Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr11 124536837 

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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 312 characters in sequence are not A, C, G, or T


File 410 of 427

Found at i:119148908 original size:20 final size:20

Alignment explanation

Indices: 119148885--119148934 Score: 57 Period size: 20 Copynumber: 2.5 Consensus size: 20 119148875 AAATCCAAAT 119148885 TAAAATACTAAAATTCAGGA 1 TAAAATACTAAAATTCAGGA * * 119148905 TAAAAT-CATGAAATTTAGGA 1 TAAAATAC-TAAAATTCAGGA 119148925 TAAGAATACT 1 TAA-AATACT 119148935 GATGTGGCAT Statistics Matches: 25, Mismatches: 2, Indels: 5 0.78 0.06 0.16 Matches are distributed among these distances: 19 1 0.04 20 19 0.76 21 4 0.16 22 1 0.04 ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28 Consensus pattern (20 bp): TAAAATACTAAAATTCAGGA Found at i:119149915 original size:26 final size:25 Alignment explanation

Indices: 119149856--119149916 Score: 63 Period size: 26 Copynumber: 2.4 Consensus size: 25 119149846 TAAGAATAAG 119149856 TAATATT-AATTAATTAATATTAAA 1 TAATATTAAATTAATTAATATTAAA * * 119149880 TATTATTTAAATTAATT-ATCAGTTAAT 1 TAATA-TTAAATTAATTAAT-A-TTAAA 119149907 TAATATTAAA 1 TAATATTAAA 119149917 ATTATACATC Statistics Matches: 30, Mismatches: 3, Indels: 6 0.77 0.08 0.15 Matches are distributed among these distances: 24 4 0.13 25 4 0.13 26 14 0.47 27 8 0.27 ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48 Consensus pattern (25 bp): TAATATTAAATTAATTAATATTAAA Found at i:119157766 original size:19 final size:19 Alignment explanation

Indices: 119157744--119157784 Score: 57 Period size: 19 Copynumber: 2.2 Consensus size: 19 119157734 ATGAACTCTG 119157744 AATATAAAG-ATAAAATTAA 1 AATATAAAGTATAAAA-TAA * 119157763 AATATATAGTATAAAATAA 1 AATATAAAGTATAAAATAA 119157782 AAT 1 AAT 119157785 TTAAGAAAAC Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 19 14 0.70 20 6 0.30 ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29 Consensus pattern (19 bp): AATATAAAGTATAAAATAA Found at i:119165509 original size:3 final size:3 Alignment explanation

Indices: 119165501--119165537 Score: 74 Period size: 3 Copynumber: 12.3 Consensus size: 3 119165491 TTTATCTCTC 119165501 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T 119165538 ATCCAATGTG Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 34 1.00 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (3 bp): TTA Found at i:119168506 original size:30 final size:29 Alignment explanation

Indices: 119168470--119168528 Score: 93 Period size: 30 Copynumber: 2.0 Consensus size: 29 119168460 ACTTAACAAG 119168470 CAAATGT-TTCTAAAATAATAACAAAATTAA 1 CAAATGTCTT-TAAAATAATAA-AAAATTAA 119168500 CAAATGTCTTTAAAATAATAAAAAATTAA 1 CAAATGTCTTTAAAATAATAAAAAATTAA 119168529 TAATAAAATA Statistics Matches: 28, Mismatches: 0, Indels: 3 0.90 0.00 0.10 Matches are distributed among these distances: 29 8 0.29 30 18 0.64 31 2 0.07 ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31 Consensus pattern (29 bp): CAAATGTCTTTAAAATAATAAAAAATTAA Found at i:119168586 original size:22 final size:22 Alignment explanation

Indices: 119168561--119168603 Score: 59 Period size: 22 Copynumber: 2.0 Consensus size: 22 119168551 TATCTAAATA 119168561 ATAACAACAAAATAGTAGCAAT 1 ATAACAACAAAATAGTAGCAAT * ** 119168583 ATAATAGTAAAATAGTAGCAA 1 ATAACAACAAAATAGTAGCAA 119168604 AATAGAGAGA Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 22 18 1.00 ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21 Consensus pattern (22 bp): ATAACAACAAAATAGTAGCAAT Found at i:119168607 original size:11 final size:11 Alignment explanation

Indices: 119168568--119168608 Score: 55 Period size: 11 Copynumber: 3.7 Consensus size: 11 119168558 ATAATAACAA 119168568 CAAAATAGTAG 1 CAAAATAGTAG * * 119168579 CAATATAATAG 1 CAAAATAGTAG * 119168590 TAAAATAGTAG 1 CAAAATAGTAG 119168601 CAAAATAG 1 CAAAATAG 119168609 AGAGAAAATA Statistics Matches: 24, Mismatches: 6, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 11 24 1.00 ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22 Consensus pattern (11 bp): CAAAATAGTAG Found at i:119168616 original size:22 final size:22 Alignment explanation

Indices: 119168569--119168618 Score: 66 Period size: 22 Copynumber: 2.3 Consensus size: 22 119168559 TAATAACAAC * * 119168569 AAAATAGTAGCAATATAATAGT 1 AAAATAGTAGCAAAATAAGAGT 119168591 AAAATAGTAGCAAAATAGAGAG- 1 AAAATAGTAGCAAAATA-AGAGT 119168613 AAAATA 1 AAAATA 119168619 ATAAGAAAAT Statistics Matches: 25, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 22 22 0.88 23 3 0.12 ACGTcount: A:0.60, C:0.04, G:0.16, T:0.20 Consensus pattern (22 bp): AAAATAGTAGCAAAATAAGAGT Found at i:119169711 original size:13 final size:14 Alignment explanation

Indices: 119169686--119169717 Score: 57 Period size: 14 Copynumber: 2.4 Consensus size: 14 119169676 ATTAGAGTAC 119169686 ATTT-GATATTTTT 1 ATTTAGATATTTTT 119169699 ATTTAGATATTTTT 1 ATTTAGATATTTTT 119169713 ATTTA 1 ATTTA 119169718 ATTAATTTTT Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 13 4 0.22 14 14 0.78 ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66 Consensus pattern (14 bp): ATTTAGATATTTTT Found at i:119174070 original size:33 final size:35 Alignment explanation

Indices: 119173975--119174071 Score: 89 Period size: 33 Copynumber: 2.8 Consensus size: 35 119173965 TTAATATTTT * 119173975 AATATATGAAATATAAATTTTAAATATTT--TTAAGC 1 AATATAT-AAAT-TATATTTTAAATATTTAATTAAGC * * 119174010 AATAAATATTAATTAT-TTATAAA-ATTTAATT-AG- 1 AAT--ATATAAATTATATTTTAAATATTTAATTAAGC 119174043 AATATATAAATTATATTTTAAATATTTAA 1 AATATATAAATTATATTTTAAATATTTAA 119174072 ATATAACCAT Statistics Matches: 51, Mismatches: 5, Indels: 14 0.73 0.07 0.20 Matches are distributed among these distances: 31 10 0.20 32 6 0.12 33 13 0.25 34 8 0.16 35 7 0.14 36 3 0.06 37 4 0.08 ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45 Consensus pattern (35 bp): AATATATAAATTATATTTTAAATATTTAATTAAGC Found at i:119174695 original size:16 final size:17 Alignment explanation

Indices: 119174664--119174696 Score: 50 Period size: 17 Copynumber: 2.0 Consensus size: 17 119174654 TTTTTAAATT 119174664 GAAATAATGAAAAGAGA 1 GAAATAATGAAAAGAGA * 119174681 GAAATTATG-AAAGAGA 1 GAAATAATGAAAAGAGA 119174697 TGCATGTTAG Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 16 7 0.47 17 8 0.53 ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15 Consensus pattern (17 bp): GAAATAATGAAAAGAGA Found at i:119191768 original size:21 final size:21 Alignment explanation

Indices: 119191714--119191772 Score: 66 Period size: 25 Copynumber: 2.7 Consensus size: 21 119191704 AATTTACATG * 119191714 TTTTTTAAA-ATTTATTTTTA 1 TTTTTTAAATATTTACTTTTA 119191734 TTTTCTTGAAAAATATTTACTTTTA 1 TTTT-TT---AAATATTTACTTTTA 119191759 TTTTTTAAATATTT 1 TTTTTTAAATATTT 119191773 TTAATGTATT Statistics Matches: 33, Mismatches: 1, Indels: 9 0.77 0.02 0.21 Matches are distributed among these distances: 20 4 0.12 21 10 0.30 24 5 0.15 25 14 0.42 ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64 Consensus pattern (21 bp): TTTTTTAAATATTTACTTTTA Found at i:119194261 original size:45 final size:50 Alignment explanation

Indices: 119194119--119194304 Score: 166 Period size: 53 Copynumber: 3.7 Consensus size: 50 119194109 ACGCATCACA * ** * * * 119194119 CACCGAAGCCATAGCCTTGCCATGGTCTTACACGG-TTCACA-TATCA-T 1 CACCGATGCCATAGCCCAGCTATGGTCTTAAACGGAGTCACATTATCATT * * * * * 119194166 -ACCGAAGCCATATCCCAGAC-ATAGTCTTATACGGAATCACATTATCACATT 1 CACCGATGCCATAGCCCAG-CTATGGTCTTAAACGGAGTCACATTAT--CATT * * 119194217 ATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATT 1 -CACCGATGCCATAGCCCAGCTATGGTCTTAAACGGAGTCACATTAT--CATT 119194270 CACCGATGCCATAGCCCAGCTATGGTCTTAAACGG 1 CACCGATGCCATAGCCCAGCTATGGTCTTAAACGG 119194305 GCACACTTGT Statistics Matches: 118, Mismatches: 12, Indels: 13 0.83 0.08 0.09 Matches are distributed among these distances: 46 27 0.23 47 6 0.05 48 3 0.03 50 2 0.02 51 1 0.01 52 34 0.29 53 45 0.38 ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25 Consensus pattern (50 bp): CACCGATGCCATAGCCCAGCTATGGTCTTAAACGGAGTCACATTATCATT Found at i:119194297 original size:52 final size:53 Alignment explanation

Indices: 119194166--119194304 Score: 201 Period size: 53 Copynumber: 2.6 Consensus size: 53 119194156 CACATATCAT * * * * 119194166 ACCGAAGCCATATCCCAGAC-ATAGTCTTATACGGAATCACATTATCACATTAT 1 ACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTATCACATTAC * 119194219 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTATCACATT-C 1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTAC * 119194271 ACCGATGCCATAGCCCAGCTATGGTCTTAAACGG 1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGG 119194305 GCACACTTGT Statistics Matches: 79, Mismatches: 6, Indels: 3 0.90 0.07 0.03 Matches are distributed among these distances: 52 34 0.43 53 45 0.57 ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25 Consensus pattern (53 bp): ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTAC Found at i:119200088 original size:29 final size:29 Alignment explanation

Indices: 119200026--119200098 Score: 78 Period size: 29 Copynumber: 2.5 Consensus size: 29 119200016 ATACATTACC * 119200026 TTTTTTTTTTCTTTCTTCTTCTTATTATT 1 TTTTTTTTTTCTTTCCTCTTCTTATTATT * * 119200055 CTTTTTTTTTCTTCTCCT-TTCTCTCTT-TT 1 TTTTTTTTTTCTT-TCCTCTTCT-TATTATT * 119200084 TTTTTTCTTTCTTTC 1 TTTTTTTTTTCTTTC 119200099 GGTGTGGATG Statistics Matches: 37, Mismatches: 5, Indels: 5 0.79 0.11 0.11 Matches are distributed among these distances: 28 2 0.05 29 29 0.78 30 6 0.16 ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77 Consensus pattern (29 bp): TTTTTTTTTTCTTTCCTCTTCTTATTATT Found at i:119200420 original size:24 final size:25 Alignment explanation

Indices: 119200390--119200444 Score: 76 Period size: 24 Copynumber: 2.2 Consensus size: 25 119200380 ATATATATTT * 119200390 AAATATTTTAATAAAAATA-AAAAA 1 AAATATTTTAATAAAAAAACAAAAA * * 119200414 TAATATTTTATTAAAAAAACAAAAA 1 AAATATTTTAATAAAAAAACAAAAA 119200439 AAATAT 1 AAATAT 119200445 AAAATAATCA Statistics Matches: 26, Mismatches: 4, Indels: 1 0.84 0.13 0.03 Matches are distributed among these distances: 24 16 0.62 25 10 0.38 ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31 Consensus pattern (25 bp): AAATATTTTAATAAAAAAACAAAAA Found at i:119201634 original size:17 final size:19 Alignment explanation

Indices: 119201609--119201646 Score: 53 Period size: 18 Copynumber: 2.1 Consensus size: 19 119201599 TATTTATGTC * 119201609 TTTTAAAATT-TTAAAAAA 1 TTTTAAAATTAATAAAAAA 119201627 TTTT-AAATTAATAAAAAA 1 TTTTAAAATTAATAAAAAA 119201645 TT 1 TT 119201647 AAATTTTGAT Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 17 5 0.28 18 13 0.72 ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45 Consensus pattern (19 bp): TTTTAAAATTAATAAAAAA Found at i:119201693 original size:29 final size:30 Alignment explanation

Indices: 119201639--119201696 Score: 75 Period size: 30 Copynumber: 2.0 Consensus size: 30 119201629 TTAAATTAAT * 119201639 AAAAAATTAAATTTTGATCTTCTAAAAATA 1 AAAAAATTAAATTTTAATCTTCTAAAAATA * 119201669 AAAAAATTTAA-TTTAATTCTT-TAAAAAT 1 AAAAAATTAAATTTTAA-TCTTCTAAAAAT 119201697 TTAAAATATA Statistics Matches: 25, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 29 11 0.44 30 14 0.56 ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40 Consensus pattern (30 bp): AAAAAATTAAATTTTAATCTTCTAAAAATA Found at i:119202748 original size:2 final size:2 Alignment explanation

Indices: 119202741--119202779 Score: 78 Period size: 2 Copynumber: 19.5 Consensus size: 2 119202731 GAAAACGGTA 119202741 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 119202780 GCTTAAAATA Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 37 1.00 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:119203317 original size:17 final size:16 Alignment explanation

Indices: 119203281--119203322 Score: 61 Period size: 16 Copynumber: 2.8 Consensus size: 16 119203271 TAAAATAATA 119203281 AAAATAATAATTCTTT 1 AAAATAATAATTCTTT 119203297 AAAATAATAATT-TTT 1 AAAATAATAATTCTTT * 119203312 AGAA-AATAATT 1 AAAATAATAATT 119203323 ATGAATGAGA Statistics Matches: 25, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 14 7 0.28 15 6 0.24 16 12 0.48 ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40 Consensus pattern (16 bp): AAAATAATAATTCTTT Found at i:119205460 original size:33 final size:33 Alignment explanation

Indices: 119205423--119205521 Score: 84 Period size: 33 Copynumber: 3.2 Consensus size: 33 119205413 GCATGAAACC 119205423 ATTGTCATTTTGCAGTTCCTGCAAATTATCTTT 1 ATTGTCATTTTGCAGTTCCTGCAAATTATCTTT * * * * * ** 119205456 ATTGT-TTTTTGGAAGTT--GGC--ATGAAC-CC 1 ATTGTCATTTT-GCAGTTCCTGCAAATTATCTTT 119205484 ATTGTCATTTTGCAGTTCCTGCAAATTATCTTT 1 ATTGTCATTTTGCAGTTCCTGCAAATTATCTTT 119205517 ATTGT 1 ATTGT 119205522 TTTCCTACCA Statistics Matches: 45, Mismatches: 14, Indels: 14 0.62 0.19 0.19 Matches are distributed among these distances: 28 10 0.22 29 8 0.18 30 2 0.04 31 2 0.04 32 8 0.18 33 15 0.33 ACGTcount: A:0.21, C:0.16, G:0.16, T:0.46 Consensus pattern (33 bp): ATTGTCATTTTGCAGTTCCTGCAAATTATCTTT Found at i:119205497 original size:61 final size:61 Alignment explanation

Indices: 119205397--119205524 Score: 238 Period size: 61 Copynumber: 2.1 Consensus size: 61 119205387 TGATTCGGAA 119205397 GTTTATTTGGAAGTTGGCATGAAACCATTGTCATTTTGCAGTTCCTGCAAATTATCTTTATT 1 GTTT-TTTGGAAGTTGGCATGAAACCATTGTCATTTTGCAGTTCCTGCAAATTATCTTTATT * 119205459 GTTTTTTGGAAGTTGGCATGAACCCATTGTCATTTTGCAGTTCCTGCAAATTATCTTTATT 1 GTTTTTTGGAAGTTGGCATGAAACCATTGTCATTTTGCAGTTCCTGCAAATTATCTTTATT 119205520 GTTTT 1 GTTTT 119205525 CCTACCATGT Statistics Matches: 65, Mismatches: 1, Indels: 1 0.97 0.01 0.01 Matches are distributed among these distances: 61 61 0.94 62 4 0.06 ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45 Consensus pattern (61 bp): GTTTTTTGGAAGTTGGCATGAAACCATTGTCATTTTGCAGTTCCTGCAAATTATCTTTATT Found at i:119210730 original size:25 final size:25 Alignment explanation

Indices: 119210667--119210730 Score: 62 Period size: 25 Copynumber: 2.6 Consensus size: 25 119210657 CCAAATTTTC * 119210667 TATAATTA-GTTTAAAATTTAAAATT 1 TATAATTATGTTT-AAATTCAAAATT * 119210692 TATTATATAT-TTTAAATTC-AAATAT 1 TATAAT-TATGTTTAAATTCAAAAT-T 119210717 TATAATTATGTTTA 1 TATAATTATGTTTA 119210731 TTTTATTATT Statistics Matches: 32, Mismatches: 3, Indels: 8 0.74 0.07 0.19 Matches are distributed among these distances: 24 7 0.22 25 20 0.62 26 5 0.16 ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52 Consensus pattern (25 bp): TATAATTATGTTTAAATTCAAAATT Found at i:119220384 original size:14 final size:14 Alignment explanation

Indices: 119220365--119220393 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 119220355 TGATAATAAG 119220365 TTTATTCACTATCA 1 TTTATTCACTATCA 119220379 TTTATTCACTATCA 1 TTTATTCACTATCA 119220393 T 1 T 119220394 GTACAAAATA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.28, C:0.21, G:0.00, T:0.52 Consensus pattern (14 bp): TTTATTCACTATCA Found at i:119221400 original size:21 final size:21 Alignment explanation

Indices: 119221337--119221402 Score: 71 Period size: 21 Copynumber: 3.1 Consensus size: 21 119221327 TCTTTTATTC * * * 119221337 ATTATAACTATTATATTATATC 1 ATTATAATTATTATATTTTA-A * 119221359 ATTATTATTATTATATTTTAA 1 ATTATAATTATTATATTTTAA 119221380 ATTATAATTATTAT-TTCTTAA 1 ATTATAATTATTATATT-TTAA 119221401 AT 1 AT 119221403 ATTAAGTAAA Statistics Matches: 38, Mismatches: 5, Indels: 3 0.83 0.11 0.07 Matches are distributed among these distances: 20 2 0.05 21 19 0.50 22 17 0.45 ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56 Consensus pattern (21 bp): ATTATAATTATTATATTTTAA Found at i:119222367 original size:28 final size:27 Alignment explanation

Indices: 119222316--119222368 Score: 72 Period size: 28 Copynumber: 1.9 Consensus size: 27 119222306 GGTTTAATTT * 119222316 TTTTGGTTTCAAATTTTGGTTTTGAGG 1 TTTTGGTTTCAAATTTTCGTTTTGAGG 119222343 TTTTGGATTTCAAA-TTTCGTATTTGA 1 TTTTGG-TTTCAAATTTTCGT-TTTGA 119222369 TTTTTTTTTA Statistics Matches: 23, Mismatches: 1, Indels: 3 0.85 0.04 0.11 Matches are distributed among these distances: 27 11 0.48 28 12 0.52 ACGTcount: A:0.19, C:0.06, G:0.21, T:0.55 Consensus pattern (27 bp): TTTTGGTTTCAAATTTTCGTTTTGAGG Found at i:119222374 original size:28 final size:27 Alignment explanation

Indices: 119222314--119222374 Score: 70 Period size: 28 Copynumber: 2.2 Consensus size: 27 119222304 TAGGTTTAAT * 119222314 TTTTTTGGTTTCAAATTTTGGTTTTGA 1 TTTTTTGGTTTCAAATTTTCGTTTTGA ** 119222341 GGTTTTGGATTTCAAA-TTTCGTATTTGA 1 TTTTTTGG-TTTCAAATTTTCGT-TTTGA 119222369 TTTTTT 1 TTTTTT 119222375 TTTATGTTTA Statistics Matches: 27, Mismatches: 5, Indels: 3 0.77 0.14 0.09 Matches are distributed among these distances: 27 11 0.41 28 16 0.59 ACGTcount: A:0.16, C:0.05, G:0.18, T:0.61 Consensus pattern (27 bp): TTTTTTGGTTTCAAATTTTCGTTTTGA Found at i:119222574 original size:15 final size:17 Alignment explanation

Indices: 119222551--119222585 Score: 56 Period size: 16 Copynumber: 2.2 Consensus size: 17 119222541 ATTCTCCCTT 119222551 AAATAATTAA-ATTTTA 1 AAATAATTAAGATTTTA 119222567 AAAT-ATTAAGATTTTA 1 AAATAATTAAGATTTTA 119222583 AAA 1 AAA 119222586 AACTTTTTAA Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 15 5 0.28 16 13 0.72 ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40 Consensus pattern (17 bp): AAATAATTAAGATTTTA Found at i:119222599 original size:26 final size:24 Alignment explanation

Indices: 119222559--119222622 Score: 65 Period size: 26 Copynumber: 2.5 Consensus size: 24 119222549 TTAAATAATT * 119222559 AAATTTTAAAATATTAAGATTTTAAA 1 AAATTTT-TAATATTAAGA-TTTAAA * * 119222585 AAACTTTTTAATATTAATATTTAAT 1 AAA-TTTTTAATATTAAGATTTAAA * 119222610 ACATTTTTAATAT 1 AAATTTTTAATAT 119222623 ATTTAAATTT Statistics Matches: 33, Mismatches: 4, Indels: 4 0.80 0.10 0.10 Matches are distributed among these distances: 24 10 0.30 25 7 0.21 26 12 0.36 27 4 0.12 ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48 Consensus pattern (24 bp): AAATTTTTAATATTAAGATTTAAA Found at i:119222798 original size:13 final size:13 Alignment explanation

Indices: 119222780--119222804 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 119222770 TAAGTCATTG 119222780 CTCTTTTTTTTTC 1 CTCTTTTTTTTTC 119222793 CTCTTTTTTTTT 1 CTCTTTTTTTTT 119222805 GCGTATCTAA 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:0.00, C:0.20, G:0.00, T:0.80 Consensus pattern (13 bp): CTCTTTTTTTTTC Found at i:119229393 original size:44 final size:45 Alignment explanation

Indices: 119229301--119229434 Score: 135 Period size: 44 Copynumber: 3.0 Consensus size: 45 119229291 ACAGGACAGA * * * * 119229301 ACAGAAATGAGCCATATAAGCCCATATTAGAAATATGGCTTTGGAG 1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG * * 119229347 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG 1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG * ** * * * 119229391 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG 1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG 119229435 CAGGATATTG Statistics Matches: 72, Mismatches: 14, Indels: 4 0.80 0.16 0.04 Matches are distributed among these distances: 44 36 0.50 45 1 0.01 46 35 0.49 ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26 Consensus pattern (45 bp): ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG Found at i:119236644 original size:46 final size:44 Alignment explanation

Indices: 119236585--119236699 Score: 149 Period size: 44 Copynumber: 2.6 Consensus size: 44 119236575 ACAGGACAGA * * 119236585 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG 1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG * * 119236631 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG 1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG * ** 119236675 ACAGGAATAATTCATGTAAGTCCAT 1 ACAGGAATGAGCCATGTAAGTCCAT 119236700 GTCAAAGACA Statistics Matches: 61, Mismatches: 8, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 44 35 0.57 46 26 0.43 ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28 Consensus pattern (44 bp): ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG Found at i:119236680 original size:44 final size:45 Alignment explanation

Indices: 119236585--119236718 Score: 153 Period size: 46 Copynumber: 3.0 Consensus size: 45 119236575 ACAGGACAGA * * 119236585 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG 1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG * * 119236631 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG 1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG * ** * * * 119236675 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG 1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG 119236719 CAGGATATTG Statistics Matches: 74, Mismatches: 12, Indels: 4 0.82 0.13 0.04 Matches are distributed among these distances: 44 36 0.49 45 1 0.01 46 37 0.50 ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27 Consensus pattern (45 bp): ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG Found at i:119245788 original size:15 final size:17 Alignment explanation

Indices: 119245765--119245799 Score: 56 Period size: 16 Copynumber: 2.2 Consensus size: 17 119245755 ATTCTGCCTT 119245765 AAATAATTAA-ATTTTA 1 AAATAATTAAGATTTTA 119245781 AAAT-ATTAAGATTTTA 1 AAATAATTAAGATTTTA 119245797 AAA 1 AAA 119245800 AACTTTTTAA Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 15 5 0.28 16 13 0.72 ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40 Consensus pattern (17 bp): AAATAATTAAGATTTTA Found at i:119245813 original size:26 final size:24 Alignment explanation

Indices: 119245773--119245836 Score: 65 Period size: 26 Copynumber: 2.5 Consensus size: 24 119245763 TTAAATAATT * 119245773 AAATTTTAAAATATTAAGATTTTAAA 1 AAATTTT-TAATATTAAGA-TTTAAA * * 119245799 AAACTTTTTAATATTAATATTTAAT 1 AAA-TTTTTAATATTAAGATTTAAA * 119245824 ACATTTTTAATAT 1 AAATTTTTAATAT 119245837 ATTTAAATTT Statistics Matches: 33, Mismatches: 4, Indels: 4 0.80 0.10 0.10 Matches are distributed among these distances: 24 10 0.30 25 7 0.21 26 12 0.36 27 4 0.12 ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48 Consensus pattern (24 bp): AAATTTTTAATATTAAGATTTAAA Found at i:119250413 original size:103 final size:103 Alignment explanation

Indices: 119250280--119250485 Score: 412 Period size: 103 Copynumber: 2.0 Consensus size: 103 119250270 ACCTTGTTCG 119250280 ATACTAGTTATACATTTTAAGTTCTACCACACAAAAGTCTCATTGAGAATTGCATGGTTACTTCT 1 ATACTAGTTATACATTTTAAGTTCTACCACACAAAAGTCTCATTGAGAATTGCATGGTTACTTCT 119250345 GTCTCTCGTATTTCTGCATTTAAGCTTTGACCAGTTTA 66 GTCTCTCGTATTTCTGCATTTAAGCTTTGACCAGTTTA 119250383 ATACTAGTTATACATTTTAAGTTCTACCACACAAAAGTCTCATTGAGAATTGCATGGTTACTTCT 1 ATACTAGTTATACATTTTAAGTTCTACCACACAAAAGTCTCATTGAGAATTGCATGGTTACTTCT 119250448 GTCTCTCGTATTTCTGCATTTAAGCTTTGACCAGTTTA 66 GTCTCTCGTATTTCTGCATTTAAGCTTTGACCAGTTTA 119250486 CTTAATGAGT Statistics Matches: 103, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 103 103 1.00 ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40 Consensus pattern (103 bp): ATACTAGTTATACATTTTAAGTTCTACCACACAAAAGTCTCATTGAGAATTGCATGGTTACTTCT GTCTCTCGTATTTCTGCATTTAAGCTTTGACCAGTTTA Found at i:119251055 original size:19 final size:20 Alignment explanation

Indices: 119251031--119251075 Score: 74 Period size: 19 Copynumber: 2.3 Consensus size: 20 119251021 ATCCAAACAC 119251031 CAGAAAAGTAAATCA-TTTT 1 CAGAAAAGTAAATCATTTTT * 119251050 CAGAAAAGTAAATTATTTTT 1 CAGAAAAGTAAATCATTTTT 119251070 CAGAAA 1 CAGAAA 119251076 TTATTTTTCG Statistics Matches: 24, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 19 14 0.58 20 10 0.42 ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31 Consensus pattern (20 bp): CAGAAAAGTAAATCATTTTT Found at i:119251078 original size:14 final size:14 Alignment explanation

Indices: 119251059--119251096 Score: 67 Period size: 14 Copynumber: 2.7 Consensus size: 14 119251049 TCAGAAAAGT 119251059 AAATTATTTTTCAG 1 AAATTATTTTTCAG * 119251073 AAATTATTTTTCGG 1 AAATTATTTTTCAG 119251087 AAATTATTTT 1 AAATTATTTT 119251097 ACTGGCAAAC Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 14 23 1.00 ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53 Consensus pattern (14 bp): AAATTATTTTTCAG Found at i:119256699 original size:19 final size:19 Alignment explanation

Indices: 119256675--119256714 Score: 80 Period size: 19 Copynumber: 2.1 Consensus size: 19 119256665 ATTTAGTTAA 119256675 AAGGTATGAAGAGAAATTG 1 AAGGTATGAAGAGAAATTG 119256694 AAGGTATGAAGAGAAATTG 1 AAGGTATGAAGAGAAATTG 119256713 AA 1 AA 119256715 ATTCAAAATA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 21 1.00 ACGTcount: A:0.50, C:0.00, G:0.30, T:0.20 Consensus pattern (19 bp): AAGGTATGAAGAGAAATTG Found at i:119256960 original size:2 final size:2 Alignment explanation

Indices: 119256955--119256997 Score: 86 Period size: 2 Copynumber: 21.5 Consensus size: 2 119256945 AGACTCACAC 119256955 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 119256997 A 1 A 119256998 AATTTTAGAA Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 41 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:119258699 original size:21 final size:20 Alignment explanation

Indices: 119258671--119258713 Score: 68 Period size: 21 Copynumber: 2.1 Consensus size: 20 119258661 AAGTGTAACC 119258671 TTTTTTATATTTTTATATAT 1 TTTTTTATATTTTTATATAT * 119258691 TTTTATTATATTTTTTTATAT 1 TTTT-TTATATTTTTATATAT 119258712 TT 1 TT 119258714 GTTAATATGA Statistics Matches: 21, Mismatches: 1, Indels: 1 0.91 0.04 0.04 Matches are distributed among these distances: 20 4 0.19 21 17 0.81 ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77 Consensus pattern (20 bp): TTTTTTATATTTTTATATAT Found at i:119258721 original size:10 final size:10 Alignment explanation

Indices: 119258671--119258713 Score: 61 Period size: 10 Copynumber: 4.3 Consensus size: 10 119258661 AAGTGTAACC 119258671 TTTTT-TATA 1 TTTTTATATA 119258680 TTTTTATATA 1 TTTTTATATA 119258690 TTTTTATTATA 1 TTTTTA-TATA * 119258701 TTTTTTTATA 1 TTTTTATATA 119258711 TTT 1 TTT 119258714 GTTAATATGA Statistics Matches: 31, Mismatches: 1, Indels: 3 0.89 0.03 0.09 Matches are distributed among these distances: 9 5 0.16 10 17 0.55 11 9 0.29 ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77 Consensus pattern (10 bp): TTTTTATATA Found at i:119259602 original size:18 final size:17 Alignment explanation

Indices: 119259581--119259634 Score: 54 Period size: 18 Copynumber: 2.9 Consensus size: 17 119259571 TTATAACTAA 119259581 TTTTATATTTTATATAAT 1 TTTTATATTTTATAT-AT * 119259599 TTTTATACTTTTTTATAT 1 TTTTATA-TTTTATATAT 119259617 TTTATAATAATTTTATAT 1 TTT-T-AT-ATTTTATAT 119259635 TATATATTTG Statistics Matches: 30, Mismatches: 2, Indels: 6 0.79 0.05 0.16 Matches are distributed among these distances: 18 12 0.40 19 8 0.27 20 9 0.30 21 1 0.03 ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67 Consensus pattern (17 bp): TTTTATATTTTATATAT Found at i:119259629 original size:11 final size:10 Alignment explanation

Indices: 119259587--119259634 Score: 55 Period size: 9 Copynumber: 4.9 Consensus size: 10 119259577 CTAATTTTAT 119259587 ATTTTATATA 1 ATTTTATATA 119259597 ATTTT-TATA 1 ATTTTATATA * * 119259606 CTTTTTTAT- 1 ATTTTATATA 119259615 ATTTTATAATA 1 ATTTTAT-ATA 119259626 ATTTTATAT 1 ATTTTATAT 119259635 TATATATTTG Statistics Matches: 32, Mismatches: 3, Indels: 6 0.78 0.07 0.15 Matches are distributed among these distances: 9 13 0.41 10 12 0.38 11 7 0.22 ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65 Consensus pattern (10 bp): ATTTTATATA Found at i:119261132 original size:12 final size:12 Alignment explanation

Indices: 119261115--119261139 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 119261105 TAAAAAAGAC 119261115 AAAAAATAAAAT 1 AAAAAATAAAAT 119261127 AAAAAATAAAAT 1 AAAAAATAAAAT 119261139 A 1 A 119261140 TTTTAAAAAA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16 Consensus pattern (12 bp): AAAAAATAAAAT Found at i:119266041 original size:20 final size:20 Alignment explanation

Indices: 119266016--119266053 Score: 58 Period size: 20 Copynumber: 1.9 Consensus size: 20 119266006 ATGTAATATT * * 119266016 TTAATTTTTATATTTTATAA 1 TTAATTTTCATATATTATAA 119266036 TTAATTTTCATATATTAT 1 TTAATTTTCATATATTAT 119266054 TTTTTGTTTT Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 16 1.00 ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63 Consensus pattern (20 bp): TTAATTTTCATATATTATAA Found at i:119270668 original size:21 final size:21 Alignment explanation

Indices: 119270625--119270668 Score: 54 Period size: 21 Copynumber: 2.1 Consensus size: 21 119270615 ATCCTCTAAA * * 119270625 AATTTTCTATTTAAAAAATTT 1 AATTTTCTACTTAAAAAAATT 119270646 AATTTT-TACTTAAAATAAATT 1 AATTTTCTACTTAAAA-AAATT 119270667 AA 1 AA 119270669 AATATTTAAA Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 20 8 0.40 21 12 0.60 ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48 Consensus pattern (21 bp): AATTTTCTACTTAAAAAAATT Found at i:119270762 original size:13 final size:13 Alignment explanation

Indices: 119270744--119270782 Score: 53 Period size: 14 Copynumber: 3.0 Consensus size: 13 119270734 TCAAATAATT 119270744 TAATTATATTAAA 1 TAATTATATTAAA * 119270757 TAATTAATTTTAAA 1 TAATT-ATATTAAA 119270771 TAA-TATATTAAA 1 TAATTATATTAAA 119270783 CAGTTTTATA Statistics Matches: 23, Mismatches: 2, Indels: 3 0.82 0.07 0.11 Matches are distributed among these distances: 12 7 0.30 13 6 0.26 14 10 0.43 ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46 Consensus pattern (13 bp): TAATTATATTAAA Found at i:119274761 original size:5 final size:5 Alignment explanation

Indices: 119274751--119274778 Score: 56 Period size: 5 Copynumber: 5.6 Consensus size: 5 119274741 CATTCTCACC 119274751 CTTTT CTTTT CTTTT CTTTT CTTTT CTT 1 CTTTT CTTTT CTTTT CTTTT CTTTT CTT 119274779 CCAATCAGAT Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 23 1.00 ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79 Consensus pattern (5 bp): CTTTT Found at i:119279572 original size:16 final size:17 Alignment explanation

Indices: 119279542--119279592 Score: 59 Period size: 16 Copynumber: 3.0 Consensus size: 17 119279532 TCACAACTTC 119279542 TTTGCCTTTTCCTTTTT 1 TTTGCCTTTTCCTTTTT * 119279559 TTTG-CTTTTTCTTTTT 1 TTTGCCTTTTCCTTTTT * * 119279575 CTTTTCCTTTACCTTTTT 1 -TTTGCCTTTTCCTTTTT 119279593 CCAATTTTCA Statistics Matches: 28, Mismatches: 4, Indels: 3 0.80 0.11 0.09 Matches are distributed among these distances: 16 11 0.39 17 7 0.25 18 10 0.36 ACGTcount: A:0.02, C:0.22, G:0.04, T:0.73 Consensus pattern (17 bp): TTTGCCTTTTCCTTTTT Found at i:119279591 original size:17 final size:17 Alignment explanation

Indices: 119279539--119279591 Score: 54 Period size: 17 Copynumber: 3.1 Consensus size: 17 119279529 CGCTCACAAC * 119279539 TTCTTTGCCTTTTCCTT 1 TTCTTTTCCTTTTCCTT * * 119279556 TT-TTTTGCTTTTTCTTT 1 TTCTTTT-CCTTTTCCTT * 119279573 TTCTTTTCCTTTACCTT 1 TTCTTTTCCTTTTCCTT 119279590 TT 1 TT 119279592 TCCAATTTTC Statistics Matches: 28, Mismatches: 6, Indels: 4 0.74 0.16 0.11 Matches are distributed among these distances: 16 3 0.11 17 21 0.75 18 4 0.14 ACGTcount: A:0.02, C:0.23, G:0.04, T:0.72 Consensus pattern (17 bp): TTCTTTTCCTTTTCCTT Found at i:119280839 original size:21 final size:21 Alignment explanation

Indices: 119280798--119280839 Score: 84 Period size: 21 Copynumber: 2.0 Consensus size: 21 119280788 AAAAAATTGC 119280798 AAATATTGCAGGCAAAAATAT 1 AAATATTGCAGGCAAAAATAT 119280819 AAATATTGCAGGCAAAAATAT 1 AAATATTGCAGGCAAAAATAT 119280840 TTATTTTACT Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 21 1.00 ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24 Consensus pattern (21 bp): AAATATTGCAGGCAAAAATAT Found at i:119284152 original size:23 final size:22 Alignment explanation

Indices: 119284122--119284229 Score: 123 Period size: 21 Copynumber: 5.0 Consensus size: 22 119284112 GCTTTACTGA * * 119284122 TCAGGCACTTTATGTGTCGTATT 1 TCAGGCACCTTGTGTGTCGTA-T * 119284145 TCAGGCACCTCGTGTGTCGTA- 1 TCAGGCACCTTGTGTGTCGTAT 119284166 TCAGGCACCTTGTGTGTCGTA- 1 TCAGGCACCTTGTGTGTCGTAT * 119284187 TCAGGCACCTCGTGTGTCGT-T 1 TCAGGCACCTTGTGTGTCGTAT * * * 119284208 TTAGGCACTTTATGTGTCGTAT 1 TCAGGCACCTTGTGTGTCGTAT 119284230 ACTGATCAGG Statistics Matches: 74, Mismatches: 9, Indels: 5 0.84 0.10 0.06 Matches are distributed among these distances: 21 55 0.74 22 1 0.01 23 18 0.24 ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37 Consensus pattern (22 bp): TCAGGCACCTTGTGTGTCGTAT Found at i:119284184 original size:44 final size:43 Alignment explanation

Indices: 119284121--119284229 Score: 166 Period size: 42 Copynumber: 2.5 Consensus size: 43 119284111 GGCTTTACTG 119284121 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGT 1 ATCAGGCACTTTATGTGTCGTA-TTCAGGCACCTCGTGTGTCGT * * 119284165 ATCAGGCACCTTGTGTGTCGTA-TCAGGCACCTCGTGTGTCGT 1 ATCAGGCACTTTATGTGTCGTATTCAGGCACCTCGTGTGTCGT * * 119284207 TTTAGGCACTTTATGTGTCGTAT 1 ATCAGGCACTTTATGTGTCGTAT 119284230 ACTGATCAGG Statistics Matches: 58, Mismatches: 6, Indels: 3 0.87 0.09 0.04 Matches are distributed among these distances: 42 38 0.66 44 20 0.34 ACGTcount: A:0.16, C:0.22, G:0.26, T:0.37 Consensus pattern (43 bp): ATCAGGCACTTTATGTGTCGTATTCAGGCACCTCGTGTGTCGT Found at i:119289339 original size:27 final size:26 Alignment explanation

Indices: 119289303--119289357 Score: 69 Period size: 27 Copynumber: 2.1 Consensus size: 26 119289293 TTCTAAAAAC 119289303 TTTTATAATTTTT-TTTACTTTTATTGAA 1 TTTTATAATTTTTATTT--TTTTA-TGAA 119289331 TTTT-TAATTTTTATTTTTTTATGAA 1 TTTTATAATTTTTATTTTTTTATGAA 119289356 TT 1 TT 119289358 ATATGTCGAT Statistics Matches: 26, Mismatches: 0, Indels: 5 0.84 0.00 0.16 Matches are distributed among these distances: 25 6 0.23 26 5 0.19 27 8 0.31 28 7 0.27 ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71 Consensus pattern (26 bp): TTTTATAATTTTTATTTTTTTATGAA Found at i:119290146 original size:21 final size:20 Alignment explanation

Indices: 119290117--119290155 Score: 51 Period size: 20 Copynumber: 1.9 Consensus size: 20 119290107 CCATTATTAA 119290117 TCCTATCATAATTTAATAACT 1 TCCTATCAT-ATTTAATAACT * * 119290138 TCCTTTCATTTTTAATAA 1 TCCTATCATATTTAATAA 119290156 TATATTAAAT Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 20 8 0.50 21 8 0.50 ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49 Consensus pattern (20 bp): TCCTATCATATTTAATAACT Found at i:119290965 original size:17 final size:18 Alignment explanation

Indices: 119290943--119290976 Score: 52 Period size: 17 Copynumber: 1.9 Consensus size: 18 119290933 ATAAACGTGG * 119290943 CTATTTTTAAA-ATTTAC 1 CTATTTATAAATATTTAC 119290960 CTATTTATAAATATTTA 1 CTATTTATAAATATTTA 119290977 ACGAAATTAA Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 17 10 0.67 18 5 0.33 ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53 Consensus pattern (18 bp): CTATTTATAAATATTTAC Found at i:119300473 original size:18 final size:18 Alignment explanation

Indices: 119300425--119300478 Score: 58 Period size: 18 Copynumber: 3.0 Consensus size: 18 119300415 TATCTATACT 119300425 AATATATTTT-TTATTTA 1 AATATATTTTATTATTTA * 119300442 AA-ATAAGTTATATTATTTA 1 AATAT-A-TTTTATTATTTA * 119300461 AATATATTTTATTTTTTA 1 AATATATTTTATTATTTA 119300479 TTAAAAATTA Statistics Matches: 30, Mismatches: 3, Indels: 7 0.75 0.08 0.17 Matches are distributed among these distances: 16 2 0.07 17 3 0.10 18 13 0.43 19 10 0.33 20 2 0.07 ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59 Consensus pattern (18 bp): AATATATTTTATTATTTA Found at i:119306584 original size:15 final size:15 Alignment explanation

Indices: 119306564--119306601 Score: 58 Period size: 15 Copynumber: 2.5 Consensus size: 15 119306554 AATTATGTAC * 119306564 TTAATTTTTTAATAT 1 TTAATTTTTTAATAG * 119306579 TTAATTTTTTAATCG 1 TTAATTTTTTAATAG 119306594 TTAATTTT 1 TTAATTTT 119306602 CCTCTCTCAA Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 15 21 1.00 ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66 Consensus pattern (15 bp): TTAATTTTTTAATAG Found at i:119325652 original size:22 final size:24 Alignment explanation

Indices: 119325622--119325673 Score: 81 Period size: 23 Copynumber: 2.2 Consensus size: 24 119325612 ACAGATACTC * 119325622 GAATTTCC-ACCCAAACACA-CCA 1 GAATATCCAACCCAAACACACCCA 119325644 GAATATCCAACCCAAACACACCCA 1 GAATATCCAACCCAAACACACCCA 119325668 GAATAT 1 GAATAT 119325674 TTTAAATCCT Statistics Matches: 27, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 22 7 0.26 23 11 0.41 24 9 0.33 ACGTcount: A:0.44, C:0.37, G:0.06, T:0.13 Consensus pattern (24 bp): GAATATCCAACCCAAACACACCCA Found at i:119326240 original size:12 final size:12 Alignment explanation

Indices: 119326225--119326255 Score: 53 Period size: 12 Copynumber: 2.6 Consensus size: 12 119326215 TTCTCTTTTA 119326225 TTTTTCTTTCCC 1 TTTTTCTTTCCC * 119326237 TTTTTCTTTCTC 1 TTTTTCTTTCCC 119326249 TTTTTCT 1 TTTTTCT 119326256 CCCGTGCTTC Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 12 18 1.00 ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74 Consensus pattern (12 bp): TTTTTCTTTCCC Found at i:119326653 original size:15 final size:14 Alignment explanation

Indices: 119326635--119326665 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 14 119326625 TTAATTTATT 119326635 TAATAATAATGCTAA 1 TAATAATAAT-CTAA 119326650 TAATAATAATCTAA 1 TAATAATAATCTAA 119326664 TA 1 TA 119326666 TAAAACCATA Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 6 0.38 15 10 0.62 ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35 Consensus pattern (14 bp): TAATAATAATCTAA Found at i:119326676 original size:21 final size:20 Alignment explanation

Indices: 119326652--119326720 Score: 70 Period size: 21 Copynumber: 3.4 Consensus size: 20 119326642 AATGCTAATA 119326652 ATAATAATCTAATATAAAACC 1 ATAATAAT-TAATATAAAACC * ** 119326673 ATAAT-GTTAAT-TAATAATT 1 ATAATAATTAATATAA-AACC 119326692 ATAATAATTTAATATAAAACC 1 ATAATAA-TTAATATAAAACC 119326713 ATAATAAT 1 ATAATAAT 119326721 AATCATTATA Statistics Matches: 38, Mismatches: 6, Indels: 9 0.72 0.11 0.17 Matches are distributed among these distances: 18 3 0.08 19 11 0.29 20 2 0.05 21 19 0.50 22 3 0.08 ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36 Consensus pattern (20 bp): ATAATAATTAATATAAAACC Found at i:119329793 original size:26 final size:27 Alignment explanation

Indices: 119329764--119329831 Score: 75 Period size: 31 Copynumber: 2.4 Consensus size: 27 119329754 ATTTTATTAT * 119329764 TTATAATAAAAATAT-TAATTTAATCA 1 TTATAATAAAAAAATATAATTTAATCA 119329790 TTATATGATAAGAAAAAATATAATTTAATCA 1 TTATA--AT-A-AAAAAATATAATTTAATCA * 119329821 TTATATTAAAA 1 TTATAATAAAA 119329832 TTTTCATCTA Statistics Matches: 35, Mismatches: 2, Indels: 9 0.76 0.04 0.20 Matches are distributed among these distances: 26 5 0.14 27 3 0.09 28 3 0.09 29 2 0.06 30 6 0.17 31 16 0.46 ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40 Consensus pattern (27 bp): TTATAATAAAAAAATATAATTTAATCA Found at i:119330567 original size:5 final size:6 Alignment explanation

Indices: 119330552--119330576 Score: 50 Period size: 6 Copynumber: 4.2 Consensus size: 6 119330542 AATACGAGAA 119330552 AAAAAG AAAAAG AAAAAG AAAAAG A 1 AAAAAG AAAAAG AAAAAG AAAAAG A 119330577 GAAATCGACA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 19 1.00 ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00 Consensus pattern (6 bp): AAAAAG Found at i:119336727 original size:35 final size:35 Alignment explanation

Indices: 119336687--119336759 Score: 146 Period size: 35 Copynumber: 2.1 Consensus size: 35 119336677 CACGAATCTT 119336687 GATCTTGAATTCGATATTTTATAAGATGACAAAAG 1 GATCTTGAATTCGATATTTTATAAGATGACAAAAG 119336722 GATCTTGAATTCGATATTTTATAAGATGACAAAAG 1 GATCTTGAATTCGATATTTTATAAGATGACAAAAG 119336757 GAT 1 GAT 119336760 TGACAAGGGA Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 35 38 1.00 ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34 Consensus pattern (35 bp): GATCTTGAATTCGATATTTTATAAGATGACAAAAG Found at i:119358960 original size:15 final size:16 Alignment explanation

Indices: 119358936--119358965 Score: 53 Period size: 15 Copynumber: 1.9 Consensus size: 16 119358926 ATCTCGTTAT 119358936 AAAAACTTACAAAATG 1 AAAAACTTACAAAATG 119358952 AAAAA-TTACAAAAT 1 AAAAACTTACAAAAT 119358966 AATTATTTAA Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 9 0.64 16 5 0.36 ACGTcount: A:0.67, C:0.10, G:0.03, T:0.20 Consensus pattern (16 bp): AAAAACTTACAAAATG Found at i:119368678 original size:27 final size:27 Alignment explanation

Indices: 119368648--119368702 Score: 110 Period size: 27 Copynumber: 2.0 Consensus size: 27 119368638 AAATAGGAGG 119368648 ATAATGCGCTTCAAAACACTTAAATTT 1 ATAATGCGCTTCAAAACACTTAAATTT 119368675 ATAATGCGCTTCAAAACACTTAAATTT 1 ATAATGCGCTTCAAAACACTTAAATTT 119368702 A 1 A 119368703 CGTCCTTCTG Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 27 28 1.00 ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33 Consensus pattern (27 bp): ATAATGCGCTTCAAAACACTTAAATTT Found at i:119369188 original size:21 final size:21 Alignment explanation

Indices: 119369134--119369189 Score: 60 Period size: 21 Copynumber: 2.6 Consensus size: 21 119369124 AAAATTTATT 119369134 TTAAATAAAAAATTATATCAA 1 TTAAATAAAAAATTATATCAA * ** 119369155 TAAAATTTTAAAATTA-ATCATA 1 TTAAA-TAAAAAATTATATCA-A 119369177 TTAAATAAAAAAT 1 TTAAATAAAAAAT 119369190 CAATTTTATT Statistics Matches: 27, Mismatches: 6, Indels: 4 0.73 0.16 0.11 Matches are distributed among these distances: 21 14 0.52 22 13 0.48 ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36 Consensus pattern (21 bp): TTAAATAAAAAATTATATCAA Found at i:119371144 original size:29 final size:29 Alignment explanation

Indices: 119371102--119371162 Score: 104 Period size: 29 Copynumber: 2.1 Consensus size: 29 119371092 GTACTACTAG ** 119371102 ATTAAATAATAGGTTAACATTGCTTGTCT 1 ATTAAATAATAGGTTAACATTGCCCGTCT 119371131 ATTAAATAATAGGTTAACATTGCCCGTCT 1 ATTAAATAATAGGTTAACATTGCCCGTCT 119371160 ATT 1 ATT 119371163 TTTCTTCAAA Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 29 30 1.00 ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39 Consensus pattern (29 bp): ATTAAATAATAGGTTAACATTGCCCGTCT Found at i:119373342 original size:51 final size:51 Alignment explanation

Indices: 119373282--119373384 Score: 154 Period size: 51 Copynumber: 2.0 Consensus size: 51 119373272 AAACCCCATT * * * 119373282 GGATTAACCAA-CTCCATTTCATAATCAAACTTTTGATGAGAAATCGGATCC 1 GGATTAACCAAGC-CCAATTCATAATCAAACGTTTGACGAGAAATCGGATCC * 119373333 GGATTAACCAAGCCCAATTCATAATCATACGTTTGACGAGAAATCGGATCC 1 GGATTAACCAAGCCCAATTCATAATCAAACGTTTGACGAGAAATCGGATCC 119373384 G 1 G 119373385 ACAGAGTTTC Statistics Matches: 47, Mismatches: 4, Indels: 2 0.89 0.08 0.04 Matches are distributed among these distances: 51 46 0.98 52 1 0.02 ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26 Consensus pattern (51 bp): GGATTAACCAAGCCCAATTCATAATCAAACGTTTGACGAGAAATCGGATCC Found at i:119373671 original size:20 final size:20 Alignment explanation

Indices: 119373625--119373672 Score: 51 Period size: 20 Copynumber: 2.4 Consensus size: 20 119373615 CGTCGGAACC ** 119373625 CTAATTTTGTTGGTGTTGAAA 1 CTAA-TTTGTTGGTACTGAAA * * 119373646 CCAATTTGTTGGTACTGAGA 1 CTAATTTGTTGGTACTGAAA 119373666 CTAATTT 1 CTAATTT 119373673 CCATGGAAAA Statistics Matches: 22, Mismatches: 5, Indels: 1 0.79 0.18 0.04 Matches are distributed among these distances: 20 19 0.86 21 3 0.14 ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44 Consensus pattern (20 bp): CTAATTTGTTGGTACTGAAA Found at i:119377532 original size:7 final size:7 Alignment explanation

Indices: 119377495--119377528 Score: 59 Period size: 7 Copynumber: 4.9 Consensus size: 7 119377485 TTTCGGTGCT 119377495 TTTAATA 1 TTTAATA 119377502 TTTAATA 1 TTTAATA 119377509 TTTAATA 1 TTTAATA * 119377516 TTTAATG 1 TTTAATA 119377523 TTTAAT 1 TTTAAT 119377529 GTTTTTCTCT Statistics Matches: 26, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 7 26 1.00 ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59 Consensus pattern (7 bp): TTTAATA Found at i:119378049 original size:13 final size:14 Alignment explanation

Indices: 119378028--119378056 Score: 51 Period size: 13 Copynumber: 2.1 Consensus size: 14 119378018 TGAAAAATAG 119378028 ATTAGAAAATATTT 1 ATTAGAAAATATTT 119378042 ATTA-AAAATATTT 1 ATTAGAAAATATTT 119378055 AT 1 AT 119378057 GAAGTTAATC Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 13 11 0.73 14 4 0.27 ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45 Consensus pattern (14 bp): ATTAGAAAATATTT Found at i:119378455 original size:25 final size:26 Alignment explanation

Indices: 119378404--119378456 Score: 63 Period size: 25 Copynumber: 2.1 Consensus size: 26 119378394 AATATAATTG ** 119378404 TATATTTACTTAATTTTAGAATAAAA 1 TATATTTACTTAATTAAAGAATAAAA * * 119378430 TATATTTA-TTAATTAAATAATTAAA 1 TATATTTACTTAATTAAAGAATAAAA 119378455 TA 1 TA 119378457 ATAAGATTTT Statistics Matches: 23, Mismatches: 4, Indels: 1 0.82 0.14 0.04 Matches are distributed among these distances: 25 15 0.65 26 8 0.35 ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47 Consensus pattern (26 bp): TATATTTACTTAATTAAAGAATAAAA Found at i:119378619 original size:31 final size:32 Alignment explanation

Indices: 119378570--119378633 Score: 87 Period size: 31 Copynumber: 2.0 Consensus size: 32 119378560 ATATTAAATA * 119378570 AGATATTTATTAATTAAATA-ATTATATTATG 1 AGATATTTATTAATTAAATATATTAAATTATG * 119378601 AGATTTTTATGTAA-TAAATATATTAAATTATG 1 AGATATTTAT-TAATTAAATATATTAAATTATG 119378633 A 1 A 119378634 CAAATGTATG Statistics Matches: 29, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 31 15 0.52 32 14 0.48 ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47 Consensus pattern (32 bp): AGATATTTATTAATTAAATATATTAAATTATG Found at i:119379584 original size:15 final size:15 Alignment explanation

Indices: 119379561--119379604 Score: 61 Period size: 15 Copynumber: 2.9 Consensus size: 15 119379551 TATCAAATTT 119379561 ATATTGATTGAAATC 1 ATATTGATTGAAATC * * * 119379576 ATTTTGATTGAATTT 1 ATATTGATTGAAATC 119379591 ATATTGATTGAAAT 1 ATATTGATTGAAAT 119379605 ATAATATATA Statistics Matches: 24, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 15 24 1.00 ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48 Consensus pattern (15 bp): ATATTGATTGAAATC Found at i:119393745 original size:13 final size:12 Alignment explanation

Indices: 119393727--119393771 Score: 54 Period size: 13 Copynumber: 3.4 Consensus size: 12 119393717 TCTCAAAGAT 119393727 AAATATTTTATTA 1 AAATATTTT-TTA 119393740 AAATATATTTTTA 1 AAATAT-TTTTTA 119393753 TAAATAATTTTTTA 1 -AAAT-ATTTTTTA 119393767 AAATA 1 AAATA 119393772 AATTTTTATA Statistics Matches: 29, Mismatches: 0, Indels: 7 0.81 0.00 0.19 Matches are distributed among these distances: 12 1 0.03 13 13 0.45 14 13 0.45 15 2 0.07 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (12 bp): AAATATTTTTTA Found at i:119393755 original size:27 final size:28 Alignment explanation

Indices: 119393725--119393791 Score: 102 Period size: 27 Copynumber: 2.5 Consensus size: 28 119393715 TATCTCAAAG * 119393725 ATAAAT-ATTTTATTAAAATATATTTTT 1 ATAAATAATTTTATTAAAATAAATTTTT 119393752 ATAAATAATTTT-TTAAAATAAATTTTT 1 ATAAATAATTTTATTAAAATAAATTTTT * 119393779 ATAATTAATTTTA 1 ATAAATAATTTTA 119393792 CTTTAGCATC Statistics Matches: 36, Mismatches: 2, Indels: 3 0.88 0.05 0.07 Matches are distributed among these distances: 27 31 0.86 28 5 0.14 ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54 Consensus pattern (28 bp): ATAAATAATTTTATTAAAATAAATTTTT Found at i:119393772 original size:13 final size:14 Alignment explanation

Indices: 119393725--119393790 Score: 68 Period size: 14 Copynumber: 4.9 Consensus size: 14 119393715 TATCTCAAAG 119393725 ATAAAT-ATTTTATT 1 ATAAATAATTTT-TT 119393739 A-AAAT-ATATTTTT 1 ATAAATAAT-TTTTT 119393752 ATAAATAATTTTTT 1 ATAAATAATTTTTT * 119393766 A-AAATAAATTTTT 1 ATAAATAATTTTTT * 119393779 ATAATTAATTTT 1 ATAAATAATTTT 119393791 ACTTTAGCAT Statistics Matches: 45, Mismatches: 3, Indels: 8 0.80 0.05 0.14 Matches are distributed among these distances: 13 21 0.47 14 22 0.49 15 2 0.04 ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55 Consensus pattern (14 bp): ATAAATAATTTTTT Found at i:119398980 original size:13 final size:13 Alignment explanation

Indices: 119398964--119398997 Score: 50 Period size: 14 Copynumber: 2.5 Consensus size: 13 119398954 TTATTTTGTA * 119398964 AAATTTTAAAATT 1 AAATTTAAAAATT 119398977 AAATTGTAAAAATT 1 AAATT-TAAAAATT 119398991 AAATTTA 1 AAATTTA 119398998 TTAATAGTTT Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 13 7 0.37 14 12 0.63 ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41 Consensus pattern (13 bp): AAATTTAAAAATT Found at i:119405040 original size:14 final size:14 Alignment explanation

Indices: 119404999--119405040 Score: 50 Period size: 14 Copynumber: 2.9 Consensus size: 14 119404989 TAACACCTAT 119404999 AAAAATAATATTTTA 1 AAAAATAATA-TTTA * 119405014 ATAAAATTA-ATTTA 1 A-AAAATAATATTTA 119405028 AAAAATAATATTT 1 AAAAATAATATTT 119405041 TAATTCAAAA Statistics Matches: 23, Mismatches: 2, Indels: 5 0.77 0.07 0.17 Matches are distributed among these distances: 13 6 0.26 14 9 0.39 15 2 0.09 16 6 0.26 ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40 Consensus pattern (14 bp): AAAAATAATATTTA Found at i:119405042 original size:15 final size:15 Alignment explanation

Indices: 119404999--119405043 Score: 58 Period size: 15 Copynumber: 3.1 Consensus size: 15 119404989 TAACACCTAT 119404999 AAAAATAATATTTTA 1 AAAAATAATATTTTA * 119405014 ATAAAAT--TAATTTA 1 A-AAAATAATATTTTA 119405028 AAAAATAATATTTTA 1 AAAAATAATATTTTA 119405043 A 1 A 119405044 TTCAAAAAAG Statistics Matches: 25, Mismatches: 2, Indels: 6 0.76 0.06 0.18 Matches are distributed among these distances: 13 5 0.20 14 7 0.28 15 8 0.32 16 5 0.20 ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40 Consensus pattern (15 bp): AAAAATAATATTTTA Found at i:119409496 original size:29 final size:28 Alignment explanation

Indices: 119409447--119409501 Score: 85 Period size: 29 Copynumber: 1.9 Consensus size: 28 119409437 TTTTTTATAA 119409447 TTTTAATGATTTTAAATTTTAAAATAGT 1 TTTTAATGATTTTAAATTTTAAAATAGT 119409475 TTTTATAT-ATTTCTAAATTTTAAAATA 1 TTTTA-ATGATTT-TAAATTTTAAAATA 119409502 TTAATTAAAT Statistics Matches: 25, Mismatches: 0, Indels: 3 0.89 0.00 0.11 Matches are distributed among these distances: 28 9 0.36 29 16 0.64 ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55 Consensus pattern (28 bp): TTTTAATGATTTTAAATTTTAAAATAGT Found at i:119409513 original size:29 final size:28 Alignment explanation

Indices: 119409455--119409513 Score: 75 Period size: 29 Copynumber: 2.1 Consensus size: 28 119409445 AATTTTAATG * * 119409455 ATTTTAAATTTTAAAATAGTTTTTATAT 1 ATTTTAAATTTTAAAATAGTTATTAAAT 119409483 ATTTCTAAATTTTAAAATA-TTAATTAAAT 1 ATTT-TAAATTTTAAAATAGTT-ATTAAAT 119409512 AT 1 AT 119409514 GAATGTGTTT Statistics Matches: 27, Mismatches: 2, Indels: 3 0.84 0.06 0.09 Matches are distributed among these distances: 28 6 0.22 29 21 0.78 ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53 Consensus pattern (28 bp): ATTTTAAATTTTAAAATAGTTATTAAAT Found at i:119419103 original size:22 final size:22 Alignment explanation

Indices: 119419075--119419142 Score: 75 Period size: 22 Copynumber: 3.0 Consensus size: 22 119419065 GGGAAAGTGA * 119419075 AAATTTAATTATAATTTTTTAT 1 AAATTTAATTATAATTTATTAT * 119419097 AAATTTAAATATAGATTTATTAT 1 AAATTTAATTATA-ATTTATTAT * 119419120 ATA-TTAATTTATAATTTCATTAT 1 AAATTTAA-TTATAATTT-ATTAT 119419143 TTTTAAAGGG Statistics Matches: 39, Mismatches: 4, Indels: 5 0.81 0.08 0.10 Matches are distributed among these distances: 22 20 0.51 23 19 0.49 ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54 Consensus pattern (22 bp): AAATTTAATTATAATTTATTAT Found at i:119419120 original size:11 final size:11 Alignment explanation

Indices: 119419076--119419142 Score: 50 Period size: 11 Copynumber: 6.0 Consensus size: 11 119419066 GGAAAGTGAA 119419076 AATTTAATTAT 1 AATTTAATTAT * 119419087 AATTT-TTTAT 1 AATTTAATTAT * 119419097 AAATTTAAATAT 1 -AATTTAATTAT 119419109 AGATTT-ATTAT 1 A-ATTTAATTAT 119419120 -ATATTAATTTAT 1 AAT-TTAA-TTAT * 119419132 AATTTCATTAT 1 AATTTAATTAT 119419143 TTTTAAAGGG Statistics Matches: 44, Mismatches: 5, Indels: 14 0.70 0.08 0.22 Matches are distributed among these distances: 9 2 0.05 10 6 0.14 11 20 0.45 12 14 0.32 13 2 0.05 ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55 Consensus pattern (11 bp): AATTTAATTAT Found at i:119423891 original size:17 final size:17 Alignment explanation

Indices: 119423871--119423915 Score: 63 Period size: 18 Copynumber: 2.6 Consensus size: 17 119423861 AGTATTGTTT 119423871 ATTAAAATTATTTTTGA 1 ATTAAAATTATTTTTGA * 119423888 ATTATAAAGTATTTTTGA 1 ATTA-AAATTATTTTTGA * 119423906 ATAAAAATTA 1 ATTAAAATTA 119423916 AATTTTTCTA Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 17 9 0.38 18 15 0.62 ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47 Consensus pattern (17 bp): ATTAAAATTATTTTTGA Found at i:119423902 original size:18 final size:17 Alignment explanation

Indices: 119423859--119423911 Score: 58 Period size: 18 Copynumber: 3.2 Consensus size: 17 119423849 GCGTTATTTG 119423859 AAAGTATTGTTT--ATTA 1 AAAGTATT-TTTGAATTA * 119423875 AAATTATTTTTGAATTA 1 AAAGTATTTTTGAATTA 119423892 TAAAGTATTTTTGAA-TA 1 -AAAGTATTTTTGAATTA 119423909 AAA 1 AAA 119423912 ATTAAATTTT Statistics Matches: 32, Mismatches: 2, Indels: 6 0.80 0.05 0.15 Matches are distributed among these distances: 15 3 0.09 16 10 0.31 17 6 0.19 18 13 0.41 ACGTcount: A:0.43, C:0.00, G:0.09, T:0.47 Consensus pattern (17 bp): AAAGTATTTTTGAATTA Found at i:119437608 original size:19 final size:19 Alignment explanation

Indices: 119437556--119437610 Score: 58 Period size: 19 Copynumber: 2.8 Consensus size: 19 119437546 GTATATATAT * 119437556 TAATAATCAAATAATAAAAA 1 TAATAAT-AAATAATTAAAA ** 119437576 TAATGAAT-TTTAATTAAAA 1 TAAT-AATAAATAATTAAAA 119437595 TAATAATAAATAATTA 1 TAATAATAAATAATTA 119437611 TCATAAATTT Statistics Matches: 28, Mismatches: 5, Indels: 5 0.74 0.13 0.13 Matches are distributed among these distances: 18 3 0.11 19 18 0.64 20 4 0.14 21 3 0.11 ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35 Consensus pattern (19 bp): TAATAATAAATAATTAAAA Found at i:119438220 original size:18 final size:18 Alignment explanation

Indices: 119438168--119438220 Score: 54 Period size: 18 Copynumber: 2.9 Consensus size: 18 119438158 TGTGTGAATG 119438168 TTAAAAAGTGTTTAAATA 1 TTAAAAAGTGTTTAAATA * * * * 119438186 ATAATATA-TATTAAAATA 1 TTAA-AAAGTGTTTAAATA 119438204 TTAAAAAGTGTTTAAAT 1 TTAAAAAGTGTTTAAAT 119438221 CATTTAAAAT Statistics Matches: 25, Mismatches: 8, Indels: 4 0.68 0.22 0.11 Matches are distributed among these distances: 17 2 0.08 18 21 0.84 19 2 0.08 ACGTcount: A:0.53, C:0.00, G:0.08, T:0.40 Consensus pattern (18 bp): TTAAAAAGTGTTTAAATA Found at i:119447928 original size:47 final size:47 Alignment explanation

Indices: 119447866--119447991 Score: 155 Period size: 47 Copynumber: 2.7 Consensus size: 47 119447856 CTTTACATAA * * * * 119447866 TGATGCCATAGCCCAGCTATGGTCTTACACA-TAATCACATATCTCAC 1 TGATGCCATATCCCAGATATGGTCTTACACAGT-AGCACATATCACAC * * * 119447913 TGATGTCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC 1 TGATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAC * * 119447960 CGATGCCATATCCCAGATATGGTCTTATACAG 1 TGATGCCATATCCCAGATATGGTCTTACACAG 119447992 AAATCACTTG Statistics Matches: 69, Mismatches: 9, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 47 68 0.99 48 1 0.01 ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29 Consensus pattern (47 bp): TGATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAC Found at i:119448043 original size:31 final size:31 Alignment explanation

Indices: 119448008--119448215 Score: 251 Period size: 31 Copynumber: 6.7 Consensus size: 31 119447998 CTTGTCACTT * 119448008 GTAGCCAAAGCTACCACTATTCACTGATCAG 1 GTAGCCAAAGCTACCACTTTTCACTGATCAG **** * 119448039 GTAGCTGGTGCTACCATTTTTCACTGATCAG 1 GTAGCCAAAGCTACCACTTTTCACTGATCAG ** * 119448070 GTAGCC-GGGCTACCACTTTTCACTTATCAG 1 GTAGCCAAAGCTACCACTTTTCACTGATCAG * * 119448100 GTAGCCGAAGCTACCACTTTTCACTGATTAG 1 GTAGCCAAAGCTACCACTTTTCACTGATCAG 119448131 GTAG-CAGAAGCTACCACTTTTCACTGATCAG 1 GTAGCCA-AAGCTACCACTTTTCACTGATCAG * 119448162 GTAGCTGAAA-CTACCACTTTTCACTGATCAG 1 GTAGC-CAAAGCTACCACTTTTCACTGATCAG ** 119448193 GTAGCTGAAGCTACCACTTTTCA 1 GTAGCCAAAGCTACCACTTTTCA 119448216 GTTGTCATTT Statistics Matches: 153, Mismatches: 19, Indels: 10 0.84 0.10 0.05 Matches are distributed among these distances: 30 30 0.20 31 120 0.78 32 2 0.01 33 1 0.01 ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29 Consensus pattern (31 bp): GTAGCCAAAGCTACCACTTTTCACTGATCAG Found at i:119448165 original size:62 final size:62 Alignment explanation

Indices: 119448015--119448215 Score: 296 Period size: 62 Copynumber: 3.3 Consensus size: 62 119448005 CTTGTAGCCA * ** * * 119448015 AAGCTACCACTATTCACTGATCAGGTAGCTGGTGCTACCATTTTTCACTGATCAGGTAGCCG 1 AAGCTACCACTTTTCACTGATCAGGTAGCTGAAGCTACCACTTTTCACTGATCAGGTAGCAG * * * * 119448077 -GGCTACCACTTTTCACTTATCAGGTAGCCGAAGCTACCACTTTTCACTGATTAGGTAGCAG 1 AAGCTACCACTTTTCACTGATCAGGTAGCTGAAGCTACCACTTTTCACTGATCAGGTAGCAG * * 119448138 AAGCTACCACTTTTCACTGATCAGGTAGCTGAAACTACCACTTTTCACTGATCAGGTAGCTG 1 AAGCTACCACTTTTCACTGATCAGGTAGCTGAAGCTACCACTTTTCACTGATCAGGTAGCAG 119448200 AAGCTACCACTTTTCA 1 AAGCTACCACTTTTCA 119448216 GTTGTCATTT Statistics Matches: 123, Mismatches: 15, Indels: 2 0.88 0.11 0.01 Matches are distributed among these distances: 61 52 0.42 62 71 0.58 ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29 Consensus pattern (62 bp): AAGCTACCACTTTTCACTGATCAGGTAGCTGAAGCTACCACTTTTCACTGATCAGGTAGCAG Found at i:119448289 original size:50 final size:51 Alignment explanation

Indices: 119448193--119448321 Score: 190 Period size: 50 Copynumber: 2.5 Consensus size: 51 119448183 CACTGATCAG * * * * 119448193 GTAGCTGAAGCTACCACTTTTCAGTTGTCATTTGCCATTGATCAGATAAGT 1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGCCATTGATCAGATAAGT 119448244 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCC-TTGATCAGATAAGT 1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTG-CCATTGATCAGATAAGT * 119448294 GTAGCCGAAGCTATCACTTGTCACTTGT 1 GTAGCCGAAGCTATCACTTATCACTTGT 119448322 TTTCATGGTC Statistics Matches: 71, Mismatches: 5, Indels: 4 0.89 0.06 0.05 Matches are distributed among these distances: 50 46 0.65 51 25 0.35 ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35 Consensus pattern (51 bp): GTAGCCGAAGCTATCACTTATCACTTGTCATTTGCCATTGATCAGATAAGT Found at i:119459012 original size:15 final size:16 Alignment explanation

Indices: 119458973--119459014 Score: 50 Period size: 15 Copynumber: 2.6 Consensus size: 16 119458963 AAAAAAATAA * 119458973 TAATAATTAAGCTCGAT 1 TAAT-ATTAAGCTCAAT 119458990 TGAATATTAA-CTCAAT 1 T-AATATTAAGCTCAAT 119459006 TAATATTAA 1 TAATATTAA 119459015 TATTATTATC Statistics Matches: 23, Mismatches: 1, Indels: 4 0.82 0.04 0.14 Matches are distributed among these distances: 15 8 0.35 16 6 0.26 17 6 0.26 18 3 0.13 ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38 Consensus pattern (16 bp): TAATATTAAGCTCAAT Found at i:119460763 original size:19 final size:21 Alignment explanation

Indices: 119460737--119460782 Score: 62 Period size: 19 Copynumber: 2.3 Consensus size: 21 119460727 ATTTATTTTT 119460737 ATATAAAAATAT-TTT-TAAAA 1 ATATAAAAA-ATCTTTGTAAAA 119460757 A-ATAAAAAATCTTTGTAAAA 1 ATATAAAAAATCTTTGTAAAA 119460777 ATATAA 1 ATATAA 119460783 TTTTCTATAA Statistics Matches: 23, Mismatches: 0, Indels: 5 0.82 0.00 0.18 Matches are distributed among these distances: 18 2 0.09 19 10 0.43 20 7 0.30 21 4 0.17 ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35 Consensus pattern (21 bp): ATATAAAAAATCTTTGTAAAA Found at i:119460764 original size:20 final size:21 Alignment explanation

Indices: 119460736--119460782 Score: 60 Period size: 20 Copynumber: 2.2 Consensus size: 21 119460726 TATTTATTTT * 119460736 TATATAAAAATATTTTTAAAAA 1 TATA-AAAAATATTTGTAAAAA * 119460758 -ATAAAAAATCTTTGTAAAAA 1 TATAAAAAATATTTGTAAAAA 119460778 TATAA 1 TATAA 119460783 TTTTCTATAA Statistics Matches: 22, Mismatches: 2, Indels: 3 0.81 0.07 0.11 Matches are distributed among these distances: 20 15 0.68 21 7 0.32 ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36 Consensus pattern (21 bp): TATAAAAAATATTTGTAAAAA Found at i:119461925 original size:47 final size:47 Alignment explanation

Indices: 119461863--119461988 Score: 155 Period size: 47 Copynumber: 2.7 Consensus size: 47 119461853 CTTTACATAA * * * * 119461863 TGATGCCATAGCCCAGCTATGGTCTTACACA-TAATCACATATCTCAC 1 TGATGCCATATCCCAGATATGGTCTTACACAGT-AGCACATATCACAC * * * 119461910 TGATGTCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC 1 TGATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAC * * 119461957 CGATGCCATATCCCAGATATGGTCTTATACAG 1 TGATGCCATATCCCAGATATGGTCTTACACAG 119461989 AAATCACTTG Statistics Matches: 69, Mismatches: 9, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 47 68 0.99 48 1 0.01 ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29 Consensus pattern (47 bp): TGATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAC Found at i:119462004 original size:7 final size:7 Alignment explanation

Indices: 119461992--119462020 Score: 58 Period size: 7 Copynumber: 4.1 Consensus size: 7 119461982 TATACAGAAA 119461992 TCACTTG 1 TCACTTG 119461999 TCACTTG 1 TCACTTG 119462006 TCACTTG 1 TCACTTG 119462013 TCACTTG 1 TCACTTG 119462020 T 1 T 119462021 AGCCAAAGCT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 22 1.00 ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45 Consensus pattern (7 bp): TCACTTG Found at i:119462054 original size:31 final size:31 Alignment explanation

Indices: 119462019--119462195 Score: 216 Period size: 31 Copynumber: 5.7 Consensus size: 31 119462009 CTTGTCACTT * 119462019 GTAGCCAAAGCTACCACTATTCACTGATCAG 1 GTAGCCAAAGCTACCACTTTTCACTGATCAG **** * 119462050 GTAGCTGGTGCTACCATTTTTCACTGATCAG 1 GTAGCCAAAGCTACCACTTTTCACTGATCAG ** 119462081 GTAGCC-GGGCTACCACTTTTCACTGATCAG 1 GTAGCCAAAGCTACCACTTTTCACTGATCAG * * 119462111 GTAGCCGAAGCTACCACTTTTCACTGATTAG 1 GTAGCCAAAGCTACCACTTTTCACTGATCAG 119462142 GTAG-CAGAAGCTACCACTTTTCACTGATCAG 1 GTAGCCA-AAGCTACCACTTTTCACTGATCAG * 119462173 GTAGCTGAAA-CTACCACTTTTCA 1 GTAGC-CAAAGCTACCACTTTTCA 119462196 GTTGTCATTT Statistics Matches: 127, Mismatches: 15, Indels: 8 0.85 0.10 0.05 Matches are distributed among these distances: 30 29 0.23 31 95 0.75 32 2 0.02 33 1 0.01 ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28 Consensus pattern (31 bp): GTAGCCAAAGCTACCACTTTTCACTGATCAG Found at i:119462104 original size:61 final size:62 Alignment explanation

Indices: 119462026--119462195 Score: 252 Period size: 61 Copynumber: 2.8 Consensus size: 62 119462016 CTTGTAGCCA * ** * * 119462026 AAGCTACCACTATTCACTGATCAGGTAGCTGGTGCTACCATTTTTCACTGATCAGGTAGCCG 1 AAGCTACCACTTTTCACTGATCAGGTAGCTGAAGCTACCACTTTTCACTGATCAGGTAGCAG * * * 119462088 -GGCTACCACTTTTCACTGATCAGGTAGCCGAAGCTACCACTTTTCACTGATTAGGTAGCAG 1 AAGCTACCACTTTTCACTGATCAGGTAGCTGAAGCTACCACTTTTCACTGATCAGGTAGCAG * 119462149 AAGCTACCACTTTTCACTGATCAGGTAGCTGAAACTACCACTTTTCA 1 AAGCTACCACTTTTCACTGATCAGGTAGCTGAAGCTACCACTTTTCA 119462196 GTTGTCATTT Statistics Matches: 96, Mismatches: 11, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 61 53 0.55 62 43 0.45 ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29 Consensus pattern (62 bp): AAGCTACCACTTTTCACTGATCAGGTAGCTGAAGCTACCACTTTTCACTGATCAGGTAGCAG Found at i:119462176 original size:92 final size:93 Alignment explanation

Indices: 119462019--119462195 Score: 257 Period size: 92 Copynumber: 1.9 Consensus size: 93 119462009 CTTGTCACTT * ** * 119462019 GTAGCCAAAGCTACCACTATTCACTGATCAGGTAGCTGGTGCTACCATTTTTCACTGATCAGGTA 1 GTAGCCAAAGCTACCACTATTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACTGATCAGGTA ** 119462084 GCCG-GGCTACCACTTTTCACTGATCAG 66 GCCGAAACTACCACTTTTCACTGATCAG * * * 119462111 GTAGCCGAAGCTACCACTTTTCACTGATTAGGTAGCAGAAGCTACCACTTTTCACTGATCAGGTA 1 GTAGCCAAAGCTACCACTATTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACTGATCAGGTA * 119462176 GCTGAAACTACCACTTTTCA 66 GCCGAAACTACCACTTTTCA 119462196 GTTGTCATTT Statistics Matches: 74, Mismatches: 10, Indels: 1 0.87 0.12 0.01 Matches are distributed among these distances: 92 61 0.82 93 13 0.18 ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28 Consensus pattern (93 bp): GTAGCCAAAGCTACCACTATTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACTGATCAGGTA GCCGAAACTACCACTTTTCACTGATCAG Found at i:119462264 original size:50 final size:51 Alignment explanation

Indices: 119462173--119462301 Score: 181 Period size: 50 Copynumber: 2.5 Consensus size: 51 119462163 CACTGATCAG * * * * * 119462173 GTAGCTGAAACTACCACTTTTCAGTTGTCATTTGCCATTGATCAGATAAGT 1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGCCATTGATCAGATAAGT 119462224 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCC-TTGATCAGATAAGT 1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTG-CCATTGATCAGATAAGT * 119462274 ATAGCCGAAGCTATCACTTATCACTTGT 1 GTAGCCGAAGCTATCACTTATCACTTGT 119462302 TTCCATGGTC Statistics Matches: 70, Mismatches: 6, Indels: 4 0.88 0.08 0.05 Matches are distributed among these distances: 50 46 0.66 51 24 0.34 ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35 Consensus pattern (51 bp): GTAGCCGAAGCTATCACTTATCACTTGTCATTTGCCATTGATCAGATAAGT Found at i:119464719 original size:23 final size:23 Alignment explanation

Indices: 119464679--119464724 Score: 58 Period size: 23 Copynumber: 2.0 Consensus size: 23 119464669 AAAAATGATC 119464679 AAAATAATATAATATATT-TTAT 1 AAAATAATATAATATATTATTAT * * 119464701 AAAATTAATATATTTTATTATTAT 1 AAAA-TAATATAATATATTATTAT 119464725 CGAATTGAAT Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 22 4 0.20 23 12 0.60 24 4 0.20 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (23 bp): AAAATAATATAATATATTATTAT Found at i:119478802 original size:31 final size:31 Alignment explanation

Indices: 119478773--119478832 Score: 93 Period size: 31 Copynumber: 1.9 Consensus size: 31 119478763 GGCACTTAAT * * 119478773 TTTTTTTTTCAATTTGGTATCTAAACTTAACA 1 TTTTTTCTT-AATTTGATATCTAAACTTAACA 119478805 TTTTTTCTTAATTTGATATCTAAACTTA 1 TTTTTTCTTAATTTGATATCTAAACTTA 119478833 TTTAGTCAAA Statistics Matches: 26, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 31 18 0.69 32 8 0.31 ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55 Consensus pattern (31 bp): TTTTTTCTTAATTTGATATCTAAACTTAACA Found at i:119479035 original size:20 final size:20 Alignment explanation

Indices: 119478989--119479028 Score: 80 Period size: 20 Copynumber: 2.0 Consensus size: 20 119478979 AATAAATGAC 119478989 ATGAAATTTCTTTTTTATAT 1 ATGAAATTTCTTTTTTATAT 119479009 ATGAAATTTCTTTTTTATAT 1 ATGAAATTTCTTTTTTATAT 119479029 TTTAAATGTT Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60 Consensus pattern (20 bp): ATGAAATTTCTTTTTTATAT Found at i:119480451 original size:18 final size:18 Alignment explanation

Indices: 119480428--119480466 Score: 62 Period size: 18 Copynumber: 2.2 Consensus size: 18 119480418 TAACTCAAAA 119480428 TTTATTTTATTAA-ATATT 1 TTTATTTTA-TAATATATT 119480446 TTTATTTTATAATATATT 1 TTTATTTTATAATATATT 119480464 TTT 1 TTT 119480467 TCTTAATTTT Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 17 3 0.15 18 17 0.85 ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69 Consensus pattern (18 bp): TTTATTTTATAATATATT Found at i:119481309 original size:16 final size:15 Alignment explanation

Indices: 119481279--119481312 Score: 50 Period size: 16 Copynumber: 2.2 Consensus size: 15 119481269 AATTGAATCA * 119481279 AATTTTAATATTTTT 1 AATTTTAAAATTTTT 119481294 AATTTTATAAATTTTT 1 AATTTTA-AAATTTTT 119481310 AAT 1 AAT 119481313 AATTTATTTA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 15 7 0.41 16 10 0.59 ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62 Consensus pattern (15 bp): AATTTTAAAATTTTT Found at i:119482706 original size:15 final size:15 Alignment explanation

Indices: 119482686--119482717 Score: 55 Period size: 15 Copynumber: 2.1 Consensus size: 15 119482676 GAGTTGTCGT 119482686 TGCTGGTACTGGTGA 1 TGCTGGTACTGGTGA * 119482701 TGCTGGTGCTGGTGA 1 TGCTGGTACTGGTGA 119482716 TG 1 TG 119482718 GCGACGGTGA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.09, C:0.12, G:0.44, T:0.34 Consensus pattern (15 bp): TGCTGGTACTGGTGA Found at i:119483035 original size:36 final size:36 Alignment explanation

Indices: 119482995--119483070 Score: 91 Period size: 36 Copynumber: 2.1 Consensus size: 36 119482985 TTGTAGCCGC * * * 119482995 TGATTGTGTTGGA-GCTGGTGTTGCTGTTGTAGATGA 1 TGATTGTGAT-GATGCTGATGTTGCTGTTGCAGATGA * * 119483031 TGATTGTGATGATGTTGATGTTGTTGTTGCAGATGA 1 TGATTGTGATGATGCTGATGTTGCTGTTGCAGATGA 119483067 TGAT 1 TGAT 119483071 GATGGTATGG Statistics Matches: 34, Mismatches: 5, Indels: 2 0.83 0.12 0.05 Matches are distributed among these distances: 35 2 0.06 36 32 0.94 ACGTcount: A:0.17, C:0.04, G:0.36, T:0.43 Consensus pattern (36 bp): TGATTGTGATGATGCTGATGTTGCTGTTGCAGATGA Found at i:119483053 original size:30 final size:30 Alignment explanation

Indices: 119483013--119483101 Score: 76 Period size: 30 Copynumber: 3.0 Consensus size: 30 119483003 TTGGAGCTGG * 119483013 TGTTGCTGTTGTAGATGATGATTGTGATGA 1 TGTTGATGTTGTAGATGATGATTGTGATGA * * 119483043 TGTTGATGTTGTTGTTGCA-GA-TGATGATGA 1 TGTTGATGTTGTAGATG-ATGATTG-TGATGA * * * 119483073 TGGT-ATGGTTGTAGGTGCTGATTGTGATG 1 TGTTGAT-GTTGTAGATGATGATTGTGATG 119483102 GTGATTGTGT Statistics Matches: 47, Mismatches: 7, Indels: 10 0.73 0.11 0.16 Matches are distributed among these distances: 29 4 0.09 30 40 0.85 31 3 0.06 ACGTcount: A:0.18, C:0.03, G:0.36, T:0.43 Consensus pattern (30 bp): TGTTGATGTTGTAGATGATGATTGTGATGA Found at i:119483083 original size:24 final size:24 Alignment explanation

Indices: 119483038--119483083 Score: 56 Period size: 24 Copynumber: 1.9 Consensus size: 24 119483028 TGATGATTGT * * * * 119483038 GATGATGTTGATGTTGTTGTTGCA 1 GATGATGATGATGGTATGGTTGCA 119483062 GATGATGATGATGGTATGGTTG 1 GATGATGATGATGGTATGGTTG 119483084 TAGGTGCTGA Statistics Matches: 18, Mismatches: 4, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 24 18 1.00 ACGTcount: A:0.20, C:0.02, G:0.37, T:0.41 Consensus pattern (24 bp): GATGATGATGATGGTATGGTTGCA Found at i:119483094 original size:27 final size:30 Alignment explanation

Indices: 119483064--119483142 Score: 76 Period size: 33 Copynumber: 2.6 Consensus size: 30 119483054 TTGTTGCAGA 119483064 TGATGATGATGGTA-TGGTT-GTA-GGTGC 1 TGATGATGATGGTAGTGGTTGGTACGGTGC * 119483091 TGATTG-TGATGGTGATTGTGTTGGTACTGGTGC 1 TGA-TGATGATGGT-AGTG-GTTGGTAC-GGTGC * 119483124 AGATGATGATGGTAGTGGT 1 TGATGATGATGGTAGTGGT 119483143 GTCGTTGCAG Statistics Matches: 42, Mismatches: 2, Indels: 12 0.75 0.04 0.21 Matches are distributed among these distances: 27 10 0.24 28 3 0.07 29 2 0.05 30 3 0.07 31 5 0.12 32 5 0.12 33 14 0.33 ACGTcount: A:0.18, C:0.04, G:0.41, T:0.38 Consensus pattern (30 bp): TGATGATGATGGTAGTGGTTGGTACGGTGC Found at i:119483178 original size:27 final size:27 Alignment explanation

Indices: 119483098--119483183 Score: 77 Period size: 27 Copynumber: 3.2 Consensus size: 27 119483088 TGCTGATTGT * * * 119483098 GATGGTGATTGTGTTGGTACTGGTGCA 1 GATGATGATTGTGTTGGTGCTGCTGCA * * 119483125 GATGATGATGGTAG-TGGTG-TCGTTGCA 1 GATGATGATTGT-GTTGGTGCT-GCTGCA * * 119483152 GCTGCTGATTGTGTTGGTGCTGCTGCA 1 GATGATGATTGTGTTGGTGCTGCTGCA 119483179 GATGA 1 GATGA 119483184 CGACGACGAT Statistics Matches: 45, Mismatches: 10, Indels: 8 0.71 0.16 0.13 Matches are distributed among these distances: 26 2 0.04 27 41 0.91 28 2 0.04 ACGTcount: A:0.15, C:0.10, G:0.40, T:0.35 Consensus pattern (27 bp): GATGATGATTGTGTTGGTGCTGCTGCA Found at i:119485515 original size:17 final size:19 Alignment explanation

Indices: 119485488--119485530 Score: 56 Period size: 19 Copynumber: 2.4 Consensus size: 19 119485478 GGTGCAATCG * 119485488 GTAAA-TATTTGTA-TTT- 1 GTAAATTATTTGGATTTTA 119485504 GTAAATTATTTGGATTTTA 1 GTAAATTATTTGGATTTTA 119485523 GTAAATTA 1 GTAAATTA 119485531 AATTTTAGTT Statistics Matches: 23, Mismatches: 1, Indels: 3 0.85 0.04 0.11 Matches are distributed among these distances: 16 5 0.22 17 7 0.30 18 3 0.13 19 8 0.35 ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51 Consensus pattern (19 bp): GTAAATTATTTGGATTTTA Found at i:119489245 original size:11 final size:11 Alignment explanation

Indices: 119489229--119489262 Score: 50 Period size: 11 Copynumber: 3.0 Consensus size: 11 119489219 AAATTTAATC 119489229 CATTTAATTTT 1 CATTTAATTTT * 119489240 CATTTAAATTT 1 CATTTAATTTT 119489251 CATTTAAATTTT 1 CATTT-AATTTT 119489263 AAAAATATCA Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 11 15 0.75 12 5 0.25 ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59 Consensus pattern (11 bp): CATTTAATTTT Found at i:119492182 original size:45 final size:44 Alignment explanation

Indices: 119492115--119492201 Score: 115 Period size: 45 Copynumber: 2.0 Consensus size: 44 119492105 AATAATTAAA 119492115 TGTTATGATTTCTACTATTTTGAAAAGT-AAATTTTTACTTTATT 1 TGTTATGATTTCTACTATTTTGAAAAGTAAAATTTTT-CTTTATT * * 119492159 TGTTATGCTTTGC-ACTAATTTTGAAATGTAAAATTTTTCTTTA 1 TGTTATGATTT-CTACT-ATTTTGAAAAGTAAAATTTTTCTTTA 119492202 GATCTAGCCA Statistics Matches: 38, Mismatches: 2, Indels: 5 0.84 0.04 0.11 Matches are distributed among these distances: 44 13 0.34 45 17 0.45 46 8 0.21 ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53 Consensus pattern (44 bp): TGTTATGATTTCTACTATTTTGAAAAGTAAAATTTTTCTTTATT Found at i:119495422 original size:19 final size:20 Alignment explanation

Indices: 119495388--119495429 Score: 68 Period size: 19 Copynumber: 2.1 Consensus size: 20 119495378 ATAAAGATAT 119495388 TTAATTATGTTTTATAATGA 1 TTAATTATGTTTTATAATGA * 119495408 TTAATTTTG-TTTATAATGA 1 TTAATTATGTTTTATAATGA 119495427 TTA 1 TTA 119495430 TGATATATTT Statistics Matches: 21, Mismatches: 1, Indels: 1 0.91 0.04 0.04 Matches are distributed among these distances: 19 13 0.62 20 8 0.38 ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57 Consensus pattern (20 bp): TTAATTATGTTTTATAATGA Found at i:119496750 original size:23 final size:25 Alignment explanation

Indices: 119496717--119496763 Score: 71 Period size: 24 Copynumber: 2.0 Consensus size: 25 119496707 TCATTCTTCT * 119496717 AAAATTTAAAAAAT-ATAATTATAC 1 AAAATTTAAAAAATAATAAATATAC 119496741 AAAA-TTAAAAAATAATAAATATA 1 AAAATTTAAAAAATAATAAATATA 119496764 TAGAATTTTT Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 23 9 0.43 24 12 0.57 ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30 Consensus pattern (25 bp): AAAATTTAAAAAATAATAAATATAC Done.