Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008138.1 Hibiscus syriacus cultivar Beakdansim tig00110694_pilon, whole genome shotgun sequence

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: 3838456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 5 of 18

Found at i:867185 original size:10 final size:10

Alignment explanation

Indices: 867170--867195 Score: 52 Period size: 10 Copynumber: 2.6 Consensus size: 10 867160 TGTTGTCACG 867170 CGGGTATGGA 1 CGGGTATGGA 867180 CGGGTATGGA 1 CGGGTATGGA 867190 CGGGTA 1 CGGGTA 867196 CAAGCCGATA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 16 1.00 ACGTcount: A:0.19, C:0.12, G:0.50, T:0.19 Consensus pattern (10 bp): CGGGTATGGA Found at i:870016 original size:51 final size:51 Alignment explanation

Indices: 869921--870032 Score: 154 Period size: 51 Copynumber: 2.2 Consensus size: 51 869911 ATTAATGAAT * * 869921 AAAATAATAATAAACTAAAGATAATGTTTGAATTATATCCTAATTCCTAAG 1 AAAATAATAATAAACTAAAAATAATATTTGAATTATATCCTAATTCCTAAG * * * * 869972 AAAATAATAATAAACTAAAAATAATATTTTAATTCA-ATCTTAATTCTTAAT 1 AAAATAATAATAAACTAAAAATAATATTTGAATT-ATATCCTAATTCCTAAG 870023 AAAATAATAA 1 AAAATAATAA 870033 ATTTAATTCT Statistics Matches: 54, Mismatches: 6, Indels: 2 0.87 0.10 0.03 Matches are distributed among these distances: 51 53 0.98 52 1 0.02 ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35 Consensus pattern (51 bp): AAAATAATAATAAACTAAAAATAATATTTGAATTATATCCTAATTCCTAAG Found at i:870798 original size:26 final size:26 Alignment explanation

Indices: 870729--870799 Score: 76 Period size: 26 Copynumber: 2.8 Consensus size: 26 870719 AATCGTCCTA * 870729 AAAATTCATATTAATG-TT-AAAAAAT 1 AAAATT-AAATTAATGATTAAAAAAAT ** 870754 AAAATTAAATTAAAAATTAAAAAAAT 1 AAAATTAAATTAATGATTAAAAAAAT 870780 AAATATTAAA-TAATGATTAA 1 AAA-ATTAAATTAATGATTAA 870800 TATTGAAAAG Statistics Matches: 38, Mismatches: 5, Indels: 5 0.79 0.10 0.10 Matches are distributed among these distances: 24 6 0.16 25 8 0.21 26 18 0.47 27 6 0.16 ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32 Consensus pattern (26 bp): AAAATTAAATTAATGATTAAAAAAAT Found at i:871750 original size:21 final size:21 Alignment explanation

Indices: 871724--871767 Score: 61 Period size: 21 Copynumber: 2.1 Consensus size: 21 871714 ACAAAAACCG * * 871724 AATAAAAAAATTAATAATAAT 1 AATAAAAAAATAAATAAAAAT * 871745 AATAAAATAATAAATAAAAAT 1 AATAAAAAAATAAATAAAAAT 871766 AA 1 AA 871768 ATAATATTAT Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 21 20 1.00 ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25 Consensus pattern (21 bp): AATAAAAAAATAAATAAAAAT Found at i:871760 original size:18 final size:18 Alignment explanation

Indices: 871724--871773 Score: 59 Period size: 18 Copynumber: 2.8 Consensus size: 18 871714 ACAAAAACCG * 871724 AATAAAAAAATTAAT-AAT 1 AATAATAAAA-TAATAAAT 871742 AATAATAAAATAATAAAT 1 AATAATAAAATAATAAAT * 871760 AAAAAT-AAATAATA 1 AATAATAAAATAATA 871774 TTATATTTTC Statistics Matches: 29, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 17 12 0.41 18 17 0.59 ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26 Consensus pattern (18 bp): AATAATAAAATAATAAAT Found at i:871790 original size:17 final size:17 Alignment explanation

Indices: 871770--871814 Score: 63 Period size: 17 Copynumber: 2.6 Consensus size: 17 871760 AAAAATAAAT * 871770 AATATTATATTTTCAAA 1 AATAATATATTTTCAAA * 871787 AATAATATGTTTTCAAA 1 AATAATATATTTTCAAA * 871804 AATTATATATT 1 AATAATATATT 871815 ATATATGTTT Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 17 24 1.00 ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47 Consensus pattern (17 bp): AATAATATATTTTCAAA Found at i:871950 original size:37 final size:36 Alignment explanation

Indices: 871859--872077 Score: 192 Period size: 37 Copynumber: 5.9 Consensus size: 36 871849 TATATATATG * * * 871859 TTTTCAAAACTATACTA-TATGTGTTTTTAAAAATCGT 1 TTTTAAAAACTATA-TATTATATGTTTTCAAAAAT-GT * 871896 TTTTAAAACTATATATATATTATATGTTTTCAAAAATGT 1 TTTTAAAA--A-CTATATATTATATGTTTTCAAAAATGT * * * * 871935 GTTTTCAAAAGTATATAATATATGTTTTCAAAAAAGT 1 -TTTTAAAAACTATATATTATATGTTTTCAAAAATGT * * * * 871972 ATTTTCAAAAC--CATATTATATATTTTCAAAAATCGA 1 -TTTTAAAAACTATATATTATATGTTTTCAAAAAT-GT * * * 872008 TTTTAAAAACTATATATTATATGCTTTAAAAAACGT 1 TTTTAAAAACTATATATTATATGTTTTCAAAAATGT * 872044 TTTCTAAAAACTATATATTATATGTTTTTAAAAA 1 TTT-TAAAAACTATATATTATATGTTTTCAAAAA 872078 AAAATATTTT Statistics Matches: 149, Mismatches: 24, Indels: 18 0.78 0.13 0.09 Matches are distributed among these distances: 35 27 0.18 36 5 0.03 37 85 0.57 38 1 0.01 39 5 0.03 40 26 0.17 ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44 Consensus pattern (36 bp): TTTTAAAAACTATATATTATATGTTTTCAAAAATGT Found at i:872054 original size:72 final size:73 Alignment explanation

Indices: 871912--872077 Score: 187 Period size: 72 Copynumber: 2.3 Consensus size: 73 871902 AACTATATAT * * * * 871912 ATATTATATGTTTTCAAAAATGTGTTTTCAAAAGTATATAATATATGTTTTCAAAAAAGTATTTT 1 ATATTATATGTTTTCAAAAATGTATTTTAAAAACTATATAATATATGCTTTCAAAAAAGTATTTT * 871977 CAAAAC-C 66 AAAAACAC * * 871984 ATATTATATATTTTCAAAAATCG-ATTTTAAAAACTATATATTATATGCTTT-AAAAAACGT-TT 1 ATATTATATGTTTTCAAAAAT-GTATTTTAAAAACTATATAATATATGCTTTCAAAAAA-GTATT * 872046 TCTAAAAACTAT 64 T-TAAAAAC-AC * 872058 ATATTATATGTTTTTAAAAA 1 ATATTATATGTTTTCAAAAA 872078 AAAATATTTT Statistics Matches: 79, Mismatches: 10, Indels: 8 0.81 0.10 0.08 Matches are distributed among these distances: 71 9 0.11 72 51 0.65 73 1 0.01 74 18 0.23 ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43 Consensus pattern (73 bp): ATATTATATGTTTTCAAAAATGTATTTTAAAAACTATATAATATATGCTTTCAAAAAAGTATTTT AAAAACAC Found at i:876905 original size:21 final size:21 Alignment explanation

Indices: 876868--876907 Score: 62 Period size: 21 Copynumber: 1.9 Consensus size: 21 876858 ACTATCCGAT ** 876868 ATGAACAATACTGTGAACAGA 1 ATGAACAATACCATGAACAGA 876889 ATGAACAATACCATGAACA 1 ATGAACAATACCATGAACA 876908 ATACCGAATT 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:0.50, C:0.17, G:0.15, T:0.17 Consensus pattern (21 bp): ATGAACAATACCATGAACAGA Found at i:877567 original size:22 final size:21 Alignment explanation

Indices: 877539--877587 Score: 71 Period size: 22 Copynumber: 2.3 Consensus size: 21 877529 GGCATATGAA * 877539 TTTTGTCCCAAAGGACCTCTG 1 TTTTGTCCCAAAGGACCTATG * 877560 TATTTGTCCCGAAGGACCTATG 1 T-TTTGTCCCAAAGGACCTATG 877582 TTTTGT 1 TTTTGT 877588 ATTTGTCCCG Statistics Matches: 25, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 21 6 0.24 22 19 0.76 ACGTcount: A:0.18, C:0.22, G:0.20, T:0.39 Consensus pattern (21 bp): TTTTGTCCCAAAGGACCTATG Found at i:878808 original size:3 final size:3 Alignment explanation

Indices: 878800--878833 Score: 50 Period size: 3 Copynumber: 10.7 Consensus size: 3 878790 AAGAGGAGAG 878800 GAA GAA GAA GGAA GAA GAA GGAA GAA GAA GAA GA 1 GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GA 878834 GAGTTTACAT Statistics Matches: 29, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 3 23 0.79 4 6 0.21 ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00 Consensus pattern (3 bp): GAA Found at i:878813 original size:10 final size:10 Alignment explanation

Indices: 878798--878833 Score: 65 Period size: 10 Copynumber: 3.7 Consensus size: 10 878788 AAAAGAGGAG 878798 AGGAAGAAGA 1 AGGAAGAAGA 878808 AGGAAGAAGA 1 AGGAAGAAGA 878818 AGGAAGAAGA 1 AGGAAGAAGA 878828 A-GAAGA 1 AGGAAGA 878834 GAGTTTACAT Statistics Matches: 26, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 9 5 0.19 10 21 0.81 ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00 Consensus pattern (10 bp): AGGAAGAAGA Found at i:878818 original size:13 final size:12 Alignment explanation

Indices: 878800--878833 Score: 50 Period size: 13 Copynumber: 2.7 Consensus size: 12 878790 AAGAGGAGAG 878800 GAAGAAGAAGGAA 1 GAAGAAGAA-GAA 878813 GAAGAAGGAAGAA 1 GAAGAA-GAAGAA 878826 GAAGAAGA 1 GAAGAAGA 878834 GAGTTTACAT Statistics Matches: 20, Mismatches: 0, Indels: 3 0.87 0.00 0.13 Matches are distributed among these distances: 12 2 0.10 13 15 0.75 14 3 0.15 ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00 Consensus pattern (12 bp): GAAGAAGAAGAA Found at i:879371 original size:57 final size:57 Alignment explanation

Indices: 879279--879397 Score: 195 Period size: 57 Copynumber: 2.1 Consensus size: 57 879269 GACATCAGTT * * 879279 TAAA-AGGGAAAGCCCCGATCTTCTTCAAGAATGAGACCAACTAATCAATATGGGTG 1 TAAATAGGGAAAGCCACGATCTTCTTCAAGAATGAGACCAACTAATCAACATGGGTG * * 879335 TAAATAGGGAAAGCCACTATCTTCTTCAAGGATGAGACCAACTAATCAACATGGGTG 1 TAAATAGGGAAAGCCACGATCTTCTTCAAGAATGAGACCAACTAATCAACATGGGTG 879392 TAAATA 1 TAAATA 879398 AACAGAGCTT Statistics Matches: 58, Mismatches: 4, Indels: 1 0.92 0.06 0.02 Matches are distributed among these distances: 56 4 0.07 57 54 0.93 ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23 Consensus pattern (57 bp): TAAATAGGGAAAGCCACGATCTTCTTCAAGAATGAGACCAACTAATCAACATGGGTG Found at i:879611 original size:11 final size:12 Alignment explanation

Indices: 879595--879623 Score: 51 Period size: 11 Copynumber: 2.5 Consensus size: 12 879585 GTTCACAAAC 879595 ATGTTCGTTTA- 1 ATGTTCGTTTAT 879606 ATGTTCGTTTAT 1 ATGTTCGTTTAT 879618 ATGTTC 1 ATGTTC 879624 AATTTTAATT Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 11 11 0.65 12 6 0.35 ACGTcount: A:0.17, C:0.10, G:0.17, T:0.55 Consensus pattern (12 bp): ATGTTCGTTTAT Found at i:889402 original size:2 final size:2 Alignment explanation

Indices: 889395--889419 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 889385 CAAAAACTAC 889395 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 A 889420 CTCCTTTCAA 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:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:889585 original size:24 final size:23 Alignment explanation

Indices: 889550--889623 Score: 62 Period size: 24 Copynumber: 3.1 Consensus size: 23 889540 CTTTTCATAA 889550 AATTTG-CACCGAAGTGCCACGTA- 1 AATTTGTC-CCGAAG-GCCACGTAG ** 889573 AATTTTGTCCCGAAAGGCCGTGTAG 1 AA-TTTGTCCCG-AAGGCCACGTAG * 889598 AATTTGTCCCGAAGGACCGCGTAG 1 AATTTGTCCCGAAGG-CCACGTAG 889622 AA 1 AA 889624 CCCTCAACTC Statistics Matches: 43, Mismatches: 3, Indels: 9 0.78 0.05 0.16 Matches are distributed among these distances: 23 6 0.14 24 31 0.72 25 6 0.14 ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23 Consensus pattern (23 bp): AATTTGTCCCGAAGGCCACGTAG Found at i:889760 original size:30 final size:30 Alignment explanation

Indices: 889724--889784 Score: 86 Period size: 30 Copynumber: 2.0 Consensus size: 30 889714 AAGTGTCTTT * 889724 TATTCACGTAGAACACATTTACATATATCA 1 TATTCACATAGAACACATTTACATATATCA * * * 889754 TATTCACATAGAACATATTTACTTATTTCA 1 TATTCACATAGAACACATTTACATATATCA 889784 T 1 T 889785 GTACTCATAC Statistics Matches: 27, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 30 27 1.00 ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39 Consensus pattern (30 bp): TATTCACATAGAACACATTTACATATATCA Found at i:889770 original size:15 final size:15 Alignment explanation

Indices: 889724--889772 Score: 53 Period size: 15 Copynumber: 3.3 Consensus size: 15 889714 AAGTGTCTTT * 889724 TATTCACGTAGAACA 1 TATTCACATAGAACA * * * * 889739 CATTTACATATATCA 1 TATTCACATAGAACA 889754 TATTCACATAGAACA 1 TATTCACATAGAACA 889769 TATT 1 TATT 889773 TACTTATTTC Statistics Matches: 25, Mismatches: 9, Indels: 0 0.74 0.26 0.00 Matches are distributed among these distances: 15 25 1.00 ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35 Consensus pattern (15 bp): TATTCACATAGAACA Found at i:894565 original size:33 final size:29 Alignment explanation

Indices: 894500--894584 Score: 98 Period size: 29 Copynumber: 2.8 Consensus size: 29 894490 ATATTAACAT * 894500 ATATAGTTTTTGAAAACATTATATATATA 1 ATATAGTTTTTGAAAACATTTTATATATA 894529 ATATAGTTTTTGAAAACATTTTGAACGTATATA 1 ATATAGTTTTTGAAAACATTTT--A--TATATA * * 894562 ATATATGGTTTTGAAAGCATTTT 1 ATATA-GTTTTTGAAAACATTTT 894585 TCGAATATAT Statistics Matches: 48, Mismatches: 3, Indels: 5 0.86 0.05 0.09 Matches are distributed among these distances: 29 21 0.44 31 1 0.02 33 11 0.23 34 15 0.31 ACGTcount: A:0.39, C:0.05, G:0.12, T:0.45 Consensus pattern (29 bp): ATATAGTTTTTGAAAACATTTTATATATA Found at i:894594 original size:34 final size:31 Alignment explanation

Indices: 894500--894595 Score: 97 Period size: 29 Copynumber: 3.0 Consensus size: 31 894490 ATATTAACAT * * 894500 ATATAGTTTTTGAAAACATTAT--ATATATA 1 ATATAGGTTTTGAAAACATTTTGAATATATA * 894529 ATATAGTTTTTGAAAACATTTTGAACGTATATA 1 ATATAGGTTTTGAAAACATTTTGAA--TATATA * 894562 ATATATGGTTTTGAAAGCATTTTTCGAATATATA 1 ATATA-GGTTTTGAAAACA-TTTT-GAATATATA 894596 TAATATTATT Statistics Matches: 57, Mismatches: 3, Indels: 9 0.83 0.04 0.13 Matches are distributed among these distances: 29 21 0.37 31 1 0.02 33 11 0.19 34 17 0.30 35 4 0.07 36 3 0.05 ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44 Consensus pattern (31 bp): ATATAGGTTTTGAAAACATTTTGAATATATA Found at i:894651 original size:22 final size:22 Alignment explanation

Indices: 894624--894665 Score: 66 Period size: 22 Copynumber: 1.9 Consensus size: 22 894614 ATAATGTCAT * 894624 TTTATTGATTTATTTATTTTCA 1 TTTATTGATTTATTCATTTTCA * 894646 TTTATTTATTTATTCATTTT 1 TTTATTGATTTATTCATTTT 894666 GTTATTTTTA Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 22 18 1.00 ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71 Consensus pattern (22 bp): TTTATTGATTTATTCATTTTCA Found at i:894654 original size:18 final size:17 Alignment explanation

Indices: 894622--894659 Score: 58 Period size: 18 Copynumber: 2.2 Consensus size: 17 894612 ATATAATGTC 894622 ATTTTATTGATTTATTT 1 ATTTTATTGATTTATTT * 894639 ATTTTCATTTATTTATTT 1 ATTTT-ATTGATTTATTT 894657 ATT 1 ATT 894660 CATTTTGTTA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 17 5 0.26 18 14 0.74 ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71 Consensus pattern (17 bp): ATTTTATTGATTTATTT Found at i:894672 original size:16 final size:16 Alignment explanation

Indices: 894624--894664 Score: 59 Period size: 14 Copynumber: 2.7 Consensus size: 16 894614 ATAATGTCAT * 894624 TTTATTGATTTATTTA 1 TTTATTCATTTATTTA 894640 -TT-TTCATTTATTTA 1 TTTATTCATTTATTTA 894654 TTTATTCATTT 1 TTTATTCATTT 894665 TGTTATTTTT Statistics Matches: 22, Mismatches: 1, Indels: 4 0.81 0.04 0.15 Matches are distributed among these distances: 14 11 0.50 15 4 0.18 16 7 0.32 ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71 Consensus pattern (16 bp): TTTATTCATTTATTTA Found at i:895789 original size:18 final size:18 Alignment explanation

Indices: 895763--895801 Score: 69 Period size: 18 Copynumber: 2.2 Consensus size: 18 895753 CTTTAGATTT * 895763 TTTATTTATTTTCTTTTA 1 TTTAATTATTTTCTTTTA 895781 TTTAATTATTTTCTTTTA 1 TTTAATTATTTTCTTTTA 895799 TTT 1 TTT 895802 TAAAAACAAC 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:0.18, C:0.05, G:0.00, T:0.77 Consensus pattern (18 bp): TTTAATTATTTTCTTTTA Found at i:895890 original size:20 final size:20 Alignment explanation

Indices: 895837--895893 Score: 59 Period size: 20 Copynumber: 3.0 Consensus size: 20 895827 TTATCTTTAC 895837 TATTATTA-TTTA--TTATT 1 TATTATTATTTTATTTTATT ** 895854 TATTA-TATTTCCCTTTTATT 1 TATTATTATTT-TATTTTATT 895874 TATTATTATTTTATTTTATT 1 TATTATTATTTTATTTTATT 895894 ATATATTTAA Statistics Matches: 31, Mismatches: 4, Indels: 7 0.74 0.10 0.17 Matches are distributed among these distances: 16 2 0.06 17 7 0.23 20 17 0.55 21 5 0.16 ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70 Consensus pattern (20 bp): TATTATTATTTTATTTTATT Found at i:895891 original size:16 final size:16 Alignment explanation

Indices: 895867--895901 Score: 54 Period size: 16 Copynumber: 2.2 Consensus size: 16 895857 TATATTTCCC 895867 TTTTATTTATTAT-TA 1 TTTTATTTATTATATA 895882 TTTTATTTTATTATATA 1 TTTTA-TTTATTATATA 895899 TTT 1 TTT 895902 AACTTTACCT Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 15 5 0.28 16 8 0.44 17 5 0.28 ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74 Consensus pattern (16 bp): TTTTATTTATTATATA Found at i:895900 original size:27 final size:28 Alignment explanation

Indices: 895827--895902 Score: 77 Period size: 27 Copynumber: 2.8 Consensus size: 28 895817 GAAACTTTTT * 895827 TTATCTTTACTATTATTATTTATTATTTA 1 TTATATTT-CTATTATTATTTATTATTTA ** 895856 TTATATTTCCCTT-TTATTTATTA-TTA 1 TTATATTTCTATTATTATTTATTATTTA * 895882 TTTTATTT-TATTATATATTTA 1 TTATATTTCTATTAT-TATTTA 895903 ACTTTACCTG Statistics Matches: 39, Mismatches: 6, Indels: 6 0.76 0.12 0.12 Matches are distributed among these distances: 25 2 0.05 26 11 0.28 27 16 0.41 28 3 0.08 29 7 0.18 ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67 Consensus pattern (28 bp): TTATATTTCTATTATTATTTATTATTTA Found at i:896291 original size:5 final size:5 Alignment explanation

Indices: 896281--896370 Score: 60 Period size: 5 Copynumber: 17.4 Consensus size: 5 896271 TTCTTTTTTA * * 896281 TATTT TATTT TGTTT TATTTT TATTT TCCCACTT T--TT TATTT TATTT 1 TATTT TATTT TATTT TA-TTT TATTT T---ATTT TATTT TATTT TATTT * * * 896328 TGTTT TATTT TATTT TCTCACT T-TTT TATTT TATTT TATTT TA 1 TATTT TATTT TATTT TAT--TT TATTT TATTT TATTT TATTT TA 896371 ACACTTTTTT Statistics Matches: 68, Mismatches: 8, Indels: 18 0.72 0.09 0.19 Matches are distributed among these distances: 3 3 0.04 4 2 0.03 5 51 0.75 6 6 0.09 7 2 0.03 8 4 0.06 ACGTcount: A:0.16, C:0.08, G:0.02, T:0.74 Consensus pattern (5 bp): TATTT Found at i:896350 original size:36 final size:37 Alignment explanation

Indices: 896275--896370 Score: 158 Period size: 36 Copynumber: 2.6 Consensus size: 37 896265 TAACACTTCT 896275 TTTTTATATTTTATTTTGTTTTATTTTTATTTTCCCAC 1 TTTTT-TATTTTATTTTGTTTTATTTTTATTTTCCCAC * 896313 TTTTTTATTTTATTTTGTTTTA-TTTTATTTTCTCAC 1 TTTTTTATTTTATTTTGTTTTATTTTTATTTTCCCAC * 896349 TTTTTTATTTTATTTTATTTTA 1 TTTTTTATTTTATTTTGTTTTA 896371 ACACTTTTTT Statistics Matches: 56, Mismatches: 2, Indels: 2 0.93 0.03 0.03 Matches are distributed among these distances: 36 34 0.61 37 17 0.30 38 5 0.09 ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75 Consensus pattern (37 bp): TTTTTTATTTTATTTTGTTTTATTTTTATTTTCCCAC Found at i:896375 original size:26 final size:26 Alignment explanation

Indices: 896325--896385 Score: 95 Period size: 26 Copynumber: 2.3 Consensus size: 26 896315 TTTTATTTTA * ** 896325 TTTTGTTTTATTTTATTTTCTCACTT 1 TTTTATTTTATTTTATTTTAACACTT 896351 TTTTATTTTATTTTATTTTAACACTT 1 TTTTATTTTATTTTATTTTAACACTT 896377 TTTTATTTT 1 TTTTATTTT 896386 TCTTCTCTGA Statistics Matches: 32, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 26 32 1.00 ACGTcount: A:0.16, C:0.08, G:0.02, T:0.74 Consensus pattern (26 bp): TTTTATTTTATTTTATTTTAACACTT Found at i:904819 original size:16 final size:16 Alignment explanation

Indices: 904798--904828 Score: 62 Period size: 16 Copynumber: 1.9 Consensus size: 16 904788 TTCCTATAGT 904798 TTTGATGCGCAATTCG 1 TTTGATGCGCAATTCG 904814 TTTGATGCGCAATTC 1 TTTGATGCGCAATTC 904829 TTTCCTTGTA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39 Consensus pattern (16 bp): TTTGATGCGCAATTCG Found at i:904882 original size:24 final size:24 Alignment explanation

Indices: 904855--904900 Score: 76 Period size: 24 Copynumber: 1.9 Consensus size: 24 904845 TAAATTTTAA 904855 CACTTCTTTTTTTT-TTTATTTTCC 1 CACTT-TTTTTTTTATTTATTTTCC 904879 CACTTTTTTTTTTATTTATTTT 1 CACTTTTTTTTTTATTTATTTT 904901 ATTTTATTTT Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 23 8 0.38 24 13 0.62 ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74 Consensus pattern (24 bp): CACTTTTTTTTTTATTTATTTTCC Found at i:904901 original size:5 final size:5 Alignment explanation

Indices: 904883--904915 Score: 50 Period size: 5 Copynumber: 6.8 Consensus size: 5 904873 TTTTCCCACT * 904883 TTTTT TTTTA -TTTA TTTTA TTTTA TTTTA TTTT 1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT 904916 CTCTTTTATC Statistics Matches: 26, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 4 4 0.15 5 22 0.85 ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85 Consensus pattern (5 bp): TTTTA Found at i:905901 original size:187 final size:186 Alignment explanation

Indices: 905558--905933 Score: 711 Period size: 187 Copynumber: 2.0 Consensus size: 186 905548 AATTGAATTT 905558 ATCCTGAATTCTCCTAAAGACTTATACACTATTCATCTTTACTTTGTAACCTAAACATTTAACTA 1 ATCCTGAATTCTCCTAAAGACTTATACACTATTCATCTTTACTTTGTAACCTAAACATTTAACTA 905623 TCACTTTCTATTCTGAAATCAATTTTAAATCCAACATTCTCAACTTCTCCCTTGCATTCGGATGT 66 TCACTTTCTATTCTGAAATCAATTTTAAATCCAACATTCTCAACTTCTCCCTTGCATTCGGATGT 905688 TCCTGAACTTCATATCCTATTTCACTTTGAGAGCCCTCGTAGTCTGACATCTATTA 131 TCCTGAACTTCATATCCTATTTCACTTTGAGAGCCCTCGTAGTCTGACATCTATTA 905744 ATCCTGAATTCTCCTAAAGACTTATACACTATTCATCTTTACTTTTGTAACCTAAAACATTTAAC 1 ATCCTGAATTCTCCTAAAGACTTATACACTATTCATCTTTAC-TTTGTAACCT-AAACATTTAAC 905809 TATCACTTTCTATTCTGAAATCAATTTTAAATCCAACATTTCTCAACTTC-CCCTT-CATTCGGA 64 TATCACTTTCTATTCTGAAATCAATTTTAAATCCAACA-TTCTCAACTTCTCCCTTGCATTCGGA 905872 TGTTCCTGAACTTCATATCCTATTTCACTTTGAGAGCCCTCGTAGTCTGACATCTATTA 128 TGTTCCTGAACTTCATATCCTATTTCACTTTGAGAGCCCTCGTAGTCTGACATCTATTA 905931 ATC 1 ATC 905934 TAATCACTTA Statistics Matches: 187, Mismatches: 0, Indels: 5 0.97 0.00 0.03 Matches are distributed among these distances: 186 42 0.22 187 80 0.43 188 54 0.29 189 11 0.06 ACGTcount: A:0.28, C:0.25, G:0.08, T:0.39 Consensus pattern (186 bp): ATCCTGAATTCTCCTAAAGACTTATACACTATTCATCTTTACTTTGTAACCTAAACATTTAACTA TCACTTTCTATTCTGAAATCAATTTTAAATCCAACATTCTCAACTTCTCCCTTGCATTCGGATGT TCCTGAACTTCATATCCTATTTCACTTTGAGAGCCCTCGTAGTCTGACATCTATTA Found at i:906761 original size:24 final size:23 Alignment explanation

Indices: 906742--906799 Score: 71 Period size: 24 Copynumber: 2.4 Consensus size: 23 906732 CACCGAAGTG * 906742 CCACGTAGATTTTGTCCCGAAAGA 1 CCACGTAGAATTTGTCCCG-AAGA * 906766 CCATGTAGAATTTGTCCCGAAGGA 1 CCACGTAGAATTTGTCCCGAA-GA * 906790 CCGCGTAGAA 1 CCACGTAGAA 906800 CCCTCGACTC Statistics Matches: 29, Mismatches: 4, Indels: 2 0.83 0.11 0.06 Matches are distributed among these distances: 23 2 0.07 24 27 0.93 ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22 Consensus pattern (23 bp): CCACGTAGAATTTGTCCCGAAGA Found at i:906936 original size:30 final size:30 Alignment explanation

Indices: 906900--906962 Score: 90 Period size: 30 Copynumber: 2.1 Consensus size: 30 906890 AAGTGTCTTT * 906900 TATTCACGTAGAACACATTTACATATATCA 1 TATTCACATAGAACACATTTACATATATCA * * * 906930 TATTCACATAGAACATATTTACTTATTTCA 1 TATTCACATAGAACACATTTACATATATCA 906960 TAT 1 TAT 906963 ACTCATACAT Statistics Matches: 29, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 30 29 1.00 ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40 Consensus pattern (30 bp): TATTCACATAGAACACATTTACATATATCA Found at i:906946 original size:15 final size:15 Alignment explanation

Indices: 906900--906948 Score: 53 Period size: 15 Copynumber: 3.3 Consensus size: 15 906890 AAGTGTCTTT * 906900 TATTCACGTAGAACA 1 TATTCACATAGAACA * * * * 906915 CATTTACATATATCA 1 TATTCACATAGAACA 906930 TATTCACATAGAACA 1 TATTCACATAGAACA 906945 TATT 1 TATT 906949 TACTTATTTC Statistics Matches: 25, Mismatches: 9, Indels: 0 0.74 0.26 0.00 Matches are distributed among these distances: 15 25 1.00 ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35 Consensus pattern (15 bp): TATTCACATAGAACA Found at i:907516 original size:22 final size:22 Alignment explanation

Indices: 907481--907522 Score: 59 Period size: 22 Copynumber: 1.9 Consensus size: 22 907471 AGTATCGGTA * 907481 CTCTTCTACTGTACTGATACTT 1 CTCTTCTACTGTACCGATACTT 907503 CTCTTCTA-TCGTACCGATAC 1 CTCTTCTACT-GTACCGATAC 907523 CCACTTCGGT Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 21 1 0.06 22 17 0.94 ACGTcount: A:0.19, C:0.31, G:0.10, T:0.40 Consensus pattern (22 bp): CTCTTCTACTGTACCGATACTT Found at i:915633 original size:6 final size:6 Alignment explanation

Indices: 915622--917805 Score: 3426 Period size: 6 Copynumber: 383.5 Consensus size: 6 915612 TTATTGACTA 915622 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 915670 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 915718 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 915766 AAACAT AAACAT AAACAT AAACAT AAACAT -AACAT -AACAT -AACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 915811 -AACAT -AACAT -AAC-- AAACA- AAACAT AAAC-- AAACAT AAACA- 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 915850 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAAC-- AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 915896 -AACAT AAACAT -AACAT AAACAT AAACAT AAACAT AAACAT -AACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 915941 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT -AACAT -AACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 915987 AAACAT AAACAT -AACAT AAACAT AAACAT AAACAT AAACAT -AA-AT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916032 AAACAT AAACAT AAAC-- AAACAT AAACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916078 -AACAT AAACAT AAACAT AAACAT -AACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916124 -AACAT AAACAT -AACAT AAACAT AAACAT -AAC-T AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916168 AAACA- AAACAT AAACAT -AACAT AAACAT AAACAT AAACAT -AACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916213 AAACAT AAACAT AAACAT -AACAT AAACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916260 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916308 AAACAT AAACAT AAAC-- AAACAT AAACAT AAACAT -AACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916353 AAACAT AAACAT AAAC-- -AACAT AAACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916398 AAACAT AAACAT -AACAT AAACAT AAACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916445 AAACAT AAACAT AAACA- AAACAT AAACAT AAACAT -AAC-- AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT * 916489 AAACAT AAACAT AAACCT AAACAT AAACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916537 AAACAT AAACAT AAACAT AAACAT -AACAT AAACAT -AA-AT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916582 AAAC-- AAACAT AAACAT AAACAT AAACAT AAACAT -AACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916627 AAACAT -AACAT AAAC-T AAACAT -AACAT AAACAT -AACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916671 AAACAT AAACAT AAACAT AAACAT AAAC-- AAACAT AAACAT AAACA- 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916716 AAACAT AAACAT AACAACAT AAACAT AAACAT AAACAT -AACAT AAACAT 1 AAACAT AAACAT -A-AACAT AAACAT AAACAT AAACAT AAACAT AAACAT * 916765 AAACAT AAACAT AAACAT AAACAT AAACAAC ATAACAT AAAC-- AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAAC-AT A-AACAT AAACAT AAACAT 916813 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916861 AAACAT AAACAT AAA-AT AAACAT AAACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916908 -AAC-- AAACAT AAACAT AAACAT --ACAT -AACAT AAA-AT -AACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916948 AAACAT AAACAT AAACAT AAACAT -AACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 916995 AAACAT AAACAT AAACAT -AACAT AAAC-T AAACAT -AACAT -AACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 917039 AAACAT AAACAT AAACAT AAACA- AAACAT AAACAT AAACAT AAAC-- 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 917084 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT --A-AT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 917129 AAACAT --ACAT AAACAT AAACAT AAACAT AAACAT -AACAT -AACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 917173 -AACAT -AACAT AAACAT AAACAT AAACAT -AACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 917218 -AACAT AAACAT AAACAT -AACAT AAACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 917264 -AACAT AAACAT -AACAT AAACAT AAACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT * 917310 AAACAT AAACAT -AACAA ACAACAT -AACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT A-AACAT AAACAT AAACAT AAACAT AAACAT 917357 AAACAT -AACAT AAACAT AAACAT -AACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 917403 AAAC-T AAACAT AAACAT -AACAT AAACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 917449 -AACAT AAACAT AAAC-- AAACAT AAACAT AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 917494 -AACAT AAACAT -AACAT -AACAT AAACAT AAAC-- AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 917537 AAACAT AAACAT -AACAT AAACAT -AAC-- AAACAT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 917581 AAACAT AAACAT AAACAT AAA-ACT AAACAT AAACAT -AACAT AAACAT 1 AAACAT AAACAT AAACAT AAACA-T AAACAT AAACAT AAACAT AAACAT 917628 -AACAT AAACAT AAACAT AAACA- AAACAT -AA-AT AAACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 917672 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT -AAC-- AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 917717 AAACAT AAACAT AAACAT -AACAT AAACAT AAACAT -AACAT AAACAT 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT 917763 AAACAT AAAC-- AAACAT AAACAT AAACAT AAACAT AAACAT AAA 1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT AAA 917806 TAGAGAAAAT Statistics Matches: 2056, Mismatches: 6, Indels: 232 0.90 0.00 0.10 Matches are distributed among these distances: 3 5 0.00 4 77 0.04 5 362 0.18 6 1593 0.77 7 11 0.01 8 8 0.00 ACGTcount: A:0.66, C:0.17, G:0.00, T:0.16 Consensus pattern (6 bp): AAACAT Found at i:918026 original size:19 final size:19 Alignment explanation

Indices: 918002--918042 Score: 73 Period size: 19 Copynumber: 2.2 Consensus size: 19 917992 AATTCGCAAC 918002 ACTGAATTTCAAATTCACA 1 ACTGAATTTCAAATTCACA * 918021 ACTGAATTTCAAATTCGCA 1 ACTGAATTTCAAATTCACA 918040 ACT 1 ACT 918043 CGAACTCTAA Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 19 21 1.00 ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32 Consensus pattern (19 bp): ACTGAATTTCAAATTCACA Found at i:918132 original size:20 final size:19 Alignment explanation

Indices: 918110--918222 Score: 93 Period size: 20 Copynumber: 5.7 Consensus size: 19 918100 AACAAAAAAG 918110 TCAAATTCGCAACGCGTTT 1 TCAAATTCGCAACGCGTTT * * 918129 GTCAAATTCGCAACACTGAATT 1 -TCAAATTCGCAACGC-G-TTT * ** 918151 TCAAATTCCCAACTG-AATT 1 TCAAATTCGCAAC-GCGTTT * 918170 TCAAATTCGCAACTCGATTT 1 TCAAATTCGCAACGCG-TTT * 918190 TCAAATTCGCAACTCGGTTT 1 TCAAATTCGCAACGC-GTTT * 918210 TCGAATTCGCAAC 1 TCAAATTCGCAAC 918223 ACAAATTTAA Statistics Matches: 77, Mismatches: 10, Indels: 12 0.78 0.10 0.12 Matches are distributed among these distances: 19 15 0.19 20 46 0.60 21 14 0.18 22 2 0.03 ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31 Consensus pattern (19 bp): TCAAATTCGCAACGCGTTT Found at i:918143 original size:141 final size:141 Alignment explanation

Indices: 917889--918186 Score: 533 Period size: 141 Copynumber: 2.1 Consensus size: 141 917879 AAATAACCAA * ** * 917889 CAAATTCGCAACGCGAACTCCAATTTCGCAACTTAGTTTCCAAATTTGTAACGTGAATTTAGAAA 1 CAAATTCGCAACTCGAACTCCAATTTCGCAACCCAGTTTCCAAATTTGTAACGCGAATTTAGAAA 917954 ATCGCAACAAAAAAGTCAAATTCGCAACGCGTTTGCCAAATTCGCAACACTGAATTTCAAATTCA 66 ATCGCAACAAAAAAGTCAAATTCGCAACGCGTTTGCCAAATTCGCAACACTGAATTTCAAATTCA 918019 CAACTGAATTT 131 CAACTGAATTT * 918030 CAAATTCGCAACTCGAACTCTAATTTCGCAACCCAGTTTCCAAATTTGTAACGCGAATTTAGAAA 1 CAAATTCGCAACTCGAACTCCAATTTCGCAACCCAGTTTCCAAATTTGTAACGCGAATTTAGAAA * * 918095 ATCGCAACAAAAAAGTCAAATTCGCAACGCGTTTGTCAAATTCGCAACACTGAATTTCAAATTCC 66 ATCGCAACAAAAAAGTCAAATTCGCAACGCGTTTGCCAAATTCGCAACACTGAATTTCAAATTCA 918160 CAACTGAATTT 131 CAACTGAATTT 918171 CAAATTCGCAACTCGA 1 CAAATTCGCAACTCGA 918187 TTTTCAAATT Statistics Matches: 150, Mismatches: 7, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 141 150 1.00 ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27 Consensus pattern (141 bp): CAAATTCGCAACTCGAACTCCAATTTCGCAACCCAGTTTCCAAATTTGTAACGCGAATTTAGAAA ATCGCAACAAAAAAGTCAAATTCGCAACGCGTTTGCCAAATTCGCAACACTGAATTTCAAATTCA CAACTGAATTT Found at i:918167 original size:19 final size:19 Alignment explanation

Indices: 918130--918222 Score: 105 Period size: 20 Copynumber: 4.7 Consensus size: 19 918120 AACGCGTTTG 918130 TCAAATTCGCAACACTGAATT 1 TCAAATTCGC-A-ACTGAATT * 918151 TCAAATTCCCAACTGAATT 1 TCAAATTCGCAACTGAATT * 918170 TCAAATTCGCAACTCGATTT 1 TCAAATTCGCAACT-GAATT ** 918190 TCAAATTCGCAACTCGGTTT 1 TCAAATTCGCAACT-GAATT * 918210 TCGAATTCGCAAC 1 TCAAATTCGCAAC 918223 ACAAATTTAA Statistics Matches: 66, Mismatches: 5, Indels: 3 0.89 0.07 0.04 Matches are distributed among these distances: 19 21 0.32 20 36 0.55 21 9 0.14 ACGTcount: A:0.32, C:0.26, G:0.11, T:0.31 Consensus pattern (19 bp): TCAAATTCGCAACTGAATT Found at i:918174 original size:40 final size:40 Alignment explanation

Indices: 917969--918230 Score: 133 Period size: 40 Copynumber: 6.5 Consensus size: 40 917959 AACAAAAAAG * * * 917969 TCAAATTCGCAACGCG--TTTGCCAAATTCGCAACACTGAATT 1 TCAAATTCGCAACACGAATTT--CAAATTCCCAACTC-GAATT * * * * 918010 TCAAATTCACAAC-TGAATTTCAAATTCGCAACTCGAA-C 1 TCAAATTCGCAACACGAATTTCAAATTCCCAACTCGAATT * * * *** * 918048 TCTAATTTCGCAAC-CCAGTTTCCAAATTTGTAACGCGAATT 1 TC-AAATTCGCAACACGAATTT-CAAATTCCCAACTCGAATT * * ** ** * * * 918089 TAGAAAATCGCAACAAAAAAGTCAAATTCGCAACGCG-TTT 1 T-CAAATTCGCAACACGAATTTCAAATTCCCAACTCGAATT 918129 GTCAAATTCGCAACACTGAATTTCAAATTCCCAACT-GAATT 1 -TCAAATTCGCAACAC-GAATTTCAAATTCCCAACTCGAATT * * * ** 918170 TCAAATTCGCAACTCGATTTTCAAATTCGCAACTCGGTTT 1 TCAAATTCGCAACACGAATTTCAAATTCCCAACTCGAATT * * 918210 TCGAATTCGCAACACAAATTT 1 TCAAATTCGCAACACGAATTT 918231 AATTTCGCAA Statistics Matches: 168, Mismatches: 42, Indels: 23 0.72 0.18 0.10 Matches are distributed among these distances: 38 2 0.01 39 33 0.20 40 76 0.45 41 52 0.31 42 5 0.03 ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29 Consensus pattern (40 bp): TCAAATTCGCAACACGAATTTCAAATTCCCAACTCGAATT Found at i:918230 original size:141 final size:141 Alignment explanation

Indices: 917889--918231 Score: 463 Period size: 141 Copynumber: 2.4 Consensus size: 141 917879 AAATAACCAA * * * ** * * *** 917889 CAAATTCGCAACGCGAACTCCAATTTCGCAACTTAGTTTCCAAATTTGTAACGTGAATTTAGAAA 1 CAAATTCGCAACTCGAACTCTAAATTCGCAACCCAGTTTCCAAATTCGCAACACAAATTTAGAAA 917954 ATCGCAACAAAAAAGTCAAATTCGCAACGCGTTTGCCAAATTCGCAACACTGAATTTCAAATTCA 66 ATCGCAACAAAAAAGTCAAATTCGCAACGCGTTTGCCAAATTCGCAACACTGAATTTCAAATTCA 918019 CAACTGAATTT 131 CAACTGAATTT * * * * * 918030 CAAATTCGCAACTCGAACTCTAATTTCGCAACCCAGTTTCCAAATTTGTAACGCGAATTTAGAAA 1 CAAATTCGCAACTCGAACTCTAAATTCGCAACCCAGTTTCCAAATTCGCAACACAAATTTAGAAA * * 918095 ATCGCAACAAAAAAGTCAAATTCGCAACGCGTTTGTCAAATTCGCAACACTGAATTTCAAATTCC 66 ATCGCAACAAAAAAGTCAAATTCGCAACGCGTTTGCCAAATTCGCAACACTGAATTTCAAATTCA 918160 CAACTGAATTT 131 CAACTGAATTT * * * * * * 918171 CAAATTCGCAACTCG-ATTTTCAAATTCGCAACTCGGTTTTCGAATTCGCAACACAAATTTA 1 CAAATTCGCAACTCGAACTCT-AAATTCGCAACCCAGTTTCCAAATTCGCAACACAAATTTA 918232 ATTTCGCAAC Statistics Matches: 183, Mismatches: 18, Indels: 2 0.90 0.09 0.01 Matches are distributed among these distances: 140 3 0.02 141 180 0.98 ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28 Consensus pattern (141 bp): CAAATTCGCAACTCGAACTCTAAATTCGCAACCCAGTTTCCAAATTCGCAACACAAATTTAGAAA ATCGCAACAAAAAAGTCAAATTCGCAACGCGTTTGCCAAATTCGCAACACTGAATTTCAAATTCA CAACTGAATTT Found at i:919209 original size:24 final size:24 Alignment explanation

Indices: 919177--919230 Score: 81 Period size: 24 Copynumber: 2.2 Consensus size: 24 919167 GTATTCGAAA * 919177 TTTGATCTTGGTCCATACCCAGAC 1 TTTGATCTTGGTCAATACCCAGAC * * 919201 TTTGATCTTGGTCAATACTCAGAT 1 TTTGATCTTGGTCAATACCCAGAC 919225 TTTGAT 1 TTTGAT 919231 GATGTTTCAG Statistics Matches: 27, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 24 27 1.00 ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41 Consensus pattern (24 bp): TTTGATCTTGGTCAATACCCAGAC Found at i:921017 original size:12 final size:12 Alignment explanation

Indices: 921000--921040 Score: 55 Period size: 12 Copynumber: 3.4 Consensus size: 12 920990 AGCAAAAGGA * 921000 AATCAAAATCGC 1 AATCAAAATCAC * 921012 AATCAAAATCAA 1 AATCAAAATCAC * 921024 AATCAAAATCCC 1 AATCAAAATCAC 921036 AATCA 1 AATCA 921041 CAACCGGCTT Statistics Matches: 25, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 12 25 1.00 ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17 Consensus pattern (12 bp): AATCAAAATCAC Found at i:921021 original size:6 final size:6 Alignment explanation

Indices: 920999--921033 Score: 52 Period size: 6 Copynumber: 5.8 Consensus size: 6 920989 AAGCAAAAGG * * 920999 AAATCA AAATCG CAATCA AAATCA AAATCA AAATC 1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC 921034 CCAATCACAA Statistics Matches: 25, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 6 25 1.00 ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17 Consensus pattern (6 bp): AAATCA Found at i:921468 original size:37 final size:36 Alignment explanation

Indices: 921418--921521 Score: 109 Period size: 37 Copynumber: 3.1 Consensus size: 36 921408 CAAATCAACT 921418 TTTACAAATCAATTAATCAAGCAAAAAATAATTCTTA 1 TTTACAAATCAATTAA-CAAGCAAAAAATAATTCTTA * * 921455 TTTACAGATCAATT-A-AA-C--AAATTAA--C-T- 1 TTTACAAATCAATTAACAAGCAAAAAATAATTCTTA 921482 TTTACAAATCAATTAAACAAGCAAAAAATAATTCTTA 1 TTTACAAATCAATT-AACAAGCAAAAAATAATTCTTA 921519 TTT 1 TTT 921522 CCTCATCAAT Statistics Matches: 53, Mismatches: 4, Indels: 20 0.69 0.05 0.26 Matches are distributed among these distances: 27 13 0.25 28 1 0.02 29 2 0.04 30 2 0.04 31 7 0.13 33 7 0.13 34 2 0.04 35 1 0.02 36 2 0.04 37 16 0.30 ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34 Consensus pattern (36 bp): TTTACAAATCAATTAACAAGCAAAAAATAATTCTTA Found at i:921486 original size:64 final size:64 Alignment explanation

Indices: 921406--921563 Score: 253 Period size: 64 Copynumber: 2.5 Consensus size: 64 921396 TTGAATAAAC * * 921406 AACAAATCAACTTTTACAAATCAATTAATCAAGCAAAAAATAATTCTTATTTACAGATCAATTA 1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA * * * 921470 AACAAATTAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA 1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA * 921534 AACAAATCAACTTTTACAAATGAATATAAA 1 AACAAATCAACTTTTACAAATCAAT-TAAA 921564 ATTCAATTAA Statistics Matches: 86, Mismatches: 7, Indels: 1 0.91 0.07 0.01 Matches are distributed among these distances: 64 82 0.95 65 4 0.05 ACGTcount: A:0.51, C:0.16, G:0.03, T:0.31 Consensus pattern (64 bp): AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA Found at i:922962 original size:21 final size:21 Alignment explanation

Indices: 922936--923054 Score: 125 Period size: 21 Copynumber: 5.7 Consensus size: 21 922926 GTGAATCGGG * * * * 922936 CTCTTGAACGGTGGGAGAGAC 1 CTCTTGAACGATGAGAGGGGC * * 922957 CTCTTGAACGATGACAGGGGG 1 CTCTTGAACGATGAGAGGGGC * 922978 CTCTTGAAC-AGTGGGAGGGGC 1 CTCTTGAACGA-TGAGAGGGGC * 922999 CTCTTGAACGATGAGAGGGCC 1 CTCTTGAACGATGAGAGGGGC * 923020 CTCTTGAACGAT-AGGAGGCGC 1 CTCTTGAACGATGA-GAGGGGC 923041 CTCTTGAACGATGA 1 CTCTTGAACGATGA 923055 CATGTGCACG Statistics Matches: 81, Mismatches: 13, Indels: 7 0.80 0.13 0.07 Matches are distributed among these distances: 20 2 0.02 21 77 0.95 22 2 0.02 ACGTcount: A:0.24, C:0.21, G:0.35, T:0.20 Consensus pattern (21 bp): CTCTTGAACGATGAGAGGGGC Found at i:922992 original size:42 final size:40 Alignment explanation

Indices: 922933--923056 Score: 149 Period size: 42 Copynumber: 3.0 Consensus size: 40 922923 CATGTGAATC * 922933 GGGCTCTTGAACGGTGGGAGAGACCTCTTGAACGATGACAGG 1 GGGCTCTTGAAC-GTGGGAG-GGCCTCTTGAACGATGACAGG * 922975 GGGCTCTTGAACAGTGGGAGGGGCCTCTTGAACGATGAGAGG 1 GGGCTCTTGAAC-GTGGGA-GGGCCTCTTGAACGATGACAGG ** * 923017 GCCCTCTTGAACGATAGGAGGCGCCTCTTGAACGATGACA 1 GGGCTCTTGAACG-TGGGAGG-GCCTCTTGAACGATGACA 923057 TGTGCACGAC Statistics Matches: 72, Mismatches: 7, Indels: 6 0.85 0.08 0.07 Matches are distributed among these distances: 41 3 0.04 42 68 0.94 43 1 0.01 ACGTcount: A:0.23, C:0.21, G:0.36, T:0.19 Consensus pattern (40 bp): GGGCTCTTGAACGTGGGAGGGCCTCTTGAACGATGACAGG Found at i:923110 original size:4 final size:4 Alignment explanation

Indices: 923089--923126 Score: 58 Period size: 4 Copynumber: 9.5 Consensus size: 4 923079 AAGCCACTAA * * 923089 AAAT AAAT TAAT ACAT AAAT AAAT AAAT AAAT AAAT AA 1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA 923127 TGCCGAAAAA Statistics Matches: 30, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 4 30 1.00 ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26 Consensus pattern (4 bp): AAAT Found at i:925077 original size:20 final size:20 Alignment explanation

Indices: 925054--925135 Score: 137 Period size: 20 Copynumber: 4.1 Consensus size: 20 925044 AAACTTAAAT 925054 TCGCAATGCGAAAATGAAAA 1 TCGCAATGCGAAAATGAAAA * 925074 TCGCAATTCGAAAATGAAAA 1 TCGCAATGCGAAAATGAAAA 925094 TCGCAATGCGAAAATGAAAA 1 TCGCAATGCGAAAATGAAAA * * 925114 TCGCAACGCGAACATGAAAA 1 TCGCAATGCGAAAATGAAAA 925134 TC 1 TC 925136 ACAACACGAA Statistics Matches: 58, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 20 58 1.00 ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16 Consensus pattern (20 bp): TCGCAATGCGAAAATGAAAA Found at i:925140 original size:20 final size:20 Alignment explanation

Indices: 925054--925146 Score: 123 Period size: 20 Copynumber: 4.7 Consensus size: 20 925044 AAACTTAAAT * 925054 TCGCAATGCGAAAATGAAAA 1 TCGCAACGCGAAAATGAAAA ** 925074 TCGCAATTCGAAAATGAAAA 1 TCGCAACGCGAAAATGAAAA * 925094 TCGCAATGCGAAAATGAAAA 1 TCGCAACGCGAAAATGAAAA * 925114 TCGCAACGCGAACATGAAAA 1 TCGCAACGCGAAAATGAAAA * * 925134 TCACAACACGAAA 1 TCGCAACGCGAAA 925147 CTAAATTCGC Statistics Matches: 66, Mismatches: 7, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 20 66 1.00 ACGTcount: A:0.49, C:0.19, G:0.17, T:0.14 Consensus pattern (20 bp): TCGCAACGCGAAAATGAAAA Found at i:925420 original size:20 final size:20 Alignment explanation

Indices: 925384--925429 Score: 58 Period size: 20 Copynumber: 2.3 Consensus size: 20 925374 TATCATCAAT * * 925384 ATAAGAAAAATATAATAATA 1 ATAAGAAAAATAAAATAAAA 925404 ATAA-AAAAATAAAAATAAAA 1 ATAAGAAAAAT-AAAATAAAA 925424 ATAAGA 1 ATAAGA 925430 GATTAAAAAA Statistics Matches: 22, Mismatches: 2, Indels: 3 0.81 0.07 0.11 Matches are distributed among these distances: 19 6 0.27 20 15 0.68 21 1 0.05 ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20 Consensus pattern (20 bp): ATAAGAAAAATAAAATAAAA Found at i:925544 original size:22 final size:22 Alignment explanation

Indices: 925517--925563 Score: 85 Period size: 22 Copynumber: 2.1 Consensus size: 22 925507 GAGATAGACA * 925517 GATTTCGTCGGAGATGGGGACG 1 GATTTCGTCGAAGATGGGGACG 925539 GATTTCGTCGAAGATGGGGACG 1 GATTTCGTCGAAGATGGGGACG 925561 GAT 1 GAT 925564 GTTGCCGGAG Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 22 24 1.00 ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23 Consensus pattern (22 bp): GATTTCGTCGAAGATGGGGACG Found at i:925711 original size:20 final size:20 Alignment explanation

Indices: 925686--925744 Score: 109 Period size: 20 Copynumber: 3.0 Consensus size: 20 925676 ATAAACGTGC 925686 TTTGACTTCTGTGTTGCGAA 1 TTTGACTTCTGTGTTGCGAA 925706 TTTGACTTCTGTGTTGCGAA 1 TTTGACTTCTGTGTTGCGAA * 925726 TTTGACTTCTTTGTTGCGA 1 TTTGACTTCTGTGTTGCGA 925745 TTTTCTAAAT Statistics Matches: 38, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 20 38 1.00 ACGTcount: A:0.14, C:0.15, G:0.24, T:0.47 Consensus pattern (20 bp): TTTGACTTCTGTGTTGCGAA Found at i:925776 original size:20 final size:20 Alignment explanation

Indices: 925738--925887 Score: 147 Period size: 20 Copynumber: 7.3 Consensus size: 20 925728 TGACTTCTTT * 925738 GTTGCGATTTTCTAAATTCGC 1 GTTGCGATTTAC-AAATTCGC * 925759 GTTGCGATTTACAAATTCAC 1 GTTGCGATTTACAAATTCGC 925779 GTTGCGATTTACAAATTCGC 1 GTTGCGATTTACAAATTCGC * 925799 GTTGCGATTTACATATTCGC 1 GTTGCGATTTACAAATTCGC ** * 925819 GTTGCGAATTTGGAAAATCGC 1 GTTGCG-ATTTACAAATTCGC ** * * 925840 AATGCGAATTTAGAAAATCGC 1 GTTGCG-ATTTACAAATTCGC ** * * 925861 AATGCGATTCACATATTCGC 1 GTTGCGATTTACAAATTCGC 925881 GTTGCGA 1 GTTGCGA 925888 ATTTGGAAAC Statistics Matches: 111, Mismatches: 17, Indels: 3 0.85 0.13 0.02 Matches are distributed among these distances: 20 66 0.59 21 45 0.41 ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33 Consensus pattern (20 bp): GTTGCGATTTACAAATTCGC Found at i:925904 original size:20 final size:20 Alignment explanation

Indices: 925815--925932 Score: 78 Period size: 20 Copynumber: 5.8 Consensus size: 20 925805 ATTTACATAT 925815 TCGCGTTGCGAATTTGGAAAA 1 TCGCGTTGCGAATTTGG-AAA ** * 925836 TCGCAATGCGAATTTAGAAAA 1 TCGCGTTGCGAATTT-GGAAA ** *** * 925857 TCGCAATGCG-ATTCACATAT 1 TCGCGTTGCGAATTTGGA-AA 925877 TCGCGTTGCGAATTTGGAAA 1 TCGCGTTGCGAATTTGGAAA * * * 925897 -CTGTGTTGCGAAATTGGAGA 1 TC-GCGTTGCGAATTTGGAAA 925917 TCGCGTTGCGAATTTG 1 TCGCGTTGCGAATTTG 925933 TTGGTCATTT Statistics Matches: 74, Mismatches: 18, Indels: 11 0.72 0.17 0.11 Matches are distributed among these distances: 19 2 0.03 20 40 0.54 21 31 0.42 22 1 0.01 ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30 Consensus pattern (20 bp): TCGCGTTGCGAATTTGGAAA Found at i:926981 original size:3 final size:3 Alignment explanation

Indices: 926958--927033 Score: 70 Period size: 3 Copynumber: 26.3 Consensus size: 3 926948 CATTTTGTTT * ** * 926958 TTA TTA CTA TTA TTA AAA TTA TTA TTA TTA TTA ATA -TA TATA TTA 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA * 927003 TTA -TA TTA -TA TTA TTA TTA -AA TTA TTA TTA T 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T 927034 AAACATGCCA Statistics Matches: 59, Mismatches: 9, Indels: 10 0.76 0.12 0.13 Matches are distributed among these distances: 2 7 0.12 3 49 0.83 4 3 0.05 ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58 Consensus pattern (3 bp): TTA Found at i:926981 original size:18 final size:17 Alignment explanation

Indices: 926958--927033 Score: 88 Period size: 16 Copynumber: 4.6 Consensus size: 17 926948 CATTTTGTTT * 926958 TTATTACTATTATTAAAA 1 TTATTATTATTATT-AAA 926976 TTATTATTATTATT-AA 1 TTATTATTATTATTAAA * 926992 -TA-TATATATTATTATA 1 TTATTAT-TATTATTAAA 927008 TTA-TATTATTATTAAA 1 TTATTATTATTATTAAA 927024 TTATTATTAT 1 TTATTATTAT 927034 AAACATGCCA Statistics Matches: 51, Mismatches: 3, Indels: 9 0.81 0.05 0.14 Matches are distributed among these distances: 14 3 0.06 15 9 0.18 16 15 0.29 17 11 0.22 18 13 0.25 ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58 Consensus pattern (17 bp): TTATTATTATTATTAAA Found at i:938369 original size:22 final size:22 Alignment explanation

Indices: 938344--938420 Score: 127 Period size: 22 Copynumber: 3.5 Consensus size: 22 938334 ATCTACACTC * * 938344 TTCAAAGATGATATATTATCTT 1 TTCAAAGATGATAGATTCTCTT 938366 TTCAAAGATGATAGATTCTCTT 1 TTCAAAGATGATAGATTCTCTT * 938388 TTTAAAGATGATAGATTCTCTT 1 TTCAAAGATGATAGATTCTCTT 938410 TTCAAAGATGA 1 TTCAAAGATGA 938421 AAGCTTTATT Statistics Matches: 51, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 22 51 1.00 ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42 Consensus pattern (22 bp): TTCAAAGATGATAGATTCTCTT Found at i:939232 original size:165 final size:165 Alignment explanation

Indices: 938919--939245 Score: 530 Period size: 165 Copynumber: 2.0 Consensus size: 165 938909 CACAAGAATG * 938919 AGCATTATCTTGAGATTGGGTCATGTTACCCAATCAACATGATATTTTGAAAAATAATGAGAAAA 1 AGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGATATTTTGAAAAATAATGAGAAAA ** * 938984 CGATTTCCATAGTTTCACATTTTATCTTTTCAAAAATGAAATTGTTGAAAAGTAAGAAAACGATT 66 CGATTTCCATAGTTTCACATTCAATCTATTCAAAAATGAAATTGTTGAAAAGTAAGAAAACGATT * * * * 939049 TTCTTAGTTTTTTTACTTAGTAAACTATTTCCAAC 131 TCCATAGTTATCTTACTTAGTAAACTATTTCCAAC * 939084 AGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTTGAAAAATAATGAGAAAA 1 AGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGATATTTTGAAAAATAATGAGAAAA * * * 939149 CGATTTTCATAGTTTCTCATTCAATCTATTCTGAAAATGAAATTGTTGAAAAGTAAGAAAACGAT 66 CGATTTCCATAGTTTCACATTCAATCTATTC-AAAAATGAAATTGTTGAAAAGTAAGAAAACGAT 939214 TTCCATAG-TATCTTACTTAGTAAACTATTTCC 130 TTCCATAGTTATCTTACTTAGTAAACTATTTCC 939246 CACATCCATA Statistics Matches: 149, Mismatches: 12, Indels: 2 0.91 0.07 0.01 Matches are distributed among these distances: 165 111 0.74 166 38 0.26 ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36 Consensus pattern (165 bp): AGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGATATTTTGAAAAATAATGAGAAAA CGATTTCCATAGTTTCACATTCAATCTATTCAAAAATGAAATTGTTGAAAAGTAAGAAAACGATT TCCATAGTTATCTTACTTAGTAAACTATTTCCAAC Found at i:939412 original size:72 final size:72 Alignment explanation

Indices: 939288--940060 Score: 1365 Period size: 72 Copynumber: 10.8 Consensus size: 72 939278 TCAAATAAAA 939288 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA 1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA 939353 ACAGAAC 66 ACAGAAC * * * 939360 TTTATCTCACTTGATATTGTTTTTCTTAAAACAAATTTGTCTCTCTTAAGACAGTTTCACTCGAA 1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA 939425 ACAGAAC 66 ACAGAAC * * 939432 --T-T-TCACTTGAGATTGTTTTTATTAAAACAAATTTGTCTCGCTTAAGACAGTTTCACTCGAA 1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA 939493 ACAGAAC 66 ACAGAAC * * 939500 TTTATCTCACTTGAGATTGTTTTGCTTAAAACAAATTTGTCTCGCTTAAGACAGTTTCACTCGAA 1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA 939565 ACAGAAC 66 ACAGAAC * 939572 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAATTTTGTCTCGCTTGAGACAGTTTCACTCGAA 1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA 939637 ACAGAAC 66 ACAGAAC 939644 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA 1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA 939709 ACAGAAC 66 ACAGAAC * * 939716 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCCCTTAAGACAGTTTCACTCGAA 1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA 939781 ACAGAAC 66 ACAGAAC * 939788 TTTATCTCACTTGAGATTGTTTTTGTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA 1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA 939853 ACAGAAC 66 ACAGAAC * 939860 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTAAGACAGTTTCACTCGAA 1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA 939925 ACAGAAC 66 ACAGAAC * * 939932 TTTATCTCACTTGATATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGATAGTTTCACTCGAA 1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA * 939997 ACACAAC 66 ACAGAAC * 940004 TTTATCTCACTTGAGATTGTTTTTCTTAAAAAAAATTTTGTCTCGCTTGAGACAGTT 1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-TTTGTCTCGCTTGAGACAGTT 940061 ATTTCGAGTT Statistics Matches: 670, Mismatches: 26, Indels: 9 0.95 0.04 0.01 Matches are distributed among these distances: 68 63 0.09 69 1 0.00 70 2 0.00 71 1 0.00 72 583 0.87 73 20 0.03 ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39 Consensus pattern (72 bp): TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA ACAGAAC Found at i:940495 original size:3 final size:3 Alignment explanation

Indices: 940487--940549 Score: 71 Period size: 3 Copynumber: 22.0 Consensus size: 3 940477 TTCCATTTTG * 940487 TTA TTA TTA TTA TTA TTA ATA TTA -TA TATA TTA TTA -TA TTA -TA 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA * 940530 TTA TTA TTA -AA TTA TTA TTA 1 TTA TTA TTA TTA TTA TTA TTA 940550 CAAACAGGCC Statistics Matches: 51, Mismatches: 4, Indels: 10 0.78 0.06 0.15 Matches are distributed among these distances: 2 7 0.14 3 41 0.80 4 3 0.06 ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60 Consensus pattern (3 bp): TTA Found at i:940523 original size:24 final size:25 Alignment explanation

Indices: 940488--940549 Score: 81 Period size: 25 Copynumber: 2.4 Consensus size: 25 940478 TCCATTTTGT * 940488 TATTATTATTATTATTAATATTATATA 1 TATTATTATTATTA-TATTATTAT-TA 940515 TATTATTA-TATTATATTATTATTA 1 TATTATTATTATTATATTATTATTA * 940539 AATTATTATTA 1 TATTATTATTA 940550 CAAACAGGCC Statistics Matches: 32, Mismatches: 2, Indels: 4 0.84 0.05 0.11 Matches are distributed among these distances: 24 9 0.28 25 10 0.31 26 5 0.16 27 8 0.25 ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60 Consensus pattern (25 bp): TATTATTATTATTATATTATTATTA Found at i:957279 original size:16 final size:15 Alignment explanation

Indices: 957249--957284 Score: 54 Period size: 16 Copynumber: 2.3 Consensus size: 15 957239 CAAATACACC * 957249 AAATTAGTAATTAGT 1 AAATTAATAATTAGT 957264 AAATTAATAGATTAGT 1 AAATTAATA-ATTAGT 957280 AAATT 1 AAATT 957285 GGTGGTAATT Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 15 8 0.42 16 11 0.58 ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39 Consensus pattern (15 bp): AAATTAATAATTAGT Found at i:964557 original size:21 final size:21 Alignment explanation

Indices: 964531--964576 Score: 74 Period size: 21 Copynumber: 2.2 Consensus size: 21 964521 CAATTAAGTA * 964531 ATATCTCGAAATCGAATCTTT 1 ATATCTCGAAATCGAATATTT * 964552 ATATCTCGAATTCGAATATTT 1 ATATCTCGAAATCGAATATTT 964573 ATAT 1 ATAT 964577 ATATGTAAAA Statistics Matches: 23, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 21 23 1.00 ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41 Consensus pattern (21 bp): ATATCTCGAAATCGAATATTT Found at i:969550 original size:2 final size:2 Alignment explanation

Indices: 969543--969570 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 969533 TTTAAGGTGC 969543 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 969571 TAACAACACA Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:969949 original size:20 final size:20 Alignment explanation

Indices: 969924--969974 Score: 59 Period size: 21 Copynumber: 2.5 Consensus size: 20 969914 AAGCATGGAA * 969924 TATCGATACCATGTTA-AGGG 1 TATCGATACCA-ATTATAGGG * 969944 TATCGATACTCAATTATATGG 1 TATCGATAC-CAATTATAGGG 969965 TATCGATACC 1 TATCGATACC 969975 CTTGGTCAGT Statistics Matches: 27, Mismatches: 2, Indels: 4 0.82 0.06 0.12 Matches are distributed among these distances: 20 13 0.48 21 14 0.52 ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33 Consensus pattern (20 bp): TATCGATACCAATTATAGGG Found at i:974140 original size:19 final size:19 Alignment explanation

Indices: 974083--974140 Score: 52 Period size: 19 Copynumber: 3.2 Consensus size: 19 974073 TAATAATGTG * * 974083 CTTTTGTCTGTTAGGTTAA 1 CTTTTGTATGTTAGGTTTA * 974102 CTTTTTGTA--TT--GTATA 1 C-TTTTGTATGTTAGGTTTA 974118 CTTTTGTATGTTAGGTTTA 1 CTTTTGTATGTTAGGTTTA 974137 CTTT 1 CTTT 974141 ACTGATTCAT Statistics Matches: 30, Mismatches: 4, Indels: 10 0.68 0.09 0.23 Matches are distributed among these distances: 15 7 0.23 16 4 0.13 17 2 0.07 18 2 0.07 19 9 0.30 20 6 0.20 ACGTcount: A:0.16, C:0.09, G:0.17, T:0.59 Consensus pattern (19 bp): CTTTTGTATGTTAGGTTTA Found at i:974365 original size:16 final size:16 Alignment explanation

Indices: 974344--974381 Score: 76 Period size: 16 Copynumber: 2.4 Consensus size: 16 974334 TTTGTATTAT 974344 AATATGCGTTTATAAA 1 AATATGCGTTTATAAA 974360 AATATGCGTTTATAAA 1 AATATGCGTTTATAAA 974376 AATATG 1 AATATG 974382 TATTAAAATA Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 22 1.00 ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37 Consensus pattern (16 bp): AATATGCGTTTATAAA Found at i:974456 original size:15 final size:16 Alignment explanation

Indices: 974438--974476 Score: 62 Period size: 15 Copynumber: 2.4 Consensus size: 16 974428 TAGATTGATA 974438 TGATTTAGGGTTTA-T 1 TGATTTAGGGTTTACT 974453 TGATTTAGGGTTTACT 1 TGATTTAGGGTTTACT 974469 TGTATTTA 1 TG-ATTTA 974477 AATATTATAG Statistics Matches: 22, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 15 14 0.64 16 3 0.14 17 5 0.23 ACGTcount: A:0.21, C:0.03, G:0.23, T:0.54 Consensus pattern (16 bp): TGATTTAGGGTTTACT Found at i:975486 original size:93 final size:96 Alignment explanation

Indices: 975323--975549 Score: 277 Period size: 93 Copynumber: 2.4 Consensus size: 96 975313 GATTCAATCA * * * * * * 975323 GTATCGATACC-GAGGA-GGTAGTATCGATACCATGATAAGGGGTATCGATACCAAGCAATATCG 1 GTATCGATACCATAGTATGGTAGTATCAATACCATGGTAAGGGGTATCAATACCAAGCAACATCG * 975386 AATCTAATTTTGGTATCGATACCGG-AAGGG 66 AACCTAATTTTGGTATCGATACCGGAAAGGG * * 975416 GTATC-ATACCATAGTATGGTAGCATCAATACCATGGTAA-GGGTATCAATACC-AGATAACATC 1 GTATCGATACCATAGTATGGTAGTATCAATACCATGGTAAGGGGTATCAATACCAAG-CAACATC 975478 GAACCTAATTTTGGTATCGATACCGGATAAGGG 65 GAACCTAATTTTGGTATCGATACCGGA-AAGGG * * * * 975511 GTATCGTTACCATAGTATAGAAGTATCAATACCAGGGTA 1 GTATCGATACCATAGTATGGTAGTATCAATACCATGGTA 975550 GTAGTATCGT Statistics Matches: 114, Mismatches: 14, Indels: 9 0.83 0.10 0.07 Matches are distributed among these distances: 92 7 0.06 93 50 0.44 94 19 0.17 95 10 0.09 96 28 0.25 ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26 Consensus pattern (96 bp): GTATCGATACCATAGTATGGTAGTATCAATACCATGGTAAGGGGTATCAATACCAAGCAACATCG AACCTAATTTTGGTATCGATACCGGAAAGGG Found at i:975957 original size:55 final size:55 Alignment explanation

Indices: 975873--976249 Score: 603 Period size: 55 Copynumber: 6.9 Consensus size: 55 975863 TGTGTACTAT 975873 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC 1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC ** * 975928 AGGCACTTCGTGTGCATATTCATAGAATTCATCATGAGTTAATGAATCACCGTAC 1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC 975983 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC 1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC * * 976038 AGGCACTTCGTGTGCATATTCATGGAATTCATCATGAGTTGATGAATCACCTTAC 1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC * * * 976093 AAGCACTTCGTGTGCATATTCACGGAATTTATCATGATTTGATGAATCACCGTAC 1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC * * 976148 AGGCACTTCGTGTGCATATTCACAGAATTCATCATGAGTTGATGAATCACCGTAT 1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC ** * * * 976203 AAACACCTT-GTGTGCAAATCCACGGATTTCATCATGAGTTGATGAAT 1 AGGCA-CTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAAT 976250 TTTTGTATGG Statistics Matches: 297, Mismatches: 24, Indels: 2 0.92 0.07 0.01 Matches are distributed among these distances: 55 294 0.99 56 3 0.01 ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31 Consensus pattern (55 bp): AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC Found at i:982584 original size:94 final size:95 Alignment explanation

Indices: 982391--982588 Score: 267 Period size: 94 Copynumber: 2.1 Consensus size: 95 982381 TGATTCAATT * * 982391 AGTATCGATACCATGATAAGGGTTATCGATACCAAGCAATATCGAATCTAATTTTGGTATCGATA 1 AGTATCGATACCATGATAAGGGTTATCGATACCAAGCAACATCGAACCTAATTTTGGTATCGATA * * * * 982456 CCTGAAGAGGTATCGGTACCATAGTATGGT 66 CCGGAAGAGGTATCAGTACCATAGTATAGA * * 982486 AGTATCGATACCATGGTAAGGG-TATCGATACC-AGACAACATCGAACCTAATTTTGGTATTGAT 1 AGTATCGATACCATGATAAGGGTTATCGATACCAAG-CAACATCGAACCTAATTTTGGTATCGAT * * 982549 ACCGGATGGGGGTATCAGTACCATAG-ATAGA 65 ACCGGA-AGAGGTATCAGTACCATAGTATAGA 982580 AGTATCGAT 1 AGTATCGAT 982589 GATACCAGGA Statistics Matches: 91, Mismatches: 10, Indels: 5 0.86 0.09 0.05 Matches are distributed among these distances: 93 2 0.02 94 52 0.57 95 37 0.41 ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28 Consensus pattern (95 bp): AGTATCGATACCATGATAAGGGTTATCGATACCAAGCAACATCGAACCTAATTTTGGTATCGATA CCGGAAGAGGTATCAGTACCATAGTATAGA Found at i:982672 original size:29 final size:29 Alignment explanation

Indices: 982625--982690 Score: 105 Period size: 29 Copynumber: 2.3 Consensus size: 29 982615 ATGGAGCCAA 982625 AATGTTAAAATAGACTGATATTGGTATAG 1 AATGTTAAAATAGACTGATATTGGTATAG ** 982654 AATGTTAAAATAGGTTGATATTGGTATAG 1 AATGTTAAAATAGACTGATATTGGTATAG * 982683 AAAGTTAA 1 AATGTTAA 982691 TGATGCGTTC Statistics Matches: 34, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 29 34 1.00 ACGTcount: A:0.42, C:0.02, G:0.21, T:0.35 Consensus pattern (29 bp): AATGTTAAAATAGACTGATATTGGTATAG Found at i:983057 original size:55 final size:55 Alignment explanation

Indices: 982971--983347 Score: 495 Period size: 55 Copynumber: 6.9 Consensus size: 55 982961 TGTGTTCTAT * * 982971 AGGCACTTCGTGTGCATATTCATGGAATTCATCATGAGTTGATGAATTACCGTAC 1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC * * ** * 983026 AAGCACTTCGTGTGTATATTCATAGAATTCATCATGAGTTGATGAATCACCGTAT 1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC * * * 983081 TGGCACTTCGTGTGCATATTCACAGAATTCATCATGAGTTGATGAATCAACGTAC 1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC * * * 983136 AGGCACTTCGTGTGCATATTCACGGAATTTATCATGAGTTGATGGATCATCGTAC 1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC * * 983191 AAGCACTTCGTGTACATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC 1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC * * * * 983246 ATGAACTTCATGTGCATATTCACGGAATTCAACATGAGTTGATGAATCACCGTAC 1 AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC * * * * * * * * 983301 GGGCACCTT-GTGTGTAAATCCATGGATTTTATCATAAGTTGATGAAT 1 AGGCA-CTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAAT 983348 TTCTATATAG Statistics Matches: 283, Mismatches: 38, Indels: 2 0.88 0.12 0.01 Matches are distributed among these distances: 55 280 0.99 56 3 0.01 ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32 Consensus pattern (55 bp): AGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC Found at i:984550 original size:21 final size:21 Alignment explanation

Indices: 984524--984573 Score: 66 Period size: 21 Copynumber: 2.4 Consensus size: 21 984514 CAAGATGAAC * 984524 AAGTAGAGGAT-AAGCAAGTTG 1 AAGTAGAAGATGAA-CAAGTTG 984545 AAGTAGAAGATGAACAAGTTG 1 AAGTAGAAGATGAACAAGTTG * 984566 AAGAAGAA 1 AAGTAGAA 984574 TAAGATGTAA Statistics Matches: 26, Mismatches: 2, Indels: 2 0.87 0.07 0.07 Matches are distributed among these distances: 21 24 0.92 22 2 0.08 ACGTcount: A:0.50, C:0.04, G:0.30, T:0.16 Consensus pattern (21 bp): AAGTAGAAGATGAACAAGTTG Found at i:984863 original size:3 final size:3 Alignment explanation

Indices: 984857--984900 Score: 61 Period size: 3 Copynumber: 14.7 Consensus size: 3 984847 GTTTATTTTT ** * 984857 TTA TTA TTA AAA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TT 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT 984901 TAAATAAATA Statistics Matches: 35, Mismatches: 6, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 3 35 1.00 ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61 Consensus pattern (3 bp): TTA Found at i:984880 original size:18 final size:18 Alignment explanation

Indices: 984857--984905 Score: 80 Period size: 18 Copynumber: 2.7 Consensus size: 18 984847 GTTTATTTTT 984857 TTATTATTAAAATTATTA 1 TTATTATTAAAATTATTA * 984875 TTATTATTATAATTATTA 1 TTATTATTAAAATTATTA * 984893 TTATTATTTAAAT 1 TTATTATTAAAAT 984906 AAATATTATA Statistics Matches: 28, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 18 28 1.00 ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59 Consensus pattern (18 bp): TTATTATTAAAATTATTA Found at i:986467 original size:3 final size:3 Alignment explanation

Indices: 986459--986494 Score: 63 Period size: 3 Copynumber: 12.0 Consensus size: 3 986449 ATTTATTTAT * 986459 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA 986495 CAAATATATA Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 3 31 1.00 ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64 Consensus pattern (3 bp): TTA Found at i:986688 original size:23 final size:22 Alignment explanation

Indices: 986658--986716 Score: 68 Period size: 21 Copynumber: 2.6 Consensus size: 22 986648 CATTTTCTGA 986658 TATTTTTAAATAAATAAATAT-TT 1 TATTTTT-AATAAAT-AATATCTT * 986681 TATTTTT-ATAAATTATATCTT 1 TATTTTTAATAAATAATATCTT 986702 TATTTTTAGATAAAT 1 TATTTTTA-ATAAAT 986717 GTTTTATTAA Statistics Matches: 32, Mismatches: 1, Indels: 6 0.82 0.03 0.15 Matches are distributed among these distances: 20 4 0.12 21 15 0.47 23 13 0.41 ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56 Consensus pattern (22 bp): TATTTTTAATAAATAATATCTT Found at i:987167 original size:12 final size:12 Alignment explanation

Indices: 987146--987180 Score: 63 Period size: 12 Copynumber: 3.0 Consensus size: 12 987136 GGCGACTCCC 987146 AAAA-CATTTTA 1 AAAATCATTTTA 987157 AAAATCATTTTA 1 AAAATCATTTTA 987169 AAAATCATTTTA 1 AAAATCATTTTA 987181 TCCACATTAC Statistics Matches: 23, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 11 4 0.17 12 19 0.83 ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40 Consensus pattern (12 bp): AAAATCATTTTA Found at i:989616 original size:22 final size:22 Alignment explanation

Indices: 989562--989650 Score: 144 Period size: 22 Copynumber: 4.1 Consensus size: 22 989552 TACATCTACA * 989562 CTCTTCAAAGATGATAGATTCT 1 CTCTCCAAAGATGATAGATTCT * 989584 ATCT-CAAAGATGATAGATTCT 1 CTCTCCAAAGATGATAGATTCT 989605 CTCTCCAAAGATGATAGATTCT 1 CTCTCCAAAGATGATAGATTCT * 989627 CTCTCCAAAGATGATAAATTCT 1 CTCTCCAAAGATGATAGATTCT 989649 CT 1 CT 989651 TTTTCAAATA Statistics Matches: 63, Mismatches: 3, Indels: 2 0.93 0.04 0.03 Matches are distributed among these distances: 21 20 0.32 22 43 0.68 ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34 Consensus pattern (22 bp): CTCTCCAAAGATGATAGATTCT Found at i:990490 original size:92 final size:92 Alignment explanation

Indices: 990327--991399 Score: 1592 Period size: 92 Copynumber: 11.7 Consensus size: 92 990317 CTATTTCCTA * * * 990327 CATCTGTAAGTCCTTTAGTGCATGATATTTTC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT * * 990391 GCATGATGTTTTCAAAAACCTTTGGGT 66 GCTTGATGTTTTCAAAAACCTTCGGGT * * 990418 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT * 990483 GCTTGATGTTTTCAAAAACTTTCGGGT 66 GCTTGATGTTTTCAAAAACCTTCGGGT * * * * 990510 CATCTGTAAGCCCTTCAGTGCTTAATGTTTTC-AAAACCTTTGGGTCATCTGTAAGTCCTTTAGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT * 990574 TCTTGATGTTTTTCAAAAACCTTCGGGT 66 GCTTGATG-TTTTCAAAAACCTTCGGGT * * * 990602 CATTTGTAAGTCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGTTATCTGTAAGTCATTCAGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT 990666 GCTTGATGTTTATCAAAAACCTTCGGGT 66 GCTTGATGTTT-TCAAAAACCTTCGGGT * * 990694 CA--TATAAGTCCTTCAGTGCTTGATGTTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAA 1 CATCTGTAAGTCCTTCAGTGCTTGATG-TTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAG 990757 TGCTTGATGTTTTTCAAAAACCTTCGGGT 65 TGCTTGATG-TTTTCAAAAACCTTCGGGT * 990786 CATCTATAAGTCCTTCAGTGCTTGATGTTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAG 1 CATCTGTAAGTCCTTCAGTGCTTGATG-TTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAG * 990851 TTCTTGATGTTTTTCAAAAACCTTCGGGT 65 TGCTTGATG-TTTTCAAAAACCTTCGGGT * 990880 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAG 1 CATCTGTAAGTCCTTCAGTGCTTGATG-TTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAG ** 990945 TGCTTGATGTTTTC-AAAACCTTTAGGT 65 TGCTTGATGTTTTCAAAAACCTTCGGGT * * 990972 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTTCAAAAACCTTCGGGTCATCTGTAAGTCTTTCAG 1 CATCTGTAAGTCCTTCAGTGCTTGATG-TTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAG * 991037 TGCTTGATGTTTTTAAAAACCTTCGGGT 65 TGCTTGATGTTTTCAAAAACCTTCGGGT * 991065 CATCTATAAGTCCTTCAGTGCTTGATGTTTTCAAAAA-CTTCGGGTCATCTGTAAGTCCTTCAGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT * 991129 GCTTGATGTTTTTCAAAAACCTTTGGGT 66 GCTTGATG-TTTTCAAAAACCTTCGGGT * * * * 991157 TATCTGTAAGCCCTTCAGTGTTTGATGTTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAG 1 CATCTGTAAGTCCTTCAGTGCTTGATG-TTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAG * * 991222 TGTTTGATGTTTTC-AAAACCTTCAGGT 65 TGCTTGATGTTTTCAAAAACCTTCGGGT * * ** 991249 CATCTATAAGTCCTTCAGTGCTTGATGCTTTCAAAAACCTTCGGGTCATCTGTAACCCCTTCAGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT * 991314 GTTTGATGTTTTCAAAAACCTTC-GGT 66 GCTTGATGTTTTCAAAAACCTTCGGGT * ** * 991340 CATATGTAAGTCCTTCAGTGCACGATGTTTTC-AAAACCTTCGGGTCATTTGTAAG-CCTTC 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTC 991400 CGAGCAAGAT Statistics Matches: 904, Mismatches: 65, Indels: 28 0.91 0.07 0.03 Matches are distributed among these distances: 89 5 0.01 90 43 0.05 91 187 0.21 92 418 0.46 93 59 0.07 94 192 0.21 ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38 Consensus pattern (92 bp): CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT GCTTGATGTTTTCAAAAACCTTCGGGT Found at i:990610 original size:47 final size:46 Alignment explanation

Indices: 990327--991399 Score: 1592 Period size: 47 Copynumber: 23.3 Consensus size: 46 990317 CTATTTCCTA * * * 990327 CATCTGTAAGTCCTTTAGTGCATGATATTTTC-AAAACCTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT * * 990372 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTTGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT * 990418 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT * * 990464 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACTTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT * * * 990510 CATCTGTAAGCCCTTCAGTGCTTAATGTTTTC-AAAACCTTTGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT * * 990555 CATCTGTAAGTCCTTTAGTTCTTGATGTTTTTCAAAAACCTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATG-TTTTCAAAAACCTTCGGGT * 990602 CATTTGTAAGTCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT * * 990647 TATCTGTAAGTCATTCAGTGCTTGATGTTTATCAAAAACCTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTT-TCAAAAACCTTCGGGT * 990694 CA--TATAAGTCCTTCAGTGCTTGATGTTTTTCAAAAACCTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATG-TTTTCAAAAACCTTCGGGT * 990739 CATCTGTAAGTCCTTCAATGCTTGATGTTTTTCAAAAACCTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATG-TTTTCAAAAACCTTCGGGT * 990786 CATCTATAAGTCCTTCAGTGCTTGATGTTTTTCAAAAACCTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATG-TTTTCAAAAACCTTCGGGT * 990833 CATCTGTAAGTCCTTCAGTTCTTGATGTTTTTCAAAAACCTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATG-TTTTCAAAAACCTTCGGGT 990880 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTTCAAAAACCTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATG-TTTTCAAAAACCTTCGGGT * ** 990927 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTTAGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT * 990972 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTTCAAAAACCTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATG-TTTTCAAAAACCTTCGGGT * * 991019 CATCTGTAAGTCTTTCAGTGCTTGATGTTTTTAAAAACCTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT * 991065 CATCTATAAGTCCTTCAGTGCTTGATGTTTTCAAAAA-CTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT * 991110 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTTCAAAAACCTTTGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATG-TTTTCAAAAACCTTCGGGT * * * 991157 TATCTGTAAGCCCTTCAGTGTTTGATGTTTTTCAAAAACCTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATG-TTTTCAAAAACCTTCGGGT * * * 991204 CATCTGTAAGCCCTTCAGTGTTTGATGTTTTC-AAAACCTTCAGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT * * 991249 CATCTATAAGTCCTTCAGTGCTTGATGCTTTCAAAAACCTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT ** * 991295 CATCTGTAACCCCTTCAGTGTTTGATGTTTTCAAAAACCTTC-GGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT * ** 991340 CATATGTAAGTCCTTCAGTGCACGATGTTTTC-AAAACCTTCGGGT 1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT * 991385 CATTTGTAAG-CCTTC 1 CATCTGTAAGTCCTTC 991400 CGAGCAAGAT Statistics Matches: 947, Mismatches: 67, Indels: 29 0.91 0.06 0.03 Matches are distributed among these distances: 44 14 0.01 45 296 0.31 46 272 0.29 47 365 0.39 ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38 Consensus pattern (46 bp): CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT Found at i:991594 original size:3 final size:3 Alignment explanation

Indices: 991588--991649 Score: 79 Period size: 3 Copynumber: 20.7 Consensus size: 3 991578 TTCATTTTTT ** * * * 991588 TTA TTA TTA AAA TTA TTA TTA TTA TTA CTA TAA ATA TTA TTA TTA TTA 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA 991636 TTA TTA TTA TTA TT 1 TTA TTA TTA TTA TT 991650 TAAATAAATA Statistics Matches: 49, Mismatches: 10, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 3 49 1.00 ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60 Consensus pattern (3 bp): TTA Found at i:996294 original size:18 final size:18 Alignment explanation

Indices: 996273--996320 Score: 51 Period size: 18 Copynumber: 2.6 Consensus size: 18 996263 CGACCTGATT * * 996273 CGACCCACCTTCCTGACC 1 CGACCCACCTGCCTAACC * * 996291 CGACCCTCATGCCTAACC 1 CGACCCACCTGCCTAACC 996309 CGACCCGACCTG 1 CGACCC-ACCTG 996321 ATCTGAACCG Statistics Matches: 23, Mismatches: 6, Indels: 1 0.77 0.20 0.03 Matches are distributed among these distances: 18 20 0.87 19 3 0.13 ACGTcount: A:0.19, C:0.52, G:0.15, T:0.15 Consensus pattern (18 bp): CGACCCACCTGCCTAACC Found at i:1014747 original size:22 final size:23 Alignment explanation

Indices: 1014701--1014750 Score: 93 Period size: 23 Copynumber: 2.2 Consensus size: 23 1014691 CGATTCCCCT 1014701 GGGGGAATCGGTTCCCCTTCAAA 1 GGGGGAATCGGTTCCCCTTCAAA 1014724 GGGGGAATCGGTTCCCCTTC-AA 1 GGGGGAATCGGTTCCCCTTCAAA 1014746 GGGGG 1 GGGGG 1014751 TGTCGATTCC Statistics Matches: 27, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 22 7 0.26 23 20 0.74 ACGTcount: A:0.18, C:0.24, G:0.38, T:0.20 Consensus pattern (23 bp): GGGGGAATCGGTTCCCCTTCAAA Found at i:1014760 original size:22 final size:23 Alignment explanation

Indices: 1014701--1014761 Score: 79 Period size: 23 Copynumber: 2.7 Consensus size: 23 1014691 CGATTCCCCT * 1014701 GGGGGAATCGGTTCCCCTTCAAA 1 GGGGGAATCGATTCCCCTTCAAA * 1014724 GGGGGAATCGGTTCCCCTTC-AA 1 GGGGGAATCGATTCCCCTTCAAA ** 1014746 GGGGGTGTCGATTCCC 1 GGGGGAATCGATTCCC 1014762 TCTGCCCTAT Statistics Matches: 35, Mismatches: 3, Indels: 1 0.90 0.08 0.03 Matches are distributed among these distances: 22 15 0.43 23 20 0.57 ACGTcount: A:0.16, C:0.26, G:0.34, T:0.23 Consensus pattern (23 bp): GGGGGAATCGATTCCCCTTCAAA Found at i:1024749 original size:41 final size:40 Alignment explanation

Indices: 1024703--1024861 Score: 210 Period size: 42 Copynumber: 3.9 Consensus size: 40 1024693 GAGCCTAGGA * 1024703 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGG 1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGG-ACCTGG * * 1024744 AAACTGTAAGGATTACCTTTGCACACAGCAAATGTACCTGAG 1 AAACTGTAAGGCTTACCTTTGCACACAGCAAA-GGACCTG-G * 1024786 AAACTGTAAGGCTTACCTTTGCACACAGTAAACGGACCTGGG 1 AAACTGTAAGGCTTACCTTTGCACACAGCAAA-GGACCT-GG * * * 1024828 AAACTATAAGGCTTTCCTTTGCACATAGCAAAGG 1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGG 1024862 GACTTGAGAA Statistics Matches: 104, Mismatches: 11, Indels: 6 0.86 0.09 0.05 Matches are distributed among these distances: 41 37 0.36 42 66 0.63 43 1 0.01 ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22 Consensus pattern (40 bp): AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGACCTGG Found at i:1025849 original size:29 final size:29 Alignment explanation

Indices: 1025807--1025891 Score: 107 Period size: 29 Copynumber: 2.9 Consensus size: 29 1025797 TATCACCCTT ** 1025807 TTTTAAAAATATTTACGAATTTAACACCC 1 TTTTAAAAATATTTACGAAACTAACACCC * * * 1025836 TTTTAAAATTATTTATGAAACTAGCACCC 1 TTTTAAAAATATTTACGAAACTAACACCC * * 1025865 TTTTAAAAATAATTACAAAACTAACAC 1 TTTTAAAAATATTTACGAAACTAACAC 1025892 ACGGTCAACA Statistics Matches: 46, Mismatches: 10, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 29 46 1.00 ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35 Consensus pattern (29 bp): TTTTAAAAATATTTACGAAACTAACACCC Found at i:1032091 original size:42 final size:42 Alignment explanation

Indices: 1031949--1032152 Score: 250 Period size: 42 Copynumber: 4.8 Consensus size: 42 1031939 CAGTACACCA * * * * 1031949 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT 1 GTAAGGCTT-ACCTTTGCACACAGCAAAGGGA-CCT-GGGAAACT * * * 1031993 GTAAGGCTTACCCTTGCACATAGCAAAGGAACCT-GGAAACT 1 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACT * 1032034 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAATCT 1 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACT * * 1032076 GTAAGGCTTACCTTTGTACACAGCAAAGGGACCTGGGAAAAT 1 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACT * * * 1032118 GTAAGGCTTACCTTTGCAGACAACAAAGAGACCTG 1 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTG 1032153 AGAATAGTTC Statistics Matches: 141, Mismatches: 17, Indels: 6 0.86 0.10 0.04 Matches are distributed among these distances: 41 37 0.26 42 76 0.54 43 17 0.12 44 11 0.08 ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20 Consensus pattern (42 bp): GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACT Found at i:1033136 original size:29 final size:29 Alignment explanation

Indices: 1033088--1033180 Score: 152 Period size: 29 Copynumber: 3.2 Consensus size: 29 1033078 ACACAATTAT * 1033088 CACCCTTTTTAAAAATATTTACCAAACTAA 1 CACCC-TTTTAAAAATATTTACAAAACTAA 1033118 CACCCTTTTAAAAATATTTACAAAACTAA 1 CACCCTTTTAAAAATATTTACAAAACTAA 1033147 CACCCTTTTAAAAAT-TATTACAAAACTAA 1 CACCCTTTTAAAAATAT-TTACAAAACTAA 1033176 CACCC 1 CACCC 1033181 AGTCAACGGT Statistics Matches: 61, Mismatches: 1, Indels: 3 0.94 0.02 0.05 Matches are distributed among these distances: 28 1 0.02 29 55 0.90 30 5 0.08 ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30 Consensus pattern (29 bp): CACCCTTTTAAAAATATTTACAAAACTAA Found at i:1034109 original size:95 final size:95 Alignment explanation

Indices: 1033987--1034177 Score: 355 Period size: 95 Copynumber: 2.0 Consensus size: 95 1033977 CCTTCGGGAC 1033987 AAATTCACATGCCCCTAGTGGAACCTTATAAGAGCTGTGGTGACAACATATGTGCACAACCTCTA 1 AAATTCACATGCCCCTAGTGGAACCTTATAAGAGCTGTGGTGACAACATATGTGCACAACCTCTA * 1034052 TGTACTCACATATCTTTAGTTCTCACATGT 66 TGTACTCACATATCTTTAGTTATCACATGT * * 1034082 AAATTCACATGCCCCTAGTGGGACCTTATACGAGCTGTGGTGACAACATATGTGCACAACCTCTA 1 AAATTCACATGCCCCTAGTGGAACCTTATAAGAGCTGTGGTGACAACATATGTGCACAACCTCTA 1034147 TGTACTCACATATCTTTAGTTATCACATGT 66 TGTACTCACATATCTTTAGTTATCACATGT 1034177 A 1 A 1034178 TACATGGGCT Statistics Matches: 93, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 95 93 1.00 ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30 Consensus pattern (95 bp): AAATTCACATGCCCCTAGTGGAACCTTATAAGAGCTGTGGTGACAACATATGTGCACAACCTCTA TGTACTCACATATCTTTAGTTATCACATGT Found at i:1035185 original size:18 final size:19 Alignment explanation

Indices: 1035139--1035203 Score: 55 Period size: 18 Copynumber: 3.6 Consensus size: 19 1035129 TACACCAACG ** 1035139 ACCTCAACAA-ACTCAGTG 1 ACCTCAACAACACTCAGCA * 1035157 ACCTCGACAACA-TCAGCA 1 ACCTCAACAACACTCAGCA * 1035175 ACCTCAACAAC-CTTAGCA 1 ACCTCAACAACACTCAGCA * * 1035193 TCCACAACAAC 1 ACCTCAACAAC 1035204 CACACCGGTC Statistics Matches: 38, Mismatches: 7, Indels: 4 0.78 0.14 0.08 Matches are distributed among these distances: 18 37 0.97 19 1 0.03 ACGTcount: A:0.40, C:0.38, G:0.08, T:0.14 Consensus pattern (19 bp): ACCTCAACAACACTCAGCA Found at i:1035932 original size:40 final size:40 Alignment explanation

Indices: 1035876--1035967 Score: 114 Period size: 40 Copynumber: 2.3 Consensus size: 40 1035866 ACACAAAAAT * * * 1035876 CATATACAAAAACCTTCACCAATTACTAT-CCATCATTACC 1 CATATACAAAAACCTTCAACAATTACT-TCCCACCATTAAC * * * 1035916 CATACACAAAATCCTTCAACGATTACTTCCCACCATTAAC 1 CATATACAAAAACCTTCAACAATTACTTCCCACCATTAAC 1035956 CATATACAAAAA 1 CATATACAAAAA 1035968 ATTACTACCC Statistics Matches: 43, Mismatches: 8, Indels: 2 0.81 0.15 0.04 Matches are distributed among these distances: 39 1 0.02 40 42 0.98 ACGTcount: A:0.42, C:0.32, G:0.01, T:0.25 Consensus pattern (40 bp): CATATACAAAAACCTTCAACAATTACTTCCCACCATTAAC Found at i:1036827 original size:29 final size:28 Alignment explanation

Indices: 1036766--1036827 Score: 72 Period size: 28 Copynumber: 2.2 Consensus size: 28 1036756 AGATCAATTG ** * 1036766 TTTTCTTTTGTTTAAATTTTTCTCTTCT 1 TTTTCTTTTGTTTAAATTTTTCTAATCA 1036794 TTTTCTTTTGTTTTGAAATTTTTC-AATCA 1 TTTTCTTTTG-TTT-AAATTTTTCTAATCA 1036823 TTTTC 1 TTTTC 1036828 GAGATAAAAA Statistics Matches: 29, Mismatches: 3, Indels: 3 0.83 0.09 0.09 Matches are distributed among these distances: 28 10 0.34 29 10 0.34 30 9 0.31 ACGTcount: A:0.15, C:0.13, G:0.05, T:0.68 Consensus pattern (28 bp): TTTTCTTTTGTTTAAATTTTTCTAATCA Found at i:1038172 original size:26 final size:26 Alignment explanation

Indices: 1038141--1038201 Score: 122 Period size: 26 Copynumber: 2.3 Consensus size: 26 1038131 GGTAACCTTT 1038141 TAAAATTTTAGAAAGAGACAAACTTA 1 TAAAATTTTAGAAAGAGACAAACTTA 1038167 TAAAATTTTAGAAAGAGACAAACTTA 1 TAAAATTTTAGAAAGAGACAAACTTA 1038193 TAAAATTTT 1 TAAAATTTT 1038202 TGGGGGGCAA Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 35 1.00 ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31 Consensus pattern (26 bp): TAAAATTTTAGAAAGAGACAAACTTA Found at i:1041033 original size:32 final size:32 Alignment explanation

Indices: 1040983--1041056 Score: 87 Period size: 32 Copynumber: 2.3 Consensus size: 32 1040973 ATTAGAATAG * ** 1040983 TAAAAAAATAAATATTAAATATTATTTAAAA- 1 TAAAAAATTAAATATTAAATATTAAGTAAAAT * 1041014 TAAAAAATTAAAGTTTTAAATATTAAGTAAAAT 1 TAAAAAATTAAA-TATTAAATATTAAGTAAAAT * 1041047 TAGAAAATTA 1 TAAAAAATTA 1041057 TAAAGCATCA Statistics Matches: 36, Mismatches: 5, Indels: 2 0.84 0.12 0.05 Matches are distributed among these distances: 31 11 0.31 32 16 0.44 33 9 0.25 ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35 Consensus pattern (32 bp): TAAAAAATTAAATATTAAATATTAAGTAAAAT Found at i:1043479 original size:20 final size:21 Alignment explanation

Indices: 1043449--1043487 Score: 62 Period size: 20 Copynumber: 1.9 Consensus size: 21 1043439 AAAGTATCCG * 1043449 AAATAATTTGATAATTAAATA 1 AAATAATTTGAAAATTAAATA 1043470 AAAT-ATTTGAAAATTAAA 1 AAATAATTTGAAAATTAAA 1043488 GACAGCATGA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 20 13 0.76 21 4 0.24 ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36 Consensus pattern (21 bp): AAATAATTTGAAAATTAAATA Found at i:1044414 original size:17 final size:17 Alignment explanation

Indices: 1044392--1044436 Score: 51 Period size: 17 Copynumber: 2.8 Consensus size: 17 1044382 TAGGGGTGTG 1044392 TATTATCGGATATCGAA 1 TATTATCGGATATCGAA * * 1044409 TATTATCCGAT-CCGAA 1 TATTATCGGATATCGAA 1044425 -ATT-TCGGATATC 1 TATTATCGGATATC 1044437 CAAAAATTTC Statistics Matches: 23, Mismatches: 4, Indels: 4 0.74 0.13 0.13 Matches are distributed among these distances: 14 5 0.22 15 4 0.17 16 4 0.17 17 10 0.43 ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36 Consensus pattern (17 bp): TATTATCGGATATCGAA Found at i:1044527 original size:21 final size:21 Alignment explanation

Indices: 1044485--1044538 Score: 58 Period size: 21 Copynumber: 2.6 Consensus size: 21 1044475 ATCCGAAAAA * 1044485 ATCGGATATCCGAAATTTCGG 1 ATCGGATATCCGAAATTCCGG * 1044506 ATCGGATATCTG-AATATCCGG 1 ATCGGATATCCGAAAT-TCCGG * 1044527 ATCCGA-ATCCGA 1 ATCGGATATCCGA 1044539 TTTTAGTCCT Statistics Matches: 27, Mismatches: 4, Indels: 4 0.77 0.11 0.11 Matches are distributed among these distances: 20 7 0.26 21 20 0.74 ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26 Consensus pattern (21 bp): ATCGGATATCCGAAATTCCGG Found at i:1062259 original size:233 final size:233 Alignment explanation

Indices: 1061735--1062666 Score: 1075 Period size: 233 Copynumber: 4.1 Consensus size: 233 1061725 TCCAAAATTG * * 1061735 GTAAGTCCTTCGAACATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGAT 1 GTAAGTCATTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGAT * * * * 1061800 AAGTCCTTC-GGCCATCCATAAGA-CTTACGGGCAGGATATTTTCACATG-TTTTCCAAAATGTG 66 AAGTCCTTCAAGCCATCCATAAGACCTT-CGGGCAGGATGTTTTCACATGTTTTTCGAAAA-ATG * 1061862 AGAAATG-TTTCTCATTTACAA-CTGAAAATTGAAATTTTTG--AA--AAGAAAAGTTTATTACC 129 AGAAA-GATTTCTCATTTA-AATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACC * ** * * * 1061921 TAGGAAACTATTTCTGAAAGTGGTAAATCCTTCGGGCCATCA 192 TAGTAAACTATTTCCAAAATTGGTAAGTCCTTCAGGCCATCA * * * * 1061963 ATAAGT-ATTTTGAGCATGATACTTAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAAGATGA 1 GTAAGTCA-TTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGA * * 1062027 AAAGTCCTTCAAGCCATCCATAAGACCTTTGGGCAGGATGTTTTCACATGTTTTTCGAAAAATGA 65 TAAGTCCTTCAAGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGTTTTTCGAAAAATGA * * * 1062092 GAAAGGTTTCTCATTTAAATCTGAAAATAGAAAATTTTGAAAAGTAAGAAAAGTTTCTTACCTAG 130 GAAAGATTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAG * * 1062157 TAAACTATTTCCAAAATTGGCAAGTCCTTCACGCCATCA 195 TAAACTATTTCCAAAATTGGTAAGTCCTTCAGGCCATCA * * * ** 1062196 GTAAGTCATTCGAGCATGATGCTTAAATCTTTCGGGTCATCTATAAGTCTTTCAAAAAAGATGAT 1 GTAAGTCATTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGAT * ** * * * * * 1062261 AAGTCATTCGGGTCATCCATAACACATTCGGGCAGGATGTTTTCACATGTTTTTCAAAAAATAAG 66 AAGTCCTTCAAGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGTTTTTCGAAAAATGAG * * * 1062326 AAAGATTTCTCATTTAAATCTGAAATTTGAAATTTTTGAAAATTAAGAAAAGTTTCTTACTTAGT 131 AAAGATTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGT 1062391 AAACTA-TTCCAAAATTGGTAAGTCCTTCAGGCCATC- 196 AAACTATTTCCAAAATTGGTAAGTCCTTCAGGCCATCA ** * * 1062427 GTAAGTTTTTCAAGCATAATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATG-- 1 GTAAGTCATTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGAT * * * * 1062490 -A-----T-AAG-------T----CCTTCGGGTAGGGTTTTTTCACATGTCTCTT-GAAAAATGA 66 AAGTCCTTCAAGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGT-TTTTCGAAAAATGA * * 1062536 CAAAGATTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAG 130 GAAAGATTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAG * * * 1062601 TAAACTATTTCCAAAATCGGTAAGTCCTTCGGGTCATCA 195 TAAACTATTTCCAAAATTGGTAAGTCCTTCAGGCCATCA * * * 1062640 GTTAGTCTTTCGAGTATGATGCTTAAA 1 GTAAGTCATTCGAGCATGATGCTTAAA 1062667 CTGTAACACC Statistics Matches: 609, Mismatches: 81, Indels: 43 0.83 0.11 0.06 Matches are distributed among these distances: 211 96 0.16 212 30 0.05 213 22 0.04 215 1 0.00 222 1 0.00 223 1 0.00 228 70 0.11 229 67 0.11 230 12 0.02 231 56 0.09 232 28 0.05 233 224 0.37 234 1 0.00 ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33 Consensus pattern (233 bp): GTAAGTCATTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGAT AAGTCCTTCAAGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGTTTTTCGAAAAATGAG AAAGATTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTCTTACCTAGT AAACTATTTCCAAAATTGGTAAGTCCTTCAGGCCATCA Found at i:1062499 original size:41 final size:41 Alignment explanation

Indices: 1062409--1062504 Score: 106 Period size: 41 Copynumber: 2.3 Consensus size: 41 1062399 CCAAAATTGG * * * * 1062409 TAAGTCCTTCAGGCCATCGTAAGTTTTTCAAGCATAATGCT 1 TAAGTCCTTCGGGTCATCGTAAGTCTTTCAAGCATAATGCA * * 1062450 TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCA-AGATG-A 1 TAAGTCCTTCGGGTCATC-GTAAGTCTTTCAAGCATA-ATGCA 1062491 TAAGTCCTTCGGGT 1 TAAGTCCTTCGGGT 1062505 AGGGTTTTTT Statistics Matches: 46, Mismatches: 7, Indels: 4 0.81 0.12 0.07 Matches are distributed among these distances: 41 29 0.63 42 17 0.37 ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33 Consensus pattern (41 bp): TAAGTCCTTCGGGTCATCGTAAGTCTTTCAAGCATAATGCA Found at i:1063423 original size:23 final size:23 Alignment explanation

Indices: 1063397--1063453 Score: 96 Period size: 23 Copynumber: 2.5 Consensus size: 23 1063387 TTCGTATAAA 1063397 TGCACCGAAGTGCCACGTAGAAT 1 TGCACCGAAGTGCCACGTAGAAT * 1063420 TGCACCGAAGTGCCGCGTAGAAT 1 TGCACCGAAGTGCCACGTAGAAT * 1063443 TGCTCCGAAGT 1 TGCACCGAAGT 1063454 TCCATATAAA Statistics Matches: 32, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 23 32 1.00 ACGTcount: A:0.26, C:0.26, G:0.28, T:0.19 Consensus pattern (23 bp): TGCACCGAAGTGCCACGTAGAAT Found at i:1064734 original size:16 final size:17 Alignment explanation

Indices: 1064715--1064749 Score: 54 Period size: 17 Copynumber: 2.1 Consensus size: 17 1064705 AAAACATATC * 1064715 AATACATA-TAATCATG 1 AATACATACAAATCATG 1064731 AATACATACAAATCATG 1 AATACATACAAATCATG 1064748 AA 1 AA 1064750 ATTCACATAC Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 16 8 0.47 17 9 0.53 ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26 Consensus pattern (17 bp): AATACATACAAATCATG Found at i:1065183 original size:64 final size:64 Alignment explanation

Indices: 1065095--1065256 Score: 173 Period size: 64 Copynumber: 2.5 Consensus size: 64 1065085 CCCTTAACAT * * * * * 1065095 GTGCATCGATGCACTACCCATGCATCGATACACAAAGCACCTTCGATGTTT-TAATCTTAAGGGG 1 GTGCATCGATGCACTTCCTATGCATCGATACACAAAGCACATTCGATATTTCCAATCTTAA-GGG * * * ** * * * 1065159 GTGTATCGATGCACTTCCTATGCATCGATGCACTAATTACATTCGATATTTCCATTTTTAATGG 1 GTGCATCGATGCACTTCCTATGCATCGATACACAAAGCACATTCGATATTTCCAATCTTAAGGG * * 1065223 GTGCATCGATGCACTTCTTGTGCATCGATACACA 1 GTGCATCGATGCACTTCCTATGCATCGATACACA 1065257 CTGAAAAATT Statistics Matches: 79, Mismatches: 18, Indels: 2 0.80 0.18 0.02 Matches are distributed among these distances: 64 73 0.92 65 6 0.08 ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32 Consensus pattern (64 bp): GTGCATCGATGCACTTCCTATGCATCGATACACAAAGCACATTCGATATTTCCAATCTTAAGGG Found at i:1066714 original size:135 final size:132 Alignment explanation

Indices: 1066440--1066886 Score: 475 Period size: 137 Copynumber: 3.3 Consensus size: 132 1066430 AAAATCGAAT * * * * * * * 1066440 TCGATTCAATCTTCCTTGGAGAAAAATTGAATGAATTAATGTCCCCATATTTGATATTTCCTTAA 1 TCGATTCAATCTTCCTTGAAGAACAATGGAATGAATCAACGTCCCCATATATGAT-TTTCCCTAA * * * * * * 1066505 GAAAAAA-GGAGCAGATCCCTCTTTTTCCAGATTTGATA-TCCCTTGAGTAATAGTGGAACAAGT 65 AAAAAAAGGGAACAAATCCCT-ATTTTCAAGATTTGATATTCCC-TAAGTAATAGTGGAACAAGT * * 1066568 TTTCC 128 CTACC * 1066573 TCGATTCAATCTTACTTGAAGAACAATGGAATGAATCAACGTCCCCATATATGATTTTCCCTAAA 1 TCGATTCAATCTTCCTTGAAGAACAATGGAATGAATCAACGTCCCCATATATGATTTTCCCTAAA * 1066638 AAAACAAGTGGAACAAATCTCTATCTTTCAAGATTTGATATTCCCTAAGTAATAGTGGAACAAGT 66 AAAA-AAG-GGAACAAATCCCTAT-TTTCAAGATTTGATATTCCCTAAGTAATAGTGGAACAAGT 1066703 CTACC 128 CTACC * * * * * * 1066708 TTGATTCAATCTTCCCTGACGAAACAGTGGAATGAATCAACATCCCCTTAGATATGATTTTCCCT 1 TCGATTCAATCTTCCTTGAAG-AACAATGGAATGAATCAACGTCCCC--ATATATGATTTTCCCT * * ** * * * * * * * 1066773 CAAGATGAAGCGAAACATATCCCTTATTTTCAAGATTTGGTCTTCCCTAAGTAACAATGGAAGAA 63 AAAAAAAAAG-GGAACAAATCCC-TATTTTCAAGATTTGATATTCCCTAAGTAATAGTGGAACAA 1066838 GTCTACC 126 GTCTACC 1066845 TCGATTCAATCTTCCTTGAAGAACAATGGAATGAATCAACGT 1 TCGATTCAATCTTCCTTGAAGAACAATGGAATGAATCAACGT 1066887 TTCTCGATCT Statistics Matches: 263, Mismatches: 42, Indels: 15 0.82 0.13 0.05 Matches are distributed among these distances: 132 12 0.05 133 50 0.19 134 1 0.00 135 63 0.24 136 46 0.17 137 70 0.27 138 21 0.08 ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31 Consensus pattern (132 bp): TCGATTCAATCTTCCTTGAAGAACAATGGAATGAATCAACGTCCCCATATATGATTTTCCCTAAA AAAAAAGGGAACAAATCCCTATTTTCAAGATTTGATATTCCCTAAGTAATAGTGGAACAAGTCTA CC Found at i:1067071 original size:3 final size:3 Alignment explanation

Indices: 1067055--1067123 Score: 59 Period size: 3 Copynumber: 22.7 Consensus size: 3 1067045 TTTGTCTAGG * * * * 1067055 TTA TTA TT- TATA TTA TTA TTA CTA CTA CTA TTA TTA TTA TTG TTA 1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA * * 1067100 ATA TTTA TTA TTG TTA TTA TTA TT 1 TTA -TTA TTA TTA TTA TTA TTA TT 1067124 TAATATATAC Statistics Matches: 55, Mismatches: 8, Indels: 6 0.80 0.12 0.09 Matches are distributed among these distances: 2 1 0.02 3 51 0.93 4 3 0.05 ACGTcount: A:0.30, C:0.04, G:0.03, T:0.62 Consensus pattern (3 bp): TTA Found at i:1067109 original size:16 final size:16 Alignment explanation

Indices: 1067088--1067120 Score: 57 Period size: 16 Copynumber: 2.1 Consensus size: 16 1067078 ACTACTATTA 1067088 TTATTATTGTTAATAT 1 TTATTATTGTTAATAT * 1067104 TTATTATTGTTATTAT 1 TTATTATTGTTAATAT 1067120 T 1 T 1067121 ATTTAATATA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67 Consensus pattern (16 bp): TTATTATTGTTAATAT Found at i:1067109 original size:19 final size:19 Alignment explanation

Indices: 1067055--1067125 Score: 65 Period size: 18 Copynumber: 3.8 Consensus size: 19 1067045 TTTGTCTAGG * 1067055 TTATTATTTATA-TTATTA 1 TTATTATTAATATTTATTA * * * 1067073 TTACTACTACTA-TTATTA 1 TTATTATTAATATTTATTA * 1067091 TTATTGTTAATATTTATTA 1 TTATTATTAATATTTATTA * * 1067110 TTGTTATTATTATTTA 1 TTATTATTAATATTTA 1067126 ATATATACAT Statistics Matches: 41, Mismatches: 11, Indels: 1 0.77 0.21 0.02 Matches are distributed among these distances: 18 22 0.54 19 19 0.46 ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62 Consensus pattern (19 bp): TTATTATTAATATTTATTA Found at i:1069641 original size:17 final size:17 Alignment explanation

Indices: 1069619--1069652 Score: 68 Period size: 17 Copynumber: 2.0 Consensus size: 17 1069609 GCCCAACTAC 1069619 TCATCTAACAAACAACT 1 TCATCTAACAAACAACT 1069636 TCATCTAACAAACAACT 1 TCATCTAACAAACAACT 1069653 AAGGTAAACT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 17 1.00 ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24 Consensus pattern (17 bp): TCATCTAACAAACAACT Found at i:1077421 original size:3 final size:3 Alignment explanation

Indices: 1077413--1077443 Score: 53 Period size: 3 Copynumber: 10.3 Consensus size: 3 1077403 ATATCATTTC * 1077413 ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT A 1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A 1077444 GCATGATTAT Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 3 26 1.00 ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61 Consensus pattern (3 bp): ATT Found at i:1077621 original size:14 final size:16 Alignment explanation

Indices: 1077591--1077626 Score: 58 Period size: 15 Copynumber: 2.4 Consensus size: 16 1077581 TATGACAACT 1077591 ATATATATATATACAC 1 ATATATATATATACAC 1077607 ATAT-TATATAT-CAC 1 ATATATATATATACAC 1077621 ATATAT 1 ATATAT 1077627 CACTTCACAG Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 14 7 0.37 15 8 0.42 16 4 0.21 ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42 Consensus pattern (16 bp): ATATATATATATACAC Found at i:1085520 original size:4 final size:4 Alignment explanation

Indices: 1085511--1085536 Score: 52 Period size: 4 Copynumber: 6.5 Consensus size: 4 1085501 TCTGAATATA 1085511 TTAT TTAT TTAT TTAT TTAT TTAT TT 1 TTAT TTAT TTAT TTAT TTAT TTAT TT 1085537 TTATTAAAAT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 22 1.00 ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77 Consensus pattern (4 bp): TTAT Found at i:1085557 original size:23 final size:23 Alignment explanation

Indices: 1085531--1085584 Score: 54 Period size: 24 Copynumber: 2.3 Consensus size: 23 1085521 ATTTATTTAT 1085531 TTATTTTTATTAAAATTTTAAAA 1 TTATTTTTATTAAAATTTTAAAA * * * * 1085554 TTATAATTTATTTAATTTTTATAA 1 TTAT-TTTTATTAAAATTTTAAAA 1085578 TATATTT 1 T-TATTT 1085585 ACATATCATA Statistics Matches: 24, Mismatches: 5, Indels: 3 0.75 0.16 0.09 Matches are distributed among these distances: 23 4 0.17 24 17 0.71 25 3 0.12 ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61 Consensus pattern (23 bp): TTATTTTTATTAAAATTTTAAAA Done.