Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr07 97507971 

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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 232 characters in sequence are not A, C, G, or T


File 190 of 328

Found at i:56622735 original size:71 final size:71

Alignment explanation

Indices: 56622614--56622778 Score: 244 Period size: 71 Copynumber: 2.3 Consensus size: 71 56622604 GAGTTAAGCC ** * * 56622614 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC 1 TTTTCAATTTTTG-TTTTCAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC 56622678 TGAGGTA 65 TGAGGTA * 56622685 TTTTCAATTTTTGTGTTT-AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC 1 TTTTCAATTTTTGT-TTTCAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC 56622749 TGAGGTA 65 TGAGGTA * 56622756 TTTTCAATTTCTGTTTTCAATTT 1 TTTTCAATTTTTGTTTTCAATTT 56622779 ACGTTGTTCA Statistics Matches: 85, Mismatches: 6, Indels: 6 0.88 0.06 0.06 Matches are distributed among these distances: 70 3 0.04 71 71 0.84 72 11 0.13 ACGTcount: A:0.22, C:0.15, G:0.21, T:0.41 Consensus pattern (71 bp): TTTTCAATTTTTGTTTTCAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCT GAGGTA Found at i:56623014 original size:72 final size:71 Alignment explanation

Indices: 56622893--56623058 Score: 244 Period size: 72 Copynumber: 2.3 Consensus size: 71 56622883 GAGTTAAGCC ** * * 56622893 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC 1 TTTTCAATTTTTGTTTTT-AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC 56622957 TGAGGTA 65 TGAGGTA * 56622964 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC 1 TTTTCAATTTTTGT-TTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC 56623029 TGAGGTA 65 TGAGGTA * * 56623036 TTTTCAATTTCTGTTTTCAATTT 1 TTTTCAATTTTTGTTTTTAATTT 56623059 ACGTTGTTCA Statistics Matches: 86, Mismatches: 7, Indels: 4 0.89 0.07 0.04 Matches are distributed among these distances: 71 12 0.14 72 70 0.81 73 4 0.05 ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42 Consensus pattern (71 bp): TTTTCAATTTTTGTTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCT GAGGTA Found at i:56623286 original size:70 final size:69 Alignment explanation

Indices: 56623167--56623589 Score: 385 Period size: 71 Copynumber: 6.2 Consensus size: 69 56623157 GAGTTAAGCC * 56623167 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC 1 TTTTCAATTTTTG-TTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC 56623231 TGAGGTA 63 TGAGGTA * * * ** * * 56623238 TTTTCAATTTTTGTGTTTTAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAAGACACGTTG 1 TTTTCAATTTTTGT-TTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTG 56623303 AGGTA 65 AGGTA * * 56623308 TTTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT 1 TTTTCAATTTTTGTTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCT 56623373 GAGGTA 64 GAGGTA * * * ** * * * 56623379 TTTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT---------TTTA 1 TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGA 56623435 ---A 66 GGTA *** ** * * 56623436 TTTTTGTTTTTCA----AAATCGACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGA 1 TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGA 56623497 GGTA 66 GGTA * * * 56623501 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC 1 TTTTCAA-TTTT-TGTTTTAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC 56623566 TGAGGTA 63 TGAGGTA * 56623573 TTTTCAATTTCTGTTTT 1 TTTTCAATTTTTGTTTT 56623590 CAATTTACGT Statistics Matches: 284, Mismatches: 45, Indels: 47 0.76 0.12 0.12 Matches are distributed among these distances: 53 32 0.11 57 9 0.03 60 2 0.01 62 2 0.01 65 5 0.02 66 4 0.01 69 34 0.12 70 64 0.23 71 69 0.24 72 63 0.22 ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39 Consensus pattern (69 bp): TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGA GGTA Found at i:56623461 original size:537 final size:539 Alignment explanation

Indices: 56622184--56623627 Score: 2373 Period size: 537 Copynumber: 2.7 Consensus size: 539 56622174 TTTCAAGGAA * 56622184 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTGTTGT 1 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT * 56622249 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTA---TT--T 66 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGT 56622309 TTA-GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAA 131 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAA 56622373 TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT 196 TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT * * * * * 56622438 TTTAA--TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAA-- 261 TTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATT * 56622499 ------TT---TTT--GTT-TTC-AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGG 326 TCTGTTTTCAATTTACGTTGTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGA 56622551 CACGCTGAGGTATTTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTT 391 CACGCTGAGGTA--TTTA-TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTT 56622616 TTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGA 453 TTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGA 56622681 GGTATTTTCAATTTTTGTGTTT 518 GGTATTTTCAATTTTTGTGTTT * * * * * 56622703 AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCT 1 AA--TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAA----- 56622768 GTTTTCAATTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCAC 59 ---TT---TTT--GTT-TTCAA-AATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCAC 56622833 GCTGAGGTATTTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTA 114 GCTGAGGTATTTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTA 56622898 ATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGT 179 ATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGT 56622963 ATTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACG 244 ATTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACG 56623028 CTGAGGTATTTTCAATTTCTGTTTTCAATTTACGTTGTTCAAAAATCAACTCATATTGCGAGAAG 309 CTGAGGTATTTTCAATTTCTGTTTTCAATTTACGTTGTTCAAAAATCAACTCATATTGCGAGAAG 56623093 TGAGTTGAGCCTCGGGACACGCTGAGGTA-TT-TTTA-GTTTTAAATTGACTCATATTGCGAGAG 374 TGAGTTGAGCCTCGGGACACGCTGAGGTATTTATTTATGTTTTAAATTGACTCATATTGCGAGAG 56623155 GTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCC 439 GTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCC 56623220 TCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT 504 TCGGGGCACGCTGAGGTATTTTCAATTTTTGTG-TTT * 56623257 AATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT 1 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT 56623322 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGT 66 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGT 56623387 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAA 131 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAA * 56623452 TCGACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT 196 TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT 56623517 TTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATT 261 TTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATT * 56623582 TCTGTTTTCAATTTACGTTGTTCAAGAATCAACTCATATTGCGAGA 326 TCTGTTTTCAATTTACGTTGTTCAAAAATCAACTCATATTGCGAGA 56623628 GGTAGGTTGA Statistics Matches: 863, Mismatches: 21, Indels: 64 0.91 0.02 0.07 Matches are distributed among these distances: 519 2 0.00 521 51 0.06 529 2 0.00 532 2 0.00 534 3 0.00 535 5 0.01 536 50 0.06 537 298 0.35 538 5 0.01 539 5 0.01 541 7 0.01 542 131 0.15 544 53 0.06 552 52 0.06 553 125 0.14 554 9 0.01 555 3 0.00 556 2 0.00 557 3 0.00 558 3 0.00 559 52 0.06 ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37 Consensus pattern (539 bp): AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGT TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAA TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT TTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATT TCTGTTTTCAATTTACGTTGTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGA CACGCTGAGGTATTTATTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTA ATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGT ATTTTCAATTTTTGTGTTT Found at i:56623475 original size:122 final size:124 Alignment explanation

Indices: 56623309--56623555 Score: 383 Period size: 122 Copynumber: 2.0 Consensus size: 124 56623299 GTTGAGGTAT 56623309 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG 1 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG * * 56623374 AGGTATTTT-TA-GTTTATGTTTTAAATT-GACTCATATTGCGAGAGGTGAGTTAAGCC 66 AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC * * * 56623430 TTTTAATTTTTGTTTTTCAAAATCGACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT 1 TTTTAATTTTTG-TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT * * * * 56623495 GAGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCC 65 GAGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC 56623555 T 1 T 56623556 CAGGTCACGC Statistics Matches: 113, Mismatches: 9, Indels: 4 0.90 0.07 0.03 Matches are distributed among these distances: 121 12 0.11 122 59 0.52 123 1 0.01 124 13 0.12 125 28 0.25 ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39 Consensus pattern (124 bp): TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC Found at i:56623551 original size:72 final size:71 Alignment explanation

Indices: 56623430--56623595 Score: 235 Period size: 72 Copynumber: 2.3 Consensus size: 71 56623420 GAGTTAAGCC ** * * * 56623430 TTTT-AATTTTTGTTTTTCAAAATCGACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC 1 TTTTCAATTTTTGTTTTT-AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC 56623494 TGAGGTA 65 TGAGGTA * 56623501 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC 1 TTTTCAATTTTTGT-TTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC 56623566 TGAGGTA 65 TGAGGTA * * 56623573 TTTTCAATTTCTGTTTTCAATTT 1 TTTTCAATTTTTGTTTTTAATTT 56623596 ACGTTGTTCA Statistics Matches: 85, Mismatches: 8, Indels: 4 0.88 0.08 0.04 Matches are distributed among these distances: 71 12 0.14 72 69 0.81 73 4 0.05 ACGTcount: A:0.22, C:0.15, G:0.22, T:0.42 Consensus pattern (71 bp): TTTTCAATTTTTGTTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCT GAGGTA Found at i:56623926 original size:74 final size:76 Alignment explanation

Indices: 56623820--56623964 Score: 224 Period size: 74 Copynumber: 1.9 Consensus size: 76 56623810 TTTTTGCCTT * 56623820 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--GACACG-CTGAGGTAATTT 1 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTC-GAGGTAATTT 56623882 CAATTTCTATTG 65 CAATTTCTATTG * * * 56623894 TCAAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTATTTTC 1 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAATTTC 56623959 AATTTC 66 AATTTC 56623965 CATTTTTCAA Statistics Matches: 64, Mismatches: 4, Indels: 4 0.89 0.06 0.06 Matches are distributed among these distances: 74 42 0.66 76 21 0.33 77 1 0.02 ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28 Consensus pattern (76 bp): TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAATTTC AATTTCTATTG Found at i:56623932 original size:165 final size:166 Alignment explanation

Indices: 56623660--56624141 Score: 677 Period size: 165 Copynumber: 2.9 Consensus size: 166 56623650 CTACTTTTTC 56623660 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT 1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT * * * 56623725 GTTGTCAAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTAT 66 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTCGAGGTAT * * 56623790 TTTCAATTTCCGTTTTTCAATTTTTGCCTTTC-AAA 131 TTTCAATTTCCGTTTTTCAATTTCTGCATTTCAAAA 56623825 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT 1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT * * * 56623890 ATTGTCAAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAT 66 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTCGAGGTAT * 56623955 TTTCAATTTCCATTTTTCAATTTCTGCATTTCAAAAAAAAAAAAA 131 TTTCAATTTCCGTTTTTCAATTTCTGCATTTC---------AAAA * 56624000 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCT 1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT * * * * ** * * 56624065 GTTTTC--AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAG--ACACGTTGAGGTAT 66 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTCGAGGTAT * 56624126 TTTCAATTTCTGTTTT 131 TTTCAATTTCCGTTTT 56624142 CAAAAAATCA Statistics Matches: 285, Mismatches: 22, Indels: 14 0.89 0.07 0.04 Matches are distributed among these distances: 165 153 0.54 171 27 0.09 173 34 0.12 175 71 0.25 ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32 Consensus pattern (166 bp): AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTCGAGGTAT TTTCAATTTCCGTTTTTCAATTTCTGCATTTCAAAA Found at i:56624082 original size:72 final size:73 Alignment explanation

Indices: 56623998--56624505 Score: 399 Period size: 72 Copynumber: 6.5 Consensus size: 73 56623988 AAAAAAAAAA * 56623998 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTT 1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTT 56624063 CTGTTTTC 66 CTGTTTTC * * ** ** * 56624071 -AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT 1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTT 56624135 CTGTTTTC 66 CTGTTTTC * * * ** * 56624143 AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATTTTCAAT 1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA--CGCTGAGGTATTTTCAAT * 56624208 TTCTATCTTTC 64 TTCTGT-TTTC * ** * 56624219 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTC 1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-G-GGACACGCTGAGGTA--TTTTC * * 56624284 AATTTATATTTTTC 61 AATTTCT-GTTTTC * * * 56624298 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTTACATG-TCGAGGTATTTTCA 1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG--ACACGCT-GAGGTATTTTCA ** 56624362 AAATCTGTTTTTC 62 ATTTCTG-TTTTC * * ** 56624375 AAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGA 1 --A----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC--GCTGA * 56624440 GCTATTTTCAATTTCTGTTTTTTTTTTC 52 GGTATTTTCAATTTCTG------TTTTC 56624468 AAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGC 1 -AAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC 56624506 TTTTTAATTT Statistics Matches: 348, Mismatches: 53, Indels: 58 0.76 0.12 0.13 Matches are distributed among these distances: 72 64 0.18 73 33 0.09 75 21 0.06 76 4 0.01 77 57 0.16 78 5 0.01 79 64 0.18 80 1 0.00 82 5 0.01 83 29 0.08 86 2 0.01 88 54 0.16 89 1 0.00 92 2 0.01 93 6 0.02 ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35 Consensus pattern (73 bp): AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTT CTGTTTTC Found at i:56624321 original size:79 final size:76 Alignment explanation

Indices: 56623997--56624715 Score: 420 Period size: 88 Copynumber: 9.0 Consensus size: 76 56623987 AAAAAAAAAA ** * 56623997 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-G-GGACACGCTGAGGTAATTTCAA 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA 56624060 TTTCTGTTTTC 66 TTTCTGTTTTC * * ** * * 56624071 --AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCA-A-GACACGTTGAGGTATTTTCAA 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA 56624132 TTTCTGTTTTC 66 TTTCTGTTTTC * * ** * ** * 56624143 -AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATTTTCAA 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA * 56624207 TTTCTATCTTTC 66 TTTCTGT-TTTC * * 56624219 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTC 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTA--TTTTC * * 56624284 AATTTATATTTTTC 64 AATTTCT-GTTTTC * * * * * * 56624298 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTTACATG-TCGAGGTATTTTCA 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCT-GAGGTATTTTCA ** 56624362 AAATCTGTTTTTC 65 ATTTCTG-TTTTC * ** * ** 56624375 AAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGA 1 -AA----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGA * 56624440 GCTATTTTCAATTTCTGTTTTTTTTTTC 55 GGTATTTTCAATTTCTG------TTTTC * * * * * * 56624468 AAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA-ATTTCTGCGAGAGTTGAGTT 1 AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--CTCAGA--TC-AC-A-CGCTGAGGT * 56624532 GAGTCTTTTAATTTCTGTTTTTC 58 -A-T-TTTCAATTTCTG-TTTTC * ** 56624555 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCCAG-TCACA-TATCGAGGTATTTTC 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-CAGATCACACGCT-GAGGTATTTTC ** 56624616 AAAATCTGCTTTTC 64 AATTTCTG-TTTTC ** * * 56624630 AAGTTAAGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGA 1 ------A-----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGA * 56624695 GCTATTTTCAATTTCTGTTTT 55 GGTATTTTCAATTTCTGTTTT 56624716 TAATGTCTGT Statistics Matches: 503, Mismatches: 84, Indels: 103 0.73 0.12 0.15 Matches are distributed among these distances: 72 64 0.13 73 31 0.06 75 36 0.07 76 5 0.01 77 63 0.13 78 7 0.01 79 64 0.13 80 2 0.00 81 2 0.00 82 6 0.01 83 30 0.06 84 29 0.06 85 7 0.01 86 2 0.00 87 12 0.02 88 114 0.23 89 8 0.02 90 1 0.00 91 1 0.00 92 13 0.03 93 6 0.01 ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36 Consensus pattern (76 bp): AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA TTTCTGTTTTC Found at i:56624375 original size:14 final size:13 Alignment explanation

Indices: 56624356--56624391 Score: 54 Period size: 14 Copynumber: 2.7 Consensus size: 13 56624346 TGTCGAGGTA 56624356 TTTTCAAAATCTG 1 TTTTCAAAATCTG * 56624369 TTTTTCAAATTCTG 1 -TTTTCAAAATCTG 56624383 TTTTCAAAA 1 TTTTCAAAA 56624392 ATCAACTCAT Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 13 8 0.40 14 12 0.60 ACGTcount: A:0.31, C:0.14, G:0.06, T:0.50 Consensus pattern (13 bp): TTTTCAAAATCTG Found at i:56624523 original size:30 final size:30 Alignment explanation

Indices: 56624487--56624548 Score: 99 Period size: 30 Copynumber: 2.1 Consensus size: 30 56624477 CAACTCATAT 56624487 TGCGAGAGGTGAGTTGAG-CTTTTTAATTTC 1 TGCGAGAGGTGAGTTGAGTC-TTTTAATTTC * 56624517 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC 1 TGCGAGAGGTGAGTTGAGTCTTTTAATTTC 56624547 TG 1 TG 56624549 TTTTTCAAAA Statistics Matches: 30, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 30 29 0.97 31 1 0.03 ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42 Consensus pattern (30 bp): TGCGAGAGGTGAGTTGAGTCTTTTAATTTC Found at i:56624649 original size:255 final size:249 Alignment explanation

Indices: 56624137--56624716 Score: 757 Period size: 255 Copynumber: 2.3 Consensus size: 249 56624127 TTCAATTTCT * * * 56624137 GTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATT 1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT * 56624202 TTCAATTTC-----TATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGA 66 TTCAATTTCTGTTTTTTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGA * * 56624262 TCACACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTG 131 TCACACACTGAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCACATTGCGAGAGGTG * ** * * * ** 56624327 AGTTGAGCCTCGGGTTACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAATTCT 195 AGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAA * * 56624382 GTTTTC-AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATT 1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT * * 56624446 TTCAATTTCTGTTTTTTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTT 66 TTCAATTTCTGTTTTTTCTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--TTC * * * * * * * 56624511 A-ATTTCTGCGAGAGTTGAGTTGAGTCTTTT-AATTTCTGTTTTTC-AAAAATCAACTCATATTG 128 AGA--TC-AC-ACA-CTGAGGT-A-TCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTG * 56624573 CGAGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAGTTAA 186 CGAGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAA 56624637 G-TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT 1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT 56624701 TTCAATTTCTGTTTTT 66 TTCAATTTCTGTTTTT 56624717 AATGTCTGTT Statistics Matches: 291, Mismatches: 28, Indels: 22 0.85 0.08 0.06 Matches are distributed among these distances: 244 62 0.21 245 6 0.02 249 13 0.04 250 30 0.10 251 1 0.00 252 3 0.01 253 2 0.01 254 5 0.02 255 146 0.50 256 5 0.02 257 13 0.04 258 5 0.02 ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37 Consensus pattern (249 bp): GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT TTCAATTTCTGTTTTTTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGA TCACACACTGAGGTATCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCGAGAGGTGA GTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAA Found at i:56625376 original size:15 final size:15 Alignment explanation

Indices: 56625358--56625397 Score: 55 Period size: 15 Copynumber: 2.7 Consensus size: 15 56625348 AACCTAACCC 56625358 AAAAAAAAACAAAGA 1 AAAAAAAAACAAAGA 56625373 AAAAAAAGAA-AAAGA 1 AAAAAAA-AACAAAGA * 56625388 AAAAGAAAAC 1 AAAAAAAAAC 56625398 CTACCCCAAA Statistics Matches: 22, Mismatches: 1, Indels: 4 0.81 0.04 0.15 Matches are distributed among these distances: 14 2 0.09 15 18 0.82 16 2 0.09 ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00 Consensus pattern (15 bp): AAAAAAAAACAAAGA Found at i:56625413 original size:15 final size:15 Alignment explanation

Indices: 56625393--56625426 Score: 59 Period size: 15 Copynumber: 2.3 Consensus size: 15 56625383 AAAGAAAAAG * 56625393 AAAACCTACCCCAAA 1 AAAACCTAACCCAAA 56625408 AAAACCTAACCCAAA 1 AAAACCTAACCCAAA 56625423 AAAA 1 AAAA 56625427 AGAAGAAAAA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.62, C:0.32, G:0.00, T:0.06 Consensus pattern (15 bp): AAAACCTAACCCAAA Found at i:56625424 original size:16 final size:15 Alignment explanation

Indices: 56625388--56625427 Score: 53 Period size: 16 Copynumber: 2.5 Consensus size: 15 56625378 AAGAAAAAGA 56625388 AAAAGAAAACCTACCC 1 AAAA-AAAACCTACCC * 56625404 CAAAAAAACCTAACCC 1 AAAAAAAACCT-ACCC 56625420 AAAAAAAA 1 AAAAAAAA 56625428 GAAGAAAAAG Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 15 7 0.33 16 14 0.67 ACGTcount: A:0.65, C:0.28, G:0.03, T:0.05 Consensus pattern (15 bp): AAAAAAAACCTACCC Found at i:56627572 original size:41 final size:42 Alignment explanation

Indices: 56627527--56627641 Score: 146 Period size: 41 Copynumber: 2.8 Consensus size: 42 56627517 TTTTGTTGCC * 56627527 TTTTTATC-AAAAACGCCACTATAGCTCAATTTTTTATGGCG 1 TTTTTACCGAAAAACGCCACTATAGCTCAATTTTTTATGGCG * * 56627568 TTTTT-CCGAAAAACGCCACTATAGCTCAACTTTTTGTGGCG 1 TTTTTACCGAAAAACGCCACTATAGCTCAATTTTTTATGGCG * * * * 56627609 -TTTTACCTAAAAACGCCCCCATTGCTCAATTTT 1 TTTTTACCGAAAAACGCCACTATAGCTCAATTTT 56627642 GATTTTTTTC Statistics Matches: 64, Mismatches: 8, Indels: 4 0.84 0.11 0.05 Matches are distributed among these distances: 40 5 0.08 41 59 0.92 ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37 Consensus pattern (42 bp): TTTTTACCGAAAAACGCCACTATAGCTCAATTTTTTATGGCG Found at i:56628467 original size:21 final size:21 Alignment explanation

Indices: 56628443--56628489 Score: 76 Period size: 21 Copynumber: 2.2 Consensus size: 21 56628433 CTCAAATACC 56628443 AAACCCCAAATCCTAGACCAT 1 AAACCCCAAATCCTAGACCAT * * 56628464 AAACCCTAAATCTTAGACCAT 1 AAACCCCAAATCCTAGACCAT 56628485 AAACC 1 AAACC 56628490 TACTCCCTAA Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 21 24 1.00 ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17 Consensus pattern (21 bp): AAACCCCAAATCCTAGACCAT Found at i:56628871 original size:14 final size:14 Alignment explanation

Indices: 56628852--56628892 Score: 64 Period size: 14 Copynumber: 2.9 Consensus size: 14 56628842 CCCCTATCCC 56628852 CATAAACCCTAAAT 1 CATAAACCCTAAAT * * 56628866 CATAAAGCATAAAT 1 CATAAACCCTAAAT 56628880 CATAAACCCTAAA 1 CATAAACCCTAAA 56628893 CCCCTAACCC Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 14 23 1.00 ACGTcount: A:0.54, C:0.24, G:0.02, T:0.20 Consensus pattern (14 bp): CATAAACCCTAAAT Found at i:56628899 original size:8 final size:7 Alignment explanation

Indices: 56628831--56628970 Score: 50 Period size: 7 Copynumber: 19.0 Consensus size: 7 56628821 CTAATTAATA 56628831 TAAACCC 1 TAAACCC 56628838 TAAACCCC 1 TAAA-CCC ** 56628846 TATCCCC 1 TAAACCC 56628853 ATAAACCC 1 -TAAACCC * * 56628861 TAAATCA 1 TAAACCC * * 56628868 TAAAGCA 1 TAAACCC * * 56628875 TAAATCA 1 TAAACCC 56628882 TAAACCC 1 TAAACCC 56628889 TAAACCCC 1 TAAA-CCC 56628897 T-AACCC 1 TAAACCC * 56628903 TTAACCC 1 TAAACCC 56628910 ATATATCACCCC 1 -TA-A--A-CCC * 56628922 TAAACCT 1 TAAACCC 56628929 TAAACCC 1 TAAACCC * 56628936 -CAACCC 1 TAAACCC * 56628942 TTAAACCA 1 -TAAACCC * 56628950 TAAACCA 1 TAAACCC * * 56628957 TAATCTC 1 TAAACCC 56628964 TAAACCC 1 TAAACCC 56628971 ATAATCCATA Statistics Matches: 101, Mismatches: 21, Indels: 22 0.70 0.15 0.15 Matches are distributed among these distances: 6 9 0.09 7 64 0.63 8 20 0.20 9 1 0.01 10 1 0.01 11 3 0.03 12 3 0.03 ACGTcount: A:0.41, C:0.38, G:0.01, T:0.20 Consensus pattern (7 bp): TAAACCC Found at i:56629034 original size:14 final size:14 Alignment explanation

Indices: 56629012--56629056 Score: 54 Period size: 14 Copynumber: 3.2 Consensus size: 14 56629002 TTTTAAAACT 56629012 TAAACCCTAAACCA 1 TAAACCCTAAACCA * * * 56629026 TACATCCTAAACTA 1 TAAACCCTAAACCA * 56629040 TAAACCCTAAACTA 1 TAAACCCTAAACCA 56629054 TAA 1 TAA 56629057 TGATAATTAA Statistics Matches: 26, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 14 26 1.00 ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22 Consensus pattern (14 bp): TAAACCCTAAACCA Found at i:56629372 original size:40 final size:40 Alignment explanation

Indices: 56629323--56629441 Score: 139 Period size: 40 Copynumber: 3.0 Consensus size: 40 56629313 ACGGTAAAGC * 56629323 TCGATCTATAGCGGCGTTTTTAAAAAAGCGCCGCTAGTGG 1 TCGATCTATAGCGGCGTTTTTAAAAAAGCGCCGCTAATGG * * * * ** * 56629363 TCGACCTATAGTGGCATTTTTTAAAAAGCGTTGCTAATGT 1 TCGATCTATAGCGGCGTTTTTAAAAAAGCGCCGCTAATGG * * * 56629403 TCAATCTATAGCAGCGTTTTTCAAAAAGCGCCGCTAATG 1 TCGATCTATAGCGGCGTTTTTAAAAAAGCGCCGCTAATG 56629442 CCGCTACAAC Statistics Matches: 63, Mismatches: 16, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 40 63 1.00 ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31 Consensus pattern (40 bp): TCGATCTATAGCGGCGTTTTTAAAAAAGCGCCGCTAATGG Found at i:56629566 original size:39 final size:40 Alignment explanation

Indices: 56629488--56629616 Score: 172 Period size: 40 Copynumber: 3.2 Consensus size: 40 56629478 AATTTTTTTA * 56629488 CGGCATTTTTCAAAAAGCGCCGCTAATGGTCGA-CTTATAG 1 CGGCATTTTTCAAAAAGCGCCGCTAATGCTCGATC-TATAG ** * * 56629528 CGGCATTTTTTGAAAAGC-CCACTAATACTCGATCTATAG 1 CGGCATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAG * 56629567 CGGTATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAG 1 CGGCATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAG * 56629607 CGGCGTTTTT 1 CGGCATTTTT 56629617 TTATCCAAAC Statistics Matches: 75, Mismatches: 12, Indels: 4 0.82 0.13 0.04 Matches are distributed among these distances: 39 31 0.41 40 44 0.59 ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31 Consensus pattern (40 bp): CGGCATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAG Found at i:56630615 original size:2 final size:2 Alignment explanation

Indices: 56630610--56630646 Score: 74 Period size: 2 Copynumber: 18.5 Consensus size: 2 56630600 GTAGTTTTCT 56630610 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 56630647 TTCTAAAATT Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (2 bp): TA Found at i:56631363 original size:26 final size:26 Alignment explanation

Indices: 56631332--56631382 Score: 77 Period size: 26 Copynumber: 2.0 Consensus size: 26 56631322 TTAACTCCCA 56631332 TTCTTTTT-TTTTCTTTCTTCTTCTTC 1 TTCTTTTTCTTTT-TTTCTTCTTCTTC * 56631358 TTCTTTTTCTTTTTTTTTTCTTCTT 1 TTCTTTTTCTTTTTTTCTTCTTCTT 56631383 GGTGTTCTTT Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 26 19 0.83 27 4 0.17 ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80 Consensus pattern (26 bp): TTCTTTTTCTTTTTTTCTTCTTCTTC Found at i:56631390 original size:29 final size:29 Alignment explanation

Indices: 56631336--56631400 Score: 78 Period size: 29 Copynumber: 2.2 Consensus size: 29 56631326 CTCCCATTCT * 56631336 TTTTTTTTCTTTCTTCTTCTTCTTCTTT- 1 TTTTTTTTCTTTCTTCTTCGTCTTCTTTA * * * 56631364 TTCTTTTTTTTTTCTTCTTGGTGTTCTTTA 1 TT-TTTTTTCTTTCTTCTTCGTCTTCTTTA 56631394 TTTTTTT 1 TTTTTTT 56631401 GATAATTTAC Statistics Matches: 31, Mismatches: 4, Indels: 3 0.82 0.11 0.08 Matches are distributed among these distances: 28 2 0.06 29 27 0.87 30 2 0.06 ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78 Consensus pattern (29 bp): TTTTTTTTCTTTCTTCTTCGTCTTCTTTA Found at i:56632550 original size:18 final size:19 Alignment explanation

Indices: 56632529--56632564 Score: 56 Period size: 18 Copynumber: 1.9 Consensus size: 19 56632519 AATAAAGAAA * 56632529 GGAATTAAA-AAGAAAAGG 1 GGAATAAAATAAGAAAAGG 56632547 GGAATAAAATAAGAAAAG 1 GGAATAAAATAAGAAAAG 56632565 AAAAAGGGGG Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 8 0.50 19 8 0.50 ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11 Consensus pattern (19 bp): GGAATAAAATAAGAAAAGG Found at i:56633958 original size:59 final size:58 Alignment explanation

Indices: 56633862--56633993 Score: 246 Period size: 59 Copynumber: 2.3 Consensus size: 58 56633852 AAAATTGTAC 56633862 AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATAT 1 AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATAT * 56633920 AGCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT 1 AGCACTAAGTGTGCGAACTGAAAA-TATATAGCACTAAGTGTGCGAGCTGAAAATATAT 56633979 AGCACTAAGTGTGCG 1 AGCACTAAGTGTGCG 56633994 GATTCACTAT Statistics Matches: 72, Mismatches: 1, Indels: 1 0.97 0.01 0.01 Matches are distributed among these distances: 58 23 0.32 59 49 0.68 ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24 Consensus pattern (58 bp): AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATAT Found at i:56633982 original size:88 final size:89 Alignment explanation

Indices: 56633832--56633993 Score: 263 Period size: 88 Copynumber: 1.8 Consensus size: 89 56633822 GACAAGATTG * * * 56633832 GCACTAAGTGTGCGGGTTTAAAAATTGTACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT 1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT 56633897 AAGTGTGCGAGCTGAAAATATATA 66 AAGTGTGCGAGCTGAAAATATATA * * * 56633921 GCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACT 1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT 56633985 AAGTGTGCG 66 AAGTGTGCG 56633994 GATTCACTAT Statistics Matches: 67, Mismatches: 6, Indels: 1 0.91 0.08 0.01 Matches are distributed among these distances: 88 52 0.78 89 15 0.22 ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25 Consensus pattern (89 bp): GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT AAGTGTGCGAGCTGAAAATATATA Found at i:56634005 original size:29 final size:29 Alignment explanation

Indices: 56633862--56633993 Score: 246 Period size: 29 Copynumber: 4.5 Consensus size: 29 56633852 AAAATTGTAC * 56633862 AGCACTAAGTGTGCGAACTGAAAATATAT 1 AGCACTAAGTGTGCGAGCTGAAAATATAT 56633891 AGCACTAAGTGTGCGAGCTGAAAATATAT 1 AGCACTAAGTGTGCGAGCTGAAAATATAT 56633920 AGCACTAAGTGTGCGAGCTGAAAATTATAT 1 AGCACTAAGTGTGCGAGCTGAAAA-TATAT 56633950 AGCACTAAGTGTGCGAGCTGAAAATATAT 1 AGCACTAAGTGTGCGAGCTGAAAATATAT 56633979 AGCACTAAGTGTGCG 1 AGCACTAAGTGTGCG 56633994 GATTCACTAT Statistics Matches: 101, Mismatches: 1, Indels: 2 0.97 0.01 0.02 Matches are distributed among these distances: 29 72 0.71 30 29 0.29 ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24 Consensus pattern (29 bp): AGCACTAAGTGTGCGAGCTGAAAATATAT Found at i:56640210 original size:18 final size:19 Alignment explanation

Indices: 56640189--56640224 Score: 56 Period size: 18 Copynumber: 1.9 Consensus size: 19 56640179 AATAAAGAAA * 56640189 GGAATTAAA-AAGAAAAGG 1 GGAATAAAATAAGAAAAGG 56640207 GGAATAAAATAAGAAAAG 1 GGAATAAAATAAGAAAAG 56640225 AAAAAGGGGG Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 8 0.50 19 8 0.50 ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11 Consensus pattern (19 bp): GGAATAAAATAAGAAAAGG Found at i:56641619 original size:59 final size:58 Alignment explanation

Indices: 56641523--56641654 Score: 246 Period size: 59 Copynumber: 2.3 Consensus size: 58 56641513 AAAATTGTAC 56641523 AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATAT 1 AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATAT * 56641581 AGCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATAT 1 AGCACTAAGTGTGCGAACTGAAAA-TATATAGCACTAAGTGTGCGAGCTGAAAATATAT 56641640 AGCACTAAGTGTGCG 1 AGCACTAAGTGTGCG 56641655 GATTCACTAT Statistics Matches: 72, Mismatches: 1, Indels: 1 0.97 0.01 0.01 Matches are distributed among these distances: 58 23 0.32 59 49 0.68 ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24 Consensus pattern (58 bp): AGCACTAAGTGTGCGAACTGAAAATATATAGCACTAAGTGTGCGAGCTGAAAATATAT Found at i:56641643 original size:88 final size:89 Alignment explanation

Indices: 56641493--56641654 Score: 263 Period size: 88 Copynumber: 1.8 Consensus size: 89 56641483 GACAAGATTG * * * 56641493 GCACTAAGTGTGCGGGTTTAAAAATTGTACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT 1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT 56641558 AAGTGTGCGAGCTGAAAATATATA 66 AAGTGTGCGAGCTGAAAATATATA * * * 56641582 GCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATAGCACT 1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT 56641646 AAGTGTGCG 66 AAGTGTGCG 56641655 GATTCACTAT Statistics Matches: 67, Mismatches: 6, Indels: 1 0.91 0.08 0.01 Matches are distributed among these distances: 88 52 0.78 89 15 0.22 ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25 Consensus pattern (89 bp): GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATAGCACT AAGTGTGCGAGCTGAAAATATATA Found at i:56641666 original size:29 final size:29 Alignment explanation

Indices: 56641523--56641654 Score: 246 Period size: 29 Copynumber: 4.5 Consensus size: 29 56641513 AAAATTGTAC * 56641523 AGCACTAAGTGTGCGAACTGAAAATATAT 1 AGCACTAAGTGTGCGAGCTGAAAATATAT 56641552 AGCACTAAGTGTGCGAGCTGAAAATATAT 1 AGCACTAAGTGTGCGAGCTGAAAATATAT 56641581 AGCACTAAGTGTGCGAGCTGAAAATTATAT 1 AGCACTAAGTGTGCGAGCTGAAAA-TATAT 56641611 AGCACTAAGTGTGCGAGCTGAAAATATAT 1 AGCACTAAGTGTGCGAGCTGAAAATATAT 56641640 AGCACTAAGTGTGCG 1 AGCACTAAGTGTGCG 56641655 GATTCACTAT Statistics Matches: 101, Mismatches: 1, Indels: 2 0.97 0.01 0.02 Matches are distributed among these distances: 29 72 0.71 30 29 0.29 ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24 Consensus pattern (29 bp): AGCACTAAGTGTGCGAGCTGAAAATATAT Found at i:56645263 original size:93 final size:93 Alignment explanation

Indices: 56645149--56645319 Score: 288 Period size: 93 Copynumber: 1.8 Consensus size: 93 56645139 GCCCATAAGT * * 56645149 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTAAACTCAGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCAGACTCAACTCAA 56645214 CGAGCTCGGATGCCTAGTTACATCTCTC 66 CGAGCTCGGATGCCTAGTTACATCTCTC * * * 56645242 GAACTCGGACTCAACTTAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCAGACTCAACTCAA * 56645307 CGAGTTCGGATGC 66 CGAGCTCGGATGC 56645320 TCAACCATCC Statistics Matches: 72, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 93 72 1.00 ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCAGACTCAACTCAA CGAGCTCGGATGCCTAGTTACATCTCTC Found at i:56645316 original size:46 final size:46 Alignment explanation

Indices: 56645141--56645316 Score: 178 Period size: 46 Copynumber: 3.8 Consensus size: 46 56645131 TGTAACCCGC * * * 56645141 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT 1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT * * 56645187 CCATAAGTAAACTCAGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT 1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACATTCGC-A--T * *** * * * 56645233 ACATCTCTCGAACTCGGACTCAACTTAACGAGTTCGGACATTCGCAT 1 CCATAAGT-GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT * 56645280 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA 1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGA 56645317 TGCTCAACCA Statistics Matches: 104, Mismatches: 19, Indels: 14 0.76 0.14 0.10 Matches are distributed among these distances: 43 1 0.01 44 3 0.03 46 66 0.63 47 29 0.28 49 4 0.04 50 1 0.01 ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22 Consensus pattern (46 bp): CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT Found at i:56647594 original size:30 final size:29 Alignment explanation

Indices: 56647550--56647638 Score: 94 Period size: 30 Copynumber: 3.0 Consensus size: 29 56647540 CAAAGATAAC 56647550 AAGAAAACC-GAATAAAGAAATCCAAGAT 1 AAGAAAACCAGAATAAAGAAATCCAAGAT * 56647578 AGAGAAACCCAGAATAAAGAAATCC-AGAAT 1 A-AGAAAACCAGAATAAAGAAATCCAAG-AT * * 56647608 AA-AAAGATCCAGGATAAAGAAACCCAAGAT 1 AAGAAA-A-CCAGAATAAAGAAATCCAAGAT 56647638 A 1 A 56647639 CGATACTATG Statistics Matches: 51, Mismatches: 4, Indels: 10 0.78 0.06 0.15 Matches are distributed among these distances: 28 4 0.08 29 10 0.20 30 35 0.69 31 2 0.04 ACGTcount: A:0.58, C:0.16, G:0.16, T:0.10 Consensus pattern (29 bp): AAGAAAACCAGAATAAAGAAATCCAAGAT Found at i:56647598 original size:15 final size:15 Alignment explanation

Indices: 56647550--56647629 Score: 85 Period size: 15 Copynumber: 5.4 Consensus size: 15 56647540 CAAAGATAAC * 56647550 AAGAAAACC-GAATA 1 AAGAAATCCAGAATA 56647564 AAGAAATCCA-AGATA 1 AAGAAATCCAGA-ATA * * 56647579 GAGAAACCCAGAATA 1 AAGAAATCCAGAATA 56647594 AAGAAATCCAGAATA 1 AAGAAATCCAGAATA * 56647609 AA-AAGATCCAGGATA 1 AAGAA-ATCCAGAATA 56647624 AAGAAA 1 AAGAAA 56647630 CCCAAGATAC Statistics Matches: 55, Mismatches: 6, Indels: 9 0.79 0.09 0.13 Matches are distributed among these distances: 14 11 0.20 15 41 0.75 16 3 0.05 ACGTcount: A:0.60, C:0.14, G:0.16, T:0.10 Consensus pattern (15 bp): AAGAAATCCAGAATA Found at i:56647638 original size:15 final size:15 Alignment explanation

Indices: 56647561--56647638 Score: 72 Period size: 15 Copynumber: 5.2 Consensus size: 15 56647551 AGAAAACCGA 56647561 ATAAAGAAATCCAAG 1 ATAAAGAAATCCAAG * * 56647576 ATAGAGAAA-CCCAG 1 ATAAAGAAATCCAAG 56647590 AATAAAGAAATCC-AG 1 -ATAAAGAAATCCAAG * 56647605 AATAAA-AAGATCCAGG 1 -ATAAAGAA-ATCCAAG * 56647621 ATAAAGAAACCCAAG 1 ATAAAGAAATCCAAG 56647636 ATA 1 ATA 56647639 CGATACTATG Statistics Matches: 52, Mismatches: 6, Indels: 10 0.76 0.09 0.15 Matches are distributed among these distances: 14 6 0.12 15 41 0.79 16 5 0.10 ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12 Consensus pattern (15 bp): ATAAAGAAATCCAAG Found at i:56650702 original size:93 final size:93 Alignment explanation

Indices: 56650574--56650744 Score: 288 Period size: 93 Copynumber: 1.8 Consensus size: 93 56650564 GCCCATACGT * * * 56650574 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 56650639 CGAGCTCGGATGCCTAGTTACATCTCTC 66 CGAGCTCGGATGCCTAGTTACATCTCTC * * 56650667 GAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA * 56650732 CGAGTTCGGATGC 66 CGAGCTCGGATGC 56650745 TCAACCATCC Statistics Matches: 72, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 93 72 1.00 ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGCTCGGATGCCTAGTTACATCTCTC Found at i:56650741 original size:46 final size:46 Alignment explanation

Indices: 56650566--56650741 Score: 187 Period size: 46 Copynumber: 3.8 Consensus size: 46 56650556 TGTAACCCGC * * * * 56650566 CCATACGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT * 56650612 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T * *** * * 56650658 ACATCTCTCGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCAT 1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT * 56650705 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA 56650742 TGCTCAACCA Statistics Matches: 107, Mismatches: 16, Indels: 14 0.78 0.12 0.10 Matches are distributed among these distances: 43 1 0.01 44 3 0.03 46 67 0.63 47 31 0.29 49 4 0.04 50 1 0.01 ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT Found at i:56650760 original size:46 final size:46 Alignment explanation

Indices: 56650572--56650760 Score: 124 Period size: 46 Copynumber: 4.1 Consensus size: 46 56650562 CCGCCCATAC * ** * * 56650572 GTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTC--GCATCCATAA 1 GTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCAACCATCC-T-A 56650618 GTGAACTCGGACTCAACTCAACGAGCTCGGATGC-CTAGTTA-CATCTCT- 1 GTGAACTCGGACTCAACTCAACGAGCTCGGATGCTC-A---ACCATC-CTA * * * * * * * 56650666 -CGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--AA 1 GTGAACTCGGACTCAACTCAACGAGCTCGG--ATGCTCAACCATCCTA * 56650711 GTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTA 1 GTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCAACCATCCTA 56650757 GTGA 1 GTGA 56650761 CATGTCACTT Statistics Matches: 112, Mismatches: 16, Indels: 30 0.71 0.10 0.19 Matches are distributed among these distances: 44 9 0.08 45 1 0.01 46 62 0.55 47 29 0.26 49 4 0.04 50 6 0.05 51 1 0.01 ACGTcount: A:0.28, C:0.29, G:0.21, T:0.23 Consensus pattern (46 bp): GTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCAACCATCCTA Found at i:56653241 original size:17 final size:18 Alignment explanation

Indices: 56653206--56653248 Score: 61 Period size: 17 Copynumber: 2.4 Consensus size: 18 56653196 ATTCTTTTCC 56653206 ATTTTCTCTATTTTCGTT 1 ATTTTCTCTATTTTCGTT * 56653224 ATTTTCTCT-TTTTTGTT 1 ATTTTCTCTATTTTCGTT * 56653241 ATATTCTC 1 ATTTTCTC 56653249 CTACCCGTTG Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 17 14 0.61 18 9 0.39 ACGTcount: A:0.12, C:0.16, G:0.05, T:0.67 Consensus pattern (18 bp): ATTTTCTCTATTTTCGTT Found at i:56653678 original size:16 final size:16 Alignment explanation

Indices: 56653659--56653689 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 56653649 TTCGATGAAA 56653659 TTCGAAAGTACATTCT 1 TTCGAAAGTACATTCT * 56653675 TTCGAAAGTGCATTC 1 TTCGAAAGTACATTC 56653690 CCGATGCCAC 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:0.29, C:0.19, G:0.16, T:0.35 Consensus pattern (16 bp): TTCGAAAGTACATTCT Found at i:56657965 original size:28 final size:27 Alignment explanation

Indices: 56657899--56657967 Score: 102 Period size: 27 Copynumber: 2.5 Consensus size: 27 56657889 ATAGTGAGTC * 56657899 CGCACACTTAGTGCTATATAATCAACT 1 CGCACACTTAGTGCTACATAATCAACT * 56657926 CGCACACTTAGTGCTACATGATCAAACT 1 CGCACACTTAGTGCTACATAATC-AACT * 56657954 CGCACACCTAGTGC 1 CGCACACTTAGTGC 56657968 CATTCTCATG Statistics Matches: 38, Mismatches: 3, Indels: 1 0.90 0.07 0.02 Matches are distributed among these distances: 27 21 0.55 28 17 0.45 ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25 Consensus pattern (27 bp): CGCACACTTAGTGCTACATAATCAACT Found at i:56667280 original size:39 final size:39 Alignment explanation

Indices: 56667234--56667375 Score: 205 Period size: 40 Copynumber: 3.6 Consensus size: 39 56667224 TGAATGATAC 56667234 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATATAT 1 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATATAT 56667273 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGA-TATAT * ** * * 56667313 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATATAT * 56667353 CCGGGCTAAG-ACCGAAGGCATTT 1 CCGGGCTAAGTCCCGAAGGCATTT 56667376 GTGCAAGTTA Statistics Matches: 94, Mismatches: 7, Indels: 4 0.90 0.07 0.04 Matches are distributed among these distances: 39 45 0.48 40 47 0.50 41 2 0.02 ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26 Consensus pattern (39 bp): CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATATAT Found at i:56667328 original size:40 final size:40 Alignment explanation

Indices: 56667234--56667438 Score: 231 Period size: 39 Copynumber: 5.2 Consensus size: 40 56667224 TGAATGATAC * * 56667234 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGA-TATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT * * 56667273 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT * * 56667313 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT * * ** * 56667353 CCGGGCTAAGA-CCGAAGGCATTTGTGCAAGTTACCAAAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT * * * * 56667392 CCGGGTTAAGACCCGAA-GCAATTGTGCTTGTGGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT 56667431 CC-GGCTAA 1 CCGGGCTAA 56667439 ATTCCGAAGA Statistics Matches: 142, Mismatches: 20, Indels: 9 0.83 0.12 0.05 Matches are distributed among these distances: 38 6 0.04 39 80 0.56 40 54 0.38 41 2 0.01 ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26 Consensus pattern (40 bp): CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT Found at i:56667368 original size:79 final size:79 Alignment explanation

Indices: 56667234--56667447 Score: 229 Period size: 79 Copynumber: 2.7 Consensus size: 79 56667224 TGAATGATAC * * * * 56667234 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATATATCCGGGCTAAGTCCCGAAGGCATTTA 1 CCGGGCTAAGACCCGAAGGCA-TTGTGCTAGTTGTTATATCCGGGCTAAGTACCGAAGGCATTTA * ** * 56667298 TGCTAGTGATTATAT 65 TGCAAGTGACCAAAT * * 56667313 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATATCCGGGCTAAG-ACCGAAGGCATTTG 1 CCGGGCTAAGACCCGAAGGCATT-GTGCTAGTTGTTATATCCGGGCTAAGTACCGAAGGCATTTA * 56667377 TGCAAGTTACCAAAT 65 TGCAAGTGACCAAAT * * * * * 56667392 CCGGGTTAAGACCCGAA-GCAATTGTGCTTGTGGTTATATCC-GGCTAAATTCCGAAG 1 CCGGGCTAAGACCCGAAGGC-ATTGTGCTAGTTGTTATATCCGGGCTAAGTACCGAAG 56667448 AGACTCGGTT Statistics Matches: 114, Mismatches: 17, Indels: 9 0.81 0.12 0.06 Matches are distributed among these distances: 77 6 0.05 78 25 0.22 79 66 0.58 80 17 0.15 ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26 Consensus pattern (79 bp): CCGGGCTAAGACCCGAAGGCATTGTGCTAGTTGTTATATCCGGGCTAAGTACCGAAGGCATTTAT GCAAGTGACCAAAT Found at i:56671388 original size:42 final size:42 Alignment explanation

Indices: 56671275--56671422 Score: 190 Period size: 43 Copynumber: 3.5 Consensus size: 42 56671265 TACAAACACA * 56671275 ATATCCCAGATATGGTCTTACATGTAATCTCATATCGATGCC 1 ATATCCCAGATATGGTCTTACATGAAATCTCATATCGATGCC * * * 56671317 AATAGCCCAGCTATGGTCTTACATGAAATCTCATATAGATGCC 1 -ATATCCCAGATATGGTCTTACATGAAATCTCATATCGATGCC * ** * 56671360 ATATCCCAAATATGGTCTTACAAAAAATCTCATA-CGATGTC 1 ATATCCCAGATATGGTCTTACATGAAATCTCATATCGATGCC * * 56671401 TTATCCCAGATATGGTGTTACA 1 ATATCCCAGATATGGTCTTACA 56671423 CATAGTCTTA Statistics Matches: 91, Mismatches: 14, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 41 24 0.26 42 29 0.32 43 38 0.42 ACGTcount: A:0.32, C:0.22, G:0.14, T:0.31 Consensus pattern (42 bp): ATATCCCAGATATGGTCTTACATGAAATCTCATATCGATGCC Found at i:56678401 original size:2 final size:2 Alignment explanation

Indices: 56678394--56678423 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 56678384 ATGTTTTGTG 56678394 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 56678424 TTAGCCATGT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:56682446 original size:32 final size:32 Alignment explanation

Indices: 56682410--56682478 Score: 86 Period size: 32 Copynumber: 2.2 Consensus size: 32 56682400 TAGGTGTGGC * * 56682410 CGTGTGGG-TCACACGGACTAGGCCAAGCTGGG 1 CGTGTGGGCT-ACACGGACAAAGCCAAGCTGGG * * 56682442 CGTGTGGGCTACACGGGCAAAGCCAATCTGGG 1 CGTGTGGGCTACACGGACAAAGCCAAGCTGGG 56682474 CGTGT 1 CGTGT 56682479 AGGCCCATAA Statistics Matches: 32, Mismatches: 4, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 32 31 0.97 33 1 0.03 ACGTcount: A:0.19, C:0.25, G:0.39, T:0.17 Consensus pattern (32 bp): CGTGTGGGCTACACGGACAAAGCCAAGCTGGG Found at i:56685468 original size:33 final size:33 Alignment explanation

Indices: 56685426--56685491 Score: 114 Period size: 33 Copynumber: 2.0 Consensus size: 33 56685416 GCTTTTTAAT 56685426 ATTCTAAATACAATTTAAAAATACATGAAAAAA 1 ATTCTAAATACAATTTAAAAATACATGAAAAAA * * 56685459 ATTCTAAATACAATTTAAAAATGCATGATAAAA 1 ATTCTAAATACAATTTAAAAATACATGAAAAAA 56685492 TTTAACTCCG Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 33 31 1.00 ACGTcount: A:0.58, C:0.09, G:0.05, T:0.29 Consensus pattern (33 bp): ATTCTAAATACAATTTAAAAATACATGAAAAAA Found at i:56685601 original size:13 final size:13 Alignment explanation

Indices: 56685583--56685609 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 56685573 TAAACCCTTT 56685583 AAATTAAGTTCTA 1 AAATTAAGTTCTA 56685596 AAATTAAGTTCTA 1 AAATTAAGTTCTA 56685609 A 1 A 56685610 TTATAAATTC 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:0.48, C:0.07, G:0.07, T:0.37 Consensus pattern (13 bp): AAATTAAGTTCTA Found at i:56686082 original size:2 final size:2 Alignment explanation

Indices: 56686075--56686111 Score: 74 Period size: 2 Copynumber: 18.5 Consensus size: 2 56686065 AACATGCCAC 56686075 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 56686112 GGTAGAAGTA Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:56686610 original size:573 final size:553 Alignment explanation

Indices: 56685636--56688368 Score: 2059 Period size: 573 Copynumber: 5.0 Consensus size: 553 56685626 AAATTACAAG * * * 56685636 ATGGGTTTATAGAAGTTTCATGATAAAAATAATAATA-TTT-T------AT-ACACAATAGATGA 1 ATGGGTTTACAGTAGTTTCATGATAAAAATAATAATATTTTATAACAAGATGACACAATAGGTGA * * *** * * * 56685692 AATCGTCGTATCAGTTTTTTTT-ATTAAAATTGTTTCAGCAATAATTTCATTATAAAAAGAATAA 66 AATCGTTGTATCAATTTTTTTTAATTAAAATTGCCACCGCAACAATTTCATGAT--AAA-AATAA * * * * * * ** * * 56685756 TATTTTTATATTAAGACGATACAATGGGTGCAATCGTTGTACCAGGCGGCAGTTTCTCATATAAA 128 TAATTTTATAATAAGACGACAAAATGGGTGAAACCGTCATATCAGGCGGCAATTTCTCATAT-AA * * * * * 56685821 AAAAAATATTTTCAAAGCCGAACATTACACCCTTGACATGTTTTAACATTTCTTAAAAAAAA-AT 192 AAAATAT-TTTTCAAAGCCGAACGTTACACCCTTGACATGTTTTAACAATTC-CAAAAAAAATTT * * * * * * * * * 56685885 TTTGAGGCGTTACACCCTTAAAG-TGAAACGTTCCTCTCTTCTTTGTCCCTTAGTT-GTATTTGC 255 TTTGGGGCATTACACCCTTAAAGCCG-AATGTTCCTCACTTCTTTCTTCCTTGGTTCG-GTTTGC * * 56685948 AC---G-AAA-A---AAA-------G-TTTTACCACCTATTCTCATTATCACATATGTTCTATTT 318 ACGAAGAAAAGATGGAAATGTTTTTGTTTTTGCCACCTATTCCCATTATCACATATGTTCTATTT 56685997 AATTAAATTTTCATTTTATAATTTTAATTACTAATGTTTTATAATATAGCATACATACTTACTTC 383 AATTAAATTTTCATTTTATAATTTTAATTACTAATGTTTTATAATATAGCATACATACTTACTTC 56686062 AATAACATGCCACATATATATATATATATATATATATATATATATATATAGGTAGAAGTACTATT 448 AATAACA-GCCAC--------------ATATATAT-TATATATATATATAGGTAGAA-TACTATT * 56686127 TAACCCCTTTAAATTAAGTTCTAATTATAAATCTTTAAGCAAGTTACAAGATGATACA 496 TAACCCCTTTAAATTAAGTTCTAATTATAAATCTTTAAGCAAATTACAAGATGATACA * *** * * * * 56686185 ATGGGTATACAACGGTTTCATGATAATAATAATAATATTTTATAATAAGATGGCACAATGGGTGA 1 ATGGGTTTACAGTAGTTTCATGATAAAAATAATAATATTTTATAACAAGATGACACAATAGGTGA * * 56686250 AATCGTTGTATCAATTTTTTTTAATTAAAATTGCCACGGCAACAATTTCATGATAATAATAATAA 66 AATCGTTGTATCAATTTTTTTTAATTAAAATTGCCACCGCAACAATTTCATGATAAAAATAATAA * * * * * 56686315 TTTTATAACAAGACGACAAAATGCGTGGAATCGTCATATCAGGTGGCAATTTCTCATATAAAAAA 131 TTTTATAATAAGACGACAAAATGGGTGAAACCGTCATATCAGGCGGCAATTTCTCATATAAAAAA * * ** ** 56686380 TATTTTTAAAAAGCCGAACATTACACCCTTGACATGTTTTAACACCTCCAAAAACGATTTTTTGG 196 TATTTTT-CAAAGCCGAACGTTACACCCTTGACATGTTTTAACAATTCCAAAAAAAATTTTTT-- * * * 56686445 GGGGCATTACACCCTTAAAGCCGAATGTTCCTCACTTCCTTATTGCTTGGTTCGGTTTGCACGAA 258 GGGGCATTACACCCTTAAAGCCGAATGTTCCTCACTTCTTTCTTCCTTGGTTCGGTTTGCACGAA * * * 56686510 GAAAAGATGGAAATGTCTTTGCTTTTGCCACCTATTCCCATTATCACATATGTTATATTTAATTA 323 GAAAAGATGGAAATGTTTTTGTTTTTGCCACCTATTCCCATTATCACATATGTTCTATTTAATTA *** * 56686575 AATTTTCATTTTATAATTTTAATTACGGGTGTTTTATAATATAACATACATACTTACTTCAATAG 388 AATTTTCATTTTATAATTTTAATTACTAATGTTTTATAATATAGCATACATACTTACTTCAATA- * * * ** * 56686640 CCCGCCACATATATATTCTAGGTATA-AT---T---ATA--ATTTAACCCCTTTAAATTAAGTTT 452 ACAGCCACATATATATTATATATATATATAGGTAGAATACTATTTAACCCCTTTAAATTAAGTTC * * 56686696 TAATTATACATCCTTAAGCAAATTACAAGATGATACA 517 TAATTATAAATCTTTAAGCAAATTACAAGATGATACA * * * * * * * 56686733 ATGAGTTTATAGTAATTTCATAATAAAAATAATAATAATTTATAACAAGATAACACAAAAGGTGA 1 ATGGGTTTACAGTAGTTTCATGATAAAAATAATAATATTTTATAACAAGATGACACAATAGGTGA * * * * 56686798 AACTGTCGTAATATAT-ATATATATATATATATATATATTTTGTTAAAATTGCCTCTGCAACGAT 66 AA---TCGT--TGTATCA-AT-T-T-T-T-T-T-TA-A-----TTAAAATTGCCACCGCAACAAT * * * 56686862 TTCATGATAAAAATAATACTATTTTTATAATAAAACGTCACAATGGGTGAAACCGTCGA-ATCAG 112 TTCATGATAAAAATAATA--A-TTTTATAATAAGACGACAAAATGGGTGAAACCGTC-ATATCAG * * ** * * * 56686926 GCGACAGTTTCTCATATAAAAAA-ATATTTTCAAAGTTTGAACGTTACACCTTTGACTTATTTTA 173 GCGGCAATTTCTCATATAAAAAATAT-TTTTCAAAG-CCGAACGTTACACCCTTGACATGTTTTA * ***** * * * * 56686990 ACATTTCCAAAACAAAAAAAAAAAAAAAT-GGGCGTTACACCCTTAAAGCCAAACT-TTTCTCTC 236 ACAATT-C----C--AAAAAAAATTTTTTGGGGCATTACACCCTTAAAGCCGAA-TGTTCCTCAC * * * 56687053 TTCTTTCCTCCTTGGTTCGGTTTGCACCAAGGAAAGATGGAAATGTTTTTGTTTTTGCCACCTAT 293 TTCTTTCTTCCTTGGTTCGGTTTGCACGAAGAAAAGATGGAAATGTTTTTGTTTTTGCCACCTAT * * * 56687118 TCCCATTATCACTTATGTTCTATTTAATTAAAATTTCATTTTATAATTTTAATTCCTAATGTTTT 358 TCCCATTATCACATATGTTCTATTTAATTAAATTTTCATTTTATAATTTTAATTACTAATGTTTT * * 56687183 ATAATATAGCATACATACTAACTTCAATAACCAG-C-C---------ATATATAT-TCTAGGTAG 423 ATAATATAGCATACATACTTACTTCAATAA-CAGCCACATATATATTATATATATATATAGGTAG * * * * * * 56687236 AATGACTATTTAACCTCTTTTAACTTAAGTTCTATTTACAAATCCTTCAA-CAAATTATAAGATG 487 AAT-ACTATTTAACC-CCTTTAAATTAAGTTCTAATTATAAAT-CTTTAAGCAAATTACAAGATG * * 56687300 ACATA 549 ATACA * 56687305 ATGGGTTTACAGTAGTTCCATGATAAAAATAATAATATTTTATAACAAGATGACACAATAGGTGA 1 ATGGGTTTACAGTAGTTTCATGATAAAAATAATAATATTTTATAACAAGATGACACAATAGGTGA ** * * * * 56687370 ACCCCTCGTATC-ATTTTTTTT-GTTAAAATTGTCACCGCAACAATTTCATGATACAAAGAATAA 66 AATCGTTGTATCAATTTTTTTTAATTAAAATTGCCACCGCAACAATTTCATGAT--AAA-AATAA * * * * * * * * 56687433 TATTTTTATAATAAGATGA-AAGGATGGGTGTAACCATCGTATAAGGCGGCATTTTCTCATATAA 128 TAATTTTATAATAAGACGACAA-AATGGGTGAAACCGTCATATCAGGCGGCAATTTCTCATATAA * * 56687497 GAAAATA-TTTTCATATCCGAACGTTACACCCTTG-CATGTTTTAACAATTCCAAGAACAAAATT 192 -AAAATATTTTTCAAAGCCGAACGTTACACCCTTGACATGTTTTAACAATTCCAA-AA-AAAATT * * * * 56687560 TTTTGGGGCATTACACCCTTAAAGCCGAACGTTCCTCATTTCTTTCTCCCTTGGTTCGATTTGCA 254 TTTTGGGGCATTACACCCTTAAAGCCGAATGTTCCTCACTTCTTTCTTCCTTGGTTCGGTTTGCA * * * 56687625 TGAAGAAAAGATGGAAATGTTTTTGTTTTTGCCACCTATTTCCATTATCACTTATGTTCTATTTA 319 CGAAGAAAAGATGGAAATGTTTTTGTTTTTGCCACCTATTCCCATTATCACATATGTTCTATTTA * * 56687690 ATTAAATTTTAATTTTATAATTTTAATTACTAATGTTTTATAATAT---AT-CATACTTACTTTA 384 ATTAAATTTTCATTTTATAATTTTAATTACTAATGTTTTATAATATAGCATACATACTTACTTCA * * 56687751 ATAACCAG-C-CATATATATTAT-TGGTATA-AT---T---AT--TGTTTAACCCCTTTAAATT- 449 ATAA-CAGCCACATATATATTATAT-ATATATATAGGTAGAATACTATTTAACCCCTTTAAATTA * * * * 56687803 AG-----A-TATAAATCCTTAAGTAAATTACAAAATGACACA 512 AGTTCTAATTATAAATCTTTAAGCAAATTACAAGATGATACA * * * 56687839 ATGGGTTTACAGCAGTTTCATGATAAAAATAATAATATTTTATAACAAGATAACACAATGGGTGA 1 ATGGGTTTACAGTAGTTTCATGATAAAAATAATAATATTTTATAACAAGATGACACAATAGGTGA * ** ** * * * 56687904 AATTGTCATATCAATTTTTTTTTTGTTAAAATTGCCTCCGCAACAATTTCATGTTAAAAATGATA 66 AATCGTTGTATCAA-TTTTTTTTAATTAAAATTGCCACCGCAACAATTTCATGATAAAAATAATA * * * * * * 56687969 ATATTT-T--T-ATA--AC--AA-----G--A-CGACACA--ATGAGGCAGTTTCTCATATAAAA 130 AT-TTTATAATAAGACGACAAAATGGGTGAAACCGTCATATCAGGCGGCAATTTCTCATATAAAA * * * * * * * * 56688016 AAAATATTGTAAAAGTCGAACGTTACACACTTGACATGTTTTAACATTTCAAAAAATAAAAATTT 194 AATAT-TTTTCAAAGCCGAACGTTACACCCTTGACATGTTTTAACAATTC-CAAAA-AAAATTTT ** * * * * * * * * 56688081 TTCTGGCATTACACTCTTAAAACAGAA-GTTACTCTCTTATTTC-TCACTTGATTTGGTTTGCAC 256 TTGGGGCATTACACCCTTAAAGCCGAATGTTCCTCACTTCTTTCTTC-CTTGGTTCGGTTTGCAC * * * * 56688144 AAAGAAAAGATGGAAA---TATT-TTTTTCCCACCTATTCCCATTATCACTTATGTTCTATTTAA 320 GAAGAAAAGATGGAAATGTTTTTGTTTTTGCCACCTATTCCCATTATCACATATGTTCTATTTAA * * * 56688205 -TAAAATTTCATTTTATAATTTTAATTACAAATGTTTTATAATATAGCATACAAACTTACTTCAA 385 TTAAATTTTCATTTTATAATTTTAATTACTAATGTTTTATAATATAGCATACATACTTACTTCAA * * * 56688269 TAACAG--AC-----CA-TATATATAT-TCTAGGTATAATTACTATTTAACCCCTTTAAATTAAG 450 TAACAGCCACATATATATTATATATATATATAGGTAGAA-TACTATTTAACCCCTTTAAATTAAG * * 56688325 TTCTAATTAAAAAT-TCTTAAGCAAATTACAAGATGACACA 514 TTCTAATTATAAATCT-TTAAGCAAATTACAAGATGATACA 56688365 ATGG 1 ATGG 56688369 TTGAAACCGC Statistics Matches: 1759, Mismatches: 288, Indels: 297 0.75 0.12 0.13 Matches are distributed among these distances: 510 7 0.00 511 2 0.00 513 42 0.02 514 39 0.02 515 3 0.00 516 12 0.01 517 35 0.02 518 61 0.03 519 67 0.04 520 5 0.00 522 1 0.00 525 1 0.00 526 32 0.02 527 1 0.00 529 1 0.00 531 2 0.00 532 1 0.00 533 4 0.00 534 97 0.06 535 7 0.00 536 8 0.00 537 28 0.02 540 2 0.00 541 8 0.00 542 29 0.02 543 4 0.00 544 2 0.00 545 8 0.00 546 154 0.09 548 110 0.06 549 32 0.02 550 18 0.01 551 28 0.02 552 81 0.05 553 10 0.01 554 16 0.01 555 57 0.03 556 56 0.03 557 54 0.03 558 40 0.02 559 35 0.02 560 4 0.00 561 5 0.00 562 8 0.00 563 1 0.00 564 1 0.00 565 5 0.00 566 38 0.02 567 3 0.00 568 9 0.01 569 86 0.05 570 2 0.00 571 9 0.01 572 97 0.06 573 281 0.16 574 3 0.00 576 7 0.00 ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37 Consensus pattern (553 bp): ATGGGTTTACAGTAGTTTCATGATAAAAATAATAATATTTTATAACAAGATGACACAATAGGTGA AATCGTTGTATCAATTTTTTTTAATTAAAATTGCCACCGCAACAATTTCATGATAAAAATAATAA TTTTATAATAAGACGACAAAATGGGTGAAACCGTCATATCAGGCGGCAATTTCTCATATAAAAAA TATTTTTCAAAGCCGAACGTTACACCCTTGACATGTTTTAACAATTCCAAAAAAAATTTTTTGGG GCATTACACCCTTAAAGCCGAATGTTCCTCACTTCTTTCTTCCTTGGTTCGGTTTGCACGAAGAA AAGATGGAAATGTTTTTGTTTTTGCCACCTATTCCCATTATCACATATGTTCTATTTAATTAAAT TTTCATTTTATAATTTTAATTACTAATGTTTTATAATATAGCATACATACTTACTTCAATAACAG CCACATATATATTATATATATATATAGGTAGAATACTATTTAACCCCTTTAAATTAAGTTCTAAT TATAAATCTTTAAGCAAATTACAAGATGATACA Found at i:56686815 original size:2 final size:2 Alignment explanation

Indices: 56686808--56686835 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 56686798 AACTGTCGTA 56686808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT 56686836 TTTGTTAAAA Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:56692576 original size:2 final size:2 Alignment explanation

Indices: 56692569--56692598 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 56692559 ATAGCCCGCC 56692569 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 56692599 TCTTGGTACA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:56693811 original size:29 final size:29 Alignment explanation

Indices: 56693750--56693811 Score: 81 Period size: 29 Copynumber: 2.1 Consensus size: 29 56693740 TGTATGGTCG * 56693750 TGTGGTTGGCCGTGTACGAGACACGATCC 1 TGTGGTTGGCCGTGTACGAGACACGAGCC ** 56693779 TGTGGTTGGCCGTGTGTGAGACACG-GCC 1 TGTGGTTGGCCGTGTACGAGACACGAGCC 56693807 ATGTG 1 -TGTG 56693812 TCTAAAGAAG Statistics Matches: 29, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 28 2 0.07 29 27 0.93 ACGTcount: A:0.15, C:0.21, G:0.39, T:0.26 Consensus pattern (29 bp): TGTGGTTGGCCGTGTACGAGACACGAGCC Found at i:56702420 original size:46 final size:45 Alignment explanation

Indices: 56702369--56702677 Score: 329 Period size: 46 Copynumber: 6.7 Consensus size: 45 56702359 GGCATCCAAA * * 56702369 CTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAATGTCCGAA 1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCCGAG * *** * * * 56702415 CTCGTTGAGTTGAGTCCGACTTCGAGAGATGTAACTAG-GCA-TCTGAG 1 CTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAGTCCGAG * 56702462 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAA 1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCCGAG *** * * 56702508 CTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-TCCGAG 1 CTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAGTCCGAG * 56702555 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAG 1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCCGAG * 56702601 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAG 1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCCGAG 56702647 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG 1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG 56702678 GCGGGTTACA Statistics Matches: 220, Mismatches: 29, Indels: 28 0.79 0.10 0.10 Matches are distributed among these distances: 43 2 0.01 44 6 0.03 45 2 0.01 46 138 0.63 47 62 0.28 48 2 0.01 49 6 0.03 50 2 0.01 ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28 Consensus pattern (45 bp): CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGTCCGAG Found at i:56702477 original size:47 final size:47 Alignment explanation

Indices: 56702409--56702577 Score: 202 Period size: 47 Copynumber: 3.6 Consensus size: 47 56702399 GATGCGAATG * * 56702409 TCCGAACTCGTTGAGTTGAGTCCGACTTCGAGAGATGTAACTAGGCA 1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA * *** * * 56702456 TCTGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAA 1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA * 56702500 TGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA 1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA 56702549 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC 1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC 56702578 ACTTATGGAT Statistics Matches: 99, Mismatches: 16, Indels: 14 0.77 0.12 0.11 Matches are distributed among these distances: 43 1 0.01 44 3 0.03 45 1 0.01 46 31 0.31 47 58 0.59 48 1 0.01 49 3 0.03 50 1 0.01 ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28 Consensus pattern (47 bp): TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA Found at i:56702518 original size:93 final size:93 Alignment explanation

Indices: 56702359--56702677 Score: 455 Period size: 93 Copynumber: 3.4 Consensus size: 93 56702349 AGGATATTTG * * * 56702359 GGCATCCAAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG 1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG 56702424 TTGAGTCCGACTTCGAGAGATGTAACTA 66 TTGAGTCCGACTTCGAGAGATGTAACTA * 56702452 GGCATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG 1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG * 56702517 TTGAGTCCGAGTTCGAGAGATGTAACTA 66 TTGAGTCCGACTTCGAGAGATGTAACTA * * * 56702545 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG 1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG * *** * * * 56702610 TTGAGTCCGAGTTC-ACTTATGGATGCGAA 66 TTGAGTCCGACTTCGAGAGATGTA-AC-TA * 56702639 CGC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG 1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG 56702678 GCGGGTTACA Statistics Matches: 208, Mismatches: 16, Indels: 5 0.91 0.07 0.02 Matches are distributed among these distances: 92 41 0.20 93 164 0.79 94 3 0.01 ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28 Consensus pattern (93 bp): GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG TTGAGTCCGACTTCGAGAGATGTAACTA Found at i:56708827 original size:46 final size:45 Alignment explanation

Indices: 56708777--56708952 Score: 212 Period size: 46 Copynumber: 3.8 Consensus size: 45 56708767 TGGTTGAGCA 56708777 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G *** * * 56708823 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA- 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG * 56708870 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G * * 56708916 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG 56708953 GCGGGTTACA Statistics Matches: 111, Mismatches: 12, Indels: 14 0.81 0.09 0.10 Matches are distributed among these distances: 43 1 0.01 44 3 0.03 45 1 0.01 46 69 0.62 47 32 0.29 48 1 0.01 49 3 0.03 50 1 0.01 ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28 Consensus pattern (45 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG Found at i:56708933 original size:93 final size:93 Alignment explanation

Indices: 56708774--56708944 Score: 306 Period size: 93 Copynumber: 1.8 Consensus size: 93 56708764 GGATGGTTGA * * 56708774 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT 56708839 TGAGTCCGAGTTCGAGAGATGTAACTAG 66 TGAGTCCGAGTTCGAGAGATGTAACTAG * * 56708867 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT 56708932 TGAGTCCGAGTTC 66 TGAGTCCGAGTTC 56708945 ACTTATGGGC Statistics Matches: 74, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 93 74 1.00 ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27 Consensus pattern (93 bp): GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT TGAGTCCGAGTTCGAGAGATGTAACTAG Found at i:56712102 original size:46 final size:47 Alignment explanation

Indices: 56712002--56712217 Score: 197 Period size: 46 Copynumber: 4.7 Consensus size: 47 56711992 AGGATATTTG * 56712002 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATG-GATGCGAA-T- 1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCG---A-GAGATG-TAACTA 56712051 -G--TCCGAACTCGTTGAG-TGAGTCCGAGTTCGAGAGATGTAACTA 1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTA * *** * 56712094 GGCATCCGAGCTCGTTGAGTTGAGT-CGAGTTC-ACTTATG-GA-T- 1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTA * 56712136 GCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTA 1 G-GCA--TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTA * 56712186 GGCATCCGAGCTCGTTGA-TTGAGTCCGAGTTC 1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC 56712218 ACTTATGGAT Statistics Matches: 138, Mismatches: 14, Indels: 33 0.75 0.08 0.18 Matches are distributed among these distances: 41 3 0.02 42 7 0.05 43 3 0.02 44 2 0.01 45 38 0.28 46 57 0.41 47 22 0.16 48 2 0.01 49 3 0.02 50 1 0.01 ACGTcount: A:0.22, C:0.20, G:0.31, T:0.28 Consensus pattern (47 bp): GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTA Found at i:56712159 original size:45 final size:45 Alignment explanation

Indices: 56712006--56712270 Score: 249 Period size: 45 Copynumber: 5.8 Consensus size: 45 56711996 TATTTGGGCA * 56712006 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G *** * * 56712052 TCCGAACTCGTTGAG-TGAGTCCGAGTTCGAGAGATGTAACTAG-GCA- 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG * 56712098 TCCGAGCTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G *** * * 56712143 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA- 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG * 56712190 TCCGAGCTCGTTGA-TTGAGTCCGAGTTCACTTATGGATGCGAACG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G * 56712235 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG 56712271 GCGGGTTACA Statistics Matches: 178, Mismatches: 24, Indels: 35 0.75 0.10 0.15 Matches are distributed among these distances: 42 2 0.01 43 6 0.03 44 15 0.08 45 63 0.35 46 60 0.34 47 23 0.13 48 4 0.02 49 4 0.02 50 1 0.01 ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28 Consensus pattern (45 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG Found at i:56712168 original size:92 final size:93 Alignment explanation

Indices: 56712002--56712262 Score: 458 Period size: 92 Copynumber: 2.8 Consensus size: 93 56711992 AGGATATTTG * * 56712002 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAATGTCCGAACTCGTTGAG 1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG 56712067 -TGAGTCCGAGTTCGAGAGATGTAACTA 66 TTGAGTCCGAGTTCGAGAGATGTAACTA 56712094 GGCATCCGAGCTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG 1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG 56712158 TTGAGTCCGAGTTCGAGAGATGTAACTA 66 TTGAGTCCGAGTTCGAGAGATGTAACTA * * 56712186 GGCATCCGAGCTCGTTGA-TTGAGTCCGAGTTCACTTATGGATGCGAACG-CCGAGCTCGTTGAG 1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG 56712249 TTGAGTCCGAGTTC 66 TTGAGTCCGAGTTC 56712263 ACTTATGGGC Statistics Matches: 163, Mismatches: 4, Indels: 5 0.95 0.02 0.03 Matches are distributed among these distances: 91 71 0.44 92 92 0.56 ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28 Consensus pattern (93 bp): GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG TTGAGTCCGAGTTCGAGAGATGTAACTA Found at i:56719979 original size:13 final size:13 Alignment explanation

Indices: 56719961--56719985 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 56719951 GCTCGACAAG 56719961 GACACGCCCGTGT 1 GACACGCCCGTGT 56719974 GACACGCCCGTG 1 GACACGCCCGTG 56719986 CGGTGTGGCT 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:0.16, C:0.40, G:0.32, T:0.12 Consensus pattern (13 bp): GACACGCCCGTGT Found at i:56721963 original size:18 final size:18 Alignment explanation

Indices: 56721940--56721975 Score: 54 Period size: 18 Copynumber: 2.0 Consensus size: 18 56721930 AAAAGTAAGT * 56721940 TAAAAAGATAAATAAATA 1 TAAAAAGAAAAATAAATA * 56721958 TAAAAATAAAAATAAATA 1 TAAAAAGAAAAATAAATA 56721976 AAAGATGAAT Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22 Consensus pattern (18 bp): TAAAAAGAAAAATAAATA Found at i:56722352 original size:160 final size:160 Alignment explanation

Indices: 56722088--56722452 Score: 561 Period size: 160 Copynumber: 2.3 Consensus size: 160 56722078 GACAGTTTTA ** * * * 56722088 ACCACGGGTGGTGGGCACGATCGTGTCGCACGCCCGTGGTAATTTCTCAGTTTTTACCATGGCTT 1 ACCACGGGTGGTGGGCACGGGCGTGTCGCACGCCCGTGTTAATTTCTCAGTTTCTACCACGGCTT ** * * 56722153 ATAGACATGGGCGTGTTGTACACCGTGTCCTACTTCGTTCGCTTCTCCCACGCCTGTGTATGTAT 66 ATAGACACAGGCGTGTTGTACACCGTATCCTACTTCGTTCGCTTCTCCCACGCCCGTGTATGTAT 56722218 GCGCACGCCCGTGTTATTTCGACAATTTCG 131 GCGCACGCCCGTGTTATTTCGACAATTTCG * * 56722248 ACCACGGGTGGTGGGTACGGGCGTGTCTCACGCCCGTGTTAATTTCTCAGTTTCTACCACGGCTT 1 ACCACGGGTGGTGGGCACGGGCGTGTCGCACGCCCGTGTTAATTTCTCAGTTTCTACCACGGCTT 56722313 ATAGACACAGGCGTGTT-TCACACCGTATCCTACTTCGTTCGCTTCTCCCACGCCCGTGTATGTA 66 ATAGACACAGGCGTGTTGT-ACACCGTATCCTACTTCGTTCGCTTCTCCCACGCCCGTGTATGTA * * * 56722377 TGTGTACGCCCGTGTTATTTCGACAATTTTG 130 TGCGCACGCCCGTGTTATTTCGACAATTTCG * * * 56722408 CCCACGGGTGGTGGGCACAGGCGTGTCGCATGCCCGTGTTAATTT 1 ACCACGGGTGGTGGGCACGGGCGTGTCGCACGCCCGTGTTAATTT 56722453 GGCAGGATTG Statistics Matches: 185, Mismatches: 19, Indels: 2 0.90 0.09 0.01 Matches are distributed among these distances: 159 1 0.01 160 184 0.99 ACGTcount: A:0.16, C:0.28, G:0.26, T:0.31 Consensus pattern (160 bp): ACCACGGGTGGTGGGCACGGGCGTGTCGCACGCCCGTGTTAATTTCTCAGTTTCTACCACGGCTT ATAGACACAGGCGTGTTGTACACCGTATCCTACTTCGTTCGCTTCTCCCACGCCCGTGTATGTAT GCGCACGCCCGTGTTATTTCGACAATTTCG Found at i:56730366 original size:49 final size:49 Alignment explanation

Indices: 56730266--56730403 Score: 152 Period size: 49 Copynumber: 2.8 Consensus size: 49 56730256 ACCATTGTTA * * * * ** 56730266 ATGAGATCTCATGTAAGACCATGTCTGGGACATGGCATTGGCATTTAAG 1 ATGAGATCTCGTGTAAGACCATGTCTGGGACATAGCATCGACATCCAAG * * 56730315 ATGAGATCTCGTGTAAGACTATGTCTGGGACATAGCATCGACATCCGAG 1 ATGAGATCTCGTGTAAGACCATGTCTGGGACATAGCATCGACATCCAAG * * * * 56730364 ATGAGAGC-CAGTATAAGACCATATCTGGGACATAACATCG 1 ATGAGATCTC-GTGTAAGACCATGTCTGGGACATAGCATCG 56730404 GCGTTGATAT Statistics Matches: 75, Mismatches: 13, Indels: 2 0.83 0.14 0.02 Matches are distributed among these distances: 48 1 0.01 49 74 0.99 ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25 Consensus pattern (49 bp): ATGAGATCTCGTGTAAGACCATGTCTGGGACATAGCATCGACATCCAAG Found at i:56730523 original size:48 final size:49 Alignment explanation

Indices: 56730473--56730641 Score: 175 Period size: 48 Copynumber: 3.5 Consensus size: 49 56730463 TGTGCCAGTG * 56730473 TAAGACCATATCTGGGATATGGCATTGGCATCAG-TATGAGATCCCATG 1 TAAGACCATATCTGGGATATGGCATTGGCATCAGATATGAGATCCCATA * * * * * 56730521 TAAGACCATATCTGGGATATGACATTGGCAT-TGCTATGAGGTCCCGTA 1 TAAGACCATATCTGGGATATGGCATTGGCATCAGATATGAGATCCCATA * * * * * * * * 56730569 TAAGACCATGTCTGAGACATGCCATCGGCA-CCGACATGAGA-CTTCATA 1 TAAGACCATATCTGGGATATGGCATTGGCATCAGATATGAGATC-CCATA 56730617 TAAGACCATATCTGGGATATGGCAT 1 TAAGACCATATCTGGGATATGGCAT 56730642 CGATATGTAG Statistics Matches: 98, Mismatches: 20, Indels: 6 0.79 0.16 0.05 Matches are distributed among these distances: 47 2 0.02 48 96 0.98 ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26 Consensus pattern (49 bp): TAAGACCATATCTGGGATATGGCATTGGCATCAGATATGAGATCCCATA Found at i:56730529 original size:96 final size:96 Alignment explanation

Indices: 56730277--56730537 Score: 231 Period size: 96 Copynumber: 2.7 Consensus size: 96 56730267 TGAGATCTCA * * * * 56730277 TGTAAGACCATGTCTGGGACATGGCATTGGCATTTAAG-ATGAGATCTCGTGTAAGACTATGTCT 1 TGTAAGACCATATCTGGGACATGGCATTGGCA--T-AGTATGAGATCCCATGTAAGACCATGTCT 56730341 GGGACATAGCATCGACATCCGAGATGAGAGCCAG 63 GGGACATAGCATCGACATCCGAGATGAGAGCCAG * ** * * * * * * * * 56730375 TATAAGACCATATCTGGGACATAACATCGGCGTTGATATGTG-TGCTAGCGTAAAACCATGTCTG 1 TGTAAGACCATATCTGGGACATGGCATTGGCATAG-TATGAGATCCCA-TGTAAGACCATGTCTG * * * * * * * 56730439 GGACATGGCATCGGCGT-TGATATGTGTGCCAG 64 GGACATAGCATCGACATCCGAGATGAGAGCCAG * * 56730471 TGTAAGACCATATCTGGGATATGGCATTGGCATCAGTATGAGATCCCATGTAAGACCATATCTGG 1 TGTAAGACCATATCTGGGACATGGCATTGGCAT-AGTATGAGATCCCATGTAAGACCATGTCTGG 56730536 GA 65 GA 56730538 TATGACATTG Statistics Matches: 123, Mismatches: 35, Indels: 12 0.72 0.21 0.07 Matches are distributed among these distances: 95 1 0.01 96 61 0.50 97 35 0.28 98 26 0.21 ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26 Consensus pattern (96 bp): TGTAAGACCATATCTGGGACATGGCATTGGCATAGTATGAGATCCCATGTAAGACCATGTCTGGG ACATAGCATCGACATCCGAGATGAGAGCCAG Found at i:56730643 original size:48 final size:48 Alignment explanation

Indices: 56730266--56730643 Score: 174 Period size: 48 Copynumber: 7.8 Consensus size: 48 56730256 ACCATTGTTA * * * * * ** * 56730266 ATGAGATCTCATGTAAGACCATGTCTGGGACATGGCATTGGCATTTAAG 1 ATGAGATCCCATATAAGACCATATCTGGGATATGGCATCGGCA-TCGAC * * * * * * * * * 56730315 ATGAGATCTCGTGTAAGACTATGTCTGGGACATAGCATCGACATCCGAG 1 ATGAGATCCCATATAAGACCATATCTGGGATATGGCATCGGCAT-CGAC * * ** * * * 56730364 ATGAGA-GCCAGTATAAGACCATATCTGGGACATAACATCGGCGTTGAT 1 ATGAGATCCCA-TATAAGACCATATCTGGGATATGGCATCGGCATCGAC * * * ** * * * * * * 56730412 ATGTG-TGCTAGCGTAAAACCATGTCTGGGACATGGCATCGGCGTTGAT 1 ATGAGATCCCA-TATAAGACCATATCTGGGATATGGCATCGGCATCGAC * * * * * 56730460 ATGTG-TGCCAGTGTAAGACCATATCTGGGATATGGCATTGGCATC-AGT 1 ATGAGATCCCA-TATAAGACCATATCTGGGATATGGCATCGGCATCGA-C * * * * 56730508 ATGAGATCCCATGTAAGACCATATCTGGGATATGACATTGGCATTG-C 1 ATGAGATCCCATATAAGACCATATCTGGGATATGGCATCGGCATCGAC * * * * * * * 56730555 TATGAGGTCCCGTATAAGACCATGTCTGAGACATGCCATCGGCACCGAC 1 -ATGAGATCCCATATAAGACCATATCTGGGATATGGCATCGGCATCGAC * 56730604 ATGAGA-CTTCATATAAGACCATATCTGGGATATGGCATCG 1 ATGAGATC-CCATATAAGACCATATCTGGGATATGGCATCG 56730644 ATATGTAGAC Statistics Matches: 264, Mismatches: 56, Indels: 19 0.78 0.17 0.06 Matches are distributed among these distances: 47 2 0.01 48 184 0.70 49 78 0.30 ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26 Consensus pattern (48 bp): ATGAGATCCCATATAAGACCATATCTGGGATATGGCATCGGCATCGAC Found at i:56733651 original size:551 final size:541 Alignment explanation

Indices: 56732454--56734132 Score: 1932 Period size: 551 Copynumber: 3.1 Consensus size: 541 56732444 TCTAGGTAAC * * * * * 56732454 TTAAGTTCTAATTTTAAATCCTTAAGTAAATTACAAGATGATGCAATGGGTTTATAGTAGTTCCA 1 TTAAGTTCTAATTATAAATCCTTAAGCAAATTACAAGATGAGGCAATGGGTTTACAGTAGTTTCA * * * *** 56732519 TGATAAAAATAACAACATTTTATAACAAGATGATACAATGGGTGAAACCG--TT-GTATCAGTTT 66 TGATAAAAATAAAAATATTTTATAACAAGATGACACAATGGGTGAAACCGTATTAGT-TTTTTTT * * * * 56732581 TTTTATTAAAATT---T---TAACAATTTCATGATAAAAAGAATAATATTTTTATAATAAGATGA 130 TTTTGTTAAAATTGCCTCCGAAACAA-TTCATGATAAAAATAATAATATTTTTATAATAAGACGA * * * ** * * * 56732640 CACAATGGGTGTAACCATCGTATGAGGTGGTAGATTCTCATATAAAAAAAATATTTTCAAAGGCT 194 CACAAT-GGTG-AAACGTCGTATCAACTGGTAGTTTCTCATAT-AAAAAAATATTTTCAAAGCCA * * * * * * * * 56732705 AATGTTACACCCTTAACAAGTTTTAGCAATTACAAGAACAAAAATTTTTGGGGTGTTACACCCTT 256 AACGTTACACCCTTGACATGTTTTAACATTTCCAAAAACAAAAATTTTTGGGGCGTTACACCCTT * * * * * * * * * 56732770 AAAGCCGAAAGCTCGTCTCTTCTTTCTCACTTTGTTCGGTTTACACAAAAAAAGATGGAAATGTT 321 AAAGCCGAACGTTCCTCTCTTATTTCTCACTTGGTTCGGTTTGCAGAAGAAAAGATGGAAATCTT * * 56732835 TTTTTTTG-CATTC-TATTCCCATGATCACTTATGTTCTATTTAATTAAAATTTCATTTTATAAT 386 TTTTTTTGCCA--CGTATTCCCATTATCACTTATGTTCTATTTAATTAAATTTTCATTTTATAAT ** * * 56732898 TTTAATTACTAACATTTTATAATATAACTTACATACTTACTTCAATAACCCGCCATATATATATA 449 TTTAATTACTAATGTTTTATAATATAACATACATACTTTCTTCAATAA-CCGCC----ATATATA * * 56732963 TTCTAGGTATAATTACTATTTAGCCCCTTTGAA 509 TTCTAGGTATAATTACTATTTAACCCCTTTAAA * ** * ** * 56732996 TTAAGATCTAATTATACTTCCTTAAGCAAATTACAAGATG-GCACAATGGGTTTACAACAATTTC 1 TTAAGTTCTAATTATAAATCCTTAAGCAAATTACAAGATGAG-GCAATGGGTTTACAGTAGTTTC * 56733060 ATGATAAAAATAAAAATATTTTATAACAAGATGACACAATGGATGAAACTAACGTATTAGTTTTT 65 ATGATAAAAATAAAAATATTTTATAACAAGATGACACAATGGGTGAAAC---CGTATTAGTTTTT 56733125 TTTTTTTGTTAAAATTGCCTCCGAAACAATATCATGATAAAAATAATAATATTTTTATAATAAGA 127 TTTTTTTGTTAAAATTGCCTCCGAAACAAT-TCATGATAAAAATAATAATATTTTTATAATAAGA * * * ** 56733190 CGACACAATAGGTGAAATCGTTGTATCAATTGGCAGTTTCTCATATAAAAAAATATTTTCAAAAT 191 CGACACAAT-GGTGAAA-CGTCGTATCAACTGGTAGTTTCTCATATAAAAAAATATTTTCAAAGC * * * 56733255 CAAACATTACACCCTTGACATGTTTTAACATTTCCAAAAACAAAAGTTTTTGGGGCATTACACCC 254 CAAACGTTACACCCTTGACATGTTTTAACATTTCCAAAAACAAAAATTTTTGGGGCGTTACACCC * * 56733320 TTAAAGTCGAACGTTCCTCTCTTATTTCTCACTTGGTTCGGTTTGTATGAAGAAAAGATGGAAAT 319 TTAAAGCCGAACGTTCCTCTCTTATTTCTCACTTGGTTCGGTTTGCA-GAAGAAAAGATGGAAAT * * * * 56733385 ATTTTTGTTTTTGCCACGTATTCCCATTATTACTTATGCTCTTTTTAATTAAATTTTCATTTTAT 383 -CTTTT-TTTTTGCCACGTATTCCCATTATCACTTATGTTCTATTTAATTAAATTTTCATTTTAT * * 56733450 AGTTTTAATTAATAATGTTTTATAATATAACATACATACTTTCTTCAATAACCGACCATATATAT 446 AATTTTAATTACTAATGTTTTATAATATAACATACATACTTTCTTCAATAACCG-CCATATATAT * * 56733515 TCTTGGTATAATTATTATTTAACCCCTTTAAA 510 TCTAGGTATAATTACTATTTAACCCCTTTAAA * * * 56733547 TTAAGTTCTAGA-TATAAATCCTTAAGCAAATCACAAGATGAGGCAACGGGTTTACAGTAGTTTT 1 TTAAGTTCTA-ATTATAAATCCTTAAGCAAATTACAAGATGAGGCAATGGGTTTACAGTAGTTTC * * ** * 56733611 ATGATAAAAATAATAATATTTTATAACAAGATGGCACAATGGGTGAAACCGTCGTA-TCAATTTT 65 ATGATAAAAATAAAAATATTTTATAACAAGATGACACAATGGGTGAAACCGTATTAGT--TTTTT * * 56733675 TTTTTTGTTAAAATTGCCTCCGCAGCAAGTTCATGATAATAATAATAATAATAATACTTTTATAA 128 TTTTTTGTTAAAATTGCCTCCGAAACAA-TTCATGAT-A-AA-AATAATAAT-AT--TTTTATAA * * * * 56733740 TAAGACGACACAATGATTGAAACTGTCGAATCAAGCT-GTA-TTTCTCATGTAAAAATATATTTT 186 TAAGACGACACAATG-GTGAAAC-GTCGTATCAA-CTGGTAGTTTCTCATATAAAAAAATATTTT * * 56733803 CAAAGCCAAACGTTACACCTTTGACATGTTTTAACATTTCCAAAAA-AAAAATTGTT---GCGTT 248 CAAAGCCAAACGTTACACCCTTGACATGTTTTAACATTTCCAAAAACAAAAATTTTTGGGGCGTT * 56733864 ACACCCTTAAAGCCAAACGTTCCTCTCTTATTTCTCACTTGGTTCGGTTTGCACGAAGAAAAGAT 313 ACACCCTTAAAGCCGAACGTTCCTCTCTTATTTCTCACTTGGTTCGGTTTGCA-GAAGAAAAGAT * 56733929 GGAAATGCTTTTTTTTTGCC-TGCTATTCCCATTATCACTTATGTTCTATTTAATTAAATTTTCA 377 GGAAAT-CTTTTTTTTTGCCACG-TATTCCCATTATCACTTATGTTCTATTTAATTAAATTTTCA * * * 56733993 TTTTATAAATTTCATTACTAATGTTTTATAATATAACATACATA---T-TTCAATAATCGGCCAT 440 TTTTATAATTTTAATTACTAATGTTTTATAATATAACATACATACTTTCTTCAATAA-CCGCCAT * * * 56734054 AAATATTCTGGGTATAATTACTATTTAACCCCTTAAAA 504 ATATATTCTAGGTATAATTACTATTTAACCCCTTTAAA * 56734092 TTAAGTTCTAATTATAAATTCTTAAGCAAATTACAAGATGA 1 TTAAGTTCTAATTATAAATCCTTAAGCAAATTACAAGATGA 56734133 CATAATGGGT Statistics Matches: 974, Mismatches: 125, Indels: 73 0.83 0.11 0.06 Matches are distributed among these distances: 542 96 0.10 544 1 0.00 545 85 0.09 546 3 0.00 547 19 0.02 548 8 0.01 549 123 0.13 550 78 0.08 551 134 0.14 552 123 0.13 553 96 0.10 554 73 0.07 555 132 0.14 556 3 0.00 ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37 Consensus pattern (541 bp): TTAAGTTCTAATTATAAATCCTTAAGCAAATTACAAGATGAGGCAATGGGTTTACAGTAGTTTCA TGATAAAAATAAAAATATTTTATAACAAGATGACACAATGGGTGAAACCGTATTAGTTTTTTTTT TTTGTTAAAATTGCCTCCGAAACAATTCATGATAAAAATAATAATATTTTTATAATAAGACGACA CAATGGTGAAACGTCGTATCAACTGGTAGTTTCTCATATAAAAAAATATTTTCAAAGCCAAACGT TACACCCTTGACATGTTTTAACATTTCCAAAAACAAAAATTTTTGGGGCGTTACACCCTTAAAGC CGAACGTTCCTCTCTTATTTCTCACTTGGTTCGGTTTGCAGAAGAAAAGATGGAAATCTTTTTTT TTGCCACGTATTCCCATTATCACTTATGTTCTATTTAATTAAATTTTCATTTTATAATTTTAATT ACTAATGTTTTATAATATAACATACATACTTTCTTCAATAACCGCCATATATATTCTAGGTATAA TTACTATTTAACCCCTTTAAA Found at i:56735568 original size:40 final size:39 Alignment explanation

Indices: 56735523--56735649 Score: 130 Period size: 40 Copynumber: 3.2 Consensus size: 39 56735513 CGGAACATAA 56735523 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC * * * * 56735563 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC * * * * * 56735603 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC 56735643 CCGGATA 1 CCGGATA 56735650 AAATTTCCAG Statistics Matches: 70, Mismatches: 13, Indels: 8 0.77 0.14 0.09 Matches are distributed among these distances: 38 1 0.01 40 67 0.96 41 1 0.01 42 1 0.01 ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24 Consensus pattern (39 bp): CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC Found at i:56735667 original size:40 final size:40 Alignment explanation

Indices: 56735539--56735689 Score: 137 Period size: 40 Copynumber: 3.8 Consensus size: 40 56735529 ATAACCATGT * * * 56735539 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC- 1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAAAATCTC-CA ** ** * * 56735579 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA 1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATAAAATCTCCA * * 56735619 GCACAATTGCCTTCGGGTCTTAACCCGGATAAAATTTCCA 1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAAAATCTCCA * * 56735659 GCATAATTGTCTTCGGGAT-TTAGCCCGGATA 1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATA 56735690 TCATTCAATT Statistics Matches: 89, Mismatches: 18, Indels: 8 0.77 0.16 0.07 Matches are distributed among these distances: 39 2 0.02 40 84 0.94 41 3 0.03 ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26 Consensus pattern (40 bp): GCACAATTGCCTTCGGGTCTTAGCCCGGATAAAATCTCCA Found at i:56735673 original size:80 final size:80 Alignment explanation

Indices: 56735539--56735688 Score: 198 Period size: 80 Copynumber: 1.9 Consensus size: 80 56735529 ATAACCATGT * * 56735539 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAAAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC 56735603 CCGGATGTAGCCACTA 65 CCGGATGTAGCCACTA * * * * 56735619 GCACAATTGCCTTCGGGTCTTAACCCGGATAAAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAAAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG 56735682 CCCGGAT 64 CCCGGAT 56735689 ATCATTCAAT Statistics Matches: 61, Mismatches: 6, Indels: 6 0.84 0.08 0.08 Matches are distributed among these distances: 79 3 0.05 80 57 0.93 81 1 0.02 ACGTcount: A:0.23, C:0.27, G:0.24, T:0.27 Consensus pattern (80 bp): GCACAAATGCCTTCGGGTCTTAACCCGGATAAAATGTCTCGCACGAATGCCTTCGGGATTTAGCC CGGATGTAGCCACTA Found at i:56741930 original size:29 final size:29 Alignment explanation

Indices: 56741897--56741970 Score: 139 Period size: 29 Copynumber: 2.6 Consensus size: 29 56741887 CCTTCGAGCT 56741897 CGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA * 56741926 TGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 56741955 CGCACACTTAGTGCCA 1 CGCACACTTAGTGCCA 56741971 ATCTCGTCAC Statistics Matches: 43, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 29 43 1.00 ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27 Consensus pattern (29 bp): CGCACACTTAGTGCCATATATTTCCAGCA Found at i:56741931 original size:58 final size:58 Alignment explanation

Indices: 56741838--56741970 Score: 133 Period size: 58 Copynumber: 2.3 Consensus size: 58 56741828 ATACTCGATT * * * * * 56741838 TCGCACACTTAGTGCCATGCGATTTAAGCCCGCACACACAGTGCCATGCCCTTCGAGC 1 TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC * * * ** * * 56741896 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGC 1 TCGCACACTTAGTGCCATGAGATTT-AAGCACGCACACACAGTGCCATACACTTCCAGC * 56741954 ACGCACACTTAGTGCCA 1 TCGCACACTTAGTGCCA 56741971 ATCTCGTCAC Statistics Matches: 61, Mismatches: 13, Indels: 2 0.80 0.17 0.03 Matches are distributed among these distances: 57 4 0.07 58 57 0.93 ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25 Consensus pattern (58 bp): TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC Found at i:56747436 original size:29 final size:29 Alignment explanation

Indices: 56747403--56747476 Score: 139 Period size: 29 Copynumber: 2.6 Consensus size: 29 56747393 CCTTCGAGCT 56747403 CGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA * 56747432 TGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 56747461 CGCACACTTAGTGCCA 1 CGCACACTTAGTGCCA 56747477 ATCTCGTCAC Statistics Matches: 43, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 29 43 1.00 ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27 Consensus pattern (29 bp): CGCACACTTAGTGCCATATATTTCCAGCA Found at i:56747437 original size:58 final size:58 Alignment explanation

Indices: 56747344--56747476 Score: 133 Period size: 58 Copynumber: 2.3 Consensus size: 58 56747334 ATACTCGATT * * * * * 56747344 TCGCACACTTAGTGCCATGCGATTTAAGCCCGCACACACAGTGCCATGCCCTTCGAGC 1 TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC * * * ** * * 56747402 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGC 1 TCGCACACTTAGTGCCATGAGATTT-AAGCACGCACACACAGTGCCATACACTTCCAGC * 56747460 ACGCACACTTAGTGCCA 1 TCGCACACTTAGTGCCA 56747477 ATCTCGTCAC Statistics Matches: 61, Mismatches: 13, Indels: 2 0.80 0.17 0.03 Matches are distributed among these distances: 57 4 0.07 58 57 0.93 ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25 Consensus pattern (58 bp): TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC Found at i:56752245 original size:40 final size:39 Alignment explanation

Indices: 56752200--56752326 Score: 130 Period size: 40 Copynumber: 3.2 Consensus size: 39 56752190 CGGAACATAA 56752200 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC * * * * 56752240 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC * * * * * 56752280 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC 56752320 CCGGATA 1 CCGGATA 56752327 AATTTCCAGC Statistics Matches: 70, Mismatches: 13, Indels: 8 0.77 0.14 0.09 Matches are distributed among these distances: 38 1 0.01 40 67 0.96 41 1 0.01 42 1 0.01 ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24 Consensus pattern (39 bp): CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC Found at i:56764481 original size:2 final size:2 Alignment explanation

Indices: 56764474--56764498 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 56764464 ATTTCAATGC 56764474 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 56764499 TAACACGTAA 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:56764767 original size:18 final size:18 Alignment explanation

Indices: 56764731--56764769 Score: 51 Period size: 18 Copynumber: 2.2 Consensus size: 18 56764721 TAAATTTTAC * ** 56764731 AATTTGAATTACTTGAAT 1 AATTTGAATAACTCAAAT 56764749 AATTTGAATAACTCAAAT 1 AATTTGAATAACTCAAAT 56764767 AAT 1 AAT 56764770 AGATTAATAT Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38 Consensus pattern (18 bp): AATTTGAATAACTCAAAT Found at i:56764862 original size:11 final size:10 Alignment explanation

Indices: 56764840--56764882 Score: 59 Period size: 10 Copynumber: 4.1 Consensus size: 10 56764830 TATATTTTTT 56764840 AAATTTAAAA 1 AAATTTAAAA 56764850 AAATTTAAAA 1 AAATTTAAAA 56764860 AAATCTTAAAA 1 AAAT-TTAAAA * 56764871 AATATATAAAA 1 AA-ATTTAAAA 56764882 A 1 A 56764883 TGTTTAAAAT Statistics Matches: 30, Mismatches: 1, Indels: 3 0.88 0.03 0.09 Matches are distributed among these distances: 10 14 0.47 11 14 0.47 12 2 0.07 ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28 Consensus pattern (10 bp): AAATTTAAAA Found at i:56764870 original size:20 final size:20 Alignment explanation

Indices: 56764847--56764900 Score: 63 Period size: 20 Copynumber: 2.7 Consensus size: 20 56764837 TTTAAATTTA 56764847 AAAAAATTTAAAAAAATCTT 1 AAAAAATTTAAAAAAATCTT * * * 56764867 AAAAAATATATAAAAATGTT 1 AAAAAATTTAAAAAAATCTT * * 56764887 TAAAATTTTAAAAA 1 AAAAAATTTAAAAA 56764901 TAAAAGTCCC Statistics Matches: 27, Mismatches: 7, Indels: 0 0.79 0.21 0.00 Matches are distributed among these distances: 20 27 1.00 ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31 Consensus pattern (20 bp): AAAAAATTTAAAAAAATCTT Found at i:56764901 original size:9 final size:10 Alignment explanation

Indices: 56764842--56764902 Score: 54 Period size: 10 Copynumber: 6.1 Consensus size: 10 56764832 TATTTTTTAA * 56764842 ATTTAAAAAA 1 ATTTAAAAAT * 56764852 ATTTAAAAAA 1 ATTTAAAAAT 56764862 ATCTTAAAAAAT 1 AT-TT-AAAAAT * 56764874 ATATAAAAAT 1 ATTTAAAAAT * 56764884 GTTT-AAAAT 1 ATTTAAAAAT 56764893 -TTTAAAAAT 1 ATTTAAAAAT 56764902 A 1 A 56764903 AAAGTCCCAA Statistics Matches: 43, Mismatches: 4, Indels: 8 0.78 0.07 0.15 Matches are distributed among these distances: 8 3 0.07 9 10 0.23 10 20 0.47 11 3 0.07 12 7 0.16 ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34 Consensus pattern (10 bp): ATTTAAAAAT Found at i:56770851 original size:26 final size:28 Alignment explanation

Indices: 56770802--56770861 Score: 79 Period size: 27 Copynumber: 2.2 Consensus size: 28 56770792 ATCATTTTTT 56770802 AAATATAAAAAGCTAAAAAGTTATTAAA 1 AAATATAAAAAGCTAAAAAGTTATTAAA * * 56770830 AAAT-TAAAAAGTTTAAAA-TTATTAAA 1 AAATATAAAAAGCTAAAAAGTTATTAAA * 56770856 ATATAT 1 AAATAT 56770862 TTTTTAATAT Statistics Matches: 28, Mismatches: 3, Indels: 3 0.82 0.09 0.09 Matches are distributed among these distances: 26 11 0.39 27 13 0.46 28 4 0.14 ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32 Consensus pattern (28 bp): AAATATAAAAAGCTAAAAAGTTATTAAA Found at i:56771381 original size:16 final size:16 Alignment explanation

Indices: 56771360--56771392 Score: 57 Period size: 16 Copynumber: 2.1 Consensus size: 16 56771350 GGGAAAAAGT * 56771360 AGGAAAACGCTTTCTC 1 AGGAAAACGCTTCCTC 56771376 AGGAAAACGCTTCCTC 1 AGGAAAACGCTTCCTC 56771392 A 1 A 56771393 AGGATGTCAT Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.33, C:0.27, G:0.18, T:0.21 Consensus pattern (16 bp): AGGAAAACGCTTCCTC Found at i:56771605 original size:11 final size:11 Alignment explanation

Indices: 56771578--56771639 Score: 53 Period size: 11 Copynumber: 5.9 Consensus size: 11 56771568 CAATCTTCAA 56771578 TCTT-TCAATAT 1 TCTTCTCAA-AT 56771589 TC-TCTCAAAT 1 TCTTCTCAAAT 56771599 TCTTCTCAAA- 1 TCTTCTCAAAT 56771609 TC-TCTCAAAT 1 TCTTCTCAAAT * 56771619 T-TCTCTTAAAT 1 TCT-TCTCAAAT * 56771630 TCCTCTCAAA 1 TCTTCTCAAA 56771640 ACTCTCGTTA Statistics Matches: 42, Mismatches: 3, Indels: 12 0.74 0.05 0.21 Matches are distributed among these distances: 9 7 0.17 10 8 0.19 11 27 0.64 ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44 Consensus pattern (11 bp): TCTTCTCAAAT Found at i:56771629 original size:20 final size:21 Alignment explanation

Indices: 56771578--56771639 Score: 67 Period size: 20 Copynumber: 3.0 Consensus size: 21 56771568 CAATCTTCAA 56771578 TCTT-TCAATATTCTCTCAAAT 1 TCTTCTCAA-ATTCTCTCAAAT 56771599 TCTTCTCAAA-TCTCTCAAAT 1 TCTTCTCAAATTCTCTCAAAT * 56771619 T-TCTCTTAAATTCCTCTCAAA 1 TCT-TCTCAAATT-CTCTCAAA 56771640 ACTCTCGTTA Statistics Matches: 36, Mismatches: 1, Indels: 7 0.82 0.02 0.16 Matches are distributed among these distances: 19 1 0.03 20 17 0.47 21 6 0.17 22 12 0.33 ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44 Consensus pattern (21 bp): TCTTCTCAAATTCTCTCAAAT Found at i:56773467 original size:18 final size:18 Alignment explanation

Indices: 56773422--56773467 Score: 65 Period size: 18 Copynumber: 2.6 Consensus size: 18 56773412 TGATGCCAGG * 56773422 TACGTATCCTAGCCCTTT 1 TACGTATCCTAGCCCTTA * 56773440 TATGTATCCTAGCCCTTA 1 TACGTATCCTAGCCCTTA * 56773458 TACGTTTCCT 1 TACGTATCCT 56773468 TTTTCTAGTT Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 18 24 1.00 ACGTcount: A:0.17, C:0.30, G:0.11, T:0.41 Consensus pattern (18 bp): TACGTATCCTAGCCCTTA Found at i:56774079 original size:54 final size:54 Alignment explanation

Indices: 56773901--56774198 Score: 174 Period size: 55 Copynumber: 5.2 Consensus size: 54 56773891 TAAAAGGTTG * * * 56773901 TTTTAAATAAAGTAATTGTAATTTACTTTTATATTTTTTAATAAAATTG-AAATTA 1 TTTTAAATAAACTAATTATAAATTACTTTTATA-TTTTTAATAAAA-TGAAAATTA * * * * * * 56773956 TTTTAAATAAGGCAATATTTTGAA-TATTTTTATATTATTTCATGTAATTAGAT-AAAAGGTTA 1 TTTTAAATAA-ACTA-ATTATAAATTACTTTTATATT-TTT-A-ATAA--A-ATGAAAA--TTA * * 56774018 TTTTAAATAAATTAATTATAAATTACTTTTATATTTTTAATAAAATGGAAATTA 1 TTTTAAATAAACTAATTATAAATTACTTTTATATTTTTAATAAAATGAAAATTA * * * * * * * 56774072 TTTTAAATAAGGCAACATTTTGAA-TATTTTTATATTATTTCATGTGATAATAT-AAAAGGTTG 1 TTTTAAATAA-ACTA-ATTATAAATTACTTTTATATT-TTT-A----ATAAAATGAAAA--TTA * ** 56774134 TTTTAAATAAAGTAATTATATTTTACTTTTATATTTTTAATAAAATGAAAATTA 1 TTTTAAATAAACTAATTATAAATTACTTTTATATTTTTAATAAAATGAAAATTA 56774188 TTTTAAATAAA 1 TTTTAAATAAA 56774199 GAAATATTTT Statistics Matches: 183, Mismatches: 35, Indels: 51 0.68 0.13 0.19 Matches are distributed among these distances: 54 26 0.14 55 32 0.17 56 30 0.16 57 7 0.04 58 6 0.03 59 2 0.01 60 24 0.13 61 31 0.17 62 25 0.14 ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48 Consensus pattern (54 bp): TTTTAAATAAACTAATTATAAATTACTTTTATATTTTTAATAAAATGAAAATTA Found at i:56774127 original size:116 final size:116 Alignment explanation

Indices: 56773852--56774237 Score: 619 Period size: 116 Copynumber: 3.3 Consensus size: 116 56773842 TATTTGTACA * * 56773852 AACATTTTGAATCTTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT 1 AACATTTTGAATATTTTTATATTATTTCATGTAATAAGATAAAAGGTTGTTTTAAATAAAGTAAT * * 56773917 TGTAATTTACTTTTATATTTTTTAATAAAATTGAAATTATTTTAAATAAGGC 66 TATAATTTACTTTTATA-TTTTTAATAAAATGGAAATTATTTTAAATAAGGC * * * * 56773969 AATATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTATTTTAAATAAATTAAT 1 AACATTTTGAATATTTTTATATTATTTCATGTAATAAGATAAAAGGTTGTTTTAAATAAAGTAAT * 56774034 TATAAATTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC 66 TATAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC * * 56774085 AACATTTTGAATATTTTTATATTATTTCATGTGATAATATAAAAGGTTGTTTTAAATAAAGTAAT 1 AACATTTTGAATATTTTTATATTATTTCATGTAATAAGATAAAAGGTTGTTTTAAATAAAGTAAT * * * * 56774150 TATATTTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGA 66 TATAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC * 56774201 AATATTTTGAATATTTTTATATTATTTCATGTAATAA 1 AACATTTTGAATATTTTTATATTATTTCATGTAATAA 56774238 AATATAAATA Statistics Matches: 249, Mismatches: 20, Indels: 1 0.92 0.07 0.00 Matches are distributed among these distances: 116 173 0.69 117 76 0.31 ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48 Consensus pattern (116 bp): AACATTTTGAATATTTTTATATTATTTCATGTAATAAGATAAAAGGTTGTTTTAAATAAAGTAAT TATAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGC Found at i:56777693 original size:251 final size:251 Alignment explanation

Indices: 56777247--56777792 Score: 837 Period size: 251 Copynumber: 2.2 Consensus size: 251 56777237 GCCCAAGTTA * * * 56777247 TTTTAGAAACCACTGTAATAAAAGAGCGTCCACGTAGG-AGCTTATTTCAGTACTTTTGCTGAAA 1 TTTTAGAGACTACTGTAACAAAAGAGCGTCCACGT-GGAAGCTTATTTCAGTACTTTTGCTGAAA * ** 56777311 ATGCATCCTGCTTGAAGCGTTTTTGACACTATTTATGCAGACACGTCTTCTCAAAATTATTTTTT 65 ATGCATCCTACTTGAAGCGTTTTTGACACTATTTACACAGACACGTCTTCTCAAAATTATTTTTT 56777376 CAGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGC 130 CAGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGC 56777441 ATCCTGCTTGAAGCGTTTTT-ACCACTATTTGCGCAGACACGTCTTCTCAAAATTATT 195 ATCCTGCTTGAAGCGTTTTTGA-CACTATTTGCGCAGACACGTCTTCTCAAAATTATT * * * 56777498 TTTTAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGACAA 1 TTTTAGAGACTACTGTAACAAAAGAGCGTCCACGTGGAAGCTTATTTCAGTACTTTTGCTGAAAA * 56777563 TGCATCCTACTTGAAGCGTTTTTTG-CACTATTTGCACAGACACGTCTTCTCAAAATTATTTTTT 66 TGCATCCTACTTGAAGCG-TTTTTGACACTATTTACACAGACACGTCTTCTCAAAATTATTTTTT * * * * * * 56777627 CAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGC 130 CAGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGC * * * 56777692 ATCCTGCTTGAAGCGTTTTTGACATTATTTGTGCAGACACGTCTTCTCAAATTTATT 195 ATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATT ** * 56777749 TTTTCAGAGACTTTTGTAACAAAAGAGCGTCCACGTAGAAGCTT 1 TTTT-AGAGACTACTGTAACAAAAGAGCGTCCACGTGGAAGCTT 56777793 TTTTAGATTA Statistics Matches: 268, Mismatches: 23, Indels: 7 0.90 0.08 0.02 Matches are distributed among these distances: 250 2 0.01 251 224 0.84 252 42 0.16 ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34 Consensus pattern (251 bp): TTTTAGAGACTACTGTAACAAAAGAGCGTCCACGTGGAAGCTTATTTCAGTACTTTTGCTGAAAA TGCATCCTACTTGAAGCGTTTTTGACACTATTTACACAGACACGTCTTCTCAAAATTATTTTTTC AGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGCA TCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATT Found at i:56777792 original size:126 final size:126 Alignment explanation

Indices: 56777266--56777784 Score: 819 Period size: 126 Copynumber: 4.1 Consensus size: 126 56777256 CCACTGTAAT * * 56777266 AAAAGAGCGTCCACGTAGGAGCTTATTTCAGTACTTTTGCTGAAAATGCATCCTGCTTGAAGCGT 1 AAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAATGCATCCTGCTTGAAGCGT ** * 56777331 TTTTGACACTATTTATGCAGACACGTCTTCTCAAAATTATTTTTTCAGAGACCACTGTAGC 66 TTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTTTTTCAGAGACTACTGTAGC * * * 56777392 AAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGCATCCTGCTTGAAGCGT 1 AAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAATGCATCCTGCTTGAAGCGT 56777457 TTTT-ACCACTATTTGCGCAGACACGTCTTCTCAAAATTATTTTTT-AGAGACTACTGTAGC 66 TTTTGA-CACTATTTGCGCAGACACGTCTTCTCAAAATTATTTTTTCAGAGACTACTGTAGC * * * 56777517 AAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGACAATGCATCCTACTTGAAGCGT 1 AAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAATGCATCCTGCTTGAAGCG- * * 56777582 TTTTTG-CACTATTTGCACAGACACGTCTTCTCAAAATTATTTTTTCAGATACTACTGTAGC 65 TTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTTTTTCAGAGACTACTGTAGC * 56777643 AAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCCTGCTTGAAGCGT 1 AAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAATGCATCCTGCTTGAAGCGT * * * ** * 56777708 TTTTGACATTATTTGTGCAGACACGTCTTCTCAAATTTATTTTTTCAGAGACTTTTGTAAC 66 TTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTTTTTCAGAGACTACTGTAGC 56777769 AAAAGAGCGTCCACGT 1 AAAAGAGCGTCCACGT 56777785 AGAAGCTTTT Statistics Matches: 362, Mismatches: 26, Indels: 10 0.91 0.07 0.03 Matches are distributed among these distances: 125 117 0.32 126 245 0.68 ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34 Consensus pattern (126 bp): AAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAATGCATCCTGCTTGAAGCGT TTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTTTTTCAGAGACTACTGTAGC Found at i:56778047 original size:96 final size:98 Alignment explanation

Indices: 56777872--56778068 Score: 253 Period size: 96 Copynumber: 2.0 Consensus size: 98 56777862 TAAATACCCT * * * ** 56777872 AAAACCCTAAACTCTAAAATCCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGTAA 1 AAAACCATAAACACTAAAATCCTAATCTAATTTTTTTAAAATTTATAATTAATTTAATCAACAAA * 56777937 CCTTAAATCCTAATTTATTTGATTTTTTCCTTA 66 CCTTAAATCCTAATTTATTTAATTTTTTCCTTA * 56777970 AAAACCATAAACACT-AAA-CCATAATCTAA-TTTTTTAAAA-TTAGTAATTAATTTAATTAACA 1 AAAACCATAAACACTAAAATCC-TAATCTAATTTTTTTAAAATTTA-TAATTAATTTAATCAACA 56778031 AACAC-TAAA-CCTTAATTTATTTAATTTTTTCCTTA 64 AAC-CTTAAATCC-TAATTTATTTAATTTTTTCCTTA 56778066 AAA 1 AAA 56778069 CCCTAAAATT Statistics Matches: 88, Mismatches: 7, Indels: 10 0.84 0.07 0.10 Matches are distributed among these distances: 95 5 0.06 96 58 0.66 97 12 0.14 98 13 0.15 ACGTcount: A:0.42, C:0.15, G:0.02, T:0.41 Consensus pattern (98 bp): AAAACCATAAACACTAAAATCCTAATCTAATTTTTTTAAAATTTATAATTAATTTAATCAACAAA CCTTAAATCCTAATTTATTTAATTTTTTCCTTA Found at i:56779103 original size:22 final size:23 Alignment explanation

Indices: 56779075--56779117 Score: 70 Period size: 22 Copynumber: 1.9 Consensus size: 23 56779065 ATTTCATAAT * 56779075 AAAAATATTAATAAA-ATTTATA 1 AAAAATAATAATAAACATTTATA 56779097 AAAAATAATAATAAACATTTA 1 AAAAATAATAATAAACATTTA 56779118 GAGTCGAAAT Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 22 14 0.74 23 5 0.26 ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33 Consensus pattern (23 bp): AAAAATAATAATAAACATTTATA Found at i:56780532 original size:25 final size:25 Alignment explanation

Indices: 56780498--56780546 Score: 98 Period size: 25 Copynumber: 2.0 Consensus size: 25 56780488 AAACAAAAAG 56780498 ATGACAAAATAAAAAAGAAAAGAAA 1 ATGACAAAATAAAAAAGAAAAGAAA 56780523 ATGACAAAATAAAAAAGAAAAGAA 1 ATGACAAAATAAAAAAGAAAAGAA 56780547 CATTAAAGGT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 24 1.00 ACGTcount: A:0.76, C:0.04, G:0.12, T:0.08 Consensus pattern (25 bp): ATGACAAAATAAAAAAGAAAAGAAA Found at i:56783138 original size:46 final size:44 Alignment explanation

Indices: 56783034--56783141 Score: 144 Period size: 44 Copynumber: 2.4 Consensus size: 44 56783024 TGTCTTTGAC ** * * * 56783034 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT 1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT * 56783078 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT 1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT 56783124 ATGGACTTACATGGCTCA 1 ATGGACTTACATGGCTCA 56783142 TTTCTGTTCT Statistics Matches: 56, Mismatches: 6, Indels: 2 0.88 0.09 0.03 Matches are distributed among these distances: 44 33 0.59 46 23 0.41 ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33 Consensus pattern (44 bp): ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT Found at i:56789447 original size:75 final size:73 Alignment explanation

Indices: 56789359--56789530 Score: 217 Period size: 75 Copynumber: 2.4 Consensus size: 73 56789349 GGTTTTCCTC *** * * ** 56789359 ATTGAAATACCATACCTACATTTTTTAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC 1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC 56789423 TCAGTATGG 65 TCAGTATGG * 56789432 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA 1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA 56789497 CTCAGTATGG 64 CTCAGTATGG 56789507 A-TG--ATACCATACCTACATTTCACA 1 ATTGAAATACCATACCTACATTTCACA 56789531 CTTTGCCATG Statistics Matches: 88, Mismatches: 8, Indels: 9 0.84 0.08 0.09 Matches are distributed among these distances: 70 21 0.24 73 3 0.03 74 7 0.08 75 57 0.65 ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32 Consensus pattern (73 bp): ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT CAGTATGG Found at i:56789528 original size:35 final size:35 Alignment explanation

Indices: 56789364--56789530 Score: 192 Period size: 35 Copynumber: 4.6 Consensus size: 35 56789354 TCCTCATTGA *** * 56789364 AATACCATACCTACATTTTTTAACTCGGTATGGGA- 1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT * ** 56789399 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT 1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT * 56789439 AATACCATACCTACATTTCACAGCTCAGTATGGAT 1 AATACCATACCTACATTTCACAACTCAGTATGGAT 56789474 AATACCATACCTACATTTCACAACTCAGTATGGAT 1 AATACCATACCTACATTTCACAACTCAGTATGGAT * 56789509 GATACCATACCTACATTTCACA 1 AATACCATACCTACATTTCACA 56789531 CTTTGCCATG Statistics Matches: 118, Mismatches: 9, Indels: 10 0.86 0.07 0.07 Matches are distributed among these distances: 35 88 0.75 39 3 0.03 40 27 0.23 ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32 Consensus pattern (35 bp): AATACCATACCTACATTTCACAACTCAGTATGGAT Found at i:56798805 original size:124 final size:124 Alignment explanation

Indices: 56798583--56798807 Score: 326 Period size: 124 Copynumber: 1.8 Consensus size: 124 56798573 GAATTATGTG * * * * * * * 56798583 AAATGAAATATGGATGTGTATTGATTATTGATTTATGTGTGTATGAGTATTTGAATGATACCCGG 1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG * ** 56798648 GCTAAGTCCCGAAGGCGATTATGCTAGTGATTATATTTGTGTTTGAGCCTTAGTAACGA 66 GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA * 56798707 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATATCCGG 1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG * 56798772 GCTAAGTCCCGAAGACG-TTATTGCTGGAAATTATAT 66 GCTAAGTCCCGAAGACGATTA-TGCTAGAAATTATAT 56798808 CCGGGTTAAG Statistics Matches: 88, Mismatches: 12, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 123 3 0.03 124 85 0.97 ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35 Consensus pattern (124 bp): AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA Found at i:56798929 original size:40 final size:40 Alignment explanation

Indices: 56798802--56798931 Score: 165 Period size: 40 Copynumber: 3.2 Consensus size: 40 56798792 TTGCTGGAAA * * * 56798802 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGG 1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG * * * 56798842 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG * 56798882 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG 56798922 TTATATCCGG 1 TTATATCCGG 56798932 TTGTATTCCG Statistics Matches: 77, Mismatches: 11, Indels: 4 0.84 0.12 0.04 Matches are distributed among these distances: 39 4 0.05 40 73 0.95 ACGTcount: A:0.22, C:0.25, G:0.29, T:0.23 Consensus pattern (40 bp): TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG Found at i:56811194 original size:124 final size:124 Alignment explanation

Indices: 56810972--56811196 Score: 326 Period size: 124 Copynumber: 1.8 Consensus size: 124 56810962 GAATTATGTG * * * * * * * 56810972 AAATGAAATATGGATGTGTATTGATTATTGATTTATGTGTGTATGAGTATTTGAATGATACCCGG 1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG * ** 56811037 GCTAAGTCCCGAAGGCGATTATGCTAGTGATTATATTTGTGTTTGAGCCTTAGTAACGA 66 GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA * 56811096 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATATCCGG 1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG * 56811161 GCTAAGTCCCGAAGACG-TTATTGCTGGAAATTATAT 66 GCTAAGTCCCGAAGACGATTA-TGCTAGAAATTATAT 56811197 CCGGGTTAAG Statistics Matches: 88, Mismatches: 12, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 123 3 0.03 124 85 0.97 ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35 Consensus pattern (124 bp): AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA Found at i:56811318 original size:40 final size:40 Alignment explanation

Indices: 56811191--56811320 Score: 165 Period size: 40 Copynumber: 3.2 Consensus size: 40 56811181 TTGCTGGAAA * * * 56811191 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGG 1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG * * * 56811231 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG * 56811271 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG 56811311 TTATATCCGG 1 TTATATCCGG 56811321 TTGTATTCCG Statistics Matches: 77, Mismatches: 11, Indels: 4 0.84 0.12 0.04 Matches are distributed among these distances: 39 4 0.05 40 73 0.95 ACGTcount: A:0.22, C:0.25, G:0.29, T:0.23 Consensus pattern (40 bp): TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG Found at i:56816057 original size:40 final size:40 Alignment explanation

Indices: 56816008--56816172 Score: 190 Period size: 40 Copynumber: 4.2 Consensus size: 40 56815998 TCTTCGGAAT * * * 56816008 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC 1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC * * *** * 56816047 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTC 1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC * * 56816087 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC 1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC * * 56816127 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC 1 TTAGCCCGGATATAA-CAACTAGCACAAATGCCTTCGGGTC 56816167 TTAGCC 1 TTAGCC 56816173 GGGTATCATT Statistics Matches: 104, Mismatches: 20, Indels: 3 0.82 0.16 0.02 Matches are distributed among these distances: 39 3 0.03 40 100 0.96 41 1 0.01 ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25 Consensus pattern (40 bp): TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC Found at i:56827715 original size:47 final size:47 Alignment explanation

Indices: 56827645--56827763 Score: 148 Period size: 47 Copynumber: 2.5 Consensus size: 47 56827635 CTTCGGGACT * * * * * 56827645 TATCACATTTATACACTTCCACATCCATCACGTTGGCCACTCGGCCC 1 TATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC * * * 56827692 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT 1 TATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC 56827739 TATCACGTATATATACACTTTCACA 1 TATCAC--ATATATACACTTTCACA 56827764 AATTTTAATA Statistics Matches: 62, Mismatches: 8, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 47 45 0.73 49 17 0.27 ACGTcount: A:0.29, C:0.32, G:0.08, T:0.31 Consensus pattern (47 bp): TATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC Found at i:56832317 original size:46 final size:46 Alignment explanation

Indices: 56832267--56832581 Score: 349 Period size: 46 Copynumber: 6.8 Consensus size: 46 56832257 TGGTTGAGCA 56832267 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * * 56832313 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G * 56832358 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG 1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * * 56832406 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * * 56832452 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G * 56832497 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG 1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * ** 56832545 CCCGAGCTCGTTGAGTTGAGTCCGAGTTTGCTTATGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG 56832582 GCGGGTTACA Statistics Matches: 227, Mismatches: 24, Indels: 36 0.79 0.08 0.13 Matches are distributed among these distances: 42 4 0.02 43 10 0.04 45 6 0.03 46 131 0.58 47 58 0.26 48 6 0.03 50 8 0.04 51 4 0.02 ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29 Consensus pattern (46 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG Found at i:56832423 original size:93 final size:93 Alignment explanation

Indices: 56832264--56832434 Score: 315 Period size: 93 Copynumber: 1.8 Consensus size: 93 56832254 GGATGGTTGA * * 56832264 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT 56832329 TGAGTCCGAGTTCGTGAGATGTAACTAG 66 TGAGTCCGAGTTCGTGAGATGTAACTAG * 56832357 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT 56832422 TGAGTCCGAGTTC 66 TGAGTCCGAGTTC 56832435 ACTTACGGAT Statistics Matches: 75, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 75 1.00 ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28 Consensus pattern (93 bp): GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT TGAGTCCGAGTTCGTGAGATGTAACTAG Found at i:56832498 original size:139 final size:139 Alignment explanation

Indices: 56832268--56832572 Score: 592 Period size: 139 Copynumber: 2.2 Consensus size: 139 56832258 GGTTGAGCAT * * 56832268 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTGAG 1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTCCGAACTCGTTGAGTTGAG 56832333 TCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA 66 TCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA 56832398 TGCGAACGC 131 TGCGAACGC 56832407 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTCCGAACTCGTTGAGTTGAG 1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTCCGAACTCGTTGAGTTGAG 56832472 TCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA 66 TCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA 56832537 TGCGAACGC 131 TGCGAACGC 56832546 CCGAGCTCGTTGAGTTGAGTCCGAGTT 1 CCGAGCTCGTTGAGTTGAGTCCGAGTT 56832573 TGCTTATGGG Statistics Matches: 164, Mismatches: 2, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 139 164 1.00 ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28 Consensus pattern (139 bp): CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTCCGAACTCGTTGAGTTGAG TCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA TGCGAACGC Found at i:56835554 original size:15 final size:15 Alignment explanation

Indices: 56835534--56835602 Score: 84 Period size: 15 Copynumber: 4.6 Consensus size: 15 56835524 GTATCTTGGG 56835534 TTTCTTTATCCTGGA 1 TTTCTTTATCCTGGA * * 56835549 TCTCTTTATTCTGGA 1 TTTCTTTATCCTGGA * * 56835564 TTTCTTTATTCTGGG 1 TTTCTTTATCCTGGA * * 56835579 TTTCTCTATCTTGGA 1 TTTCTTTATCCTGGA 56835594 TTTCTTTAT 1 TTTCTTTAT 56835603 TCGGTTTTCT Statistics Matches: 45, Mismatches: 9, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 15 45 1.00 ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58 Consensus pattern (15 bp): TTTCTTTATCCTGGA Found at i:56835603 original size:30 final size:30 Alignment explanation

Indices: 56835525--56835612 Score: 99 Period size: 30 Copynumber: 3.0 Consensus size: 30 56835515 CATAGTATCG * * * * 56835525 TATCTTGGGTTTCTTTATCCTGGATCTCTT 1 TATCTTGGATTTCTTTATTCTGGATTTCTC * 56835555 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC 1 TATCT-TGGATTTCTTTATTCTGGATTTCTC * 56835585 TATCTTGGATTTCTTTATTC-GGTTTTCT 1 TATCTTGGATTTCTTTATTCTGGATTTCT 56835613 TGTTATCTTT Statistics Matches: 50, Mismatches: 6, Indels: 5 0.82 0.10 0.08 Matches are distributed among these distances: 29 8 0.16 30 41 0.82 31 1 0.02 ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57 Consensus pattern (30 bp): TATCTTGGATTTCTTTATTCTGGATTTCTC Found at i:56838045 original size:46 final size:46 Alignment explanation

Indices: 56837995--56838309 Score: 349 Period size: 46 Copynumber: 6.8 Consensus size: 46 56837985 TGGTTGAGCA 56837995 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * * 56838041 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G * 56838086 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG 1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * * 56838134 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * * 56838180 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G * 56838225 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG 1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * * * 56838273 CCCGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG 56838310 GCGGGTTACA Statistics Matches: 227, Mismatches: 24, Indels: 36 0.79 0.08 0.13 Matches are distributed among these distances: 42 4 0.02 43 10 0.04 45 6 0.03 46 131 0.58 47 58 0.26 48 6 0.03 50 8 0.04 51 4 0.02 ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28 Consensus pattern (46 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG Found at i:56838151 original size:93 final size:93 Alignment explanation

Indices: 56837992--56838162 Score: 315 Period size: 93 Copynumber: 1.8 Consensus size: 93 56837982 GGATGGTTGA * * 56837992 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT 56838057 TGAGTCCGAGTTCGTGAGATGTAACTAG 66 TGAGTCCGAGTTCGTGAGATGTAACTAG * 56838085 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT 56838150 TGAGTCCGAGTTC 66 TGAGTCCGAGTTC 56838163 ACTTACGGAT Statistics Matches: 75, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 75 1.00 ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28 Consensus pattern (93 bp): GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT TGAGTCCGAGTTCGTGAGATGTAACTAG Found at i:56838226 original size:139 final size:139 Alignment explanation

Indices: 56837996--56838306 Score: 586 Period size: 139 Copynumber: 2.2 Consensus size: 139 56837986 GGTTGAGCAT * * 56837996 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTGAG 1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTCCGAACTCGTTGAGTTGAG 56838061 TCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA 66 TCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA 56838126 TGCGAACGC 131 TGCGAACGC 56838135 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTCCGAACTCGTTGAGTTGAG 1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTCCGAACTCGTTGAGTTGAG 56838200 TCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA 66 TCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA 56838265 TGCGAACGC 131 TGCGAACGC * * 56838274 CCGAGCTCATTGAGTTGAGTCCGAGTTCGCTTA 1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA 56838307 TGGGCGGGTT Statistics Matches: 168, Mismatches: 4, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 139 168 1.00 ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28 Consensus pattern (139 bp): CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTCCGAACTCGTTGAGTTGAG TCCGAGTTCGTGAGATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA TGCGAACGC Found at i:56841765 original size:47 final size:47 Alignment explanation

Indices: 56841677--56841793 Score: 135 Period size: 47 Copynumber: 2.4 Consensus size: 47 56841667 AAAATTTGTA * * * 56841677 AAAGTGTATATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTG 1 AAAGTGTATATAT--GTGATAAGGCCGAATGGCCAACGTGATGAATGTG * * * * 56841726 AAAGTGTATATATGTGATAGGGCCGAGTGGTCAACGTGATGGATGTG 1 AAAGTGTATATATGTGATAAGGCCGAATGGCCAACGTGATGAATGTG * * 56841773 GAAGTGTATAAATGTGATAAG 1 AAAGTGTATATATGTGATAAG 56841794 TCCCGAAGGG Statistics Matches: 58, Mismatches: 10, Indels: 2 0.83 0.14 0.03 Matches are distributed among these distances: 47 45 0.78 49 13 0.22 ACGTcount: A:0.32, C:0.08, G:0.32, T:0.28 Consensus pattern (47 bp): AAAGTGTATATATGTGATAAGGCCGAATGGCCAACGTGATGAATGTG Found at i:56843870 original size:40 final size:40 Alignment explanation

Indices: 56843821--56844012 Score: 321 Period size: 40 Copynumber: 4.8 Consensus size: 40 56843811 CCAGCATGAT * * * 56843821 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA 1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA * * * 56843861 TGCTCTTCGGGACTTAGTCCGGTTGCATCACTAGCACGAA 1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA 56843901 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA 1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA 56843941 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA 1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA * 56843981 TGCTCTTCGGAACTTAGTCCGGATATATCACT 1 TGCTCTTCGGAACTTAGTCCGGATACATCACT 56844013 CTCAATTCTC Statistics Matches: 144, Mismatches: 8, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 40 144 1.00 ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26 Consensus pattern (40 bp): TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA Found at i:56848698 original size:46 final size:45 Alignment explanation

Indices: 56848603--56848773 Score: 148 Period size: 46 Copynumber: 3.7 Consensus size: 45 56848593 CTCATAGCCA * * * * * * 56848603 ATGCATGTCCCAAACATGTCTTACACTGGCTTACGTCTCGAGGCCG 1 ATGCATGTCCCAAACATGTCTTACACTAGCCT-CATCTTGATGCTG ** 56848649 ATGCATGTCCCGGACATGTCTTACACTAGCACTCATCTTGATGCTG 1 ATGCATGTCCCAAACATGTCTTACACTAGC-CTCATCTTGATGCTG * * ** 56848695 ATGCCATATCCCAGACATGGTCTTACA-TAGGCTCTCATAATG-TGGCTG 1 ATG-CATGTCCCAAACAT-GTCTTACACTA-GC-CTCATCTTGAT-GCTG * 56848743 ATGCATGTCCCAAACATGTCTAACACTAGCC 1 ATGCATGTCCCAAACATGTCTTACACTAGCC 56848774 CACAATAACC Statistics Matches: 103, Mismatches: 16, Indels: 13 0.78 0.12 0.10 Matches are distributed among these distances: 45 1 0.01 46 48 0.47 47 30 0.29 48 24 0.23 ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27 Consensus pattern (45 bp): ATGCATGTCCCAAACATGTCTTACACTAGCCTCATCTTGATGCTG Found at i:56848721 original size:48 final size:46 Alignment explanation

Indices: 56848648--56848772 Score: 137 Period size: 47 Copynumber: 2.7 Consensus size: 46 56848638 TCTCGAGGCC * ** 56848648 GATGCATGTCCCGGACATGTCTTACACTAGCACTCATCTTGAT-GCT 1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATAATG-TGGCT * * 56848694 GATGCCATATCCCAGACATGGTCTTACA-TAGGCTCTCATAATGTGGCT 1 GATG-CATGTCCCAGACAT-GTCTTACACTA-GCACTCATAATGTGGCT * * 56848742 GATGCATGTCCCAAACATGTCTAACACTAGC 1 GATGCATGTCCCAGACATGTCTTACACTAGC 56848773 CCACAATAAC Statistics Matches: 66, Mismatches: 8, Indels: 10 0.79 0.10 0.12 Matches are distributed among these distances: 46 13 0.20 47 29 0.44 48 24 0.36 ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28 Consensus pattern (46 bp): GATGCATGTCCCAGACATGTCTTACACTAGCACTCATAATGTGGCT Done.