Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr11 ID=Chr11-JGI_221_v2.0

Parameters: 2 7 7 80 10 50 1000

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

Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33

Warning! 1052928 characters in sequence are not A, C, G, or T


File 194 of 210

Found at i:57046422 original size:24 final size:26

Alignment explanation

Indices: 57046395--57046442 Score: 73 Period size: 24 Copynumber: 1.9 Consensus size: 26 57046385 TTTGAGTAAT * 57046395 TTAACTTTTTTC-T-TTTATTTTCTG 1 TTAACTTTATTCTTCTTTATTTTCTG 57046419 TTAACTTTATTCTTCTTTATTTTC 1 TTAACTTTATTCTTCTTTATTTTC 57046443 CATTCTTTCC Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 24 11 0.52 25 1 0.05 26 9 0.43 ACGTcount: A:0.15, C:0.15, G:0.02, T:0.69 Consensus pattern (26 bp): TTAACTTTATTCTTCTTTATTTTCTG Found at i:57046732 original size:23 final size:24 Alignment explanation

Indices: 57046706--57046750 Score: 58 Period size: 23 Copynumber: 1.9 Consensus size: 24 57046696 AGAAAAGTTA 57046706 AAAAAACAT-AAAACAAA-AAAATT 1 AAAAAAC-TCAAAACAAATAAAATT * 57046729 AAAATACTCAAAACAAATAAAA 1 AAAAAACTCAAAACAAATAAAA 57046751 ATATGAGGAC Statistics Matches: 19, Mismatches: 1, Indels: 3 0.83 0.04 0.13 Matches are distributed among these distances: 22 1 0.05 23 14 0.74 24 4 0.21 ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13 Consensus pattern (24 bp): AAAAAACTCAAAACAAATAAAATT Found at i:57051323 original size:17 final size:17 Alignment explanation

Indices: 57051303--57051337 Score: 52 Period size: 17 Copynumber: 2.1 Consensus size: 17 57051293 GTTTATGAAA * * 57051303 AAATAAAATACGAAAAT 1 AAATAAAAAACAAAAAT 57051320 AAATAAAAAACAAAAAT 1 AAATAAAAAACAAAAAT 57051337 A 1 A 57051338 GTATATTTAC Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14 Consensus pattern (17 bp): AAATAAAAAACAAAAAT Found at i:57051533 original size:157 final size:158 Alignment explanation

Indices: 57051315--57051862 Score: 811 Period size: 157 Copynumber: 3.5 Consensus size: 158 57051305 ATAAAATACG * ** * 57051315 AAAATAAATAAAAAACAAAAATAGTATATTTACTGAAAGTAATAAAATTCAAAAAAAAGAAAAAT 1 AAAAT-AATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAA-TCAAAAATAAGAAAAAT * * * 57051380 ATGAACAAAGGGCCAAAATAAGGGTTTTTCACTAAATTTATAT-AAAAAA-ACACTAAAATAATA 64 ACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAAATAATA 57051443 CATTTCAAACATTATGTACTAAAATAATAT 129 CATTTCAAACATTATGTACTAAAATAATAT * * * 57051473 AAAATAATAAAACACGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATA 1 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAA-TCAAAAATAAGAAAAATA * * * 57051538 CGAATAAATGGCCAAAATAAAGGTTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATAC 65 CGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAAATAATAC * 57051603 ATTTCAAACTTTATGTACTAAAATAATAT 130 ATTTCAAACATTATGTACTAAAATAATAT * * * * 57051632 AAAATAATAAAATACGAAAGTATTATATTTTTTGAAAGTAATAAAATC--AGA-AA-AAAAATAC 1 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATCAAAAATAAGAAAAATAC * * * 57051693 GAACAAATGGCCAAAATAAGGGTTTTTTACTAGATTTACATAAAAAAGACACACTAAAACAATAC 66 GAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAA-ACACACTAAAATAATAC * 57051758 ATTTCAAATATTATGTACTAAAATAATAT 130 ATTTCAAACATTATGTACTAAAATAATAT 57051787 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATCAAAAAATAAGAAAAATA 1 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATC-AAAAATAAGAAAAATA 57051852 CGAACAAATGG 65 CGAACAAATGG 57051863 GGGTGTCGCC Statistics Matches: 353, Mismatches: 29, Indels: 14 0.89 0.07 0.04 Matches are distributed among these distances: 154 51 0.14 155 89 0.25 156 2 0.01 157 91 0.26 158 15 0.04 159 87 0.25 160 18 0.05 ACGTcount: A:0.56, C:0.09, G:0.08, T:0.28 Consensus pattern (158 bp): AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATCAAAAATAAGAAAAATAC GAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAAATAATACA TTTCAAACATTATGTACTAAAATAATAT Found at i:57051800 original size:155 final size:157 Alignment explanation

Indices: 57051315--57051862 Score: 786 Period size: 155 Copynumber: 3.5 Consensus size: 157 57051305 ATAAAATACG * ** 57051315 AAAATAAATAAAAAACAAAAATAGTATATTTACTGAAAGTAATAAAATTCAAAAAAAAGAAAAAT 1 AAAAT-AATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTC--AAAAAAGAAAAAT * * * 57051380 ATGAACAAAGGGCCAAAATAAGGGTTTTTCACTAAATTTATAT-AAAAAA-ACACTAAAATAATA 63 ACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAAATAATA * 57051443 CATTTCAAACATTATGTACTAAAATAATAT 128 CATTTCAAATATTATGTACTAAAATAATAT * * 57051473 AAAATAATAAAACACGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATA 1 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTC-AAAA-AAGAAAAATA * * * 57051538 CGAATAAATGGCCAAAATAAAGGTTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATAC 64 CGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAAATAATAC 57051603 ATTTCAAACT-TTATGTACTAAAATAATAT 129 ATTTCAAA-TATTATGTACTAAAATAATAT * * * * 57051632 AAAATAATAAAATACGAAAGTATTATATTTTTTGAAAGTAATAAAA-TC-AGAAA-AAAAATACG 1 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTCAAAAAAGAAAAATACG * * * 57051694 AACAAATGGCCAAAATAAGGGTTTTTTACTAGATTTACATAAAAAAGACACACTAAAACAATACA 66 AACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAA-ACACACTAAAATAATACA 57051759 TTTCAAATATTATGTACTAAAATAATAT 130 TTTCAAATATTATGTACTAAAATAATAT 57051787 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAA-TCAAAAAATAAGAAAAAT 1 AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTC--AAAA-AAGAAAAAT 57051851 ACGAACAAATGG 63 ACGAACAAATGG 57051863 GGGTGTCGCC Statistics Matches: 353, Mismatches: 26, Indels: 20 0.88 0.07 0.05 Matches are distributed among these distances: 154 52 0.15 155 89 0.25 156 6 0.02 157 87 0.25 158 15 0.04 159 86 0.24 160 18 0.05 ACGTcount: A:0.56, C:0.09, G:0.08, T:0.28 Consensus pattern (157 bp): AAAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTCAAAAAAGAAAAATACG AACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAAATAATACAT TTCAAATATTATGTACTAAAATAATAT Found at i:57058619 original size:31 final size:30 Alignment explanation

Indices: 57058554--57058621 Score: 82 Period size: 30 Copynumber: 2.2 Consensus size: 30 57058544 TTTCCCAAGA ** *** 57058554 GTAAATACTCAAAATTTGAAGGGTTAAAGT 1 GTAAATACAAAAAATTTGAAGGACCAAAGT 57058584 GTAAATACAAAAAATTTGAAGGACCAATAGT 1 GTAAATACAAAAAATTTGAAGGACCAA-AGT 57058615 GTAAATA 1 GTAAATA 57058622 TTTTAAGGGT Statistics Matches: 32, Mismatches: 5, Indels: 1 0.84 0.13 0.03 Matches are distributed among these distances: 30 22 0.69 31 10 0.31 ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26 Consensus pattern (30 bp): GTAAATACAAAAAATTTGAAGGACCAAAGT Found at i:57068388 original size:22 final size:22 Alignment explanation

Indices: 57068363--57068404 Score: 59 Period size: 22 Copynumber: 1.9 Consensus size: 22 57068353 AGTAAGTAAA * 57068363 TTGTTCTTTGT-TTCGTTCTCCT 1 TTGTTCTCTGTCTT-GTTCTCCT 57068385 TTGTTCTCTGTCTTGTTCTC 1 TTGTTCTCTGTCTTGTTCTC 57068405 TTCTTTTGTT Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 22 16 0.89 23 2 0.11 ACGTcount: A:0.00, C:0.24, G:0.14, T:0.62 Consensus pattern (22 bp): TTGTTCTCTGTCTTGTTCTCCT Found at i:57072368 original size:22 final size:21 Alignment explanation

Indices: 57072327--57072369 Score: 52 Period size: 22 Copynumber: 2.0 Consensus size: 21 57072317 TAATATGGGC 57072327 AATAATAAAAAAAAGGAAGTAA 1 AATAATAAAAAAAA-GAAGTAA 57072349 AATACATAAAATAAAA-AAGTA 1 AATA-ATAAAA-AAAAGAAGTA 57072370 TATATGAAGT Statistics Matches: 19, Mismatches: 0, Indels: 4 0.83 0.00 0.17 Matches are distributed among these distances: 22 9 0.47 23 6 0.32 24 4 0.21 ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16 Consensus pattern (21 bp): AATAATAAAAAAAAGAAGTAA Found at i:57077291 original size:22 final size:22 Alignment explanation

Indices: 57077266--57077309 Score: 88 Period size: 22 Copynumber: 2.0 Consensus size: 22 57077256 AACAATCAAA 57077266 GGTATTACTTGAGCAATGGTTG 1 GGTATTACTTGAGCAATGGTTG 57077288 GGTATTACTTGAGCAATGGTTG 1 GGTATTACTTGAGCAATGGTTG 57077310 CAGGTAAGTG Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 22 1.00 ACGTcount: A:0.23, C:0.09, G:0.32, T:0.36 Consensus pattern (22 bp): GGTATTACTTGAGCAATGGTTG Found at i:57087788 original size:20 final size:21 Alignment explanation

Indices: 57087763--57087807 Score: 56 Period size: 21 Copynumber: 2.2 Consensus size: 21 57087753 TTTTCCATTC * 57087763 TTTCCT-ACTTCTCCCTCTAT 1 TTTCCTCACTTCTCCATCTAT * * 57087783 TTTCCTCCCTTCTCCATCTCT 1 TTTCCTCACTTCTCCATCTAT 57087804 TTTC 1 TTTC 57087808 ATGTAGTTTT Statistics Matches: 21, Mismatches: 3, Indels: 1 0.84 0.12 0.04 Matches are distributed among these distances: 20 6 0.29 21 15 0.71 ACGTcount: A:0.07, C:0.42, G:0.00, T:0.51 Consensus pattern (21 bp): TTTCCTCACTTCTCCATCTAT Found at i:57093834 original size:6 final size:6 Alignment explanation

Indices: 57093823--57093858 Score: 63 Period size: 6 Copynumber: 6.0 Consensus size: 6 57093813 TACCAATTCA * 57093823 TATATG TATATG TATATG TATTTG TATATG TATATG 1 TATATG TATATG TATATG TATATG TATATG TATATG 57093859 CATACACACA Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 6 28 1.00 ACGTcount: A:0.31, C:0.00, G:0.17, T:0.53 Consensus pattern (6 bp): TATATG Found at i:57101352 original size:61 final size:58 Alignment explanation

Indices: 57101249--57101413 Score: 186 Period size: 61 Copynumber: 2.7 Consensus size: 58 57101239 ACCAACAGTA * * * * 57101249 GTCACCCAACTATGGATTTTTTTCTTTTTTGGTCACCTAACTATGAAAAGTTATAAATTG 1 GTCACCCAACTAT-TA-GTTTTTCTTTTTTGGTCACCCAACTATGAAAAGTTATAAAATG 57101309 GTCACCCAACTATTAGTATTTTCTTTCTCTTGGTCACCCAACTATGAAAAGTTATAAAATG 1 GTCACCCAACTATTAGT-TTTTCTTT-T-TTGGTCACCCAACTATGAAAAGTTATAAAATG * ** * * 57101370 ATCACTTAATTATTCAGTTTTATCTTTTTTGGTCAACCAACTAT 1 GTCACCCAACTATT-AGTTTT-TCTTTTTTGGTCACCCAACTAT 57101414 CTAGGATTTT Statistics Matches: 91, Mismatches: 9, Indels: 10 0.83 0.08 0.09 Matches are distributed among these distances: 58 1 0.01 59 9 0.10 60 29 0.32 61 44 0.48 62 8 0.09 ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41 Consensus pattern (58 bp): GTCACCCAACTATTAGTTTTTCTTTTTTGGTCACCCAACTATGAAAAGTTATAAAATG Found at i:57107265 original size:29 final size:28 Alignment explanation

Indices: 57107201--57107265 Score: 69 Period size: 29 Copynumber: 2.3 Consensus size: 28 57107191 TAATTTAGAC * 57107201 TTATTTAATTTTTTAATAATATAAAGAC 1 TTATTTAATTTTTTAATAATATAAAGAA * * * 57107229 TAAATTAATTTATTTAATAATA-ATGAGAA 1 TTATTTAATTT-TTTAATAATATA-AAGAA 57107258 TTATTTAA 1 TTATTTAA 57107266 CTTGGTCCTT Statistics Matches: 29, Mismatches: 6, Indels: 3 0.76 0.16 0.08 Matches are distributed among these distances: 28 10 0.34 29 19 0.66 ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48 Consensus pattern (28 bp): TTATTTAATTTTTTAATAATATAAAGAA Found at i:57109619 original size:234 final size:235 Alignment explanation

Indices: 57109207--57109684 Score: 859 Period size: 234 Copynumber: 2.0 Consensus size: 235 57109197 GATATCTTGG * 57109207 TCATTTGTTCCTATTTTCTTTTTGATCAGAATTCATCAAGATAATGTAGAATCTTGAATGTATCA 1 TCATTTGTTCCTATTTTCTTTTTAATCAGAATTCATCAAGATAATGTAGAATCTTGAATGTATCA * 57109272 TAAACATTTTTAGACATTTATTTCCATGCTTTGCTAGCATAGTTATTGACTAATTTTTAGAGGAT 66 TAAACATTTTTAGACATTTATTTCCATGCTTTGATAGCATAGTTATTGACTAATTTTTAGAGGAT * 57109337 TAGGCATTAGATGAAGTTTTGGAAAAGTCAACATTTCAGGTATGGTCATTCTGGATCTAAATCTT 131 TAGGCATTAGATGAAGTTTCGGAAAAGTCAACATTTCAGGTATGGTCATTCTGGATCTAAATCTT * 57109402 TCCCTG-AAAAAAAAAACTAAAATAAACAATCCGGATAGT 196 TCCCTGAAAAAAAAAAACTAAAATAAACAATCCGGATAGC 57109441 TCATTTGTTCCTATTTTCTTTTTAATCAGAATTCATCAAGATAATGTAGAATCTTGAATGTATCA 1 TCATTTGTTCCTATTTTCTTTTTAATCAGAATTCATCAAGATAATGTAGAATCTTGAATGTATCA * 57109506 TAAACATTTTTTGACATTTATTTCCATGCTTTGATAGCATAGTTATTGACTAATTTTTAGAGGAT 66 TAAACATTTTTAGACATTTATTTCCATGCTTTGATAGCATAGTTATTGACTAATTTTTAGAGGAT * 57109571 TAGGCATTAGATGAAGTTTCGGAAAAGTCAACATTTCAGGTGTGGTCATTCTGGATCTAAATCTT 131 TAGGCATTAGATGAAGTTTCGGAAAAGTCAACATTTCAGGTATGGTCATTCTGGATCTAAATCTT * 57109636 TCCCTGAAAAAAAAAAAAAATTAAAATAAACAATCCGGATAGC 196 TCCCTG---AAAAAAAAAAACTAAAATAAACAATCCGGATAGC 57109679 TCATTT 1 TCATTT 57109685 AAATAAAGAA Statistics Matches: 233, Mismatches: 7, Indels: 4 0.95 0.03 0.02 Matches are distributed among these distances: 234 196 0.84 238 37 0.16 ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38 Consensus pattern (235 bp): TCATTTGTTCCTATTTTCTTTTTAATCAGAATTCATCAAGATAATGTAGAATCTTGAATGTATCA TAAACATTTTTAGACATTTATTTCCATGCTTTGATAGCATAGTTATTGACTAATTTTTAGAGGAT TAGGCATTAGATGAAGTTTCGGAAAAGTCAACATTTCAGGTATGGTCATTCTGGATCTAAATCTT TCCCTGAAAAAAAAAAACTAAAATAAACAATCCGGATAGC Found at i:57112569 original size:38 final size:38 Alignment explanation

Indices: 57112526--57112605 Score: 117 Period size: 38 Copynumber: 2.1 Consensus size: 38 57112516 ATTATGGATA * 57112526 GCTAAGATTATAAGATA-CTGTTAGGGTTTAGATCTAGG 1 GCTAAGATTATAAGATATCT-TTAGGGTTTAAATCTAGG * * 57112564 GCTAAGATTATTAGTTATCTTTAGGGTTTAAATCTAGG 1 GCTAAGATTATAAGATATCTTTAGGGTTTAAATCTAGG 57112602 GCTA 1 GCTA 57112606 TTAGAAATTT Statistics Matches: 38, Mismatches: 3, Indels: 2 0.88 0.07 0.05 Matches are distributed among these distances: 38 36 0.95 39 2 0.05 ACGTcount: A:0.30, C:0.09, G:0.24, T:0.38 Consensus pattern (38 bp): GCTAAGATTATAAGATATCTTTAGGGTTTAAATCTAGG Found at i:57119775 original size:31 final size:31 Alignment explanation

Indices: 57119712--57119775 Score: 76 Period size: 31 Copynumber: 2.1 Consensus size: 31 57119702 TTAGGATTTG * * 57119712 AAAAGTAAAGGGACTAAAATTGATCAATTTA 1 AAAAGTAAAGGGACTAAAATTAATCAAATTA * * 57119743 AAAAGTATAA-GGATTAAAATTAATTAAATTA 1 AAAAGTA-AAGGGACTAAAATTAATCAAATTA 57119774 AA 1 AA 57119776 TTATAATTTG Statistics Matches: 28, Mismatches: 4, Indels: 2 0.82 0.12 0.06 Matches are distributed among these distances: 31 26 0.93 32 2 0.07 ACGTcount: A:0.56, C:0.03, G:0.12, T:0.28 Consensus pattern (31 bp): AAAAGTAAAGGGACTAAAATTAATCAAATTA Found at i:57124387 original size:20 final size:20 Alignment explanation

Indices: 57124362--57124404 Score: 68 Period size: 20 Copynumber: 2.1 Consensus size: 20 57124352 AGTTCAAGGT * 57124362 TTCGAGTTTTGGGTTTAGGG 1 TTCGAGTTTTGAGTTTAGGG * 57124382 TTCGAGTTTTGAGTTTGGGG 1 TTCGAGTTTTGAGTTTAGGG 57124402 TTC 1 TTC 57124405 TGGGTTTATG Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.09, C:0.07, G:0.37, T:0.47 Consensus pattern (20 bp): TTCGAGTTTTGAGTTTAGGG Found at i:57125929 original size:38 final size:39 Alignment explanation

Indices: 57125860--57125937 Score: 108 Period size: 38 Copynumber: 2.0 Consensus size: 39 57125850 ATAAACACCA 57125860 AAAAATTATTTTAAAAATAAAAAAAATAAAAAGTAT-TTT 1 AAAAATTATTTTAAAAATAAAAAAAATAAAAA-TATATTT * 57125899 AAAAA-TATTTTAAAATTAAAAAAACA-AAAAATATATTT 1 AAAAATTATTTTAAAAATAAAAAAA-ATAAAAATATATTT 57125937 A 1 A 57125938 TTATATTCGG Statistics Matches: 36, Mismatches: 1, Indels: 5 0.86 0.02 0.12 Matches are distributed among these distances: 37 3 0.08 38 27 0.75 39 6 0.17 ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32 Consensus pattern (39 bp): AAAAATTATTTTAAAAATAAAAAAAATAAAAATATATTT Found at i:57130560 original size:88 final size:90 Alignment explanation

Indices: 57130404--57130573 Score: 263 Period size: 88 Copynumber: 1.9 Consensus size: 90 57130394 AATCGACCAG * * * * 57130404 TTTTTTATCGATTTAATTGATTTTTTTACTAATTTAATTCTTCTTCGATTTTTTTTACTAGTTAG 1 TTTTTTATCGATTTAATTGAATTTTTTACTAATTTAATTCTTCTTCGATTTTATATACTAGTCAG 57130469 ACTATCAATTTCTAGTTAGGCTAAT 66 ACTATCAATTTCTAGTTAGGCTAAT * * * 57130494 TTTTTTATGGATTTAATT-AATTTTTTACT-GTTTAATTCTTCTTCGATTTTATATACTAGTCGG 1 TTTTTTATCGATTTAATTGAATTTTTTACTAATTTAATTCTTCTTCGATTTTATATACTAGTCAG 57130557 ACTATCAATTTCTAGTT 66 ACTATCAATTTCTAGTT 57130574 GGATGTAATT Statistics Matches: 73, Mismatches: 7, Indels: 2 0.89 0.09 0.02 Matches are distributed among these distances: 88 46 0.63 89 10 0.14 90 17 0.23 ACGTcount: A:0.24, C:0.11, G:0.09, T:0.55 Consensus pattern (90 bp): TTTTTTATCGATTTAATTGAATTTTTTACTAATTTAATTCTTCTTCGATTTTATATACTAGTCAG ACTATCAATTTCTAGTTAGGCTAAT Found at i:57135213 original size:96 final size:85 Alignment explanation

Indices: 57135143--57135307 Score: 240 Period size: 85 Copynumber: 1.9 Consensus size: 85 57135133 CTCTTTTTTT * * * 57135143 TTTTTTTGCACTCAGTTGAGCACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTCTTC 1 TTTTTTT--ACTCAATTGAGCACTTGAACTTTCAAAATGCATCAAAAAGACACTCAAAATTCTTC * * 57135208 AAAAAAGCAATTAATCCCCTGC 64 AAAAAAGTAATTAAGCCCCTGC * * * 57135230 TTTTTTTACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACACTCAAAATTTTTCAA 1 TTTTTTTACTCAATTGAGCACTTGAACTTTCAAAATGCATCAAAAAGACACTCAAAATTCTTCAA 57135295 AAAAGTAATTAAG 66 AAAAGTAATTAAG 57135308 TCCATGTTCT Statistics Matches: 70, Mismatches: 8, Indels: 2 0.88 0.10 0.03 Matches are distributed among these distances: 85 63 0.90 87 7 0.10 ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32 Consensus pattern (85 bp): TTTTTTTACTCAATTGAGCACTTGAACTTTCAAAATGCATCAAAAAGACACTCAAAATTCTTCAA AAAAGTAATTAAGCCCCTGC Found at i:57135388 original size:19 final size:19 Alignment explanation

Indices: 57135342--57135390 Score: 64 Period size: 18 Copynumber: 2.6 Consensus size: 19 57135332 AAAAAATATA * 57135342 AATAATAAATAATAAATTTT 1 AATAA-AAATATTAAATTTT * 57135362 -AGAAAAATATTAAATTTT 1 AATAAAAATATTAAATTTT 57135380 AATAAAAATAT 1 AATAAAAATAT 57135391 AAAAAATTTA Statistics Matches: 25, Mismatches: 3, Indels: 3 0.81 0.10 0.10 Matches are distributed among these distances: 18 13 0.52 19 12 0.48 ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37 Consensus pattern (19 bp): AATAAAAATATTAAATTTT Found at i:57135402 original size:27 final size:28 Alignment explanation

Indices: 57135364--57135441 Score: 79 Period size: 28 Copynumber: 2.8 Consensus size: 28 57135354 TAAATTTTAG * 57135364 AAAAATATTAAATTTTAATAAAAAT-ATA 1 AAAAATATTAAAATTT-ATAAAAATCATA * 57135392 AAAAAT-TTAAAATTTATAAAAATCGTAA 1 AAAAATATTAAAATTTATAAAAATCAT-A ** * 57135420 AAAAATAAAAAAAATTATAAAA 1 AAAAATATTAAAATTTATAAAA 57135442 TTTTATAGAA Statistics Matches: 42, Mismatches: 5, Indels: 5 0.81 0.10 0.10 Matches are distributed among these distances: 26 8 0.19 27 9 0.21 28 13 0.31 29 12 0.29 ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29 Consensus pattern (28 bp): AAAAATATTAAAATTTATAAAAATCATA Found at i:57135410 original size:26 final size:29 Alignment explanation

Indices: 57135364--57135423 Score: 81 Period size: 27 Copynumber: 2.2 Consensus size: 29 57135354 TAAATTTTAG * 57135364 AAAAATATTAAATTTTAATAAAAAT-ATA 1 AAAAATATTAAAATTTAATAAAAATCATA * 57135392 AAAAAT-TTAAAATTT-ATAAAAATCGTA 1 AAAAATATTAAAATTTAATAAAAATCATA 57135419 AAAAA 1 AAAAA 57135424 ATAAAAAAAA Statistics Matches: 29, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 26 8 0.28 27 15 0.52 28 6 0.21 ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32 Consensus pattern (29 bp): AAAAATATTAAAATTTAATAAAAATCATA Found at i:57135441 original size:9 final size:9 Alignment explanation

Indices: 57135381--57135461 Score: 58 Period size: 9 Copynumber: 8.8 Consensus size: 9 57135371 TTAAATTTTA 57135381 ATAAAAA-T 1 ATAAAAATT 57135389 ATAAAAAATT 1 AT-AAAAATT * 57135399 -TAAAATTT 1 ATAAAAATT 57135407 ATAAAAATCGT 1 ATAAAAAT--T * * 57135418 AAAAAAATA 1 ATAAAAATT * 57135427 AAAAAAATT 1 ATAAAAATT * 57135436 ATAAAATTTT 1 ATAAAA-ATT * 57135446 ATAGAAATT 1 ATAAAAATT 57135455 ATAAAAA 1 ATAAAAA 57135462 AAATCGACAA Statistics Matches: 57, Mismatches: 10, Indels: 11 0.73 0.13 0.14 Matches are distributed among these distances: 8 8 0.14 9 33 0.58 10 8 0.14 11 8 0.14 ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30 Consensus pattern (9 bp): ATAAAAATT Found at i:57135616 original size:11 final size:10 Alignment explanation

Indices: 57135596--57135738 Score: 61 Period size: 10 Copynumber: 14.4 Consensus size: 10 57135586 TTTTGGTAAG 57135596 ATAATTTTTT 1 ATAATTTTTT 57135606 ATAATTTTTT 1 ATAATTTTTT * ** 57135616 TTACGA-AATTT 1 ATA--ATTTTTT 57135627 AT-ATTTTTT 1 ATAATTTTTT * 57135636 -TACATTTTGT 1 ATA-ATTTTTT 57135646 ATAATTTTCTT 1 ATAATTTT-TT * * 57135657 ATGA--CTTT 1 ATAATTTTTT ** 57135665 ATAAAATTTT 1 ATAATTTTTT * 57135675 AAAATTTTTT 1 ATAATTTTTT 57135685 AT-ATATTTTT 1 ATAAT-TTTTT 57135695 ATATATTTTTT 1 ATA-ATTTTTT 57135706 ACT-A-TTTTT 1 A-TAATTTTTT 57135715 ATATATTTTTT 1 ATA-ATTTTTT * 57135726 AT-ATTTTTA 1 ATAATTTTTT 57135735 ATAA 1 ATAA 57135739 ATTGTTAATA Statistics Matches: 99, Mismatches: 17, Indels: 34 0.66 0.11 0.23 Matches are distributed among these distances: 8 8 0.08 9 20 0.20 10 44 0.44 11 23 0.23 12 4 0.04 ACGTcount: A:0.31, C:0.03, G:0.02, T:0.63 Consensus pattern (10 bp): ATAATTTTTT Found at i:57135697 original size:30 final size:30 Alignment explanation

Indices: 57135662--57135732 Score: 74 Period size: 30 Copynumber: 2.4 Consensus size: 30 57135652 TTCTTATGAC 57135662 TTTATAAAATTTTAAAAT-TTTTTATATATT 1 TTTAT-AAATTTTAAAATATTTTTATATATT * ** * 57135692 TTTATATATTTTTTACTATTTTTATATATT 1 TTTATAAATTTTAAAATATTTTTATATATT * 57135722 TTT-TATATTTT 1 TTTATAAATTTT 57135733 TAATAAATTG Statistics Matches: 36, Mismatches: 4, Indels: 3 0.84 0.09 0.07 Matches are distributed among these distances: 29 16 0.44 30 20 0.56 ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68 Consensus pattern (30 bp): TTTATAAATTTTAAAATATTTTTATATATT Found at i:57135711 original size:20 final size:19 Alignment explanation

Indices: 57135680--57135734 Score: 92 Period size: 20 Copynumber: 2.8 Consensus size: 19 57135670 ATTTTAAAAT 57135680 TTTTTATATATTTTTATATA 1 TTTTT-TATATTTTTATATA 57135700 TTTTTTACTATTTTTATATA 1 TTTTTTA-TATTTTTATATA 57135720 TTTTTTATATTTTTA 1 TTTTTTATATTTTTA 57135735 ATAAATTGTT Statistics Matches: 34, Mismatches: 0, Indels: 3 0.92 0.00 0.08 Matches are distributed among these distances: 19 10 0.29 20 24 0.71 ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73 Consensus pattern (19 bp): TTTTTTATATTTTTATATA Found at i:57135749 original size:20 final size:19 Alignment explanation

Indices: 57135687--57135751 Score: 58 Period size: 20 Copynumber: 3.3 Consensus size: 19 57135677 AATTTTTTAT * * 57135687 ATATTTTTATATATTTTTTA 1 ATATTTTTATA-AATTGTTA * * * * 57135707 CTATTTTTATATATTTTTT 1 ATATTTTTATAAATTGTTA 57135726 ATATTTTTAATAAATTGTTA 1 ATATTTTT-ATAAATTGTTA 57135746 ATATTT 1 ATATTT 57135752 GAATTTTTTA Statistics Matches: 36, Mismatches: 8, Indels: 2 0.78 0.17 0.04 Matches are distributed among these distances: 19 12 0.33 20 24 0.67 ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66 Consensus pattern (19 bp): ATATTTTTATAAATTGTTA Found at i:57135976 original size:90 final size:90 Alignment explanation

Indices: 57135819--57136039 Score: 284 Period size: 90 Copynumber: 2.4 Consensus size: 90 57135809 AATTTTTAAT * * * * 57135819 AAAAGCAGGGGCTTAATTGCTTTTTTTGAAAAGTTTG-GGGTCTTTTTTATGCATTTTGAAAGTT 1 AAAACCAGGGGCTTAATTGCTTTTTTTGAAAAGTTTGAGAGCCTTTTTGATGCATTTTGAAAGTT * * 57135883 CAAATACTCAATTGAGTG-AAAAAA 66 CAAATACCCAAATGAGTGCAAAAAA * * ** * 57135907 GAGAGTAGGGGATTAATTGCTTTTTTTGAAAATGTTTGAGAGCCTTTTTGATGCATTTTGAAAGT 1 AAAACCAGGGGCTTAATTGCTTTTTTTGAAAA-GTTTGAGAGCCTTTTTGATGCATTTTGAAAGT 57135972 TCAAATACCCAAATGAGTGCCAAAAAAA 65 TCAAATACCCAAATGAGTG-C-AAAAAA * 57136000 AAAACCAGAGGCTTAATTGCTTTTTTTGAAAAAGTTTGAG 1 AAAACCAGGGGCTTAATTGCTTTTTTTG-AAAAGTTTGAG 57136040 GAATTTTTGC Statistics Matches: 112, Mismatches: 15, Indels: 7 0.84 0.11 0.05 Matches are distributed among these distances: 88 28 0.25 89 5 0.04 90 40 0.36 93 35 0.31 94 4 0.04 ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35 Consensus pattern (90 bp): AAAACCAGGGGCTTAATTGCTTTTTTTGAAAAGTTTGAGAGCCTTTTTGATGCATTTTGAAAGTT CAAATACCCAAATGAGTGCAAAAAA Found at i:57143738 original size:13 final size:13 Alignment explanation

Indices: 57143722--57143752 Score: 53 Period size: 13 Copynumber: 2.4 Consensus size: 13 57143712 AGTTTAATAT 57143722 TTATTATGATTTA 1 TTATTATGATTTA * 57143735 TTATTATTATTTA 1 TTATTATGATTTA 57143748 TTATT 1 TTATT 57143753 GTACTTAAAA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 13 17 1.00 ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68 Consensus pattern (13 bp): TTATTATGATTTA Found at i:57144833 original size:30 final size:29 Alignment explanation

Indices: 57144799--57144953 Score: 138 Period size: 30 Copynumber: 5.2 Consensus size: 29 57144789 ATTTTTTTTA * * 57144799 AAAATTACATTTTGACACTTAATCTTTTCT 1 AAAATTACATTTTGACCCCTAA-CTTTTCT * ** 57144829 AAAATTACTTTTTGACCCC-AAAATTTCTT 1 AAAATTACATTTTGACCCCTAACTTTTC-T ** 57144858 AAAATTACATTTCAACCCCTGAACTTTTCT 1 AAAATTACATTTTGACCCCT-AACTTTTCT * 57144888 -AAATTACCTTTTGACCCCTAAAC-TTTCT 1 AAAATTACATTTTGACCCCT-AACTTTTCT * 57144916 AAAAATTACATTTTTACCCCTTAAC-TTTCT 1 -AAAATTACATTTTGACCCC-TAACTTTTCT 57144946 ATAAATTA 1 A-AAATTA 57144954 TGTTTTAGCC Statistics Matches: 102, Mismatches: 16, Indels: 14 0.77 0.12 0.11 Matches are distributed among these distances: 28 9 0.09 29 39 0.38 30 47 0.46 31 7 0.07 ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41 Consensus pattern (29 bp): AAAATTACATTTTGACCCCTAACTTTTCT Found at i:57144861 original size:29 final size:30 Alignment explanation

Indices: 57144799--57144950 Score: 125 Period size: 29 Copynumber: 5.1 Consensus size: 30 57144789 ATTTTTTTTA * * * * 57144799 AAAATTACATTTTGACACTTAATCTTT-TCT 1 AAAATTACTTTTTGACCCCTAAACTTTCT-T * 57144829 AAAATTACTTTTTGACCCC-AAAATTTCTT 1 AAAATTACTTTTTGACCCCTAAACTTTCTT * ** * 57144858 AAAATTACATTTCAACCCCTGAACTTT-TCT 1 AAAATTACTTTTTGACCCCTAAACTTTCT-T * * 57144888 -AAATTACCTTTTGACCCCTAAACTTTCTA 1 AAAATTACTTTTTGACCCCTAAACTTTCTT * 57144917 AAAATTACATTTTT-ACCCCTTAACTTTCTAT 1 AAAATTAC-TTTTTGACCCCTAAACTTTCT-T 57144948 AAA 1 AAA 57144951 TTATGTTTTA Statistics Matches: 97, Mismatches: 18, Indels: 13 0.76 0.14 0.10 Matches are distributed among these distances: 29 45 0.46 30 45 0.46 31 7 0.07 ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41 Consensus pattern (30 bp): AAAATTACTTTTTGACCCCTAAACTTTCTT Found at i:57144862 original size:59 final size:59 Alignment explanation

Indices: 57144797--57144953 Score: 174 Period size: 59 Copynumber: 2.6 Consensus size: 59 57144787 GAATTTTTTT * * * 57144797 TAAAAATTACATTTTGA-CACTTAATCTTTTCTAAAATTACTTTTTGACCCC-AAAATTTC 1 TAAAAATTACATTTTAACCACTGAA-CTTTTCT-AAATTACCTTTTGACCCCTAAAATTTC * * * * 57144856 TTAAAATTACATTTCAACCCCTGAACTTTTCTAAATTACCTTTTGACCCCTAAACTTTC 1 TAAAAATTACATTTTAACCACTGAACTTTTCTAAATTACCTTTTGACCCCTAAAATTTC * * * * 57144915 TAAAAATTACATTTTTACCCCTTAACTTTCTATAAATTA 1 TAAAAATTACATTTTAACCACTGAACTTT-TCTAAATTA 57144954 TGTTTTAGCC Statistics Matches: 83, Mismatches: 12, Indels: 5 0.83 0.12 0.05 Matches are distributed among these distances: 58 17 0.20 59 53 0.64 60 13 0.16 ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41 Consensus pattern (59 bp): TAAAAATTACATTTTAACCACTGAACTTTTCTAAATTACCTTTTGACCCCTAAAATTTC Found at i:57145288 original size:3 final size:3 Alignment explanation

Indices: 57145280--57145330 Score: 84 Period size: 3 Copynumber: 16.3 Consensus size: 3 57145270 GCTAAGTTTT 57145280 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GGAA GAA GGAA 1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA -GAA 57145327 GAA G 1 GAA G 57145331 GAAGGGGGAA Statistics Matches: 46, Mismatches: 0, Indels: 4 0.92 0.00 0.08 Matches are distributed among these distances: 3 40 0.87 4 6 0.13 ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00 Consensus pattern (3 bp): GAA Found at i:57145569 original size:22 final size:19 Alignment explanation

Indices: 57145522--57145558 Score: 74 Period size: 19 Copynumber: 1.9 Consensus size: 19 57145512 CAAAGTACAA 57145522 GGCCCAAAGCAAAAAAAGG 1 GGCCCAAAGCAAAAAAAGG 57145541 GGCCCAAAGCAAAAAAAG 1 GGCCCAAAGCAAAAAAAG 57145559 AAGCAGGCCA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 18 1.00 ACGTcount: A:0.54, C:0.22, G:0.24, T:0.00 Consensus pattern (19 bp): GGCCCAAAGCAAAAAAAGG Found at i:57145664 original size:13 final size:13 Alignment explanation

Indices: 57145643--57145691 Score: 66 Period size: 13 Copynumber: 3.8 Consensus size: 13 57145633 GCAGCCCAGC * 57145643 AGAGAAAAAAAAG 1 AGAGGAAAAAAAG 57145656 AGAGGAAAAAAAG 1 AGAGGAAAAAAAG 57145669 AGA-GAAGAAAAA- 1 AGAGGAA-AAAAAG 57145681 AGAGGAAAAAA 1 AGAGGAAAAAA 57145692 GAACAAAAAA Statistics Matches: 33, Mismatches: 1, Indels: 5 0.85 0.03 0.13 Matches are distributed among these distances: 12 10 0.30 13 23 0.70 ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00 Consensus pattern (13 bp): AGAGGAAAAAAAG Found at i:57145667 original size:15 final size:15 Alignment explanation

Indices: 57145647--57145681 Score: 52 Period size: 15 Copynumber: 2.3 Consensus size: 15 57145637 CCCAGCAGAG * 57145647 AAAAAAAAGAGAGGA 1 AAAAAAAAGAGAAGA * 57145662 AAAAAAGAGAGAAGA 1 AAAAAAAAGAGAAGA 57145677 AAAAA 1 AAAAA 57145682 GAGGAAAAAA Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00 Consensus pattern (15 bp): AAAAAAAAGAGAAGA Found at i:57146037 original size:12 final size:11 Alignment explanation

Indices: 57146016--57146040 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 57146006 AATTGTAAAT 57146016 ATTCAAAAAAA 1 ATTCAAAAAAA 57146027 ATTCAAAAAAA 1 ATTCAAAAAAA 57146038 ATT 1 ATT 57146041 TTCCGTGTTT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24 Consensus pattern (11 bp): ATTCAAAAAAA Found at i:57146095 original size:21 final size:22 Alignment explanation

Indices: 57146057--57146097 Score: 57 Period size: 21 Copynumber: 1.9 Consensus size: 22 57146047 GTTTCGAAAT * * 57146057 TTTCGTGTCTTCAGAAAAAAAA 1 TTTCGTATCTTCAAAAAAAAAA 57146079 TTTCGTAT-TTCAAAAAAAA 1 TTTCGTATCTTCAAAAAAAA 57146098 TATTCGCGTT Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 21 10 0.59 22 7 0.41 ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34 Consensus pattern (22 bp): TTTCGTATCTTCAAAAAAAAAA Found at i:57146273 original size:18 final size:18 Alignment explanation

Indices: 57146252--57146730 Score: 301 Period size: 18 Copynumber: 26.9 Consensus size: 18 57146242 AATTCCGGTG * * 57146252 TTTCAAAAATTTTCATGA 1 TTTCAAAAATTTTCGTGT * 57146270 TTTCAAAAATTCTCGTGT 1 TTTCAAAAATTTTCGTGT *** * 57146288 TTTCAAAAAAACTCAT-T 1 TTTCAAAAATTTTCGTGT * 57146305 TTT-AAAATTTTTCGTGT 1 TTTCAAAAATTTTCGTGT * * 57146322 TTTCTAAATATTTCCGTG- 1 TTTC-AAAAATTTTCGTGT * * * * 57146340 TCTCAATAATTTTCATGA 1 TTTCAAAAATTTTCGTGT * 57146358 TTTCAAAAATTCTCGTGT 1 TTTCAAAAATTTTCGTGT * * 57146376 TTTCAAAAAAATTT-AT-T 1 TTTC-AAAAATTTTCGTGT * 57146393 TTT-AAAATTTTTCGTGT 1 TTTCAAAAATTTTCGTGT * 57146410 TTTCTAAAAATTTCCGTG- 1 TTTC-AAAAATTTTCGTGT * * * 57146428 TCTCAAAAATTTTCATGA 1 TTTCAAAAATTTTCGTGT * 57146446 TTTCAAAAATTCTCGTGT 1 TTTCAAAAATTTTCGTGT *** * 57146464 TTTCAAAAAAAATCAT-T 1 TTTCAAAAATTTTCGTGT * * 57146481 TTT-AAAATTTTTCGTTT 1 TTTCAAAAATTTTCGTGT * 57146498 TTTCTAAAAATTTCCGTG- 1 TTTC-AAAAATTTTCGTGT * * 57146516 TCTCAAAAATTTTCATGT 1 TTTCAAAAATTTTCGTGT * 57146534 TTTCAAAAATTTTCGTGC 1 TTTCAAAAATTTTCGTGT * 57146552 TTTC-AAAATTTTTGTGT 1 TTTCAAAAATTTTCGTGT * * * 57146569 TTTTAACAATTCTCGTGT 1 TTTCAAAAATTTTCGTGT * 57146587 TTT-ACTAAATTTTCGTG- 1 TTTCA-AAAATTTTCGTGT * * 57146604 TTTCAAAAAATTGT-ATGT 1 TTTC-AAAAATTTTCGTGT * * 57146622 TTTAAAAAAAAATTCTCGTG- 1 TTT---CAAAAATTTTCGTGT 57146642 TTTCAAAAATTGTT-GTGCT 1 TTTCAAAAATT-TTCGTG-T 57146661 TTT-AAAAATTTTCGTGT 1 TTTCAAAAATTTTCGTGT * * 57146678 TTT-TAAAATTTTTGTGT 1 TTTCAAAAATTTTCGTGT * 57146695 TTTAAAAAAATTTTCGTGT 1 TTT-CAAAAATTTTCGTGT * * 57146714 TTTAAAAAAATTTCGTG 1 TTTCAAAAATTTTCGTG 57146731 CTTCAAAATT Statistics Matches: 353, Mismatches: 79, Indels: 58 0.72 0.16 0.12 Matches are distributed among these distances: 15 7 0.02 16 15 0.04 17 106 0.30 18 155 0.44 19 57 0.16 20 11 0.03 21 2 0.01 ACGTcount: A:0.32, C:0.11, G:0.09, T:0.47 Consensus pattern (18 bp): TTTCAAAAATTTTCGTGT Found at i:57146363 original size:88 final size:88 Alignment explanation

Indices: 57146238--57146559 Score: 536 Period size: 88 Copynumber: 3.6 Consensus size: 88 57146228 TGTGCTTTTA * * * 57146238 AAAAAATTCCGGTGTTTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAACTCA 1 AAAAATTTCC-GTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAAATCA 57146303 TTTTTAAAATTTTTCGTGTTTTCT 65 TTTTTAAAATTTTTCGTGTTTTCT * * * * 57146327 AAATATTTCCGTGTCTCAATAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAATTTAT 1 AAAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAAATCAT 57146392 TTTTAAAATTTTTCGTGTTTTCT 66 TTTTAAAATTTTTCGTGTTTTCT 57146415 AAAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAAATCAT 1 AAAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAAATCAT * 57146480 TTTTAAAATTTTTCGTTTTTTCT 66 TTTTAAAATTTTTCGTGTTTTCT * * * 57146503 AAAAATTTCCGTGTCTCAAAAATTTTCATGTTTTCAAAAATTTTCGTGCTTTCAAAA 1 AAAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAA 57146560 TTTTTGTGTT Statistics Matches: 219, Mismatches: 14, Indels: 1 0.94 0.06 0.00 Matches are distributed among these distances: 88 211 0.96 89 8 0.04 ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45 Consensus pattern (88 bp): AAAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAAATCAT TTTTAAAATTTTTCGTGTTTTCT Found at i:57146597 original size:88 final size:87 Alignment explanation

Indices: 57146239--57146688 Score: 516 Period size: 88 Copynumber: 5.1 Consensus size: 87 57146229 GTGCTTTTAA * * * * 57146239 AAAAATTCCGGTGTTTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAACTCAT 1 AAAATTTCC-GTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAATTTAT 57146304 TTTTAAAATTTTTCGTGTTTTCT 65 TTTTAAAATTTTTCGTGTTTTCT * 57146327 AAATATTTCCGTGTCTCAATAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAATTTAT 1 AAA-ATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAATTTAT 57146392 TTTTAAAATTTTTCGTGTTTTCT 65 TTTTAAAATTTTTCGTGTTTTCT * * 57146415 AAAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAAATCAT 1 -AAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAATTTAT * 57146480 TTTTAAAATTTTTCGTTTTTTCT 65 TTTTAAAATTTTTCGTGTTTTCT * * * *** * 57146503 AAAAATTTCCGTGTCTCAAAAATTTTCATGTTTTCAAAAATTTTCGTGCTTTCAAAATTTTTGTG 1 -AAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAATT-TA * 57146568 TTTTTAACAA-TTCTCGTGTTTTACT 64 TTTTTAA-AATTTTTCGTGTTTT-CT * * * * * * 57146593 -AAATTTTCGTGTTTCAAAAAATTGT-ATGTTTTAAAAAAAAATTCTCGTG-TTTC-AAAAATTG 1 AAAATTTCCGTGTCTC-AAAAATTTTCATGATTT---CAAAAATTCTCGTGTTTTCAAAAAAAT- * * 57146654 TTGTGCTTTTAAAAATTTTCGTGTTTT-T 61 TTAT--TTTTAAAATTTTTCGTGTTTTCT 57146682 AAAATTT 1 AAAATTT 57146689 TTGTGTTTTA Statistics Matches: 320, Mismatches: 28, Indels: 26 0.86 0.07 0.07 Matches are distributed among these distances: 88 232 0.73 89 42 0.13 90 17 0.05 91 29 0.09 ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47 Consensus pattern (87 bp): AAAATTTCCGTGTCTCAAAAATTTTCATGATTTCAAAAATTCTCGTGTTTTCAAAAAAATTTATT TTTAAAATTTTTCGTGTTTTCT Found at i:57146641 original size:38 final size:39 Alignment explanation

Indices: 57146593--57146668 Score: 111 Period size: 38 Copynumber: 2.0 Consensus size: 39 57146583 GTGTTTTACT * 57146593 AAATTTTCGTGTTTCAAAAAATTG-TATG-TTTTAAAAAA 1 AAATTCTCGTGTTTC-AAAAATTGTTATGCTTTTAAAAAA * 57146631 AAATTCTCGTGTTTCAAAAATTGTTGTGCTTTTAAAAA 1 AAATTCTCGTGTTTCAAAAATTGTTATGCTTTTAAAAA 57146669 TTTTCGTGTT Statistics Matches: 34, Mismatches: 2, Indels: 3 0.87 0.05 0.08 Matches are distributed among these distances: 37 8 0.24 38 17 0.50 39 9 0.26 ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42 Consensus pattern (39 bp): AAATTCTCGTGTTTCAAAAATTGTTATGCTTTTAAAAAA Found at i:57146738 original size:18 final size:19 Alignment explanation

Indices: 57146682--57146738 Score: 62 Period size: 19 Copynumber: 3.1 Consensus size: 19 57146672 TCGTGTTTTT * * * 57146682 AAAATTTTTGTGTTTTAAA 1 AAAATTTTCGTGCTTCAAA * * 57146701 AAAATTTTCGTGTTTTAAA 1 AAAATTTTCGTGCTTCAAA 57146720 AAAA-TTTCGTGCTTCAAA 1 AAAATTTTCGTGCTTCAAA 57146738 A 1 A 57146739 TTCCCGTGTT Statistics Matches: 35, Mismatches: 3, Indels: 1 0.90 0.08 0.03 Matches are distributed among these distances: 18 13 0.37 19 22 0.63 ACGTcount: A:0.39, C:0.07, G:0.11, T:0.44 Consensus pattern (19 bp): AAAATTTTCGTGCTTCAAA Found at i:57154305 original size:19 final size:19 Alignment explanation

Indices: 57154265--57154320 Score: 64 Period size: 19 Copynumber: 3.0 Consensus size: 19 57154255 ATTACAAAAC 57154265 AAAA-TCAAAATGATTT-TCA 1 AAAATTCAAAAT-ATTTAT-A 57154284 AAAATTCAAAATATTTATA 1 AAAATTCAAAATATTTATA * 57154303 AAAATTCCAAA-ATTTATA 1 AAAATTCAAAATATTTATA 57154321 TTTTTTTAAT Statistics Matches: 34, Mismatches: 1, Indels: 5 0.85 0.03 0.12 Matches are distributed among these distances: 18 7 0.21 19 19 0.56 20 8 0.24 ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34 Consensus pattern (19 bp): AAAATTCAAAATATTTATA Found at i:57161878 original size:19 final size:18 Alignment explanation

Indices: 57161854--57161930 Score: 59 Period size: 18 Copynumber: 4.2 Consensus size: 18 57161844 TTTTTGTATA 57161854 TTTAAAATTTATTTTTAAT 1 TTTAAAATTTA-TTTTAAT * * 57161873 TTTAAAAATTTA-ATTGAT 1 TTT-AAAATTTATTTTAAT * 57161891 TTCAAAATTTATATTTAAT 1 TTTAAAATTTAT-TTTAAT * * 57161910 TATTAACA-TTATTATAAT 1 T-TTAAAATTTATTTTAAT 57161928 TTT 1 TTT 57161931 TATGTTAAAT Statistics Matches: 46, Mismatches: 8, Indels: 10 0.72 0.12 0.16 Matches are distributed among these distances: 17 10 0.22 18 12 0.26 19 12 0.26 20 12 0.26 ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56 Consensus pattern (18 bp): TTTAAAATTTATTTTAAT Found at i:57164999 original size:24 final size:24 Alignment explanation

Indices: 57164967--57165013 Score: 76 Period size: 24 Copynumber: 2.0 Consensus size: 24 57164957 GGTGCTTCCC * 57164967 GTTAATTGCTCTTCGGAGCTACCT 1 GTTAATTGCTCTTCGAAGCTACCT * 57164991 GTTAATTGCTCTTTGAAGCTACC 1 GTTAATTGCTCTTCGAAGCTACC 57165014 CATTATAAGC Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 24 21 1.00 ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38 Consensus pattern (24 bp): GTTAATTGCTCTTCGAAGCTACCT Found at i:57166695 original size:44 final size:42 Alignment explanation

Indices: 57166627--57166767 Score: 131 Period size: 42 Copynumber: 3.3 Consensus size: 42 57166617 AATGTGACAT ** * * 57166627 CGTGTAAGACCACATCTGGAACATTGGCCTCG-ATTTGAGATTTA 1 CGTGTAAGACCATGTCTGGGACATTGGCCTCGTATAT--GA-TTA * * 57166671 CGTGTAAGATCATGTCTGGGACATTGGCGTCGTATATGATTA 1 CGTGTAAGACCATGTCTGGGACATTGGCCTCGTATATGATTA * * * * * 57166713 CGTGTAAGACCCTGTCTGCGACAGTGGCATCGTTATTTGATTA 1 CGTGTAAGACCATGTCTGGGACATTGGCCTCG-TATATGATTA * 57166756 CATGTAAGACCA 1 CGTGTAAGACCA 57166768 CGTTTGGGGC Statistics Matches: 81, Mismatches: 14, Indels: 5 0.81 0.14 0.05 Matches are distributed among these distances: 42 30 0.37 43 21 0.26 44 27 0.33 45 3 0.04 ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30 Consensus pattern (42 bp): CGTGTAAGACCATGTCTGGGACATTGGCCTCGTATATGATTA Found at i:57170137 original size:52 final size:51 Alignment explanation

Indices: 57170059--57170212 Score: 194 Period size: 52 Copynumber: 3.1 Consensus size: 51 57170049 GATCAAGTGA 57170059 CAAGTGGA-AAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT 1 CAAGT-GACAAGT-GAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT * 57170111 CAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGAT 1 CAAGTGACAAGTG-AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT * * ** 57170163 CAAGAGAC-----AAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGAT 1 CAAGTGACAAGTGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT 57170209 CAAG 1 CAAG 57170213 AAACAAAGTG Statistics Matches: 94, Mismatches: 6, Indels: 10 0.85 0.05 0.09 Matches are distributed among these distances: 46 38 0.40 51 3 0.03 52 53 0.56 ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27 Consensus pattern (51 bp): CAAGTGACAAGTGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT Found at i:57170202 original size:46 final size:43 Alignment explanation

Indices: 57170125--57170298 Score: 185 Period size: 37 Copynumber: 4.2 Consensus size: 43 57170115 TGACAAGTGA * * 57170125 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC 1 AAAGTGATAAGT-ATAGCTT--GCTACACTTATCTGATCAAGAAAC 57170171 AAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGATCAAGAAAC 1 AAAGTGATAAGT-ATAGC-TT-GCTACACTTATCTGATCAAGAAAC 57170217 AAAGTGATAAG--T-G---GCTACACTTATCTGATCAAGAAAC 1 AAAGTGATAAGTATAGCTTGCTACACTTATCTGATCAAGAAAC 57170254 AAAGTGATAAG--T-G---GCTACACTTATCTGATC-AGAAAC 1 AAAGTGATAAGTATAGCTTGCTACACTTATCTGATCAAGAAAC 57170290 AAAGTGATA 1 AAAGTGATA 57170299 GGTGGCTACA Statistics Matches: 123, Mismatches: 4, Indels: 12 0.88 0.03 0.09 Matches are distributed among these distances: 36 15 0.12 37 54 0.44 42 1 0.01 43 1 0.01 46 50 0.41 47 2 0.02 ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26 Consensus pattern (43 bp): AAAGTGATAAGTATAGCTTGCTACACTTATCTGATCAAGAAAC Found at i:57170295 original size:36 final size:37 Alignment explanation

Indices: 57170193--57170337 Score: 242 Period size: 37 Copynumber: 4.0 Consensus size: 37 57170183 AATAGCTTTA 57170193 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG 1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG 57170230 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG 1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG * 57170267 GCTACACTTATCTGATC-AGAAACAAAGTGATAGGTG 1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG ** 57170303 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG 1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG 57170338 ATCATACGTA Statistics Matches: 104, Mismatches: 4, Indels: 2 0.95 0.04 0.02 Matches are distributed among these distances: 35 11 0.11 36 39 0.38 37 54 0.52 ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25 Consensus pattern (37 bp): GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG Found at i:57170313 original size:73 final size:72 Alignment explanation

Indices: 57170193--57170337 Score: 238 Period size: 73 Copynumber: 2.0 Consensus size: 72 57170183 AATAGCTTTA 57170193 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAAACAAAG 1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATC-AGAAAC-AAG 57170258 TGATAAGTG 64 TGATAAGTG * ** 57170267 GCTACACTTATCTGATC-AGAAACAAAGTGATAGGTGGCTACACTTATCTGATCAGGGACAAGTG 1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCAGAAACAAGTG 57170331 ATAAGTG 66 ATAAGTG 57170338 ATCATACGTA Statistics Matches: 68, Mismatches: 3, Indels: 3 0.92 0.04 0.04 Matches are distributed among these distances: 71 12 0.18 72 4 0.06 73 35 0.51 74 17 0.25 ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25 Consensus pattern (72 bp): GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCAGAAACAAGTG ATAAGTG Found at i:57179119 original size:2 final size:2 Alignment explanation

Indices: 57179112--57179141 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 57179102 AATTCCTCTT 57179112 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 57179142 AGTTGTTTAC Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:57189787 original size:23 final size:23 Alignment explanation

Indices: 57189757--57189807 Score: 84 Period size: 23 Copynumber: 2.2 Consensus size: 23 57189747 CGAAATGTAT * * 57189757 AACTCTTACCAATTATAATATCA 1 AACTCTTACCAAATACAATATCA 57189780 AACTCTTACCAAATACAATATCA 1 AACTCTTACCAAATACAATATCA 57189803 AACTC 1 AACTC 57189808 AAGTATTGTA Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 23 26 1.00 ACGTcount: A:0.45, C:0.25, G:0.00, T:0.29 Consensus pattern (23 bp): AACTCTTACCAAATACAATATCA Found at i:57201947 original size:26 final size:25 Alignment explanation

Indices: 57201916--57201971 Score: 71 Period size: 24 Copynumber: 2.2 Consensus size: 25 57201906 AAAAAGTTAA 57201916 TTAATTATTTTAATGAC-TTTTAATT-T 1 TTAATTA-TTT-AT-ACTTTTTAATTAT 57201942 TTAATTATTTATACTTTTTAATTAT 1 TTAATTATTTATACTTTTTAATTAT 57201967 TTAAT 1 TTAAT 57201972 GACTTTTTTG Statistics Matches: 28, Mismatches: 0, Indels: 5 0.85 0.00 0.15 Matches are distributed among these distances: 23 2 0.07 24 10 0.36 25 9 0.32 26 7 0.25 ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62 Consensus pattern (25 bp): TTAATTATTTATACTTTTTAATTAT Found at i:57201959 original size:17 final size:19 Alignment explanation

Indices: 57201939--57201979 Score: 68 Period size: 17 Copynumber: 2.3 Consensus size: 19 57201929 TGACTTTTAA 57201939 TTTTTAATTATTT-AT-AC 1 TTTTTAATTATTTAATGAC 57201956 TTTTTAATTATTTAATGAC 1 TTTTTAATTATTTAATGAC 57201975 TTTTT 1 TTTTT 57201980 TGCTTCTATT Statistics Matches: 22, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 17 13 0.59 18 2 0.09 19 7 0.32 ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66 Consensus pattern (19 bp): TTTTTAATTATTTAATGAC Found at i:57203829 original size:57 final size:58 Alignment explanation

Indices: 57203768--57203889 Score: 158 Period size: 57 Copynumber: 2.1 Consensus size: 58 57203758 CCAGAGTTGG * * 57203768 CAACATTGGGTCCTGTGGGAATGGGACCACTGGCTGCA-GCA-CCTACACCAGGGTTCC 1 CAACAGTGGGTCCTGTGGGAATAGGACCACTGGCTGCACGCAGCC-ACACCAGGGTTCC * * * 57203825 CAACAGTGGTTCCTGTGGGAATAGGACCAGTGGCTGCACCTGCAGCCACACCAGGGTTGC 1 CAACAGTGGGTCCTGTGGGAATAGGACCACTGGCTGCA-C-GCAGCCACACCAGGGTTCC 57203885 CAACA 1 CAACA 57203890 ACGGCTCCAG Statistics Matches: 56, Mismatches: 5, Indels: 5 0.85 0.08 0.08 Matches are distributed among these distances: 57 34 0.61 60 20 0.36 61 2 0.04 ACGTcount: A:0.23, C:0.30, G:0.30, T:0.18 Consensus pattern (58 bp): CAACAGTGGGTCCTGTGGGAATAGGACCACTGGCTGCACGCAGCCACACCAGGGTTCC Found at i:57208651 original size:20 final size:22 Alignment explanation

Indices: 57208613--57208658 Score: 69 Period size: 20 Copynumber: 2.2 Consensus size: 22 57208603 AAAATAGTAG * 57208613 AAAGAAGAACCCAAGAAAGAGA 1 AAAGAAGAACCCAAGAAAGAAA 57208635 AAAGAA-AACCC-AGAAAGAAA 1 AAAGAAGAACCCAAGAAAGAAA 57208655 AAAG 1 AAAG 57208659 GGGAAAGAAA Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 20 12 0.52 21 5 0.22 22 6 0.26 ACGTcount: A:0.67, C:0.13, G:0.20, T:0.00 Consensus pattern (22 bp): AAAGAAGAACCCAAGAAAGAAA Found at i:57211946 original size:67 final size:67 Alignment explanation

Indices: 57211866--57212000 Score: 243 Period size: 67 Copynumber: 2.0 Consensus size: 67 57211856 TTTGGCATAT * 57211866 TCCCTGAAGCGAATATTGCATATAATTGTTTAGAAATTATATTTATTTTGTTGACTTAGTGACAT 1 TCCCTAAAGCGAATATTGCATATAATTGTTTAGAAATTATATTTATTTTGTTGACTTAGTGACAT 57211931 TA 66 TA * * 57211933 TCCCTAAAGCGAATATTGCATATAATTGTTTGGAAATTATATTTATTTTTTTGACTTAGTGACAT 1 TCCCTAAAGCGAATATTGCATATAATTGTTTAGAAATTATATTTATTTTGTTGACTTAGTGACAT 57211998 TA 66 TA 57212000 T 1 T 57212001 AATATTCACA Statistics Matches: 65, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 67 65 1.00 ACGTcount: A:0.31, C:0.10, G:0.14, T:0.44 Consensus pattern (67 bp): TCCCTAAAGCGAATATTGCATATAATTGTTTAGAAATTATATTTATTTTGTTGACTTAGTGACAT TA Found at i:57217694 original size:28 final size:28 Alignment explanation

Indices: 57217654--57217711 Score: 116 Period size: 28 Copynumber: 2.1 Consensus size: 28 57217644 TTAACATTAA 57217654 TATAATAATTTAAGATAAGATTGGATCG 1 TATAATAATTTAAGATAAGATTGGATCG 57217682 TATAATAATTTAAGATAAGATTGGATCG 1 TATAATAATTTAAGATAAGATTGGATCG 57217710 TA 1 TA 57217712 GTCTTAGTCT Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 30 1.00 ACGTcount: A:0.43, C:0.03, G:0.17, T:0.36 Consensus pattern (28 bp): TATAATAATTTAAGATAAGATTGGATCG Found at i:57219038 original size:17 final size:16 Alignment explanation

Indices: 57219005--57219060 Score: 53 Period size: 16 Copynumber: 3.6 Consensus size: 16 57218995 GTAATTTTCT 57219005 TTCT-ATTTTTGATCC 1 TTCTAATTTTTGATCC * 57219020 TTCTAATTTTTTATCCC 1 TTCTAATTTTTGAT-CC * * 57219037 TTC-AAATTTTCATCC 1 TTCTAATTTTTGATCC * 57219052 TTCCAATTT 1 TTCTAATTT 57219061 CCTTTCTACT Statistics Matches: 34, Mismatches: 4, Indels: 5 0.79 0.09 0.12 Matches are distributed among these distances: 15 9 0.26 16 20 0.59 17 5 0.15 ACGTcount: A:0.20, C:0.23, G:0.02, T:0.55 Consensus pattern (16 bp): TTCTAATTTTTGATCC Found at i:57223744 original size:23 final size:23 Alignment explanation

Indices: 57223714--57224292 Score: 230 Period size: 23 Copynumber: 22.9 Consensus size: 23 57223704 TACAATTTAA 57223714 TTAGGGTTTTTAATTAAATAGGG 1 TTAGGGTTTTTAATTAAATAGGG 57223737 TTAGGGTTTTTAATTTAATTAAATTA-GG 1 TTAGGG---TT--TTTAATTAAA-TAGGG * 57223765 TTAGGGTTTTTAATTAAGTAGGG 1 TTAGGGTTTTTAATTAAATAGGG * 57223788 TTAGGGTTTTTAATTAAGTAGGG 1 TTAGGGTTTTTAATTAAATAGGG * 57223811 TTAGGGTTTTTAATTTAATTAAATAAGG 1 TTAGGG---TT--TTTAATTAAATAGGG 57223839 TTAGGGTTTTTAATTAAATTA-GG 1 TTAGGGTTTTTAATTAAA-TAGGG * 57223862 TTAGGGTTTTTAATTTAATTAAATAAGG 1 TTAGGG---TT--TTTAATTAAATAGGG 57223890 TTAGGGTTTTTAATT-AA-A--- 1 TTAGGGTTTTTAATTAAATAGGG *** ** 57223908 TTA-GGTAACCTAATTAGGTTA-GG 1 TTAGGGT-TTTTAATTA-AATAGGG * 57223931 TTAGTGTTTTTAATTTAATTAAATTA-GG 1 TTAG-G--GTT--TTTAATTAAA-TAGGG 57223959 TTAGGGTTTTTAATTAAATTAGGTTAGG 1 TTAGGGTTTTTAATTAAA-TA-G---GG * 57223987 TTAGGGTTAGGGTTTTTAATTAAGTAGGG 1 TTAGGG------TTTTTAATTAAATAGGG * 57224016 TTTAGGGTTTTTAATTTAATTAAATAAGG 1 -TTAGGG---TT--TTTAATTAAATAGGG * ** 57224045 TTAGGGTTTTTAATTTAATTA-AA 1 TTAGGGTTTTTAA-TTAAATAGGG * 57224068 TTAGGGTTTTTAATTAAGTAGGG 1 TTAGGGTTTTTAATTAAATAGGG * 57224091 TTAGGGTTTTTAATTTAATTAAATAAGG 1 TTAGGG---TT--TTTAATTAAATAGGG * 57224119 TTAGGGTTTTTAATTTAAGTAGGTTAGG 1 TTAGGGTTTTTAA-TTAAATA-G---GG 57224147 TTAGGGTTTTTAATTAAATTAGGTTAGG 1 TTAGGGTTTTTAATTAAA-TA-G---GG 57224175 TTAGGGTTTTTAATTTAATTAAATTA-GG 1 TTAGGG---TT--TTTAATTAAA-TAGGG * 57224203 TTAGGGTTTTTAATTAAGTAGGG 1 TTAGGGTTTTTAATTAAATAGGG * * ** 57224226 TTTAGGATTTTTAATTTAATTA-AA 1 -TTAGGGTTTTTAA-TTAAATAGGG * * 57224250 TTATGGTTTTTAATTAAGTAGGG 1 TTAGGGTTTTTAATTAAATAGGG * * 57224273 TTAGGGATTTTAATCAAATA 1 TTAGGGTTTTTAATTAAATA 57224293 ATGTCAAAAT Statistics Matches: 442, Mismatches: 46, Indels: 136 0.71 0.07 0.22 Matches are distributed among these distances: 17 3 0.01 18 8 0.02 21 2 0.00 22 18 0.04 23 154 0.35 24 26 0.06 25 21 0.05 26 8 0.02 27 10 0.02 28 140 0.32 29 17 0.04 30 6 0.01 31 2 0.00 32 1 0.00 33 15 0.03 34 11 0.02 ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46 Consensus pattern (23 bp): TTAGGGTTTTTAATTAAATAGGG Found at i:57223766 original size:28 final size:28 Alignment explanation

Indices: 57223722--57224257 Score: 354 Period size: 28 Copynumber: 19.6 Consensus size: 28 57223712 AATTAGGGTT 57223722 TTTAATTAAA-TAGGGTTAGGGTTTTTAA 1 TTTAATTAAATTA-GGTTAGGGTTTTTAA 57223750 TTTAATTAAATTAGGTTAGGGTTTTTAA 1 TTTAATTAAATTAGGTTAGGGTTTTTAA * * 57223778 -TTAAGT--A--GGGTTAGGGTTTTTAA 1 TTTAATTAAATTAGGTTAGGGTTTTTAA * * 57223801 -TTAAGT--A--GGGTTAGGGTTTTTAA 1 TTTAATTAAATTAGGTTAGGGTTTTTAA * 57223824 TTTAATTAAATAAGGTTAGGG---TT-- 1 TTTAATTAAATTAGGTTAGGGTTTTTAA 57223847 TTTAATTAAATTAGGTTAGGGTTTTTAA 1 TTTAATTAAATTAGGTTAGGGTTTTTAA * 57223875 TTTAATTAAATAAGGTTAGGGTTTTTAA 1 TTTAATTAAATTAGGTTAGGGTTTTTAA * 57223903 TTAAATTAGGTAACCTAATTAGGTTA-GGTTAGTGTT-- 1 TTTAA-T---T-A---AATTAGGTTAGGGTT--T-TTAA * * 57223939 TTTAATTTAATTAAATTAGGTTAGGGTTTTTAA 1 TTTAATTAAATT--A--GG-TTAGGGTTTTTAA * ** * 57223972 TTAAATTAGGTTAGGTTAGGGTTAGGGTT-- 1 TTTAATTAAATTAGGTTAGGGTT---TTTAA * 57224001 TTTAATT-AAGTAGGGTTTAGGGTTTTTAA 1 TTTAATTAAATTA-GG-TTAGGGTTTTTAA * 57224030 TTTAATTAAATAAGGTTAGGGTTTTTAA 1 TTTAATTAAATTAGGTTAGGGTTTTTAA 57224058 TTTAATT-AA--A--TTAGGGTTTTTAA 1 TTTAATTAAATTAGGTTAGGGTTTTTAA * * 57224081 -TTAAGT--A--GGGTTAGGGTTTTTAA 1 TTTAATTAAATTAGGTTAGGGTTTTTAA * 57224104 TTTAATTAAATAAGGTTAGGGTTTTTAA 1 TTTAATTAAATTAGGTTAGGGTTTTTAA * ** 57224132 TTTAAGTAGGTTAGGTTAGGGTTTTTAA 1 TTTAATTAAATTAGGTTAGGGTTTTTAA * ** 57224160 TTAAATTAGGTTAGGTTAGGGTTTTTAA 1 TTTAATTAAATTAGGTTAGGGTTTTTAA 57224188 TTTAATTAAATTAGGTTAGGGTTTTTAA 1 TTTAATTAAATTAGGTTAGGGTTTTTAA * * * 57224216 -TTAAGT--A--GGGTTTAGGATTTTTAA 1 TTTAATTAAATTAGG-TTAGGGTTTTTAA 57224240 TTTAATTAAATTATGGTT 1 TTTAATTAAATTA-GGTT 57224258 TTTAATTAAG Statistics Matches: 414, Mismatches: 42, Indels: 103 0.74 0.08 0.18 Matches are distributed among these distances: 21 1 0.00 22 5 0.01 23 86 0.21 24 22 0.05 25 10 0.02 26 4 0.01 27 15 0.04 28 188 0.45 29 23 0.06 30 14 0.03 31 5 0.01 32 4 0.01 33 12 0.03 34 4 0.01 35 5 0.01 36 13 0.03 37 1 0.00 38 2 0.00 ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47 Consensus pattern (28 bp): TTTAATTAAATTAGGTTAGGGTTTTTAA Found at i:57223787 original size:51 final size:51 Alignment explanation

Indices: 57223714--57224286 Score: 353 Period size: 51 Copynumber: 10.7 Consensus size: 51 57223704 TACAATTTAA 57223714 TTAGGGTTTTTAATTAAATAGGGTTAGGGTTTTTAATTTAATTAAATTAGG 1 TTAGGGTTTTTAATTAAATAGGGTTAGGGTTTTTAATTTAATTAAATTAGG * * * 57223765 TTAGGGTTTTTAATTAAGTAGGGTTAGGGTTTTTAA-TTAAGT--A--GGG 1 TTAGGGTTTTTAATTAAATAGGGTTAGGGTTTTTAATTTAATTAAATTAGG * 57223811 TTAGGGTTTTTAATTTAATTAAATAAGGTTAGGG---TT--TTTAATTAAATTAGG 1 TTAGGG---TT--TTTAATTAAATAGGGTTAGGGTTTTTAATTTAATTAAATTAGG * * 57223862 TTAGGGTTTTTAATTTAATTAAATAAGGTTAGGGTTTTTAATTAAATTAGGTAACCTAATTAGG 1 TTAGGG---TT--TTTAATTAAATAGGGTTAGGGTTTTTAATTTAA-T---T-A---AATTAGG * * 57223926 TTAGGTTAGTGTTTTTAATTTAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGTTA 1 TTA-G---G-GTTTTT-A----ATTAAA-TAGGGTTAGGGTTTTTAATTTAATTA----A-ATTA 57223990 GGG 50 -GG * * 57223993 TTAGGGTTTTTAATTAAGTAGGGTTTAGGGTTTTTAATTTAATTAAATAAGG 1 TTAGGGTTTTTAATTAAATAGGG-TTAGGGTTTTTAATTTAATTAAATTAGG * ** * * 57224045 TTAGGGTTTTTAATTTAATTA-AATTAGGGTTTTTAA-TTAAGT--A--GGG 1 TTAGGGTTTTTAA-TTAAATAGGGTTAGGGTTTTTAATTTAATTAAATTAGG * * ** 57224091 TTAGGGTTTTTAATTTAATTAAATAAGGTTAGGGTTTTTAATTTAAGTAGGTTAGG 1 TTAGGG---TT--TTTAATTAAATAGGGTTAGGGTTTTTAATTTAATTAAATTAGG 57224147 TTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTTTTTAATTTAATTAAATTAGG 1 TTAGGGTTTTTAATTAAA-TA-G---GGTTAGGGTTTTTAATTTAATTAAATTAGG * * 57224203 TTAGGGTTTTTAATTAAGTAGGGTTTAGGATTTTTAATTTAATTAAATTA-- 1 TTAGGGTTTTTAATTAAATAGGG-TTAGGGTTTTTAATTTAATTAAATTAGG * * 57224253 -T--GGTTTTTAATTAAGTAGGGTTAGGGATTTTAAT 1 TTAGGGTTTTTAATTAAATAGGGTTAGGGTTTTTAAT 57224287 CAAATAATGT Statistics Matches: 432, Mismatches: 33, Indels: 119 0.74 0.06 0.20 Matches are distributed among these distances: 46 28 0.06 47 24 0.06 48 4 0.01 49 6 0.01 50 16 0.04 51 133 0.31 52 48 0.11 53 10 0.02 54 4 0.01 55 2 0.00 56 58 0.13 57 8 0.02 58 20 0.05 60 1 0.00 61 2 0.00 62 6 0.01 63 1 0.00 64 14 0.03 65 5 0.01 66 6 0.01 67 5 0.01 68 2 0.00 69 27 0.06 70 2 0.00 ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47 Consensus pattern (51 bp): TTAGGGTTTTTAATTAAATAGGGTTAGGGTTTTTAATTTAATTAAATTAGG Found at i:57224091 original size:17 final size:18 Alignment explanation

Indices: 57224058--57224092 Score: 54 Period size: 17 Copynumber: 2.0 Consensus size: 18 57224048 GGGTTTTTAA * 57224058 TTTAATTAAATTAGGGTT 1 TTTAATTAAAGTAGGGTT 57224076 TTTAATT-AAGTAGGGTT 1 TTTAATTAAAGTAGGGTT 57224093 AGGGTTTTTA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 17 9 0.56 18 7 0.44 ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49 Consensus pattern (18 bp): TTTAATTAAAGTAGGGTT Found at i:57224521 original size:21 final size:21 Alignment explanation

Indices: 57224480--57224524 Score: 56 Period size: 21 Copynumber: 2.1 Consensus size: 21 57224470 GGCGGTTGTT * * 57224480 GTTCTTCCGGTGGGGATTCTG 1 GTTCTTCCGGTCGGCATTCTG 57224501 GTTCTTCCGGTTCGGCA-TCTG 1 GTTCTTCCGG-TCGGCATTCTG 57224522 GTT 1 GTT 57224525 GTCGGACTTG Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 21 17 0.81 22 4 0.19 ACGTcount: A:0.04, C:0.22, G:0.33, T:0.40 Consensus pattern (21 bp): GTTCTTCCGGTCGGCATTCTG Found at i:57226592 original size:28 final size:29 Alignment explanation

Indices: 57226560--57226615 Score: 96 Period size: 28 Copynumber: 2.0 Consensus size: 29 57226550 TGAAAATATT 57226560 AAAAATTTTAAAATTAT-TTAAAAAAATA 1 AAAAATTTTAAAATTATCTTAAAAAAATA * 57226588 AAAAATTTTAAAATTTTCTTAAAAAAAT 1 AAAAATTTTAAAATTATCTTAAAAAAAT 57226616 GAAATTTAAT Statistics Matches: 26, Mismatches: 1, Indels: 1 0.93 0.04 0.04 Matches are distributed among these distances: 28 16 0.62 29 10 0.38 ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38 Consensus pattern (29 bp): AAAAATTTTAAAATTATCTTAAAAAAATA Found at i:57226687 original size:22 final size:22 Alignment explanation

Indices: 57226657--57226698 Score: 66 Period size: 22 Copynumber: 1.9 Consensus size: 22 57226647 ATTTGGAGAT * 57226657 TTTTTGAAGGAAATTGAGAGGA 1 TTTTGGAAGGAAATTGAGAGGA * 57226679 TTTTGGAAGGAATTTGAGAG 1 TTTTGGAAGGAAATTGAGAG 57226699 TTTGAGAGAA Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 22 18 1.00 ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33 Consensus pattern (22 bp): TTTTGGAAGGAAATTGAGAGGA Found at i:57226719 original size:52 final size:51 Alignment explanation

Indices: 57226648--57226750 Score: 129 Period size: 52 Copynumber: 2.0 Consensus size: 51 57226638 TTAATATAGA * * * 57226648 TTTGGAGATTTTTTGAAGGAAATTGAGAG-GATTTTGGAA-GGAATTTGAGAG 1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTT-GAAGGGAA-TTGAGAG * 57226699 TTTGAGAGAATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAATTGAGAG 1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG 57226751 AAATTTTGAA Statistics Matches: 45, Mismatches: 4, Indels: 5 0.83 0.07 0.09 Matches are distributed among these distances: 51 4 0.09 52 32 0.71 53 9 0.20 ACGTcount: A:0.35, C:0.00, G:0.32, T:0.33 Consensus pattern (51 bp): TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG Found at i:57226725 original size:22 final size:23 Alignment explanation

Indices: 57226700--57226791 Score: 111 Period size: 22 Copynumber: 4.2 Consensus size: 23 57226690 ATTTGAGAGT 57226700 TTGAGAG-AATTTTGGAAGGAAA 1 TTGAGAGAAATTTTGGAAGGAAA * * 57226722 TTGATAGAAATTTT-GAAGGGAA 1 TTGAGAGAAATTTTGGAAGGAAA * 57226744 TTGAGAGAAATTTTGAAAGG-AA 1 TTGAGAGAAATTTTGGAAGGAAA * * 57226766 TTGAGAG-AATTTTTGAAAGAAA 1 TTGAGAGAAATTTTGGAAGGAAA 57226788 TTGA 1 TTGA 57226792 TATTGAATTT Statistics Matches: 60, Mismatches: 7, Indels: 6 0.82 0.10 0.08 Matches are distributed among these distances: 21 9 0.15 22 41 0.68 23 10 0.17 ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30 Consensus pattern (23 bp): TTGAGAGAAATTTTGGAAGGAAA Found at i:57226749 original size:44 final size:44 Alignment explanation

Indices: 57226700--57226791 Score: 123 Period size: 44 Copynumber: 2.1 Consensus size: 44 57226690 ATTTGAGAGT * * * * 57226700 TTGAGAG-AATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAA 1 TTGAGAGAAATTTTGAAAGG-AATTGAGAGAAATTTTGAAAGAAA * 57226744 TTGAGAGAAATTTTGAAAGGAATTGAGAGAATTTTTGAAAGAAA 1 TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA 57226788 TTGA 1 TTGA 57226792 TATTGAATTT Statistics Matches: 42, Mismatches: 5, Indels: 2 0.86 0.10 0.04 Matches are distributed among these distances: 44 31 0.74 45 11 0.26 ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30 Consensus pattern (44 bp): TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA Found at i:57229662 original size:19 final size:19 Alignment explanation

Indices: 57229625--57229663 Score: 53 Period size: 20 Copynumber: 2.0 Consensus size: 19 57229615 ATTGATTTTT 57229625 TAAATTTTGAATTAAAATGA 1 TAAATTTTGAA-TAAAATGA 57229645 TAAATTTTGTAA-AAAATGA 1 TAAATTTTG-AATAAAATGA 57229664 GGGCTAAATT Statistics Matches: 18, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 19 7 0.39 20 9 0.50 21 2 0.11 ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38 Consensus pattern (19 bp): TAAATTTTGAATAAAATGA Found at i:57230569 original size:42 final size:37 Alignment explanation

Indices: 57230474--57230549 Score: 100 Period size: 37 Copynumber: 2.1 Consensus size: 37 57230464 ATTACTAATA * * 57230474 AAATAAA-AAGAAAAATTATATAAAATTTATAATATGT 1 AAATAAAGAA-AAAAATAATATAAAATTTATAATATAT * * 57230511 AAATTAAGTAAAAAATAATATAAAATTTATAATATAT 1 AAATAAAGAAAAAAATAATATAAAATTTATAATATAT 57230548 AA 1 AA 57230550 CCTTTATAAA Statistics Matches: 34, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 37 33 0.97 38 1 0.03 ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33 Consensus pattern (37 bp): AAATAAAGAAAAAAATAATATAAAATTTATAATATAT Found at i:57234595 original size:18 final size:17 Alignment explanation

Indices: 57234551--57234602 Score: 52 Period size: 17 Copynumber: 2.9 Consensus size: 17 57234541 ATCATTATTA * 57234551 AAAATCATT-AAAAATAT 1 AAAAT-ATTCAAAAAAAT * 57234568 ATAATATTCAAAAAAAT 1 AAAATATTCAAAAAAAT 57234585 AAAATATTTCAAAGAAAA 1 AAAATA-TTCAAA-AAAA 57234603 ATATAAGTAA Statistics Matches: 29, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 16 3 0.10 17 16 0.55 18 6 0.21 19 4 0.14 ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27 Consensus pattern (17 bp): AAAATATTCAAAAAAAT Found at i:57236528 original size:14 final size:14 Alignment explanation

Indices: 57236509--57236535 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 57236499 TTATTTAGTT 57236509 GTAGAATCAAAATA 1 GTAGAATCAAAATA 57236523 GTAGAATCAAAAT 1 GTAGAATCAAAAT 57236536 TTAAGATAAA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22 Consensus pattern (14 bp): GTAGAATCAAAATA Found at i:57245173 original size:39 final size:39 Alignment explanation

Indices: 57245119--57245196 Score: 138 Period size: 39 Copynumber: 2.0 Consensus size: 39 57245109 ATAAGTCGCC * 57245119 GGCACTCGGGGATGCGTAGGTTATATCCATTCCCGCACT 1 GGCACTCGAGGATGCGTAGGTTATATCCATTCCCGCACT * 57245158 GGCACTCGAGGATGCGTAGGTTATCTCCATTCCCGCACT 1 GGCACTCGAGGATGCGTAGGTTATATCCATTCCCGCACT 57245197 ATCGGAGCAT Statistics Matches: 37, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 39 37 1.00 ACGTcount: A:0.18, C:0.29, G:0.27, T:0.26 Consensus pattern (39 bp): GGCACTCGAGGATGCGTAGGTTATATCCATTCCCGCACT Found at i:57251745 original size:21 final size:21 Alignment explanation

Indices: 57251721--57251790 Score: 58 Period size: 19 Copynumber: 3.4 Consensus size: 21 57251711 AATTTAATTT 57251721 TTTATTTTAATATTATATATA 1 TTTATTTTAATATTATATATA * 57251742 TTTAATGTGTTATTATTA-ATA-A 1 TTT-AT-T-TTAATATTATATATA * 57251764 TTAATTTTAA-ATTATATAT- 1 TTTATTTTAATATTATATATA * 57251783 TTCATTTT 1 TTTATTTT 57251791 TTATTGTATG Statistics Matches: 40, Mismatches: 4, Indels: 12 0.71 0.07 0.21 Matches are distributed among these distances: 18 4 0.10 19 13 0.32 20 1 0.03 21 5 0.12 22 5 0.12 23 4 0.10 24 8 0.20 ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60 Consensus pattern (21 bp): TTTATTTTAATATTATATATA Found at i:57254501 original size:14 final size:14 Alignment explanation

Indices: 57254482--57254513 Score: 55 Period size: 14 Copynumber: 2.3 Consensus size: 14 57254472 TAAAATCTTC * 57254482 GATTCCAACTACAG 1 GATTCCAACTAAAG 57254496 GATTCCAACTAAAG 1 GATTCCAACTAAAG 57254510 GATT 1 GATT 57254514 TCTCCACTCG Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 14 17 1.00 ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25 Consensus pattern (14 bp): GATTCCAACTAAAG Found at i:57256242 original size:26 final size:26 Alignment explanation

Indices: 57256213--57256264 Score: 104 Period size: 26 Copynumber: 2.0 Consensus size: 26 57256203 ATAAGAAAGT 57256213 GACACGTTGATGAAAGAAACATTAGG 1 GACACGTTGATGAAAGAAACATTAGG 57256239 GACACGTTGATGAAAGAAACATTAGG 1 GACACGTTGATGAAAGAAACATTAGG 57256265 AGGTGCCACA Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 26 1.00 ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19 Consensus pattern (26 bp): GACACGTTGATGAAAGAAACATTAGG Found at i:57258801 original size:2 final size:2 Alignment explanation

Indices: 57258796--57258825 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 57258786 AGTCTAACAC 57258796 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 57258826 CAATAAGTAT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:57259973 original size:14 final size:14 Alignment explanation

Indices: 57259954--57259984 Score: 53 Period size: 14 Copynumber: 2.2 Consensus size: 14 57259944 TTCTAGTTTG 57259954 TTTTGTTCTAATAT 1 TTTTGTTCTAATAT * 57259968 TTTTGTTGTAATAT 1 TTTTGTTCTAATAT 57259982 TTT 1 TTT 57259985 AGTTTATGCG Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 14 16 1.00 ACGTcount: A:0.19, C:0.03, G:0.10, T:0.68 Consensus pattern (14 bp): TTTTGTTCTAATAT Found at i:57262981 original size:15 final size:15 Alignment explanation

Indices: 57262936--57262981 Score: 53 Period size: 15 Copynumber: 3.1 Consensus size: 15 57262926 AAGTTGTGGA 57262936 TTTAATC-TATATTT 1 TTTAATCTTATATTT 57262950 TTTAAT-TTGAT-TATT 1 TTTAATCTT-ATAT-TT 57262965 TTTAATCTTATATTT 1 TTTAATCTTATATTT 57262980 TT 1 TT 57262982 CAAAATTTGA Statistics Matches: 27, Mismatches: 0, Indels: 9 0.75 0.00 0.25 Matches are distributed among these distances: 14 8 0.30 15 16 0.59 16 3 0.11 ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67 Consensus pattern (15 bp): TTTAATCTTATATTT Found at i:57279034 original size:39 final size:39 Alignment explanation

Indices: 57278991--57279072 Score: 112 Period size: 39 Copynumber: 2.1 Consensus size: 39 57278981 TTGAGGAAGG * 57278991 ATTATTGTAAATTCTAAACATTATATCAA-AAAAGTAAAA 1 ATTATGGTAAATTCTAAACATTATATCAAGAAAA-TAAAA * * * 57279030 ATTATGGTAAATTTTAAACATTATATTAAGAAAATAAAG 1 ATTATGGTAAATTCTAAACATTATATCAAGAAAATAAAA 57279069 ATTA 1 ATTA 57279073 AGAGAGTAAA Statistics Matches: 38, Mismatches: 4, Indels: 2 0.86 0.09 0.05 Matches are distributed among these distances: 39 34 0.89 40 4 0.11 ACGTcount: A:0.52, C:0.05, G:0.07, T:0.35 Consensus pattern (39 bp): ATTATGGTAAATTCTAAACATTATATCAAGAAAATAAAA Found at i:57281448 original size:25 final size:27 Alignment explanation

Indices: 57281398--57281448 Score: 63 Period size: 25 Copynumber: 2.0 Consensus size: 27 57281388 ACAAATAATT * 57281398 AAAAAATTATAATAAAATATTAAAAAC 1 AAAAAATTATAATAAAATATCAAAAAC 57281425 AAAAAA-TAT-ATAAAAT-TCATAAAA 1 AAAAAATTATAATAAAATATCA-AAAA 57281449 ATTTAAAAAC Statistics Matches: 22, Mismatches: 1, Indels: 4 0.81 0.04 0.15 Matches are distributed among these distances: 24 2 0.09 25 11 0.50 26 3 0.14 27 6 0.27 ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25 Consensus pattern (27 bp): AAAAAATTATAATAAAATATCAAAAAC Found at i:57282179 original size:19 final size:19 Alignment explanation

Indices: 57282157--57282195 Score: 78 Period size: 19 Copynumber: 2.1 Consensus size: 19 57282147 ATCTTCATAA 57282157 AAGCTTCCACAAAAAAAAT 1 AAGCTTCCACAAAAAAAAT 57282176 AAGCTTCCACAAAAAAAAT 1 AAGCTTCCACAAAAAAAAT 57282195 A 1 A 57282196 TCCACACTTT Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.59, C:0.21, G:0.05, T:0.15 Consensus pattern (19 bp): AAGCTTCCACAAAAAAAAT Found at i:57287015 original size:11 final size:10 Alignment explanation

Indices: 57286993--57287023 Score: 53 Period size: 10 Copynumber: 3.1 Consensus size: 10 57286983 CTTGATGTCG 57286993 AAAATTAAAA 1 AAAATTAAAA * 57287003 AAACTTAAAA 1 AAAATTAAAA 57287013 AAAATTAAAA 1 AAAATTAAAA 57287023 A 1 A 57287024 TACGATCCTT Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 10 19 1.00 ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19 Consensus pattern (10 bp): AAAATTAAAA Found at i:57288086 original size:29 final size:28 Alignment explanation

Indices: 57288024--57288088 Score: 76 Period size: 30 Copynumber: 2.2 Consensus size: 28 57288014 ATAAAATTGC * * 57288024 TAAAATATGGGCTAAATCGAAATAAAAA 1 TAAAATATGGGCGAAATCGAAAGAAAAA * * 57288052 TGAAAATGTAGGGCGAAATTGAAAGAAAAA 1 T-AAAATAT-GGGCGAAATCGAAAGAAAAA 57288082 TAAAATA 1 TAAAATA 57288089 AAAGGGACTA Statistics Matches: 30, Mismatches: 5, Indels: 3 0.79 0.13 0.08 Matches are distributed among these distances: 28 1 0.03 29 11 0.37 30 18 0.60 ACGTcount: A:0.57, C:0.05, G:0.18, T:0.20 Consensus pattern (28 bp): TAAAATATGGGCGAAATCGAAAGAAAAA Found at i:57289621 original size:46 final size:45 Alignment explanation

Indices: 57289559--57289980 Score: 241 Period size: 46 Copynumber: 9.8 Consensus size: 45 57289549 CTGGCTTCAA * 57289559 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGG 1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTCGG * * * * * 57289605 TCTGTTCCACTGTAATCTCAGGGAAATAAGACCTG-A--C-GCGA 1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTCGG * ** * * ** 57289646 TCTACTCTGCTGTAA-CTTTAGAGAGATAAGATC---A-T-TT-AA 1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGAATTCTTCGG * * * * * 57289685 TCCGCTCCACTGTAATCTCAGGGAGATAGGAT-T-ACTATCTTTGA 1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTCGG * * * 57289729 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTACTTTTTCGG 1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTCGG * * * * 57289775 TCTGCTCCACTGTAATTTCAGGGAGATAAGACCT-AA---TACGA 1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTCGG ** * * ** 57289816 TCCACTCTACTGTAA-CTTCAGAGAGATAAGATCCT---TTAATC-- 1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-CTGAATTCTTCGG * * * 57289857 -C-GCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTATCTTTGA 1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTCGG * * 57289899 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGG 1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTCGG * * 57289945 TCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGA 1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGA 57289981 TATGATCCAC Statistics Matches: 290, Mismatches: 57, Indels: 59 0.71 0.14 0.15 Matches are distributed among these distances: 37 1 0.00 39 50 0.17 40 6 0.02 41 53 0.18 42 4 0.01 43 4 0.01 44 60 0.21 45 3 0.01 46 103 0.36 47 6 0.02 ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31 Consensus pattern (45 bp): TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTCGG Found at i:57289751 original size:44 final size:43 Alignment explanation

Indices: 57289688--57290070 Score: 296 Period size: 46 Copynumber: 9.0 Consensus size: 43 57289678 CATTTAATCC * 57289688 GCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTTGATCT 1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-TCTTTGATCT * * 57289732 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGTACTT-TTTCGGTCT 1 GCTCCACTGTAATCTCAGGGAGATAAGA--T-TACTTCTTT-GATCT * * * * * 57289778 GCTCCACTGTAATTTCAGGGAGATAAGACCTAATAC---GATCC 1 GCTCCACTGTAATCTCAGGGAGATAAGA-TTACTTCTTTGATCT * * * * * 57289819 ACTCTACTGTAA-CTTCAGAGAGATAAGA-T-C--CTTTAATCC 1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTTCTTTGATCT 57289858 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT 1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-TCTTTGATCT * * * 57289902 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCT 1 GCTCCACTGTAATCTCAGGGAGATAAGAT-T--ACTTCTTTGATCT * * ** * * 57289948 GTTCCACTGTAATCTCAGGGAGATAAGA--CCTGATATGATCC 1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTTCTTTGATCT * * * * 57289989 ACTCTACTGTAA-CTTCAGAGAGATAAGA-T-C--CTTTAATC- 1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTTCTTTGATCT 57290027 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT 1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-TCTTTGATCT 57290071 ACTTCACTTA Statistics Matches: 268, Mismatches: 44, Indels: 54 0.73 0.12 0.15 Matches are distributed among these distances: 36 1 0.00 38 23 0.09 39 35 0.13 40 4 0.01 41 56 0.21 43 7 0.03 44 64 0.24 45 5 0.02 46 66 0.25 47 7 0.03 ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31 Consensus pattern (43 bp): GCTCCACTGTAATCTCAGGGAGATAAGATTACTTCTTTGATCT Found at i:57290103 original size:170 final size:170 Alignment explanation

Indices: 57289558--57290070 Score: 875 Period size: 170 Copynumber: 3.0 Consensus size: 170 57289548 ACTGGCTTCA * 57289558 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGTAATCT 1 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAACTTCTTCGGTCTGTTCCACTGTAATCT * ** * * * * 57289623 CAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTTAGAGAGATAAGATCATTTAATCC 66 CAGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC * 57289688 GCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTTG 131 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG * * * * 57289728 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTACTTTTTCGGTCTGCTCCACTGTAATTT 1 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAACTTCTTCGGTCTGTTCCACTGTAATCT * 57289793 CAGGGAGATAAGACCTAATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC 66 CAGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC 57289858 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG 131 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG * 57289898 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGTTCCACTGTAATCT 1 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAACTTCTTCGGTCTGTTCCACTGTAATCT * 57289963 CAGGGAGATAAGACCTGATATGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAAT-C 66 CAGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC 57290027 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG 131 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG 57290067 ATCT 1 ATCT 57290071 ACTTCACTTA Statistics Matches: 323, Mismatches: 20, Indels: 1 0.94 0.06 0.00 Matches are distributed among these distances: 169 45 0.14 170 278 0.86 ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31 Consensus pattern (170 bp): ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAACTTCTTCGGTCTGTTCCACTGTAATCT CAGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTG Found at i:57301783 original size:9 final size:10 Alignment explanation

Indices: 57301764--57301795 Score: 55 Period size: 10 Copynumber: 3.1 Consensus size: 10 57301754 CTTGATGTCG 57301764 AAAATTAAAA 1 AAAATTAAAA 57301774 AAAATTAAAAA 1 AAAATT-AAAA 57301785 AAAATTAAAA 1 AAAATTAAAA 57301795 A 1 A 57301796 TACGATCCTT Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 10 11 0.52 11 10 0.48 ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19 Consensus pattern (10 bp): AAAATTAAAA Found at i:57301786 original size:11 final size:11 Alignment explanation

Indices: 57301764--57301795 Score: 57 Period size: 11 Copynumber: 3.0 Consensus size: 11 57301754 CTTGATGTCG 57301764 AAAATT-AAAA 1 AAAATTAAAAA 57301774 AAAATTAAAAA 1 AAAATTAAAAA 57301785 AAAATTAAAAA 1 AAAATTAAAAA 57301796 TACGATCCTT Statistics Matches: 21, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 10 6 0.29 11 15 0.71 ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19 Consensus pattern (11 bp): AAAATTAAAAA Found at i:57302860 original size:29 final size:28 Alignment explanation

Indices: 57302798--57302862 Score: 76 Period size: 30 Copynumber: 2.2 Consensus size: 28 57302788 ATAAAATTGC * * 57302798 TAAAATATGGGCTAAATCGAAATAAAAA 1 TAAAATATGGGCGAAATCGAAAGAAAAA * * 57302826 TGAAAATGTAGGGCGAAATTGAAAGAAAAA 1 T-AAAATAT-GGGCGAAATCGAAAGAAAAA 57302856 TAAAATA 1 TAAAATA 57302863 AAAGGGACTA Statistics Matches: 30, Mismatches: 5, Indels: 3 0.79 0.13 0.08 Matches are distributed among these distances: 28 1 0.03 29 11 0.37 30 18 0.60 ACGTcount: A:0.57, C:0.05, G:0.18, T:0.20 Consensus pattern (28 bp): TAAAATATGGGCGAAATCGAAAGAAAAA Found at i:57304346 original size:12 final size:12 Alignment explanation

Indices: 57304329--57304355 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 57304319 AATAAATCAT 57304329 ATATGTATATTA 1 ATATGTATATTA 57304341 ATATGTATATTA 1 ATATGTATATTA 57304353 ATA 1 ATA 57304356 GAAAATTTAA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 15 1.00 ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48 Consensus pattern (12 bp): ATATGTATATTA Found at i:57304467 original size:22 final size:21 Alignment explanation

Indices: 57304438--57304478 Score: 55 Period size: 22 Copynumber: 1.9 Consensus size: 21 57304428 TCCAAAAAAT * 57304438 ATTAATAAATAATTTAAATTA 1 ATTAATAAATAATTAAAATTA * 57304459 ATTACATAATTAATTAAAAT 1 ATTA-ATAAATAATTAAAAT 57304479 ATTGGAAGAT Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 21 4 0.24 22 13 0.76 ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41 Consensus pattern (21 bp): ATTAATAAATAATTAAAATTA Found at i:57304697 original size:21 final size:21 Alignment explanation

Indices: 57304673--57304728 Score: 76 Period size: 21 Copynumber: 2.7 Consensus size: 21 57304663 CACTATTATT * * * 57304673 TCTAATTTCACTGCTATAGTA 1 TCTAATCTCACCGCTACAGTA 57304694 TCTAATCTCACCGCTACAGTA 1 TCTAATCTCACCGCTACAGTA * 57304715 ACTAATCTCACCGC 1 TCTAATCTCACCGC 57304729 CACCGCTATT Statistics Matches: 31, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 21 31 1.00 ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32 Consensus pattern (21 bp): TCTAATCTCACCGCTACAGTA Found at i:57305556 original size:23 final size:23 Alignment explanation

Indices: 57305499--57305543 Score: 90 Period size: 23 Copynumber: 2.0 Consensus size: 23 57305489 CATATAATCA 57305499 AATCAAACTAAAAATGATAAATG 1 AATCAAACTAAAAATGATAAATG 57305522 AATCAAACTAAAAATGATAAAT 1 AATCAAACTAAAAATGATAAAT 57305544 TATAGTAAAT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 22 1.00 ACGTcount: A:0.62, C:0.09, G:0.07, T:0.22 Consensus pattern (23 bp): AATCAAACTAAAAATGATAAATG Found at i:57306989 original size:14 final size:14 Alignment explanation

Indices: 57306965--57306998 Score: 50 Period size: 14 Copynumber: 2.4 Consensus size: 14 57306955 TTTATTTTCC * 57306965 CCCTCTTTTTCTCT 1 CCCTCTCTTTCTCT * 57306979 CTCTCTCTTTCTCT 1 CCCTCTCTTTCTCT 57306993 CCCTCT 1 CCCTCT 57306999 TCAGTTTCAC Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 14 17 1.00 ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53 Consensus pattern (14 bp): CCCTCTCTTTCTCT Found at i:57320845 original size:2 final size:2 Alignment explanation

Indices: 57320838--57320877 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 57320828 NNNNNNNNNN 57320838 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 57320878 GTGACTTAAT Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:57322923 original size:42 final size:42 Alignment explanation

Indices: 57322827--57322929 Score: 129 Period size: 42 Copynumber: 2.5 Consensus size: 42 57322817 GTTTTCGAAC * * 57322827 CTTGGTCAAAATGGCTATGGCACTAGTCAAAATAATTTTTCT 1 CTTGGTCAAAATTGCTATGGCACTAGTCAAAATAATTTTGCT * * 57322869 -TCTGGTCAAAATTGCTATGG-ATTTGGTCAAAATAATTTTGCT 1 CT-TGGTCAAAATTGCTATGGCA-CTAGTCAAAATAATTTTGCT * 57322911 CTTGGTCAAAATTGTTATG 1 CTTGGTCAAAATTGCTATG 57322930 CTGATGGATA Statistics Matches: 53, Mismatches: 5, Indels: 6 0.83 0.08 0.09 Matches are distributed among these distances: 41 2 0.04 42 50 0.94 43 1 0.02 ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39 Consensus pattern (42 bp): CTTGGTCAAAATTGCTATGGCACTAGTCAAAATAATTTTGCT Found at i:57322931 original size:21 final size:20 Alignment explanation

Indices: 57322871--57322931 Score: 59 Period size: 21 Copynumber: 3.0 Consensus size: 20 57322861 ATTTTTCTTC * * 57322871 TGGTCAAAATTGCTATGGATT 1 TGGTCAAAATTGTTAT-GCTT ** * 57322892 TGGTCAAAATAATTTTGCTCT 1 TGGTCAAAATTGTTATGCT-T 57322913 TGGTCAAAATTGTTATGCT 1 TGGTCAAAATTGTTATGCT 57322932 GATGGATATA Statistics Matches: 31, Mismatches: 8, Indels: 2 0.76 0.20 0.05 Matches are distributed among these distances: 20 2 0.06 21 29 0.94 ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41 Consensus pattern (20 bp): TGGTCAAAATTGTTATGCTT Found at i:57333796 original size:3 final size:3 Alignment explanation

Indices: 57333778--57333827 Score: 52 Period size: 3 Copynumber: 17.7 Consensus size: 3 57333768 CATTAAATTA * * 57333778 ATT ATT -TT AAT ATT ATT ATT ACT ATT A-T ATT A-T ATT ATT ATT ATT 1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT * 57333823 GTT AT 1 ATT AT 57333828 GATTTACTTA Statistics Matches: 38, Mismatches: 6, Indels: 6 0.76 0.12 0.12 Matches are distributed among these distances: 2 6 0.16 3 32 0.84 ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62 Consensus pattern (3 bp): ATT Found at i:57334916 original size:21 final size:21 Alignment explanation

Indices: 57334892--57334932 Score: 57 Period size: 21 Copynumber: 2.0 Consensus size: 21 57334882 TAATGCATTG 57334892 GATATG-GCATTTTATTTTCTC 1 GATATGAGCATTTT-TTTTCTC * 57334913 GATATGAGGATTTTTTTTCT 1 GATATGAGCATTTTTTTTCT 57334933 AAAAAATAAT Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 21 12 0.67 22 6 0.33 ACGTcount: A:0.20, C:0.10, G:0.17, T:0.54 Consensus pattern (21 bp): GATATGAGCATTTTTTTTCTC Found at i:57337257 original size:22 final size:22 Alignment explanation

Indices: 57337206--57337250 Score: 65 Period size: 22 Copynumber: 2.1 Consensus size: 22 57337196 TAGTTTAAAC ** 57337206 TTTAAATTCCTTTATCCTTTAT 1 TTTAAATTTATTTATCCTTTAT 57337228 TTTAAATTTATTTAT-CTTTAT 1 TTTAAATTTATTTATCCTTTAT 57337249 TT 1 TT 57337251 ATGAATTCTG Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 21 8 0.38 22 13 0.62 ACGTcount: A:0.24, C:0.11, G:0.00, T:0.64 Consensus pattern (22 bp): TTTAAATTTATTTATCCTTTAT Found at i:57337924 original size:40 final size:41 Alignment explanation

Indices: 57337857--57337938 Score: 114 Period size: 40 Copynumber: 2.0 Consensus size: 41 57337847 AAATGTGAAG * * * 57337857 CTGCCGACTATTTGGCGGATTGAAGACATGT-GGATTGAATT 1 CTGCCGAATATTTGACGGATTAAAGACATGTAGG-TTGAATT 57337898 CTGCCGAATATTT-ACGGATTAAAGACATGTAGGTTGAATT 1 CTGCCGAATATTTGACGGATTAAAGACATGTAGGTTGAATT 57337938 C 1 C 57337939 GACAATTGTA Statistics Matches: 37, Mismatches: 3, Indels: 3 0.86 0.07 0.07 Matches are distributed among these distances: 40 23 0.62 41 14 0.38 ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32 Consensus pattern (41 bp): CTGCCGAATATTTGACGGATTAAAGACATGTAGGTTGAATT Found at i:57340720 original size:236 final size:236 Alignment explanation

Indices: 57340156--57340862 Score: 1180 Period size: 236 Copynumber: 3.0 Consensus size: 236 57340146 AGAGTTGTGT * * * * 57340156 GCTATATATAGAGAGGTTGACATGCAGCAACCAAGGGCCACAGAGAAGTGGAATGGTCAATTGTA 1 GCTATATATAGAGAGGTTAATATGCAGTAACCAAGGGCCACAGAGAAGTGGAATGGTCAA-TG-C * * * * 57340221 TAGTAAATAAGTCTTGGTGATTTACGAGTGTGATACTTCCCAATGATCTATATATCGACCACTGG 64 TAGTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATATATCTACAACTGG * 57340286 CCTCCAACATTTGTCCAGGAACTGATAACTAATGCTAATAATTACTGTCTTGGGAATTCAATAAT 129 CCTCCAACATTTGTCCAGGAACTGATAACTAATGCTAATAATTACTGTCTTGAGAATTCAATAAT * 57340351 CGATAATTATCTCTTATTTTACTTATGAGGTTACATATATCAGT 194 CGATAATTATCTCTTA-TTTACTTATGAGGTTACATATATCAGC * * 57340395 GCTATATATAGAGAGGTTAATATGCAGTAAACAAGGGCCACAGAGAAGTGGAATGGTAAATGCTA 1 GCTATATATAGAGAGGTTAATATGCAGTAACCAAGGGCCACAGAGAAGTGGAATGGTCAATGCTA * 57340460 GTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATGTATCTACAACTGGCC 66 GTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATATATCTACAACTGGCC * * ** 57340525 TCCAACATTTGACTAGGAACTGATAACTAATGCTAATAATTTGTGTCTTGAGAATTCAATAATCG 131 TCCAACATTTGTCCAGGAACTGATAACTAATGCTAATAATTACTGTCTTGAGAATTCAATAATCG * * 57340590 ATAATTATCTCTTATTTACCTATGAGGTTAAATATATCAGC 196 ATAATTATCTCTTATTTACTTATGAGGTTACATATATCAGC * 57340631 GGTATATATAGAGAGGTTAATATGCAGTAACCAAGGGCCACAGAGAAGTGGAATGGTCAATGCTA 1 GCTATATATAGAGAGGTTAATATGCAGTAACCAAGGGCCACAGAGAAGTGGAATGGTCAATGCTA 57340696 GTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATATATCTACAACTGGCC 66 GTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATATATCTACAACTGGCC * * * 57340761 TCCAACATTTGTCCAGGAACTGATAACTAATGCTGATAATTACTATCTTGAGACTTCAATAATCG 131 TCCAACATTTGTCCAGGAACTGATAACTAATGCTAATAATTACTGTCTTGAGAATTCAATAATCG 57340826 ATAATTATCTCTTATTTACTTATGAGGTTACATATAT 196 ATAATTATCTCTTATTTACTTATGAGGTTACATATAT 57340863 ACGTGATATG Statistics Matches: 436, Mismatches: 32, Indels: 3 0.93 0.07 0.01 Matches are distributed among these distances: 236 243 0.56 237 136 0.31 238 2 0.00 239 55 0.13 ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32 Consensus pattern (236 bp): GCTATATATAGAGAGGTTAATATGCAGTAACCAAGGGCCACAGAGAAGTGGAATGGTCAATGCTA GTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATATATCTACAACTGGCC TCCAACATTTGTCCAGGAACTGATAACTAATGCTAATAATTACTGTCTTGAGAATTCAATAATCG ATAATTATCTCTTATTTACTTATGAGGTTACATATATCAGC Found at i:57344996 original size:31 final size:31 Alignment explanation

Indices: 57344954--57345030 Score: 120 Period size: 31 Copynumber: 2.5 Consensus size: 31 57344944 ACTATAAAAA 57344954 TAGTCA-TTTTGTTTGCCTCAGGTTACATTT 1 TAGTCACTTTTGTTTGCCTCAGGTTACATTT * * 57344984 TAGTCACTTTTGTTTGTCTTAGGTTACATTT 1 TAGTCACTTTTGTTTGCCTCAGGTTACATTT * 57345015 TAGTCACTTATGTTTG 1 TAGTCACTTTTGTTTG 57345031 AAATGTTACG Statistics Matches: 43, Mismatches: 3, Indels: 1 0.91 0.06 0.02 Matches are distributed among these distances: 30 6 0.14 31 37 0.86 ACGTcount: A:0.17, C:0.14, G:0.17, T:0.52 Consensus pattern (31 bp): TAGTCACTTTTGTTTGCCTCAGGTTACATTT Found at i:57347460 original size:18 final size:18 Alignment explanation

Indices: 57347437--57347475 Score: 78 Period size: 18 Copynumber: 2.2 Consensus size: 18 57347427 TTTACCAACT 57347437 CCATTCTCCAAATTACCA 1 CCATTCTCCAAATTACCA 57347455 CCATTCTCCAAATTACCA 1 CCATTCTCCAAATTACCA 57347473 CCA 1 CCA 57347476 AGTCCGATAA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 21 1.00 ACGTcount: A:0.33, C:0.41, G:0.00, T:0.26 Consensus pattern (18 bp): CCATTCTCCAAATTACCA Found at i:57359472 original size:51 final size:51 Alignment explanation

Indices: 57359396--57359496 Score: 177 Period size: 51 Copynumber: 2.0 Consensus size: 51 57359386 GGCTTCAAAA 57359396 GGGTGTCTTTGTTTACTGTTGGCTGAAT-TTAGGTATCATTCATATTCTCAT 1 GGGTGTCTTTGTTTACTGTTGGCTGAATGTT-GGTATCATTCATATTCTCAT * 57359447 GGGTGTCTTTGTTTGCTGTTGGCTGAATGTTGGTATCATTCATATTCTCA 1 GGGTGTCTTTGTTTACTGTTGGCTGAATGTTGGTATCATTCATATTCTCA 57359497 AGGCTGTCAT Statistics Matches: 48, Mismatches: 1, Indels: 2 0.94 0.02 0.04 Matches are distributed among these distances: 51 46 0.96 52 2 0.04 ACGTcount: A:0.16, C:0.14, G:0.24, T:0.47 Consensus pattern (51 bp): GGGTGTCTTTGTTTACTGTTGGCTGAATGTTGGTATCATTCATATTCTCAT Found at i:57359788 original size:1 final size:1 Alignment explanation

Indices: 57359782--57359809 Score: 56 Period size: 1 Copynumber: 28.0 Consensus size: 1 57359772 CTTTGGCAGC 57359782 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 57359810 CTGAAGAACC Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 27 1.00 ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:57370273 original size:24 final size:23 Alignment explanation

Indices: 57370236--57370281 Score: 58 Period size: 23 Copynumber: 2.0 Consensus size: 23 57370226 TGAAGTTAAA 57370236 TAAATGAATGATTAAATTAAAATT 1 TAAATGAATGATTAAA-TAAAATT * 57370260 TAAAT-AATGAATTATATAAAAT 1 TAAATGAATG-ATTAAATAAAAT 57370282 AAATAAATAA Statistics Matches: 20, Mismatches: 1, Indels: 3 0.83 0.04 0.12 Matches are distributed among these distances: 23 10 0.50 24 10 0.50 ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37 Consensus pattern (23 bp): TAAATGAATGATTAAATAAAATT Found at i:57370285 original size:27 final size:28 Alignment explanation

Indices: 57370231--57370284 Score: 74 Period size: 28 Copynumber: 1.9 Consensus size: 28 57370221 AGGTGTGAAG * 57370231 TTAAATAAATGAATGATTAAATTAAAAT 1 TTAAATAAATGAATGATTAAAATAAAAT * 57370259 TTAAAT-AATGAATTATATAAAATAAA 1 TTAAATAAATGAATGAT-TAAAATAAA 57370285 TAAATAAATA Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 27 9 0.39 28 14 0.61 ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35 Consensus pattern (28 bp): TTAAATAAATGAATGATTAAAATAAAAT Found at i:57370287 original size:4 final size:4 Alignment explanation

Indices: 57370278--57370311 Score: 50 Period size: 4 Copynumber: 8.0 Consensus size: 4 57370268 GAATTATATA 57370278 AAAT AAAT AAAT AAAT AAAT AAAT CAAAGT AAAT 1 AAAT AAAT AAAT AAAT AAAT AAAT -AAA-T AAAT 57370312 GACTAAACTA Statistics Matches: 28, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 4 21 0.75 5 6 0.21 6 1 0.04 ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24 Consensus pattern (4 bp): AAAT Found at i:57370666 original size:3 final size:3 Alignment explanation

Indices: 57370658--57370716 Score: 118 Period size: 3 Copynumber: 19.7 Consensus size: 3 57370648 GTCAAAAAAG 57370658 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT 57370706 AAT AAT AAT AA 1 AAT AAT AAT AA 57370717 AACATTTCAG Statistics Matches: 56, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 56 1.00 ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32 Consensus pattern (3 bp): AAT Found at i:57373868 original size:119 final size:119 Alignment explanation

Indices: 57373657--57373897 Score: 473 Period size: 119 Copynumber: 2.0 Consensus size: 119 57373647 ACTTTTTCTT 57373657 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA 1 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA 57373722 GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA 66 GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA 57373776 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA 1 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA * 57373841 GGAGTAATTGTTAGATGATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA 66 GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA 57373895 CCA 1 CCA 57373898 CCCTCATTTG Statistics Matches: 121, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 119 121 1.00 ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32 Consensus pattern (119 bp): CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA Found at i:57387399 original size:4 final size:4 Alignment explanation

Indices: 57387392--57387425 Score: 50 Period size: 4 Copynumber: 8.5 Consensus size: 4 57387382 AGCTGTTTTT * * 57387392 TTTA TTTA TTTA TCTA TTCA TTTA TTTA TTTA TT 1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT 57387426 ACCTTTTTTA Statistics Matches: 26, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 4 26 1.00 ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71 Consensus pattern (4 bp): TTTA Found at i:57387528 original size:17 final size:16 Alignment explanation

Indices: 57387476--57387535 Score: 50 Period size: 17 Copynumber: 3.4 Consensus size: 16 57387466 TTTATGCATT * 57387476 TTTTTATTATTGTCATTA 1 TTTTT-TTATT-TTATTA 57387494 TTATTTTTA-TTTATTTA 1 TT-TTTTTATTTTA-TTA 57387511 TTTTTGTTATTTTATTA 1 TTTTT-TTATTTTATTA 57387528 TTTCTTTT 1 TTT-TTTT 57387536 TGATATTTTC Statistics Matches: 36, Mismatches: 1, Indels: 11 0.75 0.02 0.23 Matches are distributed among these distances: 16 5 0.14 17 17 0.47 18 11 0.31 19 3 0.08 ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75 Consensus pattern (16 bp): TTTTTTTATTTTATTA Found at i:57387530 original size:21 final size:22 Alignment explanation

Indices: 57387498--57387544 Score: 69 Period size: 21 Copynumber: 2.2 Consensus size: 22 57387488 TCATTATTAT * 57387498 TTTTATTTATTTATTTTTGTTA 1 TTTTATTTATTTATTTTTGATA * 57387520 TTTTA-TTATTTCTTTTTGATA 1 TTTTATTTATTTATTTTTGATA 57387541 TTTT 1 TTTT 57387545 CATGTTACGT Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 21 18 0.78 22 5 0.22 ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77 Consensus pattern (22 bp): TTTTATTTATTTATTTTTGATA Found at i:57389576 original size:13 final size:13 Alignment explanation

Indices: 57389549--57389595 Score: 76 Period size: 13 Copynumber: 3.5 Consensus size: 13 57389539 TTTTTAAGTT 57389549 TTTATTTATTTTTC 1 TTTATTTA-TTTTC 57389563 TTTATTTATTTTC 1 TTTATTTATTTTC * 57389576 TTTATTTGTTTTC 1 TTTATTTATTTTC 57389589 TTTATTT 1 TTTATTT 57389596 GTTTATTATT Statistics Matches: 32, Mismatches: 1, Indels: 1 0.94 0.03 0.03 Matches are distributed among these distances: 13 24 0.75 14 8 0.25 ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79 Consensus pattern (13 bp): TTTATTTATTTTC Found at i:57389587 original size:37 final size:36 Alignment explanation

Indices: 57389520--57389611 Score: 91 Period size: 37 Copynumber: 2.5 Consensus size: 36 57389510 TGATTTGTCC * 57389520 TTTTTCATTTCTTT-TTTTCTTTTTAAGTTTTTATTTA 1 TTTTTC-TTTATTTATTTTCTTTTTAAG-TTTTATTTA * * 57389557 TTTTTCTTTATTTATTTTCTTTATT-TGTTTTCTTTA 1 TTTTTCTTTATTTATTTTCTTT-TTAAGTTTTATTTA 57389593 TTTGTT-TATTATTTATTTT 1 TTT-TTCT-TTATTTATTTT 57389612 ATAAAATTTT Statistics Matches: 48, Mismatches: 3, Indels: 8 0.81 0.05 0.14 Matches are distributed among these distances: 36 18 0.38 37 28 0.58 38 2 0.04 ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77 Consensus pattern (36 bp): TTTTTCTTTATTTATTTTCTTTTTAAGTTTTATTTA Done.