Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold1267

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: 1050379
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.28

Warning! 150710 characters in sequence are not A, C, G, or T


File 3 of 4

Found at i:438819 original size:10 final size:10

Alignment explanation

Indices: 438793--438872 Score: 81 Period size: 8 Copynumber: 9.0 Consensus size: 10 438783 AGATATTTGC 438793 CAAAA-AAAA 1 CAAAACAAAA * 438802 -AAACCAAAA 1 CAAAACAAAA 438811 CAAAACAAAA 1 CAAAACAAAA 438821 CAAAACAAAA 1 CAAAACAAAA 438831 CAAAAC-AAA 1 CAAAACAAAA 438840 C-AAACAAAA 1 CAAAACAAAA 438849 -AAAA-AAAA 1 CAAAACAAAA 438857 -AAAA-AAAA 1 CAAAACAAAA 438865 -AAAA-AAAA 1 CAAAACAAAA 438873 AAGGGTTTAA Statistics Matches: 65, Mismatches: 2, Indels: 9 0.86 0.03 0.12 Matches are distributed among these distances: 8 27 0.42 9 14 0.22 10 24 0.37 ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00 Consensus pattern (10 bp): CAAAACAAAA Found at i:438885 original size:1 final size:1 Alignment explanation

Indices: 438794--438874 Score: 72 Period size: 1 Copynumber: 81.0 Consensus size: 1 438784 GATATTTGCC ** * * * * * * * * 438794 AAAAAAAAAAACCAAAACAAAACAAAACAAAACAAAACAAAACAAACAAACAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 438859 AAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAA 438875 GGGTTTAAAA Statistics Matches: 62, Mismatches: 18, Indels: 0 0.77 0.22 0.00 Matches are distributed among these distances: 1 62 1.00 ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:438897 original size:1 final size:1 Alignment explanation

Indices: 438893--438926 Score: 68 Period size: 1 Copynumber: 34.0 Consensus size: 1 438883 AAATTTGGGG 438893 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 438927 CGTGTATTAA Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 33 1.00 ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:447984 original size:24 final size:23 Alignment explanation

Indices: 447954--448029 Score: 62 Period size: 24 Copynumber: 3.2 Consensus size: 23 447944 AAAACATAAA * 447954 ACATTACATTGTGCATTATATTAT 1 ACATTACATTG-GCATTACATTAT * * 447978 AGATTACAGTAGGCATTACATTAT 1 ACATTACA-TTGGCATTACATTAT * * ** 448002 ACATTTCATTATGTGTTACATTAT 1 ACATTACATT-GGCATTACATTAT 448026 ACAT 1 ACAT 448030 CTCATCATGA Statistics Matches: 41, Mismatches: 9, Indels: 4 0.76 0.17 0.07 Matches are distributed among these distances: 23 1 0.02 24 38 0.93 25 2 0.05 ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42 Consensus pattern (23 bp): ACATTACATTGGCATTACATTAT Found at i:448006 original size:12 final size:12 Alignment explanation

Indices: 447954--448029 Score: 53 Period size: 12 Copynumber: 6.3 Consensus size: 12 447944 AAAACATAAA * 447954 ACATTACATTGT 1 ACATTACATTAT * * 447966 GCATTATATTAT 1 ACATTACATTAT * * * 447978 AGATTACAGTAG 1 ACATTACATTAT * 447990 GCATTACATTAT 1 ACATTACATTAT * 448002 ACATTTCATTAT 1 ACATTACATTAT *** 448014 GTGTTACATTAT 1 ACATTACATTAT 448026 ACAT 1 ACAT 448030 CTCATCATGA Statistics Matches: 43, Mismatches: 21, Indels: 0 0.67 0.33 0.00 Matches are distributed among these distances: 12 43 1.00 ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42 Consensus pattern (12 bp): ACATTACATTAT Found at i:448714 original size:11 final size:11 Alignment explanation

Indices: 448698--448734 Score: 56 Period size: 11 Copynumber: 3.4 Consensus size: 11 448688 ATATTGTGTA 448698 TTTTCAATTAC 1 TTTTCAATTAC 448709 TTTTCAATTAC 1 TTTTCAATTAC * * 448720 ATCTCAATTAC 1 TTTTCAATTAC 448731 TTTT 1 TTTT 448735 TTCCAAGTTT Statistics Matches: 22, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 11 22 1.00 ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54 Consensus pattern (11 bp): TTTTCAATTAC Found at i:449329 original size:32 final size:32 Alignment explanation

Indices: 449272--449338 Score: 100 Period size: 32 Copynumber: 2.1 Consensus size: 32 449262 AAATAAAACT * 449272 AAAGTAATTGAAATGTAATTAATTACATTTATC 1 AAAGTAATTGAAATGAAATTAATTACATTT-TC * 449305 AAAGTAATTGAGA-GAAATTAATTACATTTTC 1 AAAGTAATTGAAATGAAATTAATTACATTTTC 449336 AAA 1 AAA 449339 AATCAATGTA Statistics Matches: 32, Mismatches: 2, Indels: 2 0.89 0.06 0.06 Matches are distributed among these distances: 31 5 0.16 32 15 0.47 33 12 0.38 ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36 Consensus pattern (32 bp): AAAGTAATTGAAATGAAATTAATTACATTTTC Found at i:451589 original size:11 final size:11 Alignment explanation

Indices: 451573--451612 Score: 55 Period size: 11 Copynumber: 3.7 Consensus size: 11 451563 TAAGCAAGTC 451573 CTTAAAGGTGG 1 CTTAAAGGTGG * 451584 CTTAAAGGTGA 1 CTTAAAGGTGG * 451595 CTTAAAGG-AG 1 CTTAAAGGTGG 451605 CTTAAAGG 1 CTTAAAGG 451613 CTATACAACC Statistics Matches: 26, Mismatches: 3, Indels: 1 0.87 0.10 0.03 Matches are distributed among these distances: 10 8 0.31 11 18 0.69 ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25 Consensus pattern (11 bp): CTTAAAGGTGG Found at i:451728 original size:10 final size:11 Alignment explanation

Indices: 451682--451732 Score: 77 Period size: 11 Copynumber: 4.7 Consensus size: 11 451672 TGTCCAAACG 451682 TCTTTAAGCCA 1 TCTTTAAGCCA * 451693 CCTTTAAGCCA 1 TCTTTAAGCCA * 451704 CCTTTAAGCCA 1 TCTTTAAGCCA 451715 TCTTTAAG-CA 1 TCTTTAAGCCA 451725 TCTTTAAG 1 TCTTTAAG 451733 TGGCATTTAC Statistics Matches: 38, Mismatches: 2, Indels: 1 0.93 0.05 0.02 Matches are distributed among these distances: 10 10 0.26 11 28 0.74 ACGTcount: A:0.27, C:0.27, G:0.10, T:0.35 Consensus pattern (11 bp): TCTTTAAGCCA Found at i:451782 original size:22 final size:22 Alignment explanation

Indices: 451725--451782 Score: 64 Period size: 22 Copynumber: 2.6 Consensus size: 22 451715 TCTTTAAGCA * * 451725 TCTTTAAGTGGCATTTACGCTC 1 TCTTTAAGTGGCCTTTACACTC * * 451747 TCTTTACACT-GCCTTTACACTG 1 TCTTTA-AGTGGCCTTTACACTC 451769 TCTTTAAGTGGCCT 1 TCTTTAAGTGGCCT 451783 ATAAGTCAAT Statistics Matches: 29, Mismatches: 5, Indels: 4 0.76 0.13 0.11 Matches are distributed among these distances: 21 2 0.07 22 25 0.86 23 2 0.07 ACGTcount: A:0.17, C:0.26, G:0.16, T:0.41 Consensus pattern (22 bp): TCTTTAAGTGGCCTTTACACTC Found at i:452121 original size:2 final size:2 Alignment explanation

Indices: 452116--452161 Score: 83 Period size: 2 Copynumber: 23.0 Consensus size: 2 452106 GTGAAAAAAA * 452116 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TA 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 452158 TC TC 1 TC TC 452162 AGTTCATCCG Statistics Matches: 42, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.02, C:0.48, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:452573 original size:112 final size:112 Alignment explanation

Indices: 452376--452598 Score: 392 Period size: 112 Copynumber: 2.0 Consensus size: 112 452366 AGTTTTGTTC * * 452376 GTTTGTGTATATCTAATTAGAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA 1 GTTTGTGTACATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA * * 452441 GAATATACAAGATATACACAACAGTTGTGTCGTGTGCCAAGGTGCAT 66 GAATATACAAGATATACACAACAGGTGTGTCATGTGCCAAGGTGCAT * 452488 GTTTGTGTACATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACTCCTGGAACTAACACA 1 GTTTGTGTACATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA * 452553 GAATATACAAGATATACACAACAGGTGTGTCATGTGCCCAGGTGCA 66 GAATATACAAGATATACACAACAGGTGTGTCATGTGCCAAGGTGCA 452599 CGTCAGGGTT Statistics Matches: 105, Mismatches: 6, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 112 105 1.00 ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30 Consensus pattern (112 bp): GTTTGTGTACATCTAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACACA GAATATACAAGATATACACAACAGGTGTGTCATGTGCCAAGGTGCAT Found at i:453636 original size:11 final size:11 Alignment explanation

Indices: 453622--453673 Score: 86 Period size: 11 Copynumber: 4.7 Consensus size: 11 453612 TTTTTTAATT 453622 GCTTAAAGGTG 1 GCTTAAAGGTG * 453633 GCTTAAAGGTA 1 GCTTAAAGGTG 453644 GCTTAAAGGTG 1 GCTTAAAGGTG * 453655 GCTTAGAGGTG 1 GCTTAAAGGTG 453666 GCTTAAAG 1 GCTTAAAG 453674 AAGTTTGGAC Statistics Matches: 37, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 11 37 1.00 ACGTcount: A:0.29, C:0.10, G:0.35, T:0.27 Consensus pattern (11 bp): GCTTAAAGGTG Found at i:453793 original size:11 final size:11 Alignment explanation

Indices: 453777--453808 Score: 55 Period size: 11 Copynumber: 2.9 Consensus size: 11 453767 GCAATACATA 453777 TAGCTTAAAGG 1 TAGCTTAAAGG 453788 TAGCTTAAAGG 1 TAGCTTAAAGG * 453799 TGGCTTAAAG 1 TAGCTTAAAG 453809 ATCGTCTTTA Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 20 1.00 ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28 Consensus pattern (11 bp): TAGCTTAAAGG Found at i:453830 original size:11 final size:11 Alignment explanation

Indices: 453814--453852 Score: 53 Period size: 11 Copynumber: 3.6 Consensus size: 11 453804 TAAAGATCGT 453814 CTTTAAGCTAC 1 CTTTAAGCTAC * 453825 CTTTAAAC-AC 1 CTTTAAGCTAC * 453835 CTTTAAGCTAT 1 CTTTAAGCTAC 453846 CTTTAAG 1 CTTTAAG 453853 GAGGGCTTAA Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 10 9 0.38 11 15 0.62 ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38 Consensus pattern (11 bp): CTTTAAGCTAC Found at i:464889 original size:440 final size:441 Alignment explanation

Indices: 464053--465304 Score: 2062 Period size: 440 Copynumber: 2.8 Consensus size: 441 464043 CCGTAACTTA * 464053 AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGGAGTGCAC 1 AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTAAGAAGGAGTGCAC * 464118 GCCACCAAAAGTTTTGACTTTGACCTATTTT-TTGTTTCAAGGTCAAGCTTTTCATAAAAAATAT 66 GCCACCAAAAGTTTTGACCTTGACCTATTTTGTT-TTTCAAGGTCAAGCTTTTCATAAAAAATAT * 464182 TGTCCT-GACCATAACACAATACTCCTTTAACATACAGACTTTTAACTTGTATCATAGATAGATG 130 TGT-CTGGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCATAGATAGATG * * * * 464246 GTATATAACGTAGTTAAACCTTGACAAAATTTTTGACCTTAACCTAGAATTTTTATTTCAAGGTC 194 GTATATAACCTAGTTGAACCTTAACAAAATTTTTGACCTTGACCTAGAATTTTTATTTCAAGGTC * * * * 464311 ATATTTGAAAAAACTTCATTGTTTAACTTCTGAATATACTTTGACAGAAGGACTTCAAACTTTAT 259 ATATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAACTTTAA * 464376 ACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTGACCTTTACCTTGTTTTA 324 ACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTGACCTTGACCTTGTTTTA * * 464441 CTCAAGGTCAAATTAAGAAAAAAATAATAAAAATTTGTCTGGGTCATAAATTT 389 CGCAAGGTCAAATGAAGAAAAAAATAATAAAAATTTGTCTGGGTCATAAATTT * * * * 464494 AATACCCTTTGCCA-TAAGACTTCAAACTTGGAAGATTGGTGGATGGTATTAAGAAGGAGTGCAC 1 AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTAAGAAGGAGTGCAC 464558 GCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTCATAAAAAATATT 66 GCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTCATAAAAAATATT 464623 GTCTGGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCATAGATAGATGGT 131 GTCTGGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCATAGATAGATGGT ** 464688 ATATAACCTAGTTGAACCTTAACAAAAAATTTGACCTTGACCTAGAATTTTTATTTCAAGGTCAT 196 ATATAACCTAGTTGAACCTTAACAAAATTTTTGACCTTGACCTAGAATTTTTATTTCAAGGTCAT * 464753 ATTAAAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAACTTTAAAC 261 ATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAACTTTAAAC * * 464818 AAAGAACAATGATAATACACTTAGGTGTACTTTTGAATAATATTTGACCTTGACCTTGTTTTACG 326 AAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTGACCTTGACCTTGTTTTACG * ** * 464883 CAAGGTCAAATGAAGAAAAAAGTAATAAATTTTTGTCTGGGTCATAATTTT 391 CAAGGTCAAATGAAGAAAAAAATAATAAAAATTTGTCTGGGTCATAAATTT * * 464934 AATACCCTTTGACATTAAGACTTCAAACTTGGAACATGGGTAGATGGTATTTAGAAGGAGTGCAC 1 AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTAAGAAGGAGTGCAC * * * 464999 GCCACCAAAAGTTTTGACCTTGACCTTTTTTGTGTTTCAAAGTCAAGCTTTTCATAAAAAATATT 66 GCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTCATAAAAAATATT * * 465064 GTCCGGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATC-TTGAATAGATGG 131 GTCTGGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCATAG-ATAGATGG * * * ** * 465128 TATATAACCTAGTTGAACCGTACCAAAATTTTTGACCTTGACCTAAAAAATTTATTTCAAAGTCA 195 TATATAACCTAGTTGAACCTTAACAAAATTTTTGACCTTGACCTAGAATTTTTATTTCAAGGTCA * 465193 AATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAACTTTAAA 260 TATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAACTTTAAA * * 465258 CAAAGAACAATAATATTACACTTAGGTGTGCTATTGAATAATATTTG 325 CAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTG 465305 TTAAATTTGC Statistics Matches: 756, Mismatches: 51, Indels: 8 0.93 0.06 0.01 Matches are distributed among these distances: 439 2 0.00 440 409 0.54 441 345 0.46 ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33 Consensus pattern (441 bp): AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTAAGAAGGAGTGCAC GCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTCATAAAAAATATT GTCTGGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCATAGATAGATGGT ATATAACCTAGTTGAACCTTAACAAAATTTTTGACCTTGACCTAGAATTTTTATTTCAAGGTCAT ATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGGACTTCAAACTTTAAAC AAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTGACCTTGACCTTGTTTTACG CAAGGTCAAATGAAGAAAAAAATAATAAAAATTTGTCTGGGTCATAAATTT Found at i:470763 original size:13 final size:12 Alignment explanation

Indices: 470737--470771 Score: 52 Period size: 13 Copynumber: 2.8 Consensus size: 12 470727 TGTTTTGGGA 470737 TTTTTGGGGGTT 1 TTTTTGGGGGTT * 470749 TTTTTGGGGTTTT 1 TTTTTGGGG-GTT 470762 TTTTTGGGGG 1 TTTTTGGGGG 470772 GGGGGGGCTT Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 12 9 0.45 13 11 0.55 ACGTcount: A:0.00, C:0.00, G:0.40, T:0.60 Consensus pattern (12 bp): TTTTTGGGGGTT Found at i:470885 original size:2 final size:2 Alignment explanation

Indices: 470878--470930 Score: 106 Period size: 2 Copynumber: 26.5 Consensus size: 2 470868 ATCGAATTAA 470878 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 470920 AG AG AG AG AG A 1 AG AG AG AG AG A 470931 TTGCCAGTTT Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:474460 original size:30 final size:30 Alignment explanation

Indices: 474425--474500 Score: 116 Period size: 30 Copynumber: 2.5 Consensus size: 30 474415 AATACGTTGC * 474425 CGGTCCAATAGATCGCACTCTATTGACCGG 1 CGGTCCAATAGATCGAACTCTATTGACCGG * * 474455 TGGTCCAATAGATCGAAGTCTATTGACCGG 1 CGGTCCAATAGATCGAACTCTATTGACCGG * 474485 CAGTCCAATAGATCGA 1 CGGTCCAATAGATCGA 474501 GACCAGCGGT Statistics Matches: 41, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 30 41 1.00 ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24 Consensus pattern (30 bp): CGGTCCAATAGATCGAACTCTATTGACCGG Found at i:480869 original size:16 final size:16 Alignment explanation

Indices: 480848--480878 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 480838 CACGATTGCA * 480848 CAGACAGACGGACGGG 1 CAGACAGACAGACGGG 480864 CAGACAGACAGACGG 1 CAGACAGACAGACGG 480879 ACAAGGGGTT Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.35, C:0.26, G:0.39, T:0.00 Consensus pattern (16 bp): CAGACAGACAGACGGG Found at i:482238 original size:2 final size:2 Alignment explanation

Indices: 482231--482265 Score: 70 Period size: 2 Copynumber: 17.5 Consensus size: 2 482221 ACGCCTTAAA 482231 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 C 482266 ATATGAAGAT Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 33 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:484132 original size:31 final size:32 Alignment explanation

Indices: 484096--484204 Score: 107 Period size: 34 Copynumber: 3.4 Consensus size: 32 484086 TATTCCTGGT * * 484096 ACGACTTAACAAAATCC-GAATGATTTTAAGC 1 ACGACTTAACAAAATCCTGAATGATTTCAAGA *** 484127 ACGACTTAACAAAATCCTTCCTGATTTCAAGA 1 ACGACTTAACAAAATCCTGAATGATTTCAAGA * 484159 ACGACTTAACAAAAAAAT-CTGAATG-TGTTCAAGT 1 ACGACTTAAC---AAAATCCTGAATGAT-TTCAAGA 484193 ACGACTTAACAA 1 ACGACTTAACAA 484205 TTATTTTTGG Statistics Matches: 64, Mismatches: 9, Indels: 10 0.77 0.11 0.12 Matches are distributed among these distances: 31 19 0.30 32 19 0.30 33 1 0.02 34 20 0.31 35 5 0.08 ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26 Consensus pattern (32 bp): ACGACTTAACAAAATCCTGAATGATTTCAAGA Found at i:484163 original size:32 final size:31 Alignment explanation

Indices: 484096--484204 Score: 103 Period size: 31 Copynumber: 3.4 Consensus size: 31 484086 TATTCCTGGT * * 484096 ACGACTTAACAAAATCCGAATGATTTTAAGC 1 ACGACTTAACAAAATCCGAATGATTTCAAGA *** 484127 ACGACTTAACAAAATCCTTCCTGATTTCAAGA 1 ACGACTTAACAAAATCC-GAATGATTTCAAGA * * 484159 ACGACTTAACAAAAAAATCTGAATG-TGTTCAAGT 1 ACGACTTAAC---AAAATCCGAATGAT-TTCAAGA 484193 ACGACTTAACAA 1 ACGACTTAACAA 484205 TTATTTTTGG Statistics Matches: 63, Mismatches: 10, Indels: 10 0.76 0.12 0.12 Matches are distributed among these distances: 31 19 0.30 32 19 0.30 33 1 0.02 34 18 0.29 35 6 0.10 ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26 Consensus pattern (31 bp): ACGACTTAACAAAATCCGAATGATTTCAAGA Found at i:489125 original size:439 final size:436 Alignment explanation

Indices: 488116--489108 Score: 1072 Period size: 437 Copynumber: 2.3 Consensus size: 436 488106 TCTTCGTAGC * * * * * *** * 488116 CCCT-TTGGTCCCTTATTTGAGGGGTCA-CTCCTTTTTTCTTGATATCAAATGGAAGATCTTGTA 1 CCCTCTTGGCCCCTAATTTGAGGGGCCAGC-CCCTTTTTCTTGAAATCAAACAAAAGATCTGGTA * * * * * ** * * * * * * 488179 AATATAAACATATTTTGTTCTACATGTATTCACGAATTGTTGACCGTTCTAGAGATATCCGAACA 65 AATATAAACACATTTTGTT-AACAAGTCTTAAAAAAATATTGACCATTCAAAAGATAGCCGAACA * * * * 488244 ATTGTGTTTTAGGGGCCGACCCTTAAACTCCTTACCAGGGCCACCAACATAAATGTTTAAGATAC 129 AATGTGTTTTAGGGGCCGACCCTTAAAATCCTTACCAGGGCCACCAACAAAAATGTTTAAGAGAC * * 488309 CATATCGTTTAGAACATTATTTTAAGCATTTTTTGTTCTATAATGCTTATCAAAATATTTCTCCT 194 CATATCGTTAAGAACATTATTTTAAACATTTTTTGTTCTATAATGCTTATCAAAATATTTCTCCT * * * * ** 488374 TTTCTAGATATTAATGTTCAAAGTTTTGGACATATGGCCCCTTGAAACCCCTAATTACGTATTAT 259 TTTCTAGATATTAATGATCAAAATTTCGGACATATGGCCCCTTGAAACCCCTAATGACGTAACAT * 488439 ATGACATATGTATGGTACCGTATAGATAAACAGATGTACAATGAACATTTTTGGTTCTATAATTG 324 ATGACATATGCATGGTACCGTATAGATAAACAGATGTACAATGAACATTTTTGGTTCTATAATTG * * ** * 488504 ATAACAATTTATTTTTCAGCCAAGAGTTATGATAAAAAGAATTTACAG 389 ATAACAAATTATTTTTCAGCAAAGAAATATGACAAAAAGAATTTACAG * * * * * 488552 CCCTCTTGGCCCCTTATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCTTGTAA 1 CCCTCTTGGCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGAAATCAAACAAAAGATCTGGTAA * * * * * * * * * * 488617 ATATAAACGCATTTTGTTCAACAAGTGTTCAGAAATTGTTGACCGTTCTAAAGATATCTGAACAA 66 ATATAAACACATTTTGTT-AACAAGTCTTAAAAAAATATTGACCATTCAAAAGATAGCCGAACAA * * * * * 488682 ATGTGTTTTAGGGGCCGACCCTTAAAATCCTTA-CTGGGACCACCAACAAAAATTTTTTAGGGAG 130 ATGTGTTTTAGGGGCCGACCCTTAAAATCCTTACCAGGG-CCACCAACAAAAATGTTTAAGAGAC * 488746 CATATTGTTAAGAACATTATTTTAAACATTTTTTGTTCTATAATGCTTATCAAAATATTTCTCCT 194 CATATCGTTAAGAACATTATTTTAAACATTTTTTGTTCTATAATGCTTATCAAAATATTTCTCCT * * * * * 488811 TTTCTAGATATTTTTAA-GATCAAAATTTCGGACTTTTGGCCCCTTTAAGCCCCTAATGATGTAA 259 TTTCTAGATA---TTAATGATCAAAATTTCGGACATATGGCCCCTTGAAACCCCTAATGACGTAA * * * * 488875 CATATTACTTA-GACATGGTACTGTTTAGATAAACAGATGTACAATGAACATTTTTGGTTCTATA 321 CATATGACATATG-CATGGTACCGTATAGATAAACAGATGTACAATGAACATTTTTGGTTCTATA * * * * 488939 ATTGATAACAAATTATTTTTCAGTAAAGAAATATTG-CAAAAATACTTTAGAG 385 ATTGATAACAAATTATTTTTCAGCAAAGAAATA-TGACAAAAAGAATTTACAG * 488991 CCCTTTTGGCCCCTAATTTGAGGGGCCAGCCCCTTTTT-TCTGAAATCAAACAAAAGATCTAGGT 1 CCCTCTTGGCCCCTAATTTGAGGGGCCAGCCCCTTTTTCT-TGAAATCAAACAAAAGATCT-GGT * * * 489055 -AATCTAAACA-ACTTTTGCATT-ACATGTCTTAAAAAAATATTTACACATT-AAAAG 64 AAATATAAACACA-TTTTG--TTAACAAGTCTTAAAAAAATATTGAC-CATTCAAAAG 489109 TTAGGGCCGA Statistics Matches: 474, Mismatches: 69, Indels: 25 0.83 0.12 0.04 Matches are distributed among these distances: 436 8 0.02 437 230 0.49 438 4 0.01 439 219 0.46 440 11 0.02 441 2 0.00 ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36 Consensus pattern (436 bp): CCCTCTTGGCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGAAATCAAACAAAAGATCTGGTAA ATATAAACACATTTTGTTAACAAGTCTTAAAAAAATATTGACCATTCAAAAGATAGCCGAACAAA TGTGTTTTAGGGGCCGACCCTTAAAATCCTTACCAGGGCCACCAACAAAAATGTTTAAGAGACCA TATCGTTAAGAACATTATTTTAAACATTTTTTGTTCTATAATGCTTATCAAAATATTTCTCCTTT TCTAGATATTAATGATCAAAATTTCGGACATATGGCCCCTTGAAACCCCTAATGACGTAACATAT GACATATGCATGGTACCGTATAGATAAACAGATGTACAATGAACATTTTTGGTTCTATAATTGAT AACAAATTATTTTTCAGCAAAGAAATATGACAAAAAGAATTTACAG Found at i:489573 original size:56 final size:56 Alignment explanation

Indices: 489492--489604 Score: 199 Period size: 56 Copynumber: 2.0 Consensus size: 56 489482 AATAATAAGG 489492 AAAAGAAACAATAGAATAACAAGAGGGTCTTCCGTCGGAAACGGAAGACCCTAATA 1 AAAAGAAACAATAGAATAACAAGAGGGTCTTCCGTCGGAAACGGAAGACCCTAATA ** * 489548 AAAAGAAACCGTAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATA 1 AAAAGAAACAATAGAATAACAAGAGGGTCTTCCGTCGGAAACGGAAGACCCTAATA 489604 A 1 A 489605 TTTCTAGAGC Statistics Matches: 54, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 56 54 1.00 ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15 Consensus pattern (56 bp): AAAAGAAACAATAGAATAACAAGAGGGTCTTCCGTCGGAAACGGAAGACCCTAATA Found at i:489933 original size:62 final size:62 Alignment explanation

Indices: 489857--489976 Score: 206 Period size: 62 Copynumber: 1.9 Consensus size: 62 489847 TCAAGTACGA 489857 AATAAAAAGAAACAAT-AATATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAT 1 AATAAAAAGAAACAATGAA-ATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAT * * 489919 AATAAAAAGAAACAATGGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGATCCTAA 1 AATAAAAAGAAACAATGAAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAA 489977 AAAGAAACCG Statistics Matches: 55, Mismatches: 2, Indels: 2 0.93 0.03 0.03 Matches are distributed among these distances: 62 54 0.98 63 1 0.02 ACGTcount: A:0.47, C:0.14, G:0.20, T:0.18 Consensus pattern (62 bp): AATAAAAAGAAACAATGAAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAT Found at i:490862 original size:357 final size:354 Alignment explanation

Indices: 490207--491238 Score: 1719 Period size: 357 Copynumber: 2.9 Consensus size: 354 490197 TCTTCTGATC * * 490207 TATCCTAATAAGGTCTGGAATAAGATCTAGCATATGCATGTACAGAATATAAAATATAGTTATGA 1 TATCCTATTAAGGTCTGGAATAAGATCTAGCATATGCATGTACAGAATGTAAAATATAGTTATGA * 490272 CACTATAAATATTCAACTCAATCTTACTTATCATGAAAAGAAAACAGTTCCCCATTATTTTACTC 66 CACTATAAATATTCAACTCAATCTTACTTATCATAAAAAGAAAACAGTTCCCCATTATTTTACTC * * 490337 AGAAATGTCTTATCAAGTCTTGTTTGTTTATTTCTTGCATCTGTAAAAAAATGACAGGGAAGCCT 131 AGAAATGTCTTATCAAGTCTTGTTTG--T-TTTCTTGCATCTGTAAGAAACTGACAGGGAAGCCT 490402 CACTCGCCCACAAGCAAGAGCAAAAGGATCGGTCTGAGACACCACCTTTCTCTTACTTGGGTATC 193 CACTCGCCCACAAGCAAGAGCAAAAGGATCGGTCTGAGACACCACCTTTCTCTTACTTGGGTATC * 490467 AAGATTTGCAACTTACTGCCAGCAAAGCCCTTTCAAAATACTCTTGCATTGTCTCCTGCTTAAAA 258 AAGATCTGCAACTTACTGCCAGCAAAGCCCTTTCAAAATACTCTTGCATTGTCTCCTGCTTAAAA * 490532 TTCACTTTCAATAAAAATTCTTCTAGTCTATA 323 TTAACTTTCAATAAAAATTCTTCTAGTCTATA * * * * 490564 TATCCTATTCAGGTCTGGAATAAGATCTAACATATGCATGTACAAAATGT-AAA-ACAGTTATGA 1 TATCCTATTAAGGTCTGGAATAAGATCTAGCATATGCATGTACAGAATGTAAAATATAGTTATGA * 490627 CACTATAAAAATTCAACTCAATCTTACTTACATGTATCATAAAAAGAAAACAGTTCCCCATTATT 66 CACTATAAATATTCAACTCAA---T-CTTAC-T-TATCATAAAAAGAAAACAGTTCCCCATTATT 490692 TTACTCAGAAATGTCTTATCAAGTCTTGTTTG-TTTCTTGCATCTGTAAGAAACTGACAGGGAAG 125 TTACTCAGAAATGTCTTATCAAGTCTTGTTTGTTTTCTTGCATCTGTAAGAAACTGACAGGGAAG 490756 CCTCACTCGCCCACAAGCAAGAGCAAAAGGATCGGTCTGAGACACCACCTTTCTCTTACTTGGGT 190 CCTCACTCGCCCACAAGCAAGAGCAAAAGGATCGGTCTGAGACACCACCTTTCTCTTACTTGGGT * * * 490821 ATCAAGATCTGCAACTTACTACCAGCAAAGCCCTTTCAAAATACTCTCGCATTGTCACCTGCTTA 255 ATCAAGATCTGCAACTTACTGCCAGCAAAGCCCTTTCAAAATACTCTTGCATTGTCTCCTGCTTA * * 490886 AAATTAACTTTCAATAGAAATTCTTCTAGTCTTTA 320 AAATTAACTTTCAATAAAAATTCTTCTAGTCTATA ** * * 490921 TATCCTATTAAGGTCTTAAATAAGACCTGGCATATGCATGTACAGAATGTAAAATATAGTTATGA 1 TATCCTATTAAGGTCTGGAATAAGATCTAGCATATGCATGTACAGAATGTAAAATATAGTTATGA * 490986 CACTCTAAATATTCAACTCAATCTTACTTATCATAAAAAGAAAACAGTTCCCCATTATTTTACTC 66 CACTATAAATATTCAACTCAATCTTACTTATCATAAAAAGAAAACAGTTCCCCATTATTTTACTC * 491051 AGAAATGTCTTATCAAGTCTTGTTTGTTTATTTCTTGCACCTGTAAGAAACTGACAGGGAAGCCT 131 AGAAATGTCTTATCAAGTCTTGTTTG--T-TTTCTTGCATCTGTAAGAAACTGACAGGGAAGCCT * 491116 CACTCGCCCACAAGCAAGAGCAAAAGGATCGGTCTAAGACACCACCTTTCTCTTACTTGGGTATC 193 CACTCGCCCACAAGCAAGAGCAAAAGGATCGGTCTGAGACACCACCTTTCTCTTACTTGGGTATC 491181 AAGATCTGCAACTTACTGCCAGCAAAGCCCTTTCAAAATACTCTTGCATTGTCTCCTG 258 AAGATCTGCAACTTACTGCCAGCAAAGCCCTTTCAAAATACTCTTGCATTGTCTCCTG 491239 TATATTTTTA Statistics Matches: 631, Mismatches: 32, Indels: 24 0.92 0.05 0.03 Matches are distributed among these distances: 353 63 0.10 354 1 0.00 355 34 0.05 356 4 0.01 357 429 0.68 358 4 0.01 359 33 0.05 360 1 0.00 361 62 0.10 ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31 Consensus pattern (354 bp): TATCCTATTAAGGTCTGGAATAAGATCTAGCATATGCATGTACAGAATGTAAAATATAGTTATGA CACTATAAATATTCAACTCAATCTTACTTATCATAAAAAGAAAACAGTTCCCCATTATTTTACTC AGAAATGTCTTATCAAGTCTTGTTTGTTTTCTTGCATCTGTAAGAAACTGACAGGGAAGCCTCAC TCGCCCACAAGCAAGAGCAAAAGGATCGGTCTGAGACACCACCTTTCTCTTACTTGGGTATCAAG ATCTGCAACTTACTGCCAGCAAAGCCCTTTCAAAATACTCTTGCATTGTCTCCTGCTTAAAATTA ACTTTCAATAAAAATTCTTCTAGTCTATA Found at i:499554 original size:12 final size:13 Alignment explanation

Indices: 499523--499555 Score: 50 Period size: 12 Copynumber: 2.6 Consensus size: 13 499513 AAAAATTTTC 499523 AAGAAATGCAATT 1 AAGAAATGCAATT 499536 AAGAAATGC-ATT 1 AAGAAATGCAATT * 499548 TAGAAATG 1 AAGAAATG 499556 ACCAATATAA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 12 10 0.53 13 9 0.47 ACGTcount: A:0.52, C:0.06, G:0.18, T:0.24 Consensus pattern (13 bp): AAGAAATGCAATT Found at i:508798 original size:21 final size:21 Alignment explanation

Indices: 508695--508840 Score: 114 Period size: 21 Copynumber: 7.0 Consensus size: 21 508685 TTATGTCGAT * 508695 TCATTTCGCGACTATATG-TA 1 TCATTTCGCGACGATATGTTA * * * 508715 GACATTTCGCGCCGATATGTAA 1 -TCATTTCGCGACGATATGTTA * * * * 508737 TCATATGGCGACGGTATGTGA 1 TCATTTCGCGACGATATGTTA * * * * 508758 TTATTTTGCAATGATATGTTA 1 TCATTTCGCGACGATATGTTA 508779 TCATTTCGCGACGATATGTTA 1 TCATTTCGCGACGATATGTTA * * * 508800 TCATTTCGCAACTAAATGTTA 1 TCATTTCGCGACGATATGTTA * * * 508821 TCATTTTGCGAAGAGATGTT 1 TCATTTCGCGACGATATGTT 508841 TTCGCTTCTC Statistics Matches: 95, Mismatches: 29, Indels: 2 0.75 0.23 0.02 Matches are distributed among these distances: 21 94 0.99 22 1 0.01 ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38 Consensus pattern (21 bp): TCATTTCGCGACGATATGTTA Found at i:522156 original size:2 final size:2 Alignment explanation

Indices: 522149--522174 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 522139 NNNNNNNNNN 522149 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 522175 AAGAATAAAT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:522428 original size:21 final size:21 Alignment explanation

Indices: 522402--522493 Score: 123 Period size: 21 Copynumber: 4.4 Consensus size: 21 522392 TTATGTCTGC * 522402 TCATTTCGCAACGATATATTA 1 TCATTTCGCGACGATATATTA 522423 TCATTTCGCGACGATATATTA 1 TCATTTCGCGACGATATATTA * 522444 TTATTTTC-CGACGATATATTA 1 TCA-TTTCGCGACGATATATTA * * 522465 TCATTTTGCGACGATTTATTA 1 TCATTTCGCGACGATATATTA * 522486 TTATTTCG 1 TCATTTCG 522494 ATTAGCGTAC Statistics Matches: 62, Mismatches: 7, Indels: 4 0.85 0.10 0.05 Matches are distributed among these distances: 20 3 0.05 21 55 0.89 22 4 0.06 ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45 Consensus pattern (21 bp): TCATTTCGCGACGATATATTA Found at i:522476 original size:42 final size:42 Alignment explanation

Indices: 522412--522491 Score: 142 Period size: 42 Copynumber: 1.9 Consensus size: 42 522402 TCATTTCGCA 522412 ACGATATATTATCATTTCGCGACGATATATTATTATTTTCCG 1 ACGATATATTATCATTTCGCGACGATATATTATTATTTTCCG * * 522454 ACGATATATTATCATTTTGCGACGATTTATTATTATTT 1 ACGATATATTATCATTTCGCGACGATATATTATTATTT 522492 CGATTAGCGT Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 42 36 1.00 ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46 Consensus pattern (42 bp): ACGATATATTATCATTTCGCGACGATATATTATTATTTTCCG Found at i:526498 original size:75 final size:74 Alignment explanation

Indices: 526404--526571 Score: 191 Period size: 79 Copynumber: 2.2 Consensus size: 74 526394 TTTTATTGGC * * * * * 526404 AATATTTTAACAT-ATTTCAATAAAGTTGTACATATG-ATAAATTAAATAC-ATAATTCATGCAC 1 AATATTTGAATATAATTTCAATAAAGTTATACATATGAATAAATT-AATACTAAAATCCATGCAC * 526466 TTTTATTGATAA 65 TTTCATTG--AA 526478 AATATTTGAATATAATTTCAATAAAGTTATACATATGATTAATAAATTAATACTAAAATCCATGC 1 AATATTTGAATATAATTTCAATAAAGTTATACATATG---AATAAATTAATACTAAAATCCATGC * 526543 ACTTTCATTGAC 63 ACTTTCATTGAA 526555 AATA-TTGAATATAATTT 1 AATATTTGAATATAATTT 526572 AAAACAAGAA Statistics Matches: 81, Mismatches: 7, Indels: 10 0.83 0.07 0.10 Matches are distributed among these distances: 74 11 0.14 75 22 0.27 76 13 0.16 77 5 0.06 78 5 0.06 79 25 0.31 ACGTcount: A:0.44, C:0.10, G:0.07, T:0.40 Consensus pattern (74 bp): AATATTTGAATATAATTTCAATAAAGTTATACATATGAATAAATTAATACTAAAATCCATGCACT TTCATTGAA Found at i:530717 original size:44 final size:44 Alignment explanation

Indices: 530681--530830 Score: 291 Period size: 44 Copynumber: 3.4 Consensus size: 44 530671 ACTACACTGC * 530681 TAATCAGATAATACACAGGTGTTGATTTATTAACACTACGATGT 1 TAATCAGATAATATACAGGTGTTGATTTATTAACACTACGATGT 530725 TAATCAGATAATATACAGGTGTTGATTTATTAACACTACGATGT 1 TAATCAGATAATATACAGGTGTTGATTTATTAACACTACGATGT 530769 TAATCAGATAATATACAGGTGTTGATTTATTAACACTACGATGT 1 TAATCAGATAATATACAGGTGTTGATTTATTAACACTACGATGT 530813 TAATCAGATAATATACAG 1 TAATCAGATAATATACAG 530831 ATGTCTGTAT Statistics Matches: 105, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 44 105 1.00 ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35 Consensus pattern (44 bp): TAATCAGATAATATACAGGTGTTGATTTATTAACACTACGATGT Found at i:530725 original size:22 final size:22 Alignment explanation

Indices: 530700--530813 Score: 74 Period size: 22 Copynumber: 5.2 Consensus size: 22 530690 AATACACAGG 530700 TGTTGATTTATTAACACTACGA 1 TGTTGATTTATTAACACTACGA * * * * * 530722 TGTT-AATCAGATAATA-TACAGG 1 TGTTGATTTA-TTAACACTAC-GA 530744 TGTTGATTTATTAACACTACGA 1 TGTTGATTTATTAACACTACGA * * * * * 530766 TGTT-AATCAGATAATA-TACAGG 1 TGTTGATTTA-TTAACACTAC-GA 530788 TGTTGATTTATTAACACTACGA 1 TGTTGATTTATTAACACTACGA 530810 TGTT 1 TGTT 530814 AATCAGATAA Statistics Matches: 64, Mismatches: 20, Indels: 16 0.64 0.20 0.16 Matches are distributed among these distances: 21 12 0.19 22 40 0.62 23 12 0.19 ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39 Consensus pattern (22 bp): TGTTGATTTATTAACACTACGA Found at i:530833 original size:22 final size:22 Alignment explanation

Indices: 530720--530834 Score: 76 Period size: 22 Copynumber: 5.2 Consensus size: 22 530710 TTAACACTAC 530720 GATGTTAATCAGATAATATACA 1 GATGTTAATCAGATAATATACA * * * * * 530742 GGTGTTGATTTA-TTAACACTAC- 1 GATGTT-AATCAGATAATA-TACA 530764 GATGTTAATCAGATAATATACA 1 GATGTTAATCAGATAATATACA * * * * * 530786 GGTGTTGATTTA-TTAACACTAC- 1 GATGTT-AATCAGATAATA-TACA 530808 GATGTTAATCAGATAATATACA 1 GATGTTAATCAGATAATATACA 530830 GATGT 1 GATGT 530835 CTGTATACAC Statistics Matches: 65, Mismatches: 20, Indels: 16 0.64 0.20 0.16 Matches are distributed among these distances: 21 12 0.18 22 41 0.63 23 12 0.18 ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36 Consensus pattern (22 bp): GATGTTAATCAGATAATATACA Found at i:532231 original size:65 final size:65 Alignment explanation

Indices: 532127--532362 Score: 402 Period size: 65 Copynumber: 3.6 Consensus size: 65 532117 ACAGAGCAGA * * 532127 AAACACATGTAGATAAAGAGTAGGGACACCACACAGATGATGAAAATCACCACAACCTGAAACAT 1 AAACACATGTAGATAAAGAGTAGGGACACCACACAGATGATGAAAATCACCACAACCTGAAATAC * 532192 AAACACATGTAGATAAAGAATATGGG-CACCACACAGATGATGAAAATCACCACAACCTGAAATA 1 AAACACATGTAGATAAAGAGTA-GGGACACCACACAGATGATGAAAATCACCACAACCTGAAATA 532256 C 65 C * ** 532257 AAACACATGAAGATAAAGAGTAGGGACACCACACAGATGATGAAAATCACCACCGCCTGAAATAC 1 AAACACATGTAGATAAAGAGTAGGGACACCACACAGATGATGAAAATCACCACAACCTGAAATAC 532322 AAACACATGTAGATAAAGAGTAGGGACACCACACAGATGAT 1 AAACACATGTAGATAAAGAGTAGGGACACCACACAGATGAT 532363 ACAAACACAT Statistics Matches: 161, Mismatches: 8, Indels: 4 0.93 0.05 0.02 Matches are distributed among these distances: 64 3 0.02 65 155 0.96 66 3 0.02 ACGTcount: A:0.47, C:0.21, G:0.18, T:0.14 Consensus pattern (65 bp): AAACACATGTAGATAAAGAGTAGGGACACCACACAGATGATGAAAATCACCACAACCTGAAATAC Found at i:532366 original size:43 final size:43 Alignment explanation

Indices: 532318--532405 Score: 149 Period size: 43 Copynumber: 2.0 Consensus size: 43 532308 ACCGCCTGAA * * 532318 ATACAAACACATGTAGATAAAGAGTAGGGACACCACACAGATG 1 ATACAAACACATGTAAATAAAGAGAAGGGACACCACACAGATG * 532361 ATACAAACACATGTAAATAAAGAGAAGGGGCACCACACAGATG 1 ATACAAACACATGTAAATAAAGAGAAGGGACACCACACAGATG 532404 AT 1 AT 532406 GAAAATTAGC Statistics Matches: 42, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 43 42 1.00 ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14 Consensus pattern (43 bp): ATACAAACACATGTAAATAAAGAGAAGGGACACCACACAGATG Found at i:532395 original size:108 final size:108 Alignment explanation

Indices: 532253--532470 Score: 321 Period size: 108 Copynumber: 2.0 Consensus size: 108 532243 ACAACCTGAA * ** 532253 ATACAAACACATGAAGATAAAGAGTAGGGACACCACACAGATGATGAAAATCACCACCGCCTGAA 1 ATACAAACACATGAAGATAAAGAGAAGGGACACCACACAGATGATGAAAATCACCACAACCTGAA * * 532318 ATACAAACACATGTAGATAAAGAGTAGGGACACCACACAGATG 66 ATACAAACACAGGTAGATAAAGAGTAGGGACACCACAAAGATG * * * 532361 ATACAAACACATGTAA-ATAAAGAGAAGGGGCACCACACAGATGATGAAAATTAGCACAACCTGA 1 ATACAAACACATG-AAGATAAAGAGAAGGGACACCACACAGATGATGAAAATCACCACAACCTGA * ** 532425 AATACAAACACAGGTAGATAAAGAGTAGTGATGCCACAAAGATG 65 AATACAAACACAGGTAGATAAAGAGTAGGGACACCACAAAGATG 532469 AT 1 AT 532471 GAAAATCACC Statistics Matches: 98, Mismatches: 11, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 108 96 0.98 109 2 0.02 ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14 Consensus pattern (108 bp): ATACAAACACATGAAGATAAAGAGAAGGGACACCACACAGATGATGAAAATCACCACAACCTGAA ATACAAACACAGGTAGATAAAGAGTAGGGACACCACAAAGATG Found at i:532468 original size:65 final size:65 Alignment explanation

Indices: 532361--532633 Score: 357 Period size: 65 Copynumber: 4.2 Consensus size: 65 532351 CACACAGATG * * * * * 532361 ATACAAACACATGTAAATAAAGAGAAGGGGCACCACACAGATGATGAAAATTAGCACAACCTGAA 1 ATACAAACACATGTAGATAAAGAGAAGGGACACCACACAGATGATGAAAATCACCACCACCTGAA * * * ** * * * 532426 ATACAAACACAGGTAGATAAAGAGTAGTGATGCCACAAAGATGATGAAAATCACCACCACATAAA 1 ATACAAACACATGTAGATAAAGAGAAGGGACACCACACAGATGATGAAAATCACCACCACCTGAA * * * 532491 ACATAAACACATGTAGATAAAGAGAAGGGACACCACACAGATGATAAAAATCACCACCACCTGAA 1 ATACAAACACATGTAGATAAAGAGAAGGGACACCACACAGATGATGAAAATCACCACCACCTGAA * * * * * 532556 ACATAAACACATGTAGATAAAGAGTAGGGGCACCACACAGATGATGAAAATCACCACCATCTGAA 1 ATACAAACACATGTAGATAAAGAGAAGGGACACCACACAGATGATGAAAATCACCACCACCTGAA 532621 ATACAAACACATG 1 ATACAAACACATG 532634 GACAACAATC Statistics Matches: 178, Mismatches: 30, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 65 178 1.00 ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14 Consensus pattern (65 bp): ATACAAACACATGTAGATAAAGAGAAGGGACACCACACAGATGATGAAAATCACCACCACCTGAA Found at i:532481 original size:173 final size:173 Alignment explanation

Indices: 532192--532536 Score: 530 Period size: 173 Copynumber: 2.0 Consensus size: 173 532182 CCTGAAACAT * * 532192 AAACACATGTAGATAAAGAATATGGGCACCACACAGATGATGAAAATCACCACAACCTGAAATAC 1 AAACACATGTAAATAAAGAATAGGGGCACCACACAGATGATGAAAATCACCACAACCTGAAATAC * * * * * * 532257 AAACACATGAAGATAAAGAGTAGGGACACCACACAGATGATGAAAATCACCACCGCCTGAAATAC 66 AAACACAGGAAGATAAAGAGTAGGGACACCACAAAGATGATGAAAATCACCACCACATAAAACAC * 532322 AAACACATGTAGATAAAGAGTAGGGACACCACACAGATGATAC 131 AAACACATGTAGATAAAGAGAAGGGACACCACACAGATGATAC * * 532365 AAACACATGTAAATAAAGAGA-AGGGGCACCACACAGATGATGAAAATTAGCACAACCTGAAATA 1 AAACACATGTAAATAAAGA-ATAGGGGCACCACACAGATGATGAAAATCACCACAACCTGAAATA * * ** 532429 CAAACACAGGTAGATAAAGAGTAGTGATGCCACAAAGATGATGAAAATCACCACCACATAAAACA 65 CAAACACAGGAAGATAAAGAGTAGGGACACCACAAAGATGATGAAAATCACCACCACATAAAACA * 532494 TAAACACATGTAGATAAAGAGAAGGGACACCACACAGATGATA 130 CAAACACATGTAGATAAAGAGAAGGGACACCACACAGATGATA 532537 AAAATCACCA Statistics Matches: 155, Mismatches: 16, Indels: 2 0.90 0.09 0.01 Matches are distributed among these distances: 173 154 0.99 174 1 0.01 ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14 Consensus pattern (173 bp): AAACACATGTAAATAAAGAATAGGGGCACCACACAGATGATGAAAATCACCACAACCTGAAATAC AAACACAGGAAGATAAAGAGTAGGGACACCACAAAGATGATGAAAATCACCACCACATAAAACAC AAACACATGTAGATAAAGAGAAGGGACACCACACAGATGATAC Found at i:532545 original size:238 final size:237 Alignment explanation

Indices: 532127--532600 Score: 707 Period size: 238 Copynumber: 2.0 Consensus size: 237 532117 ACAGAGCAGA * * * 532127 AAACACATGTAGATAAAGAGTAGGGACACCACACAGATGATGAAAATCACCACAACCTGAAACAT 1 AAACACATGTAAATAAAGAGAAGGGACACCACACAGATGATGAAAATCACCACAACCTGAAACAC * * * * * 532192 AAACACATGTAGATAAAGAATATGGGCACCACACAGATGATGAAAATCACCACAACCTGAAATAC 66 AAACACAGGTAGATAAAGAATATGGG-ACCACAAAGATGATGAAAATCACCACAACATAAAACAC * * * * 532257 AAACACATGAAGATAAAGAGTAGGGACACCACACAGATGATGAAAATCACCACCGCCTGAAATAC 130 AAACACATGAAGATAAAGAGAAGGGACACCACACAGATGATAAAAATCACCACCACCTGAAACAC 532322 AAACACATGTAGATAAAGAGTAGGGACACCACACAGATGATAC 195 AAACACATGTAGATAAAGAGTAGGGACACCACACAGATGATAC * * * * 532365 AAACACATGTAAATAAAGAGAAGGGGCACCACACAGATGATGAAAATTAGCACAACCTGAAATAC 1 AAACACATGTAAATAAAGAGAAGGGACACCACACAGATGATGAAAATCACCACAACCTGAAACAC * * * 532430 AAACACAGGTAGATAAAGAGTA-GTGATGCCACAAAGATGATGAAAATCACCACCACATAAAACA 66 AAACACAGGTAGATAAAGAATATGGGA--CCACAAAGATGATGAAAATCACCACAACATAAAACA * * 532494 TAAACACATGTAGATAAAGAGAAGGGACACCACACAGATGATAAAAATCACCACCACCTGAAACA 129 CAAACACATGAAGATAAAGAGAAGGGACACCACACAGATGATAAAAATCACCACCACCTGAAACA * * 532559 TAAACACATGTAGATAAAGAGTAGGGGCACCACACAGATGAT 194 CAAACACATGTAGATAAAGAGTAGGGACACCACACAGATGAT 532601 GAAAATCACC Statistics Matches: 211, Mismatches: 23, Indels: 4 0.89 0.10 0.02 Matches are distributed among these distances: 236 1 0.00 237 2 0.01 238 208 0.99 ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14 Consensus pattern (237 bp): AAACACATGTAAATAAAGAGAAGGGACACCACACAGATGATGAAAATCACCACAACCTGAAACAC AAACACAGGTAGATAAAGAATATGGGACCACAAAGATGATGAAAATCACCACAACATAAAACACA AACACATGAAGATAAAGAGAAGGGACACCACACAGATGATAAAAATCACCACCACCTGAAACACA AACACATGTAGATAAAGAGTAGGGACACCACACAGATGATAC Found at i:538071 original size:1 final size:1 Alignment explanation

Indices: 538065--538093 Score: 58 Period size: 1 Copynumber: 29.0 Consensus size: 1 538055 TAAAACAGCG 538065 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 538094 CTATGCACTT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 28 1.00 ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:538562 original size:12 final size:12 Alignment explanation

Indices: 538542--538618 Score: 58 Period size: 12 Copynumber: 6.6 Consensus size: 12 538532 TTAGTATCTT * * 538542 ATAGCCACTCTC 1 ATAGTCACTATC 538554 ATAGTCACTATC 1 ATAGTCACTATC 538566 ATA-TCA-TAGTC 1 ATAGTCACTA-TC 538577 ACTA-TCA-TAGTC 1 A-TAGTCACTA-TC 538589 ACTA-TCA-TATC 1 A-TAGTCACTATC 538600 ATAGTCACTATC 1 ATAGTCACTATC 538612 ATAGTCA 1 ATAGTCA 538619 ACAGTCAACA Statistics Matches: 59, Mismatches: 2, Indels: 8 0.86 0.03 0.12 Matches are distributed among these distances: 10 4 0.07 11 12 0.20 12 43 0.73 ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32 Consensus pattern (12 bp): ATAGTCACTATC Found at i:538564 original size:76 final size:77 Alignment explanation

Indices: 538438--538732 Score: 356 Period size: 76 Copynumber: 4.0 Consensus size: 77 538428 CCAGTACCTG 538438 ACAGTCAGTATCTCAGAGTTAGTATCTAATAGCCACTCTCATAGTCACTATCATA-TCATAGTCA 1 ACAGTCAGTATCTCAGAGTTAGTATCTAATAGCCACTCTCATAGTCACTATCATAGTCATAGTCA 538502 CTATCATAGTCA 66 CTATCATAGTCA * 538514 ACAGTCAGTATCTCAGAGTTAGTATCTTATAGCCACTCTCATAGTCACTATCATA-TCATAGTCA 1 ACAGTCAGTATCTCAGAGTTAGTATCTAATAGCCACTCTCATAGTCACTATCATAGTCATAGTCA 538578 CTATCATAGTC- 66 CTATCATAGTCA * * * * * * 538589 ACTA-TCA-TA--TCATAGTCACTATC--ATAG----TC-AACAGTCAAC-ATCATAGTCAACAG 1 AC-AGTCAGTATCTCAGAGTTAGTATCTAATAGCCACTCTCATAGTC-ACTATCATAGTC-ATAG 538642 TCAAC-ATCATAGTCA 63 TC-ACTATCATAGTCA 538657 ACAGTCAGTATCTCAGAGTTAGTATCTAATAGCCACTCTCATAGTCACTATCATAGTCACTA-TC 1 ACAGTCAGTATCTCAGAGTTAGTATCTAATAGCCACTCTCATAGTCACTATCATAGTCA-TAGTC 538721 A-TATCATAGTCA 65 ACTATCATAGTCA 538733 CTATCATAGT Statistics Matches: 186, Mismatches: 13, Indels: 40 0.78 0.05 0.17 Matches are distributed among these distances: 65 11 0.06 66 6 0.03 67 15 0.08 68 7 0.04 69 2 0.01 70 4 0.02 71 11 0.06 72 11 0.06 73 4 0.02 74 2 0.01 75 5 0.03 76 86 0.46 77 7 0.04 78 15 0.08 ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31 Consensus pattern (77 bp): ACAGTCAGTATCTCAGAGTTAGTATCTAATAGCCACTCTCATAGTCACTATCATAGTCATAGTCA CTATCATAGTCA Found at i:538626 original size:7 final size:7 Alignment explanation

Indices: 538614--538663 Score: 54 Period size: 7 Copynumber: 7.7 Consensus size: 7 538604 TCACTATCAT 538614 AGTCAAC 1 AGTCAAC 538621 AGTCAAC 1 AGTCAAC * 538628 A-TC-AT 1 AGTCAAC 538633 AGTCAAC 1 AGTCAAC 538640 AGTCAAC 1 AGTCAAC * 538647 A-TC-AT 1 AGTCAAC 538652 AGTCAAC 1 AGTCAAC 538659 AGTCA 1 AGTCA 538664 GTATCTCAGA Statistics Matches: 35, Mismatches: 4, Indels: 8 0.74 0.09 0.17 Matches are distributed among these distances: 5 4 0.11 6 8 0.23 7 23 0.66 ACGTcount: A:0.42, C:0.26, G:0.12, T:0.20 Consensus pattern (7 bp): AGTCAAC Found at i:538631 original size:19 final size:19 Alignment explanation

Indices: 538609--538663 Score: 110 Period size: 19 Copynumber: 2.9 Consensus size: 19 538599 CATAGTCACT 538609 ATCATAGTCAACAGTCAAC 1 ATCATAGTCAACAGTCAAC 538628 ATCATAGTCAACAGTCAAC 1 ATCATAGTCAACAGTCAAC 538647 ATCATAGTCAACAGTCA 1 ATCATAGTCAACAGTCA 538664 GTATCTCAGA Statistics Matches: 36, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 36 1.00 ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22 Consensus pattern (19 bp): ATCATAGTCAACAGTCAAC Found at i:538705 original size:12 final size:12 Alignment explanation

Indices: 538685--538856 Score: 66 Period size: 12 Copynumber: 14.6 Consensus size: 12 538675 TTAGTATCTA * * 538685 ATAGCCACTCTC 1 ATAGTCACTATC 538697 ATAGTCACTATC 1 ATAGTCACTATC 538709 ATAGTCACTATC 1 ATAGTCACTATC 538721 ATA-TCA-TAGTC 1 ATAGTCACTA-TC 538732 ACTA-TCA-TAGTC 1 A-TAGTCACTA-TC * 538744 AACAGTCAAC-ATC 1 -ATAGTC-ACTATC 538757 ATAGTCA--A-C 1 ATAGTCACTATC * 538766 AGTCAGT-A-TCTC 1 A-T-AGTCACTATC * * * 538778 AGAGTTAGTATC 1 ATAGTCACTATC * * 538790 TAATAGCCACTCTC 1 -A-TAGTCACTATC 538804 ATAGTCACTATC 1 ATAGTCACTATC 538816 ATAG-CA-TAGTC 1 ATAGTCACTA-TC 538827 ACTA-TCA-TATC 1 A-TAGTCACTATC 538838 ATAGTCACTATC 1 ATAGTCACTATC 538850 ATAGTCA 1 ATAGTCA 538857 ACAGTCAATA Statistics Matches: 127, Mismatches: 14, Indels: 38 0.71 0.08 0.21 Matches are distributed among these distances: 9 2 0.02 10 12 0.09 11 22 0.17 12 76 0.60 13 7 0.06 14 8 0.06 ACGTcount: A:0.34, C:0.25, G:0.10, T:0.30 Consensus pattern (12 bp): ATAGTCACTATC Found at i:538774 original size:107 final size:108 Alignment explanation

Indices: 538594--538887 Score: 484 Period size: 107 Copynumber: 2.7 Consensus size: 108 538584 TAGTCACTAT * 538594 CATATCATAGTCACTATCATAGTCAACAGTCAAC-ATCATAGTCAACAGTCAACATCATAGTCAA 1 CATATCATAGTCACTATCATA-TC-ATAGTC-ACTATCATAGTCAACAGTCAACATCATAGTCAA 538658 CAGTCAGTATCTCAGAGTTAGTATCTAATAGCCACTCTCATAGTCA 63 CAGTCAGTATCTCAGAGTTAGTATCTAATAGCCACTCTCATAGTCA 538704 C-TATCATAGTCACTATCATATCATAGTCACTATCATAGTCAACAGTCAACATCATAGTCAACAG 1 CATATCATAGTCACTATCATATCATAGTCACTATCATAGTCAACAGTCAACATCATAGTCAACAG 538768 TCAGTATCTCAGAGTTAGTATCTAATAGCCACTCTCATAGTCA 66 TCAGTATCTCAGAGTTAGTATCTAATAGCCACTCTCATAGTCA * 538811 CTATCATAGCATAGTCACTATCATATCATAGTCACTATCATAGTCAACAGTCAATATCATAGTCA 1 C-AT-AT--CATAGTCACTATCATATCATAGTCACTATCATAGTCAACAGTCAACATCATAGTCA * 538876 ACAGTCAATATC 62 ACAGTCAGTATC 538888 ATAGTCAACA Statistics Matches: 175, Mismatches: 3, Indels: 10 0.93 0.02 0.05 Matches are distributed among these distances: 106 2 0.01 107 82 0.47 108 2 0.01 109 20 0.11 110 3 0.02 112 66 0.38 ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29 Consensus pattern (108 bp): CATATCATAGTCACTATCATATCATAGTCACTATCATAGTCAACAGTCAACATCATAGTCAACAG TCAGTATCTCAGAGTTAGTATCTAATAGCCACTCTCATAGTCA Found at i:538864 original size:7 final size:7 Alignment explanation

Indices: 538838--538935 Score: 81 Period size: 7 Copynumber: 15.4 Consensus size: 7 538828 CTATCATATC 538838 ATAGTCA 1 ATAGTCA * 538845 CTA-TC- 1 ATAGTCA 538850 ATAGTCA 1 ATAGTCA * 538857 ACAGTCA 1 ATAGTCA 538864 ATA-TC- 1 ATAGTCA 538869 ATAGTCA 1 ATAGTCA * 538876 ACAGTCA 1 ATAGTCA 538883 ATA-TC- 1 ATAGTCA 538888 ATAGTCA 1 ATAGTCA * 538895 ACAGTCA 1 ATAGTCA 538902 ATA-TC- 1 ATAGTCA 538907 ATAGTCA 1 ATAGTCA * 538914 ACAGTCA 1 ATAGTCA 538921 ATA-TC- 1 ATAGTCA 538926 ATAGTCA 1 ATAGTCA 538933 ATA 1 ATA 538936 TATATCAACG Statistics Matches: 71, Mismatches: 10, Indels: 20 0.70 0.10 0.20 Matches are distributed among these distances: 5 14 0.20 6 20 0.28 7 37 0.52 ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28 Consensus pattern (7 bp): ATAGTCA Found at i:538868 original size:19 final size:19 Alignment explanation

Indices: 538806--538933 Score: 183 Period size: 19 Copynumber: 6.9 Consensus size: 19 538796 CCACTCTCAT * * 538806 AGTCACTATCATAG-C-AT 1 AGTCAATATCATAGTCAAC * * 538823 AGTCACTATCATA-TC-AT 1 AGTCAATATCATAGTCAAC * 538840 AGTCACTATCATAGTCAAC 1 AGTCAATATCATAGTCAAC 538859 AGTCAATATCATAGTCAAC 1 AGTCAATATCATAGTCAAC 538878 AGTCAATATCATAGTCAAC 1 AGTCAATATCATAGTCAAC 538897 AGTCAATATCATAGTCAAC 1 AGTCAATATCATAGTCAAC 538916 AGTCAATATCATAGTCAA 1 AGTCAATATCATAGTCAA 538934 TATATATCAA Statistics Matches: 106, Mismatches: 2, Indels: 4 0.95 0.02 0.04 Matches are distributed among these distances: 17 29 0.27 18 2 0.02 19 75 0.71 ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28 Consensus pattern (19 bp): AGTCAATATCATAGTCAAC Found at i:538874 original size:12 final size:12 Alignment explanation

Indices: 538802--538936 Score: 70 Period size: 12 Copynumber: 11.1 Consensus size: 12 538792 ATAGCCACTC * 538802 TCATAGTCACTA 1 TCATAGTCAATA 538814 TCATAG-C-ATA 1 TCATAGTCAATA 538824 GTCACTA-TC-ATA 1 -TCA-TAGTCAATA * 538836 TCATAGTCACTA 1 TCATAGTCAATA * 538848 TCATAGTCAACA 1 TCATAGTCAATA 538860 GTCAATA-TC-ATA 1 -TC-ATAGTCAATA * 538872 GTCAACAGTCAATA 1 -TC-ATAGTCAATA * 538886 TCATAGTCAACA 1 TCATAGTCAATA 538898 GTCAATA-TC-ATA 1 -TC-ATAGTCAATA * 538910 GTCAACAGTCAATA 1 -TC-ATAGTCAATA 538924 TCATAGTCAATA 1 TCATAGTCAATA 538936 T 1 T 538937 ATATCAACGT Statistics Matches: 99, Mismatches: 11, Indels: 26 0.73 0.08 0.19 Matches are distributed among these distances: 10 4 0.04 11 9 0.09 12 58 0.59 13 16 0.16 14 12 0.12 ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30 Consensus pattern (12 bp): TCATAGTCAATA Found at i:539273 original size:15 final size:12 Alignment explanation

Indices: 539243--539284 Score: 75 Period size: 12 Copynumber: 3.5 Consensus size: 12 539233 TCATAGACGG 539243 TAATAATACAGT 1 TAATAATACAGT 539255 TAATAATACAGT 1 TAATAATACAGT 539267 TAATAATACAGT 1 TAATAATACAGT * 539279 AAATAA 1 TAATAA 539285 AATGATGTCG Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 12 29 1.00 ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31 Consensus pattern (12 bp): TAATAATACAGT Found at i:539444 original size:16 final size:16 Alignment explanation

Indices: 539420--539466 Score: 76 Period size: 16 Copynumber: 2.9 Consensus size: 16 539410 ACAACATTAC 539420 AGAGGTTGTTTCAGAA 1 AGAGGTTGTTTCAGAA * 539436 AGAGTTTGTTTCAGAA 1 AGAGGTTGTTTCAGAA * 539452 AGAGGCTGTTTCAGA 1 AGAGGTTGTTTCAGA 539467 CAGACGCTAT Statistics Matches: 28, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 16 28 1.00 ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32 Consensus pattern (16 bp): AGAGGTTGTTTCAGAA Found at i:539479 original size:16 final size:16 Alignment explanation

Indices: 539444--539485 Score: 57 Period size: 16 Copynumber: 2.6 Consensus size: 16 539434 AAAGAGTTTG * * * 539444 TTTCAGAAAGAGGCTG 1 TTTCAGACAGACGCTA 539460 TTTCAGACAGACGCTA 1 TTTCAGACAGACGCTA 539476 TTTCAGACAG 1 TTTCAGACAG 539486 GTTTAAGAAA Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 16 23 1.00 ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26 Consensus pattern (16 bp): TTTCAGACAGACGCTA Found at i:543227 original size:34 final size:34 Alignment explanation

Indices: 543181--543490 Score: 575 Period size: 34 Copynumber: 9.1 Consensus size: 34 543171 TCGATACCTC * 543181 CCTGTGAATTGAAAGGTATAAAAGATAATGTCTA 1 CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA * * 543215 CCCGTGAATTGAAAGGTATAAAAGATAATGTCTA 1 CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA 543249 CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA 1 CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA 543283 CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA 1 CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA 543317 CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA 1 CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA 543351 CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA 1 CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA 543385 CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA 1 CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA 543419 CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA 1 CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA * * 543453 CCTGTGGATTGAAGGGTATAAAAGATAATATCTA 1 CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA 543487 CCTG 1 CCTG 543491 CAGCATGGAC Statistics Matches: 271, Mismatches: 5, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 34 271 1.00 ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29 Consensus pattern (34 bp): CCTGTGGATTGAAAGGTATAAAAGATAATGTCTA Found at i:544134 original size:18 final size:18 Alignment explanation

Indices: 544111--544151 Score: 82 Period size: 18 Copynumber: 2.3 Consensus size: 18 544101 ATACTCTGAA 544111 TCCCCTACGATATGGTGT 1 TCCCCTACGATATGGTGT 544129 TCCCCTACGATATGGTGT 1 TCCCCTACGATATGGTGT 544147 TCCCC 1 TCCCC 544152 GATGTTATGC Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 23 1.00 ACGTcount: A:0.15, C:0.34, G:0.20, T:0.32 Consensus pattern (18 bp): TCCCCTACGATATGGTGT Found at i:545418 original size:78 final size:78 Alignment explanation

Indices: 544725--545403 Score: 1061 Period size: 78 Copynumber: 8.7 Consensus size: 78 544715 TTTGGTCACG * * * * 544725 TTACATTCTCTATCTAATAGTGACGTCCCTATCACAAATCATCAGTAGAGGTTGTCATTGCGTCA 1 TTACAGTCTCTATCTAATAGTGACATCTCTATCACAAATCATCAGTAGAAGTTGTCATTGCGTCA * 544790 CAATAGCTTCATA 66 CAATAGCGTCATA ** * * * 544803 TGGCAGTCTCTATCTAATAGTGACGTCCCTATCACAAATCATCAGTAAAAGTTGTCATTGCGTCA 1 TTACAGTCTCTATCTAATAGTGACATCTCTATCACAAATCATCAGTAGAAGTTGTCATTGCGTCA 544868 CAATAGCGTCATA 66 CAATAGCGTCATA ** * * * 544881 TGGCAGTCTCTATCTAATAGTGACGTCCCTATCACAAATCATCAGTAAAAGTTGTCATTGCGTCA 1 TTACAGTCTCTATCTAATAGTGACATCTCTATCACAAATCATCAGTAGAAGTTGTCATTGCGTCA 544946 CAATAGCGTCATA 66 CAATAGCGTCATA * * 544959 TTACAGTCTCTATCTTATAGTGACATCTCTATCACGAATCATCAGTAGAAGTTGTCATTGCGTCA 1 TTACAGTCTCTATCTAATAGTGACATCTCTATCACAAATCATCAGTAGAAGTTGTCATTGCGTCA * 545024 CAATAGCGGCATA 66 CAATAGCGTCATA ** * * * * 545037 TGGCAGTCTCTATCTAATAGTGACGTCCCTATCACAAATCATCAGTAAAAGTTGTCATTGCATCA 1 TTACAGTCTCTATCTAATAGTGACATCTCTATCACAAATCATCAGTAGAAGTTGTCATTGCGTCA 545102 CAATAGCGTCATA 66 CAATAGCGTCATA * * 545115 TTACAGTCTCTATCTTATAGTGACATCTCTATCACGAATCATCAGTAGAAGTTGTCATTGCGTCA 1 TTACAGTCTCTATCTAATAGTGACATCTCTATCACAAATCATCAGTAGAAGTTGTCATTGCGTCA 545180 CAATAGCGTCATA 66 CAATAGCGTCATA * * * 545193 TTACAGTCTCTATCTTATAGTGACATCTCTATCACGAATCATCAGTAGAGGTTGTCATTGCGTCA 1 TTACAGTCTCTATCTAATAGTGACATCTCTATCACAAATCATCAGTAGAAGTTGTCATTGCGTCA 545258 CAATAGCGTCATA 66 CAATAGCGTCATA * * 545271 TTACAGTCTCTATCTTATAGTGACATCTCTATCACGAATCATCAGTAGAAGTTGTCATTGCGTCA 1 TTACAGTCTCTATCTAATAGTGACATCTCTATCACAAATCATCAGTAGAAGTTGTCATTGCGTCA 545336 CAATAGCGTCATA 66 CAATAGCGTCATA * 545349 TTACAGTCTCTATCTAATAGTGGCATCTCTATCACAAATCATCAGTAGAAAGTTG 1 TTACAGTCTCTATCTAATAGTGACATCTCTATCACAAATCATCAGTAG-AAGTTG 545404 CGTCACAATA Statistics Matches: 564, Mismatches: 36, Indels: 1 0.94 0.06 0.00 Matches are distributed among these distances: 78 558 0.99 79 6 0.01 ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32 Consensus pattern (78 bp): TTACAGTCTCTATCTAATAGTGACATCTCTATCACAAATCATCAGTAGAAGTTGTCATTGCGTCA CAATAGCGTCATA Found at i:545637 original size:6 final size:7 Alignment explanation

Indices: 545620--545646 Score: 54 Period size: 7 Copynumber: 3.9 Consensus size: 7 545610 CAAAAATATT 545620 TTTTTTA 1 TTTTTTA 545627 TTTTTTA 1 TTTTTTA 545634 TTTTTTA 1 TTTTTTA 545641 TTTTTT 1 TTTTTT 545647 TTGGGTATAA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 20 1.00 ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89 Consensus pattern (7 bp): TTTTTTA Found at i:545637 original size:16 final size:16 Alignment explanation

Indices: 545616--545648 Score: 50 Period size: 16 Copynumber: 2.1 Consensus size: 16 545606 AACTCAAAAA 545616 TATTTTTTTTATTTTT 1 TATTTTTTTTATTTTT 545632 TATTTTTTATT-TTTTT 1 TATTTTTT-TTATTTTT 545648 T 1 T 545649 GGGTATAATG Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 16 14 0.88 17 2 0.12 ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88 Consensus pattern (16 bp): TATTTTTTTTATTTTT Found at i:545719 original size:31 final size:31 Alignment explanation

Indices: 545680--545867 Score: 367 Period size: 31 Copynumber: 6.1 Consensus size: 31 545670 TATCTCTATA 545680 TGCATTATAAATCTCTATAAGATCTTATCAC 1 TGCATTATAAATCTCTATAAGATCTTATCAC * 545711 TGCTTTATAAATCTCTATAAGATCTTATCAC 1 TGCATTATAAATCTCTATAAGATCTTATCAC 545742 TGCATTATAAATCTCTATAAGATCTTATCAC 1 TGCATTATAAATCTCTATAAGATCTTATCAC 545773 TGCATTATAAATCTCTATAAGATCTTATCAC 1 TGCATTATAAATCTCTATAAGATCTTATCAC 545804 TGCATTATAAATCTCTATAAGATCTTATCAC 1 TGCATTATAAATCTCTATAAGATCTTATCAC 545835 TGCATTATAAATCTCTATAAGATCTTATCAC 1 TGCATTATAAATCTCTATAAGATCTTATCAC 545866 TG 1 TG 545868 TGTATCTAAG Statistics Matches: 155, Mismatches: 2, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 31 155 1.00 ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39 Consensus pattern (31 bp): TGCATTATAAATCTCTATAAGATCTTATCAC Found at i:545735 original size:11 final size:10 Alignment explanation

Indices: 545685--545859 Score: 53 Period size: 10 Copynumber: 16.9 Consensus size: 10 545675 CTATATGCAT 545685 TATAAATCTC 1 TATAAATCTC 545695 TATAAGATCT- 1 TATAA-ATCTC * * * 545705 TATCACTGCTT 1 TATAAAT-CTC 545716 TATAAATCTC 1 TATAAATCTC 545726 TATAAGATCT- 1 TATAA-ATCTC * * 545736 TATCACTGCAT- 1 TATAAAT-C-TC 545747 TATAAATCTC 1 TATAAATCTC 545757 TATAAGATCT- 1 TATAA-ATCTC * * 545767 TATCACTGCAT- 1 TATAAAT-C-TC 545778 TATAAATCTC 1 TATAAATCTC 545788 TATAAGATCT- 1 TATAA-ATCTC * * 545798 TATCACTGCAT- 1 TATAAAT-C-TC 545809 TATAAATCTC 1 TATAAATCTC 545819 TATAAGATCT- 1 TATAA-ATCTC * * 545829 TATCACTGCAT- 1 TATAAAT-C-TC 545840 TATAAATCTC 1 TATAAATCTC 545850 TATAAGATCT 1 TATAA-ATCT 545860 TATCACTGTG Statistics Matches: 124, Mismatches: 21, Indels: 39 0.67 0.11 0.21 Matches are distributed among these distances: 9 9 0.07 10 62 0.50 11 53 0.43 ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39 Consensus pattern (10 bp): TATAAATCTC Found at i:546596 original size:2 final size:2 Alignment explanation

Indices: 546589--546649 Score: 122 Period size: 2 Copynumber: 30.5 Consensus size: 2 546579 CGATACGCCA 546589 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 546631 TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC T 546650 TCTTCTTCTT Statistics Matches: 59, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 59 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:546655 original size:3 final size:3 Alignment explanation

Indices: 546647--546688 Score: 84 Period size: 3 Copynumber: 14.0 Consensus size: 3 546637 TCTCTCTCTC 546647 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT 1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT 546689 AAATATACAT Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 39 1.00 ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67 Consensus pattern (3 bp): TCT Found at i:548468 original size:2 final size:2 Alignment explanation

Indices: 548461--548510 Score: 100 Period size: 2 Copynumber: 25.0 Consensus size: 2 548451 GAATGCCATG 548461 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 548503 TC TC TC TC 1 TC TC TC TC 548511 GTTTGTGAAG Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 48 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:548662 original size:30 final size:31 Alignment explanation

Indices: 548626--548685 Score: 95 Period size: 30 Copynumber: 1.9 Consensus size: 31 548616 ACCTTTTAAA 548626 AGTTGTTAAAGATTAC-ATATTTATATATTT 1 AGTTGTTAAAGATTACAATATTTATATATTT * 548656 AGTTGTTTAAGATTACATATATTTATATAT 1 AGTTGTTAAAGATTACA-ATATTTATATAT 548686 AAATCAGTTA Statistics Matches: 27, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 30 15 0.56 32 12 0.44 ACGTcount: A:0.37, C:0.03, G:0.10, T:0.50 Consensus pattern (31 bp): AGTTGTTAAAGATTACAATATTTATATATTT Found at i:549868 original size:16 final size:16 Alignment explanation

Indices: 549847--549877 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 549837 ATGGAATTAC 549847 TTCGTTACATCCGTAA 1 TTCGTTACATCCGTAA * 549863 TTCGTTATATCCGTA 1 TTCGTTACATCCGTA 549878 TAACGAATTC Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.23, C:0.23, G:0.13, T:0.42 Consensus pattern (16 bp): TTCGTTACATCCGTAA Found at i:550181 original size:15 final size:16 Alignment explanation

Indices: 550146--550196 Score: 59 Period size: 17 Copynumber: 3.1 Consensus size: 16 550136 TCAAAATCAG 550146 TTCGTTATATCCTTAAA 1 TTCGTTATATCC-TAAA * 550163 TTCGTTATATCC-GAA 1 TTCGTTATATCCTAAA * 550178 TTCGTTATAACCATAAA 1 TTCGTTATATCC-TAAA 550195 TT 1 TT 550197 TTGCAAAGAT Statistics Matches: 29, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 15 13 0.45 17 16 0.55 ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43 Consensus pattern (16 bp): TTCGTTATATCCTAAA Found at i:551020 original size:15 final size:14 Alignment explanation

Indices: 550993--551030 Score: 51 Period size: 15 Copynumber: 2.7 Consensus size: 14 550983 TTAAATCAGT 550993 AAAGTATAT-AACA 1 AAAGTATATAAACA 551006 AAAGTATATACAACA 1 AAAGTATATA-AACA * 551021 AAAATATATA 1 AAAGTATATA 551031 TTTAAAAACA Statistics Matches: 22, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 13 9 0.41 15 13 0.59 ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24 Consensus pattern (14 bp): AAAGTATATAAACA Found at i:552145 original size:70 final size:70 Alignment explanation

Indices: 552032--553387 Score: 1796 Period size: 70 Copynumber: 20.1 Consensus size: 70 552022 TGATGCCATG * * 552032 GTACCATATAGTGGAGTCACAGGTAAACAGATCCACCTGACTTCTCCTTCTACTGACCAAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 552097 GTAAA 66 GTAAA * 552102 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCAAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 552167 GTAAA 66 GTAAA * * 552172 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACAGACGGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 552237 GTAAA 66 GTAAA * * 552242 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACAGACGGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 552307 GTAAA 66 GTAAA * 552312 GTACCATATAGTGGAGTCACAGGTAAACAGACCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 552377 GTAAA 66 GTAAA * 552382 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACGGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT * 552447 ATAAA 66 GTAAA * 552452 GTACTATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 552517 GTAAA 66 GTAAA 552522 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 552587 GTAAA 66 GTAAA ** * 552592 GTACCATATAGTGGAACCACAGGTAAATAGATCCCCCTGA------CTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 552651 GTAAA 66 GTAAA ** 552656 GTACCATATAGTGGAACCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 552721 GTAAA 66 GTAAA * 552726 GTACCATATAGTGGAGTCACAGGTAAATAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 552791 GTAAA 66 GTAAA ** * 552796 GTACCATATAGTGGAACCACAGGTAAATAGAT---CC---CTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 552855 GTAAA 66 GTAAA ** * 552860 GTACCATATAGTGGAACCACAGGT----A-A-CCACCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 552919 GTAAA 66 GTAAA * 552924 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCGTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT ** 552989 AGTGGA 66 -GTAAA * * * * *** * * ** * * 552995 GT--C--ACAG-GTA--AACAGATCCCCCTGA----CTTTCCTTCTAC-T-GA----CCGAGTTA 1 GTACCATATAGTGGAGTCACAGGT-AAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTA * 553043 TATAAA 65 TGTAAA 553049 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT ** 553114 AGTGGA 66 -GTAAA * * * * * ** * * 553120 GT--C--ACAG-GTA--AACA-G--ATC---CCCCCGACTTTCCTTCTAC-T-GA----CCGAGT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCC--C-TGACTTCTCCTTCTACTGACCGAGT * 553166 TATATAAA 63 TATGTAAA 553174 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTT-TCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 553238 GTAAA 66 GTAAA 553243 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 553308 GTAAA 66 GTAAA * 553313 GTACCATATAGTGGAGTCACAGGTAAATAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 553378 GTAAA 66 GTAAA 553383 GTACC 1 GTACC 553388 TACATTATAG Statistics Matches: 1141, Mismatches: 84, Indels: 122 0.85 0.06 0.09 Matches are distributed among these distances: 54 8 0.01 55 18 0.02 56 2 0.00 58 10 0.01 59 7 0.01 60 7 0.01 61 27 0.02 62 1 0.00 63 3 0.00 64 192 0.17 65 6 0.01 66 5 0.00 67 12 0.01 68 1 0.00 69 59 0.05 70 774 0.68 71 9 0.01 ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27 Consensus pattern (70 bp): GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT GTAAA Found at i:552284 original size:140 final size:140 Alignment explanation

Indices: 552032--553387 Score: 2117 Period size: 140 Copynumber: 10.0 Consensus size: 140 552022 TGATGCCATG * * 552032 GTACCATATAGTGGAGTCACAGGTAAACAGATCCACCTGACTTCTCCTTCTACTGACCAAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT * 552097 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCAA 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA 552162 GTTATGTAAA 131 GTTATGTAAA * * 552172 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACAGACGGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT * * 552237 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACAGACGGA 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA 552302 GTTATGTAAA 131 GTTATGTAAA * 552312 GTACCATATAGTGGAGTCACAGGTAAACAGACCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT * 552377 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACGGA 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA * 552442 GTTATATAAA 131 GTTATGTAAA * 552452 GTACTATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 552517 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA 552582 GTTATGTAAA 131 GTTATGTAAA ** * 552592 GTACCATATAGTGGAACCACAGGTAAATAGATCCCCCTGA------CTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT ** 552651 GTAAAGTACCATATAGTGGAACCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA 552716 GTTATGTAAA 131 GTTATGTAAA * 552726 GTACCATATAGTGGAGTCACAGGTAAATAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT ** * 552791 GTAAAGTACCATATAGTGGAACCACAGGTAAATAGAT---CC---CTTCTCCTTCTACTGACCGA 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA 552850 GTTATGTAAA 131 GTTATGTAAA ** * 552860 GTACCATATAGTGGAACCACAGGT----A-A-CCACCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT * 552919 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCGTCTACTGACC-- 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA 552982 -----G---A 131 GTTATGTAAA 552984 GT----TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTT-TCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT * 553044 ATAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACC-- 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA 553107 -----G---A 131 GTTATGTAAA * 553109 GT----TATAGTGGAGTCACAGGTAAACAGATCCCCCCGACTT-TCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT * 553169 ATAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTT-TCCTTCTACTGACCGA 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA 553233 GTTATGTAAA 131 GTTATGTAAA 553243 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT * 553308 GTAAAGTACCATATAGTGGAGTCACAGGTAAATAGATCCCCCTGACTTCTCCTTCTACTGACCGA 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA 553373 GTTATGTAAA 131 GTTATGTAAA 553383 GTACC 1 GTACC 553388 TACATTATAG Statistics Matches: 1141, Mismatches: 41, Indels: 68 0.91 0.03 0.05 Matches are distributed among these distances: 120 16 0.01 124 18 0.02 125 192 0.17 126 10 0.01 127 1 0.00 128 66 0.06 129 1 0.00 130 1 0.00 131 3 0.00 134 202 0.18 137 2 0.00 138 36 0.03 139 67 0.06 140 526 0.46 ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27 Consensus pattern (140 bp): GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA GTTATGTAAA Found at i:552394 original size:210 final size:209 Alignment explanation

Indices: 552032--553387 Score: 2118 Period size: 210 Copynumber: 6.7 Consensus size: 209 552022 TGATGCCATG * * 552032 GTACCATATAGTGGAGTCACAGGTAAACAGATCCACCTGACTTCTCCTTCTACTGACCAAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT * 552097 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCAA 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA * 552162 GTTATGTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACAG 131 GTTATGTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTT-TCCTTCTACTG * 552227 ACGGAGTTATGTAAA 195 ACCGAGTTATGTAAA * * 552242 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACAGACGGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT * 552307 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGACCCCCCTGACTTCTCCTTCTACTGACCGA 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA 552372 GTTATGTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTG 131 GTTATGTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTT-TCCTTCTACTG * * 552437 ACGGAGTTATATAAA 195 ACCGAGTTATGTAAA * 552452 GTACTATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 552517 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA ** * 552582 GTTATGTAAAGTACCATATAGTGGAACCACAGGTAAATAGATCCCCCTGA-----CTTCTACTGA 131 GTTATGTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTTCCTTCTACTGA 552642 CCGAGTTATGTAAA 196 CCGAGTTATGTAAA ** 552656 GTACCATATAGTGGAACCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT * 552721 GTAAAGTACCATATAGTGGAGTCACAGGTAAATAGATCCCCCTGACTTCTCCTTCTACTGACCGA 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA ** * * 552786 GTTATGTAAAGTACCATATAGTGGAACCACAGGTAAATAGAT--CCCT---TCTCCTTCTACTGA 131 GTTATGTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTTCCTTCTACTGA 552846 CCGAGTTATGTAAA 196 CCGAGTTATGTAAA ** * 552860 GTACCATATAGTGGAACCACAGGT----A-A-CCACCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT * 552919 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCGTCTACTGACC-- 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA 552982 -----G---AGT----TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTTCCTTCTACTGA 131 GTTATGTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTTCCTTCTACTGA * 553035 CCGAGTTATATAAA 196 CCGAGTTATGTAAA 553049 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACC------- 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT * 553107 G---AGT----TATAGTGGAGTCACAGGTAAACAGATCCCCCCGACTT-TCCTTCTACTGACCGA 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA * 553164 GTTATATAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTTCCTTCTACTGA 131 GTTATGTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTTCCTTCTACTGA 553229 CCGAGTTATGTAAA 196 CCGAGTTATGTAAA 553243 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT 1 GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT * 553308 GTAAAGTACCATATAGTGGAGTCACAGGTAAATAGATCCCCCTGACTTCTCCTTCTACTGACCGA 66 GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA 553373 GTTATGTAAAGTACC 131 GTTATGTAAAGTACC 553388 TACATTATAG Statistics Matches: 1063, Mismatches: 39, Indels: 89 0.89 0.03 0.07 Matches are distributed among these distances: 180 13 0.01 181 36 0.03 184 23 0.02 185 3 0.00 186 4 0.00 188 4 0.00 189 48 0.05 190 3 0.00 191 1 0.00 193 1 0.00 194 121 0.11 195 25 0.02 198 93 0.09 199 1 0.00 200 1 0.00 201 1 0.00 202 4 0.00 204 241 0.23 208 35 0.03 209 30 0.03 210 375 0.35 ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27 Consensus pattern (209 bp): GTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTAT GTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGA GTTATGTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTTCCTTCTACTGA CCGAGTTATGTAAA Found at i:552997 original size:56 final size:55 Alignment explanation

Indices: 552930--553044 Score: 212 Period size: 56 Copynumber: 2.1 Consensus size: 55 552920 TAAAGTACCA 552930 TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCGTCTACTGACCGAGT 1 TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTT-TCCGTCTACTGACCGAGT * 552986 TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTTCCTTCTACTGACCGAGT 1 TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTTCCGTCTACTGACCGAGT 553041 TATA 1 TATA 553045 TAAAGTACCA Statistics Matches: 58, Mismatches: 1, Indels: 1 0.97 0.02 0.02 Matches are distributed among these distances: 55 21 0.36 56 37 0.64 ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27 Consensus pattern (55 bp): TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTTCCGTCTACTGACCGAGT Found at i:553066 original size:125 final size:126 Alignment explanation

Indices: 552732--553377 Score: 880 Period size: 125 Copynumber: 5.0 Consensus size: 126 552722 TAAAGTACCA * 552732 TATAGTGGAGTCACAGGTAAATAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTATGTAAAG 1 TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTATGTAAAG ** * 552797 TACCATATAGTGGAACCACAGGTAAATAGAT---CC---CTTCTCCTTCTACTGACCGAGT 66 TACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGT ** * * * * 552852 TAT-GTAAAGTACCATATAGTGGAACCACAGGTAACCACCTGACTTCTCCTTCTACTGACCGAGT 1 TATAGTGGAGT--C--ACAG-GTAA--ACA-G-ATCCCCCTGACTTCTCCTTCTACTGACCGAGT * 552916 TATGTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCGTCTACTGAC 57 TATGTAAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGAC 552981 CGAGT 122 CGAGT * 552986 TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTT-TCCTTCTACTGACCGAGTTATATAAAG 1 TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTATGTAAAG 553050 TACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGT 66 TACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGT * * 553111 TATAGTGGAGTCACAGGTAAACAGATCCCCCCGACTT-TCCTTCTACTGACCGAGTTATATAAAG 1 TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTATGTAAAG 553175 TACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTT-TCCTTCTACTGACCGAGTTATG 66 TACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACC-------G 553239 TAAAGT 124 ---AGT 553245 ACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTATGT 1 ----TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTATGT * 553310 AAAGTACCATATAGTGGAGTCACAGGTAAATAGATCCCCCTGACTTCTCCTTCTACTGACCGAGT 62 AAAGTACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGT 553375 TAT 1 TAT 553378 GTAAAGTACC Statistics Matches: 471, Mismatches: 23, Indels: 58 0.85 0.04 0.11 Matches are distributed among these distances: 119 5 0.01 120 3 0.01 121 1 0.00 123 3 0.01 124 17 0.04 125 191 0.41 126 16 0.03 127 2 0.00 128 70 0.15 130 6 0.01 131 6 0.01 133 2 0.00 134 27 0.06 135 5 0.01 138 36 0.08 139 67 0.14 140 14 0.03 ACGTcount: A:0.28, C:0.26, G:0.18, T:0.27 Consensus pattern (126 bp): TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTATGTAAAG TACCATATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGT Found at i:553122 original size:56 final size:55 Alignment explanation

Indices: 553055--553169 Score: 212 Period size: 56 Copynumber: 2.1 Consensus size: 55 553045 TAAAGTACCA * 553055 TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGT 1 TATAGTGGAGTCACAGGTAAACAGATCCCCCCGACTT-TCCTTCTACTGACCGAGT 553111 TATAGTGGAGTCACAGGTAAACAGATCCCCCCGACTTTCCTTCTACTGACCGAGT 1 TATAGTGGAGTCACAGGTAAACAGATCCCCCCGACTTTCCTTCTACTGACCGAGT 553166 TATA 1 TATA 553170 TAAAGTACCA Statistics Matches: 58, Mismatches: 1, Indels: 1 0.97 0.02 0.02 Matches are distributed among these distances: 55 22 0.38 56 36 0.62 ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27 Consensus pattern (55 bp): TATAGTGGAGTCACAGGTAAACAGATCCCCCCGACTTTCCTTCTACTGACCGAGT Found at i:553222 original size:69 final size:70 Alignment explanation

Indices: 553111--553387 Score: 513 Period size: 69 Copynumber: 4.0 Consensus size: 70 553101 CTGACCGAGT * * 553111 TATAGTGGAGTCACAGGTAAACAGATCCCCCCGACTT-TCCTTCTACTGACCGAGTTATATAAAG 1 TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTATGTAAAG 553175 TACCA 66 TACCA 553180 TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTT-TCCTTCTACTGACCGAGTTATGTAAAG 1 TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTATGTAAAG 553244 TACCA 66 TACCA 553249 TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTATGTAAAG 1 TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTATGTAAAG 553314 TACCA 66 TACCA * 553319 TATAGTGGAGTCACAGGTAAATAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTATGTAAAG 1 TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTATGTAAAG 553384 TACC 66 TACC 553388 TACATTATAG Statistics Matches: 204, Mismatches: 3, Indels: 1 0.98 0.01 0.00 Matches are distributed among these distances: 69 104 0.51 70 100 0.49 ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27 Consensus pattern (70 bp): TATAGTGGAGTCACAGGTAAACAGATCCCCCTGACTTCTCCTTCTACTGACCGAGTTATGTAAAG TACCA Found at i:559403 original size:22 final size:22 Alignment explanation

Indices: 559378--559613 Score: 141 Period size: 21 Copynumber: 10.9 Consensus size: 22 559368 CTTCTGTAAT * 559378 TTTTCCTCTGGAA-CTTTGTTAC 1 TTTTCCTCT-AAATCTTTGTTAC * * 559400 TTTT-CTCTGAATCTTTGTTAT 1 TTTTCCTCTAAATCTTTGTTAC * * 559421 TTTTTCTCTAAACCTTAT-TT-C 1 TTTTCCTCTAAATCTT-TGTTAC * 559442 TTTTCCTCTAAATTTTTGTTAC 1 TTTTCCTCTAAATCTTTGTTAC * *** * 559464 TTTTCCTGTTTGTCTTTGTT-T 1 TTTTCCTCTAAATCTTTGTTAC * * 559485 TTTTCCTCTGAATCTTTGTTAT 1 TTTTCCTCTAAATCTTTGTTAC * * 559507 TTTTTCTCTAAACCTTAT-TT-C 1 TTTTCCTCTAAATCTT-TGTTAC * * 559528 TTTTCCTCTAAATTTTTTGTTAT 1 TTTTCCTCTAAA-TCTTTGTTAC * *** * 559551 TTTTCCTGTTTGTCTTTGTT-T 1 TTTTCCTCTAAATCTTTGTTAC * 559572 TTTTCCTCTGAATCTTTGTTA- 1 TTTTCCTCTAAATCTTTGTTAC 559593 TTTTCCCTCTGAAA-CTTTGTT 1 TTTT-CCTCT-AAATCTTTGTT 559614 TACAGGATTG Statistics Matches: 166, Mismatches: 35, Indels: 26 0.73 0.15 0.11 Matches are distributed among these distances: 20 4 0.02 21 80 0.48 22 70 0.42 23 12 0.07 ACGTcount: A:0.13, C:0.19, G:0.08, T:0.60 Consensus pattern (22 bp): TTTTCCTCTAAATCTTTGTTAC Found at i:559523 original size:86 final size:87 Alignment explanation

Indices: 559400--559596 Score: 371 Period size: 87 Copynumber: 2.3 Consensus size: 87 559390 ACTTTGTTAC 559400 TTTT-CTCTGAATCTTTGTTATTTTTTCTCTAAACCTTATTTCTTTTCCTCTAAA-TTTTTGTTA 1 TTTTCCTCTGAATCTTTGTTATTTTTTCTCTAAACCTTATTTCTTTTCCTCTAAATTTTTTGTTA 559463 CTTTTCCTGTTTGTCTTTGTTT 66 CTTTTCCTGTTTGTCTTTGTTT 559485 TTTTCCTCTGAATCTTTGTTATTTTTTCTCTAAACCTTATTTCTTTTCCTCTAAATTTTTTGTTA 1 TTTTCCTCTGAATCTTTGTTATTTTTTCTCTAAACCTTATTTCTTTTCCTCTAAATTTTTTGTTA * 559550 TTTTTCCTGTTTGTCTTTGTTT 66 CTTTTCCTGTTTGTCTTTGTTT 559572 TTTTCCTCTGAATCTTTGTTATTTT 1 TTTTCCTCTGAATCTTTGTTATTTT 559597 CCCTCTGAAA Statistics Matches: 109, Mismatches: 1, Indels: 2 0.97 0.01 0.02 Matches are distributed among these distances: 85 4 0.04 86 50 0.46 87 55 0.50 ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63 Consensus pattern (87 bp): TTTTCCTCTGAATCTTTGTTATTTTTTCTCTAAACCTTATTTCTTTTCCTCTAAATTTTTTGTTA CTTTTCCTGTTTGTCTTTGTTT Found at i:559611 original size:43 final size:43 Alignment explanation

Indices: 559376--559614 Score: 205 Period size: 43 Copynumber: 5.5 Consensus size: 43 559366 TACTTCTGTA * * 559376 ATTTTTCCTCTGGAACTTTGTTACTTTT-CTCTGAATCTTTGTT 1 ATTTTTCCTCTGAAACTTTGTT-TTTTTCCTCTGAATCTTTGTT * * * * * 559419 ATTTTTTCTCT-AAACCTTATTTCTTTTCCTCTAAATTTTTGTT 1 ATTTTTCCTCTGAAACTTTGTTT-TTTTCCTCTGAATCTTTGTT * * **** 559462 ACTTTTCCTGTTTGTCTTTGTTTTTTTCCTCTGAATCTTTGTT 1 ATTTTTCCTCTGAAACTTTGTTTTTTTCCTCTGAATCTTTGTT * * * * * 559505 ATTTTTTCTCT-AAACCTTATTTCTTTTCCTCTAAATTTTTTGTT 1 ATTTTTCCTCTGAAACTTTGTTT-TTTTCCTCTGAA-TCTTTGTT * **** 559549 ATTTTTCCTGTTTGTCTTTGTTTTTTTCCTCTGAATCTTTGTT 1 ATTTTTCCTCTGAAACTTTGTTTTTTTCCTCTGAATCTTTGTT * 559592 ATTTTCCCTCTGAAACTTTGTTT 1 ATTTTTCCTCTGAAACTTTGTTT 559615 ACAGGATTGC Statistics Matches: 148, Mismatches: 42, Indels: 12 0.73 0.21 0.06 Matches are distributed among these distances: 42 17 0.11 43 92 0.62 44 33 0.22 45 6 0.04 ACGTcount: A:0.13, C:0.18, G:0.08, T:0.60 Consensus pattern (43 bp): ATTTTTCCTCTGAAACTTTGTTTTTTTCCTCTGAATCTTTGTT Found at i:559762 original size:32 final size:32 Alignment explanation

Indices: 559726--559863 Score: 154 Period size: 32 Copynumber: 4.1 Consensus size: 32 559716 ATCTGGTGAG ** 559726 TACAAACTACATTCTTCTAATCAGTCCTAACT 1 TACAAACTACACCCTTCTAATCAGTCCTAACT * 559758 TACAAACTACACCCTTCTAACCAGTCCTAACT 1 TACAAACTACACCCTTCTAATCAGTCCTAACT * 559790 TACACAA-T-CAGTCCTAACTTACACAATCAGTCCTAACT 1 TACA-AACTACA--CC---CTT-C-TAATCAGTCCTAACT 559828 TACAAACTACACCCTTCTAATCAGTCCTAACT 1 TACAAACTACACCCTTCTAATCAGTCCTAACT 559860 TACA 1 TACA 559864 CAATCAGTCC Statistics Matches: 90, Mismatches: 6, Indels: 20 0.78 0.05 0.17 Matches are distributed among these distances: 31 2 0.02 32 52 0.58 33 5 0.06 34 3 0.03 36 3 0.03 37 5 0.06 38 18 0.20 39 2 0.02 ACGTcount: A:0.36, C:0.33, G:0.04, T:0.28 Consensus pattern (32 bp): TACAAACTACACCCTTCTAATCAGTCCTAACT Found at i:559850 original size:51 final size:51 Alignment explanation

Indices: 559795--559916 Score: 199 Period size: 51 Copynumber: 2.4 Consensus size: 51 559785 TAACTTACAC 559795 AATCAGTCCTAACTTACACAATCAGTCCTAACTTACAAACTACACCCTTCT 1 AATCAGTCCTAACTTACACAATCAGTCCTAACTTACAAACTACACCCTTCT * * * * 559846 AATCAGTCCTAACTTACACAATCAGTCCTAACTTACACATTACATCCTTTT 1 AATCAGTCCTAACTTACACAATCAGTCCTAACTTACAAACTACACCCTTCT * 559897 AATCTGTCCTAACTTACACA 1 AATCAGTCCTAACTTACACA 559917 TCACATCCTT Statistics Matches: 66, Mismatches: 5, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 51 66 1.00 ACGTcount: A:0.34, C:0.31, G:0.04, T:0.30 Consensus pattern (51 bp): AATCAGTCCTAACTTACACAATCAGTCCTAACTTACAAACTACACCCTTCT Found at i:559857 original size:70 final size:70 Alignment explanation

Indices: 559744--559884 Score: 273 Period size: 70 Copynumber: 2.0 Consensus size: 70 559734 ACATTCTTCT 559744 AATCAGTCCTAACTTACAAACTACACCCTTCTAACCAGTCCTAACTTACACAATCAGTCCTAACT 1 AATCAGTCCTAACTTACAAACTACACCCTTCTAACCAGTCCTAACTTACACAATCAGTCCTAACT 559809 TACAC 66 TACAC * 559814 AATCAGTCCTAACTTACAAACTACACCCTTCTAATCAGTCCTAACTTACACAATCAGTCCTAACT 1 AATCAGTCCTAACTTACAAACTACACCCTTCTAACCAGTCCTAACTTACACAATCAGTCCTAACT 559879 TACAC 66 TACAC 559884 A 1 A 559885 TTACATCCTT Statistics Matches: 70, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 70 70 1.00 ACGTcount: A:0.36, C:0.33, G:0.04, T:0.26 Consensus pattern (70 bp): AATCAGTCCTAACTTACAAACTACACCCTTCTAACCAGTCCTAACTTACACAATCAGTCCTAACT TACAC Found at i:559893 original size:19 final size:19 Alignment explanation

Indices: 559779--559884 Score: 129 Period size: 19 Copynumber: 5.9 Consensus size: 19 559769 CCCTTCTAAC 559779 CAGTCCTAACTTACACAAT 1 CAGTCCTAACTTACACAAT 559798 CAGTCCTAACTTACACAAT 1 CAGTCCTAACTTACACAAT 559817 CAGTCCTAACTTACA-AACT 1 CAGTCCTAACTTACACAA-T * 559836 ACA--CC---CTT-C-TAAT 1 -CAGTCCTAACTTACACAAT 559849 CAGTCCTAACTTACACAAT 1 CAGTCCTAACTTACACAAT 559868 CAGTCCTAACTTACACA 1 CAGTCCTAACTTACACA 559885 TTACATCCTT Statistics Matches: 76, Mismatches: 1, Indels: 20 0.78 0.01 0.21 Matches are distributed among these distances: 12 2 0.03 13 1 0.01 14 5 0.07 15 3 0.04 17 3 0.04 18 5 0.07 19 55 0.72 20 2 0.03 ACGTcount: A:0.36, C:0.33, G:0.05, T:0.26 Consensus pattern (19 bp): CAGTCCTAACTTACACAAT Found at i:559911 original size:32 final size:32 Alignment explanation

Indices: 559865--559926 Score: 106 Period size: 32 Copynumber: 1.9 Consensus size: 32 559855 TAACTTACAC * 559865 AATCAGTCCTAACTTACACATTACATCCTTTT 1 AATCAGTCCTAACTTACACATCACATCCTTTT * 559897 AATCTGTCCTAACTTACACATCACATCCTT 1 AATCAGTCCTAACTTACACATCACATCCTT 559927 CTAAATACTA Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 32 28 1.00 ACGTcount: A:0.31, C:0.31, G:0.03, T:0.35 Consensus pattern (32 bp): AATCAGTCCTAACTTACACATCACATCCTTTT Found at i:560198 original size:32 final size:32 Alignment explanation

Indices: 560175--560741 Score: 819 Period size: 32 Copynumber: 17.6 Consensus size: 32 560165 CTTACACATT 560175 ACATCCTTCTAATCAGTCCTAACTTACATACC 1 ACATCCTTCTAATCAGTCCTAACTTACATACC * * 560207 ACATCCTTCTAATCGGTCCTAACTAACATACC 1 ACATCCTTCTAATCAGTCCTAACTTACATACC 560239 ACATCCTTCTAATCAGTCCTAACTTACATACC 1 ACATCCTTCTAATCAGTCCTAACTTACATACC * * * * 560271 ACACCCTTTTTATCAGTCCTTACTTACACATACC 1 ACATCCTTCTAATCAGTCCTAACTT--ACATACC 560305 ACATCCTTCTAATCAGTCCTAACTTACATACC 1 ACATCCTTCTAATCAGTCCTAACTTACATACC 560337 ACATCCTTCTAATCAGTCCTAACTTACATACC 1 ACATCCTTCTAATCAGTCCTAACTTACATACC * * * 560369 ACACCCTTTTTATCAGTCCTAACTTACACATACC 1 ACATCCTTCTAATCAGTCCTAACTT--ACATACC * * * 560403 ACATCCTTCTAATCAGTCTTAACTCACATTCC 1 ACATCCTTCTAATCAGTCCTAACTTACATACC * * * * ** 560435 ATATCCTTTTAATCAGTCCTATCTTACACATT 1 ACATCCTTCTAATCAGTCCTAACTTACATACC 560467 ACATCCTTCTAATCAGTCCTAACTTACATACC 1 ACATCCTTCTAATCAGTCCTAACTTACATACC * * ** 560499 ATATCCTTCTAATCAGTCCTAACTTACACATT 1 ACATCCTTCTAATCAGTCCTAACTTACATACC * * 560531 ACATTCTTCTAATCAGTCCTAACTTACACACC 1 ACATCCTTCTAATCAGTCCTAACTTACATACC * * 560563 ACATCCTTCTTATCAGTCCTAACTTACACACC 1 ACATCCTTCTAATCAGTCCTAACTTACATACC * * 560595 ACATCTTTCTTATCAGTCCTAACTTACATACC 1 ACATCCTTCTAATCAGTCCTAACTTACATACC * * 560627 ATATCCTTTTAATCAGTCCTAACTTACATACC 1 ACATCCTTCTAATCAGTCCTAACTTACATACC 560659 ACATCCTTCTAATCAGTCCTAACTTACATACC 1 ACATCCTTCTAATCAGTCCTAACTTACATACC 560691 ACATCCTTCTAATCAGTCCTAACTTACATACC 1 ACATCCTTCTAATCAGTCCTAACTTACATACC * 560723 ACATCCTTCTTATCAGTCC 1 ACATCCTTCTAATCAGTCC 560742 CTTTGCAGAA Statistics Matches: 476, Mismatches: 55, Indels: 8 0.88 0.10 0.01 Matches are distributed among these distances: 32 421 0.88 34 55 0.12 ACGTcount: A:0.30, C:0.33, G:0.03, T:0.34 Consensus pattern (32 bp): ACATCCTTCTAATCAGTCCTAACTTACATACC Found at i:572965 original size:12 final size:12 Alignment explanation

Indices: 572948--572973 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 572938 ACCTTATCGG 572948 AATAACTTTAAT 1 AATAACTTTAAT 572960 AATAACTTTAAT 1 AATAACTTTAAT 572972 AA 1 AA 572974 GGGGCATTTT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38 Consensus pattern (12 bp): AATAACTTTAAT Found at i:583070 original size:7 final size:7 Alignment explanation

Indices: 583045--583111 Score: 80 Period size: 7 Copynumber: 9.6 Consensus size: 7 583035 TTTAGATATT 583045 GAATCTC 1 GAATCTC * 583052 GAATTTC 1 GAATCTC * 583059 AAATCTC 1 GAATCTC 583066 GAATCTC 1 GAATCTC * * 583073 GTATTTC 1 GAATCTC 583080 GAATCTC 1 GAATCTC * * 583087 GTATTTC 1 GAATCTC 583094 GAATCTC 1 GAATCTC 583101 GAATCTC 1 GAATCTC 583108 GAAT 1 GAAT 583112 GATCCTTCTC Statistics Matches: 48, Mismatches: 12, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 7 48 1.00 ACGTcount: A:0.28, C:0.22, G:0.13, T:0.36 Consensus pattern (7 bp): GAATCTC Found at i:583070 original size:21 final size:21 Alignment explanation

Indices: 583045--583111 Score: 89 Period size: 21 Copynumber: 3.2 Consensus size: 21 583035 TTTAGATATT * 583045 GAATCTCGAATTTCAAATCTC 1 GAATCTCGAATTTCGAATCTC * 583066 GAATCTCGTATTTCGAATCTC 1 GAATCTCGAATTTCGAATCTC * * * 583087 GTATTTCGAATCTCGAATCTC 1 GAATCTCGAATTTCGAATCTC 583108 GAAT 1 GAAT 583112 GATCCTTCTC Statistics Matches: 39, Mismatches: 7, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 21 39 1.00 ACGTcount: A:0.28, C:0.22, G:0.13, T:0.36 Consensus pattern (21 bp): GAATCTCGAATTTCGAATCTC Found at i:583582 original size:22 final size:22 Alignment explanation

Indices: 583554--583684 Score: 244 Period size: 22 Copynumber: 6.0 Consensus size: 22 583544 TTCGAGCCGA 583554 AAACTCATATTGTCTAGGGTTT 1 AAACTCATATTGTCTAGGGTTT 583576 AAACTCATATTGTCTAGGGTTT 1 AAACTCATATTGTCTAGGGTTT * 583598 AAACTCATATTGACTAGGGTTT 1 AAACTCATATTGTCTAGGGTTT 583620 AAACTCATATTGTCTAGGGTTT 1 AAACTCATATTGTCTAGGGTTT 583642 AAACTCATATTGTCTAGGGTTT 1 AAACTCATATTGTCTAGGGTTT * 583664 AAACTCATATTGTCTGGGGTT 1 AAACTCATATTGTCTAGGGTT 583685 CTTTAAGTTA Statistics Matches: 106, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 22 106 1.00 ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40 Consensus pattern (22 bp): AAACTCATATTGTCTAGGGTTT Found at i:586046 original size:29 final size:28 Alignment explanation

Indices: 586009--586075 Score: 109 Period size: 29 Copynumber: 2.4 Consensus size: 28 585999 CGATAGTTAC 586009 TTTT-CTTTATTGACTTTACGTTTCCTT 1 TTTTACTTTATTGACTTTACGTTTCCTT * 586036 TGTTTACTTTACTGACTTTACGTTTCCTT 1 T-TTTACTTTATTGACTTTACGTTTCCTT 586065 TTTTACTTTAT 1 TTTTACTTTAT 586076 CTTAATTCAG Statistics Matches: 36, Mismatches: 2, Indels: 3 0.88 0.05 0.07 Matches are distributed among these distances: 27 1 0.03 28 12 0.33 29 23 0.64 ACGTcount: A:0.13, C:0.18, G:0.07, T:0.61 Consensus pattern (28 bp): TTTTACTTTATTGACTTTACGTTTCCTT Found at i:587359 original size:116 final size:116 Alignment explanation

Indices: 587150--587729 Score: 968 Period size: 116 Copynumber: 5.0 Consensus size: 116 587140 CCGGTGCTTT 587150 ATAACAACCAACAGGAACATAATAAACGTCTTCAACAACCAGTGTCTGAATAGACTGACCGGAAC 1 ATAACAACCAACAGGAACATAATAAACGTCTTCAACAACCAGTGTCTGAATAGACTGACCGGAAC 587215 CTTAAAGCAG-AGAGTACAACTGATGATTACAACAATCTATAACAACCAACA 66 CTTAAAGCAGAAGA-TACAACTGATGATTACAACAATCTATAACAACCAACA * * 587266 ATAACAACCAACAGGAACATAATGAACGTCTCCAACAACCAGTGTCTGAATAGACTGACCGGAAC 1 ATAACAACCAACAGGAACATAATAAACGTCTTCAACAACCAGTGTCTGAATAGACTGACCGGAAC * 587331 CTTAAAGCAGAAGATACAACTGAGGATTACAACAATCTATAACAACCAACA 66 CTTAAAGCAGAAGATACAACTGATGATTACAACAATCTATAACAACCAACA * * * 587382 ATAACAACCAACAGGAACATAATGAACTTCTTCAACACCCAGTGTCTGAATAGACTGACCGGAAC 1 ATAACAACCAACAGGAACATAATAAACGTCTTCAACAACCAGTGTCTGAATAGACTGACCGGAAC * 587447 CTTAAAGCAGAAGATACAACTGAGGATTACAACAATCTATAACAACCAACCA 66 CTTAAAGCAGAAGATACAACTGATGATTACAACAATCTATAACAACCAA-CA * * 587499 TTATAACAACCAACAGGAACATAATAAACGTCTCCAACAACCAGTGTCTGAATAGACTGACCGAA 1 --ATAACAACCAACAGGAACATAATAAACGTCTTCAACAACCAGTGTCTGAATAGACTGACCGGA * 587564 ACCTTAAAACAG-AGAGTACAACTGATGATTACAACAATCTATAACAACCAACA 64 ACCTTAAAGCAGAAGA-TACAACTGATGATTACAACAATCTATAACAACCAACA * * 587617 ATAACAACCAACAGGAACATAATTAACGTCTTCAACAACCAGTGTCTGAATAGACTGACCGAAAC 1 ATAACAACCAACAGGAACATAATAAACGTCTTCAACAACCAGTGTCTGAATAGACTGACCGGAAC * 587682 CTTAAAGCAGAAAGA-ACCACTGATGATTACAACAATCTATAACAACCA 66 CTTAAAGCAG-AAGATACAACTGATGATTACAACAATCTATAACAACCA 587730 GTGTCTAAAT Statistics Matches: 440, Mismatches: 17, Indels: 14 0.93 0.04 0.03 Matches are distributed among these distances: 116 324 0.74 117 5 0.01 118 8 0.02 119 103 0.23 ACGTcount: A:0.45, C:0.24, G:0.13, T:0.18 Consensus pattern (116 bp): ATAACAACCAACAGGAACATAATAAACGTCTTCAACAACCAGTGTCTGAATAGACTGACCGGAAC CTTAAAGCAGAAGATACAACTGATGATTACAACAATCTATAACAACCAACA Found at i:587616 original size:235 final size:232 Alignment explanation

Indices: 587150--587729 Score: 986 Period size: 235 Copynumber: 2.5 Consensus size: 232 587140 CCGGTGCTTT 587150 ATAACAACCAACAGGAACATAATAAACGTCTTCAACAACCAGTGTCTGAATAGACTGACCGGAAC 1 ATAACAACCAACAGGAACATAATAAACGTCTTCAACAACCAGTGTCTGAATAGACTGACCGGAAC 587215 CTTAAAGCAG-AGAGTACAACTGATGATTACAACAATCTATAACAACCAACAATAACAACCAACA 66 CTTAAAGCAGAAGA-TACAACTGATGATTACAACAATCTATAACAACCAACAATAACAACCAACA * * * 587279 GGAACATAATGAACGTCTCCAACAACCAGTGTCTGAATAGACTGACCGGAACCTTAAAGCAGAAG 130 GGAACATAATAAACGTCTCCAACAACCAGTGTCTGAATAGACTGACCGAAACCTTAAAACAGAAG 587344 ATACAACTGAGGATTACAACAATCTATAACAACCAACA 195 ATACAACTGAGGATTACAACAATCTATAACAACCAACA * * * 587382 ATAACAACCAACAGGAACATAATGAACTTCTTCAACACCCAGTGTCTGAATAGACTGACCGGAAC 1 ATAACAACCAACAGGAACATAATAAACGTCTTCAACAACCAGTGTCTGAATAGACTGACCGGAAC * 587447 CTTAAAGCAGAAGATACAACTGAGGATTACAACAATCTATAACAACCAACCATTATAACAACCAA 66 CTTAAAGCAGAAGATACAACTGATGATTACAACAATCTATAACAACCAA-CA--ATAACAACCAA 587512 CAGGAACATAATAAACGTCTCCAACAACCAGTGTCTGAATAGACTGACCGAAACCTTAAAACAG- 128 CAGGAACATAATAAACGTCTCCAACAACCAGTGTCTGAATAGACTGACCGAAACCTTAAAACAGA * 587576 AGAGTACAACTGATGATTACAACAATCTATAACAACCAACA 193 AGA-TACAACTGAGGATTACAACAATCTATAACAACCAACA * * 587617 ATAACAACCAACAGGAACATAATTAACGTCTTCAACAACCAGTGTCTGAATAGACTGACCGAAAC 1 ATAACAACCAACAGGAACATAATAAACGTCTTCAACAACCAGTGTCTGAATAGACTGACCGGAAC * 587682 CTTAAAGCAGAAAGA-ACCACTGATGATTACAACAATCTATAACAACCA 66 CTTAAAGCAG-AAGATACAACTGATGATTACAACAATCTATAACAACCA 587730 GTGTCTAAAT Statistics Matches: 328, Mismatches: 14, Indels: 9 0.93 0.04 0.03 Matches are distributed among these distances: 232 106 0.32 233 5 0.02 234 3 0.01 235 210 0.64 236 4 0.01 ACGTcount: A:0.45, C:0.24, G:0.13, T:0.18 Consensus pattern (232 bp): ATAACAACCAACAGGAACATAATAAACGTCTTCAACAACCAGTGTCTGAATAGACTGACCGGAAC CTTAAAGCAGAAGATACAACTGATGATTACAACAATCTATAACAACCAACAATAACAACCAACAG GAACATAATAAACGTCTCCAACAACCAGTGTCTGAATAGACTGACCGAAACCTTAAAACAGAAGA TACAACTGAGGATTACAACAATCTATAACAACCAACA Found at i:587776 original size:72 final size:72 Alignment explanation

Indices: 587650--587796 Score: 224 Period size: 72 Copynumber: 2.0 Consensus size: 72 587640 TAACGTCTTC * * 587650 AACAACCAGTGTCTGAATAGACTGACCGAAACCTTAAAGCAGAAAGAACCACTGATGATTACAAC 1 AACAACCAGTGTCTAAATAGACTGACCGAAACCTTAAAGCAGAAAGAACAACTGATGATTACAAC 587715 AATCTAT 66 AATCTAT * * * * 587722 AACAACCAGTGTCTAAATTGACTGACCGGAACCTTACAA-CAGAGAGTACAACTGATGATTACAA 1 AACAACCAGTGTCTAAATAGACTGACCGAAACCTTA-AAGCAGAAAGAACAACTGATGATTACAA 587786 CAATCTAT 65 CAATCTAT 587794 AAC 1 AAC 587797 CAGTAATAAC Statistics Matches: 68, Mismatches: 6, Indels: 2 0.89 0.08 0.03 Matches are distributed among these distances: 72 66 0.97 73 2 0.03 ACGTcount: A:0.42, C:0.22, G:0.15, T:0.20 Consensus pattern (72 bp): AACAACCAGTGTCTAAATAGACTGACCGAAACCTTAAAGCAGAAAGAACAACTGATGATTACAAC AATCTAT Found at i:588060 original size:13 final size:13 Alignment explanation

Indices: 587990--588072 Score: 60 Period size: 13 Copynumber: 6.4 Consensus size: 13 587980 TAACATTCAG * 587990 TGATAACAACCGA 1 TGATAACAACCAA * * 588003 TGGTAATAACCAA 1 TGATAACAACCAA * 588016 TGATTGA-AACCAA 1 TGA-TAACAACCAA * * * 588029 TAATAACAATCAT 1 TGATAACAACCAA * 588042 TTATAACAACCAA 1 TGATAACAACCAA * * 588055 TGATAACGATCAA 1 TGATAACAACCAA 588068 TGATA 1 TGATA 588073 TAACAACTCA Statistics Matches: 53, Mismatches: 15, Indels: 4 0.74 0.21 0.06 Matches are distributed among these distances: 12 2 0.04 13 49 0.92 14 2 0.04 ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24 Consensus pattern (13 bp): TGATAACAACCAA Found at i:588194 original size:13 final size:13 Alignment explanation

Indices: 588178--588202 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 588168 AAAACAAAAA 588178 CTATGATAACAAC 1 CTATGATAACAAC 588191 CTATGATAACAA 1 CTATGATAACAA 588203 ACATCTATAA Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24 Consensus pattern (13 bp): CTATGATAACAAC Found at i:589424 original size:59 final size:59 Alignment explanation

Indices: 588334--589412 Score: 1865 Period size: 59 Copynumber: 18.3 Consensus size: 59 588324 CAGCCGCCCT * * 588334 ATCCCTCATCCCATTGACAATGAGGGTCAGGTCTACATTACCTTGTATACAGCTGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC * * 588393 ATCCCTCATTCCATTGACCATGAGGGTCAGGTTTACATTACCTTGTATACAGCAGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC * * * 588452 ATCCCTCATTCCATTGACCATGAGGGTCAGGTTTACATTACCTTGTATACAGCTGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC * 588511 ATCCCTCATCCCATTGACAATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC * * 588570 ATCCCTCATTCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCTGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC * * 588629 ATCCCTCATCCCATTGACAATGAGGGTCAGGTCTACATTACCTTGTATACAGCTGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC * * 588688 ATCCCTCATCCCATTGACAATGAGGGTCAGGTCTACATTACCTTGTATACAGCTGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC * 588747 ATCCCTCATCCCATTGACAATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC 588806 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC 588865 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC * 588924 ATCCCTCATCCCGTTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC 588983 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC 589042 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC * 589101 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTCGTATACAGCAGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC * * * 589160 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACAATATCTTGAATACAGCAGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC * * 589219 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTCGTATACAGCTGGTAC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC * 589278 A-CCAC-CATTCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC 1 ATCC-CTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC * * * * 589336 ATCCCTCATTCCATTGACCATGAGGGTCAGGTCTACATTACCTCGTATACAGCTGGTGC 1 ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC * * * 589395 AGCCCTTATTCCATTGAC 1 ATCCCTCATCCCATTGAC 589413 ACTTGGTGTC Statistics Matches: 981, Mismatches: 36, Indels: 6 0.96 0.04 0.01 Matches are distributed among these distances: 58 54 0.06 59 927 0.94 ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28 Consensus pattern (59 bp): ATCCCTCATCCCATTGACCATGAGGGTCAGGTCTACATTACCTTGTATACAGCAGGTAC Found at i:589729 original size:32 final size:31 Alignment explanation

Indices: 589623--590846 Score: 150 Period size: 32 Copynumber: 38.3 Consensus size: 31 589613 TTATGACATA * * 589623 TTATAACATACTGTAAA-ACAAATCGCGTTTGT 1 TTATGACATACTG-AAAGACAAGTCGCGTTT-T * * * 589655 TTATGACATACTGGAGGACAAGTTG-GCTTTT 1 TTATGACATACTGAAAGACAAGTCGCG-TTTT * 589686 TTATAACATACTGAAAGACAAGTCGCGTTCTAT 1 TTATGACATACTGAAAGACAAGTCGCGTT-T-T * * 589719 TT-TGACATACTAGATA-ACAAATCG-GCTTTGT 1 TTATGACATACT-GAAAGACAAGTCGCG-TTT-T * * * 589750 TTATGACAAAGTGTAAGACAAGTCAGC-TTTGT 1 TTATGACATACTGAAAGACAAGTC-GCGTTT-T * * * 589782 TTAT-ACTTTAGTGTAAGACAAGTCGCGTTTT 1 TTATGAC-ATACTGAAAGACAAGTCGCGTTTT * * * 589813 TTCTGATATACTGAAGGA-AAGATCG-GCTTTGT 1 TTATGACATACTGAAAGACAAG-TCGCG-TTT-T * * * * 589845 TTATAACATACT-ATAGGACAAGTCGCATGTGT 1 TTATGACATACTGA-AAGACAAGTCGCGT-TTT * * ** * * * 589877 TTATAACATAGTGTTACACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * *** * * * 589909 TTATAACATAGTCTTACACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT ** * * 589941 TTAT-A-ATACAGTGTTAGACAAGTAGCGTGTGT 1 TTATGACATAC--TGAAAGACAAGTCGCGT-TTT * * ** * 589973 TTATAACATAGTGTTAGACAAGTAGCGTTTGT 1 TTATGACATACTGAAAGACAAGTCGCGTTT-T * * * * * 590005 TTATAACATAGTGTAAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * * ** * 590037 TTATAACATAGTGTAAGACAAGAAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * * ** * ** * 590069 TTATAACGTAGTGTTACACAAGTAACGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * ** * * 590101 TTATAACATAGTGTTAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * * * * * 590133 CTATAACATAGTGTAAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * ** * * 590165 TTATAACATAGTGTTAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * ** * * 590197 TTATAACATAGTGTTAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * ** * * 590229 TTATAACATAGTGTTAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * * * * 590261 TTATAACATAGTGTAAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * ** * * 590293 TTATAACATAGTGTTAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * * * * 590325 TTATAACATAGTGTAAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * ** * * 590357 TTATAACATAGTGTTAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * * * * 590389 TTATAACATAGTGTAAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * ** * * 590421 TTATAACATAGTGTTAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * *** * * 590453 TTATAACATAGTTCTAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * * * * 590485 TTATAACATAGTGTAAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * ** * * 590517 TTATAACATAGTGTTAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * * * * 590549 TTATAACATAGTGTAAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * ** * * 590581 TTATAACATAGTGTTAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * * * * 590613 TTATAACATAGTGTAAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * ** * * 590645 TTATAACATAGTGTTAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * ** * * 590677 TTATAACATAGTGTTAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * ** * * 590709 TTATAACATAGTGTTAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * ** * * 590741 TTATAACATAGTGTTAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * ** * * 590773 TTATAACATAGTGTTAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * * * * * 590805 TTATAACATAGTGTAAGACAAGTAGCGTGTGT 1 TTATGACATACTGAAAGACAAGTCGCGT-TTT * 590837 TTATAACATA 1 TTATGACATA 590847 GTGTTAGACA Statistics Matches: 1088, Mismatches: 76, Indels: 56 0.89 0.06 0.05 Matches are distributed among these distances: 30 7 0.01 31 57 0.05 32 1008 0.93 33 13 0.01 34 3 0.00 ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33 Consensus pattern (31 bp): TTATGACATACTGAAAGACAAGTCGCGTTTT Found at i:589746 original size:63 final size:64 Alignment explanation

Indices: 589623--589773 Score: 164 Period size: 63 Copynumber: 2.4 Consensus size: 64 589613 TTATGACATA * * * * * * 589623 TTATAACATACTGTAAA-ACAAATCGCGTTTGTTTATGACATACTGGAGGACAAGTTGGCTTT-T 1 TTATAACATACTG-AAAGACAAGTCGCGTTTATTTATGACATACTAGAGAACAAATCGGCTTTGT * 589686 TTATAACATACTGAAAGACAAGTCGCGTTCTATTT-TGACATACTAGATAACAAATCGGCTTTGT 1 TTATAACATACTGAAAGACAAGTCGCGTT-TATTTATGACATACTAGAGAACAAATCGGCTTTGT * * * * 589750 TTATGACAAAGTGTAAGACAAGTC 1 TTATAACATACTGAAAGACAAGTC 589774 AGCTTTGTTT Statistics Matches: 74, Mismatches: 11, Indels: 5 0.82 0.12 0.06 Matches are distributed among these distances: 62 3 0.04 63 46 0.62 64 25 0.34 ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32 Consensus pattern (64 bp): TTATAACATACTGAAAGACAAGTCGCGTTTATTTATGACATACTAGAGAACAAATCGGCTTTGT Found at i:589889 original size:95 final size:94 Alignment explanation

Indices: 589639--589904 Score: 249 Period size: 95 Copynumber: 2.8 Consensus size: 94 589629 CATACTGTAA * * * * * 589639 AACAAATC-GCGTTTGTTTATGACATACTGGAGGACAAGTTGGCTTTTTTATAACATACTGAAAG 1 AACAAATCGGC-TTTGTTTATGACATACTGTAGGACAAG-TCGCTTGTTTATAACATAGTGTAAG 589703 ACAAGTCGCGTTCTATTTTGACATACTAGAT 64 ACAAGTCGCGTTCTATTTTGACATACTAGAT * * * * 589734 AACAAATCGGCTTTGTTTATGACAAAGTGTAAGACAAGTCAGCTTTGTTTAT-ACTTTAGTGTAA 1 AACAAATCGGCTTTGTTTATGACATACTGTAGGACAAGTC-GC-TTGTTTATAAC-ATAGTGTAA * 589798 GACAAGTCGCGTT-T-TTTCTGATATACT-GA- 63 GACAAGTCGCGTTCTATTT-TGACATACTAGAT * * 589827 AGGA-AAGATCGGCTTTGTTTATAACATACTATAGGACAAGTCGCATGTGTTTATAACATAGTGT 1 A--ACAA-ATCGGCTTTGTTTATGACATACTGTAGGACAAGTCGC-T-TGTTTATAACATAGTGT * * * 589891 TACACAAGTAGCGT 61 AAGACAAGTCGCGT 589905 GTGTTTATAA Statistics Matches: 141, Mismatches: 20, Indels: 20 0.78 0.11 0.11 Matches are distributed among these distances: 93 1 0.01 94 11 0.08 95 99 0.70 96 30 0.21 ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34 Consensus pattern (94 bp): AACAAATCGGCTTTGTTTATGACATACTGTAGGACAAGTCGCTTGTTTATAACATAGTGTAAGAC AAGTCGCGTTCTATTTTGACATACTAGAT Found at i:590847 original size:32 final size:32 Alignment explanation

Indices: 589842--590857 Score: 1775 Period size: 32 Copynumber: 31.8 Consensus size: 32 589832 AGATCGGCTT * * * * 589842 TGTTTATAACATACT-ATAGGACAAGTCGCATG 1 TGTTTATAACATAGTGTTA-GACAAGTAGCGTG * 589874 TGTTTATAACATAGTGTTACACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG * * 589906 TGTTTATAACATAGTCTTACACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG * * 589938 TGTTTATAATACAGTGTTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG * 589970 TGTTTATAACATAGTGTTAGACAAGTAGCGTT 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG * 590002 TGTTTATAACATAGTGTAAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG * * 590034 TGTTTATAACATAGTGTAAGACAAGAAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG * * * 590066 TGTTTATAACGTAGTGTTACACAAGTAACGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590098 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG * * 590130 TGTCTATAACATAGTGTAAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590162 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590194 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590226 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG * 590258 TGTTTATAACATAGTGTAAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590290 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG * 590322 TGTTTATAACATAGTGTAAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590354 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG * 590386 TGTTTATAACATAGTGTAAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590418 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590450 TGTTTATAACATAGT-TCTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGT-TAGACAAGTAGCGTG * 590482 TGTTTATAACATAGTGTAAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590514 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG * 590546 TGTTTATAACATAGTGTAAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590578 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG * 590610 TGTTTATAACATAGTGTAAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590642 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590674 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590706 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590738 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590770 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG * 590802 TGTTTATAACATAGTGTAAGACAAGTAGCGTG 1 TGTTTATAACATAGTGTTAGACAAGTAGCGTG 590834 TGTTTATAACATAGTGTTAGACAA 1 TGTTTATAACATAGTGTTAGACAA 590858 AGTTATGACA Statistics Matches: 939, Mismatches: 42, Indels: 6 0.95 0.04 0.01 Matches are distributed among these distances: 31 1 0.00 32 935 1.00 33 3 0.00 ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33 Consensus pattern (32 bp): TGTTTATAACATAGTGTTAGACAAGTAGCGTG Found at i:594913 original size:21 final size:21 Alignment explanation

Indices: 594887--594965 Score: 86 Period size: 21 Copynumber: 3.8 Consensus size: 21 594877 CTATATGTTG * 594887 TTGAACAGTTTCAATAAATCA 1 TTGAACAGTTACAATAAATCA * * * 594908 TTGAACAGTTATAATACACCA 1 TTGAACAGTTACAATAAATCA * * * 594929 CTGAACAGTTACAATATATTA 1 TTGAACAGTTACAATAAATCA * 594950 TTGAACTGTTACAATA 1 TTGAACAGTTACAATA 594966 TGTTATAAGA Statistics Matches: 47, Mismatches: 11, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 21 47 1.00 ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33 Consensus pattern (21 bp): TTGAACAGTTACAATAAATCA Found at i:594966 original size:21 final size:21 Alignment explanation

Indices: 594887--595034 Score: 82 Period size: 21 Copynumber: 6.8 Consensus size: 21 594877 CTATATGTTG * * * 594887 TTGAACAGTTTCAATAAATCA 1 TTGAACAGTTACAATATATTA * * ** 594908 TTGAACAGTTATAATACACCA 1 TTGAACAGTTACAATATATTA * 594929 CTGAACAGTTACAATATATTA 1 TTGAACAGTTACAATATATTA * * 594950 TTGAACTGTTACAATATGTTA 1 TTGAACAGTTACAATATATTA * * 594971 -TAAGACAGTTGCAATATATGTA 1 TTGA-ACAGTTACAATATAT-TA * * * 594993 TATTATTAGACGATTACAATATACTA 1 T-TGA--ACA-G-TTACAATATATTA * 595019 TTGAAGAGTTACAATA 1 TTGAACAGTTACAATA 595035 CATGTATATT Statistics Matches: 98, Mismatches: 22, Indels: 14 0.73 0.16 0.10 Matches are distributed among these distances: 20 2 0.02 21 71 0.72 22 3 0.03 23 3 0.03 24 2 0.02 25 4 0.04 26 4 0.04 27 9 0.09 ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34 Consensus pattern (21 bp): TTGAACAGTTACAATATATTA Found at i:594997 original size:48 final size:47 Alignment explanation

Indices: 594943--595066 Score: 128 Period size: 48 Copynumber: 2.6 Consensus size: 47 594933 ACAGTTACAA ** * * 594943 TATATTATTGAACTGTTACAATATGTTA-T-AAGACAGTTGCAATATATG 1 TATATTATTGAAC-GTTACAATATACTATTGAAG--AGTTACAATACATG 594991 TATATTATT-AGACGATTACAATATACTATTGAAGAGTTACAATACATG 1 TATATTATTGA-ACG-TTACAATATACTATTGAAGAGTTACAATACATG * 595039 TATATTATTGGACAGTTACAATATACTA 1 TATATTATTGAAC-GTTACAATATACTA 595067 CTATTGGTCA Statistics Matches: 65, Mismatches: 5, Indels: 12 0.79 0.06 0.15 Matches are distributed among these distances: 47 2 0.03 48 58 0.89 49 2 0.03 50 3 0.05 ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38 Consensus pattern (47 bp): TATATTATTGAACGTTACAATATACTATTGAAGAGTTACAATACATG Found at i:595012 original size:27 final size:27 Alignment explanation

Indices: 594982--595063 Score: 70 Period size: 27 Copynumber: 3.3 Consensus size: 27 594972 AAGACAGTTG 594982 CAATATATGTATATTATTAGACGATTA 1 CAATATATGTATATTATTAGACGATTA * * 595009 CAATATA-CTAT-TGA--AGA-G-TTA 1 CAATATATGTATATTATTAGACGATTA * * 595030 CAATACATGTATATTATTGGAC-AGTTA 1 CAATATATGTATATTATTAGACGA-TTA 595057 CAATATA 1 CAATATA 595064 CTACTATTGG Statistics Matches: 41, Mismatches: 7, Indels: 14 0.66 0.11 0.23 Matches are distributed among these distances: 21 9 0.22 22 4 0.10 23 5 0.12 25 4 0.10 26 3 0.07 27 16 0.39 ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37 Consensus pattern (27 bp): CAATATATGTATATTATTAGACGATTA Found at i:595148 original size:82 final size:82 Alignment explanation

Indices: 595008--595252 Score: 391 Period size: 82 Copynumber: 2.9 Consensus size: 82 594998 TTAGACGATT * * 595008 ACAATATACTATTGAAGAGTTACAATACATGTATATTATTGGACAGTTACAATATACTACTATTG 1 ACAATATACTAATGAACAGTTACAATACATGTATATTATTGGACAGTTACAATATACTACTATTG * 595073 GTCAGTTACAACATACA 66 ATCAGTTACAACATACA * 595090 ACAAAATACTAATGAACAGTTACAATACATGTATATTATTGGACAGTTACAATATACTACTATTG 1 ACAATATACTAATGAACAGTTACAATACATGTATATTATTGGACAGTTACAATATACTACTATTG * 595155 ATCAGTTCCAACATACA 66 ATCAGTTACAACATACA * 595172 ACAATATACTATTGCATTGGACAGTTACAATACATGTATATTATTGGACAGTTACAATATACTAC 1 ACAATATACTA----A-TGAACAGTTACAATACATGTATATTATTGGACAGTTACAATATACTAC 595237 TATTGATCAGTTACAA 61 TATTGATCAGTTACAA 595253 TACAAGTATA Statistics Matches: 150, Mismatches: 8, Indels: 5 0.92 0.05 0.03 Matches are distributed among these distances: 82 87 0.58 86 1 0.01 87 62 0.41 ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33 Consensus pattern (82 bp): ACAATATACTAATGAACAGTTACAATACATGTATATTATTGGACAGTTACAATATACTACTATTG ATCAGTTACAACATACA Found at i:595240 original size:24 final size:24 Alignment explanation

Indices: 595172--595292 Score: 95 Period size: 27 Copynumber: 4.7 Consensus size: 24 595162 CCAACATACA 595172 ACAATATACTATTGCATTGGACAGTT 1 ACAATATACTATT--ATTGGACAGTT 595198 ACAATACATGTA-TATTATTGGACAGTT 1 ACAAT--A--TACTATTATTGGACAGTT * 595225 ACAATATACTACTATT-GATCAGTT 1 ACAATATACTATTATTGGA-CAGTT * 595249 ACAATACAAGTA-TATTACTGGACAGTT 1 ACAAT---A-TACTATTATTGGACAGTT * 595276 ACAATATACTACTATTG 1 ACAATATACTATTATTG 595293 ATCAGTGACA Statistics Matches: 78, Mismatches: 5, Indels: 26 0.72 0.05 0.24 Matches are distributed among these distances: 23 6 0.08 24 23 0.29 25 1 0.01 26 5 0.06 27 32 0.41 28 5 0.06 29 4 0.05 30 2 0.03 ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35 Consensus pattern (24 bp): ACAATATACTATTATTGGACAGTT Found at i:595256 original size:51 final size:51 Alignment explanation

Indices: 595193--595303 Score: 195 Period size: 51 Copynumber: 2.2 Consensus size: 51 595183 TTGCATTGGA * * 595193 CAGTTACAATACATGTATATTATTGGACAGTTACAATATACTACTATTGAT 1 CAGTTACAATACAAGTATATTACTGGACAGTTACAATATACTACTATTGAT 595244 CAGTTACAATACAAGTATATTACTGGACAGTTACAATATACTACTATTGAT 1 CAGTTACAATACAAGTATATTACTGGACAGTTACAATATACTACTATTGAT * 595295 CAGTGACAA 1 CAGTTACAA 595304 CATACAACAA Statistics Matches: 57, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 51 57 1.00 ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33 Consensus pattern (51 bp): CAGTTACAATACAAGTATATTACTGGACAGTTACAATATACTACTATTGAT Found at i:595262 original size:138 final size:133 Alignment explanation

Indices: 595096--595387 Score: 467 Period size: 138 Copynumber: 2.2 Consensus size: 133 595086 TACAACAAAA * * * * 595096 TACTAATGAACAGTTACAATACATGTATATTATTGGACAGTTACAATATACTACTATTGATCAGT 1 TACTATTGATCAGTTACAATACAAGTATATTACTGGACAGTTACAATATACTACTATTGATCAGT ** * 595161 TCCAACATACAACAATATACTATTGCATTGGACAGTTACAATACATGTATATTATTGGACAGTTA 66 GACAACATACAACAATATACTATTGCA---CACA--TACAATACATGTATATTATTGGACAGTTA 595226 CAATATAC 126 CAATATAC 595234 TACTATTGATCAGTTACAATACAAGTATATTACTGGACAGTTACAATATACTACTATTGATCAGT 1 TACTATTGATCAGTTACAATACAAGTATATTACTGGACAGTTACAATATACTACTATTGATCAGT * 595299 GACAACATACAACAATATACTATTGCACACATACAATACATGTATATTATTGGACAGTTACAGTA 66 GACAACATACAACAATATACTATTGCACACATACAATACATGTATATTATTGGACAGTTACAATA 595364 TAC 131 TAC 595367 TACTATTGATCAGTTACAATA 1 TACTATTGATCAGTTACAATA 595388 TACAACAATA Statistics Matches: 146, Mismatches: 8, Indels: 5 0.92 0.05 0.03 Matches are distributed among these distances: 133 57 0.39 135 3 0.02 138 86 0.59 ACGTcount: A:0.39, C:0.16, G:0.11, T:0.33 Consensus pattern (133 bp): TACTATTGATCAGTTACAATACAAGTATATTACTGGACAGTTACAATATACTACTATTGATCAGT GACAACATACAACAATATACTATTGCACACATACAATACATGTATATTATTGGACAGTTACAATA TAC Found at i:595303 original size:24 final size:24 Alignment explanation

Indices: 595220--595308 Score: 83 Period size: 24 Copynumber: 3.6 Consensus size: 24 595210 TATTATTGGA 595220 CAGTTACAATATACTACTATTGAT 1 CAGTTACAATATACTACTATTGAT * * 595244 CAGTTACAATACAAGTA-TATT-ACT 1 CAGTTACAATA-TACTACTATTGA-T 595268 GGACAGTTACAATATACTACTATTGAT 1 ---CAGTTACAATATACTACTATTGAT * * 595295 CAGTGACAACATAC 1 CAGTTACAATATAC 595309 AACAATATAC Statistics Matches: 52, Mismatches: 6, Indels: 14 0.72 0.08 0.19 Matches are distributed among these distances: 23 1 0.02 24 28 0.54 25 3 0.06 26 3 0.06 27 16 0.31 28 1 0.02 ACGTcount: A:0.39, C:0.18, G:0.11, T:0.31 Consensus pattern (24 bp): CAGTTACAATATACTACTATTGAT Found at i:595306 original size:220 final size:216 Alignment explanation

Indices: 594974--595467 Score: 710 Period size: 220 Copynumber: 2.3 Consensus size: 216 594964 TATGTTATAA * * ** 594974 GACAGTTGCAATATATGTATATTATTAGAC-GATTAC-A-ATA-TACTATTGAAGAGTTACAATA 1 GACAGTTACAATAAATGTATATTATTAGACAG-TTACAATATACTACTATTGATCAGTTACAATA * * * * 595035 CATGTATATTATTGGACAGTTACAATATACTACTATTGGTCAGTTACAACATACAACAAAATACT 65 CAAGTATATTACTGGACAGTTACAATATACTACTATTGATCAGTGACAACATACAACAAAATACT ** * 595100 AATGAACAGTTACAATACATGTATATTATTGGACAGTTACAATATACTACTATTGATCAGTTCCA 130 AATGAACACATACAATACATGTATATTATTGGACAGTTACAATATACTACTATTGATCAGTTACA 595165 ACATACAACAATATACTATTGCATT 195 ACATACAACAATATACTATTG---T * * 595190 GGACAGTTACAATACATGTATATTATTGGACAGTTACAATATACTACTATTGATCAGTTACAATA 1 -GACAGTTACAATAAATGTATATTATTAGACAGTTACAATATACTACTATTGATCAGTTACAATA * 595255 CAAGTATATTACTGGACAGTTACAATATACTACTATTGATCAGTGACAACATACAACAATATACT 65 CAAGTATATTACTGGACAGTTACAATATACTACTATTGATCAGTGACAACATACAACAAAATACT * * * 595320 ATTGCACACATACAATACATGTATATTATTGGACAGTTACAGTATACTACTATTGATCAGTTACA 130 AATGAACACATACAATACATGTATATTATTGGACAGTTACAATATACTACTATTGATCAGTTACA * 595385 ATATACAACAATATACTATTGT 195 ACATACAACAATATACTATTGT * * * * 595407 -ACAGTTACAATAAATGTATATAATTAGACAGCTACAGTATACTACTATTGATCAGTGACAA 1 GACAGTTACAATAAATGTATATTATTAGACAGTTACAATATACTACTATTGATCAGTTACAA 595468 CATACAACAA Statistics Matches: 250, Mismatches: 23, Indels: 10 0.88 0.08 0.04 Matches are distributed among these distances: 215 55 0.22 217 32 0.13 218 2 0.01 219 3 0.01 220 158 0.63 ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33 Consensus pattern (216 bp): GACAGTTACAATAAATGTATATTATTAGACAGTTACAATATACTACTATTGATCAGTTACAATAC AAGTATATTACTGGACAGTTACAATATACTACTATTGATCAGTGACAACATACAACAAAATACTA ATGAACACATACAATACATGTATATTATTGGACAGTTACAATATACTACTATTGATCAGTTACAA CATACAACAATATACTATTGT Found at i:595335 original size:82 final size:82 Alignment explanation

Indices: 595234--595582 Score: 511 Period size: 82 Copynumber: 4.3 Consensus size: 82 595224 TACAATATAC * * * 595234 TACTATTGATCAGTTACAATACAAGTATATTACTGGACAGTTACAATATACTACTATTGATCAGT 1 TACTATTGAACACTTACAATACAAGTATATTATTGGACAGTTACAATATACTACTATTGATCAGT 595299 GACAACATACAACAATA 66 GACAACATACAACAATA * * * * 595316 TACTATTGCACACATACAATACATGTATATTATTGGACAGTTACAGTATACTACTATTGATCAGT 1 TACTATTGAACACTTACAATACAAGTATATTATTGGACAGTTACAATATACTACTATTGATCAGT * * 595381 TACAATATACAACAATA 66 GACAACATACAACAATA * * * * * * 595398 TACTATTGTACAGTTACAATA-AATGTATATAATTAGACAGCTACAGTATACTACTATTGATCAG 1 TACTATTGAACACTTACAATACAA-GTATATTATTGGACAGTTACAATATACTACTATTGATCAG 595462 TGACAACATACAACAATA 65 TGACAACATACAACAATA * * 595480 TACTATTGAACAGTTACAATACAGGTATATTATTGGACAGTTACAATATACTACTATTGATCAGT 1 TACTATTGAACACTTACAATACAAGTATATTATTGGACAGTTACAATATACTACTATTGATCAGT * * 595545 TACAACATTCAACAATA 66 GACAACATACAACAATA 595562 TACTATTGAACACTTACAATA 1 TACTATTGAACACTTACAATA 595583 TATTATTTGG Statistics Matches: 238, Mismatches: 27, Indels: 4 0.88 0.10 0.01 Matches are distributed among these distances: 81 1 0.00 82 236 0.99 83 1 0.00 ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32 Consensus pattern (82 bp): TACTATTGAACACTTACAATACAAGTATATTATTGGACAGTTACAATATACTACTATTGATCAGT GACAACATACAACAATA Found at i:595404 original size:31 final size:31 Alignment explanation

Indices: 595367--595584 Score: 99 Period size: 31 Copynumber: 7.7 Consensus size: 31 595357 TACAGTATAC 595367 TACTATTGATCAGTTACAATATACAACAATA 1 TACTATTGATCAGTTACAATATACAACAATA *** 595398 TACTATTG-TACAGTTACAATA-A-ATGTATA 1 TACTATTGAT-CAGTTACAATATACAACAATA * * 595427 TA--ATTAGA-CAGCTACAGTAT---AC---- 1 TACTATT-GATCAGTTACAATATACAACAATA * * 595449 TACTATTGATCAGTGACAACATACAACAATA 1 TACTATTGATCAGTTACAATATACAACAATA * ** 595480 TACTATTGAACAGTTAC-A-ATAC-A-GGTA 1 TACTATTGATCAGTTACAATATACAACAATA * 595507 TATTATTGGA-CAGTTACAATAT---AC---- 1 TACTATT-GATCAGTTACAATATACAACAATA * * 595531 TACTATTGATCAGTTACAACATTCAACAATA 1 TACTATTGATCAGTTACAATATACAACAATA * * 595562 TACTATTGAACACTTACAATATA 1 TACTATTGATCAGTTACAATATA 595585 TTATTTGGTA Statistics Matches: 139, Mismatches: 22, Indels: 52 0.65 0.10 0.24 Matches are distributed among these distances: 22 2 0.01 23 4 0.03 24 28 0.20 27 32 0.23 28 5 0.04 29 12 0.09 30 3 0.02 31 53 0.38 ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32 Consensus pattern (31 bp): TACTATTGATCAGTTACAATATACAACAATA Found at i:595456 original size:133 final size:132 Alignment explanation

Indices: 595096--595420 Score: 389 Period size: 138 Copynumber: 2.4 Consensus size: 132 595086 TACAACAAAA * * ** * * * * 595096 TACTAATGAACAGTTACAATACATGTATATTATTGGACAGTTACAATATACTACTATTGATCAGT 1 TACTATTGATCAGTTACAATACAAATATACTACTGGACAGTTACAATAAACTACTATTAATCAG- ** * 595161 TCCAACATACAACAATATACTATTGCATTGGACAGTTACAATACATGTATATTATTGGACAGTTA 65 GACAACATACAACAATATACTATTGCA---CACA--TACAATACATGTATATTATTGGACAGTTA 595226 CAATATAC 125 CAATATAC * * * * 595234 TACTATTGATCAGTTACAATACAAGTATATTACTGGACAGTTACAATATACTACTATTGATCAGT 1 TACTATTGATCAGTTACAATACAAATATACTACTGGACAGTTACAATAAACTACTATTAATCAG- * 595299 GACAACATACAACAATATACTATTGCACACATACAATACATGTATATTATTGGACAGTTACAGTA 65 GACAACATACAACAATATACTATTGCACACATACAATACATGTATATTATTGGACAGTTACAATA 595364 TAC 130 TAC * * 595367 TACTATTGATCAGTTACAATATACAACAATATACTATTGTACAGTTACAATAAA 1 TACTATTGATCAGTTAC-A-ATAC-A-AATATACTACTGGACAGTTACAATAAA 595421 TGTATATAAT Statistics Matches: 170, Mismatches: 13, Indels: 9 0.89 0.07 0.05 Matches are distributed among these distances: 133 53 0.31 134 1 0.01 135 7 0.04 136 1 0.01 137 22 0.13 138 86 0.51 ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33 Consensus pattern (132 bp): TACTATTGATCAGTTACAATACAAATATACTACTGGACAGTTACAATAAACTACTATTAATCAGG ACAACATACAACAATATACTATTGCACACATACAATACATGTATATTATTGGACAGTTACAATAT AC Found at i:595497 original size:24 final size:24 Alignment explanation

Indices: 595470--595551 Score: 76 Period size: 24 Copynumber: 3.3 Consensus size: 24 595460 AGTGACAACA 595470 TACAACAATATACTATTGAACAGT 1 TACAACAATATACTATTGAACAGT * * * 595494 TACAATACAGGTATATTATTGGACAGT 1 TAC-A-ACA-ATATACTATTGAACAGT * * 595521 TACAA-TATACTACTATTGATCAGT 1 TACAACAATA-TACTATTGAACAGT 595545 TACAACA 1 TACAACA 595552 TTCAACAATA Statistics Matches: 44, Mismatches: 9, Indels: 9 0.71 0.15 0.15 Matches are distributed among these distances: 23 2 0.05 24 19 0.43 25 2 0.05 26 4 0.09 27 17 0.39 ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32 Consensus pattern (24 bp): TACAACAATATACTATTGAACAGT Found at i:596446 original size:51 final size:50 Alignment explanation

Indices: 596391--596964 Score: 755 Period size: 51 Copynumber: 11.3 Consensus size: 50 596381 CCATCAATTC * * * * * 596391 AAGATACATGACA-AAAGCGAGGCTTTTCATATTCGTGCAAACTATCAGTTA 1 AAGATACATGACACTAAG-G-GGCTTTTCATATACATACCAACTATCAGTTA * * * 596442 AAGATACATGACACTACGGGGGCTTTACATATACATA-CAACGATCAGTTA 1 AAGATACATGACACTA-AGGGGCTTTTCATATACATACCAACTATCAGTTA * * 596492 AAGATACATGACA-T-GGGGGGTGGGGTTTACATATACATACCAACTATCAGTTA 1 AAGATACATGACACTAAGGGGCT----TTT-CATATACATACCAACTATCAGTTA * * 596545 AAGATACATGACACTAAGGGGGCTTTACATATGCATACCAACTATCAGTTA 1 AAGATACATGACACTAA-GGGGCTTTTCATATACATACCAACTATCAGTTA * * * 596596 AAGATACATGACACTAGGGGGGCTTTACATATACATACCAACCATCAGTTA 1 AAGATACATGACACTA-AGGGGCTTTTCATATACATACCAACTATCAGTTA * 596647 AAGATACATGACACTAAAGGGG-TTTTACATATACATACCAACCATCAGTTA 1 AAGATACATGACACT-AAGGGGCTTTT-CATATACATACCAACTATCAGTTA * * 596698 AAGATAAATGACACTAAGGGGGCTTTACATATACATACCAACTATCAGTT- 1 AAGATACATGACACTAA-GGGGCTTTTCATATACATACCAACTATCAGTTA * 596748 AAGATACATGACACTAAGGGGATTTTACATATACATACCAACTATCAGTTA 1 AAGATACATGACACTAAGGGGCTTTT-CATATACATACCAACTATCAGTTA * 596799 AAGATACATGACACTAAGGGGGTTTTACATATACATACCAACTATCAGTTA 1 AAGATACATGACACTAAGGGGCTTTT-CATATACATACCAACTATCAGTTA * 596850 AAGATACATGACACTAAGGGGGTTTTACATATACATACCAACTATCAGTTA 1 AAGATACATGACACTAAGGGGCTTTT-CATATACATACCAACTATCAGTTA * 596901 AAGATACATGACACTAAGGGGGTTTTACATATACATACCAACTATCAGTTA 1 AAGATACATGACACTAAGGGGCTTTT-CATATACATACCAACTATCAGTTA 596952 AAGATACATGACA 1 AAGATACATGACA 596965 ATGGGGGAGG Statistics Matches: 478, Mismatches: 27, Indels: 36 0.88 0.05 0.07 Matches are distributed among these distances: 47 6 0.01 49 8 0.02 50 68 0.14 51 346 0.72 52 18 0.04 53 26 0.05 54 1 0.00 56 5 0.01 ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26 Consensus pattern (50 bp): AAGATACATGACACTAAGGGGCTTTTCATATACATACCAACTATCAGTTA Found at i:596663 original size:102 final size:102 Alignment explanation

Indices: 596430--596964 Score: 878 Period size: 102 Copynumber: 5.2 Consensus size: 102 596420 TATTCGTGCA * * * 596430 AACTATCAGTTAAAGATACATGACACTACGGGGGCTTTACATATACATA-CAACGATCAGTTAAA 1 AACTATCAGTTAAAGATACATGACACTAAGGGGGTTTTACATATACATACCAACTATCAGTTAAA ** * 596494 GATACATGACA-TGGGGGGTGGGGTTTACATATACATACC 66 GATACATGACACT--AAGG-GGGCTTTACATATACATACC * * 596533 AACTATCAGTTAAAGATACATGACACTAAGGGGGCTTTACATATGCATACCAACTATCAGTTAAA 1 AACTATCAGTTAAAGATACATGACACTAAGGGGGTTTTACATATACATACCAACTATCAGTTAAA * 596598 GATACATGACACTAGGGGGGCTTTACATATACATACC 66 GATACATGACACTAAGGGGGCTTTACATATACATACC * * * 596635 AACCATCAGTTAAAGATACATGACACTAAAGGGGTTTTACATATACATACCAACCATCAGTTAAA 1 AACTATCAGTTAAAGATACATGACACTAAGGGGGTTTTACATATACATACCAACTATCAGTTAAA * 596700 GATAAATGACACTAAGGGGGCTTTACATATACATACC 66 GATACATGACACTAAGGGGGCTTTACATATACATACC * 596737 AACTATCAGTT-AAGATACATGACACTAAGGGGATTTTACATATACATACCAACTATCAGTTAAA 1 AACTATCAGTTAAAGATACATGACACTAAGGGGGTTTTACATATACATACCAACTATCAGTTAAA * 596801 GATACATGACACTAAGGGGGTTTTACATATACATACC 66 GATACATGACACTAAGGGGGCTTTACATATACATACC 596838 AACTATCAGTTAAAGATACATGACACTAAGGGGGTTTTACATATACATACCAACTATCAGTTAAA 1 AACTATCAGTTAAAGATACATGACACTAAGGGGGTTTTACATATACATACCAACTATCAGTTAAA * 596903 GATACATGACACTAAGGGGGTTTTACATATACATACC 66 GATACATGACACTAAGGGGGCTTTACATATACATACC 596940 AACTATCAGTTAAAGATACATGACA 1 AACTATCAGTTAAAGATACATGACA 596965 ATGGGGGAGG Statistics Matches: 410, Mismatches: 19, Indels: 7 0.94 0.04 0.02 Matches are distributed among these distances: 101 96 0.23 102 238 0.58 103 50 0.12 104 25 0.06 105 1 0.00 ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26 Consensus pattern (102 bp): AACTATCAGTTAAAGATACATGACACTAAGGGGGTTTTACATATACATACCAACTATCAGTTAAA GATACATGACACTAAGGGGGCTTTACATATACATACC Found at i:596802 original size:203 final size:204 Alignment explanation

Indices: 596434--596964 Score: 870 Period size: 203 Copynumber: 2.6 Consensus size: 204 596424 CGTGCAAACT * * * 596434 ATCAGTTAAAGATACATGACACTACGGGGGCTTTACATATACATA-CAACGATCAGTTAAAGATA 1 ATCAGTTAAAGATACATGACACTAAGGGGGTTTTACATATACATACCAACCATCAGTTAAAGATA ** * 596498 CATGACA-TGGGGGGTGGGGTTTACATATACATACCAACTATCAGTTAAAGATACATGACACTAA 66 CATGACACT--AAGG-GGGCTTTACATATACATACCAACTATCAGTTAAAGATACATGACACTAA * * * 596562 GGGGGCTTTACATATGCATACCAACTATCAGTTAAAGATACATGACACTAGGGGGGCTTTACATA 128 GGGGACTTTACATATACATACCAACTATCAGTTAAAGATACATGACACTAAGGGGGCTTTACATA 596627 TACATACCAACC 193 TACATACCAACC * 596639 ATCAGTTAAAGATACATGACACTAAAGGGGTTTTACATATACATACCAACCATCAGTTAAAGATA 1 ATCAGTTAAAGATACATGACACTAAGGGGGTTTTACATATACATACCAACCATCAGTTAAAGATA * 596704 AATGACACTAAGGGGGCTTTACATATACATACCAACTATCAGTT-AAGATACATGACACTAAGGG 66 CATGACACTAAGGGGGCTTTACATATACATACCAACTATCAGTTAAAGATACATGACACTAAGGG * * 596768 GATTTTACATATACATACCAACTATCAGTTAAAGATACATGACACTAAGGGGGTTTTACATATAC 131 GACTTTACATATACATACCAACTATCAGTTAAAGATACATGACACTAAGGGGGCTTTACATATAC * 596833 ATACCAACT 196 ATACCAACC * 596842 ATCAGTTAAAGATACATGACACTAAGGGGGTTTTACATATACATACCAACTATCAGTTAAAGATA 1 ATCAGTTAAAGATACATGACACTAAGGGGGTTTTACATATACATACCAACCATCAGTTAAAGATA * 596907 CATGACACTAAGGGGGTTTTACATATACATACCAACTATCAGTTAAAGATACATGACA 66 CATGACACTAAGGGGGCTTTACATATACATACCAACTATCAGTTAAAGATACATGACA 596965 ATGGGGGAGG Statistics Matches: 305, Mismatches: 18, Indels: 7 0.92 0.05 0.02 Matches are distributed among these distances: 203 193 0.63 204 43 0.14 205 44 0.14 206 24 0.08 207 1 0.00 ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26 Consensus pattern (204 bp): ATCAGTTAAAGATACATGACACTAAGGGGGTTTTACATATACATACCAACCATCAGTTAAAGATA CATGACACTAAGGGGGCTTTACATATACATACCAACTATCAGTTAAAGATACATGACACTAAGGG GACTTTACATATACATACCAACTATCAGTTAAAGATACATGACACTAAGGGGGCTTTACATATAC ATACCAACC Found at i:596833 original size:27 final size:27 Alignment explanation

Indices: 596802--596936 Score: 74 Period size: 27 Copynumber: 5.2 Consensus size: 27 596792 TCAGTTAAAG 596802 ATACATGACACTAAGGGGGTTTTACAT 1 ATACATGACACTAAGGGGGTTTTACAT *** * * 596829 ATACAT-ACCAACT-A-TCAG--TTAAAG 1 ATACATGA-C-ACTAAGGGGGTTTTACAT 596853 ATACATGACACTAAGGGGGTTTTACAT 1 ATACATGACACTAAGGGGGTTTTACAT *** * * 596880 ATACAT-ACCAACT-A-TCAG--TTAAAG 1 ATACATGA-C-ACTAAGGGGGTTTTACAT 596904 ATACATGACACTAAGGGGGTTTTACAT 1 ATACATGACACTAAGGGGGTTTTACAT 596931 ATACAT 1 ATACAT 596937 ACCAACTATC Statistics Matches: 74, Mismatches: 20, Indels: 28 0.61 0.16 0.23 Matches are distributed among these distances: 23 6 0.08 24 24 0.32 25 4 0.05 26 4 0.05 27 30 0.41 28 6 0.08 ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28 Consensus pattern (27 bp): ATACATGACACTAAGGGGGTTTTACAT Found at i:597011 original size:153 final size:147 Alignment explanation

Indices: 596430--596966 Score: 664 Period size: 152 Copynumber: 3.5 Consensus size: 147 596420 TATTCGTGCA * ** * 596430 AACTATCAGTTAAAGATACATGACACTACGGGGGCTTTACATATACATA-CAACGATCAGTTAAA 1 AACTATCAGTT-AAGATACATGACACTAAGGGGATTTTACATATACATACCAACTATCAGTTAAA ** * * 596494 GATACATGAC-ATGGGGGGTGGGGTTTACATATACATACCAACTATCAGTTAAAGATACATGACA 65 GATACATGACAAT--AAGG-GGGCTTTACATATACATACCAAC-ATCACTT----ATACATGACA * 596558 CTAAGGGGGCTTTACATATGCATACC 122 CTAAGGGGGCTTTACATATACATACC * ** * 596584 AACTATCAGTTAAAGATACATGACACTAGGGGGGCTTTACATATACATACCAACCATCAGTTAAA 1 AACTATCAGTT-AAGATACATGACACTAAGGGGATTTTACATATACATACCAACTATCAGTTAAA * * * * * 596649 GATACATGACACTAAAGGGGTTTTACATATACATACCAACCATCAGTTAAAGATAAATGACACTA 65 GATACATGACAATAAGGGGGCTTTACATATACATACCAA-CATCACTT----ATACATGACACTA 596714 AGGGGGCTTTACATATACATACC 125 AGGGGGCTTTACATATACATACC 596737 AACTATCAGTTAAGATACATGACACTAAGGGGATTTTACATATACATACCAACTATCAGTTAAAG 1 AACTATCAGTTAAGATACATGACACTAAGGGGATTTTACATATACATACCAACTATCAGTTAAAG * * * 596802 ATACATGACACTAAGGGGGTTTTACATATACATACCAACTATCAGTTAAAGATACATGACACTAA 66 ATACATGACAATAAGGGGGCTTTACATATACATACCAAC-ATCACTT----ATACATGACACTAA * 596867 GGGGGTTTTACATATACATACC 126 GGGGGCTTTACATATACATACC * 596889 AACTATCAGTTAAAGATACATGACACTAAGGGGGTTTTACATATACATACCAACTATCAGTTAAA 1 AACTATCAGTT-AAGATACATGACACTAAGGGGATTTTACATATACATACCAACTATCAGTTAAA 596954 GATACATGACAAT 65 GATACATGACAAT 596967 GGGGGAGGGG Statistics Matches: 360, Mismatches: 18, Indels: 11 0.93 0.05 0.03 Matches are distributed among these distances: 151 1 0.00 152 143 0.40 153 141 0.39 154 50 0.14 155 24 0.07 156 1 0.00 ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26 Consensus pattern (147 bp): AACTATCAGTTAAGATACATGACACTAAGGGGATTTTACATATACATACCAACTATCAGTTAAAG ATACATGACAATAAGGGGGCTTTACATATACATACCAACATCACTTATACATGACACTAAGGGGG CTTTACATATACATACC Found at i:597817 original size:10 final size:10 Alignment explanation

Indices: 597804--597835 Score: 55 Period size: 10 Copynumber: 3.2 Consensus size: 10 597794 TGATATTGGG 597804 TATGTAATAA 1 TATGTAATAA * 597814 TATGTAGTAA 1 TATGTAATAA 597824 TATGTAATAA 1 TATGTAATAA 597834 TA 1 TA 597836 AAATGTTGAT Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 10 20 1.00 ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41 Consensus pattern (10 bp): TATGTAATAA Done.