Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr07 97507971 

Parameters: 2 7 7 80 10 50 1000

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

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

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


File 311 of 328

Found at i:92404429 original size:28 final size:30

Alignment explanation

Indices: 92404398--92404463 Score: 84 Period size: 27 Copynumber: 2.3 Consensus size: 30 92404388 TTACATTTTG 92404398 TATAATTTTCTTATGACT-TTAT-AAAATT 1 TATAATTTTCTTATGACTATTATAAAAATT * * 92404426 TAT-ATTTTTTTATGATTATTATAAAAATT 1 TATAATTTTCTTATGACTATTATAAAAATT * 92404455 TACAATTTT 1 TATAATTTT 92404464 TATTTTTTTT Statistics Matches: 32, Mismatches: 3, Indels: 4 0.82 0.08 0.10 Matches are distributed among these distances: 27 12 0.38 28 7 0.22 29 8 0.25 30 5 0.16 ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56 Consensus pattern (30 bp): TATAATTTTCTTATGACTATTATAAAAATT Found at i:92404463 original size:29 final size:27 Alignment explanation

Indices: 92404401--92404464 Score: 74 Period size: 29 Copynumber: 2.3 Consensus size: 27 92404391 CATTTTGTAT * 92404401 AATTTTCTTATGACTTTATAAAATTTAT 1 AATTTT-TTATGACTTTATAAAATTTAC * * 92404429 ATTTTTTTATGATTATTATAAAAATTTAC 1 AATTTTTTATGACT-TTAT-AAAATTTAC 92404458 AATTTTT 1 AATTTTT 92404465 ATTTTTTTTT Statistics Matches: 30, Mismatches: 4, Indels: 3 0.81 0.11 0.08 Matches are distributed among these distances: 27 7 0.23 28 9 0.30 29 14 0.47 ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56 Consensus pattern (27 bp): AATTTTTTATGACTTTATAAAATTTAC Found at i:92404475 original size:19 final size:20 Alignment explanation

Indices: 92404453--92404490 Score: 60 Period size: 19 Copynumber: 1.9 Consensus size: 20 92404443 ATTATAAAAA 92404453 TTTACAATTTT-TATTTTTT 1 TTTACAATTTTATATTTTTT * 92404472 TTTACTATTTTATATTTTT 1 TTTACAATTTTATATTTTT 92404491 CTAATTTTAA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 19 10 0.59 20 7 0.41 ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74 Consensus pattern (20 bp): TTTACAATTTTATATTTTTT Found at i:92406212 original size:23 final size:24 Alignment explanation

Indices: 92406173--92406219 Score: 78 Period size: 23 Copynumber: 2.0 Consensus size: 24 92406163 CAGATATAAT * 92406173 AAAAATCTATAATTAAATTATTAA 1 AAAAATATATAATTAAATTATTAA 92406197 AAAAATATATAA-TAAATTATTAA 1 AAAAATATATAATTAAATTATTAA 92406220 TTTAGTTAAG Statistics Matches: 22, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 23 11 0.50 24 11 0.50 ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36 Consensus pattern (24 bp): AAAAATATATAATTAAATTATTAA Found at i:92412753 original size:36 final size:37 Alignment explanation

Indices: 92412701--92412777 Score: 138 Period size: 36 Copynumber: 2.1 Consensus size: 37 92412691 TATGTTTGAC 92412701 TTTATGTTTGAATGTGAATCAATGTAAATTAATATCT 1 TTTATGTTTGAATGTGAATCAATGTAAATTAATATCT * 92412738 TTTA-GTTTGAATGTGAATCGATGTAAATTAATATCT 1 TTTATGTTTGAATGTGAATCAATGTAAATTAATATCT 92412774 TTTA 1 TTTA 92412778 ATTTACTGCG Statistics Matches: 39, Mismatches: 1, Indels: 1 0.95 0.02 0.02 Matches are distributed among these distances: 36 35 0.90 37 4 0.10 ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47 Consensus pattern (37 bp): TTTATGTTTGAATGTGAATCAATGTAAATTAATATCT Found at i:92413623 original size:141 final size:141 Alignment explanation

Indices: 92413368--92413646 Score: 382 Period size: 141 Copynumber: 2.0 Consensus size: 141 92413358 ACTCGTATAA * 92413368 TTTGATGTAAGTAAAAGCCTGAGTTAAAATAGATAAGCAACCGAAAGTTGATGCGTTAGGTATAC 1 TTTGATGTAAGTAAAAACCTGAGTTAAAATAGATAAGCAACCGAAAGTTGATGCGTTAGGTATAC * * * * * * 92413433 GACTTCTGTAGTATGTAGTGTCATTCACAATAATGGAATTTATAGCCCGAGACATGATTAAATGA 66 GACTTCTGCAGTATGTAGCGTCATTCACAACAATGGAATTTATAACCCGAGACATGAGTAAATAA 92413498 TATCCTTTTAC 131 TATCCTTTTAC * * * * * * 92413509 TTTGATGTAAGTAAAAACCTGATTTCAAATAGATAATG-AATCGAAAGTTGGTGTGTTGGGTATA 1 TTTGATGTAAGTAAAAACCTGAGTTAAAATAGATAA-GCAACCGAAAGTTGATGCGTTAGGTATA * * * 92413573 TGACTTCTGCAGTATGTAGCG-CAATTCACAACAGTGGAATTTATAACCCGAGACATGCGTAAAT 65 CGACTTCTGCAGTATGTAGCGTC-ATTCACAACAATGGAATTTATAACCCGAGACATGAGTAAAT 92413637 AATATCCTTT 129 AATATCCTTT 92413647 CATTAGTATT Statistics Matches: 120, Mismatches: 16, Indels: 4 0.86 0.11 0.03 Matches are distributed among these distances: 140 1 0.01 141 118 0.98 142 1 0.01 ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32 Consensus pattern (141 bp): TTTGATGTAAGTAAAAACCTGAGTTAAAATAGATAAGCAACCGAAAGTTGATGCGTTAGGTATAC GACTTCTGCAGTATGTAGCGTCATTCACAACAATGGAATTTATAACCCGAGACATGAGTAAATAA TATCCTTTTAC Found at i:92415530 original size:18 final size:18 Alignment explanation

Indices: 92415507--92415555 Score: 55 Period size: 17 Copynumber: 2.8 Consensus size: 18 92415497 AATTAATGAT * 92415507 TTGAAATAGAAAATGGTA 1 TTGAAATAGAAAATGCTA * * 92415525 TTGAAAT-GACAATGCTT 1 TTGAAATAGAAAATGCTA * 92415542 TTGAAATAGCAAAT 1 TTGAAATAGAAAAT 92415556 AAGATGAAAT Statistics Matches: 25, Mismatches: 5, Indels: 2 0.78 0.16 0.06 Matches are distributed among these distances: 17 14 0.56 18 11 0.44 ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31 Consensus pattern (18 bp): TTGAAATAGAAAATGCTA Found at i:92421953 original size:6 final size:6 Alignment explanation

Indices: 92421942--92421979 Score: 76 Period size: 6 Copynumber: 6.3 Consensus size: 6 92421932 AAAATATATC 92421942 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TA 1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TA 92421980 ACCTTTGACC Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 32 1.00 ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82 Consensus pattern (6 bp): TATTTT Found at i:92422606 original size:28 final size:29 Alignment explanation

Indices: 92422575--92422654 Score: 85 Period size: 28 Copynumber: 2.9 Consensus size: 29 92422565 GCTTATTGGT * * 92422575 TAGTTCC-TGCAAACTTTTGCTTGAAAGA 1 TAGTTCCATGCAAACTCTTACTTGAAAGA * * 92422603 TAG-TCCATGTAGACTCTTACTTGAAAGA 1 TAGTTCCATGCAAACTCTTACTTGAAAGA * * 92422631 TAGTT-CATACAGACTCTTACTTGA 1 TAGTTCCATGCAAACTCTTACTTGA 92422655 TAATAGTCCT Statistics Matches: 44, Mismatches: 6, Indels: 4 0.81 0.11 0.07 Matches are distributed among these distances: 27 3 0.07 28 40 0.91 29 1 0.02 ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35 Consensus pattern (29 bp): TAGTTCCATGCAAACTCTTACTTGAAAGA Found at i:92429578 original size:23 final size:23 Alignment explanation

Indices: 92429546--92429597 Score: 86 Period size: 23 Copynumber: 2.2 Consensus size: 23 92429536 TGAATCCCAT 92429546 TAAATTGAGTTTAATTAAAGTACC 1 TAAA-TGAGTTTAATTAAAGTACC * 92429570 TAAATGAGTTTAATTAGAGTACC 1 TAAATGAGTTTAATTAAAGTACC 92429593 TAAAT 1 TAAAT 92429598 TATATTCTCC Statistics Matches: 27, Mismatches: 1, Indels: 1 0.93 0.03 0.03 Matches are distributed among these distances: 23 23 0.85 24 4 0.15 ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37 Consensus pattern (23 bp): TAAATGAGTTTAATTAAAGTACC Found at i:92430348 original size:6 final size:6 Alignment explanation

Indices: 92430337--92430361 Score: 50 Period size: 6 Copynumber: 4.2 Consensus size: 6 92430327 GCATATGATA 92430337 TTTATT TTTATT TTTATT TTTATT T 1 TTTATT TTTATT TTTATT TTTATT T 92430362 GTAATCATAT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 19 1.00 ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84 Consensus pattern (6 bp): TTTATT Found at i:92430916 original size:5 final size:5 Alignment explanation

Indices: 92430906--92430956 Score: 50 Period size: 5 Copynumber: 10.0 Consensus size: 5 92430896 GTGGTAAGAT * * * 92430906 ATATA ATATA ATATA TATATT ATATT ATATT ATATA GA-ATA ATATA ATATA 1 ATATA ATATA ATATA -ATATA ATATA ATATA ATATA -ATATA ATATA ATATA 92430957 TAGGCCAAAG Statistics Matches: 41, Mismatches: 2, Indels: 6 0.84 0.04 0.12 Matches are distributed among these distances: 4 1 0.02 5 35 0.85 6 5 0.12 ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45 Consensus pattern (5 bp): ATATA Found at i:92430951 original size:17 final size:17 Alignment explanation

Indices: 92430908--92430959 Score: 50 Period size: 17 Copynumber: 2.9 Consensus size: 17 92430898 GGTAAGATAT ** 92430908 ATAATATAATATATATATT 1 ATAATAT-AT-TATATAGA * 92430927 ATATTATATTATATAGA 1 ATAATATATTATATAGA * 92430944 ATAATATAATATATAG 1 ATAATATATTATATAG 92430960 GCCAAAGATG Statistics Matches: 28, Mismatches: 5, Indels: 2 0.80 0.14 0.06 Matches are distributed among these distances: 17 20 0.71 18 2 0.07 19 6 0.21 ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44 Consensus pattern (17 bp): ATAATATATTATATAGA Found at i:92437459 original size:17 final size:17 Alignment explanation

Indices: 92437439--92437490 Score: 52 Period size: 20 Copynumber: 2.9 Consensus size: 17 92437429 TTATTAGATT * 92437439 TTTAT-ATTTTTATAATA 1 TTTATAATTTTAATAA-A 92437456 TTTATAATTTTAATAAA 1 TTTATAATTTTAATAAA 92437473 TTTAAATCAATTTTAATA 1 TTT--AT-AATTTTAATA 92437491 TTTTTTATAT Statistics Matches: 30, Mismatches: 1, Indels: 5 0.83 0.03 0.14 Matches are distributed among these distances: 17 9 0.30 18 9 0.30 19 2 0.07 20 10 0.33 ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56 Consensus pattern (17 bp): TTTATAATTTTAATAAA Found at i:92437515 original size:29 final size:29 Alignment explanation

Indices: 92437482--92437538 Score: 82 Period size: 29 Copynumber: 2.0 Consensus size: 29 92437472 ATTTAAATCA 92437482 ATTTTA-ATATTTTTTA-TATTTTTTATAAC 1 ATTTTACA-ATTTTTTAGT-TTTTTTATAAC 92437511 ATTTTACAATTTTTTAGTTTTTTTATAA 1 ATTTTACAATTTTTTAGTTTTTTTATAA 92437539 AAAAATTAGA Statistics Matches: 26, Mismatches: 0, Indels: 4 0.87 0.00 0.13 Matches are distributed among these distances: 29 24 0.92 30 2 0.08 ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65 Consensus pattern (29 bp): ATTTTACAATTTTTTAGTTTTTTTATAAC Found at i:92439598 original size:23 final size:23 Alignment explanation

Indices: 92439568--92439625 Score: 107 Period size: 23 Copynumber: 2.5 Consensus size: 23 92439558 GCGGATTCCT 92439568 CCCAAACACACCAGAATATCCAA 1 CCCAAACACACCAGAATATCCAA * 92439591 CCCAAACACACTAGAATATCCAA 1 CCCAAACACACCAGAATATCCAA 92439614 CCCAAACACACC 1 CCCAAACACACC 92439626 TGGAATATTA Statistics Matches: 33, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 23 33 1.00 ACGTcount: A:0.47, C:0.41, G:0.03, T:0.09 Consensus pattern (23 bp): CCCAAACACACCAGAATATCCAA Found at i:92439913 original size:8 final size:10 Alignment explanation

Indices: 92439884--92439924 Score: 50 Period size: 10 Copynumber: 4.3 Consensus size: 10 92439874 ATTCTAATAA * 92439884 TCACATATTT 1 TCACACATTT 92439894 TCACACATTT 1 TCACACATTT 92439904 TCACA-A-TT 1 TCACACATTT * 92439912 TCATACATTT 1 TCACACATTT 92439922 TCA 1 TCA 92439925 TTCAATTCAA Statistics Matches: 27, Mismatches: 2, Indels: 4 0.82 0.06 0.12 Matches are distributed among these distances: 8 6 0.22 9 2 0.07 10 19 0.70 ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44 Consensus pattern (10 bp): TCACACATTT Found at i:92440145 original size:15 final size:15 Alignment explanation

Indices: 92440127--92440176 Score: 73 Period size: 15 Copynumber: 3.3 Consensus size: 15 92440117 ATATACATAT 92440127 TATAATTTCAATCAA 1 TATAATTTCAATCAA * 92440142 TATAAATTCAATCAA 1 TATAATTTCAATCAA * * 92440157 AATGATTTCAATCAA 1 TATAATTTCAATCAA 92440172 TATAA 1 TATAA 92440177 ATTTGATAAA Statistics Matches: 29, Mismatches: 6, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 15 29 1.00 ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36 Consensus pattern (15 bp): TATAATTTCAATCAA Found at i:92440328 original size:10 final size:10 Alignment explanation

Indices: 92440313--92440348 Score: 63 Period size: 10 Copynumber: 3.6 Consensus size: 10 92440303 ACAAACCGTA * 92440313 TTTTCCGAGC 1 TTTTCCAAGC 92440323 TTTTCCAAGC 1 TTTTCCAAGC 92440333 TTTTCCAAGC 1 TTTTCCAAGC 92440343 TTTTCC 1 TTTTCC 92440349 TCGTCGACTT Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 10 25 1.00 ACGTcount: A:0.14, C:0.31, G:0.11, T:0.44 Consensus pattern (10 bp): TTTTCCAAGC Found at i:92440514 original size:15 final size:15 Alignment explanation

Indices: 92440475--92440521 Score: 58 Period size: 15 Copynumber: 2.9 Consensus size: 15 92440465 CCTGTTTCTT 92440475 CTCTGTTTCGTTTCCA 1 CTCTGTTTC-TTTCCA * 92440491 CATTCTGTTTCTTTTCA 1 C--TCTGTTTCTTTCCA 92440508 CTCTGTTTCTTTCC 1 CTCTGTTTCTTTCC 92440522 TTTATTTCAT Statistics Matches: 27, Mismatches: 2, Indels: 5 0.79 0.06 0.15 Matches are distributed among these distances: 15 12 0.44 16 1 0.04 17 6 0.22 18 8 0.30 ACGTcount: A:0.06, C:0.30, G:0.09, T:0.55 Consensus pattern (15 bp): CTCTGTTTCTTTCCA Found at i:92440751 original size:21 final size:22 Alignment explanation

Indices: 92440698--92440752 Score: 60 Period size: 21 Copynumber: 2.5 Consensus size: 22 92440688 CAATTTAAAT * 92440698 AATAATAACAATAACAATAATA 1 AATAATAATAATAACAATAATA * * 92440720 ATTAA-ATATAA-AACTATAATA 1 AATAATA-ATAATAACAATAATA 92440741 AATAATAATAAT 1 AATAATAATAAT 92440753 TTAATATATA Statistics Matches: 26, Mismatches: 4, Indels: 6 0.72 0.11 0.17 Matches are distributed among these distances: 21 18 0.69 22 8 0.31 ACGTcount: A:0.65, C:0.05, G:0.00, T:0.29 Consensus pattern (22 bp): AATAATAATAATAACAATAATA Found at i:92453770 original size:19 final size:20 Alignment explanation

Indices: 92453740--92453781 Score: 59 Period size: 19 Copynumber: 2.1 Consensus size: 20 92453730 AAATTTCAAA * * 92453740 AAAAATATAAAACTATTTTT 1 AAAAATATAAAAATATTCTT 92453760 AAAAATA-AAAAATATTCTT 1 AAAAATATAAAAATATTCTT 92453779 AAA 1 AAA 92453782 TAATTTTAAT Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 19 13 0.65 20 7 0.35 ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33 Consensus pattern (20 bp): AAAAATATAAAAATATTCTT Found at i:92454553 original size:15 final size:14 Alignment explanation

Indices: 92454527--92454568 Score: 57 Period size: 15 Copynumber: 2.9 Consensus size: 14 92454517 AAATTTTGGT 92454527 TTTTGATATTTAAGG 1 TTTTGAT-TTTAAGG 92454542 TTTGTGATTTTAAGG 1 TTT-TGATTTTAAGG * 92454557 TTTAGATTTTAA 1 TTTTGATTTTAA 92454569 AATTCTAAAA Statistics Matches: 25, Mismatches: 1, Indels: 3 0.86 0.03 0.10 Matches are distributed among these distances: 14 8 0.32 15 13 0.52 16 4 0.16 ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55 Consensus pattern (14 bp): TTTTGATTTTAAGG Found at i:92454716 original size:29 final size:31 Alignment explanation

Indices: 92454673--92454745 Score: 80 Period size: 29 Copynumber: 2.4 Consensus size: 31 92454663 GAAGAATTTG * * 92454673 AGATTTT-GGTTTTTAAGGCTTAAG-TCTTAT 1 AGATTTTAGG-TTTTAAGACTTAAGATCATAT * * 92454703 -GATTTTAGGTTTTAAGATTTATGATCATAT 1 AGATTTTAGGTTTTAAGACTTAAGATCATAT 92454733 AGATTTTAGGTTT 1 AGATTTTAGGTTT 92454746 AGGGTTTTTA Statistics Matches: 36, Mismatches: 4, Indels: 5 0.80 0.09 0.11 Matches are distributed among these distances: 29 17 0.47 30 7 0.19 31 12 0.33 ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51 Consensus pattern (31 bp): AGATTTTAGGTTTTAAGACTTAAGATCATAT Found at i:92456828 original size:15 final size:15 Alignment explanation

Indices: 92456805--92456845 Score: 50 Period size: 15 Copynumber: 2.9 Consensus size: 15 92456795 TATACAAATC * 92456805 AAAGAATTACTAGAA 1 AAAGAATTAATAGAA * 92456820 AAAGGATTAATAG-A 1 AAAGAATTAATAGAA 92456834 AAA-AATTAATAG 1 AAAGAATTAATAG 92456846 TCCACACTCG Statistics Matches: 23, Mismatches: 3, Indels: 2 0.82 0.11 0.07 Matches are distributed among these distances: 13 8 0.35 14 4 0.17 15 11 0.48 ACGTcount: A:0.61, C:0.02, G:0.15, T:0.22 Consensus pattern (15 bp): AAAGAATTAATAGAA Found at i:92458238 original size:2 final size:2 Alignment explanation

Indices: 92458231--92458256 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 92458221 TTATACCTAA 92458231 AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT 92458257 CTAACTTGAG Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:92458525 original size:21 final size:20 Alignment explanation

Indices: 92458487--92458525 Score: 51 Period size: 21 Copynumber: 1.9 Consensus size: 20 92458477 TTATTTATTG ** 92458487 TTTTATATTTAGGGTTTTGA 1 TTTTATATTTAGAATTTTGA 92458507 TTTTATAGTTTAGAATTTT 1 TTTTATA-TTTAGAATTTT 92458526 TGGATTTAAG Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 20 7 0.44 21 9 0.56 ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62 Consensus pattern (20 bp): TTTTATATTTAGAATTTTGA Found at i:92460905 original size:18 final size:18 Alignment explanation

Indices: 92460856--92460905 Score: 59 Period size: 18 Copynumber: 2.8 Consensus size: 18 92460846 AATTAATTAG 92460856 AAAAAAA-ATTATTTGTT 1 AAAAAAATATTATTTGTT * 92460873 AAAAAGGAT-TTATTTGTT 1 AAAAA-AATATTATTTGTT * 92460891 AAAAAAATATAATTT 1 AAAAAAATATTATTT 92460906 TATTTAAAAA Statistics Matches: 27, Mismatches: 3, Indels: 5 0.77 0.09 0.14 Matches are distributed among these distances: 17 7 0.26 18 20 0.74 ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40 Consensus pattern (18 bp): AAAAAAATATTATTTGTT Found at i:92461121 original size:22 final size:22 Alignment explanation

Indices: 92461079--92461121 Score: 52 Period size: 22 Copynumber: 2.0 Consensus size: 22 92461069 AAGTAAGTTA * * 92461079 TTTATAATTTTTATTTTTTATT 1 TTTATAATTTTTAGTTATTATT 92461101 TTTAT-ATTTTATAGTTATTAT 1 TTTATAATTTT-TAGTTATTAT 92461122 AATATAATAA Statistics Matches: 18, Mismatches: 2, Indels: 2 0.82 0.09 0.09 Matches are distributed among these distances: 21 5 0.28 22 13 0.72 ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72 Consensus pattern (22 bp): TTTATAATTTTTAGTTATTATT Found at i:92463603 original size:60 final size:60 Alignment explanation

Indices: 92463510--92463646 Score: 177 Period size: 60 Copynumber: 2.3 Consensus size: 60 92463500 GTCGCAGAAC ** ** ** 92463510 AGTTCATATCACCCGGACATGGGCAGTTCAAGTTCATATCACCTGGACATGGGCGGCTTG 1 AGTTCATATCACCTAGACATGGGCAGTTCAAGTTCATATCACCCAGACATAAGCGGCTTG * * * 92463570 AGTTCATATCACCTAGACATGGGCGGTTTAAGTTCATATCACCCAGACATAAGCGGTTTG 1 AGTTCATATCACCTAGACATGGGCAGTTCAAGTTCATATCACCCAGACATAAGCGGCTTG 92463630 AGTTCAT-TCCACCTAGA 1 AGTTCATAT-CACCTAGA 92463647 GCAACCACTG Statistics Matches: 67, Mismatches: 9, Indels: 2 0.86 0.12 0.03 Matches are distributed among these distances: 59 1 0.01 60 66 0.99 ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27 Consensus pattern (60 bp): AGTTCATATCACCTAGACATGGGCAGTTCAAGTTCATATCACCCAGACATAAGCGGCTTG Found at i:92463626 original size:30 final size:30 Alignment explanation

Indices: 92463510--92463636 Score: 155 Period size: 30 Copynumber: 4.2 Consensus size: 30 92463500 GTCGCAGAAC * * * 92463510 AGTTCATATCACCCGGACATGGGCAGTTCA 1 AGTTCATATCACCCAGACATGGGCGGTTTA ** * * 92463540 AGTTCATATCACCTGGACATGGGCGGCTTG 1 AGTTCATATCACCCAGACATGGGCGGTTTA * 92463570 AGTTCATATCACCTAGACATGGGCGGTTTA 1 AGTTCATATCACCCAGACATGGGCGGTTTA ** * 92463600 AGTTCATATCACCCAGACATAAGCGGTTTG 1 AGTTCATATCACCCAGACATGGGCGGTTTA 92463630 AGTTCAT 1 AGTTCAT 92463637 TCCACCTAGA Statistics Matches: 85, Mismatches: 12, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 30 85 1.00 ACGTcount: A:0.26, C:0.23, G:0.24, T:0.28 Consensus pattern (30 bp): AGTTCATATCACCCAGACATGGGCGGTTTA Found at i:92466985 original size:21 final size:22 Alignment explanation

Indices: 92466952--92466992 Score: 75 Period size: 21 Copynumber: 1.9 Consensus size: 22 92466942 CTCCACCAAA 92466952 TAAAATATTAATTTTTAAAATT 1 TAAAATATTAATTTTTAAAATT 92466974 TAAAAT-TTAATTTTTAAAA 1 TAAAATATTAATTTTTAAAA 92466993 ACGTTTGAAT Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 21 13 0.68 22 6 0.32 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (22 bp): TAAAATATTAATTTTTAAAATT Found at i:92467050 original size:30 final size:30 Alignment explanation

Indices: 92467016--92467091 Score: 82 Period size: 30 Copynumber: 2.5 Consensus size: 30 92467006 TTTAAAATTA * 92467016 ATTTAAAATTTTATAAT-TTATAAAAAATAT 1 ATTTAAAATTTTATAATATT-TAAAAAATAC ** * * 92467046 ATTTAAAATTAAAAAATATTTAAAATATAC 1 ATTTAAAATTTTATAATATTTAAAAAATAC * 92467076 ATTTAAAATATTATAA 1 ATTTAAAATTTTATAA 92467092 AACAAATAAT Statistics Matches: 36, Mismatches: 9, Indels: 2 0.77 0.19 0.04 Matches are distributed among these distances: 30 34 0.94 31 2 0.06 ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42 Consensus pattern (30 bp): ATTTAAAATTTTATAATATTTAAAAAATAC Found at i:92467059 original size:17 final size:17 Alignment explanation

Indices: 92467038--92467071 Score: 59 Period size: 17 Copynumber: 1.9 Consensus size: 17 92467028 ATAATTTATA 92467038 AAAAATATATTTAAAATT 1 AAAAA-ATATTTAAAATT 92467056 AAAAAATATTTAAAAT 1 AAAAAATATTTAAAAT 92467072 ATACATTTAA Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 17 11 0.69 18 5 0.31 ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35 Consensus pattern (17 bp): AAAAAATATTTAAAATT Found at i:92467263 original size:23 final size:23 Alignment explanation

Indices: 92467172--92467270 Score: 77 Period size: 21 Copynumber: 4.5 Consensus size: 23 92467162 ACTATATTTA * 92467172 AATATTTT-ATATTATT-AAAAAT 1 AATATTTTAAAATT-TTAAAAAAT * * 92467194 -ATA-TTTAAAA-TGTAAAAACT 1 AATATTTTAAAATTTTAAAAAAT * * 92467214 AATA-TTT-AAATTTTTAAATAT 1 AATATTTTAAAATTTTAAAAAAT 92467235 ATATATTTTAAAATTTTAAAAAAT 1 A-ATATTTTAAAATTTTAAAAAAT * 92467259 AATATTATAAAA 1 AATATTTTAAAA 92467271 CATTTCAAAT Statistics Matches: 60, Mismatches: 10, Indels: 13 0.72 0.12 0.16 Matches are distributed among these distances: 19 1 0.02 20 12 0.20 21 18 0.30 22 3 0.05 23 13 0.22 24 13 0.22 ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44 Consensus pattern (23 bp): AATATTTTAAAATTTTAAAAAAT Found at i:92470326 original size:28 final size:29 Alignment explanation

Indices: 92470257--92470327 Score: 76 Period size: 28 Copynumber: 2.5 Consensus size: 29 92470247 ACCTCAGGTT * * 92470257 ACATTTTAGTCACTTATGTTTGAAATATT 1 ACATTTTAGTCACTTACGTTTGAAATATA * 92470286 ACATTTTTA-TCACTTACG-TT-AACATGTA 1 ACA-TTTTAGTCACTTACGTTTGAA-ATATA 92470314 ACATTTTAGTCACT 1 ACATTTTAGTCACT 92470328 GAGCTGTTAA Statistics Matches: 36, Mismatches: 3, Indels: 7 0.78 0.07 0.15 Matches are distributed among these distances: 27 7 0.19 28 13 0.36 29 11 0.31 30 5 0.14 ACGTcount: A:0.31, C:0.15, G:0.08, T:0.45 Consensus pattern (29 bp): ACATTTTAGTCACTTACGTTTGAAATATA Found at i:92474049 original size:2 final size:2 Alignment explanation

Indices: 92474044--92474074 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 92474034 TGTAATTTTT 92474044 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 92474075 TCCACCAAAC Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:92483921 original size:26 final size:29 Alignment explanation

Indices: 92483876--92483932 Score: 75 Period size: 27 Copynumber: 2.1 Consensus size: 29 92483866 ATGACTTTTC * 92483876 AAAAATTCATACATGATTTAACTT-TAAA 1 AAAAATTCATACAAGATTTAACTTATAAA * 92483904 AAAAATT-ATACAAG-TTTAAGTTATAAA 1 AAAAATTCATACAAGATTTAACTTATAAA 92483931 AA 1 AA 92483933 TTATATTATA Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 26 7 0.27 27 12 0.46 28 7 0.27 ACGTcount: A:0.54, C:0.07, G:0.05, T:0.33 Consensus pattern (29 bp): AAAAATTCATACAAGATTTAACTTATAAA Found at i:92485701 original size:28 final size:28 Alignment explanation

Indices: 92485670--92485731 Score: 70 Period size: 28 Copynumber: 2.2 Consensus size: 28 92485660 ACTTTTCTAT ** 92485670 ATTTTTAATAATTTTAATAAATTTTAAA 1 ATTTTTAATAATGGTAATAAATTTTAAA * * * * 92485698 ATTTTTTATTATGGTAATAATTTTTAAT 1 ATTTTTAATAATGGTAATAAATTTTAAA 92485726 ATTTTT 1 ATTTTT 92485732 CTGTAATTTT Statistics Matches: 28, Mismatches: 6, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 28 28 1.00 ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60 Consensus pattern (28 bp): ATTTTTAATAATGGTAATAAATTTTAAA Found at i:92485703 original size:9 final size:10 Alignment explanation

Indices: 92485670--92485750 Score: 53 Period size: 9 Copynumber: 8.4 Consensus size: 10 92485660 ACTTTTCTAT 92485670 ATTTTTAATA 1 ATTTTTAATA 92485680 A-TTTTAATA 1 ATTTTTAATA * 92485689 AATTTTAA-A 1 ATTTTTAATA * * 92485698 ATTTTTTATT 1 ATTTTTAATA ** 92485708 A-TGGTAATA 1 ATTTTTAATA 92485717 ATTTTTAAT- 1 ATTTTTAATA ** 92485726 ATTTTTCTGTA 1 ATTTTT-AATA * 92485737 ATTTTTTATA 1 ATTTTTAATA 92485747 ATTT 1 ATTT 92485751 ATATAAATTT Statistics Matches: 54, Mismatches: 12, Indels: 10 0.71 0.16 0.13 Matches are distributed among these distances: 9 27 0.50 10 21 0.39 11 6 0.11 ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60 Consensus pattern (10 bp): ATTTTTAATA Found at i:92502260 original size:12 final size:12 Alignment explanation

Indices: 92502243--92502290 Score: 60 Period size: 12 Copynumber: 3.8 Consensus size: 12 92502233 TGGGAGTAAA 92502243 GTTTTATATTTG 1 GTTTTATATTTG * 92502255 GTTTTATATGTTAAA 1 GTTTTATAT-TT--G 92502270 GTTTTATATTTG 1 GTTTTATATTTG 92502282 GTTTTATAT 1 GTTTTATAT 92502291 GTTAATGACA Statistics Matches: 31, Mismatches: 2, Indels: 6 0.79 0.05 0.15 Matches are distributed among these distances: 12 18 0.58 13 2 0.06 14 2 0.06 15 9 0.29 ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62 Consensus pattern (12 bp): GTTTTATATTTG Found at i:92502273 original size:27 final size:27 Alignment explanation

Indices: 92502239--92502295 Score: 114 Period size: 27 Copynumber: 2.1 Consensus size: 27 92502229 TTAGTGGGAG 92502239 TAAAGTTTTATATTTGGTTTTATATGT 1 TAAAGTTTTATATTTGGTTTTATATGT 92502266 TAAAGTTTTATATTTGGTTTTATATGT 1 TAAAGTTTTATATTTGGTTTTATATGT 92502293 TAA 1 TAA 92502296 TGACATATTG Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 27 30 1.00 ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58 Consensus pattern (27 bp): TAAAGTTTTATATTTGGTTTTATATGT Found at i:92513455 original size:43 final size:43 Alignment explanation

Indices: 92513394--92513479 Score: 145 Period size: 43 Copynumber: 2.0 Consensus size: 43 92513384 TATATGATTG * 92513394 ATATTGAAATGACAAATATGATAAATGAATATGAGATGAGAAA 1 ATATTGAAATGACAAATATGAGAAATGAATATGAGATGAGAAA * * 92513437 ATATTGAAATGGCAAATATGAGAAATGATTATGAGATGAGAAA 1 ATATTGAAATGACAAATATGAGAAATGAATATGAGATGAGAAA 92513480 TGAGATATGA Statistics Matches: 40, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 43 40 1.00 ACGTcount: A:0.51, C:0.02, G:0.21, T:0.26 Consensus pattern (43 bp): ATATTGAAATGACAAATATGAGAAATGAATATGAGATGAGAAA Found at i:92514295 original size:24 final size:25 Alignment explanation

Indices: 92514234--92514311 Score: 113 Period size: 25 Copynumber: 3.1 Consensus size: 25 92514224 TGTGATAAAA 92514234 ATAAAATATATTTGTAATAAATATT 1 ATAAAATATATTTGTAATAAATATT * 92514259 ATAAAATATATTTGTACTAAATATT 1 ATAAAATATATTTGTAATAAATATT * * 92514284 AT-AAATACATTTGTAATATATATAT 1 ATAAAATATATTTGTAATAAATAT-T 92514309 ATA 1 ATA 92514312 TATATGTATT Statistics Matches: 47, Mismatches: 4, Indels: 3 0.87 0.07 0.06 Matches are distributed among these distances: 24 18 0.38 25 29 0.62 ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44 Consensus pattern (25 bp): ATAAAATATATTTGTAATAAATATT Found at i:92514554 original size:24 final size:23 Alignment explanation

Indices: 92514519--92514577 Score: 68 Period size: 24 Copynumber: 2.6 Consensus size: 23 92514509 TAAAAGAAAG * 92514519 ACAAGTGTATAAAATGATTTGG-T 1 ACAAGTGTATAAAAT-ATATGGAT * 92514542 ACAAGTGTAATAATATATATGGAT 1 ACAAGTGT-ATAAAATATATGGAT 92514566 ACAAGTGT-TAAA 1 ACAAGTGTATAAA 92514578 TAAATATTTG Statistics Matches: 31, Mismatches: 3, Indels: 5 0.79 0.08 0.13 Matches are distributed among these distances: 22 3 0.10 23 13 0.42 24 15 0.48 ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32 Consensus pattern (23 bp): ACAAGTGTATAAAATATATGGAT Found at i:92514643 original size:2 final size:2 Alignment explanation

Indices: 92514636--92514663 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 92514626 TTATTATTAT 92514636 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 92514664 GTAAATAAAG Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:92515592 original size:18 final size:18 Alignment explanation

Indices: 92515569--92515632 Score: 101 Period size: 18 Copynumber: 3.6 Consensus size: 18 92515559 TAAATAAATA * 92515569 TACTGAATAACTGACTAC 1 TACTGAATAACTGACTGC * 92515587 TACTGAATAACTGACTGT 1 TACTGAATAACTGACTGC * 92515605 TACTGGATAACTGACTGC 1 TACTGAATAACTGACTGC 92515623 TACTGAATAA 1 TACTGAATAA 92515633 TTTATCGTTA Statistics Matches: 41, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 18 41 1.00 ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30 Consensus pattern (18 bp): TACTGAATAACTGACTGC Found at i:92515660 original size:18 final size:18 Alignment explanation

Indices: 92515569--92515660 Score: 96 Period size: 18 Copynumber: 5.1 Consensus size: 18 92515559 TAAATAAATA ** 92515569 TACTGAATAACTGACTAC 1 TACTGAATAACTGACTGT 92515587 TACTGAATAACTGACTGT 1 TACTGAATAACTGACTGT * * 92515605 TACTGGATAACTGACTGC 1 TACTGAATAACTGACTGT * * 92515623 TACTGAATAATTTA-TCGT 1 TACTGAATAACTGACT-GT * * 92515641 TATTGAATAATTGACTGT 1 TACTGAATAACTGACTGT 92515659 TA 1 TA 92515661 AAAAGTGATT Statistics Matches: 62, Mismatches: 10, Indels: 4 0.82 0.13 0.05 Matches are distributed among these distances: 17 1 0.02 18 60 0.97 19 1 0.02 ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36 Consensus pattern (18 bp): TACTGAATAACTGACTGT Found at i:92515713 original size:18 final size:18 Alignment explanation

Indices: 92515639--92515721 Score: 62 Period size: 18 Copynumber: 4.6 Consensus size: 18 92515629 ATAATTTATC * * 92515639 GTTATTGAATAATTGACT 1 GTTATTGAATGATTGAAT ** 92515657 GTTA-AAAAGTGATTGAAT 1 GTTATTGAA-TGATTGAAT * * * 92515675 ATTATTGAACGACT-AATT 1 GTTATTGAATGATTGAA-T 92515693 GTTATTGAATGATTGAAT 1 GTTATTGAATGATTGAAT * 92515711 GTTACTGAATG 1 GTTATTGAATG 92515722 CAACTGACAA Statistics Matches: 48, Mismatches: 13, Indels: 8 0.70 0.19 0.12 Matches are distributed among these distances: 17 4 0.08 18 40 0.83 19 4 0.08 ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40 Consensus pattern (18 bp): GTTATTGAATGATTGAAT Found at i:92527872 original size:49 final size:49 Alignment explanation

Indices: 92527791--92527884 Score: 136 Period size: 49 Copynumber: 1.9 Consensus size: 49 92527781 TCAAGAAGGG * * * * 92527791 ATAAATAGTGATCAGAGTGTAAACAGTGGAAGACTAAGTTTAGCAATGT 1 ATAAATAGTGATAAGAGTGTAAACAATAGAAGACCAAGTTTAGCAATGT 92527840 ATAAATAGTGATAAGAGTGTAGAA-AATAGAAGACCAAGTTTAGCA 1 ATAAATAGTGATAAGAGTGTA-AACAATAGAAGACCAAGTTTAGCA 92527885 TTGCATAGCA Statistics Matches: 40, Mismatches: 4, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 49 38 0.95 50 2 0.05 ACGTcount: A:0.45, C:0.07, G:0.23, T:0.24 Consensus pattern (49 bp): ATAAATAGTGATAAGAGTGTAAACAATAGAAGACCAAGTTTAGCAATGT Found at i:92528768 original size:32 final size:32 Alignment explanation

Indices: 92528727--92528790 Score: 119 Period size: 32 Copynumber: 2.0 Consensus size: 32 92528717 TAGTAAGTTC * 92528727 ATAGGAATAAATCATAAATCTTACCAAGCATT 1 ATAGGAATAAATCATAAATCTTACCAAACATT 92528759 ATAGGAATAAATCATAAATCTTACCAAACATT 1 ATAGGAATAAATCATAAATCTTACCAAACATT 92528791 CATACTCTTA Statistics Matches: 31, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 32 31 1.00 ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28 Consensus pattern (32 bp): ATAGGAATAAATCATAAATCTTACCAAACATT Found at i:92529141 original size:51 final size:51 Alignment explanation

Indices: 92529060--92529176 Score: 189 Period size: 51 Copynumber: 2.3 Consensus size: 51 92529050 CGGATCACAT * * * 92529060 TTATCATTTGTCACTTGTCACTGATTAGATAAGTTTAGCTAAAGCTACCAC 1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC * * 92529111 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACTAT 1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC 92529162 TTATCACTTGTCACT 1 TTATCACTTGTCACT 92529177 GATCAAAAGT Statistics Matches: 61, Mismatches: 5, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 51 61 1.00 ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38 Consensus pattern (51 bp): TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC Found at i:92543489 original size:14 final size:15 Alignment explanation

Indices: 92543470--92543502 Score: 59 Period size: 15 Copynumber: 2.3 Consensus size: 15 92543460 AAATAATTTT 92543470 AAAATTTT-AAAAAG 1 AAAATTTTCAAAAAG 92543484 AAAATTTTCAAAAAG 1 AAAATTTTCAAAAAG 92543499 AAAA 1 AAAA 92543503 ACCAAGGTTA Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 14 8 0.44 15 10 0.56 ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24 Consensus pattern (15 bp): AAAATTTTCAAAAAG Found at i:92545404 original size:9 final size:9 Alignment explanation

Indices: 92545384--92545533 Score: 77 Period size: 10 Copynumber: 14.9 Consensus size: 9 92545374 TTTTTATTAG 92545384 AATTTATTAT 1 AATTT-TTAT 92545394 AATTTTTAT 1 AATTTTTAT * 92545403 AAACTTTTAT 1 -AATTTTTAT 92545413 GAATTTTTTAAT 1 -AA-TTTTT-AT 92545425 AATATTTTAT 1 AAT-TTTTAT 92545435 AAGTTTTTAT 1 AA-TTTTTAT * 92545445 AAGTTTATAT 1 AA-TTTTTAT * 92545455 AATTTTTTT 1 AATTTTTAT ** 92545464 AAGATTTA- 1 AATTTTTAT 92545472 ATATTTTTAAT 1 A-ATTTTT-AT * 92545483 GATTTTTAT 1 AATTTTTAT 92545492 GAAATTATTTTTAT 1 ---A--ATTTTTAT 92545506 AATTTTTAAT 1 AATTTTT-AT 92545516 AATTTTTTAT 1 AA-TTTTTAT * 92545526 GATTTTTA 1 AATTTTTA 92545534 AATAAAAAAT Statistics Matches: 111, Mismatches: 14, Indels: 31 0.71 0.09 0.20 Matches are distributed among these distances: 8 1 0.01 9 32 0.29 10 51 0.46 11 17 0.15 12 2 0.02 14 8 0.07 ACGTcount: A:0.35, C:0.01, G:0.05, T:0.60 Consensus pattern (9 bp): AATTTTTAT Found at i:92545443 original size:32 final size:31 Alignment explanation

Indices: 92545373--92545470 Score: 94 Period size: 32 Copynumber: 3.1 Consensus size: 31 92545363 ATACACTTTT 92545373 ATTTTTATTAGAATTTATTATAATTTTTATAA 1 ATTTTTA-TAGAATTTATTATAATTTTTATAA * * 92545405 ACTTTTAT-GAATTTTTTAATAATATTTTATAA 1 ATTTTTATAGAATTTATT-ATAAT-TTTTATAA * * * 92545437 GTTTTTATA-AGTTTA-TATAATTTTTTTAA 1 ATTTTTATAGAATTTATTATAATTTTTATAA 92545466 GATTT 1 -ATTT 92545471 AATATTTTTA Statistics Matches: 54, Mismatches: 8, Indels: 10 0.75 0.11 0.14 Matches are distributed among these distances: 29 7 0.13 30 16 0.30 31 7 0.13 32 24 0.44 ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59 Consensus pattern (31 bp): ATTTTTATAGAATTTATTATAATTTTTATAA Found at i:92545466 original size:19 final size:20 Alignment explanation

Indices: 92545373--92545480 Score: 84 Period size: 22 Copynumber: 5.3 Consensus size: 20 92545363 ATACACTTTT * 92545373 ATTTTTATTAGAATTTATTATA 1 ATTTTTATAAG-ATTTA-TATA 92545395 ATTTTTATAA-ACTTT-TATGA 1 ATTTTTATAAGA-TTTATAT-A * 92545415 ATTTTTTAATAATATTT-TATA 1 A-TTTTT-ATAAGATTTATATA 92545436 AGTTTTTATAAG-TTTATATA 1 A-TTTTTATAAGATTTATATA * 92545456 ATTTTTTTAAGATTTA-AT- 1 ATTTTTATAAGATTTATATA 92545474 ATTTTTA 1 ATTTTTA 92545481 ATGATTTTTA Statistics Matches: 74, Mismatches: 5, Indels: 18 0.76 0.05 0.19 Matches are distributed among these distances: 18 6 0.08 19 17 0.23 20 16 0.22 21 15 0.20 22 19 0.26 23 1 0.01 ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59 Consensus pattern (20 bp): ATTTTTATAAGATTTATATA Found at i:92545478 original size:16 final size:17 Alignment explanation

Indices: 92545454--92545487 Score: 52 Period size: 16 Copynumber: 2.1 Consensus size: 17 92545444 TAAGTTTATA * 92545454 TAATTTTTTTAA-GATT 1 TAATATTTTTAATGATT 92545470 TAATATTTTTAATGATT 1 TAATATTTTTAATGATT 92545487 T 1 T 92545488 TTATGAAATT Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 16 11 0.69 17 5 0.31 ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62 Consensus pattern (17 bp): TAATATTTTTAATGATT Found at i:92545480 original size:29 final size:28 Alignment explanation

Indices: 92545417--92545491 Score: 78 Period size: 29 Copynumber: 2.6 Consensus size: 28 92545407 TTTTATGAAT * * 92545417 TTTTTAATAATATTTTATAAGTTTTTATA 1 TTTTTAATAAT-TTTTATAAGATTTAATA ** * 92545446 AGTTTATATAATTTTTTTAAGATTTAATA 1 TTTTTA-ATAATTTTTATAAGATTTAATA * 92545475 TTTTTAATGATTTTTAT 1 TTTTTAATAATTTTTAT 92545492 GAAATTATTT Statistics Matches: 36, Mismatches: 9, Indels: 3 0.75 0.19 0.06 Matches are distributed among these distances: 28 9 0.25 29 22 0.61 30 5 0.14 ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61 Consensus pattern (28 bp): TTTTTAATAATTTTTATAAGATTTAATA Found at i:92550622 original size:28 final size:27 Alignment explanation

Indices: 92550562--92550638 Score: 79 Period size: 28 Copynumber: 2.9 Consensus size: 27 92550552 TATTTTTAAA * * * 92550562 AAATTA-AAAGATTTAAATATTA-TTT 1 AAATTATAAAAATATAAAAATTATTTT * 92550587 AAAATATAAAAATATAAAAATTATTTT 1 AAATTATAAAAATATAAAAATTATTTT * 92550614 GAAATTATAAAAATAT-ATAATTATT 1 -AAATTATAAAAATATAAAAATTATT 92550639 AAAAAAATCA Statistics Matches: 43, Mismatches: 6, Indels: 4 0.81 0.11 0.08 Matches are distributed among these distances: 25 5 0.12 26 13 0.30 27 11 0.26 28 14 0.33 ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40 Consensus pattern (27 bp): AAATTATAAAAATATAAAAATTATTTT Found at i:92551229 original size:2 final size:2 Alignment explanation

Indices: 92551222--92551249 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 92551212 TTTATTACCA 92551222 AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT 92551250 GCATTTACAT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:92556637 original size:48 final size:48 Alignment explanation

Indices: 92556585--92556685 Score: 114 Period size: 48 Copynumber: 2.1 Consensus size: 48 92556575 CCTAAACTCC * * 92556585 AAACCATGAACAACAAAC-CTTGAACCCGAATCCTGAACTTGAAACCAT 1 AAACCATGAACAACAAACACTAG-ACCCAAATCCTGAACTTGAAACCAT * * * * * * 92556633 AAACCTTGAACACCAAACACTAGATCTAAATCTTGAACTTGAAACCCT 1 AAACCATGAACAACAAACACTAGACCCAAATCCTGAACTTGAAACCAT 92556681 AAACC 1 AAACC 92556686 TCAAATCGAG Statistics Matches: 44, Mismatches: 8, Indels: 2 0.81 0.15 0.04 Matches are distributed among these distances: 48 41 0.93 49 3 0.07 ACGTcount: A:0.44, C:0.29, G:0.09, T:0.19 Consensus pattern (48 bp): AAACCATGAACAACAAACACTAGACCCAAATCCTGAACTTGAAACCAT Found at i:92556751 original size:20 final size:21 Alignment explanation

Indices: 92556726--92556765 Score: 64 Period size: 21 Copynumber: 2.0 Consensus size: 21 92556716 TTTGAGGTTC 92556726 AAGTTCAAG-TTTAGGGTTTA 1 AAGTTCAAGATTTAGGGTTTA * 92556746 AAGTTCGAGATTTAGGGTTT 1 AAGTTCAAGATTTAGGGTTT 92556766 GAGTTTGGGG Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 20 8 0.44 21 10 0.56 ACGTcount: A:0.28, C:0.05, G:0.28, T:0.40 Consensus pattern (21 bp): AAGTTCAAGATTTAGGGTTTA Found at i:92558074 original size:22 final size:22 Alignment explanation

Indices: 92558030--92558074 Score: 58 Period size: 22 Copynumber: 2.1 Consensus size: 22 92558020 TAGCAAACAA * * 92558030 ATATAAATATAAATAATTGTAT 1 ATATAAATATAAAAAATTATAT 92558052 ATATAAATA-AAAAAATTA-AT 1 ATATAAATATAAAAAATTATAT 92558072 ATA 1 ATA 92558075 AGCAAATATT Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 20 5 0.24 21 7 0.33 22 9 0.43 ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36 Consensus pattern (22 bp): ATATAAATATAAAAAATTATAT Found at i:92558116 original size:21 final size:21 Alignment explanation

Indices: 92558090--92558150 Score: 59 Period size: 21 Copynumber: 2.8 Consensus size: 21 92558080 ATATTTATAT ** 92558090 AAAAAAATTATATTTATGTAA 1 AAAAAAATTATATTTAAATAA * * 92558111 AAAAAAACTAGATTTAAATAA 1 AAAAAAATTATATTTAAATAA * 92558132 AAAATAAATAAATATTTAA 1 AAAA-AAAT-TATATTTAA 92558151 CATTAGATCT Statistics Matches: 31, Mismatches: 7, Indels: 2 0.77 0.17 0.05 Matches are distributed among these distances: 21 21 0.68 22 3 0.10 23 7 0.23 ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31 Consensus pattern (21 bp): AAAAAAATTATATTTAAATAA Found at i:92563476 original size:12 final size:13 Alignment explanation

Indices: 92563461--92563492 Score: 50 Period size: 12 Copynumber: 2.6 Consensus size: 13 92563451 ATAACACATT 92563461 TCAAAAC-ATGCA 1 TCAAAACTATGCA 92563473 TCAAAACTATGCA 1 TCAAAACTATGCA 92563486 -CAAAACT 1 TCAAAACT 92563493 TAACATTTTC Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 12 14 0.74 13 5 0.26 ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19 Consensus pattern (13 bp): TCAAAACTATGCA Found at i:92565824 original size:46 final size:46 Alignment explanation

Indices: 92565774--92565995 Score: 308 Period size: 46 Copynumber: 4.8 Consensus size: 46 92565764 TGGTTGAGCA 92565774 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG 92565820 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * * 92565866 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G * 92565911 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG 1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * * 92565959 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG 92565996 GCGGGTTACA Statistics Matches: 157, Mismatches: 10, Indels: 18 0.85 0.05 0.10 Matches are distributed among these distances: 42 2 0.01 43 5 0.03 45 3 0.02 46 109 0.69 47 29 0.18 48 3 0.02 50 4 0.03 51 2 0.01 ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29 Consensus pattern (46 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG Found at i:92565943 original size:93 final size:93 Alignment explanation

Indices: 92565820--92565988 Score: 311 Period size: 93 Copynumber: 1.8 Consensus size: 93 92565810 GATGCGAATG * * 92565820 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTGA 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTGA 92565885 GTCCGAGTTCGTGAGATGTAACTAGGCA 66 GTCCGAGTTCGTGAGATGTAACTAGGCA * 92565913 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTGA 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTGA 92565978 GTCCGAGTTCG 66 GTCCGAGTTCG 92565989 CTTATGGGCG Statistics Matches: 73, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 73 1.00 ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28 Consensus pattern (93 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTGA GTCCGAGTTCGTGAGATGTAACTAGGCA Found at i:92572950 original size:46 final size:46 Alignment explanation

Indices: 92572900--92573121 Score: 308 Period size: 46 Copynumber: 4.8 Consensus size: 46 92572890 TGGTTGAGCA 92572900 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG 92572946 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * * 92572992 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G * 92573037 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG 1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * * 92573085 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG 92573122 GCGGGTTACA Statistics Matches: 157, Mismatches: 10, Indels: 18 0.85 0.05 0.10 Matches are distributed among these distances: 42 2 0.01 43 5 0.03 45 3 0.02 46 109 0.69 47 29 0.18 48 3 0.02 50 4 0.03 51 2 0.01 ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29 Consensus pattern (46 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG Found at i:92573069 original size:93 final size:93 Alignment explanation

Indices: 92572946--92573114 Score: 311 Period size: 93 Copynumber: 1.8 Consensus size: 93 92572936 GATGCGAATG * * 92572946 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTGA 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTGA 92573011 GTCCGAGTTCGTGAGATGTAACTAGGCA 66 GTCCGAGTTCGTGAGATGTAACTAGGCA * 92573039 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTGA 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTGA 92573104 GTCCGAGTTCG 66 GTCCGAGTTCG 92573115 CTTATGGGCG Statistics Matches: 73, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 73 1.00 ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28 Consensus pattern (93 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTGA GTCCGAGTTCGTGAGATGTAACTAGGCA Found at i:92577385 original size:31 final size:31 Alignment explanation

Indices: 92577350--92577408 Score: 84 Period size: 31 Copynumber: 1.9 Consensus size: 31 92577340 AACAACTCAT ** 92577350 TGACTTAAAT-AAAAGCTTTTGAATAGTTCAG 1 TGACTTAAATGAAAA-CTTCCGAATAGTTCAG 92577381 TGACTTAAATGAAAACTTCCGAATAGTT 1 TGACTTAAATGAAAACTTCCGAATAGTT 92577409 AAATGATCAA Statistics Matches: 25, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 31 21 0.84 32 4 0.16 ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34 Consensus pattern (31 bp): TGACTTAAATGAAAACTTCCGAATAGTTCAG Found at i:92578154 original size:12 final size:12 Alignment explanation

Indices: 92578137--92578163 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 92578127 ATAAAATCAC 92578137 CCAAGTTCTGCT 1 CCAAGTTCTGCT 92578149 CCAAGTTCTGCT 1 CCAAGTTCTGCT 92578161 CCA 1 CCA 92578164 TAAAATCACC 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:0.19, C:0.37, G:0.15, T:0.30 Consensus pattern (12 bp): CCAAGTTCTGCT Found at i:92580082 original size:43 final size:43 Alignment explanation

Indices: 92580021--92580118 Score: 160 Period size: 43 Copynumber: 2.3 Consensus size: 43 92580011 CTATAGATGG * * 92580021 CGCCGCTAAAGGTCATGGCCATTAGCGGCGCTTTTCCCACAAA 1 CGCCGCTAAAGGCCATGGCCATTAGCGGCACTTTTCCCACAAA * * 92580064 CGCCGCTATAGGCCATGGCCTTTAGCGGCACTTTTCCCACAAA 1 CGCCGCTAAAGGCCATGGCCATTAGCGGCACTTTTCCCACAAA 92580107 CGCCGCTAAAGG 1 CGCCGCTAAAGG 92580119 TCATAAAATT Statistics Matches: 50, Mismatches: 5, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 43 50 1.00 ACGTcount: A:0.22, C:0.34, G:0.23, T:0.20 Consensus pattern (43 bp): CGCCGCTAAAGGCCATGGCCATTAGCGGCACTTTTCCCACAAA Found at i:92580308 original size:19 final size:19 Alignment explanation

Indices: 92580263--92580309 Score: 51 Period size: 19 Copynumber: 2.5 Consensus size: 19 92580253 ATCAAATTAA * 92580263 AATAAAAATAAAAATATAG 1 AATAAAAATAAAAATAAAG * * 92580282 AATCAAAACT-AAAATAAAT 1 AAT-AAAAATAAAAATAAAG 92580301 AATAAAAAT 1 AATAAAAAT 92580310 TAGATTAAAT Statistics Matches: 23, Mismatches: 4, Indels: 3 0.77 0.13 0.10 Matches are distributed among these distances: 18 5 0.22 19 13 0.57 20 5 0.22 ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21 Consensus pattern (19 bp): AATAAAAATAAAAATAAAG Found at i:92584718 original size:3 final size:3 Alignment explanation

Indices: 92584712--92584773 Score: 124 Period size: 3 Copynumber: 20.7 Consensus size: 3 92584702 TTTTTCTCTT 92584712 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA 92584760 TTA TTA TTA TTA TT 1 TTA TTA TTA TTA TT 92584774 TACTAAAATG Statistics Matches: 59, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 59 1.00 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (3 bp): TTA Found at i:92585480 original size:7 final size:7 Alignment explanation

Indices: 92585468--92585524 Score: 51 Period size: 7 Copynumber: 8.0 Consensus size: 7 92585458 CCCATGGCCA 92585468 TTAAACC 1 TTAAACC 92585475 TTAAACC 1 TTAAACC * 92585482 ATAAAACC 1 -TTAAACC * 92585490 CTAAACC 1 TTAAACC * * 92585497 ATAGACC 1 TTAAACC ** 92585504 TTAAATA 1 TTAAACC 92585511 TTAAACC 1 TTAAACC 92585518 TTAAACC 1 TTAAACC 92585525 CCAAAATAAA Statistics Matches: 38, Mismatches: 11, Indels: 2 0.75 0.22 0.04 Matches are distributed among these distances: 7 32 0.84 8 6 0.16 ACGTcount: A:0.47, C:0.26, G:0.02, T:0.25 Consensus pattern (7 bp): TTAAACC Found at i:92585488 original size:15 final size:15 Alignment explanation

Indices: 92585465--92585524 Score: 70 Period size: 14 Copynumber: 4.1 Consensus size: 15 92585455 ACACCCATGG 92585465 CCATTAAACCTTAAA 1 CCATTAAACCTTAAA * * 92585480 CCATAAAACCCTAAA 1 CCATTAAACCTTAAA * 92585495 CCA-TAGACCTTAAA 1 CCATTAAACCTTAAA * 92585509 -TATTAAACCTTAAA 1 CCATTAAACCTTAAA 92585523 CC 1 CC 92585525 CCAAAATAAA Statistics Matches: 35, Mismatches: 8, Indels: 4 0.74 0.17 0.09 Matches are distributed among these distances: 13 1 0.03 14 18 0.51 15 16 0.46 ACGTcount: A:0.47, C:0.28, G:0.02, T:0.23 Consensus pattern (15 bp): CCATTAAACCTTAAA Found at i:92585654 original size:16 final size:15 Alignment explanation

Indices: 92585630--92585697 Score: 68 Period size: 15 Copynumber: 4.5 Consensus size: 15 92585620 CATATGATTT 92585630 TTTTAGGGTTTAAGG 1 TTTTAGGGTTTAAGG * 92585645 TTTTAGGGGTTATA-G 1 TTTTAGGGTTTA-AGG * * 92585660 -TTTAGTGTTTATGG 1 TTTTAGGGTTTAAGG * 92585674 TTTTTAGGGTTTAGGG 1 -TTTTAGGGTTTAAGG 92585690 TTTTAGGG 1 TTTTAGGG 92585698 GTTATATGAC Statistics Matches: 43, Mismatches: 6, Indels: 8 0.75 0.11 0.14 Matches are distributed among these distances: 14 10 0.23 15 20 0.47 16 13 0.30 ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50 Consensus pattern (15 bp): TTTTAGGGTTTAAGG Found at i:92585759 original size:41 final size:40 Alignment explanation

Indices: 92585709--92585804 Score: 120 Period size: 41 Copynumber: 2.4 Consensus size: 40 92585699 TTATATGACC * * 92585709 TTTAGCGGCGTTTTGACCATAAACGCCACTATTGCTCTGTT 1 TTTAGCGGCGTTTTG-CCAAAAACGCCACTATTGCTCTATT * ** * 92585750 TTTAACGGCGTTTTTGGTAAAAACGCCGCTATTGCTCTATT 1 TTTAGCGGCG-TTTTGCCAAAAACGCCACTATTGCTCTATT 92585791 TTTAGCGGCGTTTT 1 TTTAGCGGCGTTTT 92585805 TGCTAAAACG Statistics Matches: 47, Mismatches: 7, Indels: 3 0.82 0.12 0.05 Matches are distributed among these distances: 40 4 0.09 41 38 0.81 42 5 0.11 ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40 Consensus pattern (40 bp): TTTAGCGGCGTTTTGCCAAAAACGCCACTATTGCTCTATT Found at i:92585805 original size:41 final size:41 Alignment explanation

Indices: 92585729--92585812 Score: 132 Period size: 41 Copynumber: 2.0 Consensus size: 41 92585719 TTTTGACCAT * * 92585729 AAACGCCACTATTGCTCTGTTTTTAACGGCGTTTTTGGTAA 1 AAACGCCACTATTGCTCTATTTTTAACGGCGTTTTTGCTAA * * 92585770 AAACGCCGCTATTGCTCTATTTTTAGCGGCGTTTTTGCTAA 1 AAACGCCACTATTGCTCTATTTTTAACGGCGTTTTTGCTAA 92585811 AA 1 AA 92585813 CGCAATGTAC Statistics Matches: 39, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 41 39 1.00 ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38 Consensus pattern (41 bp): AAACGCCACTATTGCTCTATTTTTAACGGCGTTTTTGCTAA Found at i:92589389 original size:100 final size:100 Alignment explanation

Indices: 92589216--92589413 Score: 351 Period size: 100 Copynumber: 2.0 Consensus size: 100 92589206 AGACGGCAAT * * * 92589216 GAGAATGTGCGATTTTCGAGGGTTTATTCAAACTTTTTCAAGCTTTCATGCTCTTTTACATCATG 1 GAGAATGTGCGATTTTCAAGGGTTTATTCAAACTTTTTCAAGCTTCCATGCTCATTTACATCATG 92589281 TCAATAGGCGTTCAAACCACGCGCCTTCCGGTTAC 66 TCAATAGGCGTTCAAACCACGCGCCTTCCGGTTAC ** 92589316 GAGAATGTGCGATTTTCAAGGGTTTATTCAAACTTTTTCAAGCTTCCATGCTCATTTACATTGTG 1 GAGAATGTGCGATTTTCAAGGGTTTATTCAAACTTTTTCAAGCTTCCATGCTCATTTACATCATG 92589381 TCAATAGGCGTTCAAACCACGCGCCTTCCGGTT 66 TCAATAGGCGTTCAAACCACGCGCCTTCCGGTT 92589414 TTAGCCCACT Statistics Matches: 93, Mismatches: 5, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 100 93 1.00 ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35 Consensus pattern (100 bp): GAGAATGTGCGATTTTCAAGGGTTTATTCAAACTTTTTCAAGCTTCCATGCTCATTTACATCATG TCAATAGGCGTTCAAACCACGCGCCTTCCGGTTAC Found at i:92589553 original size:29 final size:30 Alignment explanation

Indices: 92589518--92589574 Score: 89 Period size: 29 Copynumber: 1.9 Consensus size: 30 92589508 TGGTTTAATA * 92589518 TGTAATTGTATATATG-AATTTTGATTTTG 1 TGTAATTGTATACATGAAATTTTGATTTTG * 92589547 TGTAATTTTATACATGAAATTTTGATTT 1 TGTAATTGTATACATGAAATTTTGATTT 92589575 GATCCAATTC Statistics Matches: 25, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 29 14 0.56 30 11 0.44 ACGTcount: A:0.30, C:0.02, G:0.14, T:0.54 Consensus pattern (30 bp): TGTAATTGTATACATGAAATTTTGATTTTG Found at i:92589575 original size:29 final size:29 Alignment explanation

Indices: 92589491--92589574 Score: 89 Period size: 31 Copynumber: 2.8 Consensus size: 29 92589481 ATAAATTTTA * * * 92589491 AATT-TATACATGAATTATGGTTTAATATGT 1 AATTGTATACATGAATTTTGATTT--TGTGT * 92589521 AATTGTATATATGAATTTTGATTTTGTGT 1 AATTGTATACATGAATTTTGATTTTGTGT * 92589550 AATTTTATACATGAAATTTTGATTT 1 AATTGTATACATG-AATTTTGATTT 92589575 GATCCAATTC Statistics Matches: 46, Mismatches: 6, Indels: 4 0.82 0.11 0.07 Matches are distributed among these distances: 29 15 0.33 30 15 0.33 31 16 0.35 ACGTcount: A:0.33, C:0.02, G:0.13, T:0.51 Consensus pattern (29 bp): AATTGTATACATGAATTTTGATTTTGTGT Found at i:92589754 original size:31 final size:30 Alignment explanation

Indices: 92589686--92589742 Score: 98 Period size: 29 Copynumber: 1.9 Consensus size: 30 92589676 GACTAAATCA * 92589686 AAATTAAAATTTCATGTGTATAATTGCATC 1 AAATTAAAATTTCATGTATATAATTGCATC 92589716 AAATTAAAA-TTCATGTATATAATTGCA 1 AAATTAAAATTTCATGTATATAATTGCA 92589743 CATTAAATTA Statistics Matches: 26, Mismatches: 1, Indels: 1 0.93 0.04 0.04 Matches are distributed among these distances: 29 17 0.65 30 9 0.35 ACGTcount: A:0.44, C:0.09, G:0.09, T:0.39 Consensus pattern (30 bp): AAATTAAAATTTCATGTATATAATTGCATC Found at i:92589985 original size:20 final size:22 Alignment explanation

Indices: 92589941--92590001 Score: 72 Period size: 20 Copynumber: 2.8 Consensus size: 22 92589931 AAAGTTTTTA * * 92589941 AAATACAATTTTATTAAATAAT 1 AAATATAATTTTATTAAACAAT * 92589963 AAATA-AATTTT-TTAAACAGT 1 AAATATAATTTTATTAAACAAT 92589983 AAATATTAATTTTATTAAA 1 AAATA-TAATTTTATTAAA 92590002 AATTATATTA Statistics Matches: 34, Mismatches: 2, Indels: 5 0.83 0.05 0.12 Matches are distributed among these distances: 20 12 0.35 21 6 0.18 22 11 0.32 23 5 0.15 ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43 Consensus pattern (22 bp): AAATATAATTTTATTAAACAAT Found at i:92590023 original size:23 final size:22 Alignment explanation

Indices: 92589947--92590023 Score: 70 Period size: 23 Copynumber: 3.5 Consensus size: 22 92589937 TTTAAAATAC 92589947 AATTTTATTAAATAA-TAAATA-- 1 AATTTT-TTAAA-AAGTAAATATT * 92589968 AATTTTTTAAACAGTAAATATT 1 AATTTTTTAAAAAGTAAATATT * * 92589990 AATTTTATTAAAAATTATATTATT 1 AATTTT-TTAAAAAGTA-AATATT 92590014 AATTTTTTAA 1 AATTTTTTAA 92590024 TGCAATAAAA Statistics Matches: 47, Mismatches: 4, Indels: 8 0.80 0.07 0.14 Matches are distributed among these distances: 19 1 0.02 20 11 0.23 21 6 0.13 22 6 0.13 23 12 0.26 24 11 0.23 ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49 Consensus pattern (22 bp): AATTTTTTAAAAAGTAAATATT Found at i:92604352 original size:22 final size:22 Alignment explanation

Indices: 92604327--92604370 Score: 70 Period size: 22 Copynumber: 2.0 Consensus size: 22 92604317 TAGTCATATA 92604327 ATAAATTATTAATATAATAAAT 1 ATAAATTATTAATATAATAAAT * * 92604349 ATAAATTATTATTTTAATAAAT 1 ATAAATTATTAATATAATAAAT 92604371 TATTTAATAT Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 22 20 1.00 ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45 Consensus pattern (22 bp): ATAAATTATTAATATAATAAAT Found at i:92604416 original size:16 final size:16 Alignment explanation

Indices: 92604394--92604430 Score: 58 Period size: 16 Copynumber: 2.3 Consensus size: 16 92604384 AATTTTATTT 92604394 TAATAATAAACTTTAAA 1 TAATAATAAA-TTTAAA 92604411 -AATAATAAATTTAAA 1 TAATAATAAATTTAAA 92604426 TAATA 1 TAATA 92604431 TTATTCACAT Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 15 6 0.32 16 13 0.68 ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35 Consensus pattern (16 bp): TAATAATAAATTTAAA Found at i:92604739 original size:29 final size:29 Alignment explanation

Indices: 92604698--92604760 Score: 126 Period size: 29 Copynumber: 2.2 Consensus size: 29 92604688 TTTTTAAATA 92604698 AAAAATACTCATTTAGTAGTCATGTAATT 1 AAAAATACTCATTTAGTAGTCATGTAATT 92604727 AAAAATACTCATTTAGTAGTCATGTAATT 1 AAAAATACTCATTTAGTAGTCATGTAATT 92604756 AAAAA 1 AAAAA 92604761 ATGACGTTGT Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 29 34 1.00 ACGTcount: A:0.46, C:0.10, G:0.10, T:0.35 Consensus pattern (29 bp): AAAAATACTCATTTAGTAGTCATGTAATT Found at i:92605187 original size:18 final size:18 Alignment explanation

Indices: 92605164--92605205 Score: 59 Period size: 18 Copynumber: 2.3 Consensus size: 18 92605154 TTCAAGGTGT 92605164 AATTAATTTAAAATT-TTC 1 AATTAA-TTAAAATTATTC * 92605182 AATTAATTAAATTTATTC 1 AATTAATTAAAATTATTC 92605200 AATTAA 1 AATTAA 92605206 AAATCTACTC Statistics Matches: 22, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 17 7 0.32 18 15 0.68 ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48 Consensus pattern (18 bp): AATTAATTAAAATTATTC Found at i:92605860 original size:40 final size:41 Alignment explanation

Indices: 92605772--92605863 Score: 98 Period size: 40 Copynumber: 2.3 Consensus size: 41 92605762 AATTTTAAAA * * ** 92605772 ATTATATTTAATACAATAAAATATTCATTATATTTATTTGT 1 ATTATTTTTAATACAATAAAACATTCATTATATTTATAGGT * * * * 92605813 GTT-TTTTTAATATAATAATACATTTATTATATTTA-AGGT 1 ATTATTTTTAATACAATAAAACATTCATTATATTTATAGGT 92605852 ATTATTTTTAAT 1 ATTATTTTTAAT 92605864 GTCTTAGAAA Statistics Matches: 41, Mismatches: 9, Indels: 3 0.77 0.17 0.06 Matches are distributed among these distances: 39 4 0.10 40 35 0.85 41 2 0.05 ACGTcount: A:0.38, C:0.03, G:0.04, T:0.54 Consensus pattern (41 bp): ATTATTTTTAATACAATAAAACATTCATTATATTTATAGGT Found at i:92614088 original size:16 final size:16 Alignment explanation

Indices: 92614067--92614103 Score: 56 Period size: 16 Copynumber: 2.3 Consensus size: 16 92614057 CCGAGAAATT * 92614067 AAACACATATAATTGA 1 AAACACACATAATTGA 92614083 AAACACACATAATTGA 1 AAACACACATAATTGA * 92614099 GAACA 1 AAACA 92614104 AGATCTAAGT Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 16 19 1.00 ACGTcount: A:0.57, C:0.16, G:0.08, T:0.19 Consensus pattern (16 bp): AAACACACATAATTGA Found at i:92617215 original size:19 final size:19 Alignment explanation

Indices: 92617134--92617215 Score: 83 Period size: 19 Copynumber: 4.3 Consensus size: 19 92617124 CACCAGGATA * * 92617134 CACTTCGTGTGCCAAGATG 1 CACTTTGTGTGCCAATATG ** * 92617153 CACTACGTGTGCCAGTATG 1 CACTTTGTGTGCCAATATG * * 92617172 CACTTTGTGCGTCAATATG 1 CACTTTGTGTGCCAATATG * * 92617191 CGCTTTGTGTACCAATATG 1 CACTTTGTGTGCCAATATG 92617210 CACTTT 1 CACTTT 92617216 ACATGCCAGT Statistics Matches: 50, Mismatches: 13, Indels: 0 0.79 0.21 0.00 Matches are distributed among these distances: 19 50 1.00 ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33 Consensus pattern (19 bp): CACTTTGTGTGCCAATATG Found at i:92623190 original size:9 final size:9 Alignment explanation

Indices: 92623160--92623240 Score: 51 Period size: 10 Copynumber: 8.8 Consensus size: 9 92623150 TCTTTCATTA 92623160 AATTTTAA- 1 AATTTTAAT 92623168 AATTTATAAT 1 AATTT-TAAT 92623178 -ATTTTAAT 1 AATTTTAAT * 92623186 AATTTCTTAT 1 AATTT-TAAT * 92623196 CATTTTTAAT 1 -AATTTTAAT * * 92623206 AACTTCAAT 1 AATTTTAAT 92623215 AAATTTTAAT 1 -AATTTTAAT * 92623225 -ATTTTATAA 1 AATTTTA-AT 92623234 AATTTTA 1 AATTTTA 92623241 TTTGAAAATA Statistics Matches: 56, Mismatches: 9, Indels: 14 0.71 0.11 0.18 Matches are distributed among these distances: 8 15 0.27 9 18 0.32 10 19 0.34 11 4 0.07 ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53 Consensus pattern (9 bp): AATTTTAAT Found at i:92623228 original size:28 final size:27 Alignment explanation

Indices: 92623153--92623229 Score: 66 Period size: 28 Copynumber: 2.8 Consensus size: 27 92623143 ATTTTACTCT * * * * 92623153 TTCATTAAATTTTAAAATTTATAATAT 1 TTCAATAAATTTTAATATTTTTAATAC * * 92623180 TTTAAT-AATTTCTTATCATTTTTAATAAC 1 TTCAATAAATTT-TAAT-ATTTTTAAT-AC 92623209 TTCAATAAATTTTAATATTTT 1 TTCAATAAATTTTAATATTTT 92623230 ATAAAATTTT Statistics Matches: 38, Mismatches: 8, Indels: 7 0.72 0.15 0.13 Matches are distributed among these distances: 26 5 0.13 27 6 0.16 28 13 0.34 29 9 0.24 30 5 0.13 ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55 Consensus pattern (27 bp): TTCAATAAATTTTAATATTTTTAATAC Found at i:92623731 original size:19 final size:19 Alignment explanation

Indices: 92623707--92623746 Score: 53 Period size: 19 Copynumber: 2.1 Consensus size: 19 92623697 TTCTTTTTTT * * 92623707 TTTCACTATTTTGCTACTA 1 TTTCACAATTATGCTACTA * 92623726 TTTCACAATTATGTTACTA 1 TTTCACAATTATGCTACTA 92623745 TT 1 TT 92623747 ATTTTGTTCT Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 19 18 1.00 ACGTcount: A:0.25, C:0.17, G:0.05, T:0.53 Consensus pattern (19 bp): TTTCACAATTATGCTACTA Found at i:92629825 original size:9 final size:9 Alignment explanation

Indices: 92629811--92629837 Score: 54 Period size: 9 Copynumber: 3.0 Consensus size: 9 92629801 TCTTTCTAAA 92629811 CTCTCAAAT 1 CTCTCAAAT 92629820 CTCTCAAAT 1 CTCTCAAAT 92629829 CTCTCAAAT 1 CTCTCAAAT 92629838 TTTTTAAGTT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 18 1.00 ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33 Consensus pattern (9 bp): CTCTCAAAT Found at i:92631795 original size:38 final size:39 Alignment explanation

Indices: 92631746--92631823 Score: 113 Period size: 38 Copynumber: 2.0 Consensus size: 39 92631736 TTAATGCAAT * * 92631746 AAATATTTATTATATTTGT-TTGTGCTTTTAATATAATA 1 AAATATTTATTATATTTATATAGTGCTTTTAATATAATA * 92631784 AAATATTTATTATATTTATAGTAGTGTTTTTAATATAATA 1 AAATATTTATTATATTTATA-TAGTGCTTTTAATATAATA 92631824 TTTTTTAATA Statistics Matches: 35, Mismatches: 3, Indels: 2 0.88 0.08 0.05 Matches are distributed among these distances: 38 18 0.51 40 17 0.49 ACGTcount: A:0.37, C:0.01, G:0.08, T:0.54 Consensus pattern (39 bp): AAATATTTATTATATTTATATAGTGCTTTTAATATAATA Found at i:92633057 original size:31 final size:30 Alignment explanation

Indices: 92632984--92633057 Score: 85 Period size: 31 Copynumber: 2.4 Consensus size: 30 92632974 TATAAAACGA 92632984 TCACTAACTATTCAAAAGTTTTCATTTAAG 1 TCACTAACTATTCAAAAGTTTTCATTTAAG * * ** * 92633014 TTACAGAACTATTTGAAAGTTTTTATTTAAG 1 TCAC-TAACTATTCAAAAGTTTTCATTTAAG 92633045 TCACTAAGCTATT 1 TCACTAA-CTATT 92633058 AAGGTATTTT Statistics Matches: 35, Mismatches: 7, Indels: 3 0.78 0.16 0.07 Matches are distributed among these distances: 30 5 0.14 31 30 0.86 ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42 Consensus pattern (30 bp): TCACTAACTATTCAAAAGTTTTCATTTAAG Found at i:92634275 original size:21 final size:20 Alignment explanation

Indices: 92634237--92634275 Score: 51 Period size: 20 Copynumber: 1.9 Consensus size: 20 92634227 AGCGATATTA * 92634237 AGTTGTATATTTACTAAAAT 1 AGTTGCATATTTACTAAAAT * 92634257 AGTTGCATACTTTCCTAAA 1 AGTTGCATA-TTTACTAAA 92634276 TTCCCATTTC Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 20 8 0.50 21 8 0.50 ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41 Consensus pattern (20 bp): AGTTGCATATTTACTAAAAT Found at i:92640776 original size:17 final size:18 Alignment explanation

Indices: 92640750--92640783 Score: 52 Period size: 17 Copynumber: 1.9 Consensus size: 18 92640740 TCGCTGATGG * 92640750 CCCTTTATTTT-TTTGTT 1 CCCTTGATTTTCTTTGTT 92640767 CCCTTGATTTTCTTTGT 1 CCCTTGATTTTCTTTGT 92640784 AGGTTTCTGG Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 17 10 0.67 18 5 0.33 ACGTcount: A:0.06, C:0.21, G:0.09, T:0.65 Consensus pattern (18 bp): CCCTTGATTTTCTTTGTT Found at i:92643895 original size:16 final size:17 Alignment explanation

Indices: 92643869--92643908 Score: 55 Period size: 16 Copynumber: 2.4 Consensus size: 17 92643859 AAGGAATTTA * 92643869 ACAACAAAGAATAAAAAG 1 ACAA-AAAGAAAAAAAAG 92643887 A-AAAAAGAAAAAAAAG 1 ACAAAAAGAAAAAAAAG 92643903 ACAAAA 1 ACAAAA 92643909 TGGAAGATAG Statistics Matches: 20, Mismatches: 1, Indels: 3 0.83 0.04 0.12 Matches are distributed among these distances: 16 13 0.65 17 6 0.30 18 1 0.05 ACGTcount: A:0.80, C:0.07, G:0.10, T:0.03 Consensus pattern (17 bp): ACAAAAAGAAAAAAAAG Found at i:92644034 original size:9 final size:9 Alignment explanation

Indices: 92644022--92644064 Score: 61 Period size: 9 Copynumber: 4.7 Consensus size: 9 92644012 ACAATATCTA 92644022 AAATAACTT 1 AAATAACTT 92644031 AAATAACTCTT 1 AAATAA--CTT 92644042 AAATAACTT 1 AAATAACTT 92644051 AAAT-ACTT 1 AAATAACTT 92644059 AAATAA 1 AAATAA 92644065 TATCCAAAAT Statistics Matches: 31, Mismatches: 0, Indels: 6 0.84 0.00 0.16 Matches are distributed among these distances: 8 8 0.26 9 14 0.45 11 9 0.29 ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33 Consensus pattern (9 bp): AAATAACTT Found at i:92644937 original size:23 final size:23 Alignment explanation

Indices: 92644904--92644957 Score: 99 Period size: 23 Copynumber: 2.3 Consensus size: 23 92644894 AATTCATAAC * 92644904 CAAATATACACATATTTATAGTT 1 CAAATACACACATATTTATAGTT 92644927 CAAATACACACATATTTATAGTT 1 CAAATACACACATATTTATAGTT 92644950 CAAATACA 1 CAAATACA 92644958 TAACAATTTA Statistics Matches: 30, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 23 30 1.00 ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33 Consensus pattern (23 bp): CAAATACACACATATTTATAGTT Found at i:92644966 original size:23 final size:23 Alignment explanation

Indices: 92644904--92644967 Score: 85 Period size: 23 Copynumber: 2.8 Consensus size: 23 92644894 AATTCATAAC * * 92644904 CAAATATACACATATTTATAGTT 1 CAAATACAAACATATTTATAGTT * 92644927 CAAATACACACATATTTATAGTT 1 CAAATACAAACATATTTATAGTT 92644950 CAAATACATAACA-ATTTA 1 CAAATACA-AACATATTTA 92644968 AACACGACCA Statistics Matches: 38, Mismatches: 2, Indels: 2 0.90 0.05 0.05 Matches are distributed among these distances: 23 35 0.92 24 3 0.08 ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34 Consensus pattern (23 bp): CAAATACAAACATATTTATAGTT Found at i:92645744 original size:15 final size:15 Alignment explanation

Indices: 92645714--92645764 Score: 50 Period size: 15 Copynumber: 3.3 Consensus size: 15 92645704 GAAGATTAAT ** 92645714 TTAATTAAACCCTAA 1 TTAATTAAACTATAA 92645729 TTAATTAAACTATAA 1 TTAATTAAACTATAA * 92645744 TCCTAATT-AACTAAAA 1 T--TAATTAAACTATAA 92645760 TTAAT 1 TTAAT 92645765 GGGTTATAAC Statistics Matches: 31, Mismatches: 3, Indels: 5 0.79 0.08 0.13 Matches are distributed among these distances: 14 4 0.13 15 14 0.45 16 8 0.26 17 5 0.16 ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37 Consensus pattern (15 bp): TTAATTAAACTATAA Found at i:92649971 original size:13 final size:13 Alignment explanation

Indices: 92649921--92649988 Score: 55 Period size: 13 Copynumber: 5.2 Consensus size: 13 92649911 GTACATATAT * 92649921 TTTCATATGACCA 1 TTTCATATAACCA * * * * 92649934 ATTCCTGTAAACA 1 TTTCATATAACCA * * 92649947 TTTCACACAACCA 1 TTTCATATAACCA * 92649960 TTTTATATAACCA 1 TTTCATATAACCA * 92649973 ATTCATATAACCA 1 TTTCATATAACCA 92649986 TTT 1 TTT 92649989 GTCATCTGGT Statistics Matches: 38, Mismatches: 17, Indels: 0 0.69 0.31 0.00 Matches are distributed among these distances: 13 38 1.00 ACGTcount: A:0.37, C:0.24, G:0.03, T:0.37 Consensus pattern (13 bp): TTTCATATAACCA Found at i:92650314 original size:183 final size:183 Alignment explanation

Indices: 92650071--92650418 Score: 493 Period size: 183 Copynumber: 1.9 Consensus size: 183 92650061 TTATCTTCGA * * * 92650071 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTT 1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCACGTTGCCATGGTATCTT ** * * * * * 92650136 TCAACCATGGTCTTATTCATTTCCCCGTCATGTTGAGATGGTATCTTTCAACCATGGTCTTATTC 66 TCAACCATGGTCTTACACATTT-CACATCATGTTGACATGATATCTTTCAACCATGGTCTTATAC * * * 92650201 A-TTCTTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCTTGT 130 ATTTCATATCATGTTACCATGGTATCTTTCAACCATGGTCTTATTCATTCTTGT * * * 92650254 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGTTGCCATGGTATCT 1 CATGATGCCATAGTATCTTTCAACCATGGTCTTACTCATTTTC-TGTCACGTTGCCATGGTATCT * * 92650318 TTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATCTTTCAACCATGGTCTTATAC 65 TTCAACCATGGTCTTACACATTTCACATCATGTTGACATGATATCTTTCAACCATGGTCTTATAC * 92650383 ATTTCATATCATGTTACTATGGTATCTTTCAACCAT 130 ATTTCATATCATGTTACCATGGTATCTTTCAACCAT 92650419 AGTTTTACAC Statistics Matches: 144, Mismatches: 19, Indels: 4 0.86 0.11 0.02 Matches are distributed among these distances: 182 41 0.28 183 103 0.72 ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42 Consensus pattern (183 bp): CATGATGCCATAGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCACGTTGCCATGGTATCTT TCAACCATGGTCTTACACATTTCACATCATGTTGACATGATATCTTTCAACCATGGTCTTATACA TTTCATATCATGTTACCATGGTATCTTTCAACCATGGTCTTATTCATTCTTGT Found at i:92650387 original size:21 final size:21 Alignment explanation

Indices: 92650317--92650388 Score: 56 Period size: 21 Copynumber: 3.2 Consensus size: 21 92650307 CCATGGTATC * 92650317 TTTCAACCATGGTCTTACACA 1 TTTCAACCATGGTCTTATACA * * * 92650338 TTTCATATCATGTTGCCATGATATC- 1 TTTCA-ACCATG--GTC-TTATA-CA 92650363 TTTCAACCATGGTCTTATACA 1 TTTCAACCATGGTCTTATACA 92650384 TTTCA 1 TTTCA 92650389 TATCATGTTA Statistics Matches: 38, Mismatches: 7, Indels: 12 0.67 0.12 0.21 Matches are distributed among these distances: 20 1 0.03 21 14 0.37 22 7 0.18 24 7 0.18 25 8 0.21 26 1 0.03 ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40 Consensus pattern (21 bp): TTTCAACCATGGTCTTATACA Found at i:92650431 original size:46 final size:46 Alignment explanation

Indices: 92650071--92650435 Score: 450 Period size: 46 Copynumber: 8.0 Consensus size: 46 92650061 TTATCTTCGA * * * * 92650071 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACT-CATTTTC-TGT 1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTA-TACA-TTTCATGT * ** 92650117 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCCGT 1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATACATTT-CATGT ** * * 92650164 CATGTTGAGATGGTATCTTTCAACCATGGTCTTATTCA-TTCTTGT 1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATGT * * 92650209 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCTTGT 1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATGT * * 92650254 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGT 1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATGT * * * 92650300 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT 1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATGT * * 92650346 CATGTTGCCATGATATCTTTCAACCATGGTCTTATACATTTCATAT 1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATGT * * * * * 92650392 CATGTTACTATGGTATCTTTCAACCATAGTTTTACACATTTCAT 1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCAT 92650436 TTCAGAAAGC Statistics Matches: 288, Mismatches: 27, Indels: 8 0.89 0.08 0.02 Matches are distributed among these distances: 45 87 0.30 46 163 0.57 47 38 0.13 ACGTcount: A:0.21, C:0.22, G:0.14, T:0.42 Consensus pattern (46 bp): CATGTTGCCATGGTATCTTTCAACCATGGTCTTATACATTTCATGT Found at i:92652501 original size:11 final size:11 Alignment explanation

Indices: 92652485--92652543 Score: 64 Period size: 11 Copynumber: 5.2 Consensus size: 11 92652475 CTTTATATAC 92652485 TAATAAAATAA 1 TAATAAAATAA 92652496 TAATAAAATAA 1 TAATAAAATAA ** 92652507 TAATAATATATCT 1 TAATAA-A-ATAA * * 92652520 TATTAAAATAT 1 TAATAAAATAA 92652531 TAATAAAATAA 1 TAATAAAATAA 92652542 TA 1 TA 92652544 TTTATCTAAT Statistics Matches: 40, Mismatches: 6, Indels: 4 0.80 0.12 0.08 Matches are distributed among these distances: 11 31 0.77 12 2 0.05 13 7 0.17 ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36 Consensus pattern (11 bp): TAATAAAATAA Found at i:92655326 original size:11 final size:11 Alignment explanation

Indices: 92655310--92655341 Score: 55 Period size: 11 Copynumber: 2.9 Consensus size: 11 92655300 AACATAATAT 92655310 AAAAATTATAA 1 AAAAATTATAA 92655321 AAAAATTATAA 1 AAAAATTATAA * 92655332 AACAATTATA 1 AAAAATTATA 92655342 TAAGGATATG Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 20 1.00 ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28 Consensus pattern (11 bp): AAAAATTATAA Found at i:92657690 original size:11 final size:11 Alignment explanation

Indices: 92657674--92657707 Score: 59 Period size: 11 Copynumber: 3.1 Consensus size: 11 92657664 GATTAGGTCA 92657674 TGAATTGAATT 1 TGAATTGAATT 92657685 TGAATTGAATT 1 TGAATTGAATT * 92657696 TGAAATGAATT 1 TGAATTGAATT 92657707 T 1 T 92657708 ATGCATTTGT Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 11 22 1.00 ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44 Consensus pattern (11 bp): TGAATTGAATT Found at i:92660456 original size:2 final size:2 Alignment explanation

Indices: 92660444--92660473 Score: 51 Period size: 2 Copynumber: 15.0 Consensus size: 2 92660434 AGTATAAAAC * 92660444 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 92660474 GCAAGATAAG Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:92661247 original size:30 final size:29 Alignment explanation

Indices: 92661182--92661256 Score: 69 Period size: 30 Copynumber: 2.5 Consensus size: 29 92661172 TAGTTCATAT * 92661182 TTTTATAATTTTTAAAAAATTAAATTAAA 1 TTTTATAATTTTTAAAAAATTAAAGTAAA * ** * 92661211 TATTTATCATTTTTAACGAGTTAAAGTATAA 1 T-TTTATAATTTTTAAAAAATTAAAGTA-AA * * 92661242 TTTTATTATTATTAA 1 TTTTATAATTTTTAA 92661257 TCTAAAATTT Statistics Matches: 37, Mismatches: 7, Indels: 3 0.79 0.15 0.06 Matches are distributed among these distances: 29 1 0.03 30 33 0.89 31 3 0.08 ACGTcount: A:0.43, C:0.03, G:0.04, T:0.51 Consensus pattern (29 bp): TTTTATAATTTTTAAAAAATTAAAGTAAA Found at i:92662260 original size:66 final size:66 Alignment explanation

Indices: 92662100--92662331 Score: 358 Period size: 66 Copynumber: 3.5 Consensus size: 66 92662090 TAAAACAAGA * * 92662100 CAAAACTACGTCGTTTTGATGAA-TGTTTACTTTTTTAAAAGTTAAAATTCGAGATAATTAAGTT 1 CAAAACTACGTCGTTTTGAT-AAGTGTTTACTTTTTAAAAAGTTAAAATTC-A-A-AA-TAATTT 92662164 AAAAGG 61 AAAAGG 92662170 CAAAACTACGTCGTTTTGATAAGTGTTTACTTTTTAAAAAGTTAAAATTCAAAATAATTTAAAAG 1 CAAAACTACGTCGTTTTGATAAGTGTTTACTTTTTAAAAAGTTAAAATTCAAAATAATTTAAAAG 92662235 G 66 G * * 92662236 CAAAACTACGTCATTTTGATAAGTGTTTACTTTTTAAAAAATTAAAATTCAAAATAATTTAAAAG 1 CAAAACTACGTCGTTTTGATAAGTGTTTACTTTTTAAAAAGTTAAAATTCAAAATAATTTAAAAG 92662301 G 66 G * * 92662302 TAAAACTACGTCGTTTTGATAAATGTTTAC 1 CAAAACTACGTCGTTTTGATAAGTGTTTAC 92662332 CCATTAAGTT Statistics Matches: 154, Mismatches: 7, Indels: 6 0.92 0.04 0.04 Matches are distributed among these distances: 66 102 0.66 67 2 0.01 68 1 0.01 69 3 0.02 70 46 0.30 ACGTcount: A:0.41, C:0.09, G:0.12, T:0.37 Consensus pattern (66 bp): CAAAACTACGTCGTTTTGATAAGTGTTTACTTTTTAAAAAGTTAAAATTCAAAATAATTTAAAAG G Found at i:92663561 original size:31 final size:31 Alignment explanation

Indices: 92663493--92663561 Score: 93 Period size: 31 Copynumber: 2.2 Consensus size: 31 92663483 TGCGAACCTG ** * * 92663493 TTGAAGATGGTAAGCCAAAAGTGCGAGTCTG 1 TTGAAGACAGTAAGCCAAAAGTGCAAGTCTA * 92663524 TCGAAGACAGTAAGCCAAAAGTGCAAGTCTA 1 TTGAAGACAGTAAGCCAAAAGTGCAAGTCTA 92663555 TTGAAGA 1 TTGAAGA 92663562 GTGAGCCTAT Statistics Matches: 32, Mismatches: 6, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 31 32 1.00 ACGTcount: A:0.38, C:0.14, G:0.28, T:0.20 Consensus pattern (31 bp): TTGAAGACAGTAAGCCAAAAGTGCAAGTCTA Found at i:92674019 original size:46 final size:50 Alignment explanation

Indices: 92673947--92674051 Score: 146 Period size: 46 Copynumber: 2.2 Consensus size: 50 92673937 GACAGGACAG * * * 92673947 GACAGAAATGAGCCATGTAAGTCCATA-T-CA-A-ATATATGGCTTTGGA 1 GACAGGAATGAGCCATGTAAGCCCATATTACATATATATATGGCATTGGA * 92673993 GACAGGAATGAGCCATGTAAGCCCATATTAGATATATATATGGCATTGGA 1 GACAGGAATGAGCCATGTAAGCCCATATTACATATATATATGGCATTGGA 92674043 GACAGGAAT 1 GACAGGAAT 92674052 AATTCATGTA Statistics Matches: 51, Mismatches: 4, Indels: 4 0.86 0.07 0.07 Matches are distributed among these distances: 46 25 0.49 47 1 0.02 48 1 0.02 49 1 0.02 50 23 0.45 ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25 Consensus pattern (50 bp): GACAGGAATGAGCCATGTAAGCCCATATTACATATATATATGGCATTGGA Found at i:92680245 original size:13 final size:13 Alignment explanation

Indices: 92680227--92680254 Score: 56 Period size: 13 Copynumber: 2.2 Consensus size: 13 92680217 ATCATAAGTC 92680227 TTTTTTTTTCTTT 1 TTTTTTTTTCTTT 92680240 TTTTTTTTTCTTT 1 TTTTTTTTTCTTT 92680253 TT 1 TT 92680255 CATGCCCCTA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 15 1.00 ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93 Consensus pattern (13 bp): TTTTTTTTTCTTT Found at i:92689989 original size:2 final size:2 Alignment explanation

Indices: 92689982--92690023 Score: 84 Period size: 2 Copynumber: 21.0 Consensus size: 2 92689972 GATTGAATCA 92689982 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 92690024 GTTATTATAC Statistics Matches: 40, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 40 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:92691046 original size:20 final size:20 Alignment explanation

Indices: 92691003--92691044 Score: 61 Period size: 20 Copynumber: 2.1 Consensus size: 20 92690993 TAAAGAAAGT 92691003 AAATGCAATGTAAAGTAATG 1 AAATGCAATGTAAAGTAATG 92691023 AAATGCAAATG-AAAGTAA-G 1 AAATGC-AATGTAAAGTAATG 92691042 AAA 1 AAA 92691045 ATTTGGAAAG Statistics Matches: 21, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 19 4 0.19 20 13 0.62 21 4 0.19 ACGTcount: A:0.57, C:0.05, G:0.19, T:0.19 Consensus pattern (20 bp): AAATGCAATGTAAAGTAATG Done.