATTGGAGACCATTATTCTAAGTGAAGTAACT 55765
ii
L1PB1_3end#LI 584 TCGCAGCAACCTGGATGGAATTGGAGACCATTATTCTAAGTGAAGTAACT 633
INTRON_3 55766 AAGGAATGGAAAACCAAACGT--TATGTTCTCACTCA--GGTGGGAGCTA 55811
v i -- --i
L1PB1_3end#LI 634 CAGGAATGGAAAACCAAACATCGTATGTTCTCACTCATAAGTGGGAGCTA 683
INTRON_3 55812 AGCTATGAG-ATGCAAAGGCATAAGAATGATACAATGGACTTTGGGGACT 55860
-
L1PB1_3end#LI 684 AGCTATGAGGATGCAAAGGCATAAGAATGATACAATGGACTTTGGGGACT 733
INTRON_3 55861 CAGGGGAAAGGGTAGGAGGTAGGTGAAGGGTAAAAGACTACACATTGGCT 55910
i i vi i i v
L1PB1_3end#LI 734 CGGGGGAAAGGGTGGGAGGGGGGTGAGGGATAAAAGACTACACATTGGGT 783
INTRON_3 55911 ACAATGTATACTGCTTGGTTGATGGGGGCACCAAAAATCTCAGAAATCAC 55960
i i i v v -
L1PB1_3end#LI 784 ACAGTGTACACTGCTCGGGTGATGGGTGCACCAAAA-TCTCAGAAATCAC 832
INTRON_3 55961 CACTAAAGAACTTATTCATGTAGCCAAATACCACCTGTTTCCCCAAAACC 56010
i i i v
L1PB1_3end#LI 833 CACTAAAGAACTTATTCATGTAACCAAACACCACCTGTTCCCCAAAAACC 882
INTRON_3 56011 TATTGAAATAAATAAA 56026
v
L1PB1_3end#LI 883 TATTGAAATAAAAAAA 898
Matrix = 20p37g.matrix
Transitions / transversions = 2.36 (33 / 14)
Gap_init rate = 0.01 (5 / 701), avg. gap size = 3.00 (15 / 5)
+ 642 30.0 2.8 1.6 INTRON_3 56027 56273 (343908) C L2a LINE/L2 (254) 3172 2923 68
ANNOTATION EVIDENCE:
642 30.03 2.83 1.60 INTRON_3 56027 56273 343908 C L2a_3end LINE/L2 14 263 254 45
INTRON_3 56027 TAAATAAAGTATTGAGGGGAGAGGTCACTGGGAAAGTGGCATTTGAG-GG 56075
ii iv v i ivv i i i -ii
C L2a_3end#LINE 263 TAAATAGGGTGGTCAGGGAAGGCCTCACTGAGAAGGTGACATTTGAGCAA 214
INTRON_3 56076 AGACCTAAAGTACTTG-GGGAGCAGGTCATAAAGGTA-ATAGGGAAAG-- 56121
i v vv - ii i ivi i -v i i --
C L2a_3end#LINE 213 AGACCTGAAGGAGGTGAGGGAGCGAGCCATGCGGATATCTGGGGGAAGAG 164
INTRON_3 56122 TATTCCAAGCTGATGGGAGTATCATGGGTAAAAATCCATGAGCCGTGAGC 56171
ii i v - ii v v v i iii - v v
C L2a_3end#LINE 163 CGTTCCAGGCAGA-GGGAACAGCAAGTGCAAAGGCCC-TGAGGCGGGAGC 116
INTRON_3 56172 ATGT-TGACTGTGTTTCAGGGACTTCCAGGAGCCCAGTGTGGCTGGAGAG 56220
i i- i - iv i vv v v v
C L2a_3end#LINE 115 GTGCCTGGC-GTGTTCGAGGAACAGCAAGGAGGCCAGTGTGGCTGGAGCG 67
INTRON_3 56221 GGATGAACAAGGGGAAT-CTAGTAGGCAAATATGTTTAGAGAATTAATGA 56269
ii i i i v-v i - i iv v i iv i i
C L2a_3end#LINE 66 GAGTGAGCGAGGGGGAGAGTGGTAGG-AGATGAGGTCAGAGAGGTAACGG 18
INTRON_3 56270 GAAG 56273
ii
C L2a_3end#LINE 17 GGGG 14
Matrix = 25p37g.matrix
Transitions / transversions = 1.81 (47 / 26)
Gap_init rate = 0.04 (10 / 246), avg. gap size = 1.10 (11 / 10)
+ 431 26.8 0.0 0.0 INTRON_3 56757 56853 (343328) C MER133B DNA? (28) 112 16 70
ANNOTATION EVIDENCE:
431 26.80 0.00 0.00 INTRON_3 56757 56853 343328 C MER133B DNA? 16 112 28 122
INTRON_3 56757 ATGCAGAGGACCATAGTCTGGCCTTAGATGCGCACCCAGAATTTCCATTG 56806
i i v v v i i v iv i i
C MER133B#DNA? 112 ATACAGAGGGCCAAATTCTGCCCTCAGATACGCACGCGCAACTCCCATTG 63
INTRON_3 56807 ACGTCAATACTTATTGCTTACGTGTATCCAAGGGCAGGATCTGGTCC 56853
v ivvvi vii i i i i i
C MER133B#DNA? 62 ACTTCAATGGGAGTTGCGCGCGCGTATCCGAGGGCAGAATTTGGCCC 16
Matrix = 20p37g.matrix
Transitions / transversions = 1.60 (16 / 10)
Gap_init rate = 0.00 (0 / 96), avg. gap size = 0.0 (0 / 0)
+ 2968 0.7 0.0 0.0 INTRON_3 57587 57895 (342286) + AluYa5 SINE/Alu 1 309 (1) 71
ANNOTATION EVIDENCE:
2760 2.27 0.00 0.00 INTRON_3 57587 57895 342286 + AluY SINE/Alu 1 309 2 13
INTRON_3 57587 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 57636
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 57637 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCAGCTAAAACGG 57686
ii v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
INTRON_3 57687 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 57736
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
INTRON_3 57737 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 57786
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
INTRON_3 57787 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 57836
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
INTRON_3 57837 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 57886
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
INTRON_3 57887 AAAAAGAAA 57895
i
AluY#SINE/Alu 301 AAAAAAAAA 309
Matrix = 14p37g.matrix
Transitions / transversions = 2.50 (5 / 2)
Gap_init rate = 0.00 (0 / 308), avg. gap size = 0.0 (0 / 0)
2760 2.27 0.00 0.00 INTRON_3 57587 57895 342286 + AluY SINE/Alu 1 309 2 123
INTRON_3 57587 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 57636
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 57637 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCAGCTAAAACGG 57686
ii v
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
INTRON_3 57687 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGC 57736
i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
INTRON_3 57737 GGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGT 57786
i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
INTRON_3 57787 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTC 57836
v
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
INTRON_3 57837 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 57886
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
INTRON_3 57887 AAAAAGAAA 57895
i
AluY#SINE/Alu 301 AAAAAAAAA 309
Matrix = 14p37g.matrix
Transitions / transversions = 2.50 (5 / 2)
Gap_init rate = 0.00 (0 / 308), avg. gap size = 0.0 (0 / 0)
+ 239 37.5 4.2 8.1 INTRON_3 57968 58416 (341765) C L2c LINE/L2 (4) 3383 2951 72
ANNOTATION EVIDENCE:
239 37.55 4.23 8.08 INTRON_3 57968 58416 341765 C L2c_3end LINE/L2 42 474 4 150
INTRON_3 57968 ATTCACTTAAAGTAACATTTATTGTGTAACTCTTTTATGTTAGTT--TGA 58015
i i vi- v iiv vi v i ii v -- -
C L2c_3end#LINE 474 ATTCATTCAACA-AACATTTATTGAGCGCCTACTATGTGCCAGGTGCTG- 427
INTRON_3 58016 GGGCTAGCATTCTGGGCTAAACACTGAGTCCTAACTCTCTACTA-CTCAG 58064
v vv vvv iiiv i --i ivi i v vv - v
C L2c_3end#LINE 426 GGGATACAAAGATGAATAAGACAC--GGTCCCTGCCCTCAAGGAGCTCAC 379
INTRON_3 58065 CATACACTGAAGGGGCCAGACATACTATACTATATA--TAGAAGATAGAG 58112
vi vi v i i v ?i- v - v i -- v v i -
C L2c_3end#LINE 378 AGTCTAGTGGAGGAGACAGACANG-TAAAC-AGACAATTACAATACA-AG 332
INTRON_3 58113 T--ATGGTAAGTTCTGTAATAGGCATATAAACAAAATTCTGGAAGAGAAT 58160
-- i v i i vi i iii v ivii v i
C L2c_3end#LINE 331 TTAATGATAAGTGCTATAATGGGAGTATAGACAGGGTGCTATGGGAGCAC 282
INTRON_3 58161 GAAGTGGGGGTGAAAGAGCTTAAATTTGCCTATTTTTGGAAA--TGCCTT 58208
ii - i i- vvv vi i?i vvviv ivv i-- v v
C L2c_3end#LINE 281 AGAG-GAGGGC-ACCTAGACTAGNCTTGGGGGGTCAGGGAAGGCTTCCTG 234
INTRON_3 58209 AAGTAGCACTGATCATCTGTGGTGTACTTTGGAA-ATGAATATGATTTTG 58257
i v v-- - v v vi?i i i- i v v v
C L2c_3end#LINE 233 GAGGAGG--TGA-CATCTGAGCTGAGNCTTGAAGGATGAGTAGGAGTTAG 187
INTRON_3 58258 ACAGGTGACAGAGGTATGGGCAGGGCAATAAGAACAGTATTCTAGGTGGA 58307
v iv i--------- ----ii v i i ii
C L2c_3end#LINE 186 CCAGGTGGAAGG---------AGGG----GGGAAGAGCATTCCAGGCAGA 150
INTRON_3 58308 GTGATAACCCTGAACAAAGAATTAGATG--GG-------TGCTTGATGTG 58348
v vv v v vi iv?ii v -- ------- -- ii
C L2c_3end#LINE 149 GGGAACAGCATGTGCAAAGGCNCGGAGGCAGGAAAGAACTGC--GGCGTG 102
INTRON_3 58349 GATTTTAGGGAGCAGTGAGGCATCTGATGTGTTTAGAACATAAGTTATAT 58398
--- i ii- ii ?vi iiii vi i i - viv--
C L2c_3end#LINE 101 ---TTTGGGGAAT-GCAAGNAGTTCAGTGTGGCTGGAGCATA-GTGGG-- 59
INTRON_3 58399 TGAATAGGGATAGTGGAG 58416
i iv i-
C L2c_3end#LINE 58 CGAGGAGGGG-AGTGGAG 42
Matrix = 25p37g.matrix
Transitions / transversions = 1.24 (83 / 67)
Gap_init rate = 0.06 (26 / 448), avg. gap size = 2.08 (54 / 26)
+ 334 23.5 8.1 1.1 INTRON_3 58922 59007 (341174) + MIR3 SINE/MIR 88 179 (29) 73
ANNOTATION EVIDENCE:
334 23.52 8.14 1.09 INTRON_3 58922 59007 341174 + MIR3 SINE/MIR 88 179 29 151
INTRON_3 58922 GAGCTTGGACAAATTACTTC-----TCTAGACCTCATTTTCTTTATTATG 58966
v i i i ----- i i v i i i-
MIR3#SINE/MIR 88 GACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCATC-TG 136
INTRON_3 58967 -AAAATGAGAAG-TTGGTCTAAACAAGTTCTAGGTTCCCTTCC 59007
- ii - v i ii vi i v
MIR3#SINE/MIR 137 TAAAATGAGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCC 179
Matrix = 25p37g.matrix
Transitions / transversions = 3.00 (15 / 5)
Gap_init rate = 0.05 (4 / 85), avg. gap size = 2.00 (8 / 4)
+ 234 0.0 0.0 0.0 INTRON_3 60246 60271 (339910) + (A)n Simple_repeat 1 26 (0) 74
ANNOTATION EVIDENCE:
234 0.00 0.00 0.00 INTRON_3 60246 60271 339910 + (A)n Simple_repeat 1 26 154 259
INTRON_3 60246 AAAAAAAAAAAAAAAAAAAAAAAAAA 60271
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26
Matrix = Unknown
Transitions / transversions = 0.0 (0 / 0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
+ 207 30.8 0.0 0.0 INTRON_3 60650 60714 (339467) + MIRc SINE/MIR 197 261 (7) 75
ANNOTATION EVIDENCE:
207 30.77 0.00 0.00 INTRON_3 60650 60714 339467 + MIRc SINE/MIR 197 261 7 152
INTRON_3 60650 AAGGAAGTAAAATATTTAGAAGCCCACTGTAAATTGTGAAATGCTATCTA 60699
v ii vi v ii v vi i i i vi
MIRc#SINE/MIR 197 AATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACA 246
INTRON_3 60700 AAGGTAAGATCTTAT 60714
v ivv
MIRc#SINE/MIR 247 AATGTAAGGGGTTAT 261
Matrix = 25p37g.matrix
Transitions / transversions = 1.22 (11 / 9)
Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0)
+ 428 31.2 8.6 1.1 INTRON_3 60831 61073 (339108) C Plat_L3 LINE/CR1 (28) 3558 3298 76
ANNOTATION EVIDENCE:
428 31.22 8.64 1.15 INTRON_3 60831 61073 339108 C Plat_L3 LINE/CR1 3298 3558 28 172
INTRON_3 60831 AGTGACCTTGAG--GTTATCTAGTTCA--CATTTTCCTTTGGGCAGA--A 60874
v i -- i i i -- vii v iii i--
C Plat_L3#LINE/ 3558 AGGGACCTCGAGAGGTCATCTGGTCCAGCCCCCTGCCTCCAGGCAGGTGA 3509
INTRON_3 60875 ATCCACTTAAATCATGTTAGAAAGATGGA----TACTCTTTTCATGAAAG 60920
v- - i vivi v ?---- i v i ii
C Plat_L3#LINE/ 3508 ATG-ACT-AAACCATCCAGGACAGATGGNCGTCTATTCTTTTCTTAAAGA 3461
INTRON_3 60921 TCTATAGAGTAGGAGAATCCATA-TCTCTTTTGACAGCCTTTGCCAGTGT 60969
vi i vv v i -i ii i ii iv v
C Plat_L3#LINE/ 3460 TCTCCAGGGATGGAGACTCCACAACCTCCCTCGGTAGCCCGTTCCAGTGT 3411
INTRON_3 60970 TTCA-CATCCCTTCAGACATGAA-----TTCTGATTTTTGATCTAAAGAC 61013
i - i vv i v v ----- i v v iii i v vvi
C Plat_L3#LINE/ 3410 TTTATCACCCCGACGGTCAAGAAGTTCTTCCTTATGTCCAACCGAAATCT 3361
INTRON_3 61014 CTCCTGCTAGTAATGTAAGGCTGTT-CCT-TTGTCCCATTCTCAATGGAA 61061
-v v v ii - - i vi i ?i v
C Plat_L3#LINE/ 3360 CTCCTGCT-TTAATTTAAGCCCATTTCCTCTTGTTCGGTCCTCNGTGGAC 3312
INTRON_3 61062 AC--AGGATAGCTG 61073
-- i i i
C Plat_L3#LINE/ 3311 ACGGAGAACAACTG 3298
Matrix = 20p37g.matrix
Transitions / transversions = 1.61 (45 / 28)
Gap_init rate = 0.05 (13 / 242), avg. gap size = 1.85 (24 / 13)
+ 341 31.7 1.9 0.0 INTRON_3 61514 61617 (338564) C L2a LINE/L2 (20) 3406 3301 77
ANNOTATION EVIDENCE:
341 31.73 1.92 0.00 INTRON_3 61514 61617 338564 C L2a_3end LINE/L2 392 497 20 153
INTRON_3 61514 TTCATTCAACACAGAATGTGTATCTAGTAC-GTGCTAGGCATTATAAATT 61562
i v i i vv v i ii vi i - v ii ivii v
C L2a_3end#LINE 497 TTTATTGAGCGCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATA 448
INTRON_3 61563 TAGCAGTGAACAAAGATGATAAAA-TCTCAGCTCTCCTGGAGCCAACGTT 61611
i ivv i - i v i v iv i
C L2a_3end#LINE 447 CAGCAGTGAACAAAACAGACAAAAGTCCCTGCCCTCATGGAGCTTACATT 398
INTRON_3 61612 CTAGTG 61617
C L2a_3end#LINE 397 CTAGTG 392
Matrix = 25p37g.matrix
Transitions / transversions = 1.54 (20 / 13)
Gap_init rate = 0.02 (2 / 103), avg. gap size = 1.00 (2 / 2)
+ 243 30.8 5.6 2.7 INTRON_3 62187 62293 (337888) + L3 LINE/CR1 4235 4344 (145) 78
ANNOTATION EVIDENCE:
243 30.75 5.61 2.73 INTRON_3 62187 62293 337888 + L3 LINE/CR1 4235 4344 145 154
INTRON_3 62187 AGGATTAACCGTGG-TACAATTTAAAAGGAAACACATTTTAGTTCACTGT 62235
i --- - iv v v i ii v i i v i
L3#LINE/CR1 4235 AGGATCA---GTGGGTGGAAGTTACAGGGAGGCAGATTTCAGCTCAATAT 4281
INTRON_3 62236 GTAGAAGGGTTTT---GCAAT-AAAGCTGTCTGAAAATG-AATTGGTAGC 62280
ivi iii ---i - i ii - v iv
L3#LINE/CR1 4282 AAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGC 4331
INTRON_3 62281 TTTAAGAAATTGT 62293
i ii ii v
L3#LINE/CR1 4332 CTTGGGAGGTAGT 4344
Matrix = 25p37g.matrix
Transitions / transversions = 2.56 (23 / 9)
Gap_init rate = 0.05 (5 / 106), avg. gap size = 1.80 (9 / 5)
+ 2520 7.3 0.0 0.0 INTRON_3 62303 62605 (337576) + AluY SINE/Alu 1 303 (8) 79
ANNOTATION EVIDENCE:
2437 7.26 0.00 0.00 INTRON_3 62303 62605 337576 + AluY SINE/Alu 1 303 8 124
INTRON_3 62303 GGCTGGGCGGGGTGGCTCACGCCTGTAATTCCAGCACTTTGGGAGGCCCA 62352
i v i v
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 62353 GGCGGGCGGATCACGTGGTCAGGAGATTGAGACCTTCCTGGCTAACACAG 62402
v i v i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
INTRON_3 62403 TGATACCCTGTCTCTACTAAAAATACAAAAAATTAGCCAGGCATGGTGGC 62452
v i i i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
INTRON_3 62453 GGGGGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATGGCGT 62502
v i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
INTRON_3 62503 GAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCACGCCACTGCACTC 62552
v i
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
INTRON_3 62553 CAGCCTGGGTGACAGAGCGAGATTCCGTCTTTAAAAAAAAAAATAAAAAG 62602
i i iv v i
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
INTRON_3 62603 AAA 62605
AluY#SINE/Alu 301 AAA 303
Matrix = 14p37g.matrix
Transitions / transversions = 1.44 (13 / 9)
Gap_init rate = 0.00 (0 / 302), avg. gap size = 0.0 (0 / 0)
+ 369 0.0 0.0 0.0 INTRON_3 62616 62656 (337525) + (CAT)n Simple_repeat 3 43 (0) 80
ANNOTATION EVIDENCE:
369 0.00 0.00 0.00 INTRON_3 62616 62656 337525 + (CAT)n Simple_repeat 3 43 137 254
INTRON_3 62616 TCATCATCATCATCATCATCATCATCATCATCATCATCATC 62656
(CAT)n#Simple 3 TCATCATCATCATCATCATCATCATCATCATCATCATCATC 43
Matrix = Unknown
Transitions / transversions = 0.0 (0 / 0)
Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0)
+ 501 24.1 9.6 4.3 INTRON_3 62693 62870 (337311) C MIRb SINE/MIR (7) 261 75 81
ANNOTATION EVIDENCE:
501 24.06 9.55 4.28 INTRON_3 62693 62870 337311 C MIRb SINE/MIR 75 261 7 155
INTRON_3 62693 GAGCTAC----TAGTGAGTGCCGAGTATAT-CCAGATACTCTGCTAAGGG 62737
---- v i iv v i i - ii v v
C MIRb#SINE/MIR 261 GAGCTACCATTTATTGAGCGCTTACTGTGTGCCAGGCACTGTGCTAAGCG 212
INTRON_3 62738 CTTTAAAGACATTATTT---TTAATCTTTAGCACA-TCCTATAAAATA-- 62781
v vi i --- i i vv -i iii ii --
C MIRb#SINE/MIR 211 CTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGG 162
INTRON_3 62782 --TCATTATTCCTGTTTTGCAGATGAGGCACCTGAGACTTAGAGAGTTT- 62828
-- i i ii i v v i i v -
C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112
INTRON_3 62829 -GTGAGTT-CTCAAT-TCAGCATATAGGCTAAATGATAAATGGCA 62870
- v - i v- - i --- i---- i
C MIRb#SINE/MIR 111 AGTGACTTGCCCAAGGTCA-CACA---GCTAG----TAAGTGGCA 75
Matrix = 25p37g.matrix
Transitions / transversions = 1.93 (27 / 14)
Gap_init rate = 0.06 (11 / 177), avg. gap size = 2.27 (25 / 11)
+ 1192 18.1 8.2 0.0 INTRON_3 62913 63144 (337037) C MER45B DNA/hAT-Tip100 (220) 820 570 82
ANNOTATION EVIDENCE:
1192 18.10 8.19 0.00 INTRON_3 62913 63144 337037 C MER45B DNA/hAT-Tip100 570 820 220 263
INTRON_3 62913 TACTATCCATCTTTATATTGTGCAATGCAAGTTTTAAATACAAACAAAAG 62962
i i v i i v
C MER45B#DNA/hA 820 TACCATTCATCTTTATATTGTGCAATGCCAGTTTTAAATGCAAATATAAG 771
INTRON_3 62963 AGCATTTAACTTATATGTGGAACCACAGGA---------------TTTTA 62997
ii i i v i --------------- ii
C MER45B#DNA/hA 770 AGCATTTAACTCGTATGCGGAATCACCGAAATTACACAATTCGTATTTCG 721
INTRON_3 62998 TAGTTCATACATGCATATGTATTTCTTTCTTACCAGAACAATGGAAATGC 63047
i i v i i
C MER45B#DNA/hA 720 TAGCTCGTACATGCATATGTATTTCGTTCTTACCAGAACAGTGGAAACGC 671
INTRON_3 63048 TGTGCAAATTTAAC---AGT-TTTTTACTTTACCTTCGGATGTTTGCACA 63093
ii vi --- v - i i i iiv iivi
C MER45B#DNA/hA 670 TGCACAAAACTAACTCAACTGTTTTTATTTCACTTCTTGATACGCGCACA 621
INTRON_3 63094 CTCTACCAACATTCTCTACTTTTGGTTTACTCATGAATAAGGAAGGCCTG 63143
i i i i i v i v
C MER45B#DNA/hA 620 TTCTACCAACACTCTCTACCTTCGGCTTACTGATGAGTAAGGAAGGACTG 571
INTRON_3 63144 A 63144
C MER45B#DNA/hA 570 A 570
Matrix = 20p37g.matrix
Transitions / transversions = 3.20 (32 / 10)
Gap_init rate = 0.01 (3 / 231), avg. gap size = 6.33 (19 / 3)
+ 1143 6.7 0.0 0.0 INTRON_3 63145 63278 (336903) + AluSg SINE/Alu 1 134 (176) 83
ANNOTATION EVIDENCE:
1093 6.72 1.49 0.00 INTRON_3 63145 63278 336903 + AluSx SINE/Alu 1 136 176 137
INTRON_3 63145 GGCCGGGTGTGGTGGTTCACCCCTGTAATCCCAGCACTTTGGGAGGCCGA 63194
i i i v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 63195 GGTGGGTGGATCAC--GAGGTCAGGAGTTTGAAACCAGCCTGGCCAACAT 63242
i i -- i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
INTRON_3 63243 GGTGAAACCCCGTCTCTACTAAAAATACAAAATTTA 63278
v
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTA 136
Matrix = 14p37g.matrix
Transitions / transversions = 3.50 (7 / 2)
Gap_init rate = 0.01 (1 / 133), avg. gap size = 2.00 (2 / 1)
+ 309 25.3 0.0 0.0 INTRON_3 63572 63646 (336535) C MER121 DNA/TcMar? (175) 222 148 84
ANNOTATION EVIDENCE:
309 25.33 0.00 0.00 INTRON_3 63572 63646 336535 C MER121 DNA/TcMar? 148 222 175 264
INTRON_3 63572 TCTTAAATCTCAAAGAGCACTTGTAAAACAGCACTTTGATTTGCTAAGTG 63621
ii iv v v ii i i vv i
C MER121#DNA/Tc 222 TCTTGGACATCAAATAGCTCTTACAAAACAACATTTTGATGAGTTAAGTG 173
INTRON_3 63622 GAACTAAATCAGAAACATGTAGACT 63646
v v i i i i
C MER121#DNA/Tc 172 TAAATGAATCAGAAACATATGGATT 148
Matrix = 20p37g.matrix
Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0)
+ 2076 30.0 4.9 2.1 INTRON_3 64044 65571 (334610) + L1M3d LINE/L1 11 888 (5003) 85
ANNOTATION EVIDENCE:
1596 30.55 4.12 0.80 INTRON_3 64044 64528 335653 + L1M3d_5end LINE/L1 11 511 864 173
INTRON_3 64044 AGCAAGGATGA-AGGATAGGAAGCTCTAGACTCTCCTTTCCTGCACAAAC 64092
- i- vi i i ii i i v i
L1M3d_5end#LI 11 AGCAAG-ATGGCATAATAGGAAGCCCTGGACCTTTCTTCCCTTCACAGAC 59
INTRON_3 64093 ACATCTG-TTTAACAGCAAAACATGGACAAGTTTCTTTTTTGAGACATCC 64141
- - i i i vv i - i v i v v v
L1M3d_5end#LI 60 ACA-CTGATTCAGCAACAATTCACGGA-AAATTACCTTTGTGAGAAATGC 107
INTRON_3 64142 AAAAACTAATTGAGAGGCTTTTATATCCTGGGTGAGTGTGAAACCAG--C 64189
i i ii ii i i i i --
L1M3d_5end#LI 108 AGAAACTAGTTGAGAGGCTCCTGCACCCTGGGCGAGCGCGAAACCAGACC 157
INTRON_3 64190 CACATTAAAACTGGTATTGAAATTCAGGATACCCTTTCACAAGAATTGCT 64239
i i i vv i i i ivii i iv
L1M3d_5end#LI 158 CACATCAAAGCCGGTAGGGAGATTCAGGACACCCTCTCATCGAAGTCCCT 207
INTRON_3 64240 ACCCT-GGCACAGTACCATACAATCAGAAAGAAAC--CTCCTAATTCTCA 64286
v i- ? ii ?i i i i i v-- i i i i i
L1M3d_5end#LI 208 CCCCCCGGCWCAGCGCMGTGCGATCGGAAGGAAAAAACCCCCAACTCCCG 257
INTRON_3 64287 GCTTCTCCTTGGGAATGGAAAGAGTTGGACCACGTATCTAATACTCCAAC 64336
iv i v i vi i iii v i i i ?
L1M3d_5end#LI 258 GCTTCTCCCAGGGGAGGAAAAGAGTTGGTTCGCACGTCAAGTGCCCCRAC 307
INTRON_3 64337 TTTTTTG-GGGACTTCTGAGAAGACTGCTATATGTCTTGAGTGTCTTGGA 64385
ii - i v iv i iiv v vv? i?
L1M3d_5end#LI 308 TTTTCCGAGGGGCTACCCAGAGGACTGTCTTCTGTCTTGCCWGTCTCRGA 357
INTRON_3 64386 GTGCTGACAGGACCTGGCATACTTTAGCTGCTTGGGC---ACCAG----- 64427
iv i - i v i vii ii v--- v -----
L1M3d_5end#LI 358 GCTCTGATAGG-CCCGGCATAATCTAGACACCCGGGGGAGAACAGAGATG 406
INTRON_3 64428 ----TTTGGACTGAGTGTCACTATAGCCCATGCCCCCAACTCAGCACAAA 64473
---- i ivv vii i i?v vv vi i
L1M3d_5end#LI 407 GTGGTTTGGGCTGGTAGATGCCATAGCTNCTCACCCCTGCTCAGCACAGA 456
INTRON_3 64474 GTGAATGGATGAATAAACCCAGCTCCCAAACTTTTCCTGGTGAGAAAATG 64523
iii i?i v vv ? i ivi ii iv i v?
L1M3d_5end#LI 457 ACAAGNAGATGAAAACCCCCAGNTCTCAGCTTTCCCCTGAGGAGGAAAAN 506
INTRON_3 64524 AGTTG 64528
L1M3d_5end#LI 507 AGTTG 511
Matrix = 20p37g.matrix
Transitions / transversions = 2.29 (96 / 42)
Gap_init rate = 0.02 (12 / 484), avg. gap size = 2.00 (24 / 12)
818 32.35 2.24 2.90 INTRON_3 64448 64759 335422 + L1M3d_5end LINE/L1 201 510 865 174
INTRON_3 64448 AGCCCATGCCCCCAACTCAGCACAAAGTGAATGGATGAATAAA---CCCA 64494
i v v ii ? i ?iv i vi v i v ---
L1M3d_5end#LI 201 AGTCCCTCCCCCCGGCWCAGCGCMGTGCGATCGGAAGGAAAAAACCCCCA 250
INTRON_3 64495 GCTCCCAAACTTTTCCTGGTGAGAAAATGAGTTGGACCACACATCCAATG 64544
i iivi i i v v i v vi i i v i
L1M3d_5end#LI 251 ACTCCCGGCTTCTCCCAGGGGAGGAAAAGAGTTGGTTCGCACGTCAAGTG 300
INTRON_3 64545 CCTCAACTTCTCTGGAGG--TGCACTAAAGACTAGATCCTGTTTTGCCTG 64592
i ? i i ii -- i v vi i ivv i i ?
L1M3d_5end#LI 301 CCCCRACTTTTCCGAGGGGCTACCCAGAGGACTGTCTTCTGTCTTGCCWG 350
INTRON_3 64593 TTATGGGATGCTGACAGGTCCTGGCATATTATAG-CAGCCTTGGAACCAG 64641
ivi? iiiv i i - v v - v -- -----
L1M3d_5end#LI 351 TCTCRGAGCTCTGATAGGCCC-GGCATAATCTAGACACCC--GG-----G 392
INTRON_3 64642 TGAGATCAGACGTGGTGGTTTAGGCTGGCGTTTACCATAACCCCCAATCC 64691
v v vi i iivv i i i? iv i
L1M3d_5end#LI 393 GGAGAACAGAGATGGTGGTTTGGGCTGGTAGATGCCATAGCTNCTCACCC 442
INTRON_3 64692 CAGCTCAGCACAGAGTGAATAGGTGAATAACTCCAGATCCCGGCTTCTCC 64741
v iii i? i v v i ? i i ii
L1M3d_5end#LI 443 CTGCTCAGCACAGAACAAGNAGATGAAAACCCCCAGNTCTCAGCTTTCCC 492
INTRON_3 64742 CTT-GGATGAGATAGAGTT 64759
v- v i - ?
L1M3d_5end#LI 493 CTGAGGAGGAAA-ANAGTT 510
Matrix = 20p37g.matrix
Transitions / transversions = 1.78 (57 / 32)
Gap_init rate = 0.03 (8 / 311), avg. gap size = 2.00 (16 / 8)
1016 27.21 3.32 2.30 INTRON_3 64690 64990 335191 + L1M3d_5end LINE/L1 211 514 861 175
INTRON_3 64690 CCCAGCTCAGCACAGAGTGAAT---AGGTGAATAACTCCAGATCCCGGCT 64736
i ? i ? v i vi--- vi v v i iv
L1M3d_5end#LI 211 CCCGGCWCAGCGCMGTGCGATCGGAAGGAAAAAACCCCCAACTCCCGGCT 260
INTRON_3 64737 TCTCCCTTGGATGAGATAGAGTTTGACCATGTGTCCAATACCCCAACTTG 64786
vv iv ii v v vi iiii v i i ? v
L1M3d_5end#LI 261 TCTCCCAGGGGAGGAAAAGAGTTGGTTCGCACGTCAAGTGCCCCRACTTT 310
INTRON_3 64787 CTTG-TGGACTGCCCAAAGGACTACCATCTGTCTTGCCTG-CTCAGAGTG 64834
iii -v i i i ii v ? - ? iv
L1M3d_5end#LI 311 TCCGAGGGGCTACCCAGAGGACTGTCTTCTGTCTTGCCWGTCTCRGAGCT 360
INTRON_3 64835 CTGATGGGACCTGGCATACTCTAGCCACTTGGGGCCAGTGAGAACCGAGG 64884
i - i v v ii ----- v i
L1M3d_5end#LI 361 CTGATAGG-CCCGGCATAATCTAGACACCCGGGG-----GAGAACAGAGA 404
INTRON_3 64885 TGGAGGTTTGG--CGGT---TGTCATAGCTCCTTCCCCTGGCTCTACACA 64929
v --i --- i ? iv iv vi
L1M3d_5end#LI 405 TGGTGGTTTGGGCTGGTAGATGCCATAGCTNCTCACCCCTGCTCAGCACA 454
INTRON_3 64930 GAGCAAGCAGATGAATATACCCTAGTTCCCAGCTTCCCTCTGGGGAGGGA 64979
i ? v i- i ? i i i i i
L1M3d_5end#LI 455 GAACAAGNAGATGAAAAC-CCCCAGNTCTCAGCTTTCCCCTGAGGAGGAA 503
INTRON_3 64980 AAGAGCTGGAT 64990
? i i
L1M3d_5end#LI 504 AANAGTTGAAT 514
Matrix = 20p37g.matrix
Transitions / transversions = 1.84 (46 / 25)
Gap_init rate = 0.03 (8 / 300), avg. gap size = 2.12 (17 / 8)
2076 30.29 7.33 2.83 INTRON_3 64906 65571 334610 + L1M3d_5end LINE/L1 201 888 487 176
INTRON_3 64906 AGCTCCTTCCCCTGGCTCTACACAGAGCAAGCAGATGAATATA--CCCTA 64953
ii i i ? vi i ? v i v i v i v v -- i
L1M3d_5end#LI 201 AGTCCCTCCCCCCGGCWCAGCGCMGTGCGATCGGAAGGAAAAAACCCCCA 250
INTRON_3 64954 GTTCCCAGCTTCCCTCTGGGGAGGGAAAGAGCTGGATCACACATCCAATG 65003
ii i i i v i i v i i v i
L1M3d_5end#LI 251 ACTCCCGGCTTCTCCCAGGGGAGGAAAAGAGTTGGTTCGCACGTCAAGTG 300
INTRON_3 65004 CCCCAACTTCTCTG-TGGGCTGCC--AAAGAATGATTTCTTTCTTGCCTC 65050
? i i -v i --i i v vi v ?v
L1M3d_5end#LI 301 CCCCRACTTTTCCGAGGGGCTACCCAGAGGACTGTCTTCTGTCTTGCCWG 350
INTRON_3 65051 TTGTGGGGAACTAAGGGACCCAGCATACTTT-GCTGCCTGGGGACCAGTG 65099
ivi? i vv i vi i i v i - vii i ------
L1M3d_5end#LI 351 TCTCRGAGCTCTGATAGGCCCGGCATAATCTAGACACCCGGGG------G 394
INTRON_3 65100 CAGACAAAGACTGTGGTTTGAACTAGCACACTCTCATAGCCGCTTTCCAT 65149
vii i iv ii i i v iv - i? iv vi
L1M3d_5end#LI 395 AGAACAGAGATGGTGGTTTGGGCTGGTAGATGC-CATAGCTNCTCACCCC 443
INTRON_3 65150 GACTCAATACGGAACAAATGGGCAAAAAATCCTGCATCCCAGATTTTTCT 65199
vi ii i i?i iii vi iiv? i v ii i
L1M3d_5end#LI 444 TGCTCAGCACAGAACAAGNAGATGAAAACCCCCAGNTCTCAGCTTTCCCC 493
INTRON_3 65200 TGGGGAGGAAACGAGTTGGATAGA----------------------ACAT 65227
i v? i i ----------------------i
L1M3d_5end#LI 494 TGAGGAGGAAAANAGTTGAATGGACTGGAAAACAGAATTGAATGGAGCAT 543
INTRON_3 65228 CCAAAGATCCAACTTTTCCAGAGGCTGCCTAAGAGACTGGATTCAGTCTC 65277
vi i iivi -- ii i iv v v iiv
L1M3d_5end#LI 544 CCAACAATCCAGCTTTCTGGGAG--TGCCTAAGGAACCGATTGCATTTCA 591
INTRON_3 65278 GTTTATCTTGGAATGCTGACTGGACCCAGCATAATCTTGATGCCTAAGGG 65327
ii i vi vv i iv? ii? ? vi v? iiiiv i
L1M3d_5end#LI 592 ACTTGTCGCGCTACGCTGATANGATTNANCATACCCTANATGCTCGGCGA 641
INTRON_3 65328 TGGCTAAGAGCAAAGAAAGCAGGTTGAACCAGGACACAGGTTTGAAAAGT 65377
iv v i -- ? i i v iv i i ?
L1M3d_5end#LI 642 CTGCAAAGAACAAA--AANCAGGTTGGACTAGTACGAAGGTTTGAGAGGN 689
INTRON_3 65378 CCCCAGAATTTCTAGCTAGGCTGATTGAAGAGGGCCTTTACCTATACAAG 65427
i i i i iv i i iv ii i
L1M3d_5end#LI 690 CCCCAAAATCTCTGGCTAGGCTGATCGGTGAAGGTCTTCTCCTGCATAAG 739
INTRON_3 65428 GCCAGTCTGTGAA---------AGGTAACTG--TTCTCTAATGCACAGAT 65466
--------- ii -- v v i i
L1M3d_5end#LI 740 GCCAGTCTGTGAAGACTGAGAGAGGTGGCTGCTTTGTATAATGCGCAGAC 789
INTRON_3 65467 ACCATCACAAATAATCAAGGAAAATAAAAAAACAAGGATATATGTCCCAC 65516
vi i v i i v i v ? i v
L1M3d_5end#LI 790 ACCAATACAGAGAGTCAAGGAAAATAAAGAATCAGGGAAANATGTTCCAA 839
INTRON_3 65517 ACAAAGGAATAAAGTAAATTTCCTGAAAACAACTGTAATGAATTGGAGAT 65566
i iii v v vii iv i -
L1M3d_5end#LI 840 ACAAAGGAACAGGATAATTTTCCAGAAACTGACCCTAATAAATTGGAG-T 888
INTRON_3 65567 ACAGT 65571
-----
L1M3d_5end#LI 888 ----- 887
Matrix = 20p37g.matrix
Transitions / transversions = 2.13 (130 / 61)
Gap_init rate = 0.02 (13 / 665), avg. gap size = 4.31 (56 / 13)
+ 1634 17.2 1.8 13.4 INTRON_3 65572 65953 (334228) + MER2 DNA/TcMar-Tigger 3 345 (0) 86
ANNOTATION EVIDENCE:
1634 17.23 1.83 13.41 INTRON_3 65572 65953 334228 + MER2 DNA/TcMar-Tigger 3 345 0 139
INTRON_3 65572 GTTGGCCCTCCATATCTGTGGGTCCTGCATCCATGGATTCAACCAATGAC 65621
i i i i i i ivi
MER2#DNA/TcMa 3 GTCGGCCCTCCGTATCCGTGGGTTCCGCATCCGTGGATTCAACCAACCGC 52
INTRON_3 65622 AGATCAAAAATATTTTTTAAAAATTTATATCCCAAGGCTCAGCATCATGC 65671
i i ivvvi ---------------------------
MER2#DNA/TcMa 53 GGATCGAAAATATTCGGGGAAAA--------------------------- 75
INTRON_3 65672 AATATATGCATGTTTAAAGTAAAAAAAAATGCATCTGTATTGAACATATG 65721
--- v v v --------------- i i i i
MER2#DNA/TcMa 76 ---AAATGGATGGTT---------------GCGTCTGTACTGAACATGTA 107
INTRON_3 65722 CAGACTTTTTTGGG-GTTATTATTCCCTAAATAATA-----TAACAACTG 65765
vvv- i i ----- i
MER2#DNA/TcMa 108 CAGACTTTTTTCCTTGTCATTATTCCCTAAACAATACAGTATAACAACTA 157
INTRON_3 65766 TCTACATAGCATTTACATTGTAT-AGGTATTATAAGTAATCTAGAGATGA 65814
i -
MER2#DNA/TcMa 158 TTTACATAGCATTTACATTGTATTAGGTATTATAAGTAATCTAGAGATGA 207
INTRON_3 65815 TTTAAAGTACATGGGAGAATATGCATAGATTATATGCAAATACCATCCCA 65864
i i i i i i i iv
MER2#DNA/TcMa 208 TTTAAAGTATACGGGAGGATGTGCGTAGGTTATATGCAAATACTACGCCA 257
INTRON_3 65865 TATTATATTAGAGACTTGAGCATCCATGGATTTTGGTATCTGTGGAAGGT 65914
v ? i i i i ii
MER2#DNA/TcMa 258 TTTTATATMAGGGACTTGAGCATCCGTGGATTTTGGTATCCGCGGGGGGT 307
INTRON_3 65915 CCTGGAATCAACTCCTGATGGAAAATCCAGGGATGACTG 65953
i ii iv i v -i v i
MER2#DNA/TcMa 308 CCTGGAACCAATCCCCCACGGATA-CCGAGGGACGACTG 345
Matrix = 18p37g.matrix
Transitions / transversions = 2.73 (41 / 15)
Gap_init rate = 0.02 (6 / 381), avg. gap size = 8.83 (53 / 6)
+ 2076 30.3 7.3 2.8 INTRON_3 65954 66008 (334173) + L1M3d LINE/L1 889 958 (4933) 85
ANNOTATION EVIDENCE:
2076 30.29 7.33 2.83 INTRON_3 65954 66008 334173 + L1M3d_5end LINE/L1 889 958 417 177
INTRON_3 65954 TATATGACTTACCTGA------ATTC-----------TCTGACAGATAAT 65986
?i i ------ ----------- ? i - i-i
L1M3d_5end#LI 889 TATANAATTTACCTGACGAAGAATTCAAAACAATTGTTNTAA-AGATG-C 936
INTRON_3 65987 TCA-AAATAATCATAATGATGAT 66008
-i - i i v
L1M3d_5end#LI 937 TCATGAATAA-CATGATAAAGAT 958
Matrix = 20p37g.matrix
Transitions / transversions = 8.00 (8 / 1)
Gap_init rate = 0.11 (6 / 54), avg. gap size = 3.50 (21 / 6)
+ 2331 15.8 3.6 1.4 INTRON_3 66009 66425 (333756) C MSTB LTR/ERVL-MaLR (0) 426 1 87
ANNOTATION EVIDENCE:
2331 15.81 3.60 1.41 INTRON_3 66009 66425 333756 C MSTB LTR/ERVL-MaLR 1 426 0 140
INTRON_3 66009 TGTGTTGGTCTATT--TGTGTTACCATAAAGGAATAGCTGA--CTGGGTA 66054
i ii -- i i i i v --
C MSTB#LTR/ERVL 426 TGTGTTAGTCCGTTCTTGCGTTGCTATAAAGAAATACCTGAGGCTGGGTA 377
INTRON_3 66055 ATTTATAAAGAAAAGATGTTTTATTTTGGCTCATGGTTTTGTGGGCTGTA 66104
v v -- i i ii
C MSTB#LTR/ERVL 376 ATTTATAAAGAAAAGAGGTTTAATT--GGCTCACGGTTCTGCAGGCTGTA 329
INTRON_3 66105 CAGGAAGCATGGTGTTAGTATCTGCT-----TCTGGTGAGAGCCTCAGGA 66149
i iii i ----- -
C MSTB#LTR/ERVL 328 CAGGAAGCATGGCGCCGGCATCTGCTCGGCTTCTGGTGAG-GCCTCAGGA 280
INTRON_3 66150 ATTTTCCATTCATGGTGGAAGGTGATAGGGGAGCAGGCCCATATCACATG 66199
vi ? v ii i vi -- ii
C MSTB#LTR/ERVL 279 AGCTTNCAATCATGGCAGAAGGCGAAGGGGGAGCAGGC--ACGTCACATG 232
INTRON_3 66200 G----AACGGGAGCAAGACAGAGAGAGGGAGAAGTGTCACACTCTTTTAC 66245
---- i v i - i i ? v
C MSTB#LTR/ERVL 231 GCGAGAGCGGGAGCAAGAGAGAGAGGGGG-GAGGTGCCANACTCTTTTAA 183
INTRON_3 66246 ATAACCAGATCTTGTGTGAACTGA--GAGCAAGAATTCACTCATTACTGT 66293
i i i i -- i i i iiv
C MSTB#LTR/ERVL 182 ACAACCAGATCTCGCGTGAACTAACAGAGCGAGAACTCACTCATCACCAA 133
INTRON_3 66294 GAGTAGGGCATGAAGCCACTCGTGAGGGATCCACCTCCATGACTCAAACA 66343
i v v iiv i i i i ii
C MSTB#LTR/ERVL 132 GGGGATGGCGCCAAGCCATTCATGAGGGATCCGCCCCCATGATCCAAACA 83
INTRON_3 66344 CCTACTACCAGGCCCCACCTCCAACAGTGGGGATTTCATTTCAACATGAG 66393
v i v iv
C MSTB#LTR/ERVL 82 CCTCCCACCAGGCCCCACCTCCAACACTGGGGATCACATTTCAACATGAG 33
INTRON_3 66394 ATTTGGAGGTGACAAACATCCAAACCATATCA 66425
v
C MSTB#LTR/ERVL 32 ATTTGGAGGGGACAAACATCCAAACCATATCA 1
Matrix = 18p37g.matrix
Transitions / transversions = 2.94 (47 / 16)
Gap_init rate = 0.02 (9 / 416), avg. gap size = 2.33 (21 / 9)
+ 2076 30.3 7.3 2.8 INTRON_3 66426 66480 (333701) + L1M3d LINE/L1 959 1012 (4879) 85
ANNOTATION EVIDENCE:
2076 30.29 7.33 2.83 INTRON_3 66426 66480 333701 + L1M3d_5end LINE/L1 959 1012 363 178
INTRON_3 66426 TGATCAATGAAATCAGGAGAACAATGTATTAACAAAGTGAAAATTTCAAC 66475
- v vii i i ii v i
L1M3d_5end#LI 959 -GCTCACCAAGATCAGGAAAACAATACATGAACAAAGTGAGAATTTCAAC 1007
INTRON_3 66476 ATAGA 66480
v
L1M3d_5end#LI 1008 AAAGA 1012
Matrix = 20p37g.matrix
Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1)
+ 228 13.5 0.0 0.0 INTRON_3 66501 66537 (333644) + (CA)n Simple_repeat 2 38 (0) 88
ANNOTATION EVIDENCE:
228 13.51 0.00 0.00 INTRON_3 66501 66537 333644 + (CA)n Simple_repeat 2 38 142 260
INTRON_3 66501 ACACACACACACACACATATATATACACACATACACA 66537
i i i i i
(CA)n#Simple_ 2 ACACACACACACACACACACACACACACACACACACA 38
Matrix = Unknown
Transitions / transversions = 0.0 (5 / 0)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 212 26.0 2.7 0.0 INTRON_3 66552 66624 (333557) + (TATATG)n Simple_repeat 1 75 (0) 89
ANNOTATION EVIDENCE:
212 26.03 2.74 0.00 INTRON_3 66552 66624 333557 C (CATATA)n Simple_repeat 67 141 39 261
INTRON_3 66552 ATATATATGGATATTTATACACCTGTATATATTTA-ATGGATCTAAATAT 66600
i v v iiiv i i v - v v iv
C (CATATA)n#Sim 141 ATGTATATGTATATGTATATGTATATGTATATGTATATGTATATGTATAT 92
INTRON_3 66601 GAA-ATGGATGTGTGTATATATATG 66624
v - v i i i
C (CATATA)n#Sim 91 GTATATGTATATGTATATGTATATG 67
Matrix = Unknown
Transitions / transversions = 1.11 (10 / 9)
Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.00 (2 / 2)
+ 252 12.2 0.0 0.0 INTRON_3 66633 66673 (333508) + (CA)n Simple_repeat 2 42 (0) 90
ANNOTATION EVIDENCE:
252 12.20 0.00 0.00 INTRON_3 66633 66673 333508 + (CA)n Simple_repeat 2 42 138 255
INTRON_3 66633 ACACACACATATACACATACACACACATACACTCACACACA 66673
i i i i v
(CA)n#Simple_ 2 ACACACACACACACACACACACACACACACACACACACACA 42
Matrix = Unknown
Transitions / transversions = 4.00 (4 / 1)
Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0)
+ 2915 26.1 1.3 1.3 INTRON_3 66679 67551 (332630) + L1MB1 LINE/L1 2226 3171 (4394) 91
ANNOTATION EVIDENCE:
2915 25.94 1.08 1.08 INTRON_3 66679 67508 332673 + L1M4c_5end LINE/L1 1043 1872 628 179
INTRON_3 66679 AAACAAATCTTGAAACTGAAGAATAGAATAATTGAACTAAAAAATTCAAT 66728
v ii i i i i v i v i v
L1M4c_5end#LI 1043 AAAGAAATTCTGGAGCTGAAAAGTACAATAACTGAAATGAAAAATTCACT 1092
INTRON_3 66729 GGGAGG-TTGAATAGCAGACTAGATCAATCAGAAGAAAGGATCAGTAAAC 66777
i ii - v vi i v v iv i i
L1M4c_5end#LI 1093 AGAGGGATTCAAAGGCAGATTTGAGCAGGCAGAAGAAAGAATCAGCAAAC 1142
INTRON_3 66778 TCGAAGACAAATTACCAGAAATTATTCAGTCAGATGAACAAAAAGAAAAA 66827
i i iivi v i v v v i
L1M4c_5end#LI 1143 TTGAAGATAGGACAACGGAAATTATTGAGTCTGAGGAACAGAAAGAAAAA 1192
INTRON_3 66828 CAAGTGAAAAAGAATGAAGAAAGCTTAAGAGACTTATGGAACTCCATGAA 66877
vi v i i i v i i i i i i v v
L1M4c_5end#LI 1193 AGATTGAAGAAAAGTGAACAGAGCCTAAGGGACCTGTGGGACACCATCAA 1242
INTRON_3 66878 AGCAGACCAAGAGACATATTATGAATGTTCCTGATGGAGAAGAGGTGGAG 66927
- i v v ii i iiv i v v ivi
L1M4c_5end#LI 1243 -GCGGACCAACATACGCATTGTGGGAGTCCCAGAAGGAGAAGAGAGAGAG 1291
INTRON_3 66928 AAAGGGGGAAGAAAGCTTATTCAAAGAAGTAATGGCTGAAAACTTTTCAA 66977
v - i vv ii i ii
L1M4c_5end#LI 1292 AAAGGGGCA-GAGAGAATATTTGAAGAAATAATGGCTGAAAACTTCCCAA 1340
INTRON_3 66978 ATCTGGTAAAGAAACTTGA-CATCCAGATCCAGGAGCCCTAACAGACCTC 67026
i i i - i v -i vv v i iv ii ii ii
L1M4c_5end#LI 1341 ATTTGATGAA-AGACATGAATATAAACATCCAAGAAGCTCAACGAACTCC 1389
INTRON_3 67027 AAATAAAATGAATCCAAAGACATCCACACCAAGACACAATGTAGTCAAAT 67076
i ii ii v i i v i i i
L1M4c_5end#LI 1390 AAGTAGGATGAACTCAAAGAGACCCACACCGAGACACATTATAATCAAAC 1439
INTRON_3 67077 TGTCAAAAATCAAAGAGAAAGAGAACCTTTTGAAAGCAGTAAGAGAAGAA 67126
? i ii v ivv i i ii i
L1M4c_5end#LI 1440 TNTCGAAAGCCAAAGACAAAGAGAGAATCTTGAAAGCAGCAAGAGAGAAG 1489
INTRON_3 67127 CAATTTGTCATATACAAGAAAACCCTCATAAGACTA-CAGTGTATTTCTC 67175
i i ii i ii v iiv i - iiv
L1M4c_5end#LI 1490 CGACTCATCACATACAAGGGATCCTCAATAAGATTATCAGCAGATTTCTC 1539
INTRON_3 67176 AGCAGAAACCCTGCAGGCCAGAAGGAAAAGGGATGATATATTCAAAGTGC 67225
v ii v v iv vi
L1M4c_5end#LI 1540 ATCAGAAACTTTGGAGGCCAGAAGGCAGTGGGCCGATATATTCAAAGTGC 1589
INTRON_3 67226 TGAAGGAAACAAAAAGGCCAACCAAGAATCGTATACCTGGCAAAATTGTC 67275
i i - vv i v i i i
L1M4c_5end#LI 1590 TAAAAGAAA-AAAACTGTCAACCAAGAATCCTATATCCGGCAAAACTGTC 1638
INTRON_3 67276 CTTCAATAATGATGGAGATA--AAGACTTTCTCAGGTAAACAAAAGCTGA 67323
v i v v -- v i i
L1M4c_5end#LI 1639 CTTCAAAAGTGAGGGAGAAATTAAGACATTCCCAGATAAACAAAAGCTGA 1688
INTRON_3 67324 GAGAGTTCTTTGCGACCCAGACCTGCCTTAAAAGACTTATTAAAGGGAGT 67373
i iv i v i- i iv vv ii ?
L1M4c_5end#LI 1689 GGGAGTTTGTTACCACT-AGACCTGCCCTGCAAGAAATGCTNAAGGGAGT 1737
INTRON_3 67374 TCTTTAAGTGAAAACAAAAGGACACCTAACAGTAATACAAAAGCATAGGA 67423
i vi i vvi ii ivi ivii iv i v
L1M4c_5end#LI 1738 CCTGCAGGGTGAAATGAAAGGACACTAGACAGTAACTTGAAGCCGTATGA 1787
INTRON_3 67424 AAATGTAAA-ATTTGCTAGTAAAGGTAAATATATAGATAAATACAGAA-- 67470
i vi - i --i i i ii v i i --
L1M4c_5end#LI 1788 AGAAATAAAGATCT--CAGTAAAGGTAAATACATGGGCAATTATAAAAGC 1835
INTRON_3 67471 TAATGCAATATTGTAATGGTGGTAGGTAAGTC-ACTTTT 67508
i -- v iii vv v -
L1M4c_5end#LI 1836 TAGT--ATTATTGTAACAATGGTTTGTAACTCCACTTTT 1872
Matrix = 20p37g.matrix
Transitions / transversions = 1.97 (140 / 71)
Gap_init rate = 0.02 (14 / 829), avg. gap size = 1.29 (18 / 14)
1921 28.87 6.07 5.14 INTRON_3 66683 67551 332630 + L1M1_5end LINE/L1 2305 3171 504 180
INTRON_3 66683 AAATCTTGAAACTGAAGAATAGAATAATTGA---ACTAAAAAATTCAATG 66729
ii i ii i i---i --- i i v - v
L1M1_5end#LIN 2305 AAATTCTGGAGTTGAAAAATG---CAATTGACATACTGAAGAATGCA-TC 2350
INTRON_3 66730 GGAGGTTG--AATAGCAGACTAGATCAATCAGAAGAAAGGATCAGTAAAC 66777
i vi v-- i v v v i i i i
L1M1_5end#LIN 2351 AGAGTCTCTTAACAGCAGAATTGATCAAGCAGAAGAAAGAATTAGTGAGC 2400
INTRON_3 66778 TCGAAGACAAATTACCAGAAATTATTCAGTCAGATGAACAAAAAGAAAAA 66827
i iii iiv v iv v ivv
L1M1_5end#LIN 2401 TTGAAGACAGGCTATTTGAAAATACACAGTCAGAGGAGACAAAAGAAAAA 2450
INTRON_3 66828 CAAGTGAAAAAGAATGAAGAAAGCTTAAGAGACTTATGGAA---CTCCAT 66874
vi i i v v i vi ii vii --- ii v
L1M1_5end#LIN 2451 AGAATAAAAAAGAATGAAGCACGCCTACAAGATCTAGAAAATAGCCTCAA 2500
INTRON_3 66875 GAAAGCAGACC-AAGAGACATATTATGAATGTTCCTGATGGAGAAGAGGT 66923
i ii i i - ----- --- vi i i --- i
L1M1_5end#LIN 2501 AAGGGCAAATCTAAGAG-----TTAT---TGGCCTTAA---AGAGGAGGT 2539
INTRON_3 66924 GGAGAAAG-----GGGGAAGAAAGCTTATTCAAAGAAGTAATGGCTGAAA 66968
i i ----- v i iii ii v i
L1M1_5end#LIN 2540 AGAGAGAGAGATAGGGGTAGAAAGTTTATTCAAAGGGATAATAACAGAGA 2589
INTRON_3 66969 ACTTTTCAAATCTGG-TAAAGAAACTTGACATCCAGATCCAGGAGCCCTA 67017
ii i i -v v - ii i i ii v i ivvi
L1M1_5end#LIN 2590 ACTTCCCAAACCTAGAGAAAGATA-TCAATATTCAAGTACAAGAAGGTTA 2638
INTRON_3 67018 ACAGACCTCAAATAAAATGAATCCAAAGACATCCACACCAAGACAC--AA 67065
vvii vi ii i v v i viv i vi i i--
L1M1_5end#LIN 2639 TAGAACACCAAGCAGATTTAACCCAAAGAAGACTACCTCAAGGCATTTAA 2688
INTRON_3 67066 TGTAGTCAAATTGTCAAAAATCAAAGAGAAAGAGAACCTTTTGAAAGCAG 67115
-- i i vi ii i v i ivv ii i
L1M1_5end#LIN 2689 T--AATCAAACTCCCAAAGGTCAAGGATAAAGAAAGGATCCTAAAAGCAG 2736
INTRON_3 67116 TAAGAGAAGAACAATTTGTCATATACAAGAAAACCCTCATAAGACTA-CA 67164
i i iv ivvi v i vii i i iv v v i-
L1M1_5end#LIN 2737 CAAGAGAAAAGAAACAAATAACATACAATGGAGCTCCAATACGTCTGGCA 2786
INTRON_3 67165 GTGTATTTCTCAGCAGAAACCCTGCAGGCCAGAAGGAAAAGGGATGATAT 67214
iiv i i ii i i i ii iv v i
L1M1_5end#LIN 2787 GCAGACTTTTCAGTGGAAACCTTACAGGCCAGGAGAGAGTGGCATGACAT 2836
INTRON_3 67215 ATTCAAAGTGCTGAAGGAAACAAAAAGGCCAACCAAGAATCGTATACCTG 67264
i - vvvii v v v i ii
L1M1_5end#LIN 2837 ATTTAAAGTGCTGAAGGAAA-AAAACTTTTACCCTAGAATAGTATATCCA 2885
INTRON_3 67265 GCAAAATTGTCCTTCAATAATGATGGAGA--TAAAGACTTTCTCAGGTAA 67312
ii v i vv v -- i ii
L1M1_5end#LIN 2886 GTGAAAATATCCTTCAAACATGAAGGAGAAATAAAGACTTTCCCAGACAA 2935
INTRON_3 67313 ACAAAAGCTGAGAGAGTTCTTTGCGAC-CCAGACCTGCCTTAAAAGACTT 67361
i v v -- i - i i v vv
L1M1_5end#LIN 2936 ACAAAAGCTGAGGGATTTCAT--CAACACCAGACCTGTCCTACAAGAAAT 2983
INTRON_3 67362 ATTAAAGGGAGTTCTTTAAGTGAAAACAAAAGGACACCTAAC-AGTAATA 67410
ii i vivi v i- i- i
L1M1_5end#LIN 2984 GCTAAAGGGAGTTCTTCAATCTGAAAGAAAAGGACAT-TAATGAGCAATA 3032
INTRON_3 67411 CAAAAGCATAGGAAAATGTAAAATTTGCTAGTAAAGGTAAATATATAGAT 67460
vi v vv ii ii i ii i vi i i i v
L1M1_5end#LIN 3033 AGAAATCATCTGAAGGTACAAAACTCACTGGTAATAGTAAGTACACAGAA 3082
INTRON_3 67461 AAATACAGAATAATGCAATATTGTAATGGTGGTAGGTAAGTCACTTTTAA 67510
i v ii i i v iv iii iv v
L1M1_5end#LIN 3083 AAACACAGAATATTATAACACTGTAATTGTGGTGTGTAAACTACTCATAT 3132
INTRON_3 67511 CTCTAGTGTAAAAGCTAAAAGACAAAAGTATGAAAAATAGA 67551
iv iv ii ii vvv v --
L1M1_5end#LIN 3133 CTTAAGTAGAAAGACTAAAAGATGAACCAATCAAAAATA-- 3171
Matrix = 20p37g.matrix
Transitions / transversions = 1.98 (168 / 85)
Gap_init rate = 0.03 (22 / 868), avg. gap size = 2.09 (46 / 22)
+ 1902 18.2 0.0 0.0 INTRON_3 67552 67842 (332339) + AluSz6 SINE/Alu 2 292 (20) 92
ANNOTATION EVIDENCE:
1729 19.59 0.00 0.00 INTRON_3 67552 67842 332339 + AluSx SINE/Alu 2 292 20 125
INTRON_3 67552 GTCAGGCATGGAGGCTCACACCTGTAATCCCAGTACTTTGGGAAGCCGAG 67601
i i ii v i i i
AluSx#SINE/Al 2 GCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG 51
INTRON_3 67602 GCAGACAGATCACCTGAGACCAGGAATTCAAGACCAGCCTGACCAATGTG 67651
i i i ii i i i ii
AluSx#SINE/Al 52 GCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATG 101
INTRON_3 67652 ACAAAAGCCCGTCTCCACTAAAAATATAAAAGTTAGCCAGGTGTGGTGGC 67701
iii v i i i i i
AluSx#SINE/Al 102 GTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGC 151
INTRON_3 67702 TCATGCCTGTGGTCCCAGCTACTGGGGAGGCTGAGGAACCAGAATTGCTT 67751
v ii ii v v vv i
AluSx#SINE/Al 152 GCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTT 201
INTRON_3 67752 GAGCACAGAAGGCAGAAGTTGTAGTGAGCTGAGATCACACCACTGCTCTC 67801
i v i i i i i i i i v
AluSx#SINE/Al 202 GAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 251
INTRON_3 67802 CAGCCTGGGTGAGAAAGCAAAACTATGTATCAAAAAGAAAA 67842
i v i i i vi v i
AluSx#SINE/Al 252 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAA 292
Matrix = 14p37g.matrix
Transitions / transversions = 3.75 (45 / 12)
Gap_init rate = 0.00 (0 / 290), avg. gap size = 0.0 (0 / 0)
+ 7940 16.6 3.2 1.5 INTRON_3 67843 70581 (329600) + L1MB1 LINE/L1 3172 5962 (1597) 91
ANNOTATION EVIDENCE:
1921 28.87 6.07 5.14 INTRON_3 67843 68323 331858 + L1M1_5end LINE/L1 3172 3667 8 181
INTRON_3 67843 TATGA--AAAATAACT---------ATAAA---TATAAAAATGTGTGAAT 67878
- i -- v i --------- i --- i v vi i i
L1M1_5end#LIN 3172 -ATAACTACAACAACTTTTCAAGACATAGACAGTACAATAAGATATAAAT 3220
INTRON_3 67879 TGATACA-CAAAA---TAAAAAGATGTAAAGGGA-GAAGTAAAAGTGTAC 67923
v v - --- ---iiii - v v
L1M1_5end#LIN 3221 AGAAACAACAAAAAGTTAAAAAG---CGGGGGGACGAAGTTAAAGTGTAG 3267
INTRON_3 67924 AGGTTTT-----TCTGCAATCAAAGTTACATTATCAGCTTA---AAACAG 67965
v ----- i v -- ---v i - i iv i i--- v
L1M1_5end#LIN 3268 AGTTTTTATTAGTTTTC--TC---TTTGC-TTGTTTGTTTGTGCAATCAG 3311
INTRON_3 67966 -ATTA--TTGTAACTA---TAAGATATTTTAT-GTAAGCTCCATGGCATT 68008
-i -- v ii --- i v vvi -i ---- ivi
L1M1_5end#LIN 3312 TGTTAAGTTGTCATCAGTTTAAAATAATGGGTTATAAG----ATATTATT 3357
INTRON_3 68009 CACAAAGAAAACACCT-ATAGAAGATACACAAAAGAAAAAAAGAACCAAA 68057
ii i------- - i v --- viv vv ---- --
L1M1_5end#LIN 3358 TGCAAG-------CCTCATGGTA---ACCTCAAATCAAAAAA----CA-- 3391
INTRON_3 68058 GTATATCA-ATACAAAAAAAAATCAATGAAAAACAAGGGA---AGACA-- 68101
- i v - v ----- i i ii --- i --
L1M1_5end#LIN 3392 -TACAACAGATACACAAAAAA-----TAAAAAGCAAGAAATTAAAACATA 3435
INTRON_3 68102 --GCAAGAGAGGAGAAGAGGGAC-AAAAGAATTACAAGACAAACAGAAAG 68148
--i v ii vv vvvvv - i ----- iiv i
L1M1_5end#LIN 3436 CCACCAGAGAAAATCACCTTCACTAAAAGGA-----AGACAGGAAGGAAG 3480
INTRON_3 68149 CAATGAAAAAATTGAA------AAAACAATGAGAAAAACCTATGAAAAAA 68192
v v ii vv ------ iv - vv - v
L1M1_5end#LIN 3481 GAAAGAAGGAAGAGAAGACCACAAAACAACCAGAAAA-CAAAT-AACAAA 3528
INTRON_3 68193 ATGG----------TCCTTTCCTATCAGTGGTTACATTACATGTAAGTGG 68232
---------- v i i ii v iv i
L1M1_5end#LIN 3529 ATGGCAGGAGTAAGTCCTTACTTATCAATAATAACATTGAATGTAAATGG 3578
INTRON_3 68233 TTTGAACTACTCAGTCAGAAGGTATAGTGTGGCTGAATGAATTAAAAAAC 68282
vi i vii i i ii v i v
L1M1_5end#LIN 3579 ACTAAACTCTCCAATCAAAAGACATAGAGTGGCTGAATGGATAAAAAAAC 3628
INTRON_3 68283 AAGATCCAACTATATGTATTGTCTATAAGAAACTCATTTTA 68323
i v v -- i i v i i
L1M1_5end#LIN 3629 AAGACCCAACGATCTGT--TGCCTACAAGAAACACACTTCA 3667
Matrix = 20p37g.matrix
Transitions / transversions = 1.29 (66 / 51)
Gap_init rate = 0.07 (34 / 480), avg. gap size = 3.09 (105 / 34)
5593 14.91 2.74 0.29 INTRON_3 68196 69217 330964 + L1M3_orf2 LINE/L1 14 1060 2228 182
INTRON_3 68196 GTCCTTTCCTATCAGTGGTTACATTACATGTAAGTGGTTTGAACTACTCA 68245
i i ii v v i v i v i
L1M3_orf2#LIN 14 GTCCTTCCCTATCAATAATTACTTTAAATGTAAATGGATTAAACTCCCCA 63
INTRON_3 68246 GTCAGAAGGTATAGTGTGGCTGAATGAATTAAAAAACAAGATCCAACTAT 68295
i i ii v i v ?
L1M3_orf2#LIN 64 ATCAAAAGACATAGAGTGGCTGAATGGATAAAAAAACANGATCCAACTAT 113
INTRON_3 68296 ATGTATTGTCTATAAGAAACTCATTTTAAATTGAAACACATACATAGGCT 68345
i-- i ? i i v iv i
L1M3_orf2#LIN 114 ATGC--TGTCTACAAGANACTCACTTTAGATTTAAGGACACACATAGGCT 161
INTRON_3 68346 AAAAGTGAAGGGATAGAAAAATATATTCCATGTAAATGGTAACCAAAAGA 68395
i i v i
L1M3_orf2#LIN 162 GAAAGTGAAGGGATGGAAAAAGATATTCCATGCAAATGGTAACCAAAAGA 211
INTRON_3 68396 GAGCAG-AGTGGCTATA------TAAGACAAAATAGACTGTTAGTCATAA 68438
- ------ v ? v v v
L1M3_orf2#LIN 212 GAGCAGGAGTGGCTATACTTATATCAGANAAAATAGACTTTAAGTCAAAA 261
INTRON_3 68439 ACTGTTACAAGAGACAAAA---GATGTTATATAATAATAAAAGAGTAAAT 68485
i ? i--- ii i i v
L1M3_orf2#LIN 262 ACTGTCANAAGAGACAAAGAAGGACATTATATAATGATAAAAGGGTCAAT 311
INTRON_3 68486 TCACCAAGAAGATATAAGAATTATAAATATATATGCACCCAACATGAGAG 68535
? i i v v
L1M3_orf2#LIN 312 TCANCAGGAAAATATAACAATTATAAATATATATGCACCCAACATCAGAG 361
INTRON_3 68536 CACTTAAATATTTAAAACAAACATCGACAGAATTGAAGAGAGAAGTGGAT 68585
i v i i i i i i i
L1M3_orf2#LIN 362 CACCTAAATATATAAAGCAAACATTGACAGAACTGAAGGGAGAAATAGAC 411
INTRON_3 68586 GACAATCCTATAATAGTGGGACACTTCAGTATCCCACTTTCAATAATCAA 68635
ii iv v i v i i vi
L1M3_orf2#LIN 412 AGCAACACAATAATAGTAGGAGACTTCAATACCCCACTTTCAATAATGGA 461
INTRON_3 68636 TAGAACATCCAGATAGAA-ATCAATAAGGAAACAGCTGACTTGAAAAACA 68684
i - vv v
L1M3_orf2#LIN 462 TAGAACATCCAGACAGAAGATCAATAAGGAAACAGAGGACTTGAACAACA 511
INTRON_3 68685 CTATAGACCAAATGGACGTAACACACATATATCAATTATTTAACCCAACA 68734
v v ivi vi iv
L1M3_orf2#LIN 512 CTATAGACCAAATGGACCTAACAGACATATACAGAACATTCCACCCAACA 561
INTRON_3 68735 ACAGAGGAATATATATTTTTCTCAAAGGTAC-CA-AACATTCTCCAGGCT 68782
i vi i i i i? i - - v
L1M3_orf2#LIN 562 GCAGCAGAATACACATTCTTCTCAAGNGCACACAGAACATTCTCCAGGAT 611
INTRON_3 68783 AGATAATATGTTTAGCCACAAATCAAGTCTTAGCAAATTTAGGAATGTTA 68832
v i vi i v i i vi i
L1M3_orf2#LIN 612 AGATCACATGTTAGGTCACAAAACAAGTCTTAACAAATTTAAGAAGATTG 661
INTRON_3 68833 AAATCATACCAAGTATCTTTTCTGATCACAGTGGAATGGAAATTAGAAAT 68882
i i i - i
L1M3_orf2#LIN 662 AAATCATACCAAGTATCTTTTCCGACCACAATGGAATG-AAACTAGAAAT 710
INTRON_3 68883 AAACAGTAGATGGGAAACTGGAAAATTCACAAACATGTG-AAATTAAACA 68931
v i i v i i -
L1M3_orf2#LIN 711 CAATAGCAGAAGGAAAACTGGAAAATTCACAAATATGTGGAAATTAAACA 760
INTRON_3 68932 GCATACCCCTGAAGAGCTAATGGATCAAAGAAGAAATCATAAGGGAAATT 68981
i i i v i i i v
L1M3_orf2#LIN 761 ACACACTCCTGAACAACCAATGGGTCAAAGAAGAAATCAAAAGGGAAATT 810
INTRON_3 68982 AGAAAATATCTTGAGAGAAATGAAAATGAAAACACAACATACCAAA-CCT 69030
i v i - i
L1M3_orf2#LIN 811 AGAAAATATCTCGAGACAAATGAAAATAAAAACACAACATACCAAAACTT 860
INTRON_3 69031 ATAAGATGCAGCAAAAGTGATCCTAAGAGAAAAGTTGATAGTGATAAATG 69080
ii iii v ii v
L1M3_orf2#LIN 861 ATGGGATGCAGCAAAAGCAGTACTAAGAGGGAAGTTTATAGTGATAAATG 910
INTRON_3 69081 TCTGTATTAAAAAAGAA-AGAGATCTCAAGTAA----CCTAACTTTATAC 69125
i ii - i i ---- i
L1M3_orf2#LIN 911 CCTACATTAAAAAAGAAGAAAGATCTCAAATAAACAACCTAACTTTACAC 960
INTRON_3 69126 CTCAAAGAATTAGAAAAAGAA---CAAACTAAGCCCAAAG---GTAGAAA 69169
i i --- --- i i
L1M3_orf2#LIN 961 CTCAAGGAACTAGAAAAAGAAGAACAAACTAAGCCCAAAGTTAGCAGAAG 1010
INTRON_3 69170 G--GGAAGAAATAAAGATTAGAGCAGAAGTAAATGTAATAGAGAATAGAA 69217
-- iv i iv i ?
L1M3_orf2#LIN 1011 GAAGGAAATAATAAAGATTAGAGCAGAAATAAATAAAATAGAAANTAGAA 1060
Matrix = 20p37g.matrix
Transitions / transversions = 2.30 (101 / 44)
Gap_init rate = 0.01 (15 / 1021), avg. gap size = 2.07 (31 / 15)
7940 14.96 2.81 1.45 INTRON_3 69089 70581 329600 + L1M3_orf2 LINE/L1 922 2434 854 183
INTRON_3 69089 AAAAAAGAAAGAGATCT--CAAGTAACCTAACTTTATACCTCAAAGAATT 69136
i vv v--i ii i i i
L1M3_orf2#LIN 922 AAAGAAGAAAGATCTCAAATAAACAACCTAACTTTACACCTCAAGGAACT 971
INTRON_3 69137 AGAAAAAGAA---CAAACTAAGCCCAAAG---GTAGAAAG--GGAAGAAA 69178
--- --- i i -- iv
L1M3_orf2#LIN 972 AGAAAAAGAAGAACAAACTAAGCCCAAAGTTAGCAGAAGGAAGGAAATAA 1021
INTRON_3 69179 TAAAGATTAGAGCAGAAGTAAATGTAATAGAGA-----------ATAGAA 69217
i iv i -----------
L1M3_orf2#LIN 1022 TAAAGATTAGAGCAGAAATAAATAAAATAGAAANTAGAAAAACAATAGAA 1071
INTRON_3 69218 GAGACCAACAAAACTAATAGTGGGTTTGTTTAAAAAGAGCAACAAAATCA 69267
i i i i v v - i v? ii
L1M3_orf2#LIN 1072 AAAATCAACGAAACTAAGAGTTGGTTT-TTTGAAAAGATNAACAAAATTG 1120
INTRON_3 69268 ACAAATCTTTAGCAAGATTAACCAAGAAAGGGGAGAGGGTTCAAATAAAT 69317
i v i vv i i i ---i
L1M3_orf2#LIN 1121 ACAAACCTTTAGCTAGACTAAGAAAAAAAGAGAAGA---CTCAAATAAAT 1167
INTRON_3 69318 AAAATTATAAATGATAGAGGAGACATTACAATTGATACCACAGAAATACA 69367
i v v i i v
L1M3_orf2#LIN 1168 AAAATCAGAAATGAAAGAGGAGACATTACAACTGATGCCACAGAAATAAA 1217
INTRON_3 69368 AAGAATCATAAGAGACTACTATGAACAATTACATGCCAACAAATTGAAAA 69417
i i i i v
L1M3_orf2#LIN 1218 AAGGATCATAAGAGACTACTATGAACAATTATACGCCAACAAATTGGATA 1267
INTRON_3 69418 ACCTAGAAGAAATGGGCATATTCTTAGATATAT-CAGTCTACCAAGACTC 69466
ii v i v i - ii ?
L1M3_orf2#LIN 1268 ACCTAGAAGAAATGGATAAATTCCTAGAAACATACAACCTACCAAGACTN 1317
INTRON_3 69467 ACTCATGAAGGATTAGAAAATCTGGACGGGCCAATAATGAGTAAAGAGAT 69516
v i v i i i i ? i? i
L1M3_orf2#LIN 1318 AATCATGAAGAAATAGAAAACCTGAACAGACCNATAACNAGTAAGGAGAT 1367
INTRON_3 69517 TGAATCAGTAATCAAAAACCTCCCAACAAA---AAGCCTAGTGCTAGGTA 69563
--- i i vi i i i
L1M3_orf2#LIN 1368 TGAATCAGTAATCAAAAACCTCCCAACAAAGAAAAGTCCAGGACCAGATG 1417
INTRON_3 69564 GCTTCACTGATGAATTCTACCAAACATTTAAAGAAGAACTAATACTGATC 69613
i i i ii
L1M3_orf2#LIN 1418 GCTTCACTGGTGAATTCTACCAAACATTTAAAGAAGAATTAATGCCAATC 1467
INTRON_3 69614 CTTCTCAAACTCGTCCAAAAACATTGAAGAGGAGGGAACACTTCCAAGTC 69663
v - iii
L1M3_orf2#LIN 1468 CTTCTCAAACTCTTCCAAAAA-ATTGAAGAGGAGGGAACACTTCCAAACT 1516
INTRON_3 69664 CATTT-ATGAGGCTAGCATTACCCTGATACCAGAGCTATACAAAGACACT 69712
- i i i v ?
L1M3_orf2#LIN 1517 CATTTTATGAGGCCAGCATTACCCTGATACCAAAGCCAGACAAAGACACN 1566
INTRON_3 69713 ACAAGAAAAGAAAACTACTGGCCAATATCCCAGATAAACATAGATGCAAA 69762
v v i i
L1M3_orf2#LIN 1567 ACAAGAAAAGAAAACTACAGGCCAATATCCCTGATGAATATAGATGCAAA 1616
INTRON_3 69763 AATCCTTAACAAAATACTAGCAAACTGAATGAAAGAGCACATTAATAGGA 69812
i i vv v v
L1M3_orf2#LIN 1617 AATCCTCAACAAAATACTAGCAAACCGAATTCAACAGCACATTAAAAGGA 1666
INTRON_3 69813 AAATACACCATGATTAGATGGGATTTTTCCCTGAGATGCAAGGATGATTC 69862
vv ii ii v i i
L1M3_orf2#LIN 1667 TCATACACCATGACCAAGTGGGATTTATCCCTGGGATGCAAGGATGGTTC 1716
INTRON_3 69863 AGCTTACAAAAGTCAGTTAATGCAATATACCCCATAAACAGAATGAAGAA 69912
i v i i i i ii i v v i
L1M3_orf2#LIN 1717 AACATACGAAAATCAATCAATGTGATACACCACATTAACAGAATGAAGGA 1766
INTRON_3 69913 TAAAAATCTCATAATTATCTCAATAGATGCAGAAAAAAAATTTGACAAAA 69962
v i i iv
L1M3_orf2#LIN 1767 TAAAAATCACATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAAA 1816
INTRON_3 69963 TTCAACACGCTTTTATGATAAAAACTC--AATATATTAACTGGGAAAAGA 70010
iv i -- i ---- i v
L1M3_orf2#LIN 1817 TTCAACATCCTTTCATGATAAAAACTCTCAACA----AACTAGGAATAGA 1862
INTRON_3 70011 AGGACATTACCTCAACATAAT---GGCCATATATGAAAAGCCCACATTTA 70057
v? --- vi
L1M3_orf2#LIN 1863 AGGAANTTACCTCAACATAATAAAGGCCATATATGAAAAGCCCACAGCTA 1912
INTRON_3 70058 ACATTATATTTAATGGTGAAAAACTGAAAATTTTCCCTGTAGGATTGGGA 70107
i i i ii i v i ii
L1M3_orf2#LIN 1913 ACATCATACTCAATGGTGAAAAACTGAAAGCTTTTCCTCTAAGATCAGGA 1962
INTRON_3 70108 ACAAGGCA-TAATGCCAACTCACATCGCTTCTGTTCAAAATTATACTGGA 70156
-vi v v i i i v vi
L1M3_orf2#LIN 1963 ACAAGGCAAGGATGCCCACTCTCACCACTTCTATTCAACATAGTACTGGA 2012
INTRON_3 70157 AGTCCTAGCCAGAGCAAATAGGCAAGAAAAAGAAA----AGTCAACCAAA 70202
v ---- v v
L1M3_orf2#LIN 2013 AGTCCTAGCCAGAGCAATTAGGCAAGAAAAAGAAATAAAAGGCATCCAAA 2062
INTRON_3 70203 TCAGAAAGGAAGAAGTAAAAATTATTTCTGTTGGCAGATGACATTATCTT 70252
i - ii v v
L1M3_orf2#LIN 2063 TCGGAAAGGAAGAAGTAAAA-TTATCCCTGTTTGCAGATGACATGATCTT 2111
INTRON_3 70253 ACATGTAGAAAATTAGAAGGATTCCACCAAAAAAAAAAAAAAAAAACTTT 70302
i ? iivv i i ?------------ v
L1M3_orf2#LIN 2112 ATATNTAGAAAACCCTAAAGACTCCACCAAAAAN------------CTGT 2149
INTRON_3 70303 TGGAACTAATAAATGGATTGAGTAAAGTTTTAGGATTCAAAATCAACATA 70352
i ii v vi v
L1M3_orf2#LIN 2150 TAGAACTAATAAATAAATTCAGTAAAGTTGCAGGATACAAAATCAACATA 2199
INTRON_3 70353 TAAAAGTCACTTTTGTTTCCATACACTAACAATGAACTATCCAAAAAGGT 70402
i i v vi i ii ? ii v
L1M3_orf2#LIN 2200 CAAAAATCAGTTGCGTTTCTATACACTAACAACAAACNATCTGAAAAGGA 2249
INTRON_3 70403 A-TTAAGAAAACAATCCTACTTATGATAGCATCAAAAAGAATAAAATACA 70451
- i i ii v
L1M3_orf2#LIN 2250 AATTAAGAAAACAATCCCATTTACAATAGCATCAAAAAGAATAAAATACT 2299
INTRON_3 70452 TAGTAATAAACTTGACTAAGGAGGTGAAAAACTTGTACACAGAAAATGAC 70501
v i i i v iv
L1M3_orf2#LIN 2300 TAGGAATAAACTTAACCAAGGAGGTGAAAGACTTGTACACTGAAAACTAC 2349
INTRON_3 70502 AAAACATTGATTGCACAAATTT-----GACACACATACATGGAGAGACAG 70546
viv v v----- v v i v
L1M3_orf2#LIN 2350 AAAACATTGATGAAAGAAATTAAAGAAGACACAAATAAATGGAAAGACAT 2399
INTRON_3 70547 CTCGTGTTTATAGATTGGAAGACTGAATATTATTA 70581
i i i v v i
L1M3_orf2#LIN 2400 CCCGTGTTCATGGATTGGAAGAATTAATATTGTTA 2434
Matrix = 20p37g.matrix
Transitions / transversions = 1.89 (138 / 73)
Gap_init rate = 0.01 (20 / 1492), avg. gap size = 3.20 (64 / 20)
+ 6711 7.3 0.3 2.0 INTRON_3 70585 71280 (328901) C L1PA10 LINE/L1 (1) 6167 5483 93
ANNOTATION EVIDENCE:
6711 7.35 0.32 1.97 INTRON_3 70585 71280 328901 C L1PA10_3end LINE/L1 230 914 1 184
INTRON_3 70585 TTTTTTTAACCTTATTTTGTATTTTAAGTTCCAGGGTTCATGTGCAGATT 70634
------ v i v iv
C L1PA10_3end#L 914 TTTTTTTAA------TTTTTATTTTAAGTTCCGGGGTACATGTGCAGGAT 871
INTRON_3 70635 GTGCAGGTTTGTTATATAGGTAAACGTGTGCGATGGTGGTTTGCCGCACC 70684
i v i
C L1PA10_3end#L 870 GTGCAGGTTTGTTACATAGGTAAACGTGTGCCATGGTGGTTTGCTGCACC 821
INTRON_3 70685 TATCAACCCATCACCTATGTATTAAGCCCAGCATGCATTAGCTATGTTGC 70734
v v v
C L1PA10_3end#L 820 TATCAACCCATCACCTAGGTATTAAGCCCAGCATGCATTAGCTATTTTTC 771
INTRON_3 70735 CTAATGCTCTTCTTCCCCCA--CCCCACCCCC-AACAGGCCCCAGTGTAT 70781
i i v-- -i i
C L1PA10_3end#L 770 CTAATGCTCTCCCTCCCCCCACCCCCACCCCCCGACAGGCCCCAGTGTGT 721
INTRON_3 70782 GTTGTTCTCCTCCCTGTGTCCATGTGTTCTCATTGTTCAACTCCCACCTG 70831
i i i i
C L1PA10_3end#L 720 GTTGTTCCCCTCCCTGTGTCCATGTGTTCTCATTGTTCAGCTCCCACTTA 671
INTRON_3 70832 TAAGTGAGAACATGTGGTGCTTGGTTTTCTGTTCCTGTGTTAGTTTGCTG 70881
i i i
C L1PA10_3end#L 670 TAAGTGAGAACATGCGGTGTTTGGTTTTCTGTTCCTGCGTTAGTTTGCTG 621
INTRON_3 70882 AGGATAATGGCTTCCAGCTCCATCCATGTCCCTGCAAAGGACATGATCTT 70931
i
C L1PA10_3end#L 620 AGGATAATGGCTTCCAGCTCCATCCATGTCCCTGCAAAGGACATGATCTC 571
INTRON_3 70932 GTTCCTTTTTATGGCTGCATAGTATTCCATTGTGTATCTCTACCACATTT 70981
i v v v
C L1PA10_3end#L 570 ATTCCTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTACCACATTT 521
INTRON_3 70982 TCTTTGTCCAGTCTATCATTGATGGGCATTTTGAATGGTTCCATGTCTTT 71031
i v iv i
C L1PA10_3end#L 520 TCTTTATCCAGTCTATCATTGATGGGCATTTGGGTTGATTCCATGTCTTT 471
INTRON_3 71032 ACTATTGTGAATAGTGCTGCAATGAACATACACGTGCCTTCATCTTTGTA 71081
i v vi i
C L1PA10_3end#L 470 GCTATTGTGAATAGTGCTGCAATGAACATACACGTGCATGTATCTTTATA 421
INTRON_3 71082 ATAGAATGATTAATATTCCTTTGGGTATATACCCAGTAATGGGACTGCTG 71131
v i
C L1PA10_3end#L 420 ATAGAATGATTTATATTCCTTTGGGTATATACCCAGTAATGGGATTGCTG 371
INTRON_3 71132 GGGCAAATGGTATTTCTGGTTCTAGATCTTTGAGGAATTGCCACATCGTC 71181
v i ii
C L1PA10_3end#L 370 GGTCAAATGGTATTTCTGGTTCTAGATCTTTGAGGAATCGCCACACTGTC 321
INTRON_3 71182 TTCAACAATGGTTGAACTAATTTACATTCCCACCAACAGTGTAAAAGCAT 71231
v i
C L1PA10_3end#L 320 TTCCACAATGGTTGAACTAATTTACATTCCCACCAACAGTGTAAAAGCGT 271
INTRON_3 71232 TCCTGTTCCTCTGCAACCTCTCCAGCATCTGTTGTTTCTTGTCTTTTTT 71280
i i ii v --------
C L1PA10_3end#L 270 TCCTATTTCTCCACAACCTCGCCAGCATCTGTTGTTTCTTG-------- 230
Matrix = 20p37g.matrix
Transitions / transversions = 1.68 (32 / 19)
Gap_init rate = 0.01 (4 / 695), avg. gap size = 4.25 (17 / 4)
+ 2419 9.3 0.0 1.6 INTRON_3 71281 71593 (328588) C AluSc SINE/Alu (0) 309 2 94
ANNOTATION EVIDENCE:
2203 11.33 0.32 1.29 INTRON_3 71281 71593 328588 C AluY SINE/Alu 2 311 0 126
INTRON_3 71281 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGCCTGGCTCTGT 71330
i v
C AluY#SINE/Alu 311 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGT 262
INTRON_3 71331 CACC-AGGCTGGAGTGCAGTGGCGCAATCTCAGCTCACTGCAACCTCCAC 71379
i - i i v i
C AluY#SINE/Alu 261 CGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGC 212
INTRON_3 71380 CTCCCAGGTTCAAGCAATTCTCCTGCCTCTGCCTCACAAGTAGCTAGGAC 71429
i v v v v i i
C AluY#SINE/Alu 211 CTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGAC 162
INTRON_3 71430 TATAGGCGTGCACCACCACGCCCAGCTAATTTTTATTTTGTATTTTTAGT 71479
i iv i i ----
C AluY#SINE/Alu 161 TACAGGCGCCCGCCACCACGCCCGGCTAATTTTT----TGTATTTTTAGT 116
INTRON_3 71480 AGAGACAGGGTTTCACCATGTTGGCCAGGATGATCTCTATCTCTTGACCC 71529
i i i i v i i
C AluY#SINE/Alu 115 AGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCT 66
INTRON_3 71530 TGTTATCCACCCGCCTTGGCCTCCCAAAGTGCTGGGATTATAGGCATGAG 71579
i v i i i i
C AluY#SINE/Alu 65 CGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAG 16
INTRON_3 71580 CCGCCATGCCCGGC 71593
i ii
C AluY#SINE/Alu 15 CCACCGCGCCCGGC 2
Matrix = 14p37g.matrix
Transitions / transversions = 2.89 (26 / 9)
Gap_init rate = 0.01 (2 / 312), avg. gap size = 2.50 (5 / 2)
+ 6711 8.0 0.2 1.3 INTRON_3 71594 72035 (328146) C L1PA10 LINE/L1 (686) 5482 5045 93
ANNOTATION EVIDENCE:
6711 7.35 0.32 1.97 INTRON_3 71594 71825 328356 C L1PA10_3end LINE/L1 1 229 686 185
INTRON_3 71594 TGACTTTTTTATAATTGCCATTCTGACTGGCATGAGATGGTATCTCATTA 71643
-- v ? i i
C L1PA10_3end#L 229 --ACTTTTTAATAATNGCCATTCTGACTGGCGTGAGATGGTATCTCATTG 182
INTRON_3 71644 TGGTTTTGATTTGCATTTCTCTAATGATCAGTGATGTTGAGCTTTTTTTC 71693
C L1PA10_3end#L 181 TGGTTTTGATTTGCATTTCTCTAATGATCAGTGATGTTGAGCTTTTTTTC 132
INTRON_3 71694 ATATGTTTGTCAGCTGCATGAATGTCTTCTTTTGAGAAGTGTCTGTTCAT 71743
i ii i
C L1PA10_3end#L 131 GTATGTTTGTTGGCCGCATGAATGTCTTCTTTTGAGAAGTGTCTGTTCAT 82
INTRON_3 71744 GTCTCTTGCCCACTTTTTAATGGGGTTGGTTGTTCTTTTTCATGTAAATT 71793
ii v v - v
C L1PA10_3end#L 81 GTCCTTTGCCCACATTTTAATGGGGTTGTTTGTT-TTTTTCTTGTAAATT 33
INTRON_3 71794 TGTTTAAGTTTCTTGTTGATTCTAGATATTAG 71825
i v i
C L1PA10_3end#L 32 TGTTTAAGTTCCTTGTAGATTCTGGATATTAG 1
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (10 / 5)
Gap_init rate = 0.01 (2 / 231), avg. gap size = 1.50 (3 / 2)
2408 8.64 0.00 0.56 INTRON_3 71675 72035 328146 C L1P3_orf2 LINE/L1 2936 3294 0 186
INTRON_3 71675 TGATGTTGAGCTTTTTTTCATATGTTTGTCAGCTGCATGAATGTCTTCTT 71724
ii i i
C L1P3_orf2#LIN 3294 TGATGTTGAGCTTTTTTTCATATGTTTGTTGGCCGCATAAATGTCTTCTT 3245
INTRON_3 71725 TTGAGAAGTGTCTGTTCATGTCTCTTGCCCACTTTTTAATGGGGTTGGTT 71774
ii v
C L1P3_orf2#LIN 3244 TTGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAATGGGGTTGTTT 3195
INTRON_3 71775 GTTCTTTTTCATGTAAATTTGTTTAAGTTTCTTGTTGATTCTAGATATTA 71824
- v i v i
C L1P3_orf2#LIN 3194 GTT-TTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAGATTCTGGATATTA 3146
INTRON_3 71825 GACCTTTGTCAGATAGATAGATTGGAAAATTTTTCTCCCATTCTGTAGGT 71874
i v v
C L1P3_orf2#LIN 3145 GACCTTTGTCAGATGGATAGATTGCAAAAATTTTCTCCCATTCTGTAGGT 3096
INTRON_3 71875 TGCCTGTTTGCTCTGATGATAGTTTCTTTTGCTGTGCAAAAGCTCTTTAG 71924
i ii i
C L1P3_orf2#LIN 3095 TGTCTGTTCACTCTGATGATAGTTTCTTTTGCTGTGCAGAAGCTCTTTAG 3046
INTRON_3 71925 TTTAATTAGATCCGATTTGTCAATTTTTGCTTTAGTTGCAAATTGTTTTT 71974
v v - i
C L1P3_orf2#LIN 3045 TTTAATTAGATCCCATTTGTCAATTTTTGCTTTTGTTGCAA-TTGCTTTT 2997
INTRON_3 71975 GGTGATTTTGTCATGAAATCTTTGCTGGCGTGTATGTCCTGAATGGTATT 72024
i v ii iv i iv
C L1P3_orf2#LIN 2996 GGCGTTTTCATCATGAAATCTTTGCCCGTGCCTATGTCCTGAATGGTATT 2947
INTRON_3 72025 GCGTAGATTTT 72035
v
C L1P3_orf2#LIN 2946 GCCTAGATTTT 2936
Matrix = 20p37g.matrix
Transitions / transversions = 1.82 (20 / 11)
Gap_init rate = 0.01 (2 / 360), avg. gap size = 1.00 (2 / 2)
+ 3210 16.3 0.5 2.6 INTRON_3 72035 72651 (327530) + L1MB1 LINE/L1 5942 6545 (1014) 91 *
ANNOTATION EVIDENCE:
3210 16.31 0.49 2.65 INTRON_3 72035 72651 327530 + L1M3_orf2 LINE/L1 2414 3017 271 187
INTRON_3 72035 TTGGAAGACTTCATGTTATTAAAATGTCCATACTACCCAATGCAGTCTCT 72084
v v i i v i vi
L1M3_orf2#LIN 2414 TTGGAAGAATTAATATTGTTAAAATGTCCATACTACCCAAAGCAATCTAC 2463
INTRON_3 72085 ACATTCAATTCTATCTCTATCAAAATCTCAGTGGAATTTTTTATTTACAG 72134
v v v i i i v ----
L1M3_orf2#LIN 2464 AGATTCAATGCAATCCCTATCAAAATCCCAATGGCATTTTTTA----CAG 2509
INTRON_3 72135 AAATAGACAAAACAATTCTTAAATCCATATGTAACCACAAAGGACCCTAA 72184
v i v i v i i
L1M3_orf2#LIN 2510 AAATAGAAAAAACAATCCTAAAATTCATATGGAACCACAAAAGACCCCAA 2559
INTRON_3 72185 ATAACCAAAACAATTAAAAAAAAAAAAACAAACAAAGTTAGAGGCAATCC 72234
i ivvi i i i --- i i viv
L1M3_orf2#LIN 2560 ATAGCCAAAACAATCTTGAGAAAGAAGA---ACAAAGCTGGAGGCATCAC 2606
INTRON_3 72235 ACTTCCTGAATTCAAAATATATTATTACAAAGCTACTGGAATTAAATCAG 72284
v i --- iv v i v
L1M3_orf2#LIN 2607 ACTTCCTGACTTCAAAACATATTA---CAAAGCTATAGTAATCAAAACAG 2653
INTRON_3 72285 TATGGTACTGGCATACAGACAGACATATA--CCAATGGAACAGAATTGAG 72332
v i -- v
L1M3_orf2#LIN 2654 TATGGTACTGGCATAAAGATAGACATATAGACCAATGGAACAGAATAGAG 2703
INTRON_3 72333 AGCTCAGAAATAAACCCAGTTGACCCATTTACAGTCAACCTATCTTCAAC 72382
i ----- v v i iv i
L1M3_orf2#LIN 2704 AGCCCAGAAATAAACCCA-----CGCATATACGGTCAACTGATCTTCGAC 2748
INTRON_3 72383 AACTGTGCCAAGAATAGGCAATGAGGGAAAGATAGTCTCTTCAATAAATA 72432
vv vi i i i i i
L1M3_orf2#LIN 2749 AAGGGTGCCAAGAATACACAATGGGGAAAGGATAGTCTCTTCAACAAATG 2798
INTRON_3 72433 GTGTTGGGAAAACTGGATATTCACATGCAAAACAATGAAATTGGACCCTT 72482
i i v
L1M3_orf2#LIN 2799 GTGTTGGGAAAACTGGATATCCACATGCAGAAGAATGAAATTGGACCCTT 2848
INTRON_3 72483 TTCTTACAC-GTGGACAAAAATTAATGCAAAGTAGATTAAAGATTTAAAC 72531
v -i iv i iv i i i i
L1M3_orf2#LIN 2849 ATCTTACACCATACACAAAAATCAACTCAAAATGGATTAAAGACTTAAAT 2898
INTRON_3 72532 ATAAGATTTAAAACTGCATAACCACTAGGATAAAACATAGGAGGAAACCT 72581
i ii i i v iv i v i i v
L1M3_orf2#LIN 2899 GTAAGACCTGAAACTGTAAAACTCCTAGAAGAAAACATAGGGGAAAAGCT 2948
INTRON_3 72582 TCATGTCATTGGCATTAGCGATGGTTTCTTGGATATGACACCAAAAGCAC 72631
v iv i i i
L1M3_orf2#LIN 2949 TCATGACATTGGTCTTGGCAATGATTTCTTGGATATGACACCAAAAGCAC 2998
INTRON_3 72632 AGACAACAAAGTGTAAAGAT 72651
i i- i i
L1M3_orf2#LIN 2999 AGGCAACAAAA-GCAAAAAT 3017
Matrix = 20p37g.matrix
Transitions / transversions = 1.65 (61 / 37)
Gap_init rate = 0.01 (7 / 616), avg. gap size = 2.71 (19 / 7)
+ 4166 16.5 1.1 3.1 INTRON_3 72643 72868 (327313) + L1MB1 LINE/L1 6803 7026 (561) 91
ANNOTATION EVIDENCE:
4166 16.51 1.12 3.06 INTRON_3 72643 72868 327313 + L1MB1_3end LINE/L1 131 354 561 188
INTRON_3 72643 TGTAAAGATGCTTAAAAACATTACTTATAAGGGAAATGCATGTCAAA-CT 72691
v i v v i v i v vi - i
L1MB1_3end#LI 131 TGAAAAGATGCTCAACATCACTAATCATCAGGGAAATGCAAATCAAAACC 180
INTRON_3 72692 ACAATGAGATAGAAATCACTTCATATCTGTTAGGATGGCCATTATAAAAC 72741
---- i ii i i i v v
L1MB1_3end#LI 181 ACAATGAGATA----TCACCTCGCACCTGTTAGAATGGCTATTATCAAAA 226
INTRON_3 72742 AAACAAAAGATTAACAAATTCTGGCGAGAATGTGTAGAAATTGGAACCCT 72791
i - i i vi i v
L1MB1_3end#LI 227 AAACAAAAAAT-AATAAGTGTTGGCGAGGATGTGGAGAAATTGGAACCCT 275
INTRON_3 72792 TGTACTCAGCTGGTGGGAATGTGAAATAGTTGCAGTCACTATGAAAGA-- 72839
v v i i i - i i i --
L1MB1_3end#LI 276 TGTACACTGTTGGTGGGAATGTAAAATGGT-GCAGCCACTATGGAAAACA 324
INTRON_3 72840 -TATGACATTTCCTCAAAAAATTAAAAATA 72868
- iviv
L1MB1_3end#LI 325 GTATGGAGGTTCCTCAAAAAATTAAAAATA 354
Matrix = 20p37g.matrix
Transitions / transversions = 1.71 (24 / 14)
Gap_init rate = 0.02 (5 / 225), avg. gap size = 2.00 (10 / 5)
+ 2375 10.2 0.0 0.3 INTRON_3 72869 73171 (327010) + AluSx1 SINE/Alu 1 302 (10) 95
ANNOTATION EVIDENCE:
2284 10.59 0.00 0.33 INTRON_3 72869 73171 327010 + AluSx SINE/Alu 1 302 10 127
INTRON_3 72869 GGCCAGGCACGGCGGCTTATGCCTATAATCCCAGCAGTTTGGGAGGCTGA 72918
i i i i i i v i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 72919 GGTGGGTGGATCACCTGAGGTCAGGAGTTTGAGAACAGCCTGGCCAACAT 72968
i i i v
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
INTRON_3 72969 GGCGAAACCCCATCTCTACTAAAAGTACAAAAATTAGCTGGGCGTGGTGG 73018
i i i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGG 150
INTRON_3 73019 TGGGTGCCTGTAATCCCAGATACTCAGGAGGCTGAGTCAGGAGAATCGCT 73068
i v i v i v
AluSx#SINE/Al 151 CGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCT 200
INTRON_3 73069 TGAACCTGGGAGGCAGAGGTTGCAGTGAGCCGAGATCATGCCTCTGCACT 73118
i i ii v
AluSx#SINE/Al 201 TGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACT 250
INTRON_3 73119 TCAGCCTGGGTGACAAGAGTGAGACTCCATCTCAAAAAAAAAAAAAAAAA 73168
i i - i i
AluSx#SINE/Al 251 CCAGCCTGGGCGACA-GAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAA 299
INTRON_3 73169 GAA 73171
i
AluSx#SINE/Al 300 AAA 302
Matrix = 14p37g.matrix
Transitions / transversions = 4.33 (26 / 6)
Gap_init rate = 0.00 (1 / 302), avg. gap size = 1.00 (1 / 1)
+ 4166 16.5 1.1 3.1 INTRON_3 73172 73744 (326437) + L1MB1 LINE/L1 7027 7587 (0) 91
ANNOTATION EVIDENCE:
4166 16.51 1.12 3.06 INTRON_3 73172 73744 326437 + L1MB1_3end LINE/L1 355 915 0 189
INTRON_3 73172 TTAAAAATAGAAATACCATATTATCTAGCAATCCCACTTCTGCATACCTA 73221
--------- v v i vi ii
L1MB1_3end#LI 355 ---------GAACTACCATATGATCCAGCAATCCCACTTCTGGGTATTTA 395
INTRON_3 73222 TACAAAATAATTGAGAACAGGATATTGAAGAGATATTTTCACTCCCACGT 73271
v v i v v i ?v i
L1MB1_3end#LI 396 TCCAAAAGAATTGAAATCAGGATCTCGAAGAGATATTNGCACTCCCATGT 445
INTRON_3 73272 TTGTTGCAGCATTATTCACAACAAC--AGATGTGGAAACACTCTAAATGT 73319
ii i i -- vi
L1MB1_3end#LI 446 TCATTGCAGCATTATTCACAATAGCCAAGATGTGGAAACAACCTAAATGT 495
INTRON_3 73320 CCATTGATGGGTAGATGAATGGACAAAGAATATGTAGTAAACATGTACAA 73369
i i ---- i v i v i ii
L1MB1_3end#LI 496 CCATCGACGG----ATGAATGGATAAAGAAAATGTGGTATATACATACAA 541
INTRON_3 73370 CGAAATATTATTTAGCCTTACAAAATAAGGAAATCTTGAAATATGCAGCA 73419
i i i v v i vv ii
L1MB1_3end#LI 542 TGGAATATTATTCAGCCTTAAAAAAGAAGGAAATCCTGCCATATGCGACA 591
INTRON_3 73420 ACATGGATGAAACTGGAGGACATTATGCTAAGTCAAATAAACCAGTCACA 73469
v v v i
L1MB1_3end#LI 592 ACATGGATGAACCTTGAGGACATTATGCTAAGTGAAATAAGCCAGTCACA 641
INTRON_3 73470 GAAAGACGAATACTGTATTATTCCACATGTACAAATTATCTAAAATAGCC 73519
i i i v v i ii iv i
L1MB1_3end#LI 642 GAAGGACAAATACTGCATGATTCCACTTATATGAGGTATCTAAAATAGTC 691
INTRON_3 73520 AAACCAATGGAATCAGAAAATAGAATTGTGGCTGCCAAAGGCTGGGGGCC 73569
iv i v i i v i ii --
L1MB1_3end#LI 692 AAACTCATAGAAGCAGAGAGTAGAATGGTGGTTGCCAGGGGCTGGGGG-- 739
INTRON_3 73570 TGGGGTGGTAAATGGGGATCTGCTATCCAATGGGTATAAAATTTCAGTTA 73619
- i v - vi i i i
L1MB1_3end#LI 740 -GAGGGGG-AAATGGGGAGTTGCTGTTCAATGGGTATAAAGTTTCAGTTA 787
INTRON_3 73620 TACAAGATGAATAAGTTCTAGGCATCTGCTGTACAACATTGTACCTGTAG 73669
i iv i i
L1MB1_3end#LI 788 TGCAAGATGAATAAGTTCTAGAGATCTGCTGTACAACATTGTGCCTATAG 837
INTRON_3 73670 TTAACAATACTGAATTATATACTTGA---TTTTTTAAAATGGTAGATGCC 73716
v i i i --- v i v vi
L1MB1_3end#LI 838 TTAACAATACTGTATTGTACACTTAAAAATTTGTTAAGAGGGTAGATCTC 887
INTRON_3 73717 ATGCTAAATGTTCTTACTACAATAAAAA 73744
i i i
L1MB1_3end#LI 888 ATGTTAAGTGTTCTTACCACAATAAAAA 915
Matrix = 20p37g.matrix
Transitions / transversions = 1.87 (58 / 31)
Gap_init rate = 0.01 (6 / 572), avg. gap size = 3.67 (22 / 6)
+ 1144 20.3 3.5 0.3 INTRON_3 73783 74158 (326023) C L1M4 LINE/L1 (695) 5484 5099 96
ANNOTATION EVIDENCE:
883 20.44 2.67 0.00 INTRON_3 73783 74007 326174 C L1ME1_3end LINE/L1 1 231 695 190
INTRON_3 73783 AGTATTTTAATTTTTACCCTTTTTAGATCATAGGTAGTAGTATCTCACTG 73832
v v v v v i ivvvi iv i i
C L1ME1_3end#LI 231 AGTCTTTTTAATTTTAGCCATTCTAATGGGTGTGTAGTGGTATCTCATTG 182
INTRON_3 73833 CAGTTTTAATTTGCATTTTACTAATGAATAACAGTGTTGAGCATCATATC 73882
ii iv v iii v v
C L1ME1_3end#LI 181 TGGTTTTAATTTGCATTTCCCTAATGACTAATGATGTTGAGCATCTTTTC 132
INTRON_3 73883 ATGT-TTTATTTGCCATCAGTATATCTTCTTTGCAGAAGTGTATGTTCAA 73931
-i vi vv v
C L1ME1_3end#LI 131 ATGTGCTTATTTGCCATCCATATATCTTCTTTGGTGAAGTGTCTGTTCAA 82
INTRON_3 73932 ATATATTGTCCATTT---AAAAAATTTGGTTGTTTACTAATTATTGAGTT 73978
v v i --- vviiv v v v
C L1ME1_3end#LI 81 ATCTTTTGCCCATTTTTTAATTGGGTTGTTTGTTTTCTTATTATTGAGTT 32
INTRON_3 73979 TTGAGAGTTCTTCATAT--TGTAGATCCAAG 74007
i -- v i v
C L1ME1_3end#LI 31 TTGAGAGTTCTTTATATATTCTGGATACAAG 1
Matrix = 20p37g.matrix
Transitions / transversions = 0.70 (19 / 27)
Gap_init rate = 0.01 (3 / 224), avg. gap size = 2.00 (6 / 3)
1144 20.28 3.77 0.33 INTRON_3 73867 74158 326023 C L1MD_orf2 LINE/L1 2990 3291 3 191
INTRON_3 73867 TGTTGAGCATCATATCATGT-TTTATTTGCCATCAGTATATCTTCTTTGC 73915
i v v -i v i i v
C L1MD_orf2#LIN 3291 TGTTGAACATCTTTTCATGTGCTTATTTGCCATCTGTATATCCTCTTCGG 3242
INTRON_3 73916 AGAAGTGTATGTTCAAATATATTGTCCATTTAAAAAAT---TTGGTTGTT 73962
v i v v vi v v i vvv v --- v
C L1MD_orf2#LIN 3241 TGAAATGTCTCTTCATGTCTTTTGCCCATTTTCTAATTGGATTGTTTGTT 3192
INTRON_3 73963 TACTAATTATTGAGTTTTGAGAGTTCTTCATAT--TGTAGATCCAAGTCA 74010
vi v i i i -- v v v v
C L1MD_orf2#LIN 3191 TTTTTACTGTTGAGTTTTGAGAGTTCTTTATATATTCTAGATACTAGTCC 3142
INTRON_3 74011 TTTGTCAGATATGTGATTTGCAAATAATTTCTCCTAGT--GTGGCTTGTC 74058
i i v i ? -- i
C L1MD_orf2#LIN 3141 TTTGTCGGATATGTGGTTTGCAAATATTTTCTCCCANTCTGTAGCTTGTC 3092
INTRON_3 74059 TTTTCATTCTGTGAAT---GTCCTTCAAGCAGCAGCAGTTCTTAATTTCG 74105
i v v i--- i iviv iv i i
C L1MD_orf2#LIN 3091 TTTTCATCCTCTTAACAGGGTCTTTCGCAGAGCAAAAGTTTTTAATTTTG 3042
INTRON_3 74106 ATGAAGTCTAGTTTATCAGTTTTTTTCTTTTGTGGATAATGCTTTTGGTG 74155
i i i i- i vi
C L1MD_orf2#LIN 3041 ATGAAGTCCAATTTATCAATTTTTC-CTTTTATGGATCGTGCTTTTGGTG 2993
INTRON_3 74156 TTA 74158
i
C L1MD_orf2#LIN 2992 TCA 2990
Matrix = 20p37g.matrix
Transitions / transversions = 1.07 (30 / 28)
Gap_init rate = 0.02 (6 / 291), avg. gap size = 2.00 (12 / 6)
+ 202 19.5 2.4 0.0 INTRON_3 74465 74505 (325676) + MIRb SINE/MIR 180 221 (47) 97
ANNOTATION EVIDENCE:
202 19.51 2.44 0.00 INTRON_3 74465 74505 325676 + MIRb SINE/MIR 180 221 47 156
INTRON_3 74465 TGTGAGCATTAGATGAGATGATACATG-AAAACACTGAGTAC 74505
v i i i - i i v i
MIRb#SINE/MIR 180 TGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCAC 221
Matrix = 25p37g.matrix
Transitions / transversions = 3.00 (6 / 2)
Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1)
+ 24 86.8 0.0 0.0 INTRON_3 74687 74724 (325457) + AT_rich Low_complexity 1 38 (0) 98
ANNOTATION EVIDENCE:
24 86.84 0.00 0.00 INTRON_3 74687 74724 325457 + AT_rich Low_complexity 110 147 153 166
INTRON_3 74687 TATTTTTGTATTATATTCTTTAATATTTTATTTAAATT 74724
??????????????????????????????v vv
AT_rich#Low_c 110 WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWATTAAAAA 147
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 3)
Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0)
+ 2721 18.0 3.5 4.0 INTRON_3 75107 75609 (324572) C L1M4 LINE/L1 (2489) 3657 3144 96
ANNOTATION EVIDENCE:
2721 18.00 3.55 4.01 INTRON_3 75107 75609 324572 C L1M4_orf2 LINE/L1 1035 1548 1746 192
INTRON_3 75107 CAGGGAAGTACTGAACTTATAGAATGAGTTGGGAAGTATTCCCTGCATCT 75156
v i iv i i v -
C L1M4_orf2#LIN 1548 CAGGGTAATACTGGCCTCATAGAATGAGTTGGGAAGTGTTCCCTCC-TCT 1500
INTRON_3 75157 TC-AGTTACTGGAAGAGTTTGTGAAGGATTGGCATTATTTCTTCCT-AAA 75204
- v vi i? v i -
C L1M4_orf2#LIN 1499 TCTATTTTTTGGAAGAGTTTGTGAAGGATTGGTNTTAATTCTTCTTTAAA 1450
INTRON_3 75205 TGTTTAATAGAATTCACCAGTAAAGACAGCTGGGACTTGGCTTTTCTTTG 75254
i ii i v v v v
C L1M4_orf2#LIN 1449 CGTTTGGTAGAATTCACCAGTGAAGCCATCTGGGCCTGGGCTTTTCTTTG 1400
INTRON_3 75255 AGTGAAGATTTTTAATTACTAATTTAATCT--TTACTCATTATAGGTCTG 75302
v v v i i -- ii i
C L1M4_orf2#LIN 1399 TGGGAAGTTTTTTGATTACTAATTCAATCTCTTTACTTGTTATAGGTCTA 1350
INTRON_3 75303 TTCAATTTTTCTGTTTC--CTTGAGCCTGTTTTGGTAATTTTT--CTTTC 75348
iv i -- i v i i v --
C L1M4_orf2#LIN 1349 TTCAGATTTTCTATTTCTTCTTGAGTCAGTTTCGGTAGTTTGTGTCTTTC 1300
INTRON_3 75349 TAGGAATTTGTTCATTTCACCCAAGTTGTCTAATTTATTGGCATAAATTT 75398
i i i i i i v v
C L1M4_orf2#LIN 1299 TAGGAATTTGTCCATTTCATCTAGGTTATCTAATTTGTTGGCATACAATT 1250
INTRON_3 75399 GTTCATAATACTCATTTACA-----TTTTAAAAAATTTCTGTAGGATCAG 75443
i i vi i ----- ----- i i i
C L1M4_orf2#LIN 1249 GTTCATAGTATTCCCTTATAATCCTTTTTA-----TTTCTGTAAGGTCGG 1205
INTRON_3 75444 TGGTGATGTGCCCTCTTTCATTCATGATTTTGATGATCT----TTCCTCT 75489
i i v v ii i i ----i i
C L1M4_orf2#LIN 1204 TAGTAATGTCCCCTCTTTCATTCCTGATTTTAGTAATTTGAGTCTTCTCT 1155
INTRON_3 75490 CTTTCTTTTCATAGTGGATCTTGTTAAAAGTTTGACAATTTT-TTGAACA 75538
- v i vii v i i v - v v
C L1M4_orf2#LIN 1154 CTTT-TTTTCTTGGTCAGTCTAGCTAAAGGTTTGTCAATTTTGTTGATCT 1106
INTRON_3 75539 TTTTAGAGAA---GCTTTTAATGTT-TTG--TTTTTCTGTTGCTTTTCTA 75582
i i ---i ii v i- -- i i i
C L1M4_orf2#LIN 1105 TTTCAAAGAACCAACTTTTGGTTTCGTTGATTTTCTCTATTGTTTTTCTA 1056
INTRON_3 75583 TTGTCCATTTAATTGATTTGCACTCTC 75609
v i v v ----- -
C L1M4_orf2#LIN 1055 TTCTCTATTTCATTTATTT-----CT- 1035
Matrix = 20p37g.matrix
Transitions / transversions = 1.84 (57 / 31)
Gap_init rate = 0.03 (16 / 502), avg. gap size = 2.31 (37 / 16)
+ 1921 14.1 8.7 0.0 INTRON_3 75610 75943 (324238) + THE1B LTR/ERVL-MaLR 2 364 (0) 99
ANNOTATION EVIDENCE:
1921 14.07 8.68 0.00 INTRON_3 75610 75943 324238 + THE1B LTR/ERVL-MaLR 2 364 0 141
INTRON_3 75610 GATATGGTTCAGCTGTATCCCTACACAAATCTGACCTTGAATTGTA---- 75655
ii i i v v i ----
THE1B#LTR/ERV 2 GATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGAATTGTAGCTC 51
INTRON_3 75656 --ATAAT--CCACATGT-------GGGGCCAGGTGG-AGATAATTGAATC 75693
-- -- i ------- i v - i
THE1B#LTR/ERV 52 CCATAATTCCCACGTGTCGTGGGAGGGACCCGGTGGGAGGTAATTGAATC 101
INTRON_3 75694 ATGGGGGCAG-TTTCTTCCACACTGTTCTCATGGTAGTGAATAAGTCTCA 75742
i - i i i iii i i
THE1B#LTR/ERV 102 ATGGGGGCGGGTCTTTCCCGTGCTGTTCTCGTGATAGTGAATAAGTCTCA 151
INTRON_3 75743 CAAGATCTGATGGCTTTATAAATGGAACTTCTCCCGTACAAGCTCTCTTA 75792
i i v i v i i i ? i
THE1B#LTR/ERV 152 CGAGATCTGATGGTTTTATAAAGGGGAGTTCCCCTGCACAWGCTCTCTTG 201
INTRON_3 75793 CCTGCTGCCATGTAAGATGTGACTTTGCTCCTCATTTGCCTTCTGCCATG 75842
i i ? v i i
THE1B#LTR/ERV 202 CCTGCCGCCATGTAAGACGTGMCTTTGCTCCTCCTTCGCCTTCCGCCATG 251
INTRON_3 75843 ATTGTGAG-TCTCCCCAGCCACGTGGAACTGTG--TCAATTAAACCTCCT 75889
-i i -- v i
THE1B#LTR/ERV 252 ATTGTGAGGCCTCCCCAGCCATGTGGAACTGTGAGTCCATTAAACCTCTT 301
INTRON_3 75890 TCCTTTGCAAATTACC---------ATATGTCTTTATTAGCAACATGAGA 75930
ii ---------i i i
THE1B#LTR/ERV 302 TCCTTTATAAATTACCCAGTCTCGGGTATGTCTTTATTAGCAGCGTGAGA 351
INTRON_3 75931 ACAGACTTAGACA 75943
v v
THE1B#LTR/ERV 352 ACAGACTAATACA 364
Matrix = 18p37g.matrix
Transitions / transversions = 4.00 (36 / 9)
Gap_init rate = 0.02 (8 / 333), avg. gap size = 3.62 (29 / 8)
+10729 10.4 3.8 0.3 INTRON_3 75944 77469 (322712) + THE1B-int LTR/ERVL-MaLR 1 1579 (1) 99
ANNOTATION EVIDENCE:
10729 10.38 3.80 0.32 INTRON_3 75944 77469 322712 + THE1-int LTR/ERVL-MaLR 1 1579 1 142
INTRON_3 75944 GTAAATTGGTACCGAGTAG--TGGGGCGCTGCTGTAAAAATACCTGAAAA 75991
- -- v i i
THE1-int#LTR/ 1 GTAAATTGGTACC-AGTAGAGTGGGGCGCTGCTGAAAAGATACCCGAAAA 49
INTRON_3 75992 TGTGGAAGTGACTTTGGAACTGGGTAACAGGCAGAGACTGGAACAGTTTA 76041
i ii i
THE1-int#LTR/ 50 TGTGGAAGCGACTTTGGAACTGGGTAACAGGCAGAGGTTGGAACAGTTTG 99
INTRON_3 76042 GAGTACTCAGAAGA---CAGGAAGATGCGGGCAAGTTTGGAACTTCCTAG 76088
vi --- i i v
THE1-int#LTR/ 100 GAGGGCTCAGAAGAAGACAGGAAAATGTGGGAAAGTTTGGAACTTCCTAG 149
INTRON_3 76089 AAACTTGTTGAATGGCTTTGAGCAAAATGCTGATAGTGATATGGGCAAGA 76138
i v i v
THE1-int#LTR/ 150 AGACTTGTTGAATGGCTTTGACCAAAATGCTGATAGTGATATGGACAATA 199
INTRON_3 76139 AGGTTCAGGCTGAGGTGGTCTCAGATGGAGATGAGGAACTTGTTGGGAAC 76188
i i
THE1-int#LTR/ 200 AAGTCCAGGCTGAGGTGGTCTCAGATGGAGATGAGGAACTTGTTGGGAAC 249
INTRON_3 76189 TGGAGTAAAGGTCACTTTTGCTATG------CAAAGAGACTGGTGGCATT 76232
i v i i ------ i
THE1-int#LTR/ 250 TGGAGCAAAGGTGACTCTTGTTATGTTTTAGCAAAGAGACTGGCGGCATT 299
INTRON_3 76233 TTCCCCCTGCCTTAGAGATCTGTGGAACTTTGAACTTAAGAGTTATGATT 76282
v i i i vv
THE1-int#LTR/ 300 TTGCCCCTGCCCTAGAGATTTGTGGAACTTTGAACTTGAGAGAGATGATT 349
INTRON_3 76283 TAGGGTATCTGGCAAAAGAAATTTCTAA------AAGTATTCAAGAGG-- 76324
ii ------ ii --
THE1-int#LTR/ 350 TAGGGTATCTGGCGGAAGAAATTTCTAAGCAGCAAAGCGTTCAAGAGGTG 399
INTRON_3 76325 -------------------------------------AAGCAGAACATAA 76337
------------------------------------- i
THE1-int#LTR/ 400 ACTTGGGTGCTGTTAAAGGCATTCAGTTTTAAAAGGGAAGCAGAGCATAA 449
INTRON_3 76338 AAGTTTGGAAAATTTGTAGCCTGACAATGCAATAGAAAAGAAAAACCCAT 76387
i i i v
THE1-int#LTR/ 450 AAGTTCGGAAAATTTGCAGCCTGACAATGCGATAGAAAAGAAAATCCCAT 499
INTRON_3 76388 TTTCTGAGGAGAAATTCAAGCCTGCTGCAGAAATTTGCATAATTAACAAG 76437
v v i
THE1-int#LTR/ 500 TTTCTGAGGAGAAATTCAAGCCGGCTGCAGAAATTTGCATAAGTAACGAG 549
INTRON_3 76438 AAGCCAAATGTTATTCACTAAGACAATGGGGAAAATGTCTCCAGGACAAA 76487
i i v v i i vi
THE1-int#LTR/ 550 GAGCCGAATGTTAATCCCCAAGACAATGGGGAAAATGTCTCCAGGGCATG 599
INTRON_3 76488 TCAGAGACCTTCACAGCAGCCCCTCCCATCAAAGGCCCAGAGGCCTAGGA 76537
i i i v i
THE1-int#LTR/ 600 TCAGAGATCTTCGCGGCAGCCCCTCCCATCACAGGCCCGGAGGCCTAGGA 649
INTRON_3 76538 GGGAAAAATGGTTTTGTGGACTAGGCCCAGGG--CATGTTTTGCTGTGTG 76585
i i i i -- vi ---
THE1-int#LTR/ 650 GGAAAAAATGGTTTCGTGGGCCAGGCCCAGGGTCCCCGT---GCTGTGTG 696
INTRON_3 76586 CAGCCTTGGAACTTGGTGCCCTGTGTCCTAGCTGCTCCAGCTGTGGTTAA 76635
v i i i i ii i
THE1-int#LTR/ 697 CAGCCTAGGGACTTGGTGCCCTGCGTCCCAGCCGCTCCAGCCATGGCTAA 746
INTRON_3 76636 AAGGAGCCAACATACAGCTCAGACTATTACTTCAGAGGTTACAAGCCCTA 76685
i i i i ii vi v i i
THE1-int#LTR/ 747 AAGGGGCCAACGTACAGCTCGGGCCGTGGCTTCAGAGGGTGCAAGCCCCA 796
INTRON_3 76686 AGCTTTGGCAGCTTCCACATGACATTGGGCCCACAGGTGCAGAGAAGTCA 76735
i i iii i ii i v
THE1-int#LTR/ 797 AGCCTTGGCAGCTTCCACGTGGTGTTGAGCCTGCGGGTGCACAGAAGTCA 846
INTRON_3 76736 AGAATTGAGGTTTGGGAACCTCCACCTAGATTTCAGAGGATGTATGGAAA 76785
i
THE1-int#LTR/ 847 AGAATTGAGGTTTGGGAACCTCCGCCTAGATTTCAGAGGATGTATGGAAA 896
INTRON_3 76786 GGCCTGGATGTCCAGGCAGAATTTTGCTTCAGGGGTGGAACCGTCATGGA 76835
v v v i ii v
THE1-int#LTR/ 897 CGCCTGGATGTCCAGGCAGAAGTTTGCTGCAGGGGCGGGGCCCTCATGGA 946
INTRON_3 76836 GAACCTCTGCTAGAGCAGTATGGAAGGGAAATGTGGGGTCAGAGCCCCCA 76885
i ii i
THE1-int#LTR/ 947 GAACCTCTGCTAGGGCAGTGCGGAAGGGAAATGTGGGGTCGGAGCCCCCA 996
INTRON_3 76886 CACAGAGTCTCCAGAGGGGCACTGCATAGGGCAGCTGTGAGAAGAGGGCC 76935
i i vv v v v
THE1-int#LTR/ 997 CACAGAGTCCCTACTGGGGCACTGCCTAGTGGAGCTGTGAGAAGAGGGCC 1046
INTRON_3 76936 ACCATCCTCCAGACCCCAGAATGGTAGATCCACTGACAGATTGCACCATG 76985
i i v i
THE1-int#LTR/ 1047 ACCGTCCTCCAGACCCCAGAATGGTAGATCCACCGACAGCTTGCACCGTG 1096
INTRON_3 76986 CACCTGGAAAAGCCACAGACACTCAGCGCCAGCCTGTGAAAGTAGCCAGG 77035
i i i i i
THE1-int#LTR/ 1097 CGCCTGGAAAAGCCGCAGACACTCAACGCCAGCCCGTGAAAGCAGCCAGG 1146
INTRON_3 77036 AGGTGGGGTGTACCATGCAAAGCCACAAGGACAGAGCTGCCCAAGGCTGT 77085
vi v v i i i i ii
THE1-int#LTR/ 1147 AGGGAGGCTGTACCCTGCAAAGCCACAGGGGCGGAGCTGCCCAAGACCAT 1196
INTRON_3 77086 GGGAGCCCACCTCTCGAATCAGCATGACCTGTATGTGAGACATGGAGTCA 77135
i i v i v
THE1-int#LTR/ 1197 GGGAACCCACCTCTTGCATCAGCGTGACCTGGATGTGAGACATGGAGTCA 1246
INTRON_3 77136 AAGGAGATCATTTTGGAGCTTTAATATTTGACTGCCCCATTGGATTTTGG 77185
v ii i
THE1-int#LTR/ 1247 AAGGAGATCATTTTGGAGCTTTAAGATTTGACTGCCCCGCTGGATTTCGG 1296
INTRON_3 77186 ATTTGCATAGGGTCTATAGCTCCTTCGTTTTGGCCAGTTTCTCCCATTTG 77235
i i i i i i i
THE1-int#LTR/ 1297 ACTTGCATGGGGCCTGTAGCCCCTTTGTTTTGGCCAATTTCTCCCATTTG 1346
INTRON_3 77236 GAATGAGTGTATTTACCCAATGCCTGTACCCTCATTGTATCTAGGAAGTA 77285
iv i
THE1-int#LTR/ 1347 GAATGGCTGTATTTACCCAATGCCTGTACCCCCATTGTATCTAGGAAGTA 1396
INTRON_3 77286 ACTAACTTGCTTTTGATTTTACAGGCTCATAGGTGGAAAGGACTTACCTT 77335
i i i
THE1-int#LTR/ 1397 ACTAACTTGCTTTTGATTTTACAGGCTCATAGGCGGAAGGGACTTGCCTT 1446
INTRON_3 77336 GTCTCAGTTGAGACTTTGGACTGTGGACTTTTAAGTTAATGCTGAAATGA 77385
v i
THE1-int#LTR/ 1447 GTCTCAGATGAGACTTTGGACTGTGGACTTTTGAGTTAATGCTGAAATGA 1496
INTRON_3 77386 GTTAAGACTTTGGAGGACTGTTGGGAAGGCATGATTGGTTTTGAAATGTG 77435
i
THE1-int#LTR/ 1497 GTTAAGACTTTGGGGGACTGTTGGGAAGGCATGATTGGTTTTGAAATGTG 1546
INTRON_3 77436 AGGACATGAGATTTGCGGGGGAGTGGGGGGCAGA 77469
- i i ivi i
THE1-int#LTR/ 1547 AGGACATGAGATTTG-GGAGGGGCCAGGGGCGGA 1579
Matrix = 18p37g.matrix
Transitions / transversions = 2.95 (118 / 40)
Gap_init rate = 0.01 (9 / 1525), avg. gap size = 7.00 (63 / 9)
2721 18.00 3.55 4.01 INTRON_3 77470 77476 322705 C L1M4_orf2 LINE/L1 1034 1034 2260 193
INTRON_3 77470 GGCAGAA 77476
-------
C L1M4_orf2#LIN 1034 ------- 1035
Matrix = 20p37g.matrix
Transitions / transversions = 0.0 (0 / 0)
Gap_init rate = 0.17 (1 / 6), avg. gap size = 7.00 (7 / 1)
+ 2011 14.0 8.3 0.0 INTRON_3 77477 77812 (322369) + THE1B LTR/ERVL-MaLR 1 364 (0) 100
ANNOTATION EVIDENCE:
2011 13.99 8.33 0.00 INTRON_3 77477 77812 322369 + THE1B LTR/ERVL-MaLR 1 364 0 143
INTRON_3 77477 TGATATGGTTTAGCTGTGACCCCACCCAAATCTTACCTTGAATTGTG--- 77523
i v i i i---
THE1B#LTR/ERV 1 TGATATGGTTTGGCTGTGTCCCCACCCAAATCTCATCTTGAATTGTAGCT 50
INTRON_3 77524 ---ATAATCCCCGTGTGTCAAGGGTGGGACCAGGTGG-AGATAATGGAAT 77569
--- i ii iv v v - i v
THE1B#LTR/ERV 51 CCCATAATTCCCACGTGTCGTGGGAGGGACCCGGTGGGAGGTAATTGAAT 100
INTRON_3 77570 CATGCGGGCAG-TTTCCCCCATACTGTTCTCATGGTAGTGAATAAGTCTG 77618
v i - i ii i i i i v
THE1B#LTR/ERV 101 CATGGGGGCGGGTCTTTCCCGTGCTGTTCTCGTGATAGTGAATAAGTCTC 150
INTRON_3 77619 ACGAGATCTAATGGTTTTATAAATGGGAGTTCCCCTGAACAAGTTATCTT 77668
i v v ? i v
THE1B#LTR/ERV 151 ACGAGATCTGATGGTTTTATAAAGGGGAGTTCCCCTGCACAWGCTCTCTT 200
INTRON_3 77669 GCCTGCCACCATGTAAAACATGACTTTGCTCCTCATTTGCCTTCTGCCAT 77718
i i i ? v i i
THE1B#LTR/ERV 201 GCCTGCCGCCATGTAAGACGTGMCTTTGCTCCTCCTTCGCCTTCCGCCAT 250
INTRON_3 77719 GATTGTGAGGCCACCCCAGCCATGTGGTACTGTGAGTTGG---------- 77758
v v ivi----------
THE1B#LTR/ERV 251 GATTGTGAGGCCTCCCCAGCCATGTGGAACTGTGAGTCCATTAAACCTCT 300
INTRON_3 77759 ----------AGTTACCCAGTCTCGGATATGTTTTTATTAGCATCATGAG 77798
---------- i i i v i
THE1B#LTR/ERV 301 TTCCTTTATAAATTACCCAGTCTCGGGTATGTCTTTATTAGCAGCGTGAG 350
INTRON_3 77799 AACAGACTAATACA 77812
THE1B#LTR/ERV 351 AACAGACTAATACA 364
Matrix = 18p37g.matrix
Transitions / transversions = 2.00 (30 / 15)
Gap_init rate = 0.01 (4 / 335), avg. gap size = 7.00 (28 / 4)
+ 2721 18.0 3.5 4.0 INTRON_3 77813 77976 (322205) C L1M4 LINE/L1 (3003) 3143 2984 96
ANNOTATION EVIDENCE:
2721 18.00 3.55 4.01 INTRON_3 77813 77976 322205 C L1M4_orf2 LINE/L1 875 1034 2260 194
INTRON_3 77813 ACTCTAATCTTTATTTTTTTTCCTCTCTTTTCTTTGCTTCGGGTTGAGTT 77862
i v -- ii i vi i v
C L1M4_orf2#LIN 1034 GCTCTAATCTTTATTATTT--CCTTCCTTCTGCTTGCTTTGGGTTTAGTT 987
INTRON_3 77863 TACTCTTCCTTTTCTAGGTTCTTAAGGTAGAAACTTAGGTCACTTATTTG 77912
i i v i iv i i v
C L1M4_orf2#LIN 986 TGCTCTTCTTTTTCTAGTTTCTTAAGGTGGAAGGTTAGGTTATTGATTTG 937
INTRON_3 77913 AGAGATCTTTTTCCTTTTCTAATAGAGCCATTTAAAACTATAAATGTCCC 77962
-- i i i v v v i v
C L1M4_orf2#LIN 936 AGA--TCTTTCTTCTTTTTTAATATAGGCATTTACAGCTATAAATTTCCC 889
INTRON_3 77963 TCTAAGTATTGCTT 77976
i i
C L1M4_orf2#LIN 888 TCTAAGCACTGCTT 875
Matrix = 20p37g.matrix
Transitions / transversions = 1.80 (18 / 10)
Gap_init rate = 0.01 (2 / 163), avg. gap size = 2.00 (4 / 2)
+ 371 34.0 10.0 0.8 INTRON_3 78478 78705 (321476) + L2c LINE/L2 3067 3299 (76) 101
ANNOTATION EVIDENCE:
247 39.87 6.58 4.29 INTRON_3 78478 78705 321476 + L2b_3end LINE/L2 158 390 76 157
INTRON_3 78478 ACTTCCTTCCTCCCACCCACTTTTGTCTGGTTAATGCCTACTCACTCTTC 78527
vi -- i--i i i ii iv ii
L2b_3end#LINE 158 ACGCCCTTCC--CCACCT--CTTCGCCTGGCCAACTCCTACTCATCCTTC 203
INTRON_3 78528 AAGCCTTGGCTTAGATATT---TCTTCTAGAA----TTCTCTGAGTGTTT 78570
i i ii i i i i--- i i i ----i i viviii
L2b_3end#LINE 204 AGGTCTCAGCTCAAATGTCACCTCCTCCAGGAAGCCCTCCCTGACCCCCC 253
INTRON_3 78571 GTACTTCATTAGACCTCCTCTTTCATAACACTCT-GTCTTAACTCTATCA 78619
ivi ivvi i i vi i iiiviv v i i- i - i ii
L2b_3end#LINE 254 AGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTA-CCCTGCCA 302
INTRON_3 78620 TAGTGA-TTATTACAATTTTATGTAATTTTATGCCTGTTTATC----TGT 78664
ivv i- ? ----- i v i? vi i i vi ---- v
L2b_3end#LINE 303 CTCTGGGTTATNA-----TTGTCTGNTTACATGTCTGTCTCCCCCACTGG 347
INTRON_3 78665 TTTCCATGTTCTCTGAGGACAGGGCCCA--TCAGTTTGGTTCA 78705
vi viiv i iv i v i-- v i v
L2b_3end#LINE 348 ACTGTGAGCTCCGTGAGGGCAGGGACCGGGTCTGTCTTGTTCA 390
Matrix = 25p37g.matrix
Transitions / transversions = 2.54 (61 / 24)
Gap_init rate = 0.04 (10 / 227), avg. gap size = 2.50 (25 / 10)
371 32.61 10.87 0.00 INTRON_3 78485 78668 321513 + L2c_3end LINE/L2 164 367 111 158
INTRON_3 78485 TCCTCCCACCCACTTTTGTCTGGTTAATGCCTACTCACTCTTCAAGCCTT 78534
i v iv iiii i iv ii ? i
L2c_3end#LINE 164 TCTTCCCCCCTCCTTCCACCTGGCTAACTCCTACTCATCCTTCAAGNCTC 213
INTRON_3 78535 GGCTTAGATATT---TCTTCTAGAA----TTCTCTGAGTGTTTGTACTTC 78577
i i i i--- i i i ---- i viviiiivi?i v
L2c_3end#LINE 214 AGCTCAGATGTCACCTCCTCCAGGAAGCCTTCCCTGACCCCCCAAGNCTA 263
INTRON_3 78578 AT-TAGA---CCTCCTCTTT-----CATAACACTCTGTCTTAACTCT-AT 78617
i - i--- v ----- i i vv i-
L2c_3end#LINE 264 GTCTAGGTGCCCTCCTCTGTGCTCCCATAGCACCCTGTCTATACTCCCAT 313
INTRON_3 78618 CATAGTGATTATTAC-AATTT-TAT-GTAATTTTATGCCTGTTTATCTGT 78664
i iiv i i- i - - v v ii ii? i
L2c_3end#LINE 314 TATAGCACTTATCATTAACTTGTATTGTAATTGTCTGTTTACNTGTCTGT 363
INTRON_3 78665 TTTC 78668
i i
L2c_3end#LINE 364 CTCC 367
Matrix = 25p37g.matrix
Transitions / transversions = 3.38 (44 / 13)
Gap_init rate = 0.05 (9 / 183), avg. gap size = 2.22 (20 / 9)
+ 21 71.4 0.0 0.0 INTRON_3 78746 78773 (321408) + AT_rich Low_complexity 1 28 (0) 102
ANNOTATION EVIDENCE:
21 71.43 0.00 0.00 INTRON_3 78746 78773 321408 + AT_rich Low_complexity 123 150 150 167
INTRON_3 78746 AATAAAAATAATTGATTTTTAAAATTTA 78773
?????????????????v v v
AT_rich#Low_c 123 WWWWWWWWWWWWWWWWWATTAAAAATAA 150
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 3)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 180 0.0 0.0 0.0 INTRON_3 79614 79633 (320548) + (TA)n Simple_repeat 2 21 (0) 103
ANNOTATION EVIDENCE:
180 0.00 0.00 0.00 INTRON_3 79614 79633 320548 C (TA)n Simple_repeat 160 179 1 256
INTRON_3 79614 ATATATATATATATATATAT 79633
C (TA)n#Simple_ 179 ATATATATATATATATATAT 160
Matrix = Unknown
Transitions / transversions = 0.0 (0 / 0)
Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0)
+ 22 63.6 0.0 0.0 INTRON_3 80005 80026 (320155) + AT_rich Low_complexity 1 22 (0) 104
ANNOTATION EVIDENCE:
22 63.64 0.00 0.00 INTRON_3 80005 80026 320155 C AT_rich Low_complexity 142 163 137 168
INTRON_3 80005 GTTTATATATTTAAATAAAATA 80026
?vvvv vvvvvvvvv
C AT_rich#Low_c 163 SAAATTATATTATTTATTTTTA 142
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 13)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)
+ 2438 8.8 0.0 0.7 INTRON_3 80120 80427 (319754) C AluSc5 SINE/Alu (6) 306 1 105
ANNOTATION EVIDENCE:
2298 10.71 0.32 0.00 INTRON_3 80120 80427 319754 C AluSx SINE/Alu 1 309 3 128
INTRON_3 80120 TTTTTCTATTTTTTGTTTTTGTTTTTTGAGACGGAGTCTCACTCTGTCAC 80169
i v v v i i
C AluSx#SINE/Al 309 TTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGC 260
INTRON_3 80170 C-AGGCTGGAGTGCAGTGGCGCGATCTCAGCTCACTGCAACCTCCGACTC 80218
- i v
C AluSx#SINE/Al 259 CCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTC 210
INTRON_3 80219 CCTGGTTCAAGCAATTCTCCTGCCTCAGCTTCCTGAGTAGCTGGGATTAC 80268
v i i i
C AluSx#SINE/Al 209 CCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTAC 160
INTRON_3 80269 AGGCACGTGCCACCATGCCCAGATAATTTTTGTATTTTTAGTAGAGATGG 80318
i i i i v i
C AluSx#SINE/Al 159 AGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGG 110
INTRON_3 80319 GGTTTCACCGTGTTGGCCAGGATGATCTCAATCTCCTGACCTCAGGTGAT 80368
i v i i v
C AluSx#SINE/Al 109 GGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGAT 60
INTRON_3 80369 CCACATGGCTCAATCTCCCAAAGTGCTGGGATTACAGGTGTAAGCCACTG 80418
i vi v iii i i i
C AluSx#SINE/Al 59 CCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCG 10
INTRON_3 80419 CGCCCGGCC 80427
C AluSx#SINE/Al 9 CGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 2.30 (23 / 10)
Gap_init rate = 0.00 (1 / 307), avg. gap size = 1.00 (1 / 1)
+ 209 30.1 1.2 2.4 INTRON_3 80441 80525 (319656) + (CATATA)n Simple_repeat 5 88 (0) 106
ANNOTATION EVIDENCE:
209 30.13 1.18 2.38 INTRON_3 80441 80525 319656 + (CATATA)n Simple_repeat 5 88 92 262
INTRON_3 80441 TATATGCACATATGAACATATATTTATATTTCTATGCACATATAAGCACA 80490
i ii iv i i v i v vi ii -- i
(CATATA)n#Sim 5 TACATATACATATACATATACATATACATATACATATACATATA--CATA 52
INTRON_3 80491 TTTATATAAACATATGTA-ACAAATGCATAAATATA 80525
vi v i ii - v i v i
(CATATA)n#Sim 53 TACATATACATATACATATACATATACATATACATA 88
Matrix = Unknown
Transitions / transversions = 2.12 (17 / 8)
Gap_init rate = 0.02 (2 / 84), avg. gap size = 1.50 (3 / 2)
+ 574 24.5 16.1 2.0 INTRON_3 80578 80944 (319237) C L1M5 LINE/L1 (424) 5700 5278 107
ANNOTATION EVIDENCE:
434 30.44 11.58 1.76 INTRON_3 80578 80888 319293 C L1ME2_3end LINE/L1 104 444 467 195
INTRON_3 80578 CATCCTTTTATGTGTATTTTTATGAACTTGTGATAATATTTCTGATTGAC 80627
i v iiv v i i v i v vvi vv v ii
C L1ME2_3end#LI 444 CATTCTTGTACAAGTCTTTTTGTGGACATATGTTTTCATTTCTCTTGGGT 395
INTRON_3 80628 AATTTACTAGAAGTAGAATTGATAGACTAAAGGTTATTCACATTTTAAAC 80677
v vv i i v i iii v v vviii v v
C L1ME2_3end#LI 394 AAATACCTAGGAGTGGAATTGCTGGGTCATAGGGTAGGTGTATGTTTAAC 345
INTRON_3 80678 AGTACAGGGAAATTGCCCA--------CCTAAATGGTT---------TAC 80710
vv i i - i v -------- v i ---------
C L1ME2_3end#LI 344 TTTATAAG-AAACTGCCAAACNGTTTTCCAAAGTGGTTGTACCATTTTAC 296
INTRON_3 80711 ACTCTTTTCAACTGTGAATGTGAGTATCCTTTTTCTCCACACCATTGCCA 80760
iivi i vi v v - ivv v i v i
C L1ME2_3end#LI 295 ACTCCCACCAGCAATGTATGAGAGT-TCTAGTTGCTCCACATCCTCGCCA 247
INTRON_3 80761 ACATG-GGTATTACCGATCTTTTTAATTCTTGCCA-------AGCTGAAA 80802
v- ii ii i v -------i v vi
C L1ME2_3end#LI 246 ACATTTGGTATTGTCAGTCTTTTTAATTTTAGCCATTCTAGTGGGTGTGA 197
INTRON_3 80803 AGTGGTATCTTCCTGT---------TTGCAATTTCCTTATACCTAATGAG 80843
ivi --------- v i v iv v
C L1ME2_3end#LI 196 AGTGGTATCTCATTGTGGTTTTAATTTGCATTTCCCTGATGACTAATGAT 147
INTRON_3 80844 ATGGAGCCTCTGGCATTTCTTCTGCAAATTGCCTAT--GTATATCCT 80888
i v vi ---- v v vv v i -- i
C L1ME2_3end#LI 146 GTTGAGCACCT----TTTCATGTGCTTATTGGCCATTTGTATATCTT 104
Matrix = 20p37g.matrix
Transitions / transversions = 0.94 (45 / 48)
Gap_init rate = 0.03 (9 / 310), avg. gap size = 4.67 (42 / 9)
506 29.79 12.27 0.65 INTRON_3 80578 80854 319327 C L1ME3C_3end LINE/L1 133 441 429 196
INTRON_3 80578 CATCCTTTTATGTGTATTTTTATGAACTTGTGATAATATTTCTGATTGAC 80627
i v ii v ii i v vi vv ivi v- v iv
C L1ME3C_3end#L 441 CATTCTTGTACATGTCTCCTTGTGCACACGTGCGAGAGTTTCTC-TAGGG 393
INTRON_3 80628 AATTTAC-TAGAAGTAGAATTGATAGACTAAAGGTTATTCACATTTTAAA 80676
v v - i i v i iiiiv v v i i v
C L1ME3C_3end#L 392 TATATACCTAGGAGTGGAATTGCTGGGTCGTAGGGTATGCGCATCTTCAA 343
INTRON_3 80677 CAGTACAGGG-------AAATTGCCCACCTAAATGGTT---------TAC 80710
vv vi i------- i v v i ---------
C L1ME3C_3end#L 342 CTTTACTAGATATTGCCAAATTGCTCTCCAAAGTGGTTGTACCAATTTAC 293
INTRON_3 80711 ACTCTTTTCAACTGTGAATGTGAGTATCCTTTTTCTCCACACCATTGCCA 80760
iivi i v v v - iv v i v i
C L1ME3C_3end#L 292 ACTCCCACCAGCAGTGTATGAGAGT-TCCCGTTGCTCCACATCCTCGCCA 244
INTRON_3 80761 ACA-TGGGTATTACCGATCTTTTTAATTCTTGCCAAGCTGA-------AA 80802
- v ii iiv v i v -------i
C L1ME3C_3end#L 243 ACACTTGGTATTGTCAGACTTTTAAATTTTTGCCAATCTGATGGGTGTGA 194
INTRON_3 80803 AGTGGTATCTTCCTGT---------TTGCAATTTCCTTATACCTAATGAG 80843
i ivi --------- v i v vv i
C L1ME3C_3end#L 193 AATGGTATCTCATTGTCGTTTTAATTTGCATTTCCCTGATTACTAGTGAG 144
INTRON_3 80844 ATGGAGCCTCT 80854
i v v
C L1ME3C_3end#L 143 GTTGAGCATCT 133
Matrix = 20p37g.matrix
Transitions / transversions = 1.05 (42 / 40)
Gap_init rate = 0.03 (8 / 276), avg. gap size = 4.50 (36 / 8)
574 25.26 12.81 1.87 INTRON_3 80578 80819 319362 C L1ME4a_3end LINE/L1 180 447 424 197
INTRON_3 80578 CATCCTTTTATGTGTATTTTTATGAAC--TTGTGATAATATTTCTGATT- 80624
v ii iv i i ?v --i v -- i-- -
C L1ME4a_3end#L 447 CATCCTTGTACATAAATCTTTGTNCACATCTCTGAT--TATTTCC--TTA 402
INTRON_3 80625 -GACAATTTACTAGAAGTAGAATTGATAGACTAAAGGTTATTCACATTTT 80673
- i v v i iv i iii v v?
C L1ME4a_3end#L 401 GGATAAATTCCTAGAAGTGGAATTACTGGGTCAAAGGGTATGNACATTTT 352
INTRON_3 80674 AAA------CAGTACA----GGGAAATTGCCCACCTAAATGGTT------ 80707
v ------iii ---- vv v vi v ------
C L1ME4a_3end#L 351 TAAGGCTCTTGATACATATTGCCAAATTGCCCTCCAGAAAGGTTGTACCA 302
INTRON_3 80708 ---TACACTCTTTTCAACTGTGAATGTGAGTATCCTTTTTCTCCACACCA 80754
--- iivi i v v v ii v - ? v
C L1ME4a_3end#L 301 ATTTACACTCCCACCAGCAGTGTATGAGAGTGCCCGTTT-CNCCACACCC 253
INTRON_3 80755 TTGCCAACA-TGGGTATTACCGATCTTTTTAATTCTTGCCAA-------G 80796
i - ? i i v ii -------
C L1ME4a_3end#L 252 TCGCCAACACTGNGTATTATCAATCTTTTAAATCTTTGCCAATTTGATAG 203
INTRON_3 80797 CTGAAAAGTGGTATCTTCCTGTT 80819
v i ivi
C L1ME4a_3end#L 202 GTGAAAAATGGTATCTCATTGTT 180
Matrix = 20p37g.matrix
Transitions / transversions = 1.33 (32 / 24)
Gap_init rate = 0.04 (10 / 241), avg. gap size = 3.60 (36 / 10)
361 23.52 17.99 2.17 INTRON_3 80706 80944 319237 C L1ME3B_3end LINE/L1 25 300 689 198
INTRON_3 80706 TTTACACTCTTTTCAACTGTGAATGTGAGTATCCTTTTTCTCCACACCAT 80755
iivi i v i v v - iv v i v
C L1ME3B_3end#L 300 TTTACACTCCCACCAGCAGCGTATGAGAGT-TCCCGTTGCTCCACATCCT 252
INTRON_3 80756 TGCCAACA-TGGGTATTACCGATCTTTTTAATTCTTGCCAAGCTGAAA-- 80802
i - v ii iiv ? i v ivi--
C L1ME3B_3end#L 251 CGCCAACACTTGGTATTGTCAGACTTTTNAATTTTTGCCAATCTGGTGGG 202
INTRON_3 80803 -----AGTGGTATCTTCCTGT---------TTGCAATTTCCTTATACCTA 80838
----- ivi --------- v i v vv
C L1ME3B_3end#L 201 TGTGTAGTGGTATCTCATTGTGGTTTTAATTTGCATTTCCCTGATTACTA 152
INTRON_3 80839 ATGAGATGGAGCCTCTGGCATTTCTTCTGCAAATTGCCTAT--GTATATC 80886
i v vi ---- v v ivv v i -- v v
C L1ME3B_3end#L 151 ATGAGGTTGAGCACCT----TTTCATATGTTTATTGGCCATTTGGATTTC 106
INTRON_3 80887 CT------TG------CTGTTT-----TTTT-----TTTCTGTGTGTGTG 80914
------ ------ i----- ----- i v i - v
C L1ME3B_3end#L 105 CTCTTTTGTGAAGTGCCTGTTCAAGTCTTTTGCCCATTTTTCTAT-TGGG 57
INTRON_3 80915 TTGTTTGTATTTTTCATATTGATTTG--GGAG 80944
v v --
C L1ME3B_3end#L 56 TTGTTTGTCTTTTTCTTATTGATTTGTAGGAG 25
Matrix = 20p37g.matrix
Transitions / transversions = 0.86 (25 / 29)
Gap_init rate = 0.05 (12 / 238), avg. gap size = 4.08 (49 / 12)
+ 413 28.9 1.4 6.0 INTRON_3 81068 81207 (318974) C MIRb SINE/MIR (51) 217 84 108
ANNOTATION EVIDENCE:
413 28.86 1.43 5.97 INTRON_3 81068 81207 318974 C MIRb SINE/MIR 84 217 51 159
INTRON_3 81068 TAAGATTTTCACATATATT--CTCATATAACTCCTAAAACAAACTTATGA 81115
vvi i ii -- v ii ii v v i ii
C MIRb#SINE/MIR 217 TAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGA 168
INTRON_3 81116 AGGTAAGAATTACTATCATCATCATGTAGATGAACTAACTGAGGTTCATA 81165
- i v i vi iv ii ivv i v
C MIRb#SINE/MIR 167 -GGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGA 119
INTRON_3 81166 GGGCTTCAGTGACTTGTTCCAGAAGGAAGGGCTCACATCTAG 81207
i v v ii ------- v v v
C MIRb#SINE/MIR 118 GAGGTTAAGTGACTTGCCC-------AAGGTCACACAGCTAG 84
Matrix = 25p37g.matrix
Transitions / transversions = 1.38 (22 / 16)
Gap_init rate = 0.02 (3 / 139), avg. gap size = 3.33 (10 / 3)
+ 561 16.9 25.9 0.6 INTRON_3 82403 82574 (317607) C MIR SINE/MIR (52) 216 2 109
ANNOTATION EVIDENCE:
243 14.63 0.00 0.00 INTRON_3 82403 82443 317738 C MIRb SINE/MIR 176 216 52 160
INTRON_3 82403 AAGTACTTTATGTACAATATCTCATTTAATCCTCACAACAA 82443
ii ii i v
C MIRb#SINE/MIR 216 AAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAA 176
Matrix = 25p37g.matrix
Transitions / transversions = 5.00 (5 / 1)
Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0)
561 17.59 10.32 0.72 INTRON_3 82449 82574 317607 C MIR SINE/MIR 2 139 123 161
INTRON_3 82449 TTTGCAGATAGGGAACATGAGACACAGAGAG--TAAGTAATTTGCCCAAG 82496
i ii vv i -- i
C MIR#SINE/MIR 139 TTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAG 90
INTRON_3 82497 CTCAAACAGCTAGTAATTGGCAGAGCCAAG----GGCTCCA--TAGTCTG 82540
v v v ii ---- ivi --i
C MIR#SINE/MIR 89 GTCACACAGCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCAGTCTG 40
INTRON_3 82541 TGCTCCTAA--CCAT---CTTAACTACTATGCTGTATTG 82574
- vi -- i --- i i i
C MIR#SINE/MIR 39 -GCTCCAGAGTCCGTGCTCTTAACCACTATGCTATACTG 2
Matrix = 25p37g.matrix
Transitions / transversions = 2.14 (15 / 7)
Gap_init rate = 0.05 (6 / 125), avg. gap size = 2.33 (14 / 6)
+ 245 24.6 1.5 1.5 INTRON_3 82618 82683 (317498) C MIR SINE/MIR (0) 262 197 110
ANNOTATION EVIDENCE:
245 24.61 1.52 1.52 INTRON_3 82618 82683 317498 C MIR SINE/MIR 197 262 0 162
INTRON_3 82618 AACAATAGCTAACATTTATTGAGTTTTTATTATATTCCAGGACA-TCTAC 82666
i i i ivi i i v - - v v
C MIR#SINE/MIR 262 AATAATAACCAACATTTATTGAGCGCTTACTATGTGCCAGG-CACTGTTC 214
INTRON_3 82667 TACATACTTTACAGGTA 82683
viii v
C MIR#SINE/MIR 213 TAAGCGCTTTACATGTA 197
Matrix = 25p37g.matrix
Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2)
+ 227 37.9 5.8 0.9 INTRON_3 82679 82782 (317399) C MIR SINE/MIR (152) 110 2 110 *
ANNOTATION EVIDENCE:
227 37.85 5.77 0.92 INTRON_3 82679 82782 317399 C MIR SINE/MIR 2 110 152 163
INTRON_3 82679 AGGTAAAATG--TTACTTAAAGCCATAAAATCAATAA-TGGCAGTGCTGG 82725
v i i-- i ii i i i v iii i - v i
C MIR#SINE/MIR 110 AGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGG 61
INTRON_3 82726 AATTTAAGCATAGATTTGTCTTATGCTAGAAACTGTA---TTAACTGTCC 82772
i ii i vi iiv- viiv i iv i i--- iiiiv
C MIR#SINE/MIR 60 GATTCGAACCCAGGCA-GTCTGGCTCCAGAGTCCGTGCTCTTAACCACTA 12
INTRON_3 82773 TGCTATACTG 82782
C MIR#SINE/MIR 11 TGCTATACTG 2
Matrix = 25p37g.matrix
Transitions / transversions = 3.33 (30 / 9)
Gap_init rate = 0.04 (4 / 103), avg. gap size = 1.75 (7 / 4)
+ 31 58.1 0.0 0.0 INTRON_3 83222 83252 (316929) + AT_rich Low_complexity 1 31 (0) 111
ANNOTATION EVIDENCE:
31 58.06 0.00 0.00 INTRON_3 83222 83252 316929 + AT_rich Low_complexity 137 167 133 169
INTRON_3 83222 TTTTTTAAATAAAAAAAAAATTTAAATTTTT 83252
???v v v v v vvvvv?????
AT_rich#Low_c 137 WWWATTAAAAATAAATAATATAATTTWWWWW 167
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 10)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)
+ 1850 11.9 2.4 1.0 INTRON_3 83253 83549 (316632) C L1MA3 LINE/L1 (270) 6035 5735 112
ANNOTATION EVIDENCE:
1850 11.90 2.36 1.00 INTRON_3 83253 83549 316632 C L1MA3_3end LINE/L1 482 782 270 199
INTRON_3 83253 ATTAACTATCCTGACTCTCTTACCCCCAACA-ACTGCCATTCCCAGCCTC 83301
i iv ii --- v v- i v
C L1MA3_3end#LI 782 ATTAACCATCCCCACTTCC---CCCCCACCCCACTACCCTTCCCAGCCTC 736
INTRON_3 83302 TGATAACCATCATTCTACTCTCTATCTCCATGAATTCATTTGTTTTAATT 83351
i v i v
C L1MA3_3end#LI 735 TGGTAACCATCCTTCTACTCTCTATCTCCATGAGTTCAATTGTTTTAATT 686
INTRON_3 83352 TTTAGTTCGCACAAGTAAGTGAGAACATGCAAAGTTCATTTTTCTGTTCC 83401
i v i ii ii i v
C L1MA3_3end#LI 685 TTTAGCTCCCACAAATAAGTGAGAACATGTGAAGTTTGTCTTTCTGTGCC 636
INTRON_3 83402 TGGTTTATTTCACCTAA-----TGACCTCCAGTTCCATTTGTGTTTTTGC 83446
i i ----- iii v
C L1MA3_3end#LI 635 TGGCTTATTTCACTTAACATAATGACCTCCAGTTCCATCCATGTTGTTGC 586
INTRON_3 83447 AAATGACAGGATCTCATTCTTTTT-ATGGCTAAATAGTACTCTATTGTAT 83495
- i i i
C L1MA3_3end#LI 585 AAATGACAGGATCTCATTCTTTTTTATGGCTGAATAGTACTCCATTGTGT 536
INTRON_3 83496 GTATGTACCACATTTTCTTTATCCATTAGTCTGTTGATGGACACTTAGAT 83545
i vi i
C L1MA3_3end#LI 535 ATATGTACCACATTTTCTTTATCCATTCATCTGTTGATGGACACTTAGGT 486
INTRON_3 83546 TGCT 83549
C L1MA3_3end#LI 485 TGCT 482
Matrix = 20p37g.matrix
Transitions / transversions = 2.50 (25 / 10)
Gap_init rate = 0.01 (4 / 296), avg. gap size = 2.50 (10 / 4)
+ 698 15.5 3.9 0.0 INTRON_3 83543 83553 (316628) C L1M1 LINE/L1 (7422) 143 133 113 *
ANNOTATION EVIDENCE:
698 15.50 3.88 0.00 INTRON_3 83543 83553 316628 C L1M1_5end LINE/L1 133 143 3532 200
INTRON_3 83543 GATTGCTCACC 83553
i
C L1M1_5end#LIN 143 GATCGCTCACC 133
Matrix = 20p37g.matrix
Transitions / transversions = 0.0 (1 / 0)
Gap_init rate = 0.00 (0 / 10), avg. gap size = 0.0 (0 / 0)
+ 2413 10.4 0.3 0.0 INTRON_3 83554 83861 (316320) C AluSp SINE/Alu (4) 309 1 114
ANNOTATION EVIDENCE:
2208 12.05 0.32 0.32 INTRON_3 83554 83861 316320 C AluSx SINE/Alu 1 308 4 129
INTRON_3 83554 TTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTTTCGCTCTTATTGC 83603
i i -i i
C AluSx#SINE/Al 308 TTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCT-GTCGC 260
INTRON_3 83604 CCAGGCTGGAGCGCAATGGCCCAATCTCAGCTTACCTCAACCTCTGCTTC 83653
i i v i i i iv i i
C AluSx#SINE/Al 259 CCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTC 210
INTRON_3 83654 CCTGGTTCAAGTGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTAT 83703
v i i i
C AluSx#SINE/Al 209 CCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTAC 160
INTRON_3 83704 AGGCATGCACCACCACGCCTGGCTAATTTT-GTATTTTTAGTAGAGACAG 83752
ii i i - i
C AluSx#SINE/Al 159 AGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGG 110
INTRON_3 83753 GGTTTCTCCATGTTGGTCAGGCTGGTCCCAACCTCCTGACTTCAGGTGAT 83802
v i i i v i
C AluSx#SINE/Al 109 GGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGAT 60
INTRON_3 83803 CTGCCCACCTCAGTCTCCCAAAGTGCTGGGATTGCAGGCATGAGCCACTG 83852
i i i i i i i
C AluSx#SINE/Al 59 CCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCG 10
INTRON_3 83853 CGCCCAGCC 83861
i
C AluSx#SINE/Al 9 CGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 6.40 (32 / 5)
Gap_init rate = 0.01 (2 / 307), avg. gap size = 1.00 (2 / 2)
+ 698 15.5 3.9 0.0 INTRON_3 83862 83978 (316203) C L1M1 LINE/L1 (7433) 132 11 113
ANNOTATION EVIDENCE:
698 15.50 3.88 0.00 INTRON_3 83862 83978 316203 C L1M1_5end LINE/L1 11 132 3543 201
INTRON_3 83862 TATTTTTGTTTTTTATGAAGGTGTTTTTTTGGGTAGATAGTTGTTAAATT 83911
v v i i v i v
C L1M1_5end#LIN 132 GATTTTTGGTTCTTATGAAGGTGCTTTTTTGTGTGGATAGTTGTTCAATT 83
INTRON_3 83912 TAGTGTTCTTGTGTGGAGGA----CAATCAGTGAAAGATTCTATTTGGCC 83957
i i i v ---- i i i i v i
C L1M1_5end#LIN 82 TGGTGTTCCTGCGGGGAGGATGGACGATCGGTGGAGGCTTCTATTCGGCC 33
INTRON_3 83958 ATCTTGCTCCACCTCT-TCTAA 83978
i i-
C L1M1_5end#LIN 32 ATCTTGCTCCGCCTCCCTCTAA 11
Matrix = 20p37g.matrix
Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.02 (2 / 116), avg. gap size = 2.50 (5 / 2)
+ 23 47.8 0.0 0.0 INTRON_3 84635 84657 (315524) + AT_rich Low_complexity 1 23 (0) 115
ANNOTATION EVIDENCE:
23 47.83 0.00 0.00 INTRON_3 84635 84657 315524 C AT_rich Low_complexity 138 160 140 170
INTRON_3 84635 TTAATATTTTTATTTAAAAAAGG 84657
v v v vv vvv v??
C AT_rich#Low_c 160 ATTATATTATTTATTTTTAATSS 138
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 9)
Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0)
+ 1908 15.2 4.0 0.0 INTRON_3 85041 85337 (314844) + MER58B DNA/hAT-Charlie 1 309 (32) 116
ANNOTATION EVIDENCE:
1908 15.15 4.04 0.00 INTRON_3 85041 85337 314844 + MER58B DNA/hAT-Charlie 1 309 32 265
INTRON_3 85041 CAAGGATTGGTAAACTATGGCCCATGGGCCAAATCTGGCCTGCTTCCTGT 85090
i i i i i ii i i iv
MER58B#DNA/hA 1 CAGGGGTCGGCAAACTACGGCCCGCGGGCCAAATCCGGCCCGCCGCCTGT 50
INTRON_3 85091 TTTAGTATGGTCTGCAAACTGAGAATGGTTTTAACATTTTTAAATGATTG 85140
v i i i i i i v i
MER58B#DNA/hA 51 TTTTGTACGGCCCGCGAGCTAAGAATGGTTTTTACATTTTTAAATGGTTG 100
INTRON_3 85141 AAAAAAA--TCAAAGGAAGGATAATATTTCATGACATGTGAAAAGTATAT 85188
-- i i i i v
MER58B#DNA/hA 101 AAAAAAAAATCAAAAGAAGAATAATATTTCGTGACACGTGAAAATTATAT 150
INTRON_3 85189 GAAATCCAAATTTCAGTATTCATAAAT----------TGGAACACAGCCA 85228
i i i ----------
MER58B#DNA/hA 151 GAAATTCAAATTTCAGTGTCCATAAATAAAGTTTTATTGGAACACAGCCA 200
INTRON_3 85229 TGCTCATTCATTTACATATTGTCTATGGTTGCTTTTATGCTACAACAGCA 85278
i i i i iii i
MER58B#DNA/hA 201 CGCTCATTCGTTTACGTATTGTCTATGGCTGCTTTCGCGCTACAACGGCA 250
INTRON_3 85279 AAGTTGAATAGTTGTAACAGAGCCCATATGGCTCACAAAGCCTAAAATAA 85328
i i ii v i i i v
MER58B#DNA/hA 251 GAGTTGAGTAGTTGCGACAGAGACCGTATGGCCCGCAAAGCCTAAAATAT 300
INTRON_3 85329 TTACTATCT 85337
MER58B#DNA/hA 301 TTACTATCT 309
Matrix = 20p37g.matrix
Transitions / transversions = 6.50 (39 / 6)
Gap_init rate = 0.01 (2 / 296), avg. gap size = 6.00 (12 / 2)
+ 947 22.5 12.3 1.0 INTRON_3 87028 87415 (312766) C L1ME2 LINE/L1 (7) 6330 5899 117
ANNOTATION EVIDENCE:
947 19.43 8.29 0.43 INTRON_3 87028 87244 312937 C L1ME2_3end LINE/L1 671 904 7 202
INTRON_3 87028 TTGAAGTAAAATTTATATGTGGTAAAATGCAAACATCTTACATGTACAAT 87077
i v i iiii v v vi i
C L1ME2_3end#LI 904 TTGAGGTATAATTTACATACAATAAAATGCACAGATCTTAAGTGTACAGT 855
INTRON_3 87078 TTGATTAGTTTTGATAAAATTATACACCTATGTAACCACCACCTCAGTCA 87127
i v i vv i i i?
C L1ME2_3end#LI 854 TCGATGAGTTTTGACAAATGTATACACCCATGTAACCACCACCCCAANCA 805
INTRON_3 87128 AGATCTAGAACATTTTCATCACCC-AGAAAGTCCCCTTATCATTTCTTTC 87176
v i - i i -iiii
C L1ME2_3end#LI 804 AGATATAGAACATTTCCATCACCCCAGAAAGTTCCCTTGT-GCCCCTTTC 756
INTRON_3 87177 CAG-CAAATCCTCACCTCCC-AAAGGCAACC--------------TGTCA 87210
- vi i i -ii --------------
C L1ME2_3end#LI 755 CAGTCAATCCCCCACCCCCCCGGAGGCAACCACTGTTCTGATTTCTGTCA 706
INTRON_3 87211 CTATAGATTA-TTTCACCTGTTCATATACTTCATA 87244
i - ii vviv
C L1ME2_3end#LI 705 CCATAGATTAGTTTTGCCTGTTCTAGAACTTCATA 671
Matrix = 20p37g.matrix
Transitions / transversions = 2.42 (29 / 12)
Gap_init rate = 0.03 (6 / 216), avg. gap size = 3.17 (19 / 6)
383 26.45 6.36 1.66 INTRON_3 87243 87415 312766 C L1ME2z_3end LINE/L1 473 653 538 203
INTRON_3 87243 TACGTACTCTTTTGTTT----CTTGTTTAAGCTTAACCTAACGTTCTCAA 87288
i v ---- v v - i i v i i ii
C L1ME2z_3end#L 653 TATGTACTCTTTTGTGTAAGGCTTCTTTCA-CTCAGCATAATGTTTTTGA 605
INTRON_3 87289 TACTCATCTACTTTGCTGTATGTATCAGTAGTTCA---CTTAAAAAATTT 87335
v i i iv i ii i--- vvv -- v
C L1ME2z_3end#L 604 GATTCATCCATGTTGTTGCGTGTATCAGTAGTTCGTTCCTTTTTA--TTG 557
INTRON_3 87336 CTGGGTTGTTTTCCATTGTATGAATATCCTACAATTGATATATGATTTCT 87385
i v v v i i vi v vvv
C L1ME2z_3end#L 556 CTGAGTAGTATTCCATTGTATGAATATACCACAGTTTGTTTATCCATTCT 507
INTRON_3 87386 CATGTTAA----CTTCTAACTTGTTTTCAGTTTT 87415
v i ---- vi iivi i
C L1ME2z_3end#L 506 CCTGTTGATGGACACCTGGGCTGTTTCCAGTTTT 473
Matrix = 20p37g.matrix
Transitions / transversions = 1.14 (24 / 21)
Gap_init rate = 0.03 (5 / 172), avg. gap size = 2.80 (14 / 5)
+ 824 26.4 5.5 2.1 INTRON_3 87419 87693 (312488) C L1ME2 LINE/L1 (975) 5344 5061 117
ANNOTATION EVIDENCE:
824 26.38 5.45 2.11 INTRON_3 87419 87693 312488 C L1M5_orf2 LINE/L1 2779 3062 232 204
INTRON_3 87419 GAGTAGAAAGTTTTGATTATGATAAAATCCAGTTTATCAAAATTTTATTT 87468
ii iv i i v i v i ? i vv v?
C L1M5_orf2#LIN 3062 GAACAGAAGTTCTTAATTTTAATATAGTCNAATTTATCAATTTTTTCNTT 3013
INTRON_3 87469 TATGGTTAATGCTCTCTGTGTCCCATTTAAGAAATTGTTGTCTACTCCCA 87518
i i i ii iv i -
C L1M5_orf2#LIN 3012 TATGGTTAGTGCTTTTTGTGTCCTGTTTAAGAAATCTTTGCCTAC-CCCA 2964
INTRON_3 87519 AGGGCATAAAATTTTTTCTCCTTTGTTTTCTTCTACACATGTAATAGCTT 87568
v iv v - v ? v viiv v ? i
C L1M5_orf2#LIN 2963 AGGTCATAAAGATATT-CTCCTATGTTNTCTTCTAGAAGCTTTATNGTTT 2915
INTRON_3 87569 TAGCTCTTACGATGAAGTTTATGATCCATTTCACATCAACTAATTTTT-- 87616
v i i iv v i i i i vi---- i i --
C L1M5_orf2#LIN 2914 TACCTTTCACATTTAGGTCTATAATCCATCTGG----AATTGATTTTTGT 2869
INTRON_3 87617 ----------AGG--GAGATTAATATTCACTTTTC-CCTTATGTTTATTC 87653
---------- -- i i i v? i i- v vv i
C L1M5_orf2#LIN 2868 GTATGGTGTGAGGTAGGGGTCAAGNTTCATTTTTTTCCATATGGATATCC 2819
INTRON_3 87654 AATTGTTCCAGCAACATTTGTTGAAAAGACCACCCTTCCC 87693
?i v i i ii i
C L1M5_orf2#LIN 2818 AATTGNCCCAGCACCATTTATTGAAAAGACTATTCTTTCC 2779
Matrix = 20p37g.matrix
Transitions / transversions = 1.71 (41 / 24)
Gap_init rate = 0.02 (6 / 274), avg. gap size = 3.50 (21 / 6)
+ 1931 24.6 6.5 3.5 INTRON_3 87713 88632 (311549) C L1ME2 LINE/L1 (2434) 3885 2937 117
ANNOTATION EVIDENCE:
1906 23.72 6.80 3.89 INTRON_3 87713 88462 311719 C L1M5_orf2 LINE/L1 833 1603 1691 205
INTRON_3 87713 GGGCTATTGGTTTATAACCTTTTTTTCTTCTCAGATTAACAGCTTGTCAG 87762
? v? ii i ii ii v v vi i-----
C L1M5_orf2#LIN 1603 GNGANATTGGCCTGTAATTTTCCTTTCTTGTAATGTC-----CTTGTCAG 1559
INTRON_3 87763 ATTTTTGCATCAGGCTTAAGC-AGTCTCATAAAATGAGGTGA-AAGCATT 87810
i v i i v v -i i v i- ii
C L1M5_orf2#LIN 1558 GTTTTGGTATCAAGGTTATGCTGGCCTCATAAAATGAGTTGGGAAGTGTT 1509
INTRON_3 87811 CTTTTCTCCTTTATTTTCAGAAAGCATTTGTGTACTATTGATGTTAAGCC 87860
ii ii ii i i v i vi vv i i vvi
C L1M5_orf2#LIN 1508 CCCTCTTTTTCTATTCTCTGGAAGAGTTTGTGTAAGATTGGTATTATTTC 1459
INTRON_3 87861 TTCCTTCAAGGTT-----GAATTTACCAGTGAACCCAATTGCACCTGAAG 87905
v v ----- i i v vi vi i
C L1M5_orf2#LIN 1458 TTCCTTAAATGTTTGGNAGAATTCACCGGTGAAGCCATCTGGGCCTGGAG 1409
INTRON_3 87906 TTTTCTCTTTGGGAAATTTTT--ATTATATATTTAGTTTCTCTAATATGT 87953
i v i iv -- i v i i i v?
C L1M5_orf2#LIN 1408 TTTTCTTTGTGGAAAGGTTTTTAATTACAGATTCAATTTCTTTAATAGNT 1359
INTRON_3 87954 ATGGGAATATTCAGAT---CTGTTTTTTCATGAGTTAATTTTGTTAAGTT 88000
i v --- i i v v i i v
C L1M5_orf2#LIN 1358 ATAGGACTATTCAGATTTTCTATTTCTTCTTGTGTCAGTTTTGGTAAGTT 1309
INTRON_3 88001 GTAGTTTTTTTTTAAAGGAATTTGTTCATTTCATTTAAGTTACCAAATGT 88050
----- v? i? i i vi v
C L1M5_orf2#LIN 1308 GTA-----TTTTTCNAGGAATTTGTCNATTTCATCTAAATTTTCAAATTT 1264
INTRON_3 88051 TTTGCCATAAAGTTGTTTATAATAGTTCCATATTGTTCTTTTAATGTCTA 88100
v v i viii v i i i
C L1M5_orf2#LIN 1263 ATTGGCATAAAGTTGTTCATAATATCCTCTTATTATCCTTTTAATGTCTG 1214
INTRON_3 88101 TAGGATCTGTAGTGATGTCTGCTTTT--ATTCCTGATATTGTTAATTTGT 88148
v -- v
C L1M5_orf2#LIN 1213 TAGGATCTGTAGTGATGTCTCCTTTTTCATTCCTGATATTGGTAATTTGT 1164
INTRON_3 88149 GTTCTTAAAGTCTTTTTCCTTAT---TCTTGCTAGGTGCTTATTAGTTTT 88195
ii ivvvv i i v --- iv i i i
C L1M5_orf2#LIN 1163 GTCTTCTCTCTTTTTTTCTTGATCAGTCTTGCTAGAGGTTTATCAATTTT 1114
INTRON_3 88196 ATTAATTCTTTAAAAGAAA-AACTTTGGATTTTATTAATTTGTTCTATTG 88244
ii v v- ? v ii i i vi
C L1M5_orf2#LIN 1113 ATTAATCTTTTCAAAGAACCANCTTTTGGCTTTGTTGATTTTCTCTATTG 1064
INTRON_3 88245 TTTGCTGATTTCAACTCTGATCTTTATT-ATTCCTG-TCTTACTACTTAC 88292
? ?i vi ---- - - i - i - i------
C L1M5_orf2#LIN 1063 TNTNTTTGTTT----TCT-AT-TTCATTGATTTCTGCTCTTAT------C 1026
INTRON_3 88293 TTTGGATTTAATTTGCCCTTCCTTCT-CTAGCTT---GTTAAGGTGGAGA 88338
-- -- -- - vv --- v iv v vv?
C L1M5_orf2#LIN 1025 TTT--ATT--ATTT--CCTTCCTTCTACTTTCTTTGGGTTTAATTTGCTN 982
INTRON_3 88339 TT-------TAGATAATTGATTT-------TAAAT-ATT----------- 88362
------- v vv v? ------- ? - -----------
C L1M5_orf2#LIN 981 TTCTTTTTCTAGCTTCTTGAGNTGGANGCTTANATCATTGATTTTNAGCC 932
INTRON_3 88363 TTTCTTGTCT-CTAATATAGGCGCTTAAAGCTGTAAGTTCCCTTCTTCAA 88411
v i - v ii i i i i i --
C L1M5_orf2#LIN 931 TTTCTTCTTTTCTAATATATGCATTTAAGGCTATAAATTTCCCTCT--AA 884
INTRON_3 88412 ACACTGTTCTGGCTGCATCCCACAAATTTTGATACATTATGTTATTATTA 88461
i i i i i ii ii i v i
C L1M5_orf2#LIN 883 GCACTGCTTTAGCTGCATCCCACAAGTTTTGATATGTCGTATTTTCATTA 834
INTRON_3 88462 T 88462
C L1M5_orf2#LIN 833 T 833
Matrix = 20p37g.matrix
Transitions / transversions = 1.62 (99 / 61)
Gap_init rate = 0.04 (27 / 749), avg. gap size = 3.00 (81 / 27)
1931 28.62 4.93 1.75 INTRON_3 87801 88632 311549 C L1M3_orf2 LINE/L1 655 1512 1776 206
INTRON_3 87801 TGAAAGCATTCTTTTCTCCTTTATTTTCAGAAAGCATTTGTGTACTATTG 87850
i ii ii i i iv iv i vi v v vv
C L1M3_orf2#LIN 1512 TGGAAGTGTTCCCTCCTCTTCAATTTTTTGGAAGAGTTTGAGAAGGATTG 1463
INTRON_3 87851 ATGTTAAGCCTTCCTTCAA-----GGTTGAATTTACCAGTGAACCCAATT 87895
iii vi i v ----- v i v vi
C L1M3_orf2#LIN 1462 GCATTAATTCTTCTTTAAATGTTTGGTAGAATTCACCAGTGAAGCCATCT 1413
INTRON_3 87896 GCACCTGAAGTTTTCTCT-TTGGGAAATTTTT-ATTATATATTTAGTTTC 87943
vv i v i - ii - ivv i i i
C L1M3_orf2#LIN 1412 GGTCCTGGACTTTTCTTTGTTGGGAGGTTTTTGATTACTGATTCAATCTC 1363
INTRON_3 87944 TCTAATATGTATGGGAATATTCAGAT---CTGTTTTTTCATGAGTTAATT 87990
ii v ?vv ? vv i i --- i i v ? i i
C L1M3_orf2#LIN 1362 CTTACTNGTTATNGGTCTGTTCAGGTTTTCTATTTCTTCATGATTNAGTC 1313
INTRON_3 87991 TTGTTAAGTTGTA-GTTTTTTTTTAAAGGAATTTGTTCATTTCATTTAAG 88039
v i - i ------ i i v i i
C L1M3_orf2#LIN 1312 TTGGTAGGTTGTATGTTTCT------AGGAATTTATCCATTTCTTCTAGG 1269
INTRON_3 88040 TTACCAAATGTTTTGCCATAAAGTTGTTTATAATAGTTCCATATTGTTCT 88089
i v v v v i v i i i ii v vi i
C L1M3_orf2#LIN 1268 TTATCCAATTTGTTGGCGTATAATTGTTCATAGTAGTCTCTTATGATCCT 1219
INTRON_3 88090 TTTAATGTCTATAGGATCTGTAGTGATGTCTGCTTTT--ATTCCTGATAT 88137
v v i i v v v i v i -- i v
C L1M3_orf2#LIN 1218 TTTTATTTCTGTGGCATCAGTTGTAATGTCTCCTCTTTCATTTCTGATTT 1169
INTRON_3 88138 TGTTAATTTGTGTTCTTAAAGTCTTTTTC-CTTATTCTTGCTAGGTGCTT 88186
i v v ii i---- i- v v iiv i
C L1M3_orf2#LIN 1168 TATTTATTTGAGTCTTC----TCTTTTTTTCTTAGTCTAGCTAAAGGTTT 1123
INTRON_3 88187 ATTAGTTTTATTAATTCTTTAAAAGAAA-AACTTTGGATTTTATTAATTT 88235
i i i i ? ii v i v- i vii ii i
C L1M3_orf2#LIN 1122 GTCAATTTTGTTNATCTTTTCAAAAAACCAACTCTTAGTTTCGTTGATTT 1073
INTRON_3 88236 GTTCTATTGTTT----------------GCTGATTTCAACTCTGATCTTT 88269
v ----------------ii v vi i
C L1M3_orf2#LIN 1072 TTTCTATTGTTTTTCTANTTTCTATTTTATTTATTTCTGCTCTAATCTTT 1023
INTRON_3 88270 ATTATTCCTGTCTTACTACTTACTTTGGATTTAATTTGCCCTTCCTTCTC 88319
i iv i v i v ii i ii i i
C L1M3_orf2#LIN 1022 ATTATTTCCTTCCTTCTGCTAACTTTGGGCTTAGTTTGTTCTTCTTTTTC 973
INTRON_3 88320 TAGCTTGTTAAGGTGGAGATTTAGATAATTGATTTTAAATATTTTTCTTG 88369
i iv i v i v i vi v v i v i ii -
C L1M3_orf2#LIN 972 TAGTTCCTTGAGGTGTAAAGTTAGGTTGTTTATTTGAGATCTTTCTTCT- 924
INTRON_3 88370 TCTCTAATATAGGCGCTTAAAGCTGTAAGTTCCCTTCTTCAAACACTGTT 88419
i i i ii vvi i ii i i -- ii i
C L1M3_orf2#LIN 923 TTTTTAATGTAGGCATTTATCACTATAAACTTCCCTCTT--AGTACTGCT 876
INTRON_3 88420 CTGGCTGCATCCCACAAATTTTGATACATTATGTTATTATTATTCAGTTA 88469
i v i i i ii i v - v i
C L1M3_orf2#LIN 875 TTTGCTGCATCCCATAAGTTTTGGTATGTTGTGTTTTTATT-TTCATTTG 827
INTRON_3 88470 ----GAAATACATTCTAATTTTTCTTCTGATTTCTTCCCTGACCCATGGG 88515
---- i iv ii i ii v
C L1M3_orf2#LIN 826 TCTCGAGATATTTTCTAATTTCCCTTTTGATTTCTTCTTTGACCCATTGG 777
INTRON_3 88516 TTATTTAGAAATATGTTATTTAATTTGTAACTACTAGGAGATTATCTAGA 88565
i i i i i i vi vv i v vii v i v
C L1M3_orf2#LIN 776 TTGTTCAGGAGTGTGTTGTTTAATTTCCACATATTTGTGAATTTTCCAGT 727
INTRON_3 88566 TATCTCAGTATTATTGATTTTCAATTTAATT---TTGTGGTAAGATAACA 88612
v iivv ii ii i v --- vi v v
C L1M3_orf2#LIN 726 TTTCCTTCTGCTATTGATTTCTAGTTTCATTCCATTGTGGTCGGAAAAGA 677
INTRON_3 88613 TACTTG---TGAGTTTCAGTCTT 88632
--- - i
C L1M3_orf2#LIN 676 TACTTGGTATGA-TTTCAATCTT 655
Matrix = 20p37g.matrix
Transitions / transversions = 1.84 (149 / 81)
Gap_init rate = 0.02 (18 / 831), avg. gap size = 3.11 (56 / 18)
+ 570 26.4 9.0 5.5 INTRON_3 88619 89085 (311096) C L1ME2 LINE/L1 (5011) 1404 927 117 *
ANNOTATION EVIDENCE:
279 21.18 11.48 9.68 INTRON_3 88619 88801 311380 C L1MEc_5end LINE/L1 1190 1375 1152 207
INTRON_3 88619 TGAGTTTCAGTCTTTGGATTTTAAGGTTTACAGTGGGTGTTTTTCACCAA 88668
i ----- i vvi i ------- i
C L1MEc_5end#LI 1375 TGAGCTTC-----TTGGATCTGTGGGTTTATAGT-------TTTCATCAA 1338
INTRON_3 88669 AATT-GGGAAATTTTTGGCCGTTATTTTTTCCAATATTTTATCAG----- 88712
- i i i i v v vv-----
C L1MEc_5end#LI 1337 AATTTGGAAAATTTTTAGCCATTATTTCTTCAAATATTTTTTCTCTCTTT 1288
INTRON_3 88713 -------CTCCAGTTTCCTTCAGG-ACTC-AATTA------TATTAGGTC 88747
------- -- i ii - - ------ ii
C L1MEc_5end#LI 1287 CTCTTTTCTCC--TCTCCTTTGGGGACTCCAATTACATATATATTAGGCT 1240
INTRON_3 88748 ATTTTATATTGTTCCAAATATCCGTGAGGCTTTTATATTTTCCAATAATT 88797
i v vi i v vv vv v i v v ----
C L1MEc_5end#LI 1239 ACTTGAAGTTGTCCCACAGCTCACTGATGCTCTTTTCTTTT----TAATT 1194
INTRON_3 88798 TCTT 88801
i
C L1MEc_5end#LI 1193 TTTT 1190
Matrix = 20p37g.matrix
Transitions / transversions = 1.19 (19 / 16)
Gap_init rate = 0.05 (9 / 182), avg. gap size = 4.33 (39 / 9)
464 23.38 12.99 0.00 INTRON_3 88656 88809 311372 C L1MEf_5end LINE/L1 1016 1189 1028 208
INTRON_3 88656 TGTTTTTCACCAAAATTGGGAAATTTTTGGCCGTTATTTTTTCCAATATT 88705
i v ii i i v
C L1MEf_5end#LI 1189 TGTCTTTCACCAAATTTGGGAAATTTTCAGCCATTATTTCTTCAAATATT 1140
INTRON_3 88706 TTATCAGCTCCAGTTTCCTTC------------AGGACTC-AATTATA-- 88740
v v ? ? i i ------------i - ? i --
C L1MEf_5end#LI 1139 TTTTCTGCNCCANTCTCTTTCTCCTCTCCTTCTGGGACTCCAATNACACG 1090
INTRON_3 88741 ----TTAGGTCATTTTATATTGTTCCAAATATCCGTGAGGCTTT-TATAT 88785
---- ii v v i v vi v i - vi
C L1MEf_5end#LI 1089 NATGTTAGACCTTTTGATATTGTCCCACAGGTCCCTGAGGCTCTGTTCAT 1040
INTRON_3 88786 TTTCCAATAATTTCTTCCCTCTCT 88809
iivvi i ii
C L1MEf_5end#LI 1039 TTTTTTTCAATTTTTTTTCTCTCT 1016
Matrix = 20p37g.matrix
Transitions / transversions = 1.75 (21 / 12)
Gap_init rate = 0.03 (4 / 153), avg. gap size = 5.00 (20 / 4)
475 29.88 7.26 2.84 INTRON_3 88713 89084 311097 C L1MEg_5end LINE/L1 650 1037 1064 209
INTRON_3 88713 CTCCAGTTTCCTTC-AGGACTC-AATTATAT------TAGGTCATTTTAT 88754
-- i -i - i ------ ii v i i
C L1MEg_5end#LI 1037 CTCC--TCTCCTTCTGGGACTCCAATTACATATATGTTAGACCTTTTCAC 990
INTRON_3 88755 ATTGTTCCAAATATCCGTGAGGCTTTT----ATATTTTCCAATAATTTCT 88800
vv i v i iv v v i ----i v v- i?
C L1MEg_5end#LI 989 CGTGTCCCATATGTCTCTTACGCTCTTTTCTGTATTTTCCATTT-TTTTN 941
INTRON_3 88801 TCCCTCTCTTCTTCAAAGTGTATTATTTTTATTGACTTGTCCTCAAGCTC 88850
i v v ivv v vv i ?i i i i v i
C L1MEg_5end#LI 940 TCTCTCTGTGCTTCAGTCTGGATATTTTCTNCTGACCTATCTTCCAGTTC 891
INTRON_3 88851 ACT--TCTCTTTCTTCTAC-------AACCTGCTTTTAAGCCCATCTAGT 88891
-- - i vi ------- i v i v
C L1MEg_5end#LI 890 ACTAATC-CTCTCTTCAGCTGTGTCTAATCTGCTGTTAAACCCATCTATT 842
INTRON_3 88892 GAGTTTTTAATTCCAGTTCTAGTATTTTATTTGGTCCCTTGTATGTGTAT 88941
i i v v v v ii i - v v v vi
C L1MEg_5end#LI 841 GAGTTCTTAATTTCAGTTATTGTATATTTTTCAGTTC-TAGAATTTCCAT 793
INTRON_3 88942 TTAGTTGCCATTTCTCCACTGTTAATCTCTTAACTTACTAAAA--CTACA 88989
ii -- v i vi v?v iv vi i---- i i -- v
C L1MEg_5end#LI 792 TTGATT--CTTTTTTATAGNTTCCAGTTCTC----TGCTGAAATTCTCCA 749
INTRON_3 88990 TTTT--CCTTTAATTCTTT--ACATATTTACAATAGCTGCTCGAATGTCT 89035
i -- ? ? ii -- v iv i ii iv v i
C L1MEg_5end#LI 748 TCTTGTCNTTTANTTTCTTGAACATATTAATCATAGTTATTTTAAAGTCC 699
INTRON_3 89036 TTGTCTGCTAAGTCCAACATCTGGGCCATTTCTGATTTGGTTTCTGTTG 89084
v v v i ii ?ii v iv iv i
C L1MEg_5end#LI 698 GTGTCTGATAACTCCAATATCTGGATCNCCTGTGGGTCTGTTTCTATTG 650
Matrix = 20p37g.matrix
Transitions / transversions = 1.27 (57 / 45)
Gap_init rate = 0.04 (15 / 371), avg. gap size = 2.53 (38 / 15)
570 27.52 8.40 0.78 INTRON_3 88848 89085 311096 C L1MEf_5end LINE/L1 712 967 1250 210
INTRON_3 88848 CTCACTTCTCTTTCTTCTACAACCTGCTTTTAAGCCCATCTAGTGAGTTT 88897
vi i v v v vi v i i i
C L1MEf_5end#LI 967 CTCTTTCCTCTGTCATCTCCATTCTGCTATTGAGCCCATCCAGTGAATTT 918
INTRON_3 88898 TTAATTCCAGTTCTAGTATTTTATTTGGTCCC-----TTGTATGTGTATT 88942
? i v v v -- ii i i----- vi v vv
C L1MEf_5end#LI 917 TTNATTTCAGATATTGTATTTT--TCAGTTCTAAAATTTCCATTTGGTTT 870
INTRON_3 88943 T-------AGTTGCCATTTCTCCACTG------TTAATCTCTTAACTTAC 88979
------- v i ii ------ iv i iv i i i
C L1MEf_5end#LI 869 TTTTTTATAGTTTCTATTTCTCTGCTGAGANTTTCTATCTTTCCATTCAT 820
INTRON_3 88980 TAAAACTACATTTTCCTTTAATTCTTTA--CATATTTACAATAGCTGCTC 89027
vv v?iii ? vi ? vi-- v i i
C L1MEf_5end#LI 819 TTCAAGNGTGTTTNCCTTTACCTCNTGGAGCATAGTTATAATAGCTGCTT 770
INTRON_3 89028 GAATGTCTTTGTCTGCTAAGTCCAACATCTGGGCCATTTCTGATTTGGTT 89077
v v v v i i v iv i?
C L1MEf_5end#LI 769 TAAAGTCTTTGTCTGATAATTCCAACATCTGGGTCATCTCGGGGTTGGCN 720
INTRON_3 89078 TCTGTTGA 89085
C L1MEf_5end#LI 719 TCTGTTGA 712
Matrix = 20p37g.matrix
Transitions / transversions = 1.14 (32 / 28)
Gap_init rate = 0.02 (5 / 237), avg. gap size = 4.40 (22 / 5)
+ 250 26.6 1.5 9.4 INTRON_3 89163 89226 (310955) C L1ME2 LINE/L1 (5472) 943 883 117
ANNOTATION EVIDENCE:
250 26.60 1.46 9.45 INTRON_3 89163 89226 310955 C L1MEg_5end LINE/L1 552 612 1489 211
INTRON_3 89163 TTCTTATGTATCTGGTGAATTTTTAATTGAATACC-GACATTACAATTAA 89211
i ?i i ii ? - i i - ii vv i
C L1MEg_5end#LI 612 TCCTNGTATGCCTGGTNA-TTTTTGATTGAATGCCAGACATTGTATATGA 564
INTRON_3 89212 AAATATTGTAGAGTA 89226
- --
C L1MEg_5end#LI 563 AAA-ATTGTAGAG-- 552
Matrix = 20p37g.matrix
Transitions / transversions = 5.00 (10 / 2)
Gap_init rate = 0.06 (4 / 63), avg. gap size = 1.25 (5 / 4)
+ 2257 12.1 0.0 0.7 INTRON_3 89227 89533 (310648) + AluSx3 SINE/Alu 1 305 (7) 118
ANNOTATION EVIDENCE:
2117 12.17 0.65 0.98 INTRON_3 89227 89533 310648 + AluSx SINE/Alu 1 306 6 130
INTRON_3 89227 GGCCGGGCACAGTGGCTCACACTTGTAATCCCAGCACTTTGAGAGGCTGA 89276
i i i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 89277 GGCGGGCAGATCAC--AAGGTCAGGAGTTTGAGACCAGCCTGGCCAACAT 89324
i --i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
INTRON_3 89325 AGTAAAACCCTGTCTCTACTAAAAAAATTCAAAAAATTAGCTGGGCATGG 89374
i i i v i--- i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATAC---AAAAATTAGCCGGGCGTGG 147
INTRON_3 89375 TGCTGGGTGCCTGTAATCCCAGCTACTCAAGAGGCTGAGGCAGGAGAATC 89424
vi v i ii
AluSx#SINE/Al 148 TGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATC 197
INTRON_3 89425 GTTTGAACCCAAGAGGCGGAGGTTGCAGTGAGCCAAGATTACACAACTGC 89474
i ii i ii i v
AluSx#SINE/Al 198 GCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGC 247
INTRON_3 89475 ACTCCAGCCTGGGCCACAGTGCGAGACTCCGTCTCAAAAACGAACAAACA 89524
v v vi v v
AluSx#SINE/Al 248 ACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAA 297
INTRON_3 89525 AACAAAAAA 89533
v
AluSx#SINE/Al 298 AAAAAAAAA 306
Matrix = 14p37g.matrix
Transitions / transversions = 2.70 (27 / 10)
Gap_init rate = 0.01 (2 / 306), avg. gap size = 2.50 (5 / 2)
+ 250 26.6 1.5 9.4 INTRON_3 89534 89605 (310576) C L1ME2 LINE/L1 (5533) 882 817 117
ANNOTATION EVIDENCE:
250 26.60 1.46 9.45 INTRON_3 89534 89605 310576 C L1MEg_5end LINE/L1 486 551 1550 212
INTRON_3 89534 CAATAAATATTGTAGAGTAGTTGGATTCCATTATCTTCCTCTGAATAGTA 89583
-- - - - iv --i vvii iii v v
C L1MEg_5end#LI 551 --ATAA-T-TTG-AGGCT--CTGGATGATGTTATCTTCCTCCAGAGAGGA 509
INTRON_3 89584 TTGATTCTTATTT-TAACAGGCA 89605
v i i ii - ii
C L1MEg_5end#LI 508 TTTACTTTTGCTTCTGGCAGGCA 486
Matrix = 20p37g.matrix
Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.08 (6 / 71), avg. gap size = 1.33 (8 / 6)
+ 306 35.1 10.2 6.2 INTRON_3 90064 90202 (309979) C L1ME2 LINE/L1 (5697) 612 479 117
ANNOTATION EVIDENCE:
306 35.11 10.15 6.23 INTRON_3 90064 90202 309979 C L1MEb_5end LINE/L1 240 373 716 147
INTRON_3 90064 TGGGTCTCCCTTCTCTTCATAGCCACCTTTTCTCTGATGTCTTGTCTCGT 90113
vv ii ----i ivi ii i i ivi i -i i vi
C L1MEb_5end#LI 373 TGGGGATCCTCTCTCT----GGCTCTCTCCTTTCCGGGATTTT-CCCCTC 329
INTRON_3 90114 AGATTACAGTGACTTTCACCAGCCTGAACTCTAATTTCTGCTGCCTCAGG 90163
vv v i v viiiiv i i ?v i v v i i
C L1MEb_5end#LI 328 ACTTTCCAGTGGCTGTGGTTGCCCCGAATTCTNTTCTCTGGTTCTTCAAG 279
INTRON_3 90164 TCAGTGGGATCAC---TTTGATCTGCTAAGACTGCAACTCTT 90202
i ii i i --- -- i i ?ii vi i iv -
C L1MEb_5end#LI 278 CCAGTAAGACCGCGGGTTT--TCTACTGASGTTTTAGCCAT- 240
Matrix = Unknown
Transitions / transversions = 2.31 (37 / 16)
Gap_init rate = 0.04 (5 / 138), avg. gap size = 2.20 (11 / 5)
+ 2189 11.7 0.9 2.9 INTRON_3 90203 90518 (309663) + AluSx SINE/Alu 1 310 (2) 119
ANNOTATION EVIDENCE:
2107 12.06 0.95 2.90 INTRON_3 90203 90518 309663 + AluSx SINE/Alu 1 310 2 131
INTRON_3 90203 GACCAGGCACAGTGGCTCACGCCTATAATCCTAGCACTTTGGGAGGCCGA 90252
i i i i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 90253 GGCGGGCAGATTGCCTGAGCTCGGGAGTTCGAGACCAGCCTGAGCAACAT 90302
i ii v i iv
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
INTRON_3 90303 GGTGAAACTCCATCTCTACTAAAA-TACAAAAAAAAAAAAAATTATCTGG 90351
i i - --------- v i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAA---------TTAGCCGG 141
INTRON_3 90352 GCGTGGCAGCGTGCACCTGTAGTCCCAGC-ATTCGGGAGGCTGAGGCAAG 90400
ii i i i - i i
AluSx#SINE/Al 142 GCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGG 191
INTRON_3 90401 AGAATTGCTTGAACCCAGGAGGTGGAGGTTGCAGTGAACCAAGATTGTAC 90450
i i i i i i ii
AluSx#SINE/Al 192 AGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGC 241
INTRON_3 90451 CACTGCACTCCAGCCTGA-TGACAGAGCATGACTCTGTCTCAAAAAAAAA 90499
i-i iv i
AluSx#SINE/Al 242 CACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAA 291
INTRON_3 90500 AAAAAAAAAAAAAAAAAAA 90518
AluSx#SINE/Al 292 AAAAAAAAAAAAAAAAAAA 310
Matrix = 14p37g.matrix
Transitions / transversions = 8.25 (33 / 4)
Gap_init rate = 0.01 (4 / 315), avg. gap size = 3.00 (12 / 4)
+ 306 35.1 10.2 6.2 INTRON_3 90519 90703 (309478) C L1ME2 LINE/L1 (5831) 478 276 117
ANNOTATION EVIDENCE:
306 35.11 10.15 6.23 INTRON_3 90519 90703 309478 C L1MEb_5end LINE/L1 37 239 850 148
INTRON_3 90519 GACTGTA------ACTCTCTGTA-CTTAAT-TCAGG-AAATTGTGTCCAG 90559
-- ------ ivv ii- i iv - - vv --- -
C L1MEb_5end#LI 239 --CTGTACGACGCACCAACTGCGGCCTGCTCTCAGGCAAAAAG---CC-G 196
INTRON_3 90560 TAAGAGCTAGATGCTCACATCATTAGTTTCCTTTCTTTCAAGGGTTGTAA 90609
- iv i ivi vi i vv?v i i i v i - v
C L1MEb_5end#LI 195 TA-GAAATGGGAACTCACTCCGTGCSATTCCCTTCTTCCAGGTGTCG-AC 148
INTRON_3 90610 TCATGTCC------TATCTA---TTGCCCACTCCCTGAAAATGGTTTCA- 90649
viv ------ ii i--- vi i i--- i vi -
C L1MEb_5end#LI 147 TCCCCTCCAGTTTCTGCCTGCTTTTGGTCACTCTCC---AGTGCCTTCAA 101
INTRON_3 90650 GCAA---------ATATTTTGTTCA-AGTTTATAGTTGCTTATGT-CAGG 90688
i i---------i i - - v - i
C L1MEb_5end#LI 100 GTAGTTGTTTTTTGTATTTTGTCCAGAGTTTATAGTTG-TTATCTGCGGG 52
INTRON_3 90689 AGGGCTGGTGTAGTA 90703
i vii
C L1MEb_5end#LI 51 AGGGTTGGTCCGGTA 37
Matrix = Unknown
Transitions / transversions = 1.68 (32 / 19)
Gap_init rate = 0.09 (17 / 184), avg. gap size = 2.47 (42 / 17)
+ 3403 27.0 4.0 2.3 INTRON_3 90719 91096 (309085) C L1MEf LINE/L1 (4113) 2087 1706 120
ANNOTATION EVIDENCE:
3403 26.98 4.04 2.34 INTRON_3 90719 91096 309085 C L1MEf_5end LINE/L1 1706 2087 130 213
INTRON_3 90719 GTGGGATTCTAGGTGT--CGTTTTGTT----GTTTCCT--TTGTCCTGTC 90760
v - v -- i i ---- i -- iv
C L1MEf_5end#LI 2087 GTTGGATT-TAGGTCTACCATTTTATTATTTGTTTTCTGTTTGTCCCCTC 2039
INTRON_3 90761 TGTTTTGTTTTTCTTCTGTTTTTTAAATTCCTGCTTTATTTTGGGCTAAT 90810
- v i ii vv- i i v ii v
C L1MEf_5end#LI 2038 TGTTTT-TTGTTCCTCTGTTTCCTCT-TTTCTGCCTTCTTTTGGATTATT 1991
INTRON_3 90811 CAAAT-CTTTAAATGTTTTATTTTAATTCTTCTAATGTCTTTTTAGCTAT 90859
ii -i v i i ii iv v v
C L1MEf_5end#LI 1990 TGAATATTTTTAGTATTCCATTTTAATTTATCTATTGGCTTTTTAGCTAT 1941
INTRON_3 90860 AACTTTTTGTACTGTTTTTT-AGTGGTTGCTCTAGAGATTACAATATGGG 90908
v i i i - i ivi
C L1MEf_5end#LI 1940 ATCTCTTTGTATTATTTTTTTAGTGGTTGCTCTAGGGATTACAATATACA 1891
INTRON_3 90909 TCTTCAACTTATCACAATCTACTTAGAGTTAATATTATACTACTTC-CAT 90957
?i i v i ? i -?i
C L1MEf_5end#LI 1890 TNCTTAACTTTTCACAGTCTACTTAGAGTTAATATTNTACCACTTCANGT 1841
INTRON_3 90958 ACAATGGAAAAGTTTTGCAACGGCATAA-TTTTATTTAACTTCTCACCCA 91006
v v i iii vii i- iii v i ----
C L1MEf_5end#LI 1840 AAAATGTAGAAACCTTGCAACCATATAGGTCCCATTTACCCTC----CCA 1795
INTRON_3 91007 TCCTTTTTGGTACTGTTGTCATGTATTTTACATTTACATATATTATAATC 91056
v v iv i i v i i v
C L1MEf_5end#LI 1794 TCCTTTATGCTATAGTTGTCATATGTATTACATCTACATACATTATAAAC 1745
INTRON_3 91057 CCCACAATATAATATTATAATTTTTTCATTAAACTACCAA 91096
? v i i v v vii -
C L1MEf_5end#LI 1744 CCCACNAGACAATGTTATAATTTTTGCTTTAAACAGTCA- 1706
Matrix = 20p37g.matrix
Transitions / transversions = 1.79 (50 / 28)
Gap_init rate = 0.03 (12 / 377), avg. gap size = 1.67 (20 / 12)
+ 373 11.1 3.7 0.0 INTRON_3 91097 91177 (309004) C L1MB2 LINE/L1 (3) 6168 6085 121
ANNOTATION EVIDENCE:
373 11.11 3.70 0.00 INTRON_3 91097 91177 309004 C L1MB2_3end LINE/L1 832 915 3 146
INTRON_3 91097 TTTTTATTGTGGTAAAA-ATAAAT--TATAAAATTTATGATCATAACCAT 91143
v - i v --i iv v
C L1MB2_3end#LI 915 TTTTAATTGTGGTAAAASACACATAACATAAAATTTACCATCTTAACCAT 866
INTRON_3 91144 TTTTAAGTGTATAGTTTAGTAGTGTTAAGTATAT 91177
i i
C L1MB2_3end#LI 865 TTTTAAGTGTACAGTTCAGTAGTGTTAAGTATAT 832
Matrix = 18p37g.matrix
Transitions / transversions = 1.25 (5 / 4)
Gap_init rate = 0.03 (2 / 80), avg. gap size = 1.50 (3 / 2)
+ 3403 27.3 4.3 2.5 INTRON_3 91178 92329 (307852) C L1MEf LINE/L1 (4495) 1705 571 120
ANNOTATION EVIDENCE:
3403 26.98 4.04 2.34 INTRON_3 91178 92183 307998 C L1MEf_5end LINE/L1 680 1705 512 214
INTRON_3 91178 ATAGGCAGTTTGTTTTTTTTTCAAGAAATTAATAAAAGATGGAAAATACC 91227
- v i ---------- v ? v ii --- --
C L1MEf_5end#LI 1705 -TATGTA----------TTTTAAAGAANTTAAGAGGAGA---AAAATA-- 1672
INTRON_3 91228 ATCTGTTAAAATTATCTATATATTTATCATTTCCAGTCCCCTTTATTTCT 91277
i v v v i i v i ii? v i i? i?
C L1MEf_5end#LI 1671 GTCTTTTATATTTACCCAGATATTTACCATTTCTGNTGCTCTTCNTTCNT 1622
INTRON_3 91278 CTTTATATGTTTGAATTTCCATCTGGTATTATTTCTCTTCA-CCAGA-TA 91325
iii iv vi iii i ? i i - v -v
C L1MEf_5end#LI 1621 TCCTGAAGATCCAAGTTTCCNTCTGGTATCATTTCCCTTCAGCCTGAAGA 1572
INTRON_3 91326 ACTTC-TTTGGCAT-----GAAGTGTGTGTTTTTTCAAGATAAATCCTCT 91369
- i -----?v ? iiv i vi vivi ii i
C L1MEf_5end#LI 1571 ACTTCCTTTAGCATTTCTTNTAGNGCAGGTCTGCTGGCAACGAATTCTCT 1522
INTRON_3 91370 CTGCATTTGTTCATATGGAGATGTCTTTATTTCACTTTCATTTTTGAAGG 91419
iv iv i? i v i i i i
C L1MEf_5end#LI 1521 TAGTTTTCNTTTATCTGAAAATGTCTTTATTTCACCTTCATTTCTGAAGG 1472
INTRON_3 91420 GTATCTTACCAAGCTATAGAATTCTAAGTTGATAGTTTTTGCTTTTTATT 91469
i i vv vi v ii i vii i vi
C L1MEf_5end#LI 1471 ATATTTTCGCTGGATATAGAATTCTGGGTTGACAGTTTTTTTCTTTCAGC 1422
INTRON_3 91470 -TTTTAAA-----TGTCTTACTTTCCTCTTGGCCTTTTCTTCTTTACAGT 91513
-i ----- iii v i - ii-v ?v viii
C L1MEf_5end#LI 1421 ACTTTAAAGATGTTGTTCCACTGTCTTCT-GGCCTCC-ATNGTTTCTGAT 1374
INTRON_3 91514 GAGGAGTCAGTTTTCCTTTGCATCATTCCTCCTTTATATGTGATGTGTCA 91563
i i v i?v v i v i vi ii i i i
C L1MEf_5end#LI 1373 GAGAAATCCGCNGTCATTCGAATCGTTGTTCCCCTGTATGTAATGTGTCG 1324
INTRON_3 91564 TTTTGCTCTGGCTGCTGTCAAGATTTTCTTATTACCTTTGGTTT--GGCT 91611
v v i iv i --i v
C L1MEf_5end#LI 1323 TTTTTCTCTGGCTGCTTTCAAGATTTTTTCTTTATCTTTGGTTTTCAGCA 1274
INTRON_3 91612 ATTTTACTATG-TG---CTGTGTGTGGTTCTCTTTATGTTTTTCCTAATT 91657
i v i - --- iv i i i? v i-
C L1MEf_5end#LI 1273 GTTTGATTATGATGTGTCTAGGCGTGGTTTTCTTTGNGTTTATCCTG-TT 1225
INTRON_3 91658 TGG--TTTATTGAGCTTCTTGGATCTAAAAGTCAATGTTTTTAAATCAAA 91705
-- iii i iv i iv i v -i
C L1MEf_5end#LI 1224 TGGGGTTCGCTGAGCTTCTTGAATCTGTAAATTTATGTCTTTCA-CCAAA 1176
INTRON_3 91706 TTTGGGAAGTTTTCATCCATTTTTTTTTCATA-ATTTCCCC--CCACAAT 91752
i v v i v - iii -- ?v ?
C L1MEf_5end#LI 1175 TTTGGGAAATTTTCAGCCATTATTTCTTCAAATATTTTTTCTGCNCCANT 1126
INTRON_3 91753 TTCATACTTTTCTCTTTTTGAGATTCTAATTACACATATGGCCAACTATT 91802
i v v ii i i i i i ? i? vivi iv
C L1MEf_5end#LI 1125 CTCTTTCTCCTCTCCTTCTGGGACTCCAATNACACGNATGTTAGACCTTT 1076
INTRON_3 91803 TGATATTGTT----AACTCTATTGAAACTCTATTCATTTTGTCCTGTCTT 91848
i---- iv i-i ii i v iiiivi
C L1MEf_5end#LI 1075 TGATATTGTCCCACAGGTCC-CTGAGGCTCTGTTCATTTTTTTTCAATTT 1027
INTRON_3 91849 TTTTTCTCTGTGGTCTTTAAGGTTG------TTCTATTGTTCTGTTTTCA 91892
v v i - i ------ v i i
C L1MEf_5end#LI 1026 TTTTTCTCTCTGTTCTTCA-GATTGGATAATTTCTATTGATCTATCTTCA 978
INTRON_3 91893 AATTGG-TGAC-CTTTTCTTGGGGATGGCTTCAGTCTTCTATTAATCTCA 91940
i vi- - i iv vv -- i v v i v i
C L1MEf_5end#LI 977 AGTTCACTGACTCTTTCCTCTGTCAT--CTCCATTCTGCTATTGAGCCCA 930
INTRON_3 91941 TCTATTTACTTTTTTATTTCACATGTTGTACTTTTCATTTCTAGAGTTTC 91990
i v v v ? v i i v i i
C L1MEf_5end#LI 929 TCCAGTGAATTTTTNATTTCAGATATTGTATTTTTCAGTTCTAAAATTTC 880
INTRON_3 91991 CACTTGGTTATTTTTTATAATCTTT-----TTTACTTAGATTTTCCATCT 92035
i v i i i ----- i i v ? i
C L1MEf_5end#LI 879 CATTTGGTTTTTTTTTATAGTTTCTATTTCTCTGCTGAGANTTTCTATCT 830
INTRON_3 92036 TTTCATTCATCATGATCATTCTTTCCTATAG-TCCTTGATTATGTTTATA 92084
i ivii v?i vi ? v v- ? v vi iv
C L1MEf_5end#LI 829 TTCCATTCATTTCAAGNGTGTTTNCCTTTACCTCNTGGAGCATAGTTATA 780
INTRON_3 92085 ATATCATCTTTAAAGTTCTTGTCTG-TATTTGTAACGTCTGTGTCAGTTT 92133
v vv ii - v vi i v vi i
C L1MEf_5end#LI 779 ATAGCTGCTTTAAAGTCTTTGTCTGATAATTCCAACATCTGGGTCATCTC 730
INTRON_3 92134 GGGGTTTCTTTGTATTGACTGCTTTTTCTTTTAATTATGGGTCACATTTT 92183
vvi? v i i ii ii i vv v ?
C L1MEf_5end#LI 729 GGGGTTGGCNTCTGTTGATTGTCTTTTCCCTTGAGAATTGGTCANATTTT 680
Matrix = 20p37g.matrix
Transitions / transversions = 1.75 (166 / 95)
Gap_init rate = 0.03 (30 / 1005), avg. gap size = 2.27 (68 / 30)
1410 29.59 6.29 3.28 INTRON_3 91233 92329 307852 C L1MEg_5end LINE/L1 455 1583 518 215
INTRON_3 91233 TTAAAATTATCTATATATTTATCATTTCCAGTCCCCTTTATTTCTCTTTA 91282
i v i i i v iiv v i i i iii i
C L1MEg_5end#LI 1583 TTAGATTTACCCATATATTTACCCTTTCTGTTGCTCTTCATTCCTTCCTG 1534
INTRON_3 91283 TATGTTTGAATTTCCATCTGGTATTATTTCTCTTC-ACCAGA-TAACTTC 91330
i v iiivii v i ii -i v -v
C L1MEg_5end#LI 1533 CATTTCCATGCTTCCATCTGGGATCATTTTCCTTCTGCCTGAAGAACTTC 1484
INTRON_3 91331 -TTTGGCATGA-----AGTGTGTGTTTTTTCAAGATAAATCCTCTCTGCA 91374
- i i vv----- iv i vi viv ii i v iv
C L1MEg_5end#LI 1483 CTTTAGTATTTCTTTTAGTGTAGGTCTGCTGGTGACGAATTCTCTCAGTT 1434
INTRON_3 91375 TTTGTTCATATGGAGATGTCTTTATTTCACTTTCATTTTTGAAGGGTATC 91424
ii v i i i i i i
C L1MEg_5end#LI 1433 TTTGTTTGTCTGAAAATGTCTTTATTTCGCCTTCATTTTTGAAGGATATT 1384
INTRON_3 91425 TTACCAAGCTATAGAATTCTAAGTTGATAGTT-TTTGCTTTTTATTTTTT 91473
- vi v i ii - v iviivi
C L1MEg_5end#LI 1383 TT-CCTGGATATAGAATTCTAGGTTGGCAGTTATTTTCTTTCAGCACTTT 1335
INTRON_3 91474 AAA--TGTC-TTAC-TTTCCTCTTGGCCTTTTCTTCTTTACAGTGAGGAG 91519
-- - v - vi ii - iiv v viiv i
C L1MEg_5end#LI 1334 AAAGATGTCATTCCATTGTCTTCTGGC-TTCCATTGTTTCTGTTGAGAAG 1286
INTRON_3 91520 TCAGTTTTCCTTTGCATCATTCCTCCTTTATATGTGATGTGTCATTTTGC 91569
i v vv ivi ii v iv v i v v
C L1MEg_5end#LI 1285 TCAGCTGTCAGTCTTATTGTTGCTCCTTTGAAGGTAATGTGTCTTTTTTC 1236
INTRON_3 91570 TCTGGCTGCTGTCAAGATTTTCTTATTACCTTTGGTTT--GGCTATTTTA 91617
v i iv ii --i vi
C L1MEg_5end#LI 1235 TCTGGCTGCTTTTAAGATTTTCTCTTTGTCTTTGGTTTTCAGCAGTTTTA 1186
INTRON_3 91618 CTATG-TG---CTGTGTGTGGTTCTCTTTATGTTTTTCCTAATTTGG-TT 91662
- --- iv i i i v iv v -
C L1MEg_5end#LI 1185 CTATGATGTGCCTAGGTGTGGTTTTCTTTGTATTTATCCTGCTTGGGGTT 1136
INTRON_3 91663 TATTGAGCTTCTTGGATCTAAAAGTCAATGTTTTTAAATCAAATTTGGGA 91712
ii v ? i iviiv ii i vi- iv i
C L1MEg_5end#LI 1135 CGTAGNGCTTCTTGAATCTGTGGCTTGATGTCTTTCG-TCAGTTTTGGAA 1087
INTRON_3 91713 AGTTTTCATCCATTTTTTTTTCATA-ATTTCCCC--CCACAATTTCATAC 91759
i i v v i i v - v ii -- v v i viv
C L1MEg_5end#LI 1086 AATTCTCAGCCATTATCTCTTCAAATATTGCTTCTGCCCCATTCTCTCTC 1037
INTRON_3 91760 TTTTCTCTTTTTGAGATTCTAATTACACATATGGCCAACTATTTGATATT 91809
ii i i i i i i vivi iv v ivv
C L1MEg_5end#LI 1036 TCCTCTCCTTCTGGGACTCCAATTACATATATGTTAGACCTTTTCACCGT 987
INTRON_3 91810 GT----TAACTCTATTGAAACTCTATTC---ATTTTGTCCTGTCTTTTTT 91852
---- vv v - vi v --- -i v v i ? i
C L1MEg_5end#LI 986 GTCCCATATGTCTCTT-ACGCTCTTTTCTGTATTTT-CCATTTTTTTNTC 939
INTRON_3 91853 TCTCTGTGGTCTTTAA---GGTTGTT--CTATTGTTCTGTTTTCAAATTG 91897
-- i i--- v i -- ?i vi i i v i v
C L1MEg_5end#LI 938 TCTCTGTG--CTTCAGTCTGGATATTTTCTNCTGACCTATCTTCCAGTTC 891
INTRON_3 91898 G-TGACCTTTTCTTGGGGATGGCTTCAGTCTTCTATTAATCTCATCTATT 91946
i- i i i i vi v- vv ii i v i v i
C L1MEg_5end#LI 890 ACTAATCCTCTCTTCAGC-TGTGTCTAATCTGCTGTTAAACCCATCTATT 842
INTRON_3 91947 TACTTTTTTATTTCACATGTTGTAC--TTTTCATTTCTAGAGTTTCCACT 91994
v v i v vv i i-- v i i
C L1MEg_5end#LI 841 GAGTTCTTAATTTCAGTTATTGTATATTTTTCAGTTCTAGAATTTCCATT 792
INTRON_3 91995 TGGTTATTTTTTATAATCTTTTTTACTTAGATTTTCCA--TCTTTTC--- 92039
i v i?---------------- -- i v ---
C L1MEg_5end#LI 791 TGATTCTTTTTTATAGN----------------TTCCAGTTCTCTGCTGA 758
INTRON_3 92040 -ATTCATCATGATCATTCTTTCCTATAGTC-CTTGATTATGTTTATAATA 92087
- - ----- ii v ? v ? i- vi i v v
C L1MEg_5end#LI 757 AATTC-TC-----CATCTTGTCNTTTANTTTCTTGAACATATTAATCATA 714
INTRON_3 92088 -TCATCTTTAAAGTTCTTGTCTG-TATTTGTAACGTCTGTGTCAGTTTGG 92135
- i - i v - vi vi ii vi ?vi vv
C L1MEg_5end#LI 713 GTTAT-TTTAAAGTCCGTGTCTGATAACTCCAATATCTGGATCNCCTGTG 665
INTRON_3 92136 GGTTTCTTTGTATTGACTGCTTTTTCTTTTAATTATGGGTCACAT-TTTT 92184
i v v v - i i? v v iv - i
C L1MEg_5end#LI 664 GGTCTGTTTCTATTGTCTG-TTTTTCTCTTGNTTTTCGGTCATTTGTCTT 616
INTRON_3 92185 ATTACCCTGTA-G---AGTAATTTTT-ATTGTA-ACTGGAAATTATATTT 92228
i iv i? - ---i ? - v -i ii v i v
C L1MEg_5end#LI 615 GTCTCCTNGTATGCCTGGTNATTTTTGATTGAATGCCAGACATTGTATAT 566
INTRON_3 92229 GATATACCCTGGAGA----------ATCTGGATTTTGTTCTTGTTCCCTA 92268
v v iiv i ----------v vv v iv i i i
C L1MEg_5end#LI 565 GAAAAATTGTAGAGATAATTTGAGGCTCTGGATGATGTTATCTTCCTCCA 516
INTRON_3 92269 AAGAGTGATTTTTTTTTTTTAATTTCAAGCAGACAGC-ATAGTTATTGGC 92317
i - vi ----ii vi i - vi vi i i
C L1MEg_5end#LI 515 GAGAG-GATTTACTTTT----GCTTCTGGCAGGCAGCTAGGGGCACTAGC 471
INTRON_3 92318 --T--GATCACCTTAA 92329
-- --
C L1MEg_5end#LI 470 AATCAGATCACCTTAA 455
Matrix = 20p37g.matrix
Transitions / transversions = 1.47 (181 / 123)
Gap_init rate = 0.04 (48 / 1096), avg. gap size = 2.21 (106 / 48)
+ 379 19.7 0.0 0.0 INTRON_3 92907 92967 (307214) C Tigger1 DNA/TcMar-Tigger (0) 2418 2358 122
ANNOTATION EVIDENCE:
379 19.67 0.00 0.00 INTRON_3 92907 92967 307214 C Tigger1 DNA/TcMar-Tigger 2358 2418 0 266
INTRON_3 92907 CAGGGATATTTTGGAAATATTGCAGGTTCTGTTCCAGACCATTGCAGTAA 92956
v ii i i i v ii i
C Tigger1#DNA/T 2418 CAGGCATACCTCGGAGATATTGCGGGTTCGGTTCCAGACCACCGCAATAA 2369
INTRON_3 92957 AGCAAATATTG 92967
i i
C Tigger1#DNA/T 2368 AGCGAATATCG 2358
Matrix = 20p37g.matrix
Transitions / transversions = 5.00 (10 / 2)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 1299 7.7 0.0 6.4 INTRON_3 92968 93149 (307032) C AluY SINE/Alu (42) 269 99 123
ANNOTATION EVIDENCE:
1215 8.81 0.00 6.43 INTRON_3 92968 93149 307032 C AluY SINE/Alu 99 269 42 138
INTRON_3 92968 CACTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCA 93017
i
C AluY#SINE/Alu 269 CGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCA 220
INTRON_3 93018 ATCACTGCCTCCTGGGTTCATGCCATTCTCCTGCCTCAGCCTCCCAAGTA 93067
v v i i i i
C AluY#SINE/Alu 219 AGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTA 170
INTRON_3 93068 GCTGGCACTACAGGTGCATGCCACCATGCCCTGCTAATTTTTTTGTATTT 93117
v i vi i v -------
C AluY#SINE/Alu 169 GCTGGGACTACAGGCGCCCGCCACCACGCCCGGCTAATTTTTT------- 127
INTRON_3 93118 TTCTGTCTTTTTAGCAGAGACGGGGTTTCACC 93149
---- v i
C AluY#SINE/Alu 126 ----GTATTTTTAGTAGAGACGGGGTTTCACC 99
Matrix = 14p37g.matrix
Transitions / transversions = 1.50 (9 / 6)
Gap_init rate = 0.01 (1 / 181), avg. gap size = 11.00 (11 / 1)
+ 463 15.2 11.7 1.5 INTRON_3 93203 93262 (306919) C L1MA7 LINE/L1 (11) 6280 6209 124
ANNOTATION EVIDENCE:
463 15.23 11.67 1.52 INTRON_3 93203 93262 306919 C L1MA7_3end LINE/L1 956 1027 11 216
INTRON_3 93203 ATTAACAAATGATAACTGTATATATTTATGGGGTACAAAATGATGGTATG 93252
i i i vi v v
C L1MA7_3end#LI 1027 ATTGACAAATAATAATTGTATATATTTATGGGGTACAATGTGATGTTTTG 978
INTRON_3 93253 ATATTTTT-------------TC 93262
v v ------------- -
C L1MA7_3end#LI 977 ATATATGTATACANTGTGGAAT- 956
Matrix = 20p37g.matrix
Transitions / transversions = 0.80 (4 / 5)
Gap_init rate = 0.03 (2 / 59), avg. gap size = 7.00 (14 / 2)
+ 186 4.3 0.0 0.0 INTRON_3 93263 93285 (306896) + (CA)n Simple_repeat 1 23 (0) 125
ANNOTATION EVIDENCE:
186 4.35 0.00 0.00 INTRON_3 93263 93285 306896 + (CA)n Simple_repeat 1 23 157 257
INTRON_3 93263 CATACACACACACACACACACAC 93285
i
(CA)n#Simple_ 1 CACACACACACACACACACACAC 23
Matrix = Unknown
Transitions / transversions = 0.0 (1 / 0)
Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0)
+ 1778 22.0 4.4 4.7 INTRON_3 93286 93911 (306270) C L1MA7 LINE/L1 (83) 6208 5484 124
ANNOTATION EVIDENCE:
463 15.23 11.67 1.52 INTRON_3 93286 93344 306837 C L1MA7_3end LINE/L1 896 955 83 217
INTRON_3 93286 GATTGAATCAAGCTAATTAACATATCCA-AACCTCAAATATTTGTTATTT 93334
i -v v i i i
C L1MA7_3end#LI 955 GATTAAATCAAGCTAATTAACATATCCATCACCTCACATACTTATCATTT 906
INTRON_3 93335 ATTTCTGCTG 93344
v v v
C L1MA7_3end#LI 905 TTTTGTGGTG 896
Matrix = 20p37g.matrix
Transitions / transversions = 0.80 (4 / 5)
Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1)
1778 22.66 3.61 5.06 INTRON_3 93331 93911 306270 C L1MA7_3end LINE/L1 231 803 235 218
INTRON_3 93331 ATTTATTTCTGCTGTGTAACTTAAACATTGTACCGTTTGACTAACATCTC 93380
i i v v v v v i
C L1MA7_3end#LI 803 ACTTATTCCTCCTGTCTAACTGAAACTTTGTACCCTTTGACCAACATCTC 754
INTRON_3 93381 CTTATTATCCCTACTCTGCAGCCTTTGGTAACCACCAGTCTGCTCTCTGC 93430
ii vi i i iv i v i
C L1MA7_3end#LI 753 CCCATTCCCCCCACCCCCCAGCCTCTGGTAACCACCATTCTACTCTCTGC 704
INTRON_3 93431 TTCCCTGAGTTCGATTGTTTTAGATTTCATGTGGAATTTGTCTTCCCATG 93480
iv i v i ii iv --- vvvvi
C L1MA7_3end#LI 703 TTCTATGAGTTCGACTTTTTTAGATTCCACATATAA---GTGAGATCATG 657
INTRON_3 93481 CCTGGCTTATTTCATT-TATACTAATGACCTCCAGGTTCACC---CATGG 93526
-- iv v v v - i i i-- i i vi--- i--- ii
C L1MA7_3end#LI 656 C--GGTATTTGTCTTTCTGTGCC--TGGCTTAT---TTCACTTAGCATAA 614
INTRON_3 93527 TGTCC--CAAATGACATAATTTCCTTCTTTT---AAATGGC-TAATTTT- 93569
-- ii v- ----- v v v --- i -vi i-
C L1MA7_3end#LI 613 TGTCCTCCAGGTT-CAT-----CCATGTTGTCACAAATGACAGGATTTCC 570
INTRON_3 93570 TTCTATT----G--TGTATATATACCACATTTTCTTGGTGT-CCA---TT 93609
v ---- -- v -i iiv v v vvi i - ---
C L1MA7_3end#LI 569 TTCTTTTTTAAGGCTGAATA-GTATTCCATTGTGTATATATACCACATTT 521
INTRON_3 93610 GGTTGATGGATACTTAGGCTGATAGACACTTAGGTTGATTCCATAACTTA 93659
vv v vv v v vvii i v i
C L1MA7_3end#LI 520 TCTTTATCCATTCATCCATTGATGGACACTTAGGTTGATTCCATATCTTG 471
INTRON_3 93660 TTGCAGTAATTCCACGTTTATTGCAGCGTTATTGTGAATATGAGAGAGCA 93709
----- iv ---- vv --- i i iivi i i v
C L1MA7_3end#LI 470 -----GCTATT----GTGAAT---AGTGCTGCAATGAACATGGGAGTGCA 433
INTRON_3 93710 GTTATCTCTTTGACATACATAATTCATATCCTTTGTATATATACCCAGAA 93759
v i vv v v? v
C L1MA7_3end#LI 432 GATATCTCTTCGACATACTGATTTCAANTCCTTTGGATATATACCCAGAA 383
INTRON_3 93760 ATAGGATTGTTGGATCATATGGTAGTTCTATCTTCAGTTTTTAGAGGAAT 93809
i i i i i v i
C L1MA7_3end#LI 382 GTGGGATTGCTGGATCATATGGTAGTTCTATTTTTAGTTTTTTGAGGAAC 333
INTRON_3 93810 ATCCATACTGTTTTCCATAATGGCTGTATCAATTTATATTCCCACCAGTA 93859
v ii i ii
C L1MA7_3end#LI 332 CTCCATACTGTTTTCCATAATGGCTGTACTAATTTACATTCCCACCAACA 283
INTRON_3 93860 GTGTACAAAGGCTCCCTTTTCTCCACATTCTTACCAACACTTGTTATCTT 93909
i i i i ii
C L1MA7_3end#LI 282 GTATACAAGGGTTCCCTTTTCTCCACATCCTCGCCAACACTTGTTATCTT 233
INTRON_3 93910 TT 93911
i
C L1MA7_3end#LI 232 CT 231
Matrix = 20p37g.matrix
Transitions / transversions = 1.25 (69 / 55)
Gap_init rate = 0.03 (20 / 580), avg. gap size = 2.50 (50 / 20)
+ 1852 18.9 0.0 1.0 INTRON_3 93925 94220 (305961) C AluJr SINE/Alu (18) 294 2 126
ANNOTATION EVIDENCE:
1589 22.19 0.00 1.02 INTRON_3 93925 94220 305961 C AluJb SINE/Alu 2 294 18 132
INTRON_3 93925 TTTTTTTTTTTTGAGACAGAGTCTCACTCTTTTGTCTAGGCTTGAGTCCA 93974
i i v i i i v v
C AluJb#SINE/Al 294 TTTTTTTTTTTTGAGACAGGGTCTCGCTCTGTCGCCCAGGCTGGAGTGCA 245
INTRON_3 93975 GTGGTGCAGTCATACCCCACTACAGCCTCAGACTCCTGGGCTCAGGTGAT 94024
i ii iiv i i iiv i i i
C AluJb#SINE/Al 244 GTGGCGCGATCACGGCTCACTGCAGCCTCGACCTCCCGGGCTCAAGCGAT 195
INTRON_3 94025 CCTCTCACTTCAGCCTCCCAAGTAACTGGGATTACAGATGCATGTCACCA 94074
iii i i i i ii ii i
C AluJb#SINE/Al 194 CCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCGCGCCACCA 145
INTRON_3 94075 TGCCTGACTAATTTAAAACACTTTTTTTGTAGAGATGAGGTCTCACTATG 94124
i i i v---iiiv i i i i
C AluJb#SINE/Al 144 CGCCCGGCTAATTTT---TGTATTTTTTGTAGAGACGGGGTTTCACCATG 98
INTRON_3 94125 TTGCTCAGGCTGGTCTTAAATTTCTGGCCTGAAGCAATCTTCCTGCCTTG 94174
i ii i i v v ii i i i
C AluJb#SINE/Al 97 TTGCCCAGGCTGGTCTCGAACTCCTGGGCTCAAGTGATCCTCCCGCCTCG 48
INTRON_3 94175 GCCTCCCAAAGTGCTGGAATTATAGGCCTCAGCCACTGTGCCCAGC 94220
i i v v i i i
C AluJb#SINE/Al 47 GCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p37g.matrix
Transitions / transversions = 4.91 (54 / 11)
Gap_init rate = 0.00 (1 / 295), avg. gap size = 3.00 (3 / 1)
+ 937 19.1 5.4 0.6 INTRON_3 94221 94514 (305667) C L1MA7 LINE/L1 (740) 5424 5123 124
ANNOTATION EVIDENCE:
734 18.01 6.21 0.00 INTRON_3 94221 94381 305800 C L1ME2_3end LINE/L1 1 171 740 219
INTRON_3 94221 TTACATTTCCTTAATGACTGGTGATGTTCTCTATATTTTCATGTGCTTAT 94270
i i i ii vvvi iv
C L1ME2_3end#LI 171 TTGCATTTCCCTGATGACTAATGATGTTGAGCACCTTTTCATGTGCTTAT 122
INTRON_3 94271 TAGCCATTTATATATA-------GTGAAATGTCTGTTCAGTTCCTCTGCC 94313
i i v------- i iv i i
C L1ME2_3end#LI 121 TGGCCATTTGTATATCTTCTTTTGTGAAGTGTCTGTTCAAGTCTTTTGCC 72
INTRON_3 94314 CATTTTT-AATTGGACTGTTCAT--TTTTATTATTAAGTTGTCAGAGTTC 94360
- ii ii -- i vi
C L1ME2_3end#LI 71 CATTTTTTAATTGGGTTGTTTGTCTTTTTATTATTGAGTTGTAGGAGTTC 22
INTRON_3 94361 ATTATATATTCTGGGTAGAAG 94381
v i v
C L1ME2_3end#LI 21 TTTATATATTCTGGATACAAG 1
Matrix = 20p37g.matrix
Transitions / transversions = 2.22 (20 / 9)
Gap_init rate = 0.02 (3 / 160), avg. gap size = 3.33 (10 / 3)
937 20.44 4.40 1.42 INTRON_3 94242 94514 305667 C L1M4_orf2 LINE/L1 3014 3294 0 220
INTRON_3 94242 TGATGTTCTCTATATTTTCATGTGCTTATTAGCCATTTATATAT------ 94285
vvvi v i i ------
C L1M4_orf2#LIN 3294 TGATGTTGAGCATCTTTTCATGTGCTTATTGGCCATTTGTATATCTTCTT 3245
INTRON_3 94286 -AGTGAAATGTCTGTTCAGTTCCTCTGCCCATTTTT-AATTGGACTGTTC 94333
-i v i iv i - ii i i
C L1M4_orf2#LIN 3244 TGGAGAAATGTCTATTCAAATCCTTTGCCCATTTTTSAATTGGGTTATTT 3195
INTRON_3 94334 AT--TTTTATTATTAAGTTGTCAGAGTTCATTATATATTCTGGGTAGAAG 94381
i -- i v v i v
C L1M4_orf2#LIN 3194 GTCTTTTTATTATTGAGTTGTAAGAGTTCTTTATATATTCTGGATACAAG 3145
INTRON_3 94382 TCCTTTATTAGATAAGCAATTTGCAAAAAATATTTTCTCCTGGTCTATAG 94431
i i viii --- iiv i i
C L1M4_orf2#LIN 3144 TCCCTTATCAGATATATGATTTGCAAA---TATTTTCTCCCATTCTGTGG 3098
INTRON_3 94432 CTTGTTTTTAAACTTTTCTAAATGTTGTTTTTTGAAGAGCAAATGTTTTT 94481
v i vv - vi iv ii vi v
C L1M4_orf2#LIN 3097 GTTGTCTTTTCACTTT-CTTGATAGTGTCCTTTGAAGCACAAAAGTTTTT 3049
INTRON_3 94482 TATTT-GATAAAATCCT-TTTAATTATTATTTGTT 94514
v - i i v- vi v v
C L1M4_orf2#LIN 3048 AATTTTGATGAAGTCCAATTTATCTATTTTTTCTT 3014
Matrix = 20p37g.matrix
Transitions / transversions = 1.39 (32 / 23)
Gap_init rate = 0.03 (7 / 272), avg. gap size = 2.29 (16 / 7)
+ 894 23.5 6.7 1.0 INTRON_3 94520 94909 (305272) C L1M4b LINE/L1 (4703) 2305 1904 127
ANNOTATION EVIDENCE:
890 29.34 2.82 1.26 INTRON_3 94520 94909 305272 C L1M4c_5end LINE/L1 1286 1681 819 221
INTRON_3 94520 TTATTTATCTGGTA-TATCTTTATTATACCCTTGCATTTGTAGTATACTT 94568
i v - i v viv ii v v v i v
C L1M4c_5end#LI 1681 TTGTTTATCTGGGAATGTCTTAATTTCTCCCTCACTTTTGAAGGACAGTT 1632
INTRON_3 94569 TTGCTGGAGCTAGAAACTTTGGTAGACAAGTTGTTTTTTTTCCCTTGTAC 94618
i vv i vii v ---- iiii v i
C L1M4c_5end#LI 1631 TTGCCGGATATAGGATTCTTGGTTGACA----GTTTTTTTCTTTTAGCAC 1586
INTRON_3 94619 TTTGAATATGTCAGTCTACTGCCCTCTGTTCTCTACTGTTTCTAACTAGA 94668
i i i i i vi i vv i iv
C L1M4c_5end#LI 1585 TTTGAATATATCGGCCCACTGCCTTCTGGCCTCCAAAGTTTCTGATGAGA 1536
INTRON_3 94669 AGCTAGCCTTTAATTATATTGTTATTCTTCTGTGTATAATTAAGAGTTTT 94718
iiiv ivv iv vviv iii i i i v ivv i i
C L1M4c_5end#LI 1535 AATCTGCTGATAATCTTATTGAGGATCCCTTGTATGTGATGAGTCGCTTC 1486
INTRON_3 94719 TCTCTTGCT---TTCAAAAGTTTA-CTTTGCCTTTGTCTGTCAAAA-TTT 94763
--- i v i v- i v v i ? -
C L1M4c_5end#LI 1485 TCTCTTGCTGCTTTCAAGATTCTCTCTTTGTCTTTGGCTTTCGANAGTTT 1436
INTRON_3 94764 GACTGTGATA---CTAGGTTTGGATCTCTTGATGTTTATCTTACTTGGGG 94810
i i i i--- v v i viv i i i
C L1M4c_5end#LI 1435 GATTATAATGTGTCTCGGTGTGGGTCTCTTTGAGTTCATCCTACTTGGAG 1386
INTRON_3 94811 TTC-TTGAGCTTTTTCAATATTTA-GTTTTTATATTTTATCGTTTTGGAG 94858
- i vi i -i iv i v i ivv v i
C L1M4c_5end#LI 1385 TTCGTTGAGCTTCTTGGATGTTTATATTCATGTCTTTCATCAAATTTGGG 1336
INTRON_3 94859 ATACTTTCAGCCCCTGTTTCTTCAAATATTTTTTCTGTTCCCTTTCTCTT 94908
vii vi i i i i- i
C L1M4c_5end#LI 1335 AAGTTTTCAGCCATTATTTCTTCAAATATTCTCTCTGC-CCCTTTCTCTC 1287
INTRON_3 94909 T 94909
C L1M4c_5end#LI 1286 T 1286
Matrix = 20p37g.matrix
Transitions / transversions = 1.60 (69 / 43)
Gap_init rate = 0.02 (9 / 389), avg. gap size = 1.78 (16 / 9)
894 22.06 7.72 0.90 INTRON_3 94599 94909 305272 C L1M4b_5end LINE/L1 1904 2235 1469 222
INTRON_3 94599 TTGTTTTTTTTCCCTT--GTACTTTGAATATGTCAGTCTACTGCCCTCTG 94646
v i i -- i vi i i
C L1M4b_5end#LI 2235 TTTTTTTTTTTTCTTTCAGCACTTTGAATATGTCATCCCACTGCCTTCTG 2186
INTRON_3 94647 TTCTCTACTGTTTCTAACTAGAAGCTAGCCTTTAATTATATTG----TTA 94692
vi i i i iv ii iv iv ----???
C L1M4b_5end#LI 2185 GCCTCCATTGTTTCTGATGAGAAGTCAGCTGTTAATCTTATTGAGGTNNN 2136
INTRON_3 94693 TTCTTCTGTGTATAATTAAGAGTTTTTCTCTTGCT---TTCAAAAGTTTA 94739
iii i i i v ivvi --- i v v
C L1M4b_5end#LI 2135 TTCCCTTGTATGTGATGAGTCATTTTTCTCTTGCTGCTTTCAAGATTTTC 2086
INTRON_3 94740 -CTTTGCCTTTGTCTGTCAAAATTT-GACTGTGATA---CTAGGTTTGGA 94784
- i v v - i i--- v
C L1M4b_5end#LI 2085 TCTTTGTCTTTGTCTTTCAACATTTTGACTATGATGTGTCTAGGTGTGGA 2036
INTRON_3 94785 TCTCTTGATGTTTATCTTACTTGGGGTTC-TTGAGCTTTTTCAATAT--- 94830
viv i i i- i vi i ---
C L1M4b_5end#LI 2035 TCTCTTTGAGTTTATCCTACTTGGAGTTTATTGAGCTTCTTGGATGTGTA 1986
INTRON_3 94831 --TTAGTTTTTATATTTTATCGT----TTTGGAGATACTTTCAGCCCCTG 94874
-- i v v i - i ---- - vii i vi i
C L1M4b_5end#LI 1985 GATTAATATTAATGTTTT-TCATCAAATTTGG-GAAGTTTTTAGCCATTA 1938
INTRON_3 94875 TTTCTTCAAATATTTTTTCTGTTCCCTTTCTCTTT 94909
i - i
C L1M4b_5end#LI 1937 TTTCTTCAAATATTTTTTCTGCTCC-TTTCTCTCT 1904
Matrix = 20p37g.matrix
Transitions / transversions = 2.10 (44 / 21)
Gap_init rate = 0.04 (12 / 310), avg. gap size = 2.25 (27 / 12)
+ 4937 13.8 4.3 0.8 INTRON_3 95019 95882 (304299) C L1PA16 LINE/L1 (2) 7332 6446 128
ANNOTATION EVIDENCE:
382 14.31 0.00 4.29 INTRON_3 95019 95091 305090 C L1PA16_3end LINE/L1 842 911 2 223
INTRON_3 95019 TTTCTTTTAACTTCAACTTTTACTTTAGATATAGGGAGTACATGTGCAGA 95068
i --- i vi i i
C L1PA16_3end#L 911 TTTTTTTT---TTCAACTTTTATTTTAGATTCAGGGGGTACATGTGCAGG 865
INTRON_3 95069 TTTCTTGTATGGGTATATTGCAT 95091
v ii i
C L1PA16_3end#L 864 TTTGTTACATGGGTATATTGCGT 842
Matrix = 20p37g.matrix
Transitions / transversions = 4.00 (8 / 2)
Gap_init rate = 0.01 (1 / 72), avg. gap size = 3.00 (3 / 1)
4937 13.49 0.26 0.26 INTRON_3 95089 95861 304320 C L1PA16_3end LINE/L1 37 809 104 224
INTRON_3 95089 CATCCAGGTAGTACACATAGTACCCAACAGGCAGATTTTTCAAGCCAAGC 95138
i ivi i i - v vv
C L1PA16_3end#L 809 CACCCAGGTAGTGAGCATAGTACCCAATAGGTAG-TTTTTCAACCCTTGC 761
INTRON_3 95139 CCTTCTCCGTTCTTCCCTCCTCTAGTAGTCTACAGTGTTTATTTTTCCCA 95188
ii v i i i iv i v
C L1PA16_3end#L 760 CCCCCTCCCTCCCTCCCCCCTCTAGTAGTCCCCAGTGTCTATTGTTCCCA 711
INTRON_3 95189 TGTTTATGTCCATGTGTGCTCAATGTTTAGCTCCCACTTATAAGTGAAAA 95238
v i i i
C L1PA16_3end#L 710 TCTTTATGTCCATGTGTACCCAATGTTTAGCTCCCACTTATAAGTGAGAA 661
INTRON_3 95239 TATATGGTTCTTGGTTTTCTGTTCCTGTGTTAGTTCACTTAGGATTATGG 95288
i ii vi i i i v
C L1PA16_3end#L 660 CATGCGGTATTTGGTTTTCTGTTCCTGCGTTAATTCGCTTAGGATAATGG 611
INTRON_3 95289 CCTCCAGCTCCATCCATGTTGCTGCAAGTAACAGGATTTGATTCTTTTTT 95338
v ivi v v
C L1PA16_3end#L 610 CCTCCAGCTGCATCCATGTTGCTGCAAAGGACATGATTTCATTCTTTTTT 561
INTRON_3 95339 ATAGCTGCATAATATGCCATGGTGTATATGTACCATATTTTCTTTATCTA 95388
i i i v i i
C L1PA16_3end#L 560 ATGGCTGCGTAGTATTCCATGGTGTATATGTACCACATTTTCTTTATCCA 511
INTRON_3 95389 GTCCACCACTGATGGATACCTAGGTTGATTCCAGGACTTTGCTATTCTCA 95438
ii ii v v v v
C L1PA16_3end#L 510 GTCCACCGTTGATGGGCACCTAGGTTGATTCCATGTCTTTGCTATTGTGA 461
INTRON_3 95439 ATAGCACAGTGATGAACATAGAAGTACATGTGTCTTTTTG-TATAATGAT 95487
ii v i vi i - v
C L1PA16_3end#L 460 ATAGTGCTGCGATGAACATACGAGTGCATGTGTCTTTTTGGTAGAATGAT 411
INTRON_3 95488 CTATTTTCCTTTGGGTATATACCTAGTAATGGGATTGTGGGGTTGAATGG 95537
i i iv i
C L1PA16_3end#L 410 TTATTTTCCTTTGGGTATATACCCAGTAATGGGATTGCTGGGTCGAATGG 361
INTRON_3 95538 TAGCTCTGTTTTAAGTTATTTGAGAAACCTCTAAACTGCTTGCCACAGTG 95587
i v i i v
C L1PA16_3end#L 360 TAGTTCTGTTTTAAGTTCTTTGAGAAATCTCCAAACTGCTTTCCACAGTG 311
INTRON_3 95588 GTTGAACTAACTTACATTCCCAAAAACAGTGTATAAGCACCCCCTTTTCT 95637
i i vv iii
C L1PA16_3end#L 310 GCTGAACTAATTTACATTCCCACCAACAGTGTATAAGCGTTCCCTTTTCT 261
INTRON_3 95638 CTACAGCCTCACCAATATATCTTGTTTTTTTGACTTTTTAAAAATAGCCA 95687
ii i ii v v - v
C L1PA16_3end#L 260 CCGCAGCCTCGCCAGCATCTGTTGTTTTTT-GACTTTTTAATAATAGCCA 212
INTRON_3 95688 TTCTGACTGCTTTGAGATGGTATCTCACTGTGGTTTTGATTTGCATTTCT 95737
v v i
C L1PA16_3end#L 211 TTCTGACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCT 162
INTRON_3 95738 CTAATGATTAGTGACAGTGAGCATGTTTTCATATGTTTCTTGGCCACTTG 95787
i iiv v v i
C L1PA16_3end#L 161 CTGATGATTAGTGATGTTGAGCATTTTTTCATATGTTTGTTGGCCGCTTG 112
INTRON_3 95788 TATGTCTTCTTTTGAGAAGTGTCTGTTAATGTCCTTTGCCCCTTTTTGAA 95837
v vi v
C L1PA16_3end#L 111 TATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAA 62
INTRON_3 95838 TGGGATTGTTT-TTGCTTGCTTATT 95861
i i - vi i
C L1PA16_3end#L 61 TGGGGTTATTTGTTTTTTGCTTGTT 37
Matrix = 20p37g.matrix
Transitions / transversions = 1.67 (65 / 39)
Gap_init rate = 0.01 (4 / 772), avg. gap size = 1.00 (4 / 4)
337 23.30 0.75 7.14 INTRON_3 95749 95882 304299 C L1MD_orf2 LINE/L1 3169 3294 0 225
INTRON_3 95749 TGACAGTGAGCATGTTTTCATATGTTTCTTGGCCACTTGTATGTCTTCTT 95798
iiv i v i i v v ii i i
C L1MD_orf2#LIN 3294 TGATGTTGAACATCTTTTCATGTGCTTATTTGCCATCTGTATATCCTCTT 3245
INTRON_3 95799 TTGAGAAGTGTCTGTTAATGTCCTTTGCCCCTTTTTGAATGGGATTGTTT 95848
iv v i v v i v iv v
C L1MD_orf2#LIN 3244 CGGTGAAATGTCTCTTCATGTCTTTTGCCCATTTTCTAATTGGATTGTTT 3195
INTRON_3 95849 TTGCTTGCTTATTTTTTTTTTTTCAGTTT-GAGAG 95882
v --------- vi v v -
C L1MD_orf2#LIN 3194 GT---------TTTTTTACTGTTGAGTTTTGAGAG 3169
Matrix = 20p37g.matrix
Transitions / transversions = 0.93 (14 / 15)
Gap_init rate = 0.02 (2 / 133), avg. gap size = 5.00 (10 / 2)
+13098 15.4 2.9 1.7 INTRON_3 96620 100720 (299461) C L1PA16 LINE/L1 (849) 6465 2314 128
ANNOTATION EVIDENCE:
13098 13.72 2.23 0.92 INTRON_3 96620 98864 301317 C L1P4_orf2 LINE/L1 915 3188 106 226
INTRON_3 96620 TGCTTGTTGA----TTTAAGTCCCTTATAGATTCTGGCTATTAGACCTTG 96665
---- i v v
C L1P4_orf2#LIN 3188 TGCTTGTTGAATTGTTTAAGTTCCTTATAGATTCTGGATATTAGACCTTT 3139
INTRON_3 96666 G-CATATGCAAAGTTTGTGAATATTTTCTCCTATCGTGTAGGTTGTCTCT 96714
- iv v i i iv v
C L1P4_orf2#LIN 3138 GTCGGATGCATAGTTTGCGAATATTTTCTCCCATTCTGTAGGTTGTCTGT 3089
INTRON_3 96715 TTA----GT-AATAGTTTCTTTTGCTGTGCAGAAGCTCTTCTGTTTAATT 96759
---- -i iv
C L1P4_orf2#LIN 3088 TTACTCTGTTGATAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATT 3039
INTRON_3 96760 AGGTCCCACTCATCAATTTTTGTTTATGTTGCAATTGCTTTTGGGGACTT 96809
ii v i
C L1P4_orf2#LIN 3038 AGGTCCCACTTGTCAATTTTTGTTTTTGTTGCAATTGCTTTTGAGGACTT 2989
INTRON_3 96810 AGCCAAAAATTCTTTGCCTAGACCAATATTGAAAAGTGCATTTCCTAGGT 96859
i v v v i i i iv i vv ii
C L1P4_orf2#LIN 2988 AGTCATAAATTCTTTCCCAAGGCCGATGTCCAGAATGGTGTTTCCTAGGT 2939
INTRON_3 96860 TTTCTTCTAGGATTTTTATAGTTTGAGATTTTCCATTTACATTTTTAATC 96909
i i i v v i
C L1P4_orf2#LIN 2938 TTTCTTCTAGGATTCTTATAGTTTGAGGTCTTACATTTAAATCTTTAATC 2889
INTRON_3 96910 CATCTTAGGTTAATTTTTGTATATGGTGAAAGGTAAGGGTCTAGTTTTAT 96959
ii i i i
C L1P4_orf2#LIN 2888 CATCTTGAGTTAATTTTTGTATATGGTGAAAGGTAGGGGTCCAGTTTCAT 2839
INTRON_3 96960 TCTTCTGCATATGGATAGCCAGTTATCCCAGCACCATTAATCAAATAGGA 97009
v i v ii i
C L1P4_orf2#LIN 2838 TCTTCTGCATATGGCTAGCCAGCTATCCCAGCACCATTTATTGAATAGGG 2789
INTRON_3 97010 GTTCCTTTCCCCATTGCTTGTTTTTGTCAGCCTTGTCAAAGATCAGATGG 97059
iv i ii i i
C L1P4_orf2#LIN 2788 AGTCCTTTCCCCATTGCTTATTTTTGTCGACTTTGTCGAAGATCAGATGG 2739
INTRON_3 97060 TTGTAAATATGTGGCTGTATTTTTGAGTTTGCTACTCTGTTTCATGGATC 97109
i ii i v i i iv i i v i
C L1P4_orf2#LIN 2738 CTGTAGGTGTGTGGCTTTATTTCTGGGTTCTCTATTCTGTTCCATTGGTC 2689
INTRON_3 97110 TGTGTGTCTGTTTTTTATACCAGTTCCATGCTGTTTTGGTTACAGTAGCC 97159
i -i v v
C L1P4_orf2#LIN 2688 TATGTGTCTGTTTTT-GTACCAGTACCATGCTGTTTTGGTTACTGTAGCC 2640
INTRON_3 97160 CTATAATATCATTTGAAGTTGGGTAGCATGCTGTCTCCACATTTGTTCTT 97209
i i vi i iii v i ivv
C L1P4_orf2#LIN 2639 TTATAGTATAGTTTGAAGTCGGGTAATGTGATGCCTCCGGCTTTGTTCTT 2590
INTRON_3 97210 TGTGCTTAGGATTGCTTTGGCTATTTGGGTTCATTTTTGTTGTTATTCCA 97259
v i v -----i
C L1P4_orf2#LIN 2589 TTTGCTTAGGATTGCTTTGGCTATTTGGGCTCTTTTTTG-----GTTCCA 2545
INTRON_3 97260 TATGAATTTTAGAATATCTTTTTCTAATTTTGTGAAGAATGATGCTGGTA 97309
vi i i iii
C L1P4_orf2#LIN 2544 TATGAATTTTAGAATAGTTTTTTCTAATTCTGTGAAAAATGACATTGGTA 2495
INTRON_3 97310 GTTTGATAGGTATAGCACTGAATCTGCAGATTCCTTTGGGCAGTATGTCC 97359
v i i v v
C L1P4_orf2#LIN 2494 GTTTGATAGGAATAGCATTGAATCTGTAGATTGCTTTGGGCAGTATGGCC 2445
INTRON_3 97360 ATTTTAATGATATTGATTCTTTCCATCCA-GAGCATGGAATGTTTTTTCA 97408
i i v - i
C L1P4_orf2#LIN 2444 ATTTTAACGATATTGATTCTTCCAATCCATGAGCATGGAATGTTTTTCCA 2395
INTRON_3 97409 TTTATTTG-----------ATTTATTTCAGCAGTGTTTTGTAGTTATCCT 97447
i ----------- v v
C L1P4_orf2#LIN 2394 TTTGTTTGTGTCATCTATGATTTCTTTCAGCAGTGTTTTGTAGTTCTCCT 2345
INTRON_3 97448 TGTGGAGATCTTTCACCCCCTTAGTTAGCTATATTCCTAGGTATTTCATT 97497
i i i v i i
C L1P4_orf2#LIN 2344 TGTAGAGATCTTTCACCTCCTTGGTTAGATGTATTCCTAGGTATTTTATT 2295
INTRON_3 97498 TTCTTTGTGGCTGTTGTAAATGGGATTGTGTTCTCAATTTCACCCTCAGC 97547
i i i ii vi i
C L1P4_orf2#LIN 2294 TTTTTTGTGGCTATTGTAAATGGGATTGCGTTCTTGATTTGGCTCTCAGC 2245
INTRON_3 97548 ATGGACATTATTGGTGTTTGGAAATGCTACTGATTTGTGTATATTGATTT 97597
v i i v i v i
C L1P4_orf2#LIN 2244 TTGAACGTTATTGGTGTATAGAAATGCTACTGATTTTTGTACATTGATTT 2195
INTRON_3 97598 TGTATCCTGAAACCTTATTAAAATCATTGATCTTTTATAGTAGCCTTTTG 97647
i i i i i v vv vi v
C L1P4_orf2#LIN 2194 TGTATCCTGAAACTTTACTGAAGTCGTTTATCAGTTCCAGGAGCCTTTTG 2145
INTRON_3 97648 G-GGAGTCTTTAGGGTTTTCTAGGTATAGAATCATATCGGCAGCAAAGAG 97696
- iv i
C L1P4_orf2#LIN 2144 GCGGAGTCTTTAGGGTTTTCTAGGTATAGAATCATATCATCAGCGAAGAG 2095
INTRON_3 97697 AGAGAGTTTGATGTCTTCTTTTCCTATTTG--TG--TTTTATTTCTTTTT 97742
v iv -- -- i
C L1P4_orf2#LIN 2094 AGATAGTTTGACTTCTTCTTTTCCTATTTGGATGCCTTTTATTTCTTTCT 2045
INTRON_3 97743 TTCTTGCCTGATTGCACTGGCTAGCACTTCCAGTACTATGTTGAATAACA 97792
-- v v iv
C L1P4_orf2#LIN 2044 --CTTGCCTGATTGCTCTGGCTAGGACTTCCAGTACTATGTTGAATAGGA 1997
INTRON_3 97793 GTAGTGAGAGTGGACATTGTTGTCTTATTCCAGTTATCAAGGGGAATGCT 97842
i i iv i v
C L1P4_orf2#LIN 1996 GTGGTGAGAGTGGGCATCCTTGTCTTGTTCCAGTTCTCAAGGGGAATGCT 1947
INTRON_3 97843 TCCAGTTTTTGCCTTTTCAGTATGATGTTGGCTGAGGGTTTGTTATA--T 97890
i iv v i --
C L1P4_orf2#LIN 1946 TCCAGCTTTTGCCCGTTCAGTATGATGTTGGCTGTGGGTTTGTCATAGAT 1897
INTRON_3 97891 AGCTCTTACTATTTTGAGGTATGTTCCTTCAGTGCTTAGTTTGTTGAGGG 97940
i i ii i ?
C L1P4_orf2#LIN 1896 GGCTCTTATTATTTTGAGGTATGTTCCTTCGATGCCTAGTTTNTTGAGGG 1847
INTRON_3 97941 TTTTTATCATAAAGACATTTTGGATTTAATCAAAAGCTTTTTCTGTATTT 97990
i iv v v i i i i
C L1P4_orf2#LIN 1846 TTTTTATCATGAAGGGATGTTGGATTTTATCGAAAGCTTTTTCCGCATCT 1797
INTRON_3 97991 ATTGAAGTAATCATATGGTTTTTGCTTTTAATTCTGTTAATGTGGTGAAT 98040
ii i i v
C L1P4_orf2#LIN 1796 ATTGAGATGATCATATGGTTTTTGTTTTTAATTCTGTTTATGTGGTGAAT 1747
INTRON_3 98041 CACATTTATTGATTTGCATATGTTGAACCAGCCTTGCATCCAAGGAATTA 98090
i i v -i
C L1P4_orf2#LIN 1746 CACATTTATTGATTTGCGTATGTTGAACCAACCTTGCATCCCAGGAAT-G 1698
INTRON_3 98091 AAGCTTACTTGATTCTGGTATATTGACTTTTTAATGTGCTGCTGGATTCA 98140
i iv iv i i i
C L1P4_orf2#LIN 1697 AAGCCTACTTGATCGTGGTGAATTAACTTTTTGATGTGCTGCTGGATTCG 1648
INTRON_3 98141 GTTTGTTAGTATGTCATTGAGGATTTTTGTGTC-------ATCAGGGATA 98183
i v ii i -------
C L1P4_orf2#LIN 1647 GTTTGCTAGTATTTTGTTGAGGATTTTTGCGTCTATGTTCATCAGGGATA 1598
INTRON_3 98184 TTGGCCTAAACTTTTATTTTTTCACTGTGTTCCTGCCAGGCTTTGGTATT 98233
iv v v ii iii i i
C L1P4_orf2#LIN 1597 TTGGCCTGTAGTTTTCTTTTTTCGTTGTGTCTTTGCCAGGTTTTGGTATC 1548
INTRON_3 98234 AGGCTGATGTTGGCTTCCTAAAATAAGTTAGGGAGGAGCCTCTCCTCTTC 98283
v i v i i i i i
C L1P4_orf2#LIN 1547 AGGGTGATGCTGGCTTCATAGAATGAGTTAGGGAGGAGTCCCTCCTCCTC 1498
INTRON_3 98284 AATTTTTTGGAATAGTTTCAGTAGGATTGCTACCAGTTCTTCTTTGTACA 98333
i i v i i
C L1P4_orf2#LIN 1497 GATTTTTTGGAATAGTTTCAGTAGAATTGGTACCAGCTCTTCTTTGTACG 1448
INTRON_3 98334 TCTGATAGAATTCATCTGTGAATCCATCTGTTCCAGGGCTATTTTTGGTT 98383
i iv v i v
C L1P4_orf2#LIN 1447 TCTGGTAGAATTCGGCTGTGAATCCATCTGGTCCGGGGCTTTTTTTGGTT 1398
INTRON_3 98384 GGTAGGTTTTTTAAATTACTGATTTAATTTCAGAGTTTGATATTGGTCCA 98433
-- i i ii i ii
C L1P4_orf2#LIN 1397 GGTAGGTTTTTTA--TTACTGATTCAATTTCGGAACTCGATATTGGTCTG 1350
INTRON_3 98434 TTCAGGGTTTCAATCTCTTCCTGAGTCAATCTTGACAGATTGTGTGATTC 98483
i v iv i v
C L1P4_orf2#LIN 1349 TTCAGGGTTTCAATTTCTTCCTGATTCAATCTTGGGAGGTTGTGTGTTTC 1300
INTRON_3 98484 CAGAAATTTATTCATGTCCTCTAGATTTTCTAATTTGTGTGTATAGAGTT 98533
i i v i i v
C L1P4_orf2#LIN 1299 CAGGAATTTATCCATTTCCTCTAGATTTTCTAGTTTGTGTGCATAGAGGT 1250
INTRON_3 98534 GTTCATAGTATTCTCTGAGGATATTTTGTATTTCTATGGGATCAGTTGTA 98583
i v v i i
C L1P4_orf2#LIN 1249 GTTCATAATAGTCTCTGAGGATCTTTTGTATTTCTGTGGGATCGGTTGTA 1200
INTRON_3 98584 AAGTCATTGCTGTCTTTTCTTATTGTACTTACTTGGATCTTCTCT---TT 98630
v iivi v v i i ---
C L1P4_orf2#LIN 1199 ATGTCACCTTTGTCATTTCTGATTGTGCTTATTTGGATCTTCTCTCTTTT 1150
INTRON_3 98631 TTTCATTGCTAATCTAGCTAGCCATATGTTAATCTTGTTTATTTTTTTGG 98680
v i vi v i i ii iii
C L1P4_orf2#LIN 1149 TTTCTTTGTTAATCTAGCTAGCGGTCTATTGATCTTGTTTATCCTTTCAA 1100
INTRON_3 98681 AGAATGAATTCTTGTCTTCATTGATTTTTTCATATGGATTTTTGCATCTC 98730
iv i i vi i i -i vi
C L1P4_orf2#LIN 1099 AGAACCAACTTTTGGTTTCGTTGATTCTTT-GTATGGATTTTTGGGTCTC 1051
INTRON_3 98731 AATTTCATTTGGTTCTTCTGTAATTATTGTTAGAGAGGAA---------- 98770
ii v v i v v ------------------
C L1P4_orf2#LIN 1050 AATTTCATTCAGTTCTGCTCTGATTTTAGTTA--------TTTCTTTTCT 1009
INTRON_3 98771 -CTGCTAGCTTTAGGGTTGGTTTGTTCTTTTTTCTTCTAGTTCCTTTAGG 98819
- i i v - i
C L1P4_orf2#LIN 1008 TCTGCTAGCTTTGGGGTTAGTTTGTTCTTGTTT-TTCTAGTTCCTCTAGG 960
INTRON_3 98820 TGCAATGTTCGATTGTTAATTTGAGATCTTTCTAACTTCTCAAAG 98864
ii v i i ii i
C L1P4_orf2#LIN 959 TGTGATGTTAGATCGTTAATTTGAGATCTTTCTAACTTTTTGAGG 915
Matrix = 20p37g.matrix
Transitions / transversions = 2.13 (207 / 97)
Gap_init rate = 0.01 (20 / 2244), avg. gap size = 3.55 (71 / 20)
5137 22.89 5.10 3.73 INTRON_3 98172 99759 300422 C L1PREC2_orf2 LINE/L1 1 1609 1685 227
INTRON_3 98172 TCATCAGGGATATTGGCCTAAACTTTTATTTTTTCACTGTGTTCCTGCCA 98221
i i v v iii ii
C L1PREC2_orf2# 1609 TCATCAAGGATATTGGCCTGAAGTTTTCTTTTTTTGTTGTGTCTCTGCCA 1560
INTRON_3 98222 GGCTTTGGTATTAGGCTGATGTTGGCTTCCTAAAATAAGTTAGGGAGGAG 98271
i i v i i v i i i
C L1PREC2_orf2# 1559 GGTTTTGGTATCAGGATGATGCTGGCCTCATAGAATGAGTTGGGGAGGAG 1510
INTRON_3 98272 CCTCTCCTCTTCAATTTTTTGGAATAGTTTCAGTAGGATTGCTACCAGTT 98321
i i i v v i
C L1PREC2_orf2# 1509 TCCCTCCTCCTCAATTTTTTGGAATAGTTTCAGTAGGAATGGTACCAGCT 1460
INTRON_3 98322 CTTCTTTGTACATCTGATAGAATTCATCTGTGAATCCATCTGTTCCAGGG 98371
i iv i v v
C L1PREC2_orf2# 1459 CTTCTTTGTACATCTGGTAGAATTCGGCTGTGAATCCGTCTGGTCCTGGG 1410
INTRON_3 98372 CTATTTTTGGTTGGTAGGTTTTTTA----------AATTACTGATTTAAT 98411
v i v ---------- v v vi vi
C L1PREC2_orf2# 1409 CTTTTTTTGGTTGGTAGGCTATTTATTACTGATTCAATTTCGGAGCTCGT 1360
INTRON_3 98412 T----------TCAGAG------TTTGATATTGGTCCATTC-----AGGG 98440
---------- i ------ vv vi i v -----
C L1PREC2_orf2# 1359 TATTGGTCTGTTCAGGGAATCAATTTCTTCCTGGTTCAGTCTTGGGAGGG 1310
INTRON_3 98441 TTTCAATCTCTTCCTGAGT----CAATCTTGAC-AGATTGTGTGATTCCA 98485
v -- v v i vv i ---- v ivv - i ------ i
C L1PREC2_orf2# 1309 TGT--ATGTGTCCAGGAATTTATCCATCTCTTCTAGGTT------TTCTA 1268
INTRON_3 98486 GAAATTTATTCATGTCC-TCTAGATTTTC----TAATTTGTGTGTATAGA 98530
------- ii v - vv i v ---- i v ----- vi
C L1PREC2_orf2# 1267 G-------TTTGTGTGCATAGAGGTGTTCGTAGTAGTTTCTG-----ATG 1230
INTRON_3 98531 GTTGTTCATAGTATTCTCTGAGGATATT--TTGTATTTCTATGGGATCAG 98578
i ii v -- v i vi v -- vii ii iv v -- v
C L1PREC2_orf2# 1229 GTTATTTGTATT--TCTGTGGGGTCAGTGGTAACATCCCCTTTG--TCAT 1184
INTRON_3 98579 TTGTAAAGTCATTGCTGTCTTTTCTTATTGTACTTACTTGGATCTTCTCT 98628
v ----- - i v ----- v ii v i--- i
C L1PREC2_orf2# 1183 TTCTAA-----TTG-TGTTTATT-----TGGATCTTCTC---TCTTTTCT 1148
INTRON_3 98629 TTTTTCATTGCTAATCTAGCTAGCCATATGTTAATCTTGTTTATTTTTTT 98678
i - --- i viiv i iv i v i
C L1PREC2_orf2# 1147 TCTTT-ATT---AGTCTAGCTAGCGGCCTATCTATCTTATTAATTTTTTC 1102
INTRON_3 98679 GGAGAATGAATTCTTGTCTTCATTGATTTTTTCATATGGATTTTTGCATC 98728
ii i iv i i vv i i v - v i ii
C L1PREC2_orf2# 1101 AAAAAACCAACTCCTGGATTCGTTGATCTTTTGA-ATGGTTTTTCGTGTC 1053
INTRON_3 98729 TCAATTTCATTTGGTTC--TTCTG----TAATTATTGTTAGAGAGGAACT 98772
i i v ii --i ---- ii vi v vvvv---
C L1PREC2_orf2# 1052 TCGATCTCCTTCAGTTCAGCTCTGATTTTGGTTATTTCTTGTCTT---CT 1006
INTRON_3 98773 GCTAGCTTTAGGGTTGGTTTGTTCTTTTTTCTTCTAGTTCCTTTAGGTGC 98822
i i vi - i i v i
C L1PREC2_orf2# 1005 GCTAGCTTTGGGGTTGGTTTGCTCTTGCTTCT-CTAGTTCTTTCAGTTGT 957
INTRON_3 98823 AATGTTCGATTGTTAATTTGAGATCTTTCTAACTTCTCAA---AGGCATT 98869
i v i i ii ---i
C L1PREC2_orf2# 956 GATGTTAGGTTGTTAATTTGAGATCTTTCTAACTTTTTGATGTGGGCATT 907
INTRON_3 98870 T---------------CCTCTTA-TACTGTTTTAGCTGCATTCCAGAGAT 98903
--------------- -i ii ii i
C L1PREC2_orf2# 906 TAGTGCTATAAATTTCCCTCTTAACACTGCCTTAGCTGTGTCCCAGAGAT 857
INTRON_3 98904 GTTGGCATGTTTTGTTCCTAATTTCATTAATTTCAATGAATTTTTTAATC 98953
vi i v i iii iv i i v i i i i
C L1PREC2_orf2# 856 TCTGGTATGTTGTATCTTTGTTCTCATTAGTTTCAAAGAACTTCTTGATT 807
INTRON_3 98954 TCTGCCTTAATTTCAGTGCTTACACAGGAATTATTTGGGAGCAAATTGTT 99003
v ii v ii i i ii ii
C L1PREC2_orf2# 806 TCTGCCTTAATTTCATTATTTACCCAAAAGTCATTCAGGAGCAGGTTGTT 757
INTRON_3 99004 AAATTTCCATGTATTTGTGTAGTTTTGAG--ATATCTTTGGTTTT----- 99046
v v ii i -- v i i i -----
C L1PREC2_orf2# 756 TAATTTCCATGTAATTGCATGGTTTTGAGCGATTTTTTTAGTCTTGACTT 707
INTRON_3 99047 -TGTTTTTATTGCACTGTGGTCCAAGAGTATGGTTGATATTATTTCAATT 99095
- i i i i v i v ii
C L1PREC2_orf2# 706 CTATTTTTATTGCGCTGTGGTCCGAGAGTGTGTTTGGTATGATTTCGGTT 657
INTRON_3 99096 TTTTTGATTTTATTGAAGTTTGGTTTATGACTGTGCATGTGGTTCATCTT 99145
i vv ii i v v v iivvii iv i
C L1PREC2_orf2# 656 CTTTTGCATTTGCTGAGGATTGTTTTATGTCCAATTGTGTGGTCGATTTT 607
INTRON_3 99146 AGAATATGTTCTGTGTG-CATATGGGAAGAATGTATATTCTGTCATTGTT 99194
i v ii - - i ii v
C L1PREC2_orf2# 606 AGAGTATGTGCCATGTGGCA-ATGAGAAGAATGTATATTCTGTTGTTTTT 558
INTRON_3 99195 GGGTGGAGTGTTCTGTAGATGTCTATTAGGTCTAATTGGTTAAGTGTTGC 99244
v v i i i v iv i v
C L1PREC2_orf2# 557 GGGTGGAGAGTTCTGTAGAGGTCTATCAGATCCATTTGGTCCAATGTTGA 508
INTRON_3 99245 ATTTGAGTCCATAGTTTCTTTGTAAGTTTTCTGCCT---TGATCTGTCTA 99291
i iii vv i v v i ---
C L1PREC2_orf2# 507 GTTCAGGTCCTGAATATCTTTGTTAATTTTCTGCCTCGATGATCTGTCTA 458
INTRON_3 99292 ATGCTATCAGTGAGGTGTTGAAGTCTCCCACTATTGTTGTGTGGTTGTCT 99341
i i ii i vv
C L1PREC2_orf2# 457 ATACTGTCAGTGGAGTGTTGAAGTCTCCCACTATTATTGTGTGGGAGTCT 408
INTRON_3 99342 TAAGTCTTTTTGTGGGCCAAGAAGAACTTGTTTTATGAATCTGAGTGCCC 99391
- i i i vvv i i i
C L1PREC2_orf2# 407 -AAGTCTCTTTGTAGGTCTCTAAGAACTTGCTTTATGAATCTGGGTGCTC 359
INTRON_3 99392 CAATGTAAGTGTGTATATAT-TTTAGGATAGTTAAGTCTTCTTGTGTGCT 99440
vi vi - i - i vviv
C L1PREC2_orf2# 358 CTGTGTTGG-GTGCATATATATTTAGGATAGTTAGGTCTTCTTGTTGAAT 310
INTRON_3 99441 TGTAGTCTTTATCATTATGTAATGCCCTTCTTTGCCCTTGTTATTTTATA 99490
v vi i i i v iv i v i
C L1PREC2_orf2# 309 TGAACCCTTTACCATTATGTAATGCCCTTCTTTGTCTTTTTTGATCTTTG 260
INTRON_3 99491 CTGGTTTAAAACTTATTTTATCTGATATAAGAATAACAATTCCTGCTATT 99540
i iii i i v v i vi ii ---
C L1PREC2_orf2# 259 TTGGTTTAAAGTCTGTTTTGTCTGAAATTAGGATTGCAACCCCTGCT--- 213
INTRON_3 99541 TTTTTTGTTTGTTTGTTTTCTGTTTGCATGGTAAATGTTTCTCCATCTTT 99590
------- v i v ii v i v i ii
C L1PREC2_orf2# 212 -------TTTTTCTGATTTCCATTTGCTTGGTAGATTTTCCTCCATCCCT 170
INTRON_3 99591 TTACTTTGAGCCTGTGGGTGTTGTTACATGTGAGATGGATCTTTTGAAGA 99640
i i ii i i i i
C L1PREC2_orf2# 169 TTATTTTGAGCCTATGGGTGTCATTGCGTGTGAGATGGGTCTCTTGAAGA 120
INTRON_3 99641 CAGCAAATGGTTGGGTCTTGTCTTCTTATTCAGCTTGCCACTTTATGCCT 99690
v ivi ii i i i i
C L1PREC2_orf2# 119 CAGCATACCATTGGGTCTTGCTTTTTTATCCAGCTTGCCACTCTGTGCCT 70
INTRON_3 99691 TTTAAGTGGGGTGTTCAGTTCATTTACATTCAGCGTTACTTTTGAAATGT 99740
i ii i ii iv v v v
C L1PREC2_orf2# 69 TTTAAATGGGGCATTTAGCCCATTTACATTCAAGGTTAGTATTGATATGT 20
INTRON_3 99741 GAGATTTTGATTCTGCCAT 99759
v iv i i
C L1PREC2_orf2# 19 GTGGATTTGATCCTGTCAT 1
Matrix = 20p37g.matrix
Transitions / transversions = 1.82 (226 / 124)
Gap_init rate = 0.02 (38 / 1587), avg. gap size = 3.71 (141 / 38)
8448 12.99 2.52 1.52 INTRON_3 99610 100720 299461 C L1P4a_5end LINE/L1 1483 2596 0 228
INTRON_3 99610 GTTGTTACATGTGAGATGGATCTTTTGAAGACAGCAAATGGTTGGGTCTT 99659
i i i i
C L1P4a_5end#LI 2596 GTCGTTACATGTGAGATGGGTCTCTTGAAGACAGCAGATGGTTGGGTCTT 2547
INTRON_3 99660 GTCTTCTTATTCAGCTTGCCACTTTATGCCTTTTAAGTGGGGTGTTCAGT 99709
i i i i i i i i
C L1P4a_5end#LI 2546 GTCTTTTTATCCAGCTTGCCACTCTGTGTCTTTTAAGTGGGGCGTTTAGC 2497
INTRON_3 99710 TCATTTACATTCAGCGTTACTTTTGAAATGTGAGATTTTGATTCTGCCAT 99759
i v v v v i i
C L1P4a_5end#LI 2496 CCATTTACATTCAGGGTTAGTATTGATATGTGAGATTTTGATCCTGTCAT 2447
INTRON_3 99760 TATGTCGTTAGCTGGTTGTTTTGTCAGCTTGATTGTGTGATTGCTTTATA 99809
ii i v vii ii
C L1P4a_5end#LI 2446 CGTGTTGTTAGCTGGTTGTTATGTAGACTTGATTGTGTAGTTGCTTTATA 2397
INTRON_3 99810 GTGCCTGTGGCATATGTGCTTAAGTGTGTTTATGTGGTAGCAGGTGTTGT 99859
vv v ii
C L1P4a_5end#LI 2396 GTGCCTGTGGGCTATGTGCTTAAGTGTGTTTTTGTGGTAGCAGGTGTCAT 2347
INTRON_3 99860 TATTTTGATTCCATGTTTAGCATGCCCTTAAGGACCTCTTGTAAGGCTGG 99909
v i iv
C L1P4a_5end#LI 2346 TCTTTCGATTCCATGTTTAGCACTCCCTTAAGGACCTCTTGTAAGGCTGG 2297
INTRON_3 99910 TCTAATTGAAATGATTTCTCTCAGTGTTTGCTTGTCTGAGAAGGATTTTA 99959
i v i ii
C L1P4a_5end#LI 2296 TCTAGTTGAAATGAATTCCCTCAGCATTTGCTTGTCTGAGAAGGATTTTA 2247
INTRON_3 99960 TTTCTATTTCACATTTCAAGCTTAGTTTGGCAGGATATGAAAT-CTTACT 100008
vi v v v - iv
C L1P4a_5end#LI 2246 TTTCTCCTTCACTTATGAAGCTTAGTTTGGCAGGATATGAAATTCTTGGT 2197
INTRON_3 100009 TGGAATTTCTTTTCTTTAGGAACACTAAACAGAGGTCCCCTGATTTCTTC 100058
i i ii i v v i -i i
C L1P4a_5end#LI 2196 TGGAATTTCTTTTCTTTAAGGATGCTGAAAATAGGCCCCC-AATCTCTTC 2148
INTRON_3 100059 TGGCTTTTAAGGTTTCTGCTGAGAAGTCTCCTGTTAGCCTGATGGGGTTT 100108
v i v i i
C L1P4a_5end#LI 2147 TGGCTTGTAAGGTTTCTGCTGAGAGGTCTGCTGCTAGCCTGATGGGGTTC 2098
INTRON_3 100109 CCTCTGTAAGTGACTTGACTCTTCTCTCTAGCTGCCTTTAAGATTTTTTA 100158
v i i v
C L1P4a_5end#LI 2097 CCTCTGTATGTGACCTGACCCTTCTCTCTAGCTGCCTTTAAGATTTTTTC 2048
INTRON_3 100159 TTTTG---------TAGTGAATCTGATGACTATGTGCCTTAGGGATAGTC 100199
i --------- i i i
C L1P4a_5end#LI 2047 TTTCGCGTTGACCTTGGTGAATCTGATGACTATGTGCCTTGGGGATGGTC 1998
INTRON_3 100200 ATATTGTATAGTATCTAGCCAGGGTCCTTTGTATTTCTTGGATTTGCATA 100249
v i i i i i
C L1P4a_5end#LI 1997 ATCTTGTATAGTATCTAGCCGGGGTTCTCTGTATTTCTTGAATTTGCATG 1948
INTRON_3 100250 CCAACTTCTCCAAGAAGATTAGGGAAATTTTCGTGGACTGTATTCTCAAA 100299
i i i ivi i i i
C L1P4a_5end#LI 1947 TCAACCTCTCTAGCGAGATTAGGGAAATTTTCATGGACTATATCCTCAAA 1898
INTRON_3 100300 TATATTTTCCAAGTTGTTTAT-CTCTCTCCT---CTCTCAGGAATGCCAG 100345
i - --- i
C L1P4a_5end#LI 1897 TATATTTTCCAAGTTGCTTATTCTCTCTCCTTCTCTCTCAGGAATGCCAA 1848
INTRON_3 100346 TGAATCATAGATTTGGTCTCTTTACAGAATCTCATATTTCTTGGAGTTTT 100395
i v i i v
C L1P4a_5end#LI 1847 TGAGTCATAGATTTGGTCTCTTTACATAATCCCATATTTCTCGGAGGTTT 1798
INTRON_3 100396 T-TTTATTTTTAAAAATTCTTTCTTCTTTATTTTTATCTGATTGGGTTGA 100444
- i v i i i i
C L1P4a_5end#LI 1797 TGTTCATTTTTTAAAATTCTTTTTTCTTTATTTTTGTCTGACTGAGTTGA 1748
INTRON_3 100445 TTTGAAGAGCCAGTCTTTGAGCTGTGA--TTCTTTCCTCAGTTTGGTCTA 100492
i i i i v -- i
C L1P4a_5end#LI 1747 TTCGAAGAACCGGTCTTCGAGCTCTGAGATTCTTTCCTCAGCTTGGTCTA 1698
INTRON_3 100493 TTCTACTATTAATGCTTCTGATTGTATTACAAAATTCTTGTAGTGAATTT 100542
i i i i ii
C L1P4a_5end#LI 1697 TTCTGCTGTTAATACTTCCGATTGTATTATGAAATTCTTGTAGTGAATTT 1648
INTRON_3 100543 TTCAGCTCTAGAAGTTCAGTTTGGTTCTTTGTTAAAATTACTATTGTATC 100592
i v vi vii
C L1P4a_5end#LI 1647 TTCAGCTCCAGAAGTTCAGTTTGGTTCTTTCTTAAAATGGCTATTTCGTC 1598
INTRON_3 100593 TTTCAGCTCTTGGATCATTTTACTGCATTCCTTGGATTGGGTTTCAACTT 100642
v ? ------------
C L1P4a_5end#LI 1597 TTTCAGCTCTTGGATCATTTTACTGGATTNCTTGGATT------------ 1560
INTRON_3 100643 TCTCCTGAATCTTGATGAGCTTC--CTTGCCATCCAGATTCTGAATTA-T 100689
--i i i ----- i i -- v -- v v vi v -i
C L1P4a_5end#LI 1559 --CCTTGGAT-----TGGGTTTCAACTTTC--TCCTGAATCTCGATGAGC 1519
INTRON_3 100690 ATGTTTGTCATTT-CATTC-ACATCCAA---CTGTT 100720
v vi i ii-v -iv i v --- i
C L1P4a_5end#LI 1518 TTCCTTGCCATCCAGATTCTGAATTCTATGTCTGTC 1483
Matrix = 20p37g.matrix
Transitions / transversions = 2.35 (101 / 43)
Gap_init rate = 0.01 (15 / 1110), avg. gap size = 3.13 (47 / 15)
6337 15.06 3.72 1.78 INTRON_3 100320 100720 299461 C L1P4a_5end LINE/L1 1466 1876 720 229
INTRON_3 100320 TCTCTCTCCT---CTCTCAGGAATGCCAGTGAATCATAGATTTGGTCTCT 100366
--- i i
C L1P4a_5end#LI 1876 TCTCTCTCCTTCTCTCTCAGGAATGCCAATGAGTCATAGATTTGGTCTCT 1827
INTRON_3 100367 TTACAGAATCTCATATTTCTTGGAGTTTTT-TTTATTTTTAAAAATTCTT 100415
v i i v - i v
C L1P4a_5end#LI 1826 TTACATAATCCCATATTTCTCGGAGGTTTTGTTCATTTTTTAAAATTCTT 1777
INTRON_3 100416 TCTTCTTTATTTTTATCTGATTGGGTTGATTTGAAGAGCCAGTCTTTGAG 100465
i i i i i i i i
C L1P4a_5end#LI 1776 TTTTCTTTATTTTTGTCTGACTGAGTTGATTCGAAGAACCGGTCTTCGAG 1727
INTRON_3 100466 CTGTGA--TTCTTTCCTCAGTTTGGTCTATTCTACTATTAATGCTTCTGA 100513
v -- i i i i i
C L1P4a_5end#LI 1726 CTCTGAGATTCTTTCCTCAGCTTGGTCTATTCTGCTGTTAATACTTCCGA 1677
INTRON_3 100514 TTGTATTACAAAATTCTTGTAGTGAATTTTTCAGCTCTAGAAGTTCAGTT 100563
ii i
C L1P4a_5end#LI 1676 TTGTATTATGAAATTCTTGTAGTGAATTTTTCAGCTCCAGAAGTTCAGTT 1627
INTRON_3 100564 TGGTTCTTTGTTAAAATTACTATTGTATCTTTCAGCTCTTGGATCATTTT 100613
v vi vii
C L1P4a_5end#LI 1626 TGGTTCTTTCTTAAAATGGCTATTTCGTCTTTCAGCTCTTGGATCATTTT 1577
INTRON_3 100614 ACTG-----C----ATTCCTTGGATTGGGTTTCAACTTTCTCCTGAATCT 100654
----- ----
C L1P4a_5end#LI 1576 ACTGGATTNCTTGGATTCCTTGGATTGGGTTTCAACTTTCTCCTGAATCT 1527
INTRON_3 100655 TGATGAGCTTCCTTGCCATCCAGATTCTGAATTATATGTTTGTCATTTCA 100704
i v i
C L1P4a_5end#LI 1526 CGATGAGCTTCCTTGCCATCCAGATTCTGAATTCTATGTCTGTCATTTCA 1477
INTRON_3 100705 TTCACATCCAACTGTT 100720
v i- i --- -
C L1P4a_5end#LI 1476 GTCAT-TTCA---GT- 1466
Matrix = 20p37g.matrix
Transitions / transversions = 3.11 (28 / 9)
Gap_init rate = 0.02 (8 / 400), avg. gap size = 2.50 (20 / 8)
+ 207 0.0 0.0 0.0 INTRON_3 100721 100743 (299438) + (TTTG)n Simple_repeat 2 24 (0) 129
ANNOTATION EVIDENCE:
207 0.00 0.00 0.00 INTRON_3 100721 100743 299438 C (CAAA)n Simple_repeat 158 180 0 258
INTRON_3 100721 TTTGTTTGTTTGTTTGTTTGTTT 100743
C (CAAA)n#Simpl 180 TTTGTTTGTTTGTTTGTTTGTTT 158
Matrix = Unknown
Transitions / transversions = 0.0 (0 / 0)
Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0)
+ 2352 7.6 0.0 2.5 INTRON_3 100747 101035 (299146) C AluY SINE/Alu (29) 282 1 130
ANNOTATION EVIDENCE:
2277 7.80 0.00 2.48 INTRON_3 100747 101035 299146 C AluY SINE/Alu 1 282 29 133
INTRON_3 100747 TGAGATGGAGTCTCACTCTGTCGCCCAGGCTGGAATGCAGTGGTGCAATC 100796
i i i i i
C AluY#SINE/Alu 282 TGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATC 233
INTRON_3 100797 TCAGCTCACTGCAAGCTCCTCCTCCTGGGTCCCAGATTCATGCCATTCTC 100846
i v i ------- i
C AluY#SINE/Alu 232 TCGGCTCACTGCAAGCTCCGCCTCCCGGGT-------TCACGCCATTCTC 190
INTRON_3 100847 CTGCCTCAGCCTCCCTAGTAGCTGGAACTACAGGTGCCCACCACCACGCC 100896
v i i i
C AluY#SINE/Alu 189 CTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCACGCC 140
INTRON_3 100897 CAGCTAATTTTTTGTATTTTTAGTAGAGATGGGGTTTCACCGTGTTAGCC 100946
i i
C AluY#SINE/Alu 139 CGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCC 90
INTRON_3 100947 AGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTTGGCCTCCCA 100996
i i i
C AluY#SINE/Alu 89 AGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCA 40
INTRON_3 100997 AAGTGCTGGGATTACAGACATGAGCCACCATGCCCGGCC 101035
i i ii
C AluY#SINE/Alu 39 AAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 10.00 (20 / 2)
Gap_init rate = 0.00 (1 / 288), avg. gap size = 7.00 (7 / 1)
+ 8448 18.9 3.3 3.9 INTRON_3 101036 103067 (297114) C L1PA16 LINE/L1 (5021) 2313 2 128
ANNOTATION EVIDENCE:
6337 15.06 3.72 1.78 INTRON_3 101036 101731 298450 C L1P4a_5end LINE/L1 754 1465 1131 231
INTRON_3 101036 TCCAGCTGTTTAAGAACCATTGTTGGGGAGCTAGTGAACTTATTTGGAGG 101085
----- v i ii ii
C L1P4a_5end#LI 1465 -----CTGGTTAAGAACCATTGCTGGGGAGCTAGTGGGCTCGTTTGGAGG 1421
INTRON_3 101086 GAAGGGGACACT--GGCTTTTTGAATTGCCAGAGTTCTTACGCTGATTTT 101133
v -- i i
C L1P4a_5end#LI 1420 TAAGGGGACACTCTGGCTTTTTGAATTGCCAGAGTTCTTGCGCTGATTCT 1371
INTRON_3 101134 TTCTTATTTCGGAGGGTCGGTGTCCCTTTAACTGTGGTGTAAGTTGAGTA 101183
i i v ii i
C L1P4a_5end#LI 1370 TTCTCATCTGGGAGGGCTGGTGTTCCTTTAACTGTGGTGTAAGTTGAGTA 1321
INTRON_3 101184 TAGTCAGTTGGCTTCGTTTCTGGATGTTTTTAGTGGGTCAAGGCTCTGTG 101233
i i i v i i
C L1P4a_5end#LI 1320 TAGTCAGTTGGCTTCATTTCTGGATGCTTTCAGAGGGCCAAGGCTCTGTA 1271
INTRON_3 101234 TGGGGTCT--GTTTGTGGCTGAATTCTTGTCCTTAGTTTCACAGGGATGT 101281
ii i --i i i i
C L1P4a_5end#LI 1270 CAGGATCTTTATTTGTGGCTGAATTCTTGCCCTTGGTTTCACAGGGGTGT 1221
INTRON_3 101282 ATATTAGCAAAATATTTTTGGTGGTGTTGTTTGGACTGTGATCCAGTAGA 101331
i v v i i
C L1P4a_5end#LI 1220 ATATTAGCAGAATATTTTTGGTGTTGTAGTTTGGGCTGCGATCCAGTAGA 1171
INTRON_3 101332 TGGCGCTTAAG-------GCCAATAGA----------CTTAGTCTTGTGG 101364
------- ii ---------- i i vi i
C L1P4a_5end#LI 1170 TGGCGCTTAAGAGTAATGGCCGGTAGATAGGCTCTTACTCAGCCGCGCGG 1121
INTRON_3 101365 CTCTTTTATAGTTTCTGACATTTGCAGCCCTGCTCTGTATTGCAGTGTGG 101414
i v i vi i i v iiv i i v
C L1P4a_5end#LI 1120 CTCTTTTGTACTTCCTCGCGTTCGCAGCCGTGCTCTGCGGTGCGGCGGGG 1071
INTRON_3 101415 AGAGAGGTGACCCCCTCAGCAGGTCCACTCCTAGGCCTCTGGAGAGTCCC 101464
i v i i iv i i
C L1P4a_5end#LI 1070 AGAGAGATGACCCCCTCACCAGGTCCGCTCCTGGGCCTTGGGGGAGCCCC 1021
INTRON_3 101465 CTCTGATCACTGGGACTGCACCTTCATTTCTTTTGTTGAATGTTAGGTGA 101514
i v i i iv i iii vv ---
C L1P4a_5end#LI 1020 CTCCGATCACTGGCACCGCGCCCGCGTTTCTTTTGTTAGGTGTTCCG--- 974
INTRON_3 101515 GGGGCCACGGGGCTCTCTCTGGCAGAGGCAGTGGCAG--AGATAAGCCAC 101562
-- i i v v i -- i
C L1P4a_5end#LI 973 --GGCCGCGGGGCTCCCTCGGGCAGAGGCTGCGGCAGGGAGATAGGCCAC 926
INTRON_3 101563 ACC-TTTCTCGGTGGGCCCTTCCGAGGGAGGCATGCACTGCTCCCACGGC 101611
- v iiv viv i v i i ?v
C L1P4a_5end#LI 925 ACCCTTTCTGGACCGGCCCTGTGGAGGGAGGCACGCCCCGCTCCCGCNCC 876
INTRON_3 101612 AGTCCACAAGCCAGCCAGACTCACCCTTTTTTGTGCTCTGAG--TGTGCA 101659
i i ?i i v vviv i i iv -- v vi
C L1P4a_5end#LI 875 GGCCCANGAACCCGCGCATCTCACCCCTCTCAGTGCTCTGAGAGTGGGGG 826
INTRON_3 101660 CTGCTCTCCGGCTCCAGTGCTGGTCATAGATCTTGGCTCAGCACTCCCAA 101709
v i ? v i i i i i i
C L1P4a_5end#LI 825 CTCCTCCCCNGCTCGAGTGCCGGCCACAGATCTCGGCTCGGCACTCCCGA 776
INTRON_3 101710 GCTTTGCACTGCAGCCCTGTGG 101731
vi ?i i v
C L1P4a_5end#LI 775 GCTGCGNGCCGCAGCCCTGGGG 754
Matrix = 20p37g.matrix
Transitions / transversions = 2.30 (85 / 37)
Gap_init rate = 0.01 (9 / 695), avg. gap size = 4.00 (36 / 9)
8448 12.99 2.52 1.52 INTRON_3 101036 101350 298831 C L1P4a_5end LINE/L1 1163 1482 1114 230
INTRON_3 101036 TCCAG-CTGTTTAAGAACCATTGTTGGGGAGCTAGTGAACTTATTTGGAG 101084
i - v i ii ii
C L1P4a_5end#LI 1482 TTCAGTCTGGTTAAGAACCATTGCTGGGGAGCTAGTGGGCTCGTTTGGAG 1433
INTRON_3 101085 GGAAGGGGACACT--GGCTTTTTGAATTGCCAGAGTTCTTACGCTGATTT 101132
v -- i i
C L1P4a_5end#LI 1432 GTAAGGGGACACTCTGGCTTTTTGAATTGCCAGAGTTCTTGCGCTGATTC 1383
INTRON_3 101133 TTTCTTATTTCGGAGGGTCGGTGTCCCTTTAACTGTGGTGTAAGTTGAGT 101182
i i v ii i
C L1P4a_5end#LI 1382 TTTCTCATCTGGGAGGGCTGGTGTTCCTTTAACTGTGGTGTAAGTTGAGT 1333
INTRON_3 101183 ATAGTCAGTTGGCTTCGTTTCTGGATGTTTTTAGTGGGTCAAGGCTCTGT 101232
i i i v i
C L1P4a_5end#LI 1332 ATAGTCAGTTGGCTTCATTTCTGGATGCTTTCAGAGGGCCAAGGCTCTGT 1283
INTRON_3 101233 GTGGGGTCT--GTTTGTGGCTGAATTCTTGTCCTTAGTTTCACAGGGATG 101280
iii i --i i i i
C L1P4a_5end#LI 1282 ACAGGATCTTTATTTGTGGCTGAATTCTTGCCCTTGGTTTCACAGGGGTG 1233
INTRON_3 101281 TATATTAGCAAAATATTTTTGGTGGTGTTGTTTGGACTGTGATCCAGTAG 101330
i v v i i
C L1P4a_5end#LI 1232 TATATTAGCAGAATATTTTTGGTGTTGTAGTTTGGGCTGCGATCCAGTAG 1183
INTRON_3 101331 ATGGCGCTTAAGGCCAATAG 101350
ivi i
C L1P4a_5end#LI 1182 ATGGCGCTTAAGAGTAATGG 1163
Matrix = 20p37g.matrix
Transitions / transversions = 4.43 (31 / 7)
Gap_init rate = 0.01 (3 / 314), avg. gap size = 1.67 (5 / 3)
1476 20.12 1.80 6.25 INTRON_3 101538 101871 298310 C L1P4b_5end LINE/L1 1464 1783 0 232
INTRON_3 101538 AGAGGCAGTGGCAG--AGATAAGCCACACCTTTCTCGG-TGGGCCCTTCC 101584
v i -- i i ii -iv viv
C L1P4b_5end#LI 1783 AGAGGCCGCGGCAGGGAGACAGGCCACACCTTTTCCGGGCTGGCCCTGTG 1734
INTRON_3 101585 GAGGGAGGCATGCACTGCTCCCACGGCAGTCCACAAGCCAGCCAGACTCA 101634
v i i i ?i vi vv
C L1P4b_5end#LI 1733 GAGGGAGGCATGCCCCGCTCCCGCGGCAGCCCANGAGCCCACGCGACTCA 1684
INTRON_3 101635 CCCTTTTTTGTGCTCTGAG--TGTGCACTGCTCTCCGGCTCCAGTGCTGG 101682
i i iv -- vi v i v iv
C L1P4b_5end#LI 1683 CCCCTCTCAGTGCTCTGAGAGTGTGGGCTCCTCTTCCGCTTAAGTGCTGG 1634
INTRON_3 101683 TCATAGATCTTGGCTCAGCACTCCCAAGCTTTGCACTGCAGCCCTGTGGT 101732
i i i i i v ? i v i
C L1P4b_5end#LI 1633 CCACAGATCTCGGCTCGGCACTCCCGAGCTGTNCACCGCAGCCCTGGGGC 1584
INTRON_3 101733 GAACTCAGGCTTTTTGTTCCC-CCTTATATTGGGGGCAGCAGGAATGGGG 101781
i - ii vv iii
C L1P4b_5end#LI 1583 GAGCTCAGGCTTTTTGTTCCCTCCCCAGCTTGGGGGCAGCAGGGGCGGGG 1534
INTRON_3 101782 ACCGTAGTGGTTGGTATGGCAGAGGGACTGTCTGGGAACTCCACCCCAGA 101831
v - i iv vv v ------------------
C L1P4b_5end#LI 1533 ACCTT-GCGGCGGCAATGGCAGAGGGCCTGTC------------------ 1503
INTRON_3 101832 GAAATGCCTCTGGGAATTCCACCCCAGAGAAATGCAGAGC 101871
- iv ii ii
C L1P4b_5end#LI 1502 -AGTTGCCTCTGGGAGCTCCACCCCAGAGAAACACAGAGC 1464
Matrix = 20p37g.matrix
Transitions / transversions = 1.65 (38 / 23)
Gap_init rate = 0.02 (6 / 333), avg. gap size = 4.33 (26 / 6)
5172 21.49 3.49 4.85 INTRON_3 101836 103067 297114 C L1P4b_5end LINE/L1 2 1217 566 233
INTRON_3 101836 TGCCTCTGGGAATTCCACCCCAGAGAAATGCAGAGCTGCTTCTGCCAGTT 101885
ii i ii --- ii ?
C L1P4b_5end#LI 1217 TGCCTCTGGGAGCTCCACCCCAGAGAAACGCAGAGCCACT---GCCGATN 1171
INTRON_3 101886 GGGATAATCAGCTGTGGGTGGG-CAGCTGTGCTGTGGGCCCAAGCCAGGG 101934
i i i v - i i i -
C L1P4b_5end#LI 1170 GGAATGATCAGCCGGGGGTGGGGCGGCTGCGCTGCGGGCCCAAGCC-GGG 1122
INTRON_3 101935 ACGCCTTGTCTGGCCAAGGGTGGGGCAGGGGTCAGGAGTTTACATGGAAC 101984
v i i iv i ii --- ? i i ii i? v
C L1P4b_5end#LI 1121 AGGCCCTGCCTGGTGAAGAGCAGGG---GNGTCAGGGGCTCGCGNGGAAG 1075
INTRON_3 101985 ACAGTCTGGCCTCTTCTCCATAGGACGGCTGTCGTGGTGTGCTGTCGG-- 102032
i i i i i--- i vv --
C L1P4b_5end#LI 1074 ACAGTCTGGCCTCCTCTCCGTAGGGCAGCTGC---GGCGTGCTGGAGGCA 1028
INTRON_3 102033 TGCAGGAAAGTAGTCAGGCTCTTGGTTTCCTCCCTAGCCTGTTGGGAGGA 102082
-- i i v i i vv ? v
C L1P4b_5end#LI 1027 TGCA--AAAGCAATCAGGCTCTTTGTTCCCTCCCCAGCCTGAGGGNAGCA 980
INTRON_3 102083 AGGGCAGGGACCAGGGCAGAAGCAATAGGAGAGGGCCTGCCAGTTGTCTC 102132
v ivv i vi i v i i i
C L1P4b_5end#LI 979 AGGGCAGGTACCGCTGCGGCGGCAATGGCAGAGGGCCTGTCGGTTGCCTC 930
INTRON_3 102133 TAGGGACTTCCACCCCAGAGAAACACTGA----------ACTGAAGTGAT 102172
- vi ii v ---------- i
C L1P4b_5end#LI 929 T-GGGAGCTCCACCCCAGAGAAATGCAGAGCCGCCACCGACCGAAGTGAT 881
INTRON_3 102173 CAGGTGGGAGTGTGGTGGCTATGACTTGGGTTTTTATACCTAAAATTAAA 102222
ii i v i ii - v -------i i iivivii
C L1P4b_5end#LI 880 CAGGCAGGGGTGGGGCGGCTGCG-CTGGGG-------GCCCAGGCCAGGA 839
INTRON_3 102223 AACTATACATG-TGAAGGTCTGTGTGTACAAATATGTGTGTATGTAATAT 102271
ii iv i vi - i iv v iiv vi iiv iviii iviv i -
C L1P4b_5end#LI 838 GGCCCTGCCCGGTGAGGAGCAGCAGGGGCAGGGACCCACGTGGAAAACA- 790
INTRON_3 102272 GTGTGAGGAGCAG-TGAACCATATGGAAAACTGTCCAGCTGTCTTTTCAT 102320
v ---- v - vvv i --------- --------
C L1P4b_5end#LI 789 GTCTG----GCCGCTTTTCCGTATGG---------CAGCTGT-------- 761
INTRON_3 102321 ATGGTA-GCTGCAG-CATGTTGGAGG-CTTGTGACTGTTCTCAGGCTCTT 102367
-- ii- v - vi viv v- v i vvi i ---
C L1P4b_5end#LI 760 --GGCGTGCTGGAGGCCCGTGACAGTTCTTGAGGCATCTTT---GCTCTT 716
INTRON_3 102368 AGCTCCCTTCCCAGCCTCAGGGTAGCAGGG------ACTAT---AGAGGC 102408
v- i v i ------ ii --- v
C L1P4b_5end#LI 715 C-CTCCCTCCCCAGCCTGAGGGCAGCAGGGGTGGGGACCGTGGCAGCGGC 667
INTRON_3 102409 AATCACAACGGGCCTGTCGGTTATCTCTGTGAGCTCCATCCCAGAGAAAT 102458
i i i i v i
C L1P4b_5end#LI 666 AATCGCAGCGGGCCTGTTGGTTACCTCTGGGAGCTCTATCCCAGAGAAAT 617
INTRON_3 102459 GCAGGGCCA----------GAGTGCTTAGGTGTGGGTGGGATGACTACAC 102498
i---------- i i?v i i i i
C L1P4b_5end#LI 616 GCAGGGCCGCAACCGGCCGGAGTGCTCAGGCNGGGGTGGGGTGGCTGCGC 567
INTRON_3 102499 TGGGGGCCCAGGCCAGTTGGCTGTTCCTGGTGAGGTGCAGCAGAGGTGAG 102548
? i v iv v i i i
C L1P4b_5end#LI 566 TGGGGNCCCAGGCCGGTGGGCCTTGCCTGGCGAGGTGCAGCGGAGGTGGG 517
INTRON_3 102549 GCCTGCAATCCGTGCACTCCTCAGCACTATGGATGCGGCCCCTACCCTAA 102598
i i vii ii i i
C L1P4b_5end#LI 516 GCCTGCAGTCCATCTGCTCCTCAGCACCGTGGATGCGGCCCCTATCCTAG 467
INTRON_3 102599 GGGCACATGAGAGTGCCTGGCCTCTGTTGTTGGTGAGGCTAGGGAAGCTG 102648
i ii v iv i i v v
C L1P4b_5end#LI 466 GGGTACGCGAGAGAGCCTGGCCTCCCTTGTTGGCGGGGCTACGGCAGCTG 417
INTRON_3 102649 GTGCTGGGGTGTTCAGGAGTCCAAGGCCTGTGGGGCTCAACCTGGGTTTG 102698
i i i ii i v v ii
C L1P4b_5end#LI 416 GCGCCGGGGTGCTCAGGGATCCAAGGCCCGTGGGGCTCCACGTGGGCCTG 367
INTRON_3 102699 AGTGGGTAGTTCTGTTCAGACTCCAGGCAGCTCTCTGTGTTAGTTTGGAG 102748
i -ii i ii i ii i
C L1P4b_5end#LI 366 AGCGG-CGGCTCTGCCCAGACTCCAGGCAGCTCTCCGTGTCGGTCTGGAG 318
INTRON_3 102749 TCCCAGAGGGATTGGGGGTTGGGAGGATTGCCCATACCCAAGATTGCAAA 102798
v i i - ii ------ iv ii i i
C L1P4b_5end#LI 317 GCCCGGGGGG-TCAGGGG------GGATCTCCTGTGCCCAGGATTGCAAA 275
INTRON_3 102799 GATCCATGGCAGAAGTATGGGTCCCCAGGGGCTCTCACTCATTCACCCTT 102848
i i i i i
C L1P4b_5end#LI 274 GGTCCGTGGCAGAAGTGTGGGTCCCCAGGGGCTCTCGCTCACTCACCCTT 225
INTRON_3 102849 CCCTAGAGGTAGGGAGCCTCCCCTGGTTCTGCTGACAATCCTGGGTGGGC 102898
i iviv - i i - v ii
C L1P4b_5end#LI 224 TCCCCATGGTAGGGAGCCTCCC-TGGCTCCG-TGCCAATCCCAGGTGGGC 177
INTRON_3 102899 AGCTGTTCTGCCTCGCTCCTCTCTGCTCCTTGTGGGTTGCTGTTGCATCC 102948
i i iiii i ii v
C L1P4b_5end#LI 176 GGCTGTCCTGCCTCGCTCCTCTCTGCTCTCCATGGGTCGCCATTGCTTCC 127
INTRON_3 102949 TTTATGAATCTCAATGTGGCCTCCTGGATGATCCACTTGAAGAGCC--TG 102996
v i i--
C L1P4b_5end#LI 126 TTGATGAATCCCAATGTGGCCTCCTGGATGATCCACTTGAAGAGCTAGTG 77
INTRON_3 102997 TTTACTCACCACTCTGT----TCTCTGTGAGAGCAGTGTGCACTAGCTAC 103042
i ---- i iiii i
C L1P4b_5end#LI 76 TTTACTCGCCACTCTGTCTCCTCTCCGTGAGAGCAGCACACACTAGCTGC 27
INTRON_3 103043 TTCTAGTAAGCCATCTTGGAACTTC 103067
v vi
C L1P4b_5end#LI 26 TTCTAGTCAGCCATCTTGGTGCTTC 2
Matrix = 20p37g.matrix
Transitions / transversions = 2.62 (178 / 68)
Gap_init rate = 0.03 (32 / 1231), avg. gap size = 3.19 (102 / 32)
+ 2414 8.4 0.0 0.3 INTRON_3 103137 103432 (296749) C AluY SINE/Alu (15) 296 2 131
ANNOTATION EVIDENCE:
2345 8.48 0.00 0.34 INTRON_3 103137 103432 296749 C AluY SINE/Alu 2 296 15 134
INTRON_3 103137 TTTTTTTTTTTTTTTGAGATGGAGTCTCGCTATGTCACTCAGGCTGGAGT 103186
i v i i
C AluY#SINE/Alu 296 TTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGT 247
INTRON_3 103187 GAAGTGGCGCGATCTCTACTCACTACAAGCTCCGCCTCCCAGGTTCATGC 103236
v vi i i i
C AluY#SINE/Alu 246 GCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGC 197
INTRON_3 103237 CATTCTCCTGCCTCGGCCTCCGGAGTAGCTGGGACTATAGGCACCCGCCA 103286
i v i i
C AluY#SINE/Alu 196 CATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCA 147
INTRON_3 103287 CCACACCTGGCTAATTTTTTTGTATTTTTCGTAGAGACAGGGTTTCACTG 103336
i i - v i i
C AluY#SINE/Alu 146 CCACGCCCGGCTAATTTTTT-GTATTTTTAGTAGAGACGGGGTTTCACCG 98
INTRON_3 103337 TGTTAGCCAGGATGGTCTCGATCTCCTGATCTTGTGATCCGCTCGCCTCG 103386
i i i
C AluY#SINE/Alu 97 TGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCG 48
INTRON_3 103387 GCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCACCTGGC 103432
i i i
C AluY#SINE/Alu 47 GCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p37g.matrix
Transitions / transversions = 4.00 (20 / 5)
Gap_init rate = 0.00 (1 / 295), avg. gap size = 1.00 (1 / 1)
+ 557 29.5 1.8 0.5 INTRON_3 103901 104118 (296063) + L1MC4a LINE/L1 5696 5916 (1966) 132
ANNOTATION EVIDENCE:
557 29.49 1.83 0.45 INTRON_3 103901 104118 296063 + L1MC4a_3end LINE/L1 443 663 1966 234
INTRON_3 103901 TTCTTTATAGCATACTTTAAAATGACAAAATATTAGAAATAAT-TAAATG 103949
vi ii vv iv ii v i i i i-
L1MC4a_3end#L 443 TTCACTGCAGCATTGTTTGTAATAGCAAAAGACTGGAAACAACCTAAATG 492
INTRON_3 103950 TGCATTAATAGAGTAACGATTAGGTAAATTTTGGTATATCCATTCAATTG 103999
v i iiv vi i iii i v i v -
L1MC4a_3end#L 493 TCCATCAATAGGAGACTGGTTGAATAAACTATGGTACATCCATACAAT-G 541
INTRON_3 104000 AAATAC-ATACAACTATTAAAAAGAATGCAGTAGAACTATATGTGCTGAT 104048
i - i i i v vi v v v ?i
L1MC4a_3end#L 542 GAATACTATGCAGCTGTAAAAAAGAATGAGGAAGATCTCTATGNACTGAT 591
INTRON_3 104049 ATGGAAAGATGCCTGTGATATATTTTAAAATGAGAAATGCAATTTGAAGA 104098
iv vi iiv v v i i v vv v
L1MC4a_3end#L 592 ATGGAGTGATCTCCAGGATATATTGTTAAGTGAAAAAAGCAAGGTGCAGA 641
INTRON_3 104099 ATTATCTGTGTAGCAT--TACC 104118
?vi v i i i --
L1MC4a_3end#L 642 ANAGTGTATATAGTATGCTACC 663
Matrix = 20p37g.matrix
Transitions / transversions = 1.38 (36 / 26)
Gap_init rate = 0.02 (4 / 217), avg. gap size = 1.25 (5 / 4)
+ 34 78.3 0.0 0.0 INTRON_3 104672 104740 (295441) + AT_rich Low_complexity 1 69 (0) 133
ANNOTATION EVIDENCE:
34 78.26 0.00 0.00 INTRON_3 104672 104740 295441 + AT_rich Low_complexity 145 213 87 171
INTRON_3 104672 AAATATATATTATAATATGATGTTATATATAATATATAATATACACACAT 104721
v v v ????????????????????????????????
AT_rich#Low_c 145 AAATAAATAATATAATTTWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWW 194
INTRON_3 104722 ATATTTATATATTTAATAT 104740
???????????????????
AT_rich#Low_c 195 WWWWWWWWWWWWWWWWWWW 213
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 3)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0)
+ 274 31.6 9.0 1.8 INTRON_3 104761 104927 (295254) C MIRc SINE/MIR (39) 229 51 134
ANNOTATION EVIDENCE:
204 33.04 10.78 3.93 INTRON_3 104761 104927 295254 C MIRb SINE/MIR 51 228 40 164
INTRON_3 104761 AAGGACTTTACATAGTGATTTTACATGGACTATCTTAGTTGATTATTCCA 104810
i v v i vv i -i v i i v i iv iv
C MIRb#SINE/MIR 228 AGGCACTGTGCTAAGCG-CTTTACATGCATTATCTCATTTAATCCTCACA 180
INTRON_3 104811 GTAGTTCTGCCAGTTGGGAAAGGCAAGTATTCCTATTTTAAAAA------ 104854
ii iii v v i v ---iv v i i v i ------
C MIRb#SINE/MIR 179 ACAACCCTGCGAGGTAGGTA---TTATTATCCCCATTTTACAGATGAGGA 133
INTRON_3 104855 ----GAGGCTTGGCATGGTTG-GTGTCGTATTCAAG-----ACAGTTGAG 104894
---- ii viv i- v v iii ----- i -
C MIRb#SINE/MIR 132 AACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCT-AG 84
INTRON_3 104895 ATAAGTGGTAG--CAAGGAGTGAAAACTTAGATCT 104927
- i -- v v vi - ii i
C MIRb#SINE/MIR 83 -TAAGTGGCAGAGCCAGGATTCGAA-CCCAGGTCT 51
Matrix = 25p37g.matrix
Transitions / transversions = 1.52 (32 / 21)
Gap_init rate = 0.05 (9 / 166), avg. gap size = 2.78 (25 / 9)
274 30.43 7.61 0.00 INTRON_3 104767 104858 295323 C MIRc SINE/MIR 131 229 39 165
INTRON_3 104767 TTTACATAGTGATTTTACATGGACTATCTTAGTTGATTATTCCAGTAGTT 104816
v i v i iv i i v iv iv ii iii
C MIRc#SINE/MIR 229 TTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTCACAACAACC 180
INTRON_3 104817 CTGCCAGTTGGGAAAGGCAAGTATT------CCTATTTTAAAAA-GAGG 104858
iv v i v i i ------ i v i -
C MIRc#SINE/MIR 179 CTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTACAGATGAGG 131
Matrix = 25p37g.matrix
Transitions / transversions = 1.80 (18 / 10)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 3.50 (7 / 2)
+ 235 34.5 5.9 0.0 INTRON_3 105082 105200 (294981) C MER102c DNA/hAT-Charlie (3) 328 203 135
ANNOTATION EVIDENCE:
235 34.45 5.88 0.00 INTRON_3 105082 105200 294981 C MER102c DNA/hAT-Charlie 203 328 3 267
INTRON_3 105082 GGGTGGCAAACTCAAAAGTCTTTAAGGATTAGACAGG-ATTTTAAATGAG 105130
vi v i vi i iii i - viv
C MER102c#DNA/h 328 GGGTCACAAACTCAAATGCCTACAGGGGCCAGGCAGGTAACGTAAATGAG 279
INTRON_3 105131 TGGAGCA--CAGAGTATAAAGTTATAA--AGCAGTGGAAACTA--GTAAA 105174
i i-- v i i iiiv i-- ii ii i-- i
C MER102c#DNA/h 278 TGAAGCGGGCCGGGTGTAAGACAATAGGGAGTGGTGGGGACTGTGGCAAA 229
INTRON_3 105175 CTACAGCTGATACGCGCCCTCTGAAG 105200
iv vvvii i v v i
C MER102c#DNA/h 228 CTGGAGAGCGCATGCCCCGTCTAAAG 203
Matrix = 20p37g.matrix
Transitions / transversions = 2.15 (28 / 13)
Gap_init rate = 0.03 (4 / 118), avg. gap size = 1.75 (7 / 4)
+ 610 16.0 3.9 8.0 INTRON_3 105415 105570 (294611) C L1MC4a LINE/L1 (6) 7876 7727 136
ANNOTATION EVIDENCE:
610 16.02 3.85 8.00 INTRON_3 105415 105570 294611 C L1MC4a_3end LINE/L1 2474 2623 6 235
INTRON_3 105415 AACTTTTTATTTGGAAGCA-TTTTAGTGATAAGCAATATACAGGAA-GTT 105462
v ii - --------- iv i -
C L1MC4a_3end#L 2623 AACTTTTTATTTTGAAATAATTTTAG---------ACTTACAGAAAAGTT 2583
INTRON_3 105463 GCAAAGATAATAGAGAGCGGTCTCCTATATCCTTCACCCGGCTTCCCGAG 105512
i i v v v i v i i ---
C L1MC4a_3end#L 2582 GCAAAAATAGTACAGAGAGTTCCCGTATACCCTTCACCCAGCTTCCC--- 2536
INTRON_3 105513 TTA--GTTA-CATCTTGCATAACTGTAGTATAAT-ATCAAAACCAGGAAG 105558
i -- - i ii i - i
C L1MC4a_3end#L 2535 CTAATGTTAACATCTTACATAACCATAGTACAATTATCAAAACCAGGAAA 2486
INTRON_3 105559 TCGACATTGGTA 105570
ii
C L1MC4a_3end#L 2485 TTAACATTGGTA 2474
Matrix = 20p37g.matrix
Transitions / transversions = 2.83 (17 / 6)
Gap_init rate = 0.05 (7 / 155), avg. gap size = 2.57 (18 / 7)
+ 2776 19.0 3.8 1.4 INTRON_3 105575 106432 (293749) C L1MD2 LINE/L1 (213) 6146 5263 137
ANNOTATION EVIDENCE:
2776 20.53 3.50 0.98 INTRON_3 105575 106174 294007 C L1MD2_3end LINE/L1 279 893 213 236
INTRON_3 105575 GTGTGTGTATA---AATTCTATGTCATTTTTTCATATATATTAATATATT 105621
i --- i iv v i i i ---- v
C L1MD2_3end#LI 893 GTGTGTGTGTATTTAGTTCTATGCAATTTTATCACATGTGT----AGATT 848
INTRON_3 105622 TGTATAGCCACCGCCACAGTCAAGATACAGAAATATTCCATTGCTGCAAA 105671
i i ? i vvi ii ii i
C L1MD2_3end#LI 847 CGTGTANCCACCACCACAGTCAAGATACAGAACAGTTCCATCACCACAAG 798
INTRON_3 105672 GATCTCTTCTTGTTACCTTTTGATAGTCACACCTACTTCTTTGCTTCC-- 105719
i - v i i i v i i i ii v ii --
C L1MD2_3end#LI 797 GATCCCT-CGTGCTGCCCTTTTATAGCCACACCCACCTCCCTTCCCCCNC 749
INTRON_3 105720 ----CCCCAATTCCTAAACCCTGGCAACAACTAATCTGTTTTCTGTCTCT 105765
---- v i v v i ii
C L1MD2_3end#LI 748 NCCACCCCCATCCCTAACCCCTGGCAACCACTAATCTGTTCTCCATCTCT 699
INTRON_3 105766 ATAATTTTGTCACTTCAAGAATGTTATATAATTGAAATCATATAGTAATT 105815
i v i i vv
C L1MD2_3end#LI 698 ATAATTTTGTCATTTCAAGAATGTTATATAAATGGAATCATACAGTATGT 649
INTRON_3 105816 GACTTTTTGAGATTGTCTTTTGTTTGTCAGCATAATGCTCTTGATAGTCA 105865
i i i v v ivv v i v v
C L1MD2_3end#LI 648 AACCTTTTGGGATTGGCTTTTTTCACTCAGCATAATTCCCTTGAGATTCA 599
INTRON_3 105866 TCCAAGTCGTTATGGTTGTTAATTTTTCATTTCTTTTTATTGCCAAGTAG 105915
i ii vv i i vv i i ii
C L1MD2_3end#LI 598 TCCAAGTTGTTGCGTGTATCAATAGTTCGTTCCTTTTTATTGCTGAGTAG 549
INTRON_3 105916 TATACCATGGTGTGGCTG-ACCCCTGTTTGTTTAACCATTCACCTGTTGT 105964
v i v - v v i v
C L1MD2_3end#LI 548 TATTCCATGGTATGGATGTACCACAGTTTGTTTAACCATTCACCCGTTGA 499
INTRON_3 105965 CAGACATTTTGGTACTTTCCAGTTTTTGGCTATTGCAAAT--------TA 106006
vi i v vv i i --------
C L1MD2_3end#LI 498 AGGACATCTGGGTTGTTTCCAGTTTTTGGCTATTACGAATAAAGCTGCTA 449
INTRON_3 106007 TGAGCAATTGTGTGCATGTTGTTGTGAGGACATA-GTCTTCATTTCTCAA 106055
i v i i v v v i - i vi
C L1MD2_3end#LI 448 TGAACATTCGTGTACAGGTTTTTGTGTGAACATAAGTTTTCATTTCTCTG 399
INTRON_3 106056 GGATAAATCCTTAGGAGTATGATTGCTGGGTGGTATGGTGAGTGTATATT 106105
v ii i iii v i ? i i
C L1MD2_3end#LI 398 GGATAAATGCCCAAGAGTGCAATTGCTGGGTCGTATGGTAAKTGCATGTT 349
INTRON_3 106106 TAGTTCCTTAAGAAACTGCCAAACTATTTTCCAAAGTGACTATACCATTT 106155
iiv i i i i
C L1MD2_3end#LI 348 TAGTTTTATAAGAAACTGCCAAACTGTTTTCCAGAGTGGCTGTACCATTT 299
INTRON_3 106156 TCACACTCTTACAA--AATGT 106174
- i ii v --
C L1MD2_3end#LI 298 T-ACATTCCCACCAGCAATGT 279
Matrix = 20p37g.matrix
Transitions / transversions = 1.79 (77 / 43)
Gap_init rate = 0.02 (9 / 599), avg. gap size = 3.00 (27 / 9)
2033 17.82 5.19 0.24 INTRON_3 106005 106409 293772 C L1MD1_3end LINE/L1 26 450 539 237
INTRON_3 106005 TATGAGCAATTGTGTGCATGTTGTTGTGAGGACATA-GTCTTCATTTCTC 106053
i i v i i v v v i - i
C L1MD1_3end#LI 450 TATAAACATTCGTGTACAGGTTTTTGTGTGAACATAAGTTTTCATTTCTC 401
INTRON_3 106054 AAGGATAAATCCTTAGGAGTATGATTGCTGGGTGGTATGGTGAGTGTATA 106103
vi v ii iii v iiv i i
C L1MD1_3end#LI 400 TGGGATAAATGCCCAGGAGTGCAATTGCTGGGTCGTATGGTAGTTGCATG 351
INTRON_3 106104 TTTAGTTCCTTAAGAAACTGCCAAACTATTTTCCAAAGTGACTATACCAT 106153
ii i i i i
C L1MD1_3end#LI 350 TTTAGTTTTTTAAGAAACTGCCAAACTGTTTTCCAGAGTGGCTGTACCAT 301
INTRON_3 106154 TTTCACACTCTTACAA--AATGT--------------TTCTTTGCATTCT 106187
- i ii v -- -------------- i i i
C L1MD1_3end#LI 300 TTT-ACATTCCCACCAGCAATGTATGAGTGATCCAGTTTCTCTACATCCT 252
INTRON_3 106188 TGCTAGCATTTAATATTGCTACTACTTTTTATTTCAACTGTTGGAATAGA 106237
i i ii i ii i i i ii vvi i
C L1MD1_3end#LI 251 CGCCAGCATTTGGTGTTGTCACTATTTTTTATTTTAGCCATTCTGATAGG 202
INTRON_3 106238 TATGTAGTGATATC--ATCATGGTCTTAATTTGCATTTCCCTAATGGCTA 106285
i -- ii i
C L1MD1_3end#LI 201 TGTGTAGTGATATCTCATTGTGGTTTTAATTTGCATTTCCCTAATGGCTA 152
INTRON_3 106286 GTGATATTGAACATTTTTTCATGTGCTTATTTGTCGTCTGTATCTCCTTT 106335
i i i i i v i
C L1MD1_3end#LI 151 ATGATGTTGAACATCTTTTCATGTGCTTATTTGCCATCTGTATATCCTCT 102
INTRON_3 106336 TTGATGAAATATCTGTTTATGTCTTTTGCCCATTT-CTAAGTGGGTTGTT 106384
i i i v i - v i
C L1MD1_3end#LI 101 TCGGTGAAATGTCTCTTCATGTCTTTTGCCCATTTTCTAATTGGATTGTT 52
INTRON_3 106385 TGTTTTTTTACTGT-GAGTTTGGAGA 106409
- v
C L1MD1_3end#LI 51 TGTTTTTTTACTGTTGAGTTTTGAGA 26
Matrix = 20p37g.matrix
Transitions / transversions = 3.80 (57 / 15)
Gap_init rate = 0.02 (7 / 404), avg. gap size = 3.14 (22 / 7)
519 18.01 1.37 4.96 INTRON_3 106287 106432 293749 C L1MC_orf2 LINE/L1 3154 3294 0 238
INTRON_3 106287 TGATATTGAACATTTTTTCATGTGCTTATTTGTCGTCTGTATCTCCTTTT 106336
i v i i i i i v i i
C L1MC_orf2#LIN 3294 TGATGTGGAGCATCTTTTCATATGCTTATTTGCCATCTGTATATCTTCTT 3245
INTRON_3 106337 TGATGAAATATCTGTTTATGTCTTTTGCCCATTTCTAAGT-GGGTTGTTT 106385
i ii i v v v i ? i -
C L1MC_orf2#LIN 3244 TGGTGAGGTGTCTGTTAAGGTCTTTGGCCCATTTTTNAATCGGGTTGTTT 3195
INTRON_3 106386 GTTTTTTTACTGT-GAGTTTGGAGAAATTCGATTTGGCTTTATATTTT 106432
i i - vi i- -- ----
C L1MC_orf2#LIN 3194 GTTTTCTTATTGTTGAGTTTTAAGAG-TTC--TTTG----TATATTTT 3154
Matrix = 20p37g.matrix
Transitions / transversions = 3.00 (18 / 6)
Gap_init rate = 0.03 (5 / 145), avg. gap size = 1.80 (9 / 5)
+ 459 26.9 8.8 4.0 INTRON_3 106460 106676 (293505) C L1ME5 LINE/L1 (2) 6192 5966 138
ANNOTATION EVIDENCE:
459 26.87 8.76 3.96 INTRON_3 106460 106676 293505 C L1ME5_3end LINE/L1 713 939 2 239
INTRON_3 106460 TTTTTCTTATTTTTTAACCTAATAGGCA-AGGTATTATTGAATTAATCAT 106508
i v vi v viv - ----i i
C L1ME5_3end#LI 939 TTTTTTTTTTTTTTGGACCTCAGGTGCAGAGG----GTTGAGTTAATCAT 894
INTRON_3 106509 TTCCCTCATGTCGTAGAACATTATCATCATTGGTTGATGCAAG--TCTTC 106556
vii vv i i v ivi --i i
C L1ME5_3end#LI 893 ACTCCTCAGTTCATGGCACATTATCATCATTGGTCCGTGCAAGGCCCCTC 844
INTRON_3 106557 TCTCATTTTATTTCTTTATTCCTTT------------TAATCCCTGTACT 106594
ii v ? ------------ v ?iv i
C L1ME5_3end#LI 843 TCTTGTTTTATTTATTTATTCNTTTATTCTTTCCCTTTATTCCCTNCCCC 794
INTRON_3 106595 TTACTCTTATTCCTTTCTCCTTCTTATAAATCACAATTCTAATATATTAA 106644
i ? ii--- i ii ii iiiv v i i --
C L1ME5_3end#LI 793 CTNCTCCC---CCTTCCTCCCCCCCATAGGCAACCATTCTAATGTGTT-- 749
INTRON_3 106645 TATTATGTACA----TATATGTATGTATTCTTGCAA 106676
v i iv---- i v i i
C L1ME5_3end#LI 748 TAATGTGTATCCTTTTGTTTGTATGTGTTCTTGTAA 713
Matrix = 20p37g.matrix
Transitions / transversions = 1.94 (35 / 18)
Gap_init rate = 0.03 (7 / 216), avg. gap size = 4.00 (28 / 7)
+ 5130 21.5 2.6 2.1 INTRON_3 106770 107995 (292186) C L1MD3 LINE/L1 (88) 7907 6744 139
ANNOTATION EVIDENCE:
1840 25.88 6.13 2.36 INTRON_3 106770 107422 292759 C L1MC3_3end LINE/L1 1846 2522 10 240
INTRON_3 106770 TAAACTTTTAATTTCAAACTAATTTTATACTTAGAG-----TTGCTAAGA 106814
v i i v i v i v ----- v
C L1MC3_3end#LI 2522 TAAACTTTTTATTTTAGAATAGTTTTAGATTTACAGAAAAATTGCGAAGA 2473
INTRON_3 106815 TAGTACTC----TTTACATATATGTGTCACC-AGCTTCCCCAATATA--- 106856
vv---- iv ivivv - i v - ---
C L1MC3_3end#LI 2472 TAGTACAGAGAGTTCCCATATACCCCACACCCAGTTTCCCCTAT-TATTA 2424
INTRON_3 106857 --ATCTTGTATAACTATGGTATGATTATCAGAACTAAGAAAGAGATATTG 106904
-- ii v v iiv i v i vi vvi
C L1MC3_3end#LI 2423 ACATCTTACATTAGTATGGTACATTTGTCACAATTAATGAACCAATATTG 2374
INTRON_3 106905 -TATAATACAATTAACTGCAG-----ATTTTATTCAGATTTCCCCAGCTT 106948
- i v iv iv ----- i ii i
C L1MC3_3end#LI 2373 ATACATTATTATTAACTAAAGTCCATACTTTATTCAGATTTCCTTAGTTT 2324
INTRON_3 106949 TTCTACC-AATGTCCTTTTTGTGTCCCAGGATCTAATACAGGATACCACA 106997
-- - v i iv v
C L1MC3_3end#LI 2323 TT--ACCTAATGTCCTTTTTCTGTTCCAGGATCCCATCCAGGATACCACA 2276
INTRON_3 106998 TTAAATTTAGTTGTCATATTTCCTTAGTCTCTTCTAATATGTGGTAATTC 107047
v i i i v i vivv ii i i
C L1MC3_3end#LI 2275 TTACATTTAGTCGTCATGTCTCCTTAGGCTCCTCTTGGCTGTGACAGTTT 2226
INTRON_3 107048 CTTGCTCTTTTCTTCTTTC--ATGACCTTGACAGTTTCAAAGAATACTAG 107095
iivv i v i-- ii i i i
C L1MC3_3end#LI 2225 CTCAGACTTTCCTTGTTTTTGATGACCTTGACAGTTTTGAGGAGTACTGG 2176
INTRON_3 107096 CCAAG---------GAACGTCCCTCAATTTGGGTTTGTCTAGTGTTTTCC 107136
i i --------- i v i ii i
C L1MC3_3end#LI 2175 TCAGGTATTTTGTAGAATGTCCCTCAATTGGGATTTGTCTGATGTTTTTC 2126
INTRON_3 107137 T-ATGTTTAGACTGAAGTTATGGATTTTTGGGAAGTTTACCACAGATATG 107185
- v ii i ? i vvv vi i
C L1MC3_3end#LI 2125 TCATGATTAGACTGGGGTTATGGGTTTTKGGGAGGAAGACCACAGAGGTA 2076
INTRON_3 107186 ATGTGCCTTTCTCTTTACATCATTTCAGAGGGTACATAATACCAGTATTT 107235
v v v i v - v i ii vv
C L1MC3_3end#LI 2075 AAGTGCCATTCTCATCACATCATATCA-AGGGTACATACTATCAACATGA 2027
INTRON_3 107236 CTTCTTCTTAGTGATACTAATCTTGCTCTTTTAGTTACTGCGGTGTTTGC 107285
v ivi iv ii i i v vii i i ivv ii i
C L1MC3_3end#LI 2026 CTTATCACTGTTGATGTTGACCTTGATCACCTGGCTGAGGTAGTGTTTGT 1977
INTRON_3 107286 CAGGTTTTTTCTCTGTTAACTTACAATTTT----CCCCTTTCTTTGACTA 107331
i i v v v vv ---- ? iv - i
C L1MC3_3end#LI 1976 CAGGTTTCTCCACTGTAAAGTTACTCTTTTTTCCCCMCTTTCCAT-ACTG 1928
INTRON_3 107332 T--TCATTAGAAGCAAACAACTAAGCAACTGAGTAAGTATGCTCACTCTA 107379
-- v i v iiv v ------ i ----- i v v
C L1MC3_3end#LI 1927 TACTCTTTGGAAGGAAGTCACTATGC------GCA-----GCCCACACTT 1889
INTRON_3 107380 AAGAGGATGGGAATTAAGCTTCACCCCATGAAACGAGGAGTAT 107422
ii vv i v i i v vi iv v
C L1MC3_3end#LI 1888 AAGGAGTGGGGAGTTATGCTCCACCTCCTTGAGGGCGGAGTAT 1846
Matrix = 20p37g.matrix
Transitions / transversions = 1.26 (91 / 72)
Gap_init rate = 0.03 (18 / 652), avg. gap size = 3.11 (56 / 18)
5130 21.19 2.34 2.08 INTRON_3 106840 107991 292190 C L1MD3_3end LINE/L1 1500 2654 88 241
INTRON_3 106840 CCAGCTTCCCC-AATAT---AATCTTGTATAACTATGGTATGATTATCAG 106885
- i ---v ii i iiv i
C L1MD3_3end#LI 2654 CCAGCTTCCCCTAATGTTAACATCTTACATAACCATGGTACATTTATCAA 2605
INTRON_3 106886 AACTAAGAAAGAGATATTG-TATAATACAATTAACTG-----CAGATTTT 106929
vvi i - i v i----- i
C L1MD3_3end#LI 2604 AACTAAGAAATTAACATTGGTACAATACTATTAACTAAACTACAGACTTT 2555
INTRON_3 106930 ATTCAGATTTCCCCAGCTTTTCTACCAATGTCCTTTTTGTGTCCCAGGAT 106979
i v i i i v i
C L1MD3_3end#LI 2554 ATTCGGATTTCACCAGTTTTTCCACTAATGTCCTTTTTCTGTTCCAGGAT 2505
INTRON_3 106980 CTAATACAGGATACCACATTAAATTTAGTTGTCATATTTCCTTAGTCTCT 107029
i v i iv i i i
C L1MD3_3end#LI 2504 CCAATCCAGGATACCACGTTGCATTTAGTTGTCATGTCTCCTTAGTCTCC 2455
INTRON_3 107030 TCTAATATGTGGTAATTCCTTGCTCTTTTCTT--CTTTCATGACCTTGAC 107077
ii v ii i i iiv i --i
C L1MD3_3end#LI 2454 TCCGATCTGTGACAGTTTCTCAGTCTTTCCTTGTTTTTCATGACCTTGAC 2405
INTRON_3 107078 AGTTTCAAAGAATACTAGCCAAG---------GAACGTCCCTCAATTTGG 107118
? ii i i i i --------- i
C L1MD3_3end#LI 2404 ANTTTTGAAGAGTACTGGTCAGGTATTTTGTAGAATGTCCCTCAATTTGG 2355
INTRON_3 107119 GTTTGTCTAGTGTTTTCCTATGTTTAGACTGAAGTTATGGATTTTTGGGA 107168
ii ii v ii i
C L1MD3_3end#LI 2354 GTTTGTCTGATGTTTTCTCATGATTAGACTGGGGTTATGGGTTTTTGGGA 2305
INTRON_3 107169 AGTTTACCACAGATATGATGTGCCTTTCTCTTTACATCATTTCAGAGGGT 107218
vv vi v i v ii v i
C L1MD3_3end#LI 2304 AGAATACCACAGAGGTGAAGTGCCCTTCTCATCGCATCATATCAGGGGGT 2255
INTRON_3 107219 ACATAATACCAGTATTTCTTCTTCTTAGTGATACTAATCTTGCTCTTTTA 107268
i i ii vv v ivi i ii i v vi i
C L1MD3_3end#LI 2254 ACATGATATCAACATGACTTATCACTGGTGATGTTAACCTTGATCACTTG 2205
INTRON_3 107269 GTTACTGCGGTGTTTGCCAGGTTTTTTCTCTGTTAACTTACAATTTTCCC 107318
vv i i i i v v v v i
C L1MD3_3end#LI 2204 GTTAAGGTGGTGTCTGCCAGGTTTCTCCACTGTAAAGTTACTATTTTTCC 2155
INTRON_3 107319 CTTTCTTTGA-CTATTCATTAGAAGCAAACAACTAAG--CAACTGAGTAA 107365
iv iv- v i i iiv -- ---------
C L1MD3_3end#LI 2154 CTTTCCATACTCTATTCTTTGGAAGTAAGTCACTAAGTCCA--------- 2114
INTRON_3 107366 GTATGCTCACTCTAAAGAGGATGGGAATTAAGCTTCACCCCATGAAACGA 107415
---- i v v i v i i v i iv
C L1MD3_3end#LI 2113 ----GCCCACACTCAAGGGGAGGGGAATTAAGCTCCACCTCCTGGAGGGA 2068
INTRON_3 107416 GGAGTATGGAGGGATTTCTGGACATATGTTAAAACCACCATAGTAATTAA 107465
vi vvi v ii i
C L1MD3_3end#LI 2067 GGAGTATCAACTAATTTGTGGACATATGTTAAAACCACCGCAATAATTAA 2018
INTRON_3 107466 TAAGTATCTTGGGCAGAGATTGTTTGAAGCTATGAAAATATCCATGACCT 107515
i i v - vv i v ?vvvi
C L1MD3_3end#LI 2017 TAAATATTTTGGGGA-AGATACTTTGAGGCTATGCAAATATCCNGCTTCT 1969
INTRON_3 107516 CTTTAAACTTTTACCCACTAATTTAAGCATGCATTTGTGGACCTTGCCTG 107565
i v i v v iv i
C L1MD3_3end#LI 1968 CCTTAAAGTTTCACCCACTAATTTTAGCATCCATCGGTGGATCTTGCCTG 1919
INTRON_3 107566 TAGCAATTATTATTGTGGTGTTCTAATGCTGATTTTC-ATTTATTTCATT 107614
ii i? i vi - i vii
C L1MD3_3end#LI 1918 CGGCAATTATTACNGTAGTGTTCTAATGGCGATTTTCTACTTCCCTCATT 1869
INTRON_3 107615 CATTTTACCTTTATAATTTGAAATTCTTCTGTAAGAAAGAGTTAGTTGTC 107664
v i v ? v i v - -
C L1MD3_3end#LI 1868 CCTTCTACATNTATTATTTGGAATTCTTCTGTAAGAAAGATTT-GTT-TC 1821
INTRON_3 107665 CTTTCTTGCTCATTTATTCATTTATCCAATTTTAAATTTTGTATCACTAA 107714
i iiv ii i i vi -- --- i v v
C L1MD3_3end#LI 1820 CCTTCCCCCCTATTTATTTATTCAATCA--TTTA---TTTATATCAGTAT 1776
INTRON_3 107715 GGACTTAGGGATATTTATTTTATTCTTTAGGTAGTGATTCAATACTAATA 107764
i v v i vi i i ?i
C L1MD3_3end#LI 1775 GGACTCATGGATATTTATTTTATACTTTGGGTTATAATCCAATACTANCA 1726
INTRON_3 107765 TTATTTATTTTGTTTCTCAAATCGTTCCAGCTTTGGTCATTGAGAATTCC 107814
v i i i ii i
C L1MD3_3end#LI 1725 TTATTTATTTTGTTGCTCAAATTGTTCCAGCTTTGGCCATTGGGAGCTCT 1676
INTRON_3 107815 TTCAGGTTGACACCTGTGTTTTTTAGATATGTCTCATTCTTATTGTTTT- 107863
i v ii v i i i v? i v -
C L1MD3_3end#LI 1675 TTCAGGTTGGCTCCTGTGTCCTTTTGACATGCCCCCNTCCTTTTGTTTTT 1626
INTRON_3 107864 GAGCACCACCTGTCTTTCTAGCAACACAAGATGCTCCAGGCTCATCT-AT 107912
iv vv i i vi i -i
C L1MD3_3end#LI 1625 GAGCACTTCCTTACCTTCTGGCACTACGAGATGCTCCAGGCTCATCTTGT 1576
INTRON_3 107913 ATTTTCCCCATCTTGATTTCCTTGGAATTAACTATTTCTCTAAAGATCCC 107962
iii iiii--- i i i i i i i v
C L1MD3_3end#LI 1575 ATTTTCCCTGCCCCAG---CCCTAGAATCAGCCATTTCTCCAAGGAGCCC 1529
INTRON_3 107963 TGGTTTCTTTTATTGTAGAATCATATTTA 107991
i v vi
C L1MD3_3end#LI 1528 TGGTTCCTTTTATTGGAGAATGGTATTTA 1500
Matrix = 20p37g.matrix
Transitions / transversions = 1.95 (154 / 79)
Gap_init rate = 0.02 (18 / 1151), avg. gap size = 2.83 (51 / 18)
1755 22.57 2.19 7.32 INTRON_3 107630 107995 292186 C L1MC3_3end LINE/L1 1491 1834 698 242
INTRON_3 107630 ATTTGAAATTCTTCTGTAAGAAAGAGTTAGTTGTCCTTTCTTGCTCATTT 107679
i i v ii v ---- ii v
C L1MC3_3end#LI 1834 ATTTGGAATTCTTCTGCACGGGAGATTT----GTCTCTTCTTCCTCATTT 1789
INTRON_3 107680 ATTCATTTATCCAAT--TTTAAATTTTGTATCACTAAGGACTTAGGGATA 107727
i i -- --- i v v i v
C L1MC3_3end#LI 1788 ATTTATTTATTCAATCATTTA---TTTATATCAGTATGGACTCATGGATA 1742
INTRON_3 107728 TTTATTTTATTCTTTAGGTAGTGATTCAATACTAATATTATTTATTTTGT 107777
v i vi i i v -
C L1MC3_3end#LI 1741 TTTATTTTATACTTTGGGTTATAATCCAATACTACT-TTATTTATTTTGT 1693
INTRON_3 107778 TTCTCAAATCGTTCCAGCTTTGGTCATTGAGAATTCCTTCAGGTTGACAC 107827
v i i i ii i - i v
C L1MC3_3end#LI 1692 TGCTCAAATTGTTCCAGCTTTGGCCATTGGGAGCTCTTTCAG-TTGGCTC 1644
INTRON_3 107828 CTGTGTTTTTTAGATATGTCTC-ATTCTTATTG----TTTTGAGCACCAC 107872
iii v i ii i - iv i v ---- iv
C L1MC3_3end#LI 1643 CTGTGTCCCTTTGACATACCCCCATCATTGTGGGTTTTTTTGAGCACTTC 1594
INTRON_3 107873 CTGTCTTTCTAGCAACACAAGATGCTCCAGGCTCATCT-ATATTTTCCCC 107921
vv i vi -i v i i
C L1MC3_3end#LI 1593 CTTACTTTCTGGCACTACAAGATGCTCCAGGCTCATCTTGTATATTTCCT 1544
INTRON_3 107922 ATCTTGATTTCCTTGGAATTAACTATTTCTCTAAAGATCCCTGGTTTCTT 107971
ii iiii --- i i i i i i i v i
C L1MC3_3end#LI 1543 GCCCCAGT---CCTAGAATCAGCCATTTCTCCAAGGAGCCCTGGTTCCTT 1497
INTRON_3 107972 TTATTGTAGAATCATATTTATTTA 107995
------------------
C L1MC3_3end#LI 1496 TTATTG------------------ 1491
Matrix = 20p37g.matrix
Transitions / transversions = 2.50 (50 / 20)
Gap_init rate = 0.03 (10 / 365), avg. gap size = 3.80 (38 / 10)
864 23.01 0.41 11.31 INTRON_3 107932 107995 292186 C L1MC4a_3end LINE/L1 1525 1570 1059 243
INTRON_3 107932 CCTTGGAATTAACTATTTCTCTAAAGATCCCTGGTTTCTTTTATTGTAGA 107981
i i i i i i v i ----
C L1MC4a_3end#L 1570 CCCTGGAATCAACCACTTCTCCAAGGAGCCCTGGTTCCTTTTATTG---- 1525
INTRON_3 107982 ATCATATTTATTTA 107995
--------------
C L1MC4a_3end#L 1525 -------------- 1526
Matrix = 20p37g.matrix
Transitions / transversions = 7.00 (7 / 1)
Gap_init rate = 0.02 (1 / 63), avg. gap size = 18.00 (18 / 1)
+ 1630 20.1 1.6 2.6 INTRON_3 107996 108308 (291873) C AluJr SINE/Alu (2) 310 1 140
ANNOTATION EVIDENCE:
1318 23.28 1.60 2.58 INTRON_3 107996 108308 291873 C AluJb SINE/Alu 1 310 2 135
INTRON_3 107996 TTTTTATTTTATTTAGTTTATTTATTCTGAGTCAGGGTCTTGCCCTGTCA 108045
v v vv v v i v i i i
C AluJb#SINE/Al 310 TTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGGGTCTCGCTCTGTCG 261
INTRON_3 108046 CCCAGGCTGGAGTGCAGTGGTGCATTCATAGTTCACTTCAGCCTCCAACT 108095
i iv ii i v v v
C AluJb#SINE/Al 260 CCCAGGCTGGAGTGCAGTGGCGCGATCACGGCTCACTGCAGCCTCGACCT 211
INTRON_3 108096 CCTAGGCCCAAGCAGTTCTTCCACCTCAGCCTCCCAAGTAGCTGGGACTC 108145
ii i ii i i ii i v
C AluJb#SINE/Al 210 CCCGGGCTCAAGCGATCCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTA 161
INTRON_3 108146 TAGGCACATGGTTCTATGCCTAGTTTAAAAAAAAATTTTT----TTTTTG 108191
i i ii viv i i ii i -------- ----
C AluJb#SINE/Al 160 CAGGCGCGCGCCACCACGCCCGGCT--------AATTTTTGTATTTTTTG 119
INTRON_3 108192 TAGGAACAGGGTCTTGCTTTGTTGCCCTGTCTGGTCTTGAGCTCCTGGCT 108241
ii i i ii iv v v i i vi
C AluJb#SINE/Al 118 TAGAGACGGGGTTTCACCATGTTGCCCAGGCTGGTCTCGAACTCCTGGGC 69
INTRON_3 108242 TCAAGTAATCTTCT-GCATTGGCCTTCCAATGTGCTGGGATTACAGGCAT 108290
i i i- v i i v i
C AluJb#SINE/Al 68 TCAAGTGATCCTCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGT 19
INTRON_3 108291 AGGCCACCAGGCTCAGCC 108308
ii iv i i
C AluJb#SINE/Al 18 GAGCCACCGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 2.38 (50 / 21)
Gap_init rate = 0.01 (3 / 312), avg. gap size = 4.33 (13 / 3)
+ 1755 22.6 2.2 7.3 INTRON_3 108309 108416 (291765) C L1MD3 LINE/L1 (1042) 6743 6636 139
ANNOTATION EVIDENCE:
1755 22.57 2.19 7.32 INTRON_3 108309 108416 291765 C L1MC3_3end LINE/L1 1383 1490 1042 244
INTRON_3 108309 TAGAGAATGGTGTTTAGAGACCACTATCTGGATGTTAAATGTGCTTATTG 108358
-- i - i vv ii i ii i
C L1MC3_3end#LI 1490 --GAGAATGGTATT-AGAAACCAAGATCTGGGCGCTAGGTGTGCTCATTG 1444
INTRON_3 108359 CTGCTGGAGTGTCACTGCATCTTGGTTCTCTCATCGGACAAAGCTAGAAA 108408
i i ii ? v v ii v v i v i
C L1MC3_3end#LI 1443 CTACTGGGGTGTCGTTKCTTCTAGGCCCTCTCAGCTGACAGAGCAAGGAA 1394
INTRON_3 108409 GTAT---TGTA 108416
i --- i
C L1MC3_3end#LI 1393 ATATATGTGTG 1383
Matrix = 20p37g.matrix
Transitions / transversions = 2.57 (18 / 7)
Gap_init rate = 0.03 (3 / 107), avg. gap size = 2.00 (6 / 3)
864 23.01 0.41 11.31 INTRON_3 108309 108416 291765 C L1MC4a_3end LINE/L1 1418 1524 1105 245
INTRON_3 108309 TAGAGAATGGTGTTTAGAGACCACTATCTGGATGTTAAATGTGCTTATTG 108358
-- i i vv ii i ii i
C L1MC4a_3end#L 1524 --GAGAATGGTATTTAGAAACCAAGATCTGGGCGCTAGGTGTGCTCATTG 1477
INTRON_3 108359 CTGCTGGAGTGTCACTGCATCTTGGTTCTCTCATCGGACAAAGCTAGAAA 108408
i i i v v ii v i i
C L1MC4a_3end#L 1476 CTACTGGGGTGTCATTGCTTCTAGGCCCTCTCAGCGGACAGAGCTAGGAA 1427
INTRON_3 108409 GTAT-TGTA 108416
i -
C L1MC4a_3end#L 1426 ATATATGTA 1418
Matrix = 20p37g.matrix
Transitions / transversions = 3.20 (16 / 5)
Gap_init rate = 0.02 (2 / 107), avg. gap size = 1.50 (3 / 2)
+ 6393 13.8 6.2 1.1 INTRON_3 108417 109588 (290593) + Tigger3b DNA/TcMar-Tigger 1 1231 (0) 141
ANNOTATION EVIDENCE:
6393 13.81 6.23 1.14 INTRON_3 108417 109588 290593 + Tigger3b DNA/TcMar-Tigger 1 1231 0 144
INTRON_3 108417 CAGTCATGCACTGCATAATGACATTTCTGTCAATGATGGACTACATATAT 108466
i i i i v i i ii i
Tigger3b#DNA/ 1 CAGTCATGCGCCGCATAACGACGTTTCGGTCAACGACGGACCGCATATAC 50
INTRON_3 108467 GATGGT----TTATGAGA--AAAATTCCTGCCTGAAAAATTCCTATCACG 108510
i ----ii i -- v vv--iv i v
Tigger3b#DNA/ 51 GACGGTGGTCCCATAAGATTATAATGG--AGCTGAAAAATTCCTATCGCC 98
INTRON_3 108511 TAATGACATTGTAGCTGTCATAACATTGTAGCACAGTGCATTACTCATGT 108560
i i i ii i i i i ii i
Tigger3b#DNA/ 99 TAGTGACGTCGTAGCCATCGTAACGTCGTAGCGCAACGCATTACTCACGT 148
INTRON_3 108561 GTTTATAGTGATGCTGGTGTAAACATCATCTGTTGTGCTGCCACTTGTAT 108610
i i -v i ii i v i
Tigger3b#DNA/ 149 GTTTGTGGTGATGCTGGTGTAAACA-AACCTACTGCGCTGCCAGTCGTAT 197
INTRON_3 108611 AAAAGTATAGCTAGCACATAAAACTATATACAGCATATAATACTTGATAA 108660
---- v i i i i
Tigger3b#DNA/ 198 AAAAGTATAGC----ACATACAATTATGTACAGTACATAATACTTGATAA 243
INTRON_3 108661 TGATAATAAATGATTATGTTACTGGTTTACGTGT-----ATACTATGCTT 108705
i i i i ----- i
Tigger3b#DNA/ 244 TGATAATAAACGACTATGTTACTGGTTTATGTATTTACTATACTATACTT 293
INTRON_3 108706 ------AGTATTTTA-AGCACACTCTTTCTAGTTATTAAAAGAAAA--CT 108746
------iv - iii i v i --i
Tigger3b#DNA/ 294 TTTATCGTTATTTTAGAGTGTACTCCTTCTACTTATTAAAAAAAAAAGTT 343
INTRON_3 108747 AAGTGTAAAACAGCCTCAGGCAGGTCCTCCAGAAGGTATTCCAGAAGAAG 108796
v i i
Tigger3b#DNA/ 344 AACTGTAAAACAGCCTCAGGCAGGTCCTTCAGGAGGTATTCCAGAAGAAG 393
INTRON_3 108797 GCATTGTTATCATAGGAGATGACAGCTCCATGCAT--TATTGCCCCTGAA 108844
i --
Tigger3b#DNA/ 394 GCATTGTTATCATAGGAGATGACAGCTCCATGCGTGTTATTGCCCCTGAA 443
INTRON_3 108845 CACCTTCTAGTGAGACAAGATGTGGAGGTGGAAGACAGTGATATTGATGA 108894
v i i
Tigger3b#DNA/ 444 GACCTTCCAGTGGGACAAGATGTGGAGGTGGAAGACAGTGATATTGATGA 493
INTRON_3 108895 TCTTGATCCTGTGTAGGCCTAGG-TAATATGTGT--TCGTGTGTTTGTTT 108941
i i - i -- i v v
Tigger3b#DNA/ 494 TCCTGACCCTGTGTAGGCCTAGGCTAATGTGTGTGTTTGTGTCTTAGTTT 543
INTRON_3 108942 TTAACAAAAA-GTTTAAAAAGT----------TAAATT----AATAGAAA 108976
- ---------- ? ----
Tigger3b#DNA/ 544 TTAACAAAAAAGTTTAAAAAGTAAAAAAAAAATAAWTTTAAAAATAGAAA 593
INTRON_3 108977 AACGTTTATAGAATAAGGATTTAA-----CAACACATTTTTTGTATATTT 109021
v i v -----v v i - i vi
Tigger3b#DNA/ 594 AAAGCTTATAGAATAAGGATATAAAGAAAGAAAATATTTTT-GTACAGCT 642
INTRON_3 109022 TT------TGTTCGTGTTTTAAGCTAAGTGCTATTACAAAAGCGTCCAAA 109065
v ------ i i v v
Tigger3b#DNA/ 643 GTACAATGTGTTTGTGTTTTAAGCTAAGTGTTATTACAAAAGAGTCAAAA 692
INTRON_3 109066 AGTTAGAAAAATGTAAAAGTTTATAAAGTAAAAACGTTAAAGAAAGCTAC 109115
?i v? v v v v
Tigger3b#DNA/ 693 AGTTWAAAAAATTWAAAAGTTTATAAAGTAAAAAAGTTACAGTAAGCTAA 742
INTRON_3 109116 GGTTAATTTGTTATTGAAGAGAGAAA--TACTTTAACAAATAAATTTAGT 109163
i i -- i ? ---
Tigger3b#DNA/ 743 GGTTAATTTATTATTGAAGAAAGAAAAATATTTTWA---ATAAATTTAGT 789
INTRON_3 109164 GTACCCTAAGTGTACAGTGTTTATAAACTCTACAGTAGTGTACAATAATG 109213
v v i
Tigger3b#DNA/ 790 GTAGCCTAAGTGTACAGTGTTTATAAAGTCTACAGTAGTGTACAGTAATG 839
INTRON_3 109214 TCCTAGCTCTTCACATCTACTCACCACTCACTCACTGACACACTCAGGGA 109263
vi ii v i i v
Tigger3b#DNA/ 840 TCCTAGGCCTTCACATTCACTCACCACTCACTCACTGACTCACCCAGAGC 889
INTRON_3 109264 AACTTATGGTTCTGCAAGTTCCATTTGTGATAAATGCTCTATAAAGGTAC 109313
vii i i ii i i i v ii
Tigger3b#DNA/ 890 AACTTCCAGTCCTGCAAGCTCCATTCATGGTAAGTGCCCTATACAGGTGT 939
INTRON_3 109314 ACCATTTTAAAAAATCTTTTATACCATATTTTTACTGTATCTTTTCTATG 109363
vv --- i i
Tigger3b#DNA/ 940 ACCATTTTTTA---TCTTTTATACCGTATTTTTACTGTACCTTTTCTATG 986
INTRON_3 109364 TTTAGATATGCTTATATATACTCACAATTACCAT-GTGTTAGAATTGCCT 109412
i v i vv i v - v
Tigger3b#DNA/ 987 TTTAGATATGTTTAGATACACAAATACTTACCATTGTGTTACAATTGCCT 1036
INTRON_3 109413 ATAGTTTTCAGTACAATAACATGCTGTTCAGGTTTGTAGCCTAGGAGCA- 109461
i v i v -
Tigger3b#DNA/ 1037 ACAGTATTCAGTACAGTAACATGCTGTACAGGTTTGTAGCCTAGGAGCAA 1086
INTRON_3 109462 --------------TAGCCTAGGTGTGTAGGAGGCTATAACATCTAGATT 109497
-------------- v v i
Tigger3b#DNA/ 1087 TAGGCTATACCATATAGCCTAGGTGTGTAGTAGGCTATACCATCTAGGTT 1136
INTRON_3 109498 TGTGTAAATACACTCAATGACATTTACACAACAA---AATCACCTAACTA 109544
i v ii ii i --- i v
Tigger3b#DNA/ 1137 TGTGTAAGTACACTCTATGATGTTCGCACAACGACGAAATCGCCTAACGA 1186
INTRON_3 109545 TGCATTTCTCAGAACATATCCCT-TTGTTAAGTGATGCATGAGTG 109588
i i i- i i i v
Tigger3b#DNA/ 1187 CGCATTTCTCAGAACGTATCCCCGTCGTTAAGCGACGCATGACTG 1231
Matrix = 18p37g.matrix
Transitions / transversions = 2.18 (107 / 49)
Gap_init rate = 0.02 (25 / 1171), avg. gap size = 3.48 (87 / 25)
+ 1755 22.9 1.1 9.8 INTRON_3 109589 109659 (290522) C L1MD3 LINE/L1 (1212) 6670 6603 139
ANNOTATION EVIDENCE:
864 23.01 0.41 11.31 INTRON_3 109589 109659 290522 C L1MC4a_3end LINE/L1 1350 1417 1212 247
INTRON_3 109589 TATGTTTACTAACGTATATATATATACACACATGTGTCTGTTTTTCTATA 109638
-- v vi ii i i i iv i i - v i
C L1MC4a_3end#L 1417 --TGTATACTAACCCATGCATACACATACATCTATATCT-TATTTCTGTA 1371
INTRON_3 109639 TCTGTGTATTTATGTCTCTGT 109659
i v i i i v v
C L1MC4a_3end#L 1370 TCTATCTATCTGTATATATGT 1350
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.03 (2 / 70), avg. gap size = 1.50 (3 / 2)
1755 22.57 2.19 7.32 INTRON_3 109589 109614 290567 C L1MC3_3end LINE/L1 1357 1382 1150 246
INTRON_3 109589 TATGTTTACTAACGTATATATATATA 109614
ii v ivii i i
C L1MC3_3end#LI 1382 TATACTAACCTGTGTATATACACATA 1357
Matrix = 20p37g.matrix
Transitions / transversions = 3.50 (7 / 2)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
+ 1758 25.8 5.2 7.3 INTRON_3 109672 110433 (289748) C L1MD3 LINE/L1 (1735) 6260 5478 139
ANNOTATION EVIDENCE:
328 26.67 5.83 0.00 INTRON_3 109672 109791 290390 C L1MD3_3end LINE/L1 881 1007 1735 248
INTRON_3 109672 TGTAATACAGGTAGAATCATTTGTCACAGTTTGCATTTCATCTT-----C 109716
v v v ? i i i i -----
C L1MD3_3end#LI 1007 TGTAATACAGTTAGATTCTTTTGTCACAKTCTGTATTCCATCCTGRGATC 958
INTRON_3 109717 CTCTGACATTGTGG-TGAATTAAAAAAATT-AGAAACAATAAGCTTTACT 109764
i i iv i? ii- v vvv -?v v v iv i
C L1MD3_3end#LI 957 CCCCGATCTCYTAAATGATTTTTTAAAATTTRCATACATTAAAGTTCACT 908
INTRON_3 109765 CTTGGTGGTGTACAGTTCTATGGGTTT 109791
vi v v i
C L1MD3_3end#LI 907 CTTTATGCTGTAAAGTTCTGTGGGTTT 881
Matrix = 20p37g.matrix
Transitions / transversions = 0.93 (14 / 15)
Gap_init rate = 0.03 (3 / 119), avg. gap size = 2.33 (7 / 3)
1758 25.71 5.18 8.18 INTRON_3 109750 110433 289748 C L1ME1_3end LINE/L1 225 889 37 249
INTRON_3 109750 ACAATAAGCTTTAC-TCTTGGTGGTGTACAGTTCTATGGGTTT-GATGAA 109797
iv i - ? vvvi v i - ii
C L1ME1_3end#LI 889 ACAATAAAATTCACCTNTTTTAAGTGTACAGTTCGATGAGTTTTGACAAA 840
INTRON_3 109798 TTTAGACAGTCATGTATCCACCCCCGC--------TATAGAACAGTTCTA 109839
v v ? i v v i -------- v i
C L1ME1_3end#LI 839 TGTATACANTCGTGTAACCACCACCACAATCAAGATATAGAACATTTCCA 790
INTRON_3 109840 TTATTCACTAAATTTCCTCATGGTACCTGTTGATAGTTTATCTTTCCTTC 109889
i ii v v v i-- vi i iv vi iv --- i
C L1ME1_3end#LI 789 TCACCCCCAAAAGTTCCC--TCATGCCCCTTTGTAGTCAATC---CCCTC 745
INTRON_3 109890 ACTCCAACCCATGGCAGCCACAGATCTGTTTTTTATCCTCATAGTTTGCC 109939
v i v ---- -----i vi---- v v - ii i i
C L1ME1_3end#LI 744 CCCCCACCCC----CAGCC-----CCTGGC----AACCAC-TGATCTGCT 709
INTRON_3 109940 TTTTTCCAACGTCA-TATAA-----------ATGGAAT--CATACAATAC 109975
i ------ - i-----------v i -- i ---
C L1ME1_3end#LI 708 TTCT------GTCACTATAGTTTTGCCTTTTCTAGAATTTCATATAA--- 668
INTRON_3 109976 ATAGGTTTGTATATATACAATACAACCAGGCTTTTGGATCTGGTTTCTTT 110025
i i----- -i i ii--i v vi i
C L1ME1_3end#LI 667 ATGGA-----AT-CATACAGTATG--TAGTCTTTTGTGTCTGGCTTCTTT 626
INTRON_3 110026 CATTTAACAAAATACATTTATTATTTATCTATGTTGTTGCATAAATCA-T 110074
i i v i v ivv i i iv -
C L1ME1_3end#LI 625 CACTTAGCATAATGCTTTTGAGATTCATCCATGTTGTTGCATGTATCAAT 576
INTRON_3 110075 AGTTTGTTCCTTTTAATTGTTGAATAATATTCTATTATACGGAAGTGCCA 110124
ii v i i i i i i vi i
C L1ME1_3end#LI 575 AGTTCATTCCTTTTTATTGCTGAGTAGTATTCCATTGTATGGATATACCA 526
INTRON_3 110125 CCCTTTGTTTACTCAGGCATCTATTGAATTGCATTGGGGATCATTTTCAG 110174
vv ii vv i ?i vvvi v - ii i
C L1ME1_3end#LI 525 CAATTTGTTTATCCATTCACCNGTTGATGGACATTTGGG-TTGTTTCCAG 477
INTRON_3 110175 TTTTTG-CAGTCATGAATAAAGTTGCTAAACATATGCACATATAGGTTTT 110223
- vi i i i viv i v iii i i
C L1ME1_3end#LI 476 TTTTTGGCTATTACGAATAAAGCTGCTATGAACATTCGTGTACAGGTCTT 427
INTRON_3 110224 TG-GTGAGCAT--GTTAAAACTTCACTTGCATTTGATTCACTCTACTTTG 110270
- ii -- ----- i - vi iv v v -- i v
C L1ME1_3end#LI 426 TGTGTGGACATATGTT-----TTCATTT-CTCTTGGGTAAAT--ACCTAG 385
INTRON_3 110271 GAGTGCAGAGTGAGATTTCCAGGTCAAATG-TAAGTGTGTGTTTA----- 110314
------ - v ii v - i -----
C L1ME1_3end#LI 384 GAGTG------GA-ATTGCTGGGTCATATGGTAAGTGTATGTTTAACTTT 342
INTRON_3 110315 -TAGGAAACTGCCACACTGTTTTCCAAACTGACTGTACCATTT-GCATTT 110362
- i v v i - i
C L1ME1_3end#LI 341 ATAAGAAACTGCCAAACTGTTTTCCAAAGTGGCTGTACCATTTTGCATTC 292
INTRON_3 110363 CTACCAGGAGTGTATAAGGATTTTGGTTAGTCTTTGTCCTTTATAGCGCC 110412
i v i i ii iii iv ivii ivvi i i
C L1ME1_3end#LI 291 CCACCAGCAATGTATGAGAGTTCCAGTTGCTCCGCATCCTCGCCAGCACT 242
INTRON_3 110413 TGCTGTTGTTGCTGTTGTTGG 110433
v i -- v iv --
C L1ME1_3end#LI 241 TGGTATTGT--CAGTCTTT-- 225
Matrix = 20p37g.matrix
Transitions / transversions = 1.72 (105 / 61)
Gap_init rate = 0.05 (32 / 683), avg. gap size = 2.91 (93 / 32)
+ 2276 9.9 1.3 1.6 INTRON_3 110434 110737 (289444) C AluY SINE/Alu (8) 303 1 142
ANNOTATION EVIDENCE:
2186 10.04 1.32 1.65 INTRON_3 110434 110737 289444 C AluY SINE/Alu 1 303 8 136
INTRON_3 110434 TTTTTTGTGTTTTTTTTTTTTTGAGACGGAGTCTC----TGTCACTCAGG 110479
v v ---- i i
C AluY#SINE/Alu 303 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGG 254
INTRON_3 110480 CTGGAGTGCAGTGAGTGGCGCCATCTTGGCTTACTGCAAGCTTCACCTCC 110529
---- v i i i i
C AluY#SINE/Alu 253 CTGGAGTGCAGTG----GCGCGATCTCGGCTCACTGCAAGCTCCGCCTCC 208
INTRON_3 110530 TGGGTTCACGCTATTCTCCTGCCTCAGCCTCCTGAATAGCTGGGACTATG 110579
i i i i ii
C AluY#SINE/Alu 207 CGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACA 158
INTRON_3 110580 GGCGCCTACCACCATGCTTGGCTAATTTTTTTGTATTTTTAGTAGAGATG 110629
ii i ii - i
C AluY#SINE/Alu 157 GGCGCCCGCCACCACGCCCGGCTAATTTTTT-GTATTTTTAGTAGAGACG 109
INTRON_3 110630 AGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTTGTGATA 110679
i i v
C AluY#SINE/Alu 108 GGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATC 59
INTRON_3 110680 TGCCCGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTAAGCCACTGC 110729
i i i i i
C AluY#SINE/Alu 58 CGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGC 9
INTRON_3 110730 GCCTGGCC 110737
i
C AluY#SINE/Alu 8 GCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 6.50 (26 / 4)
Gap_init rate = 0.01 (3 / 303), avg. gap size = 3.00 (9 / 3)
+ 1758 22.7 3.3 4.1 INTRON_3 110738 110890 (289291) C L1MD3 LINE/L1 (702) 5477 5327 139
ANNOTATION EVIDENCE:
1758 25.71 5.18 8.18 INTRON_3 110738 110882 289299 C L1ME1_3end LINE/L1 83 224 702 250
INTRON_3 110738 TGTTACTGGTTTTTTAATGCTTTTCTAATAGGTATATAGTACTGTATCAT 110787
-- v ----- -- iv i i i iv i v
C L1ME1_3end#LI 224 --TTAAT-----TTTA--GCCATTCTAATGGGTGTGTAGTGGTATCTCAT 184
INTRON_3 110788 TGT---TTTGATTTGTGTGTCCCTAATGACT---GTTGTTGAATGTCATG 110831
--- i ii v --- v iii v v
C L1ME1_3end#LI 183 TGTGGTTTTAATTTGCATTTCCCTAATGACTAATGATGTTGAGCATCTTT 134
INTRON_3 110832 TCATATGCTTATTTGCCATCTGTATATCTTTTTTGGCAAAGTGTCTATTC 110881
i ii i ii i
C L1ME1_3end#LI 133 TCATGTGCTTATTTGCCATCCATATATCTTCTTTGGTGAAGTGTCTGTTC 84
INTRON_3 110882 A 110882
C L1ME1_3end#LI 83 A 83
Matrix = 20p37g.matrix
Transitions / transversions = 2.38 (19 / 8)
Gap_init rate = 0.03 (5 / 144), avg. gap size = 3.00 (15 / 5)
347 19.74 1.32 0.00 INTRON_3 110815 110890 289291 C L1MC_orf2 LINE/L1 3218 3294 0 251
INTRON_3 110815 TGTTGTTGAATGTCATGTCATATGCTTATTTGCCATCTGTATATCTTTTT 110864
v v iii v v i
C L1MC_orf2#LIN 3294 TGATGTGGAGCATCTTTTCATATGCTTATTTGCCATCTGTATATCTTCTT 3245
INTRON_3 110865 TGGCAAAGTGTCTATTCATA-CTTTGG 110890
ii i i v vi-
C L1MC_orf2#LIN 3244 TGGTGAGGTGTCTGTTAAGGTCTTTGG 3218
Matrix = 20p37g.matrix
Transitions / transversions = 1.50 (9 / 6)
Gap_init rate = 0.01 (1 / 75), avg. gap size = 1.00 (1 / 1)
+ 315 27.1 11.3 1.1 INTRON_3 110911 111078 (289103) C L1ME4a LINE/L1 (3) 6121 5937 143
ANNOTATION EVIDENCE:
315 27.08 11.31 1.08 INTRON_3 110911 111078 289103 C L1ME4a_3end LINE/L1 684 868 3 149
INTRON_3 110911 TTTTGCCTTCTTTTAAAATAAATA-ATTTTT-TTGAAGAAAAATTAGAAA 110958
vi vv v vv - vi i- v v i
C L1ME4a_3end#L 868 TTTTTTCTGATTATAAAAGTAATACATGCTCATTGTAGAAAATTTGGAAA 819
INTRON_3 110959 ATACAAATAATCTCCCCCCAAAAGGAAATAGAAA--AC-----ATTTCAC 111001
i v vivvvvvv i i -- ----- ii
C L1ME4a_3end#L 818 ATACAGAAAATACAAAGAAAAAAGAAAATAAAAATCACCCATAATCCCAC 769
INTRON_3 111002 CACCCAGTAATAACCA----TA-----TTGTTACATATCTTTCTAGACCT 111042
vi ---- ----- v ii v i i v i
C L1ME4a_3end#L 768 CACCCAGAGATAACCACTGTTAACATTTTGGTGTATTTCCTTCCAGTCTT 719
INTRON_3 111043 TTTTCTATTTGTAAATAAGAA-ATATATATGTATCTA 111078
-- i v v v - i v i ?
C L1ME4a_3end#L 718 TTTTCTAT--GCATATATGTATACATTTATATATNTA 684
Matrix = Unknown
Transitions / transversions = 0.76 (19 / 25)
Gap_init rate = 0.05 (8 / 167), avg. gap size = 2.62 (21 / 8)
+ 1982 19.8 4.2 5.0 INTRON_3 111175 111653 (288528) + MLT1D LTR/ERVL-MaLR 31 505 (0) 144
ANNOTATION EVIDENCE:
1982 19.79 4.18 5.05 INTRON_3 111175 111653 288528 + MLT1D LTR/ERVL-MaLR 31 505 0 268
INTRON_3 111175 ATATCCATGTCCTAATTTCTGGAAATCTGTGAATATGTTAACTTACATGG 111224
i i ii i -i v
MLT1D#LTR/ERV 31 ATGTCCACGTCCTAATCCCCGGAA-CCTGTGAATATGTTACCTTACATGG 79
INTRON_3 111225 CAAAGGGGAATTTAAGTTGTAGATGAAATTAAGGTTTCTAGTCAGTTGAC 111274
i v ----- i vi ----i --- -- i
MLT1D#LTR/ERV 80 CAAAAGGGACTTT-----GCAGATGTGATTAAG----TTA---AG--GAT 115
INTRON_3 111275 CTTAAAATACAGAGATTATTTTGGATTGTCTAGGTAGATCCAGTGTAATC 111324
i i ivi ii i ii i ii i
MLT1D#LTR/ERV 116 CTTGAGATGGGGAGATTATCCTGGATTATCCGGGTGGGCCCAATGTAATC 165
INTRON_3 111325 ACAAGGATCCTTAAAAGTGGAGGACCTAGGCAGAAGAGCAAATGTGAGAG 111374
i v --- i--- i i iv iv v
MLT1D#LTR/ERV 166 ACAAGGGTCCTTATAAG---AGGG---AGGCAGGAGGGTCAGAGTCAGAG 209
INTRON_3 111375 A-TTAGATGTGAT-ATG-----AGAAG--GACTTGACT-TGTTGCTGGCT 111414
-vv i- i ----- i -- ivv v-i
MLT1D#LTR/ERV 210 AAGGAGATGTGACGACGGAAGCAGAGGTCGGAGTGACGACGTTGCTGGCT 259
INTRON_3 111415 TTGAGGATGGAGGAAGTGGCTTATGAGCCAAGGAGTGTGGACAGCTTCTA 111464
i v i- i i i i i i
MLT1D#LTR/ERV 260 TTGAAGATGGAGGAAGGGGCC-ACGAGCCAAGGAATGCGGGCGGCCTCTA 308
INTRON_3 111465 GACACTGGAAAAGGAAAAGAAATAGACTCTCCCTTAGAGCTTCCAGAATG 111514
vi v i ii i i i -
MLT1D#LTR/ERV 309 GAAGCTGGAAAAGGCAAGGAAACGGATTCTCCCCTAGAGCCTCCAGAA-G 357
INTRON_3 111515 GAATGCAGCCTTCCCAATACCTTGATTTTAGCCCACTGAAATCCATTTCA 111564
i i v i i v i i i
MLT1D#LTR/ERV 358 GAACGCAGCCCTGCCGACACCTTGATTTTAGCCCAGTGAGACCCATTTCG 407
INTRON_3 111565 TACTTTT--CCATTTA----TATAAGACCA---GTTTGTATTGTTT-AAG 111604
v i -- - ii ---- i iv ---i i -
MLT1D#LTR/ERV 408 GACTTCTGACC-TCCAGAACTGTAAGATAATAAATTTGTGTTGTTTTAAG 456
INTRON_3 111605 CCATGAAGTTTGTGGTAATTTGTTATAGCAGCAATAGAAAACTGAAACA 111653
iv i i i v
MLT1D#LTR/ERV 457 CCACTAAGTTTGTGGTAATTTGTTACAGCAGCAATAGGAAACTAATACA 505
Matrix = 20p37g.matrix
Transitions / transversions = 3.09 (68 / 22)
Gap_init rate = 0.04 (19 / 478), avg. gap size = 2.32 (44 / 19)
+ 6392 11.0 2.4 1.5 INTRON_3 112948 113927 (286254) C L1MA1 LINE/L1 (0) 7721 6727 145
ANNOTATION EVIDENCE:
6392 10.97 2.41 1.53 INTRON_3 112948 113927 286254 C L1MA1_3end LINE/L1 55 1049 0 252
INTRON_3 112948 TTTTAAATTTTGTGGGTACATGGTAGGTATATGTATTTTTGGGGTACATG 112997
v i i i v
C L1MA1_3end#LI 1049 TTTTAATTTTTGTGGGTACATAGTAGGTGTATATATTTATGGGGTACATG 1000
INTRON_3 112998 AGATGTTTTGGTAT-GGCATGCAAGGTGAAATAAGCACATCTTGGAGAAT 113046
i i- v v
C L1MA1_3end#LI 999 AGATGTTTTGATACAGGCATGCAATGTGAAATAAGCACATCATGGAGAAT 950
INTRON_3 113047 GTGGTATCCGTCCCCTCAAGCATTCAGCCTTTGTGTTACAAACAATCCTA 113096
v i i v v v
C L1MA1_3end#LI 949 GGGGTATCCATCCCCTCAAGCATTTATCCTTTGAGTTACAAACAATCCAA 900
INTRON_3 113097 TTATACTCTT--AGTTATTTTAAAATGTACAGTTGAATTACTATTGACTA 113144
i -- i i i i
C L1MA1_3end#LI 899 TTACACTCTTTAAGTTATTTTAAAATGTACAATTAAGTTATTATTGACTA 850
INTRON_3 113145 TAG-AAACCTGTTGTGCTATCACATACTAGGGTTTGTTTATTCTTTCT-A 113192
-v v v v vi i i -
C L1MA1_3end#LI 849 TAGTCACCCTGTTGTGCTATCAAATAGTAGGTCTTATTCATTCTTTCTTA 800
INTRON_3 113193 TTTATTTTGGACCCATTAACCATTTCCTCCTTCTTCCTGCCCTCACCACC 113242
v v ii v i ------ i v?v
C L1MA1_3end#LI 799 TTTTTTTTGTACCCATTAACCATCCCCACCTCC------CCCCCAANCCC 756
INTRON_3 113243 TCACTACTCTTTTCAGCCTCTGGTAACCATCTTTCTACTCTCTCTGTCCA 113292
i i ii i v
C L1MA1_3end#LI 755 CCACTACCCTTCCCAGCCTCTGGTAACCATCCTTCTACTCTCTATGTCCA 706
INTRON_3 113293 TTAAGTCCAATTGTTTTGATTTTTGGATTCCACAAATAAGTGAGAACATG 113342
-i i i i
C L1MA1_3end#LI 705 T-GAGTTCAATTGTTTTGATTTTTAGATCCCACAAATAAGTGAGAACATG 657
INTRON_3 113343 CGATGTTTGTCTT-CTGTGCCTGTCTTATTTCACTTAACATAATGATCTT 113391
i - v i
C L1MA1_3end#LI 656 TGATGTTTGTCTTTCTGTGCCTGGCTTATTTCACTTAACATAATGATCTC 607
INTRON_3 113392 CA-TTTCATCCGTGTTATTGCAGATGACTAGATCTCAGTCTTTTT-ATAG 113439
- i i i i i v - i
C L1MA1_3end#LI 606 CAGTTCCATCCATGTTGTTGCAAATGACTGGATCTCATTCTTTTTTATGG 557
INTRON_3 113440 CTGAATGGTACTCCATTGTATATATATGTACTACATTTTCTTTATCCATT 113489
i i -- i
C L1MA1_3end#LI 556 CTGAATAGTACTCCATTGTGTATAT--GTACCACATTTTCTTTATCCATT 509
INTRON_3 113490 CATC-----------ACTTAGGTTGCTTCCAAATCTTGGCTATTGTGAAT 113528
----------- i i i
C L1MA1_3end#LI 508 CATCTGTTGATGGACACTTAGGTTGCTTCCAAATCTTAGCTATTGTAAAC 459
INTRON_3 113529 AGTACTGCAACAAACTTGGGAGTGCAGATGACTCTTTGATACACTGATTT 113578
i v i iv i i
C L1MA1_3end#LI 458 AGTGCTGCAACAAACATAGGAGTGCAGATATCTCTTCGATATACTGATTT 409
INTRON_3 113579 TTTTTCTTTGGGGTATATAGCCAGCAGTGGGATTGCCGGATTGTATGATA 113628
ii v v i ii i
C L1MA1_3end#LI 408 CCTTTCTTTTGGGTATATACCCAGCAGTGGGATTGCTGGATCATATGGTA 359
INTRON_3 113629 GCTCTATTTTTAGTTTTTTGAGGAACCTCCAAACTGTTCTGCTTAGTGGT 113678
v v v
C L1MA1_3end#LI 358 GCTCAATTTTTAGTTTTTTGAGGAACCTCCAAACTGTTCTCCATAGTGGT 309
INTRON_3 113679 TGTACTAACTTACATTTCCACCAATAGGGTACAAGGTTTCCCTTTTCTCT 113728
i i i v v i
C L1MA1_3end#LI 308 TGTACTAATTTACATTCCCACCAACAGTGTACAAGGGTTCCCTTTTCTCC 259
INTRON_3 113729 GCATTCTTATCAGCATGTGTTATTGCCT----TATGGCTAAAAGCCATTT 113774
i i iii v ---- v v v
C L1MA1_3end#LI 258 ACATCCTCGCCAGCATTTGTTATTGCCTGTCTTTTGGATATAAGCCATTT 209
INTRON_3 113775 TGACTGGGGCGAGATTATATCTCATTGTAGTTTTCATTTGTATTTCTCTG 113824
i i v v i
C L1MA1_3end#LI 208 TAACTGGGGTGAGATGATATCTCATTGTAGTTTTGATTTGCATTTCTCTG 159
INTRON_3 113825 ATGATCAATTATGTTGAGCACTTTTTCATATGCCTGTATGCCATTTGTAT 113874
v i v
C L1MA1_3end#LI 158 ATGATCAATGATGTTGAGCACCTTTTCATATGCCTGTTTGCCATTTGTAT 109
INTRON_3 113875 ATCTTCTTTTCAGAAATGTCTGTTCAAATATTTTGCCCATTTTT-GATTG 113923
i v i v - i
C L1MA1_3end#LI 108 GTCTTCTTTTGAGAAATGTCTATTCAAATCTTTTGCCCATTTTTTGATCG 59
INTRON_3 113924 GATT 113927
C L1MA1_3end#LI 58 GATT 55
Matrix = 20p37g.matrix
Transitions / transversions = 1.73 (69 / 40)
Gap_init rate = 0.01 (13 / 979), avg. gap size = 2.54 (33 / 13)
6300 8.40 0.87 0.87 INTRON_3 113835 113927 286254 C L1M1_orf2 LINE/L1 3199 3292 2 253
INTRON_3 113835 ATGTTGAGCACTTTTTCATATGCCTGTATGCCATTTGTATATCTTCTTTT 113884
i v i
C L1M1_orf2#LIN 3292 ATGTTGAGCACCTTTTCATATGCCTGTTTGCCATTTGTATGTCTTCTTTT 3243
INTRON_3 113885 CAGAAATGTCTGTTCAAATATTTTGCCCATTTTT-GATTGGATT 113927
v i v - i
C L1M1_orf2#LIN 3242 GAGAAATGTCTATTCAAATCTTTTGCCCATTTTTTGATCGGATT 3199
Matrix = 20p37g.matrix
Transitions / transversions = 1.33 (4 / 3)
Gap_init rate = 0.01 (1 / 92), avg. gap size = 1.00 (1 / 1)
+ 7857 6.6 0.4 0.6 INTRON_3 113928 114936 (285245) + LTR13 LTR/ERVK 1 1007 (0) 146
ANNOTATION EVIDENCE:
7857 6.58 0.40 0.60 INTRON_3 113928 114936 285245 + LTR13 LTR/ERVK 1 1007 0 145
INTRON_3 113928 TGTGGGCAGCAAGCCACCCAGGTGCCGAGGCAAGAGACCAAGGACATGAG 113977
i i i i
LTR13#LTR/ERV 1 TGTGGGCGGCAAGCCACCCAGGTGCCGAGGCAAGAGACCGAGGGCACGAG 50
INTRON_3 113978 CTGTTCCAGTATAATAAAATATA--AAACAAGAATAGTTATACCAGATAT 114025
-- i i
LTR13#LTR/ERV 51 CTGTTCCAGTATAATAAAATATATAAAATAAGAATAGTTATACTAGATAT 100
INTRON_3 114026 AGATCTTAGATACGATTATATGCGAATATCATTAATCATTAGTTGGTAGT 114075
i ii v i
LTR13#LTR/ERV 101 AGATCTTAGATATGATTATATATGAATATCATTAATCATTAGTTTGTAGC 150
INTRON_3 114076 AATTACTCTTTATCCCAATATTATAATAATCCTCGCTCTATAATCATAAC 114125
i i
LTR13#LTR/ERV 151 AATTACTCTTTATTCCAATATTATAATAATCCTCGCTCTACAATCATAAC 200
INTRON_3 114126 CTAGGAAAAACCAGGCCATACAGAGATAGGAGCTGAGGGGATGCAGTGAG 114175
iii
LTR13#LTR/ERV 201 CTAGGAAAAACCAGGCCATACAGAGATAGGAGCTGAGGGGACATAGTGAG 250
INTRON_3 114176 AAGTGACCAGAAGACAAGAGTGCGAGCCTTCTGTTATGCCCAGACAGGGC 114225
i
LTR13#LTR/ERV 251 AAGTGACCAGAAGACAAGAGTGCGAGCCTTCTGTTATGCCCGGACAGGGC 300
INTRON_3 114226 CACCAGAAGGGCTCCTTGGTCTAGCGGTGACACCAGTGTCTGGGAAGATG 114275
- i i i i
LTR13#LTR/ERV 301 CACCAGA-GGGCTCCTTGGTCTAGCGGTAACGCCAGCGTCTGGGAAGACG 349
INTRON_3 114276 CCCGTTGCCAGGCAGACCGTGGTCTAGTGGTAGCGAAAAGTGTCAAGGAA 114325
i i i vv -
LTR13#LTR/ERV 350 CCCGTTGCCAAGCGGACCGTGGTCTAGCGGTAGCGTCA-GTGTCAAGGAA 398
INTRON_3 114326 CAACATCCGCTACTTAGCAGACTGGGAAAGGGAGTCTCCTTTTCCCCCGG 114375
v i i i -
LTR13#LTR/ERV 399 AAACACCCGCTACTTAGCAGACCGGGAAAGGGAGTCTCCCTTTCCCC-GG 447
INTRON_3 114376 GGGAGTTTAGAGAAGACTCTGCTCCTCCACCTCTTGTGGAGGGCCTGATA 114425
i i
LTR13#LTR/ERV 448 GGGAGTTTAGAGAAGACTCTACTCCTCCACCTCTTGTGGAGGGCCTGACA 497
INTRON_3 114426 TTAGTCAGGCTTGCCCGCAGTTATCCGGAGGCCTAACCGTCTCCCTGTGA 114475
i ii
LTR13#LTR/ERV 498 TCAGTCAGGCCCGCCCGCAGTTATCCGGAGGCCTAACCGTCTCCCTGTGA 547
INTRON_3 114476 TGCTGTGCTTCAACGGTCACACTCCTAGTCCGCCTTCATGTTCCATCCTG 114525
ii i
LTR13#LTR/ERV 548 TGCTGTGCTTCAGTGGTCACGCTCCTAGTCCGCCTTCATGTTCCATCCTG 597
INTRON_3 114526 TACACCTGGCTCTGCCTTCTAGATAGCAGCAGAAAATTAGTGAAAGTACT 114575
i i v
LTR13#LTR/ERV 598 TACACCTGGCTCTGCCTTTTAGATAGCAGTAGCAAATTAGTGAAAGTACT 647
INTRON_3 114576 AAAAGTCTCTGATATGCTGAAATAATGGTGTAAGCTGTCTTTCTCTTTGT 114625
v v i i i --
LTR13#LTR/ERV 648 AAAAGTCTCTGATAAGCAGAAATAATGGCGTAAGCTGTCTCTCTCTCT-- 695
INTRON_3 114626 CTCCTCTCTCTCTCTGCCTTGGCTGCAAGGCAGGGAAGGGCCCCCTGTCC 114675
i v
LTR13#LTR/ERV 696 CTCCTCTCTCTCTCTGCCTCGGCTGCCAGGCAGGGAAGGGCCCCCTGTCC 745
INTRON_3 114676 AGTGGACACGTGACCCACGTGACCTTACCTATCATTGGAGATGACTCACA 114725
i
LTR13#LTR/ERV 746 AGTGGACACGTGACCCACGTGACCTTACCTATCATTGGAGATGGCTCACA 795
INTRON_3 114726 CTCTTTACCCTGCCCCTTTTGCTTTGTATCCAATAAATAACAGCGCAGCC 114775
i - ii v
LTR13#LTR/ERV 796 CTCCTTACCCTGCCCCTTT-GTCTTGTATCCAATAAATATCAGCGCAGCC 844
INTRON_3 114776 AGACATTTGGGGCCACTACCGGTCTCTGCGCATTGGTGGTAGTGGTCCCC 114825
v i i i iv
LTR13#LTR/ERV 845 TGGCATTCGGGGCCACTACCGGTCTCCGCGTCTTGGTGGTAGTGGTCCCC 894
INTRON_3 114826 CGGGCCCAGCTGGCTTTTCTTTTATCTCTTTGTCTTGAGTCTTTATTTCT 114875
v v
LTR13#LTR/ERV 895 CGGGCCCAGCTGTCTTTTCTTTTATCTCTTTGTCTTGTGTCTTTATTTCT 944
INTRON_3 114876 ACACTCTCTCGTCACCGCACATGGGGAGAGA--CCCACCGACCCTGTGGG 114923
v i i --
LTR13#LTR/ERV 945 ACACTCTCTCGTCTCCGCACACGGGGAGAAAAACCCACCGACCCTGTGGG 994
INTRON_3 114924 GCTGGTCCCTGCA 114936
v i
LTR13#LTR/ERV 995 GCTGGACCCTACA 1007
Matrix = 18p37g.matrix
Transitions / transversions = 3.40 (51 / 15)
Gap_init rate = 0.01 (7 / 1008), avg. gap size = 1.43 (10 / 7)
7857 6.58 0.40 0.60 INTRON_3 113928 114936 285245 + LTR13 LTR/ERVK 1 1007 0 276
INTRON_3 113928 TGTGGGCAGCAAGCCACCCAGGTGCCGAGGCAAGAGACCAAGGACATGAG 113977
i i i i
LTR13#LTR/ERV 1 TGTGGGCGGCAAGCCACCCAGGTGCCGAGGCAAGAGACCGAGGGCACGAG 50
INTRON_3 113978 CTGTTCCAGTATAATAAAATATA--AAACAAGAATAGTTATACCAGATAT 114025
-- i i
LTR13#LTR/ERV 51 CTGTTCCAGTATAATAAAATATATAAAATAAGAATAGTTATACTAGATAT 100
INTRON_3 114026 AGATCTTAGATACGATTATATGCGAATATCATTAATCATTAGTTGGTAGT 114075
i ii v i
LTR13#LTR/ERV 101 AGATCTTAGATATGATTATATATGAATATCATTAATCATTAGTTTGTAGC 150
INTRON_3 114076 AATTACTCTTTATCCCAATATTATAATAATCCTCGCTCTATAATCATAAC 114125
i i
LTR13#LTR/ERV 151 AATTACTCTTTATTCCAATATTATAATAATCCTCGCTCTACAATCATAAC 200
INTRON_3 114126 CTAGGAAAAACCAGGCCATACAGAGATAGGAGCTGAGGGGATGCAGTGAG 114175
iii
LTR13#LTR/ERV 201 CTAGGAAAAACCAGGCCATACAGAGATAGGAGCTGAGGGGACATAGTGAG 250
INTRON_3 114176 AAGTGACCAGAAGACAAGAGTGCGAGCCTTCTGTTATGCCCAGACAGGGC 114225
i
LTR13#LTR/ERV 251 AAGTGACCAGAAGACAAGAGTGCGAGCCTTCTGTTATGCCCGGACAGGGC 300
INTRON_3 114226 CACCAGAAGGGCTCCTTGGTCTAGCGGTGACACCAGTGTCTGGGAAGATG 114275
- i i i i
LTR13#LTR/ERV 301 CACCAGA-GGGCTCCTTGGTCTAGCGGTAACGCCAGCGTCTGGGAAGACG 349
INTRON_3 114276 CCCGTTGCCAGGCAGACCGTGGTCTAGTGGTAGCGAAAAGTGTCAAGGAA 114325
i i i vv -
LTR13#LTR/ERV 350 CCCGTTGCCAAGCGGACCGTGGTCTAGCGGTAGCGTCA-GTGTCAAGGAA 398
INTRON_3 114326 CAACATCCGCTACTTAGCAGACTGGGAAAGGGAGTCTCCTTTTCCCCCGG 114375
v i i i -
LTR13#LTR/ERV 399 AAACACCCGCTACTTAGCAGACCGGGAAAGGGAGTCTCCCTTTCCCC-GG 447
INTRON_3 114376 GGGAGTTTAGAGAAGACTCTGCTCCTCCACCTCTTGTGGAGGGCCTGATA 114425
i i
LTR13#LTR/ERV 448 GGGAGTTTAGAGAAGACTCTACTCCTCCACCTCTTGTGGAGGGCCTGACA 497
INTRON_3 114426 TTAGTCAGGCTTGCCCGCAGTTATCCGGAGGCCTAACCGTCTCCCTGTGA 114475
i ii
LTR13#LTR/ERV 498 TCAGTCAGGCCCGCCCGCAGTTATCCGGAGGCCTAACCGTCTCCCTGTGA 547
INTRON_3 114476 TGCTGTGCTTCAACGGTCACACTCCTAGTCCGCCTTCATGTTCCATCCTG 114525
ii i
LTR13#LTR/ERV 548 TGCTGTGCTTCAGTGGTCACGCTCCTAGTCCGCCTTCATGTTCCATCCTG 597
INTRON_3 114526 TACACCTGGCTCTGCCTTCTAGATAGCAGCAGAAAATTAGTGAAAGTACT 114575
i i v
LTR13#LTR/ERV 598 TACACCTGGCTCTGCCTTTTAGATAGCAGTAGCAAATTAGTGAAAGTACT 647
INTRON_3 114576 AAAAGTCTCTGATATGCTGAAATAATGGTGTAAGCTGTCTTTCTCTTTGT 114625
v v i i i --
LTR13#LTR/ERV 648 AAAAGTCTCTGATAAGCAGAAATAATGGCGTAAGCTGTCTCTCTCTCT-- 695
INTRON_3 114626 CTCCTCTCTCTCTCTGCCTTGGCTGCAAGGCAGGGAAGGGCCCCCTGTCC 114675
i v
LTR13#LTR/ERV 696 CTCCTCTCTCTCTCTGCCTCGGCTGCCAGGCAGGGAAGGGCCCCCTGTCC 745
INTRON_3 114676 AGTGGACACGTGACCCACGTGACCTTACCTATCATTGGAGATGACTCACA 114725
i
LTR13#LTR/ERV 746 AGTGGACACGTGACCCACGTGACCTTACCTATCATTGGAGATGGCTCACA 795
INTRON_3 114726 CTCTTTACCCTGCCCCTTTTGCTTTGTATCCAATAAATAACAGCGCAGCC 114775
i - ii v
LTR13#LTR/ERV 796 CTCCTTACCCTGCCCCTTT-GTCTTGTATCCAATAAATATCAGCGCAGCC 844
INTRON_3 114776 AGACATTTGGGGCCACTACCGGTCTCTGCGCATTGGTGGTAGTGGTCCCC 114825
v i i i iv
LTR13#LTR/ERV 845 TGGCATTCGGGGCCACTACCGGTCTCCGCGTCTTGGTGGTAGTGGTCCCC 894
INTRON_3 114826 CGGGCCCAGCTGGCTTTTCTTTTATCTCTTTGTCTTGAGTCTTTATTTCT 114875
v v
LTR13#LTR/ERV 895 CGGGCCCAGCTGTCTTTTCTTTTATCTCTTTGTCTTGTGTCTTTATTTCT 944
INTRON_3 114876 ACACTCTCTCGTCACCGCACATGGGGAGAGA--CCCACCGACCCTGTGGG 114923
v i i --
LTR13#LTR/ERV 945 ACACTCTCTCGTCTCCGCACACGGGGAGAAAAACCCACCGACCCTGTGGG 994
INTRON_3 114924 GCTGGTCCCTGCA 114936
v i
LTR13#LTR/ERV 995 GCTGGACCCTACA 1007
Matrix = 18p37g.matrix
Transitions / transversions = 3.40 (51 / 15)
Gap_init rate = 0.01 (7 / 1008), avg. gap size = 1.43 (10 / 7)
+12859 9.1 2.2 0.7 INTRON_3 114937 116520 (283661) C L1MA1 LINE/L1 (839) 6726 5119 145
ANNOTATION EVIDENCE:
9542 9.02 2.20 0.75 INTRON_3 114937 116295 283886 C L1M1_orf2 LINE/L1 1819 3198 96 322
INTRON_3 114937 TGGATTATTATATTTTT-CCTATAGAGTTGTTTGAGCTCCTTATATCTTC 114985
------ v - v
C L1M1_orf2#LIN 3198 ------ATTAGATTTTTTCCTATAGAGTTGTTTGAGCTCCTTATATATTC 3155
INTRON_3 114986 TGGTTAT-AATCTCTTGTCAGATGGATAGTTTGCAAATATTGTCTCCCAT 115034
- i i v
C L1M1_orf2#LIN 3154 TGGTTATTAATCCCTTGTCAGATGGGTAGTTTGCAAATATTTTCTCCCAT 3105
INTRON_3 115035 TCTGTTGTTTGTCTCTTCACTTTATTGATTGTATCCTTTGCTGTGCAGAA 115084
v v i
C L1M1_orf2#LIN 3104 TCTGTGGGTTGTCTCTTCACTTTGTTGATTGTATCCTTTGCTGTGCAGAA 3055
INTRON_3 115085 TCTTTTTAACTTGATGTGATCCCATTTGTCCGTTTCTTCTTTGGTTGCCT 115134
v i i v
C L1M1_orf2#LIN 3054 GCTTTTTAACTTGATGTGATCCCATTTGTCCATTTTTGCTTTGGTTGCCT 3005
INTRON_3 115135 ATACTTGTAAGGTATTGCTCAAGAAATCTTTGCCCAGACCAATGTGCTAG 115184
i i ii v i
C L1M1_orf2#LIN 3004 GTGCTTGTGGGGTATTGCTCAAGAAATCTTTGCCCAGACCAATGTCCTGG 2955
INTRON_3 115185 AGATTTTCCCCTATCTTTTCTTGTAGTAGTTTAATAGTTTGAGGTCTTAG 115234
v v v
C L1M1_orf2#LIN 2954 AGATTTTCCCCAATGTTTTCTTGTAGTAGTTTCATAGTTTGAGGTCTTAG 2905
INTRON_3 115235 ATTTAAGTCTTTAATCCATTTTGATTTGATTTTTATATATGGTGAGAA-- 115282
i i i--
C L1M1_orf2#LIN 2904 ATTTAAGTCTTTAATCCATTTTGATTTGATTTTTGTATATGGCGAGAGAT 2855
INTRON_3 115283 --GGACCTAGTTTCCTTTTTCTGCATATGGACATTCACTTTTCTCAGCAC 115330
-- ii v i i i v i
C L1M1_orf2#LIN 2854 AGGGGTCTAGTTTCATTCTTCTGCATATGGATATCCAGTTTTCCCAGCAC 2805
INTRON_3 115331 CATTTATTGAAGAGACCGTCTTTCCCCCAGTGTATGTTCTTGGCACTTTT 115380
i i i
C L1M1_orf2#LIN 2804 CATTTATTGAAGAGACTGTCTTTTCCCCAGTGTATGTTCTTGGCACCTTT 2755
INTRON_3 115381 GTCAAAAATGAGTTCACTGTAGGTATGTAGATT-GTTTCTGGGTTCTCCA 115429
i i - i
C L1M1_orf2#LIN 2754 GTCAAAAATGAGTTCACTGTAGGTGTGTGGATTTGTTTCTGGGTTCTCTA 2705
INTRON_3 115430 TTCTGTTCCATTGATCTATGCGTCTGTTTTTAATGATAGTATATTGCTGT 115479
i i - vi ivv
C L1M1_orf2#LIN 2704 TTCTGTTCCATTGGTCTATGTGTCTGTTTTTA-TGCCAGTACCATGCTGT 2656
INTRON_3 115480 TTTGGTTACTGTATCACTGTAGTATAATTTGCAGTCAGGTAATGTGATTT 115529
i v v v i
C L1M1_orf2#LIN 2655 TTTGGTTACTATAGCTCTGTAGTATAATTTGAAGTCAGGTAATGTGATTC 2606
INTRON_3 115530 CTCCAATTTTATTCTTTTTGCTTAGGATAGCTTTGCCTATTGTAGGTCTT 115579
i i v v i
C L1M1_orf2#LIN 2605 CTCCAGTTTTGTTCTTTTTGCTTAGGATAGCTTTGGCTATTCTGGGTCTT 2556
INTRON_3 115580 TTGTGGTTCTATATACATTTTAGGATTGTTTTTTCTATTTCTGTGAAGAA 115629
i v
C L1M1_orf2#LIN 2555 TTGTGGTTCCATATAAATTTTAGGATTGTTTTTTCTATTTCTGTGAAGAA 2506
INTRON_3 115630 TGTCATTGGTATTGTGATAGGGATTGCATAGAATCTATAAATTGCTTTGG 115679
v v i i
C L1M1_orf2#LIN 2505 TGTCATTGGTATTTTGATAGGGATTGCATTGAATCTGTAGATTGCTTTGG 2456
INTRON_3 115680 GCAGTATGAACATTTTAACAATATTGATTCTTCTGATCCATAAATATGGA 115729
i i ii i i
C L1M1_orf2#LIN 2455 GTAGTATGGACATTTTAACAATATTGATTCTTCCAATCCATGAACATGGA 2406
INTRON_3 115730 ATATTTTTCCATTCTTTGATGACCTCTTCAATTTCTTTCATCAGTGTTTT 115779
i i v
C L1M1_orf2#LIN 2405 ATATTTTTCCATTTTTTGGTGTCCTCTTCAATTTCTTTCATCAGTGTTTT 2356
INTRON_3 115780 GTAATTTTTATTACATTTATCTTTCACTTCTTTGGTTAA-----TTCCTA 115824
i i i i vvv -----
C L1M1_orf2#LIN 2355 ATAGTTTTCATTATAGAGATCTTTCACTTCTTTGGTTAAGTTAATTCCTA 2306
INTRON_3 115825 GGTATTTA------TTTGTGGCTATTGTAAATGGGATTACTTTTTAAATT 115868
------ v v
C L1M1_orf2#LIN 2305 GGTATTTAATTTTATGTGTGGCTATTGTAAATGGGATTACTTTTTTAATT 2256
INTRON_3 115869 TCTTTTTCCCATTTTTCACTGTTGACATATAGAAAATACTACTCATTTTT 115918
v v i - i v
C L1M1_orf2#LIN 2255 TCTTTTTCACATTGTTCACTGTTGGCATATAGAAA-TGCTACTGATTTTT 2207
INTRON_3 115919 GTATGTTGATTTTGTGTCCTGCAACCATACTGAATTTATT----AGTTCC 115964
i iv i ---- i
C L1M1_orf2#LIN 2206 GTATGTTGATTTTGTATCCTGCAACTTTACTGAATTTGTTTATCAGTTCT 2157
INTRON_3 115965 AATAATATATTTTAGTGGAGTCTTTAGTTTTTTCCAAATATAAGATCATG 116014
i v - i - v i
C L1M1_orf2#LIN 2156 AATAGTTT-TCTT-GTGGAGTCTTTAGGTTTTTCCAAATATAAGATCATA 2109
INTRON_3 116015 TCCTCTGCAAACAAATATAACTTGACTTCTTCCTTTCCAATTTGACTGCC 116064
v iv i iv
C L1M1_orf2#LIN 2108 TCATCTGCAAACAAGGATAATTTGACTTCTTCCTTTCCAATTTGGATGCC 2059
INTRON_3 116065 CTTTACATCTTT-----GTCTGGTTGCTCTAGCTAGGACTTCCAGTACTA 116109
i ----- i
C L1M1_orf2#LIN 2058 CTTTATATCTTTCTCTTGTCTGATTGCTCTAGCTAGGACTTCCAGTACTA 2009
INTRON_3 116110 TGTTTAATAACAGTGGTGACAGTGGTTATCATTGTCATGTTCCAAATCTT 116159
v vi v i i
C L1M1_orf2#LIN 2008 TGTTGAATAACAGTGGTGACAGTGGGCATCCTTGTCGTGTTCCAGATCTT 1959
INTRON_3 116160 AGAGGAAAGGCTTTCAGTCTTTTCTTGTTCAGTATGATACTAGCTGTGGG 116209
i i iii
C L1M1_orf2#LIN 1958 AGAGGAAAGGCTTTCAGTTTTTCCCCATTCAGTATGATACTAGCTGTGGG 1909
INTRON_3 116210 TCTGGTGTATGTGGCTTTTATTACATTGAGGTATGTTCCTTC----CCCA 116255
vii i ii ----
C L1M1_orf2#LIN 1908 TCTGTCATATATGGCTTTTATTATGTTGAGGTATGTTCCTTCTATNCCCA 1859
INTRON_3 116256 GTTTTTTGAGGGTTTGTATTATGAAGGGATGGTAAATTTT 116295
v i v i
C L1M1_orf2#LIN 1858 GTTTTTTGAGGGTTTTTATCATGAAGGGATGTTGAATTTT 1819
Matrix = 20p37g.matrix
Transitions / transversions = 1.73 (78 / 45)
Gap_init rate = 0.01 (14 / 1358), avg. gap size = 2.93 (41 / 14)
1370 7.11 0.92 3.29 INTRON_3 114937 114992 285189 C L1MA1_3end LINE/L1 4 54 995 321
INTRON_3 114937 TGGATTATTATATTTTT-CCTATAGAGTTGTTTGAGCTCCTTATATCTTC 114985
------ v - v
C L1MA1_3end#LI 54 ------ATTAGATTTTTTCCTATAGAGTTGTTTGAGCTCCTTATATATTC 11
INTRON_3 114986 TGGTTAT 114992
C L1MA1_3end#LI 10 TGGTTAT 4
Matrix = 20p37g.matrix
Transitions / transversions = 0.00 (0 / 2)
Gap_init rate = 0.04 (2 / 55), avg. gap size = 3.50 (7 / 2)
12859 9.62 2.39 0.64 INTRON_3 116075 116520 283661 C L1M1_orf2 LINE/L1 1591 2043 1251 323
INTRON_3 116075 TTGTCTGGTTGCTCTAGCTAGGACTTCCAGTACTATGTTTAATAACAGTG 116124
i v
C L1M1_orf2#LIN 2043 TTGTCTGATTGCTCTAGCTAGGACTTCCAGTACTATGTTGAATAACAGTG 1994
INTRON_3 116125 GTGACAGTGGTTATCATTGTCATGTTCCAAATCTTAGAGGAAAGGCTTTC 116174
vi v i i
C L1M1_orf2#LIN 1993 GTGACAGTGGGCATCCTTGTCGTGTTCCAGATCTTAGAGGAAAGGCTTTC 1944
INTRON_3 116175 AGTCTTTTCTTGTTCAGTATGATACTAGCTGTGGGTCTGGTGTATGTGGC 116224
i i iii vii i
C L1M1_orf2#LIN 1943 AGTTTTTCCCCATTCAGTATGATACTAGCTGTGGGTCTGTCATATATGGC 1894
INTRON_3 116225 TTTTATTACATTGAGGTATGTTCCTTC----CCCAGTTTTTTGAGGGTTT 116270
ii ----
C L1M1_orf2#LIN 1893 TTTTATTATGTTGAGGTATGTTCCTTCTATNCCCAGTTTTTTGAGGGTTT 1844
INTRON_3 116271 GTATTATGAAGGGATGGTAAATTTTCAATTAA-----TTTTCAACATCAA 116315
v i v i -- i ----- i
C L1M1_orf2#LIN 1843 TTATCATGAAGGGATGTTGAATTTT--ATCAAATGCTTTTTCAGCATCAA 1796
INTRON_3 116316 TTGAAATGATCATGTGGTTTTTATCCTTCATTTTGTTGATATGATGTATC 116365
i i
C L1M1_orf2#LIN 1795 TTGAAATGATCATATGGTTTTTATCCTTCATTCTGTTGATATGATGTATC 1746
INTRON_3 116366 ATATTGGATGATTTGCATATGTTGAAACATCCTTGCATCCCAGGGATAAA 116415
i iv v
C L1M1_orf2#LIN 1745 ACATTGATTGATTTGCATATGTTGAACCATCCTTGCATCCCAGGGATAAA 1696
INTRON_3 116416 TTCCACTTGATCATGATGAATGATCTTTCTGATGTATTGTTGAGTTTGGT 116465
i i i i i
C L1M1_orf2#LIN 1695 TCCCACTTGGTCATGATGAATGATCTTTCTAATGTATTGTTGAATTCGGT 1646
INTRON_3 116466 TTACTAGTATTTTGTTGAAGATTTTTGCATCAGTATTCATCAGAGATATT 116515
i i i
C L1M1_orf2#LIN 1645 TTGCTAGTATTTTGTTGAGGATTTTTGCATCAATATTCATCAGAGATATT 1596
INTRON_3 116516 GGCCC 116520
i
C L1M1_orf2#LIN 1595 GGCCT 1591
Matrix = 20p37g.matrix
Transitions / transversions = 3.88 (31 / 8)
Gap_init rate = 0.01 (3 / 445), avg. gap size = 3.67 (11 / 3)
+ 471 3.5 0.0 0.0 INTRON_3 116521 116577 (283604) + (TGG)n Simple_repeat 3 59 (0) 147
ANNOTATION EVIDENCE:
471 3.51 0.00 0.00 INTRON_3 116521 116577 283604 + (TGG)n Simple_repeat 3 59 121 361
INTRON_3 116521 GTAGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTAGTGGTGGT 116570
i i
(TGG)n#Simple 3 GTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGT 52
INTRON_3 116571 GGTGGTG 116577
(TGG)n#Simple 53 GGTGGTG 59
Matrix = Unknown
Transitions / transversions = 0.0 (2 / 0)
Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0)
+12859 9.7 2.3 0.7 INTRON_3 116578 118344 (281837) C L1MA1 LINE/L1 (2447) 5118 3319 145
ANNOTATION EVIDENCE:
12859 9.62 2.39 0.64 INTRON_3 116578 118138 282043 C L1M1_orf2 LINE/L1 2 1590 1704 324
INTRON_3 116578 T--TTGTC--------ATGTGTCTTTGTCTGATTTTGTTATCAGGGTAAT 116617
-- v -------- i v
C L1M1_orf2#LIN 1590 TAGTTTTCTTTTTTTGATGTGTCTTTGTCTGGTTTTGGTATCAGGGTAAT 1541
INTRON_3 116618 CCTGGCCTCATAGAATGAGTTTTGAAGTATTCCTTCCTTTCCTATTTTTC 116667
v i v i iii
C L1M1_orf2#LIN 1540 ACTGGCCTCGTAGAATGAGTTTGGAAGTATTCCCTCCTCCTCTATTTTTC 1491
INTRON_3 116668 AGAATAGTTTGAATAGGATTGGTTTTAATTCTTCCTTAAATGTTTTGTAG 116717
i i v i i v
C L1M1_orf2#LIN 1490 GGAATAGTTTGAGTAGGATTGGTATTAGTTCTTCTTTAAATGTTTGGTAG 1441
INTRON_3 116718 AATTCATCAGTGAAGCCATCAGGCCCCAGGCTTTTCTTTAGTGGGAAACT 116767
v i i v i
C L1M1_orf2#LIN 1440 AATTCAGCAGTGAAGCCATCAGGTCCCGGGCTTTTCTTTACTGGGAGACT 1391
INTRON_3 116768 TTTTATTACAACTTTGATCTTGTTATTTGTTGTTGGTCTGTTCAAGTTTT 116817
ii i i i i i
C L1M1_orf2#LIN 1390 TTTTATTACGGCTTCGATCTCGTTACTTGTTATTGGTCTGTTCAGGTTTT 1341
INTRON_3 116818 GGATTTCTTCTTGATTCAGTCTTGGTAGGTTGTGT----CTAGGAATTTG 116863
i i i i ----
C L1M1_orf2#LIN 1340 GGATTTCTTCCTGGTTCAATCTTGGTAGGTTGTATGTATCTAGGAATTTG 1291
INTRON_3 116864 TCCA---GTTCTAGATTTTCCAATTTATTGGTATATAGTTACTCATAGTA 116910
---v i i
C L1M1_orf2#LIN 1290 TCCATTTCTTCTAGATTTTCCAATTTATTGGCATATAGTTGCTCATAGTA 1241
INTRON_3 116911 GCCACTAATGATCCTTTGGATTTCTGCAGTATCACTTGTAATGTCTTTTT 116960
i v ii
C L1M1_orf2#LIN 1240 GCCACTAATGATCCTTTGAATTTCTGCAGTATCAGTTGTAATGTCTCCTT 1191
INTRON_3 116961 TTTTTTTATTTCTGATTTTCTTTATTTGGATCTTCTCTCCTTTTTT---- 117006
i--- v i ----
C L1M1_orf2#LIN 1190 TTTC---ATTTCTGATTTTATTTATTTGGATCTTCTCTCTTTTTTTCTTA 1144
INTRON_3 117007 GTCAGTCTGACTAAAGGTTTGTCAATTTTGTTTAACTTTTCAAAAAAACA 117056
i i v
C L1M1_orf2#LIN 1143 GTTAGTCTGGCTAAAGGTTTGTCAATTTTGTTTAACTTTTCAAAAAACCA 1094
INTRON_3 117057 ACTTTTGGTTTCATTGATCTTTTGTATA--TTTTTTCATTTCAATTTCAT 117104
v v--
C L1M1_orf2#LIN 1093 ACTTTTTGTTTCATTGATCTTTTGTATTGTTTTTTTCATTTCAATTTCAT 1044
INTRON_3 117105 TTATTTCTGCTTTGATCTTTATTATTTATTTTCTTCTACTATTTTTGGGT 117154
i v v
C L1M1_orf2#LIN 1043 TTATTTCTGCTCTGATCTTTATTATTTCTTTTCTTCTACTAATTTTGGGT 994
INTRON_3 117155 TTAGTTTGTTCTTGCTTTTCTAGATACTTAAGATGCATTATTAGATTTTT 117204
i i v vi ii v
C L1M1_orf2#LIN 993 TTGGTTTGCTCTTGCTTTTCTAGTTCTTTAAGATGCATCGTTAGATTGTT 944
INTRON_3 117205 CATTTGAAGTTTTTT-TCTTGTGTGATGTAAGCACTTATAGCCATAAAAT 117253
i i- v v i i v
C L1M1_orf2#LIN 943 TATTTGAAGTTTTTCCTCTTTTTTGATGTAGGCACTTATAGCTATAAACT 894
INTRON_3 117254 TCCCA--TAGTACTTCCTTTGCTGTATCCCACAGGTTTTGGTATTTTGTG 117301
v-- v i i v
C L1M1_orf2#LIN 893 TCCCTCTTAGTACTGCTTTTGCTGTATCCCATAGGTTTTGGTATGTTGTG 844
INTRON_3 117302 TTTTCATTATCATTTGTTTTCAAGAAAATTTTAAATTTTATTCTTAATTT 117351
i - v v iv
C L1M1_orf2#LIN 843 TTTCCATTATCATTTGTTT-CAAGAAATTTTTCAATTTCCTTCTTAATTT 795
INTRON_3 117352 CTTTACTGACCCATTGATCATTCAGGAGCATATTGTTTAATTTCCATGTA 117401
i i i i
C L1M1_orf2#LIN 794 CTTCATTGACCCACTGGTCATTCAGGAGCATATTGTTTAATTTCCATGTA 745
INTRON_3 117402 TTTATACAGTTTCCAAAATTATTCTTCTCCTTAATTTCTAGTTTTATTCT 117451
i i vi v iv i
C L1M1_orf2#LIN 744 TTTGTATAGTTTCCAAAATTCCTCTTGTTATTAATTTCTAGTTTTATTCC 695
INTRON_3 117452 ATTGTGGTCAGGGAAGATACTTGATACTATTTCAATTTTCT-GAATGTTT 117500
i i i i -
C L1M1_orf2#LIN 694 ATTGTGGTCAGAGAAGATGCTTGATATTATTTCAATTTTTTTGAATGTTT 645
INTRON_3 117501 TAAGACTTGTTTTGTGACCTAACCTATGGTTTATCCTTGTGAATTATCCA 117550
v i v v
C L1M1_orf2#LIN 644 TAAGACTTGTTTTGTGACCTAACATATGGTCTATCCTTGAGAATGATCCA 595
INTRON_3 117551 TGTGCTGAGGAAAATAATGCGTATTCTGCAGCTGTTGAATAAAATGTTCT 117600
v i v i i
C L1M1_orf2#LIN 594 TGTGCTGAGGAAAAGAATGTGTATTCTGCAGCTCTTGGATGAAATGTTCT 545
INTRON_3 117601 GTAAATATCT--CAGATCCATTTGATCTGTAGTGCAGATTAGTTCTGATG 117648
--i i i iv
C L1M1_orf2#LIN 544 GTAAATATCTATTAGATCCATTTGGTCTATAGTGCAGATTAAGTCTGATG 495
INTRON_3 117649 TTTCTTTATGGATTTTCTGTCTGGAATATCTGTCCAATGCTGAAAGTGTG 117698
i v v v
C L1M1_orf2#LIN 494 TTTCTTTGTTGATTTTCTGTCTGGAAGATCTGTCCAATGCTGAAAGTGGG 445
INTRON_3 117699 GTGTCGAAGTTTCCAGCTATTATTGTATTGAGGACTCTCTCTCCCTTTAC 117748
i i i v v i v
C L1M1_orf2#LIN 444 GTGTTGAAGTCTCCAGCTATTATTGTATTGGGGCCTATCTCTCTCTTTAG 395
INTRON_3 117749 CTCTAATATTAACCTTTTTGTACTTATATATCTAGGTGCTCCAGTGTTGG 117798
v ---- ?v -- i
C L1M1_orf2#LIN 394 CTCTAATAATA----TTTNCT--TTATATATCTGGGTGCTCCAGTGTTGG 351
INTRON_3 117799 GTGCATATATATTTAAAATTTTTATGTTCTCTTGCTAAATTGACCCCTTA 117848
v i i i v
C L1M1_orf2#LIN 350 GTGCATATATATTTAAAATTGTTATATCCTCTTGCTGAATTGACCCCTTT 301
INTRON_3 117849 ATCATTATATAGT-ACTTTATTTGTCTCTG---ATAGTTTTTCTCCTGAC 117894
- i v v--- v i v
C L1M1_orf2#LIN 300 ATCATTATATAGTGACCTTCTTTGTCTCTTCTTATAGTTTTTGTCTTGAA 251
INTRON_3 117895 ATCT-----GTCTGATA-AAGTATAGTGACTCCTGCTTTTTATTGGTTTC 117938
----- - i i v
C L1M1_orf2#LIN 250 ATCTATTTTGTCTGATATAAGTATAGCGACTCCTGCTCTTTTTTGGTTTC 201
INTRON_3 117939 CACTGGCATGGAATATCTTTTTCCATCCCTTTATTTTTAGTCAATTTGTG 117988
i i v v
C L1M1_orf2#LIN 200 CATTGGCATGGAATATCTTTTTCCATCCCTTTATTTTCAGTCTATGTGTG 151
INTRON_3 117989 TGTTCATAGGTGAGGTGTGTTTCTTGTAGGCAGCAGATCAATGGTTCTTA 118038
v i i i v i
C L1M1_orf2#LIN 150 TCTTTATAGGTGAAGTGTGTTTCTTGTAGGCAACAGATCAATGGGTCTTG 101
INTRON_3 118039 TTTTCTCATCCATTCAGCCAGTGTATGTTTTTTTGATTGGAGAGGTTAGT 118088
i v i - v
C L1M1_orf2#LIN 100 TTTTTTCATCCATTCAGCCAGTCTATGTCTTTT-GATTGGAGAGTTTAGT 52
INTRON_3 118089 TCATTTACATTAAATATTATTATTGATAAATAAGAACTTACTCCTGCCAT 118138
i v i i i
C L1M1_orf2#LIN 51 CCATTTACATTCAATGTTATTATTGATAAGTAAGGACTTACTCCTGCCAT 2
Matrix = 20p37g.matrix
Transitions / transversions = 1.58 (93 / 59)
Gap_init rate = 0.01 (19 / 1560), avg. gap size = 2.63 (50 / 19)
7309 10.53 1.95 1.01 INTRON_3 117991 118344 281837 C L1M1_5end LINE/L1 3319 3675 0 325
INTRON_3 117991 TTCATAGGTGAGGTGTGTTTCTTGTAGGCAGCAGATCAATGGTTCTTATT 118040
i i i iv v i
C L1M1_5end#LIN 3675 TTTATAGGTGAAGTGTGTTTCTTGTAGGCAACAGATCGTTGGGTCTTGTT 3626
INTRON_3 118041 TTCTCATCCATTCAGCCAGTGTATGTTTTTTTGATTGGAGAGGTTAGTTC 118090
i i v v i - v i
C L1M1_5end#LIN 3625 TTTTTATCCATTCAGCCACTCTATGTCTTTT-GATTGGAGAGTTTAGTCC 3577
INTRON_3 118091 ATTTACATTAAATATTATTATTGATAAATAAGAACTTACTCCTGCCATTT 118140
v i i i
C L1M1_5end#LIN 3576 ATTTACATTCAATGTTATTATTGATAAGTAAGGACTTACTCCTGCCATTT 3527
INTRON_3 118141 TGTTATGTGTTTTCTGGTTGTTTTGTGGTGTTCTCTTCCTTCTTTTTTTT 118190
v v ii -
C L1M1_5end#LIN 3526 TGTTATTTGTTTTCTGGTTGTTTTGTGGTCTTCTCTTCCTTCTTTCCTT- 3478
INTRON_3 118191 CCTTCCTGTGTTCCTCT-AGTGAAGGCAATTTTCTCCGCTCACATGATTT 118239
v i - ii i v vii v
C L1M1_5end#LIN 3477 CCTTCCTGTCTTCCTTTTAGTGAAGGTGATTTTCTCTGGTGGTATGTTTT 3428
INTRON_3 118240 AGTTTCTTGCTTTTTATTATTT-TGTATCCATTGTACGTTTTTTGGTTTG 118288
i v - ii i i
C L1M1_5end#LIN 3427 AATTTCTTGCTTTTTATTTTTTGTGTATCTGTTGTATGTTTTTTGATTTG 3378
INTRON_3 118289 AGGGTAACCTGAGGCTTGCAAATACTATTTTATAACCTATTATTTTAACC 118338
v v v v i i v
C L1M1_5end#LIN 3377 AGGTTACCATGAGGCTTGCAAATAATATCTTATAACCCATTATTTTAAAC 3328
INTRON_3 118339 TGAT---AA 118344
---
C L1M1_5end#LIN 3327 TGATGACAA 3319
Matrix = 20p37g.matrix
Transitions / transversions = 1.50 (27 / 18)
Gap_init rate = 0.01 (5 / 353), avg. gap size = 1.40 (7 / 5)
+ 4432 8.1 0.1 4.2 INTRON_3 118345 118991 (281190) C L1PA14 LINE/L1 (0) 6161 5540 148
ANNOTATION EVIDENCE:
4432 8.07 0.15 4.18 INTRON_3 118345 118991 281190 C L1PA14_3end LINE/L1 287 908 0 278
INTRON_3 118345 TTTTTTTTTAACTTTTCTTTTAGGTTTGGGGCTACATGTGAAGGTTTGTT 118394
v v
C L1PA14_3end#L 908 TTTTTTTTTAACTTTTATTTTAGGTTTGGGGGTACATGTGAAGGTTTGTT 859
INTRON_3 118395 ACATAGGTAAATACATGTCACAAGGGTTTTTTGTACATATTATTTCATCA 118444
i i ii v
C L1PA14_3end#L 858 ACATAGGTAAACACGTGTCACGGGGGTTTGTTGTACATATTATTTCATCA 809
INTRON_3 118445 CCCAATGTTATTTCATCACCCAGGTATTAAGCCCAGTACACAACAGTTAT 118494
------------------ v i
C L1PA14_3end#L 808 CCCA------------------GGTATTAAGCCCAGTACCCAATAGTTAT 777
INTRON_3 118495 CTTTTCTGCTCCTCTCTCCTCTCCCTCTTCCTACCCTCCCCACTCAGGTA 118544
------- i i v i
C L1PA14_3end#L 776 CTTTTCTGCTCCTCTC-------CCTCCTCCCACCCTCCCCCCTCAAGTA 734
INTRON_3 118545 TACCC-AGTGTCTGTTGTTTCCTTCTTTGTGTTCATAAATTCTTATAATT 118593
v - i i v
C L1PA14_3end#L 733 GACCCCAGTGTCTGTTGTTTCCTTCTTTGTGTTCATAAGTTCTCATCATT 684
INTRON_3 118594 TAGCTCCCACTTATAAGTGAGAACATGTGGTATTCAGTTTTTTGTTCCTG 118643
i ii i
C L1PA14_3end#L 683 TAGCTCCCACTTATAAGTGAGAACATGCGGTATTTGGTTTTCTGTTCCTG 634
INTRON_3 118644 TGTTAGTTTGCTAGGGATTGTAGCCTCCAGCTCTATCCATGTTCCTGCAA 118693
i i vi i i
C L1PA14_3end#L 633 CGTTAGTTTGCTAAGGATAATAGCCTCCAGCTCCATCCATGTTCCCGCAA 584
INTRON_3 118694 AATACATGATCTTGTTCTTTTTTTATGGCTGTGTAGTATTCCATGGTGTA 118743
v i - ii
C L1PA14_3end#L 583 AAGACATGATCTCGTTCTTTTTT-ATGGCTGCATAGTATTCCATGGTGTA 535
INTRON_3 118744 TATGTACCACATTTTCTTTATTCAATCTGTCATTGATGGGCATTTAGGTT 118793
i i
C L1PA14_3end#L 534 TATGTACCACATTTTCTTTATCCAGTCTGTCATTGATGGGCATTTAGGTT 485
INTRON_3 118794 GATTCCATGTCCTTGCTATTGTGAATAATGCTGCAATGAACATTTGCATG 118843
i i i i
C L1PA14_3end#L 484 GATTCCATGTCTTTGCTATTGTGAATAGTGCTGCAATGAACATTCGCGTG 435
INTRON_3 118844 CATGTGTGTTTATGGTAGAATGATTCATATTCCTCTGGGTATATACCCAG 118893
v i
C L1PA14_3end#L 434 CATGTGTCTTTATGGTAGAATGATTTATATTCCTCTGGGTATATACCCAG 385
INTRON_3 118894 TAATGGGATTGCTGGATTGAATGATAGTTCTGCTTTTAGCTCTTTGAGGA 118943
i i i
C L1PA14_3end#L 384 TAATGGGATTGCTGGGTCGAATGGTAGTTCTGCTTTTAGCTCTTTGAGGA 335
INTRON_3 118944 ATTGTCACACTGCTTTGCACAATGGTTGACCTAATTAACATTCCTACC 118991
i i i v v v i i
C L1PA14_3end#L 334 ATCGCCATACTGCTTTCCACAATGGTTGAACTAATTTACACTCCCACC 287
Matrix = 18p37g.matrix
Transitions / transversions = 2.85 (37 / 13)
Gap_init rate = 0.01 (4 / 646), avg. gap size = 6.75 (27 / 4)
+ 7309 10.5 1.9 1.0 INTRON_3 118992 119816 (280365) C L1MA1 LINE/L1 (4247) 3318 2486 145
ANNOTATION EVIDENCE:
7309 10.53 1.95 1.01 INTRON_3 118992 119816 280365 C L1M1_5end LINE/L1 2486 3318 357 326
INTRON_3 118992 TTAACACTATTTGCATAAACAAACAAAGGAGCAAAAAGAAAACCAATAAA 119041
iv i ---- i i
C L1M1_5end#LIN 3318 TTAACACTGATTGCACAAACAAACAA----GCAAAGAGAAAACTAATAAA 3273
INTRON_3 119042 AACTCTACACCTTAACTTCATCTCTCTGCTTCTTAGCTTTTTGTTGTTTC 119091
i i i i i i i
C L1M1_5end#LIN 3272 AACTCTACACTTTAACTTCGTCCCCCCGCTTTTTAACTTTTTGTTGTTTC 3223
INTRON_3 119092 TATTTATGTCTTATTGTACT----ATGTCTTGAAAAGTTGTTGTAGTTAT 119137
i ----
C L1M1_5end#LIN 3222 TATTTATATCTTATTGTACTGTCTATGTCTTGAAAAGTTGTTGTAGTTAT 3173
INTRON_3 119138 TATTTTTTATTGGTTCATTGTTTAGTTTTTCTACTTAGGATAAGAGGAGT 119187
v iv i i v v
C L1M1_5end#LIN 3172 TATTTTTGATTGGTTCATCTTTTAGTCTTTCTACTTAAGATATGAGTAGT 3123
INTRON_3 119188 TTACACACTACAGTTACCATGTTATAATATTCTGTGTTTTTCTGTGTACT 119237
i i vi
C L1M1_5end#LIN 3122 TTACACACCACAATTACAGTGTTATAATATTCTGTGTTTTTCTGTGTACT 3073
INTRON_3 119238 TACTATTATCAGTGATTATTTATTGCTTTCTG-TGATTATTTATTGCTCA 119286
i v - i -i i v - vi
C L1M1_5end#LIN 3072 TACTATTACCAGTGAGT-TTTGT-ACCTTCAGATGATTTCTTATTGCTCA 3025
INTRON_3 119287 TTAATGTCCTTTTCTTTCTGATTGAAGAACTTCCTTTAGCATTTCTTGTA 119336
v i
C L1M1_5end#LIN 3024 TTAATGTCCTTTTCTTTCAGATTGAAGAACTCCCTTTAGCATTTCTTGTA 2975
INTRON_3 119337 GGATAGGCCTGGCATTGGTGAAATCCCTCAGCTTTTGTTTGTGTGGGAAA 119386
i i ii i v
C L1M1_5end#LIN 2974 GGACAGGTCTGGTGTTGATGAAATCCCTCAGCTTTTGTTTGTCTGGGAAA 2925
INTRON_3 119387 GTCTTTATCTCTCCTTCGTGTTTCAAGGATACATT-ACTAGACATAATAT 119435
i i v iv - i i ----
C L1M1_5end#LIN 2924 GTCTTTATTTCTCCTTCATGTTTGAAGGATATTTTCACTGGATATA---- 2879
INTRON_3 119436 TTATTCTAGGGTAAATGTTTATTTTCTTCAGCACTTTAAATATGTCTTGC 119485
i v v i v
C L1M1_5end#LIN 2878 CTATTCTAGGGTAAAAGTTTTTTTCCTTCAGCACTTTAAATATGTCATGC 2829
INTRON_3 119486 CATTCTCTTCTGGCCTGTAAGGTTTCCACTGAAAAGCCTGCTATTAGACA 119535
i i i iii i
C L1M1_5end#LIN 2828 CACTCTCTCCTGGCCTGTAAGGTTTCCACTGAAAAGTCTGCTGCCAGACG 2779
INTRON_3 119536 TGTCG-----------TATATTATTTGTTTCTTTTTTCTTGCTGCTTTTA 119574
i i ----------- i i
C L1M1_5end#LIN 2778 TATTGGAGCTCCATTGTATGTTATTTGTTTCTTTTCTCTTGCTGCTTTTA 2729
INTRON_3 119575 GGGTCCCTTCTTTATCCTTGACCTTTGGGAGTTTGATTATTAAATGCCTT 119624
i i
C L1M1_5end#LIN 2728 GGATCCTTTCTTTATCCTTGACCTTTGGGAGTTTGATTATTAAATGCCTT 2679
INTRON_3 119625 GAGGTAGTCTTCTTTGGGTTAAATCTGCTTGGTGTTCTATAACCTTTTTG 119674
i
C L1M1_5end#LIN 2678 GAGGTAGTCTTCTTTGGGTTAAATCTGCTTGGTGTTCTATAACCTTCTTG 2629
INTRON_3 119675 TACTTGGATATTGATATCTTTTTCTAGGCTTGGGAAGTTCTGTGTTATTA 119724
i i i v
C L1M1_5end#LIN 2628 TACTTGAATATTGATATCTTTCTCTAGGTTTGGGAAGTTCTCTGTTATTA 2579
INTRON_3 119725 TCCCTTTGAGTAAACTTCCTACCCCTATCACT-TCTCTGCTTCCTCTTTA 119773
i i v - i i
C L1M1_5end#LIN 2578 TCCCTTTGAATAAACTTTCTACCCCTATCTCTCTCTCTACCTCCTCTTTA 2529
INTRON_3 119774 AGGCCAATAACTCTTAGTTTTGCCCTTTTGAGGCTATATTTTA 119816
v v i
C L1M1_5end#LIN 2528 AGGCCAATAACTCTTAGATTTGCCCTTTTGAGGCTATTTTCTA 2486
Matrix = 20p37g.matrix
Transitions / transversions = 2.90 (58 / 20)
Gap_init rate = 0.01 (9 / 824), avg. gap size = 3.11 (28 / 9)
+ 411 17.7 0.0 0.0 INTRON_3 119817 119895 (280286) C L1M1 LINE/L1 (4149) 3416 3338 149 *
ANNOTATION EVIDENCE:
411 17.72 0.00 0.00 INTRON_3 119817 119895 280286 C L1M1_5end LINE/L1 3338 3416 259 327
INTRON_3 119817 TTTTATTATTTGTGCATCCATTGCATGTTTTTTGGTTTGAGGATACCCCG 119866
v i ii i i v vi
C L1M1_5end#LIN 3416 TTTTATTTTTTGTGTATCTGTTGTATGTTTTTTGATTTGAGGTTACCATG 3367
INTRON_3 119867 AGGGTTGCAAATACGATTTTATAACCTAT 119895
v vv i i
C L1M1_5end#LIN 3366 AGGCTTGCAAATAATATCTTATAACCCAT 3338
Matrix = 20p37g.matrix
Transitions / transversions = 1.33 (8 / 6)
Gap_init rate = 0.00 (0 / 78), avg. gap size = 0.0 (0 / 0)
+10112 17.0 2.4 1.0 INTRON_3 119895 122179 (278002) C L1MA1 LINE/L1 (5077) 2488 151 145
ANNOTATION EVIDENCE:
4331 11.88 4.25 0.00 INTRON_3 119895 120576 279605 C L1M1_5end LINE/L1 1778 2488 1187 328
INTRON_3 119895 TCTAGATCTTGTAGGTGTGCTTCATTGTTTTTTATTCCTTTTTCTTTTGT 119944
i v i
C L1M1_5end#LIN 2488 TCTAGATCTTGTAGGCGTGCTTCATTCTTTTTTATTCTTTTTTCTTTTGT 2439
INTRON_3 119945 CTCCTCTG----TGTATTTTTAAATAGCCTGTCTTCAAGCTA-------- 119982
---- i v--------
C L1M1_5end#LIN 2438 CTCCTCTGACTGTGTATTTTCAAATAGCCTGTCTTCAAGCTCACTAATTC 2389
INTRON_3 119983 TTTCTTATGCTTGATCAGTTCTGCTATTAAAGGACTCTGATGCATTCTTC 120032
v i i ii
C L1M1_5end#LIN 2388 TTTCTTCTGCTTGATCAATTCTGCTGTTAAGAGACTCTGATGCATTCTTC 2339
INTRON_3 120033 AGTATACCAATTGCATTTTTCAGCTCCAGAATTTCTTCTTAGTTGTTTTT 120082
ii i v ii v
C L1M1_5end#LIN 2338 AGTATGTCAATTGCATTTTTCAACTCCAGAATTTCTGCTTGATTCTTTTT 2289
INTRON_3 120083 AATTATTTCAATCTCTTTGTTAAATGTATCTGATAGAATTCTGAATTCCT 120132
v i
C L1M1_5end#LIN 2288 AATTATTTCAATCTCTTTGTTAAATTTATCTGATAGGATTCTGAATTCCT 2239
INTRON_3 120133 TCTCTGGGTTATCTTGAATTTCTTTGAGTTTCCTCACA-CAGCGATTTTG 120181
v ? v - v
C L1M1_5end#LIN 2238 TCTCTGTGTTATCTTGAATTTCNTTGAGTTTCCTCAAAACAGCTATTTTG 2189
INTRON_3 120182 AATTCTCTTTCTGAAAGATCACATATCTCTGTTTCTCCAGAATTGGTCAG 120231
v i i i i vv
C L1M1_5end#LIN 2188 AATTCTCTGTCTGAAAGGTCACATATCTCTGTCTCTCCGGGATTGGTCCC 2139
INTRON_3 120232 CAGCACCTTATTTAGTTTATTTGGTGAGGTCATGTCTTCCTGGGTGGTGT 120281
ii ii i i i v
C L1M1_5end#LIN 2138 TGGTGCCTTATTTAGTTCATTTGGTGAGGTCATGTTTTCCTGGATGGTCT 2089
INTRON_3 120282 TGATGCTTATAGATGTTCTTTGGTGTGTGCACAGTGAAGAGTTAGTTATT 120331
i i v i v vi v v
C L1M1_5end#LIN 2088 TGATGCTTGTGGATGTTCGTCGGTGTCTGGGCATTGAAGAGTTAGGTATT 2039
INTRON_3 120332 TATTGTGTTCTTCACTATCTGGACTTATTTGTAGCTGTCCTTCTTGGGAA 120381
iv vi i i v i
C L1M1_5end#LIN 2038 TATTGTAGTCTTCACAGTCTGGGCTTGTTTGTACCCGTCCTTCTTGGGAA 1989
INTRON_3 120382 GGCTTTCCAGATATTTGAAAGGACTTGGGTGTTGTGATCTAAG------- 120424
i i i -------
C L1M1_5end#LIN 1988 GGCTTTCCAGGTATTCGAAGGGACTTGGGTGTTGTGATCTAAGTTTTTGG 1939
INTRON_3 120425 ---------CTGTATCTGCTTTTGGGGGCACCCCAAACCCAGTAACACTG 120465
--------- i v v i i
C L1M1_5end#LIN 1938 TCACTGCAGCCGTATCTGCATTAGGGGGCACCCCAAGCCCAGTAACGCTG 1889
INTRON_3 120466 TGGTTCTTGTTGACTCATAGAGGAACTGCCTTCATGGTCTTAGACTAGAT 120515
i iv i v i vi i iv
C L1M1_5end#LIN 1888 TGGCTCTTGCAGACTCGTAGAGGTACCGCCTTGGTGGTCTTGGATAAGAT 1839
INTRON_3 120516 CTTGAAGAATTCACTGGATTATCAGGCAGAGACTCTTGTTCTTTTCCCTT 120565
iv v i i
C L1M1_5end#LIN 1838 CCGGAAGAATTCTCTGGATTACCAGGCAGAGACTCTTGTTCTCTTCCCTT 1789
INTRON_3 120566 ATTTTCTCTCA 120576
i i
C L1M1_5end#LIN 1788 ACTTTCTCCCA 1778
Matrix = 20p37g.matrix
Transitions / transversions = 1.76 (51 / 29)
Gap_init rate = 0.01 (4 / 681), avg. gap size = 7.25 (29 / 4)
10112 19.13 1.62 1.45 INTRON_3 120423 122179 278002 C L1M1_5end LINE/L1 151 1931 1744 329
INTRON_3 120423 AGCTGTATCTGCTTTTGGGGGCACCCCAAACCCAGTAACACTGTGGTTCT 120472
i v v i i i
C L1M1_5end#LIN 1931 AGCCGTATCTGCATTAGGGGGCACCCCAAGCCCAGTAACGCTGTGGCTCT 1882
INTRON_3 120473 TGTTGACTCATAGAGGAACTGCCTTCATGGTCTTAGACTAGATCTTGAAG 120522
iv i v i vi i iv iv
C L1M1_5end#LIN 1881 TGCAGACTCGTAGAGGTACCGCCTTGGTGGTCTTGGATAAGATCCGGAAG 1832
INTRON_3 120523 AATTCACTGGATTATCAGGCAGAGACTCTTGTTCTTTTCCCTTATTTTCT 120572
v i i i
C L1M1_5end#LIN 1831 AATTCTCTGGATTACCAGGCAGAGACTCTTGTTCTCTTCCCTTACTTTCT 1782
INTRON_3 120573 CTCA--------GAGTCTCTCTCTCTGTTCTGAGCAACATAAAGCTGGAG 120614
i -------- v vi v ii i
C L1M1_5end#LIN 1781 CCCAAACAAACGGAGTCTCTCTCTCTGTGCTGAGCTGCCTGGAGCTGGGG 1732
INTRON_3 120615 CTGGAGTGACACAAGCACCTCTGTTGCCACCATTACTATGACTGTGCTGG 120664
vv i i v ii iv i
C L1M1_5end#LIN 1731 GAGGGGTGACACAAGCACCCCTGTGGCCACCACCACTGGGACTGCGCTGG 1682
INTRON_3 120665 GTCAGTCCTGAAGCCAGCATAGCACTGAGTCTTGCCCAAAGCCTGTTATA 120714
v i i i i i i?i
C L1M1_5end#LIN 1681 GTCAGACCTGAAGCCAGCACAGCACTGGGTCTCGCCCAAGGCCCGCNGTA 1632
INTRON_3 120715 TCCACTCCCTGGCTACT-CCTATGTTCATGCAAGGGCCCTGGAGCTCTAC 120763
v v i- iiiv - i i
C L1M1_5end#LIN 1631 ACCACTGCCTGGCTACCGCCTATGTTTGCTCAAGG-CCCTAGGGCTCTAC 1583
INTRON_3 120764 AATCAGCAAGTGGCAATGTCAGCCAGGCCTGTATTCTTCTTTTCAGGTCG 120813
i v i i i i ii vi
C L1M1_5end#LIN 1582 AATCAGCAGGTGGCAAAGCCAGCCAGGCTTGTGTCCTTCCCTTCAGGGTG 1533
INTRON_3 120814 GTGATGTCCCCCAG-TCCCAGCTAGGTCCAGAAGTGCCATCCTGGAGTTA 120862
i vv ? -i vii ii v ii
C L1M1_5end#LIN 1532 GCGAGTTCCCCCNGGCCCCAGGCGGGTCCAGAGATGCCATCCAGGAGCCA 1483
INTRON_3 120863 GGGACTAGAGTCAAAAACCTTAGAAGTCTACCTAGTGTTCTATTGTACTG 120912
v i i i i i i v
C L1M1_5end#LIN 1482 GGGCCTGGAGTCAGAAACCTTAGGAATCTACCTGGTGCTCTATTCTACTG 1433
INTRON_3 120913 TGGCTGACATGGCACTCAGACTACAAGATGCAGTTCTTCCCACTCTTTCC 120962
i vv i ii i iiv i i
C L1M1_5end#LIN 1432 CGGCTGAGCTGGCACCCAAGCCACAAGACAAAGTCCTTCCCACTCTTCCC 1383
INTRON_3 120963 TCCCATTTCCAAAGACAGAGGAGCCTCACCCCATAGCCACCGCCACCCCA 121012
v v i i v i i
C L1M1_5end#LIN 1382 TCCCCTTTCCACAGGCAGAGGAGTCTCTCCCCATGGCCACCACCACCCCA 1333
INTRON_3 121013 GGCC-ACAAGGAATACTGCCAGACTTTTGCTGATGTTCCCTTAAGACCCA 121061
- iiv i ? i vii i v i i
C L1M1_5end#LIN 1332 GGCCCACGGCGAGTACTGCCNGGCTACCGCCGATGTTCACTCAAGGCCCA 1283
INTRON_3 121062 CGGGCTCTTAAGTCAGTATGTGGTGAATGCTGCCTGGCCCAGGACTCACC 121111
v v iv v ii ?
C L1M1_5end#LIN 1282 AGGGCTCTTCAGTCAGCTTGTGGTGAATGCTGCCAGGCCTGGGACTCNCC 1233
INTRON_3 121112 CTTCAGGGCATTAGTTTCTCCTCTAGCCTAAGGCAGGTCCAGAAATG--G 121159
v i vi i i i i --
C L1M1_5end#LIN 1232 CTTCAGGGCAGTGGGCTCCCCTCTGGCCCAGGGCAGGTCCAGAAATGCCG 1183
INTRON_3 121160 -CCAAGAGTCAAGTCCTGGAATCAGGGACCCCAAGAGCCCACTTAGTGCT 121208
- i v i i i
C L1M1_5end#LIN 1182 TCCAAGAGCCAAGGCCTGGAATCGGGGACCCCAAGAGCCCGCTTGGTGCT 1133
INTRON_3 121209 CTATCCCACTGTGGTTGTGCTGGTACCTAAGGTGCAAGACAAAGCCGCCT 121258
i i v v i v
C L1M1_5end#LIN 1132 CTACCCCACTGTGGCTGAGCTGGTACCTAAGCTGCAAGACAAAGTCCCCT 1083
INTRON_3 121259 TTACTTTTCCCTCTGTTTTTCTCAAGCAGAGGGTGTTTTACCTTGTAGCC 121308
i vi i v i iv iii
C L1M1_5end#LIN 1082 TTACTCTTCCCTCTCCTTTTCTCAAGCAGAAGGAGTCTCTCCCCATAGCC 1033
INTRON_3 121309 AGCACAGGTGGTAATGTGGTACATCTTACCTGAAGCCAGCAAGTCTCAGA 121358
v v v v ivi vi v v
C L1M1_5end#LIN 1032 ACCACAGCTGGGAATGTGCTGGGTCACACCTGAAGCCAGCACGTCTCTGA 983
INTRON_3 121359 GGCTCACCCAAGGCCCTTGATTA-TAGTACCTGGCTATCGCTGCTAGTTA 121407
v vi iiv - v i v i ii
C L1M1_5end#LIN 982 GTCTCACCCAAGGCCCACGGCGAGTACTGCCTGGGTACCGCTGCTGATTA 933
INTRON_3 121408 TTCAGGGCCCAAAGGCTCTTCAGTTAGCAGGTAATGAATGCTGCCAGGGC 121457
i i i i v i
C L1M1_5end#LIN 932 TTCAGGGCCCAAGGGCTCTTTAGTCAGCAGGTGATGAATCCTGCCAGGAC 883
INTRON_3 121458 TGGGTATTTTTCTTCAAGGCAGGGGAATCTCTACTGGCCCAGAATGTGTC 121507
vi ii v iv i v ii
C L1M1_5end#LIN 882 TGGGTCCTTCCCTTCAAGGCAGCGGGTTCCCTTCTGGCCCAGGGTGTGTC 833
INTRON_3 121508 TAGAAATGTCATCTGGAAG-TAGGGCCTGAAACGTGGACCTCATGACTCT 121556
i i - i i v i v
C L1M1_5end#LIN 832 TAGAAATGTCGTCTGGGAGCTAGGGCCTGGAATGGGGGCCTCAGGACTCT 783
INTRON_3 121557 GATCAGTGCC-TATCCTGCTGTGGCTGAGCAGGTATCCAAGATGCAAGAC 121605
vi i - i v v
C L1M1_5end#LIN 782 GCCCGGTGCCCTATCCTACTGTGGCTGAGCTGGTATCCAAGTTGCAAGAC 733
INTRON_3 121606 AAAGTCTTCCCTACTCTT---TCTTTTCTCCTCAAGTGGAAGGAAGGGAT 121652
i ii --- ii i ii
C L1M1_5end#LIN 732 AAAGTCCTCTTTACTCTTCCCTCTCCTCTCCTCAAGCGGAAGGAAGGAGT 683
INTRON_3 121653 CTCTTACGGAGCCTTGAGCTGTGCAGCCTGGGGTTAGGGGAAGAGTCGTG 121702
iv ivi v i i i v i
C L1M1_5end#LIN 682 CTCTCCCGGAGCTGCGAGCTGTGCTGCCTGGGGTTGGGGGAGGGGTGGCG 633
INTRON_3 121703 CAAGCACTTCCTTGTCTTCTCCAGCTTGTGTCTCAGTATGTCACATGCCC 121752
i v iv i i v v v i i
C L1M1_5end#LIN 632 CAAGCACTCCCTTGGCCGCCCCGGCTGGTGTCTCACTAGGTCGCGTGCCC 583
INTRON_3 121753 CCTCAGTCCACTGTGTCTGGGCCTAGTTTAACACTAGGATTTGCCTAAGA 121802
iv vv i i ivi i i i i i
C L1M1_5end#LIN 582 CCCAAGTCCACTGGCTCTGAGCCCAGCACAGCACCAGGACTTGCCCAGGA 533
INTRON_3 121803 GTTGCAGTCCTTATGGCCTAGACTGCCTTTCAAGTTTATTTGGAGACACA 121852
i i i iiv v
C L1M1_5end#LIN 532 ATTGCAGTCCTTGTGGCCTAGACTGCCTTTCAAGTTTATTTAGGACCCCA 483
INTRON_3 121853 GAGTGCTGTAGCCCTCCCTGGCAAGGTTTGCAGGCACTCAAGTTCAGACA 121902
ii v v vv i i v v i v v
C L1M1_5end#LIN 482 GAGCACTTTAGCCCGCGGTGGCGAGGCTTGCCGGAACTCAGGTTCCGACC 433
INTRON_3 121903 GCTGGGATTGGTGATTCCCTTCTGGCTAGGTCTAGTTTAAATGCTCCCTC 121952
v i v i i
C L1M1_5end#LIN 432 GCTGGGATGGGTGATTCCCCTCTGGCTAGGGCTGGTCTAAATGCTCCCTC 383
INTRON_3 121953 CGTGGGTGGGCATCAGCTGAGTTTGGTCCAGTTTTCTTTTCTTCTTTATC 122002
i ----i i iv i i v vi iv v iv
C L1M1_5end#LIN 382 CGTGGGCG----CCGGCTGAGTTCTGCCCGGTGTTGCTTTCCGCTGTGAC 337
INTRON_3 122003 AGGATGGCACTGAGTTC-AATT-----TCTCAGAATTTCTGTGTTCTTCC 122046
iii - v----- i v iv i i i
C L1M1_5end#LIN 336 AGGGCAGCACTGAGTTCCAATGCAAAGTCCCACAATCGCTGCGCTCTCCC 287
INTRON_3 122047 TCCCCTA-GTGCCCAGAGAAACTCTCTGCACCAAGCTGCCACTGCTGGTA 122095
i - v vvvv i i vi v i i vi
C L1M1_5end#LIN 286 TCCCCCAAGTGCACAGATTCTCTCTCCGCGCCACACGGCCGCTGCCGGGG 237
INTRON_3 122096 GGCAGAGAAGGGGTGGTGTCAGAGATTCAGG-CTGTATTTTCTATC-TCT 122143
iii i i i i v i - v i i -
C L1M1_5end#LIN 236 GATGGGGGAGGGGTGGCGTCGGCGATTCAAGACTGTCTTTCCTACCCTCT 187
INTRON_3 122144 TCAGTGCCTCTTTCAGTGATATTAAGTTAAAACCAG 122179
v
C L1M1_5end#LIN 186 TCAGTGCCTCTTTCAGTGATATGAAGTTAAAACCAG 151
Matrix = 20p37g.matrix
Transitions / transversions = 1.83 (214 / 117)
Gap_init rate = 0.01 (17 / 1756), avg. gap size = 2.00 (34 / 17)
+ 1402 3.0 0.0 0.0 INTRON_3 122180 122346 (277835) + L1PA5 LINE/L1 5988 6154 (0) 150
ANNOTATION EVIDENCE:
1402 2.99 0.00 0.00 INTRON_3 122180 122346 277835 + L1PA5_3end LINE/L1 735 901 0 279
INTRON_3 122180 GTTGTGGGGTGGGGGGAGGGGGGAGGGATAGCATTAGGAGATATACCTAA 122229
L1PA5_3end#LI 735 GTTGTGGGGTGGGGGGAGGGGGGAGGGATAGCATTAGGAGATATACCTAA 784
INTRON_3 122230 TGTAAATGACGAGTTAATGGGTGCAGCACACCAACATGGCACATGTATAC 122279
L1PA5_3end#LI 785 TGTAAATGACGAGTTAATGGGTGCAGCACACCAACATGGCACATGTATAC 834
INTRON_3 122280 ATATGTAACAAACCTGCATGTTGTGCACATGTACCCTAAAACTTAAAGTA 122329
i i
L1PA5_3end#LI 835 ATATGTAACAAACCTGCACGTTGTGCACATGTACCCTAGAACTTAAAGTA 884
INTRON_3 122330 TAATAATAATAATAAAA 122346
? v v
L1PA5_3end#LI 885 TAATAAWAAAAAAAAAA 901
Matrix = 18p37g.matrix
Transitions / transversions = 1.00 (2 / 2)
Gap_init rate = 0.00 (0 / 166), avg. gap size = 0.0 (0 / 0)
+10112 19.1 1.6 1.4 INTRON_3 122347 122445 (277736) C L1MA1 LINE/L1 (7415) 150 72 145
ANNOTATION EVIDENCE:
10112 19.13 1.62 1.45 INTRON_3 122347 122445 277736 C L1M1_5end LINE/L1 72 150 3525 330
INTRON_3 122347 AAACAGGTACAATGAGTGCCTCCCTGATTTTTGGTTCTCATGAAGGTGTT 122396
------ vi vi iiv i i
C L1M1_5end#LIN 150 ------GTACTGTGATCGCTCACCTGATTTTTGGTTCTTATGAAGGTGCT 107
INTRON_3 122397 GGGGTTTTTTTTTTTTTTTGGTGTAGATAGTCATT-AACTTGGTGTTCTT 122445
--------------- v i ii - i i
C L1M1_5end#LIN 106 ---------------TTTTTGTGTGGATAGTTGTTCAATTTGGTGTTCCT 72
Matrix = 20p37g.matrix
Transitions / transversions = 2.75 (11 / 4)
Gap_init rate = 0.03 (3 / 98), avg. gap size = 7.33 (22 / 3)
+ 694 25.8 5.4 1.0 INTRON_3 122460 122643 (277538) + MLT1L LTR/ERVL-MaLR 335 526 (84) 151
ANNOTATION EVIDENCE:
694 25.81 5.43 1.04 INTRON_3 122460 122643 277538 + MLT1L LTR/ERVL-MaLR 335 526 84 365
INTRON_3 122460 TGTGTGAGGAGGTGATGTCTGCAGCTGCTGTAGCCATCTTGCTATTATTA 122509
? v i v i v ii v
MLT1L#LTR/ERV 335 TGTGTGWGGATGTGATGCCTGGAGCTGCTGCAGCCATCTTGCGACCATGA 384
INTRON_3 122510 AGGCACAAGCCTGAGGACAAAAGCCAATGTTCTAAGGACATCAGAGAAGA 122559
i v iiv iiiv i iiv vi
MLT1L#LTR/ERV 385 GGGGACAAGCCTGAGAGGAAAAGCCAACACGCTGAGGATGGCAGAGCGGA 434
INTRON_3 122560 AAT-TGGAAAGGACTTG---CATT----ATACCACTAAGCTACTCAATTA 122601
v- i i --- v ---- i i ii i ii v
MLT1L#LTR/ERV 435 AAGATGGAAAGAACCTGGGTCCTTGATGACATCGTTGAGCCGCTGAATTA 484
INTRON_3 122602 ATCAATCCTTAAAACACCTTACTTT--GTCTTCTCTTTTTATGT 122643
i i vi v i i i i-- v -- v
MLT1L#LTR/ERV 485 ACCAACCCTGGAACCGCCCTACCTCTGGACTTCT--TGTTATGT 526
Matrix = 20p37g.matrix
Transitions / transversions = 1.88 (30 / 16)
Gap_init rate = 0.03 (5 / 183), avg. gap size = 2.40 (12 / 5)
+ 694 32.0 4.7 1.8 INTRON_3 122755 123004 (277177) + MIRb SINE/MIR 2 260 (2) 152
ANNOTATION EVIDENCE:
631 33.45 5.60 1.93 INTRON_3 122755 123004 277177 + MIR SINE/MIR 2 260 2 281
INTRON_3 122755 CAATA-AATATGGTGACCAGGAACATGAGCTTTGAAGTGAATCAGATT-- 122801
i - ii i iii i i i ii i i i---- i --
MIR#SINE/MIR 2 CAGTATAGCATAGTGGTTAAGAGCACGGACTCTGGAGC----CAGACTGC 47
INTRON_3 122802 -TATATTTAAATCCCGGCTCTGGTCTTTTATAAGATGAGTAACCTTGGAT 122850
- ivi ii -i vi iv v v i ii
MIR#SINE/MIR 48 CTGGGTTCGAATCCCGGCTCTG-CCACTTACTAGCTGTGTGACCTTGGGC 96
INTRON_3 122851 GAATTATTTAACCTTGCTGATCTCTTTTTTTCTCATCTATGAAATAAGAG 122900
i i i iv vv iiivv i i i ii ii
MIR#SINE/MIR 97 AAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGA 146
INTRON_3 122901 TAATAATTTTAGCTGTTTTACAGTGTTATT---AGGGTTAA------TAA 122941
vv v iii i i v i --- i ------
MIR#SINE/MIR 147 TAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAA 196
INTRON_3 122942 TGCAT-TCACACCCTTCACATAGTATCTCTTACATACTAAGTGCTCAATA 122990
i - v vi v viv i ii vvi v i
MIR#SINE/MIR 197 TACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAATA 246
INTRON_3 122991 AACTCTTATTATTA 123004
ivi vi
MIR#SINE/MIR 247 AATGTTGGTTATTA 260
Matrix = 25p37g.matrix
Transitions / transversions = 2.42 (58 / 24)
Gap_init rate = 0.03 (7 / 249), avg. gap size = 2.71 (19 / 7)
694 31.78 4.52 1.76 INTRON_3 122772 122992 277189 + MIRb SINE/MIR 26 252 16 282
INTRON_3 122772 AGGAACATGAGCTTTGAAGTGAATCAGATTTATATTTAAATCCCGGCTCT 122821
i i i i i v iv ii ivi ii i
MIRb#SINE/MIR 26 AAGAGCACGGGCTTTGGAGTCAGGCAGACCTGGGTTCGAATCCTGGCTCT 75
INTRON_3 122822 GGTCTTTTATAAGATGAGTAACCTTGGATGAATTATTTAACCTTGCTGAT 122871
-i vi iv v v i iii i i i iv v
MIRb#SINE/MIR 76 G-CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAG 124
INTRON_3 122872 CTCTTTTTTTCTCATCTATGAAATAAGAGTAATAATTTTAGCTGTTTTAC 122921
iiivv i i i ii ii --- v iii ii
MIRb#SINE/MIR 125 CCTCAGTTTCCTCATCTGTAAAATGGGGATAATAAT---ACCTACCTCGC 171
INTRON_3 122922 AGTGTTATT---AGGGTTAA------TAATGCAT-TCACACCCTTCACAT 122961
v i --- i ------ - v vi v vi i
MIRb#SINE/MIR 172 AGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCAC 221
INTRON_3 122962 AGTATCTCTTACATACTAAGTGCTCAATAAA 122992
ii vvi i v i
MIRb#SINE/MIR 222 AGTGCCTGGCACACAGTAAGCGCTCAATAAA 252
Matrix = 25p37g.matrix
Transitions / transversions = 2.45 (49 / 20)
Gap_init rate = 0.02 (5 / 220), avg. gap size = 2.80 (14 / 5)
+ 334 24.0 15.5 0.1 INTRON_3 123770 123888 (276293) + MIR3 SINE/MIR 5 138 (130) 153
ANNOTATION EVIDENCE:
297 25.40 13.45 0.75 INTRON_3 123770 123888 276293 + MIRc SINE/MIR 5 138 130 283
INTRON_3 123770 GCACTAGGATACAGAGTAAAAGAGAACTGGGCTGGGAGCCAGGA-GACCA 123818
v iv i i v -i v i v i - v
MIRc#SINE/MIR 5 GCAGTGTGGTGCAGTG-GAAAGAGCACTGGACTTGGAGTCAGGAAGACCT 53
INTRON_3 123819 GTATTC----CATAAC----AGACTTATGA----TGGGACCTTAGA-AAG 123855
vi ---- v ii ----vv iv ---- v i i-
MIRc#SINE/MIR 54 GGGTTCGAGTCCTGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAG 103
INTRON_3 123856 TCACTTCACCTTTCTATGTCT--GTTTACTCATCT 123888
v i iv i -- v
MIRc#SINE/MIR 104 TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCT 138
Matrix = 25p37g.matrix
Transitions / transversions = 1.00 (15 / 15)
Gap_init rate = 0.06 (7 / 118), avg. gap size = 2.43 (17 / 7)
334 23.76 15.84 0.00 INTRON_3 123788 123888 276293 + MIR3 SINE/MIR 19 135 73 284
INTRON_3 123788 AAAGAGAAC-TGGGCTGGGAGCCAGGAGACCAGTATTCCA-TAACAG--- 123832
i i -i i i v vi i - vv ---
MIR3#SINE/MIR 19 AGAGAGAGCACGGACTGGGAGTCAGGAGACCTGGGTTCTAGTCCCAGCTC 68
INTRON_3 123833 --------ACTTATGATGGGACCTTAGA-AAGTCACTTCACCTTTCTATG 123873
-------- ?iivi v i i- i iv
MIR3#SINE/MIR 69 TGCCACTAACTMGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGG 118
INTRON_3 123874 TCT--GTTTACTCATCT 123888
i -- v
MIR3#SINE/MIR 119 CCTCAGTTTCCTCATCT 135
Matrix = 25p37g.matrix
Transitions / transversions = 1.88 (15 / 8)
Gap_init rate = 0.05 (5 / 100), avg. gap size = 3.20 (16 / 5)
+ 31 76.9 0.0 0.0 INTRON_3 123919 123970 (276211) + AT_rich Low_complexity 1 52 (0) 154
ANNOTATION EVIDENCE:
31 76.92 0.00 0.00 INTRON_3 123919 123970 276211 + AT_rich Low_complexity 131 182 118 316
INTRON_3 123919 TTATTTAATTTATTTAATAATTATAAGTAGTTTATGAATTATATATTTAT 123968
?????????v vvvv v vv vv v ??????????????????
AT_rich#Low_c 131 WWWWWWWWWATTAAAAATAAATAATATAATTTWWWWWWWWWWWWWWWWWW 180
INTRON_3 123969 TT 123970
??
AT_rich#Low_c 181 WW 182
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 11)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 195 34.4 5.7 9.3 INTRON_3 123977 124098 (276083) + L2b LINE/L2 3261 3378 (9) 155
ANNOTATION EVIDENCE:
190 34.35 5.74 9.32 INTRON_3 123977 124098 276083 + L2c_3end LINE/L2 352 469 9 285
INTRON_3 123977 TTACCTATTTGATTATTTAATTAAAT----ATCTCC---AGATCAGAGAC 124019
? i i vi vi iv i i i---- v --- iv i
L2c_3end#LINE 352 TTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGAC 401
INTRON_3 124020 TACGTCTGGTTCTATTTGGTATTGTAACCACTAGTATAATGCCTGATGTA 124069
iii vi - i ---- v - i i ----- iiii
L2c_3end#LINE 402 CGTGTCTTATTC-ATCT----TTGTATCC-CCAGCA-----CCTGGCACA 440
INTRON_3 124070 GAGTAAGTGCTCAATAAGTAATTATGAAA 124098
v i i i iv i vi
L2c_3end#LINE 441 TAGTAGGCGCTCAATAAATGTTTGTTGAA 469
Matrix = 25p37g.matrix
Transitions / transversions = 2.70 (27 / 10)
Gap_init rate = 0.05 (6 / 121), avg. gap size = 3.00 (18 / 6)
195 39.30 6.67 1.05 INTRON_3 124009 124098 276083 + L2b_3end LINE/L2 363 457 9 286
INTRON_3 124009 AGATCAGAGACTACGTCTGGTTCTATTTGGTATTGTA--ACCA----CTA 124052
iv i iiv - ii i iiviii i--v ---- i
L2b_3end#LINE 363 AGGGCAGGGACCGGGTCTG-TCTTGTTCACCGCTGTGTCCCCAGCGCCCA 411
INTRON_3 124053 GTATAATGCCTGATGTAGAGTAAGTGCTCAATAAGTAATTATGAAA 124098
i i iv iiii v i i i iv i vi
L2b_3end#LINE 412 GCACAGGGCCTGGCACACAGTAGGTGCTCAGTAAATGTTTGTTGAA 457
Matrix = 25p37g.matrix
Transitions / transversions = 3.38 (27 / 8)
Gap_init rate = 0.03 (3 / 89), avg. gap size = 2.33 (7 / 3)
+ 2281 11.8 0.0 0.7 INTRON_3 124227 124531 (275650) + AluSz SINE/Alu 1 303 (9) 156
ANNOTATION EVIDENCE:
2190 12.21 0.00 0.66 INTRON_3 124227 124531 275650 + AluSx SINE/Alu 1 303 9 269
INTRON_3 124227 GGCTCGGTGCGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGA 124276
iv i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 124277 GGTGGGCAGATGACTTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAGCAT 124326
i i v i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
INTRON_3 124327 GGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGG 124376
i i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGG 150
INTRON_3 124377 TGCATGCCCGTAATCTCAGCTACTAGGGAAGCTGACGGGGGAGAGAATTG 124426
i ii i i v i -- vii i
AluSx#SINE/Al 151 CGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGA--GGCAGGAGAATCG 198
INTRON_3 124427 CTTGAATCTGGGGGGCAGAGGTTGCAGTGAGCCAAGATTGCACCACTGCA 124476
i i i i i i i
AluSx#SINE/Al 199 CTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCA 248
INTRON_3 124477 CTCCAGCCTGGGGGACAGAGTGAGACTCCATCTCAAAAAAAAAAACAACA 124526
v i i v v
AluSx#SINE/Al 249 CTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 298
INTRON_3 124527 AAAAA 124531
AluSx#SINE/Al 299 AAAAA 303
Matrix = 14p37g.matrix
Transitions / transversions = 4.29 (30 / 7)
Gap_init rate = 0.00 (1 / 304), avg. gap size = 2.00 (2 / 1)
+ 395 26.3 1.1 0.0 INTRON_3 125962 126056 (274125) C MIR3 SINE/MIR (14) 194 99 157
ANNOTATION EVIDENCE:
395 26.32 1.05 0.00 INTRON_3 125962 126056 274125 C MIR3 SINE/MIR 99 194 14 287
INTRON_3 125962 TAGATTTTCATA-CTAGAGGAGACCACAAAGATCATGTGGTCAAAACCCC 126010
v v v - i i i vi i v i v v
C MIR3#SINE/MIR 194 TAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCC 145
INTRON_3 126011 TTATTTTATAGGTGGGTAAGCTGAAGTCCAAAGTGGGGAAGTGATT 126056
i i i i v i i i i v v i
C MIR3#SINE/MIR 144 TCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACT 99
Matrix = 25p37g.matrix
Transitions / transversions = 1.50 (15 / 10)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)
+ 245 22.2 1.8 1.8 INTRON_3 126356 126410 (273771) + L2b LINE/L2 3312 3366 (9) 158
ANNOTATION EVIDENCE:
245 22.22 1.82 1.82 INTRON_3 126356 126410 273771 + L2b_3end LINE/L2 403 457 9 288
INTRON_3 126356 CAGTGCCTAAGCATGGTGCCTGGCATGAAGTAGGTGTTCAA-AAATGTGT 126404
i i - ii v iiv i i- v
L2b_3end#LINE 403 CAGCGCCCA-GCACAGGGCCTGGCACACAGTAGGTGCTCAGTAAATGTTT 451
INTRON_3 126405 ATTGAA 126410
i
L2b_3end#LINE 452 GTTGAA 457
Matrix = 25p37g.matrix
Transitions / transversions = 3.00 (9 / 3)
Gap_init rate = 0.04 (2 / 54), avg. gap size = 1.00 (2 / 2)
+12058 10.7 1.6 0.4 INTRON_3 126528 128389 (271792) + L1PA13 LINE/L1 3467 5350 (824) 159
ANNOTATION EVIDENCE:
12058 10.69 1.43 0.43 INTRON_3 126528 128350 271831 + L1PREC2_orf2 LINE/L1 1358 3198 96 331
INTRON_3 126528 TAACAGGCTTTGAAATTGAGGTAGTAATAAATAGGCTATCAACCAAAAAA 126577
ii ii ivi v i
L1PREC2_orf2# 1358 TAACGAGCTCCGAAATTGAATCAGTAATAAATAGCCTACCAACCAAAAAA 1407
INTRON_3 126578 AGCTCAGGAGTAGACAGATTCACAGCCGATTTCTACCAGACATACAAAGA 126627
i vi i v ii
L1PREC2_orf2# 1408 AGCCCAGGACCAGACGGATTCACAGCCGAATTCTACCAGATGTACAAAGA 1457
INTRON_3 126628 AGAACTGGTACTAATTCTACAGAAACTATTTCAAAAAATTGAGGAGGAGG 126677
i i v i v i
L1PREC2_orf2# 1458 AGAGCTGGTACCATTCCTACTGAAACTATTCCAAAAAATTGAGGAGGAGG 1507
INTRON_3 126678 GACTCCTCCCTAACTCATTCTATAAGGCCGGCATCATCCTAATACCAAAA 126727
i i i i
L1PREC2_orf2# 1508 GACTCCTCCCCAACTCATTCTATGAGGCCAGCATCATCCTGATACCAAAA 1557
INTRON_3 126728 CCTGGCAGAGATCCAACAAAAAAAGACAACTTAAGGGCAATATCCTTGAT 126777
iv v v v
L1PREC2_orf2# 1558 CCTGGCAGAGACACAACAAAAAAAGAAAACTTCAGGCCAATATCCTTGAT 1607
INTRON_3 126778 GAACATTGATGCAAAAATCCTCAACAAAATACTGGCAAACCGAATTCAGC 126827
i v i
L1PREC2_orf2# 1608 GAACATCGATGCAAAAATCCTCAACAAAATACTTGCAAACCGAATCCAGC 1657
INTRON_3 126828 AGCATATCAAAAAGCTTATTCACCACTTGAT--AGTAGGCTTCATCCCTG 126875
i v i -- -- i i
L1PREC2_orf2# 1658 AGCACATCAAAAAGCTAATCCACCAC--GATCAAGTAGGCTTTATCCCCG 1705
INTRON_3 126876 GGATGCAAGGTTGGTGCAACATACACAAATCAATAAACATGACTCACCAC 126925
v i ii i i
L1PREC2_orf2# 1706 GGATGCAAGGTTGGTTCAACATACGCAAATCAATAAATGTGATTCATCAC 1755
INTRON_3 126926 ATAAACAGAACTGAAGACAAAA-CCACATGATTATCTCAATAGATGCAGA 126974
i -
L1PREC2_orf2# 1756 ATAAACAGAACTAAAGACAAAAACCACATGATTATCTCAATAGATGCAGA 1805
INTRON_3 126975 AAAGGATTTCCATACAATTCAACATCCATTCATGTTAAAAACTC--AATA 127022
v iv v v --
L1PREC2_orf2# 1806 AAAGGCTTTTGATAAAATTCAACATCCCTTCATGTTAAAAACTCTCAATA 1855
INTRON_3 127023 AACTAGGTATCGAAGGAACATACCTCAAAATAATAAGAGCTATGTGTGAC 127072
i i v i
L1PREC2_orf2# 1856 AACTAGGTATTGAAGGAACATACCTCAAAATAATAAGAGCCATCTATGAC 1905
INTRON_3 127073 AAACCCATAGCCATCATCATACTGAATGGGCAAAATCTAGAAGCATTCCA 127122
i v v i v
L1PREC2_orf2# 1906 AAACCCACAGCCAACATCATACTGAATGGGCAAAAGCTGGAAGCATTCCC 1955
INTRON_3 127123 CTTGAAAACTGGCACAAGACA-GGATAGTCTCTCTCACCACTCCTACTCA 127171
i - ivi i
L1PREC2_orf2# 1956 CTTGAAAACCGGCACAAGACAAGGATGCCCTCTCTCACCACTCCTATTCA 2005
INTRON_3 127172 ATATAGTATTGAAAGTTCTGGCCAGGACAATCAGGCAAGAAAAAGAAATA 127221
i i i ii i
L1PREC2_orf2# 2006 ACATAGTATTGGAAGTCCTGGCCAGAGCAATCAGGCAAGAGAAAGAAATA 2055
INTRON_3 127222 AAAGGCATGCAAATAGGAAGAGAGGAAGTCAAACTATCCTTGTTTAAAGA 127271
i v i iv
L1PREC2_orf2# 2056 AAGGGCATCCAAATAGGAAGAGAGGAAGTCAAACTATCCCTGTTTGCAGA 2105
INTRON_3 127272 TGACATGATTCTATATCTAGAAATTTCCA--GTCTCAGCCCAAAAGCTTC 127319
i vii -- i i
L1PREC2_orf2# 2106 CGACATGATTCTATATCTAGAAAACCCCATAGTCTCGGCCCAAAAGCTCC 2155
INTRON_3 127320 TTAAGAAGATAAACAACTTCAGCAAAGTCCCAGGATACAAAATAAATATG 127369
v vv ii v ii i
L1PREC2_orf2# 2156 TTCAGCTGATAAACAACTTCAGCAAAGTTTCAGGATACAAAATCAACGTA 2205
INTRON_3 127370 CAAAAATCACTAGCATTCCTA--CATCAATAACAGTCAAGCTGAGAGCCA 127417
-- i i i i
L1PREC2_orf2# 2206 CAAAAATCACTAGCATTCCTATACACCAACAACAGCCAAGCCGAGAGCCA 2255
INTRON_3 127418 AGTCAGGAATGAACTCACATTCGCAATTGCCACACACACACACACAAAAT 127467
i i v v v i v v v --- i
L1PREC2_orf2# 2256 AATCAGGAACGCAATCCCATTCACAATTGCCACAAAAAGA---ATAAAAT 2302
INTRON_3 127468 ACCTAAGAATGCAGCTAACTAGGGAGGTAAAA-ATCTCTATAAGGAGAAC 127516
i i i i - i v i
L1PREC2_orf2# 2303 ACCTAGGAATACAGCTAACCAGGGAGGTGAAAGATCTCTACAATGAGAAT 2352
INTRON_3 127517 TACAAACCACTGCTCAAAGAAATCAGAGATGACACAAACAAATGGAAAAA 127566
v
L1PREC2_orf2# 2353 TACAAAACACTGCTCAAAGAAATCAGAGATGACACAAACAAATGGAAAAA 2402
INTRON_3 127567 GATTCCATGCTCATGGATAGGAAGAATCAATATGGTTAAAATGGCCATAT 127616
v vi i
L1PREC2_orf2# 2403 CATTCCATGCTCATGGATAGGAAGAATCAATATCATTAAAATGGCCATAC 2452
INTRON_3 127617 TGCCGAAAGCAATTTATAGATTCAGTGTTATGCCTATTAAACTACCATTG 127666
v i i i v i v
L1PREC2_orf2# 2453 TGCCCAAAGCAATTTACAGATTCAATGCTATTCCTATCAAACTACCAATG 2502
INTRON_3 127667 ACATTGTTCACAGAACTAGAAAAAAAAACTATTTTAAAATTCATATGGAA 127716
v ---
L1PREC2_orf2# 2503 ACATTCTTCACAGAACTAGAAAAAA---CTATTTTAAAATTCATATGGAA 2549
INTRON_3 127717 CCAAAAAAGAGCCTGAATACCCAAGGCAACCCTAAGCAGAAAGAACAAGG 127766
i v i i i
L1PREC2_orf2# 2550 CCAAAAAAGAGCCCGAATAGCCAAGGCAATCCTAAGCAAAAAGAACAAAG 2599
INTRON_3 127767 CTGAAGG----AC--TACCTGACTTCAAACTATACCACAGGACTACAGTA 127810
i ---- -- ii i i
L1PREC2_orf2# 2600 CTGGAGGCATCACGTTACCCAACTTCAAACTATACTACAGGGCTACAGTA 2649
INTRON_3 127811 ACCAAAACATCATGGTACTGGTACAAAAACAGACACATAGACCAGTAGAA 127860
v i i
L1PREC2_orf2# 2650 ACCAAAACAGCATGGTACTGGTACAAAAACAGACACATAGACCAATGGAA 2699
INTRON_3 127861 CCAAATACAGAACTTGGAAATAAGACCACACACCTACAACTGTCTGATCT 127910
vi v i iii i i ii
L1PREC2_orf2# 2700 CAGAATAGAGAGCCCAGAAATAAGGCCGCACACCTACAACCATCTGATCT 2749
INTRON_3 127911 TCGACAAACCTGATAAAAATAAGCAATGGGGAAAGGATTCCCTATTCAAT 127960
v i i i
L1PREC2_orf2# 2750 TCGACAAAGCTGACAAAAACAAGCAATGGGGAAAGGACTCCCTATTCAAT 2799
INTRON_3 127961 AAATGGTGCTGGGATAAATGACTAGCAATATGCAGAAGATTAAAACTGGA 128010
v i v i
L1PREC2_orf2# 2800 AAATGGTGCTGGGATAACTGGCTAGCCATATGCAGAAGATTGAAACTGGA 2849
INTRON_3 128011 ACCTTTCCTTATACCATATATAAAAATTAA-----GATGGATTAAAGGCT 128055
v i i i i ----- i
L1PREC2_orf2# 2850 CCCCTTCCTTACACCATATACAAAAATCAACTCAAGATGGATTAAAGACT 2899
INTRON_3 128056 TAAATGCAACACTCAAAACTTTAAAATCCCTGGAAGGCAACCTAGACAAT 128105
i v i v v i i
L1PREC2_orf2# 2900 TAAATGTAAAACCCAAAACTATAAAAACCCTGGAAGACAACCTAGGCAAT 2949
INTRON_3 128106 ACAATTTGGGACATAGGCACAGGCAAAGATTTCATGATGAAGATGCCAAA 128155
v iv v i i i
L1PREC2_orf2# 2950 ACCATTCTGGACATAGGAACGGGCAAAGATTTCATGACGAAGACGCCAAA 2999
INTRON_3 128156 AGCAATTGCAACTAAAGCAAAAATTGACAAATGGGATCTGATTAAACTAA 128205
v i v
L1PREC2_orf2# 3000 AGCAATTGCAACAAAAGCAAAAATTGACAAATGGGATCTAATTAAACTTA 3049
INTRON_3 128206 AGAGCTTCTGCACAGCAAAAGAAACTATTAACAGAGTAAATAG----CCT 128251
i i ----
L1PREC2_orf2# 3050 AGAGCTTCTGCACAGCAAAAGAAACTATCAACAGAGTAAACAGACAACCT 3099
INTRON_3 128252 ACAGAATGGTAGAACATTTTTGCAAACTATGCATCCAACAAAGGTCAACT 128301
v v v ii v v
L1PREC2_orf2# 3100 ACAGAATGGGAGAAAATATTTGCAAACTATGCATCTGACAAAGGTCTAAT 3149
INTRON_3 128302 ATCCAGCATCTACAAGGAACTTAAGCAAATTTATAGGAAAAAAACAAGC 128350
i i i i i
L1PREC2_orf2# 3150 ATCCAGCATCTATAAGGAACTTAAACAAATTTACAAGAAAAAAACAAAC 3198
Matrix = 20p37g.matrix
Transitions / transversions = 2.03 (130 / 64)
Gap_init rate = 0.01 (14 / 1822), avg. gap size = 2.43 (34 / 14)
540 10.11 4.49 0.00 INTRON_3 128301 128389 271792 + L1PA11_3end LINE/L1 5 97 824 332
INTRON_3 128301 TATCCAGCATCTACAAGGAACTTAAGCAAATTTATAGGAAAAAAACAAGC 128350
i i i i
L1PA11_3end#L 5 TATCCAGCATCTACAAGGAACTTAAACAAATTTACAAGAAAAAAACAAAC 54
INTRON_3 128351 ----CCATAAAAAAGTGGGCAAAGGAAGTGAACAGAAACTTTT 128389
---- v vi v i
L1PA11_3end#L 55 AACCCCATTAAAAAGTGGGCAAAGGACATGAACAGACACTTCT 97
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (6 / 3)
Gap_init rate = 0.01 (1 / 88), avg. gap size = 4.00 (4 / 1)
+ 7594 2.8 0.6 0.3 INTRON_3 128407 129486 (270695) C L1PA4 LINE/L1 (3) 6152 5072 160
ANNOTATION EVIDENCE:
7594 2.24 0.45 0.33 INTRON_3 128407 129304 270877 C L1PA4_3end LINE/L1 1 899 3 333
INTRON_3 128407 TTTATTTATTTTAATTATACTTTAAGTTTTAGGGTACATGTGCACAACGT 128456
v ---
C L1PA4_3end#LI 899 TTTTTTTATT---ATTATACTTTAAGTTTTAGGGTACATGTGCACAACGT 853
INTRON_3 128457 GCAGGTTAGTTACATATGTATACATGTGCCATGTTGGTGTGCTGCACCCA 128506
v
C L1PA4_3end#LI 852 GCAGGTTTGTTACATATGTATACATGTGCCATGTTGGTGTGCTGCACCCA 803
INTRON_3 128507 TTAACTCGTCCTTTAACATTAGGTATATCTCCTAATGCTATCCCTCCCCT 128556
v i
C L1PA4_3end#LI 802 TTAACTCGTCATTTAACATTAGGTATATCTCCTAATGCTATCCCTCCCCC 753
INTRON_3 128557 CTCCCCCCACCCCACAACAGGCCCCGGTGTTTGATGTTCCCCTTCCTGTG 128606
v
C L1PA4_3end#LI 752 CTCCCCCCACCCCACAACAGGCCCCGGTGTGTGATGTTCCCCTTCCTGTG 703
INTRON_3 128607 TCCATGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAACATGCAGT 128656
i
C L1PA4_3end#LI 702 TCCATGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAACATGCGGT 653
INTRON_3 128657 GTTTGGTTTTTTGTCCTTGTGATAGTTTGCTGAGAATGATGGTTTCCAGC 128706
i
C L1PA4_3end#LI 652 GTTTGGTTTTTTGTCCTTGCGATAGTTTGCTGAGAATGATGGTTTCCAGC 603
INTRON_3 128707 TTCATCCATGTCCCTACAAAGGACACGAACTCATTATTTTTTATGGCTGC 128756
i i
C L1PA4_3end#LI 602 TTCATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGC 553
INTRON_3 128757 ATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCA 128806
C L1PA4_3end#LI 552 ATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCA 503
INTRON_3 128807 TTGTTGGACATTTGGTTTCGTTCCAAGTCTTTTCTGTTGTGAATAGTGCC 128856
v v v i
C L1PA4_3end#LI 502 TTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCC 453
INTRON_3 128857 ACAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAATC 128906
i
C L1PA4_3end#LI 452 GCAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAATC 403
INTRON_3 128907 CTTTGGATATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTA 128956
i
C L1PA4_3end#LI 402 CTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTA 353
INTRON_3 128957 GTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACT 129006
C L1PA4_3end#LI 352 GTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACT 303
INTRON_3 129007 AGTTGACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCC 129056
v
C L1PA4_3end#LI 302 AGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCC 253
INTRON_3 129057 TCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTG 129106
i
C L1PA4_3end#LI 252 TCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATCGCCATTCTAACTG 203
INTRON_3 129107 GTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCC 129156
C L1PA4_3end#LI 202 GTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCC 153
INTRON_3 129157 AGTGATGATGAGCCTTTTTTCATGTGTCTTTTGGCTGCATAAATGTCTTC 129206
v
C L1PA4_3end#LI 152 AGTGATGATGAGCATTTTTTCATGTGTCTTTTGGCTGCATAAATGTCTTC 103
INTRON_3 129207 TTTTGAGAAGCATCTGTTCATATCCTTCGCCCACTTTTTGATGGGGTTGT 129256
ii
C L1PA4_3end#LI 102 TTTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGATGGGGTTGT 53
INTRON_3 129257 TT----TTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATT 129302
----
C L1PA4_3end#LI 52 TTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATT 3
INTRON_3 129303 AG 129304
C L1PA4_3end#LI 2 AG 1
Matrix = 20p37g.matrix
Transitions / transversions = 1.22 (11 / 9)
Gap_init rate = 0.00 (2 / 897), avg. gap size = 3.50 (7 / 2)
2479 5.49 1.22 0.00 INTRON_3 129159 129486 270695 C L1P1_orf2 LINE/L1 2963 3294 0 334
INTRON_3 129159 TGATGATGAGCCTTTTTTCATGTGTCTTTTGGCTGCATAAATGTCTTCTT 129208
v i i
C L1P1_orf2#LIN 3294 TGATGATGAGCATTTCTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTT 3245
INTRON_3 129209 TTGAGAAGCATCTGTTCATATCCTTCGCCCACTTTTTGATGGGGTTGTTT 129258
ii i
C L1P1_orf2#LIN 3244 TTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTT 3195
INTRON_3 129259 ----TTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAG 129304
----
C L1P1_orf2#LIN 3194 GTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAG 3145
INTRON_3 129305 CCCTTTGTCAGATGAGTAGATTGCAAAAATTTTCTCCCATTCTGTAGGTT 129354
i i vi
C L1P1_orf2#LIN 3144 CCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATGTTGTAGGTT 3095
INTRON_3 129355 GGCTGTTCGCTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTGAGT 129404
v i v
C L1P1_orf2#LIN 3094 GCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGT 3045
INTRON_3 129405 TTAATTAGATCCCATTTGTCAATTTTGTCTTTTGTTGCCATTGCTTTTGG 129454
v
C L1P1_orf2#LIN 3044 TTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGG 2995
INTRON_3 129455 TGTTTTAGACATGAAGTCCTTGCCCATGTTTA 129486
i i ii
C L1P1_orf2#LIN 2994 TGTTTTGGACATGAAGTCCTTGCCCACGCCTA 2963
Matrix = 20p37g.matrix
Transitions / transversions = 2.60 (13 / 5)
Gap_init rate = 0.00 (1 / 327), avg. gap size = 4.00 (4 / 1)
+ 3787 8.3 2.3 0.0 INTRON_3 129484 130014 (270167) + L1PA13 LINE/L1 5350 5892 (271) 159 *
ANNOTATION EVIDENCE:
3787 8.29 2.26 0.00 INTRON_3 129484 130014 270167 + L1PA13_3end LINE/L1 97 639 271 335
INTRON_3 129484 TTAAAAGAAGACATACATGCAACCGACAGTCGT--GAAGAAAAGCTCAAC 129531
i ii i i i -- i
L1PA13_3end#L 97 TCAAAAGAAGACATACATGCGGCCAACAATCATATGAAAAAAAGCTCAAC 146
INTRON_3 129532 ATCACCAATCACTAGAGAAACGCATATCAAAACCAC---GAGATACCATC 129578
ii i i v ---
L1PA13_3end#L 147 ATCACTGATCATTAGAGAAATGCAAATCAAAACCACAATGAGATACCATC 196
INTRON_3 129579 TCACACCAGTTAGAATGACGATTATTAAAAAGTCAAAAAATAACATATGC 129628
i i v v
L1PA13_3end#L 197 TCACACCAGTCAGAATGGCTATTATTAAAAAGTCAAAAAATAACAGATGC 246
INTRON_3 129629 TGGTGAGGTTGTGGAGAAAACGGAACACTTATACACTGTTTGTGGGGGTG 129678
i i v i v i
L1PA13_3end#L 247 TGGCGAGGTTGCGGAGAAAAAGGAACGCTTATACACTGTTGGTGGGAGTG 296
INTRON_3 129679 TAAAT-AGTTCAACCATTGTGAAAAACAGTGTGGCGATTCCTCAGAGACC 129727
- i i i
L1PA13_3end#L 297 TAAATTAGTTCAACCATTGTGGAAGACAGTGTGGCGATTCCTCAAAGACC 346
INTRON_3 129728 TAAAGACAGAAATACCTTTCAACCCAGCAATCCCATTACTGAGTATATAC 129777
v i i
L1PA13_3end#L 347 TAAAGACAGAAATACCATTCGACCCAGCAATCCCATTACTGGGTATATAC 396
INTRON_3 129778 CCAAAGGAATACAAAGCATTCTATTATGAAGACACATGCATGCACATGTT 129827
i v i i i
L1PA13_3end#L 397 CCAAAGGAATATAAATCATTCTATTATAAAGACACATGCACGCATATGTT 446
INTRON_3 129828 CATTGCAACACTATTCACAATAGCAAAGACATGGAATCAACCTAAGTGGC 129877
i i v
L1PA13_3end#L 447 CATTGCAGCACTATTCACAATAGCAAAGACATGGAATCAACCTAAATGCC 496
INTRON_3 129878 CATGAATGATACACTGGATAAAGAAAACATCATACATATACACCATGGAA 129927
v v ii vi
L1PA13_3end#L 497 CATCAATGATAGACTGGATAAAGAAAATGTGGTACATATACACCATGGAA 546
INTRON_3 129928 T-----GCAGCCATAAAAA-GAATGAGATCATGTCCTTTGCAGGGACATG 129971
----- -
L1PA13_3end#L 547 TACTATGCAGCCATAAAAAAGAATGAGATCATGTCCTTTGCAGGGACATG 596
INTRON_3 129972 GATGGAGCTGGAGGCCATTATCCTTAGCAAACTAACACATGAA 130014
i v
L1PA13_3end#L 597 GATGGAGCTGGAGGCCATTATCCTTAGCAAACTAACGCAGGAA 639
Matrix = 20p37g.matrix
Transitions / transversions = 2.67 (32 / 12)
Gap_init rate = 0.01 (5 / 530), avg. gap size = 2.40 (12 / 5)
+ 2152 11.0 0.0 0.0 INTRON_3 130477 130749 (269432) + AluSx SINE/Alu 11 283 (29) 161
ANNOTATION EVIDENCE:
2078 10.99 0.00 0.00 INTRON_3 130477 130749 269432 + AluSx SINE/Alu 11 283 29 270
INTRON_3 130477 GGTAGCTCACGCCTGTAATCCCAGCGCTTTGGGAGGCTGAGGTGGGTGGA 130526
i i i i i
AluSx#SINE/Al 11 GGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGA 60
INTRON_3 130527 TCACCTGAGGTCAGGAGTTTGAGACCAGCCCAGCCAACATGGTGAAGGCC 130576
i ii iv
AluSx#SINE/Al 61 TCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCC 110
INTRON_3 130577 CGTCTCTACTAAAAATACAAAAATTAGGTGGGCATGGTGGCACGCACCTG 130626
vi i i i
AluSx#SINE/Al 111 CGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTG 160
INTRON_3 130627 TAATACCAGCTACTCGGGAGGCTGAGACAGGAGAATTGCTTGAACCTGGG 130676
v i i i
AluSx#SINE/Al 161 TAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG 210
INTRON_3 130677 AGGCGGAGGTTGCAGTGAGCTGTGATCGTGCCAGTACACTCCAGCCTGGG 130726
i v i v i
AluSx#SINE/Al 211 AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGG 260
INTRON_3 130727 TGACAAAGCAAGACTGTATCTCA 130749
i i i vii
AluSx#SINE/Al 261 CGACAGAGCGAGACTCCGTCTCA 283
Matrix = 14p37g.matrix
Transitions / transversions = 4.00 (24 / 6)
Gap_init rate = 0.00 (0 / 272), avg. gap size = 0.0 (0 / 0)
+ 213 6.5 0.0 0.0 INTRON_3 130750 130780 (269401) + (TAA)n Simple_repeat 2 32 (0) 162
ANNOTATION EVIDENCE:
213 6.45 0.00 0.00 INTRON_3 130750 130780 269401 + (TAA)n Simple_repeat 2 32 148 362
INTRON_3 130750 AATAATAATAATAATCATAATCATAATAATA 130780
v v
(TAA)n#Simple 2 AATAATAATAATAATAATAATAATAATAATA 32
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 2)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)
+ 36 89.1 0.0 0.0 INTRON_3 132103 132166 (268015) + AT_rich Low_complexity 1 64 (0) 163
ANNOTATION EVIDENCE:
36 89.06 0.00 0.00 INTRON_3 132103 132166 268015 + AT_rich Low_complexity 88 151 149 317
INTRON_3 132103 AAATAATATTCTATAAATATTATAAAATAATTTAGCTATATTATTTTTAA 132152
??????????????????????????????????????????????????
AT_rich#Low_c 88 WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWW 137
INTRON_3 132153 GTATTAAATTATAT 132166
?? vvvv v
AT_rich#Low_c 138 WWATTAAAAATAAA 151
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 5)
Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0)
+ 2366 10.4 0.0 0.0 INTRON_3 132464 132762 (267419) C AluSc SINE/Alu (10) 299 1 164
ANNOTATION EVIDENCE:
2133 11.71 1.00 0.00 INTRON_3 132464 132762 267419 C AluSx SINE/Alu 1 302 10 271
INTRON_3 132464 TTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTCGCC-AGGCT 132512
i i -
C AluSx#SINE/Al 302 TTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCT 253
INTRON_3 132513 GGAGTGCAGTGGCATGATGTCAGCTCACTGCAACCCCTGCCTCTTGGGTT 132562
ii v i i i ii
C AluSx#SINE/Al 252 GGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTT 203
INTRON_3 132563 CAAGCAATTCTCCTGCCTCAGTCTCCCGAGTAGCTGGGACTACCAGCACA 132612
i i i vi i i
C AluSx#SINE/Al 202 CAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCG 153
INTRON_3 132613 TGCCACCATGCCTGGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCA 132662
i i i i
C AluSx#SINE/Al 152 CGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCA 103
INTRON_3 132663 CGACGTTGGCTAGGATGGTCTCTATCTCTTGACGTC--GTGATCTGCCTG 132710
v i i v v v i v -- i i
C AluSx#SINE/Al 102 CCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCG 53
INTRON_3 132711 CCTCAGCCTCCCAAAGTGCTGGGATTACAGGCTTGAGCCACCACGCCCAG 132760
i v i i
C AluSx#SINE/Al 52 CCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGG 3
INTRON_3 132761 CC 132762
C AluSx#SINE/Al 2 CC 1
Matrix = 14p37g.matrix
Transitions / transversions = 3.38 (27 / 8)
Gap_init rate = 0.01 (2 / 298), avg. gap size = 1.50 (3 / 2)
+ 1950 8.0 1.8 1.1 INTRON_3 133103 133381 (266800) + L1PA13 LINE/L1 5881 6161 (2) 159
ANNOTATION EVIDENCE:
1950 7.98 1.79 1.07 INTRON_3 133103 133381 266800 + L1PA13_3end LINE/L1 628 908 2 280
INTRON_3 133103 CTAACACAGGAACAGAAAACTAAATACCACATGTTCTCATTTACAAATGG 133152
i i i i i i
L1PA13_3end#L 628 CTAACGCAGGAACAGAAAACCAAATACCGCATGTTCTCACTTATAAGTGG 677
INTRON_3 133153 GAACTAAATGATGAGAACACATGGACACATAGAGAGGAACACAACACACA 133202
i i --
L1PA13_3end#L 678 GAGCTAAATGATGAGAACACATGGACACATAGAGGGGAACA--ACACACA 725
INTRON_3 133203 TTGGGGCCTACAGAGGGGTTGAAGGGTGGGAGGAGGGAGAGGATCAGGAA 133252
i iv ii - i
L1PA13_3end#L 726 CTGGGGCCTATTGGAGGGT-GGAGGGTGGGAGGAGGGAGAGGATCAGGAA 774
INTRON_3 133253 ATATAACTGATGGGTACTAGGTTTAATACCTGGGTGATGAAATAATCTGT 133302
v i i
L1PA13_3end#L 775 AAATAACTAATGGGTACTAGGCTTAATACCTGGGTGATGAAATAATCTGT 824
INTRON_3 133303 ACAGCAAACCCCCATGACACAAGTTTAAATATGTGACAAACCTGCACATG 133352
i vv i
L1PA13_3end#L 825 ACAACAAACCCCCATGACACAAGTTTACCTATGTAACAAACCTGCACATG 874
INTRON_3 133353 TACCCCTGAACTTAACA-----GTTAAAAAAAAA 133381
v -----
L1PA13_3end#L 875 TACCCCTGAACTTAAAATAAAAGTTAAAAAAAAA 908
Matrix = 18p37g.matrix
Transitions / transversions = 3.40 (17 / 5)
Gap_init rate = 0.01 (3 / 278), avg. gap size = 2.67 (8 / 3)
+ 543 32.9 4.8 5.4 INTRON_3 133518 133832 (266349) C L3 LINE/CR1 (4) 4485 4173 165
ANNOTATION EVIDENCE:
543 32.90 4.76 5.43 INTRON_3 133518 133832 266349 C L3 LINE/CR1 4173 4485 4 289
INTRON_3 133518 GAATCCTAGATTCTTAGAGTTAGATGGCTTCTCAGAGGTTATCTGAGCTA 133567
vi v i i v vvi i i iiv i
C L3#LINE/CR1 4485 GAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCA 4436
INTRON_3 133568 ATCTACTACCT------TGATTTCCCTTTTCAGTAAAGCTGCCAAATTGT 133611
? v i i i------v v i i i v ii vvv v i v
C L3#LINE/CR1 4435 ANCTCCCATCCAATGCAGGAATCCCTTCTACAACATCCCTGACAAGTGGT 4386
INTRON_3 133612 TAACCAGGTTTTGCTTAAGCACTTCCAG-AATAGGTTGGCCTCT-CATAC 133659
i v vi i i ii i -i i vv vi v - v v
C L3#LINE/CR1 4385 CATCCAGCCTCTGCTTGAATACCTCCAGTGACAGGGAGCTCACTACCTCC 4336
INTRON_3 133660 CATGAAGTTGCCCAGTC-ATCTTTGAATTTACTTAAGAAGTTATGCCTCT 133708
-- i iv v - i i i---------- i v vi v
C L3#LINE/CR1 4335 CA--AGGCAGCCCATTCCATTTTTGGAC----------AGCTCTGATTGT 4298
INTRON_3 133709 AAAAACAAGTTCTT----ATCTTTATCTATATACTGCCTCTCTTAAAATT 133754
v i -- ---- v v v iv vv i -iv i
C L3#LINE/CR1 4297 TAGAA--AGTTCTTCCTTATATTGAGCTGAAATCTGCCTCCCT-GTAACT 4251
INTRON_3 133755 TCTGCCCATTTATGGTAATTCTGATCTCTGGAATCA-ATAGGAGTCAAGT 133803
ii i v vv i vi ii - i i --i
C L3#LINE/CR1 4250 TCCACCCACTGATCCTAGTTCTGCCCTCTGGAGCCACACAGAA--TAAGT 4203
INTRON_3 133804 A-AATCCCTCTTTCACAAGGCTGCAATTCA 133832
v- i v i v vv
C L3#LINE/CR1 4202 CTAATCCCTCTTCCACATGACAGCCCTTCA 4173
Matrix = 25p37g.matrix
Transitions / transversions = 1.16 (52 / 45)
Gap_init rate = 0.04 (12 / 314), avg. gap size = 2.67 (32 / 12)
+ 257 32.7 11.8 0.0 INTRON_3 134217 134326 (265855) + Charlie18a DNA/hAT-Charlie 6 128 (214) 166 *
ANNOTATION EVIDENCE:
257 32.73 11.82 0.00 INTRON_3 134217 134326 265855 + Charlie18a DNA/hAT-Charlie 6 128 214 366
INTRON_3 134217 GTTCCCAAACAATGGTCTGTAAATGAATTTCAGTCTATGA---AGCTTTT 134263
iivi i iii iv i vi i ii --- i i
Charlie18a#DN 6 GTTCCCAAATGCCGGTCCGCGGACCAGTGCCGGTCCGTGACGAAGTTTTC 55
INTRON_3 134264 AGCAACTTGGGAC---------AAAATAAGAACCAAGTGACAAGTTTTT- 134303
v iiiii v i --------- i v v iiii -
Charlie18a#DN 56 ACCGGTCCGCGGCGAAATGAGAAAAATAAGGACAATGTAGTGAGTTTTTC 105
INTRON_3 134304 ATGAAACTAAATTTATTTAATTT 134326
i i i
Charlie18a#DN 106 ATAAAGCTAAATTTATTCAATTT 128
Matrix = 20p37g.matrix
Transitions / transversions = 4.14 (29 / 7)
Gap_init rate = 0.03 (3 / 109), avg. gap size = 4.33 (13 / 3)
+ 667 18.8 10.2 7.0 INTRON_3 134299 134533 (265648) + Charlie18a DNA/hAT-Charlie 101 342 (0) 167
ANNOTATION EVIDENCE:
667 18.77 10.21 7.02 INTRON_3 134299 134533 265648 + Charlie18a DNA/hAT-Charlie 101 342 0 367
INTRON_3 134299 TTTTTATGAAACTAAATTTATTTAATTTTTAAG-----------TTCCAA 134337
i i i i vv i ----------- ii
Charlie18a#DN 101 TTTTCATAAAGCTAAATTTATTCAATTTAAAGGACTGTCCTTTATTCTGA 150
INTRON_3 134338 GTTTATGTCCTTCCTACGTTTTTGTTATTGAAGT----------TATGAA 134377
v v v i i i ----------
Charlie18a#DN 151 GATTATGTCCTTCCTACTTTTTTGGTGTTAAAATGTCTTTCTTTTATGAA 200
INTRON_3 134378 ATGATGTTGATAATTAATGGTAGTTGCTATTTTA--AATGTCTTTGTTTT 134425
v i vi i i v-- i ii v
Charlie18a#DN 201 ATGATGGTGATAGTAGATGGTAGTTGTTGTTTTTTTAATGTCCTTACTTG 250
INTRON_3 134426 GCAAAAGCAAATGACTATGAAAAAAATGAGCAACTCTATTTTGGTGCCCT 134475
v------------- i vi i v i v -
Charlie18a#DN 251 GCAAAAT-------------AAAAAGTTGGCAACCCTATGTCGGTCCCC- 286
INTRON_3 134476 GATATTTTTCTTTTTGAAATATTACTGGTCC-TGAAATCCCTAAGTATGT 134524
- v -- v - vv v v
Charlie18a#DN 287 -AAATTTTT--TTTTGAAATTTTACTGGTCCATGAAATCCAAAAGTCTGG 333
INTRON_3 134525 GAATCACTG 134533
i
Charlie18a#DN 334 GAACCACTG 342
Matrix = 20p37g.matrix
Transitions / transversions = 1.16 (22 / 19)
Gap_init rate = 0.03 (7 / 234), avg. gap size = 5.86 (41 / 7)
+ 351 30.2 2.8 5.8 INTRON_3 134590 134765 (265416) + AmnSINE1 SINE/Deu 62 232 (343) 168
ANNOTATION EVIDENCE:
351 30.18 2.84 5.85 INTRON_3 134590 134765 265416 + AmnSINE1 SINE/Deu 62 232 343 368
INTRON_3 134590 GGTTTAATCAG-ACTTGGACATGAAACCCCTATGGAAACC-AGGTGCTAC 134637
ii ii - iiv i i i v - i
AmnSINE1#SINE 62 GGCCTGGTCAGTACTTGGATGGGAGACCTCCAAGGAAACCCAGGTGCTGC 111
INTRON_3 134638 AGGAACTGAAGTTTGGAATTCTACAAGAAACTGGCTGCCTTTTCCCTCTG 134687
v iv i v vi ---- v iv --v i
AmnSINE1#SINE 112 AGGAAGTGGTGCTGGTGATTC----AGTAGGTGGC--ACTCTTCCCTCTG 155
INTRON_3 134688 GTCCACTGTTGAATCAGTACTTCCAG-ATGGTGGCAAGGA--AATGTGGC 134734
ivi v ii i i i- -i vi i i-- v -
AmnSINE1#SINE 156 AGTCAGTACTGAACCAGTGCC-CCAGCGTGGTGTTAGGGGGCACTGTG-C 203
INTRON_3 134735 TGCCAGTAGTAACCCGGCTCTGGAGGGAGAC 134765
ii vi i-- v i v iiv
AmnSINE1#SINE 204 TGCTGGAGGTG--CCGTCTTTCGGATGAGAC 232
Matrix = 20p37g.matrix
Transitions / transversions = 1.94 (33 / 17)
Gap_init rate = 0.05 (9 / 175), avg. gap size = 1.67 (15 / 9)
+ 1649 17.8 0.9 5.6 INTRON_3 134795 135114 (265067) C AluJr SINE/Alu (6) 306 1 169
ANNOTATION EVIDENCE:
1299 22.17 0.94 5.56 INTRON_3 134795 135114 265067 C AluJb SINE/Alu 1 306 6 272
INTRON_3 134795 TTTTTGTTTGTTTGTTTGTTTTTTGAGACTGGATCTCAGTCTGTCATCCA 134844
v v v v v i iv ii
C AluJb#SINE/Al 306 TTTTTTTTTTTTTTTTTTTTTTTTGAGACAGGGTCTCGCTCTGTCGCCCA 257
INTRON_3 134845 GGCAGGAGTGCAGTGGTGCAGTAATAGCTCATTGCAGCCTCAAACTCCTG 134894
v i ii v ii i i v i
C AluJb#SINE/Al 256 GGCTGGAGTGCAGTGGCGCGATCACGGCTCACTGCAGCCTCGACCTCCCG 207
INTRON_3 134895 GGCTCATGCAATTCACCCACCTCAGCCTCCTGAGTAGCTAGGCCTACAGG 134944
v i i v ii i i v
C AluJb#SINE/Al 206 GGCTCAAGCGATCCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGG 157
INTRON_3 134945 GCATGTACCAGCATGCCTGGC-AATGTTTTTTTTTTTTTTTTTTTTTTTT 134993
- ii ii v i i - ---------------- v v
C AluJb#SINE/Al 156 -CGCGCGCCACCACGCCCGGCTAAT----------------TTTTGTATT 124
INTRON_3 134994 TTTTGTAGACACTGGGCCTTGTTATGTTGCCCAGGCTGGTTGTGAACCCC 135043
v v ii iiii ivi i
C AluJb#SINE/Al 123 TTTTGTAGAGACGGGGTTTCACCATGTTGCCCAGGCTGGTCTCGAACTCC 74
INTRON_3 135044 TGGCTTCTAGCGATCCTCCTACCTCAGCTTTCCAGAGTGCTGGGATTATA 135093
vi v i ii i i i i i
C AluJb#SINE/Al 73 TGGGCTCAAGTGATCCTCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACA 24
INTRON_3 135094 GT--TGAGCCACTGTGTCTGGCC 135114
v-- i i i i
C AluJb#SINE/Al 23 GGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 2.19 (46 / 21)
Gap_init rate = 0.01 (4 / 319), avg. gap size = 5.00 (20 / 4)
+ 321 37.7 3.4 1.3 INTRON_3 136297 136444 (263737) + MIRb SINE/MIR 2 152 (116) 170
ANNOTATION EVIDENCE:
321 37.66 3.38 1.32 INTRON_3 136297 136444 263737 + MIRb SINE/MIR 2 152 116 290
INTRON_3 136297 AGAGGGTGGCAGCATCATGTAGCATAAAAAGCATTAGCCAGGAAGTTGGA 136346
-- i vi i iiv i ivi ivv i ii i
MIRb#SINE/MIR 2 AGAGGG--GCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGG 49
INTRON_3 136347 C---CCTGAATCTCCGCTTTAGGTCCACTGCTTACAGACTGGTTGGACCT 136393
--- ii iivviiii i v ii ii vii vv iv i
MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCTGGCTCTGCCACTTACTAGCTGTGTGACCTT 99
INTRON_3 136394 GGGTAAGGAACTTAACCTCACTGCTCCT--GCTTTCTCAGATGTGAAATA 136441
i vv v vv -- i i vv i i
MIRb#SINE/MIR 100 GGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 149
INTRON_3 136442 AGG 136444
i
MIRb#SINE/MIR 150 GGG 152
Matrix = 25p37g.matrix
Transitions / transversions = 1.89 (36 / 19)
Gap_init rate = 0.02 (3 / 147), avg. gap size = 2.33 (7 / 3)
+ 3684 29.6 5.7 5.6 INTRON_3 136632 138679 (261502) + L1M3e LINE/L1 1 2113 (4917) 171
ANNOTATION EVIDENCE:
3684 29.55 5.48 5.61 INTRON_3 136632 138363 261818 + L1M3e_5end LINE/L1 1 1730 383 336
INTRON_3 136632 GATGTCAGCAAGATGGCAGAATATGACTTTCCAGTGATTGTCCTCTGCAA 136681
ii i v i v i -i i
L1M3e_5end#LI 1 GACATCAGCAAGATGGCGGAATAGGACTTTCCAGCGCTCGTCCTC-ACAG 49
INTRON_3 136682 AAACATCACTTTGAACAACTATTCATGCATGAAAATTCCTTTACATCAGC 136731
v i i i v i vv
L1M3e_5end#LI 50 AAACATCAATTTGAACAACTATCCACGCACGAAAATACCTTCACAAGAGC 99
INTRON_3 136732 AACAGAAGCCAGGTGAGAGATTTCAGCACTTAAGTATAGCACAGAAATAA 136781
v vi i v ? i ii i
L1M3e_5end#LI 100 TAAGGAAACCAGGTGAGAGATTACAGYACCTGGGTGTAGCACAGAAATAA 149
INTRON_3 136782 GAAGGGGCACATTGAAGAGGGTAGGAAAGACAGTTTTACATCACCTGCAT 136831
ii i i i i i i
L1M3e_5end#LI 150 GAAAAGACGCATTGAAGAGGGTAGGAAGGACAGTTTTACATTACCCGCGT 199
INTRON_3 136832 CTCTCCTCCTTCAACTCCAGGCAGCAAAGTGTGGAGATAGATACTCTCTC 136881
v i ii ?i v ii v i v
L1M3e_5end#LI 200 CACCCCTCCCCCAANCCCAGGCAGCACAGCATGGAGAGAGATACCCTCTG 249
INTRON_3 136882 CTTGGGGGAGGGTCAGGGAAGTGAGCATCGGATGCTGCCTGGGACCCCAA 136931
i vv iv ivi v
L1M3e_5end#LI 250 CTTGGGGGAAGGAGAGGGAAGTGAGCACAGGACTTTGCCTTGGACCCCAA 299
INTRON_3 136932 -CACTAGCCCTATCCCAGTAAAACCCAGTGCCACACAAGCCCTCACAGCC 136980
- v iii i i vi i i i
L1M3e_5end#LI 300 ACACTAGGCCCGCCCCAGTAAAACCCAGTACTAGGCAGGCCCCCATAGCC 349
INTRON_3 136981 CCAGACTCCAGGCTGGTATGTGTGGACTCAATGTCTAGGCTCATCTTGGT 137030
ii iv ii v --------------------
L1M3e_5end#LI 350 CCAGACTCCAGGCCAGTACCTACGGACTGA-------------------- 379
INTRON_3 137031 GTCAGACCAGATCCTGAAGCTCTACACTCCAGGTCTACCCGGAGGACTTG 137080
i i? iiv i - vi i i i v ii
L1M3e_5end#LI 380 GCCGYACCAGATCCCACAGCCC-AGGCTCCAGGCCTGCCTGGTGGACTCA 428
INTRON_3 137081 TTCTATGTGC-TACCCTA-CACCAGGTTGATCCCCACAGTGCT--AGGCT 137126
v viiv - i i - iii i --- i--
L1M3e_5end#LI 429 GTCTCCAGGCCTGCCCCAGCACCAGGCCAACCCC---AGTGCCCCAGGCT 475
INTRON_3 137127 CCAGGCCACCCCCAGCAGTGGGCTAGTGTCAATAATCCCAGGCTTCAGGC 137176
i iv vii i ivi i ii i
L1M3e_5end#LI 476 CCAGACCGGCCCCAGCACCAGGCCAGCCCCAGTAGCCCCAGGCTCCAGGC 525
INTRON_3 137177 CTGCCCCAGCACCAGATTGGCCTCTAAAGCCCTGGTCTTCAGGCC----- 137221
iv? ii i i v ii v -----
L1M3e_5end#LI 526 TGSCCCCAGCACCAGGCTGGCCCCCATAGCCCCAGGCTTCAGGCCCACCC 575
INTRON_3 137222 -AATACCTG--TGGAC---ACAGCC----TC--CAGGCTGGCTTCTGCAG 137259
- ii v -- v ---? ---- -- ii vi ii
L1M3e_5end#LI 576 CAGCACCAGGCTGGCCCCTRCAGCCCTAGTCATCAGGCCAGCACCTATAG 625
INTRON_3 137260 AAACAGGCTCCAGACCCACC----TAGCCCCAGGC--CAGCTCTGGAAGC 137303
vv v i ivi ---- v v -- vi i-----
L1M3e_5end#LI 626 ACCCAGCCTCCAGGCTGGCCCCTGTAGACACAGGCTCCAGGCCTA----- 670
INTRON_3 137304 CCCAGGCTCCATACTAGTACCTGTAAATTGAGCTTCCAAGCCCACCCT-G 137352
- ? vi i iv iviiv vi i i-
L1M3e_5end#LI 671 CCCAG-CRCCAGGCCAGCCCCTGTAGCCCCAGGCTCCAGGCCCACCCCAG 719
INTRON_3 137353 GCACAAAACAGAATCCTGCAGCCCTTGGCTCCAGGCCTGACTTGCACA-- 137400
?v v i --------- --i vv i-? i iii i --
L1M3e_5end#LI 720 GYTCCAGAC---------CAGCCC--AGAGCCAGGT-YGGCCCACATAGC 757
INTRON_3 137401 -CTAGGACTTGTGGCTGCCCCGATACCAGGCC--TACCCCAGCAGCCCCA 137447
- i vi iiv v ii? i --i v -- i
L1M3e_5end#LI 758 CCCAGGCTTCAGGCCTGCCCCAGYACCAGGTCAGCACCCCTG--GCCTCA 805
INTRON_3 137448 GGCCTGAGACTGGTACCAGCACTGAGCTGGCCTCAATGGCCCTGGGTTTC 137497
i v v v ------ vi vi i v vii i i
L1M3e_5end#LI 806 GACCTTAGCCAGGTACCAG------GCTGGCACCTGTAGACACAGGCTCC 849
INTRON_3 137498 AGGCATGACATAGCACCAGGCCAACCTCTACAGACTTGGGCTGTAGGTTC 137547
v v -i i ii i iii v iiivv vi vi?
L1M3e_5end#LI 850 AGGCCTGCC-CAGTACCAGGCCAGTCCCTGTGGCCCCACCCTCCAGGGCY 898
INTRON_3 137548 AACCCTGCATGAGGCCAT-CCCCTGAAGCCCTAGTCATCAAGCTGGTACC 137596
i i-ii ivv - i v v v i vvv i iv v
L1M3e_5end#LI 899 AGCCCC-TGTGGCCCCATGCTCCAGCAGACCCAGGGTTCAGGCCTGTCCC 947
INTRON_3 137597 TATAGACCAAACCACCAAGCTGGACATCACAGATATAGGTTCTAGG---- 137642
vi vv v i i i v vi i ivi i i ----
L1M3e_5end#LI 948 AGTAGACCCCAGCACTAGGCTAGTCCCCATAGACCCAGGCTCCAGGACTG 997
INTRON_3 137643 -CCC-----ACCCAG-TGCCAGGCCAGCTTCTGGGACCCCAGGCTTCAGT 137685
- ----- - v v ii iv i vii v
L1M3e_5end#LI 998 TCCCTGTGTACCCAGGTCCCAGGGCAGCCCCTATGGCCCCAGGACCCAGG 1047
INTRON_3 137686 TCTGCCCT---AGATTTTGGAGCCT---GG--AGCCATGATAGCCCAT-- 137725
i v --- ii --- --- -- v vvii v--
L1M3e_5end#LI 1048 CCAGCCCTCAGAGACCT---AGCCTCTAGGCCAGCCCTGCAGACCCAGCC 1094
INTRON_3 137726 ----GACTG----CCAAAG--CCAGGAT---GGTTGCAGCCCCT---TTT 137759
---- i ---- ? -- i v --- i-- v i--- i
L1M3e_5end#LI 1095 TCCAGGCTGGCACCCAYAGACCCAAGCTCCAGGC--CATCCCCCAGGTTC 1142
INTRON_3 137760 CAGGCTTTAATCTCA----CTCTAG-CACCAGGTCA-TAGCCTCTGGCAT 137803
i-- ii ---- i - ii -i v v v i -i
L1M3e_5end#LI 1143 CAGGCC--AGCCTCAGTAGCTCCAGGCACCAGGCTAGCACCCACAGAC-C 1189
INTRON_3 137804 CAGATACAAGGCAAGATCCTGTGG-ATATAGGCTCTGGGCCTGCTC--AG 137850
iiv v i v -i iii v- ivivi v ii v i --i
L1M3e_5end#LI 1190 CAGGCTCCAGACTAG-CCCCACGCTACCCCAGCACCAGGCCAGCCCCAGG 1238
INTRON_3 137851 TGCCAGACTTGTCCCTGTGGTGCCATCCTCCAGGGCAGTCCTTGTGGCCA 137900
iv i v i- vv v v -- iv v v
L1M3e_5end#LI 1239 CTCCAGGCTGGTCCCTGTGGC-CCAGGCTCCAGTGGA--CCCAGGGTCCA 1285
INTRON_3 137901 --CAAGGTCCAACAGATCCAGGGTCCAGGCCTGCTCCAACAGACTCTGGT 137948
-- vv v i i ii i ii i
L1M3e_5end#LI 1286 GGCCTGCTCCAGCAGACCCAGGGTCCAGGCCCACCCCAGTAGACCCTGGT 1335
INTRON_3 137949 TCTAGACTGGTCCCCATGGATCAAGACTCTAGGACCACCT-TATAGATCC 137997
i i i i iiv i i i- ii i
L1M3e_5end#LI 1336 TCCAGGCTAGCCCCCATGGACTCAGGCTCCAGGACCACCCCTGCAGACCC 1385
INTRON_3 137998 AGAACCCAGGCTCACCCTTGTGTCCCATCCCCACTCTAGTTCCAAG--CC 138045
ivi ivi i?i vv ----------i v ? --
L1M3e_5end#LI 1386 AGGCTCCAGGCCAGCCCCYATGGACCA----------GGATCCARGGCCC 1425
INTRON_3 138046 AGCTCCT--GTGGACTCAGTTCCCAGGACCATCCCAGCACCTGGCTGACC 138093
v? i-- v --- vii v iii ii v iii
L1M3e_5end#LI 1426 ATYTCCCCAGTTG---CAGGCTCCAGGCCTGCCCCAGTGCCAGGCCAGCC 1472
INTRON_3 138094 CCTGCAGACTTGGGCTCAGAGACCACCCCAGTG---CCAGATCAGTTCAT 138140
iiii ii vii v i --- ii--- i v
L1M3e_5end#LI 1473 CCCATGGACTCAGGCTCCAGGCCCATCCCAGTGGACCCAGGC---TCCAG 1519
INTRON_3 138141 GTGGATACAGGCTTCAGGGAAGCCCCTGGAAAAATAGGTTCTAGGCCTAC 138190
ivv v vi ?vi vv ? i vvi i v i
L1M3e_5end#LI 1520 GCCCATCCCAGYACCAGGCCAGCCCCTGYAGACTCAGGCTCAAGGCCCAC 1569
INTRON_3 138191 CCTCTGTGACCTAGGCTCCAGGTCTCCTCCTGAGGAACCAATCAACAGGT 138240
i----------i v vv i v v iv vv i
L1M3e_5end#LI 1570 CCC----------AGCACCAGGTCAGCCCCTGTGGACCCAGGCTTCAGGC 1609
INTRON_3 138241 CCACTCTGGTGTGTTTAGGCCCTAGGCTTAACCCCGTGGAACCAGGTTCC 138290
vi i ivi iviivi i i i? v i i v i
L1M3e_5end#LI 1610 CAGCCCCTATAGACACAGGCTCCAGGCCYACCCTCATGGACCCAGGCTCC 1659
INTRON_3 138291 AGGCCCACCCACCTGCTGACCCAGTTACGAGG-CTACATGTCCAAAGACT 138339
? -- ii v i i vv - i ---- iv iv
L1M3e_5end#LI 1660 AGGCCCAYCC--CCACAGACCCAATCAACAGGTCCAC----CCAGTGGAT 1703
INTRON_3 138340 CCAG-CAGTAAACCCA--CCTATGGAC 138363
- vvi ii ? -- i
L1M3e_5end#LI 1704 CCAGGCTCCAGGCYCAACCCTGTGGAC 1730
Matrix = 20p37g.matrix
Transitions / transversions = 1.76 (296 / 168)
Gap_init rate = 0.04 (65 / 1731), avg. gap size = 2.95 (192 / 65)
3439 29.84 6.57 5.71 INTRON_3 136960 138679 261502 + L1M3e_5end LINE/L1 380 2113 0 337
INTRON_3 136960 GCCACACAAGCCCTCACAGCCCCAGACTCCAGGCTGGTATGTGTGGACTC 137009
i? v vi i - i iv iv -
L1M3e_5end#LI 380 GCCGYACCAGATCCCACAGCCC-AGGCTCCAGGCCTGCCTG-GTGGACTC 427
INTRON_3 137010 AATGTCTAGGCTCATCTTGGTGTCAGACCAGATCCTGAAGCTCTACACTC 137059
i v i iiii iii iii i - i iiiv i i vi
L1M3e_5end#LI 428 AGTCTCCAGGCCTGCCCCAGCACCAGGCCA-ACCCCAGTGCCCCAGGCTC 476
INTRON_3 137060 CAGGTCTACCC-GG----AGGAC--------TTGTTCTATGT-----GCT 137091
ii vi -i ---- v -------- v ii i v i-----
L1M3e_5end#LI 477 CAGACCGGCCCCAGCACCAGGCCAGCCCCAGTAGCCCCAGGCTCCAGGCT 526
INTRON_3 137092 ACCCT--ACACCAGGTTGATCCCCACAGTGCTAGGCTCCAGGCCACCCCC 137139
i? i--i i ii i iv i i vv
L1M3e_5end#LI 527 GSCCCCAGCACCAGGCTGGCCCCCATAGCCCCAGGCTTCAGGCCCACCCC 576
INTRON_3 137140 AGCAGTGGGCTAGTGTCAATAATCCCAGGCTTCAGGCCTGC--------- 137180
vii i ivi v?i ii i v v v ---------
L1M3e_5end#LI 577 AGCACCAGGCTGGCCCCTRCAGCCCTAGTCATCAGGCCAGCACCTATAGA 626
INTRON_3 137181 CCCAGCA-CCAGATTGGCCTCTAAAGCCCTGGTCTTCAGGCCAATACCTG 137229
v- ii i iv v vii v i -- --
L1M3e_5end#LI 627 CCCAGCCTCCAGGCTGGCCCCTGTAGACACAGGCTCCAGGCC--TACC-- 672
INTRON_3 137230 TGGACACAGCCTCCAGGCTGGCTTCTGCAGAAACAGGCTCCAGACCCACC 137279
------ ?- ii ii i vvv i
L1M3e_5end#LI 673 ------CAGCR-CCAGGCCAGCCCCTGTAGCCCCAGGCTCCAGGCCCACC 715
INTRON_3 137280 T--AGCCCCAGGCCAGCTCTGGAAGCCCCAGGCT---CCATACTAGTACC 137324
i--i ?i i i ---- vv i?--- i - iv
L1M3e_5end#LI 716 CCAGGYTCCAGACCAGCCC----AGAGCCAGGTYGGCCCACA-TAGCCCC 760
INTRON_3 137325 TGTAAATTGAGCTTCCAAGCCCACCCTGGCACAAAA-CAGAATCC-TG-- 137370
v -------- - i ii ii ? v ii- v i - --
L1M3e_5end#LI 761 AG--------GCTTC-AGGCCTGCCCCAGYACCAGGTCAGCACCCCTGGC 801
INTRON_3 137371 --CAGCCCTTGGCT-----CCAGGCCTG-ACTTGCACACTAGGACTTGTG 137412
-- v i i----- iv - i i v vvi i ivv
L1M3e_5end#LI 802 CTCAGACCTTAGCCAGGTACCAGGCTGGCACCTGTAGACACAGGCTCCAG 851
INTRON_3 137413 GCTGCCCCGATACCAGGCCTACCCCAGCAGCCCCAGGCCTGAGACTGGTA 137462
ivv ii vii v ii v- ---- ii vi
L1M3e_5end#LI 852 GCCTGCCCAGTACCAGGCCAGTCCCTGTGGCCCCAC-CCT----CCAGGG 896
INTRON_3 137463 CCAGCAC-TGAGCTGGCCTCAATG-----GC---CCTGGGTTTCAGGCAT 137503
? v - --- i - ----- --- ii v v
L1M3e_5end#LI 897 CYAGCCCCTG---TGGCCCCA-TGCTCCAGCAGACCCAGGGTTCAGGCCT 942
INTRON_3 137504 G----------ACATAGCACCAGGCCAACCTCTACAGACTTGGGCTGTAG 137543
----------v vi i i ii i i i iii vi
L1M3e_5end#LI 943 GTCCCAGTAGACCCCAGCACTAGGCTAGTCCCCATAGACCCAGGCTCCAG 992
INTRON_3 137544 GTTCAACCCTGCATGAGGCCATCCCCTGAAGCCCTAGTCATCAAGCTGGT 137593
viiiv ii ------ i ---- i i i ------i -i i
L1M3e_5end#LI 993 GACTGTCCCTGTGT------ACCC----AGGTCCCAG------GGC-AGC 1025
INTRON_3 137594 ACCTATAGACCAAACCACCAAGCTGGACATCACAGATATAGGTTCTAGGC 137643
v i v v ivvv i ii v v v iv vi
L1M3e_5end#LI 1026 CCCTATGGCCCCAGGACCCAGGCCAGCCCTCAGAGACCTAGCCTCTAGGC 1075
INTRON_3 137644 CCACCCAGTGCCAGGCCAGCTTC-----TGGGACCC-------CAGGCTT 137681
vi -- viiv i ----- v ------- i i
L1M3e_5end#LI 1076 CAGCCC--TGCAGACCCAGCCTCCAGGCTGGCACCCAYAGACCCAAGCTC 1123
INTRON_3 137682 CAGTTC-TGCCCTAGATTTTGGAGCCTGGAGCCATGATAGCCCATGACTG 137730
vi - v i i iii - --- viii i vv i -i
L1M3e_5end#LI 1124 CAGGCCATCCCCCAGGTTCCAG-GCC---AGCCTCAGTAGCTCCAGGC-A 1168
INTRON_3 137731 CCAAAGCCAGGATGGTTGCAGCCCC--TTTTCAGGCTTTAATCTCACTCT 137778
i- i v i--iii v --vi i i -- ii i v
L1M3e_5end#LI 1169 CCAG-GCTAGCAC--CCACAGACCCAGGCTCCAGACT--AGCCCCACGCT 1213
INTRON_3 137779 A-----GCACCAGGTCATAGCCTCTGGCATCAGA--------TACAAGGC 137815
----- i -- i v vi i-------- iiiivv
L1M3e_5end#LI 1214 ACCCCAGCACCAGGCCA--GCCCCAGGCTCCAGGCTGGTCCCTGTGGCCC 1261
INTRON_3 137816 AAGATCCTGTGGATATAGGCTCTGGGCCTGCTC-AGTGCCAGACTT---G 137861
i v v ivi v ii - --- ii---
L1M3e_5end#LI 1262 AGGCTCCAGTGGACCCAGGGTCCAGGCCTGCTCCAG---CAGACCCAGGG 1308
INTRON_3 137862 TCCCTGTGGTGCCATCCTCCAGGGCAGTCCTTGTGGCCA--CAAGGTCCA 137909
v--- i- i -- --i v i vvv -- v vi v
L1M3e_5end#LI 1309 TCCA---GGC-CCACCC--CAG--TAGACCCTGGTTCCAGGCTAGCCCCC 1350
INTRON_3 137910 ACAGATCCAGGGTCCAGGCCTGCTCCAACAGACTCTGGTTCTAGACTGGT 137959
ii ii v v ii i vi i v i i i ii i
L1M3e_5end#LI 1351 ATGGACTCAGGCTCCAGGACCACCCCTGCAGACCCAGGCTCCAGGCCAGC 1400
INTRON_3 137960 CCCCATGGATCAAGACTCTAGGACCACCTTAT-AGATCCAGAACCCAGGC 138008
? i i ii v? v i? ivi- v v ivi
L1M3e_5end#LI 1401 CCCYATGGACCAGGATCCARGGCCCATYTCCCCAGTTGCAGGCTCCAGGC 1450
INTRON_3 138009 TCACCCTTGTGTC---CCATCCCC-----ACTCTAGTTCCAAGCCAGCTC 138050
iii iv i --- v ----- vi i i viii
L1M3e_5end#LI 1451 CTGCCCCAGTGCCAGGCCAGCCCCCATGGACTCAGGCTCCAGGCCCATCC 1500
INTRON_3 138051 CTGTGGACTCAGTTCCCAGGACCATCCCAGCACCTGGCTGACCCCTGCAG 138100
v i vii v ? v iii ?
L1M3e_5end#LI 1501 CAGTGGACCCAGGCTCCAGGCCCATCCCAGYACCAGGCCAGCCCCTGYAG 1550
INTRON_3 138101 ACTTGGGCTCAGAGACCACCCCAGTGCCAGATCAGTTCATGTGGATACAG 138150
ii ii v ii i ii v iv
L1M3e_5end#LI 1551 ACTCAGGCTCAAGGCCCACCCCAGCACCAGGTCAGCCCCTGTGGACCCAG 1600
INTRON_3 138151 GCTTCAGGGAAGCCCCTGGAAAAATAGGTTCTAGGCCTACCCTC-TGTGA 138199
vv iv i v i i i ? - -
L1M3e_5end#LI 1601 GCTTCAGGCCAGCCCCTATAGACACAGGCTCCAGGCCYACCCTCATG-GA 1649
INTRON_3 138200 CCTAGGCTCCAGGTCTCCTCCTGAGGAACCAATCAACAGGTCCACTCTGG 138249
i i iv?i iivi v i -i
L1M3e_5end#LI 1650 CCCAGGCTCCAGGCCCAYCCCCACAGACCCAATCAACAGGTCCACCC-AG 1698
INTRON_3 138250 TGTGTTTAGGCCCTAGGCTTAACCCCGTGGAACCAGGTTCCAGGCCCACC 138299
vi ii i i ?i i v iv ii
L1M3e_5end#LI 1699 TGGATCCAGGCTCCAGGCYCAACCCTGTGGACCCAGGCACCAGGCCTGCC 1748
INTRON_3 138300 CACCTGCTGACCCAGTTACGAGGCTA-CATGTCCAAAGACTCCAGCAGTA 138348
- vi v i - v i i i i
L1M3e_5end#LI 1749 -ACCTGCTGACCCAGGCACCAGGCCAGCCTGCCTAAGGACTCCAGCAGCA 1797
INTRON_3 138349 AACCCACCTATGGACAACTTACTCAGAATGCCAGACAACTTACTCAGAAT 138398
i ii i ------ ----- i iii i i i
L1M3e_5end#LI 1798 AGCCTGCCTATAGAC------C-----ATACCAGATGGCCTGCCCAGAAT 1836
INTRON_3 138399 CTCTGGATGGACTGAAAAGGAAGGGCTCTCCCATACAAAGCCAGTCAGCA 138448
- i---v i v v
L1M3e_5end#LI 1837 CTCTGGATG-ACTGG---TGAAGGGCTTTCCCAGACAAAGCCAGTCTGCA 1882
INTRON_3 138449 AAAACTAGAGTGAATTCCAACTTCTTTCCATGTGCAAGCTTCAATGTAAG 138498
i i i i i i v ivv ii vi i
L1M3e_5end#LI 1883 AAGACTGGAATAAGTCCCTACTTCTTCAAATGTGCAGACACCAATGCAAG 1932
INTRON_3 138499 ATAAGAGGAAACATGACAAACCAAGGAGATATAACACTACCAAAAGAGTA 138548
iivvi - v ? vv i i i i i i i ii
L1M3e_5end#LI 1933 GCCCAAG-AATCAWGAACAATCAGGGAAACATGACACCACCAAAGGAACA 1981
INTRON_3 138549 CAATAATCTCCCAGTAGCTAACCCTCAAAGAAATAGAGAT-TATGAACTG 138597
v vi i i i - i -
L1M3e_5end#LI 1982 AAATAAATTTCCAGTAACTGACCCT-AAAGAAATGGAGATCTATGAACTG 2030
INTRON_3 138598 CCTAAAAAACAGTTCAAGATGATTGTCTTAAGGAAGCCCAGCAAAATTAA 138647
i v v i i i i i ii v ?v
L1M3e_5end#LI 2031 CCTGACAAAGAATTCAAAATAATTGTTTTAAGGAAGCTCAGTGAACTWCA 2080
INTRON_3 138648 AGAAAATACAGA-AAAAAATTGTATGAAATCAG 138679
i - i v iv
L1M3e_5end#LI 2081 AGAAAACACAGATAGACAATTAAATGAAATCAG 2113
Matrix = 20p37g.matrix
Transitions / transversions = 2.13 (317 / 149)
Gap_init rate = 0.04 (74 / 1719), avg. gap size = 2.86 (212 / 74)
+ 3435 24.6 3.4 3.0 INTRON_3 138706 140209 (259972) + L1MA8 LINE/L1 2263 3775 (3787) 172 *
ANNOTATION EVIDENCE:
3435 26.71 3.79 2.83 INTRON_3 138706 140104 260077 + L1M1_5end LINE/L1 2263 3674 1 338
INTRON_3 138706 AATTTAACAGAGAGATTGAAATTGTTTTTAAAAGTCAAACAGAAATTCTG 138755
i vi vvv i i i
L1M1_5end#LIN 2263 AATTTAACAAAGAGATTGAAATAATTAAAAAGAATCAAGCAGAAATTCTG 2312
INTRON_3 138756 GAGCTGAAAGACACAATGAATGAAGTGAAAAATGCAATAGAAAGCATCAG 138805
i i ii vi iiv v i vi ivviv i i
L1M1_5end#LIN 2313 GAGTTGAAAAATGCAATTGACATACTGAAGAATGCATCAGAGTCTCTTAA 2362
INTRON_3 138806 TAGCAGCATTGATCAAGCAGAAGAATGAATCTGTGAACTTGAAGACAGAT 138855
i v v iv i ii
L1M1_5end#LIN 2363 CAGCAGAATTGATCAAGCAGAAGAAAGAATTAGTGAGCTTGAAGACAGGC 2412
INTRON_3 138856 TATTTGAAAATATGTAGTCGAATGATA-AAAATTAAAAAGAA----AAGG 138900
iii ii v v - vv ---- i
L1M1_5end#LIN 2413 TATTTGAAAATACACAGTCAGAGGAGACAAAAGAAAAAAGAATAAAAAAG 2462
INTRON_3 138901 AGTGAAGAAAACTTACAGAATTTATGGGACAATGTAAAAAGAGCAAATGT 138950
i v vi i ii i viii i iiv v i v
L1M1_5end#LIN 2463 AATGAAGCACGCCTACAAGATCTAGAAAATAGCCTCAAAAGGGCAAATCT 2512
INTRON_3 138951 CTGAGTTATAGGATTTCAAGAAGAG----AAAGACAAAT-GGGGTAAAAA 138995
vv v vi v i ---- i v i - i
L1M1_5end#LIN 2513 AAGAGTTATTGGCCTTAAAGAGGAGGTAGAGAGAGAGATAGGGGTAGAAA 2562
INTRON_3 138996 GCTTACTGAAAGAAATAGTAACAGAAAACTTTTCAAATCTGGGAAAACAC 139045
i i v ii i i ii i i ii v i
L1M1_5end#LIN 2563 GTTTATTCAAAGGGATAATAACAGAGAACTTCCCAAACCTAGAGAAAGAT 2612
INTRON_3 139046 ATAAAGATCCAGAGATCTAGGTAAAAGAAGGTCAAAGGTATTCAATCAAA 139095
v v i i-------- v i v ivvvi v i
L1M1_5end#LIN 2613 ATCAATATTCAA--------GTACAAGAAGGTTATAGAACACCAAGCAGA 2654
INTRON_3 139096 TTCAGTTCACACAAGATTATGCCAAGACATATTATAATAAAACTGTTAAA 139145
i iii v v i ivi i v v v vii
L1M1_5end#LIN 2655 TTTAACCCAAAGAAGACTACCTCAAGGCATTTAATAATCAAACTCCCAAA 2704
INTRON_3 139146 AATCAAAGACAAAGAGAAGATCCTGAAAGCAACAAGGAAAAAGAAGCAGA 139195
ii i i i i i i ii i i
L1M1_5end#LIN 2705 GGTCAAGGATAAAGAAAGGATCCTAAAAGCAGCAAGAGAAAAGAAACAAA 2754
INTRON_3 139196 TCACATATAAGGGAGTTCCAATAAGGCTATCAGTGGACTTCTGAGCAGAA 139245
v i v i v v iv ii i v ii
L1M1_5end#LIN 2755 TAACATACAATGGAGCTCCAATACGTCTGGCAGCAGACTTTTCAGTGGAA 2804
INTRON_3 139246 ACTTTATAGGC-AGGAGATAGTGGAATGGTATATTCAAAGTACTAAAGGA 139294
i i - v v ii i i i
L1M1_5end#LIN 2805 ACCTTACAGGCCAGGAGAGAGTGGCATGACATATTTAAAGTGCTGAAGGA 2854
INTRON_3 139295 AAAAAGAAACCCTGCCAACCAAGAGTACTGTATTCAGCAAAGCTGTCCTT 139344
i----- vii v v i v i i ii iv i
L1M1_5end#LIN 2855 AAAAAA-----CTTTTACCCTAGAATAGTATATCCAGTGAAAATATCCTT 2899
INTRON_3 139345 CAGAAATGAAGGCAAGATCAAGACTTTCTCAGACAAATAAAAGCTGAGGG 139394
i v vi i v i i
L1M1_5end#LIN 2900 CAAACATGAAGGAGAAATAAAGACTTTCCCAGACAAACAAAAGCTGAGGG 2949
INTRON_3 139395 AGTTCATCACCACCAGACCCGTCTTATACAACATACTAAAGGTAGTTCTT 139444
v v i i i vi v i v
L1M1_5end#LIN 2950 ATTTCATCAACACCAGACCTGTCCTACAAGAAATGCTAAAGGGAGTTCTT 2999
INTRON_3 139445 CAAGTTGAAAGGAAAGCACACTAATTAGTGATACAAAAACTTATGAAGGT 139494
vi i v i v ii vi v v v
L1M1_5end#LIN 3000 CAATCTGAAAGAAAAGGACATTAATGAGCAATAAGAAATCATCTGAAGGT 3049
INTRON_3 139495 ATAAAACTCACTAGTAAAAGTAAGTACACAGTCAAATTTAGAATTATCTA 139544
i i v vv ivi vv v
L1M1_5end#LIN 3050 ACAAAACTCACTGGTAATAGTAAGTACACAGAAAAACACAGAATATTATA 3099
INTRON_3 139545 ATACTATAAAGGTAATATGTAAATCAC--ATATCTTTAGTATGAAGGTTA 139592
i i vv ii i ii -- v vi ii
L1M1_5end#LIN 3100 ACACTGTAATTGTGGTGTGTAAACTACTCATATCTTAAGTAGAAAGACTA 3149
INTRON_3 139593 AAAGACAAAACTATTAAAAAGATTAATAGCTACAAAAATTTCTTAAGGAT 139642
ii v v i --- i v i i i ivv
L1M1_5end#LIN 3150 AAAGATGAACCAATCAAAAA---TAATAACTACAACAACTTTTCAAGACA 3196
INTRON_3 139643 TACACACTATAACAAGATGTAAACAGTGACATCAAAAACATAAAATATTG 139692
v v i i i i vi v vv viiv
L1M1_5end#LIN 3197 TAGACAGTACAATAAGATATAAATAGAAACAACAAAAAGTTAAAAAGCGG 3246
INTRON_3 139693 GAGGAGGAA-TGAAAGTGTTTAGTTTTTTTTAATGCAATCAAATCTTTG- 139740
i v - v vv v i vi-- --- -
L1M1_5end#LIN 3247 GGGGACGAAGTTAAAGTGTAGAGTTTTTATTAGTTT--TC---TCTTTGC 3291
INTRON_3 139741 --G---GTTAACAGAGCC--TGTTACAACTATAA--GGTTTTATGTAA-G 139780
-- --- viiiv ii -- - ii i v --i v vi -
L1M1_5end#LIN 3292 TTGTTTGTTTGTGCAATCAGTGTTA-AGTTGTCATCAGTTTAAAATAATG 3340
INTRON_3 139781 CCTCA-AAG----TAACCACAAAGCAAA----AACCTATAATCGATACAC 139821
vv i - ---- viii iv vv ---- vv i v v
L1M1_5end#LIN 3341 GGTTATAAGATATTATTTGCAAGCCTCATGGTAACCTCAAATCAAAAAAC 3390
INTRON_3 139822 ---CAA-AGAT-CAGAAGTAAGATGGTAAAGCATACTTCTAGAGA--AAA 139864
--- - - v -- i ii- ------- i --
L1M1_5end#LIN 3391 ATACAACAGATACACAA--AAAATAA-AAAGCA-------AGAAATTAAA 3430
INTRON_3 139865 ATCACTTAACTGCAAAGGAAGACAGC--------AAGAGAGAAAGAAAAG 139906
- -- v vv i i iv v -------- ii v i i
L1M1_5end#LIN 3431 A-CA--TACCACCAGAGAAAATCACCTTCACTAAAAGGAAGACAGGAAGG 3477
INTRON_3 139907 AGGTTCTAAAAACAAAACAAAACAAAACAAAACAA---GAAAACAA-TAA 139952
i v--- i vii v i v vv --- -
L1M1_5end#LIN 3478 AAGG---AAAGAAGGAAGAGAAGACCACAAAACAACCAGAAAACAAATAA 3524
INTRON_3 139953 CAAAATAACAGTGATAAGCCCTTACATATTAATAATTATCTTGAATGTAA 140002
ii vii i v i v iv
L1M1_5end#LIN 3525 CAAAATGGCAGGAGTAAGTCCTTACTTATCAATAATAACATTGAATGTAA 3574
INTRON_3 140003 GTAGATTGAATTCTTCTATTAAAATACATAGAGGGGCTGAATGGATTAAA 140052
i i i i i i v i v v v
L1M1_5end#LIN 3575 ATGGACTAAACTCTCCAATCAAAAGACATAGAGTGGCTGAATGGATAAAA 3624
INTRON_3 140053 AAAAAGCTGGGCCAACTGTGTGCTGTGTACAAGAGACTTATTTCACCTTT 140102
v i-- iv vi v i iv i vi i v
L1M1_5end#LIN 3625 AAACAA--GACCCAACGATCTGTTGCCTACAAGAAACACACTTCACCTAT 3672
INTRON_3 140103 AA 140104
L1M1_5end#LIN 3673 AA 3674
Matrix = 20p37g.matrix
Transitions / transversions = 1.45 (215 / 148)
Gap_init rate = 0.03 (35 / 1398), avg. gap size = 2.66 (93 / 35)
1354 14.35 1.19 3.64 INTRON_3 139957 140209 259972 + L1M2_orf2 LINE/L1 1 247 3044 339
INTRON_3 139957 ATAACAGTGATAAGCCCTTACATATTAATAATTATCTTGAATGTAAGTAG 140006
ii ii i v i ? i i i
L1M2_orf2#LIN 1 ATGGCAGTAGTAAGTCCTTACCTATCAATAATNACCTTGAATGTAAATGG 50
INTRON_3 140007 ATTGAATTCTTCTATTAAAATACATAGAGGGGCTGAATGGATTAAAAAAA 140056
i i v v v v v
L1M2_orf2#LIN 51 ATTAAATTCTCCAATTAAAAGACATAGAGTGGCTGAATGGATAAAAAAAC 100
INTRON_3 140057 AGCTGGGCCAACTGTGTGCTGTGTACAAGAGACTTATTTCACCTTTAAGG 140106
i-- iv i i iv i i ?
L1M2_orf2#LIN 101 AA--GACCCAACTATATGCTGCCTACAAGAGACTCACTTCACCTNTAAGG 148
INTRON_3 140107 GCACACA--GGCTGAAAGTGAAGCGATGGAAAAAGATATTCCATTCAAAT 140154
i -- i v v
L1M2_orf2#LIN 149 ACACACATAGACTGAAAGTGAAGGGATGGAAAAAGATATTCCATGCAAAT 198
INTRON_3 140155 GGAAACAAACAAATGGAAAAGAGCAGG-GTAACTATACTTATATCAAATA 140203
--- ---- i - i i
L1M2_orf2#LIN 199 GGAAAC---CAAA----AGAGAGCAGGAGTAGCTATACTTATATCAGATA 241
INTRON_3 140204 AAATAG 140209
L1M2_orf2#LIN 242 AAATAG 247
Matrix = 20p37g.matrix
Transitions / transversions = 2.30 (23 / 10)
Gap_init rate = 0.02 (5 / 252), avg. gap size = 2.40 (12 / 5)
+ 3982 15.2 7.0 0.2 INTRON_3 140204 141478 (258703) + L1MA8 LINE/L1 6322 7709 (1) 172
ANNOTATION EVIDENCE:
767 19.88 0.62 0.00 INTRON_3 140204 140364 259817 + L1M3_orf2 LINE/L1 2794 2955 333 340
INTRON_3 140204 AAATAGTGTTGAGAAAACTGAATTTCCACATGCACTAGAATGAAATTAAA 140253
i i i v vv ii
L1M3_orf2#LIN 2794 AAATGGTGTTGGGAAAACTGGATATCCACATGCAGAAGAATGAAATTGGA 2843
INTRON_3 140254 ACCTTGTCTCACAACATATACAAAAATCAACCCAAAATGGATAAAAGACT 140303
v i i v i i v
L1M3_orf2#LIN 2844 CCCTTATCTTACACCATACACAAAAATCAACTCAAAATGGATTAAAGACT 2893
INTRON_3 140304 TAAATTTAGAATCTGAAACTTTATAGTCACTGGAAGAAAATCTAGGGATA 140353
v ii i v v iiiv i iv iv
L1M3_orf2#LIN 2894 TAAATGTAAGACCTGAAACTGTAAAACTCCTAGAAGAAAACATAGGGGAA 2943
INTRON_3 140354 AA-TTGCATGAC 140364
-i v
L1M3_orf2#LIN 2944 AAGCTTCATGAC 2955
Matrix = 20p37g.matrix
Transitions / transversions = 1.46 (19 / 13)
Gap_init rate = 0.01 (1 / 160), avg. gap size = 1.00 (1 / 1)
1553 14.97 3.39 0.33 INTRON_3 140362 140656 259525 + L1M2_orf2 LINE/L1 2988 3291 0 341
INTRON_3 140362 GACCTCAAAAGCATAGGCAAAAAGAGGAAAAATAGACAAATGGGATTATA 140411
i v i v i
L1M2_orf2#LIN 2988 GACCTCAAAAGCACAGGCAACAAAAGCAAAAATAGACAAATGGGATTACA 3037
INTRON_3 140412 TCAAACTAAAAAGTTTCTGCACAGCTAA--AAAAAATCAACAGAATGTTG 140459
i v -- v i vv
L1M2_orf2#LIN 3038 TCAAACTAAAAAGCTTCTGCACAGCAAAGGAAACAATCAACAGAGTGAAG 3087
INTRON_3 140460 AAAGAACCTATAGGATGGGAGAAAATATTTGCAAACCATCCATCTGGTAA 140509
i v i i i v ii
L1M2_orf2#LIN 3088 AGACAACCTACAGAATGGGAGAAAATATTTGCAAACTATGCATCTGACAA 3137
INTRON_3 140510 AGGGTTCATATCCAAAATGTGTAAGGAACTCAA----CTCAATAGCAAGA 140555
i v i i i ---- i i
L1M2_orf2#LIN 3138 GGGGTTAATATCCAGAATATATAAGGAACTCAAACAACTCAACAGCAAAA 3187
INTRON_3 140556 AGAGAAA----CTGATTAATAACTGGGCAAAGGACCTGAATAGATATATC 140601
i v ---- i ? v v i i v
L1M2_orf2#LIN 3188 AAACAAATAACCCGATTNAAAAATGGGCAAAAGACCTGAATAGACATTTC 3237
INTRON_3 140602 TCAAAAGAAGCTATAAAAATGGCCAACAGGCATACAAAAATGTGCTTAAC 140651
vi v i ii vi i
L1M2_orf2#LIN 3238 TCAAAAGAAGACATACAAATGGCCAACAGGTATATGAAAAAATGCTCAAC 3287
INTRON_3 140652 CATCA 140656
-
L1M2_orf2#LIN 3288 -ATCA 3291
Matrix = 20p37g.matrix
Transitions / transversions = 1.69 (27 / 16)
Gap_init rate = 0.01 (4 / 294), avg. gap size = 2.75 (11 / 4)
2383 15.35 6.55 0.00 INTRON_3 140514 140956 259225 + L1MA8_3end LINE/L1 1 472 566 342
INTRON_3 140514 TTCATATCCAAAATGTGTAAGGAACTCAA----CTCAATAGCAAGAAGAG 140559
v i i ---- i v
L1MA8_3end#LI 1 TTAATATCCAAAATATATAAGGAACTCAAACAACTCAATAGCAAGAAAAC 50
INTRON_3 140560 AAA----CTGATTAATAACTGGGCAAAGGACCTGAATAGATATATCTCAA 140605
---- i v v i v
L1MA8_3end#LI 51 AAATAACCCGATTAAAAAATGGGCAAAGGACCTGAATAGACATTTCTCAA 100
INTRON_3 140606 AAGAAGCTATAAAAATGGCCAACAGGCATACAAAAATGTGCTTAAC---- 140651
vi v i ii vi i ----
L1MA8_3end#LI 101 AAGAAGACATACAAATGGCCAACAGGTATATGAAAAAATGCTCAACATCA 150
INTRON_3 140652 -----CATCAGAGAAATGCAAATTAACACCACAGTGAGATATCTCCTCAC 140696
----- i i v i v
L1MA8_3end#LI 151 CTAATCATCAGGGAAATGCAAATCAAAACCACAATGAGATATCACCTCAC 200
INTRON_3 140697 ACCTATTAGAATTGCTATTATCAAAAAGACCAAAGATAAC--TTGTTGGT 140744
i v v --v ?
L1MA8_3end#LI 201 ACCTGTTAGAATGGCTATTATCAAAAAGACGAAAGATAACAAGTGTTGGW 250
INTRON_3 140745 AAGGATATGGAGTCAAGGGAACCCTTGCATGCTGTTGGTGGGTATGT--- 140791
i i vv ii v ---
L1MA8_3end#LI 251 GAGGATGTGGAGAAAAGGGAACCCTTGCACACTGTTGGTGGGAATGTAAA 300
INTRON_3 140792 ---GTATAATTATTATGAAAAATAGAATGCACATTCCTCAAAAAACTGAA 140838
--- i iii i i v v vi i i
L1MA8_3end#LI 301 TTAGTACAGCCATTATGGAAAACAGTATGGAGGTTCCTCAAAAAATTAAA 350
INTRON_3 140839 GATAGAACTATCATTTGATGCAGCAGTCTCATTAATGGGTAT----TCAA 140884
i i v v i i i ?v ----i
L1MA8_3end#LI 351 AATAGAACTACCATATGATCCAGCAATCCCACTWCTGGGTATATATCCAA 400
INTRON_3 140885 GGGAAATGAATTCAGTATATTGAAGACATATCTGCACTGAAATGTTCATT 140934
i v i ii v vvv
L1MA8_3end#LI 401 AGGAAATGAAATCAGTATGTCAAAGAGATATCTGCACTCCCATGTTCATT 450
INTRON_3 140935 GCAGCATTATTCATAATAGCCA 140956
i
L1MA8_3end#LI 451 GCAGCATTATTCACAATAGCCA 472
Matrix = 20p37g.matrix
Transitions / transversions = 1.44 (39 / 27)
Gap_init rate = 0.01 (6 / 442), avg. gap size = 4.83 (29 / 6)
2485 24.38 5.46 0.41 INTRON_3 140560 141255 258926 + L1MB4_3end LINE/L1 55 785 142 343
INTRON_3 140560 AAACTGATTAATAACTGGGCAAAGGACCTGAATAGATATATCTCAAAAGA 140609
v ii v v i i v v
L1MB4_3end#LI 55 AACCCAATTAAAAAATGGGCAAAGGACTTGAATAGACATTTCTCCAAAGA 104
INTRON_3 140610 AGCTATAAAAATGGCCAACAGGCATACAAAAATGTGCTTAAC-------- 140651
v v i i i ii vi i --------
L1MB4_3end#LI 105 AGATATACAAATGGCCAATAAGCACATGAAAAGATGCTCAACATCACTAN 154
INTRON_3 140652 -CATCAGAGAAATGCAAATTAACACCACAGTGAGATATCTCCTCACACCT 140700
- i i i v i i v i
L1MB4_3end#LI 155 TCATTAGGGAAATGCAAATCAAAACCACAATGAGATACCACCTCACACCC 204
INTRON_3 140701 ATTAGAATTGCTATTATCAAAAAGACCAAAGATAAC--TTGTTGGTAAGG 140748
i i v v i vi i --v ii
L1MB4_3end#LI 205 ACTAGGATGGCTATAATCAAAAAAACAGAAAATAACAAGTGTTGGCGAGG 254
INTRON_3 140749 ATATGGAGTCAAGGGAACCCTTGCATGC--TGTTGGTGGGTATGT----- 140791
i vv vv -- -- i v -----
L1MB4_3end#LI 255 ATGTGGAGAAATTGGAACCCT--CATGCATTGCTGGTGGGAATGTAAAAT 302
INTRON_3 140792 -GTATAATTATTATGAAAAATAGAATGCACATTCCTCAAAAAACTGAAGA 140840
- ii iiiii i i i vv vvvi ii i v
L1MB4_3end#LI 303 GGTGCAGCCGCTGTGGAAAACAGTTTGGTGGTTCCTCAAAAAGTTAAACA 352
INTRON_3 140841 TAGAACTATCATTTGATGCAGCAGTCTCATTAATGGGTAT----TCAAGG 140886
i i v iv i ii i vv i ----i ii
L1MB4_3end#LI 353 TAGAATTACCATATGACCCAGCAATTCCACTCCTAGGTATATACCCAAAA 402
INTRON_3 140887 GAAATGAATTCAGTATATTGAAGACATATCTGCACTGAAATGTTCATTGC 140936
v vv vivv i v v ii i vvv v
L1MB4_3end#LI 403 GAATTGAAAGCAGGGACTCGAACAGATACTTGTACACCAATGTTCATAGC 452
INTRON_3 140937 AGCATTATTCATAATAGCCATA-TATGGAATCAATCTAAGTGTCCACAAG 140985
i v -vi v i i i -
L1MB4_3end#LI 453 AGCATTATTCACAATAGCCAAAAGGTGGAAACAACCCAAGTGTCCATAA- 501
INTRON_3 140986 CAAATGAATTGATAAAGAAAATGTGGTATATACACACAATGGAATACTAT 141035
ii v v i i
L1MB4_3end#LI 502 CGGATGAATGGATAAACAAAATGTGGTATATACATACAATGGAATATTAT 551
INTRON_3 141036 TCAGCCTTAAAAAAGGAGGAAATCCTGTCATTTGTGACAACATGGATGAA 141085
i i i vi iv iv
L1MB4_3end#LI 552 TCAGCCTTAAAAAGGAAGGAAATTCTGATACATGCTACAACATGGATGAA 601
INTRON_3 141086 CATGGAGGACATTATATTAAGTGAAATAAAG-AGGCAAAGAAAGATAAAT 141134
v v ii ii iv- ? v i i i
L1MB4_3end#LI 602 CCTTGAAAACATTATGCTAAGTGAAATAAGCCAGWCACAAAAGGACAAAT 651
INTRON_3 141135 ACTGCATAGT---A--TATATGTGGAATCTAAAA-AATTGAACTCAGAGA 141178
i i ii --- -- v v i i - i?ii i v
L1MB4_3end#LI 652 ATTGTATGATTCCACTTATATGAGGTACCTAGAATAGKCAAATTCATAGA 701
INTRON_3 141179 AGTAGAGGGTAGAGTGGTGGTTACCAGGGGATAGGG--AGG-----ATGG 141221
iii ii i i ? v i -- -----
L1MB4_3end#LI 702 GACAGAAAGTAGAATAGWGGTTACCAGGGGCTGGGGGGAGGGGAAAATGG 751
INTRON_3 141222 GAAGATGTTGGTCAAAGAATACAAAATTTCAGTT 141255
i v ii v i v ii i i v
L1MB4_3end#LI 752 GGAGTTACTGTTTAATGGGTACAGAGTTTCTGTT 785
Matrix = 20p37g.matrix
Transitions / transversions = 1.72 (105 / 61)
Gap_init rate = 0.02 (14 / 695), avg. gap size = 2.93 (41 / 14)
3982 13.31 3.99 0.14 INTRON_3 140648 141324 258857 + L1MA8_3end LINE/L1 152 854 184 344
INTRON_3 140648 TAACCATCAGAGAAATGCAAATTAACACCACAGTGAGATATCTCCTCACA 140697
i i i v i v
L1MA8_3end#LI 152 TAATCATCAGGGAAATGCAAATCAAAACCACAATGAGATATCACCTCACA 201
INTRON_3 140698 CCTATTAGAATTGCTATTATCAAAAAGACCAAAGATAAC--TTGTTGGTA 140745
i v v --v ?i
L1MA8_3end#LI 202 CCTGTTAGAATGGCTATTATCAAAAAGACGAAAGATAACAAGTGTTGGWG 251
INTRON_3 140746 AGGATATGGAGTCAAGGGAACCCTTGCATGCTGTTGGTGGGTATGT---- 140791
i vv ii v ----
L1MA8_3end#LI 252 AGGATGTGGAGAAAAGGGAACCCTTGCACACTGTTGGTGGGAATGTAAAT 301
INTRON_3 140792 --GTATAATTATTATGAAAAATAGAATGCACATTCCTCAAAAAACTGAAG 140839
-- i iii i i v v vi i i i
L1MA8_3end#LI 302 TAGTACAGCCATTATGGAAAACAGTATGGAGGTTCCTCAAAAAATTAAAA 351
INTRON_3 140840 ATAGAACTATCATTTGATGCAGCAGTCTCATTAATGGGTAT----TCAAG 140885
i v v i i i ?v ----i i
L1MA8_3end#LI 352 ATAGAACTACCATATGATCCAGCAATCCCACTWCTGGGTATATATCCAAA 401
INTRON_3 140886 GGAAATGAATTCAGTATATTGAAGACATATCTGCACTGAAATGTTCATTG 140935
v i ii v vvv
L1MA8_3end#LI 402 GGAAATGAAATCAGTATGTCAAAGAGATATCTGCACTCCCATGTTCATTG 451
INTRON_3 140936 CAGCATTATTCATAATAGCCA-TATATGGAATCAATCTAAGTGTCCACAA 140984
i -v i iv
L1MA8_3end#LI 452 CAGCATTATTCACAATAGCCAAGATATGGAATCAACCTAAGTGTCCATCA 501
INTRON_3 140985 GCAAATGAATTGATAAAGAAAATGTGGTATATACACACAATGGAATACTA 141034
i ii v i i
L1MA8_3end#LI 502 ACGGATGAATGGATAAAGAAAATGTGGTACATATACACAATGGAATACTA 551
INTRON_3 141035 TTCAGCCTTAAAAAAGGAGGAAATCCTGTCATTTGTGACAACATGGATGA 141084
i i
L1MA8_3end#LI 552 TTCAGCCTTAAAAAAGAAGGAAATCCTGTCATTTGCGACAACATGGATGA 601
INTRON_3 141085 ACATGGAGGACATTATATTAAGTGAAATAAAG-AGGCAAAGAAAGATAAA 141133
v i iv- v i
L1MA8_3end#LI 602 ACCTGGAGGACATTATGTTAAGTGAAATAAGCCAGGCACAGAAAGACAAA 651
INTRON_3 141134 TACTGCATAGTAT-----ATATGTGGAATCTAAAAAA-TTGAACTCAGAG 141177
i ii v ----- - v
L1MA8_3end#LI 652 TACCGCATGATCTCACTTATATGTGGAATCTAAAAAAGTTGAACTCATAG 701
INTRON_3 141178 AAGTAGAGGGTAGAGTGGTGGTTACCAGGGGATAGGGAG---GA----TG 141220
i i i v i --- ----
L1MA8_3end#LI 702 AAGCAGAGAGTAGAATGGTGGTTACCAGGGGCTGGGGAGTGGGAGGATTG 751
INTRON_3 141221 GGAAGATGTTGGTCAAAGAATACAAAATTTCAGTTAGATAGGAGACATAT 141270
i i i iv v
L1MA8_3end#LI 752 GGGAGATGTTGGTCAAAGGATACAAAATTTCAGTTAGACAGGAGGAATAA 801
INTRON_3 141271 GTACAAAGGATCTATTGTACAACATGGTTAACTGTAGGTAATAACAATGT 141320
v ii -i i v
L1MA8_3end#LI 802 GTTCAAGAGATCTATTGTACAACATGGT-GACTATAGTTAATAACAATGT 850
INTRON_3 141321 ATTG 141324
L1MA8_3end#LI 851 ATTG 854
Matrix = 20p37g.matrix
Transitions / transversions = 1.75 (56 / 32)
Gap_init rate = 0.01 (10 / 676), avg. gap size = 2.80 (28 / 10)
747 14.28 5.16 0.62 INTRON_3 141324 141478 258703 + L1MA8_3end LINE/L1 876 1037 1 345
INTRON_3 141324 GAGTAGATTTTAAGTGTTCTCATCACAAAAAA--GATAGGTATGTGAGGT 141371
i -- i
L1MA8_3end#LI 876 GAGTAGATTTTAAGTGTTCTCACCACAAAAAAATGATAAGTATGTGAGGT 925
INTRON_3 141372 GATACCTATGTTAAT-AGCTTAGTTGATCCATTCCACCATGTATACATAT 141420
i i v - ii v v v
L1MA8_3end#LI 926 AATGCATATGTTAATTAGCTTGATTTAGCCATTCCACAATGTATACATAT 975
INTRON_3 141421 TTCAAAACATTATTTTGTATACGTAT-----TTTGTAATTTTTATTTTTC 141465
? i v i -i ----- v ii v
L1MA8_3end#LI 976 WTCAAAACATCATGTTGTACAC-CATAAATATATACAATTTTTATTTGTC 1024
INTRON_3 141466 TATTAAATAAAAA 141478
v ? v
L1MA8_3end#LI 1025 AATTWAAAAAAAA 1037
Matrix = 20p37g.matrix
Transitions / transversions = 1.22 (11 / 9)
Gap_init rate = 0.03 (4 / 154), avg. gap size = 2.25 (9 / 4)
+ 1215 15.9 8.1 0.4 INTRON_3 141505 141750 (258431) C L1MC3 LINE/L1 (169) 7616 7352 173
ANNOTATION EVIDENCE:
1215 15.91 8.13 0.38 INTRON_3 141505 141750 258431 C L1MC3_3end LINE/L1 2099 2363 169 346
INTRON_3 141505 ATTAACCAAAGCCCATATTTTATAGATATTTACCTAGTTTTTACATG-TG 141553
i i i vv v v i v i-
C L1MC3_3end#LI 2363 ATTAACTAAAGTCCATACTTTATTCAGATTTCCTTAGTTTTTACCTAATG 2314
INTRON_3 141554 TTCATTTTCTGTTC-AGGATCTCATCCAG-------------ATTTAGTC 141589
i v - i -------------
C L1MC3_3end#LI 2313 TCCTTTTTCTGTTCCAGGATCCCATCCAGGATACCACATTACATTTAGTC 2264
INTRON_3 141590 ATCATGTCTCTTTAGGCTCCTCTTGACTG--ACAGTTTCTCAGACTTTTC 141637
i i i -- i
C L1MC3_3end#LI 2263 GTCATGTCTCCTTAGGCTCCTCTTGGCTGTGACAGTTTCTCAGACTTTCC 2214
INTRON_3 141638 TTGTTTTTGATGATGTTGACAGTTTTGAGGAATATTGGTCAGGTATTTTA 141687
iv i i i
C L1MC3_3end#LI 2213 TTGTTTTTGATGACCTTGACAGTTTTGAGGAGTACTGGTCAGGTATTTTG 2164
INTRON_3 141688 TAAGGTGTCTGTA---TGAGATTGGTCTGCTATTTTTCTTACAATTTAAA 141734
iii iv v--- i v v i i ii - i
C L1MC3_3end#LI 2163 TAGAATGTCCCTCAATTGGGATTTGTCTGATGTTTTTCTCATGATT-AGA 2115
INTRON_3 141735 CTGAGGTTATAGATTT 141750
i i i
C L1MC3_3end#LI 2114 CTGGGGTTATGGGTTT 2099
Matrix = 20p37g.matrix
Transitions / transversions = 2.55 (28 / 11)
Gap_init rate = 0.02 (6 / 245), avg. gap size = 3.50 (21 / 6)
+ 1753 14.0 7.9 0.9 INTRON_3 141762 142177 (258004) C L1MC3 LINE/L1 (493) 7292 6854 173
ANNOTATION EVIDENCE:
1753 13.53 7.01 0.86 INTRON_3 141762 142089 258092 C L1MC3_3end LINE/L1 1692 2039 493 347
INTRON_3 141762 ACTATCAATGTGACTTATCACTGTTCATGTTGGCCTTTATCACCTGGCTG 141811
ii v i v
C L1MC3_3end#LI 2039 ACTATCAACATGACTTATCACTGTTGATGTTGACCTTGATCACCTGGCTG 1990
INTRON_3 141812 CGGTAGTGTTTGTCAGGTTTCTCCAGTGTAAAGTTACTTACCCTTCCTCG 141861
v v iviii i ?
C L1MC3_3end#LI 1989 AGGTAGTGTTTGTCAGGTTTCTCCACTGTAAAGTTACTCTTTTTTCCCCM 1940
INTRON_3 141862 GTATCCATACCGTAGTTTTTGGAAGGAAGTCACTACTATGTGCAGCCCAC 141911
v v i v i --- i
C L1MC3_3end#LI 1939 CTTTCCATACTGTACTCTTTGGAAGGAAGTCACTA---TGCGCAGCCCAC 1893
INTRON_3 141912 ACTTAAAGAGTGGAGAGTTATGCTCCACCTCCATGAGGATGGAATATCTA 141961
i i v ii i
C L1MC3_3end#LI 1892 ACTTAAGGAGTGGGGAGTTATGCTCCACCTCCTTGAGGGCGGAGTATCTA 1843
INTRON_3 141962 CATCAATTATTTGTA----TTCTGCATGAGATATTTGTCTTTTCTCCC-C 142006
v v ---- i i v i i -
C L1MC3_3end#LI 1842 CATAAATTATTTGGAATTCTTCTGCACGGGAGATTTGTCTCTTCTTCCTC 1793
INTRON_3 142007 ATTTATTGAT-----CAATTGCTTATTAATA-----GTGAAT--ATGGAT 142044
v ----- iii v -----i i i--
C L1MC3_3end#LI 1792 ATTTATTTATTTATTCAATCATTTATTTATATCAGTATGGACTCATGGAT 1743
INTRON_3 142045 ATTTATTTTATATTTTGGGTTATAAT-----ATTACTTTATTT-TGTTGT 142088
i ----- i - v
C L1MC3_3end#LI 1742 ATTTATTTTATACTTTGGGTTATAATCCAATACTACTTTATTTATTTTGT 1693
INTRON_3 142089 T 142089
C L1MC3_3end#LI 1692 T 1692
Matrix = 20p37g.matrix
Transitions / transversions = 1.87 (28 / 15)
Gap_init rate = 0.02 (8 / 327), avg. gap size = 3.25 (26 / 8)
767 15.69 11.40 0.94 INTRON_3 141985 142177 258004 C L1MC3_3end LINE/L1 1601 1813 719 348
INTRON_3 141985 GAGATATTTGTCTTTTCTCCCCATTTATTGAT-----CAATTGCTTATTA 142029
v v v i - i v ----- iii v
C L1MC3_3end#LI 1813 GAGATTTGTCTCTTCT-TCCTCATTTATTTATTTATTCAATCATTTATTT 1765
INTRON_3 142030 ATA-----GTGAAT--ATGGATATTTATTTTATATTTTGGGTTATAAT-- 142070
-----i i i-- i --
C L1MC3_3end#LI 1764 ATATCAGTATGGACTCATGGATATTTATTTTATACTTTGGGTTATAATCC 1715
INTRON_3 142071 ---ATTACTTTATTT----TGTTGTTCAAATTGTTCTAGATTTAGCTATG 142113
--- i ---- i i v i i v
C L1MC3_3end#LI 1714 AATACTACTTTATTTATTTTGTTGCTCAAATTGTTCCAGCTTTGGCCATT 1665
INTRON_3 142114 TGGAGCTCTTTCAGTTGGCTCCCATGTCTCTTTGACGTACCTCC-TCATT 142162
v ii i i i -
C L1MC3_3end#LI 1664 GGGAGCTCTTTCAGTTGGCTCCTGTGTCCCTTTGACATACCCCCATCATT 1615
INTRON_3 142163 GCAGATTTTTGTTGA 142177
ii i -
C L1MC3_3end#LI 1614 GTGGGTTTTT-TTGA 1601
Matrix = 20p37g.matrix
Transitions / transversions = 2.75 (22 / 8)
Gap_init rate = 0.04 (8 / 192), avg. gap size = 3.00 (24 / 8)
+ 954 21.9 0.0 2.2 INTRON_3 142193 142379 (257802) + MER58A DNA/hAT-Charlie 42 224 (0) 174
ANNOTATION EVIDENCE:
954 21.87 0.00 2.19 INTRON_3 142193 142379 257802 + MER58A DNA/hAT-Charlie 42 224 0 369
INTRON_3 142193 GCCATCTGTGTTTGTAAATAAAGTTTTATTGGAACACAGCCACAGTTATT 142242
ii v ivii
MER58A#DNA/hA 42 GCCGCCTGTTTTTGTAAATAAAGTTTTATTGGAACACAGCCACGCCCATT 91
INTRON_3 142243 ATCTTATATATTCTTTATGGCTACTTTTGCACTACAGTGGCAGAGTTAAT 142292
vvi ii v i i i i ii i v
MER58A#DNA/hA 92 CGTTTACGTATTGTCTATGGCTGCTTTCGCGCTACAACGGCAGAGTTGAG 141
INTRON_3 142293 TCACTGCAACAGAGACCATATTGCCTGTAAAGCCTAAACTAATTACAGTC 142342
vii i i v i i v v vi
MER58A#DNA/hA 142 TAGTTGCGACAGAGACCGTATGGCCCGCAAAGCCTAAAATATTTACTATC 191
INTRON_3 142343 TGACCTGTTACAGAAAAAAAAAATTTGCTGACTCTTG 142379
i iv i---- i i i
MER58A#DNA/hA 192 TGGCCCTTTACAGAAAAAG----TTTGCCGACCCCTG 224
Matrix = 20p37g.matrix
Transitions / transversions = 2.33 (28 / 12)
Gap_init rate = 0.01 (1 / 186), avg. gap size = 4.00 (4 / 1)
+ 28 66.7 0.0 0.0 INTRON_3 143380 143421 (256760) + AT_rich Low_complexity 1 42 (0) 175
ANNOTATION EVIDENCE:
28 66.67 0.00 0.00 INTRON_3 143380 143421 256760 + AT_rich Low_complexity 128 169 131 318
INTRON_3 143380 TTTAAAATAGAATTTTACTATAAAAATAAAAATTAAAATAAT 143421
????????????v v vv v vv v v???????
AT_rich#Low_c 128 WWWWWWWWWWWWATTAAAAATAAATAATATAATTTWWWWWWW 169
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 9)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0)
+ 323 33.2 6.3 0.8 INTRON_3 143478 143699 (256482) + L2c LINE/L2 1851 2084 (1335) 176
ANNOTATION EVIDENCE:
323 33.16 6.31 0.85 INTRON_3 143478 143699 256482 + L2 LINE/L2 1851 2084 998 291
INTRON_3 143478 CCCCCTTTTTTGT---CTTCTACTGCCAATCTTTTCAAATAAGTAATCTG 143524
vi i i i--- i i v v v ii vi vi i
L2#LINE/L2 1851 CCCATTTCTCTGCTCCCCTTTACAGCAAAACTCCTCAAAAGAGTTGTCTA 1900
INTRON_3 143525 T-CTTACATCCTCCA--TTTTCAATTCACATTCTC-CTTAG-CTCTCAGA 143569
- ii vvi -- ii vvi v - i- i v vvv
L2#LINE/L2 1901 TACTCGCTGTCTCCAATTCCTCTCCTCCCATTCTCTCTTAAACCCACTCC 1950
INTRON_3 143570 AATCTGCATTT--TCCTAATTACTTGCCTGAATCCGAGCTCTTG--AAGG 143615
v vv -- iv ii ivv i v i -- --
L2#LINE/L2 1951 AATCAGGCTTTCGTCCCCACCACTCCACCGAAACTG--CTCTTGTCAAGG 1998
INTRON_3 143616 TCACCA-TGACCTCCTAATTGTCAAATCAAATAGTCTTTTCCCAG-CCTT 143663
- vvi ii v i vv i - i
L2#LINE/L2 1999 TCACCAATGACCTCCATGTTGCTAAATCCAATGGTCAATTCTCAGTCCTC 2048
INTRON_3 143664 AGTGTCTTTGATTTGCATGCAACATTCGATACTGTT 143699
viv vi ii iivv i i i v
L2#LINE/L2 2049 ATCTTACTTGACCTATCAGCAGCATTTGACACAGTT 2084
Matrix = 25p37g.matrix
Transitions / transversions = 1.21 (40 / 33)
Gap_init rate = 0.05 (10 / 221), avg. gap size = 1.60 (16 / 10)
+ 212 41.5 7.3 1.0 INTRON_3 143820 144106 (256075) + L2c LINE/L2 2331 2635 (784) 176
ANNOTATION EVIDENCE:
212 41.52 7.32 0.98 INTRON_3 143820 144106 256075 + L2 LINE/L2 2331 2635 447 292
INTRON_3 143820 GATGATGGACAAATCTAAATTTCCAGCCT-GATCTTTCTCTTGG------ 143862
ivvv i v i i- i i i i i------
L2#LINE/L2 2331 GATGACTCCCAAATTTATATCTCCAGCCCAGACCTCTCCCCTGAACTCCA 2380
INTRON_3 143863 -----GTA-ATTG---TGTCCACAAAACATTTTCA-TGAGGCACCTTG-A 143901
----- - iv--- i i vvi i i - vi iiii vi-
L2#LINE/L2 2381 GACTCGTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATA 2430
INTRON_3 143902 GTTGTCTCAAATTTAGTGTTTCATAATCTTAACCTGTTATTTTTCTTTCT 143951
vii i iii v vv v v - vi iv i iii
L2#LINE/L2 2431 GGCATCTCAAACTTAACATGTCCAAAACTGAAC-TCCTGATCTTCCCCCT 2479
INTRON_3 143952 TAAATTTGGTTCCATTCTTCTAAATTTCTTACTTCTGTTAATGATCCCAC 144001
i ii -i - i iv vivv i ii ii v iivv v
L2#LINE/L2 2480 CAAACCTG-CTCC-TCCCACAGTCTTCCCCATCTCAGTTAATGGCAACTC 2527
INTRON_3 144002 TATCATCAAGGTTGTCTGGGTCTGA--CATTTGAGTGACAGTTAA-TACA 144048
i v ivvi iiii i vi -- v v v ivv i - v v
L2#LINE/L2 2528 CATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCT 2577
INTRON_3 144049 CACTTTCTCTTGTTTTCCATAGCCAGTAAGTTAACAAGTTCTAATGATTC 144098
v iiivii i v i vvi i i i i iv ii
L2#LINE/L2 2578 CTCTTTCTCTCACACCCCACATCCAATCCATCAGCAAATCCTGTTGGCTC 2627
INTRON_3 144099 TCTCCTCA 144106
vi i
L2#LINE/L2 2628 TACCTTCA 2635
Matrix = 25p37g.matrix
Transitions / transversions = 1.74 (75 / 43)
Gap_init rate = 0.04 (11 / 286), avg. gap size = 2.18 (24 / 11)
+ 197 34.9 11.3 0.0 INTRON_3 144543 144648 (255533) + L2c LINE/L2 3023 3140 (247) 176
ANNOTATION EVIDENCE:
197 34.91 11.32 0.00 INTRON_3 144543 144648 255533 + L2c_3end LINE/L2 114 231 247 293
INTRON_3 144543 CTTTTCTGCTTGAAAATCATGGTAGAGTCTAGTCTGCCTACCTAAAATGC 144592
i i vvi?ii v v i v vv iv ivi i ii
L2c_3end#LINE 114 CTTTCCTGCCTCCGNGCCTTTGCACATGCTGTTCCCTCTGCCTGGAATGC 163
INTRON_3 144593 TTTTCCCGTTCCTCTCCAC--AG--AAT--------ATCCTTCAATTCCC 144630
i viii ii --i -- i-------- v? i
L2c_3end#LINE 164 TCTTCCCCCCTCCTTCCACCTGGCTAACTCCTACTCATCCTTCAAGNCTC 213
INTRON_3 144631 AGCTCACATCTCACTTCC 144648
v v i
L2c_3end#LINE 214 AGCTCAGATGTCACCTCC 231
Matrix = 25p37g.matrix
Transitions / transversions = 1.69 (22 / 13)
Gap_init rate = 0.03 (3 / 105), avg. gap size = 4.00 (12 / 3)
+ 419 25.6 13.3 3.7 INTRON_3 144681 144912 (255269) + MIRb SINE/MIR 2 256 (6) 177
ANNOTATION EVIDENCE:
419 26.39 13.81 4.37 INTRON_3 144681 144890 255291 + MIRb SINE/MIR 2 230 38 294
INTRON_3 144681 AAAAAAGCAGCATGGTGCATGGGAAGAAAAACAAGAGATTTGAAGTCAGA 144730
i iii i vv -- i i v i v i i
MIRb#SINE/MIR 2 AGAGGGGCAGCGTGGTGCAGTGGAA--AGAGCACGGGCTTTGGAGTCAGG 49
INTRON_3 144731 -GGACTT-------ACTTCTAG-TCTGCACA---------TGAATGACTT 144762
-i i ------- v i i - - --------- vi i
MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCTGGCTCTGC-CACTTACTAGCTGTGTGACCT 98
INTRON_3 144763 TGGATAAATCACTT---TTGCCTGGCCAACCATTGTTTCCTCATCTATAA 144809
ii i ---i vi --- i viv i
MIRb#SINE/MIR 99 TGGGCAAGTCACTTAACCTCTCTG---AGCCTCAGTTTCCTCATCTGTAA 145
INTRON_3 144810 AAATAAGAGTATACAATTACTT---TCACAAGGATGTTGGGAAGATTAAA 144856
- ii ii - i - i --- i i v v i
MIRb#SINE/MIR 146 AA-TGGGGATA-ATAAT-ACCTACCTCGCAGGGTTGTTGTGAGGATTAAA 192
INTRON_3 144857 TAA-ATAGGCACACGTAA-GCTCTT--CA-GGCACCTGG 144890
i - i-ii i - v -- -i ii
MIRb#SINE/MIR 193 TGAGATAA-TGCATGTAAAGCGCTTAGCACAGTGCCTGG 230
Matrix = 25p37g.matrix
Transitions / transversions = 3.42 (41 / 12)
Gap_init rate = 0.08 (17 / 209), avg. gap size = 2.29 (39 / 17)
345 25.25 13.12 3.43 INTRON_3 144753 144912 255269 + MIR SINE/MIR 82 256 6 295
INTRON_3 144753 TGAATGACTTTGGATAAATCACTT---TTGCCTG-GCCAACCATTGTTTC 144798
vi i ii i i ---i vi - --i --
MIR#SINE/MIR 82 TGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGTGCC--TCA--GTTTC 127
INTRON_3 144799 CTCATCTATAAAAATAAGAGTATACAAT--TACTT---TCACAAGGATGT 144843
i - ii ii - i -- i --- i i v
MIR#SINE/MIR 128 CTCATCTGTAAAA-TGGGGATA-ATAATAGTACCTACCTCATAGGGTTGT 175
INTRON_3 144844 TGGGAAGATTAAATAAATAGGCACACGTAA-GCTCTT----CAG------ 144882
v i i i viii i - v ---- ------
MIR#SINE/MIR 176 TGTGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTG 225
INTRON_3 144883 GCACCTGGAAATTGCCCA-CAAATGTTTGTT 144912
v i v vi i -i v
MIR#SINE/MIR 226 GCACATAGTAAGCGCTCAATAAATGTTGGTT 256
Matrix = 25p37g.matrix
Transitions / transversions = 2.90 (29 / 10)
Gap_init rate = 0.08 (12 / 159), avg. gap size = 2.25 (27 / 12)
+ 408 4.0 0.0 0.0 INTRON_3 145032 145081 (255100) + (CA)n Simple_repeat 2 51 (0) 178
ANNOTATION EVIDENCE:
408 4.00 0.00 0.00 INTRON_3 145032 145081 255100 + (CA)n Simple_repeat 2 51 129 363
INTRON_3 145032 ACACACACATGCACACACACACACACACACACACACACACACACACACAC 145081
ii
(CA)n#Simple_ 2 ACACACACACACACACACACACACACACACACACACACACACACACACAC 51
Matrix = Unknown
Transitions / transversions = 0.0 (2 / 0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 533 29.2 10.8 2.6 INTRON_3 146240 146527 (253654) + AmnSINE1 SINE/Deu 193 503 (72) 179
ANNOTATION EVIDENCE:
533 29.22 10.76 2.57 INTRON_3 146240 146527 253654 + AmnSINE1 SINE/Deu 193 503 72 370
INTRON_3 146240 GGTCACTGTGCTGTGGGACATACCTTCT-----GTGAGATG--------A 146276
v iv vi i v -----i i --------
AmnSINE1#SINE 193 GGGCACTGTGCTGCTGGAGGTGCCGTCTTTCGGATGAGACGTAAAACCGA 242
INTRON_3 146277 GGCTCTGACCACTAATGA-CA--------CTTGTG---CTTTTCATTACG 146314
ii vi i- -------- iii --- iiv vi
AmnSINE1#SINE 243 GGTCCTGACCACTTGTGGTCATTAAAGATCCCATGGCACTTTTCGCAAGA 292
INTRON_3 146315 ACAGATGTGTTAACCACATCGTGCTGGTCATGCTCCAGCCCAAGCCATTG 146364
ii iv v ivi v i vii iiiiii iv i
AmnSINE1#SINE 293 GTAGGGGTGTTAACCCCGGTGTCCTGGCCAAATTCCAATTTGGGTAATTA 342
INTRON_3 146365 TAGCTTTCTGCTTCTGCAACCTTCCTCGTCTTCACTTT-GGTTGGCTGTA 146413
i --- i vivi v- i -- v v -ii v iii
AmnSINE1#SINE 343 CA---TTCTGCCTACCTAAA-TTCCCC--CTGCAGTTTCAATTGGATACG 386
INTRON_3 146414 GAATTCTTTACTTCCTGTCCTAAATTTTTGTGAGGTGTCA---TG-GCTG 146459
v i i v vi ii--- -
AmnSINE1#SINE 387 GTATTCTTCACTTCCTGTCCTAAACTGTTGTGTAGTGTTGCTGTGCGCTG 436
INTRON_3 146460 TTAAACAGCTGCCATGTTGCAGGCCAGATGTGGCTGCACTTTAGTG-CGC 146508
ii v vv v i i -i v
AmnSINE1#SINE 437 TTAAACAGCTGCCGCGTTCCACCCCAGAGGTGGCTGCATTTCAGTGGTGG 486
INTRON_3 146509 ATGAAATGTTCTTCCTATA 146527
i i v -- i
AmnSINE1#SINE 487 GTGAAGTGATC--CCTGTA 503
Matrix = 20p37g.matrix
Transitions / transversions = 1.93 (54 / 28)
Gap_init rate = 0.05 (13 / 287), avg. gap size = 3.00 (39 / 13)
+ 180 21.9 4.9 0.0 INTRON_3 146561 146601 (253580) + AmnSINE1 SINE/Deu 508 550 (25) 179
ANNOTATION EVIDENCE:
180 21.95 4.88 0.00 INTRON_3 146561 146601 253580 + AmnSINE1 SINE/Deu 508 550 25 296
INTRON_3 146561 GTTTGTAAAACACTTAGGATTCCTTCAG-ATAAGAGG-GCTAT 146601
i i i v iv i - i i -
AmnSINE1#SINE 508 GCTTGTAAAGCGCTTTGGGATCCTTCGGGATGAAAGGTGCTAT 550
Matrix = 25p37g.matrix
Transitions / transversions = 3.50 (7 / 2)
Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2)
+ 2338 10.1 0.0 1.3 INTRON_3 146823 147129 (253052) + AluSx3 SINE/Alu 1 303 (9) 180
ANNOTATION EVIDENCE:
2195 10.59 0.65 1.64 INTRON_3 146823 147129 253052 + AluSx SINE/Alu 1 304 8 273
INTRON_3 146823 GGCTGGGCACAGTGGCTGAAGCCTGTAATCCCAGCAGTTTGGGAGTCTGA 146872
i i i v v v v i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 146873 GGTGGGTGGATCAC--GAGGTCAGGAGTTCAAGACCAGCCTGGCCAATAT 146920
i i -- i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
INTRON_3 146921 GGTGAAACCCCATCTCTGTTAAAAATAGAAAAAAAAAATTAGCCGGGCAT 146970
i ii v ----- i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAA-----TTAGCCGGGCGT 145
INTRON_3 146971 GGTGGCATATGCCTGTAGTCCCAGCTACTCTGGAGGCTGAGGCAGAAGAA 147020
iiii i v i
AluSx#SINE/Al 146 GGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAA 195
INTRON_3 147021 TCACTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCTGAGATCGCTCCACT 147070
i i v
AluSx#SINE/Al 196 TCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACT 245
INTRON_3 147071 GCACTGCAGCCTGGGTGACAGAGTGAGACTCTGTCTCAAAAAAAAAAAAA 147120
v i i i
AluSx#SINE/Al 246 GCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAA 295
INTRON_3 147121 AAAAAGAAA 147129
i
AluSx#SINE/Al 296 AAAAAAAAA 304
Matrix = 14p37g.matrix
Transitions / transversions = 3.00 (24 / 8)
Gap_init rate = 0.01 (2 / 306), avg. gap size = 3.50 (7 / 2)
+ 1839 22.2 4.3 5.9 INTRON_3 147208 147949 (252232) C L1ME2 LINE/L1 (0) 6164 5423 181
ANNOTATION EVIDENCE:
1839 24.90 2.64 5.42 INTRON_3 147208 147776 252405 C L1ME2_3end LINE/L1 358 911 0 349
INTRON_3 147208 TTTTTTATTGAGATATAACTTACACACAGTGAAGTGTAAAGGTCCTAAGT 147257
v i i i i i i i v i i
C L1ME2_3end#LI 911 TTTTTTTTTGAGGTATAATTTACATACAATAAAATGCACAGATCTTAAGT 862
INTRON_3 147258 G---------ATCAGTTTTCACAAATGCCTACTCTTGTGTTACC-CCAAC 147297
--------- v v iv v iii v - v
C L1ME2_3end#LI 861 GTACAGTTCGATGAGTTTTGACAAATGTATACACCCATGTAACCACCACC 812
INTRON_3 147298 ACTATCAGCACCCAGTACGTTTTCATCATTCCCAGAGAGTTTCCTTATGC 147347
v v ? iv ivi v i i i- i i i
C L1ME2_3end#LI 811 CCAANCAAGATATAGAACATTTCCATCAC-CCCAGAAAGTTCCCTTGTGC 763
INTRON_3 147348 TCCTTCCCAGTCAG-CACTTACTTAGTCCCAATTCTAAGCAACCACTCAT 147396
i i i- v ii ii--i ii---- i vv
C L1ME2_3end#LI 762 CCCTTTCCAGTCAATCCCCCACCC--CCCCGG----AGGCAACCACTGTT 719
INTRON_3 147397 CTGATTTCTATCACTATAGATTATGTTAGACTATTGTAGAGCTTCATATA 147446
i i vv v v i v i
C L1ME2_3end#LI 718 CTGATTTCTGTCACCATAGATTAGTTTTGCCTGTTCTAGAACTTCATATA 669
INTRON_3 147447 TATAGAATCATGTAGCATGTACTTTTTTGTGTCTGGCTTCTTTCACTTGG 147496
v i ii i i ii
C L1ME2_3end#LI 668 AATGGAATCATACAGTATGTACTCTTTTGTGTCTGGCTTCTTTCACTCAG 619
INTRON_3 147497 CATAATGTTTTTGATATTCACTCATGATGTTGTTTATATAAATGCTTCAT 147546
i v ii v iv i v i iv i
C L1ME2_3end#LI 618 CATAATGTCTTTGAGATTCATCCATGTTGTTGCGTGTATCAGTAGTTCGT 569
INTRON_3 147547 CCCTTTTTTTGTTGCTGAGTACTGTTCCATTAAATGAATATACCGCA--- 147593
i --i v i iv i ---
C L1ME2_3end#LI 568 TCCTTTTT--ATTGCTGAGTAGTATTCCATTGTATGAATATACCACAATT 521
INTRON_3 147594 -GTTTATCCGTTAACCTTTTGGTGAATGTCTGAATTGTTGATGGATATCT 147642
- i v? v i i ii i ii -------- i
C L1ME2_3end#LI 520 TGTTTATCCATTCNCCTGTTGATGGACATTTGGGTTGTT--------TCC 479
INTRON_3 147643 GAATTTACTGACTGTAAAGTATTTGGTTATCATGAGTAAAGCTTCTATGG 147692
- i ?v- i i v v v vvi i iii ii ---- - v
C L1ME2_3end#LI 478 -AGTTTNG-GGCTATTATGAATAAAGCTGCTATGAACA----TTCT-TGT 436
INTRON_3 147693 ACACACCTAAGACTTTTTATAGACATAGATTTTCGTTTTTCTCATAAAAA 147742
------ v i i vi i i iiviv
C L1ME2_3end#LI 435 ACA------AGTCTTTTTGTGGACATATGTTTTCATTTCTCTTGGGTAAA 392
INTRON_3 147743 TATCTAGGAGCAGAATTTCTGAGTCATAGGGTAG 147776
i ii v i
C L1ME2_3end#LI 391 TACCTAGGAGTGGAATTGCTGGGTCATAGGGTAG 358
Matrix = 20p37g.matrix
Transitions / transversions = 2.05 (88 / 43)
Gap_init rate = 0.02 (14 / 568), avg. gap size = 3.21 (45 / 14)
1459 19.84 5.78 6.31 INTRON_3 147552 147949 252232 C L1ME2z_3end LINE/L1 170 565 626 350
INTRON_3 147552 TTTTTGTTGCTGAGTACTGTTCCATTAAATGAATATACCGCAGTTTATCC 147601
i v i iv i i --
C L1ME2z_3end#L 565 TTTTTATTGCTGAGTAGTATTCCATTGTATGAATATACCACAGTTTGT-- 518
INTRON_3 147602 GTTAACCTTTTGGTGAATGTCTGAATTGTTGATGGATATCTGAATTTACT 147651
- v v i-------- i---- i i ii----
C L1ME2z_3end#L 517 -TTATCCATTC--------TCC----TGTTGATGGACACCTGGG----CT 485
INTRON_3 147652 GACTGTAAAGTATTTGGTTATCATGAGTAAAGCTTCTATGGACACACCT- 147700
-- v vv v i i i v i iv i -
C L1ME2z_3end#L 484 G--TTTCCAGTTTTTGGCTATTATGAATAAAGCTGCTATGAACATTCTTG 437
INTRON_3 147701 ---AAGACTTTTTATAGACATAGATTTTCGTTTTTCTCATAAAAATATCT 147747
--- v i i vi i i iiviv i
C L1ME2z_3end#L 436 TACAAGTCTTTTTGTGGACATATGTTTTCATTTCTCTTGGGTAAATACCT 387
INTRON_3 147748 AGGAGCAGAATTTCTGAGTCATAGGGTAGCTAGAGATATGTTTAATGTTT 147797
ii v i v i---- i v v
C L1ME2z_3end#L 386 AGGAGTGGAATTGCTGGGTCATAGGGTAGGTG----TATGTTTAGTTTTA 341
INTRON_3 147798 TAAGAAACTGCCAAACTATTTTCCAAAGTGGTTCTACCATTTCACACTCT 147847
i iv v i i
C L1ME2z_3end#L 340 TAAGAAACTGCCAGACCTTTTTCCAAAGTGGTTGTACCATTTTACACTCC 291
INTRON_3 147848 TACCAACAATATATGAAAGTTCTGGTTGCTCCATATCCCCACCAACATT- 147896
i i i i i i i -
C L1ME2z_3end#L 290 CACCAACAATGTATGAGAGTTCCGGTTGCTCCACATCCTCGCCAACATTT 241
INTRON_3 147897 ---------AATTTTTTTACT----G--ATTCTAATGGGCGCTTAGTGTT 147931
--------- i i v ---- -- ii i iv v
C L1ME2z_3end#L 240 GGTGTTGTCAGTCTTTTTAATTTTAGCCATTCTGGTGGGTGTGTAGTGGT 191
INTRON_3 147932 ATCT---TGTTATTTTAACTT 147949
--- vi i
C L1ME2z_3end#L 190 ATCTCATTGTGGTTTTAATTT 170
Matrix = 20p37g.matrix
Transitions / transversions = 2.08 (50 / 24)
Gap_init rate = 0.03 (11 / 397), avg. gap size = 4.36 (48 / 11)
+ 776 21.9 8.2 5.3 INTRON_3 147945 148199 (251982) C L1MD3 LINE/L1 (10) 7985 7724 182 *
ANNOTATION EVIDENCE:
776 21.95 8.24 5.34 INTRON_3 147945 148199 251982 C L1MD3_3end LINE/L1 2471 2732 10 351
INTRON_3 147945 AACTTTTAATTTTCAAACAATTTTGGATTTGCAGAAGAGTTGCAA----- 147989
v v i i i i -----
C L1MD3_3end#LI 2732 AACTTTTTATTTTGAAATAATTTTAGATTTACAGAAAAGTTGCAAAGATA 2683
INTRON_3 147990 ---------GTTCCCATA-AACCTTCACTCAACTTTTCATAATATTAACA 148029
--------- i - v i i ii v i
C L1MD3_3end#LI 2682 GTACAGAGAGTTCCCGTATACCCTTCACCCAGCTTCCCCTAATGTTAACA 2633
INTRON_3 148030 TTTTATATTAATGAAAACTAATACATTGATAGGTTGGTCAAAAT----AA 148075
i i ------- i ------ i vi vi i----
C L1MD3_3end#LI 2632 TCTTACAT-------AACCA------TGGTACATTTATCAAAACTAAGAA 2596
INTRON_3 148076 ATTATAATTGTTATAATATCATTAACCAATCTGTAGATTTTATTTAAGTT 148125
vv v i ii i v ii i iiii
C L1MD3_3end#LI 2595 ATTAACATTGGTACAATACTATTAACTAAACTACAGACTTTATTCGGATT 2546
INTRON_3 148126 TCCTTAGTTTTT--ACCAATCTCTTTTTTTGGTTTTAGGATCCAATCCAA 148173
vii -- i v i iv ii i
C L1MD3_3end#LI 2545 TCACCAGTTTTTCCACTAATGTCCTTTTTCTGTTCCAGGATCCAATCCAG 2496
INTRON_3 148174 GATATGACATTGCATTTAATTTGTCA 148199
iv i i -
C L1MD3_3end#LI 2495 GATACCACGTTGCATTTAGTT-GTCA 2471
Matrix = 20p37g.matrix
Transitions / transversions = 2.79 (39 / 14)
Gap_init rate = 0.03 (7 / 254), avg. gap size = 5.00 (35 / 7)
+ 639 18.8 4.5 0.0 INTRON_3 148192 148324 (251857) C L1MD3 LINE/L1 (129) 7866 7728 183 *
ANNOTATION EVIDENCE:
639 18.80 4.51 0.00 INTRON_3 148192 148324 251857 C L1MD3_3end LINE/L1 2475 2613 129 352
INTRON_3 148192 ATTTGTCAAAAC----AAATTATCATTGTTATAATATCGTTAACTAATCT 148237
i ---- v v i iii v
C L1MD3_3end#LI 2613 ATTTATCAAAACTAAGAAATTAACATTGGTACAATACTATTAACTAAACT 2564
INTRON_3 148238 GTAGATTTTATTTGAGTTTCCTTAGTTTTT--ACCAATGTCTTTTTTTGG 148285
ii i i ii vii -- i i iv
C L1MD3_3end#LI 2563 ACAGACTTTATTCGGATTTCACCAGTTTTTCCACTAATGTCCTTTTTCTG 2514
INTRON_3 148286 TTCTAGGATCCAGTCCAGGATACCACATTGCATTTAATT 148324
i i i i
C L1MD3_3end#LI 2513 TTCCAGGATCCAATCCAGGATACCACGTTGCATTTAGTT 2475
Matrix = 20p37g.matrix
Transitions / transversions = 4.00 (20 / 5)
Gap_init rate = 0.02 (2 / 132), avg. gap size = 3.00 (6 / 2)
+ 616 21.5 2.0 10.3 INTRON_3 148322 148615 (251566) C L1ME2 LINE/L1 (721) 5443 5162 181 *
ANNOTATION EVIDENCE:
587 20.63 1.46 10.58 INTRON_3 148322 148527 251654 C L1ME2_3end LINE/L1 2 190 721 353
INTRON_3 148322 ATTTCAGTATGCTTTTAATGTGTGCTTTCCTGCTGACTAATCATG---AT 148368
i v i v v iii i v v --- v
C L1ME2_3end#LI 190 ATCTCATTGTGGTTTTAATTTGCATTTCCCTGATGACTAATGATGTTGAG 141
INTRON_3 148369 CACCTTTTCATGTACTCATTGTCCATTTATAGATTTTTCTTTTGTAAAGT 148418
i i v i v i - i
C L1ME2_3end#LI 140 CACCTTTTCATGTGCTTATTGGCCATTTGTATATCTT-CTTTTGTGAAGT 92
INTRON_3 148419 GTCTGTCCAAGTGTCTTGCCTGGTTTTCTTTTGATTCTTTTTTGAGGGGG 148468
i v i ii---- i i -----------
C L1ME2_3end#LI 91 GTCTGTTCAAGTCTTTTGCCCA----TTTTTTAATT-----------GGG 57
INTRON_3 148469 TTGATTATTGGCTTTTTATTTACTGATTTTTAAGAATTTCTTATTTGTTC 148518
v i --- - i v v i i ii v i
C L1ME2_3end#LI 56 TTGTTTGT---CTTTTTATT-ATTGAGTTGTAGGAGTTCTTTATATATTC 11
INTRON_3 148519 TGGATATAA 148527
i
C L1ME2_3end#LI 10 TGGATACAA 2
Matrix = 20p37g.matrix
Transitions / transversions = 1.92 (25 / 13)
Gap_init rate = 0.03 (6 / 205), avg. gap size = 3.83 (23 / 6)
616 23.40 3.19 9.75 INTRON_3 148365 148615 251566 C L1M5_orf2 LINE/L1 3053 3288 6 354
INTRON_3 148365 TGATCACCTTTTCATGTACTCATTGTCCATTTATAGAT-TTTTCTTTTGT 148413
v i ii i v i-- - ii
C L1M5_orf2#LIN 3288 TGAGCACCTTTTCATATGTTTATTGGCCATTTG--GATATCCTCTTTTGT 3241
INTRON_3 148414 AAAGTGTCTGTCCAAGTGTCTTGCCTGGTTTTCTTTTGATTCTTTTTTGA 148463
i i i v i iiv ---- ---------
C L1M5_orf2#LIN 3240 GAAGTGCCTGTTCAAGTCTTTTGCCCATTTTTCT----ATT--------- 3204
INTRON_3 148464 GGGGGTTGATTATTGGCTTTTTATTTACTGATTTTTAAGAATTTCTTATT 148513
-- vi i --- -i i v i i ii v
C L1M5_orf2#LIN 3203 --GGGTTGTCTGT---CTTTTT-CTTATTGATTTGTAGGAGTTCTTTATA 3160
INTRON_3 148514 TGTTCTGGATATAA---TTTTGTCAGATATAAGTGTTG----TATTTTTT 148556
i i ---i ? v i ---- ? i
C L1M5_orf2#LIN 3159 TATTCTGGATATGAGTTCTTTGTCAGNTATATGTATTGCAAATATNTTCT 3110
INTRON_3 148557 TCCTTAGCCTATTACTTGTCCATTTATTTTCTCAATGGTGTTTTTTGATA 148606
i -- vi i vi i iv i i i i i i
C L1M5_orf2#LIN 3109 CCC--ACTCTGTGGCTTGCCTTTTCACTCTCTTAATGGTGTCTTTTGATG 3062
INTRON_3 148607 AGTAGAAGT 148615
ii
C L1M5_orf2#LIN 3061 AACAGAAGT 3053
Matrix = 20p37g.matrix
Transitions / transversions = 3.64 (40 / 11)
Gap_init rate = 0.04 (9 / 250), avg. gap size = 3.44 (31 / 9)
+ 312 24.7 14.4 3.1 INTRON_3 148829 148974 (251207) C MIR SINE/MIR (0) 262 101 184
ANNOTATION EVIDENCE:
312 24.73 14.38 3.09 INTRON_3 148829 148974 251207 C MIR SINE/MIR 101 262 0 297
INTRON_3 148829 AATAGTAATTGGTAATACTTGTTGTGTGCTTACTATGTGTAGCAGAC-CC 148877
i ii--- i i i v i i-- i - i
C MIR#SINE/MIR 262 AATAATAACC---AACATTTATTGAGCGCTTACTATGTGC--CAGGCACT 218
INTRON_3 148878 GTT----GC---TTAT-TGT-TTA-------TAGGCATCAT--CAAACTC 148909
---- --- i- - ------- iv v i-- v ii
C MIR#SINE/MIR 217 GTTCTAAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCT 168
INTRON_3 148910 ATAAGGTAGA-ATTATTATTATCTACATTT-AAAGGTAAGGAAACCAAGG 148957
i i- i iv - v i i ii
C MIR#SINE/MIR 167 ATGAGGTAGGTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGG 118
INTRON_3 148958 CTTAAAGATGGTAAATA 148974
vi i v v i
C MIR#SINE/MIR 117 CACAGAGAGGTTAAGTA 101
Matrix = 25p37g.matrix
Transitions / transversions = 2.89 (26 / 9)
Gap_init rate = 0.08 (11 / 145), avg. gap size = 2.36 (26 / 11)
+ 1902 14.7 3.9 0.0 INTRON_3 148988 149293 (250888) + L1M2a1 LINE/L1 3 320 (6796) 185 *
ANNOTATION EVIDENCE:
1902 14.71 3.92 0.00 INTRON_3 148988 149293 250888 + L1M2a1_5end LINE/L1 3 320 1522 355
INTRON_3 148988 CAAGATGGCTGACTAGATGCAGGTAATATGTACCTTCTCCATGTAGAGGA 149037
i i i v
L1M2a1_5end#L 3 CAAGATGGCTGACTAGATGCAGGTAGTATGTGCCTCCTCCATGGAGAGGA 52
INTRON_3 149038 GCCAGAATAGTCA-GCAGATAT----ATTTTGAACAGATCATTTAGGAGA 149082
i i - i i---- ?? i i
L1M2a1_5end#L 53 ACCAGAATAGTTAAGTAGATACTCACATTTYRAACAGATCGTCTAGGAGA 102
INTRON_3 149083 GAATGCTAGGATTCACCAGAGAAGAGATGGGAAGCACCAGAAGCAAGTAA 149132
?i i
L1M2a1_5end#L 103 GAATGCTAGGATTCACCAGAGAAGAGAYAGGAAGCACCAGAAGTAAGTAA 152
INTRON_3 149133 GGAGAGGGTTCGAAGCACCTTCCTCAGCCAGGAACAGACTGAGAGTTGGG 149182
i i v v i v i
L1M2a1_5end#L 153 GGAGAGGGTTTGAGGCAGCTTGCCCAGCCAGGAACTGACTGAGAGCTGGG 202
INTRON_3 149183 AAAAGCTCCTGGACATGGGGAAACAGTGATAGAGAAACCCCCAGGAATCA 149232
i i ii i v iv v
L1M2a1_5end#L 203 AGAGGCTCCTGGATGTGGGGAAACAGTAAGAGAGAAACCCCCAGGGCTCC 252
INTRON_3 149233 A-------AAATGGGCTTTTGCAATCTTGGCTACATGAGAAACCATAGAC 149275
------- ?i iii iiv v v
L1M2a1_5end#L 253 ACACTCTGAAAYAGGCTTTTATGATCTTGGCTATGGGAGAAACCCTTGAC 302
INTRON_3 149276 CCACTAAGGTCTTGGCCC 149293
i i i v
L1M2a1_5end#L 303 CCACTAGGGCCTCGGGCC 320
Matrix = 20p37g.matrix
Transitions / transversions = 2.73 (30 / 11)
Gap_init rate = 0.01 (3 / 305), avg. gap size = 4.00 (12 / 3)
+ 4301 20.3 1.8 0.0 INTRON_3 149274 150115 (250066) + L1M2a1 LINE/L1 458 1335 (5781) 185
ANNOTATION EVIDENCE:
2096 23.34 2.52 0.00 INTRON_3 149274 149710 250471 + L1M2a1_5end LINE/L1 888 1335 507 356
INTRON_3 149274 ACCCACTAAGGTCTTGGCCCAAAGGTGCTGTTTTGAGAGTTTAATGCTGG 149323
v vv iii v v ii
L1M2a1_5end#L 888 ACCCTCTCTGGTCCCAGGCCCAAGGTGCCATTTTGAGAGTTTAATGCTGG 937
INTRON_3 149324 GCTGCACCCTACCCTTGGCTTGACTTTGGGCTGATGTGGCTATAGCCACC 149373
ii i vi v i ii ii ii i
L1M2a1_5end#L 938 GCTGTGCCCCACCCTTGGGCTGAGTTTGAGCTGACATGGCTGCAGCTGCT 987
INTRON_3 149374 ACTCTGCCAAGGAGGGACAGGGAAACCAGGTTATCCTATGCATATCTAGG 149423
i i v i v i
L1M2a1_5end#L 988 GCCCAGCCAAGGAGGGACAGGGAAACCAGGCTCTCCTATGCATACCTAGG 1037
INTRON_3 149424 ACAATACCCACTACCCTACAACAGGTTGCTTTGAGACTAAGATGTGAGTG 149473
i i v ii i v i iv i
L1M2a1_5end#L 1038 ACAATACCCACTGCCCTGCTATGGGCTGCTGTGAGACTGAGACTTGAGTA 1087
INTRON_3 149474 GACCACAATTCCTACAGCCTCTTGTCCATGCTGCTTGCTTGGGAGGGAAC 149523
v i i i i i i i iv
L1M2a1_5end#L 1088 GACCACACTCCCCACAGCTTCTTGCCCATGCTGCTTACCTGAGAGGGGCC 1137
INTRON_3 149524 CC-ACCGTCTCTGGTCCCATCACCAA----GGGACC----TGAGAATTCA 149564
- v v vvv v---- v ---- i i
L1M2a1_5end#L 1138 CCCACCCTCTCTGGTCACAAGCCCACAGCTGGCACCATTTTGAGAGTTTA 1187
INTRON_3 149565 ATACTGAGCTGTGCCTCACTCTTGGTCTGAGTTTGGGCTGACATGGCTAT 149614
i i i i v i v ii ii
L1M2a1_5end#L 1188 ATGCTGGGCTGTGCCCCACCCTTGGGCTGAGTTTGAGGTGATGTGGCTGC 1237
INTRON_3 149615 AGCCACTGTCTGGCCAAGG-AGAGACAGGAAA-ACCGGGCTTTACTATGC 149662
ii iii ii i i - i ii - ii i v v
L1M2a1_5end#L 1238 AGCTGCCACCCAGCTAGGGGAGGGACAGGGGAGACCAAGCTCTCCTAAGC 1287
INTRON_3 149663 ATATCTAGGACAAGATGCACTGCTCTGCAGTGGGCTGCTGTGAGACTG 149710
i ii v iv i viii iv i
L1M2a1_5end#L 1288 ACACTTAGGACAATACCCACTGCCCTGCTACAGGTGGCTGTGGGACTG 1335
Matrix = 20p37g.matrix
Transitions / transversions = 2.52 (73 / 29)
Gap_init rate = 0.01 (5 / 436), avg. gap size = 2.20 (11 / 5)
4301 20.00 1.71 0.00 INTRON_3 149356 150115 250066 + L1M2a1_5end LINE/L1 458 1230 612 357
INTRON_3 149356 GATGTGGCTATAGCCACCACTCTGC--CAAGGAGGGACAGGGAA-ACCAG 149402
ii ii ii v -- v i -
L1M2a1_5end#L 458 GACATGGCTGCAGCCACTGCACTGCTCCAAGGAGGGAGAGGGGAGACCAG 507
INTRON_3 149403 GTTATCCTATGCATATCTAGGACAATACCCACTACCCTACAACAGGTTGC 149452
ivv i ivi vii ii i i v ii i
L1M2a1_5end#L 508 GCACTCCCATGCACCCCTAGGAGGGTACCTGCTGCCCTGCTATGGGCTGC 557
INTRON_3 149453 TTTGAGACTAAGATGTGAGTGGACCACAATTCCTACAGCCTCTTGTCCAT 149502
v i ii ? v i i i i
L1M2a1_5end#L 558 TGTGAGACTGAGACATGAGTNGACCACACTCCCCACAGCTTCTTGCCCAT 607
INTRON_3 149503 GCTGCTTGCTTGGGAGGGAACCCACCGTCTCTGG-TCCCATCACCAAGG- 149550
i viv v - vvv -
L1M2a1_5end#L 608 GCTGCTTGCCTGGGAGGTGCCCCACCCTCTCTGGNTCCCAGGCCCAAGGT 657
INTRON_3 149551 GA---CC----TGAGAATTCAATACTGAGCTGTGCCTCACTCTTGGTCTG 149593
?--- ---- i i i i ii i i i
L1M2a1_5end#L 658 GNNTGCCATTTTGAGAGTTTAATGCTGGGCTGCACCCCACCCTTGGCCTG 707
INTRON_3 149594 AGTTTGGGCTGACATGGCTATAGCCACTGTCTGGCCAAGGAGAGACAGGA 149643
i ii ii iii ii i i
L1M2a1_5end#L 708 AGTTTGGGCTGACGTGGCTGCAGCTGCCACCCAGCCAAGGAGGGACAGGG 757
INTRON_3 149644 AAACCGGGCTTTACTATGCATATCTAGGACAAGATGCACTGCTCTGCAGT 149693
i i v v iv i i
L1M2a1_5end#L 758 AAACCAGGCTCTCCTATGCATATCTAGGACAATACCCACTGCCCTGCAAT 807
INTRON_3 149694 GGGCTGCTGTGAGACTGAAACATAAGCAGACCACATGCCACATAGCTACT 149743
i ii i ii iv v i v
L1M2a1_5end#L 808 GGGCTGCTGTGAGACTGAGATGTGAGTGGACCACACTCCCCACAGCTTCT 857
INTRON_3 149744 TGCCTATGATGCCTGTTTGGGAAGGGTCCCATTCTCCCTGGTTGCAGGCC 149793
i v i ii i i ii i iv
L1M2a1_5end#L 858 TGCCCATGCTGCTTGCCTGGGAGGGGCCCCACCCTCTCTGGTCCCAGGCC 907
INTRON_3 149794 CAAGGAGCCATTTTGAGAGTTTAATGCTGGGCTGTGCCCTGCCCTTAGGC 149843
v ii i
L1M2a1_5end#L 908 CAAGGTGCCATTTTGAGAGTTTAATGCTGGGCTGTGCCCCACCCTTGGGC 957
INTRON_3 149844 TGAATTTGACTTGATGTAGCTGCAGCTGCTGTCTGGTTGAGGAGGGACAT 149893
i vi ii i i ii iii v
L1M2a1_5end#L 958 TGAGTTTGAGCTGACATGGCTGCAGCTGCTGCCCAGCCAAGGAGGGACAG 1007
INTRON_3 149894 GGAAGCTAGGCTCTCCTATATATACCTAGGACAATACCCACTGCCCTCCT 149943
i i ii v
L1M2a1_5end#L 1008 GGAAACCAGGCTCTCCTATGCATACCTAGGACAATACCCACTGCCCTGCT 1057
INTRON_3 149944 ATGGGCTGCTGTGAAACTGAGACCTGGGCAGATTACAGTCCCCACAGCTT 149993
i i i i ii v
L1M2a1_5end#L 1058 ATGGGCTGCTGTGAGACTGAGACTTGAGTAGACCACACTCCCCACAGCTT 1107
INTRON_3 149994 CTTCTCCATGCTGCTTAACTGAAAGGAGGTGC-ACCTTCTGTGGTTATAA 150042
vi v i i viv - i v i i
L1M2a1_5end#L 1108 CTTGCCCATGCTGCTTACCTGAGAGGGGCCCCCACCCTCTCTGGTCACAA 1157
INTRON_3 150043 GCCCACAGCTGGTATCATTTCCAGAGTTTAACACTGGGATTTTCCCCACC 150092
i i iv ii v v v
L1M2a1_5end#L 1158 GCCCACAGCTGGCACCATTTTGAGAGTTTAATGCTGGGCTGTGCCCCACC 1207
INTRON_3 150093 CTCAGGCTGAGTTCAAGGTGATG 150115
ii ii
L1M2a1_5end#L 1208 CTTGGGCTGAGTTTGAGGTGATG 1230
Matrix = 20p37g.matrix
Transitions / transversions = 3.05 (113 / 37)
Gap_init rate = 0.01 (7 / 759), avg. gap size = 1.86 (13 / 7)
+ 252 38.8 0.0 0.0 INTRON_3 150116 150195 (249986) C MIR SINE/MIR (181) 81 2 186
ANNOTATION EVIDENCE:
252 38.75 0.00 0.00 INTRON_3 150116 150195 249986 C MIR SINE/MIR 2 81 181 298
INTRON_3 150116 GCAAGAAAATGGTGAATTAAGAGTTTAAATACAGGCAGTCTGACTTCAAA 150165
v v i iii vivi ii ii iv i i i
C MIR#SINE/MIR 81 GCTAGTAAGTGGCAGAGCCGGGATTCGAACCCAGGCAGTCTGGCTCCAGA 32
INTRON_3 150166 GCCTTCATGCTTAATTTCTGTGCTATTCTG 150195
i iviiiv iiv i v
C MIR#SINE/MIR 31 GTCCGTGCTCTTAACCACTATGCTATACTG 2
Matrix = 25p37g.matrix
Transitions / transversions = 2.44 (22 / 9)
Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.0 (0 / 0)
+ 262 27.9 10.6 5.0 INTRON_3 150587 150756 (249425) + X7A_LINE LINE/CR1 28 206 (61) 187
ANNOTATION EVIDENCE:
262 27.87 10.59 5.03 INTRON_3 150587 150756 249425 + X7A_LINE LINE/CR1 28 206 61 299
INTRON_3 150587 TAGCATTAGAGGACCAACACTGAAGCTTCCTTAATAAATGGAAGCTTA-- 150634
v ? v -- vi ----i v i v v vi --
X7A_LINE#LINE 28 TAGAATTASAGGCCC--CCTTGAAGCTT----GAAAGAGGTAATTTTAGG 71
INTRON_3 150635 AC---TAAAAGGAAATAACTCTTTTACATA------------ATTTCTGG 150669
--- i ?- vi i ------------ i v
X7A_LINE#LINE 72 ACAAATAAAAGGAAGTR-CTACTTTACACAGCAGGGGAGTAAACTTATGG 120
INTRON_3 150670 AATGTATTAACTGAAGAGGTAGTGAAGAGTAAAAATAAAAATATATTCAA 150719
ivi v iv i iv iv i v vv
X7A_LINE#LINE 121 AACTCATTACCCCAAGAGGTGGTATAGGCTGAAAATATAAATAGCTTCAA 170
INTRON_3 150720 AGTAAAGTTTCAAA-GGTTTAATGAATGGCAGTTCCAT 150756
-- v i i -iiv v i ii v
X7A_LINE#LINE 171 A--AAAGATTTAGATAAATTCATGGATGATAGATCCAT 206
Matrix = 25p37g.matrix
Transitions / transversions = 1.05 (22 / 21)
Gap_init rate = 0.05 (8 / 169), avg. gap size = 3.38 (27 / 8)
+ 187 34.4 10.4 2.2 INTRON_3 150987 151111 (249070) + L2a LINE/L2 3102 3236 (151) 188
ANNOTATION EVIDENCE:
187 34.36 10.40 2.22 INTRON_3 150987 151111 249070 + L2c_3end LINE/L2 193 327 151 300
INTRON_3 150987 CCTCTTCATTTTTTAAGGCCTAGC-CAAAAGGCATCTCTTATGTGAAAGC 151035
vi ii i ? ii - i v v i i viiv iv
L2c_3end#LINE 193 CCTACTCATCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCAGGAAGCC 242
INTRON_3 151036 TTACCCAGCATTTCCAGGCAAAT--AGTTACTCCCTGCTCTATGTTCCT- 151082
v iii viii v ? v i -- v i -- v i i i-
L2c_3end#LINE 243 TTCCCTGACCCCCCAAGNCTAGTCTAGGTGC--CCTCCTCTGTGCTCCCA 290
INTRON_3 151083 --------TGTAATTTACTCT-ATTTTAGCACTGATCA 151111
-------- v- v i- v v
L2c_3end#LINE 291 TAGCACCCTGTC-TATACTCCCATTATAGCACTTATCA 327
Matrix = 25p37g.matrix
Transitions / transversions = 1.50 (24 / 16)
Gap_init rate = 0.05 (6 / 124), avg. gap size = 2.67 (16 / 6)
+ 539 25.9 7.1 0.7 INTRON_3 151298 151437 (248744) C MIRb SINE/MIR (108) 160 12 189
ANNOTATION EVIDENCE:
539 25.88 7.14 0.67 INTRON_3 151298 151437 248744 C MIRb SINE/MIR 12 160 108 301
INTRON_3 151298 ACTATTATCCCCATT----------GTGAACTGGGACTCAAAGAAGTGAA 151337
i ---------- vi i i i i v
C MIRb#SINE/MIR 160 ATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAA 111
INTRON_3 151338 ATAATTTGTCCAAGGTCAAACAGCTGCAAAGAATTATAGCCAGGATTGGA 151387
i i i i v ivv vivi v v
C MIRb#SINE/MIR 110 GTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCAGGATTCGA 61
INTRON_3 151388 ACCCAGTGCTGTCTAACTTCAAACCCTGTGCTTCTGGCCAGTACAGTATG 151437
vv i i i v i - vv v i vi i
C MIRb#SINE/MIR 60 ACCCAGGTCTGCCTGACTCCAAAGCCCGTGCT-CTTTCCACTGCACCACG 12
Matrix = 25p37g.matrix
Transitions / transversions = 1.25 (20 / 16)
Gap_init rate = 0.01 (2 / 139), avg. gap size = 5.50 (11 / 2)
+ 274 25.9 10.5 0.9 INTRON_3 151597 151701 (248480) + L2a LINE/L2 3311 3425 (1) 188
ANNOTATION EVIDENCE:
274 25.94 10.48 0.87 INTRON_3 151597 151701 248480 + L2a_3end LINE/L2 402 516 1 302
INTRON_3 151597 TAAGATCCTTGACTGCAAG-ACTTTTCTTTGTGCTTTTC-TTGA------ 151638
v v vv i - v i vi v -i v------
L2a_3end#LINE 402 TAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATC 451
INTRON_3 151639 --CAG-ATCTAGCCCAATGCCTTGTACATAGTAGGTACTCAATGAAAACC 151685
-- -ii vv i v i ii i v ii
L2a_3end#LINE 452 CCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATT 501
INTRON_3 151686 TGTAGAATTGAATTAA 151701
v - v
L2a_3end#LINE 502 TGTTGAAT-GAATGAA 516
Matrix = 25p37g.matrix
Transitions / transversions = 0.93 (13 / 14)
Gap_init rate = 0.05 (5 / 104), avg. gap size = 2.40 (12 / 5)
+ 453 30.0 10.3 4.7 INTRON_3 152344 152567 (247614) + L2a LINE/L2 1246 1481 (1938) 190
ANNOTATION EVIDENCE:
453 29.97 10.27 4.66 INTRON_3 152344 152567 247614 + L2 LINE/L2 1246 1481 1601 303
INTRON_3 152344 GCCTGCTTCAGACCTGCTCCTAGCCAGTTTTATGTTGGTGGAG------- 152386
i i ivi v iivv i vv i v v -------
L2#LINE/L2 1246 GCCTACTCCGCGCCTGCACCCGTGCAGCTGAACGTGGCTGGAGAAAAACA 1295
INTRON_3 152387 CATGACTTTGCTAACTGGGTTTACTTTACTTTCATGATCATTAACCCAAA 152436
ii iv i vi ii vv i iv iv
L2#LINE/L2 1296 CACAACCATGCTGACTGGTCTCGCTTTAAATTCATGACCACGAACCTCAA 1345
INTRON_3 152437 ATAGGTG-TTGGTGATGCCCACCAATCTTACTGTTTTTTTTT-GTCCACC 152484
i i iv- ii v iv v iiv iii - ii
L2#LINE/L2 1346 GTGGGCCCTTAATGCTGCCCGGCAATCATACTACATTTCCCTAGTCCATT 1395
INTRON_3 152485 ACGCATTCTCCTATTCTCTT--------------CACTTTCTCTTCTCTC 152520
--- i i i i -------------- i i
L2#LINE/L2 1396 ---CACTCTCCCACTCTCCTAGATNACTATTTCACACCTTCTCCTCTCTC 1442
INTRON_3 152521 TTCAAAACCTACAGCACTTAATTTCCCTCCTTTATCCTTTACTTTCA 152567
i - v i i ------ ii i- i
L2#LINE/L2 1443 CTCAAA-CCTCCAACACCT------CCTCCCCTATCCTC-ACTCTCA 1481
Matrix = 25p37g.matrix
Transitions / transversions = 2.20 (44 / 20)
Gap_init rate = 0.04 (8 / 223), avg. gap size = 4.25 (34 / 8)
+ 798 28.3 5.6 4.3 INTRON_3 152584 153011 (247170) + L2a LINE/L2 2798 3228 (198) 190
ANNOTATION EVIDENCE:
798 27.20 3.09 5.26 INTRON_3 152584 152874 247307 + L2 LINE/L2 2798 3082 0 304
INTRON_3 152584 GATCCTTTTAAACC-TAAGTTGAACCATGTGACTCTGCTGCTCAAAACCT 152632
v - iii i v iv i
L2#LINE/L2 2798 GATCCTTTTAAAACATAAGTCAGATCATGTCACTCCTCTGCTCAAAACCC 2847
INTRON_3 152633 GTTAGTGGCTTCTCATGTCCCTCAGA-TGAAAGCTACCATC-TTGCAGTG 152680
vii i v v - i i vvi - i
L2#LINE/L2 2848 TCCAGTGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCCTTACAGTG 2897
INTRON_3 152681 ACTTACAAGGCTATAAAGTCTGCCATCTACCACCCACTTTACTCCCCACT 152730
i i iv v --- -- iviv - v ------
L2#LINE/L2 2898 GCCTACAAGGCCCTACA---TG--ATCTGGTCCCC-CGTTAC------CT 2935
INTRON_3 152731 GTCTGCCCAC-TCTCTGACCTTTCTTCTCCTACTCTCTTATTT-GTTATA 152778
v v v - iv vi i i --- v i i i- i vi
L2#LINE/L2 2936 CTCTGACCTCATCTCCTACCACTCTCCCCCT---CGCTCACTCCGCTCCA 2982
INTRON_3 152779 TTCAT--TGGCCTCTTTACTCTTCCTTAAA-ATACAGAGCATGCTCTAGT 152825
vi i-- i i v ii - ii vii i iv i
L2#LINE/L2 2983 GCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCACGCTCCTGC 3032
INTRON_3 152826 GTAAGGGCCTTTGCATTAGCTGTTCTC-CTGCTTGAAAATTTCTTCCCTC 152874
v v i v i - i i vvi i
L2#LINE/L2 3033 CTCAGGGCCTTTGCACTTGCTGTTCCCTCTGCCTGGAACGCTCTTCCCCC 3082
Matrix = 25p37g.matrix
Transitions / transversions = 1.59 (46 / 29)
Gap_init rate = 0.04 (13 / 290), avg. gap size = 1.85 (24 / 13)
635 30.50 11.03 2.37 INTRON_3 152740 153011 247170 + L2a_3end LINE/L2 25 319 198 305
INTRON_3 152740 CTCTCTGACCTT-TCTTCTCCTACTCTCTTATTTGTTATATTC------- 152781
i- i v i iivi i i -i i -------
L2a_3end#LINE 25 CTCTCTGACCTCATCTCCTACCACTCTCCCCCTCGCT-CACTCCGCTCCA 73
INTRON_3 152782 -----ATTGGCCTCTTTACTCTTCCTTAAA-ATACAGAGCATGCTCTAGT 152825
----- i i i v ii - ii vii i iv i
L2a_3end#LINE 74 GCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCACGCTCCCGC 123
INTRON_3 152826 GTAAGGGCCTTTGCATTAGCTGTTCTC-CTGCTTGAAAATTTCTTCCCTC 152874
v v i v i - i i vvi i
L2a_3end#LINE 124 CTCAGGGCCTTTGCACTTGCTGTTCCCTCTGCCTGGAACGCTCTTCCCCC 173
INTRON_3 152875 AGATGCCTGTGTGGTTT-----CTCATTTCCTTCAGGCATCTGTTCATAT 152919
ii i ii i i----- ii iv i i v
L2a_3end#LINE 174 AGATATCCGCATGGCTCGCTCCCTCACCTCCTTCAGGTCTTTGCTCAAAT 223
INTRON_3 152920 ATCA--------GAGAGGCTTTTTCCTGGCCGTC-TAAATAAAATACCAG 152960
i -------- v i i- i ii - vv ?v -
L2a_3end#LINE 224 GTCACCTTCTCAGTGAGGCCTTC-CCTGACCACCCTATTTAAAATWGCA- 271
INTRON_3 152961 TCCCCACTCTGACCTC-AGCACTTTCTAACTCCTTTATTTCTCTTCACAT 153009
---- i v? i - ? ii v i i iiiiv i iv
L2a_3end#LINE 272 ----CACCCTCNCCCCCANCACTCCCTATCCCCCTTACCCTGCTTTATTT 317
INTRON_3 153010 TT 153011
L2a_3end#LINE 318 TT 319
Matrix = 25p37g.matrix
Transitions / transversions = 2.90 (58 / 20)
Gap_init rate = 0.04 (11 / 271), avg. gap size = 3.36 (37 / 11)
+ 6624 11.2 1.8 0.4 INTRON_3 153648 154575 (245606) + Charlie3 DNA/hAT-Charlie 1 941 (1765) 191
ANNOTATION EVIDENCE:
6624 11.15 1.83 0.43 INTRON_3 153648 154575 245606 + Charlie3 DNA/hAT-Charlie 1 941 1765 371
INTRON_3 153648 CACGGGTCCCCAACCTCCAGGCCACAGACCAGGACCAGTCCATGGCCTGT 153697
v i i i i v i i
Charlie3#DNA/ 1 CAGGGGTCCCCAACCCCCGGGCCACGGACCGGTACCGGTCCGTGGCCTGT 50
INTRON_3 153698 TAGGAATCAGGCTGCATAGCAGGAGCTAAGTGGCAGGGTGAGCGAGCGAA 153747
i i i i v i i - i
Charlie3#DNA/ 51 TAGGAACCGGGCCGCACAGCAGGAGGTGAGCGGC-GGGCGAGCGAGCGAA 99
INTRON_3 153748 GCTTCATCTTTATTTACAGCCACTCCCCATCACTTGGCGTTACTGCCTGA 153797
v i i i - i i
Charlie3#DNA/ 100 GCTTCATCTGTATTTACAGCCGCTCCCCATCGCTCG-CATTACCGCCTGA 148
INTRON_3 153798 GCTCCACCTCCTGTCAGATCAGCAGCAGCAATAGATTATCATAGGAGCAC 153847
i i i v v i
Charlie3#DNA/ 149 GCTCCGCCTCCTGTCAGATCAGCGGCGGCATTAGATTCTCATAGGAGCGC 198
INTRON_3 153848 AAACCCTATTGTGAACTGCTCATGTGAGGGATCTAGGTTGTGTACTCCTT 153897
i v i i ii
Charlie3#DNA/ 199 GAACCCTATTGTGAACTGCGCATGCGAGGGATCTAGGTTGCGCGCTCCTT 248
INTRON_3 153898 ATGAGAATCTAATGCTTGATGATCTGAGGTGGAGCTGAGGCAGTGGTGCT 153947
i i i
Charlie3#DNA/ 249 ATGAGAATCTAATGCCTGATGATCTGAGGTGGAGCTGAGGCGGTGATGCT 298
INTRON_3 153948 AGTGCTGGAGAGTGGCTACAAATACAGATTAACATTAGCAGAGAAGTTTG 153997
i i i i i
Charlie3#DNA/ 299 AGCGCTGGGGAGCGGCTGCAAATACAGATTAACATTAGCAGAGAGGTTTG 348
INTRON_3 153998 ACTGCACAGAGACCATAATAAACCAATTTCTTGCAGACTGATGTCAAAAC 154047
i v v i
Charlie3#DNA/ 349 ACTGCACAGAGACCATAATAAATCAATTGCTTGCAGACTCATATCAAAAC 398
INTRON_3 154048 CCTATCAGCAAATGGCAAGTGACAATTAAGCTGCATCTGTTGGCAGG--- 154094
ii i v ---
Charlie3#DNA/ 399 CCTATCAGTGAGTGGCAAGTGACAATTAAGCTGCATCTGGTGGCAGGCTT 448
INTRON_3 154095 ------------TGAGTTGATGTACTTGAGTTGTACAGCTGCATCTGGTG 154132
------------ v i
Charlie3#DNA/ 449 TATAGTGGCAAGTGAGTTGATGTACTTCAATTGTACAGCTGCATCTGGTG 498
INTRON_3 154133 GCAGGCTTTAAGTCAGAATCTGACACTTGTTTTAATCTCCACATGGCCTG 154182
i i i iv i i i
Charlie3#DNA/ 499 GCAGGCTTTAAGTCAGAATCCGACACTTATTTTAGTCCGCGCGTGGCCCG 548
INTRON_3 154183 CCCATTACTTTTTTTACTTCTTTTGTTTGCGCCTCTTTCTAACACTGTGC 154232
i v iv ii ii ivi i
Charlie3#DNA/ 549 CCCATTATTTTATTTACCACTTCCGTCCGCGCCTCTTTCCCGCACTGCGC 598
INTRON_3 154233 ACTTGTCTCAATCACAGTTTTGGTACGCCCACAAGCTAACTCTAGGCAAA 154282
i v i v
Charlie3#DNA/ 599 ACTTGTCTCAGTCACAGTTTTGGTAAGCCCACAAGCTAACCCTAGCCAAA 648
INTRON_3 154283 ATGAGTAAAAAACAAACATCACTAGGGAGCTTCTTTGAAAAGGAGGAAAA 154332
i i i i i
Charlie3#DNA/ 649 ATGAGTAAAAAACAAACGTCACTGGAGAGCTTCTTTGAAAAGGGGGAAAG 698
INTRON_3 154333 ATTCAGTGATGAGACAGCAGAAGACTCTAAGAATGCCAACAAAA-GAAAG 154381
ii i v -
Charlie3#DNA/ 699 ACCCAATGATGAGACAGCAGAAGACTCTAAGACTGCCAACAAAAAGAAAG 748
INTRON_3 154382 CTGCATTTAAATGAAAATACCAAGAGTCCTACTTAAATTATGA-TTCATT 154430
v i i-
Charlie3#DNA/ 749 CTGCATTTAAAAGAAAATACCAAGAGTCCTACTTAAATTACGGGTTCATT 798
INTRON_3 154431 GCAACAGGTGATATACATTCTCCAAGCCTGCTTTGTATACTGTGTGGCAA 154480
vi i v i i
Charlie3#DNA/ 799 GCAACAGGTGATTCACATTCTCCAAGCCCGCTTTGTATAATATGTGGCGA 848
INTRON_3 154481 TCAGCTATCCAAAAAAGGCCATGAAATATTCAAAACTGCTTCGCCACATG 154530
i i vi - iv
Charlie3#DNA/ 849 CCGGCTATCCAACGAAG-CCATGAAACCTTCAAAACTGCTTCGCCACATG 897
INTRON_3 154531 GAGACCAAGCATCCTGGATTAAAAGACAAGCCTTTTTGAGTTTTT 154575
i v v-
Charlie3#DNA/ 898 GAGACCAAGCACCCTGCATTAAAAGACAAGCCTTTG-GAGTTTTT 941
Matrix = 20p37g.matrix
Transitions / transversions = 3.12 (78 / 25)
Gap_init rate = 0.01 (7 / 927), avg. gap size = 3.00 (21 / 7)
+26308 4.6 0.1 0.1 INTRON_3 154580 160567 (239614) C L1PA4 LINE/L1 (1) 6154 165 192
ANNOTATION EVIDENCE:
7671 2.33 0.00 0.00 INTRON_3 154580 155480 244701 C L1PA4_3end LINE/L1 1 901 1 358
INTRON_3 154580 TTTTTTTTTTTTATTATACTTTAAGTATTAGGGTACATGTGCACACCGTG 154629
v v v
C L1PA4_3end#LI 901 TTTTTTTTTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACGTG 852
INTRON_3 154630 CAGGTTTGTTACATATGTATACATGTGCCATGTTGGTGTGCTGCACCCAT 154679
C L1PA4_3end#LI 851 CAGGTTTGTTACATATGTATACATGTGCCATGTTGGTGTGCTGCACCCAT 802
INTRON_3 154680 TAACTCGTCCTTTAACATTAGGTATATCTCCTAATGCTATCCCTCCCCCC 154729
v
C L1PA4_3end#LI 801 TAACTCGTCATTTAACATTAGGTATATCTCCTAATGCTATCCCTCCCCCC 752
INTRON_3 154730 TCCCCCCACCCCACAACAGTCCCCGGTGTTTGATGTTCCCCTTCCTGTGT 154779
v v
C L1PA4_3end#LI 751 TCCCCCCACCCCACAACAGGCCCCGGTGTGTGATGTTCCCCTTCCTGTGT 702
INTRON_3 154780 CCATGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAACATGCAGTG 154829
i
C L1PA4_3end#LI 701 CCATGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAACATGCGGTG 652
INTRON_3 154830 TTTGGTTTTTTGTCCTTGCGATAGTTTGCTGAGAATGATGGTTTCCAGTT 154879
i
C L1PA4_3end#LI 651 TTTGGTTTTTTGTCCTTGCGATAGTTTGCTGAGAATGATGGTTTCCAGCT 602
INTRON_3 154880 TCATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCC 154929
v
C L1PA4_3end#LI 601 TCATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCA 552
INTRON_3 154930 TAGTATTCGATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCAT 154979
v
C L1PA4_3end#LI 551 TAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCAT 502
INTRON_3 154980 TGTTGGACATTTGGGTTGGTTCCAAGTCTTTTCTGTTGTGAATAGTGCCA 155029
v i i
C L1PA4_3end#LI 501 TGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCCG 452
INTRON_3 155030 CAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAATCC 155079
C L1PA4_3end#LI 451 CAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAATCC 402
INTRON_3 155080 TTTGGATATATACCCAGTAATGGGATGGCTGGGTCAAGTGGTATTTCTAG 155129
i i
C L1PA4_3end#LI 401 TTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAG 352
INTRON_3 155130 TTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTA 155179
C L1PA4_3end#LI 351 TTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTA 302
INTRON_3 155180 GTTGACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCT 155229
v
C L1PA4_3end#LI 301 GTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCT 252
INTRON_3 155230 CTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGG 155279
i
C L1PA4_3end#LI 251 CTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATCGCCATTCTAACTGG 202
INTRON_3 155280 TGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCA 155329
C L1PA4_3end#LI 201 TGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCA 152
INTRON_3 155330 GAGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCT 155379
v i
C L1PA4_3end#LI 151 GTGATGATGAGCATTTTTTCATGTGTCTTTTGGCTGCATAAATGTCTTCT 102
INTRON_3 155380 TTTGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTGATGGGGTTGTT 155429
i i
C L1PA4_3end#LI 101 TTTGAGAAGTGTCTGTTCATATCCTTCGCCCACTTTTTGATGGGGTTGTT 52
INTRON_3 155430 TGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTA 155479
C L1PA4_3end#LI 51 TGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTA 2
INTRON_3 155480 G 155480
C L1PA4_3end#LI 1 G 1
Matrix = 20p37g.matrix
Transitions / transversions = 0.91 (10 / 11)
Gap_init rate = 0.00 (0 / 900), avg. gap size = 0.0 (0 / 0)
26308 4.25 0.09 0.09 INTRON_3 155332 158624 241557 C L1P1_orf2 LINE/L1 1 3293 1 359
INTRON_3 155332 GATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTT 155381
i
C L1P1_orf2#LIN 3293 GATGATGAGCATTTCTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTT 3244
INTRON_3 155382 TGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTGATGGGGTTGTTTG 155431
i
C L1P1_orf2#LIN 3243 TGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTG 3194
INTRON_3 155432 TTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGC 155481
C L1P1_orf2#LIN 3193 TTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGC 3144
INTRON_3 155482 CCTTTGTCAGATGAGTAGGTTGCAAAAATTTTCTCCCATTTTGTAGGTTG 155531
i v
C L1P1_orf2#LIN 3143 CCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATGTTGTAGGTTG 3094
INTRON_3 155532 CCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTGAGTT 155581
v
C L1P1_orf2#LIN 3093 CCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTT 3044
INTRON_3 155582 TAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGGT 155631
C L1P1_orf2#LIN 3043 TAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGGT 2994
INTRON_3 155632 GTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTAATGCC 155681
i i
C L1P1_orf2#LIN 2993 GTTTTGGACATGAAGTCCTTGCCCACGCCTATGTCCTGAATGGTAATGCC 2944
INTRON_3 155682 TAGATTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAATGTTTAAGTCTT 155731
i i i
C L1P1_orf2#LIN 2943 TAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAATCTT 2894
INTRON_3 155732 TAATCCATCTTGAATTGATTTTTGTATAAGGTGTAAGGAAGGGATCCAGT 155781
C L1P1_orf2#LIN 2893 TAATCCATCTTGAATTGATTTTTGTATAAGGTGTAAGGAAGGGATCCAGT 2844
INTRON_3 155782 TTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAA 155831
C L1P1_orf2#LIN 2843 TTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAA 2794
INTRON_3 155832 TAGGGAATCCTTTCCCGATTGCTTGTTTTTCTCAGGTTTGTCAAAGATCA 155881
v
C L1P1_orf2#LIN 2793 TAGGGAATCCTTTCCCCATTGCTTGTTTTTCTCAGGTTTGTCAAAGATCA 2744
INTRON_3 155882 GATAGCTGTAGATATGTGGTGTTATTTCTGAGGGCTCTATTCTGTTCCAT 155931
i i ii i
C L1P1_orf2#LIN 2743 GATAGTTGTAGATATGCGGCATTATTTCTGAGGGCTCTGTTCTGTTCCAT 2694
INTRON_3 155932 TGATCTATATCTCTGTTTTGGTACCAGTAGCATGCTGTTTTGGTTACTGT 155981
v
C L1P1_orf2#LIN 2693 TGATCTATATCTCTGTTTTGGTACCAGTACCATGCTGTTTTGGTTACTGT 2644
INTRON_3 155982 AGCCTTGTAGTATAGTTTGAAGTCAGGTAGCATGATGCCTCCAGCTTTGT 156031
ii
C L1P1_orf2#LIN 2643 AGCCTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTCCAGCTTTGT 2594
INTRON_3 156032 TCTTTTGGCTTAGGATTGCCTTGGTGATGCGGACTCTTTTTTGGTTCCAT 156081
v i i
C L1P1_orf2#LIN 2593 TCTTTTGGCTTAGGATTGACTTGGCGATGCGGGCTCTTTTTTGGTTCCAT 2544
INTRON_3 156082 ATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGTCATTGGTAG 156131
C L1P1_orf2#LIN 2543 ATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGTCATTGGTAG 2494
INTRON_3 156132 CTTGATGGGGATGGCATTGAATCTATAAATTACCTTGGGCAGTATGGCCA 156181
i
C L1P1_orf2#LIN 2493 CTTGATGGGGATGGCATTGAATCTGTAAATTACCTTGGGCAGTATGGCCA 2444
INTRON_3 156182 TTTTCACGATATTGATTCTTCCTATCCATGAGCATGGAATGTTCTTCCAT 156231
i
C L1P1_orf2#LIN 2443 TTTTCACGATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTCCAT 2394
INTRON_3 156232 TTGTTTGTATCCTATTTTATTTCACTGAAAAGTGGTTTGTAGTTCTCCTT 156281
i v vi iv
C L1P1_orf2#LIN 2393 TTGTTTGTGTCCTCTTTTATTTCCTTGAGCAGTGGTTTGTAGTTCTCCTT 2344
INTRON_3 156282 GAAGAGGTGCTTCACATCCCTTGTAAGTTGGATTCCTAGGTATTTTATTC 156331
v
C L1P1_orf2#LIN 2343 GAAGAGGTCCTTCACATCCCTTGTAAGTTGGATTCCTAGGTATTTTATTC 2294
INTRON_3 156332 TCTTTGAAGCAATTGTGAATGGGAGTTCACTCATGATTTGGCTCTCTGTT 156381
i
C L1P1_orf2#LIN 2293 TCTTTGAAGCAATTGTGAATGGGAGTTCACCCATGATTTGGCTCTCTGTT 2244
INTRON_3 156382 TGTCTGTTATTGGTGTATAAGAATGCTTGTGATTTTTGCACATTGATTTT 156431
i i
C L1P1_orf2#LIN 2243 TGTCTGTTGTTGGTGTATAAGAATGCTTGTGATTTTTGTACATTGATTTT 2194
INTRON_3 156432 GTATGCTGAGACTTTGCTGAAGTGGCTTATCAGCTTAAGGAGATTTTGGG 156481
v v
C L1P1_orf2#LIN 2193 GTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGGAGATTTTGGG 2144
INTRON_3 156482 CTGAGACGATGGGGTTTTCTAGGTATACAATCATGTCATCTGCAAACAGG 156531
i v i
C L1P1_orf2#LIN 2143 CTGAGACGATGGGGTTTTCTAGATAAACAATCATGTCGTCTGCAAACAGG 2094
INTRON_3 156532 GACAATTTGACTTCCTCTTTTCCTAATTGAATACCCTTTATTTCCTTCTC 156581
C L1P1_orf2#LIN 2093 GACAATTTGACTTCCTCTTTTCCTAATTGAATACCCTTTATTTCCTTCTC 2044
INTRON_3 156582 CTGCCTAATTGCCCTGGCCAGAACTTCCAACATTATGTTGAATAGGAGTG 156631
i i i
C L1P1_orf2#LIN 2043 CTGCCTGATTGCCCTGGCCAGAACTTCCAACACTATGTTGAATAGGAGCG 1994
INTRON_3 156632 GTGAGAGAGGGCATCCCTGTCTTGTGCCAGTTTTCAAAGGGAGTGCTTCC 156681
i
C L1P1_orf2#LIN 1993 GTGAGAGAGGGCATCCCTGTCTTGTGCCAGTTTTCAAAGGGAATGCTTCC 1944
INTRON_3 156682 AGTTTTTGCCCATTCAGTATGATATTGGCTGTGGGTTTGTCATAGATAGC 156731
C L1P1_orf2#LIN 1943 AGTTTTTGCCCATTCAGTATGATATTGGCTGTGGGTTTGTCATAGATAGC 1894
INTRON_3 156732 TCTTATTATTTTGAGATATGTCCCATCGATACCTAATTT---GAGAGTTT 156778
i i i ---
C L1P1_orf2#LIN 1893 TCTTATTATTTTGAAATACGTCCCATCAATACCTAATTTATTGAGAGTTT 1844
INTRON_3 156779 TTAGCATGAAGGGTTGTTGAATTTTGTCAAAGGCCTTTTCTGCATCTATT 156828
i
C L1P1_orf2#LIN 1843 TTAGCATGAAGGGTTGTTGAATTTTGTCAAAGGCTTTTTCTGCATCTATT 1794
INTRON_3 156829 GAGATAATCATGTGGTTTTTGTCTTTGGTTCTGTTTATATGCTGGATTAC 156878
i
C L1P1_orf2#LIN 1793 GAGATAATCATGTGGTTTTTGTCTTTGGCTCTGTTTATATGCTGGATTAC 1744
INTRON_3 156879 GTTTATTGATTTGCTTGTGTTGAACCAGCCTTGCATCCCAGGGATGAAGC 156928
i v i i
C L1P1_orf2#LIN 1743 ATTTATTGATTTGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAGC 1694
INTRON_3 156929 CCACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATTTGGTTT 156978
i
C L1P1_orf2#LIN 1693 CCACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTTT 1644
INTRON_3 156979 GCCAGTATTTTATTGAGGATTTTTGCGTCGATGTTCATTAGGTATATTGG 157028
i i i i v
C L1P1_orf2#LIN 1643 GCCAGTATTTTATTGAGGATTTTTGCATCAATGTTCATCAAGGATATTGG 1594
INTRON_3 157029 TCTAAAATTCTCTTTTTTTTTTGTTGTCTCTCTGCCAGGCTTTGGTATCA 157078
v--- v v
C L1P1_orf2#LIN 1593 TCTAAAATTCTCTTTTTTG---GTTGTGTCTCTGCCCGGCTTTGGTATCA 1547
INTRON_3 157079 GGATGATGCTGGCCTCATAAAATGAGTTAGGGAGGATTCCCTCTTTTTCT 157128
i
C L1P1_orf2#LIN 1546 GAATGATGCTGGCCTCATAAAATGAGTTAGGGAGGATTCCCTCTTTTTCT 1497
INTRON_3 157129 ATTGATCGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCCTTGTACCT 157178
i i
C L1P1_orf2#LIN 1496 ATTGATTGGAATAGTTTCAGAAGGAATGGTACCAGTTCCTCCTTGTACCT 1447
INTRON_3 157179 CTGGTAGAATTCGGCTGTGAATCCATCTGGTCCTGGACTTTTTTTGGTTG 157228
i
C L1P1_orf2#LIN 1446 CTGGTAGAATTCGGCTGTGAATCCATCTGGTCCTGGACTCTTTTTGGTTG 1397
INTRON_3 157229 GTAGGCTGTTAATTATTGCCTCGATTTCGGAGCCTGCTATTGGTCTGTTC 157278
ii i i v i i i i
C L1P1_orf2#LIN 1396 GTAAACTATTGATTATTGCCACAATTTCAGAGCCTGTTATTGGTCTATTC 1347
INTRON_3 157279 AGAGACTCAGCTTCTTCCTGGTTTAGTCTTGGGAGGGTTTATGTGCCGAG 157328
i i i v i
C L1P1_orf2#LIN 1346 AGAGATTCAACTTCTTCCTGGTTTAGTCTTGGGAGAGTGTATGTGTCGAG 1297
INTRON_3 157329 AAATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTCCGTAGAGGTGTT 157378
i v v
C L1P1_orf2#LIN 1296 GAATGTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTT 1247
INTRON_3 157379 TATAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCGGTGGTGATA 157428
i
C L1P1_orf2#LIN 1246 TGTAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCGGTGGTGATA 1197
INTRON_3 157429 TCCCCTTTATCATTTTTTATTGCGTCTATTTGATTCTTCTCTCTTTTCTT 157478
i i
C L1P1_orf2#LIN 1196 TCCCCTTTATCATTTTTTATTGTGTCTATTTGATTCTTCTCTCTTTTTTT 1147
INTRON_3 157479 CTTTATTAGTCTAGCTAGCAGTCTATCAATTTTGTTGATCTTTTCAAAAA 157528
v i i
C L1P1_orf2#LIN 1146 CTTTATTAGTCTTGCTAGCGGTCTATCAATTTTGTTGATCCTTTCAAAAA 1097
INTRON_3 157529 ACCAGCTCCTGGATTCATTAATTTTTTGAAGGGTTTTTTGTGTCTCTATT 157578
i
C L1P1_orf2#LIN 1096 ACCAGCTCCTGGATTCATTGATTTTTTGAAGGGTTTTTTGTGTCTCTATT 1047
INTRON_3 157579 TCCTTCAGTTCTGCTCTGATCTTAGTTATTTCTTGCCTTCTGCTAGCTTT 157628
i
C L1P1_orf2#LIN 1046 TCCTTCAGTTCTGCTCTGATTTTAGTTATTTCTTGCCTTCTGCTAGCTTT 997
INTRON_3 157629 TGAATGTGTTTGCTCTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGGG 157678
i
C L1P1_orf2#LIN 996 TGAATGTGTTTGCTCTTGCTTTTCTAGTTCTTTTAATTGTGATGTTAGGG 947
INTRON_3 157679 TGTGAATTTTAGATCTTTCCTGCTTTCTCTTGTGGGCATTTAGTGCTATA 157728
v i i
C L1P1_orf2#LIN 946 TGTCAATTTTGGATCTTTCCTGCTTTCTCTTGTAGGCATTTAGTGCTATA 897
INTRON_3 157729 AATTTCCCTCTACACACTGCTTTGAATGTGTCCCAGAGATTCTGGTATGT 157778
i
C L1P1_orf2#LIN 896 AATTTCCCTCTACACACTGCTTTGAATGCGTCCCAGAGATTCTGGTATGT 847
INTRON_3 157779 TGTGTCTTTGTTCTCGTTGGTTTCAAAGAACATCTTTATTTCTGCCTTCA 157828
v
C L1P1_orf2#LIN 846 GGTGTCTTTGTTCTCGTTGGTTTCAAAGAACATCTTTATTTCTGCCTTCA 797
INTRON_3 157829 TTTCGTTATGTACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCAT 157878
C L1P1_orf2#LIN 796 TTTCGTTATGTACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCAT 747
INTRON_3 157879 GTAGTTGAGTGGTTTTGAGTGAGTTTCTTAATCCTGAGTTCTAGTTTGAT 157928
i i v
C L1P1_orf2#LIN 746 GTAGTTGAGCGGCTTTGAGTGAGATTCTTAATCCTGAGTTCTAGTTTGAT 697
INTRON_3 157929 TGCACTGTGGTCTGAGAGAGAGTTTGTTATAATTTCTGTTCTTTTACATT 157978
v
C L1P1_orf2#LIN 696 TGCACTGTGGTCTGAGAGATAGTTTGTTATAATTTCTGTTCTTTTACATT 647
INTRON_3 157979 TGCTGAGGAGTGCTTTACTTCCAACTATGTGGTCAGTTTTGGAATAGGTG 158028
v i
C L1P1_orf2#LIN 646 TGCTGAGGAGAGCTTTACTTCCAACTATGTGGTCAATTTTGGAATAGGTG 597
INTRON_3 158029 TGGTGTGGTGCTGAAAAGAATGTTTATTCTGTTGATTTGGGGTGCAGAGT 158078
i v v
C L1P1_orf2#LIN 596 TGGTGTGGTGCTGAAAAAAATGTATATTCTGTTGATTTGGGGTGGAGAGT 547
INTRON_3 158079 TCTGTAGATGTCTATTAGGTCCACTTGGTGAAGAGCTAAATTCAATTCCT 158128
ii v i i
C L1P1_orf2#LIN 546 TCTGTAGATGTCTATTAGGTCTGCTTGGTGCAGAGCTGAGTTCAATTCCT 497
INTRON_3 158129 GGATATTCTTGTTAACTTTCTGTCTCGTTGATCTGTCTAGTGTCGACAGT 158178
i i i i i
C L1P1_orf2#LIN 496 GGGTATCCTTGTTGACTTTCTGTCTCGTTGATCTGTCTAATGTTGACAGT 447
INTRON_3 158179 GGGGTGTTAAAGTCTCCCATTATTATTGTGTGGGAGTCTAAGTCTGTTTG 158228
v v
C L1P1_orf2#LIN 446 GGGGTGTTAAAGTCTCCCATTATTAATGTGTGGGAGTCTAAGTCTCTTTG 397
INTRON_3 158229 TAGGTCTCTAAGGACTTGCTTTATGAATCTGGGTGCTCCTGTGTTGGGTG 158278
v ? i
C L1P1_orf2#LIN 396 TAGGTCACTWAGGACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGGTG 347
INTRON_3 158279 CATATATATTTAGGATAGTTAGCTCTTCTTGTTGAATTGATCCCTTTACC 158328
v i
C L1P1_orf2#LIN 346 CATAAATATTTAGGATAGTTAGCTCCTCTTGTTGAATTGATCCCTTTACC 297
INTRON_3 158329 ATTATGTAATGGCCTTCTTTATCTCTTTTGATCTTTGTTGGTTTAAAGTC 158378
i
C L1P1_orf2#LIN 296 ATTATGTAATGGCCTTCTTTGTCTCTTTTGATCTTTGTTGGTTTAAAGTC 247
INTRON_3 158379 TGTTTTATGAGAGACTAGGATTGCAACCCCTGCCTTTTTTTGTTTTCCGT 158428
v i
C L1P1_orf2#LIN 246 TGTTTTATCAGAGACTAGGATTGCAACCCCTGCCTTTTTTTGTTTTCCAT 197
INTRON_3 158429 TTGCTTGGTAGATCTTCCTCCATCCGTTTATTTTGTGCCTATGTGTGTCT 158478
v v v
C L1P1_orf2#LIN 196 TGGCTTGGTAGATCTTCCTCCATCCTTTTATTTTGAGCCTATGTGTGTCT 147
INTRON_3 158479 CTGCATATGAGATGGGTTTCCTGAATATAGCACACTGATGGGTGTTTACT 158528
ii i v v
C L1P1_orf2#LIN 146 CTGCACGTGAGATGGGTTTCCTGAATACAGCACACTGATGGGTCTTGACT 97
INTRON_3 158529 CTTTATCCAATTTGCCAGTCTGTGTCTTTTAATTGGAGCATTTAGCCCAT 158578
i v v i
C L1P1_orf2#LIN 96 CTTTATCCAACTTGCCAGTCTGTGTCTTTTAATTGCAGAATTTAGTCCAT 47
INTRON_3 158579 TTACATTTAAGGTTAATATTGTTATGTGTGAATATGATCCTGTCAT 158624
i i v
C L1P1_orf2#LIN 46 TTATATTTAAAGTTAATATTGTTATGTGTGAATTTGATCCTGTCAT 1
Matrix = 20p37g.matrix
Transitions / transversions = 2.23 (96 / 43)
Gap_init rate = 0.00 (2 / 3292), avg. gap size = 3.00 (6 / 2)
16514 6.35 0.10 0.00 INTRON_3 158475 160567 239614 C L1P1_5end LINE/L1 165 2259 0 360
INTRON_3 158475 GTCTCTGCATATGAGATGGGTTTCCTGAATATAGCACACTGATGGGTGTT 158524
ii ii v
C L1P1_5end#LIN 2259 GTCTCTGCACGTGAGATGGGTTTCCTGAATACGGCACACTGATGGGTCTT 2210
INTRON_3 158525 TACTCTTTATCCAATTTGCCAGTCTGTGTCTTTTAATTGGAGCATTTAGC 158574
v
C L1P1_5end#LIN 2209 GACTCTTTATCCAATTTGCCAGTCTGTGTCTTTTAATTGGAGCATTTAGC 2160
INTRON_3 158575 CCATTTACATTTAAGGTTAATATTGTTATGTGTGAATATGATCCTGTCAT 158624
i v
C L1P1_5end#LIN 2159 CCATTTACATTTAAAGTTAATATTGTTATGTGTGAATTTGATCCTGTCAT 2110
INTRON_3 158625 TATGATGTTAGCTGGTTATTTTGCTCGTTAGTTGATGCAGTTTCTTCCTA 158674
i
C L1P1_5end#LIN 2109 TATGACGTTAGCTGGTTATTTTGCTCGTTAGTTGATGCAGTTTCTTCCTA 2060
INTRON_3 158675 GCCTTGATGGTCTTTACAATTTGGCATGTTTTTGCAGTGGCTGGTACTGG 158724
i
C L1P1_5end#LIN 2059 GCCTTGATGGTCTTTACAATTTGGCATGTTTTTGCAGCGGCTGGTACTGG 2010
INTRON_3 158725 TTGTTCCTTTCCATGTTTAGTGCTTCCTTCAGGAGCTGTTTTAGGGCAGG 158774
i v
C L1P1_5end#LIN 2009 TTGTTCCTTTCCATGTTTAGCGCTTCCTTCAGGAGCTCTTTTAGGGCAGG 1960
INTRON_3 158775 CCTGGTGGTGACAAAATCTCTCAGCATTTGCTTGTCTGTAAAGTATTTTA 158824
C L1P1_5end#LIN 1959 CCTGGTGGTGACAAAATCTCTCAGCATTTGCTTGTCTGTAAAGTATTTTA 1910
INTRON_3 158825 TTTCTCCTTCACTTATGAAGCTTAGTTTGGCTGGATATGAAATTCTTGGT 158874
i v
C L1P1_5end#LIN 1909 TTTCTCCTTCGCTTATGAAGCTTAGTTTGGCTGGATATGAAATTCTGGGT 1860
INTRON_3 158875 TAAAAATTCTTTTCTTTAAGAATGTTGAATATTGGCCCCCACTCTCTTCT 158924
ii
C L1P1_5end#LIN 1859 CGAAAATTCTTTTCTTTAAGAATGTTGAATATTGGCCCCCACTCTCTTCT 1810
INTRON_3 158925 GGCTTGTAGAGTTTCTGCCAAGAGATCAGCTGTTAGTCTGATGGACTTCC 158974
i i i
C L1P1_5end#LIN 1809 GGCTTGTAGAGTTTCTGCCGAGAGATCAGCCGTTAGTCTGATGGGCTTCC 1760
INTRON_3 158975 CTTTGTGGGTAACCTGACCTTTCTCTCTGGCTGCCCTTAACATTTTTTCC 159024
i
C L1P1_5end#LIN 1759 CTTTGTGGGTAACCCGACCTTTCTCTCTGGCTGCCCTTAACATTTTTTCC 1710
INTRON_3 159025 TTCATTTCAACTTTGGTGAATCTGACAATGATGTGTCTTGGAGTTGCTCT 159074
v
C L1P1_5end#LIN 1709 TTCATTTCAACTTTGGTGAATCTGACAATTATGTGTCTTGGAGTTGCTCT 1660
INTRON_3 159075 TCTCGAGGAGTATCTTTGTGGCGTTCTCTGTATTTCCTGAGTCTGAATGT 159124
i i
C L1P1_5end#LIN 1659 TCTCGAGGAGTATCTTTGTGGCGTTCTCTGTATTTCCTGAATCTGAACGT 1610
INTRON_3 159125 TGGCGTGCCTTGCTAGATTGGGGAAATTCTCCTGGATAATATCCTGCAGA 159174
v i
C L1P1_5end#LIN 1609 TGGCCTGCCTTGCTAGATTGGGGAAGTTCTCCTGGATAATATCCTGCAGA 1560
INTRON_3 159175 GTGTTTTCCAACTTGGTTCCATTCTCCCTGTCACTTTCAGGTACACCAAT 159224
i
C L1P1_5end#LIN 1559 GTGTTTTCCAACTTGGTTCCATTCTCCCCGTCACTTTCAGGTACACCAAT 1510
INTRON_3 159225 CATATGTAGATTTGGTCTTTTCACATAGTCCCATATTTCTTGGAGGCTTT 159274
v i i
C L1P1_5end#LIN 1509 CAGACGCAGATTTGGTCTTTTCACATAGTCCCATATTTCTTGGAGGCTTT 1460
INTRON_3 159275 GTCTGTATCTTTTTATTCTTTTTTCTCTAAACTTCCCTTCTCGCTTCATT 159324
ii v i
C L1P1_5end#LIN 1459 GTTCGTTTCTTTTTATTCTTTTTTCTCTAAACTTCTCTTCTCGCTTCATT 1410
INTRON_3 159325 TCATTCATTTGATCTTCCATCACTGATACCCTTTCTTCCAGTTGATCGAA 159374
v i v
C L1P1_5end#LIN 1409 TCATTCATTTCATCTTCCGTCACTGATACCCTTTCTTCCAGTTGATCGCA 1360
INTRON_3 159375 TTGGCTACTGACGCTTGTGCATTCGTCACGTAGTTCTCGTGCCGTGGTTT 159424
i v v v
C L1P1_5end#LIN 1359 TCGGCTACTGAGGCTTCTGCATTCGTCACGTAGTTCTCGTGCCTTGGTTT 1310
INTRON_3 159425 TCAGCTCCATCAGGTCCTTTAAGGACTTCTCTGCATTGATTATTCTAGTT 159474
i
C L1P1_5end#LIN 1309 TCAGCTCCATCAGGTCCTTTAAGGACTTCTCTGCATTGGTTATTCTAGTT 1260
INTRON_3 159475 AGCCATTCCTCTAATCTTTTTTCAAGGTTCT-AACTTCTTTGCCATGGGT 159523
v v i i i - i v
C L1P1_5end#LIN 1259 ATCCATTCATCTAATTTTTTTTCAAAGTTTTTAACTTCTTTGCCGTTGGT 1210
INTRON_3 159524 TCGAACTTCCTCCTTTAGCTCAGAGTAGTTTGATCGTCTGAAGCCTTCTT 159573
i v i
C L1P1_5end#LIN 1209 TCGAATTTCCTCCTGTAGCTCGGAGTAGTTTGATCGTCTGAAGCCTTCTT 1160
INTRON_3 159574 CTCTCAACTCGTCAAAGTCATTCTCCATCCAGCTTTGTTCCATTGCTGGT 159623
ii i
C L1P1_5end#LIN 1159 CTCTCAACTCGTCAAAGTCATTCTCTGTCCAGCTTTGTTCCGTTGCTGGT 1110
INTRON_3 159624 GAGGACCTGCGTTCCTTTGTAGGAGGAGAGGCACTCTGATTTTTAGAATT 159673
v v i i i
C L1P1_5end#LIN 1109 GAGGAGCTGCGTTCCTTTGGAGAAGGAGAGGCGCTCTGATTTTTAGAGTT 1060
INTRON_3 159674 TTCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACCT 159723
i
C L1P1_5end#LIN 1059 TCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACCT 1010
INTRON_3 159724 TTAGTCTTTGATGATGGTGACGTACAGATGGGGTTTTGGTGTGGATGTCC 159773
i v
C L1P1_5end#LIN 1009 TTGGTCTTTGATGATGGTGACGTACAGATGGGTTTTTGGTGTGGATGTCC 960
INTRON_3 159774 TTTCTGTTTGTTAGTTTTCCTTCTAAGAGTCAGGACCCTCAGCTGCAGTT 159823
v v v
C L1P1_5end#LIN 959 TTTCTGTTTGTTAGTTTTCCTTCTAACAGACAGGACCCTCAGCTGCAGGT 910
INTRON_3 159824 CTGTTGGAGTTTGCTGGAGGTCCACTCCAGATCCTGTTTGCCTGGGTATC 159873
i
C L1P1_5end#LIN 909 CTGTTGGAGTTTGCTGGAGGTCCACTCCAGACCCTGTTTGCCTGGGTATC 860
INTRON_3 159874 AGCAGCAGAGGCTGCAGAACAGCGGATATTGGCAAACAGCAAATGTTGCT 159923
i v i ii v i i
C L1P1_5end#LIN 859 AGCAGCGGTGGCTGCAGAACAGTGGATATTGGTGAACCGCAGATGCTGCT 810
INTRON_3 159924 GCCTGATCGTTCCTCTGGAAGTTTTGTCTCAGAGGAGTACCTGGCCGTGT 159973
i
C L1P1_5end#LIN 809 GCCTGATCGTTCCTCTGGAAGTTTTGTCTCAGAGGAGTACCCGGCCGTGT 760
INTRON_3 159974 GAGGTGTCAGTCTGCCCCTACTGGGGGGTGCCTCCGATTTAGGCTACTTG 160023
i v v i
C L1P1_5end#LIN 759 GAGGTGTCAGTCCGCCCCTACTGGGGGGTGCCTCCCAGTTAGGCTACTCG 710
INTRON_3 160024 GGGGTCAGGGACCTGCTTGAGGAGGCAGTCTGCCCGTTCTCAGATCTCAA 160073
ii v
C L1P1_5end#LIN 709 GGGGTCAGGGACCCACTTGAGGAGGCAGTCTGCCCGTTCTCAGATCTGAA 660
INTRON_3 160074 GCTGCGTGCTGAGAGAACCACTACTCTCTTCAAAGCTGTCAGATAAGGAC 160123
i i i i
C L1P1_5end#LIN 659 GCTGCGTGCTGGGAGAACCACTGCTCTCTTCAAAGCTGTCAGACAGGGAC 610
INTRON_3 160124 ATTTAAGTCTGCAGATGTTTTTGCTGCCTTTTGTTTTG-CTATGCTCTGC 160172
v vi i vv - i i
C L1P1_5end#LIN 609 ATTTAAGTCTGCAGAGGTTACTGCTGTCTTTTTGTTTGTCTGTGCCCTGC 560
INTRON_3 160173 CCCCAGAGGTGGAGTCTACAGAGGCAGGCAGGCCTCCTTGAGCTGCCGTG 160222
i iv
C L1P1_5end#LIN 559 CCCCAGAGGTGGAGCCTACAGAGGCAGGCAGGCCTCCTTGAGCTGTGGTG 510
INTRON_3 160223 GGCTCCACCCAGTTCCAGCTTCCTGGCTGCTTTGTTTACCTACTCAAGCC 160272
v i i v
C L1P1_5end#LIN 509 GGCTCCACCCAGTTCGAGCTTCCCGGCCGCTTTGTTTACCTAATCAAGCC 460
INTRON_3 160273 TGGGCAATGAGGGTCGCCCCTCCCCGAGCCTGGCTGCTGCCTTGCAGTTC 160322
iv v v v i i
C L1P1_5end#LIN 459 TGGGCAATGGCGGGCGCCCCTCCCCCAGCCTCGCTGCCGCCTTGCAGTTT 410
INTRON_3 160323 GATCTCAGACTGCTGTGCTAGCAATGAATGAGGCTCCATGGGCGTAGGTC 160372
i v ii i i v
C L1P1_5end#LIN 409 GATCTCGGACTGCTGTGCTAGCAATCAGCGAGACTCCGTGGGCGTAGGAC 360
INTRON_3 160373 CCTCCGAGCCAGGCGCAGGATATAATCTCCCAGTGTGCCATTTGCTAAGA 160422
i i ii i i vi v
C L1P1_5end#LIN 359 CCTCCGAGCCAGGTGCGGGATATAATCTCCTGGTGCGCCGTTTTTTAAGC 310
INTRON_3 160423 CTGTTGGAAAAGCACAGTATTAGGGTGGGAGTGACCCGATTTTCCAGGTG 160472
i i i i
C L1P1_5end#LIN 309 CCGTCGGAAAAGCGCAGTATTAGGGCGGGAGTGACCCGATTTTCCAGGTG 260
INTRON_3 160473 CCGTCTGTCACCCCTTTCCTTGGCTAGGAAAGGGAATTCCCTGACCCCTT 160522
i i
C L1P1_5end#LIN 259 CCGTCTGTCACCCCTTTCTTTGACTAGGAAAGGGAATTCCCTGACCCCTT 210
INTRON_3 160523 GCACTTCCCGGGTGAGGCGATGCCTTGCCCTGCTTTGGCTCACGC 160567
i i i
C L1P1_5end#LIN 209 GCGCTTCCCGGGTGAGGCGATGCCTCGCCCTGCTTCGGCTCACGC 165
Matrix = 20p37g.matrix
Transitions / transversions = 2.02 (89 / 44)
Gap_init rate = 0.00 (2 / 2092), avg. gap size = 1.00 (2 / 2)
+ 4577 8.5 0.2 0.2 INTRON_3 160571 161172 (239009) + Charlie3 DNA/hAT-Charlie 2105 2706 (0) 193
ANNOTATION EVIDENCE:
4577 8.48 0.17 0.17 INTRON_3 160571 161172 239009 + Charlie3 DNA/hAT-Charlie 2105 2706 0 372
INTRON_3 160571 AGTTTGAGCTTTACTTCCCAGCCACAAAAGACCCCCAACCTGGGAAGGAA 160620
v i i v
Charlie3#DNA/ 2105 AGTTTGAGCATTACTTCCCAACCACAAAAGACCCCCGAACTGGGAAGGAA 2154
INTRON_3 160621 TGGACCCACGACCCATTTGTGAATAAGCCAGGTAAATTGACTTTGTCTGT 160670
i i i i i
Charlie3#DNA/ 2155 TGGATCCGCGACCCATTTGTGAATAAGCCAGGTGAATCGACTTTGTCCGT 2204
INTRON_3 160671 GCTAGAAGAGGATCAACTGCTTGAGATCGCAAATGATGGTGGCCTTAAAA 160720
i
Charlie3#DNA/ 2205 GCTAGAAGAGGATCAACTGCTTGAGATCGCAAATGACGGTGGCCTTAAAA 2254
INTRON_3 160721 ATAAGTTTGAGACAATTTCAAATCTCCATACGTTGTGGATTAAAGTCAAA 160770
i v i v i
Charlie3#DNA/ 2255 GTATGTTTGAGACAACTTCAAATCTCCATACGTTCTGGATTAAAGTCAAG 2304
INTRON_3 160771 GTGGAATATCCCGAGATTGGCAAAAAATCACTGAAAAGCCTGCTTCCATT 160820
i i v v v
Charlie3#DNA/ 2305 GCGGAATATCCTGAGATTGCCACAAAAGCACTGAAAAGCCTGCTTCCATT 2354
INTRON_3 160821 TCCAACATCGTATCTTTGTGAAACAGGGTTTTCTGCAGCGACAGCAACCA 160870
v i i
Charlie3#DNA/ 2355 TCCAACATCCTATCTTTGTGAAGCAGGGTTTTCTGCAGTGACAGCAACCA 2404
INTRON_3 160871 AAACGAGATTACGGAGTACACTAAACATAAGCAACACACTTCTGGTTTCA 160920
v ii v v
Charlie3#DNA/ 2405 AAACGAGATTACGGAGTAGACTGGACATAAGCAACACACTTCGGGTGTCA 2454
INTRON_3 160921 CTGTCTCCCATCATCCCCAGATGGGACCATCTAGTTAGAGGAAAACAAGC 160970
i i iv
Charlie3#DNA/ 2455 CTGTCTCCCATCACCCCCAGATGGGACCGTCTAGTTGCAGGAAAACAAGC 2504
INTRON_3 160971 TCGGGGCTCCCACTGATTCTACATTATGGTGAGTTGTATAATTATTTCAT 161020
i
Charlie3#DNA/ 2505 TCAGGGCTCCCACTGATTCTACATTATGGTGAGTTGTATAATTATTTCAT 2554
INTRON_3 161021 TGTATATTACAATGAAGTAATAATAGAAATAAAGTGCACAATAAATGTAA 161070
i v i
Charlie3#DNA/ 2555 TATATATTACAATGTAATAATAATAGAAATAAAGTGCACAATAAATGTAA 2604
INTRON_3 161071 TGTGCTTGAATGATGCCGCAACCATCCCCTGC-CTTCCAGTTCTTGGAAA 161119
i v v v iv - ii i i v
Charlie3#DNA/ 2605 TGCGCTTGAATCATCCCGAAACCATCCCCCCCACCCCCGGTCCGTGGAAA 2654
INTRON_3 161120 AAATTGTCTTCCATGAAACTGGTCCCTGGTGCCAAACAGGTTGGGGACTG 161169
- i i v i
Charlie3#DNA/ 2655 AA-TTGTCTTCCACGAAACCGGTCCCTGGTGCCAAAAAGGTTGGGGACCG 2703
INTRON_3 161170 CTG 161172
Charlie3#DNA/ 2704 CTG 2706
Matrix = 20p37g.matrix
Transitions / transversions = 1.68 (32 / 19)
Gap_init rate = 0.00 (2 / 601), avg. gap size = 1.00 (2 / 2)
+ 190 27.8 1.9 0.0 INTRON_3 161173 161226 (238955) + L2a LINE/L2 3367 3421 (5) 190
ANNOTATION EVIDENCE:
190 27.78 1.85 0.00 INTRON_3 161173 161226 238955 + L2a_3end LINE/L2 458 512 5 306
INTRON_3 161173 GTTTAGCACATTGTCTGGCATTTAATAGTAGC-CAGTAAATATTGATTAT 161221
ii v v i iv i vv - i vi iv
L2a_3end#LINE 458 GCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGA 507
INTRON_3 161222 ATGAA 161226
L2a_3end#LINE 508 ATGAA 512
Matrix = 25p37g.matrix
Transitions / transversions = 1.14 (8 / 7)
Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1)
+ 288 29.1 15.8 1.7 INTRON_3 162684 162900 (237281) C MIRb SINE/MIR (7) 261 4 194
ANNOTATION EVIDENCE:
288 32.35 14.92 0.97 INTRON_3 162684 162864 237317 C MIRb SINE/MIR 56 261 7 307
INTRON_3 162684 GAATTAACATTC-TTGAAC-CTGTCTGTA-AACATATATCATGCCAA-CT 162729
ii v i- i - vv i-iv vii iii i - v
C MIRb#SINE/MIR 261 GAGCTACCATTTATTGAGCGCTTACTGTGTGCCAGGCACTGTGCTAAGCG 212
INTRON_3 162730 TTTCATAAATGTTATTTCAAT-GATTCTTACACTAAGCCTATGAGG---A 162775
i i i viii i v -i i i vi v ii ---i
C MIRb#SINE/MIR 211 CTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGG 162
INTRON_3 162776 TATGAGCCTCCCT-TTTTA--GATGAGGA----------------TGTTA 162806
v viv i- -- ----------------v
C MIRb#SINE/MIR 161 TATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTA 112
INTRON_3 162807 AGGGACTTGTCCAAGCTCTTACAGTGAGTGCACTTGGTAGAGCCAGAGTT 162856
v i v vi iv -- vv i ii
C MIRb#SINE/MIR 111 AGTGACTTGCCCAAGGTCACACAGCTAGT--AAGTGGCAGAGCCAGGATT 64
INTRON_3 162857 AAACTCCA 162864
vi vi
C MIRb#SINE/MIR 63 CGAACCCA 56
Matrix = 25p37g.matrix
Transitions / transversions = 1.64 (36 / 22)
Gap_init rate = 0.06 (10 / 180), avg. gap size = 2.90 (29 / 10)
279 25.41 16.83 2.61 INTRON_3 162800 162900 237281 C MIRb SINE/MIR 4 118 150 308
INTRON_3 162800 GATGTTAAGGGACTTGTCCAAGCTCTTACAGTGAGTGCACTTGGTAGAGC 162849
v v i v vi iv -- vv i
C MIRb#SINE/MIR 118 GAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGT--AAGTGGCAGAGC 71
INTRON_3 162850 CAGAGTT--AA--------------ACTCCAAAGCC-ATACTCTTCCTAT 162882
ii -- -------------- -i i i i i
C MIRb#SINE/MIR 70 CAGGATTCGAACCCAGGTCTGCCTGACTCCAAAGCCCGTGCTCTTTCCAC 21
INTRON_3 162883 TTATATCACATTGACTCT 162900
-ii i ii v i
C MIRb#SINE/MIR 20 T-GCACCACGCTGCCCCT 4
Matrix = 25p37g.matrix
Transitions / transversions = 2.12 (17 / 8)
Gap_init rate = 0.05 (5 / 100), avg. gap size = 4.00 (20 / 5)
+ 2634 14.4 0.7 1.6 INTRON_3 163462 163897 (236284) + MER57A1 LTR/ERV1 1 432 (0) 195
ANNOTATION EVIDENCE:
2634 14.45 0.69 1.62 INTRON_3 163462 163897 236284 + MER57A1 LTR/ERV1 1 432 0 277
INTRON_3 163462 TGTTAAATCGAACTAAATATGGCCTGAGAAAGCGTCCATACTTCCATATT 163511
v i i vv i i
MER57A1#LTR/E 1 TGTTAAAGCGAACTAAATACGGCCTGAGAAGGACTCCGTACTTCTATATT 50
INTRON_3 163512 TGAGTCTTCGTGGACAAACCGTAACCTAACTTAGTAGGTAGACAAGACTG 163561
i i i i i i i
MER57A1#LTR/E 51 TGAGTCCTTGTGGACGAACCGTAACCTAGCTTAATAGGCAGACAAGATTG 100
INTRON_3 163562 TAAACCTAACTTAGGAGTATGCTACTGTAACAACAGCTGTGTATCAGTCA 163611
v vv i v v ii i
MER57A1#LTR/E 101 AAAACCTAACTTAGGAGTATGCGCCTGTAACAATAGCTGAGTCTTGGCCA 150
INTRON_3 163612 ATCCCAGCGGCCAGACTTCAATCACTCATACACTGCTGACTGTTCGAACT 163661
v i v i vi i
MER57A1#LTR/E 151 ATCCCAGCGGCCATACTTCAACCACTCATAGACTGCCGAGCGTTCAAACT 200
INTRON_3 163662 GT--TCAAATAAGGCAAAAGCCAAGCTGTAACCAATCCAGATGTTCCTGT 163709
-- v i v i vi i
MER57A1#LTR/E 201 GTGTTCAAATAAGGCAAACGCCGACCCGTAACCAATCCAGCCGTTTCTGT 250
INTRON_3 163710 ACTACACTTCTGTTTTCTGTATGTCACTTCCCTTTTTTTGTCTATAAATT 163759
iv i v i
MER57A1#LTR/E 251 ACCTCACTTCCGATTTCTGTACGTCACTTCCCTTTTTTTGTCTATAAATT 300
INTRON_3 163760 TGCTCTGACCATGAGACATCCCTGGAGTTTCTCTTAATCTGCTGTGATTC 163809
i i i i v
MER57A1#LTR/E 301 TGTTCTGACCACGAGGCATCCCTGGAGTCTCTCTGAATCTGCTGTGATTC 350
INTRON_3 163810 TTCAGGCTGCCTGATTCATGAATTGATTTTTTTTCCTTGCTCAATTACAC 163859
vvi i ii i ------- v v
MER57A1#LTR/E 351 TGGGGGCTGCCCGATTCGCGAATCG-------TTCATTGCTCAATTAAAC 393
INTRON_3 163860 TCTGTTAAATTTAATTTGTCTGAAATTTTCCTTT-AACA 163897
iv i v i i -
MER57A1#LTR/E 394 TCCTTTAAATTTAATTCGGCTGAAGTTTTTCTTTTAACA 432
Matrix = 18p37g.matrix
Transitions / transversions = 1.70 (39 / 23)
Gap_init rate = 0.01 (3 / 435), avg. gap size = 3.33 (10 / 3)
+ 402 29.4 10.5 1.1 INTRON_3 163971 164164 (236017) C MIRb SINE/MIR (46) 222 8 196
ANNOTATION EVIDENCE:
402 29.08 10.84 0.55 INTRON_3 163971 164136 236045 C MIRb SINE/MIR 40 222 46 309
INTRON_3 163971 TGTACTAAAAGATTAACATA-ATTAT-----TTAATTCTTAAAGCAAAAT 164014
i iv v v i- ----- i i v i vvi
C MIRb#SINE/MIR 222 TGTGCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCC 173
INTRON_3 164015 TGTGAGATTGATATTATT-TCCTCTTTTTAGAGAT-------C--AGGCT 164054
i i v i - i v v ------- --
C MIRb#SINE/MIR 172 TGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCT 123
INTRON_3 164055 AAAAAATGTTAAG--AGTTGTCCAAGGGCACTTAGGTTGGATGGTAGCAA 164102
v i i v -- v i v vi v v v -i i i
C MIRb#SINE/MIR 122 CAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTA-AGTGGCAG 74
INTRON_3 164103 AGTTCGGGTTTTAGCCAAGATCTCTCTGACTTTA 164136
iiv i iv i v i vi ii
C MIRb#SINE/MIR 73 AGCCAGGATTCGAACCCAGGTCTGCCTGACTCCA 40
Matrix = 25p37g.matrix
Transitions / transversions = 1.29 (27 / 21)
Gap_init rate = 0.04 (7 / 165), avg. gap size = 2.71 (19 / 7)
311 31.37 8.20 4.21 INTRON_3 163982 164164 236017 C MIR SINE/MIR 8 197 65 310
INTRON_3 163982 ATTAACATAATTATTTAATTCTTAAAGCAAAATTGTGAGATTGATATTAT 164031
---- i i i v i vvi i i v i i
C MIR#SINE/MIR 197 ATTAAC----TCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTAT 152
INTRON_3 164032 T----TCCTCTTTTTAGAGATCAGG---CTAAA------AAATGTTAAG- 164067
---- i v v v --- i i------ i v -
C MIR#SINE/MIR 151 TATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGT 102
INTRON_3 164068 -AGTTGTCCAAGGGCACTTAGGTTGGATGGTAGCAAAGTTCGGGTTTTAG 164116
- v i v vi v v v -i i i iiv i iv i
C MIR#SINE/MIR 101 AACTTGCCCAAGGTCACACAGCTAGTA-AGTGGCAGAGCCGGGATTCGAA 53
INTRON_3 164117 CCAAGATCTCTCTGACTTTATATGTCCTGCGTTGTAGAACACTAGGTT 164164
v i- vv i ii v - - i i v vi v v i
C MIR#SINE/MIR 52 CCCAGG-CAGTCTGGCTCCAGA-GTCC-GTGCTCTTAACCACTATGCT 8
Matrix = 25p37g.matrix
Transitions / transversions = 1.29 (31 / 24)
Gap_init rate = 0.05 (9 / 182), avg. gap size = 2.56 (23 / 9)
+ 900 15.7 7.3 0.5 INTRON_3 164499 164677 (235504) + MER82 DNA/TcMar-Tigger 14 204 (449) 197
ANNOTATION EVIDENCE:
900 15.72 7.26 0.52 INTRON_3 164499 164677 235504 + MER82 DNA/TcMar-Tigger 14 204 449 373
INTRON_3 164499 TTGTTCTGTAGTAGTTCTGTACTATAAAGTTGCAGCAAACACTGAATTAG 164548
i - ii v v i v i
MER82#DNA/TcM 14 TTATTC-GCGGTAGTTATGTTCTATAAAGTCGCCGCGAACACTGAATTAG 62
INTRON_3 164549 CAAATACAGAGCCATTGCTACTAGGAGAAATACACGGTTAAGTT------ 164592
i v i v i v i ------
MER82#DNA/TcM 63 CGAATACTGAACCATTGCTCCTAGGGGAAATACAGGGTTAGGTTCCTGCG 112
INTRON_3 164593 ----TCTGGTCACAT--TTTTAATCAACCAATCAATACATAACCTTGTTT 164636
---- v-- vi i
MER82#DNA/TcM 113 AGCCTCTGGTCACAACATTTTCGTCAACCGATCAATACATAACCTTGTTT 162
INTRON_3 164637 AGTAAATGTTTCTGTTTAAAAACACCTC-TTTAATATGTCTT 164677
vi ivi i i- i v
MER82#DNA/TcM 163 TATGTGTGTTTCTGTTTAAAGACACCTTATTTAATATATATT 204
Matrix = 20p37g.matrix
Transitions / transversions = 1.55 (17 / 11)
Gap_init rate = 0.02 (4 / 178), avg. gap size = 3.50 (14 / 4)
+ 226 28.8 2.3 4.7 INTRON_3 164840 164970 (235211) C MER44C DNA/TcMar-Tigger (108) 625 498 198
ANNOTATION EVIDENCE:
226 28.83 2.29 4.69 INTRON_3 164840 164970 235211 C MER44C DNA/TcMar-Tigger 498 625 108 374
INTRON_3 164840 TCATCTCATGAACCCACAAATTTAGCCACTTTTTCATCTTTTCCATAGC- 164888
v v vv iivv i vv i - -
C MER44C#DNA/Tc 625 TCATGTCTTCCACCCACAAATTTAATGCCTTTTCCATCTTAACTA-AGCA 577
INTRON_3 164889 TTCATTATGCACTGTAGATGTTATTTTAGCACTGTCTGGTGTGGCCTCTG 164938
i i i i i vi v i v v v vv i i ----i
C MER44C#DNA/Tc 576 CTTATCACGCACTGTGGCCGTAACTTTTGCAGTTTGAGGTGCGAC----A 531
INTRON_3 164939 GTATCAATTACCA--AATTTCTTCTTTCTTTTTC 164970
i -v i v -- i i i
C MER44C#DNA/Tc 530 GCA-AAACTAGCACGAATTTCTTTTTCCTTCTTC 498
Matrix = 20p37g.matrix
Transitions / transversions = 1.12 (19 / 17)
Gap_init rate = 0.04 (5 / 130), avg. gap size = 1.80 (9 / 5)
+ 396 16.7 0.0 0.0 INTRON_3 164982 165047 (235134) + MER82 DNA/TcMar-Tigger 201 266 (387) 199
ANNOTATION EVIDENCE:
396 16.67 0.00 0.00 INTRON_3 164982 165047 235134 + MER82 DNA/TcMar-Tigger 201 266 387 375
INTRON_3 164982 TATTGTTCATTCATTAACATTGAATTCATGGCCAGCAGTACCCTAGCTCG 165031
v i i i i iv i i
MER82#DNA/TcM 201 TATTGTTGATTCATTAACATTGAACTCACGGCCAACAGCACTATAACTCA 250
INTRON_3 165032 TGCCTGAAGGAAGGTT 165047
v v
MER82#DNA/TcM 251 TGCCTGAACGAAGCTT 266
Matrix = 20p37g.matrix
Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
+ 2318 19.1 1.2 0.2 INTRON_3 165051 165459 (234722) + MER82 DNA/TcMar-Tigger 241 653 (0) 200
ANNOTATION EVIDENCE:
2318 19.12 1.22 0.24 INTRON_3 165051 165459 234722 + MER82 DNA/TcMar-Tigger 241 653 0 376
INTRON_3 165051 CTCTAGCTGGTGCCTGAAGGAGGTTTACCTAACACACATATTTTCTCCAT 165100
v i vi v i i i i i
MER82#DNA/TcM 241 CTATAACTCATGCCTGAACGAAGCTTATCTAACACACGTATTTTCTCCGT 290
INTRON_3 165101 CAGGCCTATCACAGCCTTCTTGCACTTAGAAACACTTGGCAACACTTAAG 165150
v vi i i v i i v
MER82#DNA/TcM 291 AAGGCACATCACAGCCTTCTTGCGCTTAGGAACACTAGACAGCACTTCAG 340
INTRON_3 165151 CACTGTGCTTGGAAGCCATTTTAAACAGCAGAATCACCAACAAAAAGCAC 165200
i i- ii
MER82#DNA/TcM 341 CACTATGCTTGGG-GCCATTTTAAACAGCGAAATCACCAACAAAAAGCAC 389
INTRON_3 165201 AAAAATGTAAAAACGGTGGCACTAAATAGGCCAAGAAAAGAACACGTGTT 165250
ii vv i iv i v
MER82#DNA/TcM 390 AAAAATGCGAAAAACGTGGCACTAAATAGACCGCGAAAAGGACACTTGTT 439
INTRON_3 165251 CGCAGTTCAAGAGCTGAAACAAGAAGGCAGAGCATCTCCTTGTTTGACCT 165300
ii vii i v i
MER82#DNA/TcM 440 TACAGTATGAGAGCTGAAACAAGAAGGCAGAGCGTCGCCTTGTTCGACCT 489
INTRON_3 165301 CAGTTGGGAACATGCATGTCCAGCGACTCCAATTTTTTACCTTTCTGTGT 165350
i i ii vi v ii vi i i
MER82#DNA/TcM 490 CAGCTGGGAACGTGCGCGTCGGGCGACTCAAATTTTTCGCCGCTCTGCGC 539
INTRON_3 165351 ATGTCCACAAATGACC----AAGTGTCGAGGATACTGACTTTAGGGTTAC 165396
i i ---- i i v ii i i i
MER82#DNA/TcM 540 ATGTCCGCGAATGACCGCGAAAGCGCCGCGAGTATTGATTTTGGGGTTAC 589
INTRON_3 165397 AAATAAATTTTATCAAGTAGACAAATATGCAAATGCAGAATTATCAAA-A 165445
v i i i vi i i ivv i -
MER82#DNA/TcM 590 AAATAAATTTTAGCGAGTAGGCGAATTCGCAAATACGGAATCCGCGAATA 639
INTRON_3 165446 ACAAGGATCAACTG 165459
ii i
MER82#DNA/TcM 640 ATGAGGATCGACTG 653
Matrix = 20p37g.matrix
Transitions / transversions = 2.71 (57 / 21)
Gap_init rate = 0.01 (3 / 408), avg. gap size = 2.00 (6 / 3)
+ 441 27.5 5.9 2.0 INTRON_3 166102 166280 (233901) + MIR SINE/MIR 6 199 (69) 201
ANNOTATION EVIDENCE:
441 27.25 5.73 1.84 INTRON_3 166102 166258 233923 + MIR SINE/MIR 6 168 94 311
INTRON_3 166102 ATAG--TAGTGATTAAAATCTCAGGCTGTGGAATTAA---GCGTGT-TTC 166145
-- i i v v i i v iii i--- v v-
MIR#SINE/MIR 6 ATAGCATAGTGGTTAAGAGCACGGACTCTGGAGCCAGACTGCCTGGGTTC 55
INTRON_3 166146 AAATCCTGGCTCTACCTTGTACTAGCTATGTGGATTTGGGCATTATATTT 166195
i i i viv i ivi vvv i
MIR#SINE/MIR 56 GAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTT 105
INTRON_3 166196 ATTGTCTCCGAGTTT--GTTTTCTCCATTTGAAAAACTGGTGA-AATAAT 166242
viv i v ii -- i - i v - v -
MIR#SINE/MIR 106 AACCTCTCTGTGCCTCAGTTTCCTC-ATCTGTAAAA-TGGGGATAATAAT 153
INTRON_3 166243 AATACATTATTTCATA 166258
i -i ii
MIR#SINE/MIR 154 AGTAC-CTACCTCATA 168
Matrix = 25p37g.matrix
Transitions / transversions = 1.62 (26 / 16)
Gap_init rate = 0.05 (8 / 156), avg. gap size = 1.50 (12 / 8)
407 29.59 7.19 2.87 INTRON_3 166114 166280 233901 + MIRb SINE/MIR 26 199 69 312
INTRON_3 166114 AAAATCTCAGGCTGTGGAATTAAGCGT-----GTTTCAAATCCTGGCTCT 166158
i v v i v i i i iv----- v i
MIRb#SINE/MIR 26 AAGAGCACGGGCTTTGGAGTCAGGCAGACCTGGGTTCGAATCCTGGCTCT 75
INTRON_3 166159 ACCTTGTACTAGCTATGTGGATTTGGGCATTATATTTATTGTCTCCGAGT 166208
i viv i ivi vvvi i viv i i
MIRb#SINE/MIR 76 GCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGC 125
INTRON_3 166209 TT--GTTTTCTCCATTTGAAAAACTGGTGAAATAATAATACATTATTTCA 166256
i -- i - i v - v -- -i ii i
MIRb#SINE/MIR 126 CTCAGTTTCCTC-ATCTGTAAAA-TGGGGA--TAATAATAC-CTACCTCG 170
INTRON_3 166257 TACA--TACTGTAAATAT---ATGAAATA 166280
i vi-- ii i iv --- i
MIRb#SINE/MIR 171 CAGGGTTGTTGTGAGGATTAAATGAGATA 199
Matrix = 25p37g.matrix
Transitions / transversions = 1.82 (31 / 17)
Gap_init rate = 0.05 (8 / 166), avg. gap size = 2.12 (17 / 8)
+ 27 75.6 0.0 0.0 INTRON_3 166330 166370 (233811) + AT_rich Low_complexity 1 41 (0) 202
ANNOTATION EVIDENCE:
27 75.61 0.00 0.00 INTRON_3 166330 166370 233811 + AT_rich Low_complexity 125 165 135 319
INTRON_3 166330 ATAAAAATTAGTATATAATTTATATACATAAATAATTTTTA 166370
???????????????vvvvvv vvv vvv v ???
AT_rich#Low_c 125 WWWWWWWWWWWWWWWATTAAAAATAAATAATATAATTTWWW 165
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 13)
Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0)
+ 28 74.3 0.0 0.0 INTRON_3 166424 166458 (233723) + AT_rich Low_complexity 1 35 (0) 203
ANNOTATION EVIDENCE:
28 74.29 0.00 0.00 INTRON_3 166424 166458 233723 + AT_rich Low_complexity 120 154 146 320
INTRON_3 166424 ATTTTATAAAAAGTATATATTATTATTATAAAAAA 166458
????????????????????vv v vv v
AT_rich#Low_c 120 WWWWWWWWWWWWWWWWWWWWATTAAAAATAAATAA 154
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 6)
Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0)
+ 235 23.1 3.9 0.0 INTRON_3 166997 167048 (233133) C L2c LINE/L2 (52) 3335 3282 204
ANNOTATION EVIDENCE:
235 23.08 3.85 0.00 INTRON_3 166997 167048 233133 C L2c_3end LINE/L2 373 426 52 313
INTRON_3 166997 GGGCTACAAAGATACATAAAACACAGTTCCTGTAC--AAGGACCTTCTAG 167044
v iv i i i iv -- v ivi
C L2c_3end#LINE 426 GGGATACAAAGATGAATAAGACACGGTCCCTGCCCTCAAGGAGCTCACAG 377
INTRON_3 167045 TCTA 167048
C L2c_3end#LINE 376 TCTA 373
Matrix = 25p37g.matrix
Transitions / transversions = 1.40 (7 / 5)
Gap_init rate = 0.02 (1 / 51), avg. gap size = 2.00 (2 / 1)
+ 1072 25.7 7.7 3.6 INTRON_3 167069 167481 (232700) C MLT1C LTR/ERVL-MaLR (7) 460 28 205
ANNOTATION EVIDENCE:
1072 26.73 6.81 3.03 INTRON_3 167069 167450 232731 C MLT1C LTR/ERVL-MaLR 65 460 7 377
INTRON_3 167069 GTTTCCTATGGTTGCTATAGCAAATTACCACAAACATGGTGATATAAAAC 167118
? v i ii i v vv iiv -
C MLT1C#LTR/ERV 460 GTTTNCTAGGGCTGCCGTAACAAAGTACCACAAACTGGGTGGCTTAAA-C 412
INTRON_3 167119 AATGGAAATGTACTCTCTCACAGTTCTGGAGGCCAGAGGTCTGAAATCAA 167168
ii v i v i i i i
C MLT1C#LTR/ERV 411 AACAGAAATTTATTGTCTCACAGTTCTGGAGGCTAGAAGTCCGAGATCAA 362
INTRON_3 167169 GGTGTCAGCAGGTCCAGGCTTCATTAGAAGGCTCTTGAGTAAATTCTATT 167218
i vii- i i v iv i v vii v i v i
C MLT1C#LTR/ERV 361 GGTGTCGGCAGGGTT-GGTTCCTTCTGAGGGCTGTGAGGGAGAATCTGTT 313
INTRON_3 167219 CCTTGTCTCTTAC--AGCATCTGGTGACT--CTAG---------GCATTC 167255
v i iv -- v ii -- i --------- i
C MLT1C#LTR/ERV 312 CCATGCCTCTCCCCTAGCTTCTGGTGGTTTGCTGGCAATCTTTGGCGTTC 263
INTRON_3 167256 CTTGGCTTGTGGGTGCATCACTCCAATCTCCACCTG-----TCACATTGC 167300
i i? i ii v----- v
C MLT1C#LTR/ERV 262 CTTGGCTTGTAGANGCATCACCCCAATCTCTGCCTTCATCTTCACATGGC 213
INTRON_3 167301 CTCCTCTTCTTCTATCTCTTTTCCTCTGTGTGTC----TTTTATAAGGAT 167346
v i iiiv v iiv v i viv iivi v ---- i
C MLT1C#LTR/ERV 212 GTTCTCCCTGTGTGCGTGTCTGTGTCCAAATTTCCCCTTTTTATAAGGAC 163
INTRON_3 167347 ACTTGTTATTGGATTGAA---GGCCTGCTCATATTG-TCCAGGATGATCT 167392
iv i --- i --- v-- i ivi i- v i
C MLT1C#LTR/ERV 162 ACCAGTCAT---ATTGGATTAGGG--GCCCACCCTACTCCAGTATGACCT 118
INTRON_3 167393 CATTTCAAATGCTTAATTACATCTGCAAAGCCCATTTTTTCCAAATAAAG 167442
i i ----i v v -i v i
C MLT1C#LTR/ERV 117 CATCTTAA----CTAATTACATCTGCAACGACC-CTATTTCCAAATAAGG 73
INTRON_3 167443 TAACAGTC 167450
v v
C MLT1C#LTR/ERV 72 TCACATTC 65
Matrix = 20p37g.matrix
Transitions / transversions = 1.62 (60 / 37)
Gap_init rate = 0.03 (13 / 381), avg. gap size = 2.92 (38 / 13)
561 24.71 8.53 4.09 INTRON_3 167271 167481 232700 C MLT1D LTR/ERVL-MaLR 28 247 258 378
INTRON_3 167271 CATCACTCCAATCTCCACCT-----GTCACATTGCCTCCTCTTCTTCTAT 167315
i i i ii i ----- iv i vvi iv
C MLT1D#LTR/ERV 247 CGTCACTCCGACCTCTGCTTCCGTCGTCACATCTCCTTCTCTGACTCTGA 198
INTRON_3 167316 CTCTTTT-CCTCTGTGTGTCTTTTATAAGGATACTTGTTATTGGATTGAA 167364
i ii - i------ i iv v iv --
C MLT1D#LTR/ERV 197 CCCTCCTGCCTCC------CTCTTATAAGGACCCTTGTGATTACATTG-- 156
INTRON_3 167365 GGCCTGCTCATATTGTCCAGGATGATCTC---ATTTCAA-AT-----GCT 167405
ii i iv vi i --- i - -----i
C MLT1D#LTR/ERV 155 GGCCCACCCGGATAATCCAGGATAATCTCCCCATCTCAAGATCCTTAACT 106
INTRON_3 167406 TAATTACATCTGCAAAGCCCATTTTTTCCAAATAAAGTAACAG--TCACA 167453
i i -i v vi i v--
C MLT1D#LTR/ERV 105 TAATCACATCTGCAAAGTCC-CTTTTGCCATGTAAGGTAACATATTCACA 57
INTRON_3 167454 GTTTCCAAGGATT-TGATATGGATATTTT 167481
v ii -v ii i i
C MLT1D#LTR/ERV 56 GGTTCCGGGGATTAGGACGTGGACATCTT 28
Matrix = 20p37g.matrix
Transitions / transversions = 2.57 (36 / 14)
Gap_init rate = 0.05 (10 / 210), avg. gap size = 2.70 (27 / 10)
+ 626 26.1 20.7 3.3 INTRON_3 167739 167955 (232226) + MIR SINE/MIR 8 262 (0) 206
ANNOTATION EVIDENCE:
250 36.42 5.26 7.53 INTRON_3 167739 167833 232348 + MIR SINE/MIR 8 100 162 314
INTRON_3 167739 AGGATAGTGG-----AATGCAGGCTCTGGAATTAGATTACTTGGCTATAA 167783
v ----- iii i i iii i i i v vii
MIR#SINE/MIR 8 AGCATAGTGGTTAAGAGCACGGACTCTGGAGCCAGACTGCCTGGGTTCGA 57
INTRON_3 167784 ATCCCTCATCCTATCCCCATCATTTACTAGCCACATGGCCTTAAATAAGT 167833
-------iv i iii i iiii i iiii
MIR#SINE/MIR 58 ATCCC-------GGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGT 100
Matrix = 25p37g.matrix
Transitions / transversions = 7.00 (28 / 4)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 6.00 (12 / 2)
626 18.03 10.66 0.00 INTRON_3 167834 167955 232226 + MIR SINE/MIR 128 262 0 315
INTRON_3 167834 CTTGCCTGTAAAATTGGAATTATAATTGTAC-------------TTGTTG 167870
iii v i v v -------------
MIR#SINE/MIR 128 CTCATCTGTAAAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTTG 177
INTRON_3 167871 TGAGGATTAAATGAGCTAATACATGTAAAACATTTAGAACAATACCTGGC 167920
i i ii i i
MIR#SINE/MIR 178 TGAGGATTAAATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGC 227
INTRON_3 167921 ACATAGTAAGCACTTAATATGCATTAACTATTATT 167955
i i viii iii
MIR#SINE/MIR 228 ACATAGTAAGCGCTCAATAAATGTTGGTTATTATT 262
Matrix = 25p37g.matrix
Transitions / transversions = 4.50 (18 / 4)
Gap_init rate = 0.01 (1 / 121), avg. gap size = 13.00 (13 / 1)
+ 1345 8.4 33.8 1.4 INTRON_3 169673 169909 (230272) + AluSx4 SINE/Alu 1 312 (0) 207
ANNOTATION EVIDENCE:
183 4.17 0.00 0.00 INTRON_3 169886 169909 230272 + (CAAA)n Simple_repeat 2 25 155 364
INTRON_3 169886 AAACAAACAAACAAACAAAAAAAC 169909
v
(CAAA)n#Simpl 2 AAACAAACAAACAAACAAACAAAC 25
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 1)
Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0)
1255 10.47 1.14 1.72 INTRON_3 169673 169847 230334 + AluSx SINE/Alu 1 174 138 275
INTRON_3 169673 GGCCGGGTGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGCAGGCCAA 169722
i i i v i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 169723 GGCGGGTGGATCAC--GAGGTCAGGAGTTCAAGACCAGCCTGGCCAATAT 169770
i -- i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
INTRON_3 169771 GGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGCCGGGCATTAAGG 169820
i i ---
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGT---GG 147
INTRON_3 169821 TAACACCTGCCTGTAGTCCCAACCACT 169847
ii i vi i i i
AluSx#SINE/Al 148 TGGCGCGCGCCTGTAATCCCAGCTACT 174
Matrix = 14p37g.matrix
Transitions / transversions = 8.00 (16 / 2)
Gap_init rate = 0.01 (2 / 174), avg. gap size = 2.50 (5 / 2)
304 5.26 0.00 0.00 INTRON_3 169848 169885 230296 + AluY_short_ SINE/Alu 245 282 19 379
INTRON_3 169848 GCACTCCAGCCTGGGCAACAGAGCGAGACTCCATCTCA 169885
i i
AluY_short_#S 245 GCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCA 282
Matrix = 20p37g.matrix
Transitions / transversions = 0.0 (2 / 0)
Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0)
+ 2110 12.8 2.0 0.3 INTRON_3 169926 170229 (229952) C AluSz6 SINE/Alu (3) 309 1 208
ANNOTATION EVIDENCE:
1971 13.86 1.97 0.32 INTRON_3 169926 170229 229952 C AluSx SINE/Alu 1 309 3 274
INTRON_3 169926 TTTCTTTCTTTTCTTTCTTTTTTTTTTC---CAGAGTCACTCTGTGTCGC 169972
i i i i v--- i v v v
C AluSx#SINE/Al 309 TTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGC 260
INTRON_3 169973 CCAGGCTGGAGTGCAATGGTACGATCTCAGCTCATTGCAACCTCTGCCTC 170022
i ii i i i
C AluSx#SINE/Al 259 CCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTC 210
INTRON_3 170023 CTGGGTTCGAGCAATTCTCCTGCCTCAGGCT---GAGTAGCTGTGATTAC 170069
i i i v --- v
C AluSx#SINE/Al 209 CCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTAC 160
INTRON_3 170070 GGGTGCACACCACCACACCTGGCTAATTTTTTGTATTTTTAGTAGAGATG 170119
i i i i i i - i
C AluSx#SINE/Al 159 AGGCGCGCGCCACCACGCCCGGCTAATTTTT-GTATTTTTAGTAGAGACG 111
INTRON_3 170120 GGGTTTTTCCATGTTGGCCAGGCTGGTCTCAAACTTGTTGTCTCAAGTGA 170169
iv i iv vii i
C AluSx#SINE/Al 110 GGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGA 61
INTRON_3 170170 TCCACCCACCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACC 170219
i i i
C AluSx#SINE/Al 60 TCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACC 11
INTRON_3 170220 ATGCCCAGCC 170229
ii i
C AluSx#SINE/Al 10 GCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 3.67 (33 / 9)
Gap_init rate = 0.01 (3 / 303), avg. gap size = 2.33 (7 / 3)
+ 688 28.3 5.6 1.4 INTRON_3 171705 172201 (227980) + L1ME5 LINE/L1 5005 5520 (674) 209
ANNOTATION EVIDENCE:
332 33.31 4.85 2.10 INTRON_3 171705 172075 228106 + L1M5_orf2 LINE/L1 2896 3276 18 427
INTRON_3 171705 GACCTATATGTGAAAAATAAGTCTATAAAGTTAATAGAAGAAAAAGTAAG 171754
v ii iv ? i vv ? vi i
L1M5_orf2#LIN 2896 GACCTAAATGTGAAAGGTAAAACNATAAAGCTTCTAGAAGANAACATAGG 2945
INTRON_3 171755 TGAATATCTCTGTGAACTAAGGGCTCGAGAAATGTCTTCTCAACAAAATT 171804
v i i v vi - v iv vi i ii v ii --
L1M5_orf2#LIN 2946 AGAATATCTTTATGACCTTGGGG-TAGGCAAAGATTTCTTAAACAGGA-- 2992
INTRON_3 171805 TCAACCAATAAAGCAC-AGCCAATAAAGGAAACATTAATA---------- 171843
- -- - - i vv ? i v i ----------
L1M5_orf2#LIN 2993 -CA--CAA-AAAGCACTAACCATAAANGAAAAAATTGATAAATTNGACTA 3038
INTRON_3 171844 CATTAAAATTCAGGATTTTTTTTCAACAAA-GCTTCCAGGGGCAATATTA 171892
i v i i i v v - viv vviiv ivi v
L1M5_orf2#LIN 3039 TATTAAAATTAAGAACTTCTGTTCATCAAAAGACACCATTAAGAGAGTGA 3088
INTRON_3 171893 AAAGGCACATAACATAAGGAAAGAATATTTTTGCTATGTCTGTAATCAAC 171942
viiv v iv ii ? v v iiv i ?iii
L1M5_orf2#LIN 3089 AAAGGCAAGCCACAGAGTGGGAGAANATATTTGCAATACATATANCTGAC 3138
INTRON_3 171943 AAGAGATTAGTATCTTGAATGTATA--GAATGCCTA-GAATCAACAAGAA 171989
iii i vi iv i -- iv -i i
L1M5_orf2#LIN 3139 AAAGAACTCATATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAA 3188
INTRON_3 171990 TACAGCA-ACAAG--AAAAGAAAAATAGATGAAGAATAGGAACAGAAAAT 172036
v vii - v-- v i iii ii ivv iv -i
L1M5_orf2#LIN 3189 AAAGACAGACAACCCAATAGAAAAATGGGCAAAAGACTTGAACAGGCA-C 3237
INTRON_3 172037 TTTACTTAGGAAAAAACCCTAAAAGCTAACAAACACATG 172075
i vv i ii v i v vi i i i
L1M5_orf2#LIN 3238 TTCACAAAAGAGGATATCCAAATGGCCAATAAACATATG 3276
Matrix = 20p39g.matrix
Transitions / transversions = 1.47 (69 / 47)
Gap_init rate = 0.03 (12 / 370), avg. gap size = 2.17 (26 / 12)
688 23.50 6.32 0.75 INTRON_3 171949 172201 227980 + L1ME5_3end LINE/L1 1 267 674 428
INTRON_3 171949 TTAGTATCTTGAATGTATA--GAATGCCTA-GAATCAACAAGAATACAGC 171995
i v i i -- iv i-i v ? i
L1ME5_3end#LI 1 TTAATATCTAGAATATACAAGGAACTCCTGCAAATCAACAAGAAAANAAC 50
INTRON_3 171996 AACAAG---AAAAGAAAAATAGATGAAGAATAGGAACAGAAAATTTTACT 172042
ii v--- v i iii i v i iv - v
L1ME5_3end#LI 51 GGCAACCCCAATAGAAAAATGGGCAAAGGATATGAATAGGTAATTT-ACA 99
INTRON_3 172043 TAGGAAAAAACCCTAAAAGCTAACAAACACATG--------TTCAAAATG 172084
v i ii v i i --------i v v
L1ME5_3end#LI 100 GAAGAGGAAACCCGAAAAGCTAACAAGCATATGAAGAGATGCTCAAACTC 149
INTRON_3 172085 ATTAATAATTTTAAAGATGCTAATTATAAAAACAATGAGATATTACTTTC 172134
i ivv i i v v v i v
L1ME5_3end#LI 150 ATTAGTAATCAGAGAAATGCAAATTAAAACAACAATGAGATATCACTTTA 199
INTRON_3 172135 TACCTATTAAACTGGCAAAAGT-AAAAAGTTTGATAATGCCATACGTTGA 172183
i i i - i i v vii i
L1ME5_3end#LI 200 CACCTATTAGACTGGCAAAAATTAGAAAGCTGGATAATGCCAAGTGTTGG 249
INTRON_3 172184 -AAGGCTCGAGGGGATATA 172201
-i v - v
L1ME5_3end#LI 250 TGAGGAT-GTGGGGATATA 267
Matrix = 20p39g.matrix
Transitions / transversions = 1.64 (36 / 22)
Gap_init rate = 0.03 (8 / 252), avg. gap size = 2.25 (18 / 8)
+ 888 26.4 10.8 1.1 INTRON_3 172320 172929 (227252) + L1ME5 LINE/L1 5512 6187 (7) 209
ANNOTATION EVIDENCE:
587 26.62 11.00 0.45 INTRON_3 172320 172519 227662 + L1ME5_3end LINE/L1 259 479 462 429
INTRON_3 172320 GGGGGTATAGGAACCTTCATATTCTGCTGGTGGGATTGTACACTGGTATA 172369
i i iiv v v ii
L1ME5_3end#LI 259 GGGGATATAGGAACCCTCATGCACTGCTGGTGGGAGTGTAGACTGGTGCA 308
INTRON_3 172370 GCTATTCTGGAAAACAA-------------------ATGAAGGGTATGCT 172400
i i i ------------------- v vi i v
L1ME5_3end#LI 309 GCCATTCTGGAGAGCAATCTGGCANTACTTAGTCAAATTAAGTATACGCA 358
INTRON_3 172401 CACTCTTTGAATTTGAAATTTCACTTATGTGTTTATGCCCCCACGGGAAT 172450
i i v viiv v i i iv v v ii v -i i
L1ME5_3end#LI 359 TACCCTATGACCCAGCAATTCCGCTCCTGGGTATATATCCCAA-AGAAAT 407
INTRON_3 172451 TCTCATGTGGGTCTATAAAGGGCCAGATATGAGGGTATTTGTTGTAGCTT 172500
iiii i i v vi i i i ii i v
L1ME5_3end#LI 408 TCTCACACAGGTCCATAAGGGGACATGTACGAGGATGTTCATTGCAGCGT 457
INTRON_3 172501 TATTTGTGGTGG---GGAGTTG 172519
i ---
L1ME5_3end#LI 458 TGTTTGTGGTGGCGGGGAGTTG 479
Matrix = 20p39g.matrix
Transitions / transversions = 2.12 (36 / 17)
Gap_init rate = 0.02 (3 / 199), avg. gap size = 7.67 (23 / 3)
888 28.40 7.06 0.55 INTRON_3 172384 172723 227458 + L1ME5_3end LINE/L1 342 703 238 430
INTRON_3 172384 CAAATGAAGGGTATGCTCACTCTTTGAATTTGAAATTTCACTTATGTGTT 172433
v vi i vi i v viiv v i i iv v v
L1ME5_3end#LI 342 CAAATTAAGTATACGCATACCCTATGACCCAGCAATTCCGCTCCTGGGTA 391
INTRON_3 172434 TATGCCCCCACGGGAATTCTCATGTGGGTCTATAAAGGGCCAGATATGAG 172483
ii v -i i iiii i i v vi i
L1ME5_3end#LI 392 TATATCCCAA-AGAAATTCTCACACAGGTCCATAAGGGGACATGTACGAG 440
INTRON_3 172484 GGTATTTGTTGTAGCTTTATTTGTGGTGG---GGAGTTGT-GACAATCTG 172529
i i ii i v i --- v- i
L1ME5_3end#LI 441 GATGTTCATTGCAGCGTTGTTTGTGGTGGCGGGGAGTTGGAGGCAATCTG 490
INTRON_3 172530 GATGTTCATTTCAAGGAGAATGCATAGATAAAATGTAATGATTGCACAAC 172579
i i iv vi i v i ii iv v
L1ME5_3end#LI 491 GGTGTCCATCACTGGGAGAGTGGATAGGTAAAATGTGGTGGATGCACACC 540
INTRON_3 172580 AAGGAATGTTATGCAACACTTAAAAGCAAACAGTTTGATGTTATATCTAA 172629
v i ii i v i vviii v - i iv i
L1ME5_3end#LI 541 ATGGAGTACTATGCAGCAGTTAGAAGCAACGGACTAGATGT-ACACATAG 589
INTRON_3 172630 CAACATGAGTGAAT------AACAT--TG-----TGAAATAAACGGGCAG 172666
ii i ------ -- ----- v iiii v i
L1ME5_3end#LI 590 CAACATGGATGGATCTTAAAAACATAGTGCTGAGTGAAAAAAGTAAGAAA 639
INTRON_3 172667 CA-------ATATATAGTACAATAACATTTACATGAATTAAAAATACATG 172709
------- ? ii v ii i
L1ME5_3end#LI 640 CAGAATGAGATNTATAACACAATACCATTTATGTAAATTAAAAATACATG 689
INTRON_3 172710 CTCAGATAATAATA 172723
v v v i i
L1ME5_3end#LI 690 CACACAAAACAACA 703
Matrix = 20p39g.matrix
Transitions / transversions = 1.97 (63 / 32)
Gap_init rate = 0.02 (8 / 339), avg. gap size = 3.25 (26 / 8)
450 24.23 12.56 2.11 INTRON_3 172715 172929 227252 + L1ME5_3end LINE/L1 698 934 7 431
INTRON_3 172715 ATAATAATACACATTT-ATAAAAGCATATGTAAGGAAAA----ATATATT 172759
i i - i i i i ii iv ---- i i
L1ME5_3end#LI 698 ACAACAATACACATTTTACAAGAACACATACAAACAAAAGGATACACATT 747
INTRON_3 172760 AAACACATTTAAGTGGTTGTCT----GGCTTATGAATGGGGATATGAATG 172805
vi i i ---- vvv v v --- ? v
L1ME5_3end#LI 748 AAACACATTAGAATGGTTGCCTATGGGGGGGAGGAAGGGGGA---GNAGG 794
INTRON_3 172806 TGTTATGGGTACAAAG----AGAATTAAAAAATGAA-----------AGA 172840
v v? - v i ---- v ?i i -----------
L1ME5_3end#LI 795 GGGNA-GGGAATAAAGGGAAAGAATAAANGAATAAATAAATAAAACAAGA 843
INTRON_3 172841 GAGAGGCTTTGCAAGGATCAATGATGATGAAGTGTCATTAACTGAGTAG- 172889
i i v i i v i v v -
L1ME5_3end#LI 844 GAGGGGCCTTGCACGGACCAATGATGATAATGTGCCATGAACTGAGGAGT 893
INTRON_3 172890 --AATTAATTATATCCTCTGCATTTGAGATCACAAGTAAAAA 172929
--i i vv i ii i - iv
L1ME5_3end#LI 894 ATGATTAACTCAACCCTCTGCACCTGAGGTC-CAAAAAAAAA 934
Matrix = 20p39g.matrix
Transitions / transversions = 1.53 (29 / 19)
Gap_init rate = 0.04 (9 / 214), avg. gap size = 3.56 (32 / 9)
+ 257 34.0 1.7 6.1 INTRON_3 172981 173099 (227082) + L2c LINE/L2 3274 3387 (0) 210
ANNOTATION EVIDENCE:
257 34.02 1.68 6.14 INTRON_3 172981 173099 227082 + L2c_3end LINE/L2 365 478 0 394
INTRON_3 172981 TCCTCTAC-AAATTCTAAGTTGTTTGGAAGAATGGATTATGTTGTTATTC 173029
i - i i v i i vi iii v v iii i-
L2c_3end#LINE 365 TCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTC-TTATTC 413
INTRON_3 173030 TTGTTAGTCCCTGTAACTCTGGTGCCTCACATGTAGTAGTCAGT-ATTAA 173078
------i ii v i ii ii vi ii v iv - v
L2c_3end#LINE 414 ------ATCTTTGTATCCCCAGCACCTGGCACATAGTAGGCGCTCAATAA 457
INTRON_3 173079 ACGTTTGTTAATTTAATGAAT 173099
i i v v
L2c_3end#LINE 458 ATGTTTGTTGAATGAATGAAT 478
Matrix = 25p39g.matrix
Transitions / transversions = 2.45 (27 / 11)
Gap_init rate = 0.03 (4 / 118), avg. gap size = 2.25 (9 / 4)
+ 201 33.7 9.9 4.7 INTRON_3 173354 173515 (226666) + L2c LINE/L2 2913 3082 (305) 211
ANNOTATION EVIDENCE:
201 33.69 9.88 4.71 INTRON_3 173354 173515 226666 + L2c_3end LINE/L2 4 173 305 395
INTRON_3 173354 CATGATTTGGCTTCTGATTACCTATTTTTTTGCCTCATCCTTTCC-CTCA 173402
i i ii v ---i iiv iii - v
L2c_3end#LINE 4 CACGATCTGGCCCCTGCTTACCT---CTCCAGCCTCATCTCCTCCACTCC 50
INTRON_3 173403 AGTACCTTGAGCTTTATGC------CATGGGAAACTTCTTTCATTTTACA 173446
vv - i vv vi ------ iivvi ? v iiv
L2c_3end#LINE 51 CCT-CCTCGCCCACTATGCTCCAGCCACACTGAACTNCTTGCATTCCCCA 99
INTRON_3 173447 AATGTG--GCATGTTGTTTGATGACCTTTTGCTTTTATACATTCTGATCT 173494
iii -- - v vv v iiiv? i ii v v i
L2c_3end#LINE 100 AACACGCCGCA-GTTCTTTCCTGCCTCCGNGCCTTTGCACATGCTGTTCC 148
INTRON_3 173495 -------TGAAATAAAGCTCTTTCTCTC 173515
------- i --- i i i
L2c_3end#LINE 149 CTCTGCCTGGAAT---GCTCTTCCCCCC 173
Matrix = 25p39g.matrix
Transitions / transversions = 1.63 (31 / 19)
Gap_init rate = 0.05 (8 / 161), avg. gap size = 3.00 (24 / 8)
+ 216 23.9 8.5 11.3 INTRON_3 173751 173780 (226401) C MIR3 SINE/MIR (9) 199 174 212
ANNOTATION EVIDENCE:
216 23.89 8.47 11.30 INTRON_3 173751 173780 226401 C MIR3 SINE/MIR 174 199 9 396
INTRON_3 173751 AATTATAAAGTGTCAGTGTTGCAAAGGACC 173780
i i i v i -i ---
C MIR3#SINE/MIR 199 AATCATAGAATGTCAGAGCTG-GAAGG--- 174
Matrix = 25p39g.matrix
Transitions / transversions = 5.00 (5 / 1)
Gap_init rate = 0.07 (2 / 29), avg. gap size = 2.00 (4 / 2)
+ 2399 17.4 1.4 2.8 INTRON_3 173781 173975 (226206) + MSTB LTR/ERVL-MaLR 1 198 (228) 213
ANNOTATION EVIDENCE:
2399 17.39 1.39 2.82 INTRON_3 173781 173975 226206 + MSTB LTR/ERVL-MaLR 1 198 228 386
INTRON_3 173781 TGATACGGTTTGAATATGTGTCCGCTCCAAATCTCATGTTAAAATGTGGT 173830
i i i v v i i
MSTB#LTR/ERVL 1 TGATATGGTTTGGATGTTTGTCCCCTCCAAATCTCATGTTGAAATGTGAT 50
INTRON_3 173831 CTCTGGTGTTGGAAGTGGGGCATGGTGGGAGGTGTTTGGATCATGGGGAC 173880
i ii i v i
MSTB#LTR/ERVL 51 CCCCAGTGTTGGAGGTGGGGCCTGGTGGGAGGTGTTTGGATCATGGGGGC 100
INTRON_3 173881 AGATCCCTCATAAATGGCTTGGTGCTATCCC-TTGGTGAAAAGTGACCTC 173929
i i i i - vi vi
MSTB#LTR/ERVL 101 GGATCCCTCATGAATGGCTTGGCGCCATCCCCTTGGTGATGAGTGAGTTC 150
INTRON_3 173930 TTGCTCTG--AGTTTACATGTGATCTATGTTTTTAAAAGTGGGTGACA 173975
i -- i ii v ivv v v v? i
MSTB#LTR/ERVL 151 TCGCTCTGTTAGTTCACGCGAGATCTGGTTGTTTAAAAGAGTNTGGCA 198
Matrix = 18p39g.matrix
Transitions / transversions = 2.00 (22 / 11)
Gap_init rate = 0.01 (2 / 194), avg. gap size = 1.50 (3 / 2)
+ 2323 9.4 0.3 0.3 INTRON_3 173976 174272 (225909) + AluSq2 SINE/Alu 1 297 (15) 214
ANNOTATION EVIDENCE:
2155 10.17 0.34 0.68 INTRON_3 173976 174272 225909 + AluSx SINE/Alu 1 296 16 380
INTRON_3 173976 GGCCGGGCGTGGTGGCTCAGGCCTGTAAGCCCAGCACTTTGGGAGGCCGA 174025
i v v
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 174026 GGCAGGCAGATCACCTGAAGCCAGGAGTTCCAAGACCAACCTGGCCAACG 174075
i i i i -i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTC-GAGACCAGCCTGGCCAACA 99
INTRON_3 174076 TGGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGCCTGGTGTGGTG 174125
i v i
AluSx#SINE/Al 100 TGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTG 149
INTRON_3 174126 GCGGGCACCTGTAATCTCAGCTACTTGGGAGGATGAGGCAGGAGAATCGC 174175
v i i i v
AluSx#SINE/Al 150 GCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGC 199
INTRON_3 174176 TTGAACCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATCACGCCATTGCAC 174225
i i i i i
AluSx#SINE/Al 200 TTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAC 249
INTRON_3 174226 TCCAGC-TGGGCAACAGGAGCAAAAGTGCATCTCAGAAAAAAAAAAAA 174272
- i - i i v v i i
AluSx#SINE/Al 250 TCCAGCCTGGGCGACAG-AGCGAGACTCCGTCTCAAAAAAAAAAAAAA 296
Matrix = 14p39g.matrix
Transitions / transversions = 3.29 (23 / 7)
Gap_init rate = 0.01 (3 / 296), avg. gap size = 1.00 (3 / 3)
+ 2399 17.4 1.4 2.8 INTRON_3 174273 174508 (225673) + MSTB LTR/ERVL-MaLR 199 426 (0) 213
ANNOTATION EVIDENCE:
2399 17.39 1.39 2.82 INTRON_3 174273 174508 225673 + MSTB LTR/ERVL-MaLR 199 426 0 387
INTRON_3 174273 GTGGGTGACAGCTGTTCCCCAC---CTCTTGCTCCTGCTTTTGCCACGTG 174319
----------- ivii v --- i i i i
MSTB#LTR/ERVL 199 -----------CCTCCCCCCTCTCTCTCTTGCTCCCGCTCTCGCCATGTG 237
INTRON_3 174320 AAACACCTTCTCTCCCTTCACCTTCTCCCATGATTGGAAACTTCCTGGGG 174369
viii v i i v ? i i
MSTB#LTR/ERVL 238 ACGTGCCTGCTCCCCCTTCGCCTTCTGCCATGATTGNAAGCTTCCTGAGG 287
INTRON_3 174370 TCTCTCTGGAAGCCAAGAAGATGCTGGTGCCATGCTTCCTCTACAGCCTA 174419
i v ii i v i i v i
MSTB#LTR/ERVL 288 CCTCACCAGAAGCCGAGCAGATGCCGGCGCCATGCTTCCTGTACAGCCTG 337
INTRON_3 174420 CAGAACTATGAGCCAATTAAACCTCTTTTCTTTATAAATTGCCCAGTCTC 174469
ii i i
MSTB#LTR/ERVL 338 CAGAACCGTGAGCCAATTAAACCTCTTTTCTTTATAAATTACCCAGCCTC 387
INTRON_3 174470 TGGTATTTCTTCATAGCAATGCAAGAATGGCCTAACACA 174508
v i i i v
MSTB#LTR/ERVL 388 AGGTATTTCTTTATAGCAACGCAAGAACGGACTAACACA 426
Matrix = 18p39g.matrix
Transitions / transversions = 2.80 (28 / 10)
Gap_init rate = 0.01 (2 / 235), avg. gap size = 7.00 (14 / 2)
+ 216 23.9 8.5 11.3 INTRON_3 174509 174595 (225586) C MIR3 SINE/MIR (35) 173 85 212
ANNOTATION EVIDENCE:
216 23.89 8.47 11.30 INTRON_3 174509 174595 225586 C MIR3 SINE/MIR 85 173 35 397
INTRON_3 174509 GGACCTTTTAGGTCACTATAGTACAAACCCTCAGGACATTGGTTACAAAT 174558
- vv i - v v v ii---- -- i
C MIR3#SINE/MIR 173 -GACCTTAGAGATCA-TCTAGTCCAACCCCCT----CATT--TTACAGAT 132
INTRON_3 174559 GAA-------AGG---GAATAGGAGAAGTGACTGGACTAATGTCATA 174595
i------- ---ii v v v v i v i
C MIR3#SINE/MIR 131 GAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACA 85
Matrix = 25p39g.matrix
Transitions / transversions = 0.90 (9 / 10)
Gap_init rate = 0.07 (6 / 86), avg. gap size = 3.00 (18 / 6)
+ 4654 10.3 1.5 0.0 INTRON_3 175239 175920 (224261) C L1PB2 LINE/L1 (1) 6150 5459 215
ANNOTATION EVIDENCE:
4654 10.26 1.47 0.00 INTRON_3 175239 175920 224261 C L1PB2_3end LINE/L1 206 897 1 392
INTRON_3 175239 TTTTTTATTTCAATAGTTTTTGGGATT-CAGGCAGTTTTGGGTTACATGG 175287
iv - ii v
C L1PB2_3end#LI 897 TTTTTTATTTCAATAGTTTTTGGGGGTACAGGTGGTTTTTGGTTACATGG 848
INTRON_3 175288 GTAACTTCGTTAGTGGTGATTTCTGAGATTTTGGTGAACCCGTCACCTGA 175337
i v v v i i
C L1PB2_3end#LI 847 ATAAGTTCTTTAGTGGTGATTTCTGAGATTTTGGTGCACCCATCACCCGA 798
INTRON_3 175338 GCAGTGTACACTGTACTCAATAT--AGTCTTTTATCCCTGACCCCCCTCC 175385
i -- v
C L1PB2_3end#LI 797 GCAGTGTACACTGTACCCAATATGTAGTCTTTTATCCCTCACCCCCCTCC 748
INTRON_3 175386 CACCCTTCCTCCCAACTCCCCAGAGTCTATTATATCATTCTTATGC-TTT 175434
i ii v i i -
C L1PB2_3end#LI 747 CACCCTTCCCCCTGAGTCCCCAAAGTCCATTATATCATTCTTATGCCTTT 698
INTRON_3 175435 GCATCCTCATAGCTTAGCTCCCACATATAAGTGAAAACATAAAATATTTG 175484
i v i vi
C L1PB2_3end#LI 697 GCGTCCTCATAGCTTAGCTCCCACTTATAAGTGAGAACATACGATATTTG 648
INTRON_3 175485 GTTTTTTATTTCTAAGTTACTTCACTTAGAACAACAACCTCCAGCTCCAT 175534
ii i i i iii
C L1PB2_3end#LI 647 GTTTTCCATTCCTGAGTTACTTCACTTAGAATAATGGCCTCCAGCTCCAT 598
INTRON_3 175535 CTAAGTTGCTGCAAATGCCATTATTTCATTCTGTTTTATGACTGAATAGC 175584
i v v iv i i i
C L1PB2_3end#LI 597 CCAAGTTGCTGCAAAAGACATTATTTCATTCCTTTTTATGGCTGAGTAGT 548
INTRON_3 175585 ATTCCATGGTGTATATATACCACATTTTCTTTATCTACTCATTGATTGAT 175634
i i i
C L1PB2_3end#LI 547 ATTCCATGGTGTATATATACCACATTTTCTTTATCCACTCGTTGGTTGAT 498
INTRON_3 175635 GGACATTTAGGTTGGCTCCGTATTTTTGCAATTG-----TGTGCTGCTAT 175679
i i i i i -----
C L1PB2_3end#LI 497 GGGCACTTAGGTTGGTTCCATATCTTTGCAATTGCGAATTGTGCTGCTAT 448
INTRON_3 175680 AAATATGCATGTGCATGTGTCTTTTTCATATAACAACTTATTTTTCTTTG 175729
i i ii v i
C L1PB2_3end#LI 447 AAACATGCGTGTGCATGTGTCTTTTTCATATAATGACTTCTTTTCCTTTG 398
INTRON_3 175730 CGTAAATACCCAGTAGTCGGATTGCTGGGTCAAATGGTAGTTCTACTTTT 175779
v i v i
C L1PB2_3end#LI 397 GGTAGATACCCAGTAGTGGGATTGCTGGATCAAATGGTAGTTCTACTTTT 348
INTRON_3 175780 AGTTCTTTAAGGAAGCTCCATACTGTTTTCTGTAGTGGTTATACTAGTTT 175829
v ii i
C L1PB2_3end#LI 347 AGTTCTTTAAGGAATCTCCATACTGTTTTCCATAGTGGTTGTACTAGTTT 298
INTRON_3 175830 ACACTCCCACCAGCAGT-TAAAAATGTTCCCTTTTCACCACACCCACACC 175878
i - i i i
C L1PB2_3end#LI 297 ACATTCCCACCAGCAGTGTAAAAGTGTTCCCTTTTCACCACATCCACGCC 248
INTRON_3 175879 AACATCAATTATTTTTTGGTTTTTAAATTATGGCCATTCTTG 175920
v i i v
C L1PB2_3end#LI 247 AACATCTATTGTTTTTTGATTTTTTAATTATGGCCATTCTTG 206
Matrix = 18p39g.matrix
Transitions / transversions = 2.89 (52 / 18)
Gap_init rate = 0.01 (5 / 681), avg. gap size = 2.00 (10 / 5)
+ 33 75.8 0.0 0.0 INTRON_3 176046 176078 (224103) + AT_rich Low_complexity 1 33 (0) 216
ANNOTATION EVIDENCE:
33 75.76 0.00 0.00 INTRON_3 176046 176078 224103 + AT_rich Low_complexity 120 152 148 424
INTRON_3 176046 TTTTTAAAATAATTTAAATTATTAATTTTTAAA 176078
???????????????????? vvv v v
AT_rich#Low_c 120 WWWWWWWWWWWWWWWWWWWWATTAAAAATAAAT 152
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 5)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 26 26.9 0.0 0.0 INTRON_3 176056 176081 (224100) + AT_rich Low_complexity 1 26 (0) 217 *
ANNOTATION EVIDENCE:
26 26.92 0.00 0.00 INTRON_3 176056 176081 224100 C AT_rich Low_complexity 137 162 138 425
INTRON_3 176056 AATTTAAATTATTAATTTTTAAAGGC 176081
v v v v???
C AT_rich#Low_c 162 AAATTATATTATTTATTTTTAATSSS 137
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 4)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
+ 23 52.2 0.0 0.0 INTRON_3 176535 176557 (223624) + AT_rich Low_complexity 1 23 (0) 218
ANNOTATION EVIDENCE:
23 52.17 0.00 0.00 INTRON_3 176535 176557 223624 C AT_rich Low_complexity 141 163 137 426
INTRON_3 176535 CATTATTTAAATTATTTTTTTTT 176557
? vvv v vvv v v vv
C AT_rich#Low_c 163 SAAATTATATTATTTATTTTTAA 141
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 11)
Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0)
+ 1440 13.0 0.4 0.0 INTRON_3 177327 177557 (222624) C L1MA4A LINE/L1 (22) 6281 6050 219
ANNOTATION EVIDENCE:
1440 12.99 0.43 0.00 INTRON_3 177327 177557 222624 C L1MA4A_3end LINE/L1 797 1028 22 432
INTRON_3 177327 ATATTTGTACATATTTATGGAGTACATGTGAAGTTTTGTTATATGCATAA 177376
i vi i i
C L1MA4A_3end#L 1028 ATATTTGTACATATTTATGGGGTACATGTGATATTTTGTTACATGCATAG 979
INTRON_3 177377 AATGTGTAATGATCAAGCCAGAGTATTCAGGGTATTCGTCACCT-GAACA 177425
i i i i i - ii
C L1MA4A_3end#L 978 AATGTGTAATGATCAAGTCAGGGTATTTAGGGTATCCATCACCTCGAGTA 929
INTRON_3 177426 TTTATCATTTCTACGTGTTGGGTGCATTGCAAGTTCTCTCTTGTAGCTAT 177475
i vi v i v
C L1MA4A_3end#L 928 TTTATCATTTCTATGTGTTGGGAACATTTCAAGTCCTCTCTTCTAGCTAT 879
INTRON_3 177476 TTTGAAAAATGCAATATATTGTTATTAGCTATAGTTACCCTACTCTGCTA 177525
v i i i i i
C L1MA4A_3end#L 878 TTTGAAATATACAATACATTGTTGTTAACTATAGTCACCCTACTCTGCTA 829
INTRON_3 177526 TCAGGCATTAGAACTTATTTTTTCTACCTAAC 177557
iii ii i
C L1MA4A_3end#L 828 TCGAACATTAGAACTTATTCCTTCTATCTAAC 797
Matrix = 20p39g.matrix
Transitions / transversions = 5.00 (25 / 5)
Gap_init rate = 0.00 (1 / 230), avg. gap size = 1.00 (1 / 1)
+ 407 31.1 3.2 3.0 INTRON_3 177826 178046 (222135) + L2c LINE/L2 2931 3155 (232) 220
ANNOTATION EVIDENCE:
308 33.49 4.52 4.05 INTRON_3 177826 178046 222135 + L2b_3end LINE/L2 22 243 223 398
INTRON_3 177826 CTTCTCTG---CCACCTTATGCTGCTTCTCTCTAGTGC-CTTTCTGTCTC 177871
i ---i i iv i ii iii i -- - vi -
L2b_3end#LINE 22 CCTCTCTGGCCTCATCTCCTACCACTCTCCCCT--TGCTCACTCTG-CTC 68
INTRON_3 177872 T--CTAC-CTGATCTCTTTTTCAGCTCCTTTATTTTGCAAAACTATTTTT 177918
i-- i - ii i v- v i iv vivi v ii -ivi i
L2b_3end#LINE 69 CAGCCACACTGGCCTCCTTG-CTGTTCCTCGAACACGCCAGGCT-CGCTC 116
INTRON_3 177919 CTGACCTCAGAACCTTCACACAAGCTACTCCTTCCTCCTGGAA-GCTTTC 177967
i - ii ii ?v ii i iv - ii i
L2b_3end#LINE 117 CCG-CCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACGCCCTT 165
INTRON_3 177968 CCTCCCTCTCTTTGCCTGGCCACTTTCTACTCATCCTTTAAAACTCAGTG 178017
i v - i vi i i iiv iv
L2b_3end#LINE 166 CCCCAC-CTCTTCGCCTGGCCAACTCCTACTCATCCTTCAGGTCTCAGCT 214
INTRON_3 178018 TAA--CTCAGTCCTCATCAAAGAGGGCTTTC 178046
i --v -- v v i i v i i
L2b_3end#LINE 215 CAAATGTCA--CCTCCTCCAGGAAGCCCTCC 243
Matrix = 25p39g.matrix
Transitions / transversions = 2.68 (51 / 19)
Gap_init rate = 0.06 (13 / 220), avg. gap size = 1.46 (19 / 13)
407 29.46 2.27 2.27 INTRON_3 177915 178046 222135 + L2c_3end LINE/L2 115 246 232 399
INTRON_3 177915 TTTTCTGACCTCAGAACCTTCACACAAGCTACTCCTTCCTCCTGGAA-GC 177963
i - v ?i ii v ii i iv -
L2c_3end#LINE 115 TTTCCTG-CCTCCGNGCCTTTGCACATGCTGTTCCCTCTGCCTGGAATGC 163
INTRON_3 177964 TTTCCCTCCCTCTCTTTGCCTGGCCACTTTCTACTCATCCTTTAAAACTC 178013
i i i ii iii i vi i i i?
L2c_3end#LINE 164 TCTTCCCCCCTCCTTCCACCTGGCTAACTCCTACTCATCCTTCAAGNCTC 213
INTRON_3 178014 AGTGTAA--CTCAGTCCTCATCAAAGAGGGCTTTC 178046
ivi i--v -- v v i i v i
L2c_3end#LINE 214 AGCTCAGATGTCA--CCTCCTCCAGGAAGCCTTCC 246
Matrix = 25p39g.matrix
Transitions / transversions = 3.00 (27 / 9)
Gap_init rate = 0.03 (4 / 131), avg. gap size = 1.50 (6 / 4)
+ 2262 11.9 0.0 0.3 INTRON_3 178048 178349 (221832) + AluSx1 SINE/Alu 1 301 (11) 221
ANNOTATION EVIDENCE:
2177 12.29 0.00 0.33 INTRON_3 178048 178349 221832 + AluSx SINE/Alu 1 301 11 381
INTRON_3 178048 GGCCAGGCACAGTGGCTCACGCCTGTAAGCCCAGCACTTTGGGAGGCTGA 178097
i i i v i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 178098 AGTGGGCAGATCACTTGAGGTCATGGGTTCAAGACCAGTCTGGCCAACTT 178147
i i i i v i i i v
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
INTRON_3 178148 GGTGAAACCCTGTCTCTATTAAAAACACAAAAATTATCTTGGAGTGGTGG 178197
i i i v iv v
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGG 150
INTRON_3 178198 CAGGCACCTGTAACCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCT 178247
iv i i i
AluSx#SINE/Al 151 CGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCT 200
INTRON_3 178248 TAAGCCCAGGAGGTGGAGGTTGCAGTGAGCCCAGATTCGCGCCACTGCAC 178297
i i i i v -
AluSx#SINE/Al 201 TGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGAT-CGCGCCACTGCAC 249
INTRON_3 178298 TCCAGCCTGGGTGATAGAGTGAGGCTCCATCTCAAAAAAAAGAAAAAAAA 178347
i i i i i i
AluSx#SINE/Al 250 TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAA 299
INTRON_3 178348 AA 178349
AluSx#SINE/Al 300 AA 301
Matrix = 14p39g.matrix
Transitions / transversions = 3.62 (29 / 8)
Gap_init rate = 0.00 (1 / 301), avg. gap size = 1.00 (1 / 1)
+ 198 32.5 4.6 1.1 INTRON_3 178865 178951 (221230) C MIRc SINE/MIR (162) 106 17 222
ANNOTATION EVIDENCE:
198 32.54 4.60 1.11 INTRON_3 178865 178951 221230 C MIRc SINE/MIR 17 106 162 400
INTRON_3 178865 TGACATTCATAAGATCACACAATTACCAACTAGCA---CTAGTATTTAAA 178911
v v vi i ii vi v i --- i v i ii
C MIRc#SINE/MIR 106 TGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCAGGACTCGAA 57
INTRON_3 178912 CTCCTTATCT-CCTTACTCAGAGTCTAGTATCCTTTATACT 178951
- vvi - v vi i iii vi
C MIRc#SINE/MIR 56 C-CCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTCCACT 17
Matrix = 25p39g.matrix
Transitions / transversions = 1.55 (17 / 11)
Gap_init rate = 0.03 (3 / 86), avg. gap size = 1.67 (5 / 3)
+ 363 34.8 5.8 3.0 INTRON_3 179069 179329 (220852) C L2 LINE/L2 (575) 2844 2577 223
ANNOTATION EVIDENCE:
363 34.76 5.75 2.99 INTRON_3 179069 179329 220852 C L2 LINE/L2 2577 2844 238 401
INTRON_3 179069 TTTTGATCAGAGAATTG-CATGATGAAAGTAATATTTCAGGAAGATTATT 179117
v i v - vvi v v i i ii i i i
C L2#LINE/L2 2844 TTTTGAGCAGAGGAGTGACATGATCTGACTTATGTTTTAAAAGGATCACT 2795
INTRON_3 179118 CTGGTAGGTATGTACAGGATAGGTTAGAAGTGGGT--GGTCTGTTGA--C 179163
iv v i vv i ii i? i v i-- --- v --
C L2#LINE/L2 2794 CTGGCTGCTGTGTTGAGAATAGACTGNAGGGGGGCAAGG---GTGGAAGC 2748
INTRON_3 179164 AGAGAAACTAATAAGGAAGGTATTGCAGTAGTCTCTGCATGAGATAATAA 179213
i i i i v i v i ivv iv i ii
C L2#LINE/L2 2747 AGGGAGACCAGTTAGGAGGCTATTGCAGTAATCCAGGCGAGAGATGATGG 2698
INTRON_3 179214 TAAGT-GGCTCTATCTGG--AAATTGGAAACA-TGAGAA----TCAAGTT 179255
iiv - vi vivv --iv v iiii- ---- iii
C L2#LINE/L2 2697 TGGCTTGGACCAGGGTGGTGGCAGTGGAGGTGGTGAGAAGTGGTCGGATT 2648
INTRON_3 179256 ATGAATATTAAGAAGTCT-AAGGAAGAACCAGAAGTGCTTGTTGA-GGAT 179303
v i ----- v i - v i iv vii i -
C L2#LINE/L2 2647 CTGGATAT-----ATTTTGAAGGTAGAGCCAACAGGATTTGCTGATGGAT 2603
INTRON_3 179304 TAAATGTTATGGATAAGAGAGGGAAA 179329
ii viv vi i ii i
C L2#LINE/L2 2602 TGGATGTGGGGTGTGAGAGAAAGAGA 2577
Matrix = 25p39g.matrix
Transitions / transversions = 1.72 (55 / 32)
Gap_init rate = 0.04 (11 / 260), avg. gap size = 2.09 (23 / 11)
+ 262 23.9 3.0 0.0 INTRON_3 180772 180838 (219343) C MER113 DNA/hAT-Charlie (295) 226 158 224
ANNOTATION EVIDENCE:
262 23.88 2.99 0.00 INTRON_3 180772 180838 219343 C MER113 DNA/hAT-Charlie 158 226 295 467
INTRON_3 180772 TCCTTGT--AAAAGAAAGCTTAGCAACTATTGGAGAGGTACTAATGACAT 180819
i -- ii v v i i ii v
C MER113#DNA/hA 226 TCTTTGTTAAAAAGGGAGATTAGCAAGTGTTAGAGAGGTGTTAAAGACAT 177
INTRON_3 180820 ACTAGTGTGGCACTGAGAC 180838
iiiviv
C MER113#DNA/hA 176 ACTAGCACCAAACTGAGAC 158
Matrix = 20p39g.matrix
Transitions / transversions = 2.20 (11 / 5)
Gap_init rate = 0.02 (1 / 66), avg. gap size = 2.00 (2 / 1)
+ 408 19.0 4.9 9.6 INTRON_3 180845 181007 (219174) + L1ME4a LINE/L1 5968 6123 (1) 225
ANNOTATION EVIDENCE:
408 19.01 4.91 9.62 INTRON_3 180845 181007 219174 + L1ME4a_3end LINE/L1 715 870 1 433
INTRON_3 180845 AAAAAAGACTGAAAGAAAACACTCTAAAATATGAATAGCAGTCATCTGCA 180894
i i i v i i v i ii i vii
L1ME4a_3end#L 715 AAAAAAGACTGGAAGGAAATACACCAAAATGTTAACAGTGGTTATCTCTG 764
INTRON_3 180895 GGTGTGGGAATTA-GAGTTTATTAATTTTTATACTTTACGCTTTTTGGCC 180943
vv i - i -----i -- --- --i
L1ME4a_3end#L 765 GGTGGTGGGATTATGGGT-----GATTTTTAT--TTT---CTTTTT--TC 802
INTRON_3 180944 TTTGC--TTTTTGTATTGTCTAAATTTTCTGCAAT-----TATATTTGAA 180986
i-- i v i i ----- i ---
L1ME4a_3end#L 803 TTTGTATTTTCTGTATTTTCCAAATTTTCTACAATGAGCATGTATT---A 849
INTRON_3 180987 CTTTTAAAATCAGAAAACAAA 181007
v v
L1ME4a_3end#L 850 CTTTTATAATCAGAAAAAAAA 870
Matrix = 20p39g.matrix
Transitions / transversions = 2.50 (20 / 8)
Gap_init rate = 0.05 (8 / 162), avg. gap size = 2.88 (23 / 8)
+ 3991 0.8 0.0 0.0 INTRON_3 181333 181802 (218379) C L1HS LINE/L1 (1682) 4464 3995 226 *
ANNOTATION EVIDENCE:
3991 0.85 0.00 0.00 INTRON_3 181333 181802 218379 C L1P1_orf2 LINE/L1 1886 2355 939 434
INTRON_3 181333 GTTGTTCTCCTTGAAGAGGTCCTTCACATCCCTTGTAAGTTGGATTCCTA 181382
v
C L1P1_orf2#LIN 2355 GTAGTTCTCCTTGAAGAGGTCCTTCACATCCCTTGTAAGTTGGATTCCTA 2306
INTRON_3 181383 GGTATTTTATTCTCTTTGAAGCAATTGTGAATGGGAGTTCACCCATGATT 181432
C L1P1_orf2#LIN 2305 GGTATTTTATTCTCTTTGAAGCAATTGTGAATGGGAGTTCACCCATGATT 2256
INTRON_3 181433 TGGCTCTCTGTTTGTCTGTTGTTGGTGTATAAGAATGCTTGTGATTTTTG 181482
C L1P1_orf2#LIN 2255 TGGCTCTCTGTTTGTCTGTTGTTGGTGTATAAGAATGCTTGTGATTTTTG 2206
INTRON_3 181483 TACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAA 181532
C L1P1_orf2#LIN 2205 TACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAA 2156
INTRON_3 181533 GGAGATTTTGGGCTGAGACGATGGGGTTTTCTAGATAAACAATCATGTCG 181582
C L1P1_orf2#LIN 2155 GGAGATTTTGGGCTGAGACGATGGGGTTTTCTAGATAAACAATCATGTCG 2106
INTRON_3 181583 TCTGCAAACAGGGACAATTTGACTTCCTCTTTTCCTAATTGAATACCCTT 181632
C L1P1_orf2#LIN 2105 TCTGCAAACAGGGACAATTTGACTTCCTCTTTTCCTAATTGAATACCCTT 2056
INTRON_3 181633 TATTTCCTTCTCCTGCCTGATTGCTCTGGCCAGAACTTCCAACACTATGT 181682
i
C L1P1_orf2#LIN 2055 TATTTCCTTCTCCTGCCTGATTGCCCTGGCCAGAACTTCCAACACTATGT 2006
INTRON_3 181683 TGAATAGGAGTGGTGAGAGAGGGCATCCCTGTCTTGTGCCAGTTTTCAAA 181732
i
C L1P1_orf2#LIN 2005 TGAATAGGAGCGGTGAGAGAGGGCATCCCTGTCTTGTGCCAGTTTTCAAA 1956
INTRON_3 181733 GGGAATGCTTCCAGTTTTTGCCCATTCAGTATGATATTGGCTGTGGGTTT 181782
C L1P1_orf2#LIN 1955 GGGAATGCTTCCAGTTTTTGCCCATTCAGTATGATATTGGCTGTGGGTTT 1906
INTRON_3 181783 GTCATAAATAGCTCTTATTA 181802
i
C L1P1_orf2#LIN 1905 GTCATAGATAGCTCTTATTA 1886
Matrix = 20p39g.matrix
Transitions / transversions = 3.00 (3 / 1)
Gap_init rate = 0.00 (0 / 469), avg. gap size = 0.0 (0 / 0)
+ 7884 0.6 0.0 0.1 INTRON_3 181802 183497 (216684) + L1HS LINE/L1 4460 6153 (2) 226
ANNOTATION EVIDENCE:
7884 0.42 0.00 0.00 INTRON_3 181802 182745 217436 + L1P1_orf2 LINE/L1 2351 3294 0 435
INTRON_3 181802 ACTACAAACCACTGCTCAAGGAAATAAAAGAGGACACAAACAATTGGAAG 181851
v
L1P1_orf2#LIN 2351 ACTACAAACCACTGCTCAAGGAAATAAAAGAGGACACAAACAAATGGAAG 2400
INTRON_3 181852 AACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCCAT 181901
L1P1_orf2#LIN 2401 AACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCCAT 2450
INTRON_3 181902 ACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCTACCAA 181951
L1P1_orf2#LIN 2451 ACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCTACCAA 2500
INTRON_3 181952 TGACTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATATGGAAC 182001
L1P1_orf2#LIN 2501 TGACTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATATGGAAC 2550
INTRON_3 182002 CAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAACAAAGC 182051
L1P1_orf2#LIN 2551 CAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAACAAAGC 2600
INTRON_3 182052 TGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAA 182101
L1P1_orf2#LIN 2601 TGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAA 2650
INTRON_3 182102 CCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAAC 182151
L1P1_orf2#LIN 2651 CCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAAC 2700
INTRON_3 182152 AGAACAGAGCCCTCAGAAATAATGCCGCATATCTACAACTATCTGATCTT 182201
L1P1_orf2#LIN 2701 AGAACAGAGCCCTCAGAAATAATGCCGCATATCTACAACTATCTGATCTT 2750
INTRON_3 182202 TGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATA 182251
L1P1_orf2#LIN 2751 TGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATA 2800
INTRON_3 182252 AATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGAT 182301
L1P1_orf2#LIN 2801 AATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGAT 2850
INTRON_3 182302 CCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGATTT 182351
L1P1_orf2#LIN 2851 CCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGATTT 2900
INTRON_3 182352 AAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTA 182401
i
L1P1_orf2#LIN 2901 AAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTA 2950
INTRON_3 182402 CCATTCAGGACATAGGCGTGGGCAATGACTTCATGTCCAAAACACCAAAA 182451
v
L1P1_orf2#LIN 2951 CCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAACACCAAAA 3000
INTRON_3 182452 GCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAA 182501
L1P1_orf2#LIN 3001 GCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAA 3050
INTRON_3 182502 GAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTA 182551
L1P1_orf2#LIN 3051 GAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTA 3100
INTRON_3 182552 CAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATA 182601
L1P1_orf2#LIN 3101 CAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATA 3150
INTRON_3 182602 TCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAA 182651
L1P1_orf2#LIN 3151 TCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAA 3200
INTRON_3 182652 CTCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAG 182701
i
L1P1_orf2#LIN 3201 CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAG 3250
INTRON_3 182702 ACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCA 182745
L1P1_orf2#LIN 3251 ACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCA 3294
Matrix = 20p39g.matrix
Transitions / transversions = 1.00 (2 / 2)
Gap_init rate = 0.00 (0 / 943), avg. gap size = 0.0 (0 / 0)
7581 0.89 0.00 0.22 INTRON_3 182596 183497 216684 + L1HS_3end LINE/L1 1 900 2 436
INTRON_3 182596 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 182645
L1HS_3end#LIN 1 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 50
INTRON_3 182646 AAACAACTCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAA 182695
i
L1HS_3end#LIN 51 AAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAA 100
INTRON_3 182696 AAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCA 182745
L1HS_3end#LIN 101 AAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCA 150
INTRON_3 182746 CTGGCCATCAGAGAAATGCAAATCAAAACCACTGTGAGATATCATCTCAC 182795
i
L1HS_3end#LIN 151 CTGGCCATCAGAGAAATGCAAATCAAAACCACTATGAGATATCATCTCAC 200
INTRON_3 182796 ACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGA 182845
L1HS_3end#LIN 201 ACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGA 250
INTRON_3 182846 GAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTCAA 182895
i v
L1HS_3end#LIN 251 GAGGATGCGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAA 300
INTRON_3 182896 CTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGA 182945
L1HS_3end#LIN 301 CTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGA 350
INTRON_3 182946 ACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAA 182995
L1HS_3end#LIN 351 ACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAA 400
INTRON_3 182996 ATGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATT 183045
v
L1HS_3end#LIN 401 ATGAGTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATT 450
INTRON_3 183046 GCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAAC 183095
L1HS_3end#LIN 451 GCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAAC 500
INTRON_3 183096 AATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACT 183145
L1HS_3end#LIN 501 AATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACT 550
INTRON_3 183146 ATGCAGCCATAAAAAATGATGAGTTCATATCCTTTGTAGGGACATGGATG 183195
L1HS_3end#LIN 551 ATGCAGCCATAAAAAATGATGAGTTCATATCCTTTGTAGGGACATGGATG 600
INTRON_3 183196 AAATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAA 183245
L1HS_3end#LIN 601 AAATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAA 650
INTRON_3 183246 ACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGATCACATG 183295
L1HS_3end#LIN 651 ACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGATCACATG 700
INTRON_3 183296 GACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTCGGGGG 183345
L1HS_3end#LIN 701 GACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTCGGGGG 750
INTRON_3 183346 AGGGGGGAGGGATAGCATTGGGAGATATATACCTAATGCTAGAGGACTCA 183395
-- v v
L1HS_3end#LIN 751 AGGGGGGAGGGATAGCATTGGGAGATATA--CCTAATGCTAGATGACACA 798
INTRON_3 183396 TTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAAC 183445
L1HS_3end#LIN 799 TTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAAC 848
INTRON_3 183446 CTGCACAATATGCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAA 183495
i
L1HS_3end#LIN 849 CTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAA 898
INTRON_3 183496 AA 183497
L1HS_3end#LIN 899 AA 900
Matrix = 20p39g.matrix
Transitions / transversions = 1.00 (4 / 4)
Gap_init rate = 0.00 (1 / 901), avg. gap size = 2.00 (2 / 1)
+ 258 9.5 0.0 0.0 INTRON_3 183499 183540 (216641) + (A)n Simple_repeat 1 42 (0) 227
ANNOTATION EVIDENCE:
258 9.52 0.00 0.00 INTRON_3 183499 183540 216641 + (A)n Simple_repeat 1 42 138 461
INTRON_3 183499 AAAATAAAAAAAATAAAACAAAAAAAAAAAAAAAAAAAGAAA 183540
v v v i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 42
Matrix = Unknown
Transitions / transversions = 0.33 (1 / 3)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0)
+ 1140 19.8 6.0 0.9 INTRON_3 183791 184122 (216059) C MER113 DNA/hAT-Charlie (118) 403 55 228
ANNOTATION EVIDENCE:
1140 19.75 6.02 0.86 INTRON_3 183791 184122 216059 C MER113 DNA/hAT-Charlie 55 403 118 468
INTRON_3 183791 TAAATAAATGAATTTAGAAAGTAAACTTTATTTTACTACTATAAATGGAA 183840
vv vi v v i i
C MER113#DNA/hA 403 TAAATAAATTTATTTTAAAAGGAAACTTTATATCACTACCATAAATGGAA 354
INTRON_3 183841 AAACAAT-TCAGTTGCCATAAATAGACCGTAAC--TAAAAATAAAGACAG 183887
v i - v vv -- v i
C MER113#DNA/hA 353 AACCAGTATCACTTGCCATAAATAGAAGGTAACCATAAAAATAAATACAA 304
INTRON_3 183888 TATAAACAAAATGGTGTTATTAAATTCTATCTAGGTAGTATTGCCTGTTC 183937
iv iii v i v i i-
C MER113#DNA/hA 303 TGAAAACAAAACAATGTTATTAAATTCTAGCTAGATACTGTTGCCTGC-C 255
INTRON_3 183938 CTTGGCTTTGAAACTGAG----------TCTTTGT-AACAAGAACTCTTA 183976
vvv i iv ---------- - v iivvv
C MER113#DNA/hA 254 GAAGGCTCTGAGCCTGAGGCCTGCTCTCTCTTTGTTAAAAAGGGAGATTA 205
INTRON_3 183977 ACAACTGTGGGAGAGGTGCTAATGACATACTAGCATGGCAGTGAGACATG 184026
i v vi i v iviv v v v
C MER113#DNA/hA 204 GCAAGTGTTAGAGAGGTGTTAAAGACATACTAGCACCAAACTGAGACTTT 155
INTRON_3 184027 CTTCTTAACA-AATCAGAA--ATTCAGAAAAAGCAATGAAAATAGAATAA 184073
i i i- -- -- i v v vi
C MER113#DNA/hA 154 CTCCTTGACGTAATCAGAAGGATT--GAAAGAGAATTGAAAAGGGAATAA 107
INTRON_3 184074 CTTTCTC-CTATGTGATTCAATGTTATTTCATG--GCATCCCTTAACCAC 184120
- v -- ii v vv
C MER113#DNA/hA 106 CTTTCTCACTATGTGATTCAATGTTATTTAATGCCGTGTCCATGTACCAC 57
INTRON_3 184121 TT 184122
i
C MER113#DNA/hA 56 CT 55
Matrix = 20p39g.matrix
Transitions / transversions = 0.81 (29 / 36)
Gap_init rate = 0.03 (10 / 331), avg. gap size = 2.30 (23 / 10)
+ 189 0.0 0.0 0.0 INTRON_3 184859 184879 (215302) + (T)n Simple_repeat 1 21 (0) 229
ANNOTATION EVIDENCE:
189 0.00 0.00 0.00 INTRON_3 184859 184879 215302 C (A)n Simple_repeat 160 180 0 462
INTRON_3 184859 TTTTTTTTTTTTTTTTTTTTT 184879
C (A)n#Simple_r 180 TTTTTTTTTTTTTTTTTTTTT 160
Matrix = Unknown
Transitions / transversions = 0.0 (0 / 0)
Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0)
+ 510 26.1 10.6 3.2 INTRON_3 185169 185384 (214797) C MIRb SINE/MIR (26) 242 8 230
ANNOTATION EVIDENCE:
449 30.22 10.65 3.46 INTRON_3 185169 185384 214797 C MIR SINE/MIR 8 238 24 403
INTRON_3 185169 GCTTACTACATGCTAAACATTGGTTTTGAC--TTCATATACATTATCTC- 185215
ii i ii i v i vii -- i i ii v -
C MIR#SINE/MIR 238 GCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTAACTCA 189
INTRON_3 185216 --TGCTCTTAACATCAACTCTTTAAAATAGATATTTTT------CCCACT 185257
-- iv i v v i v i ii i i v ------ i
C MIR#SINE/MIR 188 TTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCCCCATT 139
INTRON_3 185258 T--CAGATGGAGAAATTGAGGCTC-------TTATGGAACTAGCC-AGGG 185297
-- ii i v ------- v v v - i
C MIR#SINE/MIR 138 TTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTGCCCAAGG 89
INTRON_3 185298 TCACATAGCTAGCA-GTGGTTGGAGCCAGTACTTTCTAACTCTAAAAGTC 185346
i i - i-i i v -- v i viiv
C MIR#SINE/MIR 88 TCACACAGCTAGTAAGTGGC-AGAGCCGGGA--TTCGAACCCAGGCAGTC 42
INTRON_3 185347 TGTGTTGTTAAATTTG-GTTCCTAATTTGATATTATGCT 185384
- i vivi i ii - i i ii---- i
C MIR#SINE/MIR 41 TG-GCTCCAGAGTCCGTGCTCTTAACC----ACTATGCT 8
Matrix = 25p39g.matrix
Transitions / transversions = 2.50 (45 / 18)
Gap_init rate = 0.06 (12 / 215), avg. gap size = 2.58 (31 / 12)
510 25.22 10.56 3.11 INTRON_3 185169 185348 214833 C MIRb SINE/MIR 50 242 26 402
INTRON_3 185169 GCTTACTACATGCTAAACATTG-GTTTTG-ACTTCATATACATTATCTC- 185215
iii i ii i - i vv -i i i i -
C MIRb#SINE/MIR 242 GCTTACTGTGTGCCAGGCACTGTGCTAAGCGCTTTACATGCATTATCTCA 193
INTRON_3 185216 --TGCTCTTAACATCAACTCTTTAAAATAGATATTTTT---CCCACTT-- 185258
-- iv i v v i vii ii i v --- i --
C MIRb#SINE/MIR 192 TTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTA 143
INTRON_3 185259 CAGATGGAGAAATTGAGGCTC-------TTATGGAACTAGCC-AGGGTCA 185300
ii i ------- v vi v - i
C MIRb#SINE/MIR 142 CAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCA 93
INTRON_3 185301 CATAGCTAGCA-GTGGTTGGAGCCAGTACTTTCTAACTCTAAAAGTCTG 185348
i i - i-i v -- v i --- i
C MIRb#SINE/MIR 92 CACAGCTAGTAAGTGGC-AGAGCCAGGA--TTCGAACCC---AGGTCTG 50
Matrix = 25p39g.matrix
Transitions / transversions = 2.67 (32 / 12)
Gap_init rate = 0.06 (11 / 179), avg. gap size = 2.27 (25 / 11)
+ 513 29.8 4.6 6.9 INTRON_3 185523 185760 (214421) + MIRb SINE/MIR 27 259 (9) 231
ANNOTATION EVIDENCE:
513 29.78 4.62 6.87 INTRON_3 185523 185760 214421 + MIRb SINE/MIR 27 259 9 404
INTRON_3 185523 AGAGCACAGGGTTT--AGTTAGGCAGATCTGA-CTAGAGTTC-AGCTCAG 185568
i v -- i i i-i v i i -i v
MIRb#SINE/MIR 27 AGAGCACGGGCTTTGGAGTCAGGCAGACCTGGGTTCGAATCCTGGCTCTG 76
INTRON_3 185569 TCACTTACTGTTTCTCAGGTCTTGG-CAAGAAATTTAATCTTTAGTTAAA 185617
i ivi v vv ii - vv i i i --i ---
MIRb#SINE/MIR 77 CCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCT--CT--- 121
INTRON_3 185618 GAATCTATAGTTTCTTTAACTATAAAGCAGTTATAATAATACTGCCTGTC 185667
ii -i i i v i iii vv --- ii
MIRb#SINE/MIR 122 GAGCCT-CAGTTTCCTCATCTGTAAAATGGGGATAATAATAC---CTACC 167
INTRON_3 185668 TCTTAAGGTTATTTTTA---TTAAATGAGATAAGCCTTATTTCATTTAAT 185714
vi i i v v --- ------- v v v
MIRb#SINE/MIR 168 TCGCAGGGTTGTTGTGAGGATTAAATGAGATAA-------TGCATGTAAA 210
INTRON_3 185715 ATGT---GCTAATTGTTTAGCATGTAGTAAATGCTCAATAATAGATAGC 185760
ii i--- vv v ii i iii ii vv i
MIRb#SINE/MIR 211 GCGCTTAGCACAGTGCCTGGCACACAGTAAGCGCTCAATAAATGGTAGC 259
Matrix = 25p39g.matrix
Transitions / transversions = 1.87 (43 / 23)
Gap_init rate = 0.05 (11 / 237), avg. gap size = 2.45 (27 / 11)
+ 189 21.3 0.0 0.0 INTRON_3 185993 186039 (214142) + (TATATG)n Simple_repeat 4 50 (0) 232
ANNOTATION EVIDENCE:
189 21.28 0.00 0.00 INTRON_3 185993 186039 214142 C (CATATA)n Simple_repeat 130 176 4 463
INTRON_3 185993 TGTATATGTATACAAATATGTGTATGTGTAAATATATGTGTGTGCAT 186039
iiv i i vi i i i
C (CATATA)n#Sim 176 TGTATATGTATATGTATATGTATATGTATATGTATATGTATATGTAT 130
Matrix = Unknown
Transitions / transversions = 4.00 (8 / 2)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 446 23.7 5.7 1.4 INTRON_3 186601 186741 (213440) C MamRep605 Unknown (377) 499 353 233
ANNOTATION EVIDENCE:
446 23.72 5.67 1.36 INTRON_3 186601 186741 213440 C MamRep605 Unknown 353 499 377 469
INTRON_3 186601 AATCAGAAGACTGCTGTGTGGGCATGCATTTACAACAAGAAGACTTAG-- 186648
ii vv i v v i v ii v --
C MamRep605#Unk 499 AATCAGAAGGTTGCTTGGTGAGCATGGAATCAGAACAAGGGGAGTTAGTT 450
INTRON_3 186649 --ATAAATTGGATGTTTGATGGC-TCAGGCTAAGGCAGCCTTACCCTTCC 186695
-- i ? i i i - ii v iv v
C MamRep605#Unk 449 ANATGANTCGAATGTTTAATGGCATCAGGCTAAGATAGCCTGATGCATCC 400
INTRON_3 186696 TATC---ATAATGGGCATGGCCCTTTCAAGGGGACTGGAAATACTCCAA 186741
- --- i i i v i vi v i - v
C MamRep605#Unk 399 -ATCTCCACAGTAGGGATGGCCTTGCCAATGGGACCGGAA-TACTCGAA 353
Matrix = 20p39g.matrix
Transitions / transversions = 1.46 (19 / 13)
Gap_init rate = 0.04 (5 / 140), avg. gap size = 2.00 (10 / 5)
+ 2722 11.3 2.4 0.2 INTRON_3 186827 187243 (212938) C LTR47A2 LTR/ERVL (6) 426 1 234
ANNOTATION EVIDENCE:
2722 11.30 2.40 0.23 INTRON_3 186827 187243 212938 C LTR47A2 LTR/ERVL 1 426 6 470
INTRON_3 186827 ACAGTGAGCAGGTCTATGCAAAGCTACCCCTGAAGGCCGAGGGAGCTGAG 186876
i v ii i
C LTR47A2#LTR/E 426 ACGGTGAGCAGGTCTATGCAAACCTACCCCCAAAGGCTGAGGGAGCTGAG 377
INTRON_3 186877 AGGCCAGAGAAAGAGGCTGACAAAGCCAGTTTCTCAGAAAGAAACATTTA 186926
i v ?
C LTR47A2#LTR/E 376 AGGCCAAAGAAAGAGGCTGACAAATCCAGTTTCTCAGAAAGAAAYATTTA 327
INTRON_3 186927 ATAGGGACTTACAAAGAGGTGCCATTTCTTGGGTAGCTGCTAGATAGTGG 186976
v iv v v ii i iv
C LTR47A2#LTR/E 326 ATAGGGACTTACAAACAGAAGCGATGTCTCAGGTAGCCGTGAGATAGTGG 277
INTRON_3 186977 ATCCTC-ACACCTGCCCTCTAGAAAGTATCCTTCATATAGCATGCTTTTA 187025
? i -i ii i i v
C LTR47A2#LTR/E 276 ATYCCCTGCACCCACCCTCCAGAAAGTATCCTTTATATAGCAAGCTTTTA 227
INTRON_3 187026 GTGTAAAGACATGTGCAGCTGGTCATACCTCAGACTTTCTTGCCAAA-CT 187074
v ii -
C LTR47A2#LTR/E 226 GGGTAAAGACATGTGCAGCTGGTCATGTCTCAGACTTTCTTGCCAAAACT 177
INTRON_3 187075 TGCGACCACTGGGGAGGTTAGATAAGCATCTTTATGGGGGAATTATCTAT 187124
i i i-
C LTR47A2#LTR/E 176 TGTGACCACTGGGGAGGTTAGATAAGCATCTTTATGAGGGG-TTATCTAT 128
INTRON_3 187125 GCTACAAGTATTGTTCAAAGACTTTGCTGCAGAACATGTTGGTATGCA-- 187172
i i i i iv --
C LTR47A2#LTR/E 127 GCTACAGGCATTGTTTAAAGACCTTGCTGCAGAACACCTTGGTATGCAGG 78
INTRON_3 187173 ------ACATTAGTCATCATGGTGGTTTCACTTCAATATGGCATCACTCT 187216
------ ii ii v
C LTR47A2#LTR/E 77 AGTCAAACATCGGTCATCATGGTGGTTTTGCTTCAAGATGGCATCACTCT 28
INTRON_3 187217 TGGAATGCAACAGACTGTTTTCCTGCA 187243
vv i i
C LTR47A2#LTR/E 27 TGCCATGCAACAGGCTGTTTTCCTACA 1
Matrix = 20p39g.matrix
Transitions / transversions = 2.46 (32 / 13)
Gap_init rate = 0.01 (4 / 416), avg. gap size = 2.75 (11 / 4)
+ 411 35.3 7.0 0.0 INTRON_3 187244 187430 (212751) + L2b LINE/L2 2953 3152 (223) 235
ANNOTATION EVIDENCE:
411 35.29 6.95 0.00 INTRON_3 187244 187430 212751 + L2b_3end LINE/L2 44 243 223 405
INTRON_3 187244 CACTCTCTCATT---CAATTTGTACCAGT-GCCCTGGCTTTCTTGTGATT 187289
i v --- v i iv i-i v i i ivi
L2b_3end#LINE 44 CACTCTCCCCTTGCTCACTCTGCTCCAGCCACACTGGCCTCCTTGCTGTT 93
INTRON_3 187290 CCTAAGGTATACAGAGTTCTTTCCCACTTCAGGGATTTTGCACTTGTTCT 187339
viiii ii vii i vi i i vi ? i v
L2b_3end#LINE 94 CCTCGAACACGCCAGGCTCGCTCCCGCCTCAGGGCCTTTGCACNTGCTGT 143
INTRON_3 187340 CCTCTTTG---AAACCTTTCGTCTCCAGATCCTTTCATGGCTA---CCTT 187383
i i i ---ii v vii v i vv i iv v i --- v
L2b_3end#LINE 144 TCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTCGCCTGGCCAACTCCTA 193
INTRON_3 187384 TTCATCGTTGAGGCTTCAGGTCATATG---ACTCCTCAGAGAGGCCTTCC 187430
i v v ii v v ---v vii i i
L2b_3end#LINE 194 CTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCAGGAAGCCCTCC 243
Matrix = 25p39g.matrix
Transitions / transversions = 1.71 (41 / 24)
Gap_init rate = 0.03 (5 / 186), avg. gap size = 2.60 (13 / 5)
+ 1332 28.1 3.0 2.0 INTRON_3 187432 187867 (212314) + MLT1J LTR/ERVL-MaLR 70 509 (3) 236
ANNOTATION EVIDENCE:
1332 28.10 2.98 2.05 INTRON_3 187432 187867 212314 + MLT1J LTR/ERVL-MaLR 70 509 3 471
INTRON_3 187432 TTCTTTGTTAGGCACATTGCCACACAGCTGAGCAACTATATTTTCCAACG 187481
i v i i v v vvv ivi i i i v
MLT1J#LTR/ERV 70 TTTTTAGCTGGGCACATGGCCACCCAGAATAAAGACTACATTTCCCAGCC 119
INTRON_3 187482 TCCCTTGCAGCTGAGTGTGGCCCTGTGACTAAGTTCTGGCTAATGAAATG 187531
ii v i ii
MLT1J#LTR/ERV 120 TCCCTTGCAGCTAGGTGTGGCCATGTGACTAAGTTCTGGCCAATGGGATG 169
INTRON_3 187532 TAAACCAAATTGTACTGTGGTACTTTGAAAGGAACTGTA---AAAGGAAA 187578
i vi v ?vv vv ivi-- v v--- i i
MLT1J#LTR/ERV 170 TAAGCAGAAGTGNCGTGTGCAACTTCCG--GGAAGTGTCCTTAAAGGGAG 217
INTRON_3 187579 GAAGTGTATTCTTCTTTCTCCTCTTCTCTATCTGTTGTGTTCCCTGGAAT 187628
ii i iii ii ii i iv i---- i vv
MLT1J#LTR/ERV 218 GGGGCGTGCCCTTCTTTTCCCCTTCCTCCTTCC----TGCTGGCTGGAAT 263
INTRON_3 187629 ACCTAATGTGGTGGCTG-AGCTCTAGTAGCCATCTTAGACCATGGGAGAA 187677
i v-i i i - v i i i ivii
MLT1J#LTR/ERV 264 GCG-GACGTGATGGCTGGAGCTCGAGCAGCCATCTTGGACCATGAGGTGG 312
INTRON_3 187678 AGGGTATTCACTAGGTATGGTAGAG-----ATTTGGAA--AGCCTGAGTC 187720
i vi ivii ii v ii ----- vv i -- i
MLT1J#LTR/ERV 313 AAGCCACGTGCTGAGGATGGCGGAGCAACAAGATAGAAGGAGCCTGGGTC 362
INTRON_3 187721 TCTGATGAATTTGTGAGGCTCTACAATAGCCCCGAGCTATCTACCTCTAT 187770
i v v - v v i i vi i ii ii iiv
MLT1J#LTR/ERV 363 CCTGATGACTGTG-GAGCCGCCATACCAGCCCTGGACTGCCTACCTCCGG 411
INTRON_3 187771 GCTTCTTTTAAATGAGAGAGAAATAAGTTT-TATCTTACTTAATCCACTG 187819
i v ii - ii v
MLT1J#LTR/ERV 412 ACTTCTTTTACATGAGAGAGAAATAAACTTCTATCTTGTTTAAGCCACTG 461
INTRON_3 187820 TTATTTTAGGTTAGTTTGT-ATATGCAGCCAAACTTATTCCAAACCAAT 187867
i -v i - ivi i i v v ii
MLT1J#LTR/ERV 462 TTATTTTGGGTT-TTCTGTCACTCGCAGCCGAACCTAATCCTAACTGAT 509
Matrix = 20p39g.matrix
Transitions / transversions = 1.90 (78 / 41)
Gap_init rate = 0.03 (11 / 435), avg. gap size = 2.00 (22 / 11)
+ 253 32.6 10.1 2.4 INTRON_3 187896 188093 (212088) + L2b LINE/L2 3193 3405 (21) 235
ANNOTATION EVIDENCE:
253 32.59 10.10 2.35 INTRON_3 187896 188093 212088 + L2a_3end LINE/L2 284 496 21 406
INTRON_3 187896 CACCATGCTCTATCATACCATTATTCTCTGGTTTGTCTT-CTTCATGGCT 187944
? iv i v-- v -- i v i i - i i v
L2a_3end#LINE 284 CANCACTCCCTATCC--CCCTTA--CCCTGCTTTATTTTTCTCCATAGCA 329
INTRON_3 187945 TGTTTAATGACTGGAAATTCTCAT-TATTTT-CTT------TTTTTTATT 187986
iv v v iv iiv v v - - - ------ v
L2a_3end#LINE 330 CTTATCACCATCTGACATACT-ATATATTTTACTTATTTATTTGTTTATT 378
INTRON_3 187987 GTTTGTCCTTCCTGCTTTAAATATAAGCTT--TGTGGGAAGAGTCCTC-A 188033
i iii ivvi vi i i-- v v i v i i-i
L2a_3end#LINE 379 GTCTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTG 428
INTRON_3 188034 TCTTCCTTGTTTACTGTGTTGTCTTCAGAGAG-AAAACAATGTCT----- 188077
vii i ivv i ii v vv- i i i -----
L2a_3end#LINE 429 TCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCAC 478
INTRON_3 188078 --AATAGGTACTCAATAA 188093
-- i ii
L2a_3end#LINE 479 ATAGTAGGCGCTCAATAA 496
Matrix = 25p39g.matrix
Transitions / transversions = 1.48 (37 / 25)
Gap_init rate = 0.06 (11 / 197), avg. gap size = 2.27 (25 / 11)
+ 6162 8.9 1.3 0.4 INTRON_3 188114 189072 (211109) C L1PA10 LINE/L1 (1) 6167 5200 237
ANNOTATION EVIDENCE:
6162 8.87 1.33 0.33 INTRON_3 188114 189018 211163 C L1PA10_3end LINE/L1 1 914 1 437
INTRON_3 188114 TTTTTTTAAAATTTAATTTAAGTTCTGGGATACATGTGCAGGATGTTCAA 188163
vv v i i v i
C L1PA10_3end#L 914 TTTTTTTAATTTTTATTTTAAGTTCCGGGGTACATGTGCAGGATGTGCAG 865
INTRON_3 188164 GTTTGTTACATGGGTAAACGTGTGCCATGGTGGTTTGCTGTACCTATCAA 188213
i i
C L1PA10_3end#L 864 GTTTGTTACATAGGTAAACGTGTGCCATGGTGGTTTGCTGCACCTATCAA 815
INTRON_3 188214 CCCATTGCCTAGGTAATAAGCCCA-CATTCATCAACTGTTTATCCTGATG 188262
ii v - v i i i v i
C L1PA10_3end#L 814 CCCATCACCTAGGTATTAAGCCCAGCATGCATTAGCTATTTTTCCTAATG 765
INTRON_3 188263 CTCTCCCTCCCCTT-----CACTCCT-GAGAGGCCCTGGTGTGTGTTGTT 188306
ii----- i i- v ii
C L1PA10_3end#L 764 CTCTCCCTCCCCCCACCCCCACCCCCCGACAGGCCCCAGTGTGTGTTGTT 715
INTRON_3 188307 CCCCTCCCTGTGTCCATGTGTTCTTGTTGTTCAGCTCCCACTTATAAGTG 188356
ii
C L1PA10_3end#L 714 CCCCTCCCTGTGTCCATGTGTTCTCATTGTTCAGCTCCCACTTATAAGTG 665
INTRON_3 188357 AGAACATGCAGTGTTTGGTTTTCTGTTCCTGCATCAGTGTGCTGAGGATA 188406
i i i v
C L1PA10_3end#L 664 AGAACATGCGGTGTTTGGTTTTCTGTTCCTGCGTTAGTTTGCTGAGGATA 615
INTRON_3 188407 ATGGCTTCCAGCTCCATCCATGTCCCTGCAAAGGACATAATCTCATTTCT 188456
i i
C L1PA10_3end#L 614 ATGGCTTCCAGCTCCATCCATGTCCCTGCAAAGGACATGATCTCATTCCT 565
INTRON_3 188457 TTTTATGGCTGCATAGTATTCCATGGTATATATGTACCACATTTTCTTTA 188506
i
C L1PA10_3end#L 564 TTTTATGGCTGCATAGTATTCCATGGTGTATATGTACCACATTTTCTTTA 515
INTRON_3 188507 TGCAGTCTATGATTGATGGGCATTTGGGTTGATTCGATGTCTTTGCTATT 188556
v v v
C L1PA10_3end#L 514 TCCAGTCTATCATTGATGGGCATTTGGGTTGATTCCATGTCTTTGCTATT 465
INTRON_3 188557 GTGAATAGTGCTGCAGTGAACATACATGTGCATGTATCTTTATAATAGAA 188606
i i
C L1PA10_3end#L 464 GTGAATAGTGCTGCAATGAACATACACGTGCATGTATCTTTATAATAGAA 415
INTRON_3 188607 TGATTTATATTCTTTTGGGTATATACCTAGTAATGGGATTGCTGGGTCAA 188656
i i
C L1PA10_3end#L 414 TGATTTATATTCCTTTGGGTATATACCCAGTAATGGGATTGCTGGGTCAA 365
INTRON_3 188657 ATGGTATTTCTGATTCTAGGTCTTTGAAGAATCGCCAC--TGTCTTCCAC 188704
i i i --
C L1PA10_3end#L 364 ATGGTATTTCTGGTTCTAGATCTTTGAGGAATCGCCACACTGTCTTCCAC 315
INTRON_3 188705 AATGGTTGAACTAATTTATATTCCTACAAACAGTGTAAAACCATTCCTGT 188754
i i v v i i
C L1PA10_3end#L 314 AATGGTTGAACTAATTTACATTCCCACCAACAGTGTAAAAGCGTTCCTAT 265
INTRON_3 188755 TTCTCCACAGCCTCACCAGCATCTGTTGTTTCTTAACTTTCTAATAATCA 188804
i i i i ?i
C L1PA10_3end#L 264 TTCTCCACAACCTCGCCAGCATCTGTTGTTTCTTGACTTTTTAATAATNG 215
INTRON_3 188805 CCATTCTGACTGGCATGCAATGGTATCTCATTGTGGTTTTGATTTGCATT 188854
i vi
C L1PA10_3end#L 214 CCATTCTGACTGGCGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATT 165
INTRON_3 188855 TCTCTAATGATCACTGATTTTGAGCTTTTTAAAAAAATATGTTTGT---C 188901
v v vvvi--- ---
C L1PA10_3end#L 164 TCTCTAATGATCAGTGATGTTGAGCTTTTTTTCG---TATGTTTGTTGGC 118
INTRON_3 188902 CACATAAATGGCTACTTTTGGGAAATATCTGTTCACGTCCTTTGCTCACT 188951
i i v v i i i i i v
C L1PA10_3end#L 117 CGCATGAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTTGCCCACA 68
INTRON_3 188952 TTTTAATGTGGTTGTTTGTTTTTCTCTTGTAAATTTGTTCAAGTTTCTTG 189001
v i i i
C L1PA10_3end#L 67 TTTTAATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTG 18
INTRON_3 189002 TAGATTCTAGATATTAG 189018
i
C L1PA10_3end#L 17 TAGATTCTGGATATTAG 1
Matrix = 20p39g.matrix
Transitions / transversions = 2.29 (55 / 24)
Gap_init rate = 0.01 (6 / 904), avg. gap size = 2.50 (15 / 6)
1200 9.95 1.47 1.47 INTRON_3 188869 189072 211109 C L1P3_orf2 LINE/L1 3091 3294 0 438
INTRON_3 188869 TGATTTTGAGCTTTTTAAAAAAATATGTTTGT---CCACATAAATGGCTA 188915
v vvv --- --- i v v
C L1P3_orf2#LIN 3294 TGATGTTGAGCTTTTTTTCA---TATGTTTGTTGGCCGCATAAATGTCTT 3248
INTRON_3 188916 CTTTTGGGAAATATCTGTTCACGTCCTTTGCTCACTTTTTAATGTGGTTG 188965
i i i i i v
C L1P3_orf2#LIN 3247 CTTTTGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAATGGGGTTG 3198
INTRON_3 188966 TTTGTTTTTCTCTTGTAAATTTGTTCAAGTTTCTTGTAGATTCTAGATAT 189015
i i i i
C L1P3_orf2#LIN 3197 TTTGTTTTTTTCTTGTAAATTTGTTTAAGTTCCTTGTAGATTCTGGATAT 3148
INTRON_3 189016 TAGACCTTTCTCAGATGGATAGATTGCAAAAAATTTCTCCTATTCTGTAG 189065
v v i
C L1P3_orf2#LIN 3147 TAGACCTTTGTCAGATGGATAGATTGCAAAAATTTTCTCCCATTCTGTAG 3098
INTRON_3 189066 GTTGTCT 189072
C L1P3_orf2#LIN 3097 GTTGTCT 3091
Matrix = 20p39g.matrix
Transitions / transversions = 1.22 (11 / 9)
Gap_init rate = 0.01 (2 / 203), avg. gap size = 3.00 (6 / 2)
+ 327 9.6 0.0 0.0 INTRON_3 189228 189279 (210902) + (TA)n Simple_repeat 1 52 (0) 238
ANNOTATION EVIDENCE:
327 9.62 0.00 0.00 INTRON_3 189228 189279 210902 C (TA)n Simple_repeat 129 180 0 458
INTRON_3 189228 TATATATAAATAAATATGTATATATATATATAAATATGTATATATATATA 189277
v v i v i
C (TA)n#Simple_ 180 TATATATATATATATATATATATATATATATATATATATATATATATATA 131
INTRON_3 189278 TA 189279
C (TA)n#Simple_ 130 TA 129
Matrix = Unknown
Transitions / transversions = 0.67 (2 / 3)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 2399 9.3 0.3 1.0 INTRON_3 189905 190214 (209967) C AluSx3 SINE/Alu (4) 308 1 239
ANNOTATION EVIDENCE:
2273 9.47 0.97 1.29 INTRON_3 189905 190214 209967 C AluSx SINE/Alu 1 309 3 382
INTRON_3 189905 TTTTTTTTTCCTTTGTTTCTTTTTTTTGAGATGGAGTCTCACTCTCTCGC 189954
ii v i i i v
C AluSx#SINE/Al 309 TTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGC 260
INTRON_3 189955 CTAGGCTGGAGTACAGTGGTGCGATCTCTGCTCACTGCAACCTCTGCCTC 190004
i i i v i
C AluSx#SINE/Al 259 CCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTC 210
INTRON_3 190005 CCGGGTTCAAGTGAT-CTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTAC 190053
i - i i
C AluSx#SINE/Al 209 CCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTAC 160
INTRON_3 190054 AGGCATACGCCACCACACCCAGCTAATTTTTGTATATTTTTTAAGTAGAA 190103
iii i i -- -- i
C AluSx#SINE/Al 159 AGGCGCGCGCCACCACGCCCGGCTAATTTTTGTAT--TTTT--AGTAGAG 114
INTRON_3 190104 ATGGGGTTTTACCATATTGGCCAGGCTGGTCTCGAACTCCTGACCTT--G 190151
i i i i--
C AluSx#SINE/Al 113 ACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGG 64
INTRON_3 190152 TGATCCACCTGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCC 190201
i i
C AluSx#SINE/Al 63 TGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCC 14
INTRON_3 190202 ACCGCATCCGGCC 190214
ii
C AluSx#SINE/Al 13 ACCGCGCCCGGCC 1
Matrix = 14p39g.matrix
Transitions / transversions = 8.67 (26 / 3)
Gap_init rate = 0.01 (4 / 309), avg. gap size = 1.75 (7 / 4)
+ 627 38.5 1.7 0.4 INTRON_3 190254 190493 (209688) C MIRb SINE/MIR (0) 268 26 240
ANNOTATION EVIDENCE:
627 38.49 1.67 0.41 INTRON_3 190254 190493 209688 C MIRb SINE/MIR 26 268 0 407
INTRON_3 190254 AATAGTAATAACTACTATTTATTGAATGCTTATTATAGATTTGGTAGTAT 190303
i i- i i ii i i iviiiv i v i
C MIRb#SINE/MIR 268 AATAATAG-AGCTACCATTTATTGAGCGCTTACTGTGTGCCAGGCACTGT 220
INTRON_3 190304 AATCAGCATTTTGATTATGGTACCTT-TTCAATCCTGGCAAAAAC---AT 190349
iv v ii ivv iiiv i i- i vi v ---ii
C MIRb#SINE/MIR 219 GCTAAGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGC 170
INTRON_3 190350 GAATTTGGAGGTGTTATTTCCAGTTTAAAGATGAAGAAGCTGAGGCTTAG 190399
iv v viv i ii v v i i i
C MIRb#SINE/MIR 169 GAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAG 120
INTRON_3 190400 AGGAGTTGAATAGAGTATTCAATGTTGCGTAGTCACCAAAAGGCAGAGCC 190449
ii i i iivv iii v ii ii ii vi iv
C MIRb#SINE/MIR 119 AGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCC 70
INTRON_3 190450 GAGGTGAAGACCTAGGTTTATTGAGCTCTAAAGCCTGTGTTTTT 190493
ii i vvii i i iiivii i i i i
C MIRb#SINE/MIR 69 AGGATTCGAACCCAGGTCTGCCTGACTCCAAAGCCCGTGCTCTT 26
Matrix = 25p39g.matrix
Transitions / transversions = 2.83 (68 / 24)
Gap_init rate = 0.01 (3 / 239), avg. gap size = 1.67 (5 / 3)
+ 1641 19.7 3.9 3.6 INTRON_3 191255 191643 (208538) + MLT1B LTR/ERVL-MaLR 1 390 (0) 241
ANNOTATION EVIDENCE:
1641 19.73 3.86 3.59 INTRON_3 191255 191643 208538 + MLT1B LTR/ERVL-MaLR 1 390 0 472
INTRON_3 191255 TGCTTTGGACTGAATTGCTTCCCCCACCTTCCCTAATTTCGTATATTGAA 191304
i v i iv ------- v v i i
MLT1B#LTR/ERV 1 TGTTATGGGCTGAATTGTGTCCCCC-------CAAAATTCATATGTTGAA 43
INTRON_3 191305 GCCCTAACTCCCA----------ATGTGGACTATATTTGGAGACAGAGAT 191344
i i ---------- - i i i vi
MLT1B#LTR/ERV 44 GTCCTAACCCCCAGTACCTCAGAATGTG-ACTGTATTTGGAGATAGGGTC 92
INTRON_3 191345 TTTAG-GAGGTAATTAAGGTTCAATTAGGTTATCAGGGTAGGGTCCTATT 191393
i- v vv v i i - i v
MLT1B#LTR/ERV 93 TTTAAAGAGGTAATTAAGTTAAAATGAGGTCATTAGGGT-GGGCCCTAAT 141
INTRON_3 191394 CCAATAGGATTGGTGGCCTTATAAGAAGAAGAGA---GATCATGCACATG 191440
v i v i --- iv iiv ii
MLT1B#LTR/ERV 142 CCAATATGACTGGTGTCCTTATAAGAAGAGGAGATTAGGACACAGACACA 191
INTRON_3 191441 CACCAAGGGAAGGCCATGTGAGGACACAGCAAGAAGGTAGCCATCTGCAA 191490
vi i i vi iii i
MLT1B#LTR/ERV 192 CACAGAGGGAAGACCATGTGAAGACACAGGGAGAAGACGGCCATCTACAA 241
INTRON_3 191491 ATCAGGAAAAGAGCCCTCACCAGAACCCTACCATACTAGCACCCTGGTCT 191540
ii i i i v vv v v v i iii i i
MLT1B#LTR/ERV 242 GCCAAGGAGAGAGGCCTCAGAAGAAACCAACCCTGCCGACACCTTGATCT 291
INTRON_3 191541 TGGACTTCCAGCCTCCAGAATTGTGAGAAAATAA-TTTCTGTTGTTTAAA 191589
i i - i
MLT1B#LTR/ERV 292 CGGACTTCCAGCCTCCAGAACTGTGAGAAAATAAATTTCTGTTGTTTAAG 341
INTRON_3 191590 CCACTTATTATATGGTATTTTGTTATGGCAGCCCAAGCTGACTAGACTAA 191639
ii v v i i v ----- i
MLT1B#LTR/ERV 342 CCACCCAGTCTGTGGTACTTTGTTATGGCAGCCCTAGC-----AAACTAA 386
INTRON_3 191640 TACA 191643
MLT1B#LTR/ERV 387 TACA 390
Matrix = 20p39g.matrix
Transitions / transversions = 1.96 (49 / 25)
Gap_init rate = 0.02 (8 / 388), avg. gap size = 3.62 (29 / 8)
+ 408 2.0 0.0 0.0 INTRON_3 191879 191927 (208254) + (CA)n Simple_repeat 2 50 (0) 242
ANNOTATION EVIDENCE:
408 2.04 0.00 0.00 INTRON_3 191879 191927 208254 + (CA)n Simple_repeat 2 50 130 459
INTRON_3 191879 ACACACACACACACACACACACACACACACACACACACACACACAAACA 191927
v
(CA)n#Simple_ 2 ACACACACACACACACACACACACACACACACACACACACACACACACA 50
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 1)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 745 24.0 7.8 1.5 INTRON_3 192191 192433 (207748) + MIRb SINE/MIR 11 268 (0) 243
ANNOTATION EVIDENCE:
510 27.51 3.87 3.87 INTRON_3 192191 192345 207836 + MIRc SINE/MIR 11 165 103 408
INTRON_3 192191 TGGTATAGGGTTAAAAGTGGTTAAGGCTTTGGAATCAGC--TACCTGGGC 192238
ii v vv i iiv --- vi i v--v i
MIRc#SINE/MIR 11 TGGTGCAGTGGAAAGAGCACT---GGACTTGGAGTCAGGAAGACCTGGGT 57
INTRON_3 192239 TTGAATCTTGGCTCCACAA--TA-TAGTTGTAAGAACTTAGGCAAGTCAC 192285
i i i ii v -- - i iv v i
MIRc#SINE/MIR 58 TCGAGTCCTGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCAC 107
INTRON_3 192286 ATTACCTC-CTAAACTTTCATTTCCTCATCTATAAGATGGGGTTTATGGT 192334
v v - i i i ivi i i --- ii
MIRc#SINE/MIR 108 TTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGG---ATAAT 154
INTRON_3 192335 AATACCTATTC 192345
iii
MIRc#SINE/MIR 155 AATACCTGCCC 165
Matrix = 25p39g.matrix
Transitions / transversions = 2.15 (28 / 13)
Gap_init rate = 0.04 (6 / 154), avg. gap size = 2.00 (12 / 6)
745 23.59 8.22 1.28 INTRON_3 192215 192433 207748 + MIRb SINE/MIR 35 268 0 409
INTRON_3 192215 GGCTTTGGAATCAGCTA--CCTGGGCTTGAATCTTGGCTCCACAA--TA- 192259
i vi -- i i i ii v -- -
MIRb#SINE/MIR 35 GGCTTTGGAGTCAGGCAGACCTGGGTTCGAATCCTGGCTCTGCCACTTAC 84
INTRON_3 192260 TAGTTGTAAGAACTTAGGCAAGTCACATTACCTC-CTAAACTTTCATTTC 192308
i iv v i v v - i i i ivi
MIRb#SINE/MIR 85 TAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTC 134
INTRON_3 192309 CTCATCTATAAGATGGGGTTTATGGTAATACCTAT-TCAAAGGGCTG--G 192355
i i --- ii i- iv i --
MIRb#SINE/MIR 135 CTCATCTGTAAAATGGGG---ATAATAATACCTACCTCGCAGGGTTGTTG 181
INTRON_3 192356 -GGGAATTTAGTTGGATAAT-C-TGTTAAGCTTGTAGTAGAGAATCTGGC 192402
- i i v i vi - - v viv i v vii
MIRb#SINE/MIR 182 TGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGC 231
INTRON_3 192403 ------TGAGCAGTGAATAAATGTTAGCTTTATTATT 192433
------ i iv v v i
MIRb#SINE/MIR 232 ACACAGTAAGCGCTCAATAAATGGTAGCTCTATTATT 268
Matrix = 25p39g.matrix
Transitions / transversions = 1.83 (33 / 18)
Gap_init rate = 0.05 (11 / 218), avg. gap size = 1.91 (21 / 11)
+ 213 13.9 0.0 0.0 INTRON_3 193748 193783 (206398) C L2b LINE/L2 (1) 3374 3339 244
ANNOTATION EVIDENCE:
213 13.89 0.00 0.00 INTRON_3 193748 193783 206398 C L2b_3end LINE/L2 430 465 1 410
INTRON_3 193748 TTTAATCATTCAACAAACATTTACTGGGTACCTTCT 193783
i v i i v
C L2b_3end#LINE 465 TTCATTCATTCAACAAACATTTACTGAGCACCTACT 430
Matrix = 25p39g.matrix
Transitions / transversions = 1.50 (3 / 2)
Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0)
+ 758 28.1 3.6 7.9 INTRON_3 193853 194154 (206027) + MLT1F2 LTR/ERVL-MaLR 1 290 (270) 245
ANNOTATION EVIDENCE:
758 28.05 3.64 7.93 INTRON_3 193853 194154 206027 + MLT1F2 LTR/ERVL-MaLR 1 290 270 473
INTRON_3 193853 TGTGTCAGGCAGGTTGTAATATGACTGCCACTAATCCCTACTCCTGGGTA 193902
vi vi v v i iv v i ii ii iv
MLT1F2#LTR/ER 1 TGTGGTAGGCAGCCTCTAAGATGGCCCCCAATGATCCCCGCCTCCTGGTA 50
INTRON_3 193903 TTTATGCCTTTGGGTAATCCTTGTG---TGTGGGTGGGCTGGATCTAGTG 193949
i i i v iiviv--- v v i
MLT1F2#LTR/ER 51 TTCACGCCCTTGTGTAATCCCCTCCCCTTGAGTGTGGGCTGGACCTAGTG 100
INTRON_3 193950 ACTTGCTTCTTAAGAACAGAATGTGGCAAAACATACGGGTTATCACTTCA 193999
i v v i ii vvv i v i v
MLT1F2#LTR/ER 101 ACTCGCTTCTAACGAATAGAATACGGCAAAAGTGATGGGATGTCACTTCC 150
INTRON_3 194000 TA---TAGGCTACAAAA-GACTAGGACTTTAACCTTACTAGGACTTTCTC 194045
v --- i - iv i --------------------
MLT1F2#LTR/ER 151 GAGATTAGGTTACAAAAAGACTGTGGCTT--------------------C 180
INTRON_3 194046 TTTCTTGCTGGCACTCTTCTTTGCCTTCTTGCTTGCTTGTTCTGATG-AA 194094
iv -- i i iii ii i i i ? -
MLT1F2#LTR/ER 181 CGTCTTGC--GCGCCCTCTCTTGCTCTCTCGCTTGCTCGCTCTGANGGAA 228
INTRON_3 194095 GCAAGCTACCACGCTGTATCATGCTCTATGGAGAAGCTCAACGTG---AG 194141
v i i i ivvv i i i - ---
MLT1F2#LTR/ER 229 GCCAGCTGCCATGTTGTGAGCTGCCCTATGGAGAGGCCCA-CGTGGCAAG 277
INTRON_3 194142 AGACTAAAAGAAG 194154
ii i ii ?i
MLT1F2#LTR/ER 278 GAACTGAGGGNGG 290
Matrix = 20p39g.matrix
Transitions / transversions = 1.92 (50 / 26)
Gap_init rate = 0.03 (8 / 301), avg. gap size = 4.25 (34 / 8)
+ 216 29.3 0.0 3.5 INTRON_3 194466 194525 (205656) + MIRb SINE/MIR 107 164 (104) 246
ANNOTATION EVIDENCE:
216 29.34 0.00 3.45 INTRON_3 194466 194525 205656 + MIRb SINE/MIR 107 164 104 411
INTRON_3 194466 TTACTTAATTTTTTTGAACTTTAGGTTTCCTATGTGTAAAAAACAGGAAT 194515
i ii i i i i i v i ii v --ii i
MIRb#SINE/MIR 107 TCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAA--TGGGGAT 154
INTRON_3 194516 AATAATATCT 194525
i
MIRb#SINE/MIR 155 AATAATACCT 164
Matrix = 25p39g.matrix
Transitions / transversions = 7.50 (15 / 2)
Gap_init rate = 0.02 (1 / 59), avg. gap size = 2.00 (2 / 1)
+ 510 30.9 5.4 5.7 INTRON_3 194528 194898 (205283) C MLT1K LTR/ERVL-MaLR (0) 595 226 247
ANNOTATION EVIDENCE:
510 30.86 5.39 5.68 INTRON_3 194528 194898 205283 C MLT1K LTR/ERVL-MaLR 226 595 0 474
INTRON_3 194528 TATATTAGGCATGACTTTTT--ATTTCAAATGATAGAAACCCAGGTCTGT 194575
i v v i --i v i i iv viv
C MLT1K#LTR/ERV 595 TGTATTAGTCAGGACTCTTTCGGTTGCAAGTGACAGAAACCCAACTCAAA 546
INTRON_3 194576 CCAACTTAGACAAACAATAACCATATAAATTTATTGATTCAGGTAACTTC 194625
iii ii v vii------- ii v --
C MLT1K#LTR/ERV 545 CTGGCTTAAGCAAAAAAGGG-------AATTTATTGGCTCATGTAACT-- 505
INTRON_3 194626 AGAAAGG----GGTGCAATTGAGGCT-CAGGAATTACTGACATCAGGAAC 194670
- i ---- v i i? vv - v vi ivvi vi
C MLT1K#LTR/ERV 504 -GAAAAGTCCAGGGGTAGNTCTGGCTTCAGGCATGGCTGGATCCAGGTGC 456
INTRON_3 194671 TAAAATGTTGT----AAGAAT-TGCCTGATTCCATCTGTAAACTCTGCTG 194715
v i v ---- i - i vvi v vii v
C MLT1K#LTR/ERV 455 TCAAACGATGTCATCAGGAATCTGTCTCTCTCCATCTCTCGGCTCTGCTT 406
INTRON_3 194716 CTCTCTG-GTCAGCTTCATCTTGTCAGACTGGCTTTTTTCATATGGCTGG 194764
ii - ii -- v i v i iii ii iv v
C MLT1K#LTR/ERV 405 TCCTCTGTGTTGGCTTCAT--TCTCAGGCAGGCTCTCCCCACGTGGTGGC 358
INTRON_3 194765 AAGCTTGGTTACTAGCAGCTCCTATTTTTTACATCTCTGACACAACTTTG 194814
v - ii? i vivi -- - - - i v
C MLT1K#LTR/ERV 357 AAGAT-GGCCNCCAGCAGCTCCAGGCTT--ACATC-CT-AC-CAGCTTAG 314
INTRON_3 194815 C--CACCAG-AGAAAGACTGAATTTTTTCCCCA---GCTCTGGTGTGAGA 194858
-- v -i vv v? i i i --- i ii i--- i
C MLT1K#LTR/ERV 313 CAACCCCAGCGGAAAGAGAGCNTCTCTTTCCCAATAGTTCCAGC---AAA 267
INTRON_3 194859 AATGCCATAGA-AATACTGATTGGCCCACCTTGGGTTACAT 194898
i v vi v-i iv v iv i i
C MLT1K#LTR/ERV 266 AGTCCCAGGGCTGACTCTCATTGGCCCGGCTTGGGTCACGT 226
Matrix = 20p39g.matrix
Transitions / transversions = 1.50 (63 / 42)
Gap_init rate = 0.05 (19 / 370), avg. gap size = 2.16 (41 / 19)
+ 291 15.7 0.0 0.0 INTRON_3 194962 195012 (205169) + (TG)n Simple_repeat 2 52 (0) 248
ANNOTATION EVIDENCE:
291 15.69 0.00 0.00 INTRON_3 194962 195012 205169 C (CA)n Simple_repeat 130 180 0 464
INTRON_3 194962 TGTGTGTGTGTGTGTGTGTGTGTGTGCACGCATGCGTGTGCGTGTGCGTG 195011
iii ii i i i
C (CA)n#Simple_ 180 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 131
INTRON_3 195012 T 195012
C (CA)n#Simple_ 130 T 130
Matrix = Unknown
Transitions / transversions = 0.0 (8 / 0)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0)
+14759 12.9 2.1 0.8 INTRON_3 195147 197559 (202622) C Tigger2 DNA/TcMar-Tigger (0) 2718 274 249
ANNOTATION EVIDENCE:
14759 12.95 2.11 0.78 INTRON_3 195147 197559 202622 C Tigger2 DNA/TcMar-Tigger 274 2718 0 475
INTRON_3 195147 CAGTTGACCCCTGAA-AACACGGGAGTTGAGGGGGCACCAACTCCCCGTG 195195
i - i i i-- i i i i
C Tigger2#DNA/T 2718 CAGTTGACCCTTGAACAACGCGGGGGTTA--GGGGCGCCGACCCCCCGCG 2671
INTRON_3 195196 CAGCAAAAAATTTGCACATAACTTTTGACTTCCCCAAAACTTATCTATTA 195245
ivi ii ii i v i
C Tigger2#DNA/T 2670 CAGTCGAAAATCCGCGTATAACTTTTGACTCCCCCAAAACTTAACTACTA 2621
INTRON_3 195246 ATAGCCTACTGTTAACCAGAAGCCTTATTGATAACATAAACAGCCAGTTA 195295
i i ii i ii
C Tigger2#DNA/T 2620 ATAGCCTACTGTTGACCGGAAGCCTTACCGATAACATAAACAGTCGATTA 2571
INTRON_3 195296 ACACATATTTTATATGTTGTATTTATTATATTGTATATTCTTATAATAAA 195345
i i v vv i i
C Tigger2#DNA/T 2570 ACACATATTTTGTATGTTATATGTATTATATACTGTATTCTTACAATAAA 2521
INTRON_3 195346 GTAAGCTAGAGA---GAAAAGGTTATTAAGAAAATCATAAGAAAGAGAAA 195392
--- v i
C Tigger2#DNA/T 2520 GTAAGCTAGAGAAAAGAAAATGTTATTAAGAAAATCATAAGGAAGAGAAA 2471
INTRON_3 195393 ACATATTTACTATTCATTAAGTAGAAGTGGGTCATCACAAAAGCCTTCAT 195442
i i i i i i
C Tigger2#DNA/T 2470 ATATATTTACTATTCATTAAGTGGAAGTGGATCATCATAAAGGTCTTCAT 2421
INTRON_3 195443 ---------------GTTGAGAAGGCTGAGGAGGATGTGGAAGAGGAGGG 195477
--------------- v v v
C Tigger2#DNA/T 2420 CCTCATCGTCTTCACGTTGAGTAGGCTGAGGAGGAGGAGGAAGAGGAGGG 2371
INTRON_3 195478 GGTGGTCTTGCTGTCTCAGGGTGGCAGAGGGTGAAGAAGTAGATGAGGTA 195527
v vv i i v i
C Tigger2#DNA/T 2370 GTTGGTCTTGCTGTCTCAGGGTGGCAGAGGCGGAAGAGGTGGAGGAGGTG 2321
INTRON_3 195528 GAAGGTGTGGCAGGAAAGGCAGGCACACGTCTTGTAACTTTATAGAAATA 195577
v v i vivv ?
C Tigger2#DNA/T 2320 GAAGGGGAGGCAGGAGAGGCAGGCACACTCGGTGTAACTTTATNGAAATA 2271
INTRON_3 195578 CCATCATAATTTCTGGTTGACTTTTCTGCTTTTTCTTTACTCTAAAAATG 195627
- i vi i v v
C Tigger2#DNA/T 2270 C-ATCGTAATTTCTGTCTGACTTTTTTGCTTTTTCATTTCTCTAAAAATG 2222
INTRON_3 195628 TTTTTATACAGTACCAATCCTTCTTCTACCATTTGCTTTAGTTTCAGTGC 195677
i ii i i
C Tigger2#DNA/T 2221 TTTCTATATGGTACCAATCCTTCTTCCACCGTTTGCTTTAGTTTCAGTGC 2172
INTRON_3 195678 CCATATCATATAGAAGGATCCATGTTGTAAAGGAAGTCAAAAGCAGTCTT 195727
i -- i i i
C Tigger2#DNA/T 2171 CCGTATCATA--GAAGGGTCCATGTCGTAAAAGAAGTCAAAAGCAGTCTT 2124
INTRON_3 195728 GAATAATCAGAACCCTTCTGCCAGATTGTCTAATGTCAATTCGTTTTCTG 195777
i i
C Tigger2#DNA/T 2123 GAATAATCGGAACCCTTCTGCCAGATTGTCTAATGTCAATTTGTTTTCTG 2074
INTRON_3 195778 GCATTGCTTCTTCCCCTTCGTCTTTCTCATCATCTGGCATTGGTTTGGAA 195827
i iv v v i i i i
C Tigger2#DNA/T 2073 GCACTGCTTCTTCTACGTCTTCTTCCTCATCGTCTGGCACTGGTTCGGAA 2024
INTRON_3 195828 GCACTCATCTCCACCAAGTCATATTCTGTTAATTCCTCTTGTGTGGTGTC 195877
i i v v
C Tigger2#DNA/T 2023 GCACTCATCTCCATCAAGTCGTCTTCTGTTAATTCCTCTGGTGTGGTGTC 1974
INTRON_3 195878 CATTAGCATTTGAATTTTCTCTAAGATCCATACCTTGAAACCCTTTACCC 195927
i vi - i i i
C Tigger2#DNA/T 1973 TATTAGCTCTTGAATTT-CTCCAAGATCCATATCTTGAAACCCTTCACCC 1925
INTRON_3 195928 CCTCACCTTTTTTGCCATATCTATAATATCTTTCATGATTTCCTTGACTG 195977
- i i v i
C Tigger2#DNA/T 1924 CC-CACCTTTTTTGCCATATCCACAATCTCTTTCATGATTTCCTTGATTG 1876
INTRON_3 195978 GCTCTGTTATAAATCCTGTGAAGTCATGCACAAAATCTGGGCACAGTCTT 196027
ii v i i
C Tigger2#DNA/T 1875 GCTCTGTCGTAAATCCTGTGAAGTCATGCACAACATCTGGACACAGTTTT 1826
INTRON_3 196028 CTCCAGCAGGAATTTATTGTTTTGGACT--ATGGCTTTCACAGCTTTTTA 196075
i i -- i v
C Tigger2#DNA/T 1825 CTCCAGCAGGAATTTATTGTTTCGGGCTTGATGGCTTTCACGGCTTTTTC 1776
INTRON_3 196076 TTTTTAAACAATGATGGCATCTTCAATGTTGTAATCCTTCCAGACTTTCA 196125
v --- i v
C Tigger2#DNA/T 1775 TAT---AACAACGATGGCATCTTCAATGGTGTAATCCTTCCAGACTTTCA 1729
INTRON_3 196126 TGATGTTCTCTCTATTAGGGCTCTTTTCCATAGTGTTGA-AATCCTTTCC 196174
ii i i i -
C Tigger2#DNA/T 1728 TGATGTTCTCTCTATCGGGGTTCTCTTCCATAGCGTTGACAATCCTTTCC 1679
INTRON_3 196175 -TGTAGTATTACGTGTAATGACCCTTAATGGTCCTTATGACCCCTTGATC 196223
- iv iiii v v i
C Tigger2#DNA/T 1678 ATAGAGTACCGTGTGTAATGAGCCTTAAAGGTCCTTATGACCCCCTGATC 1629
INTRON_3 196224 TAGGGAGTGAATTAGAAATGTTGTGTTTGGGGACACGTAGGCCACTTTGA 196273
i iv i i i v i i
C Tigger2#DNA/T 1628 TAGAGGCTGAATTAGAGACGTTGTGTTTGGGGGCAAGTAGACCACTTCGA 1579
INTRON_3 196274 TGACTTCAGTGTTGAATCCATGGGGTTCTGGGTGGCCAGGAACGTTGTTT 196323
i v i ii ii i ii
C Tigger2#DNA/T 1578 CGCCTTCGGTGTTGAACTCATGGGGTTCTGGGTGGCCAGGGGCATTGTCC 1529
INTRON_3 196324 AATATCAAAAGAACTTTAAAAGCCA-TCCCTTACTGGAAAGGTGCTTCCT 196372
v - v i
C Tigger2#DNA/T 1528 AATATCAAAAGAACTTTAAAAGGCAGTCCCTTACTGGCAAGGTACTTCCT 1479
INTRON_3 196373 GACTTCAGGGACAAAGCATCAATGGAACCAATCCAGAAAAAGGGCTTTTC 196422
i i i iv
C Tigger2#DNA/T 1478 GACTTCAGGGACAAAGCATCGATGGAACCAATCCAGAAAAAGGGTTCTCG 1429
INTRON_3 196423 TTGTTCAGGCCTTCTTATTGTACAACTAAAAGGTGGGTAGCTTGTATTTA 196472
i i i iiv i v i
C Tigger2#DNA/T 1428 TTGTCCAGGCCTTCTTGTTGTACAACCAAAAGACTGGCAGCTGGTGTTTA 1379
INTRON_3 196473 TCTTTTTCCTTTAAGGCTTGGGG-TTAGCAGCTTCATAGATAGGGGCAGT 196521
i i i - i i
C Tigger2#DNA/T 1378 TCTTTTCCCTTCAAGGCTCGGGGGTTAGCAGCTTTATAGATAAGGGCAGT 1329
INTRON_3 196522 CCTGTTCATAAACCCTACTGTATTTACACCAAACAATAAAGTTAGCCTGT 196571
v v i i v i i i
C Tigger2#DNA/T 1328 CCTGATCATAAACCCGACTGCATTTGCACAAAACAGTAGAGTTAGCCTAT 1279
INTRON_3 196572 CTCTTCCTACCTTAAATCTTGGTACTTGCTTCTCTTTCTTACTAATAAAT 196621
i i i i i i
C Tigger2#DNA/T 1278 CCCTTCCTGCCTTAAATCCTGGTGCTCGCTTCTCTTCCTTACTAATAAAT 1229
INTRON_3 196622 GTCCTTTGTGTGGCATTTTATTCT---AGAATATGGCACTT--GTCTGCA 196666
-- v i--- v --
C Tigger2#DNA/T 1228 GTCCTTTGTG--GCATTTTTTTCCTCCAGAATAGGGCACTTTCGTCTGCA 1181
INTRON_3 196667 CCAAAAATCTGTTCAGGCAGATATCCTCTCTCCTTAA-AATTTTCTTAAT 196715
ii i i i -i
C Tigger2#DNA/T 1180 TTAAAAACCTGTTCAGGCAGATATCCTTTCTCCTCAATGATTTTCTTAAT 1131
INTRON_3 196716 GGTGCCTGGGAATTTATCCGCTGCCTCTTG-TCAGCAGGAGCTACTTCTC 196764
i i i ii i - i i i
C Tigger2#DNA/T 1130 GGCGTCTGGGAACTCGTCTGCTGCCTCTTGGTCGGCAGAAGCTGCTTCTC 1081
INTRON_3 196765 TTGTTATCTTGACTTTTTAAAAGCCACATCTCCTTCTGAAATTATCAAAC 196814
i v v? v i i i
C Tigger2#DNA/T 1080 CTGTTATCTTGACATTTTTNAAGCCAAACCTCTTTCTAAAATTATCAAAC 1031
INTRON_3 196815 CATCCTTTGCTGGCATTAAATTCTCCAGCTTTAGATACTTCACCTTCCTT 196864
v
C Tigger2#DNA/T 1030 CATCCTTTGCTGGCATTAAATTCTCCAGCTTTAGATCCTTCACCTTCCTT 981
INTRON_3 196865 TTGCTTTAAGTTGTCATATA-TGTCCTTGCTTTTTCTCTAACCATATTAT 196913
- v i i v i v
C Tigger2#DNA/T 980 TTGCTTTAAGTTGTCATATAATGACTTCGCTTTTTCTCGAATCATATTAG 931
INTRON_3 196914 AGTCTATAGGTATGCCTTTCTTATAGCAGTCCTGTACCTACATAAAAGCT 196963
i i i
C Tigger2#DNA/T 930 AGTCTATAGGTATGCCTTTCTTATAGCAATCCTGCACCCACATAAAAGCT 881
INTRON_3 196964 GCATTTTCAATATGAGATAAGAAGGTATTTTGCAAAAATTTTGCAAGGTT 197013
i i i v --
C Tigger2#DNA/T 880 GCATTTTCAATACGAGATAAAAAGGTATTTCGCAAAAAGT--GCAAGGTT 833
INTRON_3 197014 TTCACACTTTCTGGAATAGCTGCAGTGATGGCTTTATGATTTTCCTTTTC 197063
i i i v vi i i i i v
C Tigger2#DNA/T 832 TTCGCGCCTGCTGGCGTAGCTGCAGCGACGGCTTCACGAATTTCCTTTTC 783
INTRON_3 197064 TTTTTTCACCATGGTCCTTATTCTTGGTTCATTTATCTTGAAATGGTGGG 197113
i v iv v i i
C Tigger2#DNA/T 782 TTTTTTTACAATGGTCCTTACGCTGGATTCATTTATCTTGAAATGGCGGG 733
INTRON_3 197114 CATCACATCACAGCTGCAAACCTCAATCGGTGGTATGTGTCAAGCAATTC 197163
---- i i i vii ii i
C Tigger2#DNA/T 732 CA----ACCGCAGCTGCAGACCTCAATCTACGGTACATATCAAGCAATTC 687
INTRON_3 197164 AACCTTTTCTTGTAAGGTTATGACTTTCCTCTTCTGCTTGGAAGCAGTTA 197213
i v i i v v i v v
C Tigger2#DNA/T 686 AACTTTTTCTTGTAATGTCATGACTTTTCTCTGCTTCTTGGGAGCACTTC 637
INTRON_3 197214 CAGCATCACTAGTGGCACTCCTTATGGGCCCCATGGT----TTC------ 197253
i v i ---- ------
C Tigger2#DNA/T 636 CAGCATCACTAGTGGCACTTCGTATGGGTCCCATGGTGTTATTCAAGGTT 587
INTRON_3 197254 --TGGTATTGCACTTTAACATGATAAAAAATAAGTGAGAACTCCAAGTGC 197301
--i v- i i v i iv i v v
C Tigger2#DNA/T 586 TACGGTATTGCACTA-AACACGATGAAAAATACGCGAGAACCGCGAGAGA 538
INTRON_3 197302 TCACTTTTTACTGTGATATGCAATTTACTGGAGAGACAAATTGCTCACGT 197351
i i i i i
C Tigger2#DNA/T 537 TCACTTTTTACTGCGATACGCAATTTACTGGAGAGACGAACTGCTCACGC 488
INTRON_3 197352 GAAGATGATTAGCCTCACATGGTGTTTTAACGGAATAC----AACTCTTG 197397
i v i i vv i ---- v
C Tigger2#DNA/T 487 GGAGATGATTAGCGTCACACGGCGTTTTAAGCGGATACTCGCAACACTTG 438
INTRON_3 197398 AGCTCACCACAATAGCCACAGGAGGTAGCTACAGAATTATTACCATAGTA 197447
i v i ii vi
C Tigger2#DNA/T 437 AGCTCACCGCAATAGCAACAGGAGGTGGCTACGAAATTATTACAGTAGTA 388
INTRON_3 197448 CAATAGATACTA--GTTAATTTTATGTAGTTATGGCTTAATACTGCCTCT 197495
i vi -- i ii v
C Tigger2#DNA/T 387 CAGTATGTACTACAGTTAATTTTATGCAGTTATGATTTAATACTGCATCT 338
INTRON_3 197496 TTACATTTGTTTACATTTCTTTTAACTGTAAATGGTGCCATTTATAGTTT 197545
i i ii ii i v ii i
C Tigger2#DNA/T 337 TTACGTTTGTTTACATTTCTCTCGACTGCGAATGGCGCCATGTACGGTCT 288
INTRON_3 197546 ATAAGTGTTTGTGT 197559
i v i
C Tigger2#DNA/T 287 GTAAGTGTGTGCGT 274
Matrix = 20p39g.matrix
Transitions / transversions = 2.67 (224 / 84)
Gap_init rate = 0.01 (27 / 2412), avg. gap size = 2.59 (70 / 27)
+ 559 17.0 5.9 0.0 INTRON_3 197596 197730 (202451) C L1MC3 LINE/L1 (0) 7785 7643 250
ANNOTATION EVIDENCE:
559 17.04 5.93 0.00 INTRON_3 197596 197730 202451 C L1MC3_3end LINE/L1 2390 2532 0 439
INTRON_3 197596 TTTTT--AAATTAACTTTTAATTTTAGGATAGTTTTAG-TTCCCAGAACT 197642
-- v v i - iv vv
C L1MC3_3end#LI 2532 TTTTTSAAAATAAACTTTTTATTTTAGAATAGTTTTAGATTTACAGAAAA 2483
INTRON_3 197643 GCTGTGAAGATAGTA-----AGTTCCCATATACCCAACACTCTGTTTCCT 197687
ii i ----- v i v i
C L1MC3_3end#LI 2482 ATTGCGAAGATAGTACAGAGAGTTCCCATATACCCCACACCCAGTTTCCC 2433
INTRON_3 197688 CTGCTGTTCTCATTTTACATTAATATGTTGCATTTGTCACAAT 197730
ii i vv i i v i
C L1MC3_3end#LI 2432 CTATTATTAACATCTTACATTAGTATGGTACATTTGTCACAAT 2390
Matrix = 20p39g.matrix
Transitions / transversions = 1.30 (13 / 10)
Gap_init rate = 0.02 (3 / 134), avg. gap size = 2.67 (8 / 3)
+ 1884 17.3 1.3 2.3 INTRON_3 197739 198050 (202131) C AluJr SINE/Alu (3) 309 1 251
ANNOTATION EVIDENCE:
1721 19.35 1.28 2.27 INTRON_3 197739 198050 202131 C AluJb SINE/Alu 1 309 3 383
INTRON_3 197739 TTTCTTTTCTGTTTTTTTTTTTTTTTTGAGTGAGGGTCTCACTCTGTTGC 197788
i i v vv i i
C AluJb#SINE/Al 309 TTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGGGTCTCGCTCTGTCGC 260
INTRON_3 197789 CCAGGTTTGAGTGCAGTGGTATGATCATGACTTACTGCAGTCTAAAACTC 197838
i v iii i i i i vi v
C AluJb#SINE/Al 259 CCAGGCTGGAGTGCAGTGGCGCGATCACGGCTCACTGCAGCCTCGACCTC 210
INTRON_3 197839 GTGGGCTGAAACGATGCTCCTGCCTCAGCCTCCCAATTAGTGAGTAGCTA 197888
vi v i v ------- i
C AluJb#SINE/Al 209 CCGGGCTCAAGCGATCCTCCTGCCTCAGCCTCCC-------GAGTAGCTG 167
INTRON_3 197889 GGATTACAAGCATGTGCCACCACACCTGGCTACTTTTTAT----TTAATA 197934
i i ii i i i v i ---- vi
C AluJb#SINE/Al 166 GGACTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTTGTA 117
INTRON_3 197935 GAGGTGGGGTCTCACTATGCTGCTCAGGCTGGTCTGGAACTTCTGACCTC 197984
ii i i i i v i iv
C AluJb#SINE/Al 116 GAGACGGGGTTTCACCATGTTGCCCAGGCTGGTCTCGAACTCCTGGGCTC 67
INTRON_3 197985 AAGCAATCCTCCCACCTTGGCCTCCCAAAGTGCTGGAATTACAGGTGTGA 198034
ii i i i i
C AluJb#SINE/Al 66 AAGTGATCCTCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGA 17
INTRON_3 198035 GCTGCTATGTCTGGCC 198050
ii iii i i
C AluJb#SINE/Al 16 GCCACCGCGCCCGGCC 1
Matrix = 14p39g.matrix
Transitions / transversions = 3.54 (46 / 13)
Gap_init rate = 0.01 (2 / 311), avg. gap size = 5.50 (11 / 2)
+ 1382 13.8 4.5 0.7 INTRON_3 198052 198320 (201861) C Tigger2 DNA/TcMar-Tigger (2438) 280 2 252
ANNOTATION EVIDENCE:
1382 13.85 4.46 0.72 INTRON_3 198052 198320 201861 C Tigger2 DNA/TcMar-Tigger 2 280 2438 476
INTRON_3 198052 TGCACGTAAATTTTGACAAATTTTAACCTTCTATAATAGATTTGTGTAAT 198101
ii i i i i -
C Tigger2#DNA/T 280 TGTGCGTAAGTTTTGATAAATTTTAACTTTTTATAATAGATTTGTGTA-T 232
INTRON_3 198102 ATTTTATGGTAGAAAATGATAAAGTAGACTA-TAGTTATACATATTTTAT 198150
v i - vi i i
C Tigger2#DNA/T 231 ATTTTATGGTAGTAAATGATAAAATAGACTAGTATCTACATATATTTTAT 182
INTRON_3 198151 GTGCTCATCACA------ACCTTTTCCTTATTTTTTTGATATTTCTAGGC 198194
iii v ------ i i v i
C Tigger2#DNA/T 181 GCATTCATGACATACCTAACTTTTTCTTAATTTTTTCGATATTTCTAGGC 132
INTRON_3 198195 TACACAGTTTGTCTG----TTTTTTCAAATTGTCACAAATCTTGAAAAAA 198240
i i i ---- i iv
C Tigger2#DNA/T 131 TACGCGGTTCGTCTGCGAGTTTTTTCAAATTGTCGCAAATCTCCAAAAAA 82
INTRON_3 198241 ATTTCTGATATATCTTATTGAAAAAA-TCTGCATATAAGTTGACCCGCAC 198289
v ii - - i i v i
C Tigger2#DNA/T 81 TTTTCCAATATAT-TTATTGAAAAAAATCCGCGTATAAGTGGACCCGCGC 33
INTRON_3 198290 AGTTCAAACTTGTGTGGTTCAAGGATCAACT 198320
ii v i
C Tigger2#DNA/T 32 AGTTCAAACCCGTGTTGTTCAAGGGTCAACT 2
Matrix = 20p39g.matrix
Transitions / transversions = 3.62 (29 / 8)
Gap_init rate = 0.02 (6 / 268), avg. gap size = 2.33 (14 / 6)
+ 572 33.9 7.8 4.6 INTRON_3 198867 199225 (200956) + L3 LINE/CR1 3091 3460 (1029) 253
ANNOTATION EVIDENCE:
572 33.86 7.80 4.59 INTRON_3 198867 199225 200956 + L3 LINE/CR1 3091 3460 1029 412
INTRON_3 198867 GTCATTTTTTAAA----GAAAAGGAGTGAATTCTGGAAA-TATTAACCTA 198911
i v i ---- iiiii i - ivi -i
L3#LINE/CR1 3091 GCCTTCTTTTAAAAAGGGAAAAAAGACGAATCCTGGAAACTACAGACC-G 3139
INTRON_3 198912 ATAATAGAGTGCTTTTATATTTCAGTATCTGTAAAAACAACTTGGG-GAA 198960
i ------ -- - i? iii vi v? i i?- v ii-i
L3#LINE/CR1 3140 GTAA------GCTT--A-ACNTTGATCCCTGGNAAGATN-CTAGAACAAA 3179
INTRON_3 198961 TTATAAAACTTGTACATTGTGACCATTTAGAAGAAAA-CATGTTAATCAG 199009
i v vvi ivv i v ii iii - vi-- v
L3#LINE/CR1 3180 TCATTAAACAGATGGTTTGCGAGCACCTAGAAGGGGAGCAGA--AATCAC 3227
INTRON_3 199010 TAAG----AGCCGACTTAGGTTCACTAAGAAGAAATCCAGCCAAAGTAAA 199055
i ---- i ii v i i iv i vv v ?
L3#LINE/CR1 3228 TAGGTAGCAACCAGCATGGGTTCATTAAGAGCAAGTCATGCCAAACTAAN 3277
INTRON_3 199056 TTCACTTCTTTTTTTGGGTGGGGATAGTGGCTTGATGTATT-GGGGAATT 199104
? i i ? i- i v v iivvv i iv i- v
L3#LINE/CR1 3278 TTNATTTCCTTTTNTGA-TAGGGTTACTAAGAGGGTAGATCAGGGGAATG 3326
INTRON_3 199105 CCATACACAAAAGGTATATTGATTTCAGCAAAGCAATTTGCAAAGGCTTA 199154
v i ? v v v i v vi v iv
L3#LINE/CR1 3327 CCATAGATANAATGTATCTGGATTTCAGCAAGGCATTTGACAAAGTCTCT 3376
INTRON_3 199155 CATGTCATACATCTTGTAGCTAAAATGATGAATT---------------- 199188
? -- i-i i vi i i? v ----------------
L3#LINE/CR1 3377 NATG--ATAT-CCTTGTGGACAAGATGGNGAAATATGGGCTGGATGNTAG 3423
INTRON_3 199189 TGCACCTAAGTGAATTTGCAGTTGATTGAGCAACCAT 199225
?? vi i i iii i i i i
L3#LINE/CR1 3424 NNCAATTAGGTGGATTCATAGCTGGTTGAACAACTAT 3460
Matrix = 25p39g.matrix
Transitions / transversions = 1.92 (69 / 36)
Gap_init rate = 0.04 (16 / 358), avg. gap size = 2.81 (45 / 16)
+ 365 30.7 0.0 0.0 INTRON_3 199215 199315 (200866) + L3 LINE/CR1 3852 3952 (537) 253 *
ANNOTATION EVIDENCE:
365 30.69 0.00 0.00 INTRON_3 199215 199315 200866 + L3 LINE/CR1 3852 3952 537 413
INTRON_3 199215 TGAGCAACCATTGTGGCGTGACAGCAAAACAATCTAAGGCAATCTTAGGC 199264
v v v ii i v v v v v
L3#LINE/CR1 3852 TGAGCCAACAGTGTGATGTGGCTGCCAAAAAAGCTAATGCAATCTTAGGC 3901
INTRON_3 199265 TCCGTTAATAGATATGTAGTACTCATAAAAAGAGGCATAATGGTTTCCCC 199314
v i vi i iii v ?v i ivi i ii v i
L3#LINE/CR1 3902 TGCATTAATAGAAGTATAGTGTCCAGAWCAAGGGAGGTAATAGTCCCGCT 3951
INTRON_3 199315 G 199315
L3#LINE/CR1 3952 G 3952
Matrix = 25p39g.matrix
Transitions / transversions = 1.14 (16 / 14)
Gap_init rate = 0.00 (0 / 100), avg. gap size = 0.0 (0 / 0)
+ 212 37.4 0.8 8.8 INTRON_3 199544 199666 (200515) + L2b LINE/L2 3260 3373 (2) 254
ANNOTATION EVIDENCE:
212 37.43 0.81 8.77 INTRON_3 199544 199666 200515 + L2b_3end LINE/L2 351 464 2 414
INTRON_3 199544 GTGGGTCCCTTGAGGAATGGTATTGTGCCTTATTGACCTTTCTAATCCCT 199593
i ii v ivv v ii v i -----ii vi v i v
L2b_3end#LINE 351 GTGAGCTCCGTGAGGGCAGGGACCGGGTCT-----GTCTTGTTCACCGCT 395
INTRON_3 199594 -TCTCCCCTCTAAAGCTTAGTATGTTATGCCTAGAACAGAGGAAATACTC 199642
- v --- iv ii i ii--iv i v v v ii i
L2b_3end#LINE 396 GTGTCCCC---AGCGCCCAGCACA--GGGCCTGGCACACAGTAGGTGCTC 440
INTRON_3 199643 AGTAAACAATTACTGAATAAATGA 199666
iiv ii i
L2b_3end#LINE 441 AGTAAATGTTTGTTGAATGAATGA 464
Matrix = 25p39g.matrix
Transitions / transversions = 1.80 (27 / 15)
Gap_init rate = 0.03 (4 / 122), avg. gap size = 2.75 (11 / 4)
+ 202 31.3 13.4 4.3 INTRON_3 199833 199959 (200222) C MIR3 SINE/MIR (54) 154 17 255
ANNOTATION EVIDENCE:
202 31.28 13.39 4.35 INTRON_3 199833 199959 200222 C MIR3 SINE/MIR 17 154 54 415
INTRON_3 199833 TCCTATCTCTTTCCTTTTTAGATAAGAAAACTAAAGCCCCAGAGTGACCG 199882
v i i i ivi vi i i i i - v iivi
C MIR3#SINE/MIR 154 TCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCC-AGAGAGGTGA 106
INTRON_3 199883 AGAGGCTTGTTCAGTGTCCCA-------TT--TGCC----TTAAGA---- 199915
v i ii iv v ------- -- v ----i ii ----
C MIR3#SINE/MIR 105 AGTGACTTGCCCAAGGTCACACAGCKAGTTAGTGGCAGAGCTGGGACTAG 56
INTRON_3 199916 AATGCTGGTCTTTTAAATCCCAGTCCAGCAGAGCTCTTTCCTGC 199959
iv v ii i v ---- v i -
C MIR3#SINE/MIR 55 AACCCAGGTCTCCTGACTCCCAGTCC----GTGCTCTCTC-TGC 17
Matrix = 25p39g.matrix
Transitions / transversions = 1.92 (25 / 13)
Gap_init rate = 0.06 (7 / 126), avg. gap size = 3.29 (23 / 7)
+ 1567 24.1 6.3 8.6 INTRON_3 200235 200792 (199389) C MLT1F LTR/ERVL-MaLR (2) 546 1 256
ANNOTATION EVIDENCE:
1567 24.12 6.27 8.61 INTRON_3 200235 200792 199389 C MLT1F LTR/ERVL-MaLR 1 546 2 388
INTRON_3 200235 TATTAGATATCTATTTCTGTGTAACAGACTACTCCAAAACTGAGTGGCTT 200284
v v i i i i v
C MLT1F#LTR/ERV 546 TATTAGTTATCTATTGCTGCGTAACAAATTACCCCAAAACTTAGTGGCTT 497
INTRON_3 200285 AAA----CTACAAACATTCATCATCTCA----GTTTCTATGGGGAAAAAA 200326
---- v i i i ---- i vv ii
C MLT1F#LTR/ERV 496 AAAACAACAATAAACATTTATTATCTCACACAGTTTCTGTGGGTCAGGAA 447
INTRON_3 200327 TT-GGAAGCTGCTAAGCTGGGTGGATCTGATT-AAGGTCTCTCATGAGAT 200374
- i v v v ii - i i
C MLT1F#LTR/ERV 446 TTTGGGAGCGGCTTAGCTGGGTGGTTCTGGCTCAGGGTCTCTCATGAGGT 397
INTRON_3 200375 TTCATTCAAAATATTGGCTGAGGCAGCAGTCTAATCCGAAGGCTCAATTT 200424
v v i i i i i v -- i ii i v
C MLT1F#LTR/ERV 396 TGCAGTCAAGATGTCGGCCGGGGCTGCAGTC--ATCTGAAGGCTTGACTG 349
INTRON_3 200425 GGG---GAGGATACATTTAGAAAAT----CATTCCCATGGTTTTTAACAG 200467
--- v ii vv i ---- i v i ---ii -
C MLT1F#LTR/ERV 348 GGGCTGGAGGATCCGCTTCCAAGATGGCTCACTCACATGGCT---GGCA- 303
INTRON_3 200468 TCCTCAGTTCCTATCTAGCTGTTGGTCAATGGCTTTAGTTCCTTACCACA 200517
----- vv i- i iviiv i i ii i
C MLT1F#LTR/ERV 302 -----AGTTGGTG-CTGGCTGTTGGCAGGAGGCCTCAGTTCCTCGCCACG 259
INTRON_3 200518 TAGGCTT-TCTATAGG-CTTCCTGAATGTCCTCATGATATGACAGCTGGC 200565
i i i - i i - v i i i i i
C MLT1F#LTR/ERV 258 TGGACCTCTCCACAGGGCTGCTTGAGTGTCCTCACGACATGGCAGCTGGC 209
INTRON_3 200566 TTTATCCAGAGCTAGTGTATAGAGACAGCAGGGGGAGAGAGAAAAAGAGA 200615
ivi v ----- vv ------------------
C MLT1F#LTR/ERV 208 TTCCCCCAGAGCGAGTG-----ATCC------------------AAGAGA 182
INTRON_3 200616 AAGTAAGAGAATAAATAAGATGGAAGCCAT--TGTCTTT-ATCATACAGT 200662
i i i------------i i-- - v ivi i
C MLT1F#LTR/ERV 181 GAGCAAGG------------CGGAAGCCACAATGTCTTTTATGACCTAGC 144
INTRON_3 200663 CTTGGAAGTGACACACC------------ATGTGTTATTTGTCACACAGA 200700
i v ------------ i vi v i i
C MLT1F#LTR/ERV 143 CTCGGAAGTCACACACCGTCATTTCCGCAATATCCTATTGGTTACACAGG 94
INTRON_3 200701 CCTTCCTAGTATGATGTGGG-GGGTACTACACAGGGCTATGAATACGAAG 200749
i vv ivi vii? - v i vii v i
C MLT1F#LTR/ERV 93 TCAGCCCTATTCANTGTGGGAGGGGACTACACAAGGGCGTGAATACCAGG 44
INTRON_3 200750 GGGTGGGGATCATTAGGGCCTGTCTTGGAGGCTGTCTACCACA 200792
i iii i v ii v
C MLT1F#LTR/ERV 43 AGGCAAGGATCATTGGGGGCCATCTTGGAGGCTGGCTACCACA 1
Matrix = 18p39g.matrix
Transitions / transversions = 2.05 (82 / 40)
Gap_init rate = 0.03 (19 / 557), avg. gap size = 4.32 (82 / 19)
+ 191 9.5 4.8 0.0 INTRON_3 200953 200994 (199187) + (TTTTTA)n Simple_repeat 2 45 (0) 257
ANNOTATION EVIDENCE:
191 9.52 4.76 0.00 INTRON_3 200953 200994 199187 C (TAAAAA)n Simple_repeat 134 177 3 465
INTRON_3 200953 TTATTTTTATTTTTATTT--ATTTATTTTTTTATTATAATTTTT 200994
-- v v v v
C (TAAAAA)n#Sim 177 TTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTT 134
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 4)
Gap_init rate = 0.02 (1 / 41), avg. gap size = 2.00 (2 / 1)
+25636 3.9 0.2 0.1 INTRON_3 200997 207137 (193044) C L1PA3 LINE/L1 (3) 6152 7 258
ANNOTATION EVIDENCE:
7313 3.00 0.00 0.00 INTRON_3 200997 201895 198286 C L1PA3_3end LINE/L1 1 899 3 440
INTRON_3 200997 TTGTATTATTATTATACTTTAAGTTTTAGGGTATATGTGCACAATGTGCA 201046
v i
C L1PA3_3end#LI 899 TTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAATGTGCA 850
INTRON_3 201047 CGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCTGCACCCACCA 201096
v i i
C L1PA3_3end#LI 849 GGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTA 800
INTRON_3 201097 ACTCGTCATTTAGCATTAGGTATATCACCTAATGCCATCCCTCCCCCCTC 201146
i v i i
C L1PA3_3end#LI 799 ACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCCTC 750
INTRON_3 201147 CCCCCACCCCACAACAGTCCCCAGAGTGTGATGTTCCCCTTCCTGTGTCC 201196
C L1PA3_3end#LI 749 CCCCCACCCCACAACAGTCCCCAGAGTGTGATGTTCCCCTTCCTGTGTCC 700
INTRON_3 201197 ATGTGTTCTCATAGTTCAATTCCCACCTATGAGTGAGAACATGCAGCGTT 201246
v i i i
C L1PA3_3end#LI 699 ATGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTT 650
INTRON_3 201247 TGGTTTTTTGTCCTTGCGATAGTTTACTGAGAATGATGATTTCCAATTTC 201296
i
C L1PA3_3end#LI 649 TGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGATTTCCAATTTC 600
INTRON_3 201297 ATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCATA 201346
C L1PA3_3end#LI 599 ATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCATA 550
INTRON_3 201347 GTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTG 201396
C L1PA3_3end#LI 549 GTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTG 500
INTRON_3 201397 TTGGACACTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCCGCA 201446
i
C L1PA3_3end#LI 499 TTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCCGCA 450
INTRON_3 201447 ATAAACATACGTGTGCATGTATCTTTATAGCAGCATGATTTATAGTCCTT 201496
i
C L1PA3_3end#LI 449 ATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTT 400
INTRON_3 201497 TGGGTATATACCCAATAATGAGATGGCTGGGTCAAATGGTGTTTCTAGTT 201546
i i i
C L1PA3_3end#LI 399 TGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTT 350
INTRON_3 201547 CCAGATCCCTGAGGAATCGCCACACTGACTTCTACAATGGTTGAACTAGT 201596
i i
C L1PA3_3end#LI 349 CTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGT 300
INTRON_3 201597 TGACAGTCCCACCAACAGTGTGAAAGTGTTCCTATTTCTCTGCATCCTCT 201646
v i ii
C L1PA3_3end#LI 299 TTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCT 250
INTRON_3 201647 CCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTG 201696
C L1PA3_3end#LI 249 CCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTG 200
INTRON_3 201697 TGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGT 201746
C L1PA3_3end#LI 199 TGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGT 150
INTRON_3 201747 GATCGTGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTT 201796
v
C L1PA3_3end#LI 149 GATGGTGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTT 100
INTRON_3 201797 TGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTGATGGGGTTGTTTG 201846
i
C L1PA3_3end#LI 99 TGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTG 50
INTRON_3 201847 TTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAG 201895
C L1PA3_3end#LI 49 TTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAG 1
Matrix = 20p39g.matrix
Transitions / transversions = 3.50 (21 / 6)
Gap_init rate = 0.00 (0 / 898), avg. gap size = 0.0 (0 / 0)
25636 3.23 0.27 0.00 INTRON_3 201746 205030 195151 C L1P1_orf2 LINE/L1 1 3294 0 441
INTRON_3 201746 TGATCGTGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTT 201795
vi i
C L1P1_orf2#LIN 3294 TGATGATGAGCATTTCTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTT 3245
INTRON_3 201796 TTGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTGATGGGGTTGTTT 201845
i
C L1P1_orf2#LIN 3244 TTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTT 3195
INTRON_3 201846 GTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAG 201895
C L1P1_orf2#LIN 3194 GTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAG 3145
INTRON_3 201896 CCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTATAGGTT 201945
v i
C L1P1_orf2#LIN 3144 CCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATGTTGTAGGTT 3095
INTRON_3 201946 TCCTGTTCACTCTAATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTGAGT 201995
v i v
C L1P1_orf2#LIN 3094 GCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGT 3045
INTRON_3 201996 TTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGG 202045
C L1P1_orf2#LIN 3044 TTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGG 2995
INTRON_3 202046 TGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTAATGC 202095
i i
C L1P1_orf2#LIN 2994 TGTTTTGGACATGAAGTCCTTGCCCACGCCTATGTCCTGAATGGTAATGC 2945
INTRON_3 202096 CTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAATGTTTAAGTCT 202145
i i
C L1P1_orf2#LIN 2944 CTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAATCT 2895
INTRON_3 202146 TTAATCCATCTTGAATTAATTTTTGTATAAGGTGTAAGGATGGGATCCAG 202195
i v
C L1P1_orf2#LIN 2894 TTAATCCATCTTGAATTGATTTTTGTATAAGGTGTAAGGAAGGGATCCAG 2845
INTRON_3 202196 TTTCAGCTTTCTACCTATGGCTAGCCAGTTTTCCCAGCACCATTTATTAA 202245
v
C L1P1_orf2#LIN 2844 TTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAA 2795
INTRON_3 202246 ATAGGGAATCCTTTCCCCATTGCTTGTTTTTCTCAGGTTTGTCAAAGATC 202295
C L1P1_orf2#LIN 2794 ATAGGGAATCCTTTCCCCATTGCTTGTTTTTCTCAGGTTTGTCAAAGATC 2745
INTRON_3 202296 AGATAGCTGTAGATATGTGGCATTATTTCTGAGGGCTCTGTTCTGTTCCA 202345
i i
C L1P1_orf2#LIN 2744 AGATAGTTGTAGATATGCGGCATTATTTCTGAGGGCTCTGTTCTGTTCCA 2695
INTRON_3 202346 TTGATCTATATCTCTGTTTTGGTACCAGTACCATGCTGTTTTGGTTACTG 202395
C L1P1_orf2#LIN 2694 TTGATCTATATCTCTGTTTTGGTACCAGTACCATGCTGTTTTGGTTACTG 2645
INTRON_3 202396 TAGCCTTGTAGTATAGTTTGAAGTCAGGTAGCATGATGCCTCCAGCTTTG 202445
ii
C L1P1_orf2#LIN 2644 TAGCCTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTCCAGCTTTG 2595
INTRON_3 202446 TTCTTTTGGCTTAGGATTGACTTGGCGATGCGGGCTCTTTTTTGGTTCCA 202495
C L1P1_orf2#LIN 2594 TTCTTTTGGCTTAGGATTGACTTGGCGATGCGGGCTCTTTTTTGGTTCCA 2545
INTRON_3 202496 TATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGTCATTGGTA 202545
C L1P1_orf2#LIN 2544 TATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGTCATTGGTA 2495
INTRON_3 202546 GCTTGATGGGGATGGCATTGAATCTATAAATTACCTTGGGCAGTATGGCC 202595
i
C L1P1_orf2#LIN 2494 GCTTGATGGGGATGGCATTGAATCTGTAAATTACCTTGGGCAGTATGGCC 2445
INTRON_3 202596 ATTTTCACGATATTGATTCTTCCTATCCATGAGCATGGAATGTTCTTCCA 202645
i
C L1P1_orf2#LIN 2444 ATTTTCACGATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTCCA 2395
INTRON_3 202646 TTTGTTTGTATCCTCTTTTATTTCATTGAGCAGTGGTTTGTAGTTCTCCT 202695
i v
C L1P1_orf2#LIN 2394 TTTGTTTGTGTCCTCTTTTATTTCCTTGAGCAGTGGTTTGTAGTTCTCCT 2345
INTRON_3 202696 TGAAGAGGTCCTTCACAACCCTTGTAGGTTGGACTCCTAGGTATTTTATT 202745
v i i
C L1P1_orf2#LIN 2344 TGAAGAGGTCCTTCACATCCCTTGTAAGTTGGATTCCTAGGTATTTTATT 2295
INTRON_3 202746 CTCTTTGAAGCAATTGTGAATGGGAGTTCACTGATGATTTGGCTCTCTGT 202795
iv
C L1P1_orf2#LIN 2294 CTCTTTGAAGCAATTGTGAATGGGAGTTCACCCATGATTTGGCTCTCTGT 2245
INTRON_3 202796 ----CTGTTATTGGTGTATAAGAACGCTTGTGATTTTTGTACATTGATTT 202841
---- i i
C L1P1_orf2#LIN 2244 TTGTCTGTTGTTGGTGTATAAGAATGCTTGTGATTTTTGTACATTGATTT 2195
INTRON_3 202842 TGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGGAGATTTCGG 202891
i
C L1P1_orf2#LIN 2194 TGTATCCTGAGACTTTGCTGAAGTTGCTTATCAGCTTAAGGAGATTTTGG 2145
INTRON_3 202892 GCTGAGACAATGGGGTTTTCTAGATATACAATCATGTCATCTGCAAACAG 202941
i v i
C L1P1_orf2#LIN 2144 GCTGAGACGATGGGGTTTTCTAGATAAACAATCATGTCGTCTGCAAACAG 2095
INTRON_3 202942 GGACAATTTGACTTCCTCTTTTCCTAATTGAATACCCTTTATTTCCTTCT 202991
C L1P1_orf2#LIN 2094 GGACAATTTGACTTCCTCTTTTCCTAATTGAATACCCTTTATTTCCTTCT 2045
INTRON_3 202992 CCTGCCTAATTGCCCTGGCCAGAACTTCCAACACTATGTTGAATAGGAGT 203041
i i
C L1P1_orf2#LIN 2044 CCTGCCTGATTGCCCTGGCCAGAACTTCCAACACTATGTTGAATAGGAGC 1995
INTRON_3 203042 GGTGAGAGAGGGCATCCCTGTCTTGTGCCAGTTTTCTAAGGGATTGCTTC 203091
v v
C L1P1_orf2#LIN 1994 GGTGAGAGAGGGCATCCCTGTCTTGTGCCAGTTTTCAAAGGGAATGCTTC 1945
INTRON_3 203092 CAGTTTTTGCCCATTCAGGATGATACTGGCTGTGGGTTCGTCATAGATAG 203141
v i i
C L1P1_orf2#LIN 1944 CAGTTTTTGCCCATTCAGTATGATATTGGCTGTGGGTTTGTCATAGATAG 1895
INTRON_3 203142 CTCTTATTCTTTTGAGATACGTCCCATCAATACCTAATTTATTGAGAGTT 203191
v i
C L1P1_orf2#LIN 1894 CTCTTATTATTTTGAAATACGTCCCATCAATACCTAATTTATTGAGAGTT 1845
INTRON_3 203192 TT-AGCATGAAGGGTTGTTGAATTTTGTGAAAGGCCTTTTCTGCATCTAT 203240
- v i
C L1P1_orf2#LIN 1844 TTTAGCATGAAGGGTTGTTGAATTTTGTCAAAGGCTTTTTCTGCATCTAT 1795
INTRON_3 203241 TGAGATAATCATGTGGTTTTTGTCTTTGGTTCTGTTTATATGCTGGATTA 203290
i
C L1P1_orf2#LIN 1794 TGAGATAATCATGTGGTTTTTGTCTTTGGCTCTGTTTATATGCTGGATTA 1745
INTRON_3 203291 CATTTATTGATTTGTGTATATTGAACCAGCCTTGCATCCCAGGGATGAAG 203340
i
C L1P1_orf2#LIN 1744 CATTTATTGATTTGCGTATATTGAACCAGCCTTGCATCCCAGGGATGAAG 1695
INTRON_3 203341 CCCACTTGATTATGGTGGATAAGCTTTTTGATGTGCTGCTGGATTTGTTT 203390
i i v
C L1P1_orf2#LIN 1694 CCCACTTGATCATGGTGGATAAGCTTTTTGATGTGCTGCTGGATTCGGTT 1645
INTRON_3 203391 TGCCAGTATTTTATTGAGGATTTTTGCATCAATGTTCATCAAGGATATTG 203440
C L1P1_orf2#LIN 1644 TGCCAGTATTTTATTGAGGATTTTTGCATCAATGTTCATCAAGGATATTG 1595
INTRON_3 203441 GTTTAAAATTCTCTTTTTTGGTTGTGTCTCTGCCCAGCTTTGGTATCAGG 203490
i i i
C L1P1_orf2#LIN 1594 GTCTAAAATTCTCTTTTTTGGTTGTGTCTCTGCCCGGCTTTGGTATCAGA 1545
INTRON_3 203491 ATGATGCTGGCCTTATAAAATGAGTTAGGGAGGATTCCCTCTTTTTCTAT 203540
i
C L1P1_orf2#LIN 1544 ATGATGCTGGCCTCATAAAATGAGTTAGGGAGGATTCCCTCTTTTTCTAT 1495
INTRON_3 203541 TGATTGGAATAGTTTCAGAAGGAATGGTACCAGTTCCTCCTTGTACCTCT 203590
C L1P1_orf2#LIN 1494 TGATTGGAATAGTTTCAGAAGGAATGGTACCAGTTCCTCCTTGTACCTCT 1445
INTRON_3 203591 GGTAGAATTCGGCTGTGAATCCATCTGGTCCTGGACTCTTTTTGGTTGGT 203640
C L1P1_orf2#LIN 1444 GGTAGAATTCGGCTGTGAATCCATCTGGTCCTGGACTCTTTTTGGTTGGT 1395
INTRON_3 203641 AAGCTATTGATTATTGCCACAATTTCAGAGCCTGTTATTGGTCTATTCAG 203690
i
C L1P1_orf2#LIN 1394 AAACTATTGATTATTGCCACAATTTCAGAGCCTGTTATTGGTCTATTCAG 1345
INTRON_3 203691 AGATTCAACTTCTTCCTTGTTTAGTCTTGGGAGGGTGTATGTGTGGAGGA 203740
v i v
C L1P1_orf2#LIN 1344 AGATTCAACTTCTTCCTGGTTTAGTCTTGGGAGAGTGTATGTGTCGAGGA 1295
INTRON_3 203741 ATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTG 203790
v
C L1P1_orf2#LIN 1294 ATGTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTGTTTG 1245
INTRON_3 203791 TAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCGGTGGTGATATC 203840
C L1P1_orf2#LIN 1244 TAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCGGTGGTGATATC 1195
INTRON_3 203841 CCCTTTATCATTTTTTATTGCGTCTATTTGATTCTTCTCTCTTTTCTTCT 203890
i i
C L1P1_orf2#LIN 1194 CCCTTTATCATTTTTTATTGTGTCTATTTGATTCTTCTCTCTTTTTTTCT 1145
INTRON_3 203891 TTATTAGTCTTGCTAGCAGTCTGTCAATTTTGTTGATCCTTTCAAAAAAC 203940
i i
C L1P1_orf2#LIN 1144 TTATTAGTCTTGCTAGCGGTCTATCAATTTTGTTGATCCTTTCAAAAAAC 1095
INTRON_3 203941 CAGCTCCTGGATTCATTAATTTTTTGAAGGGTTTTTTGTGTCTCTATTTC 203990
i
C L1P1_orf2#LIN 1094 CAGCTCCTGGATTCATTGATTTTTTGAAGGGTTTTTTGTGTCTCTATTTC 1045
INTRON_3 203991 CTTCATTTCTGCTCTGGTTTTAGTTATTTCTTGCCTTCTACTAGCTTTTG 204040
v i i
C L1P1_orf2#LIN 1044 CTTCAGTTCTGCTCTGATTTTAGTTATTTCTTGCCTTCTGCTAGCTTTTG 995
INTRON_3 204041 AATGTGTTTGTTCTTGCTTCTCTAGTTCTTTTAATTGTGATGTTAGGGTG 204090
i i
C L1P1_orf2#LIN 994 AATGTGTTTGCTCTTGCTTTTCTAGTTCTTTTAATTGTGATGTTAGGGTG 945
INTRON_3 204091 TCAATTTTGGATCTTTCCTGCTTTCTCTTGTGGGCATTTAGTGCTATAAA 204140
i
C L1P1_orf2#LIN 944 TCAATTTTGGATCTTTCCTGCTTTCTCTTGTAGGCATTTAGTGCTATAAA 895
INTRON_3 204141 TTTCCCTCTTTACACTGCTTTGAATGTGTCCCAGAGATTCTGGTATGTTG 204190
vi i v
C L1P1_orf2#LIN 894 TTTCCCTCTACACACTGCTTTGAATGCGTCCCAGAGATTCTGGTATGTGG 845
INTRON_3 204191 TGTCTTTGTTCTCGTTGGTTTCAAAGGACATCTTTATTTCTGCCTTCATT 204240
i
C L1P1_orf2#LIN 844 TGTCTTTGTTCTCGTTGGTTTCAAAGAACATCTTTATTTCTGCCTTCATT 795
INTRON_3 204241 TCGTTGTGTACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCATGT 204290
i
C L1P1_orf2#LIN 794 TCGTTATGTACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCATGT 745
INTRON_3 204291 AGTTGAGCGGTTTTGAGTGAGTTTCTTAATCCTGAGTTCTAGTTTGATTG 204340
i v
C L1P1_orf2#LIN 744 AGTTGAGCGGCTTTGAGTGAGATTCTTAATCCTGAGTTCTAGTTTGATTG 695
INTRON_3 204341 CACTGTGGTCTGAGAGACAGTTTGTTATAATTTCTGTTCTTTTACATTTG 204390
i
C L1P1_orf2#LIN 694 CACTGTGGTCTGAGAGATAGTTTGTTATAATTTCTGTTCTTTTACATTTG 645
INTRON_3 204391 CTGAGGAGAGCTTTACTTCCACCTATGTGGTCAATTTTGGAATAGGTGTG 204440
v
C L1P1_orf2#LIN 644 CTGAGGAGAGCTTTACTTCCAACTATGTGGTCAATTTTGGAATAGGTGTG 595
INTRON_3 204441 GTGTGGTGCTGAAAAGAATGTTTATTTTGTTGATTTGTGTTGGAGAGTTC 204490
i v i v v
C L1P1_orf2#LIN 594 GTGTGGTGCTGAAAAAAATGTATATTCTGTTGATTTGGGGTGGAGAGTTC 545
INTRON_3 204491 TGTGGATGTCTATTAGGTCTGCTTGGTGCAGAGCTGAGTTCAGTTCCTGG 204540
i i
C L1P1_orf2#LIN 544 TGTAGATGTCTATTAGGTCTGCTTGGTGCAGAGCTGAGTTCAATTCCTGG 495
INTRON_3 204541 GTATCCTTGTTAACTTTCTGTCTCGTTGATCTGTCTAATGTTGACAGTGG 204590
i
C L1P1_orf2#LIN 494 GTATCCTTGTTGACTTTCTGTCTCGTTGATCTGTCTAATGTTGACAGTGG 445
INTRON_3 204591 GGTGTTAAAATCTCCCATTATTATTGTGTGGGTGTCTAAGTCTCTTTGTA 204640
i v v
C L1P1_orf2#LIN 444 GGTGTTAAAGTCTCCCATTATTAATGTGTGGGAGTCTAAGTCTCTTTGTA 395
INTRON_3 204641 GGTCACTCAGGACTTGCTTCATGAATCTGGGTGCTCCTGTATTGGGTGCA 204690
? i
C L1P1_orf2#LIN 394 GGTCACTWAGGACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGGTGCA 345
INTRON_3 204691 TATATATTTAGGATAGTTAGCTCTTCTTGTTGAATTGATCCCTTTACCAT 204740
v i
C L1P1_orf2#LIN 344 TAAATATTTAGGATAGTTAGCTCCTCTTGTTGAATTGATCCCTTTACCAT 295
INTRON_3 204741 TATGTAATGGCCTTCTTTGTCTCTTTTGATCTTT-TTGGTTTAAAGTCTG 204789
-
C L1P1_orf2#LIN 294 TATGTAATGGCCTTCTTTGTCTCTTTTGATCTTTGTTGGTTTAAAGTCTG 245
INTRON_3 204790 TTTTATGAGAGACTAGGATTGCAACCCCTGCCTTTTTTTGTTTTCCATTT 204839
v v
C L1P1_orf2#LIN 244 TTTTATCAGAGACTAGGATTGCAACCCCTGCCTTTTTTTGTTTTCCATTG 195
INTRON_3 204840 GCTTGGTAGATCTTCCTCCATCCTTTTATTTTGAGCCTATGTGTGTCTCT 204889
C L1P1_orf2#LIN 194 GCTTGGTAGATCTTCCTCCATCCTTTTATTTTGAGCCTATGTGTGTCTCT 145
INTRON_3 204890 GCACGTGAGATGGATTTCCTGAATACAGCACACTGATGGGTCTTGACTCC 204939
i i
C L1P1_orf2#LIN 144 GCACGTGAGATGGGTTTCCTGAATACAGCACACTGATGGGTCTTGACTCT 95
INTRON_3 204940 --ATCCAATTTGCCAGTCTGTGTCTTTTAATTGGAGCATTTAATCCATTT 204987
-- i v v i
C L1P1_orf2#LIN 94 TTATCCAACTTGCCAGTCTGTGTCTTTTAATTGCAGAATTTAGTCCATTT 45
INTRON_3 204988 ACAATTAAAGTTAATATTGTTATGTGTGAATTT-ATCCTGTCAT 205030
i v -
C L1P1_orf2#LIN 44 ATATTTAAAGTTAATATTGTTATGTGTGAATTTGATCCTGTCAT 1
Matrix = 20p39g.matrix
Transitions / transversions = 2.00 (70 / 35)
Gap_init rate = 0.00 (5 / 3284), avg. gap size = 1.80 (9 / 5)
17229 5.17 0.31 0.36 INTRON_3 204884 207137 193044 C L1P1_5end LINE/L1 7 2259 0 442
INTRON_3 204884 GTCTCTGCACGTGAGATGGATTTCCTGAATACAGCACACTGATGGGTCTT 204933
i i
C L1P1_5end#LIN 2259 GTCTCTGCACGTGAGATGGGTTTCCTGAATACGGCACACTGATGGGTCTT 2210
INTRON_3 204934 GACTCC--ATCCAATTTGCCAGTCTGTGTCTTTTAATTGGAGCATTTAAT 204981
i-- ii
C L1P1_5end#LIN 2209 GACTCTTTATCCAATTTGCCAGTCTGTGTCTTTTAATTGGAGCATTTAGC 2160
INTRON_3 204982 CCATTTACAATTAAAGTTAATATTGTTATGTGTGAATTT-ATCCTGTCAT 205030
v -
C L1P1_5end#LIN 2159 CCATTTACATTTAAAGTTAATATTGTTATGTGTGAATTTGATCCTGTCAT 2110
INTRON_3 205031 TATGATGTTAGCTGGTTATTTTGCTCGTTAGTTGATGCAGTTTCTTCCTA 205080
i
C L1P1_5end#LIN 2109 TATGACGTTAGCTGGTTATTTTGCTCGTTAGTTGATGCAGTTTCTTCCTA 2060
INTRON_3 205081 GCCTCGATGGTCTTTACAATTTGCCATGATTTTGCAGTGGCTGGAACTGG 205130
i v v i v
C L1P1_5end#LIN 2059 GCCTTGATGGTCTTTACAATTTGGCATGTTTTTGCAGCGGCTGGTACTGG 2010
INTRON_3 205131 TTGTTCCTTTCCATGTTTAGTGCTTCCTTCAGGAGCTGTTTTAGGGCAGG 205180
i v
C L1P1_5end#LIN 2009 TTGTTCCTTTCCATGTTTAGCGCTTCCTTCAGGAGCTCTTTTAGGGCAGG 1960
INTRON_3 205181 CCTGGTGGTGACAAAATCTCTCAGCATTTGCTTGTCTGTAAAGAATTTTA 205230
v
C L1P1_5end#LIN 1959 CCTGGTGGTGACAAAATCTCTCAGCATTTGCTTGTCTGTAAAGTATTTTA 1910
INTRON_3 205231 TTTCTCCTTCACTTATGAAGCTTAGTTTGGCTGGATATGAAATTCTTGGT 205280
i v
C L1P1_5end#LIN 1909 TTTCTCCTTCGCTTATGAAGCTTAGTTTGGCTGGATATGAAATTCTGGGT 1860
INTRON_3 205281 TGAAAATTCTTTTCTTTAAGAATGTTGAATATTGGCTCCCACTCTCTTCT 205330
i i
C L1P1_5end#LIN 1859 CGAAAATTCTTTTCTTTAAGAATGTTGAATATTGGCCCCCACTCTCTTCT 1810
INTRON_3 205331 GGCTTGTAGAGTTTCTGCCAAGAGATCAGCTGTTAGTCTGATGGACTTCC 205380
i i i
C L1P1_5end#LIN 1809 GGCTTGTAGAGTTTCTGCCGAGAGATCAGCCGTTAGTCTGATGGGCTTCC 1760
INTRON_3 205381 CTTTGTGGGTAACCTGACCTTTCTCTCTGTCTGCCCTTAACATTTTTTCC 205430
i v
C L1P1_5end#LIN 1759 CTTTGTGGGTAACCCGACCTTTCTCTCTGGCTGCCCTTAACATTTTTTCC 1710
INTRON_3 205431 TTCATTTCAACTTTGGTGAATCTGACAATGATGTGTCTTGGGGTTGCTCT 205480
v i
C L1P1_5end#LIN 1709 TTCATTTCAACTTTGGTGAATCTGACAATTATGTGTCTTGGAGTTGCTCT 1660
INTRON_3 205481 TCTTGAGGAGTATCTTTGTGGCGTTCTCTGTATTTCCTGAGTCTGAATGT 205530
i i i
C L1P1_5end#LIN 1659 TCTCGAGGAGTATCTTTGTGGCGTTCTCTGTATTTCCTGAATCTGAACGT 1610
INTRON_3 205531 TGGCGTGCCTTGCTAGATTGGGGAAGTTCTCCTGGACAATATCCTGCAGA 205580
v i
C L1P1_5end#LIN 1609 TGGCCTGCCTTGCTAGATTGGGGAAGTTCTCCTGGATAATATCCTGCAGA 1560
INTRON_3 205581 GGGTTTTCCAACTTGGTTGCATTCTCCCCCTCACTTTCAGGTACACCAAT 205630
v v v
C L1P1_5end#LIN 1559 GTGTTTTCCAACTTGGTTCCATTCTCCCCGTCACTTTCAGGTACACCAAT 1510
INTRON_3 205631 CAGACGTAGATTTGGTCTTTTCACATAGTCCCATATTACTTGGAGGCTTT 205680
i v
C L1P1_5end#LIN 1509 CAGACGCAGATTTGGTCTTTTCACATAGTCCCATATTTCTTGGAGGCTTT 1460
INTRON_3 205681 GTTTGTTT----TTATTCTTTTTTCTCTAAACTTCCCTTCTTGCTTCATT 205726
i ---- i i
C L1P1_5end#LIN 1459 GTTCGTTTCTTTTTATTCTTTTTTCTCTAAACTTCTCTTCTCGCTTCATT 1410
INTRON_3 205727 TCATTCATTTCATCTTCCATCACTGATAACCTTTCTTCCAGTTGATCACA 205776
i v i
C L1P1_5end#LIN 1409 TCATTCATTTCATCTTCCGTCACTGATACCCTTTCTTCCAGTTGATCGCA 1360
INTRON_3 205777 TTGGCTCCTGAGGCTTCTGCATTCTTCACGTAGTTCTCGAGCCTTGGCTT 205826
i v v v i
C L1P1_5end#LIN 1359 TCGGCTACTGAGGCTTCTGCATTCGTCACGTAGTTCTCGTGCCTTGGTTT 1310
INTRON_3 205827 TCAGCTCCATCAGCTACTTTAAGCACTTCTCTGTATTGGTTATTCTAGTT 205876
v v v i
C L1P1_5end#LIN 1309 TCAGCTCCATCAGGTCCTTTAAGGACTTCTCTGCATTGGTTATTCTAGTT 1260
INTRON_3 205877 ATACATTTGTCTAAATTTTTTTCAAAGTTTTTAACTTCTTTGCCTTTGGT 205926
v ii v v
C L1P1_5end#LIN 1259 ATCCATTCATCTAATTTTTTTTCAAAGTTTTTAACTTCTTTGCCGTTGGT 1210
INTRON_3 205927 TTGAATTTCCTCCTGTAGCTCGGAGTAGTTTGATCATCTGAAGCCTTCTT 205976
i i
C L1P1_5end#LIN 1209 TCGAATTTCCTCCTGTAGCTCGGAGTAGTTTGATCGTCTGAAGCCTTCTT 1160
INTRON_3 205977 CTCTCAACTCGTCAAAGTCATTCTCCGTCCAGCTTTGTTCCGTTGCTGGT 206026
i
C L1P1_5end#LIN 1159 CTCTCAACTCGTCAAAGTCATTCTCTGTCCAGCTTTGTTCCGTTGCTGGT 1110
INTRON_3 206027 GAGGAACTGCGTTCCTTTGGAGGAGGAGAGGTGCTCTGCTTTTTAGAATT 206076
i i i v i
C L1P1_5end#LIN 1109 GAGGAGCTGCGTTCCTTTGGAGAAGGAGAGGCGCTCTGATTTTTAGAGTT 1060
INTRON_3 206077 TCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACTT 206126
i
C L1P1_5end#LIN 1059 TCCAGTTTTTCTGCTCTGTTTTTTCCCCATCTTTGTGGTTTTATCTACCT 1010
INTRON_3 206127 TTGGTCTTTGATGATGGTGATGTACAGATGGGTTTTTGGTGTGGATGTCC 206176
i
C L1P1_5end#LIN 1009 TTGGTCTTTGATGATGGTGACGTACAGATGGGTTTTTGGTGTGGATGTCC 960
INTRON_3 206177 TTTCTGTTTGTTAGTTTTCCTTCTAACAGACAGGACCCTCAGCTGCAGGT 206226
C L1P1_5end#LIN 959 TTTCTGTTTGTTAGTTTTCCTTCTAACAGACAGGACCCTCAGCTGCAGGT 910
INTRON_3 206227 CTGTTGGAGTTTGCTAGAGGTCCACTCCAGACCCTGTTTGCCTGGGTATC 206276
i
C L1P1_5end#LIN 909 CTGTTGGAGTTTGCTGGAGGTCCACTCCAGACCCTGTTTGCCTGGGTATC 860
INTRON_3 206277 AGCAGAGGTGTCTGCAGAACAGTGGATTTTTATGAACCGCGAATGCTGCT 206326
v v v vi ii
C L1P1_5end#LIN 859 AGCAGCGGTGGCTGCAGAACAGTGGATATTGGTGAACCGCAGATGCTGCT 810
INTRON_3 206327 GTCTGATCGTTCCTCTGGAAGTTTTGTCTCAGAGGAGTACTGGGCCATGT 206376
i iv i
C L1P1_5end#LIN 809 GCCTGATCGTTCCTCTGGAAGTTTTGTCTCAGAGGAGTACCCGGCCGTGT 760
INTRON_3 206377 GAGGTGTCAGTCTGCCCCTACTGGGGGGTGCCTCCCAGTTAGGCTGCTTG 206426
i i i
C L1P1_5end#LIN 759 GAGGTGTCAGTCCGCCCCTACTGGGGGGTGCCTCCCAGTTAGGCTACTCG 710
INTRON_3 206427 GGGGTCAGGGGTCAGGGACCCACTTGAGGAGGCAGTCTGCCCGTTCTCAG 206476
-------
C L1P1_5end#LIN 709 GGGGTCAGGG-------ACCCACTTGAGGAGGCAGTCTGCCCGTTCTCAG 667
INTRON_3 206477 ATCTCCAGCTGCGTGCTGGGAGAACCACTGCTCTCTTCAAAGCTGTCAGA 206526
vv
C L1P1_5end#LIN 666 ATCTGAAGCTGCGTGCTGGGAGAACCACTGCTCTCTTCAAAGCTGTCAGA 617
INTRON_3 206527 CAGGGACATTTAAGTCTGCAGAGGTTACTGCTGTCTTTTTGTTTGTCTGT 206576
C L1P1_5end#LIN 616 CAGGGACATTTAAGTCTGCAGAGGTTACTGCTGTCTTTTTGTTTGTCTGT 567
INTRON_3 206577 GCCCTGCCCCCAGAGGTGGAGCCTACAGAGGCAGGCAGGCCTCCTTGAGC 206626
C L1P1_5end#LIN 566 GCCCTGCCCCCAGAGGTGGAGCCTACAGAGGCAGGCAGGCCTCCTTGAGC 517
INTRON_3 206627 TGTGGTGGGCTCCACCCAGTTCGAGCTTCCAGGCTGCTTTGTTTACCTAA 206676
v i
C L1P1_5end#LIN 516 TGTGGTGGGCTCCACCCAGTTCGAGCTTCCCGGCCGCTTTGTTTACCTAA 467
INTRON_3 206677 GAAAGCCTGGGCAATGGTGGGCACCCCTCCCCCAGCCTGGCTGCTGCCTT 206726
vv i i v i
C L1P1_5end#LIN 466 TCAAGCCTGGGCAATGGCGGGCGCCCCTCCCCCAGCCTCGCTGCCGCCTT 417
INTRON_3 206727 GCAGTTTGATCTCAGACTGCTGTGCTAGCAATCAGCGAGACTCCGTGGGC 206776
i
C L1P1_5end#LIN 416 GCAGTTTGATCTCGGACTGCTGTGCTAGCAATCAGCGAGACTCCGTGGGC 367
INTRON_3 206777 GTAGGACCCTCCAAGCCATGTGCGGGATATAATCTCCTGGTGCGCCGTTT 206826
i v
C L1P1_5end#LIN 366 GTAGGACCCTCCGAGCCAGGTGCGGGATATAATCTCCTGGTGCGCCGTTT 317
INTRON_3 206827 TTTAAGCCTGTCGGAAAAGCGCAGTATTAGGGTGGGAGTGACCCGAATTT 206876
i i v
C L1P1_5end#LIN 316 TTTAAGCCCGTCGGAAAAGCGCAGTATTAGGGCGGGAGTGACCCGATTTT 267
INTRON_3 206877 CCAGGTGCCGTCTGTCACCCCTTTCTTTGACTAGGAAAGGGAACTCCCCG 206926
i i
C L1P1_5end#LIN 266 CCAGGTGCCGTCTGTCACCCCTTTCTTTGACTAGGAAAGGGAATTCCCTG 217
INTRON_3 206927 ACTCCTTGCACTTCCTGAGTGAGGCAATGCCTTGCCCTGCTTCAGCTTGC 206976
i i i i i i i ii
C L1P1_5end#LIN 216 ACCCCTTGCGCTTCCCGGGTGAGGCGATGCCTCGCCCTGCTTCGGCTCAC 167
INTRON_3 206977 GCACGGTGCGCTGCACCCACTGTCCTGCGCCCACTGTCTGGCACTCCCTA 207026
i
C L1P1_5end#LIN 166 GCACGGTGCGCTGCACCCACTGTCCTGCGCCCACTGTCTGGCACTCCCCA 117
INTRON_3 207027 GTGAGATGAACCTGGTACCTCAGATGGAAATGCAGAAATCACCCGTGTTC 207076
v v
C L1P1_5end#LIN 116 GTGAGATGAACCTGGTACCTCAGTTGGAAATGCAGAAATCACCCGTCTTC 67
INTRON_3 207077 TGTGTCGCTTAACGCTGGGAGCTGTAGACCAGAGCTGTTCCTACTCAGCC 207126
i i - i i i
C L1P1_5end#LIN 66 TGCGTCGCTCA-CGCTGGGAGCTGTAGACCGGAGCTGTTCCTATTCGGCC 18
INTRON_3 207127 ATCTTGGCTCC 207137
C L1P1_5end#LIN 17 ATCTTGGCTCC 7
Matrix = 20p39g.matrix
Transitions / transversions = 1.90 (76 / 40)
Gap_init rate = 0.00 (5 / 2253), avg. gap size = 3.00 (15 / 5)
+ 2291 12.4 0.0 0.0 INTRON_3 207233 207539 (192642) C AluSg SINE/Alu (3) 307 1 259
ANNOTATION EVIDENCE:
2210 12.05 0.65 0.00 INTRON_3 207233 207539 192642 C AluSx SINE/Alu 1 309 3 384
INTRON_3 207233 TTTTTTTTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTCCTACTGTCGC 207282
i viv
C AluSx#SINE/Al 309 TTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGC 260
INTRON_3 207283 CCAGTTTGGAGTGTAGTAGTGCTGTCTCAGCTCACTGCAACCTCCGCCTC 207332
vi i i i vi i
C AluSx#SINE/Al 259 CCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTC 210
INTRON_3 207333 CCGGGATTAAGTGATTTTCCTGCTTCAGCCTCCTGAGTATCTGGGATTAC 207382
v i i i i i v
C AluSx#SINE/Al 209 CCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTAC 160
INTRON_3 207383 AGGTGTGTGCTACCACGCCCAGCTAATTTTTGTATTTTTAGGGGACACAG 207432
i i i i i vi v i
C AluSx#SINE/Al 159 AGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGG 110
INTRON_3 207433 GGTTTCCCCATGTTGGCCAGGCTAGTCTTGAACTTCTGACCTCA--TAAT 207480
v i i i -- i
C AluSx#SINE/Al 109 GGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGAT 60
INTRON_3 207481 CCACCCACCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCG 207530
i i
C AluSx#SINE/Al 59 CCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCG 10
INTRON_3 207531 CACCTGGCC 207539
i i
C AluSx#SINE/Al 9 CGCCCGGCC 1
Matrix = 14p39g.matrix
Transitions / transversions = 3.11 (28 / 9)
Gap_init rate = 0.00 (1 / 306), avg. gap size = 2.00 (2 / 1)
+ 372 24.1 0.0 1.2 INTRON_3 207555 207638 (192543) C MER58B DNA/hAT-Charlie (36) 305 223 260
ANNOTATION EVIDENCE:
372 24.10 0.00 1.20 INTRON_3 207555 207638 192543 C MER58B DNA/hAT-Charlie 223 305 36 477
INTRON_3 207555 AGTAAGTATTTTAGGCTTTATGGGCCATATAATCTCAGTCACAATGACTG 207604
i ii iii v i iv v
C MER58B#DNA/hA 305 AGTAAATATTTTAGGCTTTGCGGGCCATACGGTCTCTGTCGCAACTACTC 256
INTRON_3 207605 AACTCTGTTCTTGTAGCATTAAAAGCTCTCATAG 207638
iiv ii-i vvi
C MER58B#DNA/hA 255 AACTCTGCCGTTGTAGCGC-GAAAGCAGCCATAG 223
Matrix = 20p39g.matrix
Transitions / transversions = 2.33 (14 / 6)
Gap_init rate = 0.01 (1 / 83), avg. gap size = 1.00 (1 / 1)
+22324 13.9 1.6 0.9 INTRON_3 207639 210207 (189974) + L1PA10 LINE/L1 149 2708 (3753) 261
ANNOTATION EVIDENCE:
7781 18.22 2.30 1.78 INTRON_3 207639 209202 190979 + L1P3_5end LINE/L1 149 1720 7 443
INTRON_3 207639 GGAAGAGCAGAAACAGGGTGGGGCGTCACTTCACCTGGGAAGTGCACGGA 207688
iv i i i i i v i
L1P3_5end#LIN 149 GGGCGAGCAGAAGCAGGGTGGGGCGTCGCCTCACCCGGGAAGCGCAAGGG 198
INTRON_3 207689 GTTGGGGGCACCTCCCTTCTCCAGTCAAGGTA-GCAGTGAGGGACTGTGC 207737
ii -- v i i i i v - v
L1P3_5end#LIN 199 GTCAGGG--AACTCCCTCCCCTAGCCAAGGGAAGCCGTGAGGGACTGTGC 246
INTRON_3 207738 TACC----------CA--CTGG---GGGTACTATGCTTTTCCCAAAGATT 207772
i v---------- -- i ---i i vi - i
L1P3_5end#LIN 247 CACGAGGAACGRTGCATTCCGGCCCAGATACTATGCTTTTCCCATGG-TC 295
INTRON_3 207773 TTTGCTATCTGGGGATTAGGAGATTCCCTCGTGAGCCTACACCACCAGGC 207822
i v i iivi ii v v v
L1P3_5end#LIN 296 TTCGCAACCCACAGACCAGGAGATTCCCTCGGGTGCCTACACCACCAGGG 345
INTRON_3 207823 CCCTGGGTCTCAAGCAAAAAACTGGGCAGCTGTTCAGGCAGGCACTGAAC 207872
i v i ii i i i
L1P3_5end#LIN 346 CCCTGGGTTTCAAGCACAAAACTGGGCAGCCGTTTGGGCAGACACCGAGC 395
INTRON_3 207873 T----GCAG--------TTTTTACATACTCCAGTGGCACTTGGAACTCTA 207910
---- -------- v i i i i v i
L1P3_5end#LIN 396 TAGCTGCAGGAGTTTTTTTTTTTCGTACCCCAGTGGCGCCTGGAACGCCA 445
INTRON_3 207911 GTGAGACAGGAGAACAGTCCACTCCTGTGGAAAGGGGGATGAAGCCAGGG 207960
--- v i iv v
L1P3_5end#LIN 446 GTGAGACAG---AACTGTTCACTCCCCTGGAAAGGGGGCTGAAGCCAGGG 492
INTRON_3 207961 AGCCAAGTGGTCTTGCTCAGTGGGTCCCACTCCCATGGAGCCTAGCAAGC 208010
v i i i i
L1P3_5end#LIN 493 AGCCAAGTGGTCTAGCTCAGTGGATCCCACCCCCACGGAGCCCAGCAAGC 542
INTRON_3 208011 TAAGAACCACTGGCTTGAAATTCCCATTGCAAGTACAGAAGTCTGGAGTC 208060
v i ii v i v i
L1P3_5end#LIN 543 TAAGATCCACTGGCTTGAAATTCTCGCTGCCAGCACAGCAGTCTGAAGTC 592
INTRON_3 208061 TGCCTGGGGGGATCGAATTCCCAGGCAGGGGTGATGCAACTACCATTACT 208110
vi iv v ii ivvv -- v iv v ii
L1P3_5end#LIN 593 GACCTGGGATGCTCGAGCTTGGTGG--GGGGAGGGGCATCCGCCATTACT 640
INTRON_3 208111 GTGGCTTTAGTAGGCAGTTTTCCCCTGAGAGGGC---TAAGGAGACTGGG 208157
v v i v v v i---i i vv ii
L1P3_5end#LIN 641 GAGGCTTGAGTAGGCGGTTTTCCCCTCACAGTGTAAACAAAGCCACCAGG 690
INTRON_3 208158 AGGTTTGGACTGGGCAGAATTCTCCACAGTGCAGTAAAGTGGCTGTGGCC 208207
i i i i iii v iv v i ?i i
L1P3_5end#LIN 691 AAGTTCGAACTGGGCGGAGCCCACCACAGCTCCGCAAANCGGCTGTAGCC 740
INTRON_3 208208 AGACTACTTCTCTAGATACCCCCTCACCGGGCAGGGCATCCCTGCAGGAG 208257
i i v i v i i v i i
L1P3_5end#LIN 741 AGACTGCCTCTCTAGATTCCTCCTCTCTGGGCAGGGCATCTCTGAAAGAA 790
INTRON_3 208258 -TCCACCAGCTCCAGTCAGGGGCTTACAGACAGAACTCACATCTCCTTGG 208306
-vv v i i i i v i
L1P3_5end#LIN 791 AGGCAGCAGCCCCAGTCAGGGGCTTATAGATAAAACTCCCATCTCCCTGG 840
INTRON_3 208307 GACAGAGCACCTGGTGGGAGGGGTGGCTGTGGTCCCAGGTTCAGCAGACC 208356
v i i v v v i
L1P3_5end#LIN 841 GACAGAGCACCTGGGGGAAGGGGCGGCTGTGGGCGCAGCTTCAGCAGACT 890
INTRON_3 208357 TGATCTTTCTTGCCTCTTGGCTCTGAAAAGATTGGCTGATTCCGAAGAGG 208406
i v v i viii i vii --------------
L1P3_5end#LIN 891 TAAACGTTCCTGCCTGCCAGCTCTGAAGAGAGCAGC-------------- 926
INTRON_3 208407 GGGATTTCCCCCAGCACAGCACACCAGCTCTGCTAAGGGACAGACTGCCT 208456
- i -- ii v v
L1P3_5end#LIN 927 -GGATCTCCC--AGCACAGTGCTCGAGCTCTGCTAAGGGACAGACTGCCT 973
INTRON_3 208457 CCTCAGGAGGGTCCCTGACCCC-ATGCCTTCTGTCTGGGTGAGACCTCCC 208505
i v -i i v v v
L1P3_5end#LIN 974 CCTCAAGTGGGTCCCTGACCCCTGTGCCTCCTGACTGGGAGACACCTCCC 1023
INTRON_3 208506 AACAGTGGTTGGCAGATGCCTTATATAGGAGAGCTCCAGCTGGCATCAGG 208555
i v? i i ii i i i v
L1P3_5end#LIN 1024 AGCAGGRGTCGACAGACACCTCATACAGGAGAGCTCCGGCTGGCATCTGG 1073
INTRON_3 208556 TCAGTGCCCCTCTGGGATGAAGCTTCCAGAGGAAGGAGCCGGCAGCAATC 208605
vi i i v
L1P3_5end#LIN 1074 TGGGTGCCCCTCTGGGACGAAGCTTCCAGAGGAAGGAACAGGCAGCAATC 1123
INTRON_3 208606 TTTGCTGTTCTGCAATCTTCACTGGTGATACCCTGGCAAACAGGGTCTGG 208655
ii i i ? v
L1P3_5end#LIN 1124 TTTGCTGTTCTGCAGCCTCCGCTGGTGATAYCCAGGCAAACAGGGTCTGG 1173
INTRON_3 208656 AGTGGACCCCCAGCAAGCTGCAGCAGACCTGCAGAAGAGGGTCCTGACTG 208705
i i v v v
L1P3_5end#LIN 1174 AGTGGACCTCCAGCAAACTCCAGCAGACCTGCAGCAGAGGGGCCTGACTG 1223
INTRON_3 208706 TTAGAAGAAAAAGAAACAAATAGAAAGCAAAAACAAAATCAACATCAACA 208755
i vv ii v i ---
L1P3_5end#LIN 1224 TTAGAAGGAAAACTAACAAACGGAAAGCAATAGCA---TCAACATCAACA 1270
INTRON_3 208756 AAAAAGAC--CC-CACAAAAACCCTATCCAAAGGTTGTCAGCCTCAAAGA 208802
i -- - i i i iii i v
L1P3_5end#LIN 1271 AAAAGGACGTCCACACAGAAACCCCATCCGAAGGTCACCAACATCAAAGA 1320
INTRON_3 208803 TCAAAGGTAGATAAATCCAGAAAGATGAGGAAAAACCAATGCAAAAATGC 208852
i vi i v
L1P3_5end#LIN 1321 CCAAAGGTAGATAAATCCACGAAGATGAGGAAAAACCAGTGCAAAAAGGC 1370
INTRON_3 208853 TGAAAATCTCAAAAGCCAGAATGCTTCCTCTCCTCCAAATGATTGTAACT 208902
ii i i i i vi iii
L1P3_5end#LIN 1371 TGAAAATTCCAAAAACCAGAACGCCTCTTCTCCTCCAAAGAATCACAACT 1420
INTRON_3 208903 CGTCTCCAGCAAGGACACAGAATGGGGCTAAAGCTGAGATGGATGAACTG 208952
v v iv i iv i vi iiv v v i i
L1P3_5end#LIN 1421 CCTCGCCAGCAAGGGAACAAAACTGGACGGAGAATGAGTTTGACGAATTG 1470
INTRON_3 208953 ACAGAAGTAGGCTTTAGAAAGTGGGTAATAACAAATTTTATTGAGCTAAA 209002
i i i iivii
L1P3_5end#LIN 1471 ACAGAAGTAGGCTTCAGAAGGTGGGTAATAACAAACTCCTCCGAGCTAAA 1520
INTRON_3 209003 GGATTATATTCTAACCCAATGCAAAGAAGCTAAGAACCATGATAAAAGAT 209052
vi i i v v i
L1P3_5end#LIN 1521 GGAGCATGTTCTAACCCAATGCAAGGAAGCTAAGAACCTTGAAAAAAGGT 1570
INTRON_3 209053 TACAGGAGCTGTTAACTAGAATAACCAGTCTAGAGAGGAACATAAGCAAC 209102
v ii i i i iii
L1P3_5end#LIN 1571 TAGAGGAATTGCTAACTAGAATAACCAGTTTAGAGAAGAACATAAATGAC 1620
INTRON_3 209103 CTGATGGAGCTGAAAAACACAACACGAGAACTTTGTGATGCAAATAGAAG 209152
i i i v v i v
L1P3_5end#LIN 1621 CTGATGGAGCTGAAAAACACAGCATGAGAACTTCGTGAAGCATACACAAG 1670
INTRON_3 209153 TATCAATAGCCAGATCAACCAAGCAGAAGAGAGAATATCAGAGCTTGAAG 209202
ii i i i i v
L1P3_5end#LIN 1671 TATCAATAGCCGAATCGATCAAGCAGAAGAAAGGATATCAGAGATTGAAG 1720
Matrix = 20p39g.matrix
Transitions / transversions = 1.95 (183 / 94)
Gap_init rate = 0.01 (18 / 1563), avg. gap size = 3.56 (64 / 18)
11045 13.33 1.43 0.66 INTRON_3 208260 210072 190109 + L1PA10_5end LINE/L1 618 2444 0 444
INTRON_3 208260 CACCAGCTCCAGTCAGGGGCTTACAGACAGAACTCACATCTCCTTGGGAC 208309
v i i i vi vv i
L1PA10_5end#L 618 CAGCAACTCCAGCCAGGGGTTTAGGGACAGAACTCTGATCTCCCTGGGAC 667
INTRON_3 208310 AGAGCACCTGGTGGGAGGGGTGGCTGTGGTC-CCA-GGTTCAGCAGACCT 208357
v v v i i i - i- v i
L1PA10_5end#L 668 TGAGCCCCTGGGGGGAGGGGCGGCCGCGGTCTCCGCGGATCAGCAGACTT 717
INTRON_3 208358 GATCTTTCTTGCCTCTTGGCTCTGAAAAGATTGGCTGATTCCGAAGAGGG 208407
ii ii- vi ii ivii viii i v v v
L1PA10_5end#L 718 AGTCTTTCCC-CCTGCTGGCTCTGAGGAATCCGGGCAGTCCGGACGAGTG 766
INTRON_3 208408 GGATTTCCCCCAGCACAGCACACCAGCTCTGCTAAGGGACAGAC----TG 208453
i i i vv i i i v ----
L1PA10_5end#L 767 GGATTCCCCCCAGCGCAGCGCACCCCCTCCGCCAAGGGGCAGCCAGAGTG 816
INTRON_3 208454 CCTCCTCAGGAGGGTCCCTGACCCCATGCCTTCTGTCTGGGTGAGACCTC 208503
i v i i v ? i i i v i
L1PA10_5end#L 817 CTTCGTTAAGCGGGTCCCNGATCCCGTGCCTCCTGACTGGGTGAGACCCC 866
INTRON_3 208504 CCAACAGTGGTTGGCAGATGCCTTATATAGGAGAGCTCCAGCTGGCATCA 208553
v i v ii i v i v
L1PA10_5end#L 867 CCAACAGGGGTCGCCAGACACCTTATACAGGAGCGTTCCCGCTGGCATCA 916
INTRON_3 208554 GGTCAGTGCCCCTCTGGGATGAAGCTTCCAGAGGAAGGAGCCGGCAGCAA 208603
i i i v i v v
L1PA10_5end#L 917 GGTCGGTGCCCCTCTGGGACGGAGATCCCAGAGGAAGGAGCAGGCAGCCA 966
INTRON_3 208604 TCTTTGCTGTTCTGCAATCTTCACTGGTGATACC---------------- 208637
ii i i ----------------
L1PA10_5end#L 967 TCTTTGCTGTTCTGCAGCCTCCACTGGTGACACCTCCAGGTGCGGGAGGG 1016
INTRON_3 208638 ---CTGGCAAACAGGGTCTGGAGTGGACCCCCAGCAAGCTGCAGCAGACC 208684
--- v i i i i v
L1PA10_5end#L 1017 ACCCAGGCGAATAGGGTCTGGAGTGGACCCCCAGCAAACCGCAGCAGCCC 1066
INTRON_3 208685 TGCAGAAGAGGGTCCTGACTGTTAGAAGAAAAAGAAACAAATAGAAAGCA 208734
i i v i v i
L1PA10_5end#L 1067 TACGGAAGAGGGGCCTGACTGTTAAAAGAAAAACAAACAAACAGAAAGCA 1116
INTRON_3 208735 AAAACAAAATCAACATCAACAAAAAAGACCCCACAAAAACCCTATCCAAA 208784
v --- i v i
L1PA10_5end#L 1117 ACAACAA---CAGCATCAACAAAAAAGTCCCCACAAAAACCCCATCCAAA 1163
INTRON_3 208785 GGTTGTCAGCCTCAAAGATCAAAGGTAGATAAATCCAGAAAGATGAGGAA 208834
iiv i v ii vi i
L1PA10_5end#L 1164 GGTCAGCAGCCTCAAAGATCGAAGCTAGATAAACTCACGAAGATGAGAAA 1213
INTRON_3 208835 AAACCAATGCAAAAATGCTGAAAATCTCAAAAGCCAGAATGCTTCCTCTC 208884
i i i v i iiiv i i i
L1PA10_5end#L 1214 GAATCAACGAAAAAACGCTGAAAACTCAAAAAGCCAGAGTGCCTCTTCTC 1263
INTRON_3 208885 CTCCAAATGATTGTAACTCGTCTCCAGCAAGGACACAGAATGGGGCTAAA 208934
i i v v i iv vi i
L1PA10_5end#L 1264 CTCCAAATGATCGCAACACCTCTCCAGCAAGGGCACAGAACTGGGCGGAG 1313
INTRON_3 208935 GCTGAGATGGATGAACTGACAGAAGTAGGCTTTAGAAAGTGGGTAATAAC 208984
i i i
L1PA10_5end#L 1314 GCTGAGATGGATGAATTGACAGAAGTAGGCTTCAGAAGGTGGGTAATAAC 1363
INTRON_3 208985 AAATTTTATTGAGCTAAAGGATTATATTCTAACCCAATGCAAAGAAGCTA 209034
i i iii vi i
L1PA10_5end#L 1364 GAACTTCGCTGAGCTAAAGGAGCATGTTCTAACCCAATGCAAAGAAGCTA 1413
INTRON_3 209035 AGAACCATGATAAAAGATTACAGGAGCTGTTAACTAGAATAACCAGTCTA 209084
v i i
L1PA10_5end#L 1414 AGAACCATGATAAAACATTACAGGAGCTGTTAACCAGAATAACCAGTTTA 1463
INTRON_3 209085 GAGAGGAACATAAGCAACCTGATGGAGCTGAAAAACACAACACGAGAACT 209134
iii
L1PA10_5end#L 1464 GAGAGGAACATAAATGACCTGATGGAGCTGAAAAACACAACACGAGAACT 1513
INTRON_3 209135 TTGTGATGCAAATAGAAGTATCAATAGCCAGATCAACCAAGCAGAAGAGA 209184
iiii vi v ii vi i i i
L1PA10_5end#L 1514 TCACAATGCAACCACAAGTATCAATAGCCGAATAGACCAAGCGGAGGAAA 1563
INTRON_3 209185 GAATATCAGAGCTTGAAGGCTATCTTGCTGAAATAAGGCAGGCAGACAAG 209234
v i i
L1PA10_5end#L 1564 GAATTTCAGAGCTTGAAGACTATCTTGCTGAAATAAGACAGGCAGACAAG 1613
INTRON_3 209235 ATTAGAGAATAAACAATGAAAAGGAACAAACAAAACCTTTGAGAATTATG 209284
v v ii ii i
L1PA10_5end#L 1614 ATTAGAGAAAAAAGAATGAAAAGGAATGAACAAAACCTCCGAGAACTATG 1663
INTRON_3 209285 GGACTGTGTAAAAAGACCAAACCTGTGACTG-TTTGGATACCTGAAAGAG 209333
i i i i - v i
L1PA10_5end#L 1664 GGATTATGTAAAAAGACCGAACCTATGACTGATTGGGGTACCTGAAAGAG 1713
INTRON_3 209334 ATGGGGAGAATGGAACCAAGTTGTAAAACACCCTTCAGGATATCATCCAG 209383
i v iv
L1PA10_5end#L 1714 ACGGGGAGAATGGAACCAAGTTGGAAAACATACTTCAGGATATCATCCAG 1763
INTRON_3 209384 GGCAACTTCCACTTCCCCAACCTAGCAAGACAGGCCAATATTCAAATTCA 209433
iv ------ i
L1PA10_5end#L 1764 GAGAACTTCC------CCAACCTAGCAAGACAGGCCAACATTCAAATTCA 1807
INTRON_3 209434 GGAAATCCAAAGAACCCCAATAAGATACTCCACAAAAAGATCTGCCCCAA 209483
i i ii i vi
L1PA10_5end#L 1808 GGAAATCCAGAGAACCCCAGTAAGATACTCCATGAGAAGATCAACCCCAA 1857
INTRON_3 209484 GGCACATAATCATCAGATTCTCCAAGGTCAAAATGAAGGAAAAAATGTTA 209533
i i
L1PA10_5end#L 1858 GACACATAATCATCAGATTCTCCAAGGTCGAAATGAAGGAAAAAATGTTA 1907
INTRON_3 209534 AGGGCACTAAGAGAGAAAGGCCAGGTCACCTACAAAGGGAAGCCCATGAC 209583
viv v v
L1PA10_5end#L 1908 AGGGCAGCCAGAGAGAAAGGCCAGGTCACCTACAAAGGGAAGCCCATCAG 1957
INTRON_3 209584 ACTAACAGTGGACCTCTGAGCAGAAACTCTGCAAGCCAGAAGAAATTGGG 209633
i v i i i
L1PA10_5end#L 1958 ACTAACAGCGGACCTCTCAGCAGAAACCCTACAAGCCAGAAGAGATTGGG 2007
INTRON_3 209634 GGCCAATGTTCAACATTGTTAAAAAAGAGAAATTCCAACCCAGAATTTCA 209683
i v i i v
L1PA10_5end#L 2008 GGCCAATATTCAACATTCTTAAAGAAAAGAATTTCCAACCCAGAATTTCA 2057
INTRON_3 209684 TATCTGGCCAAACTAAGTTTCATAAGCAGAAGAGAAATAACATCTTTTTC 209733
i i ii i v i
L1PA10_5end#L 2058 TATCCGGCCAAACTAAGCTTCATAAGCGAAGGAGAAATAAAATCCTTTTC 2107
INTRON_3 209734 AGACAAGCAAATGCTGAAGGATTTTTGTCACCACCAGGCCTGCCTGGCAA 209783
i v i- v
L1PA10_5end#L 2108 AGACAAGCAAATGCTGAGGGAATTC-GTCACCACCAGGCCTGCCTTGCAA 2156
INTRON_3 209784 GAGCTCCTGAAAGAAGCACTAAACATGGATAAGAAAAACCATTACTAGCC 209833
i i v i i i
L1PA10_5end#L 2157 GAGCTCCTGAAGGAAGCACTAAATATGGAAAGGAAAAACCGTTACCAGCC 2206
INTRON_3 209834 ACTACAAAAACACACTGAAGTACACAGACCAATGACACTATGAAGGAACT 209883
i v v
L1PA10_5end#L 2207 ACTGCAAAAACACACTGAAGTACAAAGACCAATGACACTATGAAGCAACT 2256
INTRON_3 209884 ACATTAACAAGTCTGCAAAATTAACCAGCCAGCATCATGATGATGGGATC 209933
i - i ii
L1PA10_5end#L 2257 ACATCAACAAGTCTGCAAAAT-AACCAGCTAGCATCATGATGACAGGATC 2305
INTRON_3 209934 AAATTCACACATAACAATATTAACCTTAAATGTAAATGGGCAAAATGCCC 209983
v
L1PA10_5end#L 2306 AAATTCACACATAACAATATTAACCTTAAATGTAAATGGGCTAAATGCCC 2355
INTRON_3 209984 TGATTAAAAGACACAGAATGGCAAGCTGGATACAAAGAGAAGACCTGTTG 210033
ii v i vv ii i
L1PA10_5end#L 2356 CAATTAAAAGACACAGAATGGCAAGCTGGATAAAGAGTCAAGACCCATCG 2405
INTRON_3 210034 GTGTGCTGTATTCAAGAGACACATCTCATGTGCAAAGAC 210072
v i
L1PA10_5end#L 2406 GTGTGCTGTATTCAAGAGACCCATCTCACGTGCAAAGAC 2444
Matrix = 20p39g.matrix
Transitions / transversions = 2.27 (166 / 73)
Gap_init rate = 0.01 (10 / 1812), avg. gap size = 3.80 (38 / 10)
22324 8.43 0.94 0.67 INTRON_3 209923 210207 189974 + L1P3_orf2 LINE/L1 1 284 3010 445
INTRON_3 209923 ATGATGGGATCAAATTCACACATAACAATATTAACCTTAAATGTAAATGG 209972
ii
L1P3_orf2#LIN 1 ATGACAGGATCAAATTCACACATAACAATATTAACCTTAAATGTAAATGG 50
INTRON_3 209973 GCAAAATGCCCTGATTAAAAGACACAGAATGGCAAGCTGGATACAAAGAG 210022
v ii v i vv
L1P3_orf2#LIN 51 GCTAAATGCCCCAATTAAAAGACACAGAATGGCAAGCTGGATAAAGAGTC 100
INTRON_3 210023 AAGACCTGTTGGTGTGCTGTATTCAAGAGACACATCTCATGTGCAAAGAC 210072
ii i v i
L1P3_orf2#LIN 101 AAGACCCATCGGTGTGCTGTATTCAAGAGACCCATCTCACGTGCAAAGAC 150
INTRON_3 210073 GCACATAGACTCATAAGAAAGGGATGGAGGAAAATTTACCAAGCATATGG 210122
i i v v v
L1P3_orf2#LIN 151 ACACATAGGCTCAAAATAAAGGGATGGAGGAAAATTTACCAAGCAAATGG 200
INTRON_3 210123 AAAGCAGAAAAAAGCAGGGGTTGCAGTCATAGTTTCTGACAAAACAGACT 210172
i v
L1P3_orf2#LIN 201 AAAGCAGAAAAAAGCAGGGGTTGCAATCCTAGTTTCTGACAAAACAGACT 250
INTRON_3 210173 TTCAACCAACAAAGATAAAAAAAGACGAAGAAGGT 210207
v v i -
L1P3_orf2#LIN 251 TTAAACCAACAAAGATCAAAAAAGACAAAGAAGG- 284
Matrix = 20p39g.matrix
Transitions / transversions = 1.18 (13 / 11)
Gap_init rate = 0.00 (1 / 284), avg. gap size = 1.00 (1 / 1)
+ 2489 8.7 0.0 0.3 INTRON_3 210208 210516 (189665) + AluY SINE/Alu 2 309 (2) 262
ANNOTATION EVIDENCE:
2430 8.77 0.00 0.32 INTRON_3 210208 210516 189665 + AluY SINE/Alu 2 309 2 385
INTRON_3 210208 GCCAGGCTCACTGGCTCAAGCCTGTAATCTCAGCACTTTGGGAGGCCGAG 210257
i v iv v i
AluY#SINE/Alu 2 GCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG 51
INTRON_3 210258 GTGGGCAGATCACAAGGTCAGGAGATTGAGACCATCCTGGCTAACACAGT 210307
i i i i i
AluY#SINE/Alu 52 GCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGT 101
INTRON_3 210308 GAAACTCCGTCTCTACTAAAAATACAAAAACATTAGCCGGGTGTGGTGGT 210357
i - i i
AluY#SINE/Alu 102 GAAACCCCGTCTCTACTAAAAATACAAAAA-ATTAGCCGGGCGTGGTGGC 150
INTRON_3 210358 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 210407
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
INTRON_3 210408 GAACCCAGGAGGCGGAGCTTGCAGTGAGCCGAGATCACACTGTTGCACTC 210457
i i i iii
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
INTRON_3 210458 CAGCCTGGGCAAAAGAGCAAGACTCCATCTCAAAAAAAAAAAGAAAAGAA 210507
i v i i i i
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
INTRON_3 210508 AAAGAAAAA 210516
i
AluY#SINE/Alu 301 AAAAAAAAA 309
Matrix = 14p39g.matrix
Transitions / transversions = 5.75 (23 / 4)
Gap_init rate = 0.00 (1 / 308), avg. gap size = 1.00 (1 / 1)
+22324 8.5 1.3 0.5 INTRON_3 210517 214242 (185939) + L1PA10 LINE/L1 2709 6465 (18) 261
ANNOTATION EVIDENCE:
22324 8.43 0.94 0.67 INTRON_3 210517 213515 186666 + L1P3_orf2 LINE/L1 285 3294 0 446
INTRON_3 210517 GGCAATGAAGGGCATTACATAATGTTAAAGTGTTCAATTCAACACGAAGA 210566
----------- v v ? v
L1P3_orf2#LIN 285 -----------GCATTACATAATGGTAAAGGGNTCAATTCAACAAGAAGA 323
INTRON_3 210567 GCTAACTACCCTAAATATATATGCACCCAATACAGGAGCCCCCAGATTCA 210616
i v
L1P3_orf2#LIN 324 GCTAACTATCCTAAATATATATGCACCCAATACAGGAGCACCCAGATTCA 373
INTRON_3 210617 TAAAACAAGTTCTTAGAGACCTATTAAGAGACTTAGACCCCCACACAATA 210666
iv i
L1P3_orf2#LIN 374 TAAAACAAGTTCTTAGAGACCTACAAAGAGACTTAGACTCCCACACAATA 423
INTRON_3 210667 ATAGTCAGAGACTTTAATACCCCACTGGCAGTGTTAGACAGATCATTGAG 210716
vi i v i i i
L1P3_orf2#LIN 424 ATAGTGGGAGACTTTAACACCCCACTGTCAATATTAGACAGATCATCGAG 473
INTRON_3 210717 ACAGAAAATTAACAAAGATATCCAGGACTTGAACTCAGCTCTAAATCAAG 210766
i i ii
L1P3_orf2#LIN 474 ACAGAAAATTAACAAGGATATTCAGGACTTGAACTCAGCTCTGGATCAAG 523
INTRON_3 210767 TGGACCTGATAGATATCTATAGAACGCTCCACTCAAAAACAACAGAATAT 210816
i v i v
L1P3_orf2#LIN 524 TGGACCTGATAGATATCTACAGAACTCTCCACCCCAAAACAACAGAATAT 573
INTRON_3 210817 ACATTTCTTTTTGGTGCCACATGGCACTTATTCTAAAATTGATCACATAA 210866
- i i i i i
L1P3_orf2#LIN 574 ACATT-CTTCTCGGCGCCACATGGCACTTACTCTAAAATCGATCACATAA 622
INTRON_3 210867 TTGGAAGTAAAACACTCCTCAGCAAA------GGAACTGAAATCATAA-- 210908
------i --
L1P3_orf2#LIN 623 TTGGAAGTAAAACACTCCTCAGCAAATGCAAAAGAACTGAAATCATAACA 672
INTRON_3 210909 ----GTCTCTCAGACCACAGTGCAGTCAAATTAAAACTCAAGATTAAAAA 210954
---- i i i i
L1P3_orf2#LIN 673 AACAGTCTCTCAGACCACAGCGCAATCAAATTAGAACTCAAGATTAAGAA 722
INTRON_3 210955 GCCCACTCAAAACCACACCACTACATGGAAATTGAACAACCTGCTCCTGA 211004
i i v
L1P3_orf2#LIN 723 ACTCACTCAAAACCACACAACTACATGGAAATTGAACAACCTGCTCCTGA 772
INTRON_3 211005 ATGACTCTGGGGTAAATAATGAAATTAAGGCAGAAATCAAGAAGTTCTTT 211054
iv
L1P3_orf2#LIN 773 ATGACTCCTGGGTAAATAATGAAATTAAGGCAGAAATCAAGAAGTTCTTT 822
INTRON_3 211055 GAAACCAACTAGAACAAAGAGACAACATATCAGAATCTCTGGTACACAGC 211104
iv i i v i
L1P3_orf2#LIN 823 GAAACCAATGAGAACAAAGAGACAACGTACCAGAATCTCTGGGACGCAGC 872
INTRON_3 211105 TAAAGCAGTGTTAAGAGGGAAATCTATAGTACTAAATACTCACATCAAAA 211154
i i i i
L1P3_orf2#LIN 873 TAAAGCAGTGTTAAGAGGGAAATTTATAGCACTAAATGCCCACATCAAAA 922
INTRON_3 211155 AGCTAGAAAGATCTCAAATCAACACCTTAACATCACAACTAAAATAACTA 211204
i i v
L1P3_orf2#LIN 923 AGCTAGAAAGATCTCAAATCGACACCCTAACATCACAACTAAAAGAACTA 972
INTRON_3 211205 GAGAACCAAGAGCAAACAAACCCTAGAGCTAGCAGAAGACAGGAAATAAC 211254
i i i
L1P3_orf2#LIN 973 GAGAACCAAGAGCAAACAAACCCCAAAGCTAGCAGAAGACAAGAAATAAC 1022
INTRON_3 211255 CAAACTCGG-------------GAGATAGAGACCTGAAAAACACTTCGAA 211291
iv i ------------- vi v i
L1P3_orf2#LIN 1023 CAAGATCAGAGCGGAACTGAAGGAGATAGAGACACGAAAAACCCTTCAAA 1072
INTRON_3 211292 AAATCAACAAATCCAGGAGCTGTGTTTTTGAAAAAATCAATAAAATAGAT 211341
ii vv i
L1P3_orf2#LIN 1073 AAATCAATGAATCCAGGAGCTGGTTTTTTGAAAAAATTAATAAAATAGAT 1122
INTRON_3 211342 AGACTGTTAGCAAGACTAATAGAGAAGAAAAGAGAGGAGATTCAAATAAA 211391
i i v i i v i
L1P3_orf2#LIN 1123 AGACCGCTAGCTAGACTAATAAAGAAGAAAAGAGAGAAGAATCAAATAGA 1172
INTRON_3 211392 CACAATCAGAAATAATAAGGGGGATACCATCACTGACCCTAGAGAAATAC 211441
v i i i i i i v
L1P3_orf2#LIN 1173 CACAATAAAAAATGATAAAGGGGATATCACCACTGACCCCACAGAAATAC 1222
INTRON_3 211442 AAACAACCATCAGAGAATACTATAAACACCTCTTTAAAAACAAACTAGAA 211491
v iv i
L1P3_orf2#LIN 1223 AAACAACCATCAGAGAATACTATAAACACCTCTATGCAAATAAACTAGAA 1272
INTRON_3 211492 AATCTAGAAGAAATGCATAAATTCCTGGACACATACACCCTCCCAAGACT 211541
v
L1P3_orf2#LIN 1273 AATCTAGAAGAAATGGATAAATTCCTGGACACATACACCCTCCCAAGACT 1322
INTRON_3 211542 GCACCAGAAAGAAGTTGAATTCCTGAACAGACCAATAACAAGTTGTGAAA 211591
v i i i v
L1P3_orf2#LIN 1323 GAACCAGGAAGAAGTTGAATCCCTGAATAGACCAATAACAAGTTCTGAAA 1372
INTRON_3 211592 TTAAGGCAGTAATAAATAGCCTACCAGCCAAAAAAAAAAAAAAGCCCAGC 211641
i i ------- v
L1P3_orf2#LIN 1373 TTGAGGCAGTAATAAATAGCCTACCAACCAAAAAAA-------GCCCAGG 1415
INTRON_3 211642 TCCAGATGGAGTTACAGCTGAATTCTACCAGAGGTACAACGAGGAGCTGG 211691
v i v v
L1P3_orf2#LIN 1416 ACCAGACGGATTTACAGCTGAATTCTACCAGAGGTACAAAGAGGAGCTGG 1465
INTRON_3 211692 TACCATTTCTTCTGAAACTATTCCAAACAATTGTGAAGGAGGGACTCCCC 211741
vi i
L1P3_orf2#LIN 1466 TACCATTTCTTCTGAAACTATTCCAAACAATTGAAAAGGAGGGACTCCTC 1515
INTRON_3 211742 TCTAACTCATTTTATGAGGCCAGCATCATCCTGATTCCAAAACCTGGCAG 211791
i v
L1P3_orf2#LIN 1516 CCTAACTCATTTTATGAGGCCAGCATCATCCTGATACCAAAACCTGGCAG 1565
INTRON_3 211792 AGATATAACAAAAAAAGAAAACTTTAGGCCAATATCCTTGATGAACATCT 211841
i i i v
L1P3_orf2#LIN 1566 AGATACAACAAAAAAAGAAAACTTCAGGCCAATATCCCTGATGAACATCG 1615
INTRON_3 211842 GTGCAAAAATCCTCAATAAAATACTGGCAAACAAAATCCAGCAACACATC 211891
i vi i
L1P3_orf2#LIN 1616 ATGCAAAAATCCTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATC 1665
INTRON_3 211892 AAAAAGTTTATCCACCATGATCAGGTCGGTTTTATCCCCAGAATGCAAGG 211941
i i i i i i i
L1P3_orf2#LIN 1666 AAAAAGCTTATCCACCACGATCAAGTCGGCTTCATCCCCGGGATGCAAGG 1715
INTRON_3 211942 CTGGTTCAATATATGCAAATCAATAAATGTAATTCATCACATAAACAGAA 211991
i i i
L1P3_orf2#LIN 1716 CTGGTTCAACATACGCAAATCAATAAACGTAATTCATCACATAAACAGAA 1765
INTRON_3 211992 CTAAAGACAAAAACCATATGATTATTCCAATAGATTCAGAAAAGGCCTTC 212041
i ii iv
L1P3_orf2#LIN 1766 CTAAAGACAAAAACCACATGATTATCTCAATAGACGCAGAAAAGGCCTTC 1815
INTRON_3 212042 AGTAAAATTCAACATACCTTCATGTTAAAAACTCTCAATAAACTAGATAT 212091
ii v i
L1P3_orf2#LIN 1816 GATAAAATTCAACATCCCTTCATGTTAAAAACTCTCAATAAACTAGGTAT 1865
INTRON_3 212092 TGAAGAAACATACCTCAAAATAATAAGAACCATTTATGACAAGCCCACAG 212141
? i i i
L1P3_orf2#LIN 1866 TGANGGAACATACCTCAAAATAATAAGAGCCATTTATGACAAACCCACAG 1915
INTRON_3 212142 CCAATATCATACTAAATGGGCAAAAGCTGGAGGCATTCCCTTTGAAAAGT 212191
i i i vi
L1P3_orf2#LIN 1916 CCAATATCATACTGAATGGGCAAAAGCTGGAAGCATTCCCCTTGAAAACC 1965
INTRON_3 212192 GGCACAAGACAAGGATGCCCTCTCTCACCACTCCTTTTCAACCAAGTGCT 212241
v vv ii
L1P3_orf2#LIN 1966 GGCACAAGACAAGGATGCCCTCTCTCACCACTCCTATTCAACATAGTATT 2015
INTRON_3 212242 GGAAGTTCTGGCCAGTGCAATTAGGCAAGAGAAATAAATAAAGGAAATTT 212291
v i v iv -
L1P3_orf2#LIN 2016 GGAAGTTCTGGCCAGGGCAATCAGGCAAGAGAAAGAAATAAAGGGTATT- 2064
INTRON_3 212292 CAAATAGGAAGAGAGGAAGTCAAATTGTCTTTGTTTGCCAATGACATGAT 212341
i vi
L1P3_orf2#LIN 2065 CAAATAGGAAGAGAGGAAGTCAAATTGTCTCTGTTTGCAGATGACATGAT 2114
INTRON_3 212342 CCTGTATCTAGAAAACCCCATCATCTCAGCCCAAAAGGTTCTTAAGCTGA 212391
i i v
L1P3_orf2#LIN 2115 CCTATATCTAGAAAACCCCATCGTCTCAGCCCAAAAGCTTCTTAAGCTGA 2164
INTRON_3 212392 TATGCAACTTTAGCAAAGTCTCAGGATATAAAATCAATGTGCAGAAATCA 212441
v i i i
L1P3_orf2#LIN 2165 TAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTGCAAAAATCA 2214
INTRON_3 212442 CAAGCATTCCTATACACCAACAACAGACAAGCAGAAATCAAAATCGTGAA 212491
i v v i
L1P3_orf2#LIN 2215 CAAGCATTCCTATACACCAACAACAGACAAGCAGAGAGCCAAATCATGAA 2264
INTRON_3 212492 TGAACTCCCATTCACAATTGTGACAAAGAGAATAAAATACCTAGGAATAC 212541
iv
L1P3_orf2#LIN 2265 TGAACTCCCATTCACAATTGCTACAAAGAGAATAAAATACCTAGGAATAC 2314
INTRON_3 212542 AGCTAATGAGGGTAGTGAAGGACCTCTTCAAGGAGAACTACAAACCACTG 212591
ii v
L1P3_orf2#LIN 2315 AGCTAACAAGGGAAGTGAAGGACCTCTTCAAGGAGAACTACAAACCACTG 2364
INTRON_3 212592 CTCAAGCAAATCAGAGAGGACACAGGCAGATAGAAAAACATTCCGTGCTC 212641
v ii i i i
L1P3_orf2#LIN 2365 CTCAAGGAAATCAGAGAGGACACAAACAAATGGAAAAACATTCCATGCTC 2414
INTRON_3 212642 CTGGATAGGAAGAATCAATATTGTGAAAATGGACATACTGTCCAAAGCAA 212691
v i v i i
L1P3_orf2#LIN 2415 ATGGATAGGAAGAATCAATATCGTGAAAATGGCCATACTGCCCAAAGTAA 2464
INTRON_3 212692 CTTATAGATTCAGTGCAATTCCCATTAAGCTACCATTGACATTCTTCACA 212741
i i v i
L1P3_orf2#LIN 2465 TTTATAGATTCAATGCTATTCCCATTAAACTACCATTGACATTCTTCACA 2514
INTRON_3 212742 GAATTAGAAAAAACT--TTTAAAATTTATATGGAACCAAAAAAGAGCTTG 212789
-- i ii
L1P3_orf2#LIN 2515 GAATTAGAAAAAACTACTTTAAAATTCATATGGAACCAAAAAAGAGCCCG 2564
INTRON_3 212790 CATAGCCAAGACAACCCTAAGTAAAAAGAACAAAGCCAGAGGCATCATGC 212839
i i i ii i
L1P3_orf2#LIN 2565 TATAGCCAAGACAATCCTAAGCAAAAAGAACAAAGCTGGAGGCATCACGC 2614
INTRON_3 212840 TACCCAACTTCAAACTGTACTACAAGGCCATAGTAACCAAAATAGCATGG 212889
i i i i i
L1P3_orf2#LIN 2615 TACCCGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGG 2664
INTRON_3 212890 TACTGGTACAAAAACAGGCACATAGACAAATGGAACAGAATAGAGAACTT 212939
i v ? i
L1P3_orf2#LIN 2665 TACTGGTACAAAAACAGACACATAGACCAATGGAACAGAATAGAGANCTC 2714
INTRON_3 212940 AGAAATAAAACTGCCCATCTACAGCTATCTGATCTTTGACAGACCTGACA 212989
i i v i i i i
L1P3_orf2#LIN 2715 AGAAATAAGACCGCACATCTACAACCATCTGATCTTCGACAAACCTGACA 2764
INTRON_3 212990 AAAACATGCAATGGGGAAAAGATGCCCTATTTAATAAATGGTGCTAGGAG 213039
v i v i
L1P3_orf2#LIN 2765 AAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAG 2814
INTRON_3 213040 AACTGGCTAGTTATATGCAGAAAATTGAAATGGGATCTCTTCCTTACACC 213089
ii iv i i
L1P3_orf2#LIN 2815 AACTGGCTAGCCATATGCAGAAAATTGAAACTGGACCCCTTCCTTACACC 2864
INTRON_3 213090 TTTTACAAAAATTAACTCAAGATGGATTAAAGACTTAAATGTAAAACCGA 213139
v v
L1P3_orf2#LIN 2865 TTATACAAAAATTAACTCAAGATGGATTAAAGACTTAAATGTAAAACCCA 2914
INTRON_3 213140 AAACCATAAAAACCCTAGAAGAAAATCTAGGCAATACCATTCAGGACATA 213189
i
L1P3_orf2#LIN 2915 AAACTATAAAAACCCTAGAAGAAAATCTAGGCAATACCATTCAGGACATA 2964
INTRON_3 213190 GGCATGGGCAAAGACTTTATGAAGAAATCTCCAAAAGCAATTGCAACAAA 213239
i i i v v v
L1P3_orf2#LIN 2965 GGCACGGGCAAAGATTTCATGATGAAAACGCCAAAAGCAATTGCAACAAA 3014
INTRON_3 213240 AACAAAAATTGACAAATGGGATCTAATTAAACTAAGGAGCTTCTTCACAG 213289
i i v
L1P3_orf2#LIN 3015 AGCAAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAG 3064
INTRON_3 213290 CAAATGAAACTATCATCAGAGTGAACAGATAACCTATGGAATGGGAGGAA 213339
v i ii i
L1P3_orf2#LIN 3065 CAAAAGAAACTATCATCAGAGTGAACAGACAACCTACAGAATGGGAGAAA 3114
INTRON_3 213340 ATTTTTGCAATCTATCCATCTGACAAAGGGCTAATATCCAGAATCTACAA 213389
v
L1P3_orf2#LIN 3115 ATTTTTGCAATCTATCCATCTGACAAAGGTCTAATATCCAGAATCTACAA 3164
INTRON_3 213390 GGAACTTATGCAAATTTACAAGCAAAAAACAA----CCCCATCAAAAAGT 213435
vi v ---- i
L1P3_orf2#LIN 3165 GGAACTTAAACAAATTTACAAGAAAAAAACAAACAACCCCATTAAAAAGT 3214
INTRON_3 213436 AGGCAAAGTGTATGAACAGACACTTCTCAAAAAAAGACATACATGCAGCC 213485
i vii i vi i
L1P3_orf2#LIN 3215 GGGCAAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCGGCC 3264
INTRON_3 213486 AACAAACACATGAAAAACAGCTCAACATCA 213515
i v
L1P3_orf2#LIN 3265 AACAAACATATGAAAAAAAGCTCAACATCA 3294
Matrix = 20p39g.matrix
Transitions / transversions = 2.35 (174 / 74)
Gap_init rate = 0.00 (9 / 2998), avg. gap size = 5.67 (51 / 9)
5997 8.71 2.75 0.00 INTRON_3 213370 214242 185939 + L1PA10_3end LINE/L1 1 897 18 447
INTRON_3 213370 CTAATATCCAGAATCTACAAGGAACTTATGCAAATTTACAAGCAAAAAAC 213419
vi v
L1PA10_3end#L 1 CTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAAAAC 50
INTRON_3 213420 AA----CCCCATCAAAAAGTAGGCAAAGTGTATGAACAGACACTTCTCAA 213465
---- i v i vii
L1PA10_3end#L 51 AAACAACCCCATTAAAATGTGGGCAAAGGACATGAACAGACACTTCTCAA 100
INTRON_3 213466 AAAAAGACATACATGCAGCCAACAAACACATGAAAAACAGCTCAACATCA 213515
i v i i i v
L1PA10_3end#L 101 AAGAAGACATTCATGCGGCCAACAAACATACGAAAAAAAGCTCAACATCA 150
INTRON_3 213516 C--------AGAGAAAT------CAAAACCACAGTGAGATACCATCTCAG 213551
-------- ------ i v
L1PA10_3end#L 151 CTGATCATTAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCAC 200
INTRON_3 213552 GCCAGCCAGAATGGCGATTGTTAAAAAGTTAGGAAACAACAGATGCTGGT 213601
i ? i i i i
L1PA10_3end#L 201 GCCAGTCAGAATGGCNATTATTAAAAAGTCAAGAAACAACAGATGCTGGC 250
INTRON_3 213602 GACATTGTGGAGAAATAGGAACGCTTGTACACTGTTGGTGGGAATGTAAA 213651
vi v
L1PA10_3end#L 251 GAGGTTGTGGAGAAATAGGAACGCTTTTACACTGTTGGTGGGAATGTAAA 300
INTRON_3 213652 TTAGTTCAGCCATTGTGGAAGACAGTGTGGTAACTCCTCAAAGATTTAGA 213701
i ii i i
L1PA10_3end#L 301 TTAGTTCAACCATTGTGGAAGACAGTGTGGCGATTCCTCAAAGATCTAGA 350
INTRON_3 213702 ACCAGAAATATCATTTGACCCAGCAATCCCATTACTGGGTATATACCCAA 213751
i
L1PA10_3end#L 351 ACCAGAAATACCATTTGACCCAGCAATCCCATTACTGGGTATATACCCAA 400
INTRON_3 213752 AGGAATATAGATCATTCTTTTATAAAGATACATGCACACTTATGTTCATT 213801
i v iiv
L1PA10_3end#L 401 AGGAATATAAATCATTCTATTATAAAGATACATGCACGTGTATGTTCATT 450
INTRON_3 213802 GCAGCACTATTCACAATAGCAAAGACATGGAATCAACCCAAATGCTCATC 213851
i
L1PA10_3end#L 451 GCAGCACTATTCACAATAGCAAAGACATGGAATCAACCCAAATGCCCATC 500
INTRON_3 213852 AATGATAGACTGGATAAAGAAACTGTGGTATATATACACCATGAAATACT 213901
v i i
L1PA10_3end#L 501 AATGATAGACTGGATAAAGAAAATGTGGTACATATACACCATGGAATACT 550
INTRON_3 213902 ATGCAGCCATAAAAGGTAATGAAATCATGTCCTTTACAGGAACATAGATT 213951
i v i i i i v
L1PA10_3end#L 551 ATGCAGCCATAAAAAGGAATGAGATCATGTCCTTTGCAGGGACATGGATG 600
INTRON_3 213952 AAGCTGGAAGCCATTATCCTCAGCAGACTAACACAGGAACAGAAAACCAA 214001
i i i
L1PA10_3end#L 601 GAGCTGGAAGCCATTATCCTCAGCAAACTAACGCAGGAACAGAAAACCAA 650
INTRON_3 214002 ACACTGCATGTTCTCACTTATAAGTGGGAACTGAACAATGAGAACACATG 214051
i i
L1PA10_3end#L 651 ACACCGCATGTTCTCACTTATAAGTGGGAGCTGAACAATGAGAACACATG 700
INTRON_3 214052 GACACAGGGAGGGGAACAACACTTACTGGGGCCTGTTGTGGA-TAGTGGA 214100
vi i v i- i v v
L1PA10_3end#L 701 GACACAGGGAGGGGAACAACACACACTGGGGCCTGTCGGGGGGTGGGGGT 750
INTRON_3 214101 GGGGGGA-----AGCATTAGAGAAAAGAGCTGATGCATGCTGGGCTTAAT 214145
----- ii v i
L1PA10_3end#L 751 GGGGGGAGGGAGAGCATTAGGAAAAATAGCTAATGCATGCTGGGCTTAAT 800
INTRON_3 214146 ACATAGATGATGGGTCGACAGGTGCAGCAAACCACCATGACACACGTTTA 214195
v i i i i
L1PA10_3end#L 801 ACCTAGGTGATGGGTTGATAGGTGCAGCAAACCACCATGGCACACGTTTA 850
INTRON_3 214196 CCTATGTAACAAACTTGCACATCTTGTACAGGTATCCCAGAACTTAA 214242
i i i v i i
L1PA10_3end#L 851 CCTATGTAACAAACCTGCACATCCTGCACATGTACCCCGGAACTTAA 897
Matrix = 20p39g.matrix
Transitions / transversions = 2.57 (54 / 21)
Gap_init rate = 0.01 (5 / 872), avg. gap size = 4.80 (24 / 5)
+ 257 3.0 0.0 0.0 INTRON_3 214295 214327 (185854) C MER58B DNA/hAT-Charlie (151) 190 158 260
ANNOTATION EVIDENCE:
257 3.03 0.00 0.00 INTRON_3 214295 214327 185854 C MER58B DNA/hAT-Charlie 158 190 151 478
INTRON_3 214295 CCAATAAAACTTTATTTATGGGCACTGAAATTT 214327
i
C MER58B#DNA/hA 190 CCAATAAAACTTTATTTATGGACACTGAAATTT 158
Matrix = 20p39g.matrix
Transitions / transversions = 0.0 (1 / 0)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 610 19.1 8.7 6.0 INTRON_3 214331 214525 (185656) C MER58B DNA/hAT-Charlie (141) 200 1 263
ANNOTATION EVIDENCE:
610 19.10 8.72 6.00 INTRON_3 214331 214525 185656 C MER58B DNA/hAT-Charlie 1 200 141 479
INTRON_3 214331 TGGCTATGTGCCAATAAAACTTTATTTATGG-CACTGAAATTTTAATGTT 214379
i v - v v i
C MER58B#DNA/hA 200 TGGCTGTGTTCCAATAAAACTTTATTTATGGACACTGAAATTTGAATTTC 151
INTRON_3 214380 TAAAAATAATTTTC-TGTGTCATGAAATATT-------------CACTTT 214415
--- v -i i -------------ivi
C MER58B#DNA/hA 150 ---ATATAATTTTCACGTGTCACGAAATATTATTCTTCTTTTGATTTTTT 104
INTRON_3 214416 TTTCAACCATTAAAAAATGTAAAAATAATTCTCAGCTCATGGGCTGTTTG 214465
v iv i ii i ---
C MER58B#DNA/hA 103 TTTCAACCATTTAAAAATGTAAAAACCATTCTTAGCTCGCGGGCCGT--- 57
INTRON_3 214466 TTTTAAACAAACACAAACT-TAGGCTG-ATTTTTCCCACTGGCAGTAGAT 214513
------ v ii v-ii i - vv i v v v
C MER58B#DNA/hA 56 ------ACAAAAACAGGCGGCGGGCCGGATTTGGCCCGCGGGCCGTAGTT 13
INTRON_3 214514 TGCTGATGTCTG 214525
i ivi
C MER58B#DNA/hA 12 TGCCGACCCCTG 1
Matrix = 20p39g.matrix
Transitions / transversions = 1.33 (20 / 15)
Gap_init rate = 0.04 (7 / 194), avg. gap size = 4.14 (29 / 7)
+ 260 32.5 0.0 5.4 INTRON_3 214780 214857 (185324) C MIR3 SINE/MIR (23) 185 112 264
ANNOTATION EVIDENCE:
260 32.53 0.00 5.41 INTRON_3 214780 214857 185324 C MIR3 SINE/MIR 112 185 23 416
INTRON_3 214780 AGGGCCAGAAAGGATCTTGAGTATTATCTTTTCTACCTCCATTTTCCATT 214829
i ii i i iiiv i vv i v i v ----
C MIR3#SINE/MIR 185 AGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACCCCCT----CATT 140
INTRON_3 214830 TTGCAGACAAGAAATCTGAAGTCTAGAG 214857
i ii i v i i i
C MIR3#SINE/MIR 139 TTACAGATGAGGAAACTGAGGCCCAGAG 112
Matrix = 25p39g.matrix
Transitions / transversions = 3.00 (18 / 6)
Gap_init rate = 0.01 (1 / 77), avg. gap size = 4.00 (4 / 1)
+ 7494 2.0 0.1 0.0 INTRON_3 215218 216926 (183255) C L1PA3 LINE/L1 (0) 6155 4465 265
ANNOTATION EVIDENCE:
288 0.00 0.00 0.00 INTRON_3 215218 215249 184932 C (TAAA)n Simple_repeat 147 178 2 460
INTRON_3 215218 TATTTATTTATTTATTTATTTATTTATTTATT 215249
C (TAAA)n#Simpl 178 TATTTATTTATTTATTTATTTATTTATTTATT 147
Matrix = Unknown
Transitions / transversions = 0.0 (0 / 0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
7418 1.46 0.11 0.00 INTRON_3 215250 216137 184044 C L1PA3_3end LINE/L1 1 889 13 448
INTRON_3 215250 ATTATACTTTAAGTTTTAGGGTACATGTGCACAATGTGCAGGTTAGTTAC 215299
C L1PA3_3end#LI 889 ATTATACTTTAAGTTTTAGGGTACATGTGCACAATGTGCAGGTTAGTTAC 840
INTRON_3 215300 ATATGTATACATGTGCTATGCTGGTGCGCTGCACCCACTACCTCGTCATC 215349
i v
C L1PA3_3end#LI 839 ATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTAACTCGTCATC 790
INTRON_3 215350 TAGCATTAGGCATATCTCCCAGTGCTATCCCTCCCCCCTCCCCCCACCCC 215399
i i
C L1PA3_3end#LI 789 TAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCCTCCCCCCACCCC 740
INTRON_3 215400 ACAACAGTCCCCAGAGTGTGATGTTCCCCTTCCTGAGTCCATGTGTTCTC 215449
v
C L1PA3_3end#LI 739 ACAACAGTCCCCAGAGTGTGATGTTCCCCTTCCTGTGTCCATGTGTTCTC 690
INTRON_3 215450 ATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTG 215499
C L1PA3_3end#LI 689 ATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTG 640
INTRON_3 215500 TTCTTGCGATAGTTTACTGAGAATGATGATTTCCAATTTTATCCATGTCC 215549
i
C L1PA3_3end#LI 639 TTCTTGCGATAGTTTACTGAGAATGATGATTTCCAATTTCATCCATGTCC 590
INTRON_3 215550 CTACAAAGGACATGAACTCATCATTTTT-ATGGCTGCATAGTATTCCATG 215598
-
C L1PA3_3end#LI 589 CTACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATG 540
INTRON_3 215599 GTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTT 215648
C L1PA3_3end#LI 539 GTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTT 490
INTRON_3 215649 GGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCAATAAACATAC 215698
i
C L1PA3_3end#LI 489 GGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCCGCAATAAACATAC 440
INTRON_3 215699 GTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATA 215748
C L1PA3_3end#LI 439 GTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATA 390
INTRON_3 215749 CCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCT 215798
C L1PA3_3end#LI 389 CCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCT 340
INTRON_3 215799 GAGGAATCGCCACACTGACTTCTACAATGGTTGAACTAGTTTACAGTCCC 215848
i
C L1PA3_3end#LI 339 GAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCC 290
INTRON_3 215849 ACCAACAGTGTGAAAGTGTTCCTATTTCTTCACATCCTCTCCAGCACCTG 215898
i i
C L1PA3_3end#LI 289 ACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTG 240
INTRON_3 215899 TTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGATGGTA 215948
C L1PA3_3end#LI 239 TTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGATGGTA 190
INTRON_3 215949 TCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATCGTGAGC 215998
v
C L1PA3_3end#LI 189 TCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGGTGAGC 140
INTRON_3 215999 ATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGT 216048
C L1PA3_3end#LI 139 ATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGT 90
INTRON_3 216049 CTGTTCATGTCCTTTGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTT 216098
i
C L1PA3_3end#LI 89 CTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTT 40
INTRON_3 216099 GTAAATTTGTTAGAGTTCATTGTAGATTCTGGATATTAG 216137
v
C L1PA3_3end#LI 39 GTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAG 1
Matrix = 20p39g.matrix
Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.00 (1 / 887), avg. gap size = 1.00 (1 / 1)
7494 2.66 0.00 0.00 INTRON_3 215988 216926 183255 C L1P1_orf2 LINE/L1 2356 3294 0 449
INTRON_3 215988 TGATCGTGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTT 216037
vi i
C L1P1_orf2#LIN 3294 TGATGATGAGCATTTCTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTT 3245
INTRON_3 216038 TTGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTGATGGGGTTGTTT 216087
i
C L1P1_orf2#LIN 3244 TTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTT 3195
INTRON_3 216088 GTTTTTTTCTTGTAAATTTGTTAGAGTTCATTGTAGATTCTGGATATTAG 216137
v
C L1P1_orf2#LIN 3194 GTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAG 3145
INTRON_3 216138 CCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAGGTT 216187
v
C L1P1_orf2#LIN 3144 CCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATGTTGTAGGTT 3095
INTRON_3 216188 GCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTGAGT 216237
v
C L1P1_orf2#LIN 3094 GCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGT 3045
INTRON_3 216238 TTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGG 216287
C L1P1_orf2#LIN 3044 TTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGG 2995
INTRON_3 216288 TGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTAATGC 216337
i i
C L1P1_orf2#LIN 2994 TGTTTTGGACATGAAGTCCTTGCCCACGCCTATGTCCTGAATGGTAATGC 2945
INTRON_3 216338 CTAGATTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAATGTTTAAGTCT 216387
i i i
C L1P1_orf2#LIN 2944 CTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAATCT 2895
INTRON_3 216388 TTAATCCATCTTGAATTGATTTTTGTATAAGGCGTAAGGAAGGGATCCAG 216437
i
C L1P1_orf2#LIN 2894 TTAATCCATCTTGAATTGATTTTTGTATAAGGTGTAAGGAAGGGATCCAG 2845
INTRON_3 216438 TTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAA 216487
C L1P1_orf2#LIN 2844 TTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAA 2795
INTRON_3 216488 ATAGGGAATCCTTTCCCGATTGCTTGTTTTTCTCAGGTTTGTCAAAGATC 216537
v
C L1P1_orf2#LIN 2794 ATAGGGAATCCTTTCCCCATTGCTTGTTTTTCTCAGGTTTGTCAAAGATC 2745
INTRON_3 216538 AGATAGCTGTAGATATGTGGCATTATTTCTGAGGGCTCTATTCTGTTCCA 216587
i i i
C L1P1_orf2#LIN 2744 AGATAGTTGTAGATATGCGGCATTATTTCTGAGGGCTCTGTTCTGTTCCA 2695
INTRON_3 216588 TTGATCTATATCTCTGTTTTGGTACCAGTAGCATGCTGTTTTGGTTACTG 216637
v
C L1P1_orf2#LIN 2694 TTGATCTATATCTCTGTTTTGGTACCAGTACCATGCTGTTTTGGTTACTG 2645
INTRON_3 216638 TAGCCTTGTAGTATAGTTTGAAGTCAGGTAGCATGATGCCTCCAGCTTTG 216687
ii
C L1P1_orf2#LIN 2644 TAGCCTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTCCAGCTTTG 2595
INTRON_3 216688 TTCTTTTGGCTTAGGATTGCCTTGGTGATGCGGACTCTTTTTTGGTTCCA 216737
v i i
C L1P1_orf2#LIN 2594 TTCTTTTGGCTTAGGATTGACTTGGCGATGCGGGCTCTTTTTTGGTTCCA 2545
INTRON_3 216738 TATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGTCATTGGTA 216787
C L1P1_orf2#LIN 2544 TATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGTCATTGGTA 2495
INTRON_3 216788 GCTTGATGGGGATGGCATTGAATCTATAAATTACCTTGGGCAGTATGGCC 216837
i
C L1P1_orf2#LIN 2494 GCTTGATGGGGATGGCATTGAATCTGTAAATTACCTTGGGCAGTATGGCC 2445
INTRON_3 216838 ATTTTCACGATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTCCA 216887
C L1P1_orf2#LIN 2444 ATTTTCACGATATTGATTCTTCCTACCCATGAGCATGGAATGTTCTTCCA 2395
INTRON_3 216888 TTTGTTTGTATCCTCTTTTATTTCCTTGAGCAGTGGTTT 216926
i
C L1P1_orf2#LIN 2394 TTTGTTTGTGTCCTCTTTTATTTCCTTGAGCAGTGGTTT 2356
Matrix = 20p39g.matrix
Transitions / transversions = 2.57 (18 / 7)
Gap_init rate = 0.00 (0 / 938), avg. gap size = 0.0 (0 / 0)
+ 3768 3.5 1.0 0.0 INTRON_3 216926 217408 (182773) + L1P1 LINE/L1 2444 2931 (3215) 266 *
ANNOTATION EVIDENCE:
3768 3.52 1.04 0.00 INTRON_3 216926 217408 182773 + L1P1_orf2 LINE/L1 335 822 2472 450
INTRON_3 216926 TAAATATATATGCACCCAATACAGGAGCACCCAGATTCATAAAGCAAGTC 216975
v
L1P1_orf2#LIN 335 TAAATATTTATGCACCCAATACAGGAGCACCCAGATTCATAAAGCAAGTC 384
INTRON_3 216976 CTGAGTGACCTACAAAGAGGCTTAGACTCCCACACATTAATAATGGGAGA 217025
? i
L1P1_orf2#LIN 385 CTSAGTGACCTACAAAGAGACTTAGACTCCCACACATTAATAATGGGAGA 434
INTRON_3 217026 CTGTAACACCCCACTGTCAACATTAGACAGATCAACGAGACAGAAAGTCA 217075
v
L1P1_orf2#LIN 435 CTTTAACACCCCACTGTCAACATTAGACAGATCAACGAGACAGAAAGTCA 484
INTRON_3 217076 ACAAGGATACCCAGGAATTGAACTCAGCTCTGCACCAAGCAGACCTAATA 217125
L1P1_orf2#LIN 485 ACAAGGATACCCAGGAATTGAACTCAGCTCTGCACCAAGCAGACCTAATA 534
INTRON_3 217126 GACATCTACAGAGCTCTCCACCCCAAATCAACAGAATATACATTTTTTTC 217175
i
L1P1_orf2#LIN 535 GACATCTACAGAACTCTCCACCCCAAATCAACAGAATATACATTTTTTTC 584
INTRON_3 217176 AGCACCACGCC-----TATTCCAAAATTGGCCACATACTTGGAAGTAAAG 217220
i ----- i v
L1P1_orf2#LIN 585 AGCACCACACCACACCTATTCCAAAATTGACCACATAGTTGGAAGTAAAG 634
INTRON_3 217221 CTCTCCTCAGCAAATGTAAAAGAACAGAAATTATAACAAACTGTCTCTCA 217270
i
L1P1_orf2#LIN 635 CTCTCCTCAGCAAATGTAAAAGAACAGAAATTATAACAAACTATCTCTCA 684
INTRON_3 217271 GACCCCAGTGCAATCGAACTAGAACTCAGGATTAAGAATCTCACTCAAAA 217320
v i i
L1P1_orf2#LIN 685 GACCACAGTGCAATCAAACTAGAACTCAGGATTAAGAATCTCACTCAAAG 734
INTRON_3 217321 CCGCTCAACTACATAGAGACTGAACAACCTGCTCCTGAGTGACTACTGGG 217370
i i i
L1P1_orf2#LIN 735 CCGCTCAACTACATGGAAACTGAACAACCTGCTCCTGAATGACTACTGGG 784
INTRON_3 217371 TACATAACGAAATGAAGGTAGAAATAAAGATGTTCCTT 217408
i i
L1P1_orf2#LIN 785 TACATAACGAAATGAAGGCAGAAATAAAGATGTTCTTT 822
Matrix = 20p39g.matrix
Transitions / transversions = 3.00 (12 / 4)
Gap_init rate = 0.00 (1 / 482), avg. gap size = 5.00 (5 / 1)
+ 220 29.0 1.6 0.0 INTRON_3 218072 218133 (182048) C L2a LINE/L2 (85) 3341 3279 267
ANNOTATION EVIDENCE:
220 29.03 1.61 0.00 INTRON_3 218072 218133 182048 C L2a_3end LINE/L2 370 432 85 417
INTRON_3 218072 CATACAAAAA-GCATGCCCTTTTGAGGTTCACTTTCTACCAGGGGGATAT 218120
v i-v v iv ii i i v vii v i
C L2a_3end#LINE 432 CAGACAAAAGTCCCTGCCCTCATGGAGCTTACATTCTAGTGGGGGGAGAC 383
INTRON_3 218121 AGATAATAAAGAA 218133
i v
C L2a_3end#LINE 382 AGACAATAAACAA 370
Matrix = 25p39g.matrix
Transitions / transversions = 1.25 (10 / 8)
Gap_init rate = 0.02 (1 / 61), avg. gap size = 1.00 (1 / 1)
+ 2047 27.4 6.6 1.6 INTRON_3 218168 218909 (181272) + L1MDa LINE/L1 19 1035 (5598) 268 *
ANNOTATION EVIDENCE:
2047 27.27 6.57 0.64 INTRON_3 218168 218761 181420 + L1MDa_5end LINE/L1 19 647 2003 451
INTRON_3 218168 ACTTCTACTGCCAAAAAGACAGAGTAAATATACTTTCCCCTATTCCTCCT 218217
i v iiii ii i ii i
L1MDa_5end#LI 19 ACTTCTGCTTCTGGGAAGATGGAGTAGACGTACTTTTCCCTATTCCTCCT 68
INTRON_3 218218 ATTAAGGGTAACTAAAAACTCTAAATATTATATATAAAAAACATGTAAGA 218267
ii vii i ii i v v ii
L1MDa_5end#LI 69 GCTAAGTACAACTAAAAACCCTGGACATTATATATAAAACAAACATAAGA 118
INTRON_3 218268 AGACTC--AGAGGTTGAAA--AGAAGTCAG-CCA------------AGAA 218300
-- i v i -- v - i------------ i
L1MDa_5end#LI 119 AGACTCTGAAAGGTGGAGAGAAGAAGGCAGACCGGCTAGGGACCTCAGGA 168
INTRON_3 218301 CCCAAGGAACAACATGATGGTGAGTTCCCTGGGTTTTCTTCTTGTCTTTA 218350
i ii i i ivv
L1MDa_5end#LI 169 CCCAAGGAATAACATAGTGGTGAGTTCCCTGGGTTTTCTTTTTGCCTCAT 218
INTRON_3 218351 ATATCCCAAACTTGGCGCTGAAGAAGCTGGAAACCTGGAAATCTCAATGA 218400
i v i v i ivi i i
L1MDa_5end#LI 219 ATATCCCAGACTTGGAGCTGAAGAAGCCGGCAACCCGGAAACACCAACGG 268
INTRON_3 218401 ATACAAACACAAAAGACCCCAACAAAAGCCAGTTTTCTCTAGCCAAGGAG 218450
ii i v ii v i i i -
L1MDa_5end#LI 269 GCACAGACAAAAAAAGCCCCAACAAAAGCCTGCTCTCTCTAGCCAAAG-G 317
INTRON_3 218451 AACAATAAAGGACCAATCTAGCAAGACAGAAAGGTTTTACACAATAACCA 218500
v iv iv ii iv v i i
L1MDa_5end#LI 318 ACCAGGAAAGGGGCAGCCTAGCAAGACAGAAAACTTTTAGACAGTAACCG 367
INTRON_3 218501 CTCCACCCTAGCCAAATGTCATA-AAAAATTTGTG-TCCTATTTCT---C 218545
i i i iii i - vi i -i i iii i---
L1MDa_5end#LI 368 CTCTACTCCAGCCAAACACCACAGAAAAAACTGCGGCCCCACCCCCACCC 417
INTRON_3 218546 ACACAAACAAAGGCTGAGTAGGGAGCCTGGACTT--ACCCTCATGAAACT 218593
i v i i i i -- iiv ii
L1MDa_5end#LI 418 ACGCCAGCAAAGGCCGAGTGGGGAGCCTAGACTTCCACCCTCGCCAGGCT 467
INTRON_3 218594 CTAATGTGCTCCTGCAACATCCTTGCCAGGATGGTGTC---------CAA 218634
v i v v v iv i i iii i i --------- i
L1MDa_5end#LI 468 GTAACGAGGTACCCCAGCACCCCCACCGGGGTGGTGTCAGAGAAGGCCGA 517
INTRON_3 218635 GTAGAGAGCCTGCACTT-CATCCCCATTGGTTGATATTGAGGGAACACCC 218683
i ? v - iiii vi?i vi --- i
L1MDa_5end#LI 518 GTAGGGAGCCNGGACTTTCATCCCCGCCAGGCNGTAACGAGG---CATCC 564
INTRON_3 218684 TCCCACTTCACT---GCAGTATTAGTTGAGACT--CTGGAGATGTGGAAC 218728
v? ?? ii ?--- ii i i ?v i i--v i i vviv i
L1MDa_5end#LI 565 ANCNNCCCCACNAGGGTGGTGTCAGNGGAGGCCAAGTAGGGAGCCTGGAC 614
INTRON_3 218729 TTACCCACCTGCTCAGCAATAATGAGGAGCCTC 218761
v v v ii i?i i v i
L1MDa_5end#LI 615 TTTCACCCCCACCNGGCAGTAATGAGGCGCCCC 647
Matrix = 20p39g.matrix
Transitions / transversions = 2.92 (114 / 39)
Gap_init rate = 0.02 (14 / 593), avg. gap size = 3.07 (43 / 14)
905 27.83 6.78 5.59 INTRON_3 218556 218909 181272 + L1MDa_5end LINE/L1 678 1035 1615 452
INTRON_3 218556 AGGCTGAGTAGGGAGCCTGGACTT--ACCCTCATGAAACTCTAATGTG-- 218601
ii? i -- i ivvii vv v --
L1MDa_5end#LI 678 AGGCCANGTGGGGAGCCTGGACTTCCACCCCCACCCGGCAGTAATGAGGT 727
INTRON_3 218602 ---CTCCTGCAACATCCTTGCCAGGATGGTGTC---------CAAGTAGA 218639
--- v -----i ii ii i --------- ? i
L1MDa_5end#LI 728 CACCTCCTCC-----TCTCACTGGGGTGGTGTCAGAGGAGGCCNAGTGGA 772
INTRON_3 218640 GAGCCTGCACTT-CATCCCCATTGGTTGATATTGAGGGAACACCCTCCCA 218688
i v v - i v iiiviviii v v-- --
L1MDa_5end#LI 773 GAGTCAGGACTTTCACCACCGCCCAGCAGTAATGAGGC--CACCC--CCA 818
INTRON_3 218689 CTTCACTGCAGTATTAGTTGAGACT--CTGGAGATGTGGAACTTACCCAC 218736
??------ i i v i i--v i vvii iv v v
L1MDa_5end#LI 819 CNN------AGTGTCAGTGGAGGCCAAGTGGGGAGCCAGAACTCCCACCC 862
INTRON_3 218737 CTGCTCAGCAATAATGAGGAGCCTCCC-----TTTGGTGTGAATGAAGGC 218781
i i i i i ----- iv v i i
L1MDa_5end#LI 863 CTACCCAGCAGTAACGAGGAGCCCCCCCCACCTCGGGTGTCAACGGAGGC 912
INTRON_3 218782 TGAATGGGCAACCTGGACTTTGACATCCACCTGGCAGAAACAAAGCAGTG 218831
i i v iv vi v i i ii
L1MDa_5end#LI 913 CGAGTGGGGAACCTGGACTTCTACCCCCACCTGGCAGTAACGAGGCAGCA 962
INTRON_3 218832 CCCTCACTTATACCCTGCCAGAGCAGTGTCAAAAAAAAAAAAGCCAATTA 218881
iiv iiv v i i i ----- ii
L1MDa_5end#LI 963 CCCCTCCCCTTCCCCTGCCAGAGCGGTGTCAGAGAAA-----GCCAGCTA 1007
INTRON_3 218882 AAATAAAAGGTTTAAATAAGATCTAGGG 218909
i i i i
L1MDa_5end#LI 1008 AAACAGAAGGTTTAAATAAGATCCAGAG 1035
Matrix = 20p39g.matrix
Transitions / transversions = 2.07 (60 / 29)
Gap_init rate = 0.03 (11 / 353), avg. gap size = 4.00 (44 / 11)
+ 3027 22.8 0.8 4.1 INTRON_3 218906 219661 (180520) + L1M1 LINE/L1 14 745 (6820) 269
ANNOTATION EVIDENCE:
3027 22.76 0.79 4.10 INTRON_3 218906 219661 180520 + L1M1_5end LINE/L1 14 745 2930 453
INTRON_3 218906 AGGGAGGTGGAGCAAGATGGTTGGGATAGAAGCCTTCACTGTTTGTCCCT 218955
i ii i- i i v i v
L1M1_5end#LIN 14 AGGGAGGCGGAGCAAGATGGCCGA-ATAGAAGCCTCCACCGATCGTCCAT 62
INTRON_3 218956 CTGGCTTGAACACCAAATCTTAAC--AACTA-TCTGTACACAGAAAAGCC 219002
ivv ii -- vv vv iv i-- v - v vi i v
L1M1_5end#LIN 63 CCTCCCCG--CAGGAACACCAAATTGAACAACTATCCACACAAAAAAGCA 110
INTRON_3 219003 CCATCACAAAAACCAACAATCAAGTGTGCAATCACAGTACTTGGATTTAA 219052
v i i v i v i i v
L1M1_5end#LIN 111 CCTTCATAAGAACCAAAAATCAGGTGAGCGATCACAGTACCTGGTTTTAA 160
INTRON_3 219053 CGTCATATTCACAGTACTTGGATTTAACGACAGAGGCATTGAGGAGGGCA 219102
v i------ ---------- v i i i
L1M1_5end#LIN 161 CTTCATATC------ACT----------GAAAGAGGCACTGAAGAGGGTA 194
INTRON_3 219103 GAAGAGATACTTTAGAATCACTGACACCACCTCACCTCCATCCCCTAGCA 219152
i i i v i v i i i i v i ii
L1M1_5end#LIN 195 GGAAAGACAGTCTTGAATCGCCGACGCCACCCCTCCCCCATCCCCCGGCA 244
INTRON_3 219153 GTGGCCATGCAGTGCAGAGAGAGAACTTGAGCACTTTGGGGAGGGAGAGC 219202
i i ii i i ii v v
L1M1_5end#LIN 245 GCGGCCGTGTGGCGCGGAGAGAGAATCTGTGCACTTGGGGGAGGGAGAGC 294
INTRON_3 219203 ACAGCTGCTGGGCGACTTTACATTG-AACTCAGTGCTGCCCTGTTACAGT 219251
i vii v v i - i i
L1M1_5end#LIN 295 GCAGCGATTGTGGGACTTTGCATTGGAACTCAGTGCTGCCCTGTCACAGC 344
INTRON_3 219252 GGAGAATAAAGCTGTATTGAGCTCAGCCATTGCCTGTGCACAATGGGAGC 219301
i ii vi i viiv i ivi ---- iiv
L1M1_5end#LIN 345 GGAAAGCAACACCGGGCAGAACTCAGCCGGCGCC----CACGGAGGGAGC 390
INTRON_3 219302 ATCTGGACCAGCCCTAGCCAGAGGGGGGTCACCCATCCCAGTGGTCCAAA 219351
i i ii i vi
L1M1_5end#LIN 391 ATTTAGACCAGCCCTAGCCAGAGGGGAATCACCCATCCCAGCGGTCGGAA 440
INTRON_3 219352 CTTGAGTTTCTGTGCAAACCTCACCACTTAGGGCTAAAGTGCTCTGGGGT 219401
i i v -- i i ivv
L1M1_5end#LIN 441 CCTGAGTTCCGG--CAAGCCTCGCCACCGCGGGCTAAAGTGCTCTGGGGT 488
INTRON_3 219402 CCTAGGTAAACTTGAAAGACAGTCTAGGACACAAAGACTGCAATTCCTAG 219451
ii i v i i
L1M1_5end#LIN 489 CCTAAATAAACTTGAAAGGCAGTCTAGGCCACAAGGACTGCAATTCCTGG 538
INTRON_3 219452 GCAACTCCTAGTGCTAGGCTGGGCTTCAAGCCAGTGAACTAGGAGTGGAA 219501
v i iv ivi i v i - v
L1M1_5end#LIN 539 GCAAGTCCTGGTGCTGTGCTGGGCTCAGAGCCAGTGGACTTGGGG-GGCA 587
INTRON_3 219502 CATGACCTAGGGAGACACCAGCTGGCACAGCTATGGGAGAGTAAAGAGAA 219551
ii v i vi i i v v iv----viv
L1M1_5end#LIN 588 CGCGACCTAGTGAGACACCAGCCGGGGCGGCCAAGGGAGTGCT----TGC 633
INTRON_3 219552 GTCATCCCTCCCCCAAACCCAGG-ATTGCAGCTTGTAGCAATGGAAGTGA 219600
i i v - vii i i vvi i v
L1M1_5end#LIN 634 GCCACCCCTCCCCCAACCCCAGGCAGCACAGCTCGCAGCTCCGGGAGAGA 683
INTRON_3 219601 CTGTTTCTTTCCGTTTAAGGAGAGGAGATCAAAG-TTAAAGGGTACTTTG 219649
vi i i i vvi -v i v
L1M1_5end#LIN 684 CTCCTTCCTTCCGCTTGAGGAGAGGAGAGGGAAGAGTAAAGAGGACTTTG 733
INTRON_3 219650 TCTTACATCTTG 219661
i v
L1M1_5end#LIN 734 TCTTGCAACTTG 745
Matrix = 20p39g.matrix
Transitions / transversions = 1.75 (105 / 60)
Gap_init rate = 0.02 (13 / 755), avg. gap size = 2.77 (36 / 13)
+ 293 14.6 1.8 0.0 INTRON_3 219658 219712 (180469) + L1M1 LINE/L1 1368 1423 (6142) 269 *
ANNOTATION EVIDENCE:
293 14.55 1.82 0.00 INTRON_3 219658 219712 180469 + L1M1_5end LINE/L1 1368 1423 2252 454
INTRON_3 219658 CTTGTGGAAAGGGGAGGGAAGAATAGGAGGGACTTTGTATTGTGG-TTCA 219706
i i i i v - vi
L1M1_5end#LIN 1368 CCTGTGGAAAGGGGAGGGAAGAGTGGGAAGGACTTTGTCTTGTGGCTTGG 1417
INTRON_3 219707 GTACCA 219712
i
L1M1_5end#LIN 1418 GTGCCA 1423
Matrix = 20p39g.matrix
Transitions / transversions = 3.00 (6 / 2)
Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1)
+ 8419 12.7 8.8 0.3 INTRON_3 219758 221492 (178689) + L1M1 LINE/L1 1422 3302 (4263) 269
ANNOTATION EVIDENCE:
629 25.58 0.00 0.00 INTRON_3 219758 219886 180295 + L1M1_5end LINE/L1 1422 1550 2125 455
INTRON_3 219758 CAACTTAGCTTCCGTAGAATAGAACATCACATAAGTTTCTAAGGTTTTTG 219807
i i iv v i i vi ii i i
L1M1_5end#LIN 1422 CAGCTCAGCCGCAGTAGAATAGAGCACCAGGTAGATTCCTAAGGTTTCTG 1471
INTRON_3 219808 ACTCCAACTTCTGGCTCCCAGACAGCATCTCTGGACACACCTGGAGCCTA 219857
ivii ii ii v i i ?i
L1M1_5end#LIN 1472 ACTCCAGGCCCTGGCTCCTGGATGGCATCTCTGGACCCGCCTGGGGCCNG 1521
INTRON_3 219858 CAAGAACTCACTACCCTGACGGGAAGGGC 219886
vii i i v i
L1M1_5end#LIN 1522 GGGGAACTCGCCACCCTGAAGGGAAGGAC 1550
Matrix = 20p39g.matrix
Transitions / transversions = 3.57 (25 / 7)
Gap_init rate = 0.00 (0 / 128), avg. gap size = 0.0 (0 / 0)
1622 15.13 0.00 1.11 INTRON_3 219883 220156 180025 + L1M1_5end LINE/L1 1638 1908 1767 456
INTRON_3 219883 GGGCCTTGGGCAAGGCCCATTGCTGTGCTGGCTTTGGGTCTGACCCAGCA 219932
i i v ii i
L1M1_5end#LIN 1638 GGGCCTTGGGCGAGACCCAGTGCTGTGCTGGCTTCAGGTCTGACCCAGCG 1687
INTRON_3 219933 CAGTCCCAGTGGTGGTGGCCACAGGGGTGATTGCATCACTACACCCCCCA 219982
v ii iv -i
L1M1_5end#LIN 1688 CAGTCCCAGTGGTGGTGGCCACAGGGGTGCTTGTGTCACCCC-TCCCCCA 1736
INTRON_3 219983 GTTCCAGGTGGTTCGGCACAGAGAGAGAGAGACTCCATGTGTTTTGGGGA 220032
i ii i i -- i v v i
L1M1_5end#LIN 1737 GCTCCAGGCAGCTCAGCACAGAGAGAGAGA--CTCCGTTTGTTTGGGAGA 1784
INTRON_3 220033 AAGTAAGGGAAAAGAACAAGGGTTTCTGCCTGGTAATCCAGAGCATTCTT 220082
i i i v
L1M1_5end#LIN 1785 AAGTAAGGGAAGAGAACAAGAGTCTCTGCCTGGTAATCCAGAGAATTCTT 1834
INTRON_3 220083 CTGGATCTTACCCACAACCACCACAGCAGTACCTCTATGAGTGTACAAAA 220132
i i vi vi i i v i i
L1M1_5end#LIN 1835 CCGGATCTTATCCAAGACCACCAAGGCGGTACCTCTACGAGTCTGCAAGA 1884
INTRON_3 220133 CCCACCGTATTATTGGGCTTGGGG 220156
v v ii i
L1M1_5end#LIN 1885 GCCACAGCGTTACTGGGCTTGGGG 1908
Matrix = 20p39g.matrix
Transitions / transversions = 2.73 (30 / 11)
Gap_init rate = 0.01 (2 / 273), avg. gap size = 1.50 (3 / 2)
8419 11.02 0.75 0.22 INTRON_3 220157 221492 178689 + L1M1_5end LINE/L1 1960 3302 373 457
INTRON_3 220157 CCCAAGTCCCTTTGAATACCTAGAAAACCTTCCCAAGAAAGACAGGCACA 220206
i i i i i i
L1M1_5end#LIN 1960 CCCAAGTCCCTTCGAATACCTGGAAAGCCTTCCCAAGAAGGACGGGTACA 2009
INTRON_3 220207 AATAAGCCCAGACTGTGAAGACCACAATAAATACATAACTCTTTAATGCC 220256
i i v i
L1M1_5end#LIN 2010 AACAAGCCCAGACTGTGAAGACTACAATAAATACCTAACTCTTCAATGCC 2059
INTRON_3 220257 CAGATGCCAAAGAACTTCTACAAGTGCCAACATCATTCAGGAAAACATTA 220306
ii i v v i iii v i i v
L1M1_5end#LIN 2060 CAGACACCGACGAACATCCACAAGCATCAAGACCATCCAGGAAAACATGA 2109
INTRON_3 220307 CTTCACCAAATGAACTAAATGAGGTACCAGGGATCAATCCCAGAGAGATA 220356
i i i i i i
L1M1_5end#LIN 2110 CCTCACCAAATGAACTAAATAAGGCACCAGGGACCAATCCCGGAGAGACA 2159
INTRON_3 220357 GATATATATGACGTTTCAGACAGAGAATTCAAAATAGCTGTTTTGACGAA 220406
v i v v
L1M1_5end#LIN 2160 GAGATATGTGACCTTTCAGACAGAGAATTCAAAATAGCTGTTTTGAGGAA 2209
INTRON_3 220407 ACTCAAAGAAACTTAAGATAACACAGAGAAGGAATTCAATATTTTATCAG 220456
? i i iv ii
L1M1_5end#LIN 2210 ACTCAANGAAATTCAAGATAACACAGAGAAGGAATTCAGAATCCTATCAG 2259
INTRON_3 220457 GTAAATTTAACAAAGAGATTGAAATAATTAAATAGAATCAATCAGAAATT 220506
i v v
L1M1_5end#LIN 2260 ATAAATTTAACAAAGAGATTGAAATAATTAAAAAGAATCAAGCAGAAATT 2309
INTRON_3 220507 CTAGAATTGAAAACTGTAGTTGACATGCTGAAGAATTTATCAGAGTCTCT 220556
i i v i i i vi
L1M1_5end#LIN 2310 CTGGAGTTGAAAAATGCAATTGACATACTGAAGAATGCATCAGAGTCTCT 2359
INTRON_3 220557 TAATAGCAGAATTGATCAAGCAGAAGAAAGAATTAGTGAGCCTAGAGACA 220606
i i ii
L1M1_5end#LIN 2360 TAACAGCAGAATTGATCAAGCAGAAGAAAGAATTAGTGAGCTTGAAGACA 2409
INTRON_3 220607 GGCTATTTGAAAATACACAGTCAGAGGAGACAAAAGGGAAAAAGAATAAA 220656
i-
L1M1_5end#LIN 2410 GGCTATTTGAAAATACACAGTCAGAGGAGACAAAAGA-AAAAAGAATAAA 2458
INTRON_3 220657 AAAGAATGAAGCATGCCTACAAGATTTAGAAAGTAGCCTGAAAAGGACAA 220706
i i i v i
L1M1_5end#LIN 2459 AAAGAATGAAGCACGCCTACAAGATCTAGAAAATAGCCTCAAAAGGGCAA 2508
INTRON_3 220707 ATCTAAGAGTTATTGGCTTTAAAGAGGAGGTAGAGAAAGAGATAGGGATA 220756
i i i
L1M1_5end#LIN 2509 ATCTAAGAGTTATTGGCCTTAAAGAGGAGGTAGAGAGAGAGATAGGGGTA 2558
INTRON_3 220757 GAAAGTTTATTCAAAGGGATAGTATCAGAGAATTTCCCAAACCTAGAGAA 220806
i v i
L1M1_5end#LIN 2559 GAAAGTTTATTCAAAGGGATAATAACAGAGAACTTCCCAAACCTAGAGAA 2608
INTRON_3 220807 AGATATCAACATTCAAGTAGAAGAAG-TTATAGAACACCAGGCAGATTTA 220855
i v - i
L1M1_5end#LIN 2609 AGATATCAATATTCAAGTACAAGAAGGTTATAGAACACCAAGCAGATTTA 2658
INTRON_3 220856 ACCTAAAGAAGACTACCCCAAGGCATTTAATAATCAAACTCCCAGTGGCC 220905
i i iv i
L1M1_5end#LIN 2659 ACCCAAAGAAGACTACCTCAAGGCATTTAATAATCAAACTCCCAAAGGTC 2708
INTRON_3 220906 AAGGATAAAGAAAG-ATTCTAAAAGCAGCAAGAGAAAAGAAACAA----C 220950
- i ----
L1M1_5end#LIN 2709 AAGGATAAAGAAAGGATCCTAAAAGCAGCAAGAGAAAAGAAACAAATAAC 2758
INTRON_3 220951 ACACAGTGGAGCTCCAATAGGTCTGGCAGCAGACTTTTCAGTGCAAACCT 221000
i i v v
L1M1_5end#LIN 2759 ATACAATGGAGCTCCAATACGTCTGGCAGCAGACTTTTCAGTGGAAACCT 2808
INTRON_3 221001 TACAGGTCAGGAGAGAGTGGCATGAGATATTTAAAGTGCTGAAAGAATAA 221050
i v i v
L1M1_5end#LIN 2809 TACAGGCCAGGAGAGAGTGGCATGACATATTTAAAGTGCTGAAGGAAAAA 2858
INTRON_3 221051 AACTCTTATCTTAGATTAGTATATCTTGAGAAAATATCCTTTAAGCCTGA 221100
i i i v iv v i i v
L1M1_5end#LIN 2859 AACTTTTACCCTAGAATAGTATATCCAGTGAAAATATCCTTCAAACATGA 2908
INTRON_3 221101 AGGAGAAATAAAGACATTCTCAGACAAATAAAACCTGAGGGATTTCA--- 221147
v i i v ---
L1M1_5end#LIN 2909 AGGAGAAATAAAGACTTTCCCAGACAAACAAAAGCTGAGGGATTTCATCA 2958
INTRON_3 221148 ATACCATACCTATCCTATAAGAAAGGCTAGAGAGAGTTCTTCAATCTGAA 221197
i v i i v i i
L1M1_5end#LIN 2959 ACACCAGACCTGTCCTACAAGAAATGCTAAAGGGAGTTCTTCAATCTGAA 3008
INTRON_3 221198 AGAAAATGATGTTATTGAGCAACAAGATATCATCTGAAGATATAAAACTC 221247
v ii v i v i i
L1M1_5end#LIN 3009 AGAAAAGGACATTAATGAGCAATAAGAAATCATCTGAAGGTACAAAACTC 3058
INTRON_3 221248 ATTATTACCATAGTAAGCACACAGAAAAACACAGAATAGTATAACTTTGT 221297
i iv -- i v vi
L1M1_5end#LIN 3059 ACTGGTA--ATAGTAAGTACACAGAAAAACACAGAATATTATAACACTGT 3106
INTRON_3 221298 AGTTGTGATGTATAAACTTATCTTGACTAAAGTAGAAAGAATAAACGATG 221347
i i i vv v iv v v v
L1M1_5end#LIN 3107 AATTGTGGTGTGTAAACTACTCATATCTTAAGTAGAAAGACTAAAAGATG 3156
INTRON_3 221348 AACCAATCAAAGATAACAGCTACAACAACTTTTCAAGACATAGACAGTAC 221397
i i i
L1M1_5end#LIN 3157 AACCAATCAAAAATAATAACTACAACAACTTTTCAAGACATAGACAGTAC 3206
INTRON_3 221398 AATAAGACATAAAGAGAAACAACAAGAAGTTAAAAAGCCAGGGCACTAAG 221447
i v i vi v v
L1M1_5end#LIN 3207 AATAAGATATAAATAGAAACAACAAAAAGTTAAAAAGCGGGGGGACGAAG 3256
INTRON_3 221448 TTAACATGTGGAGTTTTT-TTAGTTTTCTTTTTCCGTGTTTGTTTG 221492
vi i - i v v
L1M1_5end#LIN 3257 TTAAAGTGTAGAGTTTTTATTAGTTTTCTCTTTGCTTGTTTGTTTG 3302
Matrix = 20p39g.matrix
Transitions / transversions = 1.98 (97 / 49)
Gap_init rate = 0.01 (7 / 1335), avg. gap size = 1.86 (13 / 7)
+ 540 33.2 3.1 3.4 INTRON_3 221597 221889 (178292) C MLT1N2 LTR/ERVL-MaLR (270) 292 1 270
ANNOTATION EVIDENCE:
540 33.22 3.07 3.42 INTRON_3 221597 221889 178292 C MLT1N2 LTR/ERVL-MaLR 1 292 270 480
INTRON_3 221597 ATTGGTGCCCATGAAAGCTGGATACCTTC-ACCATCAGCCTTGCCAGAAA 221645
i v iv i i i vv -i ii v i i
C MLT1N2#LTR/ER 292 ACTGCTGCCTCTGGAAACTGGATGCCAGCTGCCGCCACCCTCGCCAGAGA 243
INTRON_3 221646 ATTAATTCCACGTATACAGGGCCATGTTCTTCATTTTTTT-CT-GTTTAC 221693
vi i i----- v? v -- v viv i- - i vi
C MLT1N2#LTR/ER 242 ATGGATTCCGCGC-----GGTNCCTG--CTTCCTTGCGTCACTAGCTTCT 200
INTRON_3 221694 AATTCAAA-TCTCATATGGTTGTTTCTGACTGGTCAAGCATGCGTTACCT 221742
i - vi?ii v iv i ivi v iv i v
C MLT1N2#LTR/ER 199 GATTCAAAGTCTGGNGCGGGTGCGTCTGATTGGCGGAGCCTAGGTCACGT 150
INTRON_3 221743 TCCAATGCATTAGCTGAAAGGGAATCTGAGAAATTGAGTT-CTCCCTCGT 221791
v vi vi v iv i v - vv iv
C MLT1N2#LTR/ER 149 GCCCGTGCCCTAGCTGCAAGGGAGGCTGGGAAAGTGAGTTTCTGGCTTCT 100
INTRON_3 221792 ATCTTCATGAAATGAGACTCATAATATGCAAGCTACCCCAGG-ACAGAAA 221840
i viv iii i vi viiiv v ii- i i
C MLT1N2#LTR/ER 99 ACCTTGGGGAGGCGGGACTCATAAGGTGGGGAATTCCCCAAACATAGGAA 50
INTRON_3 221841 GAGTGTTCAAAAGATGCTAGGTACCCCAAAA---TGACAAACATCCATAA 221887
i ? --- i iiv v? --- ii iv
C MLT1N2#LTR/ER 49 GGGNGTTCA---GATGCTGGGCGGCCANAAAGAATGACAAATGTCCACTA 3
INTRON_3 221888 CA 221889
C MLT1N2#LTR/ER 2 CA 1
Matrix = 20p39g.matrix
Transitions / transversions = 1.43 (53 / 37)
Gap_init rate = 0.03 (10 / 292), avg. gap size = 1.90 (19 / 10)
+ 1108 17.9 6.0 5.3 INTRON_3 221944 222261 (177920) + MER33 DNA/hAT-Charlie 3 322 (2) 271
ANNOTATION EVIDENCE:
1108 17.93 5.97 5.31 INTRON_3 221944 222261 177920 + MER33 DNA/hAT-Charlie 3 322 2 389
INTRON_3 221944 GCACTATCCAATTTGGTAACCACTCTCCACATG-GACATACTGAGCACTT 221992
i i vi i vv - i - i
MER33#DNA/hAT 3 GCGCTGTCCAATACGGTAGCCACTAGCCACATGTGGC-TATTGAGCACTT 51
INTRON_3 221993 GAAATGTGGCAAGTCCAAATTGAGGTGTGCTGCAAGTATAAAATACACAT 222042
v i i i i i
MER33#DNA/hAT 52 GAAATGTGGCTAGTCCGAATTGAGATGTGCTGTAAGTGTAAAATACACAC 101
INTRON_3 222043 GGGATTTTGAAAAC--AGTATAAAA-------TATTAAAAATCACATTAA 222083
v i i -- i ------- i v v v
MER33#DNA/hAT 102 CGGATTTCGAAGACTTAGTATGAAAAAAAGAATGTAAAATATCTCATTAA 151
INTRON_3 222084 TAATTTT-ATACTGATTACATGTTAAAAG---AATGTTTTAGATATATTG 222129
- i i v--- i i
MER33#DNA/hAT 152 TAATTTTTATATTGATTACATGTTGAAATGATAATATTTTGGATATATTG 201
INTRON_3 222130 GTAATTAAATCATTTCTATTAACTAAAACTGATTTTATCTGTTAATTTTT 222179
--i v vv v -i i i i i vv
MER33#DNA/hAT 202 G--GTTAAATAAAATATATTA-TTAAAATTAATTTCACCTGTTTCTTTTT 248
INTRON_3 222180 TCTTCTT-----GTGGTTAGTAGAAAATTTAAAATTTTAAATGTAACTTG 222224
v i ----- i v -------------i
MER33#DNA/hAT 249 ACTTTTTTTAATGTGGCTACTAGAAAATTTAAAATT-------------A 285
INTRON_3 222225 CATTTGTGACTTACATTGTAATTCTGTTGGACATCAC 222261
v i ii i v i v i
MER33#DNA/hAT 286 CATATGTGGCTCGCATTATATTTCTATTGGACAGCGC 322
Matrix = 18p39g.matrix
Transitions / transversions = 1.70 (34 / 20)
Gap_init rate = 0.03 (10 / 317), avg. gap size = 3.60 (36 / 10)
+ 656 30.9 0.0 2.8 INTRON_3 222986 223241 (176940) C MIR SINE/MIR (12) 250 2 272
ANNOTATION EVIDENCE:
656 30.95 0.00 2.81 INTRON_3 222986 223241 176940 C MIR SINE/MIR 2 250 12 390
INTRON_3 222986 CAATTACTGAGTGCTCAGTATGTGCCAGAAACTGTGCTAAATGCTTCATC 223035
v i i i v iv v ii i iv
C MIR#SINE/MIR 250 CATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACA 201
INTRON_3 223036 TGCCTTGGCCCATTTAGTCCTAACAACAAGCATATGAGATAGGTACTAGT 223085
iv ii i i v v v i v
C MIR#SINE/MIR 200 TGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATT 151
INTRON_3 223086 ATTATATTCAGTTTACATATGAGAGAATGGAGGATCAGAGAGGGGCAGAG 223135
vii v v ii iv vv vvv v-
C MIR#SINE/MIR 150 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGT- 102
INTRON_3 223136 GGAAACATGCCTGAAGTCACCTAGTTTGAGCACCTAGTAGAACCAGGATT 223185
--- v ii i vi i -- i vv i i i i
C MIR#SINE/MIR 101 ---AACTTGCCCAAGGTCACACAGCT--AGTAAGTGGCAGAGCCGGGATT 57
INTRON_3 223186 TAGATGCAAGTGTGTAGGAGTACAGAGCCTGCACACTTAACTATGATGTC 223235
iii iv i ii- vv iv v i i ii v i iv ii
C MIR#SINE/MIR 56 CGAACCCAGGCA-GTCTGGCTCCAGAGTCCGTGCTCTTAACCACTATGCT 8
INTRON_3 223236 AGACTG 223241
v
C MIR#SINE/MIR 7 ATACTG 2
Matrix = 18p39g.matrix
Transitions / transversions = 1.41 (45 / 32)
Gap_init rate = 0.01 (3 / 255), avg. gap size = 2.33 (7 / 3)
+ 214 20.9 1.4 2.9 INTRON_3 223600 223668 (176513) + L3b LINE/CR1 4276 4343 (165) 273
ANNOTATION EVIDENCE:
214 20.90 1.45 2.94 INTRON_3 223600 223668 176513 + L3b_3end LINE/CR1 250 317 165 418
INTRON_3 223600 AGGGAGGTGGGTAAGTCTTTAGGAGTAAAATATC-TGACAGTGAGGGCTG 223648
vv i v viv v -- i v - i
L3b_3end#LINE 250 AGGGATTTAGGTTAGATATAAGGA--AGAATTTCCTGACAGTGAGAGCTG 297
INTRON_3 223649 TTAAACACTGGGCTGGGTTG 223668
i iv
L3b_3end#LINE 298 TTAAATACTGGAATGGGTTG 317
Matrix = 25p39g.matrix
Transitions / transversions = 0.75 (6 / 8)
Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.50 (3 / 2)
+ 2237 22.4 1.0 5.6 INTRON_3 223778 224278 (175903) C LTR16B1 LTR/ERVL (0) 480 2 274
ANNOTATION EVIDENCE:
2237 22.42 1.00 5.64 INTRON_3 223778 224278 175903 C LTR16B1 LTR/ERVL 2 480 0 391
INTRON_3 223778 TGTGTCAGTTAAGGTCCTTTGAGGAGCAGACACCAAGATGCAGTTAGACA 223827
vi ii i i i vii i
C LTR16B1#LTR/E 480 TGTGTCAGTTCGGGTCCTCCGAGAAGCAGACGCCAAGACGGGATTAGACG 431
INTRON_3 223828 --CATAAGTTTTATTTGGAGAAATATCCATGCTGAGTAAAGGGGA-AGAG 223874
-- vi v v i iii ii vv ii - i
C LTR16B1#LTR/E 430 TGCAAGAGATTTATTGGGGGAAACGCCTGTGAAGGATAAAGGGGAGAGGG 381
INTRON_3 223875 AGCAGGAGTAGGCAGGGAGAGCCTTCAGCCAGTGATGCAGGTCTGATATC 223924
v vii i i
C LTR16B1#LTR/E 380 AGCAGGAGTAGGCAGGGAGAGCCTTCAGACCACGATGCAGGTCTGACACC 331
INTRON_3 223925 TATGAAAGGAGCAGAGGAAAGAAAGAAAATTGGGCAGGAAGAGCCCCAGT 223974
i viii i i ii i i v
C LTR16B1#LTR/E 330 TGTGAAAGGAGAGAGGGAAGGAAGGAGGATTGGGTAGGAAGAGCCTCAGA 281
INTRON_3 223975 CCGTAATGCAGTTCTGAGAAAGTCTTGGCCAGGCTG--GGAACAGAAGTC 224022
i i ii i i -- ---- i
C LTR16B1#LTR/E 280 CTGCAGCGCAGTTCTGAGAAAGTCTCGGCCAGGCCGATGG----GGAGTC 235
INTRON_3 224023 TTTAAGCAAAAGTTCCCCATTATAGAAATCCCACATTACAGGGAAAGGAT 224072
iiii i v v i i i i--- v i i
C LTR16B1#LTR/E 234 CCCGAGCAAAGGTTGCCCATTAGAGGAGTCCCACGTC---GGGCAGGAAT 188
INTRON_3 224073 GGCTTAGCTTGACTGTGCCTTCTGTGCTTAGTCATTGCCTGGGAGCAGCA 224122
iii iv v iiv iv i i v v
C LTR16B1#LTR/E 187 GGCCCGGCTCTAGTACCCCCGCCGTGCTCAGTCATTGGCTGGGAGCAGCC 138
INTRON_3 224123 TAGGGGTCAGAAGGTGTGGAAGTGGGGAGCATGACCTCAGAGTGAACACT 224172
ii ------------- ------- i i v i
C LTR16B1#LTR/E 137 CGGGGG-------------AAGTG-------TGGCCTCGGCGTGAACGCT 108
INTRON_3 224173 GCAATGGATCTAAACATACAGCAGCTGGAGACTATCAGACAGCTATGCTT 224222
ii i vi i i i i v i i
C LTR16B1#LTR/E 107 GCGGTGGATCCAAAGGTGCGGCAGCTGGAGGCTGTCAGCCAACTATGCTC 58
INTRON_3 224223 CTAGCAGCAGGTTCTCTTGACAGGAGATCTGAGCAGTGCACCTCCATGTC 224272
iv vi i i v
C LTR16B1#LTR/E 57 CCCGCAGCAGGTTCTCTTGAAGGGAGATCTGAGCGGCGCACCTCCATGGC 8
INTRON_3 224273 TGCCAC 224278
i
C LTR16B1#LTR/E 7 CGCCAC 2
Matrix = 18p39g.matrix
Transitions / transversions = 3.08 (80 / 26)
Gap_init rate = 0.01 (7 / 500), avg. gap size = 4.57 (32 / 7)
+ 247 37.1 3.2 2.6 INTRON_3 224629 224783 (175398) + L2a LINE/L2 2619 2774 (645) 275
ANNOTATION EVIDENCE:
247 37.08 3.23 2.56 INTRON_3 224629 224783 175398 + L2 LINE/L2 2619 2774 308 419
INTRON_3 224629 TGTTAATTTTATCTCTTGAATATATTTAAAATGTATTCA-TTCTCTCTAT 224677
iii i i iivi ii i viivi - v i -
L2#LINE/L2 2619 TGTTGGCTCTACCTTCAAAATATATCCAGAATCCGACCACTTCTCACCA- 2667
INTRON_3 224678 TCCTGTACTGTTAGATTAGCTTAGTTC---CC-TCATCCTCACTTCCTTG 224723
- vi ii --ii v i i i --- -i v v iv i
L2#LINE/L2 2668 -CCTCCACTGCCA--CCACCCTGGTCCAAGCCACCATCATCTCTCGCCTG 2714
INTRON_3 224724 GGTTATTTTAGTAGCTTCCTATCTTTTCTCCCTACCTCTAATCTTGTCGC 224773
i i vi i i v vv i i i vi i v
L2#LINE/L2 2715 GATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCC 2764
INTRON_3 224774 GGTTTAGTTT 224783
vv ?i i
L2#LINE/L2 2765 CCTNCAGTCT 2774
Matrix = 25p39g.matrix
Transitions / transversions = 2.24 (38 / 17)
Gap_init rate = 0.03 (5 / 154), avg. gap size = 1.80 (9 / 5)
+ 307 36.1 1.4 4.3 INTRON_3 224827 224968 (175213) + L2a LINE/L2 2846 2983 (436) 275
ANNOTATION EVIDENCE:
307 36.08 1.41 4.35 INTRON_3 224827 224968 175213 + L2 LINE/L2 2846 2983 99 420
INTRON_3 224827 CCTTCAATGGCTTACTAGC--ATTTAGAAGGAAAAAATAATCCAAGCTCC 224874
i i v i v -- i i - v i----- iv
L2#LINE/L2 2846 CCTCCAGTGGCTTCCCATCTCACTCAGA-GTAAAAG-----CCAAAGTCC 2889
INTRON_3 224875 GTAGCATGGCATATGAGGCATTTCATGAATTTATCTATGTCCACTTTGCT 224924
v vvi v ii vi v vi vi ivivvii i iv
L2#LINE/L2 2890 TTACAGTGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCT 2939
INTRON_3 224925 AACTTCATCTCCTTCTATTCTCCCCTTCATGCTTTCTAGTCCAG 224968
i i v i i i iiv vi iiv
L2#LINE/L2 2940 GACCTCATCTCCTACCACTCTCCCCCTCGCTCACTCCGCTCCAG 2983
Matrix = 25p39g.matrix
Transitions / transversions = 1.45 (29 / 20)
Gap_init rate = 0.02 (3 / 141), avg. gap size = 2.67 (8 / 3)
+ 311 26.8 0.0 0.4 INTRON_3 225219 225309 (174872) + L2a LINE/L2 3277 3417 (9) 275
ANNOTATION EVIDENCE:
308 34.45 0.00 1.11 INTRON_3 225219 225309 174872 + L2b_3end LINE/L2 368 457 9 421
INTRON_3 225219 AGGCCCCAGGCTGTATCTTATTTTTCTTTACAACCCTTGCACCTAGCACA 225268
vv i - v i i ivi vi iiiv iv i i
L2b_3end#LINE 368 AGGGACCGGG-TCTGTCTTGTTCACCGCTGTGTCCCCAGCGCCCAGCACA 416
INTRON_3 225269 ATGCTTGGCCCATGAGAGGTACTCAATAAATATTGGTTGAA 225309
iv i v iiiv i i i v
L2b_3end#LINE 417 GGGCCTGGCACACAGTAGGTGCTCAGTAAATGTTTGTTGAA 457
Matrix = 25p39g.matrix
Transitions / transversions = 1.82 (20 / 11)
Gap_init rate = 0.01 (1 / 90), avg. gap size = 1.00 (1 / 1)
311 22.41 0.00 0.00 INTRON_3 225252 225309 174872 + L2a_3end LINE/L2 451 508 9 422
INTRON_3 225252 CCCTTGCACCTAGCACAATGCTTGGCCCATGAGAGGTACTCAATAAATAT 225301
iv i v i i v iiv ii
L2a_3end#LINE 451 CCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATAT 500
INTRON_3 225302 TGGTTGAA 225309
v
L2a_3end#LINE 501 TTGTTGAA 508
Matrix = 25p39g.matrix
Transitions / transversions = 1.60 (8 / 5)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0)
+ 5234 2.0 0.0 0.0 INTRON_3 225398 225993 (174188) C L1PA3 LINE/L1 (2) 6153 5558 276
ANNOTATION EVIDENCE:
5234 2.01 0.00 0.00 INTRON_3 225398 225993 174188 C L1PA3_3end LINE/L1 305 900 2 393
INTRON_3 225398 TTTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAATGTGC 225447
C L1PA3_3end#LI 900 TTTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAATGTGC 851
INTRON_3 225448 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCTGCACCCATT 225497
i i
C L1PA3_3end#LI 850 AGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACT 801
INTRON_3 225498 AACTCGTCATTTAGCATTAGGTATATCTCCTAATGCTATCCCTCCCCCCT 225547
i i
C L1PA3_3end#LI 800 AACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCCT 751
INTRON_3 225548 CCCCCCACCCCACAAGAGTCCCCAGAGTGTGATGTTCCCCATCCTGTGTC 225597
v v
C L1PA3_3end#LI 750 CCCCCCACCCCACAACAGTCCCCAGAGTGTGATGTTCCCCTTCCTGTGTC 701
INTRON_3 225598 CATGTGTTCTCATTGTTCAATTCCCATCTATGAGTGAGAACATGCGGTGT 225647
i i
C L1PA3_3end#LI 700 CATGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGT 651
INTRON_3 225648 TTGGTTTTTTGTCCTTGCGATAGTTTACTGAGAATGATGATTTCCAATTT 225697
i
C L1PA3_3end#LI 650 TTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGATTTCCAATTT 601
INTRON_3 225698 CATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCAT 225747
C L1PA3_3end#LI 600 CATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCAT 551
INTRON_3 225748 AGTATTCCGTGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATT 225797
i
C L1PA3_3end#LI 550 AGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATT 501
INTRON_3 225798 GTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCCGC 225847
C L1PA3_3end#LI 500 GTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCCGC 451
INTRON_3 225848 AATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAATCCT 225897
i
C L1PA3_3end#LI 450 AATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCT 401
INTRON_3 225898 TTGGATATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGT 225947
i
C L1PA3_3end#LI 400 TTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGT 351
INTRON_3 225948 TCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAA 225993
C L1PA3_3end#LI 350 TCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAA 305
Matrix = 18p39g.matrix
Transitions / transversions = 5.00 (10 / 2)
Gap_init rate = 0.00 (0 / 595), avg. gap size = 0.0 (0 / 0)
+ 185 18.4 0.0 4.1 INTRON_3 226466 226516 (173665) + (TTCA)n Simple_repeat 4 52 (0) 277
ANNOTATION EVIDENCE:
185 18.40 0.00 4.08 INTRON_3 226466 226516 173665 C (TGAA)n Simple_repeat 132 180 0 466
INTRON_3 226466 TTTATTTGTTCCTTCATTCATTCACTTTCACTCACCTATTTATTCATTCA 226515
i ii v -- i iii i
C (TGAA)n#Simpl 180 TTCATTCATTCATTCATTCATTCA--TTCATTCATTCATTCATTCATTCA 133
INTRON_3 226516 T 226516
C (TGAA)n#Simpl 132 T 132
Matrix = Unknown
Transitions / transversions = 8.00 (8 / 1)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 2.00 (2 / 1)
+ 284 31.8 0.0 0.0 INTRON_3 226619 226703 (173478) C MIRb SINE/MIR (75) 193 109 278
ANNOTATION EVIDENCE:
284 31.76 0.00 0.00 INTRON_3 226619 226703 173478 C MIRb SINE/MIR 109 193 75 423
INTRON_3 226619 ACTTAAATGTCAGAACAGCTCTCTGAGAGAGAAAATACTATTTTCCTTTT 226668
i viv v i i vi iv iv v i iii v
C MIRb#SINE/MIR 193 ATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTT 144
INTRON_3 226669 AAAGGTGAAGAATTGGATGCTCAGAGAAGTTAAGT 226703
v i i viv v i
C MIRb#SINE/MIR 143 ACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGT 109
Matrix = 25p39g.matrix
Transitions / transversions = 1.25 (15 / 12)
Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.0 (0 / 0)
+ 2388 10.3 0.0 0.0 INTRON_3 228792 229092 (171089) + AluY SINE/Alu 1 301 (10) 279
ANNOTATION EVIDENCE:
2331 10.30 0.00 0.00 INTRON_3 228792 229092 171089 + AluY SINE/Alu 1 301 10 481
INTRON_3 228792 GGCTGGGCGCGGTGGCTCACACCTATAATCCCAGCACTTTGGGAGGCAGA 228841
i i i v
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 228842 GGCAGGCAGATCAGGAGGTCAGGAGATCAAGACCATCCTGGCTAACACAG 228891
i i v i i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
INTRON_3 228892 TGAAACCCCGTCTCTATTAAAAATACAAAAAATTAGCCGGGCATGGTGGT 228941
i i i
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150
INTRON_3 228942 GGGTGCCTGTAGTCTTAGCTACTCGGGACGCTGAGGCAGGAGAATGGCAT 228991
i ii v i
AluY#SINE/Alu 151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200
INTRON_3 228992 GAACCTGGGATGTGGAGCTTGCAGTGAGCAGAGATCACACCACTGCACTC 229041
i v i v i i
AluY#SINE/Alu 201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250
INTRON_3 229042 CAGTTTGGGCAACAGTGTGAGACTCCATCTCAAAAAAAAAAAAAAGGAAA 229091
ii i v i i ii
AluY#SINE/Alu 251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300
INTRON_3 229092 A 229092
AluY#SINE/Alu 301 A 301
Matrix = 14p37g.matrix
Transitions / transversions = 4.17 (25 / 6)
Gap_init rate = 0.00 (0 / 300), avg. gap size = 0.0 (0 / 0)
+ 306 31.3 12.2 0.0 INTRON_3 229164 229294 (170887) C L1ME4a LINE/L1 (93) 6031 5885 280
ANNOTATION EVIDENCE:
306 31.30 12.21 0.00 INTRON_3 229164 229294 170887 C L1ME4a_3end LINE/L1 632 778 93 506
INTRON_3 229164 ATAATTATATCATC-AAAGACAAAAGCAGTCAATGATTTGGCATATTTCC 229212
ivi i i - i i vvi v i iiv ii
C L1ME4a_3end#L 778 ATAATCCCACCACCCAGAGATAACCACTGTTAACATTTTGGTGTATTTCC 729
INTRON_3 229213 TTCCAGTGGTTTTTTTTTTCA---GTGCATATG-----------ACTTTC 229248
vv i v v ---i i ii----------- i ?
C L1ME4a_3end#L 728 TTCCAGTCTTTTTTCTATGCATATATGTATACATTTATATATNTATTTTN 679
INTRON_3 229249 TAA-ATGGTTGAGATTATCCTGTGTGTATACTTTTGTATATTGCTTT 229294
- vii i i v i i i v ?vi
C L1ME4a_3end#L 678 TAACAAAATTGGGATCATACTGTATATACAGTTTTGTANCCTGCTTT 632
Matrix = Unknown
Transitions / transversions = 2.00 (26 / 13)
Gap_init rate = 0.03 (4 / 130), avg. gap size = 4.00 (16 / 4)
+ 235 6.8 0.0 4.5 INTRON_3 229531 229576 (170605) C L1MA5 LINE/L1 (0) 6300 6257 281
ANNOTATION EVIDENCE:
235 6.83 0.00 4.55 INTRON_3 229531 229576 170605 C L1MA5_3end LINE/L1 1004 1047 0 553
INTRON_3 229531 TTTTATTTTTTAAATTGACATATAAGAATTGTACATATTTATTGGG 229576
-- i v v
C L1MA5_3end#LI 1047 TTTTATTTTT--AATTGACACATAATAATTGTACATATTTATGGGG 1004
Matrix = 20p37g.matrix
Transitions / transversions = 0.50 (1 / 2)
Gap_init rate = 0.02 (1 / 45), avg. gap size = 2.00 (2 / 1)
+ 2421 11.3 0.5 3.6 INTRON_3 229828 230202 (169979) C THE1B LTR/ERVL-MaLR (0) 364 1 282
ANNOTATION EVIDENCE:
2421 11.33 0.53 3.57 INTRON_3 229828 230202 169979 C THE1B LTR/ERVL-MaLR 1 364 0 493
INTRON_3 229828 TGTATTAGTCCATTTTCACACTGCTAATAAAGACATACCCGAGGCTGACT 229877
ii i i i iv
C THE1B#LTR/ERV 364 TGTATTAGTCTGTTCTCACGCTGCTAATAAAGACATACCCGAGACTGGGT 315
INTRON_3 229878 AATTTACAAAAGAAAGAGGTTTCATTGAACGTACAGTTCCACCTGGCTGG 229927
i i v - i vi v
C THE1B#LTR/ERV 314 AATTTATAAAGGAAAGAGGTTTAAT-GGACTCACAGTTCCACATGGCTGG 266
INTRON_3 229928 GGAAGCCTCACAATCATGGTGGAAAGC-AAGGAGGAGCAA-GTCACATTT 229975
i i i - - ? i i
C THE1B#LTR/ERV 265 GGAGGCCTCACAATCATGGCGGAAGGCGAAGGAGGAGCAAAGKCACGTCT 216
INTRON_3 229976 TTACGTGGATGGTGGCAGGCAAAAAAAATGAGAGCTTGTGCAGGGAAACT 230025
- ---- i ------- ? i
C THE1B#LTR/ERV 215 T-AC----ATGGCGGCAGGCAA-------GAGAGCSTGTGCAGGGGAACT 178
INTRON_3 230026 CCCCCTTATAGAACCATCAGATCTCATGAGACCCATTCACTATCACAAGA 230075
i i i ii i
C THE1B#LTR/ERV 177 CCCCTTTATAAAACCATCAGATCTCGTGAGACTTATTCACTATCACGAGA 128
INTRON_3 230076 ACAGCACAGGAAAGACCTGTCCCCATAATTCATTCACCTCCCACTGGGTC 230125
i i i i v i i
C THE1B#LTR/ERV 127 ACAGCACGGGAAAGACCCGCCCCCATGATTCAATTACCTCCCACCGGGTC 78
INTRON_3 230126 CCTCCCACGATATGTGGGAATTGTGGGAGTTACAATTCAAGATGAGATTT 230175
i i i i
C THE1B#LTR/ERV 77 CCTCCCACGACACGTGGGAATTATGGGAGCTACAATTCAAGATGAGATTT 28
INTRON_3 230176 GGGTGGGGGCACAGCCAAACCATATCA 230202
i
C THE1B#LTR/ERV 27 GGGTGGGGACACAGCCAAACCATATCA 1
Matrix = 18p37g.matrix
Transitions / transversions = 6.80 (34 / 5)
Gap_init rate = 0.02 (6 / 374), avg. gap size = 2.50 (15 / 6)
+ 4588 9.6 3.6 0.7 INTRON_3 231154 231854 (168327) C L1MA2 LINE/L1 (0) 6304 5584 283
ANNOTATION EVIDENCE:
4588 9.63 3.57 0.69 INTRON_3 231154 231854 168327 C L1MA2_3end LINE/L1 331 1051 0 500
INTRON_3 231154 TTTTTATTTTTGTGCCTACATAGCAGGTATATATATTTATGGGGTACATG 231203
v vv i i
C L1MA2_3end#LI 1051 TTTTAATTTTTGTGGGTACATAGTAGGTGTATATATTTATGGGGTACATG 1002
INTRON_3 231204 AGATACTTAGGTATAGGCATGCAATGCGTAATAATCACATAATGGAAAAT 231253
ii v i i i v
C L1MA2_3end#LI 1001 AGATGTTTTGATACAGGCATGCAATGTGTAATAATCACATCATGGAAAAT 952
INTRON_3 231254 AGGGTATCCATTCCCTCAAGCATTTATCCGTTGTGATTCAAACAATCTAA 231303
i i v v v i
C L1MA2_3end#LI 951 GGGGTATCCATCCCCTCAAGCATTTATCCTTTGTGTTACAAACAATCCAA 902
INTRON_3 231304 TT--------TTACTTAATTTTAAGTGTACAATTAAATTATTATTGACTA 231345
-------- v v ? i
C L1MA2_3end#LI 901 TTATACTCTTTTAGTTATTTTSAAATGTACAATTAAATTATTATTGACTA 852
INTRON_3 231346 TAGTCCTCCTGTTGTGCTATCAAATAGTAGGTCTTATTAATTCTTTCTAA 231395
vi v v
C L1MA2_3end#LI 851 TAGTCACCCTGTTGTGCTATCAAATACTAGGTCTTATTCATTCTTTCTAA 802
INTRON_3 231396 CTATTTTTTTTTTGTACCCATTAACCATCCCCACCTCCTCACTG-CCCCG 231444
--- i ii- -
C L1MA2_3end#LI 801 CTATTTTTTT---GTACCCATTAACCATCCCCACCTCCCCACCAACCCC- 756
INTRON_3 231445 GCTACTATTCTTCCTAGCCTCTGGTAATCATCCTTCT--TCTCTATCTCT 231492
- i ii i i -- i
C L1MA2_3end#LI 755 -CCACTACCCTTCCCAGCCTCTGGTAACCATCCTTCTACTCTCTATCTCC 707
INTRON_3 231493 GAGAGTTCAATTGTTTTAACTTTTGGATCCCACAAATAAGTGAGGACATG 231542
iv i i i i
C L1MA2_3end#LI 706 ATGAGTTCAATTGTTTTGATTTTTAGATCCCACAAATAAGTGAGAACATG 657
INTRON_3 231543 TGATGTTTGTCTTTCTGTGTCTGGCTTATTTCATTTAGCATAATGACTTC 231592
i i i i i
C L1MA2_3end#LI 656 CGATGTTTGTCTTTCTGTGCCTGGCTTATTTCACTTAACATAATGACCTC 607
INTRON_3 231593 CGGTTT-----------TTGCAAATGACCC--TCTCATTCTTTTT-ATGT 231628
i i----------- vv-- - v
C L1MA2_3end#LI 606 CAGTTCCATCCATGTTGTTGCAAATGACAGGATCTCATTCTTTTTTATGG 557
INTRON_3 231629 CTGAATAGTACTCCATTGTGTATATGTACCACATTTTCTTTATCCATTCT 231678
v
C L1MA2_3end#LI 556 CTGAATAGTACTCCATTGTGTATATGTACCACATTTTCTTTATCCATTCA 507
INTRON_3 231679 TCTGCTGATGGACAATTAGATTGCTTCCAAATCTTAGCTATTGTGAACAG 231728
i v i i
C L1MA2_3end#LI 506 TCTGTTGATGGACACTTAGGTTGCTTCCAAATCTTGGCTATTGTGAACAG 457
INTRON_3 231729 TGCTGCAACAGGCATGGGAGTGCAGATAGCTCTTTGATATACTGATTTCC 231778
ii v i
C L1MA2_3end#LI 456 TGCTGCAACAAACATGGGAGTGCAGATATCTCTTCGATATACTGATTTCC 407
INTRON_3 231779 TTTCTTTTGGGTATATGCCCAGCAGTGGGATTGCTGGATCATATGACAGT 231828
i ii i
C L1MA2_3end#LI 406 TTTCTTTTGGGTATATACCCAGCAGTGGGATTGCTGGATCATATGGTAGC 357
INTRON_3 231829 TCAATTTTTACTTTCTTGAGGAACCT 231854
v v i
C L1MA2_3end#LI 356 TCTATTTTTAGTTTTTTGAGGAACCT 331
Matrix = 18p37g.matrix
Transitions / transversions = 2.00 (44 / 22)
Gap_init rate = 0.01 (8 / 700), avg. gap size = 3.75 (30 / 8)
+ 511 29.7 11.2 0.9 INTRON_3 232190 232386 (167795) C MIRb SINE/MIR (18) 250 34 284
ANNOTATION EVIDENCE:
511 29.71 11.17 0.92 INTRON_3 232190 232386 167795 C MIRb SINE/MIR 34 250 18 507
INTRON_3 232190 TATTTATCACTTAATATGTAGCCAGATACTAC---AAG------ACA--C 232228
v v i v i - ii ii--- ------ --
C MIRb#SINE/MIR 250 TATTGAGCGCTTACTGTGT-GCCAGGCACTGTGCTAAGCGCTTTACATGC 202
INTRON_3 232229 ATTATCATATTTAATTATCGTAACAATTCTGCAAGG---ATAATATTATT 232275
vi iv ii ii i ---i v i
C MIRb#SINE/MIR 201 ATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTATTATC 152
INTRON_3 232276 TTTATTTTATGGAAGAGGAAAC--AGGTATGAGGAGATTGTTTAGTTT-C 232322
iii ii v -- iviiii i ivv iii -
C MIRb#SINE/MIR 151 CCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGC 102
INTRON_3 232323 TCAAGGTCAAATAACT--T--GTGACAAAAGCCAGGTTTTAAACCCATAT 232368
i v i i -- -- i i - v ii vi
C MIRb#SINE/MIR 101 CCAAGGTCACACAGCTAGTAAGTGGCAGA-GCCAGGATTCGAACCCAGGT 53
INTRON_3 232369 CCATC-GATTCTAAAACTC 232386
iii - i i i i
C MIRb#SINE/MIR 52 CTGCCTGACTCCAAAGCCC 34
Matrix = 25p37g.matrix
Transitions / transversions = 3.46 (45 / 13)
Gap_init rate = 0.06 (11 / 196), avg. gap size = 2.18 (24 / 11)
+ 298 40.9 9.1 2.4 INTRON_3 232611 232996 (167185) + L2b LINE/L2 2923 3333 (42) 285
ANNOTATION EVIDENCE:
298 40.89 9.07 2.43 INTRON_3 232611 232996 167185 + L2b_3end LINE/L2 14 424 42 508
INTRON_3 232611 CTCTGATTACTCTCCTGCC-CATTTCCTATCCCTCTACCTCAGCTCCTTA 232659
i i ? vv iv - i i v v iiv vi v
L2b_3end#LINE 14 CCCCGNTACCTCTCTGGCCTCATCTCCTACCACTCTCCCCTTGCTCACTC 63
INTRON_3 232660 TGTTTCAGCTGCACCAAATGTGGTGGTATTATGTGAATGC---------- 232699
i i ii iiivivivv v i vivi ii ----------
L2b_3end#LINE 64 TGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCTCG 113
INTRON_3 232700 --------TTAATGTCTCTG----TGCTATTTCAGTTACCTAGAACACAC 232737
-------- i iv i i ---- i i vvi i i i v
L2b_3end#LINE 114 CTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACGCCC 163
INTRON_3 232738 TCCATACCTGCCCTCTTTGGTCTGTGAGCTCCTATTCATTTTCCTACACC 232787
i --- ii - i viiv iv i i ii i vivv i
L2b_3end#LINE 164 TTC---CCCACC-TCTTCGCCTGGCCAACTCCTACTCATCCTTCAGGTCT 209
INTRON_3 232788 CAGCTCCAGTGTTCCTTTCTTTGTGAGGCTTTCCCACAGCTTTCCCAAGC 232837
v i iv i i iiiv i ii vv v i-- i
L2b_3end#LINE 210 CAGCTCAAATGTCACCTCCTCCAGGAAGCCCTCCCTGACCC--CCCAGGC 257
INTRON_3 232838 AGAATTAGTAACTCTAATCTCTGCACTTCCA---TTACACATGCAAG--- 232881
v ii i vvi i vv vv v ii ---i v - v v---
L2b_3end#LINE 258 CGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCC-TGCCACTCT 306
INTRON_3 232882 GAGCCTTAATCAT----TTATGTATCTAT-TCCCCCTCAGAAGCCTGTGA 232926
i iiv ? ii ---- ii i i - v v i --
L2b_3end#LINE 307 GGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTGGA--CTGTGA 354
INTRON_3 232927 ACCCCTTACAGGCAGGAGTCCAGTAT-TATTCTTTGTACTTATCTCCTGC 232975
i i v ivi iii vi v - v v iiivvi i v i-
L2b_3end#LINE 355 GCTCCGTGAGGGCAGGGACCGGGTCTGTCTTGTTCACCGCTGTGTCCC-C 403
INTRON_3 232976 AGCTCCTAACAAACAATCTGG 232996
v i i v viii
L2b_3end#LINE 404 AGCGCCCAGCACAGGGCCTGG 424
Matrix = 25p37g.matrix
Transitions / transversions = 1.67 (95 / 57)
Gap_init rate = 0.04 (14 / 385), avg. gap size = 3.21 (45 / 14)
+ 255 21.3 14.5 1.4 INTRON_3 233771 233832 (166349) C L1ME3B LINE/L1 (95) 6147 6078 286
ANNOTATION EVIDENCE:
255 21.27 14.52 1.43 INTRON_3 233771 233832 166349 C L1ME3B_3end LINE/L1 825 894 95 554
INTRON_3 233771 CCATGTAACCA---------TCAAGAAATGGAACATTGCTGGCAGCCCTT 233811
i --------- i ii - iv
C L1ME3B_3end#L 894 CCGTGTAACCACCACCCAGGTCAAGAAATAGAACATTGCCAGCA-CCCCA 846
INTRON_3 233812 TAAGTTCCCTATGTGCCCTTT 233832
v ii iii i
C L1ME3B_3end#L 845 GAAGCCCCCCGCGTGCCCCTT 825
Matrix = 20p37g.matrix
Transitions / transversions = 5.50 (11 / 2)
Gap_init rate = 0.03 (2 / 61), avg. gap size = 5.00 (10 / 2)
+ 361 29.2 7.8 4.3 INTRON_3 234358 234561 (165620) C L1M5 LINE/L1 (303) 5821 5611 287
ANNOTATION EVIDENCE:
361 29.19 7.84 4.27 INTRON_3 234358 234561 165620 C L1ME4a_3end LINE/L1 358 568 303 555
INTRON_3 234358 TTTTAATGGTTGCCTAATATTCCATC--ACGAGT-----ATAGTTTACTA 234400
i v i-- i ii ----- i i v
C L1ME4a_3end#L 568 TTTTAATGGCTGCATAATATTCCATTNTATGGATGTACCATAATTTATTT 519
INTRON_3 234401 AACT-----TTTATGTGTGTGAATGGCATTTAAGTTGTTT---ATTTTTT 234442
i-----ii - - i --- i --- i
C L1ME4a_3end#L 518 AACCANTCCCCTAT-TGT-TGGA---CATTTAGGTTGTTTCCAATTTTTC 474
INTRON_3 234443 TAAAGTT-TTATAAGTAACCTTATAATAAACACTTTGATGTGTAAGTTTT 234491
---- i - i ivi iii i iii vi iii i i
C L1ME4a_3end#L 473 ----GCTATTATAAATAATGCTGCGATGAACATCCTTGTACATAAATCTT 428
INTRON_3 234492 TACCTGCATTTCAGTTTATTGGCTTAGGCTAAATTTCCCAAACTGAAATT 234541
ii?ii i v v vv v i ivi v i
C L1ME4a_3end#L 427 TGTNCACATCTCTGATTATTTCCTTAGGATAAATTCCTAGAAGTGGAATT 378
INTRON_3 234542 ACTGAGTTAAAAGTCATGCA 234561
i i i vi ?
C L1ME4a_3end#L 377 ACTGGGTCAAAGGGTATGNA 358
Matrix = 20p37g.matrix
Transitions / transversions = 3.58 (43 / 12)
Gap_init rate = 0.04 (9 / 203), avg. gap size = 2.78 (25 / 9)
+ 2399 9.6 0.3 1.0 INTRON_3 234578 234889 (165292) C AluSx3 SINE/Alu (2) 310 1 288
ANNOTATION EVIDENCE:
2272 9.09 0.96 1.29 INTRON_3 234578 234889 165292 C AluSx SINE/Alu 1 311 1 482
INTRON_3 234578 TTTTTTTTTCATTTTTTTTTTTTTTAAATTTTGAGACGGAGCCTCACTCT 234627
iv --- i i
C AluSx#SINE/Al 311 TTTTTTTTTTTTTTTTTTTTTTTTT---TTTTGAGACGGAGTCTCGCTCT 265
INTRON_3 234628 GTCGCCCAGGCTGG-GTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCC 234676
-
C AluSx#SINE/Al 264 GTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCC 215
INTRON_3 234677 ACCTCCTGAGTTCAAGCGATTCTTCTGCCTCAGCCTCCCGAGTAGCTGGG 234726
i i i i
C AluSx#SINE/Al 214 GCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGG 165
INTRON_3 234727 ATTACAGGCGCCCACCACCACGCCCAGCTAATTTTTTCTATCTTTAGTAG 234776
v i i -v i
C AluSx#SINE/Al 164 ATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTT-GTATTTTTAGTAG 116
INTRON_3 234777 AGACAGGGTTTCACCATGTTGGCCAGACTAGTCTTGAACTCCTGACCTCT 234826
i i i i v
C AluSx#SINE/Al 115 AGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCA 66
INTRON_3 234827 GG--ATTCACCCGCTTCGACCTCCCAAAGTGCTGGGATTAGAGGCATGAG 234874
-- i i i i v i
C AluSx#SINE/Al 65 GGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAG 16
INTRON_3 234875 CCACTGTATCCGGCC 234889
i iii
C AluSx#SINE/Al 15 CCACCGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 4.60 (23 / 5)
Gap_init rate = 0.01 (4 / 311), avg. gap size = 1.75 (7 / 4)
+ 310 25.6 14.9 2.8 INTRON_3 235006 235166 (165015) C MLT1J2 LTR/ERVL-MaLR (21) 427 248 289
ANNOTATION EVIDENCE:
310 25.55 14.91 2.78 INTRON_3 235006 235166 165015 C MLT1J2 LTR/ERVL-MaLR 248 427 21 594
INTRON_3 235006 ACTGAGGTAACAAAC---CCTGAAATGTCAGTAGCATAATACATTAGTAG 235052
vv --- iv v i v i v iv
C MLT1J2#LTR/ER 427 ACTGCTGTAACAAACAACCCCCAAATCTCAGTGGCTTAACACAATAAAAG 378
INTRON_3 235053 TTTATTTCTCTCTCA-G----AG--AAATGCAGATAAGGCCTTTCC---- 235091
v - ---- --v ii i -- --- i----
C MLT1J2#LTR/ER 377 TTTATTTCTCGCTCATGTCACAGTCCAATGTGGGT--GG---TTCTGGGG 333
INTRON_3 235092 --TGTGTGACTGTCTTTCAAGCG-----TCAGGAACCCAGGATATTTCTG 235134
-- v ? i v vi i v i----- i v vi ii
C MLT1J2#LTR/ER 332 GGTGGGNGGCTCTGCTCCACGCAGTCATTCAGGGACCCAGGCTCCTTCCA 283
INTRON_3 235135 T-TTGTGGCTCCACCATTTTGT--TGCCTCAAAGT 235166
- i iiiv --v ii
C MLT1J2#LTR/ER 282 TCTTGTGGCTCCGCCATCCCCTAGGGCCTCGGAGT 248
Matrix = 20p37g.matrix
Transitions / transversions = 1.29 (22 / 17)
Gap_init rate = 0.06 (10 / 160), avg. gap size = 2.90 (29 / 10)
+ 342 27.2 10.3 8.2 INTRON_3 235187 235390 (164791) C MLT1J2 LTR/ERVL-MaLR (226) 222 15 289
ANNOTATION EVIDENCE:
342 27.22 10.29 8.17 INTRON_3 235187 235390 164791 C MLT1J2 LTR/ERVL-MaLR 15 222 226 595
INTRON_3 235187 CTGACAG--GAGGAAAG---GAAAACGTGGAAGACCACACAT-AGATT-- 235228
i i -- i --- i i i i i iiiv- i --
C MLT1J2#LTR/ER 222 CCGGCAGATGGGGAAAGAGAGAGAGCGTGGAGGATCGCGTGGGAGGTTTT 173
INTRON_3 235229 -------CGGGCCTGGAGTTGCCCTATACCATTCCCACCCACATTCTATC 235271
------- i iv v v i i i i i i i
C MLT1J2#LTR/ER 172 TATGGGCCAGGCCTGGAAGTGGCGTACATCACTTCCGCCCACATTCCATT 123
INTRON_3 235272 A-CCTGAATTCAGTTACATGGCCAGGGGAGTGACAAAGCTATAGGGGAGA 235320
i- v i i ?v------- vv i ii i -
C MLT1J2#LTR/ER 122 GGCCAGAACTCAGTCACATGGCCNC-------ACCTAACTGCAAGGGAG- 81
INTRON_3 235321 GGGTGTTTAAGGCAGGAATGT-GTCTTTCTGTG---ACAGGAGGAAAATG 235366
---- i --- -- i - vv ---v v
C MLT1J2#LTR/ER 80 ----GCT---GG--GAAATGTAGTCTAGCTGTGTGCCCAGGAGGAAAAGG 40
INTRON_3 235367 AAATGG-CTTGGAGGAATAAATAGC 235390
i -? v iv i ?v
C MLT1J2#LTR/ER 39 AAACGGGNTTTGGTGAACANCTAGC 15
Matrix = 20p37g.matrix
Transitions / transversions = 2.20 (33 / 15)
Gap_init rate = 0.06 (12 / 203), avg. gap size = 3.17 (38 / 12)
+ 2490 8.8 0.3 0.0 INTRON_3 235529 235836 (164345) C AluSp SINE/Alu (4) 309 1 290
ANNOTATION EVIDENCE:
2310 10.42 0.32 0.32 INTRON_3 235529 235836 164345 C AluSx SINE/Alu 1 308 4 483
INTRON_3 235529 TTTTTTTTTTTTTTTTTTTTTTTTTTGAGATGGAGCTACGCTCTTGTTGC 235578
i iiv - i
C AluSx#SINE/Al 308 TTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCT-GTCGC 260
INTRON_3 235579 CTGGGCTGGAGTGCAACGGCACGATCTCGGCTCACCACAACCTCCACCTC 235628
ii ii i ii i
C AluSx#SINE/Al 259 CCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTC 210
INTRON_3 235629 CCGGATTCAAGTGATTCTCCTGCATCAGCCTCCCAAGTAGCTGGGATTAC 235678
i i v i
C AluSx#SINE/Al 209 CCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTAC 160
INTRON_3 235679 AGGCATGCACCACCATGCCCGGCTAATTTT-GTATTTTTAGTAAAGATGG 235727
ii i i - i i
C AluSx#SINE/Al 159 AGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGG 110
INTRON_3 235728 GGTTTCTCCATGTTGGTCAGGCTGGTCTTGAACTCCTGACCTCAGGTGAT 235777
v i i
C AluSx#SINE/Al 109 GGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGAT 60
INTRON_3 235778 CCACCCGCCTCAGCCTCACAAAGTGCTGGGATAACAGGCGTGAGCCACTG 235827
i i v v i
C AluSx#SINE/Al 59 CCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCG 10
INTRON_3 235828 CGCCCAGCC 235836
i
C AluSx#SINE/Al 9 CGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 5.40 (27 / 5)
Gap_init rate = 0.01 (2 / 307), avg. gap size = 1.00 (2 / 2)
+ 367 24.6 19.1 0.0 INTRON_3 236016 236125 (164056) + MIRb SINE/MIR 110 240 (28) 291
ANNOTATION EVIDENCE:
367 24.55 19.09 0.00 INTRON_3 236016 236125 164056 + MIRb SINE/MIR 110 240 28 509
INTRON_3 236016 CTTAACTTCTTTGGGTCTTGGTTTCCTTATCT------------------ 236047
i i i i ii i ------------------
MIRb#SINE/MIR 110 CTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 159
INTRON_3 236048 -ACCTACCTTATATGATTATTGTGACTAATTAACAACTTACTGCAGGTAA 236096
- iii v i i vv v v ii vv v v
MIRb#SINE/MIR 160 TACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAA 209
INTRON_3 236097 AGAGCTTAGAATAGTGCCTAGCACA--GTAA 236125
v v i i --
MIRb#SINE/MIR 210 AGCGCTTAGCACAGTGCCTGGCACACAGTAA 240
Matrix = 25p37g.matrix
Transitions / transversions = 1.45 (16 / 11)
Gap_init rate = 0.02 (2 / 109), avg. gap size = 10.50 (21 / 2)
+ 578 32.2 4.7 3.2 INTRON_3 236383 236597 (163584) C MIRb SINE/MIR (16) 252 35 292
ANNOTATION EVIDENCE:
578 32.19 4.65 3.21 INTRON_3 236383 236597 163584 C MIRb SINE/MIR 35 252 16 510
INTRON_3 236383 TTTGTTGAATATCTACCATATGCCAGACCCTGCTTTTTATACTTT-TATA 236431
i iiiii ii i i v ivi vviii -i i
C MIRb#SINE/MIR 252 TTTATTGAGCGCTTACTGTGTGCCAGGCACTGTGCTAAGCGCTTTACATG 203
INTRON_3 236432 CCATATCTCATGTAATTATCCTAGCAACCCTGGAAAGCAGGAGTAGTGTT 236481
vv v iv vi i vi i i ----- i
C MIRb#SINE/MIR 202 CATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGG-----TATT 158
INTRON_3 236482 TTTATCCAGATTGACTCAATAAGGAAAGTGAGGTTCAGATAA-TTAA--- 236527
v vv vvvivi i v i v i- ---
C MIRb#SINE/MIR 157 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTG 108
INTRON_3 236528 -----TCCAAGACCACAAATGCTAGTTAAGTAGCAAGATCAGGATTTAAA 236572
-----i ii v - - i iiii ii
C MIRb#SINE/MIR 107 ACTTGCCCAAGGTCACACA-GCTAGT-AAGTGGCAGAGCCAGGATTCGAA 60
INTRON_3 236573 TCCAGATCTGTCTCCCATCAAAGTC 236597
i i i vv vi i
C MIRb#SINE/MIR 59 CCCAGGTCTGCCTGACTCCAAAGCC 35
Matrix = 25p37g.matrix
Transitions / transversions = 1.91 (44 / 23)
Gap_init rate = 0.03 (6 / 214), avg. gap size = 2.83 (17 / 6)
+ 741 21.2 0.0 1.5 INTRON_3 236752 236883 (163298) C FLAM_A SINE/Alu (12) 130 1 293
ANNOTATION EVIDENCE:
580 27.07 0.00 0.00 INTRON_3 236752 236884 163297 C FLAM_C_short_ SINE/Alu 1 133 0 494
INTRON_3 236752 TTTTGTTTTTTTAATTAGAGAGCAGGTCTCACTATGTTGCCTAGGCTGGC 236801
v vv vvi i i i
C FLAM_C_short_ 133 TTTTTTTTTTTTTTTTAGAGACGGGGTCTCGCTATGTTGCCCAGGCTGGT 84
INTRON_3 236802 ATCAAACTCCTAGGCTCAAGCAATCCTCCTGCTTCAGCCTCTTCAGTAGC 236851
v i i i i i i iiv ivv
C FLAM_C_short_ 83 CTCGAACTCCTGGGCTCAAGCGATCCTCCCGCCTCGGCCTCCCAAAGTGC 34
INTRON_3 236852 TAAGTCTATAGGCACATGCTGCTGCACCCAGCC 236884
ii vi i iiiv ii i i i
C FLAM_C_short_ 33 TGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p37g.matrix
Transitions / transversions = 2.27 (25 / 11)
Gap_init rate = 0.00 (0 / 132), avg. gap size = 0.0 (0 / 0)
+ 513 23.7 9.0 3.3 INTRON_3 237107 237250 (162931) + MIRb SINE/MIR 97 248 (20) 294
ANNOTATION EVIDENCE:
513 23.70 9.03 3.29 INTRON_3 237107 237250 162931 + MIRb SINE/MIR 97 248 20 511
INTRON_3 237107 CTCAGACAAGTTACTTTAACTTTGTAAGCCTTAATTTCTTTGTCTATAAA 237156
ii i i v v i v i i i i ii i
MIRb#SINE/MIR 97 CTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAA 146
INTRON_3 237157 ATGGGCATAATAATTGGACTT-CCTCACAGAATTGTTGTGAGGAATTTAA 237205
v --- i - i ii --
MIRb#SINE/MIR 147 ATGGGGATAATAAT---ACCTACCTCGCAGGGTTGTTGTGAGGA--TTAA 191
INTRON_3 237206 ATAAGAT--TACGTGC---GTGCCTAG-----TTCCCAACATAGAGTAAA 237245
i -- i i i--- i i ----- v iii i v i
MIRb#SINE/MIR 192 ATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACACAGTAAG 241
INTRON_3 237246 C--TCAA 237250
--
MIRb#SINE/MIR 242 CGCTCAA 248
Matrix = 25p37g.matrix
Transitions / transversions = 4.50 (27 / 6)
Gap_init rate = 0.05 (7 / 143), avg. gap size = 2.57 (18 / 7)
+ 2300 10.9 0.0 0.0 INTRON_3 237321 237614 (162567) C AluSc SINE/Alu (15) 294 1 295
ANNOTATION EVIDENCE:
2083 11.90 1.02 0.00 INTRON_3 237321 237614 162567 C AluSx SINE/Alu 1 297 15 484
INTRON_3 237321 TTTTTTTTTTTTTTTGAGACAGAGTTTCAGTCTGTCACC-AGGCTGGAGT 237369
i i iv i -
C AluSx#SINE/Al 297 TTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGT 248
INTRON_3 237370 GCAGTGGCACAATCTCGGCTCACTGCAACCTCTGTCTCCCAGGTTCACGT 237419
i i i i i v i
C AluSx#SINE/Al 247 GCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGC 198
INTRON_3 237420 GATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACTGGTGCGTGCCA 237469
i i v i i
C AluSx#SINE/Al 197 GATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCA 148
INTRON_3 237470 CCACGCCCGGCTAAGTTTTGCACTTTTAGCAGAGACGGGGTTTAACCAAG 237519
v i i i v v
C AluSx#SINE/Al 147 CCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATG 98
INTRON_3 237520 TTGACCAGAATGGTCTCGATCTCTTGACCTCA--TGATCTGCCCTCCTCA 237567
i iv v i -- i v i
C AluSx#SINE/Al 97 TTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCG 48
INTRON_3 237568 GCCTCCCAAAATGCTGGGATTACAGGCGTGAGCCACTGCACCCAGCC 237614
i i i i
C AluSx#SINE/Al 47 GCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 2.89 (26 / 9)
Gap_init rate = 0.01 (2 / 293), avg. gap size = 1.50 (3 / 2)
+ 1603 22.0 12.1 1.3 INTRON_3 237935 238340 (161841) C LTR16A LTR/ERVL (2) 449 1 296
ANNOTATION EVIDENCE:
1603 21.96 12.07 1.34 INTRON_3 237935 238340 161841 C LTR16A LTR/ERVL 1 449 2 495
INTRON_3 237935 TTGCTGGTTGGGTTTCCAAGAAAGCAGATTCTGAGATGGAGATTGGCATG 237984
i v i vi i i i i i
C LTR16A#LTR/ER 449 TCGCAGGTTGGGTTCCCCGGGAAGCAGACTCTGAGACGGAGATTAGCGTG 400
INTRON_3 237985 AAGGGAATTT--TGGGGGGAAATTGTTCTTCAGAATCAACACTTTTGG-- 238030
v i?i -- i i ---- i -i i i v --
C LTR16A#LTR/ER 399 CAGGANGTTTATTAGGGAG----TGCTCTT-GGGATCAACACCTGTGGAA 355
INTRON_3 238031 GGAAAGGGAAGAAAGCAGAATTGGGCAGAGGAAGACATTGGTCTGTGATG 238080
i i i i vi iv i
C LTR16A#LTR/ER 354 GGGAAGGGAAGGAAGCAGGATTGGGCAGAGGGAGAAGTTGAGCTGCGATG 305
INTRON_3 238081 C-CTCCTAAACAAGGACTCAGT-GAGCCT----GAAGCTCTGGAGCTGGG 238124
-v i vv v i- v i---- i
C LTR16A#LTR/ER 304 CAGTCCCAACGAAGGCCTCAGCCGACCCCACGGGGAGCTCTGGAGCTGGG 255
INTRON_3 238125 ATGGCCTTTCAGA-TTG---------GAGATGAGAGGATCAGACCTTCAG 238164
i - --------- i ii i ii i i v
C LTR16A#LTR/ER 254 ATGGCCCTTCAGAGTTGTCCCGAGTTGGGGCGAGGGGGCCAGGCCTTTAT 205
INTRON_3 238165 ACTCTCACATTGACCAATCATTGGATGCAGGC--------------AGCA 238200
i i i i i i i --------------i i
C LTR16A#LTR/ER 204 ACCCCCGCATCGATCAGTCATTGGATGCGGGCTGCCCCGGGAAGGGGGCG 155
INTRON_3 238201 AGACCTTGGAAAAGATGACTCTTTTCAGCTAAGGACAATTCCTAGAGAGG 238250
v ivi ii i i i - i iii
C LTR16A#LTR/ER 154 TGACCTTGGGCGAGGCGGCTCTCTTCAGCTGAGG-CAATCCCCGAAGAGG 106
INTRON_3 238251 GTTGTCAGCTG--------------GCAACACTCCCAGCAGCCAGGAGAC 238286
i v -------------- i ii i v
C LTR16A#LTR/ER 105 GCTGACAGCTGAGGGCTGTCTGCCGGCAGCACTCCCAGCAGCTGGGGGAA 56
INTRON_3 238287 TAAGTTCTTCAATCCTGAAGGGAGATCTGGTGGGTGCAACATA-CATCCA 238335
i i i vv i v i - i
C LTR16A#LTR/ER 55 TAAGTCCTTCAGTCCTGAAGGGGGATCTGGGCGGCGCATCACAGCGTCCA 6
INTRON_3 238336 CTACA 238340
i
C LTR16A#LTR/ER 5 CCACA 1
Matrix = 18p37g.matrix
Transitions / transversions = 3.58 (68 / 19)
Gap_init rate = 0.03 (13 / 405), avg. gap size = 4.23 (55 / 13)
+ 2066 2.9 0.0 0.0 INTRON_3 238832 239076 (161105) + L1PA2 LINE/L1 5909 6153 (2) 297
ANNOTATION EVIDENCE:
2066 2.86 0.00 0.00 INTRON_3 238832 239076 161105 + L1PA2_3end LINE/L1 656 900 2 501
INTRON_3 238832 GTATATTCTCACTCATGGGTGGGAATTGAACAATGAGATCACATGGACAC 238881
i i
L1PA2_3end#LI 656 GCATATTCTCACTCATAGGTGGGAATTGAACAATGAGATCACATGGACAC 705
INTRON_3 238882 AGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTCGGGGGAGGGG 238931
v
L1PA2_3end#LI 706 AGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTGGGGGGAGGGG 755
INTRON_3 238932 GGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGATGAGTTAGGGG 238981
i v
L1PA2_3end#LI 756 GGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACGAGTTAGTGG 805
INTRON_3 238982 GTGCAGCACACCAGCATGGCACATGTATACATATGTAACTAAACTGCACA 239031
i v
L1PA2_3end#LI 806 GTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACA 855
INTRON_3 239032 ATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAAAAAAAAA 239076
L1PA2_3end#LI 856 ATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAAAAAAAAA 900
Matrix = 18p37g.matrix
Transitions / transversions = 1.33 (4 / 3)
Gap_init rate = 0.00 (0 / 244), avg. gap size = 0.0 (0 / 0)
+ 437 32.2 6.6 0.0 INTRON_3 240149 240300 (159881) C MIRc SINE/MIR (30) 238 77 298
ANNOTATION EVIDENCE:
437 32.24 6.58 0.00 INTRON_3 240149 240300 159881 C MIRc SINE/MIR 77 238 30 512
INTRON_3 240149 ACTATGTAGTTTATACAATACTTTTGTAGACATGTTTACATTTAATTATC 240198
v ii i v iii iii v vv iv i iv
C MIRc#SINE/MIR 238 ACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTGATCCTC 189
INTRON_3 240199 ACAATAACCCAGTGAGTTGGGT--GACA-------TTTTCTCCATTACAC 240239
i v v i i-- i ------- v i vi
C MIRc#SINE/MIR 188 ACAACAACCCTGTGAGGTAGGCAGGGCAGGTATTATTATCCCCATTTTAC 139
INTRON_3 240240 AGTTGAA-AAACTGGAACTTTGAGTAGTTAAATGACTGACTTAAGATTAT 240288
v i- iii iv vi i vi ii i i i
C MIRc#SINE/MIR 138 AGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCAC 89
INTRON_3 240289 AAAACTACTAAG 240300
v i v
C MIRc#SINE/MIR 88 ACAGCTAGTAAG 77
Matrix = 25p37g.matrix
Transitions / transversions = 1.88 (32 / 17)
Gap_init rate = 0.02 (3 / 151), avg. gap size = 3.33 (10 / 3)
+ 509 28.3 4.4 6.5 INTRON_3 240348 240551 (159630) + L2c LINE/L2 3188 3387 (0) 299
ANNOTATION EVIDENCE:
509 28.31 4.41 6.50 INTRON_3 240348 240551 159630 + L2c_3end LINE/L2 279 478 0 513
INTRON_3 240348 TCTGTTCT----TAGCACTTT-TACATGCTTGAATTATAGTAC--ATC-T 240389
v ---- ii - vi i ivv i -- -
L2c_3end#LINE 279 TCTGTGCTCCCATAGCACCCTGTCTATACTCCCATTATAGCACTTATCAT 328
INTRON_3 240390 TAATTGATAT-ATTACTGTGTGTTTATACATCTGTCTCCCTTACTAGATT 240438
i vi -i v i v i?ii iii i
L2c_3end#LINE 329 TAACTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACT 378
INTRON_3 240439 GTAAACTTTTTGATGGCAGGCACCTGGTCTTATTTGACTTTGTACTTTAG 240488
i i ii v v vv iiv iiiivi
L2c_3end#LINE 379 GTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCA 428
INTRON_3 240489 GCGTTTAACAGAGTTTCTGACACAATGTAACCACTCAGTATAAATTTGAT 240538
----- ------- i vv iv i i v vi v
L2c_3end#LINE 429 GC-----AC-------CTGGCACATAGTAGGCGCTCAATAAATGTTTGTT 466
INTRON_3 240539 AAAGTGAATGAAT 240551
i -
L2c_3end#LINE 467 GAA-TGAATGAAT 478
Matrix = 25p37g.matrix
Transitions / transversions = 1.79 (34 / 19)
Gap_init rate = 0.04 (8 / 203), avg. gap size = 2.75 (22 / 8)
+ 2701 17.9 1.7 0.6 INTRON_3 240794 241332 (158849) C L1MB8 LINE/L1 (7) 6171 5627 300
ANNOTATION EVIDENCE:
2701 17.91 1.67 0.55 INTRON_3 240794 241332 158849 C L1MB8_3end LINE/L1 374 918 7 502
INTRON_3 240794 ATAGCTTTCTTGAGATATAATTCACATACCATACAATTCATCCATTTAAA 240843
v i
C L1MB8_3end#LI 918 ATAGCTTTATTGAGATATAATTCACATACCATACAATTCACCCATTTAAA 869
INTRON_3 240844 GTGTACAATTCAATGTCTTTTAATATATTCATAAAGTTGTGCATTTAT-A 240892
vi i i i vii -
C L1MB8_3end#LI 868 GTGTACAATTCAATGGTTTTTAGTATATTCACAGAGTTGTGCAACCATCA 819
INTRON_3 240893 TTGCAATCAATTTTA---CATTTTCACTACTCCAAAAATGAAACCTGTAC 240939
iii - --- ii i v vi v i
C L1MB8_3end#LI 818 CCACAATCA-TTTTAGAACATTTTCATCACCCCCAAAAGAAACCCCGTAC 770
INTRON_3 240940 TCACTAGCCATCACTCCCCAAATCCCCACTCCCCTAGGCCTAGGCAGCCA 240989
i i vi vvi vii i v i i
C L1MB8_3end#LI 769 CCATTAGCAGTCACTCCCCATTCCCCCTTCCCCCCAGCCCCAGGCAACCA 720
INTRON_3 240990 CTAACCCACTTTCTATCTCTATAGTTTTTCTTATTCTGAGCATTTCATAT 241039
i i i i v v i ii
C L1MB8_3end#LI 719 CTAATCTACTTTCTGTCTCTATGGATTTGCCTATTCTGGACATTTCATAT 670
INTRON_3 241040 AAATGAAATAATATAATATGTAATCTTTGGTGACTGTCTTCATTCATTTA 241089
i v i ii v v v i
C L1MB8_3end#LI 669 AAATGGAATCATACAATATGTGGTCTTTTGTGACTGGCTTCTTTCACTTA 620
INTRON_3 241090 GCATAATGAAGTTAAGTTTCATTCATGTTGTTGCTTGTAAAAGTACTTG- 241138
i vvv i v i v v vv v-
C L1MB8_3end#LI 619 GCGTAATGTTTTCAAGGTTCATCCATGTTGTAGCATGTATCAGTACTTCA 570
INTRON_3 241139 ---CTTTTTATGGCTGAATAATATTCCATTGTATGACTATATCACATCTT 241185
--- v iv ii i
C L1MB8_3end#LI 569 TTCCTTTTTATTGCTGAATAATATTCCATTGTATGGATATGCCACATTTT 520
INTRON_3 241186 ATTTATCAATTCTGCTGCTGATGGACATTTAGATTATTTCTCTCTTTTAG 241235
v vv v i i i i ivii i
C L1MB8_3end#LI 519 ATTTATCCATTCATCAGTTGATGGACATTTGGGTTGTTTCCACTTTTTGG 470
INTRON_3 241236 CTATTATGAATAATACTGCTATAAGCATT-GTGTTCAAGTTTTTGTGTGG 241284
i i i - v
C L1MB8_3end#LI 469 CTATTATGAATAATGCTGCTATGAACATTCGTGTACAAGTTTTTGTGTGG 420
INTRON_3 241285 GCATATGTTTTTAATTCTCCTGGGTGTGTATATCTAGGAGTAGAATTG 241332
i ? i v i i -- i i
C L1MB8_3end#LI 419 ACNTATGTTTTCATTTCTCTTGGGTAT--ATACCTAGGAGTGGAATTG 374
Matrix = 18p37g.matrix
Transitions / transversions = 1.71 (60 / 35)
Gap_init rate = 0.01 (6 / 538), avg. gap size = 2.00 (12 / 6)
+ 825 19.5 6.1 3.9 INTRON_3 241369 241597 (158584) C L1ME1 LINE/L1 (138) 6306 6073 301
ANNOTATION EVIDENCE:
825 19.53 6.11 3.85 INTRON_3 241369 241597 158584 C L1ME2z_3end LINE/L1 820 1053 138 556
INTRON_3 241369 CACCTATCTATCCATCTATCCACCCATTAATCTGTCTTATTTTT-GGTGC 241417
i i v i i ii - i
C L1ME2z_3end#L 1053 CATCTATCCATCCCTCTATCCATCCATCAATCCATCTTATTTTTTGATGC 1004
INTRON_3 241418 CTTTTAACATAAGTTGCAGAAATCATTACACTTAAGCCCTAAACATTTTA 241467
v i vi i v v vv- i i i
C L1ME2z_3end#L 1003 ATTTCAAAGTAAATTGCAGACATCAGTACACTTCC-CCCTAAATACTTCA 955
INTRON_3 241468 GCATGCATATCATTAACTAAAATTTATTATTTGTATGTAGGGTTTTAAAA 241517
i i i v v ii vv ----
C L1ME2z_3end#L 954 GCATGCATATCATTAACTAGAGTTCAATATTTGTTTACAGTTTTTT---- 909
INTRON_3 241518 TTTTCACATAAAGTTTGCATACAATTAAATGCACCAAAAATC---AGTAT 241564
- v vi i i v --- --- i
C L1ME2z_3end#L 908 -TTTGAGGTAAAATTTACATACAATGAAATGCAC---AAATCTTAAGTGT 863
INTRON_3 241565 ATGTTCACT----------AAATGCAATCACATGTGTAACCCA 241597
ii iv ---------- vv v
C L1ME2z_3end#L 862 ACATTCGATGAGTTTTGACAAATGCATACACCTGTGTAACCCA 820
Matrix = 20p37g.matrix
Transitions / transversions = 1.39 (25 / 18)
Gap_init rate = 0.03 (6 / 228), avg. gap size = 3.83 (23 / 6)
+ 337 27.4 4.7 0.9 INTRON_3 241600 241706 (158475) C MIR3 SINE/MIR (11) 197 87 302
ANNOTATION EVIDENCE:
337 27.35 4.67 0.90 INTRON_3 241600 241706 158475 C MIR3 SINE/MIR 87 197 11 514
INTRON_3 241600 TTATAGGGTTTTA-AGTTAGAAAGTACTGTGGAGGT-AT-TAGACAACAC 241646
i ii v i - i i i v iv i i - - v v -
C MIR3#SINE/MIR 197 TCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCA-AC 149
INTRON_3 241647 CCTCCCATTTTACAGAGGA--AAACTGATATCCTGAGAGGGTGAGTAACT 241694
i i v -- vii v vvi i
C MIR3#SINE/MIR 148 CCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACT 99
INTRON_3 241695 TGTCCAAAATCA 241706
i ii
C MIR3#SINE/MIR 98 TGCCCAAGGTCA 87
Matrix = 25p37g.matrix
Transitions / transversions = 1.90 (19 / 10)
Gap_init rate = 0.05 (5 / 106), avg. gap size = 1.20 (6 / 5)
+ 711 27.6 6.3 2.0 INTRON_3 242305 242555 (157626) C MIRb SINE/MIR (6) 262 1 303
ANNOTATION EVIDENCE:
711 31.37 4.87 1.28 INTRON_3 242305 242530 157651 C MIRb SINE/MIR 29 262 6 515
INTRON_3 242305 AGAGCTGGTAATTATAATTGAGCATGTGCCATATGCCAGGCGTTATGTTA 242354
ivi v --- iiv i ii i ii i i
C MIRb#SINE/MIR 262 AGAGCTACCATTTAT---TGAGCGCTTACTGTGTGCCAGGCACTGTGCTA 216
INTRON_3 242355 ACTGCTTTACATGCATTACCTC-TTTAATCCTTATAAT---CCT-CATAG 242399
vi i - i i i--- - ivi
C MIRb#SINE/MIR 215 AGCGCTTTACATGCATTATCTCATTTAATCCTCACAACAACCCTGCGAGG 166
INTRON_3 242400 T-GCTATTATTATGAATATTTAACAGCTGAGGAAACATAGGCCTACAAAG 242448
- v vvvi v v vv ii v i
C MIRb#SINE/MIR 165 TAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAG 116
INTRON_3 242449 GTTAAGTAGCTTGCTTAAAATCATTCAA-----AAGTGATGTGGTCAGAA 242493
ii ii ii iv i----- iiivi i i
C MIRb#SINE/MIR 115 GTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCAGGA 66
INTRON_3 242494 TTAAATTCTAAGCCTGTCAGTTCTCAGAGCACATGTT 242530
vi vi i i i i v viii i v i i
C MIRb#SINE/MIR 65 TTCGAACCCAGGTCTGCCTGACTCCAAAGCCCGTGCT 29
Matrix = 25p37g.matrix
Transitions / transversions = 2.33 (49 / 21)
Gap_init rate = 0.03 (6 / 225), avg. gap size = 2.33 (14 / 6)
692 27.37 6.38 2.04 INTRON_3 242321 242555 157626 C MIR SINE/MIR 1 245 17 516
INTRON_3 242321 ATTGAGCATGTGCCATATGCCAGGCGTTATGTTAACTGCTTTACATGCAT 242370
iiv i i i ii i vi vi i
C MIR#SINE/MIR 245 ATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTAT 196
INTRON_3 242371 TACCTC-TTTAATCCTTATAAT--CCTCATA------GTGCTATTATTAT 242411
v - i i i-- ii i------ i
C MIR#SINE/MIR 195 TAACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTAT 146
INTRON_3 242412 GAATATTTAACAGCTGAGGAAACATAGGCCTACAAAGGTTAAGTAGCTTG 242461
vvvi v v vv vi v i i
C MIR#SINE/MIR 145 CCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAGGTTAAGTAACTTG 96
INTRON_3 242462 CTTAAAATCATTCAAA-AGTGATGTGGTCAGAATTAA-ATTCTAAGCCTG 242509
ii ii iv iv- i - - iiiii- v v v
C MIR#SINE/MIR 95 CCCAAGGTCACACAGCTAGTAA-GTGG-CAGAGCCGGGATTCGAACCCAG 48
INTRON_3 242510 TCAGTT---CTC-AGAGCACATGTTATATAAACTCTCTCTGTTATACTGT 242555
v i--- - iv i i v - --i v v i
C MIR#SINE/MIR 47 GCAGTCTGGCTCCAGAGTCCGTGCTCT-TAA--CCACTATGCTATACTGT 1
Matrix = 25p37g.matrix
Transitions / transversions = 1.74 (40 / 23)
Gap_init rate = 0.05 (11 / 234), avg. gap size = 1.82 (20 / 11)
+ 444 32.1 10.2 0.0 INTRON_3 242559 242815 (157366) + L3 LINE/CR1 4150 4441 (48) 304
ANNOTATION EVIDENCE:
444 32.03 9.96 0.00 INTRON_3 242559 242789 157392 + L3 LINE/CR1 4150 4403 86 517
INTRON_3 242559 CAAGATAGGCAGCTTTTAATATTTGAAGG-CTGTCA------ATAAAGAT 242601
v viiv iv - ------ v ii
L3#LINE/CR1 4150 CATGATAGCTGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGAT 4199
INTRON_3 242602 TATA-TGA----GAGTAGTTCCAGAGGGCAGAACTTGGCCAAATA--TGG 242644
v - v ---- v i i v viv i i--
L3#LINE/CR1 4200 TAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGATCAGTGGGTGG 4249
INTRON_3 242645 CCATCAGAGGGAAGTTTATTTAGACTCAGCAT--GGAAAGATTTTCTGAC 242692
vvi i v i ivv vii ii -- ii i i
L3#LINE/CR1 4250 AAGTTACAGGGAGGCAGATTTCAGCTCAATATAAGGAAGAACTTTCTAAC 4299
INTRON_3 242693 ---C-GAGCTGTCAAGAAGTGGGCAAGGCAGCCCTGTTTAGCAGCAAGCT 242738
--- - v i i ivvi v i vvvi i ii
L3#LINE/CR1 4300 AATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTTGGGAGGTAGTGAGCT 4349
INTRON_3 242739 TCA-GACATAAGAAATATTCAGGTAG-GGCTAGGTGACTG-TTGTAGAAA 242785
i v- v ivi ii i i - i i ii- viiii
L3#LINE/CR1 4350 CCCTGTCACTGGAGGTATTCAAGCAGAGGCTGGATGACCACTTGTCAGGG 4399
INTRON_3 242786 ATGT 242789
L3#LINE/CR1 4400 ATGT 4403
Matrix = 25p37g.matrix
Transitions / transversions = 1.64 (46 / 28)
Gap_init rate = 0.05 (11 / 230), avg. gap size = 2.09 (23 / 11)
333 32.93 12.80 0.00 INTRON_3 242652 242815 157366 + L3 LINE/CR1 4257 4441 48 518
INTRON_3 242652 AGGGAAGTTTATTTAGACTCAGCAT--GGAAAGATTTTCTGAC---C-GA 242695
i ivv vii ii -- ii i i --- -
L3#LINE/CR1 4257 AGGGAGGCAGATTTCAGCTCAATATAAGGAAGAACTTTCTAACAATCAGA 4306
INTRON_3 242696 GCTGTCAAGAAGTGGGCAAGGCAGCCCTGTTTAGCAGCAAGCTTCA-GAC 242744
v i i ivvi v i vvvi i ii i v- v
L3#LINE/CR1 4307 GCTGTCCAAAAATGGAATGGGCTGCCTTGGGAGGTAGTGAGCTCCCTGTC 4356
INTRON_3 242745 ATAAGAAATATTCAGGTAG-GGCTAGGTGAC-------------TGTTGT 242780
ivi ii i i - i i -------------
L3#LINE/CR1 4357 ACTGGAGGTATTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGT 4406
INTRON_3 242781 AGAAAATGTATTTGCATTCAGTTGGAGATTGGATT 242815
iivi vii vii v ? i
L3#LINE/CR1 4407 AGAAGGGATTCCTGCATTGGATGGGAGNTTGGACT 4441
Matrix = 25p37g.matrix
Transitions / transversions = 2.12 (36 / 17)
Gap_init rate = 0.04 (6 / 163), avg. gap size = 3.50 (21 / 6)
+ 2936 23.5 4.2 1.8 INTRON_3 242862 243583 (156598) C L1ME1 LINE/L1 (1) 6178 5440 305
ANNOTATION EVIDENCE:
2936 23.54 4.16 1.76 INTRON_3 242862 243583 156598 C L1ME1_3end LINE/L1 187 925 1 557
INTRON_3 242862 TTTTCCAAATCAACTGTATTGAAATAAAATTAACACACAATAAAATGTAC 242911
iv i v ii v ? i vi
C L1ME1_3end#LI 925 TTTTTAAAATCAGCTTTATTGAGGTATAATTNACATACAATAAAATTCAC 876
INTRON_3 242912 CCA----AATTGTA------AATG---TTTAACAAATTTATACAACCATG 242948
i?---- v ------i --- i v ?i i
C L1ME1_3end#LI 875 CTNTTTTAAGTGTACAGTTCGATGAGTTTTGACAAATGTATACANTCGTG 826
INTRON_3 242949 TAACTGCCATCAAAATCAAGATATAAGGTATTTCAGCAAGCTCCAAAAGT 242998
ii i v iiii viiv v i
C L1ME1_3end#LI 825 TAACCACCACCACAATCAAGATATAGAACATTTCCATCACCCCCAAAAGT 776
INTRON_3 242999 GTTGTTGTGCTCCTCCTTGGCTAA-CACCTCCTCC-ATCCCCAGCCCCAA 243046
viiv ii i iiv i ii - v i - i vi
C L1ME1_3end#LI 775 TCCCTCATGCCCCTTTGTAGTCAATCCCCTCCCCCCACCCCCAGCCCCTG 726
INTRON_3 243047 ACAATCACTAATCTGCTTTCTGTCACCTTAGGTTAAATTGTTTTTTTCTA 243096
i i i iv v ---- ii -
C L1ME1_3end#LI 725 GCAACCACTGATCTGCTTTCTGTCACTATAGTTT----TGCCTTTT-CTA 681
INTRON_3 243097 GAGTTTCGTATAAATGAAATCATTCTGTATGTCATCTTT-GTGTCTGGAG 243145
i i i v v vi - vv
C L1ME1_3end#LI 680 GAATTTCATATAAATGGAATCATACAGTATGTAGTCTTTTGTGTCTGGCT 631
INTRON_3 243146 GTCTTTGCTCAGCACAGTAACTCTGAGATTCATTCATGTTGTTGCACATA 243195
vii ii i i i ivi i i ii
C L1ME1_3end#LI 630 TCTTTCACTTAGCATAATGCTTTTGAGATTCATCCATGTTGTTGCATGTA 581
INTRON_3 243196 TCAAGCACTCATTCCTTTTTACTGCTGAGTAGTATTCTACTGTATGAATA 243245
vvii i i i i
C L1ME1_3end#LI 580 TCAATAGTTCATTCCTTTTTATTGCTGAGTAGTATTCCATTGTATGGATA 531
INTRON_3 243246 TACCACAATTTCTTTATTCATATACCTGTTGATGGACATTTGGGTTGTTT 243295
v i vi ?
C L1ME1_3end#LI 530 TACCACAATTTGTTTATCCATTCACCNGTTGATGGACATTTGGGTTGTTT 481
INTRON_3 243296 CCAGTTTTTAGCTACTATTAATAAAACTGCTATGAGTATTTATGTATACA 243345
i i iv i ii ii i vi
C L1ME1_3end#LI 480 CCAGTTTTTGGCTATTACGAATAAAGCTGCTATGAACATTCGTGTACAGG 431
INTRON_3 243346 TTTTTATATGTACATATGTGTTTGTTTCTCTTCAGTAAATAACTAGGAGT 243395
i i i v v ii vi v
C L1ME1_3end#LI 430 TCTTTGTGTGGACATATGTTTTCATTTCTCTTGGGTAAATACCTAGGAGT 381
INTRON_3 243396 GGAATTCATGGGTTGTATGGTAAATTCA--------------AGAAATTG 243431
vv ii i vi -------------- i
C L1ME1_3end#LI 380 GGAATTGCTGGGTCATATGGTAAGTGTATGTTTAACTTTATAAGAAACTG 331
INTRON_3 243432 CCAAATTGTGTTTGCAAAGTGATGGTACTATTTTACATTCCTTCAAGTAA 243481
i - v iiv i i iv v i
C L1ME1_3end#LI 330 CCAAACTGT-TTTCCAAAGTGGCTGTACCATTTTGCATTCCCACCAGCAA 282
INTRON_3 243482 TGTATGAGAGATTTGATTTTTCCACATCTTCACCAACATTTAATATTATC 243531
v iiii vi i i i i i ii i
C L1ME1_3end#LI 281 TGTATGAGAGTTCCAGTTGCTCCGCATCCTCGCCAGCACTTGGTATTGTC 232
INTRON_3 243532 AATATTTAGTATTTTACATTTTATCTACTTTGACGAACATGTACAGGTAT 243581
i v ------ - v i i i i i iiii vv
C L1ME1_3end#LI 231 AGTCTTT------TTA-ATTTTAGCCATTCTAATGGGTGTGTAGTGGTAT 189
INTRON_3 243582 CT 243583
C L1ME1_3end#LI 188 CT 187
Matrix = 20p37g.matrix
Transitions / transversions = 2.47 (116 / 47)
Gap_init rate = 0.02 (12 / 721), avg. gap size = 3.58 (43 / 12)
+ 321 16.8 4.4 2.1 INTRON_3 243595 243685 (156496) C L1MA10 LINE/L1 (1) 6333 6241 306
ANNOTATION EVIDENCE:
321 16.84 4.40 2.15 INTRON_3 243595 243685 156496 C L1MA10_3end LINE/L1 988 1080 1 503
INTRON_3 243595 TTTTTTATAACAGTTTTGTTGGAGTATAATTGACATTACAATAAGCTGCA 243644
- i i ii i - v i
C L1MA10_3end#L 1080 TTTTTTA-AACAGCTTTATTGAGGTATAATTGATAT-ACAAAAAACTGCA 1033
INTRON_3 243645 CTTA---AAAGTGTTCAATTTGATAAGTTTTGGCATAT-CATATA 243685
v --- v i v i v i - i
C L1MA10_3end#L 1032 CATATTTAATGTATACAATTTGATGAGTTTGGACATATGCATACA 988
Matrix = 18p37g.matrix
Transitions / transversions = 2.00 (10 / 5)
Gap_init rate = 0.04 (4 / 90), avg. gap size = 1.50 (6 / 4)
+ 3387 19.1 4.0 4.7 INTRON_3 243768 244226 (155955) C L1ME1 LINE/L1 (133) 6046 5579 301
ANNOTATION EVIDENCE:
3387 19.06 4.01 4.67 INTRON_3 243768 244226 155955 C L1ME1_3end LINE/L1 326 793 133 558
INTRON_3 243768 TCCATCATCCCCCAAAGTTTTCTCACGCCTCTT----ACCAACTTTTCCC 243813
i v ii i i ----ii --- i
C L1ME1_3end#LI 793 TCCATCACCCCCAAAAGTTCCCTCATGCCCCTTTGTAGTCAA---TCCCC 747
INTRON_3 243814 TCCCTTC--CTCCACTTTGTCCCAGGTAAC-ACTGATTTGCTTTTAATCA 243860
ii -- i ---- i v i - i ivi
C L1ME1_3end#LI 746 TCCCCCCACCCCCA----GCCCCTGGCAACCACTGATCTGCTTTCTGTCA 701
INTRON_3 243861 CTATATATTAGTTTGTATTTTCTTGAACTGTACATAAATGGAATATTACA 243910
----iv iv v i vi i vv
C L1ME1_3end#LI 700 CTATA----GTTTTGCCTTTTCTAGAATTTCATATAAATGGAATCATACA 655
INTRON_3 243911 GTTTGTA-----CTGGGTTTTGGCTTCTTTTACTCCGTACAATTATATTA 243955
v -----i v i - i iv i i vv v i
C L1ME1_3end#LI 654 GTATGTAGTCTTTTGTGTCT-GGCTTCTTTCACTTAGCATAATGCTTTTG 606
INTRON_3 243956 ATATTCATCCATGTTGT-------------AGT--GTTCCTTTTTATTGA 243990
v ------------- --i v
C L1ME1_3end#LI 605 AGATTCATCCATGTTGTTGCATGTATCAATAGTTCATTCCTTTTTATTGC 556
INTRON_3 243991 CAAGTGGTGTTCCATTGTATGGCTATACCACAGCTTGCTTATAAATTCAT 244040
ii i i v ii i vv i
C L1ME1_3end#LI 555 TGAGTAGTATTCCATTGTATGGATATACCACAATTTGTTTATCCATTCAC 506
INTRON_3 244041 TTATTGATGGACATTTGAGTTGTTTCTAGCTTTTGATTGTTAAAGATAAA 244090
i?i i i i ii i vii
C L1ME1_3end#LI 505 CNGTTGATGGACATTTGGGTTGTTTCCAGTTTTTGGCTATTACGAATAAA 456
INTRON_3 244091 GCTACTATGAATATGCTTGTACAAGTCTTTATGTAGACATATGCTTTTAT 244140
i i v v i i i i i
C L1ME1_3end#LI 455 GCTGCTATGAACATTCGTGTACAGGTCTTTGTGTGGACATATGTTTTCAT 406
INTRON_3 244141 TCCTTTTGGTCAAATACCTAGGAGTAGAATGGCTGAATCACAATTGGCAA 244190
i i vi i v ii i -- i
C L1ME1_3end#LI 405 TTCTCTTGGGTAAATACCTAGGAGTGGAATTGCTGGGTCATA--TGGTAA 358
INTRON_3 244191 GTGTATGTTTAACTTTGTAAGAAACTGCCAGAATAC 244226
i i ----
C L1ME1_3end#LI 357 GTGTATGTTTAACTTTATAAGAAACTGCCAAA---- 326
Matrix = 20p37g.matrix
Transitions / transversions = 2.56 (64 / 25)
Gap_init rate = 0.03 (12 / 458), avg. gap size = 3.75 (45 / 12)
+ 1631 10.1 2.0 5.0 INTRON_3 244227 244474 (155707) + AluSz6 SINE/Alu 72 312 (0) 307
ANNOTATION EVIDENCE:
1550 10.61 2.02 4.98 INTRON_3 244227 244474 155707 + AluSx SINE/Alu 72 312 0 485
INTRON_3 244227 CAGGAGTTTGAGACCAGCCTGGCCAACATGAAGAAACCCTGTCTCTACTA 244276
i iv i
AluSx#SINE/Al 72 CAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTA 121
INTRON_3 244277 AAAATACAAAA-TTAGCTGGGCGTGGTGATGCACACCTGTAATCCCAGCT 244325
- i ii i i
AluSx#SINE/Al 122 AAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCT 171
INTRON_3 244326 ACTCGGGAAGCTGAGGCATGAGAATTGCTTGAACCCAGGAGGCAGAAGTT 244375
i v i i i i
AluSx#SINE/Al 172 ACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTT 221
INTRON_3 244376 GCAGTGAGCCAAGATCGCGCCACTGCACTCCGGCCTGGGCAACAGCATG- 244424
i i i vii -
AluSx#SINE/Al 222 GCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGA 271
INTRON_3 244425 ---TTTGTCTCAACAGCAAACAAACAAACGAAACTCAAAAAAAAAAAAAA 244471
--- ii ---- v v --------
AluSx#SINE/Al 272 GACTCCGTCTCAA----AAAAAAAAAAA--------AAAAAAAAAAAAAA 309
INTRON_3 244472 AAA 244474
AluSx#SINE/Al 310 AAA 312
Matrix = 14p37g.matrix
Transitions / transversions = 4.00 (20 / 5)
Gap_init rate = 0.02 (4 / 247), avg. gap size = 4.25 (17 / 4)
+ 3387 19.6 3.5 3.4 INTRON_3 244475 244962 (155219) C L1ME1 LINE/L1 (601) 5578 5101 301
ANNOTATION EVIDENCE:
3387 19.06 4.01 4.67 INTRON_3 244475 244812 155369 C L1ME1_3end LINE/L1 1 325 601 559
INTRON_3 244475 AAAAAGACACTGCCAAAATATTTTTCAA-GTGATGGTACCATTTTACATT 244523
--------- -------- i - iiv i
C L1ME1_3end#LI 325 ---------CTG--------TTTTCCAAAGTGGCTGTACCATTTTGCATT 293
INTRON_3 244524 TCCATCAGCAATGTCTAAGAATTTTCATTCCTCTACCTCCTCACCAAAAC 244573
i i v i i iivi v ii v i iv
C L1ME1_3end#LI 292 CCCACCAGCAATGTATGAGAGTTCCAGTTGCTCCGCATCCTCGCCAGCAC 243
INTRON_3 244574 TTGCTATTGTCAGTCTTTT-ATTTTTAGCCATTTTAATAGGTGTGCAGTA 244622
v - v i i i i
C L1ME1_3end#LI 242 TTGGTATTGTCAGTCTTTTTAATTTTAGCCATTCTAATGGGTGTGTAGTG 193
INTRON_3 244623 GTCCTTCATTCTGGTTTTAATTTACATTTTCCTAATAATTTATAATGTTG 244672
vii v i i i i v i
C L1ME1_3end#LI 192 GTATCTCATTGTGGTTTTAATTTGCATTTCCCTAATGACTAATGATGTTG 143
INTRON_3 244673 AACATTTTTTTCATGGGCTTATTTGCCATCTATAT---TCCTTTGGTGAA 244719
i i - v i --- i
C L1ME1_3end#LI 142 AGCATCTTTT-CATGTGCTTATTTGCCATCCATATATCTTCTTTGGTGAA 94
INTRON_3 244720 GTATAGGTTCAAATCTTTTGCCCATTTTAAAATTTGGCTGTTTGTTTTCA 244769
i vv vv v i v
C L1ME1_3end#LI 93 GTGTCTGTTCAAATCTTTTGCCCATTTTTTAATTGGGTTGTTTGTTTTCT 44
INTRON_3 244770 TATTATTGAGTTTTAAGGGTTGTTTATATCATCTGGATACAAG 244812
i i v vv
C L1ME1_3end#LI 43 TATTATTGAGTTTTGAGAGTTCTTTATATATTCTGGATACAAG 1
Matrix = 20p37g.matrix
Transitions / transversions = 1.62 (34 / 21)
Gap_init rate = 0.02 (6 / 337), avg. gap size = 3.83 (23 / 6)
1157 20.95 2.35 0.66 INTRON_3 244665 244962 155219 C L1MD_orf2 LINE/L1 2992 3294 0 560
INTRON_3 244665 TAATGTTGAACATTTTTTTCATGGGCTTATTTGCCATCTATAT-TCCTTT 244713
i i - v i - i
C L1MD_orf2#LIN 3294 TGATGTTGAACATCTTTT-CATGTGCTTATTTGCCATCTGTATATCCTCT 3246
INTRON_3 244714 --GGTGAAGTATAGGTTCAAATCTTTTGCCCATTTTAAAATTTGGCTGTT 244761
-- i i vvv vi vv v ii
C L1MD_orf2#LIN 3245 TCGGTGAAATGTCTCTTCATGTCTTTTGCCCATTTTCTAATTGGATTGTT 3196
INTRON_3 244762 TGTTTTCATATTATTGAGTTTTAAGGGTTGTTTATATCATCTGGATACAA 244811
iv i i i i v vv i v
C L1MD_orf2#LIN 3195 TGTTTTTTTACTGTTGAGTTTTGAGAGTTCTTTATATATTCTAGATACTA 3146
INTRON_3 244812 GTCCTTTATCAGATATATGGTTTGTAAATATTTTTCTCCCTTTGTGTTAC 244861
i i i i - v? v vi
C L1MD_orf2#LIN 3145 GTCCTTTGTCGGATATGTGGTTTGCAAATATTTT-CTCCCANTCTGTAGC 3097
INTRON_3 244862 TTGTTATTTCATTCTCTTGATTGTGTCTTTCAACAAGCAAATGCTTC-AA 244910
iv i i iv v ivvi v i i-
C L1MD_orf2#LIN 3096 TTGTCTTTTCATCCTCTTAACAGGGTCTTTCGCAGAGCAAAAGTTTTTAA 3047
INTRON_3 244911 TTTTAATGAAGTCAAATTTATCGATTTTTAAA---ATAGACTATGCTTTT 244957
i v i vvv--- i iii
C L1MD_orf2#LIN 3046 TTTTGATGAAGTCCAATTTATCAATTTTTCCTTTTATGGATCGTGCTTTT 2997
INTRON_3 244958 GTTGT 244962
v
C L1MD_orf2#LIN 2996 GGTGT 2992
Matrix = 20p37g.matrix
Transitions / transversions = 1.26 (34 / 27)
Gap_init rate = 0.02 (6 / 297), avg. gap size = 1.50 (9 / 6)
+ 824 26.6 1.5 1.0 INTRON_3 244968 245168 (155013) + MER58A DNA/hAT-Charlie 15 216 (8) 308
ANNOTATION EVIDENCE:
824 26.63 1.49 0.99 INTRON_3 244968 245168 155013 + MER58A DNA/hAT-Charlie 15 216 8 596
INTRON_3 244968 CTAGAGCCCATGGGTCAAATCTGGCCTGCTGCCTGTTTTGGGCAATAAAG 245017
vi ii i i i i v vv
MER58A#DNA/hA 15 CTACGGCCCGCGGGCCAAATCCGGCCCGCCGCCTGTTTTTGTAAATAAAG 64
INTRON_3 245018 TTATTTTGGATCACAGCCATGT--ATTCTTGTTTACATGTCGTTTGCAAT 245065
v v v i i-- -- i i i i iiiii
MER58A#DNA/hA 65 TTTTATTGGAACACAGCCACGCCCATTC--GTTTACGTATTGTCTATGGC 112
INTRON_3 245066 TGCTTTCAAGCTACAAAAGCACA-CAGAATTGCTGGAACGAAGACCACAT 245114
iv vi v -iv i v i vi ii ii
MER58A#DNA/hA 113 TGCTTTCGCGCTACAACGGCAGAGTTGAGTAGTTGCGACAGAGACCGTAT 162
INTRON_3 245115 GGCACACAAAATCTGAAATATTTACTTTTTTGCCCTTTGCAGAAAAAATT 245164
v i ii i v i v i i
MER58A#DNA/hA 163 GGCCCGCAAAGCCTAAAATATTTACTATCTGGCCCTTTACAGAAAAAGTT 212
INTRON_3 245165 TATC 245168
ii
MER58A#DNA/hA 213 TGCC 216
Matrix = 20p37g.matrix
Transitions / transversions = 2.31 (37 / 16)
Gap_init rate = 0.01 (3 / 200), avg. gap size = 1.67 (5 / 3)
+ 694 25.4 6.2 0.3 INTRON_3 245169 245456 (154725) C L1ME1 LINE/L1 (1067) 5079 4775 301 *
ANNOTATION EVIDENCE:
694 25.43 6.25 0.33 INTRON_3 245169 245456 154725 C L1M4_orf2 LINE/L1 2666 2970 324 561
INTRON_3 245169 TAAGCCAAGG-CACAAAGTTTT--TCCTGTAGTTTTTGTATA---CTTTT 245212
v - i v --? i - iv v ---v
C L1M4_orf2#LIN 2970 TAACCCAAGGTCACGAAGATTTACNCCTAT-GTTTTCTTCTAAGAGTTTT 2922
INTRON_3 245213 GGAGTTTTATGTTTTGCATTTAGGTGTATTATCCATTTT----TATCTTT 245258
iv vv i i v ? v ---- vi
C L1M4_orf2#LIN 2921 ATAGTTTTAGCTCTTACATTTAGGTCTSTGATCCATTTTGAGTTAATTTT 2872
INTRON_3 245259 TTCTTATGTTTAGAGTTATGGATCAAAGTTTGCTGTTTTATACATGGACA 245308
viv v vv v v i v v iii v ii ii ?i
C L1M4_orf2#LIN 2871 TGTATATGGTGTGAGGTAGGGGTCCAACTTCATTCTTTTGCATGTGGMTA 2822
INTRON_3 245309 TA----TGTTCCAGCACAATTTGTTGAGCAAACTATTCTTTCTCCACTGA 245354
v---- i v iv i i i
C L1M4_orf2#LIN 2821 TCCAGTTGTCCCAGCACCATTTGTTGAAAAGACTATTCTTTCCCCATTGA 2772
INTRON_3 245355 ATTGCCTTTGCACTTTTGTC-AAAATCAGTTTTCCAAATAAGT-TTTGTT 245402
v i v ii - i vv v v v - vv
C L1M4_orf2#LIN 2771 ATGGTCTTGGCACCCTTGTCGAAAATCAATTGACCATAAATGTATGGGTT 2722
INTRON_3 245403 TATTTCTGGACTCT--ATTGTTTTCCATGTGTCTATCTGTTGATCTTTAC 245450
-- v v vvi v iv i i
C L1M4_orf2#LIN 2721 TATTTCTGGACTCTCAATTCTATTCCATTGATCTATATGTCTATCCTTAT 2672
INTRON_3 245451 ACCAGT 245456
i
C L1M4_orf2#LIN 2671 GCCAGT 2666
Matrix = 20p37g.matrix
Transitions / transversions = 0.79 (31 / 39)
Gap_init rate = 0.03 (9 / 287), avg. gap size = 2.11 (19 / 9)
+ 3009 17.1 3.7 2.7 INTRON_3 245453 246890 (153291) C L1MC3 LINE/L1 (1568) 6217 4643 309
ANNOTATION EVIDENCE:
3009 16.31 4.62 1.80 INTRON_3 245453 246101 154080 C L1MC3_3end LINE/L1 298 964 1568 562
INTRON_3 245453 CAGTTGGATTGTATTGTTACATTCTGCAGTCCATCTTGGAATCCTCTGAT 245502
i ? v i v i i i ii
C L1MC3_3end#LI 964 CAGTTAGATTNTTTTGTCACATTCTGCATTCCATCCTGGGATCCCCCAAT 915
INTRON_3 245503 CTCCTAAATAGTTTTCTATAATTTGCATACGTTAAGGTTCACTTTTGTGT 245552
ii i v i i -
C L1MC3_3end#LI 914 CTCCTAAATGATTTTTTAAAATTTGCATACATTAAGGTTCACTCTT-TGT 866
INTRON_3 245553 GCTGT-----TTTATTT-TTTTGTCAAATGGATTGTGTCATGTACCTACT 245596
----- i vv- v v v ? i i i
C L1MC3_3end#LI 865 GCTGTAAAGTTCTATGGGTTTTGACAAATGTATAGTGTNATGTATCCACC 816
INTRON_3 245597 GCTATAATAT---ACAGAATAGTTTCATCACCCTAAAAAAAATCTCTACT 245643
ii i i --- iii -- i --
C L1MC3_3end#LI 815 ATTACAGTATCATACAGAATAGTTTCACTGCCCTAAAAAA--TCCC--CT 770
INTRON_3 245644 GT-------CTATTCAACCAT--CCCTTCCTTCCTCTGAGCCCCT-AGAA 245683
------- v -- i v - - i - v
C L1MC3_3end#LI 769 GTGCTTCACCTATTCAACCCTTNCCCCTACT-CCTC-GAACCCCTGACAA 722
INTRON_3 245684 ACACTGATCTTTTTACTATCTTGATA-TTTTGCCTTTTCCAGAATGTCAT 245732
v v i iv -
C L1MC3_3end#LI 721 CCACTGATCTATTTACCATCTCTATAGTTTTGCCTTTTCCAGAATGTCAT 672
INTRON_3 245733 ATATTTGGAATCATACCGTACCATACCCTTTTCATGTACTAGTTTCTTTT 245782
v v i-i v - - i i i
C L1MC3_3end#LI 671 ATAATTGGAATCATACAGTAT-GTAGCCTTTTCA-G-ACTGGCTTCTTTC 625
INTRON_3 245783 ACTTAG---TATGCGTTTAAGATTAATCCATGTCTTT--GTGGCTTGATA 245827
--- i v --i
C L1MC3_3end#LI 624 ACTTAGCAATATGCATTTAAGATTCATCCATGTCTTTTTATGGCTTGATA 575
INTRON_3 245828 ATTTCTTTCCTTTTATCACTAAATGAGATTCCACTTTATG-ATGTACCAT 245876
ii iv i i i i i v i v - i
C L1MC3_3end#LI 574 GCTCATTCCTTTTTATCGCTGAATAATATTCCATTGTATGGATGTACCAC 525
INTRON_3 245877 A-TTTGTTTATACATTCACCTATTGAAGGTTATCTTGGTTACTTCCAATT 245925
- v vi i i
C L1MC3_3end#LI 524 AGTTTGTTTATCCATTCACCTATTGAAGGACATCTTGGTTGCTTCCAGTT 475
INTRON_3 245926 TGGGGCAATTATAAATAAAGATGCTGTAA-CATTCACATGTAGGGTTTCT 245974
vv i i v i - ii i i - i
C L1MC3_3end#LI 474 TTTGGCGATTATGAATAAAGCTGCTATAAACATTTGCGTGCAGG-TTTTT 426
INTRON_3 245975 TTGTGGACTGAAACATTCAAATCAGTTGGGTGAATATCTATGAGTGTGAT 246024
v vv iiv i i v ii
C L1MC3_3end#LI 425 GTGTGGACATAAGTTTTCAAATCAGTTGGGTAAATACCTAGGAGTACGAT 376
INTRON_3 246025 TGTTGGATTGTAAGGTAAGACTATGTTTAGCTTTGTAACATAGCTGCCAA 246074
i i v v - i
C L1MC3_3end#LI 375 TGCTGGATTATATGGTAAGACTATGTTTAGCTTTGTAAGA-AACTGCCAA 327
INTRON_3 246075 ACTGTCTTTTA--GTGGCAGTACTATTTT 246101
ii -- v i
C L1MC3_3end#LI 326 ACTGTCTTCCAAAGTGGCTGTACCATTTT 298
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (68 / 34)
Gap_init rate = 0.04 (23 / 648), avg. gap size = 1.83 (42 / 23)
986 15.32 0.50 2.54 INTRON_3 246084 246284 153897 C L1MC3_3end LINE/L1 1 197 2335 563
INTRON_3 246084 TAGTGGCAGTACTATTTTTATTT-GATTTGCAATACCTTAATGACAGATG 246132
i - vii v i -i v i
C L1MC3_3end#LI 197 TAGTGGTA-TCTCATTGTTGTTTTAATTTGCAATTCCTTAATGACAAATG 149
INTRON_3 246133 AGGCTGAGCATCTTTTCATATGCTTATTTGCCATCTGTATGTCTTCTTTG 246182
v i i i
C L1MC3_3end#LI 148 ATGTTGAGCATCTTTTCATATGCTTATTTGCCATCTGTGTATCTTCTTTG 99
INTRON_3 246183 ATACGGTGTCTGTTCATATCTTTTGCTTACGTTTTAATTGGGTTGAGGTT 246232
i iv i v ii iv ---
C L1MC3_3end#LI 98 GTGAGGCGTCTGTTCAGATCTTTTGCCCATTTTTTAATTGGGTTG---TT 52
INTRON_3 246233 TTTTTCCTCATTGTTGAGTTCTAAGAGTTCTTTGGTATATTTTTGGCATA 246282
v i i i - v ii i
C L1MC3_3end#LI 51 TGTTTTCTTATTGTTGAGTTTTAAGAGTTCTTTG-TATATTTTGGATACA 3
INTRON_3 246283 AG 246284
C L1MC3_3end#LI 2 AG 1
Matrix = 20p37g.matrix
Transitions / transversions = 2.33 (21 / 9)
Gap_init rate = 0.02 (4 / 200), avg. gap size = 1.50 (6 / 4)
2985 18.57 3.82 3.68 INTRON_3 246131 246890 153291 C L1MC_orf2 LINE/L1 2534 3294 0 564
INTRON_3 246131 TGAGGCTGAGCATCTTTTCATATGCTTATTTGCCATCTGTATGTCTTCTT 246180
v iv i
C L1MC_orf2#LIN 3294 TGATGTGGAGCATCTTTTCATATGCTTATTTGCCATCTGTATATCTTCTT 3245
INTRON_3 246181 TGATACGGTGTCTGTTCATATCTTTTGCTTACGTTTTAATTGGGTTGAGG 246230
i iv v vi v ii iv ? i ---
C L1MC_orf2#LIN 3244 TGGTGAGGTGTCTGTTAAGGTCTTTGGCCCATTTTTNAATCGGGTTG--- 3198
INTRON_3 246231 TTTTTTTCCTCATTGTTGAGTTCTAAGAGTTCTTTGGTATATTTTTGGCA 246280
v i i i - v ii
C L1MC_orf2#LIN 3197 TTTGTTTTCTTATTGTTGAGTTTTAAGAGTTCTTTG-TATATTTTGGATA 3149
INTRON_3 246281 TAAGTCTTTTATCAGGTATATATTTTGAAAATCTTTTTTGCCCAGTCTGT 246330
vv i i i i v v v i -
C L1MC_orf2#LIN 3148 ACAGTCCTTTATCAGATGTGTCTTTTGCAAATATTTTCT-CCCAGTCTGT 3100
INTRON_3 246331 GGCTT-----TTCGTTCCATTAATGATATCTTTTGCTGAGCAGAAGTTTT 246375
----- i iv i ii? i i v
C L1MC_orf2#LIN 3099 GGCTTGTCTTTTCATTCTCTTGACANTGTCTTTCGCAGAGCAGAAGTTTT 3050
INTRON_3 246376 CAATTTTAATAAAGGCTAACTAATCAATTTTTTTTCTTTCATGGGTCATG 246425
i i v i i v ? -- i i
C L1MC_orf2#LIN 3049 TAATTTTAATGAAGTCCAGCTTATCAATTNTTT--CTTTCATGGATCGTG 3002
INTRON_3 246426 CTTTTGGTGTTTTATCTAAAA-CTCATTACCAAACCCAAGGTC-TCAACC 246473
i v -v ii ? - v v-
C L1MC_orf2#LIN 3001 CCTTTGGTGTTGTATCTAAAAAGTCATCGCCANACCCAAGGTCATCTAG- 2953
INTRON_3 246474 ATTTTCTCCT--GTTTTTATCTAGAAGTTTT--------GCATTTTACAT 246513
-- v iv i --------
C L1MC_orf2#LIN 2952 ATTTTCTCCTATGTTATCTTCTAGGAGTTTTATAGTTTTGCATTTTACAT 2903
INTRON_3 246514 TCAAATATATAATACATGTTGAGTTAATTTTTGTGAAGGGTATGAGATCT 246563
i ii v i i v v i i i
C L1MC_orf2#LIN 2902 TTAGGTCTGTGATCCATTTTGAGTTAATTTTTGTGAAGGGTGTAAGGTCT 2853
INTRON_3 246564 GAATCTAGCTTTGTTTTTTATTGCATATGGATGTCCCATTGTTTCCATAC 246613
vi v ii -- i vi i vii
C L1MC_orf2#LIN 2852 GTGTCTAGATTCATTTTTT--TGCATGTGGATGTCCAGTTGTTCCAGCAC 2805
INTRON_3 246614 CATTTTTTTGAAAGA-TATCCTTTCTCCCTTGAATTGCCTTTGCCGGTTT 246662
v vi - i v v v ivv
C L1MC_orf2#LIN 2804 CATTTGTTGAAAAGACTATCTTTGCTCCATTGTATTGCCTTTGCTCCTTT 2755
INTRON_3 246663 ATTAAAGATCAGTTGACTTTATTTGTATG--TCATTTTCTGGACTCTCTA 246710
i i v i i -- vv i
C L1MC_orf2#LIN 2754 GTCAAAGATCAGTTGACTATATTTATGTGGGTCTATTTCTGGGCTCTCTA 2705
INTRON_3 246711 CTCTGTTCTATTAATGTGTATGTC-ATGGTGTCTTGATTACTGTCATTTT 246759
i i i v i v - vv v viv v ii- i --
C L1MC_orf2#LIN 2704 TTCTGTTCCATTGATCTATTTGTCTATTCTTTCGCCAATACCA-CACT-- 2658
INTRON_3 246760 ATTGGTCTTGATTAATGTAGCCTTATGCTGTTTTATTGTA-GTCTTTGAA 246808
---- v ---------- v - -
C L1MC_orf2#LIN 2657 ----GTCTTGATTACTGTAGC----------TTTATAGTAAGTCTT-GAA 2623
INTRON_3 246809 AT-GGATAGTGTGAGTCTTCCAATGCTGTTCTTC------AGTATTGTGT 246851
i - i v i ivi ------ i
C L1MC_orf2#LIN 2622 GTCGGGTAGTGTCAGTCCTCCAACTTTGTTCTTCTCCTTCAATATTGTGT 2573
INTRON_3 246852 TGGCTATTCTAGATCTTTTGCTTTTCCATATAAACTTTA 246890
i i i i
C L1MC_orf2#LIN 2572 TGGCTATTCTGGGTCTTTTGCCTCTCCATATAAACTTTA 2534
Matrix = 20p37g.matrix
Transitions / transversions = 1.49 (79 / 53)
Gap_init rate = 0.03 (21 / 759), avg. gap size = 2.71 (57 / 21)
+ 2189 9.7 0.3 0.3 INTRON_3 246899 247209 (152972) C L1PB2 LINE/L1 (3) 6148 5838 310
ANNOTATION EVIDENCE:
2189 9.68 0.32 0.32 INTRON_3 246899 247209 152972 C L1PB2_3end LINE/L1 585 895 3 504
INTRON_3 246899 TTTTATTTCAATAGTTTTTGGGCA-ACAGTTGGTTTTTGGTTACACGAAT 246947
vi- v i i
C L1PB2_3end#LI 895 TTTTATTTCAATAGTTTTTGGGGGTACAGGTGGTTTTTGGTTACATGGAT 846
INTRON_3 246948 AACTTCTTTAGTGGAGATTTCTGAGATTTTGGTGCACCTATCACCCAAGC 246997
v v i i
C L1PB2_3end#LI 845 AAGTTCTTTAGTGGTGATTTCTGAGATTTTGGTGCACCCATCACCCGAGC 796
INTRON_3 246998 GGTGTACACTGTACTCAATAAATAGTTTTTTATCCCTCACCCTAATCCCA 247047
i i vi i ivv
C L1PB2_3end#LI 795 AGTGTACACTGTACCCAATATGTAGTCTTTTATCCCTCACCCCCCTCCCA 746
INTRON_3 247048 CCCTTCCCTTCAAGTCCCCAAAGTCCATTATATAATTCTTATGCCTTTGC 247097
iiii v
C L1PB2_3end#LI 745 CCCTTCCCCCTGAGTCCCCAAAGTCCATTATATCATTCTTATGCCTTTGC 696
INTRON_3 247098 ATCCTCATAGCTTAGCTCCCACTTATAAGTGAGAACATACAACATTTGGT 247147
i i i
C L1PB2_3end#LI 695 GTCCTCATAGCTTAGCTCCCACTTATAAGTGAGAACATACGATATTTGGT 646
INTRON_3 247148 TTTCCATACCTGAGTTACTTCACTTAGAGTAACGGCCTCCAGCTCCATCC 247197
v i i
C L1PB2_3end#LI 645 TTTCCATTCCTGAGTTACTTCACTTAGAATAATGGCCTCCAGCTCCATCC 596
INTRON_3 247198 AAGGTTGTAGCA 247209
- iv
C L1PB2_3end#LI 595 AAG-TTGCTGCA 585
Matrix = 18p37g.matrix
Transitions / transversions = 2.00 (20 / 10)
Gap_init rate = 0.01 (2 / 310), avg. gap size = 1.00 (2 / 2)
+ 1271 17.6 4.5 2.1 INTRON_3 247210 247757 (152424) C L1MC3 LINE/L1 (2575) 3571 2974 309
ANNOTATION EVIDENCE:
1271 17.03 2.46 3.18 INTRON_3 247210 247494 152687 C L1MC_orf2 LINE/L1 1180 1462 1832 565
INTRON_3 247210 TTTCTTCCTTAAATGTTTGGCAGAATGTCCCAGTGACACCATGTGAATCT 247259
i viv vv v iii
C L1MC_orf2#LIN 1462 TTTCTTCCTTAAATGTTTGGTAGAATTCACCAGTGAACCCATCTGGGCCT 1413
INTRON_3 247260 GGTGCTTTCTTTTTTTAGAATGTCATTA----TTAATTCAACTTCTTTAA 247305
v -i v i ---- i i
C L1MC_orf2#LIN 1412 GGTGCTTTCTGTTTT-GGAAGGTTATTAATTATTGATTCAATTTCTTTAA 1364
INTRON_3 247306 TAGATATTGGCCTATTCAGATTACCTATTTCTCCTTGTGTGAGTT--GTT 247353
v ii i -- vi
C L1MC_orf2#LIN 1363 TAGATATAGGCCTATTCAGATTGTCTATTTCTTCTTGTGTGAGTTTTGGC 1314
INTRON_3 247354 AATTTGTGTCTTCTGAGGAATTGATCCATTTCATATAAGTTACCAAATTT 247403
iv iii i v i i
C L1MC_orf2#LIN 1313 AGATTGTGTCTTTCAAGGAATTGGTCCATTTCATCTAGGTTATCAAATTT 1264
INTRON_3 247404 GTGGTCACAGAGTTTTATCTAGCATTCCATTATTATCCTTTTAATATCAA 247453
v i v viv i v i v
C L1MC_orf2#LIN 1263 GTGGGCATAGAGTTGTTCATAGTATTCCTTTATTATCCTTTTAATGTCCA 1214
INTRON_3 247454 TTGGATCAGACTGGTAATTTGTGTTGGCTCTCTTT-ATTTCT 247494
v v -- i i ---- i-- i -
C L1MC_orf2#LIN 1213 TGGGATCTG--TAGTGAT----GTC--CCCTCTTTCATTTCT 1180
Matrix = 20p37g.matrix
Transitions / transversions = 1.47 (28 / 19)
Gap_init rate = 0.02 (7 / 284), avg. gap size = 2.29 (16 / 7)
1108 18.14 6.78 0.96 INTRON_3 247463 247757 152424 C L1MC_orf2 LINE/L1 865 1176 2118 566
INTRON_3 247463 ACTGGTAATTTGTGTTGGCTCTCTTTATTTCTTGGTTAGCCTGGCTAGAA 247512
i i ivv v i i
C L1MC_orf2#LIN 1176 ATTAGTAATTTGTGTCCTCTCTCTTTTTTTCTTAGTTAGCCTGGCTAGAG 1127
INTRON_3 247513 GTTTATCAGTT--ACTGAT---------------GGTTTTAGTTCCATTG 247545
i i -- i --------------- v i iii
C L1MC_orf2#LIN 1126 GCTTATCAATTTTATTGATCTTTTCAAAGAACCAGCTTTTGGTTTTGTTG 1077
INTRON_3 247546 TTTTTCCCTGTTGCTTTCTTAATTTCAATTTCATTCATTCCTGCTCTAAT 247595
v i i v i iv v i
C L1MC_orf2#LIN 1076 ATTTTCTCTATTGATTTCCTGTTTTCAATTTCATTGATTTCTGCTCTAAT 1027
INTRON_3 247596 TTTTATTAATTCTTTTTCTTCTGCTTACTTTAGGCTTAAATTGCTTTTCT 247645
v - i ii v i
C L1MC_orf2#LIN 1026 TTTTATTATTTCTTTT-CTTCTGCTTACTTTGGATTTAATTTGCTCTTCT 978
INTRON_3 247646 TTCTCTAGTTTCCTAATGTGAAACC--ATGTTATTGATTTTAGGTGTTTT 247693
i v i v -- vi ? i v i
C L1MC_orf2#LIN 977 TTTTCTAGTTTCCTAAGGTGGAAGCTTAGATNATTGATTTTAGATCTTTC 928
INTRON_3 247694 TCTGTTTTCTAATACATGCATTTTAATGCTAAAAATTTCTCT-TAAACCA 247742
- v i i- v i - i vv
C L1MC_orf2#LIN 927 T-TCTTTTCTAATATATGCATTC-AATGCTATAAATTTCCCTCTAAGCAC 880
INTRON_3 247743 TGTTTTTTCTTCATC 247757
i iv v
C L1MC_orf2#LIN 879 TGCTTTCGCTGCATC 865
Matrix = 20p37g.matrix
Transitions / transversions = 1.60 (32 / 20)
Gap_init rate = 0.02 (7 / 294), avg. gap size = 3.29 (23 / 7)
+ 347 36.7 1.6 0.0 INTRON_3 247758 247945 (152236) C ERVL-E-int LTR/ERVL (4570) 1097 907 311
ANNOTATION EVIDENCE:
347 36.70 1.60 0.00 INTRON_3 247758 247945 152236 C ERVL-E LTR/ERVL 907 1097 4570 589
INTRON_3 247758 ACCATTTTGTCCAGGTTTCAGACAACCAACCAACCATATGATTAGAACTA 247807
v vv i v i v v ?i iii
C ERVL-E#LTR/ER 1097 ACCTTTGGGTCCAGGTTTTAGTCAACCAACCGAGCAAATNGTTAGAGTCA 1048
INTRON_3 247808 CTCCCTGTTGCACTGTCTACTGTGTTGAATATAGAATCTCTGGTAAATTC 247857
v iii v viv v iiii vii v v i v
C ERVL-E#LTR/ER 1047 CTCCCAGCCACTCGAGCTAGTACACTGAATCCGGAATCTCTGCTTAGTGC 998
INTRON_3 247858 ACCTGTAGCCACAAATT-AGCTGGTTCTAAAAGTATTTTTCTCTCTCACT 247906
i ?i v v i -i iv v i v v v i ii v v
C ERVL-E#LTR/ER 997 ATCNATATCAATAAATTCGGCCTGATCCAACATTATATTCCTTCCACCCT 948
INTRON_3 247907 GGTCTAGCTCCCTCCAAATT--TCCCCCTAAATAGTTTCCA 247945
i i i vi ? ivii i-- i? v v v ?
C ERVL-E#LTR/ER 947 GATCCAACATCNTTAGGATCCATTNCCATACATATTTNCCA 907
Matrix = 20p37g.matrix
Transitions / transversions = 1.21 (35 / 29)
Gap_init rate = 0.01 (2 / 187), avg. gap size = 1.50 (3 / 2)
+ 4060 3.5 0.0 0.0 INTRON_3 248140 248619 (151562) C L1PA3 LINE/L1 (0) 6155 5676 312
ANNOTATION EVIDENCE:
4060 3.54 0.00 0.00 INTRON_3 248140 248619 151562 C L1PA3_3end LINE/L1 423 902 0 505
INTRON_3 248140 TTTTTTAATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAATGT 248189
v
C L1PA3_3end#LI 902 TTTTTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAATGT 853
INTRON_3 248190 GCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGTGCTGTACCCA 248239
i i
C L1PA3_3end#LI 852 GCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCA 803
INTRON_3 248240 TTAACTCGTCATTTAGCATTAGGCATATCTCCTAAGGCTATCCCTCCCCC 248289
i i i i v
C L1PA3_3end#LI 802 CTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCC 753
INTRON_3 248290 CTCCCCCCACCCCACAACAGTCCCCAGAGTGTGATGTTCCCCTTCCTGTG 248339
C L1PA3_3end#LI 752 CTCCCCCCACCCCACAACAGTCCCCAGAGTGTGATGTTCCCCTTCCTGTG 703
INTRON_3 248340 TCCATGTGTTCTCATTGTTCAATTCCCATCTATGAGTGAGAACATGCAGT 248389
i i i
C L1PA3_3end#LI 702 TCCATGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGT 653
INTRON_3 248390 GTTTGGTTTTTTGTCCTTGTGATAGTTTACTGAGAATGATGATTTCCAAT 248439
i i
C L1PA3_3end#LI 652 GTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGATTTCCAAT 603
INTRON_3 248440 TTCATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGC 248489
C L1PA3_3end#LI 602 TTCATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGC 553
INTRON_3 248490 ATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCA 248539
C L1PA3_3end#LI 552 ATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCA 503
INTRON_3 248540 TTGTTAGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCC 248589
i
C L1PA3_3end#LI 502 TTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCC 453
INTRON_3 248590 GCAATAAACATACATGTGCATGAGTTTTTA 248619
i v i
C L1PA3_3end#LI 452 GCAATAAACATACGTGTGCATGTGTCTTTA 423
Matrix = 18p37g.matrix
Transitions / transversions = 4.67 (14 / 3)
Gap_init rate = 0.00 (0 / 479), avg. gap size = 0.0 (0 / 0)
+ 957 30.5 6.6 5.9 INTRON_3 249148 250681 (149500) C L1MEd LINE/L1 (4644) 1581 7 313
ANNOTATION EVIDENCE:
938 30.05 3.96 2.85 INTRON_3 249148 249702 150479 C L1MEg_5end LINE/L1 880 1440 661 567
INTRON_3 249148 CTAAATTTTTTTTAAACTTCAGATGTCTTTGTTTCACTCTCATTTTTGAA 249197
v i v viv vv i i i ii
C L1MEg_5end#LI 1440 CTCAGTTTTTGTTTGTCTGAAAATGTCTTTATTTCGCCTTCATTTTTGAA 1391
INTRON_3 249198 AAATCGTTTTGGTTTGTATACAACTTGTATACAATTCCAGGTTGATGGTT 249247
ii -i --ii v --------- v i iii
C L1MEg_5end#LI 1390 GGAT-ATTTT--CCTGGATA---------TAGAATTCTAGGTTGGCAGTT 1353
INTRON_3 249248 ATTTGTTTTCTCATCACTTTCAGG-TATTATTTCACTATCTTTTGGCATC 249296
-- i i v v i - i i i i i i v
C L1MEg_5end#LI 1352 ATTT--TCTTTCAGCACTTTAAAGATGTCATTCCATTGTCTTCTGGCTTC 1305
INTRON_3 249297 CATTGTTGCTTCTGAGAGGTCAGATGTTAATGTAACTCTT---CCTGTGT 249343
v vi i v i i v v i v --- v v
C L1MEg_5end#LI 1304 CATTGTTTCTGTTGAGAAGTCAGCTGTCAGTCTTATTGTTGCTCCTTTGA 1255
INTRON_3 249344 ATACCATTTTTCTTTTCTCTCTGGCTGCTTTTAAGATCAT------GTCT 249387
viiv v v i iv ------
C L1MEg_5end#LI 1254 AGGTAATGTGTCTTTTTTCTCTGGCTGCTTTTAAGATTTTCTCTTTGTCT 1205
INTRON_3 249388 TTGATGTTTTGTATTTTCACTATG-----TCTTGGTGGAGATGTCTTTTT 249432
i v iv i v i -----i v vi v v v
C L1MEg_5end#LI 1204 TTGGTTTTCAGCAGTTTTACTATGATGTGCCTAGGTGTGGTTTTCTTTGT 1155
INTRON_3 249433 CTTTATCTTTCTTGGCAA-CATTGTTATTCCTCAATCTGAAAATTCACGT 249481
v i v viv- i v ?vv i v viiv v i
C L1MEg_5end#LI 1154 ATTTATCCTGCTTGGGGTTCGTAGNGCTTCTTGAATCTGTGGCTTGATGT 1105
INTRON_3 249482 -TTTCATCAATTCTGGAAAATTCTTAGTTAT-ATCTTTT-AAATATTGTC 249528
- i i i i ii - i - -
C L1MEg_5end#LI 1104 CTTTCGTCAGTTTTGGAAAATTCTCAGCCATTATCTCTTCAAATATTG-C 1056
INTRON_3 249529 TCCTACCCTGATTGTTCATTATTTTC--TCTGAAATTTTGTTTGGACATA 249576
i i iiv ivi vi vi i -- ii i iiiv iv i
C L1MEg_5end#LI 1055 TTCTGCCCCATTCTCTCTCTCCTCTCCTTCTGGGACTCCAATTACATATA 1006
INTRON_3 249577 TGTTGAACCTTTTCAGTCTAACCTCAT-TGTCTTTCAGTTTCTCTTTCAT 249625
ii viv iv - - i i vvi i iii
C L1MEg_5end#LI 1005 TGTTAGACCTTTTCACCGTGTCC-CATATGTCTCTTACGCTCTTTTCTGT 957
INTRON_3 249626 ATTTTCTATATCTTTGACTTTCTATGCATGTTTTTAGGTAATTTCTTTAG 249675
i v i ?v i i v vvv i i i v ?iv
C L1MEg_5end#LI 956 ATTTTCCATTTTTTTNTCTCTCTGTGCTTCAGTCTGGATATTTTCTNCTG 907
INTRON_3 249676 CTCTATCTTCCATGTCATTAATTGTCT 249702
vi vv i iv
C L1MEg_5end#LI 906 ACCTATCTTCCAGTTCACTAATCCTCT 880
Matrix = 20p37g.matrix
Transitions / transversions = 1.41 (93 / 66)
Gap_init rate = 0.03 (16 / 554), avg. gap size = 2.38 (38 / 16)
957 30.77 8.11 7.67 INTRON_3 249436 250681 149500 C L1MEd_5end LINE/L1 7 1257 0 568
INTRON_3 249436 TATCTTTCTTGGCAA-CATTGTTATTCCTCAATCTGAAAATTCACGTTTT 249484
ii v v v- vv i v ?ii i? i
C L1MEd_5end#LI 1257 TATTCTGCTTGGGATTCATTGTGCTTTCTGAATCTGANGGTTCATNTCTT 1208
INTRON_3 249485 CATCAATTCTGGAAAATTCTTAGTTAT-ATCT-TTTAAATATTGTCTCCT 249532
i ii - - ? i iii
C L1MEd_5end#LI 1207 CATCAATTCTGGAAAATTCTCAGCCATTATCTCTTTNAATATTGCCTTTC 1158
INTRON_3 249533 ACCCTGATTGTTCATTATTTTCT-CTGAAATTTTGTTTGGACATATGTTG 249581
v v v ----- v i i - i ? iivv i i ? i
C L1MEd_5end#LI 1157 CCCATCAT-----ATTCTCTCCTTCTGGAANTCCTATTAGACGTNTATTG 1113
INTRON_3 249582 AACCTTTTCAGTCTAACCTCATTGTCTTTCAGTTTCTCTTTCATATTTTC 249631
i i v v vv i i iii
C L1MEd_5end#LI 1112 GATCTTTTCATTCTATCCTCCATGTCTCTTAACCTCTCTTTCATATTTTC 1063
INTRON_3 249632 TATATCTTTGACTTTCTATGCATGTTTTTAGGTAATTTCTTTAGCTCTAT 249681
i v iv i i ? i -i i v
C L1MEd_5end#LI 1062 CATCTCTTTATCTCTCTGTGCATNTTCT-GGGTAATTTCTTCAGATCTAT 1014
INTRON_3 249682 CTTCCATGTCATTAATTGTCTGAAATTTTGCTTTCCC--ATT--CTGTTT 249727
vv i v v--- iv v ?i -- i--
C L1MEd_5end#LI 1013 CTTCCAGTTCACTAATTCTCTC---TTCAGCTGTNTCTAATCTGCTGTTT 967
INTRON_3 249728 AACCT-TTTACTGAACTTTTGCTTTC-----CCAT-TCTGTTTAATCT-- 249768
? - ii iii iv i----- i - v v v i --
C L1MEd_5end#LI 966 NACCTATCCACTGGGTTTTTAATTTTAATGACTATATATTTTTCATTTCC 917
INTRON_3 249769 ------TTTATTGAA--CTTTAAATGGTAACATTTTTCACTTCTGGAAGT 249810
------ ? vii--? vi i v v v ? -i ------
C L1MEd_5end#LI 916 AAAAGTTNTATTTGGTTNTTTTGATAGTACCTTATTNC-TTTCT------ 874
INTRON_3 249811 TCTGTTTGATTCATTTTAAATTTTGCCTCATTATTTCAGTG---TTTAAA 249857
iv --- i i v --- - v i--- v
C L1MEd_5end#LI 873 CATGTTT---TTATTTCATATT---CCT-ATTATTTCACTAACATTTTAA 831
INTRON_3 249858 GTATCCCTTATTATATCATTAAACATAGAAAACATGTTTGTCATA-TTCT 249906
ii v - v - ------------ - v v v - i
C L1MEd_5end#LI 830 ACATAC-TTATTTTAT-ATT------------C-TGTATCTGATAATTCC 796
INTRON_3 249907 G-TACCTGATAATTTCAATATCTGAAAT---ATTCTGGGGTCCAATTCTA 249952
i- i - i i ---- iv i i --- i ---- i v v v
C L1MEd_5end#LI 795 AATATCTGA-AGTTCC----TTGGGAGTCTAATCCTG----CTATTTGTT 755
INTRON_3 249953 ATATCTGCTG----TTGTACTTG-----CTATTTCTTGCTCATGGTGCCT 249993
i i ---- i iv v ----- i --- i - ii
C L1MEd_5end#LI 754 GTGTCTGCTGACTCTCGCTCATGGTAGACTGTTTC---CTCGTG-TGTTT 709
INTRON_3 249994 TGT--TTTCTG-TTGTTA-CTTATTTGGAGATGATTTTT-TC-------- 250030
-- iv - v - i v vv v? vi - --------
C L1MEd_5end#LI 708 TGTAATTTTGGATTGTGAGCTCATGTTTAGCNGAGCTTTATCTGTGGGAA 659
INTRON_3 250031 -------AGTCCTGAACTGAAGGATTGT-TTTCTTCAAAGATTATTTGAG 250072
------- v iii i -- i- ii i i vv v
C L1MEd_5end#LI 658 TCCTGTGAGGCCTGGGTTGAGGG--TGCGTCCCTCCAGAGAGGATTTGCG 611
INTRON_3 250073 TGTTGTTT-TGCCAGGTGCTTTTGGG-CACCAGCAATCTATGACCACTTA 250120
- i - iiiv - i v i iv v
C L1MEd_5end#LI 610 T-TTGCTTCTGCCAGGTGCCCCAGGGNCACTACCAACCTGGGACCACTTT 562
INTRON_3 250121 AGAATAAATAATAAGATTATGATTTTTCCAGTTATACCACTAGTGTGAAT 250170
viv v vv vi v iv i? iiiviiii ii viv i
C L1MEd_5end#LI 561 ATGTTAATTTCTCGGCTTGGGGNTTCCTGGACCACGCAGGTAGTGTAAAT 512
INTRON_3 250171 TTAGGTTCTATATTTATGTGAAGGCCAATCTGTGGC-ATATGTTTTCAGA 250219
iiiii i v iii i i viii i- vi i i
C L1MEd_5end#LI 511 TTGAACCCCAAACCCACGTGAGGGCAGGCCTGTGGTTATAAATTCTCAGG 462
INTRON_3 250220 AAATAGTTATTTTCTTTCCATCTGTCCATTTCTTGCCAAAGTCAAGAGAG 250269
ii v v v ? -- i ---- vv---- v i i?? -
C L1MEd_5end#LI 461 GGAGACTTTTNTTCT--CCACC----CAGA----GCCCAGGCNNAGAGA- 423
INTRON_3 250270 GCAGTTTTCACTGTTGCCACTTTTTATGGAATTTTTTTTTCTTTACTG-- 250317
- ------------ i ---------i ii v i i --
C L1MEd_5end#LI 422 -CAGTTT------------CTTTTCAT---------CTCCCTGTGCCGGT 395
INTRON_3 250318 ---CCTATTTTTTTTTTTTCTAGTTTACCACTTCATT-ATGGTATAGCCC 250363
--- vv v ---- i vi i - v i
C L1MEd_5end#LI 394 GGGCAGATTATTTTT----CTAGTCTACCCTTTCACTGAGGGTGTAGCCC 349
INTRON_3 250364 TTTGAGG-TCCTGGCTTTATATAGGGATCCTCTGT-CTGACTTCTTGCCT 250411
ii - i ii - v - ii iiii
C L1MEd_5end#LI 348 TTCAAGGGTCCCGGCTTTATGCAGGGATC-TCAGTTCCAACTCTCCGCCT 300
INTRON_3 250412 TGTG-AAGCTCTAGACTTTGTCTTCAGTCCTTACAGCAATGTCAAATACC 250460
i - i i v i i i vi iii vvi?i i vv
C L1MEd_5end#LI 299 TGCGTAGGCCCAAGGCCTTGTCTCCTATCCCCGCATGGNCGTTAAAACCC 250
INTRON_3 250461 A---CTCAGGGTCTCC-AGGCAGTTAGAGATGTTCCCAGGAC-------- 250498
--- i vv iv - i v vi i v- ii i i --------
C L1MEd_5end#LI 249 AAGCCCCTTGGTTACCGAGACCGGCAAAT-TGCCCTCAGGGCAGCCCACA 201
INTRON_3 250499 -TTTTGGCTTTAGTGCTTACTTTTCTTGCT--GGATTCCCTA---GTTTG 250542
-i? ii ivv i ivi v i --vii i v--- v
C L1MEd_5end#LI 200 GCNTCAGCTCACGTACTTACCGCTCTGGTTTTCAGTTCTCTCTTCGTTTT 151
INTRON_3 250543 TACCCTCTTTGGCTTTCC-TTACTTTCTTACCAGCTCACTAATGCATTTT 250591
iv i vv v - i v viv v
C L1MEd_5end#LI 150 TGGCCCCTGGGGATTTCCCTTACTTTCTTGCGAGCTCAGCTATGCATTTA 101
INTRON_3 250592 ACAAGATATTT-TTATGTTTTATTCAGAATTTTT------TTAATGCAGG 250634
v i i - i i v i ------ -- i v
C L1MEd_5end#LI 100 AAAGGATGTTTGTTATATTTTATCCAGCATTTCTAGGTGTTT--TGTAGT 53
INTRON_3 250635 TCAAGTAGTGTTCAGGGTATCTAATTTGCTATCTATCTAGAAATGGA 250681
vvi -i v v i i i i v vv ii i
C L1MEd_5end#LI 52 GGGAG-GGTTTTCAGGTTATCTAGTCTACCATATTGCCGGAAACGGA 7
Matrix = 20p37g.matrix
Transitions / transversions = 1.62 (208 / 128)
Gap_init rate = 0.06 (69 / 1245), avg. gap size = 2.86 (197 / 69)
+ 2293 11.3 0.3 0.3 INTRON_3 250871 251179 (149002) + AluSp SINE/Alu 1 309 (4) 314
ANNOTATION EVIDENCE:
2109 13.02 0.32 0.65 INTRON_3 250871 251179 149002 + AluSx SINE/Alu 1 308 4 486
INTRON_3 250871 GGCTAGGCATGGTGGCTCAACGCCTGTAATCCCAACACTTTGGGAGGCTG 250920
ii ii - i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCA-CGCCTGTAATCCCAGCACTTTGGGAGGCCG 49
INTRON_3 250921 AGGCGGCCATATCATCTGAGATCGGGAGTTCGAGACCAGCCTGACCAACA 250970
v iv i i i i
AluSx#SINE/Al 50 AGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACA 99
INTRON_3 250971 TGGAGAAACCCTGTCTCTACTAAAAATACAAAA-TTAGCCAGGTGTGGTA 251019
v i - i i i
AluSx#SINE/Al 100 TGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTG 149
INTRON_3 251020 GTGCATGCCTGTAATCCCAGCTGCTCGGGAAGATGAGGCAGGAGAACCGC 251069
i ii i i v i
AluSx#SINE/Al 150 GCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGC 199
INTRON_3 251070 TTGAACCTGGGAGGTGGAGGTTGCAGTGAGCTGAAATCACACCATTGCAC 251119
i i i i i i i
AluSx#SINE/Al 200 TTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAC 249
INTRON_3 251120 TCCAGCCTGGGCAACAAGAGCGAAACTCCATCTCAAAAATAAATAAATAA 251169
i - i i v v v
AluSx#SINE/Al 250 TCCAGCCTGGGCGACA-GAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 298
INTRON_3 251170 ATAAATAAAA 251179
v v
AluSx#SINE/Al 299 AAAAAAAAAA 308
Matrix = 14p37g.matrix
Transitions / transversions = 3.44 (31 / 9)
Gap_init rate = 0.01 (3 / 308), avg. gap size = 1.00 (3 / 3)
+ 405 28.8 0.9 0.9 INTRON_3 251201 251305 (148876) + MIR SINE/MIR 138 242 (20) 315
ANNOTATION EVIDENCE:
405 28.84 0.95 0.95 INTRON_3 251201 251305 148876 + MIR SINE/MIR 138 242 20 519
INTRON_3 251201 AAATGAAATTGATAATGATACCTACCTCATAGTACTGTTTACAAGAATTA 251250
iiiv i ii vii -iii i
MIR#SINE/MIR 138 AAATGGGGATAATAATAGTACCTACCTCATAGGGTTGTT-GTGAGGATTA 186
INTRON_3 251251 AATGAGATAATGTACCTAAAGCACTCAGACCAGTGTATGGCATTT-GTAG 251299
v ii iv i i v iv iv - i
MIR#SINE/MIR 187 AATGAGTTAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTAA 236
INTRON_3 251300 GTACCC 251305
ii i
MIR#SINE/MIR 237 GCGCTC 242
Matrix = 25p37g.matrix
Transitions / transversions = 3.29 (23 / 7)
Gap_init rate = 0.02 (2 / 104), avg. gap size = 1.00 (2 / 2)
+ 226 31.7 0.0 5.1 INTRON_3 251723 251805 (148376) + L2a LINE/L2 3343 3421 (5) 316
ANNOTATION EVIDENCE:
226 31.73 0.00 5.06 INTRON_3 251723 251805 148376 + L2a_3end LINE/L2 434 512 5 520
INTRON_3 251723 TTTGTTCATTTCTGGATTTATTTCTTTTGCTTACTCCCATGTCTTGAACA 251772
i v ---- ii ivvi i vvv vi i v v
L2a_3end#LINE 434 TTTGTTCACTGCTG----TATCCCCAGCGCCTAGAACAGTGCCTGGCACA 479
INTRON_3 251773 TGATAAGCACTCAACAAATATTTGCTGAGTTAA 251805
ii i i i i i v
L2a_3end#LINE 480 TAGTAGGCGCTCAATAAATATTTGTTGAATGAA 512
Matrix = 25p37g.matrix
Transitions / transversions = 1.50 (15 / 10)
Gap_init rate = 0.01 (1 / 82), avg. gap size = 4.00 (4 / 1)
+ 2002 14.2 0.0 0.4 INTRON_3 252168 252448 (147733) + AluJb SINE/Alu 1 280 (32) 317
ANNOTATION EVIDENCE:
1886 14.28 0.00 0.36 INTRON_3 252168 252448 147733 + AluJb SINE/Alu 1 280 32 487
INTRON_3 252168 GGCCAGGCACAGTGGCTCACACCTGTGATCCCAGCACTTTAGGAGGCTGA 252217
i i i i i i i
AluJb#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 252218 GGTGGGCAGATCACTTGAGCCCAGGAGTTCGAGTCCAGCCTGGGCAACAT 252267
i vi v
AluJb#SINE/Al 51 GGCGGGAGGATCACTTGAGCCCAGGAGTTCGAGACCAGCCTGGGCAACAT 100
INTRON_3 252268 GATGAAACCCCATCACTACTAAAAATACAAAAGTTAGCCAGTTGTGGTGG 252317
i i v v i i vi
AluJb#SINE/Al 101 GGTGAAACCCCGTCTCTACAAAAAATACAAAAATTAGCCGGGCGTGGTGG 150
INTRON_3 252318 CACACGTGTGTATTCCCAGCTACTCAGGAGGCTTGAGGTGGGAAGATCAC 252367
i i iv v i - ii i i
AluJb#SINE/Al 151 CGCGCGCCTGTAGTCCCAGCTACTCGGGAGGCT-GAGGCAGGAGGATCGC 199
INTRON_3 252368 CTGAGCCAGGGAGGTGGAGGTTGCAGTGAGCCAAGATCATGCCACTGCAC 252417
i v v i iv ii
AluJb#SINE/Al 200 TTGAGCCCGGGAGGTCGAGGCTGCAGTGAGCCGTGATCGCGCCACTGCAC 249
INTRON_3 252418 TCCAGCCTGGGCAACAGAGCAAGAGCCTGTC 252448
i i v
AluJb#SINE/Al 250 TCCAGCCTGGGCGACAGAGCGAGACCCTGTC 280
Matrix = 14p37g.matrix
Transitions / transversions = 2.64 (29 / 11)
Gap_init rate = 0.00 (1 / 280), avg. gap size = 1.00 (1 / 1)
+ 1633 19.5 0.0 2.5 INTRON_3 252485 252771 (147410) + AluJr4 SINE/Alu 3 282 (30) 318
ANNOTATION EVIDENCE:
1420 22.15 0.00 2.50 INTRON_3 252485 252771 147410 + AluJb SINE/Alu 3 282 30 488
INTRON_3 252485 CCAGGTGTGGTGGCTCATGCCTGTAATCTCAATGCTTTGAGGGGCCGAGC 252534
i i i i i iii i i v
AluJb#SINE/Al 3 CCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGG 52
INTRON_3 252535 TGGGAGGATCACTTGAGGCCAGGAGTTCAAGATCAGCTTGGGCAACACAG 252584
i v i i i ii
AluJb#SINE/Al 53 CGGGAGGATCACTTGAGCCCAGGAGTTCGAGACCAGCCTGGGCAACATGG 102
INTRON_3 252585 TGAGACCCTGTCTCTGTGAAAAAATAGAAAATAAAAATTAGTGGTGCATG 252634
i i ii- -----i iv v i
AluJb#SINE/Al 103 TGAAACCCCGTCTCTAC-AAAAAATA-----CAAAAATTAGCCGGGCGTG 146
INTRON_3 252635 GTGGTACATGCCTAATAGTCCTAGCTACTCCAGAGGCTGAGGTGGGAAGA 252684
ii ii i- i vi ii i
AluJb#SINE/Al 147 GTGGCGCGCGCCTG-TAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGGA 195
INTRON_3 252685 TTGCTTGACTCCACGAGTTCCATGTTACAGGGAGCCATGATCATGCTGCT 252734
i vi iv v v v i i v i ii ii
AluJb#SINE/Al 196 TCGCTTGAGCCCGGGAGGTCGAGGCTGCAGTGAGCCGTGATCGCGCCACT 245
INTRON_3 252735 GTATTCCAGCCTGGGTCACACAGAGAGATACTGTCTC 252771
i i iv v v iv
AluJb#SINE/Al 246 GCACTCCAGCCTGGGCGACAGAGCGAGACCCTGTCTC 282
Matrix = 14p37g.matrix
Transitions / transversions = 3.13 (47 / 15)
Gap_init rate = 0.01 (3 / 286), avg. gap size = 2.33 (7 / 3)
+ 24 50.0 0.0 0.0 INTRON_3 252775 252798 (147383) + AT_rich Low_complexity 1 24 (0) 319
ANNOTATION EVIDENCE:
24 50.00 0.00 0.00 INTRON_3 252775 252798 147383 + AT_rich Low_complexity 138 161 139 549
INTRON_3 252775 TTAAAAATAATAATAATAATATAA 252798
?? vv v vv vv vvv
AT_rich#Low_c 138 WWATTAAAAATAAATAATATAATT 161
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 10)
Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0)
+ 374 30.6 10.9 1.1 INTRON_3 253710 254039 (146142) C L1ME4a LINE/L1 (143) 5981 5620 320
ANNOTATION EVIDENCE:
374 30.64 10.91 1.10 INTRON_3 253710 254039 146142 C L1ME4a_3end LINE/L1 367 728 143 569
INTRON_3 253710 TTCCA---TCTTTTCT-TGCCTTTAT--ATACAAGTATGTAC--ATTTTA 253751
--- i - v v -- vv i i-- ?
C L1ME4a_3end#L 728 TTCCAGTCTTTTTTCTATGCATATATGTATACATTTATATATNTATTTTN 679
INTRON_3 253752 TAT---AGTTAAAATCATAATGTACAGGCAATTTGG-ATCATGCTTTCCT 253797
v--- i iii v i vi i v - ? v ii
C L1ME4a_3end#L 678 TAACAAAATTGGGATCATACTGTATATACAGTTTTGTANCCTGCTTTTTT 629
INTRON_3 253798 CAGTTAGTACTATATCATTCATATTTTCCCACAATATTGTCGACTCTTTA 253847
v ii i vvii iivi ivvv i ii
C L1ME4a_3end#L 628 CACTTAACATTATATCATGAGCATTTTCCCATGTCATTAAATATTCTTCG 579
INTRON_3 253848 TAGTAATTACTTT-AATGGCTTCTTAATTCTCTATCA---GG-------- 253885
v ivv ? i - v v vi i i?--- --------
C L1ME4a_3end#L 578 AAAACATNATTTTTAATGGCTGCATAATATTCCATTNTATGGATGTACCA 529
INTRON_3 253886 ---TTTACT--ACCACTTTTCAGTTGTTGAACATTTAGGTTTTTTTCAGT 253930
--- i -- ? iii vi i v i --
C L1ME4a_3end#L 528 TAATTTATTTAACCANTCCCCTATTGTTGGACATTTAGGTTGTTTCCA-- 481
INTRON_3 253931 TATTTTTTTCTGATTACAATCAATGATACCACAAA-----TTAT-CAAGT 253974
- iv - i vi v i v ii ----- i - viv
C L1ME4a_3end#L 480 -ATTTTTCGCT-ATTATAAATAATGCTGCGATGAACATCCTTGTACATAA 433
INTRON_3 253975 ACCTTTGTTTTTTCTTATAATGATTTCTTAGAGATAAATCCC-AGGAGTG 254023
i ?ivivii v i v i vii i - i
C L1ME4a_3end#L 432 ATCTTTGTNCACATCTCTGATTATTTCCTTAGGATAAATTCCTAGAAGTG 383
INTRON_3 254024 GGGTTATTGGGTAAAA 254039
ii i v
C L1ME4a_3end#L 382 GAATTACTGGGTCAAA 367
Matrix = 20p37g.matrix
Transitions / transversions = 1.61 (58 / 36)
Gap_init rate = 0.05 (15 / 329), avg. gap size = 2.67 (40 / 15)
+ 223 26.7 6.5 5.6 INTRON_3 254050 254156 (146025) C MIR SINE/MIR (0) 262 155 321
ANNOTATION EVIDENCE:
223 26.72 6.54 5.56 INTRON_3 254050 254156 146025 C MIR SINE/MIR 155 262 0 521
INTRON_3 254050 AATGATAACTTACATGTTTTCAGTACTTACCAAGGGCCAGGT--TGTTAG 254097
i iv v v v ii i v v i-- v-
C MIR#SINE/MIR 262 AATAATAACCAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTC- 214
INTRON_3 254098 TGGGGCAGGC-CTTTACCTGAATT---TAATTTAATTCTCGTAACA-CCC 254142
-----i i - v v --- v i ii -
C MIR#SINE/MIR 213 -----TAAGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCC 169
INTRON_3 254143 TTTCAGACAACTAC 254156
v v ii iv
C MIR#SINE/MIR 168 TATGAGGTAGGTAC 155
Matrix = 25p37g.matrix
Transitions / transversions = 1.08 (14 / 13)
Gap_init rate = 0.05 (5 / 106), avg. gap size = 2.60 (13 / 5)
+ 202 31.0 14.3 1.7 INTRON_3 254454 254558 (145623) C MIR3 SINE/MIR (4) 204 87 322
ANNOTATION EVIDENCE:
202 31.00 14.29 1.69 INTRON_3 254454 254558 145623 C MIR3 SINE/MIR 87 204 4 522
INTRON_3 254454 CATAGTTAATGATAGAATTTTGCCACTGGAAGGGAACTC---------CT 254494
-- v v iivvi v i---------
C MIR3#SINE/MIR 204 CATAG--AATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCT 157
INTRON_3 254495 GG---AATA---TCATCTTATTGATTAATTAATTCAAGTTCAGAGGAGTG 254538
i --- iv--- i iv v ivv i v i ii ii
C MIR3#SINE/MIR 156 AGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTG 107
INTRON_3 254539 AAGTAATTTTTCCAATATCA 254558
i i vi vi
C MIR3#SINE/MIR 106 AAGTGACTTGCCCAAGGTCA 87
Matrix = 25p37g.matrix
Transitions / transversions = 1.46 (19 / 13)
Gap_init rate = 0.04 (4 / 104), avg. gap size = 4.25 (17 / 4)
+ 1489 14.6 6.8 8.6 INTRON_3 254731 255038 (145143) + AluJo SINE/Alu 1 303 (9) 323
ANNOTATION EVIDENCE:
1298 17.69 6.49 8.25 INTRON_3 254731 255038 145143 + AluJb SINE/Alu 1 303 9 489
INTRON_3 254731 GGCTGGGTGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAAGCCAA 254780
i i i i i
AluJb#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 254781 GGCAGGCAGACAGCTTGAGCCCAGGAGTTTGTGACCAGCCTGGGCAACAA 254830
i vi ivi i v -
AluJb#SINE/Al 51 GGCGGGAGGATCACTTGAGCCCAGGAGTTCGAGACCAGCCTGGGCAACA- 99
INTRON_3 254831 TGGCAAGACTCTGTCACTACTGAAAATACAAAAAAAAAAAAAAGAAAAGA 254880
ii i i i v vi vv -------------
AluJb#SINE/Al 100 TGGTGAAACCCCGTCTCTACAAAAAATACAAAAATTA------------- 136
INTRON_3 254881 GAGAGAGAAAAGCCAGGCGTGGTGGTACATACCTGTGGTCCCAGCTACTC 254930
----------- i ii iii i
AluJb#SINE/Al 137 -----------GCCGGGCGTGGTGGCGCGCGCCTGTAGTCCCAGCTACTC 175
INTRON_3 254931 GGGAGGCTGAGGTAGGAGGATCGCTTGAGCCATGGGTGCAGAGGTTGCAG 254980
i vv iv iv i
AluJb#SINE/Al 176 GGGAGGCTGAGGCAGGAGGATCGCTTGAGCCCGGGAGGTCGAGGCTGCAG 225
INTRON_3 254981 TCAGCC--------------------CAACCTGGGTGACAGAATGAGATC 255010
v -------------------- i i ii i
AluJb#SINE/Al 226 TGAGCCGTGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACC 275
INTRON_3 255011 CTGTTTCCAAAATAAATAAATAAATAAA 255038
i v v v v v
AluJb#SINE/Al 276 CTGTCTCAAAAAAAAAAAAAAAAAAAAA 303
Matrix = 14p37g.matrix
Transitions / transversions = 1.94 (33 / 17)
Gap_init rate = 0.01 (3 / 307), avg. gap size = 15.00 (45 / 3)
+ 743 20.2 0.8 0.0 INTRON_3 255206 255329 (144852) C AluJr SINE/Alu (187) 125 1 324
ANNOTATION EVIDENCE:
692 20.16 0.00 0.81 INTRON_3 255205 255329 144852 C FLAM_C_short_ SINE/Alu 1 124 9 496
INTRON_3 255205 TTTTTTAATAGATTGGGGTCTTGCTATTTTGCCCAGGTGGGTCTTGAACT 255254
v v i- i v iv i
C FLAM_C_short_ 124 TTTTTTTAGAGAC-GGGGTCTCGCTATGTTGCCCAGGCTGGTCTCGAACT 76
INTRON_3 255255 CCTAGCCTCAAGTGATCCTCCTGCCTCAGCCTCCCAAAATGCCAGAATTA 255304
i v i i i i ii i
C FLAM_C_short_ 75 CCTGGGCTCAAGCGATCCTCCCGCCTCGGCCTCCCAAAGTGCTGGGATTA 26
INTRON_3 255305 TAGGGATGAGGCACCATGCCCAACC 255329
i vi v ii ii
C FLAM_C_short_ 25 CAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p37g.matrix
Transitions / transversions = 2.57 (18 / 7)
Gap_init rate = 0.01 (1 / 124), avg. gap size = 1.00 (1 / 1)
+ 382 20.2 0.0 2.7 INTRON_3 255660 255764 (144417) C MIRc SINE/MIR (122) 146 47 325
ANNOTATION EVIDENCE:
379 27.06 0.00 5.00 INTRON_3 255660 255764 144417 C MIRb SINE/MIR 47 146 122 523
INTRON_3 255660 TTTACAGATGAGAAAACTGAAGCCCAGAGAAGTTAATTGACTTGTTCAAG 255709
i i i i v ii
C MIRb#SINE/MIR 146 TTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAG 97
INTRON_3 255710 GTCAAAACAGGTAATTAGGAGGTGAGATGATATCTGATTCCATTATGGTT 255759
v - v i v vi vv viiiv ii vi ---- i
C MIRb#SINE/MIR 96 GTCACA-CAGCTAGTAAGTGGCAGAGCCAGGATTCGAACCCA----GGTC 52
INTRON_3 255760 TGTTT 255764
ii
C MIRb#SINE/MIR 51 TGCCT 47
Matrix = 25p37g.matrix
Transitions / transversions = 1.70 (17 / 10)
Gap_init rate = 0.02 (2 / 104), avg. gap size = 2.50 (5 / 2)
382 16.42 0.00 1.49 INTRON_3 255660 255727 144454 C MIRc SINE/MIR 77 143 125 524
INTRON_3 255660 TTTACAGATGAGAAAACTGAAGCCCAGAGAAGTTAATTGACTTGTTCAAG 255709
i i i i v ii
C MIRc#SINE/MIR 143 TTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAG 94
INTRON_3 255710 GTCAAAACAGGTAATTAG 255727
v - v i v
C MIRc#SINE/MIR 93 GTCACA-CAGCTAGTAAG 77
Matrix = 25p37g.matrix
Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.01 (1 / 67), avg. gap size = 1.00 (1 / 1)
+ 354 2.3 0.0 0.0 INTRON_3 256064 256106 (144075) + (TG)n Simple_repeat 2 44 (0) 326
ANNOTATION EVIDENCE:
354 2.33 0.00 0.00 INTRON_3 256064 256106 144075 C (CA)n Simple_repeat 138 180 0 590
INTRON_3 256064 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGT 256106
v
C (CA)n#Simple_ 180 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 138
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 1)
Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0)
+ 849 9.3 3.1 5.8 INTRON_3 256131 256290 (143891) C L1MA1 LINE/L1 (99) 6203 6048 327
ANNOTATION EVIDENCE:
849 9.29 3.12 5.77 INTRON_3 256131 256290 143891 C L1MA1_3end LINE/L1 795 950 99 570
INTRON_3 256131 TGTGGTATTCATCCCCTCAAGCATTTATCCTTTGAGTTACAAACGATCCA 256180
v i i
C L1MA1_3end#LI 950 TGGGGTATCCATCCCCTCAAGCATTTATCCTTTGAGTTACAAACAATCCA 901
INTRON_3 256181 GTTACATTCTTTATGTTATTTAAAGGTATACAATTA-----TTATTGACT 256225
i i v v ii i -----
C L1MA1_3end#LI 900 ATTACACTCTTTAAGTTATTTTAAAATGTACAATTAAGTTATTATTGACT 851
INTRON_3 256226 ATAGTCACATTATTGTGCTATCAAATATTAATAGTAGGTCTTATTCTTTC 256275
vi i ------ v
C L1MA1_3end#LI 850 ATAGTCACCCTGTTGTGCTATCAAATA------GTAGGTCTTATTCATTC 807
INTRON_3 256276 TTTTCTTTAATTTTT 256290
- --
C L1MA1_3end#LI 806 TTT-CTT--ATTTTT 795
Matrix = 20p37g.matrix
Transitions / transversions = 1.80 (9 / 5)
Gap_init rate = 0.03 (4 / 159), avg. gap size = 3.50 (14 / 4)
+ 254 9.8 1.9 1.9 INTRON_3 256300 256351 (143830) C L1PA3 LINE/L1 (0) 6155 6104 328
ANNOTATION EVIDENCE:
254 9.81 1.92 1.92 INTRON_3 256300 256351 143830 C L1PA3_3end LINE/L1 851 902 0 571
INTRON_3 256300 TTTTATTATTATTATTATACATTAAGTTTTAGGGTAC-TGTATACAACTG 256348
v v - ii -
C L1PA3_3end#LI 902 TTTTTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAA-TG 854
INTRON_3 256349 TAC 256351
i
C L1PA3_3end#LI 853 TGC 851
Matrix = 20p37g.matrix
Transitions / transversions = 1.50 (3 / 2)
Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.00 (2 / 2)
+ 204 36.4 0.0 3.4 INTRON_3 257523 257613 (142568) + L2b LINE/L2 3288 3375 (0) 329
ANNOTATION EVIDENCE:
204 36.40 0.00 3.41 INTRON_3 257523 257613 142568 + L2b_3end LINE/L2 379 466 0 525
INTRON_3 257523 CTGATTAGCTTACCAATCAGTCCATTCCAGTATTTTGCACTAAGCCTTTA 257572
vi v i i iv vv --- iiiiiv vii vvv
L2b_3end#LINE 379 CTGTCTTGTTCACCGCTGTGTCC---CCAGCGCCCAGCACAGGGCCTGGC 425
INTRON_3 257573 ACACGGTAGGAACTTCATGATTCTTTGTTGAATCAGTGAAT 257613
i vi ivi i v v v i
L2b_3end#LINE 426 ACACAGTAGGTGCTCAGTAAATGTTTGTTGAATGAATGAAT 466
Matrix = 25p37g.matrix
Transitions / transversions = 1.13 (17 / 15)
Gap_init rate = 0.01 (1 / 90), avg. gap size = 3.00 (3 / 1)
+ 6644 14.2 1.9 0.3 INTRON_3 258363 259410 (140771) C Tigger1 DNA/TcMar-Tigger (1) 2417 1353 330
ANNOTATION EVIDENCE:
6644 14.16 1.91 0.28 INTRON_3 258363 259410 140771 C Tigger1 DNA/TcMar-Tigger 1353 2417 1 597
INTRON_3 258363 AGACCTGCCTCAGAGATAC-ACAGGTTTGGTCCTAGACCACCAAAATAAA 258411
i v i i i-i i i i i iv
C Tigger1#DNA/T 2417 AGGCATACCTCGGAGATATTGCGGGTTCGGTTCCAGACCACCGCAATAAA 2368
INTRON_3 258412 GTGAATATCTCAATAAAGCAAGTCATATGAGGTTTTTGGTTTCACAGTGC 258461
i v i i i iv v
C Tigger1#DNA/T 2367 GCGAATATCGCAATAAAGCGAGTCACACGAATTTTTTGGTTTCCCAGTGC 2318
INTRON_3 258462 ATATAAACATTCTGTTTATACTGTACTATAGTGTATTAAGTATGAAATGG 258511
vi v i i i v i v i
C Tigger1#DNA/T 2317 ATATAAAAGTTATGTTTACACTATACTGTAGTCTATTAAGTGTGCAATAG 2268
INTRON_3 258512 CATTATGTCTTTAAAAA-----GTACATACATTAATTAAAAAAAAACTTT 258556
-- ----- v v v -
C Tigger1#DNA/T 2267 CATTATGTCT--AAAAAACAATGTACATACCTTAATTTAAAAATA-CTTT 2221
INTRON_3 258557 AGTGGCAAAAAATGCTGACAATCACCTGAAACTTCAGTGAGTTGTAATGT 258606
v vi i i i iv i i v
C Tigger1#DNA/T 2220 ATTGCTAAAAAATGCTAACGATCATCTGAGCCTTCAGCGAGTCGTAATCT 2171
INTRON_3 258607 CTGTACTAGTGGAGGGCCTTGTCTCTATGTTGACAAATGCTGACTAATCA 258656
i v i i i i v iiiv i
C Tigger1#DNA/T 2170 TTTTGCTGGTGGAGGGTCTTGCCTCGATGTTGATGGCTGCTGACTGATCA 2121
INTRON_3 258657 AGGTGGTGGTGGTTGTAGGTTGAAGTGGCTGTGGCAATTTCTTAAGATAA 258706
i v i v ii i
C Tigger1#DNA/T 2120 GGGTGGTGGTTGCTGAAGGTTGGGGTGGCTGTGGCAATTTCTTAAAATAA 2071
INTRON_3 258707 GACAGCAGTGAAGTTTGCCATATTGGTCAACTCTTCTTTTCATGAAAGTT 258756
i i ii i i ii i i v
C Tigger1#DNA/T 2070 GACAACAATGAAGTTTGCCGCATCGATTGACTCTTCCTTTCACGAAAGAT 2021
INTRON_3 258757 TTCTCTGTAGCACATGATGCTGCTTGATAGCATTTTACCCACAGTAGAAT 258806
iii i i
C Tigger1#DNA/T 2020 TTCTCTGTAGCATGCGATGCTGTTTGATAGCATTTTACCCACAGTAGAAC 1971
INTRON_3 258807 TTCTTTCAAAATTAAAGTCAA---------ACTCTGCAGTTGCTTTAT-- 258845
ii --------- i v i --
C Tigger1#DNA/T 1970 TTCTTTCAAAATTGGAGTCAATCCTCTCAAACCCTGCCGCTGCTTTATCA 1921
INTRON_3 258846 --TAAGCTTATGTAATATTTTAAATACTTTGCTGTCACTTCAACAATGTT 258893
-- i i v i i
C Tigger1#DNA/T 1920 ACTAAGTTTATGTAATATTCTAAATCCTTTGTTGTCATTTCAACAATGTT 1871
INTRON_3 258894 CAGAGCATCTTCACCAGGAATAGTTTCCATCTCAAGAGACCACTCCCTCT 258943
v i v i ii i
C Tigger1#DNA/T 1870 CACAGCATCTTCACCAGGAGTAGATTCCATCTCAAGAAACCACTTTCTTT 1821
INTRON_3 258944 GCTCATTCATGAGAATCAATTCTTCATCCATTAAAGTTTCATCATGAGGT 258993
i i v i i i v i i
C Tigger1#DNA/T 1820 GCTCATCCATAAGAAGCAACTCCTCATCCGTTCAAGTTTTATCATGAGAT 1771
INTRON_3 258994 TGTTGCAATTCAGTCACATATTCAGGCTCCACTTCTAATTCCAGTTCTTT 259043
iv v i i
C Tigger1#DNA/T 1770 TGCAGCAATTCAGTCACATCTTCAGGCTCCACTTCTAATTCTAGTTCTCT 1721
INTRON_3 259044 TGTTATTTCTACCACATCTGAAGTTACTTCCCCCACTGAAGTCTTGAACC 259093
i i v i
C Tigger1#DNA/T 1720 TGCTATTTCCACCACATCTGCAGTTACTTCCTCCACTGAAGTCTTGAACC 1671
INTRON_3 259094 CCTAAAAGTCACCAATAAGGGTTGGAATCAATTTCTTCTAAACTCCTGTT 259143
v i v i i i
C Tigger1#DNA/T 1670 CCTCAAAGTCATCCATGAGGGTTGGAATCAACTTCTTCCAAACTCCTGTT 1621
INTRON_3 259144 AATGTTGCTATTTTGACCTCCTCCCATGAATCACAAATATTCTTAATGGC 259193
v i i
C Tigger1#DNA/T 1620 AATGTTGATATTTTGACCTCCTCCCATGAATCACGAATGTTCTTAATGGC 1571
INTRON_3 259194 ATCTAGAGTGGTGAAACATTTCCATA-GGTTTTCAATTTGCTTTGCTTAG 259242
i v v v - i ii
C Tigger1#DNA/T 1570 ATCTAGAATGGTGAATCCTTTCCAGAAGGTTTTCAATTTACTTTGCCCAG 1521
INTRON_3 259243 ATCCATCAGAGGAATCACTGCCTATGGCAGTTCTGGCCTTACAAAATGTA 259292
ii i v i i
C Tigger1#DNA/T 1520 ATCCATCAGAGGAATCACTATCTATGGCAGCTATAGCCTTACGAAATGTA 1471
INTRON_3 259293 TTTCTTAAATAATAATACTTGAAAGTCCAAATTACTCCTTGATCCATGGG 259342
v v
C Tigger1#DNA/T 1470 TTTCTTAAATAATAAGACTTGAAAGTCGAAATTACTCCTTGATCCATGGG 1421
INTRON_3 259343 CTTCAGAATGGATGCTGGGTTAGCAGGCATAAAAACAACACAAGTCTCTT 259392
v i v i iv i i
C Tigger1#DNA/T 1420 CTGCAGAATGGATGTTGTGTTAGCAGGCATGAAAACAACATTAATCTCCT 1371
INTRON_3 259393 TGTACATCTCTGTCAGAG 259410
ii
C Tigger1#DNA/T 1370 TGTACATCTCCATCAGAG 1353
Matrix = 20p37g.matrix
Transitions / transversions = 2.44 (105 / 43)
Gap_init rate = 0.01 (7 / 1047), avg. gap size = 3.29 (23 / 7)
+ 1039 10.3 0.0 12.7 INTRON_3 259418 259595 (140586) + MER1B DNA/hAT-Charlie 181 338 (1) 331
ANNOTATION EVIDENCE:
1039 10.29 0.00 12.66 INTRON_3 259418 259595 140586 + MER1B DNA/hAT-Charlie 181 338 1 598
INTRON_3 259418 TGCAAGGGATCTAGGTTGTGTGCTCCTTACGAGAATCTAAGTAATGCCTG 259467
i i i ----
MER1B#DNA/hAT 181 TGCGAGGGATCTAGGTTGCGTGCTCCTTATGAGAATCTAA----TGCCTG 226
INTRON_3 259468 ATGATCTGAGGTGGAACAGTTTCACCCTGAAACCGTCCTCCTCGCCAACA 259517
i i i i i ------
MER1B#DNA/hAT 227 ATGATCTGAGGTGGAACAGTTTCATCCCGAAACCATCCCCCCC------A 270
INTRON_3 259518 CCCCACTACCTCCACCATCCATGAAAAAATTGTCTTCCACAAAACCAGTC 259567
---------- vi i i i i
MER1B#DNA/hAT 271 CCCC----------CGGTCCGTGGAAAAATTGTCTTCCACGAAACCGGTC 310
INTRON_3 259568 CCTGGTGCCAAAAAGGTTGAGGACTGCT 259595
i i
MER1B#DNA/hAT 311 CCTGGTGCCAAAAAGGTTGGGGACCGCT 338
Matrix = 20p37g.matrix
Transitions / transversions = 15.00 (15 / 1)
Gap_init rate = 0.02 (3 / 177), avg. gap size = 6.67 (20 / 3)
+ 4723 12.0 3.0 0.2 INTRON_3 259598 260413 (139768) C Tigger1 DNA/TcMar-Tigger (1163) 1255 412 330
ANNOTATION EVIDENCE:
4723 11.81 2.98 0.14 INTRON_3 259598 260301 139880 C Tigger1 DNA/TcMar-Tigger 532 1255 1163 599
INTRON_3 259598 AGTAAACCATGCTGTAAACAGATGTGCTGTCATCCAGGTTTTGTCATTCC 259647
i ii
C Tigger1#DNA/T 1255 AGTAAACCATGCTGTAAACAGATGTGCTGTCATCCAGGCTTTGTTGTTCC 1206
INTRON_3 259648 ACTTATAGAGCACAGATGGAGTAGATTTTGCATAAATCTTAGAGAACCTA 259697
i iii v v ii iv
C Tigger1#DNA/T 1205 ATTTATAGAGCACAGGCAGAGTAGATTTAGCATAATTCTTAAGGGCCCTA 1156
INTRON_3 259698 AGATTTTTGAAATGGTAAATGAGCACTGGTTTCAACTTAAAGTC--CAGC 259745
i i i i i --
C Tigger1#DNA/T 1155 GGATTTTCGGAATGGTAAATGAGCATTGGCTTCAACTTAAAGTCACCAGC 1106
INTRON_3 259746 TGCATTAGCCCCTAACGAGAGAATCAGCCTATCCTTTGAAGCTTTGAAGC 259795
i i i
C Tigger1#DNA/T 1105 TGCATTAGCCCCTAACAAGAGAGTCAGCCTGTCCTTTGAAGCTTTGAAGC 1056
INTRON_3 259796 CAGGCATTGACTTTTTCTCTCTAGTTATGAAAGTCCTAGAGGGCATTTTC 259845
i i i v i
C Tigger1#DNA/T 1055 CAGGCATTGACTTCTCCTCTCTAGCTATGAAAGTCCTAGATGGCATCTTC 1006
INTRON_3 259846 TTCCAATAGAAGGCTGTTTCAACTACGTCGAAAATCTGTTGTTCAGTGTA 259895
iv i i i
C Tigger1#DNA/T 1005 TTCCAATAGAAGGCTGTTTCGTCTACATTGAAAATCTGTTGTTTAGTGTA 956
INTRON_3 259896 GCCACCTTCAACAATTACCTTGGCTAGATCTTCTGGAGAACTTGGTACAG 259945
v v i i v v i
C Tigger1#DNA/T 955 GCCACCTTCATCAATGATCTTAGCTAGATCTTCTGGATAACTTGCTGCAG 906
INTRON_3 259946 CTTCTACATCAGGACTTGTTGCTTAATCTGGTACTTTTATGTTCTGGAGA 259995
v i v i v i v
C Tigger1#DNA/T 905 CTTCTACATCAGCACTTGCTGCTTCACCTTGCACTTTTATGTTATGGAGA 856
INTRON_3 259996 TAGCTTCTTTCCTTAAACCTCATGAACCAACTT----------------T 260029
i i ----------------
C Tigger1#DNA/T 855 TGGCTTCTTTCCTTAAACCTCATGAACCAACCTCTGCTAGCTTCAAACTT 806
INTRON_3 260030 TTCTTCAGCAGCTTCCTCACCTCTCTCAGCCTTCAGAGAATTAAAGAGAG 260079
v v i
C Tigger1#DNA/T 805 TTCTTCTGCAGCTTCCTCACCTCTCTCAGCCTTCATAGAATTGAAGAGAG 756
INTRON_3 260080 GTAAGGCCTTGCTCTGGATTAGGCTTTTGCCTAAGGGAATTCTGTGGCTG 260129
v i v i vi
C Tigger1#DNA/T 755 TTAGGGCCTTGCTCTGGATTAGGCTTTGGCTTAAGGGAATGTTGTGGCTG 706
INTRON_3 260130 GTTTGACCT---ATCTAGACCACTAAATCTTTCTCCATATCAGTAATAAG 260176
i --- i v i
C Tigger1#DNA/T 705 GTTTGATCTTCTATCCAGACCACTAAAACTTTCTCCATATCAGCAATAAG 656
INTRON_3 260177 GTTGTTGAGCTTTCTTATAACTTCTGTGTTCACTGGAGTAGAAATTTCTA 260226
i vv v i iv v v iv
C Tigger1#DNA/T 655 GCTGTTTCGCTTTCTTATCATTCGTGTGTTCACTGGAGTAGCACTTTTAA 606
INTRON_3 260227 TTTTCTTCAATAACTTTTTTCTTTACATTAACAAGTTGGCTAACTGTTTG 260276
i v i- i v v
C Tigger1#DNA/T 605 TTTCCTTCAAGAACTTTTC-CTTTGCATTCACAACTTGGCTAACTGTTTG 557
INTRON_3 260277 GTATAAGAGGCCTAGCTTTGAGCTT 260301
iii vi i
C Tigger1#DNA/T 556 GCGCAAGAGGCCTAGCTTTCGGCCT 532
Matrix = 20p37g.matrix
Transitions / transversions = 1.77 (53 / 30)
Gap_init rate = 0.01 (4 / 703), avg. gap size = 5.50 (22 / 4)
2446 13.33 2.81 0.25 INTRON_3 260023 260413 139768 C Tigger1 DNA/TcMar-Tigger 412 812 1606 600
INTRON_3 260023 CAACTTTTTCTTCAGCAGCTTCCTCACCTCTCTCAGCCTTCAGAGAATTA 260072
vi v v i
C Tigger1#DNA/T 812 CAAACTTTTCTTCTGCAGCTTCCTCACCTCTCTCAGCCTTCATAGAATTG 763
INTRON_3 260073 AAGAGAGGTAAGGCCTTGCTCTGGATTAGGCTTTTGCCTAAGGGAATTCT 260122
v i v i vi
C Tigger1#DNA/T 762 AAGAGAGTTAGGGCCTTGCTCTGGATTAGGCTTTGGCTTAAGGGAATGTT 713
INTRON_3 260123 GTGGCTGGTTTGACCT---ATCTAGACCACTAAATCTTTCTCCATATCAG 260169
i --- i v
C Tigger1#DNA/T 712 GTGGCTGGTTTGATCTTCTATCCAGACCACTAAAACTTTCTCCATATCAG 663
INTRON_3 260170 TAATAAGGTTGTTGAGCTTTCTTATAACTTCTGTGTTCACTGGAGTAGAA 260219
i i vv v i iv v
C Tigger1#DNA/T 662 CAATAAGGCTGTTTCGCTTTCTTATCATTCGTGTGTTCACTGGAGTAGCA 613
INTRON_3 260220 ATTTCTATTTTCTTCAATAACTTTTTTCTTTACATTAACAAGTTGGCTAA 260269
v iv i v i- i v v
C Tigger1#DNA/T 612 CTTTTAATTTCCTTCAAGAACTTTTC-CTTTGCATTCACAACTTGGCTAA 564
INTRON_3 260270 CTGTTTGGTATAAGAGGCCTAGCTTTGAGCTT----TAGCTTTAGACATG 260315
iii vi i ----ii v
C Tigger1#DNA/T 563 CTGTTTGGCGCAAGAGGCCTAGCTTTCGGCCTATCTCGGCTTTCGACATG 514
INTRON_3 260316 CCTTTCTCACTAAGCTTAATTGTTTTGAGCTTTTGATTTAAAATGAGAAA 260365
i ii iv i i
C Tigger1#DNA/T 513 CCTTCCTCACTAAGCTTAATCATTTCTAGCTTTTGATTTAAAGTGAGAGA 464
INTRON_3 260366 CATGTGACTCTT----TCACTTAAACACTTAGAGGCCATTGTAGGATTAT 260411
i i ---- i i
C Tigger1#DNA/T 463 CGTGCGACTCTTCCTTTCACTTGAACACTTAGAGGCCATTGTAGGGTTAT 414
INTRON_3 260412 TA 260413
C Tigger1#DNA/T 413 TA 412
Matrix = 20p37g.matrix
Transitions / transversions = 1.60 (32 / 20)
Gap_init rate = 0.01 (4 / 390), avg. gap size = 3.00 (12 / 4)
+ 1895 17.6 0.3 0.0 INTRON_3 260414 260715 (139466) C AluJr SINE/Alu (9) 303 1 332
ANNOTATION EVIDENCE:
1699 17.45 1.66 1.32 INTRON_3 260414 260715 139466 C AluJb SINE/Alu 1 303 9 490
INTRON_3 260414 TTTTATTTATTTTACTTTTTAGAGTTGGTGTCTTGCTGTGTCTCCCAGGC 260463
v v vi v vii v i v v
C AluJb#SINE/Al 303 TTTTTTTTTTTTTTTTTTTTTGAGACAGGGTCTCGCTCTGTCGCCCAGGC 254
INTRON_3 260464 TAGAGTGCAGTGGTGCAATCATAGTTCACTACAGGCTTGAACTCCTAGGC 260513
i i i ii i i v i v ii
C AluJb#SINE/Al 253 TGGAGTGCAGTGGCGCGATCACGGCTCACTGCAGCCTCGACCTCCCGGGC 204
INTRON_3 260514 TCAAGCAATCCTCCAGCCTCAGCCTCCCGACTAGCTGGCACTACAAGCAC 260563
i v v v i i
C AluJb#SINE/Al 203 TCAAGCGATCCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGC 154
INTRON_3 260564 ATGTCATTATGCCTGGCTAATTTATTTGTATTTT--GTAAAGATGGG--- 260608
ii i ii i i -- -- i i ---
C AluJb#SINE/Al 153 GCGCCACCACGCCCGGCTAATTT--TTGTATTTTTTGTAGAGACGGGGTT 106
INTRON_3 260609 TCATGCTATGTTGCCCAGGCTGGGTTTGAACTCCTGGCCTCAAGTGATCC 260658
-- i vi i v
C AluJb#SINE/Al 105 TCA--CCATGTTGCCCAGGCTGGTCTCGAACTCCTGGGCTCAAGTGATCC 58
INTRON_3 260659 TCCTGCCTCAGCCTCCCAAATTGCTGAGATTACAGGTGTGAGCCACCACA 260708
i i v i i i i
C AluJb#SINE/Al 57 TCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCG 8
INTRON_3 260709 CCCAGCC 260715
i
C AluJb#SINE/Al 7 CCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 2.25 (36 / 16)
Gap_init rate = 0.01 (4 / 301), avg. gap size = 2.25 (9 / 4)
+ 470 35.8 12.7 6.7 INTRON_3 260848 261233 (138948) C L3 LINE/CR1 (1) 4488 4078 333
ANNOTATION EVIDENCE:
222 36.66 0.73 10.40 INTRON_3 260848 260984 139197 C L3 LINE/CR1 4364 4488 1 526
INTRON_3 260848 ATAGAATTATAAAGTTTCTTGGCTGAAAGA-ATTTTAGGTTTTAACTATC 260896
i i i i i vvi i i i- ii ivv i v v-
C L3#LINE/CR1 4488 ATAGAATCACAGAATCTCAGAGTTGGAAGGGACCTTAGAGGTCATCTAG- 4440
INTRON_3 260897 TTTCAAGCTAACCATATTTTCCATATGATTTTGGAATCTTCTTTATAACA 260946
- i ? ----------i vii viv iii i i
C L3#LINE/CR1 4439 -TCCAANCT----------CCCATCCAATGCAGGAATCCCTTCTACAACA 4401
INTRON_3 260947 CCCATGCCTTGTGGTCACCTAGGTATTTACTTGGATAC 260984
i v v vv i i vi- i i i
C L3#LINE/CR1 4400 TCCCTGACAAGTGGTCATCCAGCC-TCTGCTTGAATAC 4364
Matrix = 25p37g.matrix
Transitions / transversions = 2.14 (30 / 14)
Gap_init rate = 0.03 (4 / 136), avg. gap size = 3.50 (14 / 4)
470 35.33 3.66 4.51 INTRON_3 260988 261233 138948 C L3 LINE/CR1 4078 4321 168 527
INTRON_3 260988 CCATCATTGAGAAGTTTTTACTGTTAAAAAAGTTTTTTTTTAAATTGTGC 261037
iv iiv i i v i i - i ii v v
C L3#LINE/CR1 4321 CCATTTTTGGACAGCTCTGATTGTTAGAAA-GTTCTTCCTTATATTGAGC 4273
INTRON_3 261038 CAAAATGTATATTCCTTTGATCTCTCAACCCACTACCTCTACCAAGGGTA 261087
ii v iiv i v i ii i-- ivii ------ v
C L3#LINE/CR1 4272 TGAAATCTGCCTCCCTGTAACTTCC--ACCCACTGATCCTA------GTT 4231
INTRON_3 261088 CCACATTTTTACAACAAATAAAACAAATCTTGTCTCTCTCTTCCATATGA 261137
ii vi i viviv v i i i i vi i -- i
C L3#LINE/CR1 4230 CTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCCTCT--TCCACATGA 4183
INTRON_3 261138 TAGCCCTTCAGAGCTAGGAAGATGGTCAACATAT---------GGCTTTT 261178
i i vv vv ii ii v i --------- v i
C L3#LINE/CR1 4182 CAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCCTCTAAGTCTTCT 4133
INTRON_3 261179 CCTCTCCATGCAAAACTGCTCTTATTGCTTTAAACATTGATCACAGGACA 261228
i v v vv i ivi v i v i vv i v
C L3#LINE/CR1 4132 CTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGACA 4083
INTRON_3 261229 TGTTT 261233
v
C L3#LINE/CR1 4082 TGGTT 4078
Matrix = 25p37g.matrix
Transitions / transversions = 1.52 (50 / 33)
Gap_init rate = 0.02 (5 / 245), avg. gap size = 4.00 (20 / 5)
+ 393 33.5 5.6 2.0 INTRON_3 261248 261442 (138739) + MIR SINE/MIR 10 211 (51) 334
ANNOTATION EVIDENCE:
393 33.48 5.64 1.98 INTRON_3 261248 261442 138739 + MIR SINE/MIR 10 211 51 528
INTRON_3 261248 CAGACTGATAAAGTATACAATCTTCGGCATCATACT--CTGAAGGTTCAA 261295
v v i v vii iiv ii vii v -- -- i
MIR#SINE/MIR 10 CATAGTGGTTAAGAGCACGGACTCTGGAGCCAGACTGCCTG--GGTTCGA 57
INTRON_3 261296 ATCTTATAACAACAACCTGCTAATACTGTGATATTTG-CATAGTTA-TTA 261343
iiivvv vi v i i iivv iv v - - -
MIR#SINE/MIR 58 ATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCA-AGTTACTTA 106
INTRON_3 261344 TCTCCTCTGTATCTCAGTTCCCCAAACTGTAA--TAGGGA----AATTGT 261387
v ii ii i iv v -- i ---- v
MIR#SINE/MIR 107 ACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGT 156
INTRON_3 261388 GTTTATTCCATAGTATTGTTGTAAAGAAATAGATAAAT-AATTCGTGTAG 261436
iii iii vi i i v- i i i - v i i
MIR#SINE/MIR 157 ACCTACCTCATAGGGTTGTTGTGAGGAT-TAAATGAGTTAATACATGTAA 205
INTRON_3 261437 AGCACT 261442
i
MIR#SINE/MIR 206 AGCGCT 211
Matrix = 25p37g.matrix
Transitions / transversions = 1.78 (41 / 23)
Gap_init rate = 0.05 (9 / 194), avg. gap size = 1.67 (15 / 9)
+ 379 30.3 6.5 3.3 INTRON_3 261522 261823 (138358) + MLT1I LTR/ERVL-MaLR 65 380 (169) 335
ANNOTATION EVIDENCE:
237 35.04 9.27 6.45 INTRON_3 261522 261823 138358 + MLT1H LTR/ERVL-MaLR 71 380 169 601
INTRON_3 261522 ACTATGCTGGGCCTGCCACTGTGAG-TAGAACATACTTTCCTGTCTCATT 261570
v v vv v iiiv - i iiv i i iii i -
MLT1H#LTR/ERV 71 ACTTTGCAGCTCCTCCCATCAAGAGGTGGAGTCTATTTCCCCACCCC-TT 119
INTRON_3 261571 GATGTTGGGTTTAGCCAAATGACTTGCTCTACCCAATGGAATGTTAGCAG 261620
vvi i -i vvi i iv i i-i
MLT1H#LTR/ERV 120 GAATCTGGGCT-GGCCTTGTGACTTGCTTTGGCCAATAGAATGC-GGCAG 167
INTRON_3 261621 AAGTGATA------TAAT---GAA---AAACTTTAAACATACTTGCATGG 261658
ii------i i --- i--- ii i i ivivv i -
MLT1H#LTR/ERV 168 AAGTGACGGTGTGCCAGTTCCGAGCCTAGGCCTCAAGAGGCCTTGCACG- 216
INTRON_3 261659 TTTTCTAGTCTCTTACACTCTAATGATCTT-------CTATAAGAACATG 261701
-i iiv ---- vivi i i ------- i iv v
MLT1H#LTR/ERV 217 -CTTCCGCTCTCT----CTCTTGGAACCCTGCCACCGCCATGTGAACAAG 261
INTRON_3 261702 CCCCAGAGAGTC-ACTAGTACAAGGAAAATAAGAAAGCACACAAAGCTGA 261750
vi vv i -i ------- ii i i v iiii v
MLT1H#LTR/ERV 262 CCCGGGCTAGCCTGCT-------GGAGGATGAGAGACCACGTGGAGCAGA 304
INTRON_3 261751 TTCGAACCCAGTTTACAATCTGAAGCCA----AGCCTAGCCTATTTC-AG 261795
vi i -- i-- v v i ---- v i viiii -
MLT1H#LTR/ERV 305 GCCGAGCC--GTC--CCAGCTGAGGCCATCCTAGACCAGCCAGCCCCCAG 350
INTRON_3 261796 CCATATCCAGCAGAGCCGC--AACTGACTC 261823
vivi -- v i i
MLT1H#LTR/ERV 351 CCAAGATCAGCAGAGCCGCCTACCCGACCC 380
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (66 / 33)
Gap_init rate = 0.06 (17 / 301), avg. gap size = 2.82 (48 / 17)
247 28.28 7.07 0.00 INTRON_3 261527 261625 138556 + MLT1J LTR/ERVL-MaLR 76 181 331 602
INTRON_3 261527 GCTGGGCCT---GCCACTGTGAGTA--GAACATACTTTCCTGTCTCA-TT 261570
vi--- ivv i -- vi i i i v i v-
MLT1J#LTR/ERV 76 GCTGGGCACATGGCCACCCAGAATAAAGACTACATTTCCCAGCCTCCCTT 125
INTRON_3 261571 GATGTTGGGTTTAGCCAAATGACTT-GCTCTACCCAATGGAATGTTAGCA 261619
vv i i v i vi v- i iv i v
MLT1J#LTR/ERV 126 GCAGCTAGGTGTGGCCATGTGACTAAGTTCTGGCCAATGGGATGTAAGCA 175
INTRON_3 261620 GAAGTG 261625
MLT1J#LTR/ERV 176 GAAGTG 181
Matrix = 20p37g.matrix
Transitions / transversions = 1.15 (15 / 13)
Gap_init rate = 0.04 (4 / 98), avg. gap size = 1.75 (7 / 4)
335 34.31 0.00 0.00 INTRON_3 261554 261655 138526 + MLT1H2 LTR/ERVL-MaLR 65 166 323 603
INTRON_3 261554 TACTTTCCTGTCTCATTGATGTTGGGTTTAGCCAAATGACTTGCTCTACC 261603
v ii vi v ivi i i vi i iv
MLT1H2#LTR/ER 65 TAGTCCCCTCCCACATTGACTCTGGGCTTGGCCATGTGACTTGCTTTGGC 114
INTRON_3 261604 CAATGGAATGTTAGCAGAAGTGATATAATGAAAAACTTTAAACATACTTG 261653
i ii iiv ii vv i ii v v viii
MLT1H2#LTR/ER 115 CAATGGGACATTAGCAAGCGTGATGCAAGCAGAGGCTTGATAAGCGCTTG 164
INTRON_3 261654 CA 261655
MLT1H2#LTR/ER 165 CA 166
Matrix = 20p37g.matrix
Transitions / transversions = 1.92 (23 / 12)
Gap_init rate = 0.00 (0 / 101), avg. gap size = 0.0 (0 / 0)
379 22.22 0.00 0.00 INTRON_3 261555 261626 138555 + MLT1I LTR/ERVL-MaLR 71 142 269 604
INTRON_3 261555 ACTTTCCTGTCTCATTGATGTTGGGTTTAGCCAAATGACTTGCTCTACCC 261604
i i i v v i v i vi i iv
MLT1I#LTR/ERV 71 ACTTCCCTGCCCCCTTGAAGTTAGGTGTGGCCATGTGACTTGCTTTGGCC 120
INTRON_3 261605 AATGGAATGTTAGCAGAAGTGA 261626
i v i
MLT1I#LTR/ERV 121 AATGAAATGTGAGCGGAAGTGA 142
Matrix = 20p37g.matrix
Transitions / transversions = 1.67 (10 / 6)
Gap_init rate = 0.00 (0 / 71), avg. gap size = 0.0 (0 / 0)
+ 250 30.6 9.2 3.1 INTRON_3 261910 262061 (138120) C MLT1H LTR/ERVL-MaLR (13) 536 376 336
ANNOTATION EVIDENCE:
250 30.56 9.21 3.11 INTRON_3 261910 262061 138120 C MLT1H LTR/ERVL-MaLR 376 536 13 605
INTRON_3 261910 TAGTGCTGCATAGCAAACTCCCCCAAA-CTCAATAGTCTTCAACAATAAA 261958
v i i iv - i i i ii vv i v
C MLT1H#LTR/ERV 536 TATTGCTGCGTAACAAACCACCCCAAAACTTAGTGGCTTAAAACAACAAC 487
INTRON_3 261959 CATTTATTCCTAGCTCCCTTGTCTACAGGTTGGC----TGAG----GTTC 262000
i- vivvv iii i ---- i ---- i
C MLT1H#LTR/ERV 486 CATTTATTT-TAGCTCATGATTCTGTGGGTCGGCAATTTGGGCTGGGCTC 438
INTRON_3 262001 AACTGA-----TCTAGAATGATCTTGGCTGGAATTCACTCCAAAGGCTGC 262045
i i----- vv-- i i i-i vviviv -
C MLT1H#LTR/ERV 437 AGCTGGGTGGTTCTTC--TGGTCTCGGCTGGG-CTCACTCATGCATCTG- 392
INTRON_3 262046 TGATCGGTTCTGGGTC 262061
i i i vi
C MLT1H#LTR/ERV 391 TGGTCAGCTGCGGGTC 376
Matrix = 20p37g.matrix
Transitions / transversions = 1.81 (29 / 16)
Gap_init rate = 0.05 (8 / 151), avg. gap size = 2.38 (19 / 8)
+ 238 31.7 0.0 1.2 INTRON_3 262188 262270 (137911) C MLT1H LTR/ERVL-MaLR (373) 176 95 336
ANNOTATION EVIDENCE:
238 31.72 0.00 1.22 INTRON_3 262188 262270 137911 C MLT1H LTR/ERVL-MaLR 95 176 373 606
INTRON_3 262188 CTGTCACCTCTGCTAGCTTACCATTGGTCACAGAAAGTCCTGTGCTAAGT 262237
i i i- v v i i v v viiv viv i
C MLT1H#LTR/ERV 176 CCGTCACTTCTGCC-GCATTCTATTGGCCAAAGCAAGTCACAAGGCCAGC 128
INTRON_3 262238 CCAAAGTCCAGAGGAGGGGAAGTAAACTCTGCC 262270
i v v i v i i ii
C MLT1H#LTR/ERV 127 CCAGATTCAAGGGGTGGGGAAATAGACTCCACC 95
Matrix = 20p37g.matrix
Transitions / transversions = 1.36 (15 / 11)
Gap_init rate = 0.01 (1 / 82), avg. gap size = 1.00 (1 / 1)
+ 248 28.7 4.1 3.1 INTRON_3 262281 262377 (137804) C MLT1H LTR/ERVL-MaLR (293) 118 21 336
ANNOTATION EVIDENCE:
248 28.72 4.12 3.06 INTRON_3 262281 262377 137804 C MLT1I LTR/ERVL-MaLR 21 118 293 607
INTRON_3 262281 CCAAAACAAGTCACATAGCCACATTCAACATCAAATGGGGTGGAAAAGTA 262330
i i iii v i- ii ii i
C MLT1I#LTR/ERV 118 CCAAAGCAAGTCACATGGCCACACCTAACTTCAAG-GGGGCAGGGAAGTG 70
INTRON_3 262331 TACACTTCCAATGGATGCAGGGGAGGGAG-GAGT---GAATATTTACTAA 262376
i vv i v v -- vv i ? - i---i iv i
C MLT1I#LTR/ERV 69 CAATCCTACCATG--TGCCCGGAAGGNAGAGAGCCAGAAATATTTGGTGA 22
INTRON_3 262377 A 262377
C MLT1I#LTR/ERV 21 A 21
Matrix = 20p37g.matrix
Transitions / transversions = 2.25 (18 / 8)
Gap_init rate = 0.04 (4 / 96), avg. gap size = 1.75 (7 / 4)
+ 241 33.9 6.8 1.6 INTRON_3 262487 262603 (137578) C L3 LINE/CR1 (401) 4088 3966 333
ANNOTATION EVIDENCE:
241 33.88 6.84 1.63 INTRON_3 262487 262603 137578 C L3 LINE/CR1 3966 4088 401 529
INTRON_3 262487 ATCACAGTGATTTC-GGGTTCTTCTCCATTTTGATTGTTCTCCTATAAGT 262535
v - i -i iii v ii i iii i v iiii
C L3#LINE/CR1 4088 ATGACA-TGGTTTCCAGACCCTTCACCATCCTGGTCACTCTTCTCTGGAC 4040
INTRON_3 262536 GC-----AGTTTATTATTGTCTCTCTCAAAA-GTAATATGTTGATATAGA 262579
----- i i v i i - ii iiviv - iv
C L3#LINE/CR1 4039 GCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGTGCCCAGA-ACTGA 3991
INTRON_3 262580 AAGCAATAGTT-ATATATGGTCTAA 262603
v v i- v i i
C L3#LINE/CR1 3990 ACGCAATACTCCAGATGTGGTCTGA 3966
Matrix = 25p37g.matrix
Transitions / transversions = 2.90 (29 / 10)
Gap_init rate = 0.05 (6 / 116), avg. gap size = 1.67 (10 / 6)
+ 256 28.4 9.5 0.0 INTRON_3 262804 262877 (137304) C L3 LINE/CR1 (800) 3689 3609 333
ANNOTATION EVIDENCE:
256 28.38 9.46 0.00 INTRON_3 262804 262877 137304 C L3 LINE/CR1 3609 3689 800 530
INTRON_3 262804 GTTGCAGCCTGTTCAGATAGTTTTGGATCCTGACTTTATTACTTAGCACA 262853
v iv vi i i i i i i iii ? ii
C L3#LINE/CR1 3689 GTTCCAGCCTGTCAAGATCATTTTGAATCTTGATTCTGTCATCCANCGTA 3640
INTRON_3 262854 T-------CCCTCCCAACTTCCTGTCATATG 262877
------- i iv v
C L3#LINE/CR1 3639 TTAGCTATCCCTCCCAGCTTTGTGTCATCTG 3609
Matrix = 25p37g.matrix
Transitions / transversions = 3.00 (15 / 5)
Gap_init rate = 0.01 (1 / 73), avg. gap size = 7.00 (7 / 1)
+ 235 25.3 7.5 7.5 INTRON_3 263688 263781 (136400) C MIRb SINE/MIR (125) 143 50 337
ANNOTATION EVIDENCE:
235 25.28 7.45 7.45 INTRON_3 263688 263781 136400 C MIRb SINE/MIR 50 143 125 531
INTRON_3 263688 ACATATGAAGCTCCTGAGATTCATAGAGGCTAAGTGAC------AAAGTC 263731
v i vvv ii v i ------ i
C MIRb#SINE/MIR 143 ACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTC 94
INTRON_3 263732 ACAAGTCTAA-AAGAGGCAAAAACAGTATCTGAACTGAAATGCCAGGCCT 263780
viv i- v i iv v ii ------- i
C MIRb#SINE/MIR 93 ACACAGCTAGTAAGTGGCAGAGCCAGGATTCGAAC-------CCAGGTCT 51
INTRON_3 263781 G 263781
C MIRb#SINE/MIR 50 G 50
Matrix = 25p37g.matrix
Transitions / transversions = 1.20 (12 / 10)
Gap_init rate = 0.03 (3 / 93), avg. gap size = 4.67 (14 / 3)
+ 360 6.4 0.0 0.0 INTRON_3 264351 264397 (135784) + (CA)n Simple_repeat 1 47 (0) 338
ANNOTATION EVIDENCE:
360 6.38 0.00 0.00 INTRON_3 264351 264397 135784 + (CA)n Simple_repeat 1 47 133 591
INTRON_3 264351 CACACACACACACACACACACACACACACACACACGCACATGCACAC 264397
i ii
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACAC 47
Matrix = Unknown
Transitions / transversions = 0.0 (3 / 0)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 621 33.5 7.2 3.6 INTRON_3 265024 265740 (134441) + L2c LINE/L2 2304 3082 (337) 339
ANNOTATION EVIDENCE:
621 30.72 6.53 4.36 INTRON_3 265024 265360 134821 + L2 LINE/L2 2304 2647 435 532
INTRON_3 265024 CATGACTTCTA-TACCATTTACATGGTAAAAACTCCCA------TATCTT 265066
i iv - i i v i vi ------ i
L2#LINE/L2 2304 CATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTATATCTC 2353
INTRON_3 265067 --GCT--GGCACTCTCCTCCTGAGCTCTAGACGTGTGTATTCA-----CC 265107
-- i-- i - - i i vi i i ----- i
L2#LINE/L2 2354 CAGCCCAGAC-CTCTCC-CCTGAACTCCAGACTCGTATATCCAACTGCCT 2401
INTRON_3 265108 ACATTGACAGCTCCACTAGGATATTTCACAGGCATGTCAAGTGTAATGTT 265157
- i v v i i v i v iiv ii v
L2#LINE/L2 2402 AC-TCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATG 2450
INTRON_3 265158 ATCAAAGTTGGATTTATTTTGTCTTCCTCCC--AATATGCTCCTTCTTTA 265205
vi ii i i i--i vi i i-- iv i ivi
L2#LINE/L2 2451 TCCAAAACTGAACTC--CTGATCTTCCCCCTCAAACCTGCTCCTCCCACA 2498
INTRON_3 265206 GAATTATC--TCTTTGATAAAGGACATCGTTCTTCTCCCAGTTGCT-AGA 265252
vv vi -- iv v v - v viiv i i - i
L2#LINE/L2 2499 GTCTTCCCCATCTCAGTTAATGG-CAACTCCATCCTTCCAGTTGCTCAGG 2547
INTRON_3 265253 CATAGAAACAGTGAAGTCATTCTTGACTTCCCTCTTTCCCTTTCCTCTCT 265302
-i i vv i i i i ------- v
L2#LINE/L2 2548 C-CAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTC-------TCTCA 2589
INTRON_3 265303 TGCCAGATATTTAATCTATCCTCCAGTCTCTCTCACTC-ATCTTTATACT 265351
ii vv i ii i vv v i iivi vi - i i v v
L2#LINE/L2 2590 CACCCCACATCCAATCCATCAGCAAATCCTGTTGGCTCTACCTTCAAAAT 2639
INTRON_3 265352 GTAATCCAG 265360
i -
L2#LINE/L2 2640 ATA-TCCAG 2647
Matrix = 25p37g.matrix
Transitions / transversions = 1.83 (64 / 35)
Gap_init rate = 0.05 (17 / 336), avg. gap size = 2.18 (37 / 17)
543 36.03 7.75 2.91 INTRON_3 265315 265740 134441 + L2 LINE/L2 2637 3082 0 533
INTRON_3 265315 AATCTATCC----TCCAGTCTCT-CTCACTCATCTTTAT-------ACTG 265352
v ---- iii v - - i ii i------- iv
L2#LINE/L2 2637 AATATATCCAGAATCCGACCACTTCTCAC-CACCTCCACTGCCACCACCC 2685
INTRON_3 265353 TAATCCA-GTCTCTATAATCGTTTATTGGGGCATT--TGCATTAGCTTCC 265399
ii - i v i v vi iiiiv -- -- v i
L2#LINE/L2 2686 TGGTCCAAGCCACCATCATCTCTCGCCTGG--ATTACTGCAATAGCCTCC 2733
INTRON_3 265400 TAAATGATCTCCTTGCTTCTA-----GCCCAT-TCCAACTCATTCTTGAC 265443
v i i i ----- vi- ? iiii ii
L2#LINE/L2 2734 TAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAAC 2783
INTRON_3 265444 TTGG-AGCCAGAGTAATGTTTTAATTATACAAAATTGATTCGATCTCTTG 265492
vii - i vi v vv i i iviv ivvi v iv
L2#LINE/L2 2784 ACAGCAGCCAGAGTGATCCTTTTAAAACATAAGTCAGATCATGTCACTCC 2833
INTRON_3 265493 TTTGTTTAAAAAACATCAGTGGCTTCCCATTATCATTATGA-TAAAGCAT 265541
i i i vv vi i- i vv - i-ii
L2#LINE/L2 2834 TCTGCTCAAAACCCTCCAGTGGCTTCCCATC-TCACTCAGAGTAAAA-GC 2881
INTRON_3 265542 CACATTCTTAACA-TGGCCTATAACCTGTTGCATGCTCTGATCCCTGCAT 265590
v v i v - i vvivi i v i i- i
L2#LINE/L2 2882 CAAAGTCCTTACAGTGGCCTACAAGGCCCTACATGATCTGGTCCCC-CGT 2930
INTRON_3 265591 CAT-TCTCCAGTTTAGTCATAACTCCTCAACCACAAACTCCTATTTTCAT 265639
i i- iiiii --- -- -- vvv i ivivi i
L2#LINE/L2 2931 TACCTCTCTGACCT---CAT--CTCCT--ACCACTCTCCCCCTCGCTCAC 2973
INTRON_3 265640 TCTAATCAAACTAAAT--GTCTAATCACTA------GGATACACTAGGAT 265681
iiv v i i v i-- i vv ii i------ i i i i vv
L2#LINE/L2 2974 TCCGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCA 3023
INTRON_3 265682 CTCTTCAACTTGTGGGTCATTGAACCTTCTCTTTCTTCAGTCTGGAACAT 265731
v i vi i vv i v v i v v i i v i ii
L2#LINE/L2 3024 CGCTCCTGCCTCAGGGCCTTTGCACTTGCTGTTCCCTCTGCCTGGAACGC 3073
INTRON_3 265732 TCTTTTACC 265740
iiv
L2#LINE/L2 3074 TCTTCCCCC 3082
Matrix = 25p37g.matrix
Transitions / transversions = 1.69 (93 / 55)
Gap_init rate = 0.05 (21 / 425), avg. gap size = 2.19 (46 / 21)
+ 400 26.9 6.7 3.6 INTRON_3 265760 265894 (134287) + L2a LINE/L2 3286 3424 (2) 340
ANNOTATION EVIDENCE:
400 26.90 6.67 3.60 INTRON_3 265760 265894 134287 + L2a_3end LINE/L2 377 515 2 534
INTRON_3 265760 TTATCTCTTATTCATCCACCAGAAAATAAGCTCCGTGAGAGCAAGTACCT 265809
i v i- i vi i vi i i i v i
L2a_3end#LINE 377 TTGTCTGTC-TCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTT 425
INTRON_3 265810 ACCTTGTCTTTCTTGTTTA--ACTGTGCCACCTAGCACTTAGAACAATCA 265857
--- v i i --i ii - i i i i vv
L2a_3end#LINE 426 ---TTGTCTGTTTTGTTCACTGCTGTATC-CCCAGCGCCTAGAACAGTGC 471
INTRON_3 265858 ATG-CACA-----GATGCTCAACAG-TACTTGCTGAGTGAATAA 265894
v - ----- ii i i- i i i i
L2a_3end#LINE 472 CTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAATGAATGA 515
Matrix = 25p37g.matrix
Transitions / transversions = 3.38 (27 / 8)
Gap_init rate = 0.05 (7 / 134), avg. gap size = 2.00 (14 / 7)
+ 339 35.3 0.0 1.0 INTRON_3 265899 266001 (134180) + L2c LINE/L2 3109 3210 (177) 339
ANNOTATION EVIDENCE:
339 35.30 0.00 0.98 INTRON_3 265899 266001 134180 + L2c_3end LINE/L2 200 301 177 535
INTRON_3 265899 ATCTTTCAAGTCTCAGCATAAACATCATTTCCTCAAGGAGGCCTTTCATG 265948
i ? vi i ii ii v i i v
L2c_3end#LINE 200 ATCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCAGGAAGCCTTCCCTG 249
INTRON_3 265949 ACTCCCAGGAAAAAAAATAGATCTCTTTATTATATCCTCCTATAGCATTC 265998
i viii?vv ivv i vi i iv i- i v i ii
L2c_3end#LINE 250 ACCCCCCAAGNCTAGTCTAGGTGCCCTCCTC-TGTGCTCCCATAGCACCC 298
INTRON_3 265999 TGT 266001
L2c_3end#LINE 299 TGT 301
Matrix = 25p37g.matrix
Transitions / transversions = 2.09 (23 / 11)
Gap_init rate = 0.01 (1 / 102), avg. gap size = 1.00 (1 / 1)
+ 427 28.4 4.0 0.7 INTRON_3 266050 266198 (133983) C L1MEc LINE/L1 (6210) 190 37 341
ANNOTATION EVIDENCE:
427 28.37 4.03 0.65 INTRON_3 266050 266198 133983 C L1MEc_5end LINE/L1 37 190 2337 572
INTRON_3 266050 TTTGTTTTTCTTTTCTCAGTGATCACAGCACTGTGCTGGCTGTTGTCAAA 266099
ii v i v v iv vi i v v v i
C L1MEc_5end#LI 190 TTTGTTTCCCATCTCTCAGGGATCACTGTCCTTCGTTGCCTGATGTCCAG 141
INTRON_3 266100 -GATTTGAAA-----CGTCTTGTATATTTTGTCCAGGTTTTCAGTTGTTT 266143
- vi -----i i ii i- v i
C L1MEc_5end#LI 140 TGTCTTGAAAACTATTGTTTCATATATTTTGTCT-GTTTTTTAGTTGTTT 92
INTRON_3 266144 AAGTCAAGAGGGTAATTCTGTTTCTTGTAATTCTATCTCAGCTGGAAGTG 266193
v vi i v i v i i v i i ii ii ii
C L1MEc_5end#LI 91 CAGGTAGGAGGGTAAATCCGGTCCCTGTTACTCCATCTTGGCCAGAAGCA 42
INTRON_3 266194 GAAGT 266198
C L1MEc_5end#LI 41 GAAGT 37
Matrix = 20p37g.matrix
Transitions / transversions = 1.80 (27 / 15)
Gap_init rate = 0.02 (3 / 148), avg. gap size = 2.33 (7 / 3)
+ 290 26.1 7.0 2.5 INTRON_3 266305 266418 (133763) + L2c LINE/L2 3303 3421 (5) 339
ANNOTATION EVIDENCE:
290 26.10 7.02 2.52 INTRON_3 266305 266418 133763 + L2a_3end LINE/L2 394 512 5 536
INTRON_3 266305 CTAGAAAGTTA--TCCATT-TGGCTAAGACTTT-----GTTTTGTTTATT 266346
v v -- v-v vii ----- i i
L2a_3end#LINE 394 CTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACT 443
INTRON_3 266347 TCTGTATCCCCACAGCCCACAGCATCATGTGAAGAACATAATAGACACTG 266396
v vv i v i --i ivvi v i i i v
L2a_3end#LINE 444 GCTGTATCCCCAGCGCCTAGAACA--GTGCCTGGCACATAGTAGGCGCTC 491
INTRON_3 266397 AATAAATTAAAGGTTGCATGAA 266418
- vvv v
L2a_3end#LINE 492 AATAAAT-ATTTGTTGAATGAA 512
Matrix = 25p37g.matrix
Transitions / transversions = 0.71 (12 / 17)
Gap_init rate = 0.04 (5 / 113), avg. gap size = 2.20 (11 / 5)
+ 586 30.5 7.9 0.0 INTRON_3 266627 266829 (133352) C MIR SINE/MIR (4) 258 40 342
ANNOTATION EVIDENCE:
586 30.54 7.88 0.00 INTRON_3 266627 266829 133352 C MIR SINE/MIR 40 258 4 537
INTRON_3 266627 ATACCTAATATTTCTTT-TCAGTTATGATTTGCCAAGCACTATACTAAAC 266675
v i i v v-v iv iv v i i v i
C MIR#SINE/MIR 258 ATAACCAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGC 209
INTRON_3 266676 -----------ATTAACTGATATAATCCTGCCAATAAACTTATGAGATGG 266714
----------- v v vv i v i i i
C MIR#SINE/MIR 208 GCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGGTAG 159
INTRON_3 266715 GGCCTATTTTTGTTCCCACTTTATCGATAAGAAAAA-GAGGCATTGAAAG 266763
vv v i i i iv i i v- iv i
C MIR#SINE/MIR 158 GTACTATTATTATCCCCATTTTACAGATGAGGAAACTGAGGCACAGAGAG 109
INTRON_3 266764 ATTAAACAAAATGTC-AAGATAGCA--GCTGAGAAGCAATGGAGCTAGGA 266810
i ii vv i - i vi -- iiv iiiii ii
C MIR#SINE/MIR 108 GTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCGGGA 59
INTRON_3 266811 TTTGAACACAGAGAGTTTG 266829
i v iv i
C MIR#SINE/MIR 58 TTCGAACCCAGGCAGTCTG 40
Matrix = 25p37g.matrix
Transitions / transversions = 1.48 (37 / 25)
Gap_init rate = 0.02 (5 / 202), avg. gap size = 3.20 (16 / 5)
+ 23 66.7 0.0 0.0 INTRON_3 266924 266953 (133228) + AT_rich Low_complexity 1 30 (0) 343
ANNOTATION EVIDENCE:
23 66.67 0.00 0.00 INTRON_3 266924 266953 133228 + AT_rich Low_complexity 127 156 144 550
INTRON_3 266924 ATATTATTAAAATAGAAATTTAAAATAAAA 266953
????????????? vv vvvv v
AT_rich#Low_c 127 WWWWWWWWWWWWWATTAAAAATAAATAATA 156
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 7)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 753 37.5 11.3 3.6 INTRON_3 267122 267670 (132511) C L4 LINE/RTE (330) 1699 1109 344
ANNOTATION EVIDENCE:
753 36.80 6.41 4.18 INTRON_3 267122 267589 132592 C L4 LINE/RTE 1222 1699 330 538
INTRON_3 267122 TTCTAAAAAGAATTTGTACA-GCAGGTTCTTATATAAGAGATATTT---- 267166
ii v - - ii ?ii i i i i v----
C L4#LINE/RTE 1699 TTCTAAAAGAAATTTCT-CACGTGGGNCTTTATATAGGGGACACTGAGTG 1651
INTRON_3 267167 -CACAACAAAAAATGTTTTTGA--ACATGGATTTTTTTTTACAAAATATT 267213
-i i iii v ii ii -- ?-------- i? v v
C L4#LINE/RTE 1650 ATATAATGGACAATGTCCTCAACAACAN--------TTTTACAGNAAATG 1609
INTRON_3 267214 CAATAGCATGCCCTATATAAAGGTCATGCCTAATA----CTATTAATAAA 267259
iv ii??iiii --- iii vi v ---- iv ii
C L4#LINE/RTE 1608 CAGAAGTGNNTTTCATAT---GGCTGTTTCTTATANCGACCCTCGATAAA 1562
INTRON_3 267260 CTTCAGAGGTGTAACAGAAAAGC-----TCAGTGAAGACATATGTACAGG 267304
vvi iii ii vv ----- i ?v v i
C L4#LINE/RTE 1561 AGCCGAGGGCATAACATTAAAGCGCAATTCAGTGAAGGCANTTCTGCAGG 1512
INTRON_3 267305 ATATTAAG-TAATGAGATTCAGGTAAATAGTCATCTATTGGTTTTATCTG 267353
ivii - v i i vii iiv iv i v ii
C L4#LINE/RTE 1511 GAGCTAAGNTAATGTGGTCCAGGTATGCAGCTTTCTGGTGGTCTAACTTG 1462
INTRON_3 267354 GTCTGAGAATAGAACTTGGAATTCATAGAAAAGTAGAGAGAGGTAGTATG 267403
i ii i i i i viv ii i i vi --i? i
C L4#LINE/RTE 1461 ATCCAAGGATAGAATTTAGAGTATCTAGAGGAATGGATGGA--CNGCATG 1414
INTRON_3 267404 TCTT-----CAAT-TTCTTCAACTGTTAATAATCTCAGCTAAGATTGTAG 267447
i ----- - i?i v i i ? vv i v v ii
C L4#LINE/RTE 1413 TCCTTCAGACAATCTTCCNTAAATATCANTTCTCTCAGCTGAGCTTTTGA 1364
INTRON_3 267448 CAACAATTCTGCA-AGTA-ATATTTTGAGACAGAGCTCTCTAGT--GAGT 267493
i v i-- v - i - i v ii iiv vii iii-- ? i
C L4#LINE/RTE 1363 TAAGAG--CTGGATAGCAGACAGTTCAAGGTTGTATTCTCTGACAAGNGC 1316
INTRON_3 267494 CAGCCATGAAGATATTCTGTTGATGCTGCTGCTTGCAAGAAAATTCATAT 267543
v vvi v ? ---- i v ivii ? i i
C L4#LINE/RTE 1315 CTGGAGTGCAGNTATTCT----ATGTTGCTGATTAAGGGNAGATCCATAT 1270
INTRON_3 267544 GCTTTGAATATTA-ATGTACAGTTGGCAAAGTTGCCATT-TATTATGA 267589
ii v ii - i vi v? ii v - ?
C L4#LINE/RTE 1269 GCTTTAGAAACCAGACGAGCAGGNGGCAGGGTTGACATTCTNTTATGA 1222
Matrix = 25p37g.matrix
Transitions / transversions = 2.43 (107 / 44)
Gap_init rate = 0.04 (19 / 467), avg. gap size = 2.63 (50 / 19)
201 41.56 1.30 0.00 INTRON_3 267594 267670 132511 C L4 LINE/RTE 1109 1186 843 539
INTRON_3 267594 AAAAATCCACCCTCAGTCTGCATAGAGTTAGGCTATGGGA-TGGCTGAAA 267642
i iv i ivvv ii v i iii - iv vii
C L4#LINE/RTE 1186 AGAAGGCCATCCCACCTCTGCACGGAGGTGGGCCGCGGGAGTACCTGCGG 1137
INTRON_3 267643 ATAGGCTCAATATTTTCCTTAAAAAGTA 267670
ii iivi iv i ii i
C L4#LINE/RTE 1136 GCAAAGCCAGGATTTTCCTCAGGAAGCA 1109
Matrix = 25p37g.matrix
Transitions / transversions = 2.56 (23 / 9)
Gap_init rate = 0.01 (1 / 76), avg. gap size = 1.00 (1 / 1)
+ 311 18.8 1.5 3.1 INTRON_3 267735 267800 (132381) C L2a LINE/L2 (0) 3426 3362 345
ANNOTATION EVIDENCE:
311 18.76 1.52 3.08 INTRON_3 267735 267800 132381 C L2a_3end LINE/L2 453 517 0 540
INTRON_3 267735 ATTCAT-CATTCAACAAATATTTATGGAGTGCATGCCATGTGCCAAGTTA 267783
- v i v i i i ivv
C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCAC 468
INTRON_3 267784 TGTGCTAAGTTCACTGG 267800
v i -- i
C L2a_3end#LINE 467 TGTTCTAGG--CGCTGG 453
Matrix = 25p37g.matrix
Transitions / transversions = 1.40 (7 / 5)
Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.50 (3 / 2)
+ 231 27.0 12.1 1.6 INTRON_3 267910 268082 (132099) C MER113 DNA/hAT-Charlie (1) 520 330 346
ANNOTATION EVIDENCE:
231 27.01 12.14 1.57 INTRON_3 267910 268082 132099 C MER113 DNA/hAT-Charlie 330 520 1 608
INTRON_3 267910 AGCACTTTCCAAAATTTAGTCA--------CCACCATAAGAATTTTAGCT 267951
iii i v i -------- v v vi v i
C MER113#DNA/hA 520 AGTGTTTCCCAAACTTCAGTCATTCGCGTACCACCTTCACGATTTTTGCC 471
INTRON_3 267952 ATAGCCTTCTACTAGCTATACTAT---------AATATTTTTCTCCACAT 267992
v iviv i v i --------- ii v
C MER113#DNA/hA 470 ATATCTGCATACCACCTGTACTATTATTTACTTAATATTTTTCTTTAAAT 421
INTRON_3 267993 TGAC-CACTTTTTTTTTACTTCT-CAAATTTTGTTTAAACATAAAGTTAA 268040
i - --- vv-i vv viv v v
C MER113#DNA/hA 420 CGACTCACTTTTTT---ACTTAAATAAATTTATTTTAAAAGGAAACTTTA 374
INTRON_3 268041 C-TCCTTCCTATAA-TGGGAAACCATTATCACCTCCTAAAAGTA 268082
i- vi v i - i v i v i v i
C MER113#DNA/hA 373 TATCACTACCATAAATGGAAAACCAGTATCACTTGCCATAAATA 330
Matrix = 20p37g.matrix
Transitions / transversions = 1.00 (23 / 23)
Gap_init rate = 0.04 (7 / 172), avg. gap size = 3.43 (24 / 7)
+ 583 29.6 7.7 2.3 INTRON_3 268086 268331 (131850) C MIR SINE/MIR (1) 261 3 347
ANNOTATION EVIDENCE:
583 29.55 7.72 2.32 INTRON_3 268086 268331 131850 C MIR SINE/MIR 3 261 1 541
INTRON_3 268086 ACAATAGCTGACATTTATTGAATATTTTCTA-GTGCTTCATACTATATTA 268134
i i ii iiii v - ivvii i vi
C MIR#SINE/MIR 261 ATAATAACCAACATTTATTGAGCGCTTACTATGTGCCAGGCACTGTTCTA 212
INTRON_3 268135 ----TTTTTCATGAATTAGGTC-TTTGATCCTCACATGAACCCCATTAAG 268179
----i v v iv - i vv i v i
C MIR#SINE/MIR 211 AGCGCTTTACATGTATTAACTCATTTAATCCTCACAACAACCCTATGAGG 162
INTRON_3 268180 TAGGTACCATTATTAGACCCATAT-ACAAATGACAGCAAA--GAGACACA 268226
i vv v - i -- v -- i
C MIR#SINE/MIR 161 TAGGTACTATTATTATCCCCATTTTACAGATGA--GGAAACTGAGGCACA 114
INTRON_3 268227 GA-------AGAAACCTACCCAAGA--AATCAGTCAATAGTTAGCAAA-C 268266
------- v i i i-- vv ii i iv i i -
C MIR#SINE/MIR 113 GAGAGGTTAAGTAACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGC 64
INTRON_3 268267 CTGTATTTTTTTAATTCAAGCTGAGTGACTTCAAAGCCTGTAATGCCTAA 268316
v v iv--- ii i v vv i i i i i iv - i
C MIR#SINE/MIR 63 CGGGATTCG---AACCCAGGCAGTCTGGCTCCAGAGTCCGTGCT-CTTAA 18
INTRON_3 268317 CTACTGTAGTATATT 268331
i i iv i
C MIR#SINE/MIR 17 CCACTATGCTATACT 3
Matrix = 25p37g.matrix
Transitions / transversions = 1.73 (45 / 26)
Gap_init rate = 0.04 (11 / 245), avg. gap size = 2.27 (25 / 11)
+ 259 19.9 0.0 7.9 INTRON_3 268338 268419 (131762) C MER113 DNA/hAT-Charlie (203) 318 243 346
ANNOTATION EVIDENCE:
259 19.86 0.00 7.89 INTRON_3 268338 268419 131762 C MER113 DNA/hAT-Charlie 243 318 203 609
INTRON_3 268338 TAAACATAGATACAAATGACAAACAAAACAATACTATTTAAATATAATTA 268387
v i - - ii v v v ii
C MER113#DNA/hA 318 TAAAAATAAATACAA-TGA-AAACAAAACAATGTTATTAAATTCTAGCTA 271
INTRON_3 268388 CATATTGTTGCCTGCTTGGTGAAGTTTTTGAG 268419
v i i---- vi i
C MER113#DNA/hA 270 GATACTGTTGCCTGCC----GAAGGCTCTGAG 243
Matrix = 20p37g.matrix
Transitions / transversions = 1.50 (9 / 6)
Gap_init rate = 0.04 (3 / 81), avg. gap size = 2.00 (6 / 3)
+ 4713 9.1 0.3 0.1 INTRON_3 268497 269179 (131002) C L1PA8A LINE/L1 (2444) 3702 3019 348 *
ANNOTATION EVIDENCE:
4713 9.09 0.29 0.15 INTRON_3 268497 269179 131002 C L1P3_orf2 LINE/L1 910 1593 1701 573
INTRON_3 268497 CCTGAAGTTTTCATTTTTTGTTGTGTCTCTGCCAGGTTTTGGCATCAGGA 268546
v i i
C L1P3_orf2#LIN 1593 CCTGAAGTTTTCTTTTTTTGTTGTATCTCTGCCAGGTTTTGGTATCAGGA 1544
INTRON_3 268547 TGATGTTGGCTTCATAAAATGAGTTAGGGAGGAGTCCCTCCTTTTCAATT 268596
i i
C L1P3_orf2#LIN 1543 TGATGCTGGCCTCATAAAATGAGTTAGGGAGGAGTCCCTCCTTTTCAATT 1494
INTRON_3 268597 GTTTGGAAGAGTTTCAGAAAGAAGGGTACCAGTTATTCTTTGTACCTCTG 268646
v ii v i vi
C L1P3_orf2#LIN 1493 GTTTGGAATAGTTTCAGAAGAAATGGTACCAGCTCCTCTTTGTACCTCTG 1444
INTRON_3 268647 GTAGAATTCAGCTGTGAATCCATCTGGTCATGGTTTTTTTTTTGGTTGGT 268696
i i v vi -
C L1P3_orf2#LIN 1443 GTAGAATTCAGCTGTAAATCCGTCTGGTCCTGGGCTTTTTTT-GGTTGGT 1395
INTRON_3 268697 AGGCTATTAATTACTGCCTCAATTTCAGAACTTGTTATCGGTCTATTCAG 268746
v i
C L1P3_orf2#LIN 1394 AGGCTATTTATTACTGCCTCAATTTCAGAACTTGTTATTGGTCTATTCAG 1345
INTRON_3 268747 GGATTCGACTTCTTCCTGGTTTAGTCTTGGGAGGATGTATATGTCCAGGA 268796
i i i i
C L1P3_orf2#LIN 1344 GGATTCAACTTCTTCCTGGTTCAGTCTTGGGAGGGTGTATGTGTCCAGGA 1295
INTRON_3 268797 ATTTATCAATTTCTTCTAGATTTTCTAGTTTATTTGCGTAGAGGTATTTA 268846
v i i
C L1P3_orf2#LIN 1294 ATTTATCCATTTCTTCTAGATTTTCTAGTTTATTTGCATAGAGGTGTTTA 1245
INTRON_3 268847 CAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGAGTCAGTGGTGATATC 268896
i v i
C L1P3_orf2#LIN 1244 TAGTATTCTCTGATGGTTGTTTGTATTTCTGTGGGGTCAGTGGTGATATC 1195
INTRON_3 268897 TCCTTTATCATTTTTTATTGTGACTATTTGATTCTTCTCTCTTTTCTTCT 268946
i v
C L1P3_orf2#LIN 1194 CCCTTTATCATTTTTTATTGTGTCTATTTGATTCTTCTCTCTTTTCTTCT 1145
INTRON_3 268947 TTATTAGTCTAGTTAGTGGTCCATGTATTTTGTTAATCTTTTCAAAAAGA 268996
i i i v i i iv
C L1P3_orf2#LIN 1144 TTATTAGTCTAGCTAGCGGTCTATCTATTTTATTAATTTTTTCAAAAAAC 1095
INTRON_3 268997 CAGGTTCAGGATTCATTAAGTTTTTGGAGGGTTTTTGG-ATCTCTATCTC 269045
v i v i v i v -i
C L1P3_orf2#LIN 1094 CAGCTCCTGGATTCATTGATTTTTTGAAGGGTTTTTCGTGTCTCTATCTC 1045
INTRON_3 269046 CTTCAGTTCTGCTCTGATCTTAATTATTTCTTGTCTTCTGACAGCTTTTG 269095
i ii vi v
C L1P3_orf2#LIN 1044 CTTCAGTTCCGCTCTGATCTTGGTTATTTCTTGTCTTCTGCTAGCTTTGG 995
INTRON_3 269096 GATCACTTTGCTCTTGCTTCTCTAGCTCTTTTA-TTGTGATGTTAGGGTG 269144
i ivv v i -
C L1P3_orf2#LIN 994 GGTTTGTTTGCTCTTGGTTCTCTAGTTCTTTTAGTTGTGATGTTAGGGTG 945
INTRON_3 269145 TCAATTTGAGATCTTTCTAGCTTTCTAATGTGGGC 269179
i i i
C L1P3_orf2#LIN 944 TCGATTTGAGATCTTTCTAGCTTTTTGATGTGGGC 910
Matrix = 20p37g.matrix
Transitions / transversions = 1.95 (41 / 21)
Gap_init rate = 0.00 (3 / 682), avg. gap size = 1.00 (3 / 3)
+ 5190 9.1 0.7 0.0 INTRON_3 269177 269887 (130294) + L1PA8A LINE/L1 3701 4416 (1730) 348 *
ANNOTATION EVIDENCE:
5190 9.14 0.70 0.00 INTRON_3 269177 269887 130294 + L1P3_orf2 LINE/L1 1592 2307 987 574
INTRON_3 269177 GGCCAATATCCCTAATGAACATCAGTGTGAAAATCCTCAATAAAATACTG 269226
i ii ii
L1P3_orf2#LIN 1592 GGCCAATATCCCTGATGAACATCGATGCAAAAATCCTCAATAAAATACTG 1641
INTRON_3 269227 GCAAACCGAATCCAGCAGCGCATCAAAAAACTTATCCACCACGATCAAGT 269276
i i
L1P3_orf2#LIN 1642 GCAAACCGAATCCAGCAGCACATCAAAAAGCTTATCCACCACGATCAAGT 1691
INTRON_3 269277 CAGCTTCATCCTTGGGATGCAAGGCTAGTTCAACATATGCAAATCAGTAA 269326
i ii i i i
L1P3_orf2#LIN 1692 CGGCTTCATCCCCGGGATGCAAGGCTGGTTCAACATACGCAAATCAATAA 1741
INTRON_3 269327 ATGTAATCTATCACATAAACAGAACCAAAGACAAAAACGACATGATTATC 269376
i ii i v
L1P3_orf2#LIN 1742 ACGTAATTCATCACATAAACAGAACTAAAGACAAAAACCACATGATTATC 1791
INTRON_3 269377 TTAATAGATCCGGAAAAGGCCTATGATAAAATTCAACATCCCTTCATGTT 269426
i iv i vi
L1P3_orf2#LIN 1792 TCAATAGACGCAGAAAAGGCCTTCGATAAAATTCAACATCCCTTCATGTT 1841
INTRON_3 269427 AAAAACTCTCAATAAACT-GATATTGATGGAACATACCTCAAAATAATAA 269475
- i ?
L1P3_orf2#LIN 1842 AAAAACTCTCAATAAACTAGGTATTGANGGAACATACCTCAAAATAATAA 1891
INTRON_3 269476 GAGCTATTTATGACAAACCCACAGCCAGTATCACACTGAATGGGCAAAAG 269525
i i i
L1P3_orf2#LIN 1892 GAGCCATTTATGACAAACCCACAGCCAATATCATACTGAATGGGCAAAAG 1941
INTRON_3 269526 TTGGAAGCATTGCCTTTGAAAACCGGCACAAGACAAAGACGCCCTCTCTC 269575
i v i i i
L1P3_orf2#LIN 1942 CTGGAAGCATTCCCCTTGAAAACCGGCACAAGACAAGGATGCCCTCTCTC 1991
INTRON_3 269576 ATCATTCCTATTCGACATAGTATTGGAAGTTCTGGCCAGGGCAATCAGGC 269625
i i i
L1P3_orf2#LIN 1992 ACCACTCCTATTCAACATAGTATTGGAAGTTCTGGCCAGGGCAATCAGGC 2041
INTRON_3 269626 AAAAGAAAGAAATAAAGAGTATTCAGAAAGGAAGAGAGGAAGTCAAATTG 269675
i i i v
L1P3_orf2#LIN 2042 AAGAGAAAGAAATAAAGGGTATTCAAATAGGAAGAGAGGAAGTCAAATTG 2091
INTRON_3 269676 TCTCTGTTTGCAGACAACATGATTCTATATTTAGAAAACCCCGTCATCTC 269725
ii i i i i
L1P3_orf2#LIN 2092 TCTCTGTTTGCAGATGACATGATCCTATATCTAGAAAACCCCATCGTCTC 2141
INTRON_3 269726 AGCCCAAACATTCCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGAT 269775
vii i
L1P3_orf2#LIN 2142 AGCCCAAAAGCTTCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGAT 2191
INTRON_3 269776 ACAAAATCAATGTGCAAAAATCACAAACATTCCTTTACACC--C--TAGA 269821
i v -- --i
L1P3_orf2#LIN 2192 ACAAAATCAATGTGCAAAAATCACAAGCATTCCTATACACCAACAACAGA 2241
INTRON_3 269822 CAAGCAGAGAGCCAAATCATGAATGAACTCCCATTCACAATTAACTCAAG 269871
iviv i
L1P3_orf2#LIN 2242 CAAGCAGAGAGCCAAATCATGAATGAACTCCCATTCACAATTGCTACAAA 2291
INTRON_3 269872 ATGGATGAAAGACTTA 269887
iv i i v i
L1P3_orf2#LIN 2292 GAGAATAAAATACCTA 2307
Matrix = 20p37g.matrix
Transitions / transversions = 4.82 (53 / 11)
Gap_init rate = 0.00 (3 / 710), avg. gap size = 1.67 (5 / 3)
+ 6193 8.0 1.6 1.0 INTRON_3 269860 271009 (129172) + L1PA8A LINE/L1 4983 6172 (0) 348
ANNOTATION EVIDENCE:
2679 8.71 1.93 0.48 INTRON_3 269860 270274 129907 + L1P3_orf2 LINE/L1 2874 3294 0 575
INTRON_3 269860 AATTAACTCAAGATGGATGAAAGACTTAAATGTAAAACCCAAAACCATAA 269909
v i
L1P3_orf2#LIN 2874 AATTAACTCAAGATGGATTAAAGACTTAAATGTAAAACCCAAAACTATAA 2923
INTRON_3 269910 AAACCCTATAAGAAAACTGAGGCAATACCATTCAGGACATAGGCATGGGC 269959
v iiv i
L1P3_orf2#LIN 2924 AAACCCTAGAAGAAAATCTAGGCAATACCATTCAGGACATAGGCACGGGC 2973
INTRON_3 269960 AAAGACTTCATGATGAAAACACCAAAAGCAATTGCAACAAAAGCCATAAT 270009
i i v v
L1P3_orf2#LIN 2974 AAAGATTTCATGATGAAAACGCCAAAAGCAATTGCAACAAAAGCAAAAAT 3023
INTRON_3 270010 TGACAAATAGGATCTAATTAAACTAAAGAACTTCTGCACAGCAGAAAAAA 270059
i i -- i
L1P3_orf2#LIN 3024 TGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCA--AAAGA 3071
INTRON_3 270060 AAAAAACATCAGAGTGAACACACAACATACAGAATGGGAGAAAATTTTTG 270109
vv v v v
L1P3_orf2#LIN 3072 AACTATCATCAGAGTGAACAGACAACCTACAGAATGGGAGAAAATTTTTG 3121
INTRON_3 270110 CAATCTACACATCTGACAAAGGTCTAATATGAGGAATTTACAAGGAACTT 270159
iv vvi i
L1P3_orf2#LIN 3122 CAATCTATCCATCTGACAAAGGTCTAATATCCAGAATCTACAAGGAACTT 3171
INTRON_3 270160 AAAAAAATTGATAAGAAA--------CAACTCCATCAAAAAGTAGGCAAA 270201
v v i -------- i i i
L1P3_orf2#LIN 3172 AAACAAATTTACAAGAAAAAAACAAACAACCCCATTAAAAAGTGGGCAAA 3221
INTRON_3 270202 GGATATGAACAGACACTTTTCAAAAGAAGACATTTATGTGGCCAAAAAAC 270251
i i i v
L1P3_orf2#LIN 3222 GGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCGGCCAACAAAC 3271
INTRON_3 270252 ATATGAAAAAAAGCTCAAAATCA 270274
v
L1P3_orf2#LIN 3272 ATATGAAAAAAAGCTCAACATCA 3294
Matrix = 20p37g.matrix
Transitions / transversions = 1.12 (19 / 17)
Gap_init rate = 0.00 (2 / 414), avg. gap size = 5.00 (10 / 2)
6193 7.68 1.52 1.16 INTRON_3 270133 270988 129193 + L1PA8A_3end LINE/L1 1 859 19 576
INTRON_3 270133 CTAATATGAGGAATTTACAAGGAACTTAAAAAAATTGATAAGAAA----- 270177
vvi v v i -----
L1PA8A_3end#L 1 CTAATATCCAGAATTTACAAGGAACTTAAACAAATTTACAAGAAAAAAAC 50
INTRON_3 270178 ---CAACTCCATCAAAAAGTAGGCAAAGGATATGAACAGACACTTTTCAA 270224
--- i i i
L1PA8A_3end#L 51 AAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAA 100
INTRON_3 270225 AAGAAGACATTTATGTGGCCAAAAAACATATGAAAAAAAGCTCAAAATCA 270274
i v v
L1PA8A_3end#L 101 AAGAAGACATTTATGCGGCCAACAAACATATGAAAAAAAGCTCAACATCA 150
INTRON_3 270275 CTGATCATTAGAGAAATACAAATCAAAACTGCAATGAGATACCATTTCAT 270324
i i ii i i
L1PA8A_3end#L 151 CTGATCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCAC 200
INTRON_3 270325 GCCAGTCAGAATGGAGATTATTAAAAAGTCAAGAA----TAGATGCTGTC 270370
v i ---- v
L1PA8A_3end#L 201 GCCAGTCAGAATGGCGATTATTAAAAAGTCAGGAAACAATAGATGCTGGC 250
INTRON_3 270371 AAGGCTGTGAAGAAGTAGGAATGCTTTTACAAACTGTTGGTGGGAATGTA 270420
i i i --
L1PA8A_3end#L 251 GAGGCTGTGGAGAAATAGGAATGCTTTTACA--CTGTTGGTGGGAATGTA 298
INTRON_3 270421 AATTAGCTCAACCATTGAGGAAGACAGTATGGTGATTCCTCAAAGATCTA 270470
i v i i
L1PA8A_3end#L 299 AATTAGTTCAACCATTGTGGAAGACAGTATGGCGATTCCTCAAGGATCTA 348
INTRON_3 270471 GAACGAGAAATACCATTTGACCCAGCAATCCCATTACTGG-TATATACCC 270519
v -
L1PA8A_3end#L 349 GAACCAGAAATACCATTTGACCCAGCAATCCCATTACTGGGTATATACCC 398
INTRON_3 270520 AAAAGAATAGAAATCATTCTACTATAAAGACACATGCACCTGTATGTTTA 270569
i v vi
L1PA8A_3end#L 399 AAAGGAATATAAATCATTCTACTATAAAGACACATGCACACGTATGTTTA 448
INTRON_3 270570 TTGCAACACTATTTACAATAGCAAAGACATGGAACCAACCCAAATGCCCA 270619
i
L1PA8A_3end#L 449 TTGCAGCACTATTTACAATAGCAAAGACATGGAACCAACCCAAATGCCCA 498
INTRON_3 270620 TCAATGACAGACTGGATAAAGAAAAAGTGGTACATAAATACCATCGAATA 270669
i v v i v
L1PA8A_3end#L 499 TCAATGATAGACTGGATAAAGAAAATGTGGTACATATACACCATGGAATA 548
INTRON_3 270670 CTATGCAGTATTCGATGCATAAAAAGGAATGAGATCATGTCCTTTTCAGG 270719
i-------- v
L1PA8A_3end#L 549 CTATGCAGC--------CATAAAAAGGAATGAGATCATGTCCTTTGCAGG 590
INTRON_3 270720 GGCATGGATGAAGCTGAAAGCCATCATACTCAGCAAACTAACACAGTAAC 270769
i i v v
L1PA8A_3end#L 591 GACATGGATGAAGCTGGAAGCCATCATCCTCAGCAAACTAACACAGGAAC 640
INTRON_3 270770 AGAAAACCAAACACCACATGTTCCCACTCATAAGTGGGAGTTGAGCAATG 270819
i i i
L1PA8A_3end#L 641 AGAAAACCAAACACCGCATGTTCTCACTCATAAGTGGGAGTTGAACAATG 690
INTRON_3 270820 AGAACACATGGACACAGGGAGGTAAACAACACACACCAGGGCCTGTTGCA 270869
i vi vi
L1PA8A_3end#L 691 AGAACACATGGACACAGAGAGGGGAACAACACACACCAGGGCCTGTTGGG 740
INTRON_3 270870 GGGTGGAGGGTGAGGGAAGGCAACTTAGAGGATGGGTCAATAGGTGCAGC 270919
i i v
L1PA8A_3end#L 741 GGGTGGGGGGTGAGGGGAGGGAACTTAGAGGATGGGTCAATAGGTGCAGC 790
INTRON_3 270920 AAACCACCATGGCACGTGTATACCTATGTAACAAACCTGCATGTTCTGCA 270969
ii i
L1PA8A_3end#L 791 AAACCACCATGGCACACGTATACCTATGTAACAAACCTGCACGTTCTGCA 840
INTRON_3 270970 TATGTATCCAGGAAATTAG 270988
i v ????
L1PA8A_3end#L 841 CATGTATCCCGKWWSTTAG 859
Matrix = 20p37g.matrix
Transitions / transversions = 1.77 (39 / 22)
Gap_init rate = 0.01 (5 / 855), avg. gap size = 4.60 (23 / 5)
784 12.61 0.00 0.00 INTRON_3 270891 271009 129172 + L1PA8_3end LINE/L1 801 919 0 577
INTRON_3 270891 AACTTAGAGGATGGGTCAATAGGTGCAGCAAACCACCATGGCACGTGTAT 270940
i v i ii i
L1PA8_3end#LI 801 AACCTAGATGACGGGTTGATAGGTGCAGCAAACCACCATGGCACATGTAT 850
INTRON_3 270941 ACCTATGTAACAAACCTGCATGTTCTGCATATGTATCCAGGAAATTAGTG 270990
i i vi v iv
L1PA8_3end#LI 851 ACCTATGTAACAAACCTGCACGTTCTGCACATGTATCCCAGAACTTAAAG 900
INTRON_3 270991 TAAAATAAAAATAAACAAA 271009
v v
L1PA8_3end#LI 901 TAAAATAAAAAAAAAAAAA 919
Matrix = 20p37g.matrix
Transitions / transversions = 1.50 (9 / 6)
Gap_init rate = 0.00 (0 / 118), avg. gap size = 0.0 (0 / 0)
+ 439 25.4 1.7 1.7 INTRON_3 271025 271140 (129041) C MER113 DNA/hAT-Charlie (402) 119 4 346
ANNOTATION EVIDENCE:
439 25.44 1.72 1.72 INTRON_3 271025 271140 129041 C MER113 DNA/hAT-Charlie 4 119 402 610
INTRON_3 271025 GAAACTAGAGTAACTTCCTC--TATGGGATTCAAGTGTTATTTAATACCA 271072
vvi i i -- v - i i
C MER113#DNA/hA 119 GAAAAGGGAATAACTTTCTCACTATGTGATTCAA-TGTTATTTAATGCCG 71
INTRON_3 271073 TATTCATGAACCATGTGAAATCAATTCATATACCACATAAAATTATACGT 271122
i i v iv i vi iii -i iviv ii
C MER113#DNA/hA 70 TGTCCATGTACCACCTAAAATCATCTCGCGTACCAC-CAGTGGTACGCGT 22
INTRON_3 271123 CCTATGCTTTGGGAAACA 271140
i ii
C MER113#DNA/hA 21 CCCACACTTTGGGAAACA 4
Matrix = 20p37g.matrix
Transitions / transversions = 2.62 (21 / 8)
Gap_init rate = 0.03 (3 / 115), avg. gap size = 1.33 (4 / 3)
+ 276 28.7 3.7 1.2 INTRON_3 271356 271436 (128745) C L2a LINE/L2 (5) 3421 3339 349
ANNOTATION EVIDENCE:
276 28.74 3.70 1.20 INTRON_3 271356 271436 128745 C L2a_3end LINE/L2 430 512 5 542
INTRON_3 271356 TTTATTCATACAAGT--TTACTGAGAAGTTACCACTTGCCAGAAACTGTT 271403
i - i -- i vivi i iv iv
C L2a_3end#LINE 512 TTCATTCA-ACAAATATTTATTGAGCGCCTACTATGTGCCAGGCACTGTT 464
INTRON_3 271404 CTAGTTACTGAGAGT-CAGTGATGAACATGACAG 271436
vii i ii - iii vi
C L2a_3end#LINE 463 CTAGGCGCTGGGGATACAGCAGTGAACAAAACAG 430
Matrix = 25p37g.matrix
Transitions / transversions = 2.83 (17 / 6)
Gap_init rate = 0.04 (3 / 80), avg. gap size = 1.33 (4 / 3)
+ 306 27.3 4.5 11.7 INTRON_3 271616 271835 (128346) + MER113A DNA/hAT-Charlie 97 302 (12) 350
ANNOTATION EVIDENCE:
306 27.27 4.55 11.65 INTRON_3 271616 271835 128346 + MER113A DNA/hAT-Charlie 97 302 12 611
INTRON_3 271616 ATTTAATTTCCTATGGATTA---AAAAGTATAACTAGCATATCAGACCTG 271662
v vv i v --- i i i i
MER113A#DNA/h 97 ATTTATTTTAATGTGTATTAGAAAAAAATATAACTAGCACATCAAACCCG 146
INTRON_3 271663 AGATTTTACAGATGTTTTTACCCTAGG-TGAAGTAAATATAAGTATTTAC 271711
v i i i v i i- - i iv vi i v
MER113A#DNA/h 147 TGATTTCACGGATATTATTGCT-TAGGATGAGGCTAAAGTAGGTATTTAA 195
INTRON_3 271712 ATT--AAAAAGTAAGGTGCTTTTTTGTAACACTTTAAGTTACTCCAAAGA 271759
i -- i vi v -----------------------
MER113A#DNA/h 196 GTTTTAAAAAGTGAGTCGATTT-----------------------AAAGA 222
INTRON_3 271760 AAAAT-TTAAGTTGACAATAGAAAAGATCCTAAGTGGATATGGCAAA--- 271805
- vi i v v i vv viii ---
MER113A#DNA/h 223 AAAATATTAAGTAAATAATAGTACAGGTGGTACACAGATATGGCAAAAAT 272
INTRON_3 271806 TATGAAGATAACAGAAAATTGACTAAATTT 271835
ii i iii vivi v i v
MER113A#DNA/h 273 CGTGAAGGTGGTATGCGAATGACTGAAGTT 302
Matrix = 20p37g.matrix
Transitions / transversions = 1.52 (32 / 21)
Gap_init rate = 0.03 (7 / 219), avg. gap size = 4.86 (34 / 7)
+ 28 64.3 0.0 0.0 INTRON_3 272643 272670 (127511) + AT_rich Low_complexity 1 28 (0) 351
ANNOTATION EVIDENCE:
28 64.29 0.00 0.00 INTRON_3 272643 272670 127511 + AT_rich Low_complexity 130 157 143 551
INTRON_3 272643 AATAAATAATTTTAAATAAAATATAATT 272670
??????????v v v vvv vv
AT_rich#Low_c 130 WWWWWWWWWWATTAAAAATAAATAATAT 157
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 8)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 31 76.3 0.0 0.0 INTRON_3 272715 272752 (127429) + AT_rich Low_complexity 1 38 (0) 352
ANNOTATION EVIDENCE:
31 76.32 0.00 0.00 INTRON_3 272715 272752 127429 + AT_rich Low_complexity 140 177 123 552
INTRON_3 272715 ATTAAATTATAAATAATATTAAATACTATTAAATTATT 272752
vvvv vv vvvvvvvv???????????????
AT_rich#Low_c 140 ATTAAAAATAAATAATATAATTTWWWWWWWWWWWWWWW 177
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 14)
Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0)
+ 1779 16.9 5.9 8.1 INTRON_3 273059 273486 (126695) C MSTB LTR/ERVL-MaLR (16) 410 1 353
ANNOTATION EVIDENCE:
423 18.39 2.27 1.12 INTRON_3 273059 273146 127035 C THE1D LTR/ERVL-MaLR 285 373 8 612
INTRON_3 273059 TCCACTATCTGCATTGCCATAAAGGAATACTCGAGACTGGGTAATTTACA 273108
i v -i i i i ii i
C THE1D#LTR/ERV 373 TCCATTTTC-ACACTGCTATAAAGAAATACCTGAGACTGGGTAATTTATA 325
INTRON_3 273109 AAGGAAAGAGTTTTA-TTGGCTCTTGGTTCTGCA-GGCTG 273146
v - i vii ii -
C THE1D#LTR/ERV 324 AAGGAAAGAGGTTTAATTGACTCACAGTTCCACATGGCTG 285
Matrix = 20p37g.matrix
Transitions / transversions = 4.33 (13 / 3)
Gap_init rate = 0.03 (3 / 87), avg. gap size = 1.00 (3 / 3)
1779 16.91 5.97 8.29 INTRON_3 273068 273486 126695 C MSTB LTR/ERVL-MaLR 1 410 16 613
INTRON_3 273068 TGCATTGCCATAAAGGAATACTCGAGACTGGGTAATTTACAAAGGAAAGA 273117
i i i ii i i i
C MSTB#LTR/ERVL 410 TGCGTTGCTATAAAGAAATACCTGAGGCTGGGTAATTTATAAAGAAAAGA 361
INTRON_3 273118 GTTTTA-TTGGCTCTTGGTTCTGCAGGCTGTACAAGAAGCATAGTACCAG 273166
v - vi i i ii i
C MSTB#LTR/ERVL 360 GGTTTAATTGGCTCACGGTTCTGCAGGCTGTACAGGAAGCATGGCGCCGG 311
INTRON_3 273167 CATCTGCT-----TCTGGTGAGGGCTTCAGGAAGCTTACAATCATGGCAG 273211
----- - i ?
C MSTB#LTR/ERVL 310 CATCTGCTCGGCTTCTGGTGAGG-CCTCAGGAAGCTTNCAATCATGGCAG 262
INTRON_3 273212 AAGG-GAAAGGG-AGCCAGTGCGTCCCGTGGTGAGAGAGGG--CAAGAGA 273257
- i - vi ii v i i v --
C MSTB#LTR/ERVL 261 AAGGCGAAGGGGGAGCAGGCACGTCACATGGCGAGAGCGGGAGCAAGAGA 212
INTRON_3 273258 GAGAGGAGGAAATT-CCAGCCTCTTTTTTTTTTTTTAATAATTTAAAGAT 273306
i i iv - ?v v-------- i ii---
C MSTB#LTR/ERVL 211 GAGAGGGGGGAGGTGCCANACTCTTTTA--------AACAACC---AGAT 173
INTRON_3 273307 ATCACTGTGAACT--CAGAGTGAGCACTCACTCATTACTGCAAGGATAGC 273354
v i - -- i v i iivii i
C MSTB#LTR/ERVL 172 CTCGC-GTGAACTAACAGAGCGAGAACTCACTCATCACCAAGGGGATGGC 124
INTRON_3 273355 ATCAAGCCATTCATGAGGGATCTGCCTTCATGAGGGATCTGCCTCCATGA 273404
ii i i-----------------
C MSTB#LTR/ERVL 123 GCCAAGCCATTCATGAGGGATCCGCCC-----------------CCATGA 91
INTRON_3 273405 TTCAACCACTTGTCCTACCAAGTCCTAGCTCCAACATTGGGAAT------ 273448
i v i -- i i i i v i i ------
C MSTB#LTR/ERVL 90 TCCAAACACCT--CCCACCAGGCCCCACCTCCAACACTGGGGATCACATT 43
INTRON_3 273449 ------TGTGATTTGGAGGGGGCACACATCCAAACTCAGTATCA 273486
------ v i v - -
C MSTB#LTR/ERVL 42 TCAACATGAGATTTGGAGGGGACAAACATCCAAAC-CA-TATCA 1
Matrix = 20p37g.matrix
Transitions / transversions = 3.20 (48 / 15)
Gap_init rate = 0.04 (16 / 418), avg. gap size = 3.69 (59 / 16)
+ 348 27.3 14.1 0.0 INTRON_3 273492 273612 (126569) C MIRb SINE/MIR (81) 187 50 354
ANNOTATION EVIDENCE:
348 27.27 14.05 0.00 INTRON_3 273492 273612 126569 C MIRb SINE/MIR 50 187 81 543
INTRON_3 273492 TCATGACAACAATTTTTCAAAGTAGGTAGAATTATTCTCAT----CATAT 273537
v v iii v i i vv i i ---- v
C MIRb#SINE/MIR 187 TCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGAT 138
INTRON_3 273538 G--GAAATGGAAGT---GAGA-------TCACTTTCCTAAGGTCACTTAA 273575
-- iv i i--- ------- v v i vi i
C MIRb#SINE/MIR 137 GAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAG 88
INTRON_3 273576 CT-GTAATTGTCCGAGCCAGGGTATAAACTTAGATCTG 273612
- v v v i vii ii i
C MIRb#SINE/MIR 87 CTAGTAAGTGGCAGAGCCAGGATTCGAACCCAGGTCTG 50
Matrix = 25p37g.matrix
Transitions / transversions = 1.36 (19 / 14)
Gap_init rate = 0.04 (5 / 120), avg. gap size = 3.40 (17 / 5)
+ 270 31.3 0.0 5.0 INTRON_3 274417 274500 (125681) C MIR3 SINE/MIR (78) 130 51 355
ANNOTATION EVIDENCE:
270 31.33 0.00 5.00 INTRON_3 274417 274500 125681 C MIR3 SINE/MIR 51 130 78 544
INTRON_3 274417 AGGAAACTATGGCTGAGAGGAAAAGAGAAATTACTTGCCCATGATCACAC 274466
iv iv --- i v i v v i
C MIR3#SINE/MIR 130 AGGAAACTGAGGCCCAGAG---AGGTGAAGTGACTTGCCCAAGGTCACAC 84
INTRON_3 274467 AATTTATTTAGTGTCCAAGTCAGGATCAAAATTC 274500
ii?- v v vi iii ii i ii
C MIR3#SINE/MIR 83 AGCK-AGTTAGTGGCAGAGCTGGGACTAGAACCC 51
Matrix = 25p37g.matrix
Transitions / transversions = 2.00 (16 / 8)
Gap_init rate = 0.02 (2 / 83), avg. gap size = 2.00 (4 / 2)
+ 442 31.2 16.4 3.6 INTRON_3 274507 274895 (125286) C MARNA DNA/TcMar-Mariner (105) 481 43 356
ANNOTATION EVIDENCE:
259 26.82 16.51 0.79 INTRON_3 274507 274615 125566 C MARNA DNA/TcMar-Mariner 356 481 105 614
INTRON_3 274507 CTTTAGGAAATGGTATGTTTATTCCAA--AT-TTGCCAC---------CA 274544
i i iii?i iii -- - i---------
C MARNA#DNA/TcM 481 CCTTGGGAGGCNATACACTTATTCCAACGATGTTGCCATTGCTCAAAACA 432
INTRON_3 274545 TT---GG---TTCTCCCTGGGCACTACTTTCTGAGTCTGTGGCATATTAT 274588
--- --- ii i- i i i v i i i v
C MARNA#DNA/TcM 431 TTTCTGGAACTTCTCTTTGGA-ATTGCCTTCAGAGCCTGCGGCACATTCT 383
INTRON_3 274589 TGTAAATACTCTCACTGGTGGTAAGTC 274615
v i ii v i i
C MARNA#DNA/TcM 382 TTTGAATATCCTCAATGGTGGCAAATC 356
Matrix = 20p37g.matrix
Transitions / transversions = 6.00 (24 / 4)
Gap_init rate = 0.06 (6 / 108), avg. gap size = 3.17 (19 / 6)
442 32.88 2.46 4.68 INTRON_3 274612 274895 125286 C MARNA DNA/TcMar-Mariner 43 320 266 615
INTRON_3 274612 AGTCAGAAGGCAATCTGGAGCCAAAT-TAGAGAAGAAAGTCTGTGACGGA 274660
i i v v -i i - i v v i vv ivi
C MARNA#DNA/TcM 320 AGCCAAAAGTCATTC-AGAGCCAAGTCTGGTGAATAAGGTGGGTGATCAA 272
INTRON_3 274661 ACTGTATAATCACATTTGGAGTAAAAACCAATTCTTAATTACAATAGAAT 274710
i vi vvi v?i v vii vviv i i i viv
C MARNA#DNA/TcM 271 GCTGGGTAATACTATTTTNGGTCAAAAATGAGGTGTGACTATAAAGTAAT 222
INTRON_3 274711 GAAATAGACTTTGTTCATATGAGGCCATAACATAAA--GG-TCTGGAAGC 274757
i iv i v --- v i---- -- - i i
C MARNA#DNA/TcM 221 GAGACTGATTTTCTT---ATGTGGCT----CATAAACTGGCTCTGAAGGC 179
INTRON_3 274758 TAATTCCCAAAAACCAAAGG-ACAAAAATGTTTAGAGTGATAACAACATT 274806
- v i --i? v-v i v ii? ii i i
C MARNA#DNA/TcM 178 -AATTCCAAAAGA--GNAGTTCCAGAAATGTTTTGAGCANTGGCAGCATC 132
INTRON_3 274807 GTTGTAGTAAGTGTCTGACTTCATAAGA--ACTACTTTAAAGGGATTAAA 274854
v iii viii i vi i i-- i i--i v
C MARNA#DNA/TcM 131 GTTGGAACGAGTGTACAGCCTCCCAGGGTGACTACTTTGAAGGA--CAAC 84
INTRON_3 274855 ACTCATTTGGACATTAGGGCTCTGATATGCTTGTTTTAAAA 274895
i vvii i i i i v
C MARNA#DNA/TcM 83 ACTCATTTGGACGTATAAGTTCTGGTGTGTTTGTTTAAAAA 43
Matrix = 20p37g.matrix
Transitions / transversions = 1.69 (54 / 32)
Gap_init rate = 0.04 (11 / 283), avg. gap size = 1.82 (20 / 11)
464 29.06 1.32 2.00 INTRON_3 274745 274895 125286 + MARNA DNA/TcMar-Mariner 395 544 42 616
INTRON_3 274745 AAGGTCTGGAAGCTAATTCCCAAAAACCAAAGGACAAAAATGTTTAGAGT 274794
i v i i - v i i-- ivvv i v i
MARNA#DNA/TcM 395 AGGCTCTGAAGGC-AATTCCAAAGAG--AAGTTCCAGAAATGTTTTGAGC 441
INTRON_3 274795 GATAACAACATTGTTGTAGTAAGTGTCTGACTTCATAAGA--ACTACTTT 274842
i ii i v i v ?i i vi i--
MARNA#DNA/TcM 442 AATGGCAACATCGTTGGAATAAGTGTATNGCCTCCCAAGGTGACTACTTT 491
INTRON_3 274843 AAAGGGATTAAAACTCATTTGGACATTAGGGCTCTGATATGCTTGTTTTA 274892
i ivi v ii vvii i i i ?v
MARNA#DNA/TcM 492 GAAGGGGACAACACTCATTTGGATGTATAAGTTCTGGTATGTTTGTTWAA 541
INTRON_3 274893 AAA 274895
MARNA#DNA/TcM 542 AAA 544
Matrix = 20p37g.matrix
Transitions / transversions = 1.93 (27 / 14)
Gap_init rate = 0.02 (3 / 150), avg. gap size = 1.67 (5 / 3)
+ 857 26.6 7.7 6.4 INTRON_3 274906 275571 (124610) + L1M5 LINE/L1 2401 3074 (3072) 357
ANNOTATION EVIDENCE:
857 26.62 7.66 6.38 INTRON_3 274906 275571 124610 + L1M5_orf2 LINE/L1 292 965 2329 578
INTRON_3 274906 ATAATGAAAAGAGTTTCAAGTCACCAGAAA-----AAGTATTATAA-TTT 274949
v i vv vi i ----- ?v v - ?
L1M5_orf2#LIN 292 ATAATGATAAAAGGGTCAATCCACCAGGAAGACATAANAATTCTAAATNT 341
INTRON_3 274950 TTATTTAACTAAAAACATAGCTTCAAAATATATAAAG--AAAATCATGAC 274997
v vi v v ? ? i i -- --
L1M5_orf2#LIN 342 GTATGCACCTAATAANANAGCCTCAAAATATGTAAAGCAAAAAT--TGAC 389
INTRON_3 274998 A-AACTACAAGGAGAAACAAGCAAACATATAATCATAGTGGTATACTTTA 275046
- ? v i ii ivi i v v i
L1M5_orf2#LIN 390 AGAANTAAAAGGAGAAATAGACAAATCCACAATCATAGTGGGAGATTTTA 439
INTRON_3 275047 AGATACTT-TCTTAAAAACTGACCAAACAAGCAGACAAAAAAAAATCACT 275095
v i? i - i iv ivi --- v
L1M5_orf2#LIN 440 ACACNCCTCTCTCAGTAACTGATAGAACAAGCAGACAAAAAA---TCAGT 486
INTRON_3 275096 AAGGATATAGAA-AGTTGAATCTCAAAAT-GGCAAACACATTG-TTT--T 275140
i - v ivv ?? -ii --- -ii --
L1M5_orf2#LIN 487 AAGAATATAGAAGATTTGAACAACANNATTAACAAAC---TTGACCTAAT 533
INTRON_3 275141 TGAAATAAATAGATGACTCGAAAACACACACGCGTGCGCACACATACACA 275190
? v ?v vv -----i ? -i ivvi v - ?
L1M5_orf2#LIN 534 NGACATNTATAGAACACT-----GCACNCA-ACAACTGCAGA-ATNCACA 576
INTRON_3 275191 TACT---CACATGCACACATACGCACCACACACACACAGAGACATGCACA 275237
v --- vi iiv -------- ivi vi i ?vi -
L1M5_orf2#LIN 577 TTCTTTTCAAGTGCACATGGA--------ACATTTACCAAAACNGAC-CA 617
INTRON_3 275238 CATGCAATTGGGCACCACAAAAAGCAAGTCTAAATACATTCTAGAGGACT 275287
i ?--- ---- v v i v ii i i
L1M5_orf2#LIN 618 TATN---TTGGGC----CATAAAGCAAGTCTCAACAAATTTCAAAGGATT 660
INTRON_3 275288 GAAATAATTTAGAATGTAGTTTCTGACCACAAAATAATT---TTA----- 275329
v vi i i iv i iviv ---i -----
L1M5_orf2#LIN 661 GAAATCATACAGAGTATGTTCTCTGACCACAGTGGAATTAAGCTAGAAAT 710
INTRON_3 275330 ---------AAAGATTTTAACTAGAAAAATCCACA----TTTGGAAATTC 275366
--------- --- - v ---- v
L1M5_orf2#LIN 711 CAATAACAAAAAGAT---AACTAGAAAA-TCCCCAAATGTTTGGAAATTA 756
INTRON_3 275367 A--AAAACTCCTCTAG-TAAAC-ATTAGTCAAAGAGAGAAGTATTAATCA 275412
-- v iv i i- v - vi - -- i -iv
L1M5_orf2#LIN 757 AGCAATATACTTCTAAATAACCCATGGGTCAAAGA-AGAA--ATCA-CAA 802
INTRON_3 275413 TGAAAATTAGGACAT-TTTTGAACT---TTGTAATAAAAATACAACAATC 275458
i i v - --- vi i i vvi
L1M5_orf2#LIN 803 TGGAAATTAGAAAATATTTTGAACTGAATGATAATGAAAATACGACATAT 852
INTRON_3 275459 AAAATTTCTATGATACTGCTAAGGTA--GTACT--TTAGAGAGAGAATTA 275504
v vi - i iv - -- v -- i v -- i i v
L1M5_orf2#LIN 853 CAAAACT-TGTGGGA-TGC--AGCTAAAGCAGTGCTTAGAGGGAAATTTA 898
INTRON_3 275505 TCATGCTAAATGTATATATTAGAAAATCAAGAAGACTGGAAGTTAATGTG 275554
viivi i vv ii i ?i i i vv
L1M5_orf2#LIN 899 TAGCCTTAAATGCATATATTAGAAAAGAAGAAAGGCTNAAAATCAATGAT 948
INTRON_3 275555 CTGAGCATTCATATTAA 275571
? i ? i ?v i
L1M5_orf2#LIN 949 NTAAGCNTCCANCTCAA 965
Matrix = 20p37g.matrix
Transitions / transversions = 1.24 (82 / 66)
Gap_init rate = 0.06 (38 / 665), avg. gap size = 2.47 (94 / 38)
+ 6880 9.4 1.5 2.0 INTRON_3 275585 276111 (124070) C L1MA2 LINE/L1 (0) 6304 5777 358
ANNOTATION EVIDENCE:
6880 9.43 1.52 2.01 INTRON_3 275585 276111 124070 C L1MA2_3end LINE/L1 524 1051 0 579
INTRON_3 275585 TTTTAACTTTTGTAGATACATAGTAGGTGTACATATTTATGGGGTACATG 275634
i i i i
C L1MA2_3end#LI 1051 TTTTAATTTTTGTGGGTACATAGTAGGTGTATATATTTATGGGGTACATG 1002
INTRON_3 275635 AGATATTTTGGTACAGGCATGCAATCCGTAATAATCACATCTTGGAAAAT 275684
i i vi v
C L1MA2_3end#LI 1001 AGATGTTTTGATACAGGCATGCAATGTGTAATAATCACATCATGGAAAAT 952
INTRON_3 275685 TGGGTATCGATCCCCTCAAGCATTTACCGTTTGTGTTACAAGCATTCCAA 275734
v v i v i v
C L1MA2_3end#LI 951 GGGGTATCCATCCCCTCAAGCATTTATCCTTTGTGTTACAAACAATCCAA 902
INTRON_3 275735 TTATATTCTT--AGTTATTTTTAAATGTATGATTTAATTACTATTGACTA 275782
i -- ? ii v i
C L1MA2_3end#LI 901 TTATACTCTTTTAGTTATTTTSAAATGTACAATTAAATTATTATTGACTA 852
INTRON_3 275783 CAG-AACCCTGTTGTGCTATCAAATACTAGGGTTTGTTCATTCTATTT-- 275829
i -v vi i v i --
C L1MA2_3end#LI 851 TAGTCACCCTGTTGTGCTATCAAATACTAGGTCTTATTCATTCTTTCTAA 802
INTRON_3 275830 -TTTTTATTTGGACCCATTAACCATCCCCACCTCCCCGCTGCCCACACCA 275878
- v v v i ------ v v
C L1MA2_3end#LI 801 CTATTTTTTTGTACCCATTAACCATCCCCACCTCCCCAC------CAACC 758
INTRON_3 275879 CCTCCCTACTCTTCTCAGTCTCTGGCAATTATCCTTCTATTCTCTATCTC 275928
i v i i i i ii i
C L1MA2_3end#LI 757 CCCCACTACCCTTCCCAGCCTCTGGTAACCATCCTTCTACTCTCTATCTC 708
INTRON_3 275929 CATGAATTTAATTGTTTTGATTTTTAGATCACACAAATAAGTGAGAATAT 275978
i i v i
C L1MA2_3end#LI 707 CATGAGTTCAATTGTTTTGATTTTTAGATCCCACAAATAAGTGAGAACAT 658
INTRON_3 275979 GCGATGTTTGTCTTTCTGTGTCTGGCTTATTTCATTTAACATAATAACCT 276028
i i i
C L1MA2_3end#LI 657 GCGATGTTTGTCTTTCTGTGCCTGGCTTATTTCACTTAACATAATGACCT 608
INTRON_3 276029 CCAGTTTCATCCATGTTGTTGCAAATGACAGAATCTCATTCTTTTT-ATA 276077
i i - i
C L1MA2_3end#LI 607 CCAGTTCCATCCATGTTGTTGCAAATGACAGGATCTCATTCTTTTTTATG 558
INTRON_3 276078 GCTGAATAGTACTTCATTGTGTATAAGTACCACA 276111
i v
C L1MA2_3end#LI 557 GCTGAATAGTACTCCATTGTGTATATGTACCACA 524
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (36 / 18)
Gap_init rate = 0.01 (5 / 526), avg. gap size = 2.60 (13 / 5)
+ 432 0.0 0.0 0.0 INTRON_3 276112 276159 (124022) + (TTTA)n Simple_repeat 2 49 (0) 359
ANNOTATION EVIDENCE:
432 0.00 0.00 0.00 INTRON_3 276112 276159 124022 C (TAAA)n Simple_repeat 130 177 3 592
INTRON_3 276112 ATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTT 276159
C (TAAA)n#Simpl 177 ATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTT 130
Matrix = Unknown
Transitions / transversions = 0.0 (0 / 0)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0)
+ 2201 11.4 1.3 0.7 INTRON_3 276162 276460 (123721) C AluSx1 SINE/Alu (11) 301 1 360
ANNOTATION EVIDENCE:
2076 11.79 1.34 0.66 INTRON_3 276162 276460 123721 C AluSx SINE/Alu 1 301 11 491
INTRON_3 276162 TTTCTTTCTTTTTTTTGTGGAGATGGAGTCTC----TGTCACACAGGCTG 276207
i i v v i ---- i v
C AluSx#SINE/Al 301 TTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTG 252
INTRON_3 276208 GAGTGCAGTGGCACGATCTCGGCTCACTGCAACCTCCACCTCCTGGGTTC 276257
i i i
C AluSx#SINE/Al 251 GAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTC 202
INTRON_3 276258 AAGTGATTCTCCCGCCTCACCCTCCAGAGTACCTGGGATTACAGGCATCT 276307
i i v v v iivi
C AluSx#SINE/Al 201 AAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGC 152
INTRON_3 276308 GCCACCACCCCTGGCTAATTTTTTTGTATTTTTAGTAGAGACAGGGTTTC 276357
v i -- i
C AluSx#SINE/Al 151 GCCACCACGCCCGGCTAATTTTT--GTATTTTTAGTAGAGACGGGGTTTC 104
INTRON_3 276358 GCCATGTTGGCCAGGCTGGTTTTGAACTCCTGACCTCAGGTAGTTGGCCT 276407
i i i ii iv i
C AluSx#SINE/Al 103 ACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCC 54
INTRON_3 276408 GCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCACCCA 276457
i i i i i
C AluSx#SINE/Al 53 GCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCG 4
INTRON_3 276458 GCC 276460
C AluSx#SINE/Al 3 GCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 2.89 (26 / 9)
Gap_init rate = 0.01 (2 / 298), avg. gap size = 3.00 (6 / 2)
+ 6880 7.9 1.7 2.6 INTRON_3 276461 277021 (123160) C L1MA2 LINE/L1 (528) 5776 5216 358
ANNOTATION EVIDENCE:
6880 9.43 1.52 2.01 INTRON_3 276461 276979 123202 C L1MA2_3end LINE/L1 7 523 528 580
INTRON_3 276461 CACAGTTTCTTTATCCATTCGTCTGTTGA---ACACTTAGGTTGCTTCCA 276507
----v i ---
C L1MA2_3end#LI 523 ----TTTTCTTTATCCATTCATCTGTTGATGGACACTTAGGTTGCTTCCA 478
INTRON_3 276508 AATCTTGGTTATTGTCAATAGTGCTGCAACAAAAATGGGAGTGCAGATAA 276557
i v i v v
C L1MA2_3end#LI 477 AATCTTGGCTATTGTGAACAGTGCTGCAACAAACATGGGAGTGCAGATAT 428
INTRON_3 276558 CTCTTTGATATACTAATTTTCTTTCTTTGGGGTGTATATCCAGCAGTGGG 276607
i i i v i i
C L1MA2_3end#LI 427 CTCTTCGATATACTGATTTCCTTTCTTTTGGGTATATACCCAGCAGTGGG 378
INTRON_3 276608 ATTGCTAGATCATATGGTAGC-CTATTTTTAGTTTTTTGAGAAAC-TCCA 276655
i - i -
C L1MA2_3end#LI 377 ATTGCTGGATCATATGGTAGCTCTATTTTTAGTTTTTTGAGGAACCTCCA 328
INTRON_3 276656 AACTGTTCTCTGCAGTGGTTGTACTAACTTACATTTCCACCAATAGTGTA 276705
iii i i i
C L1MA2_3end#LI 327 AACTGTTCTCCATAGTGGTTGTACTAATTTACATTCCCACCAACAGTGTA 278
INTRON_3 276706 CAAG--TTCCCTTTTCTCTACATGCTCGTCAGCATTTGTTATTGCCTGAT 276753
i -- i v i vi
C L1MA2_3end#LI 277 CGAGGGTTCCCTTTTCTCCACATCCTCGCCAGCATTTGTTATTGCCTGTC 228
INTRON_3 276754 TTTTGTATAAAAGCCATTTTGACTGGAATGAGATGATATCTCATTGTGGT 276803
v v i ii i
C L1MA2_3end#LI 227 TTTTGGATATAAGCCATTTTAACTGGGGTGAGATGATATCTCATTGTAGT 178
INTRON_3 276804 TTTGATTTCCATTTCTCTGATGATCAATGTTGTTGAGCACTTTTTCATAT 276853
v i v i
C L1MA2_3end#LI 177 TTTGATTTGCATTTCTCTGATGATCAGTGATGTTGAGCACCTTTTCATAT 128
INTRON_3 276854 GCTT-TTTGCCATTTGTATGACTTCTTTTCAGAAATGTCTATTCAAATCT 276902
i - v v
C L1MA2_3end#LI 127 GCCTGTTTGCCATTTGTATGTCTTCTTTTGAGAAATGTCTATTCAAATCT 78
INTRON_3 276903 TTTGCCCATTTTT-AATTGGATTATTAGATTTTTTTTTTTTTCCTATAGA 276951
- i -------
C L1MA2_3end#LI 77 TTTGCCCATTTTTTAATCGGATTATTAGATTTTTT-------CCTATAGA 35
INTRON_3 276952 GTTGTTTGAGTTCCTTATATATTCTGGT 276979
i
C L1MA2_3end#LI 34 GTTGTTTGAGCTCCTTATATATTCTGGT 7
Matrix = 20p37g.matrix
Transitions / transversions = 2.23 (29 / 13)
Gap_init rate = 0.02 (8 / 518), avg. gap size = 2.50 (20 / 8)
1215 4.89 2.09 3.72 INTRON_3 276831 277021 123160 C L1M1_orf2 LINE/L1 3107 3294 0 581
INTRON_3 276831 TGTTGTTGAGCACTTTTTCATATGCTT-TTTGCCATTTGTATGACTTCTT 276879
v i i - v
C L1M1_orf2#LIN 3294 TGATGTTGAGCACCTTTTCATATGCCTGTTTGCCATTTGTATGTCTTCTT 3245
INTRON_3 276880 TTCAGAAATGTCTATTCAAATCTTTTGCCCATTTTT-AATTGGATTATTA 276928
v -i i
C L1M1_orf2#LIN 3244 TTGAGAAATGTCTATTCAAATCTTTTGCCCATTTTTTGATCGGATTATTA 3195
INTRON_3 276929 GATTTTTTTTTTTTTCCTATAGAGTTGTTTGAGTTCCTTATATATTCTGG 276978
------- i
C L1M1_orf2#LIN 3194 GATTTTTT-------CCTATAGAGTTGTTTGAGCTCCTTATATATTCTGG 3152
INTRON_3 276979 T-AT-AATCCCTTGTCAGATGGGTAGTTTGCAAGTATTTTCTCCC 277021
- - i
C L1M1_orf2#LIN 3151 TTATTAATCCCTTGTCAGATGGGTAGTTTGCAAATATTTTCTCCC 3107
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (6 / 3)
Gap_init rate = 0.03 (5 / 190), avg. gap size = 2.20 (11 / 5)
+ 588 31.8 1.1 0.0 INTRON_3 277059 277237 (122944) C L1MEc LINE/L1 (6071) 329 149 361
ANNOTATION EVIDENCE:
588 31.84 1.12 0.00 INTRON_3 277059 277237 122944 C L1MEc_5end LINE/L1 149 329 2198 582
INTRON_3 277059 CTTTGGTCTCCCCAGACTGTTATCTCTATCTCCTCAAATCAAGGAGATTA 277108
i ii v i v i v i vi i
C L1MEc_5end#LI 329 CCTTGGTCTCCCTGGACTCTCAGCTCTGTCTCCTCAACTCAGGGAGTCTG 280
INTRON_3 277109 CTAAGGTCC-TTTCACTTCATCGTCTGTGTGTCATGACCTATAAACTCTG 277157
ii v i-ii viv vi v ?v iiiiiiii iv v
C L1MEc_5end#LI 279 CTGGGCTCTGCCTGGGTTCCCCCTCYCTGCACTGCAGCCTGGAAACTCTC 230
INTRON_3 277158 TTAATGCAGAAAGCTGAAA-AATTACAGTGCTCACCTTATTTGGTTGTCA 277206
i v v iii- i i v i v vi
C L1MEc_5end#LI 229 TCAAGGCAGTAAGCTGGGGCAATCATAGGGCTCACCTCATTTGTTTCCCA 180
INTRON_3 277207 TTTCTCTGTGTTCACTGTCCTTTATTGTCTG 277237
i v v v ii i
C L1MEc_5end#LI 179 TCTCTCAGGGATCACTGTCCTTCGTTGCCTG 149
Matrix = 20p37g.matrix
Transitions / transversions = 1.80 (36 / 20)
Gap_init rate = 0.01 (2 / 178), avg. gap size = 1.00 (2 / 2)
+ 2001 19.9 5.6 1.0 INTRON_3 277272 278103 (122078) C L1MEc LINE/L1 (4549) 1866 968 362
ANNOTATION EVIDENCE:
1944 26.39 3.04 3.44 INTRON_3 277272 278060 122121 C L1MEf_5end LINE/L1 866 1651 566 583
INTRON_3 277272 TAGTTACCATTTCCAGTACTCTATATTATTTCATGTTGATACAGATTTCT 277321
v ii? i vi? v? v vv v ii i
C L1MEf_5end#LI 1651 TATTTACCATTTCTGNTGCTCTTCNTTCNTTCCTGAAGATCCAAGTTTCC 1602
INTRON_3 277322 ATTTGTTATTATTTTCATTCTGCCTTAAGGACAATCTTTAACATTTCTTA 277371
? i v i i v v v i vvi i ?
C L1MEf_5end#LI 1601 NTCTGGTATCATTTCCCTTCAGCCTGAAGAACTTCCTTTAGCATTTCTTN 1552
INTRON_3 277372 TAGTTCAGGTATTCTGGTGATGAATTATTT--GTCCTTCTGTCATTTTGA 277419
?v v v ii i v i -- i- ?v i i -
C L1MEf_5end#LI 1551 TAGNGCAGGTCTGCTGGCAACGAATTCTCTTAGTT-TTCNTTTATCT-GA 1504
INTRON_3 277420 AAATGTTTTTATTTCATCTTCATTTTTTGAAAGATATTTTTACTGGCTAT 277469
i i i - i ii v
C L1MEf_5end#LI 1503 AAATGTCTTTATTTCACCTTCATTTCT-GAAGGATATTTTCGCTGGATAT 1455
INTRON_3 277470 AGCATTCTAGGTTGACAGGTTTTTTCTTGTTGTTGTTTGTTTTATTCTTT 277519
v i v ------------ iviiv
C L1MEf_5end#LI 1454 AGAATTCTGGGTTGACAGTTTTTTTCTT------------TCAGCACTTT 1417
INTRON_3 277520 AAGTACTTTAAATAT-GTTGCTCCTGTTGTCTCACTTGCATTGTTTCCAG 277568
------- i i - - iv iv vi i v ? iii
C L1MEf_5end#LI 1416 AA-------AGATGTTGTT-CCACTGTCTTCTGGCCTCCATNGTTTCTGA 1375
INTRON_3 277569 TGAGGAATCTGAAGTCTTACTTATCTTTGCTCCTCTGTAGGTAATGTGTT 277618
i i v? v v vv v i i v i
C L1MEf_5end#LI 1374 TGAGAAATCCGCNGTCATTCGAATCGTTGTTCCCCTGTATGTAATGTGTC 1325
INTRON_3 277619 TTTCTTCTCTGTCTACATTTAATATTTTCTGTTTATTATTGGTTTTGAGC 277668
v i v i v i v i v iv v
C L1MEf_5end#LI 1324 GTTTTTCTCTGGCTGCTTTCAAGATTTTTTCTTTATCTTTGGTTTTCAGC 1275
INTRON_3 277669 AATTTAGTT--------CCTTGGTATAGTTTTCTTTATGTTTCTTATGCT 277710
i ii --------i v ii i i? v iv i
C L1MEf_5end#LI 1274 AGTTTGATTATGATGTGTCTAGGCGTGGTTTTCTTTGNGTTTATCCTGTT 1225
INTRON_3 277711 TAGGATGCTTTGAGCTCTTTGAATTTGTGT-TTTATGGTTTTCATGAAAT 277759
i i v vi ii i iv- vi iv
C L1MEf_5end#LI 1224 TGGGGTTCGCTGAGCTTCTTGAATCTGTAAATTTATGTCTTTCACCAAAT 1175
INTRON_3 277760 TTGGAAAGTTGTCTGCCATAATTTCTTCAAATATATTTTTCTG-ACC--- 277805
i i v v v - -? ---
C L1MEf_5end#LI 1174 TTGGGAAATTTTCAGCCATTATTTCTTCAAATAT-TTTTTCTGCNCCANT 1126
INTRON_3 277806 ---TTTCTTCTCTCTGTTCTAAGACACCAATTATCTCTATGTTAGGCCAC 277852
--- i i- ii v ? iviv? i vi
C L1MEf_5end#LI 1125 CTCTTTCTCCTCTCC-TTCTGGGACTCCAATNACACGNATGTTAGACCTT 1077
INTRON_3 277853 TTGAAGTTGTCCCAGAGCTGACTGATGCTCTTTTCATTTTTTTGGATTCT 277902
vi v v vv v v vv v i
C L1MEf_5end#LI 1076 TTGATATTGTCCCACAGGTCCCTGAGGCTCTGTTCATTTTTTTTCAATTT 1027
INTRON_3 277903 TCTTTCTCAGTGGATTTCATTTTGGATTGTTTCTAAT-ATCACTCCTTCA 277951
i vv vvi vv vi v - vv -
C L1MEf_5end#LI 1026 TTTTTCTCTCTGTTCTTCAGATTGGATAATTTCTATTGATCTATC-TTCA 978
INTRON_3 277952 AGTTCACTAA-TGTTTTCTCTTGCATTGTCTAATCTACTGTTAAACCTTT 278000
i - v i vv i- i v i i i i iv
C L1MEf_5end#LI 977 AGTTCACTGACTCTTTCCTCTGTCATC-TCCATTCTGCTATTGAGCCCAT 929
INTRON_3 278001 ---GTGTATTTTTTGTCTCACACATTGTAGATTTCATCTCTAGAAATTCA 278047
--- v ?i i v i vv vi i v v
C L1MEf_5end#LI 928 CCAGTGAATTTTTNATTTCAGATATTGTATTTTTCAGTTCTAAAATTTCC 879
INTRON_3 278048 ATTTGGATATTTT 278060
v v
C L1MEf_5end#LI 878 ATTTGGTTTTTTT 866
Matrix = 20p37g.matrix
Transitions / transversions = 1.08 (97 / 90)
Gap_init rate = 0.02 (19 / 788), avg. gap size = 2.68 (51 / 19)
2001 18.03 5.52 0.19 INTRON_3 277509 277997 122184 C L1MEc_5end LINE/L1 1085 1599 928 584
INTRON_3 277509 TTTTATTCTTTAAGTACTTTAAATATGTTGCTCC--TGTTGTCTCACTTG 277556
v v v -- iv i
C L1MEc_5end#LI 1599 TTTTTTTCTTTCAGTACTTTAAAGATGTTGCTCCACTGTCTTCTCGCTTG 1550
INTRON_3 277557 CATTGTTTCCAGTGAGGAATCTGAAGTCTTACTTATCTTTGCTCCTCTGT 277606
i?i i i vv v v i
C L1MEc_5end#LI 1549 CATTGTTTCTRATAAGAAATCTGCTGTCATCCTTATCTTTGTTCCTCTGT 1500
INTRON_3 277607 AGGTAATGTGT-TTTTCTTCTCTGTCTACATTTAATATTTT-CTGTTTAT 277654
v - i v i v v - v
C L1MEc_5end#LI 1499 ATGTAATGTGTCTTTTTTTCTCTGGCTGCTTTTAAGATTTTTCTCTTTAT 1450
INTRON_3 277655 TATTGGTTTTGAGCAATTTAGTT--------CCTTGGTATAGTTTTCTTT 277696
i i ii -------- i i
C L1MEc_5end#LI 1449 CACTGGTTTTGAGCAATTTGATTATGATGTGCCTTGGTGTAGTTTTCTTC 1400
INTRON_3 277697 ATGTTTCTTATGCTTAGGATGCTTTGAGCTCTTTGAATTTGTGT-TTTAT 277745
i i i viv ii i i v-
C L1MEc_5end#LI 1399 ATGTTTCTTGTGCTTGGGGTTTGTTGAGCTTCTTGGATCTGTGGGTTTAT 1350
INTRON_3 277746 GGTTTTCAT-GAAATTTGGAAAGTTGTCTGCCATAATTTCTTCAAATATA 277794
i -i i v iv v -
C L1MEc_5end#LI 1349 AGTTTTCATCAAAATTTGGAAAATTTTTAGCCATTATTTCTTCAAATAT- 1301
INTRON_3 277795 TTTTTCTGACCTT-TCTTCTCTC-TGTTCT---AAGACACCAATTATCTC 277839
vv i - i - v i ---ii v iv v
C L1MEc_5end#LI 1300 TTTTTCTCTCTTTCTCTTTTCTCCTCTCCTTTGGGGACTCCAATTACATA 1251
INTRON_3 277840 TATGTTAGGCCACTTGAAGTTGTCCCAGAGCTGACTGATGCTCTTTTCAT 277889
i i v v v
C L1MEc_5end#LI 1250 TATATTAGGCTACTTGAAGTTGTCCCACAGCTCACTGATGCTCTTTTCTT 1201
INTRON_3 277890 TTT-----TTTGGATTCTTCTTTCTCAGTGGATTTCATTTTGGATTGTTT 277934
----- ii i i vv vi v
C L1MEc_5end#LI 1200 TTTAATTTTTTAAATTTTTTTTTCTCTCTGTGTTTCATTTTGGATAGTTT 1151
INTRON_3 277935 CTAATATCACTCCTTCAAGTTCACTAATGTTTTCTCTTGCA---TTGTCT 277981
v iii ivi v ii ---? ?
C L1MEc_5end#LI 1150 CTATTGCTATGTCTTCAAGTTCACTAATCTTTTCTTCTGCAATGNTNTCT 1101
INTRON_3 277982 AATCTACTGTTAAACC 277997
i i v
C L1MEc_5end#LI 1100 AATCTGCTATTAATCC 1085
Matrix = 20p37g.matrix
Transitions / transversions = 1.36 (49 / 36)
Gap_init rate = 0.02 (12 / 488), avg. gap size = 2.33 (28 / 12)
1601 18.77 6.53 0.66 INTRON_3 277675 278103 122078 C L1MEc_5end LINE/L1 968 1421 1106 585
INTRON_3 277675 GTTCCTTGGTATAGTTTTCTTTATGTTTCTTATGCTTAGGATGCTTTGAG 277724
v i i i i i viv
C L1MEc_5end#LI 1421 GTGCCTTGGTGTAGTTTTCTTCATGTTTCTTGTGCTTGGGGTTTGTTGAG 1372
INTRON_3 277725 CTCTTTGAATTTGTGT-TTTATGGTTTTCAT-GAAATTTGGAAAGTTGTC 277772
ii i i v- i -i i v i
C L1MEc_5end#LI 1371 CTTCTTGGATCTGTGGGTTTATAGTTTTCATCAAAATTTGGAAAATTTTT 1322
INTRON_3 277773 TGCCATAATTTCTTCAAATATATTTTTCTGACCTT-TCTTCTCTC-TGTT 277820
v v - vv i - i - v i
C L1MEc_5end#LI 1321 AGCCATTATTTCTTCAAATAT-TTTTTCTCTCTTTCTCTTTTCTCCTCTC 1273
INTRON_3 277821 CT---AAGACACCAATTATCTCTATGTTAGGCCACTTGAAGTTGTCCCAG 277867
---ii v iv v i i v
C L1MEc_5end#LI 1272 CTTTGGGGACTCCAATTACATATATATTAGGCTACTTGAAGTTGTCCCAC 1223
INTRON_3 277868 AGCTGACTGATGCTCTTTTCATTTT-----TTTGGATTCTTCTTTCTCAG 277912
v v ----- ii i i vv
C L1MEc_5end#LI 1222 AGCTCACTGATGCTCTTTTCTTTTTAATTTTTTAAATTTTTTTTTCTCTC 1173
INTRON_3 277913 TGGATTTCATTTTGGATTGTTTCTAATATCACTCCTTCAAGTTCACTAAT 277962
vi v v iii ivi
C L1MEc_5end#LI 1172 TGTGTTTCATTTTGGATAGTTTCTATTGCTATGTCTTCAAGTTCACTAAT 1123
INTRON_3 277963 GTTTTCTCTTGCA---TTGTCTAATCTACTGTTAAACCTTT---GTGTAT 278006
v ii ---? ? i i v iv ---
C L1MEc_5end#LI 1122 CTTTTCTTCTGCAATGNTNTCTAATCTGCTATTAATCCCATCCAGTGTAT 1073
INTRON_3 278007 TTTTTGTCTCACACATTGTAGATTTCATCTCT--AGAAATTCAATTTGGA 278054
ii v v -- i ii i
C L1MEc_5end#LI 1072 TTTTCATCTCAGACATTGTAGTTTTCATCTCTCTAGAAGTTTGATTTGGG 1023
INTRON_3 278055 TATTTTAAAATATTTTTCTTGTCTCT-CTTA-------GAACATATGGAA 278096
v vv - i i v - ------- ii
C L1MEc_5end#LI 1022 TCTTTTTTA-TATCTTCCATGTCTCTACTTAACTTTTTGAACATATAAAA 974
INTRON_3 278097 GTACAGT 278103
-
C L1MEc_5end#LI 973 -TACAGT 968
Matrix = 20p37g.matrix
Transitions / transversions = 1.52 (47 / 31)
Gap_init rate = 0.03 (14 / 428), avg. gap size = 2.21 (31 / 14)
+ 1581 24.5 7.5 0.2 INTRON_3 278118 278931 (121250) C L1MEc LINE/L1 (5471) 929 22 362
ANNOTATION EVIDENCE:
1581 23.16 8.47 0.44 INTRON_3 278118 278542 121639 C L1MEc_5end LINE/L1 471 929 1598 586
INTRON_3 278118 TAATTCTAACA--TATCTGTCAGTTCTGAGTTGTTTTGGATTAATTGATT 278165
-- v v i iiv vi i
C L1MEc_5end#LI 929 TAATTCTAACAATTCTGTGTCAGTTCTGGGTCAGTTTCAATTGATTGATT 880
INTRON_3 278166 ATTTTTCATATCATGAGTCATG---TTTTCTTGACTCTTTGCATACTAAG 278212
v i i vi i i i i--- i vi i ivi
C L1MEc_5end#LI 879 TTTCTCCTCATTATGGGTTATAATATTTTCCTGCTTCTTTGCATGCCTGG 830
INTRON_3 278213 TAATCCTTCATTGAATGAGAGATAATTGTACATTTTGCCTTGTTAAGAAG 278262
ii i i vv i - iv i ii viv
C L1MEc_5end#LI 829 TAATTTTTTATTGGATGCCAGACA-TTGTGAATTTTACCTTGTTGGGTGC 781
INTRON_3 278263 TACATATTTTTGTATT---------GTTCT-GAGCTATGTTTATGG---A 278299
iv ---------i - v i- ---
C L1MEc_5end#LI 780 TGGATATTTTTGTATTCCTATAAATATTCTTGAGCTTTGTTC-TGGGATA 732
INTRON_3 278300 GAGTTAAGTTATTTGGAAACAGTTTGATCCTTTCCTGTCTTGCTTATATG 278349
v i i vv v v
C L1MEc_5end#LI 731 CAGTTAAGTTACTTGGAAACAGTTTGATTCTTTCAGGTCTTGCTTTTAAG 682
INTRON_3 278350 ATTTGTTAGGAAGGGCTGGAGCAATGTTCAGTCTAGAGCTAAT-ATTCTC 278398
vi i ii i i i - i
C L1MEc_5end#LI 681 ATTTGTTAGGTGGGACCAGAGCAGTGTTTAGTCTAGGGCTAATTATTCCC 632
INTRON_3 278399 CATAACTGAGGCAAGACCTCTCTGAGTACTCCGTCTAATGCCCTATGAAT 278448
iv ii iii i i
C L1MEc_5end#LI 631 CACTACTGAGGCAAGACCCTTCTGAGTACTCTACCCAATGCCCTGTGAAT 582
INTRON_3 278449 TATGATTTTTTTCAGGCTTACTGGCAGGAATAAGTACTATTTTCAGTCTT 278498
vv i v vi ii i i i iii i i
C L1MEc_5end#LI 581 TATGAGGTTTTCCAGTCTGGCTGGTGGGAACAGGCACTATTCCTAGCCCT 532
INTRON_3 278499 GT---AGAAC---ACATTATTCCTTATAA-----------CTTTCAGATG 278531
--- v ---i i i i v ----------- ii i
C L1MEc_5end#LI 531 GTGTGAGTACCAGGCACTGTTCCCTCTAATCCTTTTTKTCCTTTTGGGTG 482
INTRON_3 278532 ATTCTCTACCT 278542
i i v
C L1MEc_5end#LI 481 GTTCTTTCCCT 471
Matrix = 20p37g.matrix
Transitions / transversions = 2.38 (69 / 29)
Gap_init rate = 0.03 (11 / 424), avg. gap size = 3.45 (38 / 11)
1195 27.40 6.03 0.00 INTRON_3 278533 278897 121284 C L1MEc_5end LINE/L1 90 476 2051 587
INTRON_3 278533 TTCTCTA-CCTCTGGTAGTTTCTTCATACTCATGTGCTTATTTGTATTCT 278581
i i- v i i iv v iv i
C L1MEc_5end#LI 476 TTCCCTGGCCTCAGGTAGTTTCCTCACATGCATGTGCTGATCAGTACTCT 427
INTRON_3 278582 GCTACATATTT---GAGAACTTTCTGGAGA-TGTCTAGAGTTATGTCTCC 278627
iv i i--- i i ii v - v v v i
C L1MEc_5end#LI 426 GCTGAATACTCAAGGGGGACCCTCTGCAGAATCTCTAGAGTTCTCTCTCT 377
INTRON_3 278628 ATGCATCCCTTTATTTGCTGTTAGTCTGA---ATGAAGT---GCT----T 278667
i v i i vi iv v v v--- v --- ----
C L1MEc_5end#LI 376 GTGCAGCTCTCTCCTCTCTGGTACTCTGTCCTATGAACTCTAGCTANCCT 327
INTRON_3 278668 TGGTCTTCCCAGACTCTTACCTCTATCTCCTCAAGTCAAGGAGCTTACTA 278717
i ii i v i v i ii i i
C L1MEc_5end#LI 326 TGGTCTCCCTGGACTCTCAGCTCTGTCTCCTCAACTCAGGGAGTCTGCTG 277
INTRON_3 278718 AGCTC--CTT---TTCATCTTTTCTGTGTCATGACTTGTAAACTCTCTCA 278762
i -- i --- vi i i? iiiiiiii i v
C L1MEc_5end#LI 276 GGCTCTGCCTGGGTTCCCCCTCYCTGCACTGCAGCCTGGAAACTCTCTCA 227
INTRON_3 278763 ATGCAGAAAACTGAAAAAATTACAGTGCTCAGTT-GCTTGGTTGTCATCT 278811
v v i iiiv i i v vi -ii v vi
C L1MEc_5end#LI 226 AGGCAGTAAGCTGGGGCAATCATAGGGCTCACCTCATTTGTTTCCCATCT 177
INTRON_3 278812 CTCAGAGTTCACTGTCCTTTGTTGTCTGATGTTCAGTGTTTTGGAAACCA 278861
i v i i i i i i
C L1MEc_5end#LI 176 CTCAGGGATCACTGTCCTTCGTTGCCTGATGTCCAGTGTCTTGAAAACTA 127
INTRON_3 278862 TTATTTCATATATTGAATCTGGTCCTT-GTTACTTTA 278897
i vvi v ii - ii i
C L1MEc_5end#LI 126 TTGTTTCATATATTTTGTCTGTTTTTTAGTTGTTTCA 90
Matrix = 20p37g.matrix
Transitions / transversions = 2.19 (68 / 31)
Gap_init rate = 0.03 (10 / 364), avg. gap size = 2.20 (22 / 10)
311 16.36 1.82 0.00 INTRON_3 278877 278931 121250 C L1MEc_5end LINE/L1 22 77 2450 588
INTRON_3 278877 AATCTGGTCCTTGTTACTTTATCTTGGCCAGAAGTATAAGTCTCTCAT-A 278925
i i ii i v ii -
C L1MEc_5end#LI 77 AATCCGGTCCCTGTTACTCCATCTTGGCCAGAAGCAGAAGTCTCCTATTA 28
INTRON_3 278926 TCTTTT 278931
v
C L1MEc_5end#LI 27 TATTTT 22
Matrix = 20p37g.matrix
Transitions / transversions = 3.50 (7 / 2)
Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1)
+ 312 19.1 19.8 1.8 INTRON_3 279660 279755 (120426) + MIRb SINE/MIR 99 211 (57) 363
ANNOTATION EVIDENCE:
312 19.09 19.79 1.77 INTRON_3 279660 279755 120426 + MIRb SINE/MIR 99 211 57 545
INTRON_3 279660 TGGATAACTTTATTTAGCCTCTCTCAGTCTCAGT---GTCATCTAATAAA 279706
ii v i- i i v i ---v i-
MIRb#SINE/MIR 99 TGGGCAAGTC-ACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTG-TAAA 146
INTRON_3 279707 ATGGG---AATAATACTCACTT-------------TAAGGATTATATAAG 279740
--- ii i ------------- i v i
MIRb#SINE/MIR 147 ATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAG 196
INTRON_3 279741 ATAATGAATATAAAG 279755
v i
MIRb#SINE/MIR 197 ATAATGCATGTAAAG 211
Matrix = 25p37g.matrix
Transitions / transversions = 2.60 (13 / 5)
Gap_init rate = 0.05 (5 / 95), avg. gap size = 4.20 (21 / 5)
+ 858 19.1 4.0 9.3 INTRON_3 279766 280013 (120168) + MER106A DNA/hAT-Charlie 1 236 (0) 364
ANNOTATION EVIDENCE:
858 19.12 4.03 9.32 INTRON_3 279766 280013 120168 + MER106A DNA/hAT-Charlie 1 236 0 497
INTRON_3 279766 CATATATTCTCAATAGAAGCAATATAGCCTTCAAGTTGGTGAAAAATTGG 279815
ii ii ii i v ii vv -
MER106A#DNA/h 1 CATGCATTCTCAACGGGGGCGATATCGCCCCCAAGGGGGTGAAAA-TTGG 49
INTRON_3 279816 TACTTGGTGGAGTGTGTGTGTGAGAAAA---CTTAGGTATTACAATGGTT 279862
v v ----------- --- i
MER106A#DNA/h 50 TTCTTGGGGG-----------GAGAAAAAATCTTAGATATTACAATGGTT 88
INTRON_3 279863 CGTTCTCCTCCAAAGG-TCACAGTATGAACAGTATAAAATAGATATATAG 279911
i vvi -i i------- -i i
MER106A#DNA/h 89 TGTGGCCCTCCAAAGGGCCACAGTAC-------ATAAA-CAGATATACAG 130
INTRON_3 279912 TATATGTGTAGTATTAAAATTTCATGGAGGA------CAATTAAGAAAAA 279955
v i ? i------ii i
MER106A#DNA/h 131 TATATCTGTGGTATTAAAATTTCATGGNGGGGGGGGGTGATTAGGAAAAA 180
INTRON_3 279956 TAAATATCTATAAGGGGTCCTTGGGGAGATGATAATTTAAAAACGTTGAG 280005
-- i v i v i i ii vv v
MER106A#DNA/h 181 --AATGTCTAAAAAGGCTCCTTAGGGGGGCGATAATGAAAAAAGGTTGAG 228
INTRON_3 280006 AAGCTCTG 280013
i v
MER106A#DNA/h 229 AAACACTG 236
Matrix = 18p37g.matrix
Transitions / transversions = 2.00 (28 / 14)
Gap_init rate = 0.03 (8 / 247), avg. gap size = 4.00 (32 / 8)
+ 249 34.1 4.8 1.6 INTRON_3 280144 280268 (119913) + Charlie23a DNA/hAT-Charlie 2 130 (209) 365
ANNOTATION EVIDENCE:
249 34.13 4.80 1.55 INTRON_3 280144 280268 119913 + Charlie23a DNA/hAT-Charlie 2 130 209 617
INTRON_3 280144 AATGATTCCAAACATGTGGACTAGAGGTTTCTGGGAATCTCAGAA----T 280189
i i v v i i- v vii iiv v i ----
Charlie23a#DN 2 AGTGGTTCCCAACCTGTGGGCC-GCGGACCCTGGGGGGCTCCGGAGTTAT 50
INTRON_3 280190 TAGAAGACGTTTTTTAATTCATTTACACACAAATCATCAGCTATAGGCTG 280239
iv iv iiviv i v iii v v iiv i i
Charlie23a#DN 51 TGCAAGGGGTCCGCGAATCCATATGTGCACCAAGCATTGTCTGTAGACTG 100
INTRON_3 280240 AATAAAT--TTTGTTTTGCATAGTACGTGTA 280268
-- v i i i - ii
Charlie23a#DN 101 AATAAATAATATGTCTCGCACA-TATATGTA 130
Matrix = 20p37g.matrix
Transitions / transversions = 1.80 (27 / 15)
Gap_init rate = 0.03 (4 / 124), avg. gap size = 2.00 (8 / 4)
+ 457 25.6 5.2 3.7 INTRON_3 280307 280517 (119664) + Charlie23a DNA/hAT-Charlie 124 337 (2) 366
ANNOTATION EVIDENCE:
457 25.60 5.21 3.74 INTRON_3 280307 280517 119664 + Charlie23a DNA/hAT-Charlie 124 337 2 618
INTRON_3 280307 ATATGTACAACT---TCTTGAGTATATTTATGATGATG--GTGAATAATA 280351
? --- i ii i i v - v -- v
Charlie23a#DN 124 ATATGTACNACTGTTTTTCAAATGTATGTA-GATGCTGTTGTGATTAATA 172
INTRON_3 280352 A--TG-AAATTCACTTAAAAGTTTT--TGGGTTCACAGCAGCTCTCT-TC 280395
-- i- i iv -- ii i i i i -
Charlie23a#DN 173 AAATACAAATTCATTTAAAAGCGTTACTGAATTCATAGTAGCTTTTTGTC 222
INTRON_3 280396 ATTTTGTGTTTTCTCAATTAATAGATTCTAAAAAATCCAACTACCATCAT 280445
v i i ii v i- v i
Charlie23a#DN 223 ATTATGTATTTTCTCAATCAACGGATACTAAAAG-TACAACTACTATCAT 271
INTRON_3 280446 TTGAGAGCTTGAATATAAAATATTTTTCTATTAGCAAAGGCTCATTATAC 280495
v i iiiii ----ii v vvii iv i v v i
Charlie23a#DN 272 GTGGGGATCCG----CGAAATTTTTTGACGTTAAAAAGGGGTCCTCATAC 317
INTRON_3 280496 TTCATATAAGGTTTGTAAACAC 280517
v - - v v v
Charlie23a#DN 318 TTGA-A-AAGGTTGGGAACCAC 337
Matrix = 20p37g.matrix
Transitions / transversions = 1.83 (33 / 18)
Gap_init rate = 0.05 (11 / 210), avg. gap size = 1.73 (19 / 11)
+ 205 16.2 0.0 0.0 INTRON_3 280847 280883 (119298) + (CA)n Simple_repeat 1 37 (0) 367
ANNOTATION EVIDENCE:
205 16.22 0.00 0.00 INTRON_3 280847 280883 119298 + (CA)n Simple_repeat 1 37 143 593
INTRON_3 280847 CACACACAGACACAGACACACAGATACATACAGACAC 280883
v v v i i v
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACAC 37
Matrix = Unknown
Transitions / transversions = 0.50 (2 / 4)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 1622 18.6 1.0 2.4 INTRON_3 281175 281469 (118712) + AluJr4 SINE/Alu 1 291 (21) 368
ANNOTATION EVIDENCE:
1449 20.15 1.02 2.41 INTRON_3 281175 281469 118712 + AluJb SINE/Alu 1 291 21 492
INTRON_3 281175 GGCCTTGCACAGTGGCTCACGTCTATAATGCCAGCACTTTGAGAGGCCAA 281224
vv i i i i v i i
AluJb#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 281225 GCCGAGAGGATCACATGAGCCAATGAGTTTGAGACAAGCCTGGGGAAAAT 281274
v i v v v i v v v
AluJb#SINE/Al 51 GGCGGGAGGATCACTTGAGCCCAGGAGTTCGAGACCAGCCTGGGCAACAT 100
INTRON_3 281275 AACAAAACCTCATCTCTA-ATAAAATCTTTTTAAAAAGTAGCCTGGCACA 281323
iiii i i - v vi---- v v iii
AluJb#SINE/Al 101 GGTGAAACCCCGTCTCTACAAAAAATAC----AAAAATTAGCCGGGCGTG 146
INTRON_3 281324 GTGGTACATGCCCACAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGGAT 281373
ii ii iii i
AluJb#SINE/Al 147 GTGGCGCGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGGAT 196
INTRON_3 281374 TGCTTGAGCC-GGAAGTTCAAGGTTACGGTGAGCTATGATCACACCA-TG 281421
i - i v i i i i ii i i -
AluJb#SINE/Al 197 CGCTTGAGCCCGGGAGGTCGAGGCTGCAGTGAGCCGTGATCGCGCCACTG 246
INTRON_3 281422 TCCCCCAGCCTGGGTGACAGAGCAAGACCCTATCTTTACAAAAAGAAA 281469
iv i i i i --- i
AluJb#SINE/Al 247 CACTCCAGCCTGGGCGACAGAGCGAGACCCTGTCT---CAAAAAAAAA 291
Matrix = 14p37g.matrix
Transitions / transversions = 2.62 (42 / 16)
Gap_init rate = 0.02 (5 / 294), avg. gap size = 2.00 (10 / 5)
+ 246 29.7 9.9 0.0 INTRON_3 281804 281894 (118287) C MIRc SINE/MIR (148) 120 21 369
ANNOTATION EVIDENCE:
246 29.67 9.89 0.00 INTRON_3 281804 281894 118287 C MIRc SINE/MIR 21 120 148 546
INTRON_3 281804 TCAGAGAGATTAAATA------TCAAGTTAAAAT--CTAATAAGTGGAAG 281845
i i i------i v v v i-- i v
C MIRc#SINE/MIR 120 TCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAG 71
INTRON_3 281846 TGTCAGGACTTCAAATGAAATTTTC-TGAATCCAAAACTAGGGATTTTTC 281894
v i iv viv ii i - v iv i v v i
C MIRc#SINE/MIR 70 AGCCAGGACTCGAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTTC 21
Matrix = 25p37g.matrix
Transitions / transversions = 1.25 (15 / 12)
Gap_init rate = 0.03 (3 / 90), avg. gap size = 3.00 (9 / 3)
+ 746 23.0 12.2 2.1 INTRON_3 283547 283759 (116422) + MIR SINE/MIR 12 245 (17) 370
ANNOTATION EVIDENCE:
746 23.03 12.21 2.14 INTRON_3 283547 283759 116422 + MIR SINE/MIR 12 245 17 547
INTRON_3 283547 TAGTAGTTAATAGCATAATATCTGAGATTGTGTTAGATTTCTAGGGTTTA 283596
i v iiivv - ---- ii i v iv ii
MIR#SINE/MIR 12 TAGTGGTTAAGAGCACGGACTCTG-GA----GCCAGACTGCCTGGGTTCG 56
INTRON_3 283597 TGTCCTAGCTCTAGCACTTACTAGAAGTGTGACTTGGAGCAAGT------ 283640
vi ii iv vv i v i ------
MIR#SINE/MIR 57 AATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTA 106
INTRON_3 283641 ------CTGCGTTTCAGTTTCCCCATCTGTAAA-TGGGCATATTAATAGT 283683
------ i ii i - v v
MIR#SINE/MIR 107 ACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGT 156
INTRON_3 283684 AATTATCTCAT---TCTGTTGTGTGGATTAAGTAAAGTAATACATGTAAA 283730
vi i ---vi v i i iv
MIR#SINE/MIR 157 ACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAA 206
INTRON_3 283731 ATGCTTAAAACA-TG---------TAGAAAATGCTCAAT 283759
ii i - --------- v ii
MIR#SINE/MIR 207 GCGCTTAGAACAGTGCCTGGCACATAGTAAGCGCTCAAT 245
Matrix = 25p37g.matrix
Transitions / transversions = 1.82 (31 / 17)
Gap_init rate = 0.03 (7 / 212), avg. gap size = 4.43 (31 / 7)
+ 181 29.6 1.9 0.0 INTRON_3 283805 283858 (116323) C L2c LINE/L2 (307) 3080 3026 371
ANNOTATION EVIDENCE:
181 29.63 1.85 0.00 INTRON_3 283805 283858 116323 C L2c_3end LINE/L2 117 171 307 548
INTRON_3 283805 GGGGAGAGGTATTCCAAACTGACTGAACAGCATGAGCAAAGGTA-GAAAG 283853
iii i ii v vv v i?- i i
C L2c_3end#LINE 171 GGGGAAGAGCATTCCAGGCAGAGGGAACAGCATGTGCAAAGGCNCGGAGG 122
INTRON_3 283854 TATGA 283858
i v
C L2c_3end#LINE 121 CAGGA 117
Matrix = 25p37g.matrix
Transitions / transversions = 2.00 (10 / 5)
Gap_init rate = 0.02 (1 / 53), avg. gap size = 1.00 (1 / 1)
+ 2555 20.1 4.5 5.4 INTRON_3 284041 284096 (116085) C MLT2B3 LTR/ERVL (0) 554 506 372
ANNOTATION EVIDENCE:
2555 20.05 4.47 5.42 INTRON_3 284041 284096 116085 C MLT2B3 LTR/ERVL 506 554 0 619
INTRON_3 284041 TGTATTAGTCAGAGTTCTCCAGGGAAACAGAATAAATAGGGAATATATAG 284090
i i i iv ------
C MLT2B3#LTR/ER 554 TGTATTAGTCAGGGTTCTCCAGAGAGACAGAACCAATAGG------ATAG 511
INTRON_3 284091 ATATAT 284096
v -
C MLT2B3#LTR/ER 510 ATAGA- 506
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (4 / 2)
Gap_init rate = 0.04 (2 / 55), avg. gap size = 3.50 (7 / 2)
+ 1948 13.2 4.0 0.3 INTRON_3 284097 284422 (115759) C MER44A DNA/TcMar-Tigger (1) 338 1 373
ANNOTATION EVIDENCE:
1948 13.23 3.99 0.30 INTRON_3 284097 284422 115759 C MER44A DNA/TcMar-Tigger 1 338 1 498
INTRON_3 284097 AGTAGTCCCCCCTTATCCATGAGGGATACATTCCAAGACCCCCAAAGGAT 284146
ii i i iv
C MER44A#DNA/Tc 338 AGTAGTCCCCCCTTATCCGCGGGGGATACGTTCCAAGACCCCCAGTGGAT 289
INTRON_3 284147 GCCTGAAACTGTGGATAGTACCAAACCCTA-AGACACTATGTTTTTCTCT 284195
i i i - v i - i
C MER44A#DNA/Tc 288 GCCTGAAACCGCGGATAGTACCGAACCCTATATATACTATGTTTTT-TCC 240
INTRON_3 284196 TATACTTATATACCTATGATAAAGTTTAATTTATAAATTAGGTACAGTAA 284245
v i i
C MER44A#DNA/Tc 239 TATACATACATACCTATGATAAAGTTTAATTTATAAATTAGGCACAGTAA 190
INTRON_3 284246 GAGATTATCAACAAT------TAATAAAATAGAACAATTATAACAATATA 284289
v ------
C MER44A#DNA/Tc 189 GAGATTAACAACAATAACTAATAATAAAATAGAACAATTATAACAATATA 140
INTRON_3 284290 TTATAATCATAGGCATATGAATGTGATCTCTCTCTCTCAAAATATCTTAC 284339
i i v v vi i i i
C MER44A#DNA/Tc 139 CTGTAATAAAAGTTATGTGAATGTGGTCTCTCTCTCTCAAAATATCTTAT 90
INTRON_3 284340 TGTA-TATAGTAA-----TTTTGGACTGTAATTGACTGAGGGCAACTGAA 284383
- i v v ----- i i iii i v i
C MER44A#DNA/Tc 89 TGTACTGTACTCACCTATTTTCGGACCGCGGTTGACCGCGGGTAACTGAA 40
INTRON_3 284384 ACCTCAGAAAGTGAAACCTCAGATAAGGCAAGACTACTG 284422
v i v i vii
C MER44A#DNA/Tc 39 ACCGCGGAAAGTGAAACCGCGGATAAGGGGGGACTACTG 1
Matrix = 18p37g.matrix
Transitions / transversions = 2.31 (30 / 13)
Gap_init rate = 0.02 (5 / 325), avg. gap size = 2.80 (14 / 5)
+ 2555 20.1 4.5 5.4 INTRON_3 284423 284924 (115257) C MLT2B3 LTR/ERVL (49) 505 1 372
ANNOTATION EVIDENCE:
2555 20.05 4.47 5.42 INTRON_3 284423 284924 115257 C MLT2B3 LTR/ERVL 1 505 49 620
INTRON_3 284423 TTTATATATAGGAAATTTATCATGGGAATTGACTCATGTGATTATGGAGA 284472
---------- ii i v i i i
C MLT2B3#LTR/ER 505 ----------GGGGATTTATTAGGGGAATTGGCTCACGTGATTATGGAGG 466
INTRON_3 284473 CTGAGAAGTCCCACAATATGCTTTATGTAAGCTGG--------------T 284508
i i v iv v i --------------i
C MLT2B3#LTR/ER 465 CTGAGAAGTCCCACGACAGGCCGTCTGCAAGCTGGAGAMCCAGGGAAGCC 416
INTRON_3 284509 GGTA---TACTTCAGTCCAAGTCTGAAGGCCTGAAAACCAGAGGTGGCTA 284555
--- ivi i v i i v v v
C MLT2B3#LTR/ER 415 GGTAGCGTGGCTCAGTCCAAGTCCGAAGGCCTCAGAACCAGGGGAGCCGA 366
INTRON_3 284556 TGAT-TAACTTCCAGTCTAATGCTGAAGGCCTGAGAACCTGGAAAGGGAG 284604
i - ii ii v i i --------
C MLT2B3#LTR/ER 365 TGGTGTAACTCTCAGTCCGAGGCCGAAGGCCTGAGAACCCGG-------- 324
INTRON_3 284605 AAGAGG--GTTGGTCTAAGTCCTGAAGTCCAAAGGCCTGAGAACCAGGAA 284652
-- i -- i vi i i v v i
C MLT2B3#LTR/ER 323 --GGGGCCGCTGGTGCAAGTCCCGGAGTCCAAAGGCCAGAGAACCTGGAG 276
INTRON_3 284653 CTCCATTGTCCAAGGGCAGGAGAAGATGAATGTCTCACCTCAAGGAGGGG 284702
i iiv ? ii i v v i -
C MLT2B3#LTR/ER 275 TTCTGATGTCCAAGGGCAGGAGAAGASGGGTGTCCCAGCTCCAGGAGAG- 227
INTRON_3 284703 AGAGCA--TTT---CTACTTCTCCACTTTTTATACTATTTGGGCTCTCAA 284747
-- i--- v i v - i v ii i i
C MLT2B3#LTR/ER 226 AGAGCAAATTCGCCCTTCCTCTGC-CTTTTTGTTCTATCCGGGCCCTCAG 178
INTRON_3 284748 AGGATTAGATGATGCCTGCCCACATATGTGAAAGTGGACTTTCTGCACTC 284797
v? i i i vv ii ii ii ivi
C MLT2B3#LTR/ER 177 CNGATTGGATGGTGCCCGCCCACATTGGTGAGGGCAGATCTTCCTTACTC 128
INTRON_3 284798 ACTTTTCTAATTTAAATGCTAATCTCTTCCAGAAACACCCTCACAGATAC 284847
v iiv i i i i i
C MLT2B3#LTR/ER 127 AGTCCACTGATTCAAATGCCAATCTCTTCCGGAAACACCCTCACAGACAC 78
INTRON_3 284848 ACCAAGAAATAATGTTTTATCAGCTATTTGAACATCCCTTAGCCCAGACA 284897
v i i i iii ii v
C MLT2B3#LTR/ER 77 ACCCAGAAATAATGCTTTACCAGCTATCTGGGTATCCCTTAATCCAGTCA 28
INTRON_3 284898 AGTTGACACATAATATTAACCATCACA 284924
v v
C MLT2B3#LTR/ER 27 AGTTGACACCTAAAATTAACCATCACA 1
Matrix = 20p37g.matrix
Transitions / transversions = 2.38 (69 / 29)
Gap_init rate = 0.02 (10 / 501), avg. gap size = 4.70 (47 / 10)
+ 733 21.6 3.7 6.6 INTRON_3 284927 285114 (115067) C MER58B DNA/hAT-Charlie (7) 334 152 374
ANNOTATION EVIDENCE:
733 21.63 3.72 6.56 INTRON_3 284927 285114 115067 C MER58B DNA/hAT-Charlie 152 334 7 621
INTRON_3 284927 CAGGAAACTTTTAATGTAAAGGGCCAGATAGTGTATATGTGTGTGTATAT 284976
i v vv iv -----------
C MER58B#DNA/hA 334 CGGCAAACTTTTTCTGTAAAGGGCCAGATAGTAAATAT-----------T 296
INTRON_3 284977 TTAAGGCTTTGTGAGTCATATGGTC------AAAACTACTCAACTTTGCT 285020
- i i i i ------iv i i
C MER58B#DNA/hA 295 TTA-GGCTTTGCGGGCCATACGGTCTCTGTCGCAACTACTCAACTCTGCC 247
INTRON_3 285021 GTGAT-GTGTGAAAGTAGCTGTAGGCAATACATAAACAAATAAGCATGGC 285069
vi - i i i ii i i i i i
C MER58B#DNA/hA 246 GTTGTAGCGCGAAAGCAGCCATAGACAATACGTAAACGAATGAGCGTGGC 197
INTRON_3 285070 GGCATTTCAATAAAACCTTATCAATGGATGTAGAAAATTGAATTT 285114
v ii i i iv iiiv v
C MER58B#DNA/hA 196 TGTGTTCCAATAAAACTTTATTTATGGACACTGAAATTTGAATTT 152
Matrix = 20p37g.matrix
Transitions / transversions = 2.80 (28 / 10)
Gap_init rate = 0.02 (4 / 187), avg. gap size = 4.75 (19 / 4)
+ 1050 19.1 0.0 0.0 INTRON_3 285150 285317 (114864) + FRAM SINE/Alu 5 172 (4) 375
ANNOTATION EVIDENCE:
933 17.43 0.00 4.35 INTRON_3 285150 285317 114864 + FRAM_short_ SINE/Alu 5 165 1 499
INTRON_3 285150 GGCACAGTGAAACGCACCTATGGTCCTAGCTACTCAGGAGGCTGAGGTGG 285199
i i ivi i i i i i i
FRAM_short_#S 5 GGCGCGGTGGCGCGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCGG 54
INTRON_3 285200 GAGGATTGCTTGAGCCCAGGAGTTGGAGGCTGCAGTGAGCTATGACTGTG 285249
i v ii i
FRAM_short_#S 55 GAGGATCGCTTGAGCCCAGGAGTTCGAGGCTGCAGTGAGCTATGATCGCG 104
INTRON_3 285250 CCACTGCACTCCAGCCCGGGCAATAAAGTGAGGTCTCGACTATGAAAACG 285299
i i i i i ii i v ------- i
FRAM_short_#S 105 CCACTGCACTCCAGCCTGGGCGACAGAGCGAGACCCCGTCT-------CA 147
INTRON_3 285300 AAAAACAAACAAAAAAAA 285317
v v
FRAM_short_#S 148 AAAAAAAAAAAAAAAAAA 165
Matrix = 18p37g.matrix
Transitions / transversions = 4.60 (23 / 5)
Gap_init rate = 0.01 (1 / 167), avg. gap size = 7.00 (7 / 1)
+ 361 22.8 3.2 1.1 INTRON_3 285367 285459 (114722) + MamRep1161 DNA/TcMar-Tigger 854 948 (9) 376
ANNOTATION EVIDENCE:
361 22.82 3.23 1.05 INTRON_3 285367 285459 114722 + MamRep1161 DNA/TcMar-Tigger 854 948 9 622
INTRON_3 285367 ATTTGTAACATTGTTTCCATGGTGCAATGTATTCTGCATTCTAAATAATT 285416
i i viv vi i i i
MamRep1161#DN 854 ATTTATAACATTGTTTCTATGGGAAAATGTATTCTGAGTTCCAAACAACT 903
INTRON_3 285417 AACTTTGAAATAGAA---TTAAAATACAACCTGTTGGTAAGGTAGG 285459
i vv - --- ii i ii v v i
MamRep1161#DN 904 GACTTACAAAT-GAACTTTTGGAACACAACCCATTTGTAAGTTGGG 948
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.02 (2 / 92), avg. gap size = 2.00 (4 / 2)
361 22.82 3.23 1.05 INTRON_3 285367 285459 114722 + MamRep1161 DNA/TcMar-Tigger 854 948 9 751
INTRON_3 285367 ATTTGTAACATTGTTTCCATGGTGCAATGTATTCTGCATTCTAAATAATT 285416
i i viv vi i i i
MamRep1161#DN 854 ATTTATAACATTGTTTCTATGGGAAAATGTATTCTGAGTTCCAAACAACT 903
INTRON_3 285417 AACTTTGAAATAGAA---TTAAAATACAACCTGTTGGTAAGGTAGG 285459
i vv - --- ii i ii v v i
MamRep1161#DN 904 GACTTACAAAT-GAACTTTTGGAACACAACCCATTTGTAAGTTGGG 948
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.02 (2 / 92), avg. gap size = 2.00 (4 / 2)
+ 486 23.4 4.5 0.0 INTRON_3 286091 286201 (113980) + MIRb SINE/MIR 91 206 (62) 377
ANNOTATION EVIDENCE:
486 23.42 4.50 0.00 INTRON_3 286091 286201 113980 + MIRb SINE/MIR 91 206 62 651
INTRON_3 286091 TGTAGCATTGGGCAAGCTACTTAAACTTTCTGAGCCTCAGTTAGCTTCTC 286140
ii v ii v i vv iv
MIRb#SINE/MIR 91 TGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATC 140
INTRON_3 286141 TATAAGATAGG---AAGAATAGCTAGTTTGAAAGATTGTTA--AAGATTG 286185
i i i --- v v vi i v i i i-- i i
MIRb#SINE/MIR 141 TGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTA 190
INTRON_3 286186 AATGAGATAATGTATG 286201
i
MIRb#SINE/MIR 191 AATGAGATAATGCATG 206
Matrix = 25p37g.matrix
Transitions / transversions = 1.89 (17 / 9)
Gap_init rate = 0.02 (2 / 110), avg. gap size = 2.50 (5 / 2)
+ 306 35.8 2.9 1.6 INTRON_3 286318 286561 (113620) C CR1_Mam LINE/CR1 (584) 1620 1374 378
ANNOTATION EVIDENCE:
306 35.83 2.87 1.62 INTRON_3 286318 286561 113620 C CR1_Mam LINE/CR1 1374 1620 584 702
INTRON_3 286318 CACATTTTTTCCTACTCAAAATATTTTGTGAGATTGCATTATGTTTTATG 286367
v i v i v vviii ivivi iiiv v
C CR1_Mam#LINE/ 1620 CACTTTTCTGCCCACTCACACAGCCTTGTGAGATCTTCCTGCAGTTTATC 1571
INTRON_3 286368 CTTATCA-CTTGGACATTTTATAATCTAGAAAAGACTCTATGCC--TTAC 286414
ii - - i iv i ii i - ivi i --i i
C CR1_Mam#LINE/ 1570 CCCATCAGCTTGG-CATTTCACTACCCGGAAGAG-CTTAGTGTCATCTGC 1523
INTRON_3 286415 AAATGTAAATATTCTACTCTGTATTCCCTGTTTCAGATAATGGATAAATA 286464
iv ii v ii v i i v i v vv v
C CR1_Mam#LINE/ 1522 AAACTTGGAGATTTCACTGTGCACTCCCTCTTCCAGATCATTTATAAAAA 1473
INTRON_3 286465 TGCCAAATTAAACT-GTCTTCAAT-CAAGTCCTTGGGTCCCTCCATTATT 286512
ii v i - i- ii- vii i vvv i i i
C CR1_Mam#LINE/ 1472 TGTTAAATAAGACTAGTCC-CAGCACTGATCCCTGGGGGACCCCACTGTT 1424
INTRON_3 286513 AGTACTTCATTATTAAAAGTCACATACATTTAATTCTC-ATCTTT-GCTT 286560
vii vii iv i vviiiiv - - i - i
C CR1_Mam#LINE/ 1423 TACACTTCTCCATCCAGAGAAGTGCCCATTTA-TTCTCTACCTTTTGTTT 1375
INTRON_3 286561 C 286561
C CR1_Mam#LINE/ 1374 C 1374
Matrix = 20p37g.matrix
Transitions / transversions = 1.87 (56 / 30)
Gap_init rate = 0.04 (10 / 243), avg. gap size = 1.10 (11 / 10)
+ 190 18.7 0.0 7.0 INTRON_3 287133 287178 (113003) + L3 LINE/CR1 4442 4484 (5) 379
ANNOTATION EVIDENCE:
190 18.69 0.00 6.98 INTRON_3 287133 287178 113003 + L3 LINE/CR1 4442 4484 5 652
INTRON_3 287133 AGATGATGCCTCTGAGTGACCCTACTAATTCTAACATTTTGTGATT 287178
-- i - v v i i i v i
L3#LINE/CR1 4442 AGATGA--CCTCTAAG-GTCCCTTCCAACTCTGAGATTCTGTGATT 4484
Matrix = 25p37g.matrix
Transitions / transversions = 1.67 (5 / 3)
Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.50 (3 / 2)
+ 554 11.1 12.1 0.0 INTRON_3 287504 287602 (112579) C L1MB3 LINE/L1 (11) 6172 6062 380
ANNOTATION EVIDENCE:
554 11.11 12.12 0.00 INTRON_3 287504 287602 112579 C L1MB3_3end LINE/L1 809 919 11 646
INTRON_3 287504 GTGATAAAACGTACATCACAT-----TTACCATTTTAAACATTTT----- 287543
i ii v ----- v -----
C L1MB3_3end#LI 919 GTGGTAAAATATACATAACATAAAATTTACCATTTTAACCATTTTTAAGT 870
INTRON_3 287544 --ACAGTCCAGTGGCATTAAGTACATTCAGATTGTTGTACAGCCATCACA 287591
-- i v i i v
C L1MB3_3end#LI 869 GTACAGTTCAGTGGCATTAAGTACATTCACATTGTTGTGCAACCATCACC 820
INTRON_3 287592 GCCATCCATCT 287602
i
C L1MB3_3end#LI 819 ACCATCCATCT 809
Matrix = 18p37g.matrix
Transitions / transversions = 1.75 (7 / 4)
Gap_init rate = 0.02 (2 / 98), avg. gap size = 6.00 (12 / 2)
+ 520 23.7 8.1 2.9 INTRON_3 287605 287876 (112305) C L1MCc LINE/L1 (4682) 2355 1958 381
ANNOTATION EVIDENCE:
417 26.96 10.29 4.53 INTRON_3 287605 287876 112305 C L1MEg_5end LINE/L1 1116 1402 699 703
INTRON_3 287605 TTCATATTCTGAAAGATTTTTTTTTGCTTATGAAATTCTAGGTTAACAAT 287654
- i i v ii vv ii ii i
C L1MEg_5end#LI 1402 TTCAT-TTTTGAAGGATATTTTCCTGGATATAGAATTCTAGGTTGGCAGT 1354
INTRON_3 287655 T-CTTTCTTCCAGCATTT------------------ATCTTCTGGTTTGC 287685
-i i i ------------------i i v
C L1MEg_5end#LI 1353 TATTTTCTTTCAGCACTTTAAAGATGTCATTCCATTGTCTTCTGGCTTCC 1304
INTRON_3 287686 ATGGTCCCTA---ATAAATCTACTATAATTCTTACCTTTGTTTCTTTCTA 287732
v ii i--- v i vi i v v iiv i i vv
C L1MEg_5end#LI 1303 ATTGTTTCTGTTGAGAAGTCAGCTGTCAGTCTTATTGTTGCTCCTTTGAA 1254
INTRON_3 287733 TGTAATGCATTTTTTTCCTCTAGCTGCCTTTAGGAATTTTTATTT--CCT 287780
v ii i i i i i v i v -- i
C L1MEg_5end#LI 1253 GGTAATGTGTCTTTTTTCTCTGGCTGCTTTTAAGATTTTCTCTTTGTCTT 1204
INTRON_3 287781 TGGTTTTCAGAATGTAAGTTTGAATATA---TGTCTATGTATTTTTGTTT 287827
v ----- v v i--- i v i v---
C L1MEg_5end#LI 1203 TGGTTTTCAGCA-----GTTTTACTATGATGTGCCTAGGTGTG---GTTT 1162
INTRON_3 287828 GCTTGTTTGTTTTAATCTGGTTTAATGTTCTATA-AGCTTTCTGAATCCG 287876
v --- v v iv i iiv -i -? ii i
C L1MEg_5end#LI 1161 TCTT---TGTATTTATCCTGCTTGGGGTTC-GTAGNGCTTCTTGAATCTG 1116
Matrix = 20p37g.matrix
Transitions / transversions = 1.76 (44 / 25)
Gap_init rate = 0.04 (11 / 271), avg. gap size = 3.73 (41 / 11)
520 22.59 7.35 2.34 INTRON_3 287673 287876 112305 C L1MCa_5end LINE/L1 1338 1551 883 704
INTRON_3 287673 TCTTCTGGTTTGCATGGTCCCTAAT---AAATCTACTATAATTCTTACCT 287719
v i ii i v--- i viv i i
C L1MCa_5end#LI 1551 TCTTCTTGCTTGCATGGTTTCTGAGGAGAAGTCGGATGTAATTCTTATCT 1502
INTRON_3 287720 TTGTTTCTTTCTATGTAATGCATTTTTTTCCTCTAGCTGCCTTTAGGAAT 287769
i i i v v v ii i i v i i v
C L1MCa_5end#LI 1501 TTGCTCCTCTATAGGTAAGGTGTTTTTTCCCTCTGGCTTCTTTCAGGATT 1452
INTRON_3 287770 TTTTATTT--CCTTGGTTTTCAGAATGTAAGTTTGAATAT---ATGTCTA 287814
v -- i i ---- - --- i
C L1MCa_5end#LI 1451 TTTTCTTTATCTTTGATTTTC----TGTA-GTTTGAATATGATATGCCTA 1407
INTRON_3 287815 --TGTATTTTTGTTT-GCTTGTTTGTT----TTAATCTGGTTTAATGTTC 287857
-- v - i v v ---- v iv i ii
C L1MCa_5end#LI 1406 GGTGTAGTTTTGTTTTGTTTTTTTTTTGGCATTTATCCTGCTTGGTGTTC 1357
INTRON_3 287858 TATAAGCTTTCTGAATCCG 287876
v i i i i
C L1MCa_5end#LI 1356 TCTGAGCTTCCTGGATCTG 1338
Matrix = 20p37g.matrix
Transitions / transversions = 1.81 (29 / 16)
Gap_init rate = 0.04 (8 / 203), avg. gap size = 2.50 (20 / 8)
+ 1395 28.2 4.2 4.6 INTRON_3 287893 288562 (111619) C L1MCc LINE/L1 (4940) 1483 836 381
ANNOTATION EVIDENCE:
1395 28.60 3.53 6.26 INTRON_3 287893 288515 111666 C L1MCc_5end LINE/L1 877 1483 53 705
INTRON_3 287893 CTTTTTGCCTCTGGAACTCTTAACATGTTAATTATAATTGTTTTTAAATC 287942
? v vi i v ii i i i i v v
C L1MCc_5end#LI 1483 CNTTTTTCCATTAGATCCTTTAACATATTAATCATAGTTATTTTAAATTC 1434
INTRON_3 287943 CCTATCTGATGGTTCTCACATCTAGATTATATCTGAGACTTATTTTATTG 287992
ii i ii iv ivi i v vi i i
C L1MCc_5end#LI 1433 TTTGTCTGATAATTCCAACATCTGTGTCATATCTGAGTCTGGTTCTGTTG 1384
INTRON_3 287993 ATTGTTTTGATTCTTGTTAGGGGATTGTTTTTCTT-GCTTCTTT-GTTTG 288040
i vi vi iv i i -? i -? ?
C L1MCc_5end#LI 1383 ATTGCTTTGTCTCTTGACAATGGGTTGTTTTTTTTTNCTTTTTTTNTNTG 1334
INTRON_3 288041 TCTTA-AATTTTTTGGTTGAAAGCCCAACAATTATGTGTAGGA---CAGT 288086
i- i- v ?vi - i ---
C L1MCc_5end#LI 1333 TCTTGTAATTTTTTA-TTGAATGCYAGACA-TTATGTGTAGAAGAACAGT 1286
INTRON_3 288087 AGAGACTGTGTTAAGTGGTATTTATGTCTGCCGATGGGTGTACCTCTCTT 288136
v v i i i vvi ii i i ii
C L1MCc_5end#LI 1285 AGAGACTGAGGTAAATAGTATTTATGCCTGGAAATGGGCATGCCTTTTCT 1236
INTRON_3 288137 TCTGCTAGGCCTTTAGTATGTATAGATGATGTTTGAGTCAACCT---CAG 288183
i i ------- iv - i ---
C L1MCc_5end#LI 1235 TCTGCTAGGCTTTTAGTGTG-------GGGGTT-GAGTCAATCTAGTCAG 1194
INTRON_3 288184 GAGTTTGCATTTTATGGTTTGGATTTTATTGGTAGCTG-GGTTTGGATTT 288232
- vii v--- i i v - i- --ivi?
C L1MCc_5end#LI 1193 GAGTT-GAGCTG---GGTTTGGGTTTTGTTGTT-GCTATGGTT--ACCYT 1151
INTRON_3 288233 TATTGTTGCTATGGTTACCTCATTGCAATGTC---AGTGTCAAATTCCTG 288279
i v i-i i ii --i i ---- vi --- viiiii v
C L1MCc_5end#LI 1150 CAGTGC-ACCACAG--GCTTCA----AATTCCTCTAGTGGTGGGCTGCTG 1108
INTRON_3 288280 TATCATTACCTTGTGCTTAG-GTAAGGGCTGCATTGCCAGAGGATTTTTC 288328
----- - ii vv i i
C L1MCc_5end#LI 1107 T-----TACCTTGTGCTTAGTGTGGGGGCTGGTTTGCTAGAGGGTTTTTC 1063
INTRON_3 288329 TCAATGTTCCTGTAACATCCTCAGCTTCAGGCATTCCTTGTGAGTCTACA 288378
i ivv i ivi i v i iivii iii
C L1MCc_5end#LI 1062 TCAGTGTTCCTGCTCCACCCTCAGCTTTCAGTAGTCCCTGCATACCTGTG 1013
INTRON_3 288379 CCTGAAAAGAGGGTCTTCCTTCACACTCTTGACTC---CTCAGTGGTAGA 288425
-iv i i i ii i i?? ?? ?? i --- i
C L1MCc_5end#LI 1012 CC-ACAGAGGGAGTCTCTCTCCATNNTNNTNNCCCTCCCCCAGTGGTAGA 964
INTRON_3 288426 TTGCCACTA-TTTGTTACTCATTGCTTGCTAGCTTAGTTGGGAAAGGCAA 288474
i iii i- ? iiv i vi v v v ii ?--
C L1MCc_5end#LI 963 CTGCTGTTGCTKTGTTACTTGGTGCTTGTTAGGCTTGTGGTGGGAGN--A 916
INTRON_3 288475 GGGACAGGGGTTCAGCCTAT-GTT---GTTCAGGTTCAGCCTTAG 288515
i---- --i i - i--- i vi i
C L1MCc_5end#LI 915 GGGAT----GTTC--TCTGTTGTCCTGGTCCAGCCTCAGTCTTAG 877
Matrix = 20p37g.matrix
Transitions / transversions = 2.73 (112 / 41)
Gap_init rate = 0.05 (28 / 622), avg. gap size = 2.14 (60 / 28)
1136 27.75 4.91 3.12 INTRON_3 288217 288562 111619 C L1MCc_5end LINE/L1 836 1187 349 706
INTRON_3 288217 AGCTGGGTTTGGATTTTATTGTTGCTATGGTTACC-TCATTGCAATGTCA 288265
i i - v viiivi
C L1MCc_5end#LI 1187 AGCTGGGTTTGGGTTTTGTTGTTGCTATGGTTACCYTCAGTGCACCACAG 1138
INTRON_3 288266 GTGTCAAATTCCTGTA-----------TCATTACCTTGTGCTTAG-GTAA 288303
iv v -----------iii - ii
C L1MCc_5end#LI 1137 GCTTCAAATTCCTCTAGTGGTGGGCTGCTGTTACCTTGTGCTTAGTGTGG 1088
INTRON_3 288304 GGGCTGCATTGCCAGAGGATTTTTCTCAATGTTCCTGTAACATCCTCAGC 288353
vv i i i ivv i
C L1MCc_5end#LI 1087 GGGCTGGTTTGCTAGAGGGTTTTTCTCAGTGTTCCTGCTCCACCCTCAGC 1038
INTRON_3 288354 TTCAGGCATTCCTTGTGAGTCTACACCTGAAAAGAGGGTCTTCCTTCACA 288403
ivi i v i iivii iii -iv i i i ii i i?
C L1MCc_5end#LI 1037 TTTCAGTAGTCCCTGCATACCTGTGCC-ACAGAGGGAGTCTCTCTCCATN 989
INTRON_3 288404 CTCTTGACTC---CTCAGTGGTAGATTGCCACTA-TTTGTTACTCATTGC 288449
? ?? ?? i --- i i iii i- ? iiv
C L1MCc_5end#LI 988 NTNNTNNCCCTCCCCCAGTGGTAGACTGCTGTTGCTKTGTTACTTGGTGC 939
INTRON_3 288450 TTGCTAGCTTAGTTGGGAAAGGCAAGGGACAGGGGTTCAGCCTATGTTGT 288499
i vi v v v ii ?-- i---- ---- v
C L1MCc_5end#LI 938 TTGTTAGGCTTGTGGTGGGAGN--AGGGAT----GTTC----TCTGTTGT 899
INTRON_3 288500 TCAGGTTCAGCCTTAGTCTTAGATTGGCATTGTGTCTCTGGGTCTTAGAG 288549
i v i i iiv vi ivi i i ii
C L1MCc_5end#LI 898 CCTGGTCCAGCCTCAGTCTTAGGCAGGCCCTGTGCGCCTGGGCCTCAGGA 849
INTRON_3 288550 GTGGGGCTTTCTC 288562
C L1MCc_5end#LI 848 GTGGGGCTTTCTC 836
Matrix = 20p37g.matrix
Transitions / transversions = 2.70 (62 / 23)
Gap_init rate = 0.03 (9 / 345), avg. gap size = 3.11 (28 / 9)
+ 740 30.4 6.7 9.9 INTRON_3 288828 289305 (110876) C L1MCc LINE/L1 (5943) 480 17 381
ANNOTATION EVIDENCE:
740 30.43 6.69 9.91 INTRON_3 288828 289305 110876 C L1MCc_5end LINE/L1 17 480 1056 707
INTRON_3 288828 CACCCCCATTTCCAGGCCTGAACCACCAAGGGCAGCTCTCCTTGGTCTTC 288877
i --- v v vi ? ii ivi i i ii i
C L1MCc_5end#LI 480 CACCTCC---TGCATGCCTGTGCCMCTGAGGAGGGCTTTCTTCAGTCTCC 434
INTRON_3 288878 TGCCTTGTCTCCCTCCTCTCTATCCACAATCCCCACACACCCAATCATTT 288927
i i ------------------------------ i v i
C L1MCc_5end#LI 433 TGCCCTGCC------------------------------CCCAGTCTTTC 414
INTRON_3 288928 TAAAGCGTGCCCAGTG-AGATTTAGGGATAAGAACCTGTGAGTAAATGCA 288976
v v v ii ii - iiii v v i i ii i i
C L1MCc_5end#LI 413 TCATGAGCACCTGGTGGAGGCCCATGGAAAAGAGCTTGCAAGTGAGTGCA 364
INTRON_3 288977 AAACTCTTTTGTGTGTGAGACTCCCAGGTGTTCTATACACTCATACTAGT 289026
vi ii v i i v - v vv? i i
C L1MCc_5end#LI 363 AACTTCCCTTGTGTCTGGGGCTCCCAGCT-TTCTAAACTGSCACACTAGC 315
INTRON_3 289027 CCATACTCCACCTTTTGCAATATGTTGGACCTCTTAGCTGA---GTTCTT 289073
i ivi viv v i ii vi - ---v
C L1MCc_5end#LI 314 CCACACTTGGCCTTTAAGAATTTATTAAAATT-TTAGCTGATTTCTTCTT 266
INTRON_3 289074 ACCAGCTTGTATGGTGCTTGGCATCACCTGGTCCCATTTTCTGC---AAG 289120
v v --- v i v i vv i vi --- i
C L1MCc_5end#LI 265 ACCTGCTTTTATGGTG---GCCACCTCTTCCTCCTATGCTCTGCCAAAGG 219
INTRON_3 289121 TG---CAG-----GTATTTCTTCTCTTTTTGGAGGTGCCTGTC----TGT 289158
--- ----- i iiiv ? ii v i ---- v
C L1MCc_5end#LI 218 TGAAACAGTTCRTGTGTCCTGTYTCTCCTTGGAGGGGCTTGTCACTCTTT 169
INTRON_3 289159 AGAATTCATGCTAGTTGGTTGCCCTGAGATTTTTTAACTTTCTCTGACGG 289208
i vvi v i v ii i-- i -- i
C L1MCc_5end#LI 168 GGAATTCAGTTTACTTGGTTGCCTTGTGACCTC--AGCT--CTCTGATGG 123
INTRON_3 289209 GATCTAGA---------TCCTGTAAATTATCT---TCTAAATTTTCTTGT 289246
v v --------- ii i --- i --- ?i
C L1MCc_5end#LI 122 GCTCAAGAAAAGTATRATTTTGTAGATTATCTGGCTTT---TTTTCTYAT 76
INTRON_3 289247 CATTAAGGTGACAGTGAAGTTCT-TTATAGCTTCCCGTATCCTAAGTAAA 289295
ii i i iv ii vi - i i i iii ii
C L1MCc_5end#LI 75 TGTTAGGATGGGAGCAATATTCTYTTGTGGCTTTCTACATCCTAAGTGGA 26
INTRON_3 289296 GGTCAAAACT 289305
i - i
C L1MCc_5end#LI 25 AGT-AGAACT 17
Matrix = 20p37g.matrix
Transitions / transversions = 2.17 (87 / 40)
Gap_init rate = 0.04 (18 / 477), avg. gap size = 4.33 (78 / 18)
+ 220 28.4 10.4 9.9 INTRON_3 289463 289693 (110488) + L2c LINE/L2 3149 3380 (7) 382
ANNOTATION EVIDENCE:
220 28.35 10.39 9.91 INTRON_3 289463 289693 110488 + L2c_3end LINE/L2 240 471 7 653
INTRON_3 289463 GTTTTTCTTG-CCCATCA--GCTAGTAGTGAGTGCCCTCTCTCTTAGTGC 289509
ii i i - vi --? v- ii - vv iv
L2c_3end#LINE 240 GCCTTCCCTGACCCCCCAAGNCTAGTC-TAGGTGCCCTC-CTCTGTGCTC 287
INTRON_3 289510 CCATGG-ATCCTGATTTTCATGTTTCTCAATATGTTACTTA-CAT----- 289552
i - i --- ii ii i - v ivi - -----
L2c_3end#LINE 288 CCATAGCACCCTG---TCTATACTCC-CATTATAGCACTTATCATTAACT 333
INTRON_3 289553 ---GTTATA--TGTC------CTTTTCTTTTCTCTCTACCAGAATTTCAA 289591
---i i -- ------ ? v v iii i i v v v i
L2c_3end#LINE 334 TGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAG 383
INTRON_3 289592 CTCCTTGAGGGCAGCAGTTTTATCTATTATTCATATTTGTCCTTCCCCGT 289641
viiiiv i -- v v- i v -
L2c_3end#LINE 384 CTCCTTGAGGGCAGGGACCGTGTCT--TATTCATCTTTGTA-TCCCCAG- 429
INTRON_3 289642 GTCCCCCTAGCTGTTTATGTGTAGCAGTAGGTAC---ATCCATGTTTGGT 289688
--- v i ----- ii ----- ii --- vv v
L2c_3end#LINE 430 ---CACCTGGC-----ACAT-----AGTAGGCGCTCAATAAATGTTTGTT 466
INTRON_3 289689 GAATG 289693
L2c_3end#LINE 467 GAATG 471
Matrix = 25p37g.matrix
Transitions / transversions = 1.71 (36 / 21)
Gap_init rate = 0.07 (17 / 230), avg. gap size = 2.76 (47 / 17)
+ 279 19.1 7.3 0.0 INTRON_3 290307 290374 (109807) C MIRc SINE/MIR (1) 267 195 383 *
ANNOTATION EVIDENCE:
279 19.12 7.35 0.00 INTRON_3 290307 290374 109807 C MIRc SINE/MIR 195 267 1 654
INTRON_3 290307 ATAATAATGTTCCCTTTCACTTGTCTTACACTTTACAGTTTACAAAACAA 290356
ivi v i v vi i iv
C MIRc#SINE/MIR 267 ATAATAATAACCCCTTACATTTGTATAGCACTTTACAGTTTACAAAGCGC 218
INTRON_3 290357 TTTCACGTA-----TCTCATATG 290374
i ----- v
C MIRc#SINE/MIR 217 TTTCACATACATTATCTCATTTG 195
Matrix = 25p37g.matrix
Transitions / transversions = 1.17 (7 / 6)
Gap_init rate = 0.01 (1 / 67), avg. gap size = 5.00 (5 / 1)
+ 345 25.5 2.6 6.4 INTRON_3 290373 290485 (109696) C MIRb SINE/MIR (96) 172 64 384
ANNOTATION EVIDENCE:
345 25.53 2.65 6.42 INTRON_3 290373 290485 109696 C MIRb SINE/MIR 64 172 96 655
INTRON_3 290373 TGTGAGATAGTTGGGACCCTTAGTTCCATTTAACAGATAAGTAA-CTGAA 290421
i i --- v iiv vii v i v - i
C MIRb#SINE/MIR 172 TGCGAGGTAG---GTATTATTATCCCCATTTTACAGATGAGGAAACTGAG 126
INTRON_3 290422 GCTCAGAGCAAAGTCA--TGACTGGCTCAAAAGGCCACACAGTTAGTAAG 290469
-- i i -- v i -- i i
C MIRb#SINE/MIR 125 GCTCAGAG--AGGTTAAGTGACTTGCCCAA--GGTCACACAGCTAGTAAG 80
INTRON_3 290470 AAGTAGGGTTTGGGTT 290485
vi i i iiv i
C MIRb#SINE/MIR 79 TGGCAGAGCCAGGATT 64
Matrix = 25p37g.matrix
Transitions / transversions = 2.38 (19 / 8)
Gap_init rate = 0.04 (5 / 112), avg. gap size = 2.00 (10 / 5)
+ 260 31.9 0.0 1.1 INTRON_3 290693 290787 (109394) + A-rich Low_complexity 1 94 (0) 385
ANNOTATION EVIDENCE:
260 31.92 0.00 1.06 INTRON_3 290693 290787 109394 + (GAAAA)n Simple_repeat 1 94 86 748
INTRON_3 290693 GAAAAGGGACGAGATGAAAAGAAAGGGGAGGTGATAAGGAGACAAGATAA 290742
ii v i v i ii i vi vi ii v v
(GAAAA)n#Simp 1 GAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAA 50
INTRON_3 290743 AAAAGGAGAGAAAAAAGAAAATGAGAAAAAAATAAAGATAGGGAA 290787
i i i - i vi i i iv v i i
(GAAAA)n#Simp 51 GAAAAGAAA-AGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAA 94
Matrix = Unknown
Transitions / transversions = 2.33 (21 / 9)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)
+ 364 18.1 2.7 1.4 INTRON_3 291457 291529 (108652) C MER21A LTR/ERVL (0) 868 795 386
ANNOTATION EVIDENCE:
364 18.05 2.74 1.35 INTRON_3 291457 291529 108652 C MER21B LTR/ERVL 795 868 0 752
INTRON_3 291457 TGTGTAGAAAAAAAC--AAACTAGTTTCCTTCTATTCTCACACCACAACA 291504
i v -- ? iv i i ii
C MER21B#LTR/ER 868 TGTGTAGGAAAAACCCCAAANTGTTTTTCCTCTGCTCTCACACCACAACA 819
INTRON_3 291505 GTCAATACAAGAAGACTTCTGTTAC 291529
i i - ? v
C MER21B#LTR/ER 818 ATCAACACA-GAANACTTCTGTGAC 795
Matrix = 20p37g.matrix
Transitions / transversions = 2.67 (8 / 3)
Gap_init rate = 0.03 (2 / 72), avg. gap size = 1.50 (3 / 2)
+ 1652 13.2 1.1 1.9 INTRON_3 291550 291734 (108447) C MER39 LTR/ERV1 (184) 523 339 387
ANNOTATION EVIDENCE:
1652 13.23 1.15 1.92 INTRON_3 291550 291734 108447 C MER39 LTR/ERV1 339 523 184 753
INTRON_3 291550 TAGGCGTGATTGAAGCAGGGACAGCCATGTAGAAATGTAATTGGACAAAA 291599
iv - v v i
C MER39#LTR/ERV 523 TAGGTTTGAT-GAAGAATGGACAGCCATGTAGAAATGTGATTGGACAAAA 475
INTRON_3 291600 AGAGTATGATCTAATACTAATAGACTGAGTGGGGAAACCCAGCAAGGCCT 291649
i i iv
C MER39#LTR/ERV 474 GGGGTATGATCTAATGGTAATAGACTGAGTGGGGAAACCCAGCAAGGCCT 425
INTRON_3 291650 GTCTGTTCAAATTCTTCTTGGCCTCT--GTATAGCATTCTTTTCTCTTGA 291697
i -- i i i ii i
C MER39#LTR/ERV 424 GTCTGTTCAGATTCTTCTTGGCCTCTCTGTGTAGCATTCCTTCCTCCCGG 375
INTRON_3 291698 GTATGGGGCAGGGTTCATTTTGAATTGGGAGTCTTAA 291734
iii v i i v i i -
C MER39#LTR/ERV 374 GTATGGGGCAGGACCCCTTCTGGAATGAGGGTCTTA- 339
Matrix = 20p37g.matrix
Transitions / transversions = 3.17 (19 / 6)
Gap_init rate = 0.02 (3 / 184), avg. gap size = 1.33 (4 / 3)
+ 576 21.7 7.5 0.0 INTRON_3 291735 291840 (108341) + FLAM_A SINE/Alu 1 114 (28) 388
ANNOTATION EVIDENCE:
426 24.53 7.55 0.00 INTRON_3 291735 291840 108341 + FLAM_C_short_ SINE/Alu 2 115 18 636
INTRON_3 291735 GCCAGGTACAGTGATGCACCCCTG--------GCTACCTGGGAGGCTGAG 291776
i ii i iiv v -------- vvii i
FLAM_C_short_ 2 GCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG 51
INTRON_3 291777 GCCAGAGGACCACTTGAGCCCAGGAGTTAAAGAGAAGCATAGGCAACATA 291826
vi i i vi vv v i
FLAM_C_short_ 52 GCGGGAGGATCGCTTGAGCCCAGGAGTTCGAGACCAGCCTGGGCAACATA 101
INTRON_3 291827 GTGAGATCCTGTCT 291840
i i i
FLAM_C_short_ 102 GCGAGACCCCGTCT 115
Matrix = 18p37g.matrix
Transitions / transversions = 1.89 (17 / 9)
Gap_init rate = 0.01 (1 / 105), avg. gap size = 8.00 (8 / 1)
+ 1652 13.2 1.1 1.9 INTRON_3 291841 291916 (108265) C MER39 LTR/ERV1 (369) 338 264 387
ANNOTATION EVIDENCE:
1652 13.23 1.15 1.92 INTRON_3 291841 291916 108265 C MER39 LTR/ERV1 264 338 369 754
INTRON_3 291841 TATGACCTATAATCAGACAAGGTAGGTCAGAGAATT-CTTTATGGCCAGC 291889
-- iv -
C MER39#LTR/ERV 338 --TGACCTACTATCAGACAAGGTAGGTCAGAGAATTTCTTTATGGCCAGC 291
INTRON_3 291890 TCCAACACAAAAAGCTTGGGGAAGATT 291916
v ? i viv i
C MER39#LTR/ERV 290 TCCTANACAGAAAGGCGGGGGAAGGTT 264
Matrix = 20p37g.matrix
Transitions / transversions = 1.00 (4 / 4)
Gap_init rate = 0.03 (2 / 75), avg. gap size = 1.50 (3 / 2)
+ 497 15.5 17.0 10.3 INTRON_3 291897 292061 (108120) C MER21A LTR/ERVL (733) 198 24 386 *
ANNOTATION EVIDENCE:
497 15.54 16.97 10.29 INTRON_3 291897 292061 108120 C MER21A LTR/ERVL 24 198 733 755
INTRON_3 291897 CAAAAAGCTTGGGGAAGATT-----TCTGCCTTGGGCAGAAAAGGTAGCA 291941
i v v i -----i -----------
C MER21A#LTR/ER 198 CAGAAAGGTGGGAGAAGATTAGAGTCCTGCCTTGGG-----------GCA 160
INTRON_3 291942 GGTGAAAGGAGGACTGGATAAGGTCAGAG----------TGAGAGAGATT 291981
i v v ---------- i------
C MER21A#LTR/ER 159 GGTGAAAGGAGGGCAGGAGAAGGTCAGAGATTCTGTTTCTGAGG------ 116
INTRON_3 291982 CTGTTTTCTGAGACCTAAAGTGCCCCAACATT-------------GTAAT 292018
iii- i v ii ------------- i
C MER21A#LTR/ER 115 CTGCCC-CTGAGGCCTAACGCACCCCAACATTATAACAAAAGACTGTAAC 67
INTRON_3 292019 AAGGGCTATGGGAGTTATCAGCTGGGAAGGATGGATGAAAACC 292061
v ii vvi
C MER21A#LTR/ER 66 AAGGGCTATGGGAGTTATGAGCCAGGAACTGTGGATGAAAACC 24
Matrix = 20p37g.matrix
Transitions / transversions = 1.88 (15 / 8)
Gap_init rate = 0.04 (6 / 164), avg. gap size = 7.67 (46 / 6)
+ 486 4.9 0.0 0.0 INTRON_3 292064 292124 (108057) + (CA)n Simple_repeat 2 62 (0) 389
ANNOTATION EVIDENCE:
486 4.92 0.00 0.00 INTRON_3 292064 292124 108057 + (CA)n Simple_repeat 2 62 118 745
INTRON_3 292064 ACATATATACACACACACACACACACACACACACACACACACACACACAC 292113
i i i
(CA)n#Simple_ 2 ACACACACACACACACACACACACACACACACACACACACACACACACAC 51
INTRON_3 292114 ACACACACACA 292124
(CA)n#Simple_ 52 ACACACACACA 62
Matrix = Unknown
Transitions / transversions = 0.0 (3 / 0)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 2670 4.9 0.0 0.3 INTRON_3 293480 293783 (106398) C AluY SINE/Alu (8) 303 1 390
ANNOTATION EVIDENCE:
2586 4.95 0.00 0.33 INTRON_3 293480 293783 106398 C AluY SINE/Alu 1 303 8 623
INTRON_3 293480 TTTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTCACTCTGTCACCCAGG 293529
i i i
C AluY#SINE/Alu 303 TTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGG 254
INTRON_3 293530 CTGGAGTGCAGTGGCGCGATCTCCGCTCACTGCAAGCTCCACCTCCTGGG 293579
v i i
C AluY#SINE/Alu 253 CTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGG 204
INTRON_3 293580 TTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCA 293629
i
C AluY#SINE/Alu 203 TTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCG 154
INTRON_3 293630 CCTGCCACCACGCCTGGCTAATTTTTTTGTATTTTTAGTAGAGACGGGGT 293679
i i -
C AluY#SINE/Alu 153 CCCGCCACCACGCCCGGCTAATTTTTT-GTATTTTTAGTAGAGACGGGGT 105
INTRON_3 293680 TTCACCGTGTTAGCCAGGATGGTCTCCATCTCCTAACCTCGTGATCTGCC 293729
v i i
C AluY#SINE/Alu 104 TTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCC 55
INTRON_3 293730 CGCTTCGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGTGCCC 293779
i i i
C AluY#SINE/Alu 54 CGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCC 5
INTRON_3 293780 GGCC 293783
C AluY#SINE/Alu 4 GGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 6.50 (13 / 2)
Gap_init rate = 0.00 (1 / 303), avg. gap size = 1.00 (1 / 1)
+ 2375 7.9 0.7 0.0 INTRON_3 294195 294485 (105696) + AluSx SINE/Alu 1 293 (19) 391
ANNOTATION EVIDENCE:
2280 7.90 0.69 0.00 INTRON_3 294195 294485 105696 + AluSx SINE/Alu 1 293 19 624
INTRON_3 294195 GGCTGGGCGTGGTGCCTCACAGCTGTAATCCCAGCACTTTGGGAGGCTGA 294244
i i v iv i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 294245 GGCAGCTGGATCACCTGAGGTCAGGAGTTCAAGGCCAGCCTGACAAACGT 294294
i vi i i i v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
INTRON_3 294295 GGAGAAACCCCGTCTCTACTAAAAATACAAAA-TTAGCCGGGCATGGTGA 294343
v - i i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGG 150
INTRON_3 294344 CCCATGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCT 294393
v ii
AluSx#SINE/Al 151 CGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCT 200
INTRON_3 294394 TGAACCTGGGAGGCGGAGGTTGCAGTGAGCCGAGATTGCACCACTGCACT 294443
i i i
AluSx#SINE/Al 201 TGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACT 250
INTRON_3 294444 CCAGCCTGG-CGACAGAGCGAGACTCCGTCTCAAAAAAAAAAA 294485
-
AluSx#SINE/Al 251 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAA 293
Matrix = 14p37g.matrix
Transitions / transversions = 2.83 (17 / 6)
Gap_init rate = 0.01 (2 / 290), avg. gap size = 1.00 (2 / 2)
+ 338 26.8 1.1 1.1 INTRON_3 295083 295169 (105012) + MIRc SINE/MIR 80 166 (102) 392
ANNOTATION EVIDENCE:
338 26.75 1.15 1.15 INTRON_3 295083 295169 105012 + MIRc SINE/MIR 80 166 102 656
INTRON_3 295083 ATTAGATGGTTGATTTTGGACAA-TTGCTTAACCTCTTTGGACTTCAGTT 295131
i v vv ii i - ii i ii i
MIRc#SINE/MIR 80 ACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTT 129
INTRON_3 295132 TCTTCATTTTAAAAAAGGACATAGTAACTCACTGCCCT 295169
i i vv v iv i iv -
MIRc#SINE/MIR 130 TCCTCATCTGTAAAATGGGGATAATAATAC-CTGCCCT 166
Matrix = 25p37g.matrix
Transitions / transversions = 1.88 (15 / 8)
Gap_init rate = 0.02 (2 / 86), avg. gap size = 1.00 (2 / 2)
+ 220 35.1 4.5 2.2 INTRON_3 295202 295335 (104846) + L2c LINE/L2 3246 3382 (5) 393
ANNOTATION EVIDENCE:
220 35.10 4.48 2.19 INTRON_3 295202 295335 104846 + L2c_3end LINE/L2 337 473 5 657
INTRON_3 295202 ATTATAATTTTTTTTTT-----TTTGTCTTTCCCACTCGACTGTGGGCGT 295246
i v i v ----- i iii v i vi
L2c_3end#LINE 337 ATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTC 386
INTRON_3 295247 TGGAATTGCAAAGTGAAAATCTAATTCACTTGTGTAAACCTAAAGTACTT 295296
ivvi vv ii vvvivi v ii v vv i -- i i
L2c_3end#LINE 387 CTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCA--GCACCT 434
INTRON_3 295297 TCAATATAGCTGGCCCTCAACAA-TGTCTTATGAGATGAA 295335
vvv i iv v i - i vv -
L2c_3end#LINE 435 GGCACATAGTAGGCGCTCAATAAATGTTTGTTGA-ATGAA 473
Matrix = 25p37g.matrix
Transitions / transversions = 1.00 (23 / 23)
Gap_init rate = 0.03 (4 / 133), avg. gap size = 2.25 (9 / 4)
+ 2265 11.3 0.0 0.7 INTRON_3 295800 296101 (104080) C AluSx SINE/Alu (11) 301 2 394
ANNOTATION EVIDENCE:
2224 11.34 0.00 0.67 INTRON_3 295800 296101 104080 C AluSx SINE/Alu 2 301 11 625
INTRON_3 295800 TTTTTTTAATTTTTTTTTTTTTAGACAGAGTCTCAATCTGTCACCCAGGC 295849
-- v i iv i
C AluSx#SINE/Al 301 TTTTTTT--TTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGC 254
INTRON_3 295850 TGGAATGCAGTGGTGCGATCTAGGCTCACTGTAACCTCTGCCTCCCAGGT 295899
i i v i i i
C AluSx#SINE/Al 253 TGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGT 204
INTRON_3 295900 TCAAGCGATTCTCCTGCCTCAGCTTCCTGAGTAGCTGGGATTACATGCTC 295949
i i v v
C AluSx#SINE/Al 203 TCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGC 154
INTRON_3 295950 ATACCACCATGCCTGGATAATTTTGGTATTTTTAGTAGAGACGGGCTTTC 295999
iii i i v v v
C AluSx#SINE/Al 153 GCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTC 104
INTRON_3 296000 GCCATGTTAGCCAGGCTGGTCTGGAACTCCTGACCTCAGGTGATCCACCT 296049
i i v i i
C AluSx#SINE/Al 103 ACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCC 54
INTRON_3 296050 GCCTTGGTCTCCCAAAGTACTGGGATTACAGGCGTGAGCCACCACACCTG 296099
i i i i i i
C AluSx#SINE/Al 53 GCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCG 4
INTRON_3 296100 GC 296101
C AluSx#SINE/Al 3 GC 2
Matrix = 14p37g.matrix
Transitions / transversions = 2.78 (25 / 9)
Gap_init rate = 0.00 (1 / 301), avg. gap size = 2.00 (2 / 1)
+ 358 30.5 0.8 5.2 INTRON_3 296554 296674 (103507) C MER117 DNA/hAT-Charlie (0) 197 82 395
ANNOTATION EVIDENCE:
358 30.51 0.83 5.17 INTRON_3 296554 296674 103507 C MER117 DNA/hAT-Charlie 82 197 0 756
INTRON_3 296554 CAGAGGTGGCAAATAACTGCTGCATGTATCACCACTACCATTTTTCCATC 296603
i i vv vii ii ii i v ------ v
C MER117#DNA/hA 197 CAGGGATGGCAAATACGTGGCACGCGTGCCGCCACTCCC------CCCTC 154
INTRON_3 296604 CCTTGCC-ATAGCAGACATCAATAAGCTATCATGATTCTTTTTCCCACTG 296652
v - i v v v i iiv i i
C MER117#DNA/hA 153 CCGTGCCCATGGCAGACATCACTAATCGATCACGGCACTCTTTCCCGCTG 104
INTRON_3 296653 AATTTACACTTTGCCTAAGAAT 296674
iiiiiv viv v
C MER117#DNA/hA 103 AGCCCGGACGCGGCCTCAGAAT 82
Matrix = 20p37g.matrix
Transitions / transversions = 1.50 (21 / 14)
Gap_init rate = 0.02 (2 / 120), avg. gap size = 3.50 (7 / 2)
+ 776 26.2 13.7 0.8 INTRON_3 296733 296959 (103222) + MIRb SINE/MIR 11 266 (2) 396
ANNOTATION EVIDENCE:
776 26.19 13.66 0.78 INTRON_3 296733 296959 103222 + MIRb SINE/MIR 11 266 2 658
INTRON_3 296733 GCCTGGGGTAGTGGTCAAAACCATAGGCTTCAGTGTTAGGCAAATTTGAG 296782
v v i -v i v ii ii v i i ii i
MIRb#SINE/MIR 11 GCGTGGTGCAGTGG-AAAGAGCACGGGCTTTGGAGTCAGGCAGACCTGGG 59
INTRON_3 296783 TTC-AATTCCAGCTCAACCACTTATTACCTGTGT---------------- 296815
- i ii vi i v ----------------
MIRb#SINE/MIR 60 TTCGAATCCTGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCA 109
INTRON_3 296816 ---AACCTCTCT-AGCGTTAATTCCCTTCTCTATCAAATGAGGATAATAA 296861
--- - v i i i iv i v i
MIRb#SINE/MIR 110 CTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAA 159
INTRON_3 296862 TACTT-----TTAGGGTTGTTACAGACATTAAATGCGAC----CATATGA 296902
i -----vi iiiiiv v i---- i i
MIRb#SINE/MIR 160 TACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAA 209
INTRON_3 296903 AGCACTCGGCA-AATTCCTGATGCATAACAGGTGTTCAATAAATGGTAGC 296951
i ii - i v iii i ii i i i
MIRb#SINE/MIR 210 AGCGCTTAGCACAGTGCCTGGCACACAGTAAGCGCTCAATAAATGGTAGC 259
INTRON_3 296952 TACTATTA 296959
-
MIRb#SINE/MIR 260 T-CTATTA 266
Matrix = 25p37g.matrix
Transitions / transversions = 3.21 (45 / 14)
Gap_init rate = 0.04 (8 / 226), avg. gap size = 4.12 (33 / 8)
+ 809 21.2 0.0 0.0 INTRON_3 297368 297499 (102682) + FLAM_A SINE/Alu 1 132 (10) 397
ANNOTATION EVIDENCE:
648 25.76 0.00 0.00 INTRON_3 297368 297499 102682 + FLAM_C_short_ SINE/Alu 2 133 0 637
INTRON_3 297368 GCCGGGCACAGTGATGTGTACCTGTAGTCCCAGCTACTTGGAAGGCTGAG 297417
i i iiviiii i vvi i i
FLAM_C_short_ 2 GCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG 51
INTRON_3 297418 GCAAGAATATTCCTTGAGCCCAGGAGTTTGAAACTAACTTGGGCAACATA 297467
ii iv iv i i i i i
FLAM_C_short_ 52 GCGGGAGGATCGCTTGAGCCCAGGAGTTCGAGACCAGCCTGGGCAACATA 101
INTRON_3 297468 TTAAGACCCTGTATCTAAAAAAGAAGAGAAAA 297499
vii i v i i i
FLAM_C_short_ 102 GCGAGACCCCGTCTCTAAAAAAAAAAAAAAAA 133
Matrix = 18p37g.matrix
Transitions / transversions = 3.86 (27 / 7)
Gap_init rate = 0.00 (0 / 131), avg. gap size = 0.0 (0 / 0)
+ 216 15.9 0.0 4.5 INTRON_3 297555 297600 (102581) + T-rich Low_complexity 137 180 (0) 398
ANNOTATION EVIDENCE:
216 15.95 0.00 4.55 INTRON_3 297555 297600 102581 C (CAAA)n Simple_repeat 137 180 0 749
INTRON_3 297555 TTTGTTTATTTGTTTGTTTAAATATGCTTCTTTGTTTGTTGGCTTG 297600
i i-- v i v v i
C (CAAA)n#Simpl 180 TTTGTTTGTTTGTTTGTTTG--TTTGTTTGTTTGTTTGTTTGTTTG 137
Matrix = Unknown
Transitions / transversions = 1.33 (4 / 3)
Gap_init rate = 0.02 (1 / 45), avg. gap size = 2.00 (2 / 1)
+ 206 25.7 16.2 0.0 INTRON_3 297906 297979 (102202) C MIRc SINE/MIR (24) 244 159 399
ANNOTATION EVIDENCE:
206 25.68 16.22 0.00 INTRON_3 297906 297979 102202 C MIRc SINE/MIR 159 244 24 659
INTRON_3 297906 TAGAGTATTTTGC--TTTTCAAAGCACTTTCATATAAAT-A--------G 297944
v i i i -- v i i v - --------
C MIRc#SINE/MIR 244 TATAGCACTTTACAGTTTACAAAGCGCTTTCACATACATTATCTCATTTG 195
INTRON_3 297945 ATCTGAATAATAATCTCAGGAAGTAGGCAGG-CAGG 297979
ivv i i i iiiv i -
C MIRc#SINE/MIR 194 ATCCTCACAACAACCCTGTGAGGTAGGCAGGGCAGG 159
Matrix = 25p37g.matrix
Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.05 (4 / 73), avg. gap size = 3.00 (12 / 4)
+ 591 25.0 8.0 7.5 INTRON_3 298534 298784 (101397) + MARNA DNA/TcMar-Mariner 6 257 (329) 400
ANNOTATION EVIDENCE:
591 24.99 7.97 7.54 INTRON_3 298534 298784 101397 + MARNA DNA/TcMar-Mariner 6 257 329 757
INTRON_3 298534 ACACACACCAGGTGTGACTGGAAAGTAATAAGGCTCACTTACAAACAAA- 298582
ii i v iv i v i vi -
MARNA#DNA/TcM 6 ACGTATACGAGGTGTGACTATAAAGTAATGAGGCTGATTTTTAAACAAAC 55
INTRON_3 298583 ACAAGACAAGTGAACTAAGAACAGGATTTATGCATCCAATTGAGGATTGT 298632
--- -------------- i i i i v vi
MARNA#DNA/TcM 56 ACA---C--------------CAGAACTTATACGTCCAAATGAGTGTTGT 88
INTRON_3 298633 TCCACAAAGTGGTCACCATGGAAAA-TATAAA------------ATGCTG 298669
i iv i v i ii- i v ------------
MARNA#DNA/TcM 89 CCTTCAAAGTAGTCACCCTGGGAGGCTGTACACTCGTTCCAACGATGCTG 138
INTRON_3 298670 CCATTGCTCATAACATTTTTAGAATGGCTCCTTCA-AATGGCCTGTAGAG 298718
? v i i iv? i ii- v vi
MARNA#DNA/TcM 139 CCANTGCTCAAAACATTTCTGGAACTNCTCTTTTGGAATTGCCTTCAGAG 188
INTRON_3 298719 ---GTT-ATGATTCTCTCATGAAAATTTGCC-CATTACTTTATACTCACA 298763
--- - vi v vi v iv i - v
MARNA#DNA/TcM 189 CCAGTTTATGAGCCACATAAGAAAATCAGTCTCATTACTTTATAGTCACA 238
INTRON_3 298764 TGTTGGTCTTTTAACCAAAAA 298784
iv ii--i i ?
MARNA#DNA/TcM 239 CCTCA--TTTTTGACCNAAAA 257
Matrix = 20p37g.matrix
Transitions / transversions = 1.75 (35 / 20)
Gap_init rate = 0.04 (10 / 250), avg. gap size = 3.90 (39 / 10)
+ 443 31.4 1.3 3.2 INTRON_3 299390 299547 (100634) + MIRb SINE/MIR 114 268 (0) 401
ANNOTATION EVIDENCE:
443 31.39 1.27 3.23 INTRON_3 299390 299547 100634 + MIRb SINE/MIR 114 268 0 660
INTRON_3 299390 ACTACTTTGAGCTTCAGATTTCTTATCTGTAAAATGGGAATACTGCTACC 299439
iv i i v i i i v iv
MIRb#SINE/MIR 114 ACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACC 163
INTRON_3 299440 TGTTTCTCAGGATGTGTTATAAAGTTTAAATATTAGAAACGTGTATGTAA 299489
iii v i - i i i v i-- v -i i
MIRb#SINE/MIR 164 TACCTCGCAGGGT-TGTTGTGAGGATTAAATG--AGATA-ATGCATGTAA 209
INTRON_3 299490 TATAAACCAACATAATGCCTAGAACATAGTTTATATTTAATATGTGAGAG 299539
- vvivii i i i i v i vviiii i vi iv
MIRb#SINE/MIR 210 -AGCGCTTAGCACAGTGCCTGGCACACAGTAAGCGCTCAATAAATGGTAG 258
INTRON_3 299540 CT--ATCATT 299547
-- i
MIRb#SINE/MIR 259 CTCTATTATT 268
Matrix = 25p37g.matrix
Transitions / transversions = 2.20 (33 / 15)
Gap_init rate = 0.03 (5 / 157), avg. gap size = 1.40 (7 / 5)
+ 259 24.5 0.0 0.0 INTRON_3 299559 299613 (100568) C MIRc SINE/MIR (141) 127 70 399
ANNOTATION EVIDENCE:
236 34.55 0.00 0.00 INTRON_3 299559 299613 100568 C MIR3 SINE/MIR 70 124 84 662
INTRON_3 299559 CTGAAGTTCAGAGAGGCTAAGCGACTTTCCTAAGGCCATATGGCTGATTG 299608
i ii iv i v i i i ii ?ii i
C MIR3#SINE/MIR 124 CTGAGGCCCAGAGAGGTGAAGTGACTTGCCCAAGGTCACACAGCKAGTTA 75
INTRON_3 299609 ATAAC 299613
i ii
C MIR3#SINE/MIR 74 GTGGC 70
Matrix = 25p37g.matrix
Transitions / transversions = 8.00 (16 / 2)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0)
259 22.22 0.00 0.00 INTRON_3 299559 299603 100578 C MIRc SINE/MIR 83 127 141 661
INTRON_3 299559 CTGAAGTTCAGAGAGGCTAAGCGACTTTCCTAAGGCCATATGGCT 299603
i i i i v i i i ii
C MIRc#SINE/MIR 127 CTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCT 83
Matrix = 25p37g.matrix
Transitions / transversions = 9.00 (9 / 1)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
+ 663 18.1 3.1 0.0 INTRON_3 300036 300162 (100019) C MIR3 SINE/MIR (11) 197 67 402
ANNOTATION EVIDENCE:
663 18.11 3.15 0.00 INTRON_3 300036 300162 100019 C MIR3 SINE/MIR 67 197 11 663
INTRON_3 300036 TCAGAAAATACCAAAGCTGGAAGAGACCTCAGAGATCATGTACTCCA-CT 300084
v i ii i i i v v - i
C MIR3#SINE/MIR 197 TCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTAGTCCAACC 148
INTRON_3 300085 TCCTCAGTTTGCTGGTGAGGAAACTTAGGCCCAGAGAGGGTAAGTGACTT 300134
i v i v i v vv
C MIR3#SINE/MIR 147 CCCTCATTTTACAGATGAGGAAACTGAGGCCCAGAGAGGTGAAGTGACTT 98
INTRON_3 300135 GCCCAAGGCCACATAGC---TTAGAAGTAGA 300162
i i --- vi i
C MIR3#SINE/MIR 97 GCCCAAGGTCACACAGCKAGTTAGTGGCAGA 67
Matrix = 25p37g.matrix
Transitions / transversions = 1.56 (14 / 9)
Gap_init rate = 0.02 (2 / 126), avg. gap size = 2.00 (4 / 2)
+ 2020 9.5 0.3 2.0 INTRON_3 300902 301202 (98979) + L1PA13 LINE/L1 5864 6159 (4) 403
ANNOTATION EVIDENCE:
2020 9.49 0.33 2.03 INTRON_3 300902 301202 98979 + L1PA13_3end LINE/L1 611 906 4 647
INTRON_3 300902 CTATTAACCTTAGGAAACTAACATAGGAACAGAGAACCAAATACTGCATG 300951
i v v ii i i
L1PA13_3end#L 611 CCATTATCCTTAGCAAACTAACGCAGGAACAGAAAACCAAATACCGCATG 660
INTRON_3 300952 TTTTCACTTATAAGTGGGAGCTAAATGATGAGAACGCATGGACACATAGA 301001
i i
L1PA13_3end#L 661 TTCTCACTTATAAGTGGGAGCTAAATGATGAGAACACATGGACACATAGA 710
INTRON_3 301002 GGGAAACAACAGACACTGGGGCCTATCGGAGGGTGGAGGGTGGGAGGAGG 301051
i v i
L1PA13_3end#L 711 GGGGAACAACACACACTGGGGCCTATTGGAGGGTGGAGGGTGGGAGGAGG 760
INTRON_3 301052 AGGAGGAAGAGTATCAGGAAAAATAACTAATGGGTAGTAGGCTTAATACC 301101
ii ------ v
L1PA13_3end#L 761 GAGAGGA------TCAGGAAAAATAACTAATGGGTACTAGGCTTAATACC 804
INTRON_3 301102 CGGGTGATGAAATAATCTGTATCACAAACCCCCATGACACA-GTTTACCT 301150
i iv -
L1PA13_3end#L 805 TGGGTGATGAAATAATCTGTACAACAAACCCCCATGACACAAGTTTACCT 854
INTRON_3 301151 GTATAACAAACGTGAATATGTACCCCTGAACTTAGAAGTTAAATTAAAAA 301200
i i v v i i vvv i
L1PA13_3end#L 855 ATGTAACAAACCTGCACATGTACCCCTGAACTTAAAATAAAAGTTAAAAA 904
INTRON_3 301201 AA 301202
L1PA13_3end#L 905 AA 906
Matrix = 18p37g.matrix
Transitions / transversions = 1.80 (18 / 10)
Gap_init rate = 0.01 (2 / 300), avg. gap size = 3.50 (7 / 2)
+ 2649 16.4 2.9 0.2 INTRON_3 301204 301684 (98497) + L1MC1 LINE/L1 5817 6310 (23) 404
ANNOTATION EVIDENCE:
2649 16.45 2.91 0.20 INTRON_3 301204 301684 98497 + L1MC1_3end LINE/L1 564 1057 23 708
INTRON_3 301204 AAGAAGTGAGCTATCAAGCCACGAAAAGA-ATGGAGGAAACATAAATGTA 301252
i i - v i
L1MC1_3end#LI 564 AAGAAATGAGCTATCAAGCCATGAAAAGACATGGAGGAAACTTAAATGCA 613
INTRON_3 301253 TACTACTGAGTGAAAGAAGCCTGTGTGAAAAGACTGCATACCATATGATT 301302
i i vi v i i ii
L1MC1_3end#LI 614 TATTACTAAGTGAAAGAAGCCAATCTGAAAAGGCTACATACTGTATGATT 663
INTRON_3 301303 -------TATGGCATTCTGGAAAAGGCAAAAGTATGGAGACAGTAAAAAG 301345
------- i v
L1MC1_3end#LI 664 CCAACTATATGACATTCTGGAAAAGGCAAAACTATGGAGACAGTAAAAAG 713
INTRON_3 301346 A-CAGTGGTTGCCAAGGGTTAGGGTGGGAGGGAGTGACAAGTGGGTGGTG 301394
- i i - v ii iii v
L1MC1_3end#LI 714 ATCAGTGGTTGCCAGGGGTTGGGG-GGGAGGGAGGGATGAACAGGTGGAG 762
INTRON_3 301395 AACAGAGGACTTTTAGGGAAGAGGAAATATTCTATATTAGATTATAATAG 301444
v i v v i v i i v v i i
L1MC1_3end#LI 763 CACAGAGGATTTTTAGGGCAGTGAAACTACTCTGTATGATACTATAATGG 812
INTRON_3 301445 TAGATGCATGTCATTATACAGTTTTCCAAACTTACAGAATGTACTACACG 301494
i i v v ii i v v
L1MC1_3end#LI 813 TGGATACATGTCATTATACATTTGTCCAAACCCATAGAATGTACAACACC 862
INTRON_3 301495 AAGAGTGAACCCTAAGGTAAACCATGGACTTTGGGTGACAATGATA-ATC 301543
v i i i-i
L1MC1_3end#LI 863 AAGAGTGAACCCTAATGTAAACTATGGACTTTGGGTGATAATGATGTGTC 912
INTRON_3 301544 AATGTAGGTTCATCAG----AAGAAATGTACCACTCTGGTGGGAGATGCT 301589
ii---- v i i
L1MC1_3end#LI 913 AATGTAGGTTCATCGATTGTAACAAATGTACCACTCTGGTGGGGGATGTT 962
INTRON_3 301590 GGTAACAGAGGAGACTATGCATGTGCAGGGACAGGGCATATATAGGAAAT 301639
i iii i i i ii i vi i
L1MC1_3end#LI 963 GATAGTGGGGGAGGCTGTGCATGTGTGGGGGCAGGGGGTATATGGGAAAT 1012
INTRON_3 301640 CTGTGGAACTTGCTCTCTATTTTGCTGTGGGTCCAAAACTGCTTT 301684
v v v v v v iii i i
L1MC1_3end#LI 1013 CTCTGTACCTTCCGCTCAATTTTGCTGTGAACCTAAAACTGCTCT 1057
Matrix = 20p37g.matrix
Transitions / transversions = 2.16 (54 / 25)
Gap_init rate = 0.01 (6 / 480), avg. gap size = 2.50 (15 / 6)
+ 365 14.0 0.0 0.0 INTRON_3 302046 302102 (98079) + L1MC1 LINE/L1 6053 6109 (224) 405
ANNOTATION EVIDENCE:
365 14.04 0.00 0.00 INTRON_3 302046 302102 98079 + L1MC1_3end LINE/L1 800 856 224 709
INTRON_3 302046 GAAATTACAATAGTGGATGCATGTCATTATACAATTGTCCAAACTTATAG 302095
v i i i i v ii
L1MC1_3end#LI 800 GATACTATAATGGTGGATACATGTCATTATACATTTGTCCAAACCCATAG 849
INTRON_3 302096 AATGTAC 302102
L1MC1_3end#LI 850 AATGTAC 856
Matrix = 20p37g.matrix
Transitions / transversions = 3.00 (6 / 2)
Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0)
+ 2449 6.4 1.0 0.3 INTRON_3 302135 302429 (97752) + AluSc8 SINE/Alu 1 297 (15) 406
ANNOTATION EVIDENCE:
2278 7.83 1.36 0.34 INTRON_3 302135 302429 97752 + AluSx SINE/Alu 1 298 14 626
INTRON_3 302135 GGCCGGGTGCGGTGGC--ACGCCTGTAATCCCTGCACTTTGGGAGGCTGA 302182
i -- v i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 302183 GGCAGGCGGATCAC--GAGGTCAGGAGATCGAGACCATCCTGGCTAACAT 302230
i -- v v i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACAT 100
INTRON_3 302231 GGTGAAACCCCGTCTCTACTAAAAAATACAAAACTTAGCTGGGCGTGGTG 302280
- v i
AluSx#SINE/Al 101 GGTGAAACCCCGTCTCTACTAAAAA-TACAAAAATTAGCCGGGCGTGGTG 149
INTRON_3 302281 GCACACGCCTGTAGTCCCAGCTACTCTGGAGGCTGAGGCAGGAGAATTGC 302330
i i i v i
AluSx#SINE/Al 150 GCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGC 199
INTRON_3 302331 TTGAACCCGGGAGGCAGAAGTTGCAGCGAGTTGAGATCGTGCCACTGCAC 302380
i i i ii i
AluSx#SINE/Al 200 TTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCAC 249
INTRON_3 302381 TCCAGCCTGGGTGACAGAGCAAGACTTCGTCTCAAAAAAAAAAAAAAAA 302429
i i i
AluSx#SINE/Al 250 TCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAA 298
Matrix = 14p37g.matrix
Transitions / transversions = 3.60 (18 / 5)
Gap_init rate = 0.01 (3 / 294), avg. gap size = 1.67 (5 / 3)
+ 192 23.5 0.0 9.3 INTRON_3 302444 302490 (97691) C L2a LINE/L2 (93) 3333 3291 407
ANNOTATION EVIDENCE:
192 23.46 0.00 9.30 INTRON_3 302444 302490 97691 C L2a_3end LINE/L2 382 424 93 664
INTRON_3 302444 AATCCCTGCAGAAAGTCATGAAATTTACATTCCACTGGGGGAAGATA 302490
i vv---- i ii i v i i
C L2a_3end#LINE 424 AGTCCCTGCCC----TCATGGAGCTTACATTCTAGTGGGGGGAGACA 382
Matrix = 25p37g.matrix
Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.02 (1 / 46), avg. gap size = 4.00 (4 / 1)
+ 450 27.6 4.7 10.2 INTRON_3 302649 302967 (97214) + L1ME3F LINE/L1 5822 6124 (119) 408
ANNOTATION EVIDENCE:
450 27.58 4.70 10.23 INTRON_3 302649 302967 97214 + L1ME3F_3end LINE/L1 569 871 119 710
INTRON_3 302649 ATGCATTATAGCTACATAGAA--GTAAGGATGAATTTTAGCAA--TACTA 302694
v i i iiv --ii v i v -- v
L1ME3F_3end#L 569 ATGAACTACAGCTACACGCAACAACATGGATGAATCTTAGAAACATAATA 618
INTRON_3 302695 TTGAGTGAAAAAGTTAAGTTCCGGAAGATTACTTACAGTGTGAGGGTTAA 302744
ivi i? i i v i -------
L1ME3F_3end#L 619 TTGAGTGAAAAAAGCAAGTCNCAGAAGACTACATACAGTATGA------- 661
INTRON_3 302745 AAAGTCAAGATACCTTTTTTTAATAAAGCT-AAATACAAATAAAGCTTAA 302793
---------- v -- i - v ii i v
L1ME3F_3end#L 662 ----------TACCATTTTT--ATAAAGTTCAAAAACAAGCAAAACTAAA 699
INTRON_3 302794 AAATGT-TTATTTTAGGA-ACATAGGTATG--ATCAAACTGTATTTTTTA 302839
v i - i vi - vi -- v i ------
L1ME3F_3end#L 700 CAATATATTGTTTAGGGATACATACATATGTGATAAAACTATA------A 743
INTRON_3 302840 AAAACACCAAAGGAATCCTAAA----GGACT-GGGATAATAGTGGCCTCT 302884
? v v i vv ----ii i -i i i vi
L1ME3F_3end#L 744 ANAAAAGCAAGGGAATGATAAACACAAAATTCAGGATAGTGGTTACCTCT 793
INTRON_3 302885 GAATAACAACTATCAGAGAGGTGGAGTGAAGGAATGTGGAAGAACCATAT 302934
iiviivii----- i i v i - v i iv i v i
L1ME3F_3end#L 794 GGGGGGGGG-----AGGGAAGAGGGG-GATGGGATAGGGAAGGAGCACAT 837
INTRON_3 302935 AGGTAAATGTGT-GCTATTGTAAGTATTATAGTT 302967
i iv- ? vv i i v
L1ME3F_3end#L 838 AGGTAGATGTAAAGNTATTGGTAATGTTCTAGTT 871
Matrix = 20p37g.matrix
Transitions / transversions = 1.62 (47 / 29)
Gap_init rate = 0.04 (14 / 318), avg. gap size = 3.29 (46 / 14)
+ 1777 12.9 0.4 0.8 INTRON_3 302969 303223 (96958) C AluSz6 SINE/Alu (19) 293 40 409
ANNOTATION EVIDENCE:
1634 13.84 0.39 0.79 INTRON_3 302969 303223 96958 C AluSx SINE/Alu 40 293 19 627
INTRON_3 302969 TTTTTGTTGTTGAGACAGCGTCTCTTGCTCTGCCGCCCAGGCTGGA-TGC 303017
v v i v -- i -
C AluSx#SINE/Al 293 TTTTTTTTTTTGAGACGGAGTCTC--GCTCTGTCGCCCAGGCTGGAGTGC 246
INTRON_3 303018 AGTGGTGTGATCTCGGTTCACTGTAACCTCCGCCTCCAGGGTTCAAGCGA 303067
i i i i v
C AluSx#SINE/Al 245 AGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGA 196
INTRON_3 303068 TTCTCATGCCTCAGCCTCCCAAGTAGCCATGATTACAGGCCTGCACTACC 303117
v i iiv vi i i
C AluSx#SINE/Al 195 TTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACC 146
INTRON_3 303118 AGGCTTAGCTAATATTTGTATTTTTAGTAGAGATGGGGTTTCTCCATGTT 303167
v iii v i v
C AluSx#SINE/Al 145 ACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTT 96
INTRON_3 303168 GGCCAGGCCAGTCTCCAACTCCTGGCTTCAAGTGATTCGCCCCCCTTGGC 303217
ii v i i i i v i
C AluSx#SINE/Al 95 GGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGC 46
INTRON_3 303218 CTCCCA 303223
C AluSx#SINE/Al 45 CTCCCA 40
Matrix = 14p37g.matrix
Transitions / transversions = 1.92 (23 / 12)
Gap_init rate = 0.01 (2 / 254), avg. gap size = 1.50 (3 / 2)
+ 221 30.8 2.8 1.9 INTRON_3 303390 303495 (96686) C L3 LINE/CR1 (304) 4185 4079 410 *
ANNOTATION EVIDENCE:
221 30.77 2.83 1.87 INTRON_3 303390 303495 96686 C L3 LINE/CR1 4079 4185 304 665
INTRON_3 303390 TGACAGTCCTTTAAATAGTAAAATCTGGCTAACATGACTTGCTTTTATTT 303439
i i v vi vvii v v i- i v v i
C L3#LINE/CR1 4185 TGACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTC-CTCTAAGTC 4137
INTRON_3 303440 TTTTAGT-TCCAGGCTAAAAATGCT-AATTTCTTTATATCATTT-TCATG 303486
i vv - v v i- i i i - i i i- i
C L3#LINE/CR1 4136 TTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCA-ACCGTTCCTCATA 4088
INTRON_3 303487 TATCTTGGT 303495
iv v
C L3#LINE/CR1 4087 TGACATGGT 4079
Matrix = 25p37g.matrix
Transitions / transversions = 1.29 (18 / 14)
Gap_init rate = 0.05 (5 / 105), avg. gap size = 1.00 (5 / 5)
+ 603 33.8 5.0 2.7 INTRON_3 303490 303890 (96291) + L2c LINE/L2 2442 2851 (568) 411
ANNOTATION EVIDENCE:
603 33.83 4.99 2.68 INTRON_3 303490 303890 96291 + L2 LINE/L2 2442 2851 231 666
INTRON_3 303490 CTTGGTATGACTAAAACTTGACTTATTTTCTTCCCATTC---TTTTCTTC 303536
iii v i vi iv vv vi ---ii v i
L2#LINE/L2 2442 CTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCC 2491
INTRON_3 303537 TCCA------TTTCATGTTTCAGCTGATGACG-CTATACTCCTCTGAGCC 303579
v------ i vii i i i i i- vi - iiv ii
L2#LINE/L2 2492 TCCCACAGTCTTCCCCATCTCAGTTAATGGCAACTCCA-TCCTTCCAGTT 2540
INTRON_3 303580 ACTAAGGCATGAGAATTTGGAATCATCTCTGAATCCCTCCTCATTTTTTG 303629
i v vvi i vi i ii ---- vi i v
L2#LINE/L2 2541 GCTCAGGCCAAAAACCTTGGAGTCATCCTTGA----CTCCTCTCTTTCTC 2586
INTRON_3 303630 TCTCTTCCCA-ATCCAATCAGTTTTCAAGCCCTGCGGAGTCTATCTCTG- 303677
v vi - vi ivv ii iv iv i iii-
L2#LINE/L2 2587 TCACACCCCACATCCAATCCATCAGCAAATCCTGTTGGCTCTACCTTCAA 2636
INTRON_3 303678 --CTTTTCCCGCTTCC--CTGCTGTCTTCTCTGTTCCCACTGTCATCACC 303723
--iv v v vv -- ii - - v iiiii i i
L2#LINE/L2 2637 AATATATCCAGAATCCGACCACT-TCT-CACCACCTCCACTGCCACCACC 2684
INTRON_3 303724 CTAGTCGAAGCCCTTATTATCTCTCTTCTGCAATATTGAAATAGC-TCCC 303772
i v vii i vi v v i v - i
L2#LINE/L2 2685 CTGGTCCAAGCCACCATCATCTCTCGCCTGGATTACTGCAATAGCCTCCT 2734
INTRON_3 303773 AACTGCTGTCTCTGCTTCTAGCCTATCATCTCTCCTATCAGTTTTCCACT 303822
v v i i v vv vi i ? vi vi i v v
L2#LINE/L2 2735 AACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACA 2784
INTRON_3 303823 GTGCTGTCAGATTTATTCTTTCTTCATACTT---TCAGACTTCAAGGCAT 303869
vv v i v v i -- v v v --- -- v v i
L2#LINE/L2 2785 CAGCAGCCAGAGTGATCCTTT--TAAAACATAAGTCAGA--TCATGTCAC 2830
INTRON_3 303870 TCCTCTGTTCAAAACTTTTTA 303890
i ii ii
L2#LINE/L2 2831 TCCTCTGCTCAAAACCCTCCA 2851
Matrix = 25p37g.matrix
Transitions / transversions = 1.34 (75 / 56)
Gap_init rate = 0.04 (14 / 400), avg. gap size = 2.21 (31 / 14)
+ 331 32.9 10.9 0.0 INTRON_3 304110 304293 (95888) + MIRb SINE/MIR 19 233 (35) 412
ANNOTATION EVIDENCE:
330 34.24 16.85 0.00 INTRON_3 304110 304293 95888 + MIRc SINE/MIR 19 233 35 667
INTRON_3 304110 TGAAATGAACAATGGACATAAAA-CAAGACAACTTGAGTTCAA------- 304151
i v i v v ii i- i vi i i i -------
MIRc#SINE/MIR 19 TGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCTGG 68
INTRON_3 304152 -------AATCACCAACTATAAGGCCTTGGACAAGTCACTGAATTTCTCT 304194
------- v i i i i iv i i v ii
MIRc#SINE/MIR 69 CTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCT 118
INTRON_3 304195 AAGTCCTAATGTCCATATTTGCAAAAAAGAAA-AAT-------------C 304230
i i ii i v vi i i vi ii - -------------
MIRc#SINE/MIR 119 GAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGC 168
INTRON_3 304231 CAA--TTAAATGATTGTCATAAGGTTTAAATAAGAATGTATATTTATAAA 304278
v -- i v v i ii i v i i vvi i v iv i
MIRc#SINE/MIR 169 CTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAG 218
INTRON_3 304279 TGTTTTGTAAAATAT 304293
i i v i
MIRc#SINE/MIR 219 CGCTTTGTAAACTGT 233
Matrix = 25p37g.matrix
Transitions / transversions = 2.32 (44 / 19)
Gap_init rate = 0.03 (5 / 183), avg. gap size = 6.20 (31 / 5)
331 32.20 7.63 0.00 INTRON_3 304154 304271 95910 + MIRb SINE/MIR 81 207 61 668
INTRON_3 304154 TCACCAACTATAAGGCCTTGGACAAGTCACTGAATTTCTCTAAGTCCTAA 304203
i i i i iv i i v ii i i ii i
MIRb#SINE/MIR 81 TTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAG 130
INTRON_3 304204 TGTCCATATTTGCAAAAAAGAAA-AAT----CCAA--TTAAATGATTGTC 304246
v vi i i vi ii - ---- v -- iiv v i i
MIRb#SINE/MIR 131 TTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTT 180
INTRON_3 304247 ATAAGGTTTAAATAAGA--ATGTATAT 304271
i i v i -- i i
MIRb#SINE/MIR 181 GTGAGGATTAAATGAGATAATGCATGT 207
Matrix = 25p37g.matrix
Transitions / transversions = 3.22 (29 / 9)
Gap_init rate = 0.03 (4 / 117), avg. gap size = 2.25 (9 / 4)
+ 211 25.6 8.5 4.7 INTRON_3 304568 304649 (95532) C L2c LINE/L2 (3) 3384 3300 413
ANNOTATION EVIDENCE:
211 25.60 8.54 4.71 INTRON_3 304568 304649 95532 C L2c_3end LINE/L2 391 475 3 669
INTRON_3 304568 CATTCCTTTA-TAATCATTT---GAACACCTAGCACTGTGTTCC---TGT 304610
v i -i v --- i i --- i v --- i
C L2c_3end#LINE 475 CATTCATTCAACAAACATTTATTGAGCGCCTA---CTATGTGCCAGGTGC 429
INTRON_3 304611 GAGGAATATAAAAATGAATCAGGCTTGGTCACTTGACCT 304649
vi i i i v i vi - i v
C L2c_3end#LINE 428 TGGGGATACAAAGATGAATAAGACACGGTC-CCTGCCCT 391
Matrix = 25p37g.matrix
Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.06 (5 / 81), avg. gap size = 2.20 (11 / 5)
+ 187 31.4 14.9 1.0 INTRON_3 304653 304739 (95442) + L2c LINE/L2 3238 3336 (51) 411
ANNOTATION EVIDENCE:
187 31.35 14.94 1.01 INTRON_3 304653 304739 95442 + L2c_3end LINE/L2 329 427 51 670
INTRON_3 304653 TACCTTTTATTCTAACTATTTATGTGTATCTCCTATTTCTCCTACTAAAT 304702
v v v i i i i v ii? v - i i ii i i i
L2c_3end#LINE 329 TAACTTGTATTGTAATTGTCTGTTTACNTGTC-TGTCTCCTCCACTAGAC 377
INTRON_3 304703 TGTGAGGATTTGGAGGACTGG-------------TTATCTTTGTATCCCC 304739
vvii v i v ------------- i
L2c_3end#LINE 378 TGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCC 427
Matrix = 25p37g.matrix
Transitions / transversions = 1.89 (17 / 9)
Gap_init rate = 0.02 (2 / 86), avg. gap size = 7.00 (14 / 2)
+ 1434 18.1 11.4 2.4 INTRON_3 305507 305777 (94404) + AluJr4 SINE/Alu 1 295 (17) 414
ANNOTATION EVIDENCE:
1273 19.34 11.81 2.71 INTRON_3 305507 305777 94404 + AluJb_short_ SINE/Alu 1 295 7 638
INTRON_3 305507 GGCCAGGTGTAGTGGCTTACGCCTGTAATCCCAGCATACTGGGAGGCCAA 305556
i i ii i ivi i
AluJb_short_# 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 305557 AGTGGGAGGATTGCTTGAAGCCAGGAGTTCAGGACCACCCTGGGCAGCAT 305606
i i ii iv ii v i
AluJb_short_# 51 GGCGGGAGGATCACTTGAGCCCAGGAGTTCGAGACCAGCCTGGGCAACAT 100
INTRON_3 305607 AGTGAGACCCCATCTCTAAAAAAAAAAAAAAGTTA-AAAAATTAGCCAGG 305655
i i i v -------- - i
AluJb_short_# 101 GGTGAAACCCCGTCTCTACAAAAAA--------TACAAAAATTAGCCGGG 142
INTRON_3 305656 CATGGTGGTGCATGCCTGTAATCACAGCTACTCGGGGGACTGATGCAGGG 305705
i i ii i v i i v i
AluJb_short_# 143 CGTGGTGGCGCGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGA 192
INTRON_3 305706 GGATCAATTGAGCCCAGTAGTTTGAGAC---------------------- 305733
iv i v v i i ----------------------
AluJb_short_# 193 GGATCGCTTGAGCCCGGGAGGTCGAGGCTGCAGTGAGCCGTGATCGCGCC 242
INTRON_3 305734 ---------CAGCTTGGGCAATATGATGAGACCCCATCTAAAAAAAAAAA 305774
--------- i i i viii ii v
AluJb_short_# 243 ACTGCACTCCAGCCTGGGCGACAGAGCGAGACCCTGTCTCAAAAAAAAAA 292
INTRON_3 305775 AAA 305777
AluJb_short_# 293 AAA 295
Matrix = 18p37g.matrix
Transitions / transversions = 3.64 (40 / 11)
Gap_init rate = 0.01 (3 / 270), avg. gap size = 13.33 (40 / 3)
+ 754 30.5 1.5 0.5 INTRON_3 305864 306064 (94117) C MIRb SINE/MIR (31) 237 35 415
ANNOTATION EVIDENCE:
754 30.50 1.49 0.49 INTRON_3 305864 306064 94117 C MIRb SINE/MIR 35 237 31 671
INTRON_3 305864 CTATGTGCCAGGCTCTCTGTACATTATTATTATATTTAATAT---AGTCA 305910
i v v ivv viii - i vi v --- v i
C MIRb#SINE/MIR 237 CTGTGTGCCAGGCACTGTGCTAAGCGCT-TTACATGCATTATCTCATTTA 189
INTRON_3 305911 ATCTTTACAATAAGCAGGTGAGATACATACTATTATCTACATCTTACAGA 305960
i i i v vv i i vi i iv i
C MIRb#SINE/MIR 188 ATCCTCACAACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGA 139
INTRON_3 305961 TTAGGTGACTGAGGTTCAAAGAGATAAATTAATTTGTCTATGGTTATACA 306010
v vi i i i v v i i i i v i i
C MIRb#SINE/MIR 138 TGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACTTGCCCAAGGTCACACA 89
INTRON_3 306011 ACCAGTAAGCTGTGGAGTTGGGATTTAAACACAGGTCTGCCTGATTCACA 306060
i i iv ii iii ii v i vv
C MIRb#SINE/MIR 88 GCTAGTAAGTGGCAGAGCCAGGATTCGAACCCAGGTCTGCCTGACTCCAA 39
INTRON_3 306061 AGTC 306064
i
C MIRb#SINE/MIR 38 AGCC 35
Matrix = 25p37g.matrix
Transitions / transversions = 1.77 (39 / 22)
Gap_init rate = 0.01 (2 / 200), avg. gap size = 2.00 (4 / 2)
+ 352 20.2 8.1 6.2 INTRON_3 306314 306347 (93834) C L1ME3C LINE/L1 (0) 6123 6088 416
ANNOTATION EVIDENCE:
352 20.17 8.11 6.19 INTRON_3 306314 306347 93834 C L1ME3C_3end LINE/L1 835 870 0 711
INTRON_3 306314 TTTTTAAG---CAAAACCGCACAGATATACTTGGAGG 306347
---i vvi i v i -
C L1ME3C_3end#L 870 TTTTTAAGAAATAAAACATTACAGATACAGTTGAAG- 835
Matrix = 20p37g.matrix
Transitions / transversions = 1.33 (4 / 3)
Gap_init rate = 0.06 (2 / 33), avg. gap size = 2.00 (4 / 2)
+ 2616 5.4 0.0 0.0 INTRON_3 306348 306645 (93536) C AluY SINE/Alu (13) 298 1 417
ANNOTATION EVIDENCE:
2499 5.37 0.00 0.00 INTRON_3 306348 306645 93536 C AluY SINE/Alu 1 298 13 628
INTRON_3 306348 TTTCTTTTTTTTTTTTTGAGATGGAGTCTCGCTCTGTCGCCCAGGCTGGA 306397
i i
C AluY#SINE/Alu 298 TTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGA 249
INTRON_3 306398 GTGCAGTGGCACGATCTCGGCTCACTGTAAGCTCCGCCTCTTGGGTTCAC 306447
i i ii
C AluY#SINE/Alu 248 GTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCAC 199
INTRON_3 306448 GCCATTCTGCTGCCTCAGCCTCCCCAGCAGCTGGGACTGCAGGCGCCCGC 306497
v v i i
C AluY#SINE/Alu 198 GCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGC 149
INTRON_3 306498 CACCACGCCCGGCTAATTTTTTTTATTTTTAGTAGAGACGGAGTTTCACC 306547
v i
C AluY#SINE/Alu 148 CACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACC 99
INTRON_3 306548 GTGTTAGGCAGAATGGTCTCGATCTGCTGACCTCGTGATCCGCCCGCCTC 306597
v i v
C AluY#SINE/Alu 98 GTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTC 49
INTRON_3 306598 GGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCCGGCC 306645
i
C AluY#SINE/Alu 48 GGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 2.20 (11 / 5)
Gap_init rate = 0.00 (0 / 297), avg. gap size = 0.0 (0 / 0)
+ 352 20.2 8.1 6.2 INTRON_3 306646 306721 (93460) C L1ME3C LINE/L1 (36) 6087 6011 416
ANNOTATION EVIDENCE:
352 20.17 8.11 6.19 INTRON_3 306646 306721 93460 C L1ME3C_3end LINE/L1 758 834 36 712
INTRON_3 306646 GGAGGTTTCTT-TGTATTCCTCTTAGATCCCATTTCTT---CTCTCTCCT 306691
----- ii i - i iiv i i --- i i
C L1ME3C_3end#L 834 -----TCCCCTGTGTACTCCTCCCCGATCCCATTCCCTTCCCTCCCTCCC 790
INTRON_3 306692 --GAGGTAACCACAATCCTGATTTTGGTATTT 306721
-- v v i
C L1ME3C_3end#L 789 CAGAGGTAACCACTATCCTGAATTTGGTGTTT 758
Matrix = 20p37g.matrix
Transitions / transversions = 3.67 (11 / 3)
Gap_init rate = 0.05 (4 / 75), avg. gap size = 2.75 (11 / 4)
+ 459 29.9 10.5 1.4 INTRON_3 306766 306965 (93216) + MamRep488 DNA/hAT-Tip100 1 218 (1) 418
ANNOTATION EVIDENCE:
459 29.91 10.50 1.38 INTRON_3 306766 306965 93216 + MamRep488 DNA/hAT-Tip100 1 218 1 758
INTRON_3 306766 CAGTAATAGTTCCAAGGGGTGAAATTAGATGGCAACTTTAGC---ACCTT 306812
iiii iv iv- i iv --i ---v i
MamRep488#DNA 1 CAGTGGCGGCGCCAAGGGGTGGC-TTGGGGGG--GCTTTAGCTCCCCCTC 47
INTRON_3 306813 CCATATTTTTC-TGATGCCTGCCCCATTCTTTGAAATAGACAACTGTCAT 306861
v i i - v vv iv v i i v i
MamRep488#DNA 48 CCATAATCTCCATCAGCCCCCCCCCATTCTTTGATATGGACAATTGACGT 97
INTRON_3 306862 TTT-TCTACCTTATATAAAGTACACTATAAATGCTGTTT-AAG------- 306902
- v i i i vv ii i v i - -------
MamRep488#DNA 98 TTTCTCAATCTTATGTAAAGTGCTATGCAAACGCAGCTTCAAGACAAGTC 147
INTRON_3 306903 -------CTCCCATTCTAATTAGTTTACTGCCTCTAAGTCTCTCC-ACAC 306944
------- i v i ii v i i i i i - i i
MamRep488#DNA 148 CCCTAGCCCCCCCTTCCAACCAGATTGCCGCCCCTAAGCCCCTCCTATAT 197
INTRON_3 306945 AAAATCTTTTGGGTCACCACT 306965
i vi i v i i i
MamRep488#DNA 198 AGAAATTCTGGAGCCGCCACT 218
Matrix = 20p37g.matrix
Transitions / transversions = 2.11 (40 / 19)
Gap_init rate = 0.04 (8 / 199), avg. gap size = 3.00 (24 / 8)
+ 968 25.5 2.6 7.4 INTRON_3 307041 307164 (93017) + MLT2C1 LTR/ERVL 1 124 (273) 419
ANNOTATION EVIDENCE:
968 25.49 2.65 7.41 INTRON_3 307041 307164 93017 + MLT2C1 LTR/ERVL 1 124 273 759
INTRON_3 307041 TGTGATGGT--ATTTCTGATGTGTCAACTTGAATAGGTTAAAGTCCTCAG 307088
-- i-- iv i v v i
MLT2C1#LTR/ER 1 TGTGATGGTTAATTTT--ATGTGTCAACTTGGCTAGGCTATAGTACCCAG 48
INTRON_3 307089 CTATTTAATCACAATCCAATCTAGGTATTGCTATGAAGATGTTTTTTACA 307138
i i v vv i i i i i v v
MLT2C1#LTR/ER 49 TTATTTAGTCAAACACTAATCTAGGTGTTGCTGTGAAGGTATTTTGTAGA 98
INTRON_3 307139 TGTGATTAAAGATTATAATCAGTTTA 307164
i viv i v
MLT2C1#LTR/ER 99 TGTGGTTAACATTTACAATCAGTTGA 124
Matrix = 20p37g.matrix
Transitions / transversions = 1.27 (14 / 11)
Gap_init rate = 0.02 (2 / 123), avg. gap size = 2.00 (4 / 2)
+ 2259 11.4 0.0 1.9 INTRON_3 307165 307479 (92702) C AluSg SINE/Alu (1) 309 1 420
ANNOTATION EVIDENCE:
2131 11.33 0.63 1.93 INTRON_3 307165 307479 92702 C AluSx SINE/Alu 1 311 1 629
INTRON_3 307165 TTTATTTATTTGTTTGTTTGTTTGTTTTTGAGACAGAGTCTCGCTCTGTT 307214
v v v v v v i i
C AluSx#SINE/Al 311 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTC 262
INTRON_3 307215 GCCCAGGCTAGAGTGCAGTGGCACCGTCTCAGCTCACTGCTACCTCTGCC 307264
i i vi i v i
C AluSx#SINE/Al 261 GCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
INTRON_3 307265 TCCCGGGTCCCAGTTCAAGCAATTCTCCCTCCTCAGCCTCCCGAGTAGCT 307314
------ i iv
C AluSx#SINE/Al 211 TCCCGGGT------TCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCT 168
INTRON_3 307315 GGGATTACAGGCATACGCCACCATGCCCAGCTAATTTTTGTATTTTTAGT 307364
iii i i
C AluSx#SINE/Al 167 GGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGT 118
INTRON_3 307365 AGAGACGGGGTTTCTCCATGTTGGCCAGGCTGGGCTTGAACTCCTGACCT 307414
v v i
C AluSx#SINE/Al 117 AGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCT 68
INTRON_3 307415 CA--TGATCCACCTGCCTTGGCCTCCGAAAGTGCTGGGATTACAGGTGTG 307462
-- i i i v i
C AluSx#SINE/Al 67 CAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTG 18
INTRON_3 307463 AGCCACTGTGTCTGGCC 307479
i i i i
C AluSx#SINE/Al 17 AGCCACCGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 1.92 (23 / 12)
Gap_init rate = 0.01 (2 / 314), avg. gap size = 4.00 (8 / 2)
+ 968 25.5 2.6 7.4 INTRON_3 307480 307693 (92488) + MLT2C1 LTR/ERVL 125 324 (73) 419
ANNOTATION EVIDENCE:
968 25.49 2.65 7.41 INTRON_3 307480 307693 92488 + MLT2C1 LTR/ERVL 125 324 73 760
INTRON_3 307480 CATAGTTTATTTATGAAAGATTATCCTACATAATTTAGGTAGGCCTAATT 307529
---- vv viii i v? v i i v i
MLT2C1#LTR/ER 125 C----TTTAAGTAAAGGAGATTACCCTCMATAATGTGGGTGGGCCTCATC 170
INTRON_3 307530 TAATCAGTCAAAAGCCCTTTAAAGCAAGG-TTGAGGCTTCCCCAG--AGA 307576
i ii i - v i ii-i i vi --
MLT2C1#LTR/ER 171 CAATCAGTTGAAGGCC-TTAAGAGCAAAAACTGAGGTTTCCCGGGGAAGA 219
INTRON_3 307577 ATAAATTCT---TATGGTCAGCAGCTTCAGTTCATGCTCATGAATT-CCA 307622
v --- vvi v v i v ii v i-- i -
MLT2C1#LTR/ER 220 AGAAATTCTGCCTCAAGACTGCAACATCAACTCCTGCC--TGAGTTTCCA 267
INTRON_3 307623 GTCTGTCCTTACTCATGACCTGTTCTACACATTTCAGACTTGCTAAGACA 307672
i i --------- i ii v -----
MLT2C1#LTR/ER 268 GCCTGCC---------GGCCTGCCCTACAGATTTCAGACTTGC-----CA 303
INTRON_3 307673 GATTCCATAACTGCATAAACC 307693
vii i iii i i i
MLT2C1#LTR/ER 304 GCCCCCACAATCACGTGAGCC 324
Matrix = 20p37g.matrix
Transitions / transversions = 2.18 (37 / 17)
Gap_init rate = 0.04 (9 / 213), avg. gap size = 3.11 (28 / 9)
+ 1040 18.2 5.8 1.1 INTRON_3 307970 308394 (91787) C LTR54B LTR/ERV1 (21) 477 1 421
ANNOTATION EVIDENCE:
1032 22.56 8.51 0.99 INTRON_3 307970 308251 91930 C LTR54B LTR/ERV1 175 477 21 761
INTRON_3 307970 TCAACGAATTGAGTTTTAAAGGTCTAATTGGCTTTTATCAGCAATTCACG 308019
i v v iiv iv ii i
C LTR54B#LTR/ER 477 TCAACAAATTTAGTTTAAAGATTCTAATTGGCTTTTATTTGTGATTCATG 428
INTRON_3 308020 AATGAGACAACACCTCAT-CTATGAAATA-GAAAGA-TGTTCTGCAGAGC 308066
vi i i i i - i - - i i v i
C LTR54B#LTR/ER 427 AATTGGGCAGCATCCCATTCTATAAAATAAGAAAGAGTGCTCCGCTGGGC 378
INTRON_3 308067 TAAGCAGAGGGAGTGAGCTTTATTTGTAGGAAAGGCTGAATA--AAGTAG 308114
vvi viiv vi --- iiiv vi ii -- vv
C LTR54B#LTR/ER 377 ATGGCAGAGCAGTTTGGCTTT---TGTAAAGTAGCTTGAGCAGGAACAAG 331
INTRON_3 308115 AAATCAGAAACA-------AAAAGCATATTG-CTGATTTCA--------- 308147
i v ------- iiv -i i iv ---------
C LTR54B#LTR/ER 330 GAAACAGAAACATAGTACAAAAAGTGGATTGGTTAACATCAGGGTTACTT 281
INTRON_3 308148 -AAATTACTTTCCTTGTAT-GGATTGAAGCAGAGAGGAGTTTCTTATCAT 308195
- ii - i i i v i
C LTR54B#LTR/ER 280 CAGGTTACTTTCCTTGTATAGGGTTAAAGCAGAGGGGACTTCCTTATCAT 231
INTRON_3 308196 GCTGGCTCATGTTGACTAGGCCCCTTTTGATCGATTGCTGTAAATCTCCT 308245
i v i i i i
C LTR54B#LTR/ER 230 GTTGGCTCAGGTTGACTGGGCCCCTTTTGATTGGTTGCTGTGAATCTCCT 181
INTRON_3 308246 GTTTTT 308251
C LTR54B#LTR/ER 180 GTTTTT 175
Matrix = 20p37g.matrix
Transitions / transversions = 2.15 (43 / 20)
Gap_init rate = 0.03 (9 / 281), avg. gap size = 3.00 (27 / 9)
1040 10.90 1.27 1.27 INTRON_3 308237 308394 91787 C LTR54B LTR/ERV1 1 158 340 762
INTRON_3 308237 AAATCTCCTGTTTTTAGAAATACTGTCCTGTCTTCGAGTTCAGTTTGATT 308286
i vi v i - v i ivi
C LTR54B#LTR/ER 158 AAGTCTGTTGATTTTGGAAA-ACTGGCCTGTTTCAAAGTTCAGTTTGATT 110
INTRON_3 308287 ACATGGCACC--TAGCATGAGTGACTCCATTCTGGTTTGGTTTGATTTGT 308334
i -- i i i i
C LTR54B#LTR/ER 109 ACGTGGCACCCTTAGCATGAGTGACTCCATTTTGGTTTGGTCTGGTCTGT 60
INTRON_3 308335 TGGGGGTCTAGTGCAGGAGCTCAGTCCAAAACAATGGCCTCCCATAAATT 308384
-i
C LTR54B#LTR/ER 59 TGGGG-CCTAGTGCAGGAGCTCAGTCCAAAACAATGGCCTCCCATAAATT 11
INTRON_3 308385 TTATTTGACA 308394
i
C LTR54B#LTR/ER 10 TTATTTAACA 1
Matrix = 20p37g.matrix
Transitions / transversions = 3.25 (13 / 4)
Gap_init rate = 0.02 (3 / 157), avg. gap size = 1.33 (4 / 3)
+ 259 32.8 11.4 0.7 INTRON_3 308641 308772 (91409) C L1ME3B LINE/L1 (63) 6179 6034 422
ANNOTATION EVIDENCE:
259 32.80 11.36 0.68 INTRON_3 308641 308772 91409 C L1ME3B_3end LINE/L1 781 926 63 713
INTRON_3 308641 TATGGCTTGATAAGTTATTATAAGGTAAATACCTTTATAACCAGCACTTA 308690
ii i i ii i v i ii i iv i v ii
C L1ME3B_3end#L 926 TACAGTTTAACGAATAATTATAAAGCGAACACCCGTGTAACCACCACCCA 877
INTRON_3 308691 GGTCAAGA----GAATTTTTTAAATCACCTTG--AGTCCCCTCTGTGCAT 308734
---- iv viv i- iii-- i ivi vi
C L1ME3B_3end#L 876 GGTCAAGAAATAGAACATTGCCAG-CACCCCAGAAGCCCCCCGCGTGCCC 828
INTRON_3 308735 TGCCCCAATT--AACCCTCTC---CCTACCTCC----AAAGTAACCA 308772
ivi i i-- i --- v i ----i i
C L1ME3B_3end#L 827 CTTCCCGATCGCAACCCCCTCTTCCCTCCCCCCCCCAGAGGTAACCA 781
Matrix = 20p37g.matrix
Transitions / transversions = 3.30 (33 / 10)
Gap_init rate = 0.05 (6 / 131), avg. gap size = 2.67 (16 / 6)
+ 670 23.8 5.5 5.1 INTRON_3 308879 309113 (91068) C L1MC5 LINE/L1 (435) 7526 7291 423
ANNOTATION EVIDENCE:
670 23.76 5.53 5.08 INTRON_3 308879 309113 91068 C L1MC5_3end LINE/L1 681 916 435 714
INTRON_3 308879 ATGTTTTTGAAGTGTCTTCAAAT--ATAAGCTATTTTTCTATCCTTTTCT 308926
i v v iv -- i i v i i i --
C L1MC5_3end#LI 916 ATGTCTTTTAAGTCTCTTTTAATCTATAGGTTCTTCTTCCATCTTTTT-- 869
INTRON_3 308927 GTTTCTTACAGTTTGCTTGTGGAAGAA---TTCAGGGCATTTGACCTGTA 308973
- i i i ii v --- v ---? v
C L1MC5_3end#LI 868 -TTTCTCATAATTTATTTGTTGAAGAAAAGTTAA---YATTTGTCCTGTA 823
INTRON_3 308974 AAGTGTTTTACAGTCTGAATTTTGCTGATTAGGTACTTACTAATATGTTG 309023
i v iii i ivi v i? ------ v
C L1MC5_3end#LI 822 GAGTTTCCCACAGTCTGGATTTTGCTGATTGCATCCCYA------TGGTG 779
INTRON_3 309024 CAGATCAACATGTTCATCTGTCCTCTGTATTTCCTGAAAATTGGCAACCA 309073
iviv i v v i iii
C L1MC5_3end#LI 778 TCATTTAACATGTTCCTCTGTCCTCTGTATTTCCTGTAAATTGGTAGTTA 729
INTRON_3 309074 GCTTCAGGGAC---A-CAG--TCAGGTTCCATCTCTTT--GGCAAGAC 309113
v ii i i --- - -- iv i i --
C L1MC5_3end#LI 728 GATCTAGAGGCTTGATCAGATTCAGGTTTGATTTTTTTTTGGCAAGAC 681
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (34 / 17)
Gap_init rate = 0.04 (9 / 234), avg. gap size = 2.78 (25 / 9)
+ 1846 16.5 3.0 6.2 INTRON_3 309114 309545 (90636) C Charlie1a DNA/hAT-Charlie (0) 1455 1037 424
ANNOTATION EVIDENCE:
1846 16.54 3.01 6.21 INTRON_3 309114 309545 90636 C Charlie1a DNA/hAT-Charlie 1037 1455 0 763
INTRON_3 309114 CAACAATTCTCAAACATTTTAGTTTGAGAAATAATCCTCTTTTAT-TTCT 309162
i ii v i i v i ------ i i i-i
C Charlie1a#DNA 1455 CAGCGGTTCTCAAACTTTTTGGTCTCAGGA------CCCCTTTACACTCT 1412
INTRON_3 309163 TCAAGACCACCCCCTTC----CCCCGCCAAAAGCATTTGTTTATGTGGGT 309208
v i ii ----- v---- i-- i v
C Charlie1a#DNA 1411 TAAAAATTA-----TTGAGGACCCCA--AAGAGCTTTTGTTTATGTGGGT 1369
INTRON_3 309209 CATGCTTACCAATATTTGCCATATTAGAAATTAAGATAGAGAAATTTA-A 309257
i iii i i i i iv v-
C Charlie1a#DNA 1368 TATATCTATCGATATTTACCATATTAGAAATTAAAACTGAGAAATTTTTA 1319
INTRON_3 309258 AAATATTTATGTAGTAATTCATTTTAAAATAACAATATAAACTAATTACA 309307
---- v i -- iv
C Charlie1a#DNA 1318 AAATATTTAT----TAATTCATTTAAAAATAATAATA--AACCCATTACA 1275
INTRON_3 309308 TGCTAATATAAAT-------TTTTGAAATCATAAGTAACTATATTTTGCA 309350
i i ------- --- v v i v
C Charlie1a#DNA 1274 TGTTAACATAAATAACATATTTTT---ATGAAAAATAACTATATTTTCCA 1228
INTRON_3 309351 AAACAAAAAAAAAAGCCTGGTGAGAAGAATGACATTGTTTTACATTTTTG 309400
----ii i i i
C Charlie1a#DNA 1227 AAACAAAAAAA----TTTAGTGAGAAGAGTGGCATTGTTTTACATTTTTG 1182
INTRON_3 309401 CAAATCTTTTTAAAGCCTGGCCTAATAGAAGACAGCTGGATTATCATATC 309450
i v i i v
C Charlie1a#DNA 1181 CAAATCTCTTTAATGTCTGGCTTAATAGAAGACAGCTGGATTCTCATATC 1132
INTRON_3 309451 TGCTTTTACATTCAATCTGTTGCATTGTGTTCTTTTATTTGAAGTATATG 309500
i i iv i v iv
C Charlie1a#DNA 1131 TGCTTCTGCATTCAATCTGTTGCGATATGTTGTTTTGGTTGAAGTATATG 1082
INTRON_3 309501 AAGAAAACCTGCCCTCATACAGATATGTAGCTGGAAATGTAAGGA 309545
i i v i i v vi
C Charlie1a#DNA 1081 AAGAAAATCCGGCCTCACACAGATATGTAGTTGGAAAAGGGAGGA 1037
Matrix = 20p37g.matrix
Transitions / transversions = 2.35 (47 / 20)
Gap_init rate = 0.03 (11 / 431), avg. gap size = 3.55 (39 / 11)
+ 247 23.7 20.3 0.0 INTRON_3 309544 309602 (90579) C Charlie1b DNA/hAT-Charlie (452) 71 1 425 *
ANNOTATION EVIDENCE:
247 23.73 20.34 0.00 INTRON_3 309544 309602 90579 C Charlie1b DNA/hAT-Charlie 1 71 452 764
INTRON_3 309544 GACCTCACAGATCTCCTAAA---------GGGATCC---AGGATTCTTAG 309581
i i i i i --------- i ---i i i ?ii
C Charlie1b#DNA 71 GACCTCGCGGACCCCCTGAAAGGGTCTCGGGGACCCCCAGGGGTCCNCGG 22
INTRON_3 309582 ACTACACTTTGAGAACCTCTG 309602
i v
C Charlie1b#DNA 21 ACCACACTTTGAGAACCGCTG 1
Matrix = 20p37g.matrix
Transitions / transversions = 12.00 (12 / 1)
Gap_init rate = 0.03 (2 / 58), avg. gap size = 6.00 (12 / 2)
+ 1092 22.9 4.0 7.3 INTRON_3 309669 310064 (90117) C L1MC5 LINE/L1 (722) 7239 6856 423
ANNOTATION EVIDENCE:
1092 22.88 4.04 7.29 INTRON_3 309669 310064 90117 C L1MC5_3end LINE/L1 246 629 722 715
INTRON_3 309669 TTTTTATGGTGTTAGCAGCTATTGATGCTGAGTGTACAAATGCATTAATT 309718
i i i v v v ivi i v
C L1MC5_3end#LI 629 TTTTTGTGATGTTAGCAGCCATTGATGATCATTGCCTAGATCCATTAATT 580
INTRON_3 309719 CATTGGATGTTGCAAAATGGTGATATTCTA--TC-AGTTCTTT------T 309759
i iv -- - i i ------
C L1MC5_3end#LI 579 CATTAGGGGTTGCAAAATGGTGATATTCTAATTCTAATTTTTTCTTCATT 530
INTRON_3 309760 AAATGGTCATAATACTTTTATGCAAACCTGCTTCCCCTCATTTACT---- 309805
v v i iiiv i iv i vv-iv i i? ----
C L1MC5_3end#LI 529 TATTAGCTGGAATACTTCTATAAAGAGA-AATTTCCCTCATCSACTATTT 481
INTRON_3 309806 GGCTACTCAGTGGTGCAGTTAGTACAGGAAAACTAGAATAAATCTTTGAT 309855
i i ? v i vi i ivi ii vi
C L1MC5_3end#LI 480 GGTTACCCSGAGGTACAGTTTATATAGGAAAGGCAAGATAAATGCTTGAT 431
INTRON_3 309856 TCTTTTTCCTTATTTACCATATTTTCAAGATAATGAATTGGTTCTCTATC 309905
ii i -i i i i v
C L1MC5_3end#LI 430 TCTTTCCCTTTATTTACCA-GTTTTCAAAATAATGAGTTGGTTCCCTAGC 382
INTRON_3 309906 ATC-TTGCAGATGTCACCAATTAG-TTTTTAAAGTATCA-CTAATGGATT 309952
-i v i v v - vv v v - v
C L1MC5_3end#LI 381 ATCACTCCAAAGGTGACCAATTAGATTTTTTTATTATAAACTCATGGATT 332
INTRON_3 309953 AATGGAATTAGTATATTTCATGGGTCTCAATCAATTGCAGTTATCATTTT 310002
v ------- i? v v ----- v i --
C L1MC5_3end#LI 331 TA-------AAYATATTTGATGTGT-----TAAATTGCAGTTATTATT-- 296
INTRON_3 310003 GAAGCTTATTTTGTCCCATCTTTAACAAGTCAGAACTTCCTGAAATTGTC 310052
v i vv ii v ------------ i v
C L1MC5_3end#LI 295 GATGCTCAAATTGTCCCATCTTTGGCCAGT------------AAGTTGGC 258
INTRON_3 310053 TTCTGAGTCCTT 310064
i
C L1MC5_3end#LI 257 TCCTGAGTCCTT 246
Matrix = 20p37g.matrix
Transitions / transversions = 1.31 (46 / 35)
Gap_init rate = 0.03 (13 / 395), avg. gap size = 3.38 (44 / 13)
+ 573 23.5 0.7 0.7 INTRON_3 310092 310228 (89953) + MER104 DNA/TcMar-Tc2 30 166 (15) 426
ANNOTATION EVIDENCE:
573 23.53 0.73 0.73 INTRON_3 310092 310228 89953 + MER104 DNA/TcMar-Tc2 30 166 15 765
INTRON_3 310092 TTTCTTCACAATTTGGCATCTCTGAAATAAAGGTGTGTTTTACAATCAGT 310141
i v ii vii i i i ii
MER104#DNA/Tc 30 TTTTTTCACATTTTAACATCTCTGAAATCGGGATGCGTCTTACAATCGAT 79
INTRON_3 310142 TGGGTGTTATTGTTTATTTGGCAACTTTTTTTTCTTTCTTAGTGATATGT 310191
v v i v v i v - i ii
MER104#DNA/Tc 80 GGCGTGTCATAGTTTAATTGGCAGCGTTTTTT-CTTTCTTAGTGGTACAT 128
INTRON_3 310192 AAAATGACAGTGCATAT-GCAATCAGTAGCATTTTAAA 310228
i ii v -i ii i i i
MER104#DNA/Tc 129 AAAATAATGGTGCATCTTACAATCGATGGCATCTTAGA 166
Matrix = 20p37g.matrix
Transitions / transversions = 3.00 (24 / 8)
Gap_init rate = 0.01 (2 / 136), avg. gap size = 1.00 (2 / 2)
+ 409 29.3 8.9 1.6 INTRON_3 310403 310582 (89599) C MLT1J2 LTR/ERVL-MaLR (255) 193 1 427
ANNOTATION EVIDENCE:
409 29.34 8.89 1.55 INTRON_3 310403 310582 89599 C MLT1J2 LTR/ERVL-MaLR 1 193 255 766
INTRON_3 310403 GAGGATTGTACCAGATGTTTTAAAGGTCTAGGCTCAAAAGTGGTTTCTAT 310452
i iiivi v v v v i iiii iv vi
C MLT1J2#LTR/ER 193 GAGGATCGCGTGGGAGGTTTTTATGGGCCAGGCCTGGAAGTGGCGTACAT 144
INTRON_3 310453 CACTTCTAAACATGCTTCCCCTTGGAT-GAATTTAATCACATGATTACAA 310501
iivv -- v i v vi- i i i iii? v
C MLT1J2#LTR/ER 143 CACTTCCGCCCA--CATTCCATTGGCCAGAACTCAGTCACATGGCCNCAC 96
INTRON_3 310502 CTTG-TGCAATGGATGTTGGGAAATGTAGTCT--CTGTG--CCTAGAA-- 310544
vi- v v i -- -- i i --
C MLT1J2#LTR/ER 95 CTAACTGCAAGGGAGGCTGGGAAATGTAGTCTAGCTGTGTGCCCAGGAGG 46
INTRON_3 310545 -AAAGGTGATG-----TGACGAACA--TAGCAGTGTCTCTACAACA 310582
- vi i ----- ii -- vi- i v
C MLT1J2#LTR/ER 45 AAAAGGAAACGGGNTTTGGTGAACANCTAGCCA-GTCTCTGCCACA 1
Matrix = 20p37g.matrix
Transitions / transversions = 1.68 (32 / 19)
Gap_init rate = 0.05 (9 / 179), avg. gap size = 2.11 (19 / 9)
+ 649 24.5 4.2 2.9 INTRON_3 310583 310750 (89431) + MIR SINE/MIR 91 260 (2) 428
ANNOTATION EVIDENCE:
649 24.53 4.17 2.94 INTRON_3 310583 310750 89431 + MIR SINE/MIR 91 260 2 672
INTRON_3 310583 TTAAGTAACTTGCATAACATCT--GTGTCTCAGTTTCCCCATTGGTAAAA 310630
ii i v i v v -- i i iv
MIR#SINE/MIR 91 TTGGGCAAGTTACTTAACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAA 140
INTRON_3 310631 TAAAGATAATAACAAGACATACTTTATAGGATTATGTTAAGTATTAAATG 310680
iii i iv v i i i i vv i v
MIR#SINE/MIR 141 TGGGGATAATAATAGTACCTACCTCATAGGGTTGTTGTGAGGATTAAATG 190
INTRON_3 310681 AACTAGTGTAGTACATGTAAAATGTTTGGTACAGTATCTGACA-----TA 310725
---- - i ii i i v ii i -----
MIR#SINE/MIR 191 A----GT-TAATACATGTAAAGCGCTTAGAACAGTGCCTGGCACATAGTA 235
INTRON_3 310726 AGTGCTCAATGAATGTTACCTATTA 310750
i i ivi
MIR#SINE/MIR 236 AGCGCTCAATAAATGTTGGTTATTA 260
Matrix = 25p37g.matrix
Transitions / transversions = 2.64 (29 / 11)
Gap_init rate = 0.02 (4 / 167), avg. gap size = 3.00 (12 / 4)
+ 480 28.8 2.7 2.1 INTRON_3 312416 312603 (87578) + MER5A DNA/hAT-Charlie 1 189 (0) 429
ANNOTATION EVIDENCE:
480 28.80 2.66 2.12 INTRON_3 312416 312603 87578 + MER5A DNA/hAT-Charlie 1 189 0 639
INTRON_3 312416 CAGTACTTCTCAAAATGTGGTTTTCT-ATCACCTGCATCAGAATCACCTG 312464
iv i iii v- i v v v
MER5A#DNA/hAT 1 CAGTGGTTCTCAAAGTGTGGTCCCCGGACCAGCAGCATCAGCATCACCTG 50
INTRON_3 312465 AGGCTGCTTATTAAAAA-GTAGACTTCTAGGGTCTA--CCCAGATCTCCT 312511
i i--i i i - i i - v i iv-- i v
MER5A#DNA/hAT 51 GGA--ACTTGTTAGAAATGCAAA-TTCTCGGGCCCCACCCCAGACCTACT 97
INTRON_3 312512 GGCTCACAATTATTAGACCTGTGGCTGTGGAATTTGCATTTTTAGCAGGT 312561
iv v vivi i ivv v ivv v i ii - i i i
MER5A#DNA/hAT 98 GAATCAGAAACTCTGGGGGTGGGGCCCAGCAATCTGTGTTTT-AACAAGC 146
INTRON_3 312562 ACTCTAGCTGATTCC-ATGCACACTAAAATTTGAGAACCACTG 312603
v i v i- i ? i
MER5A#DNA/hAT 147 CCTCCAGGTGATTCTGATGCACGCTMAAGTTTGAGAACCACTG 189
Matrix = 18p37g.matrix
Transitions / transversions = 1.60 (32 / 20)
Gap_init rate = 0.04 (7 / 187), avg. gap size = 1.29 (9 / 7)
+ 336 31.4 3.0 3.5 INTRON_3 313901 314083 (86098) + L2b LINE/L2 3198 3393 (33) 430
ANNOTATION EVIDENCE:
311 32.79 7.10 0.00 INTRON_3 313901 314083 86098 + L2a_3end LINE/L2 289 484 33 673
INTRON_3 313901 CTCTTCTTCCTCCTCTCCCTACCCC--TCTTCTTCATCACATTTATTATC 313948
iiiv i iv i iii-- i i vi i i i
L2a_3end#LINE 289 CTCCCTATCCCCCTTACCCTGCTTTATTTTTCTCCATAGCACTTATCACC 338
INTRON_3 313949 TTCC----TCCTCC---TTCTCTCTATTGAGTTTATTGTTTTCTGTCTTC 313991
v i---- v vi--- i vii v v vv i v i
L2a_3end#LINE 339 ATCTGACATACTATATATTTTACTTATTTATTTGTTTATTGTCTGTCTCC 388
INTRON_3 313992 CCCAA-TAGAATGTAATCTCTATTAACACAGGGACTGC-ATATGCCTCAT 314039
v - v i v ivi vi-i v ii ii
L2a_3end#LINE 389 CCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGT 438
INTRON_3 314040 TCACTGCAGTTTCCGTAGTGCTTGGAACA-TAGTAGGCA-ATAGTA 314083
v v vi i i i - iviv -
L2a_3end#LINE 439 TCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTA 484
Matrix = 25p37g.matrix
Transitions / transversions = 1.61 (37 / 23)
Gap_init rate = 0.04 (7 / 182), avg. gap size = 1.86 (13 / 7)
311 30.41 0.00 6.06 INTRON_3 313972 314076 86105 + L2c_3end LINE/L2 350 448 30 674
INTRON_3 313972 GTTTATTGTTTTCTGTCTTCCCCAATAGAATGTAATCTCTATTAACACAG 314021
i?-- v i i v v i v iv v ivi
L2c_3end#LINE 350 GTTTACN--TGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAG 397
INTRON_3 314022 GGACTGCATATGCCTCATTCACTGCAGTTTCCGTAGTGCTTGGAACATAG 314071
i ---- i i iiviv v vi ii i v
L2c_3end#LINE 398 GGACCG----TGTCTTATTCATCTTTGTATCCCCAGCACCTGGCACATAG 443
INTRON_3 314072 TAGGC 314076
L2c_3end#LINE 444 TAGGC 448
Matrix = 25p37g.matrix
Transitions / transversions = 1.42 (17 / 12)
Gap_init rate = 0.02 (2 / 104), avg. gap size = 3.00 (6 / 2)
336 33.66 1.98 0.00 INTRON_3 313983 314083 86098 + L2b_3end LINE/L2 331 433 33 675
INTRON_3 313983 TCTGTCTTCCCCAATAGAATGTAATCTCTATTAACACAGGGACTGCATAT 314032
i v i v i v ii v ivi i vi v
L2b_3end#LINE 331 TCTGTCTCCCCCACTGGACTGTGAGCTCCGTGAGGGCAGGGACCGGGTCT 380
INTRON_3 314033 GCCTCATTCACTGCAGTTTCCGTAGTGCTTGGAACATAGTA-GGCA-ATA 314080
i ii i v v vi i iii v vi iv- - i
L2b_3end#LINE 381 GTCTTGTTCACCGCTGTGTCCCCAGCGCCCAGCACAGGGCCTGGCACACA 430
INTRON_3 314081 GTA 314083
L2b_3end#LINE 431 GTA 433
Matrix = 25p37g.matrix
Transitions / transversions = 1.62 (21 / 13)
Gap_init rate = 0.02 (2 / 100), avg. gap size = 1.00 (2 / 2)
+ 378 9.1 0.0 0.0 INTRON_3 314108 314162 (86019) + (TGAA)n Simple_repeat 1 55 (0) 431
ANNOTATION EVIDENCE:
378 9.09 0.00 0.00 INTRON_3 314108 314162 86019 + (TGAA)n Simple_repeat 1 55 125 746
INTRON_3 314108 TGATTGAATAAATGAATGAATGAGTGAGTGAATGAATGAATGAATGAGTG 314157
v i i i i
(TGAA)n#Simpl 1 TGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATG 50
INTRON_3 314158 AATGA 314162
(TGAA)n#Simpl 51 AATGA 55
Matrix = Unknown
Transitions / transversions = 4.00 (4 / 1)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0)
+ 1041 11.6 0.0 3.2 INTRON_3 314208 314368 (85813) + L1PA8A LINE/L1 5967 6122 (9) 432
ANNOTATION EVIDENCE:
1041 11.55 0.00 3.21 INTRON_3 314208 314368 85813 + L1PA8A_3end LINE/L1 714 869 9 648
INTRON_3 314208 GAACAACACACACCAGGGCCTGTTGGTTGGTGGGAGTTGAGGGGCGGGGA 314257
vv i v -i
L1PA8A_3end#L 714 GAACAACACACACCAGGGCCTGTTGGGGGGTGGGGGGTGAGGGG-AGGGA 762
INTRON_3 314258 ACTTATGGGATGGGTCAATAGGTGCAGCAAACCATCATGGCACACATATA 314307
vi i i
L1PA8A_3end#L 763 ACTTAGAGGATGGGTCAATAGGTGCAGCAAACCACCATGGCACACGTATA 812
INTRON_3 314308 CCTATGTAACACAGCTGCACATTCTGCACATGTATCCTGTTGTTTTCTTA 314357
v v i i ??----??
L1PA8A_3end#L 813 CCTATGTAACAAACCTGCACGTTCTGCACATGTATCCCGKW----WSTTA 858
INTRON_3 314358 GAAGAAATAAA 314368
?
L1PA8A_3end#L 859 GAAGAAATWAA 869
Matrix = 18p37g.matrix
Transitions / transversions = 1.17 (7 / 6)
Gap_init rate = 0.01 (2 / 160), avg. gap size = 2.50 (5 / 2)
+ 22 61.1 0.0 0.0 INTRON_3 314369 314404 (85777) + AT_rich Low_complexity 1 36 (0) 433
ANNOTATION EVIDENCE:
22 61.11 0.00 0.00 INTRON_3 314369 314404 85777 + AT_rich Low_complexity 129 164 136 699
INTRON_3 314369 ATTTTAAAAAGAAAGAAAATAAATAAAAATAAAAAT 314404
??????????? vvi v vv vvv??
AT_rich#Low_c 129 WWWWWWWWWWWATTAAAAATAAATAATATAATTTWW 164
Matrix = Unknown
Transitions / transversions = 0.12 (1 / 8)
Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0)
+ 4101 15.1 5.8 4.3 INTRON_3 314564 314699 (85482) C L1MB3 LINE/L1 (2) 6181 6046 434
ANNOTATION EVIDENCE:
4101 15.05 5.85 4.32 INTRON_3 314564 314699 85482 C L1MB3_3end LINE/L1 793 928 2 716
INTRON_3 314564 TTTTTAATTGTGGTAAAATATACATGACATAAAATTTACCAGTTTAATCA 314613
i v i
C L1MB3_3end#LI 928 TTTTTAATTGTGGTAAAATATACATAACATAAAATTTACCATTTTAACCA 879
INTRON_3 314614 TTTT-AAGTGTACTATTCAGGGCCATTAAAGAGATTCACATTGTTGCGCA 314662
- vi v v iv v i
C L1MB3_3end#LI 878 TTTTTAAGTGTACAGTTCAGTGGCATTAAGTACATTCACATTGTTGTGCA 829
INTRON_3 314663 ACCATTACCATCATCTATCTCCAGAACTTTCTTCATC 314699
i i i -
C L1MB3_3end#LI 828 ACCATCACCACCATCCATCTCCAGAACTTT-TTCATC 793
Matrix = 20p37g.matrix
Transitions / transversions = 1.33 (8 / 6)
Gap_init rate = 0.01 (2 / 135), avg. gap size = 1.00 (2 / 2)
+ 2192 11.0 2.4 0.0 INTRON_3 314700 314990 (85191) C AluSg SINE/Alu (12) 298 1 435
ANNOTATION EVIDENCE:
2056 11.00 3.09 0.00 INTRON_3 314700 314990 85191 C AluSx SINE/Alu 1 300 12 630
INTRON_3 314700 TTTTTTTTTGTTTTTTTTGAGATGGAGTCTCACTGTGTCGCCCAGGCTGG 314749
v i i v
C AluSx#SINE/Al 300 TTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGG 251
INTRON_3 314750 AGTGGAGTGGCATGATCTTGGCTCACTGCAACCTCCACCTCCTGGGTTCA 314799
v ii i i i
C AluSx#SINE/Al 250 AGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCA 201
INTRON_3 314800 AGCAGTTCTTCTGCCTTAGCCTCCTGAG--GCTAACCTCAC-----CACG 314842
ii i i i -- iivv i ----- i
C AluSx#SINE/Al 200 AGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCG 151
INTRON_3 314843 CCACCACACCTGGCTAATTTTTGTATTTTTAGTAGAGAAGGGGTTTCGCT 314892
i i v i i
C AluSx#SINE/Al 150 CCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACC 101
INTRON_3 314893 ATATTGGCCAGGCTGGTCTCGAACTCCTGACCTC--GTGATCCACCTGCC 314940
i -- i i
C AluSx#SINE/Al 100 ATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCC 51
INTRON_3 314941 TCGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCGCCCAGCC 314990
i i i
C AluSx#SINE/Al 50 TCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 4.33 (26 / 6)
Gap_init rate = 0.01 (3 / 290), avg. gap size = 3.00 (9 / 3)
+ 4101 15.1 5.8 4.3 INTRON_3 314991 315742 (84439) C L1MB3 LINE/L1 (138) 6045 5281 434
ANNOTATION EVIDENCE:
4101 15.05 5.85 4.32 INTRON_3 314991 315742 84439 C L1MB3_3end LINE/L1 28 792 138 717
INTRON_3 314991 C----AACT----TTCTTCATCTTGTAAA-ACTGAAACTCTTTATTCATT 315031
i---- ----i vi i ivv - ? -- iii ---
C L1MB3_3end#LI 792 TCCCAAACTGAAACTCTGTACCCATTAAACAMT--AACTCCCCATTC--- 748
INTRON_3 315032 AAACAATAAGGCCCCATTCTCTC--TTCCTGTTATCCCCTGGCAACCA-- 315077
----------- v i i i --ii vi v ------- --
C L1MB3_3end#LI 747 -----------CCCCCTCCCCCCAGCCCCTGGCAACC-------ACCATT 716
INTRON_3 315078 CCATTCTTCTAACTCTATGAATTTGACTATTCTAAGTACCTCATATGAAT 315127
i i - iv i i i i
C L1MB3_3end#LI 715 CTACT-TTCTGTCTCTATGAATTTGACTACTCTAGGTACCTCATATAAGT 667
INTRON_3 315128 GGAATCAT-CAGTATTTGCCCTTTTCTGAGCAGCTTATTTCACTTAACAT 315176
- i v vii i
C L1MB3_3end#LI 666 GGAATCATACAGTATTTGTCCTTTTGTGACTGGCTTATTTCACTTAGCAT 617
INTRON_3 315177 TAATGTCTTCAAGGTTCACCTATGTTGTAGCACATGTCAGAATTTCCTTC 315226
- i i i ii
C L1MB3_3end#LI 616 -AATGTCCTCAAGGTTCATCCATGTTGTAGCATGTGTCAGAATTTCCTTC 568
INTRON_3 315227 CTTTTTAAGGCCAAATAATATTCCATT----------------TTTTTTT 315260
ii ---------------- v
C L1MB3_3end#LI 567 CTTTTTAAGGCTGAATAATATTCCATTGTATGTATATACCACATTTTGTT 518
INTRON_3 315261 AATTCATTCATCTGCCTATG-ACACTTGGGTTTCTTCTACCTTTTAGCTA 315309
v i i i v - v i i
C L1MB3_3end#LI 517 TATCCATTCATCCGTCGATGGACACTTGGGTTGCTTCCACCTTTTGGCTA 468
INTRON_3 315310 TTATGAATAATGCTACTATAAA--TGAGTGTACAAATACCTGTTCATGTT 315357
i i i -- i i iv i
C L1MB3_3end#LI 467 TTGTGAATAATGCTGCTATGAACATGGGTGTACAAATATCTGTTCGAGTC 418
INTRON_3 315358 CCTGCTTTCAGTTCTTTTGGTTATATAGTCAGAAATGGAATTGCTGGATC 315407
i ? v vi i
C L1MB3_3end#LI 417 CCTGCTTTCAATTMTTTTGGGTATATACCCAGAAGTGGAATTGCTGGATC 368
INTRON_3 315408 ATATGGTAATTCTAATTTTAATTTTTTGAAGGACTACTATACAGTTTT-- 315455
v i i ii i v --
C L1MB3_3end#LI 367 ATATGGTAATTCTATTTTTAATTTTTTGAGGAACCGCCATACTGTTTTCC 318
INTRON_3 315456 ATA-------CACCATTTTACATTCCTACCAGCAGCACACAAGGATTCAA 315498
-------i i i ii i v
C L1MB3_3end#LI 317 ATAGCGGCTGTACCATTTTACATTCCCACCAACAGTGCACAAGGGTTCCA 268
INTRON_3 315499 ATTTCTCTCCACTCTTACCAGCCGACACTTACCTTCTGGGGTTTTTGTTT 315548
iv ii ii ---- i-- v ---- i
C L1MB3_3end#LI 267 ATTTCTCCACATCCTCGCCA----ACACTTG--TTAT----TTTCTGTTT 228
INTRON_3 315549 GTTTATTGTAATAGTCATTCTAATGGATGTGAAGTGACATCTCATTGTGA 315598
v i--i i i i i i ii i
C L1MB3_3end#LI 227 TTTTG--ATAATAGCCATCCTAACGGGTGTGAGGTGGTATCTCATTGTGG 180
INTRON_3 315599 TTTTGATTTGCATTTCCTGAATGATTAGTGATGGTTGAACATATTTTTAT 315648
iv - i v i
C L1MB3_3end#LI 179 TTTTGATTTGCATTTCCCTAATGATTAGTGATG-TTGAGCATCTTTTCAT 131
INTRON_3 315649 GTACTTATTGGCCATTTGTATACCTT---TGGAGAAATGTCTATTTAAGT 315695
i i i ii --- i
C L1MB3_3end#LI 130 GTGCCTGTTGGCCATTTGTATGTCTTCTTTGGAGAAATGTCTATTCAAGT 81
INTRON_3 315696 CCTATGCCCATTTTT-AATT-GGTT--TTGTTTTT--GCTGTTGAGTTTT 315739
v - i- -- -- i v
C L1MB3_3end#LI 80 CCTTTGCCCATTTTTTAATCAGGTTATTTGTTTTTTTGTTGTTGAGTTGT 31
INTRON_3 315740 AGG 315742
C L1MB3_3end#LI 30 AGG 28
Matrix = 20p37g.matrix
Transitions / transversions = 3.31 (86 / 26)
Gap_init rate = 0.03 (26 / 751), avg. gap size = 3.42 (89 / 26)
+ 465 31.1 11.0 1.2 INTRON_3 315785 316012 (84169) + MIRc SINE/MIR 1 248 (20) 436
ANNOTATION EVIDENCE:
375 36.39 7.65 0.48 INTRON_3 315785 315980 84201 + MIRb SINE/MIR 1 210 58 676
INTRON_3 315785 CAGAAGG-CAAGATGATATAGTACAAATAAT-TGGTACCAGGAATCAGAC 315832
i - ivi i ii iv v ii-i vviiv i i
MIRb#SINE/MIR 1 CAGAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGGC 50
INTRON_3 315833 GATTATGAGTTCTAG-CCAGGCTCTACCACTTACTTAGCCTTGTGACTTT 315881
iiviv i v i- v i - iv i
MIRb#SINE/MIR 51 AGACCTGGGTTCGAATCCTGGCTCTGCCACTTACT-AGCTGTGTGACCTT 99
INTRON_3 315882 GGAAAAATTCTTTATTCTTTCCCAACTTCA------CCATCCTTGAAATT 315925
iv i ivi vi i iv i i ------i iv i v
MIRb#SINE/MIR 100 GGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATG 149
INTRON_3 315926 T---TCATTCTGCTTACCTTTCAAGGTTGT---GGGCATATAATAAGACA 315969
v--- v vv i i iv i --- i v vv i i
MIRb#SINE/MIR 150 GGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATA 199
INTRON_3 315970 ATATACATGAA 315980
ii ii i
MIRb#SINE/MIR 200 ATGCATGTAAA 210
Matrix = 25p37g.matrix
Transitions / transversions = 1.84 (46 / 25)
Gap_init rate = 0.04 (7 / 195), avg. gap size = 2.29 (16 / 7)
465 30.41 11.50 1.36 INTRON_3 315813 316012 84169 + MIRc SINE/MIR 29 248 20 677
INTRON_3 315813 ATTGGTACCAGGAATCAG-ACGATTATGAGTTCTAG-CCAGGCTCTACCA 315860
i - iv i - v ii- i v - v i
MIRc#SINE/MIR 29 ACTGG-ACTTGGAGTCAGGAAGACC-TGGGTTCGAGTCCTGGCTCTGCCA 76
INTRON_3 315861 CTTACTTAGCCTTGTGACTTTGGAAAAATTCTTTATTCTTTCCCAACTTC 315910
- iv i iv i ivi vi i iv i i
MIRc#SINE/MIR 77 CTTACT-AGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTC 125
INTRON_3 315911 A------CCATCCTTGAAAT-----------TTTC-ATTCTGCTTACCTT 315942
------i iv i ----------- vi -iii i i
MIRc#SINE/MIR 126 AGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTC 175
INTRON_3 315943 TCAAGGTTGT---GGGCATATAATAAGACAATATACATGAACATTCTTTG 315989
v i --- i v vv i i i ii viiv
MIRc#SINE/MIR 176 ACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTG 225
INTRON_3 315990 AAAACTACAAAGCATTATTCAAA 316012
v ii iii v
MIRc#SINE/MIR 226 TAAACTGTAAAGTGCTATACAAA 248
Matrix = 25p37g.matrix
Transitions / transversions = 2.16 (41 / 19)
Gap_init rate = 0.05 (9 / 199), avg. gap size = 2.89 (26 / 9)
+ 1957 18.1 4.6 5.8 INTRON_3 316026 316442 (83739) C MLT2D LTR/ERVL (2) 412 1 437
ANNOTATION EVIDENCE:
1957 18.08 4.56 5.83 INTRON_3 316026 316442 83739 C MLT2D LTR/ERVL 1 412 2 640
INTRON_3 316026 TATTAGTTACGGTTCTACAGAGAAACAGAACCAATAGACTATGTCTGAGA 316075
i v v iv i v ----
C MLT2D#LTR/ERV 412 TATTAGTCAGGGTTCTCCAGAGAAACAGAACCAATAGGGTGTGTGT---- 367
INTRON_3 316076 GACAGAGAGATAGAGATTTATTTTAAGGAATTGGCTTATATGATTGTAAA 316125
------- v i iii ii
C MLT2D#LTR/ERV 366 -------AGAGAGAGATTTATTTTAAGGAATTGGCTCACGCGATTGTGGA 324
INTRON_3 316126 GATTGG-AAGCTCTAAATCTGCAGGGTAGGCTGGTAGGCAGGACACCCAG 316174
ii - ii v i i i v v
C MLT2D#LTR/ERV 323 GGCTGGCAAGTCCGAAATCTGCAGGGCAGGCCGGCAGGCTGGAGACCCAG 274
INTRON_3 316175 AGAAGAGTTGA------AGTTTGAGTTCAAAGGCAGTCTGCTGGCAGACT 316218
i ------ i i i i vv v
C MLT2D#LTR/ERV 273 GGAAGAGTTGATGTTGCAGCTCGAGTCCGAAGGCAGTCTGGAGGCAGAAT 224
INTRON_3 316219 TTTGTCTTTTCCTGGGGAGGCCAATCTTTTCAAATTGAAGCTTTCAACTG 316268
iiv iii v vvi i ivvv i i i
C MLT2D#LTR/ERV 223 TCCCTCTTCCTCGGGGGACCTCAGTCTTTTTCTCTTAAGGCCTTCAACTG 174
INTRON_3 316269 ATTGGATGAGGTTTACTCACATTATGGAGAGTAATCTGCTTTACTCAAGG 316318
iii i i i
C MLT2D#LTR/ERV 173 ATTGGATGAGGCCCACCCACATTATGGAGGGTAATCTGCTTTACTCAAAG 124
INTRON_3 316319 TCTACTGATTTAAATGTTAATCTTATCTAAATAAATAAATAAAATAAAAC 316368
?i - ------------
C MLT2D#LTR/ERV 123 TCTACTGATTTAAATGTTAATCSCATCTAAA-AAATA------------C 87
INTRON_3 316369 CTTCACAGAAACATCTAGAATAATGTTTGACCCAATATCTAGGTATTGTG 316418
v v ii v i iii
C MLT2D#LTR/ERV 86 CTTCACAGCAACATCTAGACTGGTGTTTGACCAAATATCTGGGTACCATG 37
INTRON_3 316419 ATCTA------------CATAAAATTAGCTATCACA 316442
ii ------------ i i
C MLT2D#LTR/ERV 36 GCCTAGCCAAGTTGACACATAAAATTAACCATCACA 1
Matrix = 18p37g.matrix
Transitions / transversions = 2.33 (49 / 21)
Gap_init rate = 0.01 (6 / 416), avg. gap size = 7.17 (43 / 6)
+ 1176 28.7 6.5 6.9 INTRON_3 316677 316732 (83449) C MLT1G1 LTR/ERVL-MaLR (0) 579 526 438
ANNOTATION EVIDENCE:
1176 28.70 6.48 6.90 INTRON_3 316677 316732 83449 C MLT1G1 LTR/ERVL-MaLR 526 579 0 767
INTRON_3 316677 TGTTTCAGTTTTATGTTGCTGCGTAACAAACCACTGTTGAAAACCTAGTG 316726
i i v v i ivi-- i
C MLT1G1#LTR/ER 579 TGTTCCGGTTATCTATTGCTGCGTAACAAACCACCCC--AAAACTTAGTG 532
INTRON_3 316727 GTGTAG 316732
iv i
C MLT1G1#LTR/ER 531 GCTTAA 526
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (8 / 4)
Gap_init rate = 0.02 (1 / 55), avg. gap size = 2.00 (2 / 1)
+ 2425 9.1 0.0 0.3 INTRON_3 316733 317039 (83142) + AluY SINE/Alu 1 306 (5) 439
ANNOTATION EVIDENCE:
2346 9.15 0.00 0.33 INTRON_3 316733 317039 83142 + AluY SINE/Alu 1 306 5 631
INTRON_3 316733 GGCCGGGCGCAGTGGCTCAAACCTGTAATCCCAGTACTTTGGGAGGCCGA 316782
i vi i
AluY#SINE/Alu 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
INTRON_3 316783 GGTGGGCGGATCACGAAGTCAGGAGATCCAGACCATCCTGGCTAACATGG 316832
i i v i
AluY#SINE/Alu 51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100
INTRON_3 316833 TGAAACCCTGTCTCTACTAAAAATACAAAAAAATTAGCCGGGCGTGGTGG 316882
i -
AluY#SINE/Alu 101 TGAAACCCCGTCTCTACTAAAAATACAAAAAA-TTAGCCGGGCGTGGTGG 149
INTRON_3 316883 TGCATGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGAAGAATGGCT 316932
i vii i v
AluY#SINE/Alu 150 CGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCG 199
INTRON_3 316933 TGAACCCAGGACACAGAGCTTGTGGTGAGCCGAGATTGTGCCACTGCACT 316982
i vi i ii i i
AluY#SINE/Alu 200 TGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACT 249
INTRON_3 316983 CCAGCCTGGGCGACAGAGCAAGACTCCGTCTCAAAAAACAAACAAACAAA 317032
i v v v
AluY#SINE/Alu 250 CCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAA 299
INTRON_3 317033 CAAAAAA 317039
v
AluY#SINE/Alu 300 AAAAAAA 306
Matrix = 14p37g.matrix
Transitions / transversions = 2.11 (19 / 9)
Gap_init rate = 0.00 (1 / 306), avg. gap size = 1.00 (1 / 1)
+ 1176 28.7 6.5 6.9 INTRON_3 317040 317077 (83104) C MLT1G1 LTR/ERVL-MaLR (54) 525 501 438
ANNOTATION EVIDENCE:
1176 28.70 6.48 6.90 INTRON_3 317040 317077 83104 C MLT1G1 LTR/ERVL-MaLR 501 525 54 768
INTRON_3 317040 CCA-CAATAATTATTTAGCTTTGGTTTTTTAAAAAAAAA 317077
v - i i -- v i i------------
C MLT1G1#LTR/ER 525 ACAACAACAATCATTTA--TTTTGCTC------------ 501
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (4 / 2)
Gap_init rate = 0.08 (3 / 37), avg. gap size = 5.00 (15 / 3)
+ 1866 17.3 0.0 1.0 INTRON_3 317078 317372 (82809) C AluJr SINE/Alu (20) 292 1 440
ANNOTATION EVIDENCE:
1602 20.55 0.00 1.03 INTRON_3 317078 317372 82809 C AluJb SINE/Alu 1 292 20 632
INTRON_3 317078 TTTTTTTTTAGAGACAGGGTCTTGCTCTGTTGCCTGGGCCTGAGTGCAGT 317127
v i i ii iv
C AluJb#SINE/Al 292 TTTTTTTTTTGAGACAGGGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGT 243
INTRON_3 317128 GACACAATCCTAGCTCATTGCAGCCTCTAACTCCTGGTCTCAAGCTATTC 317177
i i i vii i v v i v v i
C AluJb#SINE/Al 242 GGCGCGATCACGGCTCACTGCAGCCTCGACCTCCCGGGCTCAAGCGATCC 193
INTRON_3 317178 TCCCACCTCAGCCTCCAGAGTAGCTGAGAATACAGGCATATACCACGACA 317227
ii v i v iiiii v i
C AluJb#SINE/Al 192 TCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCGCGCCACCACG 143
INTRON_3 317228 CCCAGCTAATTTTTTAAAAAAATTTTGTAGTGATGAGGTCTTCCTATGTT 317277
i ---iv vv v i i i iv i
C AluJb#SINE/Al 142 CCCGGCTAATTTTT---GTATTTTTTGTAGAGACGGGGTTTCACCATGTT 96
INTRON_3 317278 GCCCAGGCTGGTCCCAAACTCCTGGTCTCAAGCGATCCTCCTGCCCTGGC 317327
i i v i i ii
C AluJb#SINE/Al 95 GCCCAGGCTGGTCTCGAACTCCTGGGCTCAAGTGATCCTCCCGCCTCGGC 46
INTRON_3 317328 CTCCCAAAGTGCTGGGATTGTAAGTGTGAGCCGCCATGCCTTGCC 317372
ii i i i ii iv
C AluJb#SINE/Al 45 CTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 2.53 (43 / 17)
Gap_init rate = 0.00 (1 / 294), avg. gap size = 3.00 (3 / 1)
+ 1176 28.7 6.5 6.9 INTRON_3 317373 317785 (82396) C MLT1G1 LTR/ERVL-MaLR (79) 500 74 438
ANNOTATION EVIDENCE:
1176 28.70 6.48 6.90 INTRON_3 317373 317785 82396 C MLT1G1 LTR/ERVL-MaLR 74 500 79 769
INTRON_3 317373 TGATAAGTGTTCAATTTGTGCAGTGCTTG-TGAAAGCAGGCTCACCTCTC 317421
-- ii i v v v v i -i iiii - ii v
C MLT1G1#LTR/ER 500 --ACGAATCTGCAATTTGGGCAGGGCTCGGCGGGGACAG-CTCGTCTCTG 454
INTRON_3 317422 TTCTATGTGGTATCATCCAACTGGGCAGCTTGA--GCTAG----TGGATT 317465
i i i?i i v ii--- i ii -- i ---- v
C MLT1G1#LTR/ER 453 CTCCACNCGGCATCAGCTG---GGGCGGCTCAAAGGCTGGGGGCTGGAAT 407
INTRON_3 317466 TACTCCCAATATGGCTGACTCACATGGCTGGTAAATTGTGGCTAGCACAA 317515
i ii? v v ? i i vv i ----
C MLT1G1#LTR/ER 406 CACCTNCAAGATGGCTCACTCACATGNCTGGCAAGTTGATGCTGGC---- 361
INTRON_3 317516 TGTCTACTGA------AGCTGAAGC------CTAGGGGCCTCATTTCCTC 317553
vi i------ ii ------ ii ii v
C MLT1G1#LTR/ER 360 TGTCGGCTGGGACCTCAGCTGGGGCTGTCGGCCGGAAGCCTCAGTTCCTC 311
INTRON_3 317554 TTTAC-TGGGTCTCTTCTTGGGATATTTGT-TTTCCTCATGGCATGATGG 317601
ii - i i v v ii v-i ii i
C MLT1G1#LTR/ER 310 TCCACGTGGGCCTCTCCATGGGCTGCTTGGGCTTCCTCACAGCATGGTGG 261
INTRON_3 317602 CTAGGTACCAACAGTAAGCATTATAAGAGA-TAAGAAGAGGAAGCTGC-- 317648
i v v ii i ivi -i -- vi --
C MLT1G1#LTR/ER 260 CTGGGTTCCAAGAGCGAGCGTCCCAAGAGAGCAAG--GCAGAAGCTGCAT 213
INTRON_3 317649 --CAGTTTTGTAAGAAGCCTGGTCCTAGAAACTGGCACACTGTCATTCCT 317696
-- v i i ---- i i ii i- vi i vi i i
C MLT1G1#LTR/ER 212 GGCACTTTTATGA----CCTAGCCTCAGAAG-TCACATAGCGTCACTTCT 168
INTRON_3 317697 GGAATATTCTATTACTTGAG-TAGTCACAGAG-----TCTGAATTCAAGG 317740
vv i iv i -i i -----i iiii
C MLT1G1#LTR/ER 167 GCCACATTCTATTGGTCGAGGCAGTCACAAAGGCCCGCCCAGGTTCAAGG 118
INTRON_3 317741 ACAGGAGATATATACCCCAACCTTTCTATGAAAATAGTGTCAAAG 317785
iv ii i v - i v ii iv ?
C MLT1G1#LTR/ER 117 GGAGGGAACATAGACCCCA-CCTCTCGATGGGAGGAGTGTCAANG 74
Matrix = 20p37g.matrix
Transitions / transversions = 2.80 (84 / 30)
Gap_init rate = 0.05 (19 / 412), avg. gap size = 2.63 (50 / 19)
+ 702 24.1 1.1 3.5 INTRON_3 317990 318165 (82016) C L2a LINE/L2 (0) 3426 3255 441
ANNOTATION EVIDENCE:
702 24.14 1.14 3.49 INTRON_3 317990 318165 82016 C L2a_3end LINE/L2 346 517 0 678
INTRON_3 317990 ATGTATTCATTCAATAAATATTTATTGAGCATCTGCTATGTACTTGGCAC 318039
vi i ii i i iv
C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCAC 468
INTRON_3 318040 CATTCTAAATACTTGGAATACAGTGGTGAACAAGATAGACAAA-GTCTTT 318088
ii iiii v i ii i i - ii
C L2a_3end#LINE 467 TGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCT 418
INTRON_3 318089 GCATTCTTTGGAGCATACATTTTAGTGGGGAAATAAAAACA-TAAAAATC 318137
vi v - v i ii v v i - ---
C L2a_3end#LINE 417 GCCCTCAT-GGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAA---C 372
INTRON_3 318138 AAATGATGATAGATACAATGCAGAGAAT 318165
i -- ii v ii v v
C L2a_3end#LINE 371 AAATAA--ATAAGTAAAATATATAGTAT 346
Matrix = 25p37g.matrix
Transitions / transversions = 2.73 (30 / 11)
Gap_init rate = 0.03 (5 / 175), avg. gap size = 1.60 (8 / 5)
+ 690 26.4 17.6 5.0 INTRON_3 318249 318598 (81583) C MLT1L LTR/ERVL-MaLR (86) 524 131 442
ANNOTATION EVIDENCE:
435 23.16 3.16 0.00 INTRON_3 318249 318343 81838 C MLT1L LTR/ERVL-MaLR 427 524 86 770
INTRON_3 318249 ATGATGAGGAGTCTGGAAGTAGGGTGGTTCT--GGCTGGTTAATTTAGTG 318296
i ii i ii i i i-- i i i
C MLT1L#LTR/ERV 524 ATAACAAGAAGTCCAGAGGTAGGGCGGTTCCAGGGTTGGTTAATTCAGCG 475
INTRON_3 318297 G-TCAGAGACATCATCAAGAATCCAGGTGCTGTCCATCTTTCTCCTCT 318343
- iv ii i i v v iv
C MLT1L#LTR/ERV 474 GCTCAACGATGTCATCAAGGACCCAGGTTCTTTCCATCTTTCCGCTCT 427
Matrix = 20p37g.matrix
Transitions / transversions = 4.50 (18 / 4)
Gap_init rate = 0.02 (2 / 94), avg. gap size = 1.50 (3 / 2)
690 27.66 6.06 6.87 INTRON_3 318335 318598 81583 C MLT1L LTR/ERVL-MaLR 131 392 218 771
INTRON_3 318335 TTCTCCTCTCATAGTCATAAAATGGCTGCAGCTGTTT--GGCACCACATG 318382
v i i ii i v i i-- i v
C MLT1L#LTR/ERV 392 TTGTCCCCTCATGGTCGCAAGATGGCTGCAGCAGCTCCAGGCATCACATC 343
INTRON_3 318383 CATTCATGACCATGTCCAATGACAAAGAAGGGGGAAAAGGAGTGTGTGTA 318432
?iv ii v i iv i -------- ii -------
C MLT1L#LTR/ERV 342 CSCACACAACAACGTCCAGAGGCAA--------GAAAAGAGG-------A 308
INTRON_3 318433 TATAAGTCTTCTCT-TTTCCTTTTGCTTAAG--TGAGATAAATTTTCTCA 318479
i v-- ii - v -i --i iv ?i i
C MLT1L#LTR/ERV 307 CATC--TCTTCCTTATGTCCTTTT-TTTAAGAGCGAGGAAAMCTTTCCCA 261
INTRON_3 318480 ---------TAGTAGGTTTCTTTT-ATGTCTCATTGGGTAGAACTGTGTC 318519
---------i i ii iii - vi i
C MLT1L#LTR/ERV 260 GAAGCCCCCCAGCAGACTTCCCCTCATGTCTCATTGGCCAGAATTGTGTC 211
INTRON_3 318520 ACATGCCCATGCTTGAGCCAATC-CTAGCAATGGTAGTGAGACCACTATA 318568
v i i i - i v v i ii ii i i
C MLT1L#LTR/ERV 210 ACATGCCCATTCCTAAACCAATCACTGGCAAGGGGAATGGAATTACCATG 161
INTRON_3 318569 ATCAACTTACACCAATTAGGTTTCACTCCC 318598
iii v i i i v i
C MLT1L#LTR/ERV 160 ATTGGCTTAGACTAATCAAGATTCACCCCC 131
Matrix = 20p37g.matrix
Transitions / transversions = 3.40 (51 / 15)
Gap_init rate = 0.04 (10 / 263), avg. gap size = 3.40 (34 / 10)
+ 224 29.4 7.1 1.1 INTRON_3 318733 318833 (81348) C L2a LINE/L2 (212) 3175 3072 441
ANNOTATION EVIDENCE:
214 38.00 0.99 0.99 INTRON_3 318733 318833 81348 C L2c_3end LINE/L2 166 266 212 679
INTRON_3 318733 GACTAGG-TTCAGATGTTAGGGAAGGCCTCCCTTGAATAGTTGTTGTTTA 318781
?- vi iv i i - v iv v vii i i
C L2c_3end#LINE 266 GACTAGNCTTGGGGGGTCAGGGAAGGCTTCC-TGGAGGAGGTGACATCTG 218
INTRON_3 318782 AGGTGAAATCTGAATGACAGGAAAGAGCTAGCCTTGCTCGAGGAAGAGCA 318831
v i?ii v iii v i i vv ivvi i i vi
C L2c_3end#LINE 217 AGCTGAGNCTTGAAGGATGAGTAGGAGTTAGCCAGGTGGAAGGAGGGGGG 168
INTRON_3 318832 AA 318833
C L2c_3end#LINE 167 AA 166
Matrix = 25p37g.matrix
Transitions / transversions = 1.57 (22 / 14)
Gap_init rate = 0.02 (2 / 100), avg. gap size = 1.00 (2 / 2)
224 27.69 8.33 1.11 INTRON_3 318747 318830 81351 C L2a_3end LINE/L2 163 252 265 680
INTRON_3 318747 GTTAGGGAAGGCCTCCCTTGAATAGTTGTTGTTTAAGGTGAAATCTGAAT 318796
i v - iv v vii i vvi i i v
C L2a_3end#LINE 252 GTCAGGGAAGGCCTCACT-GAGAAGGTGACATTTGAGCAAAGACCTGAAG 204
INTRON_3 318797 GACAGGAAAGAGCTAGCCTTGC-----TC--GAGGAAGAGC 318830
viv ii v v ----- -- i
C L2a_3end#LINE 203 GAGGTGAGGGAGCGAGCCATGCGGATATCTGGGGGAAGAGC 163
Matrix = 25p37g.matrix
Transitions / transversions = 1.09 (12 / 11)
Gap_init rate = 0.04 (3 / 83), avg. gap size = 2.67 (8 / 3)
+ 370 37.1 3.8 0.0 INTRON_3 319159 319290 (80891) + L2b LINE/L2 3238 3374 (1) 443
ANNOTATION EVIDENCE:
370 37.12 3.79 0.00 INTRON_3 319159 319290 80891 + L2b_3end LINE/L2 329 465 1 681
INTRON_3 319159 TGTGTGCAGCTCCTACTCTACTGTTG--TTTGCAAGAATAAAGATCATAT 319206
v ivv i i vv vi-- ii ii iii ii i ivi
L2b_3end#LINE 329 TGTCTGTCTCCCCCACTGGACTGTGAGCTCCGTGAGGGCAGGGACCGGGT 378
INTRON_3 319207 CCAGTTTTTTC---TTTGTATCCCTAATGACTATCACAGTGCCTGACAGA 319253
iivi v ---vi i i ii v i v v i v
L2b_3end#LINE 379 CTGTCTTGTTCACCGCTGTGTCCCCAGCGCCCAGCACAGGGCCTGGCACA 428
INTRON_3 319254 CAGTAGATTATTGATAAATGTCTGTTGAGTGAATAAA 319290
i vv iii i i i
L2b_3end#LINE 429 CAGTAGGTGCTCAGTAAATGTTTGTTGAATGAATGAA 465
Matrix = 25p37g.matrix
Transitions / transversions = 2.06 (33 / 16)
Gap_init rate = 0.02 (2 / 131), avg. gap size = 2.50 (5 / 2)
+ 204 37.5 5.1 2.5 INTRON_3 319307 319462 (80719) C L2c LINE/L2 (69) 3318 3159 444
ANNOTATION EVIDENCE:
204 37.48 5.13 2.50 INTRON_3 319307 319462 80719 C L2c_3end LINE/L2 250 409 69 682
INTRON_3 319307 AGGACATGTT---TACCGTTATGAAACATACAGGCTACTGAGGAAGATGG 319353
i i v --- i v i v i i vi v v ii i ii
C L2c_3end#LINE 409 AAGACACGGTCCCTGCCCTCAAGGAGCTCACAGTCTAGTGGAGGAGACAG 360
INTRON_3 319354 GGAAATAAGCAAATAACTGCAATG-AAGCC--TGCTAAGTGCTATACCAC 319400
iv ?i i i i i i i- ii-- v vii-
C L2c_3end#LINE 359 ACANGTAAACAGACAATTACAATACAAGTTAATGATAAGTGCTATAATG- 311
INTRON_3 319401 AAGGAACATTTGAAGAG-GTTTTAAGAGCAGAAGCAACAGCAGCTAC-CT 319448
-- ii vviv i - i v ii v iivi vi v v-
C L2c_3end#LINE 310 --GGAGTATAGACAGGGTGCTATGGGAGCACAGAGGAGGGCACCTAGACT 263
INTRON_3 319449 GTGACTTGAGGGGT 319462
i- ? i
C L2c_3end#LINE 262 A-GNCTTGGGGGGT 250
Matrix = 25p37g.matrix
Transitions / transversions = 2.06 (37 / 18)
Gap_init rate = 0.05 (7 / 155), avg. gap size = 1.71 (12 / 7)
+ 180 35.3 4.8 2.3 INTRON_3 319618 319701 (80480) C MIR3 SINE/MIR (3) 205 120 445
ANNOTATION EVIDENCE:
180 35.34 4.76 2.33 INTRON_3 319618 319701 80480 C MIR3 SINE/MIR 120 205 3 683
INTRON_3 319618 TTATAGAACCATAAAAGATTAGAAATGAGATGCATTTCTGAAGGCACCTA 319667
i i i vi i iv ii v v ii iv iiv i
C MIR3#SINE/MIR 205 TCATAGAATCATAGAATGTCAGAGCTGGAAGGGACCTTAGAGATCATCTA 156
INTRON_3 319668 AAAATTAGCTCCATCATTTTAAAGAT----AAATTGAG 319701
iv--ii i i v v ---- i
C MIR3#SINE/MIR 155 GT--CCAACCCCCTCATTTTACAGATGAGGAAACTGAG 120
Matrix = 25p37g.matrix
Transitions / transversions = 2.22 (20 / 9)
Gap_init rate = 0.02 (2 / 83), avg. gap size = 3.00 (6 / 2)
+ 909 23.7 1.4 7.4 INTRON_3 319820 320106 (80075) C L1ME3A LINE/L1 (9) 6164 5894 446
ANNOTATION EVIDENCE:
909 23.70 1.39 7.38 INTRON_3 319820 320106 80075 C L1ME3A_3end LINE/L1 641 911 9 718
INTRON_3 319820 AACATTTTAGTGAATTAAAACATACATGCAGAAAAGTGCACACAGTATTA 319869
v v v v i i v vi v
C L1ME3A_3end#L 911 AACTTTTTATTGAAGTATAATATACATACAGAAAAGTGCACAAATCATAA 862
INTRON_3 319870 GTGAATAGCTAGATGCATTTTCATAG--TGAACACACA-GTGAACACAAC 319916
v i v v i i-- v- v - v v
C L1ME3A_3end#L 861 GTGTACAGCTCGATGAATTTTCACAAACTGAACACACCCGTGTA-ACCAG 813
INTRON_3 319917 CGCTCAGATCAGAAAATAGATCATTACCAGCACTA-AGATGGTCCTTCCA 319965
i i ii i v iv- v vi i iii
C L1ME3A_3end#L 812 CACCCAGATCAAGAAACAGAACATTACCAGCACCCCAGAAGCCCCCTTTG 763
INTRON_3 319966 TGACCACCCCCGCTCACTAACCTTAATCTCCTCTTTGAAGATAACCATTG 320015
vi v ii iv -------- i i iiii i i i -
C L1ME3A_3end#L 762 TGCTCCCTTCCAGTCACTA--------CCCCCCCCCAAGGGTAACCACT- 722
INTRON_3 320016 TTTATCTTCTTATTGACTTTAAAAACCATGAAATTAGTTTTGCCTGGTTT 320065
--- i ------ iv v ? - i v
C L1ME3A_3end#L 721 ---ATCCT------GACTTCTAACANCAT-AGATTAGTTTTGCCTGTTTT 682
INTRON_3 320066 TGAACTTTGTATATGTGGAATCATACAGTATACACTCTTTT 320106
i vi ii
C L1ME3A_3end#L 681 TGAACTTTATATAAATGGAATCATACAGTATGTACTCTTTT 641
Matrix = 20p37g.matrix
Transitions / transversions = 1.48 (37 / 25)
Gap_init rate = 0.03 (8 / 286), avg. gap size = 3.00 (24 / 8)
+ 651 22.3 14.4 0.8 INTRON_3 320106 320597 (79584) C L1MEg LINE/L1 (3201) 4036 3473 447 *
ANNOTATION EVIDENCE:
383 21.35 0.00 0.00 INTRON_3 320106 320194 79987 C L1M5_orf2 LINE/L1 748 836 2458 719
INTRON_3 320106 TTATTGTTCAATTCAAGATATTTTCCAATTTCCCTTTTGAACTATTGTTT 320155
ii i i i v v vi v v
C L1M5_orf2#LIN 836 TTATCATTCAGTTCAAAATATTTTCTAATTTCCATTGTGATTTCTTCTTT 787
INTRON_3 320156 GACCTGTGAGTTATTTTAAAGAATGTTGCTTAATTTCTA 320194
ii i vi v i i
C L1M5_orf2#LIN 786 GACCCATGGGTTATTTAGAAGTATATTGCTTAATTTCCA 748
Matrix = 20p37g.matrix
Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.00 (0 / 88), avg. gap size = 0.0 (0 / 0)
651 21.37 16.45 0.75 INTRON_3 320189 320419 79762 C L1M5_orf2 LINE/L1 468 734 2560 720
INTRON_3 320189 TTTCTAGTTATCTTTTAATC-----TTCTTCATTTAATTCGACTGT---- 320229
vi i----- ii vii v ----
C L1M5_orf2#LIN 734 TTTCTAGTTATCTTTTTGTTATTGATTTCTAGCTTAATTCCACTGTGGTC 685
INTRON_3 320230 AGAGAACATACTC---AT-----CAATCCTTTAAAATTTGTTAGGACCTG 320271
--- ----- i ii i
C L1M5_orf2#LIN 684 AGAGAACATACTCTGTATGATTTCAATCCTTTGAAATTTGTTGAGACTTG 635
INTRON_3 320272 CTTTGTAACCCAGCATATATTCTGTTATGGTAAATGTT--------GATT 320313
i ii i? iv ? v --------iv
C L1M5_orf2#LIN 634 CTTTATGGCCCAANATATGGTCNGTTTTGGTAAATGTTCCATGTGCACTT 585
INTRON_3 320314 GAAAAGCATG---------CATTTTTTCTGTTTGGAGTTCTATAAAT--- 320351
v --------- v v v? vii v ? ---
C L1M5_orf2#LIN 584 GAAAAGAATGTGNATTCTGCAGTTGTTGNGTGCAGTGTTCTATANATGTC 535
INTRON_3 320352 -ATTAGGTGACGTTTGTTGATTATGTCCTTTAAATCTTATATTATCTTAT 320400
- v v i ?? iv i v vv i
C L1M5_orf2#LIN 534 NATTAGGTCAAGTTTGTTAATNNTGTTGTTCAAATCTTCTATATTCTTAC 485
INTRON_3 320401 TGACAGTTTCTATCTGCTT 320419
i-- i i
C L1M5_orf2#LIN 484 TGAT--TTTTTGTCTGCTT 468
Matrix = 20p37g.matrix
Transitions / transversions = 1.39 (25 / 18)
Gap_init rate = 0.03 (8 / 230), avg. gap size = 5.00 (40 / 8)
616 23.87 8.33 1.36 INTRON_3 320322 320597 79584 C L1M5_orf2 LINE/L1 273 567 2727 721
INTRON_3 320322 TGCATTTTTTCTGTTTGGAGTTCTATAAAT----ATTAGGTGACGTTTGT 320367
v v v? vii v ? ---- v v
C L1M5_orf2#LIN 567 TGCAGTTGTTGNGTGCAGTGTTCTATANATGTCNATTAGGTCAAGTTTGT 518
INTRON_3 320368 TGATTATGTCCTTTAAATCTTATATTATCTTATTGACAGTTTCTATCTGC 320417
i ?? iv i v vv i i-- i i
C L1M5_orf2#LIN 517 TAATNNTGTTGTTCAAATCTTCTATATTCTTACTGAT--TTTTTGTCTGC 470
INTRON_3 320418 TT---CTAAAGGTTATTGTTAGAGGTATGTTAAAATGTCTCACTGTGACT 320464
--- vvi i vv ?i v i i -
C L1M5_orf2#LIN 469 TTGTTCTATCAGTTACTGAGAGAGGNGTGTTAAAATCTCCCACTATGA-T 421
INTRON_3 320465 TGTGTACTTGTTTATGTATGCTGTT--TTCT-----TTTTTAAT--GCAT 320505
v i i v v v v -- ----- iv --i
C L1M5_orf2#LIN 420 TGTGGATTTGTCTATTTCTCCTTTTANTTCTGTCAATTTTTGCTTTACAT 371
INTRON_3 320506 -TTTTGAGGCTATATTTTTATGGACATGAAAATTTAGAATT---ATATCT 320551
- ? ? v v vi iv ? --- i
C L1M5_orf2#LIN 370 ATTTTGAGGCTNTNTTATTAGGTGCATACANATTTAGAATTNTTATGTCT 321
INTRON_3 320552 TCTTGGTAGATTTATGCTTTAAATCATTATCTA---TCTCTATCTATCT 320597
i i v iv v - v? --- v i
C L1M5_orf2#LIN 320 TCCTGGTGGATTGACCCTTTTA-TCATTATGNAATGTCTCTCTTTATCT 273
Matrix = 20p37g.matrix
Transitions / transversions = 0.81 (25 / 31)
Gap_init rate = 0.04 (11 / 275), avg. gap size = 2.45 (27 / 11)
+ 2014 14.3 0.3 2.4 INTRON_3 320599 320899 (79282) C AluJr SINE/Alu (15) 297 3 448
ANNOTATION EVIDENCE:
1730 18.04 0.33 2.37 INTRON_3 320599 320899 79282 C AluJb SINE/Alu 3 297 15 633
INTRON_3 320599 TTTATTTATTTTTTAGAGATGGGGTCTTGCTTCGTCACC-AGGCTGCAGT 320647
v v v ii i ii i - v
C AluJb#SINE/Al 297 TTTTTTTTTTTTTTTGAGACAGGGTCTCGCTCTGTCGCCCAGGCTGGAGT 248
INTRON_3 320648 GCAGTGGCATGATCATAGCTCACTGCATCCTTGAACTCCTGGGATCAAGC 320697
ii ii v i v i v
C AluJb#SINE/Al 247 GCAGTGGCGCGATCACGGCTCACTGCAGCCTCGACCTCCCGGGCTCAAGC 198
INTRON_3 320698 AATCCTCTCACCTCAGCCTCCTGAGTGGCTGGGACTACAGGCATGTGCTA 320747
i iii i i ii i i
C AluJb#SINE/Al 197 GATCCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCGCGCCA 148
INTRON_3 320748 CCACGCCCAGCTAATTTTTTTGTTTTCTAGTTTTTGTAGAGATTGGATCT 320797
i v i ------- iv i i
C AluJb#SINE/Al 147 CCACGCCCGGCTAATTTTTGTATTTT-------TTGTAGAGACGGGGTTT 105
INTRON_3 320798 CGCTATATTGCCCAGGCTGGTCTTGAACTCCTGGCCTCAAGCAGTCCTCC 320847
i i i i v iii
C AluJb#SINE/Al 104 CACCATGTTGCCCAGGCTGGTCTCGAACTCCTGGGCTCAAGTGATCCTCC 55
INTRON_3 320848 TGCCTTGGCCTCTCAAAGCGCTGGGATTACAGATGTGAGCCACTGTGCCT 320897
i i i i ii i i i
C AluJb#SINE/Al 54 CGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCC 5
INTRON_3 320898 GG 320899
C AluJb#SINE/Al 4 GG 3
Matrix = 14p37g.matrix
Transitions / transversions = 4.30 (43 / 10)
Gap_init rate = 0.01 (2 / 300), avg. gap size = 4.00 (8 / 2)
+ 1886 21.6 6.5 6.1 INTRON_3 320942 321430 (78751) C MLT1D LTR/ERVL-MaLR (14) 491 1 449
ANNOTATION EVIDENCE:
1886 21.57 6.54 6.11 INTRON_3 320942 321430 78751 C MLT1D LTR/ERVL-MaLR 1 491 14 772
INTRON_3 320942 ACTGCTGCTGTAACAAATCAC----AAGTTAGTGGCTTTAAACAATGCAA 320987
i i ---- v v ii
C MLT1D#LTR/ERV 491 ATTGCTGCTGTAACAAATTACCACAAACTTAGTGGCTTAAAACAACACAA 442
INTRON_3 320988 ATTTATCATCCTACACTTTGGGAGATCAGAAGTCTAAAAT-----TCATT 321032
i i v iv i ii ----- i
C MLT1D#LTR/ERV 441 ATTTATTATCTTACAGTTCTGGAGGTCAGAAGTCCGAAATGGGTCTCACT 392
INTRON_3 321033 ------------------CTCCACAGCTGTGTTCCTTCCAGACGTTCCAA 321064
------------------ vv vi i ii v i i i
C MLT1D#LTR/ERV 391 GGGCTAAAATCAAGGTGTCGGCAGGGCTGCGTTCCTTCTGGAGGCTCTAG 342
INTRON_3 321065 GAGAGAATCTGTTTCCTTGACCTTTTCAGATTCAGGAGGCTGCCTACATT 321114
i i v i i v vi i ii
C MLT1D#LTR/ERV 341 GGGAGAATCCGTTTCCTTGCCTTTTCCAGCTTCTAGAGGCCGCCCGCATT 292
INTRON_3 321115 CTTTGGCTTCTGGCTCCTTTCTTCCATCTTCAAAGCCAGAAGCATAACAT 321164
i iv i i - -----i i
C MLT1D#LTR/ERV 291 CCTTGGCTCGTGGCCCCTTCCT-CCATCTTCAAAGCCAG-----CAACGT 248
INTRON_3 321165 ATTCAAATCTCTTTCTCTCTGTCCCTCTGCTGCTTTTGTCACATTGCCTC 321214
vv ----------- i -v v iv i iv i
C MLT1D#LTR/ERV 247 CGTCA-----------CTCCG-ACCTCTGCTTCCGTCGTCACATCTCCTT 210
INTRON_3 321215 CTATCTAACTTTGACCCCACCTGTATCTCTTTTACAAGA---CTTGTAAT 321261
-- i i i- iv i i i i--- i
C MLT1D#LTR/ERV 209 CT--CTGACTCTGACCCT-CCTGCCTCCCTCTTATAAGGACCCTTGTGAT 163
INTRON_3 321262 TATATCAGGCTCACTTGGATAATTTAGAATAATCTCCCCATCTAAAAATT 321311
i ii i ii ii i v i i
C MLT1D#LTR/ERV 162 TACATTGGGCCCACCCGGATAATCCAGGATAATCTCCCCATCTCAAGATC 113
INTRON_3 321312 CTCCATTTGATCACATCTTCAAAATCTCTTTTGCCCCATAAAGTAACAT- 321360
iv i i v i i vii i -
C MLT1D#LTR/ERV 112 CTTAACTTAATCACATCTGCAAAGTCCCTTTTGCCATGTAAGGTAACATA 63
INTRON_3 321361 -TCGTAGGTTCTAGGGATTAGGATGTAAACATTTTGGTTGGGAGAGGGCA 321409
- ii ii i ii i --- i ------
C MLT1D#LTR/ERV 62 TTCACAGGTTCCGGGGATTAGGACGTGGACATCTT---TGGGGG------ 22
INTRON_3 321410 GCCATCATTCCGCCTACCACA 321430
i ?
C MLT1D#LTR/ERV 21 GCCATTATTCSGCCTACCACA 1
Matrix = 20p37g.matrix
Transitions / transversions = 3.26 (75 / 23)
Gap_init rate = 0.03 (13 / 488), avg. gap size = 4.77 (62 / 13)
+ 806 24.2 6.3 1.5 INTRON_3 321449 321839 (78342) C L1MEg LINE/L1 (3801) 3456 3018 447
ANNOTATION EVIDENCE:
619 27.81 2.97 1.09 INTRON_3 321449 321717 78464 C L1MEe_5end LINE/L1 780 1053 111 723
INTRON_3 321449 TTGTCCGATAGAAATATATAGGTACATACAACTTCCTTTTGGTTAGTGTT 321498
i vv vvvi - i i - i
C L1MEe_5end#LI 1053 TTGTCTGATATTAATATAGCCATACAT-CAGCTTTCTTT-GGTTAGTATT 1006
INTRON_3 321499 TGCATAGCGT-TATCTCCCATCTTGTTACTTTTATCATTTTTGTATCCTT 321547
? i ii - v i i v i v ? i i i
C L1MEe_5end#LI 1005 TGCNTGGTATATTTTTCTCATCTTTTTACTTTCAACNTTTCTGTGTCTTT 956
INTRON_3 321548 ATAGTTAAAGTTGGCCTCTTTTTCAGTAACATATTATGGGTTTTGTTTTC 321597
iv v ii vv i v -v ii i viiv vv i
C L1MEe_5end#LI 955 ATGTTTTAGATATGTCTCTTGT-AAACAGCATATAGCTGGAATTGTTTTT 907
INTRON_3 321598 T--GTTTAG-CTGACAGTCTTTGTCTTTTAATTGGAATTCTTAATCCATT 321644
--i ii ?- i i vvvv vi
C L1MEe_5end#LI 906 TTAATCCANTCTGACAATCTTTGTCTTTTAACTGGATAGATTTGTCCATT 857
INTRON_3 321645 TCCACTGAATGTTGTTACTGATATATTTGGATTTACATCTAC-ACCTTAT 321693
v i v ? vi iv - ii
C L1MEe_5end#LI 856 TACATTTANTGTGATTACTGATATATTTGGATTTATTTCTACCATTTTAT 807
INTRON_3 321694 T---TATTTTCTAATCATCCTACATTT 321717
--- ii v ii i ii
C L1MEe_5end#LI 806 TCTGTGCTTTCTATTTGTTCTATGTTT 780
Matrix = 20p37g.matrix
Transitions / transversions = 1.50 (42 / 28)
Gap_init rate = 0.03 (8 / 268), avg. gap size = 1.38 (11 / 8)
806 23.17 2.52 2.09 INTRON_3 321449 321686 78495 C L1M5_orf2 LINE/L1 4 242 3052 722
INTRON_3 321449 TTGTCCGATAGAAATATATAGGTACATACAACTTCCTTTTGGTTAGTGTT 321498
i vv i -- v - i i ?
C L1M5_orf2#LIN 242 TTGTCTGATATTAGTATA--GCTACAT-CAGCTTTCTTTTGNTTAGTGTT 196
INTRON_3 321499 TGCATAGCGTTATCTC---CCATCTTGTTACTTTTATCATTTTTGTATCC 321545
?i ii - i--- ?i v i v v i i i
C L1M5_orf2#LIN 195 TGCANGGTAT-ATCTTTTTCCATNCTTTTACTTTCAACCTTTCTGTGTTC 147
INTRON_3 321546 TTATAGTTAAAGTTGGCCTCTTTTTCAGTAACATATTAT-GGGTTTTGTT 321594
v v? i v -v ii i vi - ?i ?
C L1M5_orf2#LIN 146 TTATATTTAAAGTGNGTCTCTTGT-AAACAGCATATAGTTGNATNTTGTT 98
INTRON_3 321595 TTCT-GTTTAG-CTGACAGTCTTTGTCTTTTAATTGGAATTCTTAATCCA 321642
i -i ii - i i vi i?
C L1M5_orf2#LIN 97 TTTTTATCCAGTCTGACAATCTTTGTCTTTTAATTGGAGTATTTAGNCCA 48
INTRON_3 321643 TTTCCACTGAATGTTGTTACTGATATATTTGGATTTACATCTAC 321686
v i v vi i i i
C L1M5_orf2#LIN 47 TTTACATTTAATGTAATTACTGATATGTTTGGGTTTATATCTAC 4
Matrix = 20p37g.matrix
Transitions / transversions = 2.13 (32 / 15)
Gap_init rate = 0.03 (8 / 237), avg. gap size = 1.38 (11 / 8)
306 25.20 14.47 0.37 INTRON_3 321605 321839 78342 C L1MEf_5end LINE/L1 1885 2152 65 724
INTRON_3 321605 CTGACAGTCTTTGTCTTTTAATTGGAATTCTTAATCCATTTCCACTGAAT 321654
i i vi vi i? v i v
C L1MEf_5end#LI 2152 CTGACAATCTCTGTCTTTTAATTGGTGTGTTTAGNCCATTTACATTTAAT 2103
INTRON_3 321655 GTTGTTACTGATATATTTGGATTTACATCTAC-ACCTTATT---TATTTT 321700
vi i iv vi - ii --- i
C L1MEf_5end#LI 2102 GTAATTATTGATATGGTTGGATTTAGGTCTACCATTTTATTATTTGTTTT 2053
INTRON_3 321701 CTAATCATCC--TACATTTTCATGTTC----ATTTCCTGTATT-----TA 321739
iv ii -- vii i- ----i v v ----- v
C L1MEf_5end#LI 2052 CTGTTTGTCCCCTCTGTTTTT-TGTTCCTCTGTTTCCTCTTTTCTGCCTT 2004
INTRON_3 321740 ATTTTAAA--ATTCG----TGCTTAGTATTTCATTTTC-----TCTATAA 321778
v ii -- i ---- vi i v----- vi
C L1MEf_5end#LI 2003 CTTTTGGATTATTTGAATATTTTTAGTATTCCATTTTAATTTATCTATTG 1954
INTRON_3 321779 GCAGTTTA-TTAAA---CATTATA--ATTTTT--AGTGATTATTCTTGAA 321820
vv -i v --- v i -- -- i ii v ii
C L1MEf_5end#LI 1953 GCTTTTTAGCTATATCTCTTTGTATTATTTTTTTAGTGGTTGCTCTAGGG 1904
INTRON_3 321821 ATTATATAATACATTCTTA 321839
i vv ?
C L1MEf_5end#LI 1903 ATTACAATATACATNCTTA 1885
Matrix = 20p37g.matrix
Transitions / transversions = 1.48 (34 / 23)
Gap_init rate = 0.06 (13 / 234), avg. gap size = 2.69 (35 / 13)
+ 2318 33.7 5.0 4.7 INTRON_3 321899 322728 (77453) C PRIMAX-int LTR/ERV1 (313) 3789 2978 450
ANNOTATION EVIDENCE:
2318 33.70 5.05 4.73 INTRON_3 321899 322728 77453 C PRIMAX-int LTR/ERV1 2978 3789 313 742
INTRON_3 321899 TACAAATTTTAACTAGAACATATTTATAATCTTGATAT-GGAGGTGGCTG 321947
i iv v i i vi - iv- v ii
C PRIMAX-int#LT 3789 TGCAAATCATTACCAGAACATATTTGTATCCTTG-TGADGGTGGCAGCTG 3741
INTRON_3 321948 AATGAAATCCATTTGCCAAACCTCAGAGTGTCCATTAGGTAGGTTAAAAT 321997
i i i v v i i v vv v ii iivv i
C PRIMAX-int#LT 3740 GATAAAATCTAATTGCCATACTTCAAAGGGGGCCTCGGGTAAAGGAAAGT 3691
INTRON_3 321998 GACCT--GGAACTATCTGAATTGTCTTTCCTGGGTTGAATTTTGGACAAA 322045
v -- v - v - i iv i
C PRIMAX-int#LT 3690 GTCCTTGGGAACTATGT-AATGGT-TTTCCTGGATTATATTTTGGGCAAA 3643
INTRON_3 322046 CAGTACAAGACAGTTGTA-ACTATTTG-GC---AGCCCTTGAAATGTTTC 322090
i vv i-- ii - iv v - --- i vvv -
C PRIMAX-int#LT 3642 TATGACAG--CGATTGTATACCTTATGAGCTATAGTCAGAGAAA-GTTTC 3596
INTRON_3 322091 CCCACTAATAATACTGCTTT------ATAA--AATTTATCAGTTGCCCAG 322132
----- i i ------ii -- v i vvvi
C PRIMAX-int#LT 3595 C-----AATAATATTGTTTTCCCCAAGCAACCATTTTGTCAGGACTCCAG 3551
INTRON_3 322133 TTAGTCATCTGAT-ATGT-CATTTTGAGTAAGGTTTTTAAAA----GACA 322176
v i --- - i - -------- --- ---- -
C PRIMAX-int#LT 3550 TGAGTTA---GATCACGTACAT--------AGGTT---AAAATGATGAC- 3516
INTRON_3 322177 TATAGATTCTG------GTAATAGCAGTTTATTATTGGGACCATACCGTA 322220
i - v ------ vvi i---? ii v v i
C PRIMAX-int#LT 3515 TGTA-ATTCAGCAGAAAGTATGGGCAA---RTCGTTTGGCCCATACCATA 3470
INTRON_3 322221 AATTTGTTGTTGGGCAA--AAAATGCAATTGTTATCAGCTCAATATGATT 322268
v-i ii iv vi -- v v v vvi v i i-v i i----
C PRIMAX-int#LT 3469 C-CTCATCTTTGGGGGAGTATATTCCCCCTTTTGTT-TCCCAAC----TT 3426
INTRON_3 322269 TTTTAT-ATGAT------GCCCAAGACTGAGCACCTTTCACAACATCATT 322311
i -v ------ i vi i vvv i iiv -v
C PRIMAX-int#LT 3425 TTTTGTTCTGATTTTGGAGCTCTGGATTGAGCTAATTTTATGTCA-AATT 3377
INTRON_3 322312 TAAATCCTTTTTTGGAAAACAATCCATATCAGCTATAAGGTTTTAAGTCT 322361
i ii vi ii ---- v i iv vi i ----- ---
C PRIMAX-int#LT 3376 CAGGTGTTTCCTT----AAAAGTTAATATAGGTT-----GTTTT---TCT 3339
INTRON_3 322362 TAGTGGAAC---TCTAG-GTAGTTGCTTTTGCTGCATGATTAGCCAAGTC 322407
iv vii i--- i - i i vi i v v i i - ii
C PRIMAX-int#LT 3338 TGTTTAGATGCGTTTAGAGCAGCTCTTTTTGCTACTTTATCAGCTA-GCT 3290
INTRON_3 322408 GTTTTTCTTAGCCTT--------TCTAATTTAGAGTGCCCAGAAATTTTG 322449
v i v i -------- i i i v v i i
C PRIMAX-int#LT 3289 GATTTCCTTTGCTTTCTGGAGTATCTGATTTGGAATGACCTGGAATTTTA 3240
INTRON_3 322450 ATTATAGCCAAGGCAGAGGGAAGTTGAAT-TGAATT-TAATAAATTATTG 322497
v i iv vvvvv v i -- - iv - - i -
C PRIMAX-int#LT 3239 ATAATGGCCAGTGATTTTGGTAAT--AATATGGCTTCTAATAA-TTGT-G 3194
INTRON_3 322498 ACAAAAG--TTCCATTTTTAATTTGGTTCCCTCTG--GAGGTTAAAAATC 322543
v v --v v -- v ivvi v -- i i
C PRIMAX-int#LT 3193 AAATAAGATGTCCATTTTTTAT--GGATTGACCAGAAGAGGTTAAGAACC 3146
INTRON_3 322544 CTTTTTGTTTCCAAAGCACACCAAAATCACGAACAACCCCAAAGGCGTAA 322593
i v ivi i i v i i i v
C PRIMAX-int#LT 3145 CTCTTTGTTTCCATAGCATTTCAAAATCATGAGCTACTCCAAAAGCATAT 3096
INTRON_3 322594 CGGCTGTTGGTGTAAACGTTTGCAGTT-TTATTTTCACCAGAATATAAGC 322642
vi iv i ii v - vi ii ivvv i i
C PRIMAX-int#LT 3095 CTACTGTCTGTATAAATATTAGCAGTTATTCCTTTTGCCAATTGACAGGC 3046
INTRON_3 322643 CCTGATTAAGGC-ATAAAGTTCTGCTTGTTGGGCTGAAGTAGCCATCAGC 322691
i v - v - i i i -------
C PRIMAX-int#LT 3045 CCTAATTAATGCTATTAA-TTCTGCTTGTTGAGCTGAGGTGGC------- 3004
INTRON_3 322692 AGTGCAGCTTCTTCAACTATAGTCACGTGCTGCATGT 322728
-------- vv v- iv v v -- v
C PRIMAX-int#LT 3003 --------TTCTGGAAG-ATAAGCACTTTCT--ATTT 2978
Matrix = 20p37g.matrix
Transitions / transversions = 1.20 (121 / 101)
Gap_init rate = 0.06 (51 / 829), avg. gap size = 2.59 (132 / 51)
+ 1652 15.6 8.0 1.4 INTRON_3 322729 323054 (77127) + Tigger3a DNA/TcMar-Tigger 2 348 (0) 451
ANNOTATION EVIDENCE:
1652 15.56 7.98 1.44 INTRON_3 322729 323054 77127 + Tigger3a DNA/TcMar-Tigger 2 348 0 641
INTRON_3 322729 AGTCATGTGCTGCA------CATTTTTGTCAACT---GACCACATATATG 322769
i ii ------ i iv v--- i i
Tigger3a#DNA/ 2 AGTCATGCGCCACATAACGACGTTTCGGTCAACGACGGACCGCATATACG 51
INTRON_3 322770 ACAGTG-TCCCATAA--TTGTAATACCTTATTTTTACTGTACCTTTTCTA 322816
i - -- i v
Tigger3a#DNA/ 52 ACGGTGGTCCCATAAGATTATAATACCGTATTTTTACTGTACCTTTTCTA 101
INTRON_3 322817 TGTTGAGATATGTTTAAATATACAAATACTTAGCATCATGCTATAATTAC 322866
v i i v ii i i i
Tigger3a#DNA/ 102 TGTTTAGATATGTTTAGATACACAAATACTTACCATTGTGTTACAATTGC 151
INTRON_3 322867 CTACAGTATTTAGTACAGTAATATGCTATACAGGTTTTTAGCCTAGGAGC 322916
i i i v
Tigger3a#DNA/ 152 CTACAGTATTCAGTACAGTAACATGCTGTACAGGTTTGTAGCCTAGGAGC 201
INTRON_3 322917 AGTAGGCAATATCATATAAC-TAGGTATGTAG-AAGC--------CTAGG 322956
i v i i - i - i --------
Tigger3a#DNA/ 202 AATAGGCTATACCATATAGCCTAGGTGTGTAGTAGGCTATACCATCTAGG 251
INTRON_3 322957 TTT----AAGTATACTCTATAATATTCTGTTCATACAATGATGAAATTAC 323002
---- i i ----- ii i i ii
Tigger3a#DNA/ 252 TTTGTGTAAGTACACTCTATGAT-----GTTCGCACAACGACGAAATCGC 296
INTRON_3 323003 CCAACAATGCACTTCTCAGAATGTATTCCCGTACTTAAGAGATGCATGTC 323052
i i i i i i vv v i v
Tigger3a#DNA/ 297 CTAACGACGCATTTCTCAGAACGTATCCCCGTCGTTAAGCGACGCATGAC 346
INTRON_3 323053 TG 323054
Tigger3a#DNA/ 347 TG 348
Matrix = 18p37g.matrix
Transitions / transversions = 3.55 (39 / 11)
Gap_init rate = 0.03 (9 / 325), avg. gap size = 3.44 (31 / 9)
+ 2318 33.7 5.0 4.7 INTRON_3 323055 324521 (75660) C PRIMAX-int LTR/ERV1 (1125) 2977 1485 450
ANNOTATION EVIDENCE:
2318 33.70 5.05 4.73 INTRON_3 323055 324521 75660 C PRIMAX-int LTR/ERV1 1485 2977 1125 743
INTRON_3 323055 TACTTCAAGAAAAG---TTATAGTATATCTAGCACAATATTCTCCTATAT 323101
-- ivv ---i ii v iv ii vvi - v
C PRIMAX-int#LT 2977 --CTTCAGTTAAAGATACTATAGCGTAGCCTGCACGGTAGATTCC-AGAT 2931
INTRON_3 323102 TTTAATCTGTCATTTATGATGTGTCAGTAAACCATGAAAGTTCTGTATTT 323151
i-- iv i vv v vii v viv vv v ii v
C PRIMAX-int#LT 2930 TC--ATCCTTTAAGTAAGATCCATCTGTAAACCAAACAACATCAGCGTTA 2883
INTRON_3 323152 GGTCTAGGAATTTCATGTAAATTGACTTTAGGTTTTAG---CTGGCCACT 323198
vvvvi i i v ii iviiii vvvv ---i ii v
C PRIMAX-int#LT 2882 GTAAGGGGAGTCTCTTGTAGGTCTGTCCTAGGAGAGAGAAGTTGATCAGT 2833
INTRON_3 323199 TAGATTTGAACAGTCATGATGTGTCTCATCAACAGGTAGGGGAAGGAGGG 323248
iiv ivi i i vv ii i viv i ii v i i
C PRIMAX-int#LT 2832 TAAGGTTATGCAATCGTGCGGCATTTCATCTGAAAGTAAAGGCAGAAGAG 2783
INTRON_3 323249 TTACTGGATTAAGAGTATTGCAGTGAGAAAGAATG---TGAGAAATCAAC 323295
i v v vii i viv i vii --- iiii v
C PRIMAX-int#LT 2782 TTGCAGGATTTAGATCGTTACACCTAGAGATGGTGATATGAGAAGCTGAA 2733
INTRON_3 323296 AG---CAAGATCTCATAAGAAGTTAGTCTGCT--CAGAATAATACTGAGT 323340
--- i ii v ii -- v ii
C PRIMAX-int#LT 2732 AGAAGCAAAACTTCATATGAAGCCAGTCTGCTAACTGAATAATGTTGAGT 2683
INTRON_3 323341 ATGATGAGAGTTCTCTACGGTTTCTACAAAGCTTCTACAGCATGAAGAAC 323390
i v i --- --------i v i v i i
C PRIMAX-int#LT 2682 ATGGTGTGAATT---TA--------GCAATGCTTCCACAGAATGAGGGAC 2644
INTRON_3 323391 ATAGACAGTGAGAGTAGAGTTCGTGATTATCTCTTCTGTAGAGTTAATTA 323440
iv i i vv vvii i v iv i v v vv i
C PRIMAX-int#LT 2643 GAAGACAGTAAGGGGTGTTCCCATCACAATTTCTTCAGTTGCCTTAACTA 2594
INTRON_3 323441 AAGCTGTAGTGGCTGATATAGCTGTCATGCAGAGAGGGAGTC----AGCT 323486
vivv i v i v i ii v v i ---- i
C PRIMAX-int#LT 2593 ACAGAGCAGTGGCTGTTATGGCTCTCATACAAGGTGGCAATCCTCTAGCC 2544
INTRON_3 323487 ATTGAACCTAATTGCTGGCTATAATAGCCAATGGGTCTGTGTTGAACTCA 323536
iv iii i v v i i v v -
C PRIMAX-int#LT 2543 ACAGGGTCTAATTGTTGGCTATAATACCCTATAGGTCTATTTTGATCTC- 2495
INTRON_3 323537 ATGTTTTGGGGTAAAGAACCCCCAACACATTTATTTATTTTTCATGCACA 323586
- v i v i v iv vi i vivivvi i
C PRIMAX-int#LT 2494 -TGTTTTTGAGTTAGGACCCCTAAAAGCGTTTCCACCACTTTCATGTACA 2446
INTRON_3 323587 AA-AATGAAGAAAGAGAGCTGATGATTGGGGTACCTTAAGGCAGGAAGAC 323635
- i vi iv i - i v i i ii i v iiv i
C PRIMAX-int#LT 2445 AATAATGAAAATGGAATGTT-ATAATTTGGATGCCCCAAAGCTGGGGTAT 2397
INTRON_3 323636 TTAGAAATCCTTCTTTTGATAG-----AAGGCCATACAGGCATTCT-CTT 323679
v ivi v - vi----- v ii -i v iiv - v
C PRIMAX-int#LT 2396 TTACAAGGTCAT-TTTTGATCATTTCTAATGTTA-GCTGATTTTCTTCTG 2349
INTRON_3 323680 TTTAGCCCAGGGGATCTGGGTTGTCAAATTTCTGAAGAGCATATAAGGGT 323729
ii ii i i i vv vvi ivii i
C PRIMAX-int#LT 2348 TCCAATCTAGAGGGTCTGGCATGTCTTGTTTTAAGAGAGCATATAAGGGC 2299
INTRON_3 323730 TATGCTATCAAAGGAAAATTAGGTATTCAGTTTTGACAGAA-CCTGCCAG 323778
iv v i i i v v i i iv iv -
C PRIMAX-int#LT 2298 TGAGCTTTTAAAGAAAAGTTTGGAATCCAATTTCTACAATATCCTGCCAG 2249
INTRON_3 323779 CCCCTATCTCCTTTGTAATAGTCTC--AGTCTGAGATTG-AGGAAAGTTT 323825
i i vvv i iv iv i --i iivv i v - i i v
C PRIMAX-int#LT 2248 TCCCCAAAACCCTCTTAACTGTTTCTTGGTTCTCGGTGGCAGAAAAGCTA 2199
INTRON_3 323826 AAATACCATTAAGTCTGTCAGGATCCAAGAGAAGTCCTTGGTTTTATATC 323875
v v v i i v iv vi i vv vv i
C PRIMAX-int#LT 2198 AAATTCCTTTTAATCTATCTGGATTAATAAAAAGTCCTTCCTTGGATATT 2149
INTRON_3 323876 ATGTATCCCAAATGTTTGACATGGTCCTGGGTAAATTATAGTCTTTCCCT 323925
v iv i i ii v v v ii ivv iv i ii
C PRIMAX-int#LT 2148 AGGTGACCTAAGTACTTTACTTGTTTTTGACAAAATTGAAGTTTTTCTTT 2099
INTRON_3 323926 GGAAACTTTGTGGATTTTGTCTGCTAGAAGTT-TAAGGAGATGAA---CA 323971
i i i vvii vvvv i ivv - vi - ---
C PRIMAX-int#LT 2098 AGAAACCTTATGTCCCTTTAGGGCCAATTGTTGTAACAAG-TGAATCCCA 2050
INTRON_3 323972 T---------AATCATGTTCA--CAAGGAACAAAGAAGGAGGTCATCAAC 324010
--------- v v i -- vvv i i v ii i v i
C PRIMAX-int#LT 2049 TCTTCTATGGAAGCTTGTTTATCCTCTGAGCAGAGAAGTAAATTATCTAT 2000
INTRON_3 324011 ATACTGCAAGAGAGTCAATCCTTGGGGGAAAGACATGTCTG-TTAAATAT 324059
i i i vv iii vi iii vii ivvv ii -vv ii v
C PRIMAX-int#LT 1999 GTATTGTATTAAGATGGATTTCTCAAGGAAGTCAACATCTGAGGAGGTCT 1950
INTRON_3 324060 GTCTTCAGTATCTG--AAAAGTAGGGAGGGCTTTTGGTATACCCTCAAGA 324107
i i i i -- i vv i ii i i iii i
C PRIMAX-int#LT 1949 GTTTTTAATATTTGTGAAAAGTAAGTTGGGCTCTCAGTGTATCCCTGAGG 1900
INTRON_3 324108 CATTACTATCTAGGTATATTGTTGACTTTCCTACGTGAAGACAAATAAAA 324157
v i i i i iviii i v i v i
C PRIMAX-int#LT 1899 CATGACTGTCCAAGTGTATTGTCTGTCTTCCCAAGTGAAGGCAAAGAGAA 1850
INTRON_3 324158 TTTGACTCCCAGTGTCCACATGAATGCTTTTTTTAAAAAA-GTA--ATAT 324204
v viivv i i i v ------ i - i -- i
C PRIMAX-int#LT 1849 ATTGACTGTTTTTATCTATAGGAATGCT------AAAGAATGCACTACAT 1806
INTRON_3 324205 AAAAGTATGTCACTATAAAA------TTTACATTCTGTGAGGATGGAAGT 324248
vv v v v i ------ i ? vvi - i i v ?
C PRIMAX-int#LT 1805 AAATCTATGACAGTAAAGAAAARAATTCTWCATTAGATG-GAATAGCAGY 1757
INTRON_3 324249 CATGAGAGTATGGAGATTTGGAATGACAGGGTGTCAAAGAGTGACAATAT 324298
v vv iv ?i v iv v i ?ii i i v i
C PRIMAX-int#LT 1756 GAACAATGTATGRGGATTTGGCACTACTGGATGWTGAGGAATGACTATGT 1707
INTRON_3 324299 TATTAATGTTTCATAGGTCTTGTATAAATCTCCATCCATGTCCATGAGAT 324348
i vvi vi ?i i i i vivv vv i
C PRIMAX-int#LT 1706 TGTTAATTGCTCTCARATCCTGTACAAACCTCCATCCTCTACCATTTGGT 1657
INTRON_3 324349 GTCTTTATAGGAAGGTTAGGAGTACTACAGGGGCTAGTACTAGGCGCCAC 324398
v ii iv ? iv v ? i ? v vi? viiv i
C PRIMAX-int#LT 1656 TTTCTTACCGGNAGAATTGGSGTATTACASGGGCTTGTACAGRGAATGAT 1607
INTRON_3 324399 AAGATTCCTAGCTTTACATTCTTCTGTAATT---GGCTTAATTTCTGCAG 324445
v -- vvi i vv - iv --- i v i v ?i
C PRIMAX-int#LT 1606 CAG--TCCTCTTTTTATATAAT-CTAAAATTATAGGTTTTATTCCTTCNA 1560
INTRON_3 324446 AAGTTTCAGGATTTAAGGAGTATTGTCTGATATTAGGAAGGGGCTTGTTT 324495
i i vvi i ii i v i i vvv
C PRIMAX-int#LT 1559 AGGCTTCAGTTCTCAAGGGATATTGTTTGATATTTGGAAGAGGTTTTGAT 1510
INTRON_3 324496 GGGTCAATTTGAGTCTTTATCAGGAG 324521
i v i i i-
C PRIMAX-int#LT 1509 GAGTCTATTTGAATTTTTATT-GGAG 1485
Matrix = 20p37g.matrix
Transitions / transversions = 1.34 (289 / 216)
Gap_init rate = 0.03 (37 / 1466), avg. gap size = 2.49 (92 / 37)
+ 361 33.6 2.5 6.6 INTRON_3 324700 324935 (75246) C MER101-int LTR/ERV1 (1025) 5614 5388 452
ANNOTATION EVIDENCE:
361 33.58 2.54 6.61 INTRON_3 324700 324935 75246 C MER101-int LTR/ERV1 5388 5614 1025 744
INTRON_3 324700 TTAAGAATTATCTTACCCTTATGGGAAAAGGTAAT---GGCCACATGATG 324746
i v i iv v i v --- --- iii
C MER101-int#LT 5614 TCAAGCATTATTTCCCCCTTTTGGGAGAAGGAAATATGGGCC---TGGCA 5568
INTRON_3 324747 TTTTCCTAAGAAGTCCCTTCCAAGTAAGTGAACTGGGGCCAAGAGAACTG 324796
vv i i v v i v iv i vi i --
C MER101-int#LT 5567 GGTTTCTAAGAAGTCCCTTTCCAGGAGGTGTATGGGGGCCGATGGGAC-- 5520
INTRON_3 324797 GTTAAAAAAAAAAAAAAAAAGAATGATTGT-AGAA--CCTAATTGAAAAA 324843
------ ivi iv v v viv - ii-- i i ii
C MER101-int#LT 5519 ------AAGCGAAAAGCAATGACTGCCAGTGAGGGGTCCTAGTTGGAAGG 5476
INTRON_3 324844 GCAAGGGGAAAGATTTGTAAACTGTTAAAGGTATATTAGAAACTCCTACC 324893
v vi v i ivi ii i v ivvi i vv i v
C MER101-int#LT 5475 GAATAGGTAGAGATTTAGGAACCATCATAGGCTGGTTGGCTACCCCGACC 5426
INTRON_3 324894 ATTTGCATTTTTTTTCAGTACTTCAAGGAAGGAACTGGTTGA 324935
i v vvv -- v i ii i i? --
C MER101-int#LT 5425 ATCTGGATGAATT--CAGAACTCCGGGGAGGGGNC--GTTGA 5388
Matrix = 20p37g.matrix
Transitions / transversions = 1.28 (41 / 32)
Gap_init rate = 0.03 (7 / 235), avg. gap size = 3.00 (21 / 7)
+ 1932 15.8 3.0 2.1 INTRON_3 325667 326002 (74179) + MER1B DNA/hAT-Charlie 1 339 (0) 453
ANNOTATION EVIDENCE:
1932 15.81 2.98 2.06 INTRON_3 325667 326002 74179 + MER1B DNA/hAT-Charlie 1 339 0 642
INTRON_3 325667 CAGGGATCCACAACACCTGGGCCACAGAGGGGTACTGGTCCATGGCCTGC 325716
i v v i i i vv i i i
MER1B#DNA/hAT 1 CAGGGGTCCCCAACCCCCGGGCCGCGGACCGGTACCGGTCCGTGGCCTGT 50
INTRON_3 325717 TAGGAACAGGTCCACATGGCAGGAGGTGAGTAGCAGGCAAGCAAGTTGAG 325766
v v i ii ii i i -----
MER1B#DNA/hAT 51 TAGGAACCGGGCCGCACAGCAGGAGGTGAGCGGCGGGCGAGC-----GAG 95
INTRON_3 325767 TGCTGACTACCTGAGCTCTGCCTTCTATCAGATCAGCAGTGGCATTAGAT 325816
iii - ii i i i i i
MER1B#DNA/hAT 96 CATT-ACCGCCTGAGCTCCGCCTCCTGTCAGATCAGCGGCGGCATTAGAT 144
INTRON_3 325817 TCTCACAGGAGCATGAACCCTACTGTGAACTGCACAAGCGAGGGATATAG 325866
i ii i i v v
MER1B#DNA/hAT 145 TCTCATAGGAGCGCGAACCCTATTGTGAACTGCGCATGCGAGGGATCTAG 194
INTRON_3 325867 GTTGTGTGGTCCTTATGAGAATCTAATGCCTACCGATTGGAGGTGGAACA 325916
i v ivi iv
MER1B#DNA/hAT 195 GTTGCGTGCTCCTTATGAGAATCTAATGCCTGATGATCTGAGGTGGAACA 244
INTRON_3 325917 ATTTCATC--------ATCCCCC--ACCCCCAGCCTGTGGAAAAAATTGT 325956
i -------- -- i i i -
MER1B#DNA/hAT 245 GTTTCATCCCGAAACCATCCCCCCCACCCCCGGTCCGTGGAAAAA-TTGT 293
INTRON_3 325957 CTTCCAAGAAACCGGTCCCTGGTGTCAAAAAGATTGGGGACTGCTG 326002
v i i i
MER1B#DNA/hAT 294 CTTCCACGAAACCGGTCCCTGGTGCCAAAAAGGTTGGGGACCGCTG 339
Matrix = 18p37g.matrix
Transitions / transversions = 3.33 (40 / 12)
Gap_init rate = 0.01 (5 / 335), avg. gap size = 3.40 (17 / 5)
+ 1250 20.8 1.3 0.0 INTRON_3 326074 326309 (73872) + MER8 DNA/TcMar-Tigger 1 239 (0) 454
ANNOTATION EVIDENCE:
1250 20.76 1.27 0.00 INTRON_3 326074 326309 73872 + MER8 DNA/TcMar-Tigger 1 239 0 643
INTRON_3 326074 CAGCTAAACATTGAATAACACAGATTTGAAGTACATGGGTCCACTTATAT 326123
i i v v i i i v i ii i
MER8#DNA/TcMa 1 CAGTTGACCCTTGAACAACACGGGTTTGAACTGCGCGGGTCCACTTATAC 50
INTRON_3 326124 GTGGATTTTTT-CAACCAAAAGTGGATTGAAAATACGGTATTCACAGGAT 326172
i - v i i i i i
MER8#DNA/TcMa 51 GCGGATTTTTTTCAACCAAACGCGGATCGAAAATACAGTATTCGCGGGAT 100
INTRON_3 326173 GCAAAAGCTGCATATATGGAGGGCCAACTTTTCATATATGCTGATTG-GT 326221
i v i i i i i i v i v- i
MER8#DNA/TcMa 101 GCGAAACCCGCGTATACGGAGGGCCGACTTTTCGTATACGCGGGTTCCGC 150
INTRON_3 326222 GGGGCCAACTGAGGGACTGGAGTATGAACAGATTTGGGTATA-GCATGGG 326270
i i v v vi i v - iv
MER8#DNA/TcMa 151 AGGGCCGACTGCGGGACTTGAGTATGCGCGGATTTTGGTATACGCGGGGG 200
INTRON_3 326271 TCCGGAAACCAATCCCTTGTGTATACTGAGAGATGACTG 326309
v i ii i i i i
MER8#DNA/TcMa 201 TCCTGGAACCAATCCCCCGCGTATACCGAGGGACGACTG 239
Matrix = 18p37g.matrix
Transitions / transversions = 2.77 (36 / 13)
Gap_init rate = 0.01 (3 / 235), avg. gap size = 1.00 (3 / 3)
+ 28 53.6 0.0 0.0 INTRON_3 327344 327371 (72810) + AT_rich Low_complexity 1 28 (0) 455
ANNOTATION EVIDENCE:
28 53.57 0.00 0.00 INTRON_3 327344 327371 72810 + AT_rich Low_complexity 142 169 131 700
INTRON_3 327344 TAAAAAATAAAATAAAAATAAAAAAAAA 327371
vv v vv v vv???????
AT_rich#Low_c 142 TAAAAATAAATAATATAATTTWWWWWWW 169
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 8)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 430 27.8 0.0 1.5 INTRON_3 327758 327892 (72289) C L1MEg LINE/L1 (4330) 3003 2871 447
ANNOTATION EVIDENCE:
430 27.83 0.00 1.50 INTRON_3 327758 327892 72289 C L1MEg_5end LINE/L1 1622 1754 347 725
INTRON_3 327758 AATGTAAATTAGTAATTTTATAATGTACTCGACAACACAAGGGCCATAAA 327807
i -i iv iv v iv ii i v i
C L1MEg_5end#LI 1754 AATATAAATTAGTA-CTTTACCACTTCCCGGACAATGCAAGGACCTTAGA 1706
INTRON_3 327808 ATACTTTAAATCTATTTATCCACTCTCCATCGTTTATGCTGCTGTTGTCA 327857
i v i i v i -i v i i ii
C L1MEg_5end#LI 1705 ACACTTTAACTCCATTTACCCTCTCTTC-CCTTTTGTGTTATTGTTGTCA 1657
INTRON_3 327858 TTTGCCTTATTACTCTGTATATTTTGCAGCCCACA 327892
v iii v v ? i iv v
C L1MEg_5end#LI 1656 TGTATTTTAATTCTNTATATATTTTAAACCCCACA 1622
Matrix = 20p37g.matrix
Transitions / transversions = 1.77 (23 / 13)
Gap_init rate = 0.01 (2 / 134), avg. gap size = 1.00 (2 / 2)
+ 197 3.3 3.3 0.0 INTRON_3 327960 327989 (72192) + (CAAA)n Simple_repeat 2 32 (0) 456
ANNOTATION EVIDENCE:
197 3.33 3.33 0.00 INTRON_3 327960 327989 72192 + (CAAA)n Simple_repeat 6 36 144 747
INTRON_3 327960 AAACAAACAAAAAAACAAA-AAACAAACAAA 327989
v -
(CAAA)n#Simpl 6 AAACAAACAAACAAACAAACAAACAAACAAA 36
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 1)
Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1)
+ 2804 3.0 0.0 0.3 INTRON_3 328050 328384 (71797) C L1PA4 LINE/L1 (3) 6152 5819 457
ANNOTATION EVIDENCE:
2804 3.00 0.00 0.30 INTRON_3 328050 328384 71797 C L1PA4_3end LINE/L1 566 899 3 649
INTRON_3 328050 TTTTATTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACATGCA 328099
v i
C L1PA4_3end#LI 899 TTTTTTTATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACGTGCA 850
INTRON_3 328100 GGTTTGTAACATATGTATACGTGTGCCATGTTGGTGTGCTGCACCCATTA 328149
v i
C L1PA4_3end#LI 849 GGTTTGTTACATATGTATACATGTGCCATGTTGGTGTGCTGCACCCATTA 800
INTRON_3 328150 ACTCGTCATTTAGCATTAGGTATATCTCCTAATGCTATCCCTCCCCCCTC 328199
i
C L1PA4_3end#LI 799 ACTCGTCATTTAACATTAGGTATATCTCCTAATGCTATCCCTCCCCCCTC 750
INTRON_3 328200 CCCCCCACCCCACAACAGTCCCTGGTGTGTGATGTTCCCCTTCCTGTGTT 328249
- v i i
C L1PA4_3end#LI 749 CCCCC-ACCCCACAACAGGCCCCGGTGTGTGATGTTCCCCTTCCTGTGTC 701
INTRON_3 328250 CATGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAACATGCGGTGT 328299
C L1PA4_3end#LI 700 CATGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAACATGCGGTGT 651
INTRON_3 328300 TTGGTTTTTCGTCCTTGCGATAGTTTGCTGAGAATGATGGTTTCCAGCTT 328349
i
C L1PA4_3end#LI 650 TTGGTTTTTTGTCCTTGCGATAGTTTGCTGAGAATGATGGTTTCCAGCTT 601
INTRON_3 328350 CATCCGTGTCCCTACAAAGGACATGAACTCATCAT 328384
i
C L1PA4_3end#LI 600 CATCCATGTCCCTACAAAGGACATGAACTCATCAT 566
Matrix = 18p37g.matrix
Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.00 (1 / 334), avg. gap size = 1.00 (1 / 1)
+ 574 25.6 0.8 0.0 INTRON_3 328385 328505 (71676) C MLT2E LTR/ERVL (506) 122 1 458
ANNOTATION EVIDENCE:
574 25.62 0.83 0.00 INTRON_3 328385 328505 71676 C MLT2E LTR/ERVL 1 122 506 773
INTRON_3 328385 GCATTTTAAATCTTACGTAAATTCGTTGTTGGCCAACTCTAACATAGAAC 328434
v iii ii i ? v iv vi
C MLT2E#LTR/ERV 122 GCCTCCCAAATCTCGCGCAANTTCCTCTTTGGCCAACTCTAACCCAGAAC 73
INTRON_3 328435 GATAGGGAGAAGAGGACGTGGAGAAATGTAGTTTCCAGCTTAACCAAGTT 328484
v vi i i iviv i i i
C MLT2E#LTR/ERV 72 CATACAGGGAAGGGGATTCTGGGAAACGTAGTTCCCAGCTTAACCAAGTT 23
INTRON_3 328485 AGCA-CAACACAAACCATCACA 328505
ii - i? ? ?
C MLT2E#LTR/ERV 22 GACAACAGNACAASCCAWCACA 1
Matrix = 20p37g.matrix
Transitions / transversions = 2.38 (19 / 8)
Gap_init rate = 0.01 (1 / 120), avg. gap size = 1.00 (1 / 1)
+ 835 28.3 8.9 4.0 INTRON_3 328506 328948 (71233) C L1MEg LINE/L1 (5556) 1777 1338 447
ANNOTATION EVIDENCE:
835 25.76 10.92 2.94 INTRON_3 328506 328789 71392 C L1MEg_5end LINE/L1 223 528 1573 726
INTRON_3 328506 TCATTTTCTTTCAGTAAATATTTACT---------GGCAGACAGATTAGG 328546
i i i i vi iv --------- i -i
C L1MEg_5end#LI 528 TTATCTTCCTCCAGAGAGGATTTACTTTTGCTTCTGGCAGGCAG-CTAGG 480
INTRON_3 328547 GGC---------CAG-TTATCTCAATCCTAGTTGGAACCCCGCTGACTTG 328586
--------- - i i i v viv i iivv ? i i
C L1MEg_5end#LI 479 GGCACTAGCAATCAGATCACCTTAATCCAATCAGGGATTGAGNTGATTCG 430
INTRON_3 328587 AAGCTTG-TTTCTGTCTTTGTAAGGACCATTTTATTTCTGGTTCATTCTT 328635
v -i v i i iiv i i iii
C L1MEg_5end#LI 429 AAGCTGGGCTTCAGTCTTTGTGAGGGCTGGTCTATTTCCGGTTCGCCCTT 380
INTRON_3 328636 ACTCTTAGGTTGCATCCTTTCAGGTTCCCAACAGGAAGCATAGGAAATTT 328685
i v i v i i v v i - i i--
C L1MEg_5end#LI 379 ACTCCTAGGGTGTAGCCCTTCGGGGTCCCAACTGAAAGC-TGGGG--TTT 333
INTRON_3 328686 ACCAGGGCATATCCTCCC-----------AAACTACAAGTGCTGTACTTG 328724
viv i-----------i v v vi - i-
C L1MEg_5end#LI 332 ACCAGGGCCCCTCCTCCTTGGCGGGCCCTGAACTCCAATTTTTGT-CTC- 285
INTRON_3 328725 TATCCCAGCACTGTGAGACTGCCAGAAACTGTGCTCAGAGTCTTAGCCTC 328774
--- v i ii i v vv i
C L1MEg_5end#LI 284 ---CCCAGCCCCGTGAGACTGCCGAAAGCTCTGCTCAGCTTCTCAGCCTC 238
INTRON_3 328775 TTAGCTGCTGCTTTC 328789
i i i
C L1MEg_5end#LI 237 TCAGCCGCCGCTTTC 223
Matrix = 20p37g.matrix
Transitions / transversions = 2.04 (47 / 23)
Gap_init rate = 0.04 (10 / 283), avg. gap size = 4.00 (40 / 10)
386 35.00 8.44 3.58 INTRON_3 328722 328948 71233 C L1MEg1_5end LINE/L1 97 336 447 727
INTRON_3 328722 TTGTATC-CCAGCACTGTGAGACTGCCAGAAACTGTGCTCAGAGTCTTAG 328770
v? - v iii i i i v -i vv iv
C L1MEg1_5end#L 336 TTGTCNCTCCAGCCCCACGAGACCGCCAAAAGCTCTGCT-GGTTTCTCTG 288
INTRON_3 328771 CCTCTTAGCTGCTGCTTTCTCCTTA-------TTCAGCTTCTTGGCTCTG 328813
i i ii v v ii v iii-------ii i v ii i---
C L1MEg1_5end#L 287 TCCCCCAGCAGCGGCCCTCTGCCCGGGCAAAGCCCGGATTCTCAGCC--- 241
INTRON_3 328814 TTTTGCATGTG-----AATCAGCAACTGCTTTGAAAGGAAA-GCCATGAA 328857
i vi ----- i v iiiv ii i - viiviv
C L1MEg1_5end#L 240 TCTTGCCCGTGCCCAGAATCGGCAAATGCCCCCAGGGAAAAAGCGGCTGC 191
INTRON_3 328858 AGA----CAGCTAACCTCAATTAGGGATTTTTCTTTC-ATAGA-TCT-AC 328900
---- v -- i?i? i i i ii -v i - - v
C L1MEg1_5end#L 190 AGATCGTCAGCTCACCTC--TCNANGGTTCTCCCCTCTCTGGAATCTTAG 143
INTRON_3 328901 CTGTTATA-TACTGCCTGTCTTGACAACTATATGATGCCTTCAAACTGA 328948
ivi v - v vvi ii iii i v v i ---
C L1MEg1_5end#L 142 CCCCTCTAGTCCTCGTTGCTTCAGCAGCTCTCTGATGCCTTTAAAC--- 97
Matrix = 20p37g.matrix
Transitions / transversions = 2.04 (53 / 26)
Gap_init rate = 0.06 (13 / 226), avg. gap size = 2.38 (31 / 13)
479 26.68 6.88 5.43 INTRON_3 328797 328948 71233 C L1MEg_5end LINE/L1 89 245 1856 728
INTRON_3 328797 TCAGCTTCTTGGCT-CTGTTTTGCATGTGAATCAGCAACTGCTTTGAAAG 328845
i ii i- i i ---i - i v i i ii
C L1MEg_5end#LI 245 TCAGCCTCTCAGCCGCCGCTTT---CG-GAATCGGCAAATGCCTCGAGGG 200
INTRON_3 328846 GAAA----GCCATGAAAGACAG-CTAACCTCAATTAGGGATTT--TTCTT 328888
---- ?vi v v i - v -- iv v i-- i
C L1MEg_5end#LI 199 GAAAAGCGGCNCCGAATGTCGGGCTCACCTC--TCTGGGCTTCCCTTCTC 152
INTRON_3 328889 TCATAGATCT--ACCTGTTATATACTGC-CTGTCTTGACAACTATATGAT 328935
vvi --i iv i v v iv - i ii i v vi
C L1MEg_5end#LI 151 TCCGGGATCTTGGCCCCTCAAATTCCTCGCTGCCTTGGTAGCTCTCCGAT 102
INTRON_3 328936 GCCTTCAAACTGA 328948
v
C L1MEg_5end#LI 101 GCCTTCAAACAGA 89
Matrix = 20p37g.matrix
Transitions / transversions = 1.69 (27 / 16)
Gap_init rate = 0.06 (9 / 151), avg. gap size = 1.89 (17 / 9)
+ 1688 14.8 2.4 5.2 INTRON_3 328949 329246 (70935) C AluJr SINE/Alu (22) 290 1 459
ANNOTATION EVIDENCE:
1462 16.28 2.35 5.17 INTRON_3 328949 329246 70935 C AluJb SINE/Alu 1 290 22 634
INTRON_3 328949 TTTTTTTCGAGGTAGTGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGG 328998
i ii v i i
C AluJb#SINE/Al 290 TTTTTTTTGAGACAGGGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGG 241
INTRON_3 328999 TGCCATCATGGCTCGCTGCAGCCTCAACCTCTCAGGCTCCAGTGATCCTC 329048
i v i i i i i v i
C AluJb#SINE/Al 240 CGCGATCACGGCTCACTGCAGCCTCGACCTCCCGGGCTCAAGCGATCCTC 191
INTRON_3 329049 CTGCCTCAGCCTCCTGAGTA-CTGGGACCACAGGTGCATGCTACCACACC 329097
i - i i ii i i
C AluJb#SINE/Al 190 CTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCGCGCCACCACGCC 141
INTRON_3 329098 AGGCTAATTTTATTTTTATTTATTGTTTTACTTTTGTGGAGATGGGTGTC 329147
v --- v ----------- i i - i
C AluJb#SINE/Al 140 CGGCTAATTTT---TGTATTT-----------TTTGTAGAGACGGG-GTT 106
INTRON_3 329148 TCCCTTTGTTGCCTGGGCTGGTCTAGAATTCCTGGCCTCAAGCAGTCCTC 329197
v iv ii v i v iii
C AluJb#SINE/Al 105 TCACCATGTTGCCCAGGCTGGTCTCGAACTCCTGGGCTCAAGTGATCCTC 56
INTRON_3 329198 CTGCCTTGGCCTCCCAAAGTGCTGG----ACAGGCTCGGGCAACTGC--C 329241
i i ---- vi i v i --
C AluJb#SINE/Al 55 CCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCC 6
INTRON_3 329242 TGGCC 329246
i
C AluJb#SINE/Al 5 CGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 3.18 (35 / 11)
Gap_init rate = 0.02 (6 / 297), avg. gap size = 3.67 (22 / 6)
+ 479 29.1 7.3 4.9 INTRON_3 329247 329338 (70843) C L1MEg LINE/L1 (5996) 1337 1274 447
ANNOTATION EVIDENCE:
386 35.00 8.44 3.58 INTRON_3 329247 329338 70843 C L1MEg1_5end LINE/L1 2 96 687 729
INTRON_3 329247 AAACTGATTTTTAAAATT-GTTT---TTTTCTAGTTATTCTCAGCAGGAA 329292
- ?v iv v -i i --- i i i i
C L1MEg1_5end#L 96 -ANATGATTTTTGTATTTTATCTAGCTTTTCTAGTTGTTCTCGGCGGGAG 48
INTRON_3 329293 GATTGGTCTGATACAGCCTGACTCT-TCCTAACCAAGAATGGAAATC 329338
v vii iv - i- v iii iii i
C L1MEg1_5end#L 47 CATTGGTCTGCCGCAAGCT-ACTCCATCCTACCCGGAAGCAGAAGTC 2
Matrix = 20p37g.matrix
Transitions / transversions = 2.57 (18 / 7)
Gap_init rate = 0.05 (5 / 91), avg. gap size = 1.40 (7 / 5)
479 26.68 6.88 5.43 INTRON_3 329247 329311 70870 C L1MEg_5end LINE/L1 25 88 2013 730
INTRON_3 329247 AAACTGATTTTTAAAATT-GTTT---TTTTCTAGTTATTCTCAGCAGGAA 329292
---- v v v - ii--- i i i
C L1MEg_5end#LI 88 ----TGTTTTTTATATTTTGTCCAGCTTTTCTAGTTGTTCTCAGCGGGAG 43
INTRON_3 329293 GATTGGTCTGATACAGCCT 329311
i - i?
C L1MEg_5end#LI 42 GGTTGGTCTGA-ACAANCT 25
Matrix = 20p37g.matrix
Transitions / transversions = 2.33 (7 / 3)
Gap_init rate = 0.06 (4 / 64), avg. gap size = 2.25 (9 / 4)
+ 436 25.5 9.7 1.9 INTRON_3 329459 329602 (70579) C Helitron3Na_Mam RC/Helitron (3) 483 329 460
ANNOTATION EVIDENCE:
436 25.49 9.72 1.94 INTRON_3 329459 329602 70579 C Helitron3Na_Mam RC/Helitron 329 483 3 774
INTRON_3 329459 GCTGATCTCCCTA---CTGCTGAAGAGAATTGTCTGCCATAGTTAAATTA 329505
ii ii---i vii ii ivi v v
C Helitron3Na_M 483 GCTGGCCTCCCCGGCGTTGCTCGGGAGAATCATTAACCATCGTTAAATAA 434
INTRON_3 329506 ATAAAACTCTGCTGCTTCTTACCCTGGAGCATTGTAATACTTGAAGTTGC 329555
v i v i i- i-- v ii
C Helitron3Na_M 433 ATAAATCCCTGCTGCTACTCACCCTGGAGCAC-GC--TACATAGAGTTGC 387
INTRON_3 329556 CCAAATAACAAGCA-------TGCAA-TAAAT---TGCAGTTTGATGTAT 329594
vi i v ------- - v i--- i i iv ii
C Helitron3Na_M 386 CCATGTGAGAAGCAGCTCGATTGCAAATCAACGCCTGCAATTCGGAGCGT 337
INTRON_3 329595 CTGCCCTT 329602
C Helitron3Na_M 336 CTGCCCTT 329
Matrix = 20p37g.matrix
Transitions / transversions = 2.27 (25 / 11)
Gap_init rate = 0.04 (6 / 143), avg. gap size = 2.83 (17 / 6)
+ 351 33.1 0.0 0.0 INTRON_3 329616 329742 (70439) C Helitron3Na_Mam RC/Helitron (191) 295 169 460
ANNOTATION EVIDENCE:
351 33.07 0.00 0.00 INTRON_3 329616 329742 70439 C Helitron3Na_Mam RC/Helitron 169 295 191 775
INTRON_3 329616 ATTGATTGTTTTCTCTGTCTCTGGTATTTTAATCAATGTTGCCTTTTCCT 329665
i v ivi i i vvi i v v v ii
C Helitron3Na_M 295 ACTGTTTGTTTTCTCTGTCCACGGCATCTTAATACGTATGGCATGTCTCT 246
INTRON_3 329666 TTCGTTGGGCAGTCATGTGGGTCTGCAATCATGCTTCACTTTCAGCTGCT 329715
ii v v iii i vivi ii i i v
C Helitron3Na_M 245 CCCGATCGGCAGTCACACGGGCCTCTCGTTGTACCTCAGTTTCAGCTGCT 196
INTRON_3 329716 TGTGATGATGATTGTCTGCCTCTTTAA 329742
ivv v i i ii i
C Helitron3Na_M 195 CTGGAGGATGACTGCCTATCTCTTTGA 169
Matrix = 20p37g.matrix
Transitions / transversions = 1.80 (27 / 15)
Gap_init rate = 0.00 (0 / 126), avg. gap size = 0.0 (0 / 0)
+ 244 29.9 1.5 0.0 INTRON_3 329793 329859 (70322) C Helitron3Na_Mam RC/Helitron (394) 92 25 460
ANNOTATION EVIDENCE:
244 29.85 1.49 0.00 INTRON_3 329793 329859 70322 C Helitron3Na_Mam RC/Helitron 25 92 394 776
INTRON_3 329793 ATATTTTCCAAATTTGATAAAAATTTATGTAGTCATTTTTACTTGACATG 329842
iii i i ii vi i iiiv iii
C Helitron3Na_M 92 ATACCCTCCAAATTTGGTGAAAATCCATCCAGCCATTTTCGTGTGATGCG 43
INTRON_3 329843 G-AACAGAGAAATAGACA 329859
- v i ?
C Helitron3Na_M 42 GTAACAGACAAACAGANA 25
Matrix = 20p37g.matrix
Transitions / transversions = 5.33 (16 / 3)
Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1)
+ 455 24.9 3.3 1.6 INTRON_3 329883 330066 (70115) + L1M5 LINE/L1 4247 4433 (1713) 461
ANNOTATION EVIDENCE:
455 24.86 3.26 1.60 INTRON_3 329883 330066 70115 + L1M5_orf2 LINE/L1 2138 2324 970 731
INTRON_3 329883 AATCTACAAAAATACTGGCAGGACTAATAAGTGAGTTTAGCTAAATTATA 329932
i v v i ivi i i i v ii iv
L1M5_orf2#LIN 2138 AATCTACAGATAAATTATTAGAATTAATAAGTGAATTTAGCAAGGTTACT 2187
INTRON_3 329933 GGCTATAAAGTCAATACACAAAAATCTATTATATTTCAATATATTAGTCA 329982
v i i v i v i iv
L1M5_orf2#LIN 2188 GGATACAAAGTCAATATACAAAAATCAATTGTATTTCTATATACTAGCAA 2237
INTRON_3 329983 CAAATAACTGGAAAATAAAATATTTTAAA-----TTTTTTTTTCAATTTT 330027
i i i -- ? ----- viiv v vvi
L1M5_orf2#LIN 2238 CAAACAATTGGAAAATGAAAT--TTNAAAAACAATACCATTTACAATAGC 2285
INTRON_3 330028 ATTAAAAA-CATTAAAAAACTCAGTATCAAATTTGATAAA 330066
i - i v v vi v - i i
L1M5_orf2#LIN 2286 ATCAAAAAACATCAAATACCTAGGAAT-AAATCTAATAAA 2324
Matrix = 20p37g.matrix
Transitions / transversions = 1.44 (26 / 18)
Gap_init rate = 0.02 (4 / 183), avg. gap size = 2.25 (9 / 4)
+ 574 31.1 7.8 0.0 INTRON_3 330115 330307 (69874) + MIRb SINE/MIR 15 222 (46) 462
ANNOTATION EVIDENCE:
574 31.09 7.77 0.00 INTRON_3 330115 330307 69874 + MIRb SINE/MIR 15 222 46 684
INTRON_3 330115 GGTATAGTGGAAAGGCCAAGGCCTTTTGGGTAAAACAAA------TTCAA 330158
ii iv v v v i v ii i ------ i
MIRb#SINE/MIR 15 GGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGGCAGACCTGGGTTCGA 64
INTRON_3 330159 ACTCTTGCTCCACTACTTACTTGCAGGGTAACCTATAACAAGGTACTTAG 330208
ii v ii i v v v i vvii vi i
MIRb#SINE/MIR 65 ATCCTGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAA 114
INTRON_3 330209 ACTCTCTAGACTTCAGTTTCCCCTTTTTTAAAGTGAGAATAGTAGAAATT 330258
v iii i i v i v i i i i iv vi
MIRb#SINE/MIR 115 CCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCT 164
INTRON_3 330259 ACCTCA-AGGG--GTTGAAATGATT---TGACATA---TATGGCAAATGT 330299
i- -- vi v --- v ---i vv ii i
MIRb#SINE/MIR 165 ACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGC 214
INTRON_3 330300 TTAATACA 330307
ii
MIRb#SINE/MIR 215 TTAGCACA 222
Matrix = 25p37g.matrix
Transitions / transversions = 1.73 (38 / 22)
Gap_init rate = 0.03 (5 / 192), avg. gap size = 3.00 (15 / 5)
+ 185 36.3 2.4 3.7 INTRON_3 331328 331410 (68771) + MER5A DNA/hAT-Charlie 68 149 (40) 463
ANNOTATION EVIDENCE:
185 36.27 2.41 3.66 INTRON_3 331328 331410 68771 + MER5A DNA/hAT-Charlie 68 149 40 685
INTRON_3 331328 CATATTCTTAGGGTTTCCTATCC-AAACCTACAGATTTAGAACTTTCAGG 331376
v ii ---i i i - i v v i vi iii
MER5A#DNA/hAT 68 CAAATTCTCGGG---CCCCACCCCAGACCTACTGAATCAGAAACTCTGGG 114
INTRON_3 331377 GGAGAAGCTTATTAATTTAT-TGTAAAAAAGCTTT 331410
v ii ii vi i i - v v v ii
MER5A#DNA/hAT 115 GGTGGGGCCCAGCAATCTGTGTTTTAACAAGCCCT 149
Matrix = 25p37g.matrix
Transitions / transversions = 2.22 (20 / 9)
Gap_init rate = 0.04 (3 / 82), avg. gap size = 1.67 (5 / 3)
+ 390 17.6 0.0 1.5 INTRON_3 331502 331570 (68611) + Charlie5 DNA/hAT-Charlie 3 70 (2554) 464 *
ANNOTATION EVIDENCE:
390 17.65 0.00 1.47 INTRON_3 331502 331570 68611 + Charlie5 DNA/hAT-Charlie 3 70 2554 777
INTRON_3 331502 GTGCTGTTTCAGATGAATAGCCACTAGCCACATGTGGCTACTGAGTGCTT 331551
i iiv v i i- i ii
Charlie5#DNA/ 3 GCGCTGTCCAATACGG-TAGCCACTAGCCACATGTGGCTATTGAGCACTT 51
INTRON_3 331552 GAAATGTGGCCAGTGCCAC 331570
i v
Charlie5#DNA/ 52 GAAATGTGGCTAGTGCGAC 70
Matrix = 20p37g.matrix
Transitions / transversions = 3.00 (9 / 3)
Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1)
+ 527 14.1 15.3 1.3 INTRON_3 331569 331705 (68476) + Charlie5 DNA/hAT-Charlie 2469 2624 (0) 465
ANNOTATION EVIDENCE:
527 14.05 15.33 1.28 INTRON_3 331569 331705 68476 + Charlie5 DNA/hAT-Charlie 2469 2624 0 778
INTRON_3 331569 ACATGTCAAAATGATAATATTTTGGATATATTGGGCCAACAAAAATATAT 331618
ii ii vv
Charlie5#DNA/ 2469 ACATGTTGAAATGATAATATTTTGGATATATTGGGTTAAATAAAATATAT 2518
INTRON_3 331619 TGTTAAAATTAAATTTATCT-----TTTTTA--------AAAGTAGGACT 331655
i v i i ----- -------- v i --
Charlie5#DNA/ 2519 TATTAAAATTAATTTCACCTGTTTCTTTTTACTTTTTTTAATGTGG--CT 2566
INTRON_3 331656 ACCAAAAAATTTTAAATTACATATGTGCCTTGC-TT----TTCT---GGG 331697
i i v v i - ---- --- i
Charlie5#DNA/ 2567 ACTAGAAAATTTAAAATTACATATGTGGCTCGCATTATATTTCTATTGGA 2616
INTRON_3 331698 CAGTGCTG 331705
i
Charlie5#DNA/ 2617 CAGCGCTG 2624
Matrix = 20p37g.matrix
Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.04 (6 / 136), avg. gap size = 3.83 (23 / 6)
+ 231 26.7 2.5 5.2 INTRON_3 331731 331809 (68372) + MER5A DNA/hAT-Charlie 2 78 (111) 466
ANNOTATION EVIDENCE:
231 26.71 2.53 5.19 INTRON_3 331731 331809 68372 + MER5A DNA/hAT-Charlie 2 78 111 686
INTRON_3 331731 AGTATTCCTCAA-GTATGGTTCATGGACCATCTGCATCAGACTCATCTGA 331779
iv i - i i vi v v vv i i
MER5A#DNA/hAT 2 AGTGGTTCTCAAAGTGTGGTCCCCGGACCAGCAGCATCAGCATCACCTGG 51
INTRON_3 331780 GGTGGCTTGCTA-AAATGGTTGAAGTCTCAG 331809
i--i i - --ii v i
MER5A#DNA/hAT 52 GA--ACTTGTTAGAAATG--CAAATTCTCGG 78
Matrix = 25p37g.matrix
Transitions / transversions = 1.86 (13 / 7)
Gap_init rate = 0.05 (4 / 78), avg. gap size = 1.50 (6 / 4)
+ 202 30.7 1.3 4.0 INTRON_3 331796 331873 (68308) + MER5A DNA/hAT-Charlie 114 189 (0) 467 *
ANNOTATION EVIDENCE:
202 30.70 1.28 3.95 INTRON_3 331796 331873 68308 + MER5A DNA/hAT-Charlie 114 189 0 687
INTRON_3 331796 GGTTGAAGTCTCAGAAATCTGTATTTTTAATAGGTGTTCACAGGGGATTC 331845
v ii i - v i - i i ivi - v
MER5A#DNA/hAT 114 GGGTGGGGCC-CAGCAATCTGTGTTTT-AACAAGCCCTC-CAGGTGATTC 160
INTRON_3 331846 CTGTGTATA-TAAATTTTGAGAATTCCTG 331873
ivi i ii- ? v iiv
MER5A#DNA/hAT 161 TGATGCACGCTMAAGTTTGAGAACCACTG 189
Matrix = 25p37g.matrix
Transitions / transversions = 2.14 (15 / 7)
Gap_init rate = 0.05 (4 / 77), avg. gap size = 1.00 (4 / 4)
+ 1063 25.5 6.6 1.2 INTRON_3 332154 332562 (67619) + L1M5 LINE/L1 4221 4651 (1495) 468
ANNOTATION EVIDENCE:
1063 25.48 6.60 1.16 INTRON_3 332154 332562 67619 + L1M5_orf2 LINE/L1 2112 2542 752 732
INTRON_3 332154 GATTGTCTA---GGAAACTTCAAAA-AATCTACAAAAATGTCGCTGGAAC 332199
? ---i v i - i v vi iii i i
L1M5_orf2#LIN 2112 GATTGTNTACATAGAAAATCCAAAAGAATCTACAGATAAATTATTAGAAT 2161
INTRON_3 332200 TAAC---TGAGATTAATAAGGTGAA-GGATACAAGATCAATA---AAAAG 332242
i--- iv ii v v- ii --- i
L1M5_orf2#LIN 2162 TAATAAGTGAATTTAGCAAGGTTACTGGATACAAAGTCAATATACAAAAA 2211
INTRON_3 332243 --AATTGTATTTCTATATCCTAACAATTAACAATCACAAATTGAGACTTT 332290
-- v i iv iiv v i i ?
L1M5_orf2#LIN 2212 TCAATTGTATTTCTATATACTAGCAACAAACAATTGGAAAATGAAATTTN 2261
INTRON_3 332291 AAAATATAGTATTATTCACAATAGAACACTAAACCATGAAATGACTAGGT 332340
- i i ii i v ivvv v v iv v
L1M5_orf2#LIN 2262 AAAA-ACAATACCATTTACAATAGCATCAAAAAACATCAAATACCTAGGA 2310
INTRON_3 332341 ATAACTCTAACAAAATTTGTGTAAGATCTG-ATGCTGAAAACTGTAAAAC 332389
v i ?v ii i ?- i ? ii
L1M5_orf2#LIN 2311 ATAAATCTAATAAAANATGTACAAGACCTNTATACNGAAAACTACAAAAC 2360
INTRON_3 332390 A--AT-------GATAAAAGAATACCTGAATAAATGGAGATATTTGCTAT 332430
-- -------i v v i v v i i
L1M5_orf2#LIN 2361 ATTATTGAGAGAAATTAAAGAAGACCTAAATAAATGGAGAGATATACCAT 2410
INTRON_3 332431 GTTTATGGTTTACAATAC---ACATTGTTAAGATGTCAGTCTGATCTTTA 332477
i v iv v --- i v i ii-- iii
L1M5_orf2#LIN 2411 GTTCATGGATTGGAAGACTCAATATTGTAAAGATGTCAATTC--TCCCCA 2458
INTRON_3 332478 GAGTGATCTGTAGAGTGAACACAATCTCGTTCAAAATCC-AGAAGGATTT 332526
i v i v v ii i iv ? - v --
L1M5_orf2#LIN 2459 AATTGATCTATAGATTCAATGCAATCCCAATNAAAATCCCAGCAGG--TT 2506
INTRON_3 332527 TTTTGGTCAAAATCAACAAGTTTATTCTAATATCTA 332562
v vi ii i v v i
L1M5_orf2#LIN 2507 TTTTTGTGGAAATTGACAAGCTGATTCTAAAATTTA 2542
Matrix = 20p37g.matrix
Transitions / transversions = 1.62 (60 / 37)
Gap_init rate = 0.03 (14 / 408), avg. gap size = 2.29 (32 / 14)
+ 318 24.0 5.9 5.9 INTRON_3 332563 332664 (67517) + MIRb SINE/MIR 167 268 (0) 469
ANNOTATION EVIDENCE:
318 23.96 5.88 5.88 INTRON_3 332563 332664 67517 + MIRb SINE/MIR 167 268 0 688
INTRON_3 332563 CTTGCTAGATTCTTCTGAGGATCGAATGAGATAATTGCATATAAAGATAA 332612
i vi i v v ii - i ----
MIRb#SINE/MIR 167 CTCGCAGGGTTGTTGTGAGGATTAAATGAGATAAT-GCATGTAAAG---- 211
INTRON_3 332613 TTGCATACTACAAAGTCTAACATTCAGCAAGC----AATAAATATTAGCT 332658
-i v vi iv i ii iv i ---- iv
MIRb#SINE/MIR 212 -CGCTTAGCACAGTGCCTGGCACACAGTAAGCGCTCAATAAATGGTAGCT 260
INTRON_3 332659 --ATTATT 332664
--
MIRb#SINE/MIR 261 CTATTATT 268
Matrix = 25p37g.matrix
Transitions / transversions = 1.88 (15 / 8)
Gap_init rate = 0.04 (4 / 101), avg. gap size = 3.00 (12 / 4)
+ 573 31.3 13.4 5.3 INTRON_3 332783 333266 (66915) C L2c LINE/L2 (1) 3386 2836 470
ANNOTATION EVIDENCE:
573 30.72 9.74 6.65 INTRON_3 332783 333162 67019 C L2c_3end LINE/L2 87 477 1 689
INTRON_3 332783 TTCATTAATTCTACAAATATTTATTGAGCACCTACTCTGTATACAGCATT 332832
v v i i v ii- ----
C L2c_3end#LINE 477 TTCATTCATTCAACAAACATTTATTGAGCGCCTACTATGTGC-CAG---- 433
INTRON_3 332833 GTGGTAAACTGGGGAAACAATAAATAAACAAACACACTGTCACCCCTACT 332882
----- v - i i i i- v --- i i
C L2c_3end#LINE 432 GTG-----CTGGGGATACAA-AGATGAATAAG-ACACGGTC---CCTGCC 393
INTRON_3 332883 TTCATAGAGTTTTCATTCCAGT--AGCAAATAGGTAT-TAAACAACTTTT 332929
i vi i iv v i -- v i i ii ?- ivivv
C L2c_3end#LINE 392 CTCAAGGAGCTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAAT 343
INTRON_3 332930 TACAAAACTCTGTAATTACAATTGTGAGGAGTGTTTTTGAGGAAGTAGGG 332979
v v---- i -----i vi i v viv i vi
C L2c_3end#LINE 342 TACAATACA----AGTTA-----ATGATAAGTGCTATAATGGGAGTATAG 302
INTRON_3 332980 A-ATATCGTGAATGAGATTACTG-GGAG---ACTTAAACTAGGCTT---- 333020
- vivi iv - i vi v - --- i i ? ----
C L2c_3end#LINE 301 ACAGGGTGCTA-TGGGAGCACAGAGGAGGGCACCTAGACTAGNCTTGGGG 253
INTRON_3 333021 ---CA----AGTCTTTCTTGACAAAGTAGCATTTGAACTGAGCTGTAAAT 333063
--- ---- v i v vi i ii i i ?iv i v
C L2c_3end#LINE 252 GGTCAGGGAAGGCTTCCTGGAGGAGGTGACATCTGAGCTGAGNCTTGAAG 203
INTRON_3 333064 G----GTAG-AGTTGG---GATGGGAAGAGGAG----------TCTGGGC 333095
---- - i --- i i i i ---------- ii
C L2c_3end#LINE 202 GATGAGTAGGAGTTAGCCAGGTGGAAGGAGGGGGGAAGAGCATTCCAGGC 153
INTRON_3 333096 AAAGGAAACTACCTATGGACAGGTCCTAAGGCAGTAAGAGAAGGTTAATG 333145
i i vi v i v v i? vi v - vvviiii
C L2c_3end#LINE 152 AGAGGGAACAGCATGTGCAAAGGCNCGGAGGCAGGAA-AGAACTGCGGCG 104
INTRON_3 333146 TAGTTGGAGTATAGAAG 333162
iv i v iv
C L2c_3end#LINE 103 TGTTTGGGGAATGCAAG 87
Matrix = 25p37g.matrix
Transitions / transversions = 1.56 (64 / 41)
Gap_init rate = 0.06 (21 / 379), avg. gap size = 3.00 (63 / 21)
197 36.90 4.76 0.00 INTRON_3 333134 333217 66964 C L2c_3end LINE/L2 1 88 390 690
INTRON_3 333134 AGAAGGTTAATGTAGTTGGAGTATAGAAGGTAAAGAAGAGATCA----AG 333179
? v i i i i i vi ii i i i vii----
C L2c_3end#LINE 88 AGNAGTTCAGTGTGGCTGGAGCATAGTGGGCGAGGAGGGGAGTGGAGGAG 39
INTRON_3 333180 ATGCAGTTGGAGAGGAAGGCAAAGGCTGGGTTATACAG 333217
vi i v i ii ii i ii i?
C L2c_3end#LINE 38 ATGAGGCTGGAGAGGTAAGCAGGGGCCAGATCGTGNAG 1
Matrix = 25p37g.matrix
Transitions / transversions = 4.80 (24 / 5)
Gap_init rate = 0.01 (1 / 83), avg. gap size = 4.00 (4 / 1)
183 29.55 0.00 0.00 INTRON_3 333223 333266 66915 C L2 LINE/L2 2836 2879 203 691
INTRON_3 333223 TTTTATCTTAAGAGCGGTAGGAAGCCATTAAAGGGTTTGTAGCA 333266
iii i v v i i i ii vv
C L2#LINE/L2 2879 TTTTACTCTGAGTGAGATGGGAAGCCACTGGAGGGTTTTGAGCA 2836
Matrix = 25p37g.matrix
Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0)
+ 1369 13.4 1.7 7.0 INTRON_3 333343 333583 (66598) + MER30 DNA/hAT-Charlie 2 230 (0) 471
ANNOTATION EVIDENCE:
1369 13.39 1.66 6.99 INTRON_3 333343 333583 66598 + MER30 DNA/hAT-Charlie 2 230 0 644
INTRON_3 333343 AAACTTGTCCAAACCATGGCCCACGGGCTGCATGTGGCCCAGGACAGCTT 333392
i v ii i i i i
MER30#DNA/hAT 2 AAGCTTGTCCAACCCGCGGCCCGCGGGCCGCATGCGGCCCAGGACGGCTT 51
INTRON_3 333393 TGAATGTGACACAACACAAATTTGTAAAGTTTCTTAAA----CAAGAGAT 333438
i i v i v ----i v
MER30#DNA/hAT 52 TGAATGCGGCCCAACACAAATTCGTAAACTTTCTTAAAACATTATGAGAT 101
INTRON_3 333439 ATTTTTGTGTGTGATTTATTTTTATTTTTATTTTTTTTTTTTAGTTCATC 333488
v i -------------- -- ? i
MER30#DNA/hAT 102 TTTTTTGCG--------------ATTTTT--TTTTTTTTTTWAGCTCATC 135
INTRON_3 333489 AACTGTCATTATTGTTAGCATATTTTATGTGTGGCCCAAGACAATTCTTC 333538
i i i v ii
MER30#DNA/hAT 136 AGCTATCGTTAGTGTTAGTGTATTTTATGTGTGGCCCAAGACAATTCTTC 185
INTRON_3 333539 TTCTTCCAGTGTGGCCCAGGGAAGCCAAAAGACCGTATACCCCTG 333583
i ii v i
MER30#DNA/hAT 186 TTCTTCCAATGTGGCCCAGGGAAGCCAAAAGATTGGACACCCCTG 230
Matrix = 18p37g.matrix
Transitions / transversions = 3.14 (22 / 7)
Gap_init rate = 0.01 (3 / 240), avg. gap size = 6.67 (20 / 3)
+ 238 31.1 0.0 0.0 INTRON_3 333584 333644 (66537) C L2a LINE/L2 (30) 3396 3336 472
ANNOTATION EVIDENCE:
238 31.15 0.00 0.00 INTRON_3 333584 333644 66537 C L2a_3end LINE/L2 427 487 30 692
INTRON_3 333584 GTCTAATACATTTAAGGCACTGTGCTGAGTGCTGAGAATACAGCAATAAA 333633
i v ii viv v ii i i i i i
C L2a_3end#LINE 487 GCCTACTATGTGCCAGGCACTGTTCTAGGCGCTGGGGATACAGCAGTGAA 438
INTRON_3 333634 GAAGTCACACA 333644
v iv v
C L2a_3end#LINE 437 CAAAACAGACA 427
Matrix = 25p37g.matrix
Transitions / transversions = 1.71 (12 / 7)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 313 27.9 0.0 0.0 INTRON_3 333646 333713 (66468) + Arthur1C DNA/hAT-Tip100 8 75 (288) 473
ANNOTATION EVIDENCE:
313 27.94 0.00 0.00 INTRON_3 333646 333713 66468 + Arthur1C DNA/hAT-Tip100 8 75 288 779
INTRON_3 333646 GGATTTACCGTGAAGTTAATGAAGCTCATACTTCAGTATATACCACTTTC 333695
i i vi viivivi v
Arthur1C#DNA/ 8 GGATTTACCGTGAAGCTAATGAAGCTTAAGCTTCAGGGCCCCTCACTTGC 57
INTRON_3 333696 CTAGGCTCTTGTAAATGC 333713
vii i i i i
Arthur1C#DNA/ 58 ACGGGCCCCTGTGAGTGC 75
Matrix = 20p37g.matrix
Transitions / transversions = 2.17 (13 / 6)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 1342 19.8 1.2 0.4 INTRON_3 333720 333972 (66209) + Arthur1C DNA/hAT-Tip100 109 363 (0) 474
ANNOTATION EVIDENCE:
1342 19.84 1.19 0.39 INTRON_3 333720 333972 66209 + Arthur1C DNA/hAT-Tip100 109 363 0 780
INTRON_3 333720 TGGGAAGGGAAAGCCGGGTTGTAACTGAAATGCATTTCTATGTAAACATT 333769
i i i i iiiii v i
Arthur1C#DNA/ 109 TGGGGAGGGGAAGCCAGGTTGCAATCAGGAAGCATTTCTATGTAAGCATT 158
INTRON_3 333770 TCTGGTAAATTGTCTAAAGAAGTCTCAGAAGAGAAGGATCTTAATCGCTA 333819
i ii i i i v v i
Arthur1C#DNA/ 159 TCTGGTAAATTGCCTAAAGAGATCTCAGAAGAAAGGGACCTGAATCTCCA 208
INTRON_3 333820 AACCTTCAAGAATGTGTTGTGATTTTTTTTTCTCATTTTAAATAAATATA 333869
iv i iv v i - i v
Arthur1C#DNA/ 209 AGGCTCCAGTAATTTGTTGTGATTTCTTTT-CTCATTCTAAATAAATATT 257
INTRON_3 333870 CATATTTATACATAATTTGATATTTGTAATTTTGTATATTTTTT---AAT 333916
iv ii v vi i vi --- v
Arthur1C#DNA/ 258 CACTTTCGTACCTAATTTTGTATTCGTAATTTTGTATTCTTTTTCTTAAA 307
INTRON_3 333917 GTAGGCTCCCTAAATTGTATTAGTTTCAAGCCCCATAAAACTTGGATCCA 333966
vi i i v i i i i i
Arthur1C#DNA/ 308 GAGGGCCCCCCAAATTGTATAAGCTTCAGGCCCCACAAAACCTGGATCCG 357
INTRON_3 333967 CCCCTG 333972
Arthur1C#DNA/ 358 CCCCTG 363
Matrix = 20p37g.matrix
Transitions / transversions = 2.57 (36 / 14)
Gap_init rate = 0.01 (2 / 252), avg. gap size = 2.00 (4 / 2)
+ 203 25.0 11.8 0.0 INTRON_3 333984 334059 (66122) C L2a LINE/L2 (95) 3292 3208 472
ANNOTATION EVIDENCE:
203 25.00 11.84 0.00 INTRON_3 333984 334059 66122 C L2c_3end LINE/L2 299 383 95 693
INTRON_3 333984 CTTGCAGTCTTACAGGGGAAGCAGATAAGTAAACA----ATTTCGGTA-G 334028
ii viii i ii i ? ---- v ii -i
C L2c_3end#LINE 383 CTCACAGTCTAGTGGAGGAGACAGACANGTAAACAGACAATTACAATACA 334
INTRON_3 334029 AGT--ATGACAAGTGTTATAATAG-AGGA-AGACA 334059
-- i i i - v -
C L2c_3end#LINE 333 AGTTAATGATAAGTGCTATAATGGGAGTATAGACA 299
Matrix = 25p37g.matrix
Transitions / transversions = 5.00 (15 / 3)
Gap_init rate = 0.07 (5 / 75), avg. gap size = 1.80 (9 / 5)
+ 243 17.1 0.0 0.0 INTRON_3 334693 334733 (65448) + (CATATA)n Simple_repeat 2 42 (0) 475
ANNOTATION EVIDENCE:
243 17.07 0.00 0.00 INTRON_3 334693 334733 65448 + (CATATA)n Simple_repeat 2 42 138 750
INTRON_3 334693 ATATACAAATATATATATATACACATAAACACATACATACA 334733
v i i i v i i
(CATATA)n#Sim 2 ATATACATATACATATACATATACATATACATATACATATA 42
Matrix = Unknown
Transitions / transversions = 2.50 (5 / 2)
Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0)
+ 412 13.7 14.2 3.4 INTRON_3 334901 335006 (65175) C L1MC5 LINE/L1 (51) 7910 7794 476
ANNOTATION EVIDENCE:
412 13.68 14.15 3.42 INTRON_3 334901 335006 65175 C L1MC5_3end LINE/L1 1184 1300 51 733
INTRON_3 334901 AAATTTTAAACATATGCAAAAAAGTAGAGAGAATTATATAATGAAC---- 334946
i i i---- vi ----
C L1MC5_3end#LI 1300 AAATTTCAAATATAC----AAAAGTAGAGAGAATAGTATAATGAACTTCC 1255
INTRON_3 334947 ------CCATCACTGAATTTCAACAATTACCAACTCATGAC-AATTTTGT 334989
------ iv ii i i i -
C L1MC5_3end#LI 1254 ACATACCCATCACCCAGCTTCAACAATTATCAATTCATGGCCAATTTTGT 1205
INTRON_3 334990 TTCATCAATA----CACTTAC 335006
v ---- i
C L1MC5_3end#LI 1204 TTCATCTATAGCTCCACCTAC 1184
Matrix = 20p37g.matrix
Transitions / transversions = 3.67 (11 / 3)
Gap_init rate = 0.04 (4 / 105), avg. gap size = 4.75 (19 / 4)
+ 196 26.3 14.3 1.6 INTRON_3 335923 336034 (64147) C L2a LINE/L2 (849) 2570 2445 472
ANNOTATION EVIDENCE:
196 26.31 14.29 1.59 INTRON_3 335923 336034 64147 C L2 LINE/L2 2445 2570 512 694
INTRON_3 335923 AAGGATGAGTCTCTAAGAC----AGTCTGA-CA-CAGGAGTGATGGCAT- 335965
-- i ii----i i - - v iv vi -
C L2#LINE/L2 2570 AAGGATGA--CTCCAAGGTTTTTGGCCTGAGCAACTGGAAGGATGGAGTT 2523
INTRON_3 335966 --CATCAACAGAAACAGAGG-GTTTCTGAGAGG-----GTTTGAGGGGGT 336007
-- i v i ii i i- vi v i ----- v
C L2#LINE/L2 2522 GCCATTAACTGAGATGGGGAAGACTGTGGGAGGAGCAGGTTTGAGGGGGA 2473
INTRON_3 336008 -GATGATGAGTTTAGGTTTGAATATGCT 336034
- v v i v i i i
C L2#LINE/L2 2472 AGATCAGGAGTTCAGTTTTGGACATGTT 2445
Matrix = 25p37g.matrix
Transitions / transversions = 1.90 (19 / 10)
Gap_init rate = 0.07 (8 / 111), avg. gap size = 2.25 (18 / 8)
+ 238 22.4 6.9 0.0 INTRON_3 336742 336799 (63382) C MIRb SINE/MIR (89) 179 118 477
ANNOTATION EVIDENCE:
238 22.41 6.90 0.00 INTRON_3 336742 336799 63382 C MIRb SINE/MIR 118 179 89 695
INTRON_3 336742 ACAACTTTGAGAGATGGATGCTATGAT----ATTTTGCTGAAGAGGAAAC 336787
ii v i i i ii v ---- i v v
C MIRb#SINE/MIR 179 ACAACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAAC 130
INTRON_3 336788 TGAGGCTTAGAG 336799
i
C MIRb#SINE/MIR 129 TGAGGCTCAGAG 118
Matrix = 25p37g.matrix
Transitions / transversions = 2.25 (9 / 4)
Gap_init rate = 0.02 (1 / 57), avg. gap size = 4.00 (4 / 1)
+ 457 13.0 7.6 0.0 INTRON_3 336922 337013 (63168) + L1MB3 LINE/L1 6084 6182 (1) 478
ANNOTATION EVIDENCE:
457 13.04 7.61 0.00 INTRON_3 336922 337013 63168 + L1MB3_3end LINE/L1 831 929 1 650
INTRON_3 336922 CACAGCAATATGAATGTAGTTAATGTCATTGAACTGTGCTCTTAAAA-TG 336970
i i v i i i v -
L1MB3_3end#LI 831 CACAACAATGTGAATGTACTTAATGCCACTGAACTGTACACTTAAAAATG 880
INTRON_3 336971 GTTAAAATGGTATATTT------ATGTATGTTTTGCCACATATAAAAAA 337013
v ------ i i vv
L1MB3_3end#LI 881 GTTAAAATGGTAAATTTTATGTTATGTATATTTTACCACAATTAAAAAA 929
Matrix = 18p37g.matrix
Transitions / transversions = 1.40 (7 / 5)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 3.50 (7 / 2)
+ 2460 7.5 0.0 0.7 INTRON_3 337082 337375 (62806) C AluSx3 SINE/Alu (19) 293 2 479
ANNOTATION EVIDENCE:
2329 7.21 0.68 1.02 INTRON_3 337082 337375 62806 C AluSx SINE/Alu 2 294 18 635
INTRON_3 337082 TTTTTTTAATTTTTGAGACGGAGTCTCGCTCTGTTGCCCAGGCTGGAGTG 337131
-- i
C AluSx#SINE/Al 294 TTTTTTT--TTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTG 247
INTRON_3 337132 CAGTGGCATGGTCTCAGCTCACTGCAACATCCACCTCCTGGGTTCAAGCA 337181
ii i i v i i i
C AluSx#SINE/Al 246 CAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCG 197
INTRON_3 337182 ATTCTCCTGCCTCAGCCTCCCAAATAGCTGGGATTACAGATGCCTGCCAC 337231
i i ii vi
C AluSx#SINE/Al 196 ATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCAC 147
INTRON_3 337232 CACGCCCAGCTAATTTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATG 337281
i - i
C AluSx#SINE/Al 146 CACGCCCGGCTAATTTTT-GTATTTTTAGTAGAGACGGGGTTTCACCATG 98
INTRON_3 337282 TTGGCCAGGCTGGTCTCGAACTCCTGACCTC--GTGATTCGCCTGCCTCG 337329
-- i i
C AluSx#SINE/Al 97 TTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCG 48
INTRON_3 337330 GCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCCAGC 337375
i i
C AluSx#SINE/Al 47 GCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p37g.matrix
Transitions / transversions = 9.50 (19 / 2)
Gap_init rate = 0.01 (3 / 293), avg. gap size = 1.67 (5 / 3)
+ 552 24.7 12.8 1.1 INTRON_3 337641 337804 (62377) C MIRb SINE/MIR (65) 203 21 480
ANNOTATION EVIDENCE:
552 24.66 12.80 1.09 INTRON_3 337641 337804 62377 C MIRb SINE/MIR 21 203 65 696
INTRON_3 337641 GCACTTTCACATTGAATATACGTAACATTTTTATGAAGTAGGTCTTAAGC 337690
i v v v viv ii viii ii i v -vi
C MIRb#SINE/MIR 203 GCATTATCTCATTTAATCCTCACAACAACCCTGCGAGGTAGGTATTA-TT 155
INTRON_3 337691 ATTCCCATTTT--------------------TCAGAGAGCTGAAGTGACT 337720
i -------------------- v v
C MIRb#SINE/MIR 154 ATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTGACT 105
INTRON_3 337721 TGCCCATGGTCTCATAGGAAGTAAGAGGCAGAGCTGAGATTCAAATACAA 337770
v v i vv v iii i iv i
C MIRb#SINE/MIR 104 TGCCCAAGGTCACACAGCTAGTAAGTGGCAGAGCCAGGATTCGAACCCAG 55
INTRON_3 337771 GTTTGC-TGACTCTAAGTCCAGTGCTCTATTCCAC 337804
i - i iv v -
C MIRb#SINE/MIR 54 GTCTGCCTGACTCCAAAGCCCGTGCTCT-TTCCAC 21
Matrix = 25p37g.matrix
Transitions / transversions = 1.22 (22 / 18)
Gap_init rate = 0.02 (4 / 163), avg. gap size = 5.75 (23 / 4)
+ 356 26.4 4.6 2.7 INTRON_3 337909 338017 (62164) + MIR3 SINE/MIR 83 193 (15) 481
ANNOTATION EVIDENCE:
356 26.40 4.59 2.70 INTRON_3 337909 338017 62164 + MIR3 SINE/MIR 83 193 15 697
INTRON_3 337909 TGGGTGACTTTGGGCAAGTCAGTTAACTTTAATTCACTTCATTTTCCTCA 337958
v i v v i ivv vvi i v
MIR3#SINE/MIR 83 TGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTTCCTCA 132
INTRON_3 337959 TTTGAAAACTGAGGGAACTGGACCTGATGAAAGTCTT---GGTT--TTTC 338003
i v v iii iv --- i--- i-- i
MIR3#SINE/MIR 133 TCTGTAAAATGAGGGGGTTGGACTAGATGA---TCTCTAAGGTCCCTTCC 179
INTRON_3 338004 ATTTCTAAAATTCT 338017
vi i v
MIR3#SINE/MIR 180 AGCTCTGACATTCT 193
Matrix = 25p37g.matrix
Transitions / transversions = 1.15 (15 / 13)
Gap_init rate = 0.03 (3 / 108), avg. gap size = 2.67 (8 / 3)
+ 288 32.3 10.4 0.7 INTRON_3 338046 338179 (62002) + L3 LINE/CR1 3907 4053 (436) 482
ANNOTATION EVIDENCE:
288 32.31 10.45 0.68 INTRON_3 338046 338179 62002 + L3 LINE/CR1 3907 4053 436 698
INTRON_3 338046 TAATAGAGTTCTGGTGATCAAA---AGGGAAACAGTTGTCCTGATGTA-- 338090
iv v i vi i --- iii i v i v --
L3#LINE/CR1 3907 TAATAGAAGTATAGTGTCCAGAWCAAGGGAGGTAATAGTCCCGCTGTACT 3956
INTRON_3 338091 -TGCGC----CAGGTCACATACAGACTTTAGCTTTTATTTTTGCATACTA 338135
- ---- ii vii v v v v i v i vii i
L3#LINE/CR1 3957 CTGCGCTGGTCAGACCACATCTGGAGTATTGCGTTCAGTTCTGGGCACCA 4006
INTRON_3 338136 TATCTTAAGGGAGAC--TGATAAA--GAAAACTATACCAGAGAACAAT 338179
i i i i -- i -- i ivvii - v i
L3#LINE/CR1 4007 CATTTTAAGAGGGACATTGACAAACTGGAGCGCGT-CCAGAGAAGAGT 4053
Matrix = 25p37g.matrix
Transitions / transversions = 1.87 (28 / 15)
Gap_init rate = 0.05 (6 / 133), avg. gap size = 2.50 (15 / 6)
+ 26 84.8 0.0 0.0 INTRON_3 338545 338577 (61604) + AT_rich Low_complexity 1 33 (0) 483
ANNOTATION EVIDENCE:
26 84.85 0.00 0.00 INTRON_3 338545 338577 61604 + AT_rich Low_complexity 113 145 155 701
INTRON_3 338545 TATTTTATTTAACTATATAAATTTATATTTAAA 338577
???????????????????????????v
AT_rich#Low_c 113 WWWWWWWWWWWWWWWWWWWWWWWWWWWATTAAA 145
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 1)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 311 9.0 0.0 10.7 INTRON_3 338674 338735 (61446) C L1MA3 LINE/L1 (1) 6304 6249 484
ANNOTATION EVIDENCE:
311 9.03 0.00 10.71 INTRON_3 338674 338735 61446 C L1MA3_3end LINE/L1 996 1051 1 734
INTRON_3 338674 TTTTTATTTTTGTGGATACATAGTAGGTGTATGTGTATATATTTATGAGG 338723
v i ------ i
C L1MA3_3end#LI 1051 TTTTAATTTTTGTGGGTACATAGTAGGTGTAT------ATATTTATGGGG 1008
INTRON_3 338724 TACACAAGATAT 338735
ii
C L1MA3_3end#LI 1007 TACATGAGATAT 996
Matrix = 20p37g.matrix
Transitions / transversions = 4.00 (4 / 1)
Gap_init rate = 0.02 (1 / 61), avg. gap size = 6.00 (6 / 1)
+ 5112 13.1 29.4 0.5 INTRON_3 338765 338929 (61252) C L1MA2 LINE/L1 (53) 7670 7453 485
ANNOTATION EVIDENCE:
794 13.49 0.79 0.00 INTRON_3 338765 338890 61291 C L1MA2_3end LINE/L1 872 998 53 735
INTRON_3 338765 TGCTTTGCAATAGGCATGCAACACATACTAATCACATTATGGAAAATGGG 338814
i vv i iiii v i
C L1MA2_3end#LI 998 TGTTTTGATACAGGCATGCAATGTGTAATAATCACATCATGGAAAATGGG 949
INTRON_3 338815 GTATCTATCCCCTCAGATTTTTATCCTTTGTGTTATAAACAATCCAATTA 338864
i iiiv i
C L1MA2_3end#LI 948 GTATCCATCCCCTCAAGCATTTATCCTTTGTGTTACAAACAATCCAATTA 899
INTRON_3 338865 TACTCTTTTAGCTATTTT-AAATGTAC 338890
i -
C L1MA2_3end#LI 898 TACTCTTTTAGTTATTTTSAAATGTAC 872
Matrix = 20p37g.matrix
Transitions / transversions = 3.25 (13 / 4)
Gap_init rate = 0.01 (1 / 125), avg. gap size = 1.00 (1 / 1)
5112 11.75 1.20 1.81 INTRON_3 338888 338929 61252 C L1MA2_3end LINE/L1 781 827 224 736
INTRON_3 338888 TACCAGGTCTTATTCATTCTTTCTA-----TTTTTTGAACCCATTAA 338929
i ----- v
C L1MA2_3end#LI 827 TACTAGGTCTTATTCATTCTTTCTAACTATTTTTTTGTACCCATTAA 781
Matrix = 20p37g.matrix
Transitions / transversions = 1.00 (1 / 1)
Gap_init rate = 0.02 (1 / 41), avg. gap size = 5.00 (5 / 1)
+ 886 6.3 9.4 0.0 INTRON_3 338930 339056 (61125) C MER85 DNA/PiggyBac (0) 139 1 486
ANNOTATION EVIDENCE:
886 6.30 9.45 0.00 INTRON_3 338930 339056 61125 C MER85 DNA/PiggyBac 1 139 0 645
INTRON_3 338930 CCCATTTATGCCAAAGGTTACAATTTTTT---TTT--------GTGAAAA 338968
vi i --- --------
C MER85#DNA/Pig 139 CCCATTTATGCCTGAGGTTGCAATTTTTTGAATTTTTGCATGAGTGAAAA 90
INTRON_3 338969 ATCAGACCTTGGCGATGACCTTGAGTAGTAGGATATAAATAACTCCCACA 339018
i
C MER85#DNA/Pig 89 ATCAGACCTTGGCGATGACCTTGAGCAGTAGGATATAAATAACTCCCACA 40
INTRON_3 339019 -GCTTAGCATTCCAGTAATAGAACACTGGGCATAAATGG 339056
- i i i i
C MER85#DNA/Pig 39 TGCTTAGCGTTCCAATAATGGAACACTAGGCATAAATGG 1
Matrix = 18p37g.matrix
Transitions / transversions = 7.00 (7 / 1)
Gap_init rate = 0.02 (3 / 126), avg. gap size = 4.00 (12 / 3)
+ 5112 12.0 1.0 1.5 INTRON_3 339057 340024 (60157) C L1MA2 LINE/L1 (271) 7452 6493 485 *
ANNOTATION EVIDENCE:
5112 11.75 1.20 1.81 INTRON_3 339057 339845 60336 C L1MA2_3end LINE/L1 1 780 271 737
INTRON_3 339057 GTTAATCATACC-ACCTCCTCTGCACCCAGCTTCCCACTACCTTTCCCAG 339105
-----i v - i ----v i ii i
C L1MA2_3end#LI 780 -----CCATCCCCACCTCCCC----ACCAACCCCCCACTACCCTTCCCAG 740
INTRON_3 339106 CCTCTGACAACCATCCTTCTACTCTCTTATCTCCATGAGTTCAATTGTTT 339155
ii -
C L1MA2_3end#LI 739 CCTCTGGTAACCATCCTTCTACTCTCT-ATCTCCATGAGTTCAATTGTTT 691
INTRON_3 339156 TGATTTTTAGATCTT-CAGGTAAGTAAGAACATGCGATGTTTGTCTTCCC 339204
ii- ii i i i
C L1MA2_3end#LI 690 TGATTTTTAGATCCCACAAATAAGTGAGAACATGCGATGTTTGTCTTTCT 641
INTRON_3 339205 TTGCCTGGCTTATTTCATGTAGCATAATGACTGCCAGATCCATCCATGTT 339254
v iv i iv v
C L1MA2_3end#LI 640 GTGCCTGGCTTATTTCACTTAACATAATGACCTCCAGTTCCATCCATGTT 591
INTRON_3 339255 GTTGTTGCAAATGACAGGATCTGATTCTTTTTC-TGGCTGAATATTACTC 339303
--- v i- v
C L1MA2_3end#LI 590 GTTG---CAAATGACAGGATCTCATTCTTTTTTATGGCTGAATAGTACTC 544
INTRON_3 339304 TATTGTGTATAAGTATCACATTTTATTTATTTATTTATATGTT-ATGGAC 339352
i v i v ii i v -
C L1MA2_3end#LI 543 CATTGTGTATATGTACCACATTTTCTTTATCCATTCATCTGTTGATGGAC 494
INTRON_3 339353 ACTTGGGTTGCTTGCAAATCTTGGCTTTTGTGAACAGTGCTGCAACAAAC 339402
i v v
C L1MA2_3end#LI 493 ACTTAGGTTGCTTCCAAATCTTGGCTATTGTGAACAGTGCTGCAACAAAC 444
INTRON_3 339403 ATGGAAATGCAGGTATCTCTTCGATACACTGATTTCCTTTCTTTTGGGTA 339452
i i i i
C L1MA2_3end#LI 443 ATGGGAGTGCAGATATCTCTTCGATATACTGATTTCCTTTCTTTTGGGTA 394
INTRON_3 339453 TATACCCAGCAATGGGATTGCTGAATCCTATAGTAGCTCTATTTTTAGTT 339502
i i v i
C L1MA2_3end#LI 393 TATACCCAGCAGTGGGATTGCTGGATCATATGGTAGCTCTATTTTTAGTT 344
INTRON_3 339503 TTCTGAGGAACCTCCAAACTTTTTTCCATAGTAGTCGTACTAATTTACAT 339552
i v i i i
C L1MA2_3end#LI 343 TTTTGAGGAACCTCCAAACTGTTCTCCATAGTGGTTGTACTAATTTACAT 294
INTRON_3 339553 TTCCACCAACAGCATAGGAGCATTTCCGTACCGTATACATCCTCTCCAGC 339602
i ii v vi i v vi - vi v
C L1MA2_3end#LI 293 TCCCACCAACAGTGTACGAGGGTTCCCTTTTC-TCCACATCCTCGCCAGC 245
INTRON_3 339603 ATTTGTTATTGCCTGTCTTT-GGATGAAAGACATTTTAAATGGGGTGAGA 339651
- iv v v
C L1MA2_3end#LI 244 ATTTGTTATTGCCTGTCTTTTGGATATAAGCCATTTTAACTGGGGTGAGA 195
INTRON_3 339652 TGGTATCTCATTGTAGTTTTCATTTGCATTTCTCTGATGATCAATGATGT 339701
i v i
C L1MA2_3end#LI 194 TGATATCTCATTGTAGTTTTGATTTGCATTTCTCTGATGATCAGTGATGT 145
INTRON_3 339702 TGAGCCCCATTTCATGTGCCTGTATGCCATTTGTATGTCTTATTTTCAGA 339751
v v i v v v
C L1MA2_3end#LI 144 TGAGCACCTTTTCATATGCCTGTTTGCCATTTGTATGTCTTCTTTTGAGA 95
INTRON_3 339752 AATGCCTATTTAAGTCTTTTGCTTGTTTTAAAATTAAATTTTTAGATTTT 339801
i i i iii vv iii v
C L1MA2_3end#LI 94 AATGTCTATTCAAATCTTTTGCCCATTTTTTAATCGGATTATTAGATTTT 45
INTRON_3 339802 TTCCTGTAGAGTTGTTTGGGTTCCTTATATAGTTTGGTTATTAA 339845
i i i v i
C L1MA2_3end#LI 44 TTCCTATAGAGTTGTTTGAGCTCCTTATATATTCTGGTTATTAA 1
Matrix = 20p37g.matrix
Transitions / transversions = 1.76 (60 / 34)
Gap_init rate = 0.01 (10 / 788), avg. gap size = 1.90 (19 / 10)
2026 13.07 0.30 0.00 INTRON_3 339696 340024 60157 C L1M1_orf2 LINE/L1 2965 3294 0 738
INTRON_3 339696 TGATGTTGAGCCCCATTTCATGTGCCTGTATGCCATTTGTATGTCTTATT 339745
v v i v v
C L1M1_orf2#LIN 3294 TGATGTTGAGCACCTTTTCATATGCCTGTTTGCCATTTGTATGTCTTCTT 3245
INTRON_3 339746 TTCAGAAATGCCTATTTAAGTCTTTTGCTTGTTTTAAAATTAAATTTTTA 339795
v i i i iii vvi iii v
C L1M1_orf2#LIN 3244 TTGAGAAATGTCTATTCAAATCTTTTGCCCATTTTTTGATCGGATTATTA 3195
INTRON_3 339796 GATTTTTTCCTGTAGAGTTGTTTGGGTTCCTTATATAGTTTGGTTATTAA 339845
i i i v i
C L1M1_orf2#LIN 3194 GATTTTTTCCTATAGAGTTGTTTGAGCTCCTTATATATTCTGGTTATTAA 3145
INTRON_3 339846 TTCCTTGTCAGATGGGGAGTTTGCAAACATTTTCTCTTATTCTGTGGGTT 339895
i v i ii
C L1M1_orf2#LIN 3144 TCCCTTGTCAGATGGGTAGTTTGCAAATATTTTCTCCCATTCTGTGGGTT 3095
INTRON_3 339896 ATCTCTTCATTTTGTTGACTGATTCCTTTGCTGTGCAAAAGTGTTTTAAC 339945
i i i vv i iv
C L1M1_orf2#LIN 3094 GTCTCTTCACTTTGTTGATTGTATCCTTTGCTGTGCAGAAGCTTTTTAAC 3045
INTRON_3 339946 TTGGTGTGATCCCATTTGTCCATTTTTGCTTTGGTTGCCTGTGCTTGCGG 339995
i i
C L1M1_orf2#LIN 3044 TTGATGTGATCCCATTTGTCCATTTTTGCTTTGGTTGCCTGTGCTTGTGG 2995
INTRON_3 339996 GGTATTGCTTAAGAAAT-TTTGCCAAAATC 340024
i - v i i
C L1M1_orf2#LIN 2994 GGTATTGCTCAAGAAATCTTTGCCCAGACC 2965
Matrix = 20p37g.matrix
Transitions / transversions = 2.07 (29 / 14)
Gap_init rate = 0.00 (1 / 328), avg. gap size = 1.00 (1 / 1)
+ 9570 2.3 0.0 0.2 INTRON_3 340017 341920 (58261) + L1PA3 LINE/L1 4254 6154 (1) 487
ANNOTATION EVIDENCE:
9570 2.70 0.00 0.00 INTRON_3 340017 341166 59015 + L1P1_orf2 LINE/L1 2145 3294 0 739
INTRON_3 340017 CCAAAATCTCCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACA 340066
L1P1_orf2#LIN 2145 CCAAAATCTCCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACA 2194
INTRON_3 340067 AAATCAATGTACAAAAATCACAAGCATTCTTATACACTAATAACAGATAA 340116
i i i
L1P1_orf2#LIN 2195 AAATCAATGTACAAAAATCACAAGCATTCTTATACACCAACAACAGACAA 2244
INTRON_3 340117 ACAGAGGGCCAAATCATGAGTGAACTCCCATTCACAATTGCTTCAAAGAG 340166
i i
L1P1_orf2#LIN 2245 ACAGAGAGCCAAATCATGGGTGAACTCCCATTCACAATTGCTTCAAAGAG 2294
INTRON_3 340167 AATAAAATACCTAGGAATCCAACTTACAAGGGACGTGAAGGACCTCTTCA 340216
i
L1P1_orf2#LIN 2295 AATAAAATACCTAGGAATCCAACTTACAAGGGATGTGAAGGACCTCTTCA 2344
INTRON_3 340217 AGGAGAACTACAAACCACTGCTCAATGAAATAAAAGAGGATACAAACAAA 340266
v i
L1P1_orf2#LIN 2345 AGGAGAACTACAAACCACTGCTCAAGGAAATAAAAGAGGACACAAACAAA 2394
INTRON_3 340267 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCATGAAAAT 340316
i
L1P1_orf2#LIN 2395 TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAAT 2444
INTRON_3 340317 GGCCATACTGCCCAAGGTAATTTATAGATTCACTGCCATCCCCATCAAGC 340366
i v
L1P1_orf2#LIN 2445 GGCCATACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGC 2494
INTRON_3 340367 TACCAATGACTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATA 340416
L1P1_orf2#LIN 2495 TACCAATGACTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATA 2544
INTRON_3 340417 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 340466
L1P1_orf2#LIN 2545 TGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAA 2594
INTRON_3 340467 CAAAGCTGGAGGCATCATGCTACCTGACTTCAAACTATACTACAAGGCTA 340516
ii
L1P1_orf2#LIN 2595 CAAAGCTGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTA 2644
INTRON_3 340517 CAGTAACCAAAACAGCATGCTACTGGTACCAAAACAGAGATATAGATCAA 340566
v
L1P1_orf2#LIN 2645 CAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAA 2694
INTRON_3 340567 TGGAACAGAACAGAGCCCTCAGAAATAATGCCGCATATCTACAACTATCT 340616
L1P1_orf2#LIN 2695 TGGAACAGAACAGAGCCCTCAGAAATAATGCCGCATATCTACAACTATCT 2744
INTRON_3 340617 GATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGTTTCCCTAT 340666
v
L1P1_orf2#LIN 2745 GATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTAT 2794
INTRON_3 340667 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGGAGAAAGCTGAAA 340716
v
L1P1_orf2#LIN 2795 TTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAA 2844
INTRON_3 340717 CTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAA 340766
i
L1P1_orf2#LIN 2845 CTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAA 2894
INTRON_3 340767 AGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 340816
i
L1P1_orf2#LIN 2895 AGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAG 2944
INTRON_3 340817 GCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACA 340866
i i
L1P1_orf2#LIN 2945 GCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAACA 2994
INTRON_3 340867 CCAAAAGCAATGGAAACAAAAGCCAAAATTGACAAATGGGATCTAATTAA 340916
v
L1P1_orf2#LIN 2995 CCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAA 3044
INTRON_3 340917 ACTAAAGGGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGC 340966
i
L1P1_orf2#LIN 3045 ACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGC 3094
INTRON_3 340967 AACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAGGG 341016
v i
L1P1_orf2#LIN 3095 AACCTACAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGG 3144
INTRON_3 341017 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTGCAAGAAAAAAAC 341066
i
L1P1_orf2#LIN 3145 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 3194
INTRON_3 341067 AAACAACGCCATCAAAAAGTGGGCAAAGGACATGAACAAACACTTCTCAA 341116
v i i
L1P1_orf2#LIN 3195 AAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAA 3244
INTRON_3 341117 AAGAAGACATATATGCAGCCAAAAAACACATGAAAAAATGCTCACCATCA 341166
v i i
L1P1_orf2#LIN 3245 AAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCA 3294
Matrix = 20p37g.matrix
Transitions / transversions = 2.44 (22 / 9)
Gap_init rate = 0.00 (0 / 1149), avg. gap size = 0.0 (0 / 0)
7763 1.78 0.00 0.33 INTRON_3 341017 341920 58261 + L1PA3_3end LINE/L1 1 901 1 740
INTRON_3 341017 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTGCAAGAAAAAAAC 341066
i
L1PA3_3end#LI 1 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 50
INTRON_3 341067 AAACAACGCCATCAAAAAGTGGGCAAAGGACATGAACAAACACTTCTCAA 341116
v i i
L1PA3_3end#LI 51 AAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAA 100
INTRON_3 341117 AAGAAGACATATATGCAGCCAAAAAACACATGAAAAAATGCTCACCATCA 341166
v
L1PA3_3end#LI 101 AAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCATCA 150
INTRON_3 341167 CTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCAC 341216
L1PA3_3end#LI 151 CTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCAC 200
INTRON_3 341217 ACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGA 341266
L1PA3_3end#LI 201 ACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGA 250
INTRON_3 341267 GAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTCAA 341316
v
L1PA3_3end#LI 251 GAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAA 300
INTRON_3 341317 CTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGA 341366
L1PA3_3end#LI 301 CTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGA 350
INTRON_3 341367 ACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAA 341416
L1PA3_3end#LI 351 ACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAA 400
INTRON_3 341417 AGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATT 341466
L1PA3_3end#LI 401 AGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATT 450
INTRON_3 341467 GTGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAAC 341516
i
L1PA3_3end#LI 451 GCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAAC 500
INTRON_3 341517 AATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACT 341566
L1PA3_3end#LI 501 AATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACT 550
INTRON_3 341567 ATGCAGCCATAAAATATGATGAGTGCATGTCCTTTGTAGGGACATGGATG 341616
v v
L1PA3_3end#LI 551 ATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATG 600
INTRON_3 341617 AAATTGGAAATCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAA 341666
L1PA3_3end#LI 601 AAATTGGAAATCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAA 650
INTRON_3 341667 ACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGAACACATG 341716
L1PA3_3end#LI 651 ACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGAACACATG 700
INTRON_3 341717 GACACAGGAAGGGGAACATCACACTCTGGGGACTGTTGTGGGGTGGGGGG 341766
L1PA3_3end#LI 701 GACACAGGAAGGGGAACATCACACTCTGGGGACTGTTGTGGGGTGGGGGG 750
INTRON_3 341767 AGGGGGGAGGGATAGCTTTAGGAGTTATACCTAATGCTAAATGACGAGTT 341816
v i v i
L1PA3_3end#LI 751 AGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACGAGTT 800
INTRON_3 341817 AATGGGTGCAGCACACCAGCATGGCACATGTATACATATGTAACTAACCT 341866
i i
L1PA3_3end#LI 801 AGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCT 850
INTRON_3 341867 GCACATTGTGCACATGTACCCTAAAACTTAAAGTACAATAATAATTTTAA 341916
i ---
L1PA3_3end#LI 851 GCACATTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAAT---AA 897
INTRON_3 341917 AAAA 341920
L1PA3_3end#LI 898 AAAA 901
Matrix = 20p37g.matrix
Transitions / transversions = 1.29 (9 / 7)
Gap_init rate = 0.00 (1 / 903), avg. gap size = 3.00 (3 / 1)
+ 7854 10.9 2.4 0.1 INTRON_3 341960 343723 (56458) C L1MA2 LINE/L1 (1053) 6512 4698 485
ANNOTATION EVIDENCE:
7854 11.23 3.00 0.15 INTRON_3 341960 343226 56955 C L1M1_orf2 LINE/L1 1682 2984 310 741
INTRON_3 341960 AAGAAAT-TTTGCCTAGTCCACTGTCCTGGAGAGTTTTCCCAATGTTTTC 342008
- i v v v i
C L1M1_orf2#LIN 2984 AAGAAATCTTTGCCCAGACCAATGTCCTGGAGATTTTCCCCAATGTTTTC 2935
INTRON_3 342009 TCTTGGTAGTTTTATAGTTTGAGGTCTAACATTTAAGTCTTTAATCCATT 342058
iv i i v v
C L1M1_orf2#LIN 2934 TTGTAGTAGTTTCATAGTTTGAGGTCTTAGATTTAAGTCTTTAATCCATT 2885
INTRON_3 342059 TTGATTTTATTTTTGT-------GAGAGATAGGAATCTAGTTTTATTCCT 342101
v ------- ii i i
C L1M1_orf2#LIN 2884 TTGATTTGATTTTTGTATATGGCGAGAGATAGGGGTCTAGTTTCATTCTT 2835
INTRON_3 342102 CTATATATGCATATCCAATTTTTCTAGCATTCTTTATTGAAGTGACTGTC 342151
ii v i i i iiv v
C L1M1_orf2#LIN 2834 CTGCATATGGATATCCAGTTTTCCCAGCACCATTTATTGAAGAGACTGTC 2785
INTRON_3 342152 TTTTCTCCAAC--ATGTTCTTGGAAACT--GTCAAAAATGAGTTCACTAT 342197
i ii-- v v -- i
C L1M1_orf2#LIN 2784 TTTTCCCCAGTGTATGTTCTTGGCACCTTTGTCAAAAATGAGTTCACTGT 2735
INTRON_3 342198 AGATGTGTGGATTTGTTTCTGGTGTTCTTGATTTTGTTCTGTTGGTCTAT 342247
i - iv i ii
C L1M1_orf2#LIN 2734 AGGTGTGTGGATTTGTTTCTGG-GTTCTCTATTCTGTTCCATTGGTCTAT 2686
INTRON_3 342248 GT------TTTTAAGCCAGTACGGTGCTATATTGGCTACTACAAGCTCTG 342291
------ v vi i v i i -
C L1M1_orf2#LIN 2685 GTGTCTGTTTTTATGCCAGTACCATGCTGTTTTGGTTACTATA-GCTCTG 2637
INTRON_3 342292 TAGTATAATTTGAAGTCAGGTAATGTGATTATTTCAGTTTTGTTCTTTTT 342341
vi i
C L1M1_orf2#LIN 2636 TAGTATAATTTGAAGTCAGGTAATGTGATTCCTCCAGTTTTGTTCTTTTT 2587
INTRON_3 342342 GCCCAGGGTAGGTTCGGCTATTCTGGATCTTCTGTG-TTCCATATAAATT 342390
ii i v i i i -
C L1M1_orf2#LIN 2586 GCTTAGGATAGCTTTGGCTATTCTGGGTCTTTTGTGGTTCCATATAAATT 2537
INTRON_3 342391 TTAGGATTGTTTTTTCTATTTCTAGGAAGAATGTCATTGGTATTTTGATA 342440
iv
C L1M1_orf2#LIN 2536 TTAGGATTGTTTTTTCTATTTCTGTGAAGAATGTCATTGGTATTTTGATA 2487
INTRON_3 342441 GGGATTGCATTGAATCTGTAGATTGGTCTGGGTAGTGTGAACACTTTAAC 342490
v i i i i
C L1M1_orf2#LIN 2486 GGGATTGCATTGAATCTGTAGATTGCTTTGGGTAGTATGGACATTTTAAC 2437
INTRON_3 342491 AGTATTGATTCTTCCAATCCATGAACATGGAATATCTTTTCATTTTTTTG 342540
i i i v
C L1M1_orf2#LIN 2436 AATATTGATTCTTCCAATCCATGAACATGGAATATTTTTCCATTTTTTGG 2387
INTRON_3 342541 TGTCCTTTTCCATTTTTTTCATCAGTGTTTTATAGTTTTTATTGTAGAGA 342590
i v i i i
C L1M1_orf2#LIN 2386 TGTCCTCTTCAATTTCTTTCATCAGTGTTTTATAGTTTTCATTATAGAGA 2337
INTRON_3 342591 TATTTCACTTATTTGA-------AATTTCTAGGTATTCAATTTTATTTGT 342633
v v i------- i i v
C L1M1_orf2#LIN 2336 TCTTTCACTTCTTTGGTTAAGTTAATTCCTAGGTATTTAATTTTATGTGT 2287
INTRON_3 342634 GGCTAATGTACATGGGATTACTTGTTTGATTTCTTTTTCATATTGTTCAC 342683
v v v i i
C L1M1_orf2#LIN 2286 GGCTATTGTAAATGGGATTACTTTTTTAATTTCTTTTTCACATTGTTCAC 2237
INTRON_3 342684 TGTTGACATATAGAAATACTACTGGTTTTTTCATGTTGATTTTGTATCCT 342733
i i i vi
C L1M1_orf2#LIN 2236 TGTTGGCATATAGAAATGCTACTGATTTTTGTATGTTGATTTTGTATCCT 2187
INTRON_3 342734 GCAACTT-ACTGAATTCATTTA--------GATAGTTTTTTGATGGGGTC 342774
- ii --------i i vi i
C L1M1_orf2#LIN 2186 GCAACTTTACTGAATTTGTTTATCAGTTCTAATAGTTTTCTTGTGGAGTC 2137
INTRON_3 342775 TTTAGGTTTTTCCAAATGTAAGATCATATAATCTGCAAACAAGGA-AATT 342823
i v -
C L1M1_orf2#LIN 2136 TTTAGGTTTTTCCAAATATAAGATCATATCATCTGCAAACAAGGATAATT 2087
INTRON_3 342824 TGACTTCTTTCTTTCCAATTTGGATGCCCTTTATTTTTTTTTCTTGTCTG 342873
i v i i
C L1M1_orf2#LIN 2086 TGACTTCTTCCTTTCCAATTTGGATGCCCTTTATATCTTTCTCTTGTCTG 2037
INTRON_3 342874 ATTTCTCTAGCTAGGACTTCCAGTACTATGTTAAATAACAGTGGTAAAAG 342923
v i i v
C L1M1_orf2#LIN 2036 ATTGCTCTAGCTAGGACTTCCAGTACTATGTTGAATAACAGTGGTGACAG 1987
INTRON_3 342924 TGGGTATTTTTGTTTTGTTCCATATATTAGAGGAAAGATTTTCAGTTTGT 342973
i ii iv v v ii v
C L1M1_orf2#LIN 1986 TGGGCATCCTTGTCGTGTTCCAGATCTTAGAGGAAAGGCTTTCAGTTTTT 1937
INTRON_3 342974 CCCTGTACAGTATGATACTAGCCGTGGGTCTGTTGTATCTAGCTTTTAT- 343022
ii v i ii v i -
C L1M1_orf2#LIN 1936 CCCCATTCAGTATGATACTAGCTGTGGGTCTGTCATATATGGCTTTTATT 1887
INTRON_3 343023 GTGTTGAGGCATGTTCCTTCAGTACCTAGTTATTTGACAGTTTT-ATCAT 343071
i i vi ? i v vi -
C L1M1_orf2#LIN 1886 ATGTTGAGGTATGTTCCTTCTATNCCCAGTTTTTTGAGGGTTTTTATCAT 1837
INTRON_3 343072 GAAGGGATGTTAAATGTAATCAAATGCTTTTTCAGCATTAATTGAAATGA 343121
i v v i
C L1M1_orf2#LIN 1836 GAAGGGATGTTGAATTTTATCAAATGCTTTTTCAGCATCAATTGAAATGA 1787
INTRON_3 343122 TCATATGGTTTTTGTCCTTCATTTTGTTGATATGATGTATCACATTGATT 343171
i i
C L1M1_orf2#LIN 1786 TCATATGGTTTTTATCCTTCATTCTGTTGATATGATGTATCACATTGATT 1737
INTRON_3 343172 GATTTGCATATGTTGAATTATCCTTGCATACCTGGGATAAATCTCACTTG 343221
ii v v i
C L1M1_orf2#LIN 1736 GATTTGCATATGTTGAACCATCCTTGCATCCCAGGGATAAATCCCACTTG 1687
INTRON_3 343222 GTCAT 343226
C L1M1_orf2#LIN 1686 GTCAT 1682
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (94 / 47)
Gap_init rate = 0.01 (14 / 1266), avg. gap size = 2.86 (40 / 14)
7854 11.23 3.00 0.15 INTRON_3 341960 343226 56955 C L1M1_orf2 LINE/L1 1682 2984 310 818
INTRON_3 341960 AAGAAAT-TTTGCCTAGTCCACTGTCCTGGAGAGTTTTCCCAATGTTTTC 342008
- i v v v i
C L1M1_orf2#LIN 2984 AAGAAATCTTTGCCCAGACCAATGTCCTGGAGATTTTCCCCAATGTTTTC 2935
INTRON_3 342009 TCTTGGTAGTTTTATAGTTTGAGGTCTAACATTTAAGTCTTTAATCCATT 342058
iv i i v v
C L1M1_orf2#LIN 2934 TTGTAGTAGTTTCATAGTTTGAGGTCTTAGATTTAAGTCTTTAATCCATT 2885
INTRON_3 342059 TTGATTTTATTTTTGT-------GAGAGATAGGAATCTAGTTTTATTCCT 342101
v ------- ii i i
C L1M1_orf2#LIN 2884 TTGATTTGATTTTTGTATATGGCGAGAGATAGGGGTCTAGTTTCATTCTT 2835
INTRON_3 342102 CTATATATGCATATCCAATTTTTCTAGCATTCTTTATTGAAGTGACTGTC 342151
ii v i i i iiv v
C L1M1_orf2#LIN 2834 CTGCATATGGATATCCAGTTTTCCCAGCACCATTTATTGAAGAGACTGTC 2785
INTRON_3 342152 TTTTCTCCAAC--ATGTTCTTGGAAACT--GTCAAAAATGAGTTCACTAT 342197
i ii-- v v -- i
C L1M1_orf2#LIN 2784 TTTTCCCCAGTGTATGTTCTTGGCACCTTTGTCAAAAATGAGTTCACTGT 2735
INTRON_3 342198 AGATGTGTGGATTTGTTTCTGGTGTTCTTGATTTTGTTCTGTTGGTCTAT 342247
i - iv i ii
C L1M1_orf2#LIN 2734 AGGTGTGTGGATTTGTTTCTGG-GTTCTCTATTCTGTTCCATTGGTCTAT 2686
INTRON_3 342248 GT------TTTTAAGCCAGTACGGTGCTATATTGGCTACTACAAGCTCTG 342291
------ v vi i v i i -
C L1M1_orf2#LIN 2685 GTGTCTGTTTTTATGCCAGTACCATGCTGTTTTGGTTACTATA-GCTCTG 2637
INTRON_3 342292 TAGTATAATTTGAAGTCAGGTAATGTGATTATTTCAGTTTTGTTCTTTTT 342341
vi i
C L1M1_orf2#LIN 2636 TAGTATAATTTGAAGTCAGGTAATGTGATTCCTCCAGTTTTGTTCTTTTT 2587
INTRON_3 342342 GCCCAGGGTAGGTTCGGCTATTCTGGATCTTCTGTG-TTCCATATAAATT 342390
ii i v i i i -
C L1M1_orf2#LIN 2586 GCTTAGGATAGCTTTGGCTATTCTGGGTCTTTTGTGGTTCCATATAAATT 2537
INTRON_3 342391 TTAGGATTGTTTTTTCTATTTCTAGGAAGAATGTCATTGGTATTTTGATA 342440
iv
C L1M1_orf2#LIN 2536 TTAGGATTGTTTTTTCTATTTCTGTGAAGAATGTCATTGGTATTTTGATA 2487
INTRON_3 342441 GGGATTGCATTGAATCTGTAGATTGGTCTGGGTAGTGTGAACACTTTAAC 342490
v i i i i
C L1M1_orf2#LIN 2486 GGGATTGCATTGAATCTGTAGATTGCTTTGGGTAGTATGGACATTTTAAC 2437
INTRON_3 342491 AGTATTGATTCTTCCAATCCATGAACATGGAATATCTTTTCATTTTTTTG 342540
i i i v
C L1M1_orf2#LIN 2436 AATATTGATTCTTCCAATCCATGAACATGGAATATTTTTCCATTTTTTGG 2387
INTRON_3 342541 TGTCCTTTTCCATTTTTTTCATCAGTGTTTTATAGTTTTTATTGTAGAGA 342590
i v i i i
C L1M1_orf2#LIN 2386 TGTCCTCTTCAATTTCTTTCATCAGTGTTTTATAGTTTTCATTATAGAGA 2337
INTRON_3 342591 TATTTCACTTATTTGA-------AATTTCTAGGTATTCAATTTTATTTGT 342633
v v i------- i i v
C L1M1_orf2#LIN 2336 TCTTTCACTTCTTTGGTTAAGTTAATTCCTAGGTATTTAATTTTATGTGT 2287
INTRON_3 342634 GGCTAATGTACATGGGATTACTTGTTTGATTTCTTTTTCATATTGTTCAC 342683
v v v i i
C L1M1_orf2#LIN 2286 GGCTATTGTAAATGGGATTACTTTTTTAATTTCTTTTTCACATTGTTCAC 2237
INTRON_3 342684 TGTTGACATATAGAAATACTACTGGTTTTTTCATGTTGATTTTGTATCCT 342733
i i i vi
C L1M1_orf2#LIN 2236 TGTTGGCATATAGAAATGCTACTGATTTTTGTATGTTGATTTTGTATCCT 2187
INTRON_3 342734 GCAACTT-ACTGAATTCATTTA--------GATAGTTTTTTGATGGGGTC 342774
- ii --------i i vi i
C L1M1_orf2#LIN 2186 GCAACTTTACTGAATTTGTTTATCAGTTCTAATAGTTTTCTTGTGGAGTC 2137
INTRON_3 342775 TTTAGGTTTTTCCAAATGTAAGATCATATAATCTGCAAACAAGGA-AATT 342823
i v -
C L1M1_orf2#LIN 2136 TTTAGGTTTTTCCAAATATAAGATCATATCATCTGCAAACAAGGATAATT 2087
INTRON_3 342824 TGACTTCTTTCTTTCCAATTTGGATGCCCTTTATTTTTTTTTCTTGTCTG 342873
i v i i
C L1M1_orf2#LIN 2086 TGACTTCTTCCTTTCCAATTTGGATGCCCTTTATATCTTTCTCTTGTCTG 2037
INTRON_3 342874 ATTTCTCTAGCTAGGACTTCCAGTACTATGTTAAATAACAGTGGTAAAAG 342923
v i i v
C L1M1_orf2#LIN 2036 ATTGCTCTAGCTAGGACTTCCAGTACTATGTTGAATAACAGTGGTGACAG 1987
INTRON_3 342924 TGGGTATTTTTGTTTTGTTCCATATATTAGAGGAAAGATTTTCAGTTTGT 342973
i ii iv v v ii v
C L1M1_orf2#LIN 1986 TGGGCATCCTTGTCGTGTTCCAGATCTTAGAGGAAAGGCTTTCAGTTTTT 1937
INTRON_3 342974 CCCTGTACAGTATGATACTAGCCGTGGGTCTGTTGTATCTAGCTTTTAT- 343022
ii v i ii v i -
C L1M1_orf2#LIN 1936 CCCCATTCAGTATGATACTAGCTGTGGGTCTGTCATATATGGCTTTTATT 1887
INTRON_3 343023 GTGTTGAGGCATGTTCCTTCAGTACCTAGTTATTTGACAGTTTT-ATCAT 343071
i i vi ? i v vi -
C L1M1_orf2#LIN 1886 ATGTTGAGGTATGTTCCTTCTATNCCCAGTTTTTTGAGGGTTTTTATCAT 1837
INTRON_3 343072 GAAGGGATGTTAAATGTAATCAAATGCTTTTTCAGCATTAATTGAAATGA 343121
i v v i
C L1M1_orf2#LIN 1836 GAAGGGATGTTGAATTTTATCAAATGCTTTTTCAGCATCAATTGAAATGA 1787
INTRON_3 343122 TCATATGGTTTTTGTCCTTCATTTTGTTGATATGATGTATCACATTGATT 343171
i i
C L1M1_orf2#LIN 1786 TCATATGGTTTTTATCCTTCATTCTGTTGATATGATGTATCACATTGATT 1737
INTRON_3 343172 GATTTGCATATGTTGAATTATCCTTGCATACCTGGGATAAATCTCACTTG 343221
ii v v i
C L1M1_orf2#LIN 1736 GATTTGCATATGTTGAACCATCCTTGCATCCCAGGGATAAATCCCACTTG 1687
INTRON_3 343222 GTCAT 343226
C L1M1_orf2#LIN 1686 GTCAT 1682
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (94 / 47)
Gap_init rate = 0.01 (14 / 1266), avg. gap size = 2.86 (40 / 14)
6383 10.64 1.86 0.00 INTRON_3 342756 343723 56458 C L1M1_orf2 LINE/L1 1170 2155 1139 819
INTRON_3 342756 ATAGTTTTTTGATGGGGTCTTTAGGTTTTTCCAAATGTAAGATCATATAA 342805
i vi i i v
C L1M1_orf2#LIN 2155 ATAGTTTTCTTGTGGAGTCTTTAGGTTTTTCCAAATATAAGATCATATCA 2106
INTRON_3 342806 TCTGCAAACAAGGA-AATTTGACTTCTTTCTTTCCAATTTGGATGCCCTT 342854
- i
C L1M1_orf2#LIN 2105 TCTGCAAACAAGGATAATTTGACTTCTTCCTTTCCAATTTGGATGCCCTT 2056
INTRON_3 342855 TATTTTTTTTTCTTGTCTGATTTCTCTAGCTAGGACTTCCAGTACTATGT 342904
v i i v
C L1M1_orf2#LIN 2055 TATATCTTTCTCTTGTCTGATTGCTCTAGCTAGGACTTCCAGTACTATGT 2006
INTRON_3 342905 TAAATAACAGTGGTAAAAGTGGGTATTTTTGTTTTGTTCCATATATTAGA 342954
i i v i ii iv v v
C L1M1_orf2#LIN 2005 TGAATAACAGTGGTGACAGTGGGCATCCTTGTCGTGTTCCAGATCTTAGA 1956
INTRON_3 342955 GGAAAGATTTTCAGTTTGTCCCTGTACAGTATGATACTAGCCGTGGGTCT 343004
ii v ii v i
C L1M1_orf2#LIN 1955 GGAAAGGCTTTCAGTTTTTCCCCATTCAGTATGATACTAGCTGTGGGTCT 1906
INTRON_3 343005 GTTGTATCTAGCTTTTAT-GTGTTGAGGCATGTTCCTTCAGTACCTAGTT 343053
ii v i -i i vi ? i
C L1M1_orf2#LIN 1905 GTCATATATGGCTTTTATTATGTTGAGGTATGTTCCTTCTATNCCCAGTT 1856
INTRON_3 343054 ATTTGACAGTTTT-ATCATGAAGGGATGTTAAATGTAATCAAATGCTTTT 343102
v vi - i v v
C L1M1_orf2#LIN 1855 TTTTGAGGGTTTTTATCATGAAGGGATGTTGAATTTTATCAAATGCTTTT 1806
INTRON_3 343103 TCAGCATTAATTGAAATGATCATATGGTTTTTGTCCTTCATTTTGTTGAT 343152
i i i
C L1M1_orf2#LIN 1805 TCAGCATCAATTGAAATGATCATATGGTTTTTATCCTTCATTCTGTTGAT 1756
INTRON_3 343153 ATGATGTATCACATTGATTGATTTGCATATGTTGAATTATCCTTGCATAC 343202
ii v
C L1M1_orf2#LIN 1755 ATGATGTATCACATTGATTGATTTGCATATGTTGAACCATCCTTGCATCC 1706
INTRON_3 343203 CTGGGATAAATCTCACTTGGTCAT---------------CAGTGTATTGT 343237
v i ---------------i i
C L1M1_orf2#LIN 1705 CAGGGATAAATCCCACTTGGTCATGATGAATGATCTTTCTAATGTATTGT 1656
INTRON_3 343238 TGAATTTAGGTTGCTAGTATTTTGTTGAGGATTTTTGCATGAATAATCAT 343287
ii v v v
C L1M1_orf2#LIN 1655 TGAATTCGGTTTGCTAGTATTTTGTTGAGGATTTTTGCATCAATATTCAT 1606
INTRON_3 343288 CAGAGATATTGGCCTGTAGTTTTCTGTTTTTGATGTGTCTTTGTCTGGTT 343337
v
C L1M1_orf2#LIN 1605 CAGAGATATTGGCCTGTAGTTTTCTTTTTTTGATGTGTCTTTGTCTGGTT 1556
INTRON_3 343338 TAGCTATCAGGGTATCACTAGCCTCACAGAATGAGTTTGGAAGTATTCCG 343387
v v vi i ii v
C L1M1_orf2#LIN 1555 TTGGTATCAGGGTAATACTGGCCTCGTAGAATGAGTTTGGAAGTATTCCC 1506
INTRON_3 343388 TCCTCCTCTATTTTTCAGAATAGTTTGAGTAGGATTGGTATTAGGTGTTC 343437
i v v
C L1M1_orf2#LIN 1505 TCCTCCTCTATTTTTCGGAATAGTTTGAGTAGGATTGGTATTAGTTCTTC 1456
INTRON_3 343438 TTTAAATGTATGGTAAAATTCAGCTGTGAAGCTATCAGGTCCTGACCTTT 343487
v i v i i iv
C L1M1_orf2#LIN 1455 TTTAAATGTTTGGTAGAATTCAGCAGTGAAGCCATCAGGTCCCGGGCTTT 1406
INTRON_3 343488 CCTTTACTGTGAGACTTTTTATTATGACTTCAATTTCATTACTTGTTATT 343537
i v i i i i i
C L1M1_orf2#LIN 1405 TCTTTACTGGGAGACTTTTTATTACGGCTTCGATCTCGTTACTTGTTATT 1356
INTRON_3 343538 TTTCTGTTCAGATTTTGGATTTCTTCATGGTTCAATCTTGGTAGGTTGTA 343587
vv i v
C L1M1_orf2#LIN 1355 GGTCTGTTCAGGTTTTGGATTTCTTCCTGGTTCAATCTTGGTAGGTTGTA 1306
INTRON_3 343588 TGTGTCTAGGAATTTGTCTATTTCTGCTAGATTTTCCAATTTACTGGCAT 343637
i i v i
C L1M1_orf2#LIN 1305 TGTATCTAGGAATTTGTCCATTTCTTCTAGATTTTCCAATTTATTGGCAT 1256
INTRON_3 343638 ATAGTTCCTCATGATAGCCACTAATTATCCTTTGAATTTTTGCAATATCA 343687
v ii v i i
C L1M1_orf2#LIN 1255 ATAGTTGCTCATAGTAGCCACTAATGATCCTTTGAATTTCTGCAGTATCA 1206
INTRON_3 343688 GTTGTAATATCTCCTTTTTAATCCCTGATTTTATTT 343723
i v ii
C L1M1_orf2#LIN 1205 GTTGTAATGTCTCCTTTTTCATTTCTGATTTTATTT 1170
Matrix = 20p37g.matrix
Transitions / transversions = 1.62 (63 / 39)
Gap_init rate = 0.00 (4 / 967), avg. gap size = 4.50 (18 / 4)
+ 83 91.4 0.0 0.0 INTRON_3 343724 343862 (56319) + AT_rich Low_complexity 1 139 (0) 488
ANNOTATION EVIDENCE:
83 91.37 0.00 0.00 INTRON_3 343724 343862 56319 + AT_rich Low_complexity 96 234 66 815
INTRON_3 343724 TATTATATATGTTATATTTATATATTGTATAAATATACATTTTATATAAA 343773
????????????????????????????????????????????vv
AT_rich#Low_c 96 WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWATTAAA 145
INTRON_3 343774 ATCATATATGTTATATAAAATTATAATATATTTTATGTATATTATATTTA 343823
vi v vvv vv v?????????????????????????????????
AT_rich#Low_c 146 AATAAATAATATAATTTWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWW 195
INTRON_3 343824 TATAGATATAAATATATATTTATGTATATATTTTATATA 343862
???????????????????????????????????????
AT_rich#Low_c 196 WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWW 234
Matrix = Unknown
Transitions / transversions = 0.10 (1 / 10)
Gap_init rate = 0.00 (0 / 138), avg. gap size = 0.0 (0 / 0)
+ 1879 16.9 0.3 0.3 INTRON_3 343863 344152 (56029) C AluJo SINE/Alu (22) 290 1 489
ANNOTATION EVIDENCE:
1757 17.99 0.34 0.34 INTRON_3 343863 344152 56029 C AluJb SINE/Alu 1 290 22 781
INTRON_3 343863 TTTTTTTTGAGATAGGGTCTCACTCTGTCATCCAGG-TAGAGTGCAGTGG 343911
i i ii - i
C AluJb#SINE/Al 290 TTTTTTTTGAGACAGGGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGG 241
INTRON_3 343912 TGCAATCAGAGCTCACTGCAGCCTTGACCTTCTGGGATCAAGAGAGCCTC 343961
i i vi i i i v v v
C AluJb#SINE/Al 240 CGCGATCACGGCTCACTGCAGCCTCGACCTCCCGGGCTCAAGCGATCCTC 191
INTRON_3 343962 CCAACTCAGGCTCCTGAGTAGCTGGGACTACAGGCATGTGCCACCATGCC 344011
iiv v i ii i i
C AluJb#SINE/Al 190 CTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCGCGCCACCACGCC 141
INTRON_3 344012 TAGCTAGTATTTTGTATTTTTAGTAGAGATGAAGTCTCGCCATTTTGCCC 344061
ii i - v i ii i i v
C AluJb#SINE/Al 140 CGGCTAAT-TTTTGTATTTTTTGTAGAGACGGGGTTTCACCATGTTGCCC 92
INTRON_3 344062 AGGCTGGTCTTGAACTCCTGGGCTCAAGCAATTTGCCCACCACAGCCTCC 344111
i ii iiv i v i
C AluJb#SINE/Al 91 AGGCTGGTCTCGAACTCCTGGGCTCAAGTGATCCTCCCGCCTCGGCCTCC 42
INTRON_3 344112 TGAAGTGCCGGGATTACAGGCATGAGCCAGCACTCCCAACC 344152
ii i i v i v ii
C AluJb#SINE/Al 41 CAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 3.33 (40 / 12)
Gap_init rate = 0.01 (2 / 289), avg. gap size = 1.00 (2 / 2)
+ 7442 9.8 0.9 0.3 INTRON_3 344153 345308 (54873) C L1MA2 LINE/L1 (2857) 4708 3547 485
ANNOTATION EVIDENCE:
7442 9.81 0.87 0.34 INTRON_3 344153 345308 54873 C L1M1_orf2 LINE/L1 19 1180 2114 820
INTRON_3 344153 TGGTTTTATTTATTAGGGTCTTCTCCCTTTTTTTTTCTTTGTTAGTTGAA 344202
i v i i -- v ivii
C L1M1_orf2#LIN 1180 TGATTTTATTTATTTGGATCTTCTCTCTTTTTTT--CTTAGTTAGTCTGG 1133
INTRON_3 344203 CTAGAGGTTTGTCAATTTTGTTTATCTTTTCAAAAAAACAACTTTTTGTT 344252
i v v
C L1M1_orf2#LIN 1132 CTAAAGGTTTGTCAATTTTGTTTAACTTTTCAAAAAACCAACTTTTTGTT 1083
INTRON_3 344253 TCATTGA-CTTTTGTGTTGTTTTCCTCATTTCAAATTCATTTATTTCTGC 344301
- i ii v
C L1M1_orf2#LIN 1082 TCATTGATCTTTTGTATTGTTTTTTTCATTTCAATTTCATTTATTTCTGC 1033
INTRON_3 344302 TCTGATCTTTATTATTTCTTTTCTTCTACTAATTTTGAGTTCAGTTTGCT 344351
i ii
C L1M1_orf2#LIN 1032 TCTGATCTTTATTATTTCTTTTCTTCTACTAATTTTGGGTTTGGTTTGCT 983
INTRON_3 344352 CTTGCATTTCTAATTCTTTAAGATGCATCATTAGGTTTTTTTAATTGAAG 344401
v i i i v - v
C L1M1_orf2#LIN 982 CTTGCTTTTCTAGTTCTTTAAGATGCATCGTTAGATTGTTT-ATTTGAAG 934
INTRON_3 344402 TTTTTATTCTTTTTTGATGTAGGCACTTACAGCTGTATATTTTCCTCTTA 344451
vi i i v i i
C L1M1_orf2#LIN 933 TTTTTCCTCTTTTTTGATGTAGGCACTTATAGCTATAAACTTCCCTCTTA 884
INTRON_3 344452 GTATTGCTTCTGCTGTATCCCATAGGTTGTGGTATGTTGTGTTTTCATTA 344501
i i v i
C L1M1_orf2#LIN 883 GTACTGCTTTTGCTGTATCCCATAGGTTTTGGTATGTTGTGTTTCCATTA 834
INTRON_3 344502 TCTTTTTTTTCAAGAAATTTTGCAATTT---TCTTAATTCCTTCATGGAC 344548
v v v --- i v
C L1M1_orf2#LIN 833 TCATTTGTTTCAAGAAATTTTTCAATTTCCTTCTTAATTTCTTCATTGAC 784
INTRON_3 344549 TTACTTGTCAGGCAGGAGCATATTGTTTAATTTCCATGTGTTTGTATAGT 344598
ii v vv i
C L1M1_orf2#LIN 783 CCACTGGTCATTCAGGAGCATATTGTTTAATTTCCATGTATTTGTATAGT 734
INTRON_3 344599 GTCCAAAATTCCTCTTGTTATTAATTTATAGTTTTATTCCATTATGGTCA 344648
v v i
C L1M1_orf2#LIN 733 TTCCAAAATTCCTCTTGTTATTAATTTCTAGTTTTATTCCATTGTGGTCA 684
INTRON_3 344649 ---AAAATGCTGTATATTATTTCAGTTTTTT-GAGTATTTTAAGACTTGT 344694
--- i vv i - i i
C L1M1_orf2#LIN 683 GAGAAGATGCTTGATATTATTTCAATTTTTTTGAATGTTTTAAGACTTGT 634
INTRON_3 344695 TTTGTGACCTAACATATAGTCTATCCTTGAGAATGATCCATGTGCTGAGC 344744
i v
C L1M1_orf2#LIN 633 TTTGTGACCTAACATATGGTCTATCCTTGAGAATGATCCATGTGCTGAGG 584
INTRON_3 344745 AGAACTATGTATATTCTGCAGCCAGTGGATGGAATGTTCTGTAAATAACT 344794
i vv i ivv i v
C L1M1_orf2#LIN 583 AAAAGAATGTGTATTCTGCAGCTCTTGGATGAAATGTTCTGTAAATATCT 534
INTRON_3 344795 ATTAGGTCCATTTGTTCTATAGCGCAGATGAAGTCCGATGTTTCCTTCTT 344844
i v i v i i v
C L1M1_orf2#LIN 533 ATTAGATCCATTTGGTCTATAGTGCAGATTAAGTCTGATGTTTCTTTGTT 484
INTRON_3 344845 GATTTTCCATCTGAGAGATCTGTCCAATGCTGAAAGTGGGGTGTTGAAGT 344894
ii ii
C L1M1_orf2#LIN 483 GATTTTCTGTCTGGAAGATCTGTCCAATGCTGAAAGTGGGGTGTTGAAGT 434
INTRON_3 344895 CTCCAGCTATTAT-GTATTGGGCCCTATCTCTCTCTTTAGCTCTAATAAT 344943
- v
C L1M1_orf2#LIN 433 CTCCAGCTATTATTGTATTGGGGCCTATCTCTCTCTTTAGCTCTAATAAT 384
INTRON_3 344944 ATTTGCTTTACATATCTGGGCACTCCAGTATTGGGTACATATATATTTAC 344993
? i ii i i v
C L1M1_orf2#LIN 383 ATTTNCTTTATATATCTGGGTGCTCCAGTGTTGGGTGCATATATATTTAA 334
INTRON_3 344994 AATTGTTATATCCTCTTGCAGAATTGACCCCTTTATCATTATATAATGAC 345043
v i
C L1M1_orf2#LIN 333 AATTGTTATATCCTCTTGCTGAATTGACCCCTTTATCATTATATAGTGAC 284
INTRON_3 345044 CTTCTTTGTCTCTTTTTATAGCTTTTATCTTGAAATCTGTTTTGTCTGAT 345093
i i i i
C L1M1_orf2#LIN 283 CTTCTTTGTCTCTTCTTATAGTTTTTGTCTTGAAATCTATTTTGTCTGAT 234
INTRON_3 345094 ATAAGTATGACT-CTCCTGCTGTTTTTTGGTTTTCATTGGCATGGAATAT 345142
ii v- v i
C L1M1_orf2#LIN 233 ATAAGTATAGCGACTCCTGCTCTTTTTTGGTTTCCATTGGCATGGAATAT 184
INTRON_3 345143 CTTTTTCCATCCCTTTATTTTCAGTCTATGTGTATCTTTATAGGTGAAGT 345192
i
C L1M1_orf2#LIN 183 CTTTTTCCATCCCTTTATTTTCAGTCTATGTGTGTCTTTATAGGTGAAGT 134
INTRON_3 345193 GTGTTTCTTATAGACAACAAATAATTTGGTCTTATTTTTACATCCATTCA 345242
i i i v v v i v
C L1M1_orf2#LIN 133 GTGTTTCTTGTAGGCAACAGATCAATGGGTCTTGTTTTTTCATCCATTCA 84
INTRON_3 345243 GTCACTTTATGTCTTTTGATTGTGGAGTTTAGTCCATTTTCCATTCAATG 345292
i v i vi -v
C L1M1_orf2#LIN 83 GCCAGTCTATGTCTTTTGATTGGAGAGTTTAGTCCATTT-ACATTCAATG 35
INTRON_3 345293 TTATCATTGATAAGTA 345308
i
C L1M1_orf2#LIN 34 TTATTATTGATAAGTA 19
Matrix = 20p37g.matrix
Transitions / transversions = 1.55 (68 / 44)
Gap_init rate = 0.01 (9 / 1155), avg. gap size = 1.56 (14 / 9)
+ 8579 14.8 1.8 2.3 INTRON_3 345312 346364 (53817) C L1MA2 LINE/L1 (3972) 3593 2532 485
ANNOTATION EVIDENCE:
8579 14.76 1.77 2.26 INTRON_3 345312 346364 53817 C L1M1_5end LINE/L1 2532 3593 82 821
INTRON_3 345312 ATTGCGGAGTTTAGTCCATTTTCCATTCAATGTTATCACTGATAAGTACA 345361
vi -v i i vi
C L1M1_5end#LIN 3593 ATTGGAGAGTTTAGTCCATTT-ACATTCAATGTTATTATTGATAAGTAAG 3545
INTRON_3 345362 GACTTACTCTTGCCATTTTTAGATTTGTTTTCTGGTTGTTTCATGGTCTT 345411
i vvv ii
C L1M1_5end#LIN 3544 GACTTACTCCTGCCATTTTGTTATTTGTTTTCTGGTTGTTTTGTGGTCTT 3495
INTRON_3 345412 CTCTTCCTTCTTTCCTTCCTTCTTGTATTTCTTTTAGTGAAGGTGATTTT 345461
i v i
C L1M1_5end#LIN 3494 CTCTTCCTTCTTTCCTTCCTTCCTGTCTTCCTTTTAGTGAAGGTGATTTT 3445
INTRON_3 345462 CTCTGGTGATACAATTTAATAGCTCATTTTATATTTTT-GTGTATTTGTT 345510
i iiv vv iii v - i
C L1M1_5end#LIN 3444 CTCTGGTGGTATGTTTTAATTTCTTGCTTTTTATTTTTTGTGTATCTGTT 3395
INTRON_3 345511 CTAAGTTTCTTGATTTGAGGTTACAATGAGGCTTGCAAATATTATCTTAC 345560
v v i v v i
C L1M1_5end#LIN 3394 GTATGTTTTTTGATTTGAGGTTACCATGAGGCTTGCAAATAATATCTTAT 3345
INTRON_3 345561 AACTCGTTATTTAAAACTGATGACAACTTAACACTGATTATATAAACAAA 345610
i i v ii i
C L1M1_5end#LIN 3344 AACCCATTATTTTAAACTGATGACAACTTAACACTGATTGCACAAACAAA 3295
INTRON_3 345611 CAGACAAAAAGAAAACTAATTAAAACTCTATACTTTAACTTCATCCCCTC 345660
ii i v i i i
C L1M1_5end#LIN 3294 CAAGCAAAGAGAAAACTAATAAAAACTCTACACTTTAACTTCGTCCCCCC 3245
INTRON_3 345661 AATTTTTAACTTTT-GTTGTTTCTCTTTATGTCTTACTGTACTGCCTATG 345709
iv - v i i i
C L1M1_5end#LIN 3244 GCTTTTTAACTTTTTGTTGTTTCTATTTATATCTTATTGTACTGTCTATG 3195
INTRON_3 345710 TCTTGAAAATTTGTTGTAGTTATTGTTTCTGATTGATTCATCATTTCTTC 345759
v i i i v vv
C L1M1_5end#LIN 3194 TCTTGAAAAGTTGTTGTAGTTATTATTTTTGATTGGTTCATCTTTTAGTC 3145
INTRON_3 345760 TTCCTACTTAAGA-----ATAGTTTACACACTATAATTACAGTGTTACAA 345804
i -----i i i i
C L1M1_5end#LIN 3144 TTTCTACTTAAGATATGAGTAGTTTACACACCACAATTACAGTGTTATAA 3095
INTRON_3 345805 TATGCTATGTTTTCATGTGTGCTTACTGTTACCATTGAGTTTTGTACCTT 345854
v i iv i i v
C L1M1_5end#LIN 3094 TATTCTGTGTTTTTCTGTGTACTTACTATTACCAGTGAGTTTTGTACCTT 3045
INTRON_3 345855 TCAATGATTTCTTCTTGCTCATTAACATCTTTTTCTTTCAGAATGAAGAA 345904
ivi v ii i v
C L1M1_5end#LIN 3044 CAGATGATTTCTTATTGCTCATTAATGTCCTTTTCTTTCAGATTGAAGAA 2995
INTRON_3 345905 CTCCCATTAGCATTTCTTGTAAGACAGGTGTGGTGGTGATGAAATTCTTC 345954
v i v v i i
C L1M1_5end#LIN 2994 CTCCCTTTAGCATTTCTTGTAGGACAGGTCTGGTGTTGATGAAATCCCTC 2945
INTRON_3 345955 ACCCCTAGTTTGTCTCAGAAGGTCTTTATTTCTCCTGCATGCTTGAAGGA 346004
v ii v vi i v i
C L1M1_5end#LIN 2944 AGCTTTTGTTTGTCTGGGAAAGTCTTTATTTCTCCTTCATGTTTGAAGGA 2895
INTRON_3 346005 TATTTT-ACCAGATATATCACTTTAGGGTAAAAGTTTTTTTTTTTATTTA 346053
- ii ii i i ii ---i
C L1M1_5end#LIN 2894 TATTTTCACTGGATATACTATTCTAGGGTAAAAGTTTTTTTCCTT---CA 2848
INTRON_3 346054 GCATTTTTAATATGTCATGCTCCTCTTCTCCTGGAGTGTGAGGTTTCCAC 346103
i v iv - vv i
C L1M1_5end#LIN 2847 GCACTTTAAATATGTCATGCCACTCT-CTCCTGGCCTGTAAGGTTTCCAC 2799
INTRON_3 346104 TGAAAAATCTGCTGCCAGACCTATTGCAGCTCCATTGTATGTTATTCCAT 346153
i v v ivv
C L1M1_5end#LIN 2798 TGAAAAGTCTGCTGCCAGACGTATTGGAGCTCCATTGTATGTTATTTGTT 2749
INTRON_3 346154 CCTTTTCTCTTGCTGCTTTTAGGGTCCTTTCCTTATTCTTGACCTTTGGG 346203
i i i i
C L1M1_5end#LIN 2748 TCTTTTCTCTTGCTGCTTTTAGGATCCTTTCTTTATCCTTGACCTTTGGG 2699
INTRON_3 346204 AGCTTGATTATTGAATACCTTGAGTTAGTCTTCTTTGAGATAAACCTGCT 346253
i i i v i v i
C L1M1_5end#LIN 2698 AGTTTGATTATTAAATGCCTTGAGGTAGTCTTCTTTGGGTTAAATCTGCT 2649
INTRON_3 346254 TGGTGTTCAATAACCTTCTTGTACTTGAATGTTGGTATCTT-CTCCAGGT 346302
v i i - i
C L1M1_5end#LIN 2648 TGGTGTTCTATAACCTTCTTGTACTTGAATATTGATATCTTTCTCTAGGT 2599
INTRON_3 346303 TTGAGAAATTCT-TGATATCATCCCTTTGAATAAACTTTCTACCCC-ATC 346350
i i - v i -
C L1M1_5end#LIN 2598 TTGGGAAGTTCTCTGTTATTATCCCTTTGAATAAACTTTCTACCCCTATC 2549
INTRON_3 346351 TCTTTTTGT---TTTTG 346364
i i v --- ii v
C L1M1_5end#LIN 2548 TCTCTCTCTACCTCCTC 2532
Matrix = 20p37g.matrix
Transitions / transversions = 1.82 (91 / 50)
Gap_init rate = 0.01 (11 / 1052), avg. gap size = 1.73 (19 / 11)
+ 2540 8.0 0.0 0.3 INTRON_3 346365 346675 (53506) C AluY SINE/Alu (0) 311 2 490
ANNOTATION EVIDENCE:
2448 8.07 0.00 0.32 INTRON_3 346365 346675 53506 C AluY SINE/Alu 2 311 0 782
INTRON_3 346365 TTTTTTTGTTTTTTTGTTTTTTGTTTTTTTGAGGCGGAGTCTCACTTTGT 346414
v v v i i i
C AluY#SINE/Alu 311 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGT 262
INTRON_3 346415 CGCCCAGGCTGGAGTACAGTGGCGTGATCTCGGCTCACCGCAACCTCCGT 346464
i i i v i
C AluY#SINE/Alu 261 CGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGC 212
INTRON_3 346465 CTCCCAGGTTCATGCCATTCTTCTGCCTCAGCCTCCCGAGTAGCTGGGAC 346514
i i i
C AluY#SINE/Alu 211 CTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGAC 162
INTRON_3 346515 TACAGACGCCCACCACCACGCTCGGCTAATTTTTTGTATTTTTTAGTAGA 346564
i i i -
C AluY#SINE/Alu 161 TACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTT-AGTAGA 113
INTRON_3 346565 GACGGGGTTTCACCGTGTTAGCCAGGATGGTCTTGATCGCCTGATCTCGT 346614
i v i
C AluY#SINE/Alu 112 GACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGT 63
INTRON_3 346615 GATCTGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAAACATGAGCCA 346664
i ii i
C AluY#SINE/Alu 62 GATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCA 13
INTRON_3 346665 CTGCGCCCGGC 346675
i
C AluY#SINE/Alu 12 CCGCGCCCGGC 2
Matrix = 14p37g.matrix
Transitions / transversions = 4.00 (20 / 5)
Gap_init rate = 0.00 (1 / 310), avg. gap size = 1.00 (1 / 1)
+10476 17.5 4.0 1.5 INTRON_3 346676 349147 (51034) C L1MA2 LINE/L1 (5034) 2531 12 485
ANNOTATION EVIDENCE:
8579 14.76 1.77 2.26 INTRON_3 346676 347263 52918 C L1M1_5end LINE/L1 1961 2531 1144 822
INTRON_3 346676 TTA---CCCTCATCTCTT-TATCTGCATCCTCTTTAAGGCCAATATCTCT 346721
--- vvi v -v i -- - i --- i ii
C L1M1_5end#LIN 2531 TTAAGGCCAATAACTCTTAGATTTGC--CCT-TTTGAGGC---TATTTTC 2488
INTRON_3 346722 TAGATTACCCTTTTGAGGTTATTTCGTAGATCCTGTAGGCATGCTTCATT 346771
---- v ii vv ii ---- i v -------- i
C L1M1_5end#LIN 2487 TAGAT----CTTGTAGGCGTGCTTC----ATTCTTT--------TTTATT 2454
INTRON_3 346772 CTGTTTTATTCTTTTCTTTCT---TTTGTATCCTCTGACTGTATGTTTTC 346818
v v i v iiii --- v ii vi iv iv i
C L1M1_5end#LIN 2453 CTTTTTTCTTTTGTCTCCTCTGACTGTGTATTTTCAAATAGCCTGTCTTC 2404
INTRON_3 346819 AAATAGCATGTCTTCAAGTTTACTAATTCTTTCTTGATCAATTTTGCTAT 346868
--- --- vii v i -- vv v- i i
C L1M1_5end#LIN 2403 AA---GC---TCACTAATTCT--TTCTTCTG-CTTGATCAATTCTGCTGT 2363
INTRON_3 346869 TAAGAGACT--GATACAGTTTTCAGCATATCAATTGCCTTTTTCAACTAT 346916
-- i v i i i v vi
C L1M1_5end#LIN 2362 TAAGAGACTCTGATGCATTCTTCAGTATGTCAATTGCATTTTTCAACTCC 2313
INTRON_3 346917 AGAATTTCTGCTT----CTTTTTCATTATTTCGAGCTCTTTGTTAAATTT 346962
---- v i v
C L1M1_5end#LIN 2312 AGAATTTCTGCTTGATTCTTTTTAATTATTTCAATCTCTTTGTTAAATTT 2263
INTRON_3 346963 ATCTGATAAAATTCTGAATTCTTTCTCTGTGTTACCTTGAATTTCTTTCG 347012
ii i i ? -
C L1M1_5end#LIN 2262 ATCTGATAGGATTCTGAATTCCTTCTCTGTGTTATCTTGAATTTCNTT-G 2214
INTRON_3 347013 AGTTTGCTTAAAACAGCTGTTTTGAATACTCTGTCTGGAAGGTCATATAT 347062
v i i v i i
C L1M1_5end#LIN 2213 AGTTTCCTCAAAACAGCTATTTTGAATTCTCTGTCTGAAAGGTCACATAT 2164
INTRON_3 347063 CT--GTTTCTCCAGGATTGATCTCTGGTGCCTCATTTAGTTCATTTGGTG 347110
-- i i i i i
C L1M1_5end#LIN 2163 CTCTGTCTCTCCGGGATTGGTCCCTGGTGCCTTATTTAGTTCATTTGGTG 2114
INTRON_3 347111 AAGTAAGATTTTCCTGGATGGTGTTGATGCTCGTAGATGTTCTTCAGTGT 347160
i v vi v i i v i
C L1M1_5end#LIN 2113 AGGTCATGTTTTCCTGGATGGTCTTGATGCTTGTGGATGTTCGTCGGTGT 2064
INTRON_3 347161 CTGGGCATTAAATAATTGGGTATTTATTATAGTCTTCACAGTCTGGGCTT 347210
i v i i i
C L1M1_5end#LIN 2063 CTGGGCATTGAAGAGTTAGGTATTTATTGTAGTCTTCACAGTCTGGGCTT 2014
INTRON_3 347211 ATTTGCGCCTGTCCTTCTTGAGAATGCTTTCCAGGTATTCAAAGGGACTT 347260
i ii i i v i
C L1M1_5end#LIN 2013 GTTTGTACCCGTCCTTCTTGGGAAGGCTTTCCAGGTATTCGAAGGGACTT 1964
INTRON_3 347261 GGG 347263
C L1M1_5end#LIN 1963 GGG 1961
Matrix = 20p37g.matrix
Transitions / transversions = 1.88 (62 / 33)
Gap_init rate = 0.03 (17 / 587), avg. gap size = 2.76 (47 / 17)
10476 18.33 1.96 1.27 INTRON_3 347264 349147 51034 C L1M1_5end LINE/L1 12 1908 1767 823
INTRON_3 347264 CTCCAAGCC---TAACACTGTGGTTTTTGCAGACTCGTAGAGCTACCACC 347310
i --- i i i v i
C L1M1_5end#LIN 1908 CCCCAAGCCCAGTAACGCTGTGGCTCTTGCAGACTCGTAGAGGTACCGCC 1859
INTRON_3 347311 TTGGTGGTCTTGGATAAGATTTTGAAGAGTTATCTGGATTACCAAGCAGA 347360
iiv i v i
C L1M1_5end#LIN 1858 TTGGTGGTCTTGGATAAGATCCGGAAGAATTCTCTGGATTACCAGGCAGA 1809
INTRON_3 347361 GACTCTTGTTCTTTTTCCTTACTTTCTCCCAAACAAATGTAGTCTCTCTC 347410
i i i v
C L1M1_5end#LIN 1808 GACTCTTGTTCTCTTCCCTTACTTTCTCCCAAACAAACGGAGTCTCTCTC 1759
INTRON_3 347411 TGTCTGTACTGAGGTGC-TGGAACTGGGAT-GTAGTGATGCAAGCACCCC 347458
-- i v - i iv- vi ii
C L1M1_5end#LIN 1758 T--CTGTGCTGAGCTGCCTGGAGCTGGGGGAGGGGTGACACAAGCACCCC 1711
INTRON_3 347459 TGTGGTCACTACCACTGGGACTGCACTGGCTTAGATCTGATGCTATCCCA 347508
i i i v i i v i v v
C L1M1_5end#LIN 1710 TGTGGCCACCACCACTGGGACTGCGCTGGGTCAGACCTGAAGCCAGCACA 1661
INTRON_3 347509 GCACTGGGTCTTGCCCAAGGCCTGTTGTAACCACTTACCAGGCTGCCATC 347558
i i i? -i v i ii
C L1M1_5end#LIN 1660 GCACTGGGTCTCGCCCAAGGCCCGCNGTAACCACT-GCCTGGCTACCGCC 1612
INTRON_3 347559 TGTGTTCACTCAAAGCTCAATGTCTCTATGATCAACCAGTGGTGAAGCTA 347608
i ii i i v v v ii i vi ii i
C L1M1_5end#LIN 1611 TATGTTTGCTCAAGGCCCTAGGGCTCTACAATCAGCAGGTGGCAAAGCCA 1562
INTRON_3 347609 ACCAGCTTTGTGTTCTTCCCT-CAAGGCAGCAAGTTCCTCCAGACCCCAG 347657
i vi i - i ii i i ? i
C L1M1_5end#LIN 1561 GCCAGGCTTGTGTCCTTCCCTTCAGGGTGGCGAGTTCCCCCNGGCCCCAG 1512
INTRON_3 347658 GCAGGTTCAGAGATGT-ATCTTGGAGCCGGGGATTGGAGTCAAAAACTTT 347706
i i i- iv i vi i i
C L1M1_5end#LIN 1511 GCGGGTCCAGAGATGCCATCCAGGAGCCAGGGCCTGGAGTCAGAAACCTT 1462
INTRON_3 347707 AGAAATTTACCTGATGTTCCATTTTACTGTGGTTAAGCTGGCACTCACAC 347756
i i i i i i i i i i vi
C L1M1_5end#LIN 1461 AGGAATCTACCTGGTGCTCTATTCTACTGCGGCTGAGCTGGCACCCAAGC 1412
INTRON_3 347757 CACAATACAAAGTCCTTCCCACTCTTCTCTCCGCTTTTCACAGGCAGAGG 347806
v i v i
C L1M1_5end#LIN 1411 CACAAGACAAAGTCCTTCCCACTCTTCCCTCCCCTTTCCACAGGCAGAGG 1362
INTRON_3 347807 AGCCTTTCTGTGTGGCCACCACCATCAGCAGCCCATGGGAGGTTCTGCCA 347856
i i ivii i vvvi i vii v ?
C L1M1_5end#LIN 1361 AGTCTCTCCCCATGGCCACCACCACCCCAGGCCCACGGCGAGTACTGCCN 1312
INTRON_3 347857 GGCCACTGCTGATGTTCACTTAAAGCCCAAGGGCTCTTT-GTTTGCTTGT 347905
i i i i i i- iv
C L1M1_5end#LIN 1311 GGCTACCGCCGATGTTCACTCAAGGCCCAAGGGCTCTTCAGTCAGCTTGT 1262
INTRON_3 347906 GGTGAATGCTGCCAGGCCTGGGACTAACTCTTCAGGGAAGTGAGCTCCTC 347955
v? i v i i
C L1M1_5end#LIN 1261 GGTGAATGCTGCCAGGCCTGGGACTCNCCCTTCAGGGCAGTGGGCTCCCC 1212
INTRON_3 347956 TCTGACCCAGGGAAAGTCCAGAAATGCTGTCCAAGAGCCTAGGCCTGGAC 348005
i v i i v v
C L1M1_5end#LIN 1211 TCTGGCCCAGGGCAGGTCCAGAAATGCCGTCCAAGAGCCAAGGCCTGGAA 1162
INTRON_3 348006 TCAGGGACCCCCAGAAACTGCTTGTCGCTTTACCTCACTGTGGCTGAGCT 348055
i v iv i vi i i
C L1M1_5end#LIN 1161 TCGGGGACCCCAAGAGCCCGCTTGGTGCTCTACCCCACTGTGGCTGAGCT 1112
INTRON_3 348056 GATACCTAAGGCAAGGTGCAAGACAAAGTCCTCTTTACTTTTCCCTCT-- 348103
i - ---- i i --
C L1M1_5end#LIN 1111 GGTACCTAAG-C----TGCAAGACAAAGTCCCCTTTACTCTTCCCTCTCC 1067
INTRON_3 348104 --TTCTCAAACACAAGGAGTCTTTCACTGTAGCCACCACAACTGAGAATG 348151
-- i v i v ii i i
C L1M1_5end#LIN 1066 TTTTCTCAAGCAGAAGGAGTCTCTCCCCATAGCCACCACAGCTGGGAATG 1017
INTRON_3 348152 TCTTGGGTCACACCCTAAAGTGAGCACATCTCAGAG-----CCCAAAGCC 348196
vi - i iv i v ----- i
C L1M1_5end#LIN 1016 TGCTGGGTCACACC-TGAAGCCAGCACGTCTCTGAGTCTCACCCAAGGCC 968
INTRON_3 348197 AATGGCA--TACTACTTGGGTATCATTGGTGGTTATTCAGGACCCAAGGG 348244
v i i-- i i i ii v i i
C L1M1_5end#LIN 967 CACGGCGAGTACTGCCTGGGTACCGCTGCTGATTATTCAGGGCCCAAGGG 918
INTRON_3 348245 CTCTTCAGTCAGCAG-CAATGAATCCTGCCAGGACTAGGACCTTCTCATC 348293
i -ii i v i v
C L1M1_5end#LIN 917 CTCTTTAGTCAGCAGGTGATGAATCCTGCCAGGACTGGGTCCTTCCCTTC 868
INTRON_3 348294 AAGGCAGCTGGTTCCATTTTGGATTGGGGTGTGTCTAGAAATGTCA---G 348340
v v i viii i---
C L1M1_5end#LIN 867 AAGGCAGCGGGTTCCCTTCTGGCCCAGGGTGTGTCTAGAAATGTCGTCTG 818
INTRON_3 348341 TGAGCTAGGGCCTAGAATGAGGGCCGCACCATTCTGTGCAGTGCTCTCTC 348390
v i i v vv i iv i i v
C L1M1_5end#LIN 817 GGAGCTAGGGCCTGGAATGGGGGCCTCAGGACTCTGCCCGGTGCCCTATC 768
INTRON_3 348391 CTACTGTGACTGAGCTGGTATCCAAGATACA-GACAAAGTCCTCTTTACT 348439
i v i -
C L1M1_5end#LIN 767 CTACTGTGGCTGAGCTGGTATCCAAGTTGCAAGACAAAGTCCTCTTTACT 718
INTRON_3 348440 CTTAGCTCTCCTCTGTATAAGTAGAAGGAAGGAGTCACTTTCATTGCTAC 348489
vv vivi ii v ii ivv i
C L1M1_5end#LIN 717 CTTCCCTCTCCTCTCCTCAAGCGGAAGGAAGGAGTCTCTCCCGGAGCTGC 668
INTRON_3 348490 TAGCTGCACTGATTAGG-CTGGGGGAGTGGCGGCACAAGCACTCCCTTAG 348538
v ii vi i -i v i i i
C L1M1_5end#LIN 667 GAGCTGTGCTGCCTGGGGTTGGGGGAGGGGTGGCGCAAGCACTCCCTTGG 618
INTRON_3 348539 CCACCCTGGCTGGTATCTTCCTAGGTAACATGTCACCTGAGTCTACTGGC 348588
i i i iv vi i i v ii i
C L1M1_5end#LIN 617 CCGCCCCGGCTGGTGTCTCACTAGGTCGCGTGCCCCCCAAGTCCACTGGC 568
INTRON_3 348589 TCTGAGCCCAGCCTAGCTCTAGGAGTTGCCTAGGAATTGCAGTCCCTGTG 348638
vi v i v i i
C L1M1_5end#LIN 567 TCTGAGCCCAGCACAGCACCAGGACTTGCCCAGGAATTGCAGTCCTTGTG 518
INTRON_3 348639 GCCTAGACTGC-TTTCAGGTTTACCTGGAACCCCAGAGCACTTTGACCTG 348687
- i ii i i ii i
C L1M1_5end#LIN 517 GCCTAGACTGCCTTTCAAGTTTATTTAGGACCCCAGAGCACTTTAGCCCG 468
INTRON_3 348688 TGGCGGTGAGACTTTCTAAGAAACTCAAGCTCTGACTGCTAGGATAGGTG 348737
i i i i v i-- i i i i i i i
C L1M1_5end#LIN 467 CGGTGGCGAGGCTTGCC--GGAACTCAGGTTCCGACCGCTGGGATGGGTG 420
INTRON_3 348738 ATTTCCCTCTGGCTAGT-CTGGTCCAAATGCTCCCTCCATGCACAGGCAC 348786
i v- i i ---- i
C L1M1_5end#LIN 419 ATTCCCCTCTGGCTAGGGCTGGTCTAAATGCTCCCTCCGTG----GGCGC 374
INTRON_3 348787 TGGCTGAGTGCAGCACAGCTTTGCTCTC---TGTGACAAGGCAGCACTGA 348833
i v v v i iv i --- i
C L1M1_5end#LIN 373 CGGCTGAGTTCTGCCCGGTGTTGCTTTCCGCTGTGACAGGGCAGCACTGA 324
INTRON_3 348834 GTTC-AATGTAAAGTCCCCCATCTGCTGTGCTGTCTCTCCCCCAAGTGCA 348882
- i v vii i v i
C L1M1_5end#LIN 323 GTTCCAATGCAAAGTCCCACAATCGCTGCGCTCTCCCTCCCCCAAGTGCA 274
INTRON_3 348883 CAGA----CTTTCCGTGCCGTAAGGCTGCTGCCAGGGGATGTGGGAGGGT 348928
---- i i ii v i i v v
C L1M1_5end#LIN 273 CAGATTCTCTCTCCGCGCCACACGGCCGCTGCCGGGGGATGGGGGAGGGG 224
INTRON_3 348929 TGGTGTTGGTGACTCAAGACTGTCTCTCCTACCCTCTTCAATGCCTCTTT 348978
i i i i i i
C L1M1_5end#LIN 223 TGGCGTCGGCGATTCAAGACTGTCTTTCCTACCCTCTTCAGTGCCTCTTT 174
INTRON_3 348979 TCAGTTATATGAAGTTAAAACCAGGTAGTGTGATTATTCACCTGATTTTT 349028
- v v iii
C L1M1_5end#LIN 173 -CAGTGATATGAAGTTAAAACCAGGTACTGTGATCGCTCACCTGATTTTT 125
INTRON_3 349029 GGTTCTTGTGACAGTGATTTTCTGTGTGCAAACAGTTGTTAATATTTGAT 349078
i vi v i --i i v - i
C L1M1_5end#LIN 124 GGTTCTTATGAAGGTGCTTTTTTGTGTG--GATAGTTGTTCA-ATTTGGT 78
INTRON_3 349079 ATTCTTGGGATGGGGGACAGGGAGACACATGCTATAGGCTTCTATTCTTC 349128
i i v i- i ii ---- ivvi v iv vv
C L1M1_5end#LIN 77 GTTCCTGCGG-GGAGGATGG----ACGATCGGTGGAGGCTTCTATTCGGC 33
INTRON_3 349129 CATCTTGCCCT--TTCCTTCT 349147
i i--i i
C L1M1_5end#LIN 32 CATCTTGCTCCGCCTCCCTCT 12
Matrix = 20p37g.matrix
Transitions / transversions = 2.51 (241 / 96)
Gap_init rate = 0.02 (31 / 1883), avg. gap size = 1.97 (61 / 31)
+ 669 11.0 0.0 0.0 INTRON_3 349148 349247 (50934) + (TTCC)n Simple_repeat 1 100 (0) 491
ANNOTATION EVIDENCE:
669 11.00 0.00 0.00 INTRON_3 349148 349247 50934 C (GGAA)n Simple_repeat 81 180 0 867
INTRON_3 349148 TTCCTTCTTTCCTTCCTTCCTTCTTTCCTTCCTTCCTTCCTTCCTTCCTT 349197
i i
C (GGAA)n#Simpl 180 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 131
INTRON_3 349198 CCTTCCTTCCTTCCTTCCTTCTCTCTCTCTCTCCTTCCTCCCTCCCCTCC 349247
ii ii ii i i i
C (GGAA)n#Simpl 130 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 81
Matrix = Unknown
Transitions / transversions = 0.0 (11 / 0)
Gap_init rate = 0.00 (0 / 99), avg. gap size = 0.0 (0 / 0)
+ 210 10.7 0.0 0.0 INTRON_3 349248 349275 (50906) + (TCCCC)n Simple_repeat 5 32 (0) 492
ANNOTATION EVIDENCE:
210 10.71 0.00 0.00 INTRON_3 349248 349275 50906 C (GGGGA)n Simple_repeat 150 177 3 871
INTRON_3 349248 CTTTCCCTCCCCTCCCCTCCCCTCCCTT 349275
i i i
C (GGGGA)n#Simp 177 CCTCCCCTCCCCTCCCCTCCCCTCCCCT 150
Matrix = Unknown
Transitions / transversions = 0.0 (3 / 0)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 968 22.4 11.3 9.7 INTRON_3 349467 349694 (50487) + L1MC4 LINE/L1 7387 7651 (391) 493
ANNOTATION EVIDENCE:
968 22.43 11.33 9.66 INTRON_3 349467 349694 50487 + L1MC4_3end LINE/L1 2134 2398 391 824
INTRON_3 349467 AGTAATGGAACAAGGTGACACTCTGTACCTCTCCTGATATGCTATATTGA 349516
i ivi iiv ii -- v ii i
L1MC4_3end#LI 2134 AGTAATGGGACAAATCGACATCATGCGCCTC--CTGATATGATGCACTGA 2181
INTRON_3 349517 AAAGGATA-------ACTTTTTT---AT--------AACGTGTGTCACCT 349548
i i ------- i v --- -------- vi ii v
L1MC4_3end#LI 2182 GAAGGACACAACATCACTTCTGTGGTATTCCTGCCAAAAATGCATAACCT 2231
INTRON_3 349549 GAATCTAATCTCAAAGAAACATCAAACAAACCTAAATTGAAGGACATACT 349598
vii i i i i v
L1MC4_3end#LI 2232 GAATCTAATCATGAGGAAACATCAGACAAACCCAAATTGAGGGACATTCT 2281
INTRON_3 349599 GCAAAATAAATGGCAAGTTCTTTAAAAAAATTTCAAGTTCATGAAAGACA 349648
i v vv v i vv v v
L1MC4_3end#LI 2282 ACAAAATAACTGGCCTGTACTCTTCAAAAATGTCAAGGTCATGAAAGACA 2331
INTRON_3 349649 AGAAAA-----------TATT---------AGGA-ACTAAAGAGGCATGA 349677
ii ----------- ? --------- - i
L1MC4_3end#LI 2332 AAGAAAGACTGAGGAACTNTTCCAGATTAAAGGAGACTAAAGAGACATGA 2381
INTRON_3 349678 ACATTAAATGCAATGCA 349694
vv i i
L1MC4_3end#LI 2382 CAACTAAATGCAACGCA 2398
Matrix = 20p37g.matrix
Transitions / transversions = 1.61 (29 / 18)
Gap_init rate = 0.03 (7 / 227), avg. gap size = 5.86 (41 / 7)
+ 2110 13.3 0.0 1.4 INTRON_3 349695 349994 (50187) + AluSz6 SINE/Alu 2 297 (15) 494
ANNOTATION EVIDENCE:
2024 13.86 0.00 1.35 INTRON_3 349695 349994 50187 + AluSx SINE/Alu 2 297 15 783
INTRON_3 349695 GCCAGGTGCAGTGGCTCATGCCTGTAAGCCCAACACTTCGGGAGGCCAAG 349744
i i i i v i i i
AluSx#SINE/Al 2 GCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAG 51
INTRON_3 349745 GCAGGTGGGTCACTTGAGGCCAGGAATTCAAGACCAGCCTAGCCAACATA 349794
i i i i i i i i i
AluSx#SINE/Al 52 GCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATG 101
INTRON_3 349795 GTGAAACTCCATCTCTACTAAAAATACAAAATAATAGCTGGGCATGGTGG 349844
i i - v i i
AluSx#SINE/Al 102 GTGAAACCCCGTCTCTACTAAAAATACAAAA-ATTAGCCGGGCGTGGTGG 150
INTRON_3 349845 TTCGCACCTGTAATCCCAGCTACTCAGGAGGCTGCGGCATGAGAATCTCT 349894
iv i i v v v
AluSx#SINE/Al 151 CGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCT 200
INTRON_3 349895 TGAACCTGGGAGGCAGAGGTTGCAGTGGAGAGCTCAGATCTCACCACTGC 349944
i i --- iv v i
AluSx#SINE/Al 201 TGAACCCGGGAGGCGGAGGTTGCAGTG---AGCCGAGATCGCGCCACTGC 247
INTRON_3 349945 ATTCTAGCCTCGGTGACAGAGTGAGACTCTGTCTCAAAAAAAAAAAAAAA 349994
i i v i i i
AluSx#SINE/Al 248 ACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAA 297
Matrix = 14p37g.matrix
Transitions / transversions = 3.56 (32 / 9)
Gap_init rate = 0.01 (2 / 299), avg. gap size = 2.00 (4 / 2)
+ 968 22.4 11.3 9.7 INTRON_3 349995 350224 (49957) + L1MC4 LINE/L1 7652 7852 (190) 493
ANNOTATION EVIDENCE:
968 22.43 11.33 9.66 INTRON_3 349995 350224 49957 + L1MC4_3end LINE/L1 2399 2599 190 825
INTRON_3 349995 TTAATGCAATGTAT--AATGCTGGGCTCTCAATAACTTTT--CTATAAAG 350040
- i v -- v --i v i- vv v ?vi --
L1MC4_3end#LI 2399 -TGATCC--TGGATTGGATCCTGGA-TCAGACTNTTTTTTTGCTATAAAG 2444
INTRON_3 350041 GACATTTTGGGGGCCATTAGTGAAGTTTAAGAAAGGTTTATAAATTAGAT 350090
v v i v i i i i iv i i i
L1MC4_3end#LI 2445 GACATTATTGGGACAATTGGCGAAATTTGAATAAGGTCTGTAGATTAGAT 2494
INTRON_3 350091 AAAATATATTCATATTATTTTCCGATTTCAATAACTGTACTATGGTTATA 350140
---------- v -----i v ------------ --
L1MC4_3end#LI 2495 AA----------TAGTATT-----GTATCAAT------------GTTA-- 2515
INTRON_3 350141 ACAATGAAAATTTCCTCATTTTGGTAACTGTACTTTCAT---------AA 350181
--------- v i i v vi ---------i
L1MC4_3end#LI 2516 ---------ATTTCCTGATTTTGATAATTGTACTGTGGTTATGTAAGAGA 2556
INTRON_3 350182 CTGTCCTTGATCCCAGGAAAAATACACTAAAATATTTAGGAGT 350224
v v iii v i i i i
L1MC4_3end#LI 2557 ATGTCCTTGTTTTTAGGAAATACACACTGAAGTATTTAGGGGT 2599
Matrix = 20p37g.matrix
Transitions / transversions = 1.32 (25 / 19)
Gap_init rate = 0.04 (10 / 229), avg. gap size = 5.50 (55 / 10)
+ 632 34.6 5.8 4.5 INTRON_3 350290 350791 (49390) + L2a LINE/L2 2919 3426 (0) 495
ANNOTATION EVIDENCE:
632 34.64 5.78 4.53 INTRON_3 350290 350791 49390 + L2a_3end LINE/L2 10 517 0 797
INTRON_3 350290 CTTGCCTCTTGG-ATTTCTCAGAACTCATATCCTACCTGCCACTTCCTT- 350337
v i ii v- ii v v v vvi v ii i-
L2a_3end#LINE 10 CTGGCCCCCCGTTACCTCTCTGACCTCATCTCCTACCACTCTCCCCCTCG 59
INTRON_3 350338 -TTATTAGTATTCAACAACCTTGGCTTTCTTTTTGCTCCTCAAAGATTCC 350386
- i i vvvv i i v vi i i vi i i v iv
L2a_3end#LINE 60 CTCACTCCGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCC 109
INTRON_3 350387 AAGCTTGTTCTACTTTCAAA-CCTTTGTACTTGCTGTTTTCTCTGCTTAC 350435
i vi i ivvii ii- i ii i iv
L2a_3end#LINE 110 AGGCACGCTCCCGCCTCAGGGCCTTTGCACTTGCTGTTCCCTCTGCCTGG 159
INTRON_3 350436 AGCATTCTCCTCCCAGACCTGTACATG-CTGGCTTCTTGTCATCATT-GG 350483
i ii i i iv vii - v i i vv v v -i
L2a_3end#LINE 160 AACGCTCTTCCCCCAGATATCCGCATGGCTCGCTCCCTCACCTCCTTCAG 209
INTRON_3 350484 GCCCTAACTCAAAAGTGACACTT-----TAACACCTCATCTCACAGCAGC 350528
i i vi v v - ----- i vi ivi v -- v
L2a_3end#LINE 210 GTCTTTGCTCAAATGTCAC-CTTCTCAGTGAGGCCTTCCCTGAC--CACC 256
INTRON_3 350529 AGTTTTTTATTATTCAGACAAAAGTAGTTCTCCATACATTATCAATTACA 350578
--i v vv ?---i v vvivv?i i ?- i vi v iv v
L2a_3end#LINE 257 --CTATTTAAAATW---GCACACCCTCNCCCCCAN-CACTCCCTATCCCC 300
INTRON_3 350579 -TTAACCTGTTTT-CTTATCTTCATGTGACTTATCACTATCTTAATGTAT 350626
- v i -i v i ivv i v ---i
L2a_3end#LINE 301 CTTACCCTGCTTTATTTTTCTCCATAGCACTTATCACCATCTGA---CAT 347
INTRON_3 350627 GTTGTTTAAGTATTGCCTGTTACTTCCCTCATCCCACACTCTTCTGTTCC 350676
ii i v -- v i i i vv ivi i iv-------- ii
L2a_3end#LINE 348 ACTATATA--TTTTACTTATTTATTTGTTTATTG--------TCTGTCTC 387
INTRON_3 350677 TACCTATCTGGAATGTAGG-TCCATATAGCCAG--ACCTT-GTCTGTTCT 350722
iv i - i i - ivi v -- i - i
L2a_3end#LINE 388 CCCCCA-CTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTT 436
INTRON_3 350723 GATGACTTCCATAATCCCTTTGTCTAGAACA-----------ATAGCAGG 350761
v v v ii vi vvi i ----------- i
L2a_3end#LINE 437 GTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGG 486
INTRON_3 350762 TGCTCAGTAA-TATTCGTTGAATGGATGGAT 350791
i i - i i i
L2a_3end#LINE 487 CGCTCAATAAATATTTGTTGAATGAATGAAT 517
Matrix = 25p37g.matrix
Transitions / transversions = 1.43 (96 / 67)
Gap_init rate = 0.04 (22 / 501), avg. gap size = 2.36 (52 / 22)
+ 228 29.8 9.5 1.0 INTRON_3 352380 352474 (47707) + MIRc SINE/MIR 16 118 (150) 496
ANNOTATION EVIDENCE:
228 29.76 9.47 0.97 INTRON_3 352380 352474 47707 + MIRc SINE/MIR 16 118 150 798
INTRON_3 352380 CAATAAAATGAGTA-TGGAATTATACATCAGAAA-AC-----TTTGACTC 352422
i ii v i - v iv -i i - ----- i v
MIRc#SINE/MIR 16 CAGTGGAAAGAGCACTGGACTTGGA-GTCAGGAAGACCTGGGTTCGAGTC 64
INTRON_3 352423 ATGGCTCTGTTTCTCTCTAGCTGTGGAATGTCAGGCAAATC--TTATGTT 352470
v iiv iv vi iv ii i -- vvi
MIRc#SINE/MIR 65 CTGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCT 114
INTRON_3 352471 CTCT 352474
MIRc#SINE/MIR 115 CTCT 118
Matrix = 25p37g.matrix
Transitions / transversions = 1.55 (17 / 11)
Gap_init rate = 0.05 (5 / 94), avg. gap size = 2.00 (10 / 5)
+ 458 21.4 6.0 2.6 INTRON_3 353090 353238 (46943) + MamRep564 Unknown 131 284 (73) 497
ANNOTATION EVIDENCE:
458 21.37 6.04 2.60 INTRON_3 353090 353238 46943 + MamRep564 Unknown 131 284 73 876
INTRON_3 353090 ACATGAAACACAATGCTA--TAAGTTGTGAAACATAAG--ATAGT-CTCT 353134
i- -- -- i -- ii - v
MamRep564#Unk 131 ACATGAAAT-CA--GCTACGTAAATTGTGAAACATAAGTCACGGTTCTAT 177
INTRON_3 353135 TTGTTCTATAACAATAAAAAATTTGCAGAATATTTATT--GATAGAAACT 353182
iii i iv v i i v v i i-- v
MamRep564#Unk 178 TTGTTCTGCGACAGTGTAAAAATCGCAAATTTTTCATCAAGATAGAAAAT 227
INTRON_3 353183 CAGAA-AAAGAAGGAACTATGAGTGCCATCTTGTGGCAAAGCATGCC-CT 353230
v i - i- i i vi ii v -
MamRep564#Unk 228 AAAAACAAAGAAA-AACTATGAGCGCCATCTCGTGGAGAGACCTGCCACT 276
INTRON_3 353231 ATCACATC 353238
i i
MamRep564#Unk 277 ACCACGTC 284
Matrix = 20p37g.matrix
Transitions / transversions = 2.44 (22 / 9)
Gap_init rate = 0.06 (9 / 148), avg. gap size = 1.44 (13 / 9)
+ 2041 14.5 4.2 7.5 INTRON_3 353437 353892 (46289) C L1MA7 LINE/L1 (0) 6291 5850 498
ANNOTATION EVIDENCE:
2041 14.46 4.17 7.47 INTRON_3 353437 353892 46289 C L1MA7_3end LINE/L1 597 1038 0 826
INTRON_3 353437 TTTTATTTT-AATTGACAAATTATAATTATGTATGATAAATATACATACA 353485
- v i --------- iv --
C L1MA7_3end#LI 1038 TTTTATTTTTAATTGACAAATAATAATTGT---------ATATATTTA-- 1000
INTRON_3 353486 TACTGACCACACTCCAGTACAATGTGATATTTTGATCTGTGTACACATTG 353535
--- i---------i i v i i ?
C L1MA7_3end#LI 999 ---TGG---------GGTACAATGTGATGTTTTGATATATGTATACANTG 962
INTRON_3 353536 TAGAAATATTCAGTAAAGCTAA----CATATCCATCACCTCATCAACTTA 353581
i vv v i v ---- ivv
C L1MA7_3end#LI 961 TGGAATGATTAAATCAAGCTAATTAACATATCCATCACCTCACATACTTA 912
INTRON_3 353582 TGATTTTTTTGTGGTGAGAACATT---AATCTATTCTTTTAGCGATTTTG 353628
v --- i i i
C L1MA7_3end#LI 911 TCATTTTTTTGTGGTGAGAACATTTAAAATCTACTCTCTTAGCAATTTTG 862
INTRON_3 353629 AAATACACA-----TTGTTATCAATTGTGGTCAGCATGCAGTACAATGGA 353673
i ----- i i i i i v v i i
C L1MA7_3end#LI 861 AAATATACAATACATTATTATTAACTATAGTCACCATGCTGTGCAATAGA 812
INTRON_3 353674 TCACCAAAACTTAATCCTC-TG-CT--CTGAGAGTTTGTACCCTTTGATC 353719
? i v - - -- i v i
C L1MA7_3end#LI 811 TCNCTAAAACTTATTCCTCCTGTCTAACTGAAACTTTGTACCCTTTGACC 762
INTRON_3 353720 AACATATTCCCTTTCCTCATCCCTCCTTCTCCCTCCCAGCCTCTGGTAAC 353769
v i v i ---------- iv i
C L1MA7_3end#LI 761 AACATCTCCCCATTCCCC----------CCACCCCCCAGCCTCTGGTAAC 722
INTRON_3 353770 CTCCTTTCTAATTT--GTTTCTATGAGATCGACTTTTTTAGATTCCACAT 353817
v v v i -- i v
C L1MA7_3end#LI 721 CACCATTCTACTCTCTGCTTCTATGAGTTCGACTTTTTTAGATTCCACAT 672
INTRON_3 353818 ATAAGTGAGATCATACAGTATTTGTCTCTTTGTGCCTGGCTTATTTCACT 353867
i i i i
C L1MA7_3end#LI 671 ATAAGTGAGATCATGCGGTATTTGTCTTTCTGTGCCTGGCTTATTTCACT 622
INTRON_3 353868 TAGCATAATGCCCTCCAGTTCCACC 353892
i v i i
C L1MA7_3end#LI 621 TAGCATAATGTCCTCCAGGTTCATC 597
Matrix = 20p37g.matrix
Transitions / transversions = 1.68 (37 / 22)
Gap_init rate = 0.03 (12 / 455), avg. gap size = 4.33 (52 / 12)
+ 1183 16.1 1.9 0.5 INTRON_3 353883 354088 (46093) + L1MA7 LINE/L1 5627 5835 (456) 498 *
ANNOTATION EVIDENCE:
1183 16.10 1.94 0.48 INTRON_3 353883 354088 46093 + L1MA7_3end LINE/L1 374 582 456 827
INTRON_3 353883 CAGTTCCACCTTCTGAGTTTATATCCAAAGGAATTGAAATTGGCATATTG 353932
i i - i v ? ii i i i
L1MA7_3end#LI 374 CAATCCCAC-TTCTGGGTATATATCCAAAGGANTTGAAATCAGTATGTCG 422
INTRON_3 353933 AAGAGATATCTGCATTCCTGTATTCCTTGCAGCATTATTTACAATAGCCA 353982
i ii i v i i
L1MA7_3end#LI 423 AAGAGATATCTGCACTCCCATGTTCATTGCAGCACTATTCACAATAGCCA 472
INTRON_3 353983 AGGTATGGAATCAACTTATTTGTCTATCAA-GGA---ATGAATAAATAAA 354028
i i vv i - --- i v
L1MA7_3end#LI 473 AGATATGGAATCAACCTAAGTGTCCATCAATGGATGAATGGATAAAGAAA 522
INTRON_3 354029 ATGTGGCACATATACACAATGGAATATTATTCAGTCTTCTAAAAATAGGA 354078
i i i i vv iv
L1MA7_3end#LI 523 ATGTGGTATATATACACAATGGAATACTATTCAGCCTTAAAAAAGAAGGA 572
INTRON_3 354079 AATTCTGTCA 354088
i
L1MA7_3end#LI 573 AATCCTGTCA 582
Matrix = 20p37g.matrix
Transitions / transversions = 3.00 (24 / 8)
Gap_init rate = 0.01 (3 / 205), avg. gap size = 1.67 (5 / 3)
+ 810 20.9 1.0 0.5 INTRON_3 354248 354439 (45742) C MER53 DNA/hAT (0) 193 1 499
ANNOTATION EVIDENCE:
810 20.94 1.04 0.52 INTRON_3 354248 354439 45742 C MER53 DNA/hAT 1 193 0 793
INTRON_3 354248 TAGAGCTGACAAATAAA-CACAGGACACTCAGTTAAATTTGAATTTTAAA 354296
i i v i -i i i i i
C MER53#DNA/hAT 193 TAGGGTTGCCAGATAAAATACAGGACGCCCAGTTAAATTTGAATTTCAGA 144
INTRON_3 354297 TAAACAACAAATAATTTGTTAGCATAATTGTGATTCAACTATTACGTGGG 354346
i v i v i vii vvi v iv
C MER53#DNA/hAT 143 TAAACAACGAATAATTTTTTAGTATAAGTATGTCCCATGCAATATTTGGG 94
INTRON_3 354347 A-ATATTTATATTAATAACTCACTTTGCTATTTATCTGAAATTTAAATTT 354395
- i i v v i - i i i i
C MER53#DNA/hAT 93 ACATACTTATACTAAAAAATTA-TTCGTTGTTTATCTGAAATTCAAATTT 45
INTRON_3 354396 GAATGGGTGTCTTATATTTATACTTGCTAAATCTGGCAACTCTA 354439
i v i i i v i i
C MER53#DNA/hAT 44 AACTGGGCGTCCTGTATTTTTATTTGCTAAATCTGGCAACCCTA 1
Matrix = 18p37g.matrix
Transitions / transversions = 2.33 (28 / 12)
Gap_init rate = 0.02 (3 / 191), avg. gap size = 1.00 (3 / 3)
+ 846 33.0 11.0 0.4 INTRON_3 354464 354871 (45310) + LTR16A LTR/ERVL 1 451 (0) 500
ANNOTATION EVIDENCE:
846 32.99 11.03 0.44 INTRON_3 354464 354871 45310 + LTR16A LTR/ERVL 1 451 0 794
INTRON_3 354464 TGTGGTAGATATGGAGATATACTGCTCATATTTCCCTTAAAAA---AAGT 354510
i iiiv v iii i i v ii v ii --- v
LTR16A#LTR/ER 1 TGTGGTGGACGCTGTGATGCGCCGCCCAGATCCCCCTTCAGGACTGAAGG 50
INTRON_3 354511 ACTTGC-CATCCAGCTATAAGAAATGAGGTCAATAGACAGCTTCCGGCTG 354559
ii- vi iivi i i vv i iii iii i
LTR16A#LTR/ER 51 ACTTATTCCCCCAGCTGCTGGGAGTGCTGCCGGCAGACAGCCCTCAGCTG 100
INTRON_3 354560 TCATCTC-CTTTAGGATCTGCCTTATCTGCAGAGAGTAGCCTCATCCAAG 354608
v i - ii ivi i v v iv ii
LTR16A#LTR/ER 101 TCAGCCCTCTTCGGGGATTGCCTCAGCTGAAGAGAGCCGCCTCGCCCAAG 150
INTRON_3 354609 GTCAG---CCCTACTCAAGACAGCCCACATC-AGTGACTGAATGAGATGG 354654
v--- v i ii i i - i vi vii
LTR16A#LTR/ER 151 GTCACGCCCCCTTCCCGGGGCAGCCCGCATCCAATGACTGATCGATGCGG 200
INTRON_3 354655 GGCTATAAAGGTCCAACTATTTGGGTCTATTTCAGGACAACTCTGACAGG 354704
v i iii ivii v vi i vi i vi
LTR16A#LTR/ER 201 GGGTATAAAGGCCTGGCCCCCTCGCCCCAACTCGGGACAACTCTGAAGGG 250
INTRON_3 354705 CAGCATTT--ACTTCACAGTTTTCTACCAGTTTGGCTGAGGTATT--TCC 354750
-- ii--i i v i ii iiivi v i iv -- iv
LTR16A#LTR/ER 251 C--CATCCCAGCTCCAGAGCTCCCCGTGGGGTCGGCTGAGGCCTTCGTTG 298
INTRON_3 354751 AGCCTGCATTGCAATTTGACTTCTTTCTCTAACCAGTC-TGCTTCCTTTC 354799
i v i ii ii ii iv i - i
LTR16A#LTR/ER 299 GGACTGCATCGCAGCTCAACTTCTCCCTCTGCCCAATCCTGCTTCCTTCC 348
INTRON_3 354800 ----------AAAGTTGTCGATCCT------------TAATAAACACCCA 354827
---------- v v i i------------ ?i v
LTR16A#LTR/ER 349 CTTCCCTTCCACAGGTGTTGATCCCAAGAGCACTCCCTAATAAACNTCCT 398
INTRON_3 354828 G-ACTCTTA-------CTCAGGATTTGCT-CTTGAAAAACCCATCCTGCA 354868
- v v ------- ii i - ii iii v i
LTR16A#LTR/ER 399 GCACGCTAATCTCCGTCTCAGAGTCTGCTTCCCGGGGAACCCAACCTGCG 448
INTRON_3 354869 ACA 354871
LTR16A#LTR/ER 449 ACA 451
Matrix = 18p37g.matrix
Transitions / transversions = 2.59 (96 / 37)
Gap_init rate = 0.03 (14 / 407), avg. gap size = 3.36 (47 / 14)
+ 857 23.4 7.9 0.0 INTRON_3 355047 355260 (44921) C L2a LINE/L2 (0) 3426 3196 501
ANNOTATION EVIDENCE:
857 23.36 7.94 0.00 INTRON_3 355047 355260 44921 C L2a_3end LINE/L2 287 517 0 799
INTRON_3 355047 ATTCATTTATCCAACAAATATCTATTGAATGTCTGCCATGTTCCAAGCCC 355096
i i i ii i i i v i v
C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCAC 468
INTRON_3 355097 TGT----ATCACCGGG----CTGTAACAAACCAAACAGATACAAATTTCT 355138
----iv i i ---- v i iii v i v i ii
C L2a_3end#LINE 467 TGTTCTAGGCGCTGGGGATACAGCAGTGAACAAAACAGACAAAAGTCCCT 418
INTRON_3 355139 GTCCTCATGGAGCTTACATTCTACTGGGGA-AGAGAGATAATAA-CA--T 355184
i v i- v i - --
C L2a_3end#LINE 417 GCCCTCATGGAGCTTACATTCTAGTGGGGGGAGACAGACAATAAACAAAT 368
INTRON_3 355185 AAATAGGTAAAATTTACTGTAAGTTATAGAGTGACAAGTGCTAAAAAGAA 355234
i v iv v i v vi i vii
C L2a_3end#LINE 367 AAATAAGTAAAATATATAGTATGTCAGATGGTGATAAGTGCTATGGAGAA 318
INTRON_3 355235 AAAAAAAG-----TGAGAAGGATAAGAAGTG 355260
v ----- i ii i i
C L2a_3end#LINE 317 AAATAAAGCAGGGTAAGGGGGATAGGGAGTG 287
Matrix = 25p37g.matrix
Transitions / transversions = 2.33 (35 / 15)
Gap_init rate = 0.03 (6 / 213), avg. gap size = 2.83 (17 / 6)
+28763 0.6 0.0 0.0 INTRON_3 355267 361296 (38885) + L1HS LINE/L1 124 6153 (2) 502
ANNOTATION EVIDENCE:
19017 0.61 0.00 0.00 INTRON_3 355267 357402 42779 + L1HS_5end LINE/L1 1 2136 0 828
INTRON_3 355267 GGAGGAGGAGCCAAGATGGCCGAATAGGAACAGCTCCGGTCTACAGCTCC 355316
i
L1HS_5end#LIN 1 GGGGGAGGAGCCAAGATGGCCGAATAGGAACAGCTCCGGTCTACAGCTCC 50
INTRON_3 355317 CAGCGTGAGCGACGCAGAAGACGGGTGATTTCTGCATTTCCATCTGAGGT 355366
L1HS_5end#LIN 51 CAGCGTGAGCGACGCAGAAGACGGGTGATTTCTGCATTTCCATCTGAGGT 100
INTRON_3 355367 ACCGGGTTCACCTCACTAGGGAGTGCCAGACAGTGGGTGCAGGCCAGTGT 355416
i i
L1HS_5end#LIN 101 ACCGGGTTCATCTCACTAGGGAGTGCCAGACAGTGGGCGCAGGCCAGTGT 150
INTRON_3 355417 GTGTGCGCACCGTGCTCGAGCCGAAGCAGGGCGAGGCATTGCCTCACCTG 355466
v
L1HS_5end#LIN 151 GTGTGCGCACCGTGCGCGAGCCGAAGCAGGGCGAGGCATTGCCTCACCTG 200
INTRON_3 355467 GGAAGCGCAAGGGGTCAGGGAGTTCCCTTTCCGAGTCAAAGAAAGGGGTG 355516
L1HS_5end#LIN 201 GGAAGCGCAAGGGGTCAGGGAGTTCCCTTTCCGAGTCAAAGAAAGGGGTG 250
INTRON_3 355517 ACGGACGCACCTGGAAAATCGGGTCACTCCCACCCAAATATTGCGCTTTT 355566
i
L1HS_5end#LIN 251 ACGGACGCACCTGGAAAATCGGGTCACTCCCACCCGAATATTGCGCTTTT 300
INTRON_3 355567 CAGACCGGCTTAAGAAACAGCGCACCACGAGACGATATCCCACACCTGGC 355616
i v
L1HS_5end#LIN 301 CAGACCGGCTTAAGAAACGGCGCACCACGAGACTATATCCCACACCTGGC 350
INTRON_3 355617 TCAGAGGGTCCTACGCCCACGGAATCTCGCTAATTGCTAGCACAGCAGTC 355666
i
L1HS_5end#LIN 351 TCAGAGGGTCCTACGCCCACGGAATCTCGCTGATTGCTAGCACAGCAGTC 400
INTRON_3 355667 TGAGATCAAACTGCAAGGCGGCAACGAGGCTGGGGGAGGGGCGCCTGCCA 355716
i
L1HS_5end#LIN 401 TGAGATCAAACTGCAAGGCGGCAACGAGGCTGGGGGAGGGGCGCCCGCCA 450
INTRON_3 355717 TTGCCCAGGCTTGCTTACGTAAACAAAGCAGCCGGGAAGCTCGAACTGGG 355766
v
L1HS_5end#LIN 451 TTGCCCAGGCTTGCTTAGGTAAACAAAGCAGCCGGGAAGCTCGAACTGGG 500
INTRON_3 355767 TGGAGCCCACCACAGCTCAAGGAGGCCTGCCTGCCTCTGTAGGCTCCATC 355816
i
L1HS_5end#LIN 501 TGGAGCCCACCACAGCTCAAGGAGGCCTGCCTGCCTCTGTAGGCTCCACC 550
INTRON_3 355817 TCTGGGGGCAGGGCACAGACAAACAAAAAGACAGCAGTAACCTCTGCAGA 355866
L1HS_5end#LIN 551 TCTGGGGGCAGGGCACAGACAAACAAAAAGACAGCAGTAACCTCTGCAGA 600
INTRON_3 355867 CTTAAGTGTCCCTGTCTGACAGCTTTGAAGAGAGCAGTGGTTCTCCCAGC 355916
L1HS_5end#LIN 601 CTTAAGTGTCCCTGTCTGACAGCTTTGAAGAGAGCAGTGGTTCTCCCAGC 650
INTRON_3 355917 ACGCAGCTGGAGGTCTGAGAACGGGCAGACTGCCTCCTCAAGTGGGTCCC 355966
i
L1HS_5end#LIN 651 ACGCAGCTGGAGATCTGAGAACGGGCAGACTGCCTCCTCAAGTGGGTCCC 700
INTRON_3 355967 TGACCCCTGACCCCCGAGCAGCCTAACTGGGAGGCACCCCCCAGCAGGGG 356016
L1HS_5end#LIN 701 TGACCCCTGACCCCCGAGCAGCCTAACTGGGAGGCACCCCCCAGCAGGGG 750
INTRON_3 356017 CACACTGACACCTCACACGGCAGGGTATTCCAACAGACCTGCAGCTGAGG 356066
L1HS_5end#LIN 751 CACACTGACACCTCACACGGCAGGGTATTCCAACAGACCTGCAGCTGAGG 800
INTRON_3 356067 GTCCTGTCTGTTAGAAGGAAAACTAACAACCAGAAAGGACATCTACACCG 356116
L1HS_5end#LIN 801 GTCCTGTCTGTTAGAAGGAAAACTAACAACCAGAAAGGACATCTACACCG 850
INTRON_3 356117 AAAACCCATCTGTACATCACCACCATCAAAGACCAAAAGTAGATAAAACC 356166
i
L1HS_5end#LIN 851 AAAACCCATCTGTACATCACCATCATCAAAGACCAAAAGTAGATAAAACC 900
INTRON_3 356167 ACAAAGATGGGGAAAAAACAGAACAGAAAAACTGGAAACTCTAAAACGCA 356216
L1HS_5end#LIN 901 ACAAAGATGGGGAAAAAACAGAACAGAAAAACTGGAAACTCTAAAACGCA 950
INTRON_3 356217 GAGCGCCTCTCCTCCTCCAAAGGAACGCAGTTCCTCACCAGCAACAGAAC 356266
L1HS_5end#LIN 951 GAGCGCCTCTCCTCCTCCAAAGGAACGCAGTTCCTCACCAGCAACAGAAC 1000
INTRON_3 356267 AAAGCTGGATGGAGAATGATTTTGACGAGCTGAGAGAAGAAGGCTTCAGA 356316
L1HS_5end#LIN 1001 AAAGCTGGATGGAGAATGATTTTGACGAGCTGAGAGAAGAAGGCTTCAGA 1050
INTRON_3 356317 CGATCAAATTACTCTGAGCTACGGGAGGACATTCAAACCAAAGGCAAAGA 356366
L1HS_5end#LIN 1051 CGATCAAATTACTCTGAGCTACGGGAGGACATTCAAACCAAAGGCAAAGA 1100
INTRON_3 356367 AGTTGAAAACTTTGAAAAAAATTTAGAAGAATGTATAACTAGAATAACCA 356416
L1HS_5end#LIN 1101 AGTTGAAAACTTTGAAAAAAATTTAGAAGAATGTATAACTAGAATAACCA 1150
INTRON_3 356417 ATACAGAGAAGTGCTTAAAGGAGCTGATGGAGCTGAAAACCAAGGCTCGA 356466
L1HS_5end#LIN 1151 ATACAGAGAAGTGCTTAAAGGAGCTGATGGAGCTGAAAACCAAGGCTCGA 1200
INTRON_3 356467 GAACTACGTGAAGAATGCAGAAGCCTCAGGAGCCGATGCGATCAACTGGA 356516
L1HS_5end#LIN 1201 GAACTACGTGAAGAATGCAGAAGCCTCAGGAGCCGATGCGATCAACTGGA 1250
INTRON_3 356517 AGAAAGGGTATCAGCAATGGAAGATGAAATGAATGAAATGAAGCGAGAAG 356566
L1HS_5end#LIN 1251 AGAAAGGGTATCAGCAATGGAAGATGAAATGAATGAAATGAAGCGAGAAG 1300
INTRON_3 356567 GGAAGTTTAGAGAAAAAAGAATAAAAAGAAATGAGCAAAGCCTCCAAGAA 356616
L1HS_5end#LIN 1301 GGAAGTTTAGAGAAAAAAGAATAAAAAGAAATGAGCAAAGCCTCCAAGAA 1350
INTRON_3 356617 ATATGGGACTATGTGAAAAGACCAAATCTACGTCTGATTGGTGTACCTGA 356666
L1HS_5end#LIN 1351 ATATGGGACTATGTGAAAAGACCAAATCTACGTCTGATTGGTGTACCTGA 1400
INTRON_3 356667 AAGTGATGTGGAGAATGGAACCAAGTTGGAAAACACTCTGCAGGATATTA 356716
L1HS_5end#LIN 1401 AAGTGATGTGGAGAATGGAACCAAGTTGGAAAACACTCTGCAGGATATTA 1450
INTRON_3 356717 TCCAGGAGAACTTCCCCAATCTAGCAAGGCAGGCCAACGTTCAGATTCAG 356766
L1HS_5end#LIN 1451 TCCAGGAGAACTTCCCCAATCTAGCAAGGCAGGCCAACGTTCAGATTCAG 1500
INTRON_3 356767 GAAATACAGAGAACGCCACAAAGATACTCCTCGAGAAGAGCAACTCCAAG 356816
L1HS_5end#LIN 1501 GAAATACAGAGAACGCCACAAAGATACTCCTCGAGAAGAGCAACTCCAAG 1550
INTRON_3 356817 ACACATAATTGTCAGATTCACCAAAGTTGAAATGAAGGAAAAAATGTTAA 356866
L1HS_5end#LIN 1551 ACACATAATTGTCAGATTCACCAAAGTTGAAATGAAGGAAAAAATGTTAA 1600
INTRON_3 356867 GGGCAGCCAGAGAGAAAGGTCGGGTTACCCTCAAAGGAAAGCCCATCAGA 356916
L1HS_5end#LIN 1601 GGGCAGCCAGAGAGAAAGGTCGGGTTACCCTCAAAGGAAAGCCCATCAGA 1650
INTRON_3 356917 CTAACAGCGGATCTCTCGGCAGAAACCCTACAAGCCAGAAGAGAGTGGGG 356966
L1HS_5end#LIN 1651 CTAACAGCGGATCTCTCGGCAGAAACCCTACAAGCCAGAAGAGAGTGGGG 1700
INTRON_3 356967 GCCAATATTCAACATTCTTAAAGAAAAGAATTTTCAACCCAGAATTTCAT 357016
L1HS_5end#LIN 1701 GCCAATATTCAACATTCTTAAAGAAAAGAATTTTCAACCCAGAATTTCAT 1750
INTRON_3 357017 ATCCAGCCAAACTAAGCTTCATAAGTGAAGGAGAAATAAAATACTTTATA 357066
L1HS_5end#LIN 1751 ATCCAGCCAAACTAAGCTTCATAAGTGAAGGAGAAATAAAATACTTTATA 1800
INTRON_3 357067 GACAAGCAAATGCTGAGAGATTTTGTCACCACCAGGCCTGCCCTAAAAGA 357116
L1HS_5end#LIN 1801 GACAAGCAAATGCTGAGAGATTTTGTCACCACCAGGCCTGCCCTAAAAGA 1850
INTRON_3 357117 GCTCCTGAAGGAAGCGCTAAACATGGAAAGGAACAACCGGTACCAGCCGC 357166
L1HS_5end#LIN 1851 GCTCCTGAAGGAAGCGCTAAACATGGAAAGGAACAACCGGTACCAGCCGC 1900
INTRON_3 357167 TGCAAAATCATGCCAAAATGTAAAGACCATCGAGACTAGGAAGAAACTGC 357216
L1HS_5end#LIN 1901 TGCAAAATCATGCCAAAATGTAAAGACCATCGAGACTAGGAAGAAACTGC 1950
INTRON_3 357217 ATCAACTAATGAGCAAAATCACCAGCTAACATCATAATGACAGGATCAAA 357266
L1HS_5end#LIN 1951 ATCAACTAATGAGCAAAATCACCAGCTAACATCATAATGACAGGATCAAA 2000
INTRON_3 357267 TTCACACATAACAATATTAACTTTAAATATAAATGGACTAAATTCTGCAA 357316
L1HS_5end#LIN 2001 TTCACACATAACAATATTAACTTTAAATATAAATGGACTAAATTCTGCAA 2050
INTRON_3 357317 TTAAAAGACACAGACTGGCAAGTTGGATAAAGAGTCAAGACCCATCAGTG 357366
L1HS_5end#LIN 2051 TTAAAAGACACAGACTGGCAAGTTGGATAAAGAGTCAAGACCCATCAGTG 2100
INTRON_3 357367 TGCTGTATTCAGGAAACCCATCTCACGTGCAGAGAC 357402
L1HS_5end#LIN 2101 TGCTGTATTCAGGAAACCCATCTCACGTGCAGAGAC 2136
Matrix = 20p37g.matrix
Transitions / transversions = 3.33 (10 / 3)
Gap_init rate = 0.00 (0 / 2135), avg. gap size = 0.0 (0 / 0)
28763 0.55 0.00 0.00 INTRON_3 357253 360546 39635 + L1P1_orf2 LINE/L1 1 3294 0 829
INTRON_3 357253 ATGACAGGATCAAATTCACACATAACAATATTAACTTTAAATATAAATGG 357302
L1P1_orf2#LIN 1 ATGACAGGATCAAATTCACACATAACAATATTAACTTTAAATATAAATGG 50
INTRON_3 357303 ACTAAATTCTGCAATTAAAAGACACAGACTGGCAAGTTGGATAAAGAGTC 357352
L1P1_orf2#LIN 51 ACTAAATTCTGCAATTAAAAGACACAGACTGGCAAGTTGGATAAAGAGTC 100
INTRON_3 357353 AAGACCCATCAGTGTGCTGTATTCAGGAAACCCATCTCACGTGCAGAGAC 357402
L1P1_orf2#LIN 101 AAGACCCATCAGTGTGCTGTATTCAGGAAACCCATCTCACGTGCAGAGAC 150
INTRON_3 357403 ACACATAGGCTCAAAATAAAAGGATGGAGGAAGATCTACCAAGCAAATGG 357452
v
L1P1_orf2#LIN 151 ACACATAGGCTCAAAATAAAAGGATGGAGGAAGATCTACCAAGCCAATGG 200
INTRON_3 357453 AAAACAAAAAAAGGCAGGGGTTGCAATCCTAGTCTCTGATAAAACAGACT 357502
L1P1_orf2#LIN 201 AAAACAAAAAAAGGCAGGGGTTGCAATCCTAGTCTCTGATAAAACAGACT 250
INTRON_3 357503 TTAAACCAACAAAGATCAAAAGAGACAAAGAAGGCCATTACATAATGGTA 357552
L1P1_orf2#LIN 251 TTAAACCAACAAAGATCAAAAGAGACAAAGAAGGCCATTACATAATGGTA 300
INTRON_3 357553 AAGGGATCAATTCAACAAGAGGAGCTAACTATCCTAAATATTTATGCACC 357602
L1P1_orf2#LIN 301 AAGGGATCAATTCAACAAGAGGAGCTAACTATCCTAAATATTTATGCACC 350
INTRON_3 357603 CAATACAGGAGCACCCAGATTCATAAAGCAAGTCCTGAGTGACCTACAAA 357652
?
L1P1_orf2#LIN 351 CAATACAGGAGCACCCAGATTCATAAAGCAAGTCCTSAGTGACCTACAAA 400
INTRON_3 357653 GAGACTTAGACTCCCACACATTAATAATGGGAGACTTTAACACCCCACTG 357702
L1P1_orf2#LIN 401 GAGACTTAGACTCCCACACATTAATAATGGGAGACTTTAACACCCCACTG 450
INTRON_3 357703 TCAACATTAGACAGATCAATGAGACAGAAAGTCAACAAGGATACCCAGGA 357752
i
L1P1_orf2#LIN 451 TCAACATTAGACAGATCAACGAGACAGAAAGTCAACAAGGATACCCAGGA 500
INTRON_3 357753 ATTGAACTCAGCTCTGCACCAAGCAGACCTAATAGACATCTACAGAGCTC 357802
i
L1P1_orf2#LIN 501 ATTGAACTCAGCTCTGCACCAAGCAGACCTAATAGACATCTACAGAACTC 550
INTRON_3 357803 TCCACCCCAAATCAACAGAATATACATTTTTTTCAGCACCACACCACACC 357852
L1P1_orf2#LIN 551 TCCACCCCAAATCAACAGAATATACATTTTTTTCAGCACCACACCACACC 600
INTRON_3 357853 TATTCCAAAATTGACCACATAGTTGGAAGTAAAGCTCTCCTCAGCAAATG 357902
L1P1_orf2#LIN 601 TATTCCAAAATTGACCACATAGTTGGAAGTAAAGCTCTCCTCAGCAAATG 650
INTRON_3 357903 TAAAAGAACAGAAATTATAACAAACTATCTCTCAGACCACAGTGCAATCA 357952
L1P1_orf2#LIN 651 TAAAAGAACAGAAATTATAACAAACTATCTCTCAGACCACAGTGCAATCA 700
INTRON_3 357953 AACTAGAACTCAGGATTAAGAATCTCACTCAAAGCCGCTCAACTACATGG 358002
L1P1_orf2#LIN 701 AACTAGAACTCAGGATTAAGAATCTCACTCAAAGCCGCTCAACTACATGG 750
INTRON_3 358003 AAACTGAACAACCTGCTCCTGAATGACTACTGGGTACATAACGAAATGAA 358052
L1P1_orf2#LIN 751 AAACTGAACAACCTGCTCCTGAATGACTACTGGGTACATAACGAAATGAA 800
INTRON_3 358053 GGCAGAAATAAAGATGTTCTTTGAAACCAACGAGAACAAAGACACCACAT 358102
L1P1_orf2#LIN 801 GGCAGAAATAAAGATGTTCTTTGAAACCAACGAGAACAAAGACACCACAT 850
INTRON_3 358103 ACCAGAATCTCTGGGACGCATTCAAAGCAGTGTGTAGAGGGAAATTTATA 358152
L1P1_orf2#LIN 851 ACCAGAATCTCTGGGACGCATTCAAAGCAGTGTGTAGAGGGAAATTTATA 900
INTRON_3 358153 GCACTAAATGCCCACAAGAGAAAGCAGGAAAGATCCAAAATTGACACCCT 358202
i
L1P1_orf2#LIN 901 GCACTAAATGCCTACAAGAGAAAGCAGGAAAGATCCAAAATTGACACCCT 950
INTRON_3 358203 AACATCACAATTAAAAGAACTAGAAAAGCAAGAGCAAACACATTCAAAAG 358252
L1P1_orf2#LIN 951 AACATCACAATTAAAAGAACTAGAAAAGCAAGAGCAAACACATTCAAAAG 1000
INTRON_3 358253 CTAGCAGAAGGCAAGAAATAACTAAAATCAGAGCAGAACTGAAGGAAATA 358302
L1P1_orf2#LIN 1001 CTAGCAGAAGGCAAGAAATAACTAAAATCAGAGCAGAACTGAAGGAAATA 1050
INTRON_3 358303 GAGACACAAAAAACCCTTCAAAAAATCAATGAATCCAGGAGCTGGTTTTT 358352
L1P1_orf2#LIN 1051 GAGACACAAAAAACCCTTCAAAAAATCAATGAATCCAGGAGCTGGTTTTT 1100
INTRON_3 358353 TGAAAGGATCAACAAAATTGATAGACCGCTAGCAAGACTAATAAAGAAAA 358402
L1P1_orf2#LIN 1101 TGAAAGGATCAACAAAATTGATAGACCGCTAGCAAGACTAATAAAGAAAA 1150
INTRON_3 358403 AAAGAGAGAAGAGTCAAATAGACACAATAAAAAATGATAAAGGGGATATC 358452
i
L1P1_orf2#LIN 1151 AAAGAGAGAAGAATCAAATAGACACAATAAAAAATGATAAAGGGGATATC 1200
INTRON_3 358453 ACCACCGATCCCACAGAAATACAAACTACCATCAGAGAATACTACAAACA 358502
L1P1_orf2#LIN 1201 ACCACCGATCCCACAGAAATACAAACTACCATCAGAGAATACTACAAACA 1250
INTRON_3 358503 CCTCTATGCAAATAAACTAGAAAATCTAGAAGAAATGGATACATTCCTCG 358552
i
L1P1_orf2#LIN 1251 CCTCTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATACATTCCTCG 1300
INTRON_3 358553 ACACATACACTCTCCTAAGACTAAACCAGGAAGAAGTTGACTCTCTGAAT 358602
i v
L1P1_orf2#LIN 1301 ACACATACACTCTCCCAAGACTAAACCAGGAAGAAGTTGAATCTCTGAAT 1350
INTRON_3 358603 AGACCAATAACAGGCTCTGAAATTGTGGCAATAATCAATAGTTTACCAAC 358652
L1P1_orf2#LIN 1351 AGACCAATAACAGGCTCTGAAATTGTGGCAATAATCAATAGTTTACCAAC 1400
INTRON_3 358653 CAAAAAGAGTCCAGGACCAGATGGATTCACAGCCGAATTCTACCAGAGGT 358702
L1P1_orf2#LIN 1401 CAAAAAGAGTCCAGGACCAGATGGATTCACAGCCGAATTCTACCAGAGGT 1450
INTRON_3 358703 ACAAGGAGGAACTGGTACCATTCCTTCTGAAACTATTCCAATCAATAGAA 358752
L1P1_orf2#LIN 1451 ACAAGGAGGAACTGGTACCATTCCTTCTGAAACTATTCCAATCAATAGAA 1500
INTRON_3 358753 AAAGAGGGAATCCTCCCTAACTCATTTTATGAGGCCAGCATCATTCTGAT 358802
L1P1_orf2#LIN 1501 AAAGAGGGAATCCTCCCTAACTCATTTTATGAGGCCAGCATCATTCTGAT 1550
INTRON_3 358803 ACCAAAGCCGGGCAGAGACACAACCAAAAAAGAGAATTTTAGACCAATAT 358852
L1P1_orf2#LIN 1551 ACCAAAGCCGGGCAGAGACACAACCAAAAAAGAGAATTTTAGACCAATAT 1600
INTRON_3 358853 CCTTGATGAACATTGATGCAAAAATCCTCAATAAAATACTGGCAAAACAA 358902
v i
L1P1_orf2#LIN 1601 CCTTGATGAACATTGATGCAAAAATCCTCAATAAAATACTGGCAAACCGA 1650
INTRON_3 358903 ATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTGGGCTTCAT 358952
L1P1_orf2#LIN 1651 ATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTGGGCTTCAT 1700
INTRON_3 358953 CCCTGGGATGCAAGGCTGGTTCAATATACGCAAATCAATAAATGTAATCC 359002
L1P1_orf2#LIN 1701 CCCTGGGATGCAAGGCTGGTTCAATATACGCAAATCAATAAATGTAATCC 1750
INTRON_3 359003 AGCATATAAACAGAGCCAAAGACAAAAACCACATGATTATCTCAATAGAT 359052
L1P1_orf2#LIN 1751 AGCATATAAACAGAGCCAAAGACAAAAACCACATGATTATCTCAATAGAT 1800
INTRON_3 359053 GCAGAAAAGGCCTTTGACAAAATTCAACAACCCTTCATGCTAAAAACTCT 359102
i
L1P1_orf2#LIN 1801 GCAGAAAAAGCCTTTGACAAAATTCAACAACCCTTCATGCTAAAAACTCT 1850
INTRON_3 359103 CAATAAATTAGGTATTGATGGGATGTATTTCAAAATAATAAGAGCTATCT 359152
i
L1P1_orf2#LIN 1851 CAATAAATTAGGTATTGATGGGACGTATTTCAAAATAATAAGAGCTATCT 1900
INTRON_3 359153 ATGACAAACCCACAGCCAATATCATACTGAATGGGCAAAAACTGGAAGCA 359202
L1P1_orf2#LIN 1901 ATGACAAACCCACAGCCAATATCATACTGAATGGGCAAAAACTGGAAGCA 1950
INTRON_3 359203 TTCCCTTTGAAAACTGGCACAAGACAGGGATGCCCTCTCTCACCACTCCT 359252
i
L1P1_orf2#LIN 1951 TTCCCTTTGAAAACTGGCACAAGACAGGGATGCCCTCTCTCACCGCTCCT 2000
INTRON_3 359253 ATTCAACATAGTGTTGGAAGTTCTGGCCAGGGCAATCAGGCAGGAGAAGG 359302
L1P1_orf2#LIN 2001 ATTCAACATAGTGTTGGAAGTTCTGGCCAGGGCAATCAGGCAGGAGAAGG 2050
INTRON_3 359303 AAATAAAGGGTATTCAATTAGGAAAAGAGGAAGTCAAATTGTCCCTGTTT 359352
L1P1_orf2#LIN 2051 AAATAAAGGGTATTCAATTAGGAAAAGAGGAAGTCAAATTGTCCCTGTTT 2100
INTRON_3 359353 GCAGACGACATGATTGTTTATCTAGAAAACCCCATTGTCTCAGCCCAAAA 359402
i
L1P1_orf2#LIN 2101 GCAGACGACATGATTGTTTATCTAGAAAACCCCATCGTCTCAGCCCAAAA 2150
INTRON_3 359403 TCTCCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCA 359452
L1P1_orf2#LIN 2151 TCTCCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCA 2200
INTRON_3 359453 ATGTACAAAAATCACAAGCATTCTTATACACCAACAACAGACAAACAGAG 359502
L1P1_orf2#LIN 2201 ATGTACAAAAATCACAAGCATTCTTATACACCAACAACAGACAAACAGAG 2250
INTRON_3 359503 AGCCAAATCATGAGTGAACTCCCATTCACAATTGCTTCAAAGAGAATAAA 359552
i
L1P1_orf2#LIN 2251 AGCCAAATCATGGGTGAACTCCCATTCACAATTGCTTCAAAGAGAATAAA 2300
INTRON_3 359553 ATACCTAGGAATCCAACTTACAAGGGATGTGAAGGACCTCTTCAAGGAGA 359602
L1P1_orf2#LIN 2301 ATACCTAGGAATCCAACTTACAAGGGATGTGAAGGACCTCTTCAAGGAGA 2350
INTRON_3 359603 ACTACAAACCACTGCTCAAGGAAATAAAAGAGGACACAAACAAATGGAAG 359652
L1P1_orf2#LIN 2351 ACTACAAACCACTGCTCAAGGAAATAAAAGAGGACACAAACAAATGGAAG 2400
INTRON_3 359653 AACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCCAT 359702
L1P1_orf2#LIN 2401 AACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCCAT 2450
INTRON_3 359703 ACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCTACCAA 359752
L1P1_orf2#LIN 2451 ACTGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCTACCAA 2500
INTRON_3 359753 TGACTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATATGGAAC 359802
L1P1_orf2#LIN 2501 TGACTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATATGGAAC 2550
INTRON_3 359803 CAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAACAAAGC 359852
L1P1_orf2#LIN 2551 CAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAACAAAGC 2600
INTRON_3 359853 TGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAA 359902
L1P1_orf2#LIN 2601 TGGAGGCATCACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAA 2650
INTRON_3 359903 CCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAAC 359952
L1P1_orf2#LIN 2651 CCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAAC 2700
INTRON_3 359953 AGAACAGAGCCCTCAGAAATAATGCCGCATATCTACAACTATCTGATCTT 360002
L1P1_orf2#LIN 2701 AGAACAGAGCCCTCAGAAATAATGCCGCATATCTACAACTATCTGATCTT 2750
INTRON_3 360003 TGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAACA 360052
i
L1P1_orf2#LIN 2751 TGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATA 2800
INTRON_3 360053 AATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGAT 360102
L1P1_orf2#LIN 2801 AATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGAT 2850
INTRON_3 360103 CCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGATTT 360152
L1P1_orf2#LIN 2851 CCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGATTT 2900
INTRON_3 360153 AAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTA 360202
L1P1_orf2#LIN 2901 AAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTA 2950
INTRON_3 360203 CCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAACACCAAAA 360252
L1P1_orf2#LIN 2951 CCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAACACCAAAA 3000
INTRON_3 360253 GCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAA 360302
L1P1_orf2#LIN 3001 GCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAA 3050
INTRON_3 360303 GAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTA 360352
L1P1_orf2#LIN 3051 GAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTA 3100
INTRON_3 360353 CAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATA 360402
L1P1_orf2#LIN 3101 CAACATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATA 3150
INTRON_3 360403 TCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAA 360452
L1P1_orf2#LIN 3151 TCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAA 3200
INTRON_3 360453 CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAG 360502
L1P1_orf2#LIN 3201 CCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAG 3250
INTRON_3 360503 ACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCACCATCA 360546
i
L1P1_orf2#LIN 3251 ACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCA 3294
Matrix = 20p37g.matrix
Transitions / transversions = 4.67 (14 / 3)
Gap_init rate = 0.00 (0 / 3293), avg. gap size = 0.0 (0 / 0)
7926 1.00 0.00 0.00 INTRON_3 360397 361296 38885 + L1HS_3end LINE/L1 1 900 2 830
INTRON_3 360397 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 360446
L1HS_3end#LIN 1 CTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAAC 50
INTRON_3 360447 AAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAA 360496
L1HS_3end#LIN 51 AAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAA 100
INTRON_3 360497 AAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCACCATCA 360546
i
L1HS_3end#LIN 101 AAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCA 150
INTRON_3 360547 CTGGCCATCAGAGAAATGCAAATCAAAACCACTATGAGATATCATCTCAC 360596
L1HS_3end#LIN 151 CTGGCCATCAGAGAAATGCAAATCAAAACCACTATGAGATATCATCTCAC 200
INTRON_3 360597 ACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGA 360646
L1HS_3end#LIN 201 ACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGA 250
INTRON_3 360647 GAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTCAA 360696
i v
L1HS_3end#LIN 251 GAGGATGCGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAA 300
INTRON_3 360697 CTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGA 360746
L1HS_3end#LIN 301 CTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGA 350
INTRON_3 360747 ACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAA 360796
L1HS_3end#LIN 351 ACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAA 400
INTRON_3 360797 AGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATT 360846
v v
L1HS_3end#LIN 401 ATGAGTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATT 450
INTRON_3 360847 GCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAAC 360896
L1HS_3end#LIN 451 GCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAAC 500
INTRON_3 360897 AATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACT 360946
L1HS_3end#LIN 501 AATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACT 550
INTRON_3 360947 ATGCAGCCATAAAAAATGATGAGTTCACGTCCTTTGTAGGGACATGGATG 360996
ii
L1HS_3end#LIN 551 ATGCAGCCATAAAAAATGATGAGTTCATATCCTTTGTAGGGACATGGATG 600
INTRON_3 360997 AAATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAA 361046
L1HS_3end#LIN 601 AAATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAA 650
INTRON_3 361047 ACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGATCACATG 361096
L1HS_3end#LIN 651 ACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGATCACATG 700
INTRON_3 361097 GACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTCGGGGG 361146
L1HS_3end#LIN 701 GACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTCGGGGG 750
INTRON_3 361147 AGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACACGTT 361196
i
L1HS_3end#LIN 751 AGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACACATT 800
INTRON_3 361197 AGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCT 361246
L1HS_3end#LIN 801 AGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCT 850
INTRON_3 361247 GCACAATGTGCACATGTTCCCTAAAACTTAGAGTATAATAAAAAAAAAAA 361296
v
L1HS_3end#LIN 851 GCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAA 900
Matrix = 20p37g.matrix
Transitions / transversions = 1.25 (5 / 4)
Gap_init rate = 0.00 (0 / 899), avg. gap size = 0.0 (0 / 0)
+ 795 21.0 1.7 0.0 INTRON_3 361324 361499 (38682) + FordPrefect DNA/hAT-Tip100 1504 1682 (1) 503
ANNOTATION EVIDENCE:
795 21.02 1.70 0.00 INTRON_3 361324 361499 38682 + FordPrefect DNA/hAT-Tip100 1504 1682 1 877
INTRON_3 361324 AATAAACAAACAGGGAAGTAGACCCACTCAACCCATTATTCTAACTCTTC 361373
i v v vvi iv v v
FordPrefect#D 1504 AATAAACAAATACGTAAGTACCTCTTCTCTACCCATTATTCTAAATCTTC 1553
INTRON_3 361374 ATCAA-AAATTCTTAAGTCTCATTTGGGCCCATACATTTTGTAATACATT 361422
i - ivi vii iv iv
FordPrefect#D 1554 ATCGATAAATCACTATACCTCACATGGGCCCATGAATTTTGTAATACATT 1603
INTRON_3 361423 TT-AATCAAAT-ATTTATATAGTCAGGAGCCCTACAGAACATATTTTCCC 361470
- -i v i ii i v v
FordPrefect#D 1604 TTTAATCAAATTGTTTATATAGACAGGGGCCCCGCAAAAAATATTTGCCC 1653
INTRON_3 361471 AGGGTCCTACATACCCTACCAGTGGCCCT 361499
i ii i vvi i
FordPrefect#D 1654 AGGGCCCCGCACACCCTAGGGGCGGCCCT 1682
Matrix = 20p37g.matrix
Transitions / transversions = 1.31 (21 / 16)
Gap_init rate = 0.02 (3 / 175), avg. gap size = 1.00 (3 / 3)
+ 1614 23.0 0.9 4.7 INTRON_3 361503 361922 (38259) C L1M5 LINE/L1 (1296) 4850 4446 504
ANNOTATION EVIDENCE:
1614 22.98 0.95 4.69 INTRON_3 361503 361922 38259 C L1M5_orf2 LINE/L1 2337 2741 553 831
INTRON_3 361503 TGACTAAATATGTGTGGATCTGTTTCTGGACTCT--AGTCTATTCCACTG 361550
? i v i -- v i i
C L1M5_orf2#LIN 2741 TGNCCATATATGTGTGGGTCTGTTTCTGGACTCTCTATTCTGTTCCATTG 2692
INTRON_3 361551 GCCAATATGTCTCTCCTCTCATCAACATTACATTGGCTTAATTATTATAG 361600
i v v v i? ii i ii i v i i
C L1M5_orf2#LIN 2691 GTCTATTTGTCTATCCTTNCGCCAATACCACACTGTCTTAATTACTGTAG 2642
INTRON_3 361601 CTTTATAATAGGTCTTGACATCTACTTATGTAAAATCTTCAACTTCATT- 361649
i i iv vi? ivi i ii -
C L1M5_orf2#LIN 2641 CTTTATAATAAGTCTTGATATCTGGTAGNGTAAGTCCTCCAACTTTGTTC 2592
INTRON_3 361650 -TCTTCTCTAACACAGTCTTGAATATTCTTGGATGTTTGCACTTCTGTAT 361698
- i ii v iv iv viv i ii
C L1M5_orf2#LIN 2591 TTCTTTTTCAAGATTGTCTTGGCTATTCTTGGCCCTTTGCATTTCCATAT 2542
INTRON_3 361699 AAATTTTACACCAATTGTCTTCTCTCCTTCCACATACACAAACATGCACA 361748
v --- iiv v vvi ----- --------
C L1M5_orf2#LIN 2541 AAATTTTAGA---ATCAGCTTGTCAATTTCCACA-----AAA-------- 2508
INTRON_3 361749 CACAAACATGCTGGGAAATTGATTGGGATTTTATTGAATCTAAAAATCAA 361798
--- v vv ? vi v i
C L1M5_orf2#LIN 2507 ---AAACCTGCTGGGATTTTNATTGGGATTGCATTGAATCTATAGATCAA 2461
INTRON_3 361799 TTTGGGGGGAATTGCTATTTTTACCATATTGAATCTTCCAACCCATCAAC 361848
i vi i v i i v
C L1M5_orf2#LIN 2460 TTTGGGGAGAATTGACATCTTTACAATATTGAGTCTTCCAATCCATGAAC 2411
INTRON_3 361849 ATCATATATCTTTCCATTTATTCCAGTCTTCATTAAATGCCCTCAGCAAC 361898
vi i ivi v v v i ii i
C L1M5_orf2#LIN 2410 ATGGTATATCTCTCCATTTATTTAGGTCTTCTTTAATTTCTCTCAATAAT 2361
INTRON_3 361899 GTTTTATAGTTTTTGGTTTTCAGG 361922
i i? v v?
C L1M5_orf2#LIN 2360 GTTTTGTAGTTTTCNGTATANAGG 2337
Matrix = 20p37g.matrix
Transitions / transversions = 1.53 (52 / 34)
Gap_init rate = 0.01 (5 / 419), avg. gap size = 4.60 (23 / 5)
+ 25 83.8 0.0 0.0 INTRON_3 361972 362045 (38136) + AT_rich Low_complexity 1 74 (0) 505
ANNOTATION EVIDENCE:
25 83.78 0.00 0.00 INTRON_3 361972 362045 38136 + AT_rich Low_complexity 88 161 139 816
INTRON_3 361972 TATTTTATTTTAAATTTCTTTTAGATTTTATTGTTAAATGTATAATATAT 362021
??????????????????????????????????????????????????
AT_rich#Low_c 88 WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWW 137
INTRON_3 362022 GATTGATAAATATATACATATATA 362045
??v v v v vvvvv v
AT_rich#Low_c 138 WWATTAAAAATAAATAATATAATT 161
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 10)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0)
+ 1133 26.2 8.3 2.2 INTRON_3 362086 362721 (37460) C L1ME4a LINE/L1 (163) 5961 5296 506
ANNOTATION EVIDENCE:
1133 27.78 6.28 2.34 INTRON_3 362086 362579 37602 C L1ME4a_3end LINE/L1 196 708 163 832
INTRON_3 362086 ATATATGTACATATAAGTGTTATAAATAGTATCTTCTTATAAAATTAAGG 362135
i i ----- v ?- i ? v i ii i
C L1ME4a_3end#L 708 ATATATGTATACAT-----TTATATATN-TATTTTNTAACAAAATTGGGA 665
INTRON_3 362136 TTACATTTTATGTAATGTTTCATTATGTACTTCT---ACTTCACATTA-A 362181
i i i v i vv ii v?iv i i --- v -
C L1ME4a_3end#L 664 TCATACTGTATATACAGTTTTGTANCCTGCTTTTTTCACTTAACATTATA 615
INTRON_3 362182 TCA---ACATTTTCTCACATAGCTAAATGTTTCTTAAAA---TACTTTTT 362225
---i i ii vii i ii ii --- ?v
C L1ME4a_3end#L 614 TCATGAGCATTTTCCCATGTCATTAAATATTCTTCGAAAACATNATTTTT 565
INTRON_3 362226 AAAAAATTTCTGCATAGTATTTCATCATATTAATGTACCATAAATTATTT 362275
---- vv i i i? vi v
C L1ME4a_3end#L 564 AA----TGGCTGCATAATATTCCATTNTATGGATGTACCATAATTTATTT 519
INTRON_3 362276 TAGCCAATGTTCTATTTTGGGTTACTTAGATTAAT-CCAATTT---GAAA 362321
- i ? vii v v vi i i iv - --- vv
C L1ME4a_3end#L 518 -AACCANTCCCCTATTGTTGGACATTTAGGTTGTTTCCAATTTTTCGCTA 470
INTRON_3 362322 ATGTAAATATTTCAACAAAAAACATCCATATATATAAATCTTTGTACACA 362371
v i v v vi i vi v i i ?
C L1ME4a_3end#L 469 TTATAAATAATGCTGCGATGAACATCCTTGTACATAAATCTTTGTNCACA 420
INTRON_3 362372 TCTCTAATTAGTTCTTTTGGATAAATTTCTAGAAGTGAAATGACTAGATC 362421
i v i v i i v i i
C L1ME4a_3end#L 419 TCTCTGATTATTTCCTTAGGATAAATTCCTAGAAGTGGAATTACTGGGTC 370
INTRON_3 362422 CAACGATATAAA--TTTTTCAAGATTTGGATATACATTGCCAAGTTGCCC 362469
v v i i? -- v i v i v i i i
C L1ME4a_3end#L 369 AAAGGGTATGNACATTTTTAAGGCTCTTGATACATATTGCCAAATTGCCC 320
INTRON_3 362470 TTCAGGTAGAT---GCTGGGTTACATTCCCACCAGCAGACTA--AAAGCT 362514
i iv i ---i iiiv i vv -- i -
C L1ME4a_3end#L 319 TCCAGAAAGGTTGTACCAATTTACACTCCCACCAGCAGTGTATGAGAG-T 271
INTRON_3 362515 GATTGTTCATTCTCTTCCTCATTAATATTGGATATTA--AATT------A 362556
vii iv?i v vi iii i i ?i -- i------
C L1ME4a_3end#L 270 GCCCGTTTCNCCACACCCTCGCCAACACTGNGTATTATCAATCTTTTAAA 221
INTRON_3 362557 T-TCTGCCAATTTGGT-GGAGAAAA 362579
- i i - v
C L1ME4a_3end#L 220 TCTTTGCCAATTTGATAGGTGAAAA 196
Matrix = 20p37g.matrix
Transitions / transversions = 1.82 (80 / 44)
Gap_init rate = 0.04 (18 / 493), avg. gap size = 2.39 (43 / 18)
524 22.41 13.09 1.89 INTRON_3 362531 362721 37460 C L1ME4a_3end LINE/L1 43 254 617 833
INTRON_3 362531 CCTCATTAATATTGGATATTA--AATT------AT-TCTGCCAATTTGGT 362571
iii i i ?i -- i------ - i i
C L1ME4a_3end#L 254 CCTCGCCAACACTGNGTATTATCAATCTTTTAAATCTTTGCCAATTTGAT 205
INTRON_3 362572 -GGAGAAAA---------------TGTTTTAATTTATATTTCTTTGATTA 362605
- v --------------- ii
C L1ME4a_3end#L 204 AGGTGAAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCTTTGATTA 155
INTRON_3 362606 CAAGTAAAGTTGAAATATGTATTTTTATATGTTTCTTGGGATTTTTATAT 362655
? i i ---ii ? i i v v-iv i
C L1ME4a_3end#L 154 CNAGTGAGGTTGAA---CATNTTTTCACATGTTTATTGGC-CATTTGTAT 109
INTRON_3 362656 TTTTTCTTTTATAAATTACTTGCTTACGTCTTTTGCCAATTTTTCTATTT 362705
i i i iii i i i i vi v
C L1ME4a_3end#L 108 TTCTTCTTTTGTGAATTGTCTGTTCATGTCTTTTGTCCGTTTTTCTATTG 59
INTRON_3 362706 AGGTGTACGTCTTTCT 362721
i v i
C L1ME4a_3end#L 58 GGGTGTTCGTCTTTTT 43
Matrix = 20p37g.matrix
Transitions / transversions = 4.57 (32 / 7)
Gap_init rate = 0.04 (7 / 190), avg. gap size = 4.14 (29 / 7)
+ 198 7.1 0.0 0.0 INTRON_3 362926 362953 (37228) + (A)n Simple_repeat 1 28 (0) 507
ANNOTATION EVIDENCE:
198 7.14 0.00 0.00 INTRON_3 362926 362953 37228 + (A)n Simple_repeat 1 28 152 868
INTRON_3 362926 AAAAATAAAAAAAAAAAAAAAAAAAGAA 362953
v i
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28
Matrix = Unknown
Transitions / transversions = 1.00 (1 / 1)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 308 32.9 10.8 1.6 INTRON_3 363027 363193 (36988) C MLT1J1 LTR/ERVL-MaLR (0) 448 267 508
ANNOTATION EVIDENCE:
308 32.88 10.78 1.65 INTRON_3 363027 363193 36988 C MLT1J2 LTR/ERVL-MaLR 267 448 0 878
INTRON_3 363027 TGTATTAATAAAAATAAGCTATGCTATGCTGTAGCA--CTAAATCTAGAT 363074
i v iii i -i -- i -- v vvi i i
C MLT1J2#LTR/ER 448 TGTATTAGTCAGGGTAGGCTA-ACT--GCTGTAACAAACAACCCCCAAAT 402
INTRON_3 363075 GTTAGTGGTTTAGCCCAACAAAAGTTTAGCTTTTGTTCAGAATA-AGTCT 363123
v i i i v i vi i i i vivi - i
C MLT1J2#LTR/ER 401 CTCAGTGGCTTAACACAATAAAAGTTTATTTCTCGCTCATGTCACAGTCC 352
INTRON_3 363124 GATATAGGTGGCTC---ATCGTG------------TCATCTAGTGACTCA 363158
i i i i ---ivv ------------i ivi v i
C MLT1J2#LTR/ER 351 AATGTGGGTGGTTCTGGGGGGTGGGNGGCTCTGCTCCACGCAGTCATTCA 302
INTRON_3 363159 GGATTCCAGGCTTCCTACATATCGTGATGCCGCCA 363193
ivi i i v v i iiv
C MLT1J2#LTR/ER 301 GGGACCCAGGCTCCTTCCATCTTGTGGCTCCGCCA 267
Matrix = 20p37g.matrix
Transitions / transversions = 2.18 (37 / 17)
Gap_init rate = 0.04 (6 / 166), avg. gap size = 3.50 (21 / 6)
+ 586 17.2 6.5 0.8 INTRON_3 363256 363378 (36803) C MLT1J1 LTR/ERVL-MaLR (282) 162 33 508
ANNOTATION EVIDENCE:
586 17.20 6.50 0.77 INTRON_3 363256 363378 36803 C MLT1J1 LTR/ERVL-MaLR 33 162 282 879
INTRON_3 363256 GGCCTGGAAGTGGCACA--TCACTCCTACATACATCCCACTGGCCAAAAC 363303
-- i i vi i i i
C MLT1J1#LTR/ER 162 GGCCTGGAAGTGGCACACATCACTTCTGCCCACATTCCATTGGCCAGAAC 113
INTRON_3 363304 TAAGTCATATGCTCCCACCCTAACTACAAGGGAATCCAGGAAATGT--TC 363351
v i vi v - i iv ii --
C MLT1J1#LTR/ER 112 TCAGTCACATGGCCACACC-TAACTGCAAGGGAGGCTGGGAAATGTAGTC 64
INTRON_3 363352 T-TTTGTCTGCCCAGGAAGA---GGAAATGG 363378
-vi v --- i
C MLT1J1#LTR/ER 63 TAGCTGTGTGCCCAGGAAGAAAAGGAAACGG 33
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (14 / 7)
Gap_init rate = 0.04 (5 / 122), avg. gap size = 1.80 (9 / 5)
+ 250 19.3 0.0 0.0 INTRON_3 363414 363458 (36723) C L2a LINE/L2 (272) 3154 3106 501
ANNOTATION EVIDENCE:
183 33.33 0.00 0.00 INTRON_3 363414 363458 36723 C L2b_3end LINE/L2 197 241 225 801
INTRON_3 363414 AAGACTTCACTGAAAAAGTGACATTTGAGTCAAGTCCTGAGAAAT 363458
i i viv ii i iii v iii
C L2b_3end#LINE 241 AGGGCTTCCTGGAGGAGGTGACATTTGAGCTGAGACCTGAAGGAT 197
Matrix = 25p37g.matrix
Transitions / transversions = 4.00 (12 / 3)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)
250 17.50 0.00 0.00 INTRON_3 363414 363453 36728 C L2a_3end LINE/L2 206 245 272 800
INTRON_3 363414 AAGACTTCACTGAAAAAGTGACATTTGAGTCAAGTCCTGA 363453
i i i i iv v
C L2a_3end#LINE 245 AAGGCCTCACTGAGAAGGTGACATTTGAGCAAAGACCTGA 206
Matrix = 25p37g.matrix
Transitions / transversions = 2.50 (5 / 2)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 306 28.0 2.7 6.5 INTRON_3 364433 364543 (35638) + L2c LINE/L2 3281 3387 (0) 509
ANNOTATION EVIDENCE:
306 27.96 2.70 6.54 INTRON_3 364433 364543 35638 + L2c_3end LINE/L2 372 478 0 802
INTRON_3 364433 CTAGTTTGTGAGCTTTTAGAAATTAGGGAC--TGTCTTATTCAT-TTTAT 364479
vi ii v iivi -- - i
L2c_3end#LINE 372 CTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGT 421
INTRON_3 364480 ATTCCTTTTACCTCAGTGCATGCTATGACTCGATATTCAATAAATGTTGA 364529
i ivvi -i ii iv ------ iiii vi
L2c_3end#LINE 422 ATCCCCAGCACCT-GGCACATAGTA------GGCGCTCAATAAATGTTTG 464
INTRON_3 364530 ATAAATTAATGAAT 364543
v i v
L2c_3end#LINE 465 TTGAATGAATGAAT 478
Matrix = 25p37g.matrix
Transitions / transversions = 2.22 (20 / 9)
Gap_init rate = 0.04 (4 / 110), avg. gap size = 2.50 (10 / 4)
+ 392 24.2 2.5 6.1 INTRON_3 365411 365529 (34652) C MIR3 SINE/MIR (3) 205 91 510
ANNOTATION EVIDENCE:
392 24.16 2.52 6.09 INTRON_3 365411 365529 34652 C MIR3 SINE/MIR 91 205 3 803
INTRON_3 365411 TCATAGATTCATGGACATTGAGAGCACAGAGC--AAATGAACATTGGAGA 365458
v i - ----- i- --i v i v i
C MIR3#SINE/MIR 205 TCATAGAATCATAGA-AT-----GT-CAGAGCTGGAAGGGACCTTAGAGA 163
INTRON_3 365459 TCATCTGATTTAATCATCT-ACTTTATAGATGAACAAACTGAGGCTCATT 365507
ii ii i vi - i i iv i vv
C MIR3#SINE/MIR 162 TCATCTAGTCCAACCCCCTCATTTTACAGATGAGGAAACTGAGGCCCAGA 113
INTRON_3 365508 GAGGATAAGGGATTTGCCTAAG 365529
vv v i i
C MIR3#SINE/MIR 112 GAGGTGAAGTGACTTGCCCAAG 91
Matrix = 25p37g.matrix
Transitions / transversions = 1.70 (17 / 10)
Gap_init rate = 0.04 (5 / 118), avg. gap size = 2.00 (10 / 5)
+ 3006 18.7 5.2 3.8 INTRON_3 365548 366240 (33941) + MER54A LTR/ERVL 1 642 (259) 511
ANNOTATION EVIDENCE:
3006 18.08 5.41 3.27 INTRON_3 365548 366176 34005 + MER54A LTR/ERVL 1 642 259 880
INTRON_3 365548 TGTAGTGAATTCTTGTAAGTGTGCATTGCCTCGGCATCCATTTTGAATAT 365597
i v v iii
MER54A#LTR/ER 1 TGTAGTGAATTCTTATAATTTTATGTTGCCTCGGCATCCATTTTGAATAT 50
INTRON_3 365598 AAATTTTACTTCCTTATACCAGAAGCAGGGCTCAGTCACCCTTGACA--G 365645
ii ?v i i i --
MER54A#LTR/ER 51 AGGTTNGACTTTCTCATACCAGAAGCAGGGCTTAGTCACCCTTGACACAG 100
INTRON_3 365646 TTTCCA--TTTACACCTCCTCCCAGTTTCTCAGTGTGGTTGATCCAGATA 365693
-- i v i i i i
MER54A#LTR/ER 101 TTTCCAGTTCTCCGCCTCCTCCCAGTTCCTCAATGTGGTCGATCCAGATA 150
INTRON_3 365694 T-----------AACTGCCTCCTG---ACCACTTCCCTGTGGGACAGCTA 365729
----------- i --- i i
MER54A#LTR/ER 151 TCTGCCTTATACAACCGCCTCCTGGTGACCACCTCCCTATGGGACAGCTA 200
INTRON_3 365730 GATAAAACTTACTTGACTTGCCCCACTGACCCTCACATCCCGCACTAACT 365779
v i i i i i ivi
MER54A#LTR/ER 201 GATACAACCTACTTGACTCGCCCCACTGACCCCCACACCCCACATGGACT 250
INTRON_3 365780 GTGTAGATATGCCACAGAGACCACATCTCAGTCACAGTGTGACCCCCCAG 365829
i i i v v i v i
MER54A#LTR/ER 251 GCGCAGATATGCCGCAGTGACCACCTCTCAGTCACAGCGTGACCCCACGG 300
INTRON_3 365830 AACTCATGCCTTCTTGCTCTAAACCCACCAGTTAGAGCTTCGTAAGAGAA 365879
i v i i i viiv i
MER54A#LTR/ER 301 AACTCGTGCCTGCTTGCTCTAAACCCACCAATTAGAACTCCCCGCGGGAA 350
INTRON_3 365880 ACCTAGTTGGGTAATACCCTAGATCCCAATAAAGGCTTTGGCTAACAGGT 365929
iv i i i i ivi
MER54A#LTR/ER 351 ACCTGCTTGGGTAATGCCCTGGACCCCAATAAAGGCTTCGGCCCGCAGGT 400
INTRON_3 365930 CTTTCTTGCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTCTCT 365979
i---------- v i - v i v -----
MER54A#LTR/ER 401 CC----------CTCTCTCTCTCTCTCTCGCTCCC-CACCCGCTG----- 434
INTRON_3 365980 CTCTCACTGAGCA------TCCTGCA-GTCTCCAGATTTCTTGTTGGTCC 366022
-----ii ------ i v - v vvvi ii i
MER54A#LTR/ER 435 -----GTTGAGCACGCGTGTCCCGGACGGCTCCCCCCTTCCCGTTGGCCC 479
INTRON_3 366023 TCATGGGCATG-TGC----TTCTCCCATGGATCTTTAA----TAAAATTA 366063
vvvi i - ---- i vv v ---- ? v vv
MER54A#LTR/ER 480 TGCGAGGCGTGCTGCCCTCTTCTCTCTGGGATCTGTAAGTAATAMACTGC 529
INTRON_3 366064 TTCTGTTATTTCATGTGTTTTGTTATGCACCCACCTCTGTGTCCCACCTA 366113
i ivv v i i
MER54A#LTR/ER 530 TTCTGTTATTTCATGTGTTTTGTTGTGTTGCCTCCTCTGTGTCTCACCTG 579
INTRON_3 366114 ACTGACACACCTGACCCTAACTTTCCTCCCATTTGGGGCTCTCCCTGAAA 366163
i i v i iv ii iv i
MER54A#LTR/ER 580 ACCGACACACCCGAACCTAACTCTCCTCCCGGTCAGGGCTCTCCTAGAGA 629
INTRON_3 366164 GTGGGTGTCCTGG 366176
v i i
MER54A#LTR/ER 630 GTGGCTATCTTGG 642
Matrix = 20p37g.matrix
Transitions / transversions = 1.84 (70 / 38)
Gap_init rate = 0.02 (12 / 628), avg. gap size = 4.58 (55 / 12)
936 24.79 3.68 8.61 INTRON_3 365888 366240 33941 + MER73 LTR/ERVL 303 639 5 881
INTRON_3 365888 GGGTAATACCC-TAGATCCCAATAAAGGCTTTGGCTAACAGGTCTTTCTT 365936
i i - i i ii v v v iv --------
MER73#LTR/ERV 303 GGATAATGCCCATGGACCTTAATAAAGGCATAGTCCCACAGG-------- 344
INTRON_3 365937 GCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTCTCTCTCTCAC 365986
--------- i --- iv i --- v i v vii
MER73#LTR/ERV 345 ---------CTCTCTCCC---CTCTCTCTTGCTCCC---CACCCACTGGT 379
INTRON_3 365987 TGAGCATCCTGCAGTCTCCAGATTTCTTGTTGGTC-CTCATGGGCATGTG 366035
vi v i i i ii i i - i i v ivi-
MER73#LTR/ERV 380 TGAGCTCCCTGCCGCCTCCGGACTTCCCGTCGGCCTCCCGTCGGCACCC- 428
INTRON_3 366036 CT--TCTCCCATGGATCTTT----AATAAAATTATTCTGTTATTTCATGT 366079
--i i vv i v ---- v v --- i
MER73#LTR/ERV 429 CTAACCTCTCTGGGACCTGTGAGTAATAAATTTCTTCTGTT---TCATGC 475
INTRON_3 366080 GTTTTGTTATGCACCCACCTC--TGTGTCCCACCTAACTGACACACCTGA 366127
i v - v i- -- i i ?? i
MER73#LTR/ERV 476 ATTTTGGT-TTCACCT-CCTCATTGTGTCTCACCTGACNNACACACCCGA 523
INTRON_3 366128 CCCTAACTTTCCTCCCATTTGGGGCTCTCCCTGAAAGTGGGTGTCCTGGA 366177
v i i v ii iv i v i i v
MER73#LTR/ERV 524 ACCTAACTCTCCCCCCAGTCAGGGCTCTCCTAGAGAGTGGCTATCTTGGC 573
INTRON_3 366178 TTATGGCCTCTAT--GGAGAGAAACCTCAAGGCCAAACCAGAA-GAAATC 366224
v v --i i i ii - i
MER73#LTR/ERV 574 TTATGGCCACTCTCAAGAGAGAGACCTCAAGACCAAATTAGAAAGAAACC 623
INTRON_3 366225 ATAGCAAGCAGAATCA 366240
i vv i
MER73#LTR/ERV 624 ATAACAATAAAAATCA 639
Matrix = 20p37g.matrix
Transitions / transversions = 1.79 (50 / 28)
Gap_init rate = 0.04 (14 / 352), avg. gap size = 3.00 (42 / 14)
+ 281 27.5 7.5 0.0 INTRON_3 366774 366853 (33328) + MIRb SINE/MIR 124 209 (59) 512
ANNOTATION EVIDENCE:
281 27.50 7.50 0.00 INTRON_3 366774 366853 33328 + MIRb SINE/MIR 124 209 59 804
INTRON_3 366774 GCCTTGGTTTTCCCATTTCTAAAATGAAGCTAA------GTATCTCATTT 366817
ii i i i v ii v ------v i iivv
MIRb#SINE/MIR 124 GCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAG 173
INTRON_3 366818 GGTTATTATGAAGATTCAATGAGAGTTTGCATGTAA 366853
i i i v vvv
MIRb#SINE/MIR 174 GGTTGTTGTGAGGATTAAATGAGATAATGCATGTAA 209
Matrix = 25p37g.matrix
Transitions / transversions = 1.44 (13 / 9)
Gap_init rate = 0.01 (1 / 79), avg. gap size = 6.00 (6 / 1)
+ 1135 28.6 4.3 3.5 INTRON_3 367227 367743 (32438) C L1MC4 LINE/L1 (75) 7967 7447 513
ANNOTATION EVIDENCE:
1135 28.65 4.26 3.45 INTRON_3 367227 367743 32438 C L1MC4_3end LINE/L1 2194 2714 75 834
INTRON_3 367227 CTAAATTAATCAATTGTTTACATTTTACCAAATTTGTTTT----CTCTCT 367272
i i vvi v v i v i ----i
C L1MC4_3end#LI 2714 CCAGATTCCCCAAATGTTAACATTTTGCCACATTTGCTTTATCATTCTCT 2665
INTRON_3 367273 ATC-ACCTATGTAAGATTGG----CTGAATTGTTTGAGAGTAAGTTGCAA 367317
i ?-i v ii viv vv---- iii i
C L1MC4_3end#LI 2664 GTNTGCATATACATATTTTTTTTTCTGAACCATTTGAGAGTAAGTTGCAG 2615
INTRON_3 367318 ACATCATGACATTTTAGCCCT--------TAGCATGCATCTCCTATAC-T 367358
v v vi? v --------i ii i i v v-i
C L1MC4_3end#LI 2614 ACATGATGCCCCSTTACCCCTAAATACTTCAGTGTGTATTTCCTAAAAAC 2565
INTRON_3 367359 AAGAACATTCTCCTGAATAATCACAATACTATTACTACACCTAAGAAACC 367408
i i iv i i v ii v vii i ii
C L1MC4_3end#LI 2564 AAGGACATTCTCTTACATAACCACAGTACAATTATCAAAATCAGGAAATT 2515
INTRON_3 367409 CAATATTCATTGATTCAATA--ATCATCTAATACACAGTTTGTATACTAA 367456
v ----- v -- i vi viiv v v
C L1MC4_3end#LI 2514 AA-----CATTGATACAATACTATTATCTAATCTACAGACCTTATTCAAA 2470
INTRON_3 367457 TTTTTCCTAATTATTC-AATAATGTGTATGCTGGCTATTCCCACCCACTA 367505
iv - i i - viv vv i v ---vv vv? v -
C L1MC4_3end#LI 2469 TTTCGCC-AATTGTCCCAATAATGTCCTTTATAGCAA---AAAAANAGT- 2425
INTRON_3 367506 CCCCACCAATCTCGGATCCAAGCAAGAATCACAC-TTACATTTAGTTTTC 367554
----- ii iv v v i ii - i v
C L1MC4_3end#LI 2424 -----CTGATCCAGGATCCAATCCAGGATCATGCGTTGCATTTAGTTGTC 2380
INTRON_3 367555 TTGTCTCTTTAGTCTTTTAAAATCTAGACTCGTTTCCCTAATTATATTTT 367604
v ii vv i v?v i i - i iv vi
C L1MC4_3end#LI 2379 ATGTCTCTTTAGTCTCCTTTAATCTGGAANAGTTCCTC-AGTCTTTCTTT 2331
INTRON_3 367605 GTCTTGTGTGACATTGACATTTTTTTAAGAGTGCAAGCAAGTTTTCTTAT 367654
vii v v- i i v v i i
C L1MC4_3end#LI 2330 GTCTTTCATGACCTTGACATTTTTG-AAGAGTACAGGCCAGTTATTTTGT 2282
INTRON_3 367655 AAAATGCACCTAAATCTGGATTTATCTGATTGCTTCCTTATTGTTAGATT 367704
i iv v i i i - i i vi
C L1MC4_3end#LI 2281 AGAATGTCCCTCAATTTGGGTTTGTCTGAT-GTTTCCTCATGATTAGATT 2233
INTRON_3 367705 CTGTTTAAATATGTTTGGCAAGAATACTACATAGGTGAT 367743
v v vii v i i v i
C L1MC4_3end#LI 2232 CAGGTTATGCATTTTTGGCAGGAATACCACAGAAGTGAT 2194
Matrix = 20p37g.matrix
Transitions / transversions = 1.24 (77 / 62)
Gap_init rate = 0.03 (15 / 516), avg. gap size = 2.67 (40 / 15)
+ 219 6.9 0.0 0.0 INTRON_3 367759 367787 (32394) + (TTA)n Simple_repeat 2 30 (0) 514
ANNOTATION EVIDENCE:
219 6.90 0.00 0.00 INTRON_3 367759 367787 32394 C (TAA)n Simple_repeat 152 180 0 864
INTRON_3 367759 TTATTATTATTATTATCGTTATTATTATT 367787
ii
C (TAA)n#Simple 180 TTATTATTATTATTATTATTATTATTATT 152
Matrix = Unknown
Transitions / transversions = 0.0 (2 / 0)
Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0)
+ 2152 11.0 0.0 4.9 INTRON_3 367788 368087 (32094) C AluSq2 SINE/Alu (26) 286 1 515
ANNOTATION EVIDENCE:
2028 11.96 0.00 5.26 INTRON_3 367788 368087 32094 C AluSx SINE/Alu 1 285 27 784
INTRON_3 367788 TTTGAGACAGAGTTTCACTCTTGTTGCCTAGCCTGGAGTACAATGGCGTG 367837
i i i - i i v i i i
C AluSx#SINE/Al 285 TTTGAGACGGAGTCTCGCTCT-GTCGCCCAGGCTGGAGTGCAGTGGCGCG 237
INTRON_3 367838 ATCTCGGCTTACTGCAACCTCTACCTCCTGGGTTCAAGTGATTCTCCTGC 367887
i ii i i
C AluSx#SINE/Al 236 ATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGC 187
INTRON_3 367888 TTCAGCCTCCCTAGTAGCTGGGATTACAGGCATGCGCCACCACACCCAGC 367937
i v ii i i
C AluSx#SINE/Al 186 CTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGC 137
INTRON_3 367938 TGAATTTTTTTTTTTTTTTTTTGTATTTTTAGTAGAGATGGGGTTTCACC 367987
i -------------- i
C AluSx#SINE/Al 136 TAA--------------TTTTTGTATTTTTAGTAGAGACGGGGTTTCACC 101
INTRON_3 367988 ATGTTGGTCAGGCTGGTCTCAAACTCTTGACCTCAAGTGATCCACCTGCC 368037
i i i i i i
C AluSx#SINE/Al 100 ATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCC 51
INTRON_3 368038 TCAGCCTCCCAGAGTGCTGGGATTACAGGCGTGGGCCACTGTGCCTGGCC 368087
i i i i i i
C AluSx#SINE/Al 50 TCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 16.00 (32 / 2)
Gap_init rate = 0.01 (2 / 299), avg. gap size = 7.50 (15 / 2)
+ 464 31.4 10.6 4.2 INTRON_3 368241 368599 (31582) C L2 LINE/L2 (787) 2632 2252 516
ANNOTATION EVIDENCE:
464 31.40 10.58 4.20 INTRON_3 368241 368599 31582 C L2 LINE/L2 2252 2632 450 805
INTRON_3 368241 AGGAAGAGTTTAAAAGATGAACTTGATGACCTGTTTTGGTTATGA----T 368286
v iiv v i ---- v -- vv v i i----
C L2#LINE/L2 2632 AGGTAGAGCCAACAGGAT----TTGCTGA--TGGATTGGATGTGGGGTGT 2589
INTRON_3 368287 TAGATAATAGAGAGGAACCTAGGACAATTTCCAGGTT------------- 368323
v v - ii v ii i i v -------------
C L2#LINE/L2 2588 GAGAGAA-AGAGAGGAGTCAAGGATGACTCCAAGGTTTTTGGCCTGAGCA 2540
INTRON_3 368324 ACTGAAAT-ATGACTGTGTTATTCATCAATTCAGGGAATATAAAAAAAGA 368372
i v- ivvv ii v iii vvii v iviviii i
C L2#LINE/L2 2539 ACTGGAAGGATGGAGTTGCCATTAACTGAGATGGGGAAGACTGTGGGAGG 2490
INTRON_3 368373 AACAGATTTATTGGGGTAGCTGATGAATTTATTTTTTCACATGCACCAGT 368422
i i ivv v v v v i i v vv i-iv
C L2#LINE/L2 2489 AGCAGGTTTGAGGGGGAAGATCAGGAGTTCAGTTTTGGACATGT-TAAGT 2441
INTRON_3 368423 T-GAAATGCCTGTGAGTTGTTCAGATAGAAATG-----------ATTG-A 368459
- i i v vii i ii i i -----------i -
C L2#LINE/L2 2440 TTGAGATGCCTATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGA 2391
INTRON_3 368460 TATCGCTGGCCTGGAGTTCAGA--AGAAGCCTGGACTGGAGATTTAAATT 368507
-i vi i i-- i i i v
C L2#LINE/L2 2390 TAT-ACGAGTCTGGAGTTCAGGGGAGAGGTCTGGGCTGGAGATATAAATT 2342
INTRON_3 368508 TCGGACTACAATATTAGTATATAGGTAGGGGGTAAAGCCATAAGGGATAG 368557
v v ----i i i i i vivv i iv- i
C L2#LINE/L2 2341 TGGGAGT----CATCAGCATATAGATGGTATTTAAAGCCATGAGAC-TGG 2297
INTRON_3 368558 ATGAGTTTGCCTAGACAG--AGTATTAGAT---GAAGAGAGATAGGT 368599
v ii v iv -- i - --- - v
C L2#LINE/L2 2296 ATGAGATCACCAAGGGAGTGAGTGT-AGATAGAGAAGAGA-AGAGGT 2252
Matrix = 25p37g.matrix
Transitions / transversions = 1.40 (63 / 45)
Gap_init rate = 0.05 (18 / 358), avg. gap size = 3.00 (54 / 18)
+ 206 26.4 1.4 2.7 INTRON_3 370050 370123 (30058) + (TATG)n Simple_repeat 4 76 (0) 517
ANNOTATION EVIDENCE:
206 26.40 1.35 2.74 INTRON_3 370050 370123 30058 C (CATA)n Simple_repeat 104 176 4 872
INTRON_3 370050 TGTGTATGTGTGTATAGATAGGAATGTATATATGTATTTACAGACATATG 370099
i i iv -- v i v iiv ii
C (CATA)n#Simpl 176 TATGTATGTATGTATGTAT--GTATGTATGTATGTATGTATGTATGTATG 129
INTRON_3 370100 AAAATATGTTT-TAAGTATATATAT 370123
v vi v - v i i
C (CATA)n#Simpl 128 TATGTATGTATGTATGTATGTATGT 104
Matrix = Unknown
Transitions / transversions = 1.38 (11 / 8)
Gap_init rate = 0.03 (2 / 73), avg. gap size = 1.50 (3 / 2)
+ 1532 17.4 5.1 3.7 INTRON_3 370159 370452 (29729) C AluJr SINE/Alu (14) 298 1 518
ANNOTATION EVIDENCE:
1396 19.43 5.10 3.69 INTRON_3 370159 370452 29729 C AluJb_short_ SINE/Alu 1 298 4 795
INTRON_3 370159 TTTTTATCCTTTTTTTGCTACAGGATGTCACTCCGTCACCCATACTGGAG 370208
v ii vv i v i i i vi
C AluJb_short_# 298 TTTTTTTTTTTTTTTTGAGACAGGGTCTCGCTCTGTCGCCCAGGCTGGAG 249
INTRON_3 370209 TGCAGTGACACAGTCATGGCTCACTGCACCCTGCACCCTTGACCTCCTTG 370258
i i ii i v -------i i-
C AluJb_short_# 248 TGCAGTGGCGCGATCACGGCTCACTGCAGCCT-------CGACCTCCC-G 207
INTRON_3 370259 GGCTCAAGTGATCCTCCCACCTCAGCCCCCC-AGTAGGTGGAACTACAGG 370307
i ii i - v i
C AluJb_short_# 206 GGCTCAAGCGATCCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGG 157
INTRON_3 370308 CATGTACCACAATGCCTGGCTAATTTTTAAAATTTTTTGTAGAGATAAGG 370357
ii ii v i i iv - iii
C AluJb_short_# 156 CGCGCGCCACCACGCCCGGCTAATTTTTGTA-TTTTTTGTAGAGACGGGG 108
INTRON_3 370358 TCTCACTATGTTGCCCAGGCTGATCTCAAACTCCTGAGCTCAAAAGCAAT 370407
i i i i i -- ii
C AluJb_short_# 107 TTTCACCATGTTGCCCAGGCTGGTCTCGAACTCCTGGGCTCAA--GTGAT 60
INTRON_3 370408 CCTTTCACCTTAGCCTCCCAAAG--------------GCATGAGCCACTG 370443
ii i ii -------------- i i
C AluJb_short_# 59 CCTCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCG 10
INTRON_3 370444 TCCCTGGCC 370452
iv i
C AluJb_short_# 9 CGCCCGGCC 1
Matrix = 18p37g.matrix
Transitions / transversions = 4.50 (45 / 10)
Gap_init rate = 0.02 (6 / 293), avg. gap size = 4.33 (26 / 6)
+ 643 19.9 4.5 3.8 INTRON_3 370553 370709 (29472) C L1M5 LINE/L1 (406) 5718 5561 519
ANNOTATION EVIDENCE:
643 19.86 4.46 3.80 INTRON_3 370553 370709 29472 C L1ME4a_3end LINE/L1 308 465 406 835
INTRON_3 370553 AAATAAAGCTGAGATGAACATTCTTATGCAC------TTGTGCATCCCAT 370596
v v i i i i------ ? ---
C L1ME4a_3end#L 465 AAATAATGCTGCGATGAACATCCTTGTACATAAATCTTTGTNCA---CAT 419
INTRON_3 370597 -TCTGATTATTTCCTCAGAAAAAAATTTTAGAAGTGGAGATTTTTAGTCA 370645
- i i v v ii iv vi vi
C L1ME4a_3end#L 418 CTCTGATTATTTCCTTAGGATAAATTCCTAGAAGTGGAATTACTGGGTCA 369
INTRON_3 370646 AAGCATATATACGTTTTTAAAGCTTTTGATACATATTGCCAAAATGTCCC 370695
vi i? i i i v i -
C L1ME4a_3end#L 368 AAGGGTATGNACATTTTTAAGGCTCTTGATACATATTGCCAAATTGCCC- 320
INTRON_3 370696 TTTCCAGAAGTGTT 370709
-- iv
C L1ME4a_3end#L 319 --TCCAGAAAGGTT 308
Matrix = 20p37g.matrix
Transitions / transversions = 1.80 (18 / 10)
Gap_init rate = 0.03 (4 / 156), avg. gap size = 3.25 (13 / 4)
+ 3671 25.6 6.6 4.5 INTRON_3 371566 373351 (26830) C ERV3-16A3_I-int LTR/ERVL (3315) 1911 102 520
ANNOTATION EVIDENCE:
3671 23.19 5.30 5.96 INTRON_3 371566 372679 27502 C ERV3-16A3_I LTR/ERVL 805 1911 3315 861
INTRON_3 371566 CTAGGATTCCACTTATTGCCTGGCCTCCATAAATTCCT-CTGGAATAAGG 371614
i i i i i vi i i- vv i iv
C ERV3-16A3_I#L 1911 CCAGGATTCCATTTATTACCTGGCCCCTATATGTCCCCACTCTAACAGTG 1862
INTRON_3 371615 AGGGCATGATAATACTTTGGGTTTCCAGGTGTCACTGTCTGCTCAGAGCC 371664
- v i i i i i v vi v
C ERV3-16A3_I#L 1861 -GGCCATGATGATGCTTTGGGTCTCTAGGTATCAATGTCAACTCAGACCC 1813
INTRON_3 371665 TGTATTAAATATTCCTCAAAATGTATTTGTTTTCTCCTTTTCCTTAGTTT 371714
i iv v ? v vv v i i i -- v
C ERV3-16A3_I#L 1812 TGTGTCCAATAGTCCTCRAAATGTCTGGGTATTCCCTTTCTCC--AGTGT 1765
INTRON_3 371715 ACAGTCACCTGAGTAAATGACCATAGGTCCCTTT--GAGGAAGGAGAATT 371762
i i i i vi-- i vv
C ERV3-16A3_I#L 1764 ACAGTTACCTGAGTAAATGGCTATAGGTCTCTGCAGGAGGAAAGAGAAGA 1715
INTRON_3 371763 ATAATATATAATGCTACAGCACCC---CTCCTAAAGTCCTGGCCATGTCT 371809
v --------- i iii --- ii v ? iv
C ERV3-16A3_I#L 1714 ATCAT---------TGCAGTGTCCTTYCTCCTAGGGACCTGRCCACCTCT 1674
INTRON_3 371810 TCAGTCAAAGGGTTCTGGATCTGCAAATTGGCTCGGGACCAGGGACTAAC 371859
v i v i v i ii i -
C ERV3-16A3_I#L 1673 TCAGTCAATGGGTTCTAGATCTGAAAATTGGCTCAGGTCTAGAAACTGA- 1625
INTRON_3 371860 TAGCAAAGGATCAGGACTCTTG-ATTGGGGCAACCATCCTCAGTTTCCCA 371908
-- i v i v- i ii i i ii
C ERV3-16A3_I#L 1624 --GCAAGGGATCATGACTTTTTTATTGGAGTGACTACCCTCAGCCTCCCA 1577
INTRON_3 371909 GTCATCCATTTTTGTCTTTTTTTTGTGATTACAGTTGTTAACTAACACTC 371958
--------------v i ivi i-- v? i
C ERV3-16A3_I#L 1576 G--------------ATTTTTTCTGCTGTTACAA--GTTAAGYAGCACTC 1543
INTRON_3 371959 ATGTAGTCTGCTCATCTATTATATTTGCCCCTGGGGATGTCATGCTCTGT 372008
v -------iv ---- i ii i i
C ERV3-16A3_I#L 1542 TTGT-------CAATCTATT----TTGCCCCTAGGGATACCATGTTCTAT 1504
INTRON_3 372009 TAACCATTTGTGTAACTGTC-TGCCAGTCAAGGACCCTTGGCTGCCCCTC 372057
i viii v - --i vv v
C ERV3-16A3_I#L 1503 TAACCATCTCCACAACTCTCYTG--GGTCAAGCCCCCTTGGCTGCCACTC 1456
INTRON_3 372058 TGACCTTGCTAGTCATTATAGTAATTGTAACTTTTTGGCTTCTGGAAGTT 372107
- i i i i i ii v
C ERV3-16A3_I#L 1455 TGACCTT-CTGGTCATTATAATAATTGCAGCCTCCTGGCTTCTGGCAGTT 1407
INTRON_3 372108 AAGCACCGACACCTAAGGCTCTATTGCTTT---GCCTCTCCAACCACCAT 372154
ii iiv i- v i --- i ivi v -
C ERV3-16A3_I#L 1406 AAGTGCTACCACCTG-GCCTCTATTGTTTTAGGGTCTTATCATCC-CCAT 1359
INTRON_3 372155 CCTTAC----------GGTTAT----TGCCCAGTCC-------AAAACTG 372183
ivi i----------i i ---- v vv ------- ivv
C ERV3-16A3_I#L 1358 TGCTATYAATGAGCCAAGTTGTGTAATGGCCTCTCCTACCATCAGCCCTG 1309
INTRON_3 372184 GCCTGCAGATAACAGCCATCACTGAACTTCTTAGTGAT--GCTG-TGTGC 372230
vi v i -- - iv
C ERV3-16A3_I#L 1308 GCCTGCAGAGGAGAGCCACCACTGAACTTCTTAGTGATTTGCTGGTGCCC 1259
INTRON_3 372231 CTCTCACCAGCACATTCCTAATGGCCTTAGCAAATGGTGTCCTTTGGGTT 372280
i i i ii ----- ii
C ERV3-16A3_I#L 1258 CTCTCACCAGTACATTCCTGATGGCCTTGGTGAATGGTGT-----GGGCC 1214
INTRON_3 372281 CTCCCCTGGAACAT---CCTCTGATGAATCTTCTGTCCTTAT-TAAT-AT 372325
? i v --- i ii iv i- -
C ERV3-16A3_I#L 1213 YTTCCATGGAACATAATCCTCTGGTGGGTCTTCTAGCCTTACATAATGAT 1164
INTRON_3 372326 ATCCATTCCAAC-----CACTTCCTTCAGTCTCTTTTATACATACCTGTC 372370
i i i ----- i v i --- --- v i vi
C ERV3-16A3_I#L 1163 ATCTATTCTAGCATGCCCACTTCCCTGAGCCT---TTA---ATCCTTTCC 1120
INTRON_3 372371 TTTACCATCTGCCAGGGCAACTCAGGTACTTCTACGTTGCTCAACATGG- 372419
i ? i v i i v v ii i -
C ERV3-16A3_I#L 1119 TCTACCATCTGCCAKGGCAATTCTGGCATTTCAACTTCACTCAGCATGGG 1070
INTRON_3 372420 CTATTACTTTTTGCAGACCTCTAAAAGTCACCCTAGCAGGGAGTTTGCCC 372469
i -i i ----i ii i i vi v
C ERV3-16A3_I#L 1069 CCATT-TTTCTTGC----TTCTAGGAGCCATCCTAGCAGTAAGTTTGCAC 1025
INTRON_3 372470 CATCCACTGGGATCCATGCCAGAGTGTTAAATCCCACATCTCAAGAGAGT 372519
iv i v i iii i i i
C ERV3-16A3_I#L 1024 CATCTCCTGGGGTCCTTGCCAGGGTGTTAAATCCTGTATCCCGAGAAAGT 975
INTRON_3 372520 AACCTGAAGTCACTGAATTCTTG-GTTATCCAGTTGTAC-------ATCC 372561
ivi iv v v-i i i iv ------- i
C ERV3-16A3_I#L 974 GCTCCCAAGTCAATGAATTCTTCCATTATCTAATCTTACTGCTTATATTC 925
INTRON_3 372562 TGGCCCCCTTGATCAAGCTCTTTCAAAATCCAATCCTAGGAGTATAT--C 372609
? i v ii i i v v i--
C ERV3-16A3_I#L 924 TRGCCTCCTTGATCAAGCACCCTCAAAATCCAGTCCCATGTGTATACTCC 875
INTRON_3 372610 TCTGGCTCCTATTGATACATCTTAGCTAATTTTCATAACTCCT---GGCT 372656
i ii i vi i i iii i --- v
C ERV3-16A3_I#L 874 CCTGGCTCCTGCTGGTACATGCTGGCTAATTCTTGCAGCTCCTTTGGGGT 825
INTRON_3 372657 ACATAGTCTCATTTGTTTTCTTA 372679
-- i - vi ?i
C ERV3-16A3_I#L 824 A--TAGTCCC-TTTCCTYCCTTA 805
Matrix = 20p37g.matrix
Transitions / transversions = 2.23 (163 / 73)
Gap_init rate = 0.04 (39 / 1113), avg. gap size = 3.21 (125 / 39)
1591 27.75 9.65 2.21 INTRON_3 372609 373157 27024 C ERV3-16A3_I LTR/ERVL 287 875 4351 862
INTRON_3 372609 CTCTGGCTCCTATTGATACATCTTAGCTAATTTTCATAACTCCT---GGC 372655
i ii i vi i i iii i --- v
C ERV3-16A3_I#L 875 CCCTGGCTCCTGCTGGTACATGCTGGCTAATTCTTGCAGCTCCTTTGGGG 826
INTRON_3 372656 TACATAGTCTCATTTGTTTTCTTA--------------------GTTGGG 372685
-- i - vi ?i -------------------- i
C ERV3-16A3_I#L 825 TA--TAGTCCC-TTTCCTYCCTTATCAGGCCCAGCATGTCCCCAGCTGGG 779
INTRON_3 372686 CTATCCTGGGCTTTAATTCTAGTTATCAGCCTGGTATCCAGGAGAGGAGG 372735
i v ? vi ii ii i v ii
C ERV3-16A3_I#L 778 TTATGCTGKGACTTAACCCTAGTTATTGGCCTAGTAGCCAGGAGGAGAGG 729
INTRON_3 372736 TGGGAGTGGCTCCCAA-AGGGATCAACTGTTGCCTTGCAGGGATAGGCTT 372784
i iiiv ii? - iv v ii v i
C ERV3-16A3_I#L 728 TGGGGGCAAGTCTTRAGAGGGGGCACCTGTTGCCTTGTGGGGAGAGGCCT 679
INTRON_3 372785 CTGCCAGGTTTTCCAACACAGG-GCAGG-----TGCTACCTCTTATTAGG 372828
v?v i iiiii - i ----- v ?
C ERV3-16A3_I#L 678 CTGCAKTGTCTTCCAGTGTGGGTGCAAGAGGAGTGCTAGCTCTTAWTAGG 629
INTRON_3 372829 GAAGGGTGG-TCACT-----AAACTCTGAGGGTTCAGGGAGGTCTTCAGC 372872
i? -i ----- ?i v i ii vv v
C ERV3-16A3_I#L 628 GAGRGGTGGGCCACTTCTGCARGCTCAGAGGGTTCAGAGGAGTCTAGAGA 579
INTRON_3 372873 TCCAATATTT---GGAGCTGAAATCCATCTAAATGGGCCTATCTCATATT 372919
v i i --- i ---- i i vv i iii i
C ERV3-16A3_I#L 578 GCCAACATCTTTAGGGGC----ATCCACCTAGATGTCCCCATCCTGTGTT 533
INTRON_3 372920 TCAGGGTACTGGGTTTTTCCAAT--ATAGCCCTGA---TAGCATAACAGA 372964
ii--- ? ii i i-- v i iv--- v v
C ERV3-16A3_I#L 532 CT---GTYCCAGGTTTTCCCAACCAAGAGCCTTACCTTTAGCATAAAAGT 486
INTRON_3 372965 CC-AGCTTAATTGATTGAGTATTCAAACATCTCTGAATCCCTATAACTCC 373013
i -v i --- ii i i i i v i i i
C ERV3-16A3_I#L 485 TCTCGCCT---TGGCTGAGCATTTAAACGTCTCTGGAGCTCTGTAACTCT 439
INTRON_3 373014 A----TCAGATCTTCAGTTTTCTGCTTAGCCATGTCTGTTTTTCCACCAC 373059
---- ? i v i v ? i iv i i ii
C ERV3-16A3_I#L 438 AACTATYAGATCCTGAGTCTGCTWCTCAGCTTTGTCTGTTCTTTCACTGC 389
INTRON_3 373060 AGGATATAACAGCCCTTTTATTAATGACCAG---AGAAGTCCTCTGGCTC 373106
v vii ?ii i v iiv --- i i ?
C ERV3-16A3_I#L 388 AGGAGATAAGGACYTCTTTGTAAGCTACCAGCAAAGAGGCCCTCTGGCTY 339
INTRON_3 373107 TCCCATTTAGCCATTAGTTACTTGTTAAC-TCCCTCAGTTTCTCATTTTT 373155
v i iv i i i-v i v i
C ERV3-16A3_I#L 338 TCACACTTAGCTTTTAATTGCTTGTTAATAGCCCTCAGTTTTTCATTATC 289
INTRON_3 373156 TC 373157
C ERV3-16A3_I#L 288 TC 287
Matrix = 20p37g.matrix
Transitions / transversions = 2.70 (100 / 37)
Gap_init rate = 0.03 (19 / 548), avg. gap size = 3.47 (66 / 19)
1150 34.47 6.74 1.86 INTRON_3 372684 373351 26830 C HERV16 LTR/ERVL 102 801 4195 863
INTRON_3 372684 GGCTATCCTGGGCTTTAATTCTAGTTATCAGCCTGGTATCCAGGAGAGGA 372733
i iv? v v? ii ii i iv v
C HERV16#LTR/ER 801 GGTTACGYTGTGAYTTAACCCTAGTTATTGGCCTAGTGGCCAGGAGATGA 752
INTRON_3 372734 GGTGGGAGTGGCTCCCAAAGGGATCAACTGTTGCCTTGC--AGGGATAGG 372781
ii ii v ii?i ii v vvv i -- v
C HERV16#LTR/ER 751 GGTGGAGGCAGATCCTGRGGAAAACCCATGTTGTCTTGCNAAGGGAGAGG 702
INTRON_3 372782 CTTCTGCCAGGTTTTCCAACACAGG-----GCAGGTGCTACCTCTTATTA 372826
i i ivvv i v i v ?----- iii ? v i v
C HERV16#LTR/ER 701 CCTCCGTACTGTCTTCCCATAAAGNAAGAAGCGAATGCYAGCCCTTAATA 652
INTRON_3 372827 GGGAAGGGT-GGTCACT-----AAACTCTGAGGGTTCAGGGAGGTCTTCA 372870
i i - ----- ii vi iii vvi
C HERV16#LTR/ER 651 GGGAGGAGTAGGTCACTTCTGCAGGCTCAAAGGGTTCAGGGGAATCTGGG 602
INTRON_3 372871 GCTCCAATATTT---GGAGCTGAAATCCATCTAAATGGGCCTATCTCATA 372917
v i v --- i ---- v i i i vv i ?i i i
C HERV16#LTR/ER 601 GATTCAAGATTTTTAGGGGC----ATCAATCCAGACGTCCCCATYCCGTG 556
INTRON_3 372918 TTTCAGGGTACTGGGTTTTTCCAAT-ATAGCCCTGA---TAGCATAACAG 372963
v v i vvi ?i i i-ivi v ---?i iv
C HERV16#LTR/ER 555 TGTCAGGGTCCCGTTCTTWCCTAACCGGGGCGCTGAMCTNGGCATAGAAG 506
INTRON_3 372964 ACCAGCTTAATTGATTGAGTATTCAAACATCTCTGAATCCCTATAACTCC 373013
v i --- i i v i v v i v ii iiv ii
C HERV16#LTR/ER 505 ACCTGCCT---TGGTTGGGAATTTAACCTTCTTTGAAGCTTTGCTACTTT 459
INTRON_3 373014 -ATCAGATCTTCAGTTTTCTGCTTAGCCATGTCTGTTTTTCCACCACAGG 373062
- i ii vi i vv v i ?iv v ii? i i ii
C HERV16#LTR/ER 458 GATCAAATTCTGGGTCTGATCCTCAGWTTTCTCTGCCNTCCCGCTGCAGG 409
INTRON_3 373063 ATATAACAGCCCTTTTATTAATG--ACCAGAGAAGTCCTCTGGCTCTCCC 373110
v i v ii -- -- i i i i vi
C HERV16#LTR/ER 408 AGATGAGAGCCTCTTTAT--ATGCTACCAAAGAGGCCCTCTGGCTTTCAT 361
INTRON_3 373111 ATTTAGCCATTAGTTACTTGTTAA-CTCCCTCAGTTTCTCATT---TTTT 373156
ii iiv i i i ivi - v i i ?i i ---i
C HERV16#LTR/ER 360 GCTTAGTTTTCAATTGCCAATTAATCGCTCTCAGCTYTTTATTGTTCTTT 311
INTRON_3 373157 CCCAGGGCCTCAATATAATTTTGCGGTAGCC-TGCAACTCTGCTCTCTTG 373205
i? i iv i vv ii v ii - v i ii? v i v
C HERV16#LTR/ER 310 TMCAGAGTGTCAGTCAAGCTTAGCGACAGCCATCCAATTCCAYTGTCCTT 261
INTRON_3 373206 ----ATAGATATTTTCTCCTCATGTCTTTTAAATCCCAGAATTATTGCA- 373250
----i ?? v iv - i i i i iv v vi -
C HERV16#LTR/ER 260 CCATGTANNTAATTCATCC-CATATTTCTCAAACGCCTGAAGCATTGCAC 212
INTRON_3 373251 --GCT---GCATCC-CTCT--ACCTG---GCTAAATTCTTAGATAACCAC 373289
-- --- i i - i -- v --- i --- ii v v
C HERV16#LTR/ER 211 CAGCTAGTGCGTTCTCTTTTCACCAGTACGCCA---TCCCAGTTCACCAC 165
INTRON_3 373290 TAATGAAATATTTAGTAAATGAGCCATCACCTTTTGTCAGGGGCTGTTCA 373339
i i vv ii v ?vi i ii v i i i ii
C HERV16#LTR/ER 164 CAGTGAAAGTTTTAACAATTWCACTACTACCTTGTGCCAGAGGCTATCTA 115
INTRON_3 373340 TGCTC-ACCTACC 373351
-
C HERV16#LTR/ER 114 TGCTCCACCTACC 102
Matrix = 20p37g.matrix
Transitions / transversions = 1.96 (139 / 71)
Gap_init rate = 0.04 (24 / 667), avg. gap size = 2.42 (58 / 24)
+ 1355 27.3 8.8 1.2 INTRON_3 373453 373871 (26310) C LTR16B LTR/ERVL (5) 457 8 521
ANNOTATION EVIDENCE:
286 25.96 19.23 0.00 INTRON_3 373453 373556 26625 C LTR16B2 LTR/ERVL 334 457 5 882
INTRON_3 373453 TAGATTGAGTCTACCAAGAAGCAGACACTAAGATACGATTAGATGTTCCA 373502
vii i iv i i i iiv i v v
C LTR16B2#LTR/E 457 TAGTCCGGGTCCTCCGAGAAGCAGACGCCAAGACGGGATTAGACGTGCAA 408
INTRON_3 373503 GAGATTGATTGG---AAGC-------AGGGA----------GGAACTGGT 373532
v --- i ------- ---------- i i v
C LTR16B2#LTR/E 407 GAGATTTATTGGGGGAAACGCCTGTGAGGGAAAATGGGGAGGGAGCCGGA 358
INTRON_3 373533 GAAGGTGAAGAAAGCCTTCAGACC 373556
i ivii i v
C LTR16B2#LTR/E 357 GGAGGCTGGGAGAGCCATCAGACC 334
Matrix = 20p37g.matrix
Transitions / transversions = 2.00 (18 / 9)
Gap_init rate = 0.03 (3 / 103), avg. gap size = 6.67 (20 / 3)
1355 27.72 5.40 1.64 INTRON_3 373520 373871 26310 C LTR16B LTR/ERVL 8 372 91 883
INTRON_3 373520 GGGAGGAA-CTGGTGAAGGTGAAGAAAGCCTTCAGACCA--------GTC 373560
i - v v ? iiii i --------
C LTR16B#LTR/ER 372 GGGAGGGAGCAGGAGNAGGCAGGGAGAGCCTTCAGACCACGATGCAGGTC 323
INTRON_3 373561 TAATGTCTGTGGTTGGGGGAAGGGGAGGCGAGGAGAA--GGGAAGGCA-- 373606
i i?i i--i i i i vi i -- v v --
C LTR16B#LTR/ER 322 TGACNCCTGTGA--AGGAGAGGGGGAAGGAAGGAGGATTGGGTAGGAAGA 275
INTRON_3 373607 -TCTTAGACT--AGGGCATTTCCAAAAATGATTCAGCCAGGCTCATGGGG 373653
- i -- v v i i v v i iv
C LTR16B#LTR/ER 274 GTCTCAGACTGCAGCGCAGTTCTAAGAAAGTTTCGGCCAGGCCGATGGGG 225
INTRON_3 373654 AGTCCTCAAGCCAAAATTATCTGCAGGAAGAGTCCTATAATTTGCTGGAA 373703
i i iii i ivi i iiivi i v
C LTR16B#LTR/ER 224 AGTCCTCGAGCCAAAGTCGCCCGTTAGAGGAGTCCTGCGTCTCGCAGGAA 175
INTRON_3 373704 TAAACCTGCCTTAATATCCTTGGCTACTGTGTTCAGTCATTGACTAGAAG 373753
iii v i i ii ---- i i i i i
C LTR16B#LTR/ER 174 TGGGCCTGCATTAGTACCCCCG----CCGTGCTCAGTCATTGGCTGGGAG 129
INTRON_3 373754 CAGCTCATGGGAAGTGTGACCTTGGCACAAATGCAGTGATATATGTAGAA 373803
i i? i i i i i i i i iv vi i
C LTR16B#LTR/ER 128 CAGCCCGNGGGAAGCGTGGCCTCGGCGCGAACGCGGTGGTGGATCCAGAG 79
INTRON_3 373804 GAGGAGTAGCTAGAACCATTAATCAGTTATGCTCCCTGTGGCAG---ATG 373850
i v i i ii i i i ii i ii --- v
C LTR16B#LTR/ER 78 GGGCAGCAGCTGGGGCCGTCAGTCAACTATGCTCCCCGCAGCAGGAGATC 29
INTRON_3 373851 TGAGTGGTGCATTTTCATGGC 373871
i i
C LTR16B#LTR/ER 28 TGAGCGGCGCATTTTCATGGC 8
Matrix = 20p37g.matrix
Transitions / transversions = 4.17 (75 / 18)
Gap_init rate = 0.02 (8 / 351), avg. gap size = 3.12 (25 / 8)
+ 203 13.8 0.0 0.0 INTRON_3 373872 373900 (26281) + (CA)n Simple_repeat 2 30 (0) 522
ANNOTATION EVIDENCE:
203 13.79 0.00 0.00 INTRON_3 373872 373900 26281 + (CA)n Simple_repeat 2 30 150 873
INTRON_3 373872 ACACACATACACATGCACACACATACACA 373900
i ii i
(CA)n#Simple_ 2 ACACACACACACACACACACACACACACA 30
Matrix = Unknown
Transitions / transversions = 0.0 (4 / 0)
Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0)
+ 369 35.7 1.3 1.3 INTRON_3 373901 374129 (26052) + Tigger16b DNA/TcMar-Tigger 103 307 (30) 523
ANNOTATION EVIDENCE:
369 35.64 1.46 1.46 INTRON_3 373901 374105 26076 + Tigger16b DNA/TcMar-Tigger 103 307 30 884
INTRON_3 373901 AACACATATATACACACAGATA--GTTACACCTAGGGATCAGATTCCACC 373948
i v viv v i i -- i ?v i v i i i i iv
Tigger16b#DNA 103 AACGCATTTTCCCACAGAAACANTGTTATANATGGTGGTTAGGTTCTATA 152
INTRON_3 373949 ATTCCATTAGTATTATAATTC-CTTATTCAGAATGGATTTGTACAACCTT 373997
i v i i v -v? -- vv i vi- i iv
Tigger16b#DNA 153 GTACCGTTAGTACTATACTTCAGNTA--CATTATGGGTTAA-ATAGGCTT 199
INTRON_3 373998 TTTTTGGCCCATCTAAAGAAATGACCCTCACTTGTGGCTTTCTTTCAATG 374047
v v ivii iiii vv i vi i i ii v v v
Tigger16b#DNA 200 TTGTGGGCTGGCCTGGGAACCTAACCACCATTTATAACATTGTTTCTATG 249
INTRON_3 374048 TGAAAACACATACCAAGTTTCCAACAGCTGACTCACAAGTAAGTCTTTGG 374097
v ii i v i i v i i iii iii
Tigger16b#DNA 250 GGAAAATGCGTTCCGAGTTCCAAACAACTGACTTACAAACGAACTTTTGG 299
INTRON_3 374098 AACACAAC 374105
Tigger16b#DNA 300 AACACAAC 307
Matrix = 20p37g.matrix
Transitions / transversions = 1.69 (44 / 26)
Gap_init rate = 0.02 (4 / 204), avg. gap size = 1.50 (6 / 4)
316 36.30 0.00 0.00 INTRON_3 373995 374129 26052 + MamRep1161 DNA/TcMar-Tigger 822 956 1 885
INTRON_3 373995 CTTTTTTTGGCCCATCTAAAGAAATGACCCTCACTTGTGGCTTTCTTTCA 374044
v v ivii iiii vv i vi i i ii v v v
MamRep1161#DN 822 CTTTTGTGGGCTAGCCTGGGAACCTAACCACCATTTATAACATTGTTTCT 871
INTRON_3 374045 ATGTGAAAACACATACCAAGTTTCCAACAGCTGACTCACAAGTAAGTCTT 374094
v iii v ii i v i i i i iii
MamRep1161#DN 872 ATGGGAAAATGTATTCTGAGTTCCAAACAACTGACTTACAAATGAACTTT 921
INTRON_3 374095 TGGAACACAACAAAATTAAAAGCGGAGAACTTTCT 374129
vv v iv iv i i vi
MamRep1161#DN 922 TGGAACACAACCCATTTGTAAGTTGGGGACTGCCT 956
Matrix = 20p37g.matrix
Transitions / transversions = 1.72 (31 / 18)
Gap_init rate = 0.00 (0 / 134), avg. gap size = 0.0 (0 / 0)
+ 276 25.0 7.5 6.3 INTRON_3 374436 374529 (25652) + L2c LINE/L2 3283 3377 (10) 524
ANNOTATION EVIDENCE:
276 24.98 7.45 6.32 INTRON_3 374436 374529 25652 + L2c_3end LINE/L2 374 468 10 806
INTRON_3 374436 AGCCTATAAATTCCTTGAAAGCAAGGACCATGTCT----CAGCTTTGATT 374481
v i i ii ii i i ---- v --
L2c_3end#LINE 374 AGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTG--T 421
INTRON_3 374482 ATACTCAGTACCCAAGTGACTAAT--TCAGTGC-CAACAAATATTTGGTG 374528
v i i ---- i vv -- vi i - i i v
L2c_3end#LINE 422 ATCCCCAGCACC----TGGCACATAGTAGGCGCTCAATAAATGTTTGTTG 467
INTRON_3 374529 A 374529
L2c_3end#LINE 468 A 468
Matrix = 25p37g.matrix
Transitions / transversions = 2.14 (15 / 7)
Gap_init rate = 0.05 (5 / 93), avg. gap size = 2.60 (13 / 5)
+ 366 30.7 3.8 6.3 INTRON_3 375067 375164 (25017) C MIRc SINE/MIR (10) 258 164 525
ANNOTATION EVIDENCE:
366 30.70 3.77 6.28 INTRON_3 375067 375164 25017 C MIRc SINE/MIR 164 258 10 807
INTRON_3 375067 ATTTCTTCAATTTGCGTA-TACTTTATACCTTTCAAGAACAGTTTATTGA 375115
iii vv ii -i i vi v - i - i -- v
C MIRc#SINE/MIR 258 ACCCCTTACATTTGTATAGCACTTTACAGTTTACAA-AGC-GCTT--TCA 213
INTRON_3 375116 TATCCATTTTCTTATTTGAAACTTAAAATAATGTTGGGACATAGACAAG 375164
i v v i vv i v i ivi v vi i i
C MIRc#SINE/MIR 212 CATACATTATCTCATTTGATCCTCACAACAACCCTGTGAGGTAGGCAGG 164
Matrix = 25p37g.matrix
Transitions / transversions = 1.46 (19 / 13)
Gap_init rate = 0.04 (4 / 97), avg. gap size = 1.25 (5 / 4)
+ 180 7.7 0.0 0.0 INTRON_3 375165 375190 (24991) + (TTA)n Simple_repeat 2 27 (0) 526
ANNOTATION EVIDENCE:
180 7.69 0.00 0.00 INTRON_3 375165 375190 24991 C (TAA)n Simple_repeat 149 174 6 865
INTRON_3 375165 TTATTATTATGATTATTACTATTATT 375190
v i
C (TAA)n#Simple 174 TTATTATTATTATTATTATTATTATT 149
Matrix = Unknown
Transitions / transversions = 1.00 (1 / 1)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
+ 2017 12.3 1.8 0.0 INTRON_3 375191 375467 (24714) C AluSz SINE/Alu (29) 283 2 527
ANNOTATION EVIDENCE:
1918 12.64 1.81 0.00 INTRON_3 375191 375467 24714 C AluSx SINE/Alu 2 283 29 785
INTRON_3 375191 TGAGATGGAGTCTTGCTCTGTCATGCAGGCTGGAGTGCAGTGGCGCGATC 375240
i i iiv
C AluSx#SINE/Al 283 TGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATC 234
INTRON_3 375241 TCCCTTCACTGCAACCTCTGCCTCCCAGGTTCAAGCAATTCTCCTGCTTC 375290
vvi i i i i
C AluSx#SINE/Al 233 TCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTC 184
INTRON_3 375291 GGTCT---GAGTAGCTGGGATTACAGGTGCTTGCCACCA-GCCTGGCTAA 375336
i i --- i vi - i
C AluSx#SINE/Al 183 AGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAA 134
INTRON_3 375337 TTTTTGTATTTTTAGCAGAGATGAGGTTTCACGATGTTGGCCAGGCTGGT 375386
i i i v
C AluSx#SINE/Al 133 TTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGT 84
INTRON_3 375387 CTTGAACTCCTGACCTCAAGT-ATCCACCTGCCTCAACATCCCGAAGTGC 375435
i i - i i ii v i
C AluSx#SINE/Al 83 CTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGC 34
INTRON_3 375436 TGGGATTACAGGCGTGGGCCACCATGACCAGC 375467
i ii v i
C AluSx#SINE/Al 33 TGGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p37g.matrix
Transitions / transversions = 4.00 (28 / 7)
Gap_init rate = 0.01 (3 / 276), avg. gap size = 1.67 (5 / 3)
+ 366 30.7 3.8 6.3 INTRON_3 375468 375579 (24602) C MIRc SINE/MIR (105) 163 52 525
ANNOTATION EVIDENCE:
366 30.70 3.77 6.28 INTRON_3 375468 375579 24602 C MIRc SINE/MIR 52 163 105 808
INTRON_3 375468 TGAGACAAGTATTATTATTGACTTTTGTA-AAACAAGGAATCTGAAGTAC 375516
----i i ivv v - - i ii v i i-i
C MIRc#SINE/MIR 163 ----GCAGGTATTATTATCCCCATTT-TACAGATGAGGAAACTGAGGC-T 120
INTRON_3 375517 CATAGAG-TTAAATGATTTGTCCAAGG--GAACAG--AATAAATT-TGGG 375560
v - i i i --iv -- i i v-ii i
C MIRc#SINE/MIR 119 CAGAGAGGTTAAGTGACTTGCCCAAGGTCACACAGCTAGTAAGTGGCAGA 70
INTRON_3 375561 GCCAGTGATTAGAAAACAG 375579
- i v vv
C MIRc#SINE/MIR 69 GCCAG-GACTCGAACCCAG 52
Matrix = 25p37g.matrix
Transitions / transversions = 1.90 (19 / 10)
Gap_init rate = 0.08 (9 / 111), avg. gap size = 1.56 (14 / 9)
+ 184 33.3 1.7 1.7 INTRON_3 375633 375690 (24491) C L2b LINE/L2 (11) 3364 3307 528
ANNOTATION EVIDENCE:
184 33.33 1.72 1.72 INTRON_3 375633 375690 24491 C L2b_3end LINE/L2 398 455 11 809
INTRON_3 375633 CAGTAAACATGTACTTAGTAACCACTCTGTGCTGGGTACTGATGCTAAAC 375682
ii v v i v i v ii iv - iii
C L2b_3end#LINE 455 CAACAAACATTTACTGAGCACCTACTGTGTGCCAGGCCCTG-TGCTGGGC 407
INTRON_3 375683 -TTGAAAAC 375690
-i iii
C L2b_3end#LINE 406 GCTGGGGAC 398
Matrix = 25p37g.matrix
Transitions / transversions = 2.80 (14 / 5)
Gap_init rate = 0.04 (2 / 57), avg. gap size = 1.00 (2 / 2)
+ 251 30.0 3.5 2.8 INTRON_3 376101 376244 (23937) C L1ME3C LINE/L1 (5) 6118 5974 529
ANNOTATION EVIDENCE:
251 30.00 3.47 2.76 INTRON_3 376101 376244 23937 C L1ME3C_3end LINE/L1 721 865 5 836
INTRON_3 376101 AAGAAATAAGAG--TATAGACATAATTTAAACCTGCCTGAGTATTTCTCT 376148
i v-- i i i i v ii i- v i i i
C L1ME3C_3end#L 865 AAGAAATAAAACATTACAGATACAGTTGAAGTCC-CCTGTGTACTCCTCC 817
INTRON_3 376149 CCAATCCCATTATTTTCCAGTATAACACAGAGGAGGTAA--AGTATCCTG 376196
i vii vvivivv v --- -- v
C L1ME3C_3end#L 816 CCGATCCCATTCCCTTCCCTCCCTCCCCAGAGG---TAACCACTATCCTG 770
INTRON_3 376197 AATTTTTAATTTA-CATTTCCCTTTGTTTTATTTTACTTATACTATATA 376244
vvvi - i v vii v v v ? v i
C L1ME3C_3end#L 769 AATTTGGTGTTTATCATTCCCATGCATGTTTTTATANTTTTACTACATA 721
Matrix = 20p37g.matrix
Transitions / transversions = 1.05 (21 / 20)
Gap_init rate = 0.03 (5 / 143), avg. gap size = 1.80 (9 / 5)
+ 380 21.8 3.5 1.7 INTRON_3 376441 376613 (23568) + (TA)n Simple_repeat 2 177 (0) 530
ANNOTATION EVIDENCE:
380 21.76 3.47 1.70 INTRON_3 376441 376613 23568 C (TA)n Simple_repeat 4 179 1 874
INTRON_3 376441 ATTTATACATATTTATATATGATGTAGTAATATATAACTATATAGTATTG 376490
v i v - i vvv vv - vv
C (TA)n#Simple_ 179 ATATATATATATATATATAT-ATATATATATATATATATATATA-TATAT 132
INTRON_3 376491 ATACAT-TAAAAATACATGTATGTTTATATATGAATTTAT-TATATATCA 376538
i - v v i i i v iv v - -
C (TA)n#Simple_ 131 ATATATATATATATATATATATATATATATATATATATATATATATAT-A 83
INTRON_3 376539 TGTATAAAAATATTGATATA-ATTTATAGATACATAAATA-ATATATTTA 376586
i v v vv - v v i v - v
C (TA)n#Simple_ 82 TATATATATATATATATATATATATATATATATATATATATATATATATA 33
INTRON_3 376587 AA-ATAAATATTAATAAATAT-TACATAT 376613
v - v vv v - i
C (TA)n#Simple_ 32 TATATATATATATATATATATATATATAT 4
Matrix = Unknown
Transitions / transversions = 0.37 (10 / 27)
Gap_init rate = 0.05 (9 / 172), avg. gap size = 1.00 (9 / 9)
+ 359 13.7 5.7 4.0 INTRON_3 376643 376764 (23417) + (TA)n Simple_repeat 1 124 (0) 530
ANNOTATION EVIDENCE:
359 13.66 5.74 4.03 INTRON_3 376643 376764 23417 C (TA)n Simple_repeat 57 180 0 875
INTRON_3 376643 TATATAACTACATAT-TATATATAGCAT-TACATA-ATATACATATATGT 376689
vv i - -i - i - i i
C (TA)n#Simple_ 180 TATATATATATATATATATATATA-TATATATATATATATATATATATAT 132
INTRON_3 376690 ATATACAGTATA-ATATATATAGTATATATAGTGCA-ATATGCATA-ACA 376736
i - - - - ii - ii - i
C (TA)n#Simple_ 131 ATATATA-TATATATATATATA-TATATATA-TATATATATATATATATA 85
INTRON_3 376737 TATACATGTATATATCATGTAT-TATATA 376764
i i - i -
C (TA)n#Simple_ 84 TATATATATATATAT-ATATATATATATA 57
Matrix = Unknown
Transitions / transversions = 7.00 (14 / 2)
Gap_init rate = 0.10 (12 / 121), avg. gap size = 1.00 (12 / 12)
+ 551 21.4 1.2 4.3 INTRON_3 376766 376931 (23250) C L1ME3C LINE/L1 (145) 5978 5818 529
ANNOTATION EVIDENCE:
551 21.41 1.20 4.35 INTRON_3 376766 376931 23250 C L1ME3C_3end LINE/L1 565 725 145 837
INTRON_3 376766 ACATATA-ATGTATTTCCATAATAAATTGTATAGTACTATTTTGTATGTC 376814
i- -- i vv --- i i ii i
C L1ME3C_3end#L 725 ACATATGTATGTAT--CCGTAAACAAT---ATAGTATTGTTTTGCGTGTT 681
INTRON_3 376815 TT-AACCATCATACAAATAGTATCATGCTGCATGTATTATTAGGCAACTC 376863
- v v i i i i i i v vv i
C L1ME3C_3end#L 680 TTTAAACTTTATATAAATGGTATCATACTGTACGTATTCTTCTGCAACTT 631
INTRON_3 376864 CCTTGTTTTTCTCTGTAAATTATGTTTTTGAGATTTATTTCTGTTAATAC 376913
v -- v vv v iiv i
C L1ME3C_3end#L 630 GCTT--TTTTCGCTCAACATTATGTTTTTGAGATTTATCCATGTTGATAC 583
INTRON_3 376914 ATGTAACTCTGGTTTATT 376931
i i i i
C L1ME3C_3end#L 582 GTGTAGCTCTAGTTCATT 565
Matrix = 20p37g.matrix
Transitions / transversions = 1.62 (21 / 13)
Gap_init rate = 0.03 (5 / 165), avg. gap size = 1.80 (9 / 5)
+ 486 25.0 1.6 0.0 INTRON_3 376942 377065 (23116) C L1MEf LINE/L1 (352) 6169 6044 531 *
ANNOTATION EVIDENCE:
486 25.00 1.61 0.00 INTRON_3 376942 377065 23116 C L1ME3C_3end LINE/L1 393 518 352 838
INTRON_3 376942 TTACTTATCAATTCT--TATAGATGGACATTTAGGCTATTTCTAATTTAT 376989
i v -- i v i i i v
C L1ME3C_3end#L 518 TTATTTATCCATTCTCCTGTTGATGGACATTTAGGTTGTTTCCAATTTTT 469
INTRON_3 376990 TCTTATTGCAAATAGCCTTTCAGTCAAAATTCTTGTTCTTGTCTCCTTGT 377039
ivi i i iivi v i v v v v
C L1ME3C_3end#L 468 CGCTATTACAAACAATGCTGCAATGAACATTCTTGTACATGTCTCCTTGT 419
INTRON_3 377040 ACACAAGTGAAAAAGCTTCTCTGGAG 377065
i v vi i i i i
C L1ME3C_3end#L 418 GCACACGTGCGAGAGTTTCTCTAGGG 393
Matrix = 20p37g.matrix
Transitions / transversions = 1.58 (19 / 12)
Gap_init rate = 0.01 (1 / 123), avg. gap size = 2.00 (2 / 1)
+ 2569 24.4 8.0 6.4 INTRON_3 377064 377287 (22894) C L1MEf LINE/L1 (2079) 4465 4234 531
ANNOTATION EVIDENCE:
2569 24.41 7.96 6.36 INTRON_3 377064 377287 22894 C L1M5_orf2 LINE/L1 1727 1958 1336 839
INTRON_3 377064 AGAGAGAAAACATTCAATTTTTCACTATTAAATATGACATTAGCTGGAA- 377112
i i ? v i i ii v v i-
C L1M5_orf2#LIN 1958 AGAGGGAAAGCNTTCAATATTTCACCATTAAGTATGATGTTTGCTGTAGG 1909
INTRON_3 377113 CATTTTGTAGATGCCATTTATCAAACTAAAGAAGTTCA----TA------ 377152
iv i iv i i i v---- ------
C L1M5_orf2#LIN 1908 TTTTTTGTAGATACTCTTTATCAGATTAAGGAAGTTCCCTTCTATTCCTA 1859
INTRON_3 377153 ----GCTATGAATTTTTTAAAATAATGAATTAATGTTGAATTTTGTCGGA 377198
---- v i ---- v vii i ii
C L1M5_orf2#LIN 1858 GTTTGCTAAGAGTTTTT----ATCATGAATGGGTGTTGAATTTTATCAAA 1813
INTRON_3 377199 TATATTCTCAGCATCTGTTGAAATTATCATGTGCTGTTTCTTATGTAGTC 377248
iiv i v i i v i v v iv v v
C L1M5_orf2#LIN 1812 TGCTTTTTCTGCATCTATTGAGATGATCATATGATTTTTCTCCTTTATTC 1763
INTRON_3 377249 TGTTAATATGGTGAATTACATTGAGTTAATATTGTGGGG 377287
i - i - v ii-
C L1M5_orf2#LIN 1762 TGTTAATGTGGTGAATTACATTGA-TTGAT-TTTTGAA- 1727
Matrix = 20p37g.matrix
Transitions / transversions = 1.67 (30 / 18)
Gap_init rate = 0.03 (7 / 223), avg. gap size = 3.14 (22 / 7)
+ 2285 13.0 0.0 0.0 INTRON_3 377288 377595 (22586) C AluJb SINE/Alu (4) 308 1 532
ANNOTATION EVIDENCE:
2193 12.99 0.00 0.00 INTRON_3 377288 377595 22586 C AluJb SINE/Alu 1 308 4 786
INTRON_3 377288 TTTTTTTTGTTTTGTTTTTTGTTTTTGAGACAGGGTCTTGCTCTGTCACC 377337
v v v i i
C AluJb#SINE/Al 308 TTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGGGTCTCGCTCTGTCGCC 259
INTRON_3 377338 CAGGCTGGAGTGCAGTGGTGTGATCATGGCTCACTGCAGCCTCGACCTCC 377387
i i i
C AluJb#SINE/Al 258 CAGGCTGGAGTGCAGTGGCGCGATCACGGCTCACTGCAGCCTCGACCTCC 209
INTRON_3 377388 CAGGCTCAGGTGATCCTCCCATCTCAGTCTCCTGAGTAGCTGGGACTACA 377437
i i i iii i i
C AluJb#SINE/Al 208 CGGGCTCAAGCGATCCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACA 159
INTRON_3 377438 GGTGTGCACCACCATGCCCAGCTAATTTTTGTATTTTTAGTAGAGATTGG 377487
i i i i i v iv
C AluJb#SINE/Al 158 GGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTTGTAGAGACGGG 109
INTRON_3 377488 GTTTCGCCATGTTGCCCAGGCTGGTCTCCAATTCCTGAGCTCAAGCAATC 377537
i v i i ii
C AluJb#SINE/Al 108 GTTTCACCATGTTGCCCAGGCTGGTCTCGAACTCCTGGGCTCAAGTGATC 59
INTRON_3 377538 TGCCTGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCATGCGTCACCAC 377587
iv i i i v i i
C AluJb#SINE/Al 58 CTCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGC 9
INTRON_3 377588 ACCCTGCC 377595
i v
C AluJb#SINE/Al 8 GCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 3.44 (31 / 9)
Gap_init rate = 0.00 (0 / 307), avg. gap size = 0.0 (0 / 0)
+ 2569 24.4 8.0 6.4 INTRON_3 377596 378380 (21801) C L1MEf LINE/L1 (2311) 4233 3432 531
ANNOTATION EVIDENCE:
2569 24.41 7.96 6.36 INTRON_3 377596 378380 21801 C L1M5_orf2 LINE/L1 925 1726 1568 840
INTRON_3 377596 CATTGATTTAATTTTGAAT--GTTGAATCAGCCTTTCATTGCTGGAATAA 377643
ii i vii ii v --v v v i i?v - -- vv i
C L1M5_orf2#LIN 1726 TGTTAAACCAACCTTGCATTCCTGGAATAAACCCNAC-TTG--GTCATGA 1680
INTRON_3 377644 ACTCCACTTGGTTGTGTTATTTTTCCT-TACATTTGTGAATT-AATTTGT 377691
------------ i ii ii - i vv i -i i
C L1M5_orf2#LIN 1679 ------------TGTATTATCCTTTTTATATATTGCTGGATTCGATTTGC 1642
INTRON_3 377692 TAATATTTTGTTGGGGATTTTTGT-TACATTTTTATGAGAGATGTTGGCT 377740
vi i- vi v i ? ?i i
C L1M5_orf2#LIN 1641 TAATATTTTGTTTAGGATTTTTGCATCTATGTTCATGAGNGANATTGGCC 1592
INTRON_3 377741 TATATCTTTTATTTCTTGTAATGTCTTTATTTCATTTTGTTA-CAAGGAT 377789
i vi iv i i ivvi v - v
C L1M5_orf2#LIN 1591 TGTAATTTTCCTTTCTTGTAATGTCCTTGTCAGGTTTTGGTATCAAGGTT 1542
INTRON_3 377790 AATGCTGGCCTCA--AAATGCATTAAGAACTATTTCCT-----TCTGTTT 377832
- -- vi ii v i i ----- i i
C L1M5_orf2#LIN 1541 A-TGCTGGCCTCATAAAATGAGTTGGGAAGTGTTCCCTCTTTTTCTATTC 1493
INTRON_3 377833 TCAGGAAGAGATTGTTTAGAAATGGTATTATTTCTTCCTTAAATGTTTAC 377882
v v v ii v i-
C L1M5_orf2#LIN 1492 TCTGGAAGAGTTTGTGTAAGATTGGTATTATTTCTTCCTTAAATGTTTG- 1444
INTRON_3 377883 TGATGTAGAATTGGTGTCAGCAGTGAAATCAACTAG---TGTA-TGTTCT 377928
---- ? ----- v i ii v i --- v - v
C L1M5_orf2#LIN 1443 ----GNAGAATT-----CACCGGTGAAGCCATCTGGGCCTGGAGTTTTCT 1403
INTRON_3 377929 --GTGG---TTTTCTTTGTTGAAGGTT--------TTAA--ACTAT--GA 377961
-- ---vv i vi iv i -------- --i? --
C L1M5_orf2#LIN 1402 TTGTGGAAAGGTTTTTAATTACAGATTCAATTTCTTTAATAGNTATAGGA 1353
INTRON_3 377962 --ATTCA-ATTTCCTTGGTAGATATATGATTATTCCTATTTT------CT 378002
-- - i ------ v v vv i vi vi ------i
C L1M5_orf2#LIN 1352 CTATTCAGATTTTCT------ATTTCTTCTTGTGTCAGTTTTGGTAAGTT 1309
INTRON_3 378003 GTTTTTTCTCGAATGAATTTTGGTAGTTTGTGTC-TCTCAAGGCATTGTT 378051
v - ? i- ----- i?i v - v ----- v
C L1M5_orf2#LIN 1308 GTATTTT-TCNAG-GAATTT-----GTCNATTTCATCTAAA-----TTTT 1271
INTRON_3 378052 CTGTTTTATGGACGTTATTCTTGAATTTATGGATAGTGGATAGTTCATAA 378101
viv v i i -------i v i vv i -- v-i v v
C L1M5_orf2#LIN 1270 CAAATTTATTGGCAT-------AAAGTTGTTCATAAT--ATC-CTCTTAT 1231
INTRON_3 378102 TAT---TTTATTTTCCTTTTAATATTTATATGGTTTATATTGATTCATCT 378148
--- v v -- v iv i i ------i iv vi --
C L1M5_orf2#LIN 1230 TATCCTTTTAATGTC--TGTAGGATCTGTA------GTGATGTCTC--CT 1191
INTRON_3 378149 CTTCCCTTCTTGATACTGGTAATTTGTATGT-CTCTCAGCTCGTTTTTGG 378197
i i v i i i v - -vi iv i i
C L1M5_orf2#LIN 1190 TTTTCATTCCTGATATTGGTAATTTGTGTCTTCTCTC-TTTTTTTCTTGA 1142
INTRON_3 378198 TC-----TGTTAGAGTTTTATCAATTTTACTGATCTTTTTGAAGAGCCAG 378242
----- i v i i ii i ?
C L1M5_orf2#LIN 1141 TCAGTCTTGCTAGAGGTTTATCAATTTTATTAATCTTTTCAAAGAACCAN 1092
INTRON_3 378243 CTTTTAG-TTGATTGATTTT----------TATTTATTT-CAATTTTATT 378280
i - vi ---------- ? i - v i
C L1M5_orf2#LIN 1091 CTTTTGGCTTTGTTGATTTTCTCTATTGTNTNTTTGTTTTCTATTTCATT 1042
INTRON_3 378281 ----TCTACTCT-AT-------------TTCTTTCTGCTTGCTTTAGATT 378312
---- i - ------------- i i v i i
C L1M5_orf2#LIN 1041 GATTTCTGCTCTTATCTTTATTATTTCCTTCCTTCTACTTTCTTTGGGTT 992
INTRON_3 378313 TTATTTGCTTTTCTTTTTATAGCTTCTTAAGGTAGATGATTAGATTAATG 378362
v ? v i ? i ? v ? i v
C L1M5_orf2#LIN 991 TAATTTGCTNTTCTTTTTCTAGCTTCTTGAGNTGGANGCTTANATCATTG 942
INTRON_3 378363 ATGTGAAACCTCTCTTCA 378380
v v? i i -
C L1M5_orf2#LIN 941 ATTTTNAGCCTTTCTTC- 925
Matrix = 20p37g.matrix
Transitions / transversions = 1.40 (101 / 72)
Gap_init rate = 0.06 (46 / 784), avg. gap size = 3.24 (149 / 46)
+ 2297 9.3 0.0 1.7 INTRON_3 378381 378680 (21501) C AluSg4 SINE/Alu (17) 295 1 533
ANNOTATION EVIDENCE:
2209 9.84 0.67 1.68 INTRON_3 378381 378680 21501 C AluSx SINE/Alu 1 297 15 787
INTRON_3 378381 TTTTATTTTTTTATTTAGACAGAGTCTTGCTCTGTCACCCAGGCTGGAGT 378430
v v v i i i
C AluSx#SINE/Al 297 TTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGT 248
INTRON_3 378431 GCAGTGGCGTGATCTTGGCTCATTGCAACCTCTGCCACCAGGGTTCAAGT 378480
i i i i v v i
C AluSx#SINE/Al 247 GCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGC 198
INTRON_3 378481 GATTCTCCTGCCTCAGCCTCCTGAGTAACTGGGATTACAGGCACGTGCCA 378530
i i i i
C AluSx#SINE/Al 197 GATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCA 148
INTRON_3 378531 CCATGCCATGCCTGGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCA 378580
i -----i i
C AluSx#SINE/Al 147 CCACGCC-----CGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCA 103
INTRON_3 378581 GCATCTTGGCCAGGCTGGTCTTGAACTCCTGACCTCA--TGATCCACCCG 378628
v v i -- i
C AluSx#SINE/Al 102 CCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCG 53
INTRON_3 378629 TCTCGGCCTCCCAAAGTGCTGGGATTACAGACGTGAGCCACCATGCCTGG 378678
i i ii i
C AluSx#SINE/Al 52 CCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGG 3
INTRON_3 378679 CC 378680
C AluSx#SINE/Al 2 CC 1
Matrix = 14p37g.matrix
Transitions / transversions = 3.14 (22 / 7)
Gap_init rate = 0.01 (2 / 299), avg. gap size = 3.50 (7 / 2)
+ 2569 25.0 8.2 4.4 INTRON_3 378681 379322 (20859) C L1MEf LINE/L1 (3113) 3431 2761 531
ANNOTATION EVIDENCE:
2569 24.41 7.96 6.36 INTRON_3 378681 379126 21055 C L1M5_orf2 LINE/L1 480 924 2370 841
INTRON_3 378681 TCTTCATTTTAAATAAGAGCATTTTTTGCTATCAATTTTCCTGTAAGCAC 378730
-- -- i - viv vvv v i v
C L1M5_orf2#LIN 924 --TT--TTCTAA-TATATGCATTTAAGGCTATAAATTTCCCTCTAAGCAC 880
INTRON_3 378731 TGCTTTGGCTACATCACACAAATTTCGATATGTTCTATTTTCATTTTTAT 378780
i i v i i iv v i
C L1M5_orf2#LIN 879 TGCTTTAGCTGCATCCCACAAGTTTTGATATGTCGTATTTTCATTATCAT 830
INTRON_3 378781 TCCATTGAATATATGTTATGATTTCCCTTCTGACTTGT-CTTTTACCTAA 378829
vi v v v v i v v i v - v i v
C L1M5_orf2#LIN 829 TCAGTTCAAAATATTTTCTAATTTCCATTGTGATTTCTTCTTTGACCCAT 780
INTRON_3 378830 AAGTAACTTATAGCAGTA----GTTTAATTTCCCAATATTTGGGAGAATT 378875
ii v i -- v ---- i v i i--
C L1M5_orf2#LIN 779 GGGTTATTTA--GAAGTATATTGCTTAATTTCCAAACATTTGGGG--ATT 734
INTRON_3 378876 TTCCAGATGTTACCTTTCTGTTACTAATTTCTGGGTTAATGCCATTATGG 378925
i --- i i i i i v v i i
C L1M5_orf2#LIN 733 TTCTAG---TTATCTTTTTGTTATTGATTTCTAGCTTAATTCCACTGTGG 687
INTRON_3 378926 TCATATAAAATACTTTGTATGATTTGAGTTCTTTTATATTTGCTTAAG-- 378973
v v v i v i i v v - i --
C L1M5_orf2#LIN 686 TCAGAGAACATACTCTGTATGATTTCAATCCTTTGAAATTTG-TTGAGAC 638
INTRON_3 378974 -----TTATGGCCCAGAATATGGTCTGTCTTGGTGAGTGTT--ATGAGCA 379016
----- i? ? i i i -- v
C L1M5_orf2#LIN 637 TTGCTTTATGGCCCAANATATGGTCNGTTTTGGTAAATGTTCCATGTGCA 588
INTRON_3 379017 CTGCTAAAGAATGTACTTTACTATAGTTGTC---TTCAGTGTTCTTCAAG 379063
vvv i?v - ii i--- v vi ?i
C L1M5_orf2#LIN 587 CTTGAAAAGAATGTGNATT-CTGCAGTTGTTGNGTGCAGTGTTCTATANA 539
INTRON_3 379064 TTTCTGTTAGGTTAAGTAGGTTGATAGTATTGTTCAGGTCTCCATCTACT 379113
v ?i i vv i ?? i ii --- --
C L1M5_orf2#LIN 538 TGTCNATTAGGTCAAGTTTGTTAATNNTGTTGTTCAAATCT---TCTA-- 494
INTRON_3 379114 TGTTCT-ATTGATT 379126
i - i
C L1M5_orf2#LIN 493 TATTCTTACTGATT 480
Matrix = 20p37g.matrix
Transitions / transversions = 1.20 (49 / 41)
Gap_init rate = 0.04 (16 / 445), avg. gap size = 2.31 (37 / 16)
834 26.44 8.81 0.00 INTRON_3 379028 379322 20859 C L1MD_orf2 LINE/L1 254 574 2720 842
INTRON_3 379028 TGTACTTTACTATAGTTGTCTTCAGTGTTCTTCAAGTTTCTGTTAGGTTA 379077
i i i i v vv vv vi i v vi i iv
C L1MD_orf2#LIN 574 TGTATTCTGCTGTTGTTGGGTGGAGTGTTCTATAAATGTCGATTAGATCC 525
INTRON_3 379078 AGTAGGTTGATAGTATTGTTCAGGTCTCC--------------------A 379107
v v i i v v i --------------------i
C L1MD_orf2#LIN 524 TGTTGGTTGATGGTGTTGTTGAGTTCTTCTATATCCTTGCTGATTTTCTG 475
INTRON_3 379108 TCTACTTGTTCTATTGATTACTGAGAGAGAAGTGTTGAAGTCTCCATTTG 379157
v ii ii ii vi i
C L1MD_orf2#LIN 474 TCTAGTTGTTCTATCAATTGTTGAGAGAGGGGTGTTGAAGTCTCCAACTA 425
INTRON_3 379158 TAATTGCAGATTTGGCTGTTTCTTCTTTGAGTTATGTCAATTTTTGCTTC 379207
ii v i i v v i i
C L1MD_orf2#LIN 424 TAATTGTGGATTTGTCTATTTCTCCTTTCAGTTCTATCAGTTTTTGCTTC 375
INTRON_3 379208 ATATGTTTTGGAAGTTTATTA---GGTACATGTACTTTTAGGATTGTTAT 379254
i i v iv i i i--- i ii v i
C L1MD_orf2#LIN 374 ACATATTTTGCAGCTCTGTTGTTTGGTGCATACACATTTAGGATTGCTAT 325
INTRON_3 379255 ATTTTGTTTGTGAATTGACCTGTTTATCATAATTTTATGGCCTTTTTTAT 379304
i i v v i iv v v v v i i i i
C L1MD_orf2#LIN 324 GTCTTCTTGGTGGATTGACCCTTTTATCATTATATAATGTCCCTCTCTGT 275
INTRON_3 379305 TCCT---AAGTTTCCTTTCTC 379322
ii --- v i v
C L1MD_orf2#LIN 274 CTCTGGTAATTTTCTTTGCTC 254
Matrix = 20p37g.matrix
Transitions / transversions = 1.60 (48 / 30)
Gap_init rate = 0.01 (3 / 294), avg. gap size = 8.67 (26 / 3)
+ 183 4.2 0.0 0.0 INTRON_3 379345 379368 (20813) + (TTTG)n Simple_repeat 2 25 (0) 534
ANNOTATION EVIDENCE:
183 4.17 0.00 0.00 INTRON_3 379345 379368 20813 C (CAAA)n Simple_repeat 154 177 3 866
INTRON_3 379345 GTTTTTTTGTTTGTTTGTTTGTTT 379368
v
C (CAAA)n#Simpl 177 GTTTGTTTGTTTGTTTGTTTGTTT 154
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 1)
Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0)
+ 2157 8.2 0.0 4.7 INTRON_3 379374 379665 (20516) C AluSz SINE/Alu (32) 280 2 535
ANNOTATION EVIDENCE:
2008 8.98 0.00 4.66 INTRON_3 379374 379665 20516 C AluSx SINE/Alu 2 280 32 788
INTRON_3 379374 GACGGAGTCTGGCTCTCTGGCTCTCTGTCACCCAGGCTGGAGTGCAGTGG 379423
v ---------- i
C AluSx#SINE/Al 280 GACGGAGTCTCGCTCT----------GTCGCCCAGGCTGGAGTGCAGTGG 241
INTRON_3 379424 TGCCATCTCGGCTCACTGCAACCTCCGCCTCCCTGGTTCAAGTGATTCTC 379473
i v v i
C AluSx#SINE/Al 240 CGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTC 191
INTRON_3 379474 CTGCCTCAGCCTCCAGAGGAGCCAGGATTACAGGCACGTGCCACCACACC 379523
v v ii i i i
C AluSx#SINE/Al 190 CTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCC 141
INTRON_3 379524 CGGCTAATTTTTGTGTTTTTTTAGTAGAAGACAGGGTTTCACCATGTTGG 379573
i -- - i
C AluSx#SINE/Al 140 CGGCTAATTTTTGTATTTTT--AGTAGA-GACGGGGTTTCACCATGTTGG 94
INTRON_3 379574 TCTGGCTGGTCTCGAACTTCTGACCTCAAGTGATCTGCCTGCCTCTGCCT 379623
i v i i i i v
C AluSx#SINE/Al 93 CCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCT 44
INTRON_3 379624 CCCAAGGTGCTGGGATTACAGGCGTGAGCCACCACGCCTGGC 379665
i i i
C AluSx#SINE/Al 43 CCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 2
Matrix = 14p37g.matrix
Transitions / transversions = 2.57 (18 / 7)
Gap_init rate = 0.01 (3 / 291), avg. gap size = 4.33 (13 / 3)
+ 353 19.7 13.1 1.5 INTRON_3 379669 379853 (20328) C L1MEf LINE/L1 (3859) 2685 2484 531
ANNOTATION EVIDENCE:
353 19.54 14.29 1.27 INTRON_3 379669 379808 20373 C L1MD_orf2 LINE/L1 21 178 3116 843
INTRON_3 379669 TCCATCCTTTTA------ACCTATTTATATAATTATATTTTAAGTGGGTT 379712
------ iii vi v i
C L1MD_orf2#LIN 178 TCCATCCTTTTACTTTCAACCTGCCTATATCGTTATATTTGAAGTGAGTT 129
INTRON_3 379713 TCTTGT-CATAGTGTATAATTGGATT-TATTTTTAAAAATCAAATCTAAC 379760
-v i ii i i i- i v -- v v iv
C L1MD_orf2#LIN 128 TCTTGTAGACAGCATATAGTTGGGTCATGTTTTTTAA--TCCACTCTGCC 81
INTRON_3 379761 AA-GTTTGTACTTT--TTGGTA---------CGTTTACATTTAATCTAAT 379798
-v i vi -- i--------- i v
C L1MD_orf2#LIN 80 AATCTCTGTCTTTTAATTGGTGTATTTAGACCATTTACATTTAATGTAAT 31
INTRON_3 379799 TATTGATATG 379808
C L1MD_orf2#LIN 30 TATTGATATG 21
Matrix = 20p37g.matrix
Transitions / transversions = 1.70 (17 / 10)
Gap_init rate = 0.05 (7 / 139), avg. gap size = 3.14 (22 / 7)
336 20.09 9.20 2.30 INTRON_3 379691 379853 20328 C L1MEf_5end LINE/L1 2044 2217 0 844
INTRON_3 379691 ATAATTATATTTTAAGTGGGTTTCTTGT-CATAGTGTATAATTGGAT-TT 379738
v? v ? -v i ii i i -
C L1MEf_5end#LI 2217 ATCNTTATATTTAAAGTGNGTTTCTTGTAGACAGCATATAGTTGGGTCTT 2168
INTRON_3 379739 ATTTTTAAAAATCAAATCTAACAA-GTTTGTACTTT--TTGGTACGTTTA 379785
i v -- v ? i -v i vi -- ii
C L1MEf_5end#LI 2167 GTTTTTTAA--TCCANTCTGACAATCTCTGTCTTTTAATTGGTGTGTTTA 2120
INTRON_3 379786 ---------CATTTAATCTAATTATTGATATGGTTCTATAGATTTCTAA- 379825
--------- v vv vv vv v-
C L1MEf_5end#LI 2119 GNCCATTTACATTTAATGTAATTATTGATATGGTTGGATTTAGGTCTACC 2070
INTRON_3 379826 ATTTGTTTTTATTTGCTTTCTTTTTGTC 379853
-- v i v
C L1MEf_5end#LI 2069 ATTT--TATTATTTGTTTTCTGTTTGTC 2044
Matrix = 20p37g.matrix
Transitions / transversions = 0.71 (12 / 17)
Gap_init rate = 0.05 (8 / 162), avg. gap size = 2.38 (19 / 8)
+ 634 21.8 6.0 1.9 INTRON_3 379874 380074 (20107) C L1MEf LINE/L1 (4147) 2493 2285 531
ANNOTATION EVIDENCE:
634 21.81 5.97 1.91 INTRON_3 379874 380074 20107 C L1MEf_5end LINE/L1 1845 2053 164 845
INTRON_3 379874 TTTATTTATACCCCTCATGTTTTTTTGGTACCTCTATTCCCCCATTTCTC 379923
i i i - - -- v i i i v v
C L1MEf_5end#LI 2053 TCTGTTTGT-CCCCTC-TGTTTTTT--GTTCCTCTGTTTCCTCTTTTCTG 2008
INTRON_3 379924 CCATTGTTTGGATTAAATGAATATTTTTAGTGTTCCATTTGAATTTATT- 379972
v iv vv i v i-
C L1MEf_5end#LI 2007 CCTTCTTTTGGATTATTTGAATATTTTTAGTATTCCATTTTAATTTATCT 1958
INTRON_3 379973 ----GATTTTTGACTACAT----TTGCAGTATTTT---AATGACCTCTTC 380011
---- v ii i ---- i v --- i iiiv ii
C L1MEf_5end#LI 1957 ATTGGCTTTTTAGCTATATCTCTTTGTATTATTTTTTTAGTGGTTGCTCT 1908
INTRON_3 380012 AGGAATTAAAAAATACATACATAACCTTTCTCAGTTTACTTAGAATTAGT 380061
i v v ? v i v i i i
C L1MEf_5end#LI 1907 AGGGATTACAATATACATNCTTAACTTTTCACAGTCTACTTAGAGTTAAT 1858
INTRON_3 380062 ATTTGACCATTTC 380074
?v i
C L1MEf_5end#LI 1857 ATTNTACCACTTC 1845
Matrix = 20p37g.matrix
Transitions / transversions = 1.56 (25 / 16)
Gap_init rate = 0.03 (6 / 200), avg. gap size = 2.67 (16 / 6)
+ 1311 21.2 6.3 1.5 INTRON_3 380193 380582 (19599) C L1MEf LINE/L1 (4417) 2223 1807 531
ANNOTATION EVIDENCE:
1311 23.26 4.04 1.21 INTRON_3 380193 380514 19667 C L1MEf_5end LINE/L1 1453 1783 434 846
INTRON_3 380193 ATAGTTGTTTGATGTATTACATCTATGTATGTTG-AAGTTCCTTCAGACA 380241
ivv ii ii i- iii vi?
C L1MEf_5end#LI 1783 ATAGTTGTCATATGTATTACATCTACATACATTATAAACCCCACNAGACA 1734
INTRON_3 380242 GTGTTGTGATTTTTGCTTTAAACTGCCATACATCTTTTAAATTATTTGAG 380291
i i i v i ii v vv ? i
C L1MEf_5end#LI 1733 ATGTTATAATTTTTGCTTTAAACAGTCATATGTATTTTAAAGAANTTAAG 1684
INTRON_3 380292 AGGAGAAAAATAGCCTATTACCTTTACCCCCAAATTTACTATTTCTGTTG 380341
i v iv vv v i ?
C L1MEf_5end#LI 1683 AGGAGAAAAATAGTCTTTTATATTTACCCAGATATTTACCATTTCTGNTG 1634
INTRON_3 380342 CTTCTCCTTTGTTC------------ATTTCCCTTTGGCATCATTTCTGT 380379
ii ? i? ------------i ? i i iv
C L1MEf_5end#LI 1633 CTCTTCNTTCNTTCCTGAAGATCCAAGTTTCCNTCTGGTATCATTTCCCT 1584
INTRON_3 380380 TTAGCCTAAAGGACTTCCTTTTGCATTTCTTTTAGAGCAAGTTTCTTCAC 380429
i i i v ? ? i i vi vi
C L1MEf_5end#LI 1583 TCAGCCTGAAGAACTTCCTTTAGCATTTCTTNTAGNGCAGGTCTGCTGGC 1534
INTRON_3 380430 AATGGATTCTACTAGTTTTTTTTTTTTCATCTGAAAATGTCTTTGTAACA 380479
i i vi i? ---- i vv
C L1MEf_5end#LI 1533 AACGAATTCTCTTAGTTTTCNTTT----ATCTGAAAATGTCTTTATTTCA 1488
INTRON_3 380480 CCTTTATTCCTGAAAAATATATTCTCTAGATATAG 380514
i i ii v v i
C L1MEf_5end#LI 1487 CCTTCATTTCTGAAGGATATTTTCGCTGGATATAG 1453
Matrix = 20p37g.matrix
Transitions / transversions = 2.10 (44 / 21)
Gap_init rate = 0.01 (3 / 321), avg. gap size = 5.67 (17 / 3)
936 19.80 7.96 1.67 INTRON_3 380357 380582 19599 C L1MEf_5end LINE/L1 1367 1606 611 847
INTRON_3 380357 TTTCCCTTTGGCATCATTTCTGTTTAGCCTAAAGGACTTCCTTTTGCATT 380406
? i i iv i i i v
C L1MEf_5end#LI 1606 TTTCCNTCTGGTATCATTTCCCTTCAGCCTGAAGAACTTCCTTTAGCATT 1557
INTRON_3 380407 TCTTTTAGAGCAAGTTTCTTCACAATGGATTCTACTAGTTTTTTTTTTTT 380456
? ? i i vi vi i i vi i? ---
C L1MEf_5end#LI 1556 TCTTNTAGNGCAGGTCTGCTGGCAACGAATTCTCTTAGTTTTCNTTT--- 1510
INTRON_3 380457 CATCTGAAAATGTCTTTGTAACACCTTTATTCCTGAAAAATATATTCTCT 380506
- i vv i i ii v v
C L1MEf_5end#LI 1509 -ATCTGAAAATGTCTTTATTTCACCTTCATTTCTGAAGGATATTTTCGCT 1461
INTRON_3 380507 AGATATAG---TCT------------TTTCTTTTTCAGCACTTTGAAGAT 380541
i --- ------------ i i i
C L1MEf_5end#LI 1460 GGATATAGAATTCTGGGTTGACAGTTTTTTTCTTTCAGCACTTTAAAGAT 1411
INTRON_3 380542 ATT---TCACTTTCTTCTGATCTCCATAGTTTCTTATGATAAAT 380582
i ---i v ii ? v v
C L1MEf_5end#LI 1410 GTTGTTCCACTGTCTTCTGGCCTCCATNGTTTCTGATGAGAAAT 1367
Matrix = 20p37g.matrix
Transitions / transversions = 2.25 (27 / 12)
Gap_init rate = 0.02 (4 / 225), avg. gap size = 5.50 (22 / 4)
+ 2468 26.2 5.6 4.7 INTRON_3 380716 381824 (18357) C L1MEf LINE/L1 (4825) 1815 786 531
ANNOTATION EVIDENCE:
2468 24.85 5.90 5.54 INTRON_3 380716 381614 18567 C L1MEf_5end LINE/L1 474 1375 842 848
INTRON_3 380716 ATGAGAAGTACATGATCATTTAAATCATTTTTCTCTTATATGTAATATGT 380765
i v ii?i ii i v i i i i
C L1MEf_5end#LI 1375 ATGAGAAATCCGCNGTCATTCGAATCGTTGTTCCCCTGTATGTAATGTGT 1326
INTRON_3 380766 TGCTTTTCTCTGGCTATTTTCAAGATTTTTTTTCTTTATACTTGGATTTA 380815
i i ii -- vi v v
C L1MEf_5end#LI 1325 CGTTTTTCTCTGGCTGCTTTCAAGATTTTTT--CTTTATCTTTGGTTTTC 1278
INTRON_3 380816 ATCAGTTTTATGATTATGTGTCTGGGTATGTATGGGTTTTGTTTTGGTTT 380865
v v v v i ii ----- -i ?---
C L1MEf_5end#LI 1277 AGCAGTTTGATTATGATGTGTCTAGGCGTG-----GTTTT-CTTTGN--- 1237
INTRON_3 380866 TTAGTTTACATTGTTTTGAGAGTCACTGAGAATCTTGATTTTGTTAAGTT 380915
--- ivi - i iv i vv v i - i
C L1MEf_5end#LI 1236 ---GTTTATCCTGTTT-GGGGTTCGCTGAGCTTCTTGAATCTGT-AAATT 1192
INTRON_3 380916 TATTTTTTAAATCAAATTTGGGAAGTTTTCAACTACTGTTTCTTTAAATG 380965
v i vv i i i i i i i i
C L1MEf_5end#LI 1191 TATGTCTTTCACCAAATTTGGGAAATTTTCAGCCATTATTTCTTCAAATA 1142
INTRON_3 380966 TTTTTTTCCTGTAGTAATGTCTTTCTTTTCTCATT-TGGGATGCCAATGA 381014
-- i?vi ? v ii v - iv ?
C L1MEf_5end#LI 1141 TTTTTT--CTGCNCCANTCTCTTTCTCCTCTCCTTCTGGGACTCCAATNA 1094
INTRON_3 381015 CATGAGTCTTAAACCTTTTGATATTGTCTCACAGTTCACTGAGACTATGT 381064
i ?i v i i v v i v
C L1MEf_5end#LI 1093 CACGNATGTTAGACCTTTTGATATTGTCCCACAGGTCCCTGAGGCTCTGT 1044
INTRON_3 381065 TCATTAAAAAAAAAT-----------CTGT-CTTTAAATTGTATA-TTTC 381101
vvvvvvv ----------- - i i v -
C L1MEf_5end#LI 1043 TCATTTTTTTTCAATTTTTTTTCTCTCTGTTCTTCAGATTGGATAATTTC 994
INTRON_3 381102 TCCTGTTTTATCTTTAAGTTTATTGATTTTTTTCTTCTGTCATTTTTGTT 381151
vi v i i i i i i i - i iii
C L1MEf_5end#LI 993 TATTGATCTATCTTCAAGTTCACTGACTCTTTCCT-CTGTCATCTCCATT 945
INTRON_3 381152 CTGGTATTAGGCCCATCAAGTAAAGGTTTTATTTCAAATATTATATATTT 381201
v ii v i vv ? i i v
C L1MEf_5end#LI 944 CTGCTATTGAGCCCATCCAGTGAATTTTTNATTTCAGATATTGTATTTTT 895
INTRON_3 381202 TAGCTCTAAAATTTTCATCTGGTTCTATTTTATGGTTTCTAGTTCTT--- 381248
i i i i i v i v i---
C L1MEf_5end#LI 894 CAGTTCTAAAATTTCCATTTGGTTTTTTTTTATAGTTTCTATTTCTCTGC 845
INTRON_3 381249 --AGGC-----ATATTTT-ATTCATTTAAAACATGTTCATCACTACATCA 381290
-- i?----- v i- v i?i i?i vi v ?
C L1MEf_5end#LI 844 TGAGANTTTCTATCTTTCCATTCATTTCAAGNGTGTTTNCCTTTACCTCN 795
INTRON_3 381291 TGGGTGATGGCTATACTGGCTGCTTTCAAGTCTTTGATAATTGTTATTAT 381340
ivv i i v i v --------------
C L1MEf_5end#LI 794 TGGAGCATAGTTATAATAGCTGCTTTAAAGTCTTTG-------------- 759
INTRON_3 381341 TATTTGATAAT-ACAATGTCTGGATCATCTCAGGATTGTCCTCTGCTGAT 381389
-- i -v ii i i i v ? i
C L1MEf_5end#LI 758 --TCTGATAATTCCAACATCTGGGTCATCTCGGGGTTGGCNTCTGTTGAT 711
INTRON_3 381390 TGTCTTTTCTCTTGAGAATTGGTCAGATTTTCTTTTTGTTTTGTTTTATT 381439
i ? i vv vi i ------
C L1MEf_5end#LI 710 TGTCTTTTCCCTTGAGAATTGGTCANATTTTCCTGGTTCTTCGT------ 667
INTRON_3 381440 ATTTTTTTCATGTGGCTTAATAT-GAATCATATTCTGGACATTTTGAATG 381488
--------- v vv v - i ii i ? i
C L1MEf_5end#LI 666 ---------ATGTCGAGTAATTTTGGATTGTATCCTGGACATTNTGAATA 626
INTRON_3 381489 TTACATTGTCAGAACCTGTGTCCC------------------------AT 381514
ii v vi v i------------------------
C L1MEf_5end#LI 625 TTATGTTGTGAGACTCTGGGTCCTGTTANANTCCTCTGGAGAATGTTGAT 576
INTRON_3 381515 TTTTTTTTAAA--AGTATGGGATCAATGTGGTTATGTTCAGACTGTAAAT 381562
ivv-- i v vi ivi iv ii i
C L1MEf_5end#LI 575 TTTTTTTTGTTTTAGCAGGCAATCAACCCGGTTGGGTTCAGACTACAAGT 526
INTRON_3 381563 TTGGTCTCATCTCCCATGCATGGTGGTTTCAATGTCAGTTCTGTTATTAA 381612
iv iii i ii vii iv v v v i
C L1MEf_5end#LI 525 TCTGTCTTGCCTTCTGTGGGCGGTGGTTCAAATCTCAGTTCAGTTCTCAA 476
INTRON_3 381613 AG 381614
C L1MEf_5end#LI 475 AG 474
Matrix = 20p37g.matrix
Transitions / transversions = 1.66 (123 / 74)
Gap_init rate = 0.02 (21 / 898), avg. gap size = 4.90 (103 / 21)
455 32.64 7.77 1.83 INTRON_3 381514 381719 18462 C L1MD2_5end LINE/L1 797 1014 55 849
INTRON_3 381514 TTTTTTTTTAAAAGTATGGGATCAATGTGGTTATGTTCAGACTGTAAATT 381563
v iv --- vi iv iv i i i i
C L1MD2_5end#LI 1014 TTTTGTTTTAGCAG---GCAATCAACCTGGTTGGGTTCAGGCCGCAAGTT 968
INTRON_3 381564 TGGTCTCATCTCCCATGCATGGTGGTTTCAATGTCAGTTCTGTTATTAAA 381613
iv v ivii i ii vi v i ? v i
C L1MD2_5end#LI 967 CCGACCAGCCTTCTGTGGGTTGTGGTTCCAATGTCAGTTCSGTTTTCAAA 918
INTRON_3 381614 G--------------TTTGAGTCTACCCAGTACATGTACCACTCAGAAAT 381649
-------------- i ii ii vi iii i i viii
C L1MD2_5end#LI 917 GCCTTTGCAGTGCTATTCGGATCTGTCCCATGTGTGTGCCACCCAGTGGC 868
INTRON_3 381650 TAGTTTGGGACTTGGCCCATGGTTTTATCACAT--TTCAATTCTTAAATA 381697
i i i v vi i - vii -- i i vv
C L1MD2_5end#LI 867 CAGTCTGGGACCTGGGCAGTGGTCT-ATCCTGTAGTTCAGTTCTCAAAGT 819
INTRON_3 381698 CTTTTCTGTGCTTCTTTGGGTC 381719
vv i vi v
C L1MD2_5end#LI 818 CTTTGGTATGCTGTTTAGGGTC 797
Matrix = 20p37g.matrix
Transitions / transversions = 1.95 (43 / 22)
Gap_init rate = 0.02 (4 / 205), avg. gap size = 5.00 (20 / 4)
412 31.48 1.23 0.61 INTRON_3 381662 381824 18357 C L1MEf_5end LINE/L1 346 509 1708 850
INTRON_3 381662 TGGCCCATGGTTTTA-TCACATTTCAATTCTTAAATACTTTTCTGTGCTT 381710
v vi iv - v v i i vv v i v
C L1MEf_5end#LI 509 TGGGCGGTGGTTCAAATCTCAGTTCAGTTCTCAAAGCCTTTGCTATGCTG 460
INTRON_3 381711 CTTTGGGTCTCTTTTGCCTGCAGGTAACTCCAGCATGATCCTGGTACTTC 381760
? v iiii viiiiv i i vi vi ? v v v
C L1MEf_5end#LI 459 NTTTGGGTCTGTCCCACACATGCGCAGCTCAGGGGTNAGCCTGGGACTTG 410
INTRON_3 381761 TGCTGTTTCATATCCAGAATTAGATGAGTCCCCTTCTCCAGTGTTCTCTT 381810
i? v iv iv v - ivi i
C L1MEf_5end#LI 409 TGTNGGTTCATACACAGAATTAGGGGATTCCCCT-CTCCAGCTCTCTCCT 361
INTRON_3 381811 CT-TGGGAATCCTCC 381824
- v i i
C L1MEf_5end#LI 360 CTCTGGGATTTCCCC 346
Matrix = 20p37g.matrix
Transitions / transversions = 1.09 (25 / 23)
Gap_init rate = 0.02 (3 / 162), avg. gap size = 1.00 (3 / 3)
+ 332 34.5 3.4 8.3 INTRON_3 381836 382012 (18169) C L1MEf LINE/L1 (5834) 806 638 531
ANNOTATION EVIDENCE:
332 34.50 3.39 8.28 INTRON_3 381836 382012 18169 C L1MEf_5end LINE/L1 198 366 1851 796
INTRON_3 381836 TTTTCTCTCTG---TCTCTCTCCTTCTCTCTGGATTTAAGAGACT--TTT 381880
i i --- i i i viv i v iiv i i i--
C L1MEf_5end#LI 366 TCTCCTCTCTGGGATTTCCCCCACACTCTCCGGCTCCCAGGGGCCCCTTT 317
INTRON_3 381881 CCTCACTTCTTTTGTTCCAAATATATTATCTTTTTTCTCAAGGTTTTAGC 381930
i i iv i i? v- i v v vivv i ?- ii
C L1MEf_5end#LI 316 TCCCGGTTCCTCNGG-CCAGAAAGATGGGGTTTCTN-TCGGGGTTTTAGC 269
INTRON_3 381931 ACCCCCCACCCCCCACCCCCGCCAGGTTTTCAGTTCTGTGAGACTGGGAC 381980
vv v i v i --iv i v------- i i -- i
C L1MEf_5end#LI 268 TGCCCGCGCCGCTC--TGCTGCA-------CAGCTCCGTGA--CTGGGGC 230
INTRON_3 381981 TTCTTTAGAGGCAAA-CTGGTGAGAAAGAGGGA 382012
iv ii v i - i - i
C L1MEf_5end#LI 229 CGCCCTCGGGGCAAAGCCGG-GAGAAAGAAGGA 198
Matrix = Unknown
Transitions / transversions = 1.84 (35 / 19)
Gap_init rate = 0.05 (9 / 176), avg. gap size = 2.22 (20 / 9)
+ 363 15.4 0.0 0.0 INTRON_3 382204 382268 (17913) + G-rich Low_complexity 3 67 (0) 536
ANNOTATION EVIDENCE:
363 15.38 0.00 0.00 INTRON_3 382204 382268 17913 + (GGGGA)n Simple_repeat 3 67 113 869
INTRON_3 382204 GGAAAGGAGAGGAGAAGAGGGGAGGGGAGGGGAAGACAGGGGAGAGGAGG 382253
ii i ii i iv i
(GGGGA)n#Simp 3 GGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGG 52
INTRON_3 382254 GGAGGGGAGGGAAGG 382268
i
(GGGGA)n#Simp 53 GGAGGGGAGGGGAGG 67
Matrix = Unknown
Transitions / transversions = 9.00 (9 / 1)
Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0)
+ 864 31.5 2.1 2.7 INTRON_3 382281 382613 (17568) C L1MEf LINE/L1 (5853) 787 457 531
ANNOTATION EVIDENCE:
864 31.49 2.10 2.72 INTRON_3 382281 382613 17568 C L1MEf_5end LINE/L1 17 347 1870 851
INTRON_3 382281 CTCAAACTGTCTGGCATGTTGCGGGGGGCCTCTTTTTCTGATTC-TATGG 382329
i v v i ---- v vi i i i i - v?
C L1MEf_5end#LI 347 CCCACACTCTCCGGC----TCCCAGGGGCCCCTTTTCCCGGTTCCTCNGG 302
INTRON_3 382330 CTAGAAATAATGCTTTGTTTTTCAGAATTTCTACTTTTAGCGCC----TA 382375
i -i vvv v i ? i ii ivi viiv ---- i
C L1MEf_5end#LI 301 CCAGAAA-GATGGGGTTTCTNTCGGGGTTTTAGCTGCCCGCGCCGCTCTG 253
INTRON_3 382376 TCACACTGTTCTGCCACTTGGGCCTTATCTTAGTCAAAGACTGGAGGTAA 382425
iii v i i iv v viviiivi v v v --
C L1MEf_5end#LI 252 CTGCACAGCTCCGTGACTGGGGCCGCCCTCGGGGCAAAGCCGGGAG--AA 205
INTRON_3 382426 AGGAAGAACATAAGACCATGAAACTCACCTTCATTACAGATCA-TTGTCC 382474
i i v - i iiv vi i -i i?i - v
C L1MEf_5end#LI 204 AGAAGGAAAA-AAAACTGGGAAACTCACCGCCGT-GCGNGTCACTTCTCC 157
INTRON_3 382475 AGATTGTAAGTTAAGTCCCCAGTCCGCTTGCTACTGTTTACTTTTCGGAG 382524
ii v i v ivvv v i i i vi i
C L1MEf_5end#LI 156 AAGTTTTGACTCCCCTCCACAATCTGCCTGCTTTTGTTTACTTTTCAGAG 107
INTRON_3 382525 TTCTTAGGTCATTGCCATTTGTATTCTGTCCAGAGATTTTAGTTGTAGTC 382574
i i vi iv i v i
C L1MEf_5end#LI 106 TCCTCAGGTAGTTGCTTTTTGTATTTTGTCCAGAGTTTTTAGTTGTAATC 57
INTRON_3 382575 AGTATGAAATATACA-CTGTAGTTGGCTTACTCCATATTG 382613
iv i v vi- v i v?
C L1MEf_5end#LI 56 AGTGGGAGAGATAGGGCTGTAGTGGGCTTACTCCGTCNTG 17
Matrix = 20p37g.matrix
Transitions / transversions = 1.45 (58 / 40)
Gap_init rate = 0.03 (9 / 332), avg. gap size = 1.78 (16 / 9)
+ 996 16.2 4.3 0.0 INTRON_3 382708 382917 (17264) + L1M3 LINE/L1 2994 3212 (2928) 537
ANNOTATION EVIDENCE:
996 16.19 4.29 0.00 INTRON_3 382708 382917 17264 + L1M3_orf2 LINE/L1 885 1103 2185 852
INTRON_3 382708 AAGAAGGAGGTTTATAGTAATAAATGCCTACATTAAGAAAAAAGAAAGAT 382757
i i i i i
L1M3_orf2#LIN 885 AAGAGGGAAGTTTATAGTGATAAATGCCTACATTAAAAAAGAAGAAAGAT 934
INTRON_3 382758 CTTAA---------TGAACTTTTTATCTCAAGGAATTAGAAAAAGAAGAA 382798
i ---------iv vi i i
L1M3_orf2#LIN 935 CTCAAATAAACAACCTAACTTTACACCTCAAGGAACTAGAAAAAGAAGAA 984
INTRON_3 382799 CAAATGAAACCGAAAGTTAGCAGAAGGAAGGAAATAATAAAGACGAGAAC 382848
iv i v iv i
L1M3_orf2#LIN 985 CAAACTAAGCCCAAAGTTAGCAGAAGGAAGGAAATAATAAAGATTAGAGC 1034
INTRON_3 382849 AGAAGTAAATGAAATAGAGATTAAGAAACAAATAGAAAAGATCAAGAAAG 382898
i i i ? ii vv i vi i
L1M3_orf2#LIN 1035 AGAAATAAATAAAATAGAAANTAGAAAAACAATAGAAAAAATCAACGAAA 1084
INTRON_3 382899 CTAGGAGTTGCTTTGTTGA 382917
i v v
L1M3_orf2#LIN 1085 CTAAGAGTTGGTTTTTTGA 1103
Matrix = 20p37g.matrix
Transitions / transversions = 2.30 (23 / 10)
Gap_init rate = 0.00 (1 / 209), avg. gap size = 9.00 (9 / 1)
+ 500 15.3 0.0 0.0 INTRON_3 382920 383017 (17164) C L1M3 LINE/L1 (2920) 3220 3123 537
ANNOTATION EVIDENCE:
500 15.31 0.00 0.00 INTRON_3 382920 383017 17164 C L1M3_orf2 LINE/L1 1014 1111 2177 853
INTRON_3 382920 TTATCTTTTCAAAAAGCCAACTCTTAGCTTCCTTGATCTTTTCTACGGGT 382969
? i i v i iv v
C L1M3_orf2#LIN 1111 TNATCTTTTCAAAAAACCAACTCTTAGTTTCGTTGATTTTTTCTATTGTT 1062
INTRON_3 382970 TTTCTAATGTCTATTTCATTTATTTCTGTTCTCATTTTTATTATTCCC 383017
? v i i v i i
C L1M3_orf2#LIN 1061 TTTCTANTTTCTATTTTATTTATTTCTGCTCTAATCTTTATTATTTCC 1014
Matrix = 20p37g.matrix
Transitions / transversions = 1.60 (8 / 5)
Gap_init rate = 0.00 (0 / 97), avg. gap size = 0.0 (0 / 0)
+ 8489 17.2 2.4 3.5 INTRON_3 383021 384890 (15291) + L1M3 LINE/L1 3238 5087 (1053) 537 *
ANNOTATION EVIDENCE:
8489 17.23 2.41 3.51 INTRON_3 383021 384890 15291 + L1M3_orf2 LINE/L1 1129 2978 310 854
INTRON_3 383021 TTAGTTAGACTAAACAAAAAAGAGAGAAGACT----TAAATAAAATTATA 383066
i i-- i ---- i v
L1M3_orf2#LIN 1129 TTAGCTAGACTAAG--AAAAAAAGAGAAGACTCAAATAAATAAAATCAGA 1176
INTRON_3 383067 AAGGAAAAAGGGGATGTTACAACTGATACCACAGAAATACAAAGGATTAT 383116
v i i ii i v i
L1M3_orf2#LIN 1177 AATGAAAGAGGAGACATTACAACTGATGCCACAGAAATAAAAAGGATCAT 1226
INTRON_3 383117 AAGAGACTACTACAAGCAATTGTACACCA-CATATTGGATAACCTAGACA 383165
ii i i i - v vi
L1M3_orf2#LIN 1227 AAGAGACTACTATGAACAATTATACGCCAACAAATTGGATAACCTAGAAG 1276
INTRON_3 383166 AAATGGAGAAATTTCTGGAAGCATACAACCTATGAAGATTAAACCATAAA 383215
v i i i iv i ? i i
L1M3_orf2#LIN 1277 AAATGGATAAATTCCTAGAAACATACAACCTACCAAGACTNAATCATGAA 1326
INTRON_3 383216 CAAATAGAAAACCTGAACAGACCAAAAATAAGTAAG---ATTC--TCAGT 383260
v ? v i? --- v--
L1M3_orf2#LIN 1327 GAAATAGAAAACCTGAACAGACCNATAACNAGTAAGGAGATTGAATCAGT 1376
INTRON_3 383261 TGTCAAAAACCTTCTAACAAAGTAAAGCCCAGGACCAGATGGATTCACAA 383310
vi i i v i v vi
L1M3_orf2#LIN 1377 AATCAAAAACCTCCCAACAAAGAAAAGTCCAGGACCAGATGGCTTCACTG 1426
INTRON_3 383311 GTGAACTCTACCAAACATTTAAAGAA---TTAATACCATTCCTTCTCAAA 383357
i --- i v
L1M3_orf2#LIN 1427 GTGAATTCTACCAAACATTTAAAGAAGAATTAATGCCAATCCTTCTCAAA 1476
INTRON_3 383358 CTCATCCAAAAAATTGAAGAGGAGGGAACACTTTCAAAGCCATTTTATGA 383407
v i vi
L1M3_orf2#LIN 1477 CTCTTCCAAAAAATTGAAGAGGAGGGAACACTTCCAAACTCATTTTATGA 1526
INTRON_3 383408 GACCAACTTTAGTGATACCAAAGCTCATATCAAAGACCTGATACCAAAGC 383457
i i v ------------------- -----
L1M3_orf2#LIN 1527 GGCCAGCATTA-------------------C-----CCTGATACCAAAGC 1552
INTRON_3 383458 TGGACAAGGTCACTACAAGAAAAGAAAATTATAGGAAAGTATCACTGATG 383507
ii i v ? i i vv i v
L1M3_orf2#LIN 1553 CAGACAAAGACACNACAAGAAAAGAAAACTACAGGCCAATATCCCTGATG 1602
INTRON_3 383508 GACAAAAATGCAAAAATTCTCAGTAAAATACTAGCAAAGCAAATTCAACA 383557
i i v i i ii v i
L1M3_orf2#LIN 1603 AATATAGATGCAAAAATCCTCAACAAAATACTAGCAAACCGAATTCAACA 1652
INTRON_3 383558 GCACAGTAAGAGACTAATTTATCATGATCAAGTGAGATTTATTCCGAAGA 383607
v i iv v vi i i i i vii
L1M3_orf2#LIN 1653 GCACATTAAAAGGATCATACACCATGACCAAGTGGGATTTATCCCTGGGA 1702
INTRON_3 383608 TGCAAG-ATG-TTCAGTATACACAAATCACTAAATGTGATATACCATATT 383655
- - ii iv v v i i
L1M3_orf2#LIN 1703 TGCAAGGATGGTTCAACATACGAAAATCAATCAATGTGATACACCACATT 1752
INTRON_3 383656 AACAGACTAAAGGACAAAAACCATGTGATCATCTCAATAGATGCAGAAAA 383705
v i i i ii
L1M3_orf2#LIN 1753 AACAGAATGAAGGATAAAAATCACATGATCATCTCAATAGATGCAGAAAA 1802
INTRON_3 383706 ATTATTGGATAAAATTCAACATTCTTT-ATGATAAAA-CTCTAAACAAAT 383753
vi v i i - - v i
L1M3_orf2#LIN 1803 AGCATTTGACAAAATTCAACATCCTTTCATGATAAAAACTCTCAACAAAC 1852
INTRON_3 383754 T-GATATACAAAGAATGTATCTCAACATAATAAAGGTCATATATGACATG 383802
- iv v i ?v i i v v
L1M3_orf2#LIN 1853 TAGGAATAGAAGGAANTTACCTCAACATAATAAAGGCCATATATGAAAAG 1902
INTRON_3 383803 CCCACAGCCAAAATCATATTCAACAGTAAAAAGCCAAAAGCTTTTCTTCT 383852
i v i ii i i ii i
L1M3_orf2#LIN 1903 CCCACAGCTAACATCATACTCAATGGTGAAAAACTGAAAGCTTTTCCTCT 1952
INTRON_3 383853 AAGATTAGTAACAAGACAAGGATGTCCATTCTTATCACTTATATTCAACA 383902
i v i i i i i v
L1M3_orf2#LIN 1953 AAGATCAGGAACAAGGCAAGGATGCCCACTCTCACCACTTCTATTCAACA 2002
INTRON_3 383903 TAGTACTAGAAGTCCTACCCAGACCAAGTGGACAACAAAAAAGAAATGAA 383952
i v v v i i -i i
L1M3_orf2#LIN 2003 TAGTACTGGAAGTCCTAGCCAGAGCAATTAGGCAA-GAAAAAGAAATAAA 2051
INTRON_3 383953 ACCTGCCAAGGCTAAATCATAAACAAATTATTAATAAAAAGGAAAAAGTG 384002
-------- --- ----- iivv vi i i v v -
L1M3_orf2#LIN 2052 A--------GGC---ATC-----CAAATCGGAAAGGAAGAAGTAAAATT- 2084
INTRON_3 384003 AAATTGTCTGTTTACAGATGACATCGTTTTATATAGGGAAAACCCTAAAT 384052
-- i-i i vi i ?vi v
L1M3_orf2#LIN 2085 --ATC-CCTGTTTGCAGATGACATGATCTTATATNTAGAAAACCCTAAAG 2131
INTRON_3 384053 ACTTCACTAAAAAATTGTTAGAATTAATAAATGAATTCAGTA------CA 384096
i i ?i i i ------
L1M3_orf2#LIN 2132 ACTCCACCAAAAANCTGTTAGAACTAATAAATAAATTCAGTAAAGTTGCA 2181
INTRON_3 384097 GGTTGCAGGATATAAAAT-CAACATACAAATATCAGTAGTGCTTATATA- 384144
v i ii -i v - v vv iv ii----- vii i -
L1M3_orf2#LIN 2182 GGATACAAAAT-CAACATACAAAAATCAGTTGC-----GTTTCTATACAC 2225
INTRON_3 384145 TATTAACAA-CAAGCT-ATCTGAAAAT---GATATTTTTTAAAACCCCAT 384189
vi - ? v - vvv i --- v ------ v i
L1M3_orf2#LIN 2226 TAACAACAAACNATCTGAAAAGGAAATTAAGAAA------ACAATCCCAT 2269
INTRON_3 384190 T-ACAATAGCATCA----GAACAAAATACTTAAGAATAAAATTAACCAAA 384234
- ---- i i v i
L1M3_orf2#LIN 2270 TTACAATAGCATCAAAAAGAATAAAATACTTAGGAATAAACTTAACCAAG 2319
INTRON_3 384235 AAG-TGAAAGATTTGCATACTAAAAACTATAAAACATTAATGAAAGAAAT 384283
i - i i i i i i
L1M3_orf2#LIN 2320 GAGGTGAAAGACTTGTACACTGAAAACTACAAAACATTGATGAAAGAAAT 2369
INTRON_3 384284 -AAATAAGATACAAATAAATGGGAAGATA-CCCATGTTTATGAATTCAAA 384331
- v i i i - i i i vi
L1M3_orf2#LIN 2370 TAAAGAAGACACAAATAAATGGAAAGACATCCCGTGTTCATGGATTGGAA 2419
INTRON_3 384332 ----TAATATTGTTAAAATGTCTCTACTACAAAAAGCCATCTACAGATTC 384377
---- iv vv v
L1M3_orf2#LIN 2420 GAATTAATATTGTTAAAATGTCCATACTACCCAAAGCAATCTACAGATTC 2469
INTRON_3 384378 AATGCAATTCATATCAAAATTCCAATGGCATTTTTCACAGAAATAGTAAA 384427
i v i i v
L1M3_orf2#LIN 2470 AATGCAATCCCTATCAAAATCCCAATGGCATTTTTTACAGAAATAGAAAA 2519
INTRON_3 384428 A-CAATTCTAAAATTCACATGGAACCACAAAAGACCCTGAATAGTCAAAG 384476
- i i ii i i
L1M3_orf2#LIN 2520 AACAATCCTAAAATTCATATGGAACCACAAAAGACCCCAAATAGCCAAAA 2569
INTRON_3 384477 CAATCTTGAGCAAGAAGAACAAAGTTGGAGGCATCATACTCTCTGATTTC 384526
v i i ii i
L1M3_orf2#LIN 2570 CAATCTTGAGAAAGAAGAACAAAGCTGGAGGCATCACACTTCCTGACTTC 2619
INTRON_3 384527 AAAATATTATTACAAAGCTAAGCTAATAAAAAGAGAATGGTTCTGGCATA 384576
i - viv v v v v
L1M3_orf2#LIN 2620 AAAACAT-ATTACAAAGCTATAGTAATCAAAACAGTATGGTACTGGCATA 2668
INTRON_3 384577 AAAATAGACATATAGATCAATGTAACAGAACAGAGAACCCAGCAATAAAC 384626
i i v i i v
L1M3_orf2#LIN 2669 AAGATAGACATATAGACCAATGGAACAGAATAGAGAGCCCAGAAATAAAC 2718
INTRON_3 384627 CCACACATTTTTAGTCAACTGATCTTTAACAACGGTTCTGAGAACTCACA 384676
i v vii ii v v ii iv
L1M3_orf2#LIN 2719 CCACGCATATACGGTCAACTGATCTTCGACAAGGGTGCCAAGAATACACA 2768
INTRON_3 384677 ATGGGGAAGAGATAATGTCTTTAATGTATGATATTGGGATA-CTGGATAT 384725
ii i v i iiv i i v -
L1M3_orf2#LIN 2769 ATGGGGAAAGGATAGTCTCTTCAACAAATGGTGTTGGGAAAACTGGATAT 2818
INTRON_3 384726 ACACACACTGAGGAATGAAATTGGATCCTTATTTAACACCATATGCAAAA 384775
v ii v i i i v ii
L1M3_orf2#LIN 2819 CCACATGCAGAAGAATGAAATTGGACCCTTATCTTACACCATACACAAAA 2868
INTRON_3 384776 TTTAATTCAAAATGGATGAAAAACTAAAACAATAAGACCCAAAACTTGTA 384825
v i i v i v ii- ii -
L1M3_orf2#LIN 2869 ATCAACTCAAAATGGATTAAAGACTTAAATG-TAAGACCTGAAACT-GTA 2916
INTRON_3 384826 AAATTGCTAGAAGATATCACAGGGGAAAAGTGTCTTGACATTGGTCTGGG 384875
i v v v i iv v v
L1M3_orf2#LIN 2917 AAACTCCTAGAAGAAAACATAGGGGAAAAGCTTCATGACATTGGTCTTGG 2966
INTRON_3 384876 CAATTACCTTTTCTT 384890
v ---
L1M3_orf2#LIN 2967 CAATGA---TTTCTT 2978
Matrix = 20p37g.matrix
Transitions / transversions = 1.81 (195 / 108)
Gap_init rate = 0.02 (40 / 1869), avg. gap size = 2.75 (110 / 40)
+18416 14.3 0.9 1.0 INTRON_3 384884 388218 (11963) C L1PA15 LINE/L1 (4) 6781 3452 538
ANNOTATION EVIDENCE:
6066 12.57 0.11 0.33 INTRON_3 384884 385793 14388 C L1PA15_3end LINE/L1 1 908 4 855
INTRON_3 384884 TTTTCTTCCAACTTTTATTTTAGGTTCAGAGGAGACACGTGCAGGTTTGT 384933
i ii i -v i
C L1PA15_3end#L 908 TTTTTTTTTAACTTTTATTTTAGGTTCAGGGG-TACATGTGCAGGTTTGT 860
INTRON_3 384934 TGCATGGGTAAATTGTGTGTCATGAGTATTTGGCATACAAATTATTTCAT 384983
ii i i i i vi ii i i
C L1PA15_3end#L 859 TATATAGGTAAATTGCGTGTCACGGGGGTTTGGTGTACAGATTATTTCGT 810
INTRON_3 384984 CACTCAGGTAATAAGCATAGCACCCAATAGGTAGTTTTTCAATCCTCACC 385033
i i i i
C L1PA15_3end#L 809 CACCCAGGTAATAAGCATAGTACCCGATAGGTAGTTTTTCGATCCTCACC 760
INTRON_3 385034 CTCCTCCCACACTCTACCCTCAAGTAGGCCCTGGTATCTATTTTTCCCTT 385083
v i i i i v
C L1PA15_3end#L 759 CTCCTCCCACCCTCCACCCTCAAGTAGGCCCCGGTGTCTGTTGTTCCCTT 710
INTRON_3 385084 CTTTGTGTCCATGTATACTCAGTGTTTAGCAATAACATGTCAGTGAGAAT 385133
i i vviv v i v i
C L1PA15_3end#L 709 CTTTGTGTCCATGTGTACTCAATGTTTAGCTCCCACTTATAAGTGAGAAC 660
INTRON_3 385134 GTGCAGTGTTTGGTTTTCTGTTCCTGCATTAATTCACTTAGGATAATGGT 385183
i i i i i i i
C L1PA15_3end#L 659 ATGCGGTATTTGGTTTTCTGTTCCTGCGTTAGTTCGCTTAGGATAATGGC 610
INTRON_3 385184 CTCCAGTTCTATCCATGTTGCTGCAAAGGACATGAGCTCATTCTTTTT-G 385232
i i v i -i
C L1PA15_3end#L 609 CTCCAGCTCCATCCATGTTGCTGCAAAGGACATGATCTCGTTCTTTTTTA 560
INTRON_3 385233 TGGCTTCATACTATTTCATGCTGTGTATATACCACATTTTCTTTATCCAG 385282
v i v i v i i
C L1PA15_3end#L 559 TGGCTGCGTAGTATTCCATGGTGTATATGTACCACATTTTCTTTATCCAG 510
INTRON_3 385283 TCCACCATTGATGGGCATTTAGGTTGATTCCATGTCTTCACTATTGTGAC 385332
i i ii v
C L1PA15_3end#L 509 TCTACCGTTGATGGGCATTTAGGTTGATTCCATGTCTTTGCTATTGTGAA 460
INTRON_3 385333 TAGCACTGCATTGAACATATGCATGCATGTATCTTTATGGTAGAATGATT 385382
ii iv i i i
C L1PA15_3end#L 459 TAGTGCTGCGATGAACATACGCGTGCATGTGTCTTTATGGTAGAATGATT 410
INTRON_3 385383 TATATTCCTTTGGGTGTATACCCAGTAAAGGGATTACTGTGTCAAGTTCT 385432
i i v i v i i vv
C L1PA15_3end#L 409 TATATTCCTTTGGGTATATACCCAATAATGGGATTGCTGGGTCGAATGGT 360
INTRON_3 385433 AGTTCTGTTTTGAATTCTTTGAGAAATCTCCAAACTGCTTCCCACAATGG 385482
i i v i
C L1PA15_3end#L 359 AGTTCTGTTTTAAGTTCTTTGAGAAATCGCCAAACTGCTTTCCACAATGG 310
INTRON_3 385483 CTGAACTAATTTGCATTCCTACCAACAGTGTATACGCATTCGTTTTTCTC 385532
i i i v i vi
C L1PA15_3end#L 309 CTGAACTAATTTACATTCCCACCAGCAGTGTATAAGCGTTCCCTTTTCTC 260
INTRON_3 385533 CGCAAGCTCACCAGCATCTGTTATTTTTTGACATTTTAATAACAGCCATT 385582
v i v i
C L1PA15_3end#L 259 CGCAACCTCGCCAGCATCTGTTATTTTTTGACTTTTTAATAATAGCCATT 210
INTRON_3 385583 CTGCCTGGTATGATATGATGTCTCATTGTGGTTTTGATTTGCATTTCTCT 385632
v i v i i
C L1PA15_3end#L 209 CTGACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCT 160
INTRON_3 385633 AATGATTAGCAATGTGTTGAGCATTTCTTTATATGCTTGTGGGCCATGTG 385682
ii -- i i v i
C L1PA15_3end#L 159 AATGATTAGTGATGT--TGAGCATTTTTTCATATGCTTGTTGGCCACGTG 112
INTRON_3 385683 TATGTCTTCTTTTGAGAAGTGTCTGCTCATGCCCTTTGGCCAATTTTTAG 385732
i i v v i
C L1PA15_3end#L 111 TATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTAA 62
INTRON_3 385733 TGGGATTGTTTGGCTTTTGCTTGTTAATTTGTTCAAGTTCCTTATATATT 385782
i vi i v
C L1PA15_3end#L 61 TGGGGTTGTTTGTTTTTTGCTTGTTAATTTGTTTAAGTTCCTTATAGATT 12
INTRON_3 385783 CTGGATATTAG 385793
C L1PA15_3end#L 11 CTGGATATTAG 1
Matrix = 20p37g.matrix
Transitions / transversions = 2.68 (83 / 31)
Gap_init rate = 0.00 (3 / 909), avg. gap size = 1.33 (4 / 3)
18416 14.95 1.22 1.22 INTRON_3 385647 388218 11963 C L1P4_orf2 LINE/L1 723 3291 3 856
INTRON_3 385647 TGTTGAGCATTTCTTTATATGCTTGTGGGCCATGTGTATGTCTTCTTTTG 385696
i i i v iiv
C L1P4_orf2#LIN 3291 TGTTGAGCATTTTTTCATATGTTTGTTGGCCGCTTGTATGTCTTCTTTTG 3242
INTRON_3 385697 AGAAGTGTCTGCTCATGCCCTTTGGCCAATTTTTAGTGGGATTGTTTGGC 385746
i i i v v i i i vi
C L1P4_orf2#LIN 3241 AGAAGTGTCTGTTCATGTCTTTTGCCCACTTTTTAATGGGGTTATTTGTT 3192
INTRON_3 385747 TTTTGCTTGTTAATTTGTTCAAGTTCCTTATATATTCTGGATATTAGACC 385796
i v i v
C L1P4_orf2#LIN 3191 TTTTGCTTGTTGAATTGTTTAAGTTCCTTATAGATTCTGGATATTAGACC 3142
INTRON_3 385797 TTTTTTGGATACATAGATTGCAAATATTCTCTCCCATTCTGTAGGTTGTC 385846
v i i v i i
C L1P4_orf2#LIN 3141 TTTGTCGGATGCATAGTTTGCGAATATTTTCTCCCATTCTGTAGGTTGTC 3092
INTRON_3 385847 TGTTT-----GCTGATAGTTCATTTTGCTGTGCAGAAGCTCTTTAGTTTA 385891
----- i iv
C L1P4_orf2#LIN 3091 TGTTTACTCTGTTGATAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTA 3042
INTRON_3 385892 ATTAGGTCCCATTTGTCAATTTTTTTTTTT-TTGTAATTGCTTTTGGAGT 385940
i v - i ii v
C L1P4_orf2#LIN 3041 ATTAGGTCCCACTTGTCAATTTTTGTTTTTGTTGCAATTGCTTTTGAGGA 2992
INTRON_3 385941 TTTCATCATGAAATCTTTGCCAGGGCATATGTCCAGAATGCTATATCCTA 385990
i vi i v v i vv v i v
C L1P4_orf2#LIN 2991 CTTAGTCATAAATTCTTTCCCAAGGCCGATGTCCAGAATGGTGTTTCCTA 2942
INTRON_3 385991 GGTCTTTTTCTAGGGTTTTTATAGTTCTACATTTTACATTTACATCTTTA 386040
i i i i iv vi i v
C L1P4_orf2#LIN 2941 GGTTTTCTTCTAGGATTCTTATAGTTTGAGGTCTTACATTTAAATCTTTA 2892
INTRON_3 386041 ACCCATCTTGAGTTGATTTTT-TATATGGTGGAAGGAAGGGGTTCAGTTT 386089
i i - i v i
C L1P4_orf2#LIN 2891 ATCCATCTTGAGTTAATTTTTGTATATGGTGAAAGGTAGGGGTCCAGTTT 2842
INTRON_3 386090 CAATCTTCTGCATATGGCTAGCCAGTTATCCCAACACCAGTTATTGAATA 386139
v i i v
C L1P4_orf2#LIN 2841 CATTCTTCTGCATATGGCTAGCCAGCTATCCCAGCACCATTTATTGAATA 2792
INTRON_3 386140 GGCAGTCTTTTCCTCATTGCTTGTTTTTGTCAAGGTTGTTGAAAATTGGA 386189
v i i i i vv i i ii
C L1P4_orf2#LIN 2791 GGGAGTCCTTTCCCCATTGCTTATTTTTGTCGACTTTGTCGAAGATCAGA 2742
INTRON_3 386190 TGGTTGTAGATGTGCAGCTTTATTTCTCAGTATTGTAACC-ATTCCATTG 386238
i i ii vi vi v vi -i
C L1P4_orf2#LIN 2741 TGGCTGTAGGTGTGTGGCTTTATTTCTGGGTTCTCTATTCTGTTCCATTG 2692
INTRON_3 386239 GCCTATTTGTCAGTTTTTGTACCAGTACTGTGCTGTTTTGGTTTTTGTAG 386288
i v v ii vi
C L1P4_orf2#LIN 2691 GTCTATGTGTCTGTTTTTGTACCAGTACCATGCTGTTTTGGTTACTGTAG 2642
INTRON_3 386289 CCTTGTAGCATAATTCAAAGTCAGGTAATGTGATGCCTCTGGCTTTGTTC 386338
i i i ii i i
C L1P4_orf2#LIN 2641 CCTTATAGTATAGTTTGAAGTCGGGTAATGTGATGCCTCCGGCTTTGTTC 2592
INTRON_3 386339 TTTTTGTTTAGGATTGCTTTGGCTATTTGGGTTCTTTCTTG-TTCCATAT 386387
i i i -
C L1P4_orf2#LIN 2591 TTTTTGCTTAGGATTGCTTTGGCTATTTGGGCTCTTTTTTGGTTCCATAT 2542
INTRON_3 386388 GAATTTTAAAATATTTTTTTCTAATTCTGTGGAAAATGTCATTGGTAGTT 386437
i v i v
C L1P4_orf2#LIN 2541 GAATTTTAGAATAGTTTTTTCTAATTCTGTGAAAAATGACATTGGTAGTT 2492
INTRON_3 386438 TGATAGGAATAGCACTGGATCTGTAAATTGCTTTGGGCAGTATGGCCATT 386487
i i i
C L1P4_orf2#LIN 2491 TGATAGGAATAGCATTGAATCTGTAGATTGCTTTGGGCAGTATGGCCATT 2442
INTRON_3 386488 TTAACAATATTGATTCTTACTATCCATGTGCATGAAATGTTTTTCCACTT 386537
i v v v i i
C L1P4_orf2#LIN 2441 TTAACGATATTGATTCTTCCAATCCATGAGCATGGAATGTTTTTCCATTT 2392
INTRON_3 386538 ATTAATATTTGTGTTGTCTCTAATTTCTCTCAGCAGCGTTTCATAATTTT 386587
i ------ ii v i i i ii i i
C L1P4_orf2#LIN 2391 GTT------TGTGTCATCTATGATTTCTTTCAGCAGTGTTTTGTAGTTCT 2348
INTRON_3 386588 TGGTGTAGAGATCTTTCATTTCTCTGGTTAGCTGTCTTCCTAGGTATTTT 386637
ivv ii ii v v
C L1P4_orf2#LIN 2347 CCTTGTAGAGATCTTTCACCTCCTTGGTTAGATGTATTCCTAGGTATTTT 2298
INTRON_3 386638 ATAATTTTTTTATGGCTATGGTGAATGGAATTGCATTTTTGATTTGGCTC 386687
-- i v i i i i
C L1P4_orf2#LIN 2297 AT--TTTTTTTGTGGCTATTGTAAATGGGATTGCGTTCTTGATTTGGCTC 2250
INTRON_3 386688 TCAGCTTGGACAATGTTGGTGTATAGAAATCCTACTGATTTTTGTATATT 386737
i iv i v i
C L1P4_orf2#LIN 2249 TCAGCTTGAACGTTATTGGTGTATAGAAATGCTACTGATTTTTGTACATT 2200
INTRON_3 386738 GACTTTGTATCCTGAAACTTTACTGAAGTTGTTTATCCATTCCAGGAGCC 386787
i i vi
C L1P4_orf2#LIN 2199 GATTTTGTATCCTGAAACTTTACTGAAGTCGTTTATCAGTTCCAGGAGCC 2150
INTRON_3 386788 TTTTGGTGGAGTCTTTAGGGTTTTCTAGGTGTAGAATCATATTGTCTGTG 386837
i i ii v i
C L1P4_orf2#LIN 2149 TTTTGGCGGAGTCTTTAGGGTTTTCTAGGTATAGAATCATATCATCAGCG 2100
INTRON_3 386838 AAGAGAGATCATTTGAACTTCCTCACTTCTTATTTAGATGCATTTTGTTT 386887
vi - i vi i i v i
C L1P4_orf2#LIN 2099 AAGAGAGATAGTTTGA-CTTCTTCTTTTCCTATTTGGATGCCTTTTATTT 2051
INTRON_3 386888 CTTTCCCTTATCTGATTGCTCTGACTAGGACTTCCAGTACTATGTTGAAT 386937
i ii i
C L1P4_orf2#LIN 2050 CTTTCTCTTGCCTGATTGCTCTGGCTAGGACTTCCAGTACTATGTTGAAT 2001
INTRON_3 386938 AGAGGTGCTAAGAGTGGCCATTCTTATCTTGTTCTGGTTCTCAAGGGAAA 386987
ii v i v i i ii i
C L1P4_orf2#LIN 2000 AGGAGTGGTGAGAGTGGGCATCCTTGTCTTGTTCCAGTTCTCAAGGGGAA 1951
INTRON_3 386988 TGCTTCTAGCTTTTGTCCATTCAATATATTACTGGCCGTGGGTTTGCCAT 387037
i i i i iv ii i i
C L1P4_orf2#LIN 1950 TGCTTCCAGCTTTTGCCCGTTCAGTATGATGTTGGCTGTGGGTTTGTCAT 1901
INTRON_3 387038 AGATGGCTCTTATTATTTTGAGATATGTTTCTTTGATGCCTACTTTGTTG 387087
i i i v ?
C L1P4_orf2#LIN 1900 AGATGGCTCTTATTATTTTGAGGTATGTTCCTTCGATGCCTAGTTTNTTG 1851
INTRON_3 387088 AGCATGTTTAACATGAAGG-ATGTTGAATTTTATGGAAAGCCTTTTCTGT 387136
vi v v - i v i i i
C L1P4_orf2#LIN 1850 AGGGTTTTTATCATGAAGGGATGTTGGATTTTATCGAAAGCTTTTTCCGC 1801
INTRON_3 387137 GTCTATTGAGATGATTATGTGGGTTTTGTTTTTTGTTCTATTTATGTGAT 387186
i i i v vi i i
C L1P4_orf2#LIN 1800 ATCTATTGAGATGATCATATGGTTTTTGTTTTTAATTCTGTTTATGTGGT 1751
INTRON_3 387187 GAATCACATTTATTAATTTGAGTAT--TAATATGCAATGTTGCATCCCAG 387234
i v -- i - i- iv
C L1P4_orf2#LIN 1750 GAATCACATTTATTGATTTGCGTATGTTGA-AC-CAACCTTGCATCCCAG 1703
INTRON_3 387235 GAATAAAGCCTACTTGATTGTGGTGGATTAACTTTTTGATGTGCTGCCAG 387284
i i i ii
C L1P4_orf2#LIN 1702 GAATGAAGCCTACTTGATCGTGGTGAATTAACTTTTTGATGTGCTGCTGG 1653
INTRON_3 387285 ATTAGTTAGTTTGCTAGTATTTTGTTGAGGATTTTTGCATCTATGTTCAT 387334
v --- i
C L1P4_orf2#LIN 1652 ATTCG---GTTTGCTAGTATTTTGTTGAGGATTTTTGCGTCTATGTTCAT 1606
INTRON_3 387335 TAGAGACATTGGCCTAAAGTTTCCTTTTTTTGTTTCCTTCCTCTGCCAGG 387384
i i i iv i i viv -- i
C L1P4_orf2#LIN 1605 CAGGGATATTGGCCTGTAGTTTTCTTTTTTCGTTGTGT--CTTTGCCAGG 1558
INTRON_3 387385 TTTTGGTACCAGAATGATTCTGGCCTCAT-GAATAAGTCAGAGAAGAGGT 387433
i ii v i - i i i i vi
C L1P4_orf2#LIN 1557 TTTTGGTATCAGGGTGATGCTGGCTTCATAGAATGAGTTAGGGAGGAGTC 1508
INTRON_3 387434 TCTTCTCCTGGATTTTTTGGAATAGTTTCAGTGTGATTGGTACCAACTCT 387483
i i v ivi i
C L1P4_orf2#LIN 1507 CCTCCTCCTCGATTTTTTGGAATAGTTTCAGTAGAATTGGTACCAGCTCT 1458
INTRON_3 387484 TCTTTATATGTTTGGTGGAATTTGGCTGTAAATCCTTCTGGTCCAGGGCT 387533
i i i i i i v i
C L1P4_orf2#LIN 1457 TCTTTGTACGTCTGGTAGAATTCGGCTGTGAATCCATCTGGTCCGGGGCT 1408
INTRON_3 387534 TTTTTGTTTTTTGGTTGGTAGGCTTGTAACTACTGATTGAATTTTAGAAC 387583
------ i v v i v ii
C L1P4_orf2#LIN 1407 TTTTT------TGGTTGGTAGGTTTTTTATTACTGATTCAATTTCGGAAC 1364
INTRON_3 387584 TTGTTATTGGTCTGTTCAGGGTTTCAATTTATTCCTTGTTCAGTCATGAC 387633
i v v vi i v iv
C L1P4_orf2#LIN 1363 TCGATATTGGTCTGTTCAGGGTTTCAATTTCTTCCTGATTCAATCTTGGG 1314
INTRON_3 387634 AGGTTGTATGTTTCCAGGAATTTATCC---TGGT-TAGGTTTCCTAGTTT 387679
i --- vv - i i
C L1P4_orf2#LIN 1313 AGGTTGTGTGTTTCCAGGAATTTATCCATTTCCTCTAGATTTTCTAGTTT 1264
INTRON_3 387680 GTGTGCATAGAGGTGTTCATAACAGTCTCTGAGGGTTTTTTTAATTATTA 387729
i i i v------
C L1P4_orf2#LIN 1263 GTGTGCATAGAGGTGTTCATAATAGTCTCTGAGGATCTTTTG------TA 1220
INTRON_3 387730 TTTCTGTAGGTTCAGTGGTAATGTCCCCTTTGTCATTTCTGATTGTGTTT 387779
i v i v v i
C L1P4_orf2#LIN 1219 TTTCTGTGGGATCGGTTGTAATGTCACCTTTGTCATTTCTGATTGTGCTT 1170
INTRON_3 387780 ATTTGGATCTTCTTTCTTCTTT-CTTTATTAGTCTAGCTAGTGGTCTATC 387828
i i - i i i i
C L1P4_orf2#LIN 1169 ATTTGGATCTTCTCTCTTTTTTTCTTTGTTAATCTAGCTAGCGGTCTATT 1120
INTRON_3 387829 AATCTTATT----CTTTCAAAAAACAAACTTTTAGTTTTATTGATATTTT 387874
i i ---- i v i ii vi
C L1P4_orf2#LIN 1119 GATCTTGTTTATCCTTTCAAAGAACCAACTTTTGGTTTCGTTGATTCTTT 1070
INTRON_3 387875 GTATGGTTTTTCACATCTCAATTTCATTCAGTTCAGCTCTGATTTTGGTT 387924
v iivi v i
C L1P4_orf2#LIN 1069 GTATGGATTTTTGGGTCTCAATTTCATTCAGTTCTGCTCTGATTTTAGTT 1020
INTRON_3 387925 ATTTATTTTCTTCTGCTAGCTTTGGCATT-GTTTTCTCTTGTTTTCCTTG 387973
v vi - vi i v
C L1P4_orf2#LIN 1019 ATTTCTTTTCTTCTGCTAGCTTTGGGGTTAGTTTGTTCTTGTTTTTCTAG 970
INTRON_3 387974 TTCCTCTAGGTGTGATGTTAGGTTGTTAATTTGAGGCATTTCTACCTTTT 388023
i i iiv v
C L1P4_orf2#LIN 969 TTCCTCTAGGTGTGATGTTAGATCGTTAATTTGAGATCTTTCTAACTTTT 920
INTRON_3 388024 TCATGTGGGTGTTTAGTGCTATAAACTTTCTTTTTAACACTGCTTTAACT 388073
v v i ii i i i vi
C L1P4_orf2#LIN 919 TGAGGTAGGCATTTAGCGCTATAAACTTTCCTCTTAACACTGCTTTTGCT 870
INTRON_3 388074 GTGTCC--GAGATTCTAGTATGTTGTATCTTTGTTTTCATTCGTCTTAAA 388121
ii -- i i i i ii i i
C L1P4_orf2#LIN 869 GCATCCCAGAGATTTTGGTATGTTGTGTCTCTGTTTTCATTTATTTCAAA 820
INTRON_3 388122 GAATTTCTTGATTTCTGCCTTAATTTCATTGCTTACCTAAAAGTCATTCG 388171
? i i i i i
C L1P4_orf2#LIN 819 NAATTTTTTGATTTCTGCCTTAATTTCGTTGTTTACCCAAAAGTCATTCA 770
INTRON_3 388172 GGAACAGGTTGTTTAATTTCCATGTAATTATATGGTTTTGAGAGATC 388218
i i i i
C L1P4_orf2#LIN 769 GGAGCAAGTTGTTTAATTTCCATGTAATTGTGTGGTTTTGAGAGATC 723
Matrix = 20p37g.matrix
Transitions / transversions = 2.54 (259 / 102)
Gap_init rate = 0.01 (23 / 2571), avg. gap size = 2.30 (53 / 23)
+ 2289 11.8 0.0 0.0 INTRON_3 388219 388522 (11659) C AluSc5 SINE/Alu (8) 304 1 539
ANNOTATION EVIDENCE:
2027 13.82 0.99 0.00 INTRON_3 388219 388522 11659 C AluSx SINE/Alu 1 307 5 789
INTRON_3 388219 TTTTTTGTTTGTTTTTTGTTTTTTTGAGACAGAATCTCTCTCTGTTGCC- 388267
v v v i i v i -
C AluSx#SINE/Al 307 TTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCC 258
INTRON_3 388268 AGGCTGGGGTGCAGTGGCACCATCTCGGCTCACTGCAACCTCCAACTCCC 388317
i i v iv
C AluSx#SINE/Al 257 AGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCC 208
INTRON_3 388318 TGGTTCAAGCAGTTCTCTCACCTCAGCCTCCCGAGTAGCTGGGATTACAG 388367
v ii iii
C AluSx#SINE/Al 207 GGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAG 158
INTRON_3 388368 GCATGTGCTACTACGCCCAACTAATTTTTGCATTTTTCATAGAGATGGGG 388417
ii i i i ii i vi i
C AluSx#SINE/Al 157 GCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGG 108
INTRON_3 388418 TTTCACCATGTTGGCCAGGATGGTCTCGATCTCCTGACATC--GTGATCT 388465
v v v -- i
C AluSx#SINE/Al 107 TTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCC 58
INTRON_3 388466 GCCCACCTGAAACTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCACA 388515
i viiv i i i
C AluSx#SINE/Al 57 GCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCG 8
INTRON_3 388516 CCCAGCC 388522
i
C AluSx#SINE/Al 7 CCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 2.23 (29 / 13)
Gap_init rate = 0.01 (2 / 303), avg. gap size = 1.50 (3 / 2)
+18416 17.3 1.4 1.9 INTRON_3 388523 390661 (9520) C L1PA15 LINE/L1 (3315) 3451 1322 538
ANNOTATION EVIDENCE:
18416 14.95 1.22 1.22 INTRON_3 388523 389240 10941 C L1P4_orf2 LINE/L1 1 722 2572 857
INTRON_3 388523 AAGAGATCTGTTTAGTATTCATTTCTATTTGTATTGCACTGTGGTCTGAG 388572
-------- vi i v v v i
C L1P4_orf2#LIN 722 --------TTCTTGGTATTGATTTCTATTTTTATTCCACTGTGGTCCGAG 681
INTRON_3 388573 AGGGTGGGTGATATGATTT-------TTTAAAATTTTTTTGAAAATTGTT 388615
vi v i ------- i -- v i v i
C L1P4_orf2#LIN 680 AGTATGGTTGGTATGATTTCGATTTTTTTGAA--TTTATTGAGACTTGCT 633
INTRON_3 388616 TTATGACCGAGCATGTCTTCTATTATAGAACATGTGCCATGTGCAAATGA 388665
i i vv v iv i ii v i i
C L1P4_orf2#LIN 632 TTATGGCTGAGCATGTGGTCGATCTTGGAGTATGTTCCGTGTGCAGATGA 583
INTRON_3 388666 GAAGAATGTATATTCCGTTGTTGTTGGGTGGAGTGTTCTGCAGATATCTG 388715
i v v i i i i
C L1P4_orf2#LIN 582 GAAGAATGTATATTCTGTGGTTGATGGGTGGAGTATTCTGTAGATGTCTA 533
INTRON_3 388716 TTAGGTCCATTTGGTCAAGTGCTGAGTTTTAGTTCCCAAATATCTTTGG- 388764
v ii i v - vi v v-
C L1P4_orf2#LIN 532 TTAGGTCCAATTGGTCAAGTGTCGAATTTAAGT-CCAGAATTTCTTTGTT 484
INTRON_3 388765 AGTTTTCTGCCTCGATGATCT----AATACTGTCAGTGTGGTGTTGAAGT 388810
---- ii v
C L1P4_orf2#LIN 483 AGTTTTCTGCCTCGATGATCTGTCTAACGCTGTCAGTGGGGTGTTGAAGT 434
INTRON_3 388811 TTCCCATTATTATTGTGTGGGTATCTAAATCTCTTCATAGTTCTCTAATA 388860
ii i v i i i i v vv vv
C L1P4_orf2#LIN 433 CCCCCACTATTATTGTGTGGCTGTCTAAGTCTTTTCGTAGGTCTAGAAGT 384
INTRON_3 388861 ACTTGTTTTATGAATCTGGGTGCTCCAGTGTTGAGTGCATATATGTTTAG 388910
i i i
C L1P4_orf2#LIN 383 ACTTGTTTTATGAATCTGGGTGCTCCAATGTTGGGTGCATATATATTTAG 334
INTRON_3 388911 GATATTTAAGTCTTCTTGTTGAAT-GAACCTTTTTTCATTATGTAATGCC 388959
v - i v
C L1P4_orf2#LIN 333 GATAGTTAAGTCTTCTTGTTGAATTGAACCCTTTATCATTATGTAATGCC 284
INTRON_3 388960 TTTCTTTGCCTTTTCTGATCATTGTTGGTTTAGAGTCCATTTTGTCTTAA 389009
i i i i v iii i ii i v v
C L1P4_orf2#LIN 283 CTTCTTTGTCCTTTTTTACTGTTGTTGGTTTAAAGTCTGTTTTATCTGAT 234
INTRON_3 389010 ATTGGATTAGCAACCCTTACTCTTTTTTGTTTTCTGTTTGCTTGGTAGAT 389059
vi v i i i i v i
C L1P4_orf2#LIN 233 ATAAGAATAGCGACCCCTGCTCTTTTTTGTTTTCCGTTTGCGTGATAGAT 184
INTRON_3 389060 TTTTCTCCATCTCTTTACTTTGAGCTTATGAAT--CATTGCATGTGAGAT 389107
i v i i ii -- i i i
C L1P4_orf2#LIN 183 CTTTCTCCAACCCTTTACTTTGAGCCTATGGGTGTCGTTACGTGTGAGAT 134
INTRON_3 389108 GGGTCTCCTGAATACAGCATATAGTTGGGTCTTGCTTCTTTATCCTACTT 389157
i v v ii v i i v
C L1P4_orf2#LIN 133 GGGTCTCTTGAAGACAGCAGACGGATGGGTCTTGTTTTTTTATCCAACTT 84
INTRON_3 389158 GCCACTTTGTGCCTTTTTTGTGGGGCGTTTAGCTGATTTACATTCAAGGT 389207
i vv i viv
C L1P4_orf2#LIN 83 GCCACTCTGTGCCTTTTAAGTGGGGCATTTAGACCATTTACATTCAAGGT 34
INTRON_3 389208 TACTACTGACATGTATAGATTTGATCCTGTCAT 389240
v i i ivi v i
C L1P4_orf2#LIN 33 TAATATTGATATGTGAGGTTTTGATCCTATCAT 1
Matrix = 20p37g.matrix
Transitions / transversions = 1.62 (76 / 47)
Gap_init rate = 0.01 (8 / 717), avg. gap size = 3.25 (26 / 8)
8114 18.49 1.46 2.18 INTRON_3 389092 390661 9520 C L1PA13_5end LINE/L1 1322 2880 1 858
INTRON_3 389092 TCATTGCATGTGAGATGGGTCTCCTGAATACAGCATATAGTTGGGTCTTG 389141
i v ivi?
C L1PA13_5end#L 2880 TCATTGCATGTGAGATGGGTCTCTTGAAGACAGCATACCANTGGGTCTTG 2831
INTRON_3 389142 CTTCTTTATCCTACTTGCCACTTTGTGCCTTTTTTGTGGGGCGTTTAGCT 389191
v vi i vvv i i
C L1PA13_5end#L 2830 GTTCTTTATCCAGCTTGCCACTCTGTGCCTTTTAATTGGGGCATTTAGCC 2781
INTRON_3 389192 GATTTACATTCAAGGTTACTACTGACATGTATAGATTTGATCCTGTCATC 389241
vi v i i i i
C L1PA13_5end#L 2780 CGTTTACATTCAAGGTTAGTATTGATATGTGTGGATTTGATCCTGTCATC 2731
INTRON_3 389242 TTGTTATTAGCTGGTGTTTATGCAGACTTGATTGTGTAGTTGCTTTATAG 389291
v ? i vv v i
C L1PA13_5end#L 2730 ATGNTGTTAGCTGGTTATTATGCAGACTTGTTTGTGTGGTTGCTTTATAG 2681
INTRON_3 389292 TGTCA---ATC---------AAGTGTGTTTTTGTAATGACCAGTAAAACA 389329
---i --------- i i ii -- i
C L1PA13_5end#L 2680 TGTCACTGGTCTGTGTACTTAAGTGTGTTTTTGTAGTGGCTGGTAA--CG 2633
INTRON_3 389330 GTCTTTTGTTTTCATGTTTAGTACTCTGTTAAGAACCTCTTTTAAGGAAG 389379
iv i i i iiv v i v v v
C L1PA13_5end#L 2632 GTCTTTCCTTTCCATATTTAGTGCTTCCTTCAGGAGCTCTTGTAAGGCAG 2583
INTRON_3 389380 GTCAGGTGGTAACAAATTCCCTTACCTTTTGCTTGTCTGAAAAGGATTTT 389429
v i i v v i
C L1PA13_5end#L 2582 GTCTGGTGGTAACGAATTCCCTCAGCATTTGCTTGTCTGAAAAGGATCTT 2533
INTRON_3 389430 ATTTCTCTTTTGCTTATGAATCTTAGTTTGGCTGGATTGGGCACCTGTAG 389479
i i v i -------------
C L1PA13_5end#L 2532 ATTTCTCCTTCGCTTATGAAGCTTAGTTTGGCCGGAT------------- 2496
INTRON_3 389480 TCAGCATTCTTAAAGAAAAATTCTAACCCCAAATTTTTTTTCTTTAAGAA 389529
----- ---------i ?iviivi i
C L1PA13_5end#L 2495 -----AT---------GAAATTCTNGGTTGGAATTTCTTTTCTTTAAGAA 2460
INTRON_3 389530 TGCTGACTACAGGTGCCCAGTCTCTTCTGGCTTGTAGAGTTTCTGCTGAA 389579
i v iv iv i i i
C L1PA13_5end#L 2459 TGTTGAATATTGGCCCCCAATCTCTTCTGGCTTGTAGGGTTTCTGCTGAG 2410
INTRON_3 389580 AGGTCCACTGTTTGCCTGATAAAGTTCCCTCTGTAGGTGACCTGCCCCTT 389629
i v i iiiv i v i
C L1PA13_5end#L 2409 AGGTCCGCTGTTAGTCTGATGGGCTTCCCTTTGTAGGTGACCTGACCTTT 2360
INTRON_3 389630 CTCTCTAGCTGCTTTTAATATTTTTT--TTCACATCAACCTTGGAGAATC 389677
i i -- iv i
C L1PA13_5end#L 2359 CTCTCTAGCTGCCTTTAACATTTTTTCTTTCATTTCGACCTTGGAGAATC 2310
INTRON_3 389678 TGATGACTGTGTGCCTTGGAGATGGTCTTCTTGGATAGTATCTTACAGGG 389727
i i i i i viv i v
C L1PA13_5end#L 2309 TGATGATTATGTGTCTTGGGGATGATCTTCTTGTGAAGTATCTTGCTGGG 2260
INTRON_3 389728 GTTCTCTGAATTTCCTAAATTTAAATGTCAAACTCTATAGTGAGGTTGGG 389777
v i i iiiv v iv
C L1PA13_5end#L 2259 GTTCTCTGCATTTCCTGAATTTGAATGTTGGCCTCTCTAGCTAGGTTGGG 2210
INTRON_3 389778 GAATTTTTCATGGAAAAAATCCTCAAATATGTTTTTCAAGTTGCTTGTGC 389827
v i vi v v i viii
C L1PA13_5end#L 2209 GAAGTTCTCATGGATGATATCCTGAAATATGTTTTCCAAGTTGCTTCCAT 2160
INTRON_3 389828 TCTCTCTCTC-CTTTCAAGAATGCCAGCGAGTCATAGATTTGGTCTTTTT 389876
i iv - i i ii ii i
C L1PA13_5end#L 2159 TCTCCCCATCTCTTTCAGGGACACCAATGAGTCATAGATTTGGTCTCTTT 2110
INTRON_3 389877 ACGTAATCTCATATTTCTCAGAGGTTTTCTTCATTACATTGTATTCTTTT 389926
i i i v i v v vi
C L1PA13_5end#L 2109 ACATAATCCCATATTTCTCGGAGGTTTTGTTCGTTCCTTTTCATTCTTTT 2060
INTRON_3 389927 TTCCCTATGTTTGTCTGATTGACTTGATTCAAAGAACTAGCCTTCGAGCT 389976
i vi i v iv i i i i i i
C L1PA13_5end#L 2059 TTCTCTATTCTTGTCTGACTGTCTTATTTCAGAAAGCCAGTCTTCAAGCT 2010
INTRON_3 389977 CTGAGATTCTTTCCTCAGCTTGATCTATTCTGCTGTTAATACTTCCAGAT 390026
? i i vi-
C L1PA13_5end#L 2009 CTGAGATTCTTTCCTCNGCTTGGTCTATTCTGCTATTAATACTTGT-GAT 1961
INTRON_3 390027 TGTATCACGAAATTTTTGTAGTGAGTTTTTCAACTCTATCAGATCAGTTT 390076
i i i i v i i v
C L1PA13_5end#L 1960 TGCATTATGAAATTCTTGTAGTGTGTTTTTCAGCTCTATCAGGTCAGTTA 1911
INTRON_3 390077 GGTTCTTTCTTAAAATGACTGTTTCATCTTTCAGCTCTTGTATCATTTTA 390126
v ii v v i i ii v i i
C L1PA13_5end#L 1910 CGTTCTTTTCTATACTGGCTATTTTGTCTGTCAGCTCCTGTATCGTTTTA 1861
INTRON_3 390127 TTGGATTTTTTAGATTTTTTGGATTCAGTTTTGACTTTCTCCTGAATCTC 390176
viv i v ii vi ii v v v
C L1PA13_5end#L 1860 TTGTGATTCTTAGCTTCCTTGGATTGGGTTTCAACGTACTCCTGCATCTC 1811
INTRON_3 390177 AGTGATCTCCATTGCAATCCAGATTCTGAATTCTATATCT--CACTTCAG 390224
ii i i v v v v -- i
C L1PA13_5end#L 1810 GATGATCTTCGTTCCTATCCATATTCTGAATTCTATTTCTGTCATTTCAG 1761
INTRON_3 390225 CCATTTCAGCCTGGTTAAGAACCATTGCTGGGAAGCTAGTGTGGTCATTT 390274
i i v v ii ? i i
C L1PA13_5end#L 1760 CCATCTCAGCCCGGTTCAGAACCCTTGCTGGAGAGNTAGTGCGGTCGTTT 1711
INTRON_3 390275 GGAGGTAAGAAGACACTCTGGGTTTTTGAGTTGCCAGAGTTCCTATTCTG 390324
v i v i i iiv
C L1PA13_5end#L 1710 GGAGGAAAGAAGGCACTCTGGCTTTTTGAGTTGTCAGAGTTCTTGCGCTG 1661
INTRON_3 390325 GTTCTTTCTCATCTGTGGGTGCTGATGTTCCTTTAAT-TTTGAAGTTACT 390373
v v v i - i
C L1PA13_5end#L 1660 GTTCTTTCTCATCTTTGTGGGCTGATGTTCCTTCAATCTTTGAAGTTGCT 1611
INTRON_3 390374 GTCATTTGGATAGGGTTTTTTGCTTTTATATTCTTTGATGCCCTTGAAGG 390423
? v i vv v vi v v i
C L1PA13_5end#L 1610 GNCCTTTGGATGGTTTTTTTTTCTTTTATCCTATTTGATGACCTTGAGGG 1561
INTRON_3 390424 TTTGACTGTGGTATAAGCTGGATTCAGTTGACTAGTTTCTTTTCTGGA-- 390471
i v i i i i v --
C L1PA13_5end#L 1560 TTTGATTGTGGTATAAGGTGGGTTCAGTCGACTGGCTTCATTTCTGGAAG 1511
INTRON_3 390472 --TTTCAGGGGCCGAGGCTCAGCTAAGCATTTCTGGGCTGCATGCTCTAA 390519
-- vi i v?vv i i i i
C L1PA13_5end#L 1510 ATTTTAGGGGGCCAAGGCTCAGCTCNCGACTCCTGGACTGCGTGCTCTAA 1461
INTRON_3 390520 CCCTGGGGGGCTGGTACCAGGCCCAAGGCTTTGTCCTCCGGCCCC-CAAG 390568
i i ? i i v- i i i - i
C L1PA13_5end#L 1460 CTCTGGGGGACTNGTATCGGGCCCC-GGCTTTGTTCTCTGGCTCCTCGAG 1412
INTRON_3 390569 GTTAAGCACTTGCTGCTGTGCTGGAGGGGCCAATATGTTCCCAGTCTGCT 390618
i v ii --- i i vi i i v i
C L1PA13_5end#L 1411 GTTAGGAACCCGCTGC---GCTGGGGGGGCCGAGGTGCTCCCGGACCGCT 1365
INTRON_3 390619 GGCCACAACACTCTGATGGAAGGTGCCAGCAAAAGTGCTTCAT 390661
i ? i iv v i i i
C L1PA13_5end#L 1364 GGTCACNACACTCCGATGGGTGGTGCCAGCCAAAGCGTTTCGT 1322
Matrix = 20p37g.matrix
Transitions / transversions = 1.84 (178 / 97)
Gap_init rate = 0.01 (14 / 1569), avg. gap size = 4.07 (57 / 14)
+ 2047 13.3 1.4 0.9 INTRON_3 390657 391004 (9177) C L1MB4 LINE/L1 (355) 5825 5476 540 *
ANNOTATION EVIDENCE:
2047 13.33 1.44 0.86 INTRON_3 390657 391004 9177 C L1MB4_3end LINE/L1 223 572 355 859
INTRON_3 390657 TTCATTCCTTTTTATGGGTGAATAATATTCCAATGTATTGATATACCACA 390706
v v v v vv
C L1MB4_3end#LI 572 TTCCTTCCTTTTTAAGGCTGAATAATATTCCATTGTATGTATATACCACA 523
INTRON_3 390707 TTTTGTTTATATATTTATTAGTAATGGACACTTGAGTTTTTTCCACCTTT 390756
vi i iv v i v
C L1MB4_3end#LI 522 TTTTGTTTATCCATTCATCCGTTATGGACACTTGGGTTGTTTCCACCTTT 473
INTRON_3 390757 TTGGCTATTGTGAATAATGCTGCTATTAACATTGATGTACAAGTATCCTT 390806
- v i iv
C L1MB4_3end#LI 472 T-GGCTATTGTGAATAATGCTGCTATGAACATTGGTGTACAAGTATCTGT 424
INTRON_3 390807 TTGAGTCCCCACTGTCAGTTCTTCTGGATATATACCTAGGAGTGAAATTG 390856
i ii v i i i i
C L1MB4_3end#LI 423 TCGAGTCCCTGCTTTCAATTCTTTTGGGTATATACCTAGGAGTGGAATTG 374
INTRON_3 390857 -TGAATCATATGGTAATTTTAGATCTAGCTTTTTGAGAAACCACCA--CT 390903
- ii i vi i i i --
C L1MB4_3end#LI 373 CTGGGTCATATGGTAATTCTATGTTTAACTTTTTGAGGAACCACCAAACT 324
INTRON_3 390904 GTTTTCCACAGAGGCTGCAGCATTTTACATTCCCACCAGCAATGCA-AAG 390952
v v -i
C L1MB4_3end#LI 323 GTTTTCCACAGCGGCTGCACCATTTTACATTCCCACCAGCAATGCATGAG 274
INTRON_3 390953 CGTTCCAATTTCTCT-TACCCACGCCAGCACTTGTCATTACCTGACTTTT 391001
v i-i i v i i vi --
C L1MB4_3end#LI 273 GGTTCCAATTTCTCCACATCCTCGCCAACACTTGTTATTTTCTG--TTTT 226
INTRON_3 391002 TTT 391004
C L1MB4_3end#LI 225 TTT 223
Matrix = 20p37g.matrix
Transitions / transversions = 1.42 (27 / 19)
Gap_init rate = 0.02 (6 / 347), avg. gap size = 1.33 (8 / 6)
+ 2821 14.6 0.6 2.4 INTRON_3 391005 391516 (8665) C L1MA8 LINE/L1 (115) 6176 5674 541
ANNOTATION EVIDENCE:
2821 14.61 0.59 2.39 INTRON_3 391005 391516 8665 C L1MA8_3end LINE/L1 421 923 115 860
INTRON_3 391005 CTCACATAGTTATCATTTTTTTA--GTGATAATACATAACATCTGTTCTC 391052
v i-- v i v v ii
C L1MA8_3end#LI 923 CTCACATACTTATCATTTTTTTGTGGTGAGAACACTTAAAATCTACTCTC 874
INTRON_3 391053 TTTACATTTTTACAGAATACAATGTATCATCATTACCTATAGTTGCCTTG 391102
vi v vv v ii ii i v ii v
C L1MA8_3end#LI 873 TTAGCAATTTTCAAGTATACAATACATTGTTATTAACTATAGTCACCATG 824
INTRON_3 391103 TTCCACAATAGATCTCTTGGAAATTATTCCTCCTATGTAACTGTAATTAT 391152
vi - v i v v v
C L1MA8_3end#LI 823 TTGTACAATAGATCTCTTG-AACTTATTCCTCCTGTCTAACTGAAATTTT 775
INTRON_3 391153 GTATTCTTTAATCAACACCTCCTCACCCCCACCTCCCAACTAAAGTCCTC 391202
i i i i i vi ---- - ----- i
C L1MA8_3end#LI 774 GTATCCTTTGACCAACATCTCCCCAATCC----TCCCA-CT-----CCCC 735
INTRON_3 391203 AGCATCTGGTATCCACCATTCTACCCTCTGCTTCTTTGAGATCAACTTAT 391252
vi v i v v -
C L1MA8_3end#LI 734 AGCCCCTGGTAACCACCATTCTACTCTCTGCTTCTATGAGTTCAACTT-T 686
INTRON_3 391253 TTTAGATTCCACATATGAGTAAAATCATGCAGTATTTGTCTTTCTGTGCC 391302
i i i i
C L1MA8_3end#LI 685 TTTAGATTCCACATATAAGTGAGATCATGCGGTATTTGTCTTTCTGTGCC 636
INTRON_3 391303 TGGCTTATTTCACTTCACGTACTGTCCTCCATGTTCATCCACATTGTCAC 391352
v i v v ii i
C L1MA8_3end#LI 635 TGGCTTATTTCACTTAACATAATGTCCTCCAGGTTCATCCATGTTGTCGC 586
INTRON_3 391353 AAATGACAGGATTTTATTCTTTTT-ATGGCTGAGTAGTATTCCATTGTGT 391401
iv - v i
C L1MA8_3end#LI 585 AAATGACAGGATTTCCTTCTTTTTTAAGGCTGAATAGTATTCCATTGTGT 536
INTRON_3 391402 ATGTGTGCTACATATTCTTTATCCATTCATCTGTTGATGGACACTTAGGC 391451
i i i v i i
C L1MA8_3end#LI 535 ATATGTACCACATTTTCTTTATCCATTCATCCGTTGATGGACACTTAGGT 486
INTRON_3 391452 TGATTCCATATCATGGCTACTGTAAATAGTGCTGTGATAAACATGGGAGT 391501
v i i i ii i
C L1MA8_3end#LI 485 TGATTCCATATCTTGGCTATTGTGAATAATGCTGCAATGAACATGGGAGT 436
INTRON_3 391502 GCAGATATCTTTTTG 391516
i
C L1MA8_3end#LI 435 GCAGATATCTCTTTG 421
Matrix = 20p37g.matrix
Transitions / transversions = 1.61 (45 / 28)
Gap_init rate = 0.01 (7 / 511), avg. gap size = 2.14 (15 / 7)
+ 570 26.3 0.7 0.7 INTRON_3 392923 393075 (7106) C MamRep488 DNA/hAT-Tip100 (0) 219 67 542
ANNOTATION EVIDENCE:
570 26.31 0.65 0.65 INTRON_3 392923 393075 7106 C MamRep488 DNA/hAT-Tip100 67 219 0 886
INTRON_3 392923 CAGTTGTTGCTCCATCATTTCTATGGAAGAGGAGCTTAGAGGGGGCCATC 392972
v iv vv iv i i i v v
C MamRep488#DNA 219 CAGTGGCGGCTCCAGAATTTCTATATAGGAGGGGCTTAGGGGCGGCAATC 170
INTRON_3 392973 AATTTGAAAAGTGAGGGCT-GGAGCCATGTCTATAAGCTTTGTTTGCATA 393021
viv i i - i - i v v vv vi
C MamRep488#DNA 169 TGGTTGGAAGG-GGGGGCTAGGGGACTTGTCTTGAAGCTGCGTTTGCATA 121
INTRON_3 393022 GTAGCTTACAAAACATGAAGAAAATGTTAATCGTCTCTGTCAAATAATGG 393071
i vi v v vi i i i iv i v
C MamRep488#DNA 120 GCACTTTACATAAGATTGAGAAAACGTCAATTGTCCATATCAAAGAATGG 71
INTRON_3 393072 AGGG 393075
i
C MamRep488#DNA 70 GGGG 67
Matrix = 20p37g.matrix
Transitions / transversions = 1.00 (20 / 20)
Gap_init rate = 0.01 (2 / 152), avg. gap size = 1.00 (2 / 2)
+ 2346 26.1 12.2 1.9 INTRON_3 393351 394266 (5915) + L2a LINE/L2 2344 3359 (67) 543
ANNOTATION EVIDENCE:
2346 26.20 5.47 2.04 INTRON_3 393351 394063 6118 + L2 LINE/L2 2344 3080 2 810
INTRON_3 393351 TTTATACTTCCCATCCACATCCCACTGCTTAACTCTGGATTTGCATATTC 393400
ii vii v i i v iv v ii i i i i
L2#LINE/L2 2344 TTTATATCTCCAGCCCAGACCTCTCCCCTGAACTCCAGACTCGTATATCC 2393
INTRON_3 393401 ---TGCCCACTCAAATTATTTACCTATACATCTAA-GGACATTACAAACT 393446
--- i i vv v ii i iv ii -i i iv
L2#LINE/L2 2394 AACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACT 2443
INTRON_3 393447 TAACATGCCCCAAGCCCAAATTCTCATCTTGGCCTTCT--TCT-CTCTTC 393493
i v i iv v i v vv i v--i - i
L2#LINE/L2 2444 TAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTC 2493
INTRON_3 393494 TCCCAATCTTTCACACTTCCTTCATAAATATCAAGTTTATCTTTCT-GTT 393542
i v i i v ii v---i v iv v ii i i-
L2#LINE/L2 2494 CCACAGTCTTCCCCATCTCA---GTTAATGGCAACTCCATCCTTCCAGTT 2540
INTRON_3 393543 GCTTAAGCCAAAAACTTCAGAGT--TTCTTGACTCTT---TTTTTCTCAC 393587
i i i ii -- i i --- i
L2#LINE/L2 2541 GCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCAC 2590
INTRON_3 393588 ACACCACATTCCAATCCTTCAGCAAATCTTACTGGCTCAACCTTTAAAAC 393637
v - v i ii v i i
L2#LINE/L2 2591 ACCCCACAT-CCAATCCATCAGCAAATCCTGTTGGCTCTACCTTCAAAAT 2639
INTRON_3 393638 ATCCCCAGAAACCAACCACTTCT-ACCGC-TCTGCTGCTACCACCCTGGT 393685
vi v i - i - ii i
L2#LINE/L2 2640 ATATCCAGAATCCGACCACTTCTCACCACCTCCACTGCCACCACCCTGGT 2689
INTRON_3 393686 CCAAGCCACAATGATCCCTTGCTTCAATTATTGCTATAGACTCCTAATT- 393734
v v i i i vi i v v i -
L2#LINE/L2 2690 CCAAGCCACCATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTG 2739
INTRON_3 393735 ---TCCTTGCTTTCACCCTTGCTCTTCCCATCCCCTTCAGTCTCTTC--A 393779
--- i i i -------- ? v --
L2#LINE/L2 2740 GTCTCCCTGCTTCCACCCTTGCCC--------CCCTNCAGTCTATTCTCA 2781
INTRON_3 393780 GCTCAGCAGCCAGAGTGATGATTTCACAGTGTGAGTTGGGTCATAT---- 393825
i v vv i v iii i ii i i ----
L2#LINE/L2 2782 ACACAGCAGCCAGAGTGATCCTTTTAAAACATAAGTCAGATCATGTCACT 2831
INTRON_3 393826 -------TCAAAACCATCTAATGGCTTCT-ATGTCAATGAGGGCAAAAGC 393867
------- v i i i- v v v i i
L2#LINE/L2 2832 CCTCTGCTCAAAACCCTCCAGTGGCTTCCCATCTCACTCAGAGTAAAAGC 2881
INTRON_3 393868 CAAAGTTCTTATAATGACCAGTAAGGCCCTTCGTGACATG--TCCTTGCT 393915
i i i i vii v i iv --i ii i
L2#LINE/L2 2882 CAAAGTCCTTACAGTGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTT 2931
INTRON_3 393916 ACCACTGTGATCTCATCTCCTACTGCTCTCCCTCTCATTCATTCTGGGGC 393965
v v i ii i ii i i vvv
L2#LINE/L2 2932 ACCTCTCTGACCTCATCTCCTACCACTCTCCCCCTCGCTCACTCCGCTCC 2981
INTRON_3 393966 AGCTACACCAGCCTC-TCAGTGTTCTTCACATTCATCAGTCTCACATGAG 394014
i ii - iiv i iv iv ii v v i vivv
L2#LINE/L2 2982 AGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCACGCTCCTG 3031
INTRON_3 394015 TCTT-GGGCCTTTGCCCTTACTGTAGGACCCTCTGCCTGGAAT--TCTTT 394061
i i- v i v--- i-- i
L2#LINE/L2 3032 CCTCAGGGCCTTTGCACTTGCTGTT---CCCTCTGCCTGGAACGCTCTTC 3078
INTRON_3 394062 CC 394063
L2#LINE/L2 3079 CC 3080
Matrix = 25p37g.matrix
Transitions / transversions = 2.03 (122 / 60)
Gap_init rate = 0.03 (21 / 712), avg. gap size = 2.57 (54 / 21)
772 28.95 7.59 2.30 INTRON_3 393909 394198 5983 + L2a_3end LINE/L2 16 320 197 811
INTRON_3 393909 CCTTGCTACCACTGTGATCTCATCTCCTACTGCTCTCCCTCTCATTCATT 393958
ii i v v i ii i ii i
L2a_3end#LINE 16 CCCCGTTACCTCTCTGACCTCATCTCCTACCACTCTCCCCCTCGCTCACT 65
INTRON_3 393959 CTGGGGCAGCTACACCAGCCTC-TCAGTGTTCTTCACATTCATCAGTCTC 394007
i vvv i ii - iiv i iv iv ii v v
L2a_3end#LINE 66 CCGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCAC 115
INTRON_3 394008 ACATGAGTCTT-GGGCCTTTGCCCTTACTGTAGGACCCTCTGCCTGGAAT 394056
i vivv i i- v i v--- i
L2a_3end#LINE 116 GCTCCCGCCTCAGGGCCTTTGCACTTGCTGTT---CCCTCTGCCTGGAAC 162
INTRON_3 394057 --TCTTTCCATAGTTATCTACTTGACTTGCTCCCTTCTTTCCATTGGGTC 394104
-- i vi v ii v i i ivii v ii
L2a_3end#LINE 163 GCTCTTCCCCCAGATATCCGCATGGCTCGCTCCCTCACCTCCTTCAGGTC 212
INTRON_3 394105 TCTGATCAAATGACACCTTAATTGTGATGCTT--------------ATTT 394140
i v v vviv v i --------------
L2a_3end#LINE 213 TTTGCTCAAATGTCACCTTCTCAGTGAGGCCTTCCCTGACCACCCTATTT 262
INTRON_3 394141 AAAATAGCATAC--TAGCTACTATTGGTTCTATACTATCTCC--TACCCT 394186
? i -- v? iv i ?iiv i ---- i --
L2a_3end#LINE 263 AAAATWGCACACCCTCNCCCCCANCACTCC----CTATCCCCCTTACCCT 308
INTRON_3 394187 GCTTTACTTCTC 394198
i i
L2a_3end#LINE 309 GCTTTATTTTTC 320
Matrix = 25p37g.matrix
Transitions / transversions = 1.72 (50 / 29)
Gap_init rate = 0.03 (8 / 289), avg. gap size = 3.62 (29 / 8)
315 18.03 1.64 0.00 INTRON_3 394206 394266 5915 + L2a_3end LINE/L2 389 450 67 812
INTRON_3 394206 CCACATTA-AATGTAACCTCCATGAGGGTAGGGCCTGTTTTCTGTTTTGC 394254
v i - v i v v v i
L2a_3end#LINE 389 CCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGT 438
INTRON_3 394255 TCATTGCAATAT 394266
i vi
L2a_3end#LINE 439 TCACTGCTGTAT 450
Matrix = 25p37g.matrix
Transitions / transversions = 0.83 (5 / 6)
Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1)
+ 23 60.9 0.0 0.0 INTRON_3 394312 394334 (5847) + AT_rich Low_complexity 1 23 (0) 544
ANNOTATION EVIDENCE:
23 60.87 0.00 0.00 INTRON_3 394312 394334 5847 C AT_rich Low_complexity 140 162 138 817
INTRON_3 394312 TTAATATATATATATAAAATATA 394334
vv v vvv vvvvvv vv
C AT_rich#Low_c 162 AAATTATATTATTTATTTTTAAT 140
Matrix = Unknown
Transitions / transversions = 0.00 (0 / 14)
Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0)
+ 2217 10.5 2.2 0.0 INTRON_3 394348 394662 (5519) C MER47A DNA/TcMar-Tigger (0) 366 45 545
ANNOTATION EVIDENCE:
2217 10.48 2.22 0.00 INTRON_3 394348 394662 5519 C MER47A DNA/TcMar-Tigger 45 366 0 887
INTRON_3 394348 CAGATGCTCCTCAACTTATGA---GGTTATGTCCCAATAAACTCATCATA 394394
i i --- i i i i
C MER47A#DNA/Tc 366 CAGATGCTCCTCGACTTACGATGGGGTTACGTCCCGATAAACCCATCGTA 317
INTRON_3 394395 AGTTGAAACTATGGTAAGTCAAAAATGCATTTAATACACCTAACCTACTG 394444
v v i i
C MER47A#DNA/Tc 316 AGTTGAAAATATCGTAAGTCGAAAATGCATTTAATACACCTAACCTACCG 267
INTRON_3 394445 AACATCATAGCTTAGCCGGGCCTACCTTAAATGCACTCAGAACACTTACA 394494
vi i ii
C MER47A#DNA/Tc 266 AACATCATAGCTTAGCCTAGCCTACCTTAAACGTGCTCAGAACACTTACA 217
INTRON_3 394495 TCAGCCTACTGTTGGGCAAAATCATCTAACTGAAAGCCTATCTTATAATA 394544
i v vv i
C MER47A#DNA/Tc 216 TTAGCCTACAGTTGGGCAAAATCATCTAACACAAAGCCTATTTTATAATA 167
INTRON_3 394545 AAGTATTGAATATTTCAAGTAATTTATTGAATACTATACTGAAAGTGAAA 394594
i i v i
C MER47A#DNA/Tc 166 AAGTGTTGAATATCTCATGTAATTTATTGAATACTGTACTGAAAGTGAAA 117
INTRON_3 394595 AACAAAATGGTTGT----GTATTTGAAGTACGATTTCTACTGAGTGTGTA 394640
i ---- i i i i i
C MER47A#DNA/Tc 116 AACAGAATGGTTGTATGGGTACTCGAAGTACGGTTTCTACTGAATGCGTA 67
INTRON_3 394641 TTGCTTTTGCACCATCATAAAG 394662
i i i
C MER47A#DNA/Tc 66 TCGCTTTCGCACCATCGTAAAG 45
Matrix = 20p37g.matrix
Transitions / transversions = 3.71 (26 / 7)
Gap_init rate = 0.01 (2 / 314), avg. gap size = 3.50 (7 / 2)
+ 581 23.0 0.6 0.0 INTRON_3 394695 394872 (5309) + (TA)n Simple_repeat 2 180 (0) 546
ANNOTATION EVIDENCE:
581 23.03 0.56 0.00 INTRON_3 394695 394872 5309 C (TA)n Simple_repeat 2 180 0 870
INTRON_3 394695 TATATATGTATATCTATCTTCTTGTATGTATGTATATATGCATATATATA 394744
i v v viv i i i ii
C (TA)n#Simple_ 180 TATATATATATATATATATATATATATATATATATATATATATATATATA 131
INTRON_3 394745 TCTGTATATATACATGCATGTATATATGTATATATGCATGCATATATGTA 394794
v i i ii i i ii ii i
C (TA)n#Simple_ 130 TATATATATATATATATATATATATATATATATATATATATATATATATA 81
INTRON_3 394795 TATATACAGA-ACAGATATATATATGCATGTATATGTACAGATATACACG 394843
i v - i v ii i i i v i ii
C (TA)n#Simple_ 80 TATATATATATATATATATATATATATATATATATATATATATATATATA 31
INTRON_3 394844 CATGTATATCTGTATATATAGATATATAT 394872
i i v i v
C (TA)n#Simple_ 30 TATATATATATATATATATATATATATAT 2
Matrix = Unknown
Transitions / transversions = 3.10 (31 / 10)
Gap_init rate = 0.01 (1 / 177), avg. gap size = 1.00 (1 / 1)
+ 283 21.1 0.0 0.0 INTRON_3 394909 394965 (5216) + L2a LINE/L2 3370 3426 (0) 543
ANNOTATION EVIDENCE:
283 21.05 0.00 0.00 INTRON_3 394909 394965 5216 + L2a_3end LINE/L2 461 517 0 813
INTRON_3 394909 TATAATAGTGCCTGTCACGTAGTAACTGCTTAATAAATATTTGTTGAGTA 394958
v i v i ivi i i i
L2a_3end#LINE 461 TAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAATG 510
INTRON_3 394959 ATTTAAT 394965
v v
L2a_3end#LINE 511 AATGAAT 517
Matrix = 25p37g.matrix
Transitions / transversions = 1.40 (7 / 5)
Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0)
+ 2169 10.8 0.3 2.4 INTRON_3 395927 396221 (3960) C AluSq2 SINE/Alu (23) 289 1 547
ANNOTATION EVIDENCE:
2066 11.51 0.34 2.78 INTRON_3 395927 396221 3960 C AluSx SINE/Alu 1 288 24 790
INTRON_3 395927 TTTTTTGAGACGGATTTTCACTCTTGTCACCCAGGCTGGAGTGCAATGGT 395976
v i i - i i i
C AluSx#SINE/Al 288 TTTTTTGAGACGGAGTCTCGCTCT-GTCGCCCAGGCTGGAGTGCAGTGGC 240
INTRON_3 395977 GTGATCTTGGCTCACTGCAATCTCCACCTCCCAGGTTCAAGCGATTCTCC 396026
i i i i i
C AluSx#SINE/Al 239 GCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCC 190
INTRON_3 396027 TGCCTCAGCCTCCTAAGTAGAGTAGCTGGGATTACAGGCATGTGCCACCA 396076
i----- ii i
C AluSx#SINE/Al 189 TGCCTCAGCCTCCC-----GAGTAGCTGGGATTACAGGCGCGCGCCACCA 145
INTRON_3 396077 CACCCAGCTAATTTTTTTGTATTTTTGGTAGAGACCAG-TTTCACTATGT 396125
i i -- i vi - i
C AluSx#SINE/Al 144 CGCCCGGCTAATTTTT--GTATTTTTAGTAGAGACGGGGTTTCACCATGT 97
INTRON_3 396126 TGGTTAGGCTGGTCTCGAACTCCTGACTTCAGATGATTCACCCACCTCAG 396175
ii i i i i i i
C AluSx#SINE/Al 96 TGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGG 47
INTRON_3 396176 CCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCATTGCGCCCAGCC 396221
i ii i
C AluSx#SINE/Al 46 CCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 15.50 (31 / 2)
Gap_init rate = 0.01 (4 / 294), avg. gap size = 2.25 (9 / 4)
+ 212 29.8 10.3 1.2 INTRON_3 396344 396421 (3760) C L2c LINE/L2 (33) 3354 3270 548
ANNOTATION EVIDENCE:
212 29.84 10.26 1.18 INTRON_3 396344 396421 3760 C L2c_3end LINE/L2 361 445 33 814
INTRON_3 396344 TGCTGTGTGTTAGATGCTATG-----AAGGAT--ATAAGATACGGTACC- 396385
i i ii i iv ----- i -- i v -
C L2c_3end#LINE 445 TACTATGTGCCAGGTGCTGGGGATACAAAGATGAATAAGACACGGTCCCT 396
INTRON_3 396386 AAACTTAAGAAACTTCACAGTTTAACTGGGAAAACA 396421
ivv i i i - i iiv i i i
C L2c_3end#LINE 395 GCCCTCAAGGAGCT-CACAGTCTAGTGGAGGAGACA 361
Matrix = 25p37g.matrix
Transitions / transversions = 3.60 (18 / 5)
Gap_init rate = 0.05 (4 / 77), avg. gap size = 2.25 (9 / 4)
+ 369 24.4 5.5 2.4 INTRON_3 396625 396788 (3393) C MER113B DNA/hAT-Charlie (1) 301 133 549
ANNOTATION EVIDENCE:
369 24.36 5.49 2.37 INTRON_3 396625 396788 3393 C MER113B DNA/hAT-Charlie 133 301 1 888
INTRON_3 396625 AGTATTTCCCAAACTTTTAGCATT------CTAG-TTCCCAATTTTTGC- 396666
iviv ------ v- vi -
C MER113B#DNA/h 301 AGTATTTCCCAAACTTCAGTCATTTGTGTACTACCTTCATAATTTTTGCC 252
INTRON_3 396667 -TATGTGAACAAACTATCCATACTGTTTCTCCCATACTGCTCTTTATGTT 396715
- v v v i v - i i viiiv i vi vi
C MER113B#DNA/h 251 ATATGTGTACCACCTGTAC-TATTATTTACTTAATATTTTTCTTTAAATT 203
INTRON_3 396716 GACACATTTTTTGTAAATACATTTTGCCTTGCCTTAAACCATCAAATCCA 396765
vi i - - - v iii i i v v v i
C MER113B#DNA/h 202 GACTTACTTTTT-TAAA-AC-TTTAGCCTCATCCTAAGCAATAATATCTA 156
INTRON_3 396766 TGAAATCAAAGGTTTGATATGCT 396788
v i
C MER113B#DNA/h 155 TGAAATCATAGGTTTGATGTGCT 133
Matrix = 20p37g.matrix
Transitions / transversions = 1.17 (21 / 18)
Gap_init rate = 0.04 (7 / 163), avg. gap size = 1.86 (13 / 7)
+ 1634 22.5 6.6 5.0 INTRON_3 397173 398243 (1938) C Charlie6 DNA/hAT-Charlie (39) 3461 2371 550
ANNOTATION EVIDENCE:
1446 20.79 4.17 2.46 INTRON_3 397173 397532 2649 C Charlie6 DNA/hAT-Charlie 3096 3461 39 889
INTRON_3 397173 AATAATTCTCAAATCTCAAGGAAACTTCTGGATAAAAGTTATTATATCTA 397222
i ii i - ii v ?i -i
C Charlie6#DNA/ 3461 AATAATTTTCAGGTCTCAGGGAA-CCCCTGCATAAANAT-GTTATATCTA 3414
INTRON_3 397223 AAGCTCATAGTATATTAGAATGACTATTGAGTTGTAGATATATAATTATC 397272
v i vi ?i v i -- v
C Charlie6#DNA/ 3413 CAGCTCATGGTATATTAGCGTGANCAGTAAGTTGTAGATATA--ATAATC 3366
INTRON_3 397273 CAATA----TTGCCAGTGTTCTGTTAAATAGAGAGTTATATTTTCCTTAG 397318
---- i i i ? v i i i v v i vv
C Charlie6#DNA/ 3365 CAATAATAATTGTCAATGCTNTTTTGAGTAGAGAATGATTTTTTTCTGTG 3316
INTRON_3 397319 AATCTGTTTAGTTTGGCCAGTTTCTTAACCTATTTATTTTTTGCATTGTT 397368
i i v ii v i ?i i-- ii v
C Charlie6#DNA/ 3315 GATCTGCTTATTTTGGCCAACTTATTAGCCTNCTC--TTTTTGTGTGGTT 3268
INTRON_3 397369 TCCCTCTCCCCACAAAGGATACCAATTCTAATG----------GTATAGA 397408
? - i i ---------- i i
C Charlie6#DNA/ 3267 NCCC-CTCCCCACAAAGGATATCAACTCTAATGCAAGTCAGTAGTGTAGG 3219
INTRON_3 397409 TAAAAGAAACTTCAGTTTTTCTTTTTAAAAAAAAATCCTACTAGATTTTT 397458
i i v v vv v
C Charlie6#DNA/ 3218 TAAAGGAAACTTCAGTTTTTTTTTTTTAATAAATTTCCTACTTGATTTTT 3169
INTRON_3 397459 TTTGTATCTTATACAAGTGGGCCTCAAAGTCTTAACACAAATTTCTGTTG 397508
v--iv ii v i ? v ii i
C Charlie6#DNA/ 3168 A--AAACTTTATCCAAGTAGGCCTNAAAGTCTTATCACAAATTTCTACTA 3121
INTRON_3 397509 TATCA-ATACTACTGAGGTATGGTA 397532
iv - i v
C Charlie6#DNA/ 3120 TACAAGATGCTAATGAGGTATGGTA 3096
Matrix = 20p37g.matrix
Transitions / transversions = 1.79 (43 / 24)
Gap_init rate = 0.03 (9 / 359), avg. gap size = 2.67 (24 / 9)
1634 23.41 7.85 6.36 INTRON_3 397391 398243 1938 C Charlie6 DNA/hAT-Charlie 2371 3235 265 890
INTRON_3 397391 CAATTCTAATGGTATAGATAAAAGAAACTTCAGTTTTTCTTTTTAAAAAA 397440
v - i i i i i i v v
C Charlie6#DNA/ 3235 CAAGTC-AGTAGTGTAGGTAAAGGAAACTTCAGTTTTTTTTTTTTAATAA 3187
INTRON_3 397441 AAATCCTACTAGATTTTT----TTTGTATCT---TATAC----AAGTGGG 397479
vv v ----i - i--- vi ---- ---
C Charlie6#DNA/ 3186 ATTTCCTACTTGATTTTTAAAACTT-TATCCAAGTAGGCCTNAAAGT--- 3141
INTRON_3 397480 CCT----CAAAGTCTTA--ACACAAATTTCTGTTGTATCAATACTACTGA 397523
i ---- v ii -- i iv v iv - vvv iv - v
C Charlie6#DNA/ 3140 CTTATCACAAATTTCTACTATACAAGATGCTAATG-AGGTATGGTA-TGT 3093
INTRON_3 397524 GGTA--TGGTAAATGCAAG----------TCCT-ATTTAAAACTAAATAG 397560
-- ivi ---------- -? ---
C Charlie6#DNA/ 3092 GGTACATGGTGTGTGCAAGAGTANCTTTTTCCTTNTTTAAAACTAAA--- 3046
INTRON_3 397561 GACAACTATTTTAGACAACTATGATTGAAAAGAAAAAAAAGAGTAG--TT 397608
i ii - v iv vv - iv iiv ? i--
C Charlie6#DNA/ 3045 AATGACT-TTTTAGCCAACCTTTCTTGAAAA-AAGTAAGGTANTAAGCTT 2998
INTRON_3 397609 ATCT-GTCTTTCTTGAAATTAATTTCATCATTTCCTTTTCATAAATTTGA 397657
v -ii ----- i v
C Charlie6#DNA/ 2997 AGCTTACCTTTCTTGAAATTAATTTC-----TTTCTTTTCATAAATTTTA 2953
INTRON_3 397658 AAATCTTATAAGGCAAACATAATTTGTTTTTGTTAAGTAACTAGTTTAAG 397707
v i vvi i i i i
C Charlie6#DNA/ 2952 AAAACTCATAAGGCAAACATAATAAATTTCTGTTAAATAACTGGCTTAAG 2903
INTRON_3 397708 CCACAATGGGATAAAATTTTTCTAAGGGTAGGTTTGTTAGGTTTAATTTA 397757
v vv - i ? ? i iiv i
C Charlie6#DNA/ 2902 CCAAAATGGGATTTAATTTTT-TAAAGNTANGCTCAGTAGATTTAATTTA 2854
INTRON_3 397758 AATAAAGGTTATGAATTTACTTTAAT----ATTATTTTGAATAT-AAAAT 397802
i i v i ----i vi- i -
C Charlie6#DNA/ 2853 AATAAAGGTTGTAAATTGATTTTAATTAATGTTATTAC-AACATGAAAAT 2805
INTRON_3 397803 GTATTAATGATGTTGAATAGTAAAGCATGTAAAACTATACATCAAAGCAA 397852
v i ii vvv ii vii
C Charlie6#DNA/ 2804 TTATTGACAATGTTGAATAGTAAAGCTACTAAAACCGTAAGCCAAAGCAA 2755
INTRON_3 397853 TATGAATAAAATTATAGCCTATGATACAATTTTATATGATACTTTGACAA 397902
i v v i v ii v v
C Charlie6#DNA/ 2754 TGTGAATAAAAATATAGCCTAAGACAAAATTTTATACAAGACTTTGAAAA 2705
INTRON_3 397903 AAATTATTTTTTTACCTAATGGCATG--------------TAGAT----- 397933
--i i ? iv i i -------------- ii-----
C Charlie6#DNA/ 2704 AA--CATTTTCTTSCTGAGTGACATGATCAGGCTCAAATATAGGCCTAGC 2657
INTRON_3 397934 AATTATAAAATTATTATATACTGGTTTCATGATCACTTTA-CTAAGCTAT 397982
i i ? i vv iv -- i iv ? v - vvvi
C Charlie6#DNA/ 2656 AGTTACAAAANTATTATACACATGCGT--TGGTTTCNTGATCTTTTTTAT 2609
INTRON_3 397983 AAATGCATTT-TAATTTTAATTGTTATTTTGGAA-CTAAAAATAATAATT 398030
iiivi v - ivv v v i v - v -
C Charlie6#DNA/ 2608 AGGCCTATATATGCATTAAAATGCTATTTTTGAANCTAAAAATAAAAAT- 2560
INTRON_3 398031 AAATGT-ATTTCCTGAATGTGAAATTTATTCCTTTTGTTGTTGTTGTTGT 398079
-- - ? i v -i ii i v -- v v ---- i
C Charlie6#DNA/ 2559 --ATGTTANTTCTTCA-CGTGAAACCTGTGC--TTAGTTTTT----TTGC 2519
INTRON_3 398080 TGCCCAATTACTCAATTCTGGGTAGAGTATGATGTAAGTTGACATCGATT 398129
v iv vi iiv vi ivv ??
C Charlie6#DNA/ 2518 TGCACAGATACTCAATTCTGGGTCAAACTTGAGATAAGCACACANNGATT 2469
INTRON_3 398130 TTATTTCTGGGTAGAGTATGATATAAGTTGACAGAAATGAGACAATTTCT 398179
i --------------------- ii v i ?
C Charlie6#DNA/ 2468 TCATTT---------------------TCAACTGAGATGAGACNATTTCT 2440
INTRON_3 398180 GTCCTTGTTCTTGGTGCTTCTTAA----GAAATACTTT--CTTATATATG 398223
i i v ---- - v -- i i i
C Charlie6#DNA/ 2439 GTCCTTGCTCTTGATGCTTGTTAAATAAGAAA-ACTGTTGCTCACACATG 2391
INTRON_3 398224 TAAGAAGATGAAAATGGCAG 398243
v iv
C Charlie6#DNA/ 2390 TAAGAAGTTGAAAACCGCAG 2371
Matrix = 20p37g.matrix
Transitions / transversions = 1.29 (99 / 77)
Gap_init rate = 0.05 (39 / 852), avg. gap size = 3.13 (122 / 39)
+ 376 27.1 36.5 1.5 INTRON_3 398240 398436 (1745) C Charlie6 DNA/hAT-Charlie (3234) 266 1 551 *
ANNOTATION EVIDENCE:
376 28.78 7.94 0.74 INTRON_3 398240 398365 1816 C Charlie6 DNA/hAT-Charlie 132 266 3234 891
INTRON_3 398240 GCAGTCTTCCTATATCCTGCTTCAAAAACTGATAAAATACTCAACCCAAT 398289
i i i i- i v v viv v
C Charlie6#DNA/ 266 GTAGCCTCCCC-TATCTTGCATCAAAAACTGAGAATGGACTCAACCAAAT 218
INTRON_3 398290 GATAATGGTTCTTTTT----------TAAAGGACTAAAAGATCTATAACA 398329
vv ii i vi v---------- v i i i iv ii
C Charlie6#DNA/ 217 GAGCACAGTCCTACTGCACACTGCCATACAGGGCTGAAAGACCCCTAATG 168
INTRON_3 398330 AAATTGCTAATGGGGTAACTTGGACACTCTGCATCA 398365
i ivi i v viv
C Charlie6#DNA/ 167 AAATTGCTAACGGGGCTGCTCGGTCACTGCCCATCA 132
Matrix = 20p37g.matrix
Transitions / transversions = 1.40 (21 / 15)
Gap_init rate = 0.02 (2 / 125), avg. gap size = 5.50 (11 / 2)
286 24.30 1.39 2.82 INTRON_3 398365 398436 1745 C Charlie6 DNA/hAT-Charlie 1 71 3429 892
INTRON_3 398365 ATCTCTTGCAGAACCTCTGGTGACCTCTTGTGGAACCCTAGTGTTTCACA 398414
i i ii i - i i v i i i - i ii
C Charlie6#DNA/ 71 ATTTCTCGTGGAGCC-CTAGCGACATCTCGCGGAACTCTAG-GTTCCGTA 24
INTRON_3 398415 GAACCCCA-TTTGAGAAACTCTG 398436
v -? i
C Charlie6#DNA/ 23 GAAACCCAANTTGAGAAACTTTG 1
Matrix = 20p37g.matrix
Transitions / transversions = 7.00 (14 / 2)
Gap_init rate = 0.04 (3 / 71), avg. gap size = 1.00 (3 / 3)
+ 2479 9.1 0.0 0.0 INTRON_3 399008 399316 (865) C AluY SINE/Alu (1) 310 2 552
ANNOTATION EVIDENCE:
2392 9.06 0.00 0.00 INTRON_3 399008 399316 865 C AluY SINE/Alu 2 310 1 791
INTRON_3 399008 TTTCTTTTTTTTATTTTATTTATTTATTTGAGACGGAGCCTCACTCTGTC 399057
i v v v v i i
C AluY#SINE/Alu 310 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTC 261
INTRON_3 399058 ACCCAGGCTGGAGTACAGTGGCGCAATCGCGGCTTACCGCAAGCTCTGTC 399107
i i i v i i i i
C AluY#SINE/Alu 260 GCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCC 211
INTRON_3 399108 TCCCAGGTTCACGCCATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACT 399157
i i
C AluY#SINE/Alu 210 TCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACT 161
INTRON_3 399158 ACAGGCAGCCGCCACCGCGCCTGGCTAATTTTTTGTATTTTTAACAGAGA 399207
iv i i ii
C AluY#SINE/Alu 160 ACAGGCGCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGA 111
INTRON_3 399208 CGGGGTTTCACCGTGTTAGCCAGGATGGTCTCCATCTCCTGACCTCGAGA 399257
v v
C AluY#SINE/Alu 110 CGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGA 61
INTRON_3 399258 TCCACCCGCCTCGGCCTCCCAAAGTGCTGGAATTACAGGCGTGAGCCACC 399307
i i
C AluY#SINE/Alu 60 TCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACC 11
INTRON_3 399308 ACGCCCGGC 399316
i
C AluY#SINE/Alu 10 GCGCCCGGC 2
Matrix = 14p37g.matrix
Transitions / transversions = 2.50 (20 / 8)
Gap_init rate = 0.00 (0 / 308), avg. gap size = 0.0 (0 / 0)
+ 413 29.0 3.5 3.1 INTRON_3 399478 399645 (536) C MER102a DNA/hAT-Charlie (141) 189 1 553
ANNOTATION EVIDENCE:
369 29.46 8.33 7.06 INTRON_3 399478 399645 536 C MER102c DNA/hAT-Charlie 1 170 161 894
INTRON_3 399478 TGTCCTGTAGGAATATGGACCTAGCAGTGCCATATTGTCTGACTTTTCAA 399527
i v i ii i i iiv v iv i i
C MER102c#DNA/h 170 TGCCATGTGGGAATGCGGGCCCAGTGTTGCCAGATCTTCCGATTTTTCAA 121
INTRON_3 399528 GGAAAATTAAGAAATTCAGCTACTT-TGTGAAATCTTCCCATTTTCAAAC 399576
ii iii - i i v vi - i v i -
C MER102c#DNA/h 120 GAGAAGCCA-GAAATCCGGATTTTTATGTGAAATCTCCCGATTTTTAAA- 73
INTRON_3 399577 ATCAGCAATTTAACTTTGTTAAATAAAACATA-TGAT----GGACTAGAT 399621
i---------- v iviivi v - i ---- i ii i
C MER102c#DNA/h 72 AC----------ACTGTGCGGGCCAAAACAAACTGGTCTGTGGGCCGGAC 33
INTRON_3 399622 TTGGTT--------GCCAATTTGCAACCTCTG 399645
? ii-------- i
C MER102c#DNA/h 32 NTGGCCCGCGGGCCGCCAGTTTGCAACCTCTG 1
Matrix = 20p37g.matrix
Transitions / transversions = 3.09 (34 / 11)
Gap_init rate = 0.04 (7 / 167), avg. gap size = 3.71 (26 / 7)
## Batch Overlap Boundaries
## INTRON_3 58882, 56883, 115765, 113766, 172648, 170649, 229531, 227532, 286414, 284415, 343297, 341298
## Total Sequences: 1
## Total Length: 400181
## Total NonMask ( excluding >20bp runs of N/X bases ): 400181
## Total NonSub ( excluding all non ACGT bases ):400181
RepeatMasker version open-3.2.9 , default mode
run with blastp version 3.0SE-AB [2009-10-30] [linux26-x64-I32LPF64 2009-10-30T17:06:09]
RepBase Update 20090604, RM database version 20090604
413 28.70 0.92 0.92 INTRON_3 399478 399586 595 C MER102a DNA/hAT-Charlie 81 189 141 893
INTRON_3 399478 TGTCCTGTAGGAATATGGACCTAGCAGTGCCATATTGTCTGACTTTTCAA 399527
i v i ii i i iiv v iv i
C MER102a#DNA/h 189 TGCCATGTGGGAATGCGGGCCCAGTGTTGCCAGATCTTCTGATTTTTCAA 140
INTRON_3 399528 GGAAAATTAAGAAATTCAGCTACTT-TGTGAAATCTTCCCATTTTCAAAC 399576
ii iii - i v vi - i v i i
C MER102a#DNA/h 139 GAGAAGCCA-GAAATCCAGATTTTTATGTGAAATCTCCCGATTTTTAAAT 91
INTRON_3 399577 ATCAGCAATT 399586
i ii i
C MER102a#DNA/h 90 GTTGGCAACT 81
Matrix = 20p37g.matrix
Transitions / transversions = 3.43 (24 / 7)
Gap_init rate = 0.02 (2 / 108), avg. gap size = 1.00 (2 / 2)
+ 2518 8.1 0.3 0.0 INTRON_3 399683 399992 (189) C AluSp SINE/Alu (2) 311 1 554
ANNOTATION EVIDENCE:
2281 10.35 0.32 0.32 INTRON_3 399683 399992 189 C AluSx SINE/Alu 1 310 2 792
INTRON_3 399683 TTTTGTTTTTTTGTTTTGTTTTGTTTTTGAGACGGAGTTTCGCTCTTGTT 399732
v v v v i - i
C AluSx#SINE/Al 310 TTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCT-GTC 262
INTRON_3 399733 GCCCAGGCTGGAGTGCAATGGTGCAATCTCGGCTCACCACAACCTCAGCT 399782
i i i ii v i
C AluSx#SINE/Al 261 GCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCC 212
INTRON_3 399783 TCCCAGGTTCAAGCGATTCTCCTGCCTCAGCCTTCTGAGTAGCTGGGACT 399832
i i i i
C AluSx#SINE/Al 211 TCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATT 162
INTRON_3 399833 ACAGGCATACACCACCACGCCCAGCAAATTTT-GTATTTTTAGTAGAGAT 399881
iii i i v - i
C AluSx#SINE/Al 161 ACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGAC 112
INTRON_3 399882 GGGGTTTCTCCAGGTTGGTCAGGCTGGTCTCGAACTCCCGACCTTAGGTG 399931
v v i i i
C AluSx#SINE/Al 111 GGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTG 62
INTRON_3 399932 ATCTGCCCACCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC 399981
i i
C AluSx#SINE/Al 61 ATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCAC 12
INTRON_3 399982 CGCGCCCAGCC 399992
i
C AluSx#SINE/Al 11 CGCGCCCGGCC 1
Matrix = 14p37g.matrix
Transitions / transversions = 3.00 (24 / 8)
Gap_init rate = 0.01 (2 / 309), avg. gap size = 1.00 (2 / 2)