Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr04 98600468 

Parameters: 2 7 7 80 10 50 1000

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

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

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


File 275 of 325

Found at i:85353239 original size:19 final size:18

Alignment explanation

Indices: 85353203--85353250 Score: 53 Period size: 19 Copynumber: 2.6 Consensus size: 18 85353193 ACAAAGTTAC * 85353203 AGAGAAAGAAATGTGAAA 1 AGAGAAAGAAATGAGAAA 85353221 GAGAGAAAGAAA-GAAGAAA 1 -AGAGAAAGAAATG-AGAAA * 85353240 AGAAAAAGAAA 1 AGAGAAAGAAA 85353251 AAGGATTAAG Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 18 11 0.42 19 15 0.58 ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04 Consensus pattern (18 bp): AGAGAAAGAAATGAGAAA Found at i:85354639 original size:13 final size:13 Alignment explanation

Indices: 85354603--85354639 Score: 56 Period size: 13 Copynumber: 2.8 Consensus size: 13 85354593 TGATAGTTTG * 85354603 GTATGAATTTATAT 1 GTATG-ATTTGTAT 85354617 GTATGATTTGTAT 1 GTATGATTTGTAT 85354630 GTATGATTTG 1 GTATGATTTG 85354640 CTAATTATCT Statistics Matches: 22, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 13 17 0.77 14 5 0.23 ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51 Consensus pattern (13 bp): GTATGATTTGTAT Found at i:85355151 original size:20 final size:20 Alignment explanation

Indices: 85355123--85355180 Score: 82 Period size: 20 Copynumber: 2.9 Consensus size: 20 85355113 TGCCCATGGG * 85355123 CAGGCCACACGGGCGTG-CTC 1 CAGGCCACACGGGCATGTC-C * 85355143 CAGGTCACACGGGCATGTCC 1 CAGGCCACACGGGCATGTCC 85355163 CAGGCCACACGGGCATGT 1 CAGGCCACACGGGCATGT 85355181 GCCCCTATCT Statistics Matches: 34, Mismatches: 3, Indels: 2 0.87 0.08 0.05 Matches are distributed among these distances: 20 33 0.97 21 1 0.03 ACGTcount: A:0.19, C:0.36, G:0.33, T:0.12 Consensus pattern (20 bp): CAGGCCACACGGGCATGTCC Found at i:85355854 original size:114 final size:112 Alignment explanation

Indices: 85355728--85356068 Score: 372 Period size: 114 Copynumber: 3.0 Consensus size: 112 85355718 CCAGCACTAG * * * 85355728 AGACTAGTAAAAAAAACAATTTTTTTTGTTCTGGCCTTCTAATGGCTGGCACCAGGGACTTTTTT 1 AGACCAGTAAAAAAAA-AATTTTTTTTGTTCTGGCCTTCTAATGGCCGGCACCAAGGACTTTTTT * * * 85355793 CGTGTCCTAATGCAATTTTTTTTA-TTGTTCTACACTGATGGTCAGCACC 65 -GTGTCCCAATGCAATTTTTTTTACTT-TTCTACACTGATGGTCGGCACT * * * 85355842 AGACCAGTAAAAAAAAAA------TAGTTTTGGCCTTCTAATGGCCGGCACCAAGGATTTTTTTT 1 AGACCAGTAAAAAAAAAATTTTTTTTGTTCTGGCCTTCTAATGGCCGGCACCAAGGA-CTTTTTT * * 85355901 GTGTCCCAATGCAATTTTTTTTTTACTTTTCTATATTGATGGTCGGCACT 65 GTGTCCCAATGCAA--TTTTTTTTACTTTTCTACACTGATGGTCGGCACT ******* 85355951 AGACCAGTAAATTTTGTTTTTTTTTTTGGTTCTGGCCTTCTAATGGCCGGCACCAAGGACTTTTT 1 AGACCAGTAAA-AAAAAAATTTTTTTT-GTTCTGGCCTTCTAATGGCCGGCACCAAGGACTTTTT * * * 85356016 TGTGCCCCAATGCAAATTATTTTACTTTTCTACACTGATGGTCGGCACT 64 TGTGTCCCAATGCAATTTTTTTTACTTTTCTACACTGATGGTCGGCACT 85356065 AGAC 1 AGAC 85356069 TAGCAATTTA Statistics Matches: 189, Mismatches: 26, Indels: 24 0.79 0.11 0.10 Matches are distributed among these distances: 107 42 0.22 108 6 0.03 109 38 0.20 110 2 0.01 113 2 0.01 114 49 0.26 116 20 0.11 117 30 0.16 ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39 Consensus pattern (112 bp): AGACCAGTAAAAAAAAAATTTTTTTTGTTCTGGCCTTCTAATGGCCGGCACCAAGGACTTTTTTG TGTCCCAATGCAATTTTTTTTACTTTTCTACACTGATGGTCGGCACT Found at i:85355887 original size:107 final size:106 Alignment explanation

Indices: 85355759--85356108 Score: 351 Period size: 109 Copynumber: 3.2 Consensus size: 106 85355749 TTTTTTGTTC * * * 85355759 TGGCCTTCTAATGGCTGGCACCAGGGACTTTTTTCGTGTCCTAATGCAATTTTTTTTA-TTGTTC 1 TGGCCTTCTAATGGCCGGCACCAAGGACTTTTTT-GTGTCCCAATGCAATTTTTTTTACTT-TTC * * * 85355823 TACACTGATGGTCAGCACCAGACCAGTAAAAAAAAAATAGTTT 64 TACACTGATGGTCGGCACTAGACCAGTAAAAAAAAAATGGTTT * 85355866 TGGCCTTCTAATGGCCGGCACCAAGGATTTTTTTTGTGTCCCAATGCAATTTTTTTTTTACTTTT 1 TGGCCTTCTAATGGCCGGCACCAAGGA-CTTTTTTGTGTCCCAATGCAA--TTTTTTTTACTTTT * * ******* * 85355931 CTATATTGATGGTCGGCACTAGACCAGTAAATTTTGTTTTTTTTTTTGGTTC 63 CTACACTGATGGTCGGCACTAGACCAGTAAA--------AAAAAAATGGTTT * * * 85355983 TGGCCTTCTAATGGCCGGCACCAAGGACTTTTTTGTGCCCCAATGCAAATTATTTTACTTTTCTA 1 TGGCCTTCTAATGGCCGGCACCAAGGACTTTTTTGTGTCCCAATGCAATTTTTTTTACTTTTCTA * * 85356048 CACTGATGGTCGGCACTAGACTAGCAATTTAAAAAAAATGGTTT 66 CACTGATGGTCGGCACTAGACCAGTAA---AAAAAAAATGGTTT 85356092 TGGCCTTCTAATGGCCG 1 TGGCCTTCTAATGGCCG 85356109 AGACCAGAGT Statistics Matches: 195, Mismatches: 33, Indels: 28 0.76 0.13 0.11 Matches are distributed among these distances: 107 38 0.19 108 6 0.03 109 60 0.31 110 2 0.01 114 38 0.19 116 19 0.10 117 32 0.16 ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38 Consensus pattern (106 bp): TGGCCTTCTAATGGCCGGCACCAAGGACTTTTTTGTGTCCCAATGCAATTTTTTTTACTTTTCTA CACTGATGGTCGGCACTAGACCAGTAAAAAAAAAATGGTTT Found at i:85356410 original size:27 final size:27 Alignment explanation

Indices: 85356373--85356435 Score: 92 Period size: 27 Copynumber: 2.3 Consensus size: 27 85356363 ATCATGAAAT * 85356373 GAGTTTGTTTGTAGTGGATTGTATG-TGG 1 GAGTTT-TTTGTAGTGGATTGTA-GATGA 85356401 GAGTTTTTTGTAGTGGATTGTAGATGA 1 GAGTTTTTTGTAGTGGATTGTAGATGA 85356428 GAGTTTTT 1 GAGTTTTT 85356436 CATAGTGTAC Statistics Matches: 33, Mismatches: 1, Indels: 3 0.89 0.03 0.08 Matches are distributed among these distances: 26 1 0.03 27 26 0.79 28 6 0.18 ACGTcount: A:0.17, C:0.00, G:0.35, T:0.48 Consensus pattern (27 bp): GAGTTTTTTGTAGTGGATTGTAGATGA Found at i:85356441 original size:27 final size:27 Alignment explanation

Indices: 85356384--85356442 Score: 75 Period size: 27 Copynumber: 2.2 Consensus size: 27 85356374 AGTTTGTTTG * ** 85356384 TAGTGGATTGTATGTGGGAGTTTTTTG 1 TAGTGGATTGTATGTGAGAGTTTTTCA 85356411 TAGTGGATTGTA-GATGAGAGTTTTTCA 1 TAGTGGATTGTATG-TGAGAGTTTTTCA 85356438 TAGTG 1 TAGTG 85356443 TACAACCAAA Statistics Matches: 28, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 26 1 0.04 27 27 0.96 ACGTcount: A:0.20, C:0.02, G:0.34, T:0.44 Consensus pattern (27 bp): TAGTGGATTGTATGTGAGAGTTTTTCA Found at i:85357152 original size:20 final size:20 Alignment explanation

Indices: 85357115--85357153 Score: 53 Period size: 20 Copynumber: 1.9 Consensus size: 20 85357105 GTGCGTATTA * 85357115 TTTTTGTTTGAATCTTTTAT 1 TTTTTGTTTGAATATTTTAT 85357135 TTTTTGTATT-AATATTTTA 1 TTTTTGT-TTGAATATTTTA 85357154 GAATGTTTGT Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 20 15 0.88 21 2 0.12 ACGTcount: A:0.21, C:0.03, G:0.08, T:0.69 Consensus pattern (20 bp): TTTTTGTTTGAATATTTTAT Found at i:85359681 original size:21 final size:22 Alignment explanation

Indices: 85359635--85359682 Score: 57 Period size: 21 Copynumber: 2.3 Consensus size: 22 85359625 GATTTCCATT 85359635 TCATTTAAATTATCTATCTTTC 1 TCATTTAAATTATCTATCTTTC * 85359657 -CATTTAAATTTAT-T-TTTTTC 1 TCATTTAAA-TTATCTATCTTTC 85359677 TCATTT 1 TCATTT 85359683 CAAAGTTTTT Statistics Matches: 23, Mismatches: 1, Indels: 5 0.79 0.03 0.17 Matches are distributed among these distances: 20 5 0.22 21 14 0.61 22 4 0.17 ACGTcount: A:0.25, C:0.15, G:0.00, T:0.60 Consensus pattern (22 bp): TCATTTAAATTATCTATCTTTC Found at i:85359772 original size:5 final size:5 Alignment explanation

Indices: 85359742--85359864 Score: 61 Period size: 5 Copynumber: 22.6 Consensus size: 5 85359732 TTTTTTTAAA * * * 85359742 ATTTC ATTCC ATTTC ATAATC A--TC ATTTC ATTTT ATATTC ATTTAAC 1 ATTTC ATTTC ATTTC AT-TTC ATTTC ATTTC ATTTC AT-TTC ATTT--C * * * * 85359789 ATTTC ATTTA ATTTC ATATTC ATTAC AAATTAC ATTTC TTTTC ATATTC 1 ATTTC ATTTC ATTTC AT-TTC ATTTC --ATTTC ATTTC ATTTC AT-TTC 85359838 ATATTTC ATTTAAC ATTTC ATTTC ATT 1 --ATTTC ATTT--C ATTTC ATTTC ATT 85359865 AATTTTTTTT Statistics Matches: 93, Mismatches: 11, Indels: 28 0.70 0.08 0.21 Matches are distributed among these distances: 3 3 0.03 5 55 0.59 6 15 0.16 7 18 0.19 8 2 0.02 ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53 Consensus pattern (5 bp): ATTTC Found at i:85359796 original size:28 final size:28 Alignment explanation

Indices: 85359764--85359864 Score: 103 Period size: 28 Copynumber: 3.4 Consensus size: 28 85359754 TTCATAATCA * 85359764 TCATTTCATTTTATATTCATTTAACATT 1 TCATTTCATTTCATATTCATTTAACATT * * 85359792 TCATTTAATTTCATATTCATTACAAATTACATT 1 TCATTTCATTTCATATTCATT-----TAACATT * 85359825 TCTTTTCATATTCATATTTCATTTAACATT 1 TCATTTCAT-TTCATA-TTCATTTAACATT 85359855 TCATTTCATT 1 TCATTTCATT 85359865 AATTTTTTTT Statistics Matches: 59, Mismatches: 7, Indels: 13 0.75 0.09 0.16 Matches are distributed among these distances: 28 19 0.32 29 1 0.02 30 14 0.24 33 13 0.22 34 6 0.10 35 6 0.10 ACGTcount: A:0.30, C:0.16, G:0.00, T:0.54 Consensus pattern (28 bp): TCATTTCATTTCATATTCATTTAACATT Found at i:85360026 original size:16 final size:16 Alignment explanation

Indices: 85359986--85360027 Score: 52 Period size: 15 Copynumber: 2.7 Consensus size: 16 85359976 TATTAAGGTC 85359986 ATTTAAATTTTTTCGA 1 ATTTAAATTTTTTCGA * 85360002 ATTT-TATTTTTATC-A 1 ATTTAAATTTTT-TCGA 85360017 ATTTAAATTTT 1 ATTTAAATTTT 85360028 AAATTTAAAA Statistics Matches: 22, Mismatches: 2, Indels: 4 0.79 0.07 0.14 Matches are distributed among these distances: 15 11 0.50 16 11 0.50 ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62 Consensus pattern (16 bp): ATTTAAATTTTTTCGA Found at i:85360245 original size:16 final size:16 Alignment explanation

Indices: 85360226--85360270 Score: 56 Period size: 16 Copynumber: 2.8 Consensus size: 16 85360216 CACTTTTTTT 85360226 TTTCATTTCATTTTCA 1 TTTCATTTCATTTTCA * 85360242 TTTCATTTC-GTTTCA 1 TTTCATTTCATTTTCA 85360257 TTTCCATTCTCATT 1 TTT-CATT-TCATT 85360271 CCTATTTCAT Statistics Matches: 24, Mismatches: 2, Indels: 4 0.80 0.07 0.13 Matches are distributed among these distances: 15 8 0.33 16 13 0.54 17 2 0.08 18 1 0.04 ACGTcount: A:0.16, C:0.22, G:0.02, T:0.60 Consensus pattern (16 bp): TTTCATTTCATTTTCA Found at i:85360255 original size:10 final size:10 Alignment explanation

Indices: 85360226--85360282 Score: 60 Period size: 11 Copynumber: 5.3 Consensus size: 10 85360216 CACTTTTTTT 85360226 TTTCATTTCA 1 TTTCATTTCA 85360236 TTTTCATTTCA 1 -TTTCATTTCA * 85360247 TTTCGTTTCA 1 TTTCATTTCA 85360257 TTTCCATTCTCA 1 TTT-CATT-TCA * 85360269 TTCCTATTTCA 1 TTTC-ATTTCA 85360280 TTT 1 TTT 85360283 AAATTATATT Statistics Matches: 39, Mismatches: 4, Indels: 6 0.80 0.08 0.12 Matches are distributed among these distances: 10 12 0.31 11 19 0.49 12 8 0.21 ACGTcount: A:0.16, C:0.23, G:0.02, T:0.60 Consensus pattern (10 bp): TTTCATTTCA Found at i:85360255 original size:21 final size:22 Alignment explanation

Indices: 85360226--85360282 Score: 71 Period size: 21 Copynumber: 2.6 Consensus size: 22 85360216 CACTTTTTTT * 85360226 TTTCATTTCATTTTCATT-TCA 1 TTTCATTTCATTTCCATTCTCA * 85360247 TTTCGTTTCATTTCCATTCTCA 1 TTTCATTTCATTTCCATTCTCA * 85360269 TTCCTATTTCATTT 1 TTTC-ATTTCATTT 85360283 AAATTATATT Statistics Matches: 30, Mismatches: 4, Indels: 2 0.83 0.11 0.06 Matches are distributed among these distances: 21 16 0.53 22 6 0.20 23 8 0.27 ACGTcount: A:0.16, C:0.23, G:0.02, T:0.60 Consensus pattern (22 bp): TTTCATTTCATTTCCATTCTCA Found at i:85360271 original size:6 final size:5 Alignment explanation

Indices: 85360226--85360282 Score: 60 Period size: 5 Copynumber: 10.6 Consensus size: 5 85360216 CACTTTTTTT * * 85360226 TTTCA TTTCA TTTTCA TTTCA TTTCG TTTCA TTTCCA TTCTCA TTCCTA 1 TTTCA TTTCA -TTTCA TTTCA TTTCA TTTCA TTT-CA TT-TCA TTTC-A 85360275 TTTCA TTT 1 TTTCA TTT 85360283 AAATTATATT Statistics Matches: 44, Mismatches: 4, Indels: 8 0.79 0.07 0.14 Matches are distributed among these distances: 5 26 0.59 6 17 0.39 7 1 0.02 ACGTcount: A:0.16, C:0.23, G:0.02, T:0.60 Consensus pattern (5 bp): TTTCA Found at i:85360308 original size:15 final size:16 Alignment explanation

Indices: 85360290--85360324 Score: 54 Period size: 15 Copynumber: 2.2 Consensus size: 16 85360280 TTTAAATTAT 85360290 ATTTTTTTC-AATTTA 1 ATTTTTTTCTAATTTA * 85360305 ATTTTTTTCTAATTTC 1 ATTTTTTTCTAATTTA 85360321 ATTT 1 ATTT 85360325 ATATTATCTA Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 15 9 0.50 16 9 0.50 ACGTcount: A:0.23, C:0.09, G:0.00, T:0.69 Consensus pattern (16 bp): ATTTTTTTCTAATTTA Found at i:85360369 original size:49 final size:48 Alignment explanation

Indices: 85360299--85360427 Score: 188 Period size: 49 Copynumber: 2.7 Consensus size: 48 85360289 TATTTTTTTC * * * 85360299 AATTTAATTTTTTTCTAATTTCATTTATATTATCTATTTTTCCATGCA 1 AATTTAATTTTTTTCTCATTTCATTTAAATTATCTATCTTTCCATGCA * 85360347 AATTTAATTTTTTTTCTCATTTCATTTAAATCATCTATCTTTCCATGCA 1 AATTTAA-TTTTTTTCTCATTTCATTTAAATTATCTATCTTTCCATGCA * 85360396 AATTAAATTTTTTTCTCAATTT-ATTTAAATTA 1 AATTTAATTTTTTTCTC-ATTTCATTTAAATTA 85360428 AATTTTTTTC Statistics Matches: 73, Mismatches: 6, Indels: 4 0.88 0.07 0.05 Matches are distributed among these distances: 48 26 0.36 49 47 0.64 ACGTcount: A:0.29, C:0.13, G:0.02, T:0.56 Consensus pattern (48 bp): AATTTAATTTTTTTCTCATTTCATTTAAATTATCTATCTTTCCATGCA Found at i:85360427 original size:27 final size:27 Alignment explanation

Indices: 85360395--85360735 Score: 221 Period size: 27 Copynumber: 13.2 Consensus size: 27 85360385 CTTTCCATGC 85360395 AAATTAAATTTTTTTCTCAATTT-ATTT 1 AAATTAAATTTTTTTCTC-ATTTCATTT 85360422 AAATTAAATTTTTTTCTCATTTCATTT 1 AAATTAAATTTTTTTCTCATTTCATTT * * 85360449 AAATTTAATTTTTTTCTCATTTCTTTT 1 AAATTAAATTTTTTTCTCATTTCATTT * 85360476 GAATT-AATTTTTTTC-C---TCATTT 1 AAATTAAATTTTTTTCTCATTTCATTT * * 85360498 CAATTAAATTTATCTT-TC-TTTCAATTT 1 AAATTAAATTT-TTTTCTCATTTC-ATTT * 85360525 TAA-TATAA-TTTTTTCTCAGTTT-ATTT 1 AAATTA-AATTTTTTTCTCA-TTTCATTT 85360551 AAATT-AATTTTTTTCCTCATTTCATTT 1 AAATTAAATTTTTTT-CTCATTTCATTT * * * * 85360578 CAATT-TATCTTTCTT-TCA-AT--TTT 1 AAATTAAAT-TTTTTTCTCATTTCATTT * * * 85360601 AATTTTAA-TTTTTTCTCATTTCTTTT 1 AAATTAAATTTTTTTCTCATTTCATTT * 85360627 AAATTAAA-ATTTTTCTTCATTTCATTT 1 AAATTAAATTTTTTTC-TCATTTCATTT * * 85360654 AAA-T---TTATCTT-TC-TTTCAATTT 1 AAATTAAATTTTTTTCTCATTTC-ATTT * * * 85360676 TAATTCAAA-TTTTGTCTCATTTCTTTT 1 AAATT-AAATTTTTTTCTCATTTCATTT * 85360703 AAATTAATTTTTTTTCCTCATTTCATTT 1 AAATTAAATTTTTTT-CTCATTTCATTT 85360731 AAATT 1 AAATT 85360736 TTTCTTTCTT Statistics Matches: 247, Mismatches: 34, Indels: 65 0.71 0.10 0.19 Matches are distributed among these distances: 21 4 0.02 22 22 0.09 23 15 0.06 24 9 0.04 25 7 0.03 26 61 0.25 27 101 0.41 28 28 0.11 ACGTcount: A:0.27, C:0.12, G:0.01, T:0.60 Consensus pattern (27 bp): AAATTAAATTTTTTTCTCATTTCATTT Found at i:85360497 original size:129 final size:129 Alignment explanation

Indices: 85360350--85360584 Score: 332 Period size: 129 Copynumber: 1.8 Consensus size: 129 85360340 CCATGCAAAT * * * 85360350 TTAATTTTTTTTCTCATTTCATTTAAA-TCATCTATCTTTCCATGCAAAT-TAAATTTTTTTCTC 1 TTAATTTTTTTCCTCATTTCAATTAAATTCATCTATCTTTCAATGCAAATAT-AA-TTTTTTCTC 85360413 AATTTATTTAAATTAAATTTTTTT-CTCATTTCATTTAAATTTAATTTTTTTCTCATTTCTTTTG 64 AATTTATTTAAATT-AATTTTTTTCCTCATTTCATTTAAATTTAATTTTTTTCTCATTTCTTTTG 85360477 AA 128 AA * * *** * 85360479 TTAATTTTTTTCCTCATTTCAATTAAATTTATCTTTCTTTCAATTTTAATATAATTTTTTCTCAG 1 TTAATTTTTTTCCTCATTTCAATTAAATTCATCTATCTTTCAATGCAAATATAATTTTTTCTCAA * 85360544 TTTATTTAAATTAATTTTTTTCCTCATTTCATTTCAATTTA 66 TTTATTTAAATTAATTTTTTTCCTCATTTCATTTAAATTTA 85360585 TCTTTCTTTC Statistics Matches: 93, Mismatches: 10, Indels: 6 0.85 0.09 0.06 Matches are distributed among these distances: 128 9 0.10 129 65 0.70 130 18 0.19 131 1 0.01 ACGTcount: A:0.27, C:0.13, G:0.01, T:0.59 Consensus pattern (129 bp): TTAATTTTTTTCCTCATTTCAATTAAATTCATCTATCTTTCAATGCAAATATAATTTTTTCTCAA TTTATTTAAATTAATTTTTTTCCTCATTTCATTTAAATTTAATTTTTTTCTCATTTCTTTTGAA Found at i:85360553 original size:151 final size:150 Alignment explanation

Indices: 85360418--85360767 Score: 397 Period size: 151 Copynumber: 2.3 Consensus size: 150 85360408 TTCTCAATTT * * 85360418 ATTTAAATTAAATTT-TTTTCTCATTTC-A-TTTAAATTTAATTTTTTTCTCATTTCTTTTGAAT 1 ATTTAAATTAAATTTATCTT-TC-TTTCAATTTTAAATTTAA-TTTTTTCTCATTTCTTTTAAAT ** 85360480 TAATTTTTTTCCTCATTTCAATTAAATTTATCTTTCTTTCAATTTTAATATAATTTTTTCTCAGT 63 TAAAATTTTTCCTCATTTCAATTAAATTTATCTTTCTTTCAATTTTAATATAATTTTTTCTCAGT * 85360545 TTATTTAAATTAATTTTTTTCCTC 128 TTATTTAAATT-ATTTTTCTCCTC * * * * 85360569 ATTTCATTTCAATTTATCTTTCTTTCAATTTTAATTTTAATTTTTTCTCATTTCTTTTAAATTAA 1 ATTTAAATTAAATTTATCTTTCTTTCAATTTTAAATTTAATTTTTTCTCATTTCTTTTAAATTAA * * * 85360634 AATTTTTCTTCATTTCATTTAAATTTATCTTTCTTTCAATTTTAAT-TCAAATTTTGTCTCA-TT 66 AATTTTTCCTCATTTCAATTAAATTTATCTTTCTTTCAATTTTAATAT--AATTTTTTCTCAGTT * * 85360697 TCTTTTAAATTAATTTTTTTTCCTC 129 T-ATTTAAATT-A-TTTTTCTCCTC * * * * * * 85360722 ATTTCATTTAAATTTTTCTTTCTTTC-CTTGTAAATTTAAATTTTTC 1 ATTTAAATTAAATTTATCTTTCTTTCAATTTTAAATTTAATTTTTTC 85360768 CTCAATTCAC Statistics Matches: 174, Mismatches: 18, Indels: 13 0.85 0.09 0.06 Matches are distributed among these distances: 150 5 0.03 151 84 0.48 152 50 0.29 153 35 0.20 ACGTcount: A:0.25, C:0.13, G:0.01, T:0.61 Consensus pattern (150 bp): ATTTAAATTAAATTTATCTTTCTTTCAATTTTAAATTTAATTTTTTCTCATTTCTTTTAAATTAA AATTTTTCCTCATTTCAATTAAATTTATCTTTCTTTCAATTTTAATATAATTTTTTCTCAGTTTA TTTAAATTATTTTTCTCCTC Found at i:85360631 original size:76 final size:76 Alignment explanation

Indices: 85360446--85360843 Score: 463 Period size: 76 Copynumber: 5.3 Consensus size: 76 85360436 TCTCATTTCA * * * 85360446 TTTAAATTTAATTTTTTTCTCATTTCTTTTGAATTAATTTTTTTCCTCATTTCAATTAAATTTAT 1 TTTAATTTTAA-TTTTTTCTCATTTCTTTTAAATTAATTTTTTTCCTCATTTCATTTAAATTTAT 85360511 CTTTCTTTCAAT 65 CTTTCTTTCAAT * * * 85360523 TTTAA-TATAATTTTTTCTCAGTTT-ATTTAAATTAATTTTTTTCCTCATTTCATTTCAATTTAT 1 TTTAATTTTAATTTTTTCTCA-TTTCTTTTAAATTAATTTTTTTCCTCATTTCATTTAAATTTAT 85360586 CTTTCTTTCAAT 65 CTTTCTTTCAAT ** * 85360598 TTTAATTTTAATTTTTTCTCATTTCTTTTAAATTAAAATTTTTCTTCATTTCATTTAAATTTATC 1 TTTAATTTTAATTTTTTCTCATTTCTTTTAAATTAATTTTTTTCCTCATTTCATTTAAATTTATC 85360663 TTTCTTTCAAT 66 TTTCTTTCAAT ** * * 85360674 TTTAATTCAAATTTTGTCTCATTTCTTTTAAATTAATTTTTTTTCCTCATTTCATTTAAATTTTT 1 TTTAATTTTAATTTTTTCTCATTTCTTTTAAATTAA-TTTTTTTCCTCATTTCATTTAAATTTAT * 85360739 CTTTCTTTC-CT 65 CTTTCTTTCAAT * * * * ** * 85360750 TGTAAATTTAAATTTTTCCTCAATTCACTTATATT--TTTTTTT--TCATTTCATTTAAA-TTAT 1 T-TTAATTTTAATTTTTTCTCATTTCTTTTAAATTAATTTTTTTCCTCATTTCATTTAAATTTAT * * 85360810 CTATCTTTCCA- 65 CTTTCTTTCAAT * * 85360821 TGTAATTTTCATTTTCTTCTCAT 1 TTTAATTTTAATTTT-TTCTCAT 85360844 ACCATTTATC Statistics Matches: 278, Mismatches: 36, Indels: 20 0.83 0.11 0.06 Matches are distributed among these distances: 70 10 0.04 71 17 0.06 72 14 0.05 74 7 0.03 75 65 0.23 76 102 0.37 77 63 0.23 ACGTcount: A:0.24, C:0.14, G:0.01, T:0.60 Consensus pattern (76 bp): TTTAATTTTAATTTTTTCTCATTTCTTTTAAATTAATTTTTTTCCTCATTTCATTTAAATTTATC TTTCTTTCAAT Found at i:85360632 original size:129 final size:128 Alignment explanation

Indices: 85360404--85360716 Score: 289 Period size: 129 Copynumber: 2.5 Consensus size: 128 85360394 CAAATTAAAT * 85360404 TTTTTTCTCAATTTATTTAAATTAAATTTTTTTCTCATTTCATTTAAATTTAATTTTTTTCTCAT 1 TTTTTTCTCAATTTATTTAAATTAAATTTTTTTCTCATTTCATTTAAATTTAATTTTTTTCTAAT * * 85360469 TTCTTTTGAATTAATTTTTTTCCTCATTTCAATT-AAATTTATCTTTCTTTCAATTTTAATATAA 66 TTCTATT--ATTAATTTTTTTCCTCATTTAAATTAAAATTTATCTTTCTTTCAATTTTAATATAA * * 85360533 TTTTTTCTCAGTTTATTTAAATT-AATTTTTTTCCTCATTTCATTTCAATTT-ATCTTTCTTTC- 1 TTTTTTCTCAATTTATTTAAATTAAATTTTTTT-CTCATTTCATTTAAATTTAAT-TTT-TTTCT * * * * 85360595 AATTT-TAATT-TTAATTTTTTCTCATTTCTTTTAAATTAAAATTTTTC-TTCATTTC-ATTTAA 63 AATTTCT-ATTATTAATTTTTT-TC--CTCATTTAAATTAAAATTTATCTTTC-TTTCAATTTTA * 85360656 AT-TTA 123 ATATAA * * 85360661 TCTTTCTT-TCAA--T-TTT-AATTCAAA-TTTTGTCTCATTTCTTTTAAA-TTAATTTTTTT 1 T-TTT-TTCTCAATTTATTTAAATT-AAATTTTTTTCTCATTTCATTTAAATTTAATTTTTTT 85360717 TCCTCATTTC Statistics Matches: 156, Mismatches: 14, Indels: 34 0.76 0.07 0.17 Matches are distributed among these distances: 123 3 0.02 124 5 0.03 125 19 0.12 126 18 0.12 127 5 0.03 128 15 0.10 129 73 0.47 130 18 0.12 ACGTcount: A:0.26, C:0.12, G:0.01, T:0.61 Consensus pattern (128 bp): TTTTTTCTCAATTTATTTAAATTAAATTTTTTTCTCATTTCATTTAAATTTAATTTTTTTCTAAT TTCTATTATTAATTTTTTTCCTCATTTAAATTAAAATTTATCTTTCTTTCAATTTTAATATAA Found at i:85360670 original size:21 final size:22 Alignment explanation

Indices: 85360628--85360680 Score: 56 Period size: 21 Copynumber: 2.5 Consensus size: 22 85360618 ATTTCTTTTA * * 85360628 AATTAAAATTTTTCTTCATTTC 1 AATTTAAATTTATCTTCATTTC 85360650 -ATTTAAATTTATCTTTC-TTTC 1 AATTTAAATTTATC-TTCATTTC * 85360671 AATTTTAATT 1 AATTTAAATT 85360681 CAAATTTTGT Statistics Matches: 26, Mismatches: 3, Indels: 4 0.79 0.09 0.12 Matches are distributed among these distances: 21 15 0.58 22 11 0.42 ACGTcount: A:0.30, C:0.11, G:0.00, T:0.58 Consensus pattern (22 bp): AATTTAAATTTATCTTCATTTC Found at i:85360675 original size:22 final size:23 Alignment explanation

Indices: 85360619--85360680 Score: 58 Period size: 22 Copynumber: 2.8 Consensus size: 23 85360609 TTTTTTCTCA * * * * 85360619 TTTCTTTTAAATTAAAATTTTTC 1 TTTCATTTCAATTTAAATTTATC 85360642 -TTCATTTC-ATTTAAATTTATC 1 TTTCATTTCAATTTAAATTTATC * 85360663 TTTC-TTTCAATTTTAATT 1 TTTCATTTCAATTTAAATT 85360681 CAAATTTTGT Statistics Matches: 32, Mismatches: 5, Indels: 5 0.76 0.12 0.12 Matches are distributed among these distances: 21 15 0.47 22 17 0.53 ACGTcount: A:0.27, C:0.11, G:0.00, T:0.61 Consensus pattern (23 bp): TTTCATTTCAATTTAAATTTATC Found at i:85360735 original size:49 final size:48 Alignment explanation

Indices: 85360418--85360740 Score: 158 Period size: 49 Copynumber: 6.4 Consensus size: 48 85360408 TTCTCAATTT * * 85360418 ATTTAAATTAAATTTTTTTCTCATTTCATTTAAATTTAATTTTTTTCTCATTTC 1 ATTTAATTTAAA--TTTTTCTCATTTCATTTAAA-TTAATTTTTTT-TC--CTC * * * * * * 85360472 TTTTGAA-TTAATTTTTTTCCTCATTTCAATTAAATTTATCTTTCTTT-C-A 1 ATTT-AATTTAA-ATTTTT-CTCATTTCATTTAAATTAAT-TTTTTTTCCTC * * 85360521 ATTTTAATATAATTTTTTCTCAGTTT-ATTTAAATTAA-TTTTTTTCCTC 1 A-TTTAATTTAAATTTTTCTCA-TTTCATTTAAATTAATTTTTTTTCCTC * * * * * * 85360569 ATTTCATTTCAATTTATCTTTC-TTTCAATTTTAATTTTAATTTTTTCTCATTTC 1 ATTTAATTTAAATTT-T-TCTCATTTC-A-TTTAA-ATTAATTTTTTTTC--CTC * * * * * 85360623 TTTTAAATTAAAATTTTTCTTCATTTCATTTAAATTTATCTTTCTTT-C-A 1 ATTT-AATTTAAATTTTTC-TCATTTCATTTAAATTAAT-TTTTTTTCCTC * * 85360672 ATTTTAATTCAAATTTTGTCTCATTTCTTTTAAATTAATTTTTTTTCCTC 1 A-TTTAATTTAAATTTT-TCTCATTTCATTTAAATTAATTTTTTTTCCTC * 85360722 ATTTCATTTAAATTTTTCT 1 ATTTAATTTAAATTTTTCT 85360741 TTCTTTCCTT Statistics Matches: 203, Mismatches: 40, Indels: 58 0.67 0.13 0.19 Matches are distributed among these distances: 46 6 0.03 47 14 0.07 48 24 0.12 49 57 0.28 50 17 0.08 51 4 0.02 52 11 0.05 53 21 0.10 54 35 0.17 55 14 0.07 ACGTcount: A:0.26, C:0.13, G:0.01, T:0.61 Consensus pattern (48 bp): ATTTAATTTAAATTTTTCTCATTTCATTTAAATTAATTTTTTTTCCTC Found at i:85360850 original size:153 final size:149 Alignment explanation

Indices: 85360481--85360827 Score: 386 Period size: 153 Copynumber: 2.3 Consensus size: 149 85360471 CTTTTGAATT * * * * * 85360481 AATT-TTTTTCCTCATTTCAATTAAATTTATCTTTCTTTCAATTTTAA-T-ATAATTTTTTCTCA 1 AATTATTTTTCTTCATTTCATTTAAATTTATCTATCTTTCAATTGTAATTCA-AATTTTCTCTCA * * * * 85360543 GTTT-ATTTAAATTAATTTTTTTCCTCATTTCATTTCAATTTATCTTTCTTTCAATTTTAATTTT 65 -TTTCTTTTAAATTAATTTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATTTAAATTTA * * ** 85360607 AATTTTTTCTCATTTCTTTTA 129 AATTTTTCCTCAATTCACTTA * * * 85360628 AATTAAAATTTTTCTTCATTTCATTTAAATTTATCTTTCTTTCAATTTTAATTCAAATTTTGTCT 1 AATT---ATTTTTCTTCATTTCATTTAAATTTATCTATCTTTCAATTGTAATTCAAATTTTCTCT * * 85360693 CATTTCTTTTAAATTAATTTTTTTTCCTCATTTCATTTAAATTTTTCTTTCTTTC-CTTGTAAAT 63 CATTTCTTTTAAATTAA-TTTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATT-TAAAT 85360757 TTAAATTTTTCCTCAATTCACTTA 126 TTAAATTTTTCCTCAATTCACTTA * * * 85360781 TATT-TTTTTTTTCATTTCATTTAAA-TTATCTATCTTTCCA-TGTAATT 1 AATTATTTTTCTTCATTTCATTTAAATTTATCTATCTTTCAATTGTAATT 85360828 TTCATTTTCT Statistics Matches: 173, Mismatches: 18, Indels: 18 0.83 0.09 0.09 Matches are distributed among these distances: 147 10 0.06 148 13 0.08 149 20 0.12 151 44 0.25 152 24 0.14 153 62 0.36 ACGTcount: A:0.25, C:0.14, G:0.01, T:0.60 Consensus pattern (149 bp): AATTATTTTTCTTCATTTCATTTAAATTTATCTATCTTTCAATTGTAATTCAAATTTTCTCTCAT TTCTTTTAAATTAATTTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATTTAAATTTAAA TTTTTCCTCAATTCACTTA Found at i:85364255 original size:116 final size:108 Alignment explanation

Indices: 85363988--85364589 Score: 644 Period size: 117 Copynumber: 5.4 Consensus size: 108 85363978 AGAATGAAAA * * * * 85363988 ATTGGAACACGAAAAAATTCCTTAGTGCCGGCCATTAGAAGGCCAGAACCAAAATTTTTTTTTAC 1 ATTGGGACACGAAAAAAGTCCCTAGTGCCGACCATTAGAAGGCCAGAACC--AATTTTTTTTTAC * * 85364053 TGGTCTGGTGCTGGCAATCAGTGTAGAAAAGT-AAAAAAATTTAA 64 TGGTCTGGTGCTGGCCATCAGTGTAGAAAAGTAAAAAAAATTTAC * * * 85364097 ATTGGGACACGAAAAAAGTCCCTGGTGCCGGCCATTAGAAGGCCAAAACCAATTTTTTTTGAAAA 1 ATTGGGACACGAAAAAAGTCCCTAGTGCCGACCATTAGAAGGCCAGAACCAA-TTTTTTT----- 85364162 ATTACTGGTCTGGTGCTGGCCATCAGTGTAGAAAAGTAAAAAAAAAATTT-C 60 -TTACTGGTCTGGTGCTGGCCATCAGTGTAGAAAAGT--AAAAAAAATTTAC * * * 85364213 ATTGGGAGACGAAAAAAGTCCCTAGTGCCGACCATTAAAAGGCCAAGAACGAATTTTTTTTAAAA 1 ATTGGGACACGAAAAAAGTCCCTAGTGCCGACCATTAGAAGGCC-AGAACCAA-TTTTTTT---- * * * 85364278 TTATTGGTTTGGTGCTGACCATCAGTGTAGAAAAGTAAAAAAAAAAATTTAC 60 TTACTGGTCTGGTGCTGGCCATCAGTGTAGAAAAGT---AAAAAAAATTTAC * * * * * 85364330 ATTGGGACACGAAAAAAGTCCTTGGTGCCGACCATTAAAAGGCTAGAACCAAATTTTTTTTACTG 1 ATTGGGACACGAAAAAAGTCCCTAGTGCCGACCATTAGAAGGCCAGAACCAATTTTTTTTTACTG * * * * 85364395 GTTTGGTG-TCGGCCATTAGTGTAGAAAAGTAAAAATAATTTGC 66 GTCTGGTGCT-GGCCATCAGTGTAGAAAAGTAAAAAAAATTTAC * * * * * * 85364438 ATTGGGAAACAAAAAAAGTCCCTGGTGCC-AGCTATTAGAAGGCTAGAA-CAA-ATTTTTTTA-T 1 ATTGGGACACGAAAAAAGTCCCTAGTGCCGA-CCATTAGAAGGCCAGAACCAATTTTTTTTTACT * * * 85364499 GGTCTGGTGTTGGCCATCAGTGTAGAAAAGT-AAAAAATTTTGC 65 GGTCTGGTGCTGGCCATCAGTGTAGAAAAGTAAAAAAAATTTAC * 85364542 ATTGGGACACGAAAAAAGTCCCTAGTGCCGACCATTAGAAGGCTAGAA 1 ATTGGGACACGAAAAAAGTCCCTAGTGCCGACCATTAGAAGGCCAGAA 85364590 TAAAAAAAAT Statistics Matches: 435, Mismatches: 41, Indels: 39 0.84 0.08 0.08 Matches are distributed among these distances: 104 52 0.12 105 29 0.07 106 9 0.02 107 6 0.01 108 59 0.14 109 45 0.10 110 1 0.00 111 31 0.07 114 35 0.08 115 43 0.10 116 60 0.14 117 65 0.15 ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27 Consensus pattern (108 bp): ATTGGGACACGAAAAAAGTCCCTAGTGCCGACCATTAGAAGGCCAGAACCAATTTTTTTTTACTG GTCTGGTGCTGGCCATCAGTGTAGAAAAGTAAAAAAAATTTAC Found at i:85364581 original size:104 final size:106 Alignment explanation

Indices: 85364163--85364589 Score: 486 Period size: 104 Copynumber: 3.9 Consensus size: 106 85364153 TTTTGAAAAA * 85364163 TTACTGGTCTGGTGCTGGCCATCAGTGTAGAAAAGTAAAAAAAAAATTT-CATTGGGAGACGAAA 1 TTACTGGTCTGGTGCTGGCCATCAGTGTAGAAAAGT--AAAAAAAATTTGCATTGGGACACGAAA * * 85364227 AAAGTCCCTAGTGCCGACCATTAAAAGGCCAAGAACGAATTTTTTTT 64 AAAGTCCCTAGTGCCGACCATTAAAAGG-CTAGAAC-AA--ATTTTT * * * * 85364274 AAAATTATTGGTTTGGTGCTGACCATCAGTGTAGAAAAGTAAAAAAAAAAATTTACATTGGGACA 1 ----TTACTGGTCTGGTGCTGGCCATCAGTGTAGAAAAGT---AAAAAAAATTTGCATTGGGACA * * 85364339 CGAAAAAAGTCCTTGGTGCCGACCATTAAAAGGCTAGAACCAAATTTTTT 59 CGAAAAAAGTCCCTAGTGCCGACCATTAAAAGGCTAGAA-CAAA-TTTTT * * * * * 85364389 TTACTGGTTTGGTG-TCGGCCATTAGTGTAGAAAAGTAAAAATAATTTGCATTGGGAAACAAAAA 1 TTACTGGTCTGGTGCT-GGCCATCAGTGTAGAAAAGTAAAAAAAATTTGCATTGGGACACGAAAA * * * 85364453 AAGTCCCTGGTGCC-AGCTATTAGAAGGCTAGAACAAATTTTT 65 AAGTCCCTAGTGCCGA-CCATTAAAAGGCTAGAACAAATTTTT * * 85364495 TTA-TGGTCTGGTGTTGGCCATCAGTGTAGAAAAGT-AAAAAATTTTGCATTGGGACACGAAAAA 1 TTACTGGTCTGGTGCTGGCCATCAGTGTAGAAAAGTAAAAAAAATTTGCATTGGGACACGAAAAA * 85364558 AGTCCCTAGTGCCGACCATTAGAAGGCTAGAA 66 AGTCCCTAGTGCCGACCATTAAAAGGCTAGAA 85364590 TAAAAAAAAT Statistics Matches: 278, Mismatches: 26, Indels: 27 0.84 0.08 0.08 Matches are distributed among these distances: 104 52 0.19 105 29 0.10 106 9 0.03 107 5 0.02 108 52 0.19 110 1 0.00 111 31 0.11 115 38 0.14 116 20 0.07 117 41 0.15 ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27 Consensus pattern (106 bp): TTACTGGTCTGGTGCTGGCCATCAGTGTAGAAAAGTAAAAAAAATTTGCATTGGGACACGAAAAA AGTCCCTAGTGCCGACCATTAAAAGGCTAGAACAAATTTTT Found at i:85369453 original size:74 final size:74 Alignment explanation

Indices: 85369332--85369480 Score: 289 Period size: 74 Copynumber: 2.0 Consensus size: 74 85369322 CCATAGTTAT 85369332 TTGTTGACTATCTGAAGAATAAACTAATAACAAAATGATAGTAAATCATAAAGAAAACAATGGTT 1 TTGTTGACTATCTGAAGAATAAACTAATAACAAAATGATAGTAAATCATAAAGAAAACAATGGTT 85369397 CAATCATGA 66 CAATCATGA * 85369406 TTGTTGACTATCTGAAGAATAAACTAATAACAAAATGATAGTAAATCATATAGAAAACAATGGTT 1 TTGTTGACTATCTGAAGAATAAACTAATAACAAAATGATAGTAAATCATAAAGAAAACAATGGTT 85369471 CAATCATGA 66 CAATCATGA 85369480 T 1 T 85369481 CCTCTTACTT Statistics Matches: 74, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 74 74 1.00 ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28 Consensus pattern (74 bp): TTGTTGACTATCTGAAGAATAAACTAATAACAAAATGATAGTAAATCATAAAGAAAACAATGGTT CAATCATGA Found at i:85373156 original size:23 final size:24 Alignment explanation

Indices: 85373115--85373168 Score: 65 Period size: 23 Copynumber: 2.2 Consensus size: 24 85373105 AAAAAAAAAT * 85373115 CTATTGTTTTGTTATTGTTTTGCTG 1 CTATT-TTTTGTTACTGTTTTGCTG * 85373140 CTATTTTTT-TTACTGTTTTGTTG 1 CTATTTTTTGTTACTGTTTTGCTG * 85373163 TTATTT 1 CTATTT 85373169 CACAATTATG Statistics Matches: 26, Mismatches: 3, Indels: 2 0.84 0.10 0.06 Matches are distributed among these distances: 23 17 0.65 24 4 0.15 25 5 0.19 ACGTcount: A:0.09, C:0.07, G:0.15, T:0.69 Consensus pattern (24 bp): CTATTTTTTGTTACTGTTTTGCTG Found at i:85373997 original size:23 final size:22 Alignment explanation

Indices: 85373971--85374013 Score: 59 Period size: 22 Copynumber: 1.9 Consensus size: 22 85373961 AATTCTTATG 85373971 AATTTTAAACTTTAGATTTTTTT 1 AATTTTAAA-TTTAGATTTTTTT * * 85373994 AATTTTTAATTTATATTTTT 1 AATTTTAAATTTAGATTTTT 85374014 AAAAATTAAT Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 22 10 0.56 23 8 0.44 ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65 Consensus pattern (22 bp): AATTTTAAATTTAGATTTTTTT Found at i:85382200 original size:19 final size:21 Alignment explanation

Indices: 85382166--85382206 Score: 59 Period size: 19 Copynumber: 2.0 Consensus size: 21 85382156 ATTGGATGGA 85382166 TCAGCTCTTACGAGCTTCTGT 1 TCAGCTCTTACGAGCTTCTGT * 85382187 TCAGCT-TT-CGAGCTTTTGT 1 TCAGCTCTTACGAGCTTCTGT 85382206 T 1 T 85382207 GGCATATTCG Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 19 11 0.58 20 2 0.11 21 6 0.32 ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44 Consensus pattern (21 bp): TCAGCTCTTACGAGCTTCTGT Found at i:85386674 original size:43 final size:44 Alignment explanation

Indices: 85386613--85386707 Score: 115 Period size: 43 Copynumber: 2.2 Consensus size: 44 85386603 AATGCCAACA * * * 85386613 TCCCAGAC-GTGGTCTTACATGTAAT-TCAGTATCGAAGCCTCTG 1 TCCCAGACAGTGGTCTTACACGAAATCTCA-AATCGAAGCCTCTG * * 85386656 TCCCAGACAG-GGTCTTACACGAAATCTCAAATCGAGGCCTGTG 1 TCCCAGACAGTGGTCTTACACGAAATCTCAAATCGAAGCCTCTG 85386699 TCCCAGACA 1 TCCCAGACA 85386708 CTGTATTGCA Statistics Matches: 45, Mismatches: 5, Indels: 4 0.83 0.09 0.07 Matches are distributed among these distances: 43 41 0.91 44 4 0.09 ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24 Consensus pattern (44 bp): TCCCAGACAGTGGTCTTACACGAAATCTCAAATCGAAGCCTCTG Found at i:85393784 original size:622 final size:622 Alignment explanation

Indices: 85392601--85393846 Score: 2438 Period size: 622 Copynumber: 2.0 Consensus size: 622 85392591 ACAAAAAATG * 85392601 ATTTAGACTCTAATGAGTCTTCATTGAGACAGATAAAGTATGAGGACATTAAGGTAAGCAATGAA 1 ATTTAGACTCTAATGAGTCTTCACTGAGACAGATAAAGTATGAGGACATTAAGGTAAGCAATGAA 85392666 TTGAAATTAAAACCCTCTATTGAAGAACCTCCCAAATTGGAACTGAAGCAATTACCAAATCACCT 66 TTGAAATTAAAACCCTCTATTGAAGAACCTCCCAAATTGGAACTGAAGCAATTACCAAATCACCT 85392731 AGAGTATGTGTTTCTTGAAAACAATTAGACATTACCAGTGATTATTGCTTTAGATTTAAAGTCAA 131 AGAGTATGTGTTTCTTGAAAACAATTAGACATTACCAGTGATTATTGCTTTAGATTTAAAGTCAA 85392796 ATGAGAAAGATGAGTTATTGAAAGTGTTGAAGGAACATAAAAGAGCTATAGCCTGGAAGATTTCT 196 ATGAGAAAGATGAGTTATTGAAAGTGTTGAAGGAACATAAAAGAGCTATAGCCTGGAAGATTTCT * 85392861 GACATTAGAGGGATCAATCCTTCTTTTAGCATATATAAAATTTTAATGGAGGCTGAATACAAACC 261 AACATTAGAGGGATCAATCCTTCTTTTAGCATATATAAAATTTTAATGGAGGCTGAATACAAACC * 85392926 ATGTGTACAATCTCAAAAACGACTAAATCTTAACATAAATGAAGTCGTTAAGGCTGAGGTAATTA 326 ATGTGTACAATCTCAAAAACGACTAAATCCTAACATAAATGAAGTCGTTAAGGCTGAGGTAATTA 85392991 AACTTCTAGATGCTGGAGTTATTCATTCTATTTCTGATAGTACTTGGGTGAGTTCTGTGCAGGTT 391 AACTTCTAGATGCTGGAGTTATTCATTCTATTTCTGATAGTACTTGGGTGAGTTCTGTGCAGGTT 85393056 GTTCCTGAGAAGGGATACATGACTGTTGTAGCCAAAAAGCAGAACGAGTTGATTCCAACGAGAAT 456 GTTCCTGAGAAGGGATACATGACTGTTGTAGCCAAAAAGCAGAACGAGTTGATTCCAACGAGAAT 85393121 AGTCACAAGATGGAGAGTTTGTATTGACTATAGGAAGTTGAATGATGCCACGAGAAAAGATCATT 521 AGTCACAAGATGGAGAGTTTGTATTGACTATAGGAAGTTGAATGATGCCACGAGAAAAGATCATT 85393186 TTCCTCTACCATTCATAGATCAAATGTTGGAAAGATT 586 TTCCTCTACCATTCATAGATCAAATGTTGGAAAGATT 85393223 ATTTAGACTCTAATGAGTCTTCACTGAGACAGATAAAGTATGAGGACATTAAGGTAAGCAATGAA 1 ATTTAGACTCTAATGAGTCTTCACTGAGACAGATAAAGTATGAGGACATTAAGGTAAGCAATGAA * 85393288 TTGAAATTAAAACCTTCTATTGAAGAACCTCCCAAATTGGAACTGAAGCAATTACCAAATCACCT 66 TTGAAATTAAAACCCTCTATTGAAGAACCTCCCAAATTGGAACTGAAGCAATTACCAAATCACCT 85393353 AGAGTATGTGTTTCTTGAAAACAATTAGACATTACCAGTGATTATTGCTTTAGATTTAAAGTCAA 131 AGAGTATGTGTTTCTTGAAAACAATTAGACATTACCAGTGATTATTGCTTTAGATTTAAAGTCAA 85393418 ATGAGAAAGATGAGTTATTGAAAGTGTTGAAGGAACATAAAAGAGCTATAGCCTGGAAGATTTCT 196 ATGAGAAAGATGAGTTATTGAAAGTGTTGAAGGAACATAAAAGAGCTATAGCCTGGAAGATTTCT 85393483 AACATTAGAGGGATCAATCCTTCTTTTAGCATATATAAAATTTTAATGGAGGCTGAATACAAACC 261 AACATTAGAGGGATCAATCCTTCTTTTAGCATATATAAAATTTTAATGGAGGCTGAATACAAACC * 85393548 ATGTGTACAATCTCAAAAATGACTAAATCCTAACATAAATGAAGTCGTTAAGGCTGAGGTAATTA 326 ATGTGTACAATCTCAAAAACGACTAAATCCTAACATAAATGAAGTCGTTAAGGCTGAGGTAATTA * 85393613 AACTTCTAGATGCTGGAGTTATTCATTCTATTTCTGATAGTACTTGGGTGAGTTCTGTGTAGGTT 391 AACTTCTAGATGCTGGAGTTATTCATTCTATTTCTGATAGTACTTGGGTGAGTTCTGTGCAGGTT 85393678 GTTCCTGAGAAGGGATACATGACTGTTGTAGCCAAAAAGCAGAACGAGTTGATTCCAACGAGAAT 456 GTTCCTGAGAAGGGATACATGACTGTTGTAGCCAAAAAGCAGAACGAGTTGATTCCAACGAGAAT 85393743 AGTCACAAGATGGAGAGTTTGTATTGACTATAGGAAGTTGAATGATGCCACGAGAAAAGATCATT 521 AGTCACAAGATGGAGAGTTTGTATTGACTATAGGAAGTTGAATGATGCCACGAGAAAAGATCATT 85393808 TTCCTCTACCATTCATAGATCAAATGTTGGAAAGATT 586 TTCCTCTACCATTCATAGATCAAATGTTGGAAAGATT 85393845 AT 1 AT 85393847 CTGGGCATAT Statistics Matches: 618, Mismatches: 6, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 622 618 1.00 ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30 Consensus pattern (622 bp): ATTTAGACTCTAATGAGTCTTCACTGAGACAGATAAAGTATGAGGACATTAAGGTAAGCAATGAA TTGAAATTAAAACCCTCTATTGAAGAACCTCCCAAATTGGAACTGAAGCAATTACCAAATCACCT AGAGTATGTGTTTCTTGAAAACAATTAGACATTACCAGTGATTATTGCTTTAGATTTAAAGTCAA ATGAGAAAGATGAGTTATTGAAAGTGTTGAAGGAACATAAAAGAGCTATAGCCTGGAAGATTTCT AACATTAGAGGGATCAATCCTTCTTTTAGCATATATAAAATTTTAATGGAGGCTGAATACAAACC ATGTGTACAATCTCAAAAACGACTAAATCCTAACATAAATGAAGTCGTTAAGGCTGAGGTAATTA AACTTCTAGATGCTGGAGTTATTCATTCTATTTCTGATAGTACTTGGGTGAGTTCTGTGCAGGTT GTTCCTGAGAAGGGATACATGACTGTTGTAGCCAAAAAGCAGAACGAGTTGATTCCAACGAGAAT AGTCACAAGATGGAGAGTTTGTATTGACTATAGGAAGTTGAATGATGCCACGAGAAAAGATCATT TTCCTCTACCATTCATAGATCAAATGTTGGAAAGATT Found at i:85396824 original size:5 final size:5 Alignment explanation

Indices: 85396814--85396893 Score: 56 Period size: 5 Copynumber: 15.0 Consensus size: 5 85396804 CCCTTTCCAT * * * 85396814 TTTTA TTTTA TTTTA TTTTA TCCTTA TTATTA TTTTTC TTTCTT TCTTTA 1 TTTTA TTTTA TTTTA TTTTA T-TTTA TT-TTA -TTTTA TTT-TA T-TTTA 85396864 TTTTTA TTTTA TTATTA -TTT- TTTTA TTTTA 1 -TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA 85396894 AAGTATTATT Statistics Matches: 61, Mismatches: 5, Indels: 18 0.73 0.06 0.21 Matches are distributed among these distances: 4 5 0.08 5 32 0.52 6 19 0.31 7 5 0.08 ACGTcount: A:0.17, C:0.06, G:0.00, T:0.76 Consensus pattern (5 bp): TTTTA Found at i:85396889 original size:11 final size:11 Alignment explanation

Indices: 85396814--85396890 Score: 52 Period size: 11 Copynumber: 6.9 Consensus size: 11 85396804 CCCTTTCCAT 85396814 TTTTATT-TTA 1 TTTTATTATTA 85396824 TTTTATT-TTA 1 TTTTATTATTA * 85396834 TCCTTATTATTA 1 T-TTTATTATTA * * 85396846 TTTT-TCTTTCTT 1 TTTTAT-TAT-TA * 85396858 TCTTTATTTTTA 1 T-TTTATTATTA 85396870 TTTTATTATTA 1 TTTTATTATTA * 85396881 TTTTTTTATT 1 TTTTATTATT 85396891 TTAAAGTATT Statistics Matches: 54, Mismatches: 7, Indels: 11 0.75 0.10 0.15 Matches are distributed among these distances: 10 12 0.22 11 27 0.50 12 8 0.15 13 6 0.11 14 1 0.02 ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77 Consensus pattern (11 bp): TTTTATTATTA Found at i:85396892 original size:6 final size:6 Alignment explanation

Indices: 85396812--85396885 Score: 50 Period size: 6 Copynumber: 13.0 Consensus size: 6 85396802 TTCCCTTTCC ** * * 85396812 ATTTTT A-TTTT A-TTTT A-TTTT ATCCTT ATTATT ATTTTT CTTTCTT 1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTT-TT * * 85396858 -TCTTT ATTTTT A-TTTT ATTATT ATTTTT 1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT 85396886 TTATTTTAAA Statistics Matches: 54, Mismatches: 10, Indels: 8 0.75 0.14 0.11 Matches are distributed among these distances: 5 22 0.41 6 30 0.56 7 2 0.04 ACGTcount: A:0.18, C:0.07, G:0.00, T:0.76 Consensus pattern (6 bp): ATTTTT Found at i:85396902 original size:21 final size:19 Alignment explanation

Indices: 85396864--85396906 Score: 59 Period size: 21 Copynumber: 2.2 Consensus size: 19 85396854 TCTTTCTTTA * 85396864 TTTTTATTTTATTATTATT 1 TTTTTATTTTAGTATTATT 85396883 TTTTTATTTTAAAGTATTATT 1 TTTTTATTTT--AGTATTATT 85396904 TTT 1 TTT 85396907 ACTAATTCTT Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 19 10 0.48 21 11 0.52 ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74 Consensus pattern (19 bp): TTTTTATTTTAGTATTATT Found at i:85396905 original size:19 final size:20 Alignment explanation

Indices: 85396861--85396907 Score: 62 Period size: 19 Copynumber: 2.5 Consensus size: 20 85396851 CTTTCTTTCT * * 85396861 TTATTTTTATTTTATTATTA 1 TTATTTTTATTTTATAAGTA 85396881 TT-TTTTTATTTTA-AAGTA 1 TTATTTTTATTTTATAAGTA 85396899 TTATTTTTA 1 TTATTTTTA 85396908 CTAATTCTTA Statistics Matches: 24, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 18 5 0.21 19 17 0.71 20 2 0.08 ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72 Consensus pattern (20 bp): TTATTTTTATTTTATAAGTA Found at i:85397145 original size:23 final size:22 Alignment explanation

Indices: 85397083--85397146 Score: 65 Period size: 23 Copynumber: 2.8 Consensus size: 22 85397073 TTCACTATTG * 85397083 TATTATTTAGGTTTATATTTGAT 1 TATTATTTA-GTTTATTTTTGAT * * * 85397106 TATCACTTAGTTCTATTTTTGGT 1 TATTATTTAGTT-TATTTTTGAT 85397129 TATTATTATAGTTTATTT 1 TATTATT-TAGTTTATTT 85397147 GATATTTTTG Statistics Matches: 33, Mismatches: 6, Indels: 4 0.77 0.14 0.09 Matches are distributed among these distances: 22 3 0.09 23 25 0.76 24 5 0.15 ACGTcount: A:0.23, C:0.05, G:0.11, T:0.61 Consensus pattern (22 bp): TATTATTTAGTTTATTTTTGAT Found at i:85399436 original size:45 final size:45 Alignment explanation

Indices: 85399346--85399476 Score: 176 Period size: 45 Copynumber: 3.0 Consensus size: 45 85399336 CCGAATTTAT * ** * 85399346 TCACCGGCATT-TTGCCTGCTAGGCT-TGAGGCCCGAAAAATATC 1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC * * 85399389 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATGTC 1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC * * 85399434 TCACCAGCATTATAGCCTGCTAGGCTCCAAGGCCCGAATAATA 1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATA 85399477 CTGTACAACA Statistics Matches: 76, Mismatches: 10, Indels: 2 0.86 0.11 0.02 Matches are distributed among these distances: 43 10 0.13 44 13 0.17 45 53 0.70 ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24 Consensus pattern (45 bp): TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC Found at i:85403202 original size:45 final size:45 Alignment explanation

Indices: 85403112--85403242 Score: 176 Period size: 45 Copynumber: 3.0 Consensus size: 45 85403102 CCGAATTTAT * ** * 85403112 TCACCGGCATT-TTGCCTGCTAGGCT-TGAGGCCCGAAAAATATC 1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC * * 85403155 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATGTC 1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC * * 85403200 TCACCAGCATTATAGCCTGCTAGGCTCCAAGGCCCGAATAATA 1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATA 85403243 CTGTACAACA Statistics Matches: 76, Mismatches: 10, Indels: 2 0.86 0.11 0.02 Matches are distributed among these distances: 43 10 0.13 44 13 0.17 45 53 0.70 ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24 Consensus pattern (45 bp): TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC Found at i:85404233 original size:5 final size:5 Alignment explanation

Indices: 85404225--85404252 Score: 56 Period size: 5 Copynumber: 5.6 Consensus size: 5 85404215 TTGTTTTCTT 85404225 TTTTA TTTTA TTTTA TTTTA TTTTA TTT 1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT 85404253 CTCTTTTTAG Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 23 1.00 ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82 Consensus pattern (5 bp): TTTTA Found at i:85412688 original size:57 final size:58 Alignment explanation

Indices: 85412608--85412726 Score: 190 Period size: 57 Copynumber: 2.1 Consensus size: 58 85412598 TGGTTCATAT 85412608 TAAAATAATGTTAATTTTATAGGAATTTAAATTTTTATGGAAAA-ACAAAAATTGATGA 1 TAAAATAATGTTAATTTTATAGGAATTTAAATTTTTATGGAAAACA-AAAAATTGATGA * * 85412666 TAAAATAATTTTCA-TTTATAGGAATTTAAATTTTTATGGAAAACAAAAAATTGATGA 1 TAAAATAATGTTAATTTTATAGGAATTTAAATTTTTATGGAAAACAAAAAATTGATGA 85412723 -AAAA 1 TAAAA 85412727 GTAAAATCAC Statistics Matches: 58, Mismatches: 2, Indels: 4 0.91 0.03 0.06 Matches are distributed among these distances: 56 4 0.07 57 41 0.71 58 13 0.22 ACGTcount: A:0.50, C:0.03, G:0.11, T:0.37 Consensus pattern (58 bp): TAAAATAATGTTAATTTTATAGGAATTTAAATTTTTATGGAAAACAAAAAATTGATGA Found at i:85412849 original size:17 final size:17 Alignment explanation

Indices: 85412823--85412865 Score: 50 Period size: 17 Copynumber: 2.5 Consensus size: 17 85412813 AAAAATTATC * 85412823 AAATAGAATTGATTTCAA 1 AAATA-AATTAATTTCAA * * 85412841 AATTAAATTAATTTGAA 1 AAATAAATTAATTTCAA 85412858 AAATAAAT 1 AAATAAAT 85412866 AAAAATATGT Statistics Matches: 21, Mismatches: 4, Indels: 1 0.81 0.15 0.04 Matches are distributed among these distances: 17 17 0.81 18 4 0.19 ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35 Consensus pattern (17 bp): AAATAAATTAATTTCAA Found at i:85414201 original size:13 final size:13 Alignment explanation

Indices: 85414183--85414209 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 85414173 GCTCGGTAGG 85414183 GACACGCCCGTGT 1 GACACGCCCGTGT 85414196 GACACGCCCGTGT 1 GACACGCCCGTGT 85414209 G 1 G 85414210 CGATTACTTC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15 Consensus pattern (13 bp): GACACGCCCGTGT Found at i:85416437 original size:34 final size:34 Alignment explanation

Indices: 85416399--85416474 Score: 98 Period size: 34 Copynumber: 2.2 Consensus size: 34 85416389 TTAGCCCCTC * * 85416399 TTTCAGTAGCAGTAGTAGTTTGGGCCTGAGCCCA 1 TTTCAGTAACAGTAGTAGTCTGGGCCTGAGCCCA * * * * 85416433 TTTCAGTAACAGTGGTAGTCTGTGCCTTAGCCTA 1 TTTCAGTAACAGTAGTAGTCTGGGCCTGAGCCCA 85416467 TTTCAGTA 1 TTTCAGTA 85416475 CAATATGCAC Statistics Matches: 36, Mismatches: 6, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 34 36 1.00 ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34 Consensus pattern (34 bp): TTTCAGTAACAGTAGTAGTCTGGGCCTGAGCCCA Found at i:85417323 original size:17 final size:18 Alignment explanation

Indices: 85417283--85417323 Score: 57 Period size: 17 Copynumber: 2.3 Consensus size: 18 85417273 CTATGGTCAA * 85417283 CCAAAACCTCTCATTAGT 1 CCAAAACCTCTCATTAAT * 85417301 CTAAAACC-CTCATTAAT 1 CCAAAACCTCTCATTAAT 85417318 CCAAAA 1 CCAAAA 85417324 ACATAATAAT Statistics Matches: 20, Mismatches: 3, Indels: 1 0.83 0.12 0.04 Matches are distributed among these distances: 17 13 0.65 18 7 0.35 ACGTcount: A:0.41, C:0.32, G:0.02, T:0.24 Consensus pattern (18 bp): CCAAAACCTCTCATTAAT Found at i:85423662 original size:21 final size:20 Alignment explanation

Indices: 85423628--85423666 Score: 51 Period size: 21 Copynumber: 1.9 Consensus size: 20 85423618 GAGTATTTTT 85423628 ATGTTTAATGATAGATTATGA 1 ATGTTTAATGATAG-TTATGA * * 85423649 ATGTTTGATTATAGTTAT 1 ATGTTTAATGATAGTTAT 85423667 ACAAGTTTTG Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 20 4 0.25 21 12 0.75 ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49 Consensus pattern (20 bp): ATGTTTAATGATAGTTATGA Found at i:85424287 original size:48 final size:48 Alignment explanation

Indices: 85424214--85424355 Score: 212 Period size: 48 Copynumber: 3.0 Consensus size: 48 85424204 GTCATTAGGG * * 85424214 GATACATTAAGTTGGCTTCGGGCCATGACATTGGCACTTCGGGTGCAA 1 GATACATTAATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCAA * ** 85424262 GTTACATTAATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGTGA 1 GATACATTAATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCAA * * * 85424310 GATACATTGATTTGGCTTCGGGCCATGATATTGGTACTTAGGGTGC 1 GATACATTAATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGC 85424356 GAGACTCCCA Statistics Matches: 84, Mismatches: 10, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 48 84 1.00 ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32 Consensus pattern (48 bp): GATACATTAATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCAA Found at i:85426039 original size:43 final size:43 Alignment explanation

Indices: 85425991--85426146 Score: 179 Period size: 43 Copynumber: 3.6 Consensus size: 43 85425981 TATTGAGATG * * * 85425991 TGATTACATGTAAGACCATGTCTGGGACATTTGAATTGTATTA 1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTA * * * 85426034 TGATTACGTGTAAGACCATGTTTGGGACATTGGCATCGTATAA 1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTA * * * * * 85426077 TGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCG-ATATG 1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT-TA * * 85426120 TGATAACATGTAAGACCATATCTGGGA 1 TGATTACATGTAAGACCATGTCTGGGA 85426147 TATGGCACTG Statistics Matches: 95, Mismatches: 17, Indels: 2 0.83 0.15 0.02 Matches are distributed among these distances: 42 2 0.02 43 93 0.98 ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32 Consensus pattern (43 bp): TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTA Found at i:85441302 original size:47 final size:47 Alignment explanation

Indices: 85441229--85441322 Score: 179 Period size: 47 Copynumber: 2.0 Consensus size: 47 85441219 ACAACCAAAG 85441229 ACGTATGGCATCATCAGAAACACCATTGATTTTAAATGTATCGCATA 1 ACGTATGGCATCATCAGAAACACCATTGATTTTAAATGTATCGCATA * 85441276 ACGTATGGCATCATCAGAAACGCCATTGATTTTAAATGTATCGCATA 1 ACGTATGGCATCATCAGAAACACCATTGATTTTAAATGTATCGCATA 85441323 GTTCCAAGAA Statistics Matches: 46, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 47 46 1.00 ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30 Consensus pattern (47 bp): ACGTATGGCATCATCAGAAACACCATTGATTTTAAATGTATCGCATA Found at i:85447270 original size:21 final size:20 Alignment explanation

Indices: 85447246--85447284 Score: 60 Period size: 21 Copynumber: 1.9 Consensus size: 20 85447236 GAGTATTTTT 85447246 ATGTTTAATGATAGATTATGA 1 ATGTTTAATGATAG-TTATGA * 85447267 ATGTTTGATGATAGTTAT 1 ATGTTTAATGATAGTTAT 85447285 ACAAGTTTTG Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 20 4 0.24 21 13 0.76 ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46 Consensus pattern (20 bp): ATGTTTAATGATAGTTATGA Found at i:85447902 original size:48 final size:48 Alignment explanation

Indices: 85447829--85447971 Score: 205 Period size: 48 Copynumber: 3.0 Consensus size: 48 85447819 CATTAGGGGA * * * ** 85447829 TACATTGAGTTGGCTTCGGGCCATGATATTGGCACTTTGGGTGTGAGT 1 TACATTGAGTTGGCTTCAGGTCATGATATTGGCACTTAGGGTGCAAGT ** * 85447877 TACATTGAGTTGGCTTTTGGTCATGATATTGGCACTTCGGGTGCAAGT 1 TACATTGAGTTGGCTTCAGGTCATGATATTGGCACTTAGGGTGCAAGT * 85447925 TACATTGATTTGGCTTCAGGTCATGATATTGGCACTTAGGGTGCAAG 1 TACATTGAGTTGGCTTCAGGTCATGATATTGGCACTTAGGGTGCAAG 85447972 ACTCTCAAAT Statistics Matches: 85, Mismatches: 10, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 48 85 1.00 ACGTcount: A:0.20, C:0.15, G:0.30, T:0.36 Consensus pattern (48 bp): TACATTGAGTTGGCTTCAGGTCATGATATTGGCACTTAGGGTGCAAGT Found at i:85460801 original size:35 final size:35 Alignment explanation

Indices: 85460762--85460832 Score: 124 Period size: 35 Copynumber: 2.0 Consensus size: 35 85460752 AAAATGAATG 85460762 TTGTAAAAATCTTAGTTTTGAGGTTTTTGAATCTT 1 TTGTAAAAATCTTAGTTTTGAGGTTTTTGAATCTT * * 85460797 TTGTAAAAATCTTGGTTTTGAGGTTTTTGTATCTT 1 TTGTAAAAATCTTAGTTTTGAGGTTTTTGAATCTT 85460832 T 1 T 85460833 CATAGAAATT Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 35 34 1.00 ACGTcount: A:0.23, C:0.06, G:0.18, T:0.54 Consensus pattern (35 bp): TTGTAAAAATCTTAGTTTTGAGGTTTTTGAATCTT Found at i:85467050 original size:30 final size:30 Alignment explanation

Indices: 85467015--85467149 Score: 166 Period size: 30 Copynumber: 4.5 Consensus size: 30 85467005 ACACCCATGA * 85467015 GCTGACCAACACCAGGATTGCTGATGTGTT 1 GCTGACCAACACCAGGATAGCTGATGTGTT * * * 85467045 GCTGACCAACTCCGGGATAGCTAAT-TAGTT 1 GCTGACCAACACCAGGATAGCTGATGT-GTT * * 85467075 GCTGACCAACACCAGGATTGTTGATGTGTT 1 GCTGACCAACACCAGGATAGCTGATGTGTT * * * 85467105 GCTGACCAACTCCGGGATAGCTGATGAGTT 1 GCTGACCAACACCAGGATAGCTGATGTGTT 85467135 GCTGACCAAC-CCAGG 1 GCTGACCAACACCAGG 85467150 GTTATTGAGG Statistics Matches: 88, Mismatches: 15, Indels: 5 0.81 0.14 0.05 Matches are distributed among these distances: 29 5 0.06 30 82 0.93 31 1 0.01 ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24 Consensus pattern (30 bp): GCTGACCAACACCAGGATAGCTGATGTGTT Found at i:85467086 original size:60 final size:60 Alignment explanation

Indices: 85467015--85467149 Score: 236 Period size: 60 Copynumber: 2.3 Consensus size: 60 85467005 ACACCCATGA * 85467015 GCTGACCAACACCAGGATTGCTGATGTGTTGCTGACCAACTCCGGGATAGCTAATTAGTT 1 GCTGACCAACACCAGGATTGCTGATGTGTTGCTGACCAACTCCGGGATAGCTAATGAGTT * * 85467075 GCTGACCAACACCAGGATTGTTGATGTGTTGCTGACCAACTCCGGGATAGCTGATGAGTT 1 GCTGACCAACACCAGGATTGCTGATGTGTTGCTGACCAACTCCGGGATAGCTAATGAGTT 85467135 GCTGACCAAC-CCAGG 1 GCTGACCAACACCAGG 85467150 GTTATTGAGG Statistics Matches: 72, Mismatches: 3, Indels: 1 0.95 0.04 0.01 Matches are distributed among these distances: 59 5 0.07 60 67 0.93 ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24 Consensus pattern (60 bp): GCTGACCAACACCAGGATTGCTGATGTGTTGCTGACCAACTCCGGGATAGCTAATGAGTT Found at i:85467988 original size:11 final size:12 Alignment explanation

Indices: 85467966--85467997 Score: 50 Period size: 11 Copynumber: 2.8 Consensus size: 12 85467956 AAAGTATAAA 85467966 TCAATATG-AAT 1 TCAATATGTAAT 85467977 TCAA-ATGTAAT 1 TCAATATGTAAT 85467988 TCAATATGTA 1 TCAATATGTA 85467998 TTGGAGTTTA Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 10 3 0.16 11 11 0.58 12 5 0.26 ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38 Consensus pattern (12 bp): TCAATATGTAAT Found at i:85475105 original size:41 final size:41 Alignment explanation

Indices: 85475060--85475192 Score: 142 Period size: 41 Copynumber: 3.2 Consensus size: 41 85475050 ACAAAGGCTA * * * 85475060 CTAGGCTTAAGGCCTAATTTCA-TACACTGACACGAAGTCTG 1 CTAGGCTCAAGGCCTAA-TTCATTACACCGACACGAAGCCTG * * 85475101 CTAGGCTCAAAGCCTAATTCATTACACCGACATGAAGCCTG 1 CTAGGCTCAAGGCCTAATTCATTACACCGACACGAAGCCTG * * * * ** 85475142 CTTGGCTCAAGGCCTAAATCGTTACACCAACATAAAGCCTG 1 CTAGGCTCAAGGCCTAATTCATTACACCGACACGAAGCCTG * 85475183 CTAGGTTCAA 1 CTAGGCTCAA 85475193 AACCTGATAC Statistics Matches: 78, Mismatches: 13, Indels: 2 0.84 0.14 0.02 Matches are distributed among these distances: 40 4 0.05 41 74 0.95 ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24 Consensus pattern (41 bp): CTAGGCTCAAGGCCTAATTCATTACACCGACACGAAGCCTG Found at i:85476495 original size:21 final size:20 Alignment explanation

Indices: 85476471--85476522 Score: 52 Period size: 21 Copynumber: 2.6 Consensus size: 20 85476461 CCATAACATG * 85476471 AAATTTGGATTAAATTGAGTA 1 AAATTTGGATTAAAAT-AGTA * * * 85476492 AAATATGAATTAAAATAGTT 1 AAATTTGGATTAAAATAGTA 85476512 AAATTT-GATTA 1 AAATTTGGATTA 85476523 TATAGATCAA Statistics Matches: 25, Mismatches: 6, Indels: 2 0.76 0.18 0.06 Matches are distributed among these distances: 19 4 0.16 20 8 0.32 21 13 0.52 ACGTcount: A:0.48, C:0.00, G:0.13, T:0.38 Consensus pattern (20 bp): AAATTTGGATTAAAATAGTA Found at i:85483173 original size:10 final size:10 Alignment explanation

Indices: 85483158--85483187 Score: 51 Period size: 10 Copynumber: 2.9 Consensus size: 10 85483148 CTCTATTCTC 85483158 TTGTTATTTA 1 TTGTTATTTA 85483168 TTGTTATTTA 1 TTGTTATTTA 85483178 TTGTTTATTT 1 TTG-TTATTT 85483188 GAATGTTTTG Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 10 13 0.68 11 6 0.32 ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73 Consensus pattern (10 bp): TTGTTATTTA Found at i:85486086 original size:29 final size:29 Alignment explanation

Indices: 85486058--85486159 Score: 150 Period size: 29 Copynumber: 3.5 Consensus size: 29 85486048 CCTCCGAGCT ** * * * 85486058 CGCACACCCAGTGCCGTATTTTTCCAGCT 1 CGCACACTTAGTGCCATATATTTCCAGCA * 85486087 TGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 85486116 CGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 85486145 CGCACACTTAGTGCC 1 CGCACACTTAGTGCC 85486160 GATCTCGTCA Statistics Matches: 66, Mismatches: 7, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 29 66 1.00 ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27 Consensus pattern (29 bp): CGCACACTTAGTGCCATATATTTCCAGCA Found at i:85493948 original size:29 final size:29 Alignment explanation

Indices: 85493920--85494021 Score: 150 Period size: 29 Copynumber: 3.5 Consensus size: 29 85493910 CCTCCGAGCT ** * * * 85493920 CGCACACCCAGTGCCGTATTTTTCCAGCT 1 CGCACACTTAGTGCCATATATTTCCAGCA * 85493949 TGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 85493978 CGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 85494007 CGCACACTTAGTGCC 1 CGCACACTTAGTGCC 85494022 GATCTCGTCA Statistics Matches: 66, Mismatches: 7, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 29 66 1.00 ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27 Consensus pattern (29 bp): CGCACACTTAGTGCCATATATTTCCAGCA Found at i:85495731 original size:16 final size:14 Alignment explanation

Indices: 85495704--85495738 Score: 52 Period size: 16 Copynumber: 2.4 Consensus size: 14 85495694 TTAAACTTAC 85495704 TTTTTTTTATTTTA 1 TTTTTTTTATTTTA 85495718 TTTTTCTTTAATTTTA 1 TTTTT-TTT-ATTTTA 85495734 TTTTT 1 TTTTT 85495739 ACTACATCCT Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 14 5 0.26 15 3 0.16 16 11 0.58 ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83 Consensus pattern (14 bp): TTTTTTTTATTTTA Found at i:85497716 original size:25 final size:25 Alignment explanation

Indices: 85497682--85497733 Score: 95 Period size: 25 Copynumber: 2.1 Consensus size: 25 85497672 TCCGCACACT 85497682 TAGTGCCATCTCAAATAACCGAGAC 1 TAGTGCCATCTCAAATAACCGAGAC * 85497707 TAGTGCCATCTCAAATAACTGAGAC 1 TAGTGCCATCTCAAATAACCGAGAC 85497732 TA 1 TA 85497734 AGTCAGTATC Statistics Matches: 26, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 25 26 1.00 ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23 Consensus pattern (25 bp): TAGTGCCATCTCAAATAACCGAGAC Found at i:85497812 original size:30 final size:29 Alignment explanation

Indices: 85497766--85497832 Score: 125 Period size: 30 Copynumber: 2.3 Consensus size: 29 85497756 CCTCAAGTAA 85497766 CCAAAGCTAGTTAAATCGCACACTTAGTG 1 CCAAAGCTAGTTAAATCGCACACTTAGTG 85497795 CCAAAGCTAGTTTAAATCGCACACTTAGTG 1 CCAAAGCTAG-TTAAATCGCACACTTAGTG 85497825 CCAAAGCT 1 CCAAAGCT 85497833 TCTGATTCAT Statistics Matches: 37, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 29 10 0.27 30 27 0.73 ACGTcount: A:0.34, C:0.25, G:0.16, T:0.24 Consensus pattern (29 bp): CCAAAGCTAGTTAAATCGCACACTTAGTG Found at i:85504257 original size:23 final size:23 Alignment explanation

Indices: 85504229--85504288 Score: 77 Period size: 23 Copynumber: 2.6 Consensus size: 23 85504219 ACATGATAAA * 85504229 TAAAAATAAAAATAAAAACAAAAG 1 TAAAAATAAAAAGAAAAAC-AAAG * 85504253 -AAAAAGAAAAAGAAAAACAAAG 1 TAAAAATAAAAAGAAAAACAAAG * 85504275 TGAAAATAAAAAGA 1 TAAAAATAAAAAGA 85504289 CTCAAAAGTC Statistics Matches: 31, Mismatches: 4, Indels: 3 0.82 0.11 0.08 Matches are distributed among these distances: 22 4 0.13 23 27 0.87 ACGTcount: A:0.78, C:0.03, G:0.10, T:0.08 Consensus pattern (23 bp): TAAAAATAAAAAGAAAAACAAAG Found at i:85505800 original size:30 final size:30 Alignment explanation

Indices: 85505745--85505875 Score: 171 Period size: 30 Copynumber: 4.5 Consensus size: 30 85505735 ATAGTGAATC * 85505745 CGCACACTTAGTGCTATAT-ATTTTCAGCT 1 CGCACACTTAGTGCTATATAATTTTCAACT * 85505774 CGCACACTTAGTGCTATATAATTTTCAGCT 1 CGCACACTTAGTGCTATATAATTTTCAACT 85505804 CGCACACTTAGTGCTATATAA---TCAAACT 1 CGCACACTTAGTGCTATATAATTTTC-AACT * * * * 85505832 CGCACACTTAGTGCTGTACAATTTTAAACC 1 CGCACACTTAGTGCTATATAATTTTCAACT 85505862 CGCACACTTAGTGC 1 CGCACACTTAGTGC 85505876 CAATCTTGTC Statistics Matches: 92, Mismatches: 5, Indels: 9 0.87 0.05 0.08 Matches are distributed among these distances: 27 2 0.02 28 22 0.24 29 19 0.21 30 48 0.52 31 1 0.01 ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32 Consensus pattern (30 bp): CGCACACTTAGTGCTATATAATTTTCAACT Found at i:85505855 original size:58 final size:58 Alignment explanation

Indices: 85505744--85505875 Score: 176 Period size: 58 Copynumber: 2.3 Consensus size: 58 85505734 TATAGTGAAT * * * * * 85505744 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGC 1 CCGCACACTTAGTGCTATATA-TATCAACTCGCACACTTAGTGCTATACAATTTTAAAC * * 85505803 TCGCACACTTAGTGCTATATA-ATCAAACTCGCACACTTAGTGCTGTACAATTTTAAAC 1 CCGCACACTTAGTGCTATATATATC-AACTCGCACACTTAGTGCTATACAATTTTAAAC 85505861 CCGCACACTTAGTGC 1 CCGCACACTTAGTGC 85505876 CAATCTTGTC Statistics Matches: 64, Mismatches: 8, Indels: 3 0.85 0.11 0.04 Matches are distributed among these distances: 57 2 0.03 58 42 0.66 59 20 0.31 ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32 Consensus pattern (58 bp): CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATACAATTTTAAAC Found at i:85513755 original size:27 final size:29 Alignment explanation

Indices: 85513670--85513796 Score: 136 Period size: 29 Copynumber: 4.5 Consensus size: 29 85513660 ATAGTGAATC * * 85513670 CGCACACTTAGTGCTATATATTTC-AGCT 1 CGCACACTTAGTGCTATATAATTCAAACT **** 85513698 CGCACACTTAGTGCTATATAATTTTCGCT 1 CGCACACTTAGTGCTATATAATTCAAACT 85513727 CGCACACTTAGTGCTATA-AA-TCAAACT 1 CGCACACTTAGTGCTATATAATTCAAACT * * * 85513754 CGCACACTTAGTGCTGTACAATTTTAAAC- 1 CGCACACTTAGTGCTATATAA-TTCAAACT 85513783 CGCACACTTAGTGC 1 CGCACACTTAGTGC 85513797 CATCTTGTCA Statistics Matches: 86, Mismatches: 9, Indels: 7 0.84 0.09 0.07 Matches are distributed among these distances: 27 20 0.23 28 26 0.30 29 35 0.41 30 5 0.06 ACGTcount: A:0.28, C:0.26, G:0.14, T:0.31 Consensus pattern (29 bp): CGCACACTTAGTGCTATATAATTCAAACT Found at i:85513777 original size:56 final size:57 Alignment explanation

Indices: 85513669--85513796 Score: 163 Period size: 56 Copynumber: 2.3 Consensus size: 57 85513659 AATAGTGAAT * * * ** 85513669 CCGCACACTTAGTGCTATATATTTCAGCTCGCACACTTAGTGCTATATAATTTT-CG 1 CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATACAATTTTAAA * 85513725 CTCGCACACTTAGTGCTATA-A-ATCAAACTCGCACACTTAGTGCTGTACAATTTTAAA 1 C-CGCACACTTAGTGCTATATATATC-AACTCGCACACTTAGTGCTATACAATTTTAAA 85513782 CCGCACACTTAGTGC 1 CCGCACACTTAGTGC 85513797 CATCTTGTCA Statistics Matches: 63, Mismatches: 6, Indels: 6 0.84 0.08 0.08 Matches are distributed among these distances: 55 2 0.03 56 42 0.67 57 19 0.30 ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31 Consensus pattern (57 bp): CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATACAATTTTAAA Found at i:85515208 original size:4 final size:4 Alignment explanation

Indices: 85515199--85515226 Score: 56 Period size: 4 Copynumber: 7.0 Consensus size: 4 85515189 GCACAAAAGT 85515199 ATAA ATAA ATAA ATAA ATAA ATAA ATAA 1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA 85515227 GAAAGAAAGA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 24 1.00 ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25 Consensus pattern (4 bp): ATAA Found at i:85515852 original size:12 final size:12 Alignment explanation

Indices: 85515835--85515861 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 85515825 ATGTGTCGAC 85515835 TACTATTACTGT 1 TACTATTACTGT 85515847 TACTATTACTGT 1 TACTATTACTGT 85515859 TAC 1 TAC 85515862 CGATTCGACA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 15 1.00 ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48 Consensus pattern (12 bp): TACTATTACTGT Found at i:85515900 original size:51 final size:50 Alignment explanation

Indices: 85515818--85515959 Score: 145 Period size: 45 Copynumber: 2.9 Consensus size: 50 85515808 TTACTGATCA * * * 85515818 AGCAC-TTATGTGTCGACTACTATTACTGTTACTATTACTGTTACCGATTC 1 AGCACTTTGTGTGTTGAATACTATTACTGTTACTATTACTG-TACCGATTC * 85515868 -GACACTTTGTGTGTTGAATACTATTACCGTTACTATTA---TA--GATTC 1 AG-CACTTTGTGTGTTGAATACTATTACTGTTACTATTACTGTACCGATTC * * * 85515913 AGTACTTTGTGTGTTGAATACTGTTACTGTTACTGTTACTGCTACCG 1 AGCACTTTGTGTGTTGAATACTATTACTGTTACTATTACTG-TACCG 85515960 TTACTGATTA Statistics Matches: 75, Mismatches: 8, Indels: 17 0.75 0.08 0.17 Matches are distributed among these distances: 45 37 0.49 46 1 0.01 47 2 0.03 49 3 0.04 50 3 0.04 51 29 0.39 ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42 Consensus pattern (50 bp): AGCACTTTGTGTGTTGAATACTATTACTGTTACTATTACTGTACCGATTC Found at i:85515942 original size:6 final size:6 Alignment explanation

Indices: 85515931--85515971 Score: 55 Period size: 6 Copynumber: 6.7 Consensus size: 6 85515921 GTGTGTTGAA * * 85515931 TACTGT TACTGT TACTGT TACTGC TACCGT TACTGAT TACT 1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACT 85515972 ATTTAGGTAC Statistics Matches: 30, Mismatches: 4, Indels: 1 0.86 0.11 0.03 Matches are distributed among these distances: 6 25 0.83 7 5 0.17 ACGTcount: A:0.20, C:0.22, G:0.15, T:0.44 Consensus pattern (6 bp): TACTGT Found at i:85522616 original size:48 final size:47 Alignment explanation

Indices: 85522508--85522676 Score: 216 Period size: 48 Copynumber: 3.6 Consensus size: 47 85522498 TGATATGTGT * * * * 85522508 GCTAGTGTAAGACATGTTTGGGACATGCATCGGCCAC-A-TTATGAGA 1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATAT-AAA * * * 85522554 GCCAGTGTAAGACATGTCTGGGATATGCATCTGCCTCGAGATATACAA 1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATA-AA * 85522602 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATATATAA 1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATA-AA * 85522650 GCTAGTGTAAGACCTGTCTGGGACATG 1 GCTAGTGTAAGACATGTCTGGGACATG 85522677 GCGTCAGCTT Statistics Matches: 106, Mismatches: 14, Indels: 4 0.85 0.11 0.03 Matches are distributed among these distances: 46 32 0.30 47 2 0.02 48 72 0.68 ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25 Consensus pattern (47 bp): GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATAAA Found at i:85522784 original size:49 final size:49 Alignment explanation

Indices: 85522731--85522824 Score: 125 Period size: 49 Copynumber: 1.9 Consensus size: 49 85522721 ACATTGACAC * * 85522731 CGATAGATGAGAGCCAGTGTAAAACCTATCTGGGACACAGCATCGGCCT 1 CGATAGATGAAAGCCAGTGTAAAACCTACCTGGGACACAGCATCGGCCT * * * * * 85522780 CGATATATGAAAGTCAGTGTAAGACCTGCCTGGGACATAGCATCG 1 CGATAGATGAAAGCCAGTGTAAAACCTACCTGGGACACAGCATCG 85522825 ACTTTGATGT Statistics Matches: 38, Mismatches: 7, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 49 38 1.00 ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20 Consensus pattern (49 bp): CGATAGATGAAAGCCAGTGTAAAACCTACCTGGGACACAGCATCGGCCT Found at i:85525607 original size:46 final size:46 Alignment explanation

Indices: 85525557--85525681 Score: 214 Period size: 46 Copynumber: 2.7 Consensus size: 46 85525547 GGTTGAGCAT * 85525557 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC 1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC * 85525603 CCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGC 1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC * * 85525649 CCGAGCTCGTTGAGTTGAGTCCGAGTTTACTTA 1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA 85525682 GGGGCGCGTT Statistics Matches: 74, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 46 74 1.00 ACGTcount: A:0.21, C:0.22, G:0.28, T:0.30 Consensus pattern (46 bp): CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC Found at i:85525943 original size:19 final size:20 Alignment explanation

Indices: 85525906--85525943 Score: 53 Period size: 19 Copynumber: 1.9 Consensus size: 20 85525896 ATAAGGTGGT 85525906 AAGATGATGAATGATGTTTA 1 AAGATGATGAATGATGTTTA 85525926 AAGATG-TGATAT-ATGTTT 1 AAGATGATGA-ATGATGTTT 85525944 TGATGGTACC Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 19 9 0.53 20 8 0.47 ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39 Consensus pattern (20 bp): AAGATGATGAATGATGTTTA Found at i:85532903 original size:40 final size:39 Alignment explanation

Indices: 85532743--85532905 Score: 254 Period size: 39 Copynumber: 4.2 Consensus size: 39 85532733 TGTGTATGAA * 85532743 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT 1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT * 85532782 TGTGCGAGTTGTGATGTCCGGGCTAAGCCCGAAGGCAAT 1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT * * * 85532821 GGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT 1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT * * 85532860 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT 1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT 85532900 TGTGCG 1 TGTGCG 85532906 GGTTACCATA Statistics Matches: 112, Mismatches: 11, Indels: 1 0.90 0.09 0.01 Matches are distributed among these distances: 39 95 0.85 40 17 0.15 ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24 Consensus pattern (39 bp): TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT Found at i:85532921 original size:40 final size:40 Alignment explanation

Indices: 85532760--85532941 Score: 154 Period size: 39 Copynumber: 4.6 Consensus size: 40 85532750 ATTGTGATAT * *** ** 85532760 CCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTGTGATGT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA * * * ** * 85532799 CCGGGCTAAG-CCCGAAGGCAATGGTGCGAGCTATGATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA * *** * 85532838 CCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTGTGATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA * * 85532877 CCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTACCATAA 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA * * 85532917 CCGGGCTATGTCCCGAAGGCGTTTG 1 CCGGGCTAAGTCCCGAAGGCATTTG 85532942 AACGAGTAGC Statistics Matches: 125, Mismatches: 17, Indels: 1 0.87 0.12 0.01 Matches are distributed among these distances: 39 80 0.64 40 45 0.36 ACGTcount: A:0.21, C:0.23, G:0.34, T:0.23 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA Found at i:85544112 original size:46 final size:46 Alignment explanation

Indices: 85543988--85544151 Score: 144 Period size: 46 Copynumber: 3.6 Consensus size: 46 85543978 GCCATTTCCA * * * * 85543988 TGTCCCAGATATGGTCTTACACTA--ACACATCTCGTAGCCGATGCA 1 TGTCCCAGACATGGTCTTACACTAGCACTCGTCTCG-AGCCGATGCT * * 85544033 TGTCCCAGACAT-GTCTTACACTGGCTTA-T-GTCTCGAGGCCGAAGCT 1 TGTCCCAGACATGGTCTTACACTAGC--ACTCGTCTCGA-GCCGATGCT * 85544079 TGTCCCAGACAT-GTCTTACACTAGCACTCGTCTCAATGCCGATG-T 1 TGTCCCAGACATGGTCTTACACTAGCACTCGTCTCGA-GCCGATGCT * 85544124 CGTGCCTCAGACATGGTCTTACACTAGC 1 TGT-CC-CAGACATGGTCTTACACTAGC 85544152 TCTCAAAATG Statistics Matches: 98, Mismatches: 11, Indels: 17 0.78 0.09 0.13 Matches are distributed among these distances: 44 11 0.11 45 16 0.16 46 50 0.51 47 7 0.07 48 14 0.14 ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27 Consensus pattern (46 bp): TGTCCCAGACATGGTCTTACACTAGCACTCGTCTCGAGCCGATGCT Found at i:85551641 original size:44 final size:45 Alignment explanation

Indices: 85551575--85551686 Score: 120 Period size: 46 Copynumber: 2.5 Consensus size: 45 85551565 TCATTTTCAT * * 85551575 GTCCCAAACATGGTCTTACACTGAC-ACATCTCGTA-GCCGATGCAG 1 GTCCCAGACAT-GTCTTACACTGACTACATCTCG-AGGCCGAAGCAG * * ** 85551620 GTCCCAGACATGTCTTACACTGGCTTACGTCTCGAGGCCGAAGCTT 1 GTCCCAGACATGTCTTACACTGAC-TACATCTCGAGGCCGAAGCAG * 85551666 GTCCCAGACAAGTCTTACACT 1 GTCCCAGACATGTCTTACACT 85551687 AGCACTCGTC Statistics Matches: 57, Mismatches: 7, Indels: 5 0.83 0.10 0.07 Matches are distributed among these distances: 44 12 0.21 45 11 0.19 46 34 0.60 ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24 Consensus pattern (45 bp): GTCCCAGACATGTCTTACACTGACTACATCTCGAGGCCGAAGCAG Found at i:85552553 original size:49 final size:49 Alignment explanation

Indices: 85552499--85552593 Score: 181 Period size: 49 Copynumber: 1.9 Consensus size: 49 85552489 TTAAAAATGT 85552499 AAAAATCATCAAGAAAAACTATCAAAATCACTTACTTGTAAGGATTTTA 1 AAAAATCATCAAGAAAAACTATCAAAATCACTTACTTGTAAGGATTTTA * 85552548 AAAAATCATCAAGAAAAACTATCAAAATCACTTACTTGTGAGGATT 1 AAAAATCATCAAGAAAAACTATCAAAATCACTTACTTGTAAGGATT 85552594 ACAAGTTGCT Statistics Matches: 45, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 49 45 1.00 ACGTcount: A:0.48, C:0.15, G:0.09, T:0.27 Consensus pattern (49 bp): AAAAATCATCAAGAAAAACTATCAAAATCACTTACTTGTAAGGATTTTA Found at i:85554407 original size:24 final size:24 Alignment explanation

Indices: 85554380--85554436 Score: 69 Period size: 24 Copynumber: 2.3 Consensus size: 24 85554370 GATTACTAAT 85554380 TTCAACTCGTAAGAGCTTACCGAC 1 TTCAACTCGTAAGAGCTTACCGAC * * * * 85554404 TTCAGCTCGTGAGAGTTTACCGAT 1 TTCAACTCGTAAGAGCTTACCGAC 85554428 TCTCAACTC 1 T-TCAACTC 85554437 ATATGATCTT Statistics Matches: 27, Mismatches: 5, Indels: 1 0.82 0.15 0.03 Matches are distributed among these distances: 24 21 0.78 25 6 0.22 ACGTcount: A:0.25, C:0.28, G:0.18, T:0.30 Consensus pattern (24 bp): TTCAACTCGTAAGAGCTTACCGAC Found at i:85555635 original size:15 final size:16 Alignment explanation

Indices: 85555615--85555644 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 85555605 TGATGCTTTG 85555615 TTGAT-ATGTGTTAAT 1 TTGATAATGTGTTAAT 85555630 TTGATAATGTGTTAA 1 TTGATAATGTGTTAA 85555645 ATCATGTTTG Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 5 0.36 16 9 0.64 ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50 Consensus pattern (16 bp): TTGATAATGTGTTAAT Found at i:85559908 original size:13 final size:14 Alignment explanation

Indices: 85559887--85559919 Score: 50 Period size: 14 Copynumber: 2.4 Consensus size: 14 85559877 TTTATTAATG 85559887 AAATATATTAAA-AT 1 AAAT-TATTAAATAT 85559901 AAATTATTAAATAT 1 AAATTATTAAATAT 85559915 AAATT 1 AAATT 85559920 TATATTTTAT Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 13 7 0.39 14 11 0.61 ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39 Consensus pattern (14 bp): AAATTATTAAATAT Found at i:85572937 original size:19 final size:21 Alignment explanation

Indices: 85572896--85572944 Score: 66 Period size: 19 Copynumber: 2.3 Consensus size: 21 85572886 AATCATTTCT 85572896 TTATTTATTATTTTGAATTTTTA 1 TTATTTATTA-TTTGAA-TTTTA 85572919 TTATTTATTA-TTGAA-TTTA 1 TTATTTATTATTTGAATTTTA 85572938 TTATTTA 1 TTATTTA 85572945 ATTTTTTCTT Statistics Matches: 26, Mismatches: 0, Indels: 4 0.87 0.00 0.13 Matches are distributed among these distances: 19 11 0.42 21 5 0.19 23 10 0.38 ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67 Consensus pattern (21 bp): TTATTTATTATTTGAATTTTA Found at i:85572938 original size:12 final size:12 Alignment explanation

Indices: 85572903--85572948 Score: 55 Period size: 12 Copynumber: 4.2 Consensus size: 12 85572893 TCTTTATTTA 85572903 TTATT-TTGAAT 1 TTATTATTGAAT 85572914 TT-TTATT--AT 1 TTATTATTGAAT 85572923 TTATTATTGAAT 1 TTATTATTGAAT * 85572935 TTATTATTTAAT 1 TTATTATTGAAT 85572947 TT 1 TT 85572949 TTTCTTCTTG Statistics Matches: 30, Mismatches: 1, Indels: 7 0.79 0.03 0.18 Matches are distributed among these distances: 9 4 0.13 10 7 0.23 11 4 0.13 12 15 0.50 ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67 Consensus pattern (12 bp): TTATTATTGAAT Found at i:85573876 original size:40 final size:40 Alignment explanation

Indices: 85573830--85573907 Score: 156 Period size: 40 Copynumber: 1.9 Consensus size: 40 85573820 TGTGAATATA 85573830 TTGTTTCCAATGTCATTCAACCTTCTATTGTTCATGGATG 1 TTGTTTCCAATGTCATTCAACCTTCTATTGTTCATGGATG 85573870 TTGTTTCCAATGTCATTCAACCTTCTATTGTTCATGGA 1 TTGTTTCCAATGTCATTCAACCTTCTATTGTTCATGGA 85573908 CTTGTCAAGA Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 40 38 1.00 ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45 Consensus pattern (40 bp): TTGTTTCCAATGTCATTCAACCTTCTATTGTTCATGGATG Found at i:85574359 original size:30 final size:30 Alignment explanation

Indices: 85574325--85574385 Score: 104 Period size: 30 Copynumber: 2.0 Consensus size: 30 85574315 AAGTTTATAG * 85574325 TAATAGTGCGAACTATGATAATAGTAATAA 1 TAATAGTGAGAACTATGATAATAGTAATAA * 85574355 TAATAGTGAGAACTATGATAATAGTGATAA 1 TAATAGTGAGAACTATGATAATAGTAATAA 85574385 T 1 T 85574386 GAACTTTGTG Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 30 29 1.00 ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31 Consensus pattern (30 bp): TAATAGTGAGAACTATGATAATAGTAATAA Found at i:85574381 original size:18 final size:18 Alignment explanation

Indices: 85574325--85574381 Score: 63 Period size: 18 Copynumber: 3.5 Consensus size: 18 85574315 AAGTTTATAG * 85574325 TAATAGTGCGAACTATGA 1 TAATAGTGAGAACTATGA 85574343 TAATAGT---AA-TA--A 1 TAATAGTGAGAACTATGA 85574355 TAATAGTGAGAACTATGA 1 TAATAGTGAGAACTATGA 85574373 TAATAGTGA 1 TAATAGTGA 85574382 TAATGAACTT Statistics Matches: 33, Mismatches: 0, Indels: 12 0.73 0.00 0.27 Matches are distributed among these distances: 12 8 0.24 14 2 0.06 15 4 0.12 16 2 0.06 18 17 0.52 ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30 Consensus pattern (18 bp): TAATAGTGAGAACTATGA Found at i:85576861 original size:29 final size:30 Alignment explanation

Indices: 85576806--85576863 Score: 73 Period size: 29 Copynumber: 2.0 Consensus size: 30 85576796 TACACGGGCA ** * 85576806 GACACACGGGCTTGTGTCTTGGCCATGTGT 1 GACACACGGGCTTGTCCCATGGCCATGTGT * 85576836 GACACAC-GGCTTGTCCCATGGGCATGTG 1 GACACACGGGCTTGTCCCATGGCCATGTG 85576864 GTCCGGCCAT Statistics Matches: 24, Mismatches: 4, Indels: 1 0.83 0.14 0.03 Matches are distributed among these distances: 29 17 0.71 30 7 0.29 ACGTcount: A:0.16, C:0.26, G:0.33, T:0.26 Consensus pattern (30 bp): GACACACGGGCTTGTCCCATGGCCATGTGT Found at i:85582580 original size:65 final size:65 Alignment explanation

Indices: 85582476--85582669 Score: 289 Period size: 65 Copynumber: 3.0 Consensus size: 65 85582466 GAATCTCGAG * *** * * 85582476 TGTTCATTATTTTCCAATCTTGTTCTTCACCAGTGCTTGAAGTATTTGGCACTAGTCTATAGCAT 1 TGTTCATTATTTTTCTGCCTTGTTCTTCACTAGTGCTTGAAGTAGTTGGCACTAGTCTATAGCAT * * 85582541 TGTTCATTTTTTTTCTGCCTTGTTCTTCACTAATGCTTGAAGTAGTTGGCACTAGTCTATAGCAT 1 TGTTCATTATTTTTCTGCCTTGTTCTTCACTAGTGCTTGAAGTAGTTGGCACTAGTCTATAGCAT * * * 85582606 TGTTTATTATTTTTCTGCCTTGTTCTTCACTGGTGCTTGAAGTAGTTGGCACTAATCTATAGCA 1 TGTTCATTATTTTTCTGCCTTGTTCTTCACTAGTGCTTGAAGTAGTTGGCACTAGTCTATAGCA 85582670 CTGCTTGTTT Statistics Matches: 116, Mismatches: 13, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 65 116 1.00 ACGTcount: A:0.20, C:0.19, G:0.17, T:0.45 Consensus pattern (65 bp): TGTTCATTATTTTTCTGCCTTGTTCTTCACTAGTGCTTGAAGTAGTTGGCACTAGTCTATAGCAT Found at i:85587299 original size:39 final size:40 Alignment explanation

Indices: 85587247--85587334 Score: 117 Period size: 39 Copynumber: 2.2 Consensus size: 40 85587237 AAAATTTATA * * * 85587247 TTTAATACAATAAAATATTTATTATATCTAT-TTATGT-TT 1 TTTAATATAATAAAACATTTATTATATCTATGGTA-GTATT * 85587286 TTTAATATAATAAAACATTTATTATATTTATGGTAGTATT 1 TTTAATATAATAAAACATTTATTATATCTATGGTAGTATT 85587326 TTTAATATA 1 TTTAATATA 85587335 CATACTTTTT Statistics Matches: 43, Mismatches: 4, Indels: 3 0.86 0.08 0.06 Matches are distributed among these distances: 39 30 0.70 40 13 0.30 ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52 Consensus pattern (40 bp): TTTAATATAATAAAACATTTATTATATCTATGGTAGTATT Found at i:85587451 original size:12 final size:11 Alignment explanation

Indices: 85587430--85587459 Score: 51 Period size: 12 Copynumber: 2.6 Consensus size: 11 85587420 AAAATTAATT 85587430 TTAAATAAAAA 1 TTAAATAAAAA 85587441 TTAATATAAAAA 1 TTAA-ATAAAAA 85587453 TTAAATA 1 TTAAATA 85587460 TGGGCGAGCC Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 11 7 0.39 12 11 0.61 ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33 Consensus pattern (11 bp): TTAAATAAAAA Found at i:85588715 original size:11 final size:11 Alignment explanation

Indices: 85588699--85588732 Score: 59 Period size: 11 Copynumber: 3.1 Consensus size: 11 85588689 CGCATCTAGT 85588699 TTTGTTCTTGA 1 TTTGTTCTTGA 85588710 TTTGTTCTTGA 1 TTTGTTCTTGA * 85588721 TTTATTCTTGA 1 TTTGTTCTTGA 85588732 T 1 T 85588733 GATTTGACAT Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 11 22 1.00 ACGTcount: A:0.12, C:0.09, G:0.15, T:0.65 Consensus pattern (11 bp): TTTGTTCTTGA Found at i:85594713 original size:7 final size:6 Alignment explanation

Indices: 85594692--85594725 Score: 52 Period size: 6 Copynumber: 5.7 Consensus size: 6 85594682 GTAGCTTTCC 85594692 CTTTTT CTTTTT CTTTTCT CTTTTT -TTTTT CTTT 1 CTTTTT CTTTTT CTTTT-T CTTTTT CTTTTT CTTT 85594726 CCCTGCTAAC Statistics Matches: 26, Mismatches: 0, Indels: 4 0.87 0.00 0.13 Matches are distributed among these distances: 5 5 0.19 6 15 0.58 7 6 0.23 ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82 Consensus pattern (6 bp): CTTTTT Found at i:85600877 original size:16 final size:16 Alignment explanation

Indices: 85600852--85600886 Score: 61 Period size: 16 Copynumber: 2.2 Consensus size: 16 85600842 CAAAAATATT 85600852 AAATAATTTTTTGAGA 1 AAATAATTTTTTGAGA * 85600868 AAATAGTTTTTTGAGA 1 AAATAATTTTTTGAGA 85600884 AAA 1 AAA 85600887 AAATAAAAAA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 16 18 1.00 ACGTcount: A:0.46, C:0.00, G:0.14, T:0.40 Consensus pattern (16 bp): AAATAATTTTTTGAGA Found at i:85601091 original size:23 final size:23 Alignment explanation

Indices: 85601063--85601111 Score: 64 Period size: 23 Copynumber: 2.1 Consensus size: 23 85601053 TAAAAATAAT ** 85601063 TTTAAATTC-TTGTTATTTATTAA 1 TTTAAATTCATT-TTACATATTAA 85601086 TTTAAATTCATTTTACATATTAA 1 TTTAAATTCATTTTACATATTAA 85601109 TTT 1 TTT 85601112 CTTTTTTCTT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 23 21 0.91 24 2 0.09 ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59 Consensus pattern (23 bp): TTTAAATTCATTTTACATATTAA Found at i:85602422 original size:86 final size:86 Alignment explanation

Indices: 85602277--85602448 Score: 344 Period size: 86 Copynumber: 2.0 Consensus size: 86 85602267 AGGTTAAAGT 85602277 GAATGGAAGCTGTGCACCAGGTAGGAAACCGGAAAAGATGAGGTGAGTCCATCGGACTGCTTAAG 1 GAATGGAAGCTGTGCACCAGGTAGGAAACCGGAAAAGATGAGGTGAGTCCATCGGACTGCTTAAG 85602342 TACCAAACTCCCTTCGGATCC 66 TACCAAACTCCCTTCGGATCC 85602363 GAATGGAAGCTGTGCACCAGGTAGGAAACCGGAAAAGATGAGGTGAGTCCATCGGACTGCTTAAG 1 GAATGGAAGCTGTGCACCAGGTAGGAAACCGGAAAAGATGAGGTGAGTCCATCGGACTGCTTAAG 85602428 TACCAAACTCCCTTCGGATCC 66 TACCAAACTCCCTTCGGATCC 85602449 AATCCTAGAC Statistics Matches: 86, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 86 86 1.00 ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19 Consensus pattern (86 bp): GAATGGAAGCTGTGCACCAGGTAGGAAACCGGAAAAGATGAGGTGAGTCCATCGGACTGCTTAAG TACCAAACTCCCTTCGGATCC Found at i:85603189 original size:27 final size:27 Alignment explanation

Indices: 85603141--85603299 Score: 166 Period size: 27 Copynumber: 5.9 Consensus size: 27 85603131 GCGAGGCTGC * * 85603141 CAGATATTGTGAC-GAAGTCACCAGATA 1 CAGATATTGTGGCAG-AGCCACCAGATA 85603168 CAGATATTGTGGCAGAGCCACCAGA-A 1 CAGATATTGTGGCAGAGCCACCAGATA * 85603194 CAGATATATGTGGCAGAGCCATCAGAT- 1 CAGATAT-TGTGGCAGAGCCACCAGATA * * * 85603221 CAGATAATCGTGGCATAACCACCAGA-A 1 CAGAT-ATTGTGGCAGAGCCACCAGATA * 85603248 CAGATATATGGGGCAGAGCCACCAGAT- 1 CAGATAT-TGTGGCAGAGCCACCAGATA * 85603275 CAGATAATTGTGGCATAGCCACCAG 1 CAGAT-ATTGTGGCAGAGCCACCAG 85603300 GACGCTTCCT Statistics Matches: 111, Mismatches: 13, Indels: 16 0.79 0.09 0.11 Matches are distributed among these distances: 26 10 0.09 27 96 0.86 28 5 0.05 ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18 Consensus pattern (27 bp): CAGATATTGTGGCAGAGCCACCAGATA Found at i:85603243 original size:54 final size:54 Alignment explanation

Indices: 85603159--85603299 Score: 221 Period size: 54 Copynumber: 2.6 Consensus size: 54 85603149 GTGACGAAGT * * 85603159 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC 1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGGGGCAGAGC * * * 85603213 CATCAGATCAGATAATCGTGGCATAACCACCAGAACAGATATATGGGGCAGAGC 1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGGGGCAGAGC 85603267 CACCAGATCAGATAATTGTGGCATAGCCACCAG 1 CACCAGATCAGATAATTGTGGCATAGCCACCAG 85603300 GACGCTTCCT Statistics Matches: 78, Mismatches: 8, Indels: 2 0.89 0.09 0.02 Matches are distributed among these distances: 53 5 0.06 54 73 0.94 ACGTcount: A:0.35, C:0.23, G:0.24, T:0.17 Consensus pattern (54 bp): CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGGGGCAGAGC Found at i:85604964 original size:26 final size:26 Alignment explanation

Indices: 85604908--85605012 Score: 178 Period size: 26 Copynumber: 4.1 Consensus size: 26 85604898 ATGAAATTCC * 85604908 TATCAT-GAGCATTTACCTAA-CCAT 1 TATCATGGAACATTTACCTAACCCAT 85604932 TATCATGGAACATTTACCTAACCCAT 1 TATCATGGAACATTTACCTAACCCAT * 85604958 TATCATGAAACATTTACCTAACCCAT 1 TATCATGGAACATTTACCTAACCCAT 85604984 TATCATGGAACATTTACCTAACCCAT 1 TATCATGGAACATTTACCTAACCCAT 85605010 TAT 1 TAT 85605013 AAATTTGTAT Statistics Matches: 76, Mismatches: 3, Indels: 2 0.94 0.04 0.02 Matches are distributed among these distances: 24 6 0.08 25 13 0.17 26 57 0.75 ACGTcount: A:0.35, C:0.26, G:0.07, T:0.32 Consensus pattern (26 bp): TATCATGGAACATTTACCTAACCCAT Found at i:85610283 original size:27 final size:28 Alignment explanation

Indices: 85610241--85610379 Score: 168 Period size: 27 Copynumber: 5.2 Consensus size: 28 85610231 GTGACGAAGT 85610241 CACCAGATACAG--ATATTGT-GCAGAGC 1 CACCAGA-ACAGATATATTGTGGCAGAGC 85610267 CACCAGAACAGATATA-TGTGGCAGAGC 1 CACCAGAACAGATATATTGTGGCAGAGC * * * 85610294 CACCAGATCAGATA-ATCGTGGCATAGC 1 CACCAGAACAGATATATTGTGGCAGAGC 85610321 CACCAGAACAGATATA-TG-GGCAGAGC 1 CACCAGAACAGATATATTGTGGCAGAGC * * 85610347 CACCAGATCAGATA-ATTGTGGCATAGC 1 CACCAGAACAGATATATTGTGGCAGAGC 85610374 CACCAG 1 CACCAG 85610380 GACGCTTCTC Statistics Matches: 98, Mismatches: 8, Indels: 13 0.82 0.07 0.11 Matches are distributed among these distances: 25 5 0.05 26 33 0.34 27 59 0.60 28 1 0.01 ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17 Consensus pattern (28 bp): CACCAGAACAGATATATTGTGGCAGAGC Found at i:85610300 original size:53 final size:53 Alignment explanation

Indices: 85610241--85610379 Score: 228 Period size: 53 Copynumber: 2.6 Consensus size: 53 85610231 GTGACGAAGT * 85610241 CACCAGATACAGAT-ATTGT-GCAGAGCCACCAGAACAGATATATGTGGCAGAGC 1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATG-GGCAGAGC * 85610294 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGGGCAGAGC 1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGGGCAGAGC 85610347 CACCAGATCAGATAATTGTGGCATAGCCACCAG 1 CACCAGATCAGATAATTGTGGCATAGCCACCAG 85610380 GACGCTTCTC Statistics Matches: 81, Mismatches: 3, Indels: 4 0.92 0.03 0.05 Matches are distributed among these distances: 52 5 0.06 53 52 0.64 54 24 0.30 ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17 Consensus pattern (53 bp): CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGGGCAGAGC Found at i:85612022 original size:26 final size:26 Alignment explanation

Indices: 85611992--85612099 Score: 189 Period size: 26 Copynumber: 4.2 Consensus size: 26 85611982 TGAAATTCCC 85611992 ATCATGGAACATTTACCTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT * 85612018 ATCATGGAACATTTACTTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT * * 85612044 ATCATGAAACATTTACTTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT 85612070 ATCATGGAACATTTACCTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT 85612096 ATCA 1 ATCA 85612100 ATTTGTATCA Statistics Matches: 78, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 26 78 1.00 ACGTcount: A:0.36, C:0.25, G:0.06, T:0.32 Consensus pattern (26 bp): ATCATGGAACATTTACCTAACCCATT Found at i:85613410 original size:20 final size:21 Alignment explanation

Indices: 85613374--85613416 Score: 61 Period size: 20 Copynumber: 2.1 Consensus size: 21 85613364 ATATATATAT * * 85613374 ATATATATTTGTGAATTTTAA 1 ATATATATATGTGAATTTGAA 85613395 ATATATATAT-TGAATTTGAA 1 ATATATATATGTGAATTTGAA 85613415 AT 1 AT 85613417 TCATGTTTCT Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 20 11 0.55 21 9 0.45 ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49 Consensus pattern (21 bp): ATATATATATGTGAATTTGAA Found at i:85619488 original size:16 final size:15 Alignment explanation

Indices: 85619462--85619495 Score: 50 Period size: 16 Copynumber: 2.2 Consensus size: 15 85619452 TGTGGAATCC * 85619462 TTTCTAAAAATAGTT 1 TTTCTAAAAATAATT 85619477 TTTCTGAAAAATAATT 1 TTTCT-AAAAATAATT 85619493 TTT 1 TTT 85619496 TAAGGATAAA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 15 5 0.29 16 12 0.71 ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50 Consensus pattern (15 bp): TTTCTAAAAATAATT Found at i:85620915 original size:23 final size:23 Alignment explanation

Indices: 85620889--85620937 Score: 64 Period size: 23 Copynumber: 2.1 Consensus size: 23 85620879 GATTTTAAAC * 85620889 AAATACTCAT-TTTTATATTATGA 1 AAATACTCATATTTTATACTAT-A * 85620912 AAATATTCATATTTTATACTATA 1 AAATACTCATATTTTATACTATA 85620935 AAA 1 AAA 85620938 CATTTAATAC Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 23 13 0.57 24 10 0.43 ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45 Consensus pattern (23 bp): AAATACTCATATTTTATACTATA Found at i:85625413 original size:23 final size:23 Alignment explanation

Indices: 85625373--85625416 Score: 61 Period size: 23 Copynumber: 1.9 Consensus size: 23 85625363 AGAACTTTTA * 85625373 ATCGGGAGGATCACAAAGAGCCT 1 ATCGGGAAGATCACAAAGAGCCT * * 85625396 ATCGGGAAGCTCATAAAGAGC 1 ATCGGGAAGATCACAAAGAGC 85625417 TATGTAACGG Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 23 18 1.00 ACGTcount: A:0.36, C:0.20, G:0.30, T:0.14 Consensus pattern (23 bp): ATCGGGAAGATCACAAAGAGCCT Found at i:85626280 original size:28 final size:28 Alignment explanation

Indices: 85626240--85626296 Score: 114 Period size: 28 Copynumber: 2.0 Consensus size: 28 85626230 GAAAATTCAC 85626240 TTCACAAAAGTTGTTTATCTATCAACAA 1 TTCACAAAAGTTGTTTATCTATCAACAA 85626268 TTCACAAAAGTTGTTTATCTATCAACAA 1 TTCACAAAAGTTGTTTATCTATCAACAA 85626296 T 1 T 85626297 CTTTCAATTT Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 29 1.00 ACGTcount: A:0.39, C:0.18, G:0.07, T:0.37 Consensus pattern (28 bp): TTCACAAAAGTTGTTTATCTATCAACAA Found at i:85633218 original size:23 final size:23 Alignment explanation

Indices: 85633177--85633220 Score: 70 Period size: 23 Copynumber: 1.9 Consensus size: 23 85633167 AGAACTTTGA ** 85633177 ATCGGGAAGCTCATGAAGAGCAT 1 ATCGGGAAGCTCACAAAGAGCAT 85633200 ATCGGGAAGCTCACAAAGAGC 1 ATCGGGAAGCTCACAAAGAGC 85633221 CATGTAACAG Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 23 19 1.00 ACGTcount: A:0.36, C:0.20, G:0.30, T:0.14 Consensus pattern (23 bp): ATCGGGAAGCTCACAAAGAGCAT Found at i:85633334 original size:75 final size:73 Alignment explanation

Indices: 85633194--85633334 Score: 158 Period size: 75 Copynumber: 1.9 Consensus size: 73 85633184 AGCTCATGAA * * * * * * 85633194 GAGCATATCGGGAAGCTCACAAAGAGCCATGTAACAGGAAGCTCCGGGTAGCCATATATTGGGAA 1 GAGCATATCGGGAAGCTCACAAAGAGCAATGTAACAGGAAGCTCCAGGAAGCAATATAATCGGAA 85633259 TTTCAAGC 66 TTTCAAGC * * * * 85633267 GAGCACTATTGGGAAGCTCACAAAGAGCTAATTTAACAGGAAGCT-TATGAAGACAATATAATCG 1 GAGCA-TATCGGGAAGCTCACAAAGAGC-AATGTAACAGGAAGCTCCAGGAAG-CAATATAATCG 85633331 GAAT 63 GAAT 85633335 GCTTATAAGA Statistics Matches: 55, Mismatches: 10, Indels: 4 0.80 0.14 0.06 Matches are distributed among these distances: 73 5 0.09 74 24 0.44 75 26 0.47 ACGTcount: A:0.37, C:0.18, G:0.25, T:0.21 Consensus pattern (73 bp): GAGCATATCGGGAAGCTCACAAAGAGCAATGTAACAGGAAGCTCCAGGAAGCAATATAATCGGAA TTTCAAGC Found at i:85641314 original size:21 final size:21 Alignment explanation

Indices: 85641288--85641331 Score: 72 Period size: 21 Copynumber: 2.1 Consensus size: 21 85641278 AGGCCTAAAA 85641288 AAACCAAGTGCATA-GAAGGTT 1 AAACCAAGTGCATAGGAA-GTT 85641309 AAACCAAGTGCATAGGAAGTT 1 AAACCAAGTGCATAGGAAGTT 85641330 AA 1 AA 85641332 GTATTTTAAG Statistics Matches: 22, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 21 19 0.86 22 3 0.14 ACGTcount: A:0.45, C:0.14, G:0.23, T:0.18 Consensus pattern (21 bp): AAACCAAGTGCATAGGAAGTT Found at i:85641523 original size:68 final size:67 Alignment explanation

Indices: 85641381--85641581 Score: 165 Period size: 68 Copynumber: 3.0 Consensus size: 67 85641371 TTAAGAAGCC * * * * ** 85641381 AAGTTCTTGAGAAAG-TTAAATAATTTAAGAAGTACGCA-ACCTTGGAAGGTTGAGAGCTTTGAA 1 AAGTTCTTGA-AAAGATTAAATACTTTAAAAAGTATG-AGA-CTTAGAAGGTCAAGAGCTTTGAA * ** 85641444 ATTTT 63 AATAA ** * * 85641449 GGGTTCTTGAAAAGGTTAAGTACTTTAAAAAGTACATGAG-CTTAGAAGGTCAAGAGCTTTGAAA 1 AAGTTCTTGAAAAGATTAAATACTTTAAAAAGT--ATGAGACTTAGAAGGTCAAGAGCTTTGAAA 85641513 ATAA 64 ATAA * * * ** 85641517 AAGTTCTTGAGATGATTAAATACTTTAAAGAGTATGAGACCTTAGAAGGTCAAGATTTTTGAAAA 1 AAGTTCTTGAAAAGATTAAATACTTTAAAAAGTATGAGA-CTTAGAAGGTCAAGAGCTTTGAAAA 85641582 GGAGGGTGCT Statistics Matches: 106, Mismatches: 21, Indels: 12 0.76 0.15 0.09 Matches are distributed among these distances: 66 5 0.05 67 4 0.04 68 94 0.89 69 1 0.01 70 2 0.02 ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31 Consensus pattern (67 bp): AAGTTCTTGAAAAGATTAAATACTTTAAAAAGTATGAGACTTAGAAGGTCAAGAGCTTTGAAAAT AA Found at i:85641594 original size:68 final size:67 Alignment explanation

Indices: 85641464--85641618 Score: 152 Period size: 68 Copynumber: 2.3 Consensus size: 67 85641454 CTTGAAAAGG * * * 85641464 TTAAGTACTTTAAAAAGTACATGAGCTTAGAAGGTCAAGAGCTTTGAAAATAAAAGTTCTTGA-G 1 TTAAATACTTTAAAAAGTA-ATGAGCTTAGAAGGTCAAGAGCTTTGAAAAGAAAAGTGCTTGAGG 85641528 ATGA 65 A-GA * ** * ** 85641532 TTAAATACTTTAAAGAGT-ATGAGACCTTAGAAGGTCAAGATTTTTGAAAAGGAGGGTGCTTGAG 1 TTAAATACTTTAAAAAGTAATGAG--CTTAGAAGGTCAAGAGCTTTGAAAAGAAAAGTGCTTGAG * 85641596 GAGG 64 GAGA * * 85641600 CTAAATACTTTAAGAAGTA 1 TTAAATACTTTAAAAAGTA 85641619 CGCAACCTTG Statistics Matches: 70, Mismatches: 13, Indels: 7 0.78 0.14 0.08 Matches are distributed among these distances: 66 5 0.07 68 63 0.90 69 2 0.03 ACGTcount: A:0.39, C:0.08, G:0.23, T:0.29 Consensus pattern (67 bp): TTAAATACTTTAAAAAGTAATGAGCTTAGAAGGTCAAGAGCTTTGAAAAGAAAAGTGCTTGAGGA GA Found at i:85641627 original size:68 final size:64 Alignment explanation

Indices: 85641533--85641726 Score: 151 Period size: 68 Copynumber: 2.8 Consensus size: 64 85641523 TTGAGATGAT * * * 85641533 TAAATACTTTAAAGAGTATG-AGACCTTAGAAGGTCAAGATTTTTGAAAAG-GAGGGTGCTTGAG 1 TAAATACTTTAAA-AGTACGCA-ACCTT-GAAGGTCAAGA--TTTGAAAAGCGA-AGTGCTTAAG 85641596 -GAGGC 60 AG-GGC * * * 85641601 TAAATACTTTAAGAAGTACGCAACCTTGAAAGGCTGAAAGATTTGAAAAGCTAAGTTCTTAAGAG 1 TAAATACTTTAA-AAGTACGCAACCTTG-AAGG-T-CAAGATTTGAAAAGCGAAGTGCTTAAGAG 85641666 GGC 62 GGC * * * 85641669 TAAGTACTTTAATAAGTACGCAACCTTTGAAGGTCAAAAGCTTTGAAAAGCTAAGTGC 1 TAAATACTTTAA-AAGTACGCAACC-TTGAAGGTC--AAGATTTGAAAAGCGAAGTGC 85641727 CTGGAAGGTA Statistics Matches: 105, Mismatches: 11, Indels: 20 0.77 0.08 0.15 Matches are distributed among these distances: 67 2 0.02 68 91 0.87 69 8 0.08 70 4 0.04 ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26 Consensus pattern (64 bp): TAAATACTTTAAAAGTACGCAACCTTGAAGGTCAAGATTTGAAAAGCGAAGTGCTTAAGAGGGC Found at i:85641854 original size:67 final size:68 Alignment explanation

Indices: 85641747--85641889 Score: 157 Period size: 67 Copynumber: 2.1 Consensus size: 68 85641737 AAGAGTTCTA ** * ** * 85641747 AAAAGCTAAGTGCTGAAGAAGGCTAAGTATTTTAAAAAGTATGTGACCA-TGGAAGGTTGAGAGC 1 AAAAGCTAAGTGCTGAAGAAGGCTAAGTACATTAAAAAGTACGTGA-CATTGGAAGGCCGAGAGA 85641811 TTT- 65 TTTG * ** * 85641814 AAAAGCTAAGTGCTTAAGAATTCTCAA-TACATTAAGAAGTACGTGACATTGGAAGGCCGAGAGA 1 AAAAGCTAAGTGCTGAAGAAGGCT-AAGTACATTAAAAAGTACGTGACATTGGAAGGCCGAGAGA 85641878 TTTG 65 TTTG 85641882 AAAAGCTA 1 AAAAGCTA 85641890 TTCTTTCATA Statistics Matches: 63, Mismatches: 10, Indels: 5 0.81 0.13 0.06 Matches are distributed among these distances: 66 2 0.03 67 51 0.81 68 10 0.16 ACGTcount: A:0.39, C:0.11, G:0.24, T:0.25 Consensus pattern (68 bp): AAAAGCTAAGTGCTGAAGAAGGCTAAGTACATTAAAAAGTACGTGACATTGGAAGGCCGAGAGAT TTG Done.