Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold501

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 1397941
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31

Warning! 110142 characters in sequence are not A, C, G, or T


File 2 of 5

Found at i:4746 original size:2 final size:2

Alignment explanation

Indices: 4739--4800 Score: 124 Period size: 2 Copynumber: 31.0 Consensus size: 2 4729 ACGCAATGAA 4739 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 4781 AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG 4801 GGGGGTTAAA Statistics Matches: 60, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 60 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:12251 original size:21 final size:20 Alignment explanation

Indices: 12213--12251 Score: 51 Period size: 20 Copynumber: 1.9 Consensus size: 20 12203 TCTTGTGGTT * * 12213 TTTTTTTTTTTTGGTTTGTA 1 TTTTTTTTTTCTGATTTGTA 12233 TTTTTTTTTTCTGTATTTG 1 TTTTTTTTTTCTG-ATTTG 12252 AAAAAGTTCT Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 20 12 0.75 21 4 0.25 ACGTcount: A:0.05, C:0.03, G:0.13, T:0.79 Consensus pattern (20 bp): TTTTTTTTTTCTGATTTGTA Found at i:13302 original size:21 final size:22 Alignment explanation

Indices: 13254--13302 Score: 73 Period size: 22 Copynumber: 2.3 Consensus size: 22 13244 ATTTAACAAG * * 13254 ATATTTAAAATATTTTTTAAAA 1 ATATTGAAAATATTCTTTAAAA 13276 ATATTGAAAATATTCTTTAAAA 1 ATATTGAAAATATTCTTTAAAA 13298 A-ATTG 1 ATATTG 13303 CATTAAATTT Statistics Matches: 25, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 21 4 0.16 22 21 0.84 ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45 Consensus pattern (22 bp): ATATTGAAAATATTCTTTAAAA Found at i:18998 original size:42 final size:42 Alignment explanation

Indices: 18945--19407 Score: 398 Period size: 42 Copynumber: 10.8 Consensus size: 42 18935 TCTTCATAAT * * * 18945 ATGATGATACTTTAACATTACGT-ACTGATACTTCAACATTAC 1 ATGATGATACTTCAACATTACATGA-TGGTACTTCAACATTAC * 18987 ATGATGGTACTTCAACATTACATGATGGTACTTCAACATTAC 1 ATGATGATACTTCAACATTACATGATGGTACTTCAACATTAC * 19029 ATGATGGA-ACTTCAACATTACATGATGGTTCTTCAACATTAC 1 ATGAT-GATACTTCAACATTACATGATGGTACTTCAACATTAC * * * * 19071 ATGCTGATACTTCAACATAACATCATGGTTCTTCAACATTAC 1 ATGATGATACTTCAACATTACATGATGGTACTTCAACATTAC * * 19113 ATGCTGATACTTTAACATTACATGATGGTACTTCAACATTAC 1 ATGATGATACTTCAACATTACATGATGGTACTTCAACATTAC * * * 19155 AAGCTGATACTTTAACATTACATGATGGTACCTT-AACATTAC 1 ATGATGATACTTCAACATTACATGATGGTA-CTTCAACATTAC * * * 19197 GA-GGTGATACTTCAACATTACATGATGGCCATGGTACTTTAACATTGC 1 -ATGATGATACTTCAACATTAC---AT-G--ATGGTACTTCAACATTAC * * * * 19245 GTGCTGATATTTCAACATTACATGATGGTACTTTAACATTAC 1 ATGATGATACTTCAACATTACATGATGGTACTTCAACATTAC * * * * ** * ** * 19287 GTGCTGATACTTTAACATTACATGTTCATGCTGAAACTTCTTTA- 1 ATGATGATACTTCAACATTACATGATGGTACTTCAA---CATTAC * * * * 19331 ATTTATGATACTTTAACATTACATGCTGATACTT-AACATTAC 1 A-TGATGATACTTCAACATTACATGATGGTACTTCAACATTAC * * * * * 19373 ATGCTGAAACTTCAACATTATATGCTGGTATTTCA 1 ATGATGATACTTCAACATTACATGATGGTACTTCA 19408 TAAAATGATT Statistics Matches: 357, Mismatches: 45, Indels: 38 0.81 0.10 0.09 Matches are distributed among these distances: 41 31 0.09 42 249 0.70 43 6 0.02 44 3 0.01 45 34 0.10 46 1 0.00 47 3 0.01 48 30 0.08 ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36 Consensus pattern (42 bp): ATGATGATACTTCAACATTACATGATGGTACTTCAACATTAC Found at i:19368 original size:20 final size:20 Alignment explanation

Indices: 19336--19399 Score: 92 Period size: 20 Copynumber: 3.1 Consensus size: 20 19326 CTTTAATTTA 19336 TGATACTTTAACATTACATGC 1 TGATAC-TTAACATTACATGC 19357 TGATACTTAACATTACATGC 1 TGATACTTAACATTACATGC * * 19377 TGAAACTTCAACATTATATGC 1 TGATACTT-AACATTACATGC 19398 TG 1 TG 19400 GTATTTCATA Statistics Matches: 40, Mismatches: 2, Indels: 2 0.91 0.05 0.05 Matches are distributed among these distances: 20 21 0.52 21 19 0.47 ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36 Consensus pattern (20 bp): TGATACTTAACATTACATGC Found at i:19407 original size:21 final size:21 Alignment explanation

Indices: 18949--19399 Score: 347 Period size: 21 Copynumber: 21.1 Consensus size: 21 18939 CATAATATGA * * * 18949 TGATACTTTAACATTACGTAC 1 TGATACTTCAACATTACATGC * 18970 TGATACTTCAACATTACATGA 1 TGATACTTCAACATTACATGC * * 18991 TGGTACTTCAACATTACATGA 1 TGATACTTCAACATTACATGC * * 19012 TGGTACTTCAACATTACATGA 1 TGATACTTCAACATTACATGC * 19033 TGGA-ACTTCAACATTACATGA 1 T-GATACTTCAACATTACATGC * * 19054 TGGTTCTTCAACATTACATGC 1 TGATACTTCAACATTACATGC * 19075 TGATACTTCAACATAACAT-C 1 TGATACTTCAACATTACATGC * * 19095 ATGGTTCTTCAACATTACATGC 1 -TGATACTTCAACATTACATGC * * 19117 TGATACTTTAACATTACATGA 1 TGATACTTCAACATTACATGC * * 19138 TGGTACTTCAACATTACAAGC 1 TGATACTTCAACATTACATGC * * 19159 TGATACTTTAACATTACATGA 1 TGATACTTCAACATTACATGC * * 19180 TGGTACCTT-AACATTACGA-GG 1 TGATA-CTTCAACATTAC-ATGC 19201 TGATACTTCAACATTACATGATGGCC 1 TGATACTTCAACATTAC---AT-G-C * * * * 19227 ATGGTACTTTAACATTGCGTGC 1 -TGATACTTCAACATTACATGC * * 19249 TGATATTTCAACATTACATGA 1 TGATACTTCAACATTACATGC * * * 19270 TGGTACTTTAACATTACGTGC 1 TGATACTTCAACATTACATGC * * 19291 TGATACTTTAACATTACATGT 1 TGATACTTCAACATTACATGC * * ** * ** 19312 TCATGCTGAAACTTCTTTA-ATTTA 1 TGATACTTCAA---CATTACA-TGC * 19336 TGATACTTTAACATTACATGC 1 TGATACTTCAACATTACATGC 19357 TGATACTT-AACATTACATGC 1 TGATACTTCAACATTACATGC * * 19377 TGAAACTTCAACATTATATGC 1 TGATACTTCAACATTACATGC 19398 TG 1 TG 19400 GTATTTCATA Statistics Matches: 346, Mismatches: 65, Indels: 38 0.77 0.14 0.08 Matches are distributed among these distances: 20 24 0.07 21 282 0.82 22 8 0.02 23 4 0.01 24 13 0.04 25 1 0.00 27 14 0.04 ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35 Consensus pattern (21 bp): TGATACTTCAACATTACATGC Found at i:25544 original size:13 final size:13 Alignment explanation

Indices: 25526--25550 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 25516 TATCATGTAC 25526 TGTATGTAAAACA 1 TGTATGTAAAACA 25539 TGTATGTAAAAC 1 TGTATGTAAAAC 25551 CTTCAATAGT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATGTAAAACA Found at i:26466 original size:180 final size:180 Alignment explanation

Indices: 26164--26523 Score: 639 Period size: 180 Copynumber: 2.0 Consensus size: 180 26154 GCTGCCAAAT * * 26164 GGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCAG 1 GGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAG * 26229 ATCAATTGTACATATATCAGAGGTGTGCATATCGCTAGGATTTTGATTTCCGATAATTTATCGAA 66 ATCAATTGTACATATATCAGAGGTGTGCATATCGCTAGGATTTTGATTTCCGATAATTTATCAAA * 26294 AAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATA 131 AAAATACCAGCTTTTGAACTTAGTAATTTTTTGGCAAAATATTGCATATA 26344 GGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAG 1 GGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAG * 26409 ATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCAAA 66 ATCAATTGTACATATATCAGAGGTGTGCATATCGCTAGGATTTTGATTTCCGATAATTTATCAAA ** * * 26474 AAAATATTAGCTTTTGAACTTAGTAATTTTTTTGCAAAATGTTGCATATA 131 AAAATACCAGCTTTTGAACTTAGTAATTTTTTGGCAAAATATTGCATATA 26524 CATGTAGGGT Statistics Matches: 171, Mismatches: 9, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 180 171 1.00 ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37 Consensus pattern (180 bp): GGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAG ATCAATTGTACATATATCAGAGGTGTGCATATCGCTAGGATTTTGATTTCCGATAATTTATCAAA AAAATACCAGCTTTTGAACTTAGTAATTTTTTGGCAAAATATTGCATATA Found at i:36008 original size:16 final size:16 Alignment explanation

Indices: 35987--36021 Score: 61 Period size: 16 Copynumber: 2.2 Consensus size: 16 35977 TAAAGGTGGT 35987 CTCATAAAGCTGATGC 1 CTCATAAAGCTGATGC * 36003 CTCATAAAGGTGATGC 1 CTCATAAAGCTGATGC 36019 CTC 1 CTC 36022 GTCTCTGTGT 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:0.29, C:0.26, G:0.20, T:0.26 Consensus pattern (16 bp): CTCATAAAGCTGATGC Found at i:36568 original size:14 final size:13 Alignment explanation

Indices: 36535--36569 Score: 52 Period size: 14 Copynumber: 2.5 Consensus size: 13 36525 ACTTTTGCTC 36535 CTTCGCCTTTGCA 1 CTTCGCCTTTGCA 36548 CTATCGCCTTTGCAA 1 CT-TCGCCTTTGC-A 36563 CTTCGCC 1 CTTCGCC 36570 CTAAGGTCGA Statistics Matches: 20, Mismatches: 0, Indels: 3 0.87 0.00 0.13 Matches are distributed among these distances: 13 2 0.10 14 15 0.75 15 3 0.15 ACGTcount: A:0.11, C:0.40, G:0.14, T:0.34 Consensus pattern (13 bp): CTTCGCCTTTGCA Found at i:37648 original size:32 final size:32 Alignment explanation

Indices: 37602--37663 Score: 88 Period size: 32 Copynumber: 1.9 Consensus size: 32 37592 TCCAGGCAAA * * 37602 GGGGTCATTTTTCTACGTAGAATAATGACCGG 1 GGGGTCATTATTCTACGTAGAAAAATGACCGG * * 37634 GGGGTTATTATTCTACGTCGAAAAATGACC 1 GGGGTCATTATTCTACGTAGAAAAATGACC 37664 CCCGGTCATA Statistics Matches: 26, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 32 26 1.00 ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31 Consensus pattern (32 bp): GGGGTCATTATTCTACGTAGAAAAATGACCGG Found at i:37789 original size:11 final size:11 Alignment explanation

Indices: 37773--37797 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 37763 CTACCAAATG 37773 AAGTCCTGAAT 1 AAGTCCTGAAT 37784 AAGTCCTGAAT 1 AAGTCCTGAAT 37795 AAG 1 AAG 37798 GCATGGCCAA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24 Consensus pattern (11 bp): AAGTCCTGAAT Found at i:39120 original size:12 final size:12 Alignment explanation

Indices: 39103--39136 Score: 59 Period size: 12 Copynumber: 2.8 Consensus size: 12 39093 TGCTAAAACG 39103 CGGAACGGAAAA 1 CGGAACGGAAAA * 39115 CGGAACGGAAAG 1 CGGAACGGAAAA 39127 CGGAACGGAA 1 CGGAACGGAA 39137 CGCAAGACGG Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 12 21 1.00 ACGTcount: A:0.44, C:0.18, G:0.38, T:0.00 Consensus pattern (12 bp): CGGAACGGAAAA Found at i:43219 original size:16 final size:17 Alignment explanation

Indices: 43193--43228 Score: 56 Period size: 16 Copynumber: 2.2 Consensus size: 17 43183 AAACTGAAGT 43193 GGAACAGACAGACGGAC 1 GGAACAGACAGACGGAC * 43210 GGAA-AGACAGACTGAC 1 GGAACAGACAGACGGAC 43226 GGA 1 GGA 43229 CGCAGAGGAA Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 16 14 0.78 17 4 0.22 ACGTcount: A:0.42, C:0.19, G:0.36, T:0.03 Consensus pattern (17 bp): GGAACAGACAGACGGAC Found at i:51196 original size:2 final size:2 Alignment explanation

Indices: 51191--51236 Score: 74 Period size: 2 Copynumber: 23.0 Consensus size: 2 51181 AAAAAGTCTT * * 51191 TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 51233 TA TA 1 TA TA 51237 AGTCACGTTT Statistics Matches: 40, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 2 40 1.00 ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46 Consensus pattern (2 bp): TA Found at i:54760 original size:2 final size:2 Alignment explanation

Indices: 54753--54802 Score: 100 Period size: 2 Copynumber: 25.0 Consensus size: 2 54743 AAAAGCATAT 54753 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 54795 GA GA GA GA 1 GA GA GA GA 54803 TTTCCAGTCT Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 48 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:62567 original size:20 final size:20 Alignment explanation

Indices: 62522--62568 Score: 58 Period size: 20 Copynumber: 2.4 Consensus size: 20 62512 GGTATTATAT * 62522 TGTATCATATTAAACAATAG 1 TGTATCATATTAAACAATAC * * 62542 TGTATCATATTATACGATAC 1 TGTATCATATTAAACAATAC * 62562 TTTATCA 1 TGTATCA 62569 AAGGGATCAT Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 20 23 1.00 ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40 Consensus pattern (20 bp): TGTATCATATTAAACAATAC Found at i:64481 original size:3 final size:3 Alignment explanation

Indices: 64475--64512 Score: 76 Period size: 3 Copynumber: 12.7 Consensus size: 3 64465 TGTTAATGTA 64475 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC 1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC 64513 ATAATACTGA Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 35 1.00 ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66 Consensus pattern (3 bp): TCT Found at i:65977 original size:23 final size:23 Alignment explanation

Indices: 65931--65990 Score: 74 Period size: 23 Copynumber: 2.8 Consensus size: 23 65921 TTTTTTGAAT 65931 AATCAAATTAATAA---TTCTTA 1 AATCAAATTAATAATTTTTCTTA * * 65951 AATCAAATTAATAATTTTTTTTG 1 AATCAAATTAATAATTTTTCTTA 65974 AATCAAATTAAT-ATTTT 1 AATCAAATTAATAATTTT 65991 GTAAATCTAA Statistics Matches: 35, Mismatches: 2, Indels: 4 0.85 0.05 0.10 Matches are distributed among these distances: 20 14 0.40 22 5 0.14 23 16 0.46 ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47 Consensus pattern (23 bp): AATCAAATTAATAATTTTTCTTA Found at i:65985 original size:20 final size:20 Alignment explanation

Indices: 65960--66012 Score: 63 Period size: 20 Copynumber: 2.6 Consensus size: 20 65950 AAATCAAATT * * 65960 AATAATTTTTTTTGAATC-A 1 AATAATTTTTTGTAAATCTA * 65979 AATTAATATTTTGTAAATCTA 1 AA-TAATTTTTTGTAAATCTA 66000 AATAATTTTTTGT 1 AATAATTTTTTGT 66013 TTTTTGTTTC Statistics Matches: 28, Mismatches: 4, Indels: 3 0.80 0.11 0.09 Matches are distributed among these distances: 19 2 0.07 20 23 0.82 21 3 0.11 ACGTcount: A:0.38, C:0.04, G:0.06, T:0.53 Consensus pattern (20 bp): AATAATTTTTTGTAAATCTA Found at i:66869 original size:4 final size:4 Alignment explanation

Indices: 66853--66893 Score: 64 Period size: 4 Copynumber: 10.2 Consensus size: 4 66843 CTTTCCTCTG * * 66853 CGTC CGTC AGTC CGTC CGTC CGTC CGTC CGTC CGTC TGTC C 1 CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC C 66894 CACTTCAGTT Statistics Matches: 33, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 4 33 1.00 ACGTcount: A:0.02, C:0.46, G:0.24, T:0.27 Consensus pattern (4 bp): CGTC Found at i:76979 original size:12 final size:13 Alignment explanation

Indices: 76934--76967 Score: 54 Period size: 12 Copynumber: 2.8 Consensus size: 13 76924 TGCTAAAACG 76934 CGGAACGGAAA-A 1 CGGAACGGAAAGA 76946 CGGAACGGAAAGA 1 CGGAACGGAAAGA 76959 -GGAACGGAA 1 CGGAACGGAA 76968 CGGAAAACGG Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 12 20 0.95 13 1 0.05 ACGTcount: A:0.47, C:0.15, G:0.38, T:0.00 Consensus pattern (13 bp): CGGAACGGAAAGA Found at i:92806 original size:35 final size:35 Alignment explanation

Indices: 92760--92879 Score: 154 Period size: 35 Copynumber: 3.4 Consensus size: 35 92750 GGGTCCCTGC * 92760 ATGGTGTCAACCCAGGTTCCATTCCTTAAATCCCG 1 ATGGTGTCAACCCGGGTTCCATTCCTTAAATCCCG ** 92795 ATGGTGTCAACCCGGGAACCATTCCTTAAATCCCG 1 ATGGTGTCAACCCGGGTTCCATTCCTTAAATCCCG * * 92830 ATGGTGTCAACCCGGGAATT--ACTCTTTAAATCCCG 1 ATGGTGTCAACCCGGG--TTCCATTCCTTAAATCCCG * 92865 ATGATGTCAACCCGG 1 ATGGTGTCAACCCGG 92880 AAACCATTAT Statistics Matches: 75, Mismatches: 8, Indels: 4 0.86 0.09 0.05 Matches are distributed among these distances: 35 75 1.00 ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26 Consensus pattern (35 bp): ATGGTGTCAACCCGGGTTCCATTCCTTAAATCCCG Found at i:95212 original size:2 final size:2 Alignment explanation

Indices: 95197--95232 Score: 58 Period size: 2 Copynumber: 19.0 Consensus size: 2 95187 ATGTGTGGCA 95197 AT AT A- AT AT A- 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 AT AT AT 95233 CCAGAGCCGA Statistics Matches: 32, Mismatches: 0, Indels: 4 0.89 0.00 0.11 Matches are distributed among these distances: 1 2 0.06 2 30 0.94 ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47 Consensus pattern (2 bp): AT Found at i:95330 original size:22 final size:22 Alignment explanation

Indices: 95305--95346 Score: 66 Period size: 22 Copynumber: 1.9 Consensus size: 22 95295 AATCATTTGT * 95305 ATTTTCTGATATCAGAAAATCG 1 ATTTTCTGATATAAGAAAATCG * 95327 ATTTTTTGATATAAGAAAAT 1 ATTTTCTGATATAAGAAAAT 95347 AAGACCTAAT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 22 18 1.00 ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40 Consensus pattern (22 bp): ATTTTCTGATATAAGAAAATCG Found at i:114024 original size:13 final size:13 Alignment explanation

Indices: 114006--114031 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 113996 GTGTAATGAT 114006 AATATCATAACAA 1 AATATCATAACAA 114019 AATATCATAACAA 1 AATATCATAACAA 114032 CAACAACAAC 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:0.62, C:0.15, G:0.00, T:0.23 Consensus pattern (13 bp): AATATCATAACAA Found at i:114068 original size:3 final size:3 Alignment explanation

Indices: 114027--114060 Score: 68 Period size: 3 Copynumber: 11.3 Consensus size: 3 114017 AAAATATCAT 114027 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A 1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A 114061 GAACAACAGT Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 31 1.00 ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00 Consensus pattern (3 bp): AAC Found at i:114478 original size:36 final size:36 Alignment explanation

Indices: 114431--114501 Score: 133 Period size: 36 Copynumber: 2.0 Consensus size: 36 114421 TTTCAAAAAT * 114431 AAAAGTTCCAAGAACGCACTAGTTCTTTTGTCTTTC 1 AAAAGTTCCAAGAACGCACTAGTTCTTTTCTCTTTC 114467 AAAAGTTCCAAGAACGCACTAGTTCTTTTCTCTTT 1 AAAAGTTCCAAGAACGCACTAGTTCTTTTCTCTTT 114502 ATTATACGAC Statistics Matches: 34, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 36 34 1.00 ACGTcount: A:0.28, C:0.23, G:0.13, T:0.37 Consensus pattern (36 bp): AAAAGTTCCAAGAACGCACTAGTTCTTTTCTCTTTC Found at i:116906 original size:1 final size:1 Alignment explanation

Indices: 116900--116924 Score: 50 Period size: 1 Copynumber: 25.0 Consensus size: 1 116890 GAAAAGGTGT 116900 GGGGGGGGGGGGGGGGGGGGGGGGG 1 GGGGGGGGGGGGGGGGGGGGGGGGG 116925 AGATGTTTCA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 24 1.00 ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00 Consensus pattern (1 bp): G Found at i:118453 original size:20 final size:19 Alignment explanation

Indices: 118424--118466 Score: 59 Period size: 20 Copynumber: 2.2 Consensus size: 19 118414 TTGTTGTTGA * * 118424 ATAAATTTAAAATACAATC 1 ATAAATTTAAAAAACAAAC 118443 ATAAGATTTAAAAAACAAAC 1 ATAA-ATTTAAAAAACAAAC 118463 ATAA 1 ATAA 118467 CAAATCTACG Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 19 4 0.19 20 17 0.81 ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26 Consensus pattern (19 bp): ATAAATTTAAAAAACAAAC Found at i:143241 original size:41 final size:41 Alignment explanation

Indices: 143123--143250 Score: 107 Period size: 41 Copynumber: 3.1 Consensus size: 41 143113 ACAAACATTT * 143123 AAAAATGACAAAGTCCAAATTAGTTACAAAAAAGTTATACTG 1 AAAAATGACAAAGTCCAAA-TAGGTACAAAAAAGTTATACTG * * * ** * **** 143165 AACAAT-TCTAAGTCTGAATAAGGCACAGTTTAGTTATACT- 1 AAAAATGACAAAGTCCAAAT-AGGTACAAAAAAGTTATACTG * 143205 AAGAAATGACAAAGTCCAAATAGGTACAAAAAAGTTATAGTG 1 AA-AAATGACAAAGTCCAAATAGGTACAAAAAAGTTATACTG 143247 AAAA 1 AAAA 143251 TTTTCTAAGT Statistics Matches: 60, Mismatches: 22, Indels: 9 0.66 0.24 0.10 Matches are distributed among these distances: 40 3 0.05 41 41 0.68 42 16 0.27 ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24 Consensus pattern (41 bp): AAAAATGACAAAGTCCAAATAGGTACAAAAAAGTTATACTG Found at i:143342 original size:84 final size:84 Alignment explanation

Indices: 143121--143402 Score: 337 Period size: 84 Copynumber: 3.4 Consensus size: 84 143111 AAACAAACAT * * * 143121 TTAA-AAATGACAAAGTCCAAATTAGTTACAAAAAAGTTATACTGAACAA-TTCTAAGTCTGA-A 1 TTAAGAAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAA-AATTTCTAAGTGTGATA * * 143183 TAAGGCACAGTTTAGTTATAC 65 T-AGGTACATTTTAGTTATAC 143204 -TAAGAAATGACAAAGTCCAAA-TAGGTACAAAAAAGTTATAGTGAAAATTTTCTAAGTGTGATA 1 TTAAGAAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAAAA-TTTCTAAGTGTGATA 143267 TAGGTACATTTTAGTTATAC 65 TAGGTACATTTTAGTTATAC * * * * * 143287 TTTA-ATATGACTAAGTTCAAATTAGGTACAGAAAAGTTATAGTGAAAATTGTCTAAGTGTGATA 1 TTAAGAAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAAAATT-TCTAAGTGTGATA 143351 TAGGTACATTTTAGTTATAC 65 TAGGTACATTTTAGTTATAC * * * * 143371 TTCA-AAACGACAAAG-ACAAATATAGTTACAAA 1 TTAAGAAATGACAAAGTCCAAAT-TAGGTACAAA 143403 TCAGTCATAA Statistics Matches: 174, Mismatches: 17, Indels: 15 0.84 0.08 0.07 Matches are distributed among these distances: 81 2 0.01 82 25 0.14 83 66 0.38 84 81 0.47 ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31 Consensus pattern (84 bp): TTAAGAAATGACAAAGTCCAAATTAGGTACAAAAAAGTTATAGTGAAAATTTCTAAGTGTGATAT AGGTACATTTTAGTTATAC Found at i:143367 original size:42 final size:42 Alignment explanation

Indices: 143237--143369 Score: 135 Period size: 42 Copynumber: 3.2 Consensus size: 42 143227 GGTACAAAAA * 143237 AGTTATAGTGAAAATTTTCTAAGTGTGATATAGGTACATTTT 1 AGTTATAGTGAAAATTGTCTAAGTGTGATATAGGTACATTTT * ** * * * **** 143279 AGTTATACT-TTAATATGACTAAGT-TCAAATTAGGTACAGAAA 1 AGTTATAGTGAAAAT-TGTCTAAGTGTGATA-TAGGTACATTTT 143321 AGTTATAGTGAAAATTGTCTAAGTGTGATATAGGTACATTTT 1 AGTTATAGTGAAAATTGTCTAAGTGTGATATAGGTACATTTT 143363 AGTTATA 1 AGTTATA 143370 CTTCAAAACG Statistics Matches: 66, Mismatches: 21, Indels: 8 0.69 0.22 0.08 Matches are distributed among these distances: 41 6 0.09 42 54 0.82 43 6 0.09 ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39 Consensus pattern (42 bp): AGTTATAGTGAAAATTGTCTAAGTGTGATATAGGTACATTTT Found at i:147807 original size:2 final size:2 Alignment explanation

Indices: 147800--147852 Score: 106 Period size: 2 Copynumber: 26.5 Consensus size: 2 147790 CGAGATTTTG 147800 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 147842 GA GA GA GA GA G 1 GA GA GA GA GA G 147853 GCGCATGGCA Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:151293 original size:2 final size:2 Alignment explanation

Indices: 151286--151338 Score: 106 Period size: 2 Copynumber: 26.5 Consensus size: 2 151276 GTCTGATCTC 151286 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 151328 AG AG AG AG AG A 1 AG AG AG AG AG A 151339 TATGCTGCAG Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:163720 original size:13 final size:13 Alignment explanation

Indices: 163702--163726 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 163692 TAGATACACA 163702 TGCAAAAGCTGGG 1 TGCAAAAGCTGGG 163715 TGCAAAAGCTGG 1 TGCAAAAGCTGG 163727 ATCCACCCCT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16 Consensus pattern (13 bp): TGCAAAAGCTGGG Found at i:169291 original size:23 final size:23 Alignment explanation

Indices: 169235--169291 Score: 55 Period size: 22 Copynumber: 2.5 Consensus size: 23 169225 ACCTAATTAA * * 169235 TGCAAATAAAAACTGTATTTTTG 1 TGCAAATAACAACTGCATTTTTG * * 169258 TG-AAGTTACAA-TGCATATTTTG 1 TGCAAATAACAACTGCAT-TTTTG 169280 TGCAAATAACAA 1 TGCAAATAACAA 169292 AATAAATAAT Statistics Matches: 26, Mismatches: 6, Indels: 4 0.72 0.17 0.11 Matches are distributed among these distances: 21 4 0.15 22 13 0.50 23 9 0.35 ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35 Consensus pattern (23 bp): TGCAAATAACAACTGCATTTTTG Found at i:174532 original size:69 final size:69 Alignment explanation

Indices: 174421--174647 Score: 341 Period size: 69 Copynumber: 3.3 Consensus size: 69 174411 AGTTGTACAT ** * * * * 174421 CTACCCATCTTCTCCATGTCTAGTACATAGCCCCCTCTGACATGCCTACCATTGATTATCTTTCT 1 CTACCCATCTTCTCGGTGTCTAGTATATAACCCCCTTTGACATGCCTACCATTGATTACCTTTCT 174486 GCAC 66 GCAC 174490 CTACCCATCTTCTCGGTGTCTAGTATATAACCCCCTTTGACATGCCTA-CAGTTG-TTAACCTTT 1 CTACCCATCTTCTCGGTGTCTAGTATATAACCCCCTTTGACATGCCTACCA-TTGATT-ACCTTT 174553 CTGCAC 64 CTGCAC * * * 174559 CTACCCATATTCTCAGTGTCTAGTATATAACCCCCTTTGACATGCCTACCATTGATAACCTTTCT 1 CTACCCATCTTCTCGGTGTCTAGTATATAACCCCCTTTGACATGCCTACCATTGATTACCTTTCT 174624 GCAC 66 GCAC 174628 CTACCCATCTTCTCGGTGTC 1 CTACCCATCTTCTCGGTGTC 174648 GAGGTCCATC Statistics Matches: 143, Mismatches: 11, Indels: 8 0.88 0.07 0.05 Matches are distributed among these distances: 68 4 0.03 69 136 0.95 70 3 0.02 ACGTcount: A:0.21, C:0.34, G:0.11, T:0.34 Consensus pattern (69 bp): CTACCCATCTTCTCGGTGTCTAGTATATAACCCCCTTTGACATGCCTACCATTGATTACCTTTCT GCAC Found at i:208143 original size:16 final size:16 Alignment explanation

Indices: 208105--208135 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 208095 CAAACAAGGT * 208105 TTAGGGCAAACGATAA 1 TTAGAGCAAACGATAA 208121 TTAGAGCAAACGATA 1 TTAGAGCAAACGATA 208136 TTAAGAGCGA Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19 Consensus pattern (16 bp): TTAGAGCAAACGATAA Found at i:226111 original size:2 final size:2 Alignment explanation

Indices: 226104--226159 Score: 112 Period size: 2 Copynumber: 28.0 Consensus size: 2 226094 TCTTTCAATT 226104 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 226146 GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA 226160 AAANNNNNNN Statistics Matches: 54, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 54 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:231024 original size:2 final size:2 Alignment explanation

Indices: 231019--231057 Score: 69 Period size: 2 Copynumber: 19.5 Consensus size: 2 231009 TATATATATT * 231019 TG TG TG TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG T 1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T 231058 CCTATTTAGC Statistics Matches: 35, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.00, C:0.03, G:0.49, T:0.49 Consensus pattern (2 bp): TG Found at i:234042 original size:2 final size:2 Alignment explanation

Indices: 234035--234083 Score: 98 Period size: 2 Copynumber: 24.5 Consensus size: 2 234025 TCTTTCAATT 234035 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 234077 GA GA GA G 1 GA GA GA G 234084 CATGCTGAAT Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 47 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:250047 original size:196 final size:188 Alignment explanation

Indices: 249688--250058 Score: 580 Period size: 196 Copynumber: 1.9 Consensus size: 188 249678 CTACTCATTC * 249688 GGAGGACACTCGAGGAAGACTCGAAAAACAATCGCAGGAACTCGTTAGTTTTCTATGAATGTTAA 1 GGAGGACACTCGAGGAAGACTCGAAAAACAATCGCAGGAACTCGTAAGTTTTCTATGAATGTTAA * * 249753 AGATTTACTGCGCATGTGTGCAGTGCGAGTGTCATACGAAAGTCTAAAAATAACTAAAAATCCTA 66 AGATTTACTGCGCATGAGTGCAGTGCGAGTGTCACACGAAAGTCTAAAAATAACTAAAAATCCTA * * 249818 TTGTGGGCACAATTGTTTTTAATATGCTCTCAACAATTGTCGTATTTAGCTATTATTT 131 CTGTGGGCACAATTGTTTTTAATATGCTCTCAACAATTGCCGTATTTAGCTATTATTT * * 249876 GGAGGACACTCGAGGAGGACTCGAAAAACAATCGCAGGAACTCGTAAGTTTTCTATGAATGTTTA 1 GGAGGACACTCGAGGAAGACTCGAAAAACAATCGCAGGAACTCGTAAGTTTTCTATGAATGTTAA * ** 249941 AGATTTACTGCGATTATGTGCATGAGTGCAGTGCGAGTGTCACACGAAAGTCTAAGAATGCCTAA 66 AGATTTACTGC--------GCATGAGTGCAGTGCGAGTGTCACACGAAAGTCTAAAAATAACTAA 250006 AAATCCTACTGTGGGCACAATTGTTTTTAATATGCTCTCAACAATTGCCGTAT 123 AAATCCTACTGTGGGCACAATTGTTTTTAATATGCTCTCAACAATTGCCGTAT 250059 ATTTCAATGA Statistics Matches: 165, Mismatches: 10, Indels: 8 0.90 0.05 0.04 Matches are distributed among these distances: 188 73 0.44 196 92 0.56 ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30 Consensus pattern (188 bp): GGAGGACACTCGAGGAAGACTCGAAAAACAATCGCAGGAACTCGTAAGTTTTCTATGAATGTTAA AGATTTACTGCGCATGAGTGCAGTGCGAGTGTCACACGAAAGTCTAAAAATAACTAAAAATCCTA CTGTGGGCACAATTGTTTTTAATATGCTCTCAACAATTGCCGTATTTAGCTATTATTT Found at i:256641 original size:39 final size:39 Alignment explanation

Indices: 256582--256662 Score: 117 Period size: 39 Copynumber: 2.1 Consensus size: 39 256572 TGCTATCCAG * * * 256582 CACCAAATGCCCAGTTTATTGAACGTGGATACGGATTTC 1 CACCAAATGCCCAGTATATTGAACGCGGAGACGGATTTC * * 256621 CACCAAATGCCCAGTATATTGATCGCGGCGACGGATTTC 1 CACCAAATGCCCAGTATATTGAACGCGGAGACGGATTTC 256660 CAC 1 CAC 256663 AATCAAATAT Statistics Matches: 37, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 39 37 1.00 ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25 Consensus pattern (39 bp): CACCAAATGCCCAGTATATTGAACGCGGAGACGGATTTC Found at i:258216 original size:11 final size:11 Alignment explanation

Indices: 258200--258250 Score: 57 Period size: 12 Copynumber: 4.3 Consensus size: 11 258190 CCCCCCCAAA 258200 AAAAAAAAAAC 1 AAAAAAAAAAC 258211 AAAAAAAAAAAC 1 -AAAAAAAAAAC 258223 AACAACAACAAAAC 1 AA-AA-AA-AAAAC * 258237 AAACAAAAAAC 1 AAAAAAAAAAC 258248 AAA 1 AAA 258251 CGTTTTAATA Statistics Matches: 35, Mismatches: 1, Indels: 7 0.81 0.02 0.16 Matches are distributed among these distances: 11 10 0.29 12 15 0.43 13 3 0.09 14 7 0.20 ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00 Consensus pattern (11 bp): AAAAAAAAAAC Found at i:258217 original size:15 final size:15 Alignment explanation

Indices: 258197--258246 Score: 64 Period size: 15 Copynumber: 3.3 Consensus size: 15 258187 CCCCCCCCCC 258197 AAAAAAAAAAAAACA 1 AAAAAAAAAAAAACA * 258212 AAAAAAAAAACAACA 1 AAAAAAAAAAAAACA * * * 258227 ACAACAAAACAAACA 1 AAAAAAAAAAAAACA 258242 AAAAA 1 AAAAA 258247 CAAACGTTTT Statistics Matches: 28, Mismatches: 7, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 15 28 1.00 ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00 Consensus pattern (15 bp): AAAAAAAAAAAAACA Found at i:258251 original size:15 final size:14 Alignment explanation

Indices: 258196--258251 Score: 58 Period size: 14 Copynumber: 3.8 Consensus size: 14 258186 CCCCCCCCCC * 258196 CAAAAAAAAAAAAA 1 CAAAAAAAAACAAA * 258210 CAAAAAAAAAAACAA 1 CAAAAAAAAACA-AA * 258225 CAACAACAAAACAAA 1 CAA-AAAAAAACAAA 258240 CAAAAAACAAAC 1 CAAAAAA-AAAC 258252 GTTTTAATAT Statistics Matches: 36, Mismatches: 3, Indels: 5 0.82 0.07 0.11 Matches are distributed among these distances: 14 15 0.42 15 14 0.39 16 7 0.19 ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00 Consensus pattern (14 bp): CAAAAAAAAACAAA Found at i:263786 original size:17 final size:18 Alignment explanation

Indices: 263764--263797 Score: 61 Period size: 17 Copynumber: 1.9 Consensus size: 18 263754 AGACATTGCG 263764 TTTCTTAAAA-ACATTTA 1 TTTCTTAAAAGACATTTA 263781 TTTCTTAAAAGACATTT 1 TTTCTTAAAAGACATTT 263798 TTATGCATAT Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 17 10 0.62 18 6 0.38 ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47 Consensus pattern (18 bp): TTTCTTAAAAGACATTTA Found at i:264119 original size:44 final size:44 Alignment explanation

Indices: 264069--264156 Score: 167 Period size: 44 Copynumber: 2.0 Consensus size: 44 264059 TGTACTTGTT 264069 AAATCTATAAATCCATTTGTTTAATCTCATTGCTTACTATATAA 1 AAATCTATAAATCCATTTGTTTAATCTCATTGCTTACTATATAA * 264113 AAATCTATAAATCCATTTGTTTAATCTCATTGCTTATTATATAA 1 AAATCTATAAATCCATTTGTTTAATCTCATTGCTTACTATATAA 264157 TTATAACATC Statistics Matches: 43, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 44 43 1.00 ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44 Consensus pattern (44 bp): AAATCTATAAATCCATTTGTTTAATCTCATTGCTTACTATATAA Found at i:265024 original size:2 final size:2 Alignment explanation

Indices: 265017--265041 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 265007 ATATGTGAAT 265017 TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA T 265042 NNNNNNNNNN Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:268663 original size:20 final size:20 Alignment explanation

Indices: 268640--268682 Score: 77 Period size: 20 Copynumber: 2.1 Consensus size: 20 268630 TCATCATGTG * 268640 CTACTAGTGAGTTTATAATT 1 CTACTAGTGAGTTGATAATT 268660 CTACTAGTGAGTTGATAATT 1 CTACTAGTGAGTTGATAATT 268680 CTA 1 CTA 268683 TTATATATAT Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 20 22 1.00 ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42 Consensus pattern (20 bp): CTACTAGTGAGTTGATAATT Found at i:276564 original size:1 final size:1 Alignment explanation

Indices: 276560--276589 Score: 60 Period size: 1 Copynumber: 30.0 Consensus size: 1 276550 TTTAATATTG 276560 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 276590 GAAATAAATA Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 29 1.00 ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00 Consensus pattern (1 bp): T Found at i:278050 original size:119 final size:119 Alignment explanation

Indices: 277839--278059 Score: 442 Period size: 119 Copynumber: 1.9 Consensus size: 119 277829 ATATTAGGCC 277839 ACCTTTGAATTTGCTTGTTTGCTCTTGTCCTAGTGAATTCTCATGGTAAATATAATAAAGATTCT 1 ACCTTTGAATTTGCTTGTTTGCTCTTGTCCTAGTGAATTCTCATGGTAAATATAATAAAGATTCT 277904 AAGAATTTGTTTTTTCTCAACGCACTTGTTCGTAAATAAAGTCGTATTTTCTAT 66 AAGAATTTGTTTTTTCTCAACGCACTTGTTCGTAAATAAAGTCGTATTTTCTAT 277958 ACCTTTGAATTTGCTTGTTTGCTCTTGTCCTAGTGAATTCTCATGGTAAATATAATAAAGATTCT 1 ACCTTTGAATTTGCTTGTTTGCTCTTGTCCTAGTGAATTCTCATGGTAAATATAATAAAGATTCT 278023 AAGAATTTGTTTTTTCTCAACGCACTTGTTCGTAAAT 66 AAGAATTTGTTTTTTCTCAACGCACTTGTTCGTAAAT 278060 GCTATAATAT Statistics Matches: 102, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 119 102 1.00 ACGTcount: A:0.27, C:0.15, G:0.14, T:0.43 Consensus pattern (119 bp): ACCTTTGAATTTGCTTGTTTGCTCTTGTCCTAGTGAATTCTCATGGTAAATATAATAAAGATTCT AAGAATTTGTTTTTTCTCAACGCACTTGTTCGTAAATAAAGTCGTATTTTCTAT Found at i:288011 original size:35 final size:35 Alignment explanation

Indices: 287972--288040 Score: 120 Period size: 35 Copynumber: 2.0 Consensus size: 35 287962 ACTGTATTAT 287972 ATTGTGCTTTTATGTATACAAACGTTATGTATAAC 1 ATTGTGCTTTTATGTATACAAACGTTATGTATAAC ** 288007 ATTGTGCTTTTATGTATACCGACGTTATGTATAA 1 ATTGTGCTTTTATGTATACAAACGTTATGTATAA 288041 TATTTCAAAC Statistics Matches: 32, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 35 32 1.00 ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43 Consensus pattern (35 bp): ATTGTGCTTTTATGTATACAAACGTTATGTATAAC Found at i:290856 original size:18 final size:18 Alignment explanation

Indices: 290823--290857 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 290813 TTTGCCGTTA * * 290823 CAGTCATTTAACCATTTG 1 CAGTCATTAAAACATTTG 290841 CAGTCATTAAAACATTT 1 CAGTCATTAAAACATTT 290858 AAAATTTGAT Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 15 1.00 ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37 Consensus pattern (18 bp): CAGTCATTAAAACATTTG Found at i:304020 original size:15 final size:15 Alignment explanation

Indices: 304000--304031 Score: 64 Period size: 15 Copynumber: 2.1 Consensus size: 15 303990 ATAATGAGGC 304000 TTGTGATTAAATAAA 1 TTGTGATTAAATAAA 304015 TTGTGATTAAATAAA 1 TTGTGATTAAATAAA 304030 TT 1 TT 304032 AAGAGGAATT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 17 1.00 ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44 Consensus pattern (15 bp): TTGTGATTAAATAAA Found at i:308915 original size:15 final size:15 Alignment explanation

Indices: 308897--308939 Score: 59 Period size: 15 Copynumber: 2.9 Consensus size: 15 308887 CTAGAATGAA * 308897 GTTCTCTATCTCTGG 1 GTTCCCTATCTCTGG * * 308912 GTTCCCTATCCCTTG 1 GTTCCCTATCTCTGG 308927 GTTCCCTATCTCT 1 GTTCCCTATCTCT 308940 AGACATGTGA Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 15 24 1.00 ACGTcount: A:0.07, C:0.35, G:0.14, T:0.44 Consensus pattern (15 bp): GTTCCCTATCTCTGG Found at i:320881 original size:33 final size:33 Alignment explanation

Indices: 320838--320918 Score: 153 Period size: 33 Copynumber: 2.5 Consensus size: 33 320828 AGACAATGTC * 320838 GTCTAACTGTGTCCCAAAGTATATACAGGTAAA 1 GTCTACCTGTGTCCCAAAGTATATACAGGTAAA 320871 GTCTACCTGTGTCCCAAAGTATATACAGGTAAA 1 GTCTACCTGTGTCCCAAAGTATATACAGGTAAA 320904 GTCTACCTGTGTCCC 1 GTCTACCTGTGTCCC 320919 CTTAGAGGGC Statistics Matches: 47, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 33 47 1.00 ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28 Consensus pattern (33 bp): GTCTACCTGTGTCCCAAAGTATATACAGGTAAA Found at i:334206 original size:33 final size:33 Alignment explanation

Indices: 334168--334269 Score: 114 Period size: 33 Copynumber: 3.0 Consensus size: 33 334158 GGGCTTGGGA * 334168 GGACCTCCAAATGGAGGTGGTGGAGGGGGAGGG 1 GGACCTCCAAATGGAGGTGGTGGAGGAGGAGGG * * * * * * 334201 GGACCTCCAAAAGGTGGAGGAGGCGGTGGAGGG 1 GGACCTCCAAATGGAGGTGGTGGAGGAGGAGGG 334234 GGACCTCCAAAGGGTGGAGGTGGTGGAGGAGGAGGG 1 GGACCTCCAAA---TGGAGGTGGTGGAGGAGGAGGG 334270 ATCATTCCTG Statistics Matches: 54, Mismatches: 12, Indels: 3 0.78 0.17 0.04 Matches are distributed among these distances: 33 38 0.70 36 16 0.30 ACGTcount: A:0.23, C:0.13, G:0.54, T:0.11 Consensus pattern (33 bp): GGACCTCCAAATGGAGGTGGTGGAGGAGGAGGG Found at i:353994 original size:95 final size:95 Alignment explanation

Indices: 353831--354020 Score: 380 Period size: 95 Copynumber: 2.0 Consensus size: 95 353821 NAGCCTATGC 353831 TAGGATAAAAGTTTTGTTTTTACCGGTAGATTATCACCCTTTTACTACTCAGAAAAACAGTGTGG 1 TAGGATAAAAGTTTTGTTTTTACCGGTAGATTATCACCCTTTTACTACTCAGAAAAACAGTGTGG 353896 AAATAGAACCACTGTAAAATTTGCATATAT 66 AAATAGAACCACTGTAAAATTTGCATATAT 353926 TAGGATAAAAGTTTTGTTTTTACCGGTAGATTATCACCCTTTTACTACTCAGAAAAACAGTGTGG 1 TAGGATAAAAGTTTTGTTTTTACCGGTAGATTATCACCCTTTTACTACTCAGAAAAACAGTGTGG 353991 AAATAGAACCACTGTAAAATTTGCATATAT 66 AAATAGAACCACTGTAAAATTTGCATATAT 354021 ATATATANTA Statistics Matches: 95, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 95 95 1.00 ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34 Consensus pattern (95 bp): TAGGATAAAAGTTTTGTTTTTACCGGTAGATTATCACCCTTTTACTACTCAGAAAAACAGTGTGG AAATAGAACCACTGTAAAATTTGCATATAT Found at i:364896 original size:2 final size:2 Alignment explanation

Indices: 364889--364938 Score: 100 Period size: 2 Copynumber: 25.0 Consensus size: 2 364879 CATTCTACTA 364889 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 364931 AG AG AG AG 1 AG AG AG AG 364939 GGGATGTTTT Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 48 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:366442 original size:2 final size:2 Alignment explanation

Indices: 366435--366474 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 366425 CAGGAACCGG 366435 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 366475 CCCCTCCCCC Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:366611 original size:2 final size:2 Alignment explanation

Indices: 366604--366629 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 366594 NNNNNNNNNN 366604 TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC 366630 GGGGTAGGGG Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:372807 original size:2 final size:2 Alignment explanation

Indices: 372800--372834 Score: 70 Period size: 2 Copynumber: 17.5 Consensus size: 2 372790 CAACAACAAC 372800 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 372835 TCCCTTACGA Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 33 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:381635 original size:2 final size:2 Alignment explanation

Indices: 381630--381668 Score: 78 Period size: 2 Copynumber: 19.5 Consensus size: 2 381620 TCCGATTGAT 381630 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 381669 TTTGCTCACT Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 37 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:382596 original size:26 final size:26 Alignment explanation

Indices: 382563--382614 Score: 95 Period size: 26 Copynumber: 2.0 Consensus size: 26 382553 AATAAATATG 382563 AAACATATCACAAAATGAAAGTAATA 1 AAACATATCACAAAATGAAAGTAATA * 382589 AAACATATCACAAAATGGAAGTAATA 1 AAACATATCACAAAATGAAAGTAATA 382615 TTATATTATC Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 25 1.00 ACGTcount: A:0.60, C:0.12, G:0.10, T:0.19 Consensus pattern (26 bp): AAACATATCACAAAATGAAAGTAATA Found at i:385747 original size:129 final size:128 Alignment explanation

Indices: 385517--385763 Score: 485 Period size: 129 Copynumber: 1.9 Consensus size: 128 385507 ATAATTTAAC 385517 GCTGTGAATTTCACTAAAATAATGTTAAAGTGTTGTTTCTGTTCACACCAATCATCATTATAAAA 1 GCTGTGAATTTCACTAAAATAATGTTAAAGTGTTGTTTCTGTTCACACCAATCATCATTATAAAA 385582 TTGTTGAAATTGGAAAAAAATAATTTCATCAGTTGCCTTTATTGGGGGGGGGGGGGGGGGGGG 66 TTGTTGAAATTGGAAAAAAATAATTTCATCAGTTGCCTTTATTGGGGGGGGGGGGGGGGGGGG 385645 NGCTGTGAATTTCACTAAAATAATGTTAAAGTGTTGTTTCTGTTCACACCAATCATCATTATAAA 1 -GCTGTGAATTTCACTAAAATAATGTTAAAGTGTTGTTTCTGTTCACACCAATCATCATTATAAA 385710 ATTGTTGAAATTGGAAAAAAATAATTTCATCAGTTGCCTTTATTGGGGGGGGGG 65 ATTGTTGAAATTGGAAAAAAATAATTTCATCAGTTGCCTTTATTGGGGGGGGGG 385764 TGTAAGTGTT Statistics Matches: 118, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 129 118 1.00 ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34 Consensus pattern (128 bp): GCTGTGAATTTCACTAAAATAATGTTAAAGTGTTGTTTCTGTTCACACCAATCATCATTATAAAA TTGTTGAAATTGGAAAAAAATAATTTCATCAGTTGCCTTTATTGGGGGGGGGGGGGGGGGGGG Found at i:397408 original size:16 final size:17 Alignment explanation

Indices: 397377--397408 Score: 57 Period size: 17 Copynumber: 1.9 Consensus size: 17 397367 CTTGAATATA 397377 ATAAATATCTTTAACAG 1 ATAAATATCTTTAACAG 397394 ATAAATATC-TTAACA 1 ATAAATATCTTTAACA 397409 AGAAATCCAG Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 6 0.40 17 9 0.60 ACGTcount: A:0.50, C:0.12, G:0.03, T:0.34 Consensus pattern (17 bp): ATAAATATCTTTAACAG Found at i:406149 original size:22 final size:22 Alignment explanation

Indices: 406121--406166 Score: 92 Period size: 22 Copynumber: 2.1 Consensus size: 22 406111 GAAATCACAA 406121 AACTTCATTACTCTTACATGAT 1 AACTTCATTACTCTTACATGAT 406143 AACTTCATTACTCTTACATGAT 1 AACTTCATTACTCTTACATGAT 406165 AA 1 AA 406167 AACAGTCATT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 24 1.00 ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39 Consensus pattern (22 bp): AACTTCATTACTCTTACATGAT Found at i:411730 original size:2 final size:2 Alignment explanation

Indices: 411725--411790 Score: 125 Period size: 2 Copynumber: 33.5 Consensus size: 2 411715 CCCTTCTTCA 411725 TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 411766 TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC T 411791 GTACAACATT Statistics Matches: 63, Mismatches: 0, Indels: 2 0.97 0.00 0.03 Matches are distributed among these distances: 1 1 0.02 2 62 0.98 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:415266 original size:2 final size:2 Alignment explanation

Indices: 415259--415317 Score: 118 Period size: 2 Copynumber: 29.5 Consensus size: 2 415249 GTCATGAATT 415259 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 415301 GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA G 415318 TACCTGTTCT Statistics Matches: 57, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 57 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:421566 original size:13 final size:13 Alignment explanation

Indices: 421548--421578 Score: 62 Period size: 13 Copynumber: 2.4 Consensus size: 13 421538 CTTCCAACAC 421548 AAAAAAAAATGGA 1 AAAAAAAAATGGA 421561 AAAAAAAAATGGA 1 AAAAAAAAATGGA 421574 AAAAA 1 AAAAA 421579 CCTTGCCACA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 18 1.00 ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06 Consensus pattern (13 bp): AAAAAAAAATGGA Found at i:421770 original size:18 final size:18 Alignment explanation

Indices: 421747--421782 Score: 56 Period size: 18 Copynumber: 2.0 Consensus size: 18 421737 AGCATGAACA 421747 AGTGGT-TTTCACAGCATT 1 AGTGGTATTTCACA-CATT 421765 AGTGGTATTTCACACATT 1 AGTGGTATTTCACACATT 421783 TTTGCTGAAT Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 18 10 0.59 19 7 0.41 ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39 Consensus pattern (18 bp): AGTGGTATTTCACACATT Found at i:425858 original size:12 final size:12 Alignment explanation

Indices: 425841--425866 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 425831 TTTTTCTGTT 425841 TGTCGAATTGTC 1 TGTCGAATTGTC 425853 TGTCGAATTGTC 1 TGTCGAATTGTC 425865 TG 1 TG 425867 CAACTTGACT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.15, C:0.15, G:0.27, T:0.42 Consensus pattern (12 bp): TGTCGAATTGTC Found at i:427839 original size:4 final size:4 Alignment explanation

Indices: 427830--427858 Score: 51 Period size: 4 Copynumber: 7.5 Consensus size: 4 427820 CTTCCCAGTT 427830 TTGA TTGA TTGA TTGA TTGA TTG- TTGA TT 1 TTGA TTGA TTGA TTGA TTGA TTGA TTGA TT 427859 TACATCCGGT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 3 3 0.12 4 21 0.88 ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55 Consensus pattern (4 bp): TTGA Found at i:431232 original size:26 final size:26 Alignment explanation

Indices: 431211--431283 Score: 78 Period size: 29 Copynumber: 2.7 Consensus size: 26 431201 GTAAAATCAA 431211 CAGGTATGATTAGTGCACAAAA-AAC 1 CAGGTATGATTAGTGCACAAAACAAC * 431236 CAGGTATGCATGATTAGTGCAC-GAACAAGC 1 CAGG--T--ATGATTAGTGCACAAAACAA-C 431266 CAGGTATGATTAGTGCAC 1 CAGGTATGATTAGTGCAC 431284 GAACAAGTAT Statistics Matches: 41, Mismatches: 1, Indels: 11 0.77 0.02 0.21 Matches are distributed among these distances: 25 4 0.10 26 13 0.32 27 1 0.02 28 3 0.07 29 15 0.37 30 5 0.12 ACGTcount: A:0.36, C:0.18, G:0.25, T:0.22 Consensus pattern (26 bp): CAGGTATGATTAGTGCACAAAACAAC Found at i:431248 original size:29 final size:30 Alignment explanation

Indices: 431216--431273 Score: 91 Period size: 29 Copynumber: 2.0 Consensus size: 30 431206 ATCAACAGGT 431216 ATGATTAGTGCAC-AAAAAACCAGGTATGC 1 ATGATTAGTGCACGAAAAAACCAGGTATGC * * 431245 ATGATTAGTGCACGAACAAGCCAGGTATG 1 ATGATTAGTGCACGAAAAAACCAGGTATG 431274 ATTAGTGCAC Statistics Matches: 26, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 29 13 0.50 30 13 0.50 ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21 Consensus pattern (30 bp): ATGATTAGTGCACGAAAAAACCAGGTATGC Found at i:431284 original size:26 final size:26 Alignment explanation

Indices: 431211--431290 Score: 99 Period size: 26 Copynumber: 3.0 Consensus size: 26 431201 GTAAAATCAA * * 431211 CAGGTATGATTAGTGCAC-AAAAAAC 1 CAGGTATGATTAGTGCACGAACAAGC 431236 CAGGTATGCATGATTAGTGCACGAACAAGC 1 CAGG--T--ATGATTAGTGCACGAACAAGC 431266 CAGGTATGATTAGTGCACGAACAAG 1 CAGGTATGATTAGTGCACGAACAAG 431291 TATCATCCAT Statistics Matches: 48, Mismatches: 2, Indels: 9 0.81 0.03 0.15 Matches are distributed among these distances: 25 4 0.08 26 20 0.42 27 1 0.02 28 1 0.02 29 13 0.27 30 9 0.19 ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20 Consensus pattern (26 bp): CAGGTATGATTAGTGCACGAACAAGC Found at i:446938 original size:29 final size:29 Alignment explanation

Indices: 446896--446956 Score: 97 Period size: 29 Copynumber: 2.1 Consensus size: 29 446886 AATCCTACGC * 446896 AATCTTTAATCATATACATGT-TCATAGAG 1 AATCTTCAATCATATACATGTAT-ATAGAG 446925 AATCTTCAATCATATACATGTATATAGAG 1 AATCTTCAATCATATACATGTATATAGAG 446954 AAT 1 AAT 446957 ACAAATAGTT Statistics Matches: 30, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 29 29 0.97 30 1 0.03 ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36 Consensus pattern (29 bp): AATCTTCAATCATATACATGTATATAGAG Found at i:458155 original size:5 final size:5 Alignment explanation

Indices: 458145--458203 Score: 79 Period size: 5 Copynumber: 12.4 Consensus size: 5 458135 AAGCAATCAA * 458145 AAAAT AAAAT AAAAT AAAAT -AAAT -AAAT AGAAT AAAAT AAAAT -AAAT 1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT * 458192 AAAAA AAAAT AA 1 AAAAT AAAAT AA 458204 GAAAAAAACT Statistics Matches: 48, Mismatches: 4, Indels: 4 0.86 0.07 0.07 Matches are distributed among these distances: 4 12 0.25 5 36 0.75 ACGTcount: A:0.80, C:0.00, G:0.02, T:0.19 Consensus pattern (5 bp): AAAAT Found at i:458178 original size:23 final size:23 Alignment explanation

Indices: 458146--458199 Score: 90 Period size: 23 Copynumber: 2.3 Consensus size: 23 458136 AGCAATCAAA 458146 AAATAAAATAAAATAAAATAAAT 1 AAATAAAATAAAATAAAATAAAT * 458169 AAATAGAATAAAATAAAATAAAT 1 AAATAAAATAAAATAAAATAAAT * 458192 AAAAAAAA 1 AAATAAAA 458200 ATAAGAAAAA Statistics Matches: 28, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 23 28 1.00 ACGTcount: A:0.80, C:0.00, G:0.02, T:0.19 Consensus pattern (23 bp): AAATAAAATAAAATAAAATAAAT Found at i:458208 original size:10 final size:9 Alignment explanation

Indices: 458143--458211 Score: 59 Period size: 9 Copynumber: 7.6 Consensus size: 9 458133 TGAAGCAATC 458143 AAAAAATAA 1 AAAAAATAA 458152 AATAAAATAA 1 AA-AAAATAA * 458162 AATAAATAA 1 AAAAAATAA * * 458171 ATAGAATAA 1 AAAAAATAA 458180 AATAAAATAA 1 AA-AAAATAA * 458190 ATAAAA-AA 1 AAAAAATAA * * 458198 AAATAAGAA 1 AAAAAATAA 458207 AAAAA 1 AAAAA 458212 CTTTGCAGCC Statistics Matches: 47, Mismatches: 10, Indels: 6 0.75 0.16 0.10 Matches are distributed among these distances: 8 6 0.13 9 25 0.53 10 16 0.34 ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16 Consensus pattern (9 bp): AAAAAATAA Found at i:458209 original size:9 final size:8 Alignment explanation

Indices: 458143--458198 Score: 51 Period size: 8 Copynumber: 6.8 Consensus size: 8 458133 TGAAGCAATC 458143 AAAAAATA 1 AAAAAATA * 458151 AAATAA-A 1 AAAAAATA * 458158 ATAAAATA 1 AAAAAATA * 458166 AATAAATA 1 AAAAAATA 458174 GAATAAAATA 1 -AA-AAAATA 458184 AAATAAATA 1 AAA-AAATA 458193 AAAAAA 1 AAAAAA 458199 AATAAGAAAA Statistics Matches: 38, Mismatches: 6, Indels: 8 0.73 0.12 0.15 Matches are distributed among these distances: 7 5 0.13 8 16 0.42 9 12 0.32 10 5 0.13 ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18 Consensus pattern (8 bp): AAAAAATA Found at i:458209 original size:14 final size:13 Alignment explanation

Indices: 458143--458211 Score: 57 Period size: 13 Copynumber: 5.1 Consensus size: 13 458133 TGAAGCAATC 458143 AAAAAATAAAATAA 1 AAAAAATAAAA-AA * 458157 AATAAAATAAATAA 1 AA-AAAATAAAAAA * * 458171 ATAGAATAAAATAA 1 AAAAAATAAAA-AA * 458185 AATAAATAAAAAA 1 AAAAAATAAAAAA * * 458198 AAATAAGAAAAAA 1 AAAAAATAAAAAA 458211 A 1 A 458212 CTTTGCAGCC Statistics Matches: 43, Mismatches: 10, Indels: 5 0.74 0.17 0.09 Matches are distributed among these distances: 13 20 0.47 14 15 0.35 15 8 0.19 ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16 Consensus pattern (13 bp): AAAAAATAAAAAA Found at i:466741 original size:12 final size:12 Alignment explanation

Indices: 466724--466758 Score: 52 Period size: 12 Copynumber: 2.9 Consensus size: 12 466714 GATGTATCTA 466724 TTTCAGACTTGT 1 TTTCAGACTTGT * * 466736 TTTCAGTCATGT 1 TTTCAGACTTGT 466748 TTTCAGACTTG 1 TTTCAGACTTG 466759 GCACAACTAA Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 12 19 1.00 ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49 Consensus pattern (12 bp): TTTCAGACTTGT Found at i:469702 original size:2 final size:2 Alignment explanation

Indices: 469697--469725 Score: 58 Period size: 2 Copynumber: 14.5 Consensus size: 2 469687 TGGATTTAAC 469697 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 469726 TGAAACACAA Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 27 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:472058 original size:99 final size:99 Alignment explanation

Indices: 471909--472091 Score: 242 Period size: 99 Copynumber: 1.8 Consensus size: 99 471899 TGTACTTTTA * * * 471909 TTACTGAGTAATGGAGCAGACATTAATTTGTGCAAAGAAAACAGAACCAGTCCTCTCCT-TATAG 1 TTACTGAGTAATGAAGCAGACATTAATTTATGCAAAGAAAACAGAACCAGTCCTCT-CTATAAAG 471973 CTTGCGAAAACGGACATGATAGCACTGTACAGGTT 65 CTTGCGAAAACGGACATGATAGCACTGTACAGGTT * *** * * 472008 TTACTGAGTAATGAAGCAGACATTAATTTATGCACAGTGGACGGAGCCAGTCCTCTCTATAAAGC 1 TTACTGAGTAATGAAGCAGACATTAATTTATGCAAAGAAAACAGAACCAGTCCTCTCTATAAAGC *** 472073 TTGTTTAAACGGACATGAT 66 TTGCGAAAACGGACATGAT 472092 GCAATTGCGA Statistics Matches: 71, Mismatches: 12, Indels: 2 0.84 0.14 0.02 Matches are distributed among these distances: 98 2 0.03 99 69 0.97 ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27 Consensus pattern (99 bp): TTACTGAGTAATGAAGCAGACATTAATTTATGCAAAGAAAACAGAACCAGTCCTCTCTATAAAGC TTGCGAAAACGGACATGATAGCACTGTACAGGTT Found at i:472646 original size:99 final size:99 Alignment explanation

Indices: 472543--472734 Score: 217 Period size: 99 Copynumber: 1.9 Consensus size: 99 472533 TGCTCAAACC * ** 472543 ACGGAACCAGTCCGCTCTATACAGCCTGTTACGAAGGACATTG-TAACATTGTAC-AACTTTTAC 1 ACGGAACCAGTCCGCTCTATACAGCCTGTCAAAAAGGACA-TGATAACATTGT-CGAACTTTTAC * * 472606 TTAGTAATGGAGCAGACACCAGTTTATGTTGTATTG 64 TTAGCAATGGAGCAGACACCAATTTATGTTGTATTG ** * * * * * * * 472642 ACGGATTCAGTCCTCTCTTTGCCGCTTGTCAAAAAGGATATGATAGCATTGTCGAACTTTTACTT 1 ACGGAACCAGTCCGCTCTATACAGCCTGTCAAAAAGGACATGATAACATTGTCGAACTTTTACTT * 472707 AGCAATGGAGCAGACATCAATTTATGTT 66 AGCAATGGAGCAGACACCAATTTATGTT 472735 CAAAAGATAA Statistics Matches: 76, Mismatches: 15, Indels: 4 0.80 0.16 0.04 Matches are distributed among these distances: 98 3 0.04 99 73 0.96 ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32 Consensus pattern (99 bp): ACGGAACCAGTCCGCTCTATACAGCCTGTCAAAAAGGACATGATAACATTGTCGAACTTTTACTT AGCAATGGAGCAGACACCAATTTATGTTGTATTG Found at i:475389 original size:11 final size:11 Alignment explanation

Indices: 475373--475397 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 475363 TAGCCATTAA 475373 ATTTTCTTGCT 1 ATTTTCTTGCT 475384 ATTTTCTTGCT 1 ATTTTCTTGCT 475395 ATT 1 ATT 475398 GGAATTAATT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.12, C:0.16, G:0.08, T:0.64 Consensus pattern (11 bp): ATTTTCTTGCT Found at i:479920 original size:14 final size:14 Alignment explanation

Indices: 479870--479919 Score: 57 Period size: 14 Copynumber: 3.6 Consensus size: 14 479860 CATTCATACA 479870 CCTCTCTCACTACTC 1 CCTCTCTCACT-CTC * 479885 TCT-TCTCACTCTC 1 CCTCTCTCACTCTC * * 479898 CCTTTCTCTCTCTC 1 CCTCTCTCACTCTC 479912 CCTCTCTC 1 CCTCTCTC 479920 TATTTTCTCA Statistics Matches: 30, Mismatches: 4, Indels: 3 0.81 0.11 0.08 Matches are distributed among these distances: 13 5 0.17 14 23 0.77 15 2 0.07 ACGTcount: A:0.06, C:0.52, G:0.00, T:0.42 Consensus pattern (14 bp): CCTCTCTCACTCTC Found at i:480442 original size:13 final size:13 Alignment explanation

Indices: 480428--480518 Score: 69 Period size: 13 Copynumber: 7.0 Consensus size: 13 480418 ACACCACCCT 480428 CTCACTCCTCACT- 1 CTCACT-CTCACTC * 480441 CTCAATCTCACTC 1 CTCACTCTCACTC * * * 480454 CCCAGTCTCTCTC 1 CTCACTCTCACTC * 480467 CTC-CTTCACACTC 1 CTCAC-TCTCACTC 480480 CTCACTCTCACTC 1 CTCACTCTCACTC * * 480493 CTCCCTCTCATTC 1 CTCACTCTCACTC * * 480506 CCCACTCTTACTC 1 CTCACTCTCACTC 480519 TTCCCGCTCA Statistics Matches: 60, Mismatches: 15, Indels: 6 0.74 0.19 0.07 Matches are distributed among these distances: 12 6 0.10 13 53 0.88 14 1 0.02 ACGTcount: A:0.14, C:0.53, G:0.01, T:0.32 Consensus pattern (13 bp): CTCACTCTCACTC Found at i:480449 original size:19 final size:18 Alignment explanation

Indices: 480427--480503 Score: 59 Period size: 19 Copynumber: 4.1 Consensus size: 18 480417 CACACCACCC 480427 TCTCACTCCTCACTCTCAA 1 TCTCACTCCTCACTCTC-A * * 480446 TCTCACTCCCCAGTCTC- 1 TCTCACTCCTCACTCTCA 480463 TCTC-CTCCTTCACACTCCTCA 1 TCTCACTCC-T--CACT-CTCA * 480484 CTCTCACTCCTCCCTCTCA 1 -TCTCACTCCTCACTCTCA 480503 T 1 T 480504 TCCCCACTCT Statistics Matches: 46, Mismatches: 5, Indels: 15 0.70 0.08 0.23 Matches are distributed among these distances: 16 4 0.09 17 4 0.09 18 1 0.02 19 22 0.48 20 6 0.13 22 5 0.11 23 4 0.09 ACGTcount: A:0.14, C:0.52, G:0.01, T:0.32 Consensus pattern (18 bp): TCTCACTCCTCACTCTCA Found at i:480469 original size:32 final size:31 Alignment explanation

Indices: 480350--480456 Score: 101 Period size: 32 Copynumber: 3.4 Consensus size: 31 480340 TATTCCTTAC * * 480350 TCTCACTCCCCCTCTCTCT-CTCCACTCTCAC 1 TCTCACTCCCCCTCTCACTCCT-CACTCTCAA * * * 480381 TCCTCCCTCCCCACTCTCAC-CTCTCTCTCTCTA 1 T-CTCACTCCCC-CTCTCACTC-CTCACTCTCAA * 480414 TCTCACACCACCCTCTCACTCCTCACTCTCAA 1 TCTCACTCC-CCCTCTCACTCCTCACTCTCAA 480446 TCTCACTCCCC 1 TCTCACTCCCC 480457 AGTCTCTCTC Statistics Matches: 60, Mismatches: 10, Indels: 12 0.73 0.12 0.15 Matches are distributed among these distances: 31 3 0.05 32 39 0.65 33 16 0.27 34 2 0.03 ACGTcount: A:0.13, C:0.57, G:0.00, T:0.30 Consensus pattern (31 bp): TCTCACTCCCCCTCTCACTCCTCACTCTCAA Found at i:480511 original size:26 final size:26 Alignment explanation

Indices: 480348--480700 Score: 143 Period size: 26 Copynumber: 13.8 Consensus size: 26 480338 ATTATTCCTT * * 480348 ACTCTCACTCC-CCCTCTCTCTCTCC 1 ACTCTCACTCCTCCCTCTCACTCCCC * * 480373 ACTCTCACTCCTCCCTCCCCACT-CTC 1 ACTCTCACTCCTCCCT-CTCACTCCCC * ** * 480399 AC-CTCTCTCTCTCTATCTCACACCACC 1 ACTCTCACTC-CTCCCTCTCACTCC-CC 480426 -CTCTCACTCCTCACTCTCAATCTCACTCCCC 1 ACTCTCACTCCT--C-C-C--TCTCACTCCCC * * * * * 480457 AGTCTCTCTCCTCCTTCACACTCCTC 1 ACTCTCACTCCTCCCTCTCACTCCCC * 480483 ACTCTCACTCCTCCCTCTCATTCCCC 1 ACTCTCACTCCTCCCTCTCACTCCCC * * * * 480509 ACTCTTACTCTTCCCGCTCACTCACC 1 ACTCTCACTCCTCCCTCTCACTCCCC * * * * * 480535 AATCTTACTCCCTTCCCTCT--TTGCCA 1 ACTCTCACT-CC-TCCCTCTCACTCCCC * * * * 480561 ACTCTCACTACATCCCTCGCTCTTCCC 1 ACTCTCACT-CCTCCCTCTCACTCCCC * 480588 ACTCTCACTCCTCACTCTCA-----C 1 ACTCTCACTCCTCCCTCTCACTCCCC * * * 480609 -CTCTCTCTCC-CCACTTTTACTCCCC 1 ACTCTCACTCCTCC-CTCTCACTCCCC * * 480634 ACTCTCAGTCCTCCCTCTCTCTCCTCC 1 ACTCTCACTCCTCCCTCTCACTCC-CC 480661 -CTCTCA--CCT--CTCT--CTCCCC 1 ACTCTCACTCCTCCCTCTCACTCCCC 480680 ACTCTCACTCCTCCCTCTCAC 1 ACTCTCACTCCTCCCTCTCAC 480701 CTCTCTCTCC Statistics Matches: 237, Mismatches: 58, Indels: 65 0.66 0.16 0.18 Matches are distributed among these distances: 19 3 0.01 20 23 0.10 21 1 0.00 22 7 0.03 24 7 0.03 25 28 0.12 26 112 0.47 27 28 0.12 28 7 0.03 29 1 0.00 30 1 0.00 31 2 0.01 32 17 0.07 ACGTcount: A:0.13, C:0.54, G:0.01, T:0.31 Consensus pattern (26 bp): ACTCTCACTCCTCCCTCTCACTCCCC Found at i:480605 original size:13 final size:13 Alignment explanation

Indices: 480587--480700 Score: 55 Period size: 13 Copynumber: 9.2 Consensus size: 13 480577 TCGCTCTTCC 480587 CACT-CTCACTCCT 1 CACTCCTCACT-CT 480600 CACT-CTCACCTCT 1 CACTCCTCA-CTCT * * * 480613 CTCTCCCCACTTT 1 CACTCCTCACTCT * * 480626 TACTCCCCACTCT 1 CACTCCTCACTCT * * 480639 CAGTCCTCCCTCT 1 CACTCCTCACTCT * * 480652 CTCTCCTCCCTCT 1 CACTCCTCACTCT 480665 CA--CCT--CTCT 1 CACTCCTCACTCT * 480674 --CTCCCCACTCT 1 CACTCCTCACTCT * 480685 CACTCCTCCCTCT 1 CACTCCTCACTCT 480698 CAC 1 CAC 480701 CTCTCTCTCC Statistics Matches: 77, Mismatches: 16, Indels: 16 0.71 0.15 0.15 Matches are distributed among these distances: 9 6 0.08 11 7 0.09 13 59 0.77 14 5 0.06 ACGTcount: A:0.11, C:0.57, G:0.01, T:0.32 Consensus pattern (13 bp): CACTCCTCACTCT Found at i:480623 original size:33 final size:33 Alignment explanation

Indices: 480575--480710 Score: 117 Period size: 33 Copynumber: 4.3 Consensus size: 33 480565 TCACTACATC * * 480575 CCTCGCTCTTCCCACTCTCACTCCTCACTCTCA 1 CCTCGCTCTCCCCACTCTCACTCCCCACTCTCA * * * 480608 CCTCTCTCTCCCCACTTTTACTCCCCACTCTCA 1 CCTCGCTCTCCCCACTCTCACTCCCCACTCTCA * * * 480641 -GTC-CTC-CCTCTCTCTC-CT--CC-CTCTCA 1 CCTCGCTCTCCCCACTCTCACTCCCCACTCTCA * 480667 CCTCTCTCTCCCCACTCTCACTCCTCC-CTCTCA 1 CCTCGCTCTCCCCACTCTCACTCC-CCACTCTCA * 480700 CCTCTCTCTCC 1 CCTCGCTCTCC 480711 AATTTTACTC Statistics Matches: 83, Mismatches: 13, Indels: 14 0.75 0.12 0.13 Matches are distributed among these distances: 26 6 0.07 27 4 0.05 28 3 0.04 29 10 0.12 30 8 0.10 31 3 0.04 32 2 0.02 33 47 0.57 ACGTcount: A:0.09, C:0.57, G:0.01, T:0.32 Consensus pattern (33 bp): CCTCGCTCTCCCCACTCTCACTCCCCACTCTCA Found at i:480670 original size:11 final size:11 Alignment explanation

Indices: 480650--480709 Score: 52 Period size: 11 Copynumber: 5.5 Consensus size: 11 480640 AGTCCTCCCT * 480650 CTCTCTCCTCC 1 CTCTCACCTCC * 480661 CTCTCACCTCT 1 CTCTCACCTCC * 480672 CTCTC-CC-CA 1 CTCTCACCTCC 480681 CTCTCACTCCTCC 1 CTCTCA--CCTCC * 480694 CTCTCACCTCT 1 CTCTCACCTCC 480705 CTCTC 1 CTCTC 480710 CAATTTTACT Statistics Matches: 40, Mismatches: 5, Indels: 8 0.75 0.09 0.15 Matches are distributed among these distances: 9 6 0.15 10 2 0.05 11 23 0.57 12 2 0.05 13 7 0.17 ACGTcount: A:0.07, C:0.60, G:0.00, T:0.33 Consensus pattern (11 bp): CTCTCACCTCC Found at i:480704 original size:20 final size:20 Alignment explanation

Indices: 480647--480710 Score: 70 Period size: 20 Copynumber: 3.5 Consensus size: 20 480637 CTCAGTCCTC 480647 CCTCTCTCTCCTCCCTCTCA 1 CCTCTCTCTCCTCCCTCTCA 480667 -C-CTCTCT-CT-CC-C-CA 1 CCTCTCTCTCCTCCCTCTCA * 480681 -CTCTCACTCCTCCCTCTCA 1 CCTCTCTCTCCTCCCTCTCA 480700 CCTCTCTCTCC 1 CCTCTCTCTCC 480711 AATTTTACTC Statistics Matches: 36, Mismatches: 2, Indels: 12 0.72 0.04 0.24 Matches are distributed among these distances: 14 3 0.08 15 6 0.17 16 4 0.11 17 4 0.11 18 7 0.19 19 3 0.08 20 9 0.25 ACGTcount: A:0.06, C:0.61, G:0.00, T:0.33 Consensus pattern (20 bp): CCTCTCTCTCCTCCCTCTCA Found at i:480731 original size:46 final size:45 Alignment explanation

Indices: 480585--480789 Score: 165 Period size: 46 Copynumber: 4.5 Consensus size: 45 480575 CCTCGCTCTT * 480585 CCCACTCTCACTCCTCACTCTCACCTCTCTCTCCCCACTTTTACT-C 1 CCCACTCTCACTCCTCCCTCTCACCTCTCTCT--CCACTTTTACTCC * * * * * 480631 CCCACTCTCAGTCCTCCCTCTC-TCTCCTCCCTCTCACCTCT-CTCTC 1 CCCACTCTCACTCCTCCCTCTCACCT-CTCTCTC-CACTTTTACTC-C * 480677 CCCACTCTCACTCCTCCCTCTCACCTCTCTCTCCAATTTTACTCC 1 CCCACTCTCACTCCTCCCTCTCACCTCTCTCTCCACTTTTACTCC * * * 480722 CCC-CTCTCTCT-CTCCCTCTTA-CTCCTCCCTCACACATTTCT-CTCTC 1 CCCACTCTCACTCCTCCCTCTCACCT-CTCTCTC-CAC-TTT-TACTC-C 480768 CCCACTCTCACTTCC-CCCTCTC 1 CCCACTCTCAC-TCCTCCCTCTC 480790 CCTACTCACC Statistics Matches: 127, Mismatches: 18, Indels: 26 0.74 0.11 0.15 Matches are distributed among these distances: 42 2 0.02 43 15 0.12 44 12 0.09 45 21 0.17 46 61 0.48 47 8 0.06 48 7 0.06 49 1 0.01 ACGTcount: A:0.10, C:0.56, G:0.00, T:0.33 Consensus pattern (45 bp): CCCACTCTCACTCCTCCCTCTCACCTCTCTCTCCACTTTTACTCC Found at i:484007 original size:12 final size:12 Alignment explanation

Indices: 483990--484017 Score: 56 Period size: 12 Copynumber: 2.3 Consensus size: 12 483980 TTTTGTTTAG 483990 CATTGTATAAAA 1 CATTGTATAAAA 484002 CATTGTATAAAA 1 CATTGTATAAAA 484014 CATT 1 CATT 484018 AAATTCGCGG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 16 1.00 ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36 Consensus pattern (12 bp): CATTGTATAAAA Found at i:489562 original size:3 final size:3 Alignment explanation

Indices: 489554--489583 Score: 60 Period size: 3 Copynumber: 10.0 Consensus size: 3 489544 GCTGATGTCT 489554 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA 1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA 489584 CGGCGATGGT Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 27 1.00 ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33 Consensus pattern (3 bp): TGA Found at i:490777 original size:21 final size:21 Alignment explanation

Indices: 490733--490778 Score: 65 Period size: 21 Copynumber: 2.2 Consensus size: 21 490723 AAAAAATCTG * * 490733 ATTTGTTCGGACGAATTAGAT 1 ATTTGTTCGGACAAATAAGAT * 490754 ATTTGTTCGGACAAATAAGTT 1 ATTTGTTCGGACAAATAAGAT 490775 ATTT 1 ATTT 490779 ATATCAACAC Statistics Matches: 22, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 21 22 1.00 ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41 Consensus pattern (21 bp): ATTTGTTCGGACAAATAAGAT Found at i:491034 original size:2 final size:2 Alignment explanation

Indices: 491029--491054 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 491019 AAAGCACAAT 491029 TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC 491055 CAATTGCAGT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:498016 original size:398 final size:397 Alignment explanation

Indices: 497280--498074 Score: 1536 Period size: 398 Copynumber: 2.0 Consensus size: 397 497270 GTGGGCAGTA 497280 ATGGCCAACAGCAGGAAGACCGAACGGATGGGCCGTGGAAGGAATTTGGTCCTTTGTGGAAAACT 1 ATGGCCAACAGCAGGAAGACCGAACGGATGGGCCGTGGAAGGAATTTGGTCCTTTGTGGAAAACT 497345 GATAAAAATCGAGAATTGGGTGTAGATATCGATGGAGCTTCATCTGTATGGGCCGTCGATGCCAA 66 GATAAAAATCGAGAATTGGGTGTAGATATCGATGGAGCTTCATCTGTATGGGCCGTCGATGCCAA 497410 GAAGAAAACCATTCTTGAAATATCTCCATCTTCTGGAAACATATTGAAAAGTTTGAATGTTTCTC 131 GAAGAAAACCATTCTTGAAATATCTCCATCTTCTGGAAACATATTGAAAAGTTTGAATGTTTCTC * 497475 AGCTGTTACAAGCTAAAGCGGTTGTAACATCAGATCTAATGGTCACCAGAGCAGACAAGAAAGAC 196 AGCTGTTACAAGCTAAAGCGGTTGTAACATCAGATCTAATGATCACCAGAGCAGACAAGAAAGAC 497540 GAGGACCATCTTGTGTTTGCTGTTACTCTTGTCAACGGGCCATCTACTGCGTTTCACTCTCTTTT 261 GAGGACCATCTTGTGTTTGCTGTTACTCTTGTCAACGGGCCATCTACTGCGTTTCACTCTCTTTT 497605 GAAATCGTTTGGTGGCGATCGATCAGACAACAAGAACTACGTGATTCAGATGAAAGGTGACACAG 326 GAAATCGTTTGGTGGCGATCGATCAGACAACAAGAACTACGTGATTCAGATGAAAGGTGACACAG 497670 TAGAATG 391 TAGAATG 497677 NATGGCCAACAGCAGGAAGACCGAACGGATGGGCCGTGGAAGGAATTTGGTCCTTTGTGGAAAAC 1 -ATGGCCAACAGCAGGAAGACCGAACGGATGGGCCGTGGAAGGAATTTGGTCCTTTGTGGAAAAC 497742 TGATAAAAATCGAGAATTGGGTGTAGATATCGATGGAGCTTCATCTGTATGGGCCGTCGATGCCA 65 TGATAAAAATCGAGAATTGGGTGTAGATATCGATGGAGCTTCATCTGTATGGGCCGTCGATGCCA 497807 AGAAGAAAACCATTCTTGAAATATCTCCATCTTCTGGAAACATATTGAAAAGTTTGAATGTTTCT 130 AGAAGAAAACCATTCTTGAAATATCTCCATCTTCTGGAAACATATTGAAAAGTTTGAATGTTTCT * * * 497872 CAGCTGTTACAAGCTAAAGCGGTTGTAACTTCAGATCTAATGATCACCAGATCAGACAAGAATGA 195 CAGCTGTTACAAGCTAAAGCGGTTGTAACATCAGATCTAATGATCACCAGAGCAGACAAGAAAGA * 497937 TGAGGACCATCTTGTGTTTGCTGTTACTCTTGTCAACGGGCCATCTACTGCGTTTCACTCTCTTT 260 CGAGGACCATCTTGTGTTTGCTGTTACTCTTGTCAACGGGCCATCTACTGCGTTTCACTCTCTTT 498002 TGAAATCGTTTGGTGGCGATCGATCAGACAACAAGAACTACGTGATTCAGATGAAAGGTGACACA 325 TGAAATCGTTTGGTGGCGATCGATCAGACAACAAGAACTACGTGATTCAGATGAAAGGTGACACA 498067 GTAGAATG 390 GTAGAATG 498075 GGCCGTGCCA Statistics Matches: 392, Mismatches: 5, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 398 392 1.00 ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27 Consensus pattern (397 bp): ATGGCCAACAGCAGGAAGACCGAACGGATGGGCCGTGGAAGGAATTTGGTCCTTTGTGGAAAACT GATAAAAATCGAGAATTGGGTGTAGATATCGATGGAGCTTCATCTGTATGGGCCGTCGATGCCAA GAAGAAAACCATTCTTGAAATATCTCCATCTTCTGGAAACATATTGAAAAGTTTGAATGTTTCTC AGCTGTTACAAGCTAAAGCGGTTGTAACATCAGATCTAATGATCACCAGAGCAGACAAGAAAGAC GAGGACCATCTTGTGTTTGCTGTTACTCTTGTCAACGGGCCATCTACTGCGTTTCACTCTCTTTT GAAATCGTTTGGTGGCGATCGATCAGACAACAAGAACTACGTGATTCAGATGAAAGGTGACACAG TAGAATG Found at i:498895 original size:492 final size:490 Alignment explanation

Indices: 497971--498952 Score: 1865 Period size: 492 Copynumber: 2.0 Consensus size: 490 497961 TACTCTTGTC * 497971 AACGGGCCATCTACTGCGTTTCACTCTCTTTTGAAATCGTTTGGTGGCGATCGATCAGACAACAA 1 AACGGGCCATCTACTGCGTTTCACTCTCTTCTGAAATCGTTTGGTGGCGATCGATCAGACAACAA 498036 GAACTACGTGATTCAGATGAAAGGTGACACAGTAGAATGGGCCGTGCCAACCGTTGAAGATCTAC 66 GAACTACGTGATTCAGATGAAAGGTGACACAGTAGAATGGGCCGTGCCAACCGTTGAAGATCTAC * * 498101 CAGGGGTAGGGCAAATTGCCGGCATCAAAACACATGACAGCACGGACGATGACTTGAAAGATTTG 131 CAGGGGTAGGCCAAATTGCCGGCATCAAAACACATGACAGCACGGAAGATGACTTGAAAGATTTG 498166 TATGTTGTGTTCGCTGGCGATGACAAATCGTCGGTGGTCTTTGGTATTCATTAGATACTAGTGGA 196 TATGTTGTGTTCGCTGGCGATGACAAATCGTCGGTGGTCTTTGGTATTCATTAGATACTAGTGGA * 498231 TAAAACAACAGCATCAACGAAACACTAACTAATGTCGATTATATGTAGATATCCTTAATTCATGT 261 TAAAACAACAGCATCAACGAAACACTAACTAATGTCGATTATATGTAGATATCCATAATTCATGT * * 498296 ACATGTATATTGTAAAATATGACAGTGGAGCCAAAAGAAAAAGAAAAGAAAATTGATATAAAACG 326 ACATGAATATTGTAAAATATGACAATGGAGCCAAAAGAAAAAGAAAAGAAAATTGATATAAAACG 498361 TATTCATGTTACAATGTATAATAAAGTAAGACGGGTGTGGAATTGTTCATGGAATGGTTTATTTG 391 TATTCATGTTACAATGTATAATAAAGTAAGACGGGTGTGGAATTGTTCATGGAATGGTTTATTTG 498426 AGAAAAAAAACTACACGTATGCAATCAATATTATAT 456 AG-AAAAAAACTACACGTATGCAATCAATATTATAT 498462 NAACGGGCCATCTACTGCGTTTCACTCTCTTCTGAAATCGTTTGGTGGCGATCGATCAGACAACA 1 -AACGGGCCATCTACTGCGTTTCACTCTCTTCTGAAATCGTTTGGTGGCGATCGATCAGACAACA * 498527 AGAACTACGTGATTCAGATGAAAGGTGACACAGTAGAATGGGTCGTGCCAACCGTTGAAGATCTA 65 AGAACTACGTGATTCAGATGAAAGGTGACACAGTAGAATGGGCCGTGCCAACCGTTGAAGATCTA 498592 CCAGGGGTAGGCCAAATTGCCGGCATCAAAACACATGACAGCACGGAAGATGACTTGAAAGATTT 130 CCAGGGGTAGGCCAAATTGCCGGCATCAAAACACATGACAGCACGGAAGATGACTTGAAAGATTT 498657 GTATGTTGTGTTCGCTGGCGATGACAAATCGTCGGTGGTCTTTGGTATTCATTAGATACTAGTGG 195 GTATGTTGTGTTCGCTGGCGATGACAAATCGTCGGTGGTCTTTGGTATTCATTAGATACTAGTGG * 498722 ATAAAACAACAGCATCAACGAAACACTAACTGATGTCGATTATATGTAGATATCCATAATTCATG 260 ATAAAACAACAGCATCAACGAAACACTAACTAATGTCGATTATATGTAGATATCCATAATTCATG * 498787 TACATGAATATTGTAAAATATGACAATGGAGCCAAAATAAAAAGAAAAGAAAATTGATATAAAAC 325 TACATGAATATTGTAAAATATGACAATGGAGCCAAAAGAAAAAGAAAAGAAAATTGATATAAAAC 498852 GTATTCATGTTACAATGTATAATAAAGTAAGACGGGTGTGGAATTGTTCATGGAATGGTTTATTT 390 GTATTCATGTTACAATGTATAATAAAGTAAGACGGGTGTGGAATTGTTCATGGAATGGTTTATTT 498917 GAGAAAAAAACTACACGTATGCAATCAATATTATAT 455 GAGAAAAAAACTACACGTATGCAATCAATATTATAT 498953 GGCAATAACA Statistics Matches: 481, Mismatches: 9, Indels: 1 0.98 0.02 0.00 Matches are distributed among these distances: 491 33 0.07 492 448 0.93 ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27 Consensus pattern (490 bp): AACGGGCCATCTACTGCGTTTCACTCTCTTCTGAAATCGTTTGGTGGCGATCGATCAGACAACAA GAACTACGTGATTCAGATGAAAGGTGACACAGTAGAATGGGCCGTGCCAACCGTTGAAGATCTAC CAGGGGTAGGCCAAATTGCCGGCATCAAAACACATGACAGCACGGAAGATGACTTGAAAGATTTG TATGTTGTGTTCGCTGGCGATGACAAATCGTCGGTGGTCTTTGGTATTCATTAGATACTAGTGGA TAAAACAACAGCATCAACGAAACACTAACTAATGTCGATTATATGTAGATATCCATAATTCATGT ACATGAATATTGTAAAATATGACAATGGAGCCAAAAGAAAAAGAAAAGAAAATTGATATAAAACG TATTCATGTTACAATGTATAATAAAGTAAGACGGGTGTGGAATTGTTCATGGAATGGTTTATTTG AGAAAAAAACTACACGTATGCAATCAATATTATAT Found at i:502103 original size:126 final size:125 Alignment explanation

Indices: 501878--502128 Score: 493 Period size: 126 Copynumber: 2.0 Consensus size: 125 501868 ATTTATATCT 501878 TATAAACATCACATTAGAATTATATCTTAGTTTTTTTTAACCTATTCAAAACCATTAACTGAAAA 1 TATAAACATCACATTAGAATTATATCTTAGTTTTTTTTAACCTATTCAAAACCATTAACTGAAAA 501943 TTAGAAAGATAACTATAAGATCGTAGTCCAAGACATTTTCAAAAGATCTGACAGTGTGTG 66 TTAGAAAGATAACTATAAGATCGTAGTCCAAGACATTTTCAAAAGATCTGACAGTGTGTG 502003 NTATAAACATCACATTAGAATTATATCTTAGTTTTTTTTAACCTATTCAAAACCATTAACTGAAA 1 -TATAAACATCACATTAGAATTATATCTTAGTTTTTTTTAACCTATTCAAAACCATTAACTGAAA 502068 ATTAGAAAGATAACTATAAGATCGTAGTCCAAGACATTTTCAAAAGATCTGACAGTGTGTG 65 ATTAGAAAGATAACTATAAGATCGTAGTCCAAGACATTTTCAAAAGATCTGACAGTGTGTG 502129 CATGAATATC Statistics Matches: 125, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 126 125 1.00 ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33 Consensus pattern (125 bp): TATAAACATCACATTAGAATTATATCTTAGTTTTTTTTAACCTATTCAAAACCATTAACTGAAAA TTAGAAAGATAACTATAAGATCGTAGTCCAAGACATTTTCAAAAGATCTGACAGTGTGTG Found at i:502556 original size:17 final size:18 Alignment explanation

Indices: 502534--502568 Score: 54 Period size: 19 Copynumber: 1.9 Consensus size: 18 502524 TGATGATTTC 502534 TTTTTT-ACCTTATATGT 1 TTTTTTAACCTTATATGT 502551 TTTTTTAAACCTTATATG 1 TTTTTT-AACCTTATATG 502569 CTATGACCAC Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 17 6 0.38 19 10 0.62 ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60 Consensus pattern (18 bp): TTTTTTAACCTTATATGT Found at i:506632 original size:54 final size:54 Alignment explanation

Indices: 506550--506656 Score: 205 Period size: 54 Copynumber: 2.0 Consensus size: 54 506540 GGTAGTTTTA * 506550 ATGAAAAAATTAACTGGTACGTTAAAAAACAATCAATCAATCAATCAATCAATT 1 ATGAAAAAATTAACTGGGACGTTAAAAAACAATCAATCAATCAATCAATCAATT 506604 ATGAAAAAATTAACTGGGACGTTAAAAAACAATCAATCAATCAATCAATCAAT 1 ATGAAAAAATTAACTGGGACGTTAAAAAACAATCAATCAATCAATCAATCAAT 506657 CAATTAAATG Statistics Matches: 52, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 54 52 1.00 ACGTcount: A:0.52, C:0.15, G:0.08, T:0.24 Consensus pattern (54 bp): ATGAAAAAATTAACTGGGACGTTAAAAAACAATCAATCAATCAATCAATCAATT Found at i:506642 original size:4 final size:4 Alignment explanation

Indices: 506633--506660 Score: 56 Period size: 4 Copynumber: 7.0 Consensus size: 4 506623 CGTTAAAAAA 506633 CAAT CAAT CAAT CAAT CAAT CAAT CAAT 1 CAAT CAAT CAAT CAAT CAAT CAAT CAAT 506661 TAAATGTAAG 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:0.50, C:0.25, G:0.00, T:0.25 Consensus pattern (4 bp): CAAT Found at i:506912 original size:17 final size:17 Alignment explanation

Indices: 506892--506925 Score: 59 Period size: 17 Copynumber: 2.0 Consensus size: 17 506882 TGATAAATGA * 506892 AACGAGTTATCAAATTT 1 AACGAGTTAACAAATTT 506909 AACGAGTTAACAAATTT 1 AACGAGTTAACAAATTT 506926 TAAAAATATC Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32 Consensus pattern (17 bp): AACGAGTTAACAAATTT Found at i:508338 original size:15 final size:15 Alignment explanation

Indices: 508318--508348 Score: 62 Period size: 15 Copynumber: 2.1 Consensus size: 15 508308 AATAACCCTT 508318 ATTATAAAAAAAAAA 1 ATTATAAAAAAAAAA 508333 ATTATAAAAAAAAAA 1 ATTATAAAAAAAAAA 508348 A 1 A 508349 GAAATTACAG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19 Consensus pattern (15 bp): ATTATAAAAAAAAAA Found at i:518464 original size:7 final size:7 Alignment explanation

Indices: 518452--518476 Score: 50 Period size: 7 Copynumber: 3.6 Consensus size: 7 518442 GTTTTTAGAA 518452 CGCAGTT 1 CGCAGTT 518459 CGCAGTT 1 CGCAGTT 518466 CGCAGTT 1 CGCAGTT 518473 CGCA 1 CGCA 518477 ATTGAATAGT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 18 1.00 ACGTcount: A:0.16, C:0.32, G:0.28, T:0.24 Consensus pattern (7 bp): CGCAGTT Found at i:518548 original size:56 final size:57 Alignment explanation

Indices: 518477--518586 Score: 204 Period size: 58 Copynumber: 1.9 Consensus size: 57 518467 GCAGTTCGCA 518477 ATTGAATAGTGAACTGCGTTCTA-TAGAACGCAGTTCGCAATTCAAAATTTAGTTCG 1 ATTGAATAGTGAACTGCGTTCTACTAGAACGCAGTTCGCAATTCAAAATTTAGTTCG 518533 ATTGAATAGTGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAG 1 ATTGAATAGTGAACTGCGTTCTA-CTAGAACGCAGTTCGCAATTCAAAATTTAG 518587 AATTCATATT Statistics Matches: 52, Mismatches: 0, Indels: 2 0.96 0.00 0.04 Matches are distributed among these distances: 56 23 0.44 58 29 0.56 ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32 Consensus pattern (57 bp): ATTGAATAGTGAACTGCGTTCTACTAGAACGCAGTTCGCAATTCAAAATTTAGTTCG Found at i:518680 original size:86 final size:86 Alignment explanation

Indices: 518533--518881 Score: 653 Period size: 86 Copynumber: 4.0 Consensus size: 86 518523 ATTTAGTTCG * 518533 ATTGAATAGTGAACTGCGTTCTATCTAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATATTT 1 ATTGAATAGTGAACTGCGTTCTA--TAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATACTT * 518598 GGGGCCCGATTGCCTTATATGCA 64 GGGGCCCGCTTGCCTTATATGCA * 518621 ATTGAATAGTGAACTGCGTTCTATAGAATGCAGTTCGCAATTCAAAATTTAGAATTCATACTTGG 1 ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATACTTGG 518686 GGCCCGCTTGCCTTATATGCA 66 GGCCCGCTTGCCTTATATGCA 518707 ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATACTTGG 1 ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATACTTGG 518772 GGCCCGCTTGCCTTATATGCA 66 GGCCCGCTTGCCTTATATGCA 518793 ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATACTTGG 1 ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATACTTGG 518858 GGCCCGCTTGCCTTATATGCA 66 GGCCCGCTTGCCTTATATGCA 518879 ATT 1 ATT 518882 NNNNNNNNNN Statistics Matches: 257, Mismatches: 4, Indels: 2 0.98 0.02 0.01 Matches are distributed among these distances: 86 234 0.91 88 23 0.09 ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32 Consensus pattern (86 bp): ATTGAATAGTGAACTGCGTTCTATAGAACGCAGTTCGCAATTCAAAATTTAGAATTCATACTTGG GGCCCGCTTGCCTTATATGCA Found at i:528804 original size:14 final size:13 Alignment explanation

Indices: 528784--528819 Score: 54 Period size: 14 Copynumber: 2.7 Consensus size: 13 528774 TTTTTGCATT 528784 TTTAATTTTTAGG 1 TTTAATTTTTAGG * 528797 TTTAAATTTTTTGG 1 TTT-AATTTTTAGG 528811 TTTAATTTT 1 TTTAATTTT 528820 GCGTTTCACT Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 13 9 0.43 14 12 0.57 ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67 Consensus pattern (13 bp): TTTAATTTTTAGG Found at i:545590 original size:20 final size:22 Alignment explanation

Indices: 545561--545610 Score: 70 Period size: 20 Copynumber: 2.4 Consensus size: 22 545551 AATACAAATA 545561 TCTT-ATATCAGAAA-ATGAAT 1 TCTTGATATCAGAAATATGAAT * 545581 T-TTGATATCAGAAATTTGAAT 1 TCTTGATATCAGAAATATGAAT 545602 TCTTGATAT 1 TCTTGATAT 545611 TATAAAAAAT Statistics Matches: 26, Mismatches: 1, Indels: 4 0.84 0.03 0.13 Matches are distributed among these distances: 19 2 0.08 20 11 0.42 21 6 0.23 22 7 0.27 ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42 Consensus pattern (22 bp): TCTTGATATCAGAAATATGAAT Found at i:548960 original size:12 final size:12 Alignment explanation

Indices: 548943--548967 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 548933 ATAAATATCT 548943 AATTATTATATA 1 AATTATTATATA 548955 AATTATTATATA 1 AATTATTATATA 548967 A 1 A 548968 TTGGAAAGCT 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:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (12 bp): AATTATTATATA Found at i:555142 original size:12 final size:12 Alignment explanation

Indices: 555106--555144 Score: 51 Period size: 12 Copynumber: 3.2 Consensus size: 12 555096 TTCACTTATG * 555106 TTTTTAATGCAA 1 TTTTTAATTCAA * 555118 TTTCTTAAGTCAA 1 TTT-TTAATTCAA 555131 TTTTTAATTCAA 1 TTTTTAATTCAA 555143 TT 1 TT 555145 GCATTAATTC Statistics Matches: 23, Mismatches: 3, Indels: 2 0.82 0.11 0.07 Matches are distributed among these distances: 12 13 0.57 13 10 0.43 ACGTcount: A:0.31, C:0.10, G:0.05, T:0.54 Consensus pattern (12 bp): TTTTTAATTCAA Found at i:565430 original size:165 final size:165 Alignment explanation

Indices: 565125--565518 Score: 436 Period size: 165 Copynumber: 2.4 Consensus size: 165 565115 ATGCATAATA * * * 565125 ATCTCACAAACTGTAGCATTATAGTTCTCGAGAAAAA-ACTTTTTAATAACATTTTCAATATATC 1 ATCTCACAAACTGAAGCATTATAGTTCTCGAGAAAAAGA-TTTTT-A-AACATTTTCCATATATA * * * * * 565189 TTTCTATGTTAAACTTTGAACCCCTCTTGGGGCCACAGTATTAGTCCAGGGCTAAAGTTTTAATT 63 TTTCTATGCTAAACTTTGAACACCTCTTGGGGCCACAGTATTAGTCCAAGACTAAAGTTTTAATA * * * 565254 ATTTGGAATCTACATTATTCAAGGATGCTTGCATAGTT 128 ATTTCGAATCTACACTATTCAAGGATGCTTACATAGTT * * * * * * 565292 ATCTCACAAGCTGAAGCATTATAGTTCCCTAGAAAAAGATTTTTCAACATTTTCCCTCTATATTT 1 ATCTCACAAACTGAAGCATTATAGTTCTCGAGAAAAAGATTTTTAAACATTTTCCATATATATTT * ** ** 565357 CTATGCTAAACTTTGAACACCTCTTGGGGCCCCAGTATTAGATTGAAGAC-ACGGCTTTT-ATAA 66 CTATGCTAAACTTTGAACACCTCTTGGGGCCACAGTATTAG-TCCAAGACTAAAG-TTTTAATAA ** * * 565420 TTTCGAATCTACACTATTTGAGGGTGCTTACGTAGTT 129 TTTCGAATCTACACTATTCAAGGATGCTTACATAGTT * * * * 565457 ATCTGACAAATTGATGCATTGTAGTTCTCGA-AAAGAAGATTTTTAAACATTTTCCATATATA 1 ATCTCACAAACTGAAGCATTATAGTTCTCGAGAAA-AAGATTTTTAAACATTTTCCATATATA 565519 CTGGTACTTC Statistics Matches: 187, Mismatches: 36, Indels: 10 0.80 0.15 0.04 Matches are distributed among these distances: 164 3 0.02 165 137 0.73 166 8 0.04 167 38 0.20 168 1 0.01 ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36 Consensus pattern (165 bp): ATCTCACAAACTGAAGCATTATAGTTCTCGAGAAAAAGATTTTTAAACATTTTCCATATATATTT CTATGCTAAACTTTGAACACCTCTTGGGGCCACAGTATTAGTCCAAGACTAAAGTTTTAATAATT TCGAATCTACACTATTCAAGGATGCTTACATAGTT Found at i:566614 original size:332 final size:332 Alignment explanation

Indices: 566070--566985 Score: 1489 Period size: 332 Copynumber: 2.8 Consensus size: 332 566060 GGTCACGATT * * * ** * * 566070 TTTACAATCTTCACTATGTATACAACCTTTTGTGTATGTATTGGCATTTTTGGTGAAGTGGTTCT 1 TTTAAAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT * * * 566135 TGAGAAGAAAATTTTTAAACATTTTTCATATGTAGTTCTATGTTAAACTTTGAACCCCGCCTGGG 66 TGAGAAGAAGATTTTTAAACA-TTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCCTGGG * * * * 566200 GCCCCAGTCTTGGTCCGAGGGTCACGATTTCTACAATTTAGAATCTTCATTATACATACAAGCTT 130 GCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAAGCTT * * * * * 566265 TTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCTTGAGAACAACATTTTTTAAACATTTT-CC 195 TTGTGTAAATATTGGCATTTCTGGTGCTGTGGTTCTTGAGAAGAAGATTTTTAAAAAATTTTCCC * 566329 TAAGGTAT-TTCTATGTTAAACTTTGAACCCCGCCTGGGGCCCCAGTCTTGGTCCGAGGGGCACG 260 T-AGGT-TGTTCTATGTTAAACTTTGAACCCCGCCTGGGGCCCCAGTCTTGGTCCGAGGGGCACC 566393 ATTTTTACAA 323 ATTTTTACAA 566403 TTTAAAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT 1 TTTAAAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT * * 566468 TGAGAAGAAGATTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTAAACCCCGCTTGGGG 66 TGAGAAGAAGATTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCCTGGGG * 566533 CCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAAAATCTTCACTATATATACAAGCTTT 131 CCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAAGCTTT 566598 TGTGTAAATATTGGCATTTCTGGTGCTGTGGTTCTTGAGAAGAAGATTTTTAAAAAATTTTCCCT 196 TGTGTAAATATTGGCATTTCTGGTGCTGTGGTTCTTGAGAAGAAGATTTTTAAAAAATTTTCCCT * * * 566663 ATGTTGTTCTATGTTAAACTTTGAACCCCGCCTGGGGCCCCAGTTTTGGTCCGAGGGTCACCATT 261 AGGTTGTTCTATGTTAAACTTTGAACCCCGCCTGGGGCCCCAGTCTTGGTCCGAGGGGCACCATT 566728 TTTACAA 326 TTTACAA * 566735 TTTAGAATCTTCACTATATATGA-AAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTC 1 TTTAAAATCTTCACTATATAT-ACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTC * 566799 TTGAGAAGAAGATTTTTAAAAAATTTTCCATATGT-TGTTCTATGTTAAACTTTGAACCCCGCCT 65 TTGAGAAGAAGATTTTT-AAACATTTTCC-TATGTAT-TTCTATGTTAAACTTTGAACCCCGCCT 566863 GGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAAG 127 GGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAAG 566928 CTTTTGTGTAAATATTGGCATTTCTGGTGCTGTGGTTCTTGAGAAGAAGATTTTTAAA 192 CTTTTGTGTAAATATTGGCATTTCTGGTGCTGTGGTTCTTGAGAAGAAGATTTTTAAA 566986 GACATGCACC Statistics Matches: 546, Mismatches: 31, Indels: 11 0.93 0.05 0.02 Matches are distributed among these distances: 331 1 0.00 332 300 0.55 333 93 0.17 334 152 0.28 ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38 Consensus pattern (332 bp): TTTAAAATCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTGGTTCT TGAGAAGAAGATTTTTAAACATTTTCCTATGTATTTCTATGTTAAACTTTGAACCCCGCCTGGGG CCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAAGCTTT TGTGTAAATATTGGCATTTCTGGTGCTGTGGTTCTTGAGAAGAAGATTTTTAAAAAATTTTCCCT AGGTTGTTCTATGTTAAACTTTGAACCCCGCCTGGGGCCCCAGTCTTGGTCCGAGGGGCACCATT TTTACAA Done.