Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold481

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: 1334154
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30

Warning! 122349 characters in sequence are not A, C, G, or T


File 3 of 4

Found at i:355685 original size:67 final size:67

Alignment explanation

Indices: 355604--355833 Score: 388 Period size: 67 Copynumber: 3.4 Consensus size: 67 355594 TTACCCTCAA * * 355604 ATAGAGTATCCTTACCCTCCCATGGAGTACCCCAGCCTTCCCATAGAGTAAAAACCCTAATCCTC 1 ATAGAGTATCCTTACTCTCCCATGGAGTACCCCAGCCTTCCCATAGAGTAAATACCCTAATCCTC 355669 CC 66 CC * 355671 ATTGAGTATCCTTACTCTCCCATGGAGTACCCCAGCCTTCCCATAGAGTAAATACCCTAATCCTC 1 ATAGAGTATCCTTACTCTCCCATGGAGTACCCCAGCCTTCCCATAGAGTAAATACCCTAATCCTC 355736 CC 66 CC * 355738 ATAGAGTATCCTTACTCTCCCATGGAGTACCCCAGCCTTCCCATAGAGTAGATACCCTAATCCTC 1 ATAGAGTATCCTTACTCTCCCATGGAGTACCCCAGCCTTCCCATAGAGTAAATACCCTAATCCTC 355803 CC 66 CC * * * * 355805 ATAGGGTACCCTAACTCTCCCATAGAGTA 1 ATAGAGTATCCTTACTCTCCCATGGAGTA 355834 TTCTCACTCT Statistics Matches: 154, Mismatches: 9, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 67 154 1.00 ACGTcount: A:0.27, C:0.35, G:0.13, T:0.25 Consensus pattern (67 bp): ATAGAGTATCCTTACTCTCCCATGGAGTACCCCAGCCTTCCCATAGAGTAAATACCCTAATCCTC CC Found at i:355793 original size:25 final size:25 Alignment explanation

Indices: 355698--355794 Score: 61 Period size: 25 Copynumber: 4.2 Consensus size: 25 355688 TCCCATGGAG * 355698 TACCCCAGCCTTCCCATAGAGTAAA 1 TACCCCAGCCTTCCCATAGAGTAGA * * 355723 TACCCTAATCC-TCCCATAGAGT--A 1 TACCC-CAGCCTTCCCATAGAGTAGA ** 355746 T-CCTTA--CTCTCCCAT-G-G-AG- 1 TACCCCAGCCT-TCCCATAGAGTAGA 355765 TACCCCAGCCTTCCCATAGAGTAGA 1 TACCCCAGCCTTCCCATAGAGTAGA 355790 TACCC 1 TACCC 355795 TAATCCTCCC Statistics Matches: 54, Mismatches: 6, Indels: 24 0.64 0.07 0.29 Matches are distributed among these distances: 19 3 0.06 20 4 0.07 21 13 0.24 22 5 0.09 23 3 0.06 24 2 0.04 25 21 0.39 26 3 0.06 ACGTcount: A:0.27, C:0.37, G:0.12, T:0.24 Consensus pattern (25 bp): TACCCCAGCCTTCCCATAGAGTAGA Found at i:360468 original size:2 final size:2 Alignment explanation

Indices: 360463--360514 Score: 86 Period size: 2 Copynumber: 26.0 Consensus size: 2 360453 TACCAAAAAG * * 360463 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA AA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 360505 GA GA GA GA GA 1 GA GA GA GA GA 360515 TGTCATTGCT Statistics Matches: 46, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 2 46 1.00 ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00 Consensus pattern (2 bp): GA Found at i:365103 original size:51 final size:50 Alignment explanation

Indices: 365055--365450 Score: 517 Period size: 51 Copynumber: 7.7 Consensus size: 50 365045 ATTCAGAATG ** * 365055 ATGTCAAAGACCCAAACAATCTTTA-AGACTTACGACTGTAGAACCAGAACA 1 ATGTCAAAG-CCTGAACAATC-TTAGAGACTTACAACTGTAGAACCAGAACA * 365106 ATGTCAAACGCCTGAACAATCTTAGAGACTTAAAACTGTAGAACCAGAACA 1 ATGTCAAA-GCCTGAACAATCTTAGAGACTTACAACTGTAGAACCAGAACA * * 365157 ATGTTAAAGGTCTGAACAATCTTAGAGACTTACAACTGTAGAACCAGAACA 1 ATGTCAAA-GCCTGAACAATCTTAGAGACTTACAACTGTAGAACCAGAACA ** * 365208 ATGTCAAACGCCTGAACAATCTTAGAGACTTACATTGAACCCTAGAACAAGAACA 1 ATGTCAAA-GCCTGAACAATCTTAGAGACTTAC----AACTGTAGAACCAGAACA * * 365263 ATGTCAAAGACCCGAACAATCTTTA-AGACTTACGACTGTAGAACCAGAACA 1 ATGTCAAAG-CCTGAACAATC-TTAGAGACTTACAACTGTAGAACCAGAACA * * 365314 ATGTTAAAGGCCTGAACAATCTTAGAGACTTACAACTGTAGAACTAGAACA 1 ATGTCAAA-GCCTGAACAATCTTAGAGACTTACAACTGTAGAACCAGAACA * 365365 ATGTCAAACGCCTGAACAATCTTAGAGACTTACAACTGTAGAACTAGAACA 1 ATGTCAAA-GCCTGAACAATCTTAGAGACTTACAACTGTAGAACCAGAACA * 365416 ATGTCAAAGGCCTGGACAATCTTAGAGACTTACAA 1 ATGTCAAA-GCCTGAACAATCTTAGAGACTTACAA 365451 GGATGTAAAA Statistics Matches: 308, Mismatches: 27, Indels: 20 0.87 0.08 0.06 Matches are distributed among these distances: 50 6 0.02 51 255 0.83 52 2 0.01 54 1 0.00 55 41 0.13 56 3 0.01 ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21 Consensus pattern (50 bp): ATGTCAAAGCCTGAACAATCTTAGAGACTTACAACTGTAGAACCAGAACA Found at i:365293 original size:157 final size:152 Alignment explanation

Indices: 365069--365447 Score: 546 Period size: 157 Copynumber: 2.4 Consensus size: 152 365059 CAAAGACCCA * ** * 365069 AACAATCTTTA-AGACTTACGACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAG 1 AACAATC-TTAGAGACTTACAACCCTAGAACAAGAACAATGTCAAA-GCCTGAACAATCTTAGAG * 365133 ACTTAAAACTGTAGAACCAGAACAATGTTAAAGGTCTGAACAATCTTAGAGACTTACAACTGTAG 64 ACTTAAAACTGTAGAACCAGAACAATGTTAAAGGCCTGAACAATCTTAGAGACTTACAACTGTAG 365198 AACCAGAACAATGTCAAACGCCTG 129 AACCAGAACAATGTCAAACGCCTG * 365222 AACAATCTTAGAGACTTACATTGAACCCTAGAACAAGAACAATGTCAAAGACCCGAACAATCTTT 1 AACAATCTTAGAGACTTAC----AACCCTAGAACAAGAACAATGTCAAAG-CCTGAACAATC-TT ** 365287 A-AGACTTACGACTGTAGAACCAGAACAATGTTAAAGGCCTGAACAATCTTAGAGACTTACAACT 60 AGAGACTTAAAACTGTAGAACCAGAACAATGTTAAAGGCCTGAACAATCTTAGAGACTTACAACT * 365351 GTAGAACTAGAACAATGTCAAACGCCTG 125 GTAGAACCAGAACAATGTCAAACGCCTG ** * * 365379 AACAATCTTAGAGACTTACAACTGTAGAACTAGAACAATGTCAAAGGCCTGGACAATCTTAGAGA 1 AACAATCTTAGAGACTTACAACCCTAGAACAAGAACAATGTCAAA-GCCTGAACAATCTTAGAGA 365444 CTTA 65 CTTA 365448 CAAGGATGTA Statistics Matches: 203, Mismatches: 14, Indels: 18 0.86 0.06 0.08 Matches are distributed among these distances: 152 6 0.03 153 54 0.27 154 1 0.00 156 1 0.00 157 138 0.68 158 3 0.01 ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22 Consensus pattern (152 bp): AACAATCTTAGAGACTTACAACCCTAGAACAAGAACAATGTCAAAGCCTGAACAATCTTAGAGAC TTAAAACTGTAGAACCAGAACAATGTTAAAGGCCTGAACAATCTTAGAGACTTACAACTGTAGAA CCAGAACAATGTCAAACGCCTG Found at i:365329 original size:208 final size:208 Alignment explanation

Indices: 365055--365449 Score: 691 Period size: 208 Copynumber: 1.9 Consensus size: 208 365045 ATTCAGAATG 365055 ATGTCAAAGACCCAAACAATCTTTAAGACTTACGACTGTAGAACCAGAACAATGTCAAACGCCTG 1 ATGTCAAAGACCCAAACAATCTTTAAGACTTACGACTGTAGAACCAGAACAATGTCAAACGCCTG * * * 365120 AACAATCTTAGAGACTTAAAACTGTAGAACCAGAACAATGTTAAAGGTCTGAACAATCTTAGAGA 66 AACAATCTTAGAGACTTAAAACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAGA 365185 CTTACAACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAGACTTACATTGAACCC 131 CTTACAACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAGACTTACATTGAACCC 365250 TAGAACAAGAACA 196 TAGAACAAGAACA * * * 365263 ATGTCAAAGACCCGAACAATCTTTAAGACTTACGACTGTAGAACCAGAACAATGTTAAAGGCCTG 1 ATGTCAAAGACCCAAACAATCTTTAAGACTTACGACTGTAGAACCAGAACAATGTCAAACGCCTG * * 365328 AACAATCTTAGAGACTTACAACTGTAGAACTAGAACAATGTCAAACGCCTGAACAATCTTAGAGA 66 AACAATCTTAGAGACTTAAAACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAGA * * * 365393 CTTACAACTGTAGAACTAGAACAATGTCAAAGGCCTGGACAATCTTAGAGACTTACA 131 CTTACAACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAGACTTACA 365450 AGGATGTAAA Statistics Matches: 176, Mismatches: 11, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 208 176 1.00 ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21 Consensus pattern (208 bp): ATGTCAAAGACCCAAACAATCTTTAAGACTTACGACTGTAGAACCAGAACAATGTCAAACGCCTG AACAATCTTAGAGACTTAAAACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAGA CTTACAACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAGACTTACATTGAACCC TAGAACAAGAACA Found at i:365482 original size:37 final size:37 Alignment explanation

Indices: 365416--365599 Score: 251 Period size: 37 Copynumber: 5.0 Consensus size: 37 365406 AACTAGAACA * * * 365416 ATGTCAAAGGCCTGGACAATCTTAGAGACTTACAAGG 1 ATGTAAAAGGCCTGAACAATCTTAGAGACTTACAACG * * * 365453 ATGTAAAAGACCTGAACAATCTTACAGACTGACAACG 1 ATGTAAAAGGCCTGAACAATCTTAGAGACTTACAACG * * * 365490 ATGTAAAGGGTCTGAAAAATCTTAGAGACTTACAACG 1 ATGTAAAAGGCCTGAACAATCTTAGAGACTTACAACG * * * 365527 ATGTAAAAGGTCTGAAAAATTTTAGAGACTTACAACG 1 ATGTAAAAGGCCTGAACAATCTTAGAGACTTACAACG * 365564 ATGTAAAAGGCCTGGACAATCTTAGAGACTTACAAC 1 ATGTAAAAGGCCTGAACAATCTTAGAGACTTACAAC 365600 TGTAGAAGCA Statistics Matches: 129, Mismatches: 18, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 37 129 1.00 ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23 Consensus pattern (37 bp): ATGTAAAAGGCCTGAACAATCTTAGAGACTTACAACG Found at i:365645 original size:51 final size:51 Alignment explanation

Indices: 365564--365735 Score: 281 Period size: 51 Copynumber: 3.4 Consensus size: 51 365554 ACTTACAACG * 365564 ATGTAAAAGGCCTGGACAATCTTAGAGACTTACAACTGTAGAAGCAGAACA 1 ATGTCAAAGGCCTGGACAATCTTAGAGACTTACAACTGTAGAAGCAGAACA 365615 ATGTCAAAGGCCTGGACAATCTTAGAGACTTACAACTGTAGAAGCAGAACA 1 ATGTCAAAGGCCTGGACAATCTTAGAGACTTACAACTGTAGAAGCAGAACA * * * ** 365666 ATGTCAAAGGCCTGGGCAATCTTAGAGACTTACAACTGTAGAACCAGGATG 1 ATGTCAAAGGCCTGGACAATCTTAGAGACTTACAACTGTAGAAGCAGAACA * 365717 ATGTCAAAGGCCTGAACAA 1 ATGTCAAAGGCCTGGACAA 365736 GTCCACAGCT Statistics Matches: 113, Mismatches: 8, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 51 113 1.00 ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20 Consensus pattern (51 bp): ATGTCAAAGGCCTGGACAATCTTAGAGACTTACAACTGTAGAAGCAGAACA Found at i:374206 original size:157 final size:157 Alignment explanation

Indices: 373920--374224 Score: 493 Period size: 157 Copynumber: 1.9 Consensus size: 157 373910 TTTATAAATT * 373920 CATTATTTTAACTGATCAAATGTAAGCTGCAAGTTTTCAGTGTTTAATTTCAATTTGAATAGACT 1 CATTATTTTAACTGATCAAATGTAAGCTGCAAGTTTTCAGTGTTTAATTTCAATTTGAACAGACT * * 373985 GAGAAATTATATTTTTGAAATTTAAAAAAAAAAAAATGATACCATAAATCTGAAAGTGTTTATGT 66 GAGAAATTATACTTTGGAAATTTAAAAAAAAAAAAATGATACCATAAATCTGAAAGTGTTTATGT 374050 CGATAAATTTTTGCGAATACATATCTG 131 CGATAAATTTTTGCGAATACATATCTG 374077 CATTATTTTAACTGATCAAATGTAAGCTGCAAGTTTTCAGTGTTTAATTTCAATTTGAACAGACT 1 CATTATTTTAACTGATCAAATGTAAGCTGCAAGTTTTCAGTGTTTAATTTCAATTTGAACAGACT ********* * 374142 GAGAAATTATACTTTGGAAATTTTTTTTTTTTAAAATGATACCGTAAATCTGAAAGTGTTTATGT 66 GAGAAATTATACTTTGGAAATTTAAAAAAAAAAAAATGATACCATAAATCTGAAAGTGTTTATGT 374207 CGATAAATTTTTGCGAAT 131 CGATAAATTTTTGCGAAT 374225 CCGAGTCATA Statistics Matches: 135, Mismatches: 13, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 157 135 1.00 ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40 Consensus pattern (157 bp): CATTATTTTAACTGATCAAATGTAAGCTGCAAGTTTTCAGTGTTTAATTTCAATTTGAACAGACT GAGAAATTATACTTTGGAAATTTAAAAAAAAAAAAATGATACCATAAATCTGAAAGTGTTTATGT CGATAAATTTTTGCGAATACATATCTG Found at i:376602 original size:72 final size:72 Alignment explanation

Indices: 376518--376661 Score: 288 Period size: 72 Copynumber: 2.0 Consensus size: 72 376508 TAGTAGATAT 376518 TATTAAACTAAAATAAAATAAAATTTACTCATACCTGAGGAAAATCCTAATTGAATATTAGAATT 1 TATTAAACTAAAATAAAATAAAATTTACTCATACCTGAGGAAAATCCTAATTGAATATTAGAATT 376583 AATCCAA 66 AATCCAA 376590 TATTAAACTAAAATAAAATAAAATTTACTCATACCTGAGGAAAATCCTAATTGAATATTAGAATT 1 TATTAAACTAAAATAAAATAAAATTTACTCATACCTGAGGAAAATCCTAATTGAATATTAGAATT 376655 AATCCAA 66 AATCCAA 376662 AATATAAAAT Statistics Matches: 72, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 72 72 1.00 ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31 Consensus pattern (72 bp): TATTAAACTAAAATAAAATAAAATTTACTCATACCTGAGGAAAATCCTAATTGAATATTAGAATT AATCCAA Found at i:377325 original size:18 final size:18 Alignment explanation

Indices: 377302--377340 Score: 78 Period size: 18 Copynumber: 2.2 Consensus size: 18 377292 TTGATTTCTG 377302 ATAATTTATTTATGCAAA 1 ATAATTTATTTATGCAAA 377320 ATAATTTATTTATGCAAA 1 ATAATTTATTTATGCAAA 377338 ATA 1 ATA 377341 TTGCATATAG Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 21 1.00 ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44 Consensus pattern (18 bp): ATAATTTATTTATGCAAA Found at i:377641 original size:179 final size:178 Alignment explanation

Indices: 377333--377890 Score: 863 Period size: 176 Copynumber: 3.1 Consensus size: 178 377323 ATTTATTTAT * 377333 GCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAACTCTTCCTACAGTTCTCAAGATAGG 1 GCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGG * * * 377398 AAGTTGTTCTTTTGCAGATCAATTGTACATATATAAGAGGTGTGCATATTGCTGGGATTTTGATT 66 AAGTTGTTCTTTTGCAGATTAATTGTACATATAT-AGAGGTGTGCATATTGCTAGAATTTTGATT * * * 377463 TCCGATAATTTATCAAAAAATACAAGCTTTTGAACTTAGTCATTTTTTG 130 TCTGATAATTTATAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTG * * * 377512 GCAAAATATTGCATATAGGGTTCCTTCATTGTACGGATAATTCCTCCTACAGTTCTCAAGATAGG 1 GCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGG * * * * 377577 AAGTTGTTCTTTTGCAGATTAATTGTACATATATCTGAGGTGTGTATATTTCTAGAAATTTGATT 66 AAGTTGTTCTTTTGCAGATTAATTGTACATATAT-AGAGGTGTGCATATTGCTAGAATTTTGATT * 377642 TCTGATAATTTATGAAAGAAATACCAGCTTTTGAAC-T--T-ATTTTTTG 130 TCTGATAATTTAT-AAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTG * * * 377688 GCAAAATATTGCATATAGGGTACCCTCATTGTACGGAAAACTCCTCCTACAGTTATCAAGATAAG 1 GCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGG 377753 AAGTTGTTCTTTTGCAGATTAATTGTACATATAATAGAGGTGTGCATATTGCTAGAATTTTGATT 66 AAGTTGTTCTTTTGCAGATTAATTGTACATAT-ATAGAGGTGTGCATATTGCTAGAATTTTGATT * 377818 TCTGATAATTCATGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTG 130 TCTGATAATTTAT-AAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTG * 377868 GCAAAATGTTGCATATAGGGTAC 1 GCAAAATATTGCATATAGGGTAC 377891 TCCATTTCAC Statistics Matches: 344, Mismatches: 29, Indels: 11 0.90 0.08 0.03 Matches are distributed among these distances: 176 159 0.46 177 4 0.01 179 132 0.38 180 49 0.14 ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37 Consensus pattern (178 bp): GCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGG AAGTTGTTCTTTTGCAGATTAATTGTACATATATAGAGGTGTGCATATTGCTAGAATTTTGATTT CTGATAATTTATAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTG Found at i:381758 original size:24 final size:22 Alignment explanation

Indices: 381707--381793 Score: 63 Period size: 24 Copynumber: 3.9 Consensus size: 22 381697 AATCTACCAT * 381707 ATCTAAAGTTAAAAGTAAC-CGTA 1 ATCTACAGTTAAAAGTAACAC--A 381730 TATCTACAGTTAAAAGTAACAACAA 1 -ATCTACAGTTAAAAGTAAC-AC-A * * * 381755 ATCTACATTTCAAACT-ACAC- 1 ATCTACAGTTAAAAGTAACACA * 381775 ATTTACAGTTAAAAGTAAC 1 ATCTACAGTTAAAAGTAAC 381794 GACATAGCGT Statistics Matches: 51, Mismatches: 9, Indels: 9 0.74 0.13 0.13 Matches are distributed among these distances: 20 12 0.24 21 2 0.04 22 2 0.04 23 2 0.04 24 31 0.61 25 1 0.02 26 1 0.02 ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28 Consensus pattern (22 bp): ATCTACAGTTAAAAGTAACACA Found at i:382048 original size:23 final size:24 Alignment explanation

Indices: 382022--382079 Score: 73 Period size: 26 Copynumber: 2.4 Consensus size: 24 382012 AAAAATCAAT * * 382022 AAAAGTTTGCTTGCCTCAAAGAAAA 1 AAAAGTTTGCTTGACTCAAA-CAAA 382047 AAATAGTTTGCTTGACTCAAAC-AA 1 AAA-AGTTTGCTTGACTCAAACAAA 382071 AAAAGTTTG 1 AAAAGTTTG 382080 ATCGTCTCAA Statistics Matches: 30, Mismatches: 2, Indels: 4 0.83 0.06 0.11 Matches are distributed among these distances: 23 6 0.20 24 5 0.17 25 3 0.10 26 16 0.53 ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28 Consensus pattern (24 bp): AAAAGTTTGCTTGACTCAAACAAA Found at i:382055 original size:26 final size:26 Alignment explanation

Indices: 382025--382074 Score: 82 Period size: 26 Copynumber: 1.9 Consensus size: 26 382015 AATCAATAAA * * 382025 AGTTTGCTTGCCTCAAAGAAAAAAAT 1 AGTTTGCTTGACTCAAACAAAAAAAT 382051 AGTTTGCTTGACTCAAACAAAAAA 1 AGTTTGCTTGACTCAAACAAAAAA 382075 GTTTGATCGT Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 26 22 1.00 ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26 Consensus pattern (26 bp): AGTTTGCTTGACTCAAACAAAAAAAT Found at i:383023 original size:2 final size:2 Alignment explanation

Indices: 383018--383061 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 383008 TGTGTGTGTG 383018 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 383060 TC 1 TC 383062 CATCACATAA 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:394761 original size:2 final size:2 Alignment explanation

Indices: 394754--394784 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 394744 ATTATGTGAT 394754 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 394785 CAGACAGACA Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00 Consensus pattern (2 bp): AG Found at i:394789 original size:4 final size:4 Alignment explanation

Indices: 394782--394824 Score: 77 Period size: 4 Copynumber: 10.8 Consensus size: 4 394772 AGAGAGAGAG * 394782 AGAC AGAC AGAC AGAC AGAC GGAC AGAC AGAC AGAC AGAC AGA 1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGA 394825 GAAGGAGAGG Statistics Matches: 37, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 4 37 1.00 ACGTcount: A:0.49, C:0.23, G:0.28, T:0.00 Consensus pattern (4 bp): AGAC Found at i:397364 original size:2 final size:2 Alignment explanation

Indices: 397359--397437 Score: 149 Period size: 2 Copynumber: 39.5 Consensus size: 2 397349 ATGTGTGGTG 397359 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 * 397401 GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 397438 TTTTTCAGCT Statistics Matches: 75, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 2 75 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): GA Found at i:400097 original size:2 final size:2 Alignment explanation

Indices: 400090--400183 Score: 145 Period size: 2 Copynumber: 47.0 Consensus size: 2 400080 GTGTATAATG * * * 400090 GA GA GA GA GA GA GA GA GA GA GA GA G- GCA GA CA GA GA AA GA CA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA GA GA GA GA GA 400132 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 400174 GA GA GA GA GA 1 GA GA GA GA GA 400184 TTCATGATAG Statistics Matches: 84, Mismatches: 6, Indels: 4 0.89 0.06 0.04 Matches are distributed among these distances: 1 1 0.01 2 82 0.98 3 1 0.01 ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00 Consensus pattern (2 bp): GA Found at i:404659 original size:11 final size:11 Alignment explanation

Indices: 404643--404667 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 404633 ACATTTTGAA 404643 AAAATACAGGT 1 AAAATACAGGT 404654 AAAATACAGGT 1 AAAATACAGGT 404665 AAA 1 AAA 404668 TTTGTGTTGG Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16 Consensus pattern (11 bp): AAAATACAGGT Found at i:406891 original size:2 final size:2 Alignment explanation

Indices: 406884--406925 Score: 84 Period size: 2 Copynumber: 21.0 Consensus size: 2 406874 CCGTTTAAAC 406884 AG AG AG AG AG AG AG AG AG AG AG 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 406926 TTACAGTTTT Statistics Matches: 40, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 40 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:416550 original size:20 final size:20 Alignment explanation

Indices: 416525--416565 Score: 82 Period size: 20 Copynumber: 2.0 Consensus size: 20 416515 TTATCAAGTC 416525 CTAAGATTTTTTTATGAGTA 1 CTAAGATTTTTTTATGAGTA 416545 CTAAGATTTTTTTATGAGTA 1 CTAAGATTTTTTTATGAGTA 416565 C 1 C 416566 ATTTCAATAA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49 Consensus pattern (20 bp): CTAAGATTTTTTTATGAGTA Found at i:421958 original size:156 final size:159 Alignment explanation

Indices: 421690--422082 Score: 392 Period size: 156 Copynumber: 2.5 Consensus size: 159 421680 TATCTTCCTA * * * * * * 421690 AGTAAAATTTCATCCCCCATTGTGGCCTCACCCTA-CCCCTGGACTATTATTTAAACAAACTTGA 1 AGTAAAAATTGATCCCCCATTGTGGCCCCACCCTACCCCCGGGACTATGATTTGAACAAACTTGA * * * * * * 421754 ATCTATATGATCTGGAGATGCCTCCACTCAAATTTGGGCTTTCCTGGCCTAATACTT-TTGAGAA 66 ATCTACATGATCTGGAGATGCCTACACTCAAATTTGAGATTTCCTGGCCAAATACTTATT-AAAA 421818 GAAGA-CTTTT-AAAGATTTTCTC-TATA-T 130 GAA-ATCTTTTAAAAGATTTTCTCATATACT * * 421845 A-TAAAAA-TGTATCCCCCATTGTGGCCCCGCCCTACCCCCAGGGACCATGATTTGAACAAACTT 1 AGTAAAAATTG-ATCCCCCATTGTGGCCCCACCCTACCCCC-GGGACTATGATTTGAACAAACTT * ** * * * 421908 GAATCTACATTATCT-GAGGATGGTTACA-TGCCAATTTGAGATTTCTTGGCCAAATAGTTATTA 64 GAATCTACATGATCTGGA-GATGCCTACACT-CAAATTTGAGATTTCCTGGCCAAATACTTATTA * 421971 AAAGAAATTTTTTAAAAGATTTTCTCTATATACTCTT 127 AAAGAAATCTTTTAAAAGATTTTCTC-ATATA--C-T * * 422008 ATGTAAAAATTGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGACTATGATTTGAAGAAACG 1 A-GTAAAAATTGATCCCCC-ATTGTGGCCCCACCCTACCCCC-GGGACTATGATTTGAACAAACT 422073 TGAATCTACA 63 TGAATCTACA 422083 CTTCTTCCAT Statistics Matches: 194, Mismatches: 26, Indels: 25 0.79 0.11 0.10 Matches are distributed among these distances: 153 1 0.01 154 27 0.14 155 9 0.05 156 72 0.37 157 14 0.07 159 4 0.02 163 2 0.01 165 13 0.07 166 52 0.27 ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32 Consensus pattern (159 bp): AGTAAAAATTGATCCCCCATTGTGGCCCCACCCTACCCCCGGGACTATGATTTGAACAAACTTGA ATCTACATGATCTGGAGATGCCTACACTCAAATTTGAGATTTCCTGGCCAAATACTTATTAAAAG AAATCTTTTAAAAGATTTTCTCATATACT Found at i:422479 original size:166 final size:166 Alignment explanation

Indices: 422182--423099 Score: 1292 Period size: 166 Copynumber: 5.5 Consensus size: 166 422172 AACTTGTACA * * 422182 ATTTGAACAGACTTAAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCTTTTCTGGCC 1 ATTTGAACAAACTTAAATCTACACTACCTGAGGATGCTTCCAATTTAATTTGAGCTTTTCTGGCC * * * * ** 422247 AAATAATTTTTGAGAAGAGGATTTTTAAAGATTTTCTCTATATATTCCCT-TTTAAAACACGATC 66 TAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATT-CCTATGTAAAACTTGATC * ** * 422311 CCCCTATTGTGGCCCCACCCTACATCTGGGGACCATG 130 CCCCAATTGTGGCCCCACCCTACCCCCGGGGACCATG * * * ** * * 422348 ATTTAAACAAACTTGAATCTACACTACCTGAGGATGCTTCCACTCAAAGTTGAGCTTTCCTGGCC 1 ATTTGAACAAACTTAAATCTACACTACCTGAGGATGCTTCCAATTTAATTTGAGCTTTTCTGGCC * 422413 TCATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC 66 TAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC ** 422478 CCCAATTGTGGCCCCATACTACCCCCGGGGACCATG 131 CCCAATTGTGGCCCCACCCTACCCCCGGGGACCATG * * * * * 422514 ATTTGAACAAACTTAAATATTCACTTCCTGAGCATGCTTCCAATTTAATTTCAGCTTTTCTGGCC 1 ATTTGAACAAACTTAAATCTACACTACCTGAGGATGCTTCCAATTTAATTTGAGCTTTTCTGGCC * * 422579 TAATAGTTTTTGAGTAGAAGATTCTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC 66 TAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC * * 422644 CCCAATTGTGGCCCCACCCTACCCCCAGGGATCATG 131 CCCAATTGTGGCCCCACCCTACCCCCGGGGACCATG * 422680 ATTTGAACATACTTAAATCTACACTACCTGAGGATGCTTCCAATTTAATTTGAGCTTTTCTGGCC 1 ATTTGAACAAACTTAAATCTACACTACCTGAGGATGCTTCCAATTTAATTTGAGCTTTTCTGGCC * * 422745 TAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCCATATATTCCTATGTACAACTTGATCC 66 TAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC * * 422810 CCCAATTGTGGCCCCACCCTACCCCCGGGAACTATG 131 CCCAATTGTGGCCCCACCCTACCCCCGGGGACCATG * * * * 422846 ATTTGAATAAACTTGAATCTACACTACCTGAGGATGCTCCCATTTTAATTTGAGCTTTTCTGGCC 1 ATTTGAACAAACTTAAATCTACACTACCTGAGGATGCTTCCAATTTAATTTGAGCTTTTCTGGCC * 422911 TGATAGTTTTTGAG-A-AA-ATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC 66 TAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC ** * * 422973 CCCTCTTGTGGCCCCTCCCTACCCCCGGGGACTATG 131 CCCAATTGTGGCCCCACCCTACCCCCGGGGACCATG * * * * * * 423009 ATTTGAACAAACGTGAATCTACACTACCTGAGGATGCCTCCACA--CAAGTTTAAGCTTTTCCGG 1 ATTTGAACAAACTTAAATCTACACTACCTGAGGATGCTTCCA-ATTTAA-TTTGAGCTTTTCTGG 423072 -CTGAATAGTTTTTGAGAAGAAGATTTTT 64 CCT-AATAGTTTTTGAGAAGAAGATTTTT 423100 GAAAAATACC Statistics Matches: 670, Mismatches: 75, Indels: 14 0.88 0.10 0.02 Matches are distributed among these distances: 162 4 0.01 163 138 0.21 164 3 0.00 165 6 0.01 166 519 0.77 ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34 Consensus pattern (166 bp): ATTTGAACAAACTTAAATCTACACTACCTGAGGATGCTTCCAATTTAATTTGAGCTTTTCTGGCC TAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC CCCAATTGTGGCCCCACCCTACCCCCGGGGACCATG Found at i:424447 original size:165 final size:165 Alignment explanation

Indices: 424222--425345 Score: 1640 Period size: 166 Copynumber: 6.8 Consensus size: 165 424212 TGAATATGAT * * * * * * * * 424222 AAATAAGCAAAGTCGACATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACAA 1 AAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA * * * 424287 TATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGAA 66 TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA * * 424352 ATCTTTGAGGAAAATTTGTTTGAAAATTTTGGCTAA 131 ATCTTTGA-CAAAATTTGTTTGAAAATTTTGGCAAA * * * * * 424388 AAA-AAACAAAGTCATTATTTAACAGGAAGTTGACATCCGATTGATACAAAAATATATCCCACAA 1 AAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA * * * * * * 424452 TATGGCATGCCAAAACAAACAGTGTGTTAAAATTTCAAGCATCTGCGATATATAGCTGCTGAGAA 66 TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA * * 424517 ATCTTTGACAAAATTTGTTTCAAAATTTTGACAAA 131 ATCTTTGACAAAATTTGTTTGAAAATTTTGGCAAA * * * * 424552 AAATAAACAAAGTCGTCATTTGACAGTAAGTTGACGTCTGATTGGTACAAAAATACATCCCACGA 1 AAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA * * * 424617 TATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCAATAAACAGTTGCTGAGAA 66 TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA * * * 424682 ATCTTTGACGGAAATTTGTTTGAAAATTTTTGCTAA 131 ATCTTTGAC-AAAATTTGTTTGAAAATTTTGGCAAA * * 424718 AAAT-AACTAAAGTCGTCATTTAACAGGAAGTTGATGTCTGATTGGTACAAAAATATATCCCACG 1 AAATAAAC-AAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG * * 424782 ATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGA 65 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA * 424847 ATTCTTTGACAGAAATTTGTTTGAAAATTTTGGCAAA 130 AATCTTTGACA-AAATTTGTTTGAAAATTTTGGCAAA * * * * 424884 AAATAAACAAAGTCGTCATTTAACAGAAAGCTGGCATCCGATTGGTACAAAAATATATCCCACGA 1 AAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA 424949 TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA 66 TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA * 425014 TTCTTTGACAGAAATTTGTTTGAAAATTTTGGCAAA 131 ATCTTTGACA-AAATTTGTTTGAAAATTTTGGCAAA * * 425050 AAATAAACAAAGTCGTCATTTGACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCACGA 1 AAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA * * * * 425115 TATGGCATGCCTATACAAATACCGTGTAAAAATTTCAAGCATCTGCGATAAACAATTGCTGAGAA 66 TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA ** 425180 ATCTTTGACGAAAATTTGTTTGAAAATTTTAGTTAAA 131 ATCTTTGAC-AAAATTTGTTTGAAAATTTT-GGCAAA * 425217 AAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA 1 AAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA * * * * 425282 TATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAGCATCTGCGATTAATAGTTGCTGAGA 66 TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA 425346 TTAATGCGAC Statistics Matches: 871, Mismatches: 80, Indels: 13 0.90 0.08 0.01 Matches are distributed among these distances: 164 26 0.03 165 242 0.28 166 477 0.55 167 126 0.14 ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29 Consensus pattern (165 bp): AAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA ATCTTTGACAAAATTTGTTTGAAAATTTTGGCAAA Found at i:425382 original size:8 final size:8 Alignment explanation

Indices: 425369--425427 Score: 64 Period size: 8 Copynumber: 7.4 Consensus size: 8 425359 AATTTTTGTT 425369 ACAGACGG 1 ACAGACGG * 425377 ACAGACAG 1 ACAGACGG 425385 ACAGACGG 1 ACAGACGG * 425393 ACGGACGG 1 ACAGACGG * * 425401 ACGGACAG 1 ACAGACGG * 425409 ACGGACGG 1 ACAGACGG * 425417 ACAGACAG 1 ACAGACGG 425425 ACA 1 ACA 425428 CACAAGGGTA Statistics Matches: 44, Mismatches: 7, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 8 44 1.00 ACGTcount: A:0.39, C:0.25, G:0.36, T:0.00 Consensus pattern (8 bp): ACAGACGG Found at i:425385 original size:4 final size:4 Alignment explanation

Indices: 425369--425427 Score: 55 Period size: 4 Copynumber: 14.8 Consensus size: 4 425359 AATTTTTGTT * * * * * * * 425369 ACAG ACGG ACAG ACAG ACAG ACGG ACGG ACGG ACGG ACAG ACGG ACGG 1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG 425417 ACAG ACAG ACA 1 ACAG ACAG ACA 425428 CACAAGGGTA Statistics Matches: 49, Mismatches: 6, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 4 49 1.00 ACGTcount: A:0.39, C:0.25, G:0.36, T:0.00 Consensus pattern (4 bp): ACAG Found at i:425386 original size:12 final size:12 Alignment explanation

Indices: 425369--425422 Score: 81 Period size: 12 Copynumber: 4.5 Consensus size: 12 425359 AATTTTTGTT * 425369 ACAGACGGACAG 1 ACAGACGGACGG * 425381 ACAGACAGACGG 1 ACAGACGGACGG * 425393 ACGGACGGACGG 1 ACAGACGGACGG 425405 ACAGACGGACGG 1 ACAGACGGACGG 425417 ACAGAC 1 ACAGAC 425423 AGACACACAA Statistics Matches: 37, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 12 37 1.00 ACGTcount: A:0.37, C:0.26, G:0.37, T:0.00 Consensus pattern (12 bp): ACAGACGGACGG Found at i:426405 original size:63 final size:63 Alignment explanation

Indices: 426306--426623 Score: 411 Period size: 63 Copynumber: 4.9 Consensus size: 63 426296 CTTGTTACAC * * 426306 CAGCTCTCAGACACTTAATACTGTGATCAGTAACTACTTACTGTTCTGTGTTAGAGTAGCTCA 1 CAGCTCTCAGACACTGAATACTGTGATCAGTTACTACTTACTGTTCTGTGTTAGAGTAGCTCA * 426369 CAGCTCTCAGACACTGAATACTGTAATCAGTTACTACCGGTACTTACTGTTCTGTGTTAGAGTAG 1 CAGCTCTCAGACACTGAATACTGTGATCAG-T--TA-C--TACTTACTGTTCTGTGTTAGAGTAG ** 426434 CTTG 60 CTCA * * * * 426438 CAGCTCTCAGACACTTAATACTATGATCAGTTAACTACTTACTTTTCTGTGTTAGAGTAACTCA 1 CAGCTCTCAGACACTGAATACTGTGATCAGTT-ACTACTTACTGTTCTGTGTTAGAGTAGCTCA * * * * ** 426502 CAGCTCTCAGACATTGAATACTGTGATTAGTTACAACTCACTGTTCTGTGTTAGAGTAGCTTG 1 CAGCTCTCAGACACTGAATACTGTGATCAGTTACTACTTACTGTTCTGTGTTAGAGTAGCTCA * * * 426565 CAGCTCTCAGACACTGAATATTGTGATCAGTAACTACTTACTGTTCTGTGTTAGCGTAG 1 CAGCTCTCAGACACTGAATACTGTGATCAGTTACTACTTACTGTTCTGTGTTAGAGTAG 426624 ACCTCAACAT Statistics Matches: 219, Mismatches: 29, Indels: 14 0.84 0.11 0.05 Matches are distributed among these distances: 63 105 0.48 64 54 0.25 66 3 0.01 67 2 0.01 68 1 0.00 69 54 0.25 ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34 Consensus pattern (63 bp): CAGCTCTCAGACACTGAATACTGTGATCAGTTACTACTTACTGTTCTGTGTTAGAGTAGCTCA Found at i:429293 original size:21 final size:21 Alignment explanation

Indices: 429269--429309 Score: 64 Period size: 21 Copynumber: 2.0 Consensus size: 21 429259 ATTCAGGTAA * * 429269 ATGACACACTTCATTGTCTTC 1 ATGACACACTCCACTGTCTTC 429290 ATGACACACTCCACTGTCTT 1 ATGACACACTCCACTGTCTT 429310 GATGGTACAT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 21 18 1.00 ACGTcount: A:0.24, C:0.32, G:0.10, T:0.34 Consensus pattern (21 bp): ATGACACACTCCACTGTCTTC Found at i:430782 original size:2 final size:2 Alignment explanation

Indices: 430775--430819 Score: 90 Period size: 2 Copynumber: 22.5 Consensus size: 2 430765 GCATGACAGT 430775 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 430817 TC T 1 TC T 430820 TTTTCTGTTG Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 43 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:435692 original size:4 final size:4 Alignment explanation

Indices: 435693--435734 Score: 66 Period size: 4 Copynumber: 10.5 Consensus size: 4 435683 CTGTCTGTCT * * 435693 GTCC GTCC GTCC GTCC GTCC GTCC GTCT GTCT GTCC GTCC GT 1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GT 435735 AACAAAAATT Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 4 36 1.00 ACGTcount: A:0.00, C:0.43, G:0.26, T:0.31 Consensus pattern (4 bp): GTCC Found at i:436306 original size:166 final size:167 Alignment explanation

Indices: 435758--436666 Score: 1266 Period size: 166 Copynumber: 5.5 Consensus size: 167 435748 GTCGCATTTA * * * 435758 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAAGCATGCTATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT * * 435823 CGTGGGATGTATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATGACG-ACTTTGCTTATT 66 CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATGA-GTACTTTGTTTA-T * * * 435887 TTTTAACTAAAATTTTCAAACAAATTTTCGTCAAAGATT 129 TTTTAGCAAAAATTTTCAAACAAATTTCCGTCAAAGATT * * 435926 TCTCAGCAACTATCTATCGCAGATGCTTGAAATTTTTACACAATATTTGTATAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT ** 435991 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGT-TAAATGCA-T-CTTTGTTTATT 66 CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATG-AGTACTTTGTTTATT ** * 436053 TTTAGCAAAAATTTTCAAACAAATTTTTGTCAAAGAAT 130 TTTAGCAAAAATTTTCAAACAAATTTCCGTCAAAGATT * * * 436091 TCTCAGCAACTGTTTATCGCAGATACTTGAAATTTTTACACAGTATTTGTATAGGCATGCTATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT 436156 CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGT-AATGAGTACTTTGTTTATTT 66 CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATGAGTACTTTGTTTATTT * 436220 TTAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATT 131 TTAGCAAAAATTTTCAAACAAATTTCCGTCAAAGATT * * * * * 436257 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTTGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT * ** * 436322 TGTGGGATATATTTTTGTACCAATCAGATGTCAACTTCCTGT-TAAATGACG-ACTTTGTTTATT 66 CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATGA-GTACTTTGTTTATT * * 436385 TTTAGCAAAAAATTTCAAACAAATAATT--GTCAAAGAAT 130 TTTAGCAAAAATTTTCAAACAAAT--TTCCGTCAAAGATT * * * * * 436423 TCTCAGCAACTGTTTATCGCAGATGCTTGACATTTTTACACAGTGTTTGTATAAGCATGCTATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT ** 436488 CGTGGGATGCATTTTTGTACCAATTGGACGTCAACTTCCTGTGT-AATGAGTACTTTGTTTATTT 66 CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATGAGTACTTTGTTTATTT ** * 436552 TTAGCCCAAATTTTCAAACCAATTTTCC-TCAAAGATT 131 TTAGCAAAAATTTTCAAA-CAAATTTCCGTCAAAGATT * * * * 436589 TCTCAGCAGCTATTTATCGCAGATGCTTGAAA-TTTAACACACTATTTGTTTAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT * 436653 TGTGGGATATATTT 66 CGTGGGATATATTT 436667 CTACCAATCG Statistics Matches: 655, Mismatches: 72, Indels: 31 0.86 0.09 0.04 Matches are distributed among these distances: 164 1 0.00 165 182 0.28 166 358 0.55 167 12 0.02 168 102 0.16 ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39 Consensus pattern (167 bp): TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATGAGTACTTTGTTTATTT TTAGCAAAAATTTTCAAACAAATTTCCGTCAAAGATT Found at i:436362 original size:331 final size:332 Alignment explanation

Indices: 435758--436715 Score: 1543 Period size: 332 Copynumber: 2.9 Consensus size: 332 435748 GTCGCATTTA * 435758 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAAGCATGCTATAT 1 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAAGCATGCTATAT * 435823 CGTGGGATGTATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATGACG-ACTTTGCTTATT 66 CGTGGGATGTATTTTTGTACCAATTGGACGTCAACTTCCTGTGT-AATGA-GTACTTTGTTTA-T * * * * * 435887 TTTTAACTAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATCTATCGCAGATGC 128 TTTTAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGC * * * * 435952 TTGAAATTTTTACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCA 193 TTGAAATTTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTTTGTACCAATCA * * ** 436017 GACGTCAACTTCCTGTTAAATG-C-ATCTTTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTT 258 GATGTCAACTTCCTGTTAAATGACGA-CTTTGTTTATTTTTAGCAAAAAATTTCAAACAAATAAT 436080 TGTCAAAGAAT 322 TGTCAAAGAAT * * * 436091 TCTCAGCAACTGTTTATCGCAGATACTTGAAATTTTTACACAGTATTTGTATAGGCATGCTATAT 1 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAAGCATGCTATAT * 436156 CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAATGAGTACTTTGTTTATTTT 66 CGTGGGATGTATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAATGAGTACTTTGTTTATTTT 436221 TAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTG 131 TAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTG * 436286 AAATTTTAACACACTATTTGTTTTGGCATGCCATATTGTGGGATATATTTTTGTACCAATCAGAT 196 AAATTTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTTTGTACCAATCAGAT 436351 GTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAAAAATTTCAAACAAATAATTGTC 261 GTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAAAAATTTCAAACAAATAATTGTC 436416 AAAGAAT 326 AAAGAAT * 436423 TCTCAGCAACTGTTTATCGCAGATGCTTGACATTTTTACACAGTGTTTGTATAAGCATGCTATAT 1 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAAGCATGCTATAT * 436488 CGTGGGATGCATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAATGAGTACTTTGTTTATTTT 66 CGTGGGATGTATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAATGAGTACTTTGTTTATTTT * * 436553 TAGCCCAAATTTTCAAACCAATTTTCC-TCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTT 131 TAGCCAAAATTTTCAAA-CAAATTTCCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTT * * 436617 GAAA-TTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATA--TTTCTACCAATCGGA 195 GAAATTTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTTTGTACCAATCAGA * * * * * 436679 TGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT 260 TGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT 436716 GCATATTCAC Statistics Matches: 585, Mismatches: 36, Indels: 12 0.92 0.06 0.02 Matches are distributed among these distances: 329 45 0.08 331 185 0.32 332 242 0.41 333 113 0.19 ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39 Consensus pattern (332 bp): TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAAGCATGCTATAT CGTGGGATGTATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAATGAGTACTTTGTTTATTTT TAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTG AAATTTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTTTGTACCAATCAGAT GTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAAAAATTTCAAACAAATAATTGTC AAAGAAT Found at i:442746 original size:26 final size:25 Alignment explanation

Indices: 442695--442752 Score: 71 Period size: 25 Copynumber: 2.3 Consensus size: 25 442685 ATTTGTATTT * * 442695 AAAAAAAACCAACAACAACAACAAAA 1 AAAAAAAACCAACAA-AAAAAAAAAA * * 442721 GAAAAAAACCACCAAAAAAAAAAAA 1 AAAAAAAACCAACAAAAAAAAAAAA 442746 AAAAAAA 1 AAAAAAA 442753 TAGAAGCTGT Statistics Matches: 27, Mismatches: 5, Indels: 1 0.82 0.15 0.03 Matches are distributed among these distances: 25 14 0.52 26 13 0.48 ACGTcount: A:0.81, C:0.17, G:0.02, T:0.00 Consensus pattern (25 bp): AAAAAAAACCAACAAAAAAAAAAAA Found at i:446674 original size:2 final size:2 Alignment explanation

Indices: 446667--446723 Score: 114 Period size: 2 Copynumber: 28.5 Consensus size: 2 446657 GAAAACTTTC 446667 AG AG AG AG AG AG AG AG AG AG AG 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 446709 AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG A 446724 TTGTGTATGA Statistics Matches: 55, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 55 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:448552 original size:2 final size:2 Alignment explanation

Indices: 448545--448585 Score: 82 Period size: 2 Copynumber: 20.5 Consensus size: 2 448535 TCGACCTTTG 448545 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 448586 GGAGGGGGGG Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 39 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:450277 original size:12 final size:12 Alignment explanation

Indices: 450260--450287 Score: 56 Period size: 12 Copynumber: 2.3 Consensus size: 12 450250 TAACAACTCA 450260 GAAATTCTATAG 1 GAAATTCTATAG 450272 GAAATTCTATAG 1 GAAATTCTATAG 450284 GAAA 1 GAAA 450288 CCAACTCTAG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 16 1.00 ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29 Consensus pattern (12 bp): GAAATTCTATAG Found at i:456562 original size:14 final size:12 Alignment explanation

Indices: 456545--456614 Score: 70 Period size: 13 Copynumber: 5.5 Consensus size: 12 456535 CTTAAATGCC * 456545 AAAATACAAATAA 1 AAAAAACAAA-AA 456558 AAAAAACAAAAAA 1 AAAAAAC-AAAAA 456571 CAAAAAACAAAAA 1 -AAAAAACAAAAA 456584 AAACCAAA-AAAAA 1 AAA--AAACAAAAA * 456597 AAAAACCAAAAA 1 AAAAAACAAAAA 456609 AAAAAA 1 AAAAAA 456615 ACCCCATAAA Statistics Matches: 49, Mismatches: 3, Indels: 11 0.78 0.05 0.17 Matches are distributed among these distances: 11 2 0.04 12 13 0.27 13 21 0.43 14 13 0.27 ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03 Consensus pattern (12 bp): AAAAAACAAAAA Found at i:456568 original size:7 final size:7 Alignment explanation

Indices: 456544--456616 Score: 69 Period size: 7 Copynumber: 10.1 Consensus size: 7 456534 TCTTAAATGC * 456544 CAAAATA 1 CAAAAAA * 456551 CAAATAA 1 CAAAAAA 456558 -AAAAAA 1 CAAAAAA 456564 CAAAAAA 1 CAAAAAA 456571 CAAAAAA 1 CAAAAAA 456578 CAAAAAAAA 1 C--AAAAAA 456587 CCAAAAAA 1 -CAAAAAA * 456595 AAAAAAA 1 CAAAAAA 456602 CCAAAAAA 1 -CAAAAAA 456610 -AAAAAA 1 CAAAAAA 456616 C 1 C 456617 CCCATAAAAA Statistics Matches: 55, Mismatches: 5, Indels: 12 0.76 0.07 0.17 Matches are distributed among these distances: 6 11 0.20 7 25 0.45 8 12 0.22 9 6 0.11 10 1 0.02 ACGTcount: A:0.84, C:0.14, G:0.00, T:0.03 Consensus pattern (7 bp): CAAAAAA Found at i:456577 original size:16 final size:15 Alignment explanation

Indices: 456556--456615 Score: 84 Period size: 15 Copynumber: 3.9 Consensus size: 15 456546 AAATACAAAT 456556 AAAAAAAACAAAAAAC 1 AAAAAAAA-AAAAAAC 456572 AAAAAACAAAAAAAAC 1 AAAAAA-AAAAAAAAC * 456588 CAAAAAAAAAAAAAC 1 AAAAAAAAAAAAAAC * 456603 CAAAAAAAAAAAA 1 AAAAAAAAAAAAA 456616 CCCCATAAAA Statistics Matches: 42, Mismatches: 1, Indels: 3 0.91 0.02 0.07 Matches are distributed among these distances: 15 22 0.52 16 18 0.43 17 2 0.05 ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00 Consensus pattern (15 bp): AAAAAAAAAAAAAAC Found at i:456591 original size:24 final size:24 Alignment explanation

Indices: 456556--456615 Score: 88 Period size: 24 Copynumber: 2.5 Consensus size: 24 456546 AAATACAAAT * 456556 AAAAAAAACAAAAAACAAAAAA-C 1 AAAAAAAACAAAAAAAAAAAAACC 456579 AAAAAAAACCAAAAAAAAAAAAACC 1 AAAAAAAA-CAAAAAAAAAAAAACC 456604 AAAAAAAA-AAAA 1 AAAAAAAACAAAA 456616 CCCCATAAAA Statistics Matches: 34, Mismatches: 1, Indels: 4 0.87 0.03 0.10 Matches are distributed among these distances: 23 12 0.35 24 13 0.38 25 9 0.26 ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00 Consensus pattern (24 bp): AAAAAAAACAAAAAAAAAAAAACC Found at i:456626 original size:1 final size:1 Alignment explanation

Indices: 456556--456615 Score: 57 Period size: 1 Copynumber: 60.0 Consensus size: 1 456546 AAATACAAAT * * * ** ** 456556 AAAAAAAACAAAAAACAAAAAACAAAAAAAACCAAAAAAAAAAAAACCAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 456616 CCCCATAAAA Statistics Matches: 49, Mismatches: 10, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 1 49 1.00 ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:456626 original size:15 final size:14 Alignment explanation

Indices: 456558--456617 Score: 75 Period size: 16 Copynumber: 4.0 Consensus size: 14 456548 ATACAAATAA * 456558 AAAAAACAAAAAACAA 1 AAAAAA-AAAAAAC-C 456574 AAAACAAAAAAAACC 1 AAAA-AAAAAAAACC 456589 AAAAAAAAAAAAACC 1 -AAAAAAAAAAAACC 456604 AAAAAAAAAAAACC 1 AAAAAAAAAAAACC 456618 CCATAAAAAC Statistics Matches: 41, Mismatches: 1, Indels: 6 0.85 0.02 0.12 Matches are distributed among these distances: 14 14 0.34 15 10 0.24 16 15 0.37 17 2 0.05 ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00 Consensus pattern (14 bp): AAAAAAAAAAAACC Found at i:457592 original size:2 final size:2 Alignment explanation

Indices: 457585--457637 Score: 106 Period size: 2 Copynumber: 26.5 Consensus size: 2 457575 TTTATTCAAT 457585 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 457627 GA GA GA GA GA G 1 GA GA GA GA GA G 457638 GTGTGTGTAT Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:464590 original size:22 final size:23 Alignment explanation

Indices: 464543--464591 Score: 64 Period size: 22 Copynumber: 2.2 Consensus size: 23 464533 GAATTATTTT * * 464543 TTTTCCTTGACTGCATTTTTACA 1 TTTTCCTTGACTGCAGTTTTAAA * 464566 TTTTCCTTTACT-CAGTTTTAAA 1 TTTTCCTTGACTGCAGTTTTAAA 464588 TTTT 1 TTTT 464592 TTTGTACCAC Statistics Matches: 23, Mismatches: 3, Indels: 1 0.85 0.11 0.04 Matches are distributed among these distances: 22 12 0.52 23 11 0.48 ACGTcount: A:0.18, C:0.18, G:0.06, T:0.57 Consensus pattern (23 bp): TTTTCCTTGACTGCAGTTTTAAA Found at i:464592 original size:23 final size:24 Alignment explanation

Indices: 464542--464592 Score: 61 Period size: 23 Copynumber: 2.2 Consensus size: 24 464532 AGAATTATTT * * 464542 TTTTTCCTTGACTGCATTTTTACA 1 TTTTTCCTTGACTGCAGTTTTAAA * 464566 -TTTTCCTTTACT-CAGTTTTAAA 1 TTTTTCCTTGACTGCAGTTTTAAA 464588 TTTTT 1 TTTTT 464593 TTGTACCACT Statistics Matches: 23, Mismatches: 3, Indels: 3 0.79 0.10 0.10 Matches are distributed among these distances: 22 8 0.35 23 15 0.65 ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59 Consensus pattern (24 bp): TTTTTCCTTGACTGCAGTTTTAAA Found at i:471330 original size:19 final size:20 Alignment explanation

Indices: 471291--471338 Score: 73 Period size: 19 Copynumber: 2.5 Consensus size: 20 471281 CACTAAATAT 471291 AAAA-ATATATTAAAAGTCA 1 AAAAGATATATTAAAAGTCA 471310 AAAAGATATATTAAAAG-CA 1 AAAAGATATATTAAAAGTCA * 471329 AAAAGGTATA 1 AAAAGATATA 471339 GAGAATGTTT Statistics Matches: 27, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 19 15 0.56 20 12 0.44 ACGTcount: A:0.62, C:0.04, G:0.10, T:0.23 Consensus pattern (20 bp): AAAAGATATATTAAAAGTCA Found at i:482824 original size:7 final size:7 Alignment explanation

Indices: 482812--482842 Score: 62 Period size: 7 Copynumber: 4.4 Consensus size: 7 482802 TGAACATTTG 482812 TTTGTTT 1 TTTGTTT 482819 TTTGTTT 1 TTTGTTT 482826 TTTGTTT 1 TTTGTTT 482833 TTTGTTT 1 TTTGTTT 482840 TTT 1 TTT 482843 TGCAATTATG Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 24 1.00 ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87 Consensus pattern (7 bp): TTTGTTT Found at i:491679 original size:15 final size:15 Alignment explanation

Indices: 491659--491689 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 491649 AAATATATAG 491659 ACTTTGATTTTAAAA 1 ACTTTGATTTTAAAA * 491674 ACTTTGCTTTTAAAA 1 ACTTTGATTTTAAAA 491689 A 1 A 491690 ATGAATGAAC Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45 Consensus pattern (15 bp): ACTTTGATTTTAAAA Found at i:495955 original size:15 final size:15 Alignment explanation

Indices: 495935--495963 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 495925 CGATACAAGA 495935 TATTACTATTCTTAC 1 TATTACTATTCTTAC 495950 TATTACTATTCTTA 1 TATTACTATTCTTA 495964 ATTTGCAATA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55 Consensus pattern (15 bp): TATTACTATTCTTAC Found at i:503933 original size:12 final size:12 Alignment explanation

Indices: 503918--503946 Score: 58 Period size: 12 Copynumber: 2.4 Consensus size: 12 503908 CAATCCACCA 503918 AATCCTCCATTT 1 AATCCTCCATTT 503930 AATCCTCCATTT 1 AATCCTCCATTT 503942 AATCC 1 AATCC 503947 ACCCAATCCT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 17 1.00 ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38 Consensus pattern (12 bp): AATCCTCCATTT Found at i:503954 original size:21 final size:21 Alignment explanation

Indices: 503930--504018 Score: 142 Period size: 21 Copynumber: 4.2 Consensus size: 21 503920 TCCTCCATTT ** 503930 AATCCTCCATTTAATCCACCC 1 AATCCTCCGGTTAATCCACCC 503951 AATCCTCCGGTTAATCCACCC 1 AATCCTCCGGTTAATCCACCC * 503972 AATCCTCCGGTTAATCCTCCC 1 AATCCTCCGGTTAATCCACCC * 503993 AATCCGCCGGTTAATCCACCC 1 AATCCTCCGGTTAATCCACCC 504014 AATCC 1 AATCC 504019 ACCGAACCCT Statistics Matches: 63, Mismatches: 5, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 21 63 1.00 ACGTcount: A:0.25, C:0.43, G:0.08, T:0.25 Consensus pattern (21 bp): AATCCTCCGGTTAATCCACCC Found at i:504092 original size:18 final size:18 Alignment explanation

Indices: 504065--504106 Score: 57 Period size: 18 Copynumber: 2.3 Consensus size: 18 504055 GTTAGACCCC * * * 504065 AATCCTCCCAAACTTCCT 1 AATCCACCCAAACCTCCA 504083 AATCCACCCAAACCTCCA 1 AATCCACCCAAACCTCCA 504101 AATCCA 1 AATCCA 504107 GTATTGTAAG Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 21 1.00 ACGTcount: A:0.36, C:0.45, G:0.00, T:0.19 Consensus pattern (18 bp): AATCCACCCAAACCTCCA Found at i:504651 original size:21 final size:21 Alignment explanation

Indices: 504627--504722 Score: 147 Period size: 21 Copynumber: 4.6 Consensus size: 21 504617 CACCAAATCC * ** 504627 TCCACCTAATCCTCCATTTAA 1 TCCACCCAATCCTCCGGTTAA 504648 TCCACCCAATCCTCCGGTTAA 1 TCCACCCAATCCTCCGGTTAA 504669 TCCACCCAATCCTCCGGTTAA 1 TCCACCCAATCCTCCGGTTAA * * 504690 TCCTCCCAATCCGCCGGTTAA 1 TCCACCCAATCCTCCGGTTAA 504711 TCCACCCAATCC 1 TCCACCCAATCC 504723 ACCGAACCCT Statistics Matches: 69, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 21 69 1.00 ACGTcount: A:0.24, C:0.44, G:0.07, T:0.25 Consensus pattern (21 bp): TCCACCCAATCCTCCGGTTAA Found at i:504796 original size:18 final size:18 Alignment explanation

Indices: 504769--504810 Score: 57 Period size: 18 Copynumber: 2.3 Consensus size: 18 504759 GTTAGACCCC * * * 504769 AATCCTCCCAAACTTCCT 1 AATCCACCCAAACCTCCA 504787 AATCCACCCAAACCTCCA 1 AATCCACCCAAACCTCCA 504805 AATCCA 1 AATCCA 504811 GTATTGTAAG Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 21 1.00 ACGTcount: A:0.36, C:0.45, G:0.00, T:0.19 Consensus pattern (18 bp): AATCCACCCAAACCTCCA Found at i:511427 original size:18 final size:18 Alignment explanation

Indices: 511400--511441 Score: 57 Period size: 18 Copynumber: 2.3 Consensus size: 18 511390 GTTAGACCCC * * * 511400 AATCCTCCCAAACTTCCT 1 AATCCACCCAAACCTCCA 511418 AATCCACCCAAACCTCCA 1 AATCCACCCAAACCTCCA 511436 AATCCA 1 AATCCA 511442 GTATTGTAGG Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 21 1.00 ACGTcount: A:0.36, C:0.45, G:0.00, T:0.19 Consensus pattern (18 bp): AATCCACCCAAACCTCCA Found at i:511704 original size:33 final size:36 Alignment explanation

Indices: 511628--511704 Score: 88 Period size: 36 Copynumber: 2.2 Consensus size: 36 511618 GAGTCCAGTG * ** 511628 CCTAAACCTCCCAAGGAGCCAAGACCACTATTAAGT 1 CCTAAACCTCCCAAGGAACCAAGACCACTACCAAGT * * 511664 CCCAAACCTCCCAAGGAACCAAG-CC-C-GCCAAGT 1 CCTAAACCTCCCAAGGAACCAAGACCACTACCAAGT 511697 CCTAAACC 1 CCTAAACC 511705 ACCACCCAAG Statistics Matches: 35, Mismatches: 6, Indels: 3 0.80 0.14 0.07 Matches are distributed among these distances: 33 11 0.31 34 1 0.03 35 2 0.06 36 21 0.60 ACGTcount: A:0.35, C:0.40, G:0.13, T:0.12 Consensus pattern (36 bp): CCTAAACCTCCCAAGGAACCAAGACCACTACCAAGT Found at i:514273 original size:1 final size:1 Alignment explanation

Indices: 514267--514295 Score: 58 Period size: 1 Copynumber: 29.0 Consensus size: 1 514257 CATTTCTTTC 514267 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 514296 GGTTTTAAGA 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:0.00, G:0.00, T:1.00 Consensus pattern (1 bp): T Found at i:515010 original size:2 final size:2 Alignment explanation

Indices: 515003--515028 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 514993 ATACAAACAT 515003 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 515029 ACATATGTAC Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:519686 original size:2 final size:2 Alignment explanation

Indices: 519679--519763 Score: 152 Period size: 2 Copynumber: 42.5 Consensus size: 2 519669 TCTAAGTGAA 519679 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 * * 519721 TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC CC 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 519763 T 1 T 519764 GTTTACCATT Statistics Matches: 79, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 79 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:527186 original size:12 final size:12 Alignment explanation

Indices: 527171--527195 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 527161 AAATTTTCAA 527171 ATTCCTCAACTC 1 ATTCCTCAACTC 527183 ATTCCTCAACTC 1 ATTCCTCAACTC 527195 A 1 A 527196 AATCCTTTAA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.28, C:0.40, G:0.00, T:0.32 Consensus pattern (12 bp): ATTCCTCAACTC Found at i:527449 original size:2 final size:2 Alignment explanation

Indices: 527442--527493 Score: 104 Period size: 2 Copynumber: 26.0 Consensus size: 2 527432 TAATAAACCA 527442 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 527484 TC TC TC TC TC 1 TC TC TC TC TC 527494 AATGATCATT Statistics Matches: 50, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 50 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:529570 original size:32 final size:32 Alignment explanation

Indices: 529529--529605 Score: 136 Period size: 32 Copynumber: 2.4 Consensus size: 32 529519 GTAAATCACG * 529529 GTGGCATGGTTTGAATGACTGAGAGAATTCCT 1 GTGGCATGGTTTGAATAACTGAGAGAATTCCT 529561 GTGGCATGGTTTGAATAACTGAGAGAATTCCT 1 GTGGCATGGTTTGAATAACTGAGAGAATTCCT * 529593 TTGGCATGGTTTG 1 GTGGCATGGTTTG 529606 TGTCACAATG Statistics Matches: 43, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 32 43 1.00 ACGTcount: A:0.23, C:0.12, G:0.31, T:0.34 Consensus pattern (32 bp): GTGGCATGGTTTGAATAACTGAGAGAATTCCT Found at i:530845 original size:10 final size:10 Alignment explanation

Indices: 530830--530855 Score: 52 Period size: 10 Copynumber: 2.6 Consensus size: 10 530820 TCTCTTTGGA 530830 CAAGTGTACT 1 CAAGTGTACT 530840 CAAGTGTACT 1 CAAGTGTACT 530850 CAAGTG 1 CAAGTG 530856 CATTTGTTAT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 16 1.00 ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27 Consensus pattern (10 bp): CAAGTGTACT Found at i:535660 original size:41 final size:41 Alignment explanation

Indices: 535610--537183 Score: 1978 Period size: 41 Copynumber: 38.6 Consensus size: 41 535600 AGAGTATGCT * * * 535610 ATCAAATCACCTTTTTGTAGGTCTATATACCAGGGTGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * * ** * * ** 535651 ATCAGATCACTTTTTTGTAAATCTTTATACCAGAATGTAAT 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC 535692 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC ** * ** 535733 ATCACATCACCTTTCTGTATATCTATATACCAGGATGAATT 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * 535774 ATCACATCACCTTTCTGTAGGTCTATATACCAGGGTGTACT 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * * * ** 535815 AACACATCACCTTTCTATAGGTCTATATACAAGGAGGTATA 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * * 535856 ATCAAATCACCTTTCTCTAGGTCCATATACCA-GAGTGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGA-TGTACC ** * ** 535897 ATCACATCACCTTTCTGTATATCTATATACCAGGATGAATT 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * 535938 ATCACATCACATTTCTGTAGGTCTATATACCAGGGTGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * 535979 ATCACATCACCTTTCTGTAGGTCTATATACCAGGGTGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC 536020 ATCACATCACCTTTCTGTAGGTCTATATACCAGG--G---- 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * ** * * * ** 536055 -T-GCATCACCTTTCTGTATATCTATGTTCCAGGATGAATT 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * * 536094 AACGCATCACCTTTCCGTAGGTCTATATACCAGGATGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * ** 536135 ATCACATCACATTTCTGTACATCTATATACCAAGG-TGT-CC 1 ATCACATCACCTTTCTGTAGGTCTATATACC-AGGATGTACC * * 536175 TATCACATCACCTTTCTGTAGATCTATATATCAGGATGTACC 1 -ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * 536217 AT--CATCACCTTTCTGTAGGTCTATATATCAGGATGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * * 536256 ATCACATCACCTTTCTGTAGATCTATAAATCAGGATGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * * 536297 ATCACATCACCTTTCTGTAGATCTATAAATCAGGATGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * 536338 ATCACATCACCTTTCTGTAGGTCTATATATCAGGATGTACT 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * 536379 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATCTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * * 536420 ATCACATCACCTTTCTGTAGATCTATAAATCAGGATGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * * * 536461 ATCACATCACATTTCTGTAGGTCTATATATCAGGATTTACA 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * 536502 ATCACATCACCTTTTTGTAGGTCTATATATCAGGATGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * 536543 ATCACATCACCCTTCTGTAGGTCTATATACCAGGATGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * 536584 AT--CATCACCTTTCTGTATGTCTATATACCAGGGTGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * 536623 ATCACATCACCTTTCTGTAGGTCTGTATACCAGGATGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * * 536664 ATGACATCACCTTTCTGTTGGTCTATATACCAGAATGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * 536705 ATCACATCACCTTTCTGTAGGTCTATATACCAGAATGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * 536746 ATCACATCACCTTTCTGTATGTCTATATACCAGGGTGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * 536787 ATCACATCACCTTTCTGTAGGTCTGTATACCAGGATGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * 536828 ATCACATCACCTTTCTGTTGGTCTATATACCAGAATGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC 536869 ATCACATCACCTTTCTGTAGGTCTATATACCA-GAGTGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGA-TGTACC ** * ** 536910 ATCACATCACCTTTCTGTATATCTATATACCAGGGTG-ATTT 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTA-CC * * * 536951 ATCACATCACCTTTCTGAAGGTCTATATAACA-GAGTGTACT 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGA-TGTACC * * * 536992 ATCATATCACCTTCCTGTAGGTCTATATACCAAGGTAGGTGAACC 1 ATCACATCACCTTTCTGTAGGTCTATATACC-AGG-A--TGTACC * * * 537037 ATCACATCACCTTTCTGTAGGTCTATATACCAGGGTATATC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * 537078 ATTACTTCACCTTTCTGTAGGTCTATATACCAGGATGTACC 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * * * 537119 ATCACATCACTTTTCTGTAGGTCTATATACCAGGGTGAACT 1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC * * 537160 ATCATATCACCTTCCTGTAGGTCT 1 ATCACATCACCTTTCTGTAGGTCT 537184 TTATGCGTAA Statistics Matches: 1339, Mismatches: 167, Indels: 54 0.86 0.11 0.03 Matches are distributed among these distances: 33 26 0.02 34 1 0.00 35 1 0.00 39 75 0.06 40 10 0.01 41 1177 0.88 42 10 0.01 43 1 0.00 44 4 0.00 45 34 0.03 ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34 Consensus pattern (41 bp): ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC Found at i:544794 original size:28 final size:28 Alignment explanation

Indices: 544752--544817 Score: 114 Period size: 28 Copynumber: 2.4 Consensus size: 28 544742 AGAAGAAATT * 544752 TTTTTGAGATTTTATTGTTCTATATGAC 1 TTTTTGAGATGTTATTGTTCTATATGAC 544780 TTTTTGAGATGTTATTGTTCTATATGAC 1 TTTTTGAGATGTTATTGTTCTATATGAC * 544808 TTTTTAAGAT 1 TTTTTGAGAT 544818 ATGAACAGGT Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 28 36 1.00 ACGTcount: A:0.23, C:0.06, G:0.15, T:0.56 Consensus pattern (28 bp): TTTTTGAGATGTTATTGTTCTATATGAC Found at i:548959 original size:21 final size:21 Alignment explanation

Indices: 548889--548953 Score: 85 Period size: 21 Copynumber: 3.1 Consensus size: 21 548879 CTTTGAAATT * * * * 548889 AAGATTTGGAATATATATTAC 1 AAGATTTTGAACATACATCAC * 548910 AAGATTTCGAACATACATCAC 1 AAGATTTTGAACATACATCAC 548931 AAGATTTTGAACATACATCAC 1 AAGATTTTGAACATACATCAC 548952 AA 1 AA 548954 TTTTTTCAAA Statistics Matches: 39, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 21 39 1.00 ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29 Consensus pattern (21 bp): AAGATTTTGAACATACATCAC Found at i:549429 original size:2 final size:2 Alignment explanation

Indices: 549422--549453 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 549412 TCTGAGTAGG 549422 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 549454 ATTTGCATCC Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:565076 original size:38 final size:38 Alignment explanation

Indices: 565019--565149 Score: 203 Period size: 38 Copynumber: 3.5 Consensus size: 38 565009 GTCAAGCATC * * 565019 TGAGATCTGACCTTTTCAAACATTTAAACACATGATAT 1 TGAGATCTGACCTTGTCAAACATTTAAACACATGACAT * * 565057 TGA-ACTCTGACCTTGTCAAACATATCAACACATGACAT 1 TGAGA-TCTGACCTTGTCAAACATTTAAACACATGACAT 565095 TGAGATCTGACCTTGTCAAACATTTAAACACATGACAT 1 TGAGATCTGACCTTGTCAAACATTTAAACACATGACAT 565133 TGAGA-CTGACCTTGTCA 1 TGAGATCTGACCTTGTCA 565150 CTAGCATCTG Statistics Matches: 85, Mismatches: 6, Indels: 5 0.89 0.06 0.05 Matches are distributed among these distances: 37 13 0.15 38 71 0.84 39 1 0.01 ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30 Consensus pattern (38 bp): TGAGATCTGACCTTGTCAAACATTTAAACACATGACAT Found at i:577161 original size:32 final size:32 Alignment explanation

Indices: 577116--577918 Score: 844 Period size: 32 Copynumber: 25.3 Consensus size: 32 577106 CGTGGAGAAT ** 577116 GGCTGTAGAGGATTCCCAACCCAGTCTACCTA 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * * * 577148 GGCAGTAGAGGATTCCCGACCCAGTCTACCTC 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * * * 577180 GGCTGTAGAGGATTTCCGG-CCATATCTACCTT 1 GGCTGTAGAGGATTCCCGGCCCA-GTCTACCTA * 577212 GGCTGTAGAGGATTCCCGGTCCAGTCTACCTTA 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACC-TA * 577245 -GCT-TA-AGGATTCCCGACCCAGTCTACCTA 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * * * * * 577274 GGCTGTGGGGGAGTCTCGACCCAGTCTACCTA 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * * 577306 GGCTGTAGGGGATTTCCGG-CCAGGT-TACCTA 1 GGCTGTAGAGGATTCCCGGCCCA-GTCTACCTA * 577337 GGCTGTAGAGGAATCCCGGCCCAGTCTACCTA 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * * * 577369 GGCTGAACG-GGATTCCCGACCCAGTCTTCCTA 1 GGCTGTA-GAGGATTCCCGGCCCAGTCTACCTA * * * 577401 GGCTGTAGGGGATTCCCGACCCAGTCTTCCTA 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * * * 577433 GGCTGTAGGGGATTCCCGACCCAGTCTTCCTA 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * * 577465 GGCTGTAGAGGATTCCCGACCCAGTCTATCTA 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * 577497 CGCTGTAGAGGATTCCCGGCCCAGTCTACCTA 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * * * 577529 GGTTGTAGGGGATTCCCGGCCCAGTCTACCTT 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA 577561 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTTA 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACC-TA * * 577594 -GCT-TA-AGGATTCCCGGTCCAGTCTTCCTA 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * * 577623 GGCTGTAAAGGATTTCCGGCCCAGTCTACC-A 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * * * * 577654 TTGCTATAGAGGATTCCCGGCCAAGTTTACCTA 1 -GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * * 577687 GGCTGTACAGGATTCCCGGCCCAGTCTACCTT 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * * * 577719 GGCTGTAGGGGATTCCCGACCCAGTCTACCTT 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * * * * 577751 GGCTGTAGGGGATTCCCGACCCATTCTACCTT 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * * * 577783 GACTGTAGAGGATTCCCGG-TCAGGT-TACCTT 1 GGCTGTAGAGGATTCCCGGCCCA-GTCTACCTA ** * * 577814 GGCTGTAGAGGATTTTCGGCCCAGTCTATCTT 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA * * * 577846 GGCTGTAGAGGCTTCCCGGCCCTA-TTTACCTT 1 GGCTGTAGAGGATTCCCGGCCC-AGTCTACCTA * * * * 577878 GGCTGTAGGGGATTCCCGACCCTGTC-ACCTTG 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACC-TA 577910 GGCTGTAGA 1 GGCTGTAGA 577919 TTATCCGGCT Statistics Matches: 662, Mismatches: 86, Indels: 46 0.83 0.11 0.06 Matches are distributed among these distances: 29 4 0.01 30 46 0.07 31 68 0.10 32 536 0.81 33 8 0.01 ACGTcount: A:0.18, C:0.29, G:0.27, T:0.26 Consensus pattern (32 bp): GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA Found at i:577966 original size:32 final size:32 Alignment explanation

Indices: 577925--578280 Score: 440 Period size: 32 Copynumber: 11.3 Consensus size: 32 577915 TAGATTATCC * * * 577925 GGCTGTAGAGGATTCCCGACTCAGTTTACCTT 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT * 577957 GGCTGTAGAGGATTCCCGGCCCAGTCTATCTT 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT * * 577989 GGCTGTAGAGGATTCCCGGTCCAGTCTATCTT 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT * 578021 GGCT-TA-AGGATTCTCGGCCCAGTCTACCTT 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT * * * 578051 GGCT-TA-AGGATTCTCGGCCCATTCAACCTT 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT * * 578081 GGCTGTAGGGGATTCCCGACCCAGTCTACCTT 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT * * 578113 GGCTGTAGGGGATTCCCGACCCAGTCTACCTT 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT 578145 GGCTGTAGAGGATTCCCGG-CCAGGT-TACCTT 1 GGCTGTAGAGGATTCCCGGCCCA-GTCTACCTT * 578176 GGCTGTAGAGGATTCCCGGCCCAGTCTATCTT 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT * * * 578208 GGCTGTAGGGGCTTCCCGGCCCTA-TTTACCTT 1 GGCTGTAGAGGATTCCCGGCCC-AGTCTACCTT * * * 578240 GGCTGTAGGGGATTCCCGACCCTGTC-ACCTT 1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT 578271 GGGCTGTAGA 1 -GGCTGTAGA 578281 TTATCCGGCT Statistics Matches: 289, Mismatches: 27, Indels: 16 0.87 0.08 0.05 Matches are distributed among these distances: 30 53 0.18 31 39 0.13 32 196 0.68 33 1 0.00 ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28 Consensus pattern (32 bp): GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT Found at i:577993 original size:79 final size:79 Alignment explanation

Indices: 577846--577997 Score: 209 Period size: 79 Copynumber: 1.9 Consensus size: 79 577836 AGTCTATCTT * * * * 577846 GGCTGTAGAGGCTTCCCGGCCCTATTTACCTTGGCTGTAGGGGATTCCCGACCCTGTCACCTTGG 1 GGCTGTAGAGGATTCCCGACCCTATTTACCTTGGCTGTAGAGGATTCCCGACCCAGTCACCTTGG 577911 GCTGTAGATTATCC 66 GCTGTAGATTATCC * * * 577925 GGCTGTAGAGGATTCCCGACTC-AGTTTACCTTGGCTGTAGAGGATTCCCGGCCCAGTCTATCTT 1 GGCTGTAGAGGATTCCCGACCCTA-TTTACCTTGGCTGTAGAGGATTCCCGACCCAGTC-ACCTT 577989 -GGCTGTAGA 64 GGGCTGTAGA 577998 GGATTCCCGG Statistics Matches: 64, Mismatches: 7, Indels: 4 0.85 0.09 0.05 Matches are distributed among these distances: 78 1 0.02 79 59 0.92 80 4 0.06 ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29 Consensus pattern (79 bp): GGCTGTAGAGGATTCCCGACCCTATTTACCTTGGCTGTAGAGGATTCCCGACCCAGTCACCTTGG GCTGTAGATTATCC Found at i:578190 original size:95 final size:95 Alignment explanation

Indices: 577925--578280 Score: 438 Period size: 95 Copynumber: 3.8 Consensus size: 95 577915 TAGATTATCC * * * 577925 GGCTGTAGAGGATTCCCGACTCAGTTTACCTTGGCTGTAGAGGATTCCCGGCCCAGTCTATCTTG 1 GGCTGTAGAGGATTCCCGACCCAGTCTACCTTGGCTGTAGAGGATTCCCGGCCCAGT-TACCTTG * 577990 GCTGTAGAGGATTCCCGGTCCAGTCTATCTT 65 GCTGTAGAGGATTCCCGGCCCAGTCTATCTT * * * 578021 GGCT-TA-AGGATTCTCGGCCCAGTCTACCTTGGCT-TA-AGGATTCTCGGCCCA-TTCAACCTT 1 GGCTGTAGAGGATTCCCGACCCAGTCTACCTTGGCTGTAGAGGATTCCCGGCCCAGTT--ACCTT * * * 578081 GGCTGTAGGGGATTCCCGACCCAGTCTACCTT 64 GGCTGTAGAGGATTCCCGGCCCAGTCTATCTT * 578113 GGCTGTAGGGGATTCCCGACCCAGTCTACCTTGGCTGTAGAGGATTCCCGG-CCAGGTTACCTTG 1 GGCTGTAGAGGATTCCCGACCCAGTCTACCTTGGCTGTAGAGGATTCCCGGCCCA-GTTACCTTG 578177 GCTGTAGAGGATTCCCGGCCCAGTCTATCTT 65 GCTGTAGAGGATTCCCGGCCCAGTCTATCTT * * * * * * * * 578208 GGCTGTAGGGGCTTCCCGGCCCTA-TTTACCTTGGCTGTAGGGGATTCCCGACCCTGTCACCTTG 1 GGCTGTAGAGGATTCCCGACCC-AGTCTACCTTGGCTGTAGAGGATTCCCGGCCCAGTTACCTT- 578272 GGCTGTAGA 64 GGCTGTAGA 578281 TTATCCGGCT Statistics Matches: 225, Mismatches: 24, Indels: 22 0.83 0.09 0.08 Matches are distributed among these distances: 90 1 0.00 91 1 0.00 92 50 0.22 93 4 0.02 94 49 0.22 95 92 0.41 96 26 0.12 97 2 0.01 ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28 Consensus pattern (95 bp): GGCTGTAGAGGATTCCCGACCCAGTCTACCTTGGCTGTAGAGGATTCCCGGCCCAGTTACCTTGG CTGTAGAGGATTCCCGGCCCAGTCTATCTT Found at i:580112 original size:185 final size:185 Alignment explanation

Indices: 579813--580154 Score: 524 Period size: 185 Copynumber: 1.8 Consensus size: 185 579803 ATAAATATAG * * * 579813 GTAATAAGGAATCATTCTCTGAATATTATGTGGTTATAATTTCGGTCGGAGTGTGGTCAAATCTA 1 GTAATAAGGAATCATTCTCTGAATATTATGAGGTGATAATTTCGGTCGGAGCGTGGTCAAATCTA ** * * * * 579878 TTTTAAAATCTTTCGGCCTTTATTGGATTTGACCACGCCCCGACCGAAATTATCACCTCATAATA 66 TCATAAAACCCTACGGCCTTTATTGGATTTGACCACGCCCCGACCGAAATTATAACCTCATAATA * 579943 CTTAAAGAATGATTCCTTATTCCTTAATCTATAGTGTACAAAAATATAAATGCAA 131 CTCAAAGAATGATTCCTTATTCCTTAATCTATAGTGTACAAAAATATAAATGCAA ** * 579998 GTAATAAGTTATCATTTTCTGAATATTATGAGGTGATAATTTCGGTCGGAGCGTGGTCAAATCTA 1 GTAATAAGGAATCATTCTCTGAATATTATGAGGTGATAATTTCGGTCGGAGCGTGGTCAAATCTA * * * 580063 TCATAAAGCCCTACGGGCTTTAATT-GATTTGACCACGCCCCGACCGAAATTATAACGTCATAAT 66 TCATAAAACCCTACGGCCTTT-ATTGGATTTGACCACGCCCCGACCGAAATTATAACCTCATAAT 580127 ACTCAAAGAATGATTCCTTATTCCTTAA 130 ACTCAAAGAATGATTCCTTATTCCTTAA 580155 ATAAAACAAA Statistics Matches: 140, Mismatches: 16, Indels: 2 0.89 0.10 0.01 Matches are distributed among these distances: 185 137 0.98 186 3 0.02 ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34 Consensus pattern (185 bp): GTAATAAGGAATCATTCTCTGAATATTATGAGGTGATAATTTCGGTCGGAGCGTGGTCAAATCTA TCATAAAACCCTACGGCCTTTATTGGATTTGACCACGCCCCGACCGAAATTATAACCTCATAATA CTCAAAGAATGATTCCTTATTCCTTAATCTATAGTGTACAAAAATATAAATGCAA Found at i:583210 original size:4 final size:4 Alignment explanation

Indices: 583201--583247 Score: 76 Period size: 4 Copynumber: 11.8 Consensus size: 4 583191 GTTTTTGTTG * * 583201 TTGT TTGT TTGT TTGT TTGT ATGC TTGT TTGT TTGT TTGT TTGT TTG 1 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTG 583248 AGTTACCTTT Statistics Matches: 39, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 4 39 1.00 ACGTcount: A:0.02, C:0.02, G:0.26, T:0.70 Consensus pattern (4 bp): TTGT Found at i:584376 original size:35 final size:35 Alignment explanation

Indices: 584337--584647 Score: 424 Period size: 35 Copynumber: 8.9 Consensus size: 35 584327 GCCTATGCTT 584337 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC 1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC * * * 584372 TTGAAAACAAGTATTTTGAATGAATGGCTCAAATC 1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC * * 584407 TTGAAAACAAGTATTTTGTATGCATGCCTCAAACC 1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC * * * * * 584442 CTGAAAACAAGTATTTTGCATGACTGGCTCAGATC 1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC * * 584477 TTGAAAACAAGTATTTTGTATGCATGCCTCAAACC 1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC * * 584512 TTGAAAACAAGTATTTTGCATGAATGTCTCAAACA 1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC ** * 584547 TTGAAAACAAGTATTAAGCATGAATGCCTCAAACA 1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC * * * * 584582 TTGAAAACAAGTATTATGCATGAATACCCCAAACA 1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC * 584617 TTGAAAACAAGTATTTTGCATAAATGCCTCA 1 TTGAAAACAAGTATTTTGCATGAATGCCTCA 584648 GAACTTACAG Statistics Matches: 241, Mismatches: 35, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 35 241 1.00 ACGTcount: A:0.39, C:0.18, G:0.15, T:0.29 Consensus pattern (35 bp): TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC Found at i:589787 original size:2 final size:2 Alignment explanation

Indices: 589780--589812 Score: 66 Period size: 2 Copynumber: 16.5 Consensus size: 2 589770 TCGATCGATC 589780 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 589813 GGATGTACTA Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 31 1.00 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): GA Found at i:599467 original size:20 final size:20 Alignment explanation

Indices: 599437--600961 Score: 1436 Period size: 20 Copynumber: 75.8 Consensus size: 20 599427 TTGCAAGCCA * * 599437 TGTCAATTGGTGTGTCATGC 1 TGTCTATTGGTGTGTCATGT * * 599457 TGTTTATTGGTGTGCCATGT 1 TGTCTATTGGTGTGTCATGT * 599477 TGTCTACTGGTGTGTCA--- 1 TGTCTATTGGTGTGTCATGT * 599494 --T-TA---GTGTGCCATGT 1 TGTCTATTGGTGTGTCATGT 599508 TGTCTATTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT * 599528 TGTCTACTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT * 599548 TGTCTATTAGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT * * * 599568 TGTCTATTTGTTTGTTATGT 1 TGTCTATTGGTGTGTCATGT 599588 TGTCTATTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT * * 599608 TGTCTATTGGCGTGTCATATAT 1 TGTCTATTGGTGTGTC--ATGT * * 599630 TGTCAATTGGTGTGTCATTT 1 TGTCTATTGGTGTGTCATGT * * 599650 TGTGTCTTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT * * 599670 TGTCTATTTGATGAGTC-T-T 1 TGTCTA-TTGGTGTGTCATGT * * 599689 ATGTCTACTGGTGTGTTATGT 1 -TGTCTATTGGTGTGTCATGT * * * 599710 CGTCTTTTGGTGTGTCAAGT 1 TGTCTATTGGTGTGTCATGT * * ** 599730 TGTCTATTGGCGAGTCATAA 1 TGTCTATTGGTGTGTCATGT * * 599750 TCTCTATTGGTGTGCCATGT 1 TGTCTATTGGTGTGTCATGT * * * * * 599770 TATCTAATGGGGTATTATGT 1 TGTCTATTGGTGTGTCATGT * 599790 TGTCCATTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT 599810 TGTCTATTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT * * * 599830 TGTATTTTGGTGTG--GTGT 1 TGTCTATTGGTGTGTCATGT * 599848 TGTCTATTGGCT-TATCATGT 1 TGTCTATTGG-TGTGTCATGT * * * * 599868 TGTTTATTGATGTGCCACGT 1 TGTCTATTGGTGTGTCATGT ** 599888 TGTCTATTGGTGTGTCATAC 1 TGTCTATTGGTGTGTCATGT * * * * * 599908 TCTATGTTGGTGTTTTATGT 1 TGTCTATTGGTGTGTCATGT * * * * 599928 TGTCTTTTTGTGTGTTAT-A 1 TGTCTATTGGTGTGTCATGT 599947 TGTTCTATTGGTGTGTCATGT 1 TG-TCTATTGGTGTGTCATGT * 599968 TGTCT-TTAGGTGTGTAATGT 1 TGTCTATT-GGTGTGTCATGT * 599988 TGTTTATTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT * * 600008 TGTCTATTGATGTGCCATGT 1 TGTCTATTGGTGTGTCATGT * 600028 TGTCTATTGGTGTGTCATAT 1 TGTCTATTGGTGTGTCATGT * 600048 TGTCTATTGGTGTATCATGT 1 TGTCTATTGGTGTGTCATGT ** * 600068 TGT-TAATTGGTGTACCATCAT 1 TGTCT-ATTGGTGTGTCAT-GT * 600089 T-TCTATTAGTGTGTTGTGCCATTT 1 TGTCTATT-G-GTG-TGT--CATGT * * 600113 TGTCTATTGATGTGCCATGT 1 TGTCTATTGGTGTGTCATGT * * 600133 TGTCTATTGATGTGCCATGT 1 TGTCTATTGGTGTGTCATGT * 600153 TGTCTATTGGTGTGCCATGT 1 TGTCTATTGGTGTGTCATGT * * 600173 TGTCTATTGGTGTGTCCTAT 1 TGTCTATTGGTGTGTCATGT * * * 600193 TGTCTATTGGTTTGCCATCAT 1 TGTCTATTGGTGTGTCAT-GT * * * * * 600214 TTTAATAATGTGTTGTGCCATTT 1 TGT-CT-AT-TGGTGTGTCATGT * * 600237 TGTCTTTTGGTGTGTCACGT 1 TGTCTATTGGTGTGTCATGT 600257 TGTCTATTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT * * * 600277 TGTCTAGTGGTCTGTCACGT 1 TGTCTATTGGTGTGTCATGT * * 600297 AGTCTATTGGTGTGCCATGT 1 TGTCTATTGGTGTGTCATGT * * 600317 TGTCTATTGATGTGTCACGTT 1 TGTCTATTGGTGTGTCATG-T * * 600338 TTTCTATTGGTGTGTCATAT 1 TGTCTATTGGTGTGTCATGT * 600358 TGTCTATTGGTGTGTCACGT 1 TGTCTATTGGTGTGTCATGT * 600378 TTTCTATTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT * 600398 TGTCGATTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT * 600418 TGTCTATTGGTGTGCCATGT 1 TGTCTATTGGTGTGTCATGT * * 600438 TGTCTATTGATGTGTCACGT 1 TGTCTATTGGTGTGTCATGT * 600458 TTTCTATTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT * 600478 TGTCTATTGGTGTGCCATGT 1 TGTCTATTGGTGTGTCATGT * 600498 TGTCTATTGGTGTGCCATGT 1 TGTCTATTGGTGTGTCATGT * 600518 TGTCTATTGATGTGTCACAT-T 1 TGTCTATTGGTGTGT--CATGT * * 600539 TTTCTATTGGTGTGTCATAT 1 TGTCTATTGGTGTGTCATGT * 600559 TGTCTATTGGTGTGTCACGT 1 TGTCTATTGGTGTGTCATGT * 600579 TTTCTATTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT * 600599 TGTCTATTGGTGTGCCATGT 1 TGTCTATTGGTGTGTCATGT 600619 TGTCTATTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT * 600639 TGTCTATTGGTGTGCCATGT 1 TGTCTATTGGTGTGTCATGT 600659 TGTCTATTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT ** * 600679 TGTCTATTATTGTGCCATGT 1 TGTCTATTGGTGTGTCATGT * 600699 TGTCTATTGGTGTGTCATAT 1 TGTCTATTGGTGTGTCATGT * * 600719 TGTCAATTGGTTTGCCATCAT-T 1 TGTCTATTGGTGTG---TCATGT * * * * * 600741 TTTTTAATGTGTTGTGCCATTT 1 TGTCT-AT-TGGTGTGTCATGT * 600763 TGTCTATTGGTGTGTCACGT 1 TGTCTATTGGTGTGTCATGT 600783 TGTCTATTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT * 600803 TGTCTATTGGTGTGCCATGT 1 TGTCTATTGGTGTGTCATGT * * 600823 TGTTTATTGGTGTGTCATAT 1 TGTCTATTGGTGTGTCATGT * 600843 TGTCTATTGGTTTGCCATCAT-T 1 TGTCTATTGGTGTG---TCATGT * * * * * 600865 TTTTTAATGTGTTGTGCCATTT 1 TGTCT-AT-TGGTGTGTCATGT * 600887 TGTCTATTGGTGTGTCACGT 1 TGTCTATTGGTGTGTCATGT 600907 TGTCTATTGGTGTGTCATGT 1 TGTCTATTGGTGTGTCATGT * 600927 TGTCTATTGGTGTGCCATGT 1 TGTCTATTGGTGTGTCATGT * * 600947 TGTTTATTTGTGTGT 1 TGTCTATTGGTGTGT 600962 TGTATGACTG Statistics Matches: 1221, Mismatches: 232, Indels: 104 0.78 0.15 0.07 Matches are distributed among these distances: 11 7 0.01 14 2 0.00 15 1 0.00 16 1 0.00 17 2 0.00 18 12 0.01 19 17 0.01 20 1024 0.84 21 62 0.05 22 42 0.03 23 20 0.02 24 22 0.02 25 9 0.01 ACGTcount: A:0.13, C:0.12, G:0.26, T:0.49 Consensus pattern (20 bp): TGTCTATTGGTGTGTCATGT Found at i:599501 original size:31 final size:31 Alignment explanation

Indices: 599466--599525 Score: 111 Period size: 31 Copynumber: 1.9 Consensus size: 31 599456 CTGTTTATTG 599466 GTGTGCCATGTTGTCTACTGGTGTGTCATTA 1 GTGTGCCATGTTGTCTACTGGTGTGTCATTA * 599497 GTGTGCCATGTTGTCTATTGGTGTGTCAT 1 GTGTGCCATGTTGTCTACTGGTGTGTCAT 599526 GTTGTCTACT Statistics Matches: 28, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 31 28 1.00 ACGTcount: A:0.12, C:0.15, G:0.30, T:0.43 Consensus pattern (31 bp): GTGTGCCATGTTGTCTACTGGTGTGTCATTA Found at i:599516 original size:51 final size:51 Alignment explanation

Indices: 599446--599545 Score: 164 Period size: 51 Copynumber: 2.0 Consensus size: 51 599436 ATGTCAATTG * * 599446 GTGTGTCATGCTGTTTATTGGTGTGCCATGTTGTCTACTGGTGTGTCATTA 1 GTGTGCCATGCTGTCTATTGGTGTGCCATGTTGTCTACTGGTGTGTCATTA * * 599497 GTGTGCCATGTTGTCTATTGGTGTGTCATGTTGTCTACTGGTGTGTCAT 1 GTGTGCCATGCTGTCTATTGGTGTGCCATGTTGTCTACTGGTGTGTCAT 599546 GTTGTCTATT Statistics Matches: 45, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 51 45 1.00 ACGTcount: A:0.11, C:0.14, G:0.30, T:0.45 Consensus pattern (51 bp): GTGTGCCATGCTGTCTATTGGTGTGCCATGTTGTCTACTGGTGTGTCATTA Found at i:599663 original size:10 final size:11 Alignment explanation

Indices: 599437--599667 Score: 57 Period size: 10 Copynumber: 22.5 Consensus size: 11 599427 TTGCAAGCCA 599437 TGTCAATTGGTG 1 TGTC-ATTGGTG * 599449 TGTCA-TGCTG 1 TGTCATTGGTG * 599459 T-TTATTGGTG 1 TGTCATTGGTG * 599469 TGCCA-T-GT- 1 TGTCATTGGTG * 599477 TGTCTACTGGTG 1 TGTC-ATTGGTG * 599489 TGTCATTAGTG 1 TGTCATTGGTG * 599500 TGCCA-T-GT- 1 TGTCATTGGTG 599508 TGTCTATTGGTG 1 TGTC-ATTGGTG 599520 TGTCA-T-GT- 1 TGTCATTGGTG * 599528 TGTCTACTGGTG 1 TGTC-ATTGGTG 599540 TGTCA-T-GT- 1 TGTCATTGGTG * 599548 TGTCTATTAGTG 1 TGTC-ATTGGTG 599560 TGTCA-T-GT- 1 TGTCATTGGTG * * 599568 TGTCTATTTGTT 1 TGTC-ATTGGTG * 599580 TGTTA-T-GT- 1 TGTCATTGGTG 599588 TGTCTATTGGTG 1 TGTC-ATTGGTG 599600 TGTCA-T-GT- 1 TGTCATTGGTG * 599608 TGTCTATTGGCG 1 TGTC-ATTGGTG * 599620 TGTCATAT-AT- 1 TGTCAT-TGGTG 599630 TGTCAATTGGTG 1 TGTC-ATTGGTG * 599642 TGTCATT-TTG 1 TGTCATTGGTG 599652 TGTC-TTGGTG 1 TGTCATTGGTG 599662 TGTCAT 1 TGTCAT 599668 GTTGTCTATT Statistics Matches: 165, Mismatches: 18, Indels: 73 0.64 0.07 0.29 Matches are distributed among these distances: 8 25 0.15 9 25 0.15 10 41 0.25 11 38 0.23 12 36 0.22 ACGTcount: A:0.12, C:0.12, G:0.28, T:0.48 Consensus pattern (11 bp): TGTCATTGGTG Found at i:604815 original size:70 final size:70 Alignment explanation

Indices: 604702--604839 Score: 231 Period size: 70 Copynumber: 2.0 Consensus size: 70 604692 TTGATAGGTC * * * 604702 ATTCCTAGTGCATAAAGAAATATGCAAAATACTTTGAAATTGTCTTATCTTAAAAAAGCCTCTTT 1 ATTCCTAGTGCATAAAAAAATATGCAAAATACTTTGAAATTGTCTAATCTTAAAAAACCCTCTTT 604767 GATTA 66 GATTA * * 604772 ATTCCTAGTGCATAAAAAAATATGCAAAATACTTTGAAGTTGTCTAATCTTAAAATACCCTCTTT 1 ATTCCTAGTGCATAAAAAAATATGCAAAATACTTTGAAATTGTCTAATCTTAAAAAACCCTCTTT 604837 GAT 66 GAT 604840 AAAACATAAA Statistics Matches: 63, Mismatches: 5, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 70 63 1.00 ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36 Consensus pattern (70 bp): ATTCCTAGTGCATAAAAAAATATGCAAAATACTTTGAAATTGTCTAATCTTAAAAAACCCTCTTT GATTA Found at i:610092 original size:14 final size:12 Alignment explanation

Indices: 610056--610094 Score: 51 Period size: 12 Copynumber: 3.1 Consensus size: 12 610046 ATACTAGTGT * 610056 AATTATAGTATT 1 AATTATAGTATC 610068 AATTATAGTATC 1 AATTATAGTATC 610080 AATATACTAGTATC 1 AAT-TA-TAGTATC 610094 A 1 A 610095 TTTTATTGCT Statistics Matches: 24, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 12 14 0.58 13 2 0.08 14 8 0.33 ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41 Consensus pattern (12 bp): AATTATAGTATC Found at i:610796 original size:17 final size:17 Alignment explanation

Indices: 610776--610815 Score: 53 Period size: 17 Copynumber: 2.4 Consensus size: 17 610766 TTGTATTTTG 610776 TTTTTGTTTGGGTTGTT 1 TTTTTGTTTGGGTTGTT * * * 610793 TTTTTGTTTTGTTTTTT 1 TTTTTGTTTGGGTTGTT 610810 TTTTTG 1 TTTTTG 610816 GGGGGGGGGG Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 17 20 1.00 ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80 Consensus pattern (17 bp): TTTTTGTTTGGGTTGTT Found at i:623491 original size:2 final size:2 Alignment explanation

Indices: 623486--623572 Score: 174 Period size: 2 Copynumber: 43.5 Consensus size: 2 623476 GTAAAACACA 623486 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 623528 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 623570 CT C 1 CT C 623573 NNNNNNNNNN Statistics Matches: 85, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 85 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:624023 original size:2 final size:2 Alignment explanation

Indices: 624010--624081 Score: 135 Period size: 2 Copynumber: 36.0 Consensus size: 2 624000 NNNNNACTAA * 624010 CT CT CG CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 624052 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 624082 TATTTATATC Statistics Matches: 68, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 2 68 1.00 ACGTcount: A:0.00, C:0.50, G:0.01, T:0.49 Consensus pattern (2 bp): CT Found at i:631992 original size:17 final size:17 Alignment explanation

Indices: 631949--631992 Score: 56 Period size: 15 Copynumber: 2.7 Consensus size: 17 631939 TTTGCAAATT * 631949 TTTACGGTTATAACGAA 1 TTTACGGATATAACGAA * 631966 -TT-CAGATATAACGAA 1 TTTACGGATATAACGAA 631981 TTTACGGATATA 1 TTTACGGATATA 631993 GCAAACTGAT Statistics Matches: 22, Mismatches: 3, Indels: 4 0.76 0.10 0.14 Matches are distributed among these distances: 15 11 0.50 16 4 0.18 17 7 0.32 ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34 Consensus pattern (17 bp): TTTACGGATATAACGAA Found at i:638868 original size:16 final size:17 Alignment explanation

Indices: 638836--638870 Score: 54 Period size: 16 Copynumber: 2.1 Consensus size: 17 638826 TGATTTCATA 638836 TTAATTGGAGGACAAAT 1 TTAATTGGAGGACAAAT * 638853 TTAATT-GAGGAGAAAT 1 TTAATTGGAGGACAAAT 638869 TT 1 TT 638871 TTAAGGACCA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 16 11 0.65 17 6 0.35 ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34 Consensus pattern (17 bp): TTAATTGGAGGACAAAT Found at i:650221 original size:28 final size:28 Alignment explanation

Indices: 650153--650313 Score: 254 Period size: 28 Copynumber: 5.8 Consensus size: 28 650143 ATAGAACGTG * 650153 TGTGATTTTACATGATGTGATCAATGTC 1 TGTGATTTTACAGGATGTGATCAATGTC * 650181 --TGATTTTACAGGATATGATCAATGTC 1 TGTGATTTTACAGGATGTGATCAATGTC * 650207 TGTGATTTTACAGGATTTGATCAATGTC 1 TGTGATTTTACAGGATGTGATCAATGTC * * * 650235 TCTGATTTTACAGTATGTGATCAGTGTC 1 TGTGATTTTACAGGATGTGATCAATGTC 650263 TGTGATTTTACAGGATGTGATCAATGTC 1 TGTGATTTTACAGGATGTGATCAATGTC 650291 TGTGATTTTACAGGATGTGATCA 1 TGTGATTTTACAGGATGTGATCA 650314 GCTATGGCTG Statistics Matches: 121, Mismatches: 10, Indels: 4 0.90 0.07 0.03 Matches are distributed among these distances: 26 24 0.20 28 97 0.80 ACGTcount: A:0.25, C:0.11, G:0.22, T:0.41 Consensus pattern (28 bp): TGTGATTTTACAGGATGTGATCAATGTC Found at i:655061 original size:1 final size:1 Alignment explanation

Indices: 655057--655088 Score: 55 Period size: 1 Copynumber: 32.0 Consensus size: 1 655047 NNNNNGCGTC * 655057 GGGGGGCGGGGGGGGGGGGGGGGGGGGGGGGG 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 655089 TAGGACCTAG Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 1 29 1.00 ACGTcount: A:0.00, C:0.03, G:0.97, T:0.00 Consensus pattern (1 bp): G Found at i:657551 original size:42 final size:40 Alignment explanation

Indices: 657457--657573 Score: 156 Period size: 42 Copynumber: 3.0 Consensus size: 40 657447 GTATGAGGTC 657457 TACATGTTTACTAGTGGCTCCCCT-GGTATGTGG-T-T--G 1 TACATGTTTACTAGTGGCT-CCCTAGGTATGTGGTTGTACG 657493 TACATGTTTACTAGTGGCTCCCTAGGTATGTGGTTGTACCGG 1 TACATGTTTACTAGTGGCTCCCTAGGTATGTGGTTGTA-C-G 657535 TACATGTTTACTAGTGGCTCCAC-AGGTATGTGGTTGTAC 1 TACATGTTTACTAGTGGCTCC-CTAGGTATGTGGTTGTAC 657574 ATGTTAACCA Statistics Matches: 73, Mismatches: 0, Indels: 11 0.87 0.00 0.13 Matches are distributed among these distances: 35 4 0.05 36 28 0.38 37 1 0.01 38 1 0.01 41 1 0.01 42 37 0.51 43 1 0.01 ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37 Consensus pattern (40 bp): TACATGTTTACTAGTGGCTCCCTAGGTATGTGGTTGTACG Found at i:657592 original size:36 final size:36 Alignment explanation

Indices: 657444--657593 Score: 169 Period size: 36 Copynumber: 4.0 Consensus size: 36 657434 GCTGGTGGCC * * * 657444 CAGGTATGAGG-TCTACATGTTTACTAGTGGCTCCC 1 CAGGTATGTGGTTGTACATGTTTACTAGTGGCTCCA * 657479 CTGGTATGTGGTTGTACATGTTTACTAGTGGCTCC- 1 CAGGTATGTGGTTGTACATGTTTACTAGTGGCTCCA 657514 CTAGGTATGTGGTTGTACCGGTACATGTTTACTAGTGGCTCCA 1 C-AGGTATGTGG-T-T----GTACATGTTTACTAGTGGCTCCA * * 657557 CAGGTATGTGGTTGTACATGTTAACCAGTGGCTCCA 1 CAGGTATGTGGTTGTACATGTTTACTAGTGGCTCCA 657593 C 1 C 657594 TGTCCATGTG Statistics Matches: 100, Mismatches: 6, Indels: 17 0.81 0.05 0.14 Matches are distributed among these distances: 35 10 0.10 36 53 0.53 37 1 0.01 38 1 0.01 40 1 0.01 41 1 0.01 42 32 0.32 43 1 0.01 ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34 Consensus pattern (36 bp): CAGGTATGTGGTTGTACATGTTTACTAGTGGCTCCA Found at i:658429 original size:77 final size:77 Alignment explanation

Indices: 658276--658418 Score: 250 Period size: 77 Copynumber: 1.9 Consensus size: 77 658266 AGATTGAGGA * * 658276 TTGTATTGAAGTTCTCTCCAACATACTGAATCTCACATTCTCCAGGGACATGGTAAGAAACTCGC 1 TTGTATTGAAGTTCTCTCCAACATACTGAATCTCACATTCTCCAGAGACATGGTAAGAAACTCAC 658341 TTAGAAGGGGGG 66 TTAGAAGGGGGG * * 658353 TTGTATTGAAGTTCTCTCCAACATATTGAATCTCACATTCTCCAGAGACATGGTAAGAAATTCAC 1 TTGTATTGAAGTTCTCTCCAACATACTGAATCTCACATTCTCCAGAGACATGGTAAGAAACTCAC 658418 T 66 T 658419 GTGACAGGGG Statistics Matches: 62, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 77 62 1.00 ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30 Consensus pattern (77 bp): TTGTATTGAAGTTCTCTCCAACATACTGAATCTCACATTCTCCAGAGACATGGTAAGAAACTCAC TTAGAAGGGGGG Found at i:661171 original size:78 final size:79 Alignment explanation

Indices: 661040--661191 Score: 218 Period size: 78 Copynumber: 1.9 Consensus size: 79 661030 TGCCTCTGAT * * * * 661040 ATTTAACTGTTTGCCCTTGATTTTCATAGAACTCAAGAAAGCCATGAATCCGATCTTCTTTGACA 1 ATTTAAATGTGTGCCCTTGATTTTCACAGAACTCAAGAAAGCCACGAATCCGATCTTCTTTGACA 661105 TGATGGTGTCTAAC 66 TGATGGTGTCTAAC * * * 661119 ATTTAAATGTGTGCCCTTTATTTT-ACAGAACTTAGGAAAGCCACG-ATCCCGATCTTCTTTGAC 1 ATTTAAATGTGTGCCCTTGATTTTCACAGAACTCAAGAAAGCCACGAAT-CCGATCTTCTTTGAC 661182 ATGATGGTGT 65 ATGATGGTGT 661192 GCGAATTCAT Statistics Matches: 65, Mismatches: 7, Indels: 3 0.87 0.09 0.04 Matches are distributed among these distances: 77 2 0.03 78 42 0.65 79 21 0.32 ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36 Consensus pattern (79 bp): ATTTAAATGTGTGCCCTTGATTTTCACAGAACTCAAGAAAGCCACGAATCCGATCTTCTTTGACA TGATGGTGTCTAAC Found at i:670370 original size:44 final size:44 Alignment explanation

Indices: 670304--670570 Score: 489 Period size: 44 Copynumber: 6.1 Consensus size: 44 670294 CAGTGTATTT 670304 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA 1 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA * * 670348 TGTTTAGTTAATTTTTATGTCTCAGTGGTGTGAATTGCCTTGAA 1 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA * 670392 TGTTTAGTTAATCTTTACGTCTCAGTGGTATGAATTGCCTTGAA 1 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA * * 670436 TGTTTAGTTAATTTTTATGTCTCAGTGGTGTGAATTGCCTTGAA 1 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA 670480 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA 1 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA 670524 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA 1 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA 670568 TGT 1 TGT 670571 AGTGCTGTCA Statistics Matches: 213, Mismatches: 10, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 44 213 1.00 ACGTcount: A:0.21, C:0.12, G:0.22, T:0.45 Consensus pattern (44 bp): TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA Found at i:672372 original size:12 final size:12 Alignment explanation

Indices: 672355--672383 Score: 58 Period size: 12 Copynumber: 2.4 Consensus size: 12 672345 TGCTGAGATG 672355 TGTGTATTGGAT 1 TGTGTATTGGAT 672367 TGTGTATTGGAT 1 TGTGTATTGGAT 672379 TGTGT 1 TGTGT 672384 TTGCTTTAGT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 17 1.00 ACGTcount: A:0.14, C:0.00, G:0.34, T:0.52 Consensus pattern (12 bp): TGTGTATTGGAT Found at i:674348 original size:2 final size:2 Alignment explanation

Indices: 674343--674388 Score: 92 Period size: 2 Copynumber: 23.0 Consensus size: 2 674333 GAGAGTGTGT 674343 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 674385 GA GA 1 GA GA 674389 ACAGCTGTTG Statistics Matches: 44, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 44 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:677824 original size:2 final size:2 Alignment explanation

Indices: 677817--677863 Score: 94 Period size: 2 Copynumber: 23.5 Consensus size: 2 677807 TATATCAATG 677817 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 677859 GA GA G 1 GA GA G 677864 TTTTTAATAT Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 45 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:681555 original size:2 final size:2 Alignment explanation

Indices: 681548--681582 Score: 70 Period size: 2 Copynumber: 17.5 Consensus size: 2 681538 TAATCACAAA 681548 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 681583 GACATTTATA Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 33 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:684740 original size:20 final size:20 Alignment explanation

Indices: 684723--684760 Score: 58 Period size: 20 Copynumber: 1.9 Consensus size: 20 684713 ATGTAATACA * 684723 ATATCATATTATACAATAAT 1 ATATCATATGATACAATAAT * 684743 ATCTCATATGATACAATA 1 ATATCATATGATACAATA 684761 TACAAGTAAT Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 16 1.00 ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37 Consensus pattern (20 bp): ATATCATATGATACAATAAT Found at i:684757 original size:35 final size:35 Alignment explanation

Indices: 684679--684761 Score: 94 Period size: 35 Copynumber: 2.4 Consensus size: 35 684669 TTGAATATCG * * * * 684679 TATGATACATTATCATGGGATACAATAATATGTTA 1 TATGATACAATATCATAGGATACAATAATATCTCA * * ** 684714 TGTAATACAATATCATATTATACAATAATATCTCA 1 TATGATACAATATCATAGGATACAATAATATCTCA 684749 TATGATACAATAT 1 TATGATACAATAT 684762 ACAAGTAATA Statistics Matches: 38, Mismatches: 10, Indels: 0 0.79 0.21 0.00 Matches are distributed among these distances: 35 38 1.00 ACGTcount: A:0.43, C:0.11, G:0.08, T:0.37 Consensus pattern (35 bp): TATGATACAATATCATAGGATACAATAATATCTCA Found at i:688549 original size:104 final size:104 Alignment explanation

Indices: 688436--688891 Score: 765 Period size: 104 Copynumber: 4.4 Consensus size: 104 688426 GCAGGTGACT * 688436 TGTATAATACTTTTGAATTCATTAATTTCAAA-TGAATCACATTTGATAACTGTGATATTGCCTA 1 TGTATAATACTTTTGAATTCATTAATTT-AAATTGAATCACATTTGATAACTGTGATATTGCCCA 688500 TCTGTGATTTGTTGCATATTTTACAAATGCAAATATTACA 65 TCTGTGATTTGTTGCATATTTTACAAATGCAAATATTACA 688540 TGTATAATACTTTTGAATTCATTAATTTAAATTGAATCACATTTGATAACTGTGATATTGCCCAT 1 TGTATAATACTTTTGAATTCATTAATTTAAATTGAATCACATTTGATAACTGTGATATTGCCCAT * 688605 CTGTGATTTGTTGCATATTTTACAAATGTAAATATTACA 66 CTGTGATTTGTTGCATATTTTACAAATGCAAATATTACA 688644 TGTATAATACTTTTGAATTCATTAATTTAAATTGAATCACATTTGATAACTGTGATATTGCCCAT 1 TGTATAATACTTTTGAATTCATTAATTTAAATTGAATCACATTTGATAACTGTGATATTGCCCAT * 688709 CTGTGATTTGTTGCATATTTTACAAATGTAAATATTACA 66 CTGTGATTTGTTGCATATTTTACAAATGCAAATATTACA * * * * * 688748 TGTATAATACTTTTGAATTCATTAATTTCAATTGAATAACATGTGATAACTGTGGTATTGCCTAT 1 TGTATAATACTTTTGAATTCATTAATTTAAATTGAATCACATTTGATAACTGTGATATTGCCCAT * 688813 CTGTGATTTGTTGCATATTTTACAAATGCAAGTA--ACA 66 CTGTGATTTGTTGCATATTTTACAAATGCAAATATTACA * * * * 688850 TGTAAAATTCTTTTGAATTCATTAAATTAAATTTAATCACAT 1 TGTATAATACTTTTGAATTCATTAATTTAAATTGAATCACAT 688892 GTACTGACTG Statistics Matches: 336, Mismatches: 15, Indels: 4 0.95 0.04 0.01 Matches are distributed among these distances: 102 39 0.12 103 3 0.01 104 294 0.88 ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43 Consensus pattern (104 bp): TGTATAATACTTTTGAATTCATTAATTTAAATTGAATCACATTTGATAACTGTGATATTGCCCAT CTGTGATTTGTTGCATATTTTACAAATGCAAATATTACA Found at i:690111 original size:78 final size:79 Alignment explanation

Indices: 689878--690119 Score: 378 Period size: 79 Copynumber: 3.1 Consensus size: 79 689868 TTCTGATTAT 689878 ATGGACTTTAAAATTGAGCATATTTGGTTTTCTGAAAATATTTTACTCGTATGATGTCACAGTAA 1 ATGGACTTTAAAATTGAGCATATTTGGTTTTCTGAAAATATTTTACTCGTATGATGTCACAGTAA * 689943 ATTTTACCTCCTGA 66 ATTTAACCTCCTGA * * * * * 689957 ATGGACTTTAAAATTGAGCATATTTGTTTTTCTGAAAATATTTTACTTGTATTATGTCACAATAT 1 ATGGACTTTAAAATTGAGCATATTTGGTTTTCTGAAAATATTTTACTCGTATGATGTCACAGTAA * 690022 ATTTAAACTCCTGA 66 ATTTAACCTCCTGA * * 690036 ATGGACTTTAAAATTGAGC-TGTTTGGTTTTCTGGAAATATTTTACTCGTATGATGTCACAGTAA 1 ATGGACTTTAAAATTGAGCATATTTGGTTTTCTGAAAATATTTTACTCGTATGATGTCACAGTAA * * 690100 ACTTAACCTCCTAA 66 ATTTAACCTCCTGA 690114 ATGGAC 1 ATGGAC 690120 GGTTTTGAAA Statistics Matches: 146, Mismatches: 17, Indels: 1 0.89 0.10 0.01 Matches are distributed among these distances: 78 55 0.38 79 91 0.62 ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40 Consensus pattern (79 bp): ATGGACTTTAAAATTGAGCATATTTGGTTTTCTGAAAATATTTTACTCGTATGATGTCACAGTAA ATTTAACCTCCTGA Found at i:693423 original size:1 final size:1 Alignment explanation

Indices: 693417--693450 Score: 68 Period size: 1 Copynumber: 34.0 Consensus size: 1 693407 GCGGGTGGGT 693417 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 693451 TTCATGTATA Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 33 1.00 ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00 Consensus pattern (1 bp): G Found at i:698087 original size:2 final size:2 Alignment explanation

Indices: 698080--698104 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 698070 GTAAATAGAT 698080 GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA G 698105 TGTGTGTTTT Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): GA Found at i:708849 original size:25 final size:25 Alignment explanation

Indices: 708821--708870 Score: 91 Period size: 25 Copynumber: 2.0 Consensus size: 25 708811 ATTAATTTTG 708821 TCTTCAGCCTTAGGCAATTCAATCA 1 TCTTCAGCCTTAGGCAATTCAATCA * 708846 TCTTTAGCCTTAGGCAATTCAATCA 1 TCTTCAGCCTTAGGCAATTCAATCA 708871 AATTTTACTG Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 25 24 1.00 ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34 Consensus pattern (25 bp): TCTTCAGCCTTAGGCAATTCAATCA Found at i:722352 original size:1 final size:1 Alignment explanation

Indices: 722346--722387 Score: 75 Period size: 1 Copynumber: 42.0 Consensus size: 1 722336 TTTTAGTGCT * 722346 CCCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 722388 TTTTATTGAA Statistics Matches: 39, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 1 39 1.00 ACGTcount: A:0.00, C:0.98, G:0.00, T:0.00 Consensus pattern (1 bp): C Found at i:725746 original size:6 final size:6 Alignment explanation

Indices: 725735--725772 Score: 60 Period size: 6 Copynumber: 6.3 Consensus size: 6 725725 TGCTATACCC 725735 TCGGCG TCGGCGG T-GGCG TCGGCG TCGGCG TCGGCG TC 1 TCGGCG TCGGC-G TCGGCG TCGGCG TCGGCG TCGGCG TC 725773 CGGACCTGGT Statistics Matches: 30, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 5 2 0.07 6 26 0.87 7 2 0.07 ACGTcount: A:0.00, C:0.32, G:0.50, T:0.18 Consensus pattern (6 bp): TCGGCG Found at i:726119 original size:19 final size:19 Alignment explanation

Indices: 726097--726136 Score: 62 Period size: 19 Copynumber: 2.1 Consensus size: 19 726087 TTTCGGATGC * * 726097 TGGAGGAGGTTAAGGTTTT 1 TGGAGCAGGTTAAAGTTTT 726116 TGGAGCAGGTTAAAGTTTT 1 TGGAGCAGGTTAAAGTTTT 726135 TG 1 TG 726137 TTGCGGGTGC Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.23, C:0.03, G:0.38, T:0.38 Consensus pattern (19 bp): TGGAGCAGGTTAAAGTTTT Found at i:726127 original size:177 final size:177 Alignment explanation

Indices: 725818--726603 Score: 910 Period size: 177 Copynumber: 4.4 Consensus size: 177 725808 TCTAAGCTAT * * * * * * * * 725818 TACTTGTCCTATCTTCACCAAACTTGCATGGATGATGCATC-T-GGACCTACTTATGGACTTGA- 1 TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGA--TACTGATGCACCTGAC * * * * * * 725880 AAGACTTGGATGCTGAATCTGGGTCCTA-A-ATTTCAGATGCTGGAGGAGGTTAAGGTTGTTGGA 64 AAG-CTTGAATGCTGAATCTGAG--CTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGA * * 725943 CCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAGTATCTTAGTTAC 126 GCAGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGATAGCAGTATCTTAGTTAC * * * * * * 725995 TGCTGGT-CTGTACTTCACCAAACTTGCATGGATGGTGTGCCTTATGATACTGATGCTCCAGACA 1 TACTGGTCCT-AACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACA * * * 726059 GGCTTGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAG 65 AGCTTGAATGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAG * * * 726124 GTTAAAGTTTTTGTTGCGGGTGCCCAT-TGATAGCAATATCTAAGTTAC 130 GTTAAAGTTTTTGTTGCAGGTGCCC-TCTGATAGCAGTATCTTAGTTAC * * 726172 TACTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGAAAA 1 TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA * * 726237 GCTTGAATGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTTAGAGCTGG 66 GCTTGAATGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGG ** 726302 TT-AAGTTTTTGTTGCAGGTGCCCTCTGATGATTA-TATCTTAGTTAC 131 TTAAAGTTTTTGTTGCAGGTGCCCTCTGAT-AGCAGTATCTTAGTTAC * * * 726348 TATTGGTCCTAACTTCACCAAACATGTATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA 1 TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA * * * * 726413 GCTTGAATGCTGAATCTGAGCAATAGGTTTCTGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGG 66 GCTTGAATGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGG *** * 726478 TTAGATAAAGTTTTTGAAACAGGTGCCCTCTGAT-G-ATGATATCTTAGTTAT 131 -T---TAAAGTTTTTGTTGCAGGTGCCCTCTGATAGCA-G-TATCTTAGTTAC * * * * * * 726529 TACTTGTCCTTACTTCACCAGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCTGACAG 1 TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA 726594 GCTTGAATGC 66 GCTTGAATGC 726604 ATAGTCTGGT Statistics Matches: 528, Mismatches: 63, Indels: 32 0.85 0.10 0.05 Matches are distributed among these distances: 175 4 0.01 176 161 0.30 177 252 0.48 178 7 0.01 179 2 0.00 180 1 0.00 181 101 0.19 ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34 Consensus pattern (177 bp): TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA GCTTGAATGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGG TTAAAGTTTTTGTTGCAGGTGCCCTCTGATAGCAGTATCTTAGTTAC Found at i:726453 original size:353 final size:354 Alignment explanation

Indices: 725806--726603 Score: 943 Period size: 353 Copynumber: 2.2 Consensus size: 354 725796 GCATGTCCTG * * * * * 725806 TATCTAAGCTATTACTTGTCCTATCTTCACCAAACTTGCATGGATGATGCATC-T-GGACCTACT 1 TATCTAAGTTATTACTTGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGA--TACT * * * * * * 725869 TATGGACTTG-AAAGACTTGGATGCTGAATCTGGGTCCTAAATTTCAGATGCTGGAGGAGGTTAA 64 GATGCACCTGAAAAG-CTTGAATGCTGAATCTGAG-CCTAAATTTCAGATGCTGGAAGAGGTTAA * * * 725933 GGTTGTTGGACCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAGTATCTTAGTTACTGC 127 GGTTGTTAGACCAGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGATAGCAGTATCTTAGTTACTAC * * * * * 725998 TGGTCTGTACTTCACCAAACTTGCATGGATGGTGTGCCTTATGATACTGATGCTCCAGACAGGCT 192 TGGTCTGAACTTCACCAAACATGCATGGATGGTGCGCCTTATGATACTGATGCACCAGACAAGCT * * ** 726063 TGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGG-T- 257 TGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCAGGTTA *** * 726126 TAAAGTTTTTGTTGCGGGTGCCCAT-TGAT-AGCAA 322 TAAAGTTTTTGAAACAGGTGCCC-TCTGATGAG--A * * * 726160 TATCTAAGTTACTACTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGA 1 TATCTAAGTTATTACTTGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGA * * 726225 TGCACCTGAAAAGCTTGAATGCTGAATCTGAG-CTATAGGTTTCGGATGCTGGAAGAGGTTAAGG 66 TGCACCTGAAAAGCTTGAATGCTGAATCTGAGCCTA-A-ATTTCAGATGCTGGAAGAGGTTAAGG * * * ** * 726289 TTTTTAGAGCTGGTT-AAGTTTTTGTTGCAGGTGCCCTCTGATGATTA-TATCTTAGTTACTATT 129 TTGTTAGACCAGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGAT-AGCAGTATCTTAGTTACTACT * * * 726352 GGTCCT-AACTTCACCAAACATGTATGGATGGTGCGTCTTATGATACTGATGCACCTGACAAGCT 193 GGT-CTGAACTTCACCAAACATGCATGGATGGTGCGCCTTATGATACTGATGCACCAGACAAGCT * * 726416 TGAATGCTGAATCTGAGCAATAGGTTTCTGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTTA 257 TGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCAGGTT- 726481 GATAAAGTTTTTGAAACAGGTGCCCTCTGATGATGA 321 -ATAAAGTTTTTGAAACAGGTGCCCTCTGATGA-GA * * * * * 726517 TATCTTAGTTATTACTTGTCCTTACTTCACCAGACTTCCATGGATGGTGTGTCTTATGATACTGA 1 TATCTAAGTTATTACTTGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGA * * 726582 TGCACCTGACAGGCTTGAATGC 66 TGCACCTGAAAAGCTTGAATGC 726604 ATAGTCTGGT Statistics Matches: 377, Mismatches: 53, Indels: 25 0.83 0.12 0.05 Matches are distributed among these distances: 352 3 0.01 353 150 0.40 354 113 0.30 355 5 0.01 356 3 0.01 357 101 0.27 358 1 0.00 359 1 0.00 ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34 Consensus pattern (354 bp): TATCTAAGTTATTACTTGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGA TGCACCTGAAAAGCTTGAATGCTGAATCTGAGCCTAAATTTCAGATGCTGGAAGAGGTTAAGGTT GTTAGACCAGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGATAGCAGTATCTTAGTTACTACTGGT CTGAACTTCACCAAACATGCATGGATGGTGCGCCTTATGATACTGATGCACCAGACAAGCTTGAA TGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCAGGTTATAAA GTTTTTGAAACAGGTGCCCTCTGATGAGA Found at i:727291 original size:20 final size:20 Alignment explanation

Indices: 727268--727310 Score: 68 Period size: 20 Copynumber: 2.1 Consensus size: 20 727258 TATGATAAAG 727268 TATTGTATGATATGAAACAA 1 TATTGTATGATATGAAACAA * * 727288 TATTGTTTGATATGATACAA 1 TATTGTATGATATGAAACAA 727308 TAT 1 TAT 727311 GATATCATAT Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42 Consensus pattern (20 bp): TATTGTATGATATGAAACAA Found at i:727582 original size:15 final size:15 Alignment explanation

Indices: 727549--727695 Score: 73 Period size: 15 Copynumber: 9.3 Consensus size: 15 727539 ATATTCTATA * ** 727549 ATATTGTATCATACA 1 ATATTGTATAATATG 727564 ATATTGTATAATATG 1 ATATTGTATAATATG 727579 ATATTGATTTCAGTAATATAG 1 ATATTG---T-A-TAATAT-G * * * 727600 A-ATTATATCACATG 1 ATATTGTATAATATG * * 727614 AAATTGTATTATATG 1 ATATTGTATAATATG * 727629 ATATTGTAATATTATATA 1 ATATTGT-ATA--ATATG * * 727647 ATATTGTATCATACG 1 ATATTGTATAATATG * 727662 ATATTGTATGATATG 1 ATATTGTATAATATG * 727677 ATATTGGT-TTATATG 1 ATATT-GTATAATATG 727692 ATAT 1 ATAT 727696 ATTATCATAT Statistics Matches: 103, Mismatches: 18, Indels: 22 0.72 0.13 0.15 Matches are distributed among these distances: 14 2 0.02 15 69 0.67 16 5 0.05 17 3 0.03 18 12 0.12 19 1 0.01 20 9 0.09 21 2 0.02 ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45 Consensus pattern (15 bp): ATATTGTATAATATG Found at i:727628 original size:50 final size:46 Alignment explanation

Indices: 727566--727733 Score: 156 Period size: 50 Copynumber: 3.4 Consensus size: 46 727556 ATCATACAAT * 727566 ATTGTATAATATGATATTGATTTCAGTAATATAGAATTATATCACATGAA 1 ATTGTATTATATGATATTG-TTT-A-TAATATA-AATTATATCACATGAA * * * * * * 727616 ATTGTATTATATGATATTGTAATATTATATAATATTGTATCATACGAT 1 ATTGTATTATATGATATTGT-TTATAATATAA-ATTATATCACATGAA * * * 727664 ATTGTATGATATGATATTGGTTTATATGATATATTATCATATCACATGAA 1 ATTGTATTATATGATATT-GTTTATA--ATATA-AATTATATCACATGAA 727714 ATTGTATTATATGATATTGT 1 ATTGTATTATATGATATTGT 727734 AATATATTTT Statistics Matches: 95, Mismatches: 17, Indels: 13 0.76 0.14 0.10 Matches are distributed among these distances: 47 1 0.01 48 37 0.39 49 6 0.06 50 51 0.54 ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45 Consensus pattern (46 bp): ATTGTATTATATGATATTGTTTATAATATAAATTATATCACATGAA Found at i:727643 original size:18 final size:18 Alignment explanation

Indices: 727620--727654 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 727610 CATGAAATTG * 727620 TATTATATGATATTGTAA 1 TATTATATAATATTGTAA 727638 TATTATATAATATTGTA 1 TATTATATAATATTGTA 727655 TCATACGATA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51 Consensus pattern (18 bp): TATTATATAATATTGTAA Found at i:727659 original size:98 final size:97 Alignment explanation

Indices: 727532--727738 Score: 310 Period size: 98 Copynumber: 2.1 Consensus size: 97 727522 CTATGATACA * 727532 ATATTGT-ATATTCTATAATATTGTATCATACAATATTGTATAATATGATATTGATTTCAGTA-A 1 ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGATTT-A-TAGA * 727595 TATAGAATTATATCACATGAAATTGTATTATATG 64 TATAGAATCATATCACATGAAATTGTATTATATG * * * 727629 ATATTGTAATATTATATAATATTGTATCATACGATATTGTATGATATGATATTGGTTTATATGAT 1 ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGATTTATA-GAT ** 727694 ATATTATCATATCACATGAAATTGTATTATATG 65 ATAGAATCATATCACATGAAATTGTATTATATG 727727 ATATTGTAATAT 1 ATATTGTAATAT 727739 ATTTTATTGT Statistics Matches: 100, Mismatches: 7, Indels: 5 0.89 0.06 0.04 Matches are distributed among these distances: 96 2 0.02 97 8 0.08 98 90 0.90 ACGTcount: A:0.38, C:0.05, G:0.11, T:0.45 Consensus pattern (97 bp): ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGATTTATAGATA TAGAATCATATCACATGAAATTGTATTATATG Found at i:727732 original size:15 final size:15 Alignment explanation

Indices: 727611--727740 Score: 93 Period size: 15 Copynumber: 8.1 Consensus size: 15 727601 ATTATATCAC * 727611 ATGAAATTGTATTAT 1 ATGATATTGTATTAT 727626 ATGATATTGTAATATTAT 1 ATGATATTG---TATTAT * * 727644 ATAATATTGTATCAT 1 ATGATATTGTATTAT * * 727659 ACGATATTGTATGAT 1 ATGATATTGTATTAT 727674 ATGATATTGGT-TTAT 1 ATGATATT-GTATTAT 727689 ATGATATAT-TATCATAT 1 ATGATAT-TGTAT--TAT * 727706 CACATGAAATTGTATTAT 1 ---ATGATATTGTATTAT * 727724 ATGATATTGTAATAT 1 ATGATATTGTATTAT 727739 AT 1 AT 727741 TTTATTGTGT Statistics Matches: 92, Mismatches: 11, Indels: 24 0.72 0.09 0.19 Matches are distributed among these distances: 14 1 0.01 15 58 0.63 16 3 0.03 17 3 0.03 18 17 0.18 19 1 0.01 20 9 0.10 ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46 Consensus pattern (15 bp): ATGATATTGTATTAT Found at i:727754 original size:50 final size:50 Alignment explanation

Indices: 727604--727755 Score: 156 Period size: 50 Copynumber: 3.1 Consensus size: 50 727594 ATATAGAATT * 727604 ATATCACATGAAATTGTATTATATGATATTGTAATATTATATAATATTGT- 1 ATATCACATGAAATTGTATTATATGATATTGTAATA-TATATTATATTGTC * * * * 727654 ATCAT-AC--GATATTGTATGATATGATATTGGT-TTATATGA-TATATTATC 1 AT-ATCACATGAAATTGTATTATATGATATT-GTAATATAT-ATTATATTGTC * 727702 ATATCACATGAAATTGTATTATATGATATTGTAATATATTTTAT-TGTGTC 1 ATATCACATGAAATTGTATTATATGATATTGTAATATATATTATAT-TGTC 727752 ATAT 1 ATAT 727756 GATGCAATAT Statistics Matches: 82, Mismatches: 10, Indels: 20 0.73 0.09 0.18 Matches are distributed among these distances: 47 11 0.13 48 26 0.32 49 5 0.06 50 38 0.46 51 2 0.02 ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47 Consensus pattern (50 bp): ATATCACATGAAATTGTATTATATGATATTGTAATATATATTATATTGTC Done.