Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold226

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 1071921
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.31

Warning! 95108 characters in sequence are not A, C, G, or T


File 2 of 3

Found at i:5680 original size:49 final size:48

Alignment explanation

Indices: 5622--5719 Score: 178 Period size: 49 Copynumber: 2.0 Consensus size: 48 5612 CGCTTTGAAT 5622 ACAGATCGGACTTTAATTTTTGCAATTTATATTCGCACTCCCATAAGG 1 ACAGATCGGACTTTAATTTTTGCAATTTATATTCGCACTCCCATAAGG * 5670 ANCAGATCGGACTTTAATTTTTGCAATTTATATTCGCCCTCCCATAAGG 1 A-CAGATCGGACTTTAATTTTTGCAATTTATATTCGCACTCCCATAAGG 5719 A 1 A 5720 TGCTTTGTGC Statistics Matches: 48, Mismatches: 1, Indels: 1 0.96 0.02 0.02 Matches are distributed among these distances: 48 1 0.02 49 47 0.98 ACGTcount: A:0.29, C:0.21, G:0.14, T:0.35 Consensus pattern (48 bp): ACAGATCGGACTTTAATTTTTGCAATTTATATTCGCACTCCCATAAGG Found at i:5806 original size:4 final size:4 Alignment explanation

Indices: 5793--5854 Score: 72 Period size: 4 Copynumber: 15.8 Consensus size: 4 5783 AAAGTTTACA * * * * * 5793 GACG GACA GACA GACG GACA GACG GACA GACG GACG GACG GACG GACA 1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG 5841 GACG GAC- GACG GAC 1 GACG GACG GACG GAC 5855 AAAAAGTGAT Statistics Matches: 49, Mismatches: 8, Indels: 2 0.83 0.14 0.03 Matches are distributed among these distances: 3 3 0.06 4 46 0.94 ACGTcount: A:0.34, C:0.26, G:0.40, T:0.00 Consensus pattern (4 bp): GACG Found at i:5815 original size:20 final size:20 Alignment explanation

Indices: 5790--5848 Score: 100 Period size: 20 Copynumber: 3.0 Consensus size: 20 5780 TAAAAAGTTT * 5790 ACAGACGGACAGACAGACGG 1 ACAGACGGACAGACGGACGG 5810 ACAGACGGACAGACGGACGG 1 ACAGACGGACAGACGGACGG * 5830 ACGGACGGACAGACGGACG 1 ACAGACGGACAGACGGACG 5849 ACGGACAAAA Statistics Matches: 37, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 37 1.00 ACGTcount: A:0.36, C:0.25, G:0.39, T:0.00 Consensus pattern (20 bp): ACAGACGGACAGACGGACGG Found at i:10988 original size:7 final size:7 Alignment explanation

Indices: 10976--11042 Score: 89 Period size: 7 Copynumber: 9.6 Consensus size: 7 10966 GAGAAGGATC 10976 ATTCGAG 1 ATTCGAG 10983 ATTCGAG 1 ATTCGAG * 10990 ATTCGAA 1 ATTCGAG * 10997 ATACGAG 1 ATTCGAG * 11004 ATTCGAA 1 ATTCGAG * 11011 ATACGAG 1 ATTCGAG 11018 ATTCGAG 1 ATTCGAG * 11025 ATTCGAA 1 ATTCGAG 11032 ATTCGAG 1 ATTCGAG 11039 ATTC 1 ATTC 11043 AATATCTAAA Statistics Matches: 50, Mismatches: 10, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 7 50 1.00 ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27 Consensus pattern (7 bp): ATTCGAG Found at i:37641 original size:55 final size:56 Alignment explanation

Indices: 37530--37642 Score: 133 Period size: 55 Copynumber: 2.0 Consensus size: 56 37520 GGCCGGAATG * * * * * 37530 TAAAAAAGGGGGAAAATCCACTATATAGTAGGTTTTCCGTGGGGGTAATCTGGCTA 1 TAAAAAAGGGGGAAAACCCACTATATAGTAGGCTTTCCCTGGGGGAAAACTGGCTA * 37586 TAAAAAA-GGGGAAAGCCCACTATATAGTCA-GCTTTCCCTGGGGGAAAAACT-GCTA 1 TAAAAAAGGGGGAAAACCCACTATATAGT-AGGCTTTCCCTGGGGG-AAAACTGGCTA 37641 TA 1 TA 37643 TAGCCATTTT Statistics Matches: 49, Mismatches: 6, Indels: 5 0.82 0.10 0.08 Matches are distributed among these distances: 55 37 0.76 56 12 0.24 ACGTcount: A:0.35, C:0.16, G:0.26, T:0.24 Consensus pattern (56 bp): TAAAAAAGGGGGAAAACCCACTATATAGTAGGCTTTCCCTGGGGGAAAACTGGCTA Found at i:37642 original size:33 final size:32 Alignment explanation

Indices: 37605--37696 Score: 112 Period size: 32 Copynumber: 2.8 Consensus size: 32 37595 GGAAAGCCCA * * 37605 CTATATAGTCAGCTTTCCCTGGGGGAAAAACTG 1 CTATATAGCCA-CTTTCCCGGGGGGAAAAACTG * * * 37638 CTATATAGCCATTTTTCCGGGGGGAAGAACTG 1 CTATATAGCCACTTTCCCGGGGGGAAAAACTG * * 37670 CTATATAGCCATTTTTCCGGGGGGAAA 1 CTATATAGCCACTTTCCCGGGGGGAAA 37697 GATGGCTAGG Statistics Matches: 53, Mismatches: 6, Indels: 1 0.88 0.10 0.02 Matches are distributed among these distances: 32 43 0.81 33 10 0.19 ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28 Consensus pattern (32 bp): CTATATAGCCACTTTCCCGGGGGGAAAAACTG Found at i:37669 original size:32 final size:32 Alignment explanation

Indices: 37625--37696 Score: 135 Period size: 32 Copynumber: 2.2 Consensus size: 32 37615 AGCTTTCCCT 37625 GGGGGAAAAACTGCTATATAGCCATTTTTCCG 1 GGGGGAAAAACTGCTATATAGCCATTTTTCCG * 37657 GGGGGAAGAACTGCTATATAGCCATTTTTCCG 1 GGGGGAAAAACTGCTATATAGCCATTTTTCCG 37689 GGGGGAAA 1 GGGGGAAA 37697 GATGGCTAGG Statistics Matches: 38, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 32 38 1.00 ACGTcount: A:0.28, C:0.17, G:0.31, T:0.25 Consensus pattern (32 bp): GGGGGAAAAACTGCTATATAGCCATTTTTCCG Found at i:43131 original size:15 final size:15 Alignment explanation

Indices: 43111--43140 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 43101 AGTGGGGCCT * 43111 CAGATATCCGGACGC 1 CAGATAACCGGACGC 43126 CAGATAACCGGACGC 1 CAGATAACCGGACGC 43141 TTCAGTTTAC Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.30, C:0.33, G:0.27, T:0.10 Consensus pattern (15 bp): CAGATAACCGGACGC Found at i:44474 original size:11 final size:11 Alignment explanation

Indices: 44448--44559 Score: 66 Period size: 11 Copynumber: 10.1 Consensus size: 11 44438 ACTAAACCCT 44448 GGGTTTACTTTTG 1 GGGTTTAC--TTG 44461 GGGTTTACTTG 1 GGGTTTACTTG 44472 GGGTTTACTCT- 1 GGGTTTACT-TG * 44483 GGGTTTACTTT 1 GGGTTTACTTG ** ** * * 44494 TTG-AAAATTT 1 GGGTTTACTTG ** * 44504 GGGTCCACTCG 1 GGGTTTACTTG * 44515 GGGTTTACTTT 1 GGGTTTACTTG * 44526 GGGTTTACTCG 1 GGGTTTACTTG * 44537 GGGTTTACTTT 1 GGGTTTACTTG 44548 GGGTTTACTTG 1 GGGTTTACTTG 44559 G 1 G 44560 AAATTGCTTT Statistics Matches: 75, Mismatches: 21, Indels: 8 0.72 0.20 0.08 Matches are distributed among these distances: 10 6 0.08 11 60 0.80 12 1 0.01 13 8 0.11 ACGTcount: A:0.12, C:0.12, G:0.30, T:0.46 Consensus pattern (11 bp): GGGTTTACTTG Found at i:44489 original size:22 final size:22 Alignment explanation

Indices: 44448--44559 Score: 100 Period size: 22 Copynumber: 5.0 Consensus size: 22 44438 ACTAAACCCT 44448 GGGTTTACTTTTGGGGTTTACTTG 1 GGGTTTAC-TTT-GGGTTTACTTG * * 44472 GGGTTTACTCTGGGTTTACTTT 1 GGGTTTACTTTGGGTTTACTTG ** ** * ** * 44494 TTG-AAAATTTGGGTCCACTCG 1 GGGTTTACTTTGGGTTTACTTG * 44515 GGGTTTACTTTGGGTTTACTCG 1 GGGTTTACTTTGGGTTTACTTG 44537 GGGTTTACTTTGGGTTTACTTG 1 GGGTTTACTTTGGGTTTACTTG 44559 G 1 G 44560 AAATTGCTTT Statistics Matches: 67, Mismatches: 20, Indels: 4 0.74 0.22 0.04 Matches are distributed among these distances: 21 11 0.16 22 46 0.69 23 2 0.03 24 8 0.12 ACGTcount: A:0.12, C:0.12, G:0.30, T:0.46 Consensus pattern (22 bp): GGGTTTACTTTGGGTTTACTTG Found at i:44741 original size:11 final size:11 Alignment explanation

Indices: 44723--44764 Score: 66 Period size: 11 Copynumber: 3.8 Consensus size: 11 44713 CTCTGTGTCC 44723 ACTCTGGGTTT 1 ACTCTGGGTTT * 44734 ACTTTGGGTTT 1 ACTCTGGGTTT 44745 ACTCTGGGTTT 1 ACTCTGGGTTT * 44756 ACTCAGGGT 1 ACTCTGGGT 44765 CCACTCTAGT Statistics Matches: 28, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 11 28 1.00 ACGTcount: A:0.12, C:0.17, G:0.29, T:0.43 Consensus pattern (11 bp): ACTCTGGGTTT Found at i:44770 original size:22 final size:22 Alignment explanation

Indices: 44719--44771 Score: 70 Period size: 22 Copynumber: 2.4 Consensus size: 22 44709 TACTCTCTGT ** 44719 GTCCACTCTGGGTTTACTTTGG 1 GTCCACTCTGGGTTTACTCAGG ** 44741 GTTTACTCTGGGTTTACTCAGG 1 GTCCACTCTGGGTTTACTCAGG 44763 GTCCACTCT 1 GTCCACTCT 44772 AGTAAACCCG Statistics Matches: 25, Mismatches: 6, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 22 25 1.00 ACGTcount: A:0.11, C:0.25, G:0.25, T:0.40 Consensus pattern (22 bp): GTCCACTCTGGGTTTACTCAGG Found at i:80294 original size:14 final size:14 Alignment explanation

Indices: 80277--80312 Score: 54 Period size: 14 Copynumber: 2.6 Consensus size: 14 80267 TAAAATTTGA * 80277 TACTAGTAACTGGC 1 TACTAGAAACTGGC 80291 TACTAGAAACTGGC 1 TACTAGAAACTGGC * 80305 TACGAGAA 1 TACTAGAA 80313 GTAAGAAAAG Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 14 20 1.00 ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22 Consensus pattern (14 bp): TACTAGAAACTGGC Found at i:80377 original size:37 final size:37 Alignment explanation

Indices: 80292--80370 Score: 131 Period size: 37 Copynumber: 2.1 Consensus size: 37 80282 GTAACTGGCT * 80292 ACTAGAAACTGGCTACGAGAAGTAAGAAAAGCTAGCC 1 ACTAGAAACTAGCTACGAGAAGTAAGAAAAGCTAGCC * * 80329 GCTAGAAACTAGCTACGAGAAGTAAGAAAATCTAGCC 1 ACTAGAAACTAGCTACGAGAAGTAAGAAAAGCTAGCC 80366 ACTAG 1 ACTAG 80371 TCACTAGTTA Statistics Matches: 38, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 37 38 1.00 ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15 Consensus pattern (37 bp): ACTAGAAACTAGCTACGAGAAGTAAGAAAAGCTAGCC Found at i:82166 original size:2 final size:2 Alignment explanation

Indices: 82161--82214 Score: 99 Period size: 2 Copynumber: 27.0 Consensus size: 2 82151 ATTTTTCAGT * 82161 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 82203 TC TC TC TC TC TC 1 TC TC TC TC TC TC 82215 ATTAGATTAT Statistics Matches: 50, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 2 50 1.00 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): TC Found at i:97407 original size:3 final size:3 Alignment explanation

Indices: 97401--97438 Score: 76 Period size: 3 Copynumber: 12.7 Consensus size: 3 97391 TTGTTGTTGT 97401 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG 1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG 97439 TACCTTTTGT Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 35 1.00 ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34 Consensus pattern (3 bp): TGA Found at i:100853 original size:14 final size:14 Alignment explanation

Indices: 100834--100866 Score: 66 Period size: 14 Copynumber: 2.4 Consensus size: 14 100824 GGTAAAGTTA 100834 GCTACTAGTAACTG 1 GCTACTAGTAACTG 100848 GCTACTAGTAACTG 1 GCTACTAGTAACTG 100862 GCTAC 1 GCTAC 100867 GAGAAGTAAG Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 19 1.00 ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27 Consensus pattern (14 bp): GCTACTAGTAACTG Found at i:100900 original size:37 final size:37 Alignment explanation

Indices: 100850--100940 Score: 121 Period size: 37 Copynumber: 2.5 Consensus size: 37 100840 AGTAACTGGC * 100850 TACTAGTAACTGGCTACGAGAAGT-AAGAAAAGATAGT 1 TACTAGTAACTGGCTACGAG-AGTAAAGAAAAGATAGG * * * * 100887 TACTAGTAACTGGCTACGAGATTAAATAAAAGTTGGG 1 TACTAGTAACTGGCTACGAGAGTAAAGAAAAGATAGG 100924 TACTAGTAACTGGCTAC 1 TACTAGTAACTGGCTAC 100941 TAGTAACTGG Statistics Matches: 48, Mismatches: 5, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 36 2 0.04 37 46 0.96 ACGTcount: A:0.38, C:0.13, G:0.23, T:0.25 Consensus pattern (37 bp): TACTAGTAACTGGCTACGAGAGTAAAGAAAAGATAGG Found at i:100942 original size:51 final size:51 Alignment explanation

Indices: 100887--100991 Score: 149 Period size: 51 Copynumber: 2.1 Consensus size: 51 100877 AAAAGATAGT * * * * * 100887 TACTAGTAACTGGCTACGAG-ATTAAATAAAAGTTGGGTACTAGTAACTGGC 1 TACTAGTAACTGGCTACGAGAAGT-AAGAAAAGCTAGCTACTAGTAACTGGC 100938 TACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTAGTAACTGGC 1 TACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTAGTAACTGGC 100989 TAC 1 TAC 100992 GAGAAGTAAG Statistics Matches: 48, Mismatches: 5, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 51 46 0.96 52 2 0.04 ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25 Consensus pattern (51 bp): TACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTAGTAACTGGC Found at i:100943 original size:14 final size:14 Alignment explanation

Indices: 100924--100954 Score: 62 Period size: 14 Copynumber: 2.2 Consensus size: 14 100914 AAAAGTTGGG 100924 TACTAGTAACTGGC 1 TACTAGTAACTGGC 100938 TACTAGTAACTGGC 1 TACTAGTAACTGGC 100952 TAC 1 TAC 100955 GAGAAGTAAG Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 17 1.00 ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29 Consensus pattern (14 bp): TACTAGTAACTGGC Found at i:101006 original size:88 final size:88 Alignment explanation

Indices: 100836--101006 Score: 290 Period size: 88 Copynumber: 1.9 Consensus size: 88 100826 TAAAGTTAGC * 100836 TACTAGTAACTGGCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGATAGTTACTAGTAACTGGC 1 TACTAGTAACTGGCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGATAGCTACTAGTAACTGGC * * 100901 TACGAGATTAAATAAAAGTTGGG 66 TACGAGAGTAAAGAAAAGTTGGG * 100924 TACTAGTAACTGGCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTAGCTACTAGTAACTGGC 1 TACTAGTAACTGGCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGATAGCTACTAGTAACTGGC 100989 TACGAGAAGT-AAGAAAAG 66 TACGAG-AGTAAAGAAAAG 101007 CTAGCTACAT Statistics Matches: 78, Mismatches: 4, Indels: 2 0.93 0.05 0.02 Matches are distributed among these distances: 88 76 0.97 89 2 0.03 ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23 Consensus pattern (88 bp): TACTAGTAACTGGCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGATAGCTACTAGTAACTGGC TACGAGAGTAAAGAAAAGTTGGG Found at i:101047 original size:43 final size:37 Alignment explanation

Indices: 100936--101014 Score: 158 Period size: 37 Copynumber: 2.1 Consensus size: 37 100926 CTAGTAACTG 100936 GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTA 1 GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTA 100973 GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTA 1 GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTA 101010 GCTAC 1 GCTAC 101015 ATGTATTAGT Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 37 42 1.00 ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19 Consensus pattern (37 bp): GCTACTAGTAACTGGCTACGAGAAGTAAGAAAAGCTA Found at i:101440 original size:177 final size:176 Alignment explanation

Indices: 101144--101542 Score: 618 Period size: 177 Copynumber: 2.3 Consensus size: 176 101134 TCACTGTCAA * * * * 101144 TTGTCAATATATCTCAAGTAGCTGTATATATAAACTAAAGATATATGCCCGACTTGCTAAAATCA 1 TTGTCAATATATCTCAAGTAGCTGTATATATAGATTGAAGATATATGCCCGACATGCTAAAATCA * * 101209 ACATTCTGTCAAGTCATCCACATAATATTACGACACAATTACTCAGATATCTCTCTTTATGTAGT 66 ACATTCTGTCAAGTCATCCACATAATATAACGACACAATCACTCAGATATCTCTCTTTATGTAGT * * 101274 CAGCTACTTGTGCGTTTCGTTCCAAATATCTTTATGTTTTGGAGGTT 131 CAGCTACTTGTGCATTTCGTTACAAATATCTTTAT-TTTTGGAGGTT * * * * 101321 TTGTCAATATATCTCAAGTAGTTGTTTATATAGATTGAAGATATATGCCGGACATGCTAATATCA 1 TTGTCAATATATCTCAAGTAGCTGTATATATAGATTGAAGATATATGCCCGACATGCTAAAATCA * * 101386 ACATTCTGTGAAGTCATCCACTTAATATAACGACACAATCACTCAGATATCTCTCTTTATGTAGT 66 ACATTCTGTCAAGTCATCCACATAATATAACGACACAATCACTCAGATATCTCTCTTTATGTAGT * ** 101451 CAGCTACTTGTGCATTTCGTTACAAATATCTTTATTTTTTGCTGTT 131 CAGCTACTTGTGCATTTCGTTACAAATATCTTTATTTTTGGAGGTT * * 101497 GTGTCTATATATCTCAAGTAGCTGTATATATAGATTGAAGATATAT 1 TTGTCAATATATCTCAAGTAGCTGTATATATAGATTGAAGATATAT 101543 AGTGTTGTGC Statistics Matches: 201, Mismatches: 21, Indels: 1 0.90 0.09 0.00 Matches are distributed among these distances: 176 50 0.25 177 151 0.75 ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38 Consensus pattern (176 bp): TTGTCAATATATCTCAAGTAGCTGTATATATAGATTGAAGATATATGCCCGACATGCTAAAATCA ACATTCTGTCAAGTCATCCACATAATATAACGACACAATCACTCAGATATCTCTCTTTATGTAGT CAGCTACTTGTGCATTTCGTTACAAATATCTTTATTTTTGGAGGTT Found at i:102391 original size:2 final size:2 Alignment explanation

Indices: 102384--102426 Score: 77 Period size: 2 Copynumber: 21.5 Consensus size: 2 102374 CCCCCTTCCC * 102384 AG AG AG AG AG AG AG AG AG AG AT AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 102426 A 1 A 102427 CCGGAACCTG Statistics Matches: 39, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 39 1.00 ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02 Consensus pattern (2 bp): AG Found at i:102976 original size:22 final size:22 Alignment explanation

Indices: 102926--102978 Score: 70 Period size: 22 Copynumber: 2.4 Consensus size: 22 102916 TATAAGTATT * 102926 GCTTAAAGGTGGCTTAAAGAAA 1 GCTTAAAGATGGCTTAAAGAAA * ** 102948 GCGTAAAGATGGCTTAAAGGCA 1 GCTTAAAGATGGCTTAAAGAAA 102970 GCTTAAAGA 1 GCTTAAAGA 102979 CTATCTTTAA Statistics Matches: 26, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 22 26 1.00 ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21 Consensus pattern (22 bp): GCTTAAAGATGGCTTAAAGAAA Found at i:102999 original size:11 final size:11 Alignment explanation

Indices: 102983--103011 Score: 58 Period size: 11 Copynumber: 2.6 Consensus size: 11 102973 TAAAGACTAT 102983 CTTTAAGCCAC 1 CTTTAAGCCAC 102994 CTTTAAGCCAC 1 CTTTAAGCCAC 103005 CTTTAAG 1 CTTTAAG 103012 GACAACTTAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:103059 original size:11 final size:11 Alignment explanation

Indices: 103043--103096 Score: 99 Period size: 11 Copynumber: 4.9 Consensus size: 11 103033 GTCCAAACTT 103043 CTTTAAGCCAC 1 CTTTAAGCCAC 103054 CTTTAAGCCAC 1 CTTTAAGCCAC * 103065 CTTTAAGCTAC 1 CTTTAAGCCAC 103076 CTTTAAGCCAC 1 CTTTAAGCCAC 103087 CTTTAAGCCA 1 CTTTAAGCCA 103097 TTAAAAAAAT Statistics Matches: 41, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 41 1.00 ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:104443 original size:2 final size:2 Alignment explanation

Indices: 104436--104483 Score: 96 Period size: 2 Copynumber: 24.0 Consensus size: 2 104426 CTGATGAACT 104436 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 104478 GA GA GA 1 GA GA GA 104484 TTTTTTTCAC Statistics Matches: 46, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 46 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:104892 original size:11 final size:11 Alignment explanation

Indices: 104869--104918 Score: 75 Period size: 11 Copynumber: 4.6 Consensus size: 11 104859 GTAAATGCCA * 104869 CTTAAAGAT-G 1 CTTAAAGGTGG 104879 CTTAAAGGTGG 1 CTTAAAGGTGG 104890 CTTAAAGGTGG 1 CTTAAAGGTGG * 104901 CTTAAAGGTAG 1 CTTAAAGGTGG 104912 CTTAAAG 1 CTTAAAG 104919 AAGTTTGGAC Statistics Matches: 37, Mismatches: 2, Indels: 1 0.93 0.05 0.03 Matches are distributed among these distances: 10 8 0.22 11 29 0.78 ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28 Consensus pattern (11 bp): CTTAAAGGTGG Found at i:105004 original size:10 final size:11 Alignment explanation

Indices: 104989--105028 Score: 55 Period size: 11 Copynumber: 3.7 Consensus size: 11 104979 GGTTGTATAG * 104989 CCTTTAAG-CT 1 CCTTTAAGCCA * 104999 CCTTTAAGTCA 1 CCTTTAAGCCA 105010 CCTTTAAGCCA 1 CCTTTAAGCCA 105021 CCTTTAAG 1 CCTTTAAG 105029 GACTTGCTTA Statistics Matches: 27, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 10 8 0.30 11 19 0.70 ACGTcount: A:0.25, C:0.30, G:0.10, T:0.35 Consensus pattern (11 bp): CCTTTAAGCCA Found at i:114705 original size:2 final size:2 Alignment explanation

Indices: 114698--114747 Score: 100 Period size: 2 Copynumber: 25.0 Consensus size: 2 114688 ATTAATATAC 114698 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 114740 GA GA GA GA 1 GA GA GA GA 114748 AAATAAGTAA Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 48 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:118970 original size:95 final size:95 Alignment explanation

Indices: 118801--118982 Score: 249 Period size: 95 Copynumber: 1.9 Consensus size: 95 118791 TCAATAAGTG * * * * 118801 CCAAAATTAAGTACTTTACTTAACAAGCAATCTTTGTTCCATTCCCACACGTGCAGCTCTATAAG 1 CCAAAATTAAGTACTATAATTAACAAGCAACCTTTGCTCCATTCCCACACGTGCAGCTCTATAAG 118866 TTAAACATTCTCAAAACATTTGGAATGGTA 66 TTAAACATTCTCAAAACATTTGGAATGGTA * * * * * * 118896 CCAAAATTAAGTGCTATAATTCACAAGCGACCTTTGCTCCATTCCCATACGTGCAGGTCTTTGAA 1 CCAAAATTAAGTACTATAATTAACAAGCAACCTTTGCTCCATTCCCACACGTGCAGCTCTAT-AA * 118961 -TTAAGCATTCTCAAAACATTTG 65 GTTAAACATTCTCAAAACATTTG 118983 TAATAATAAG Statistics Matches: 75, Mismatches: 11, Indels: 2 0.85 0.12 0.02 Matches are distributed among these distances: 95 73 0.97 96 2 0.03 ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31 Consensus pattern (95 bp): CCAAAATTAAGTACTATAATTAACAAGCAACCTTTGCTCCATTCCCACACGTGCAGCTCTATAAG TTAAACATTCTCAAAACATTTGGAATGGTA Found at i:119006 original size:31 final size:31 Alignment explanation

Indices: 118971--119032 Score: 115 Period size: 31 Copynumber: 2.0 Consensus size: 31 118961 TTAAGCATTC 118971 TCAAAACATTTGTAATAATAAGGCAATGGTG 1 TCAAAACATTTGTAATAATAAGGCAATGGTG * 119002 TCAAAACATTTGTAATATTAAGGCAATGGTG 1 TCAAAACATTTGTAATAATAAGGCAATGGTG 119033 GTGTCCATCA Statistics Matches: 30, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 31 30 1.00 ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31 Consensus pattern (31 bp): TCAAAACATTTGTAATAATAAGGCAATGGTG Found at i:121989 original size:3 final size:3 Alignment explanation

Indices: 121983--122009 Score: 54 Period size: 3 Copynumber: 9.0 Consensus size: 3 121973 TTGTTGTTGT 121983 TGA TGA TGA TGA TGA TGA TGA TGA TGA 1 TGA TGA TGA TGA TGA TGA TGA TGA TGA 122010 AGATTTACCT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 24 1.00 ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33 Consensus pattern (3 bp): TGA Found at i:124142 original size:16 final size:16 Alignment explanation

Indices: 124121--124155 Score: 61 Period size: 16 Copynumber: 2.2 Consensus size: 16 124111 ATCTGAATTT * 124121 ATTCTTTCATAATGTC 1 ATTCTTACATAATGTC 124137 ATTCTTACATAATGTC 1 ATTCTTACATAATGTC 124153 ATT 1 ATT 124156 TTCTCACAGT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 16 18 1.00 ACGTcount: A:0.29, C:0.17, G:0.06, T:0.49 Consensus pattern (16 bp): ATTCTTACATAATGTC Found at i:129747 original size:40 final size:40 Alignment explanation

Indices: 129692--129770 Score: 158 Period size: 40 Copynumber: 2.0 Consensus size: 40 129682 AGCGATCAAA 129692 TAGTAAACTAGACTCTTGTTACAAATACAACAAAATGTTT 1 TAGTAAACTAGACTCTTGTTACAAATACAACAAAATGTTT 129732 TAGTAAACTAGACTCTTGTTACAAATACAACAAAATGTT 1 TAGTAAACTAGACTCTTGTTACAAATACAACAAAATGTT 129771 CTTCCGTTTT Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 40 39 1.00 ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32 Consensus pattern (40 bp): TAGTAAACTAGACTCTTGTTACAAATACAACAAAATGTTT Found at i:133295 original size:23 final size:24 Alignment explanation

Indices: 133263--133309 Score: 69 Period size: 23 Copynumber: 2.0 Consensus size: 24 133253 CGCTATACGT 133263 TTATAACGAATTCG-TAAAAAATA 1 TTATAACGAATTCGTTAAAAAATA * * 133286 TTATAGCGAATTCGTTATAAAATA 1 TTATAACGAATTCGTTAAAAAATA 133310 ATTAAGGGTT Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 23 13 0.62 24 8 0.38 ACGTcount: A:0.47, C:0.09, G:0.11, T:0.34 Consensus pattern (24 bp): TTATAACGAATTCGTTAAAAAATA Found at i:133583 original size:15 final size:16 Alignment explanation

Indices: 133546--133586 Score: 57 Period size: 17 Copynumber: 2.6 Consensus size: 16 133536 TTAAAATTAC 133546 TTCGTTATAGCCGTAAA 1 TTCGTTATAGCCGT-AA * 133563 TTCGTTATAGCCGT-G 1 TTCGTTATAGCCGTAA 133578 TTCGTTATA 1 TTCGTTATA 133587 TACATCAATT Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 15 9 0.39 17 14 0.61 ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41 Consensus pattern (16 bp): TTCGTTATAGCCGTAA Found at i:146723 original size:6 final size:6 Alignment explanation

Indices: 146712--146736 Score: 50 Period size: 6 Copynumber: 4.2 Consensus size: 6 146702 TTGCAATAAA 146712 GAAATT GAAATT GAAATT GAAATT G 1 GAAATT GAAATT GAAATT GAAATT G 146737 TATGAGTATA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 19 1.00 ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32 Consensus pattern (6 bp): GAAATT Found at i:148306 original size:20 final size:19 Alignment explanation

Indices: 148269--148309 Score: 57 Period size: 20 Copynumber: 2.1 Consensus size: 19 148259 ATACTCCACT 148269 AAAACAAAAAACCAAAACC 1 AAAACAAAAAACCAAAACC 148288 AAAACAACAACAA-CAAAACC 1 AAAACAA-AA-AACCAAAACC 148308 AA 1 AA 148310 CAACCATGTA Statistics Matches: 20, Mismatches: 0, Indels: 3 0.87 0.00 0.13 Matches are distributed among these distances: 19 7 0.35 20 11 0.55 21 2 0.10 ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00 Consensus pattern (19 bp): AAAACAAAAAACCAAAACC Found at i:148312 original size:15 final size:15 Alignment explanation

Indices: 148271--148313 Score: 51 Period size: 12 Copynumber: 3.2 Consensus size: 15 148261 ACTCCACTAA 148271 AACAA-AAAACCAA- 1 AACAACAAAACCAAC 148284 AAC--CAAAA-CAAC 1 AACAACAAAACCAAC 148296 AACAACAAAACCAAC 1 AACAACAAAACCAAC 148311 AAC 1 AAC 148314 CATGTACATG Statistics Matches: 25, Mismatches: 0, Indels: 8 0.76 0.00 0.24 Matches are distributed among these distances: 11 3 0.12 12 7 0.28 13 3 0.12 14 5 0.20 15 7 0.28 ACGTcount: A:0.70, C:0.30, G:0.00, T:0.00 Consensus pattern (15 bp): AACAACAAAACCAAC Found at i:159659 original size:254 final size:257 Alignment explanation

Indices: 159206--159704 Score: 916 Period size: 254 Copynumber: 1.9 Consensus size: 257 159196 GTTTTCATAT 159206 TTTTTACATTTAATATTTATTTAAAAAAAAAAAAACCCTCACATTTCTGTTTTTCAGTCTAGGTG 1 TTTTTACATTTAATATTTATTT-AAAAAAAAAAAACCCTCACATTTCTGTTTTTCAGTCTAGGTG 159271 TGTATAAGTGTAATAAAGTCACACATGAAAATATTTTTTTTTGGTCATTATTGCCATTGATTTTT 65 TGTATAAGTGTAATAAAGTCACACATGAAAATATTTTTTTTTGGTCATTATTGCCATTGATTTTT 159336 ACCTTGTCTTACATTATCATTAGATCGATCTTTGATAGTATCTATTTCCATTGAAAAGTAAAGGT 130 ACCTTGTCTTACATTATCATTAGATCGATCTTTGATAGTATCTATTTCCATTGAAAAGTAAAGGT * * 159401 GTGTTATTTTTCTTCCTATAA-TTTTTTTTTATTTTTTTAAACTGAAAAAAGCCGGNTTTCAAA 195 GTGTTATTTTTCTTCCTATAATTTTTTTTTTATTATTTAAAACTGAAAAAAGCCGG-TTTCAAA * * 159464 TTTTTACATTTAATATTTATTT-TAAGAAAAAAACCCTCACATTTCTG-TTTTCAGTCTAGGTGT 1 TTTTTACATTTAATATTTATTTAAAAAAAAAAAACCCTCACATTTCTGTTTTTCAGTCTAGGTGT 159527 GTATAAGTGTAATAAAGTCACACATGAAAATA-TTTTTTTTGGTCATTATTGCCATTGATTTTTA 66 GTATAAGTGTAATAAAGTCACACATGAAAATATTTTTTTTTGGTCATTATTGCCATTGATTTTTA 159591 CCTTGTCTTACATTATCATTAGATCGATCTTTGATAGTATCTATTTCCATTGAAAAGTAAAGGTG 131 CCTTGTCTTACATTATCATTAGATCGATCTTTGATAGTATCTATTTCCATTGAAAAGTAAAGGTG 159656 TGTTATTTTTCTTCCTATAATTTTTTTTTTATTATTTAAAACTGAAAAA 196 TGTTATTTTTCTTCCTATAATTTTTTTTTTATTATTTAAAACTGAAAAA 159705 TCCAGGTCAA Statistics Matches: 236, Mismatches: 4, Indels: 5 0.96 0.02 0.02 Matches are distributed among these distances: 254 117 0.50 255 74 0.31 256 23 0.10 258 22 0.09 ACGTcount: A:0.31, C:0.12, G:0.11, T:0.45 Consensus pattern (257 bp): TTTTTACATTTAATATTTATTTAAAAAAAAAAAACCCTCACATTTCTGTTTTTCAGTCTAGGTGT GTATAAGTGTAATAAAGTCACACATGAAAATATTTTTTTTTGGTCATTATTGCCATTGATTTTTA CCTTGTCTTACATTATCATTAGATCGATCTTTGATAGTATCTATTTCCATTGAAAAGTAAAGGTG TGTTATTTTTCTTCCTATAATTTTTTTTTTATTATTTAAAACTGAAAAAAGCCGGTTTCAAA Found at i:160533 original size:12 final size:12 Alignment explanation

Indices: 160513--160548 Score: 56 Period size: 12 Copynumber: 3.0 Consensus size: 12 160503 TAGTGTTCCA 160513 AATAATAACAAT 1 AATAATAACAAT 160525 -ATAAATAACAAT 1 AAT-AATAACAAT 160537 AATAATAACAAT 1 AATAATAACAAT 160549 CTTAACAAAT Statistics Matches: 22, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 11 2 0.09 12 18 0.82 13 2 0.09 ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25 Consensus pattern (12 bp): AATAATAACAAT Found at i:184747 original size:19 final size:19 Alignment explanation

Indices: 184723--184760 Score: 76 Period size: 19 Copynumber: 2.0 Consensus size: 19 184713 ATATGCTACT 184723 ATACAGTAATGATACTGAA 1 ATACAGTAATGATACTGAA 184742 ATACAGTAATGATACTGAA 1 ATACAGTAATGATACTGAA 184761 TTGTTTTCTC Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26 Consensus pattern (19 bp): ATACAGTAATGATACTGAA Found at i:184857 original size:11 final size:11 Alignment explanation

Indices: 184841--184871 Score: 55 Period size: 11 Copynumber: 2.9 Consensus size: 11 184831 ATAAAAACTT 184841 TTATTATTGTA 1 TTATTATTGTA 184852 TTATTATTGTA 1 TTATTATTGTA 184863 TTATT-TTGT 1 TTATTATTGT 184872 TTTTTGTAGC Statistics Matches: 20, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 10 4 0.20 11 16 0.80 ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68 Consensus pattern (11 bp): TTATTATTGTA Found at i:194665 original size:17 final size:16 Alignment explanation

Indices: 194643--194684 Score: 57 Period size: 17 Copynumber: 2.4 Consensus size: 16 194633 TTTGGTCGTG 194643 TGTTTTTTTATTTTGTT 1 TGTTTTTTTATTTT-TT 194660 TGTTTTATTTATTTTTT 1 TGTTTT-TTTATTTTTT 194677 TGTGTTTT 1 TGT-TTTT 194685 ATTCATTTAT Statistics Matches: 23, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 17 12 0.52 18 11 0.48 ACGTcount: A:0.07, C:0.00, G:0.12, T:0.81 Consensus pattern (16 bp): TGTTTTTTTATTTTTT Found at i:194682 original size:19 final size:19 Alignment explanation

Indices: 194641--194697 Score: 73 Period size: 19 Copynumber: 3.1 Consensus size: 19 194631 TCTTTGGTCG * 194641 TGTGTTTT-TTTATTTTGT 1 TGTGTTTTATTTATTTTTT 194659 T-TGTTTTATTTATTTTTT 1 TGTGTTTTATTTATTTTTT * 194677 TGTGTTTTATTCATTTATTT 1 TGTGTTTTATTTATTT-TTT 194697 T 1 T 194698 TTCGGGGGGT Statistics Matches: 34, Mismatches: 2, Indels: 4 0.85 0.05 0.10 Matches are distributed among these distances: 17 6 0.18 18 11 0.32 19 13 0.38 20 4 0.12 ACGTcount: A:0.11, C:0.02, G:0.11, T:0.77 Consensus pattern (19 bp): TGTGTTTTATTTATTTTTT Found at i:197248 original size:20 final size:20 Alignment explanation

Indices: 197219--197268 Score: 57 Period size: 20 Copynumber: 2.5 Consensus size: 20 197209 TTGTCTTTAT 197219 TATTTAGATTGCCCTGACTA 1 TATTTAGATTGCCCTGACTA * * * 197239 TATTTGGATTGTCTTGACTA 1 TATTTAGATTGCCCTGACTA * 197259 TTTTTA-ATTG 1 TATTTAGATTG 197269 TCTTGGCTAT Statistics Matches: 25, Mismatches: 5, Indels: 1 0.81 0.16 0.03 Matches are distributed among these distances: 19 4 0.16 20 21 0.84 ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50 Consensus pattern (20 bp): TATTTAGATTGCCCTGACTA Found at i:197261 original size:38 final size:37 Alignment explanation

Indices: 197200--197299 Score: 103 Period size: 38 Copynumber: 2.6 Consensus size: 37 197190 ACTGTCGTGA * * * 197200 ATATTTTGATTGTCTTTATTATTTAGATTGCCCTGACT 1 ATATTTGGATTGTCTTGACTATTTA-ATTGCCCTGACT * * * 197238 ATATTTGGATTGTCTTGACTATTTTTAATTGTCTTGGCT 1 ATATTTGGATTGTCTTGACTA--TTTAATTGCCCTGACT * 197277 ATTTTTGG-TTGTCTTGACTATTT 1 ATATTTGGATTGTCTTGACTATTT 197300 TTATTTGTCT Statistics Matches: 53, Mismatches: 7, Indels: 6 0.80 0.11 0.09 Matches are distributed among these distances: 36 3 0.06 38 30 0.57 39 16 0.30 40 4 0.08 ACGTcount: A:0.18, C:0.11, G:0.16, T:0.55 Consensus pattern (37 bp): ATATTTGGATTGTCTTGACTATTTAATTGCCCTGACT Found at i:197270 original size:19 final size:19 Alignment explanation

Indices: 197246--197354 Score: 123 Period size: 19 Copynumber: 5.8 Consensus size: 19 197236 CTATATTTGG 197246 ATTGTCTTGACTATTTTTA 1 ATTGTCTTGACTATTTTTA * * 197265 ATTGTCTTGGCTATTTTTG 1 ATTGTCTTGACTATTTTTA * 197284 GTTGTCTTGACTATTTTTA 1 ATTGTCTTGACTATTTTTA * * 197303 TTTGTCTTGACTATTCTT- 1 ATTGTCTTGACTATTTTTA * * * * 197321 ATTTTCCTGAATA-TTTTG 1 ATTGTCTTGACTATTTTTA 197339 ATTGTCTTGACTATTT 1 ATTGTCTTGACTATTT 197355 GGATTATACG Statistics Matches: 73, Mismatches: 15, Indels: 4 0.79 0.16 0.04 Matches are distributed among these distances: 17 3 0.04 18 19 0.26 19 51 0.70 ACGTcount: A:0.17, C:0.12, G:0.14, T:0.58 Consensus pattern (19 bp): ATTGTCTTGACTATTTTTA Found at i:197300 original size:18 final size:18 Alignment explanation

Indices: 197155--197359 Score: 178 Period size: 18 Copynumber: 11.1 Consensus size: 18 197145 TTTCGACTAC * 197155 TTGTCTTGACTATTTTGC 1 TTGTCTTGACTATTTTGA * * 197173 TTGTATTGTCTATTTTGA 1 TTGTCTTGACTATTTTGA * * * 197191 CTGTCGTGAATATTTTGA 1 TTGTCTTGACTATTTTGA * * * 197209 TTGTCTTTATTATTTAGA 1 TTGTCTTGACTATTTTGA * * 197227 TTGCCCTGACTATATTTGGA 1 TTGTCTTGACTAT-TTT-GA * 197247 TTGTCTTGACTATTTTTAA 1 TTGTCTTGACTA-TTTTGA * * 197266 TTGTCTTGGCTATTTTTGG 1 TTGTCTTGACTA-TTTTGA * 197285 TTGTCTTGACTATTTTTA 1 TTGTCTTGACTATTTTGA 197303 TTTGTCTTGACTATTCTT-A 1 -TTGTCTTGACTATT-TTGA * * * 197322 TTTTCCTGAATATTTTGA 1 TTGTCTTGACTATTTTGA * 197340 TTGTCTTGACTATTTGGA 1 TTGTCTTGACTATTTTGA 197358 TT 1 TT 197360 ATACGATTGT Statistics Matches: 147, Mismatches: 34, Indels: 12 0.76 0.18 0.06 Matches are distributed among these distances: 17 2 0.01 18 82 0.56 19 45 0.31 20 17 0.12 21 1 0.01 ACGTcount: A:0.17, C:0.12, G:0.16, T:0.55 Consensus pattern (18 bp): TTGTCTTGACTATTTTGA Found at i:197308 original size:57 final size:55 Alignment explanation

Indices: 197247--197354 Score: 144 Period size: 55 Copynumber: 1.9 Consensus size: 55 197237 TATATTTGGA * * ** * 197247 TTGTCTTGACTATTTTTAATTGTCTTGGCTATTTTTGGTTGTCTTGACTATTTTTAT 1 TTGTCTTGACTATTCTT-ATTGTCCTGAATA-TTTTGATTGTCTTGACTATTTTTAT * 197304 TTGTCTTGACTATTCTTATTTTCCTGAATATTTTGATTGTCTTGACTATTT 1 TTGTCTTGACTATTCTTATTGTCCTGAATATTTTGATTGTCTTGACTATTT 197355 GGATTATACG Statistics Matches: 45, Mismatches: 6, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 55 20 0.44 56 9 0.20 57 16 0.36 ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58 Consensus pattern (55 bp): TTGTCTTGACTATTCTTATTGTCCTGAATATTTTGATTGTCTTGACTATTTTTAT Found at i:202573 original size:168 final size:168 Alignment explanation

Indices: 202317--202732 Score: 649 Period size: 168 Copynumber: 2.5 Consensus size: 168 202307 AAAAACTGGT * * * 202317 TGCATGGTTATGATGTCCAT-AAGGCCCTCTACCAAAATTGTG--AATTATTGGCCCCTGGGTCA 1 TGCATGGTTATGATGTCCATGAA-GCCCTCTACCTAAATTGTGAAAATCA-TGACCCCTGGGTCA * * * 202379 GGGGTTCTGGGTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAA 64 GGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAA * * 202444 TCTTCTTCTCTACTACCATATATATTTTTTGAAAACTAAA 129 TCTTCTTCTCTACTACCATATATATTTGTTAAAAACTAAA * * 202484 TGCATGATTATGATGTCCATGAAGCCCTGTACCTAAATTGTGAAAATCATGACCCCTGGGTCAGG 1 TGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAAATCATGACCCCTGGGTCAGG 202549 GGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAATC 66 GGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAATC * * 202614 TTCTTCTCTTCTATCATATATATTTGTTAAAAACTAAA 131 TTCTTCTCTACTACCATATATATTTGTTAAAAACTAAA * * * * 202652 TGTATGGTTATGATGTCCATGAAGCCCTCAACCTAAATTGTGAAATTCATGACCCCTTGGTCAGG 1 TGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAAATCATGACCCCTGGGTCAGG 202717 GGTTCAGGCTCTAGGG 66 GGTTCAGGCTCTAGGG 202733 NNNNNNNNNN Statistics Matches: 228, Mismatches: 18, Indels: 5 0.91 0.07 0.02 Matches are distributed among these distances: 167 36 0.16 168 188 0.82 169 4 0.02 ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32 Consensus pattern (168 bp): TGCATGGTTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAAATCATGACCCCTGGGTCAGG GGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAGAAAATC TTCTTCTCTACTACCATATATATTTGTTAAAAACTAAA Found at i:207084 original size:49 final size:49 Alignment explanation

Indices: 207029--208203 Score: 1538 Period size: 49 Copynumber: 24.0 Consensus size: 49 207019 ACCAGGTAAG * 207029 TACTATGTCAAGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * ** 207078 TACTATGTCAAGTCTTACAC--TGTCAGAATAAAAGTCAACATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * * * * 207125 TAATTTGTCAGGTCTTACACTTTGTCAGAATAGTAGTCAACATATGGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * * 207174 TTCTATGTCAGGTCTTACACTGTGT-TGTAATAGTAGTCAACATAT-GTTC 1 TACTATGTCAGGTCTTACACTGTGTCAG-AATAGTAGTCAACATGTAG-TC * 207223 TACTATGTCAGGCCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * ** * * 207272 TACTATGTCAGGTCTTACACTTTGTCAGAATAGTAGTCTTCGTGTGGT- 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * * * 207320 TGTCTATGTCAGGTCTTACACTGTGTTATAATAGTAGTCAACATAT-GTTC 1 T-ACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAG-TC * * 207370 TACTATGTCAGGTCTTACATTGTGTCAGAATAGTAATCAACATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * * * * 207419 TACTATGTCAGGTCTTACACTGTGTTAGAATAATAGTCATCGTGTGGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * 207468 TACTATGTCAGGT-TTACACTGTGTTAGAATAGTAGTCAACATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * * 207516 TACTATGTCATGTCTTACACTGTGTCAGAATAGTAGTCAATAAGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * * 207565 T-GTAATGTCAGGTCTTACACTGTGTCAAAATAGTAGTCAAGATGTAGTC 1 TACT-ATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * * 207614 TACTATGTCATGTTTTACACTGTGTCAGAATGGTAGTCAACATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * * 207663 TACTAAGTCAGGTCTTACACTGTGTCGGAATAGTAGTCAAGATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * 207712 TACTATGTCATGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * * 207761 TACTATGTCATGTCTTACACTGTGTCGGAATAGTAGTCAAGATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * * 207810 TACTATGCCATGTCTTACACTGTGTCAGAATGGTAGTCAACATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * * 207859 TACTAAGTCAGGTCTTACACTGTGTCGGAATAGTAGTCAAGATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * * 207908 TACTATGCCATGTCTTACACTGTGTCAGAATAGTAGTCAATATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * ** * 207957 TACAATGTCATGTCTTACACTGTGTTGGAATAGTAGTCATCATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * * * 208006 TTCTATGTCATGTCTTACTCTTTGTCAGAATAGTAGTCAACATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * * 208055 TACTATGTCAGGTCTTACACTGTGTTAGAAAAAGTAGTCATCATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAG-AATAGTAGTCAACATGTAGTC * * * * ** * 208105 TTCTATGTCATGTCTTACTCTGTGTCAGAATAGTAGTCAACATCTTTTT 1 TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC * * * 208154 TACTATGTCAGGTCTTACACTGTGTTAGAAAAAGTAGTTAACATGTAGTC 1 TACTATGTCAGGTCTTACACTGTGTCAG-AATAGTAGTCAACATGTAGTC 208204 GGTTGTTCAA Statistics Matches: 980, Mismatches: 131, Indels: 29 0.86 0.11 0.03 Matches are distributed among these distances: 47 42 0.04 48 48 0.05 49 827 0.84 50 63 0.06 ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35 Consensus pattern (49 bp): TACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCAACATGTAGTC Found at i:210552 original size:65 final size:65 Alignment explanation

Indices: 210465--210614 Score: 273 Period size: 65 Copynumber: 2.3 Consensus size: 65 210455 GTTTTCATTC * * 210465 CAAGAAAAGAGAAAAGAAGTATGCCTAACAATGAAGTATTCTACACTGTTTGTGATGTTTGATTT 1 CAAGTAAAGAGAAAAGAAGTATGCCTAACAATGAAGTATTCTACACTGTTTGGGATGTTTGATTT 210530 CAAGTAAAGAGAAAAGAAGTATGCCTAACAATGAAGTATTCTACACTGTTTGGGATGTTTGATTT 1 CAAGTAAAGAGAAAAGAAGTATGCCTAACAATGAAGTATTCTACACTGTTTGGGATGTTTGATTT * 210595 CAAGTAAAGAAAAAAGAAGT 1 CAAGTAAAGAGAAAAGAAGT 210615 TTTTGTGAAG Statistics Matches: 82, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 65 82 1.00 ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28 Consensus pattern (65 bp): CAAGTAAAGAGAAAAGAAGTATGCCTAACAATGAAGTATTCTACACTGTTTGGGATGTTTGATTT Found at i:211355 original size:49 final size:49 Alignment explanation

Indices: 211279--211726 Score: 680 Period size: 49 Copynumber: 9.1 Consensus size: 49 211269 CATGGAGATT * * * 211279 ACATGTAGTTTACTATGTCATGCCTTACACTGTGTCAGAATAGTAGTCA 1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA * * * * 211328 ACATGTAGTCTACTCTTTCAAGTCTTACACTGTGTCAGAATAGTAGTGA 1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA * * * 211377 ACATGTAGCCTACTATGTCATGCCTTACACTGTGTCAGAATAGTAGTCA 1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA * 211426 ACATGTAGTCTACTATGTCAGGTGTTACACTGTGTCAGAATAGTAGTCA 1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA * * 211475 ACATGTGGTCTTCTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA 1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA * * * * 211524 ACATGTAGTCTACTCTTTCAAGTCTTACACTGTGTCAGAATAGTAGTGA 1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA * * 211573 ACATGTAGCCTACTATGTCAGGTCTTACACTGTGTCAGAATAATAGTCA 1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA * * 211622 ACATGTAGTCTACTATGCCATGTCTTACACTGTGTCAGAATAGTAGTCA 1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA * * * 211671 ACATGTAGTCTACTATGTCAGGTGTTACACTGTGTTAAAATAGTAGTCA 1 ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA 211720 ACATGTA 1 ACATGTA 211727 TATATTTTAT Statistics Matches: 359, Mismatches: 40, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 49 359 1.00 ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33 Consensus pattern (49 bp): ACATGTAGTCTACTATGTCAGGTCTTACACTGTGTCAGAATAGTAGTCA Found at i:217374 original size:448 final size:448 Alignment explanation

Indices: 216539--217435 Score: 1733 Period size: 448 Copynumber: 2.0 Consensus size: 448 216529 CATATGTTAT 216539 GATCTCTACTGTAAAAAAAACTGTAAAATGGTCTTTTCATTTGACTCGTTTGGTCCGAAACAAAA 1 GATCTCTACTGTAAAAAAAACTGTAAAATGGTCTTTTCATTTGACTCGTTTGGTCCGAAACAAAA 216604 ATTAACACATAATTTTGATTGCACCATCTAAGTTTGACCAGTTTCACTGCATAATAGTTTAACAT 66 ATTAACACATAATTTTGATTGCACCATCTAAGTTTGACCAGTTTCACTGCATAATAGTTTAACAT * 216669 AACAAGCCTTGATTACAGAGAAGCACTAATCTGTGACTAATGAGTATTAAAGGGACTGATGGCGT 131 AACAAGCCTTGATTACAAAGAAGCACTAATCTGTGACTAATGAGTATTAAAGGGACTGATGGCGT 216734 GTCAGATTCACTAACTATGAAGTGAATAATTAAACACTGTACAAAAATAATGTTTGGAAAATATA 196 GTCAGATTCACTAACTATGAAGTGAATAATTAAACACTGTACAAAAATAATGTTTGGAAAATATA 216799 AAGTATTGCATCTTGTATGCTTTCACAAGCATGGAGTATTCTATGAAGTACATCTACAAATGATA 261 AAGTATTGCATCTTGTATGCTTTCACAAGCATGGAGTATTCTATGAAGTACATCTACAAATGATA 216864 AATTGAAATCATCTAGCGGGCTGTTATATGTTCAAATGGATTTCTTAGATCTGGGATCC-ATATA 326 AATTGAAATCATCTAGCGGGCTGTTATATGTTCAAATGGATTTCTTAGATCTGGGATCCAATATA * 216928 TATATTGCTGGGTTAAGATCTATGACAACAAACTGAGACATTTTCAGATCTTTAAGNAG 391 TATATTGCTGGGTTAAAATCTATGACAACAAACTGAGACATTTTCAGATCTTTAAG-AG 216987 GATCTCTACTGTAAAAAAAACTGTAAAATGGTCTTTTCATTTGACTCGTTTGGTCCGAAACAAAA 1 GATCTCTACTGTAAAAAAAACTGTAAAATGGTCTTTTCATTTGACTCGTTTGGTCCGAAACAAAA 217052 ATTAACACATAATTTTGATTGCACCATCTAAGTTTGACCAGTTTCACTGCATAATAGTTTAACAT 66 ATTAACACATAATTTTGATTGCACCATCTAAGTTTGACCAGTTTCACTGCATAATAGTTTAACAT 217117 AACAAGCCTTGATTACAAAGAAGCACTAATCTGTGACTAATGAGTATTAAAGGGACTGATGGCGT 131 AACAAGCCTTGATTACAAAGAAGCACTAATCTGTGACTAATGAGTATTAAAGGGACTGATGGCGT 217182 GTCAGATTCACTAACTATGAAGTGAATAATTAAACACTGTACAAAAATAATGTTTGGAAAATATA 196 GTCAGATTCACTAACTATGAAGTGAATAATTAAACACTGTACAAAAATAATGTTTGGAAAATATA 217247 AAGTATTGCATCTTGTATGCTTTCACAAGCATGGAGTATTCTATGAAGTACATCTACAAATGATA 261 AAGTATTGCATCTTGTATGCTTTCACAAGCATGGAGTATTCTATGAAGTACATCTACAAATGATA 217312 AATTGAAATCATCTAGCGGGCTGTTATATGTTCAAATGGATTTCTTAGATCTGGGATCCATATAT 326 AATTGAAATCATCTAGCGGGCTGTTATATGTTCAAATGGATTTCTTAGATCTGGGATCC--A-AT 217377 ATATATATTGCTGGGTTAAAATCTATGACAACAAACTGAGACATTTTCAGATCTTTAAG 388 ATATATATTGCTGGGTTAAAATCTATGACAACAAACTGAGACATTTTCAGATCTTTAAG 217436 GGTAACTTAC Statistics Matches: 443, Mismatches: 2, Indels: 4 0.99 0.00 0.01 Matches are distributed among these distances: 448 383 0.86 452 60 0.14 ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32 Consensus pattern (448 bp): GATCTCTACTGTAAAAAAAACTGTAAAATGGTCTTTTCATTTGACTCGTTTGGTCCGAAACAAAA ATTAACACATAATTTTGATTGCACCATCTAAGTTTGACCAGTTTCACTGCATAATAGTTTAACAT AACAAGCCTTGATTACAAAGAAGCACTAATCTGTGACTAATGAGTATTAAAGGGACTGATGGCGT GTCAGATTCACTAACTATGAAGTGAATAATTAAACACTGTACAAAAATAATGTTTGGAAAATATA AAGTATTGCATCTTGTATGCTTTCACAAGCATGGAGTATTCTATGAAGTACATCTACAAATGATA AATTGAAATCATCTAGCGGGCTGTTATATGTTCAAATGGATTTCTTAGATCTGGGATCCAATATA TATATTGCTGGGTTAAAATCTATGACAACAAACTGAGACATTTTCAGATCTTTAAGAG Found at i:233800 original size:5 final size:5 Alignment explanation

Indices: 233799--233833 Score: 61 Period size: 5 Copynumber: 6.8 Consensus size: 5 233789 AAAAAAACAA 233799 AAAAC AAAAC AAAAC AAAAAC AAAAC AAAAC AAAA 1 AAAAC AAAAC AAAAC -AAAAC AAAAC AAAAC AAAA 233834 AACGACGCCG Statistics Matches: 29, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 5 24 0.83 6 5 0.17 ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00 Consensus pattern (5 bp): AAAAC Found at i:233819 original size:16 final size:16 Alignment explanation

Indices: 233792--233834 Score: 77 Period size: 16 Copynumber: 2.6 Consensus size: 16 233782 CCCCCCCAAA 233792 AAAACAAAAAACAAAAC 1 AAAAC-AAAAACAAAAC 233809 AAAACAAAAACAAAAC 1 AAAACAAAAACAAAAC 233825 AAAACAAAAA 1 AAAACAAAAA 233835 ACGACGCCGC Statistics Matches: 26, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 16 21 0.81 17 5 0.19 ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00 Consensus pattern (16 bp): AAAACAAAAACAAAAC Found at i:233834 original size:11 final size:11 Alignment explanation

Indices: 233791--233833 Score: 61 Period size: 11 Copynumber: 3.9 Consensus size: 11 233781 CCCCCCCCAA * 233791 AAAAACAAAAA 1 AAAAACAAAAC 233802 ACAAAACAAAAC 1 A-AAAACAAAAC 233814 AAAAACAAAAC 1 AAAAACAAAAC 233825 -AAAACAAAA 1 AAAAACAAAA 233834 AACGACGCCG Statistics Matches: 30, Mismatches: 1, Indels: 3 0.88 0.03 0.09 Matches are distributed among these distances: 10 9 0.30 11 11 0.37 12 10 0.33 ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00 Consensus pattern (11 bp): AAAAACAAAAC Found at i:238384 original size:16 final size:16 Alignment explanation

Indices: 238363--238394 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 238353 CCGAATTAAA * 238363 TTGATTTTATTTATTT 1 TTGATTTGATTTATTT 238379 TTGATTTGATTTATTT 1 TTGATTTGATTTATTT 238395 GATCCATCTA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72 Consensus pattern (16 bp): TTGATTTGATTTATTT Found at i:250427 original size:18 final size:18 Alignment explanation

Indices: 250404--250453 Score: 100 Period size: 18 Copynumber: 2.8 Consensus size: 18 250394 TGCAATATGG 250404 TCAAAGTTCAATCAGAGT 1 TCAAAGTTCAATCAGAGT 250422 TCAAAGTTCAATCAGAGT 1 TCAAAGTTCAATCAGAGT 250440 TCAAAGTTCAATCA 1 TCAAAGTTCAATCA 250454 AAGCTGCATT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 32 1.00 ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28 Consensus pattern (18 bp): TCAAAGTTCAATCAGAGT Found at i:251285 original size:18 final size:18 Alignment explanation

Indices: 251262--251311 Score: 100 Period size: 18 Copynumber: 2.8 Consensus size: 18 251252 TGCAATATGG 251262 TCAAAGTTCAATCAGAGT 1 TCAAAGTTCAATCAGAGT 251280 TCAAAGTTCAATCAGAGT 1 TCAAAGTTCAATCAGAGT 251298 TCAAAGTTCAATCA 1 TCAAAGTTCAATCA 251312 AAGCTGCATT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 32 1.00 ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28 Consensus pattern (18 bp): TCAAAGTTCAATCAGAGT Found at i:256406 original size:16 final size:16 Alignment explanation

Indices: 256385--256415 Score: 62 Period size: 16 Copynumber: 1.9 Consensus size: 16 256375 GCCTGAAGTG 256385 GGACAGACAGACGGAC 1 GGACAGACAGACGGAC 256401 GGACAGACAGACGGA 1 GGACAGACAGACGGA 256416 GTGACGGACG Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.39, C:0.23, G:0.39, T:0.00 Consensus pattern (16 bp): GGACAGACAGACGGAC Found at i:266092 original size:16 final size:17 Alignment explanation

Indices: 266073--266107 Score: 54 Period size: 16 Copynumber: 2.1 Consensus size: 17 266063 TATGTATTGA * 266073 ATAGGTATTGTAT-GGT 1 ATAGGTATAGTATAGGT 266089 ATAGGTATAGTATAGGT 1 ATAGGTATAGTATAGGT 266106 AT 1 AT 266108 CGTATAAGTG Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 16 12 0.71 17 5 0.29 ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40 Consensus pattern (17 bp): ATAGGTATAGTATAGGT Found at i:266096 original size:27 final size:27 Alignment explanation

Indices: 266061--266112 Score: 68 Period size: 27 Copynumber: 1.9 Consensus size: 27 266051 AGATATCGTA * * * 266061 TATATGTATTGAATAGGTATTGTATGG 1 TATAGGTATAGAATAGGTATCGTATGG * 266088 TATAGGTATAGTATAGGTATCGTAT 1 TATAGGTATAGAATAGGTATCGTAT 266113 AAGTGTCGAA Statistics Matches: 21, Mismatches: 4, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 27 21 1.00 ACGTcount: A:0.31, C:0.02, G:0.25, T:0.42 Consensus pattern (27 bp): TATAGGTATAGAATAGGTATCGTATGG Found at i:272375 original size:18 final size:18 Alignment explanation

Indices: 272352--272473 Score: 172 Period size: 18 Copynumber: 6.8 Consensus size: 18 272342 ACCATCAAGA * 272352 ACCACAAGACGTCCGTAC 1 ACCACACGACGTCCGTAC * 272370 ACCACAAGACGTCCGTAC 1 ACCACACGACGTCCGTAC * 272388 ACCACACGGCGTCCGTAC 1 ACCACACGACGTCCGTAC * 272406 ACCACTCGACGTCCGTAC 1 ACCACACGACGTCCGTAC * * 272424 ACCACTCGACGTCCTTAC 1 ACCACACGACGTCCGTAC * 272442 ACCACTCGACGTCCGTAC 1 ACCACACGACGTCCGTAC * 272460 ACCACTCGACGTCC 1 ACCACACGACGTCC 272474 TTACCCCAGG Statistics Matches: 98, Mismatches: 6, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 98 1.00 ACGTcount: A:0.25, C:0.43, G:0.16, T:0.15 Consensus pattern (18 bp): ACCACACGACGTCCGTAC Found at i:275557 original size:2 final size:2 Alignment explanation

Indices: 275550--275607 Score: 116 Period size: 2 Copynumber: 29.0 Consensus size: 2 275540 GTAAGGTTTT 275550 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 275592 TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC 275608 AGTATTTGAG Statistics Matches: 56, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 56 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:276139 original size:17 final size:18 Alignment explanation

Indices: 276114--276151 Score: 51 Period size: 17 Copynumber: 2.2 Consensus size: 18 276104 AATTGATTTT * 276114 TTAATTTTTTTCA-TAAA 1 TTAACTTTTTTCATTAAA * 276131 TTAACTTTTTTGATTAAA 1 TTAACTTTTTTCATTAAA 276149 TTA 1 TTA 276152 GTAATGTAGA Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 17 11 0.61 18 7 0.39 ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58 Consensus pattern (18 bp): TTAACTTTTTTCATTAAA Found at i:277826 original size:50 final size:50 Alignment explanation

Indices: 277687--277826 Score: 181 Period size: 50 Copynumber: 2.8 Consensus size: 50 277677 TGTACCTTCA *** * * * * 277687 TAACGCACTTTGAAAATTTTTTTCAAAGTGGGTTAACTTGGTCCAAAATT 1 TAACGCACTTTGAAAAAAATTTTCAAAGTGCGTTAATTTTGTCCAAAACT * * 277737 TAACGCACTTTGAAAAAAAATTTCAAAGTGCGTTGATTTTGTCCAAAACT 1 TAACGCACTTTGAAAAAAATTTTCAAAGTGCGTTAATTTTGTCCAAAACT * * 277787 TAACGCAATTTGAAAAAAATTTTCAAAGTGCGTAAATTTT 1 TAACGCACTTTGAAAAAAATTTTCAAAGTGCGTTAATTTT 277827 TCAAAGTGCG Statistics Matches: 77, Mismatches: 13, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 50 77 1.00 ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35 Consensus pattern (50 bp): TAACGCACTTTGAAAAAAATTTTCAAAGTGCGTTAATTTTGTCCAAAACT Found at i:284352 original size:12 final size:13 Alignment explanation

Indices: 284335--284372 Score: 53 Period size: 12 Copynumber: 3.1 Consensus size: 13 284325 GATAATACCA 284335 TCAATGAAT-TTT 1 TCAATGAATGTTT 284347 TCAATG-ATGTTT 1 TCAATGAATGTTT * 284359 TCAATGAACGTTT 1 TCAATGAATGTTT 284372 T 1 T 284373 TTTAATGATG Statistics Matches: 23, Mismatches: 1, Indels: 3 0.85 0.04 0.11 Matches are distributed among these distances: 11 2 0.09 12 15 0.65 13 6 0.26 ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47 Consensus pattern (13 bp): TCAATGAATGTTT Found at i:286251 original size:12 final size:12 Alignment explanation

Indices: 286234--286259 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 286224 TGTCTTTCTA 286234 AAAAAAAAAAAC 1 AAAAAAAAAAAC 286246 AAAAAAAAAAAC 1 AAAAAAAAAAAC 286258 AA 1 AA 286260 CCAAACAAAC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00 Consensus pattern (12 bp): AAAAAAAAAAAC Found at i:297889 original size:2 final size:2 Alignment explanation

Indices: 297882--297917 Score: 72 Period size: 2 Copynumber: 18.0 Consensus size: 2 297872 AATATCAAAT 297882 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG 1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG 297918 GTTAAGTGAA Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50 Consensus pattern (2 bp): TG Found at i:309869 original size:28 final size:28 Alignment explanation

Indices: 309829--309927 Score: 126 Period size: 28 Copynumber: 3.5 Consensus size: 28 309819 AAATCAGTGA 309829 ATATCGCCAATGTGTGATTATCCTATTG 1 ATATCGCCAATGTGTGATTATCCTATTG * * 309857 ATATCTCCAATGTGTGATTATCTTATTG 1 ATATCGCCAATGTGTGATTATCCTATTG * * * ** 309885 ATATCACCAATGTTTGAATATCGAATTG 1 ATATCGCCAATGTGTGATTATCCTATTG * 309913 ATATCGCCATTGTGT 1 ATATCGCCAATGTGT 309928 AAGCTCTCTG Statistics Matches: 61, Mismatches: 10, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 28 61 1.00 ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40 Consensus pattern (28 bp): ATATCGCCAATGTGTGATTATCCTATTG Found at i:315899 original size:2 final size:2 Alignment explanation

Indices: 315886--315923 Score: 67 Period size: 2 Copynumber: 19.0 Consensus size: 2 315876 ACCAAATAAT * 315886 GA GA GC GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 315924 AAATAAATAT Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:327412 original size:21 final size:21 Alignment explanation

Indices: 327385--327830 Score: 460 Period size: 21 Copynumber: 20.9 Consensus size: 21 327375 ATACATAATC * * * 327385 ATCTCGTTATTACGAGATCTT 1 ATCTCGTAATAACGAGATATT * 327406 TTCTCGTAATAACGAGATAATT 1 ATCTCGTAATAACGAGAT-ATT * * 327428 AACTCGTAATAACGAGATCTT 1 ATCTCGTAATAACGAGATATT * 327449 TTCTCGTAATAACGAGATAATT 1 ATCTCGTAATAACGAGAT-ATT * * 327471 AACTCGTAATAACGAGATCTT 1 ATCTCGTAATAACGAGATATT * * 327492 TTCTCGTTATAACGAGATAATT 1 ATCTCGTAATAACGAGAT-ATT * * 327514 AACTCGTAATAACGAGATCTT 1 ATCTCGTAATAACGAGATATT * * 327535 TTCTCGTTATAACGAGATAATT 1 ATCTCGTAATAACGAGAT-ATT * * 327557 AACTCGTAATAACGAGATCTT 1 ATCTCGTAATAACGAGATATT * * 327578 TTCTCGTAATAACGAGATCTT 1 ATCTCGTAATAACGAGATATT * * 327599 AACTCGTTATAACGAGATAATT 1 ATCTCGTAATAACGAGAT-ATT * 327621 AACTCGTAATAACGAGATATT 1 ATCTCGTAATAACGAGATATT * * * 327642 AACTCGTAATTACGAGATCTT 1 ATCTCGTAATAACGAGATATT * 327663 TTCTCGTAATAACGAGATATT 1 ATCTCGTAATAACGAGATATT * * * 327684 AACTCGTTATAATGAGATAATT 1 ATCTCGTAATAACGAGAT-ATT * * 327706 AACTCGTAATAACGAGATCTT 1 ATCTCGTAATAACGAGATATT * 327727 TTCTCGTAATAACGAGATAATT 1 ATCTCGTAATAACGAGAT-ATT * * * 327749 AACTCGTTATAACGAGATCTT 1 ATCTCGTAATAACGAGATATT * * 327770 TTCTCGTAATTACGAGATATT 1 ATCTCGTAATAACGAGATATT * * 327791 TTCTCGTAATAACGAGATCTT 1 ATCTCGTAATAACGAGATATT * * 327812 TTCTCGTAATTACGAGATA 1 ATCTCGTAATAACGAGATA 327831 AAAATATTTT Statistics Matches: 353, Mismatches: 65, Indels: 14 0.82 0.15 0.03 Matches are distributed among these distances: 21 228 0.65 22 125 0.35 ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35 Consensus pattern (21 bp): ATCTCGTAATAACGAGATATT Found at i:327443 original size:43 final size:42 Alignment explanation

Indices: 327396--327829 Score: 544 Period size: 43 Copynumber: 10.2 Consensus size: 42 327386 TCTCGTTATT 327396 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATA 1 ACGAGATCTTTTCTCGTAATAACGAGAT-ATTAACTCGTAATA 327439 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATA 1 ACGAGATCTTTTCTCGTAATAACGAGAT-ATTAACTCGTAATA * 327482 ACGAGATCTTTTCTCGTTATAACGAGATAATTAACTCGTAATA 1 ACGAGATCTTTTCTCGTAATAACGAGAT-ATTAACTCGTAATA * 327525 ACGAGATCTTTTCTCGTTATAACGAGATAATTAACTCGTAATA 1 ACGAGATCTTTTCTCGTAATAACGAGAT-ATTAACTCGTAATA * * 327568 ACGAGATCTTTTCTCGTAATAACGAGATCTTAACTCGTTATA 1 ACGAGATCTTTTCTCGTAATAACGAGATATTAACTCGTAATA * ** * 327610 ACGAGATAATTAACTCGTAATAACGAGATATTAACTCGTAATT 1 ACGAGAT-CTTTTCTCGTAATAACGAGATATTAACTCGTAATA * 327653 ACGAGATCTTTTCTCGTAATAACGAGATATTAACTCGTTATA 1 ACGAGATCTTTTCTCGTAATAACGAGATATTAACTCGTAATA * * ** * ** 327695 ATGAGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAATA 1 ACGAGAT-CTTTTCTCGTAATAACGAGATATTAACTCGTAATA * ** * * ** * 327738 ACGAGATAATTAACTCGTTATAACGAGATCTTTTCTCGTAATT 1 ACGAGAT-CTTTTCTCGTAATAACGAGATATTAACTCGTAATA * * ** * 327781 ACGAGATATTTTCTCGTAATAACGAGATCTTTTCTCGTAATT 1 ACGAGATCTTTTCTCGTAATAACGAGATATTAACTCGTAATA 327823 ACGAGAT 1 ACGAGAT 327830 AAAAATATTT Statistics Matches: 360, Mismatches: 29, Indels: 5 0.91 0.07 0.01 Matches are distributed among these distances: 42 94 0.26 43 266 0.74 ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35 Consensus pattern (42 bp): ACGAGATCTTTTCTCGTAATAACGAGATATTAACTCGTAATA Found at i:327498 original size:64 final size:64 Alignment explanation

Indices: 327396--327830 Score: 552 Period size: 64 Copynumber: 6.8 Consensus size: 64 327386 TCTCGTTATT * ** 327396 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAATA 1 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATATTAACTCGTAATA * ** * ** * 327460 ACGAGATAATTAACTCGTAATAACGAGAT-CTTTTCTCGTTATAACGAGATAATTAACTCGTAAT 1 ACGAGAT-CTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGAT-ATTAACTCGTAAT 327524 A 64 A * * ** 327525 ACGAGATCTTTTCTCGTTATAACGAGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAATA 1 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATATTAACTCGTAATA ** * * 327589 ACGAGATCTTAACTCGTTATAACGAGATAATTAACTCGTAATAACGAGATATTAACTCGTAATT 1 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATATTAACTCGTAATA * * 327653 ACGAGATCTTTTCTCGTAATAACGAGAT-ATTAACTCGTTATAATGAGATAATTAACTCGTAATA 1 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGAT-ATTAACTCGTAATA * * ** * 327717 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTTATAACGAGATCTTTTCTCGTAATT 1 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATATTAACTCGTAATA * * ** * 327781 ACGAGATATTTTCTCGTAATAACGAGAT-CTTTTCTCGTAATTACGAGATA 1 ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATA 327831 AAAATATTTT Statistics Matches: 321, Mismatches: 45, Indels: 11 0.85 0.12 0.03 Matches are distributed among these distances: 63 35 0.11 64 213 0.66 65 73 0.23 ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34 Consensus pattern (64 bp): ACGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATATTAACTCGTAATA Found at i:340490 original size:2 final size:2 Alignment explanation

Indices: 340485--340528 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 340475 TTAACCAGAA 340485 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 340527 TC 1 TC 340529 ATGTGTTAAA Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:341843 original size:11 final size:11 Alignment explanation

Indices: 341823--341869 Score: 58 Period size: 11 Copynumber: 4.1 Consensus size: 11 341813 TCAGAAGACA 341823 TTGAATCAACG 1 TTGAATCAACG * 341834 TTGAAACAACG 1 TTGAATCAACG * 341845 TCAGAATTCAACG 1 T-TGAA-TCAACG 341858 TTGAATCAACG 1 TTGAATCAACG 341869 T 1 T 341870 CGGAATTTCA Statistics Matches: 30, Mismatches: 4, Indels: 4 0.79 0.11 0.11 Matches are distributed among these distances: 11 18 0.60 12 6 0.20 13 6 0.20 ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26 Consensus pattern (11 bp): TTGAATCAACG Found at i:341856 original size:24 final size:25 Alignment explanation

Indices: 341828--341883 Score: 87 Period size: 24 Copynumber: 2.3 Consensus size: 25 341818 AGACATTGAA 341828 TCAACGTTGAAACAACGTCAGAA-T 1 TCAACGTTGAAACAACGTCAGAATT * * 341852 TCAACGTTGAATCAACGTCGGAATT 1 TCAACGTTGAAACAACGTCAGAATT 341877 TCAACGT 1 TCAACGT 341884 CCATTCAACT Statistics Matches: 29, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 24 21 0.72 25 8 0.28 ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25 Consensus pattern (25 bp): TCAACGTTGAAACAACGTCAGAATT Found at i:341891 original size:25 final size:24 Alignment explanation

Indices: 341840--341892 Score: 61 Period size: 25 Copynumber: 2.2 Consensus size: 24 341830 AACGTTGAAA ** 341840 CAACGTCAGAATTCAACGTTGAAT 1 CAACGTCAGAATTCAACGTCCAAT * * 341864 CAACGTCGGAATTTCAACGTCCATT 1 CAACGTCAGAA-TTCAACGTCCAAT 341889 CAAC 1 CAAC 341893 TTTCATATTC Statistics Matches: 24, Mismatches: 4, Indels: 1 0.83 0.14 0.03 Matches are distributed among these distances: 24 10 0.42 25 14 0.58 ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25 Consensus pattern (24 bp): CAACGTCAGAATTCAACGTCCAAT Found at i:343812 original size:4 final size:4 Alignment explanation

Indices: 343797--343853 Score: 53 Period size: 4 Copynumber: 14.2 Consensus size: 4 343787 TGATAGAGAG * ** * * 343797 AGAC AGAG AGAC AGAC AGAC CTAC ATAC AGA- AGGAC AGAC AGAC GGAC 1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC A-GAC AGAC AGAC AGAC 343845 AGAC AGAC A 1 AGAC AGAC A 343854 TACAAAACAT Statistics Matches: 43, Mismatches: 8, Indels: 4 0.78 0.15 0.07 Matches are distributed among these distances: 3 1 0.02 4 41 0.95 5 1 0.02 ACGTcount: A:0.47, C:0.23, G:0.26, T:0.04 Consensus pattern (4 bp): AGAC Found at i:343852 original size:12 final size:12 Alignment explanation

Indices: 343797--343852 Score: 60 Period size: 12 Copynumber: 4.7 Consensus size: 12 343787 TGATAGAGAG 343797 AGACAGA-GAGAC 1 AGACAGACG-GAC ** 343809 AGACAGACCTAC 1 AGACAGACGGAC * * 343821 ATACAGAAGGAC 1 AGACAGACGGAC 343833 AGACAGACGGAC 1 AGACAGACGGAC 343845 AGACAGAC 1 AGACAGAC 343853 ATACAAAACA Statistics Matches: 35, Mismatches: 8, Indels: 2 0.78 0.18 0.04 Matches are distributed among these distances: 12 35 1.00 ACGTcount: A:0.46, C:0.23, G:0.27, T:0.04 Consensus pattern (12 bp): AGACAGACGGAC Found at i:344150 original size:25 final size:25 Alignment explanation

Indices: 344116--344658 Score: 753 Period size: 25 Copynumber: 22.1 Consensus size: 25 344106 TATCGATCAA * * 344116 TGCTAGTATCACTTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC 344141 TGCTAATATCA-TTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC * 344165 TGCTCATATCATTTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC * * 344190 TGTTAATATCACTTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC * 344215 TGCTAATAT-AATTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC * 344239 TGCTCATATCATTTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC * * 344264 TGTTAATATCACTTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC 344289 TGCTAATATCA-TTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC 344313 TG---ATATCATTTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC * * * 344335 TGTTAATATCACTTTTGTACTGTGC 1 TGCTAATATCATTTTTGTACTTTGC 344360 TGCTAATATCA-TTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC * * 344384 TGCTCATATCAATTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC * * 344409 TGTTAATATCACTTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC * 344434 TGCTCATATCATTTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC * * 344459 TGTTAATATCACTTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC 344484 TGCTAATATCA-TTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC * 344508 TGCTCATATCATTTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC * * 344533 TGCTAATATCACTTTTGTACTTTTC 1 TGCTAATATCATTTTTGTACTTTGC 344558 TGCTAATATCATTTTTGTACTTTGC 1 TGCTAATATCATTTTTGTACTTTGC * * 344583 TGTTAATATCA-TTTTGTGCTTTGC 1 TGCTAATATCATTTTTGTACTTTGC * * * 344607 TGCTCATATCATTTTTGCACGTTGC 1 TGCTAATATCATTTTTGTACTTTGC * * * 344632 TGTTAATATCATTTTTGAATTTTGC 1 TGCTAATATCATTTTTGTACTTTGC 344657 TG 1 TG 344659 ATATTTGGTA Statistics Matches: 463, Mismatches: 46, Indels: 18 0.88 0.09 0.03 Matches are distributed among these distances: 21 6 0.01 22 15 0.03 24 126 0.27 25 316 0.68 ACGTcount: A:0.19, C:0.17, G:0.13, T:0.51 Consensus pattern (25 bp): TGCTAATATCATTTTTGTACTTTGC Found at i:344243 original size:74 final size:74 Alignment explanation

Indices: 344122--344658 Score: 839 Period size: 74 Copynumber: 7.3 Consensus size: 74 344112 TCAATGCTAG 344122 TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT 1 TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT 344187 TGCTGTTAA 66 TGCTGTTAA * 344196 TATCACTTTTGTACTTTGCTGCTAATATAATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT 1 TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT 344261 TGCTGTTAA 66 TGCTGTTAA 344270 TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTG---ATATCATTTTTGTACTT 1 TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT 344332 TGCTGTTAA 66 TGCTGTTAA * * 344341 TATCACTTTTGTACTGTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCAATTTTGTACTT 1 TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT 344406 TGCTGTTAA 66 TGCTGTTAA * * * * 344415 TATCACTTTTGTACTTTGCTGCTCATATCATTTTTGTACTTTGCTGTTAATATCACTTTTGTACT 1 TATCACTTTTGTACTTTGCTGCTAATATCA-TTTTGTACTTTGCTGCTCATATCATTTTTGTACT * 344480 TTGCTGCTAA 65 TTGCTGTTAA * * * 344490 TATCA-TTTTGTACTTTGCTGCTCATATCATTTTTGTACTTTGCTGCTAATATCACTTTTGTACT 1 TATCACTTTTGTACTTTGCTGCTAATATCA-TTTTGTACTTTGCTGCTCATATCATTTTTGTACT * * 344554 TTTCTGCTAA 65 TTGCTGTTAA * * * * * 344564 TATCATTTTTGTACTTTGCTGTTAATATCATTTTGTGCTTTGCTGCTCATATCATTTTTGCACGT 1 TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT 344629 TGCTGTTAA 66 TGCTGTTAA * * * 344638 TATCATTTTTGAATTTTGCTG 1 TATCACTTTTGTACTTTGCTG 344659 ATATTTGGTA Statistics Matches: 435, Mismatches: 23, Indels: 10 0.93 0.05 0.02 Matches are distributed among these distances: 71 70 0.16 74 298 0.69 75 67 0.15 ACGTcount: A:0.19, C:0.17, G:0.13, T:0.51 Consensus pattern (74 bp): TATCACTTTTGTACTTTGCTGCTAATATCATTTTGTACTTTGCTGCTCATATCATTTTTGTACTT TGCTGTTAA Found at i:344287 original size:99 final size:99 Alignment explanation

Indices: 344116--344658 Score: 774 Period size: 99 Copynumber: 5.5 Consensus size: 99 344106 TATCGATCAA * * * * 344116 TGCTAGTATCACTTTTGTACTTTGCTGCTAATATCA-TTTTGTACTTTGCTGCTCATATCATTTT 1 TGCTAATATCATTTTTGTACTTTGCTGCTAATATCATTTTTGTACTTTGCTGCTAATATCACTTT * 344180 TGTACTTTGCTGTTAATATCACTTTTGTACTTTGC 66 TGTACTTTGCTGCTAATATCA-TTTTGTACTTTGC * * * 344215 TGCTAATAT-AATTTTGTACTTTGCTGCTCATATCATTTTTGTACTTTGCTGTTAATATCACTTT 1 TGCTAATATCATTTTTGTACTTTGCTGCTAATATCATTTTTGTACTTTGCTGCTAATATCACTTT 344279 TGTACTTTGCTGCTAATATCATTTTGTACTTTGC 66 TGTACTTTGCTGCTAATATCATTTTGTACTTTGC * * * 344313 TG---ATATCATTTTTGTACTTTGCTGTTAATATCACTTTTGTACTGTGCTGCTAATATCA-TTT 1 TGCTAATATCATTTTTGTACTTTGCTGCTAATATCATTTTTGTACTTTGCTGCTAATATCACTTT * 344374 TGTACTTTGCTGCTCATATCAATTTTGTACTTTGC 66 TGTACTTTGCTGCTAATATC-ATTTTGTACTTTGC * * * * 344409 TGTTAATATCACTTTTGTACTTTGCTGCTCATATCATTTTTGTACTTTGCTGTTAATATCACTTT 1 TGCTAATATCATTTTTGTACTTTGCTGCTAATATCATTTTTGTACTTTGCTGCTAATATCACTTT 344474 TGTACTTTGCTGCTAATATCATTTTGTACTTTGC 66 TGTACTTTGCTGCTAATATCATTTTGTACTTTGC * * * * 344508 TGCTCATATCATTTTTGTACTTTGCTGCTAATATCACTTTTGTACTTTTCTGCTAATATCATTTT 1 TGCTAATATCATTTTTGTACTTTGCTGCTAATATCATTTTTGTACTTTGCTGCTAATATCACTTT * * 344573 TGTACTTTGCTGTTAATATCATTTTGTGCTTTGC 66 TGTACTTTGCTGCTAATATCATTTTGTACTTTGC * * * * * * 344607 TGCTCATATCATTTTTGCACGTTGCTGTTAATATCATTTTTGAATTTTGCTG 1 TGCTAATATCATTTTTGTACTTTGCTGCTAATATCATTTTTGTACTTTGCTG 344659 ATATTTGGTA Statistics Matches: 399, Mismatches: 38, Indels: 14 0.88 0.08 0.03 Matches are distributed among these distances: 95 26 0.07 96 61 0.15 98 39 0.10 99 251 0.63 100 22 0.06 ACGTcount: A:0.19, C:0.17, G:0.13, T:0.51 Consensus pattern (99 bp): TGCTAATATCATTTTTGTACTTTGCTGCTAATATCATTTTTGTACTTTGCTGCTAATATCACTTT TGTACTTTGCTGCTAATATCATTTTGTACTTTGC Found at i:356751 original size:14 final size:14 Alignment explanation

Indices: 356732--356775 Score: 70 Period size: 14 Copynumber: 3.0 Consensus size: 14 356722 GTACGGTAAT 356732 AAACTCTCTCTCTC 1 AAACTCTCTCTCTC 356746 AAACTCTCTCTCTCTC 1 AAA--CTCTCTCTCTC 356762 AAACTCTCTCTCTC 1 AAACTCTCTCTCTC 356776 TCAATTTGAT Statistics Matches: 28, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 14 14 0.50 16 14 0.50 ACGTcount: A:0.20, C:0.43, G:0.00, T:0.36 Consensus pattern (14 bp): AAACTCTCTCTCTC Found at i:356756 original size:16 final size:16 Alignment explanation

Indices: 356735--356779 Score: 90 Period size: 16 Copynumber: 2.8 Consensus size: 16 356725 CGGTAATAAA 356735 CTCTCTCTCTCAAACT 1 CTCTCTCTCTCAAACT 356751 CTCTCTCTCTCAAACT 1 CTCTCTCTCTCAAACT 356767 CTCTCTCTCTCAA 1 CTCTCTCTCTCAA 356780 TTTGATAAGT Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 29 1.00 ACGTcount: A:0.18, C:0.44, G:0.00, T:0.38 Consensus pattern (16 bp): CTCTCTCTCTCAAACT Found at i:359488 original size:15 final size:15 Alignment explanation

Indices: 359468--359497 Score: 60 Period size: 15 Copynumber: 2.0 Consensus size: 15 359458 AGTGGAGCCT 359468 CAGATATCCGGACGC 1 CAGATATCCGGACGC 359483 CAGATATCCGGACGC 1 CAGATATCCGGACGC 359498 TTCACTTTCC Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13 Consensus pattern (15 bp): CAGATATCCGGACGC Found at i:361207 original size:11 final size:11 Alignment explanation

Indices: 361191--361241 Score: 77 Period size: 11 Copynumber: 4.7 Consensus size: 11 361181 TAAGCAAGTC 361191 CTTAAAGGTGG 1 CTTAAAGGTGG 361202 CTTAAAGGTGG 1 CTTAAAGGTGG * 361213 CTTAAAGGTGA 1 CTTAAAGGTGG * 361224 CTTAAAGG-AG 1 CTTAAAGGTGG 361234 CTTAAAGG 1 CTTAAAGG 361242 CTATACAACC Statistics Matches: 37, Mismatches: 3, Indels: 1 0.90 0.07 0.02 Matches are distributed among these distances: 10 8 0.22 11 29 0.78 ACGTcount: A:0.33, C:0.10, G:0.31, T:0.25 Consensus pattern (11 bp): CTTAAAGGTGG Found at i:361328 original size:11 final size:10 Alignment explanation

Indices: 361312--361361 Score: 64 Period size: 11 Copynumber: 4.7 Consensus size: 10 361302 GTCCAAACTT 361312 CTTTAAGCTAC 1 CTTTAAGC-AC 361323 CTTTAAGCCAC 1 CTTTAAG-CAC 361334 CTTTAAGCAAC 1 CTTTAAGC-AC * 361345 CTTTAAGCAT 1 CTTTAAGCAC 361355 CTTTAAG 1 CTTTAAG 361362 TGGCATTTAC Statistics Matches: 36, Mismatches: 1, Indels: 5 0.86 0.02 0.12 Matches are distributed among these distances: 10 9 0.25 11 26 0.72 12 1 0.03 ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34 Consensus pattern (10 bp): CTTTAAGCAC Found at i:361340 original size:22 final size:21 Alignment explanation

Indices: 361312--361361 Score: 73 Period size: 22 Copynumber: 2.3 Consensus size: 21 361302 GTCCAAACTT * 361312 CTTTAAGCTACCTTTAAGCCAC 1 CTTTAAGCAACCTTTAAG-CAC * 361334 CTTTAAGCAACCTTTAAGCAT 1 CTTTAAGCAACCTTTAAGCAC 361355 CTTTAAG 1 CTTTAAG 361362 TGGCATTTAC Statistics Matches: 26, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 21 9 0.35 22 17 0.65 ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34 Consensus pattern (21 bp): CTTTAAGCAACCTTTAAGCAC Found at i:361361 original size:10 final size:11 Alignment explanation

Indices: 361312--361353 Score: 66 Period size: 11 Copynumber: 3.8 Consensus size: 11 361302 GTCCAAACTT * 361312 CTTTAAGCTAC 1 CTTTAAGCAAC * 361323 CTTTAAGCCAC 1 CTTTAAGCAAC 361334 CTTTAAGCAAC 1 CTTTAAGCAAC 361345 CTTTAAGCA 1 CTTTAAGCA 361354 TCTTTAAGTG Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 11 29 1.00 ACGTcount: A:0.31, C:0.29, G:0.10, T:0.31 Consensus pattern (11 bp): CTTTAAGCAAC Found at i:361411 original size:22 final size:22 Alignment explanation

Indices: 361354--361414 Score: 70 Period size: 22 Copynumber: 2.8 Consensus size: 22 361344 CCTTTAAGCA * * 361354 TCTTTAAGTGGCATTTACGCTC 1 TCTTTAAGTGGCCTTTACACTC * * 361376 TCTTTACACT-GCCTTTACACTG 1 TCTTTA-AGTGGCCTTTACACTC 361398 TCTTTAAGTGGCCTTTA 1 TCTTTAAGTGGCCTTTA 361415 AGTCAATATT Statistics Matches: 32, Mismatches: 5, Indels: 4 0.78 0.12 0.10 Matches are distributed among these distances: 21 2 0.06 22 28 0.88 23 2 0.06 ACGTcount: A:0.18, C:0.25, G:0.15, T:0.43 Consensus pattern (22 bp): TCTTTAAGTGGCCTTTACACTC Found at i:361752 original size:2 final size:2 Alignment explanation

Indices: 361745--361810 Score: 114 Period size: 2 Copynumber: 33.0 Consensus size: 2 361735 CGGTGAAAAA 361745 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC * * 361787 TC TT TC TC TT TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC 361811 AATCGGTCAC Statistics Matches: 60, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 60 1.00 ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53 Consensus pattern (2 bp): TC Found at i:367638 original size:167 final size:166 Alignment explanation

Indices: 367189--368206 Score: 1734 Period size: 166 Copynumber: 6.1 Consensus size: 166 367179 AACATTACAT ** * * 367189 TTCTTGAGAAGAA-AACTTTTAAACATTTTTCAC-ATGTAGTTCTATGTTAAACTTTAAACCCCG 1 TTCTTGAGAAGAAGATTTTTTAAACA-TTTTC-CTATGTATTTCTATGTTAAACTTTGAACCCCG * * * * * 367252 CCTGTGGCCCCAGTTTTGGTCCGGGGGTCACTATTTTTACAATTTAGAATCTTCACTATATATAA 64 CATGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATAC 367317 AAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG 129 AAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG * 367355 TTCTTGAGAAAAAGATTTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCA 1 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCA * * * 367420 TGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTCTACAATTTAGAATCTTCATTATACATACAA 66 TGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAA 367485 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG 131 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG * * 367521 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTAAGGTATTTCTATGTTAAACTTTTAACCCCGC 1 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCT-ATGTATTTCTATGTTAAACTTTGAACCCCGC * * 367586 ATGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTCTACAATTTAGAATCTTCACTATACATACA 65 ATGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACA 367651 AGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG 130 AGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG * 367688 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATTGTATTTCTATGTTAAACTTTTAACCCCGC 1 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTA-TGTATTTCTATGTTAAACTTTGAACCCCGC * 367753 ATGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATGTATACA 65 ATGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACA 367818 AGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG 130 AGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG * * * 367855 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGGTAAAATTTGAACCCCGCC 1 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCA * * 367920 TGGGGCCCCAGTTTTGGCCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATAAAA 66 TGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAA 367985 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG 131 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG * * * 368021 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGGTAAAATTTGAACCCCGCC 1 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCA * 368086 TGGGGCCCCAGTTTTGGCCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAA 66 TGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAA 368151 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG 131 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG 368187 TTCTTGAGAAGAAGATTTTT 1 TTCTTGAGAAGAAGATTTTT 368207 AAAAACATGC Statistics Matches: 819, Mismatches: 29, Indels: 8 0.96 0.03 0.01 Matches are distributed among these distances: 165 1 0.00 166 483 0.59 167 335 0.41 ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38 Consensus pattern (166 bp): TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCA TGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAA GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGG Found at i:367896 original size:333 final size:332 Alignment explanation

Indices: 367189--368206 Score: 1752 Period size: 333 Copynumber: 3.1 Consensus size: 332 367179 AACATTACAT ** * 367189 TTCTTGAGAAGAA-AACTTTTAAACATTTTTCAC-ATGTAGTTCTATGTTAAACTTTAAACCCCG 1 TTCTTGAGAAGAAGATTTTTTAAACA-TTTTC-CTATGTATTTCTATGTTAAACTTTAAACCCCG * * * 367252 CCTGTGGCCCCAGTTTTGGTCCGGGGGTCACTATTTTTACAATTTAGAATCTTCACTATATATAA 64 CCTGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATAA * 367317 AAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAAAAAGATTTTTTAAACAT 129 AAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAAGAAGATTTTTTAAACAT 367382 TTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCATGGGGCCCCAGTTTTGGTCCGAGGGTC 194 TTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCATGGGGCCCCAGTTTTGGTCCGAGGGTC * * * 367447 ACGATTTCTACAATTTAGAATCTTCATTATACATACAAGCTTTTGTGTAAATATTGGCATTTCTG 259 ACGATTTTTACAATTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTG 367512 GTGCAGTGG 324 GTGCAGTGG * * 367521 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTAAGGTATTTCTATGTTAAACTTTTAACCCCGC 1 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCT-ATGTATTTCTATGTTAAACTTTAAACCCCGC * * * * 367586 ATGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTCTACAATTTAGAATCTTCACTATACATACA 65 CTGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATAAA 367651 AGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAAGAAGATTTTTTAAACATT 130 AGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAAGAAGATTTTTTAAACATT * 367716 TTCCTATTGTATTTCTATGTTAAACTTTTAACCCCGCATGGGGCCCCAGTTTTGGTCCGAGGGTC 195 TTCCTA-TGTATTTCTATGTTAAACTTTGAACCCCGCATGGGGCCCCAGTTTTGGTCCGAGGGTC * 367781 ACGATTTTTACAATTTAGAATCTTCACTATGTATACAAGCTTTTGTGTAAATATTGGCATTTCTG 259 ACGATTTTTACAATTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTG 367846 GTGCAGTGG 324 GTGCAGTGG * * * 367855 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGGTAAAATTTGAACCCCGCC 1 TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTAAACCCCGCC * 367920 TGGGGCCCCAGTTTTGGCCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATAAAA 66 TGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATAAAA 367985 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAAGAAGATTTTTTAAACATTT 131 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAAGAAGATTTTTTAAACATTT * * * * 368050 TCCTATGTATTTCTATGGTAAAATTTGAACCCCGCCTGGGGCCCCAGTTTTGGCCCGAGGGTCAC 196 TCCTATGTATTTCTATGTTAAACTTTGAACCCCGCATGGGGCCCCAGTTTTGGTCCGAGGGTCAC 368115 GATTTTTACAATTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGT 261 GATTTTTACAATTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGT 368180 GCAGTGG 326 GCAGTGG 368187 TTCTTGAGAAGAAGATTTTT 1 TTCTTGAGAAGAAGATTTTT 368207 AAAAACATGC Statistics Matches: 649, Mismatches: 33, Indels: 8 0.94 0.05 0.01 Matches are distributed among these distances: 331 1 0.00 332 164 0.25 333 324 0.50 334 160 0.25 ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38 Consensus pattern (332 bp): TTCTTGAGAAGAAGATTTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTAAACCCCGCC TGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATAAAA GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAAGAAGATTTTTTAAACATTT TCCTATGTATTTCTATGTTAAACTTTGAACCCCGCATGGGGCCCCAGTTTTGGTCCGAGGGTCAC GATTTTTACAATTTAGAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGT GCAGTGG Found at i:368388 original size:4 final size:4 Alignment explanation

Indices: 368379--368424 Score: 58 Period size: 4 Copynumber: 11.8 Consensus size: 4 368369 AAAGTTTACA * * * 368379 GACG GACG GACA GACA GATG GACG GACG GACG GACG GAC- GACG GAC 1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GAC 368425 AACGGGTGAT Statistics Matches: 37, Mismatches: 4, Indels: 2 0.86 0.09 0.05 Matches are distributed among these distances: 3 3 0.08 4 34 0.92 ACGTcount: A:0.30, C:0.24, G:0.43, T:0.02 Consensus pattern (4 bp): GACG Found at i:368393 original size:12 final size:12 Alignment explanation

Indices: 368376--368429 Score: 58 Period size: 12 Copynumber: 4.7 Consensus size: 12 368366 TGAAAAGTTT 368376 ACAGACGGACGG 1 ACAGACGGACGG * * 368388 ACAGACAGATGG 1 ACAGACGGACGG * 368400 ACGGACGGACGG 1 ACAGACGGACGG * 368412 ACGGAC-GACGG 1 ACAGACGGACGG 368423 ACA-ACGG 1 ACAGACGG 368430 GTGATCAGAA Statistics Matches: 35, Mismatches: 6, Indels: 3 0.80 0.14 0.07 Matches are distributed among these distances: 10 2 0.06 11 8 0.23 12 25 0.71 ACGTcount: A:0.33, C:0.24, G:0.41, T:0.02 Consensus pattern (12 bp): ACAGACGGACGG Found at i:374484 original size:101 final size:100 Alignment explanation

Indices: 374309--374510 Score: 368 Period size: 101 Copynumber: 2.0 Consensus size: 100 374299 AGCATCATAA * 374309 CAATTCTTTTTCAAATTTATATAAATCAGTGCACTAGCTAGCTTTTTTAAAAATTCAATTAATTT 1 CAATTCTTTTTCAAATTTATATAAATCAGTGCACTAGCTAGCTTTTTTAAAAATTCAATTAAATT * 374374 CTTAAACTCCCACTTGTAATATAGCTCCTCAATGCT 66 CTTAAACTCCCACTTGTAA-ATAGCCCCTCAATGCT * 374410 CAATTCTTTTTCAAATTTATATAAATCCGTGCACTAGCTAGCTTTTTTAAAAATTCAATTAAATT 1 CAATTCTTTTTCAAATTTATATAAATCAGTGCACTAGCTAGCTTTTTTAAAAATTCAATTAAATT 374475 CTTAAACTCCCACTTGTAAATAGCCCCTCAATGCT 66 CTTAAACTCCCACTTGTAAATAGCCCCTCAATGCT 374510 C 1 C 374511 CTATTGGTCA Statistics Matches: 98, Mismatches: 3, Indels: 1 0.96 0.03 0.01 Matches are distributed among these distances: 100 16 0.16 101 82 0.84 ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39 Consensus pattern (100 bp): CAATTCTTTTTCAAATTTATATAAATCAGTGCACTAGCTAGCTTTTTTAAAAATTCAATTAAATT CTTAAACTCCCACTTGTAAATAGCCCCTCAATGCT Found at i:380443 original size:62 final size:61 Alignment explanation

Indices: 380363--380490 Score: 238 Period size: 62 Copynumber: 2.1 Consensus size: 61 380353 ATCCGCCAAA * 380363 CTTAAACAAATACAAAAATAAATTAATGAAGTTAGGAATTTTTACCATATGCATTTGTCAT 1 CTTAAACAAATACAAAAATAAATTAATGAAGTTAGGAATTTTTACCATATACATTTGTCAT 380424 CTTANAACAAATACAAAAATAAATTAATGAAGTTAGGAATTTTTACCATATACATTTGTCAT 1 CTTA-AACAAATACAAAAATAAATTAATGAAGTTAGGAATTTTTACCATATACATTTGTCAT 380486 CTTAA 1 CTTAA 380491 GTTCGTAATT Statistics Matches: 65, Mismatches: 1, Indels: 2 0.96 0.01 0.03 Matches are distributed among these distances: 61 5 0.08 62 60 0.92 ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34 Consensus pattern (61 bp): CTTAAACAAATACAAAAATAAATTAATGAAGTTAGGAATTTTTACCATATACATTTGTCAT Found at i:380734 original size:33 final size:32 Alignment explanation

Indices: 380646--380724 Score: 140 Period size: 32 Copynumber: 2.4 Consensus size: 32 380636 CCTAGCCATC 380646 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT 1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT * 380678 CTTCCCCCCGGAAAAATGGCTATATAGCAGTT 1 TTTCCCCCCGGAAAAATGGCTATATAGCAGTT 380710 TTTCCCCCACGGAAA 1 TTTCCCCC-CGGAAA 380725 GCTGACTATA Statistics Matches: 44, Mismatches: 2, Indels: 1 0.94 0.04 0.02 Matches are distributed among these distances: 32 38 0.86 33 6 0.14 ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25 Consensus pattern (32 bp): TTTCCCCCCGGAAAAATGGCTATATAGCAGTT Found at i:381888 original size:13 final size:13 Alignment explanation

Indices: 381870--381919 Score: 72 Period size: 13 Copynumber: 4.2 Consensus size: 13 381860 AGGGTAATTA 381870 AAAAAAAACAACC 1 AAAAAAAACAACC 381883 -AAAAAAA-AA-- 1 AAAAAAAACAACC 381892 AAAAAAAACAACC 1 AAAAAAAACAACC 381905 AAAAAAAACAACC 1 AAAAAAAACAACC 381918 AA 1 AA 381920 CACATATATT Statistics Matches: 33, Mismatches: 0, Indels: 8 0.80 0.00 0.20 Matches are distributed among these distances: 10 7 0.21 11 4 0.12 12 7 0.21 13 15 0.45 ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00 Consensus pattern (13 bp): AAAAAAAACAACC Found at i:381897 original size:22 final size:22 Alignment explanation

Indices: 381869--381912 Score: 88 Period size: 22 Copynumber: 2.0 Consensus size: 22 381859 AAGGGTAATT 381869 AAAAAAAAACAACCAAAAAAAA 1 AAAAAAAAACAACCAAAAAAAA 381891 AAAAAAAAACAACCAAAAAAAA 1 AAAAAAAAACAACCAAAAAAAA 381913 CAACCAACAC Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 22 1.00 ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00 Consensus pattern (22 bp): AAAAAAAAACAACCAAAAAAAA Found at i:391040 original size:1 final size:1 Alignment explanation

Indices: 391036--391064 Score: 58 Period size: 1 Copynumber: 29.0 Consensus size: 1 391026 TAGCCATCTT 391036 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC 391065 GGAAAAATGG Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 28 1.00 ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00 Consensus pattern (1 bp): C Found at i:391095 original size:32 final size:32 Alignment explanation

Indices: 391059--391134 Score: 134 Period size: 32 Copynumber: 2.3 Consensus size: 32 391049 CCCCCCCCCC 391059 CCCCCCGGAAAAATGGCTATATAGCAGTTCTT 1 CCCCCCGGAAAAATGGCTATATAGCAGTTCTT * 391091 CCCCCCGGAAAAATGGCTATATAGCAGTTTTT 1 CCCCCCGGAAAAATGGCTATATAGCAGTTCTT 391123 CCCCCACGGAAA 1 CCCCC-CGGAAA 391135 GCTGACTATA Statistics Matches: 42, Mismatches: 1, Indels: 1 0.95 0.02 0.02 Matches are distributed among these distances: 32 36 0.86 33 6 0.14 ACGTcount: A:0.29, C:0.30, G:0.18, T:0.22 Consensus pattern (32 bp): CCCCCCGGAAAAATGGCTATATAGCAGTTCTT Found at i:391144 original size:33 final size:32 Alignment explanation

Indices: 391059--391147 Score: 124 Period size: 32 Copynumber: 2.8 Consensus size: 32 391049 CCCCCCCCCC * 391059 CCCCCCGGAAAAATGGCTATATAGCAGTTCTT 1 CCCCCCGGAAAAATGACTATATAGCAGTTCTT * * 391091 CCCCCCGGAAAAATGGCTATATAGCAGTTTTT 1 CCCCCCGGAAAAATGACTATATAGCAGTTCTT ** 391123 CCCCCACGGAAAGCTGACTATATAG 1 CCCCC-CGGAAAAATGACTATATAG 391148 TGGGCTTTCC Statistics Matches: 52, Mismatches: 4, Indels: 1 0.91 0.07 0.02 Matches are distributed among these distances: 32 36 0.69 33 16 0.31 ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24 Consensus pattern (32 bp): CCCCCCGGAAAAATGACTATATAGCAGTTCTT Found at i:392312 original size:12 final size:12 Alignment explanation

Indices: 392297--392322 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 392287 ACCAAAAAAA 392297 AAAAAAACAACC 1 AAAAAAACAACC 392309 AAAAAAACAACC 1 AAAAAAACAACC 392321 AA 1 AA 392323 CACATATATT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00 Consensus pattern (12 bp): AAAAAAACAACC Found at i:392323 original size:16 final size:15 Alignment explanation

Indices: 392280--392324 Score: 54 Period size: 15 Copynumber: 2.9 Consensus size: 15 392270 AGGGTAATTT * 392280 AAAAAAAACCAAAAA 1 AAAAAAAACCAACAA * 392295 AAAAAAAAACAACCAA 1 AAAAAAAACCAA-CAA * 392311 AAAAACAACCAACA 1 AAAAAAAACCAACA 392325 CATATATTGT Statistics Matches: 25, Mismatches: 4, Indels: 2 0.81 0.13 0.06 Matches are distributed among these distances: 15 13 0.52 16 12 0.48 ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00 Consensus pattern (15 bp): AAAAAAAACCAACAA Found at i:392324 original size:19 final size:19 Alignment explanation

Indices: 392280--392315 Score: 65 Period size: 19 Copynumber: 1.9 Consensus size: 19 392270 AGGGTAATTT 392280 AAAAAA-AACCAAAAAAAA 1 AAAAAACAACCAAAAAAAA 392298 AAAAAACAACCAAAAAAA 1 AAAAAACAACCAAAAAAA 392316 CAACCAACAC Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 18 6 0.35 19 11 0.65 ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00 Consensus pattern (19 bp): AAAAAACAACCAAAAAAAA Found at i:393187 original size:17 final size:17 Alignment explanation

Indices: 393154--393187 Score: 50 Period size: 17 Copynumber: 2.0 Consensus size: 17 393144 GGTTTTCCGG * 393154 GGGGGAAAAGCTACTAT 1 GGGGGAAAAACTACTAT * 393171 GGGGGAAAAACTGCTAT 1 GGGGGAAAAACTACTAT 393188 ACAACACCGG Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.35, C:0.12, G:0.35, T:0.18 Consensus pattern (17 bp): GGGGGAAAAACTACTAT Found at i:394119 original size:2 final size:2 Alignment explanation

Indices: 394112--394163 Score: 95 Period size: 2 Copynumber: 26.0 Consensus size: 2 394102 AGCACATACA * 394112 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 394154 AG AG AG AG AG 1 AG AG AG AG AG 394164 TGGGTGGGTG Statistics Matches: 48, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 2 48 1.00 ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00 Consensus pattern (2 bp): AG Found at i:397045 original size:2 final size:2 Alignment explanation

Indices: 397038--397069 Score: 55 Period size: 2 Copynumber: 15.5 Consensus size: 2 397028 TAGCCGATTT 397038 TA TA TA TA TA TA TA NTA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T 397070 TTCATCATAG Statistics Matches: 29, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 2 27 0.93 3 2 0.07 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:397058 original size:15 final size:14 Alignment explanation

Indices: 397038--397069 Score: 55 Period size: 15 Copynumber: 2.2 Consensus size: 14 397028 TAGCCGATTT 397038 TATATATATATATA 1 TATATATATATATA 397052 NTATATATATATATA 1 -TATATATATATATA 397067 TAT 1 TAT 397070 TTCATCATAG Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 3 0.18 15 14 0.82 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.50 Consensus pattern (14 bp): TATATATATATATA Found at i:403090 original size:22 final size:22 Alignment explanation

Indices: 403040--403092 Score: 70 Period size: 22 Copynumber: 2.4 Consensus size: 22 403030 TATACGTGTT * 403040 GCTTAAAGGTGGCTTAAAGAAA 1 GCTTAAAGATGGCTTAAAGAAA * ** 403062 GCGTAAAGATGGCTTAAAGGCA 1 GCTTAAAGATGGCTTAAAGAAA 403084 GCTTAAAGA 1 GCTTAAAGA 403093 CTATCTTTAA Statistics Matches: 26, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 22 26 1.00 ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21 Consensus pattern (22 bp): GCTTAAAGATGGCTTAAAGAAA Found at i:403113 original size:11 final size:11 Alignment explanation

Indices: 403097--403125 Score: 58 Period size: 11 Copynumber: 2.6 Consensus size: 11 403087 TAAAGACTAT 403097 CTTTAAGCCAC 1 CTTTAAGCCAC 403108 CTTTAAGCCAC 1 CTTTAAGCCAC 403119 CTTTAAG 1 CTTTAAG 403126 GACAACTTAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:403173 original size:11 final size:11 Alignment explanation

Indices: 403157--403210 Score: 99 Period size: 11 Copynumber: 4.9 Consensus size: 11 403147 GTCCAAACTT 403157 CTTTAAGCCAC 1 CTTTAAGCCAC 403168 CTTTAAGCCAC 1 CTTTAAGCCAC * 403179 CTTTAAGCTAC 1 CTTTAAGCCAC 403190 CTTTAAGCCAC 1 CTTTAAGCCAC 403201 CTTTAAGCCA 1 CTTTAAGCCA 403211 TTAAAAAAAA Statistics Matches: 41, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 41 1.00 ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:406570 original size:6 final size:6 Alignment explanation

Indices: 406559--406583 Score: 50 Period size: 6 Copynumber: 4.2 Consensus size: 6 406549 GAATAAAGAA 406559 ATTGTC ATTGTC ATTGTC ATTGTC A 1 ATTGTC ATTGTC ATTGTC ATTGTC A 406584 AATATATTGA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 19 1.00 ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48 Consensus pattern (6 bp): ATTGTC Found at i:412798 original size:15 final size:15 Alignment explanation

Indices: 412774--412803 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 412764 GCGTTAATCT 412774 CAATCCCATAGCATA 1 CAATCCCATAGCATA * 412789 CAATCTCATAGCATA 1 CAATCCCATAGCATA 412804 TTATTAGACA Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.40, C:0.30, G:0.07, T:0.23 Consensus pattern (15 bp): CAATCCCATAGCATA Done.