Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold204

Parameters: 2 7 7 80 10 50 500

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

Length: 1152859
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.31

Warning! 64757 characters in sequence are not A, C, G, or T


File 4 of 3

Found at i:762974 original size:17 final size:18

Alignment explanation

Indices: 762952--762987 Score: 56 Period size: 17 Copynumber: 2.1 Consensus size: 18 762942 CGGTGGTTTG * 762952 ACTTAAACTC-TTCTGTA 1 ACTTAAACCCATTCTGTA 762969 ACTTAAACCCATTCTGTA 1 ACTTAAACCCATTCTGTA 762987 A 1 A 762988 TTTGTTTCAA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 17 9 0.53 18 8 0.47 ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36 Consensus pattern (18 bp): ACTTAAACCCATTCTGTA Found at i:766248 original size:18 final size:18 Alignment explanation

Indices: 766225--766262 Score: 67 Period size: 18 Copynumber: 2.1 Consensus size: 18 766215 TGTTATCAGT 766225 AAGTACTTGATACGAATA 1 AAGTACTTGATACGAATA * 766243 AAGTACTTGATACTAATA 1 AAGTACTTGATACGAATA 766261 AA 1 AA 766263 TTGATATGGT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29 Consensus pattern (18 bp): AAGTACTTGATACGAATA Found at i:771275 original size:19 final size:19 Alignment explanation

Indices: 771253--771306 Score: 72 Period size: 19 Copynumber: 2.8 Consensus size: 19 771243 AATGTTCGTA * 771253 AAAGTACTCAAATAACCTT 1 AAAGTACTCAAATAACATT * 771272 AAAGAACTCAAATAACATT 1 AAAGTACTCAAATAACATT * * 771291 AAATTACTGAAATAAC 1 AAAGTACTCAAATAAC 771307 TATATATATT Statistics Matches: 30, Mismatches: 5, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 19 30 1.00 ACGTcount: A:0.54, C:0.17, G:0.06, T:0.24 Consensus pattern (19 bp): AAAGTACTCAAATAACATT Found at i:775341 original size:2 final size:2 Alignment explanation

Indices: 775334--775385 Score: 104 Period size: 2 Copynumber: 26.0 Consensus size: 2 775324 GTTTGGGAGG 775334 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 775376 GA GA GA GA GA 1 GA GA GA GA GA 775386 ATGCACTCTC Statistics Matches: 50, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 50 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:797148 original size:20 final size:20 Alignment explanation

Indices: 797123--797160 Score: 76 Period size: 20 Copynumber: 1.9 Consensus size: 20 797113 AACAAAAATC 797123 TTATATCACACCCCTAGGGT 1 TTATATCACACCCCTAGGGT 797143 TTATATCACACCCCTAGG 1 TTATATCACACCCCTAGG 797161 CGAATTTTCG Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.26, C:0.32, G:0.13, T:0.29 Consensus pattern (20 bp): TTATATCACACCCCTAGGGT Found at i:798910 original size:38 final size:38 Alignment explanation

Indices: 798859--798935 Score: 145 Period size: 38 Copynumber: 2.0 Consensus size: 38 798849 GACAGTACTT 798859 AAAATCCCTTTTACATGCGTATGCACCTAAATAATGCA 1 AAAATCCCTTTTACATGCGTATGCACCTAAATAATGCA * 798897 AAAATCCCTTTTACATGCGTATGCACCTAATTAATGCA 1 AAAATCCCTTTTACATGCGTATGCACCTAAATAATGCA 798935 A 1 A 798936 TTATGAGCCT Statistics Matches: 38, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 38 38 1.00 ACGTcount: A:0.36, C:0.23, G:0.10, T:0.30 Consensus pattern (38 bp): AAAATCCCTTTTACATGCGTATGCACCTAAATAATGCA Found at i:799576 original size:180 final size:175 Alignment explanation

Indices: 799226--799762 Score: 723 Period size: 180 Copynumber: 3.0 Consensus size: 175 799216 GGCTGCCAAA * 799226 AGGGTACACTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA * 799291 GATCAATTGTACATATATCAGAGGTGTGCATATTTCTAGGATTTTGATTTCTGATACTTTTTGAA 66 GATCAATTGTACATATATCAGAGGTGTGCATA-TTCTA-GATTTTGATTT-TAATA--TTTTGAA * 799356 AAAAATACCACCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT 126 AAAAATACCACCTTTTGAACTTAGTCATTTTTTTGCAAAATATTGCATAT * * * 799406 AGGGTACCCTCATTGTACGGATAACTCCTCCGACAGTTTTCAAGATAGGAATTTGTTCTTTTGTA 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA * * * 799471 GATCAATTGTACATATATCAAAAGTGTGCATATTGCTAGATTTTGATTTTTAATAATTTATGACA 66 GATCAATTGTACATATATCAGAGGTGTGCATATT-CTAGATTTTGA-TTTTAAT-ATTT-TGAAA * * 799536 AAAATACCAGCC-TTTGAACTTAGTCATTTTTTTTGCAAAATATTACATAA 127 AAAATACCA-CCTTTTGAACTTAGTCA-TTTTTTTGCAAAATATTGCATAT * * 799586 AGGGTACCCTCA-T-TACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCA 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA * * * 799649 GATCAATTGTATATGTATATTAGAGGTGTGCATATT-TCGATTTCTGA---TAAT-TTTTGAAAA 66 GATCAATTGTACA--TATATCAGAGGTGTGCATATTCTAGATTT-TGATTTTAATATTTTGAAAA * * 799709 AAATACCACCTTTTGAACTTAGTCA-CTTTTTGCAAAAAATTGCATAT 128 AAATACCACCTTTTGAACTTAGTCATTTTTTTGCAAAATATTGCATAT 799756 AGGGTAC 1 AGGGTAC 799763 TCCATTTCAC Statistics Matches: 322, Mismatches: 25, Indels: 30 0.85 0.07 0.08 Matches are distributed among these distances: 170 25 0.08 171 2 0.01 172 27 0.08 173 3 0.01 175 4 0.01 178 67 0.21 179 44 0.14 180 150 0.47 ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38 Consensus pattern (175 bp): AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAATTGTTCTTTTGCA GATCAATTGTACATATATCAGAGGTGTGCATATTCTAGATTTTGATTTTAATATTTTGAAAAAAA TACCACCTTTTGAACTTAGTCATTTTTTTGCAAAATATTGCATAT Found at i:800823 original size:15 final size:15 Alignment explanation

Indices: 800803--800833 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 800793 ACAGAATATG 800803 GGACATATGAAGGAA 1 GGACATATGAAGGAA * 800818 GGACATATGAATGAA 1 GGACATATGAAGGAA 800833 G 1 G 800834 ACTTGCTGCA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.45, C:0.06, G:0.32, T:0.16 Consensus pattern (15 bp): GGACATATGAAGGAA Found at i:805486 original size:322 final size:322 Alignment explanation

Indices: 804892--805673 Score: 1115 Period size: 322 Copynumber: 2.4 Consensus size: 322 804882 GTGAATATGC * * * * * * 804892 AAAATAAGCAAAGTCGTCATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACA 1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA * * * * 804957 ATATGGCATGCCAAAACAAATAGTGTGTTTAAATTTCAAGCATCTGCGATATATAGTTGCTGAGA 66 ATATGGCATGCCAAAACAAATAGTGTG-TAAAAATTCAAGCATCTGCGATAAACAGTTGCTGAGA 805022 AATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAAGTCATTTAACAGGAAGT 130 AA----T-A--GAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAAGTCATTTAACAGGAAGT * * 805087 TGACGCCCGATTGGTTAAAAAATATATCCCACGATATGGCATGCTTAAACAAATATTGTGTTAAA 188 TGACACCCGATTGGTTAAAAAATATATCCCACGATATGGCATGCCTAAACAAATATTGTGTTAAA 805152 ATGTCAAGCATCTGCGATAAATAGTTGCTAAGAAATCTTTGACGAAAATTTGTTTGAAAAATTTT 253 ATGTCAAGCATCTGCGATAAATAGTTGCTAAGAAATCTTTGACGAAAATTTGTTTG-AAAATTTT 805217 GATTAA 317 GATTAA * 805223 AAAATAAGCAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA 1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA * * * 805288 ATATGGCATGCCAAAACAAATAGTGTGAAAAAATTCAAGCATCTGCGATAAACATTTGCTGA-CA 66 ATATGGCATGCCAAAACAAATAGTGTGTAAAAATTCAAGCATCTGCGATAAACAGTTGCTGAGAA * * 805352 A-A-AAA-TTGTTTGAAAATTTTTGCTAAAAATGAACAAAGTCGTCATTTAACAGGAAGTTGACA 131 ATAGAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAA---GTCATTTAACAGGAAGTTGACA ** * ** * 805414 TGCGATTGG-TACAAAAATATATCCCACGATATGGCATGCCTATACAAATATTGTGTTTTAATTT 193 CCCGATTGGTTA-AAAAATATATCCCACGATATGGCATGCCTAAACAAATATTGTGTTAAAATGT * * 805478 TAAGCATCTGCGATAAATAGTTGCTAAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTA 257 CAAGCATCTGCGATAAATAGTTGCTAAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGATTA 805543 A 322 A * * 805544 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATAAATCCCACG 1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA ** * * 805609 ATATGGCATGCCTTAACAAACACTGTGTAAAAATGTCAAGCATCTGCGATAAACAGTTGCTGAGA 66 ATATGGCATGCCAAAACAAATAGTGTGTAAAAAT-TCAAGCATCTGCGATAAACAGTTGCTGAGA 805674 TAAATGCGAC Statistics Matches: 409, Mismatches: 36, Indels: 20 0.88 0.08 0.04 Matches are distributed among these distances: 319 30 0.07 320 3 0.01 321 106 0.26 322 153 0.37 323 1 0.00 329 2 0.00 330 29 0.07 331 85 0.21 ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29 Consensus pattern (322 bp): AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA ATATGGCATGCCAAAACAAATAGTGTGTAAAAATTCAAGCATCTGCGATAAACAGTTGCTGAGAA ATAGAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAAGTCATTTAACAGGAAGTTGACACCC GATTGGTTAAAAAATATATCCCACGATATGGCATGCCTAAACAAATATTGTGTTAAAATGTCAAG CATCTGCGATAAATAGTTGCTAAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGATTAA Found at i:805521 original size:154 final size:159 Alignment explanation

Indices: 805220--805669 Score: 502 Period size: 167 Copynumber: 2.8 Consensus size: 159 805210 AAATTTTGAT * 805220 TAAAAAATAAGCAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCC 1 TAAAAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCC * * * * * * * 805285 ACAATATGGCATGCCAAAACAAATAGTGTG-AAAAAATTCAAGCATCTGCGATAAACATTTGCTG 66 ACGATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTA ** 805349 ACAAAAAATTGTTTGAAAA-T-TTTT-GC 131 ACAAAAAATTGTACGAAAATTATTTTGGC * * * 805375 T-AAAAATGAA-CAAAGTCGTCATTTAACAGGAAGTTGACATGCGATTGGTACAAAAATATATCC 1 TAAAAAAT-AAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCC * *** * * 805438 CACGATATGGCATGCCTATACAAATATTGTGTTTTAATTTTAAGCATCTGCGATAAATAGTTGCT 65 CACGATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCT * *** * 805503 AAGAAATCTTTG-ACGAAAATTTGTTTGAAAATTTTGGT 130 AACAAAAAATTGTACGAAAA-----TT----ATTTTGGC * 805541 TAAAAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATAAATCCC 1 TAAAAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCC * * 805606 ACGATATGGCATGCCT-TAACAAACACTGTGTAAAAATGTCAAGCATCTGCGATAAACAGTTGCT 66 ACGATATGGCATGCCTAT-ACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCT 805670 GAGATAAATG Statistics Matches: 243, Mismatches: 35, Indels: 22 0.81 0.12 0.07 Matches are distributed among these distances: 154 87 0.36 155 36 0.15 160 1 0.00 165 4 0.02 166 5 0.02 167 110 0.45 ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28 Consensus pattern (159 bp): TAAAAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCC ACGATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTA ACAAAAAATTGTACGAAAATTATTTTGGC Found at i:807361 original size:167 final size:168 Alignment explanation

Indices: 806989--807607 Score: 897 Period size: 167 Copynumber: 3.6 Consensus size: 168 806979 TCACACTTTT * * * * * 806989 TTGTAAGCGCTCTCATACCTACAAATTTTCACGGATTTTCATTACATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA * 807054 CCACTCTTAC-CTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG 66 CCA--CTAACACTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTT---GTTATGGG * 807118 ACTTTGACCACAATAATGACCCTGTTTTATCCAAAAATTGACC 126 ACTTTGACCACAATAATGACTCTGTTTTATCCAAAAATTGACC 807161 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA * 807226 CCACTAACACTTCGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTG-T-TTATGGGACTA 66 CCACTAACACTT-GGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGTTATGGGACTT * * 807289 TGACCACAATAATGACTCTGTTTTATCCTAAAATTGACA 130 TGACCACAATAATGACTCTGTTTTATCCAAAAATTGACC * 807328 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCAAT-AAATTTATACCAAATGTTTAT 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTAC-ATGAAATTTATACCAAATGTTTAT * * 807392 ACCACTAATACTTTGGTCAAGTTTGAAAATCAGCATTGGTCGATA-TTTTTGTTGGAGTTATGGG 65 ACCACTAACAC-TTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTT---GTTATGGG * * * * 807456 ACTTTGTCCACAATAATGACTCCGTTTTATCCCAAAATTCACC 126 ACTTTGACCACAATAATGACTCTGTTTTATCCAAAAATTGACC 807499 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA * *** * 807564 CCACTAATACCTTGGTCAAGTTCCTGAATCAGCCTTGGTCGATA 66 CCACTAACA-CTTGGTCAAGTTCGAAAATCAGCATTGGTCGATA 807608 TTAGTATACT Statistics Matches: 411, Mismatches: 25, Indels: 23 0.90 0.05 0.05 Matches are distributed among these distances: 166 6 0.01 167 147 0.36 168 4 0.01 170 6 0.01 171 146 0.36 172 102 0.25 ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36 Consensus pattern (168 bp): TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA CCACTAACACTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGTTATGGGACTTT GACCACAATAATGACTCTGTTTTATCCAAAAATTGACC Found at i:807606 original size:338 final size:339 Alignment explanation

Indices: 806989--807607 Score: 1055 Period size: 338 Copynumber: 1.8 Consensus size: 339 806979 TCACACTTTT * * 806989 TTGTAAGCGCTCTCATACCTACAAATTTTCACGGATTTTCATTACATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATACCTACAAATTTTCACGGATTTTCAATAAATTTATACCAAATGTTTATA ** 807054 CCACTCTTACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA 66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA * 807119 CTTTGACCACAATAATGACCCTGTTTTATCCAAAAATTGACCTTGTAAGCGCTCTCATGCCTACA 131 CTTTGACCACAATAATGACCCTGTTTTATCCAAAAATTCACCTTGTAAGCGCTCTCATGCCTACA 807184 AATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATACCACTAACACTTCGGTCAAGTTC 196 AATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATACCACTAACACTTCGGTCAAGTTC * 807249 GAAAATCAGCATTGGTCGATACTTTTTGTTTATGGGACTATGACCACAATAATGACTCTGTTTTA 261 CAAAATCAGCATTGGTCGATACTTTTTGTTTATGGGACTATGACCACAATAATGACTCTGTTTTA 807314 TCCTAAAATTGACA 326 TCCTAAAATTGACA * * 807328 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCAATAAATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATACCTACAAATTTTCACGGATTTTCAATAAATTTATACCAAATGTTTATA * * 807393 CCACTAATACTTTGGTCAAGTTTGAAAATCAGCATTGGTCGATA-TTTTTGTTGGAGTTATGGGA 66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA * * 807457 CTTTGTCCACAATAATGACTCC-GTTTTATCCCAAAATTCACCTTGTAAGCGCTCTCATGCCTAC 131 CTTTGACCACAATAATGAC-CCTGTTTTATCCAAAAATTCACCTTGTAAGCGCTCTCATGCCTAC * 807521 AAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATACCACTAATACCTT-GGTCAAGT 195 AAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATACCACTAACA-CTTCGGTCAAGT ** * 807585 TCCTGAATCAGCCTTGGTCGATA 259 TCCAAAATCAGCATTGGTCGATA 807608 TTAGTATACT Statistics Matches: 262, Mismatches: 16, Indels: 5 0.93 0.06 0.02 Matches are distributed among these distances: 338 156 0.60 339 106 0.40 ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36 Consensus pattern (339 bp): TTGTAAGCGCTCTCATACCTACAAATTTTCACGGATTTTCAATAAATTTATACCAAATGTTTATA CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA CTTTGACCACAATAATGACCCTGTTTTATCCAAAAATTCACCTTGTAAGCGCTCTCATGCCTACA AATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATACCACTAACACTTCGGTCAAGTTC CAAAATCAGCATTGGTCGATACTTTTTGTTTATGGGACTATGACCACAATAATGACTCTGTTTTA TCCTAAAATTGACA Found at i:807609 original size:171 final size:172 Alignment explanation

Indices: 806989--807607 Score: 950 Period size: 171 Copynumber: 3.6 Consensus size: 172 806979 TCACACTTTT * * * * * 806989 TTGTAAGCGCTCTCATACCTACAAATTTTCACGGATTTTCATTACATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA ** 807054 CCACTCTTACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA 66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA 807119 CTTTGACCACAATAATGAC-CCTGTTTTATCCAAAAATTGACC 131 CTTTGACCACAATAATGACTCC-GTTTTATCCAAAAATTGACC 807161 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA * 807226 CCACTAACA-CTTCGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTG-T----TTATGGG 66 CCACTAATACCTT-GGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG * * * * 807285 ACTATGACCACAATAATGACTCTGTTTTATCCTAAAATTGACA 130 ACTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC * 807328 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCAAT-AAATTTATACCAAATGTTTAT 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTAC-ATGAAATTTATACCAAATGTTTAT * * 807392 ACCACTAATACTTTGGTCAAGTTTGAAAATCAGCATTGGTCGATA-TTTTTGTTGGAGTTATGGG 65 ACCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG * * * 807456 ACTTTGTCCACAATAATGACTCCGTTTTATCCCAAAATTCACC 130 ACTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC 807499 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA *** * 807564 CCACTAATACCTTGGTCAAGTTCCTGAATCAGCCTTGGTCGATA 66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATA 807608 TTAGTATACT Statistics Matches: 408, Mismatches: 29, Indels: 21 0.89 0.06 0.05 Matches are distributed among these distances: 166 6 0.01 167 144 0.35 168 5 0.01 170 2 0.00 171 147 0.36 172 104 0.25 ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36 Consensus pattern (172 bp): TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTACATGAAATTTATACCAAATGTTTATA CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC Found at i:807898 original size:2 final size:2 Alignment explanation

Indices: 807891--807924 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 807881 CTATATTTAC 807891 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 807925 CTGGTGTAAC Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:819998 original size:2 final size:2 Alignment explanation

Indices: 819949--819987 Score: 78 Period size: 2 Copynumber: 19.5 Consensus size: 2 819939 GCTTTTCATA 819949 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 819988 CATGATCTCT Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 37 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:820117 original size:2 final size:2 Alignment explanation

Indices: 820110--820137 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 820100 CACTGTAATT 820110 AC AC AC AC AC AC AC AC AC AC AC AC AC AC 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC 820138 TCTCTCTCTC 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:0.50, G:0.00, T:0.00 Consensus pattern (2 bp): AC Found at i:820181 original size:2 final size:2 Alignment explanation

Indices: 820137--820164 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 820127 CACACACACA 820137 CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT 820165 GAGTCTATCT 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:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:824388 original size:166 final size:165 Alignment explanation

Indices: 824013--824557 Score: 821 Period size: 166 Copynumber: 3.3 Consensus size: 165 824003 TAAAGAATCA * * 824013 TCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTCCTCTATATATTCCTATGTAAAAC 1 TCTGGCTGATGAGTTTCTGAGAAGAAGATTTTTAAAGATTTCCTCAATATATTCCTATGTAAAAC * 824078 TTCGACCCTCCATTGTGGCTCCACCCTACCCCC-GGGGTCATGATTTTCACAACTTTGAATTTAC 66 TTCGACCCTCCATTGTGGCTCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATATAC * 824142 ACTACCTGAGGAT-TCTTCCAAACAAGTTTCAGCTT 131 ACTACCTGAGGATGT-TTCCACACAAGTTTCAGCTT * 824177 TCCTGGCTGATGAGTTTCTGAGAAGAAGATTTTTAAAGATTTCCTCAAAATATTCCTATGTAAAA 1 T-CTGGCTGATGAGTTTCTGAGAAGAAGATTTTTAAAGATTTCCTCAATATATTCCTATGTAAAA * * 824242 CTTCGACCCTCCATTGTGGCTCCACCCTACCCCCGGGGGTAATGAATTTCACAACTTTGAATATA 65 CTTCGACCCTCCATTGTGGCTCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATATA * 824307 CACTACCTGAGGATGTTTCCACACAAGTTTCAACTT 130 CACTACCTGAGGATGTTTCCACACAAGTTTCAGCTT * * 824343 TCGTGGCTGATGAGTTTCTGAGAAGAAGATTTCTAAAGGTTTCCTCAATATATTCCTATGTAAAA 1 TC-TGGCTGATGAGTTTCTGAGAAGAAGATTTTTAAAGATTTCCTCAATATATTCCTATGTAAAA * * * * 824408 CTTCGACCCCCCATTGTGGCCCCACCCTACCCACGGGGGGTCATGATTTTTCTCAACTTTGAATA 65 CTTCGACCCTCCATTGTGGCTCCACCCTACCC-CCGGGGGTCATGA-TTTTCACAACTTTGAATA * * 824473 TACACTACCTGATGATGCTTCCACACAAGTTTCAGCTTT 128 TACACTACCTGAGGATGTTTCCACACAAGTTTCAGC-TT * * 824512 TCTGGCTTTATG-GTTTTTGAGAAGAAGATTTTTGAAA-ATTT-CTCAA 1 TCTGGC-TGATGAGTTTCTGAGAAGAAGATTTTT-AAAGATTTCCTCAA 824558 ATTTTTTCAT Statistics Matches: 348, Mismatches: 24, Indels: 15 0.90 0.06 0.04 Matches are distributed among these distances: 164 1 0.00 165 95 0.27 166 149 0.43 167 17 0.05 168 75 0.22 169 11 0.03 ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34 Consensus pattern (165 bp): TCTGGCTGATGAGTTTCTGAGAAGAAGATTTTTAAAGATTTCCTCAATATATTCCTATGTAAAAC TTCGACCCTCCATTGTGGCTCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATATAC ACTACCTGAGGATGTTTCCACACAAGTTTCAGCTT Found at i:824667 original size:95 final size:95 Alignment explanation

Indices: 824504--824693 Score: 380 Period size: 95 Copynumber: 2.0 Consensus size: 95 824494 CACACAAGTT 824504 TCAGCTTTTCTGGCTTTATGGTTTTTGAGAAGAAGATTTTTGAAAATTTCTCAAATTTTTTCATT 1 TCAGCTTTTCTGGCTTTATGGTTTTTGAGAAGAAGATTTTTGAAAATTTCTCAAATTTTTTCATT 824569 AATTTCTAATTATCTCCCCTTGAAAAAAGG 66 AATTTCTAATTATCTCCCCTTGAAAAAAGG 824599 TCAGCTTTTCTGGCTTTATGGTTTTTGAGAAGAAGATTTTTGAAAATTTCTCAAATTTTTTCATT 1 TCAGCTTTTCTGGCTTTATGGTTTTTGAGAAGAAGATTTTTGAAAATTTCTCAAATTTTTTCATT 824664 AATTTCTAATTATCTCCCCTTGAAAAAAGG 66 AATTTCTAATTATCTCCCCTTGAAAAAAGG 824694 CGTGACCCTT Statistics Matches: 95, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 95 95 1.00 ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44 Consensus pattern (95 bp): TCAGCTTTTCTGGCTTTATGGTTTTTGAGAAGAAGATTTTTGAAAATTTCTCAAATTTTTTCATT AATTTCTAATTATCTCCCCTTGAAAAAAGG Found at i:824749 original size:11 final size:11 Alignment explanation

Indices: 824733--824771 Score: 60 Period size: 11 Copynumber: 3.5 Consensus size: 11 824723 CATTCAGTCA 824733 ACTGAAAGGTG 1 ACTGAAAGGTG * 824744 ACTGAAAGGTA 1 ACTGAAAGGTG * 824755 ACTGAAAAGTG 1 ACTGAAAGGTG 824766 ACTGAA 1 ACTGAA 824772 TGGCATAGCT Statistics Matches: 25, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 11 25 1.00 ACGTcount: A:0.44, C:0.10, G:0.28, T:0.18 Consensus pattern (11 bp): ACTGAAAGGTG Found at i:827227 original size:12 final size:12 Alignment explanation

Indices: 827210--827249 Score: 62 Period size: 12 Copynumber: 3.3 Consensus size: 12 827200 TTTCCTCTGC 827210 GTCCGTCTGTCT 1 GTCCGTCTGTCT * * 827222 GTCCGTCCGTCA 1 GTCCGTCTGTCT 827234 GTCCGTCTGTCT 1 GTCCGTCTGTCT 827246 GTCC 1 GTCC 827250 CACTTCAGTT Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 12 24 1.00 ACGTcount: A:0.03, C:0.38, G:0.25, T:0.35 Consensus pattern (12 bp): GTCCGTCTGTCT Found at i:834621 original size:8 final size:8 Alignment explanation

Indices: 834608--834677 Score: 86 Period size: 8 Copynumber: 8.8 Consensus size: 8 834598 CCGGGCGTCC * 834608 GTCCGTGT 1 GTCCGTGG 834616 GTCCGTGG 1 GTCCGTGG * 834624 GTCCGTGT 1 GTCCGTGG 834632 GTCCGTGG 1 GTCCGTGG * * 834640 GTCTGTGT 1 GTCCGTGG * 834648 GTCCGTGC 1 GTCCGTGG 834656 GTCCGTGG 1 GTCCGTGG * 834664 GTCCGTGC 1 GTCCGTGG 834672 GTCCGT 1 GTCCGT 834678 CCGTCACACT Statistics Matches: 53, Mismatches: 9, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 8 53 1.00 ACGTcount: A:0.00, C:0.27, G:0.41, T:0.31 Consensus pattern (8 bp): GTCCGTGG Found at i:834629 original size:16 final size:16 Alignment explanation

Indices: 834607--834677 Score: 106 Period size: 16 Copynumber: 4.4 Consensus size: 16 834597 GCCGGGCGTC 834607 CGTCCGTGTGTCCGTG 1 CGTCCGTGTGTCCGTG * 834623 GGTCCGTGTGTCCGTG 1 CGTCCGTGTGTCCGTG * * 834639 GGTCTGTGTGTCCGTG 1 CGTCCGTGTGTCCGTG * 834655 CGTCCGTGGGTCCGTG 1 CGTCCGTGTGTCCGTG 834671 CGTCCGT 1 CGTCCGT 834678 CCGTCACACT Statistics Matches: 50, Mismatches: 5, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 16 50 1.00 ACGTcount: A:0.00, C:0.28, G:0.41, T:0.31 Consensus pattern (16 bp): CGTCCGTGTGTCCGTG Found at i:834651 original size:24 final size:24 Alignment explanation

Indices: 834607--834682 Score: 98 Period size: 24 Copynumber: 3.2 Consensus size: 24 834597 GCCGGGCGTC * * 834607 CGTCCGTGTGTCCGTGGGTCCGTG 1 CGTCCGTGGGTCCGTGCGTCCGTG * * * 834631 TGTCCGTGGGTCTGTGTGTCCGTG 1 CGTCCGTGGGTCCGTGCGTCCGTG * 834655 CGTCCGTGGGTCCGTGCGTCCGTC 1 CGTCCGTGGGTCCGTGCGTCCGTG 834679 CGTC 1 CGTC 834683 ACACTTTTTT Statistics Matches: 44, Mismatches: 8, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 24 44 1.00 ACGTcount: A:0.00, C:0.30, G:0.39, T:0.30 Consensus pattern (24 bp): CGTCCGTGGGTCCGTGCGTCCGTG Found at i:834977 original size:172 final size:172 Alignment explanation

Indices: 834691--835143 Score: 834 Period size: 172 Copynumber: 2.6 Consensus size: 172 834681 TCACACTTTT * * 834691 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTTATTAAATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAACTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA * * * 834756 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA 66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTCATCGAA 834821 CTATGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC 131 CTATGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC 834863 TTGTAAGCGCTCTCATGCCTACAAACTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAACTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA * 834928 CCACGAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTCATCGAA 66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTCATCGAA * 834993 CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC 131 CTATGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC 835035 TTGTAAGCGCTCTCATGCCTACAAACTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAACTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA * 835100 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCCTTGGTCGATA 66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATA 835144 GACTCGATAC Statistics Matches: 272, Mismatches: 9, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 172 272 1.00 ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34 Consensus pattern (172 bp): TTGTAAGCGCTCTCATGCCTACAAACTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTCATCGAA CTATGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC Found at i:837737 original size:21 final size:21 Alignment explanation

Indices: 837713--837779 Score: 91 Period size: 21 Copynumber: 3.2 Consensus size: 21 837703 ATCTGCCACC 837713 ACTTGTCAGATAATTATGTCG 1 ACTTGTCAGATAATTATGTCG * 837734 ACTTGTCAGAT-CTTGATGTCG 1 ACTTGTCAGATAATT-ATGTCG * * 837755 ACTTGTCAGATAATCATGTTG 1 ACTTGTCAGATAATTATGTCG 837776 ACTT 1 ACTT 837780 ATAATATGAA Statistics Matches: 40, Mismatches: 4, Indels: 4 0.83 0.08 0.08 Matches are distributed among these distances: 20 2 0.05 21 37 0.93 22 1 0.03 ACGTcount: A:0.25, C:0.16, G:0.19, T:0.39 Consensus pattern (21 bp): ACTTGTCAGATAATTATGTCG Found at i:837854 original size:21 final size:20 Alignment explanation

Indices: 837838--837905 Score: 82 Period size: 21 Copynumber: 3.3 Consensus size: 20 837828 CTGTCAGATA 837838 ATTATGTTAACTTGTCAAAT 1 ATTATGTTAACTTGTCAAAT * ** 837858 CTTCATGTCGACTTGTCAAAT 1 ATT-ATGTTAACTTGTCAAAT * 837879 AATTATGTTAACTTGTCAGAT 1 -ATTATGTTAACTTGTCAAAT 837900 ATTATG 1 ATTATG 837906 ATGACAGGAA Statistics Matches: 39, Mismatches: 7, Indels: 4 0.78 0.14 0.08 Matches are distributed among these distances: 20 8 0.21 21 29 0.74 22 2 0.05 ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43 Consensus pattern (20 bp): ATTATGTTAACTTGTCAAAT Found at i:838010 original size:21 final size:21 Alignment explanation

Indices: 837984--838077 Score: 100 Period size: 21 Copynumber: 4.5 Consensus size: 21 837974 ATGGTTATTT * * 837984 TCTGACAAGTAAACATAAAGA 1 TCTGACAAGTTAACATAAATA * * 838005 TCTGACAAGTTGACATTAATA 1 TCTGACAAGTTAACATAAATA ** 838026 TCTGACAAGTCGACAT-AATCA 1 TCTGACAAGTTAACATAAAT-A * * 838047 TCTGACAATTTAACATAATTA 1 TCTGACAAGTTAACATAAATA 838068 TCTGACAAGT 1 TCTGACAAGT 838078 GGTGGCAGAT Statistics Matches: 61, Mismatches: 10, Indels: 4 0.81 0.13 0.05 Matches are distributed among these distances: 20 3 0.05 21 56 0.92 22 2 0.03 ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29 Consensus pattern (21 bp): TCTGACAAGTTAACATAAATA Found at i:838043 original size:42 final size:42 Alignment explanation

Indices: 837984--838077 Score: 118 Period size: 42 Copynumber: 2.2 Consensus size: 42 837974 ATGGTTATTT * * 837984 TCTGACAAGTAAACATAAAGATCTGACAAGTTGACATTAA-TA 1 TCTGACAAGTAAACATAAACATCTGACAAGTTAACA-TAATTA ** * * 838026 TCTGACAAGTCGACATAATCATCTGACAATTTAACATAATTA 1 TCTGACAAGTAAACATAAACATCTGACAAGTTAACATAATTA 838068 TCTGACAAGT 1 TCTGACAAGT 838078 GGTGGCAGAT Statistics Matches: 45, Mismatches: 6, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 41 3 0.07 42 42 0.93 ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29 Consensus pattern (42 bp): TCTGACAAGTAAACATAAACATCTGACAAGTTAACATAATTA Found at i:839435 original size:160 final size:161 Alignment explanation

Indices: 839150--839511 Score: 539 Period size: 160 Copynumber: 2.3 Consensus size: 161 839140 ACTTCAAATT * * * * * * 839150 AATTTTTATAAGTCCAAGGGCCATTACTCTGTCGAAAATTGCTCGATCGTACCCAATATCCAACT 1 AATTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGATCGATCATACCCAAAATCCAACT * * 839215 TGACCTAGATATTATCGTGATAAACCTGTATACTAAATTTCATTTCAAAATGTTCATCCTCTGCG 66 TGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTTCAAAATGTTCATCCTCTGCG * 839280 AAGAAAATGAGCGGAAACTGCAAAAAACTAG 131 AAGAAAATGAGCGGAAACTGCAAAAAACTAA * 839311 AATTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGATCTATCATACCCAAAAT-CAGAC 1 AATTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGATCGATCATACCCAAAATCCA-AC * * * 839375 TTG-CCTAGATATTATCATGATTAACCTGTATACCAAATTTTATTTCAATATGTTCATCCTCTGC 65 TTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTTCAAAATGTTCATCCTCTGC * * * 839439 GAAGAAAATGAGCGGAAACTTCAATAAATTAA 130 GAAGAAAATGAGCGGAAACTGCAAAAAACTAA * * 839471 AATTTTTCTACATCTAAGGGCCATAACTCTGTCGAAAATTG 1 AATTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTG 839512 TTCATCCTCT Statistics Matches: 182, Mismatches: 18, Indels: 3 0.90 0.09 0.01 Matches are distributed among these distances: 160 125 0.69 161 57 0.31 ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31 Consensus pattern (161 bp): AATTTTTCTACGTCCAAGGGCCATAACTCTGTCGAAAATTGATCGATCATACCCAAAATCCAACT TGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCATTTCAAAATGTTCATCCTCTGCG AAGAAAATGAGCGGAAACTGCAAAAAACTAA Found at i:855060 original size:172 final size:172 Alignment explanation

Indices: 854774--855395 Score: 1064 Period size: 172 Copynumber: 3.6 Consensus size: 172 854764 GTATCGAGTC * ** * ** * 854774 TATCGACCAAGGCTGATTTAGGAACTTGACCAAGGTATTAAAGGTATAAACATTTAGTATAAATT 1 TATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAATT * 854839 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTAAAAGGTCAATTTTTGGATAAAACG 66 TAATGAAAATCCGTCAAAATTTGTAGGCATGATAGCGCTTAAAAGGTCAATTTTTGGATAAAACG 854904 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG 131 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG * 854946 TATCGACAAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAATT 1 TATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAATT * 855011 TAATGAAAATCCGTCAAAATTTGTAGGCATGATAGCGCTTATAAGGTCAATTTTTGGATAAAACG 66 TAATGAAAATCCGTCAAAATTTGTAGGCATGATAGCGCTTAAAAGGTCAATTTTTGGATAAAACG * * 855076 GAGTTATTATTGTGGTCAAAGTCCCGTAACTCCAACAAAAAG 131 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG * * 855118 TATCGGCCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTTGTATAAACATTTGGTATAAATT 1 TATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAATT * * * * 855183 TAATGAACATCCGTCTAAATTTGTAGGCATGATAACGCTTACAAGGTCAATTTTTGGATAAAACG 66 TAATGAAAATCCGTCAAAATTTGTAGGCATGATAGCGCTTAAAAGGTCAATTTTTGGATAAAACG 855248 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG 131 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG * * 855290 TATCGACCAATGCTGATTTTAGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT 1 TATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAATT 855355 TAATGAAAATCCGTCAAAATTTGTAGGCATGATAGCGCTTA 66 TAATGAAAATCCGTCAAAATTTGTAGGCATGATAGCGCTTA 855396 CAAAAAAGTG Statistics Matches: 422, Mismatches: 28, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 172 422 1.00 ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31 Consensus pattern (172 bp): TATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAATT TAATGAAAATCCGTCAAAATTTGTAGGCATGATAGCGCTTAAAAGGTCAATTTTTGGATAAAACG GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG Found at i:855773 original size:12 final size:12 Alignment explanation

Indices: 855746--855778 Score: 50 Period size: 12 Copynumber: 2.8 Consensus size: 12 855736 ATCACATTTT * 855746 GTCTGT-CGTTC 1 GTCTGTCCGTCC 855757 GTCTGTCCGTCC 1 GTCTGTCCGTCC 855769 GTCTGTCCGT 1 GTCTGTCCGT 855779 AAACTTTTCA Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 11 6 0.30 12 14 0.70 ACGTcount: A:0.00, C:0.33, G:0.27, T:0.39 Consensus pattern (12 bp): GTCTGTCCGTCC Found at i:856227 original size:166 final size:167 Alignment explanation

Indices: 855971--856334 Score: 523 Period size: 166 Copynumber: 2.1 Consensus size: 167 855961 AGAACCAGAA * * * * * * 855971 AGCCAGAAAATCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAATT 1 AGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAAATTCAAAGTTATGAAAAT * * 856036 CATGACCCCCGGGGGTAGGGTGGGGCCACAAT-GGGGGGTCGAAGTTTAACATAGGAATATATAG 66 CATGAACCCCGGGGGTAGGGTGGGGCCACAATGGGGGGGGCGAAGTTTAACATAGGAATATATAG * 856100 AGTAAATCTTTAGAAATCTTCTTCTCAGAAACTAATC 131 AGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC * 856137 AGCCAGGAAAGCTGAAACTTTTGTGAAAGCATCCTCAGGTAGTGTAAATTCAAAGTTATGAAAAT 1 AGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAAATTCAAAGTTATGAAAAT * * 856202 CATGAACCCGGGGGGTAGGGTGGGGCCACAATGGGGGGAGGGGGGGGGGCGAAGTTTTACATAGG 66 CATGAACCCCGGGGGTAGGGTGGGGCCACAAT---------GGGGGGGGCGAAGTTTAACATAGG 856267 AATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC 122 AATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC * 856313 AGCCAGGAAAGTTGAAACTTGT 1 AGCCAGGAAAGCTGAAACTTGT 856335 TATTTGTTTA Statistics Matches: 174, Mismatches: 14, Indels: 10 0.88 0.07 0.05 Matches are distributed among these distances: 166 88 0.51 176 86 0.49 ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25 Consensus pattern (167 bp): AGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAAATTCAAAGTTATGAAAAT CATGAACCCCGGGGGTAGGGTGGGGCCACAATGGGGGGGGCGAAGTTTAACATAGGAATATATAG AGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC Found at i:859453 original size:11 final size:11 Alignment explanation

Indices: 859437--859461 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 859427 TATCCACGTT 859437 GGCATCTAGAA 1 GGCATCTAGAA 859448 GGCATCTAGAA 1 GGCATCTAGAA 859459 GGC 1 GGC 859462 CAAGCGCTGC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.32, C:0.20, G:0.32, T:0.16 Consensus pattern (11 bp): GGCATCTAGAA Found at i:861267 original size:2 final size:2 Alignment explanation

Indices: 861260--861289 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 861250 TTAAAAGCAT 861260 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 861290 TTTTCAGTCT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:863004 original size:30 final size:30 Alignment explanation

Indices: 862968--863028 Score: 104 Period size: 30 Copynumber: 2.0 Consensus size: 30 862958 AGGGAAACGT 862968 TGATTTATATGAAATGCTATTCCAATAGGA 1 TGATTTATATGAAATGCTATTCCAATAGGA * * 862998 TGATTTATATGAATTGTTATTCCAATAGGA 1 TGATTTATATGAAATGCTATTCCAATAGGA 863028 T 1 T 863029 TATTCTATGT Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 30 29 1.00 ACGTcount: A:0.34, C:0.08, G:0.16, T:0.41 Consensus pattern (30 bp): TGATTTATATGAAATGCTATTCCAATAGGA Found at i:867858 original size:30 final size:30 Alignment explanation

Indices: 867822--867879 Score: 107 Period size: 30 Copynumber: 1.9 Consensus size: 30 867812 AAAGGCGAGG * 867822 CTCCGCCTCGCTTTCTATGGACTTTACCGA 1 CTCCGCCTCGCCTTCTATGGACTTTACCGA 867852 CTCCGCCTCGCCTTCTATGGACTTTACC 1 CTCCGCCTCGCCTTCTATGGACTTTACC 867880 AACCCCACAC Statistics Matches: 27, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 30 27 1.00 ACGTcount: A:0.12, C:0.40, G:0.16, T:0.33 Consensus pattern (30 bp): CTCCGCCTCGCCTTCTATGGACTTTACCGA Found at i:871915 original size:1 final size:1 Alignment explanation

Indices: 871909--871934 Score: 52 Period size: 1 Copynumber: 26.0 Consensus size: 1 871899 GCCCTCTCCC 871909 AAAAAAAAAAAAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 871935 TCGGGAGAGG Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 25 1.00 ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:872592 original size:18 final size:18 Alignment explanation

Indices: 872569--872604 Score: 72 Period size: 18 Copynumber: 2.0 Consensus size: 18 872559 GGGACATTGT 872569 AAATTATACACCGGTAAG 1 AAATTATACACCGGTAAG 872587 AAATTATACACCGGTAAG 1 AAATTATACACCGGTAAG 872605 TTTTTGACAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22 Consensus pattern (18 bp): AAATTATACACCGGTAAG Found at i:882727 original size:2 final size:2 Alignment explanation

Indices: 882720--882753 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 882710 TTTATAGGTG 882720 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 882754 CACCTATAAA Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:900482 original size:165 final size:166 Alignment explanation

Indices: 900239--900595 Score: 457 Period size: 165 Copynumber: 2.1 Consensus size: 166 900229 TCCATGAAGC * * 900239 CCTCTACCAAAACTGTGAAATTCATGGCCCCTGGGTCAGACGTTCAGGCTCTAGGGTGGGGCCAC 1 CCTCTACCAAAACTGTAAAATTCAAGGCCCCTGGGTCAGACGTTCAGGCTCTAGGGTGGGGCCAC * 900304 TTTGGCCATATAGTGAAAATGTATTAAATCTTAGAAAA-TCTTTTCTTCTTCCATATACATTTCA 66 TTTGGCCATATAGTGAAAATGTATTAAATCTTAGAAAATTCTTTTCTTCTCCCATATACATTTCA 900368 ATAAAACTGAGTGTATGGTTATGATATCCACTGACT 131 ATAAAACTGAGTGTATGGTTATGATATCCACTGACT * * ** * 900404 CCTCTACCAAAATTGTAAAATTCAAAGG-GCCTGGGTCAGGGGTTCAGGCTTTAGGGTGGGGCCA 1 CCTCTACCAAAACTGTAAAATTC-AAGGCCCCTGGGTCAGACGTTCAGGCTCTAGGGTGGGGCCA ** * 900468 CTTTGGTGATATAGTGAAAATGTATTAAATCTTAGAAAATCTTCTTTTCTTCTCCCATATATATT 65 CTTTGGCCATATAGTGAAAATGTATTAAATCTTAGAAAA--TTCTTTTCTTCTCCCATATACATT * * * ** * * * ** 900533 TGAATAAATCTTAGTACATGGTTATTATGTCAAAGGACT 128 TCAATAAAACTGAGTGTATGGTTATGATATCCACTGACT * * * 900572 CCTTTACCTAAGCTGTAAAATTCA 1 CCTCTACCAAAACTGTAAAATTCA 900596 TTACCTCTGG Statistics Matches: 163, Mismatches: 25, Indels: 6 0.84 0.13 0.03 Matches are distributed among these distances: 165 90 0.55 166 3 0.02 167 1 0.01 168 69 0.42 ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33 Consensus pattern (166 bp): CCTCTACCAAAACTGTAAAATTCAAGGCCCCTGGGTCAGACGTTCAGGCTCTAGGGTGGGGCCAC TTTGGCCATATAGTGAAAATGTATTAAATCTTAGAAAATTCTTTTCTTCTCCCATATACATTTCA ATAAAACTGAGTGTATGGTTATGATATCCACTGACT Found at i:906616 original size:17 final size:17 Alignment explanation

Indices: 906594--906626 Score: 66 Period size: 17 Copynumber: 1.9 Consensus size: 17 906584 CTGGTACTGT 906594 ACCAGTTATCGGCTAAG 1 ACCAGTTATCGGCTAAG 906611 ACCAGTTATCGGCTAA 1 ACCAGTTATCGGCTAA 906627 ACTGAGAGTT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24 Consensus pattern (17 bp): ACCAGTTATCGGCTAAG Found at i:907747 original size:4 final size:4 Alignment explanation

Indices: 907716--907803 Score: 117 Period size: 4 Copynumber: 22.5 Consensus size: 4 907706 GCATTATAGG * * * * 907716 ATCT ATCC ATCC ATCG ATCT ATCG ATCT ATCT ATCT ATCT ATCT ATCT 1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT * 907764 ATCT ATCT ATCT ATCT ATCT ATC- -TCT ATCT TTCT ATCT AT 1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT 907804 AGATTCAACT Statistics Matches: 75, Mismatches: 7, Indels: 4 0.87 0.08 0.05 Matches are distributed among these distances: 2 2 0.03 4 73 0.97 ACGTcount: A:0.24, C:0.27, G:0.02, T:0.47 Consensus pattern (4 bp): ATCT Found at i:907940 original size:17 final size:17 Alignment explanation

Indices: 907918--907953 Score: 54 Period size: 17 Copynumber: 2.1 Consensus size: 17 907908 ATATCGCCAG 907918 TGTTTGGGGTTTTTGTT 1 TGTTTGGGGTTTTTGTT * * 907935 TGTTTGGGTTTTTTTTT 1 TGTTTGGGGTTTTTGTT 907952 TG 1 TG 907954 GGGGGGGGGG Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 17 17 1.00 ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69 Consensus pattern (17 bp): TGTTTGGGGTTTTTGTT Found at i:912489 original size:13 final size:13 Alignment explanation

Indices: 912471--912501 Score: 53 Period size: 13 Copynumber: 2.4 Consensus size: 13 912461 TTATTAGTAA 912471 AAAAAACAAAAAC 1 AAAAAACAAAAAC * 912484 AAAAAACAAAAAG 1 AAAAAACAAAAAC 912497 AAAAA 1 AAAAA 912502 CAATTCTTGT Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 13 17 1.00 ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00 Consensus pattern (13 bp): AAAAAACAAAAAC Found at i:913590 original size:21 final size:21 Alignment explanation

Indices: 913541--913624 Score: 78 Period size: 21 Copynumber: 4.0 Consensus size: 21 913531 ATTTTTCAAT 913541 TAATTATGTCGACATGCAAGA 1 TAATTATGTCGACATGCAAGA * * * 913562 TAAATATGTTGATATGCAAGA 1 TAATTATGTCGACATGCAAGA * * * * 913583 TAGTTATGTCAACATGTAACA 1 TAATTATGTCGACATGCAAGA * * * 913604 TAACTATGTTGACATGTAAGA 1 TAATTATGTCGACATGCAAGA 913625 AAACTACAAT Statistics Matches: 48, Mismatches: 15, Indels: 0 0.76 0.24 0.00 Matches are distributed among these distances: 21 48 1.00 ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32 Consensus pattern (21 bp): TAATTATGTCGACATGCAAGA Found at i:913612 original size:42 final size:42 Alignment explanation

Indices: 913544--913624 Score: 108 Period size: 42 Copynumber: 1.9 Consensus size: 42 913534 TTTCAATTAA * * * 913544 TTATGTCGACATGCAAGATAAATATGTTGATATGCAAGATAG 1 TTATGTCAACATGCAACATAAATATGTTGACATGCAAGATAG * * * 913586 TTATGTCAACATGTAACATAACTATGTTGACATGTAAGA 1 TTATGTCAACATGCAACATAAATATGTTGACATGCAAGA 913625 AAACTACAAT Statistics Matches: 33, Mismatches: 6, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 42 33 1.00 ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32 Consensus pattern (42 bp): TTATGTCAACATGCAACATAAATATGTTGACATGCAAGATAG Found at i:914110 original size:20 final size:20 Alignment explanation

Indices: 914085--914124 Score: 80 Period size: 20 Copynumber: 2.0 Consensus size: 20 914075 TGCCAGTTAT 914085 AAACACAATAATGTAAAGCA 1 AAACACAATAATGTAAAGCA 914105 AAACACAATAATGTAAAGCA 1 AAACACAATAATGTAAAGCA 914125 GTAAACGTAA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.60, C:0.15, G:0.10, T:0.15 Consensus pattern (20 bp): AAACACAATAATGTAAAGCA Found at i:915275 original size:63 final size:63 Alignment explanation

Indices: 915161--915317 Score: 199 Period size: 63 Copynumber: 2.5 Consensus size: 63 915151 CTACCTACTG * * * * *** * 915161 ATGTCAACATGCAACTCATTTATGTTAACATGCAACTTCTTTATGTCGACATGCAACTTATTT 1 ATGTCGACATGCAACTAAGTTATGTTAACATGCAAATAAATTATGTCGACATGCAACATATTT * 915224 ATGTCGACATGCAACTAAGTTATGTTAACATGCAAGATAAATT-TGTTGACATGCAACATATTT 1 ATGTCGACATGCAACTAAGTTATGTTAACATGCAA-ATAAATTATGTCGACATGCAACATATTT * * 915287 ATGTCGACATGCAACTTAGTTATGTTGACAT 1 ATGTCGACATGCAACTAAGTTATGTTAACAT 915318 ACAACTTATA Statistics Matches: 82, Mismatches: 11, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 63 79 0.96 64 3 0.04 ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36 Consensus pattern (63 bp): ATGTCGACATGCAACTAAGTTATGTTAACATGCAAATAAATTATGTCGACATGCAACATATTT Found at i:915324 original size:21 final size:21 Alignment explanation

Indices: 915167--915326 Score: 169 Period size: 21 Copynumber: 7.6 Consensus size: 21 915157 ACTGATGTCA * * 915167 ACATGCAACTCATTTATGTTA 1 ACATGCAACTTATTTATGTTG * * 915188 ACATGCAACTTCTTTATGTCG 1 ACATGCAACTTATTTATGTTG * 915209 ACATGCAACTTATTTATGTCG 1 ACATGCAACTTATTTATGTTG * * * 915230 ACATGCAACTAAGTTATGTTA 1 ACATGCAACTTATTTATGTTG * * * 915251 ACATGCAAGATAAATT-TGTTG 1 ACATGCAA-CTTATTTATGTTG * * 915272 ACATGCAACATATTTATGTCG 1 ACATGCAACTTATTTATGTTG * 915293 ACATGCAACTTAGTTATGTTG 1 ACATGCAACTTATTTATGTTG * 915314 ACATACAACTTAT 1 ACATGCAACTTAT 915327 AAGTTGCATG Statistics Matches: 115, Mismatches: 22, Indels: 4 0.82 0.16 0.03 Matches are distributed among these distances: 20 3 0.03 21 107 0.93 22 5 0.04 ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36 Consensus pattern (21 bp): ACATGCAACTTATTTATGTTG Found at i:915356 original size:21 final size:21 Alignment explanation

Indices: 915332--915407 Score: 80 Period size: 21 Copynumber: 3.6 Consensus size: 21 915322 CTTATAAGTT 915332 GCATGTCAACATATTTATCTC 1 GCATGTCAACATATTTATCTC * ** ** * 915353 GCATGTAAACATAACTAAGTT 1 GCATGTCAACATATTTATCTC * 915374 GCATGTCAACATATTCATCTC 1 GCATGTCAACATATTTATCTC * 915395 GTATGTCAACATA 1 GCATGTCAACATA 915408 AAAAAGTTGC Statistics Matches: 41, Mismatches: 14, Indels: 0 0.75 0.25 0.00 Matches are distributed among these distances: 21 41 1.00 ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33 Consensus pattern (21 bp): GCATGTCAACATATTTATCTC Found at i:915385 original size:42 final size:42 Alignment explanation

Indices: 915325--915463 Score: 161 Period size: 42 Copynumber: 3.3 Consensus size: 42 915315 CATACAACTT * 915325 ATAAGTTGCATGTCAACATATTTATCTCGCATGTAAACATAA 1 ATAAGTTGCATGTCAACATATTCATCTCGCATGTAAACATAA * * * 915367 CTAAGTTGCATGTCAACATATTCATCTCGTATGTCAACATAA 1 ATAAGTTGCATGTCAACATATTCATCTCGCATGTAAACATAA * ** * ** * * 915409 AAAAGTTGCATGTTGACATAATCAAGTTGCATGTCAACATAA 1 ATAAGTTGCATGTCAACATATTCATCTCGCATGTAAACATAA * 915451 ATAAGTTCCATGT 1 ATAAGTTGCATGT 915464 TGACATAAAT Statistics Matches: 82, Mismatches: 15, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 42 82 1.00 ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32 Consensus pattern (42 bp): ATAAGTTGCATGTCAACATATTCATCTCGCATGTAAACATAA Found at i:915421 original size:21 final size:21 Alignment explanation

Indices: 915397--915537 Score: 104 Period size: 21 Copynumber: 6.7 Consensus size: 21 915387 TTCATCTCGT 915397 ATGTCAACATAAAAAAGTTGC 1 ATGTCAACATAAAAAAGTTGC ** ** 915418 ATGTTGACATAATCAAGTTGC 1 ATGTCAACATAAAAAAGTTGC * * 915439 ATGTCAACATAAATAAGTTCC 1 ATGTCAACATAAAAAAGTTGC ** * 915460 ATGTTGACATAAATATA-TTGC 1 ATGTCAACATAAA-AAAGTTGC * ** ** 915481 ATGTCAGCATATTAATCTTGC 1 ATGTCAACATAAAAAAGTTGC * * 915502 ATGTTAACATAAATAAGTTGC 1 ATGTCAACATAAAAAAGTTGC * * 915523 AAGTCGACATAAAAA 1 ATGTCAACATAAAAA 915538 GGCACCATCC Statistics Matches: 86, Mismatches: 32, Indels: 4 0.70 0.26 0.03 Matches are distributed among these distances: 20 1 0.01 21 84 0.98 22 1 0.01 ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30 Consensus pattern (21 bp): ATGTCAACATAAAAAAGTTGC Found at i:915464 original size:42 final size:42 Alignment explanation

Indices: 915397--915535 Score: 158 Period size: 42 Copynumber: 3.3 Consensus size: 42 915387 TTCATCTCGT * 915397 ATGTCAACATAAAAAAGTTGCATGTTGACAT-AATCAAGTTGC 1 ATGTCAACATAAATAAGTTGCATGTTGACATAAAT-AAGTTGC * 915439 ATGTCAACATAAATAAGTTCCATGTTGACATAAATATA-TTGC 1 ATGTCAACATAAATAAGTTGCATGTTGACATAAATA-AGTTGC * * * * 915481 ATGTCAGCAT-ATTAATCTTGCATGTTAACATAAATAAGTTGC 1 ATGTCAACATAAATAA-GTTGCATGTTGACATAAATAAGTTGC * * 915523 AAGTCGACATAAA 1 ATGTCAACATAAA 915536 AAGGCACCAT Statistics Matches: 81, Mismatches: 11, Indels: 9 0.80 0.11 0.09 Matches are distributed among these distances: 41 5 0.06 42 71 0.88 43 5 0.06 ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31 Consensus pattern (42 bp): ATGTCAACATAAATAAGTTGCATGTTGACATAAATAAGTTGC Found at i:915470 original size:63 final size:62 Alignment explanation

Indices: 915403--915537 Score: 148 Period size: 63 Copynumber: 2.1 Consensus size: 62 915393 TCGTATGTCA * * * * 915403 ACATAAAAAAGTTGCATGT-TGACATAATCAA-GTTGCATGTCAACATAAATAAGTTCCATGTTG 1 ACATAAAAAA-TTGCATGTCAG-CAT-ATCAATCTTGCATGTCAACATAAATAAGTTCCAAGTCG * * * * 915466 ACATAAATATATTGCATGTCAGCATATTAATCTTGCATGTTAACATAAATAAGTTGCAAGTCG 1 ACATAAA-AAATTGCATGTCAGCATATCAATCTTGCATGTCAACATAAATAAGTTCCAAGTCG 915529 ACATAAAAA 1 ACATAAAAA 915538 GGCACCATCC Statistics Matches: 60, Mismatches: 9, Indels: 7 0.79 0.12 0.09 Matches are distributed among these distances: 62 5 0.08 63 52 0.87 64 3 0.05 ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30 Consensus pattern (62 bp): ACATAAAAAATTGCATGTCAGCATATCAATCTTGCATGTCAACATAAATAAGTTCCAAGTCG Found at i:915650 original size:21 final size:21 Alignment explanation

Indices: 915619--915703 Score: 107 Period size: 21 Copynumber: 4.0 Consensus size: 21 915609 ATCTGATTGC * * 915619 AATTTTCTTGCATGTCAACGT 1 AATTATCTTGCATGTCAACAT * * 915640 AATTATGTTGCATGTTAACAT 1 AATTATCTTGCATGTCAACAT 915661 AATTATCTTGCATGTCAACAT 1 AATTATCTTGCATGTCAACAT * * * 915682 ATTTATCTTGCATATCGACAT 1 AATTATCTTGCATGTCAACAT 915703 A 1 A 915704 TTTGATTGAA Statistics Matches: 55, Mismatches: 9, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 21 55 1.00 ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41 Consensus pattern (21 bp): AATTATCTTGCATGTCAACAT Found at i:918434 original size:33 final size:33 Alignment explanation

Indices: 918394--918470 Score: 127 Period size: 33 Copynumber: 2.3 Consensus size: 33 918384 AGCCATCTTT 918394 CCCCCCGGAAAAATGGCTATATAGCAGTTCATC 1 CCCCCCGGAAAAATGGCTATATAGCAGTTCATC ** 918427 CCCCCCGGAAAAATGGCTATATAGCAGTTTTTC 1 CCCCCCGGAAAAATGGCTATATAGCAGTTCATC * 918460 CCCCACGGAAA 1 CCCCCCGGAAA 918471 GCTGACTATA Statistics Matches: 41, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 33 41 1.00 ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21 Consensus pattern (33 bp): CCCCCCGGAAAAATGGCTATATAGCAGTTCATC Found at i:926754 original size:28 final size:28 Alignment explanation

Indices: 926714--926769 Score: 112 Period size: 28 Copynumber: 2.0 Consensus size: 28 926704 CTCTAGCAAA 926714 TTGTAATGTTAACAAAATGCGGTTATAT 1 TTGTAATGTTAACAAAATGCGGTTATAT 926742 TTGTAATGTTAACAAAATGCGGTTATAT 1 TTGTAATGTTAACAAAATGCGGTTATAT 926770 AAACCAACGC Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 28 1.00 ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39 Consensus pattern (28 bp): TTGTAATGTTAACAAAATGCGGTTATAT Found at i:929647 original size:2 final size:2 Alignment explanation

Indices: 929640--929688 Score: 98 Period size: 2 Copynumber: 24.5 Consensus size: 2 929630 TCTAATGACC 929640 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 929682 AG AG AG A 1 AG AG AG A 929689 CTGGGTTCAA Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 47 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:932836 original size:2 final size:2 Alignment explanation

Indices: 932829--932868 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 932819 TCTTATTAAT 932829 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 932869 TGGATGGATA Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:933139 original size:326 final size:325 Alignment explanation

Indices: 932547--933193 Score: 1285 Period size: 326 Copynumber: 2.0 Consensus size: 325 932537 GAAGGTTACA 932547 ATGGATAATAGACTCTGCAAGTTTTTTGGAAAAGAATTCAAGAGTAGATCTGCTTTTAAAATATG 1 ATGGATAATAGACTCTGCAAGTTTTTTGGAAAAGAATTCAAGAGTAGATCTGCTTTTAAAATATG 932612 ATCATGAAAAGGGACACGTAGGGAAGGCACCACACATGTGTTGCTCCAAGAGGTTTTACAGCAAA 66 ATCATGAAAAGGGACACGTAGGGAAGGCACCACACATGTGTTGCTCCAAGAGGTTTTACAGCAAA 932677 GCTAATCTTAAAAGACCTAGATTAGAATATTTTGTGCCGATATTTGACTTAAAACATTGAAATAA 131 GCTAATCTTAAAAGACCTAGATTAGAATATTTTGTGCCGATATTTGACTTAAAACATTGAAATAA 932742 TGTGTACAACTATGTAAATCTAATTTTTATTATGAAGTAAGTGCGTTTTTTTTTTTTACAGAGTC 196 TGTGTACAACTATGTAAATCTAATTTTTATTATGAAGTAAGTGCGTTTTTTTTTTTTACAGAGTC 932807 GTCAGTTTGTTCTCTTATTAATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATGG 261 GTCAGTTTGTTCTCTTATTAATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATGG 932872 ATGGATAATAGACTCTGCAAGTTTTTTTGGAAAAGAATTCAAGAGTAGATCTGCTTTTAAAATAT 1 ATGGATAATAGACTCTGCAAG-TTTTTTGGAAAAGAATTCAAGAGTAGATCTGCTTTTAAAATAT 932937 GATCATGAAAAGGGACACGTAGGGAAGGCACCACACATGTGTTGCTCCAAGAGGTTTTACAGCAA 65 GATCATGAAAAGGGACACGTAGGGAAGGCACCACACATGTGTTGCTCCAAGAGGTTTTACAGCAA 933002 AGCTAATCTTAAAAGACCTAGATTAGAATATTTTGTGCCGATATTTGACTTAAAACATTGAAATA 130 AGCTAATCTTAAAAGACCTAGATTAGAATATTTTGTGCCGATATTTGACTTAAAACATTGAAATA 933067 ATGTGTACAACTATGTAAATCTAATTTTTATTATGAAGTAAGTGCGTTTTTTTTTTTTACAGAGT 195 ATGTGTACAACTATGTAAATCTAATTTTTATTATGAAGTAAGTGCGTTTTTTTTTTTTACAGAGT 933132 CGTCAGTTTGTTCTCTTATTAATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 260 CGTCAGTTTGTTCTCTTATTAATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 933194 TGAGAGTGAG Statistics Matches: 321, Mismatches: 0, Indels: 1 1.00 0.00 0.00 Matches are distributed among these distances: 325 21 0.07 326 300 0.93 ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31 Consensus pattern (325 bp): ATGGATAATAGACTCTGCAAGTTTTTTGGAAAAGAATTCAAGAGTAGATCTGCTTTTAAAATATG ATCATGAAAAGGGACACGTAGGGAAGGCACCACACATGTGTTGCTCCAAGAGGTTTTACAGCAAA GCTAATCTTAAAAGACCTAGATTAGAATATTTTGTGCCGATATTTGACTTAAAACATTGAAATAA TGTGTACAACTATGTAAATCTAATTTTTATTATGAAGTAAGTGCGTTTTTTTTTTTTACAGAGTC GTCAGTTTGTTCTCTTATTAATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATGG Found at i:933233 original size:2 final size:2 Alignment explanation

Indices: 933155--933214 Score: 102 Period size: 2 Copynumber: 30.0 Consensus size: 2 933145 TCTTATTAAT * 933155 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GT GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA * 933197 GA GT GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA 933215 ATTTAGTTCT Statistics Matches: 54, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 2 54 1.00 ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03 Consensus pattern (2 bp): GA Found at i:936429 original size:2 final size:2 Alignment explanation

Indices: 936422--936469 Score: 96 Period size: 2 Copynumber: 24.0 Consensus size: 2 936412 TAATGCATGA 936422 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 936464 AG AG AG 1 AG AG AG 936470 GTGTAAATCC Statistics Matches: 46, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 46 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:948644 original size:17 final size:17 Alignment explanation

Indices: 948624--948666 Score: 59 Period size: 17 Copynumber: 2.5 Consensus size: 17 948614 GTGCAAACAT * * 948624 GGATATAGTGAATTCTC 1 GGATATAGCGAATTCCC 948641 GGATATAGCGAATTCCC 1 GGATATAGCGAATTCCC * 948658 AGATATAGC 1 GGATATAGC 948667 AAAGTTTTTT Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 17 23 1.00 ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28 Consensus pattern (17 bp): GGATATAGCGAATTCCC Found at i:948744 original size:15 final size:16 Alignment explanation

Indices: 948724--948763 Score: 55 Period size: 15 Copynumber: 2.6 Consensus size: 16 948714 ATTTTACGGT * 948724 TATAACGAATT-CGGA 1 TATAACGAATTAAGGA 948739 TATAACGAATTAAGGA 1 TATAACGAATTAAGGA * 948755 TATAGCGAA 1 TATAACGAA 948764 CTGATTTTGA Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 15 11 0.50 16 11 0.50 ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25 Consensus pattern (16 bp): TATAACGAATTAAGGA Found at i:949056 original size:16 final size:16 Alignment explanation

Indices: 949035--949066 Score: 64 Period size: 16 Copynumber: 2.0 Consensus size: 16 949025 CGAATTCAGT 949035 TTACGGATATAACAAA 1 TTACGGATATAACAAA 949051 TTACGGATATAACAAA 1 TTACGGATATAACAAA 949067 GTAATTCCAT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25 Consensus pattern (16 bp): TTACGGATATAACAAA Found at i:950472 original size:180 final size:179 Alignment explanation

Indices: 950170--950708 Score: 963 Period size: 180 Copynumber: 3.0 Consensus size: 179 950160 CCTACATGTT * * * 950170 TATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCT-AGTATTTTTTTCATGAATTATCGG 1 TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGA-TA-TTTTTTCATAAATTATCCG * 950234 AAATCGAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACT 64 AAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACT * 950299 TCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACCATGAGGGTACCCTA 129 TCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCTA * 950350 TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGTTGATATTTTTTCAATAAATTATCCGA 1 TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGATATTTTTTC-ATAAATTATCCGA * 950415 AATCAAAATCCTAGCAATATGCACACATCTGATATATGTACAATTGATCTGCAAAAGAACAACTT 65 AATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACTT 950480 CCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCTA 130 CCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCTA * 950530 TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCCGA 1 TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGATATTTTTTC-ATAAATTATCCGA 950595 AATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACTT 65 AATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACTT 950660 CCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCT 130 CCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCT 950709 TTTGGCAGCC Statistics Matches: 346, Mismatches: 11, Indels: 4 0.96 0.03 0.01 Matches are distributed among these distances: 179 7 0.02 180 338 0.98 181 1 0.00 ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30 Consensus pattern (179 bp): TATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGATATTTTTTCATAAATTATCCGAA ATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAACTTC CTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCTA Found at i:953694 original size:22 final size:19 Alignment explanation

Indices: 953653--953697 Score: 54 Period size: 20 Copynumber: 2.3 Consensus size: 19 953643 ACGGTCAAAA 953653 TTATATATAATCAAAATTT 1 TTATATATAATCAAAATTT * * 953672 TTATCATATAATTAACAACTT 1 TTAT-ATATAATCAA-AATTT 953693 TTATA 1 TTATA 953698 ACATTGGTGC Statistics Matches: 22, Mismatches: 2, Indels: 3 0.81 0.07 0.11 Matches are distributed among these distances: 19 4 0.18 20 10 0.45 21 8 0.36 ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47 Consensus pattern (19 bp): TTATATATAATCAAAATTT Found at i:957482 original size:24 final size:26 Alignment explanation

Indices: 957448--957499 Score: 81 Period size: 25 Copynumber: 2.1 Consensus size: 26 957438 AAAATGTTTT * 957448 AATTTCAAATTAATCC-AAGAGCAAA 1 AATTTCAAATTAATCCAAAAAGCAAA 957473 AATTT-AAATTAATCCAAAAAGCAAA 1 AATTTCAAATTAATCCAAAAAGCAAA 957498 AA 1 AA 957500 ACTACATAAC Statistics Matches: 25, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 24 10 0.40 25 15 0.60 ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23 Consensus pattern (26 bp): AATTTCAAATTAATCCAAAAAGCAAA Found at i:958797 original size:4 final size:4 Alignment explanation

Indices: 958752--958790 Score: 60 Period size: 4 Copynumber: 9.8 Consensus size: 4 958742 GTTTCACCCT * * 958752 GTCC GTCT GTCT GTCC GTCC GTCC GTCC GTCC GTCC GTC 1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC 958791 TGTCTGTAGA Statistics Matches: 33, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 4 33 1.00 ACGTcount: A:0.00, C:0.44, G:0.26, T:0.31 Consensus pattern (4 bp): GTCC Found at i:966944 original size:17 final size:19 Alignment explanation

Indices: 966922--966957 Score: 58 Period size: 18 Copynumber: 2.0 Consensus size: 19 966912 TCTGTAAGTA 966922 AAAAT-ATTCCTT-TTTTT 1 AAAATAATTCCTTATTTTT 966939 AAAATAATTCCTTATTTTT 1 AAAATAATTCCTTATTTTT 966958 TTTTCTAAAC Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 17 5 0.29 18 7 0.41 19 5 0.29 ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56 Consensus pattern (19 bp): AAAATAATTCCTTATTTTT Found at i:967318 original size:4 final size:4 Alignment explanation

Indices: 967309--967352 Score: 61 Period size: 4 Copynumber: 11.0 Consensus size: 4 967299 TACCCTTGTG * * * 967309 TGTC TGTC TGTC CGTC CGTC TGTC TGTC TGTC CGTC TGTC TGTC 1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC 967353 CGTCCGTAAC Statistics Matches: 36, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 4 36 1.00 ACGTcount: A:0.00, C:0.32, G:0.25, T:0.43 Consensus pattern (4 bp): TGTC Found at i:967331 original size:12 final size:12 Alignment explanation

Indices: 967310--967359 Score: 55 Period size: 12 Copynumber: 4.2 Consensus size: 12 967300 ACCCTTGTGT * 967310 GTCTGTCTGTCC 1 GTCTGTCCGTCC * * * 967322 GTCCGTCTGTCT 1 GTCTGTCCGTCC * 967334 GTCTGTCCGTCT 1 GTCTGTCCGTCC 967346 GTCTGTCCGTCC 1 GTCTGTCCGTCC 967358 GT 1 GT 967360 AACAAAAATT Statistics Matches: 33, Mismatches: 5, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 12 33 1.00 ACGTcount: A:0.00, C:0.34, G:0.26, T:0.40 Consensus pattern (12 bp): GTCTGTCCGTCC Found at i:967331 original size:16 final size:16 Alignment explanation

Indices: 967310--967359 Score: 91 Period size: 16 Copynumber: 3.1 Consensus size: 16 967300 ACCCTTGTGT 967310 GTCTGTCTGTCCGTCC 1 GTCTGTCTGTCCGTCC * 967326 GTCTGTCTGTCTGTCC 1 GTCTGTCTGTCCGTCC 967342 GTCTGTCTGTCCGTCC 1 GTCTGTCTGTCCGTCC 967358 GT 1 GT 967360 AACAAAAATT Statistics Matches: 32, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 32 1.00 ACGTcount: A:0.00, C:0.34, G:0.26, T:0.40 Consensus pattern (16 bp): GTCTGTCTGTCCGTCC Found at i:967658 original size:167 final size:167 Alignment explanation

Indices: 967383--968508 Score: 1682 Period size: 165 Copynumber: 6.8 Consensus size: 167 967373 GTCGCATTTA * 967383 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGT-TAAGGCATGCCATA 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTAT-AGGCATGCCATA * * 967447 TCATGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAACGACGACTTTGCTTATTT 65 TCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTT * ** 967512 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAAA 130 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * 967550 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTAACACAGTATTGGTATAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT * 967615 CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGA-GTACTTTG-TT-TAT 66 CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACG-ACTTTGCTTATTT ** 967677 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAAA 130 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * 967715 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTAACACAGTATTGGTATAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT * * 967780 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 66 CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT * 967845 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT 131 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * 967882 TCTCAGCAGCTATTTATCGCAGATGCTTGAAA-TTTATACACAATATTTGTATAGGCATGCCATA 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTA-ACACAGTATTTGTATAGGCATGCCATA * * 967946 TCGTGGGATATATTTTTGTACCAATCGG-CGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TT 65 TCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTT * 968009 TTTAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATT 130 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * 968047 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT * * * * * * 968112 TGTGGGATATATTTTTGTATCAATCGGACGTCAAACTTCCTGTGAAATGATGACTTTGTTTA-TT 66 CGTGGGATATATTTTTGTACCAATCGGACG-CCAACTTCCTGTTAAATGACGACTTTGCTTATTT 968176 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT 130 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * * * * 968214 TCTCAGCAGCTATTTATCGCAGATGCTTAAAATTTTTACACAGTGTTTGT-TAAGGCATGCCGTA 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTAT-AGGCATGCCATA * * 968278 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGA-GTACTTTG-TT-TA 65 TCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACG-ACTTTGCTTATT * 968340 TTTTAGCCAAAATTTTCAAACAAATTTTCCTCAAAGATT 129 TTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * * * 968379 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCTATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT * * * * * * * * 968444 TGTGGAATATATTTCTGTACCAATCGAATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT 66 CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 968509 GCATATTCAC Statistics Matches: 882, Mismatches: 61, Indels: 32 0.90 0.06 0.03 Matches are distributed among these distances: 165 420 0.48 166 75 0.09 167 386 0.44 168 1 0.00 ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37 Consensus pattern (167 bp): TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT CGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATTTT TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT Found at i:968014 original size:332 final size:331 Alignment explanation

Indices: 967381--968508 Score: 1771 Period size: 332 Copynumber: 3.4 Consensus size: 331 967371 CTGTCGCATT * * 967381 TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGT-TAAGGCATGCCA 1 TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTAT-AGGCATGCCA * * 967445 TATCATGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAACGACGACTTTGCTTAT 65 TATCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTAT ** * * 967510 TTTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGAAATCTCAGCAACTGTTTATCGCAGATG 130 TTTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATG * 967575 CTTGAAATTTTAACACAGTATTGGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATC 195 CTTGAAATTTT-ACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATC * 967640 GGACGCCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTAGCCAAAATTTTCAAACAAATTTTC 259 GGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTAGCCAAAATTTTCAAACAAATTTTC 967705 GTCAAAGA 324 GTCAAAGA * * * * 967713 AATCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTAACACAGTATTGGTATAGGCATGCCAT 1 TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATGCCAT * * 967778 ATCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATT 66 ATCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATT 967843 TTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGC 131 TTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGC * 967908 TTGAAATTTATACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCG 196 TTGAAATTT-TACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCG * 967973 G-CGTCAACTTCCTGTTAAATGACG-ACTTTGTTTATTTTTAGCCAAAATTTTCAAACAAATTTC 260 GACGTCAACTTCCTGTTAAATGA-GTACTTTGTTTA-TTTTAGCCAAAATTTTCAAACAAATTTT 968036 CGTCAAAGA 323 CGTCAAAGA * 968045 TTTCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATGCCAT 1 TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATGCCAT * * * * * * 968110 ATTGTGGGATATATTTTTGTATCAATCGGACGTCAAACTTCCTGTGAAATGATGACTTTGTTTA- 66 ATCGTGGGATATATTTTTGTACCAATCGGACG-CCAACTTCCTGTTAAATGACGACTTTGCTTAT * 968174 TTTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATG 130 TTTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATG * * * 968239 CTTAAAATTTTTACACAGTGTTTGT-TAAGGCATGCCGTATCGTGGGATATATTTTTGTACCAAT 195 CTTGAAA-TTTTACACAGTATTTGTAT-AGGCATGCCATATCGTGGGATATATTTTTGTACCAAT 968303 CGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTAGCCAAAATTTTCAAACAAATTTT 258 CGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTAGCCAAAATTTTCAAACAAATTTT * 968368 CCTCAAAGA 323 CGTCAAAGA * * * * 968377 TTTCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCTAT 1 TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATGCCAT * * * * * * * * 968442 ATTGTGGAATATATTTCTGTACCAATCGAATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATT 66 ATCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATT 968507 TT 131 TT 968509 GCATATTCAC Statistics Matches: 735, Mismatches: 51, Indels: 20 0.91 0.06 0.02 Matches are distributed among these distances: 331 55 0.07 332 618 0.84 333 62 0.08 ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37 Consensus pattern (331 bp): TATCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATGCCAT ATCGTGGGATATATTTTTGTACCAATCGGACGCCAACTTCCTGTTAAATGACGACTTTGCTTATT TTTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGC TTGAAATTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGG ACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTAGCCAAAATTTTCAAACAAATTTTCGT CAAAGA Found at i:979700 original size:17 final size:18 Alignment explanation

Indices: 979680--979713 Score: 61 Period size: 17 Copynumber: 1.9 Consensus size: 18 979670 AACCCTCAGT 979680 TTAGCCGA-TAACTGGTC 1 TTAGCCGATTAACTGGTC 979697 TTAGCCGATTAACTGGT 1 TTAGCCGATTAACTGGT 979714 ACAGTACCAG Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 17 8 0.50 18 8 0.50 ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32 Consensus pattern (18 bp): TTAGCCGATTAACTGGTC Found at i:982155 original size:17 final size:17 Alignment explanation

Indices: 982117--982155 Score: 51 Period size: 17 Copynumber: 2.3 Consensus size: 17 982107 TTAAAAATTC * 982117 CTTTAAATTTAACCTTT 1 CTTTAAATTTAACCATT * * 982134 TTTTAAATTTAAGCATT 1 CTTTAAATTTAACCATT 982151 CTTTA 1 CTTTA 982156 TATATTTGTA Statistics Matches: 18, Mismatches: 4, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 17 18 1.00 ACGTcount: A:0.31, C:0.13, G:0.03, T:0.54 Consensus pattern (17 bp): CTTTAAATTTAACCATT Found at i:987793 original size:13 final size:13 Alignment explanation

Indices: 987775--987804 Score: 60 Period size: 13 Copynumber: 2.3 Consensus size: 13 987765 GTAGAGTGTA 987775 TTTTTTTTTTCTT 1 TTTTTTTTTTCTT 987788 TTTTTTTTTTCTT 1 TTTTTTTTTTCTT 987801 TTTT 1 TTTT 987805 GCAACAGCAA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 17 1.00 ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93 Consensus pattern (13 bp): TTTTTTTTTTCTT Found at i:990790 original size:23 final size:23 Alignment explanation

Indices: 990760--990816 Score: 89 Period size: 23 Copynumber: 2.5 Consensus size: 23 990750 ATTGCAGTTT 990760 GATTGACACAACGCACACAGACG 1 GATTGACACAACGCACACAGACG * 990783 GATTGACACAACGCGCACAGACG 1 GATTGACACAACGCACACAGACG 990806 GATATGA-ACAA 1 GAT-TGACACAA 990817 AAGTTCACTG Statistics Matches: 32, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 23 29 0.91 24 3 0.09 ACGTcount: A:0.40, C:0.26, G:0.23, T:0.11 Consensus pattern (23 bp): GATTGACACAACGCACACAGACG Found at i:995042 original size:21 final size:21 Alignment explanation

Indices: 995018--995095 Score: 68 Period size: 21 Copynumber: 3.8 Consensus size: 21 995008 GCATATCATT * * 995018 GCATTAAAATCTCATAGAATA 1 GCATTAAAATATCATACAATA ** * * 995039 GCATTGGAATCTCATACCATA 1 GCATTAAAATATCATACAATA * * 995060 GCATTGAAATATCATACCATA 1 GCATTAAAATATCATACAATA * 995081 GCA-TACAATATCATA 1 GCATTAAAATATCATA 995096 GATTCTCATT Statistics Matches: 49, Mismatches: 8, Indels: 1 0.84 0.14 0.02 Matches are distributed among these distances: 20 10 0.20 21 39 0.80 ACGTcount: A:0.42, C:0.19, G:0.10, T:0.28 Consensus pattern (21 bp): GCATTAAAATATCATACAATA Found at i:995362 original size:21 final size:21 Alignment explanation

Indices: 995326--995403 Score: 77 Period size: 21 Copynumber: 3.7 Consensus size: 21 995316 CATTTCACTT * 995326 TCTCATAGCAAAGCA-TACAAA 1 TCTCATAGCATAGCATTA-AAA * 995347 TCTCATAGCATTGCATTAAAA 1 TCTCATAGCATAGCATTAAAA * * * 995368 TCTCGTAGCATATCATTTAAA 1 TCTCATAGCATAGCATTAAAA * * 995389 TCGCATACCATAGCA 1 TCTCATAGCATAGCA 995404 AAGCATAAAA Statistics Matches: 46, Mismatches: 10, Indels: 2 0.79 0.17 0.03 Matches are distributed among these distances: 21 44 0.96 22 2 0.04 ACGTcount: A:0.38, C:0.23, G:0.10, T:0.28 Consensus pattern (21 bp): TCTCATAGCATAGCATTAAAA Found at i:997800 original size:7 final size:7 Alignment explanation

Indices: 997788--997817 Score: 51 Period size: 7 Copynumber: 4.3 Consensus size: 7 997778 CTTGATTTAA 997788 AAAACAC 1 AAAACAC 997795 AAAACAC 1 AAAACAC * 997802 AAAACAT 1 AAAACAC 997809 AAAACAC 1 AAAACAC 997816 AA 1 AA 997818 GTGGGTTATT Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 7 21 1.00 ACGTcount: A:0.73, C:0.23, G:0.00, T:0.03 Consensus pattern (7 bp): AAAACAC Found at i:1007037 original size:53 final size:53 Alignment explanation

Indices: 1006970--1007074 Score: 158 Period size: 53 Copynumber: 2.0 Consensus size: 53 1006960 ATTTCTAAAG * * * 1006970 AAAAAAAAGAAAAATACAAAAATACATTTTCGGGTTAAAATTTTAATTAATTA 1 AAAAAAAAGAAAAATACAAAAATACATATACGGGTTAAAATTTTAACTAATTA * 1007023 AAAAAAAATG-AAAATACAAAAATACATATACGGGTTAAAGTTTTAACTAATT 1 AAAAAAAA-GAAAAATACAAAAATACATATACGGGTTAAAATTTTAACTAATT 1007075 GGCCCTATTT Statistics Matches: 47, Mismatches: 4, Indels: 2 0.89 0.08 0.04 Matches are distributed among these distances: 53 46 0.98 54 1 0.02 ACGTcount: A:0.56, C:0.07, G:0.09, T:0.29 Consensus pattern (53 bp): AAAAAAAAGAAAAATACAAAAATACATATACGGGTTAAAATTTTAACTAATTA Found at i:1009230 original size:48 final size:47 Alignment explanation

Indices: 1009178--1009273 Score: 122 Period size: 48 Copynumber: 2.0 Consensus size: 47 1009168 GTAAGTATTC * 1009178 ATGTTGT-AGAATATGATTTTTACAGATATCAAAAACATCCATCACAGA 1 ATGTTGTCA-AATAGGATTTTTACAGATATC-AAAACATCCATCACAGA * * * * 1009226 ATGTTGTCAAATAGGATTTTTGCAGATATCGAAACATTCATCCCAGA 1 ATGTTGTCAAATAGGATTTTTACAGATATCAAAACATCCATCACAGA 1009273 A 1 A 1009274 AATTTTACAG Statistics Matches: 42, Mismatches: 5, Indels: 3 0.84 0.10 0.06 Matches are distributed among these distances: 47 15 0.36 48 26 0.62 49 1 0.02 ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31 Consensus pattern (47 bp): ATGTTGTCAAATAGGATTTTTACAGATATCAAAACATCCATCACAGA Found at i:1009800 original size:1 final size:1 Alignment explanation

Indices: 1009794--1009819 Score: 52 Period size: 1 Copynumber: 26.0 Consensus size: 1 1009784 AGAATATACG 1009794 TTTTTTTTTTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTT 1009820 GGTATATAAT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 25 1.00 ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00 Consensus pattern (1 bp): T Found at i:1014951 original size:2 final size:2 Alignment explanation

Indices: 1014944--1015024 Score: 155 Period size: 2 Copynumber: 41.0 Consensus size: 2 1014934 TGTGGACCAT 1014944 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1014985 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1015025 CTTTAATTCA Statistics Matches: 78, Mismatches: 0, Indels: 2 0.98 0.00 0.03 Matches are distributed among these distances: 1 1 0.01 2 77 0.99 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:1017369 original size:414 final size:411 Alignment explanation

Indices: 1016546--1017374 Score: 1523 Period size: 413 Copynumber: 2.0 Consensus size: 411 1016536 TACTCTGAAA ** 1016546 GTCAAAAGTCGAGTTGCAAATTAAACGAAATATAGAGAGCCCCCCCACCCCCATTAAATACTGAT 1 GTCAAAAGTCGAGTTGCAAATTAAACGAAATATAGAGAGCCCCCCCACCCCCACCAAATACTGAT * 1016611 AATGTTATCGAAAGTAATCATAATTAAGTTATCATGGTTACAAGAAGGAAAAGTAATCTTATGTA 66 AATGTAATCGAAAGTAATCATAATTAAGTTATCATGGTTACAAGAAGGAAAAGTAATCTTATGTA 1016676 ATCGATTACTCCTAAAATTGGATGTAATCGGTTTGTAATCAATTTATTTTAAAATCCAGAGTAAT 131 ATCGATTACTCCTAAAATTGGATGTAATCGGTTTGTAATCAATTTATTTTAAAATCCAGAGTAAT 1016741 TGTAATTTAATCGATTACTTTTGAAAGGAATCAACTACATCGCTTGTCACAATCAACGTTATTTC 196 TGTAATTTAATCGATTACTTTTGAAAGGAATCAACTACATCGCTTGTCACAATCAACGTTATTTC * * 1016806 TTATTTTCTAACGATACAATGGGTTAATTGAAGTTGAAAACACGTGTGAATGAAATCTAGGCATT 261 TTATCTTCTAACGATACAATGGGTTAATTGAAGCTGAAAACACGTGTGAATGAAATCTAGGCATT * 1016871 AAAATATGCTTTTTTGGCGTACTGATTGAAAGGTTACGATAAGTTTAACTATAAGATAACATTTA 326 AAAATATCCTTTTTTGGCGTACTGATTGAAAGGTTACGATAAGTTTAACTATAAGATAACATTTA 1016936 CGTACATTTATTTTTTCTTCT 391 CGTACATTTATTTTTTCTTCT * 1016957 GTCAAAAGTCGAGTTGCAAATTAAACGAAATATAGAGAGCCCCCCCCCCCCTCCACCAAATACTG 1 GTCAAAAGTCGAGTTGCAAATTAAACGAAATATAGAGAG-CCCCCCCACCC-CCACCAAATACTG 1017022 ATAATGTAATCGAAAGTAATCATAATTAAGTTATCATGGTTACAAGAAGGAAAAGTAATCTTATG 64 ATAATGTAATCGAAAGTAATCATAATTAAGTTATCATGGTTACAAGAAGGAAAAGTAATCTTATG 1017087 TAATCGATTACTCCTAAAATTGGATGTAATCGGTTTGTAATCAATTTATTTTAAAATCCAGAGTA 129 TAATCGATTACTCCTAAAATTGGATGTAATCGGTTTGTAATCAATTTATTTTAAAATCCAGAGTA * 1017152 ATTGTAATTTAATCGATTACTTTTGACAGGAATCAACTACATCGCTTGTCACAATCAACGGTTAT 194 ATTGTAATTTAATCGATTACTTTTGAAAGGAATCAACTACATCGCTTGTCACAATCAAC-GTTAT * * 1017217 TTCTTATCTTCTAATGATACAATGGGTTAATTGAAGCTGAACACACGTGTGAATGAAATCTAGGC 258 TTCTTATCTTCTAACGATACAATGGGTTAATTGAAGCTGAAAACACGTGTGAATGAAATCTAGGC * * 1017282 ATTGAAATATCCTTTTTTGGCGTACTGATTGAAAGGTTACGATAAGTTTAATTATAAGATAACAT 323 ATTAAAATATCCTTTTTTGGCGTACTGATTGAAAGGTTACGATAAGTTTAACTATAAGATAACAT 1017347 TTACGTACATTTATTTTTTCTTCT 388 TTACGTACATTTATTTTTTCTTCT 1017371 GTCA 1 GTCA 1017375 TTGATTTTTT Statistics Matches: 403, Mismatches: 12, Indels: 3 0.96 0.03 0.01 Matches are distributed among these distances: 411 39 0.10 412 10 0.02 413 198 0.49 414 156 0.39 ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34 Consensus pattern (411 bp): GTCAAAAGTCGAGTTGCAAATTAAACGAAATATAGAGAGCCCCCCCACCCCCACCAAATACTGAT AATGTAATCGAAAGTAATCATAATTAAGTTATCATGGTTACAAGAAGGAAAAGTAATCTTATGTA ATCGATTACTCCTAAAATTGGATGTAATCGGTTTGTAATCAATTTATTTTAAAATCCAGAGTAAT TGTAATTTAATCGATTACTTTTGAAAGGAATCAACTACATCGCTTGTCACAATCAACGTTATTTC TTATCTTCTAACGATACAATGGGTTAATTGAAGCTGAAAACACGTGTGAATGAAATCTAGGCATT AAAATATCCTTTTTTGGCGTACTGATTGAAAGGTTACGATAAGTTTAACTATAAGATAACATTTA CGTACATTTATTTTTTCTTCT Found at i:1020005 original size:21 final size:21 Alignment explanation

Indices: 1019976--1020050 Score: 62 Period size: 21 Copynumber: 3.6 Consensus size: 21 1019966 TATGCTATGC * * 1019976 TATGGTATGCGATTTAAATGA 1 TATGCTATGAGATTTAAATGA * 1019997 TATGCTATGAGATTTTAATGCA 1 TATGCTATGAGATTTAAATG-A * ** * 1020019 -ATACTATGAGATTTGTATGC 1 TATGCTATGAGATTTAAATGA * 1020039 TTTGCTATGAGA 1 TATGCTATGAGA 1020051 AATCGAAATG Statistics Matches: 43, Mismatches: 9, Indels: 4 0.77 0.16 0.07 Matches are distributed among these distances: 21 42 0.98 22 1 0.02 ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40 Consensus pattern (21 bp): TATGCTATGAGATTTAAATGA Found at i:1026208 original size:2 final size:2 Alignment explanation

Indices: 1026201--1026251 Score: 102 Period size: 2 Copynumber: 25.5 Consensus size: 2 1026191 GACCGAGCCC 1026201 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1026243 CT CT CT CT C 1 CT CT CT CT C 1026252 AACAGAATAA Statistics Matches: 49, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 49 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:1027130 original size:2 final size:2 Alignment explanation

Indices: 1027123--1027185 Score: 126 Period size: 2 Copynumber: 31.5 Consensus size: 2 1027113 CGCCTAAACG 1027123 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1027165 TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC T 1027186 TGTAAGGTGT Statistics Matches: 61, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 61 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:1028611 original size:4 final size:4 Alignment explanation

Indices: 1028602--1028643 Score: 50 Period size: 4 Copynumber: 10.8 Consensus size: 4 1028592 AAAGTTTACA * * * 1028602 GACG GACG GACG GACA GACA GACG GACA GACG GAC- GACG GAC 1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GAC 1028644 AAAATGTGAT Statistics Matches: 33, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 3 3 0.09 4 30 0.91 ACGTcount: A:0.33, C:0.26, G:0.40, T:0.00 Consensus pattern (4 bp): GACG Found at i:1030582 original size:2 final size:2 Alignment explanation

Indices: 1030577--1030642 Score: 132 Period size: 2 Copynumber: 33.0 Consensus size: 2 1030567 TTATATACGA 1030577 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1030619 CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT 1030643 TATTTTTTCT Statistics Matches: 64, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 64 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:1031157 original size:1 final size:1 Alignment explanation

Indices: 1031151--1031180 Score: 60 Period size: 1 Copynumber: 30.0 Consensus size: 1 1031141 TTAGACCGTC 1031151 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 1031181 NNNNNNNNNN Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 29 1.00 ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00 Consensus pattern (1 bp): T Found at i:1031246 original size:1 final size:1 Alignment explanation

Indices: 1031242--1031273 Score: 64 Period size: 1 Copynumber: 32.0 Consensus size: 1 1031232 TTTTAGCCGC 1031242 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 1031274 GGATTACAGG Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 31 1.00 ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00 Consensus pattern (1 bp): T Found at i:1048649 original size:112 final size:112 Alignment explanation

Indices: 1048452--1048782 Score: 565 Period size: 111 Copynumber: 3.0 Consensus size: 112 1048442 TCCCCCGATT * * 1048452 CACATACTCACACTCACAAACCAATTGACAGTGAGACTGCCTCCCTTCATACCCACCCACACACT 1 CACATACTCACACTCACAAACCAATTGACAGTGAGATTGCCTCCCTTCACACCCACCCACACACT * * * 1048517 TACCAATGAATGGTGCATCCTTGTCGTTGGGACCTGCCGCCCCTAGA 66 TACCAATGGATGGTGCATCCTTGTCGTTAGGACCCGCCGCCCCTAGA * 1048564 CACATACTCACACTCACAAACCAATTGACAGTGAGATTACCTCCCTTCACACCCACCCACACACT 1 CACATACTCACACTCACAAACCAATTGACAGTGAGATTGCCTCCCTTCACACCCACCCACACACT * * 1048629 TACCAATGGATAGTGCATCCTTGTCGTTAGGACCCGCTG-CCCTAGA 66 TACCAATGGATGGTGCATCCTTGTCGTTAGGACCCGCCGCCCCTAGA * 1048675 CACATACTCACACTCACAAACCAACTGACAGTGAGATTGCCTCCCTTCACACCCACCCACACACT 1 CACATACTCACACTCACAAACCAATTGACAGTGAGATTGCCTCCCTTCACACCCACCCACACACT * 1048740 TACCAATGGAGGGTGCATCCTTGTCGTTAGGACCCGCCGCCCC 66 TACCAATGGATGGTGCATCCTTGTCGTTAGGACCCGCCGCCCC 1048783 CTTCACACCC Statistics Matches: 205, Mismatches: 13, Indels: 2 0.93 0.06 0.01 Matches are distributed among these distances: 111 106 0.52 112 99 0.48 ACGTcount: A:0.27, C:0.37, G:0.15, T:0.21 Consensus pattern (112 bp): CACATACTCACACTCACAAACCAATTGACAGTGAGATTGCCTCCCTTCACACCCACCCACACACT TACCAATGGATGGTGCATCCTTGTCGTTAGGACCCGCCGCCCCTAGA Found at i:1057148 original size:101 final size:101 Alignment explanation

Indices: 1056965--1057168 Score: 336 Period size: 101 Copynumber: 2.0 Consensus size: 101 1056955 TCTGTAAAAC * * * * 1056965 AATCACAGAAAGAGAGTCACTGGTAAAGTACATTATAACTTGAAAAAAAAGATTTAAGGCAACAA 1 AATCAAAGAAAGAGAGTCACTGGTAAAATACATGATAACTTGAAAAAAAAGATTTAAGACAACAA * 1057030 ATAAAAAACAATGTATTGCTGCATACTGAGAAATGA 66 ATAAAAAAAAATGTATTGCTGCATACTGAGAAATGA * * 1057066 AATCAAAGAAAGAGTGTCACTGGTAAAATACATGATAACTTGACAAAAAAGATTTAAGACAACAA 1 AATCAAAGAAAGAGAGTCACTGGTAAAATACATGATAACTTGAAAAAAAAGATTTAAGACAACAA * 1057131 ATAAAAAAAAATTTATTGCTGCATACTGAGAAATGA 66 ATAAAAAAAAATGTATTGCTGCATACTGAGAAATGA 1057167 AA 1 AA 1057169 AATTGTGTAT Statistics Matches: 95, Mismatches: 8, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 101 95 1.00 ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22 Consensus pattern (101 bp): AATCAAAGAAAGAGAGTCACTGGTAAAATACATGATAACTTGAAAAAAAAGATTTAAGACAACAA ATAAAAAAAAATGTATTGCTGCATACTGAGAAATGA Found at i:1087310 original size:177 final size:177 Alignment explanation

Indices: 1087065--1087634 Score: 781 Period size: 177 Copynumber: 3.2 Consensus size: 177 1087055 ACTTGAAAGA ** * * * * * 1087065 CTTGGATGCTGAATCTGAGTCC-TAAATTCCAGATGCTGGAGGAGGTTAAGGTTGTTGGACCAGG 1 CTTGGATGCTGAATCTGAG-CCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGG * * * * * 1087129 TTAAAGTTTTTGTTGCAGGTGCCCTTTGAT-AGTAATATCTAAGTTACTGCTGGTCCGT-ACTTC 65 TTAAAGTTTTTGTTGCAGGTGCCCTCTGATGA-TTATATCTTAGTTACTACTTGTCC-TAACTTC * * * * 1087192 ACCAAACTTGCATTGATGGTGTGTCTTATGATACTGATGCACCAGGCAGG 128 ACCAGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCAGACAGG * * * 1087242 CTTGGATGCTGAATCTGAGCTATAGGTTACAGATGCTGAAGGAGGTTAAGGTTTTTAGAGCTGGT 1 CTTGGATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGT 1087307 TAAAGTTTTTGTTGCAGGTGCCCTCTGATGATTATATCTTAGTTACTACTTGTCCTAACTTCACC 66 TAAAGTTTTTGTTGCAGGTGCCCTCTGATGATTATATCTTAGTTACTACTTGTCCTAACTTCACC * 1087372 AGACTTCCATGGATGGTGTGTCTTATGCTACTGATGCACCAGACAGG 131 AGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCAGACAGG * 1087419 CTT-GATTGCTGAATCTGAGCCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGG 1 CTTGGA-TGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGG *** * * 1087483 TTAAAGTTTTTGAAACAGGTGCCCTCTGATGATTATATCTTAGTTATTACTTGTCCTAACTACAC 65 TTAAAGTTTTTGTTGCAGGTGCCCTCTGATGATTATATCTTAGTTACTACTTGTCCTAACTTCAC * * * 1087548 CGGACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCTGACA-G 130 CAGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCAGACAGG * * * 1087595 CTTGAATGCTGAGTCTGAGCCATAGGTTTCAGACGCTGGA 1 CTTGGATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGA 1087635 TATGGTTAAG Statistics Matches: 352, Mismatches: 36, Indels: 11 0.88 0.09 0.03 Matches are distributed among these distances: 176 39 0.11 177 312 0.89 178 1 0.00 ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33 Consensus pattern (177 bp): CTTGGATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGT TAAAGTTTTTGTTGCAGGTGCCCTCTGATGATTATATCTTAGTTACTACTTGTCCTAACTTCACC AGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCAGACAGG Found at i:1088558 original size:36 final size:32 Alignment explanation

Indices: 1088516--1088580 Score: 94 Period size: 36 Copynumber: 1.9 Consensus size: 32 1088506 TATTGCAAAA 1088516 TATAATATTGTATCCTATGATCGATATTGTATATTC 1 TATAATATTGTAT--TAT-AT-GATATTGTATATTC 1088552 TATAATATTGTATTATATGATATTGTATA 1 TATAATATTGTATTATATGATATTGTATA 1088581 ATATGATATT Statistics Matches: 29, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 32 11 0.38 33 2 0.07 34 3 0.10 36 13 0.45 ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49 Consensus pattern (32 bp): TATAATATTGTATTATATGATATTGTATATTC Found at i:1088574 original size:15 final size:15 Alignment explanation

Indices: 1088515--1088590 Score: 62 Period size: 15 Copynumber: 4.7 Consensus size: 15 1088505 ATATTGCAAA * 1088515 ATATAATATTGTATCCT 1 ATATGATATTGTAT--T 1088532 ATGATCGATATTGTATATT 1 AT-AT-GATATTG--TATT * * 1088551 CTATAATATTGTATT 1 ATATGATATTGTATT * 1088566 ATATGATATTGTATA 1 ATATGATATTGTATT 1088581 ATATGATATT 1 ATATGATATT 1088591 AGTTTCTGTA Statistics Matches: 49, Mismatches: 6, Indels: 10 0.75 0.09 0.15 Matches are distributed among these distances: 15 26 0.53 17 8 0.16 18 4 0.08 19 8 0.16 21 3 0.06 ACGTcount: A:0.36, C:0.05, G:0.11, T:0.49 Consensus pattern (15 bp): ATATGATATTGTATT Found at i:1088687 original size:15 final size:15 Alignment explanation

Indices: 1088556--1088703 Score: 73 Period size: 15 Copynumber: 9.1 Consensus size: 15 1088546 ATATTCTATA * 1088556 ATATTGTATTATATG 1 ATATTGTATAATATG 1088571 ATATTGTATAATATG 1 ATATTGTATAATATG * 1088586 ATATTAGTTTCTGTAATATAG 1 ATATT-G----TATAATAT-G * * * 1088607 A-ATTATATCACATG 1 ATATTGTATAATATG * * 1088621 AAAATGTATAATATG 1 ATATTGTATAATATG * * 1088636 ATACTGTAATATTATATA 1 ATATTGT-ATA--ATATG * * * 1088654 ACATTGTATCATACG 1 ATATTGTATAATATG 1088669 ATATTGTATAATATG 1 ATATTGTATAATATG 1088684 ATATTGGTTTATAATATG 1 ATATT-G--TATAATATG 1088702 AT 1 AT 1088704 GTATTATCGC Statistics Matches: 99, Mismatches: 21, Indels: 23 0.69 0.15 0.16 Matches are distributed among these distances: 14 2 0.02 15 58 0.59 16 5 0.05 17 2 0.02 18 20 0.20 20 10 0.10 21 2 0.02 ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44 Consensus pattern (15 bp): ATATTGTATAATATG Found at i:1088751 original size:98 final size:97 Alignment explanation

Indices: 1088552--1088769 Score: 248 Period size: 98 Copynumber: 2.2 Consensus size: 97 1088542 TTGTATATTC * * * 1088552 TATAATATTGTATTATATGATATTGTATAATATGATATTAGTTTCTGTAATATAGAATTATATCA 1 TATAATATTGTATCATATGATATTGTATAATATGATATTAGGTTCTATAATATAGAATTATATCA 1088617 CATGAAAATGTATAATATGATACTGTAATATTA 66 CATGAAAATGTATAATATGATACTGTAATA-TA * * * 1088650 TATAACATTGTATCATACGATATTGTATAATATGATATT-GGTT-TATAATATGATGTATTATCG 1 TATAATATTGTATCATATGATATTGTATAATATGATATTAGGTTCTATAATAT-A-GAATTAT-- * ** 1088713 CATCACATGAAATTGTATTGTATGAT-CTTGTAA-A-A 62 -ATCACATGAAAATGTATAATATGATAC-TGTAATATA * 1088748 TATATTATTGTATCATATGATA 1 TATAATATTGTATCATATGATA 1088770 CAATATGTAT Statistics Matches: 102, Mismatches: 12, Indels: 12 0.81 0.10 0.10 Matches are distributed among these distances: 96 7 0.07 97 4 0.04 98 62 0.61 100 2 0.02 101 27 0.26 ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44 Consensus pattern (97 bp): TATAATATTGTATCATATGATATTGTATAATATGATATTAGGTTCTATAATATAGAATTATATCA CATGAAAATGTATAATATGATACTGTAATATA Found at i:1090867 original size:21 final size:21 Alignment explanation

Indices: 1090843--1090896 Score: 108 Period size: 21 Copynumber: 2.6 Consensus size: 21 1090833 ATTTTAATAA 1090843 TATGCTATGAGATTTGTATGC 1 TATGCTATGAGATTTGTATGC 1090864 TATGCTATGAGATTTGTATGC 1 TATGCTATGAGATTTGTATGC 1090885 TATGCTATGAGA 1 TATGCTATGAGA 1090897 AATTGAAATG Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 33 1.00 ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41 Consensus pattern (21 bp): TATGCTATGAGATTTGTATGC Found at i:1090878 original size:42 final size:42 Alignment explanation

Indices: 1090817--1090896 Score: 108 Period size: 42 Copynumber: 1.9 Consensus size: 42 1090807 AAATTTATGC * * 1090817 TATGCTATGGTATGCGATTT-TAATAATATGCTATGAGATTTG 1 TATGCTATGCTATGAGATTTGT-ATAATATGCTATGAGATTTG ** 1090859 TATGCTATGCTATGAGATTTGTATGCTATGCTATGAGA 1 TATGCTATGCTATGAGATTTGTATAATATGCTATGAGA 1090897 AATTGAAATG Statistics Matches: 33, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 42 32 0.97 43 1 0.03 ACGTcount: A:0.28, C:0.09, G:0.23, T:0.41 Consensus pattern (42 bp): TATGCTATGCTATGAGATTTGTATAATATGCTATGAGATTTG Found at i:1091167 original size:21 final size:21 Alignment explanation

Indices: 1091141--1091216 Score: 125 Period size: 21 Copynumber: 3.6 Consensus size: 21 1091131 ATGAGAGTGT * * 1091141 ATGCTATGGTATGAGATTCCA 1 ATGCTATGCTATGAGATTTCA 1091162 ATGCTATGCTATGAGATTTCA 1 ATGCTATGCTATGAGATTTCA * 1091183 ACGCTATGCTATGAGATTTCA 1 ATGCTATGCTATGAGATTTCA 1091204 ATGCTATGCTATG 1 ATGCTATGCTATG 1091217 CTATGGTGTA Statistics Matches: 51, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 21 51 1.00 ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36 Consensus pattern (21 bp): ATGCTATGCTATGAGATTTCA Found at i:1091563 original size:10 final size:10 Alignment explanation

Indices: 1091534--1091576 Score: 52 Period size: 10 Copynumber: 4.4 Consensus size: 10 1091524 TTGCGTAAAT 1091534 TATATTA-TG 1 TATATTATTG * * 1091543 TAAAGTATTG 1 TATATTATTG * 1091553 TTTATTATTG 1 TATATTATTG 1091563 TATATTATTG 1 TATATTATTG 1091573 TATA 1 TATA 1091577 ATATGATATT Statistics Matches: 27, Mismatches: 6, Indels: 1 0.79 0.18 0.03 Matches are distributed among these distances: 9 5 0.19 10 22 0.81 ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56 Consensus pattern (10 bp): TATATTATTG Found at i:1095800 original size:2 final size:2 Alignment explanation

Indices: 1095793--1095838 Score: 92 Period size: 2 Copynumber: 23.0 Consensus size: 2 1095783 CAGGTACCGG 1095793 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1095835 TC TC 1 TC TC 1095839 GGGGTAGGGG Statistics Matches: 44, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 44 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:1100281 original size:27 final size:27 Alignment explanation

Indices: 1100248--1100409 Score: 236 Period size: 27 Copynumber: 6.0 Consensus size: 27 1100238 TCATCCCCAG * 1100248 GATCGTCTGCTTCCACTTCTAGATCCC 1 GATCGTCTGCCTCCACTTCTAGATCCC * 1100275 GATCGTCTGCTTCCACTTCTAGATCCC 1 GATCGTCTGCCTCCACTTCTAGATCCC * 1100302 GATCGGCTGCCTCCACTTCTAGATCCC 1 GATCGTCTGCCTCCACTTCTAGATCCC * 1100329 GATCGTCTGCTTCCACTTCTAGATCCC 1 GATCGTCTGCCTCCACTTCTAGATCCC * * 1100356 CATCGGCTGCCTCCACTTCTAGATCCC 1 GATCGTCTGCCTCCACTTCTAGATCCC ** 1100383 CTTCGGT-TGCCTCCACTTCTAGATCCC 1 GATC-GTCTGCCTCCACTTCTAGATCCC 1100410 CCTCGTATCC Statistics Matches: 125, Mismatches: 9, Indels: 2 0.92 0.07 0.01 Matches are distributed among these distances: 27 124 0.99 28 1 0.01 ACGTcount: A:0.14, C:0.40, G:0.15, T:0.31 Consensus pattern (27 bp): GATCGTCTGCCTCCACTTCTAGATCCC Found at i:1100394 original size:81 final size:81 Alignment explanation

Indices: 1100248--1100409 Score: 270 Period size: 81 Copynumber: 2.0 Consensus size: 81 1100238 TCATCCCCAG * * * * 1100248 GATCGTCTGCTTCCACTTCTAGATCCCGATCGTCTGCTTCCACTTCTAGATCCCGATCGGCTGCC 1 GATCGTCTGCTTCCACTTCTAGATCCCCATCGGCTGCCTCCACTTCTAGATCCCCATCGGCTGCC 1100313 TCCACTTCTAGATCCC 66 TCCACTTCTAGATCCC * * 1100329 GATCGTCTGCTTCCACTTCTAGATCCCCATCGGCTGCCTCCACTTCTAGATCCCCTTCGGTTGCC 1 GATCGTCTGCTTCCACTTCTAGATCCCCATCGGCTGCCTCCACTTCTAGATCCCCATCGGCTGCC 1100394 TCCACTTCTAGATCCC 66 TCCACTTCTAGATCCC 1100410 CCTCGTATCC Statistics Matches: 75, Mismatches: 6, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 81 75 1.00 ACGTcount: A:0.14, C:0.40, G:0.15, T:0.31 Consensus pattern (81 bp): GATCGTCTGCTTCCACTTCTAGATCCCCATCGGCTGCCTCCACTTCTAGATCCCCATCGGCTGCC TCCACTTCTAGATCCC Found at i:1100482 original size:18 final size:18 Alignment explanation

Indices: 1100441--1100593 Score: 114 Period size: 18 Copynumber: 8.6 Consensus size: 18 1100431 GGTCTACGTC * * * 1100441 TGGGTTTCCTAGGGGGGT 1 TGGGTTTTCTTGGGGGAT * * 1100459 TTGGTTTTCTTGGTGGAT 1 TGGGTTTTCTTGGGGGAT * * 1100477 TGGG-TTTCCTGGGGGGT 1 TGGGTTTTCTTGGGGGAT * * 1100494 TGGGTTTCCTAGGGGGAT 1 TGGGTTTTCTTGGGGGAT ** * 1100512 TGGGTTCCCTGGGGGGAT 1 TGGGTTTTCTTGGGGGAT * 1100530 TGGG-TTTCCTGAGGGGAT 1 TGGGTTTTCTTG-GGGGAT * * 1100548 TGGGTTTCCTAGGGGGAT 1 TGGGTTTTCTTGGGGGAT * 1100566 TGGG-TTTCTTGGGAGCAT 1 TGGGTTTTCTTGGG-GGAT * 1100584 CGGGTTTTCT 1 TGGGTTTTCT 1100594 GTCGGGTTTA Statistics Matches: 104, Mismatches: 26, Indels: 9 0.75 0.19 0.06 Matches are distributed among these distances: 17 24 0.23 18 71 0.68 19 9 0.09 ACGTcount: A:0.07, C:0.12, G:0.44, T:0.37 Consensus pattern (18 bp): TGGGTTTTCTTGGGGGAT Found at i:1100484 original size:17 final size:17 Alignment explanation

Indices: 1100453--1100578 Score: 126 Period size: 18 Copynumber: 7.2 Consensus size: 17 1100443 GGTTTCCTAG * * 1100453 GGGGGTTTGGTTTTCTT 1 GGGGGATTGGGTTTCTT * * 1100470 GGTGGATTGGGTTTCCT 1 GGGGGATTGGGTTTCTT * * 1100487 GGGGGGTTGGGTTTCCTA 1 GGGGGATTGGGTTT-CTT * * 1100505 GGGGGATTGGGTTCCCTG 1 GGGGGATTGGGTT-TCTT * 1100523 GGGGGATTGGGTTTCCT 1 GGGGGATTGGGTTTCTT * 1100540 GAGGGGATTGGGTTTCCTA 1 G-GGGGATTGGGTTT-CTT 1100559 GGGGGATTGGGTTTCTT 1 GGGGGATTGGGTTTCTT 1100576 GGG 1 GGG 1100579 AGCATCGGGT Statistics Matches: 88, Mismatches: 17, Indels: 8 0.78 0.15 0.07 Matches are distributed among these distances: 17 32 0.36 18 54 0.61 19 2 0.02 ACGTcount: A:0.06, C:0.10, G:0.47, T:0.37 Consensus pattern (17 bp): GGGGGATTGGGTTTCTT Found at i:1100492 original size:36 final size:35 Alignment explanation

Indices: 1100441--1100578 Score: 179 Period size: 36 Copynumber: 3.9 Consensus size: 35 1100431 GGTCTACGTC * * * 1100441 TGGGTTTCCTAGGGGGGTTTGGTTTTCTTGGTGGAT 1 TGGGTTTCCT-GGGGGGATTGGGTTTCTTGGGGGAT * 1100477 TGGGTTTCCTGGGGGG-TTGGGTTTCCTAGGGGGAT 1 TGGGTTTCCTGGGGGGATTGGGTTT-CTTGGGGGAT * * 1100512 TGGGTTCCCTGGGGGGATTGGGTTTCCTGAGGGGAT 1 TGGGTTTCCTGGGGGGATTGGGTTTCTTG-GGGGAT * 1100548 TGGGTTTCCTAGGGGGATTGGGTTTCTTGGG 1 TGGGTTTCCTGGGGGGATTGGGTTTCTTGGG 1100579 AGCATCGGGT Statistics Matches: 90, Mismatches: 9, Indels: 7 0.85 0.08 0.07 Matches are distributed among these distances: 34 7 0.08 35 33 0.37 36 50 0.56 ACGTcount: A:0.07, C:0.11, G:0.46, T:0.37 Consensus pattern (35 bp): TGGGTTTCCTGGGGGGATTGGGTTTCTTGGGGGAT Found at i:1100530 original size:53 final size:54 Alignment explanation

Indices: 1100441--1100571 Score: 192 Period size: 53 Copynumber: 2.4 Consensus size: 54 1100431 GGTCTACGTC * * ** * * * 1100441 TGGGTTTCCTAGGGGGGTTTGGTTTTCTTGGTGGATTGGGTTTCCTG-GGGGGT 1 TGGGTTTCCTAGGGGGATTGGGTTCCCTGGGGGGATTGGGTTTCCTGAGGGGAT 1100494 TGGGTTTCCTAGGGGGATTGGGTTCCCTGGGGGGATTGGGTTTCCTGAGGGGAT 1 TGGGTTTCCTAGGGGGATTGGGTTCCCTGGGGGGATTGGGTTTCCTGAGGGGAT 1100548 TGGGTTTCCTAGGGGGATTGGGTT 1 TGGGTTTCCTAGGGGGATTGGGTT 1100572 TCTTGGGAGC Statistics Matches: 70, Mismatches: 7, Indels: 1 0.90 0.09 0.01 Matches are distributed among these distances: 53 41 0.59 54 29 0.41 ACGTcount: A:0.07, C:0.11, G:0.46, T:0.37 Consensus pattern (54 bp): TGGGTTTCCTAGGGGGATTGGGTTCCCTGGGGGGATTGGGTTTCCTGAGGGGAT Found at i:1100719 original size:90 final size:90 Alignment explanation

Indices: 1100562--1101193 Score: 1066 Period size: 90 Copynumber: 7.0 Consensus size: 90 1100552 TTTCCTAGGG * * ** * 1100562 GGATTGGGTTTCTTGGGAGCATCGGGTTTTCTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT 1 GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT * 1100627 AAGCTTCGGATAATCGTCGGGGTTA 66 AAGCTTCGGATAATCGTCGGGTTTA * * * 1100652 GTATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGGTTAGGACTTGCATAATCGTCGGGGGT 1 GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT 1100717 AAGCTTCGGATAATCGTCGGGTTTA 66 AAGCTTCGGATAATCGTCGGGTTTA * * * 1100742 GGATTGGCTTTCTTGGAAGCATCACGTTTACTGTCGGGGTTAGGACTTGCATAATCGTCGGGGGT 1 GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT 1100807 AAGCTTCGGATAATCGTCGGGTTTA 66 AAGCTTCGGATAATCGTCGGGTTTA * 1100832 GGATTGGCTTTCTTGGAAGCATCACGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT 1 GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT 1100897 AAGCTTCGGATAATCGTCGGGTTTA 66 AAGCTTCGGATAATCGTCGGGTTTA * * 1100922 GGATTGGCATTCTTGGAAGCATCAAGTTTACTGTCGGCTTTAGGACTTGCATAATCGTCGGGTGT 1 GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT 1100987 AAGCTTCGGATAATCGTCGGGTTTA 66 AAGCTTCGGATAATCGTCGGGTTTA * * 1101012 GTATTGGCTTTCTTGGAAGCATCACGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT 1 GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT 1101077 AAGCTTCGGATAATCGTCGGGTTTA 66 AAGCTTCGGATAATCGTCGGGTTTA * * 1101102 GTATTGGCTTTCTTGGAAGCATCAAGTTAACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT 1 GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT * * * 1101167 ATGCTTCGGATAATCGTAGAGTTTA 66 AAGCTTCGGATAATCGTCGGGTTTA 1101192 GG 1 GG 1101194 TTTAGGGTTA Statistics Matches: 516, Mismatches: 26, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 90 516 1.00 ACGTcount: A:0.19, C:0.16, G:0.31, T:0.34 Consensus pattern (90 bp): GGATTGGCTTTCTTGGAAGCATCAAGTTTACTGTCGGGTTTAGGACTTGCATAATCGTCGGGTGT AAGCTTCGGATAATCGTCGGGTTTA Found at i:1104454 original size:13 final size:13 Alignment explanation

Indices: 1104432--1104474 Score: 50 Period size: 13 Copynumber: 3.3 Consensus size: 13 1104422 TACTTGCTAG * 1104432 AAAAAGAAAAAAC 1 AAAAACAAAAAAC 1104445 AAAAACAAAAAAC 1 AAAAACAAAAAAC * * * 1104458 AAATACCAAAAAT 1 AAAAACAAAAAAC 1104471 AAAA 1 AAAA 1104475 TAAAAAGGGT Statistics Matches: 25, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 13 25 1.00 ACGTcount: A:0.81, C:0.12, G:0.02, T:0.05 Consensus pattern (13 bp): AAAAACAAAAAAC Found at i:1111923 original size:2 final size:2 Alignment explanation

Indices: 1111916--1111959 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 1111906 TAAAGACTGA 1111916 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1111958 TC 1 TC 1111960 GTTTTAATGT Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:1118514 original size:31 final size:31 Alignment explanation

Indices: 1118472--1118531 Score: 102 Period size: 31 Copynumber: 1.9 Consensus size: 31 1118462 TAGTAACTTT * 1118472 TATCAAGTCTGTAAAAACATTGACCCAGTTC 1 TATCAACTCTGTAAAAACATTGACCCAGTTC * 1118503 TATCAACTCTGTATAAACATTGACCCAGT 1 TATCAACTCTGTAAAAACATTGACCCAGT 1118532 CACCAGCAGC Statistics Matches: 27, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 31 27 1.00 ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30 Consensus pattern (31 bp): TATCAACTCTGTAAAAACATTGACCCAGTTC Done.