Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_D12

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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33

Warning! 639818 characters in sequence are not A, C, G, or T


File 107 of 196

Found at i:32266053 original size:41 final size:39

Alignment explanation

Indices: 32265958--32266053 Score: 113 Period size: 41 Copynumber: 2.4 Consensus size: 39 32265948 AAAAAGAGAA * * 32265958 TATTGAAATATTAT-AAAATTATTAAAGATTACAAAAAT 1 TATTTAAATATTATAAAAAATATTAAAGATTACAAAAAT * * 32265996 AATTTATAAAATTTATAAAAAATATTAAAGAGTTACTAAAAAT 1 TATTTA-AATA-TTATAAAAAATATTAAAGA-TTAC-AAAAAT 32266039 TATTTAAATATTATA 1 TATTTAAATATTATA 32266054 GAACTTCTAG Statistics Matches: 47, Mismatches: 6, Indels: 7 0.78 0.10 0.12 Matches are distributed among these distances: 38 4 0.09 39 3 0.06 40 4 0.09 41 18 0.38 42 7 0.15 43 11 0.23 ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39 Consensus pattern (39 bp): TATTTAAATATTATAAAAAATATTAAAGATTACAAAAAT Found at i:32266126 original size:19 final size:18 Alignment explanation

Indices: 32266102--32266154 Score: 65 Period size: 19 Copynumber: 2.9 Consensus size: 18 32266092 AAAAAAATAG 32266102 TTATAAAATTATAGAAAAA 1 TTATAAAATTAT-GAAAAA * 32266121 TTATAAAA--ATGAGAAA 1 TTATAAAATTATGAAAAA 32266137 TTATAGAAATTATGAAAA 1 TTATA-AAATTATGAAAA 32266155 TTCTACAAAA Statistics Matches: 29, Mismatches: 2, Indels: 6 0.78 0.05 0.16 Matches are distributed among these distances: 16 10 0.34 17 5 0.17 19 14 0.48 ACGTcount: A:0.60, C:0.00, G:0.09, T:0.30 Consensus pattern (18 bp): TTATAAAATTATGAAAAA Found at i:32270635 original size:12 final size:13 Alignment explanation

Indices: 32270618--32270646 Score: 51 Period size: 12 Copynumber: 2.3 Consensus size: 13 32270608 GTTTTGATTC 32270618 TTTAATTCTTT-A 1 TTTAATTCTTTAA 32270630 TTTAATTCTTTAA 1 TTTAATTCTTTAA 32270643 TTTA 1 TTTA 32270647 GTGGAAAACG Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 12 11 0.69 13 5 0.31 ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66 Consensus pattern (13 bp): TTTAATTCTTTAA Found at i:32282678 original size:20 final size:22 Alignment explanation

Indices: 32282655--32282695 Score: 59 Period size: 22 Copynumber: 2.0 Consensus size: 22 32282645 AATTAAGGAA 32282655 ATATA-TCAAAAA-TTTAAAAG 1 ATATATTCAAAAATTTTAAAAG * 32282675 ATATATTTAAAAATTTTAAAA 1 ATATATTCAAAAATTTTAAAA 32282696 AATAAAATAA Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 20 5 0.28 21 6 0.33 22 7 0.39 ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37 Consensus pattern (22 bp): ATATATTCAAAAATTTTAAAAG Found at i:32283372 original size:21 final size:21 Alignment explanation

Indices: 32283348--32283404 Score: 62 Period size: 21 Copynumber: 2.7 Consensus size: 21 32283338 CTTGAATGTC 32283348 AAGTCTTGAAACTTGACCTAT 1 AAGTCTTGAAACTTGACCTAT * * 32283369 AAGT-TTTAATACTTAACCTAT 1 AAGTCTTGAA-ACTTGACCTAT * * 32283390 AAGTCTAGAGACTTG 1 AAGTCTTGAAACTTG 32283405 GCTTGTTTAT Statistics Matches: 28, Mismatches: 6, Indels: 4 0.74 0.16 0.11 Matches are distributed among these distances: 20 4 0.14 21 22 0.79 22 2 0.07 ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35 Consensus pattern (21 bp): AAGTCTTGAAACTTGACCTAT Found at i:32285954 original size:44 final size:44 Alignment explanation

Indices: 32285889--32286062 Score: 181 Period size: 44 Copynumber: 3.9 Consensus size: 44 32285879 TGAGTTCAGA * * 32285889 AAATGAGAAATACCATGGTTGAAAGATA-TCATGGCATTATACCG 1 AAATGAGAAAGACCATAGTTGAAAGATACT-ATGGCATTATACCG * * 32285933 AAATGAGAAAGACCATAGTTGAAAGATACTATGGCATTAAACCA 1 AAATGAGAAAGACCATAGTTGAAAGATACTATGGCATTATACCG * * * * * * * 32285977 AAATGGGTAAGACCTTAGTTAAAAGATACTACGACACTATACCGG 1 AAATGAGAAAGACCATAGTTGAAAGATACTATGGCATTATACC-G * 32286022 AAAATGA-ACAAGACCATAGTTGAAAAGATACTATGACATTA 1 -AAATGAGA-AAGACCATAGTTG-AAAGATACTATGGCATTA 32286063 AATATGATTG Statistics Matches: 106, Mismatches: 19, Indels: 7 0.80 0.14 0.05 Matches are distributed among these distances: 44 73 0.69 45 1 0.01 46 16 0.15 47 16 0.15 ACGTcount: A:0.45, C:0.14, G:0.18, T:0.22 Consensus pattern (44 bp): AAATGAGAAAGACCATAGTTGAAAGATACTATGGCATTATACCG Found at i:32291114 original size:59 final size:59 Alignment explanation

Indices: 32291042--32291160 Score: 229 Period size: 59 Copynumber: 2.0 Consensus size: 59 32291032 ACATAATAGT * 32291042 AAAATACTACAGAACATACAAGCATAATAGACATATTCATAACAGTAATATACCACATA 1 AAAATACTACAGAACATACAAGCATAACAGACATATTCATAACAGTAATATACCACATA 32291101 AAAATACTACAGAACATACAAGCATAACAGACATATTCATAACAGTAATATACCACATA 1 AAAATACTACAGAACATACAAGCATAACAGACATATTCATAACAGTAATATACCACATA 32291160 A 1 A 32291161 CTATTACATA Statistics Matches: 59, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 59 59 1.00 ACGTcount: A:0.53, C:0.19, G:0.07, T:0.21 Consensus pattern (59 bp): AAAATACTACAGAACATACAAGCATAACAGACATATTCATAACAGTAATATACCACATA Found at i:32291160 original size:33 final size:31 Alignment explanation

Indices: 32291079--32291250 Score: 112 Period size: 33 Copynumber: 5.7 Consensus size: 31 32291069 TAGACATATT * 32291079 CATAACAGTAATATACCACAT-A-AAA-ATA 1 CATAACAATAATATACCACATAACAAACATA * * * * 32291107 C-T-AC-AGAACATACAAGCATAACAGACATA 1 CATAACAATAATATACCA-CATAACAAACATA * * 32291136 TTCATAACAGTAATATACCACATAACTATTACATA 1 --CATAACAATAATATACCACATAAC-A-AACATA * ** 32291171 CATAACAACAATATACCATGTAACAAACATA 1 CATAACAATAATATACCACATAACAAACATA * 32291202 CATAACAATAATAT---ACATAACATACATA 1 CATAACAATAATATACCACATAACAAACATA * * 32291230 CATAACAACAATA-ACAACATA 1 CATAACAATAATATACCACATA 32291251 CATAACAGTA Statistics Matches: 110, Mismatches: 20, Indels: 26 0.71 0.13 0.17 Matches are distributed among these distances: 25 7 0.06 26 5 0.05 27 2 0.02 28 26 0.24 29 3 0.03 30 5 0.05 31 19 0.17 32 2 0.02 33 28 0.25 34 8 0.07 35 5 0.05 ACGTcount: A:0.54, C:0.21, G:0.03, T:0.22 Consensus pattern (31 bp): CATAACAATAATATACCACATAACAAACATA Found at i:32291204 original size:31 final size:28 Alignment explanation

Indices: 32291166--32291242 Score: 109 Period size: 28 Copynumber: 2.6 Consensus size: 28 32291156 CATAACTATT 32291166 ACATACATAACAACAATATACCATGTAACAA 1 ACATACATAACAACAATATA-CA--TAACAA * * 32291197 ACATACATAACAATAATATACATAACAT 1 ACATACATAACAACAATATACATAACAA 32291225 ACATACATAACAACAATA 1 ACATACATAACAACAATA 32291243 ACAACATACA Statistics Matches: 43, Mismatches: 3, Indels: 3 0.88 0.06 0.06 Matches are distributed among these distances: 28 22 0.51 30 2 0.05 31 19 0.44 ACGTcount: A:0.57, C:0.21, G:0.01, T:0.21 Consensus pattern (28 bp): ACATACATAACAACAATATACATAACAA Found at i:32291221 original size:9 final size:9 Alignment explanation

Indices: 32291196--32291275 Score: 62 Period size: 9 Copynumber: 8.8 Consensus size: 9 32291186 CCATGTAACA 32291196 AACATACAT 1 AACATACAT 32291205 AACAATA-AT 1 AAC-ATACAT 32291214 ATACATAACAT 1 A-ACAT-ACAT 32291225 -ACATACAT 1 AACATACAT 32291233 AACA-ACAAT 1 AACATAC-AT 32291242 AACA-ACAT 1 AACATACAT 32291250 -ACATAACAGT 1 AACAT-ACA-T * 32291260 AATATACAT 1 AACATACAT 32291269 AACATAC 1 AACATAC 32291276 TTTGGTAAAG Statistics Matches: 59, Mismatches: 2, Indels: 20 0.73 0.02 0.25 Matches are distributed among these distances: 7 3 0.05 8 8 0.14 9 33 0.56 10 10 0.17 11 5 0.08 ACGTcount: A:0.57, C:0.20, G:0.01, T:0.21 Consensus pattern (9 bp): AACATACAT Found at i:32291243 original size:31 final size:30 Alignment explanation

Indices: 32291155--32291254 Score: 100 Period size: 28 Copynumber: 3.3 Consensus size: 30 32291145 GTAATATACC 32291155 ACATAACTATTACATACATAACAACAAT-ATA 1 ACATAAC-A-TACATACATAACAACAATAATA * * * 32291186 CCATGTAACAAACATACATAACAATAAT-AT- 1 ACA--TAACATACATACATAACAACAATAATA * 32291216 ACATAACATACATACATAACAACAATAACA 1 ACATAACATACATACATAACAACAATAATA 32291246 ACAT-ACATA 1 ACATAACATA 32291255 ACAGTAATAT Statistics Matches: 58, Mismatches: 7, Indels: 10 0.77 0.09 0.13 Matches are distributed among these distances: 28 21 0.36 29 6 0.10 30 6 0.10 31 20 0.34 32 1 0.02 33 4 0.07 ACGTcount: A:0.56, C:0.21, G:0.01, T:0.22 Consensus pattern (30 bp): ACATAACATACATACATAACAACAATAATA Found at i:32291263 original size:21 final size:22 Alignment explanation

Indices: 32291196--32291275 Score: 74 Period size: 21 Copynumber: 3.5 Consensus size: 22 32291186 CCATGTAACA * 32291196 AACATACATAACAATAATATAC-AT 1 AACATACAT-AC-ATAACA-ACAAT 32291220 AACATACATACATAACAACAAT 1 AACATACATACATAACAACAAT ** 32291242 AACA-ACATACATAACAGTAAT 1 AACATACATACATAACAACAAT 32291263 ATACATAACATAC 1 A-ACAT-ACATAC 32291276 TTTGGTAAAG Statistics Matches: 49, Mismatches: 3, Indels: 8 0.82 0.05 0.13 Matches are distributed among these distances: 21 18 0.37 22 14 0.29 23 2 0.04 24 15 0.31 ACGTcount: A:0.57, C:0.20, G:0.01, T:0.21 Consensus pattern (22 bp): AACATACATACATAACAACAAT Found at i:32291408 original size:31 final size:29 Alignment explanation

Indices: 32291372--32291437 Score: 87 Period size: 31 Copynumber: 2.2 Consensus size: 29 32291362 GAATGCCAAC 32291372 AAAAAAAAATTGAAGTAAGATATAATACGA 1 AAAAAAAAATTGAAGTAAGATATAATAC-A * ** 32291402 ATAAAAAAATTTGAAGTCTGATATAATACA 1 A-AAAAAAAATTGAAGTAAGATATAATACA 32291432 AAAAAA 1 AAAAAA 32291438 TACAAAAATT Statistics Matches: 32, Mismatches: 3, Indels: 3 0.84 0.08 0.08 Matches are distributed among these distances: 29 5 0.16 30 3 0.09 31 24 0.75 ACGTcount: A:0.62, C:0.05, G:0.11, T:0.23 Consensus pattern (29 bp): AAAAAAAAATTGAAGTAAGATATAATACA Found at i:32291563 original size:54 final size:57 Alignment explanation

Indices: 32291462--32291569 Score: 143 Period size: 55 Copynumber: 1.9 Consensus size: 57 32291452 AATATCAAAC * * 32291462 TAGAAAAATTTGTTTTCCCAAACCCTAAACCAAAAAACTAAATGTTCC-AAAAAGAA 1 TAGAAAAATTTGTTTTCCCAAACCATAAACCAAAAAACCAAATGTTCCTAAAAAGAA * * 32291518 TAGAAAAA-TTG-TTTCCCTAAACCATATACCAAAAAACCGAA-GTTCCTAAAAA 1 TAGAAAAATTTGTTTTCCC-AAACCATAAACCAAAAAACCAAATGTTCCTAAAAA 32291570 ATTGTCAGTT Statistics Matches: 46, Mismatches: 4, Indels: 5 0.84 0.07 0.09 Matches are distributed among these distances: 54 11 0.24 55 27 0.59 56 8 0.17 ACGTcount: A:0.49, C:0.20, G:0.07, T:0.23 Consensus pattern (57 bp): TAGAAAAATTTGTTTTCCCAAACCATAAACCAAAAAACCAAATGTTCCTAAAAAGAA Found at i:32305178 original size:28 final size:29 Alignment explanation

Indices: 32305138--32305204 Score: 93 Period size: 28 Copynumber: 2.4 Consensus size: 29 32305128 AATTTAAAAC * * * 32305138 GAGAAAGTTGAGAGAG-TTGAGAGGGTTT 1 GAGAGAGTTGAGAGAGTTTGAGAGAGTTG 32305166 GAGAGAGTTGAGAGAGTTTGAGAGAGTTG 1 GAGAGAGTTGAGAGAGTTTGAGAGAGTTG 32305195 GA-AGAGTTGA 1 GAGAGAGTTGA 32305205 AAGAAGGATG Statistics Matches: 35, Mismatches: 3, Indels: 2 0.88 0.08 0.05 Matches are distributed among these distances: 28 23 0.66 29 12 0.34 ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24 Consensus pattern (29 bp): GAGAGAGTTGAGAGAGTTTGAGAGAGTTG Found at i:32305202 original size:19 final size:19 Alignment explanation

Indices: 32305145--32305194 Score: 91 Period size: 19 Copynumber: 2.6 Consensus size: 19 32305135 AACGAGAAAG * 32305145 TTGAGAGAGTTGAGAGGGT 1 TTGAGAGAGTTGAGAGAGT 32305164 TTGAGAGAGTTGAGAGAGT 1 TTGAGAGAGTTGAGAGAGT 32305183 TTGAGAGAGTTG 1 TTGAGAGAGTTG 32305195 GAAGAGTTGA Statistics Matches: 30, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 19 30 1.00 ACGTcount: A:0.28, C:0.00, G:0.44, T:0.28 Consensus pattern (19 bp): TTGAGAGAGTTGAGAGAGT Found at i:32305208 original size:9 final size:9 Alignment explanation

Indices: 32305138--32305204 Score: 82 Period size: 9 Copynumber: 7.2 Consensus size: 9 32305128 AATTTAAAAC * 32305138 GAGAAAGTT 1 GAGAGAGTT 32305147 GAGAGAGTT 1 GAGAGAGTT * 32305156 GAGAGGGTTT 1 GAGAGAG-TT 32305166 GAGAGAGTT 1 GAGAGAGTT 32305175 GAGAGAGTTT 1 GAGAGAG-TT 32305185 GAGAGAGTT 1 GAGAGAGTT 32305194 G-GAAGAGTT 1 GAG-AGAGTT 32305203 GA 1 GA 32305205 AAGAAGGATG Statistics Matches: 51, Mismatches: 3, Indels: 7 0.84 0.05 0.11 Matches are distributed among these distances: 8 1 0.02 9 33 0.65 10 17 0.33 ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24 Consensus pattern (9 bp): GAGAGAGTT Found at i:32310960 original size:27 final size:26 Alignment explanation

Indices: 32310929--32311125 Score: 216 Period size: 27 Copynumber: 7.3 Consensus size: 26 32310919 TCATCTTCTA ** 32310929 GGGGTATAACAGTCATTTTACCCTAT 1 GGGGTATTTCAGTCATTTTACCCTAT * * 32310955 GAGGGTATTTCGGTCATTTTACCCCAT 1 G-GGGTATTTCAGTCATTTTACCCTAT * * 32310982 GGGGTATTTCACTCATTCTACCCTAT 1 GGGGTATTTCAGTCATTTTACCCTAT * 32311008 GGGGGTATTCCAGTCATTTTACCCTAT 1 -GGGGTATTTCAGTCATTTTACCCTAT 32311035 GGGGATATTTCAGTCATTTTACCCTAT 1 GGGG-TATTTCAGTCATTTTACCCTAT * * * 32311062 AGGGGTATTTCGGTTATTTTATCCTAT 1 -GGGGTATTTCAGTCATTTTACCCTAT * * 32311089 GGGGGTATTTC-GCTCATTTTATCTTAT 1 -GGGGTATTTCAG-TCATTTTACCCTAT 32311116 GGGGGTATTT 1 -GGGGTATTT 32311126 TGGTTATTTT Statistics Matches: 148, Mismatches: 18, Indels: 9 0.85 0.10 0.05 Matches are distributed among these distances: 26 27 0.18 27 117 0.79 28 4 0.03 ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41 Consensus pattern (26 bp): GGGGTATTTCAGTCATTTTACCCTAT Found at i:32311067 original size:54 final size:53 Alignment explanation

Indices: 32310929--32311137 Score: 249 Period size: 54 Copynumber: 3.9 Consensus size: 53 32310919 TCATCTTCTA ** * * 32310929 GGGGTATAACAGTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCCAT 1 GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTAT * * * * 32310982 GGGGTATTTCACTCATTCTACCCTATGGGGGTATTCCAGTCATTTTACCCTAT 1 GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTAT * * * 32311035 GGGGATATTTCAGTCATTTTACCCTATAGGGGTATTTCGGTTATTTTATCCTAT 1 GGGG-TATTTCAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTAT * * * * 32311089 GGGGGTATTTC-GCTCATTTTATCTTATGGGGGTATTTTGGTTATTTTAC 1 -GGGGTATTTCAG-TCATTTTACCCTATGGGGGTATTTCGGTCATTTTAC 32311138 TCATTTTAGG Statistics Matches: 133, Mismatches: 20, Indels: 5 0.84 0.13 0.03 Matches are distributed among these distances: 53 50 0.38 54 79 0.59 55 4 0.03 ACGTcount: A:0.19, C:0.18, G:0.22, T:0.42 Consensus pattern (53 bp): GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTAT Found at i:32311135 original size:81 final size:80 Alignment explanation

Indices: 32310929--32311137 Score: 249 Period size: 81 Copynumber: 2.6 Consensus size: 80 32310919 TCATCTTCTA ** * 32310929 GGGGTATAACAGTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCCATGGGGTATTTCAC 1 GGGGTATTCCAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCCATGGGGTATTTCAC 32310994 TCATTCTACCCTATG 66 TCATTCTACCCTATG * * * * 32311009 GGGGTATTCCAGTCATTTTACCCTATGGGGATATTTCAGTCATTTTACCCTATAGGGGTATTTCG 1 GGGGTATTCCAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCCAT-GGGGTATTTCA * * * * 32311074 GTTATTTTATCCTATG 65 CTCATTCTACCCTATG * * * * * 32311090 GGGGTATTTC-GCTCATTTTATCTTATGGGGGTATTTTGGTTATTTTAC 1 GGGGTATTCCAG-TCATTTTACCCTATGGGGGTATTTCGGTCATTTTAC 32311138 TCATTTTAGG Statistics Matches: 109, Mismatches: 18, Indels: 3 0.84 0.14 0.02 Matches are distributed among these distances: 80 48 0.44 81 61 0.56 ACGTcount: A:0.19, C:0.18, G:0.22, T:0.42 Consensus pattern (80 bp): GGGGTATTCCAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCCATGGGGTATTTCAC TCATTCTACCCTATG Found at i:32318518 original size:12 final size:12 Alignment explanation

Indices: 32318501--32318534 Score: 50 Period size: 12 Copynumber: 2.8 Consensus size: 12 32318491 TTAGAGCAAT 32318501 TGCAAGAACAGA 1 TGCAAGAACAGA ** 32318513 TGCAAGCCCAGA 1 TGCAAGAACAGA 32318525 TGCAAGAACA 1 TGCAAGAACA 32318535 ACTAGAAAAA Statistics Matches: 18, Mismatches: 4, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 12 18 1.00 ACGTcount: A:0.44, C:0.24, G:0.24, T:0.09 Consensus pattern (12 bp): TGCAAGAACAGA Found at i:32320760 original size:5 final size:5 Alignment explanation

Indices: 32320747--32320788 Score: 52 Period size: 5 Copynumber: 8.8 Consensus size: 5 32320737 AGAATGTTCA * * 32320747 AAAAA AAAAG AAAAG AAAA- AATA- AAAAG AAAAG AAAAG AAAA 1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA 32320789 AGGAGAGGCC Statistics Matches: 33, Mismatches: 3, Indels: 2 0.87 0.08 0.05 Matches are distributed among these distances: 4 6 0.18 5 27 0.82 ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02 Consensus pattern (5 bp): AAAAG Found at i:32320767 original size:18 final size:18 Alignment explanation

Indices: 32320746--32320789 Score: 70 Period size: 18 Copynumber: 2.4 Consensus size: 18 32320736 AAGAATGTTC 32320746 AAAAAAAAAAGAAAAGAA 1 AAAAAAAAAAGAAAAGAA * 32320764 AAAATAAAAAGAAAAGAA 1 AAAAAAAAAAGAAAAGAA 32320782 AAGAAAAA 1 AA-AAAAA 32320790 GGAGAGGCCA Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 18 19 0.83 19 4 0.17 ACGTcount: A:0.86, C:0.00, G:0.11, T:0.02 Consensus pattern (18 bp): AAAAAAAAAAGAAAAGAA Found at i:32320772 original size:23 final size:23 Alignment explanation

Indices: 32320746--32320789 Score: 79 Period size: 23 Copynumber: 1.9 Consensus size: 23 32320736 AAGAATGTTC 32320746 AAAAAAAAAAGAAAAGAAAAAAT 1 AAAAAAAAAAGAAAAGAAAAAAT * 32320769 AAAAAGAAAAGAAAAGAAAAA 1 AAAAAAAAAAGAAAAGAAAAA 32320790 GGAGAGGCCA Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 23 20 1.00 ACGTcount: A:0.86, C:0.00, G:0.11, T:0.02 Consensus pattern (23 bp): AAAAAAAAAAGAAAAGAAAAAAT Found at i:32321255 original size:108 final size:108 Alignment explanation

Indices: 32321064--32321265 Score: 314 Period size: 108 Copynumber: 1.9 Consensus size: 108 32321054 TTCATCTTAT * * * * 32321064 TATCTTAGCAAAATTTGGTATCTTGATTAATTTATTCATTTCGAGCTTTGCACTCAATAAAATTC 1 TATCTTAGCAAAATTTGCTATATTGATTAATTTATTCATTTCGAGCCTTACACTCAATAAAATTC 32321129 CATCTTATCCATTGTGATAATATTTTTCATCTTATTCAGTTCG 66 CATCTTATCCATTGTGATAATATTTTTCATCTTATTCAGTTCG * ** 32321172 TATCTTAGCAAAATTTGCTATATTGATTAATTTATTCATTTTGAGCCTTATTCTCAATAAAATTC 1 TATCTTAGCAAAATTTGCTATATTGATTAATTTATTCATTTCGAGCCTTACACTCAATAAAATTC * * * 32321237 CATCTTGTCCATTTTGATAATCTTTTTCA 66 CATCTTATCCATTGTGATAATATTTTTCA 32321266 AGCATATTTC Statistics Matches: 84, Mismatches: 10, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 108 84 1.00 ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47 Consensus pattern (108 bp): TATCTTAGCAAAATTTGCTATATTGATTAATTTATTCATTTCGAGCCTTACACTCAATAAAATTC CATCTTATCCATTGTGATAATATTTTTCATCTTATTCAGTTCG Found at i:32321778 original size:24 final size:24 Alignment explanation

Indices: 32321733--32321787 Score: 76 Period size: 24 Copynumber: 2.3 Consensus size: 24 32321723 ATGTCCCAAA * 32321733 ATTACAGTGGACTTAACCTTGAAG 1 ATTACAGCGGACTTAACCTTGAAG * 32321757 ATTACAGCGGA-TTGAACTTTGAAG 1 ATTACAGCGGACTT-AACCTTGAAG 32321781 ATTACAG 1 ATTACAG 32321788 TGGGGGCAAT Statistics Matches: 28, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 23 2 0.07 24 26 0.93 ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29 Consensus pattern (24 bp): ATTACAGCGGACTTAACCTTGAAG Found at i:32322470 original size:44 final size:44 Alignment explanation

Indices: 32322421--32322720 Score: 148 Period size: 44 Copynumber: 6.8 Consensus size: 44 32322411 AAGCACCAGC * * * 32322421 CTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTGTAGAT 1 CTTATCTCCCTGAGGAGCAGTGGAGCAGATCGAAGATTGTAGAT * * * * * * 32322465 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAAT 1 CTTATCTCCCTGAGGAGCAGTGGAGCAGATCGAAGATTGTAGAT * * ** ***** 32322509 CTTATCTTCCC--AAGA-TAGTAGGAAGCAGATTTAAGCCACCAG-T 1 CTTATC-TCCCTGAGGAGCAGT-GG-AGCAGATCGAAGATTGTAGAT * * * * * * 32322552 CCTATCTCCCTGAGTAGCAGCGGAGTAGGTCAAAGATTGTAGAT 1 CTTATCTCCCTGAGGAGCAGTGGAGCAGATCGAAGATTGTAGAT * * * * * * 32322596 CTTGTCTTCCTGTACTG-GCAGTGAAGCAGATCGAAAGCA--CTAG-C 1 CTTATCTCCCTG-A-GGAGCAGTGGAGCAGATCG-AAG-ATTGTAGAT * * * * 32322640 CTTATCTCCTTGAGGAGCAGTGGAGTAGGTTGAAGATTGTAGAT 1 CTTATCTCCCTGAGGAGCAGTGGAGCAGATCGAAGATTGTAGAT * * * 32322684 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT 1 CTTATCTCCCTGAGGAGCAGTGGAGCAGATCGAAGAT 32322721 GGCGAATCTT Statistics Matches: 180, Mismatches: 61, Indels: 30 0.66 0.23 0.11 Matches are distributed among these distances: 41 1 0.01 42 12 0.07 43 36 0.20 44 106 0.59 45 21 0.12 46 3 0.02 47 1 0.01 ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26 Consensus pattern (44 bp): CTTATCTCCCTGAGGAGCAGTGGAGCAGATCGAAGATTGTAGAT Found at i:32322565 original size:219 final size:219 Alignment explanation

Indices: 32322116--32323088 Score: 1492 Period size: 219 Copynumber: 4.5 Consensus size: 219 32322106 CATCATATCA ** * 32322116 AGTCCTATCTCCCTGAGCAGCAATGGAGTAGGTCGAAGATTGCAGATCTTGTCTTCCTGTACTGG 1 AGTCCTATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG * * * * 32322181 CAGTGAAGTAGATTGAAAGCACCACCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTG 66 CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTG * * * * * 32322246 CAG-----ATCTCCCTAAGAAGTAGTGGAGTAGATCGAAGACGGTGAATCTTATCTTCCCAAGAT 131 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT 32322306 AGTAGGAAGCAGATTTAAGCCACC 196 AGTAGGAAGCAGATTTAAGCCACC * * 32322330 AGTCCTATCTCCCTGAGCAGCAGCGGAGTAGGTCTAAGATTATAGATCTTGTCTTCCTGTACTGG 1 AGTCCTATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG * 32322395 CAGTGAAGCAGATCAAAAGCACCAGCCTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTG 66 CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTG * 32322460 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTCCCAAGAT 131 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT 32322525 AGTAGGAAGCAGATTTAAGCCACC 196 AGTAGGAAGCAGATTTAAGCCACC * * 32322549 AGTCCTATCTCCCTGAGTAGCAGCGGAGTAGGTCAAAGATTGTAGATCTTGTCTTCCTGTACTGG 1 AGTCCTATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG * * 32322614 CAGTGAAGCAGATCGAAAGCACTAGCCTTATCTCCTTGAGGAGCAGTGGAGTAGGTTGAAGATTG 66 CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTG * 32322679 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGAT 131 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT * 32322744 AGTAGGAAGTAGATTTAAGCCACC 196 AGTAGGAAGCAGATTTAAGCCACC * * * 32322768 AGTCCTATCTCCTTGAGCAGTAGCGAAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG 1 AGTCCTATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG * * * * 32322833 CAATGAAGCAGATCAAAAGCACCAGCCTTATCTCCCTGAAGAGCAGTGGAGTAGATTGAAGATTG 66 CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTG * * ** * 32322898 TAGATCTTATCTCCCGAGGCAGTAGTGGAGCAGATTAAAGATGGCGAATCTTATCTTCCCAAGGT 131 TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT * * ** 32322963 AGTAGGGAAGTAGATTTAAGCGATT 196 AGTA-GGAAGCAGATTTAAGCCACC * * * * 32322988 AG-CCTTATCTCCCTAAGCAGTAGTGGAGTAGGTCGATGATTGTAGATCTTGTCTTCCTGTACTG 1 AGTCC-TATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTG * 32323052 GCAGTGAAGCAGATTGAAAGCACCAGCCTTATC-CCCT 65 GCAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCT 32323089 AAAGTTGCAG Statistics Matches: 699, Mismatches: 53, Indels: 9 0.92 0.07 0.01 Matches are distributed among these distances: 214 122 0.17 219 474 0.68 220 103 0.15 ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26 Consensus pattern (219 bp): AGTCCTATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGATTGTAGATCTTGTCTTCCTGTACTGG CAGTGAAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGGAGCAGTGGAGTAGGTTGAAGATTG TAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCAAGAT AGTAGGAAGCAGATTTAAGCCACC Found at i:32322925 original size:44 final size:43 Alignment explanation

Indices: 32322859--32323037 Score: 125 Period size: 44 Copynumber: 4.1 Consensus size: 43 32322849 AAGCACCAGC * 32322859 CTTATCTCCCTGAAG-AGCAGTGGAGTAGATTGAAGATTGTAGAT 1 CTTATCTCCC-GAAGCAGTAGTGGAGTAGATTGAAGA-TGTAGAT * * * ** 32322903 CTTATCTCCCGAGGCAGTAGTGGAGCAGATTAAAGATGGCGAAT 1 CTTATCTCCCGAAGCAGTAGTGGAGTAGATTGAAGATGTAG-AT * * * 32322947 CTTATCTTCCC-AAGGTAGTAG-GGAAGTAGATTTAAGCGAT-TAG-C 1 CTTATC-TCCCGAA-GCAGTAGTGG-AGTAGATTGAA--GATGTAGAT * * * * 32322991 CTTATCTCCCTAAGCAGTAGTGGAGTAGGTCGATGATTGTAGAT 1 CTTATCTCCCGAAGCAGTAGTGGAGTAGATTGAAGA-TGTAGAT 32323035 CTT 1 CTT 32323038 GTCTTCCTGT Statistics Matches: 104, Mismatches: 19, Indels: 24 0.71 0.13 0.16 Matches are distributed among these distances: 41 2 0.02 42 1 0.01 43 26 0.25 44 52 0.50 45 19 0.18 46 1 0.01 47 3 0.03 ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29 Consensus pattern (43 bp): CTTATCTCCCGAAGCAGTAGTGGAGTAGATTGAAGATGTAGAT Found at i:32325370 original size:18 final size:18 Alignment explanation

Indices: 32325329--32325367 Score: 51 Period size: 18 Copynumber: 2.1 Consensus size: 18 32325319 TTATTTTATT * 32325329 TTTATTTTTATAATTTTA 1 TTTATTTTCATAATTTTA * 32325347 TTTATTTTCATTATTGTTA 1 TTTATTTTCATAATT-TTA 32325366 TT 1 TT 32325368 ATTGTCTTAT Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 18 13 0.72 19 5 0.28 ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72 Consensus pattern (18 bp): TTTATTTTCATAATTTTA Found at i:32327351 original size:31 final size:30 Alignment explanation

Indices: 32327297--32327358 Score: 79 Period size: 30 Copynumber: 2.0 Consensus size: 30 32327287 ATTTTAAAAA * * * 32327297 TAAAAATAAAAAAGTATTTTAAAAATATAT 1 TAAAAATAAAAAAATATTATAAAAAAATAT * 32327327 TAAAATTAAAAAAATATATATAAAAAAATAT 1 TAAAAATAAAAAAATAT-TATAAAAAAATAT 32327358 T 1 T 32327359 TATTATATAT Statistics Matches: 27, Mismatches: 4, Indels: 1 0.84 0.12 0.03 Matches are distributed among these distances: 30 15 0.56 31 12 0.44 ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32 Consensus pattern (30 bp): TAAAAATAAAAAAATATTATAAAAAAATAT Found at i:32327885 original size:15 final size:16 Alignment explanation

Indices: 32327859--32327890 Score: 57 Period size: 15 Copynumber: 2.1 Consensus size: 16 32327849 AATTTCTATA 32327859 TAATCAAGTTAAAATT 1 TAATCAAGTTAAAATT 32327875 TAATC-AGTTAAAATT 1 TAATCAAGTTAAAATT 32327890 T 1 T 32327891 GATATTTAAC Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 15 11 0.69 16 5 0.31 ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41 Consensus pattern (16 bp): TAATCAAGTTAAAATT Found at i:32328361 original size:27 final size:27 Alignment explanation

Indices: 32328322--32328399 Score: 77 Period size: 29 Copynumber: 2.8 Consensus size: 27 32328312 TCATGTTAGC * 32328322 AATTAATTAATTTTTTAAAATT-AAAA 1 AATTAATAAATTTTTTAAAATTCAAAA * 32328348 AATTACATAAATTTTTTAGAAATTCAAAG 1 AATTA-ATAAATTTTTTA-AAATTCAAAA * * * 32328377 AAGTATATATATATTTTAAAATT 1 AATTA-ATAAATTTTTTAAAATT 32328400 TAAATAAAAA Statistics Matches: 43, Mismatches: 6, Indels: 4 0.81 0.11 0.08 Matches are distributed among these distances: 26 5 0.12 27 11 0.26 28 10 0.23 29 17 0.40 ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44 Consensus pattern (27 bp): AATTAATAAATTTTTTAAAATTCAAAA Found at i:32328418 original size:21 final size:21 Alignment explanation

Indices: 32328389--32328464 Score: 55 Period size: 21 Copynumber: 3.4 Consensus size: 21 32328379 GTATATATAT * 32328389 ATTTTAAAATTTAAATAAAAA 1 ATTTAAAAATTTAAATAAAAA * * 32328410 ATTTCAAAATTCAGAA-AAAATA 1 ATTTAAAAATTTA-AATAAAA-A * 32328432 ATTTAAAAGCATATAAATAAAAAA 1 ATTTAAAA--ATTTAAAT-AAAAA * 32328456 ATATAAAAA 1 ATTTAAAAA 32328465 ATATTTTAAA Statistics Matches: 43, Mismatches: 6, Indels: 11 0.72 0.10 0.18 Matches are distributed among these distances: 21 15 0.35 22 11 0.26 23 2 0.05 24 11 0.26 25 4 0.09 ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29 Consensus pattern (21 bp): ATTTAAAAATTTAAATAAAAA Found at i:32330746 original size:21 final size:21 Alignment explanation

Indices: 32330721--32330762 Score: 59 Period size: 21 Copynumber: 2.0 Consensus size: 21 32330711 ATCCGCCCTC * 32330721 TCTTTTTTC-TCAATTTGTGTT 1 TCTTTTTCCTTCAATTT-TGTT 32330742 TCTTTTTCCTTCAATTTTGTT 1 TCTTTTTCCTTCAATTTTGTT 32330763 CAATTACAAA Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 21 12 0.63 22 7 0.37 ACGTcount: A:0.10, C:0.17, G:0.07, T:0.67 Consensus pattern (21 bp): TCTTTTTCCTTCAATTTTGTT Found at i:32334780 original size:43 final size:41 Alignment explanation

Indices: 32334688--32334836 Score: 158 Period size: 43 Copynumber: 3.6 Consensus size: 41 32334678 GTTACTCTGT * * * 32334688 GGAATCAGCACTTAACAACCACC-TTATATTC-AGTGATACGG 1 GGAATCAGCACTTAGCAACC-CCTTTACAATCAAG-GATACGG * 32334729 GGAATCAGCACATAGCAACCCCTTTCACAATCAAGGATACGG 1 GGAATCAGCACTTAGCAACCCCTTT-ACAATCAAGGATACGG * ** * 32334771 TGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTCGG 1 -GGAATCAGCACTTAGCAACC-CCTTTACAATCAAGGATACGG * 32334814 GGAATCAACACTTAGCAACCCCT 1 GGAATCAGCACTTAGCAACCCCT 32334837 CAAGGAATCT Statistics Matches: 93, Mismatches: 10, Indels: 10 0.82 0.09 0.09 Matches are distributed among these distances: 40 2 0.02 41 23 0.25 42 30 0.32 43 33 0.35 44 5 0.05 ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21 Consensus pattern (41 bp): GGAATCAGCACTTAGCAACCCCTTTACAATCAAGGATACGG Found at i:32334828 original size:42 final size:42 Alignment explanation

Indices: 32334688--32334833 Score: 170 Period size: 42 Copynumber: 3.5 Consensus size: 42 32334678 GTTACTCTGT * * * * 32334688 GGAATCAGCACTTAACAACCACC-TTATATTCAGTGATACGG 1 GGAATCAGCACTTAGCAACCACCTTTACAATCAATGATACGG * * 32334729 GGAATCAGCACATAGCAACC-CCTTTCACAATCAAGGATACGG 1 GGAATCAGCACTTAGCAACCACCTTT-ACAATCAATGATACGG * * * 32334771 TGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTCGG 1 -GGAATCAGCACTTAGCAACCACCTTTACAATCAATGATACGG * 32334814 GGAATCAACACTTAGCAACC 1 GGAATCAGCACTTAGCAACC 32334834 CCTCAAGGAA Statistics Matches: 89, Mismatches: 12, Indels: 7 0.82 0.11 0.06 Matches are distributed among these distances: 40 2 0.02 41 20 0.22 42 31 0.35 43 31 0.35 44 5 0.06 ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21 Consensus pattern (42 bp): GGAATCAGCACTTAGCAACCACCTTTACAATCAATGATACGG Found at i:32334893 original size:67 final size:68 Alignment explanation

Indices: 32334772--32334903 Score: 187 Period size: 67 Copynumber: 2.0 Consensus size: 68 32334762 AGGATACGGT 32334772 GGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTCGGGGAATCAACACTTAGCAACCCCT 1 GGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTCGGGGAATCAACACTTAGCAACCCCT 32334837 CAA 66 CAA * * * * ** 32334840 GGAATCTGCACTTAGCAACC-CCTTTTTG-ATCAGTGATTCGGGGAATCTGCACTTAGCAACCCC 1 GGAATCAGCACTTAGCAACCACC-TTTAGAATCAATAATTCGGGGAATCAACACTTAGCAACCCC 32334903 T 65 T 32334904 TACATCCAAT Statistics Matches: 57, Mismatches: 6, Indels: 3 0.86 0.09 0.05 Matches are distributed among these distances: 67 34 0.60 68 23 0.40 ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24 Consensus pattern (68 bp): GGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTCGGGGAATCAACACTTAGCAACCCCT CAA Found at i:32339420 original size:25 final size:25 Alignment explanation

Indices: 32339375--32339425 Score: 59 Period size: 25 Copynumber: 2.0 Consensus size: 25 32339365 ACTTTTCTCA * * 32339375 TCTCTTCAGTTCTCTCTCATTTTTC 1 TCTCTTCAGTTCCCTCTCATTATTC * 32339400 TCTCTTCATTTCCCT-TCCATTATTC 1 TCTCTTCAGTTCCCTCT-CATTATTC 32339425 T 1 T 32339426 TCATTTCCTT Statistics Matches: 22, Mismatches: 3, Indels: 2 0.81 0.11 0.07 Matches are distributed among these distances: 24 1 0.05 25 21 0.95 ACGTcount: A:0.10, C:0.33, G:0.02, T:0.55 Consensus pattern (25 bp): TCTCTTCAGTTCCCTCTCATTATTC Found at i:32341589 original size:30 final size:30 Alignment explanation

Indices: 32341551--32341716 Score: 126 Period size: 30 Copynumber: 5.5 Consensus size: 30 32341541 TTCAACTATC 32341551 AATTATGAAAAGGGATGGTGATGACCATCA 1 AATTATGAAAAGGGATGGTGATGACCATCA * * * * 32341581 ACTTATGAAAAGGGATGGCT--TCGGCTAT-T 1 AATTATGAAAAGGGATGG-TGAT-GACCATCA * * * * * 32341610 GATATCTGAAAAGGGATGGCT-TTGGCTATCA 1 AAT-TATGAAAAGGGATGG-TGATGACCATCA * 32341641 AATTATGAAAAGGAATGGTGATGACCATCA 1 AATTATGAAAAGGGATGGTGATGACCATCA ** * * 32341671 AAAAAT-AGAAAGGAATGGTGAAGACCATCA 1 AATTATGA-AAAGGGATGGTGATGACCATCA 32341701 AATTATGAAAAGGGAT 1 AATTATGAAAAGGGAT 32341717 AGCTTCAGCT Statistics Matches: 108, Mismatches: 20, Indels: 16 0.75 0.14 0.11 Matches are distributed among these distances: 29 4 0.04 30 99 0.92 31 5 0.05 ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24 Consensus pattern (30 bp): AATTATGAAAAGGGATGGTGATGACCATCA Found at i:32341743 original size:60 final size:59 Alignment explanation

Indices: 32341526--32341746 Score: 173 Period size: 60 Copynumber: 3.7 Consensus size: 59 32341516 TCATCAACGA * * * 32341526 ATGAAAATGGATAGCTTCAACTATC-AATTATGAAAAGGGATGGTGATGACCATCAACTT 1 ATGAAAAGGGATAGCTTCAGCTATCGAA-TATGAAAAGGGATGGTGATGACCATCAAATT * * * * * * * 32341585 ATGAAAAGGGATGGCTTCGGCTATTGATATCTGAAAAGGGATGGCT-TTGGCTATCAAATT 1 ATGAAAAGGGATAGCTTCAGCTATCGA-ATATGAAAAGGGATGG-TGATGACCATCAAATT * * * * * * * * 32341645 ATGAAAAGGAAT-G-GTGATGACCATCAAAAAAT-AGAAAGGAATGGTGAAGACCATCAAATT 1 ATGAAAAGGGATAGCTTCA-G-CTATC-GAATATGA-AAAGGGATGGTGATGACCATCAAATT 32341705 ATGAAAAGGGATAGCTTCAGCTATCGAACTATGAAAAGGGAT 1 ATGAAAAGGGATAGCTTCAGCTATCGAA-TATGAAAAGGGAT 32341747 AACTTCGTTT Statistics Matches: 119, Mismatches: 31, Indels: 23 0.69 0.18 0.13 Matches are distributed among these distances: 58 1 0.01 59 26 0.22 60 84 0.71 61 6 0.05 62 2 0.02 ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24 Consensus pattern (59 bp): ATGAAAAGGGATAGCTTCAGCTATCGAATATGAAAAGGGATGGTGATGACCATCAAATT Found at i:32341771 original size:30 final size:30 Alignment explanation

Indices: 32341701--32341773 Score: 94 Period size: 30 Copynumber: 2.4 Consensus size: 30 32341691 AAGACCATCA * 32341701 AATTATGAAAAGGGATAGCTTCAGCTATCG 1 AATTATGAAAAGGGATAACTTCAGCTATCG * * 32341731 AACTATGAAAAGGGATAACTTC-GTTTATCG 1 AATTATGAAAAGGGATAACTTCAG-CTATCG * 32341761 AATTACGAAAAGG 1 AATTATGAAAAGG 32341774 AATATGTCAA Statistics Matches: 37, Mismatches: 5, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 29 1 0.03 30 36 0.97 ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26 Consensus pattern (30 bp): AATTATGAAAAGGGATAACTTCAGCTATCG Found at i:32341772 original size:120 final size:120 Alignment explanation

Indices: 32341559--32341776 Score: 294 Period size: 120 Copynumber: 1.8 Consensus size: 120 32341549 TCAATTATGA * * * * * * * 32341559 AAAGGGATGGTGATGACCATCAACTTATGAAAAGGGATGGCTTCGGCTATTGATATCTGAAAAGG 1 AAAGGAATGGTGAAGACCATCAAATTATGAAAAGGGATAGCTTCAGCTATCGATATATGAAAAGG ** * * 32341624 GATGGCTTTGGCTATCAAATTATGAAAAGGAATGGTGATGACCATCAAAAAATAG 66 GATAACTTCGGCTATCAAATTACGAAAAGGAATGGTGATGACCATCAAAAAATAG 32341679 AAAGGAATGGTGAAGACCATCAAATTATGAAAAGGGATAGCTTCAGCTATCGA-ACTATGAAAAG 1 AAAGGAATGGTGAAGACCATCAAATTATGAAAAGGGATAGCTTCAGCTATCGATA-TATGAAAAG ** * 32341743 GGATAACTTCGTTTATCGAATTACGAAAAGGAAT 65 GGATAACTTCGGCTATCAAATTACGAAAAGGAAT 32341777 ATGTCAACCA Statistics Matches: 83, Mismatches: 14, Indels: 2 0.84 0.14 0.02 Matches are distributed among these distances: 119 1 0.01 120 82 0.99 ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24 Consensus pattern (120 bp): AAAGGAATGGTGAAGACCATCAAATTATGAAAAGGGATAGCTTCAGCTATCGATATATGAAAAGG GATAACTTCGGCTATCAAATTACGAAAAGGAATGGTGATGACCATCAAAAAATAG Found at i:32353739 original size:43 final size:43 Alignment explanation

Indices: 32353692--32353775 Score: 134 Period size: 43 Copynumber: 2.0 Consensus size: 43 32353682 TATGTGATTT 32353692 ATATTGAAATGGAAAAA-ATGAAAAATGAATATGAGATGAGAAA 1 ATATTGAAAT-GAAAAATATGAAAAATGAATATGAGATGAGAAA * * 32353735 ATATTGAAATGAAAAATATGATAAATGATTATGAGATGAGA 1 ATATTGAAATGAAAAATATGAAAAATGAATATGAGATGAGA 32353776 TATGAGATAT Statistics Matches: 38, Mismatches: 2, Indels: 2 0.90 0.05 0.05 Matches are distributed among these distances: 42 6 0.16 43 32 0.84 ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25 Consensus pattern (43 bp): ATATTGAAATGAAAAATATGAAAAATGAATATGAGATGAGAAA Found at i:32353750 original size:15 final size:16 Alignment explanation

Indices: 32353707--32353762 Score: 53 Period size: 16 Copynumber: 3.4 Consensus size: 16 32353697 GAAATGGAAA 32353707 AAATGAAAAATGAATATG 1 AAATGAAAAAT--ATATG * 32353725 AGATGAGAAAATAT-TG 1 AAATGA-AAAATATATG 32353741 AAATGAAAAATATGAT- 1 AAATGAAAAATAT-ATG 32353757 AAATGA 1 AAATGA 32353763 TTATGAGATG Statistics Matches: 33, Mismatches: 2, Indels: 8 0.77 0.05 0.19 Matches are distributed among these distances: 15 7 0.21 16 13 0.39 17 3 0.09 18 5 0.15 19 5 0.15 ACGTcount: A:0.59, C:0.00, G:0.18, T:0.23 Consensus pattern (16 bp): AAATGAAAAATATATG Found at i:32357833 original size:54 final size:54 Alignment explanation

Indices: 32357763--32357921 Score: 147 Period size: 54 Copynumber: 3.1 Consensus size: 54 32357753 TATTATAAAG * * 32357763 AATTTTATGAAATCATATATTATTATTAAATTATATTTAATAATAATTATTTTA 1 AATTGTATCAAATCATATATTATTATTAAATTATATTTAATAATAATTATTTTA * * 32357817 AATTGTA-CAAATTCATATA--A-GA--AAATT-TA-TTAGTAATAATTATTTTA 1 AATTGTATCAAA-TCATATATTATTATTAAATTATATTTAATAATAATTATTTTA * * * * * * 32357864 AATTTTATTAAAGCATATATT-TTAATTAAAATATATTTAATAATTATTATTTCA 1 AATTGTATCAAATCATATATTATT-ATTAAATTATATTTAATAATAATTATTTTA 32357918 AATT 1 AATT 32357922 ATATTTTATA Statistics Matches: 83, Mismatches: 12, Indels: 20 0.72 0.10 0.17 Matches are distributed among these distances: 47 29 0.35 48 5 0.06 49 5 0.06 50 1 0.01 51 1 0.01 52 5 0.06 53 5 0.06 54 32 0.39 ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48 Consensus pattern (54 bp): AATTGTATCAAATCATATATTATTATTAAATTATATTTAATAATAATTATTTTA Found at i:32357930 original size:59 final size:58 Alignment explanation

Indices: 32357865--32358279 Score: 212 Period size: 59 Copynumber: 6.9 Consensus size: 58 32357855 ATTATTTTAA * 32357865 ATTTTATTAAAGCATATATTTTAATTAAAATATATTTAATAATTATTATTTCAAATTAT 1 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATTATTATTT-AAATTAT * * * * * * * 32357924 ATTTTA-TAGTATCATATACTATGATTTTAGTAAAT-TCATATAAGAA-TATTGA-TT-AATAAG 1 ATTTTATTA-AATCATATA-TTTTA-ATTA--AAATAT-ATTTAATAATTATT-ATTTAAATTA- * 32357984 A 58 T 32357985 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATTATTATTTCAAATTAT 1 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATTATTATTT-AAATTAT * * * * * * * 32358044 ATTTTA-TAGTATCATATATTATGATTTTAGTAAAT-TCATATAAGAA-TATTGATTATTAA-GA 1 ATTTTATTA-AATCATATATT-TTA-ATTA--AAATAT-ATTTAATAATTATT-ATT-TAAATTA 32358105 - 58 T * * * 32358105 ATTTTATTAATTTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTAT 1 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATTATTAT-TTAAATTAT * * * * * * * 32358164 ATTTTA-TAGTATCATATATTATGATTTTAGTAAAT-TCATATAAGAA-TATTGATTATTAA-GA 1 ATTTTATTA-AATCATATATT-TTA-ATTA--AAATAT-ATTTAATAATTATT-ATT-TAAATTA 32358225 - 58 T * * * 32358225 ATTTTATTAATTTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA 1 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATTATTAT-TTAAA 32358280 ATATGATTAA Statistics Matches: 263, Mismatches: 53, Indels: 82 0.66 0.13 0.21 Matches are distributed among these distances: 57 44 0.17 58 24 0.09 59 52 0.20 60 22 0.08 61 51 0.19 62 25 0.10 63 44 0.17 64 1 0.00 ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49 Consensus pattern (58 bp): ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATTATTATTTAAATTAT Found at i:32358279 original size:120 final size:120 Alignment explanation

Indices: 32357864--32358273 Score: 723 Period size: 120 Copynumber: 3.4 Consensus size: 120 32357854 AATTATTTTA * * 32357864 AATTTTATTAAAGCATATATTTTAATTAAAATATATTTAATAATTATTATTTCAAATTATATTTT 1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT * * 32357929 ATAGTATCATATACTATGATTTTAGTAAATTCATATAAGAATATTGATTAATAAG 66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG * 32357984 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATTATTATTTCAAATTATATTTT 1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT 32358049 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG 66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG * * 32358104 AATTTTATTAATTTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT 1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTT 32358168 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG 65 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG * * 32358224 AATTTTATTAATTTATATATTTTAATTAAAATATATTTAATAATAATTAT 1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT 32358274 GTTAAAATAT Statistics Matches: 283, Mismatches: 6, Indels: 2 0.97 0.02 0.01 Matches are distributed among these distances: 120 281 0.99 121 2 0.01 ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49 Consensus pattern (120 bp): AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG Found at i:32358508 original size:45 final size:44 Alignment explanation

Indices: 32358417--32358513 Score: 135 Period size: 45 Copynumber: 2.2 Consensus size: 44 32358407 CTATTACACC * 32358417 TCCATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTAT 1 TCCATTACATTCAACCAAACACAAGAATACTATTACGCCTCTAT * 32358461 TCCATTACATTCAACCAAA-A-AATTGAATTGCTATTACGCCTCTAT 1 TCCATTACATTCAACCAAACACAA--GAA-TACTATTACGCCTCTAT 32358506 TCCATTAC 1 TCCATTAC 32358514 GTCTCTATTC Statistics Matches: 48, Mismatches: 2, Indels: 5 0.87 0.04 0.09 Matches are distributed among these distances: 42 2 0.04 43 1 0.02 44 21 0.44 45 24 0.50 ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31 Consensus pattern (44 bp): TCCATTACATTCAACCAAACACAAGAATACTATTACGCCTCTAT Found at i:32358514 original size:16 final size:16 Alignment explanation

Indices: 32358493--32358557 Score: 121 Period size: 16 Copynumber: 4.1 Consensus size: 16 32358483 TTGAATTGCT 32358493 ATTACGCCTCTATTCC 1 ATTACGCCTCTATTCC * 32358509 ATTACGTCTCTATTCC 1 ATTACGCCTCTATTCC 32358525 ATTACGCCTCTATTCC 1 ATTACGCCTCTATTCC 32358541 ATTACGCCTCTATTCC 1 ATTACGCCTCTATTCC 32358557 A 1 A 32358558 ATACAGCGAA Statistics Matches: 47, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 16 47 1.00 ACGTcount: A:0.20, C:0.35, G:0.06, T:0.38 Consensus pattern (16 bp): ATTACGCCTCTATTCC Found at i:32365608 original size:18 final size:18 Alignment explanation

Indices: 32365585--32365620 Score: 63 Period size: 18 Copynumber: 2.0 Consensus size: 18 32365575 TACGGTGTGC * 32365585 GAAACTATTTTTATGCTT 1 GAAACTATTTTGATGCTT 32365603 GAAACTATTTTGATGCTT 1 GAAACTATTTTGATGCTT 32365621 CCTATTCTTG Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47 Consensus pattern (18 bp): GAAACTATTTTGATGCTT Found at i:32368993 original size:40 final size:40 Alignment explanation

Indices: 32368895--32369064 Score: 218 Period size: 40 Copynumber: 4.3 Consensus size: 40 32368885 TCCTCGTTCA * * * * 32368895 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC- 1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG * 32368934 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG 1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG * * 32368974 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG 1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG * * * 32369014 AATGCCTTCGGGACTTAACCCGGA-TTAAGTATCTCGCACA 1 AATGCCTTCGGGACATAACCCGGATTTAA-TAACTCGCACG * 32369054 AAGGCCTTCGG 1 AATGCCTTCGG 32369065 ATCTTAATCC Statistics Matches: 117, Mismatches: 12, Indels: 3 0.89 0.09 0.02 Matches are distributed among these distances: 39 38 0.32 40 79 0.68 ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24 Consensus pattern (40 bp): AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG Found at i:32369037 original size:80 final size:79 Alignment explanation

Indices: 32368893--32369117 Score: 238 Period size: 80 Copynumber: 2.8 Consensus size: 79 32368883 GCTCCTCGTT * * * * * * 32368893 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA 32368958 TTTAA-CAACTCGCA 66 -TTAAGCAACTCGCA * * 32368972 CGACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGG 1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC-AATGCCTTCGGGACTTAACCCGG * * 32369037 ATTAAGTATCTCGCA 65 ATTAAGCAACTCGCA * * * * * * * * 32369052 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG 1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACAATGCCTTCGGGACTTAACCCG 32369116 GA 64 GA 32369118 CAGCATTCAA Statistics Matches: 122, Mismatches: 20, Indels: 7 0.82 0.13 0.05 Matches are distributed among these distances: 79 41 0.34 80 76 0.62 81 5 0.04 ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24 Consensus pattern (79 bp): CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA TTAAGCAACTCGCA Found at i:32369071 original size:40 final size:39 Alignment explanation

Indices: 32368893--32369117 Score: 186 Period size: 40 Copynumber: 5.7 Consensus size: 39 32368883 GCTCCTCGTT * * * * * * 32368893 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA 1 CAAAGGCCTTCGGGACTTAACCCGG-ATTAATAACTCGCA * * * 32368933 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA 1 CAAAGGCCTTCGGGACTTAACCCGGA-TTAATAACTCGCA * ** 32368972 CGACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA 1 CAAAGGCCTTCGGGACTTAACCCGGA-TTAATAACTCGCA * * * 32369012 CGAATGCCTTCGGGACTTAACCCGGATTAAGTATCTCGCA 1 CAAAGGCCTTCGGGACTTAACCCGGATTAA-TAACTCGCA * * * * 32369052 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA 1 CAAAGGCCTTCGGGA-CTTAACCCGGAT-TAATAAC-TCGCA * 32369093 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAAGGCCTTCGGGACTTAACCCGGA 32369118 CAGCATTCAA Statistics Matches: 159, Mismatches: 19, Indels: 14 0.83 0.10 0.07 Matches are distributed among these distances: 39 40 0.25 40 106 0.67 41 13 0.08 ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24 Consensus pattern (39 bp): CAAAGGCCTTCGGGACTTAACCCGGATTAATAACTCGCA Found at i:32374392 original size:30 final size:30 Alignment explanation

Indices: 32374356--32374417 Score: 124 Period size: 30 Copynumber: 2.1 Consensus size: 30 32374346 AATCCCTAAT 32374356 TCCCCAAATTCTCTCAAATCTTTCAAAACC 1 TCCCCAAATTCTCTCAAATCTTTCAAAACC 32374386 TCCCCAAATTCTCTCAAATCTTTCAAAACC 1 TCCCCAAATTCTCTCAAATCTTTCAAAACC 32374416 TC 1 TC 32374418 TTAAACCCAA Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 30 32 1.00 ACGTcount: A:0.32, C:0.37, G:0.00, T:0.31 Consensus pattern (30 bp): TCCCCAAATTCTCTCAAATCTTTCAAAACC Found at i:32379981 original size:19 final size:20 Alignment explanation

Indices: 32379943--32379987 Score: 65 Period size: 19 Copynumber: 2.3 Consensus size: 20 32379933 AAGGATCAAA 32379943 TTGGAACAAAATAGAAAATT 1 TTGGAACAAAATAGAAAATT ** 32379963 TTGGAACAACTTA-AAAATT 1 TTGGAACAAAATAGAAAATT 32379982 TTGGAA 1 TTGGAA 32379988 GTAGGGATCA Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 19 12 0.52 20 11 0.48 ACGTcount: A:0.49, C:0.07, G:0.16, T:0.29 Consensus pattern (20 bp): TTGGAACAAAATAGAAAATT Found at i:32389150 original size:15 final size:15 Alignment explanation

Indices: 32389130--32389158 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 32389120 GTAATCAGAT 32389130 ATCTTTGTTCAAACC 1 ATCTTTGTTCAAACC 32389145 ATCTTTGTTCAAAC 1 ATCTTTGTTCAAAC 32389159 TGGGTACACA 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:0.24, G:0.07, T:0.41 Consensus pattern (15 bp): ATCTTTGTTCAAACC Found at i:32395598 original size:39 final size:39 Alignment explanation

Indices: 32395540--32395677 Score: 224 Period size: 39 Copynumber: 3.5 Consensus size: 39 32395530 AACATGTTTT * * 32395540 TGAGTATTGTGATAGATGCTTGAATGTTATGTGATTAAA 1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA 32395579 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA 1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA * 32395618 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA 1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA * 32395657 T-ATGTAATGTGATATATGCTT 1 TGA-GTATTGTGATATATGCTT 32395678 AAAAGTGCAT Statistics Matches: 94, Mismatches: 4, Indels: 2 0.94 0.04 0.02 Matches are distributed among these distances: 38 1 0.01 39 93 0.99 ACGTcount: A:0.30, C:0.03, G:0.22, T:0.45 Consensus pattern (39 bp): TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA Found at i:32395611 original size:22 final size:22 Alignment explanation

Indices: 32395586--32395657 Score: 66 Period size: 22 Copynumber: 3.5 Consensus size: 22 32395576 AAATGAGTAT 32395586 TGTGATATATGCTTGAATGTTA 1 TGTGATATATGCTTGAATGTTA * 32395608 TGTGAT-TAT--ATG-A-G-TA 1 TGTGATATATGCTTGAATGTTA * 32395624 TTGTGATATATGCTTAAATGTTA 1 -TGTGATATATGCTTGAATGTTA 32395647 TGTGATTATAT 1 TGTGA-TATAT 32395658 ATGTAATGTG Statistics Matches: 39, Mismatches: 3, Indels: 15 0.68 0.05 0.26 Matches are distributed among these distances: 16 2 0.05 17 7 0.18 18 4 0.10 19 2 0.05 20 1 0.03 21 4 0.10 22 12 0.31 23 7 0.18 ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47 Consensus pattern (22 bp): TGTGATATATGCTTGAATGTTA Found at i:32395678 original size:39 final size:39 Alignment explanation

Indices: 32395540--32395694 Score: 222 Period size: 39 Copynumber: 3.9 Consensus size: 39 32395530 AACATGTTTT * * * 32395540 TGAGTATTGTGATAGATGCTTGAATGTTATGTGATTAAA 1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA * 32395579 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA 1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA 32395618 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA 1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA * * * 32395657 T-ATGTAATGTGATATATGCTTAAAAGTGCATGTGATTA 1 TGA-GTATTGTGATATATGCTTAAATGT-TATGTGATTA 32395695 CCATGTAAAT Statistics Matches: 108, Mismatches: 6, Indels: 3 0.92 0.05 0.03 Matches are distributed among these distances: 38 1 0.01 39 98 0.91 40 9 0.08 ACGTcount: A:0.31, C:0.03, G:0.23, T:0.43 Consensus pattern (39 bp): TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA Found at i:32398604 original size:20 final size:20 Alignment explanation

Indices: 32398576--32398643 Score: 75 Period size: 20 Copynumber: 3.4 Consensus size: 20 32398566 CTTACGTGCT * 32398576 CCTATTTGTACTTCGATACC 1 CCTAATTGTACTTCGATACC * * 32398596 CCTGATTGTACTTGCG-TGCC 1 CCTAATTGTACTT-CGATACC * 32398616 CCTAATTGTACTTCAATACC 1 CCTAATTGTACTTCGATACC * 32398636 CCTTATTG 1 CCTAATTG 32398644 CAGTTACGTG Statistics Matches: 39, Mismatches: 7, Indels: 4 0.78 0.14 0.08 Matches are distributed among these distances: 19 1 0.03 20 36 0.92 21 2 0.05 ACGTcount: A:0.19, C:0.29, G:0.13, T:0.38 Consensus pattern (20 bp): CCTAATTGTACTTCGATACC Found at i:32398614 original size:40 final size:40 Alignment explanation

Indices: 32398558--32398686 Score: 159 Period size: 40 Copynumber: 3.2 Consensus size: 40 32398548 AATTATACCA * * 32398558 TGATTGCACTTACGTGCTCCTATTTGTACTTCGATACCCC 1 TGATTGCACTTACGTGCCCCTATTTGTACTTCAATACCCC * * * 32398598 TGATTGTACTTGCGTGCCCCTAATTGTACTTCAATACCCC 1 TGATTGCACTTACGTGCCCCTATTTGTACTTCAATACCCC * * * * * 32398638 TTATTGCAGTTACGTGCCCCTGTTTGTACTTCAGTACCCT 1 TGATTGCACTTACGTGCCCCTATTTGTACTTCAATACCCC * 32398678 TGAATGCAC 1 TGATTGCAC 32398687 ATCGGTGCCC Statistics Matches: 73, Mismatches: 16, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 40 73 1.00 ACGTcount: A:0.19, C:0.29, G:0.16, T:0.36 Consensus pattern (40 bp): TGATTGCACTTACGTGCCCCTATTTGTACTTCAATACCCC Found at i:32398714 original size:20 final size:20 Alignment explanation

Indices: 32398651--32398716 Score: 60 Period size: 20 Copynumber: 3.3 Consensus size: 20 32398641 TTGCAGTTAC * * 32398651 GTGCCCCTGTTTGTACTTCA 1 GTGCCCATGTTTGCACTTCA * * ** * * 32398671 GTACCCTTGAATGCACATCG 1 GTGCCCATGTTTGCACTTCA 32398691 GTGCCCATGTTTGCACTTCA 1 GTGCCCATGTTTGCACTTCA 32398711 GTGCCC 1 GTGCCC 32398717 CTAGTTGCAC Statistics Matches: 33, Mismatches: 13, Indels: 0 0.72 0.28 0.00 Matches are distributed among these distances: 20 33 1.00 ACGTcount: A:0.15, C:0.32, G:0.21, T:0.32 Consensus pattern (20 bp): GTGCCCATGTTTGCACTTCA Found at i:32403764 original size:18 final size:18 Alignment explanation

Indices: 32403738--32403778 Score: 73 Period size: 18 Copynumber: 2.3 Consensus size: 18 32403728 TTTGAAGCAT 32403738 GATGCTGGTTTTGATGAA 1 GATGCTGGTTTTGATGAA * 32403756 GATGTTGGTTTTGATGAA 1 GATGCTGGTTTTGATGAA 32403774 GATGC 1 GATGC 32403779 AATCTTAGTC Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 18 21 1.00 ACGTcount: A:0.22, C:0.05, G:0.34, T:0.39 Consensus pattern (18 bp): GATGCTGGTTTTGATGAA Found at i:32411273 original size:18 final size:18 Alignment explanation

Indices: 32411250--32411287 Score: 58 Period size: 18 Copynumber: 2.1 Consensus size: 18 32411240 AATTTGAAAT 32411250 AAAACAAAAAATTTTGGA 1 AAAACAAAAAATTTTGGA ** 32411268 AAAACATGAAATTTTGGA 1 AAAACAAAAAATTTTGGA 32411286 AA 1 AA 32411288 CAGAGGTCAA Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.58, C:0.05, G:0.13, T:0.24 Consensus pattern (18 bp): AAAACAAAAAATTTTGGA Found at i:32413927 original size:41 final size:41 Alignment explanation

Indices: 32413867--32413944 Score: 138 Period size: 41 Copynumber: 1.9 Consensus size: 41 32413857 CTCACTTATC 32413867 GAAATCATGGTCCCAAAACCATTATTTCTGACACCACCGAA 1 GAAATCATGGTCCCAAAACCATTATTTCTGACACCACCGAA * * 32413908 GAAATCATGGTCCCGAAACCATTATTTCTGGCACCAC 1 GAAATCATGGTCCCAAAACCATTATTTCTGACACCAC 32413945 TGAAAATGAA Statistics Matches: 35, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 41 35 1.00 ACGTcount: A:0.33, C:0.29, G:0.14, T:0.23 Consensus pattern (41 bp): GAAATCATGGTCCCAAAACCATTATTTCTGACACCACCGAA Found at i:32418800 original size:20 final size:19 Alignment explanation

Indices: 32418776--32418823 Score: 51 Period size: 20 Copynumber: 2.5 Consensus size: 19 32418766 TTTTTAACCC * * 32418776 AAATTAATTATTTTCTCTA 1 AAATTAATTAATTACTCTA * * 32418795 ATAATTATTTAATTACTTTA 1 A-AATTAATTAATTACTCTA 32418815 AAATTAATT 1 AAATTAATT 32418824 TTCCCAAAAA Statistics Matches: 23, Mismatches: 5, Indels: 2 0.77 0.17 0.07 Matches are distributed among these distances: 19 8 0.35 20 15 0.65 ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52 Consensus pattern (19 bp): AAATTAATTAATTACTCTA Found at i:32419649 original size:37 final size:37 Alignment explanation

Indices: 32419599--32419673 Score: 132 Period size: 37 Copynumber: 2.0 Consensus size: 37 32419589 AGAGTATGAG * * 32419599 TACAGTGGACGACATCCCTTAGTATTCCTGCTAGGGT 1 TACAGTGGACGACACCCCTTAGTATTCCTCCTAGGGT 32419636 TACAGTGGACGACACCCCTTAGTATTCCTCCTAGGGT 1 TACAGTGGACGACACCCCTTAGTATTCCTCCTAGGGT 32419673 T 1 T 32419674 GTTGCCCCTT Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 37 36 1.00 ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29 Consensus pattern (37 bp): TACAGTGGACGACACCCCTTAGTATTCCTCCTAGGGT Found at i:32420065 original size:12 final size:12 Alignment explanation

Indices: 32420042--32420077 Score: 54 Period size: 12 Copynumber: 2.9 Consensus size: 12 32420032 GCAAATATAT 32420042 CATTTCTCATTTC 1 CATTT-TCATTTC 32420055 CATTTTCATTTC 1 CATTTTCATTTC * 32420067 CATTTCCATTT 1 CATTTTCATTT 32420078 TGAGAAACCT Statistics Matches: 22, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 12 17 0.77 13 5 0.23 ACGTcount: A:0.17, C:0.28, G:0.00, T:0.56 Consensus pattern (12 bp): CATTTTCATTTC Found at i:32420072 original size:18 final size:19 Alignment explanation

Indices: 32420041--32420078 Score: 69 Period size: 18 Copynumber: 2.1 Consensus size: 19 32420031 TGCAAATATA 32420041 TCATTTCTCATTTCCATTT 1 TCATTTCTCATTTCCATTT 32420060 TCATTTC-CATTTCCATTT 1 TCATTTCTCATTTCCATTT 32420078 T 1 T 32420079 GAGAAACCTA Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 18 12 0.63 19 7 0.37 ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58 Consensus pattern (19 bp): TCATTTCTCATTTCCATTT Found at i:32427195 original size:40 final size:40 Alignment explanation

Indices: 32427150--32427436 Score: 346 Period size: 40 Copynumber: 7.2 Consensus size: 40 32427140 CGGAATTTGG * * 32427150 CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC * * * * * * 32427190 CCGGATTTAGTAACTCGCACAAATGCCTTCGGATCTTAGT 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC * * * 32427230 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC * * 32427270 CCGG-TAT-AGCAACTCGCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAATC-ACTAGCACAAATGCCTTCGGGTCTTAGC * * * 32427309 CCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC * * 32427349 CCGGATAT-AGCAACTCGCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAATC-ACTAGCACAAATGCCTTCGGGTCTTAGC * * * 32427389 CCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC 32427429 CCGGATAT 1 CCGGATAT 32427437 CATTCAAATG Statistics Matches: 204, Mismatches: 38, Indels: 10 0.81 0.15 0.04 Matches are distributed among these distances: 38 2 0.01 39 33 0.16 40 165 0.81 41 4 0.02 ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24 Consensus pattern (40 bp): CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:32427391 original size:80 final size:80 Alignment explanation

Indices: 32427150--32427436 Score: 468 Period size: 80 Copynumber: 3.6 Consensus size: 80 32427140 CGGAATTTGG * * * * * * * 32427150 CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAGTAACTCGCACAAATG 1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG * * 32427215 CCTTCGGATCTTAGT 66 CCTTCGGGTCTTAGC * * 32427230 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGG-TATAGCAACTCGCACAAATG 1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG 32427294 CCTTCGGGTCTTAGC 66 CCTTCGGGTCTTAGC 32427309 CCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG 1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG 32427374 CCTTCGGGTCTTAGC 66 CCTTCGGGTCTTAGC 32427389 CCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATAT 1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATAT 32427437 CATTCAAATG Statistics Matches: 195, Mismatches: 11, Indels: 2 0.94 0.05 0.01 Matches are distributed among these distances: 79 73 0.37 80 122 0.63 ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24 Consensus pattern (80 bp): CCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG CCTTCGGGTCTTAGC Found at i:32435382 original size:79 final size:82 Alignment explanation

Indices: 32435271--32435455 Score: 229 Period size: 79 Copynumber: 2.3 Consensus size: 82 32435261 GCTACTCGTT * * * 32435271 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC 1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC * * 32435334 GGATTTAGTAAC-TCGCA 65 GGATATAGTAACTTAGCA * ** 32435351 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG 1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG * * 32435414 GATATGGTCACTTAGCA 66 GATATAGTAACTTAGCA 32435431 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 32435456 CATCATTCAA Statistics Matches: 91, Mismatches: 10, Indels: 8 0.83 0.09 0.07 Matches are distributed among these distances: 78 3 0.03 79 54 0.59 80 34 0.37 ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25 Consensus pattern (82 bp): CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG GATATAGTAACTTAGCA Found at i:32435455 original size:40 final size:40 Alignment explanation

Indices: 32435252--32435455 Score: 229 Period size: 40 Copynumber: 5.1 Consensus size: 40 32435242 CGGAATTTAA ** * 32435252 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC 1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC * * * 32435292 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC 1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC * 32435332 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC 1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC * * 32435371 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT 1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC * * * 32435411 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC 1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC 32435451 CCGGA 1 CCGGA 32435456 CATCATTCAA Statistics Matches: 139, Mismatches: 18, Indels: 14 0.81 0.11 0.08 Matches are distributed among these distances: 38 2 0.01 39 33 0.24 40 92 0.66 41 12 0.09 ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25 Consensus pattern (40 bp): CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC Found at i:32437395 original size:10 final size:10 Alignment explanation

Indices: 32437382--32437408 Score: 54 Period size: 10 Copynumber: 2.7 Consensus size: 10 32437372 GAAAAACCAT 32437382 AAAAAAAGAA 1 AAAAAAAGAA 32437392 AAAAAAAGAA 1 AAAAAAAGAA 32437402 AAAAAAA 1 AAAAAAA 32437409 ACAACAAAAA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 17 1.00 ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00 Consensus pattern (10 bp): AAAAAAAGAA Found at i:32437396 original size:11 final size:11 Alignment explanation

Indices: 32437382--32437419 Score: 51 Period size: 11 Copynumber: 3.5 Consensus size: 11 32437372 GAAAAACCAT 32437382 AAAAAAAG-AA 1 AAAAAAAGAAA 32437392 AAAAAAAGAAA 1 AAAAAAAGAAA * 32437403 AAAAAAACAACA 1 AAAAAAAGAA-A 32437415 AAAAA 1 AAAAA 32437420 CCAGCAAAAC Statistics Matches: 25, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 10 8 0.32 11 11 0.44 12 6 0.24 ACGTcount: A:0.89, C:0.05, G:0.05, T:0.00 Consensus pattern (11 bp): AAAAAAAGAAA Found at i:32449367 original size:6 final size:6 Alignment explanation

Indices: 32449345--32449397 Score: 52 Period size: 6 Copynumber: 8.3 Consensus size: 6 32449335 GAAAGTATAA * * * 32449345 AAAAAT AATAAT AAAAAAT AAAAGT AACAAGAA AAAAAT AAAAAT AAAAAT 1 AAAAAT AAAAAT -AAAAAT AAAAAT AA-AA-AT AAAAAT AAAAAT AAAAAT 32449396 AA 1 AA 32449398 CTATAAAAGA Statistics Matches: 38, Mismatches: 6, Indels: 6 0.76 0.12 0.12 Matches are distributed among these distances: 6 27 0.71 7 9 0.24 8 2 0.05 ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15 Consensus pattern (6 bp): AAAAAT Found at i:32449405 original size:12 final size:12 Alignment explanation

Indices: 32449345--32449397 Score: 52 Period size: 13 Copynumber: 4.2 Consensus size: 12 32449335 GAAAGTATAA * 32449345 AAAAATAATAAT 1 AAAAATAAAAAT * 32449357 AAAAAATAAAAGT 1 -AAAAATAAAAAT * 32449370 AACAAGAAAAAAAT 1 AA-AA-ATAAAAAT 32449384 AAAAATAAAAAT 1 AAAAATAAAAAT 32449396 AA 1 AA 32449398 CTATAAAAGA Statistics Matches: 33, Mismatches: 5, Indels: 5 0.77 0.12 0.12 Matches are distributed among these distances: 12 11 0.33 13 14 0.42 14 8 0.24 ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15 Consensus pattern (12 bp): AAAAATAAAAAT Found at i:32451208 original size:4 final size:4 Alignment explanation

Indices: 32451201--32451239 Score: 53 Period size: 4 Copynumber: 9.8 Consensus size: 4 32451191 ACAAAACAGT * 32451201 TTTA TTTA -ATA TTCTA TTTA TTTA TTTA TTTA TTTA TTT 1 TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTT 32451240 CAATTTTTGA Statistics Matches: 31, Mismatches: 2, Indels: 4 0.84 0.05 0.11 Matches are distributed among these distances: 3 2 0.06 4 25 0.81 5 4 0.13 ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72 Consensus pattern (4 bp): TTTA Found at i:32452777 original size:15 final size:15 Alignment explanation

Indices: 32452757--32452793 Score: 56 Period size: 15 Copynumber: 2.4 Consensus size: 15 32452747 GTCGCCCTTT * 32452757 TTATTTTTTATTTTA 1 TTATTTTTTATATTA 32452772 TTATTTTTTATATTA 1 TTATTTTTTATATTA 32452787 TGTATTT 1 T-TATTT 32452794 AATATATATA Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 15 15 0.75 16 5 0.25 ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76 Consensus pattern (15 bp): TTATTTTTTATATTA Found at i:32453921 original size:44 final size:44 Alignment explanation

Indices: 32453629--32454706 Score: 539 Period size: 44 Copynumber: 23.9 Consensus size: 44 32453619 GATTCATCGT * * ** * 32453629 TTTAAT-TCGCTCCACTGCAACTTCAAGGAGATAGGATTAATAGC 1 TTTAATCT-GCTCCACTGCAACTTCAGGGAGATAAGATTTGTATC * * 32453673 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATC 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATC * * * ** 32453717 TTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGGC 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATC * * 32453761 TTTAATATGCTCCATTGCAACTTCAGGGAGATAAGATTTGTAGCCTATC 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TT-T-G--TATC * * * 32453810 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATT 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT--TGTATC * * * * * 32453856 TTTAA-CTTGTTCCAGTGCAACTTCAGGGGGATAAGGTTTGTGTC 1 TTTAATC-TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATC * * 32453900 TTTAATCTGCCCCACTGCAACTTCAGGGAGATAAGATTTGTTTATT 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG--TATC * * * * 32453946 TTTAACCTGTTCCACTGCAGCTTCAGGGAGATAAGGTTTG-A-- 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATC * * * * * * 32453987 TATGATTTGCTCTACTGTAACTTCAGAGAGATAAGATTTGTAATTTATAGC 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-----TAT--C * * * ** 32454038 TTTAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTCACTATC 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TGTATC * * * * * * * 32454083 TTCAGTCTGTTCCATTGCAGCTTCAGGGAGATAAGACTTGTAAC 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATC * * * * * 32454127 TTCAACCTGCTCCACTGCAACTTCTGAGAGATAAGGTTTG---C 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATC * * * * * * * 32454168 TATGATCTGTTCTACTGTAACTTCAGAGAGATAAGATCTGAAATTTATAGC 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T----TGTAT--C * * * * * * * 32454219 TTCAATATGTTCCACTGCAACTTCAAGAAAATAAGATTCGCTATC 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATC ** * * * * * * * 32454264 TCCAGTCTGTTCTACTGCAGCTTCAAGGAGATAAGACTTGTAAC 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATC * * * * 32454308 TTCAACCTGCTCCATTGCAACTTCAGGGAGATAAGGTTTG---C 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATC * * * * ** * 32454349 TATGATTTGCTCTACTGCAACTTCAAAGAGATAAGATCTGCAATTTATAGC 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T----TGTAT--C * ** * * * * 32454400 TTCAATCTATTCCAATACAACTTCAGGGAAATAAGATTCGCTATC 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATC * * * * * * 32454445 TTCAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTTGTAGC 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATC * * * * 32454489 TTCAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTTG---C 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATC * * * * * * 32454530 TATGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTAATTTATAGC 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T-T--TGTAT--C * ** * * * * 32454581 TTCAATCTATTCCATTGCAACTTTAGGGAAATAAGATTCGCTATC 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATC * * * * * * ** 32454626 TTCAGTCTGCTCCACT-TAACTTCAGAGAGATAAGACTAGTGGC 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATC * * 32454669 TTCAATCTGCTCCACTGCAACTTCAGGGGGATAAGATT 1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT 32454707 CGCCATGATG Statistics Matches: 774, Mismatches: 204, Indels: 112 0.71 0.19 0.10 Matches are distributed among these distances: 41 115 0.15 42 2 0.00 43 19 0.02 44 282 0.36 45 115 0.15 46 75 0.10 47 14 0.02 48 3 0.00 49 38 0.05 50 2 0.00 51 109 0.14 ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32 Consensus pattern (44 bp): TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATC Found at i:32453923 original size:139 final size:134 Alignment explanation

Indices: 32453640--32454166 Score: 474 Period size: 137 Copynumber: 3.9 Consensus size: 134 32453630 TTAATTCGCT * * ** * 32453640 CCACTGCAACTTCAAGGAGATAGGA-TT-AATAGCTTCAATCTGCTCCACTGCAACTTCAGGGAG 1 CCACTGCAACTTCAGGGAGATAAGATTTGTCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAG 32453703 ATAAGATTGGTATCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGGCTTTAATA 66 ATAAGATTGGTATCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGGCTTTAATA * 32453768 TGCT 131 TGCC * 32453772 CCATTGCAACTTCAGGGAGATAAGATTTGTAGCCTATCTTCAATCTGCTCCACTGCAACTTCAGG 1 CCACTGCAACTTCAGGGAGATAAGATTTGT---CTATCTTCAATCTGCTCCACTGCAACTTCAGG * * * * * * * 32453837 GAGATAAGATTGGTTTATTTTTAACTTGTTCCAGTGCAACTTCAGGGGGATAAGGTTTGTGTCTT 63 GAGATAAGATTGG--TATCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGGCTT * 32453902 TAATCTGCC 126 TAATATGCC * * * * * * 32453911 CCACTGCAACTTCAGGGAGATAAGATTTGTTTATTTTTAACCTGTTCCACTGCAGCTTCAGGGAG 1 CCACTGCAACTTCAGGGAGATAAGATTTGTCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAG * * * * ** * * * * * 32453976 ATAAGGTTTG-AT-AT-GATTTGCTCTACTGTAACTTCAGAGAGATAAGATTTGTAATTTATAGC 66 ATAAGATTGGTATCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAG----G---TTTGTGGC * ** 32454038 TTTAATCTGTT 124 TTTAATATGCC * * ** * * * * 32454049 CCACTGCAACTTTAGGGAAATAAGA-TTCACTATCTTCAGTCTGTTCCATTGCAGCTTCAGGGAG 1 CCACTGCAACTTCAGGGAGATAAGATTTGTCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAG * * * 32454113 ATAAGACTT-GTAACTTCAACCTGCTCCACTGCAACTTCTGAGAGATAAGGTTTG 66 ATAAGA-TTGGTATCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG 32454167 CTATGATCTG Statistics Matches: 319, Mismatches: 58, Indels: 35 0.77 0.14 0.08 Matches are distributed among these distances: 131 24 0.08 132 23 0.07 133 7 0.02 135 1 0.00 136 38 0.12 137 80 0.25 138 40 0.13 139 80 0.25 140 26 0.08 ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33 Consensus pattern (134 bp): CCACTGCAACTTCAGGGAGATAAGATTTGTCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAG ATAAGATTGGTATCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGGCTTTAATA TGCC Found at i:32453932 original size:90 final size:89 Alignment explanation

Indices: 32453683--32454660 Score: 392 Period size: 92 Copynumber: 10.8 Consensus size: 89 32453673 TTCAATCTGC * * * 32453683 TCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGCTCCACTGCAACTTCAGGGAGA 1 TCCACTGCAACTTCAGGGAGATAAGATTTGTGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGA * * *** * 32453748 TAAGGTT-TGTGGCTTTAA-TATGC 66 TAAGATTGTTTATTTTTAACT-TGT * 32453771 TCCATTGCAACTTCAGGGAGATAAGATTTGTAGCCTATCTTCAATCTGCTCCACTGCAACTTCAG 1 TCCACTGCAACTTCAGGGAGATAAGATTTGT-G----TCTTCAATCTGCTCCACTGCAACTTCAG 32453836 GGAGATAAGATTGGTTTATTTTTAACTTGT 61 GGAGATAAGATT-GTTTATTTTTAACTTGT * * * * * 32453866 TCCAGTGCAACTTCAGGGGGATAAGGTTTGTGTCTTTAATCTGCCCCACTGCAACTTCAGGGAGA 1 TCCACTGCAACTTCAGGGAGATAAGATTTGTGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGA * 32453931 TAAGATTTGTTTATTTTTAACCTGT 66 TAAGA-TTGTTTATTTTTAACTTGT * * * * * * * * * 32453956 TCCACTGCAGCTTCAGGGAGATAAGGTTTG-AT-AT-GATTTGCTCTACTGTAACTTCAGAGAGA 1 TCCACTGCAACTTCAGGGAGATAAGATTTGTGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGA * 32454018 TAAGATTTGTAATTTATAGCTTTAA-TCTGT 66 TAAGA-TTG---TTTAT--TTTTAACT-TGT * * ** * * * * * 32454048 TCCACTGCAACTTTAGGGAAATAAGATTCACTATCTTCAGTCTGTTCCATTGCAGCTTCAGGGAG 1 TCCACTGCAACTTCAGGGAGATAAGATT-TGTGTCTTCAATCTGCTCCACTGCAACTTCAGGGAG ** * * * 32454113 ATAAGACTTG--TAACTTCAACCTGC 65 ATAAGA-TTGTTTATTTTTAACTTGT * * * * * * * * 32454137 TCCACTGCAACTTCTGAGAGATAAG-GTT-TG-CTAT-GATCTGTTCTACTGTAACTTCAGAGAG 1 TCCACTGCAACTTCAGGGAGATAAGATTTGTGTCT-TCAATCTGCTCCACTGCAACTTCAGGGAG * * 32454198 ATAAGATCTGAAATTTATAGCTTCAA-TATGT 65 ATAAGAT-TG---TTTAT--TTTTAACT-TGT * * * * * * * * * * * 32454229 TCCACTGCAACTTCAAGAAAATAAGATTCGCTATCTCCAGTCTGTTCTACTGCAGCTTCAAGGAG 1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TGTCTTCAATCTGCTCCACTGCAACTTCAGGGAG ** * * * 32454294 ATAAGACTTG--TAACTTCAACCTGC 65 ATAAGA-TTGTTTATTTTTAACTTGT * * * * * ** 32454318 TCCATTGCAACTTCAGGGAGATAAG-GTT-TG-CTAT-GATTTGCTCTACTGCAACTTCAAAGAG 1 TCCACTGCAACTTCAGGGAGATAAGATTTGTGTCT-TCAATCTGCTCCACTGCAACTTCAGGGAG * * * 32454379 ATAAGATCTGCAATTTATAGCTTCAA-TCTAT 65 ATAAGAT-TG---TTTAT--TTTTAACT-TGT * * * * * * * * 32454410 TCCAATACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTACTCCACTGCAACTTTAGGGAG 1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TGTCTTCAATCTGCTCCACTGCAACTTCAGGGAG ** * * ** 32454475 ATAAGACTTG--TAGCTTCAACCTAC 65 ATAAGA-TTGTTTATTTTTAACTTGT * * * * * 32454499 TCCACTGCAACTTCAGGGAGATAAG-GTT-TG-CTAT-GATCTGCTCTACTGTAACTTCAGAGAG 1 TCCACTGCAACTTCAGGGAGATAAGATTTGTGTCT-TCAATCTGCTCCACTGCAACTTCAGGGAG * * * 32454560 ATAAGATCTGTAATTTATAGCTTCAA-TCTAT 65 ATAAGAT-TG---TTTAT--TTTTAACT-TGT * * * * * * * * 32454591 TCCATTGCAACTTTAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACT-TAACTTCAGAGAG 1 TCCACTGCAACTTCAGGGAGATAAGATTTG-TGTCTTCAATCTGCTCCACTGCAACTTCAGGGAG 32454655 ATAAGA 65 ATAAGA 32454661 CTAGTGGCTT Statistics Matches: 676, Mismatches: 145, Indels: 131 0.71 0.15 0.14 Matches are distributed among these distances: 84 3 0.00 85 91 0.13 86 5 0.01 87 31 0.05 88 33 0.05 89 88 0.13 90 90 0.13 91 8 0.01 92 119 0.18 93 41 0.06 94 3 0.00 95 62 0.09 96 100 0.15 97 2 0.00 ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33 Consensus pattern (89 bp): TCCACTGCAACTTCAGGGAGATAAGATTTGTGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGA TAAGATTGTTTATTTTTAACTTGT Found at i:32454066 original size:92 final size:89 Alignment explanation

Indices: 32453814--32454660 Score: 533 Period size: 92 Copynumber: 9.4 Consensus size: 89 32453804 CCTATCTTCA * * * * * * * 32453814 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTAT--TTTTAACTTGTTCCAGTGCAAC 1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTTTATAGCTTCAACCTGTTCCACTGCAAC ** * * 32453877 TTCAGGGGGATAAGGTTTGTGTCTTTA 66 TTCAGGGAAATAAGG-TT-TG-CTATG * * * * * * 32453904 ATCTGCCCCACTGCAACTTCAGGGAGATAAGATTTGTTTAT--TTTTAACCTGTTCCACTGCAGC 1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTTTATAGCTTCAACCTGTTCCACTGCAAC * * 32453967 TTCAGGGAGATAAGGTTTGATATG 66 TTCAGGGAAATAAGGTTTGCTATG * * * * 32453991 ATTTGCTCTACTGTAACTTCAGAGAGATAAGATTTGTAATTTATAGCTTTAATCTGTTCCACTGC 1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTG---TTTATAGCTTCAACCTGTTCCACTGC * * ** * 32454056 AACTTTAGGGAAATAAGATTCACTATCTTC 63 AACTTCAGGGAAATAAGGTTTGCTA---TG * * * * * * * 32454086 AGTCTGTTCCATTGCAGCTTCAGGGAGATAAGACTTG--TA-A-CTTCAACCTGCTCCACTGCAA 1 A-TCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTTTATAGCTTCAACCTGTTCCACTGCAA * * * 32454147 CTTCTGAGAGATAAGGTTTGCTATG 65 CTTCAGGGAAATAAGGTTTGCTATG * * * ** 32454172 ATCTGTTCTACTGTAACTTCAGAGAGATAAGATCTGAAATTTATAGCTTCAATATGTTCCACTGC 1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTG---TTTATAGCTTCAACCTGTTCCACTGC * * * * * 32454237 AACTTCAAGAAAATAAGATTCGCTATCTCC 63 AACTTCAGGGAAATAAGGTTTGCTA--T-G * * * * * 32454267 AGTCTGTTCTACTGCAGCTTCA-AGGAGATAAGACTTG--TA-A-CTTCAACCTGCTCCATTGCA 1 A-TCTGCTCTACTGCAACTTCAGA-GAGATAAGATTTGTTTATAGCTTCAACCTGTTCCACTGCA * 32454327 ACTTCAGGGAGATAAGGTTTGCTATG 64 ACTTCAGGGAAATAAGGTTTGCTATG * * * * * * * 32454353 ATTTGCTCTACTGCAACTTCAAAGAGATAAGATCTGCAATTTATAGCTTCAATCTATTCCAATAC 1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTG---TTTATAGCTTCAACCTGTTCCACTGC * * * 32454418 AACTTCAGGGAAATAAGATTCGCTATCTTC 63 AACTTCAGGGAAATAAGGTTTGCTA---TG * * * * * ** 32454448 AGTCTACTCCACTGCAACTTTAGGGAGATAAGACTTG----TAGCTTCAACCTACTCCACTGCAA 1 A-TCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTTTATAGCTTCAACCTGTTCCACTGCAA * 32454509 CTTCAGGGAGATAAGGTTTGCTATG 65 CTTCAGGGAAATAAGGTTTGCTATG * * * * * 32454534 ATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTATTCCATTGC 1 ATCTGCTCTACTGCAACTTCAGAGAGATAAGAT-T-T-GTTTATAGCTTCAACCTGTTCCACTGC * * * * 32454599 AACTTTAGGGAAATAAGATTCGCTATCTTC 63 AACTTCAGGGAAATAAGGTTTGCTA---TG * * 32454629 AGTCTGCTCCACT-TAACTTCAGAGAGATAAGA 1 A-TCTGCTCTACTGCAACTTCAGAGAGATAAGA 32454661 CTAGTGGCTT Statistics Matches: 592, Mismatches: 121, Indels: 83 0.74 0.15 0.10 Matches are distributed among these distances: 85 82 0.14 86 7 0.01 87 35 0.06 88 2 0.00 89 111 0.19 90 83 0.14 91 6 0.01 92 145 0.24 94 1 0.00 95 27 0.05 96 93 0.16 ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33 Consensus pattern (89 bp): ATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTTTATAGCTTCAACCTGTTCCACTGCAAC TTCAGGGAAATAAGGTTTGCTATG Found at i:32454096 original size:227 final size:228 Alignment explanation

Indices: 32453639--32454166 Score: 566 Period size: 227 Copynumber: 2.3 Consensus size: 228 32453629 TTTAATTCGC * * * * * 32453639 TCCACTGCAACTTCAAGGAGATAGGA-TTAATAGCTTCAATCTGCTCCACTGCAACTTCAGGGAG 1 TCCAGTGCAACTTCAGGGAGATAAGACTT-GTAACTTCAATCTGCTCCACTGCAACTTCAGGGAG * * 32453703 ATAAGA-TTGGTATCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGGCTTTAAT 65 ATAAGATTTGGTATCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGGATATAAT * * * 32453767 ATGCTCCATTGCAACTTCAGGGAGATAAGATTTGTAGCCTATCTTCAATCTGCTCCACTGCAACT 130 ATGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAACCTATCTTCAATCTGCTCCACTGCAACT * *** * * 32453832 TCAGGGAGATAAGATTGGTTTATTTTTAACTTGT 195 TCAGGGAAATAAGATTGCACTATCTTCAACTTGT * ** ** * * 32453866 TCCAGTGCAACTTCAGGGGGATAAGGTTTGTGTCTTTAATCTGCCCCACTGCAACTTCAGGGAGA 1 TCCAGTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGA * * * * * * 32453931 TAAGATTTGTTTATTTTTAACCTGTTCCACTGCAGCTTCAGGGAGATAAGG-TT-T-GATATGAT 66 TAAGATTTG-GTATCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGGATATAAT * * * ** * * 32453993 TTGCTCTACTGTAACTTCAGAGAGATAAGATTTGTAATTTATAGCTTTAATCTGTTCCACTGCAA 130 ATGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAACCTAT--CTTCAATCTGCTCCACTGCAA * * 32454058 CTTTAGGGAAATAAGATT-CACTATCTTC-AGTCTGT 193 CTTCAGGGAAATAAGATTGCACTATCTTCAACT-TGT * * * * * 32454093 TCCATTGCAGCTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCTGAGAGA 1 TCCAGTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGA * 32454158 TAAGGTTTG 66 TAAGATTTG 32454167 CTATGATCTG Statistics Matches: 246, Mismatches: 49, Indels: 12 0.80 0.16 0.04 Matches are distributed among these distances: 226 41 0.17 227 127 0.52 228 42 0.17 229 36 0.15 ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33 Consensus pattern (228 bp): TCCAGTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGA TAAGATTTGGTATCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGGATATAATA TGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAACCTATCTTCAATCTGCTCCACTGCAACTT CAGGGAAATAAGATTGCACTATCTTCAACTTGT Found at i:32454163 original size:181 final size:181 Alignment explanation

Indices: 32453668--32454703 Score: 1181 Period size: 181 Copynumber: 5.7 Consensus size: 181 32453658 GATAGGATTA ** * * ** 32453668 ATAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GGTATCTTCAACCTGCTCCAC 1 ATAGCTTCAATCTATTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCAC ** ** * ** * 32453732 TGCAACTTCAGGGAGATAAGGTTTGTGGCTTTAATATGCTCCATTGCAACTTCAGGGAGATAAGA 66 TGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAG- * * * * * * 32453797 TTTGTAGCCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG--GTTT 130 GTT-T-G-CTA---T-GATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTAATTT * * * * ** * * * * * * 32453853 AT--TTTTAA-CTTGTTCCAGTGCAACTTCAGGGGGATAAGGTTTG-TGTCTTTAATCTGCCCCA 1 ATAGCTTCAATC-TATTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCA * ** * * * 32453914 CTGCAACTTCAGGGAGATAAGATTTGTTTATTTTTAACCTGTTCCACTGCAGCTTCAGGGAGATA 65 CTGCAACTTCAGGGAGATAAGACTTG--TAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATA * * * 32453979 AGGTTTGATATGATTTGCTCTACTGTAACTTCAGAGAGATAAGATTTGTAATTT 128 AGGTTTGCTATGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTAATTT * * * * * * 32454033 ATAGCTTTAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTCACTATCTTCAGTCTGTTCCAT 1 ATAGCTTCAATCTATTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCAC * * * 32454098 TGCAGCTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCTGAGAGATAAGG 66 TGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGG * * 32454163 TTTGCTATGATCTGTTCTACTGTAACTTCAGAGAGATAAGATCTGAAATTT 131 TTTGCTATGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTAATTT * * * * * * * 32454214 ATAGCTTCAATATGTTCCACTGCAACTTCAAGAAAATAAGATTCGCTATCTCCAGTCTGTTCTAC 1 ATAGCTTCAATCTATTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCAC * * * 32454279 TGCAGCTTCAAGGAGATAAGACTTGTAACTTCAACCTGCTCCATTGCAACTTCAGGGAGATAAGG 66 TGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGG * * * * 32454344 TTTGCTATGATTTGCTCTACTGCAACTTCAAAGAGATAAGATCTGCAATTT 131 TTTGCTATGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTAATTT * * * 32454395 ATAGCTTCAATCTATTCCAATACAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTACTCCAC 1 ATAGCTTCAATCTATTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCAC * * * 32454460 TGCAACTTTAGGGAGATAAGACTTGTAGCTTCAACCTACTCCACTGCAACTTCAGGGAGATAAGG 66 TGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGG 32454525 TTTGCTATGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTAATTT 131 TTTGCTATGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTAATTT * * 32454576 ATAGCTTCAATCTATTCCATTGCAACTTTAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCAC 1 ATAGCTTCAATCTATTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCAC * * * ** * * 32454641 T-TAACTTCAGAGAGATAAGACTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGGGGATAAG 66 TGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAG 32454704 ATTCGCCATG Statistics Matches: 735, Mismatches: 105, Indels: 27 0.85 0.12 0.03 Matches are distributed among these distances: 177 29 0.04 178 3 0.00 180 59 0.08 181 467 0.64 182 33 0.04 183 108 0.15 184 3 0.00 185 33 0.04 ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32 Consensus pattern (181 bp): ATAGCTTCAATCTATTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCAC TGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGG TTTGCTATGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTAATTT Found at i:32459091 original size:50 final size:50 Alignment explanation

Indices: 32458983--32459221 Score: 239 Period size: 50 Copynumber: 4.7 Consensus size: 50 32458973 ATTTGGGTAA * * 32458983 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGTATCATTGAGGCTATG 1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGG---CACTGA-G--ATG * * * 32459039 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACTGAGATG 1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG * ** * * * 32459089 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG 1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG * * * * * 32459139 AGA-ACTCCCATGTAAGACCATATCTGGGACATGACATTGGCAGT-ACAAG 1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG * * 32459188 AAACATCCCATGTAAGACCATGTCTGGGACATGG 1 AGAGATCCCATGTAAGACCATGTCTGGGACATGG 32459222 TTTTGGCATA Statistics Matches: 156, Mismatches: 25, Indels: 11 0.81 0.13 0.06 Matches are distributed among these distances: 49 32 0.21 50 82 0.53 52 1 0.01 53 5 0.03 56 36 0.23 ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22 Consensus pattern (50 bp): AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG Found at i:32460553 original size:12 final size:12 Alignment explanation

Indices: 32460523--32460580 Score: 62 Period size: 12 Copynumber: 4.6 Consensus size: 12 32460513 AGTATAAAAT * 32460523 AATAATAATAAC 1 AATAAAAATAAC * 32460535 AAATAAAAGTAAC 1 -AATAAAAATAAC * 32460548 AATAAAAAAATAAA 1 AAT--AAAAATAAC 32460562 AATAAAAATAAC 1 AATAAAAATAAC 32460574 AATAAAA 1 AATAAAA 32460581 GAGTAATATA Statistics Matches: 38, Mismatches: 5, Indels: 5 0.79 0.10 0.10 Matches are distributed among these distances: 12 18 0.47 13 10 0.26 14 10 0.26 ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17 Consensus pattern (12 bp): AATAAAAATAAC Found at i:32460566 original size:26 final size:27 Alignment explanation

Indices: 32460511--32460580 Score: 88 Period size: 26 Copynumber: 2.6 Consensus size: 27 32460501 AGAAAACATG * * 32460511 AAAGTATAAAATAATAATAATAACAAATA 1 AAAGTA-ACAATAA-AAAAATAACAAATA 32460540 AAAGTAACAATAAAAAAATAA-AAATA 1 AAAGTAACAATAAAAAAATAACAAATA * 32460566 AAAATAACAATAAAA 1 AAAGTAACAATAAAA 32460581 GAGTAATATA Statistics Matches: 38, Mismatches: 3, Indels: 3 0.86 0.07 0.07 Matches are distributed among these distances: 26 19 0.50 27 7 0.18 28 6 0.16 29 6 0.16 ACGTcount: A:0.74, C:0.04, G:0.03, T:0.19 Consensus pattern (27 bp): AAAGTAACAATAAAAAAATAACAAATA Found at i:32462156 original size:23 final size:24 Alignment explanation

Indices: 32462101--32462199 Score: 89 Period size: 23 Copynumber: 4.3 Consensus size: 24 32462091 AGTGTTATTG * * * 32462101 ATCAGTGGCAGCTTCAGTTACATT 1 ATCAGTGGTAGCTTCGGCTACATT ** * 32462125 -TCAACGGTAGCTACGGCTACATT 1 ATCAGTGGTAGCTTCGGCTACATT ** 32462148 A-CAGTGGTAGCTTCAACTACA-T 1 ATCAGTGGTAGCTTCGGCTACATT * 32462170 ATCAGTGGTAGCTTTGGCTACA-T 1 ATCAGTGGTAGCTTCGGCTACATT 32462193 ATCAGTG 1 ATCAGTG 32462200 TGACACTTAT Statistics Matches: 59, Mismatches: 14, Indels: 5 0.76 0.18 0.06 Matches are distributed among these distances: 22 2 0.03 23 57 0.97 ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30 Consensus pattern (24 bp): ATCAGTGGTAGCTTCGGCTACATT Found at i:32462199 original size:46 final size:46 Alignment explanation

Indices: 32462101--32462199 Score: 110 Period size: 46 Copynumber: 2.2 Consensus size: 46 32462091 AGTGTTATTG ** * 32462101 ATCAGTGGCAGCTTCAGTTACATTTCAACGGTAGCTACGGCTACAT 1 ATCAGTGGCAGCTTCAACTACATATCAACGGTAGCTACGGCTACAT * ** ** 32462147 -TACAGTGGTAGCTTCAACTACATATCAGTGGTAGCTTTGGCTACAT 1 AT-CAGTGGCAGCTTCAACTACATATCAACGGTAGCTACGGCTACAT 32462193 ATCAGTG 1 ATCAGTG 32462200 TGACACTTAT Statistics Matches: 43, Mismatches: 8, Indels: 4 0.78 0.15 0.07 Matches are distributed among these distances: 45 1 0.02 46 41 0.95 47 1 0.02 ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30 Consensus pattern (46 bp): ATCAGTGGCAGCTTCAACTACATATCAACGGTAGCTACGGCTACAT Found at i:32462449 original size:23 final size:25 Alignment explanation

Indices: 32462403--32462449 Score: 62 Period size: 23 Copynumber: 2.0 Consensus size: 25 32462393 GAAATTGCTA * * 32462403 AGAAATGTTTGATTAGTTATATGAG 1 AGAAATGTTTAATTAGTTAAATGAG 32462428 AGAAATG-TTAATT-GTTAAATGA 1 AGAAATGTTTAATTAGTTAAATGA 32462450 ATATTTATAG Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 23 8 0.40 24 5 0.25 25 7 0.35 ACGTcount: A:0.40, C:0.00, G:0.21, T:0.38 Consensus pattern (25 bp): AGAAATGTTTAATTAGTTAAATGAG Found at i:32469763 original size:25 final size:22 Alignment explanation

Indices: 32469733--32469844 Score: 91 Period size: 25 Copynumber: 4.6 Consensus size: 22 32469723 CTTGAGCTAT 32469733 ATAACGGGAAGCTCATGTGAGCC 1 ATAACGGGAAGCTCATG-GAGCC 32469756 ATGCAACGGGAAGCTCATAGGAGCC 1 AT--AACGGGAAGCTCAT-GGAGCC * 32469781 ATAATCAGGAAGCTCATGCGAGCC 1 ATAA-CGGGAAGCTCATG-GAGCC * * 32469805 AAGAACGGGTAGCTC-TGAAGAGCC 1 -ATAACGGGAAGCTCATG--GAGCC 32469829 ATTAATCGGGAAGCTC 1 A-TAA-CGGGAAGCTC 32469845 CGAATAGTCA Statistics Matches: 73, Mismatches: 7, Indels: 16 0.76 0.07 0.17 Matches are distributed among these distances: 23 8 0.11 24 31 0.42 25 33 0.45 26 1 0.01 ACGTcount: A:0.32, C:0.22, G:0.29, T:0.16 Consensus pattern (22 bp): ATAACGGGAAGCTCATGGAGCC Found at i:32469804 original size:49 final size:49 Alignment explanation

Indices: 32469739--32469844 Score: 135 Period size: 49 Copynumber: 2.2 Consensus size: 49 32469729 CTATATAACG * * * 32469739 GGAAGCTCATGTGAGCCATGCAACGGGAAGCTCAT-AGGAGCCA-TAATCA 1 GGAAGCTCATGCGAGCCAAG-AACGGGAAGCTC-TGAAGAGCCATTAATCA * * 32469788 GGAAGCTCATGCGAGCCAAGAACGGGTAGCTCTGAAGAGCCATTAATCG 1 GGAAGCTCATGCGAGCCAAGAACGGGAAGCTCTGAAGAGCCATTAATCA 32469837 GGAAGCTC 1 GGAAGCTC 32469845 CGAATAGTCA Statistics Matches: 50, Mismatches: 5, Indels: 4 0.85 0.08 0.07 Matches are distributed among these distances: 47 1 0.02 48 18 0.36 49 31 0.62 ACGTcount: A:0.31, C:0.23, G:0.30, T:0.16 Consensus pattern (49 bp): GGAAGCTCATGCGAGCCAAGAACGGGAAGCTCTGAAGAGCCATTAATCA Found at i:32469818 original size:24 final size:23 Alignment explanation

Indices: 32469735--32469819 Score: 82 Period size: 24 Copynumber: 3.5 Consensus size: 23 32469725 TGAGCTATAT * 32469735 AACGGGAAGCTCATGTGAGCCATG 1 AACGGGAAGCTCATG-GAGCCAAG 32469759 CAACGGGAAGCTCATAGGAGCCATA- 1 -AACGGGAAGCTCAT-GGAGCCA-AG * * 32469784 ATCAGGAAGCTCATGCGAGCCAAG 1 AACGGGAAGCTCATG-GAGCCAAG * 32469808 AACGGGTAGCTC 1 AACGGGAAGCTC 32469820 TGAAGAGCCA Statistics Matches: 50, Mismatches: 6, Indels: 9 0.77 0.09 0.14 Matches are distributed among these distances: 23 2 0.04 24 27 0.54 25 20 0.40 26 1 0.02 ACGTcount: A:0.32, C:0.24, G:0.31, T:0.14 Consensus pattern (23 bp): AACGGGAAGCTCATGGAGCCAAG Found at i:32472087 original size:25 final size:25 Alignment explanation

Indices: 32472049--32472129 Score: 78 Period size: 26 Copynumber: 3.3 Consensus size: 25 32472039 AAGTTTAAGC 32472049 GAGCCA-T-ATTAGGAAGCTCCAAA 1 GAGCCATTAATTAGGAAGCTCCAAA * 32472072 GAGCCATTAATTAGGAAGCTCACATCA 1 GAGCCATTAATTAGGAAGCTC-CA-AA * ** * 32472099 -AGCCTTTAATCGGGAAGCTCCGAA 1 GAGCCATTAATTAGGAAGCTCCAAA 32472123 GAGCCAT 1 GAGCCAT 32472130 ATATCGGGTC Statistics Matches: 46, Mismatches: 7, Indels: 8 0.75 0.11 0.13 Matches are distributed among these distances: 23 6 0.13 24 2 0.04 25 18 0.39 26 19 0.41 27 1 0.02 ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20 Consensus pattern (25 bp): GAGCCATTAATTAGGAAGCTCCAAA Found at i:32490010 original size:22 final size:21 Alignment explanation

Indices: 32489977--32490027 Score: 61 Period size: 21 Copynumber: 2.4 Consensus size: 21 32489967 TAATATTTCA 32489977 AAAGAAAA-AAAATTAG-TAAT 1 AAAGAAAATAAAA-TAGATAAT * 32489997 CAAGCAAAATAAAATAGATAAT 1 AAAG-AAAATAAAATAGATAAT 32490019 AAAGAAAAT 1 AAAGAAAAT 32490028 GTTACTTATT Statistics Matches: 26, Mismatches: 2, Indels: 5 0.79 0.06 0.15 Matches are distributed among these distances: 20 3 0.12 21 12 0.46 22 11 0.42 ACGTcount: A:0.69, C:0.04, G:0.10, T:0.18 Consensus pattern (21 bp): AAAGAAAATAAAATAGATAAT Found at i:32492525 original size:12 final size:12 Alignment explanation

Indices: 32492504--32492538 Score: 61 Period size: 12 Copynumber: 2.9 Consensus size: 12 32492494 CACATGGCCA * 32492504 TGTCCCTGCCCG 1 TGTCCTTGCCCG 32492516 TGTCCTTGCCCG 1 TGTCCTTGCCCG 32492528 TGTCCTTGCCC 1 TGTCCTTGCCC 32492539 ATGTAACATT Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 12 22 1.00 ACGTcount: A:0.00, C:0.46, G:0.23, T:0.31 Consensus pattern (12 bp): TGTCCTTGCCCG Found at i:32492598 original size:54 final size:54 Alignment explanation

Indices: 32492513--32492695 Score: 235 Period size: 54 Copynumber: 3.4 Consensus size: 54 32492503 ATGTCCCTGC ** * * * 32492513 CCGTGTCCTTGCCCGTGTC-CTTGCCCATGTAACATTCGAACTAGAGACACATGC 1 CCGTGTCCCAGCCCGTGTCTC-TGACCATGTAACATTCGAACTAGAGACACACGG * ** * 32492567 CCGTGTCCCAGCTCGTGTCTCTGACTGTGTAACATTCTAACTAGAGACACACGG 1 CCGTGTCCCAGCCCGTGTCTCTGACCATGTAACATTCGAACTAGAGACACACGG * * * 32492621 TCGTGTCCCAGCCCGTGTCTCTGCCCATGTAACATTTGAACTAGAGACACACGG 1 CCGTGTCCCAGCCCGTGTCTCTGACCATGTAACATTCGAACTAGAGACACACGG 32492675 CCGTGT-CCAGCCCGTGTCTCT 1 CCGTGTCCCAGCCCGTGTCTCT 32492696 ACCCGTCTAA Statistics Matches: 111, Mismatches: 17, Indels: 3 0.85 0.13 0.02 Matches are distributed among these distances: 53 15 0.14 54 95 0.86 55 1 0.01 ACGTcount: A:0.20, C:0.33, G:0.22, T:0.26 Consensus pattern (54 bp): CCGTGTCCCAGCCCGTGTCTCTGACCATGTAACATTCGAACTAGAGACACACGG Found at i:32492745 original size:108 final size:108 Alignment explanation

Indices: 32492525--32492746 Score: 247 Period size: 108 Copynumber: 2.1 Consensus size: 108 32492515 GTGTCCTTGC * * 32492525 CCGTGTCCTTGCCCATGTAACATTCGAACTAGAGACACATGCCCGTGTCCCAGCTCGTGTCTCTG 1 CCGTGTCCTTGCCCATGTAACATTCGAACTAGAGACACACGCCCGTGTCCCAGCCCGTGTCTCTG * * * * * 32492590 ACTGTGTAACATTCTAACTAGAGACACACGGTCGTGTCCCAGC 66 ACCGTCTAACATACTAACTAGAGACACACGGTCGTGTCACAGA * * 32492633 CCGTGT-CTCTGCCCATGTAACATTTGAACTAGAGACACACGGCCGTGT-CCAGCCCGTGTCTCT 1 CCGTGTCCT-TGCCCATGTAACATTCGAACTAGAGACACACGCCCGTGTCCCAGCCCGTGTCTCT * * * * 32492696 -ACCCGTCTAAC-TCACTAAGTAGGGTCACATGG-CTGTGTCACACGA 65 GA-CCGTCTAACAT-ACTAACTAGAGACACACGGTC-GTGTCACA-GA 32492741 CCGTGT 1 CCGTGT 32492747 GCTAGGTCGT Statistics Matches: 96, Mismatches: 13, Indels: 10 0.81 0.11 0.08 Matches are distributed among these distances: 106 3 0.03 107 44 0.46 108 49 0.51 ACGTcount: A:0.22, C:0.32, G:0.22, T:0.25 Consensus pattern (108 bp): CCGTGTCCTTGCCCATGTAACATTCGAACTAGAGACACACGCCCGTGTCCCAGCCCGTGTCTCTG ACCGTCTAACATACTAACTAGAGACACACGGTCGTGTCACAGA Found at i:32494628 original size:20 final size:20 Alignment explanation

Indices: 32494593--32494641 Score: 66 Period size: 20 Copynumber: 2.5 Consensus size: 20 32494583 ATCATGGTCT * 32494593 TTGCTT-CTTCTTTACTTAC 1 TTGCTTACTTTTTTACTTAC 32494612 TCT-CTTACTTTTTTACTTAC 1 T-TGCTTACTTTTTTACTTAC 32494632 TTGCTTACTT 1 TTGCTTACTT 32494642 AAATAACTCA Statistics Matches: 26, Mismatches: 1, Indels: 5 0.81 0.03 0.16 Matches are distributed among these distances: 19 5 0.19 20 21 0.81 ACGTcount: A:0.12, C:0.24, G:0.04, T:0.59 Consensus pattern (20 bp): TTGCTTACTTTTTTACTTAC Found at i:32494967 original size:50 final size:49 Alignment explanation

Indices: 32494843--32494987 Score: 168 Period size: 50 Copynumber: 2.9 Consensus size: 49 32494833 GATAATAACA * * 32494843 TGCCAAAGCCATGTCTCAGACATGGTCTTACATGGGATGTT-TCATGTAC 1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATATAC * * * * 32494892 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATAT-C 1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAC * ** 32494940 GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA 1 --TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATA 32494988 AACTTAATAA Statistics Matches: 81, Mismatches: 12, Indels: 5 0.83 0.12 0.05 Matches are distributed among these distances: 48 4 0.05 49 37 0.46 50 40 0.49 ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29 Consensus pattern (49 bp): TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAC Found at i:32499585 original size:40 final size:38 Alignment explanation

Indices: 32499523--32499635 Score: 145 Period size: 40 Copynumber: 2.9 Consensus size: 38 32499513 CGTCAGATAG * 32499523 ACCGAACACACCAAACAGAAGCTCATAAAAGCTGGTCCA 1 ACCGAA-ACACCAAACAGAAGCTCATAAGAGCTGGTCCA * 32499562 ACTGAAATACACCAAACAGAAGCTCATAAGAGCTGGTCCA 1 ACCG-AA-ACACCAAACAGAAGCTCATAAGAGCTGGTCCA * ** 32499602 CCCGAAACACGTGAACAGAAGCTCATAAGAGCTG 1 ACCGAAACAC-CAAACAGAAGCTCATAAGAGCTG 32499636 AACAGAAGAT Statistics Matches: 65, Mismatches: 7, Indels: 4 0.86 0.09 0.05 Matches are distributed among these distances: 38 4 0.06 39 26 0.40 40 35 0.54 ACGTcount: A:0.42, C:0.27, G:0.19, T:0.12 Consensus pattern (38 bp): ACCGAAACACCAAACAGAAGCTCATAAGAGCTGGTCCA Found at i:32499639 original size:21 final size:21 Alignment explanation

Indices: 32499613--32499657 Score: 81 Period size: 21 Copynumber: 2.1 Consensus size: 21 32499603 CCGAAACACG * 32499613 TGAACAGAAGCTCATAAGAGC 1 TGAACAGAAGATCATAAGAGC 32499634 TGAACAGAAGATCATAAGAGC 1 TGAACAGAAGATCATAAGAGC 32499655 TGA 1 TGA 32499658 TCCACCCGAA Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 21 23 1.00 ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16 Consensus pattern (21 bp): TGAACAGAAGATCATAAGAGC Found at i:32514418 original size:13 final size:13 Alignment explanation

Indices: 32514400--32514424 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 32514390 AAAATCTGAT 32514400 TTCAAGTGTATTC 1 TTCAAGTGTATTC 32514413 TTCAAGTGTATT 1 TTCAAGTGTATT 32514425 GTGTATAAGA 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:0.24, C:0.12, G:0.16, T:0.48 Consensus pattern (13 bp): TTCAAGTGTATTC Found at i:32519729 original size:19 final size:20 Alignment explanation

Indices: 32519707--32519744 Score: 51 Period size: 19 Copynumber: 1.9 Consensus size: 20 32519697 CACAATTTAT * 32519707 CTTAAACATATTA-AAAGCA 1 CTTAAACACATTATAAAGCA * 32519726 CTTATACACATTATAAAGC 1 CTTAAACACATTATAAAGC 32519745 TTACAAATTT Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 19 11 0.69 20 5 0.31 ACGTcount: A:0.47, C:0.18, G:0.05, T:0.29 Consensus pattern (20 bp): CTTAAACACATTATAAAGCA Found at i:32521512 original size:19 final size:19 Alignment explanation

Indices: 32521488--32521550 Score: 51 Period size: 19 Copynumber: 3.3 Consensus size: 19 32521478 ATATATATAT 32521488 TAATAAATGATGAATTTAA 1 TAATAAATGATGAATTTAA * * 32521507 TAATAATATG-TCAAGTTAAA 1 TAATAA-ATGATGAA-TTTAA 32521527 TTTAAT-AAT-ATGAATTTAA 1 --TAATAAATGATGAATTTAA 32521546 TAATA 1 TAATA 32521551 GTAATATTAT Statistics Matches: 34, Mismatches: 4, Indels: 13 0.67 0.08 0.25 Matches are distributed among these distances: 17 4 0.12 19 13 0.38 20 12 0.35 21 1 0.03 22 4 0.12 ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40 Consensus pattern (19 bp): TAATAAATGATGAATTTAA Found at i:32523303 original size:45 final size:44 Alignment explanation

Indices: 32523254--32523338 Score: 116 Period size: 45 Copynumber: 1.9 Consensus size: 44 32523244 ATTTGCTATT * 32523254 CTCAGTCTACCCCACTGCAACTTCAAGGGGGATAAGACCTGTTTA 1 CTCAGTCTACCCCACTGCAACTTC-AGGGAGATAAGACCTGTTTA * * ** 32523299 CTCAGTCTGCTCTGCTGCAACTTCAGGGAGATAAGACCTG 1 CTCAGTCTACCCCACTGCAACTTCAGGGAGATAAGACCTG 32523339 ATGCGATCCA Statistics Matches: 35, Mismatches: 5, Indels: 1 0.85 0.12 0.02 Matches are distributed among these distances: 44 15 0.43 45 20 0.57 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25 Consensus pattern (44 bp): CTCAGTCTACCCCACTGCAACTTCAGGGAGATAAGACCTGTTTA Found at i:32523409 original size:44 final size:44 Alignment explanation

Indices: 32523265--32523935 Score: 315 Period size: 44 Copynumber: 15.5 Consensus size: 44 32523255 TCAGTCTACC * * * * 32523265 CCACTGCAACTTCAAGGGGGATAAGACCTGTTTAC-TCAGTCTGCT 1 CCACTGCAACTTC-AGGGAGATAAGATCT-ATTACTTCAATCTGCT ** * * * * ** 32523310 CTGCTGCAACTTCAGGGAGATAAGA-C-CTGA-TGCGATCCACT 1 CCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCT * * * * 32523351 CTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCT 1 CCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCT * * ** 32523395 CCACTACAACTTCAGGGAGATAGGAT-TATCGGCTTCAATCTGCT 1 CCACTGCAACTTCAGGGAGATAAGATCTAT-TACTTCAATCTGCT * *** * 32523439 CCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCGATCTGC- 1 CCACTGCAACTTCAGGGAGATAAGATCTATTA-CTTCAATCTGCT * * * * * * * ** 32523483 CCTATTGTAACCTCA-GGAGGATAAGA-C--CTGCTGCGATCCACT 1 CC-ACTGCAACTTCAGGGA-GATAAGATCTATTACTTCAATCTGCT * * * * * 32523525 CTACTGCAACTTCAGAGAGATAAGATTTATTACTTTAATCCGCT 1 CCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCT * ** 32523569 CCACTACAACTTCAGGGAGAT-AGTAT-TATCGGCTTCAATCTGCT 1 CCACTGCAACTTCAGGGAGATAAG-ATCTAT-TACTTCAATCTGCT * * * *** * * * 32523613 CCACTGTAACTTTAGGGAGATAAGATTTGCCATCTTCGATCTACC 1 CCACTGCAACTTCAGGGAGATAAGATCTATTA-CTTCAATCTGCT * * * * * * * 32523658 CCACTGCAACCTCAGGGGGATAATA-C--TTGCTACGATCTACT 1 CCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCT * * * * * 32523699 CTATTGCAACTTCAGAGAGGTAAGATCTATTACTTTAATCTGCT 1 CCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCT * * ** 32523743 CCACTACAACTTCAGGGAGATAGGAT-TATCGGCTTCAATCTGCT 1 CCACTGCAACTTCAGGGAGATAAGATCTAT-TACTTCAATCTGCT * ** * ** 32523787 -CACTACTGCTT-AGGGAGATAAGATCTGCTT-CTTCGGTCTGCT 1 CCACTGCAACTTCAGGGAGATAAGATCT-ATTACTTCAATCTGCT * * * * * * * 32523829 CTACTGTAACCTCAGGGAGATAAGATC--TGA-TGCGATCTACT 1 CCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCT * * * * 32523870 CTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCT 1 CCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCT * * 32523914 CCACTACATCTTCAGGGAGATA 1 CCACTGCAACTTCAGGGAGATA 32523936 GGATTTGTGG Statistics Matches: 462, Mismatches: 133, Indels: 63 0.70 0.20 0.10 Matches are distributed among these distances: 41 115 0.25 42 28 0.06 43 31 0.07 44 218 0.47 45 70 0.15 ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29 Consensus pattern (44 bp): CCACTGCAACTTCAGGGAGATAAGATCTATTACTTCAATCTGCT Found at i:32523508 original size:174 final size:172 Alignment explanation

Indices: 32523321--32523957 Score: 938 Period size: 174 Copynumber: 3.7 Consensus size: 172 32523311 TGCTGCAACT 32523321 TCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTT 1 TCAGGG-GATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTT 32523386 TAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACTT 65 TAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACTT * 32523451 CAGGGAGATAAGATTTGCCATCTTCGATCTGCCCTATTGTAACC 130 -AGGGAGATAAGATTTGCCATCTTCGATCTGCCCTACTGTAACC * * 32523495 TCAGGAGGATAAGACCTGCTGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATTTATTACTT 1 TCAGG-GGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTT * * 32523560 TAATCCGCTCCACTACAACTTCAGGGAGATAGTATTATCGGCTTCAATCTGCTCCACTGTAACTT 65 TAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAAC-T * * * 32523625 TAGGGAGATAAGATTTGCCATCTTCGATCTACCCCACTGCAACC 129 TAGGGAGATAAGATTTGCCATCTTCGATCTGCCCTACTGTAACC * * * * * * * 32523669 TCAGGGGGATAATACTTGCTACGATCTACTCTATTGCAACTTCAGAGAGGTAAGATCTATTACTT 1 TCA-GGGGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTT * * ** 32523734 TAATCTGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCT-CACTACTGCTT 65 TAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACTT * * * * 32523798 AGGGAGATAAGATCTG-CTTCTTCGGTCTGCTCTACTGTAACC 130 AGGGAGATAAGATTTGCCATCTTCGATCTGCCCTACTGTAACC * * 32523840 TCAGGGAGATAAGATCTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTT 1 TCAGGG-GATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTT * * * 32523905 TAATCCGCTCCACTACATCTTCAGGGAGATAGGATT-TGTGGCTTAAATCTGCT 65 TAATCCGCTCCACTACAACTTCAGGGAGATAGGATTAT-CGGCTTCAATCTGCT 32523958 TCCTTACTCT Statistics Matches: 419, Mismatches: 39, Indels: 13 0.89 0.08 0.03 Matches are distributed among these distances: 170 4 0.01 171 121 0.29 172 17 0.04 173 5 0.01 174 267 0.64 175 5 0.01 ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29 Consensus pattern (172 bp): TCAGGGGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTT AATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACTTA GGGAGATAAGATTTGCCATCTTCGATCTGCCCTACTGTAACC Found at i:32523956 original size:345 final size:348 Alignment explanation

Indices: 32523313--32523957 Score: 1003 Period size: 345 Copynumber: 1.9 Consensus size: 348 32523303 GTCTGCTCTG * * 32523313 CTGCAACTTCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATC 1 CTGCAACCTCAGGGAGATAAGACCTGATACGATCCACTCTACTGCAACTTCAGAGAGATAAGATC 32523378 TATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCAC 66 TATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCAC * * * 32523443 TGCAACTTCAGGGAGATAAGATTTGCCATCTTCGATCTGCCCTATTGTAACCTCAGGAGGATAAG 131 TACAACTTCAGGGAGATAAGATCTGCCATCTTCGATCTGCCCTACTGTAACCTCAGGAGGATAAG * * 32523508 ACCTGCTGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATTTATTACTTTAATCCGCTCCAC 196 ACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCAC * * 32523573 TACAACTTCAGGGAGATAGTATTATCGGCTTCAATCTGCTCCACTGTAACTTTAGGGAGATAAGA 261 TACAACTTCAGGGAGATAGGATTATCGGCTTAAATCTGCTCCACTGTAACTTTAGGGAGATAAGA 32523638 TTTGCCATCTTCGATCTACCCCA 326 TTTGCCATCTTCGATCTACCCCA * * * * * * * 32523661 CTGCAACCTCAGGGGGATAATACTTGCTACGATCTACTCTATTGCAACTTCAGAGAGGTAAGATC 1 CTGCAACCTCAGGGAGATAAGACCTGATACGATCCACTCTACTGCAACTTCAGAGAGATAAGATC * 32523726 TATTACTTTAATCTGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCT-CAC 66 TATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCAC ** * * * 32523790 TACTGCTT-AGGGAGATAAGATCTG-CTTCTTCGGTCTGCTCTACTGTAACCTCAGG-GAGATAA 131 TACAACTTCAGGGAGATAAGATCTGCCATCTTCGATCTGCCCTACTGTAACCTCAGGAG-GATAA * * 32523852 GATCTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCA 195 GACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCA * * 32523917 CTACATCTTCAGGGAGATAGGATT-TGTGGCTTAAATCTGCT 260 CTACAACTTCAGGGAGATAGGATTAT-CGGCTTAAATCTGCT 32523958 TCCTTACTCT Statistics Matches: 269, Mismatches: 26, Indels: 7 0.89 0.09 0.02 Matches are distributed among these distances: 344 2 0.01 345 128 0.48 346 15 0.06 347 8 0.03 348 116 0.43 ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29 Consensus pattern (348 bp): CTGCAACCTCAGGGAGATAAGACCTGATACGATCCACTCTACTGCAACTTCAGAGAGATAAGATC TATTACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCAC TACAACTTCAGGGAGATAAGATCTGCCATCTTCGATCTGCCCTACTGTAACCTCAGGAGGATAAG ACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCAC TACAACTTCAGGGAGATAGGATTATCGGCTTAAATCTGCTCCACTGTAACTTTAGGGAGATAAGA TTTGCCATCTTCGATCTACCCCA Found at i:32524076 original size:129 final size:129 Alignment explanation

Indices: 32523926--32524330 Score: 684 Period size: 129 Copynumber: 3.1 Consensus size: 129 32523916 ACTACATCTT * * * ** 32523926 CAGGGAGATAGGATTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTACCGTCTTC 1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTC * 32523991 GATCTGCTCTGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC 66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC * 32524055 TAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTC 1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTC * * 32524120 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGAAATTTCCCAACCTATTCCACTGTTGAC 66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC * * 32524184 CAGGGATATAGGACTTGTGGCTTAAATTTGATTCCTTACACTTGAAGATAAGATTCGCCGTCTTC 1 CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTC * * * 32524249 GATCTGCTCCACTATTGCTTAGGAAGACAAGATCTGTACTTTCCCAACCTATTCCACTGCTGAC 66 GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC 32524313 CAGGGATATAGGACTTGT 1 CAGGGATATAGGACTTGT 32524331 AATCTTCAAC Statistics Matches: 259, Mismatches: 17, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 129 259 1.00 ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32 Consensus pattern (129 bp): CAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTC GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGAC Found at i:32524342 original size:44 final size:44 Alignment explanation

Indices: 32524293--32524626 Score: 431 Period size: 44 Copynumber: 7.6 Consensus size: 44 32524283 TGTACTTTCC ** * 32524293 CAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTAATCTT 1 CAACCTATTCCACTGCTGGTCAGGGATATAGGACTTGCAATCTT * * * * 32524337 CAACCTATTCCATTGATGGTTAGGGAGT-TAGGATTTGCAATCTT 1 CAACCTATTCCACTGCTGGTCAGGGA-TATAGGACTTGCAATCTT * * 32524381 CTACCTATTCCACTACTGGTCAGGGAGT-TAGGACTTGCAATCTT 1 CAACCTATTCCACTGCTGGTCAGGGA-TATAGGACTTGCAATCTT 32524425 CAACCTATTCCACTGCTGGTCAGGGAGT-TAGGACTTGCAATCTT 1 CAACCTATTCCACTGCTGGTCAGGGA-TATAGGACTTGCAATCTT * * * * 32524469 CTACCTATTCCTCTACTGGTCAGGGAGATAGGACTTGCAATCTT 1 CAACCTATTCCACTGCTGGTCAGGGATATAGGACTTGCAATCTT * * * * * 32524513 CTACCTATTCCTCTACTGGTCAGGGAGATAGGACTTACAATCTT 1 CAACCTATTCCACTGCTGGTCAGGGATATAGGACTTGCAATCTT ** * 32524557 CAACCTATTCCACTGCTGACCAGGGATATAGGACTTACAATCTT 1 CAACCTATTCCACTGCTGGTCAGGGATATAGGACTTGCAATCTT 32524601 CAACCTATTCCACTGCTGGTCAGGGA 1 CAACCTATTCCACTGCTGGTCAGGGA 32524627 GCTAGGTTTT Statistics Matches: 260, Mismatches: 28, Indels: 4 0.89 0.10 0.01 Matches are distributed among these distances: 44 259 1.00 45 1 0.00 ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31 Consensus pattern (44 bp): CAACCTATTCCACTGCTGGTCAGGGATATAGGACTTGCAATCTT Found at i:32524457 original size:132 final size:132 Alignment explanation

Indices: 32524293--32524637 Score: 507 Period size: 132 Copynumber: 2.6 Consensus size: 132 32524283 TGTACTTTCC * * 32524293 CAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTAATCTTCAACCTATTCCATTGATGGTT 1 CAACCTATTCCACTGCTGACCAGGGATATAGGACTTGCAATCTTCAACCTATTCCATTGATGGTC * * * 32524358 AGGGAGTTAGGATTTGCAATCTTCTACCTATTCCACTACTGGTCAGGGAGTTAGGACTTGCAATC 66 AGGGAGATAGGATTTGCAATCTTCTACCTATTCCACTACTGGTCAGGGAGATAGGACTTACAATC 32524423 TT 131 TT ** * 32524425 CAACCTATTCCACTGCTGGTCAGGGAGT-TAGGACTTGCAATCTTCTACCTATTCC-TCT-ACTG 1 CAACCTATTCCACTGCTGACCAGGGA-TATAGGACTTGCAATCTTCAACCTATTCCAT-TGA-TG * * 32524487 GTCAGGGAGATAGGACTTGCAATCTTCTACCTATTCCTCTACTGGTCAGGGAGATAGGACTTACA 63 GTCAGGGAGATAGGATTTGCAATCTTCTACCTATTCCACTACTGGTCAGGGAGATAGGACTTACA 32524552 ATCTT 128 ATCTT * * * 32524557 CAACCTATTCCACTGCTGACCAGGGATATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC 1 CAACCTATTCCACTGCTGACCAGGGATATAGGACTTGCAATCTTCAACCTATTCCATTGATGGTC * * 32524622 AGGGAGCTAGGTTTTG 66 AGGGAGATAGGATTTG 32524638 TGGTTTTACC Statistics Matches: 188, Mismatches: 19, Indels: 12 0.86 0.09 0.05 Matches are distributed among these distances: 131 3 0.02 132 184 0.98 133 1 0.01 ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31 Consensus pattern (132 bp): CAACCTATTCCACTGCTGACCAGGGATATAGGACTTGCAATCTTCAACCTATTCCATTGATGGTC AGGGAGATAGGATTTGCAATCTTCTACCTATTCCACTACTGGTCAGGGAGATAGGACTTACAATC TT Found at i:32525872 original size:14 final size:14 Alignment explanation

Indices: 32525845--32525904 Score: 50 Period size: 14 Copynumber: 4.1 Consensus size: 14 32525835 TTAGCCTCTC * 32525845 TATTTTTACTTTTT 1 TATTTTTATTTTTT 32525859 TATTTTT-TTATTTT 1 TATTTTTATT-TTTT * 32525873 TCATTTTCATTTTTT 1 T-ATTTTTATTTTTT * 32525888 CATTTTTCATATTTTT 1 TATTTTT-AT-TTTTT 32525904 T 1 T 32525905 CCGACTTAAA Statistics Matches: 36, Mismatches: 5, Indels: 8 0.73 0.10 0.16 Matches are distributed among these distances: 13 1 0.03 14 17 0.47 15 11 0.31 16 7 0.19 ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77 Consensus pattern (14 bp): TATTTTTATTTTTT Found at i:32525872 original size:15 final size:16 Alignment explanation

Indices: 32525847--32525879 Score: 50 Period size: 15 Copynumber: 2.1 Consensus size: 16 32525837 AGCCTCTCTA * 32525847 TTTTTACTTTTTTATT 1 TTTTTACTTTTTCATT 32525863 TTTTTA-TTTTTCATT 1 TTTTTACTTTTTCATT 32525878 TT 1 TT 32525880 CATTTTTTCA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 15 10 0.62 16 6 0.38 ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82 Consensus pattern (16 bp): TTTTTACTTTTTCATT Found at i:32525887 original size:15 final size:16 Alignment explanation

Indices: 32525869--32525905 Score: 51 Period size: 17 Copynumber: 2.4 Consensus size: 16 32525859 TATTTTTTTA 32525869 TTTTTCA-TTTTC-AT 1 TTTTTCATTTTTCAAT 32525883 TTTTTCATTTTTCATAT 1 TTTTTCATTTTTCA-AT 32525900 TTTTTC 1 TTTTTC 32525906 CGACTTAAAG Statistics Matches: 20, Mismatches: 0, Indels: 3 0.87 0.00 0.13 Matches are distributed among these distances: 14 7 0.35 15 5 0.25 17 8 0.40 ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73 Consensus pattern (16 bp): TTTTTCATTTTTCAAT Found at i:32526796 original size:19 final size:18 Alignment explanation

Indices: 32526761--32526801 Score: 55 Period size: 19 Copynumber: 2.2 Consensus size: 18 32526751 TCATTTTTCA * 32526761 TTTTCTTTTTCTCTTTAT 1 TTTTCTTTTTATCTTTAT * 32526779 TTTTCATTTTTATTTTTAT 1 TTTTC-TTTTTATCTTTAT 32526798 TTTT 1 TTTT 32526802 TTCATTTTTG Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 18 5 0.25 19 15 0.75 ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80 Consensus pattern (18 bp): TTTTCTTTTTATCTTTAT Found at i:32526802 original size:13 final size:13 Alignment explanation

Indices: 32526753--32526801 Score: 59 Period size: 12 Copynumber: 4.0 Consensus size: 13 32526743 TTGGCCTCTC 32526753 ATTTTTCA-TTTT 1 ATTTTTCATTTTT * * 32526765 CTTTTTC-TCTTT 1 ATTTTTCATTTTT 32526777 ATTTTTCATTTTT 1 ATTTTTCATTTTT 32526790 ATTTTT-ATTTTT 1 ATTTTTCATTTTT 32526802 TTCATTTTTG Statistics Matches: 31, Mismatches: 4, Indels: 4 0.79 0.10 0.10 Matches are distributed among these distances: 12 21 0.68 13 10 0.32 ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78 Consensus pattern (13 bp): ATTTTTCATTTTT Found at i:32526861 original size:6 final size:6 Alignment explanation

Indices: 32526848--32526916 Score: 111 Period size: 6 Copynumber: 11.3 Consensus size: 6 32526838 TTTTCTTATT * * 32526848 TTTTGA TTTAGA TTTAGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA 1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA 32526896 TTTTGA TTTTGA TTTTTGA TT 1 TTTTGA TTTTGA -TTTTGA TT 32526917 GAATCTGAGC Statistics Matches: 60, Mismatches: 2, Indels: 2 0.94 0.03 0.03 Matches are distributed among these distances: 6 54 0.90 7 6 0.10 ACGTcount: A:0.19, C:0.00, G:0.16, T:0.65 Consensus pattern (6 bp): TTTTGA Done.