Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold173

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 2040036
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


File 8 of 16

Found at i:983735 original size:21 final size:21

Alignment explanation

Indices: 983709--983772 Score: 76 Period size: 21 Copynumber: 3.1 Consensus size: 21 983699 ATCATATCAC 983709 ATCAAAAGTTATTAAAATTAT 1 ATCAAAAGTTATTAAAATTAT * * 983730 ATCAAAAGTTA-TAAACTTAA 1 ATCAAAAGTTATTAAAATTAT * * * 983750 AACAAAAGTTTTTAAGATTAT 1 ATCAAAAGTTATTAAAATTAT 983771 AT 1 AT 983773 TAATGAAAAA Statistics Matches: 34, Mismatches: 8, Indels: 2 0.77 0.18 0.05 Matches are distributed among these distances: 20 16 0.47 21 18 0.53 ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36 Consensus pattern (21 bp): ATCAAAAGTTATTAAAATTAT Found at i:983755 original size:20 final size:21 Alignment explanation

Indices: 983711--983769 Score: 66 Period size: 20 Copynumber: 2.9 Consensus size: 21 983701 CATATCACAT * * 983711 CAAAAGTTATTAAAATTATAT 1 CAAAAGTTATTAAAATTAAAA * 983732 CAAAAGTTA-TAAACTTAAAA 1 CAAAAGTTATTAAAATTAAAA * * 983752 CAAAAGTTTTTAAGATTA 1 CAAAAGTTATTAAAATTA 983770 TATTAATGAA Statistics Matches: 31, Mismatches: 6, Indels: 2 0.79 0.15 0.05 Matches are distributed among these distances: 20 16 0.52 21 15 0.48 ACGTcount: A:0.53, C:0.07, G:0.07, T:0.34 Consensus pattern (21 bp): CAAAAGTTATTAAAATTAAAA Found at i:988060 original size:28 final size:32 Alignment explanation

Indices: 988001--988060 Score: 83 Period size: 32 Copynumber: 2.0 Consensus size: 32 987991 TTTGACAATT * 988001 TGTAATTATCATTATTTTAGTGTAATAAAGTA 1 TGTAATTATCATTATTGTAGTGTAATAAAGTA 988033 TGTAATTATCA-T-TTGTA-TGT-ATAAAGTA 1 TGTAATTATCATTATTGTAGTGTAATAAAGTA 988061 ATTTTATACT Statistics Matches: 27, Mismatches: 1, Indels: 4 0.84 0.03 0.12 Matches are distributed among these distances: 28 8 0.30 29 3 0.11 30 4 0.15 31 1 0.04 32 11 0.41 ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47 Consensus pattern (32 bp): TGTAATTATCATTATTGTAGTGTAATAAAGTA Found at i:990569 original size:16 final size:16 Alignment explanation

Indices: 990548--990581 Score: 59 Period size: 16 Copynumber: 2.1 Consensus size: 16 990538 TGTTCAGTAT 990548 ATTAAAAAAATTAAAA 1 ATTAAAAAAATTAAAA * 990564 ATTAAAAATATTAAAA 1 ATTAAAAAAATTAAAA 990580 AT 1 AT 990582 GTATTAATTT Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29 Consensus pattern (16 bp): ATTAAAAAAATTAAAA Found at i:991162 original size:20 final size:20 Alignment explanation

Indices: 991122--991175 Score: 63 Period size: 20 Copynumber: 2.6 Consensus size: 20 991112 TCACGATAGC * * 991122 ATAAATATTATTTTATTAAAA 1 ATAATTATTAATTT-TTAAAA * * 991143 ATATTTTTTAATTTTTAAAA 1 ATAATTATTAATTTTTAAAA 991163 ATAATTATTAATT 1 ATAATTATTAATT 991176 ATTTTTAATT Statistics Matches: 27, Mismatches: 6, Indels: 1 0.79 0.18 0.03 Matches are distributed among these distances: 20 17 0.63 21 10 0.37 ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54 Consensus pattern (20 bp): ATAATTATTAATTTTTAAAA Found at i:992499 original size:2 final size:2 Alignment explanation

Indices: 992492--992527 Score: 72 Period size: 2 Copynumber: 18.0 Consensus size: 2 992482 GAGTTATTGT 992492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 992528 AACATGGAAG Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:992823 original size:21 final size:21 Alignment explanation

Indices: 992796--992873 Score: 74 Period size: 20 Copynumber: 3.7 Consensus size: 21 992786 TTGTGTTTTT 992796 TTATAAAATTA-TATCAACTA 1 TTATAAAATTATTATCAACTA * 992816 TTA-ATAAATTATTAT-AAATA 1 TTATA-AAATTATTATCAACTA 992836 TTATCAAAATTATTATCAAGCTA 1 TTAT-AAAATTATTATCAA-CTA 992859 -TATAAATAATTATTA 1 TTAT-AA-AATTATTA 992874 AAACTACTTC Statistics Matches: 48, Mismatches: 3, Indels: 11 0.77 0.05 0.18 Matches are distributed among these distances: 19 1 0.02 20 16 0.33 21 13 0.27 22 8 0.17 23 10 0.21 ACGTcount: A:0.50, C:0.06, G:0.01, T:0.42 Consensus pattern (21 bp): TTATAAAATTATTATCAACTA Found at i:992886 original size:31 final size:31 Alignment explanation

Indices: 992828--992886 Score: 75 Period size: 31 Copynumber: 1.9 Consensus size: 31 992818 AATAAATTAT * * 992828 TATAAATATTATCAAAATTATTATCAAGCTA 1 TATAAATATTATCAAAACTACTATCAAGCTA * 992859 TATAAATAATTATTAAAACTACT-TCAAG 1 TATAAAT-ATTATCAAAACTACTATCAAG 992887 TGTTACTTAA Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 31 12 0.50 32 12 0.50 ACGTcount: A:0.49, C:0.10, G:0.03, T:0.37 Consensus pattern (31 bp): TATAAATATTATCAAAACTACTATCAAGCTA Found at i:993011 original size:21 final size:21 Alignment explanation

Indices: 992987--993092 Score: 77 Period size: 21 Copynumber: 5.4 Consensus size: 21 992977 AAGTCACATT 992987 AAAGATTATCAAAATTATATC 1 AAAGATTATCAAAATTATATC * * 993008 AAAGCTTACCAAAATTATATC 1 AAAGATTATCAAAATTATATC * * 993029 AAATATTAT--AAA-GATATC 1 AAAGATTATCAAAATTATATC * 993047 ACAA-A-TAT---TATTATATC 1 A-AAGATTATCAAAATTATATC * 993064 AAAAATTATCAAAATTATAT- 1 AAAGATTATCAAAATTATATC 993084 AAATGATTA 1 AAA-GATTA 993093 AAAAAATACT Statistics Matches: 67, Mismatches: 10, Indels: 16 0.72 0.11 0.17 Matches are distributed among these distances: 16 3 0.04 17 10 0.15 18 10 0.15 19 5 0.07 20 3 0.04 21 36 0.54 ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34 Consensus pattern (21 bp): AAAGATTATCAAAATTATATC Found at i:993172 original size:21 final size:20 Alignment explanation

Indices: 993106--993250 Score: 64 Period size: 21 Copynumber: 7.0 Consensus size: 20 993096 AAATACTAGT * * * 993106 ATTAAATTAAAAGTTATTAAA 1 ATTATATTAAAAATTA-TCAA * 993127 ATCATA-TAAAAGATTATC-A 1 ATTATATTAAAA-ATTATCAA * 993146 ACTATATTAAAAATTATCCAA 1 ATTATATTAAAAATTAT-CAA * * 993167 ATTATATCAAAAGTTATCAGA 1 ATTATATTAAAAATTATCA-A * * * 993188 ATTATTATCAAAGATTAACAAA 1 ATTA-TATTAAAAATTATC-AA * 993210 ATTATA--AAAAGGTTATCAAA 1 ATTATATTAAAA-ATTATC-AA * * * 993230 ATTAAATCAAAGATTATCAA 1 ATTATATTAAAAATTATCAA 993250 A 1 A 993251 ATGACAAACA Statistics Matches: 96, Mismatches: 18, Indels: 21 0.71 0.13 0.16 Matches are distributed among these distances: 19 13 0.14 20 29 0.30 21 34 0.35 22 19 0.20 23 1 0.01 ACGTcount: A:0.54, C:0.08, G:0.06, T:0.32 Consensus pattern (20 bp): ATTATATTAAAAATTATCAA Found at i:993194 original size:40 final size:38 Alignment explanation

Indices: 993111--993252 Score: 106 Period size: 40 Copynumber: 3.5 Consensus size: 38 993101 CTAGTATTAA * * * * 993111 ATTAAAAGTTATTAAAATCATATAAAAGATTATCAACTAT 1 ATTAAAAATTATCAAAATTATATAAAAG-TTATCAAAT-T * 993151 ATTAAAAATTATCCAAATTATATCAAAAGTTATCAGAATT 1 ATTAAAAATTATCAAAATTATAT-AAAAGTTATCA-AATT * 993191 ATTATCAAAGATTAACAAAATTATA-AAAAGGTTATCAAAATT 1 ATTA--AAA-ATTATCAAAATTATATAAAA-GTTATC-AAATT * * 993233 AAATCAAAGATTATCAAAAT 1 --ATTAAAAATTATCAAAAT 993253 GACAAACATA Statistics Matches: 83, Mismatches: 10, Indels: 17 0.75 0.09 0.15 Matches are distributed among these distances: 40 30 0.36 41 21 0.25 42 15 0.18 43 14 0.17 44 3 0.04 ACGTcount: A:0.54, C:0.08, G:0.06, T:0.32 Consensus pattern (38 bp): ATTAAAAATTATCAAAATTATATAAAAGTTATCAAATT Found at i:993239 original size:41 final size:42 Alignment explanation

Indices: 993165--993252 Score: 117 Period size: 41 Copynumber: 2.1 Consensus size: 42 993155 AAAATTATCC * * 993165 AAATTATATCAAAAGTTATCAGAATTATTATCAAAGATTAACA 1 AAATTATA-CAAAAGTTATCAAAATTATAATCAAAGATTAACA * 993208 AAATTATA-AAAAGGTTATCAAAATTA-AATCAAAGATTATCA 1 AAATTATACAAAA-GTTATCAAAATTATAATCAAAGATTAACA 993249 AAAT 1 AAAT 993253 GACAAACATA Statistics Matches: 41, Mismatches: 3, Indels: 4 0.85 0.06 0.08 Matches are distributed among these distances: 41 21 0.51 42 12 0.29 43 8 0.20 ACGTcount: A:0.55, C:0.08, G:0.07, T:0.31 Consensus pattern (42 bp): AAATTATACAAAAGTTATCAAAATTATAATCAAAGATTAACA Found at i:993251 original size:21 final size:22 Alignment explanation

Indices: 993158--993252 Score: 101 Period size: 21 Copynumber: 4.5 Consensus size: 22 993148 TATATTAAAA * 993158 ATTATCCAAATTAT-ATCAAA- 1 ATTATCAAAATTATAATCAAAG * * 993178 AGTTATCAGAATTATTATCAAAG 1 A-TTATCAAAATTATAATCAAAG * 993201 ATTAACAAAATTATAA--AAAG 1 ATTATCAAAATTATAATCAAAG * 993221 GTTATCAAAATTA-AATCAAAG 1 ATTATCAAAATTATAATCAAAG 993242 ATTATCAAAAT 1 ATTATCAAAAT 993253 GACAAACATA Statistics Matches: 62, Mismatches: 8, Indels: 9 0.78 0.10 0.11 Matches are distributed among these distances: 19 2 0.03 20 16 0.26 21 25 0.40 22 18 0.29 23 1 0.02 ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32 Consensus pattern (22 bp): ATTATCAAAATTATAATCAAAG Found at i:993312 original size:21 final size:21 Alignment explanation

Indices: 993289--993359 Score: 60 Period size: 21 Copynumber: 3.5 Consensus size: 21 993279 TCATAATTTG 993289 TTACCAAAATTATATTGAATG- 1 TTACCAAAATTATATT-AATGA * * * 993310 TTACCAAGATTA-GTTAATGC 1 TTACCAAAATTATATTAATGA * 993330 TT-TCAAAATTATATTCAA-GA 1 TTACCAAAATTATATT-AATGA 993350 TTACCAAAAT 1 TTACCAAAAT 993360 AGTTATAAAG Statistics Matches: 39, Mismatches: 7, Indels: 8 0.72 0.13 0.15 Matches are distributed among these distances: 19 11 0.28 20 9 0.23 21 19 0.49 ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37 Consensus pattern (21 bp): TTACCAAAATTATATTAATGA Found at i:993530 original size:21 final size:20 Alignment explanation

Indices: 993506--993578 Score: 65 Period size: 21 Copynumber: 3.5 Consensus size: 20 993496 CATATCAACT * 993506 ATTATTAAAATTATATAAAAA 1 ATTATCAAAATTATA-AAAAA 993527 ATTATCAAAATTATAACAAAA 1 ATTATCAAAATTATAA-AAAA * * * * 993548 TTTACCCAAATTATATCAAAA 1 ATTATCAAAATTATA-AAAAA * 993569 GTTATCAAAA 1 ATTATCAAAA 993579 CCAAAATTAT Statistics Matches: 42, Mismatches: 8, Indels: 4 0.78 0.15 0.07 Matches are distributed among these distances: 20 1 0.02 21 41 0.98 ACGTcount: A:0.56, C:0.10, G:0.01, T:0.33 Consensus pattern (20 bp): ATTATCAAAATTATAAAAAA Found at i:993642 original size:21 final size:21 Alignment explanation

Indices: 993580--994080 Score: 146 Period size: 21 Copynumber: 24.2 Consensus size: 21 993570 TTATCAAAAC * * * 993580 CAAAATTATAACAAAGGTTAA 1 CAAAATTATATCAAAGATTAT * ** 993601 CAAAATCATAGAAAACG-TTAT 1 CAAAATTATATCAAA-GATTAT * * 993622 CGAAATTATATCAAATATTAT 1 CAAAATTATATCAAAGATTAT * * 993643 -AGAAATTATATTAAAGATTAC 1 CA-AAATTATATCAAAGATTAT 993664 CAAAATTATA-CTAAAGATTAT 1 CAAAATTATATC-AAAGATTAT * * * 993685 TAAAATTATATCAAATACTAT 1 CAAAATTATATCAAAGATTAT * * * 993706 TAAAATCTAT-T-GAAGGTTA- 1 CAAAAT-TATATCAAAGATTAT * * 993725 CTAAATTATACCAAATG-TTA- 1 CAAAATTATATCAAA-GATTAT * ** 993745 CTAAAATTATATTTAAAG-TTGC 1 C-AAAATTATA-TCAAAGATTAT * * * 993767 CAAAATTATATTTAACG-TTAG 1 CAAAATTATA-TCAAAGATTAT * * * 993788 GAAAATTATAT-ATGAGGTTAT 1 CAAAATTATATCA-AAGATTAT * * * * 993809 C-AAATTCATCTTAAAAACTAT 1 CAAAATT-ATATCAAAGATTAT * * * 993830 TAAAATCATATCAAAG-TTAAC 1 CAAAATTATATCAAAGATT-AT ** * * * 993851 CGGAATCATTTCAAA-AGTTAA 1 CAAAATTATATCAAAGA-TTAT * * * 993872 C-AAATTATATCCAAGGTTGT 1 CAAAATTATATCAAAGATTAT * 993892 C-AAATTACATCAAA-AGTTAT 1 CAAAATTATATCAAAGA-TTAT * * * 993912 TAAAACTATATCAAAGACTAAT 1 CAAAATTATATCAAAGA-TTAT * * 993934 -AAAATTATATCAAAGCTTCT 1 CAAAATTATATCAAAGATTAT * * 993954 TAAAATTATAT-AAACATTAT 1 CAAAATTATATCAAAGATTAT * ** 993974 CAAAATTATATTAAA-AGTGGT 1 CAAAATTATATCAAAGA-TTAT * * * * 993995 CAAAATTAGATAAAAAATTAC 1 CAAAATTATATCAAAGATTAT * * * 994016 CAAAATTATCTTAAAGGTTAT 1 CAAAATTATATCAAAGATTAT * * 994037 C-AAATTATATCAAAAATTAC 1 CAAAATTATATCAAAGATTAT * 994057 CAAAATTATATCGAAGATTA- 1 CAAAATTATATCAAAGATTAT 994077 CAAA 1 CAAA 994081 TCAAAATTTT Statistics Matches: 351, Mismatches: 99, Indels: 61 0.69 0.19 0.12 Matches are distributed among these distances: 18 3 0.01 19 5 0.01 20 82 0.23 21 239 0.68 22 22 0.06 ACGTcount: A:0.49, C:0.11, G:0.08, T:0.33 Consensus pattern (21 bp): CAAAATTATATCAAAGATTAT Found at i:994000 original size:41 final size:42 Alignment explanation

Indices: 993955--994067 Score: 140 Period size: 41 Copynumber: 2.7 Consensus size: 42 993945 AAAGCTTCTT * * * 993955 AAAATTATAT-AAACATTATCAAAATTATATTAAAAGTGGTC 1 AAAATTATATAAAAAATTACCAAAATTATATTAAAAGTGATC * * * * 993996 AAAATTAGATAAAAAATTACCAAAATTATCTTAAAGGTTATC 1 AAAATTATATAAAAAATTACCAAAATTATATTAAAAGTGATC * 994038 -AAATTATATCAAAAATTACCAAAATTATAT 1 AAAATTATATAAAAAATTACCAAAATTATAT 994068 CGAAGATTAC Statistics Matches: 61, Mismatches: 10, Indels: 2 0.84 0.14 0.03 Matches are distributed among these distances: 41 36 0.59 42 25 0.41 ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33 Consensus pattern (42 bp): AAAATTATATAAAAAATTACCAAAATTATATTAAAAGTGATC Found at i:994121 original size:25 final size:26 Alignment explanation

Indices: 994070--994132 Score: 65 Period size: 25 Copynumber: 2.4 Consensus size: 26 994060 AATTATATCG * *** 994070 AAGATTACAAATCAAAATTTTCTTTA 1 AAGATTACAAATCAAAAATTAAATTA 994096 AAGATT-CAAATCAAAAATTAAATTA 1 AAGATTACAAATCAAAAATTAAATTA * 994121 AAGTTTAACAAA 1 AAGATT-ACAAA 994133 AATAGGTAAA Statistics Matches: 30, Mismatches: 5, Indels: 3 0.79 0.13 0.08 Matches are distributed among these distances: 25 20 0.67 26 6 0.20 27 4 0.13 ACGTcount: A:0.54, C:0.10, G:0.05, T:0.32 Consensus pattern (26 bp): AAGATTACAAATCAAAAATTAAATTA Found at i:995017 original size:15 final size:15 Alignment explanation

Indices: 994999--995049 Score: 61 Period size: 14 Copynumber: 3.5 Consensus size: 15 994989 ATTTAGTGTC * 994999 AATATTTTTACACAT 1 AATATTTTTACATAT * * 995014 AATATATATA-ATAT 1 AATATTTTTACATAT 995028 AATATTTTTACATAT 1 AATATTTTTACATAT 995043 AAT-TTTT 1 AATATTTT 995050 CTCCAAGCAA Statistics Matches: 30, Mismatches: 5, Indels: 3 0.79 0.13 0.08 Matches are distributed among these distances: 14 15 0.50 15 15 0.50 ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51 Consensus pattern (15 bp): AATATTTTTACATAT Found at i:996534 original size:20 final size:20 Alignment explanation

Indices: 996509--996553 Score: 81 Period size: 20 Copynumber: 2.2 Consensus size: 20 996499 AAATATTATT * 996509 TTATTAAAAATAATTTTTAA 1 TTATTAAAAATAATTATTAA 996529 TTATTAAAAATAATTATTAA 1 TTATTAAAAATAATTATTAA 996549 TTATT 1 TTATT 996554 TTTAATCTCT Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 20 24 1.00 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (20 bp): TTATTAAAAATAATTATTAA Found at i:997125 original size:20 final size:20 Alignment explanation

Indices: 997100--997140 Score: 73 Period size: 20 Copynumber: 2.0 Consensus size: 20 997090 AAATATTATT * 997100 TTATTAAAAATAATTTTTAA 1 TTATTAAAAATAATTATTAA 997120 TTATTAAAAATAATTATTAA 1 TTATTAAAAATAATTATTAA 997140 T 1 T 997141 CATTTTCAAT Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (20 bp): TTATTAAAAATAATTATTAA Found at i:997289 original size:294 final size:293 Alignment explanation

Indices: 996463--997358 Score: 1304 Period size: 285 Copynumber: 3.0 Consensus size: 293 996453 ACATTTGAGA * * 996463 AATATAATTTTATAATACATTCAATCACAGTAACATAAATATTATTTTATTAAAAATAATTTTTA 1 AATATAAGTTTATAATGCATTCAATCACAGTAACATAAATATTATTTTATTAAAAATAATTTTTA * * 996528 ATTATTAAAAATAATTATTAATTATTTTTAATCTCTTTAAACGTAAATTTAATAATACGTTCAAA 66 ATTATTAAAAATAATTATTAA-TA---TT--T-TC----AA--TAAATTTAATAATACATCCAAA * * * * * 996593 TGACTTAAATAGTGGTTGAAATTTTATGGTACAAGCGTGCAGTTAGTTACGTAAAGTCCACAAGA 118 TGACTTAAATAGTGATTGAAATTTTATGGTACAAGTGTGTAGTTAGCTATGTAAAGTCCACAAGA * 996658 ATGAACAATAGTTGGTGTCGACAATAAATGAATTCACACTATGATTTTATTTCTTTTGTCCAATG 183 ATGAACAATAGTTGGTGTCGATAATAAATGAATTCACACTATGATTTTATTTCTTTTGTCCAATG * 996723 TCTTCTCTTTCTTCATTCGTTTACCATGTAACTTTACATGAACTTT 248 TCTTCTCTTTCTTCATTCGTTTACCATGTAACTTAACATGAACTTT * * 996769 AATATAAGTTTATAATGCATTCAATTACAGTAACATAAATATTATTTTATTAAAAATAATTATTA 1 AATATAAGTTTATAATGCATTCAATCACAGTAACATAAATATTATTTTATTAAAAATAATTTTTA *** * * * 996834 ATTATTTTTAAT--TTTTTAA-A---T--GTAAATTTAATAATACATCCAAATCACTTAAATAGT 66 ATTATTAAAAATAATTATTAATATTTTCAATAAATTTAATAATACATCCAAATGACTTAAATAGT * * 996891 GATTGAAATTTTATGGTACAAGTATGTAGTTAGCTATGTAAAGTCCACAAGGATGAACAATAGTT 131 GATTGAAATTTTATGGTACAAGTGTGTAGTTAGCTATGTAAAGTCCACAAGAATGAACAATAGTT * * 996956 GGTGTCGATAATAAATGAATTCACACTATGATCTTATTTCTTTTGTCTAATGTCTTCTCTTTCTT 196 GGTGTCGATAATAAATGAATTCACACTATGATTTTATTTCTTTTGTCCAATGTCTTCTCTTTCTT * ** * 997021 CATTTGTTTATTATGTAACTTAAAATGAACTTT 261 CATTCGTTTACCATGTAACTTAACATGAACTTT 997054 AATATAAGTTTATAATGCATTCAATCACAGTAACATAAATATTATTTTATTAAAAATAATTTTTA 1 AATATAAGTTTATAATGCATTCAATCACAGTAACATAAATATTATTTTATTAAAAATAATTTTTA 997119 ATTATTAAAAATAATTATTAATCATTTTCAATAAATTTAATAATACATCCAAATGACTTAAATAG 66 ATTATTAAAAATAATTATTAAT-ATTTTCAATAAATTTAATAATACATCCAAATGACTTAAATAG * * * * 997184 TAATTAAAATTTTATGGTACAAGTGTGTAGTTAGCTATGTAAAGTCCGCAAGAATAAACAATAGT 130 TGATTGAAATTTTATGGTACAAGTGTGTAGTTAGCTATGTAAAGTCCACAAGAATGAACAATAGT * * * 997249 TGGTGTCGATAATAAATGAATTCACATTGTGATTTTATTTCTTTTGTCCAATGTCTTCTCTTTTT 195 TGGTGTCGATAATAAATGAATTCACACTATGATTTTATTTCTTTTGTCCAATGTCTTCTCTTTCT 997314 TCATTCGTTTACCATGTAACTTAACATGAACTTT 260 TCATTCGTTTACCATGTAACTTAACATGAACTTT 997348 AATATAAGTTT 1 AATATAAGTTT 997359 GTTTCTAATA Statistics Matches: 531, Mismatches: 50, Indels: 30 0.87 0.08 0.05 Matches are distributed among these distances: 285 252 0.47 287 6 0.01 289 1 0.00 292 1 0.00 293 1 0.00 294 193 0.36 302 1 0.00 304 6 0.01 306 70 0.13 ACGTcount: A:0.37, C:0.11, G:0.10, T:0.41 Consensus pattern (293 bp): AATATAAGTTTATAATGCATTCAATCACAGTAACATAAATATTATTTTATTAAAAATAATTTTTA ATTATTAAAAATAATTATTAATATTTTCAATAAATTTAATAATACATCCAAATGACTTAAATAGT GATTGAAATTTTATGGTACAAGTGTGTAGTTAGCTATGTAAAGTCCACAAGAATGAACAATAGTT GGTGTCGATAATAAATGAATTCACACTATGATTTTATTTCTTTTGTCCAATGTCTTCTCTTTCTT CATTCGTTTACCATGTAACTTAACATGAACTTT Found at i:998673 original size:15 final size:14 Alignment explanation

Indices: 998641--998713 Score: 59 Period size: 14 Copynumber: 5.6 Consensus size: 14 998631 TGCATATAAA * 998641 TAATATA-ATAAAT 1 TAATATATATAATT * * 998654 TAATATTATTTATTT 1 TAATA-TATATAATT 998669 TAATATATATAATT 1 TAATATATATAATT * 998683 TAATA-ATATACTT 1 TAATATATATAATT 998696 T--TATATA-AATT 1 TAATATATATAATT 998707 T-ATATAT 1 TAATATAT 998714 TACTGTTTTT Statistics Matches: 49, Mismatches: 7, Indels: 9 0.75 0.11 0.14 Matches are distributed among these distances: 11 6 0.12 12 8 0.16 13 13 0.27 14 14 0.29 15 8 0.16 ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52 Consensus pattern (14 bp): TAATATATATAATT Found at i:998756 original size:20 final size:21 Alignment explanation

Indices: 998728--998784 Score: 82 Period size: 21 Copynumber: 2.8 Consensus size: 21 998718 GTTTTTTTGT 998728 ACAAAATTA-TATTAAATATTA 1 ACAAAATTATTA-TAAATATTA 998749 AC-AAATTATTATAAATATTA 1 ACAAAATTATTATAAATATTA * 998769 TCAAAATTATTATAAA 1 ACAAAATTATTATAAA 998785 GTTACATAAA Statistics Matches: 33, Mismatches: 1, Indels: 4 0.87 0.03 0.11 Matches are distributed among these distances: 20 16 0.48 21 17 0.52 ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39 Consensus pattern (21 bp): ACAAAATTATTATAAATATTA Found at i:998877 original size:20 final size:19 Alignment explanation

Indices: 998836--998881 Score: 60 Period size: 20 Copynumber: 2.4 Consensus size: 19 998826 AAATTATATC 998836 AAAAATT-TTTAAAATTAT 1 AAAAATTATTTAAAATTAT 998854 AAAAATTATATTAAATATTA- 1 AAAAATTAT-TTAAA-ATTAT 998874 AAAAATTA 1 AAAAATTA 998882 CCAAAATTAC Statistics Matches: 25, Mismatches: 0, Indels: 4 0.86 0.00 0.14 Matches are distributed among these distances: 18 7 0.28 19 1 0.04 20 13 0.52 21 4 0.16 ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39 Consensus pattern (19 bp): AAAAATTATTTAAAATTAT Found at i:998991 original size:21 final size:21 Alignment explanation

Indices: 998967--999066 Score: 96 Period size: 20 Copynumber: 4.8 Consensus size: 21 998957 CCATGTCACA * * 998967 AAAAATTATTAAAATTGTATC 1 AAAAGTTATAAAAATTGTATC ** 998988 AAAAGTTA-AAAAATTAAATC 1 AAAAGTTATAAAAATTGTATC * 999008 AAAAGTTATCAAAATTGTATC 1 AAAAGTTATAAAAATTGTATC ** 999029 AAAAGTTA-AAAAATTAAATC 1 AAAAGTTATAAAAATTGTATC * 999049 AAAAAAGTTATCAAAATT 1 --AAAAGTTATAAAAATT 999067 ATATTAATGA Statistics Matches: 64, Mismatches: 11, Indels: 6 0.79 0.14 0.07 Matches are distributed among these distances: 20 26 0.41 21 24 0.38 22 8 0.12 23 6 0.09 ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30 Consensus pattern (21 bp): AAAAGTTATAAAAATTGTATC Found at i:999000 original size:20 final size:20 Alignment explanation

Indices: 998977--999043 Score: 98 Period size: 20 Copynumber: 3.3 Consensus size: 20 998967 AAAAATTATT 998977 AAAATTGTATCAAAAGTTAA 1 AAAATTGTATCAAAAGTTAA ** * 998997 AAAATTAAATCAAAAGTTATC 1 AAAATTGTATCAAAAGTTA-A 999018 AAAATTGTATCAAAAGTTAA 1 AAAATTGTATCAAAAGTTAA 999038 AAAATT 1 AAAATT 999044 AAATCAAAAA Statistics Matches: 40, Mismatches: 6, Indels: 2 0.83 0.12 0.04 Matches are distributed among these distances: 20 23 0.57 21 17 0.43 ACGTcount: A:0.57, C:0.06, G:0.07, T:0.30 Consensus pattern (20 bp): AAAATTGTATCAAAAGTTAA Found at i:999024 original size:41 final size:42 Alignment explanation

Indices: 998965--999066 Score: 170 Period size: 41 Copynumber: 2.4 Consensus size: 42 998955 TACCATGTCA * * 998965 CAAAAAATTATTAAAATTGTATCAAAAGTTAAAAAATTAAAT 1 CAAAAAGTTATCAAAATTGTATCAAAAGTTAAAAAATTAAAT 999007 C-AAAAGTTATCAAAATTGTATCAAAAGTTAAAAAATTAAAT 1 CAAAAAGTTATCAAAATTGTATCAAAAGTTAAAAAATTAAAT 999048 CAAAAAAGTTATCAAAATT 1 C-AAAAAGTTATCAAAATT 999067 ATATTAATGA Statistics Matches: 56, Mismatches: 2, Indels: 3 0.92 0.03 0.05 Matches are distributed among these distances: 41 39 0.70 42 1 0.02 43 16 0.29 ACGTcount: A:0.58, C:0.07, G:0.06, T:0.29 Consensus pattern (42 bp): CAAAAAGTTATCAAAATTGTATCAAAAGTTAAAAAATTAAAT Found at i:999049 original size:20 final size:20 Alignment explanation

Indices: 998985--999052 Score: 100 Period size: 20 Copynumber: 3.4 Consensus size: 20 998975 TTAAAATTGT 998985 ATCAAAAGTTAAAAAATTAA 1 ATCAAAAGTTAAAAAATTAA * ** 999005 ATCAAAAGTTATCAAAATTGT 1 ATCAAAAGTTA-AAAAATTAA 999026 ATCAAAAGTTAAAAAATTAA 1 ATCAAAAGTTAAAAAATTAA 999046 ATCAAAA 1 ATCAAAA 999053 AAGTTATCAA Statistics Matches: 41, Mismatches: 6, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 20 24 0.59 21 17 0.41 ACGTcount: A:0.60, C:0.07, G:0.06, T:0.26 Consensus pattern (20 bp): ATCAAAAGTTAAAAAATTAA Found at i:1003583 original size:38 final size:38 Alignment explanation

Indices: 1003541--1003625 Score: 107 Period size: 38 Copynumber: 2.2 Consensus size: 38 1003531 ATATAAATTG * * 1003541 AATTCTCTAGTAGCTAGCCACCTGTCAATTCCAAAGTA 1 AATTCTCTAGTAGCTAGCCACCAGCCAATTCCAAAGTA * * * * * 1003579 AATTCTCTAGTTGTTAGCCACCAGCCAATTTCATATTA 1 AATTCTCTAGTAGCTAGCCACCAGCCAATTCCAAAGTA 1003617 AATTCTCTA 1 AATTCTCTA 1003626 ACCGTCAGCC Statistics Matches: 40, Mismatches: 7, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 38 40 1.00 ACGTcount: A:0.31, C:0.25, G:0.11, T:0.34 Consensus pattern (38 bp): AATTCTCTAGTAGCTAGCCACCAGCCAATTCCAAAGTA Found at i:1008250 original size:38 final size:39 Alignment explanation

Indices: 1008208--1008296 Score: 112 Period size: 38 Copynumber: 2.4 Consensus size: 39 1008198 ATTCACGTTG 1008208 GAATTCCT-TAGTCACCAGCCACTAGCCAATTCCAAATT 1 GAATTCCTCTAGTCACCAGCCACTAGCCAATTCCAAATT * * * * * 1008246 GAATT-CTCTAGTCGCTAGCCATTGGCCAATTCTAAATT 1 GAATTCCTCTAGTCACCAGCCACTAGCCAATTCCAAATT 1008284 GAATT-CTCTAGTC 1 GAATTCCTCTAGTC 1008297 GTCAGTCGCC Statistics Matches: 45, Mismatches: 5, Indels: 2 0.87 0.10 0.04 Matches are distributed among these distances: 37 2 0.04 38 43 0.96 ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31 Consensus pattern (39 bp): GAATTCCTCTAGTCACCAGCCACTAGCCAATTCCAAATT Found at i:1008321 original size:38 final size:38 Alignment explanation

Indices: 1008279--1008370 Score: 148 Period size: 38 Copynumber: 2.4 Consensus size: 38 1008269 GGCCAATTCT * * 1008279 AAATTGAATTCTCTAGTCGTCAGTCGCCAGCTAATTTC 1 AAATTGAATTCTCTAATCGGCAGTCGCCAGCTAATTTC * * 1008317 AAATTAAATTCTCTAATCGGCAGTTGCCAGCTAATTTC 1 AAATTGAATTCTCTAATCGGCAGTCGCCAGCTAATTTC 1008355 AAATTGAATTCTCTAA 1 AAATTGAATTCTCTAA 1008371 CCGTCAGCCA Statistics Matches: 49, Mismatches: 5, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 38 49 1.00 ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35 Consensus pattern (38 bp): AAATTGAATTCTCTAATCGGCAGTCGCCAGCTAATTTC Found at i:1009962 original size:11 final size:13 Alignment explanation

Indices: 1009945--1010010 Score: 50 Period size: 13 Copynumber: 5.2 Consensus size: 13 1009935 TACAAACACA * 1009945 TTTTTT-TCCTTC 1 TTTTTTCTCTTTC 1009957 TTTTTTCTCTTTC 1 TTTTTTCTCTTTC * 1009970 --TTTTCTCTATC 1 TTTTTTCTCTTTC * * 1009981 TTTTCTTCCCTTTT 1 TTTT-TTCTCTTTC 1009995 TATTTTTCT-TTTC 1 T-TTTTTCTCTTTC 1010008 TTT 1 TTT 1010011 CTTCCCTTCT Statistics Matches: 42, Mismatches: 7, Indels: 10 0.71 0.12 0.17 Matches are distributed among these distances: 11 10 0.24 12 8 0.19 13 11 0.26 14 10 0.24 15 3 0.07 ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74 Consensus pattern (13 bp): TTTTTTCTCTTTC Found at i:1013572 original size:17 final size:17 Alignment explanation

Indices: 1013520--1013574 Score: 55 Period size: 17 Copynumber: 3.4 Consensus size: 17 1013510 ATATATATTT 1013520 TAAAATTTATAT-AATA 1 TAAAATTTATATAAATA * 1013536 T-AAA-TTAT-TAATGTA 1 TAAAATTTATATAA-ATA 1013551 CTAAAATTTATATAAATA 1 -TAAAATTTATATAAATA 1013569 TAAAAT 1 TAAAAT 1013575 ATTTTAAACA Statistics Matches: 31, Mismatches: 2, Indels: 11 0.70 0.05 0.25 Matches are distributed among these distances: 13 1 0.03 14 5 0.16 15 5 0.16 16 2 0.06 17 9 0.29 18 6 0.19 19 3 0.10 ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42 Consensus pattern (17 bp): TAAAATTTATATAAATA Found at i:1015521 original size:18 final size:18 Alignment explanation

Indices: 1015498--1015537 Score: 55 Period size: 18 Copynumber: 2.2 Consensus size: 18 1015488 TATCGTACAT * 1015498 AAATTTATTT-AATTTTTA 1 AAATTT-TTTAAATATTTA 1015516 AAATTTTTTAAATATTTA 1 AAATTTTTTAAATATTTA 1015534 AAAT 1 AAAT 1015538 ATCATACATT Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 17 3 0.15 18 17 0.85 ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55 Consensus pattern (18 bp): AAATTTTTTAAATATTTA Found at i:1021922 original size:22 final size:24 Alignment explanation

Indices: 1021897--1021946 Score: 68 Period size: 22 Copynumber: 2.1 Consensus size: 24 1021887 TTTTTATTAT * 1021897 TTTTTATTATTATT-T-AATATAA 1 TTTTAATTATTATTATAAATATAA 1021919 TTTTAATTATTATTCATAAATATAA 1 TTTTAATTATTATT-ATAAATATAA 1021944 TTT 1 TTT 1021947 GTATAATTCA Statistics Matches: 24, Mismatches: 1, Indels: 3 0.86 0.04 0.11 Matches are distributed among these distances: 22 13 0.54 24 1 0.04 25 10 0.42 ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60 Consensus pattern (24 bp): TTTTAATTATTATTATAAATATAA Found at i:1023726 original size:13 final size:15 Alignment explanation

Indices: 1023702--1023733 Score: 50 Period size: 14 Copynumber: 2.3 Consensus size: 15 1023692 TTGATATTTA 1023702 TTTATATATTTAAT- 1 TTTATATATTTAATG 1023716 TTTATAT-TTTAATG 1 TTTATATATTTAATG 1023730 TTTA 1 TTTA 1023734 AAAATTAATT Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 13 6 0.35 14 11 0.65 ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66 Consensus pattern (15 bp): TTTATATATTTAATG Found at i:1030455 original size:2 final size:2 Alignment explanation

Indices: 1030448--1030516 Score: 57 Period size: 2 Copynumber: 33.5 Consensus size: 2 1030438 CTTTTAATGA * * * 1030448 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT GT AT GCT CAT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT -AT AT AT * * * * 1030492 AC GT AC AT AC AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT A 1030517 ATGATACATT Statistics Matches: 51, Mismatches: 15, Indels: 2 0.75 0.22 0.03 Matches are distributed among these distances: 2 49 0.96 3 2 0.04 ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42 Consensus pattern (2 bp): AT Found at i:1030952 original size:7 final size:7 Alignment explanation

Indices: 1030942--1030967 Score: 52 Period size: 7 Copynumber: 3.7 Consensus size: 7 1030932 TTTAATTATG 1030942 AATTTTC 1 AATTTTC 1030949 AATTTTC 1 AATTTTC 1030956 AATTTTC 1 AATTTTC 1030963 AATTT 1 AATTT 1030968 CTAAAGCTTG Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 19 1.00 ACGTcount: A:0.31, C:0.12, G:0.00, T:0.58 Consensus pattern (7 bp): AATTTTC Found at i:1032572 original size:16 final size:16 Alignment explanation

Indices: 1032553--1032586 Score: 52 Period size: 16 Copynumber: 2.1 Consensus size: 16 1032543 TTTTTTGTTT 1032553 TTAATTATT-TATTATA 1 TTAA-TATTCTATTATA 1032569 TTAATATTCTATTATA 1 TTAATATTCTATTATA 1032585 TT 1 TT 1032587 TTTTTGGTAC Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 15 4 0.24 16 13 0.76 ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62 Consensus pattern (16 bp): TTAATATTCTATTATA Found at i:1034717 original size:21 final size:21 Alignment explanation

Indices: 1034692--1034733 Score: 66 Period size: 21 Copynumber: 2.0 Consensus size: 21 1034682 TAAATATTCG * 1034692 ATATAAATATGTATTTAATAT 1 ATATAAATATATATTTAATAT * 1034713 ATATATATATATATTTAATAT 1 ATATAAATATATATTTAATAT 1034734 TTTTTAAATT Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 21 19 1.00 ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50 Consensus pattern (21 bp): ATATAAATATATATTTAATAT Found at i:1036756 original size:27 final size:26 Alignment explanation

Indices: 1036726--1036776 Score: 66 Period size: 26 Copynumber: 1.9 Consensus size: 26 1036716 TTGTAATTAA ** 1036726 ATTTTAATATTTATGTTTTTTTTATGT 1 ATTTTAATA-TTATGACTTTTTTATGT * 1036753 ATTTTCATATTATGACTTTTTTAT 1 ATTTTAATATTATGACTTTTTTAT 1036777 ATGAAAAATA Statistics Matches: 21, Mismatches: 3, Indels: 1 0.84 0.12 0.04 Matches are distributed among these distances: 26 13 0.62 27 8 0.38 ACGTcount: A:0.24, C:0.04, G:0.06, T:0.67 Consensus pattern (26 bp): ATTTTAATATTATGACTTTTTTATGT Found at i:1037161 original size:32 final size:31 Alignment explanation

Indices: 1037115--1037190 Score: 102 Period size: 32 Copynumber: 2.5 Consensus size: 31 1037105 ATAACTATAA * * 1037115 ATATTT-TTTATATAAATTTTAATATATTA- 1 ATATTTATTTATATAAATTTTAAAAAATTAT 1037144 ATAATTTATATTATATAAATTTTAAAAAATTAT 1 AT-ATTTAT-TTATATAAATTTTAAAAAATTAT 1037177 ATATTTATTTATAT 1 ATATTTATTTATAT 1037191 TATATTTTTT Statistics Matches: 41, Mismatches: 2, Indels: 6 0.84 0.04 0.12 Matches are distributed among these distances: 29 2 0.05 30 4 0.10 31 7 0.17 32 26 0.63 33 2 0.05 ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55 Consensus pattern (31 bp): ATATTTATTTATATAAATTTTAAAAAATTAT Found at i:1037164 original size:15 final size:14 Alignment explanation

Indices: 1037110--1037167 Score: 53 Period size: 15 Copynumber: 3.8 Consensus size: 14 1037100 ATATTATAAC * 1037110 TATAAATATTTTTTA 1 TATAAAT-TTTATTA * 1037125 TATAAATTTTAATA 1 TATAAATTTTATTA 1037139 TATTAATAATTTATATTA 1 TA-T-A-AATTT-TATTA 1037157 TATAAATTTTA 1 TATAAATTTTA 1037168 AAAAATTATA Statistics Matches: 36, Mismatches: 3, Indels: 9 0.75 0.06 0.19 Matches are distributed among these distances: 14 9 0.25 15 13 0.36 16 2 0.06 17 6 0.17 18 6 0.17 ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55 Consensus pattern (14 bp): TATAAATTTTATTA Found at i:1037208 original size:13 final size:15 Alignment explanation

Indices: 1037176--1037208 Score: 52 Period size: 15 Copynumber: 2.3 Consensus size: 15 1037166 TAAAAAATTA 1037176 TATATTTATTTATAT 1 TATATTTATTTATAT 1037191 TATATTT-TTTAT-T 1 TATATTTATTTATAT 1037204 TATAT 1 TATAT 1037209 AAATACCATA Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 13 6 0.33 14 5 0.28 15 7 0.39 ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70 Consensus pattern (15 bp): TATATTTATTTATAT Found at i:1038365 original size:26 final size:26 Alignment explanation

Indices: 1038318--1038368 Score: 77 Period size: 26 Copynumber: 2.0 Consensus size: 26 1038308 TATCATAATT * 1038318 AATTTTAATATATTTTATATTTATAA 1 AATTTTAATATATTATATATTTATAA 1038344 AATTTTAATATATTA-ATAATTTATA 1 AATTTTAATATATTATAT-ATTTATA 1038369 TTATATATAT Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 25 2 0.09 26 21 0.91 ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55 Consensus pattern (26 bp): AATTTTAATATATTATATATTTATAA Found at i:1038367 original size:32 final size:33 Alignment explanation

Indices: 1038316--1038406 Score: 109 Period size: 32 Copynumber: 2.8 Consensus size: 33 1038306 TATATCATAA 1038316 TTAAT-TTTAATATATTTTATATTTATA-AAATT 1 TTAATATTTAATATA-TTTATATTTATATAAATT * 1038348 TTAATATATTAATA-ATTTATA-TTATATATATT 1 TTAATAT-TTAATATATTTATATTTATATAAATT 1038380 TTAATATTTATATAATATTTATATTTA 1 TTAATATTTA-AT-ATATTTATATTTA 1038407 ATTTTTAAAT Statistics Matches: 51, Mismatches: 1, Indels: 11 0.81 0.02 0.17 Matches are distributed among these distances: 31 8 0.16 32 24 0.47 33 3 0.06 34 13 0.25 35 3 0.06 ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58 Consensus pattern (33 bp): TTAATATTTAATATATTTATATTTATATAAATT Found at i:1038397 original size:11 final size:11 Alignment explanation

Indices: 1038352--1038403 Score: 50 Period size: 11 Copynumber: 4.5 Consensus size: 11 1038342 AAAATTTTAA 1038352 TATATTAATAATT 1 TATA-TAAT-ATT * * 1038365 TATATTATATA 1 TATATAATATT * 1038376 TATTTTAATATT 1 TA-TATAATATT 1038388 TATATAATATT 1 TATATAATATT 1038399 TATAT 1 TATAT 1038404 TTAATTTTTA Statistics Matches: 32, Mismatches: 6, Indels: 4 0.76 0.14 0.10 Matches are distributed among these distances: 11 17 0.53 12 11 0.34 13 4 0.12 ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58 Consensus pattern (11 bp): TATATAATATT Found at i:1038406 original size:17 final size:17 Alignment explanation

Indices: 1038280--1038406 Score: 76 Period size: 16 Copynumber: 7.7 Consensus size: 17 1038270 ATAATGTATG * 1038280 TATTTATA-TTATGTTAA 1 TATTTATATTTAT-ATAA * * 1038297 TA-TTATTTTTATATCA 1 TATTTATATTTATATAA * 1038313 TAATTA-ATTT-TA-ATA 1 TATTTATATTTATATA-A * 1038328 TATTTTATATTTATAAAA 1 TA-TTTATATTTATATAA * 1038346 T-TTTA-ATATAT-TAA 1 TATTTATATTTATATAA 1038360 TAATTTATA-TTATAT-A 1 T-ATTTATATTTATATAA 1038376 TATTTTAATATTTATATAA 1 TA-TTT-ATATTTATATAA 1038395 TATTTATATTTA 1 TATTTATATTTA 1038407 ATTTTTAAAT Statistics Matches: 86, Mismatches: 9, Indels: 30 0.69 0.07 0.24 Matches are distributed among these distances: 14 3 0.03 15 11 0.13 16 30 0.35 17 25 0.29 18 13 0.15 19 4 0.05 ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58 Consensus pattern (17 bp): TATTTATATTTATATAA Found at i:1038769 original size:5 final size:5 Alignment explanation

Indices: 1038761--1038790 Score: 53 Period size: 5 Copynumber: 6.2 Consensus size: 5 1038751 TGAAATCTAA 1038761 AATTT AATTT AATTT AATTT AATTT -ATTT A 1 AATTT AATTT AATTT AATTT AATTT AATTT A 1038791 TATAATCACT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 4 4 0.17 5 20 0.83 ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60 Consensus pattern (5 bp): AATTT Found at i:1039537 original size:17 final size:18 Alignment explanation

Indices: 1039506--1039540 Score: 54 Period size: 17 Copynumber: 2.0 Consensus size: 18 1039496 TCATTAGTAA * 1039506 ATTTAAATATGAATATAT 1 ATTTAAATATAAATATAT 1039524 ATTT-AATATAAATATAT 1 ATTTAAATATAAATATAT 1039541 TTAAAATTTT Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 17 12 0.75 18 4 0.25 ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46 Consensus pattern (18 bp): ATTTAAATATAAATATAT Found at i:1039540 original size:15 final size:17 Alignment explanation

Indices: 1039506--1039544 Score: 55 Period size: 15 Copynumber: 2.4 Consensus size: 17 1039496 TCATTAGTAA 1039506 ATTTAAATATGAATATAT 1 ATTT-AATATGAATATAT 1039524 ATTTAATAT-AA-ATAT 1 ATTTAATATGAATATAT 1039539 ATTTAA 1 ATTTAA 1039545 AATTTTTTAA Statistics Matches: 21, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 15 10 0.48 16 2 0.10 17 5 0.24 18 4 0.19 ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46 Consensus pattern (17 bp): ATTTAATATGAATATAT Found at i:1041975 original size:23 final size:24 Alignment explanation

Indices: 1041942--1041991 Score: 75 Period size: 23 Copynumber: 2.1 Consensus size: 24 1041932 ATATTTTTTA * 1041942 TTTTGAGTTTTTTA-TTTATATTT 1 TTTTGAATTTTTTATTTTATATTT * 1041965 TTTTGAATTTTTTATTTTTTATTT 1 TTTTGAATTTTTTATTTTATATTT 1041989 TTT 1 TTT 1041992 CATGGGGATT Statistics Matches: 24, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 23 13 0.54 24 11 0.46 ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78 Consensus pattern (24 bp): TTTTGAATTTTTTATTTTATATTT Found at i:1041982 original size:6 final size:7 Alignment explanation

Indices: 1041933--1041991 Score: 50 Period size: 7 Copynumber: 8.1 Consensus size: 7 1041923 AGCCTATAAA 1041933 TATTTTT 1 TATTTTT 1041940 TA-TTTT 1 TATTTTT * 1041946 GAGTTTTT 1 TA-TTTTT 1041954 TATTTATAT 1 TATTT-T-T 1041963 T-TTTTT 1 TATTTTT * 1041969 GAATTTTT 1 -TATTTTT 1041977 TATTTTT 1 TATTTTT 1041984 TATTTTT 1 TATTTTT 1041991 T 1 T 1041992 CATGGGGATT Statistics Matches: 42, Mismatches: 4, Indels: 12 0.72 0.07 0.21 Matches are distributed among these distances: 6 6 0.14 7 20 0.48 8 14 0.33 9 2 0.05 ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78 Consensus pattern (7 bp): TATTTTT Found at i:1042204 original size:15 final size:15 Alignment explanation

Indices: 1042184--1042219 Score: 54 Period size: 15 Copynumber: 2.4 Consensus size: 15 1042174 AATTTTTAAA * 1042184 AATTTAAATTGATAT 1 AATTTAAATTAATAT * 1042199 AATTTAAATTAATTT 1 AATTTAAATTAATAT 1042214 AATTTA 1 AATTTA 1042220 TTAAATTTTT Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 15 19 1.00 ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50 Consensus pattern (15 bp): AATTTAAATTAATAT Found at i:1042240 original size:35 final size:35 Alignment explanation

Indices: 1042201--1042284 Score: 95 Period size: 35 Copynumber: 2.4 Consensus size: 35 1042191 ATTGATATAA 1042201 TTTAAATTAATTTAATTTATTAA-ATTTTTAAAATT 1 TTTAAATTAATTTAATTTA-TAATATTTTTAAAATT * 1042236 TTTAAAATTATATTT--TTTATAATATTTTTAAATTT 1 TTT-AAATTA-ATTTAATTTATAATATTTTTAAAATT * 1042271 TTTATA-TAATTTAA 1 TTTAAATTAATTTAA 1042285 AAATAAAATA Statistics Matches: 42, Mismatches: 2, Indels: 11 0.76 0.04 0.20 Matches are distributed among these distances: 32 4 0.10 33 2 0.05 34 5 0.12 35 21 0.50 36 6 0.14 37 4 0.10 ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60 Consensus pattern (35 bp): TTTAAATTAATTTAATTTATAATATTTTTAAAATT Found at i:1042246 original size:26 final size:26 Alignment explanation

Indices: 1042219--1042267 Score: 68 Period size: 26 Copynumber: 2.0 Consensus size: 26 1042209 AATTTAATTT 1042219 ATTA-AATTTTTA-AA-ATTTTTAAA 1 ATTATAATTTTTATAATATTTTTAAA * 1042242 ATTATATTTTTTATAATATTTTTAAA 1 ATTATAATTTTTATAATATTTTTAAA 1042268 TTTTTTATAT Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 23 4 0.18 24 7 0.32 25 2 0.09 26 9 0.41 ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57 Consensus pattern (26 bp): ATTATAATTTTTATAATATTTTTAAA Found at i:1042288 original size:20 final size:20 Alignment explanation

Indices: 1042247--1042288 Score: 50 Period size: 20 Copynumber: 2.1 Consensus size: 20 1042237 TTAAAATTAT ** 1042247 ATTTTTTATAATATTTTTAA 1 ATTTTTTATAATATTTAAAA 1042267 ATTTTTTAT-ATAATTTAAAA 1 ATTTTTTATAAT-ATTTAAAA 1042287 AT 1 AT 1042289 AAAATATTTA Statistics Matches: 19, Mismatches: 2, Indels: 2 0.83 0.09 0.09 Matches are distributed among these distances: 19 2 0.11 20 17 0.89 ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60 Consensus pattern (20 bp): ATTTTTTATAATATTTAAAA Found at i:1042460 original size:37 final size:40 Alignment explanation

Indices: 1042419--1042498 Score: 112 Period size: 37 Copynumber: 2.0 Consensus size: 40 1042409 TTATTAATCC * 1042419 TTAAAATAAAATCAAAT-TA-AATTT-AATAAAATTTTAA 1 TTAAAATAAAATCAAATAAATAATTTAAATAAAATTTTAA * 1042456 TTAAAATTAAATCAAATACAATAATTTAAATAAAATTTTAA 1 TTAAAATAAAATCAAATA-AATAATTTAAATAAAATTTTAA 1042497 TT 1 TT 1042499 TTTTATATTT Statistics Matches: 37, Mismatches: 2, Indels: 4 0.86 0.05 0.09 Matches are distributed among these distances: 37 16 0.43 39 1 0.03 40 5 0.14 41 15 0.41 ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39 Consensus pattern (40 bp): TTAAAATAAAATCAAATAAATAATTTAAATAAAATTTTAA Found at i:1043054 original size:12 final size:12 Alignment explanation

Indices: 1043021--1043059 Score: 51 Period size: 12 Copynumber: 3.2 Consensus size: 12 1043011 CTAAAATATA * 1043021 TAAAAAATAATT 1 TAAAAAATATTT 1043033 TAAAAAATATTT 1 TAAAAAATATTT * * 1043045 TAACAAATATCT 1 TAAAAAATATTT 1043057 TAA 1 TAA 1043060 GTCAGAACTA Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 12 24 1.00 ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36 Consensus pattern (12 bp): TAAAAAATATTT Found at i:1043611 original size:23 final size:23 Alignment explanation

Indices: 1043576--1043621 Score: 60 Period size: 23 Copynumber: 2.0 Consensus size: 23 1043566 AAAAATATTA 1043576 TAAATATTAAAAT-TTAAATTTTT 1 TAAATATTAAAATATT-AATTTTT 1043599 TAAATTATT-AAATATTAATTTTT 1 TAAA-TATTAAAATATTAATTTTT 1043622 AATCATAACT Statistics Matches: 21, Mismatches: 0, Indels: 4 0.84 0.00 0.16 Matches are distributed among these distances: 23 15 0.71 24 6 0.29 ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54 Consensus pattern (23 bp): TAAATATTAAAATATTAATTTTT Found at i:1045271 original size:29 final size:30 Alignment explanation

Indices: 1045210--1045273 Score: 87 Period size: 30 Copynumber: 2.2 Consensus size: 30 1045200 ATTAAAAGAA * * 1045210 AAAAACTTATTTGAATGTAAATTAAAAATT 1 AAAAACTTATTTAAATATAAATTAAAAATT 1045240 AAAAACTTATTTAAATAT-AA-TAAAAATAT 1 AAAAACTTATTTAAATATAAATTAAAAAT-T 1045269 AAAAA 1 AAAAA 1045274 TTAAAATTAA Statistics Matches: 31, Mismatches: 2, Indels: 3 0.86 0.06 0.08 Matches are distributed among these distances: 28 7 0.23 29 8 0.26 30 16 0.52 ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33 Consensus pattern (30 bp): AAAAACTTATTTAAATATAAATTAAAAATT Found at i:1045362 original size:3 final size:3 Alignment explanation

Indices: 1045354--1045391 Score: 76 Period size: 3 Copynumber: 12.7 Consensus size: 3 1045344 ATGTTTACTT 1045354 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT 1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT 1045392 TAATCTCTTT Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 35 1.00 ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34 Consensus pattern (3 bp): ATA Found at i:1046501 original size:47 final size:49 Alignment explanation

Indices: 1046448--1046570 Score: 124 Period size: 51 Copynumber: 2.5 Consensus size: 49 1046438 AATTTATAAT * 1046448 TATTTATCAACATGTTCA-ATAA-TATACTTATGAACATATTTGTTCAA 1 TATTTATCAACAAGTTCATATAATTATACTTATGAACATATTTGTTCAA * * * * * 1046495 TATTTATGAATAAGTTCATTTAATTTTGTTCTTATGAACATATTTGTTCAA 1 TATTTATCAACAAGTTCATATAA--TTATACTTATGAACATATTTGTTCAA * * * * 1046546 TATTCATGAATAAGTTCATTTAATT 1 TATTTATCAACAAGTTCATATAATT 1046571 TAAATAAAAA Statistics Matches: 65, Mismatches: 7, Indels: 6 0.83 0.09 0.08 Matches are distributed among these distances: 47 15 0.23 48 3 0.05 49 2 0.03 51 45 0.69 ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47 Consensus pattern (49 bp): TATTTATCAACAAGTTCATATAATTATACTTATGAACATATTTGTTCAA Found at i:1046536 original size:51 final size:51 Alignment explanation

Indices: 1046474--1046571 Score: 187 Period size: 51 Copynumber: 1.9 Consensus size: 51 1046464 CAATAATATA * 1046474 CTTATGAACATATTTGTTCAATATTTATGAATAAGTTCATTTAATTTTGTT 1 CTTATGAACATATTTGTTCAATATTCATGAATAAGTTCATTTAATTTTGTT 1046525 CTTATGAACATATTTGTTCAATATTCATGAATAAGTTCATTTAATTT 1 CTTATGAACATATTTGTTCAATATTCATGAATAAGTTCATTTAATTT 1046572 AAATAAAAAA Statistics Matches: 46, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 51 46 1.00 ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49 Consensus pattern (51 bp): CTTATGAACATATTTGTTCAATATTCATGAATAAGTTCATTTAATTTTGTT Found at i:1049162 original size:2 final size:2 Alignment explanation

Indices: 1049155--1049179 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 1049145 TTAATCAAAT 1049155 TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA T 1049180 TTTTGGCCTT 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:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:1057862 original size:268 final size:268 Alignment explanation

Indices: 1057385--1057920 Score: 1054 Period size: 268 Copynumber: 2.0 Consensus size: 268 1057375 ACTCGAATTT 1057385 TTAAAGAGATGCCTCCAACCACTTTTCGAACAGGCTTCAGTTTGAACGTTTTGTGCTTTGGTGGA 1 TTAAAGAGATGCCTCCAACCACTTTTCGAACAGGCTTCAGTTTGAACGTTTTGTGCTTTGGTGGA 1057450 AAGATAAACAACATGTTGACACACCTAATTCTCAGGGAAATATGATTTTTCTAAAAACAACTATT 66 AAGATAAACAACATGTTGACACACCTAATTCTCAGGGAAATATGATTTTTCTAAAAACAACTATT 1057515 CCAACTATATCATATTCTTTAAGTTCTTTTCATCCTTTAAGTTTACCTGCAAATTTGACCCATTA 131 CCAACTATATCATATTCTTTAAGTTCTTTTCATCCTTTAAGTTTACCTGCAAATTTGACCCATTA 1057580 TTTGCACCCAAAATATTTGTTTCATAACATGCAAATATGCATCATTCCAGATGATTGAAGGGGGC 196 TTTGCACCCAAAATATTTGTTTCATAACATGCAAATATGCATCATTCCAGATGATTGAAGGGGGC 1057645 TCTGACAC 261 TCTGACAC 1057653 TTAAAGAGATGCCTCCAACCACTTTTCGAACAGGCTTCAGTTTGAACGTTTTGTGCTTTGGTGGA 1 TTAAAGAGATGCCTCCAACCACTTTTCGAACAGGCTTCAGTTTGAACGTTTTGTGCTTTGGTGGA 1057718 AAGATAAACAACATGTTGACACACCTAATTCTCAGGGAAATATGATTTTTCTAAAAACAACTATT 66 AAGATAAACAACATGTTGACACACCTAATTCTCAGGGAAATATGATTTTTCTAAAAACAACTATT * 1057783 CCAACTATATCATATTCTTTAAGTTCTTTTCATCCTTTAAGTTTACCTGCAAATTTTACCCATTA 131 CCAACTATATCATATTCTTTAAGTTCTTTTCATCCTTTAAGTTTACCTGCAAATTTGACCCATTA * 1057848 TTTGCACCCAAAATATTTGTTTCATAACATGCAAATATGCATCATTCTAGATGATTGAAGGGGGC 196 TTTGCACCCAAAATATTTGTTTCATAACATGCAAATATGCATCATTCCAGATGATTGAAGGGGGC 1057913 TCTGACAC 261 TCTGACAC 1057921 CATTGTTAAG Statistics Matches: 266, Mismatches: 2, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 268 266 1.00 ACGTcount: A:0.31, C:0.20, G:0.14, T:0.34 Consensus pattern (268 bp): TTAAAGAGATGCCTCCAACCACTTTTCGAACAGGCTTCAGTTTGAACGTTTTGTGCTTTGGTGGA AAGATAAACAACATGTTGACACACCTAATTCTCAGGGAAATATGATTTTTCTAAAAACAACTATT CCAACTATATCATATTCTTTAAGTTCTTTTCATCCTTTAAGTTTACCTGCAAATTTGACCCATTA TTTGCACCCAAAATATTTGTTTCATAACATGCAAATATGCATCATTCCAGATGATTGAAGGGGGC TCTGACAC Found at i:1062840 original size:21 final size:21 Alignment explanation

Indices: 1062793--1062850 Score: 73 Period size: 21 Copynumber: 2.8 Consensus size: 21 1062783 AAAATTTATC * 1062793 CAAATGTATCGATACATTTGT 1 CAAATGTATCGATACATTTGA ** 1062814 GGAATGTATCGATACATTCT-A 1 CAAATGTATCGATACATT-TGA 1062835 CAAATGTATCGATACA 1 CAAATGTATCGATACA 1062851 GGGTCCCAAC Statistics Matches: 31, Mismatches: 5, Indels: 2 0.82 0.13 0.05 Matches are distributed among these distances: 21 30 0.97 22 1 0.03 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33 Consensus pattern (21 bp): CAAATGTATCGATACATTTGA Found at i:1062910 original size:19 final size:19 Alignment explanation

Indices: 1062886--1062953 Score: 78 Period size: 19 Copynumber: 3.9 Consensus size: 19 1062876 AATTCAACAA 1062886 TTTGTATCGATACATAAGT 1 TTTGTATCGATACATAAGT 1062905 TTTGTATCGATAC--AA-- 1 TTTGTATCGATACATAAGT 1062920 --TGTATCGATACATAAGT 1 TTTGTATCGATACATAAGT 1062937 ATTT-TATCGATACATAA 1 -TTTGTATCGATACATAA 1062954 TTAGCTACTG Statistics Matches: 42, Mismatches: 0, Indels: 14 0.75 0.00 0.25 Matches are distributed among these distances: 13 11 0.26 15 2 0.05 17 2 0.05 19 26 0.62 20 1 0.02 ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40 Consensus pattern (19 bp): TTTGTATCGATACATAAGT Found at i:1062925 original size:13 final size:13 Alignment explanation

Indices: 1062907--1062931 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 1062897 ACATAAGTTT 1062907 TGTATCGATACAA 1 TGTATCGATACAA 1062920 TGTATCGATACA 1 TGTATCGATACA 1062932 TAAGTATTTT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:1062929 original size:32 final size:32 Alignment explanation

Indices: 1062888--1062950 Score: 110 Period size: 32 Copynumber: 2.0 Consensus size: 32 1062878 TTCAACAATT 1062888 TGTATCGATACATAAGT-TTTGTATCGATACAA 1 TGTATCGATACATAAGTATTT-TATCGATACAA 1062920 TGTATCGATACATAAGTATTTTATCGATACA 1 TGTATCGATACATAAGTATTTTATCGATACA 1062951 TAATTAGCTA Statistics Matches: 30, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 32 27 0.90 33 3 0.10 ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38 Consensus pattern (32 bp): TGTATCGATACATAAGTATTTTATCGATACAA Found at i:1063011 original size:13 final size:13 Alignment explanation

Indices: 1062993--1063018 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 1062983 CATTTTTCTG 1062993 TGTATCGATACAT 1 TGTATCGATACAT 1063006 TGTATCGATACAT 1 TGTATCGATACAT 1063019 GGATCTTTGT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38 Consensus pattern (13 bp): TGTATCGATACAT Found at i:1063015 original size:33 final size:33 Alignment explanation

Indices: 1062973--1063039 Score: 98 Period size: 33 Copynumber: 2.0 Consensus size: 33 1062963 GCCAAGGAAA *** 1062973 TGTATCGATACATTTTTCTGTGTATCGATACAT 1 TGTATCGATACATGGATCTGTGTATCGATACAT * 1063006 TGTATCGATACATGGATCTTTGTATCGATACAT 1 TGTATCGATACATGGATCTGTGTATCGATACAT 1063039 T 1 T 1063040 TGAAAATTTT Statistics Matches: 30, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 33 30 1.00 ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43 Consensus pattern (33 bp): TGTATCGATACATGGATCTGTGTATCGATACAT Found at i:1063679 original size:28 final size:27 Alignment explanation

Indices: 1063581--1063658 Score: 156 Period size: 27 Copynumber: 2.9 Consensus size: 27 1063571 TTTCTTCACA 1063581 ATCGGGGATACTCCAACCCCGTTAATC 1 ATCGGGGATACTCCAACCCCGTTAATC 1063608 ATCGGGGATACTCCAACCCCGTTAATC 1 ATCGGGGATACTCCAACCCCGTTAATC 1063635 ATCGGGGATACTCCAACCCCGTTA 1 ATCGGGGATACTCCAACCCCGTTA 1063659 TTTCCGAGGG Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 27 51 1.00 ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22 Consensus pattern (27 bp): ATCGGGGATACTCCAACCCCGTTAATC Found at i:1063694 original size:31 final size:28 Alignment explanation

Indices: 1063584--1063679 Score: 106 Period size: 27 Copynumber: 3.5 Consensus size: 28 1063574 CTTCACAATC * *** 1063584 GGGGATACTCCAACCCCGTTA-ATCATC 1 GGGGATACTCCAACCCCGTTATTTCCGA * *** 1063611 GGGGATACTCCAACCCCGTTA-ATCATC 1 GGGGATACTCCAACCCCGTTATTTCCGA 1063638 GGGGATACTCCAACCCCGTTATTTCCGA 1 GGGGATACTCCAACCCCGTTATTTCCGA 1063666 GGGGATACTCCAAC 1 GGGGATACTCCAAC 1063680 TCCGATTTTA Statistics Matches: 64, Mismatches: 4, Indels: 1 0.93 0.06 0.01 Matches are distributed among these distances: 27 48 0.75 28 16 0.25 ACGTcount: A:0.25, C:0.32, G:0.21, T:0.22 Consensus pattern (28 bp): GGGGATACTCCAACCCCGTTATTTCCGA Found at i:1063738 original size:80 final size:80 Alignment explanation

Indices: 1063635--1063852 Score: 228 Period size: 79 Copynumber: 2.7 Consensus size: 80 1063625 CCCGTTAATC * 1063635 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACTCC-GATTTTATTTCCAAAA 1 ATCGAGGATACTCCAA-CCCGTTATTTCCGAGGGGATACTCCAACTCCTGATTTTATTTCCAAAA * 1063699 ATACCAATTTTTCACA 65 ATACCAATTTCTCACA * *** * * * 1063715 GTCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCTG-CTTTA-TTCCCAAA 1 ATCGAGGATACTCCAACC-CGTTATTTCCGAGGGGATACTCCAACTCCTGATTTTATTTCCAAAA *** * 1063778 ATATTGATTTCTCATA 65 ATACCAATTTCTCACA * * * * 1063794 ATTGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAA-TCCTGATTTTTTTTC 1 ATCGAGGATACTCCAACCC-GTTATTTCCGAGGGGATACTCCAACTCCTGATTTTATTTC 1063853 TAATCATCGA Statistics Matches: 110, Mismatches: 23, Indels: 10 0.77 0.16 0.07 Matches are distributed among these distances: 78 5 0.05 79 58 0.53 80 46 0.42 81 1 0.01 ACGTcount: A:0.25, C:0.26, G:0.15, T:0.33 Consensus pattern (80 bp): ATCGAGGATACTCCAACCCGTTATTTCCGAGGGGATACTCCAACTCCTGATTTTATTTCCAAAAA TACCAATTTCTCACA Found at i:1063829 original size:79 final size:80 Alignment explanation

Indices: 1063635--1063920 Score: 226 Period size: 79 Copynumber: 3.6 Consensus size: 80 1063625 CCCGTTAATC * * * * 1063635 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACTCCGATTTTATTTCCAAAAA 1 ATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAAA * 1063700 TACCAATTTTTCACA 66 TACCAATTTCTCACA * * * 1063715 GTCGAGGATACTCCAA-CCTCGTTA-TTTC-ATCGGGGATACTCCAACCCCTG-CTTTA-TTCCC 1 ATCGGGGATACTCCAACCCT-GTTATTTTCGA--GGGGATACTCCAACCCC-GACTTTATTTCCA *** * 1063775 AAAATATTGATTTCTCATA 62 AAAATACCAATTTCTCACA * * * * * * ** 1063794 ATTGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAATCCTGATTTTTTTTCTAATCA 1 ATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAAA * * 1063859 T--CGATTTCTTACA 66 TACCAATTTCTCACA * * * * * * * 1063872 ACCGGGGATACTCCAGCCCCGTTATTTTCAAGAGAACACTCCAACCCCG 1 ATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCG 1063921 TTATTATCTC Statistics Matches: 161, Mismatches: 36, Indels: 20 0.74 0.17 0.09 Matches are distributed among these distances: 78 50 0.31 79 58 0.36 80 51 0.32 81 2 0.01 ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31 Consensus pattern (80 bp): ATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAAA TACCAATTTCTCACA Found at i:1074264 original size:15 final size:14 Alignment explanation

Indices: 1074240--1074333 Score: 72 Period size: 15 Copynumber: 6.9 Consensus size: 14 1074230 ACCTTCTCTT * 1074240 CAAAA-AAAAAAAG 1 CAAAAGAAAAAAAA 1074253 CAAAAGAAAAAAAA 1 CAAAAGAAAAAAAA ** 1074267 -AGGA-AAAAAAAA 1 CAAAAGAAAAAAAA * 1074279 CAAAAAAACAAAAAA 1 CAAAAGAA-AAAAAA * 1074294 CAAAA-AAACAAAA 1 CAAAAGAAAAAAAA * 1074307 C-AAAGAAAAAGAGA 1 CAAAAGAAAAA-AAA * 1074321 GAAAAGAAAAAAA 1 CAAAAGAAAAAAA 1074334 CCTACTTAAG Statistics Matches: 64, Mismatches: 10, Indels: 13 0.74 0.11 0.15 Matches are distributed among these distances: 12 11 0.17 13 19 0.30 14 14 0.22 15 20 0.31 ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00 Consensus pattern (14 bp): CAAAAGAAAAAAAA Found at i:1074265 original size:8 final size:8 Alignment explanation

Indices: 1074246--1074333 Score: 56 Period size: 8 Copynumber: 10.8 Consensus size: 8 1074236 TCTTCAAAAA 1074246 AAAAAAGCA 1 AAAAAAG-A 1074255 AAAGAAA-A 1 AAA-AAAGA * 1074263 AAAAAGGA 1 AAAAAAGA 1074271 AAAAAA-A 1 AAAAAAGA * 1074278 ACAAAAAAA 1 A-AAAAAGA * 1074287 CAAAAAACA 1 -AAAAAAGA * 1074296 AAAAAACA 1 AAAAAAGA 1074304 AAACAAAGA 1 AAA-AAAGA * 1074313 AAAAGAG- 1 AAAAAAGA * 1074320 AGAAAAGA 1 AAAAAAGA 1074328 AAAAAA 1 AAAAAA 1074334 CCTACTTAAG Statistics Matches: 64, Mismatches: 8, Indels: 15 0.74 0.09 0.17 Matches are distributed among these distances: 7 9 0.14 8 34 0.53 9 17 0.27 10 4 0.06 ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00 Consensus pattern (8 bp): AAAAAAGA Found at i:1074272 original size:11 final size:10 Alignment explanation

Indices: 1074241--1074331 Score: 62 Period size: 10 Copynumber: 8.8 Consensus size: 10 1074231 CCTTCTCTTC 1074241 AAAAAAAA-A 1 AAAAAAAAGA ** 1074250 AAGCAAAAGA 1 AAAAAAAAGA 1074260 AAAAAAAAGGA 1 AAAAAAAA-GA * 1074271 AAAAAAAACA 1 AAAAAAAAGA 1074281 AAAAAACAA-A 1 AAAAAA-AAGA 1074291 AAACAAAAA-A 1 AAA-AAAAAGA 1074301 ACAAAACAAAGA 1 A-AAAA-AAAGA * * 1074313 AAAAGAGAGA 1 AAAAAAAAGA 1074323 AAAGAAAAA 1 AAA-AAAAA 1074332 AACCTACTTA Statistics Matches: 65, Mismatches: 9, Indels: 14 0.74 0.10 0.16 Matches are distributed among these distances: 9 6 0.09 10 31 0.48 11 26 0.40 12 2 0.03 ACGTcount: A:0.84, C:0.07, G:0.10, T:0.00 Consensus pattern (10 bp): AAAAAAAAGA Found at i:1074333 original size:1 final size:1 Alignment explanation

Indices: 1074241--1074316 Score: 53 Period size: 1 Copynumber: 76.0 Consensus size: 1 1074231 CCTTCTCTTC ** * ** * * * * 1074241 AAAAAAAAAAAGCAAAAGAAAAAAAAAGGAAAAAAAAACAAAAAAACAAAAAACAAAAAAACAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA * * 1074306 ACAAAGAAAAA 1 AAAAAAAAAAA 1074317 GAGAGAAAAG Statistics Matches: 56, Mismatches: 19, Indels: 0 0.75 0.25 0.00 Matches are distributed among these distances: 1 56 1.00 ACGTcount: A:0.86, C:0.08, G:0.07, T:0.00 Consensus pattern (1 bp): A Found at i:1075476 original size:59 final size:59 Alignment explanation

Indices: 1075282--1076300 Score: 1332 Period size: 59 Copynumber: 17.3 Consensus size: 59 1075272 TCCGCTTTTT * * * * * ** 1075282 AGTCCTCAGAGAGCAGGATGCCTTTTCCTTTTAAAAACCCCCACAAGTTGGTGACATTTTCC 1 AGTCCTCAAAGAGCAGGACGCCTTTT-CTTTT-AAAGCCCACACAAGTTGGTGGCACCTT-C * * ** 1075344 AGTCCTCAAAAAGCAGGACGCCTTTTCTTTTAAAGCCCATACAAGTTGGTGGCATTTTC 1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC * * 1075403 TAGTCCTCAAAGAGCAGGACGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC 1 -AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC * ** * 1075463 AGTCCTCAAAGAGCGGGACGTTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC 1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC * 1075522 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC 1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC * * 1075581 AGTCCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC 1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC * 1075640 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC 1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC * * 1075699 AGTCCTCAAAGAGC-GAGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTCC 1 AGTCCTCAAAGAGCAG-GACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC * * 1075758 AGTCCTCAAAAAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC 1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC * * 1075817 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTC 1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC * * * * 1075876 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCGAGTTGGTGGCACCTTT 1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC * * 1075935 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC 1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTC * * 1075996 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC 1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTC * * * * 1076057 AGTCCCCAAAAAGCAGGAC-CC---CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC 1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTC * * ** 1076113 AGTCCCCAAAGAGCAGGAC-AC----CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC 1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C * * 1076168 AGTCCTCAAAGAGCAGGACACC---TC--TTAAAGCCCACACAAGTTGGTGGCACCTTT 1 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC * * * * * 1076222 AGTCCTCAAAGAGCAGGATG-CTTTTGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT 1 AGTCCTCAAAGAGCAGGACGCCTTTT--CTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTC * * 1076283 ACTCCTCAATGAGCAGGA 1 AGTCCTCAAAGAGCAGGA 1076301 TACACTTTAT Statistics Matches: 881, Mismatches: 60, Indels: 33 0.90 0.06 0.03 Matches are distributed among these distances: 53 1 0.00 54 20 0.02 55 73 0.08 56 50 0.06 57 5 0.01 58 2 0.00 59 479 0.54 60 125 0.14 61 103 0.12 62 23 0.03 ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26 Consensus pattern (59 bp): AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC Found at i:1077083 original size:21 final size:21 Alignment explanation

Indices: 1077036--1077093 Score: 73 Period size: 21 Copynumber: 2.8 Consensus size: 21 1077026 AAATTTTATC * 1077036 CAAATGTATCGATACATTTGT 1 CAAATGTATCGATACATTTGA ** 1077057 GGAATGTATCGATACATTCT-A 1 CAAATGTATCGATACATT-TGA 1077078 CAAATGTATCGATACA 1 CAAATGTATCGATACA 1077094 GGGTCCCAAC Statistics Matches: 31, Mismatches: 5, Indels: 2 0.82 0.13 0.05 Matches are distributed among these distances: 21 30 0.97 22 1 0.03 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33 Consensus pattern (21 bp): CAAATGTATCGATACATTTGA Found at i:1077153 original size:19 final size:19 Alignment explanation

Indices: 1077129--1077196 Score: 85 Period size: 19 Copynumber: 3.9 Consensus size: 19 1077119 AATTCAACAA 1077129 TTTGTATCGATACATAAGT 1 TTTGTATCGATACATAAGT 1077148 TTTGTATCGATAC--AA-- 1 TTTGTATCGATACATAAGT 1077163 --TGTATCGATACATAAGT 1 TTTGTATCGATACATAAGT * 1077180 ATTGTATCGATACATAA 1 TTTGTATCGATACATAA 1077197 TTAGCTACTG Statistics Matches: 43, Mismatches: 0, Indels: 12 0.78 0.00 0.22 Matches are distributed among these distances: 13 11 0.26 15 2 0.05 17 2 0.05 19 28 0.65 ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38 Consensus pattern (19 bp): TTTGTATCGATACATAAGT Found at i:1077168 original size:13 final size:13 Alignment explanation

Indices: 1077150--1077174 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 1077140 ACATAAGTTT 1077150 TGTATCGATACAA 1 TGTATCGATACAA 1077163 TGTATCGATACA 1 TGTATCGATACA 1077175 TAAGTATTGT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:1077172 original size:32 final size:32 Alignment explanation

Indices: 1077131--1077193 Score: 117 Period size: 32 Copynumber: 2.0 Consensus size: 32 1077121 TTCAACAATT * 1077131 TGTATCGATACATAAGTTTTGTATCGATACAA 1 TGTATCGATACATAAGTATTGTATCGATACAA 1077163 TGTATCGATACATAAGTATTGTATCGATACA 1 TGTATCGATACATAAGTATTGTATCGATACA 1077194 TAATTAGCTA Statistics Matches: 30, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 32 30 1.00 ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37 Consensus pattern (32 bp): TGTATCGATACATAAGTATTGTATCGATACAA Found at i:1077254 original size:13 final size:13 Alignment explanation

Indices: 1077236--1077261 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 1077226 CATTTTTCTG 1077236 TGTATCGATACAT 1 TGTATCGATACAT 1077249 TGTATCGATACAT 1 TGTATCGATACAT 1077262 GGATCTTTGT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38 Consensus pattern (13 bp): TGTATCGATACAT Found at i:1077258 original size:33 final size:33 Alignment explanation

Indices: 1077216--1077282 Score: 98 Period size: 33 Copynumber: 2.0 Consensus size: 33 1077206 GCCAAGGAAA *** 1077216 TGTATCGATACATTTTTCTGTGTATCGATACAT 1 TGTATCGATACATGGATCTGTGTATCGATACAT * 1077249 TGTATCGATACATGGATCTTTGTATCGATACAT 1 TGTATCGATACATGGATCTGTGTATCGATACAT 1077282 T 1 T 1077283 TGGAAATTTT Statistics Matches: 30, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 33 30 1.00 ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43 Consensus pattern (33 bp): TGTATCGATACATGGATCTGTGTATCGATACAT Found at i:1077994 original size:28 final size:27 Alignment explanation

Indices: 1077936--1078006 Score: 81 Period size: 28 Copynumber: 2.6 Consensus size: 27 1077926 TCACAGTCGA * * 1077936 GGATACTCCAACCTCGTTATTTCATCGG 1 GGATACTCCAACCCCGTTACTTCA-CGG 1077964 GGATACTCCAACCCCGTTACTTC-CGAAG 1 GGATACTCCAACCCCGTTACTTCACG--G * 1077992 GGATACTCGAACCCC 1 GGATACTCCAACCCC 1078007 TGCTTTATTC Statistics Matches: 38, Mismatches: 3, Indels: 4 0.84 0.07 0.09 Matches are distributed among these distances: 26 2 0.05 28 36 0.95 ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24 Consensus pattern (27 bp): GGATACTCCAACCCCGTTACTTCACGG Found at i:1077997 original size:108 final size:108 Alignment explanation

Indices: 1077803--1077999 Score: 299 Period size: 108 Copynumber: 1.8 Consensus size: 108 1077793 AAAAAAACCA * * 1077803 AAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCCGTTAATCATTGGGGATACTCCAAC 1 AAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCGTTAATCATCGGGGATACTCCAAC * 1077868 CCCGTTATTTCCGAGGAGATACTCCAACTCCGATTTTATTTCC 66 CCCGTTACTTCCGAGGAGATACTCCAACTCCGATTTTATTTCC * * * * 1077911 AAAAATACCAATTT-TTCACAGTCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAA 1 AAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCGTTA-ATCATCGGGGATACTCCAA 1077975 CCCCGTTACTTCCGAAGG-GATACTC 65 CCCCGTTACTTCCG-AGGAGATACTC 1078000 GAACCCCTGC Statistics Matches: 80, Mismatches: 7, Indels: 4 0.88 0.08 0.04 Matches are distributed among these distances: 107 27 0.34 108 50 0.62 109 3 0.04 ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27 Consensus pattern (108 bp): AAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCGTTAATCATCGGGGATACTCCAAC CCCGTTACTTCCGAGGAGATACTCCAACTCCGATTTTATTTCC Found at i:1078014 original size:108 final size:108 Alignment explanation

Indices: 1077803--1078061 Score: 294 Period size: 108 Copynumber: 2.4 Consensus size: 108 1077793 AAAAAAACCA * * 1077803 AAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCCGTTAATCATTGGGGATACTCCAAC 1 AAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCGTTAATCATCGGGGATACTCCAAC * * * * 1077868 CCCGTTATTTCCGAGGAGATACTCCAACTCCGATTTTATTTCC 66 CCCGTTACTTCCGAGGAGATACTCCAACCCCGACTTTATTCCC * * * * 1077911 AAAAATACCAATTT-TTCACAGTCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAA 1 AAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCGTTA-ATCATCGGGGATACTCCAA * 1077975 CCCCGTTACTTCCGAAGG-GATACTCGAACCCCTG-CTTTATTCCC 65 CCCCGTTACTTCCG-AGGAGATACTCCAACCCC-GACTTTATTCCC * *** * * * 1078019 -AAAATATTGATTTC-TCATAATTGGGGATACTCCAACCCCGTTA 1 AAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCGTTA 1078062 TTTTTGAGGG Statistics Matches: 128, Mismatches: 19, Indels: 9 0.82 0.12 0.06 Matches are distributed among these distances: 107 61 0.48 108 63 0.49 109 4 0.03 ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29 Consensus pattern (108 bp): AAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCGTTAATCATCGGGGATACTCCAAC CCCGTTACTTCCGAGGAGATACTCCAACCCCGACTTTATTCCC Found at i:1078081 original size:28 final size:28 Alignment explanation

Indices: 1078041--1078094 Score: 83 Period size: 28 Copynumber: 1.9 Consensus size: 28 1078031 TCTCATAATT 1078041 GGGGATACTCCAACCCCG-TTATTTTTGA 1 GGGGATACTCCAACCCCGATT-TTTTTGA * 1078069 GGGGATACTCCAATCCCGATTTTTTT 1 GGGGATACTCCAACCCCGATTTTTTT 1078095 CTAATCATCG Statistics Matches: 24, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 28 22 0.92 29 2 0.08 ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35 Consensus pattern (28 bp): GGGGATACTCCAACCCCGATTTTTTTGA Found at i:1083210 original size:20 final size:20 Alignment explanation

Indices: 1083157--1083211 Score: 76 Period size: 20 Copynumber: 2.8 Consensus size: 20 1083147 AAAATTCCAG ** 1083157 ATGTATCGATACAAAGATCA 1 ATGTATCGATACATTGATCA 1083177 ATGTATCGATACATTGAGT-A 1 ATGTATCGATACATTGA-TCA 1083197 ATGTATCGATACATT 1 ATGTATCGATACATT 1083212 TCCTTGGCAG Statistics Matches: 32, Mismatches: 2, Indels: 2 0.89 0.06 0.06 Matches are distributed among these distances: 20 31 0.97 21 1 0.03 ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33 Consensus pattern (20 bp): ATGTATCGATACATTGATCA Found at i:1083249 original size:13 final size:13 Alignment explanation

Indices: 1083227--1083284 Score: 53 Period size: 13 Copynumber: 4.0 Consensus size: 13 1083217 GGCAGTAGCT * 1083227 TTGTAGCGATACA 1 TTGTATCGATACA 1083240 TTGTATCGATACAACA 1 TTGTATCGAT---ACA 1083256 CTTATGTATCGATACA 1 --T-TGTATCGATACA 1083272 TTGTATCGATACA 1 TTGTATCGATACA 1083285 AAACTTATGT Statistics Matches: 38, Mismatches: 1, Indels: 12 0.75 0.02 0.24 Matches are distributed among these distances: 13 21 0.55 14 1 0.03 16 6 0.16 18 1 0.03 19 9 0.24 ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34 Consensus pattern (13 bp): TTGTATCGATACA Found at i:1083265 original size:19 final size:19 Alignment explanation

Indices: 1083241--1083303 Score: 75 Period size: 19 Copynumber: 3.6 Consensus size: 19 1083231 AGCGATACAT 1083241 TGTATCGATACAACACTTA 1 TGTATCGATACAACACTTA 1083260 TGTATCGAT---ACA--T- 1 TGTATCGATACAACACTTA * 1083273 TGTATCGATACAAAACTTA 1 TGTATCGATACAACACTTA 1083292 TGTATCGATACA 1 TGTATCGATACA 1083304 TTTACTGTTT Statistics Matches: 37, Mismatches: 1, Indels: 12 0.74 0.02 0.24 Matches are distributed among these distances: 13 9 0.24 14 1 0.03 16 5 0.14 18 1 0.03 19 21 0.57 ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33 Consensus pattern (19 bp): TGTATCGATACAACACTTA Found at i:1083274 original size:32 final size:32 Alignment explanation

Indices: 1083228--1083305 Score: 138 Period size: 32 Copynumber: 2.4 Consensus size: 32 1083218 GCAGTAGCTT * * 1083228 TGTAGCGATACATTGTATCGATACAACACTTA 1 TGTATCGATACATTGTATCGATACAAAACTTA 1083260 TGTATCGATACATTGTATCGATACAAAACTTA 1 TGTATCGATACATTGTATCGATACAAAACTTA 1083292 TGTATCGATACATT 1 TGTATCGATACATT 1083306 TACTGTTTGT Statistics Matches: 44, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 32 44 1.00 ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35 Consensus pattern (32 bp): TGTATCGATACATTGTATCGATACAAAACTTA Found at i:1084408 original size:20 final size:20 Alignment explanation

Indices: 1084365--1084418 Score: 63 Period size: 20 Copynumber: 2.7 Consensus size: 20 1084355 AAGTACCCAG * * ** 1084365 ATGTATCGATACATTTTTTC 1 ATGTATCGATACATGTATGA 1084385 ATGTATCGATACATGTATGA 1 ATGTATCGATACATGTATGA * 1084405 ATGTATTGATACAT 1 ATGTATCGATACAT 1084419 CCTTCAATAT Statistics Matches: 29, Mismatches: 5, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 20 29 1.00 ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43 Consensus pattern (20 bp): ATGTATCGATACATGTATGA Found at i:1085387 original size:20 final size:21 Alignment explanation

Indices: 1085350--1085388 Score: 53 Period size: 20 Copynumber: 1.9 Consensus size: 21 1085340 GGCCTTTGAC ** 1085350 CATGCATTTTTTTTTATGTTT 1 CATGCATTTTTTAATATGTTT 1085371 CATGCA-TTTTTAATATGT 1 CATGCATTTTTTAATATGT 1085389 CTAGCATCTC Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 20 10 0.62 21 6 0.38 ACGTcount: A:0.21, C:0.10, G:0.10, T:0.59 Consensus pattern (21 bp): CATGCATTTTTTAATATGTTT Found at i:1089024 original size:42 final size:42 Alignment explanation

Indices: 1088946--1089031 Score: 106 Period size: 42 Copynumber: 2.0 Consensus size: 42 1088936 CTCCAATTTT * 1088946 TTAATTTATGCTTTTCCATCACTTCTTCTTTCAATTTAATTCC 1 TTAATTTATGCTTTTCCATCACTTCTTCTTTAAATTTAA-TCC * 1088989 TTAATTT-TGCTTTTCCAT-ACTT-TGATTTTTAAATTTAATCC 1 TTAATTTATGCTTTTCCATCACTTCT--TCTTTAAATTTAATCC 1089030 TT 1 TT 1089032 CCACTAAAAT Statistics Matches: 39, Mismatches: 2, Indels: 6 0.83 0.04 0.13 Matches are distributed among these distances: 40 1 0.03 41 9 0.23 42 22 0.56 43 7 0.18 ACGTcount: A:0.22, C:0.19, G:0.03, T:0.56 Consensus pattern (42 bp): TTAATTTATGCTTTTCCATCACTTCTTCTTTAAATTTAATCC Found at i:1094054 original size:18 final size:21 Alignment explanation

Indices: 1094015--1094054 Score: 59 Period size: 18 Copynumber: 2.0 Consensus size: 21 1094005 TTCTTAAACG 1094015 TTTTTGATATTATTTATATTA 1 TTTTTGATATTATTTATATTA 1094036 TTTTT-ATA-TATTT-TATTA 1 TTTTTGATATTATTTATATTA 1094054 T 1 T 1094055 ATTATAATCA Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 18 6 0.32 19 5 0.26 20 3 0.16 21 5 0.26 ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70 Consensus pattern (21 bp): TTTTTGATATTATTTATATTA Found at i:1094147 original size:18 final size:18 Alignment explanation

Indices: 1094126--1094188 Score: 53 Period size: 18 Copynumber: 3.6 Consensus size: 18 1094116 AATTTTAAAA 1094126 TATATATTTATATTATAT 1 TATATATTTATATTATAT 1094144 TATAT-TTTA-ATTAT-T 1 TATATATTTATATTATAT * 1094159 TA-AAATATTATATTTATAT 1 TATATAT-TTATA-TTATAT * 1094178 AAATATATTTA 1 -TATATATTTA 1094189 AAATTATTGT Statistics Matches: 35, Mismatches: 3, Indels: 12 0.70 0.06 0.24 Matches are distributed among these distances: 14 1 0.03 15 4 0.11 16 8 0.23 17 5 0.14 18 9 0.26 19 1 0.03 20 4 0.11 21 3 0.09 ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57 Consensus pattern (18 bp): TATATATTTATATTATAT Found at i:1094194 original size:38 final size:38 Alignment explanation

Indices: 1094119--1094196 Score: 106 Period size: 38 Copynumber: 2.1 Consensus size: 38 1094109 ATTACAAAAT * * 1094119 TTTAAAATATATATTTATATTATATTATATTTTAATTA 1 TTTAAAATATATATTTATATTATAATATATTTAAATTA 1094157 TTTAAAATATTATATTTATA-TA-AATATATTTAAAATTA 1 TTTAAAATA-TATATTTATATTATAATATATTT-AAATTA 1094195 TT 1 TT 1094197 GTAATTATTA Statistics Matches: 36, Mismatches: 2, Indels: 4 0.86 0.05 0.10 Matches are distributed among these distances: 37 8 0.22 38 18 0.50 39 10 0.28 ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55 Consensus pattern (38 bp): TTTAAAATATATATTTATATTATAATATATTTAAATTA Found at i:1094725 original size:29 final size:30 Alignment explanation

Indices: 1094683--1094744 Score: 74 Period size: 29 Copynumber: 2.1 Consensus size: 30 1094673 TTATCGTATT * 1094683 TATATTTAAAATTT-TA-ATATATATAATAA 1 TATATGTAAAATTTATATATATATA-AATAA * * 1094712 TATATGTAATATTTATATTTATATAAATAA 1 TATATGTAAAATTTATATATATATAAATAA 1094742 TAT 1 TAT 1094745 TAAAAGAAAT Statistics Matches: 28, Mismatches: 3, Indels: 3 0.82 0.09 0.09 Matches are distributed among these distances: 29 12 0.43 30 10 0.36 31 6 0.21 ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50 Consensus pattern (30 bp): TATATGTAAAATTTATATATATATAAATAA Found at i:1094735 original size:21 final size:21 Alignment explanation

Indices: 1094679--1094745 Score: 55 Period size: 21 Copynumber: 3.2 Consensus size: 21 1094669 ATATTTATCG * * 1094679 TATTTATATTTA-AAATTTTAA 1 TATTTATATTTATATA-TATAA * * * * 1094700 TATATATAATAATATATGTAA 1 TATTTATATTTATATATATAA * 1094721 TATTTATATTTATATAAATAA 1 TATTTATATTTATATATATAA 1094742 TATT 1 TATT 1094746 AAAAGAAATA Statistics Matches: 35, Mismatches: 10, Indels: 2 0.74 0.21 0.04 Matches are distributed among these distances: 21 33 0.94 22 2 0.06 ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52 Consensus pattern (21 bp): TATTTATATTTATATATATAA Found at i:1095314 original size:43 final size:40 Alignment explanation

Indices: 1095264--1095364 Score: 107 Period size: 40 Copynumber: 2.5 Consensus size: 40 1095254 ATTTAAAATA ** 1095264 ATTTAATTTAAATTATTATTTAAATAATA-AAAAATATTATTTT 1 ATTTAATTTAAATTA-TAAAT-AATAATATAAAAATA--ATTTT 1095307 ATTTAATTT-AATTATAAATAATAATATAAAAATAATTTT 1 ATTTAATTTAAATTATAAATAATAATATAAAAATAATTTT * * * 1095346 ATATATTTTAAATAATAAA 1 ATTTAATTTAAATTATAAA 1095365 ATTAATTTTC Statistics Matches: 51, Mismatches: 5, Indels: 7 0.81 0.08 0.11 Matches are distributed among these distances: 39 12 0.24 40 15 0.29 41 10 0.20 42 5 0.10 43 9 0.18 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (40 bp): ATTTAATTTAAATTATAAATAATAATATAAAAATAATTTT Found at i:1095345 original size:39 final size:38 Alignment explanation

Indices: 1095258--1095356 Score: 103 Period size: 39 Copynumber: 2.6 Consensus size: 38 1095248 TTTTTAATTT * * 1095258 AAAATAATTTAATTTAAATT-ATTATTTAAATAATAAAA 1 AAAATAATTTTATTTAATTTAATTA-TTAAATAATAAAA * * 1095296 AATATTATTTTATTTAATTTAATTA-TAAATAATAATATA 1 AAAATAATTTTATTTAATTTAATTATTAAATAATAA-A-A * * 1095335 AAAATAATTTTATATATTTTAA 1 AAAATAATTTTATTTAATTTAA 1095357 ATAATAAAAT Statistics Matches: 50, Mismatches: 8, Indels: 5 0.79 0.13 0.08 Matches are distributed among these distances: 37 10 0.20 38 17 0.34 39 23 0.46 ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47 Consensus pattern (38 bp): AAAATAATTTTATTTAATTTAATTATTAAATAATAAAA Found at i:1102502 original size:27 final size:28 Alignment explanation

Indices: 1102471--1102524 Score: 76 Period size: 28 Copynumber: 2.0 Consensus size: 28 1102461 ATATTTTAAT * 1102471 ATATTT-ATTTTGTGTTG-TTTTTTTTAG 1 ATATTTGATTTGGT-TTGATTTTTTTTAG 1102498 ATATTTGATTTGGTTTGATTTTTTTTA 1 ATATTTGATTTGGTTTGATTTTTTTTA 1102525 TTTTATATTT Statistics Matches: 24, Mismatches: 1, Indels: 3 0.86 0.04 0.11 Matches are distributed among these distances: 27 9 0.38 28 15 0.62 ACGTcount: A:0.17, C:0.00, G:0.15, T:0.69 Consensus pattern (28 bp): ATATTTGATTTGGTTTGATTTTTTTTAG Found at i:1102785 original size:19 final size:18 Alignment explanation

Indices: 1102745--1102786 Score: 50 Period size: 18 Copynumber: 2.3 Consensus size: 18 1102735 AAATAAGAAT * 1102745 TTTAATTTATAAATTATT 1 TTTAATTTATAAATTATA 1102763 TTTAATTT-TAAATAATATA 1 TTTAATTTATAAAT--TATA 1102782 TTTAA 1 TTTAA 1102787 AGAAATTTGA Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 17 5 0.24 18 8 0.38 19 8 0.38 ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57 Consensus pattern (18 bp): TTTAATTTATAAATTATA Found at i:1105907 original size:29 final size:29 Alignment explanation

Indices: 1105877--1105935 Score: 73 Period size: 29 Copynumber: 2.0 Consensus size: 29 1105867 TAATTTTTTT 1105877 AAATATAATATAAAAATAAAATATTGTTTAA 1 AAATAT-ATATAAAAA-AAAATATTGTTTAA * * * 1105908 AAATATATATGATAAAAAATATTTTTTA 1 AAATATATATAAAAAAAAATATTGTTTA 1105936 GATTGACAAG Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 29 12 0.48 30 7 0.28 31 6 0.24 ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39 Consensus pattern (29 bp): AAATATATATAAAAAAAAATATTGTTTAA Found at i:1108880 original size:3 final size:3 Alignment explanation

Indices: 1108872--1108898 Score: 54 Period size: 3 Copynumber: 9.0 Consensus size: 3 1108862 ACCAATAAAA 1108872 TAT TAT TAT TAT TAT TAT TAT TAT TAT 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT 1108899 AGAACATGAT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 24 1.00 ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67 Consensus pattern (3 bp): TAT Found at i:1109628 original size:56 final size:54 Alignment explanation

Indices: 1109474--1109631 Score: 126 Period size: 53 Copynumber: 2.9 Consensus size: 54 1109464 AAAAATTTAA * * * * 1109474 ATTTTTTATTTAAATTTAAATTTAATCTATTTTAATTTTTTAAATTATTTATATTTATT 1 ATTTTATAATTAAATTTAAA-ATAAT-TATTTTAA--TTTTAAA-TATTAATATTTATT * ** ** * * 1109533 A-TTTATACTT-AATAAAAAATAAAAAATTT-ATTTT-TATATTAATATTTATAT 1 ATTTTATAATTAAATTTAAAATAATTATTTTAATTTTAAATATTAATATTTAT-T 1109584 ATTTTATAATTAAATTTAAAATAATTATTTTAATTATTAAATATTAAT 1 ATTTTATAATTAAATTTAAAATAATTATTTTAATT-TTAAATATTAAT 1109632 TTAAGTTAAT Statistics Matches: 76, Mismatches: 17, Indels: 15 0.70 0.16 0.14 Matches are distributed among these distances: 50 12 0.16 51 3 0.04 52 12 0.16 53 14 0.18 54 4 0.05 55 6 0.08 56 11 0.14 57 6 0.08 58 7 0.09 59 1 0.01 ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56 Consensus pattern (54 bp): ATTTTATAATTAAATTTAAAATAATTATTTTAATTTTAAATATTAATATTTATT Found at i:1109829 original size:18 final size:19 Alignment explanation

Indices: 1109806--1109854 Score: 59 Period size: 18 Copynumber: 2.7 Consensus size: 19 1109796 ATTTAAAATA * 1109806 ATATTAAAAATT-ATTTTT 1 ATATTAAAAATTAATATTT * 1109824 ATATT-AATATTAATATTT 1 ATATTAAAAATTAATATTT 1109842 ATATT-AAAATTAA 1 ATATTAAAAATTAA 1109855 AATAATTTTT Statistics Matches: 27, Mismatches: 3, Indels: 2 0.84 0.09 0.06 Matches are distributed among these distances: 17 5 0.19 18 22 0.81 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (19 bp): ATATTAAAAATTAATATTT Found at i:1109843 original size:24 final size:25 Alignment explanation

Indices: 1109790--1109851 Score: 67 Period size: 24 Copynumber: 2.6 Consensus size: 25 1109780 AAAAGTTTAT 1109790 TTTATTATTTAAAATAATATTAAAA 1 TTTATTATTTAAAATAATATTAAAA * * * * 1109815 ATTATT-TTTATATTAATATTAATA 1 TTTATTATTTAAAATAATATTAAAA 1109839 TTTA-TA-TTAAAAT 1 TTTATTATTTAAAAT 1109852 TAAAATAATT Statistics Matches: 29, Mismatches: 7, Indels: 4 0.73 0.17 0.10 Matches are distributed among these distances: 23 6 0.21 24 18 0.62 25 5 0.17 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (25 bp): TTTATTATTTAAAATAATATTAAAA Found at i:1109916 original size:10 final size:9 Alignment explanation

Indices: 1109900--1109926 Score: 54 Period size: 9 Copynumber: 3.0 Consensus size: 9 1109890 AAATTAGATT 1109900 AAATTTTTA 1 AAATTTTTA 1109909 AAATTTTTA 1 AAATTTTTA 1109918 AAATTTTTA 1 AAATTTTTA 1109927 TCCAGATCTC Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 18 1.00 ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56 Consensus pattern (9 bp): AAATTTTTA Found at i:1110576 original size:21 final size:21 Alignment explanation

Indices: 1110529--1110576 Score: 53 Period size: 21 Copynumber: 2.3 Consensus size: 21 1110519 TTGAATAGAT * 1110529 TTAATAGTTAAAAGAAAAAAA 1 TTAAAAGTTAAAAGAAAAAAA * * 1110550 TCAAAAGTTAAAA-ATAAATAA 1 TTAAAAGTTAAAAGA-AAAAAA 1110571 TTAAAA 1 TTAAAA 1110577 AATAATAATA Statistics Matches: 22, Mismatches: 4, Indels: 2 0.79 0.14 0.07 Matches are distributed among these distances: 20 1 0.05 21 21 0.95 ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25 Consensus pattern (21 bp): TTAAAAGTTAAAAGAAAAAAA Found at i:1111775 original size:28 final size:28 Alignment explanation

Indices: 1111734--1111788 Score: 76 Period size: 28 Copynumber: 2.0 Consensus size: 28 1111724 TAGTATTTTA * * 1111734 ATTTTTTTTAATAATTTAAAATTAAAAT 1 ATTTTTTTTAATAATATAAAAATAAAAT 1111762 ATTTATTTTT-ATAATATAAAAATAAAA 1 ATTT-TTTTTAATAATATAAAAATAAAA 1111789 ATAAATAATA Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 28 19 0.79 29 5 0.21 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (28 bp): ATTTTTTTTAATAATATAAAAATAAAAT Found at i:1111783 original size:29 final size:28 Alignment explanation

Indices: 1111734--1111791 Score: 73 Period size: 29 Copynumber: 2.0 Consensus size: 28 1111724 TAGTATTTTA * * 1111734 ATTTTTTTTAATAATTTAAAATTAAAAT 1 ATTTTTTTTAATAATTAAAAATAAAAAT 1111762 ATTTATTTTT-ATAATATAAAAATAAAAAT 1 ATTT-TTTTTAATAAT-TAAAAATAAAAAT 1111791 A 1 A 1111792 AATAATAATA Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 28 9 0.35 29 17 0.65 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (28 bp): ATTTTTTTTAATAATTAAAAATAAAAAT Found at i:1113205 original size:10 final size:10 Alignment explanation

Indices: 1113192--1113224 Score: 57 Period size: 10 Copynumber: 3.3 Consensus size: 10 1113182 AAAGCTCAGA 1113192 AAAAAAAAAG 1 AAAAAAAAAG 1113202 AAAAAAAAAG 1 AAAAAAAAAG * 1113212 AAAAGAAAAG 1 AAAAAAAAAG 1113222 AAA 1 AAA 1113225 GAAACCAGAT Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 10 22 1.00 ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00 Consensus pattern (10 bp): AAAAAAAAAG Found at i:1113209 original size:15 final size:15 Alignment explanation

Indices: 1113191--1113220 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 1113181 AAAAGCTCAG 1113191 AAAAAAAAAAGAAAA 1 AAAAAAAAAAGAAAA * 1113206 AAAAAGAAAAGAAAA 1 AAAAAAAAAAGAAAA 1113221 GAAAGAAACC Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00 Consensus pattern (15 bp): AAAAAAAAAAGAAAA Found at i:1113374 original size:2 final size:2 Alignment explanation

Indices: 1113369--1113403 Score: 61 Period size: 2 Copynumber: 17.5 Consensus size: 2 1113359 TTCTCTCTTT * 1113369 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG CG TG T 1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T 1113404 TTTGTTCTTA Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 31 1.00 ACGTcount: A:0.00, C:0.03, G:0.49, T:0.49 Consensus pattern (2 bp): TG Done.