Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold433

Parameters: 2 7 7 80 10 50 500

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

Length: 1285081
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29

Warning! 132229 characters in sequence are not A, C, G, or T


File 4 of 4

Found at i:682279 original size:38 final size:38

Alignment explanation

Indices: 682204--682341 Score: 231 Period size: 38 Copynumber: 3.6 Consensus size: 38 682194 TAGACAGGTT * * 682204 AGCTGTTACAATGGTTACTAGTGTAGACAGGTACATGTATA 1 AGCTGTTACAATGGTTA--A-AGAAGACAGGTACATGTATA 682245 AGCTGTTACAATGGTTAAAGAAGACAGGTACATGTATA 1 AGCTGTTACAATGGTTAAAGAAGACAGGTACATGTATA 682283 AGCTGTTACAATGGTTAAAGAAGACAGGTACATGTATA 1 AGCTGTTACAATGGTTAAAGAAGACAGGTACATGTATA 682321 AGCTGTTACAATGGTTAAAGA 1 AGCTGTTACAATGGTTAAAGA 682342 CAGGTAAGCT Statistics Matches: 95, Mismatches: 2, Indels: 3 0.95 0.02 0.03 Matches are distributed among these distances: 38 77 0.81 39 1 0.01 41 17 0.18 ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28 Consensus pattern (38 bp): AGCTGTTACAATGGTTAAAGAAGACAGGTACATGTATA Found at i:682573 original size:35 final size:35 Alignment explanation

Indices: 682532--682630 Score: 162 Period size: 35 Copynumber: 2.8 Consensus size: 35 682522 TATAGACAGG * 682532 TAAGCTGTTAGAATGGTTAAAGACAGGTACATGTA 1 TAAGCTGTTACAATGGTTAAAGACAGGTACATGTA * * 682567 TTAGCTGTTACATTGGTTAAAGACAGGTACATGTA 1 TAAGCTGTTACAATGGTTAAAGACAGGTACATGTA * 682602 TAAGCTGTTACAATGGTTATAGACAGGTA 1 TAAGCTGTTACAATGGTTAAAGACAGGTA 682631 AGCTGTTACA Statistics Matches: 58, Mismatches: 6, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 35 58 1.00 ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31 Consensus pattern (35 bp): TAAGCTGTTACAATGGTTAAAGACAGGTACATGTA Found at i:688417 original size:2 final size:2 Alignment explanation

Indices: 688410--688453 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 688400 TTTAAAGCCT 688410 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 688452 GA 1 GA 688454 TGAATATCAC Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:689379 original size:74 final size:75 Alignment explanation

Indices: 689279--689426 Score: 253 Period size: 74 Copynumber: 2.0 Consensus size: 75 689269 ATTTTAGTTT * 689279 GTTTTATTCGAGAGCTTTTTTTATCATCAAAATAGTCATATTGTCGGAATTTACAATCAATACAA 1 GTTTTATTCGAAAGC-TTTTTTATCATCAAAATAGTCATATTGTCGGAATTTACAATCAATACAA 689344 TGCACAATTTA 65 TGCACAATTTA ** 689355 GTTTTATTCGAAAG-TTTTTTATCATCAAAATAGTTTTATTGTCGGAATTTACAATCAATACAAT 1 GTTTTATTCGAAAGCTTTTTTATCATCAAAATAGTCATATTGTCGGAATTTACAATCAATACAAT 689419 GCACAATT 66 GCACAATT 689427 CATTTTTAAA Statistics Matches: 69, Mismatches: 3, Indels: 2 0.93 0.04 0.03 Matches are distributed among these distances: 74 56 0.81 76 13 0.19 ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41 Consensus pattern (75 bp): GTTTTATTCGAAAGCTTTTTTATCATCAAAATAGTCATATTGTCGGAATTTACAATCAATACAAT GCACAATTTA Found at i:692889 original size:2 final size:2 Alignment explanation

Indices: 692882--692934 Score: 106 Period size: 2 Copynumber: 26.5 Consensus size: 2 692872 CTAGAATCCC 692882 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 692924 CT CT CT CT CT C 1 CT CT CT CT CT C 692935 CGAAAACAAT Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:698633 original size:101 final size:102 Alignment explanation

Indices: 698457--699496 Score: 1855 Period size: 101 Copynumber: 10.3 Consensus size: 102 698447 GAACATGACA * 698457 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGG-CGGTTATGTTGGAGAC 1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC * * 698521 CCCATCCGTCTCCCTCTCTTTTATTGGGAGGGGGACG 66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG * 698558 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGGCGGTTATGTT-GAGAC 1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC * 698622 CCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGGCG 66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG * 698659 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACAGTTATGTTGGAGAC 1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC 698724 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG 66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG * 698761 GTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGATATGTTGGAGAC 1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC 698825 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG 66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG 698862 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTT-GAGAC 1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC * * 698926 CCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG 66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG * * 698963 GATATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC 1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC 699028 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG 66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG 699065 GTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC 1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC 699129 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG 66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG * 699166 GTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGATATGTTGGAGAC 1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC * 699230 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACG 66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG 699267 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTT-GAGAC 1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC * * 699331 CCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG 66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG * 699368 GTTATGTTGGAGACCCCATCCGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTT-GAGAC 1 GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC * * 699432 CCCATCAGCCTCCTTCTCTTTTATTGGGA-GGGGGCG 66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG 699468 GTTATGTTGGAGACCCCATCAGTCTCCTT 1 GTTATGTTGGAGACCCCATCAGTCTCCTT 699497 TTCTCATTTT Statistics Matches: 908, Mismatches: 26, Indels: 11 0.96 0.03 0.01 Matches are distributed among these distances: 100 34 0.04 101 670 0.74 102 204 0.22 ACGTcount: A:0.15, C:0.23, G:0.29, T:0.33 Consensus pattern (102 bp): GTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCG Found at i:698733 original size:152 final size:152 Alignment explanation

Indices: 698457--699496 Score: 1838 Period size: 152 Copynumber: 6.9 Consensus size: 152 698447 GAACATGACA * 698457 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGG-CGGTTATGTTGGAGAC 1 GTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC * 698521 CCCATCCGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCT 65 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCT * 698586 TCTCTTTTATTGGGAGGGGGGCG 130 TCTCTTTTATTGGGAGGGGGACG * 698609 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGGCGGTTATGTTGGAGACC 1 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACC * * * 698674 CCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACAGTTATGTTGGAGACCCCATCAGTCTCCCT 66 CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTT * 698739 CTCTTTTATTGGGAGGGGGGCG 131 CTCTTTTATTGGGAGGGGGACG * 698761 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGATATGTTGGAGACC 1 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACC * 698826 CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCGGTTATGTTGGAGACCCCATCAGTCTCCTT 66 CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTT 698891 CTCTTTTATTGGGAGGGGGACG 131 CTCTTTTATTGGGAGGGGGACG * 698913 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGATATGTTGGAGACC 1 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACC * 698978 CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCCT 66 CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTT * 699043 CTCTTTTATTGGGAGGGGGGCG 131 CTCTTTTATTGGGAGGGGGACG 699065 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACC 1 GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACC * 699130 CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCGGTTATGTT-GAGACCCCATCAGTCTCCTT 66 CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTT 699194 CTCTTTTATTGGGAGGGGGACG 131 CTCTTTTATTGGGAGGGGGACG * * 699216 GATATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC 1 GTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC * 699281 CCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTT-GAGACCCCATCAGTCTCCT 65 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCT 699345 TCTCTTTTATTGGGAGGGGGACG 130 TCTCTTTTATTGGGAGGGGGACG * 699368 GTTATGTTGGAGACCCCATCCGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTT-GAGAC 1 GTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC * * 699432 CCCATCAGCCTCCTTCTCTTTTATTGGGAGGGGG-CGGTTATGTTGGAGACCCCATCAGTCTCCT 65 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCT 699496 T 130 T 699497 TTCTCATTTT Statistics Matches: 858, Mismatches: 27, Indels: 7 0.96 0.03 0.01 Matches are distributed among these distances: 150 10 0.01 151 143 0.17 152 705 0.82 ACGTcount: A:0.15, C:0.23, G:0.29, T:0.33 Consensus pattern (152 bp): GTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACC CCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTT CTCTTTTATTGGGAGGGGGACG Found at i:698927 original size:253 final size:253 Alignment explanation

Indices: 698457--699494 Score: 1868 Period size: 253 Copynumber: 4.1 Consensus size: 253 698447 GAACATGACA 698457 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGG-CGGTTATGTTGGAGAC 1 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC * 698521 CCCATCCGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCT 66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTT-GAGACCCCATCAGTCTCCT * 698586 TCTCTTTTATTGGGAGGGGGGCGGTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGG 130 TCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGG * * 698650 AGGGGGGCGGTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACA 195 AGGGGGACGGTTATGTT-GAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG * 698710 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCGGTTATGTT-GAGAC 1 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC * * * 698774 CCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGATATGTTGGAGACCCCATCAGTCTCCC 66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTT-GAGACCCCATCAGTCTCCT * 698839 TCTCTTTTATTGGGAGGGGGGCGGTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGG 130 TCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGG 698904 AGGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG 195 AGGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG * 698963 GATATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC 1 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC * 699028 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGGCGGTTATGTTGAGACCCCATCAGTCTCCTT 66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTT * 699093 CTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGA 131 CTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGA * 699158 GGGGGGCGGTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG 196 GGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG * 699216 GATATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC 1 GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC * 699281 CCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTT 66 CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTT * 699346 CTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCCGTCTCCTTCTCTTTTATTGGGA 131 CTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGA * 699411 GGGGGACGGTTATGTTGAGACCCCATCAGCCTCCTTCTCTTTTATTGGGAGGGGG-CG 196 GGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG 699468 GTTATGTTGGAGACCCCATCAGTCTCC 1 GTTATGTTGGAGACCCCATCAGTCTCC 699495 TTTTCTCATT Statistics Matches: 760, Mismatches: 22, Indels: 7 0.96 0.03 0.01 Matches are distributed among these distances: 252 28 0.04 253 626 0.82 254 106 0.14 ACGTcount: A:0.15, C:0.23, G:0.29, T:0.32 Consensus pattern (253 bp): GTTATGTTGGAGACCCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGAC CCCATCAGTCTCCCTCTCTTTTATTGGGAGGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTT CTCTTTTATTGGGAGGGGGACGGTTATGTTGGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGA GGGGGACGGTTATGTTGAGACCCCATCAGTCTCCTTCTCTTTTATTGGGAGGGGGACG Found at i:702156 original size:48 final size:48 Alignment explanation

Indices: 702084--702178 Score: 172 Period size: 48 Copynumber: 2.0 Consensus size: 48 702074 ATGACCTTGG 702084 ATGGATTAACTATAATTATCAAATGGAATGTCTCAATGGAATTATAGT 1 ATGGATTAACTATAATTATCAAATGGAATGTCTCAATGGAATTATAGT * * 702132 ATGGATTAACTATAATTATTAAATGGAATGTCTCTATGGAATTATAG 1 ATGGATTAACTATAATTATCAAATGGAATGTCTCAATGGAATTATAG 702179 GAGAAAATAA Statistics Matches: 45, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 48 45 1.00 ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37 Consensus pattern (48 bp): ATGGATTAACTATAATTATCAAATGGAATGTCTCAATGGAATTATAGT Found at i:704716 original size:16 final size:16 Alignment explanation

Indices: 704697--704729 Score: 66 Period size: 16 Copynumber: 2.1 Consensus size: 16 704687 AAATGTAGAA 704697 GGGCGAAAATAACACG 1 GGGCGAAAATAACACG 704713 GGGCGAAAATAACACG 1 GGGCGAAAATAACACG 704729 G 1 G 704730 TATACAGTAT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.42, C:0.18, G:0.33, T:0.06 Consensus pattern (16 bp): GGGCGAAAATAACACG Found at i:704949 original size:35 final size:35 Alignment explanation

Indices: 704903--705037 Score: 227 Period size: 35 Copynumber: 3.9 Consensus size: 35 704893 GATGACACTA * * * 704903 TCCATAATCTAAAATACAGGTACAGGTAATCACAG 1 TCCATACTCTAAAATACAGGTACAGGTAATCGCTG 704938 TCCATACTCTAAAATACAGGTACAGGTAAAT-GCTG 1 TCCATACTCTAAAATACAGGTACAGGT-AATCGCTG 704973 TCCATACTCTAAAATACAGGTACAGGTAATCGCTG 1 TCCATACTCTAAAATACAGGTACAGGTAATCGCTG 705008 TCCATACTCTAAAATACAGGTACAGGTAAT 1 TCCATACTCTAAAATACAGGTACAGGTAAT 705038 TCAAAAACAA Statistics Matches: 95, Mismatches: 3, Indels: 4 0.93 0.03 0.04 Matches are distributed among these distances: 34 3 0.03 35 89 0.94 36 3 0.03 ACGTcount: A:0.39, C:0.21, G:0.16, T:0.25 Consensus pattern (35 bp): TCCATACTCTAAAATACAGGTACAGGTAATCGCTG Found at i:709392 original size:30 final size:31 Alignment explanation

Indices: 709333--709405 Score: 103 Period size: 30 Copynumber: 2.3 Consensus size: 31 709323 ATATAAATAA * 709333 TTCCTTTATACAAGAAACGTAAATTAAGATTAT 1 TTCCTTTATACAAGAAACCT--ATTAAGATTAT * 709366 TTCCTATATACAAGAAACCT-TTAAGATTAT 1 TTCCTTTATACAAGAAACCTATTAAGATTAT 709396 TTCCTTTATA 1 TTCCTTTATA 709406 TGATGAGCAT Statistics Matches: 37, Mismatches: 3, Indels: 3 0.86 0.07 0.07 Matches are distributed among these distances: 30 19 0.51 33 18 0.49 ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40 Consensus pattern (31 bp): TTCCTTTATACAAGAAACCTATTAAGATTAT Found at i:717510 original size:48 final size:48 Alignment explanation

Indices: 717439--717539 Score: 184 Period size: 48 Copynumber: 2.1 Consensus size: 48 717429 NNNNNNNNNN * 717439 GCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAATTTGCC 1 GCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCC * 717487 GCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCG 1 GCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCC 717535 GCAAA 1 GCAAA 717540 TTTGCCGCAA Statistics Matches: 51, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 48 51 1.00 ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27 Consensus pattern (48 bp): GCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCC Found at i:717551 original size:59 final size:59 Alignment explanation

Indices: 717479--717667 Score: 315 Period size: 59 Copynumber: 3.2 Consensus size: 59 717469 ACGAATTCTG * 717479 AATTTGCCGCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCGGCA 1 AATTTGCCGCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCCGCA * * 717538 AATTTGCCGCAAACAGTTTCCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCTGCA 1 AATTTGCCGCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCCGCA * * * 717597 ACTTTGCCGCAAACAGTTTGCCAGAAGCTAATTTGCAAACGAATTCTGAACCTGCCGCA 1 AATTTGCCGCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCCGCA * 717656 AATTTGCGGCAA 1 AATTTGCCGCAA 717668 CTGTTTGTCG Statistics Matches: 121, Mismatches: 9, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 59 121 1.00 ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26 Consensus pattern (59 bp): AATTTGCCGCAAACAGTTTGCCAGAAGCTAATTTGCATACGAATTCTGAACTTGCCGCA Found at i:717684 original size:24 final size:24 Alignment explanation

Indices: 717652--717720 Score: 81 Period size: 24 Copynumber: 3.0 Consensus size: 24 717642 CTGAACCTGC 717652 CGCAAATTTGCGGCAACTGTTTGT 1 CGCAAATTTGCGGCAACTGTTTGT * * * 717676 CGCAAATTTGCAGCAAAC--TCTCT 1 CGCAAATTTGCGGC-AACTGTTTGT 717699 -GCAAATTTGCGGCAACTGTTTG 1 CGCAAATTTGCGGCAACTGTTTG 717721 CCAGAGGCCT Statistics Matches: 36, Mismatches: 6, Indels: 7 0.73 0.12 0.14 Matches are distributed among these distances: 21 3 0.08 22 12 0.33 23 5 0.14 24 13 0.36 25 3 0.08 ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30 Consensus pattern (24 bp): CGCAAATTTGCGGCAACTGTTTGT Found at i:727483 original size:2 final size:2 Alignment explanation

Indices: 727476--727527 Score: 104 Period size: 2 Copynumber: 26.0 Consensus size: 2 727466 AAGGCACAAC 727476 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 727518 CT CT CT CT CT 1 CT CT CT CT CT 727528 GAAAGGAAAG Statistics Matches: 50, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 50 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:730278 original size:20 final size:20 Alignment explanation

Indices: 729931--730623 Score: 625 Period size: 20 Copynumber: 34.6 Consensus size: 20 729921 CCATGATCCG * 729931 CCACGCTCCACAACGACCCA 1 CCACGCTCCACAATGACCCA * * * ** 729951 CCATGCTTCACAACGAATCA 1 CCACGCTCCACAATGACCCA * * * 729971 CCACGATTCACAATGATCCA 1 CCACGCTCCACAATGACCCA ** 729991 CCACGCTCCACAATGAATCA 1 CCACGCTCCACAATGACCCA * 730011 CCACGCTCCACAACGACCCA 1 CCACGCTCCACAATGACCCA * * * ** 730031 CCATGCTTCACAACGAATCA 1 CCACGCTCCACAATGACCCA * * ** 730051 CCACGATTCACAATGATTCA 1 CCACGCTCCACAATGACCCA * ** 730071 CCACGCTCCATAATGAATCA 1 CCACGCTCCACAATGACCCA * 730091 CCACGCTCCACAATGATCCA 1 CCACGCTCCACAATGACCCA 730111 CCTA-GCTCCACAATGACCCA 1 CC-ACGCTCCACAATGACCCA * * 730131 CAACGCTCCACAATGATCCA 1 CCACGCTCCACAATGACCCA * * * 730151 CCACCCTCCACAATTATCCA 1 CCACGCTCCACAATGACCCA 730171 CCACGCTCCACAATGACCCA 1 CCACGCTCCACAATGACCCA * * * 730191 CTACGCTCCACAATTATCCA 1 CCACGCTCCACAATGACCCA 730211 CCACGCTCCACAATGACCCA 1 CCACGCTCCACAATGACCCA 730231 CCACGCTCCACAATGACCCA 1 CCACGCTCCACAATGACCCA 730251 CCACGCTCCACAATGACCCA 1 CCACGCTCCACAATGACCCA * 730271 TCACG-----C--T---CCA 1 CCACGCTCCACAATGACCCA * * * 730281 CCATGCTCCACTATAACCCA 1 CCACGCTCCACAATGACCCA * 730301 TCACGCTCCACAATGACCCA 1 CCACGCTCCACAATGACCCA * * * 730321 CCACGCCCCAAAATAACCCA 1 CCACGCTCCACAATGACCCA ** 730341 CCACGCTCCACAATGAATCA 1 CCACGCTCCACAATGACCCA * 730361 CCACGCTCCACAATGATCCA 1 CCACGCTCCACAATGACCCA 730381 CCACGCTCCACAATGACCCATAA 1 CCACGCTCCACAATGACCC---A * * 730404 CGCTCCACCATGCTCCACAATAACCTA 1 ----CCA-C--GCTCCACAATGACCCA * 730431 TCACGCTCCACAATGACCCA 1 CCACGCTCCACAATGACCCA ** 730451 CCACGCTCCACAATGAATCA 1 CCACGCTCCACAATGACCCA * * * 730471 CCACCCTCCACAATTATCCA 1 CCACGCTCCACAATGACCCA 730491 CCACGCTCCACAATGACCCA 1 CCACGCTCCACAATGACCCA * 730511 CTACGCTCCACAATGACCCA 1 CCACGCTCCACAATGACCCA * * 730531 CCACGATCCACAATAACCCA 1 CCACGCTCCACAATGACCCA * 730551 CCACGCTCCACAATGATCCA 1 CCACGCTCCACAATGACCCA * ** * 730571 CCATGCTCCACAATGATGCG 1 CCACGCTCCACAATGACCCA * * * ** 730591 TCACGCTTCACAATAAATCA 1 CCACGCTCCACAATGACCCA 730611 CCACGCTCCACAA 1 CCACGCTCCACAA 730624 AGATCCAGTA Statistics Matches: 552, Mismatches: 99, Indels: 44 0.79 0.14 0.06 Matches are distributed among these distances: 10 6 0.01 13 1 0.00 15 2 0.00 17 1 0.00 19 1 0.00 20 518 0.94 21 1 0.00 22 1 0.00 23 3 0.01 27 4 0.01 28 1 0.00 30 13 0.02 ACGTcount: A:0.32, C:0.44, G:0.09, T:0.15 Consensus pattern (20 bp): CCACGCTCCACAATGACCCA Found at i:730289 original size:30 final size:30 Alignment explanation

Indices: 730248--730441 Score: 113 Period size: 30 Copynumber: 6.1 Consensus size: 30 730238 CCACAATGAC 730248 CCACCACGCTCCACAATGACCCATCACGCT 1 CCACCACGCTCCACAATGACCCATCACGCT * * * 730278 CCACCATGCTCCACTATAACCCATCACGCT 1 CCACCACGCTCCACAATGACCCATCACGCT * * * * * ** ** 730308 CCACAATGAC-CCACCACGCCCCAAAATAAC- 1 CCACCACG-CTCCACAATGACCCATCA-CGCT * 730338 CCACCACGCTCCACAATGAATCACCACGCTCCACAATGAT 1 CCACCACGCTCCACAATG-A-C-CCA---T-CAC---GCT * 730378 CCACCACGCTCCACAATGACCCATAACGCT 1 CCACCACGCTCCACAATGACCCATCACGCT * * * 730408 CCACCATGCTCCACAATAACCTATCACGCT 1 CCACCACGCTCCACAATGACCCATCACGCT 730438 CCAC 1 CCAC 730442 AATGACCCAC Statistics Matches: 122, Mismatches: 28, Indels: 28 0.69 0.16 0.16 Matches are distributed among these distances: 29 1 0.01 30 88 0.72 31 2 0.02 32 1 0.01 33 5 0.04 34 1 0.01 37 4 0.03 38 1 0.01 39 1 0.01 40 18 0.15 ACGTcount: A:0.31, C:0.46, G:0.08, T:0.14 Consensus pattern (30 bp): CCACCACGCTCCACAATGACCCATCACGCT Found at i:730342 original size:130 final size:129 Alignment explanation

Indices: 730156--730623 Score: 569 Period size: 130 Copynumber: 3.7 Consensus size: 129 730146 ATCCACCACC * * * * * 730156 CTCCACAATTATCCACCACGCTCCACAATGACCCACTACGCTCCACAATTATCCACCACGCTCCA 1 CTCCACAATAACCCATCACGCTCCACAATGACCCACCACGCTCCACAA-TAACCACCACGCTCCA * 730221 CAATGACCCACCACGCTCCACAATGACCCACCACGCTCCACAATGACCCATCACGCTCCACCATG 65 CAATGAACCACCACGCTCCACAATGACCCACCACGCTCCACAATGACCCATCACGCTCCACCATG * * * 730286 CTCCACTATAACCCATCACGCTCCACAATGACCCACCACGCCCCAAAATAACCCACCACGCTCCA 1 CTCCACAATAACCCATCACGCTCCACAATGACCCACCACGCTCCACAATAA-CCACCACGCTCCA * * * 730351 CAATGAATCACCACGCTCCACAATGATCCACCACGCTCCACAATGACCCATAACGCTCCACCATG 65 CAATGAACCACCACGCTCCACAATGACCCACCACGCTCCACAATGACCCATCACGCTCCACCATG * * * 730416 CTCCACAATAACCTATCACGCTCCACAATGACCCACCACGCTCCACAATGAATCACCACCCTCCA 1 CTCCACAATAACCCATCACGCTCCACAATGACCCACCACGCTCCACAAT-AACCACCACGCTCCA * * * 730481 CAATTATCCACCACGCTCCACAATGACCCACTACGCTCCACAATGA-CC--CA----CCA-C--G 65 CAATGAACCACCACGCTCCACAATGACCCACCACGCTCCACAATGACCCATCACGCTCCACCATG * * * * ** ** * 730536 ATCCACAATAACCCACCACGCTCCACAATGATCCACCATGCTCCACAATGATGCGTCACGCTTCA 1 CTCCACAATAACCCATCACGCTCCACAATGACCCACCACGCTCCACAAT-AACCACCACGCTCCA * * 730601 CAATAAATCACCACGCTCCACAA 65 CAATGAACCACCACGCTCCACAA 730624 AGATCCAGTA Statistics Matches: 298, Mismatches: 38, Indels: 14 0.85 0.11 0.04 Matches are distributed among these distances: 120 75 0.25 122 1 0.00 123 3 0.01 127 1 0.00 129 4 0.01 130 212 0.71 131 2 0.01 ACGTcount: A:0.32, C:0.45, G:0.08, T:0.15 Consensus pattern (129 bp): CTCCACAATAACCCATCACGCTCCACAATGACCCACCACGCTCCACAATAACCACCACGCTCCAC AATGAACCACCACGCTCCACAATGACCCACCACGCTCCACAATGACCCATCACGCTCCACCATG Found at i:741462 original size:2 final size:2 Alignment explanation

Indices: 741455--741517 Score: 126 Period size: 2 Copynumber: 31.5 Consensus size: 2 741445 TTACATTGTG 741455 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 741497 TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA T 741518 GATNNNNNNN Statistics Matches: 61, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 61 1.00 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (2 bp): TA Found at i:743185 original size:2 final size:2 Alignment explanation

Indices: 743178--743209 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 743168 GAATAGAACG 743178 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 743210 NNNNNNNNNN Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:746459 original size:12 final size:12 Alignment explanation

Indices: 746442--746468 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 746432 TCACACCCCG 746442 ACCAAAATTATC 1 ACCAAAATTATC 746454 ACCAAAATTATC 1 ACCAAAATTATC 746466 ACC 1 ACC 746469 TCCTAATACT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 15 1.00 ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22 Consensus pattern (12 bp): ACCAAAATTATC Found at i:775901 original size:17 final size:17 Alignment explanation

Indices: 775879--775915 Score: 56 Period size: 17 Copynumber: 2.2 Consensus size: 17 775869 CATTCGCTAT * 775879 ATGAAATTGGGTATAAA 1 ATGAAATCGGGTATAAA * 775896 ATGAAATCGGGTATATA 1 ATGAAATCGGGTATAAA 775913 ATG 1 ATG 775916 TCATTTTACA Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 17 18 1.00 ACGTcount: A:0.43, C:0.03, G:0.24, T:0.30 Consensus pattern (17 bp): ATGAAATCGGGTATAAA Found at i:781173 original size:15 final size:15 Alignment explanation

Indices: 781153--781183 Score: 62 Period size: 15 Copynumber: 2.1 Consensus size: 15 781143 CGTGTTGTTA 781153 TAATTATACATGTAT 1 TAATTATACATGTAT 781168 TAATTATACATGTAT 1 TAATTATACATGTAT 781183 T 1 T 781184 TTGAACAAAT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48 Consensus pattern (15 bp): TAATTATACATGTAT Found at i:784530 original size:15 final size:15 Alignment explanation

Indices: 784512--784542 Score: 62 Period size: 15 Copynumber: 2.1 Consensus size: 15 784502 TTCCCCGGGG 784512 TGTTTTTGTTGTTGT 1 TGTTTTTGTTGTTGT 784527 TGTTTTTGTTGTTGT 1 TGTTTTTGTTGTTGT 784542 T 1 T 784543 TTGGGGTTTT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74 Consensus pattern (15 bp): TGTTTTTGTTGTTGT Found at i:784535 original size:12 final size:12 Alignment explanation

Indices: 784520--784544 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 784510 GGTGTTTTTG 784520 TTGTTGTTGTTT 1 TTGTTGTTGTTT 784532 TTGTTGTTGTTT 1 TTGTTGTTGTTT 784544 T 1 T 784545 GGGGTTTTTT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76 Consensus pattern (12 bp): TTGTTGTTGTTT Found at i:794371 original size:45 final size:45 Alignment explanation

Indices: 794320--794409 Score: 180 Period size: 45 Copynumber: 2.0 Consensus size: 45 794310 GATAACTGGA 794320 GGACTATACACAGGTGGTCTAACTGACTGGTTAGGTATAGGCCGC 1 GGACTATACACAGGTGGTCTAACTGACTGGTTAGGTATAGGCCGC 794365 GGACTATACACAGGTGGTCTAACTGACTGGTTAGGTATAGGCCGC 1 GGACTATACACAGGTGGTCTAACTGACTGGTTAGGTATAGGCCGC 794410 TTTGGAGCTT Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 45 45 1.00 ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24 Consensus pattern (45 bp): GGACTATACACAGGTGGTCTAACTGACTGGTTAGGTATAGGCCGC Found at i:794999 original size:49 final size:49 Alignment explanation

Indices: 794927--795026 Score: 200 Period size: 49 Copynumber: 2.0 Consensus size: 49 794917 AACATGCCTG 794927 GAAACAACAAATATACATTTATGTTTAACATTAACTTTTATTCAGAATA 1 GAAACAACAAATATACATTTATGTTTAACATTAACTTTTATTCAGAATA 794976 GAAACAACAAATATACATTTATGTTTAACATTAACTTTTATTCAGAATA 1 GAAACAACAAATATACATTTATGTTTAACATTAACTTTTATTCAGAATA 795025 GA 1 GA 795027 CTCATGTACA Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 49 51 1.00 ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36 Consensus pattern (49 bp): GAAACAACAAATATACATTTATGTTTAACATTAACTTTTATTCAGAATA Found at i:798123 original size:14 final size:14 Alignment explanation

Indices: 798077--798130 Score: 56 Period size: 14 Copynumber: 3.9 Consensus size: 14 798067 GAACGAGCAA * 798077 GAGAGAGACAGACG 1 GAGAGAGACAGAGG * * 798091 GACG-GACAAAGAGG 1 GA-GAGAGACAGAGG * 798105 AAGAGAGACAGAGG 1 GAGAGAGACAGAGG 798119 GAGAGAGACAGA 1 GAGAGAGACAGA 798131 TTTTCGACCT Statistics Matches: 31, Mismatches: 7, Indels: 4 0.74 0.17 0.10 Matches are distributed among these distances: 13 1 0.03 14 29 0.94 15 1 0.03 ACGTcount: A:0.46, C:0.11, G:0.43, T:0.00 Consensus pattern (14 bp): GAGAGAGACAGAGG Found at i:799169 original size:10 final size:10 Alignment explanation

Indices: 799154--799309 Score: 66 Period size: 10 Copynumber: 16.1 Consensus size: 10 799144 ATATTGTTTG 799154 TATTGTATAT 1 TATTGTATAT * 799164 TTTTGTATGA- 1 TATTGTAT-AT 799174 TATTGT-T-T 1 TATTGTATAT 799182 GTATTGTATAT 1 -TATTGTATAT * 799193 TTTTGTATGA- 1 TATTGTAT-AT ** 799203 TATTGT-TCG 1 TATTGTATAT 799212 TATTGTATAT 1 TATTGTATAT * 799222 TTTTGTATGA- 1 TATTGTAT-AT ** 799232 TATTGT-TCG 1 TATTGTATAT 799241 TATTGTATAT 1 TATTGTATAT * 799251 TTTTGTATGA- 1 TATTGTAT-AT 799261 TATTGT-TCA- 1 TATTGTAT-AT 799270 TATTGTATAT 1 TATTGTATAT * 799280 TTTTGTATGA- 1 TATTGTAT-AT ** 799290 TATTGT-TCG 1 TATTGTATAT 799299 TATTGTATAT 1 TATTGTATAT 799309 T 1 T 799310 TTCTCTGTGA Statistics Matches: 109, Mismatches: 20, Indels: 34 0.67 0.12 0.21 Matches are distributed among these distances: 9 37 0.34 10 66 0.61 11 6 0.06 ACGTcount: A:0.22, C:0.03, G:0.16, T:0.60 Consensus pattern (10 bp): TATTGTATAT Found at i:799175 original size:29 final size:29 Alignment explanation

Indices: 799133--799311 Score: 331 Period size: 29 Copynumber: 6.2 Consensus size: 29 799123 AACACTCTTG * 799133 ATTTTTGTATGATATTGTTTGTATTGTAT 1 ATTTTTGTATGATATTGTTCGTATTGTAT * 799162 ATTTTTGTATGATATTGTTTGTATTGTAT 1 ATTTTTGTATGATATTGTTCGTATTGTAT 799191 ATTTTTGTATGATATTGTTCGTATTGTAT 1 ATTTTTGTATGATATTGTTCGTATTGTAT 799220 ATTTTTGTATGATATTGTTCGTATTGTAT 1 ATTTTTGTATGATATTGTTCGTATTGTAT * 799249 ATTTTTGTATGATATTGTTCATATTGTAT 1 ATTTTTGTATGATATTGTTCGTATTGTAT 799278 ATTTTTGTATGATATTGTTCGTATTGTAT 1 ATTTTTGTATGATATTGTTCGTATTGTAT 799307 ATTTT 1 ATTTT 799312 CTCTGTGATG Statistics Matches: 147, Mismatches: 3, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 29 147 1.00 ACGTcount: A:0.21, C:0.02, G:0.16, T:0.60 Consensus pattern (29 bp): ATTTTTGTATGATATTGTTCGTATTGTAT Found at i:801295 original size:34 final size:34 Alignment explanation

Indices: 801208--801331 Score: 160 Period size: 34 Copynumber: 3.6 Consensus size: 34 801198 GAATAACAGT * 801208 TAATAAACATACTGACTAAAACTTACAGACTAGC 1 TAATAAGCATACTGACTAAAACTTACAGACTAGC * * * 801242 TAATTAGCATATACTGACTAAAATTTACGGACTAGC 1 TAATAAGC--ATACTGACTAAAACTTACAGACTAGC * 801278 TAATAAGCATACTGACTAAAACTTACAGTCTAGC 1 TAATAAGCATACTGACTAAAACTTACAGACTAGC * 801312 TAA-CAGCCATACTGACTAAA 1 TAATAAG-CATACTGACTAAA 801332 GAATTATGGA Statistics Matches: 78, Mismatches: 9, Indels: 6 0.84 0.10 0.06 Matches are distributed among these distances: 33 2 0.03 34 45 0.58 36 31 0.40 ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26 Consensus pattern (34 bp): TAATAAGCATACTGACTAAAACTTACAGACTAGC Found at i:804184 original size:2 final size:2 Alignment explanation

Indices: 804177--804291 Score: 216 Period size: 2 Copynumber: 58.5 Consensus size: 2 804167 TTCATAAATA 804177 CT CT CT CT CT C- CT CT CT CT CT -T CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 804217 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 804259 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 804292 CAGGAAAGTT Statistics Matches: 111, Mismatches: 0, Indels: 4 0.97 0.00 0.03 Matches are distributed among these distances: 1 2 0.02 2 109 0.98 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:805426 original size:3 final size:3 Alignment explanation

Indices: 805420--805457 Score: 58 Period size: 3 Copynumber: 12.7 Consensus size: 3 805410 TGACAACAAA * * 805420 GAT GAT GAT GAT GAT GAT GAT GAT GAT GGT GAT TAT GA 1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA 805458 CTCGGCATTT Statistics Matches: 31, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 3 31 1.00 ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34 Consensus pattern (3 bp): GAT Found at i:809457 original size:37 final size:38 Alignment explanation

Indices: 809416--809995 Score: 677 Period size: 37 Copynumber: 15.7 Consensus size: 38 809406 ACTCAAATTG * 809416 CAATGACAAATCTTACTTTCTGTTCATG-AATAGACAC 1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC ** * * 809453 CAATGGA-AGGTATTA-TTTCTGTTCATGTAATAGAAAC 1 CAAT-GACAATTCTTACTTTCTGTTCATGTAATAGACAC * ** 809490 CAATGGCAATTC-TAAATTCTGTTCATGTAATAGACAC 1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC * 809527 CAATGACAAGTCTTACTTTCTGTTCATG-AATAGACAC 1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC * * * 809564 CAATGGA-AGGTATATATTA-TTCCTGTTCATGTAATAGAAAC 1 CAAT-GACA---AT-TCTTACTTTCTGTTCATGTAATAGACAC * 809605 CAATGGCAATTCTTAC-TTCTGTTCATGTAATAGACAC 1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC 809642 CAATGACAATTCTTA-TTTCTGTTCATG-AATAGACAC 1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC * * * 809678 CAATGGCAAGTATTA-TTTCTGTTCATG-AATAGACAC 1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC * * * * * 809714 CAATGGCAAGTCTT-CTTTCTGTTCACGAAAAAGACAC 1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC * * * 809751 CAATGGCAAGTATTA-TTTCTGTTCATGTAATAGACAC 1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC * 809788 CAATGACAATTCTTAC-TTCTGTTTATGTAAT---CAC 1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC * 809822 CAATGGCAATTCTTAC-TTCTGTTCATG-AATAGACAC 1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC * 809858 CAATGACAAGTCTTAC-TTCTGTTCATGTAATAGACAC 1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC 809895 CAATGACAATTCTTAC-TTCTGTTCATGTAATAGACAC 1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC * 809932 CAATGGCAATTCTTAC-TTCTGTTCATGTAATAGACAC 1 CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC * 809969 CAATGGCAATTCTTAC-TTCTGTTCATG 1 CAATGACAATTCTTACTTTCTGTTCATG 809996 AAAAAACAAT Statistics Matches: 478, Mismatches: 43, Indels: 44 0.85 0.08 0.08 Matches are distributed among these distances: 33 3 0.01 34 28 0.06 36 109 0.23 37 289 0.60 38 19 0.04 40 13 0.03 41 17 0.04 ACGTcount: A:0.32, C:0.19, G:0.14, T:0.34 Consensus pattern (38 bp): CAATGACAATTCTTACTTTCTGTTCATGTAATAGACAC Found at i:816209 original size:16 final size:17 Alignment explanation

Indices: 816170--816212 Score: 52 Period size: 18 Copynumber: 2.5 Consensus size: 17 816160 ATTTTTTCAT 816170 TGAAACTAAAAAAAAACCA 1 TGAAA-TAAAAAAAAA-CA * 816189 CGAAATAAAAAAAAA-A 1 TGAAATAAAAAAAAACA 816205 TGAAATAA 1 TGAAATAA 816213 TTATGACGTC Statistics Matches: 22, Mismatches: 2, Indels: 3 0.81 0.07 0.11 Matches are distributed among these distances: 16 8 0.36 18 10 0.45 19 4 0.18 ACGTcount: A:0.72, C:0.09, G:0.07, T:0.12 Consensus pattern (17 bp): TGAAATAAAAAAAAACA Found at i:823063 original size:25 final size:25 Alignment explanation

Indices: 823021--823112 Score: 89 Period size: 25 Copynumber: 3.7 Consensus size: 25 823011 TGTACCAAAG ** * 823021 GTGCTATGTTTAAATGTCTGTTAAT 1 GTGCTATGTTGCACTGTCTGTTAAT * 823046 GTGCTATGTTGCACTGTCTGCTAAT 1 GTGCTATGTTGCACTGTCTGTTAAT * * 823071 G-G-TGATATTGCACTGACTGTTAAT 1 GTGCT-ATGTTGCACTGTCTGTTAAT * 823095 GATGCTATGTTGCTCTGT 1 G-TGCTATGTTGCACTGT 823113 TAGTTTATGG Statistics Matches: 53, Mismatches: 10, Indels: 7 0.76 0.14 0.10 Matches are distributed among these distances: 23 1 0.02 24 19 0.36 25 22 0.42 26 10 0.19 27 1 0.02 ACGTcount: A:0.20, C:0.14, G:0.24, T:0.42 Consensus pattern (25 bp): GTGCTATGTTGCACTGTCTGTTAAT Found at i:834300 original size:16 final size:16 Alignment explanation

Indices: 834279--834309 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 834269 ATTAAATTTT * 834279 GAGAGATCAAGAGTTC 1 GAGAGATCAAAAGTTC 834295 GAGAGATCAAAAGTT 1 GAGAGATCAAAAGTT 834310 AAAAAACAAT 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:0.42, C:0.10, G:0.29, T:0.19 Consensus pattern (16 bp): GAGAGATCAAAAGTTC Found at i:837758 original size:23 final size:23 Alignment explanation

Indices: 837726--837773 Score: 71 Period size: 23 Copynumber: 2.1 Consensus size: 23 837716 GGGACCAAAT 837726 TTGGCCCTTA-CCTTACCTTGTTC 1 TTGGCCCTTATCC-TACCTTGTTC * 837749 TTGGCTCTTATCCTACCTTGTTC 1 TTGGCCCTTATCCTACCTTGTTC 837772 TT 1 TT 837774 TAATGATAAA Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 23 21 0.91 24 2 0.09 ACGTcount: A:0.08, C:0.31, G:0.12, T:0.48 Consensus pattern (23 bp): TTGGCCCTTATCCTACCTTGTTC Found at i:843769 original size:14 final size:14 Alignment explanation

Indices: 843750--843777 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 843740 TTTTAATGTC 843750 TGTATATGTGCAGA 1 TGTATATGTGCAGA 843764 TGTATATGTGCAGA 1 TGTATATGTGCAGA 843778 GAACCCAAAA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36 Consensus pattern (14 bp): TGTATATGTGCAGA Found at i:847486 original size:2 final size:2 Alignment explanation

Indices: 847479--847520 Score: 77 Period size: 2 Copynumber: 21.5 Consensus size: 2 847469 GAAAGTGATT 847479 GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 847520 G 1 G 847521 TGTTTCAGAG Statistics Matches: 39, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 1 1 0.03 2 38 0.97 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): GA Found at i:860950 original size:20 final size:20 Alignment explanation

Indices: 860925--860962 Score: 76 Period size: 20 Copynumber: 1.9 Consensus size: 20 860915 TTATTTAATC 860925 ATATGGTATGGTACAAAATT 1 ATATGGTATGGTACAAAATT 860945 ATATGGTATGGTACAAAA 1 ATATGGTATGGTACAAAA 860963 ACTGGCATTG Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32 Consensus pattern (20 bp): ATATGGTATGGTACAAAATT Found at i:870199 original size:34 final size:34 Alignment explanation

Indices: 870158--871022 Score: 639 Period size: 34 Copynumber: 25.0 Consensus size: 34 870148 TCATAGTGTT * 870158 CGTAAATACTAAAGGACCATAGTGGCACCACGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * 870192 CGTAAATAATGAAA-TACCATAGTGGCACCACGTA 1 CGTAAATACT-AAAGTACCATAGTGGCACCACGTA * * 870226 CGTAAATAATAAAATACCATAGTGGCACCACGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * 870260 CGTAAATAATAAAATACCATAGTGGCACCACGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * ** * 870294 CATAAATACTAAAGTATCATAGTAACACGACGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * 870328 CGTAAATACTAAAGGACCATAGTGGCACTAC-TCA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGT-A * * * * * * 870362 TGTAAATGCTAAGGTACTATAGTAGCACCAGGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * * * 870396 CGTAAATAATAAAGGACCACAGTGGCACCTC-TCA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGT-A ** * * 870430 TTTAAATACTAAAGTACCATAGTAGTACCACGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * 870464 CGTAAATACTAAAGTACC--AGTGACATCACGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * * 870496 CCTAAATATTAAAGTACCATAGTGGCACAACGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * * * * * 870530 CGTAAATATTAAAGAAACACAGTAGTACCACGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * 870564 CGTAAATAATAAAATACCATAGTGGCACCACGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * * * 870598 CCTAAATATTAAAGTACCATAGTGCCACTACGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * * * 870632 CGTAAATACTAAAGTAACACAGTAGTACCACGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * * * 870666 CGTGAATAATAAAATACCATAGTGGAACCACGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * * * * 870700 CGTAAATACTAAAGTACCATAATCGTACAACCTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * * ** 870734 AGTAAATAGTAAAGTACCATAGTGGAACCACCCA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * * * * * * 870768 CGTTAATTCTAAAGTACGTAAATATTAAAGTACTACAGTA 1 CGTAAATACTAAAGTAC---CATAGT--GGCACCAC-GTA * * * 870808 -GTACCACGTACTTAAATGATAAAGTACTATAGTGGCACCACGTT 1 CGTA--A-ATAC-T--A-----AAGTACCATAGTGGCACCACGTA * * * * 870852 CGTAAATAATAAAGAACCATGGTGGCACCATGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * ** * 870886 CGTAAATACTGAAGTACCATTTTGGTACCACGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * * * 870920 AGTAAATACTTAAGTACCAT-GATGGTACCATGTA 1 CGTAAATACTAAAGTACCATAG-TGGCACCACGTA * * * * * 870954 CGTTAATACTAAAATATCATAGTGGTACCATGTA 1 CGTAAATACTAAAGTACCATAGTGGCACCACGTA * * * * 870988 CATAAATA-TCAAAGAACCATAATGTCACCACGTA 1 CGTAAATACT-AAAGTACCATAGTGGCACCACGTA 871022 C 1 C 871023 ACTCCCGATA Statistics Matches: 649, Mismatches: 153, Indels: 58 0.75 0.18 0.07 Matches are distributed among these distances: 32 26 0.04 33 6 0.01 34 569 0.88 35 6 0.01 37 4 0.01 39 8 0.01 40 1 0.00 41 2 0.00 42 4 0.01 43 2 0.00 44 2 0.00 45 9 0.01 47 4 0.01 50 6 0.01 ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23 Consensus pattern (34 bp): CGTAAATACTAAAGTACCATAGTGGCACCACGTA Found at i:870935 original size:152 final size:152 Alignment explanation

Indices: 870629--870936 Score: 339 Period size: 152 Copynumber: 2.0 Consensus size: 152 870619 GTGCCACTAC * 870629 GTACGTAAATACTAAAGTAACACAGTAGTACCACGTACGTGAATAATAAAATACCATAGTGGAAC 1 GTACGTAAATACTAAAGTAACACAGTAGTACCACGTACGTAAATAATAAAATACCATAGTGGAAC * * * * 870694 CACGTACGTAAATACTAAAGTACCATAATCGTACAACCTAAGTAAATAGTAAAGTACCATAGTGG 66 CACGTACGTAAATAATAAAGAACCATAATCGCACAACCTAAGTAAATACTAAAGTACCATAGTGG * * * 870759 AACCACCCACGTTAATTCTAAA 131 AACCACCCAAGTAAATACTAAA * * * * * * 870781 GTACGTAAATATTAAAGT-ACTACAGTAGTACCACGTACTTAAATGATAAAGTACTATAGTGGCA 1 GTACGTAAATACTAAAGTAAC-ACAGTAGTACCACGTACGTAAATAATAAAATACCATAGTGGAA * ** * * ** * * ** 870845 CCACGTTCGTAAATAATAAAGAACCATGGTGGCACCATGTACGTAAATACTGAAGTACCATTTTG 65 CCACGTACGTAAATAATAAAGAACCATAATCGCACAACCTAAGTAAATACTAAAGTACCATAGTG * ** * 870910 GTACCACGTAAGTAAATACTTAA 130 GAACCACCCAAGTAAATACTAAA 870933 GTAC 1 GTAC 870937 CATGATGGTA Statistics Matches: 126, Mismatches: 29, Indels: 2 0.80 0.18 0.01 Matches are distributed among these distances: 151 2 0.02 152 124 0.98 ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25 Consensus pattern (152 bp): GTACGTAAATACTAAAGTAACACAGTAGTACCACGTACGTAAATAATAAAATACCATAGTGGAAC CACGTACGTAAATAATAAAGAACCATAATCGCACAACCTAAGTAAATACTAAAGTACCATAGTGG AACCACCCAAGTAAATACTAAA Found at i:873616 original size:21 final size:21 Alignment explanation

Indices: 873590--873630 Score: 57 Period size: 21 Copynumber: 2.0 Consensus size: 21 873580 ATCTTTTTTC 873590 GCATGTCAACAT-ATATAAGTT 1 GCATGTCAACATGA-ATAAGTT * 873611 GCATGTCGACATGAATAAGT 1 GCATGTCAACATGAATAAGT 873631 AGAATGCAGC Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 21 17 0.94 22 1 0.06 ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29 Consensus pattern (21 bp): GCATGTCAACATGAATAAGTT Found at i:873739 original size:21 final size:21 Alignment explanation

Indices: 873712--873791 Score: 115 Period size: 21 Copynumber: 3.8 Consensus size: 21 873702 ACCGCAATTT 873712 TCTTGCATGTCAACATAACTA 1 TCTTGCATGTCAACATAACTA * * 873733 TGTTGCATGTTAACATAACTA 1 TCTTGCATGTCAACATAACTA ** 873754 TCTTGCATGTCAACATATTTA 1 TCTTGCATGTCAACATAACTA * 873775 TCTTGCATGTCGACATA 1 TCTTGCATGTCAACATA 873792 TTCTATAGGA Statistics Matches: 52, Mismatches: 7, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 21 52 1.00 ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38 Consensus pattern (21 bp): TCTTGCATGTCAACATAACTA Found at i:876951 original size:31 final size:31 Alignment explanation

Indices: 876145--876940 Score: 1402 Period size: 31 Copynumber: 25.7 Consensus size: 31 876135 GCGATCTTGA * 876145 TTATATGACTCTATCAACTACACATTATGAT 1 TTATATGACTCTATCAACTACACATTATGTT 876176 TTATATGACTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT * 876207 TTATATGA--CTATCAAATACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT 876236 TTATATGACTCTATCAACTACACATTATGTTT 1 TTATATGACTCTATCAACTACACATTATG-TT 876268 GTANTATATGACTCTATCAACTACACATTATGTT 1 -T--TATATGACTCTATCAACTACACATTATGTT 876302 TTATATGACTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT 876333 TTATATGACTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT 876364 TTATATGACTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT * 876395 TTATGTGACTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT 876426 TTATATGACTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT 876457 TTATATGACTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT 876488 TTATATGACTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT 876519 TTATATGACTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT 876550 TTATATGACTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT * 876581 TTATGTGACTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT * * * 876612 TTATGTAAATCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT * * 876643 TTATGTGACTCTATCAACTACACATTATGAT 1 TTATATGACTCTATCAACTACACATTATGTT 876674 TTATATGACTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT 876705 TTATATGA--CTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT * 876734 TTATATGTCTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT 876765 TTATATGACTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT * 876796 TTATGTGACTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT * 876827 TTATATGTCTCTATCAACTACACATTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT * 876858 TTATATGACTCTATCAACTACACAGTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT * 876889 TTATATGACTCTATCAACTACACAGTATGTT 1 TTATATGACTCTATCAACTACACATTATGTT 876920 TTATATGACTCTATCAACTAC 1 TTATATGACTCTATCAACTAC 876941 TCGTTTTGTT Statistics Matches: 737, Mismatches: 20, Indels: 16 0.95 0.03 0.02 Matches are distributed among these distances: 29 56 0.08 31 647 0.88 32 2 0.00 33 2 0.00 34 2 0.00 35 28 0.04 ACGTcount: A:0.32, C:0.19, G:0.07, T:0.41 Consensus pattern (31 bp): TTATATGACTCTATCAACTACACATTATGTT Found at i:877696 original size:30 final size:30 Alignment explanation

Indices: 877660--877760 Score: 166 Period size: 30 Copynumber: 3.4 Consensus size: 30 877650 TTAGGTATTT * 877660 AGTGATGGAAATATTGTGTAATGGGTTATG 1 AGTGATGAAAATATTGTGTAATGGGTTATG * 877690 AGTGATGAAAATATTATGTAATGGGTTATG 1 AGTGATGAAAATATTGTGTAATGGGTTATG * 877720 AGTGATGAAAATATTGTGTAATGGGTTGTG 1 AGTGATGAAAATATTGTGTAATGGGTTATG * 877750 AGTGAAGAAAA 1 AGTGATGAAAA 877761 AATGATGTAT Statistics Matches: 66, Mismatches: 5, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 30 66 1.00 ACGTcount: A:0.36, C:0.00, G:0.31, T:0.34 Consensus pattern (30 bp): AGTGATGAAAATATTGTGTAATGGGTTATG Found at i:877709 original size:60 final size:60 Alignment explanation

Indices: 877645--877791 Score: 179 Period size: 60 Copynumber: 2.5 Consensus size: 60 877635 TGAACAAAGC * * * * * 877645 ATGTATTAGG-TATTTAGTGATGGAAATATTGTGTAATGGGTTATGAGTGATGAAAATATT 1 ATGTATTAGGTTA-TGAGTGATGAAAATATTGTGTAATGGGTTATGAGTGAAGAAAAAATG * * * 877705 ATGTAATGGGTTATGAGTGATGAAAATATTGTGTAATGGGTTGTGAGTGAAGAAAAAATG 1 ATGTATTAGGTTATGAGTGATGAAAATATTGTGTAATGGGTTATGAGTGAAGAAAAAATG ** * 877765 ATGTATTAAATAATGAGTGATGAAAAT 1 ATGTATTAGGTTATGAGTGATGAAAAT 877792 CATTCAGGTT Statistics Matches: 73, Mismatches: 13, Indels: 2 0.83 0.15 0.02 Matches are distributed among these distances: 60 71 0.97 61 2 0.03 ACGTcount: A:0.37, C:0.00, G:0.27, T:0.35 Consensus pattern (60 bp): ATGTATTAGGTTATGAGTGATGAAAATATTGTGTAATGGGTTATGAGTGAAGAAAAAATG Found at i:878160 original size:32 final size:32 Alignment explanation

Indices: 878119--879457 Score: 1799 Period size: 32 Copynumber: 41.7 Consensus size: 32 878109 AAAACTCTTT * * 878119 CTTAGTAATACCAGTACATTATATCCTAGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC 878151 CTTAGTAATATCAGTACATTATATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC 878183 CTTAGTAATATCAGTACATTATATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC 878215 CTTAGTAATATCAGTACATTATATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * 878247 CTTAGTAATATCAGTACATTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * 878279 CCTAG-ATATATCAGTACATTATATCCTCGGTC 1 CTTAGTA-ATATCAGTACATTATATCCTCGGTC * * 878311 CTTAGTCATATCAGTACATTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * * * * 878343 CCTAGTAATATCAGAAGTCCCTGGTA-AT-ATCAGTAC 1 CTTAGTAATATC---AGTACAT--TATATCCTCGGT-C * * * ** * * * 878379 ATTA-T-ATCCTCGGCCCCTAGTAATATCAGT-AGTC 1 CTTAGTAAT-ATCAG-TAC-A-TTATATC-CTCGGTC * * * * 878413 CCTGGTGATATCAGTACATTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * 878445 CTTAGTAATATCAGTACATTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC 878477 CTTAGTAATATCAGTACATTATATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * 878509 CTTAGTAATATCAGTACATTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC 878541 CTTAGTAATATCAGTACATTATATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * 878573 CTTAGTAATATCAGTACACTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * 878605 CTTAGTAATATCAGTACATTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * 878637 CCTAGTAATATCAGTACATTATATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * 878669 CTTAGTAATATCAGTACATTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * * 878701 CCTAGTAATATTAGTACATTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * * * 878733 CCTGGTAATATCAATACATTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * * 878765 CCTAGTACTATCAGTACATTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * 878797 CCTGGTAATATCAGTACATTATATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * 878829 CTTAGTAATATTAGTACATTATATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * 878861 CCTAGTAATATCAGTACATTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * 878893 CCTGGTAATATCAGTACATTATATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * 878925 CTTAGTAATTTCAGTACATTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * 878957 CCTAGTAATATCAGTATATTATATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * 878989 CTTAGTAATTTCAGTACATTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * * 879021 CCTAGTAATATCAGTACATTATATCCTCAGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * 879053 CTTAGTAATATCAGTATATTGTATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC 879085 CTTAGTAATATCAGTACATTATATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * 879117 CTTAGTAATATCAGTACATTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * * * 879149 CCTAGTGATATCAGTACATTGTATCTTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * * 879181 CCTGGTAATATCAGTTCATTATATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * 879213 CTTAGTAATATCAGTACATTGTATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC 879245 CTTAGTAATATCAGTACATTATATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * 879277 CTTAGTAATATCAGTACATTATATCCTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * * * 879309 CCTAGTGATATCAGTACATTGTATCTTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * * 879341 CCTGGTAATATCAGTTCATTATATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC 879373 CTTAGTAATATCAGTACATTATATCCTCGGTC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * * 879405 CTTAGTAATATCAGTACATTGTATCTTCGGCC 1 CTTAGTAATATCAGTACATTATATCCTCGGTC * * * 879437 CCTACTAATATTAGTACATTA 1 CTTAGTAATATCAGTACATTA 879458 GAAGTTCTAT Statistics Matches: 1164, Mismatches: 125, Indels: 36 0.88 0.09 0.03 Matches are distributed among these distances: 31 2 0.00 32 1122 0.96 33 4 0.00 34 7 0.01 35 19 0.02 36 8 0.01 37 2 0.00 ACGTcount: A:0.27, C:0.24, G:0.13, T:0.35 Consensus pattern (32 bp): CTTAGTAATATCAGTACATTATATCCTCGGTC Found at i:878459 original size:51 final size:51 Alignment explanation

Indices: 878318--878460 Score: 259 Period size: 51 Copynumber: 2.8 Consensus size: 51 878308 GTCCTTAGTC * 878318 ATATCAGTACATTATATCCTCGGCCCCTAGTAATATCAGAAGTCCCTGGTA 1 ATATCAGTACATTATATCCTCGGCCCCTAGTAATATCAGTAGTCCCTGGTA * 878369 ATATCAGTACATTATATCCTCGGCCCCTAGTAATATCAGTAGTCCCTGGTG 1 ATATCAGTACATTATATCCTCGGCCCCTAGTAATATCAGTAGTCCCTGGTA * 878420 ATATCAGTACATTATATCCTCGGCCCTTAGTAATATCAGTA 1 ATATCAGTACATTATATCCTCGGCCCCTAGTAATATCAGTA 878461 CATTATATCC Statistics Matches: 89, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 51 89 1.00 ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31 Consensus pattern (51 bp): ATATCAGTACATTATATCCTCGGCCCCTAGTAATATCAGTAGTCCCTGGTA Found at i:878520 original size:83 final size:81 Alignment explanation

Indices: 878267--878520 Score: 246 Period size: 83 Copynumber: 3.1 Consensus size: 81 878257 TCAGTACATT * * 878267 ATATCCTCGGCCCCTAG-ATATATCAGTACATTATATCCTCGGTCCTTAGTCATATCAGTACATT 1 ATATCCTCGG-CCCTAGTA-ATATCAGTACATTATATCCTCGGCCCTTAGTAATATCAGTACATT * 878331 ATATCCTCGGCCCCTAGTA 64 ATATCCTCGG-TCCTAGTA *** * * * * 878350 ATATCAGAAGTCCCTGGTAATATCAGTACATTATATCCTCGGCCCCTAGTAATATCAGTAGTCCC 1 ATATC-CTCGGCCCTAGTAATATCAGTACATTATATCCTCGGCCCTTAGTAATATCAGTA---CA ** * * * * 878415 TGGTGAT-ATCAGTAC-A-TT 62 TTAT-ATCCTCGGTCCTAGTA 878433 ATATCCTCGGCCCTTAGTAATATCAGTACATTATATCCTCGGCCCTTAGTAATATCAGTACATTA 1 ATATCCTCGGCCC-TAGTAATATCAGTACATTATATCCTCGGCCCTTAGTAATATCAGTACATTA 878498 TATCCTCGGTCCTTAGTA 65 TATCCTCGGTCC-TAGTA 878516 ATATC 1 ATATC 878521 AGTACATTAT Statistics Matches: 131, Mismatches: 29, Indels: 22 0.72 0.16 0.12 Matches are distributed among these distances: 79 2 0.02 80 8 0.06 82 5 0.04 83 104 0.79 84 3 0.02 85 1 0.01 86 6 0.05 87 2 0.02 ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33 Consensus pattern (81 bp): ATATCCTCGGCCCTAGTAATATCAGTACATTATATCCTCGGCCCTTAGTAATATCAGTACATTAT ATCCTCGGTCCTAGTA Found at i:881548 original size:18 final size:18 Alignment explanation

Indices: 881525--881560 Score: 54 Period size: 18 Copynumber: 2.0 Consensus size: 18 881515 TATAAGTTTG 881525 AATTAATCAAAGAGTCTT 1 AATTAATCAAAGAGTCTT * * 881543 AATTAATTAAGGAGTCTT 1 AATTAATCAAAGAGTCTT 881561 CTCGTTTTCA 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:0.42, C:0.08, G:0.14, T:0.36 Consensus pattern (18 bp): AATTAATCAAAGAGTCTT Found at i:889631 original size:41 final size:41 Alignment explanation

Indices: 889579--889660 Score: 155 Period size: 41 Copynumber: 2.0 Consensus size: 41 889569 ACCAGAGATC 889579 ATCCCCAAGACATAGAGGGAGTGAAGTATCAGCAAACAGAG 1 ATCCCCAAGACATAGAGGGAGTGAAGTATCAGCAAACAGAG * 889620 ATCCCCAAGACATAGATGGAGTGAAGTATCAGCAAACAGAG 1 ATCCCCAAGACATAGAGGGAGTGAAGTATCAGCAAACAGAG 889661 GATGATAGAC Statistics Matches: 40, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 41 40 1.00 ACGTcount: A:0.41, C:0.20, G:0.26, T:0.13 Consensus pattern (41 bp): ATCCCCAAGACATAGAGGGAGTGAAGTATCAGCAAACAGAG Found at i:893163 original size:62 final size:62 Alignment explanation

Indices: 893093--893224 Score: 219 Period size: 62 Copynumber: 2.1 Consensus size: 62 893083 TATTAAATGA ** * 893093 TTTTATTATACTTTTTTGTTAAATACTGAAATCTGATTGGTTTAGACGCAGTTGGTAATTCG 1 TTTTATTATACTTTCATGTTAAATACTGAAATCTGATTGGTTTAGACGCAGTTGGTAATCCG * 893155 TTTTATTATACTTTCATGTTCAATACTGAAATCTGATTGGTTTAGACGCAGTTGGTAATCCG 1 TTTTATTATACTTTCATGTTAAATACTGAAATCTGATTGGTTTAGACGCAGTTGGTAATCCG * 893217 TTCTATTA 1 TTTTATTA 893225 CCCTCAGCGT Statistics Matches: 65, Mismatches: 5, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 62 65 1.00 ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45 Consensus pattern (62 bp): TTTTATTATACTTTCATGTTAAATACTGAAATCTGATTGGTTTAGACGCAGTTGGTAATCCG Found at i:893462 original size:43 final size:43 Alignment explanation

Indices: 893401--893485 Score: 143 Period size: 43 Copynumber: 2.0 Consensus size: 43 893391 GTTTGAGAGG * 893401 GTAACTGTTGAAATTGACACCCCGAGAAAACCATTGTCAACCA 1 GTAACTGTTGAAACTGACACCCCGAGAAAACCATTGTCAACCA ** 893444 GTAACTGTTGAAACTGACACCCCTCGAAAACCATTGTCAACC 1 GTAACTGTTGAAACTGACACCCCGAGAAAACCATTGTCAACC 893486 TCCGCTTTGC Statistics Matches: 39, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 43 39 1.00 ACGTcount: A:0.35, C:0.28, G:0.15, T:0.21 Consensus pattern (43 bp): GTAACTGTTGAAACTGACACCCCGAGAAAACCATTGTCAACCA Found at i:894175 original size:21 final size:21 Alignment explanation

Indices: 894149--894276 Score: 179 Period size: 21 Copynumber: 6.1 Consensus size: 21 894139 ATAATATTTT * 894149 TTTCGCGAATAAACGCGTAAC 1 TTTCGCGAATAAACGCGAAAC 894170 TTTCGCGAATAAACGCGAAAC 1 TTTCGCGAATAAACGCGAAAC * ** * 894191 TTTTGCG-ATATAACGCGTTAG 1 TTTCGCGAATA-AACGCGAAAC 894212 TTTCGCGAATAAACGCGAAAC 1 TTTCGCGAATAAACGCGAAAC 894233 TTTCGCGAATAAACGCGAAAC 1 TTTCGCGAATAAACGCGAAAC 894254 TTTCGC-AATTAAACGCGAAAC 1 TTTCGCGAA-TAAACGCGAAAC 894275 TT 1 TT 894277 AAAAATAAAT Statistics Matches: 95, Mismatches: 9, Indels: 6 0.86 0.08 0.05 Matches are distributed among these distances: 20 5 0.05 21 87 0.92 22 3 0.03 ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25 Consensus pattern (21 bp): TTTCGCGAATAAACGCGAAAC Found at i:894269 original size:63 final size:63 Alignment explanation

Indices: 894149--894270 Score: 201 Period size: 63 Copynumber: 1.9 Consensus size: 63 894139 ATAATATTTT * * * 894149 TTTCGCGAATAAACGCGTAACTTTCGCGAATAAACGCGAAACTTTTGCGATATAACGCGTTAG 1 TTTCGCGAATAAACGCGAAACTTTCGCGAATAAACGCGAAACTTTCGCAATATAACGCGTTAG 894212 TTTCGCGAATAAACGCGAAACTTTCGCGAATAAACGCGAAACTTTCGCAAT-TAAACGCG 1 TTTCGCGAATAAACGCGAAACTTTCGCGAATAAACGCGAAACTTTCGCAATAT-AACGCG 894271 AAACTTAAAA Statistics Matches: 55, Mismatches: 3, Indels: 2 0.92 0.05 0.03 Matches are distributed among these distances: 62 1 0.02 63 54 0.98 ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25 Consensus pattern (63 bp): TTTCGCGAATAAACGCGAAACTTTCGCGAATAAACGCGAAACTTTCGCAATATAACGCGTTAG Found at i:895162 original size:21 final size:21 Alignment explanation

Indices: 895132--895262 Score: 192 Period size: 21 Copynumber: 6.2 Consensus size: 21 895122 TAATAGTTTT * * * 895132 GCGTTAATTCGCGAAACTTAC 1 GCGTTTATTCGCGAAAGTAAC 895153 GCGTTTATTCGCGAAAGTAAC 1 GCGTTTATTCGCGAAAGTAAC 895174 GCGTTTATTCGCGAAAGTAAC 1 GCGTTTATTCGCGAAAGTAAC 895195 GCGTTTATTCGCGAAAGTAAC 1 GCGTTTATTCGCGAAAGTAAC ** 895216 GCGTTTATTCGCGAAAGTTTC 1 GCGTTTATTCGCGAAAGTAAC * 895237 GCG-TTATATCGCGAAAGTTAC 1 GCGTTTAT-TCGCGAAAGTAAC 895258 GCGTT 1 GCGTT 895263 NNNNNNNNNN Statistics Matches: 102, Mismatches: 6, Indels: 3 0.92 0.05 0.03 Matches are distributed among these distances: 20 4 0.04 21 97 0.95 22 1 0.01 ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31 Consensus pattern (21 bp): GCGTTTATTCGCGAAAGTAAC Found at i:897248 original size:13 final size:12 Alignment explanation

Indices: 897227--897258 Score: 55 Period size: 13 Copynumber: 2.6 Consensus size: 12 897217 ATGCTTATAG 897227 TCTTATACATAA 1 TCTTATACATAA 897239 TCTGTATACATAA 1 TCT-TATACATAA 897252 TCTTATA 1 TCTTATA 897259 TCTAAATACC Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 12 7 0.37 13 12 0.63 ACGTcount: A:0.38, C:0.16, G:0.03, T:0.44 Consensus pattern (12 bp): TCTTATACATAA Found at i:898694 original size:2 final size:2 Alignment explanation

Indices: 898687--898713 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 898677 CTGTAATGCA 898687 TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC T 898714 GTAAAAAAAT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): TC Found at i:903142 original size:41 final size:41 Alignment explanation

Indices: 903085--903169 Score: 161 Period size: 41 Copynumber: 2.1 Consensus size: 41 903075 CTTTAGTATA 903085 GGTTTAGGCTTTTACAAGGTAGATTATACTGAGGTAGAGGT 1 GGTTTAGGCTTTTACAAGGTAGATTATACTGAGGTAGAGGT * 903126 GGTTTAGGCTTTTACAAGGTAGATTATACTGAGGTTGAGGT 1 GGTTTAGGCTTTTACAAGGTAGATTATACTGAGGTAGAGGT 903167 GGT 1 GGT 903170 GATTTGGTAG Statistics Matches: 43, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 41 43 1.00 ACGTcount: A:0.25, C:0.07, G:0.33, T:0.35 Consensus pattern (41 bp): GGTTTAGGCTTTTACAAGGTAGATTATACTGAGGTAGAGGT Found at i:903999 original size:60 final size:60 Alignment explanation

Indices: 903906--904028 Score: 210 Period size: 60 Copynumber: 2.0 Consensus size: 60 903896 GAATTTATCA * * * 903906 TCACATTTTCGCGTTTGTAGAAGTTGAAATCTACTTGTTCATTTAATCAAAATGGTTTAT 1 TCACATTTTCGCCTTTGTAGAACTTGAAATCTACTTGTTCATTTAATCAAAATGGCTTAT * 903966 TCACATTTTCGCCTTTGTAGAACTTGAAATCTACTTGTTCTTTTAATCAAAATGGCTTAT 1 TCACATTTTCGCCTTTGTAGAACTTGAAATCTACTTGTTCATTTAATCAAAATGGCTTAT 904026 TCA 1 TCA 904029 TTCTATGTAC Statistics Matches: 59, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 60 59 1.00 ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43 Consensus pattern (60 bp): TCACATTTTCGCCTTTGTAGAACTTGAAATCTACTTGTTCATTTAATCAAAATGGCTTAT Found at i:910432 original size:41 final size:41 Alignment explanation

Indices: 910372--910451 Score: 133 Period size: 41 Copynumber: 2.0 Consensus size: 41 910362 GTATAAGTTA * 910372 AGGCTTTTACAAGGTAGATTATACTGAGGTAGAGGTGGTTT 1 AGGCTTTTACAAGGAAGATTATACTGAGGTAGAGGTGGTTT * * 910413 AGGCTTTTACAAGGAAGATTATACTGAGTTTGAGGTGGT 1 AGGCTTTTACAAGGAAGATTATACTGAGGTAGAGGTGGT 910452 GATTTGGTAG Statistics Matches: 36, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 41 36 1.00 ACGTcount: A:0.28, C:0.07, G:0.31, T:0.34 Consensus pattern (41 bp): AGGCTTTTACAAGGAAGATTATACTGAGGTAGAGGTGGTTT Found at i:911082 original size:2 final size:2 Alignment explanation

Indices: 911075--911147 Score: 146 Period size: 2 Copynumber: 36.5 Consensus size: 2 911065 CGTCATTGAT 911075 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 911117 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 911148 TTTATAAATC Statistics Matches: 71, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 71 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:914296 original size:20 final size:20 Alignment explanation

Indices: 914271--914328 Score: 80 Period size: 20 Copynumber: 2.9 Consensus size: 20 914261 TTTACGATAT 914271 CATATGATACAATATCATAA 1 CATATGATACAATATCATAA * * 914291 CATATGATACATTATCATAT 1 CATATGATACAATATCATAA ** 914311 CATATGATTTAATATCAT 1 CATATGATACAATATCAT 914329 GGGAATAGGA Statistics Matches: 33, Mismatches: 5, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 20 33 1.00 ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38 Consensus pattern (20 bp): CATATGATACAATATCATAA Found at i:915408 original size:19 final size:19 Alignment explanation

Indices: 915374--915410 Score: 56 Period size: 19 Copynumber: 1.9 Consensus size: 19 915364 AAGGGCACCT * 915374 GCTCCAAAAACTTTAACCA 1 GCTCCAAAAACCTTAACCA * 915393 GCTCCAAAAGCCTTAACC 1 GCTCCAAAAACCTTAACC 915411 TCATCCAGCA Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 16 1.00 ACGTcount: A:0.38, C:0.35, G:0.08, T:0.19 Consensus pattern (19 bp): GCTCCAAAAACCTTAACCA Found at i:917788 original size:12 final size:12 Alignment explanation

Indices: 917771--917797 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 917761 ACTGATTTGA 917771 CACCTATTACGT 1 CACCTATTACGT 917783 CACCTATTACGT 1 CACCTATTACGT 917795 CAC 1 CAC 917798 AGCAATGGCA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 15 1.00 ACGTcount: A:0.26, C:0.37, G:0.07, T:0.30 Consensus pattern (12 bp): CACCTATTACGT Found at i:925948 original size:4 final size:4 Alignment explanation

Indices: 925947--926004 Score: 62 Period size: 4 Copynumber: 14.5 Consensus size: 4 925937 GGGACAGACA * * * * * 925947 GACG GACG GACG GACG GACG GACA GACA GACG GACG GACA GACA GAAG 1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG * 925995 GACT GACG GA 1 GACG GACG GA 926005 TGCAGAGGAA Statistics Matches: 46, Mismatches: 8, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 4 46 1.00 ACGTcount: A:0.34, C:0.22, G:0.41, T:0.02 Consensus pattern (4 bp): GACG Found at i:925966 original size:16 final size:16 Alignment explanation

Indices: 925938--925997 Score: 83 Period size: 16 Copynumber: 4.0 Consensus size: 16 925928 AATTGAAGTG 925938 GGACAGACAGACGGAC 1 GGACAGACAGACGGAC 925954 GGAC-G---GACGGAC 1 GGACAGACAGACGGAC 925966 GGACAGACAGACGGAC 1 GGACAGACAGACGGAC * 925982 GGACAGACAGAAGGAC 1 GGACAGACAGACGGAC 925998 TGACGGATGC Statistics Matches: 39, Mismatches: 1, Indels: 8 0.81 0.02 0.17 Matches are distributed among these distances: 12 11 0.28 13 1 0.03 15 1 0.03 16 26 0.67 ACGTcount: A:0.37, C:0.23, G:0.40, T:0.00 Consensus pattern (16 bp): GGACAGACAGACGGAC Found at i:926551 original size:12 final size:11 Alignment explanation

Indices: 926534--926587 Score: 63 Period size: 12 Copynumber: 4.5 Consensus size: 11 926524 CCCCCCCCAA 926534 AAAAAAAAAACC 1 AAAAAAAAAA-C 926546 AAAAAAACAAAAC 1 -AAAAAA-AAAAC 926559 AAAACAAAAAAC 1 AAAA-AAAAAAC 926571 AAAACAAAAAAC 1 AAAA-AAAAAAC 926583 AAAAA 1 AAAAA 926588 CAAAGTATCC Statistics Matches: 39, Mismatches: 0, Indels: 6 0.87 0.00 0.13 Matches are distributed among these distances: 11 1 0.03 12 25 0.64 13 9 0.23 14 4 0.10 ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00 Consensus pattern (11 bp): AAAAAAAAAAC Found at i:926557 original size:17 final size:17 Alignment explanation

Indices: 926547--926591 Score: 72 Period size: 17 Copynumber: 2.6 Consensus size: 17 926537 AAAAAAACCA 926547 AAAAAACAAAACAAAAC 1 AAAAAACAAAACAAAAC * 926564 AAAAAACAAAACAAAAA 1 AAAAAACAAAACAAAAC 926581 ACAAAAACAAA 1 A-AAAAACAAA 926592 GTATCCCCCA Statistics Matches: 26, Mismatches: 1, Indels: 1 0.93 0.04 0.04 Matches are distributed among these distances: 17 17 0.65 18 9 0.35 ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00 Consensus pattern (17 bp): AAAAAACAAAACAAAAC Found at i:926579 original size:30 final size:31 Alignment explanation

Indices: 926533--926591 Score: 86 Period size: 30 Copynumber: 1.9 Consensus size: 31 926523 CCCCCCCCCA 926533 AAAAAAAAAAACCAAAAAA-ACAAAACAAAAC 1 AAAAAAAAAAACCAAAAAACA-AAAACAAAAC * 926564 AAAAAACAAAA-CAAAAAACAAAAACAAA 1 AAAAAAAAAAACCAAAAAACAAAAACAAA 926592 GTATCCCCCA Statistics Matches: 26, Mismatches: 1, Indels: 3 0.87 0.03 0.10 Matches are distributed among these distances: 30 15 0.58 31 11 0.42 ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00 Consensus pattern (31 bp): AAAAAAAAAAACCAAAAAACAAAAACAAAAC Found at i:927582 original size:18 final size:18 Alignment explanation

Indices: 927559--927594 Score: 72 Period size: 18 Copynumber: 2.0 Consensus size: 18 927549 AAAAATTGAT 927559 AGTGAAAGTTGAAATGTC 1 AGTGAAAGTTGAAATGTC 927577 AGTGAAAGTTGAAATGTC 1 AGTGAAAGTTGAAATGTC 927595 GTATTCATCG Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.39, C:0.06, G:0.28, T:0.28 Consensus pattern (18 bp): AGTGAAAGTTGAAATGTC Found at i:935426 original size:3 final size:3 Alignment explanation

Indices: 935418--935452 Score: 70 Period size: 3 Copynumber: 11.7 Consensus size: 3 935408 AACTTGCCAA 935418 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA 1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA 935453 TAACCCAACC Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 32 1.00 ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00 Consensus pattern (3 bp): AAC Found at i:944886 original size:66 final size:66 Alignment explanation

Indices: 944810--944942 Score: 230 Period size: 66 Copynumber: 2.0 Consensus size: 66 944800 AAGATACAAG * * * 944810 TATTTACATTTGCAAATATGTTTTCTGATATGAACCTATAGAATAGCGAAAACGTTCAATTCTGT 1 TATTTACATTTGCAAATATGTTTCCTGATATGAACCTAGAGAATAGCAAAAACGTTCAATTCTGT 944875 A 66 A * 944876 TATTTACATTTGCAAATATGTTTCCTTATATGAACCTAGAGAATAGCAAAAACGTTCAATTCTGT 1 TATTTACATTTGCAAATATGTTTCCTGATATGAACCTAGAGAATAGCAAAAACGTTCAATTCTGT 944941 A 66 A 944942 T 1 T 944943 GAACTTTTTC Statistics Matches: 63, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 66 63 1.00 ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38 Consensus pattern (66 bp): TATTTACATTTGCAAATATGTTTCCTGATATGAACCTAGAGAATAGCAAAAACGTTCAATTCTGT A Found at i:946889 original size:66 final size:66 Alignment explanation

Indices: 946812--946945 Score: 205 Period size: 66 Copynumber: 2.0 Consensus size: 66 946802 ACTGATACAA * * * * * 946812 ATATTAACATTTGCAAATATGTTTTCTTATATGAACCTATAGAATAGCGAAAACGTTCAGTTCTG 1 ATATTAACATTTGCAAAAATGTTTCCTTACATGAACCTATAGAATAGCAAAAACGTTCAATTCTG 946877 T 66 T * * 946878 ATATTCACATTTGCAAAAATGTTTCCTTGCATGAACCTATAGAATAGCAAAAACGTTCAATTCTG 1 ATATTAACATTTGCAAAAATGTTTCCTTACATGAACCTATAGAATAGCAAAAACGTTCAATTCTG 946943 T 66 T 946944 AT 1 AT 946946 GAACTTTTTC Statistics Matches: 61, Mismatches: 7, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 66 61 1.00 ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36 Consensus pattern (66 bp): ATATTAACATTTGCAAAAATGTTTCCTTACATGAACCTATAGAATAGCAAAAACGTTCAATTCTG T Found at i:950295 original size:11 final size:11 Alignment explanation

Indices: 950279--950303 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 950269 GCGATAGTTT 950279 TTCCTGTATCA 1 TTCCTGTATCA 950290 TTCCTGTATCA 1 TTCCTGTATCA 950301 TTC 1 TTC 950304 ATAAACTAAG Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.16, C:0.28, G:0.08, T:0.48 Consensus pattern (11 bp): TTCCTGTATCA Found at i:950519 original size:2 final size:2 Alignment explanation

Indices: 950512--950570 Score: 118 Period size: 2 Copynumber: 29.5 Consensus size: 2 950502 TATGTACACA 950512 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 950554 TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC T 950571 ACAACATTGA Statistics Matches: 57, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 57 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:972512 original size:2 final size:2 Alignment explanation

Indices: 972505--972566 Score: 124 Period size: 2 Copynumber: 31.0 Consensus size: 2 972495 NNNNNNNNNN 972505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 972547 TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA 972567 AATCACAATC Statistics Matches: 60, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 60 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:973081 original size:22 final size:22 Alignment explanation

Indices: 973053--973177 Score: 178 Period size: 22 Copynumber: 5.7 Consensus size: 22 973043 GTAAAATATC 973053 ATTGTAAAGCCTGTTAAACATT 1 ATTGTAAAGCCTGTTAAACATT * * 973075 ATTGTAAAGCCTGGTACACATT 1 ATTGTAAAGCCTGTTAAACATT * * 973097 ACTGTAAGGCCTGTTAAACATT 1 ATTGTAAAGCCTGTTAAACATT * * 973119 ATTGTAAAGCCTGGTACACATT 1 ATTGTAAAGCCTGTTAAACATT * * 973141 ACTGTAAGGCCTGTTAAACATT 1 ATTGTAAAGCCTGTTAAACATT 973163 ATTGTAAAGCCTGTT 1 ATTGTAAAGCCTGTT 973178 TAAAAAATTA Statistics Matches: 87, Mismatches: 16, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 22 87 1.00 ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34 Consensus pattern (22 bp): ATTGTAAAGCCTGTTAAACATT Found at i:973109 original size:44 final size:44 Alignment explanation

Indices: 973055--973175 Score: 233 Period size: 44 Copynumber: 2.8 Consensus size: 44 973045 AAAATATCAT * 973055 TGTAAAGCCTGTTAAACATTATTGTAAAGCCTGGTACACATTAC 1 TGTAAGGCCTGTTAAACATTATTGTAAAGCCTGGTACACATTAC 973099 TGTAAGGCCTGTTAAACATTATTGTAAAGCCTGGTACACATTAC 1 TGTAAGGCCTGTTAAACATTATTGTAAAGCCTGGTACACATTAC 973143 TGTAAGGCCTGTTAAACATTATTGTAAAGCCTG 1 TGTAAGGCCTGTTAAACATTATTGTAAAGCCTG 973176 TTTAAAAAAT Statistics Matches: 76, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 44 76 1.00 ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32 Consensus pattern (44 bp): TGTAAGGCCTGTTAAACATTATTGTAAAGCCTGGTACACATTAC Found at i:973162 original size:66 final size:66 Alignment explanation

Indices: 973053--973205 Score: 180 Period size: 66 Copynumber: 2.3 Consensus size: 66 973043 GTAAAATATC * * * * 973053 ATTGTAAAGCCTGTTAAACATTATTGTAAAGCCTGGTACACATTACTGTAAGGCCTGTTAAACAT 1 ATTGTAAAGCCTGGTAAACATTACTGTAAAGCCTGGTAAACATTACTGTAAAGCCTGTTAAACAT 973118 T 66 T * * * * * 973119 ATTGTAAAGCCTGGTACACATTACTGTAAGGCCTGTTAAACATTATTGTAAAGCCTGTTTAAAAA 1 ATTGTAAAGCCTGGTAAACATTACTGTAAAGCCTGGTAAACATTACTGTAAAGCCTG-TT-AAAC 973184 ATT 64 ATT ** 973187 ATAACTAAAGCCTGGTAAA 1 AT-TGTAAAGCCTGGTAAA 973206 GTATTTAATG Statistics Matches: 72, Mismatches: 12, Indels: 3 0.83 0.14 0.03 Matches are distributed among these distances: 66 49 0.68 67 2 0.03 68 8 0.11 69 13 0.18 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (66 bp): ATTGTAAAGCCTGGTAAACATTACTGTAAAGCCTGGTAAACATTACTGTAAAGCCTGTTAAACAT T Found at i:974733 original size:165 final size:166 Alignment explanation

Indices: 974362--974812 Score: 510 Period size: 165 Copynumber: 2.7 Consensus size: 166 974352 AGCTGATCAC * * * * * 974362 AAAAATCATCTTCTCGGAAACTAATCAGCCAGGAAAGATGAAAGTTGTGTGGAAGCATCCTCACG 1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG * * * * * * 974427 TACTGTAGATTCAAAGTTGTAAAAATCATGACCCCCTCGGTGTAGGGTTGGCCACAGGGGGGGGG 66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCC-AGGGGTAGGGTGGGCCACA-------GA * * * 974492 GGGGGGGGCGAAGTTTTACATAGGAATATATTCAGTAAATCTTT 123 GGGAGGGGCGAAGTTTTACATACGAATATATACAGTAAATCTTT * * * * 974536 AAAAATATTCTTCTTAGAAACTAATTAGCCAGGAAAGCTGAAACTTGTGTGGATGCATCCTCAGG 1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG * * * * 974601 TAGTCTAGATTTAAA-TTGATGAAAATCATGACCCCCAGGGGTAGGGTGGGGCACA-ATGGAGGG 66 TAGTGTAGATTCAAAGTTG-TGAAAATCATGACCCCCAGGGGTAGGGTGGGCCACAGAGGGAGGG * * * 974664 TCGAAGTTTTACATTCGAATATATAGAGTAAATCTTT 130 GCGAAGTTTTACATACGAATATATACAGTAAATCTTT * ** * * 974701 AAAAATCTTCTTCGCAGAAACTAATCAGCCAGGAACTCTGAAACTTCTTTGGAAGCATCCTCAGG 1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG * ** 974766 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGT 66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGT 974813 AGGGTAGGGC Statistics Matches: 236, Mismatches: 39, Indels: 13 0.82 0.14 0.05 Matches are distributed among these distances: 165 131 0.56 166 3 0.01 173 18 0.08 174 84 0.36 ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27 Consensus pattern (166 bp): AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGGGTGGGCCACAGAGGGAGGGG CGAAGTTTTACATACGAATATATACAGTAAATCTTT Found at i:976347 original size:15 final size:16 Alignment explanation

Indices: 976322--976353 Score: 57 Period size: 15 Copynumber: 2.1 Consensus size: 16 976312 CCCATGGGCC 976322 TCTTGTATTATCTTTA 1 TCTTGTATTATCTTTA 976338 TCTT-TATTATCTTTA 1 TCTTGTATTATCTTTA 976353 T 1 T 976354 TTACCTTAAC Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 15 12 0.75 16 4 0.25 ACGTcount: A:0.19, C:0.12, G:0.03, T:0.66 Consensus pattern (16 bp): TCTTGTATTATCTTTA Found at i:981483 original size:88 final size:88 Alignment explanation

Indices: 981334--981544 Score: 334 Period size: 88 Copynumber: 2.4 Consensus size: 88 981324 AAAATATAAA * * ** 981334 AAGTTTCAGTAAGTTT-CAGTTGCGGAAACCCTTTGTAAACAATATGTTTCCCAATTGTATATGG 1 AAGTTTCAGTAAGTTTCCA-TTGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGG * * 981398 AGGTTGAAACTATGCAGAAACTTC 65 AGATTGAAACCATGCAGAAACTTC * 981422 AAGTTTCAGTAAGTTTCCATCGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGGA 1 AAGTTTCAGTAAGTTTCCATTGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGGA 981487 GATTGAAACCATGCAGAAACTTC 66 GATTGAAACCATGCAGAAACTTC * 981510 AAGTTTCAGCAAGTTTCCATTGCGGAAACCATTTG 1 AAGTTTCAGTAAGTTTCCATTGCGGAAACCATTTG 981545 GATTCATGGA Statistics Matches: 113, Mismatches: 9, Indels: 2 0.91 0.07 0.02 Matches are distributed among these distances: 88 111 0.98 89 2 0.02 ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30 Consensus pattern (88 bp): AAGTTTCAGTAAGTTTCCATTGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGGA GATTGAAACCATGCAGAAACTTC Found at i:981949 original size:22 final size:23 Alignment explanation

Indices: 981924--981969 Score: 76 Period size: 22 Copynumber: 2.0 Consensus size: 23 981914 TCATGAATTT 981924 GTGAGTTTGATATGATTT-TTAA 1 GTGAGTTTGATATGATTTCTTAA * 981946 GTGATTTTGATATGATTTCTTAA 1 GTGAGTTTGATATGATTTCTTAA 981969 G 1 G 981970 AAAAGTTTTT Statistics Matches: 22, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 22 17 0.77 23 5 0.23 ACGTcount: A:0.26, C:0.02, G:0.22, T:0.50 Consensus pattern (23 bp): GTGAGTTTGATATGATTTCTTAA Found at i:994441 original size:21 final size:21 Alignment explanation

Indices: 994409--994515 Score: 142 Period size: 21 Copynumber: 5.1 Consensus size: 21 994399 GCTGCACGCT * * * 994409 CGCTAAACGGTTCACATGAAA 1 CGCTGAACGGTTTACACGAAA * 994430 CGCTGAATGGTTTACACGAAA 1 CGCTGAACGGTTTACACGAAA 994451 CGCTGAACGGTTTACACGAAA 1 CGCTGAACGGTTTACACGAAA ** * * 994472 CGCCAAACGATTTACACAAAA 1 CGCTGAACGGTTTACACGAAA 994493 CGCTGAACGGTTTACACGAAA 1 CGCTGAACGGTTTACACGAAA 994514 CG 1 CG 994516 ATTCTCGCAC Statistics Matches: 73, Mismatches: 13, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 21 73 1.00 ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19 Consensus pattern (21 bp): CGCTGAACGGTTTACACGAAA Found at i:996037 original size:23 final size:21 Alignment explanation

Indices: 996007--996087 Score: 81 Period size: 21 Copynumber: 3.8 Consensus size: 21 995997 TTCTCGCACG * 996007 CTTTGCCCGAAACGATTTACACA 1 CTTTGCCCGAAACG--CTACACA * * 996030 CTTTGCCCGAAACGCTGCACG 1 CTTTGCCCGAAACGCTACACA * 996051 CTTTGCCCGAAACGCTAAACA 1 CTTTGCCCGAAACGCTACACA * * * 996072 GTTTACACGAAACGCT 1 CTTTGCCCGAAACGCT 996088 TCACGATTCA Statistics Matches: 49, Mismatches: 9, Indels: 2 0.82 0.15 0.03 Matches are distributed among these distances: 21 35 0.71 23 14 0.29 ACGTcount: A:0.28, C:0.32, G:0.17, T:0.22 Consensus pattern (21 bp): CTTTGCCCGAAACGCTACACA Found at i:996056 original size:21 final size:21 Alignment explanation

Indices: 996002--996066 Score: 85 Period size: 21 Copynumber: 3.0 Consensus size: 21 995992 CACGGTTCTC * 996002 GCACGCTTTGCCCGAAACGATTT 1 GCACGCTTTGCCCGAAACG--CT * * 996025 ACACACTTTGCCCGAAACGCT 1 GCACGCTTTGCCCGAAACGCT 996046 GCACGCTTTGCCCGAAACGCT 1 GCACGCTTTGCCCGAAACGCT 996067 AAACAGTTTA Statistics Matches: 37, Mismatches: 5, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 21 20 0.54 23 17 0.46 ACGTcount: A:0.23, C:0.35, G:0.20, T:0.22 Consensus pattern (21 bp): GCACGCTTTGCCCGAAACGCT Found at i:996082 original size:21 final size:21 Alignment explanation

Indices: 996058--996148 Score: 137 Period size: 21 Copynumber: 4.3 Consensus size: 21 996048 ACGCTTTGCC * 996058 CGAAACGCTAAACAGTTTACA 1 CGAAACGCTAAACGGTTTACA ** * * 996079 CGAAACGCTTCACGATTCACA 1 CGAAACGCTAAACGGTTTACA 996100 CGAAACGCTAAACGGTTTACA 1 CGAAACGCTAAACGGTTTACA 996121 CGAAACGCTAAACGGTTTACA 1 CGAAACGCTAAACGGTTTACA 996142 CGAAACG 1 CGAAACG 996149 TTTCTCGCAC Statistics Matches: 61, Mismatches: 9, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 21 61 1.00 ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18 Consensus pattern (21 bp): CGAAACGCTAAACGGTTTACA Found at i:997191 original size:54 final size:54 Alignment explanation

Indices: 997126--997400 Score: 487 Period size: 54 Copynumber: 5.1 Consensus size: 54 997116 ACATTGCTTT * * 997126 CAGTCGGGCAGGAGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA 1 CAGTCCGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA * 997180 CAGTCCTGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA 1 CAGTCCGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA * 997234 CAGTCCTGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA 1 CAGTCCGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA * 997288 CAGTCGGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA 1 CAGTCCGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA * * 997342 CAGTCGGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTACGTAACTTGA 1 CAGTCCGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA 997396 CAGTC 1 CAGTC 997401 AGTTAGACAA Statistics Matches: 215, Mismatches: 6, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 54 215 1.00 ACGTcount: A:0.23, C:0.13, G:0.37, T:0.28 Consensus pattern (54 bp): CAGTCCGGCAGGGGGTGGAAGAGATATGTTTGCTAGTGTCGGTATGTAACTTGA Found at i:1000476 original size:31 final size:31 Alignment explanation

Indices: 1000441--1000508 Score: 136 Period size: 31 Copynumber: 2.2 Consensus size: 31 1000431 ACTATGCATA 1000441 AGAATGAATGGGCAAAGAGAGATAACTGCTG 1 AGAATGAATGGGCAAAGAGAGATAACTGCTG 1000472 AGAATGAATGGGCAAAGAGAGATAACTGCTG 1 AGAATGAATGGGCAAAGAGAGATAACTGCTG 1000503 AGAATG 1 AGAATG 1000509 TTACCATTGT Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 31 37 1.00 ACGTcount: A:0.43, C:0.09, G:0.32, T:0.16 Consensus pattern (31 bp): AGAATGAATGGGCAAAGAGAGATAACTGCTG Found at i:1015692 original size:63 final size:63 Alignment explanation

Indices: 1015593--1016106 Score: 949 Period size: 63 Copynumber: 8.2 Consensus size: 63 1015583 NNNNNNNNNN 1015593 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT 1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT 1015656 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT 1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT 1015719 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT 1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT 1015782 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT 1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT 1015845 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT 1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT 1015908 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT 1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT * * ** 1015971 CGTCCCTACAACTCAAATAATATCTCTATAGCAACCACAGAGCACTTGATGTGCCAGCCAGGT 1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT * * * 1016034 CGTCCCTATAACACAAATAATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAACCAGGAT 1 CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGG-T 1016098 -GTCCCTACA 1 CGTCCCTACA 1016107 CAAATATCTT Statistics Matches: 440, Mismatches: 10, Indels: 2 0.97 0.02 0.00 Matches are distributed among these distances: 63 439 1.00 64 1 0.00 ACGTcount: A:0.33, C:0.33, G:0.14, T:0.20 Consensus pattern (63 bp): CGTCCCTACAACACAAATCATATCTCTATAGCAACCACAGAGCACTCAATGTGCCAGCCAGGT Found at i:1020679 original size:166 final size:165 Alignment explanation

Indices: 1020388--1020729 Score: 492 Period size: 166 Copynumber: 2.0 Consensus size: 165 1020378 AAAGAATCAG * * 1020388 CTGGCTGATTAGTTTCTGAGAAGATTTTAAAAGATTTACTCTATATATTTCTATGTAAAACTTTA 1 CTGGCTGATTAGTTTCTGAGAAGATTTTAAAAGATTTACTCTATAAATTCCTATGTAAAACTTT- * 1020453 ACACCCCCCCCCCCAATGTGGCCCAACCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATC 65 ACA----CCCCCCCAATGTGGCCCAACCCTACCCCCAGGGATCATGAATTTCACAACTTTGAATC 1020518 TACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC 126 TACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC * * 1020558 CTGGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATAAATTCCTATGTAAAAC- 1 CTGGCTGATTAGTTTCT--G-AGAAGATTTTAAAAGATTTACTCTATAAATTCCTATGTAAAACT * * * * 1020622 TT-CGA-CCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGAATTTCACAACTTTGAATCT 63 TTAC-ACCCCCCCAATGTGGCCCAACCCTACCCCCAGGGATCATGAATTTCACAACTTTGAATCT * 1020685 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC 127 ACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC 1020724 CTGGCT 1 CTGGCT 1020730 TTATGGATCT Statistics Matches: 158, Mismatches: 10, Indels: 12 0.88 0.06 0.07 Matches are distributed among these distances: 166 97 0.61 170 17 0.11 171 1 0.01 172 3 0.02 173 40 0.25 ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31 Consensus pattern (165 bp): CTGGCTGATTAGTTTCTGAGAAGATTTTAAAAGATTTACTCTATAAATTCCTATGTAAAACTTTA CACCCCCCCAATGTGGCCCAACCCTACCCCCAGGGATCATGAATTTCACAACTTTGAATCTACAC TACCTGAGGATACTTCCACACAAGTTTCAGCTTTC Found at i:1042752 original size:2 final size:2 Alignment explanation

Indices: 1042745--1042771 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 1042735 ATTACTTCTG 1042745 CT CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT C 1042772 AAAAAGCTGA Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48 Consensus pattern (2 bp): CT Found at i:1046834 original size:46 final size:45 Alignment explanation

Indices: 1046782--1047149 Score: 335 Period size: 46 Copynumber: 8.9 Consensus size: 45 1046772 TGTAATAACT * 1046782 GCTGGCTCAAACCAATCTATACCCCTGTACTGATTTCTGGCTTATA 1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTT-TA * 1046828 GCTGGCTCACACCGATCTATACCCCTGTACTGATTTCT-G----- 1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTTTA * * * 1046867 GCT--CACACATCAATCTATACCCCTATACTGATTTCTGGCTTATA 1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTT-TA 1046911 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGC-TTA 1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTTTA * 1046955 ------T---ACCAATCTATACCCCTATACTGATTTCTGGC--T- 1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTTTA * 1046988 --T--CT---ACCAATCTATACCCCTATACTGATTTCTGGC--T- 1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTTTA * ** 1047023 --T--CT---ACCAATCTACACCAATGTACTGATTTCTGGCTTATA 1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTT-TA 1047062 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTTATA 1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTT-TA * 1047108 GCTGGCTCACACCAATCTACACCCCTGTACTGATTTCTGGCT 1 GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCT 1047150 CACACCAATC Statistics Matches: 282, Mismatches: 18, Indels: 44 0.82 0.05 0.13 Matches are distributed among these distances: 34 1 0.00 35 93 0.33 37 29 0.10 38 3 0.01 39 3 0.01 41 1 0.00 43 2 0.01 44 5 0.02 45 2 0.01 46 143 0.51 ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33 Consensus pattern (45 bp): GCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTTTA Found at i:1046952 original size:35 final size:35 Alignment explanation

Indices: 1046912--1047431 Score: 553 Period size: 35 Copynumber: 14.2 Consensus size: 35 1046902 TGGCTTATAG 1046912 CTGGCTCACACCAATCTATACCCCTGTACTGATTT 1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT * * * 1046947 CTGGCTTATACCAATCTATACCCCTATACTGATTT 1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT * * 1046982 CTGGCTTC-TACCAATCTATACCCCTATACTGATTT 1 CTGGC-TCACACCAATCTATACCCCTGTACTGATTT * * ** 1047017 CTGGCTTC-TACCAATCTACACCAATGTACTGATTTCTGGCTTAT 1 CTGGC-TCACACCAATCTATACCCCTGTACTGA--------TT-T 1047061 AGCTGGCTCACACCAATCTATACCCCTGTACTGATTTCTGGCTTAT 1 --CTGGCTCACACCAATCTATACCCCTGTACTGA--------TT-T * 1047107 AGCTGGCTCACACCAATCTACACCCCTGTACTGATTT 1 --CTGGCTCACACCAATCTATACCCCTGTACTGATTT * 1047144 CTGGCTCACACCAATCTATACCCCTGTATTGATTT 1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT ** 1047179 CTGGCTCACACCAATCTATACCCCAATACTGATTT 1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT * * 1047214 CTGGCTTC-TACCAATCTATACCCCTATACTGATTT 1 CTGGC-TCACACCAATCTATACCCCTGTACTGATTT * * * 1047249 CTGTCTTATACCAATCTATACCCCTGTACTGATTT 1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT * 1047284 CTGGCTCACACCAATCTATACCCCTATACTGATTT 1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT * 1047319 CTGGCTCACACCAATCTATACCCCTGTATTGATTT 1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT * ** 1047354 CTGGCTCACACAAATCTATACCCCAATACTGATTT 1 CTGGCTCACACCAATCTATACCCCTGTACTGATTT * * 1047389 CTGGCTTC-TACCAATCTATACCCCTGTATTGATTT 1 CTGGC-TCACACCAATCTATACCCCTGTACTGATTT 1047424 CTGGCTCA 1 CTGGCTCA 1047432 TACCTACTGA Statistics Matches: 430, Mismatches: 38, Indels: 34 0.86 0.08 0.07 Matches are distributed among these distances: 34 3 0.01 35 344 0.80 36 5 0.01 37 1 0.00 38 2 0.00 43 2 0.00 44 1 0.00 45 2 0.00 46 70 0.16 ACGTcount: A:0.24, C:0.31, G:0.11, T:0.34 Consensus pattern (35 bp): CTGGCTCACACCAATCTATACCCCTGTACTGATTT Found at i:1071486 original size:63 final size:63 Alignment explanation

Indices: 1071387--1071513 Score: 254 Period size: 63 Copynumber: 2.0 Consensus size: 63 1071377 TCATGGCCAT 1071387 TTGCCTAGTGGTTATCAAACCATAAGGTGAATGGTTCAAATTCAGTTGCAATAGATTCACCAA 1 TTGCCTAGTGGTTATCAAACCATAAGGTGAATGGTTCAAATTCAGTTGCAATAGATTCACCAA 1071450 TTGCCTAGTGGTTATCAAACCATAAGGTGAATGGTTCAAATTCAGTTGCAATAGATTCACCAA 1 TTGCCTAGTGGTTATCAAACCATAAGGTGAATGGTTCAAATTCAGTTGCAATAGATTCACCAA 1071513 T 1 T 1071514 AAGTAACCTT Statistics Matches: 64, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 63 64 1.00 ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31 Consensus pattern (63 bp): TTGCCTAGTGGTTATCAAACCATAAGGTGAATGGTTCAAATTCAGTTGCAATAGATTCACCAA Found at i:1072935 original size:13 final size:13 Alignment explanation

Indices: 1072917--1072942 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 1072907 ATCCAAATTA 1072917 TTATTTTTTAAAT 1 TTATTTTTTAAAT 1072930 TTATTTTTTAAAT 1 TTATTTTTTAAAT 1072943 GATAAATGTG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69 Consensus pattern (13 bp): TTATTTTTTAAAT Found at i:1076323 original size:18 final size:18 Alignment explanation

Indices: 1076279--1076326 Score: 53 Period size: 18 Copynumber: 2.7 Consensus size: 18 1076269 CTACACCATT * 1076279 ACAGGTAGACAGTTCTAG 1 ACAGGTAGACAATTCTAG ** 1076297 ACACATAGACAATTAC-AG 1 ACAGGTAGACAATT-CTAG 1076315 ACAGGTAGACAA 1 ACAGGTAGACAA 1076327 AATTCAATTG Statistics Matches: 24, Mismatches: 5, Indels: 2 0.77 0.16 0.06 Matches are distributed among these distances: 18 23 0.96 19 1 0.04 ACGTcount: A:0.44, C:0.19, G:0.21, T:0.17 Consensus pattern (18 bp): ACAGGTAGACAATTCTAG Found at i:1077414 original size:26 final size:27 Alignment explanation

Indices: 1077365--1077423 Score: 109 Period size: 27 Copynumber: 2.2 Consensus size: 27 1077355 AGTGCCAGGT 1077365 AAAATCCACAGCGATAAAGAAAAACAA 1 AAAATCCACAGCGATAAAGAAAAACAA * 1077392 AAAATCCACGGCGATAAAGAAAAACAA 1 AAAATCCACAGCGATAAAGAAAAACAA 1077419 AAAAT 1 AAAAT 1077424 TTTCTGAATC Statistics Matches: 31, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 27 31 1.00 ACGTcount: A:0.63, C:0.17, G:0.12, T:0.08 Consensus pattern (27 bp): AAAATCCACAGCGATAAAGAAAAACAA Found at i:1081224 original size:389 final size:388 Alignment explanation

Indices: 1080507--1081279 Score: 1519 Period size: 389 Copynumber: 2.0 Consensus size: 388 1080497 TTTACTCTTT * 1080507 TTTTTTTATATCCTGTATTATGTTCCATATAACCTTCATTTTAAGAATACTTATTAGTGAATATT 1 TTTTTTTATATCCTGTATTATGTTCCATATAACCTTCATTTTAAGAATACATATTAGTGAATATT 1080572 TTTTAAAACAAAGGTGTCAGTTTCTATCATATTAAATGAAAAGGACACACCAAACATTTTAAAAA 66 TTTTAAAACAAAGGTGTCAGTTTCTATCATATTAAATGAAAAGGACACACCAAACATTTTAAAAA 1080637 ATAGTGATGCATTTCTTTGCAAATTCATTCACATTTTTGCAATTCATTCAACATGCATTTGTAAG 131 ATAGTGATGCATTTCTTTGCAAATTCATTCACATTTTTGCAATTCATTCAACATGCATTTGTAAG 1080702 TTTATTACATGTATTATATTTCACATTGTTTATATGCTTTAAGTTTGAATTACAAAGTTACATGT 196 TTTATTACATGTATTATATTTCACATTGTTTATATGCTTTAAGTTTGAATTACAAAGTTACATGT 1080767 ATTTCTAAGCTATTTTCATACATTAATGAATGATTTTGTTTTGTATTGTATTCAATGTATCATGA 261 ATTTCTAAGCTATTTTCATACATTAATGAATGATTTTGTTTTGTATTGTATTCAATGTATCATGA 1080832 ACTACCTATGCTGTGATATTAGTTGGCAGAGTTTTTGTATGAAGTAGATTAGAACATANTTAAC 326 ACTACCTATGCTGTGATATTAGTTGGCAGAGTTTTTGTATGAAGTAGATTAGAACATA-TTAAC 1080896 TTTTTTTATATCCTGTATTATGTTCCATATAACCTTCATTTTAAGAATACATATTAGTGAATATT 1 TTTTTTTATATCCTGTATTATGTTCCATATAACCTTCATTTTAAGAATACATATTAGTGAATATT * 1080961 TTTTAAAACAAAGGTGTCAGTTTCTATCGTATTAAATGAAAAGGACACACCAAACATTTTAAAAA 66 TTTTAAAACAAAGGTGTCAGTTTCTATCATATTAAATGAAAAGGACACACCAAACATTTTAAAAA 1081026 ATAGTGATGCATTTCTTTGCAAATTCATTCACATTTTTGCAATTCATTCAACATGCATTTGTAAG 131 ATAGTGATGCATTTCTTTGCAAATTCATTCACATTTTTGCAATTCATTCAACATGCATTTGTAAG 1081091 TTTATTACATGTATTATATTTCACATTGTTTATATGCTTTAAGTTTGAATTACAAAGTTACATGT 196 TTTATTACATGTATTATATTTCACATTGTTTATATGCTTTAAGTTTGAATTACAAAGTTACATGT 1081156 ATTTCTAAGCTATTTTCATACATTAATGAATGATTTTGTTTTGTATTGTATTCAATGTATCATGA 261 ATTTCTAAGCTATTTTCATACATTAATGAATGATTTTGTTTTGTATTGTATTCAATGTATCATGA 1081221 ACTACCTATGCTGTGATATTAGTTGGCAGAGTTTTTGTATGAAGTAGATTAGAACATAT 326 ACTACCTATGCTGTGATATTAGTTGGCAGAGTTTTTGTATGAAGTAGATTAGAACATAT 1081280 AACATTCAAC Statistics Matches: 382, Mismatches: 2, Indels: 1 0.99 0.01 0.00 Matches are distributed among these distances: 388 1 0.00 389 381 1.00 ACGTcount: A:0.33, C:0.12, G:0.13, T:0.43 Consensus pattern (388 bp): TTTTTTTATATCCTGTATTATGTTCCATATAACCTTCATTTTAAGAATACATATTAGTGAATATT TTTTAAAACAAAGGTGTCAGTTTCTATCATATTAAATGAAAAGGACACACCAAACATTTTAAAAA ATAGTGATGCATTTCTTTGCAAATTCATTCACATTTTTGCAATTCATTCAACATGCATTTGTAAG TTTATTACATGTATTATATTTCACATTGTTTATATGCTTTAAGTTTGAATTACAAAGTTACATGT ATTTCTAAGCTATTTTCATACATTAATGAATGATTTTGTTTTGTATTGTATTCAATGTATCATGA ACTACCTATGCTGTGATATTAGTTGGCAGAGTTTTTGTATGAAGTAGATTAGAACATATTAAC Found at i:1082676 original size:31 final size:31 Alignment explanation

Indices: 1082638--1082704 Score: 125 Period size: 31 Copynumber: 2.2 Consensus size: 31 1082628 CATTTCAATG * 1082638 TAAATAAGTCATCAGCATTTTACTTTCGCTT 1 TAAATAAGTCATCAGCATTTTACTTTCACTT 1082669 TAAATAAGTCATCAGCATTTTACTTTCACTT 1 TAAATAAGTCATCAGCATTTTACTTTCACTT 1082700 TAAAT 1 TAAAT 1082705 GCAATTGTTC Statistics Matches: 35, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 31 35 1.00 ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42 Consensus pattern (31 bp): TAAATAAGTCATCAGCATTTTACTTTCACTT Found at i:1085484 original size:16 final size:16 Alignment explanation

Indices: 1085465--1085499 Score: 61 Period size: 16 Copynumber: 2.2 Consensus size: 16 1085455 TCACCGAGAC * 1085465 GAGGCATCACCTTTAT 1 GAGGAATCACCTTTAT 1085481 GAGGAATCACCTTTAT 1 GAGGAATCACCTTTAT 1085497 GAG 1 GAG 1085500 ACCACCTTTA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 16 18 1.00 ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29 Consensus pattern (16 bp): GAGGAATCACCTTTAT Found at i:1085507 original size:14 final size:16 Alignment explanation

Indices: 1085472--1085510 Score: 55 Period size: 16 Copynumber: 2.6 Consensus size: 16 1085462 GACGAGGCAT * 1085472 CACCTTTATGAGGAAT 1 CACCTTTATGAGGAAC 1085488 CACCTTTATGA-G-AC 1 CACCTTTATGAGGAAC 1085502 CACCTTTAT 1 CACCTTTAT 1085511 CATTTTATTT Statistics Matches: 22, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 14 10 0.45 15 1 0.05 16 11 0.50 ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33 Consensus pattern (16 bp): CACCTTTATGAGGAAC Found at i:1085857 original size:10 final size:10 Alignment explanation

Indices: 1085851--1085888 Score: 51 Period size: 10 Copynumber: 3.8 Consensus size: 10 1085841 TATTGATATT 1085851 ATATGATACA 1 ATATGATACA * 1085861 ATATAATA-A 1 ATATGATACA 1085870 TATATGATACA 1 -ATATGATACA 1085881 ATATGATA 1 ATATGATA 1085889 TCACATAATA Statistics Matches: 24, Mismatches: 2, Indels: 4 0.80 0.07 0.13 Matches are distributed among these distances: 9 1 0.04 10 22 0.92 11 1 0.04 ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34 Consensus pattern (10 bp): ATATGATACA Found at i:1086019 original size:35 final size:35 Alignment explanation

Indices: 1085980--1086060 Score: 101 Period size: 35 Copynumber: 2.3 Consensus size: 35 1085970 ATAAAATTAG * 1085980 ATACAATATCATGTGATA-TAGTACTATATTATATC 1 ATACAATATCATATGATACTA-TACTATATTATATC * * * * 1086015 ATACAATATCATATTATACTATATTGTATTATATG 1 ATACAATATCATATGATACTATACTATATTATATC 1086050 ATACAATATCA 1 ATACAATATCA 1086061 CATCATACAA Statistics Matches: 40, Mismatches: 5, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 35 38 0.95 36 2 0.05 ACGTcount: A:0.42, C:0.11, G:0.06, T:0.41 Consensus pattern (35 bp): ATACAATATCATATGATACTATACTATATTATATC Found at i:1086044 original size:15 final size:15 Alignment explanation

Indices: 1086001--1086047 Score: 58 Period size: 15 Copynumber: 3.1 Consensus size: 15 1085991 TGTGATATAG * 1086001 TACTATATTATATCA 1 TACTATATTATATTA * * 1086016 TACAATATCATATTA 1 TACTATATTATATTA * 1086031 TACTATATTGTATTA 1 TACTATATTATATTA 1086046 TA 1 TA 1086048 TGATACAATA Statistics Matches: 26, Mismatches: 6, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 15 26 1.00 ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47 Consensus pattern (15 bp): TACTATATTATATTA Found at i:1086083 original size:15 final size:15 Alignment explanation

Indices: 1085995--1086084 Score: 54 Period size: 15 Copynumber: 5.7 Consensus size: 15 1085985 ATATCATGTG * * * 1085995 ATATAGTACTATATT 1 ATATAATACAATATC * 1086010 ATATCATACAATATC 1 ATATAATACAATATC * * 1086025 ATATTATACTATATTGTATT 1 ATATAATAC-A-A---TATC * 1086045 ATATGATACAATATC 1 ATATAATACAATATC * * 1086060 ACATCATACAATATC 1 ATATAATACAATATC 1086075 ATATAATACA 1 ATATAATACA 1086085 TTTTCGTATG Statistics Matches: 58, Mismatches: 12, Indels: 10 0.73 0.15 0.12 Matches are distributed among these distances: 15 43 0.74 16 1 0.02 17 1 0.02 18 1 0.02 19 1 0.02 20 11 0.19 ACGTcount: A:0.44, C:0.13, G:0.03, T:0.39 Consensus pattern (15 bp): ATATAATACAATATC Found at i:1086143 original size:20 final size:20 Alignment explanation

Indices: 1086120--1086163 Score: 61 Period size: 20 Copynumber: 2.2 Consensus size: 20 1086110 ATATAAACCA ** 1086120 ATATCATATTTTACAATATC 1 ATATCATATGATACAATATC * 1086140 ATATCATATGATACAATATT 1 ATATCATATGATACAATATC 1086160 ATAT 1 ATAT 1086164 GTTGCAATAT Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43 Consensus pattern (20 bp): ATATCATATGATACAATATC Found at i:1086158 original size:15 final size:15 Alignment explanation

Indices: 1086140--1086180 Score: 55 Period size: 15 Copynumber: 2.7 Consensus size: 15 1086130 TTACAATATC 1086140 ATATCATATGATACA 1 ATATCATATGATACA * * * 1086155 ATATTATATGTTGCA 1 ATATCATATGATACA 1086170 ATATCATATGA 1 ATATCATATGA 1086181 AATAGCATGT Statistics Matches: 21, Mismatches: 5, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 15 21 1.00 ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39 Consensus pattern (15 bp): ATATCATATGATACA Found at i:1086160 original size:50 final size:50 Alignment explanation

Indices: 1085980--1086178 Score: 170 Period size: 50 Copynumber: 4.0 Consensus size: 50 1085970 ATAAAATTAG * * 1085980 ATACAATATCATGTGATAT-AGTACTATATTATATCATACAATATCATATT 1 ATACAATATCATATGATATGA-TACAATATTATATCATACAATATCATATT * ** * * * * 1086030 ATACTATATTGTATTATATGATACAATATCACATCATACAATATCATATA 1 ATACAATATCATATGATATGATACAATATTATATCATACAATATCATATT * * * * * * 1086080 ATACATTTTCGTATGATATAATA-ATTTATTATAT-AAACCAATATCATATT 1 ATACAATATCATATGATATGATACA-ATATTATATCATA-CAATATCATATT * * ** * 1086130 TTACAATATCATATCATATGATACAATATTATATGTTGCAATATCATAT 1 ATACAATATCATATGATATGATACAATATTATATCATACAATATCATAT 1086179 GAAATAGCAT Statistics Matches: 114, Mismatches: 30, Indels: 10 0.74 0.19 0.06 Matches are distributed among these distances: 49 3 0.03 50 109 0.96 51 2 0.02 ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41 Consensus pattern (50 bp): ATACAATATCATATGATATGATACAATATTATATCATACAATATCATATT Found at i:1086338 original size:15 final size:15 Alignment explanation

Indices: 1086318--1086379 Score: 53 Period size: 15 Copynumber: 4.3 Consensus size: 15 1086308 AATTGATACA 1086318 ATATAATATTGTATC 1 ATATAATATTGTATC * 1086333 ATATAACT-TTTTA-C 1 ATATAA-TATTGTATC * 1086347 AATATAATA---TATG 1 -ATATAATATTGTATC 1086360 ATATAATATTGTATC 1 ATATAATATTGTATC 1086375 ATATA 1 ATATA 1086380 GAACAATAGT Statistics Matches: 37, Mismatches: 3, Indels: 14 0.69 0.06 0.26 Matches are distributed among these distances: 12 10 0.27 14 2 0.05 15 24 0.65 16 1 0.03 ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45 Consensus pattern (15 bp): ATATAATATTGTATC Found at i:1086405 original size:20 final size:20 Alignment explanation

Indices: 1086364--1086417 Score: 56 Period size: 20 Copynumber: 2.7 Consensus size: 20 1086354 TATATGATAT * 1086364 AATATTGTATCATATAGAAC 1 AATACTGTATCATATAGAAC * * 1086384 AATAGTGTATCATATCA-TAC 1 AATACTGTATCATAT-AGAAC * 1086404 AATACTATATCATA 1 AATACTGTATCATA 1086418 GGAATCATAT Statistics Matches: 29, Mismatches: 4, Indels: 2 0.83 0.11 0.06 Matches are distributed among these distances: 20 28 0.97 21 1 0.03 ACGTcount: A:0.44, C:0.13, G:0.07, T:0.35 Consensus pattern (20 bp): AATACTGTATCATATAGAAC Found at i:1087341 original size:19 final size:19 Alignment explanation

Indices: 1087314--1087350 Score: 56 Period size: 19 Copynumber: 1.9 Consensus size: 19 1087304 AAGTGCACCT * 1087314 GCTCCAAAAACTTTAACCA 1 GCTCCAAAAACCTTAACCA * 1087333 GCTCTAAAAACCTTAACC 1 GCTCCAAAAACCTTAACC 1087351 TCATCCAGCA Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 16 1.00 ACGTcount: A:0.41, C:0.32, G:0.05, T:0.22 Consensus pattern (19 bp): GCTCCAAAAACCTTAACCA Found at i:1087385 original size:177 final size:174 Alignment explanation

Indices: 1087089--1087811 Score: 909 Period size: 177 Copynumber: 4.2 Consensus size: 174 1087079 AGATTCAGCA * * 1087089 TGAAGTTAGGACCAGTAATAACTAAGATATAATCATCAGAGGGCACCTGCTCCAAAAGCTTTAAC 1 TGAAGTTAGGACCAGTAATAACT-AG--ATAATCATCAAAGGGCACCTGCTCCAAAAACTTTAAC * * * 1087154 AAGCTCTTAAAACCTTAACCTCATCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTCATGCC 63 CAGCTCTAAAAACCTTAACCTCATCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCC * * 1087219 TGTCAGGTACATCAGTATCATAAGACGCACCATCTATGCAAGTTCGT 128 TGTCAGGTACATCAGTATCATAAGACGCACCATCCATGCAAGTTCGG * 1087266 TGAAGTTAGGACCAGTAATAACTAAGTTATAATCATCAAAGTGCACCTGCTCCAAAAACTTTAAC 1 TGAAGTTAGGACCAGTAATAACT-AG--ATAATCATCAAAGGGCACCTGCTCCAAAAACTTTAAC * ** 1087331 CAGCTCTAAAAACCTTAACCTCATCCAGCATCAGAAACCTATGGCTCAGATTCAGCATTCCTGCC 63 CAGCTCTAAAAACCTTAACCTCATCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCC * * 1087396 TGCCAGGTACATCAGTATCATAAGACGCACCATCTATGCAAGTTCGG 128 TGTCAGGTACATCAGTATCATAAGACGCACCATCCATGCAAGTTCGG 1087443 TGAAGTTAGGA-C--------C-AG-TAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACCAG 1 TGAAGTTAGGACCAGTAATAACTAGATAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACCAG * * 1087497 CTCTAAAAACCTTAACCTCATCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTAAAGCATGT 66 CTCTAAAAACCTTAACCTCATCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGT * * * * 1087562 CTGGTGCATCAGTATCATAAGATGCACCATCCATGCAAGTTTGG 131 CAGGTACATCAGTATCATAAGACGCACCATCCATGCAAGTTCGG * * 1087606 TGAAGTTAGGACCAGTAGTAACCTAGA-AATTGCTATCAAAGGGCACCTGCACCAAAAACTTTAA 1 TGAAGTTAGGACCAGTAATAA-CTAGATAA-T-C-ATCAAAGGGCACCTGCTCCAAAAACTTTAA * * * * 1087670 CCTGCTCTAAAAACCTTAACCTCCTCCAGCATCTGAAA-CTCATGGCCCTGATTCAGCATTCAAG 62 CCAGCTCTAAAAACCTTAACCTCATCCAGCATCTGAAACCT-ATGGCTCAGATTCAGCATTCAAG * * * * * * * 1087734 TCTTTCAAGTCCATGAGTAGGTC--AAGATGCACCATCCATGCAAGTTTGG 126 CCTGTCAGGTACATCAGTA--TCATAAGACGCACCATCCATGCAAGTTCGG * * 1087783 TGAAGATAGGACAAGTAATAACTTAGATA 1 TGAAGTTAGGACCAGTAATAAC-TAGATA 1087812 CAGGACCTGC Statistics Matches: 488, Mismatches: 38, Indels: 39 0.86 0.07 0.07 Matches are distributed among these distances: 163 147 0.30 164 1 0.00 166 2 0.00 168 1 0.00 173 1 0.00 174 4 0.01 175 1 0.00 176 5 0.01 177 323 0.66 178 1 0.00 179 2 0.00 ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25 Consensus pattern (174 bp): TGAAGTTAGGACCAGTAATAACTAGATAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACCAG CTCTAAAAACCTTAACCTCATCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGT CAGGTACATCAGTATCATAAGACGCACCATCCATGCAAGTTCGG Found at i:1087480 original size:163 final size:165 Alignment explanation

Indices: 1087294--1087801 Score: 591 Period size: 163 Copynumber: 3.0 Consensus size: 165 1087284 TAACTAAGTT * 1087294 ATAATCATCAAAGTGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCATCCAG 1 ATAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCATCCAG * ** * 1087359 CATCAGAAACCTATGGCTCAGATTCAGCATTCCTGCCTGCCAGGTACATCAGTATCATAAGACGC 66 CATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCATGCCAGGTACATCAGTATCATAAGACGC * 1087424 ACCATCTATGCAAGTTCGGTGAAGTTAGGACC-AG 131 ACCATCCATGCAAGTTCGGTGAAGTTAGGACCAAG 1087458 -TAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCATCCAG 1 ATAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCATCCAG * * * * * 1087522 CATCTGAAACCTATGGCTCAGATTCAGCATTAAAGCATGTCTGGTGCATCAGTATCATAAGATGC 66 CATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCATGCCAGGTACATCAGTATCATAAGACGC * 1087587 ACCATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAG 131 ACCATCCATGCAAGTTCGGTGAAGTTAGGACCA--AG * * 1087624 TAACCTAGAAATTGCTATCAAAGGGCACCTGCACCAAAAACTTTAACCTGCTCTAAAAACCTTAA 1 --A--T---AA-T-C-ATCAAAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTTAA * * * ** * * * 1087689 CCTCCTCCAGCATCTGAAA-CTCATGGCCCTGATTCAGCATTCAAGTC-TTTCAAGTCCATGAGT 56 CCTCATCCAGCATCTGAAACCT-ATGGCTCAGATTCAGCATTCAAG-CATGCCAGGTACATCAGT * * * 1087752 AGGTC--AAGATGCACCATCCATGCAAGTTTGGTGAAGATAGGA-CAAG 119 A--TCATAAGACGCACCATCCATGCAAGTTCGGTGAAGTTAGGACCAAG 1087798 -TAAT 1 ATAAT 1087802 AACTTAGATA Statistics Matches: 302, Mismatches: 24, Indels: 35 0.84 0.07 0.10 Matches are distributed among these distances: 163 149 0.49 165 1 0.00 166 4 0.01 169 1 0.00 171 1 0.00 174 4 0.01 175 1 0.00 176 5 0.02 177 133 0.44 178 1 0.00 179 2 0.01 ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24 Consensus pattern (165 bp): ATAATCATCAAAGGGCACCTGCTCCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCATCCAG CATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCATGCCAGGTACATCAGTATCATAAGACGC ACCATCCATGCAAGTTCGGTGAAGTTAGGACCAAG Found at i:1087504 original size:19 final size:19 Alignment explanation

Indices: 1087477--1087513 Score: 56 Period size: 19 Copynumber: 1.9 Consensus size: 19 1087467 AAGGGCACCT * 1087477 GCTCCAAAAACTTTAACCA 1 GCTCCAAAAACCTTAACCA * 1087496 GCTCTAAAAACCTTAACC 1 GCTCCAAAAACCTTAACC 1087514 TCATCCAGCA Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 16 1.00 ACGTcount: A:0.41, C:0.32, G:0.05, T:0.22 Consensus pattern (19 bp): GCTCCAAAAACCTTAACCA Found at i:1087674 original size:19 final size:19 Alignment explanation

Indices: 1087650--1087691 Score: 57 Period size: 19 Copynumber: 2.2 Consensus size: 19 1087640 ATCAAAGGGC * 1087650 ACCTGCACCAAAAACTTTA 1 ACCTGCACCAAAAACCTTA * * 1087669 ACCTGCTCTAAAAACCTTA 1 ACCTGCACCAAAAACCTTA 1087688 ACCT 1 ACCT 1087692 CCTCCAGCAT Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.38, C:0.33, G:0.05, T:0.24 Consensus pattern (19 bp): ACCTGCACCAAAAACCTTA Done.