Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12

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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 1700 characters in sequence are not A, C, G, or T


File 53 of 135

Found at i:18589156 original size:19 final size:20

Alignment explanation

Indices: 18589132--18589199 Score: 70 Period size: 19 Copynumber: 3.3 Consensus size: 20 18589122 AACCCTAATT 18589132 AATAAACACTTAAAAAT-TA 1 AATAAACACTTAAAAATATA 18589151 AATAAAACAC-TAAAAATCATAA 1 AAT-AAACACTTAAAAAT-AT-A 18589173 TTAATAAACACTT-AAAATATA 1 --AATAAACACTTAAAAATATA 18589194 AATAAA 1 AATAAA 18589200 ACCTTAATTT Statistics Matches: 42, Mismatches: 0, Indels: 14 0.75 0.00 0.25 Matches are distributed among these distances: 19 16 0.38 20 6 0.14 21 2 0.05 22 3 0.07 23 11 0.26 24 4 0.10 ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25 Consensus pattern (20 bp): AATAAACACTTAAAAATATA Found at i:18589157 original size:42 final size:42 Alignment explanation

Indices: 18589111--18589206 Score: 131 Period size: 43 Copynumber: 2.3 Consensus size: 42 18589101 CATTTTTTCT * * 18589111 TAAAACTTTAAAACCCTAATTAATAAACACTTAAAA-ATTAAA 1 TAAAACCTTAAAACCATAATTAATAAACACTTAAAATA-TAAA * * 18589153 TAAAACACTAAAAATCATAATTAATAAACACTTAAAATATAAA 1 TAAAAC-CTTAAAACCATAATTAATAAACACTTAAAATATAAA 18589196 TAAAACCTTAA 1 TAAAACCTTAA 18589207 TTTAAATTAC Statistics Matches: 47, Mismatches: 5, Indels: 4 0.84 0.09 0.07 Matches are distributed among these distances: 42 10 0.21 43 36 0.77 44 1 0.02 ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27 Consensus pattern (42 bp): TAAAACCTTAAAACCATAATTAATAAACACTTAAAATATAAA Found at i:18589160 original size:20 final size:21 Alignment explanation

Indices: 18589135--18589206 Score: 80 Period size: 20 Copynumber: 3.5 Consensus size: 21 18589125 CCTAATTAAT 18589135 AAACACTTAAAAAT-TAAATA 1 AAACACTTAAAAATATAAATA * 18589155 AAACAC-TAAAAATCATAATTAA 1 AAACACTTAAAAAT-ATAAAT-A 18589177 TAAACACTT-AAAATATAAATA 1 -AAACACTTAAAAATATAAATA 18589198 AAAC-CTTAA 1 AAACACTTAA 18589207 TTTAAATTAC Statistics Matches: 44, Mismatches: 2, Indels: 12 0.76 0.03 0.21 Matches are distributed among these distances: 19 10 0.23 20 11 0.25 21 5 0.11 22 6 0.14 23 11 0.25 24 1 0.02 ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25 Consensus pattern (21 bp): AAACACTTAAAAATATAAATA Found at i:18598206 original size:31 final size:31 Alignment explanation

Indices: 18598171--18598236 Score: 105 Period size: 31 Copynumber: 2.1 Consensus size: 31 18598161 AACAACCCAA * * 18598171 TGACTTAAATAAAAACTTTTGAATAGTTCAG 1 TGACTTAAATAAAAAATTTTGAAAAGTTCAG * 18598202 TGACTTAAATAAAAAATTTTGAAAATTTCAG 1 TGACTTAAATAAAAAATTTTGAAAAGTTCAG 18598233 TGAC 1 TGAC 18598237 CATGTTGTAA Statistics Matches: 32, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 31 32 1.00 ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35 Consensus pattern (31 bp): TGACTTAAATAAAAAATTTTGAAAAGTTCAG Found at i:18600450 original size:18 final size:18 Alignment explanation

Indices: 18600427--18600480 Score: 108 Period size: 18 Copynumber: 3.0 Consensus size: 18 18600417 AATCGACCCC 18600427 AACCGAATTAATTCGATT 1 AACCGAATTAATTCGATT 18600445 AACCGAATTAATTCGATT 1 AACCGAATTAATTCGATT 18600463 AACCGAATTAATTCGATT 1 AACCGAATTAATTCGATT 18600481 TTACCCGAAA Statistics Matches: 36, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 36 1.00 ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33 Consensus pattern (18 bp): AACCGAATTAATTCGATT Found at i:18601185 original size:20 final size:20 Alignment explanation

Indices: 18601160--18601197 Score: 58 Period size: 20 Copynumber: 1.9 Consensus size: 20 18601150 GTCAAAATTT * 18601160 AATAGAAAGTATACGTAATC 1 AATAGAAAATATACGTAATC * 18601180 AATAGAAAATATATGTAA 1 AATAGAAAATATACGTAA 18601198 GTGCTGGTAG Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 16 1.00 ACGTcount: A:0.55, C:0.05, G:0.13, T:0.26 Consensus pattern (20 bp): AATAGAAAATATACGTAATC Found at i:18601575 original size:58 final size:58 Alignment explanation

Indices: 18601513--18601644 Score: 167 Period size: 58 Copynumber: 2.3 Consensus size: 58 18601503 AAACCTATCA * ** 18601513 ATAAACTAAACCCAAATAATTGTAAAC-CAAAATATAATTTCATTCTTAAAAAATATTC 1 ATAAACTAAACCCAAATAATTGTAAACAC-AAATATAATTTCATTATTAAAAAATACCC * * * * 18601571 ATAAACTAAACCCAATTATTTTTAAACACAAATATAATTTTATTATTAAAAAATACCC 1 ATAAACTAAACCCAAATAATTGTAAACACAAATATAATTTCATTATTAAAAAATACCC * * 18601629 ATAAATTAAACTCAAA 1 ATAAACTAAACCCAAA 18601645 ATCAATTTTT Statistics Matches: 63, Mismatches: 10, Indels: 2 0.84 0.13 0.03 Matches are distributed among these distances: 58 62 0.98 59 1 0.02 ACGTcount: A:0.52, C:0.15, G:0.01, T:0.32 Consensus pattern (58 bp): ATAAACTAAACCCAAATAATTGTAAACACAAATATAATTTCATTATTAAAAAATACCC Found at i:18601652 original size:42 final size:40 Alignment explanation

Indices: 18601592--18601682 Score: 96 Period size: 42 Copynumber: 2.2 Consensus size: 40 18601582 CCAATTATTT * * 18601592 TTAAACACAAATATAATTTTATTAT-TAAAAAATACCCATAAA 1 TTAAACTCAAATATAATTTT-TCATCTAAAAAA-ACCC-TAAA * 18601634 TTAAACTCAAA-ATCAATTTTTCATCCTAAAAAAATCCTAAA 1 TTAAACTCAAATAT-AATTTTTCAT-CTAAAAAAACCCTAAA 18601675 TTAAACTC 1 TTAAACTC 18601683 TCATTTAGTC Statistics Matches: 43, Mismatches: 3, Indels: 7 0.81 0.06 0.13 Matches are distributed among these distances: 41 17 0.40 42 19 0.44 43 7 0.16 ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33 Consensus pattern (40 bp): TTAAACTCAAATATAATTTTTCATCTAAAAAAACCCTAAA Found at i:18602177 original size:34 final size:34 Alignment explanation

Indices: 18602123--18602198 Score: 125 Period size: 34 Copynumber: 2.2 Consensus size: 34 18602113 CAGTTTTTGT * * 18602123 TTTGTACTGTAATACACAAAGCTGAATTTTAGTA 1 TTTGAACTGCAATACACAAAGCTGAATTTTAGTA * 18602157 TTTGAACTGCAATACCCAAAGCTGAATTTTAGTA 1 TTTGAACTGCAATACACAAAGCTGAATTTTAGTA 18602191 TTTGAACT 1 TTTGAACT 18602199 AGCAGCTAGG Statistics Matches: 39, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 34 39 1.00 ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37 Consensus pattern (34 bp): TTTGAACTGCAATACACAAAGCTGAATTTTAGTA Found at i:18623992 original size:24 final size:24 Alignment explanation

Indices: 18623965--18624016 Score: 79 Period size: 23 Copynumber: 2.2 Consensus size: 24 18623955 GAAATGTGAT * 18623965 TATTAAGAATGTGATTGTTAAAAA 1 TATTAAGAATATGATTGTTAAAAA 18623989 TATT-AGAATATGATTGTTAAAAA 1 TATTAAGAATATGATTGTTAAAAA * 18624012 AATTA 1 TATTA 18624017 CTTTACAACG Statistics Matches: 25, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 23 21 0.84 24 4 0.16 ACGTcount: A:0.48, C:0.00, G:0.13, T:0.38 Consensus pattern (24 bp): TATTAAGAATATGATTGTTAAAAA Found at i:18626685 original size:15 final size:15 Alignment explanation

Indices: 18626665--18626702 Score: 67 Period size: 15 Copynumber: 2.5 Consensus size: 15 18626655 ACACAGAACT 18626665 GGGTTCCTGATTCTA 1 GGGTTCCTGATTCTA 18626680 GGGTTCCTGATTCTA 1 GGGTTCCTGATTCTA * 18626695 GTGTTCCT 1 GGGTTCCT 18626703 CATCACATCA Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 15 22 1.00 ACGTcount: A:0.11, C:0.21, G:0.26, T:0.42 Consensus pattern (15 bp): GGGTTCCTGATTCTA Found at i:18632295 original size:17 final size:19 Alignment explanation

Indices: 18632249--18632297 Score: 57 Period size: 20 Copynumber: 2.6 Consensus size: 19 18632239 AGCATTTTGT * 18632249 TAATTTCATATTAAAGTGA 1 TAATTTAATATTAAAGTGA * 18632268 TTATCTTAATATTAAA-T-A 1 TAAT-TTAATATTAAAGTGA 18632286 TAATTTAATATT 1 TAATTTAATATT 18632298 TATCTTGTAG Statistics Matches: 26, Mismatches: 3, Indels: 4 0.79 0.09 0.12 Matches are distributed among these distances: 17 8 0.31 18 4 0.15 19 4 0.15 20 10 0.38 ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49 Consensus pattern (19 bp): TAATTTAATATTAAAGTGA Found at i:18632341 original size:57 final size:59 Alignment explanation

Indices: 18632273--18632384 Score: 165 Period size: 57 Copynumber: 1.9 Consensus size: 59 18632263 AGTGATTATC * * * 18632273 TTAATATTAAATATAATTTAATATTTATCTTG-T-AGAATTTTATTAATTTAATACGAT 1 TTAATATTAAATATAATCTAATAATTATCTTGATAAGAATTATATTAATTTAATACGAT * * 18632330 TTAATATTAAATATAATCTAATAATTATCTTGATAAGTATTATATTGATTTAATA 1 TTAATATTAAATATAATCTAATAATTATCTTGATAAGAATTATATTAATTTAATA 18632385 TTAAAGTAAT Statistics Matches: 48, Mismatches: 5, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 57 30 0.62 58 1 0.02 59 17 0.35 ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49 Consensus pattern (59 bp): TTAATATTAAATATAATCTAATAATTATCTTGATAAGAATTATATTAATTTAATACGAT Found at i:18636252 original size:17 final size:19 Alignment explanation

Indices: 18636225--18636263 Score: 55 Period size: 18 Copynumber: 2.2 Consensus size: 19 18636215 TTCTACATAC * 18636225 TTTTATATA-TTTAGAATT 1 TTTTATATATTTTAAAATT 18636243 TTTTAT-TATTTTAAAATT 1 TTTTATATATTTTAAAATT 18636261 TTT 1 TTT 18636264 ATTTTTCCTT Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 17 2 0.11 18 17 0.89 ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67 Consensus pattern (19 bp): TTTTATATATTTTAAAATT Found at i:18637310 original size:18 final size:18 Alignment explanation

Indices: 18637274--18637317 Score: 54 Period size: 18 Copynumber: 2.4 Consensus size: 18 18637264 TCTTTAAGCA * 18637274 ATAAATATTAATTATTTAT 1 ATAAAT-TTAATTAATTAT 18637293 A-AAATTTAATTAGATTAT 1 ATAAATTTAATTA-ATTAT 18637311 ATAAATT 1 ATAAATT 18637318 ATATTTTAAA Statistics Matches: 22, Mismatches: 1, Indels: 4 0.81 0.04 0.15 Matches are distributed among these distances: 17 7 0.32 18 9 0.41 19 6 0.27 ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48 Consensus pattern (18 bp): ATAAATTTAATTAATTAT Found at i:18642149 original size:21 final size:23 Alignment explanation

Indices: 18642123--18642177 Score: 69 Period size: 24 Copynumber: 2.4 Consensus size: 23 18642113 CCTGCAACTT * 18642123 CTACCGATACA-AGTA-TACATA 1 CTACCGATACACAGTACTACAAA * 18642144 CTACCGATACATCAGTACTATAAA 1 CTACCGATACA-CAGTACTACAAA 18642168 CTACCGATAC 1 CTACCGATAC 18642178 TTGTAATTTA Statistics Matches: 29, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 21 11 0.38 23 4 0.14 24 14 0.48 ACGTcount: A:0.40, C:0.27, G:0.09, T:0.24 Consensus pattern (23 bp): CTACCGATACACAGTACTACAAA Found at i:18645787 original size:24 final size:21 Alignment explanation

Indices: 18645735--18645789 Score: 56 Period size: 24 Copynumber: 2.5 Consensus size: 21 18645725 CCTGCAACTT * 18645735 CTACCGATACAAGTATACATA 1 CTACCGATACAAGTATACAAA * * 18645756 CTATCGATACATCAGTACTATAAA 1 CTACCGATACA--AGTA-TACAAA 18645780 CTACCGATAC 1 CTACCGATAC 18645790 TTGTAATTTA Statistics Matches: 27, Mismatches: 4, Indels: 3 0.79 0.12 0.09 Matches are distributed among these distances: 21 10 0.37 23 4 0.15 24 13 0.48 ACGTcount: A:0.40, C:0.25, G:0.09, T:0.25 Consensus pattern (21 bp): CTACCGATACAAGTATACAAA Found at i:18648057 original size:22 final size:22 Alignment explanation

Indices: 18648029--18648090 Score: 72 Period size: 21 Copynumber: 2.9 Consensus size: 22 18648019 CTATAACTAT 18648029 TAATTTAAAATACCCTAAACCC 1 TAATTTAAAATACCCTAAACCC * * * 18648051 TTATTTAAAATA-CCAAAACTC 1 TAATTTAAAATACCCTAAACCC * * 18648072 TAATTTAAAAAACCTTAAA 1 TAATTTAAAATACCCTAAA 18648091 ACTAATTGAA Statistics Matches: 32, Mismatches: 7, Indels: 2 0.78 0.17 0.05 Matches are distributed among these distances: 21 17 0.53 22 15 0.47 ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31 Consensus pattern (22 bp): TAATTTAAAATACCCTAAACCC Found at i:18648174 original size:30 final size:31 Alignment explanation

Indices: 18648138--18648199 Score: 99 Period size: 30 Copynumber: 2.0 Consensus size: 31 18648128 CAAAATAGCA * 18648138 AAATTTAGATATATTA-TTTTGAATTTTTAG 1 AAATTTAGATATATTAGTTTTGAAATTTTAG * 18648168 AAATTTAGATATGTTAGTTTTGAAATTTTAG 1 AAATTTAGATATATTAGTTTTGAAATTTTAG 18648199 A 1 A 18648200 CTTTAAATTT Statistics Matches: 29, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 30 15 0.52 31 14 0.48 ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50 Consensus pattern (31 bp): AAATTTAGATATATTAGTTTTGAAATTTTAG Found at i:18657865 original size:52 final size:52 Alignment explanation

Indices: 18657778--18657921 Score: 236 Period size: 52 Copynumber: 2.8 Consensus size: 52 18657768 CCGTAAATGG 18657778 AAGAGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATT 1 AAGAGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATT * * 18657830 AAGAAGTCTGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATT 1 AAGAGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATT * * 18657882 ATA-AGGTCCGATGGCTATGTGTCATCGTGAGTATATGAAT 1 A-AGAGGTCCGATGACTACGTGTCATCGTGAGTATATGAAT 18657922 GAAGTGAATC Statistics Matches: 85, Mismatches: 6, Indels: 2 0.91 0.06 0.02 Matches are distributed among these distances: 52 84 0.99 53 1 0.01 ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32 Consensus pattern (52 bp): AAGAGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATT Found at i:18657980 original size:12 final size:12 Alignment explanation

Indices: 18657963--18657987 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 18657953 TGACTCTGTG 18657963 TCATCGTGAGTA 1 TCATCGTGAGTA 18657975 TCATCGTGAGTA 1 TCATCGTGAGTA 18657987 T 1 T 18657988 ATGAATGAAG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36 Consensus pattern (12 bp): TCATCGTGAGTA Found at i:18658020 original size:72 final size:72 Alignment explanation

Indices: 18657903--18658047 Score: 272 Period size: 72 Copynumber: 2.0 Consensus size: 72 18657893 TGGCTATGTG * 18657903 TCATCGTGAGTATATGAATGAAGTGAATCCATTGCGAATTAAAGGTTCGATGACTCTGTGTCATC 1 TCATCGTGAGTATATGAATGAAGTGAATCCATTGCGAATTAAAGGTCCGATGACTCTGTGTCATC 18657968 GTGAGTA 66 GTGAGTA * 18657975 TCATCGTGAGTATATGAATGAAGTGAATCCATTGCGGATTAAAGGTCCGATGACTCTGTGTCATC 1 TCATCGTGAGTATATGAATGAAGTGAATCCATTGCGAATTAAAGGTCCGATGACTCTGTGTCATC 18658040 GTGAGTA 66 GTGAGTA 18658047 T 1 T 18658048 ATGAATCCTT Statistics Matches: 71, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 72 71 1.00 ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32 Consensus pattern (72 bp): TCATCGTGAGTATATGAATGAAGTGAATCCATTGCGAATTAAAGGTCCGATGACTCTGTGTCATC GTGAGTA Found at i:18658093 original size:50 final size:50 Alignment explanation

Indices: 18657998--18658157 Score: 160 Period size: 51 Copynumber: 3.0 Consensus size: 50 18657988 ATGAATGAAG * * 18657998 TGAATCCATTGCGGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTATA 1 TGAATCCATTACGGATTAAAGGTCCGATGA-GCTGTGTCATCGTGAGTATA * 18658049 TGAATCCTTTACGGATTATAAGGTCCGATG-GCTGTGTCATCGTGAGTATATGAATGAA 1 TGAATCCATTACGGATTA-AAGGTCCGATGAGCTGTGTCATCGTGAG----T--AT--A * * 18658107 GTGAATCCATTGCGGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTAT 1 -TGAATCCATTACGGATTAAAGGTCCGATGA-GCTGTGTCATCGTGAGTAT 18658158 CAAATGCAAA Statistics Matches: 91, Mismatches: 6, Indels: 21 0.77 0.05 0.18 Matches are distributed among these distances: 50 15 0.16 51 16 0.18 52 11 0.12 54 3 0.03 56 3 0.03 58 12 0.13 59 16 0.18 60 15 0.16 ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32 Consensus pattern (50 bp): TGAATCCATTACGGATTAAAGGTCCGATGAGCTGTGTCATCGTGAGTATA Found at i:18658139 original size:182 final size:184 Alignment explanation

Indices: 18657813--18658159 Score: 601 Period size: 182 Copynumber: 1.9 Consensus size: 184 18657803 CGTGAGTATA * * 18657813 TGAATCCTTTACGGATTAAGAAGTCTGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACG 1 TGAATCCATTACGGATTAAGAAGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACG 18657878 GATTATAAGGTCCGATGGCTATGTGTCATCGTGAGTATATGAATGAAGTGAATCCATTGCGAATT 66 GATTATAAGGTCCGATGGC-ATGTGTCATCGTGAGTATATGAATGAAGTGAATCCATTGCGAATT * 18657943 AAAGGTTCGATGACTCTGTGTCATCGTGAGTATCATCGTGAGTATATGAATGAAG 130 AAAGGTCCGATGACTCTGTGTCATCGTGAGTATCATCGTGAGTATATGAATGAAG * * 18657998 TGAATCCATTGCGGATTAA-AGGTCCGATGACT-CTGTGTCATCGTGAGTATATGAATCCTTTAC 1 TGAATCCATTACGGATTAAGAAGTCCGATGACTAC-GTGTCATCGTGAGTATATGAATCCTTTAC * 18658061 GGATTATAAGGTCCGATGGC-TGTGTCATCGTGAGTATATGAATGAAGTGAATCCATTGCGGATT 65 GGATTATAAGGTCCGATGGCATGTGTCATCGTGAGTATATGAATGAAGTGAATCCATTGCGAATT 18658125 AAAGGTCCGATGACTCTGTGTCATCGTGAGTATCA 130 AAAGGTCCGATGACTCTGTGTCATCGTGAGTATCA 18658160 AATGCAAATT Statistics Matches: 155, Mismatches: 6, Indels: 5 0.93 0.04 0.03 Matches are distributed among these distances: 182 77 0.50 183 1 0.01 184 60 0.39 185 17 0.11 ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32 Consensus pattern (184 bp): TGAATCCATTACGGATTAAGAAGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACG GATTATAAGGTCCGATGGCATGTGTCATCGTGAGTATATGAATGAAGTGAATCCATTGCGAATTA AAGGTCCGATGACTCTGTGTCATCGTGAGTATCATCGTGAGTATATGAATGAAG Found at i:18658743 original size:21 final size:23 Alignment explanation

Indices: 18658714--18658767 Score: 58 Period size: 24 Copynumber: 2.4 Consensus size: 23 18658704 ACTTGAATTA * * 18658714 TATCAGTAGT-TGAAT-TGTAAG 1 TATCGGTAGTATGAATGTGAAAG * 18658735 TATCGGTAGTACTGTATGTGAAAG 1 TATCGGTAGTA-TGAATGTGAAAG 18658759 TATCGGTAG 1 TATCGGTAG 18658768 ATTGTGTGAT Statistics Matches: 27, Mismatches: 3, Indels: 3 0.82 0.09 0.09 Matches are distributed among these distances: 21 9 0.33 23 4 0.15 24 14 0.52 ACGTcount: A:0.30, C:0.07, G:0.28, T:0.35 Consensus pattern (23 bp): TATCGGTAGTATGAATGTGAAAG Found at i:18661427 original size:151 final size:151 Alignment explanation

Indices: 18661242--18661551 Score: 593 Period size: 151 Copynumber: 2.1 Consensus size: 151 18661232 GAAGCTCCAT * 18661242 ATATTGTGTGTCTAGTGTATCCCTTTTGATACTTTTGGATGGCTTCATGAACTATTCAGTAGTTT 1 ATATTGTGTGTCTAGTGTATCCCCTTTGATACTTTTGGATGGCTTCATGAACTATTCAGTAGTTT * 18661307 TCATTGGAACTCCGGCTCTTTTGCACCAAGCTATCACTGAATGGGGAGAGAAAACCCTTACTTTC 66 TCATTGGAACTCCGGCTCTTTTGCACCAAGCCATCACTGAATGGGGAGAGAAAACCCTTACTTTC 18661372 TGGCCATTGATGCACCAGTTC 131 TGGCCATTGATGCACCAGTTC 18661393 ATATTGTGTGTCTAGTGTATCCCCTTTGATACTTTTGGATGGCTTCATGAACTATTCAGTAGTTT 1 ATATTGTGTGTCTAGTGTATCCCCTTTGATACTTTTGGATGGCTTCATGAACTATTCAGTAGTTT 18661458 TCATTGGAACTCCGGCTCTTTTGCACCAAGCCATCACTGAATGGGGAGAGAAAACCCTTACTTTC 66 TCATTGGAACTCCGGCTCTTTTGCACCAAGCCATCACTGAATGGGGAGAGAAAACCCTTACTTTC * 18661523 TGGCCATTGATGCACCATTTC 131 TGGCCATTGATGCACCAGTTC 18661544 ATATTGTG 1 ATATTGTG 18661552 ATAGATCCAT Statistics Matches: 156, Mismatches: 3, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 151 156 1.00 ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36 Consensus pattern (151 bp): ATATTGTGTGTCTAGTGTATCCCCTTTGATACTTTTGGATGGCTTCATGAACTATTCAGTAGTTT TCATTGGAACTCCGGCTCTTTTGCACCAAGCCATCACTGAATGGGGAGAGAAAACCCTTACTTTC TGGCCATTGATGCACCAGTTC Found at i:18667781 original size:3 final size:3 Alignment explanation

Indices: 18667773--18667797 Score: 50 Period size: 3 Copynumber: 8.3 Consensus size: 3 18667763 ATACTATTAC 18667773 TAA TAA TAA TAA TAA TAA TAA TAA T 1 TAA TAA TAA TAA TAA TAA TAA TAA T 18667798 TAAGAATCAT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 22 1.00 ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36 Consensus pattern (3 bp): TAA Found at i:18670510 original size:24 final size:24 Alignment explanation

Indices: 18670483--18670530 Score: 96 Period size: 24 Copynumber: 2.0 Consensus size: 24 18670473 ACCTTAAATA 18670483 TTAAAATGTTAGCAAATATTTATT 1 TTAAAATGTTAGCAAATATTTATT 18670507 TTAAAATGTTAGCAAATATTTATT 1 TTAAAATGTTAGCAAATATTTATT 18670531 AATAATTTTA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 24 1.00 ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46 Consensus pattern (24 bp): TTAAAATGTTAGCAAATATTTATT Found at i:18677655 original size:24 final size:24 Alignment explanation

Indices: 18677628--18677674 Score: 76 Period size: 24 Copynumber: 2.0 Consensus size: 24 18677618 TTTGCTATGA * 18677628 TTTAAAGAATAGTCAGTTTTTTTT 1 TTTAAAGAATAGTCAGTTATTTTT * 18677652 TTTAAAGAATAGTTAGTTATTTT 1 TTTAAAGAATAGTCAGTTATTTT 18677675 ATAATAATTG Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 24 21 1.00 ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53 Consensus pattern (24 bp): TTTAAAGAATAGTCAGTTATTTTT Found at i:18679100 original size:25 final size:23 Alignment explanation

Indices: 18679072--18679117 Score: 65 Period size: 24 Copynumber: 1.9 Consensus size: 23 18679062 GTTGGATTCA 18679072 AATTAAATTCTAAAAAGATAATTAG 1 AATTAAA-TCTAAAAA-ATAATTAG * 18679097 AATTAAATCTAAACAATAATT 1 AATTAAATCTAAAAAATAATT 18679118 CCCTAATTTG Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 23 6 0.30 24 7 0.35 25 7 0.35 ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33 Consensus pattern (23 bp): AATTAAATCTAAAAAATAATTAG Found at i:18680182 original size:18 final size:17 Alignment explanation

Indices: 18680159--18680196 Score: 58 Period size: 17 Copynumber: 2.2 Consensus size: 17 18680149 TCTTCTCTTA * 18680159 TTTTTTCTCAATTTTCC 1 TTTTTTTTCAATTTTCC * 18680176 TTTTTTTTCAATTTTTC 1 TTTTTTTTCAATTTTCC 18680193 TTTT 1 TTTT 18680197 CGACTTTTCT Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 17 19 1.00 ACGTcount: A:0.11, C:0.16, G:0.00, T:0.74 Consensus pattern (17 bp): TTTTTTTTCAATTTTCC Found at i:18680430 original size:6 final size:6 Alignment explanation

Indices: 18680421--18680519 Score: 75 Period size: 6 Copynumber: 17.2 Consensus size: 6 18680411 TTAAGTTTAC ** * 18680421 TTTAAA TTTAAA TTT--A TGTTAAA TTTAAA TTT-GT TTTAAG TTTAAA 1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA * ** * 18680467 TTT-AA TTTAAG TTTAAA TTTATT TTTAAA TTTAAA ATT--A TTCTAAA 1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA 18680513 TTTAAA T 1 TTTAAA T 18680520 GATGAAAGCC Statistics Matches: 72, Mismatches: 13, Indels: 16 0.71 0.13 0.16 Matches are distributed among these distances: 4 4 0.06 5 11 0.15 6 52 0.72 7 5 0.07 ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55 Consensus pattern (6 bp): TTTAAA Found at i:18680431 original size:17 final size:17 Alignment explanation

Indices: 18680396--18680519 Score: 142 Period size: 17 Copynumber: 7.2 Consensus size: 17 18680386 CCATTTTTTA 18680396 AAATTTATTTTAAGA-TT 1 AAATTTATTTTAA-ATTT * * 18680413 AAGTTTACTTTAAATTT 1 AAATTTATTTTAAATTT * 18680430 AAATTTATGTTAAATTT 1 AAATTTATTTTAAATTT * * 18680447 AAATTTGTTTTAAGTTT 1 AAATTTATTTTAAATTT * * 18680464 AAATTTAATTTAAGTTT 1 AAATTTATTTTAAATTT 18680481 AAATTTATTTTTAAATTT 1 AAATTTA-TTTTAAATTT * * 18680499 AAAATTATTCTAAATTT 1 AAATTTATTTTAAATTT 18680516 AAAT 1 AAAT 18680520 GATGAAAGCC Statistics Matches: 90, Mismatches: 15, Indels: 4 0.83 0.14 0.04 Matches are distributed among these distances: 16 1 0.01 17 75 0.83 18 14 0.16 ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53 Consensus pattern (17 bp): AAATTTATTTTAAATTT Found at i:18680447 original size:23 final size:22 Alignment explanation

Indices: 18680421--18680519 Score: 76 Period size: 23 Copynumber: 4.3 Consensus size: 22 18680411 TTAAGTTTAC 18680421 TTTAAATTTAAATTTATGTTAAA 1 TTTAAATTTAAATTTAT-TTAAA ** 18680444 TTTAAATTT-GTTTTAAGTTTAAA 1 TTTAAATTTAAATTT-A-TTTAAA * ** 18680467 TTT-AATTTAAGTTTAAATTTATT 1 TTTAAATTTAAATTT--ATTTAAA * 18680490 TTTAAATTTAAAATTATTCTAAA 1 TTTAAATTTAAATTTATT-TAAA 18680513 TTTAAAT 1 TTTAAAT 18680520 GATGAAAGCC Statistics Matches: 60, Mismatches: 10, Indels: 12 0.73 0.12 0.15 Matches are distributed among these distances: 22 11 0.18 23 37 0.62 24 12 0.20 ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55 Consensus pattern (22 bp): TTTAAATTTAAATTTATTTAAA Found at i:18681268 original size:3 final size:3 Alignment explanation

Indices: 18681260--18681293 Score: 50 Period size: 3 Copynumber: 11.0 Consensus size: 3 18681250 TTAATAGCAT * 18681260 TAA TAA TAA TAA TGAT TAA TAA TAA TAA TAA TAA 1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA 18681294 AGAAAATAAG Statistics Matches: 28, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 3 26 0.93 4 2 0.07 ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35 Consensus pattern (3 bp): TAA Found at i:18681279 original size:16 final size:16 Alignment explanation

Indices: 18681258--18681288 Score: 62 Period size: 16 Copynumber: 1.9 Consensus size: 16 18681248 TTTTAATAGC 18681258 ATTAATAATAATAATG 1 ATTAATAATAATAATG 18681274 ATTAATAATAATAAT 1 ATTAATAATAATAAT 18681289 AATAAAGAAA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39 Consensus pattern (16 bp): ATTAATAATAATAATG Found at i:18682266 original size:30 final size:29 Alignment explanation

Indices: 18682226--18682432 Score: 172 Period size: 30 Copynumber: 7.0 Consensus size: 29 18682216 AAAGGTCCCT * * 18682226 AAACTGTCCAAAAATTATATTTTGACCCCC 1 AAACTTTCCAAAAATTACATTTT-ACCCCC * 18682256 AAACTTTCCAAAAAATACATTTTAACCCCC 1 AAACTTTCCAAAAATTACATTTT-ACCCCC * * * 18682286 AAACTTTTCAAAAATCACATTTTTGCCCCC 1 AAACTTTCCAAAAATTACA-TTTTACCCCC * 18682316 AAAC-ATCC-AAAATTACCATTTTTACCCCCC 1 AAACTTTCCAAAAATTA-CA-TTTTA-CCCCC * * * 18682346 GAAC-ATCCAAAAATTACCATTTTACCCTC 1 AAACTTTCCAAAAATTA-CATTTTACCCCC * * 18682375 AAA-TGTCCAAAAATTATCGTTTTACCCCC 1 AAACTTTCCAAAAATTA-CATTTTACCCCC * * 18682404 -AAGTTTCTAAAAATTACCATTTTACCCCC 1 AAACTTTCCAAAAATTA-CATTTTACCCCC 18682433 GGACATCCAG Statistics Matches: 148, Mismatches: 23, Indels: 13 0.80 0.12 0.07 Matches are distributed among these distances: 28 8 0.05 29 58 0.39 30 68 0.46 31 14 0.09 ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30 Consensus pattern (29 bp): AAACTTTCCAAAAATTACATTTTACCCCC Found at i:18682446 original size:29 final size:29 Alignment explanation

Indices: 18682232--18682454 Score: 134 Period size: 29 Copynumber: 7.6 Consensus size: 29 18682222 CCCTAAACTG * * * 18682232 TCCAAAAATTA-TATTTTGACCCCCAAACTT 1 TCCAAAAATTACCATTTT-ACCCCCGAAC-A * * * 18682262 TCCAAAAAATA-CATTTTAACCCCCAAACTT 1 TCCAAAAATTACCATTTT-ACCCCCGAAC-A * * * * 18682292 TTCAAAAATCA-CATTTTTGCCCCCAAACA 1 TCCAAAAATTACCA-TTTTACCCCCGAACA 18682321 TCC-AAAATTACCATTTTTACCCCCCGAACA 1 TCCAAAAATTACCA-TTTTA-CCCCCGAACA * * ** 18682351 TCCAAAAATTACCATTTTACCCTCAAATG 1 TCCAAAAATTACCATTTTACCCCCGAACA * * ** 18682380 TCCAAAAATTATCGTTTTACCCCC-AAGTT 1 TCCAAAAATTACCATTTTACCCCCGAA-CA * * 18682409 TCTAAAAATTACCATTTTACCCCCGGACA 1 TCCAAAAATTACCATTTTACCCCCGAACA * * 18682438 TCCAGAAATCA-CATTTT 1 TCCAAAAATTACCATTTT 18682455 TGACTCCGAT Statistics Matches: 158, Mismatches: 29, Indels: 14 0.79 0.14 0.07 Matches are distributed among these distances: 28 14 0.09 29 66 0.42 30 64 0.41 31 14 0.09 ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30 Consensus pattern (29 bp): TCCAAAAATTACCATTTTACCCCCGAACA Found at i:18694158 original size:201 final size:201 Alignment explanation

Indices: 18693812--18694207 Score: 603 Period size: 201 Copynumber: 2.0 Consensus size: 201 18693802 GCGATTACCC ** * 18693812 GAAACAAGTGAGGCGGTTATCTTCCTGATGAGATACAGAAAAGTATACCAACTCAAGGCTCAAAG 1 GAAACAAGTGAGGCGGCCATCTTCCTAATGAGATACAGAAAAGTATACCAACTCAAGGCTCAAAG * * ** 18693877 TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAATG 66 TGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACA * * * * 18693942 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG 131 GTTACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAGAGAAG 18694007 CGGATT 196 CGGATT * * 18694013 GAAACAAGTGAGGTGGCCATCTTCCTAATGAGATACAGAGAAGTATACCAACTCAAGGCTCAAAG 1 GAAACAAGTGAGGCGGCCATCTTCCTAATGAGATACAGAAAAGTATACCAACTCAAGGCTCAAAG * * * 18694078 TGAGCAAATCTTCAAACCCCAGCTTTCTGATGAGATACTGAGGAGCAGGTCGAAGCAATAAAGCA 66 TGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACA * * * * * 18694143 GTTACCTTTCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTTCTGATGAGGTACTGAGAAG 131 GTTACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAGAGAAG 18694208 TAGACCAAAT Statistics Matches: 174, Mismatches: 21, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 201 174 1.00 ACGTcount: A:0.34, C:0.19, G:0.24, T:0.22 Consensus pattern (201 bp): GAAACAAGTGAGGCGGCCATCTTCCTAATGAGATACAGAAAAGTATACCAACTCAAGGCTCAAAG TGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAACA GTTACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAGAGAAG CGGATT Found at i:18694465 original size:208 final size:209 Alignment explanation

Indices: 18694184--18694638 Score: 619 Period size: 208 Copynumber: 2.2 Consensus size: 209 18694174 ACCAGATCCG * * * 18694184 TCTTTCTGATGAGGTACTGAGAAGTAGACCAAATTAATGAAGCCAAGCTCAAAGTGAGCAAATCT 1 TCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAATCT * * *** * 18694249 TCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCT 66 TCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCAAAGCAATAAAACAATTACCTTCCT * * * * * * ** 18694314 AATGAGATACTGAGAAATGGACTAAAT-TCGTCTTCCTGATGAGATATAGAGAAGCGGATTGAAA 131 AATAAGATACAGAGAAATGAACCAAATCT-GTCTTCCTGATGAGACACAGAGAAGCGGATCAAAA 18694378 CAAGTGATGTAG-TCA 195 CAAGTGATG-AGATCA * * * 18694393 TC-TCTTGATGAGATACTAAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAATCT 1 TCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAATCT * * 18694457 TCGAACCCCAGCTTCTTGATGAGATACTAAGAAGCAGGTCAAAGCAATAAAGCAATTACCTTCCT 66 TCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCAAAGCAATAAAACAATTACCTTCCT * * * * 18694522 GATAAGATACAGAGAAGTGAACCAAATCTGTCTTCCTGATGGGACACAGAGAAGTGGATCAAAAC 131 AATAAGATACAGAGAAATGAACCAAATCTGTCTTCCTGATGAGACACAGAGAAGCGGATCAAAAC * 18694587 AAGTGATGCGATCA 196 AAGTGATGAGATCA * 18694601 TCTTCCTGATGAGATATTGAGAAGTAGACCAAATCAAT 1 TCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAAT 18694639 AACACCAAAC Statistics Matches: 212, Mismatches: 31, Indels: 6 0.85 0.12 0.02 Matches are distributed among these distances: 207 1 0.00 208 177 0.83 209 34 0.16 ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23 Consensus pattern (209 bp): TCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAATCT TCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCAAAGCAATAAAACAATTACCTTCCT AATAAGATACAGAGAAATGAACCAAATCTGTCTTCCTGATGAGACACAGAGAAGCGGATCAAAAC AAGTGATGAGATCA Found at i:18706569 original size:17 final size:17 Alignment explanation

Indices: 18706526--18706571 Score: 65 Period size: 18 Copynumber: 2.6 Consensus size: 17 18706516 ATGCATTTTA * * 18706526 TTTAGTTGTTATTGCAT 1 TTTATTTGTTACTGCAT 18706543 TTTCATTTGTTACTGCAT 1 TTT-ATTTGTTACTGCAT 18706561 TTTATTTGTTA 1 TTTATTTGTTA 18706572 GTACATCTGC Statistics Matches: 26, Mismatches: 2, Indels: 2 0.87 0.07 0.07 Matches are distributed among these distances: 17 11 0.42 18 15 0.58 ACGTcount: A:0.17, C:0.09, G:0.13, T:0.61 Consensus pattern (17 bp): TTTATTTGTTACTGCAT Found at i:18709911 original size:2 final size:2 Alignment explanation

Indices: 18709904--18709931 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 18709894 CTACTACATC 18709904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT 18709932 CAACCTAAGA Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:18718277 original size:19 final size:17 Alignment explanation

Indices: 18718237--18718278 Score: 50 Period size: 19 Copynumber: 2.4 Consensus size: 17 18718227 TTCAATTAAA * 18718237 AAATT-ATAATATATTG 1 AAATTAATAATATATTC 18718253 AAATTAATAATAATAGTTC 1 AAATTAATAAT-ATA-TTC 18718272 AAATTAA 1 AAATTAA 18718279 AAATCTATAA Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 16 5 0.23 17 5 0.23 18 3 0.14 19 9 0.41 ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38 Consensus pattern (17 bp): AAATTAATAATATATTC Found at i:18718562 original size:18 final size:18 Alignment explanation

Indices: 18718539--18718590 Score: 95 Period size: 18 Copynumber: 2.9 Consensus size: 18 18718529 ATTTTTTTTC * 18718539 TTGTTTTGTTTTGTTCAT 1 TTGTTTTATTTTGTTCAT 18718557 TTGTTTTATTTTGTTCAT 1 TTGTTTTATTTTGTTCAT 18718575 TTGTTTTATTTTGTTC 1 TTGTTTTATTTTGTTC 18718591 TTATTATCGA Statistics Matches: 33, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 18 33 1.00 ACGTcount: A:0.08, C:0.06, G:0.13, T:0.73 Consensus pattern (18 bp): TTGTTTTATTTTGTTCAT Found at i:18734577 original size:123 final size:123 Alignment explanation

Indices: 18734185--18734738 Score: 722 Period size: 123 Copynumber: 4.5 Consensus size: 123 18734175 TGCTTTACAG * * * * 18734185 GAAGCGAAGCTCAATGTGAGTGAAACTTCAAACTCTCGTCTTCCTAATGAGATACAGAGAAGT-G 1 GAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCTTGATGAGATACAGAGAAGTGG ** * * * * * * 18734249 AGTCAAA-ATGATTAAACGGTCATCTTCTTGACGAGATACAGGGACGTGGACCAAAACAAC 66 A-TCAAACA--ACGAAGCGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAAACAAT * * * * * 18734309 GAAGTGAAACTCAATGTGAGTGAAACTTTAAACCC-CTATCTTCTTGATGAGATATAAAGAAGTG 1 GAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTC-ATCTTCTTGATGAGATACAGAGAAGTG * ** * 18734373 GATCAAACAACGAACCCCT-ATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAAT 65 GATCAAACAACGAAGCGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAAACAAT * * * * 18734431 GAAGCGAAGCTCAATGTGAGTGAAATTTCAAACCCCCATATTCTTGATGAGATACAAAGAAGTGG 1 GAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCTTGATGAGATACAGAGAAGTGG * 18734496 ATCAAACAACGAAGCGGTCATCTTCTTGATGAGATATAGAGAAGTAGACCAAAACAAT 66 ATCAAACAACGAAGCGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAAACAAT * * 18734554 GAAGCGAGGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCCTGATGAGATACAGAGAAGTGG 1 GAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCTTGATGAGATACAGAGAAGTGG * * * * 18734619 ATCAAACAATGAAGCGATCATCTTCCTGATGAAATACAGAGAAGTAGACCAAAACAAT 66 ATCAAACAACGAAGCGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAAACAAT * * * 18734677 AAAGCGAAGCTCCATGTGAGTAAAACTTCAAA-CCTCATCTTCTTGATGAGATACAGAGAAGT 1 GAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCTTGATGAGATACAGAGAAGT 18734739 AGACCAAAAT Statistics Matches: 380, Mismatches: 45, Indels: 12 0.87 0.10 0.03 Matches are distributed among these distances: 122 136 0.36 123 184 0.48 124 57 0.15 125 3 0.01 ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22 Consensus pattern (123 bp): GAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCTTGATGAGATACAGAGAAGTGG ATCAAACAACGAAGCGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAAACAAT Found at i:18734617 original size:245 final size:246 Alignment explanation

Indices: 18734185--18734738 Score: 731 Period size: 245 Copynumber: 2.3 Consensus size: 246 18734175 TGCTTTACAG * * * * 18734185 GAAGCGAAGCTCAATGTGAGTGAAACTTCAAACTCTCGTCTTCCTAATGAGATACAGAGAAGTGA 1 GAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCTTGATGAGATACAGAGAAGTGA ** * * * * 18734250 GTCAAAATGATTAAACGGTCATCTTCTTGACGAGATACAGGGACGTGGACCAAAACAACGAAGTG 66 GTCAAAA-GACGAAACGGTCATCTTCTTGACGAGATACAGAGAAGTAGACCAAAACAACGAAGCG * * * 18734315 AAACTCAATGTGAGTGAAACTTTAAACCCCTATCTTCTTGATGAGATATAAAGAAGTGGATCAAA 130 AAACTCAATGTGAGTGAAACTTCAAACCCCTATCTTCCTGATGAGATACAAAGAAGTGGATCAAA * * * * 18734380 CAACGAACCCCT-ATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAAT 195 CAACGAACCCATCATCTTCCTGATGAAATACAGAGAAGTAGACCAAAACAAT * * * * 18734431 GAAGCGAAGCTCAATGTGAGTGAAATTTCAAACCCCCATATTCTTGATGAGATACAAAGAAGTG- 1 GAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCTTGATGAGATACAGAGAAGTGA * * * * 18734495 GATCAAACA-ACGAAGCGGTCATCTTCTTGATGAGATATAGAGAAGTAGACCAAAACAATGAAGC 66 G-TCAAA-AGACGAAACGGTCATCTTCTTGACGAGATACAGAGAAGTAGACCAAAACAACGAAGC ** * 18734559 GAGGCTCAATGTGAGTGAAACTTCAAA-CCCTCATCTTCCTGATGAGATACAGAGAAGTGGATCA 129 GAAACTCAATGTGAGTGAAACTTCAAACCCCT-ATCTTCCTGATGAGATACAAAGAAGTGGATCA * * * 18734623 AACAATGAAGCGATCATCTTCCTGATGAAATACAGAGAAGTAGACCAAAACAAT 193 AACAACGAACCCATCATCTTCCTGATGAAATACAGAGAAGTAGACCAAAACAAT * * * 18734677 AAAGCGAAGCTCCATGTGAGTAAAACTTCAAA-CCTCATCTTCTTGATGAGATACAGAGAAGT 1 GAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCTTGATGAGATACAGAGAAGT 18734739 AGACCAAAAT Statistics Matches: 266, Mismatches: 38, Indels: 9 0.85 0.12 0.03 Matches are distributed among these distances: 244 4 0.02 245 136 0.51 246 125 0.47 247 1 0.00 ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22 Consensus pattern (246 bp): GAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTTCTTGATGAGATACAGAGAAGTGA GTCAAAAGACGAAACGGTCATCTTCTTGACGAGATACAGAGAAGTAGACCAAAACAACGAAGCGA AACTCAATGTGAGTGAAACTTCAAACCCCTATCTTCCTGATGAGATACAAAGAAGTGGATCAAAC AACGAACCCATCATCTTCCTGATGAAATACAGAGAAGTAGACCAAAACAAT Found at i:18734658 original size:47 final size:48 Alignment explanation

Indices: 18734589--18734683 Score: 147 Period size: 47 Copynumber: 2.0 Consensus size: 48 18734579 CTTCAAACCC * * * * 18734589 TCATCTTCCTGATGAGATACAGAGAAGTGGATC-AAACAATGAAGCGA 1 TCATCTTCCTGATGAAATACAGAGAAGTAGACCAAAACAATAAAGCGA 18734636 TCATCTTCCTGATGAAATACAGAGAAGTAGACCAAAACAATAAAGCGA 1 TCATCTTCCTGATGAAATACAGAGAAGTAGACCAAAACAATAAAGCGA 18734684 AGCTCCATGT Statistics Matches: 43, Mismatches: 4, Indels: 1 0.90 0.08 0.02 Matches are distributed among these distances: 47 30 0.70 48 13 0.30 ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20 Consensus pattern (48 bp): TCATCTTCCTGATGAAATACAGAGAAGTAGACCAAAACAATAAAGCGA Found at i:18735933 original size:27 final size:27 Alignment explanation

Indices: 18735903--18735955 Score: 63 Period size: 27 Copynumber: 2.0 Consensus size: 27 18735893 TAAAAAAACT * * 18735903 AAAAAGAGAA-ATAAATCAATTTTAAAA 1 AAAAAGAAAATATAAAAC-ATTTTAAAA * 18735930 AAAACGAAAATATAAAACATTTTAAA 1 AAAAAGAAAATATAAAACATTTTAAA 18735956 GATCGCTTTT Statistics Matches: 22, Mismatches: 3, Indels: 2 0.81 0.11 0.07 Matches are distributed among these distances: 27 16 0.73 28 6 0.27 ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23 Consensus pattern (27 bp): AAAAAGAAAATATAAAACATTTTAAAA Found at i:18736670 original size:31 final size:30 Alignment explanation

Indices: 18736557--18736875 Score: 194 Period size: 30 Copynumber: 10.8 Consensus size: 30 18736547 AAAATTATGT * * 18736557 TTTGACCCCTAAATTTTCTAAAAATTTAGA 1 TTTGACCCCTAAACTTTCCAAAAATTTAGA * * * * 18736587 TTTAACCCTTAAAC-TACCTAAAAATTTGGA 1 TTTGACCCCTAAACTTTCC-AAAAATTTAGA *** 18736617 TTTGACCCCTAAACAACCCAAAAAGTTTAGA 1 TTTGACCCCTAAACTTTCCAAAAA-TTTAGA * * 18736648 TTTGACCCCTGAACTTTTCAAAAA-TTA-A 1 TTTGACCCCTAAACTTTCCAAAAATTTAGA * **** * * 18736676 GTTGGTTTCTAAACTTTCCAAAAATTAAGT 1 TTTGACCCCTAAACTTTCCAAAAATTTAGA * * 18736706 TTTGA-CCCTCGAACTTTCAAAAAATTTAGA 1 TTTGACCCCT-AAACTTTCCAAAAATTTAGA * * 18736736 TTTGA-CCCTAAAC-TTCACAAAAATTCATA 1 TTTGACCCCTAAACTTTC-CAAAAATTTAGA * * * 18736765 TTTGA-CCCTCGAAC-ATCCTAAAAATTTGGA 1 TTTGACCCCT-AAACTTTCC-AAAAATTTAGA * * * 18736795 TTTAACCCC-AAACTTTCCAAAAATTCATA 1 TTTGACCCCTAAACTTTCCAAAAATTTAGA ** * 18736824 TTTGACTTCTGAAC-TTCTCAAAAATTT-GAA 1 TTTGACCCCTAAACTTTC-CAAAAATTTAG-A * 18736854 TTT-ACCCCCAAACTTTCCAAAA 1 TTTGACCCCTAAACTTTCCAAAA 18736876 TTTCATTTTT Statistics Matches: 216, Mismatches: 58, Indels: 31 0.71 0.19 0.10 Matches are distributed among these distances: 28 21 0.10 29 62 0.29 30 104 0.48 31 29 0.13 ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33 Consensus pattern (30 bp): TTTGACCCCTAAACTTTCCAAAAATTTAGA Found at i:18736757 original size:59 final size:58 Alignment explanation

Indices: 18736606--18736891 Score: 192 Period size: 59 Copynumber: 4.8 Consensus size: 58 18736596 TAAACTACCT * *** * * 18736606 AAAAATTTGGATTTGACCCCTAAACAACCCAAAAAGTTTAGATTTGACCC-CTGAACTTTTC 1 AAAAATTTAGATTTGA-CCCTAAACTTTCCAAAAA-TTAAGTTTTGACCCTC-GAAC-TTTC * * *** 18736667 AAAAATTAAG-TTGGTTTCTAAACTTTCCAAAAATTAAGTTTTGACCCTCGAACTTTC 1 AAAAATTTAGATTTGACCCTAAACTTTCCAAAAATTAAGTTTTGACCCTCGAACTTTC * * * 18736724 AAAAAATTTAGATTTGACCCTAAAC-TTCACAAAAATTCA-TATTTGACCCTCGAACATCC 1 -AAAAATTTAGATTTGACCCTAAACTTTC-CAAAAATTAAGT-TTTGACCCTCGAACTTTC * * * * * 18736783 TAAAAATTTGGATTTAACCCCAAACTTTCCAAAAATTCA-TATTTGA-CTTCTGAACTTCTC 1 -AAAAATTTAGATTTGACCCTAAACTTTCCAAAAATTAAGT-TTTGACCCTC-GAACTT-TC * * * * 18736843 AAAAATTT-GAATTT-ACCCCCAAACTTTCCAAAATTTCATTTTTGACCCT 1 AAAAATTTAG-ATTTGA-CCCTAAACTTTCCAAAAATTAAGTTTTGACCCT 18736892 ATTATTCCTT Statistics Matches: 185, Mismatches: 28, Indels: 25 0.78 0.12 0.11 Matches are distributed among these distances: 57 4 0.02 58 34 0.18 59 129 0.70 60 10 0.05 61 8 0.04 ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34 Consensus pattern (58 bp): AAAAATTTAGATTTGACCCTAAACTTTCCAAAAATTAAGTTTTGACCCTCGAACTTTC Found at i:18739482 original size:34 final size:34 Alignment explanation

Indices: 18739415--18739484 Score: 95 Period size: 34 Copynumber: 2.1 Consensus size: 34 18739405 CCAAAAAAAA * * * * 18739415 AACATGATAAGCTTGATGTGGATGTGTTGAATAT 1 AACATGATAACCTTGATGTGAATGTATTCAATAT * 18739449 AACATGATAACCTTGATGTTAATGTATTCAATAT 1 AACATGATAACCTTGATGTGAATGTATTCAATAT 18739483 AA 1 AA 18739485 AATATAAACA Statistics Matches: 31, Mismatches: 5, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 34 31 1.00 ACGTcount: A:0.37, C:0.09, G:0.19, T:0.36 Consensus pattern (34 bp): AACATGATAACCTTGATGTGAATGTATTCAATAT Found at i:18743618 original size:3 final size:3 Alignment explanation

Indices: 18743610--18743677 Score: 111 Period size: 3 Copynumber: 23.0 Consensus size: 3 18743600 AAAGCAGTAG 18743610 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA 1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA * * 18743658 AG- AGA AGG AGG AGA AGA AGA 1 AGA AGA AGA AGA AGA AGA AGA 18743678 GAAAAATTCT Statistics Matches: 62, Mismatches: 2, Indels: 2 0.94 0.03 0.03 Matches are distributed among these distances: 2 2 0.03 3 60 0.97 ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00 Consensus pattern (3 bp): AGA Found at i:18743841 original size:3 final size:3 Alignment explanation

Indices: 18743833--18743861 Score: 58 Period size: 3 Copynumber: 9.7 Consensus size: 3 18743823 TCATCTCCAT 18743833 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT 1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT 18743862 TTACTGTTAA Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 26 1.00 ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69 Consensus pattern (3 bp): TTC Found at i:18745045 original size:6 final size:6 Alignment explanation

Indices: 18745034--18745095 Score: 56 Period size: 6 Copynumber: 9.8 Consensus size: 6 18745024 AAAACCAGCA * 18745034 GAGAGG GAGAGG GAGAGG GAGA-G GAGAGG GACG-GTG GTAGGAAGG GAGGGG 1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GA-GAG-G G-A-G-AGG GAGAGG 18745085 GAGAGG GAGAG 1 GAGAGG GAGAG 18745096 AGACGGGATG Statistics Matches: 47, Mismatches: 3, Indels: 12 0.76 0.05 0.19 Matches are distributed among these distances: 5 5 0.11 6 32 0.68 7 4 0.09 8 3 0.06 9 2 0.04 10 1 0.02 ACGTcount: A:0.31, C:0.02, G:0.65, T:0.03 Consensus pattern (6 bp): GAGAGG Found at i:18759139 original size:7 final size:8 Alignment explanation

Indices: 18759122--18759150 Score: 51 Period size: 8 Copynumber: 3.8 Consensus size: 8 18759112 AACTAGAGGC 18759122 AAAAAAGG 1 AAAAAAGG 18759130 AAAAAA-G 1 AAAAAAGG 18759137 AAAAAAGG 1 AAAAAAGG 18759145 AAAAAA 1 AAAAAA 18759151 CCATAGCTGA Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 7 7 0.35 8 13 0.65 ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00 Consensus pattern (8 bp): AAAAAAGG Found at i:18759142 original size:15 final size:15 Alignment explanation

Indices: 18759122--18759150 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 18759112 AACTAGAGGC 18759122 AAAAAAGGAAAAAAG 1 AAAAAAGGAAAAAAG 18759137 AAAAAAGGAAAAAA 1 AAAAAAGGAAAAAA 18759151 CCATAGCTGA 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:0.83, C:0.00, G:0.17, T:0.00 Consensus pattern (15 bp): AAAAAAGGAAAAAAG Found at i:18762338 original size:19 final size:19 Alignment explanation

Indices: 18762316--18762374 Score: 68 Period size: 19 Copynumber: 3.1 Consensus size: 19 18762306 ATATTAATTA * 18762316 AATTATAAAATAAAAAAAT 1 AATTAAAAAATAAAAAAAT 18762335 AATTAAAAAAT-AAAAAA- 1 AATTAAAAAATAAAAAAAT * 18762352 AATTAAATAATATTAAAAAAT 1 AATTAAA-AA-ATAAAAAAAT 18762373 AA 1 AA 18762375 AATTAACTCT Statistics Matches: 35, Mismatches: 1, Indels: 6 0.83 0.02 0.14 Matches are distributed among these distances: 17 7 0.20 18 8 0.23 19 12 0.34 20 6 0.17 21 2 0.06 ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25 Consensus pattern (19 bp): AATTAAAAAATAAAAAAAT Found at i:18762345 original size:27 final size:27 Alignment explanation

Indices: 18762322--18762376 Score: 83 Period size: 27 Copynumber: 2.0 Consensus size: 27 18762312 ATTAAATTAT 18762322 AAAATAAAAAAATAATTAAAAAATAAAA 1 AAAATAAAAAAAT-ATTAAAAAATAAAA * * 18762350 AAAATTAAATAATATTAAAAAATAAAA 1 AAAATAAAAAAATATTAAAAAATAAAA 18762377 TTAACTCTTA Statistics Matches: 25, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 27 14 0.56 28 11 0.44 ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22 Consensus pattern (27 bp): AAAATAAAAAAATATTAAAAAATAAAA Found at i:18762349 original size:17 final size:17 Alignment explanation

Indices: 18762315--18762376 Score: 63 Period size: 17 Copynumber: 3.5 Consensus size: 17 18762305 AATATTAATT * 18762315 AAATTATAAAATAAAAAA 1 AAATTAAAAAAT-AAAAA 18762333 ATAATTAAAAAATAAAAA 1 A-AATTAAAAAATAAAAA * * 18762351 AAATTAAATAATATTAAA 1 AAATTAAAAAATA-AAAA 18762369 AAA-TAAAA 1 AAATTAAAA 18762377 TTAACTCTTA Statistics Matches: 38, Mismatches: 4, Indels: 5 0.81 0.09 0.11 Matches are distributed among these distances: 17 15 0.39 18 13 0.34 19 10 0.26 ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24 Consensus pattern (17 bp): AAATTAAAAAATAAAAA Found at i:18762366 original size:10 final size:10 Alignment explanation

Indices: 18762291--18762373 Score: 63 Period size: 9 Copynumber: 8.9 Consensus size: 10 18762281 ACTATTCACA * 18762291 TAAAAATTA- 1 TAAAAAATAT 18762300 TAAAAAATAT 1 TAAAAAATAT ** 18762310 TAATTAA-AT 1 TAAAAAATAT * 18762319 TATAAAATA- 1 TAAAAAATAT 18762328 -AAAAAATAAT 1 TAAAAAAT-AT 18762338 TAAAAAATA- 1 TAAAAAATAT 18762347 -AAAAAA-AT 1 TAAAAAATAT * 18762355 TAAATAATAT 1 TAAAAAATAT 18762365 TAAAAAATA 1 TAAAAAATA 18762374 AAATTAACTC Statistics Matches: 57, Mismatches: 9, Indels: 15 0.70 0.11 0.19 Matches are distributed among these distances: 7 1 0.02 8 12 0.21 9 20 0.35 10 17 0.30 11 7 0.12 ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29 Consensus pattern (10 bp): TAAAAAATAT Found at i:18762541 original size:19 final size:20 Alignment explanation

Indices: 18762487--18762541 Score: 53 Period size: 19 Copynumber: 2.8 Consensus size: 20 18762477 TTAAGAAATT * * 18762487 TAAAGAATTATAGAGAAATTA 1 TAAAAAATT-TAGAGAAATAA 18762508 TAAAAAAGTTT--AGAAA-AA 1 TAAAAAA-TTTAGAGAAATAA 18762526 TAAAAAATTTAGAGAA 1 TAAAAAATTTAGAGAA 18762542 CTTTGAGAGC Statistics Matches: 29, Mismatches: 2, Indels: 8 0.74 0.05 0.21 Matches are distributed among these distances: 17 3 0.10 18 8 0.28 19 9 0.31 21 7 0.24 22 2 0.07 ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25 Consensus pattern (20 bp): TAAAAAATTTAGAGAAATAA Found at i:18766885 original size:23 final size:23 Alignment explanation

Indices: 18766859--18766904 Score: 92 Period size: 23 Copynumber: 2.0 Consensus size: 23 18766849 TATATATATG 18766859 GTAATTCCTCACATCAGAGGAGT 1 GTAATTCCTCACATCAGAGGAGT 18766882 GTAATTCCTCACATCAGAGGAGT 1 GTAATTCCTCACATCAGAGGAGT 18766905 TATAGACAAG Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 23 1.00 ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26 Consensus pattern (23 bp): GTAATTCCTCACATCAGAGGAGT Found at i:18782440 original size:17 final size:16 Alignment explanation

Indices: 18782401--18782441 Score: 50 Period size: 17 Copynumber: 2.6 Consensus size: 16 18782391 TAAAAAGATA 18782401 AATAAT-TTTTATTTT 1 AATAATATTTTATTTT 18782416 AACT-ATATTTATATTTT 1 AA-TAATATTT-TATTTT 18782433 AATAATATT 1 AATAATATT 18782442 ATAGATTGAG Statistics Matches: 22, Mismatches: 0, Indels: 6 0.79 0.00 0.21 Matches are distributed among these distances: 15 4 0.18 16 5 0.23 17 13 0.59 ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59 Consensus pattern (16 bp): AATAATATTTTATTTT Found at i:18783283 original size:22 final size:21 Alignment explanation

Indices: 18783243--18783283 Score: 57 Period size: 21 Copynumber: 1.9 Consensus size: 21 18783233 CTATAACACA 18783243 ATTTAATTTAAAAATTAAATT 1 ATTTAATTTAAAAATTAAATT 18783264 ATTT-ATTATAAATAATTAAA 1 ATTTAATT-TAAA-AATTAAA 18783284 AATGAAACCT Statistics Matches: 18, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 20 3 0.17 21 8 0.44 22 7 0.39 ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46 Consensus pattern (21 bp): ATTTAATTTAAAAATTAAATT Found at i:18790474 original size:88 final size:88 Alignment explanation

Indices: 18790296--18790497 Score: 250 Period size: 89 Copynumber: 2.3 Consensus size: 88 18790286 CTTTAAAAAA * * * * * 18790296 AAAAAAAGCAATTAAGTCCCTCCTTTTTTTGCATTCATTTGGGTACTTAAATTTTTAAAATGCAT 1 AAAAAAAGCAATTAAGTCCCTCCTTTTTTTGCACTCAATTAGATACTTAAACTTTTAAAATGCAT * ** 18790361 TAAAAAGGTCTTCAAACCTTTTC 66 CAAAAAGACCTTCAAACCTTTTC * * 18790384 AAAAAAAGCAATTAAG-CTCCTACTTTTTTTTGCACTCAATTAGATACTTGAACTTTTAAAATGC 1 AAAAAAAGCAATTAAGTC-CCT-CCTTTTTTTGCACTCAATTAGATACTTAAACTTTTAAAATGC 18790448 ATCAAAAAGACCTTCAAA-CTTTTC 64 ATCAAAAAGACCTTCAAACCTTTTC * 18790472 AAAAAAA--AATTTAAGTCCCTGCTTTT 1 AAAAAAAGCAA-TTAAGTCCCTCCTTTT 18790498 ATTAAAAAAT Statistics Matches: 98, Mismatches: 12, Indels: 10 0.82 0.10 0.08 Matches are distributed among these distances: 86 6 0.06 87 9 0.09 88 33 0.34 89 50 0.51 ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36 Consensus pattern (88 bp): AAAAAAAGCAATTAAGTCCCTCCTTTTTTTGCACTCAATTAGATACTTAAACTTTTAAAATGCAT CAAAAAGACCTTCAAACCTTTTC Found at i:18790581 original size:8 final size:9 Alignment explanation

Indices: 18790560--18790741 Score: 91 Period size: 9 Copynumber: 19.0 Consensus size: 9 18790550 ATTTTAATAA 18790560 AAAAATTAT 1 AAAAATTAT 18790569 AAAAATTAT 1 AAAAATTAT 18790578 AAAAATTAT 1 AAAAATTAT * 18790587 AAAAAATAT 1 AAAAATTAT * 18790596 AAAAAATTGT 1 -AAAAATTAT * 18790606 AAAATTTTAT 1 AAAA-ATTAT * 18790616 AAAAATCGTAA 1 AAAAAT--TAT * 18790627 AAAAAATAT 1 AAAAATTAT 18790636 -AAAATATAT 1 AAAAAT-TAT * * 18790645 AGAAATATAAA 1 A-AAA-ATTAT 18790656 AAAAATTAT 1 AAAAATTAT * 18790665 -AAAATTTT 1 AAAAATTAT * * * 18790673 GTAAAGTCAT 1 -AAAAATTAT 18790683 AAGAAAATTAT 1 -A-AAAATTAT 18790694 AGAAAA-TAT 1 A-AAAATTAT * 18790703 AAAGAAATAT 1 AAA-AATTAT * * 18790713 AAAATTCGTAA 1 AAAAAT--TAT 18790724 AAAAATTAT 1 AAAAATTAT 18790733 AAAAATTAT 1 AAAAATTAT 18790742 CATACCAAAA Statistics Matches: 131, Mismatches: 27, Indels: 30 0.70 0.14 0.16 Matches are distributed among these distances: 8 13 0.10 9 57 0.44 10 34 0.26 11 25 0.19 12 2 0.02 ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30 Consensus pattern (9 bp): AAAAATTAT Found at i:18790588 original size:29 final size:28 Alignment explanation

Indices: 18790556--18790670 Score: 99 Period size: 28 Copynumber: 4.0 Consensus size: 28 18790546 TTAAATTTTA * 18790556 ATAAAAAAATTATAAAAATTATAAAAATT 1 ATAAAAAAATTAAAAAAATTAT-AAAATT * 18790585 AT-AAAAAA-TATAAAAAATTGTAAAATT 1 ATAAAAAAATTA-AAAAAATTATAAAATT * * * 18790612 TTATAAAAATCGTAAAAAAAATATAAAATAT 1 ATAAAAAAAT--TAAAAAAATTATAAAAT-T * * * 18790643 ATAGAAATATAAAAAAAATTATAAAATT 1 ATAAAAAAATTAAAAAAATTATAAAATT 18790671 TTGTAAAGTC Statistics Matches: 69, Mismatches: 11, Indels: 13 0.74 0.12 0.14 Matches are distributed among these distances: 27 9 0.13 28 20 0.29 29 17 0.25 30 13 0.19 31 10 0.14 ACGTcount: A:0.67, C:0.01, G:0.03, T:0.30 Consensus pattern (28 bp): ATAAAAAAATTAAAAAAATTATAAAATT Found at i:18790598 original size:38 final size:40 Alignment explanation

Indices: 18790556--18790639 Score: 111 Period size: 37 Copynumber: 2.1 Consensus size: 40 18790546 TTAAATTTTA * 18790556 ATAAAAAAATTATAAAA-ATTATAAAAAT-TATAAAAAAT 1 ATAAAAAAATTATAAAATATTATAAAAATCTAAAAAAAAT * * 18790594 AT-AAAAAATTGTAAAATTTTATAAAAATCGTAAAAAAAAT 1 ATAAAAAAATTATAAAATATTATAAAAATC-TAAAAAAAAT 18790634 ATAAAA 1 ATAAAA 18790640 TATATAGAAA Statistics Matches: 39, Mismatches: 3, Indels: 5 0.83 0.06 0.11 Matches are distributed among these distances: 37 13 0.33 38 12 0.31 40 11 0.28 41 3 0.08 ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29 Consensus pattern (40 bp): ATAAAAAAATTATAAAATATTATAAAAATCTAAAAAAAAT Found at i:18790611 original size:59 final size:59 Alignment explanation

Indices: 18790542--18790677 Score: 150 Period size: 59 Copynumber: 2.3 Consensus size: 59 18790532 GGTTATAAAT * * * * * 18790542 ATTATTAAATTTTAATAAAAAAATTATAAAAATTATAAAA-ATTATA-AAAAATATAAAAA 1 ATTATAAAATTTT-ATAAAAAAAGTAAAAAAAATATAAAATA-TATAGAAAAATAAAAAAA * ** * 18790601 ATTGTAAAATTTTATAAAAATCGTAAAAAAAATATAAAATATATAGAAATATAAAAAAA 1 ATTATAAAATTTTATAAAAAAAGTAAAAAAAATATAAAATATATAGAAAAATAAAAAAA * 18790660 ATTATAAAATTTTGTAAA 1 ATTATAAAATTTTATAAA 18790678 GTCATAAGAA Statistics Matches: 64, Mismatches: 11, Indels: 4 0.81 0.14 0.05 Matches are distributed among these distances: 58 25 0.39 59 39 0.61 ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33 Consensus pattern (59 bp): ATTATAAAATTTTATAAAAAAAGTAAAAAAAATATAAAATATATAGAAAAATAAAAAAA Found at i:18790777 original size:11 final size:11 Alignment explanation

Indices: 18790761--18790793 Score: 50 Period size: 11 Copynumber: 3.1 Consensus size: 11 18790751 AGAAGTATTT 18790761 TATAATTTTTA 1 TATAATTTTTA 18790772 TATAATTTTTA 1 TATAATTTTTA * 18790783 T-TGATTTTTA 1 TATAATTTTTA 18790793 T 1 T 18790794 TTTTTATCAT Statistics Matches: 21, Mismatches: 1, Indels: 1 0.91 0.04 0.04 Matches are distributed among these distances: 10 9 0.43 11 12 0.57 ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67 Consensus pattern (11 bp): TATAATTTTTA Found at i:18791193 original size:89 final size:89 Alignment explanation

Indices: 18791098--18791266 Score: 268 Period size: 89 Copynumber: 1.9 Consensus size: 89 18791088 TTTTAATAAG * * 18791098 AGCAAGGGCTTATTTG-TTTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCA 1 AGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTT-ATGCATTTTGAAAGTTCA 18791162 AGTACCCAATTGAGTGGGGGGAAAA 65 AGTACCCAATTGAGTGGGGGGAAAA * * 18791187 AGCAAGGGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGTCTTTTTATGTATTTTGAAAGTTCAA 1 AGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTATGCATTTTGAAAGTTCAA * * 18791252 GTGCTCAATTGAGTG 66 GTACCCAATTGAGTG 18791267 AAAAAAAAAG Statistics Matches: 73, Mismatches: 6, Indels: 2 0.90 0.07 0.02 Matches are distributed among these distances: 89 46 0.63 90 27 0.37 ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39 Consensus pattern (89 bp): AGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTATGCATTTTGAAAGTTCAA GTACCCAATTGAGTGGGGGGAAAA Found at i:18791300 original size:90 final size:90 Alignment explanation

Indices: 18791098--18791292 Score: 252 Period size: 89 Copynumber: 2.2 Consensus size: 90 18791088 TTTTAATAAG * * 18791098 AGCAAGGGCTTATTTG-TTTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCA 1 AGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCA **** 18791162 AGTACCCAATTGAGTGGGGGGAAAA 66 AGTACCCAATTGAGTGGAAAAAAAA * * 18791187 AGCAAGGGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGTCTTTTT-ATGTATTTTGAAAGTTCA 1 AGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCA * * 18791251 AGTGCTCAATTGAGT-GAAAAAAAA 66 AGTACCCAATTGAGTGGAAAAAAAA * * * 18791275 AGGAGGGGTTTAATTGCT 1 AGCAAGGGCTTAATTGCT 18791293 CTATTTTTTT Statistics Matches: 92, Mismatches: 13, Indels: 3 0.85 0.12 0.03 Matches are distributed among these distances: 88 20 0.22 89 45 0.49 90 27 0.29 ACGTcount: A:0.29, C:0.08, G:0.26, T:0.37 Consensus pattern (90 bp): AGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCA AGTACCCAATTGAGTGGAAAAAAAA Found at i:18794787 original size:60 final size:60 Alignment explanation

Indices: 18794676--18794847 Score: 190 Period size: 60 Copynumber: 2.9 Consensus size: 60 18794666 TTAACATAAT * * * 18794676 ATTTGGTA-TCTGAATTTGATATTTTTTTTCTAATTTGGTAACTAAACTTTTTTTT-ATC-CA 1 ATTTGGTACT-TGAATTTGACA-TTTTTTCCTAATTTGGTACCTAAACTTTTTTTTGA-CACA * * 18794736 ATTTGGTACTTGAATTTGACACTTTTTCCTACTTTGGTACCTAAACTTTTTTTTGACACA 1 ATTTGGTACTTGAATTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTTTGACACA * * * * * * 18794796 ATTTAGTACTTGAACTTGGCATTTTTTCTTAATTTGTTACCT-AAGTTTTTTT 1 ATTTGGTACTTGAATTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTT 18794848 AGATTCAATT Statistics Matches: 96, Mismatches: 13, Indels: 7 0.83 0.11 0.06 Matches are distributed among these distances: 59 39 0.41 60 56 0.58 61 1 0.01 ACGTcount: A:0.23, C:0.13, G:0.11, T:0.52 Consensus pattern (60 bp): ATTTGGTACTTGAATTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTTTGACACA Found at i:18800116 original size:30 final size:31 Alignment explanation

Indices: 18800080--18800147 Score: 104 Period size: 31 Copynumber: 2.2 Consensus size: 31 18800070 GATTTTAATC 18800080 CAGTCACTCAAC-TT-TTAAAAAATAACAAAT 1 CAGTCACT-AACATTATTAAAAAATAACAAAT 18800110 CAGTCACTAACATTATTAAAAAATAACAAAT 1 CAGTCACTAACATTATTAAAAAATAACAAAT * 18800141 CAATCAC 1 CAGTCAC 18800148 CCATTAACAT Statistics Matches: 35, Mismatches: 1, Indels: 3 0.90 0.03 0.08 Matches are distributed among these distances: 29 3 0.09 30 10 0.29 31 22 0.63 ACGTcount: A:0.51, C:0.21, G:0.03, T:0.25 Consensus pattern (31 bp): CAGTCACTAACATTATTAAAAAATAACAAAT Found at i:18806363 original size:27 final size:28 Alignment explanation

Indices: 18806309--18806403 Score: 83 Period size: 27 Copynumber: 3.5 Consensus size: 28 18806299 ACAGAACATA * * * 18806309 GCTCTTTCGAGCCCATAATAG-ATTATT 1 GCTCTTTCGAGCCAAGAATAGAATAATT * 18806336 GCTCTTTCGAGCCAA-AATCATAA-AATT 1 GCTCTTTCGAGCCAAGAAT-AGAATAATT * * 18806363 GCT-TATTCGAGGCAAGGATAGAATAA-T 1 GCTCT-TTCGAGCCAAGAATAGAATAATT 18806390 GCTCTTTCGAGCCA 1 GCTCTTTCGAGCCA 18806404 GATACGTATT Statistics Matches: 55, Mismatches: 7, Indels: 12 0.74 0.09 0.16 Matches are distributed among these distances: 26 4 0.07 27 45 0.82 28 6 0.11 ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31 Consensus pattern (28 bp): GCTCTTTCGAGCCAAGAATAGAATAATT Found at i:18807935 original size:45 final size:44 Alignment explanation

Indices: 18807886--18808087 Score: 197 Period size: 45 Copynumber: 4.5 Consensus size: 44 18807876 GAAGTGGTGT * 18807886 CATAGTATGTTTCAACTATGGTCTTGTTAATTTTCGATGTATTGC 1 CATAGTATCTTTCAACTATGGTCTTGTT-ATTTTCGATGTATTGC * * * * 18807931 CATAGTATCTTTTAACTATTGTCTTGTTCATTTCCAATGTATTGC 1 CATAGTATCTTTCAACTATGGTCTTGTT-ATTTTCGATGTATTGC * ** * * * 18807976 CATAGTATCTTTCAACCATGGTCTTGTTCGTTTCTGGTATAGTGC 1 CATAGTATCTTTCAACTATGGTCTTGTTATTTTC-GATGTATTGC * * * * * * * 18808021 CATAGTATCTTTCAACTATGGTCTTTCTTGTTTTGGGTATAATGT 1 CATAGTATCTTTCAACTATGGTC-TTGTTATTTTCGATGTATTGC * 18808066 CATAGTATCTTTCAACCATGGT 1 CATAGTATCTTTCAACTATGGT 18808088 TTTTTTTCGT Statistics Matches: 131, Mismatches: 24, Indels: 4 0.82 0.15 0.03 Matches are distributed among these distances: 44 3 0.02 45 121 0.92 46 7 0.05 ACGTcount: A:0.21, C:0.17, G:0.16, T:0.46 Consensus pattern (44 bp): CATAGTATCTTTCAACTATGGTCTTGTTATTTTCGATGTATTGC Found at i:18809973 original size:17 final size:17 Alignment explanation

Indices: 18809933--18809975 Score: 50 Period size: 17 Copynumber: 2.5 Consensus size: 17 18809923 TATTGCTAAT * * 18809933 ATTTTACTTTGTTTAAA 1 ATTTTAATTTATTTAAA * * 18809950 ATATTAATTTATTTATA 1 ATTTTAATTTATTTAAA 18809967 ATTTTAATT 1 ATTTTAATT 18809976 CAATATGCTT Statistics Matches: 21, Mismatches: 5, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 17 21 1.00 ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60 Consensus pattern (17 bp): ATTTTAATTTATTTAAA Found at i:18822277 original size:18 final size:18 Alignment explanation

Indices: 18822254--18822297 Score: 61 Period size: 18 Copynumber: 2.4 Consensus size: 18 18822244 CTATCTAGTA * 18822254 ATGCTCTTACGAGCCAGT 1 ATGCTCTTACGAGCAAGT ** 18822272 ATGCTCAAACGAGCAAGT 1 ATGCTCTTACGAGCAAGT 18822290 ATGCTCTT 1 ATGCTCTT 18822298 GATCGCGCTA Statistics Matches: 21, Mismatches: 5, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 18 21 1.00 ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27 Consensus pattern (18 bp): ATGCTCTTACGAGCAAGT Found at i:18823491 original size:21 final size:20 Alignment explanation

Indices: 18823465--18823503 Score: 69 Period size: 21 Copynumber: 1.9 Consensus size: 20 18823455 TTAAACAAAG 18823465 AATCACTAAGTTAGAAAATGC 1 AATCACTAAGTTA-AAAATGC 18823486 AATCACTAAGTTAAAAAT 1 AATCACTAAGTTAAAAAT 18823504 TCTAAAAATG Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 20 5 0.28 21 13 0.72 ACGTcount: A:0.51, C:0.13, G:0.10, T:0.26 Consensus pattern (20 bp): AATCACTAAGTTAAAAATGC Found at i:18833153 original size:52 final size:52 Alignment explanation

Indices: 18833001--18833244 Score: 339 Period size: 52 Copynumber: 4.7 Consensus size: 52 18832991 ATAAACAAAA * * 18833001 AGGTCCGATAACTAAGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAG 1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG * * 18833053 AGGTCTGATGATTAAGTGTCAT-GTGAGTATATGAATCCTTTACGGATTAAG 1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG * * 18833104 AGGTCCGATGACTAAGTGTCATCGTGAGTATATAAATCCTTCACGGATTAAG 1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG ** * * 18833156 AGGTCCGATGACTCTGTGTCATCATGAGTATATGAATCCCTTACGGATTATA- 1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTA-AG * ** * 18833208 AGGTCCGGTCTCTATGTGTCATCGTGAGTATATGAAT 1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAAT 18833245 AAAGTGAAAT Statistics Matches: 171, Mismatches: 19, Indels: 4 0.88 0.10 0.02 Matches are distributed among these distances: 51 48 0.28 52 122 0.71 53 1 0.01 ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33 Consensus pattern (52 bp): AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG Found at i:18833239 original size:104 final size:103 Alignment explanation

Indices: 18833001--18833240 Score: 329 Period size: 103 Copynumber: 2.3 Consensus size: 103 18832991 ATAAACAAAA * * * * * * 18833001 AGGTCCGATAACTAAGTGTCATCGTGAGTATATGAATCCTTTATGGATTAAGAGGTCTGATGATT 1 AGGTCCGATCACTAAGTGTCATCGTGAGTATATAAATCCTTCACGGATTAAGAGGTCCGATGACT * * 18833066 AAGTGTCATGTGAGTATATGAATCCTTTACGGATTAAG 66 AAGTGTCATATGAGTATATGAATCCCTTACGGATTAAG * 18833104 AGGTCCGATGACTAAGTGTCATCGTGAGTATATAAATCCTTCACGGATTAAGAGGTCCGATGACT 1 AGGTCCGATCACTAAGTGTCATCGTGAGTATATAAATCCTTCACGGATTAAGAGGTCCGATGACT ** 18833169 CTGTGTCATCATGAGTATATGAATCCCTTACGGATTATA- 66 AAGTGTCAT-ATGAGTATATGAATCCCTTACGGATTA-AG * * * 18833208 AGGTCCGGTCTCTATGTGTCATCGTGAGTATAT 1 AGGTCCGATCACTAAGTGTCATCGTGAGTATAT 18833241 GAATAAAGTG Statistics Matches: 121, Mismatches: 14, Indels: 3 0.88 0.10 0.02 Matches are distributed among these distances: 103 66 0.55 104 54 0.45 105 1 0.01 ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33 Consensus pattern (103 bp): AGGTCCGATCACTAAGTGTCATCGTGAGTATATAAATCCTTCACGGATTAAGAGGTCCGATGACT AAGTGTCATATGAGTATATGAATCCCTTACGGATTAAG Found at i:18834226 original size:14 final size:15 Alignment explanation

Indices: 18834201--18834229 Score: 51 Period size: 14 Copynumber: 2.0 Consensus size: 15 18834191 ATAATATAAC 18834201 GATAAGATGAATAGT 1 GATAAGATGAATAGT 18834216 GATAA-ATGAATAGT 1 GATAAGATGAATAGT 18834230 AAAACACCAA Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 14 9 0.64 15 5 0.36 ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28 Consensus pattern (15 bp): GATAAGATGAATAGT Found at i:18839722 original size:52 final size:52 Alignment explanation

Indices: 18839634--18839826 Score: 235 Period size: 52 Copynumber: 3.7 Consensus size: 52 18839624 ATAAACGAAG * * 18839634 AGGTCCGATAACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAT 1 AGGTCTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAT * * * 18839686 AGGTTTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACTGATTAAG 1 AGGTCTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAT * ** * * * 18839738 AGGTCTAATGACTTTGTGTCATCGTGAGTATATGAATCCCTTGCGAATT-AT 1 AGGTCTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAT * ** * 18839789 AAGGTCCGATGGTTATGTGTCATCGTGAGTATATGAAT 1 -AGGTCTGATGACTAAGTGTCATCGTGAGTATATGAAT 18839827 GAAGTGAAAT Statistics Matches: 121, Mismatches: 19, Indels: 2 0.85 0.13 0.01 Matches are distributed among these distances: 51 1 0.01 52 120 0.99 ACGTcount: A:0.28, C:0.13, G:0.23, T:0.35 Consensus pattern (52 bp): AGGTCTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAT Found at i:18840808 original size:14 final size:15 Alignment explanation

Indices: 18840783--18840811 Score: 51 Period size: 14 Copynumber: 2.0 Consensus size: 15 18840773 ATAATATAAC 18840783 GATAAGATGAACAGT 1 GATAAGATGAACAGT 18840798 GATAA-ATGAACAGT 1 GATAAGATGAACAGT 18840812 AAAACACCGA Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 14 9 0.64 15 5 0.36 ACGTcount: A:0.48, C:0.07, G:0.24, T:0.21 Consensus pattern (15 bp): GATAAGATGAACAGT Found at i:18843071 original size:20 final size:21 Alignment explanation

Indices: 18843033--18843074 Score: 77 Period size: 21 Copynumber: 2.0 Consensus size: 21 18843023 TAAACCAAGC 18843033 ATCACTAAGTTAGAAAATGCA 1 ATCACTAAGTTAGAAAATGCA 18843054 ATCACTAAGTTA-AAAATGCA 1 ATCACTAAGTTAGAAAATGCA 18843074 A 1 A 18843075 GCTAAAAAAT Statistics Matches: 21, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 20 9 0.43 21 12 0.57 ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24 Consensus pattern (21 bp): ATCACTAAGTTAGAAAATGCA Found at i:18843904 original size:16 final size:16 Alignment explanation

Indices: 18843883--18843913 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 18843873 GTTTTTTCTT * 18843883 GAAGAAGAAAATGAAA 1 GAAGAACAAAATGAAA 18843899 GAAGAACAAAATGAA 1 GAAGAACAAAATGAA 18843914 TTTTAATCTT Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.68, C:0.03, G:0.23, T:0.06 Consensus pattern (16 bp): GAAGAACAAAATGAAA Found at i:18846594 original size:52 final size:52 Alignment explanation

Indices: 18846452--18846784 Score: 404 Period size: 52 Copynumber: 6.4 Consensus size: 52 18846442 AAAAGGTCTA * 18846452 ATGACTATGTGTCATCATGAGAATATGAATCCTTTACGGA-TATGAGGTCCG 1 ATGACTATGTGTCATCGTGAGAATATGAATCCTTTACGGATTATGAGGTCCG * * ** * * 18846503 ATGACAACGCATTATCGTGA-ATATATGAATCCTTTTACGGATTATGAGGTTCG 1 ATGACTATGTGTCATCGTGAGA-ATATGAATCC-TTTACGGATTATGAGGTCCG 18846556 ATGACTATGTGTCATCGTGAGAATATGAATCCTTTACGGATTATGAGGTCCG 1 ATGACTATGTGTCATCGTGAGAATATGAATCCTTTACGGATTATGAGGTCCG * * * * * 18846608 ATGACTACGTGTCATCATGAGTATATGAATCCTTTACGAATTATGAGGTTCCA 1 ATGACTATGTGTCATCGTGAGAATATGAATCCTTTACGGATTATGAGG-TCCG * * 18846661 ATGACTATGTGTCATCGTGAGTATAAGAATCCTTTACGGATTATGAGGTCCG 1 ATGACTATGTGTCATCGTGAGAATATGAATCCTTTACGGATTATGAGGTCCG ** * * * * 18846713 ATGACTATGTGTCATCGTGATTAT-TTAATCCTTCTATGGATTA-AAGGTCCA 1 ATGACTATGTGTCATCGTGAGAATATGAATCCTT-TACGGATTATGAGGTCCG * * 18846764 ATAACTTTGTGTCATCGTGAG 1 ATGACTATGTGTCATCGTGAG 18846785 TATCAAATAT Statistics Matches: 244, Mismatches: 32, Indels: 12 0.85 0.11 0.04 Matches are distributed among these distances: 50 1 0.00 51 55 0.23 52 105 0.43 53 82 0.34 54 1 0.00 ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34 Consensus pattern (52 bp): ATGACTATGTGTCATCGTGAGAATATGAATCCTTTACGGATTATGAGGTCCG Found at i:18846674 original size:105 final size:105 Alignment explanation

Indices: 18846451--18846784 Score: 453 Period size: 105 Copynumber: 3.2 Consensus size: 105 18846441 AAAAAGGTCT * * ** 18846451 AATGACTATGTGTCATCATGAGAATATGAATCCTTTACGGA-TATGAGGTCCGATGACAACGCAT 1 AATGACTATGTGTCATCGTGAGAATATGAATCCTTTACGGATTATGAGGTCCGATGACTACGTGT * 18846515 TATCGTGAATATATGAATCCTTTTACGGATTATGAGGTT-C 66 CATCGTGAATATATGAATCC-TTTACGGATTATGAGGTTCC * 18846555 GATGACTATGTGTCATCGTGAGAATATGAATCCTTTACGGATTATGAGGTCCGATGACTACGTGT 1 AATGACTATGTGTCATCGTGAGAATATGAATCCTTTACGGATTATGAGGTCCGATGACTACGTGT * * * 18846620 CATCATGAGTATATGAATCCTTTACGAATTATGAGGTTCC 66 CATCGTGAATATATGAATCCTTTACGGATTATGAGGTTCC * * * 18846660 AATGACTATGTGTCATCGTGAGTATAAGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGT 1 AATGACTATGTGTCATCGTGAGAATATGAATCCTTTACGGATTATGAGGTCCGATGACTACGTGT * * * * 18846725 CATCGTGATTAT-TTAATCCTTCTATGGATTA-AAGG-TCC 66 CATCGTGAATATATGAATCCTT-TACGGATTATGAGGTTCC * * 18846763 AATAACTTTGTGTCATCGTGAG 1 AATGACTATGTGTCATCGTGAG 18846785 TATCAAATAT Statistics Matches: 206, Mismatches: 21, Indels: 7 0.88 0.09 0.03 Matches are distributed among these distances: 103 23 0.11 104 67 0.33 105 116 0.56 ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34 Consensus pattern (105 bp): AATGACTATGTGTCATCGTGAGAATATGAATCCTTTACGGATTATGAGGTCCGATGACTACGTGT CATCGTGAATATATGAATCCTTTACGGATTATGAGGTTCC Found at i:18850315 original size:50 final size:51 Alignment explanation

Indices: 18850239--18850422 Score: 208 Period size: 52 Copynumber: 3.6 Consensus size: 51 18850229 GGAAAAAAAG * * * * 18850239 GGTCCGGTGACTATGTGTCATTGTGAGCATATGAATCCTTTACGGA-TTGA 1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTTAA * * * * 18850289 GGTCCGATGACTAAGTGTCATCGTGAGTGTATGAATCCTTTATGAATTATAA 1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATT-TAA * * * * 18850341 GGTTCGATGACTATGTGTCATCGTGAGTATGTGGATCCTATTACAGATTTAA 1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCT-TTACGGATTTAA * * * 18850393 GGTCTGATGACTTTGTGTCATTGTGAGTAT 1 GGTCCGATGACTATGTGTCATCGTGAGTAT 18850423 TAAATGAGAA Statistics Matches: 111, Mismatches: 20, Indels: 4 0.82 0.15 0.03 Matches are distributed among these distances: 50 39 0.35 51 1 0.01 52 65 0.59 53 6 0.05 ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36 Consensus pattern (51 bp): GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTTAA Found at i:18855220 original size:52 final size:52 Alignment explanation

Indices: 18855137--18855275 Score: 176 Period size: 52 Copynumber: 2.7 Consensus size: 52 18855127 TGAAAAAAAG * * * * * 18855137 GGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCT-TTACGGATTATGA 1 GGTCCGATGATTATGTGTCATCGTGAGTATATAAATCCTATTACAGATT-TAA * 18855189 TGTCCGATGATTATGTGTCATCGTGAGTATATAAATCCTATTACAGATTTAA 1 GGTCCGATGATTATGTGTCATCGTGAGTATATAAATCCTATTACAGATTTAA * 18855241 GGTCCGTTGACTT-TGTGTCATCGTGAGTAT-TAAAT 1 GGTCCGATGA-TTATGTGTCATCGTGAGTATATAAAT 18855276 GGGAAATGAG Statistics Matches: 77, Mismatches: 8, Indels: 5 0.86 0.09 0.06 Matches are distributed among these distances: 51 5 0.06 52 62 0.81 53 10 0.13 ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38 Consensus pattern (52 bp): GGTCCGATGATTATGTGTCATCGTGAGTATATAAATCCTATTACAGATTTAA Found at i:18860815 original size:17 final size:18 Alignment explanation

Indices: 18860772--18860818 Score: 51 Period size: 21 Copynumber: 2.5 Consensus size: 18 18860762 GTGTTAAGGG * 18860772 AATGATTAATTAAGGATT 1 AATGATTAAGTAAGGATT 18860790 AGGAGTGATTAAGTAAGG-TT 1 A--A-TGATTAAGTAAGGATT 18860810 AATGATTAA 1 AATGATTAA 18860819 AGTCACAAAA Statistics Matches: 25, Mismatches: 1, Indels: 7 0.76 0.03 0.21 Matches are distributed among these distances: 17 7 0.28 18 2 0.08 20 4 0.16 21 12 0.48 ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34 Consensus pattern (18 bp): AATGATTAAGTAAGGATT Found at i:18861756 original size:52 final size:52 Alignment explanation

Indices: 18861676--18862017 Score: 490 Period size: 52 Copynumber: 6.6 Consensus size: 52 18861666 TAAATGAAAA * 18861676 AGGTCTGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG 1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG * * * * * 18861728 AGGTCTGATGACTACATGTTATCATGAGTATATGAATCCTTTACAGATTATG 1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG * 18861780 AGGTTCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG 1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG * * 18861832 AGGTCCGATGACTACGTGTCATCCTGAGTATATGAATCCTTTACGGAGTATG 1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG * * * * 18861884 AGGTCCGGTGACTACGAGTCATCGTGAGTATAAGAATCCTTTACGGATTATA 1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG * * * * 18861936 AGGTCCGATGACTATGTGTCATTGTGAGTATATG-ATCCCTCTACGGATTA-A 1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAAT-CCTTTACGGATTATG ** 18861987 AGGTCCGATGACTTTGTGTCATCGTGAGTAT 1 AGGTCCGATGACTACGTGTCATCGTGAGTAT 18862018 CAAATATGCA Statistics Matches: 262, Mismatches: 27, Indels: 3 0.90 0.09 0.01 Matches are distributed among these distances: 51 32 0.12 52 230 0.88 ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33 Consensus pattern (52 bp): AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG Found at i:18862745 original size:21 final size:22 Alignment explanation

Indices: 18862701--18862752 Score: 72 Period size: 22 Copynumber: 2.5 Consensus size: 22 18862691 TAGAAGTAAG * 18862701 ACTTGTATCGGTACAAAGAGTC 1 ACTTGTATCGGTACAAACAGTC * 18862723 ACTTGTATCGGTA-AGACAGTC 1 ACTTGTATCGGTACAAACAGTC 18862744 ACTT-TATCG 1 ACTTGTATCG 18862753 ATAGAATTCT Statistics Matches: 28, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 20 5 0.18 21 10 0.36 22 13 0.46 ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31 Consensus pattern (22 bp): ACTTGTATCGGTACAAACAGTC Found at i:18867748 original size:25 final size:26 Alignment explanation

Indices: 18867694--18867748 Score: 85 Period size: 27 Copynumber: 2.1 Consensus size: 26 18867684 TTATTTATCA * 18867694 ATATATAAAAAGAGAAGTTGAATTTTT 1 ATATATAAAAAGAGAAGTTGAA-TTCT 18867721 ATATATAAAAAGAGAAGTTGAA-TCT 1 ATATATAAAAAGAGAAGTTGAATTCT 18867746 ATA 1 ATA 18867749 CAAAAAGCTT Statistics Matches: 27, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 25 5 0.19 27 22 0.81 ACGTcount: A:0.51, C:0.02, G:0.15, T:0.33 Consensus pattern (26 bp): ATATATAAAAAGAGAAGTTGAATTCT Found at i:18868402 original size:30 final size:31 Alignment explanation

Indices: 18868368--18868426 Score: 84 Period size: 31 Copynumber: 1.9 Consensus size: 31 18868358 AAAAAGACTT 18868368 AATAACTCAGT-ACTCAAATAAAAACTTTTG 1 AATAACTCAGTAACTCAAATAAAAACTTTTG * * * 18868398 AATAATTCAGTAACTTAAATGAAAACTTT 1 AATAACTCAGTAACTCAAATAAAAACTTT 18868427 CAAATGGTTT Statistics Matches: 25, Mismatches: 3, Indels: 1 0.86 0.10 0.03 Matches are distributed among these distances: 30 10 0.40 31 15 0.60 ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32 Consensus pattern (31 bp): AATAACTCAGTAACTCAAATAAAAACTTTTG Found at i:18868932 original size:16 final size:15 Alignment explanation

Indices: 18868895--18868933 Score: 51 Period size: 16 Copynumber: 2.5 Consensus size: 15 18868885 GTCACAATTA 18868895 AATTTTAATTTTTAT 1 AATTTTAATTTTTAT * * 18868910 TAGTTTATATTTTTAT 1 AATTTTA-ATTTTTAT 18868926 AATTTTAA 1 AATTTTAA 18868934 GAGAGTTAAA Statistics Matches: 19, Mismatches: 4, Indels: 2 0.76 0.16 0.08 Matches are distributed among these distances: 15 6 0.32 16 13 0.68 ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64 Consensus pattern (15 bp): AATTTTAATTTTTAT Found at i:18868986 original size:53 final size:53 Alignment explanation

Indices: 18868874--18868983 Score: 132 Period size: 52 Copynumber: 2.1 Consensus size: 53 18868864 ATAGAAAATT * * * ** * * * 18868874 ATTTTAAGAGGGTCACAATTAAATTTTAATTTTTATTAGTTTATATTTTTATA 1 ATTTTAAGAGAGTTAAAATTAAATTTTAATTTTTATTAAATTAAAATTTTAAA * 18868927 ATTTTAAGAGAGTTAAAATTTAATTTT-ATTTTTATTAAATTAAAATTTTAAA 1 ATTTTAAGAGAGTTAAAATTAAATTTTAATTTTTATTAAATTAAAATTTTAAA 18868979 ATTTT 1 ATTTT 18868984 TAAAAGATTT Statistics Matches: 48, Mismatches: 9, Indels: 1 0.83 0.16 0.02 Matches are distributed among these distances: 52 25 0.52 53 23 0.48 ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53 Consensus pattern (53 bp): ATTTTAAGAGAGTTAAAATTAAATTTTAATTTTTATTAAATTAAAATTTTAAA Found at i:18868996 original size:53 final size:53 Alignment explanation

Indices: 18868890--18868996 Score: 126 Period size: 53 Copynumber: 2.0 Consensus size: 53 18868880 AGAGGGTCAC ** * * * * 18868890 AATTAAATTTTAATTTTTATTAGTTTATATTTTTATAATTTTAAGAGAGTTAA 1 AATTAAATTTTAATTTTTATTAAATTAAAATTTTAAAATTTTAAAAGAGTTAA * * 18868943 AATTTAATTTT-ATTTTTATTAAATTAAAATTTTAAAATTTTTAAAAGATTTAA 1 AATTAAATTTTAATTTTTATTAAATTAAAATTTTAAAA-TTTTAAAAGAGTTAA 18868996 A 1 A 18868997 TAGATGATTT Statistics Matches: 45, Mismatches: 8, Indels: 2 0.82 0.15 0.04 Matches are distributed among these distances: 52 21 0.47 53 24 0.53 ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53 Consensus pattern (53 bp): AATTAAATTTTAATTTTTATTAAATTAAAATTTTAAAATTTTAAAAGAGTTAA Found at i:18885845 original size:30 final size:29 Alignment explanation

Indices: 18885809--18885888 Score: 97 Period size: 30 Copynumber: 2.7 Consensus size: 29 18885799 AATTCGAAAG * * 18885809 TTATTAATATTTATTTATAATAATTATAA 1 TTATTAATATTTATTTATAATAAATAAAA ** * 18885838 TTAATTAATATTTAAATATATTTAAATAAAA 1 TT-ATTAATATTTATTTATA-ATAAATAAAA 18885869 TTATTAATATTTATTTATAA 1 TTATTAATATTTATTTATAA 18885889 GTCTTTAATA Statistics Matches: 41, Mismatches: 8, Indels: 4 0.77 0.15 0.08 Matches are distributed among these distances: 29 2 0.05 30 30 0.73 31 9 0.22 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (29 bp): TTATTAATATTTATTTATAATAAATAAAA Found at i:18886372 original size:15 final size:15 Alignment explanation

Indices: 18886352--18886384 Score: 50 Period size: 15 Copynumber: 2.2 Consensus size: 15 18886342 AATTTTTTAA 18886352 AAATTA-TAAAAATAT 1 AAATTATTAAAAAT-T 18886367 AAATTATTAAAAATT 1 AAATTATTAAAAATT 18886382 AAA 1 AAA 18886385 ATTTAATTTC Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 15 10 0.59 16 7 0.41 ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33 Consensus pattern (15 bp): AAATTATTAAAAATT Found at i:18891924 original size:32 final size:32 Alignment explanation

Indices: 18891885--18891949 Score: 130 Period size: 32 Copynumber: 2.0 Consensus size: 32 18891875 CGAATCCGGT 18891885 AGTAAGACTTAAAGGTAAAATAGGTGGTACTA 1 AGTAAGACTTAAAGGTAAAATAGGTGGTACTA 18891917 AGTAAGACTTAAAGGTAAAATAGGTGGTACTA 1 AGTAAGACTTAAAGGTAAAATAGGTGGTACTA 18891949 A 1 A 18891950 CTTATGTATA Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 32 33 1.00 ACGTcount: A:0.45, C:0.06, G:0.25, T:0.25 Consensus pattern (32 bp): AGTAAGACTTAAAGGTAAAATAGGTGGTACTA Found at i:18896950 original size:28 final size:28 Alignment explanation

Indices: 18896917--18896990 Score: 85 Period size: 28 Copynumber: 2.6 Consensus size: 28 18896907 TTTCTTCGTG * * ** 18896917 GCTTCATTGTTACAGCTCGTACTTCACA 1 GCTTCACTGTAACAGCTCAAACTTCACA * 18896945 GCTTCACTGTAATAGCTCAAACTTCACA 1 GCTTCACTGTAACAGCTCAAACTTCACA * * 18896973 GCTTCACAGTAATAGCTC 1 GCTTCACTGTAACAGCTC 18896991 GCACTTCGTA Statistics Matches: 40, Mismatches: 6, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 28 40 1.00 ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31 Consensus pattern (28 bp): GCTTCACTGTAACAGCTCAAACTTCACA Found at i:18896996 original size:28 final size:28 Alignment explanation

Indices: 18896930--18896997 Score: 100 Period size: 28 Copynumber: 2.4 Consensus size: 28 18896920 TCATTGTTAC * * 18896930 AGCTCGTACTTCACAGCTTCACTGTAAT 1 AGCTCGAACTTCACAGCTTCACAGTAAT * 18896958 AGCTCAAACTTCACAGCTTCACAGTAAT 1 AGCTCGAACTTCACAGCTTCACAGTAAT * 18896986 AGCTCGCACTTC 1 AGCTCGAACTTC 18896998 GTAGCATTAT Statistics Matches: 35, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 28 35 1.00 ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28 Consensus pattern (28 bp): AGCTCGAACTTCACAGCTTCACAGTAAT Found at i:18899462 original size:20 final size:20 Alignment explanation

Indices: 18899439--18899487 Score: 62 Period size: 20 Copynumber: 2.5 Consensus size: 20 18899429 GTATTGATTC * 18899439 GGTATCGATACTTTTGAGGA 1 GGTATCGATAATTTTGAGGA * ** 18899459 GGTACCGATAATTTTGTTGA 1 GGTATCGATAATTTTGAGGA 18899479 GGTATCGAT 1 GGTATCGAT 18899488 TTTTAATGGT Statistics Matches: 24, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 20 24 1.00 ACGTcount: A:0.24, C:0.10, G:0.29, T:0.37 Consensus pattern (20 bp): GGTATCGATAATTTTGAGGA Found at i:18909751 original size:17 final size:18 Alignment explanation

Indices: 18909712--18909753 Score: 59 Period size: 18 Copynumber: 2.4 Consensus size: 18 18909702 ATGCATCTCA * * 18909712 TTTAGTTGTCATTGCATT 1 TTTATTTGTCACTGCATT 18909730 TTTATTTGTCACTGCA-T 1 TTTATTTGTCACTGCATT 18909747 TTTATTT 1 TTTATTT 18909754 ATTAGTACAT Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 17 8 0.36 18 14 0.64 ACGTcount: A:0.17, C:0.12, G:0.12, T:0.60 Consensus pattern (18 bp): TTTATTTGTCACTGCATT Found at i:18913998 original size:13 final size:13 Alignment explanation

Indices: 18913980--18914004 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 18913970 TTGTAGGACA 18913980 TAAATTTTTATGG 1 TAAATTTTTATGG 18913993 TAAATTTTTATG 1 TAAATTTTTATG 18914005 ATATATCTTC 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:0.32, C:0.00, G:0.12, T:0.56 Consensus pattern (13 bp): TAAATTTTTATGG Found at i:18917127 original size:16 final size:16 Alignment explanation

Indices: 18917106--18917136 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 18917096 GATACTTTTC * 18917106 TAAAAATATTGATACG 1 TAAAAATATCGATACG 18917122 TAAAAATATCGATAC 1 TAAAAATATCGATAC 18917137 CACTGGCCTT Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29 Consensus pattern (16 bp): TAAAAATATCGATACG Found at i:18932883 original size:18 final size:18 Alignment explanation

Indices: 18932860--18932899 Score: 53 Period size: 18 Copynumber: 2.2 Consensus size: 18 18932850 TCTGTTAAAC * * * 18932860 AAGAAGAAGATCTTGATG 1 AAGAAGAAAATCCTGAGG 18932878 AAGAAGAAAATCCTGAGG 1 AAGAAGAAAATCCTGAGG 18932896 AAGA 1 AAGA 18932900 TACTGTGGAG Statistics Matches: 19, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.50, C:0.07, G:0.28, T:0.15 Consensus pattern (18 bp): AAGAAGAAAATCCTGAGG Found at i:18938429 original size:28 final size:28 Alignment explanation

Indices: 18938340--18938460 Score: 107 Period size: 28 Copynumber: 4.2 Consensus size: 28 18938330 TGGTGTTGAT * * 18938340 ATTTCAACAAAATCCAGCCACAAAGGCTC 1 ATTTTAACAGAAT-CAGCCACAAAGGCTC * * * * * 18938369 ATTTTAACAGAATCAACTATAAAGACAC 1 ATTTTAACAGAATCAGCCACAAAGGCTC * * * 18938397 CTTTTAATAGAATCAGCCATAAAGGCTC 1 ATTTTAACAGAATCAGCCACAAAGGCTC * * 18938425 ATTTTAACAAAATTAGCCACAAAGGCTTC 1 ATTTTAACAGAATCAGCCACAAAGGC-TC 18938454 ACTTTTA 1 A-TTTTA 18938461 CGGAAACTGG Statistics Matches: 72, Mismatches: 18, Indels: 3 0.77 0.19 0.03 Matches are distributed among these distances: 28 53 0.74 29 14 0.19 30 5 0.07 ACGTcount: A:0.41, C:0.22, G:0.10, T:0.26 Consensus pattern (28 bp): ATTTTAACAGAATCAGCCACAAAGGCTC Found at i:18943720 original size:20 final size:21 Alignment explanation

Indices: 18943673--18943720 Score: 53 Period size: 20 Copynumber: 2.3 Consensus size: 21 18943663 ATTAAAATTT * * 18943673 ATAAAAAAATATTAAATATAA 1 ATAAAAAAATATCAAATAAAA * * 18943694 TTTAAAAAAT-TCAAATAAAA 1 ATAAAAAAATATCAAATAAAA 18943714 ATAAAAA 1 ATAAAAA 18943721 TTAATAAAAA Statistics Matches: 21, Mismatches: 6, Indels: 1 0.75 0.21 0.04 Matches are distributed among these distances: 20 13 0.62 21 8 0.38 ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27 Consensus pattern (21 bp): ATAAAAAAATATCAAATAAAA Found at i:18943878 original size:16 final size:18 Alignment explanation

Indices: 18943859--18943892 Score: 54 Period size: 16 Copynumber: 2.0 Consensus size: 18 18943849 TTTAAAAATA 18943859 TTAAAAAT-T-ATTTTTT 1 TTAAAAATATGATTTTTT 18943875 TTAAAAATATGATTTTTT 1 TTAAAAATATGATTTTTT 18943893 GTATAATTTT Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 16 8 0.50 17 1 0.06 18 7 0.44 ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59 Consensus pattern (18 bp): TTAAAAATATGATTTTTT Found at i:18944665 original size:35 final size:33 Alignment explanation

Indices: 18944610--18944674 Score: 94 Period size: 35 Copynumber: 1.9 Consensus size: 33 18944600 CAGTAAAACC 18944610 TAAAAAATATTTCTTTTAATTTCTTTTATTTTT 1 TAAAAAATATTTCTTTTAATTTCTTTTATTTTT * * 18944643 TAAAAAATTGATTTTTTTTAATTTTTTTTATT 1 TAAAAAA-T-ATTTCTTTTAATTTCTTTTATT 18944675 GTTGTGGCAA Statistics Matches: 28, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 33 7 0.25 34 1 0.04 35 20 0.71 ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65 Consensus pattern (33 bp): TAAAAAATATTTCTTTTAATTTCTTTTATTTTT Found at i:18947333 original size:17 final size:16 Alignment explanation

Indices: 18947301--18947334 Score: 50 Period size: 17 Copynumber: 2.1 Consensus size: 16 18947291 TCGTCTGGAT 18947301 AAATATTTAAATAATA 1 AAATATTTAAATAATA * 18947317 AAATATATTATATAATA 1 AAATAT-TTAAATAATA 18947334 A 1 A 18947335 TTCTATCGAT Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 16 6 0.38 17 10 0.62 ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38 Consensus pattern (16 bp): AAATATTTAAATAATA Found at i:18948291 original size:16 final size:17 Alignment explanation

Indices: 18948265--18948297 Score: 50 Period size: 16 Copynumber: 2.0 Consensus size: 17 18948255 CTGAGAGAAC 18948265 AAATACTTAAAAAAATT 1 AAATACTTAAAAAAATT * 18948282 AAAT-CTTAAAACAATT 1 AAATACTTAAAAAAATT 18948298 TTCTTACACA Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 16 11 0.73 17 4 0.27 ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30 Consensus pattern (17 bp): AAATACTTAAAAAAATT Found at i:18955733 original size:82 final size:81 Alignment explanation

Indices: 18955622--18955818 Score: 236 Period size: 82 Copynumber: 2.4 Consensus size: 81 18955612 TAAATCTTTA * * * 18955622 AATGAAGCCTTTGTGGAAATATCTATAAAGGAATGCCCTTAT-GATAATCTT-TGTAAAGGAAAC 1 AATGAAGCCTTTGTGGCAATTTCTGTAAAGGAATGCCCTTATGGA-AAT-TTCTGTAAAGGAAAC * 18955685 ATTTCTGGTAATCTCTGT 64 ATTTCTGGCAATCTCTGT * * * * 18955703 AATGAATGCCTTTGTGGCAATTTTTGTAAAGGAATGCCTTTATGGAAATTTCTGTAAAGGAAGCC 1 AATGAA-GCCTTTGTGGCAATTTCTGTAAAGGAATGCCCTTATGGAAATTTCTGTAAAGGAAACA * 18955768 TTTGTGGCAATCTCTGT 65 TTTCTGGCAATCTCTGT * ** 18955785 AATGAAAGCCTTTGTGGCTATTTGGGTAAAGGAA 1 AATG-AAGCCTTTGTGGCAATTTCTGTAAAGGAA 18955819 GCCTTTGTGG Statistics Matches: 100, Mismatches: 12, Indels: 7 0.84 0.10 0.06 Matches are distributed among these distances: 81 8 0.08 82 88 0.88 83 4 0.04 ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35 Consensus pattern (81 bp): AATGAAGCCTTTGTGGCAATTTCTGTAAAGGAATGCCCTTATGGAAATTTCTGTAAAGGAAACAT TTCTGGCAATCTCTGT Found at i:18955829 original size:27 final size:27 Alignment explanation

Indices: 18955565--18955829 Score: 187 Period size: 27 Copynumber: 9.7 Consensus size: 27 18955555 AAAAACACCA * * 18955565 GTAATGGAAGCCTTTTTGGCAATTTCT 1 GTAAAGGAAGCCTTTGTGGCAATTTCT ** * 18955592 GTAAAGGAATGAATTTGT-GCTAA-ATCT 1 GTAAAGGAA-GCCTTTGTGGC-AATTTCT * * * * 18955619 TTAAATGAAGCCTTTGTGGAAATATCT 1 GTAAAGGAAGCCTTTGTGGCAATTTCT * * * ** 18955646 ATAAAGGAATGCCCTTATGATAATCTT-T 1 GTAAAGGAA-GCCTTTGTGGCAAT-TTCT * * * * * 18955674 GTAAAGGAAACATTTCTGGTAATCTCT 1 GTAAAGGAAGCCTTTGTGGCAATTTCT * * 18955701 GT-AATGAATGCCTTTGTGGCAATTTTT 1 GTAAAGGAA-GCCTTTGTGGCAATTTCT * * 18955728 GTAAAGGAATGCCTTTATGGAAATTTCT 1 GTAAAGGAA-GCCTTTGTGGCAATTTCT * 18955756 GTAAAGGAAGCCTTTGTGGCAATCTCT 1 GTAAAGGAAGCCTTTGTGGCAATTTCT * * * ** 18955783 GTAATGAAAGCCTTTGTGGCTATTTGG 1 GTAAAGGAAGCCTTTGTGGCAATTTCT 18955810 GTAAAGGAAGCCTTTGTGGC 1 GTAAAGGAAGCCTTTGTGGC 18955830 GAATGTGGGA Statistics Matches: 183, Mismatches: 46, Indels: 18 0.74 0.19 0.07 Matches are distributed among these distances: 26 14 0.08 27 112 0.61 28 56 0.31 29 1 0.01 ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35 Consensus pattern (27 bp): GTAAAGGAAGCCTTTGTGGCAATTTCT Found at i:18957530 original size:13 final size:13 Alignment explanation

Indices: 18957507--18957555 Score: 57 Period size: 13 Copynumber: 3.8 Consensus size: 13 18957497 GGGTTAAATT 18957507 AATTAAATTAACTC 1 AATT-AATTAACTC 18957521 AATTAATTAA--C 1 AATTAATTAACTC 18957532 AATTTAATTAACTC 1 AA-TTAATTAACTC * 18957546 AATTTATTAA 1 AATTAATTAA 18957556 TGAAATAATT Statistics Matches: 31, Mismatches: 1, Indels: 7 0.79 0.03 0.18 Matches are distributed among these distances: 11 3 0.10 12 8 0.26 13 13 0.42 14 7 0.23 ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41 Consensus pattern (13 bp): AATTAATTAACTC Found at i:18957540 original size:25 final size:25 Alignment explanation

Indices: 18957507--18957555 Score: 80 Period size: 25 Copynumber: 2.0 Consensus size: 25 18957497 GGGTTAAATT 18957507 AATTAAATTAACTCAATTAATTAAC 1 AATTAAATTAACTCAATTAATTAAC * * 18957532 AATTTAATTAACTCAATTTATTAA 1 AATTAAATTAACTCAATTAATTAA 18957556 TGAAATAATT Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 25 22 1.00 ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41 Consensus pattern (25 bp): AATTAAATTAACTCAATTAATTAAC Found at i:18960623 original size:16 final size:16 Alignment explanation

Indices: 18960583--18960626 Score: 63 Period size: 16 Copynumber: 2.8 Consensus size: 16 18960573 TAACTACGAA * 18960583 AAGAAATATAAATGCTT 1 AAGAAA-ATAAATACTT 18960600 AA-AAAATAAATACTT 1 AAGAAAATAAATACTT 18960615 AAGAAAATAAAT 1 AAGAAAATAAAT 18960627 TTCCCCCCTT Statistics Matches: 25, Mismatches: 1, Indels: 3 0.86 0.03 0.10 Matches are distributed among these distances: 15 11 0.44 16 12 0.48 17 2 0.08 ACGTcount: A:0.64, C:0.05, G:0.07, T:0.25 Consensus pattern (16 bp): AAGAAAATAAATACTT Found at i:18965750 original size:14 final size:16 Alignment explanation

Indices: 18965719--18965750 Score: 50 Period size: 16 Copynumber: 2.1 Consensus size: 16 18965709 CTACTTTATG 18965719 TATTAAAAGTACATTA 1 TATTAAAAGTACATTA 18965735 TATTAAAA-TA-ATTA 1 TATTAAAAGTACATTA 18965749 TA 1 TA 18965751 AAATAAGTCA Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 14 6 0.38 15 2 0.12 16 8 0.50 ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41 Consensus pattern (16 bp): TATTAAAAGTACATTA Done.