Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr04 98600468 

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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32

Warning! 273 characters in sequence are not A, C, G, or T


File 319 of 325

Found at i:96539196 original size:2 final size:2

Alignment explanation

Indices: 96539189--96539220 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 96539179 TCAATTAAAT 96539189 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 96539221 ATAAAGAAAA Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:96539489 original size:18 final size:17 Alignment explanation

Indices: 96539466--96539506 Score: 64 Period size: 18 Copynumber: 2.4 Consensus size: 17 96539456 GAGGTTAGGT 96539466 TTTTTTTCTTTTTCTTCA 1 TTTTTTTCTTTTT-TTCA * 96539484 TTTTTTTCTTTTTTTTA 1 TTTTTTTCTTTTTTTCA 96539501 TTTTTT 1 TTTTTT 96539507 ATTTTGGGTT Statistics Matches: 22, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 17 9 0.41 18 13 0.59 ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85 Consensus pattern (17 bp): TTTTTTTCTTTTTTTCA Found at i:96539496 original size:9 final size:9 Alignment explanation

Indices: 96539465--96539506 Score: 57 Period size: 9 Copynumber: 4.7 Consensus size: 9 96539455 AGAGGTTAGG 96539465 TTTTTTTTC 1 TTTTTTTTC * 96539474 TTTTTCTTC 1 TTTTTTTTC * 96539483 ATTTTTTTC 1 TTTTTTTTC * 96539492 TTTTTTTTA 1 TTTTTTTTC 96539501 TTTTTT 1 TTTTTT 96539507 ATTTTGGGTT Statistics Matches: 28, Mismatches: 5, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 9 28 1.00 ACGTcount: A:0.05, C:0.10, G:0.00, T:0.86 Consensus pattern (9 bp): TTTTTTTTC Found at i:96540639 original size:21 final size:21 Alignment explanation

Indices: 96540610--96540663 Score: 56 Period size: 22 Copynumber: 2.4 Consensus size: 21 96540600 CTTTTACGTA 96540610 TTATATATTTTAAACTT-CTTAT 1 TTAT-TATTTTAAA-TTACTTAT 96540632 TTATTATTTTTAAATTAACTTAT 1 TTATTA-TTTTAAATT-ACTTAT * 96540655 ATATTATTT 1 TTATTATTT 96540664 ATTTTAAAGT Statistics Matches: 28, Mismatches: 1, Indels: 6 0.80 0.03 0.17 Matches are distributed among these distances: 21 4 0.14 22 14 0.50 23 10 0.36 ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61 Consensus pattern (21 bp): TTATTATTTTAAATTACTTAT Found at i:96540721 original size:53 final size:52 Alignment explanation

Indices: 96540664--96540785 Score: 120 Period size: 52 Copynumber: 2.3 Consensus size: 52 96540654 TATATTATTT * * * * * 96540664 ATTTTAAAGTGATTCATATACGTCATTT-TTTAAATTTGCTTTGTGTATTATAG 1 ATTTTAAAATGATT--TATACATCATTTATTTAAACTTGCTTTATGTATTATAC * * * * 96540717 ATTTTAAAATGCTTTATACATTATTTATTTAAACTTGTTTTATGTATTATTC 1 ATTTTAAAATGATTTATACATCATTTATTTAAACTTGCTTTATGTATTATAC * * 96540769 ATTTTAAATTGTTTTAT 1 ATTTTAAAATGATTTAT 96540786 TATTTACTTT Statistics Matches: 57, Mismatches: 11, Indels: 3 0.80 0.15 0.04 Matches are distributed among these distances: 51 10 0.18 52 35 0.61 53 12 0.21 ACGTcount: A:0.30, C:0.07, G:0.09, T:0.55 Consensus pattern (52 bp): ATTTTAAAATGATTTATACATCATTTATTTAAACTTGCTTTATGTATTATAC Found at i:96540748 original size:52 final size:51 Alignment explanation

Indices: 96540688--96540785 Score: 124 Period size: 52 Copynumber: 1.9 Consensus size: 51 96540678 CATATACGTC * * * 96540688 ATTTTTTAAATTTGCTTTGTGTATTATAGATTTTAAAATGCTTTATACATT 1 ATTTTTTAAACTTGCTTTATGTATTATACATTTTAAAATGCTTTATACATT * * * * 96540739 ATTTATTTAAACTTGTTTTATGTATTATTCATTTTAAATTGTTTTAT 1 ATTT-TTTAAACTTGCTTTATGTATTATACATTTTAAAATGCTTTAT 96540786 TATTTACTTT Statistics Matches: 39, Mismatches: 7, Indels: 1 0.83 0.15 0.02 Matches are distributed among these distances: 51 4 0.10 52 35 0.90 ACGTcount: A:0.29, C:0.05, G:0.08, T:0.58 Consensus pattern (51 bp): ATTTTTTAAACTTGCTTTATGTATTATACATTTTAAAATGCTTTATACATT Found at i:96540758 original size:26 final size:26 Alignment explanation

Indices: 96540717--96540785 Score: 77 Period size: 26 Copynumber: 2.7 Consensus size: 26 96540707 TGTATTATAG * * * 96540717 ATTTTAAAATGCTTTATACATTATTT 1 ATTTTAAATTGTTTTATACATTATTC ** 96540743 A-TTTAAACTTGTTTTATGTATTATTC 1 ATTTTAAA-TTGTTTTATACATTATTC 96540769 ATTTTAAATTGTTTTAT 1 ATTTTAAATTGTTTTAT 96540786 TATTTACTTT Statistics Matches: 36, Mismatches: 5, Indels: 4 0.80 0.11 0.09 Matches are distributed among these distances: 25 6 0.17 26 24 0.67 27 6 0.17 ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58 Consensus pattern (26 bp): ATTTTAAATTGTTTTATACATTATTC Found at i:96540796 original size:22 final size:22 Alignment explanation

Indices: 96540736--96540797 Score: 63 Period size: 26 Copynumber: 2.6 Consensus size: 22 96540726 TGCTTTATAC 96540736 ATTATTTATTTAAACTTGTTTT 1 ATTATTTATTTAAACTTGTTTT 96540758 ATGTATTATTCATTTTAAA-TTGTTTT 1 AT-TA-T-TT-A-TTTAAACTTGTTTT 96540784 ATTATTTACTTTAA 1 ATTATTTA-TTTAA 96540798 TTTTTTTTTC Statistics Matches: 34, Mismatches: 1, Indels: 10 0.76 0.02 0.22 Matches are distributed among these distances: 22 8 0.24 23 4 0.12 24 2 0.06 25 4 0.12 26 10 0.29 27 6 0.18 ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61 Consensus pattern (22 bp): ATTATTTATTTAAACTTGTTTT Found at i:96540828 original size:50 final size:47 Alignment explanation

Indices: 96540736--96540834 Score: 110 Period size: 49 Copynumber: 2.0 Consensus size: 47 96540726 TGCTTTATAC * * 96540736 ATTATTTATTTAAACTTGTTTTATGTATTATTCATTTTAAATTGTTTT 1 ATTATTTATTTAAACTTGTTTTATATATTATTCATTTCAAATT-TTTT ** * 96540784 ATTATTTACTTTAATTTTTTTTTCATATATTA-TCAATTTCAAATTTTTT 1 ATTATTTA-TTTAAACTTGTTTT-ATATATTATTC-ATTTCAAATTTTTT 96540833 AT 1 AT 96540835 ATGTATTATC Statistics Matches: 43, Mismatches: 5, Indels: 5 0.81 0.09 0.09 Matches are distributed among these distances: 48 8 0.19 49 19 0.44 50 16 0.37 ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63 Consensus pattern (47 bp): ATTATTTATTTAAACTTGTTTTATATATTATTCATTTCAAATTTTTT Found at i:96543715 original size:23 final size:23 Alignment explanation

Indices: 96543685--96543732 Score: 87 Period size: 23 Copynumber: 2.1 Consensus size: 23 96543675 TGGCTAGTTC 96543685 CTCGTGTTACAAAACAAACCAAA 1 CTCGTGTTACAAAACAAACCAAA * 96543708 CTCGTGTTAGAAAACAAACCAAA 1 CTCGTGTTACAAAACAAACCAAA 96543731 CT 1 CT 96543733 TTTCAAAGTA Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 23 24 1.00 ACGTcount: A:0.46, C:0.25, G:0.10, T:0.19 Consensus pattern (23 bp): CTCGTGTTACAAAACAAACCAAA Found at i:96549889 original size:2 final size:2 Alignment explanation

Indices: 96549882--96549906 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 96549872 AGCCCGTATG 96549882 TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA T 96549907 GAAAGTTGAG Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:96551726 original size:2 final size:2 Alignment explanation

Indices: 96551719--96551743 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 96551709 AGCCCGTATG 96551719 TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA T 96551744 GAAAGTTGAG Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:96562410 original size:21 final size:21 Alignment explanation

Indices: 96562384--96562424 Score: 64 Period size: 21 Copynumber: 2.0 Consensus size: 21 96562374 ATCTGTTCAA * * 96562384 ACTCCACCTGTTTTGGAGTAC 1 ACTCCACCTGCTGTGGAGTAC 96562405 ACTCCACCTGCTGTGGAGTA 1 ACTCCACCTGCTGTGGAGTA 96562425 TTGTTCGTCT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 21 18 1.00 ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29 Consensus pattern (21 bp): ACTCCACCTGCTGTGGAGTAC Found at i:96567308 original size:30 final size:30 Alignment explanation

Indices: 96567274--96567332 Score: 91 Period size: 30 Copynumber: 2.0 Consensus size: 30 96567264 CTTAACAAGC * 96567274 AAATGACTCTAAAATAGTAACAAAATTAAT 1 AAATGACTCTAAAATAATAACAAAATTAAT * * 96567304 AAATGCCTTTAAAATAATAACAAAATTAA 1 AAATGACTCTAAAATAATAACAAAATTAA 96567333 CAAAAAAATA Statistics Matches: 26, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 30 26 1.00 ACGTcount: A:0.58, C:0.10, G:0.05, T:0.27 Consensus pattern (30 bp): AAATGACTCTAAAATAATAACAAAATTAAT Found at i:96568721 original size:22 final size:23 Alignment explanation

Indices: 96568695--96568737 Score: 61 Period size: 22 Copynumber: 1.9 Consensus size: 23 96568685 CAACAAGAAG * 96568695 AGGGTGACTAAA-GCAGCAGCGA 1 AGGGTGACAAAATGCAGCAGCGA * 96568717 AGGGTTACAAAATGCAGCAGC 1 AGGGTGACAAAATGCAGCAGC 96568738 AGAAAGTTAG Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 22 10 0.56 23 8 0.44 ACGTcount: A:0.37, C:0.19, G:0.33, T:0.12 Consensus pattern (23 bp): AGGGTGACAAAATGCAGCAGCGA Found at i:96571953 original size:12 final size:12 Alignment explanation

Indices: 96571936--96571965 Score: 51 Period size: 12 Copynumber: 2.5 Consensus size: 12 96571926 ATTTATCAAG 96571936 ATAAATATTAGA 1 ATAAATATTAGA 96571948 ATAAATATTAGA 1 ATAAATATTAGA * 96571960 TTAAAT 1 ATAAAT 96571966 TTAATATTAA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 12 17 1.00 ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37 Consensus pattern (12 bp): ATAAATATTAGA Found at i:96572063 original size:20 final size:19 Alignment explanation

Indices: 96572013--96572064 Score: 65 Period size: 20 Copynumber: 2.8 Consensus size: 19 96572003 CTACAAGATA 96572013 AATATTAAATT-A-ACTTT 1 AATATTAAATTAATACTTT 96572030 AATATTAAGA-TAATCACTTT 1 AATATTAA-ATTAAT-ACTTT 96572050 AATATTAAATTAATA 1 AATATTAAATTAATA 96572065 AAATACTATT Statistics Matches: 30, Mismatches: 0, Indels: 8 0.79 0.00 0.21 Matches are distributed among these distances: 17 9 0.30 18 2 0.07 19 2 0.07 20 17 0.57 ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42 Consensus pattern (19 bp): AATATTAAATTAATACTTT Found at i:96573755 original size:16 final size:16 Alignment explanation

Indices: 96573734--96573764 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 96573724 CCATGCATGC * 96573734 AAAATATAAAAGACAA 1 AAAATACAAAAGACAA 96573750 AAAATACAAAAGACA 1 AAAATACAAAAGACA 96573765 TAATAGTGAA Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10 Consensus pattern (16 bp): AAAATACAAAAGACAA Found at i:96580870 original size:16 final size:17 Alignment explanation

Indices: 96580839--96580871 Score: 50 Period size: 17 Copynumber: 2.0 Consensus size: 17 96580829 TTCTTCTTTC * 96580839 ATTATTTTTTCATTTAT 1 ATTATTTTCTCATTTAT 96580856 ATTATTTTCTC-TTTAT 1 ATTATTTTCTCATTTAT 96580872 TTTTTCTTCT Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 16 5 0.33 17 10 0.67 ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70 Consensus pattern (17 bp): ATTATTTTCTCATTTAT Found at i:96584320 original size:5 final size:5 Alignment explanation

Indices: 96584304--96584345 Score: 50 Period size: 5 Copynumber: 8.4 Consensus size: 5 96584294 AGATTATTGG * * 96584304 GTTTT GGTTTT GTTTT GTTTT GTTTT -TTTT TTTTT TTTTT GT 1 GTTTT -GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GT 96584346 GTAGGACAAC Statistics Matches: 34, Mismatches: 1, Indels: 3 0.89 0.03 0.08 Matches are distributed among these distances: 4 4 0.12 5 25 0.74 6 5 0.15 ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83 Consensus pattern (5 bp): GTTTT Found at i:96587158 original size:37 final size:37 Alignment explanation

Indices: 96587079--96587161 Score: 114 Period size: 37 Copynumber: 2.2 Consensus size: 37 96587069 AACCTTTAGT * * * 96587079 TCGGGGCTTACCCGGACAAAATCTCCACCCGTGGTCA 1 TCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCA * 96587116 TCGGGTCTTACCCGGGA-ATAATCTCCACACGTAGTCA 1 TCGGGTCTTACCC-GGACAAAATCTCCACACGTAGTCA 96587153 TCGGGTCTT 1 TCGGGTCTT 96587162 TAGAGCTCGG Statistics Matches: 41, Mismatches: 4, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 37 38 0.93 38 3 0.07 ACGTcount: A:0.20, C:0.31, G:0.24, T:0.24 Consensus pattern (37 bp): TCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCA Found at i:96587348 original size:47 final size:47 Alignment explanation

Indices: 96587279--96587669 Score: 629 Period size: 47 Copynumber: 8.3 Consensus size: 47 96587269 CTCTTCGGGA * * * * 96587279 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCACTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC * 96587326 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC * * 96587373 CTTATCACATATATGCACTTTCACATTCATCACATGGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC * * 96587420 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC * * * 96587467 CTTATCTCATATATGCACTTTCACATTCATCACATTGGCCATTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC * 96587514 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC * * 96587561 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC * * 96587608 CTTATCACATATATGCACTTTCACATTCATCACATTGGCCATTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC 96587655 CTTATCACATATATA 1 CTTATCACATATATA 96587670 TATCTCATAC Statistics Matches: 320, Mismatches: 24, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 47 320 1.00 ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33 Consensus pattern (47 bp): CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC Found at i:96587357 original size:25 final size:25 Alignment explanation

Indices: 96587329--96587407 Score: 76 Period size: 25 Copynumber: 3.3 Consensus size: 25 96587319 ACTCGGCCTT * 96587329 ATCACATATATACACTTTCACATTC 1 ATCACATATATGCACTTTCACATTC * * * * 96587354 ATCACAT-T-GGC-CATTCGGCCTT- 1 ATCACATATATGCACTTTC-ACATTC 96587376 ATCACATATATGCACTTTCACATTC 1 ATCACATATATGCACTTTCACATTC 96587401 ATCACAT 1 ATCACAT 96587408 GGGCCATTAG Statistics Matches: 40, Mismatches: 9, Indels: 10 0.68 0.15 0.17 Matches are distributed among these distances: 22 11 0.28 23 5 0.12 24 6 0.15 25 18 0.45 ACGTcount: A:0.30, C:0.29, G:0.06, T:0.34 Consensus pattern (25 bp): ATCACATATATGCACTTTCACATTC Found at i:96587537 original size:141 final size:141 Alignment explanation

Indices: 96587283--96587669 Score: 693 Period size: 141 Copynumber: 2.7 Consensus size: 141 96587273 TCGGGACTTA * * * * * * 96587283 TCACATTTATACACTTTCACATCCATCACATTGGCCACTCGGCCTTATCACATATATACACTTTC 1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATGCACTTTC * * 96587348 ACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCACTTTCACATTCATCACATGGGCC 66 ACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCC 96587413 ATTAGGCCTTG 131 ATTAGGCCTTG * 96587424 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATGCACTTTC 1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATGCACTTTC 96587489 ACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCC 66 ACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCC 96587554 ATTAGGCCTTG 131 ATTAGGCCTTG 96587565 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATGCACTTTC 1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATGCACTTTC 96587630 ACATTCATCACATTGGCCATTCGGCCTTATCACATATATA 66 ACATTCATCACATTGGCCATTCGGCCTTATCACATATATA 96587670 TATCTCATAC Statistics Matches: 236, Mismatches: 10, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 141 236 1.00 ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33 Consensus pattern (141 bp): TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATGCACTTTC ACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCC ATTAGGCCTTG Found at i:96591895 original size:27 final size:27 Alignment explanation

Indices: 96591857--96591910 Score: 99 Period size: 27 Copynumber: 2.0 Consensus size: 27 96591847 AACATAAAGC 96591857 AATACTATGATAAAAGTTCCACTATCA 1 AATACTATGATAAAAGTTCCACTATCA * 96591884 AATACTATGATAAAATTTCCACTATCA 1 AATACTATGATAAAAGTTCCACTATCA 96591911 TAACTTCTCA Statistics Matches: 26, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 27 26 1.00 ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31 Consensus pattern (27 bp): AATACTATGATAAAAGTTCCACTATCA Found at i:96595694 original size:29 final size:28 Alignment explanation

Indices: 96595606--96595696 Score: 78 Period size: 29 Copynumber: 3.2 Consensus size: 28 96595596 TGTGTCCCCT * * 96595606 ATTTTTCAAATTTTACAGTTTT-CCTCTA 1 ATTTTACAAATTTTACAGTTTTACCT-AA * * * * 96595634 CTTTTA-AGATTTTACAGTTTTATCCCAT 1 ATTTTACAAATTTTACAGTTTTA-CCTAA * 96595662 ATTTTACAAATTTTATAGTTTTACCTAGA 1 ATTTTACAAATTTTACAGTTTTACCTA-A 96595691 ATTTTA 1 ATTTTA 96595697 TGATTTGTTT Statistics Matches: 48, Mismatches: 11, Indels: 7 0.73 0.17 0.11 Matches are distributed among these distances: 27 14 0.29 28 12 0.25 29 22 0.46 ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52 Consensus pattern (28 bp): ATTTTACAAATTTTACAGTTTTACCTAA Found at i:96596093 original size:227 final size:227 Alignment explanation

Indices: 96595698--96596132 Score: 800 Period size: 227 Copynumber: 1.9 Consensus size: 227 96595688 AGAATTTTAT * 96595698 GATTTGTTTAGATTAGTCCATGATTGTTTCACGACCTGTTTTTAGTGTTAAATTTATTCAATTAA 1 GATTTGTTTAGATTAGTCCATGATTGTTTCACGACCTATTTTTAGTGTTAAATTTATTCAATTAA * 96595763 TCCATTATCTAAATGACTGAAATAATATTATACTTATATATATTTTTATGAATTGTGAATAAATA 66 TCCATTATCTAAATGACTGAAATAATATTATACTTATATATATTTGTATGAATTGTGAATAAATA * 96595828 TGTTTAATGTATCGTATTTGTGATTGTTCGTATAACATACTTTATGATA-CAGCTAAATTGGATC 131 TGTTTAATGTATCGTATTTGTGATTGTTCGTATAACATACTTTATGATATC-GCTAAATTAGATC * 96595892 CTTTGGAAAACATATGTGTTAGGCTACCGTATC 195 CTTTAGAAAACATATGTGTTAGGCTACCGTATC 96595925 GATTTGTTTAGATTAGTCCATGATTGTTTCACGACCTATTTTTAGTGTTAAATTTATTCAATTAA 1 GATTTGTTTAGATTAGTCCATGATTGTTTCACGACCTATTTTTAGTGTTAAATTTATTCAATTAA * 96595990 TCCATTATCTAAGTGACTGAAATAATATTATACTTATATATATTTGTATGAATTGTGAATAAATA 66 TCCATTATCTAAATGACTGAAATAATATTATACTTATATATATTTGTATGAATTGTGAATAAATA 96596055 TGTTTAATGTATCGTATTTGTGATTGTTCGTATAACATACTTTATGATATCGCTAAATTAGATCC 131 TGTTTAATGTATCGTATTTGTGATTGTTCGTATAACATACTTTATGATATCGCTAAATTAGATCC * 96596120 TTTAGAAAGCATA 196 TTTAGAAAACATA 96596133 ATTATTGCTG Statistics Matches: 201, Mismatches: 6, Indels: 2 0.96 0.03 0.01 Matches are distributed among these distances: 227 200 1.00 228 1 0.00 ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43 Consensus pattern (227 bp): GATTTGTTTAGATTAGTCCATGATTGTTTCACGACCTATTTTTAGTGTTAAATTTATTCAATTAA TCCATTATCTAAATGACTGAAATAATATTATACTTATATATATTTGTATGAATTGTGAATAAATA TGTTTAATGTATCGTATTTGTGATTGTTCGTATAACATACTTTATGATATCGCTAAATTAGATCC TTTAGAAAACATATGTGTTAGGCTACCGTATC Found at i:96596583 original size:91 final size:92 Alignment explanation

Indices: 96596413--96596583 Score: 211 Period size: 91 Copynumber: 1.9 Consensus size: 92 96596403 CTTGAGTAGT * * * * * 96596413 GGTTTATCCACAACGTATTCTAGTCGGTAGTCATCTACTCGACCAGTGGTTTATTCACAATGTAT 1 GGTTCATCCACAACATATTCTAGTCGGCAGCCATCTACTCGACCAGTGGTTTATTCACAACGTAT ** * 96596478 TTGCATCTTTTATCTGCAAAAATGGAC 66 TAACAGCTTTTATCTGCAAAAATGGAC * * * 96596505 GGTTCATCCACAA-ATATTCTAGTTGGCAGCCATCTGCTCGACTAGTGGTTTA-TCTACAACGTA 1 GGTTCATCCACAACATATTCTAGTCGGCAGCCATCTACTCGACCAGTGGTTTATTC-ACAACGTA * 96596568 TTAATAGCTTTTATCT 65 TTAACAGCTTTTATCT 96596584 TCATAGACGA Statistics Matches: 66, Mismatches: 12, Indels: 3 0.81 0.15 0.04 Matches are distributed among these distances: 90 2 0.03 91 52 0.79 92 12 0.18 ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36 Consensus pattern (92 bp): GGTTCATCCACAACATATTCTAGTCGGCAGCCATCTACTCGACCAGTGGTTTATTCACAACGTAT TAACAGCTTTTATCTGCAAAAATGGAC Found at i:96598361 original size:24 final size:24 Alignment explanation

Indices: 96598316--96598362 Score: 67 Period size: 24 Copynumber: 2.0 Consensus size: 24 96598306 AGTATGGTGT * 96598316 TGGAAATATATACATGGGATAATA 1 TGGAAATATATACATAGGATAATA * * 96598340 TGGAAATATGTACATAGTATAAT 1 TGGAAATATATACATAGGATAAT 96598363 GTTAAGAATA Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 24 20 1.00 ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32 Consensus pattern (24 bp): TGGAAATATATACATAGGATAATA Found at i:96599693 original size:42 final size:43 Alignment explanation

Indices: 96599613--96599697 Score: 163 Period size: 42 Copynumber: 2.0 Consensus size: 43 96599603 GCCTAAAACG 96599613 GCGCCGTTTTAATTTTAAAAGGGGGGGACCAAAACGGTGCGTT 1 GCGCCGTTTTAATTTTAAAAGGGGGGGACCAAAACGGTGCGTT 96599656 GCGCCGTTTTAATTTTAAAA-GGGGGGACCAAAACGGTGCGTT 1 GCGCCGTTTTAATTTTAAAAGGGGGGGACCAAAACGGTGCGTT 96599698 TTGGTCCCTA Statistics Matches: 42, Mismatches: 0, Indels: 1 0.98 0.00 0.02 Matches are distributed among these distances: 42 22 0.52 43 20 0.48 ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26 Consensus pattern (43 bp): GCGCCGTTTTAATTTTAAAAGGGGGGGACCAAAACGGTGCGTT Found at i:96599791 original size:16 final size:16 Alignment explanation

Indices: 96599770--96599813 Score: 63 Period size: 16 Copynumber: 2.8 Consensus size: 16 96599760 AAGAAAAAAG 96599770 AAGAGAGAAGGGAGAA 1 AAGAGAGAAGGGAGAA * 96599786 AAGAGAGAGGGGAGAA 1 AAGAGAGAAGGGAGAA * 96599802 AGGAGAG-AGGGA 1 AAGAGAGAAGGGA 96599814 TTCCGGCCAG Statistics Matches: 25, Mismatches: 3, Indels: 1 0.86 0.10 0.03 Matches are distributed among these distances: 15 4 0.16 16 21 0.84 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (16 bp): AAGAGAGAAGGGAGAA Found at i:96601356 original size:18 final size:18 Alignment explanation

Indices: 96601320--96601362 Score: 50 Period size: 18 Copynumber: 2.4 Consensus size: 18 96601310 AACAAAATAA * * * 96601320 TTTTAATATTTTTTTTAT 1 TTTTAATAATTTATATAT 96601338 TTTTAATAATTTATATAT 1 TTTTAATAATTTATATAT * 96601356 TTCTAAT 1 TTTTAAT 96601363 TTTAAAATTT Statistics Matches: 21, Mismatches: 4, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 18 21 1.00 ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67 Consensus pattern (18 bp): TTTTAATAATTTATATAT Found at i:96606046 original size:18 final size:18 Alignment explanation

Indices: 96606023--96606057 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 96606013 ACCAAATATT * 96606023 TATTTTAATTTTTTTATA 1 TATTTTAATTTTATTATA 96606041 TATTTTAATTTTATTAT 1 TATTTTAATTTTATTAT 96606058 GCGCATTTTA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71 Consensus pattern (18 bp): TATTTTAATTTTATTATA Found at i:96607794 original size:10 final size:10 Alignment explanation

Indices: 96607779--96607809 Score: 62 Period size: 10 Copynumber: 3.1 Consensus size: 10 96607769 GTTGACCATA 96607779 TTATGATGCC 1 TTATGATGCC 96607789 TTATGATGCC 1 TTATGATGCC 96607799 TTATGATGCC 1 TTATGATGCC 96607809 T 1 T 96607810 AACTTAGTGA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 21 1.00 ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42 Consensus pattern (10 bp): TTATGATGCC Found at i:96613534 original size:46 final size:46 Alignment explanation

Indices: 96613482--96613795 Score: 450 Period size: 46 Copynumber: 6.8 Consensus size: 46 96613472 AGTGTGCTCT * 96613482 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 96613528 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC * * 96613574 GTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 96613620 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC * * * 96613666 CTGACATGAAATGAGTAAGACCATGGTTGAAAAATACCATGGCAAC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC * *** ** 96613712 ATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC * * * * * 96613759 ATGACA-GAAAATGAGTAAAACCATAGTTGAAAGATAC 1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATAC 96613796 TATGACATCG Statistics Matches: 250, Mismatches: 17, Indels: 2 0.93 0.06 0.01 Matches are distributed among these distances: 46 209 0.84 47 41 0.16 ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22 Consensus pattern (46 bp): CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC Found at i:96619246 original size:2 final size:2 Alignment explanation

Indices: 96619236--96619269 Score: 50 Period size: 2 Copynumber: 16.5 Consensus size: 2 96619226 AATATAAAAA * 96619236 AT AT GAT AT AT AT AT AT AT AT AT AA AT AT AT AT A 1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 96619270 ATTGAATATA Statistics Matches: 29, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 2 27 0.93 3 2 0.07 ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44 Consensus pattern (2 bp): AT Found at i:96619270 original size:10 final size:10 Alignment explanation

Indices: 96619241--96619283 Score: 52 Period size: 10 Copynumber: 4.3 Consensus size: 10 96619231 AAAAAATATG * 96619241 ATATATATAT 1 ATATATATAA 96619251 ATATATATAA 1 ATATATATAA 96619261 ATATATATAA 1 ATATATATAA * 96619271 TTGA-ATATAA 1 AT-ATATATAA 96619281 ATA 1 ATA 96619284 CATCAATTAC Statistics Matches: 29, Mismatches: 3, Indels: 3 0.83 0.09 0.09 Matches are distributed among these distances: 9 1 0.03 10 27 0.93 11 1 0.03 ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42 Consensus pattern (10 bp): ATATATATAA Found at i:96623638 original size:19 final size:20 Alignment explanation

Indices: 96623606--96623646 Score: 57 Period size: 19 Copynumber: 2.1 Consensus size: 20 96623596 ATGTTTAGTA 96623606 ATTTTTCTATATTTTATATT 1 ATTTTTCTATATTTTATATT * * 96623626 ATTTTTGTA-ATTTTATTTT 1 ATTTTTCTATATTTTATATT 96623645 AT 1 AT 96623647 ATATATTTAA Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 19 11 0.58 20 8 0.42 ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71 Consensus pattern (20 bp): ATTTTTCTATATTTTATATT Found at i:96623644 original size:34 final size:34 Alignment explanation

Indices: 96623608--96623673 Score: 91 Period size: 34 Copynumber: 2.0 Consensus size: 34 96623598 GTTTAGTAAT * * 96623608 TTTTCTATAT-TTTATATTATT-TTTGTAATTTTA 1 TTTTATATATATTTA-ATAATTCTTTGTAATTTTA 96623641 TTTTATATATATTTAATAATTCTTTGTAATTTT 1 TTTTATATATATTTAATAATTCTTTGTAATTTT 96623674 TTATTTTTAA Statistics Matches: 29, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 33 14 0.48 34 15 0.52 ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67 Consensus pattern (34 bp): TTTTATATATATTTAATAATTCTTTGTAATTTTA Found at i:96623660 original size:24 final size:24 Alignment explanation

Indices: 96623615--96623661 Score: 60 Period size: 24 Copynumber: 2.0 Consensus size: 24 96623605 AATTTTTCTA ** 96623615 TATTTTATATTATTTTTGTAATTT 1 TATTTTATATTATTTTAATAATTT 96623639 TATTTTATA-TATATTTAATAATT 1 TATTTTATATTAT-TTTAATAATT 96623662 CTTTGTAATT Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 23 3 0.15 24 17 0.85 ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66 Consensus pattern (24 bp): TATTTTATATTATTTTAATAATTT Found at i:96627272 original size:43 final size:43 Alignment explanation

Indices: 96627217--96627438 Score: 317 Period size: 43 Copynumber: 5.2 Consensus size: 43 96627207 GGTTCCTACA * 96627217 TTATATACTTCAAATTATTATATCTTGTTTATTTTGAAATTAT 1 TTATATACTTCAAATTATTATATCTTATTTATTTTGAAATTAT * 96627260 TTATATACTTCAAATTATTATATCTTATTTATTTTGAAATTAC 1 TTATATACTTCAAATTATTATATCTTATTTATTTTGAAATTAT * * 96627303 TTATATACTTCAAACTATTATATCTTATTTCTTTTGAAATTAT 1 TTATATACTTCAAATTATTATATCTTATTTATTTTGAAATTAT * * 96627346 TTATATACTTTAAACTT-TTATATATTATTTATTTTGAAATTAT 1 TTATATACTTCAAA-TTATTATATCTTATTTATTTTGAAATTAT * * 96627389 TTATATACTTTAAACTT-TTATA-CATTATTTATTTTG-GATTAT 1 TTATATACTTCAAA-TTATTATATC-TTATTTATTTTGAAATTAT 96627431 TTATATAC 1 TTATATAC 96627439 ATATGTTTTT Statistics Matches: 166, Mismatches: 11, Indels: 5 0.91 0.06 0.03 Matches are distributed among these distances: 42 13 0.08 43 152 0.92 44 1 0.01 ACGTcount: A:0.33, C:0.08, G:0.03, T:0.55 Consensus pattern (43 bp): TTATATACTTCAAATTATTATATCTTATTTATTTTGAAATTAT Found at i:96627554 original size:26 final size:26 Alignment explanation

Indices: 96627516--96627600 Score: 88 Period size: 24 Copynumber: 3.4 Consensus size: 26 96627506 TTCTAATTAT * * 96627516 TTTTATACGTTATTTATGTTAAACCA 1 TTTTATATGTTATTTATGTTATACCA * * 96627542 TTTTATATATTATCTAT-TT-TA-CA 1 TTTTATATGTTATTTATGTTATACCA * 96627565 TTTTTATATGTTATTT-TGTTATACTA 1 -TTTTATATGTTATTTATGTTATACCA 96627591 TTTTATATGT 1 TTTTATATGT 96627601 GAATAATTTT Statistics Matches: 48, Mismatches: 7, Indels: 9 0.75 0.11 0.14 Matches are distributed among these distances: 23 3 0.06 24 16 0.33 25 14 0.29 26 15 0.31 ACGTcount: A:0.27, C:0.07, G:0.06, T:0.60 Consensus pattern (26 bp): TTTTATATGTTATTTATGTTATACCA Found at i:96627610 original size:49 final size:50 Alignment explanation

Indices: 96627514--96627611 Score: 119 Period size: 49 Copynumber: 2.0 Consensus size: 50 96627504 TATTCTAATT * * 96627514 ATTTTTATACGTTATTTATGTTAAACCATTTTATATATTATCTATTTTAC 1 ATTTTTATACGTTATTTATGTTAAACCATTTTATATATAATCAATTTTAC * * * * 96627564 ATTTTTATATGTTATTT-TGTTATACTATTTTATATGTGAAT-AATTTTA 1 ATTTTTATACGTTATTTATGTTAAACCATTTTATATAT-AATCAATTTTA 96627612 AATTCTTTTA Statistics Matches: 41, Mismatches: 6, Indels: 3 0.82 0.12 0.06 Matches are distributed among these distances: 49 23 0.56 50 18 0.44 ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58 Consensus pattern (50 bp): ATTTTTATACGTTATTTATGTTAAACCATTTTATATATAATCAATTTTAC Found at i:96627719 original size:20 final size:20 Alignment explanation

Indices: 96627691--96627728 Score: 58 Period size: 20 Copynumber: 1.9 Consensus size: 20 96627681 TATATTAAAT * 96627691 TATTTTATATACTTTTTATA 1 TATTATATATACTTTTTATA * 96627711 TATTATATATATTTTTTA 1 TATTATATATACTTTTTA 96627729 AAATTTGTTT 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:0.32, C:0.03, G:0.00, T:0.66 Consensus pattern (20 bp): TATTATATATACTTTTTATA Found at i:96629396 original size:2 final size:2 Alignment explanation

Indices: 96629389--96629449 Score: 115 Period size: 2 Copynumber: 31.0 Consensus size: 2 96629379 AATGTTCTTT 96629389 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 96629430 TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA 96629450 CTTTATAATA Statistics Matches: 58, Mismatches: 0, Indels: 2 0.97 0.00 0.03 Matches are distributed among these distances: 1 1 0.02 2 57 0.98 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (2 bp): TA Found at i:96629667 original size:2 final size:2 Alignment explanation

Indices: 96629660--96629689 Score: 51 Period size: 2 Copynumber: 15.0 Consensus size: 2 96629650 TTTCCTTTAA * 96629660 AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 96629690 TAACATTTAT Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:96629934 original size:2 final size:2 Alignment explanation

Indices: 96629927--96629967 Score: 82 Period size: 2 Copynumber: 20.5 Consensus size: 2 96629917 TCTCCTGTTT 96629927 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 96629968 GTTTTATAAA Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 39 1.00 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (2 bp): TA Found at i:96630203 original size:2 final size:2 Alignment explanation

Indices: 96630196--96630230 Score: 70 Period size: 2 Copynumber: 17.5 Consensus size: 2 96630186 AATACTCATT 96630196 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 96630231 TAATGATTGC Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 33 1.00 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (2 bp): TA Found at i:96630863 original size:131 final size:132 Alignment explanation

Indices: 96630621--96630903 Score: 361 Period size: 131 Copynumber: 2.2 Consensus size: 132 96630611 GTATTCATTC * * * *** 96630621 AAAAATTCTTCAAAACGAAGATGAGATTCAATGTTTGGTGTTTCGAGGAATCGTGCCCTAACACG 1 AAAAATTCTTCAAAACGAAGACGAGATTCAATATTTAGCAATTCGAGGAATCGTGCCCTAACACG * * * * 96630686 TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCATGTCTT 66 TTGGGTTGCAATTTCGCGTCTGCTCAAAATAATCGAATACCACTTCAAAATTCCACTCATATCTT 96630751 -T 131 CT * * * * ** 96630752 TAAAATTCTTCAAAACGAAGACGAGATTCTATATTTAGCAATTCGTGGAATTGTGCCCTAACGTG 1 AAAAATTCTTCAAAACGAAGACGAGATTCAATATTTAGCAATTCGAGGAATCGTGCCCTAACACG * * * * 96630817 TTGGTTTGCAATTTTGCGTCTGCTTAAAATAATCGAATACCCCTTCAAAATTCCACTCATATCTT 66 TTGGGTTGCAATTTCGCGTCTGCTCAAAATAATCGAATACCACTTCAAAATTCCACTCATATCTT 96630882 CT 131 CT * * 96630884 AAAAATTATTTAAAACGAAG 1 AAAAATTCTTCAAAACGAAG 96630904 GCAATATTTG Statistics Matches: 128, Mismatches: 23, Indels: 1 0.84 0.15 0.01 Matches are distributed among these distances: 131 110 0.86 132 18 0.14 ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34 Consensus pattern (132 bp): AAAAATTCTTCAAAACGAAGACGAGATTCAATATTTAGCAATTCGAGGAATCGTGCCCTAACACG TTGGGTTGCAATTTCGCGTCTGCTCAAAATAATCGAATACCACTTCAAAATTCCACTCATATCTT CT Found at i:96630940 original size:131 final size:130 Alignment explanation

Indices: 96630662--96630942 Score: 305 Period size: 131 Copynumber: 2.1 Consensus size: 130 96630652 TGTTTGGTGT * * 96630662 TTCGAGGAATCGTGCCCTAACACGTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATC 1 TTCGA-GAATCGTGCCCTAACACGTTGGGTTGCAATTTCGCGTCTGCTCAAAATAATCGAATACC * * * * * * 96630727 ACTTCAAAATTTCACTCATGTCTTTTAAAATTCTTCAAAACGAAGACGAGATTCTATATTTAGCA 65 ACTTCAAAATTCCACTCATATCTTTAAAAATTATTCAAAACGAAGACAAGATTCTACATTTAGCA 96630792 A 130 A * * ** * * * 96630793 TTCGTGGAATTGTGCCCTAACGTGTTGGTTTGCAATTTTGCGTCTGCTTAAAATAATCGAATACC 1 TTCG-AGAATCGTGCCCTAACACGTTGGGTTGCAATTTCGCGTCTGCTCAAAATAATCGAATACC * * * * * * 96630858 CCTTCAAAATTCCACTCATATCTTCTAAAAATTATTTAAAACGAAGGCAATATT-TGGCGTTT-G 65 ACTTCAAAATTCCACTCATATCTT-TAAAAATTATTCAAAACGAAGACAAGATTCT-ACATTTAG 96630921 ACAA 128 -CAA * 96630925 TTCGAGAATCATGCCCTA 1 TTCGAGAATCGTGCCCTA 96630943 TTGTGCTGGG Statistics Matches: 122, Mismatches: 24, Indels: 8 0.79 0.16 0.05 Matches are distributed among these distances: 131 89 0.73 132 33 0.27 ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33 Consensus pattern (130 bp): TTCGAGAATCGTGCCCTAACACGTTGGGTTGCAATTTCGCGTCTGCTCAAAATAATCGAATACCA CTTCAAAATTCCACTCATATCTTTAAAAATTATTCAAAACGAAGACAAGATTCTACATTTAGCAA Found at i:96633641 original size:10 final size:11 Alignment explanation

Indices: 96633624--96633649 Score: 52 Period size: 11 Copynumber: 2.4 Consensus size: 11 96633614 ATTTCTCTGC 96633624 CAAAAAAAAAA 1 CAAAAAAAAAA 96633635 CAAAAAAAAAA 1 CAAAAAAAAAA 96633646 CAAA 1 CAAA 96633650 CAAACAAGGG Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 15 1.00 ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00 Consensus pattern (11 bp): CAAAAAAAAAA Found at i:96637066 original size:18 final size:18 Alignment explanation

Indices: 96637043--96637081 Score: 69 Period size: 18 Copynumber: 2.2 Consensus size: 18 96637033 CCCCTCACTC * 96637043 TCCACCTTTTTGTTTTTT 1 TCCACCTTTTTGTTTGTT 96637061 TCCACCTTTTTGTTTGTT 1 TCCACCTTTTTGTTTGTT 96637079 TCC 1 TCC 96637082 TCTTCACTTT Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 20 1.00 ACGTcount: A:0.05, C:0.26, G:0.08, T:0.62 Consensus pattern (18 bp): TCCACCTTTTTGTTTGTT Found at i:96643025 original size:4 final size:4 Alignment explanation

Indices: 96643016--96643046 Score: 55 Period size: 4 Copynumber: 8.0 Consensus size: 4 96643006 TTCAAACTTC 96643016 AATT AATT AATT AATT AATT AATT AA-T AATT 1 AATT AATT AATT AATT AATT AATT AATT AATT 96643047 TAAAAAACCA Statistics Matches: 26, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 3 3 0.12 4 23 0.88 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (4 bp): AATT Found at i:96644036 original size:74 final size:75 Alignment explanation

Indices: 96643927--96644075 Score: 266 Period size: 74 Copynumber: 2.0 Consensus size: 75 96643917 CCTAAGATAA * 96643927 AGTATCTCCCGAATTGGATTTGATAGACAATATATTAGTCTTTCAATTGGTTTGCTCATTTCTGA 1 AGTATCTCCCGAATTGGACTTGATAGACAATATATTAGTCTTTCAATTGGTTTGCTCATTTCTGA 96643992 TTAGACTAAG 66 TTAGACTAAG 96644002 AGTATCTTCCC-AATTGGACTT-ATAGACAATATATTAGTCTTTCAATTGGTTTGCTCATTTCTG 1 AGTATC-TCCCGAATTGGACTTGATAGACAATATATTAGTCTTTCAATTGGTTTGCTCATTTCTG 96644065 ATTAGACTAAG 65 ATTAGACTAAG 96644076 GACATGTTTA Statistics Matches: 72, Mismatches: 1, Indels: 3 0.95 0.01 0.04 Matches are distributed among these distances: 74 53 0.74 75 15 0.21 76 4 0.06 ACGTcount: A:0.28, C:0.15, G:0.16, T:0.40 Consensus pattern (75 bp): AGTATCTCCCGAATTGGACTTGATAGACAATATATTAGTCTTTCAATTGGTTTGCTCATTTCTGA TTAGACTAAG Found at i:96648591 original size:20 final size:20 Alignment explanation

Indices: 96648566--96648605 Score: 80 Period size: 20 Copynumber: 2.0 Consensus size: 20 96648556 ACAGACTTAC 96648566 TTGTGTGAAACATGTAATTG 1 TTGTGTGAAACATGTAATTG 96648586 TTGTGTGAAACATGTAATTG 1 TTGTGTGAAACATGTAATTG 96648606 AGGGCATACT 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:0.25, T:0.40 Consensus pattern (20 bp): TTGTGTGAAACATGTAATTG Found at i:96654071 original size:22 final size:22 Alignment explanation

Indices: 96654046--96654097 Score: 68 Period size: 22 Copynumber: 2.4 Consensus size: 22 96654036 AATGTTTTTG * * * * 96654046 TGTCTCGAGACATTGGGGTTTA 1 TGTCTCAAAACATTGAGCTTTA 96654068 TGTCTCAAAACATTGAGCTTTA 1 TGTCTCAAAACATTGAGCTTTA 96654090 TGTCTCAA 1 TGTCTCAA 96654098 CTCGAGATAT Statistics Matches: 26, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 22 26 1.00 ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37 Consensus pattern (22 bp): TGTCTCAAAACATTGAGCTTTA Found at i:96661375 original size:27 final size:28 Alignment explanation

Indices: 96661337--96661398 Score: 67 Period size: 27 Copynumber: 2.3 Consensus size: 28 96661327 TAACTTTTTT * 96661337 TAAAAT-TAAAAA-GCTAAATAAATTATA 1 TAAAATATAAAAATACT-AATAAATTATA * * 96661364 TAAAATAT-AAAATACTCATCAATTATA 1 TAAAATATAAAAATACTAATAAATTATA 96661391 TAAAATAT 1 TAAAATAT 96661399 TCTTTAGGTT Statistics Matches: 30, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 27 27 0.90 28 3 0.10 ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32 Consensus pattern (28 bp): TAAAATATAAAAATACTAATAAATTATA Found at i:96662139 original size:28 final size:28 Alignment explanation

Indices: 96662107--96662160 Score: 74 Period size: 28 Copynumber: 1.9 Consensus size: 28 96662097 TTAATTGTCT * 96662107 ATTTAATTATAAATTA-TTATATAATAAA 1 ATTTAATT-TAAACTATTTATATAATAAA * 96662135 ATTTAATTTAAACTATTTTTATAATA 1 ATTTAATTTAAACTATTTATATAATA 96662161 GTTAAATTCT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 27 6 0.26 28 17 0.74 ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50 Consensus pattern (28 bp): ATTTAATTTAAACTATTTATATAATAAA Found at i:96665511 original size:19 final size:19 Alignment explanation

Indices: 96665480--96665520 Score: 66 Period size: 19 Copynumber: 2.2 Consensus size: 19 96665470 AAAAGCAGGG 96665480 AAAGAAAGAAAGAAAGGAGA 1 AAAGAAAGAAAGAAAGGA-A 96665500 AAAGAAAG-AAGAAAGGAA 1 AAAGAAAGAAAGAAAGGAA 96665518 AAA 1 AAA 96665521 TTGAAGGTTT Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 18 4 0.19 19 9 0.43 20 8 0.38 ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00 Consensus pattern (19 bp): AAAGAAAGAAAGAAAGGAA Found at i:96669186 original size:39 final size:39 Alignment explanation

Indices: 96669105--96669306 Score: 350 Period size: 39 Copynumber: 5.2 Consensus size: 39 96669095 CATGGTAACC * 96669105 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT 1 CGCACAATTGCCTTCGGG-CTTAACCCGGATATCACAACT * * * 96669145 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT 1 CGCACAATTGCCTTCGGGCTTAACCCGGATATCACAACT 96669184 CGCACAATTGCCTTCGGGCTTAACCCGGATATCACAACT 1 CGCACAATTGCCTTCGGGCTTAACCCGGATATCACAACT 96669223 CGCACAATTGCCTTCGGGCTTAACCCGGATATCACAACT 1 CGCACAATTGCCTTCGGGCTTAACCCGGATATCACAACT * 96669262 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT 1 CGCACAATTGCCTTCGGGCTTAACCCGGATATCACAACT 96669301 CGCACA 1 CGCACA 96669307 TTCATACACA Statistics Matches: 154, Mismatches: 8, Indels: 1 0.94 0.05 0.01 Matches are distributed among these distances: 39 137 0.89 40 17 0.11 ACGTcount: A:0.25, C:0.33, G:0.19, T:0.22 Consensus pattern (39 bp): CGCACAATTGCCTTCGGGCTTAACCCGGATATCACAACT Found at i:96677094 original size:39 final size:39 Alignment explanation

Indices: 96677013--96677214 Score: 350 Period size: 39 Copynumber: 5.2 Consensus size: 39 96677003 CATGGTAACC * 96677013 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT 1 CGCACAATTGCCTTCGGG-CTTAACCCGGATATCACAACT * * * 96677053 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT 1 CGCACAATTGCCTTCGGGCTTAACCCGGATATCACAACT 96677092 CGCACAATTGCCTTCGGGCTTAACCCGGATATCACAACT 1 CGCACAATTGCCTTCGGGCTTAACCCGGATATCACAACT 96677131 CGCACAATTGCCTTCGGGCTTAACCCGGATATCACAACT 1 CGCACAATTGCCTTCGGGCTTAACCCGGATATCACAACT * 96677170 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT 1 CGCACAATTGCCTTCGGGCTTAACCCGGATATCACAACT 96677209 CGCACA 1 CGCACA 96677215 TTCATACACA Statistics Matches: 154, Mismatches: 8, Indels: 1 0.94 0.05 0.01 Matches are distributed among these distances: 39 137 0.89 40 17 0.11 ACGTcount: A:0.25, C:0.33, G:0.19, T:0.22 Consensus pattern (39 bp): CGCACAATTGCCTTCGGGCTTAACCCGGATATCACAACT Found at i:96679126 original size:23 final size:23 Alignment explanation

Indices: 96679091--96679134 Score: 70 Period size: 23 Copynumber: 1.9 Consensus size: 23 96679081 TTTAGGCAAT 96679091 AGAAGAAGAAGAAGAGAAAAAGA 1 AGAAGAAGAAGAAGAGAAAAAGA * * 96679114 AGAAGGAGGAGAAGAGAAAAA 1 AGAAGAAGAAGAAGAGAAAAA 96679135 ATAGATATGC Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 23 19 1.00 ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00 Consensus pattern (23 bp): AGAAGAAGAAGAAGAGAAAAAGA Found at i:96684294 original size:17 final size:16 Alignment explanation

Indices: 96684272--96684314 Score: 50 Period size: 17 Copynumber: 2.6 Consensus size: 16 96684262 TTTAGGGCCT 96684272 AAATTGAATAAATTGCA 1 AAATTGAATAAATTG-A * 96684289 AAATTGGTATAAATTGA 1 AAATT-GAATAAATTGA * 96684306 TAATTGAAT 1 AAATTGAAT 96684315 GTGAAATGGT Statistics Matches: 22, Mismatches: 3, Indels: 3 0.79 0.11 0.11 Matches are distributed among these distances: 16 3 0.14 17 10 0.45 18 9 0.41 ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35 Consensus pattern (16 bp): AAATTGAATAAATTGA Found at i:96697500 original size:13 final size:13 Alignment explanation

Indices: 96697484--96697516 Score: 50 Period size: 13 Copynumber: 2.6 Consensus size: 13 96697474 TTTAATTAAA * 96697484 TTAGTTAATTAGT 1 TTAGATAATTAGT 96697497 TTAGATAATTAGT 1 TTAGATAATTAGT 96697510 TTA-ATAA 1 TTAGATAA 96697517 ACAAACCCTT Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 12 4 0.21 13 15 0.79 ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48 Consensus pattern (13 bp): TTAGATAATTAGT Found at i:96702900 original size:22 final size:21 Alignment explanation

Indices: 96702872--96702964 Score: 83 Period size: 22 Copynumber: 4.7 Consensus size: 21 96702862 CATTGAATCC 96702872 TCTTATTTTT-TTATCTATTTAT 1 TCTTATTTTTATT-TCTATTT-T * 96702894 TCTTATTTTTATTTTTATTTT 1 TCTTATTTTTATTTCTATTTT * 96702915 T-TTATTTTTATTT-T-TCTT 1 TCTTATTTTTATTTCTATTTT * 96702933 T-TGATTTTTATTTCTA-TTT 1 TCTTATTTTTATTTCTATTTT * 96702952 TATTA-TTTTATTT 1 TCTTATTTTTATTT 96702965 TCAAAGACAT Statistics Matches: 62, Mismatches: 5, Indels: 11 0.79 0.06 0.14 Matches are distributed among these distances: 18 15 0.24 19 13 0.21 20 14 0.23 21 2 0.03 22 16 0.26 23 2 0.03 ACGTcount: A:0.16, C:0.05, G:0.01, T:0.77 Consensus pattern (21 bp): TCTTATTTTTATTTCTATTTT Found at i:96702905 original size:6 final size:6 Alignment explanation

Indices: 96702879--96702965 Score: 77 Period size: 6 Copynumber: 13.7 Consensus size: 6 96702869 TCCTCTTATT * * 96702879 TTTTTA TCTATTTA TTCTTA TTTTTA TTTTTA TTTTTTTA TTTTTA TTTTTC 1 TTTTTA T-T-TTTA TTTTTA TTTTTA TTTTTA --TTTTTA TTTTTA TTTTTA * * 96702931 TTTTGA TTTTTA TTTCTA -TTTTA TTATTTTA TTTT 1 TTTTTA TTTTTA TTTTTA TTTTTA -T-TTTTA TTTT 96702966 CAAAGACATA Statistics Matches: 66, Mismatches: 8, Indels: 14 0.75 0.09 0.16 Matches are distributed among these distances: 5 4 0.06 6 43 0.65 7 3 0.05 8 16 0.24 ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78 Consensus pattern (6 bp): TTTTTA Found at i:96702918 original size:26 final size:26 Alignment explanation

Indices: 96702879--96702965 Score: 81 Period size: 26 Copynumber: 3.4 Consensus size: 26 96702869 TCCTCTTATT * * 96702879 TTTTTATCTATTTATTCTTATTTTTA 1 TTTTTATTTTTTTATTCTTATTTTTA * * 96702905 TTTTTATTTTTTTATTTTTATTTTTC 1 TTTTTATTTTTTTATTCTTATTTTTA * * 96702931 TTTTGATTTTTAT-TTC-TA-TTTTA 1 TTTTTATTTTTTTATTCTTATTTTTA 96702954 TTATTTTATTTT 1 -T-TTTTATTTT 96702966 CAAAGACATA Statistics Matches: 50, Mismatches: 9, Indels: 5 0.78 0.14 0.08 Matches are distributed among these distances: 23 4 0.08 24 3 0.06 25 10 0.20 26 33 0.66 ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78 Consensus pattern (26 bp): TTTTTATTTTTTTATTCTTATTTTTA Found at i:96702958 original size:32 final size:32 Alignment explanation

Indices: 96702874--96702965 Score: 89 Period size: 32 Copynumber: 2.8 Consensus size: 32 96702864 TTGAATCCTC * * * 96702874 TTATTTTTTTATCTATTTATTCTTATTTTTATTT 1 TTATTTTATTAT-TA-TTATTTTTATTTTGATTT * * * 96702908 TTATTTTTTTATTTTTATTTTTCTTTTGATTT 1 TTATTTTATTATTATTATTTTTATTTTGATTT 96702940 TTATTTCTATT-TTATTA-TTTTATTTT 1 TTATTT-TATTATTATTATTTTTATTTT 96702966 CAAAGACATA Statistics Matches: 50, Mismatches: 7, Indels: 5 0.81 0.11 0.08 Matches are distributed among these distances: 31 8 0.16 32 26 0.52 33 4 0.08 34 12 0.24 ACGTcount: A:0.16, C:0.04, G:0.01, T:0.78 Consensus pattern (32 bp): TTATTTTATTATTATTATTTTTATTTTGATTT Found at i:96705869 original size:13 final size:13 Alignment explanation

Indices: 96705853--96705885 Score: 50 Period size: 13 Copynumber: 2.6 Consensus size: 13 96705843 TTTAATTAAA * 96705853 TTAGTTAATTAGT 1 TTAGATAATTAGT 96705866 TTAGATAATTAGT 1 TTAGATAATTAGT 96705879 TTA-ATAA 1 TTAGATAA 96705886 AAAACCCTTT Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 12 4 0.21 13 15 0.79 ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48 Consensus pattern (13 bp): TTAGATAATTAGT Found at i:96723029 original size:20 final size:21 Alignment explanation

Indices: 96722985--96723029 Score: 58 Period size: 20 Copynumber: 2.2 Consensus size: 21 96722975 CCTTCTCGTA 96722985 TCTTTAATTTTGTTTTTACAC 1 TCTTTAATTTTGTTTTTACAC * * 96723006 -CTTTACTTTTGTTTTT-CTC 1 TCTTTAATTTTGTTTTTACAC 96723025 TCTTT 1 TCTTT 96723030 TGGACTAATA Statistics Matches: 21, Mismatches: 2, Indels: 3 0.81 0.08 0.12 Matches are distributed among these distances: 19 2 0.10 20 19 0.90 ACGTcount: A:0.11, C:0.18, G:0.04, T:0.67 Consensus pattern (21 bp): TCTTTAATTTTGTTTTTACAC Found at i:96726209 original size:17 final size:17 Alignment explanation

Indices: 96726178--96726210 Score: 50 Period size: 17 Copynumber: 1.9 Consensus size: 17 96726168 TGTATAAAAC 96726178 TTATTTTATTGTTAATT 1 TTATTTTATTGTTAATT 96726195 TTATTATTATT-TTAAT 1 TTATT-TTATTGTTAAT 96726211 GACATTTGTT Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 17 10 0.67 18 5 0.33 ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70 Consensus pattern (17 bp): TTATTTTATTGTTAATT Found at i:96726222 original size:30 final size:30 Alignment explanation

Indices: 96726186--96726248 Score: 92 Period size: 30 Copynumber: 2.1 Consensus size: 30 96726176 ACTTATTTTA * 96726186 TTGTTAATTTTATTATTATTTTA-ATGACAT 1 TTGTTAATTTTATTATTAGTTTAGA-GACAT * 96726216 TTGTTAATTTTGTTATTAGTTTAGAGACAT 1 TTGTTAATTTTATTATTAGTTTAGAGACAT 96726246 TTG 1 TTG 96726249 CTTATTTAGT Statistics Matches: 30, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 30 29 0.97 31 1 0.03 ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57 Consensus pattern (30 bp): TTGTTAATTTTATTATTAGTTTAGAGACAT Found at i:96726331 original size:18 final size:18 Alignment explanation

Indices: 96726310--96726349 Score: 55 Period size: 18 Copynumber: 2.2 Consensus size: 18 96726300 AAAATATTTA * 96726310 TTTTGATGT-TTTTAGTAT 1 TTTTGATGTATTATA-TAT 96726328 TTTTGATGTATTATATAT 1 TTTTGATGTATTATATAT 96726346 TTTT 1 TTTT 96726350 TAAAATAATA Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 18 16 0.80 19 4 0.20 ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68 Consensus pattern (18 bp): TTTTGATGTATTATATAT Found at i:96730047 original size:20 final size:19 Alignment explanation

Indices: 96730024--96730088 Score: 69 Period size: 20 Copynumber: 3.3 Consensus size: 19 96730014 CAAAAAAACA 96730024 TCAAAATAATTTTCAAAGAT 1 TCAAAATAATTTTCAAA-AT * * 96730044 TCAACATAATTTTTAAAAT 1 TCAAAATAATTTTCAAAAT * 96730063 TCAAAAT-ATTTATAAAAATT 1 TCAAAATAATTT-TCAAAA-T 96730083 TCAAAA 1 TCAAAA 96730089 CTTATATATT Statistics Matches: 39, Mismatches: 4, Indels: 4 0.83 0.09 0.09 Matches are distributed among these distances: 18 4 0.10 19 13 0.33 20 22 0.56 ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37 Consensus pattern (19 bp): TCAAAATAATTTTCAAAAT Found at i:96730126 original size:21 final size:21 Alignment explanation

Indices: 96730100--96730139 Score: 62 Period size: 21 Copynumber: 1.9 Consensus size: 21 96730090 TTATATATTT 96730100 AAAAAAAATTATAAAAATTGC 1 AAAAAAAATTATAAAAATTGC * * 96730121 AAAAAAGATTCTAAAAATT 1 AAAAAAAATTATAAAAATT 96730140 ATTTGATGGG Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 21 17 1.00 ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25 Consensus pattern (21 bp): AAAAAAAATTATAAAAATTGC Found at i:96732087 original size:20 final size:19 Alignment explanation

Indices: 96732040--96732087 Score: 51 Period size: 20 Copynumber: 2.4 Consensus size: 19 96732030 AAGGACTTTT * 96732040 ATTTATTTTATTCCAATCA 1 ATTTATTTAATTCCAATCA ** 96732059 ATTTGATTTAATTTTAATCAA 1 ATTT-ATTTAATTCCAATC-A 96732080 ATTTATTT 1 ATTTATTT 96732088 GTTGACTCTT Statistics Matches: 24, Mismatches: 3, Indels: 3 0.80 0.10 0.10 Matches are distributed among these distances: 19 4 0.17 20 15 0.62 21 5 0.21 ACGTcount: A:0.33, C:0.08, G:0.02, T:0.56 Consensus pattern (19 bp): ATTTATTTAATTCCAATCA Found at i:96734928 original size:11 final size:11 Alignment explanation

Indices: 96734905--96734971 Score: 82 Period size: 11 Copynumber: 6.2 Consensus size: 11 96734895 TATGAACTTG * 96734905 TTCGACCATGA 1 TTCGACAATGA * 96734916 TTTGACAATGA 1 TTCGACAATGA 96734927 TTCGACAATGA 1 TTCGACAATGA * 96734938 TTCGACAGTGA 1 TTCGACAATGA * 96734949 TTTGA-AATGA 1 TTCGACAATGA * 96734959 TTCGACTATGA 1 TTCGACAATGA 96734970 TT 1 TT 96734972 TGGTATTGGA Statistics Matches: 47, Mismatches: 8, Indels: 2 0.82 0.14 0.04 Matches are distributed among these distances: 10 8 0.17 11 39 0.83 ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34 Consensus pattern (11 bp): TTCGACAATGA Found at i:96734959 original size:21 final size:21 Alignment explanation

Indices: 96734912--96734973 Score: 72 Period size: 21 Copynumber: 2.9 Consensus size: 21 96734902 TTGTTCGACC * * 96734912 ATGATTTGACAATGATTCGACA 1 ATGATTCGAC-ATGATTTGACA 96734934 ATGATTCGACAGTGATTTGA-A 1 ATGATTCGACA-TGATTTGACA 96734955 ATGATTCGACTATGATTTG 1 ATGATTCGAC-ATGATTTG 96734974 GTATTGGAAA Statistics Matches: 36, Mismatches: 2, Indels: 5 0.84 0.05 0.12 Matches are distributed among these distances: 21 19 0.53 22 17 0.47 ACGTcount: A:0.32, C:0.11, G:0.21, T:0.35 Consensus pattern (21 bp): ATGATTCGACATGATTTGACA Found at i:96738891 original size:44 final size:44 Alignment explanation

Indices: 96738828--96738921 Score: 170 Period size: 44 Copynumber: 2.1 Consensus size: 44 96738818 CTGATCACAT 96738828 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCAC 1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCAC * * 96738872 TTATCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCAC 1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCAC 96738916 TTATCA 1 TTATCA 96738922 TTTTTTAGCT Statistics Matches: 48, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 44 48 1.00 ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32 Consensus pattern (44 bp): TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCAC Found at i:96738965 original size:116 final size:118 Alignment explanation

Indices: 96738825--96739044 Score: 363 Period size: 123 Copynumber: 1.8 Consensus size: 118 96738815 ACACTGATCA * 96738825 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACT-AC-CACTTATCACTTGTCATTG 1 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTCACTCACTTATCACTTGTCATTA * 96738888 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCATTTTTTAGCTACCACTTAT 66 ATCAGATAAATGTAGCTAAAGCTACCACTTATCATTTTTTAGCTACCACTTAT 96738941 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTATCACTTGT 1 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACT--CAC---TCACTTATCACTTGT 96739006 CATTAATCAGATAAATGTAGCTAAAGCTACCACTTATCA 61 CATTAATCAGATAAATGTAGCTAAAGCTACCACTTATCA 96739045 CTTGTCACTG Statistics Matches: 95, Mismatches: 2, Indels: 7 0.91 0.02 0.07 Matches are distributed among these distances: 116 42 0.44 119 2 0.02 123 51 0.54 ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34 Consensus pattern (118 bp): CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTCACTCACTTATCACTTGTCATTA ATCAGATAAATGTAGCTAAAGCTACCACTTATCATTTTTTAGCTACCACTTAT Found at i:96739006 original size:51 final size:51 Alignment explanation

Indices: 96738930--96739053 Score: 194 Period size: 51 Copynumber: 2.4 Consensus size: 51 96738920 CATTTTTTAG * * * 96738930 CTACCACTTATCATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAA 1 CTACCACTTATCACTTATCACTTGTCACTAATCAGATAAATGTAGCTAAAA * * 96738981 CTACCACTTATCACTTATCACTTGTCATTAATCAGATAAATGTAGCTAAAG 1 CTACCACTTATCACTTATCACTTGTCACTAATCAGATAAATGTAGCTAAAA * 96739032 CTACCACTTATCACTTGTCACT 1 CTACCACTTATCACTTATCACT 96739054 GATCAGAAGT Statistics Matches: 67, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 51 67 1.00 ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34 Consensus pattern (51 bp): CTACCACTTATCACTTATCACTTGTCACTAATCAGATAAATGTAGCTAAAA Found at i:96740317 original size:51 final size:51 Alignment explanation

Indices: 96740252--96740374 Score: 158 Period size: 51 Copynumber: 2.4 Consensus size: 51 96740242 TCCCAAATTT * * * ** 96740252 ACTTTATACTTCATCCGGA-ATTATTACTTTGTTGTTCTAGCTTCAACAAGA 1 ACTTCATATTTCATCCGGATA-TATTACTTTATTACTCTAGCTTCAACAAGA * 96740303 ACTTCATATTTCATCCGGATATATTACTTTATTACTCTAGTTTCAACAAGA 1 ACTTCATATTTCATCCGGATATATTACTTTATTACTCTAGCTTCAACAAGA * * 96740354 GCTTCATATTTCATCCAGATA 1 ACTTCATATTTCATCCGGATA 96740375 ACTTAGTTCT Statistics Matches: 63, Mismatches: 8, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 51 62 0.98 52 1 0.02 ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41 Consensus pattern (51 bp): ACTTCATATTTCATCCGGATATATTACTTTATTACTCTAGCTTCAACAAGA Found at i:96740921 original size:25 final size:26 Alignment explanation

Indices: 96740895--96740943 Score: 66 Period size: 26 Copynumber: 2.0 Consensus size: 26 96740885 TCTTTTTCCT * 96740895 TTTA-TTTCATTT-TATTCTATTTAC 1 TTTATTTTAATTTGTATTCTATTTAC * 96740919 TTTATTTTAATTTGTTTTCTATTTA 1 TTTATTTTAATTTGTATTCTATTTA 96740944 ATTAATTAAT Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 24 4 0.19 25 7 0.33 26 10 0.48 ACGTcount: A:0.20, C:0.08, G:0.02, T:0.69 Consensus pattern (26 bp): TTTATTTTAATTTGTATTCTATTTAC Found at i:96742049 original size:137 final size:137 Alignment explanation

Indices: 96741803--96742076 Score: 397 Period size: 137 Copynumber: 2.0 Consensus size: 137 96741793 GTTTTTCTTC * * ** 96741803 ATGTTTGATAGCCCCTTGAACTGCATGTTTTGTCACTGTGTTTAATCCCTTATTTGAACAGTTGT 1 ATGTTTGATAGCCCATTGAACTACATGTTTTGTCACTGTGTTTAATCCCTTATTCAAACAGTTGT * * * * 96741868 CTAAACTAACTTTTGAACGACAGTCTAGACAAACTTTTAGGACAACTCAAGTGTAGTATAAAGTG 66 CTAAACTAACTTTTGAACAACAATCTAGACAAACTTTCAGGACAACTCAAGTGTAATATAAAGTG 96741933 AGCATTT 131 AGCATTT * * 96741940 ATGTTTGATAGCTCATTGAACTACATGTTTTGTCACTGTGTTTAATCCCTTATTCAAATAGTTGT 1 ATGTTTGATAGCCCATTGAACTACATGTTTTGTCACTGTGTTTAATCCCTTATTCAAACAGTTGT * * * * 96742005 CTAGATTAACTTTTGGACAACAATCTAGACATGA-TTTCAGGACAACTCAAGTGTAATATAAAGT 66 CTAAACTAACTTTTGAACAACAATCTAGACA-AACTTTCAGGACAACTCAAGTGTAATATAAAGT * 96742069 TAGCATTT 130 GAGCATTT 96742077 TTTTTTTTGA Statistics Matches: 121, Mismatches: 15, Indels: 2 0.88 0.11 0.01 Matches are distributed among these distances: 137 120 0.99 138 1 0.01 ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37 Consensus pattern (137 bp): ATGTTTGATAGCCCATTGAACTACATGTTTTGTCACTGTGTTTAATCCCTTATTCAAACAGTTGT CTAAACTAACTTTTGAACAACAATCTAGACAAACTTTCAGGACAACTCAAGTGTAATATAAAGTG AGCATTT Found at i:96743633 original size:21 final size:22 Alignment explanation

Indices: 96743581--96743635 Score: 58 Period size: 21 Copynumber: 2.5 Consensus size: 22 96743571 GTGTAATAGT * 96743581 TTTTGGGTATTTTCGAGTGTGAG 1 TTTTGAGT-TTTTCGAGTGTGAG * * * 96743604 TTGTAAGTTTTTCGAGT-TGTG 1 TTTTGAGTTTTTCGAGTGTGAG 96743625 TTTTGAGTTTT 1 TTTTGAGTTTT 96743636 AGAACACTTG Statistics Matches: 26, Mismatches: 6, Indels: 2 0.76 0.18 0.06 Matches are distributed among these distances: 21 12 0.46 22 9 0.35 23 5 0.19 ACGTcount: A:0.13, C:0.04, G:0.29, T:0.55 Consensus pattern (22 bp): TTTTGAGTTTTTCGAGTGTGAG Found at i:96756104 original size:22 final size:22 Alignment explanation

Indices: 96756061--96756105 Score: 54 Period size: 22 Copynumber: 2.0 Consensus size: 22 96756051 TATCCAAACA * 96756061 ATAATAATAAAATAGTAACAAC 1 ATAATAATAAAATAGCAACAAC * * * 96756083 ATAATAGTAGAATAGCAGCAAC 1 ATAATAATAAAATAGCAACAAC 96756105 A 1 A 96756106 CGTGAGAAAA Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 22 19 1.00 ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20 Consensus pattern (22 bp): ATAATAATAAAATAGCAACAAC Found at i:96756562 original size:2 final size:2 Alignment explanation

Indices: 96756550--96756579 Score: 51 Period size: 2 Copynumber: 15.0 Consensus size: 2 96756540 AAAAGAGGGT * 96756550 GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 96756580 TGATGGGCAA Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00 Consensus pattern (2 bp): GA Found at i:96759574 original size:25 final size:25 Alignment explanation

Indices: 96759544--96759593 Score: 91 Period size: 25 Copynumber: 2.0 Consensus size: 25 96759534 AAAAATGAGA * 96759544 TTATTTTCTAAATATGGGTTGTAGG 1 TTATTTTCTAAATATGAGTTGTAGG 96759569 TTATTTTCTAAATATGAGTTGTAGG 1 TTATTTTCTAAATATGAGTTGTAGG 96759594 AGTTCATCTA Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 25 24 1.00 ACGTcount: A:0.26, C:0.04, G:0.22, T:0.48 Consensus pattern (25 bp): TTATTTTCTAAATATGAGTTGTAGG Found at i:96761054 original size:53 final size:54 Alignment explanation

Indices: 96760996--96761105 Score: 204 Period size: 53 Copynumber: 2.1 Consensus size: 54 96760986 TGAAGATAAG 96760996 TTGATGCACGTTCACCATAACCAACAATGGACAGAATTTCCTGAT-AAACTACC 1 TTGATGCACGTTCACCATAACCAACAATGGACAGAATTTCCTGATAAAACTACC * 96761049 TTGATGCACGTTCACCATAACCAACAATGGACGGAATTTCCTGATAAAACTACC 1 TTGATGCACGTTCACCATAACCAACAATGGACAGAATTTCCTGATAAAACTACC 96761103 TTG 1 TTG 96761106 TAAATTATCA Statistics Matches: 55, Mismatches: 1, Indels: 1 0.96 0.02 0.02 Matches are distributed among these distances: 53 44 0.80 54 11 0.20 ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25 Consensus pattern (54 bp): TTGATGCACGTTCACCATAACCAACAATGGACAGAATTTCCTGATAAAACTACC Found at i:96766503 original size:24 final size:24 Alignment explanation

Indices: 96766471--96766519 Score: 98 Period size: 24 Copynumber: 2.0 Consensus size: 24 96766461 TTCAATTGAA 96766471 ATTTTGCATAATTGAACCTTCCTC 1 ATTTTGCATAATTGAACCTTCCTC 96766495 ATTTTGCATAATTGAACCTTCCTC 1 ATTTTGCATAATTGAACCTTCCTC 96766519 A 1 A 96766520 AAGGGTTTGG Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 25 1.00 ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41 Consensus pattern (24 bp): ATTTTGCATAATTGAACCTTCCTC Found at i:96774019 original size:8 final size:8 Alignment explanation

Indices: 96774006--96774032 Score: 54 Period size: 8 Copynumber: 3.4 Consensus size: 8 96773996 ATCATATTTA 96774006 TTTATCTC 1 TTTATCTC 96774014 TTTATCTC 1 TTTATCTC 96774022 TTTATCTC 1 TTTATCTC 96774030 TTT 1 TTT 96774033 CACTTGAAAC Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 19 1.00 ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67 Consensus pattern (8 bp): TTTATCTC Found at i:96779221 original size:31 final size:31 Alignment explanation

Indices: 96779177--96779283 Score: 87 Period size: 31 Copynumber: 3.5 Consensus size: 31 96779167 AACAAAAAAA 96779177 TTAGGTA-TCAAATTAGGAAAAAGAGTCAAGT 1 TTAGGTACT-AAATTAGGAAAAAGAGTCAAGT * ** * 96779208 TCAGGTACTAAATT-GGACCTAA-A-TAAAGT 1 TTAGGTACTAAATTAGGA-AAAAGAGTCAAGT * * * * 96779237 TTAAGTACTAACTTAAGAAAAAGTGTCAAGT 1 TTAGGTACTAAATTAGGAAAAAGAGTCAAGT * 96779268 TTAGGTACCAAATTAG 1 TTAGGTACTAAATTAG 96779284 ACAAAAAATT Statistics Matches: 55, Mismatches: 16, Indels: 10 0.68 0.20 0.12 Matches are distributed among these distances: 29 18 0.33 30 6 0.11 31 30 0.55 32 1 0.02 ACGTcount: A:0.43, C:0.10, G:0.19, T:0.28 Consensus pattern (31 bp): TTAGGTACTAAATTAGGAAAAAGAGTCAAGT Found at i:96782605 original size:31 final size:31 Alignment explanation

Indices: 96782548--96782615 Score: 79 Period size: 31 Copynumber: 2.3 Consensus size: 31 96782538 CTTTAACAAA * * * 96782548 ATAAAAATAATTTTTAAAATTCTAAAAATAT 1 ATAAAAATAATTATTAAAAATATAAAAATAT 96782579 ATAACAAATAA-TATTAAAAATATAAAAATA- 1 ATAA-AAATAATTATTAAAAATATAAAAATAT 96782609 A-AAAAAT 1 ATAAAAAT 96782616 TCAATTTTTT Statistics Matches: 33, Mismatches: 3, Indels: 5 0.80 0.07 0.12 Matches are distributed among these distances: 28 4 0.12 29 2 0.06 30 1 0.03 31 20 0.61 32 6 0.18 ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31 Consensus pattern (31 bp): ATAAAAATAATTATTAAAAATATAAAAATAT Found at i:96782753 original size:9 final size:9 Alignment explanation

Indices: 96782739--96782773 Score: 56 Period size: 9 Copynumber: 4.1 Consensus size: 9 96782729 TCAACTGATG 96782739 AATTTTTTT 1 AATTTTTTT 96782748 AA--TTTTT 1 AATTTTTTT 96782755 AATTTTTTT 1 AATTTTTTT 96782764 AATTTTTTT 1 AATTTTTTT 96782773 A 1 A 96782774 TATAATTTTA Statistics Matches: 24, Mismatches: 0, Indels: 4 0.86 0.00 0.14 Matches are distributed among these distances: 7 7 0.29 9 17 0.71 ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74 Consensus pattern (9 bp): AATTTTTTT Found at i:96782760 original size:16 final size:16 Alignment explanation

Indices: 96782739--96782770 Score: 64 Period size: 16 Copynumber: 2.0 Consensus size: 16 96782729 TCAACTGATG 96782739 AATTTTTTTAATTTTT 1 AATTTTTTTAATTTTT 96782755 AATTTTTTTAATTTTT 1 AATTTTTTTAATTTTT 96782771 TTATATAATT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75 Consensus pattern (16 bp): AATTTTTTTAATTTTT Found at i:96784918 original size:24 final size:25 Alignment explanation

Indices: 96784891--96784940 Score: 75 Period size: 24 Copynumber: 2.0 Consensus size: 25 96784881 AATATATAAT * 96784891 ATTAATTTTAAATATTT-TTAAGTA 1 ATTAATATTAAATATTTATTAAGTA * 96784915 ATTAATATTAATTATTTATTAAGTA 1 ATTAATATTAAATATTTATTAAGTA 96784940 A 1 A 96784941 ACAAAAAAAA Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 24 15 0.65 25 8 0.35 ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52 Consensus pattern (25 bp): ATTAATATTAAATATTTATTAAGTA Found at i:96787594 original size:23 final size:23 Alignment explanation

Indices: 96787564--96787610 Score: 94 Period size: 23 Copynumber: 2.0 Consensus size: 23 96787554 CCCAAGTACC 96787564 TATTGTTGTTGCTTTTCTTTTGG 1 TATTGTTGTTGCTTTTCTTTTGG 96787587 TATTGTTGTTGCTTTTCTTTTGG 1 TATTGTTGTTGCTTTTCTTTTGG 96787610 T 1 T 96787611 CCTATAAGGT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 24 1.00 ACGTcount: A:0.04, C:0.09, G:0.21, T:0.66 Consensus pattern (23 bp): TATTGTTGTTGCTTTTCTTTTGG Found at i:96792891 original size:20 final size:20 Alignment explanation

Indices: 96792861--96792901 Score: 66 Period size: 19 Copynumber: 2.0 Consensus size: 20 96792851 TACGAGTACA 96792861 GTTTTTGTTTTTGTATTTTTT 1 GTTTTTGTTTTTGT-TTTTTT 96792882 GTTTTT-TTTTTGTTTTTTT 1 GTTTTTGTTTTTGTTTTTTT 96792901 G 1 G 96792902 CAATGAAACA Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 19 7 0.35 20 7 0.35 21 6 0.30 ACGTcount: A:0.02, C:0.00, G:0.15, T:0.83 Consensus pattern (20 bp): GTTTTTGTTTTTGTTTTTTT Found at i:96792892 original size:11 final size:11 Alignment explanation

Indices: 96792876--96792900 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 96792866 TGTTTTTGTA 96792876 TTTTTTGTTTT 1 TTTTTTGTTTT 96792887 TTTTTTGTTTT 1 TTTTTTGTTTT 96792898 TTT 1 TTT 96792901 GCAATGAAAC 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:0.00, C:0.00, G:0.08, T:0.92 Consensus pattern (11 bp): TTTTTTGTTTT Found at i:96796942 original size:21 final size:21 Alignment explanation

Indices: 96796916--96796956 Score: 64 Period size: 21 Copynumber: 2.0 Consensus size: 21 96796906 AGACAAGCGA * * 96796916 TACTCCACAGCAGGTGGAGTG 1 TACTCCAAAACAGGTGGAGTG 96796937 TACTCCAAAACAGGTGGAGT 1 TACTCCAAAACAGGTGGAGT 96796957 TTGAGCAGAT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 21 18 1.00 ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20 Consensus pattern (21 bp): TACTCCAAAACAGGTGGAGTG Found at i:96804783 original size:7 final size:7 Alignment explanation

Indices: 96804771--96804795 Score: 50 Period size: 7 Copynumber: 3.6 Consensus size: 7 96804761 TAAAAAAACC 96804771 CAAATTT 1 CAAATTT 96804778 CAAATTT 1 CAAATTT 96804785 CAAATTT 1 CAAATTT 96804792 CAAA 1 CAAA 96804796 ACTTGACAAG Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 18 1.00 ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36 Consensus pattern (7 bp): CAAATTT Found at i:96809829 original size:15 final size:16 Alignment explanation

Indices: 96809803--96809836 Score: 61 Period size: 15 Copynumber: 2.2 Consensus size: 16 96809793 ATATAATTAT 96809803 TATAATTTAACATATA 1 TATAATTTAACATATA 96809819 TATAA-TTAACATATA 1 TATAATTTAACATATA 96809834 TAT 1 TAT 96809837 TCAGATTAGG Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 15 13 0.72 16 5 0.28 ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44 Consensus pattern (16 bp): TATAATTTAACATATA Found at i:96813336 original size:24 final size:24 Alignment explanation

Indices: 96813304--96813350 Score: 94 Period size: 24 Copynumber: 2.0 Consensus size: 24 96813294 GATTCAAATG 96813304 TATACACCGAACTTTTATTTTGAA 1 TATACACCGAACTTTTATTTTGAA 96813328 TATACACCGAACTTTTATTTTGA 1 TATACACCGAACTTTTATTTTGA 96813351 TTCAATTTAC Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 23 1.00 ACGTcount: A:0.32, C:0.17, G:0.09, T:0.43 Consensus pattern (24 bp): TATACACCGAACTTTTATTTTGAA Found at i:96813362 original size:28 final size:28 Alignment explanation

Indices: 96813282--96813362 Score: 80 Period size: 24 Copynumber: 2.9 Consensus size: 28 96813272 ATATACATTA * * 96813282 AACTTTGATTATGATTCAAATGTATACACCG 1 AACTTTTATTTTGATTC-AAT-T-TACACCG * 96813313 AACTTTTATTTTG----AATATACACCG 1 AACTTTTATTTTGATTCAATTTACACCG 96813337 AACTTTTATTTTGATTCAATTTACAC 1 AACTTTTATTTTGATTCAATTTACAC 96813363 ATTTAAAAAA Statistics Matches: 42, Mismatches: 4, Indels: 11 0.74 0.07 0.19 Matches are distributed among these distances: 24 20 0.48 26 3 0.07 28 8 0.19 31 11 0.26 ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42 Consensus pattern (28 bp): AACTTTTATTTTGATTCAATTTACACCG Found at i:96813797 original size:2 final size:2 Alignment explanation

Indices: 96813792--96813823 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 96813782 AAAAGGGCCA 96813792 AT 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 AT 96813824 TTTTTTTGCA Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:96816600 original size:239 final size:239 Alignment explanation

Indices: 96816181--96816874 Score: 1086 Period size: 239 Copynumber: 2.9 Consensus size: 239 96816171 ATGCTTATGT * * 96816181 TGGTTTTAGATAAAAAAAATGAAGAGGAATTTGAGAAAGCCTTGGTGGAAGGCTTTCATCACCAA 1 TGGTTTTGGATAAAAAAAATGAAGAGGAATTTGAGAAAGCCTTGGTGGAAGGCTTTCATCATCAA 96816246 ACTTTTAGGTAAAACTTTAGCTTACAGAATACTAGTGTCTCGAATCTCCATTCTTTATACTTTGA 66 ACTTTTAGGTAAAACTTTAGCTTACAGAATACTAGTGTCTCGAATCTCCATTCTTTATACTTTGA * * 96816311 TGGGTAATTTTGAATGCATTGGTATGGGTAATGACTTCTATGTCGTTAAGTTTAATAATGAAGAA 131 TGGGCAATTTTGAATGCATTGATATGGGTAATGACTTCTATGTCGTTAAGTTTAATAATGAAGAA * 96816376 GACAGGGCTAAAGTTTTTATTGTTACGATGGTGTTCTCCTACGA 196 GACAGGGCTAAAGTTTTGATTGTTACGATGGTGTTCTCCTACGA 96816420 TGGTTTTGGATAAAAAAAATGAAGAGGAATTTGAGAAAGCCTTGGTGGAAGGCTTTCATCATCAA 1 TGGTTTTGGATAAAAAAAATGAAGAGGAATTTGAGAAAGCCTTGGTGGAAGGCTTTCATCATCAA 96816485 ACTTTTAGGTAAAACTTTAGCTTACAGAATACTAGTGTCTCGAATCTCCATTCTTTATACTTTGA 66 ACTTTTAGGTAAAACTTTAGCTTACAGAATACTAGTGTCTCGAATCTCCATTCTTTATACTTTGA * 96816550 TGGGCAATTTTGAATGCAATGATATGGGTAATGACTTCTATGTCGTTAAGTTTAATAATGAAGAA 131 TGGGCAATTTTGAATGCATTGATATGGGTAATGACTTCTATGTCGTTAAGTTTAATAATGAAGAA * * 96816615 GACAGGGCTAAAATTTTGATTGTTATGATGGTGTTCTCCTACGA 196 GACAGGGCTAAAGTTTTGATTGTTACGATGGTGTTCTCCTACGA * * 96816659 TGGTTTTGGATTAAAAAAAATGAAGAGGAATTTGAGAAAGCCTTGGTGGAAGGCTCTCATAATCA 1 TGGTTTTGGA-TAAAAAAAATGAAGAGGAATTTGAGAAAGCCTTGGTGGAAGGCTTTCATCATCA * * * * * * * * 96816724 AAATTTTAGGCAAAACTTTAACTTTCA-AGATGCTACTGTCTCAAATCTCCATTCTTTGTACTTT 65 AACTTTTAGGTAAAACTTTAGCTTACAGA-ATACTAGTGTCTCGAATCTCCATTCTTTATACTTT * * * * * * * 96816788 GGTGGGCAATTTTGAATGTATTGATATAGCTAAT-AGCTTTTATGTTGTTAAGTTTGATAATGAA 129 GATGGGCAATTTTGAATGCATTGATATGGGTAATGA-CTTCTATGTCGTTAAGTTTAATAATGAA * * * * 96816852 GAGGATAGGGCTGAAGTCTTGAT 193 GAAGACAGGGCTAAAGTTTTGAT 96816875 CAAGAGACTA Statistics Matches: 421, Mismatches: 31, Indels: 5 0.92 0.07 0.01 Matches are distributed among these distances: 239 243 0.58 240 178 0.42 ACGTcount: A:0.31, C:0.12, G:0.21, T:0.35 Consensus pattern (239 bp): TGGTTTTGGATAAAAAAAATGAAGAGGAATTTGAGAAAGCCTTGGTGGAAGGCTTTCATCATCAA ACTTTTAGGTAAAACTTTAGCTTACAGAATACTAGTGTCTCGAATCTCCATTCTTTATACTTTGA TGGGCAATTTTGAATGCATTGATATGGGTAATGACTTCTATGTCGTTAAGTTTAATAATGAAGAA GACAGGGCTAAAGTTTTGATTGTTACGATGGTGTTCTCCTACGA Found at i:96819742 original size:59 final size:60 Alignment explanation

Indices: 96819660--96819787 Score: 186 Period size: 59 Copynumber: 2.1 Consensus size: 60 96819650 ATTTATCTAG ** * 96819660 ATATTAATATGAGATATTAAATTTAACTTAAAATTTATCTAAATAGTATTTTATTAATTTA 1 ATATTAATATGAGA-ATTAAATTTAACTTAAAATTTATCTAAATAAAATTATATTAATTTA * * * 96819721 ATATTAATATGAG-ATTAAATTTAATTTAATATTTATCTAGATAAAATTATATTAATTTA 1 ATATTAATATGAGAATTAAATTTAACTTAAAATTTATCTAAATAAAATTATATTAATTTA 96819780 ATATTAAT 1 ATATTAAT 96819788 TTGATTAATT Statistics Matches: 61, Mismatches: 6, Indels: 2 0.88 0.09 0.03 Matches are distributed among these distances: 59 48 0.79 61 13 0.21 ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48 Consensus pattern (60 bp): ATATTAATATGAGAATTAAATTTAACTTAAAATTTATCTAAATAAAATTATATTAATTTA Found at i:96819779 original size:31 final size:31 Alignment explanation

Indices: 96819682--96819784 Score: 88 Period size: 31 Copynumber: 3.4 Consensus size: 31 96819672 GATATTAAAT * * * ** * 96819682 TTAACTTAAAATTTATCTAAATAGTATTTTA 1 TTAATTTAATATTTATCTAGATAAAATTATA * * * 96819713 TTAATTTAATATTAATATGAGAT-TAA--AT- 1 TTAATTTAATATTTATCT-AGATAAAATTATA 96819741 TTAATTTAATATTTATCTAGATAAAATTATA 1 TTAATTTAATATTTATCTAGATAAAATTATA 96819772 TTAATTTAATATT 1 TTAATTTAATATT 96819785 AATTTGATTA Statistics Matches: 56, Mismatches: 11, Indels: 10 0.73 0.14 0.13 Matches are distributed among these distances: 27 4 0.07 28 18 0.32 29 1 0.02 30 2 0.04 31 28 0.50 32 3 0.05 ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50 Consensus pattern (31 bp): TTAATTTAATATTTATCTAGATAAAATTATA Found at i:96819811 original size:20 final size:20 Alignment explanation

Indices: 96819771--96819811 Score: 57 Period size: 20 Copynumber: 2.0 Consensus size: 20 96819761 ATAAAATTAT * 96819771 ATTAATTTAATATTAATTTG 1 ATTAATTTAATATTAAGTTG 96819791 ATTAATTCTAATATT-AGTTG 1 ATTAATT-TAATATTAAGTTG 96819811 A 1 A 96819812 ACTGTCTCTA Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 20 12 0.63 21 7 0.37 ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51 Consensus pattern (20 bp): ATTAATTTAATATTAAGTTG Found at i:96819994 original size:16 final size:16 Alignment explanation

Indices: 96819973--96820003 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 96819963 GAACTTTAAA * 96819973 GAAATTACTAAATTAT 1 GAAATTACGAAATTAT 96819989 GAAATTACGAAATTA 1 GAAATTACGAAATTA 96820004 CCCCATTGGA Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32 Consensus pattern (16 bp): GAAATTACGAAATTAT Found at i:96830262 original size:29 final size:28 Alignment explanation

Indices: 96830230--96830292 Score: 67 Period size: 28 Copynumber: 2.2 Consensus size: 28 96830220 TTTGTTTTCC * * 96830230 ATTTATTTTAATTTTTAATT-TATTTTGTA 1 ATTTATTTAAAATTTTAATTATA-TTT-TA * 96830259 ATTT-TCTAAAATTTTAATTATATTTTA 1 ATTTATTTAAAATTTTAATTATATTTTA 96830286 ATTTATT 1 ATTTATT 96830293 AAGCCTAAAT Statistics Matches: 28, Mismatches: 4, Indels: 5 0.76 0.11 0.14 Matches are distributed among these distances: 27 6 0.21 28 16 0.57 29 6 0.21 ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65 Consensus pattern (28 bp): ATTTATTTAAAATTTTAATTATATTTTA Found at i:96831659 original size:30 final size:29 Alignment explanation

Indices: 96831588--96831659 Score: 76 Period size: 30 Copynumber: 2.4 Consensus size: 29 96831578 ACTTAATCAT * 96831588 TTTTAGTCTCTATATTTTTAAATCTATTTA 1 TTTTAGTC-CTATATTTTTAAATCTATTAA 96831618 TTTTAGTTCCTATACTTTTTAAAAT-T-TTAAA 1 TTTTAG-TCCTATA-TTTTT-AAATCTATT-AA 96831649 TTTTAGTCCTA 1 TTTTAGTCCTA 96831660 ACCCACACAA Statistics Matches: 37, Mismatches: 1, Indels: 8 0.80 0.02 0.17 Matches are distributed among these distances: 30 18 0.49 31 15 0.41 32 4 0.11 ACGTcount: A:0.28, C:0.11, G:0.04, T:0.57 Consensus pattern (29 bp): TTTTAGTCCTATATTTTTAAATCTATTAA Found at i:96832241 original size:54 final size:58 Alignment explanation

Indices: 96832120--96832243 Score: 134 Period size: 54 Copynumber: 2.2 Consensus size: 58 96832110 TTAGGACCTA * * * 96832120 AACTTGGTAATTGTTCGCACATTAAAATTTGAACTTTTTTTATCTAAGTTAGTCTCTG 1 AACTTGGCAATTGTTCGCACATTAAAACTTGAACTTTTTTTATCTAAGTTACTCTCTG ** * 96832178 AA-TTCGGCAATTGTTC-CACATTGGAGCTTGAA-TTTTTTT-T-TAAGTTACTC-CATG 1 AACTT-GGCAATTGTTCGCACATTAAAACTTGAACTTTTTTTATCTAAGTTACTCTC-TG 96832232 AACTTGGCAATT 1 AACTTGGCAATT 96832244 ATTTTTAAAT Statistics Matches: 57, Mismatches: 6, Indels: 10 0.78 0.08 0.14 Matches are distributed among these distances: 53 1 0.02 54 20 0.35 55 3 0.05 56 7 0.12 57 14 0.25 58 12 0.21 ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43 Consensus pattern (58 bp): AACTTGGCAATTGTTCGCACATTAAAACTTGAACTTTTTTTATCTAAGTTACTCTCTG Found at i:96832797 original size:25 final size:25 Alignment explanation

Indices: 96832756--96832829 Score: 64 Period size: 25 Copynumber: 3.0 Consensus size: 25 96832746 AGTCTTTATA * 96832756 TTTTTTTTGTACA-TTTAAATTTTAG 1 TTTTTTTT-TATATTTTAAATTTTAG * 96832781 TTTTTTTTTATATTTTATGAAATTTAG 1 TTTTTTTTTATATTTTA--AATTTTAG * * 96832808 --TCTTTTTATTTTTTAAATTTTA 1 TTTTTTTTTATATTTTAAATTTTA 96832830 AAATTTAGGT Statistics Matches: 41, Mismatches: 5, Indels: 8 0.76 0.09 0.15 Matches are distributed among these distances: 23 6 0.15 24 3 0.07 25 25 0.61 27 7 0.17 ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68 Consensus pattern (25 bp): TTTTTTTTTATATTTTAAATTTTAG Found at i:96841652 original size:88 final size:89 Alignment explanation

Indices: 96841498--96841678 Score: 235 Period size: 88 Copynumber: 2.0 Consensus size: 89 96841488 CTCCTATTTA * 96841498 TTTTGCACTCAATTGGATACTTAAACTTTCAAAATGCATAAAAAATGCCTTCAAGCTTAAAAAAA 1 TTTTGCACTCAATTGGATACTTAAACTTTCAAAATGCATAAAAAATGCCTTCAAACTTAAAAAAA 96841563 AAAA-CAATTAAGCCCCTG-TTTTT 66 AAAAGCAATTAAGCCCC-GCTTTTT * * * **** 96841586 TTTTGCACTCAATTGTATACTTAAA-TTGTCAAAATGCATAAAAAA-GAGCTTCAAATTTTTTCA 1 TTTTGCACTCAATTGGATACTTAAACTT-TCAAAATGCATAAAAAATG-CCTTCAAACTTAAAAA 96841649 AAAAAAGCAATTAAGCCCCGCTTTTT 64 AAAAAAGCAATTAAGCCCCGCTTTTT 96841675 TTTT 1 TTTT 96841679 CTTTTTTTTG Statistics Matches: 81, Mismatches: 8, Indels: 7 0.84 0.08 0.07 Matches are distributed among these distances: 87 3 0.04 88 57 0.70 89 21 0.26 ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35 Consensus pattern (89 bp): TTTTGCACTCAATTGGATACTTAAACTTTCAAAATGCATAAAAAATGCCTTCAAACTTAAAAAAA AAAAGCAATTAAGCCCCGCTTTTT Found at i:96841858 original size:9 final size:9 Alignment explanation

Indices: 96841822--96841916 Score: 79 Period size: 9 Copynumber: 10.4 Consensus size: 9 96841812 ATATGACAAA 96841822 AAAAATTAT 1 AAAAATTAT 96841831 AAAAA--AT 1 AAAAATTAT * 96841838 AAAAATCAAT 1 AAAAAT-TAT 96841848 AAAAATTAT 1 AAAAATTAT 96841857 AAAAATTAT 1 AAAAATTAT * * 96841866 TAAACTT-T 1 AAAAATTAT * 96841874 AAAAAAATAT 1 -AAAAATTAT * 96841884 AAAATTTTAT 1 AAAA-ATTAT * 96841894 AAAATTTTAT 1 AAAA-ATTAT 96841904 AAAAATTAT 1 AAAAATTAT 96841913 AAAA 1 AAAA 96841917 TGCATAAAAA Statistics Matches: 71, Mismatches: 9, Indels: 12 0.77 0.10 0.13 Matches are distributed among these distances: 7 7 0.10 8 1 0.01 9 37 0.52 10 26 0.37 ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33 Consensus pattern (9 bp): AAAAATTAT Found at i:96841858 original size:19 final size:19 Alignment explanation

Indices: 96841822--96841916 Score: 74 Period size: 19 Copynumber: 5.2 Consensus size: 19 96841812 ATATGACAAA 96841822 AAAAATT-ATAAAAA--AT 1 AAAAATTAATAAAAATTAT * 96841838 AAAAATCAATAAAAATTAT 1 AAAAATTAATAAAAATTAT * ** 96841857 AAAAATTATTAAACTTTA- 1 AAAAATTAATAAAAATTAT * * 96841875 AAAAAAT-ATAAAATTTTAT 1 AAAAATTAATAAAA-ATTAT * * 96841894 AAAATTTTATAAAAATTAT 1 AAAAATTAATAAAAATTAT 96841913 AAAA 1 AAAA 96841917 TGCATAAAAA Statistics Matches: 62, Mismatches: 11, Indels: 9 0.76 0.13 0.11 Matches are distributed among these distances: 16 6 0.10 17 11 0.18 18 10 0.16 19 29 0.47 20 6 0.10 ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33 Consensus pattern (19 bp): AAAAATTAATAAAAATTAT Found at i:96841879 original size:28 final size:29 Alignment explanation

Indices: 96841820--96841917 Score: 91 Period size: 28 Copynumber: 3.6 Consensus size: 29 96841810 ACATATGACA * * 96841820 AAAAAAATTATAAAA-A--ATAAAA-ATC 1 AAAAAAATTATAAAATATTATAAAACTTT * 96841845 AATAAAAATTATAAAA-ATTATTAAACTTT 1 AA-AAAAATTATAAAATATTATAAAACTTT * * 96841874 AAAAAAA-TATAAAATTTTATAAAATTTT 1 AAAAAAATTATAAAATATTATAAAACTTT * 96841902 ATAAAAATTATAAAAT 1 AAAAAAATTATAAAAT 96841918 GCATAAAAAG Statistics Matches: 60, Mismatches: 7, Indels: 8 0.80 0.09 0.11 Matches are distributed among these distances: 25 2 0.03 26 14 0.23 27 7 0.12 28 26 0.43 29 11 0.18 ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33 Consensus pattern (29 bp): AAAAAAATTATAAAATATTATAAAACTTT Found at i:96841910 original size:11 final size:10 Alignment explanation

Indices: 96841881--96841917 Score: 58 Period size: 10 Copynumber: 3.8 Consensus size: 10 96841871 TTTAAAAAAA 96841881 TATAAAATTT 1 TATAAAATTT 96841891 TATAAAATTT 1 TATAAAATTT * 96841901 TATAAAA-AT 1 TATAAAATTT 96841910 TATAAAAT 1 TATAAAAT 96841918 GCATAAAAAG Statistics Matches: 25, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 9 8 0.32 10 17 0.68 ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43 Consensus pattern (10 bp): TATAAAATTT Found at i:96842202 original size:19 final size:20 Alignment explanation

Indices: 96842180--96842219 Score: 64 Period size: 19 Copynumber: 2.0 Consensus size: 20 96842170 TTTAAACTTG 96842180 ATAATCTTTTAC-AATTTTT 1 ATAATCTTTTACTAATTTTT * 96842199 ATAATCTTTTTCTAATTTTT 1 ATAATCTTTTACTAATTTTT 96842219 A 1 A 96842220 ATAAAAATAA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 19 11 0.58 20 8 0.42 ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60 Consensus pattern (20 bp): ATAATCTTTTACTAATTTTT Done.