186 20.93 0.00 0.00 INTRON_3 1248 1290 (398891) C (CA)n Simple_repeat (0) 180 138 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) 2234 9.69 0.69 0.00 INTRON_3 3193 3481 (396700) C AluSx SINE/Alu (21) 291 1 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 60.00 0.00 0.00 INTRON_3 4774 4803 (395378) + AT_rich Low_complexity 140 169 (131) 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 13.44 0.96 0.00 INTRON_3 4805 5325 (394856) C L1PB3_3end LINE/L1 (10) 891 366 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) 6943 6.26 0.11 0.11 INTRON_3 5355 6234 (393947) C L1PA7_3end LINE/L1 (21) 880 1 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 (0) 3294 950 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 (1886) 1408 1 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 (0) 2275 528 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 (0) 1727 1 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 10.30 2.61 6.61 INTRON_3 11889 11959 (388222) C L1PB1_3end LINE/L1 (3) 895 831 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 9.38 0.00 1.56 INTRON_3 11960 12089 (388092) C (GAAA)n Simple_repeat (52) 128 1 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 (68) 830 830 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) 2129 14.52 0.00 0.32 INTRON_3 12098 12408 (387773) C AluSx SINE/Alu (2) 310 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 10.30 2.61 6.61 INTRON_3 12409 12718 (387463) C L1PB1_3end LINE/L1 (68) 830 528 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 12.77 0.00 0.00 INTRON_3 12719 12765 (387416) C (TA)n Simple_repeat (0) 180 134 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 10.30 2.61 6.61 INTRON_3 12766 12986 (387195) C L1PB1_3end LINE/L1 (371) 527 306 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 11.84 0.97 0.78 INTRON_3 12988 13198 (386983) C L1PB_orf2 LINE/L1 (1354) 1940 1732 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) 4338 5.06 0.72 0.36 INTRON_3 13199 13754 (386427) + LTR6B LTR/ERV1 1 558 (0) 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) 7600 21.89 1.55 2.45 INTRON_3 13755 15388 (384793) C L1M2_orf2 LINE/L1 (1563) 1728 101 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 (1563) 1731 398 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 9.70 0.32 0.48 INTRON_3 15389 16010 (384171) C L1PA10_3end LINE/L1 (6) 909 289 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) 7600 21.89 1.55 2.45 INTRON_3 16011 16102 (384079) C L1M2_orf2 LINE/L1 (3191) 100 16 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 (53) 2909 1734 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 (617) 2354 710 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 (2289) 682 1 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 23.18 1.79 7.55 INTRON_3 19158 19213 (380968) C L2b_3end LINE/L2 (4) 462 410 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) 686 25.11 8.10 7.08 INTRON_3 19279 19488 (380693) + MER52A LTR/ERV1 1 212 (1543) 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) 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) 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) 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) 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) 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 26.27 8.72 0.47 INTRON_3 20809 21003 (379178) C L1ME4a_3end LINE/L1 (642) 229 19 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 (14) 3280 3101 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) 283 32.87 5.46 4.15 INTRON_3 21114 21351 (378830) C L1M5_orf2 LINE/L1 (409) 2885 2645 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 (664) 2630 2287 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 (1035) 2259 1986 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) 230 30.69 5.22 3.15 INTRON_3 22183 22431 (377750) C L1MB7_3end LINE/L1 (253) 678 425 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 (296) 575 422 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 (475) 396 85 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 10.64 2.36 0.00 INTRON_3 22779 23455 (376726) C L1PA13_3end LINE/L1 (3) 907 215 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) 2168 11.60 0.68 0.34 INTRON_3 23467 23760 (376421) + AluSx SINE/Alu 1 295 (17) 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 12.90 0.00 0.00 INTRON_3 23761 23822 (376359) + L1MA4A_3end LINE/L1 206 267 (783) 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) 1226 6.45 6.38 1.01 INTRON_3 23843 24030 (376151) C L1PA12_3end LINE/L1 (716) 199 2 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 (0) 3294 2066 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 17.46 0.00 0.00 INTRON_3 25116 25178 (375003) C (GA)n Simple_repeat (0) 180 118 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 9.66 0.45 3.75 INTRON_3 25181 25199 (374982) C L1PREC2_orf2 LINE/L1 (1211) 2083 2066 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) 1926 14.80 2.63 0.00 INTRON_3 25200 25503 (374678) C AluSx SINE/Alu (0) 312 1 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 9.66 0.45 3.75 INTRON_3 25504 25696 (374485) C L1PREC2_orf2 LINE/L1 (1229) 2065 1874 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) 2412 9.36 0.00 0.00 INTRON_3 25697 25995 (374186) C AluY SINE/Alu (11) 300 2 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 9.66 0.45 3.75 INTRON_3 25996 26222 (373959) C L1PREC2_orf2 LINE/L1 (1421) 1873 1657 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 12.98 0.90 3.71 INTRON_3 26205 26980 (373201) C L1PREC2_orf2 LINE/L1 (1597) 1697 943 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 60.00 0.00 0.00 INTRON_3 27014 27038 (373143) C AT_rich Low_complexity (136) 164 140 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 70.00 0.00 0.00 INTRON_3 27016 27045 (373136) + AT_rich Low_complexity 127 156 (144) 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 18.60 2.33 0.00 INTRON_3 27198 27240 (372941) C (GAAA)n Simple_repeat (2) 178 135 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 22.92 2.08 0.00 INTRON_3 27641 27688 (372493) C L2a_3end LINE/L2 (253) 264 216 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 17.07 5.81 9.33 INTRON_3 28483 28637 (371544) C Charlie10 DNA/hAT-Charlie (143) 2679 2530 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 22.00 0.61 5.77 INTRON_3 28644 28784 (371397) + AluJb SINE/Alu 1 133 (179) 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) 2474 5.06 0.00 0.68 INTRON_3 28785 29082 (371099) + AluY SINE/Alu 1 296 (15) 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 22.00 0.61 5.77 INTRON_3 29083 29268 (370913) + AluJb SINE/Alu 134 312 (0) 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) 2264 8.36 4.01 0.00 INTRON_3 29307 29605 (370576) C AluY SINE/Alu (0) 311 1 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 27.78 0.00 0.00 INTRON_3 30157 30228 (369953) + Charlie7 DNA/hAT-Charlie 270 341 (2271) 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 27.18 7.04 4.11 INTRON_3 30210 30393 (369788) + Charlie7 DNA/hAT-Charlie 374 554 (2058) 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 16.07 1.19 3.66 INTRON_3 30394 30477 (369704) + L1PB4_3end LINE/L1 821 902 (1) 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 27.18 7.04 4.11 INTRON_3 30478 30576 (369605) + Charlie7 DNA/hAT-Charlie 555 665 (1947) 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 24.88 5.86 4.23 INTRON_3 30588 30843 (369338) + Charlie7 DNA/hAT-Charlie 2351 2610 (2) 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 31.86 0.00 1.77 INTRON_3 30873 30987 (369194) + MIR SINE/MIR 2 114 (148) 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 6.99 2.45 0.00 INTRON_3 31650 31776 (368405) + AluY SINE/Alu 1 127 (184) 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 3.45 0.00 0.00 INTRON_3 31777 31834 (368347) + (CAAAA)n Simple_repeat 2 59 (121) 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 6.99 2.45 0.00 INTRON_3 31835 31992 (368189) + AluY SINE/Alu 128 292 (19) 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 30.10 24.27 0.00 INTRON_3 32069 32171 (368010) + MIRc SINE/MIR 39 166 (102) 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 35.33 5.08 9.35 INTRON_3 32180 32435 (367746) C L2b_3end LINE/L2 (4) 462 217 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) 468 21.67 10.00 0.00 INTRON_3 32822 32941 (367240) C Arthur1B DNA/hAT-Tip100 (0) 1225 1094 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 (0) 177 90 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 16.52 1.19 0.89 INTRON_3 32942 33277 (366904) + L1MC_orf2 LINE/L1 2561 2897 (397) 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 12.05 0.00 0.00 INTRON_3 33312 33394 (366787) + L1MC_orf2 LINE/L1 2879 2961 (333) 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 18.18 0.00 0.00 INTRON_3 33387 33463 (366718) + L1MC_orf2 LINE/L1 2930 3006 (288) 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 28.72 14.86 1.19 INTRON_3 34962 35035 (365146) C MIRc SINE/MIR (171) 97 14 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 28.37 13.38 3.21 INTRON_3 35241 35382 (364799) C L2c_3end LINE/L2 (134) 344 189 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) 2104 14.29 0.00 0.00 INTRON_3 37068 37368 (362813) + AluSx SINE/Alu 1 301 (11) 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 29.05 8.33 0.45 INTRON_3 37388 37591 (362590) + MIRb SINE/MIR 40 259 (9) 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 6.45 0.00 0.00 INTRON_3 37593 37623 (362558) C (TAA)n Simple_repeat (2) 178 148 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 17.59 7.09 5.23 INTRON_3 37624 37905 (362276) + L1M4_orf2 LINE/L1 1615 1901 (1393) 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 23.40 4.00 0.45 INTRON_3 37911 38760 (361421) + L1M4_orf2 LINE/L1 2314 3193 (101) 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) 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) 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 17.88 0.56 0.00 INTRON_3 38787 38965 (361216) + L1MB4_3end LINE/L1 33 212 (715) 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 28.27 0.00 2.17 INTRON_3 38968 39014 (361167) C L2c_3end LINE/L2 (84) 394 349 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 4.60 0.00 0.14 INTRON_3 39164 39904 (360277) C L1PA5_3end LINE/L1 (0) 901 162 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 5.28 0.25 0.00 INTRON_3 39906 43127 (357054) C L1P1_orf2 LINE/L1 (64) 3230 1 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 (0) 2259 11 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 18.32 3.96 0.00 INTRON_3 45809 46010 (354171) C MER2 DNA/TcMar-Tigger (0) 345 136 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 (132) 213 1 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 31.68 5.98 0.52 INTRON_3 46355 46538 (353643) + MIRc SINE/MIR 45 238 (30) 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 50.00 0.00 0.00 INTRON_3 46823 46852 (353329) + AT_rich Low_complexity 132 161 (139) 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) 505 29.14 9.09 2.27 INTRON_3 47752 47916 (352265) + MIRb SINE/MIR 93 268 (0) 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) 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 24.82 7.55 1.18 INTRON_3 47982 48140 (352041) + L1ME4a_3end LINE/L1 527 695 (176) 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 30.02 6.35 5.30 INTRON_3 48233 48374 (351807) + L1MC4_5end LINE/L1 2224 2369 (186) 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 14.46 8.39 1.37 INTRON_3 48375 48851 (351330) + L1MB8_3end LINE/L1 416 925 (0) 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 30.02 6.35 5.30 INTRON_3 48852 49007 (351174) + L1MC4_5end LINE/L1 2370 2525 (30) 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) 1781 17.43 0.97 1.63 INTRON_3 49023 49331 (350850) C AluJb SINE/Alu (4) 308 2 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) 2219 13.14 0.00 0.00 INTRON_3 49382 49693 (350488) + AluSx SINE/Alu 1 312 (0) 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 0.00 0.00 0.00 INTRON_3 49697 49722 (350459) C (TA)n Simple_repeat (1) 179 154 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 27.10 6.83 10.60 INTRON_3 49986 50278 (349903) + L1M5_orf2 LINE/L1 696 978 (2316) 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 25.00 4.64 4.93 INTRON_3 50436 50801 (349380) + MLT1A0 LTR/ERVL-MaLR 1 365 (0) 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 71.88 0.00 0.00 INTRON_3 50843 50874 (349307) + AT_rich Low_complexity 122 153 (147) 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) 1981 11.84 1.73 0.68 INTRON_3 51001 51289 (348892) C AluSx SINE/Alu (20) 292 1 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 30.08 15.47 4.50 INTRON_3 51445 51625 (348556) C MIRb SINE/MIR (64) 204 5 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 26.27 7.14 0.96 INTRON_3 51980 52175 (348006) + MER103C DNA/hAT-Charlie 34 241 (56) 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 27.27 3.90 0.00 INTRON_3 52798 52874 (347307) + MIRc SINE/MIR 31 110 (158) 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 33.75 0.00 3.37 INTRON_3 53310 53401 (346780) C MER5B DNA/hAT-Charlie (0) 178 90 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 23.61 0.00 5.88 INTRON_3 53332 53403 (346778) + MER5A DNA/hAT-Charlie 34 101 (88) 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 23.70 4.00 2.97 INTRON_3 53641 53740 (346441) C (TAAA)n Simple_repeat (2) 178 78 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) 283 30.00 1.23 1.23 INTRON_3 53836 53916 (346265) C L2a_3end LINE/L2 (1) 516 436 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 (116) 401 285 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 8.56 1.48 0.46 INTRON_3 54026 55305 (344876) + L1PB_orf2 LINE/L1 2002 3294 (0) 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) 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) 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 30.03 2.83 1.60 INTRON_3 56027 56273 (343908) C L2a_3end LINE/L2 (254) 263 14 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 26.80 0.00 0.00 INTRON_3 56757 56853 (343328) C MER133B DNA? (28) 112 16 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) 2760 2.27 0.00 0.00 INTRON_3 57587 57895 (342286) + AluY SINE/Alu 1 309 (2) 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 37.55 4.23 8.08 INTRON_3 57968 58416 (341765) C L2c_3end LINE/L2 (4) 474 42 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 23.52 8.14 1.09 INTRON_3 58922 59007 (341174) + MIR3 SINE/MIR 88 179 (29) 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 0.00 0.00 0.00 INTRON_3 60246 60271 (339910) + (A)n Simple_repeat 1 26 (154) 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 30.77 0.00 0.00 INTRON_3 60650 60714 (339467) + MIRc SINE/MIR 197 261 (7) 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 31.22 8.64 1.15 INTRON_3 60831 61073 (339108) C Plat_L3 LINE/CR1 (28) 3558 3298 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 31.73 1.92 0.00 INTRON_3 61514 61617 (338564) C L2a_3end LINE/L2 (20) 497 392 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 30.75 5.61 2.73 INTRON_3 62187 62293 (337888) + L3 LINE/CR1 4235 4344 (145) 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) 2437 7.26 0.00 0.00 INTRON_3 62303 62605 (337576) + AluY SINE/Alu 1 303 (8) 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 0.00 0.00 0.00 INTRON_3 62616 62656 (337525) + (CAT)n Simple_repeat 3 43 (137) 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 24.06 9.55 4.28 INTRON_3 62693 62870 (337311) C MIRb SINE/MIR (7) 261 75 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 18.10 8.19 0.00 INTRON_3 62913 63144 (337037) C MER45B DNA/hAT-Tip100 (220) 820 570 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) 1093 6.72 1.49 0.00 INTRON_3 63145 63278 (336903) + AluSx SINE/Alu 1 136 (176) 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 25.33 0.00 0.00 INTRON_3 63572 63646 (336535) C MER121 DNA/TcMar? (175) 222 148 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) 1596 30.55 4.12 0.80 INTRON_3 64044 64528 (335653) + L1M3d_5end LINE/L1 11 511 (864) 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) 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) 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) 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 17.23 1.83 13.41 INTRON_3 65572 65953 (334228) + MER2 DNA/TcMar-Tigger 3 345 (0) 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 30.29 7.33 2.83 INTRON_3 65954 66008 (334173) + L1M3d_5end LINE/L1 889 958 (417) 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 15.81 3.60 1.41 INTRON_3 66009 66425 (333756) C MSTB LTR/ERVL-MaLR (0) 426 1 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 30.29 7.33 2.83 INTRON_3 66426 66480 (333701) + L1M3d_5end LINE/L1 959 1012 (363) 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 13.51 0.00 0.00 INTRON_3 66501 66537 (333644) + (CA)n Simple_repeat 2 38 (142) 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 26.03 2.74 0.00 INTRON_3 66552 66624 (333557) C (CATATA)n Simple_repeat (39) 141 67 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 12.20 0.00 0.00 INTRON_3 66633 66673 (333508) + (CA)n Simple_repeat 2 42 (138) 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 25.94 1.08 1.08 INTRON_3 66679 67508 (332673) + L1M4c_5end LINE/L1 1043 1872 (628) 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) 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) 1729 19.59 0.00 0.00 INTRON_3 67552 67842 (332339) + AluSx SINE/Alu 2 292 (20) 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) 1921 28.87 6.07 5.14 INTRON_3 67843 68323 (331858) + L1M1_5end LINE/L1 3172 3667 (8) 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) 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) 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 7.35 0.32 1.97 INTRON_3 70585 71280 (328901) C L1PA10_3end LINE/L1 (1) 914 230 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) 2203 11.33 0.32 1.29 INTRON_3 71281 71593 (328588) C AluY SINE/Alu (0) 311 2 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 7.35 0.32 1.97 INTRON_3 71594 71825 (328356) C L1PA10_3end LINE/L1 (686) 229 1 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 (0) 3294 2936 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 16.31 0.49 2.65 INTRON_3 72035 72651 (327530) + L1M3_orf2 LINE/L1 2414 3017 (271) 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 16.51 1.12 3.06 INTRON_3 72643 72868 (327313) + L1MB1_3end LINE/L1 131 354 (561) 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) 2284 10.59 0.00 0.33 INTRON_3 72869 73171 (327010) + AluSx SINE/Alu 1 302 (10) 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 16.51 1.12 3.06 INTRON_3 73172 73744 (326437) + L1MB1_3end LINE/L1 355 915 (0) 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) 883 20.44 2.67 0.00 INTRON_3 73783 74007 (326174) C L1ME1_3end LINE/L1 (695) 231 1 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 (3) 3291 2990 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 19.51 2.44 0.00 INTRON_3 74465 74505 (325676) + MIRb SINE/MIR 180 221 (47) 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 86.84 0.00 0.00 INTRON_3 74687 74724 (325457) + AT_rich Low_complexity 110 147 (153) 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 18.00 3.55 4.01 INTRON_3 75107 75609 (324572) C L1M4_orf2 LINE/L1 (1746) 1548 1035 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 14.07 8.68 0.00 INTRON_3 75610 75943 (324238) + THE1B LTR/ERVL-MaLR 2 364 (0) 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 10.38 3.80 0.32 INTRON_3 75944 77469 (322712) + THE1-int LTR/ERVL-MaLR 1 1579 (1) 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 (2260) 1034 1034 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 13.99 8.33 0.00 INTRON_3 77477 77812 (322369) + THE1B LTR/ERVL-MaLR 1 364 (0) 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 18.00 3.55 4.01 INTRON_3 77813 77976 (322205) C L1M4_orf2 LINE/L1 (2260) 1034 875 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) 247 39.87 6.58 4.29 INTRON_3 78478 78705 (321476) + L2b_3end LINE/L2 158 390 (76) 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) 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 71.43 0.00 0.00 INTRON_3 78746 78773 (321408) + AT_rich Low_complexity 123 150 (150) 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 0.00 0.00 0.00 INTRON_3 79614 79633 (320548) C (TA)n Simple_repeat (1) 179 160 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 63.64 0.00 0.00 INTRON_3 80005 80026 (320155) C AT_rich Low_complexity (137) 163 142 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) 2298 10.71 0.32 0.00 INTRON_3 80120 80427 (319754) C AluSx SINE/Alu (3) 309 1 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 30.13 1.18 2.38 INTRON_3 80441 80525 (319656) + (CATATA)n Simple_repeat 5 88 (92) 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) 434 30.44 11.58 1.76 INTRON_3 80578 80888 (319293) C L1ME2_3end LINE/L1 (467) 444 104 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 (429) 441 133 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 (424) 447 180 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 (689) 300 25 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 28.86 1.43 5.97 INTRON_3 81068 81207 (318974) C MIRb SINE/MIR (51) 217 84 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) 243 14.63 0.00 0.00 INTRON_3 82403 82443 (317738) C MIRb SINE/MIR (52) 216 176 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 (123) 139 2 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 24.61 1.52 1.52 INTRON_3 82618 82683 (317498) C MIR SINE/MIR (0) 262 197 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 37.85 5.77 0.92 INTRON_3 82679 82782 (317399) C MIR SINE/MIR (152) 110 2 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 58.06 0.00 0.00 INTRON_3 83222 83252 (316929) + AT_rich Low_complexity 137 167 (133) 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 11.90 2.36 1.00 INTRON_3 83253 83549 (316632) C L1MA3_3end LINE/L1 (270) 782 482 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 15.50 3.88 0.00 INTRON_3 83543 83553 (316628) C L1M1_5end LINE/L1 (3532) 143 133 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) 2208 12.05 0.32 0.32 INTRON_3 83554 83861 (316320) C AluSx SINE/Alu (4) 308 1 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 15.50 3.88 0.00 INTRON_3 83862 83978 (316203) C L1M1_5end LINE/L1 (3543) 132 11 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 47.83 0.00 0.00 INTRON_3 84635 84657 (315524) C AT_rich Low_complexity (140) 160 138 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 15.15 4.04 0.00 INTRON_3 85041 85337 (314844) + MER58B DNA/hAT-Charlie 1 309 (32) 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 19.43 8.29 0.43 INTRON_3 87028 87244 (312937) C L1ME2_3end LINE/L1 (7) 904 671 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 (538) 653 473 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 26.38 5.45 2.11 INTRON_3 87419 87693 (312488) C L1M5_orf2 LINE/L1 (232) 3062 2779 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) 1906 23.72 6.80 3.89 INTRON_3 87713 88462 (311719) C L1M5_orf2 LINE/L1 (1691) 1603 833 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 (1776) 1512 655 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) 279 21.18 11.48 9.68 INTRON_3 88619 88801 (311380) C L1MEc_5end LINE/L1 (1152) 1375 1190 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 (1028) 1189 1016 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 (1064) 1037 650 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 (1250) 967 712 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 26.60 1.46 9.45 INTRON_3 89163 89226 (310955) C L1MEg_5end LINE/L1 (1489) 612 552 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) 2117 12.17 0.65 0.98 INTRON_3 89227 89533 (310648) + AluSx SINE/Alu 1 306 (6) 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 26.60 1.46 9.45 INTRON_3 89534 89605 (310576) C L1MEg_5end LINE/L1 (1550) 551 486 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 35.11 10.15 6.23 INTRON_3 90064 90202 (309979) C L1MEb_5end LINE/L1 (716) 373 240 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) 2107 12.06 0.95 2.90 INTRON_3 90203 90518 (309663) + AluSx SINE/Alu 1 310 (2) 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 35.11 10.15 6.23 INTRON_3 90519 90703 (309478) C L1MEb_5end LINE/L1 (850) 239 37 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 26.98 4.04 2.34 INTRON_3 90719 91096 (309085) C L1MEf_5end LINE/L1 (130) 2087 1706 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 11.11 3.70 0.00 INTRON_3 91097 91177 (309004) C L1MB2_3end LINE/L1 (3) 915 832 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 26.98 4.04 2.34 INTRON_3 91178 92183 (307998) C L1MEf_5end LINE/L1 (512) 1705 680 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 (518) 1583 455 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 19.67 0.00 0.00 INTRON_3 92907 92967 (307214) C Tigger1 DNA/TcMar-Tigger (0) 2418 2358 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) 1215 8.81 0.00 6.43 INTRON_3 92968 93149 (307032) C AluY SINE/Alu (42) 269 99 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 15.23 11.67 1.52 INTRON_3 93203 93262 (306919) C L1MA7_3end LINE/L1 (11) 1027 956 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 4.35 0.00 0.00 INTRON_3 93263 93285 (306896) + (CA)n Simple_repeat 1 23 (157) 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) 463 15.23 11.67 1.52 INTRON_3 93286 93344 (306837) C L1MA7_3end LINE/L1 (83) 955 896 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 (235) 803 231 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) 1589 22.19 0.00 1.02 INTRON_3 93925 94220 (305961) C AluJb SINE/Alu (18) 294 2 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) 734 18.01 6.21 0.00 INTRON_3 94221 94381 (305800) C L1ME2_3end LINE/L1 (740) 171 1 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 (0) 3294 3014 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) 890 29.34 2.82 1.26 INTRON_3 94520 94909 (305272) C L1M4c_5end LINE/L1 (819) 1681 1286 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 (1469) 2235 1904 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) 382 14.31 0.00 4.29 INTRON_3 95019 95091 (305090) C L1PA16_3end LINE/L1 (2) 911 842 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 (104) 809 37 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 (0) 3294 3169 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 13.72 2.23 0.92 INTRON_3 96620 98864 (301317) C L1P4_orf2 LINE/L1 (106) 3188 915 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 (1685) 1609 1 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 (0) 2596 1483 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) 207 0.00 0.00 0.00 INTRON_3 100721 100743 (299438) C (CAAA)n Simple_repeat (0) 180 158 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) 2277 7.80 0.00 2.48 INTRON_3 100747 101035 (299146) C AluY SINE/Alu (29) 282 1 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) 6337 15.06 3.72 1.78 INTRON_3 101036 101731 (298450) C L1P4a_5end LINE/L1 (1131) 1465 754 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 (1114) 1482 1163 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 (0) 1783 1464 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 (566) 1217 2 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) 2345 8.48 0.00 0.34 INTRON_3 103137 103432 (296749) C AluY SINE/Alu (15) 296 2 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 29.49 1.83 0.45 INTRON_3 103901 104118 (296063) + L1MC4a_3end LINE/L1 443 663 (1966) 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 78.26 0.00 0.00 INTRON_3 104672 104740 (295441) + AT_rich Low_complexity 145 213 (87) 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) 204 33.04 10.78 3.93 INTRON_3 104761 104927 (295254) C MIRb SINE/MIR (40) 228 51 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 (39) 229 131 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 34.45 5.88 0.00 INTRON_3 105082 105200 (294981) C MER102c DNA/hAT-Charlie (3) 328 203 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 16.02 3.85 8.00 INTRON_3 105415 105570 (294611) C L1MC4a_3end LINE/L1 (6) 2623 2474 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 20.53 3.50 0.98 INTRON_3 105575 106174 (294007) C L1MD2_3end LINE/L1 (213) 893 279 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 (539) 450 26 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 (0) 3294 3154 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 26.87 8.76 3.96 INTRON_3 106460 106676 (293505) C L1ME5_3end LINE/L1 (2) 939 713 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) 1840 25.88 6.13 2.36 INTRON_3 106770 107422 (292759) C L1MC3_3end LINE/L1 (10) 2522 1846 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 (88) 2654 1500 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 (698) 1834 1491 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) 1318 23.28 1.60 2.58 INTRON_3 107996 108308 (291873) C AluJb SINE/Alu (2) 310 1 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 22.57 2.19 7.32 INTRON_3 108309 108416 (291765) C L1MC3_3end LINE/L1 (1042) 1490 1383 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) 6393 13.81 6.23 1.14 INTRON_3 108417 109588 (290593) + Tigger3b DNA/TcMar-Tigger 1 1231 (0) 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) 864 23.01 0.41 11.31 INTRON_3 109589 109659 (290522) C L1MC4a_3end LINE/L1 (1212) 1417 1350 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 (1150) 1382 1357 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) 328 26.67 5.83 0.00 INTRON_3 109672 109791 (290390) C L1MD3_3end LINE/L1 (1735) 1007 881 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 (37) 889 225 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) 2186 10.04 1.32 1.65 INTRON_3 110434 110737 (289444) C AluY SINE/Alu (8) 303 1 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 25.71 5.18 8.18 INTRON_3 110738 110882 (289299) C L1ME1_3end LINE/L1 (702) 224 83 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 (0) 3294 3218 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 27.08 11.31 1.08 INTRON_3 110911 111078 (289103) C L1ME4a_3end LINE/L1 (3) 868 684 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 19.79 4.18 5.05 INTRON_3 111175 111653 (288528) + MLT1D LTR/ERVL-MaLR 31 505 (0) 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 10.97 2.41 1.53 INTRON_3 112948 113927 (286254) C L1MA1_3end LINE/L1 (0) 1049 55 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) 7857 6.58 0.40 0.60 INTRON_3 113928 114936 (285245) + LTR13 LTR/ERVK 1 1007 (0) 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) 9542 9.02 2.20 0.75 INTRON_3 114937 116295 (283886) C L1M1_orf2 LINE/L1 (96) 3198 1819 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) 12859 9.62 2.39 0.64 INTRON_3 116075 116520 (283661) C L1M1_orf2 LINE/L1 (1251) 2043 1591 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 3.51 0.00 0.00 INTRON_3 116521 116577 (283604) + (TGG)n Simple_repeat 3 59 (121) 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 9.62 2.39 0.64 INTRON_3 116578 118138 (282043) C L1M1_orf2 LINE/L1 (1704) 1590 2 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 (0) 3675 3319 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 8.07 0.15 4.18 INTRON_3 118345 118991 (281190) C L1PA14_3end LINE/L1 (0) 908 287 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 10.53 1.95 1.01 INTRON_3 118992 119816 (280365) C L1M1_5end LINE/L1 (357) 3318 2486 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 17.72 0.00 0.00 INTRON_3 119817 119895 (280286) C L1M1_5end LINE/L1 (259) 3416 3338 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) 4331 11.88 4.25 0.00 INTRON_3 119895 120576 (279605) C L1M1_5end LINE/L1 (1187) 2488 1778 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 (1744) 1931 151 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 2.99 0.00 0.00 INTRON_3 122180 122346 (277835) + L1PA5_3end LINE/L1 735 901 (0) 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 19.13 1.62 1.45 INTRON_3 122347 122445 (277736) C L1M1_5end LINE/L1 (3525) 150 72 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 25.81 5.43 1.04 INTRON_3 122460 122643 (277538) + MLT1L LTR/ERVL-MaLR 335 526 (84) 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) 631 33.45 5.60 1.93 INTRON_3 122755 123004 (277177) + MIR SINE/MIR 2 260 (2) 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) 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) 297 25.40 13.45 0.75 INTRON_3 123770 123888 (276293) + MIRc SINE/MIR 5 138 (130) 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) 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 76.92 0.00 0.00 INTRON_3 123919 123970 (276211) + AT_rich Low_complexity 131 182 (118) 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) 190 34.35 5.74 9.32 INTRON_3 123977 124098 (276083) + L2c_3end LINE/L2 352 469 (9) 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) 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) 2190 12.21 0.00 0.66 INTRON_3 124227 124531 (275650) + AluSx SINE/Alu 1 303 (9) 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 26.32 1.05 0.00 INTRON_3 125962 126056 (274125) C MIR3 SINE/MIR (14) 194 99 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 22.22 1.82 1.82 INTRON_3 126356 126410 (273771) + L2b_3end LINE/L2 403 457 (9) 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 10.69 1.43 0.43 INTRON_3 126528 128350 (271831) + L1PREC2_orf2 LINE/L1 1358 3198 (96) 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) 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 2.24 0.45 0.33 INTRON_3 128407 129304 (270877) C L1PA4_3end LINE/L1 (3) 899 1 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 (0) 3294 2963 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 8.29 2.26 0.00 INTRON_3 129484 130014 (270167) + L1PA13_3end LINE/L1 97 639 (271) 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) 2078 10.99 0.00 0.00 INTRON_3 130477 130749 (269432) + AluSx SINE/Alu 11 283 (29) 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 6.45 0.00 0.00 INTRON_3 130750 130780 (269401) + (TAA)n Simple_repeat 2 32 (148) 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 89.06 0.00 0.00 INTRON_3 132103 132166 (268015) + AT_rich Low_complexity 88 151 (149) 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) 2133 11.71 1.00 0.00 INTRON_3 132464 132762 (267419) C AluSx SINE/Alu (10) 302 1 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 7.98 1.79 1.07 INTRON_3 133103 133381 (266800) + L1PA13_3end LINE/L1 628 908 (2) 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 32.90 4.76 5.43 INTRON_3 133518 133832 (266349) C L3 LINE/CR1 (4) 4485 4173 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 32.73 11.82 0.00 INTRON_3 134217 134326 (265855) + Charlie18a DNA/hAT-Charlie 6 128 (214) 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 18.77 10.21 7.02 INTRON_3 134299 134533 (265648) + Charlie18a DNA/hAT-Charlie 101 342 (0) 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 30.18 2.84 5.85 INTRON_3 134590 134765 (265416) + AmnSINE1 SINE/Deu 62 232 (343) 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) 1299 22.17 0.94 5.56 INTRON_3 134795 135114 (265067) C AluJb SINE/Alu (6) 306 1 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 37.66 3.38 1.32 INTRON_3 136297 136444 (263737) + MIRb SINE/MIR 2 152 (116) 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 29.55 5.48 5.61 INTRON_3 136632 138363 (261818) + L1M3e_5end LINE/L1 1 1730 (383) 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) 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 26.71 3.79 2.83 INTRON_3 138706 140104 (260077) + L1M1_5end LINE/L1 2263 3674 (1) 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) 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) 767 19.88 0.62 0.00 INTRON_3 140204 140364 (259817) + L1M3_orf2 LINE/L1 2794 2955 (333) 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) 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) 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) 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) 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) 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 15.91 8.13 0.38 INTRON_3 141505 141750 (258431) C L1MC3_3end LINE/L1 (169) 2363 2099 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 13.53 7.01 0.86 INTRON_3 141762 142089 (258092) C L1MC3_3end LINE/L1 (493) 2039 1692 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 (719) 1813 1601 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 21.87 0.00 2.19 INTRON_3 142193 142379 (257802) + MER58A DNA/hAT-Charlie 42 224 (0) 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 66.67 0.00 0.00 INTRON_3 143380 143421 (256760) + AT_rich Low_complexity 128 169 (131) 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 33.16 6.31 0.85 INTRON_3 143478 143699 (256482) + L2 LINE/L2 1851 2084 (998) 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 41.52 7.32 0.98 INTRON_3 143820 144106 (256075) + L2 LINE/L2 2331 2635 (447) 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 34.91 11.32 0.00 INTRON_3 144543 144648 (255533) + L2c_3end LINE/L2 114 231 (247) 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 26.39 13.81 4.37 INTRON_3 144681 144890 (255291) + MIRb SINE/MIR 2 230 (38) 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) 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 4.00 0.00 0.00 INTRON_3 145032 145081 (255100) + (CA)n Simple_repeat 2 51 (129) 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 29.22 10.76 2.57 INTRON_3 146240 146527 (253654) + AmnSINE1 SINE/Deu 193 503 (72) 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 21.95 4.88 0.00 INTRON_3 146561 146601 (253580) + AmnSINE1 SINE/Deu 508 550 (25) 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) 2195 10.59 0.65 1.64 INTRON_3 146823 147129 (253052) + AluSx SINE/Alu 1 304 (8) 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 24.90 2.64 5.42 INTRON_3 147208 147776 (252405) C L1ME2_3end LINE/L1 (0) 911 358 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 (626) 565 170 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 21.95 8.24 5.34 INTRON_3 147945 148199 (251982) C L1MD3_3end LINE/L1 (10) 2732 2471 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 18.80 4.51 0.00 INTRON_3 148192 148324 (251857) C L1MD3_3end LINE/L1 (129) 2613 2475 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) 587 20.63 1.46 10.58 INTRON_3 148322 148527 (251654) C L1ME2_3end LINE/L1 (721) 190 2 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 (6) 3288 3053 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 24.73 14.38 3.09 INTRON_3 148829 148974 (251207) C MIR SINE/MIR (0) 262 101 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 14.71 3.92 0.00 INTRON_3 148988 149293 (250888) + L1M2a1_5end LINE/L1 3 320 (1522) 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) 2096 23.34 2.52 0.00 INTRON_3 149274 149710 (250471) + L1M2a1_5end LINE/L1 888 1335 (507) 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) 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 38.75 0.00 0.00 INTRON_3 150116 150195 (249986) C MIR SINE/MIR (181) 81 2 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 27.87 10.59 5.03 INTRON_3 150587 150756 (249425) + X7A_LINE LINE/CR1 28 206 (61) 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 34.36 10.40 2.22 INTRON_3 150987 151111 (249070) + L2c_3end LINE/L2 193 327 (151) 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 25.88 7.14 0.67 INTRON_3 151298 151437 (248744) C MIRb SINE/MIR (108) 160 12 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 25.94 10.48 0.87 INTRON_3 151597 151701 (248480) + L2a_3end LINE/L2 402 516 (1) 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 29.97 10.27 4.66 INTRON_3 152344 152567 (247614) + L2 LINE/L2 1246 1481 (1601) 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 27.20 3.09 5.26 INTRON_3 152584 152874 (247307) + L2 LINE/L2 2798 3082 (0) 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) 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 11.15 1.83 0.43 INTRON_3 153648 154575 (245606) + Charlie3 DNA/hAT-Charlie 1 941 (1765) 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) 7671 2.33 0.00 0.00 INTRON_3 154580 155480 (244701) C L1PA4_3end LINE/L1 (1) 901 1 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 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 (0) 2259 165 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 8.48 0.17 0.17 INTRON_3 160571 161172 (239009) + Charlie3 DNA/hAT-Charlie 2105 2706 (0) 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 27.78 1.85 0.00 INTRON_3 161173 161226 (238955) + L2a_3end LINE/L2 458 512 (5) 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 32.35 14.92 0.97 INTRON_3 162684 162864 (237317) C MIRb SINE/MIR (7) 261 56 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 (150) 118 4 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 14.45 0.69 1.62 INTRON_3 163462 163897 (236284) + MER57A1 LTR/ERV1 1 432 (0) 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 29.08 10.84 0.55 INTRON_3 163971 164136 (236045) C MIRb SINE/MIR (46) 222 40 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 (65) 197 8 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 15.72 7.26 0.52 INTRON_3 164499 164677 (235504) + MER82 DNA/TcMar-Tigger 14 204 (449) 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 28.83 2.29 4.69 INTRON_3 164840 164970 (235211) C MER44C DNA/TcMar-Tigger (108) 625 498 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 16.67 0.00 0.00 INTRON_3 164982 165047 (235134) + MER82 DNA/TcMar-Tigger 201 266 (387) 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 19.12 1.22 0.24 INTRON_3 165051 165459 (234722) + MER82 DNA/TcMar-Tigger 241 653 (0) 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 27.25 5.73 1.84 INTRON_3 166102 166258 (233923) + MIR SINE/MIR 6 168 (94) 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) 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 75.61 0.00 0.00 INTRON_3 166330 166370 (233811) + AT_rich Low_complexity 125 165 (135) 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 74.29 0.00 0.00 INTRON_3 166424 166458 (233723) + AT_rich Low_complexity 120 154 (146) 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 23.08 3.85 0.00 INTRON_3 166997 167048 (233133) C L2c_3end LINE/L2 (52) 426 373 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 26.73 6.81 3.03 INTRON_3 167069 167450 (232731) C MLT1C LTR/ERVL-MaLR (7) 460 65 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 (258) 247 28 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) 250 36.42 5.26 7.53 INTRON_3 167739 167833 (232348) + MIR SINE/MIR 8 100 (162) 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) 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) 1255 10.47 1.14 1.72 INTRON_3 169673 169847 (230334) + AluSx SINE/Alu 1 174 (138) 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) 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) 183 4.17 0.00 0.00 INTRON_3 169886 169909 (230272) + (CAAA)n Simple_repeat 2 25 (155) 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) 1971 13.86 1.97 0.32 INTRON_3 169926 170229 (229952) C AluSx SINE/Alu (3) 309 1 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) 332 33.31 4.85 2.10 INTRON_3 171705 172075 (228106) + L1M5_orf2 LINE/L1 2896 3276 (18) 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) 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) 587 26.62 11.00 0.45 INTRON_3 172320 172519 (227662) + L1ME5_3end LINE/L1 259 479 (462) 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) 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) 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 34.02 1.68 6.14 INTRON_3 172981 173099 (227082) + L2c_3end LINE/L2 365 478 (0) 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 33.69 9.88 4.71 INTRON_3 173354 173515 (226666) + L2c_3end LINE/L2 4 173 (305) 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 23.89 8.47 11.30 INTRON_3 173751 173780 (226401) C MIR3 SINE/MIR (9) 199 174 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 17.39 1.39 2.82 INTRON_3 173781 173975 (226206) + MSTB LTR/ERVL-MaLR 1 198 (228) 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) 2155 10.17 0.34 0.68 INTRON_3 173976 174272 (225909) + AluSx SINE/Alu 1 296 (16) 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 17.39 1.39 2.82 INTRON_3 174273 174508 (225673) + MSTB LTR/ERVL-MaLR 199 426 (0) 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 23.89 8.47 11.30 INTRON_3 174509 174595 (225586) C MIR3 SINE/MIR (35) 173 85 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 10.26 1.47 0.00 INTRON_3 175239 175920 (224261) C L1PB2_3end LINE/L1 (1) 897 206 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 75.76 0.00 0.00 INTRON_3 176046 176078 (224103) + AT_rich Low_complexity 120 152 (148) 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 26.92 0.00 0.00 INTRON_3 176056 176081 (224100) C AT_rich Low_complexity (138) 162 137 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 52.17 0.00 0.00 INTRON_3 176535 176557 (223624) C AT_rich Low_complexity (137) 163 141 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 12.99 0.43 0.00 INTRON_3 177327 177557 (222624) C L1MA4A_3end LINE/L1 (22) 1028 797 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) 308 33.49 4.52 4.05 INTRON_3 177826 178046 (222135) + L2b_3end LINE/L2 22 243 (223) 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) 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) 2177 12.29 0.00 0.33 INTRON_3 178048 178349 (221832) + AluSx SINE/Alu 1 301 (11) 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 32.54 4.60 1.11 INTRON_3 178865 178951 (221230) C MIRc SINE/MIR (162) 106 17 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 34.76 5.75 2.99 INTRON_3 179069 179329 (220852) C L2 LINE/L2 (238) 2844 2577 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 23.88 2.99 0.00 INTRON_3 180772 180838 (219343) C MER113 DNA/hAT-Charlie (295) 226 158 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 19.01 4.91 9.62 INTRON_3 180845 181007 (219174) + L1ME4a_3end LINE/L1 715 870 (1) 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 0.85 0.00 0.00 INTRON_3 181333 181802 (218379) C L1P1_orf2 LINE/L1 (939) 2355 1886 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 0.42 0.00 0.00 INTRON_3 181802 182745 (217436) + L1P1_orf2 LINE/L1 2351 3294 (0) 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) 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 9.52 0.00 0.00 INTRON_3 183499 183540 (216641) + (A)n Simple_repeat 1 42 (138) 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 19.75 6.02 0.86 INTRON_3 183791 184122 (216059) C MER113 DNA/hAT-Charlie (118) 403 55 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 0.00 0.00 0.00 INTRON_3 184859 184879 (215302) C (A)n Simple_repeat (0) 180 160 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) 449 30.22 10.65 3.46 INTRON_3 185169 185384 (214797) C MIR SINE/MIR (24) 238 8 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 (26) 242 50 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 29.78 4.62 6.87 INTRON_3 185523 185760 (214421) + MIRb SINE/MIR 27 259 (9) 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 21.28 0.00 0.00 INTRON_3 185993 186039 (214142) C (CATATA)n Simple_repeat (4) 176 130 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 23.72 5.67 1.36 INTRON_3 186601 186741 (213440) C MamRep605 Unknown (377) 499 353 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 11.30 2.40 0.23 INTRON_3 186827 187243 (212938) C LTR47A2 LTR/ERVL (6) 426 1 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 35.29 6.95 0.00 INTRON_3 187244 187430 (212751) + L2b_3end LINE/L2 44 243 (223) 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 28.10 2.98 2.05 INTRON_3 187432 187867 (212314) + MLT1J LTR/ERVL-MaLR 70 509 (3) 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 32.59 10.10 2.35 INTRON_3 187896 188093 (212088) + L2a_3end LINE/L2 284 496 (21) 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 8.87 1.33 0.33 INTRON_3 188114 189018 (211163) C L1PA10_3end LINE/L1 (1) 914 1 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 (0) 3294 3091 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 9.62 0.00 0.00 INTRON_3 189228 189279 (210902) C (TA)n Simple_repeat (0) 180 129 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) 2273 9.47 0.97 1.29 INTRON_3 189905 190214 (209967) C AluSx SINE/Alu (3) 309 1 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 38.49 1.67 0.41 INTRON_3 190254 190493 (209688) C MIRb SINE/MIR (0) 268 26 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 19.73 3.86 3.59 INTRON_3 191255 191643 (208538) + MLT1B LTR/ERVL-MaLR 1 390 (0) 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 2.04 0.00 0.00 INTRON_3 191879 191927 (208254) + (CA)n Simple_repeat 2 50 (130) 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) 510 27.51 3.87 3.87 INTRON_3 192191 192345 (207836) + MIRc SINE/MIR 11 165 (103) 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) 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 13.89 0.00 0.00 INTRON_3 193748 193783 (206398) C L2b_3end LINE/L2 (1) 465 430 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 28.05 3.64 7.93 INTRON_3 193853 194154 (206027) + MLT1F2 LTR/ERVL-MaLR 1 290 (270) 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 29.34 0.00 3.45 INTRON_3 194466 194525 (205656) + MIRb SINE/MIR 107 164 (104) 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 30.86 5.39 5.68 INTRON_3 194528 194898 (205283) C MLT1K LTR/ERVL-MaLR (0) 595 226 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 15.69 0.00 0.00 INTRON_3 194962 195012 (205169) C (CA)n Simple_repeat (0) 180 130 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 12.95 2.11 0.78 INTRON_3 195147 197559 (202622) C Tigger2 DNA/TcMar-Tigger (0) 2718 274 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 17.04 5.93 0.00 INTRON_3 197596 197730 (202451) C L1MC3_3end LINE/L1 (0) 2532 2390 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) 1721 19.35 1.28 2.27 INTRON_3 197739 198050 (202131) C AluJb SINE/Alu (3) 309 1 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 13.85 4.46 0.72 INTRON_3 198052 198320 (201861) C Tigger2 DNA/TcMar-Tigger (2438) 280 2 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 33.86 7.80 4.59 INTRON_3 198867 199225 (200956) + L3 LINE/CR1 3091 3460 (1029) 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 30.69 0.00 0.00 INTRON_3 199215 199315 (200866) + L3 LINE/CR1 3852 3952 (537) 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 37.43 0.81 8.77 INTRON_3 199544 199666 (200515) + L2b_3end LINE/L2 351 464 (2) 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 31.28 13.39 4.35 INTRON_3 199833 199959 (200222) C MIR3 SINE/MIR (54) 154 17 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 24.12 6.27 8.61 INTRON_3 200235 200792 (199389) C MLT1F LTR/ERVL-MaLR (2) 546 1 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 9.52 4.76 0.00 INTRON_3 200953 200994 (199187) C (TAAAAA)n Simple_repeat (3) 177 134 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) 7313 3.00 0.00 0.00 INTRON_3 200997 201895 (198286) C L1PA3_3end LINE/L1 (3) 899 1 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 (0) 3294 1 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 (0) 2259 7 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) 2210 12.05 0.65 0.00 INTRON_3 207233 207539 (192642) C AluSx SINE/Alu (3) 309 1 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 24.10 0.00 1.20 INTRON_3 207555 207638 (192543) C MER58B DNA/hAT-Charlie (36) 305 223 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) 7781 18.22 2.30 1.78 INTRON_3 207639 209202 (190979) + L1P3_5end LINE/L1 149 1720 (7) 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) 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) 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) 2430 8.77 0.00 0.32 INTRON_3 210208 210516 (189665) + AluY SINE/Alu 2 309 (2) 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 8.43 0.94 0.67 INTRON_3 210517 213515 (186666) + L1P3_orf2 LINE/L1 285 3294 (0) 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) 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 3.03 0.00 0.00 INTRON_3 214295 214327 (185854) C MER58B DNA/hAT-Charlie (151) 190 158 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 19.10 8.72 6.00 INTRON_3 214331 214525 (185656) C MER58B DNA/hAT-Charlie (141) 200 1 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 32.53 0.00 5.41 INTRON_3 214780 214857 (185324) C MIR3 SINE/MIR (23) 185 112 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) 288 0.00 0.00 0.00 INTRON_3 215218 215249 (184932) C (TAAA)n Simple_repeat (2) 178 147 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 (13) 889 1 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 (0) 3294 2356 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 3.52 1.04 0.00 INTRON_3 216926 217408 (182773) + L1P1_orf2 LINE/L1 335 822 (2472) 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 29.03 1.61 0.00 INTRON_3 218072 218133 (182048) C L2a_3end LINE/L2 (85) 432 370 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 27.27 6.57 0.64 INTRON_3 218168 218761 (181420) + L1MDa_5end LINE/L1 19 647 (2003) 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) 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 22.76 0.79 4.10 INTRON_3 218906 219661 (180520) + L1M1_5end LINE/L1 14 745 (2930) 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 14.55 1.82 0.00 INTRON_3 219658 219712 (180469) + L1M1_5end LINE/L1 1368 1423 (2252) 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) 629 25.58 0.00 0.00 INTRON_3 219758 219886 (180295) + L1M1_5end LINE/L1 1422 1550 (2125) 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) 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) 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 33.22 3.07 3.42 INTRON_3 221597 221889 (178292) C MLT1N2 LTR/ERVL-MaLR (270) 292 1 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 17.93 5.97 5.31 INTRON_3 221944 222261 (177920) + MER33 DNA/hAT-Charlie 3 322 (2) 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 30.95 0.00 2.81 INTRON_3 222986 223241 (176940) C MIR SINE/MIR (12) 250 2 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 20.90 1.45 2.94 INTRON_3 223600 223668 (176513) + L3b_3end LINE/CR1 250 317 (165) 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 22.42 1.00 5.64 INTRON_3 223778 224278 (175903) C LTR16B1 LTR/ERVL (0) 480 2 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 37.08 3.23 2.56 INTRON_3 224629 224783 (175398) + L2 LINE/L2 2619 2774 (308) 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 36.08 1.41 4.35 INTRON_3 224827 224968 (175213) + L2 LINE/L2 2846 2983 (99) 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) 308 34.45 0.00 1.11 INTRON_3 225219 225309 (174872) + L2b_3end LINE/L2 368 457 (9) 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) 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 2.01 0.00 0.00 INTRON_3 225398 225993 (174188) C L1PA3_3end LINE/L1 (2) 900 305 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 18.40 0.00 4.08 INTRON_3 226466 226516 (173665) C (TGAA)n Simple_repeat (0) 180 132 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 31.76 0.00 0.00 INTRON_3 226619 226703 (173478) C MIRb SINE/MIR (75) 193 109 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) 2331 10.30 0.00 0.00 INTRON_3 228792 229092 (171089) + AluY SINE/Alu 1 301 (10) 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 31.30 12.21 0.00 INTRON_3 229164 229294 (170887) C L1ME4a_3end LINE/L1 (93) 778 632 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 6.83 0.00 4.55 INTRON_3 229531 229576 (170605) C L1MA5_3end LINE/L1 (0) 1047 1004 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 11.33 0.53 3.57 INTRON_3 229828 230202 (169979) C THE1B LTR/ERVL-MaLR (0) 364 1 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 9.63 3.57 0.69 INTRON_3 231154 231854 (168327) C L1MA2_3end LINE/L1 (0) 1051 331 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 29.71 11.17 0.92 INTRON_3 232190 232386 (167795) C MIRb SINE/MIR (18) 250 34 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 40.89 9.07 2.43 INTRON_3 232611 232996 (167185) + L2b_3end LINE/L2 14 424 (42) 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 21.27 14.52 1.43 INTRON_3 233771 233832 (166349) C L1ME3B_3end LINE/L1 (95) 894 825 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 29.19 7.84 4.27 INTRON_3 234358 234561 (165620) C L1ME4a_3end LINE/L1 (303) 568 358 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) 2272 9.09 0.96 1.29 INTRON_3 234578 234889 (165292) C AluSx SINE/Alu (1) 311 1 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 25.55 14.91 2.78 INTRON_3 235006 235166 (165015) C MLT1J2 LTR/ERVL-MaLR (21) 427 248 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 27.22 10.29 8.17 INTRON_3 235187 235390 (164791) C MLT1J2 LTR/ERVL-MaLR (226) 222 15 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) 2310 10.42 0.32 0.32 INTRON_3 235529 235836 (164345) C AluSx SINE/Alu (4) 308 1 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 24.55 19.09 0.00 INTRON_3 236016 236125 (164056) + MIRb SINE/MIR 110 240 (28) 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 32.19 4.65 3.21 INTRON_3 236383 236597 (163584) C MIRb SINE/MIR (16) 252 35 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) 580 27.07 0.00 0.00 INTRON_3 236752 236884 (163297) C FLAM_C_short_ SINE/Alu (0) 133 1 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 23.70 9.03 3.29 INTRON_3 237107 237250 (162931) + MIRb SINE/MIR 97 248 (20) 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) 2083 11.90 1.02 0.00 INTRON_3 237321 237614 (162567) C AluSx SINE/Alu (15) 297 1 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 21.96 12.07 1.34 INTRON_3 237935 238340 (161841) C LTR16A LTR/ERVL (2) 449 1 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 2.86 0.00 0.00 INTRON_3 238832 239076 (161105) + L1PA2_3end LINE/L1 656 900 (2) 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 32.24 6.58 0.00 INTRON_3 240149 240300 (159881) C MIRc SINE/MIR (30) 238 77 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 28.31 4.41 6.50 INTRON_3 240348 240551 (159630) + L2c_3end LINE/L2 279 478 (0) 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 17.91 1.67 0.55 INTRON_3 240794 241332 (158849) C L1MB8_3end LINE/L1 (7) 918 374 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 19.53 6.11 3.85 INTRON_3 241369 241597 (158584) C L1ME2z_3end LINE/L1 (138) 1053 820 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 27.35 4.67 0.90 INTRON_3 241600 241706 (158475) C MIR3 SINE/MIR (11) 197 87 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 31.37 4.87 1.28 INTRON_3 242305 242530 (157651) C MIRb SINE/MIR (6) 262 29 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 (17) 245 1 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 32.03 9.96 0.00 INTRON_3 242559 242789 (157392) + L3 LINE/CR1 4150 4403 (86) 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) 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 23.54 4.16 1.76 INTRON_3 242862 243583 (156598) C L1ME1_3end LINE/L1 (1) 925 187 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 16.84 4.40 2.15 INTRON_3 243595 243685 (156496) C L1MA10_3end LINE/L1 (1) 1080 988 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 19.06 4.01 4.67 INTRON_3 243768 244226 (155955) C L1ME1_3end LINE/L1 (133) 793 326 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) 1550 10.61 2.02 4.98 INTRON_3 244227 244474 (155707) + AluSx SINE/Alu 72 312 (0) 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 19.06 4.01 4.67 INTRON_3 244475 244812 (155369) C L1ME1_3end LINE/L1 (601) 325 1 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 (0) 3294 2992 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 26.63 1.49 0.99 INTRON_3 244968 245168 (155013) + MER58A DNA/hAT-Charlie 15 216 (8) 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 25.43 6.25 0.33 INTRON_3 245169 245456 (154725) C L1M4_orf2 LINE/L1 (324) 2970 2666 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 16.31 4.62 1.80 INTRON_3 245453 246101 (154080) C L1MC3_3end LINE/L1 (1568) 964 298 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 (2335) 197 1 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 (0) 3294 2534 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 9.68 0.32 0.32 INTRON_3 246899 247209 (152972) C L1PB2_3end LINE/L1 (3) 895 585 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 17.03 2.46 3.18 INTRON_3 247210 247494 (152687) C L1MC_orf2 LINE/L1 (1832) 1462 1180 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 (2118) 1176 865 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 36.70 1.60 0.00 INTRON_3 247758 247945 (152236) C ERVL-E LTR/ERVL (4570) 1097 907 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 3.54 0.00 0.00 INTRON_3 248140 248619 (151562) C L1PA3_3end LINE/L1 (0) 902 423 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) 938 30.05 3.96 2.85 INTRON_3 249148 249702 (150479) C L1MEg_5end LINE/L1 (661) 1440 880 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 (0) 1257 7 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) 2109 13.02 0.32 0.65 INTRON_3 250871 251179 (149002) + AluSx SINE/Alu 1 308 (4) 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 28.84 0.95 0.95 INTRON_3 251201 251305 (148876) + MIR SINE/MIR 138 242 (20) 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 31.73 0.00 5.06 INTRON_3 251723 251805 (148376) + L2a_3end LINE/L2 434 512 (5) 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) 1886 14.28 0.00 0.36 INTRON_3 252168 252448 (147733) + AluJb SINE/Alu 1 280 (32) 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) 1420 22.15 0.00 2.50 INTRON_3 252485 252771 (147410) + AluJb SINE/Alu 3 282 (30) 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 50.00 0.00 0.00 INTRON_3 252775 252798 (147383) + AT_rich Low_complexity 138 161 (139) 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 30.64 10.91 1.10 INTRON_3 253710 254039 (146142) C L1ME4a_3end LINE/L1 (143) 728 367 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 26.72 6.54 5.56 INTRON_3 254050 254156 (146025) C MIR SINE/MIR (0) 262 155 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 31.00 14.29 1.69 INTRON_3 254454 254558 (145623) C MIR3 SINE/MIR (4) 204 87 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) 1298 17.69 6.49 8.25 INTRON_3 254731 255038 (145143) + AluJb SINE/Alu 1 303 (9) 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) 692 20.16 0.00 0.81 INTRON_3 255205 255329 (144852) C FLAM_C_short_ SINE/Alu (9) 124 1 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) 379 27.06 0.00 5.00 INTRON_3 255660 255764 (144417) C MIRb SINE/MIR (122) 146 47 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 (125) 143 77 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 2.33 0.00 0.00 INTRON_3 256064 256106 (144075) C (CA)n Simple_repeat (0) 180 138 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 9.29 3.12 5.77 INTRON_3 256131 256290 (143891) C L1MA1_3end LINE/L1 (99) 950 795 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 9.81 1.92 1.92 INTRON_3 256300 256351 (143830) C L1PA3_3end LINE/L1 (0) 902 851 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 36.40 0.00 3.41 INTRON_3 257523 257613 (142568) + L2b_3end LINE/L2 379 466 (0) 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 14.16 1.91 0.28 INTRON_3 258363 259410 (140771) C Tigger1 DNA/TcMar-Tigger (1) 2417 1353 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 10.29 0.00 12.66 INTRON_3 259418 259595 (140586) + MER1B DNA/hAT-Charlie 181 338 (1) 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 11.81 2.98 0.14 INTRON_3 259598 260301 (139880) C Tigger1 DNA/TcMar-Tigger (1163) 1255 532 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 (1606) 812 412 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) 1699 17.45 1.66 1.32 INTRON_3 260414 260715 (139466) C AluJb SINE/Alu (9) 303 1 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) 222 36.66 0.73 10.40 INTRON_3 260848 260984 (139197) C L3 LINE/CR1 (1) 4488 4364 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 (168) 4321 4078 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 33.48 5.64 1.98 INTRON_3 261248 261442 (138739) + MIR SINE/MIR 10 211 (51) 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) 237 35.04 9.27 6.45 INTRON_3 261522 261823 (138358) + MLT1H LTR/ERVL-MaLR 71 380 (169) 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) 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) 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) 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 30.56 9.21 3.11 INTRON_3 261910 262061 (138120) C MLT1H LTR/ERVL-MaLR (13) 536 376 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 31.72 0.00 1.22 INTRON_3 262188 262270 (137911) C MLT1H LTR/ERVL-MaLR (373) 176 95 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 28.72 4.12 3.06 INTRON_3 262281 262377 (137804) C MLT1I LTR/ERVL-MaLR (293) 118 21 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 33.88 6.84 1.63 INTRON_3 262487 262603 (137578) C L3 LINE/CR1 (401) 4088 3966 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 28.38 9.46 0.00 INTRON_3 262804 262877 (137304) C L3 LINE/CR1 (800) 3689 3609 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 25.28 7.45 7.45 INTRON_3 263688 263781 (136400) C MIRb SINE/MIR (125) 143 50 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 6.38 0.00 0.00 INTRON_3 264351 264397 (135784) + (CA)n Simple_repeat 1 47 (133) 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 30.72 6.53 4.36 INTRON_3 265024 265360 (134821) + L2 LINE/L2 2304 2647 (435) 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) 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 26.90 6.67 3.60 INTRON_3 265760 265894 (134287) + L2a_3end LINE/L2 377 515 (2) 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 35.30 0.00 0.98 INTRON_3 265899 266001 (134180) + L2c_3end LINE/L2 200 301 (177) 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 28.37 4.03 0.65 INTRON_3 266050 266198 (133983) C L1MEc_5end LINE/L1 (2337) 190 37 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 26.10 7.02 2.52 INTRON_3 266305 266418 (133763) + L2a_3end LINE/L2 394 512 (5) 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 30.54 7.88 0.00 INTRON_3 266627 266829 (133352) C MIR SINE/MIR (4) 258 40 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 66.67 0.00 0.00 INTRON_3 266924 266953 (133228) + AT_rich Low_complexity 127 156 (144) 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 36.80 6.41 4.18 INTRON_3 267122 267589 (132592) C L4 LINE/RTE (330) 1699 1222 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 (843) 1186 1109 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 18.76 1.52 3.08 INTRON_3 267735 267800 (132381) C L2a_3end LINE/L2 (0) 517 453 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 27.01 12.14 1.57 INTRON_3 267910 268082 (132099) C MER113 DNA/hAT-Charlie (1) 520 330 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 29.55 7.72 2.32 INTRON_3 268086 268331 (131850) C MIR SINE/MIR (1) 261 3 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 19.86 0.00 7.89 INTRON_3 268338 268419 (131762) C MER113 DNA/hAT-Charlie (203) 318 243 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 9.09 0.29 0.15 INTRON_3 268497 269179 (131002) C L1P3_orf2 LINE/L1 (1701) 1593 910 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 9.14 0.70 0.00 INTRON_3 269177 269887 (130294) + L1P3_orf2 LINE/L1 1592 2307 (987) 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) 2679 8.71 1.93 0.48 INTRON_3 269860 270274 (129907) + L1P3_orf2 LINE/L1 2874 3294 (0) 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) 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) 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 25.44 1.72 1.72 INTRON_3 271025 271140 (129041) C MER113 DNA/hAT-Charlie (402) 119 4 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 28.74 3.70 1.20 INTRON_3 271356 271436 (128745) C L2a_3end LINE/L2 (5) 512 430 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 27.27 4.55 11.65 INTRON_3 271616 271835 (128346) + MER113A DNA/hAT-Charlie 97 302 (12) 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 64.29 0.00 0.00 INTRON_3 272643 272670 (127511) + AT_rich Low_complexity 130 157 (143) 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 76.32 0.00 0.00 INTRON_3 272715 272752 (127429) + AT_rich Low_complexity 140 177 (123) 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) 423 18.39 2.27 1.12 INTRON_3 273059 273146 (127035) C THE1D LTR/ERVL-MaLR (8) 373 285 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 (16) 410 1 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 27.27 14.05 0.00 INTRON_3 273492 273612 (126569) C MIRb SINE/MIR (81) 187 50 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 31.33 0.00 5.00 INTRON_3 274417 274500 (125681) C MIR3 SINE/MIR (78) 130 51 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) 259 26.82 16.51 0.79 INTRON_3 274507 274615 (125566) C MARNA DNA/TcMar-Mariner (105) 481 356 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 (266) 320 43 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) 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 26.62 7.66 6.38 INTRON_3 274906 275571 (124610) + L1M5_orf2 LINE/L1 292 965 (2329) 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 9.43 1.52 2.01 INTRON_3 275585 276111 (124070) C L1MA2_3end LINE/L1 (0) 1051 524 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 0.00 0.00 0.00 INTRON_3 276112 276159 (124022) C (TAAA)n Simple_repeat (3) 177 130 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) 2076 11.79 1.34 0.66 INTRON_3 276162 276460 (123721) C AluSx SINE/Alu (11) 301 1 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 9.43 1.52 2.01 INTRON_3 276461 276979 (123202) C L1MA2_3end LINE/L1 (528) 523 7 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 (0) 3294 3107 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 31.84 1.12 0.00 INTRON_3 277059 277237 (122944) C L1MEc_5end LINE/L1 (2198) 329 149 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) 1944 26.39 3.04 3.44 INTRON_3 277272 278060 (122121) C L1MEf_5end LINE/L1 (566) 1651 866 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 (928) 1599 1085 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 (1106) 1421 968 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 23.16 8.47 0.44 INTRON_3 278118 278542 (121639) C L1MEc_5end LINE/L1 (1598) 929 471 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 (2051) 476 90 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 (2450) 77 22 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 19.09 19.79 1.77 INTRON_3 279660 279755 (120426) + MIRb SINE/MIR 99 211 (57) 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 19.12 4.03 9.32 INTRON_3 279766 280013 (120168) + MER106A DNA/hAT-Charlie 1 236 (0) 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 34.13 4.80 1.55 INTRON_3 280144 280268 (119913) + Charlie23a DNA/hAT-Charlie 2 130 (209) 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 25.60 5.21 3.74 INTRON_3 280307 280517 (119664) + Charlie23a DNA/hAT-Charlie 124 337 (2) 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 16.22 0.00 0.00 INTRON_3 280847 280883 (119298) + (CA)n Simple_repeat 1 37 (143) 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) 1449 20.15 1.02 2.41 INTRON_3 281175 281469 (118712) + AluJb SINE/Alu 1 291 (21) 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 29.67 9.89 0.00 INTRON_3 281804 281894 (118287) C MIRc SINE/MIR (148) 120 21 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 23.03 12.21 2.14 INTRON_3 283547 283759 (116422) + MIR SINE/MIR 12 245 (17) 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 29.63 1.85 0.00 INTRON_3 283805 283858 (116323) C L2c_3end LINE/L2 (307) 171 117 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 20.05 4.47 5.42 INTRON_3 284041 284096 (116085) C MLT2B3 LTR/ERVL (0) 554 506 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 13.23 3.99 0.30 INTRON_3 284097 284422 (115759) C MER44A DNA/TcMar-Tigger (1) 338 1 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 20.05 4.47 5.42 INTRON_3 284423 284924 (115257) C MLT2B3 LTR/ERVL (49) 505 1 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 21.63 3.72 6.56 INTRON_3 284927 285114 (115067) C MER58B DNA/hAT-Charlie (7) 334 152 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) 933 17.43 0.00 4.35 INTRON_3 285150 285317 (114864) + FRAM_short_ SINE/Alu 5 165 (1) 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 22.82 3.23 1.05 INTRON_3 285367 285459 (114722) + MamRep1161 DNA/TcMar-Tigger 854 948 (9) 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 23.42 4.50 0.00 INTRON_3 286091 286201 (113980) + MIRb SINE/MIR 91 206 (62) 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 35.83 2.87 1.62 INTRON_3 286318 286561 (113620) C CR1_Mam LINE/CR1 (584) 1620 1374 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 18.69 0.00 6.98 INTRON_3 287133 287178 (113003) + L3 LINE/CR1 4442 4484 (5) 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 11.11 12.12 0.00 INTRON_3 287504 287602 (112579) C L1MB3_3end LINE/L1 (11) 919 809 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) 417 26.96 10.29 4.53 INTRON_3 287605 287876 (112305) C L1MEg_5end LINE/L1 (699) 1402 1116 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 (883) 1551 1338 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 28.60 3.53 6.26 INTRON_3 287893 288515 (111666) C L1MCc_5end LINE/L1 (53) 1483 877 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 (349) 1187 836 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 30.43 6.69 9.91 INTRON_3 288828 289305 (110876) C L1MCc_5end LINE/L1 (1056) 480 17 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 28.35 10.39 9.91 INTRON_3 289463 289693 (110488) + L2c_3end LINE/L2 240 471 (7) 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 19.12 7.35 0.00 INTRON_3 290307 290374 (109807) C MIRc SINE/MIR (1) 267 195 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 25.53 2.65 6.42 INTRON_3 290373 290485 (109696) C MIRb SINE/MIR (96) 172 64 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 31.92 0.00 1.06 INTRON_3 290693 290787 (109394) + (GAAAA)n Simple_repeat 1 94 (86) 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 18.05 2.74 1.35 INTRON_3 291457 291529 (108652) C MER21B LTR/ERVL (0) 868 795 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 13.23 1.15 1.92 INTRON_3 291550 291734 (108447) C MER39 LTR/ERV1 (184) 523 339 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) 426 24.53 7.55 0.00 INTRON_3 291735 291840 (108341) + FLAM_C_short_ SINE/Alu 2 115 (18) 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 13.23 1.15 1.92 INTRON_3 291841 291916 (108265) C MER39 LTR/ERV1 (369) 338 264 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 15.54 16.97 10.29 INTRON_3 291897 292061 (108120) C MER21A LTR/ERVL (733) 198 24 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 4.92 0.00 0.00 INTRON_3 292064 292124 (108057) + (CA)n Simple_repeat 2 62 (118) 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) 2586 4.95 0.00 0.33 INTRON_3 293480 293783 (106398) C AluY SINE/Alu (8) 303 1 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) 2280 7.90 0.69 0.00 INTRON_3 294195 294485 (105696) + AluSx SINE/Alu 1 293 (19) 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 26.75 1.15 1.15 INTRON_3 295083 295169 (105012) + MIRc SINE/MIR 80 166 (102) 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 35.10 4.48 2.19 INTRON_3 295202 295335 (104846) + L2c_3end LINE/L2 337 473 (5) 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) 2224 11.34 0.00 0.67 INTRON_3 295800 296101 (104080) C AluSx SINE/Alu (11) 301 2 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 30.51 0.83 5.17 INTRON_3 296554 296674 (103507) C MER117 DNA/hAT-Charlie (0) 197 82 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 26.19 13.66 0.78 INTRON_3 296733 296959 (103222) + MIRb SINE/MIR 11 266 (2) 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) 648 25.76 0.00 0.00 INTRON_3 297368 297499 (102682) + FLAM_C_short_ SINE/Alu 2 133 (0) 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 15.95 0.00 4.55 INTRON_3 297555 297600 (102581) C (CAAA)n Simple_repeat (0) 180 137 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 25.68 16.22 0.00 INTRON_3 297906 297979 (102202) C MIRc SINE/MIR (24) 244 159 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 24.99 7.97 7.54 INTRON_3 298534 298784 (101397) + MARNA DNA/TcMar-Mariner 6 257 (329) 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 31.39 1.27 3.23 INTRON_3 299390 299547 (100634) + MIRb SINE/MIR 114 268 (0) 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) 236 34.55 0.00 0.00 INTRON_3 299559 299613 (100568) C MIR3 SINE/MIR (84) 124 70 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 (141) 127 83 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 18.11 3.15 0.00 INTRON_3 300036 300162 (100019) C MIR3 SINE/MIR (11) 197 67 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 9.49 0.33 2.03 INTRON_3 300902 301202 (98979) + L1PA13_3end LINE/L1 611 906 (4) 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 16.45 2.91 0.20 INTRON_3 301204 301684 (98497) + L1MC1_3end LINE/L1 564 1057 (23) 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 14.04 0.00 0.00 INTRON_3 302046 302102 (98079) + L1MC1_3end LINE/L1 800 856 (224) 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) 2278 7.83 1.36 0.34 INTRON_3 302135 302429 (97752) + AluSx SINE/Alu 1 298 (14) 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 23.46 0.00 9.30 INTRON_3 302444 302490 (97691) C L2a_3end LINE/L2 (93) 424 382 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 27.58 4.70 10.23 INTRON_3 302649 302967 (97214) + L1ME3F_3end LINE/L1 569 871 (119) 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) 1634 13.84 0.39 0.79 INTRON_3 302969 303223 (96958) C AluSx SINE/Alu (19) 293 40 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 30.77 2.83 1.87 INTRON_3 303390 303495 (96686) C L3 LINE/CR1 (304) 4185 4079 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 33.83 4.99 2.68 INTRON_3 303490 303890 (96291) + L2 LINE/L2 2442 2851 (231) 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) 330 34.24 16.85 0.00 INTRON_3 304110 304293 (95888) + MIRc SINE/MIR 19 233 (35) 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) 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 25.60 8.54 4.71 INTRON_3 304568 304649 (95532) C L2c_3end LINE/L2 (3) 475 391 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 31.35 14.94 1.01 INTRON_3 304653 304739 (95442) + L2c_3end LINE/L2 329 427 (51) 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) 1273 19.34 11.81 2.71 INTRON_3 305507 305777 (94404) + AluJb_short_ SINE/Alu 1 295 (7) 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 30.50 1.49 0.49 INTRON_3 305864 306064 (94117) C MIRb SINE/MIR (31) 237 35 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 20.17 8.11 6.19 INTRON_3 306314 306347 (93834) C L1ME3C_3end LINE/L1 (0) 870 835 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) 2499 5.37 0.00 0.00 INTRON_3 306348 306645 (93536) C AluY SINE/Alu (13) 298 1 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 20.17 8.11 6.19 INTRON_3 306646 306721 (93460) C L1ME3C_3end LINE/L1 (36) 834 758 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 29.91 10.50 1.38 INTRON_3 306766 306965 (93216) + MamRep488 DNA/hAT-Tip100 1 218 (1) 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 25.49 2.65 7.41 INTRON_3 307041 307164 (93017) + MLT2C1 LTR/ERVL 1 124 (273) 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) 2131 11.33 0.63 1.93 INTRON_3 307165 307479 (92702) C AluSx SINE/Alu (1) 311 1 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 25.49 2.65 7.41 INTRON_3 307480 307693 (92488) + MLT2C1 LTR/ERVL 125 324 (73) 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) 1032 22.56 8.51 0.99 INTRON_3 307970 308251 (91930) C LTR54B LTR/ERV1 (21) 477 175 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 (340) 158 1 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 32.80 11.36 0.68 INTRON_3 308641 308772 (91409) C L1ME3B_3end LINE/L1 (63) 926 781 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 23.76 5.53 5.08 INTRON_3 308879 309113 (91068) C L1MC5_3end LINE/L1 (435) 916 681 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 16.54 3.01 6.21 INTRON_3 309114 309545 (90636) C Charlie1a DNA/hAT-Charlie (0) 1455 1037 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 23.73 20.34 0.00 INTRON_3 309544 309602 (90579) C Charlie1b DNA/hAT-Charlie (452) 71 1 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 22.88 4.04 7.29 INTRON_3 309669 310064 (90117) C L1MC5_3end LINE/L1 (722) 629 246 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 23.53 0.73 0.73 INTRON_3 310092 310228 (89953) + MER104 DNA/TcMar-Tc2 30 166 (15) 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 29.34 8.89 1.55 INTRON_3 310403 310582 (89599) C MLT1J2 LTR/ERVL-MaLR (255) 193 1 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 24.53 4.17 2.94 INTRON_3 310583 310750 (89431) + MIR SINE/MIR 91 260 (2) 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 28.80 2.66 2.12 INTRON_3 312416 312603 (87578) + MER5A DNA/hAT-Charlie 1 189 (0) 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) 311 32.79 7.10 0.00 INTRON_3 313901 314083 (86098) + L2a_3end LINE/L2 289 484 (33) 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) 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) 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 9.09 0.00 0.00 INTRON_3 314108 314162 (86019) + (TGAA)n Simple_repeat 1 55 (125) 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 11.55 0.00 3.21 INTRON_3 314208 314368 (85813) + L1PA8A_3end LINE/L1 714 869 (9) 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 61.11 0.00 0.00 INTRON_3 314369 314404 (85777) + AT_rich Low_complexity 129 164 (136) 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 15.05 5.85 4.32 INTRON_3 314564 314699 (85482) C L1MB3_3end LINE/L1 (2) 928 793 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) 2056 11.00 3.09 0.00 INTRON_3 314700 314990 (85191) C AluSx SINE/Alu (12) 300 1 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 15.05 5.85 4.32 INTRON_3 314991 315742 (84439) C L1MB3_3end LINE/L1 (138) 792 28 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) 375 36.39 7.65 0.48 INTRON_3 315785 315980 (84201) + MIRb SINE/MIR 1 210 (58) 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) 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 18.08 4.56 5.83 INTRON_3 316026 316442 (83739) C MLT2D LTR/ERVL (2) 412 1 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 28.70 6.48 6.90 INTRON_3 316677 316732 (83449) C MLT1G1 LTR/ERVL-MaLR (0) 579 526 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) 2346 9.15 0.00 0.33 INTRON_3 316733 317039 (83142) + AluY SINE/Alu 1 306 (5) 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 28.70 6.48 6.90 INTRON_3 317040 317077 (83104) C MLT1G1 LTR/ERVL-MaLR (54) 525 501 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) 1602 20.55 0.00 1.03 INTRON_3 317078 317372 (82809) C AluJb SINE/Alu (20) 292 1 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 28.70 6.48 6.90 INTRON_3 317373 317785 (82396) C MLT1G1 LTR/ERVL-MaLR (79) 500 74 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 24.14 1.14 3.49 INTRON_3 317990 318165 (82016) C L2a_3end LINE/L2 (0) 517 346 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) 435 23.16 3.16 0.00 INTRON_3 318249 318343 (81838) C MLT1L LTR/ERVL-MaLR (86) 524 427 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 (218) 392 131 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) 214 38.00 0.99 0.99 INTRON_3 318733 318833 (81348) C L2c_3end LINE/L2 (212) 266 166 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 (265) 252 163 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 37.12 3.79 0.00 INTRON_3 319159 319290 (80891) + L2b_3end LINE/L2 329 465 (1) 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 37.48 5.13 2.50 INTRON_3 319307 319462 (80719) C L2c_3end LINE/L2 (69) 409 250 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 35.34 4.76 2.33 INTRON_3 319618 319701 (80480) C MIR3 SINE/MIR (3) 205 120 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 23.70 1.39 7.38 INTRON_3 319820 320106 (80075) C L1ME3A_3end LINE/L1 (9) 911 641 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) 383 21.35 0.00 0.00 INTRON_3 320106 320194 (79987) C L1M5_orf2 LINE/L1 (2458) 836 748 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 (2560) 734 468 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 (2727) 567 273 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) 1730 18.04 0.33 2.37 INTRON_3 320599 320899 (79282) C AluJb SINE/Alu (15) 297 3 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 21.57 6.54 6.11 INTRON_3 320942 321430 (78751) C MLT1D LTR/ERVL-MaLR (14) 491 1 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) 619 27.81 2.97 1.09 INTRON_3 321449 321717 (78464) C L1MEe_5end LINE/L1 (111) 1053 780 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 (3052) 242 4 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 (65) 2152 1885 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 33.70 5.05 4.73 INTRON_3 321899 322728 (77453) C PRIMAX-int LTR/ERV1 (313) 3789 2978 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 15.56 7.98 1.44 INTRON_3 322729 323054 (77127) + Tigger3a DNA/TcMar-Tigger 2 348 (0) 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 33.70 5.05 4.73 INTRON_3 323055 324521 (75660) C PRIMAX-int LTR/ERV1 (1125) 2977 1485 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 33.58 2.54 6.61 INTRON_3 324700 324935 (75246) C MER101-int LTR/ERV1 (1025) 5614 5388 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 15.81 2.98 2.06 INTRON_3 325667 326002 (74179) + MER1B DNA/hAT-Charlie 1 339 (0) 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 20.76 1.27 0.00 INTRON_3 326074 326309 (73872) + MER8 DNA/TcMar-Tigger 1 239 (0) 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 53.57 0.00 0.00 INTRON_3 327344 327371 (72810) + AT_rich Low_complexity 142 169 (131) 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 27.83 0.00 1.50 INTRON_3 327758 327892 (72289) C L1MEg_5end LINE/L1 (347) 1754 1622 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 3.33 3.33 0.00 INTRON_3 327960 327989 (72192) + (CAAA)n Simple_repeat 6 36 (144) 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 3.00 0.00 0.30 INTRON_3 328050 328384 (71797) C L1PA4_3end LINE/L1 (3) 899 566 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 25.62 0.83 0.00 INTRON_3 328385 328505 (71676) C MLT2E LTR/ERVL (506) 122 1 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 25.76 10.92 2.94 INTRON_3 328506 328789 (71392) C L1MEg_5end LINE/L1 (1573) 528 223 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 (447) 336 97 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 (1856) 245 89 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) 1462 16.28 2.35 5.17 INTRON_3 328949 329246 (70935) C AluJb SINE/Alu (22) 290 1 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) 386 35.00 8.44 3.58 INTRON_3 329247 329338 (70843) C L1MEg1_5end LINE/L1 (687) 96 2 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 (2013) 88 25 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 25.49 9.72 1.94 INTRON_3 329459 329602 (70579) C Helitron3Na_Mam RC/Helitron (3) 483 329 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 33.07 0.00 0.00 INTRON_3 329616 329742 (70439) C Helitron3Na_Mam RC/Helitron (191) 295 169 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 29.85 1.49 0.00 INTRON_3 329793 329859 (70322) C Helitron3Na_Mam RC/Helitron (394) 92 25 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 24.86 3.26 1.60 INTRON_3 329883 330066 (70115) + L1M5_orf2 LINE/L1 2138 2324 (970) 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 31.09 7.77 0.00 INTRON_3 330115 330307 (69874) + MIRb SINE/MIR 15 222 (46) 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 36.27 2.41 3.66 INTRON_3 331328 331410 (68771) + MER5A DNA/hAT-Charlie 68 149 (40) 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 17.65 0.00 1.47 INTRON_3 331502 331570 (68611) + Charlie5 DNA/hAT-Charlie 3 70 (2554) 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 14.05 15.33 1.28 INTRON_3 331569 331705 (68476) + Charlie5 DNA/hAT-Charlie 2469 2624 (0) 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 26.71 2.53 5.19 INTRON_3 331731 331809 (68372) + MER5A DNA/hAT-Charlie 2 78 (111) 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 30.70 1.28 3.95 INTRON_3 331796 331873 (68308) + MER5A DNA/hAT-Charlie 114 189 (0) 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 25.48 6.60 1.16 INTRON_3 332154 332562 (67619) + L1M5_orf2 LINE/L1 2112 2542 (752) 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 23.96 5.88 5.88 INTRON_3 332563 332664 (67517) + MIRb SINE/MIR 167 268 (0) 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 30.72 9.74 6.65 INTRON_3 332783 333162 (67019) C L2c_3end LINE/L2 (1) 477 87 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 (390) 88 1 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 (203) 2879 2836 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 13.39 1.66 6.99 INTRON_3 333343 333583 (66598) + MER30 DNA/hAT-Charlie 2 230 (0) 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 31.15 0.00 0.00 INTRON_3 333584 333644 (66537) C L2a_3end LINE/L2 (30) 487 427 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 27.94 0.00 0.00 INTRON_3 333646 333713 (66468) + Arthur1C DNA/hAT-Tip100 8 75 (288) 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 19.84 1.19 0.39 INTRON_3 333720 333972 (66209) + Arthur1C DNA/hAT-Tip100 109 363 (0) 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 25.00 11.84 0.00 INTRON_3 333984 334059 (66122) C L2c_3end LINE/L2 (95) 383 299 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 17.07 0.00 0.00 INTRON_3 334693 334733 (65448) + (CATATA)n Simple_repeat 2 42 (138) 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 13.68 14.15 3.42 INTRON_3 334901 335006 (65175) C L1MC5_3end LINE/L1 (51) 1300 1184 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 26.31 14.29 1.59 INTRON_3 335923 336034 (64147) C L2 LINE/L2 (512) 2570 2445 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 22.41 6.90 0.00 INTRON_3 336742 336799 (63382) C MIRb SINE/MIR (89) 179 118 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 13.04 7.61 0.00 INTRON_3 336922 337013 (63168) + L1MB3_3end LINE/L1 831 929 (1) 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) 2329 7.21 0.68 1.02 INTRON_3 337082 337375 (62806) C AluSx SINE/Alu (18) 294 2 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 24.66 12.80 1.09 INTRON_3 337641 337804 (62377) C MIRb SINE/MIR (65) 203 21 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 26.40 4.59 2.70 INTRON_3 337909 338017 (62164) + MIR3 SINE/MIR 83 193 (15) 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 32.31 10.45 0.68 INTRON_3 338046 338179 (62002) + L3 LINE/CR1 3907 4053 (436) 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 84.85 0.00 0.00 INTRON_3 338545 338577 (61604) + AT_rich Low_complexity 113 145 (155) 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 9.03 0.00 10.71 INTRON_3 338674 338735 (61446) C L1MA3_3end LINE/L1 (1) 1051 996 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) 794 13.49 0.79 0.00 INTRON_3 338765 338890 (61291) C L1MA2_3end LINE/L1 (53) 998 872 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 (224) 827 781 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 6.30 9.45 0.00 INTRON_3 338930 339056 (61125) C MER85 DNA/PiggyBac (0) 139 1 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 11.75 1.20 1.81 INTRON_3 339057 339845 (60336) C L1MA2_3end LINE/L1 (271) 780 1 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 (0) 3294 2965 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 2.70 0.00 0.00 INTRON_3 340017 341166 (59015) + L1P1_orf2 LINE/L1 2145 3294 (0) 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) 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 11.23 3.00 0.15 INTRON_3 341960 343226 (56955) C L1M1_orf2 LINE/L1 (310) 2984 1682 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 (1139) 2155 1170 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 91.37 0.00 0.00 INTRON_3 343724 343862 (56319) + AT_rich Low_complexity 96 234 (66) 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) 1757 17.99 0.34 0.34 INTRON_3 343863 344152 (56029) C AluJb SINE/Alu (22) 290 1 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 9.81 0.87 0.34 INTRON_3 344153 345308 (54873) C L1M1_orf2 LINE/L1 (2114) 1180 19 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 14.76 1.77 2.26 INTRON_3 345312 346364 (53817) C L1M1_5end LINE/L1 (82) 3593 2532 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) 2448 8.07 0.00 0.32 INTRON_3 346365 346675 (53506) C AluY SINE/Alu (0) 311 2 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) 8579 14.76 1.77 2.26 INTRON_3 346676 347263 (52918) C L1M1_5end LINE/L1 (1144) 2531 1961 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 (1767) 1908 12 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 11.00 0.00 0.00 INTRON_3 349148 349247 (50934) C (GGAA)n Simple_repeat (0) 180 81 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 10.71 0.00 0.00 INTRON_3 349248 349275 (50906) C (GGGGA)n Simple_repeat (3) 177 150 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 22.43 11.33 9.66 INTRON_3 349467 349694 (50487) + L1MC4_3end LINE/L1 2134 2398 (391) 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) 2024 13.86 0.00 1.35 INTRON_3 349695 349994 (50187) + AluSx SINE/Alu 2 297 (15) 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 22.43 11.33 9.66 INTRON_3 349995 350224 (49957) + L1MC4_3end LINE/L1 2399 2599 (190) 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 34.64 5.78 4.53 INTRON_3 350290 350791 (49390) + L2a_3end LINE/L2 10 517 (0) 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 29.76 9.47 0.97 INTRON_3 352380 352474 (47707) + MIRc SINE/MIR 16 118 (150) 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 21.37 6.04 2.60 INTRON_3 353090 353238 (46943) + MamRep564 Unknown 131 284 (73) 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 14.46 4.17 7.47 INTRON_3 353437 353892 (46289) C L1MA7_3end LINE/L1 (0) 1038 597 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 16.10 1.94 0.48 INTRON_3 353883 354088 (46093) + L1MA7_3end LINE/L1 374 582 (456) 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 20.94 1.04 0.52 INTRON_3 354248 354439 (45742) C MER53 DNA/hAT (0) 193 1 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 32.99 11.03 0.44 INTRON_3 354464 354871 (45310) + LTR16A LTR/ERVL 1 451 (0) 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 23.36 7.94 0.00 INTRON_3 355047 355260 (44921) C L2a_3end LINE/L2 (0) 517 287 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) 19017 0.61 0.00 0.00 INTRON_3 355267 357402 (42779) + L1HS_5end LINE/L1 1 2136 (0) 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) 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) 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 21.02 1.70 0.00 INTRON_3 361324 361499 (38682) + FordPrefect DNA/hAT-Tip100 1504 1682 (1) 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 22.98 0.95 4.69 INTRON_3 361503 361922 (38259) C L1M5_orf2 LINE/L1 (553) 2741 2337 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 83.78 0.00 0.00 INTRON_3 361972 362045 (38136) + AT_rich Low_complexity 88 161 (139) 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 27.78 6.28 2.34 INTRON_3 362086 362579 (37602) C L1ME4a_3end LINE/L1 (163) 708 196 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 (617) 254 43 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 7.14 0.00 0.00 INTRON_3 362926 362953 (37228) + (A)n Simple_repeat 1 28 (152) 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 32.88 10.78 1.65 INTRON_3 363027 363193 (36988) C MLT1J2 LTR/ERVL-MaLR (0) 448 267 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 17.20 6.50 0.77 INTRON_3 363256 363378 (36803) C MLT1J1 LTR/ERVL-MaLR (282) 162 33 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) 183 33.33 0.00 0.00 INTRON_3 363414 363458 (36723) C L2b_3end LINE/L2 (225) 241 197 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 (272) 245 206 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 27.96 2.70 6.54 INTRON_3 364433 364543 (35638) + L2c_3end LINE/L2 372 478 (0) 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 24.16 2.52 6.09 INTRON_3 365411 365529 (34652) C MIR3 SINE/MIR (3) 205 91 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 18.08 5.41 3.27 INTRON_3 365548 366176 (34005) + MER54A LTR/ERVL 1 642 (259) 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) 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 27.50 7.50 0.00 INTRON_3 366774 366853 (33328) + MIRb SINE/MIR 124 209 (59) 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 28.65 4.26 3.45 INTRON_3 367227 367743 (32438) C L1MC4_3end LINE/L1 (75) 2714 2194 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 6.90 0.00 0.00 INTRON_3 367759 367787 (32394) C (TAA)n Simple_repeat (0) 180 152 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) 2028 11.96 0.00 5.26 INTRON_3 367788 368087 (32094) C AluSx SINE/Alu (27) 285 1 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 31.40 10.58 4.20 INTRON_3 368241 368599 (31582) C L2 LINE/L2 (450) 2632 2252 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 26.40 1.35 2.74 INTRON_3 370050 370123 (30058) C (CATA)n Simple_repeat (4) 176 104 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) 1396 19.43 5.10 3.69 INTRON_3 370159 370452 (29729) C AluJb_short_ SINE/Alu (4) 298 1 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 19.86 4.46 3.80 INTRON_3 370553 370709 (29472) C L1ME4a_3end LINE/L1 (406) 465 308 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 23.19 5.30 5.96 INTRON_3 371566 372679 (27502) C ERV3-16A3_I LTR/ERVL (3315) 1911 805 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 (4351) 875 287 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 (4195) 801 102 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) 286 25.96 19.23 0.00 INTRON_3 373453 373556 (26625) C LTR16B2 LTR/ERVL (5) 457 334 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 (91) 372 8 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 13.79 0.00 0.00 INTRON_3 373872 373900 (26281) + (CA)n Simple_repeat 2 30 (150) 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 35.64 1.46 1.46 INTRON_3 373901 374105 (26076) + Tigger16b DNA/TcMar-Tigger 103 307 (30) 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) 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 24.98 7.45 6.32 INTRON_3 374436 374529 (25652) + L2c_3end LINE/L2 374 468 (10) 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 30.70 3.77 6.28 INTRON_3 375067 375164 (25017) C MIRc SINE/MIR (10) 258 164 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 7.69 0.00 0.00 INTRON_3 375165 375190 (24991) C (TAA)n Simple_repeat (6) 174 149 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) 1918 12.64 1.81 0.00 INTRON_3 375191 375467 (24714) C AluSx SINE/Alu (29) 283 2 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 30.70 3.77 6.28 INTRON_3 375468 375579 (24602) C MIRc SINE/MIR (105) 163 52 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 33.33 1.72 1.72 INTRON_3 375633 375690 (24491) C L2b_3end LINE/L2 (11) 455 398 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 30.00 3.47 2.76 INTRON_3 376101 376244 (23937) C L1ME3C_3end LINE/L1 (5) 865 721 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 21.76 3.47 1.70 INTRON_3 376441 376613 (23568) C (TA)n Simple_repeat (1) 179 4 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 13.66 5.74 4.03 INTRON_3 376643 376764 (23417) C (TA)n Simple_repeat (0) 180 57 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 21.41 1.20 4.35 INTRON_3 376766 376931 (23250) C L1ME3C_3end LINE/L1 (145) 725 565 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 25.00 1.61 0.00 INTRON_3 376942 377065 (23116) C L1ME3C_3end LINE/L1 (352) 518 393 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 24.41 7.96 6.36 INTRON_3 377064 377287 (22894) C L1M5_orf2 LINE/L1 (1336) 1958 1727 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) 2193 12.99 0.00 0.00 INTRON_3 377288 377595 (22586) C AluJb SINE/Alu (4) 308 1 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 24.41 7.96 6.36 INTRON_3 377596 378380 (21801) C L1M5_orf2 LINE/L1 (1568) 1726 925 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) 2209 9.84 0.67 1.68 INTRON_3 378381 378680 (21501) C AluSx SINE/Alu (15) 297 1 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 24.41 7.96 6.36 INTRON_3 378681 379126 (21055) C L1M5_orf2 LINE/L1 (2370) 924 480 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 (2720) 574 254 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 4.17 0.00 0.00 INTRON_3 379345 379368 (20813) C (CAAA)n Simple_repeat (3) 177 154 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) 2008 8.98 0.00 4.66 INTRON_3 379374 379665 (20516) C AluSx SINE/Alu (32) 280 2 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 19.54 14.29 1.27 INTRON_3 379669 379808 (20373) C L1MD_orf2 LINE/L1 (3116) 178 21 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 (0) 2217 2044 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 21.81 5.97 1.91 INTRON_3 379874 380074 (20107) C L1MEf_5end LINE/L1 (164) 2053 1845 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 23.26 4.04 1.21 INTRON_3 380193 380514 (19667) C L1MEf_5end LINE/L1 (434) 1783 1453 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 (611) 1606 1367 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 24.85 5.90 5.54 INTRON_3 380716 381614 (18567) C L1MEf_5end LINE/L1 (842) 1375 474 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 (55) 1014 797 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 (1708) 509 346 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 34.50 3.39 8.28 INTRON_3 381836 382012 (18169) C L1MEf_5end LINE/L1 (1851) 366 198 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 15.38 0.00 0.00 INTRON_3 382204 382268 (17913) + (GGGGA)n Simple_repeat 3 67 (113) 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 31.49 2.10 2.72 INTRON_3 382281 382613 (17568) C L1MEf_5end LINE/L1 (1870) 347 17 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 16.19 4.29 0.00 INTRON_3 382708 382917 (17264) + L1M3_orf2 LINE/L1 885 1103 (2185) 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 15.31 0.00 0.00 INTRON_3 382920 383017 (17164) C L1M3_orf2 LINE/L1 (2177) 1111 1014 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 17.23 2.41 3.51 INTRON_3 383021 384890 (15291) + L1M3_orf2 LINE/L1 1129 2978 (310) 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) 6066 12.57 0.11 0.33 INTRON_3 384884 385793 (14388) C L1PA15_3end LINE/L1 (4) 908 1 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 (3) 3291 723 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) 2027 13.82 0.99 0.00 INTRON_3 388219 388522 (11659) C AluSx SINE/Alu (5) 307 1 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 14.95 1.22 1.22 INTRON_3 388523 389240 (10941) C L1P4_orf2 LINE/L1 (2572) 722 1 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 (1) 2880 1322 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 13.33 1.44 0.86 INTRON_3 390657 391004 (9177) C L1MB4_3end LINE/L1 (355) 572 223 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 14.61 0.59 2.39 INTRON_3 391005 391516 (8665) C L1MA8_3end LINE/L1 (115) 923 421 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 26.31 0.65 0.65 INTRON_3 392923 393075 (7106) C MamRep488 DNA/hAT-Tip100 (0) 219 67 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 26.20 5.47 2.04 INTRON_3 393351 394063 (6118) + L2 LINE/L2 2344 3080 (2) 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) 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) 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 60.87 0.00 0.00 INTRON_3 394312 394334 (5847) C AT_rich Low_complexity (138) 162 140 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 10.48 2.22 0.00 INTRON_3 394348 394662 (5519) C MER47A DNA/TcMar-Tigger (0) 366 45 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 23.03 0.56 0.00 INTRON_3 394695 394872 (5309) C (TA)n Simple_repeat (0) 180 2 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 21.05 0.00 0.00 INTRON_3 394909 394965 (5216) + L2a_3end LINE/L2 461 517 (0) 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) 2066 11.51 0.34 2.78 INTRON_3 395927 396221 (3960) C AluSx SINE/Alu (24) 288 1 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 29.84 10.26 1.18 INTRON_3 396344 396421 (3760) C L2c_3end LINE/L2 (33) 445 361 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 24.36 5.49 2.37 INTRON_3 396625 396788 (3393) C MER113B DNA/hAT-Charlie (1) 301 133 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) 1446 20.79 4.17 2.46 INTRON_3 397173 397532 (2649) C Charlie6 DNA/hAT-Charlie (39) 3461 3096 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 (265) 3235 2371 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 28.78 7.94 0.74 INTRON_3 398240 398365 (1816) C Charlie6 DNA/hAT-Charlie (3234) 266 132 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 (3429) 71 1 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) 2392 9.06 0.00 0.00 INTRON_3 399008 399316 (865) C AluY SINE/Alu (1) 310 2 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) 369 29.46 8.33 7.06 INTRON_3 399478 399645 (536) C MER102c DNA/hAT-Charlie (161) 170 1 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 (141) 189 81 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) 2281 10.35 0.32 0.32 INTRON_3 399683 399992 (189) C AluSx SINE/Alu (2) 310 1 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)