Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr13 124041150 

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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32

Warning! 335 characters in sequence are not A, C, G, or T


File 360 of 410

Found at i:110902061 original size:11 final size:11

Alignment explanation

Indices: 110902025--110902081 Score: 59 Period size: 11 Copynumber: 5.5 Consensus size: 11 110902015 ACATGGTATG * 110902025 TATGGTATGCA 1 TATGATATGCA * 110902036 TATGACATG-- 1 TATGATATGCA 110902045 TATGATATGCA 1 TATGATATGCA 110902056 TATGATATG-- 1 TATGATATGCA 110902065 TATGATATGCA 1 TATGATATGCA * 110902076 CATGAT 1 TATGAT 110902082 GTATTCGTAA Statistics Matches: 38, Mismatches: 4, Indels: 8 0.76 0.08 0.16 Matches are distributed among these distances: 9 17 0.45 11 21 0.55 ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37 Consensus pattern (11 bp): TATGATATGCA Found at i:110902081 original size:20 final size:20 Alignment explanation

Indices: 110902015--110902081 Score: 89 Period size: 20 Copynumber: 3.4 Consensus size: 20 110902005 ATTTTGATAA * * 110902015 ACATGGTATGTATGGTATGC 1 ACATGATATGTATGATATGC * * 110902035 ATATGACATGTATGATATGC 1 ACATGATATGTATGATATGC * 110902055 ATATGATATGTATGATATGC 1 ACATGATATGTATGATATGC 110902075 ACATGAT 1 ACATGAT 110902082 GTATTCGTAA Statistics Matches: 41, Mismatches: 6, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 20 41 1.00 ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36 Consensus pattern (20 bp): ACATGATATGTATGATATGC Found at i:110902189 original size:24 final size:24 Alignment explanation

Indices: 110902130--110902250 Score: 165 Period size: 24 Copynumber: 5.0 Consensus size: 24 110902120 GGAGGAAGTG 110902130 TAAAAGGGCTTATGCCCCAGTTAT 1 TAAAAGGGCTTATGCCCCAGTTAT * * * 110902154 GATAAAGAGCTTATGCCCCAATTAT 1 TA-AAAGGGCTTATGCCCCAGTTAT 110902179 TAAAAGGGCTTATGCCCCAGTTAT 1 TAAAAGGGCTTATGCCCCAGTTAT 110902203 TAAAAGGGCTT-TGCCCCAGTTAT 1 TAAAAGGGCTTATGCCCCAGTTAT * 110902226 TAAAAGAGGC-TAGGCCTCCAGTTAT 1 TAAAAG-GGCTTATGCC-CCAGTTAT 110902251 ATGATAAAGC Statistics Matches: 86, Mismatches: 7, Indels: 7 0.86 0.07 0.07 Matches are distributed among these distances: 23 19 0.22 24 38 0.44 25 29 0.34 ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28 Consensus pattern (24 bp): TAAAAGGGCTTATGCCCCAGTTAT Found at i:110902202 original size:49 final size:49 Alignment explanation

Indices: 110902130--110902268 Score: 169 Period size: 49 Copynumber: 2.8 Consensus size: 49 110902120 GGAGGAAGTG 110902130 TAAAAGGGCTTATGCCCCAGTTATGATAAAGAGCTTATGCCCCAATTAT 1 TAAAAGGGCTTATGCCCCAGTTATGATAAAGAGCTTATGCCCCAATTAT * * * 110902179 TAAAAGGGCTTATGCCCCAGTTATTA-AAAGGGCTT-TGCCCCAGTTAT 1 TAAAAGGGCTTATGCCCCAGTTATGATAAAGAGCTTATGCCCCAATTAT * 110902226 TAAAAGAGGC-TAGGCCTCCAGTTATATGATAAAGCAGC-TATGC 1 TAAAAG-GGCTTATGCC-CCAG-T-TATGATAAAG-AGCTTATGC 110902269 TGCCAGTGGA Statistics Matches: 77, Mismatches: 6, Indels: 11 0.82 0.06 0.12 Matches are distributed among these distances: 47 22 0.29 48 15 0.19 49 26 0.34 50 4 0.05 51 5 0.06 52 5 0.06 ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27 Consensus pattern (49 bp): TAAAAGGGCTTATGCCCCAGTTATGATAAAGAGCTTATGCCCCAATTAT Found at i:110902480 original size:30 final size:31 Alignment explanation

Indices: 110902444--110902506 Score: 92 Period size: 31 Copynumber: 2.1 Consensus size: 31 110902434 CGTTTACAAT 110902444 AAAGGCTTC-GCCCAGTAATACGAAATATGA 1 AAAGGCTTCGGCCCAGTAATACGAAATATGA ** * 110902474 AAAGGCTTCGGCCCAGTGTTATGAAATATGA 1 AAAGGCTTCGGCCCAGTAATACGAAATATGA 110902505 AA 1 AA 110902507 TATGAAAAGG Statistics Matches: 29, Mismatches: 3, Indels: 1 0.88 0.09 0.03 Matches are distributed among these distances: 30 9 0.31 31 20 0.69 ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22 Consensus pattern (31 bp): AAAGGCTTCGGCCCAGTAATACGAAATATGA Found at i:110910174 original size:20 final size:20 Alignment explanation

Indices: 110910108--110910174 Score: 89 Period size: 20 Copynumber: 3.4 Consensus size: 20 110910098 ATTTTGATAA * * 110910108 ACATGGTATGTATGGTATGC 1 ACATGATATGTATGATATGC * * 110910128 ATATGACATGTATGATATGC 1 ACATGATATGTATGATATGC * 110910148 ACATGATATGTGTGATATGC 1 ACATGATATGTATGATATGC 110910168 ACATGAT 1 ACATGAT 110910175 GTATTCGTAA Statistics Matches: 40, Mismatches: 7, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 20 40 1.00 ACGTcount: A:0.31, C:0.10, G:0.24, T:0.34 Consensus pattern (20 bp): ACATGATATGTATGATATGC Found at i:110910282 original size:24 final size:24 Alignment explanation

Indices: 110910223--110910343 Score: 183 Period size: 24 Copynumber: 5.0 Consensus size: 24 110910213 GGAGGAAGTG 110910223 TAAAAGGGCTTATGCCCCAGTTAT 1 TAAAAGGGCTTATGCCCCAGTTAT * 110910247 GATAAAGGGCTTATGCCCCAGTTAT 1 TA-AAAGGGCTTATGCCCCAGTTAT 110910272 TAAAAGGGCTTATGCCCCAGTTAT 1 TAAAAGGGCTTATGCCCCAGTTAT 110910296 TAAAAGGGCTT-TGCCCCAGTTAT 1 TAAAAGGGCTTATGCCCCAGTTAT * 110910319 TAAAAGAGGC-TAGGCCTCCAGTTAT 1 TAAAAG-GGCTTATGCC-CCAGTTAT 110910344 ATGATAAAGC Statistics Matches: 90, Mismatches: 3, Indels: 7 0.90 0.03 0.07 Matches are distributed among these distances: 23 19 0.21 24 40 0.44 25 31 0.34 ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28 Consensus pattern (24 bp): TAAAAGGGCTTATGCCCCAGTTAT Found at i:110910295 original size:49 final size:48 Alignment explanation

Indices: 110910223--110910352 Score: 183 Period size: 49 Copynumber: 2.6 Consensus size: 48 110910213 GGAGGAAGTG 110910223 TAAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTAT 1 TAAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTT-TGCCCCAGTTAT * 110910272 TAAAAGGGCTTATGCCCCAGTTATTA-AAAGGGCTTTGCCCCAGTTAT 1 TAAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTTGCCCCAGTTAT * 110910319 TAAAAGAGGC-TAGGCCTCCAGTTATATGATAAAG 1 TAAAAG-GGCTTATGCC-CCAG-T-TATGATAAAG 110910353 CAGCTATGCT Statistics Matches: 73, Mismatches: 3, Indels: 8 0.87 0.04 0.10 Matches are distributed among these distances: 47 23 0.32 48 16 0.22 49 26 0.36 50 4 0.05 51 4 0.05 ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28 Consensus pattern (48 bp): TAAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTTGCCCCAGTTAT Found at i:110910572 original size:31 final size:31 Alignment explanation

Indices: 110910537--110910600 Score: 110 Period size: 31 Copynumber: 2.1 Consensus size: 31 110910527 TGTTTACAGT 110910537 AAAGGCTTCGGCCCAGTAATATGAAATATGA 1 AAAGGCTTCGGCCCAGTAATATGAAATATGA ** 110910568 AAAGGCTTCGGCCCAGTGTTATGAAATATGA 1 AAAGGCTTCGGCCCAGTAATATGAAATATGA 110910599 AA 1 AA 110910601 TATGAAAAGG Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 31 31 1.00 ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23 Consensus pattern (31 bp): AAAGGCTTCGGCCCAGTAATATGAAATATGA Found at i:110911427 original size:17 final size:18 Alignment explanation

Indices: 110911397--110911430 Score: 52 Period size: 17 Copynumber: 1.9 Consensus size: 18 110911387 CCTTCATTTC * 110911397 TTTCTTTTATTCTTTTAG 1 TTTCTTTTAATCTTTTAG 110911415 TTTC-TTTAATCTTTTA 1 TTTCTTTTAATCTTTTA 110911431 TTTTTATTTA Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 17 11 0.73 18 4 0.27 ACGTcount: A:0.15, C:0.12, G:0.03, T:0.71 Consensus pattern (18 bp): TTTCTTTTAATCTTTTAG Found at i:110911833 original size:28 final size:29 Alignment explanation

Indices: 110911786--110911842 Score: 107 Period size: 28 Copynumber: 2.0 Consensus size: 29 110911776 ATGCAATCTA 110911786 AGAAAAATATTAGATTTTTCAATTCATTT 1 AGAAAAATATTAGATTTTTCAATTCATTT 110911815 AGAAAAATATTAGA-TTTTCAATTCATTT 1 AGAAAAATATTAGATTTTTCAATTCATTT 110911843 GCCACCTCAA Statistics Matches: 28, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 28 14 0.50 29 14 0.50 ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44 Consensus pattern (29 bp): AGAAAAATATTAGATTTTTCAATTCATTT Found at i:110928130 original size:18 final size:19 Alignment explanation

Indices: 110928096--110928135 Score: 64 Period size: 18 Copynumber: 2.2 Consensus size: 19 110928086 AACACAACTA * 110928096 AAATTAATAATAATAAAAT 1 AAATGAATAATAATAAAAT 110928115 AAATGAATAA-AATAAAAT 1 AAATGAATAATAATAAAAT 110928133 AAA 1 AAA 110928136 AACAAAAAAA Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 18 11 0.55 19 9 0.45 ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25 Consensus pattern (19 bp): AAATGAATAATAATAAAAT Found at i:110935608 original size:14 final size:13 Alignment explanation

Indices: 110935591--110935633 Score: 50 Period size: 14 Copynumber: 3.2 Consensus size: 13 110935581 TTTAGTTTCA 110935591 TTTATTTATTTATT 1 TTTATTT-TTTATT * * 110935605 TTTATTTCTTACT 1 TTTATTTTTTATT 110935618 TTTATTTTTTTATT 1 TTTA-TTTTTTATT 110935632 TT 1 TT 110935634 AGTTTTAGTT Statistics Matches: 24, Mismatches: 4, Indels: 2 0.80 0.13 0.07 Matches are distributed among these distances: 13 8 0.33 14 16 0.67 ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79 Consensus pattern (13 bp): TTTATTTTTTATT Found at i:110937164 original size:13 final size:12 Alignment explanation

Indices: 110937146--110937196 Score: 66 Period size: 12 Copynumber: 4.1 Consensus size: 12 110937136 TCTGAGTTCA 110937146 TTTATTTTATTTT 1 TTTATTTT-TTTT * 110937159 TTTATTTTTGTT 1 TTTATTTTTTTT * 110937171 TTTATTTTTTCT 1 TTTATTTTTTTT 110937183 TTTATTTATTTTT 1 TTTATTT-TTTTT 110937196 T 1 T 110937197 GAAGACTTCT Statistics Matches: 33, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 12 20 0.61 13 13 0.39 ACGTcount: A:0.12, C:0.02, G:0.02, T:0.84 Consensus pattern (12 bp): TTTATTTTTTTT Found at i:110950641 original size:20 final size:19 Alignment explanation

Indices: 110950618--110950660 Score: 59 Period size: 20 Copynumber: 2.2 Consensus size: 19 110950608 TGTTATTATA * 110950618 TTATATTATTTTATATTTGT 1 TTATATTATTTTAT-TTTCT * 110950638 TTATTTTATTTTATTTTCT 1 TTATATTATTTTATTTTCT 110950657 TTAT 1 TTAT 110950661 CAACTAAATT Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 19 8 0.38 20 13 0.62 ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74 Consensus pattern (19 bp): TTATATTATTTTATTTTCT Found at i:110951715 original size:11 final size:10 Alignment explanation

Indices: 110951699--110951764 Score: 62 Period size: 10 Copynumber: 6.5 Consensus size: 10 110951689 ATGATTTTTC 110951699 AAAAAATTAT 1 AAAAAATTAT * 110951709 AAAAAAATAT 1 AAAAAATTAT 110951719 AAAAAATTATT 1 AAAAAATTA-T * 110951730 AAGAAA-TAT 1 AAAAAATTAT * * 110951739 GAGAAATTAT 1 AAAAAATTAT * 110951749 TAAAAATTAAT 1 AAAAAATT-AT 110951760 AAAAA 1 AAAAA 110951765 TATTTAAATT Statistics Matches: 46, Mismatches: 7, Indels: 5 0.79 0.12 0.09 Matches are distributed among these distances: 9 6 0.13 10 28 0.61 11 12 0.26 ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27 Consensus pattern (10 bp): AAAAAATTAT Found at i:110951724 original size:20 final size:20 Alignment explanation

Indices: 110951699--110951764 Score: 78 Period size: 20 Copynumber: 3.2 Consensus size: 20 110951689 ATGATTTTTC * 110951699 AAAAAATTATAAAAAAATAT 1 AAAAAATTATTAAAAAATAT * 110951719 AAAAAATTATTAAGAAATAT 1 AAAAAATTATTAAAAAATAT * * * 110951739 GAGAAATTATTAAAAATTAAT 1 AAAAAATTATTAAAAAAT-AT 110951760 AAAAA 1 AAAAA 110951765 TATTTAAATT Statistics Matches: 37, Mismatches: 8, Indels: 1 0.80 0.17 0.02 Matches are distributed among these distances: 20 32 0.86 21 5 0.14 ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27 Consensus pattern (20 bp): AAAAAATTATTAAAAAATAT Found at i:110952184 original size:30 final size:31 Alignment explanation

Indices: 110952133--110952222 Score: 112 Period size: 30 Copynumber: 2.9 Consensus size: 31 110952123 TGCTAATAAG * * 110952133 AAAGGCTTAATTAATTTTTAAATTATTTTGC 1 AAAGACTTAATTAATTTTTAAATTATTTTAC * 110952164 -AAGAACTTAATTAA-TTTTAAATTATTTTAT 1 AAAG-ACTTAATTAATTTTTAAATTATTTTAC * 110952194 AAAGATTTAATTAATTTTTTAAATTATTT 1 AAAGACTTAATTAA-TTTTTAAATTATTT 110952223 AAGACTAAAA Statistics Matches: 51, Mismatches: 4, Indels: 7 0.82 0.06 0.11 Matches are distributed among these distances: 30 26 0.51 31 12 0.24 32 13 0.25 ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51 Consensus pattern (31 bp): AAAGACTTAATTAATTTTTAAATTATTTTAC Found at i:110952560 original size:9 final size:9 Alignment explanation

Indices: 110952538--110952589 Score: 54 Period size: 9 Copynumber: 5.9 Consensus size: 9 110952528 TAAATATATG 110952538 TTTTTAT-A 1 TTTTTATAA 110952546 -TTTTATAA 1 TTTTTATAA * 110952554 TTTTTATTA 1 TTTTTATAA * 110952563 TTTTAATAA 1 TTTTTATAA 110952572 TTTTTATATA 1 TTTTTATA-A * 110952582 ATTTTATA 1 TTTTTATA 110952590 TAACTCTTTA Statistics Matches: 36, Mismatches: 5, Indels: 4 0.80 0.11 0.09 Matches are distributed among these distances: 7 6 0.17 8 1 0.03 9 21 0.58 10 8 0.22 ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67 Consensus pattern (9 bp): TTTTTATAA Found at i:110952599 original size:12 final size:10 Alignment explanation

Indices: 110952549--110952604 Score: 62 Period size: 10 Copynumber: 5.5 Consensus size: 10 110952539 TTTTATATTT 110952549 TATAATTTT- 1 TATAATTTTA * 110952558 TATTATTTTA 1 TATAATTTTA 110952568 -ATAATTTTTA 1 TATAA-TTTTA 110952578 TATAATTTTA 1 TATAATTTTA 110952588 TATAACTCTTTA 1 TATAA-T-TTTA 110952600 TATAA 1 TATAA 110952605 AATTTATCAA Statistics Matches: 40, Mismatches: 2, Indels: 7 0.82 0.04 0.14 Matches are distributed among these distances: 9 11 0.28 10 15 0.38 11 5 0.12 12 9 0.22 ACGTcount: A:0.38, C:0.04, G:0.00, T:0.59 Consensus pattern (10 bp): TATAATTTTA Found at i:110952608 original size:24 final size:20 Alignment explanation

Indices: 110952545--110952609 Score: 55 Period size: 18 Copynumber: 3.2 Consensus size: 20 110952535 ATGTTTTTAT * 110952545 ATTTT-ATAATTTTTAT--T 1 ATTTTAATAATTTTTATAAA * 110952562 ATTTTAATAATTTTTATATA 1 ATTTTAATAATTTTTATAAA 110952582 ATTTTATATAACTCTTTATATAAA 1 ATTTTA-ATAA-T-TTT-TATAAA 110952606 ATTT 1 ATTT 110952610 ATCAAAATGG Statistics Matches: 39, Mismatches: 2, Indels: 7 0.81 0.04 0.15 Matches are distributed among these distances: 17 5 0.13 18 11 0.28 20 6 0.15 21 4 0.10 22 1 0.03 23 3 0.08 24 9 0.23 ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60 Consensus pattern (20 bp): ATTTTAATAATTTTTATAAA Found at i:110952850 original size:9 final size:9 Alignment explanation

Indices: 110952836--110952924 Score: 58 Period size: 9 Copynumber: 9.9 Consensus size: 9 110952826 ATTATCTATG 110952836 ATTTTTTAT 1 ATTTTTTAT 110952845 A-TTTTTAT 1 ATTTTTTAT * 110952853 AATTTTTTTT 1 -ATTTTTTAT * 110952863 ATAATTTTA- 1 AT-TTTTTAT ** 110952872 ATAATTTAT 1 ATTTTTTAT * 110952881 ATTTTCTAT 1 ATTTTTTAT 110952890 -TTTTTTAT 1 ATTTTTTAT * 110952898 AGTTTTTAT 1 ATTTTTTAT ** 110952907 AACTTTTAT 1 ATTTTTTAT 110952916 AATTTTTTA 1 -ATTTTTTA 110952925 AACTTGTTAT Statistics Matches: 61, Mismatches: 13, Indels: 11 0.72 0.15 0.13 Matches are distributed among these distances: 8 19 0.31 9 26 0.43 10 16 0.26 ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69 Consensus pattern (9 bp): ATTTTTTAT Found at i:110952859 original size:18 final size:18 Alignment explanation

Indices: 110952836--110952922 Score: 65 Period size: 18 Copynumber: 4.8 Consensus size: 18 110952826 ATTATCTATG 110952836 ATTTTTTATATTTTTATA 1 ATTTTTTATATTTTTATA * * 110952854 ATTTTTTTTATAATTT-TA 1 ATTTTTTATAT-TTTTATA ** 110952872 ATAATTTATATTTTCTAT- 1 ATTTTTTATATTTT-TATA 110952890 -TTTTTTATAGTTTTTATA 1 ATTTTTTATA-TTTTTATA * 110952908 A-CTTTTATAATTTTT 1 ATTTTTTAT-ATTTTT 110952923 TAAACTTGTT Statistics Matches: 53, Mismatches: 9, Indels: 14 0.70 0.12 0.18 Matches are distributed among these distances: 17 12 0.23 18 36 0.68 19 5 0.09 ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69 Consensus pattern (18 bp): ATTTTTTATATTTTTATA Found at i:110952863 original size:12 final size:12 Alignment explanation

Indices: 110952846--110952870 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 110952836 ATTTTTTATA 110952846 TTTTTATAATTT 1 TTTTTATAATTT 110952858 TTTTTATAATTT 1 TTTTTATAATTT 110952870 T 1 T 110952871 AATAATTTAT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76 Consensus pattern (12 bp): TTTTTATAATTT Found at i:110952928 original size:18 final size:19 Alignment explanation

Indices: 110952900--110952944 Score: 65 Period size: 19 Copynumber: 2.4 Consensus size: 19 110952890 TTTTTTATAG 110952900 TTTTTATAACTT-TTATAAT 1 TTTTTA-AACTTGTTATAAT 110952919 TTTTTAAACTTGTTATAAT 1 TTTTTAAACTTGTTATAAT * 110952938 ATTTTAA 1 TTTTTAA 110952945 TAATATTTGG Statistics Matches: 24, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 18 5 0.21 19 19 0.79 ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60 Consensus pattern (19 bp): TTTTTAAACTTGTTATAAT Found at i:110956243 original size:25 final size:25 Alignment explanation

Indices: 110956215--110956277 Score: 69 Period size: 23 Copynumber: 2.6 Consensus size: 25 110956205 ATATACAAAT * 110956215 ATAAGTATAAGTATAAGTATAT-ATA 1 ATAAGTATAA-TATAACTATATAATA * * 110956240 ATAAATATAATA-ATCTATATAATA 1 ATAAGTATAATATAACTATATAATA 110956264 AT-AGTATAATATAA 1 ATAAGTATAATATAA 110956278 AATATTAAAA Statistics Matches: 31, Mismatches: 5, Indels: 5 0.76 0.12 0.12 Matches are distributed among these distances: 23 14 0.45 24 8 0.26 25 9 0.29 ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37 Consensus pattern (25 bp): ATAAGTATAATATAACTATATAATA Found at i:110963095 original size:33 final size:33 Alignment explanation

Indices: 110963040--110963114 Score: 80 Period size: 33 Copynumber: 2.3 Consensus size: 33 110963030 TAGTCCAACT ** * * 110963040 ATGGTCTTACACTTGTATTGCCATGA-CCCAGCC 1 ATGGTCTTACACACGTAGTGCCAT-ATCCCAGAC * * 110963073 ATGGTCTTACTCACGTAGTGCCATATCCCAGAT 1 ATGGTCTTACACACGTAGTGCCATATCCCAGAC 110963106 ATGGTCTTA 1 ATGGTCTTA 110963115 TCATCTTCAT Statistics Matches: 35, Mismatches: 6, Indels: 2 0.81 0.14 0.05 Matches are distributed among these distances: 32 1 0.03 33 34 0.97 ACGTcount: A:0.23, C:0.27, G:0.19, T:0.32 Consensus pattern (33 bp): ATGGTCTTACACACGTAGTGCCATATCCCAGAC Found at i:110966722 original size:3 final size:3 Alignment explanation

Indices: 110966714--110966787 Score: 148 Period size: 3 Copynumber: 24.7 Consensus size: 3 110966704 TATGTATGTA 110966714 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT 110966762 TAT TAT TAT TAT TAT TAT TAT TAT TA 1 TAT TAT TAT TAT TAT TAT TAT TAT TA 110966788 AGAACAAATC Statistics Matches: 71, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 71 1.00 ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66 Consensus pattern (3 bp): TAT Found at i:110971922 original size:3 final size:3 Alignment explanation

Indices: 110971903--110971943 Score: 55 Period size: 3 Copynumber: 13.0 Consensus size: 3 110971893 GTATATGCAT * 110971903 ATA ATA AAA ATA TATA ATA ATA CATA ATA ATA ATA ATA ATA 1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA 110971944 TGAAAATACA Statistics Matches: 34, Mismatches: 2, Indels: 4 0.85 0.05 0.10 Matches are distributed among these distances: 3 28 0.82 4 6 0.18 ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32 Consensus pattern (3 bp): ATA Found at i:110971924 original size:16 final size:15 Alignment explanation

Indices: 110971903--110971941 Score: 51 Period size: 16 Copynumber: 2.5 Consensus size: 15 110971893 GTATATGCAT 110971903 ATAATAAAAATATATA 1 ATAATAAAAATA-ATA * 110971919 ATAATACATAATAATA 1 ATAATA-AAAATAATA 110971935 ATAATAA 1 ATAATAA 110971942 TATGAAAATA Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 15 1 0.05 16 15 0.71 17 5 0.24 ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31 Consensus pattern (15 bp): ATAATAAAAATAATA Found at i:110973613 original size:45 final size:45 Alignment explanation

Indices: 110973553--110973697 Score: 227 Period size: 45 Copynumber: 3.2 Consensus size: 45 110973543 CACTGCGACC * * * 110973553 TCAGGGATACCAGACTTGGAACTTTTGACCGGCTCCACTGCAGCT 1 TCAGGGAGACAAGACTTGCAACTTTTGACCGGCTCCACTGCAGCT * 110973598 TCAGGGAGACAAGACTTGCAACTTTTGATCGGCTCCACTGCAGCT 1 TCAGGGAGACAAGACTTGCAACTTTTGACCGGCTCCACTGCAGCT * * 110973643 TCAGGGAGACAAGACTTGTAACTTTTGACCGGCTCCACTGCAGTT 1 TCAGGGAGACAAGACTTGCAACTTTTGACCGGCTCCACTGCAGCT * 110973688 TTAGGGAGAC 1 TCAGGGAGAC 110973698 CAAGTCTGGT Statistics Matches: 92, Mismatches: 8, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 45 92 1.00 ACGTcount: A:0.24, C:0.26, G:0.26, T:0.25 Consensus pattern (45 bp): TCAGGGAGACAAGACTTGCAACTTTTGACCGGCTCCACTGCAGCT Found at i:110974097 original size:109 final size:102 Alignment explanation

Indices: 110973916--110974124 Score: 285 Period size: 109 Copynumber: 2.0 Consensus size: 102 110973906 CATATGACCC * * * 110973916 AAGGCTCAACTCACTTCTCGCAATATGGGTGGATTTTTGAAAAACAAAAAGGTACAACTCACCTC 1 AAGGCTCAACTCACCTCTCGCAATATGAGTGGATTTTTGAAAAAAAAAAAGGTACAACTCACCTC * 110973981 TCGCAATATGAGTTGCTTTTTGAAAAACAGAAATTAA 66 TCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA * 110974018 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATATAAATTGAAAGGCT-CAA 1 AAGGCTCAACTCACCTCTCGCAATATGAGTGGA-TTTTTG-AAAA-A-AAA---AAAGG-TACAA * 110974082 CTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATT 58 CTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT 110974125 GGAAAGTAGA Statistics Matches: 93, Mismatches: 6, Indels: 9 0.86 0.06 0.08 Matches are distributed among these distances: 102 30 0.32 103 6 0.06 104 4 0.04 105 1 0.01 106 2 0.02 109 49 0.53 110 1 0.01 ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29 Consensus pattern (102 bp): AAGGCTCAACTCACCTCTCGCAATATGAGTGGATTTTTGAAAAAAAAAAAGGTACAACTCACCTC TCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA Found at i:110974130 original size:55 final size:54 Alignment explanation

Indices: 110973916--110974130 Score: 282 Period size: 55 Copynumber: 4.1 Consensus size: 54 110973906 CATATGACCC * * * 110973916 AAGGCTCAACTCACTTCTCGCAATATGGGTGGATTTTTGAAAAAC---AA---A 1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGA * * 110973964 AAGG-TACAACTCACCTCTCGCAATATGAGTTGCTTTTTGAAAAACAGAAATTAA 1 AAGGCT-CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGA * * 110974018 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATATAAATTGA 1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGA * 110974073 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTGGA 1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-GA 110974128 AAG 1 AAG 110974131 TAGAAATTGA Statistics Matches: 146, Mismatches: 11, Indels: 13 0.86 0.06 0.08 Matches are distributed among these distances: 47 1 0.01 48 39 0.27 51 2 0.01 54 47 0.32 55 57 0.39 ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28 Consensus pattern (54 bp): AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGA Found at i:110974249 original size:71 final size:70 Alignment explanation

Indices: 110974134--110974271 Score: 222 Period size: 71 Copynumber: 2.0 Consensus size: 70 110974124 TGGAAAGTAG * * 110974134 AAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA 1 AAATTGAAAATACCTCAACGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGGA 110974199 AACAT 66 AACAT * ** 110974204 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGG 1 AAATTGAAAATACCTCAACGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGG 110974269 AAA 65 AAA 110974272 AGTAAAAATT Statistics Matches: 62, Mismatches: 5, Indels: 1 0.91 0.07 0.01 Matches are distributed among these distances: 70 20 0.32 71 42 0.68 ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29 Consensus pattern (70 bp): AAATTGAAAATACCTCAACGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGGA AACAT Found at i:110974457 original size:173 final size:170 Alignment explanation

Indices: 110974132--110974535 Score: 526 Period size: 173 Copynumber: 2.4 Consensus size: 170 110974122 ATTGGAAAGT 110974132 AGAAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT 1 AGAAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT * 110974197 GAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTG 66 GAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGGTG * 110974262 ATTTTGGAAAAGTAAAAATTAAAGACAGGATTTGAACAAG 131 ATTTTGGAAAAGCAAAAATTAAAGACAGGATTTGAACAAG * * * 110974302 AGAATTTGAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT 1 AGAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT * * 110974367 TTTGAAGCATAAATTGAAATTACCTCAACGTGTCTTGAGGCTGAACTCACCTCTCGCAATATGAG 63 TTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG * ** * 110974432 GTGATTTTCTGAAAA-CATGAATTAAA-A-A--A----AGCAA- 128 GTGATTTT-GGAAAAGCAAAAATTAAAGACAGGATTTGAACAAG * * * 110974466 A-AAA-TGAAAATACCTCGGCATGCGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATT 1 AGAAATTGAAAATACCTCAGCGTGC---CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT * 110974529 TCTGAAA 63 TTTGAAA 110974536 GCAGAAGTAA Statistics Matches: 210, Mismatches: 17, Indels: 22 0.84 0.07 0.09 Matches are distributed among these distances: 161 1 0.00 162 24 0.11 163 2 0.01 164 34 0.16 165 4 0.02 169 1 0.00 170 22 0.10 171 36 0.17 172 1 0.00 173 80 0.38 174 5 0.02 ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27 Consensus pattern (170 bp): AGAAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT GAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGGTG ATTTTGGAAAAGCAAAAATTAAAGACAGGATTTGAACAAG Found at i:110977570 original size:3 final size:3 Alignment explanation

Indices: 110977562--110977632 Score: 135 Period size: 3 Copynumber: 24.0 Consensus size: 3 110977552 TGTATATGAT 110977562 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA 1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA 110977610 AT- ATA ATA ATA ATA ATA ATA ATA 1 ATA ATA ATA ATA ATA ATA ATA ATA 110977633 TGAAAATACA Statistics Matches: 67, Mismatches: 0, Indels: 2 0.97 0.00 0.03 Matches are distributed among these distances: 2 2 0.03 3 65 0.97 ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34 Consensus pattern (3 bp): ATA Found at i:110978117 original size:19 final size:19 Alignment explanation

Indices: 110978095--110978133 Score: 78 Period size: 19 Copynumber: 2.1 Consensus size: 19 110978085 GAAGGGGAGA 110978095 AAGAAAAAAAAAGGAGAGG 1 AAGAAAAAAAAAGGAGAGG 110978114 AAGAAAAAAAAAGGAGAGG 1 AAGAAAAAAAAAGGAGAGG 110978133 A 1 A 110978134 GAAGAGAGAA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00 Consensus pattern (19 bp): AAGAAAAAAAAAGGAGAGG Found at i:110978124 original size:21 final size:20 Alignment explanation

Indices: 110978098--110978158 Score: 70 Period size: 19 Copynumber: 3.0 Consensus size: 20 110978088 GGGGAGAAAG * 110978098 AAAAAAAAAGGAGAGGA-AG 1 AAAAAAAAAGGAGAGGAGAA 110978117 AAAAAAAAAGGAGAGGAGAA 1 AAAAAAAAAGGAGAGGAGAA * * * 110978137 GAGAGAAAAGGGAGAGGAGAA 1 -AAAAAAAAAGGAGAGGAGAA 110978158 A 1 A 110978159 GGAGAGAGGG Statistics Matches: 36, Mismatches: 4, Indels: 3 0.84 0.09 0.07 Matches are distributed among these distances: 19 17 0.47 20 2 0.06 21 17 0.47 ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00 Consensus pattern (20 bp): AAAAAAAAAGGAGAGGAGAA Found at i:110978163 original size:21 final size:21 Alignment explanation

Indices: 110978102--110978157 Score: 73 Period size: 21 Copynumber: 2.8 Consensus size: 21 110978092 AGAAAGAAAA 110978102 AAAAAGGAGAGGAAGAA-A-A- 1 AAAAAGGAGAGG-AGAAGAGAG 110978121 AAAAAGGAGAGGAGAAGAGAG 1 AAAAAGGAGAGGAGAAGAGAG * 110978142 AAAAGGGAGAGGAGAA 1 AAAAAGGAGAGGAGAA 110978158 AGGAGAGAGG Statistics Matches: 33, Mismatches: 1, Indels: 4 0.87 0.03 0.11 Matches are distributed among these distances: 18 4 0.12 19 13 0.39 20 1 0.03 21 15 0.45 ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00 Consensus pattern (21 bp): AAAAAGGAGAGGAGAAGAGAG Found at i:110985116 original size:166 final size:169 Alignment explanation

Indices: 110984800--110985131 Score: 526 Period size: 166 Copynumber: 2.0 Consensus size: 169 110984790 CACAATGCGA * * 110984800 AATGTCCGGACCAGTCGGGCCTTCTAGGCCTGCAAATGTTTTAGCCCAATATATAATCTTATTTT 1 AATGTCCGGACCAGTCGGGCCTTCTAGGCCTGCAAATATTTTAGCCCAATACATAATCTTATTTT * * * * 110984865 CTTTCCTCAGCAGAACTTATCAATTTGGAATTAAAAAGGAGTTAATGGCTTATTTAACTCAAACA 66 CTTTCCTCAACAGAACTTATCAATTTGGAATTAAAAAAGAGTTAATAGCTCATTTAACTCAAACA 110984930 TTAATTTGGGATTAATGGCTCATTAATTAACAGACATAT 131 TTAATTTGGGATTAATGGCTCATTAATTAACAGACATAT * * 110984969 AATGTCTGGACCAGTTGGGCCTTCTAGGCCTGCAAATATTTTAGCCCAATACATAATCTT-TTTT 1 AATGTCCGGACCAGTCGGGCCTTCTAGGCCTGCAAATATTTTAGCCCAATACATAATCTTATTTT * * * 110985033 -TTT-CTCAACAGAATTTATCAGTTTGGAATTAAAAAAGAGTTAATAGCTCATTTAATTCAAACA 66 CTTTCCTCAACAGAACTTATCAATTTGGAATTAAAAAAGAGTTAATAGCTCATTTAACTCAAACA * * 110985096 TTAATTTGGGATTAATGGCTCCTTAATTCACAGACA 131 TTAATTTGGGATTAATGGCTCATTAATTAACAGACA 110985132 CATTATTGGC Statistics Matches: 150, Mismatches: 13, Indels: 3 0.90 0.08 0.02 Matches are distributed among these distances: 166 87 0.58 167 3 0.02 168 4 0.03 169 56 0.37 ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35 Consensus pattern (169 bp): AATGTCCGGACCAGTCGGGCCTTCTAGGCCTGCAAATATTTTAGCCCAATACATAATCTTATTTT CTTTCCTCAACAGAACTTATCAATTTGGAATTAAAAAAGAGTTAATAGCTCATTTAACTCAAACA TTAATTTGGGATTAATGGCTCATTAATTAACAGACATAT Found at i:110986354 original size:27 final size:27 Alignment explanation

Indices: 110986289--110986405 Score: 110 Period size: 27 Copynumber: 4.4 Consensus size: 27 110986279 ACGGGCTTTC * * * 110986289 CCCATATTAGATAGACCTCACAGACTT 1 CCCACATTAGATAGTCCTAACAGACTT ** * 110986316 -CCACAGAAGATGGTCCTAACAGACTT 1 CCCACATTAGATAGTCCTAACAGACTT * * * 110986342 CCCACATTAGATGGTCCTAACTGGCTT 1 CCCACATTAGATAGTCCTAACAGACTT * * * * 110986369 CCCACAGTAGATAGTCCTGACGGGCTT 1 CCCACATTAGATAGTCCTAACAGACTT 110986396 CCCACATTAG 1 CCCACATTAG 110986406 TTAGATTGGT Statistics Matches: 74, Mismatches: 15, Indels: 2 0.81 0.16 0.02 Matches are distributed among these distances: 26 20 0.27 27 54 0.73 ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24 Consensus pattern (27 bp): CCCACATTAGATAGTCCTAACAGACTT Found at i:110987390 original size:2 final size:2 Alignment explanation

Indices: 110987383--110987414 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 110987373 CAATTAAGTA 110987383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 110987415 TTTGTGAAGC Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:110988474 original size:21 final size:21 Alignment explanation

Indices: 110988435--110988490 Score: 55 Period size: 21 Copynumber: 2.8 Consensus size: 21 110988425 AACAACCTGT * * * 110988435 ATCATCATAATAATAATCACA 1 ATCATAATAATAGTCATCACA * 110988456 ATCATAATAATAGTCATCACT 1 ATCATAATAATAGTCATCACA 110988477 AT--TAA-AATAGTCAT 1 ATCATAATAATAGTCAT 110988491 TTTTATTTAC Statistics Matches: 31, Mismatches: 4, Indels: 3 0.82 0.11 0.08 Matches are distributed among these distances: 18 9 0.29 19 3 0.10 21 19 0.61 ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32 Consensus pattern (21 bp): ATCATAATAATAGTCATCACA Found at i:110992348 original size:3 final size:3 Alignment explanation

Indices: 110992328--110992457 Score: 77 Period size: 3 Copynumber: 42.7 Consensus size: 3 110992318 TTTGTTTTTC * * 110992328 TAT TAT CAT TAT TA- TAT TAT TAT TAT TAT TCAT GTACA TAT TAT T-T 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT -TA-T TAT TAT TAT * * * * * * 110992374 ATAT TAT TTT TAT GAT TAT TAT T-G TATT TAT TTT TAC TAC TAT TAT 1 -TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT * * * * * 110992420 TTT TAT TAT TAG TAT TAG TAT TAT AAT TAC TAT TAT TA 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA 110992458 CACTTATATA Statistics Matches: 95, Mismatches: 24, Indels: 16 0.70 0.18 0.12 Matches are distributed among these distances: 2 4 0.04 3 82 0.86 4 8 0.08 5 1 0.01 ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60 Consensus pattern (3 bp): TAT Found at i:110992450 original size:39 final size:39 Alignment explanation

Indices: 110992375--110992457 Score: 105 Period size: 39 Copynumber: 2.1 Consensus size: 39 110992365 ATATTATTTA * ** 110992375 TATTATTTTTATGATTATTATTGTATTTATTTTTACTAC 1 TATTATTTTTATGATTAGTATTGTATTTATAATTACTAC * * 110992414 TATTATTTTTATTATTAGTATTAGTA-TTATAATTACTAT 1 TATTATTTTTATGATTAGTATT-GTATTTATAATTACTAC 110992453 TATTA 1 TATTA 110992458 CACTTATATA Statistics Matches: 38, Mismatches: 5, Indels: 2 0.84 0.11 0.04 Matches are distributed among these distances: 39 35 0.92 40 3 0.08 ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61 Consensus pattern (39 bp): TATTATTTTTATGATTAGTATTGTATTTATAATTACTAC Found at i:110992646 original size:14 final size:14 Alignment explanation

Indices: 110992627--110992653 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 110992617 CATCATGTTT 110992627 TTTTAATACTATAC 1 TTTTAATACTATAC 110992641 TTTTAATACTATA 1 TTTTAATACTATA 110992654 TTATGTATAT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52 Consensus pattern (14 bp): TTTTAATACTATAC Found at i:110992734 original size:64 final size:59 Alignment explanation

Indices: 110992654--110992776 Score: 140 Period size: 64 Copynumber: 2.0 Consensus size: 59 110992644 TAATACTATA * * 110992654 TTATGTATATA-TTTTTACATGTATTATGGACATATTTTCAATAACTATATCATATGTATATATT 1 TTATGTACATACTTTTAACAT-TATTATGGACATATTTT---TAA-TATAT-ATATGTATATATT * ** 110992718 TTATGTACATACTTTTAACATTATTATGTATTTATTTTTAATATATATATGTATATATT 1 TTATGTACATACTTTTAACATTATTATGGACATATTTTTAATATATATATGTATATATT 110992777 CATGTAGTAT Statistics Matches: 53, Mismatches: 5, Indels: 7 0.82 0.08 0.11 Matches are distributed among these distances: 59 13 0.25 60 5 0.09 61 3 0.06 64 24 0.45 65 8 0.15 ACGTcount: A:0.34, C:0.07, G:0.07, T:0.53 Consensus pattern (59 bp): TTATGTACATACTTTTAACATTATTATGGACATATTTTTAATATATATATGTATATATT Found at i:110992756 original size:23 final size:23 Alignment explanation

Indices: 110992719--110992776 Score: 64 Period size: 23 Copynumber: 2.5 Consensus size: 23 110992709 GTATATATTT * * 110992719 TATGTACATACTTTTAACAT-TA 1 TATGTATATATTTTTAACATATA * * 110992741 TTATGTATTTATTTTTAATATATA 1 -TATGTATATATTTTTAACATATA 110992765 TATGTATATATT 1 TATGTATATATT 110992777 CATGTAGTAT Statistics Matches: 29, Mismatches: 5, Indels: 2 0.81 0.14 0.06 Matches are distributed among these distances: 23 27 0.93 24 2 0.07 ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55 Consensus pattern (23 bp): TATGTATATATTTTTAACATATA Found at i:110992986 original size:27 final size:26 Alignment explanation

Indices: 110992939--110993032 Score: 100 Period size: 27 Copynumber: 3.6 Consensus size: 26 110992929 ATTATATTAC * * 110992939 ATTTTTTACATATTATCTTATGTATAT 1 ATTTTTTA-ATACTATATTATGTATAT * 110992966 ATTTTTTAATAACTATATTATGTATGT 1 ATTTTTTAAT-ACTATATTATGTATAT ** * * 110992993 ATTTTTTAACGCTATATTATGTACAC 1 ATTTTTTAATACTATATTATGTATAT 110993019 A-TTTTTAATACTAT 1 ATTTTTTAATACTAT 110993033 GTATATACCT Statistics Matches: 56, Mismatches: 10, Indels: 4 0.80 0.14 0.06 Matches are distributed among these distances: 25 11 0.20 26 15 0.27 27 30 0.54 ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54 Consensus pattern (26 bp): ATTTTTTAATACTATATTATGTATAT Found at i:110993142 original size:19 final size:19 Alignment explanation

Indices: 110993100--110993142 Score: 52 Period size: 19 Copynumber: 2.3 Consensus size: 19 110993090 TCATATATCG ** 110993100 TTATTATTAGTTTTTTATA 1 TTATTATTAGTTTTCAATA 110993119 TTATTATT-GTTTTCAATA 1 TTATTATTAGTTTTCAATA 110993137 TATATT 1 T-TATT 110993143 GTATATATTT Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 18 9 0.43 19 12 0.57 ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65 Consensus pattern (19 bp): TTATTATTAGTTTTCAATA Found at i:110996890 original size:27 final size:28 Alignment explanation

Indices: 110996860--110996912 Score: 72 Period size: 27 Copynumber: 1.9 Consensus size: 28 110996850 TGAAATCAAC 110996860 ACTAAAATTCTTGCAT-ATTTATTCATG 1 ACTAAAATTCTTGCATCATTTATTCATG * * * 110996887 ACTAACATTCTTTCGTCATTTATTCA 1 ACTAAAATTCTTGCATCATTTATTCA 110996913 ACATTCATTT Statistics Matches: 22, Mismatches: 3, Indels: 1 0.85 0.12 0.04 Matches are distributed among these distances: 27 13 0.59 28 9 0.41 ACGTcount: A:0.30, C:0.19, G:0.06, T:0.45 Consensus pattern (28 bp): ACTAAAATTCTTGCATCATTTATTCATG Found at i:110996915 original size:22 final size:22 Alignment explanation

Indices: 110996890--110996944 Score: 76 Period size: 22 Copynumber: 2.5 Consensus size: 22 110996880 ATTCATGACT 110996890 AACATTC-TTTCGTCATTTATTC 1 AACATTCATTT-GTCATTTATTC 110996912 AACATTCATTTGTCATTTATTC 1 AACATTCATTTGTCATTTATTC * 110996934 ATTCATTCATT 1 A-ACATTCATT 110996945 CATTGCATGT Statistics Matches: 30, Mismatches: 1, Indels: 3 0.88 0.03 0.09 Matches are distributed among these distances: 22 19 0.63 23 11 0.37 ACGTcount: A:0.25, C:0.20, G:0.04, T:0.51 Consensus pattern (22 bp): AACATTCATTTGTCATTTATTC Found at i:111004363 original size:41 final size:41 Alignment explanation

Indices: 111004318--111004398 Score: 110 Period size: 41 Copynumber: 2.0 Consensus size: 41 111004308 ATTATGCTTG * 111004318 AAAAAAGAA-AATCAAGATGAAAAACCGAAAAGGGCATCTT 1 AAAAAAAAAGAATCAAGATGAAAAACCGAAAAGGGCATCTT * * * * 111004358 AAAAAAAAAGGATCAAGGTGAAAACCCGAAAAGGGCGTCTT 1 AAAAAAAAAGAATCAAGATGAAAAACCGAAAAGGGCATCTT 111004399 GATTAACACA Statistics Matches: 35, Mismatches: 5, Indels: 1 0.85 0.12 0.02 Matches are distributed among these distances: 40 8 0.23 41 27 0.77 ACGTcount: A:0.53, C:0.14, G:0.21, T:0.12 Consensus pattern (41 bp): AAAAAAAAAGAATCAAGATGAAAAACCGAAAAGGGCATCTT Found at i:111017898 original size:135 final size:134 Alignment explanation

Indices: 111016918--111017871 Score: 1297 Period size: 133 Copynumber: 7.1 Consensus size: 134 111016908 GATTACAGAT * * 111016918 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGACCAGGCTAA-ATACTAGATCTTATCTTCACT 1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAATATACCAGATCTTATCTTCACT * * 111016982 GAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTACCGGCGATGGAGCAGAT 66 GAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCATGTACCGGCAATGGAGCAGAT 111017047 TCCA 131 TCCA * * * * 111017051 ATCATCAGCCTTATCTTCACTAAGCAGGAGTGGGGCAGGCTAA-ATACTAGATCTTATCTTCGCT 1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAATATACCAGATCTTATCTTCACT * * * * * * 111017115 GAGTAAGAGTGGAGCAGATCAAATTTTGGTGAATCTTATCTCCATGTATCGGCAATGGAGCAGAT 66 GAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCATGTACCGGCAATGGAGCAGAT * 111017180 TTCA 131 TCCA * * * * 111017184 ACCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-ATATACTAGATCTTATCTTCGCT 1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAATATACCAGATCTTATCTTCACT ** * * ** * 111017248 GAGCAGGAGCAAAGCAGATCAAATTTT-GATGAATCTTATCTTCATGTATTGGTAATGGAGCAGA 66 GAGCAGGAGTGAAGCAGATCGAATTTTGGA-GAATCTTATCTCCATGTACCGGCAATGGAGCAGA 111017312 TTCCA 130 TTCCA * 111017317 ATCATCAGCCTTATCTTCACTGAGCAAGAGTGGAGCAGGCTAA-ATACCAGATCTTATCTTCACT 1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAATATACCAGATCTTATCTTCACT * 111017381 GAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTACCGGCAATGGAGCAGAT 66 GAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCATGTACCGGCAATGGAGCAGAT * 111017446 TCTA 131 TCCA * * * * 111017450 ATCATCAACCTTATCTTCACTGTGCAGGAGTAGAGCAGGCTAAATATACCAGATCTTATCTTCAT 1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AATATACCAGATCTTATCTTCAC * * * ** 111017515 TGAGCAGGAGTGAAGCAGATCGAATTTTGGAAAATCTTATCTCTACGTACCGGTGATGGAGCAGA 65 TGAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCATGTACCGGCAATGGAGCAGA 111017580 TTCCA 130 TTCCA * * ** 111017585 ATCATCAGCTTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGGTCTTATCTTTGC 1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AATATACCAGATCTTATCTTCAC * * * * * * * * 111017650 TGAGCAGGAGCGGAGCAGATCAAATTTTGGTGAATCTTATCTCTATGTATCGACAATGGAGCAGG 65 TGAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCATGTACCGGCAATGGAGCAGA * 111017715 TTTCA 130 TTCCA ** * * * * 111017720 GCCACCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGACTAAATATACCAGATCTTATCTTCAT 1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AATATACCAGATCTTATCTTCAC ** 111017785 TGAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCATGTACCGGTGATGGAGCAGA 65 TGAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCATGTACCGGCAATGGAGCAGA 111017850 TTCCA 130 TTCCA * 111017855 ATCATCAGCTTTATCTT 1 ATCATCAGCCTTATCTT 111017872 TACTAAACAG Statistics Matches: 718, Mismatches: 97, Indels: 10 0.87 0.12 0.01 Matches are distributed among these distances: 132 2 0.00 133 386 0.54 134 5 0.01 135 325 0.45 ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28 Consensus pattern (134 bp): ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAATATACCAGATCTTATCTTCACT GAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCATGTACCGGCAATGGAGCAGAT TCCA Found at i:111017974 original size:85 final size:85 Alignment explanation

Indices: 111017874--111018071 Score: 317 Period size: 85 Copynumber: 2.3 Consensus size: 85 111017864 TTTATCTTTA * 111017874 CTAAACAGTAGGGTAACAGGCTAAAATTTACAGATCCTGGCTCTCCGAGCAGTGATGGAGCAAGT 1 CTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCCTGGCTCTCCGAGCAGTGATGGAGCAAGT 111017939 CGAAGA-TCCGCCTTAACCCC 66 CGAAGACT-CGCCTTAACCCC * * * 111017959 CTAAGCAGTAGGGTAACAGGCTAAAATTTATAGATCCTGGCTCTCCGAGCAGTGGTGGAGCAGGT 1 CTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCCTGGCTCTCCGAGCAGTGATGGAGCAAGT * 111018024 CGAAGACTCGCCTTAATCCC 66 CGAAGACTCGCCTTAACCCC * * 111018044 CTAAGCAATAGGGTAACAGGTTAAAATT 1 CTAAGCAGTAGGGTAACAGGCTAAAATT 111018072 GCAGATCTTA Statistics Matches: 105, Mismatches: 7, Indels: 2 0.92 0.06 0.02 Matches are distributed among these distances: 85 104 0.99 86 1 0.01 ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22 Consensus pattern (85 bp): CTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCCTGGCTCTCCGAGCAGTGATGGAGCAAGT CGAAGACTCGCCTTAACCCC Found at i:111021734 original size:3 final size:3 Alignment explanation

Indices: 111021714--111021843 Score: 68 Period size: 3 Copynumber: 42.7 Consensus size: 3 111021704 TTTGTTTTTC * * * 111021714 TAT TAT CAT TAT TA- TAT TAT TAT TAT TTT TCAT GTACA TAT TAT T-T 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT -TA-T TAT TAT TAT * * * * * * 111021760 ATAT TAT TTT TAT GAT TAT TAT T-G TATT TAT TTT TAC TAC TAT TAT 1 -TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT * * * * * 111021806 TTT TAT TAT TAG TAT TAG TAT TAT AAT TAC TAT TAT TA 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA 111021844 CACTTATATA Statistics Matches: 93, Mismatches: 26, Indels: 16 0.69 0.19 0.12 Matches are distributed among these distances: 2 4 0.04 3 81 0.87 4 7 0.08 5 1 0.01 ACGTcount: A:0.31, C:0.05, G:0.04, T:0.61 Consensus pattern (3 bp): TAT Found at i:111021777 original size:12 final size:12 Alignment explanation

Indices: 111021752--111021866 Score: 67 Period size: 12 Copynumber: 9.0 Consensus size: 12 111021742 TTCATGTACA 111021752 TATTATTTATAT 1 TATTATTTATAT 111021764 TATT-TTTATGAT 1 TATTATTTAT-AT 111021776 TATTATTGTAT-T 1 TATTATT-TATAT * 111021788 TATT-TTTACTAC 1 TATTATTTA-TAT * 111021800 TATTATTTTTAT 1 TATTATTTATAT 111021812 TATTAGTATTAGTAT 1 TATTA-T-TTA-TAT * 111021827 TA-TAATTACTAT 1 TATTATTTA-TAT * 111021839 TATTACACTTATAT 1 TATT--ATTTATAT 111021853 ATATATATTTATAT 1 -TAT-TATTTATAT 111021867 GTAAAATTAT Statistics Matches: 81, Mismatches: 8, Indels: 26 0.70 0.07 0.23 Matches are distributed among these distances: 10 2 0.02 11 8 0.10 12 34 0.42 13 7 0.09 14 17 0.21 15 12 0.15 16 1 0.01 ACGTcount: A:0.32, C:0.04, G:0.03, T:0.60 Consensus pattern (12 bp): TATTATTTATAT Found at i:111021779 original size:24 final size:24 Alignment explanation

Indices: 111021716--111021815 Score: 87 Period size: 24 Copynumber: 4.0 Consensus size: 24 111021706 TGTTTTTCTA * 111021716 TTATCATTATTATATTATTATTATTT 1 TTATGATTATTAT-TTA-TATTATTT * 111021742 TTCATGTACATATTATTTATATTATTT 1 TT-ATG-A-TTATTATTTATATTATTT 111021769 TTATGATTATTATTGTAT-TTATTT 1 TTATGATTATTATT-TATATTATTT * * 111021793 TTACT-ACTATTATTTTTATTATT 1 TTA-TGATTATTATTTATATTATT 111021816 AGTATTAGTA Statistics Matches: 63, Mismatches: 5, Indels: 14 0.77 0.06 0.17 Matches are distributed among these distances: 23 2 0.03 24 29 0.46 25 5 0.08 26 5 0.08 27 12 0.19 28 4 0.06 29 6 0.10 ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64 Consensus pattern (24 bp): TTATGATTATTATTTATATTATTT Found at i:111021836 original size:39 final size:39 Alignment explanation

Indices: 111021761--111021843 Score: 105 Period size: 39 Copynumber: 2.1 Consensus size: 39 111021751 ATATTATTTA * ** 111021761 TATTATTTTTATGATTATTATTGTATTTATTTTTACTAC 1 TATTATTTTTATGATTAGTATTGTATTTATAATTACTAC * * 111021800 TATTATTTTTATTATTAGTATTAGTA-TTATAATTACTAT 1 TATTATTTTTATGATTAGTATT-GTATTTATAATTACTAC 111021839 TATTA 1 TATTA 111021844 CACTTATATA Statistics Matches: 38, Mismatches: 5, Indels: 2 0.84 0.11 0.04 Matches are distributed among these distances: 39 35 0.92 40 3 0.08 ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61 Consensus pattern (39 bp): TATTATTTTTATGATTAGTATTGTATTTATAATTACTAC Found at i:111022034 original size:14 final size:14 Alignment explanation

Indices: 111022015--111022041 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 111022005 CATCATGTTT 111022015 TTTTAATACTATAG 1 TTTTAATACTATAG 111022029 TTTTAATACTATA 1 TTTTAATACTATA 111022042 TTATGTATAT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52 Consensus pattern (14 bp): TTTTAATACTATAG Found at i:111022133 original size:23 final size:23 Alignment explanation

Indices: 111022101--111022158 Score: 66 Period size: 23 Copynumber: 2.6 Consensus size: 23 111022091 TCATATGTAT 111022101 ATATT-TTATGTACATACTTTTA 1 ATATTATTATGTACATACTTTTA ** * 111022123 ATATTATTATGTATTTATTTTTA 1 ATATTATTATGTACATACTTTTA 111022146 ATA-TATATATGTA 1 ATATTAT-TATGTA 111022159 TATATTCATG Statistics Matches: 31, Mismatches: 3, Indels: 3 0.84 0.08 0.08 Matches are distributed among these distances: 22 8 0.26 23 23 0.74 ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57 Consensus pattern (23 bp): ATATTATTATGTACATACTTTTA Found at i:111022164 original size:23 final size:23 Alignment explanation

Indices: 111022024--111022107 Score: 53 Period size: 25 Copynumber: 3.3 Consensus size: 23 111022014 TTTTTAATAC * 111022024 TATAGTTTTAATACTATATTATGTA 1 TATATTTTTAATA-TATA-TATGTA * * 111022049 TATATTTTTACATGTAT-TATGGA 1 TATATTTTTA-ATATATATATGTA * 111022072 CATATTTTCAATAACTATATCATATGTA 1 TATATTTT---TAA-TATAT-ATATGTA 111022100 TATATTTT 1 TATATTTT 111022108 ATGTACATAC Statistics Matches: 45, Mismatches: 7, Indels: 11 0.71 0.11 0.17 Matches are distributed among these distances: 23 12 0.27 25 13 0.29 26 8 0.18 28 12 0.27 ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51 Consensus pattern (23 bp): TATATTTTTAATATATATATGTA Found at i:111022258 original size:21 final size:21 Alignment explanation

Indices: 111022232--111022342 Score: 63 Period size: 21 Copynumber: 5.4 Consensus size: 21 111022222 ACTTTAATAC 111022232 TATATTATGTATACATTTCTA 1 TATATTATGTATACATTTCTA * * * * 111022253 TATATTACGTATATATATCTT 1 TATATTATGTATACATTTCTA * * 111022274 TTTAATATTGTAT---TTT-TA 1 TATATTA-TGTATACATTTCTA * 111022292 TATATGTCATGTATATATTTCTA 1 TATAT-T-ATGTATACATTTCTA * * 111022315 -ATATTATAT-TACATTTTTTA 1 TATATTATGTATACA-TTTCTA 111022335 TATATTAT 1 TATATTAT 111022343 CTTATGTATA Statistics Matches: 67, Mismatches: 14, Indels: 18 0.68 0.14 0.18 Matches are distributed among these distances: 18 4 0.06 19 11 0.16 20 9 0.13 21 30 0.45 22 11 0.16 23 2 0.03 ACGTcount: A:0.32, C:0.06, G:0.05, T:0.57 Consensus pattern (21 bp): TATATTATGTATACATTTCTA Found at i:111022374 original size:27 final size:26 Alignment explanation

Indices: 111022327--111022420 Score: 91 Period size: 27 Copynumber: 3.6 Consensus size: 26 111022317 ATTATATTAC * * 111022327 ATTTTTTATATATTATCTTATGTATAT 1 ATTTTTTATA-ACTATATTATGTATAT * 111022354 ATTTTTTAATAACTATATTATGTATGT 1 ATTTTTT-ATAACTATATTATGTATAT ** * * 111022381 ATTTTTTATCGCTATATTATGTACAC 1 ATTTTTTATAACTATATTATGTATAT * 111022407 ATTTTTAAT-ACTAT 1 ATTTTTTATAACTAT 111022421 GTATATACCT Statistics Matches: 56, Mismatches: 10, Indels: 4 0.80 0.14 0.06 Matches are distributed among these distances: 25 4 0.07 26 22 0.39 27 27 0.48 28 3 0.05 ACGTcount: A:0.31, C:0.07, G:0.05, T:0.56 Consensus pattern (26 bp): ATTTTTTATAACTATATTATGTATAT Found at i:111022524 original size:18 final size:18 Alignment explanation

Indices: 111022487--111022529 Score: 52 Period size: 18 Copynumber: 2.3 Consensus size: 18 111022477 TTCATATATC * 111022487 ATTATTATTAGTTTTTAT 1 ATTATTATTAGTTTTAAT 111022505 ATTATTATT-GTTTTCAAT 1 ATTATTATTAGTTTT-AAT 111022523 ATATATT 1 AT-TATT 111022530 GTATATATTT Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 17 5 0.23 18 13 0.59 19 4 0.18 ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63 Consensus pattern (18 bp): ATTATTATTAGTTTTAAT Found at i:111023118 original size:17 final size:18 Alignment explanation

Indices: 111023081--111023118 Score: 51 Period size: 17 Copynumber: 2.2 Consensus size: 18 111023071 CTCGGCCTTC * 111023081 TTTTTGTTTAAAAAATAA 1 TTTTTGTTTAAAAAAGAA * 111023099 TTTTT-TTTAAAAAAGGA 1 TTTTTGTTTAAAAAAGAA 111023116 TTT 1 TTT 111023119 ATTAGGTGTC Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 17 13 0.72 18 5 0.28 ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53 Consensus pattern (18 bp): TTTTTGTTTAAAAAAGAA Found at i:111023881 original size:26 final size:24 Alignment explanation

Indices: 111023841--111023900 Score: 75 Period size: 26 Copynumber: 2.4 Consensus size: 24 111023831 TTATTTCATT * * * 111023841 AAATAAAAAAATTTAAAAATATAA 1 AAATAAATATATTTAAAAACATAA 111023865 TAAATCAAATATATTTAAAAACATAA 1 -AAAT-AAATATATTTAAAAACATAA 111023891 AAATAAATAT 1 AAATAAATAT 111023901 TAAAACAAAT Statistics Matches: 31, Mismatches: 3, Indels: 3 0.84 0.08 0.08 Matches are distributed among these distances: 24 6 0.19 25 8 0.26 26 17 0.55 ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28 Consensus pattern (24 bp): AAATAAATATATTTAAAAACATAA Found at i:111023912 original size:22 final size:22 Alignment explanation

Indices: 111023871--111023929 Score: 70 Period size: 21 Copynumber: 2.8 Consensus size: 22 111023861 ATAATAAATC * * 111023871 AAATATAT-TTAAAA-ACATAA 1 AAATAAATATTAAAACAAATAA 111023891 AAATAAATATTAAAACAAATAA 1 AAATAAATATTAAAACAAATAA * 111023913 AAAT-AATACTAAAACAA 1 AAATAAATATTAAAACAA 111023930 TTCTTAAAAC Statistics Matches: 34, Mismatches: 3, Indels: 3 0.85 0.08 0.08 Matches are distributed among these distances: 20 7 0.21 21 18 0.53 22 9 0.26 ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24 Consensus pattern (22 bp): AAATAAATATTAAAACAAATAA Found at i:111024006 original size:15 final size:16 Alignment explanation

Indices: 111023976--111024008 Score: 50 Period size: 15 Copynumber: 2.1 Consensus size: 16 111023966 AAATAGTTAT 111023976 ATTAAAAATTTAAAATA 1 ATTAAAAA-TTAAAATA 111023993 ATTAAAAA-TAAAATA 1 ATTAAAAATTAAAATA 111024008 A 1 A 111024009 AAATATATAT Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 15 8 0.50 17 8 0.50 ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30 Consensus pattern (16 bp): ATTAAAAATTAAAATA Found at i:111024525 original size:25 final size:25 Alignment explanation

Indices: 111024475--111024525 Score: 68 Period size: 25 Copynumber: 2.0 Consensus size: 25 111024465 GCAATTTGAA * 111024475 TTTTTTTCTTTTTTTTAATTTTTCT 1 TTTTTTTCTTTTTTTTAATTTATCT * 111024500 TTTTTTTCTTTCTTTTTCA-TTATCT 1 TTTTTTTCTTT-TTTTTAATTTATCT 111024525 T 1 T 111024526 CTGCTCCTCC Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 25 17 0.74 26 6 0.26 ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80 Consensus pattern (25 bp): TTTTTTTCTTTTTTTTAATTTATCT Found at i:111025101 original size:23 final size:24 Alignment explanation

Indices: 111025061--111025118 Score: 59 Period size: 23 Copynumber: 2.5 Consensus size: 24 111025051 GAAGAAAATG * 111025061 AAAAA-AAAAAGTTAAAATAACAT- 1 AAAAAGAAAAAATTAAAATAAC-TC * 111025084 AAAAAGAAAAAATT-AAATTACTC 1 AAAAAGAAAAAATTAAAATAACTC * 111025107 AAAACGAAAAAA 1 AAAAAGAAAAAA 111025119 ATATAGGGAC Statistics Matches: 30, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 22 1 0.03 23 22 0.73 24 7 0.23 ACGTcount: A:0.72, C:0.07, G:0.05, T:0.16 Consensus pattern (24 bp): AAAAAGAAAAAATTAAAATAACTC Found at i:111028648 original size:52 final size:52 Alignment explanation

Indices: 111028591--111028690 Score: 191 Period size: 52 Copynumber: 1.9 Consensus size: 52 111028581 CTAAAGAAAA 111028591 TAAATATTTGACATATAAATATTATACATAAAGAAAAAAATATATATAATAT 1 TAAATATTTGACATATAAATATTATACATAAAGAAAAAAATATATATAATAT * 111028643 TAAATATTTGACATATAAATATTATACATAAAGAAAAATATATATATA 1 TAAATATTTGACATATAAATATTATACATAAAGAAAAAAATATATATA 111028691 TAAAAAATGA Statistics Matches: 47, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 52 47 1.00 ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35 Consensus pattern (52 bp): TAAATATTTGACATATAAATATTATACATAAAGAAAAAAATATATATAATAT Found at i:111028671 original size:15 final size:16 Alignment explanation

Indices: 111028628--111028672 Score: 51 Period size: 15 Copynumber: 2.9 Consensus size: 16 111028618 ATAAAGAAAA 111028628 AAATATATATA-ATATT 1 AAATAT-TATACATATT 111028644 AAATATT-TGACATA-T 1 AAATATTAT-ACATATT 111028659 AAATATTATACATA 1 AAATATTATACATA 111028673 AAGAAAAATA Statistics Matches: 26, Mismatches: 0, Indels: 7 0.79 0.00 0.21 Matches are distributed among these distances: 14 1 0.04 15 15 0.58 16 10 0.38 ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40 Consensus pattern (16 bp): AAATATTATACATATT Found at i:111028683 original size:25 final size:25 Alignment explanation

Indices: 111028603--111028689 Score: 68 Period size: 25 Copynumber: 3.4 Consensus size: 25 111028593 AATATTTGAC 111028603 ATATAAATATTATACATAAAGAAAA 1 ATATAAATATTATACATAAAGAAAA * * * * * * * 111028628 AAATATATATAATA-TTAAATATTTGAC 1 ATATAAATATTATACATAAAGA---AAA 111028655 ATATAAATATTATACATAAAGAAAA 1 ATATAAATATTATACATAAAGAAAA * 111028680 ATATATATAT 1 ATATAAATAT 111028690 ATAAAAAATG Statistics Matches: 43, Mismatches: 15, Indels: 8 0.65 0.23 0.12 Matches are distributed among these distances: 24 5 0.12 25 21 0.49 27 12 0.28 28 5 0.12 ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34 Consensus pattern (25 bp): ATATAAATATTATACATAAAGAAAA Found at i:111028685 original size:27 final size:26 Alignment explanation

Indices: 111028603--111028691 Score: 65 Period size: 27 Copynumber: 3.4 Consensus size: 26 111028593 AATATTTGAC 111028603 ATATAAATATTATACATAAAGAAAAA 1 ATATAAATATTATACATAAAGAAAAA * * * * ** * 111028629 A-ATATATATAATA-TTAAATATTTGAC 1 ATATAAATATTATACATAAAGA--AAAA 111028655 ATATAAATATTATACATAAAGAAAAA 1 ATATAAATATTATACATAAAGAAAAA * 111028681 TATATATATAT 1 -ATATAAATAT 111028692 AAAAAATGAG Statistics Matches: 43, Mismatches: 15, Indels: 9 0.64 0.22 0.13 Matches are distributed among these distances: 24 5 0.12 25 10 0.23 26 4 0.09 27 19 0.44 28 5 0.12 ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35 Consensus pattern (26 bp): ATATAAATATTATACATAAAGAAAAA Found at i:111031710 original size:43 final size:44 Alignment explanation

Indices: 111031600--111031721 Score: 128 Period size: 43 Copynumber: 2.8 Consensus size: 44 111031590 AAATAGGATT * * * 111031600 CCGATATGTGATTTACGTGTAAGACCATGTCTGGGACATCGACA 1 CCGATATGTGAGTTACATGTAAGACCCTGTCTGGGACATCGACA * * * * 111031644 TCG-TATATAAGTT-CATGTAAGACCCTGTCTGGGACAGT-GGCA 1 CCGATATGTGAGTTACATGTAAGACCCTGTCTGGGACA-TCGACA 111031686 CCGATATGTGA-TTACATGTAAGACCAC-GTCTGGGAC 1 CCGATATGTGAGTTACATGTAAGACC-CTGTCTGGGAC 111031722 GTTGGCGTTA Statistics Matches: 64, Mismatches: 10, Indels: 9 0.77 0.12 0.11 Matches are distributed among these distances: 42 28 0.44 43 33 0.52 44 3 0.05 ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27 Consensus pattern (44 bp): CCGATATGTGAGTTACATGTAAGACCCTGTCTGGGACATCGACA Found at i:111033393 original size:20 final size:20 Alignment explanation

Indices: 111033356--111033393 Score: 51 Period size: 20 Copynumber: 1.9 Consensus size: 20 111033346 AAAAAGTGTG * 111033356 AATTTGGCTTGATGTTTGCA 1 AATTTGGCTTGATATTTGCA 111033376 AATTTGG-TTGAGTATTTG 1 AATTTGGCTTGA-TATTTG 111033394 TAAAGAAATT Statistics Matches: 16, Mismatches: 1, Indels: 2 0.84 0.05 0.11 Matches are distributed among these distances: 19 4 0.25 20 12 0.75 ACGTcount: A:0.21, C:0.05, G:0.26, T:0.47 Consensus pattern (20 bp): AATTTGGCTTGATATTTGCA Found at i:111034583 original size:46 final size:46 Alignment explanation

Indices: 111034521--111034818 Score: 328 Period size: 46 Copynumber: 6.9 Consensus size: 46 111034511 TTTGACATGA * * * * * * * 111034521 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT * *** * * 111034567 TGTCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT * 111034613 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT 111034659 TGCC-----A------AACCATGGTCTTACACATTTTATATCAGGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT 111034694 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT 111034740 TGCCATGGTATCTTTCAACCATGGTCTTACAC--------TCAGGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT * 111034778 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT 111034819 TAGAGAGCAC Statistics Matches: 217, Mismatches: 16, Indels: 38 0.80 0.06 0.14 Matches are distributed among these distances: 35 33 0.15 38 38 0.18 40 1 0.00 41 1 0.00 46 144 0.66 ACGTcount: A:0.22, C:0.23, G:0.15, T:0.39 Consensus pattern (46 bp): TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT Found at i:111034675 original size:35 final size:35 Alignment explanation

Indices: 111034629--111034698 Score: 131 Period size: 35 Copynumber: 2.0 Consensus size: 35 111034619 GGTATCTTTC 111034629 AACCATGGTCTTACACATTTCATATCAGGTTGCCA 1 AACCATGGTCTTACACATTTCATATCAGGTTGCCA * 111034664 AACCATGGTCTTACACATTTTATATCAGGTTGCCA 1 AACCATGGTCTTACACATTTCATATCAGGTTGCCA 111034699 TGGTATCTTT Statistics Matches: 34, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 35 34 1.00 ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33 Consensus pattern (35 bp): AACCATGGTCTTACACATTTCATATCAGGTTGCCA Found at i:111034718 original size:81 final size:78 Alignment explanation

Indices: 111034583--111034818 Score: 287 Period size: 81 Copynumber: 2.9 Consensus size: 78 111034573 GGTATCTTTC *** * * 111034583 AACCATGGTCTTGTTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT 1 AACCATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT 111034648 TCATATCAGGTTG 66 TCATATCAGGTTG 111034661 CCAAACCATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC 1 ---AACCATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC * 111034726 ATTTTATATCAGGTTG 63 ATTTCATATCAGGTTG * * 111034742 --CCATGGTATCTTTCAACCATGGTCTTACACTCAGGTTGCCATGGTATCTTTCAACCATGGTCT 1 AACCATGG--TCTTAC-A-CAT--T-TTATA-TCAGGTTGCCATGGTATCTTTCAACCATGGTCT 111034805 TACACATTTCATAT 58 TACACATTTCATAT 111034819 TAGAGAGCAC Statistics Matches: 138, Mismatches: 9, Indels: 13 0.86 0.06 0.08 Matches are distributed among these distances: 76 6 0.04 78 5 0.04 79 1 0.01 80 3 0.02 81 72 0.52 82 1 0.01 83 4 0.03 84 46 0.33 ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37 Consensus pattern (78 bp): AACCATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT TCATATCAGGTTG Found at i:111034767 original size:127 final size:127 Alignment explanation

Indices: 111034541--111034771 Score: 372 Period size: 127 Copynumber: 1.8 Consensus size: 127 111034531 TCTTTCAACT * * * * * *** 111034541 ATGGTCTTACTCATTTTCTGTCATGTTGTCATGGTATCTTTCAACCATGGTCTTGTTCATTTCAT 1 ATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT 111034606 ATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCAAACC 66 ATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCAAACC * 111034668 ATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTAT 1 ATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT * 111034733 ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC 66 ATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACAC 111034772 TCAGGTTGCC Statistics Matches: 94, Mismatches: 10, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 127 94 1.00 ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39 Consensus pattern (127 bp): ATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT ATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCAAACC Found at i:111034785 original size:38 final size:38 Alignment explanation

Indices: 111034734--111034809 Score: 152 Period size: 38 Copynumber: 2.0 Consensus size: 38 111034724 ACATTTTATA 111034734 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC 1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC 111034772 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC 1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC 111034810 ATTTCATATT Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 38 38 1.00 ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34 Consensus pattern (38 bp): TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC Found at i:111036970 original size:11 final size:11 Alignment explanation

Indices: 111036954--111037005 Score: 52 Period size: 11 Copynumber: 4.7 Consensus size: 11 111036944 TATACTAAAT 111036954 AAATAATAATA 1 AAATAATAATA * 111036965 AAATAAT-ATT 1 AAATAATAATA * * 111036975 AAATATCTCATA 1 AAATA-ATAATA * 111036987 AAATATTAATA 1 AAATAATAATA 111036998 AAATAATA 1 AAATAATA 111037006 TTTATCTAAT Statistics Matches: 33, Mismatches: 6, Indels: 4 0.77 0.14 0.09 Matches are distributed among these distances: 10 7 0.21 11 19 0.58 12 7 0.21 ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33 Consensus pattern (11 bp): AAATAATAATA Found at i:111038217 original size:20 final size:20 Alignment explanation

Indices: 111038134--111038218 Score: 75 Period size: 20 Copynumber: 4.2 Consensus size: 20 111038124 AGATGCAAAA * 111038134 CAGGGGCACAGATGTGCAAT 1 CAGGGGCACCGATGTGCAAT * * * 111038154 CAAGGGTATCGATGTGCAAAT 1 CAGGGGCACCGATGTGC-AAT * * * 111038175 -AGGGGTACCGATGTGAAAA 1 CAGGGGCACCGATGTGCAAT 111038194 CAGGGGCA-CGATTGTGCAAT 1 CAGGGGCACCGA-TGTGCAAT 111038214 CAGGG 1 CAGGG 111038219 ATACTAAAGT Statistics Matches: 51, Mismatches: 11, Indels: 6 0.75 0.16 0.09 Matches are distributed among these distances: 19 5 0.10 20 43 0.84 21 3 0.06 ACGTcount: A:0.31, C:0.16, G:0.35, T:0.18 Consensus pattern (20 bp): CAGGGGCACCGATGTGCAAT Found at i:111040403 original size:22 final size:22 Alignment explanation

Indices: 111040375--111040429 Score: 110 Period size: 22 Copynumber: 2.5 Consensus size: 22 111040365 AATTTGTATA 111040375 TTTCAACTAATAATATTATTAG 1 TTTCAACTAATAATATTATTAG 111040397 TTTCAACTAATAATATTATTAG 1 TTTCAACTAATAATATTATTAG 111040419 TTTCAACTAAT 1 TTTCAACTAAT 111040430 TGCTTTTCAA Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 33 1.00 ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45 Consensus pattern (22 bp): TTTCAACTAATAATATTATTAG Found at i:111040845 original size:24 final size:25 Alignment explanation

Indices: 111040805--111040855 Score: 77 Period size: 24 Copynumber: 2.1 Consensus size: 25 111040795 AATCCCTCTG * 111040805 TTCGGATCCCTCGGTTTCTCCCACT 1 TTCGGATCCCTCCGTTTCTCCCACT * 111040830 TTCGGAT-CCTCCGTTTCTCCCTCT 1 TTCGGATCCCTCCGTTTCTCCCACT 111040854 TT 1 TT 111040856 TTCGCCGGTG Statistics Matches: 24, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 24 17 0.71 25 7 0.29 ACGTcount: A:0.06, C:0.39, G:0.14, T:0.41 Consensus pattern (25 bp): TTCGGATCCCTCCGTTTCTCCCACT Found at i:111041614 original size:34 final size:34 Alignment explanation

Indices: 111041575--111041666 Score: 112 Period size: 34 Copynumber: 2.7 Consensus size: 34 111041565 ACTTAGGAAC * * * 111041575 TTGTGAATGAGTAATGGTTTACTGTGGAGGAAAG 1 TTGTGAATGAGTGATGGTTTACTCTGAAGGAAAG * * 111041609 TTGTGACTGAGTGATGTTTTACTCTGAAGGAAAG 1 TTGTGAATGAGTGATGGTTTACTCTGAAGGAAAG * * * 111041643 TCGTTAATGATTGATGGTTTACTC 1 TTGTGAATGAGTGATGGTTTACTC 111041667 CAGGGTCTAG Statistics Matches: 48, Mismatches: 10, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 34 48 1.00 ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37 Consensus pattern (34 bp): TTGTGAATGAGTGATGGTTTACTCTGAAGGAAAG Found at i:111073368 original size:6 final size:6 Alignment explanation

Indices: 111073354--111073395 Score: 57 Period size: 6 Copynumber: 6.8 Consensus size: 6 111073344 TTGAGTCCGA * * 111073354 TTATTT TTATGT TTATGT TTATCTT TTATTT TTATTT TTATT 1 TTATTT TTATTT TTATTT TTAT-TT TTATTT TTATTT TTATT 111073396 CTTCTTGTTA Statistics Matches: 33, Mismatches: 2, Indels: 2 0.89 0.05 0.05 Matches are distributed among these distances: 6 28 0.85 7 5 0.15 ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76 Consensus pattern (6 bp): TTATTT Found at i:111079215 original size:20 final size:21 Alignment explanation

Indices: 111079185--111079224 Score: 64 Period size: 20 Copynumber: 2.0 Consensus size: 21 111079175 TTTATTTTTT * 111079185 AAAATTATTAAGAATTATAAG 1 AAAATTATTAAAAATTATAAG 111079206 AAAA-TATTAAAAATTATAA 1 AAAATTATTAAAAATTATAA 111079225 TAAATATTTA Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 20 14 0.78 21 4 0.22 ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33 Consensus pattern (21 bp): AAAATTATTAAAAATTATAAG Found at i:111081529 original size:13 final size:13 Alignment explanation

Indices: 111081511--111081536 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 111081501 TTCAACAAGC 111081511 TTCTATATTTATA 1 TTCTATATTTATA 111081524 TTCTATATTTATA 1 TTCTATATTTATA 111081537 GTTTTTATGT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62 Consensus pattern (13 bp): TTCTATATTTATA Found at i:111083995 original size:13 final size:13 Alignment explanation

Indices: 111083977--111084035 Score: 58 Period size: 13 Copynumber: 5.0 Consensus size: 13 111083967 CAAATTACTA 111083977 AATAATATCCCAT 1 AATAATATCCCAT 111083990 AATAATAT-CC-T 1 AATAATATCCCAT * 111084001 -ATCATATCCCAT 1 AATAATATCCCAT * 111084013 AAAAATAT--CAT 1 AATAATATCCCAT 111084024 -ATAATATCCCAT 1 AATAATATCCCAT 111084036 TAGGAATAAA Statistics Matches: 37, Mismatches: 4, Indels: 11 0.71 0.08 0.21 Matches are distributed among these distances: 10 12 0.32 11 6 0.16 12 6 0.16 13 13 0.35 ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32 Consensus pattern (13 bp): AATAATATCCCAT Found at i:111084011 original size:23 final size:23 Alignment explanation

Indices: 111083978--111084035 Score: 89 Period size: 23 Copynumber: 2.5 Consensus size: 23 111083968 AAATTACTAA * * 111083978 ATAATATCCCATAATAATATCCT 1 ATAATATCCCATAAAAATATCAT * 111084001 ATCATATCCCATAAAAATATCAT 1 ATAATATCCCATAAAAATATCAT 111084024 ATAATATCCCAT 1 ATAATATCCCAT 111084036 TAGGAATAAA Statistics Matches: 31, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 23 31 1.00 ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33 Consensus pattern (23 bp): ATAATATCCCATAAAAATATCAT Found at i:111085968 original size:16 final size:15 Alignment explanation

Indices: 111085949--111085983 Score: 52 Period size: 16 Copynumber: 2.3 Consensus size: 15 111085939 TACATTTTAT 111085949 AAACAAAATCCAAAAC 1 AAACAAAATCC-AAAC * 111085965 AAACCAAATCCAAAC 1 AAACAAAATCCAAAC 111085980 AAAC 1 AAAC 111085984 CAAACCTAAA Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 15 8 0.44 16 10 0.56 ACGTcount: A:0.66, C:0.29, G:0.00, T:0.06 Consensus pattern (15 bp): AAACAAAATCCAAAC Found at i:111085981 original size:15 final size:16 Alignment explanation

Indices: 111085949--111085987 Score: 62 Period size: 15 Copynumber: 2.5 Consensus size: 16 111085939 TACATTTTAT * 111085949 AAACAAAATCCAAAAC 1 AAACCAAATCCAAAAC 111085965 AAACCAAATCC-AAAC 1 AAACCAAATCCAAAAC 111085980 AAACCAAA 1 AAACCAAA 111085988 CCTAAACCAT Statistics Matches: 22, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 15 12 0.55 16 10 0.45 ACGTcount: A:0.67, C:0.28, G:0.00, T:0.05 Consensus pattern (16 bp): AAACCAAATCCAAAAC Found at i:111097573 original size:44 final size:43 Alignment explanation

Indices: 111097504--111097938 Score: 248 Period size: 44 Copynumber: 9.7 Consensus size: 43 111097494 TATTATGGCG ** ** * 111097504 AATCTTATCTCTTTGAAGTTGTAGTGGAGCAGATTAAATCCATA 1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAT-TATA * * * * * 111097548 AACCTTATCTCCCTGAAGTTATAGTGGAGTAGGTTGAAGTTATA 1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAATTATA * ** * * 111097592 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAA-GATA 1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAATTATA * * * ** * * 111097634 GCGAATCTTATTTCCTTAAAGTTGTAGTGGAACAGATTAAAGCTACAAATTACA 1 ---AATCTTATCTCCCTGAAGTTACAGTGGAGCAGA-T-----T--AAATTATA * * 111097688 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAATTATA 1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAATTATA * * * * * * * ** 111097732 GATCTTATCTCTCTAAAATTACAGTAGAGTAGATCGAAGA-TAGCG 1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGAT-TAA-ATTA-TA * * * 111097777 AATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTATA 1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAATTATA * * * 111097821 GATCTTATCTCCCTGAAGTTACAGTGGAGAAGATTGAAGA-TAGCA 1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-AA-ATTA-TA * * * 111097866 AATCTTATCTCTCTGAAGTTACAGTAGAGCAGATTAAAGCTATA 1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA-TTATA * 111097910 AA-CGTTATCTCCCTGAAGTTACAATGGAG 1 AATC-TTATCTCCCTGAAGTTACAGTGGAG 111097939 TGGATCGAAG Statistics Matches: 301, Mismatches: 67, Indels: 46 0.73 0.16 0.11 Matches are distributed among these distances: 42 3 0.01 43 4 0.01 44 163 0.54 45 97 0.32 50 1 0.00 51 28 0.09 53 3 0.01 54 2 0.01 ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31 Consensus pattern (43 bp): AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAATTATA Found at i:111097739 original size:140 final size:140 Alignment explanation

Indices: 111097551--111097904 Score: 341 Period size: 140 Copynumber: 2.6 Consensus size: 140 111097541 ATCCATAAAC * * * * * * * ** 111097551 CTTATCTCCCTGAAGTTATAGTGGAGTAGGTTGAAGTTATAAGTCTTATCTCCCTGAAGTTGTAG 1 CTTATCTCCCTGAAGTTACAGTAGAGCAGATTGAAATTATAAGTCTTATCTCCCTAAAATTACAG * * * 111097616 TGGAGCAGA-CTAAAGATAGCGAATCTTATTTCCTTAAAGTTGTAGTGGAACAGATTAAAGCTAC 66 TAGAGCAGATC-AAAGATAGCGAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTAAAGCTAC 111097680 AAATTACAAAT 130 AAATTACAAAT * * 111097691 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAATTAT-AGATCTTATCTCTCTAAAATTACA 1 CTTATCTCCCTGAAGTTACAGTAGAGCAGATTGAAATTATAAG-TCTTATCTCCCTAAAATTACA * * * * 111097755 GTAGAGTAGATCGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATT---G---- 65 GTAGAGCAGATCAAAGATAGCGAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTAAAGCTAC * * * 111097813 AAGTTATAGAT 130 AAATTACAAAT * * * * * * * 111097824 CTTATCTCCCTGAAGTTACAGTGGAGAAGATTGAAGA-TAGCAAATCTTATCTCTCTGAAGTTAC 1 CTTATCTCCCTGAAGTTACAGTAGAGCAGATTGAA-ATTA-TAAGTCTTATCTCCCTAAAATTAC * 111097888 AGTAGAGCAGATTAAAG 64 AGTAGAGCAGATCAAAG 111097905 CTATAAACGT Statistics Matches: 178, Mismatches: 31, Indels: 16 0.79 0.14 0.07 Matches are distributed among these distances: 133 42 0.24 134 33 0.19 135 1 0.01 137 1 0.01 139 2 0.01 140 98 0.55 141 1 0.01 ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31 Consensus pattern (140 bp): CTTATCTCCCTGAAGTTACAGTAGAGCAGATTGAAATTATAAGTCTTATCTCCCTAAAATTACAG TAGAGCAGATCAAAGATAGCGAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTAAAGCTACA AATTACAAAT Found at i:111097843 original size:89 final size:89 Alignment explanation

Indices: 111097686--111097948 Score: 357 Period size: 89 Copynumber: 3.0 Consensus size: 89 111097676 CTACAAATTA * * * * 111097686 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAATTATAGATCTTATCTCTCTAAAAT 1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTATAGATCTTATCTCCCTGAAGT * 111097751 TACAGTAGAGTAGATCGAAGATAG 66 TACAGTGGAGTAGATCGAAGATAG * * * 111097775 CGAATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTATAGATCTTATCTCCCTGAAGT 1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTATAGATCTTATCTCCCTGAAGT * * 111097840 TACAGTGGAGAAGATTGAAGATAG 66 TACAGTGGAGTAGATCGAAGATAG * * * * * 111097864 CAAATCTTATCTCTCTGAAGTTACAGTAGAGCAGATTAAAGCTATA-AACGTTATCTCCCTGAAG 1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTATAGATC-TTATCTCCCTGAAG * * 111097928 TTACAATGGAGTGGATCGAAG 65 TTACAGTGGAGTAGATCGAAG 111097949 CAACAATTCC Statistics Matches: 151, Mismatches: 22, Indels: 2 0.86 0.13 0.01 Matches are distributed among these distances: 88 2 0.01 89 149 0.99 ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30 Consensus pattern (89 bp): CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTATAGATCTTATCTCCCTGAAGT TACAGTGGAGTAGATCGAAGATAG Found at i:111097928 original size:133 final size:132 Alignment explanation

Indices: 111097689--111097938 Score: 306 Period size: 133 Copynumber: 1.9 Consensus size: 132 111097679 CAAATTACAA * * * * 111097689 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAATTATAGATCTTATCTCTCTAAAATTAC 1 ATCTTATCTCCCTGAAGTTACAGTAGAGAAGATTGAAATTACAAATCTTATCTCTCTAAAATTAC * * * * * * 111097754 AGTAGAGTAGATCGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTA 66 AGTAGAGCAGATCAAAGATA-CGAAACTTATCTCCCTGAAGTTACAATGGAGCAGATTGAAGTTA 111097819 TAG 130 TAG * * * 111097822 ATCTTATCTCCCTGAAGTTACAGTGGAGAAGATTGAAGA-TAGCAAATCTTATCTCTCTGAAGTT 1 ATCTTATCTCCCTGAAGTTACAGTAGAGAAGATTGAA-ATTA-CAAATCTTATCTCTCTAAAATT * * * 111097886 ACAGTAGAGCAGATTAAAGCTA-TAAACGTTATCTCCCTGAAGTTACAATGGAG 64 ACAGTAGAGCAGATCAAAGATACGAAAC-TTATCTCCCTGAAGTTACAATGGAG 111097939 TGGATCGAAG Statistics Matches: 98, Mismatches: 16, Indels: 6 0.82 0.13 0.05 Matches are distributed among these distances: 132 3 0.03 133 58 0.59 134 37 0.38 ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30 Consensus pattern (132 bp): ATCTTATCTCCCTGAAGTTACAGTAGAGAAGATTGAAATTACAAATCTTATCTCTCTAAAATTAC AGTAGAGCAGATCAAAGATACGAAACTTATCTCCCTGAAGTTACAATGGAGCAGATTGAAGTTAT AG Found at i:111099308 original size:3 final size:3 Alignment explanation

Indices: 111099300--111099386 Score: 51 Period size: 3 Copynumber: 30.7 Consensus size: 3 111099290 TAATTTAATG * * * ** 111099300 TTA TTA TTA CTA TAA TTA -TA TT- TTA TTT TTA TGC TTA TTA TTA TTA 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA * * * 111099346 -TA TTA TTA -TA TCA TTAA TT- TTA -TA TTA CTA TTA TCA TTA TT 1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TT 111099387 CTTGTGTTTC Statistics Matches: 61, Mismatches: 16, Indels: 14 0.67 0.18 0.15 Matches are distributed among these distances: 2 12 0.20 3 46 0.75 4 3 0.05 ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61 Consensus pattern (3 bp): TTA Found at i:111099325 original size:22 final size:21 Alignment explanation

Indices: 111099300--111099376 Score: 63 Period size: 22 Copynumber: 3.6 Consensus size: 21 111099290 TAATTTAATG 111099300 TTATTATTACTATAATTATATT 1 TTATTATTACTAT-ATTATATT * 111099322 TTATTTTTATGCT-TATTATTATT 1 TTATTATTA--CTATATTA-TATT * 111099345 ATATTATTA-TATCATTA-ATT 1 TTATTATTACTAT-ATTATATT 111099365 TTA-TATTACTAT 1 TTATTATTACTAT 111099377 TATCATTATT Statistics Matches: 45, Mismatches: 4, Indels: 14 0.71 0.06 0.22 Matches are distributed among these distances: 19 5 0.11 20 9 0.20 21 1 0.02 22 16 0.36 23 12 0.27 24 2 0.04 ACGTcount: A:0.32, C:0.05, G:0.01, T:0.61 Consensus pattern (21 bp): TTATTATTACTATATTATATT Found at i:111099351 original size:11 final size:11 Alignment explanation

Indices: 111099335--111099386 Score: 54 Period size: 11 Copynumber: 4.6 Consensus size: 11 111099325 TTTTTATGCT 111099335 TATTATTATTA 1 TATTATTATTA 111099346 TATTATTA-TA 1 TATTATTATTA 111099356 TCATTAATT-TTA 1 T-ATT-ATTATTA * 111099368 TATTACTATTA 1 TATTATTATTA 111099379 TCATTATT 1 T-ATTATT 111099387 CTTGTGTTTC Statistics Matches: 34, Mismatches: 2, Indels: 9 0.76 0.04 0.20 Matches are distributed among these distances: 10 5 0.15 11 18 0.53 12 11 0.32 ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60 Consensus pattern (11 bp): TATTATTATTA Found at i:111100499 original size:26 final size:26 Alignment explanation

Indices: 111100470--111100629 Score: 257 Period size: 26 Copynumber: 6.2 Consensus size: 26 111100460 TGGTACAAAT 111100470 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA * * * 111100496 TGATAATAGATTAGGTAAATATTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA 111100522 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA * * * 111100548 TGATAATGGATTAGGTAAATATTCTA 1 TGATAATGGGTTAGGTAAATGTTCCA 111100574 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA * 111100600 TGATAATGGTTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA 111100626 TGAT 1 TGAT 111100630 GGGCATTTCA Statistics Matches: 121, Mismatches: 13, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 26 121 1.00 ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36 Consensus pattern (26 bp): TGATAATGGGTTAGGTAAATGTTCCA Found at i:111100532 original size:52 final size:52 Alignment explanation

Indices: 111100470--111100629 Score: 284 Period size: 52 Copynumber: 3.1 Consensus size: 52 111100460 TGGTACAAAT * 111100470 TGATAATGGGTTAGGTAAATGTTCCATGATAATAGATTAGGTAAATATTCCA 1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA * 111100522 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCTA 1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA * * 111100574 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA 111100626 TGAT 1 TGAT 111100630 GGGCATTTCA Statistics Matches: 103, Mismatches: 5, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 52 103 1.00 ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36 Consensus pattern (52 bp): TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA Found at i:111102145 original size:26 final size:26 Alignment explanation

Indices: 111102115--111102167 Score: 63 Period size: 26 Copynumber: 2.0 Consensus size: 26 111102105 TTTATAGTTT 111102115 TACCCCTAGGAGATAAATT-ACCGAAA 1 TACCCCTAGG-GATAAATTGACCGAAA * * * 111102141 TACCCTTAGGGTTAAATTGACCTAAA 1 TACCCCTAGGGATAAATTGACCGAAA 111102167 T 1 T 111102168 GCATGTTTGA Statistics Matches: 23, Mismatches: 3, Indels: 2 0.82 0.11 0.07 Matches are distributed among these distances: 25 7 0.30 26 16 0.70 ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26 Consensus pattern (26 bp): TACCCCTAGGGATAAATTGACCGAAA Found at i:111107411 original size:16 final size:17 Alignment explanation

Indices: 111107392--111107439 Score: 55 Period size: 17 Copynumber: 2.9 Consensus size: 17 111107382 ACTTTAATTT 111107392 AATATAAAAATT-TAAA 1 AATATAAAAATTATAAA * * 111107408 AATATATAAATTATTAA 1 AATATAAAAATTATAAA 111107425 AATA-ATAAAATTATA 1 AATATA-AAAATTATA 111107440 TTTTAACTCA Statistics Matches: 26, Mismatches: 4, Indels: 3 0.79 0.12 0.09 Matches are distributed among these distances: 16 12 0.46 17 14 0.54 ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35 Consensus pattern (17 bp): AATATAAAAATTATAAA Found at i:111108574 original size:28 final size:27 Alignment explanation

Indices: 111108543--111108617 Score: 69 Period size: 30 Copynumber: 2.6 Consensus size: 27 111108533 TAATATGAAT 111108543 ATATGTATTATATATTTTATAACTATTC 1 ATATGTATTAT-TATTTTATAACTATTC * ** * 111108571 ATATTGTTATTATCTATTATATATTTTTTC 1 ATA-TG-TATTAT-TATTTTATAACTATTC * 111108601 ATATATATTATTATTTT 1 ATATGTATTATTATTTT 111108618 CATATTGAAT Statistics Matches: 38, Mismatches: 7, Indels: 5 0.76 0.14 0.10 Matches are distributed among these distances: 27 5 0.13 28 9 0.24 29 3 0.08 30 21 0.55 ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60 Consensus pattern (27 bp): ATATGTATTATTATTTTATAACTATTC Found at i:111108619 original size:18 final size:18 Alignment explanation

Indices: 111108571--111108622 Score: 56 Period size: 18 Copynumber: 3.0 Consensus size: 18 111108561 ATAACTATTC * * 111108571 ATATTGTTATTATC-TAT 1 ATATTATTATTTTCATAT 111108588 -TATATATT-TTTTCATAT 1 ATAT-TATTATTTTCATAT 111108605 ATATTATTATTTTCATAT 1 ATATTATTATTTTCATAT 111108623 TGAATTGATA Statistics Matches: 29, Mismatches: 2, Indels: 7 0.76 0.05 0.18 Matches are distributed among these distances: 16 7 0.24 17 10 0.34 18 12 0.41 ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62 Consensus pattern (18 bp): ATATTATTATTTTCATAT Found at i:111115990 original size:47 final size:47 Alignment explanation

Indices: 111115937--111116032 Score: 192 Period size: 47 Copynumber: 2.0 Consensus size: 47 111115927 ATTAATGTTG 111115937 TACACGATGAAGGATTGGAGAAAGGAAGCCTCGAGGGCATTCGCCCT 1 TACACGATGAAGGATTGGAGAAAGGAAGCCTCGAGGGCATTCGCCCT 111115984 TACACGATGAAGGATTGGAGAAAGGAAGCCTCGAGGGCATTCGCCCT 1 TACACGATGAAGGATTGGAGAAAGGAAGCCTCGAGGGCATTCGCCCT 111116031 TA 1 TA 111116033 TGAACTAGAG Statistics Matches: 49, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 47 49 1.00 ACGTcount: A:0.30, C:0.21, G:0.31, T:0.18 Consensus pattern (47 bp): TACACGATGAAGGATTGGAGAAAGGAAGCCTCGAGGGCATTCGCCCT Found at i:111121076 original size:206 final size:206 Alignment explanation

Indices: 111120716--111121087 Score: 609 Period size: 206 Copynumber: 1.8 Consensus size: 206 111120706 TAGGCCACAG * * * * 111120716 CATAGCAGATCCAACCTTCAGATGTTTCTGCTGAAGTAGATCTAAGATGGTTTGGCATCCTTGTG 1 CATAGCAGATCCAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTG * * * * 111120781 CTTACAAGGAGCAAATCGAAAACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAGTCT 66 CTTACAAGGAGAAAATCGAAAACATAGCTGATTTGGCTTTCACATGCTTACGCTGAAGCAAATCT * 111120846 AAGATGATTTGGCATCTTTGTATTGTCAGAGAACAATTTGAAGTTTGGCGTCTCCATATTCGACG 131 AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAATTTGAAGTTTGGCGTCTCCATATTCGACG 111120911 GAGGGCAGACA 196 GAGGGCAGACA * 111120922 CATAGCAGATCCAACCTTCATATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTG 1 CATAGCAGATCCAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTG * * ** * 111120987 CTTACAAGGAGAAAATCGAAGACATAGCTGATTTGGTTTTTGCATGCTTACGCTGAAGCAAATGT 66 CTTACAAGGAGAAAATCGAAAACATAGCTGATTTGGCTTTCACATGCTTACGCTGAAGCAAATCT 111121052 AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA 131 AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAA 111121088 ATCAAAGAAG Statistics Matches: 151, Mismatches: 15, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 206 151 1.00 ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30 Consensus pattern (206 bp): CATAGCAGATCCAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTG CTTACAAGGAGAAAATCGAAAACATAGCTGATTTGGCTTTCACATGCTTACGCTGAAGCAAATCT AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAATTTGAAGTTTGGCGTCTCCATATTCGACG GAGGGCAGACA Found at i:111122855 original size:30 final size:30 Alignment explanation

Indices: 111122801--111122889 Score: 83 Period size: 30 Copynumber: 3.0 Consensus size: 30 111122791 TGAATATACG * * * 111122801 TATTATATATTTTATAATTATTCATATTGT 1 TATTATATATTATATATTTTTTCATATTGT * * * 111122831 TATTATCTATTATATATTTTTTCATGTATAT 1 TATTATATATTATATATTTTTTCATAT-TGT * 111122862 TATTATTTA-TAT-TATTATTTTCATATTG 1 TATTATATATTATATATT-TTTTCATATTG 111122890 AATTGATAGT Statistics Matches: 48, Mismatches: 9, Indels: 5 0.77 0.15 0.08 Matches are distributed among these distances: 29 5 0.10 30 33 0.69 31 10 0.21 ACGTcount: A:0.30, C:0.04, G:0.03, T:0.62 Consensus pattern (30 bp): TATTATATATTATATATTTTTTCATATTGT Found at i:111122874 original size:12 final size:12 Alignment explanation

Indices: 111122801--111122881 Score: 53 Period size: 12 Copynumber: 6.9 Consensus size: 12 111122791 TGAATATACG 111122801 TATTATATATTT- 1 TATTAT-TATTTA * * 111122813 TATAATTATTCA 1 TATTATTATTTA * 111122825 TATTGTTA-TTA 1 TATTATTATTTA * * 111122836 T-CTATTATATA 1 TATTATTATTTA * * 111122847 T-TTTTTCATGTA 1 TATTATT-ATTTA 111122859 TATTATTATTTA 1 TATTATTATTTA 111122871 TATTATTATTT 1 TATTATTATTT 111122882 TCATATTGAA Statistics Matches: 52, Mismatches: 13, Indels: 8 0.71 0.18 0.11 Matches are distributed among these distances: 10 4 0.08 11 13 0.25 12 31 0.60 13 4 0.08 ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63 Consensus pattern (12 bp): TATTATTATTTA Found at i:111124454 original size:4 final size:4 Alignment explanation

Indices: 111124443--111124484 Score: 61 Period size: 4 Copynumber: 10.8 Consensus size: 4 111124433 TAAATATTTA 111124443 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAAT -AAT AGAAT AAA 1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAA 111124485 AAGTGGAAGA Statistics Matches: 35, Mismatches: 0, Indels: 6 0.85 0.00 0.15 Matches are distributed among these distances: 3 6 0.17 4 25 0.71 5 4 0.11 ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24 Consensus pattern (4 bp): AAAT Found at i:111124456 original size:12 final size:13 Alignment explanation

Indices: 111124431--111124484 Score: 53 Period size: 12 Copynumber: 4.5 Consensus size: 13 111124421 AAGAATAAAG ** 111124431 AATAAATATTTAA 1 AATAAATAAATAA 111124444 AAT-AATAAAT-A 1 AATAAATAAATAA 111124455 AATAAATAAAT-A 1 AATAAATAAATAA * 111124467 AATAAAT-AATAG 1 AATAAATAAATAA 111124479 AATAAA 1 AATAAA 111124485 AAGTGGAAGA Statistics Matches: 36, Mismatches: 3, Indels: 5 0.82 0.07 0.11 Matches are distributed among these distances: 11 7 0.19 12 26 0.72 13 3 0.08 ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28 Consensus pattern (13 bp): AATAAATAAATAA Found at i:111124482 original size:16 final size:16 Alignment explanation

Indices: 111124424--111124484 Score: 63 Period size: 16 Copynumber: 3.9 Consensus size: 16 111124414 TAAACTTAAG 111124424 AATAA-AGAATAAATA 1 AATAATAGAATAAATA ** * * 111124439 TTTAAAATAATAAATA 1 AATAATAGAATAAATA 111124455 AATAAATA-AATAAATA 1 AAT-AATAGAATAAATA 111124471 AATAATAGAATAAA 1 AATAATAGAATAAA 111124485 AAGTGGAAGA Statistics Matches: 37, Mismatches: 6, Indels: 5 0.77 0.12 0.10 Matches are distributed among these distances: 15 7 0.19 16 27 0.73 17 3 0.08 ACGTcount: A:0.70, C:0.00, G:0.03, T:0.26 Consensus pattern (16 bp): AATAATAGAATAAATA Found at i:111128600 original size:21 final size:23 Alignment explanation

Indices: 111128567--111128619 Score: 56 Period size: 24 Copynumber: 2.3 Consensus size: 23 111128557 CCATTTTTAT * * 111128567 TTTTATTACAATT-TAA-TTTTG 1 TTTTATTTCAATTATAATTTTTC * 111128588 TTTTATTTTAATTACTAATTTTTC 1 TTTTATTTCAATTA-TAATTTTTC 111128612 TTTTATTT 1 TTTTATTT 111128620 GCTTTTGACA Statistics Matches: 26, Mismatches: 3, Indels: 3 0.81 0.09 0.09 Matches are distributed among these distances: 21 11 0.42 23 3 0.12 24 12 0.46 ACGTcount: A:0.25, C:0.06, G:0.02, T:0.68 Consensus pattern (23 bp): TTTTATTTCAATTATAATTTTTC Found at i:111134031 original size:21 final size:21 Alignment explanation

Indices: 111133992--111134031 Score: 55 Period size: 21 Copynumber: 1.9 Consensus size: 21 111133982 GGGAAATGGG * 111133992 AAAAGAAAGGGGAAGAAAGAA 1 AAAAGAAAGGGGAAAAAAGAA 111134013 AAAAG-AAGGGAGAAAAAAG 1 AAAAGAAAGGG-GAAAAAAG 111134032 GTAGGGGTAG Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 20 5 0.29 21 12 0.71 ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00 Consensus pattern (21 bp): AAAAGAAAGGGGAAAAAAGAA Found at i:111134870 original size:8 final size:8 Alignment explanation

Indices: 111134849--111134926 Score: 80 Period size: 7 Copynumber: 10.5 Consensus size: 8 111134839 TTAATATCTG 111134849 AAAATAAT 1 AAAATAAT 111134857 -AAATAAT 1 AAAATAAT 111134864 AAAATAAT 1 AAAATAAT 111134872 AAAATAA- 1 AAAATAAT 111134879 AATAA-AA- 1 AA-AATAAT 111134886 AAAATAA- 1 AAAATAAT 111134893 AAAATAA- 1 AAAATAAT * 111134900 AAAAAAAT 1 AAAATAAT 111134908 AAAA-AAT 1 AAAATAAT * 111134915 AAAAAAAT 1 AAAATAAT 111134923 AAAA 1 AAAA 111134927 ATTGGGTTTC Statistics Matches: 64, Mismatches: 1, Indels: 10 0.85 0.01 0.13 Matches are distributed among these distances: 6 2 0.03 7 35 0.55 8 27 0.42 ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17 Consensus pattern (8 bp): AAAATAAT Found at i:111134927 original size:8 final size:8 Alignment explanation

Indices: 111134849--111134927 Score: 79 Period size: 8 Copynumber: 9.2 Consensus size: 8 111134839 TTAATATCTG 111134849 AAAATAATA 1 AAAATAA-A 111134858 AATAATAAA 1 AA-AATAAA * 111134867 ATAATAAAA 1 AAAAT-AAA 111134876 TAAAATAAA 1 -AAAATAAA 111134885 AAAA-ATAA 1 AAAATA-AA 111134893 AAAATAAA 1 AAAATAAA * 111134901 AAAAAATAA 1 AAAATA-AA 111134910 AAAATAAA 1 AAAATAAA 111134918 AAAATAAA 1 AAAATAAA 111134926 AA 1 AA 111134928 TTGGGTTTCC Statistics Matches: 60, Mismatches: 4, Indels: 13 0.78 0.05 0.17 Matches are distributed among these distances: 7 1 0.02 8 32 0.53 9 18 0.30 10 9 0.15 ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16 Consensus pattern (8 bp): AAAATAAA Found at i:111137885 original size:12 final size:12 Alignment explanation

Indices: 111137868--111137900 Score: 57 Period size: 12 Copynumber: 2.8 Consensus size: 12 111137858 TTCCCTGTAA * 111137868 AATAGTAAACAT 1 AATAGTAAAAAT 111137880 AATAGTAAAAAT 1 AATAGTAAAAAT 111137892 AATAGTAAA 1 AATAGTAAA 111137901 GGGGAAGTAG Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 12 20 1.00 ACGTcount: A:0.64, C:0.03, G:0.09, T:0.24 Consensus pattern (12 bp): AATAGTAAAAAT Found at i:111138078 original size:17 final size:18 Alignment explanation

Indices: 111138058--111138091 Score: 61 Period size: 17 Copynumber: 1.9 Consensus size: 18 111138048 AAGTGAATTG 111138058 AAATTGCA-AAATTAAAT 1 AAATTGCAGAAATTAAAT 111138075 AAATTGCAGAAATTAAA 1 AAATTGCAGAAATTAAA 111138092 ATGAGGAATA Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 17 8 0.50 18 8 0.50 ACGTcount: A:0.59, C:0.06, G:0.09, T:0.26 Consensus pattern (18 bp): AAATTGCAGAAATTAAAT Done.