Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold107

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: 1028272
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.29

Warning! 136574 characters in sequence are not A, C, G, or T


File 2 of 3

Found at i:1865 original size:49 final size:49

Alignment explanation

Indices: 1793--1892 Score: 191 Period size: 49 Copynumber: 2.0 Consensus size: 49 1783 AAAATACTCA 1793 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGAGATTGTAAGGTTT 1 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGAGATTGTAAGGTTT * 1842 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTAAGGTTT 1 TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGAGATTGTAAGGTTT 1891 TT 1 TT 1893 TATTATTATT Statistics Matches: 50, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 49 50 1.00 ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37 Consensus pattern (49 bp): TTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGAGATTGTAAGGTTT Found at i:4531 original size:174 final size:176 Alignment explanation

Indices: 4197--4546 Score: 508 Period size: 176 Copynumber: 2.0 Consensus size: 176 4187 GTTTTAGCTA * * *** * * 4197 TTTCGATGAATAATAATGTAAGATAGGCCAGAAAACAAGAATAAAAAAAATTAATTTTCATTTAG 1 TTTCGATGAAAAATAATGTAAAATAGAAAAGAAAACAAGAATAAAAAAAATTAAGTTTCATTAAG * * * 4262 CACTTCCGTTTGCCCGTTTCCTGTCCCGGGACAAAAAAACCTTATATCGATGAGATCTCAAAAAC 66 CACTTCCGTTTGCCCGTTTCCTGTCCCGAGACAAAAAAACCATATATCGACGAGATCTCAAAAAC * * * * 4327 GGTAAAGACTTCAACAACCAAACTTTGTAGGATTATAGACCTGTGT 131 AGTAAAGACTTAAACAACCAAACTTTGTAGGATGATAGACCAGTGT * 4373 TTTCGATGAAAAATAATGTAAAATAGAAAAGTAAACAAG-ATAAAAAAAATTTAAGTTTCATTAA 1 TTTCGATGAAAAATAATGTAAAATAGAAAAGAAAACAAGAATAAAAAAAA-TTAAGTTTCATTAA * 4437 GCACTTCCGTTTGTCCGTTTCCTGTCCCGAGAC-AAAAAA-CATATATCGACGAGATCTCAAAAA 65 GCACTTCCGTTTGCCCGTTTCCTGTCCCGAGACAAAAAAACCATATATCGACGAGATCTCAAAAA ** 4500 CAGTAGCGACTTAAACAACCAAACTTTGTAGGATGATAGACCAGTGT 130 CAGTAAAGACTTAAACAACCAAACTTTGTAGGATGATAGACCAGTGT 4547 ATGGACATGT Statistics Matches: 155, Mismatches: 18, Indels: 4 0.88 0.10 0.02 Matches are distributed among these distances: 174 63 0.41 175 16 0.10 176 76 0.49 ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27 Consensus pattern (176 bp): TTTCGATGAAAAATAATGTAAAATAGAAAAGAAAACAAGAATAAAAAAAATTAAGTTTCATTAAG CACTTCCGTTTGCCCGTTTCCTGTCCCGAGACAAAAAAACCATATATCGACGAGATCTCAAAAAC AGTAAAGACTTAAACAACCAAACTTTGTAGGATGATAGACCAGTGT Found at i:6037 original size:36 final size:36 Alignment explanation

Indices: 5990--6066 Score: 145 Period size: 36 Copynumber: 2.1 Consensus size: 36 5980 AGCTCAGTAA * 5990 ATTTGGAGCCATCAAAGTTTGAGTGAATAGTGATTT 1 ATTTGGAGCCATCAAAGTGTGAGTGAATAGTGATTT 6026 ATTTGGAGCCATCAAAGTGTGAGTGAATAGTGATTT 1 ATTTGGAGCCATCAAAGTGTGAGTGAATAGTGATTT 6062 ATTTG 1 ATTTG 6067 AGTATATGTA Statistics Matches: 40, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 36 40 1.00 ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36 Consensus pattern (36 bp): ATTTGGAGCCATCAAAGTGTGAGTGAATAGTGATTT Found at i:6196 original size:54 final size:54 Alignment explanation

Indices: 6116--6229 Score: 192 Period size: 54 Copynumber: 2.1 Consensus size: 54 6106 CCTTAGAATA * * * 6116 AAATTAAACAAACTTGTCAAGCCATGAACAATTATGGAATGCTGTTATTATCAT 1 AAATTGAACAAACTTGTCAAGCCATGAACAATTATGGAATACTGTTATCATCAT * 6170 AAATTGAACAAACTTGTCAAGCCATGAACAATTATTGAATACTGTTATCATCAT 1 AAATTGAACAAACTTGTCAAGCCATGAACAATTATGGAATACTGTTATCATCAT 6224 AAATTG 1 AAATTG 6230 GCATTGATTT Statistics Matches: 56, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 54 56 1.00 ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32 Consensus pattern (54 bp): AAATTGAACAAACTTGTCAAGCCATGAACAATTATGGAATACTGTTATCATCAT Found at i:9818 original size:2 final size:2 Alignment explanation

Indices: 9811--10028 Score: 420 Period size: 2 Copynumber: 109.0 Consensus size: 2 9801 CAGACAACAA 9811 AC AC AC AC -C AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 9852 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 9894 AC AC AC AC AC AC AC AC NAC AC AC AC AC AC AC AC AC AC AC AC AC 1 AC AC AC AC AC AC AC AC -AC AC AC AC AC AC AC AC AC AC AC AC AC 9937 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 9979 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 10021 AC AC AC AC 1 AC AC AC AC 10029 TTTTCCTTTT Statistics Matches: 214, Mismatches: 0, Indels: 4 0.98 0.00 0.02 Matches are distributed among these distances: 1 1 0.00 2 211 0.99 3 2 0.01 ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00 Consensus pattern (2 bp): AC Found at i:13910 original size:2 final size:2 Alignment explanation

Indices: 13903--13945 Score: 77 Period size: 2 Copynumber: 21.5 Consensus size: 2 13893 CGACTGGCGC * 13903 AT AT AT AT AT AT AT AT AT AT AT AT NT 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 13945 A 1 A 13946 CACCACTGTT Statistics Matches: 39, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 39 1.00 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:17025 original size:16 final size:16 Alignment explanation

Indices: 17004--17034 Score: 62 Period size: 16 Copynumber: 1.9 Consensus size: 16 16994 AGAACATTTT 17004 ACCTTCATTTTAAAAA 1 ACCTTCATTTTAAAAA 17020 ACCTTCATTTTAAAA 1 ACCTTCATTTTAAAA 17035 TATAGTTTAA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39 Consensus pattern (16 bp): ACCTTCATTTTAAAAA Found at i:17495 original size:10 final size:10 Alignment explanation

Indices: 17479--17697 Score: 54 Period size: 10 Copynumber: 20.9 Consensus size: 10 17469 CCGTATGAAA 17479 ATCCCCTGTC 1 ATCCCCTGTC * 17489 TTCCCCTGTC 1 ATCCCCTGTC * * 17499 ACCCCCTGTGT 1 ATCCCCTGT-C * * * 17510 TTTCACTGTC 1 ATCCCCTGTC 17520 ATCCCCTGTAC 1 ATCCCCTGT-C 17531 ATCCCCTGT- 1 ATCCCCTGTC * * 17540 GTGCCACTGTAC 1 AT-CCCCTGT-C * 17552 GGAGCCCCTGT- 1 --ATCCCCTGTC * 17563 ATACCCTGTC 1 ATCCCCTGTC 17573 ATCCCCTGTGC 1 ATCCCCTGT-C * 17584 -GCCCCTGTACAC 1 ATCCCCTGT---C 17596 ATCCCCCTGT- 1 AT-CCCCTGTC * * * 17606 GTGCCACTGTA 1 AT-CCCCTGTC * 17617 AGCCCCTGTC 1 ATCCCCTGTC * 17627 ACCCCCTGT- 1 ATCCCCTGTC * 17636 ACGCCCCTGTC 1 A-TCCCCTGTC * 17647 ATCCCCTGTA 1 ATCCCCTGTC * * 17657 AGCCACTGT- 1 ATCCCCTGTC * 17666 ATACCCTTGTGC 1 AT-CCCCTGT-C * 17678 ATGCCCCTGAC 1 AT-CCCCTGTC 17689 ATCCCCTGT 1 ATCCCCTGT 17698 ACGGCTTTTG Statistics Matches: 147, Mismatches: 43, Indels: 38 0.64 0.19 0.17 Matches are distributed among these distances: 9 10 0.07 10 96 0.65 11 20 0.14 12 8 0.05 13 6 0.04 14 7 0.05 ACGTcount: A:0.13, C:0.43, G:0.16, T:0.27 Consensus pattern (10 bp): ATCCCCTGTC Found at i:17603 original size:43 final size:43 Alignment explanation

Indices: 17523--17605 Score: 105 Period size: 42 Copynumber: 1.9 Consensus size: 43 17513 CACTGTCATC * ** * 17523 CCCTGTACATCCCCTGTGTGCCACTGTACGGAGCCCCTGTATA 1 CCCTGTACATCCCCTGTGCGCCACTGTACACACCCCCTGTATA * 17566 CCCTGT-CATCCCCTGTGCGCCCCTGTACACATCCCCCTGT 1 CCCTGTACATCCCCTGTGCGCCACTGTACACA-CCCCCTGT 17606 GTGCCACTGT Statistics Matches: 34, Mismatches: 5, Indels: 2 0.83 0.12 0.05 Matches are distributed among these distances: 42 21 0.62 43 13 0.38 ACGTcount: A:0.13, C:0.43, G:0.18, T:0.25 Consensus pattern (43 bp): CCCTGTACATCCCCTGTGCGCCACTGTACACACCCCCTGTATA Found at i:17635 original size:20 final size:20 Alignment explanation

Indices: 17612--17665 Score: 81 Period size: 20 Copynumber: 2.7 Consensus size: 20 17602 CTGTGTGCCA 17612 CTGTAAGCCCCTGTCACCCC 1 CTGTAAGCCCCTGTCACCCC * * 17632 CTGTACGCCCCTGTCATCCC 1 CTGTAAGCCCCTGTCACCCC * 17652 CTGTAAGCCACTGT 1 CTGTAAGCCCCTGT 17666 ATACCCTTGT Statistics Matches: 30, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 20 30 1.00 ACGTcount: A:0.15, C:0.44, G:0.17, T:0.24 Consensus pattern (20 bp): CTGTAAGCCCCTGTCACCCC Found at i:18646 original size:2 final size:2 Alignment explanation

Indices: 18641--18694 Score: 108 Period size: 2 Copynumber: 27.0 Consensus size: 2 18631 AAAATGATTA 18641 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 18683 AG AG AG AG AG AG 1 AG AG AG AG AG AG 18695 TTTGCATTGA Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 52 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:18894 original size:2 final size:2 Alignment explanation

Indices: 18887--18937 Score: 102 Period size: 2 Copynumber: 25.5 Consensus size: 2 18877 GAGTTTATAC 18887 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 18929 AG AG AG AG A 1 AG AG AG AG A 18938 TTGCATTGAT Statistics Matches: 49, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 49 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:19943 original size:2 final size:2 Alignment explanation

Indices: 19938--19986 Score: 98 Period size: 2 Copynumber: 24.5 Consensus size: 2 19928 AAAAAATCAA 19938 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 19980 CT CT CT C 1 CT CT CT C 19987 ACATGATTTA Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 47 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:20548 original size:20 final size:20 Alignment explanation

Indices: 20498--20586 Score: 90 Period size: 20 Copynumber: 4.3 Consensus size: 20 20488 AGTAAAAGAC * 20498 CGTACAGGGGATGTCAGGGG 1 CGTACAGGGGATGACAGGGG * * 20518 CATGCACAGGGGTAT-ACAGTGG 1 C--GTACAGGGG-ATGACAGGGG * 20540 CTTACAGGGGATGACAGGGG 1 CGTACAGGGGATGACAGGGG * 20560 CGTACAGGGGGTGACAGGGG 1 CGTACAGGGGATGACAGGGG * 20580 CTTACAG 1 CGTACAG 20587 TGGCACACAG Statistics Matches: 56, Mismatches: 9, Indels: 8 0.77 0.12 0.11 Matches are distributed among these distances: 19 2 0.04 20 38 0.68 22 14 0.25 23 2 0.04 ACGTcount: A:0.24, C:0.17, G:0.44, T:0.16 Consensus pattern (20 bp): CGTACAGGGGATGACAGGGG Found at i:20586 original size:10 final size:10 Alignment explanation

Indices: 20523--20586 Score: 58 Period size: 10 Copynumber: 6.4 Consensus size: 10 20513 AGGGGCATGC 20523 ACAGGGG-TAT 1 ACAGGGGCT-T * 20533 ACAGTGGCTT 1 ACAGGGGCTT * * 20543 ACAGGGGATG 1 ACAGGGGCTT * 20553 ACAGGGGCGT 1 ACAGGGGCTT * * 20563 ACAGGGGGTG 1 ACAGGGGCTT 20573 ACAGGGGCTT 1 ACAGGGGCTT 20583 ACAG 1 ACAG 20587 TGGCACACAG Statistics Matches: 41, Mismatches: 12, Indels: 2 0.75 0.22 0.04 Matches are distributed among these distances: 10 40 0.98 11 1 0.02 ACGTcount: A:0.25, C:0.16, G:0.44, T:0.16 Consensus pattern (10 bp): ACAGGGGCTT Found at i:20611 original size:23 final size:22 Alignment explanation

Indices: 20582--20672 Score: 73 Period size: 23 Copynumber: 4.2 Consensus size: 22 20572 GACAGGGGCT * 20582 TACAGTGGCACACAGGGGTTGTG 1 TACAGTGGCACACAGGGG-TATG ** 20605 TACAGTGGCGGACAGGGG-ATG 1 TACAGTGGCACACAGGGGTATG * * * 20626 -ACAG-GGTATACAGGGGCTCTG 1 TACAGTGGCACACAGGGG-TATG * 20647 TACAGTGGCACACAGGAG-ATG 1 TACAGTGGCACACAGGGGTATG 20668 TACAG 1 TACAG 20673 GGGATGACAG Statistics Matches: 53, Mismatches: 11, Indels: 10 0.72 0.15 0.14 Matches are distributed among these distances: 19 9 0.17 20 4 0.08 21 11 0.21 22 4 0.08 23 25 0.47 ACGTcount: A:0.26, C:0.18, G:0.38, T:0.18 Consensus pattern (22 bp): TACAGTGGCACACAGGGGTATG Found at i:20651 original size:42 final size:43 Alignment explanation

Indices: 20593--20674 Score: 112 Period size: 42 Copynumber: 1.9 Consensus size: 43 20583 ACAGTGGCAC * * ** * 20593 ACAGGGGTTGTGTACAGTGGCGGACAGGGGATG-ACAGGGTAT 1 ACAGGGGCTCTGTACAGTGGCACACAGGAGATGTACAGGGTAT 20635 ACAGGGGCTCTGTACAGTGGCACACAGGAGATGTACAGGG 1 ACAGGGGCTCTGTACAGTGGCACACAGGAGATGTACAGGG 20675 GATGACAGTG Statistics Matches: 34, Mismatches: 5, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 42 28 0.82 43 6 0.18 ACGTcount: A:0.26, C:0.16, G:0.41, T:0.17 Consensus pattern (43 bp): ACAGGGGCTCTGTACAGTGGCACACAGGAGATGTACAGGGTAT Found at i:20682 original size:63 final size:62 Alignment explanation

Indices: 20542--20682 Score: 144 Period size: 63 Copynumber: 2.2 Consensus size: 62 20532 TACAGTGGCT * * * 20542 TACAGGGGATGACAGGGGCGTACAGGGGGTGACAGGGGCTTACAGTGGCACACAGGGGTTGTG 1 TACAGGGGATGACAGGGGCGTACAGGGGATGACAGGGGCTTACAGTGGCACACAGGAG-TATG * ** * * 20605 TACAGTGGCGGACAGGGG-ATGACAGGGTAT-ACAGGGGCTCTGTACAGTGGCACACAGGAG-AT 1 TACAGGGGATGACAGGGGCGT-ACAGGGGATGACAGGGG--CT-TACAGTGGCACACAGGAGTAT 20667 G 62 G 20668 TACAGGGGATGACAG 1 TACAGGGGATGACAG 20683 TGAAAACACA Statistics Matches: 63, Mismatches: 11, Indels: 8 0.77 0.13 0.10 Matches are distributed among these distances: 62 8 0.13 63 36 0.57 64 2 0.03 65 17 0.27 ACGTcount: A:0.26, C:0.16, G:0.43, T:0.16 Consensus pattern (62 bp): TACAGGGGATGACAGGGGCGTACAGGGGATGACAGGGGCTTACAGTGGCACACAGGAGTATG Found at i:22034 original size:2 final size:2 Alignment explanation

Indices: 22021--22089 Score: 129 Period size: 2 Copynumber: 34.5 Consensus size: 2 22011 AATTAAGTAC * 22021 AG AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 22063 AG AG AG AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG AG A 22090 CTTCATACTG Statistics Matches: 65, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 2 65 1.00 ACGTcount: A:0.51, C:0.01, G:0.48, T:0.00 Consensus pattern (2 bp): AG Found at i:25745 original size:11 final size:10 Alignment explanation

Indices: 25710--25745 Score: 54 Period size: 11 Copynumber: 3.4 Consensus size: 10 25700 ATATAAAACG 25710 AAAGCATTAAA 1 AAAGCATT-AA 25721 AAAGCATTAA 1 AAAGCATTAA 25731 AAAGCAATTAA 1 AAAGC-ATTAA 25742 AAAG 1 AAAG 25746 TGAATCTGTC Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 10 7 0.29 11 17 0.71 ACGTcount: A:0.64, C:0.08, G:0.11, T:0.17 Consensus pattern (10 bp): AAAGCATTAA Found at i:26037 original size:316 final size:316 Alignment explanation

Indices: 25663--26294 Score: 1228 Period size: 316 Copynumber: 2.0 Consensus size: 316 25653 CAGTACACAA 25663 ATATCTATTTATAAAACTAAAACTGATTGGGCAGAAAATATAAAACGAAAGCATTAAAAAAGCAT 1 ATATCTATTTATAAAACTAAAACTGATTGGGCAGAAAATATAAAACGAAAGCATTAAAAAAGCAT * * 25728 TAAAAAGCAATTAAAAAGTGAATCTGTCATTTTTGCAAAAAAAGGTGTCTCTCCTTCCTAAAAGA 66 TAAAAAGCAATTAAAAAGTAAATCTGTCATTTATGCAAAAAAAGGTGTCTCTCCTTCCTAAAAGA 25793 TTACGTAACCGCTAAGCACATTGAGAACAAATAGAAAAATATTAGAAATTAATATATAAAAGACG 131 TTACGTAACCGCTAAGCACATTGAGAACAAATAGAAAAATATTAGAAATTAATATATAAAAGACG 25858 GGCCAGCACCCAATCTCTATTAATATCTGAATTACCTTTCTGAAAAGCCTAAAAAGCCCTCCAAG 196 GGCCAGCACCCAATCTCTATTAATATCTGAATTACCTTTCTGAAAAGCCTAAAAAGCCCTCCAAG 25923 TGAATCCCGGTAACAGAACACCAATTTTGTAGTAAGTTACGATAAAATAATTATGT 261 TGAATCCCGGTAACAGAACACCAATTTTGTAGTAAGTTACGATAAAATAATTATGT 25979 ATATCTATTTATAAAACTAAAACTGATTGGGCAGAAAATATAAAACGAAAGCATTAAAAAAGCAT 1 ATATCTATTTATAAAACTAAAACTGATTGGGCAGAAAATATAAAACGAAAGCATTAAAAAAGCAT 26044 TAAAAAGCAATTAAAAAGTAAATCTGTCATTTATGCAAAAAAAGGTGTCTCTCCTTCCTAAAAGA 66 TAAAAAGCAATTAAAAAGTAAATCTGTCATTTATGCAAAAAAAGGTGTCTCTCCTTCCTAAAAGA 26109 TTACGTAACCGCTAAGCACATTGAGAACAAATAGAAAAATATTAGAAATTAATATATAAAAGACG 131 TTACGTAACCGCTAAGCACATTGAGAACAAATAGAAAAATATTAGAAATTAATATATAAAAGACG * 26174 GGCCAGCACCCAATCTTTATTAATATCTGAATTACCTTTCTGAAAAGCCTAAAAAGCCCTCCAAG 196 GGCCAGCACCCAATCTCTATTAATATCTGAATTACCTTTCTGAAAAGCCTAAAAAGCCCTCCAAG * 26239 TGAATCCCGGTAACAGAACCCCAATTTTGTAGTAAGTTACGATAAAATAATTATGT 261 TGAATCCCGGTAACAGAACACCAATTTTGTAGTAAGTTACGATAAAATAATTATGT 26295 GTTTATATCT Statistics Matches: 312, Mismatches: 4, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 316 312 1.00 ACGTcount: A:0.44, C:0.16, G:0.13, T:0.26 Consensus pattern (316 bp): ATATCTATTTATAAAACTAAAACTGATTGGGCAGAAAATATAAAACGAAAGCATTAAAAAAGCAT TAAAAAGCAATTAAAAAGTAAATCTGTCATTTATGCAAAAAAAGGTGTCTCTCCTTCCTAAAAGA TTACGTAACCGCTAAGCACATTGAGAACAAATAGAAAAATATTAGAAATTAATATATAAAAGACG GGCCAGCACCCAATCTCTATTAATATCTGAATTACCTTTCTGAAAAGCCTAAAAAGCCCTCCAAG TGAATCCCGGTAACAGAACACCAATTTTGTAGTAAGTTACGATAAAATAATTATGT Found at i:26061 original size:11 final size:10 Alignment explanation

Indices: 26026--26061 Score: 54 Period size: 11 Copynumber: 3.4 Consensus size: 10 26016 ATATAAAACG 26026 AAAGCATTAAA 1 AAAGCATT-AA 26037 AAAGCATTAA 1 AAAGCATTAA 26047 AAAGCAATTAA 1 AAAGC-ATTAA 26058 AAAG 1 AAAG 26062 TAAATCTGTC Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 10 7 0.29 11 17 0.71 ACGTcount: A:0.64, C:0.08, G:0.11, T:0.17 Consensus pattern (10 bp): AAAGCATTAA Found at i:42045 original size:14 final size:14 Alignment explanation

Indices: 42026--42053 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 42016 GTCGCACAAA 42026 AATCTGTGCTAGTT 1 AATCTGTGCTAGTT 42040 AATCTGTGCTAGTT 1 AATCTGTGCTAGTT 42054 TTAGACTGAC 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:0.21, C:0.14, G:0.21, T:0.43 Consensus pattern (14 bp): AATCTGTGCTAGTT Found at i:42286 original size:21 final size:20 Alignment explanation

Indices: 42262--42324 Score: 54 Period size: 21 Copynumber: 3.0 Consensus size: 20 42252 ACATTTTAAA 42262 CTGATACGTCTTCATTATATG 1 CTGATAC-TCTTCATTATATG * * * 42283 CTGATACTTTATCTTTATATA 1 CTGATACTCT-TCATTATATG ** 42304 AAGATACTTCTTCATTATATG 1 CTGATAC-TCTTCATTATATG 42325 ATGGTAATTC Statistics Matches: 32, Mismatches: 8, Indels: 4 0.73 0.18 0.09 Matches are distributed among these distances: 20 2 0.06 21 28 0.88 22 2 0.06 ACGTcount: A:0.29, C:0.16, G:0.10, T:0.46 Consensus pattern (20 bp): CTGATACTCTTCATTATATG Found at i:43273 original size:2 final size:2 Alignment explanation

Indices: 43260--43304 Score: 81 Period size: 2 Copynumber: 22.5 Consensus size: 2 43250 CCCCCTTCAC * 43260 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 43302 AG A 1 AG A 43305 CCGGTACCTG Statistics Matches: 41, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 41 1.00 ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00 Consensus pattern (2 bp): AG Found at i:47169 original size:1 final size:1 Alignment explanation

Indices: 47163--47212 Score: 55 Period size: 1 Copynumber: 50.0 Consensus size: 1 47153 ATGATTGTCG * * * * * 47163 TTTTTTTTTGTTTTTTGTTTTGTTTTGTTTTTTTTTTTTTGTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 47213 GGGGGGGGGG Statistics Matches: 39, Mismatches: 10, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 1 39 1.00 ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90 Consensus pattern (1 bp): T Found at i:47177 original size:10 final size:10 Alignment explanation

Indices: 47162--47213 Score: 70 Period size: 10 Copynumber: 5.1 Consensus size: 10 47152 GATGATTGTC 47162 GTTTTTTTTT 1 GTTTTTTTTT 47172 GTTTTTTGTTTT 1 G-TTTTT-TTTT * 47184 GTTTTGTTTT 1 GTTTTTTTTT 47194 -TTTTTTTTT 1 GTTTTTTTTT 47203 GTTTTTTTTT 1 GTTTTTTTTT 47213 G 1 G 47214 GGGGGGGGGT Statistics Matches: 37, Mismatches: 2, Indels: 6 0.82 0.04 0.13 Matches are distributed among these distances: 9 8 0.22 10 15 0.41 11 9 0.24 12 5 0.14 ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87 Consensus pattern (10 bp): GTTTTTTTTT Found at i:47193 original size:24 final size:24 Alignment explanation

Indices: 47166--47213 Score: 78 Period size: 24 Copynumber: 2.0 Consensus size: 24 47156 ATTGTCGTTT 47166 TTTTTTGTTTTTTGTTTTGTTTTG 1 TTTTTTGTTTTTTGTTTTGTTTTG * * 47190 TTTTTTTTTTTTTGTTTTTTTTTG 1 TTTTTTGTTTTTTGTTTTGTTTTG 47214 GGGGGGGGGT Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 24 22 1.00 ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88 Consensus pattern (24 bp): TTTTTTGTTTTTTGTTTTGTTTTG Found at i:47195 original size:19 final size:18 Alignment explanation

Indices: 47162--47212 Score: 68 Period size: 19 Copynumber: 2.8 Consensus size: 18 47152 GATGATTGTC * 47162 GTTTT-TTTTTGTTTTTT 1 GTTTTGTTTTTTTTTTTT 47179 GTTTTGTTTTGTTTTTTTT 1 GTTTTGTTTT-TTTTTTTT * 47198 TTTTTGTTTTTTTTT 1 GTTTTGTTTTTTTTT 47213 GGGGGGGGGG Statistics Matches: 30, Mismatches: 2, Indels: 3 0.86 0.06 0.09 Matches are distributed among these distances: 17 5 0.17 18 9 0.30 19 16 0.53 ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88 Consensus pattern (18 bp): GTTTTGTTTTTTTTTTTT Found at i:58421 original size:16 final size:16 Alignment explanation

Indices: 58400--58435 Score: 72 Period size: 16 Copynumber: 2.2 Consensus size: 16 58390 GCATGGTCAC 58400 GTTTTTGGATTTTAAT 1 GTTTTTGGATTTTAAT 58416 GTTTTTGGATTTTAAT 1 GTTTTTGGATTTTAAT 58432 GTTT 1 GTTT 58436 ACAGTGCTTC Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 20 1.00 ACGTcount: A:0.17, C:0.00, G:0.19, T:0.64 Consensus pattern (16 bp): GTTTTTGGATTTTAAT Found at i:61419 original size:16 final size:16 Alignment explanation

Indices: 61398--61433 Score: 72 Period size: 16 Copynumber: 2.2 Consensus size: 16 61388 GAAGCACTGT 61398 AAACATTAAAATCCAA 1 AAACATTAAAATCCAA 61414 AAACATTAAAATCCAA 1 AAACATTAAAATCCAA 61430 AAAC 1 AAAC 61434 GTGACCATGC Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 20 1.00 ACGTcount: A:0.64, C:0.19, G:0.00, T:0.17 Consensus pattern (16 bp): AAACATTAAAATCCAA Found at i:63291 original size:441 final size:442 Alignment explanation

Indices: 62445--63328 Score: 1299 Period size: 441 Copynumber: 2.0 Consensus size: 442 62435 ATGTTACCCA * * *** ** * * 62445 GACCCAGACAAATTTTGTTATCTATTTCTTAATTTGACCTTGAGTGGTCACGGTCACGGTCATAT 1 GACCCAGACAAATTTTATCATCTATTTCTTAATTTGACCTTGAGTAAACAAAGTCAAGGTCAAAT * * 62510 ATAAATCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTAAAATTTTGAAGTCCTTCTGT 66 ATAAATCAATAGTACACATAAGTGTATTATTATTGTTCTTTGTTAAAAGTTTGAAGTCCTTCTGT * * * * * 62575 CAAAGTATATTCAGGAGTTGAACAATGACGTTTTTCTAATTTGACCTTGAAATAAAATTTTTGGG 131 CAAAGTATATTCAGAAGTTGAACAATGAAGTTTTTCTAATTTGACCTTGAAATAAAAATTCTAGG * 62640 TCAAGGTCAAAAATAATAATTTAATAAGGTTCAACTAGGTTATATACCATCTATCCGTGATACAA 196 TCAAGGT--AAAATAATAATTTAATAAGGTTCAACTAGGTTATATACCATCTATCCATGATACAA * * 62705 GTTAAAAGTCTATATGTTAAAGGAGTCTTTTGTTATGGCCCGGACAATATTTTTTTATGAAAAGC 259 GTTAAAAGTCTATATCTTAAAGGAGTCTTGTGTTATGGCCCGGACAATATTTTTTTATGAAAAGC * * * * ** 62770 TTGACCTTGAAGAACAAAATAGGTCATGGTCAAAACTTTTTGTGGTGTGCACTCCTTCTCAATAC 324 TTGACCTTGAAGAACAAAATAGATCAAGATCAAAACTTTTGGTGGCATGCACTCCTTCTCAATAC 62835 CATCTACCTATGTTCCAAGATTGAAGTCTTAATGTCAAAGGGTATTAAAGTTAT 389 CATCTACCTATGTTCCAAGATTGAAGTCTTAATGTCAAAGGGTATTAAAGTTAT * * 62889 GACCCAGACAAAATTTTATCATTTTTTTCTTAATTTGACCTTGAGTAAAACAAAGTCAAGGTCAA 1 GACCCAGAC-AAATTTTATCATCTATTTCTTAATTTGACCTTGAGT-AAACAAAGTCAAGGTCAA * * * 62954 ATATTATTCAATAGTACACATAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCT 64 ATATAAATCAATAGTACACATAAGTGTATTATTATTGTTCTTTGTTAAAAGTTTGAAGTCCTTCT 63019 GTCAAAGTATATTCAGAAGTTGAACAATGAAGTTTTTTCTAATTTGACCTTGAAATAAAAATTCT 129 GTCAAAGTATATTCAGAAGTTGAACAATGAAG-TTTTTCTAATTTGACCTTGAAATAAAAATTCT * ** * * * 63084 AGGTCAAGGT-AAA-AAT-GTTTGGTAAGGTTCAACTAGGTTATCTACCATTTATCTATGATACA 193 AGGTCAAGGTAAAATAATAATTTAATAAGGTTCAACTAGGTTATATACCATCTATCCATGATACA * * * * 63146 AGTTAAAAGTTTTTATCTTAAAGGAGTCTTGTGTTATTGTCCGGACAATA-TTTTTTATGAAAAG 258 AGTTAAAAGTCTATATCTTAAAGGAGTCTTGTGTTATGGCCCGGACAATATTTTTTTATGAAAAG ** 63210 CTTGACCTTGAAGAACAAAATAGATCAAGATCAAAACTTTTGGTGGCATGCACTTTTTCTCAATA 323 CTTGACCTTGAAGAACAAAATAGATCAAGATCAAAACTTTTGGTGGCATGCACTCCTTCTCAATA * * 63275 CCATCTACCTATGTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTTAAGTTA 388 CCATCTACCTATGTTCCAAGATTGAAGTCTTAATGTCAAAGGGTATTAAAGTTA 63329 CGGCATGTCC Statistics Matches: 393, Mismatches: 44, Indels: 9 0.88 0.10 0.02 Matches are distributed among these distances: 441 123 0.31 442 83 0.21 443 3 0.01 444 12 0.03 445 32 0.08 446 101 0.26 447 39 0.10 ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37 Consensus pattern (442 bp): GACCCAGACAAATTTTATCATCTATTTCTTAATTTGACCTTGAGTAAACAAAGTCAAGGTCAAAT ATAAATCAATAGTACACATAAGTGTATTATTATTGTTCTTTGTTAAAAGTTTGAAGTCCTTCTGT CAAAGTATATTCAGAAGTTGAACAATGAAGTTTTTCTAATTTGACCTTGAAATAAAAATTCTAGG TCAAGGTAAAATAATAATTTAATAAGGTTCAACTAGGTTATATACCATCTATCCATGATACAAGT TAAAAGTCTATATCTTAAAGGAGTCTTGTGTTATGGCCCGGACAATATTTTTTTATGAAAAGCTT GACCTTGAAGAACAAAATAGATCAAGATCAAAACTTTTGGTGGCATGCACTCCTTCTCAATACCA TCTACCTATGTTCCAAGATTGAAGTCTTAATGTCAAAGGGTATTAAAGTTAT Found at i:64159 original size:437 final size:429 Alignment explanation

Indices: 63352--64223 Score: 1250 Period size: 437 Copynumber: 2.0 Consensus size: 429 63342 CCTAACTACA * 63352 TAACATAGGAGTAAATGATTGCCATATATAGGTGAATACTGTTAGAATGAACATAATTGCTTCTA 1 TAACATAGGAGTAAATGATTGCCATATATAGGTGAATACTGTTAGAATAAACATAATTGCTTCTA * * * * 63417 TAACGTATCACAAAATATTTCACAGTAAAAAGTTATCATTAAAAGACTTTAGAGCCCCCTTAGTC 66 TAACGTATCACAAAATATTTCACAGTAAAAAGTTATCATTAAAAAACTTGAGAGCCCCCTCAGCC * * * * 63482 CCTTATTTGAAGGGTCAGCCCTTGATGTCATAAGAATGTTCTTGTCAATTCAAACACATTTTGTT 131 CCTTATTTGAAGAGCCAGCCCTTGATGTCATAAGAAAGCTCTTGTCAATTCAAACACATTTTGTT * ** * * * 63547 CAAGAAGTGTTTAGAAATTCTGTACTGTTCTCGAGATATCTTGAGAGAGTCGTATTAGGGGCCGA 196 CAACAAGTAATTACAAATTCTGTACCGTTATCGAGATATCTTGAGAGAGTCGTATTAGGGGCCGA * 63612 CCCTGTAACTACCTTTAAGGACCGCATAACAAAGAAATTATGGTTGATTATTGTTAAGCTTAATA 261 CCCTGTAAC-ACCTTTAAGGACCGCATAACAAAGAAATTATGGTTGATTATTGTTAAGCTCAATA 63677 TTTTGAGCATATTTTGTTCAATATTGTTTATCAAAATGTTCCTCCATTTTGAGATATTGAGCATC 325 TTTTGAGCATATTTTGTTCAATATTGTTTATCAAAATGTTCCTCCATTTTGAGATATTGAGCAT- * * 63742 AA-AGTTTTGGACATCTGGCCCCTTAAAATCCCGAATTACG 389 AAGAGTTTTGGACATCTGGCCCCTAAAAACCCCGAATTACG * * * 63782 TAACATAGGAGTAAATTATTGCCATGTATAGGTGAATACTGTTGGAATAAACATAATTGCTTCTA 1 TAACATAGGAGTAAATGATTGCCATATATAGGTGAATACTGTTAGAATAAACATAATTGCTTCTA * * * 63847 TAACGTATTACAAAATATTTTACAGTAAAAAGTTATCATTAAAAAACTTGAGAGTCCCCTCAGCC 66 TAACGTATCACAAAATATTTCACAGTAAAAAGTTATCATTAAAAAACTTGAGAGCCCCCTCAGCC * 63912 CCTTATTTGAAGAGCCAGCCCCTTTTTCATGATTTCA-AATGAAAGCTCTTGTCAATTCAAACAC 131 CCTTATTTGAAGAGCCAG-CCC----T--TGATGTCATAA-GAAAGCTCTTGTCAATTCAAACAC * * * * * 63976 TTTTTGTTCAACAAGTAATTACAAATTTTGTACCGTTATTGAGATATCTTGAGAGGGTCGTTTTA 188 ATTTTGTTCAACAAGTAATTACAAATTCTGTACCGTTATCGAGATATCTTGAGAGAGTCGTATTA * * 64041 GGGGCCGACCCTGTTAGC-CCTTTTAAGGACTGCATAACAAAGAAATTATGGTTGATTATTGTTA 253 GGGGCCGACCCTG-TAACACC-TTTAAGGACCGCATAACAAAGAAATTATGGTTGATTATTGTTA * * 64105 AGCTCAATATTTTGAGCTTCTTTTGTTCAATATTGCTTT-TCAAAAT-TGTCCTCCATTTTGAGA 316 AGCTCAATATTTTGAGCATATTTTGTTCAATATTG-TTTATCAAAATGT-TCCTCCATTTTGAGA * * * 64168 TATTGAGCATAAGAGTTTTGGACTTCTGTCCCCTAAAAACCCCTAATTACG 379 TATTGAGCATAAGAGTTTTGGACATCTGGCCCCTAAAAACCCCGAATTACG 64219 TAACA 1 TAACA 64224 CATAATTACA Statistics Matches: 392, Mismatches: 37, Indels: 19 0.88 0.08 0.04 Matches are distributed among these distances: 430 135 0.34 431 3 0.01 435 1 0.00 436 7 0.02 437 240 0.61 438 6 0.02 ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35 Consensus pattern (429 bp): TAACATAGGAGTAAATGATTGCCATATATAGGTGAATACTGTTAGAATAAACATAATTGCTTCTA TAACGTATCACAAAATATTTCACAGTAAAAAGTTATCATTAAAAAACTTGAGAGCCCCCTCAGCC CCTTATTTGAAGAGCCAGCCCTTGATGTCATAAGAAAGCTCTTGTCAATTCAAACACATTTTGTT CAACAAGTAATTACAAATTCTGTACCGTTATCGAGATATCTTGAGAGAGTCGTATTAGGGGCCGA CCCTGTAACACCTTTAAGGACCGCATAACAAAGAAATTATGGTTGATTATTGTTAAGCTCAATAT TTTGAGCATATTTTGTTCAATATTGTTTATCAAAATGTTCCTCCATTTTGAGATATTGAGCATAA GAGTTTTGGACATCTGGCCCCTAAAAACCCCGAATTACG Found at i:67286 original size:29 final size:29 Alignment explanation

Indices: 67228--67292 Score: 76 Period size: 29 Copynumber: 2.2 Consensus size: 29 67218 TTAATGGTTT * * 67228 ATAACCCCATTATAAAGAAACAAGGGAAG 1 ATAACTCCATTATAAAGAAACAAGAGAAG * * * 67257 ATAACTCCATTATGAAGAAGCAAGATAAG 1 ATAACTCCATTATAAAGAAACAAGAGAAG * 67286 ATGACTC 1 ATAACTC 67293 ATTTAACTTT Statistics Matches: 30, Mismatches: 6, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 29 30 1.00 ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18 Consensus pattern (29 bp): ATAACTCCATTATAAAGAAACAAGAGAAG Found at i:73580 original size:21 final size:21 Alignment explanation

Indices: 73556--73626 Score: 90 Period size: 21 Copynumber: 3.4 Consensus size: 21 73546 CGATAAACCT 73556 GATAGGATTAACGCACGATAG 1 GATAGGATTAACGCACGATAG * 73577 GATAGCATTAACGCACGATAG 1 GATAGGATTAACGCACGATAG * * * 73598 AACAGTA-TACACGCACGATAG 1 GATAGGATTA-ACGCACGATAG 73619 GATAGGAT 1 GATAGGAT 73627 ATATATATAT Statistics Matches: 41, Mismatches: 7, Indels: 3 0.80 0.14 0.06 Matches are distributed among these distances: 20 2 0.05 21 39 0.95 ACGTcount: A:0.39, C:0.17, G:0.25, T:0.18 Consensus pattern (21 bp): GATAGGATTAACGCACGATAG Found at i:76811 original size:10 final size:10 Alignment explanation

Indices: 76802--76852 Score: 57 Period size: 10 Copynumber: 5.1 Consensus size: 10 76792 ATATACTATT * 76802 ATATTATATT 1 ATATTATATC * 76812 AAATTATATC 1 ATATTATATC * 76822 ATATTACATC 1 ATATTATATC * * 76832 ATATCATGTC 1 ATATTATATC 76842 ATATTATATC 1 ATATTATATC 76852 A 1 A 76853 GTTAAGGTTG Statistics Matches: 32, Mismatches: 9, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 10 32 1.00 ACGTcount: A:0.41, C:0.12, G:0.02, T:0.45 Consensus pattern (10 bp): ATATTATATC Found at i:76817 original size:15 final size:15 Alignment explanation

Indices: 76799--76852 Score: 54 Period size: 15 Copynumber: 3.6 Consensus size: 15 76789 TATATATACT * 76799 ATTATATTATATTAA 1 ATTATATCATATTAA * 76814 ATTATATCATATTAC 1 ATTATATCATATTAA * * * * 76829 ATCATATCATGTCAT 1 ATTATATCATATTAA 76844 ATTATATCA 1 ATTATATCA 76853 GTTAAGGTTG Statistics Matches: 32, Mismatches: 7, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 15 32 1.00 ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46 Consensus pattern (15 bp): ATTATATCATATTAA Found at i:77597 original size:11 final size:11 Alignment explanation

Indices: 77581--77605 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 77571 TCTCAAAAAT 77581 AAATGCATGCA 1 AAATGCATGCA 77592 AAATGCATGCA 1 AAATGCATGCA 77603 AAA 1 AAA 77606 CAAAGTCACA 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:0.52, C:0.16, G:0.16, T:0.16 Consensus pattern (11 bp): AAATGCATGCA Found at i:77761 original size:4 final size:4 Alignment explanation

Indices: 77752--77835 Score: 161 Period size: 4 Copynumber: 21.2 Consensus size: 4 77742 GAGTGCGAAG 77752 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA 1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA 77800 AGAA AGAA AGAA AGAA A-AA AGAA AGAA AGAA AGAA A 1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A 77836 AAATACCTAT Statistics Matches: 79, Mismatches: 0, Indels: 2 0.98 0.00 0.02 Matches are distributed among these distances: 3 3 0.04 4 76 0.96 ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00 Consensus pattern (4 bp): AGAA Found at i:78285 original size:15 final size:15 Alignment explanation

Indices: 78265--78294 Score: 60 Period size: 15 Copynumber: 2.0 Consensus size: 15 78255 GAAAAAATCG 78265 TAATGTAATAATAAA 1 TAATGTAATAATAAA 78280 TAATGTAATAATAAA 1 TAATGTAATAATAAA 78295 CTGTATAGAT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33 Consensus pattern (15 bp): TAATGTAATAATAAA Found at i:78659 original size:20 final size:21 Alignment explanation

Indices: 78612--78660 Score: 57 Period size: 20 Copynumber: 2.4 Consensus size: 21 78602 TTGTTTCATC 78612 TTGTTTGTTGGTTTGTTTGGGT 1 TTGTTT-TTGGTTTGTTTGGGT ** 78634 TT-TTTTTGGTTT-TTTTTGT 1 TTGTTTTTGGTTTGTTTGGGT 78653 TTGTTTTT 1 TTGTTTTT 78661 TTTTGCTTTT Statistics Matches: 24, Mismatches: 2, Indels: 4 0.80 0.07 0.13 Matches are distributed among these distances: 19 7 0.29 20 12 0.50 21 3 0.12 22 2 0.08 ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76 Consensus pattern (21 bp): TTGTTTTTGGTTTGTTTGGGT Found at i:78662 original size:16 final size:15 Alignment explanation

Indices: 78633--78684 Score: 52 Period size: 16 Copynumber: 3.4 Consensus size: 15 78623 TTTGTTTGGG * 78633 TTTTTTTTG-GTTTT 1 TTTTTTTTGTTTTTT * 78647 TTTTGTTTGTTTTTT 1 TTTTTTTTGTTTTTT * 78662 TTTGCTTTTGTTTTTGT 1 TTT-TTTTTGTTTTT-T 78679 TTTTTT 1 TTTTTT 78685 GTATTTTTAA Statistics Matches: 30, Mismatches: 5, Indels: 4 0.77 0.13 0.10 Matches are distributed among these distances: 14 8 0.27 15 7 0.23 16 11 0.37 17 4 0.13 ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85 Consensus pattern (15 bp): TTTTTTTTGTTTTTT Found at i:78662 original size:22 final size:22 Alignment explanation

Indices: 78632--78684 Score: 70 Period size: 23 Copynumber: 2.4 Consensus size: 22 78622 GTTTGTTTGG * * 78632 GTTTTTTTTGGTTTTTTTTGTTT 1 GTTTTTTTTGGCTTTTGTT-TTT * 78655 GTTTTTTTTTGCTTTTGTTTTT 1 GTTTTTTTTGGCTTTTGTTTTT 78677 GTTTTTTT 1 GTTTTTTT 78685 GTATTTTTAA Statistics Matches: 27, Mismatches: 3, Indels: 1 0.87 0.10 0.03 Matches are distributed among these distances: 22 11 0.41 23 16 0.59 ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83 Consensus pattern (22 bp): GTTTTTTTTGGCTTTTGTTTTT Found at i:78670 original size:20 final size:20 Alignment explanation

Indices: 78647--78685 Score: 62 Period size: 20 Copynumber: 1.9 Consensus size: 20 78637 TTTTGGTTTT 78647 TTTTGTTTGTT-TTTTTTTGC 1 TTTTGTTT-TTGTTTTTTTGC 78667 TTTTGTTTTTGTTTTTTTG 1 TTTTGTTTTTGTTTTTTTG 78686 TATTTTTAAC Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 19 2 0.11 20 16 0.89 ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82 Consensus pattern (20 bp): TTTTGTTTTTGTTTTTTTGC Found at i:78684 original size:14 final size:13 Alignment explanation

Indices: 78633--78692 Score: 57 Period size: 14 Copynumber: 4.2 Consensus size: 13 78623 TTTGTTTGGG * 78633 TTTTTTTTGGTTT 1 TTTTTTTTTGTTT * 78646 TTTTTGTTTGTTTT 1 TTTTTTTTTG-TTT 78660 TTTTTGCTTTTGTTT 1 TTTTT--TTTTGTTT 78675 TTGTTTTTTTGTATT 1 TT-TTTTTTTGT-TT 78690 TTT 1 TTT 78693 AACTAAGTTG Statistics Matches: 39, Mismatches: 3, Indels: 9 0.76 0.06 0.18 Matches are distributed among these distances: 13 8 0.21 14 15 0.38 15 9 0.23 16 7 0.18 ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83 Consensus pattern (13 bp): TTTTTTTTTGTTT Found at i:78692 original size:22 final size:21 Alignment explanation

Indices: 78634--78692 Score: 59 Period size: 22 Copynumber: 2.7 Consensus size: 21 78624 TTGTTTGGGT 78634 TTTTTTTGGTTTTTTTTGTTTG 1 TTTTTTT-GTTTTTTTTGTTTG 78656 TTTTTTT-TTGCTTTTGTT-TTTG 1 TTTTTTTGTT--TTTT-TTGTTTG * 78678 TTTTTTTGTATTTTT 1 TTTTTTTGTTTTTTT 78693 AACTAAGTTG Statistics Matches: 32, Mismatches: 1, Indels: 10 0.74 0.02 0.23 Matches are distributed among these distances: 20 3 0.09 21 4 0.12 22 22 0.69 23 3 0.09 ACGTcount: A:0.02, C:0.02, G:0.14, T:0.83 Consensus pattern (21 bp): TTTTTTTGTTTTTTTTGTTTG Found at i:82634 original size:64 final size:63 Alignment explanation

Indices: 82533--82660 Score: 247 Period size: 64 Copynumber: 2.0 Consensus size: 63 82523 ACTTGCAATT 82533 TCACTGTGTAAAGTCAGCACAACAGTCATAGCCGCAGGTTTCGCATTTTACTTCTGATTCTCA 1 TCACTGTGTAAAGTCAGCACAACAGTCATAGCCGCAGGTTTCGCATTTTACTTCTGATTCTCA 82596 NTCACTGTGTAAAGTCAGCACAACAGTCATAGCCGCAGGTTTCGCATTTTACTTCTGATTCTCA 1 -TCACTGTGTAAAGTCAGCACAACAGTCATAGCCGCAGGTTTCGCATTTTACTTCTGATTCTCA 82660 T 1 T 82661 GTACCCAAGA Statistics Matches: 64, Mismatches: 0, Indels: 1 0.98 0.00 0.02 Matches are distributed among these distances: 63 1 0.02 64 63 0.98 ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32 Consensus pattern (63 bp): TCACTGTGTAAAGTCAGCACAACAGTCATAGCCGCAGGTTTCGCATTTTACTTCTGATTCTCA Found at i:94210 original size:11 final size:11 Alignment explanation

Indices: 94194--94230 Score: 56 Period size: 11 Copynumber: 3.4 Consensus size: 11 94184 TTGAAGAAAA 94194 AAAAGTAATTG 1 AAAAGTAATTG * * 94205 AAAAGTATTTT 1 AAAAGTAATTG 94216 AAAAGTAATTG 1 AAAAGTAATTG 94227 AAAA 1 AAAA 94231 TACATGCCAT Statistics Matches: 22, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 11 22 1.00 ACGTcount: A:0.57, C:0.00, G:0.14, T:0.30 Consensus pattern (11 bp): AAAAGTAATTG Found at i:100804 original size:21 final size:21 Alignment explanation

Indices: 100704--101054 Score: 185 Period size: 22 Copynumber: 15.9 Consensus size: 21 100694 TTTTTGAGGT * * 100704 ATTTTCTGATATCAAAATATAA 1 ATTTT-TGATATCAAAAAATTA * * 100726 ATATTTGATATC-AATAATTCGA 1 ATTTTTGATATCAAAAAATT--A * 100748 ATTTTTGATATCAAAAAA-CA 1 ATTTTTGATATCAAAAAATTA * * 100768 ATTCTGGATATC-AAAAATTA 1 ATTTTTGATATCAAAAAATTA * 100788 ATTCTTGATATCAAAAAATCT- 1 ATTTTTGATATCAAAAAAT-TA * * 100809 ATTTTGTGATATCAGAAAATCA 1 ATTTT-TGATATCAAAAAATTA * * 100831 TTTTTTTGATATC-ACAAATTCGA 1 -ATTTTTGATATCAAAAAATT--A * * 100854 ATTCTTGATATCAAAAAA-TG 1 ATTTTTGATATCAAAAAATTA * 100874 ATTTTCTGATATCACAAAA-TA 1 ATTTT-TGATATCAAAAAATTA * 100895 GATTTTCTGATATCAAGAATTAAAGTTG 1 -ATTTT-TGATATC-A-AA--AAA-TTA * * 100923 ATTTTGGACATCAAAAAATTGA 1 ATTTTTGATATCAAAAAATT-A * * * * 100945 AATCTTGATATCACAAAATCA 1 ATTTTTGATATCAAAAAATTA * * 100966 TTTTTTGATATCAAAAAATCA 1 ATTTTTGATATCAAAAAATTA * 100987 TTTTTTGATATCAAAAAATCATTTA 1 ATTTTTGATATC-AAAAA--A-TTA * 101012 CATTTTCTGATATCAGAAAATCTA 1 -ATTTT-TGATATCAAAAAAT-TA * * 101036 TTTTTTGATATCAGAAAAT 1 ATTTTTGATATCAAAAAAT 101055 AAGACTTACA Statistics Matches: 257, Mismatches: 44, Indels: 56 0.72 0.12 0.16 Matches are distributed among these distances: 19 5 0.02 20 31 0.12 21 66 0.26 22 97 0.38 23 19 0.07 24 7 0.03 25 3 0.01 26 16 0.06 27 12 0.05 28 1 0.00 ACGTcount: A:0.42, C:0.11, G:0.09, T:0.39 Consensus pattern (21 bp): ATTTTTGATATCAAAAAATTA Found at i:100906 original size:43 final size:41 Alignment explanation

Indices: 100704--101010 Score: 140 Period size: 42 Copynumber: 7.1 Consensus size: 41 100694 TTTTTGAGGT * * * 100704 ATTTTCTGATATCAAAATATAAATATT-TGATATCAATAATTCG 1 ATTTT-TGATATCAAAA-ATAGATATTCTGATATCAAAAAAT-G * * * 100747 AATTTTTGATATCAAAAA-ACA-ATTCTGGATATCAAAAATTA 1 -ATTTTTGATATCAAAAATAGATATTCT-GATATCAAAAAATG * ** * * * * 100788 ATTCTTGATATCAAAAAATCTATTTTGTGATATCAGAAAATC 1 ATTTTTGATATC-AAAAATAGATATTCTGATATCAAAAAATG * * 100830 ATTTTTTTGATATCACAAATTCGA-ATTCTTGATATCAAAAAATG 1 A--TTTTTGATATCA-AAAATAGATATTC-TGATATCAAAAAATG * 100874 ATTTTCTGATATCACAAAATAGATTTTCTGATATCAAGAATTAAAGTTG 1 ATTTT-TGATATCA-AAAATAGATATTCTGATATC-A-AA--AAA--TG * * * * * * 100923 ATTTTGGACATCAAAAAATTGA-AATCTTGATATCACAAAATC 1 ATTTTTGATATC-AAAAATAGATATTC-TGATATCAAAAAATG * * * * 100965 ATTTTTTGATATCAAAAA-ATCATTTTTTGATATCAAAAAATC 1 A-TTTTTGATATCAAAAATA-GATATTCTGATATCAAAAAATG 101007 ATTT 1 ATTT 101011 ACATTTTCTG Statistics Matches: 205, Mismatches: 36, Indels: 47 0.71 0.12 0.16 Matches are distributed among these distances: 40 14 0.07 41 11 0.05 42 53 0.26 43 49 0.24 44 42 0.20 45 2 0.01 46 1 0.00 47 6 0.03 48 19 0.09 49 8 0.04 ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39 Consensus pattern (41 bp): ATTTTTGATATCAAAAATAGATATTCTGATATCAAAAAATG Found at i:101015 original size:27 final size:28 Alignment explanation

Indices: 100985--101038 Score: 83 Period size: 27 Copynumber: 2.0 Consensus size: 28 100975 ATCAAAAAAT * 100985 CATTTTTTGATATCAAAAAATC-ATTTA 1 CATTTTCTGATATCAAAAAATCTATTTA * 101012 CATTTTCTGATATCAGAAAATCTATTT 1 CATTTTCTGATATCAAAAAATCTATTT 101039 TTTGATATCA Statistics Matches: 24, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 27 20 0.83 28 4 0.17 ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44 Consensus pattern (28 bp): CATTTTCTGATATCAAAAAATCTATTTA Found at i:101044 original size:91 final size:86 Alignment explanation

Indices: 100748--101054 Score: 262 Period size: 91 Copynumber: 3.5 Consensus size: 86 100738 AATAATTCGA * * * * 100748 ATTTTTGATATCAAAAAA-C-AATTCTGGATATCAAAAATTAATTCTTGATATCAAAAAATCTAT 1 ATTTTTGATATCAAAAAATCTAATTCTTGATATCAAAAATCATTTTTTGATATCAAAAAATC-AT * * 100811 TTTGTGATATCAGAAAATCATT 65 TTTCTGATATCAAAAAATCATT * * * * * * * 100833 -TTTTTGATATCACAAATTCGAATTCTTGATATCAAAAAATGATTTTCTGATATCACAAAATAGA 1 ATTTTTGATATCAAAAAATCTAATTCTTGATATC-AAAAATCATTTTTTGATATCAAAAAAT-CA * * * 100897 TTTTCTGATATCAAGAATTAAAGTT 64 TTTTCTGATATCAAAAAAT-CA-TT * * * 100922 GATTTTGGACATCAAAAAAT-TGAAATCTTGATATCACAAAATCATTTTTTGATATCAAAAAATC 1 -ATTTTTGATATCAAAAAATCT-AATTCTTGATATCA-AAAATCATTTTTTGATATCAAAAAATC * 100986 ATTTTTTGATATCAAAAAATCATTT 63 ATTTTCTGATATCAAAAAATCA-TT * * * 101011 ACATTTTCTGATATCAGAAAATCTATTTTTTGATATCAGAAAAT 1 --ATTTT-TGATATCAAAAAATCTAATTCTTGATATCA-AAAAT 101055 AAGACTTACA Statistics Matches: 172, Mismatches: 37, Indels: 20 0.75 0.16 0.09 Matches are distributed among these distances: 84 15 0.09 85 1 0.01 86 12 0.07 87 38 0.22 88 1 0.01 89 5 0.03 90 23 0.13 91 76 0.44 92 1 0.01 ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39 Consensus pattern (86 bp): ATTTTTGATATCAAAAAATCTAATTCTTGATATCAAAAATCATTTTTTGATATCAAAAAATCATT TTCTGATATCAAAAAATCATT Found at i:101531 original size:30 final size:29 Alignment explanation

Indices: 101492--101555 Score: 76 Period size: 29 Copynumber: 2.2 Consensus size: 29 101482 AATTTCTGAT 101492 ATCAAAAAAT-ATAATTCTTGATATCAAAAA 1 ATCAAAAAATGAT-ATTC-TGATATCAAAAA * * * 101522 ATCACAAAATGATTTTCTGATATCAGAAA 1 ATCAAAAAATGATATTCTGATATCAAAAA 101551 ATCAA 1 ATCAA 101556 TTTTTGGATA Statistics Matches: 29, Mismatches: 4, Indels: 3 0.81 0.11 0.08 Matches are distributed among these distances: 29 15 0.52 30 12 0.41 31 2 0.07 ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30 Consensus pattern (29 bp): ATCAAAAAATGATATTCTGATATCAAAAA Found at i:101593 original size:27 final size:24 Alignment explanation

Indices: 101533--101687 Score: 75 Period size: 22 Copynumber: 6.8 Consensus size: 24 101523 TCACAAAATG 101533 ATTTTCTGATATCAGAAAATCAAT 1 ATTTTCTGATATCAGAAAATCAAT * * 101557 -TTTT-GGATATCAGAAAATGGATAGT 1 ATTTTCTGATATCAGAAAAT-CA-A-T * * 101582 ATTTTCTGATATCA-AGAATTCGA- 1 ATTTTCTGATATCAGA-AAATCAAT * 101605 A-TTTCTGATATCAAAAAATC--- 1 ATTTTCTGATATCAGAAAATCAAT * * * * 101625 ATTTCCTGATATTAGAAATTCGA- 1 ATTTTCTGATATCAGAAAATCAAT * * 101648 ATTCT-TGATATCAAAAAATC--- 1 ATTTTCTGATATCAGAAAATCAAT * 101668 ATTTTCTGACATCAGAAAAT 1 ATTTTCTGATATCAGAAAAT 101688 ACCTCAAAAA Statistics Matches: 101, Mismatches: 19, Indels: 25 0.70 0.13 0.17 Matches are distributed among these distances: 20 5 0.05 21 27 0.27 22 41 0.41 23 10 0.10 24 1 0.01 25 2 0.02 26 5 0.05 27 10 0.10 ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37 Consensus pattern (24 bp): ATTTTCTGATATCAGAAAATCAAT Found at i:101635 original size:43 final size:44 Alignment explanation

Indices: 101582--101685 Score: 144 Period size: 43 Copynumber: 2.4 Consensus size: 44 101572 AATGGATAGT 101582 ATTTTCTGATATCAAG-AATTCGAATT-TCTGATATCAAAAAATC 1 ATTTTCTGATATCAAGAAATTCGAATTCT-TGATATCAAAAAATC * * 101625 ATTTCCTGATAT-TAGAAATTCGAATTCTTGATATCAAAAAATC 1 ATTTTCTGATATCAAGAAATTCGAATTCTTGATATCAAAAAATC * 101668 ATTTTCTGACATC-AGAAA 1 ATTTTCTGATATCAAGAAA 101686 ATACCTCAAA Statistics Matches: 54, Mismatches: 4, Indels: 6 0.84 0.06 0.09 Matches are distributed among these distances: 42 2 0.04 43 51 0.94 44 1 0.02 ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37 Consensus pattern (44 bp): ATTTTCTGATATCAAGAAATTCGAATTCTTGATATCAAAAAATC Found at i:101674 original size:22 final size:21 Alignment explanation

Indices: 101584--101687 Score: 86 Period size: 22 Copynumber: 4.9 Consensus size: 21 101574 TGGATAGTAT * * 101584 TTTCTGATATCAAGAATTCGAA 1 TTTCTGATATCAAAAAATCG-A 101606 TTTCTGATATCAAAAAATC-A 1 TTTCTGATATCAAAAAATCGA * * * 101626 TTTCCTGATATTAGAAATTCGA 1 TTT-CTGATATCAAAAAATCGA * 101648 ATTCTTGATATCAAAAAATC-A 1 TTTC-TGATATCAAAAAATCGA * * 101669 TTTTCTGACATCAGAAAAT 1 -TTTCTGATATCAAAAAAT 101688 ACCTCAAAAA Statistics Matches: 66, Mismatches: 12, Indels: 9 0.76 0.14 0.10 Matches are distributed among these distances: 20 4 0.06 21 27 0.41 22 35 0.53 ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37 Consensus pattern (21 bp): TTTCTGATATCAAAAAATCGA Found at i:109949 original size:24 final size:23 Alignment explanation

Indices: 109912--109958 Score: 67 Period size: 24 Copynumber: 2.0 Consensus size: 23 109902 GATCTTTTTT * * 109912 TTTTTTTTGCTTTTGAATTATTG 1 TTTTTTGTGCTTTTGAATCATTG 109935 TTTTTTGTGCATTTTGAATCATTG 1 TTTTTTGTGC-TTTTGAATCATTG 109959 ACTTAAATTT Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 23 9 0.43 24 12 0.57 ACGTcount: A:0.15, C:0.06, G:0.15, T:0.64 Consensus pattern (23 bp): TTTTTTGTGCTTTTGAATCATTG Found at i:115037 original size:20 final size:20 Alignment explanation

Indices: 115012--115050 Score: 60 Period size: 20 Copynumber: 1.9 Consensus size: 20 115002 AATTGTTTTG * * 115012 GTATCATGTGATATGATATT 1 GTATCATATCATATGATATT 115032 GTATCATATCATATGATAT 1 GTATCATATCATATGATAT 115051 GATATTGAAT Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 17 1.00 ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44 Consensus pattern (20 bp): GTATCATATCATATGATATT Found at i:119969 original size:21 final size:21 Alignment explanation

Indices: 119943--120030 Score: 108 Period size: 21 Copynumber: 4.2 Consensus size: 21 119933 TACGCCATAG 119943 CATAGCATAGCATTGAAATCT 1 CATAGCATAGCATTGAAATCT * * 119964 CATAGCATAGCATTAAAATAT 1 CATAGCATAGCATTGAAATCT * * 119985 CATAGCATAGCATTGGAATCC 1 CATAGCATAGCATTGAAATCT * 120006 CATACCATAGCA-T-ACAATCT 1 CATAGCATAGCATTGA-AATCT 120026 CATAG 1 CATAG 120031 AATTGCATCC Statistics Matches: 56, Mismatches: 10, Indels: 3 0.81 0.14 0.04 Matches are distributed among these distances: 20 9 0.16 21 47 0.84 ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26 Consensus pattern (21 bp): CATAGCATAGCATTGAAATCT Found at i:120061 original size:10 final size:10 Alignment explanation

Indices: 120043--120076 Score: 50 Period size: 10 Copynumber: 3.4 Consensus size: 10 120033 TTGCATCCGT * 120043 CATATCATAC 1 CATAGCATAC 120053 CATAGCATAC 1 CATAGCATAC * 120063 CATAGCATAG 1 CATAGCATAC 120073 CATA 1 CATA 120077 CAACATTATT Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 10 22 1.00 ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24 Consensus pattern (10 bp): CATAGCATAC Found at i:120066 original size:15 final size:15 Alignment explanation

Indices: 120043--120077 Score: 52 Period size: 15 Copynumber: 2.3 Consensus size: 15 120033 TTGCATCCGT * 120043 CATATCATACCATAG 1 CATACCATACCATAG * 120058 CATACCATAGCATAG 1 CATACCATACCATAG 120073 CATAC 1 CATAC 120078 AACATTATTT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.40, C:0.29, G:0.09, T:0.23 Consensus pattern (15 bp): CATACCATACCATAG Found at i:120238 original size:5 final size:5 Alignment explanation

Indices: 120225--120258 Score: 50 Period size: 5 Copynumber: 6.8 Consensus size: 5 120215 GTTCAAATCT * * 120225 CATAG CATAC CATAG CATAG CATAG CATAC CATA 1 CATAG CATAG CATAG CATAG CATAG CATAG CATA 120259 TCATTAAGCC Statistics Matches: 26, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 5 26 1.00 ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21 Consensus pattern (5 bp): CATAG Found at i:120240 original size:10 final size:10 Alignment explanation

Indices: 120225--120258 Score: 59 Period size: 10 Copynumber: 3.4 Consensus size: 10 120215 GTTCAAATCT 120225 CATAGCATAC 1 CATAGCATAC * 120235 CATAGCATAG 1 CATAGCATAC 120245 CATAGCATAC 1 CATAGCATAC 120255 CATA 1 CATA 120259 TCATTAAGCC Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 10 22 1.00 ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21 Consensus pattern (10 bp): CATAGCATAC Found at i:120305 original size:21 final size:21 Alignment explanation

Indices: 120281--120360 Score: 99 Period size: 21 Copynumber: 3.8 Consensus size: 21 120271 TCATTCAATT 120281 TCTCATAGCATAGCATACAAA 1 TCTCATAGCATAGCATACAAA * 120302 TCTCATAGCATAACATACAAA 1 TCTCATAGCATAGCATACAAA * * 120323 TCTCATAGCATATCGTTA-AAA 1 TCTCATAGCATAGC-ATACAAA * * 120344 TCGCATACCATAGCATA 1 TCTCATAGCATAGCATA 120361 GTATTAAATT Statistics Matches: 51, Mismatches: 7, Indels: 3 0.84 0.11 0.05 Matches are distributed among these distances: 20 2 0.04 21 47 0.92 22 2 0.04 ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26 Consensus pattern (21 bp): TCTCATAGCATAGCATACAAA Found at i:122665 original size:8 final size:8 Alignment explanation

Indices: 122652--122677 Score: 52 Period size: 8 Copynumber: 3.2 Consensus size: 8 122642 GAATATACAC 122652 TGCTTATA 1 TGCTTATA 122660 TGCTTATA 1 TGCTTATA 122668 TGCTTATA 1 TGCTTATA 122676 TG 1 TG 122678 TATGTAAATT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 18 1.00 ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50 Consensus pattern (8 bp): TGCTTATA Found at i:126541 original size:27 final size:27 Alignment explanation

Indices: 126503--126556 Score: 108 Period size: 27 Copynumber: 2.0 Consensus size: 27 126493 TTCGAACTTT 126503 CGCCTTTGTCAATTTTATGTTTGTGGA 1 CGCCTTTGTCAATTTTATGTTTGTGGA 126530 CGCCTTTGTCAATTTTATGTTTGTGGA 1 CGCCTTTGTCAATTTTATGTTTGTGGA 126557 GCTCTCTATA Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 27 27 1.00 ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48 Consensus pattern (27 bp): CGCCTTTGTCAATTTTATGTTTGTGGA Found at i:126678 original size:6 final size:6 Alignment explanation

Indices: 126667--126724 Score: 57 Period size: 6 Copynumber: 9.7 Consensus size: 6 126657 TTTTTTTCGG * * 126667 TTTTGT TTTTGT TTTTGT TTTTGT TTTT-T TGGTTT-T TTTTGT TTGTCT 1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT T--TTTGT TTTTGT TTTTGT * 126715 GTTTGT TTTT 1 TTTTGT TTTT 126725 TGCTGCTTTC Statistics Matches: 43, Mismatches: 6, Indels: 6 0.78 0.11 0.11 Matches are distributed among these distances: 5 5 0.12 6 33 0.77 7 5 0.12 ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81 Consensus pattern (6 bp): TTTTGT Found at i:126703 original size:22 final size:22 Alignment explanation

Indices: 126674--126726 Score: 56 Period size: 22 Copynumber: 2.5 Consensus size: 22 126664 CGGTTTTGTT * * 126674 TTTG-TTTTTGTT-TTTGTTTT 1 TTTGTTTTTTGTTGTTTGTCTG * * 126694 TTTGGTTTTTTTTGTTTGTCTG 1 TTTGTTTTTTGTTGTTTGTCTG 126716 TTTGTTTTTTG 1 TTTGTTTTTTG 126727 CTGCTTTCTT Statistics Matches: 26, Mismatches: 5, Indels: 2 0.79 0.15 0.06 Matches are distributed among these distances: 20 4 0.15 21 7 0.27 22 15 0.58 ACGTcount: A:0.00, C:0.02, G:0.19, T:0.79 Consensus pattern (22 bp): TTTGTTTTTTGTTGTTTGTCTG Found at i:136205 original size:11 final size:11 Alignment explanation

Indices: 136191--136215 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 136181 TTTTTGAGAT 136191 TTTTTTGTTTG 1 TTTTTTGTTTG 136202 TTTTTTGTTTG 1 TTTTTTGTTTG 136213 TTT 1 TTT 136216 GTATTTTTTT 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:0.00, C:0.00, G:0.16, T:0.84 Consensus pattern (11 bp): TTTTTTGTTTG Found at i:136212 original size:15 final size:15 Alignment explanation

Indices: 136190--136226 Score: 58 Period size: 15 Copynumber: 2.5 Consensus size: 15 136180 GTTTTTGAGA 136190 TTTTTTTGTTTGT-T 1 TTTTTTTGTTTGTAT 136204 TTTTGTTTGTTTGTAT 1 TTTT-TTTGTTTGTAT 136220 TTTTTTT 1 TTTTTTT 136227 TTATTTTATT Statistics Matches: 21, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 14 4 0.19 15 12 0.57 16 5 0.24 ACGTcount: A:0.03, C:0.00, G:0.14, T:0.84 Consensus pattern (15 bp): TTTTTTTGTTTGTAT Found at i:141828 original size:19 final size:19 Alignment explanation

Indices: 141800--141842 Score: 52 Period size: 19 Copynumber: 2.3 Consensus size: 19 141790 AAAGCAGGTT * * 141800 TAAATGATACATGAATAG-A 1 TAAATCATACACGAA-AGAA 141819 TAAATCATACACGAAAGAA 1 TAAATCATACACGAAAGAA 141838 TAAAT 1 TAAAT 141843 TTTAATATCA Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 18 2 0.10 19 19 0.90 ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23 Consensus pattern (19 bp): TAAATCATACACGAAAGAA Found at i:143560 original size:2 final size:2 Alignment explanation

Indices: 143553--143597 Score: 90 Period size: 2 Copynumber: 22.5 Consensus size: 2 143543 CACCTAATTA 143553 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 143595 AG A 1 AG A 143598 AATAATACTT Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 43 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:147227 original size:51 final size:51 Alignment explanation

Indices: 147172--147268 Score: 176 Period size: 51 Copynumber: 1.9 Consensus size: 51 147162 TTTTACAAGC 147172 ATTTAATGAGAAATCTCATGTTTTCAACATTTGCAAAATTGATTTACAAAT 1 ATTTAATGAGAAATCTCATGTTTTCAACATTTGCAAAATTGATTTACAAAT * * 147223 ATTTAATGAGTAGTCTCATGTTTTCAACATTTGCAAAATTGATTTA 1 ATTTAATGAGAAATCTCATGTTTTCAACATTTGCAAAATTGATTTA 147269 AATCAAATCA Statistics Matches: 44, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 51 44 1.00 ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41 Consensus pattern (51 bp): ATTTAATGAGAAATCTCATGTTTTCAACATTTGCAAAATTGATTTACAAAT Found at i:162584 original size:70 final size:69 Alignment explanation

Indices: 162501--162639 Score: 251 Period size: 70 Copynumber: 2.0 Consensus size: 69 162491 TCTTTGAAGT * * 162501 AGCGATCTTGACGGTAGTTCTTATGACATCACCGCTTTAGTATATGGCGGGTCACTTTCTTGGTT 1 AGCGACCTTGACGGTAGTTCTTATGACATCACCGCTTTAGTATATAGCGGGTCACTTTCTTGGTT 162566 TTCA 66 TTCA 162570 NAGCGACCTTGACGGTAGTTCTTATGACATCACCGCTTTAGTATATAGCGGGTCACTTTCTTGGT 1 -AGCGACCTTGACGGTAGTTCTTATGACATCACCGCTTTAGTATATAGCGGGTCACTTTCTTGGT 162635 TTTCA 65 TTTCA 162640 TATCAGAGGT Statistics Matches: 67, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 70 67 1.00 ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37 Consensus pattern (69 bp): AGCGACCTTGACGGTAGTTCTTATGACATCACCGCTTTAGTATATAGCGGGTCACTTTCTTGGTT TTCA Found at i:180534 original size:194 final size:194 Alignment explanation

Indices: 180205--180583 Score: 749 Period size: 194 Copynumber: 2.0 Consensus size: 194 180195 CAACATGCGG * 180205 CGAATCAAACTTCAGACAACTTTTAAAGATCTGTATTTGCTTATATACATGTACTTTGTTTCTTT 1 CGAATCAAACTTCAGACAACTTTTAAAGATCTGTATTTGCTTACATACATGTACTTTGTTTCTTT 180270 TACACAGTGTTTATACATCTAATATTGCACCATGGTCAGGTATCAATTTTTGTATTACGTCACAA 66 TACACAGTGTTTATACATCTAATATTGCACCATGGTCAGGTATCAATTTTTGTATTACGTCACAA 180335 GTATGACGCAGCTACGACGGAAGACCTAATCGTTGCTTGCAACGAGCTCGTCTCTGCAAAAAAA 131 GTATGACGCAGCTACGACGGAAGACCTAATCGTTGCTTGCAACGAGCTCGTCTCTGCAAAAAAA 180399 CGAATCAAACTTCAGACAACTTTTAAAGATCTGTATTTGCTTACATACATGTACTTTGTTTCTTT 1 CGAATCAAACTTCAGACAACTTTTAAAGATCTGTATTTGCTTACATACATGTACTTTGTTTCTTT 180464 TACACAGTGTTTATACATCTAATATTGCACCATGGTCAGGTATCAATTTTTGTATTACGTCACAA 66 TACACAGTGTTTATACATCTAATATTGCACCATGGTCAGGTATCAATTTTTGTATTACGTCACAA 180529 GTATGACGCAGCTACGACGGAAGACCTAATCGTTGCTTGCAACGAGCTCGTCTCT 131 GTATGACGCAGCTACGACGGAAGACCTAATCGTTGCTTGCAACGAGCTCGTCTCT 180584 AGTTTTTATT Statistics Matches: 184, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 194 184 1.00 ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34 Consensus pattern (194 bp): CGAATCAAACTTCAGACAACTTTTAAAGATCTGTATTTGCTTACATACATGTACTTTGTTTCTTT TACACAGTGTTTATACATCTAATATTGCACCATGGTCAGGTATCAATTTTTGTATTACGTCACAA GTATGACGCAGCTACGACGGAAGACCTAATCGTTGCTTGCAACGAGCTCGTCTCTGCAAAAAAA Found at i:181206 original size:28 final size:28 Alignment explanation

Indices: 181172--181227 Score: 112 Period size: 28 Copynumber: 2.0 Consensus size: 28 181162 CCTGGATTTT 181172 ATACGAAGCTACCGATATGTACTTTATA 1 ATACGAAGCTACCGATATGTACTTTATA 181200 ATACGAAGCTACCGATATGTACTTTATA 1 ATACGAAGCTACCGATATGTACTTTATA 181228 CGAAACTCTC Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 28 1.00 ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32 Consensus pattern (28 bp): ATACGAAGCTACCGATATGTACTTTATA Found at i:186236 original size:19 final size:19 Alignment explanation

Indices: 186217--186254 Score: 58 Period size: 19 Copynumber: 1.9 Consensus size: 19 186207 CTAGATGAGG 186217 TAAATGATTTTAGAGCAGGT 1 TAAA-GATTTTAGAGCAGGT * 186237 TAAAGTTTTTAGAGCAGG 1 TAAAGATTTTAGAGCAGG 186255 CGCTGTTTGA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 19 13 0.76 20 4 0.24 ACGTcount: A:0.34, C:0.05, G:0.26, T:0.34 Consensus pattern (19 bp): TAAAGATTTTAGAGCAGGT Found at i:186450 original size:15 final size:15 Alignment explanation

Indices: 186426--186457 Score: 55 Period size: 15 Copynumber: 2.1 Consensus size: 15 186416 TATTGAATTG 186426 TATCAAATTATACAA 1 TATCAAATTATACAA * 186441 TATCATATTATACAA 1 TATCAAATTATACAA 186456 TA 1 TA 186458 CAATTTTGTA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38 Consensus pattern (15 bp): TATCAAATTATACAA Found at i:195080 original size:59 final size:56 Alignment explanation

Indices: 195004--195170 Score: 261 Period size: 59 Copynumber: 3.0 Consensus size: 56 194994 CAAATATATA * * 195004 TTATTAGGGTCTTCCGTTTCCGACGGAAGACCCTCTTGTTATTCTATTGTTTCTTTT 1 TTATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTT-TTTT 195061 CCTTATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTG---TTTT 1 --TTATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTTT 195116 TT-TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTTT 1 TTATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTTT 195171 NGCTGGCTGC Statistics Matches: 103, Mismatches: 2, Indels: 10 0.90 0.02 0.09 Matches are distributed among these distances: 52 46 0.45 53 2 0.02 55 8 0.08 59 47 0.46 ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48 Consensus pattern (56 bp): TTATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTTT Found at i:195123 original size:52 final size:52 Alignment explanation

Indices: 195007--195170 Score: 247 Period size: 52 Copynumber: 3.0 Consensus size: 52 194997 ATATATATTA * * 195007 TTAGGGTCTTCCGTTTCCGACGGAAGACCCTCTTGTTATTCTATTGTTTCTTTTCCTT 1 TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTG----TTTT--TT 195065 ATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTT 1 -TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTT 195118 TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTT 1 TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTT 195170 T 1 T 195171 NGCTGGCTGC Statistics Matches: 103, Mismatches: 2, Indels: 7 0.92 0.02 0.06 Matches are distributed among these distances: 52 53 0.51 53 2 0.02 55 4 0.04 59 44 0.43 ACGTcount: A:0.15, C:0.21, G:0.17, T:0.48 Consensus pattern (52 bp): TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTT Found at i:197944 original size:2 final size:2 Alignment explanation

Indices: 197937--198001 Score: 121 Period size: 2 Copynumber: 32.5 Consensus size: 2 197927 GTGCCTCAGA * 197937 TC TC TC TC TG 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 197979 TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC T 198002 TTTAATCTTG Statistics Matches: 61, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 2 61 1.00 ACGTcount: A:0.00, C:0.48, G:0.02, T:0.51 Consensus pattern (2 bp): TC Found at i:201596 original size:32 final size:31 Alignment explanation

Indices: 201560--201636 Score: 91 Period size: 32 Copynumber: 2.5 Consensus size: 31 201550 CAAAAAAAAC * * * 201560 TTGTTAAGTCGTACTTGAAATTAGTAAGGTTT 1 TTGTTAAGTCGTACTTAAAATCA-TAAGGATT * ** 201592 TTGTTAAGTTGTACTTAAAATCATTCGGATT 1 TTGTTAAGTCGTACTTAAAATCATAAGGATT 201623 TTGTTAAGTCGTAC 1 TTGTTAAGTCGTAC 201637 CAGGAATAAT Statistics Matches: 38, Mismatches: 7, Indels: 1 0.83 0.15 0.02 Matches are distributed among these distances: 31 18 0.47 32 20 0.53 ACGTcount: A:0.27, C:0.09, G:0.19, T:0.44 Consensus pattern (31 bp): TTGTTAAGTCGTACTTAAAATCATAAGGATT Found at i:202460 original size:31 final size:30 Alignment explanation

Indices: 202401--202465 Score: 76 Period size: 31 Copynumber: 2.1 Consensus size: 30 202391 TCGGAAAGGT * * 202401 TTTTGTTAAGTCGTACGTAAAATCATTCGGA 1 TTTTGTTAAGTCGTACCTAAAATAATTC-GA ** * 202432 TTTTGTTAAGTCGTACCTGGAGTAATTCGA 1 TTTTGTTAAGTCGTACCTAAAATAATTCGA 202462 TTTT 1 TTTT 202466 TTTTCATTTT Statistics Matches: 29, Mismatches: 5, Indels: 1 0.83 0.14 0.03 Matches are distributed among these distances: 30 6 0.21 31 23 0.79 ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43 Consensus pattern (30 bp): TTTTGTTAAGTCGTACCTAAAATAATTCGA Found at i:203263 original size:31 final size:31 Alignment explanation

Indices: 203201--203269 Score: 86 Period size: 31 Copynumber: 2.2 Consensus size: 31 203191 AAATCGGAAA * * 203201 GGTTTTTGTTAAGTCGTACGTAAAATTATTC 1 GGTTTTTGTTAAGTCGTACGCAAAATAATTC * 203232 GGTTTTTGTTAAGTCGTAC-CAGGAATAATTC 1 GGTTTTTGTTAAGTCGTACGCA-AAATAATTC * 203263 GATTTTT 1 GGTTTTT 203270 TCATGTTTTT Statistics Matches: 33, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 30 1 0.03 31 32 0.97 ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45 Consensus pattern (31 bp): GGTTTTTGTTAAGTCGTACGCAAAATAATTC Found at i:204036 original size:31 final size:31 Alignment explanation

Indices: 203934--204044 Score: 114 Period size: 32 Copynumber: 3.5 Consensus size: 31 203924 CCAAAAATTA * * 203934 TTGTTAAGTCGTACTTGAACTCATTTGGATTTTT 1 TTGTTAAGTCGTACTTGAAATCATTAGGA---TT * ** * 203968 TTGTTAAGTCGTTCTTGAAATCAGGAAGGTTT 1 TTGTTAAGTCGTACTTGAAATCA-TTAGGATT * * 204000 TTGTTAAGTCGTACTTAAAATCATTCGGATT 1 TTGTTAAGTCGTACTTGAAATCATTAGGATT 204031 TTGTTAAGTCGTAC 1 TTGTTAAGTCGTAC 204045 CAGGAATAAT Statistics Matches: 64, Mismatches: 12, Indels: 5 0.79 0.15 0.06 Matches are distributed among these distances: 31 18 0.28 32 23 0.36 34 21 0.33 35 2 0.03 ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44 Consensus pattern (31 bp): TTGTTAAGTCGTACTTGAAATCATTAGGATT Found at i:204057 original size:31 final size:31 Alignment explanation

Indices: 203998--204063 Score: 80 Period size: 31 Copynumber: 2.1 Consensus size: 31 203988 TCAGGAAGGT * * * 203998 TTTTGTTAAGTCGTACTTAAAATCATTCGGA 1 TTTTGTTAAGTCGTACTCAAAATAATTCGAA * 204029 TTTTGTTAAGTCGTAC-CAGGAATAATTCGAA 1 TTTTGTTAAGTCGTACTCA-AAATAATTCGAA 204060 TTTT 1 TTTT 204064 CATTTTTTTT Statistics Matches: 30, Mismatches: 4, Indels: 2 0.83 0.11 0.06 Matches are distributed among these distances: 30 1 0.03 31 29 0.97 ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42 Consensus pattern (31 bp): TTTTGTTAAGTCGTACTCAAAATAATTCGAA Found at i:205382 original size:437 final size:433 Alignment explanation

Indices: 204627--205578 Score: 1194 Period size: 437 Copynumber: 2.2 Consensus size: 433 204617 TTAACTAGGA * * * * 204627 CTTTTGTTTGATTTCAAGAAAAAGGGGCTGGCCCGTCAAATTAGGGGCCAAAAGGGCTCAAAATT 1 CTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGCCAAAAGGGCTC-AAAGT * ** * * 204692 ATTTTTGCAATAACTCTTTACTGAAAAATAATTTGTAATCGATCATAGAACCAAAAGTGTTCATT 65 CTTTTTAAAATAACTCTTTACTGAAAAATAATTTATAATCAATCATAGAACCAAAAGTGTTCATT * * 204757 GTACATCTGTTTATCTACAAAGAACCATACCTAAGTCATATGTTACGTAATTATGGGTTTCAAGG 130 GTACAGCTGTTTATCTACAAAGAACCATACCTAAGTCATATGTTACGTAATTAGGGGTTTCAAGG * ** * * * * 204822 GGCCAGAAGTCCAAAATTTTGATCTTTAATATCTAGAAAAGGAGAAATATTTTGATAAGCATTGT 195 GACCAGAAGTAAAAAACTTTGATCATTAATATCTAGAAAAAGAGAAATATTTTGAAAAGCATTGT * * ** * * 204887 AGAACTAAAAATGCTTAGAATAATGTTTTTAACAATATGCTACCTAAATAATTTTTGTTGGTGGC 260 AGAACTAAAAATGCTCAAAATAATGTTTTTAACAATATGAAACCTAAAAAAATTTTGTTGGTGGC * * * * * 204952 CCCAGTAAGGATTTTAAGGGTCGGCCCCTAAAACACATTTGTTCAGATATCTTTAGAACGGTCAA 325 CCCAGTAAAGAGTTAAAGGGTCGGCCCCTAAAACACAGTTGTTCAGATATCTCTAGAACGGT-AA * * 205017 CAATTTCCG-AACACTTGTTGAACAAAATGTGTTTATATTTACAAGAC 389 CAA-TT-CGAAACACTTGTTGAAAAAAATATGTTTAT-TTTACAAGAC * * * 205064 CTTTTATTTGATATCTAGAAATAA-GGGTTGGCCCCTCAAATTAGGGGCCAAGAGGGCTCTAAAG 1 CTTTTATTTGATATCAAGAAA-AAGGGGCTGGCCCCTCAAATTAGGGGCCAAAAGGGCTC-AAAG * * * * 205128 TCTTTTTAAAATAACTCTTTACTGAAAAATAATTTATTATCAATTATAGAAGCAACAA-TGTTTA 64 TCTTTTTAAAATAACTCTTTACTGAAAAATAATTTATAATCAATCATAGAACCAA-AAGTGTTCA * * * 205192 TTGTACAGCTGTTTATCTATACAGTACCATACCTAAGTCATATGTTACGTAATTAGGGGTTTCAA 128 TTGTACAGCTGTTTATCTACAAAGAACCATACCTAAGTCATATGTTACGTAATTAGGGGTTTCAA * 205257 GGGACCAGAAGTAAAAAACTTTGATCATTAATATCTAGAAAAAGAGAAATATTTTGAAAAGTATT 193 GGGACCAGAAGTAAAAAACTTTGATCATTAATATCTAGAAAAAGAGAAATATTTTGAAAAGCATT * ** * 205322 GTAGAAC-AAAAGTTGCTCAAAATAATGTTATTT-ATGATATGAAATCTAAAAAAATTTTGTTGG 258 GTAGAACTAAAA-ATGCTCAAAATAATGTT-TTTAACAATATGAAACCTAAAAAAATTTTGTTGG * * * 205385 TGGCCCCAGTAAAGAGTTAAAGGGTGGGCCCCTAAAACAGAGTTGTTCGGATATCTCTAGAACGG 321 TGGCCCCAGTAAAGAGTTAAAGGGTCGGCCCCTAAAACACAGTTGTTCAGATATCTCTAGAACGG * * * * * * 205450 TTAGAATTCGTAAATACTTGTTGAAAAAAATATGTTTGTTTTTCGAGAC 386 TAACAATTCG-AAACACTTGTTGAAAAAAATATGTTTATTTTACAAGAC * ** * * * 205499 CTTTCATTTGATATCAAGAAAAAGGGGCCAGCCCCTCAAATAAAGAGCCAAAAGGGCTACAAAGT 1 CTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGCCAAAAGGGCT-CAAAGT * * 205564 CTTTTCATAATAACT 65 CTTTTTAAAATAACT 205579 TATTTTTAAG Statistics Matches: 440, Mismatches: 67, Indels: 18 0.84 0.13 0.03 Matches are distributed among these distances: 434 4 0.01 435 74 0.17 436 31 0.07 437 324 0.74 438 7 0.02 ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32 Consensus pattern (433 bp): CTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGCCAAAAGGGCTCAAAGTC TTTTTAAAATAACTCTTTACTGAAAAATAATTTATAATCAATCATAGAACCAAAAGTGTTCATTG TACAGCTGTTTATCTACAAAGAACCATACCTAAGTCATATGTTACGTAATTAGGGGTTTCAAGGG ACCAGAAGTAAAAAACTTTGATCATTAATATCTAGAAAAAGAGAAATATTTTGAAAAGCATTGTA GAACTAAAAATGCTCAAAATAATGTTTTTAACAATATGAAACCTAAAAAAATTTTGTTGGTGGCC CCAGTAAAGAGTTAAAGGGTCGGCCCCTAAAACACAGTTGTTCAGATATCTCTAGAACGGTAACA ATTCGAAACACTTGTTGAAAAAAATATGTTTATTTTACAAGAC Found at i:235495 original size:4 final size:4 Alignment explanation

Indices: 235488--235531 Score: 61 Period size: 4 Copynumber: 11.0 Consensus size: 4 235478 GGGACAGACA * * * 235488 GACG GACG GACG GACG GATG GACG GACA GACG GACT GACG GACG 1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG 235532 CAGAGGAAAG Statistics Matches: 34, Mismatches: 6, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 4 34 1.00 ACGTcount: A:0.27, C:0.23, G:0.45, T:0.05 Consensus pattern (4 bp): GACG Found at i:266084 original size:54 final size:53 Alignment explanation

Indices: 266014--266119 Score: 140 Period size: 54 Copynumber: 2.0 Consensus size: 53 266004 AAATAATAAT * * * 266014 AAGAAACAGTAGAATAACAGAAGGGTTTTCCGTTGAAAAACGGAAAACCCTAAA 1 AAGAAACAGTACAATAACAGAAGGGTCTTCCGCTG-AAAACGGAAAACCCTAAA * * * * 266068 AAGAAACATTACAATAATAGAAGGGTCTTCCGCTGAAGACGGAAGACCCTAA 1 AAGAAACAGTACAATAACAGAAGGGTCTTCCGCTGAAAACGGAAAACCCTAA 266120 TTACTTGCAA Statistics Matches: 45, Mismatches: 7, Indels: 1 0.85 0.13 0.02 Matches are distributed among these distances: 53 15 0.33 54 30 0.67 ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17 Consensus pattern (53 bp): AAGAAACAGTACAATAACAGAAGGGTCTTCCGCTGAAAACGGAAAACCCTAAA Found at i:268705 original size:13 final size:13 Alignment explanation

Indices: 268687--268711 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 268677 TTCTACGGGC 268687 TTAGTGGCTGCTG 1 TTAGTGGCTGCTG 268700 TTAGTGGCTGCT 1 TTAGTGGCTGCT 268712 AGCTTCAGCC Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.08, C:0.16, G:0.36, T:0.40 Consensus pattern (13 bp): TTAGTGGCTGCTG Found at i:268770 original size:2 final size:2 Alignment explanation

Indices: 268763--268802 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 268753 GATGAATGAA 268763 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 268803 ATTGAATACA Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:275809 original size:146 final size:146 Alignment explanation

Indices: 275171--276008 Score: 1189 Period size: 146 Copynumber: 5.7 Consensus size: 146 275161 CTTCCTCAAT * * * * * * * * * 275171 TGACCTTTGGTCAAGGTCATGACATACTCTCAGGTTATGAGCATTC-TAGATGTGAATTAAGAAC 1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTG-TGTGAAGTAAGAAC * * * * * * ** * 275235 TTCCAATATTTGTCCATTAGAAAGATATGGACTGAACACGAGTTTTATAC-TTTTCTGCAAGTGA 65 TTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGA * 275299 CCTTGACCTTGCCCAAA 130 CCTTGACCTTGCCCGAA * * * * * 275316 TGACCTTGGGTCAAGGTCATGACAAACCCTTAGCTTATAAGCAATCTTTGTGTGAACTGAGAACT 1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT * * 275381 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACAAGAATTTTGCACTTTTTTCTGCCATTGA 66 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCAC-TTTTTCTGCCAGTGA * * 275446 CCTTGACCTTGTCCAAA 130 CCTTGACCTTGCCCGAA 275463 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT 1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT * * * 275528 TCCAATGTTTCTCCATTAA-AAAGATATGGACCAGACACGAATTTTGCAATTTTTTCTGTCAGTG 66 TCCAATGTTTCTCCA-TAAGAAAGATATGGACCGGACACGAATTTTGC-ACTTTTTCTGCCAGTG 275592 ACCTTGACCTTGCCCGAA 129 ACCTTGACCTTGCCCGAA * * 275610 TGACCTTGGGTTAAGGTCATGACACACCCTTAGGTCATTAGCAATCTTTGTGTGAAGTTAA-AAC 1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAG-TAAGAAC *** 275674 TTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGTTGGTGA 65 TTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGA 275739 CCTTGACCTTGCCCGAA 130 CCTTGACCTTGCCCGAA * ** * * * 275756 TGACCATGCTTTAAGGTCATGACACACCCTCAGGTCATAAGCATTCTTTGTGTGAAGTAAGAACT 1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT * 275821 TCTAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGAC 66 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGAC 275886 CTTGACCTTGCCCGAA 131 CTTGACCTTGCCCGAA * * 275902 TGACCTTGGTTCAAGGTCATGACACATCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT 1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT * 275967 TCCAATGTTTCTTCATAAGAAAGATATGGACCGGACACGAAT 66 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAAT 276009 CGAACAGACA Statistics Matches: 627, Mismatches: 58, Indels: 15 0.90 0.08 0.02 Matches are distributed among these distances: 145 95 0.15 146 267 0.43 147 258 0.41 148 7 0.01 ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31 Consensus pattern (146 bp): TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCTGCCAGTGAC CTTGACCTTGCCCGAA Found at i:276034 original size:4 final size:4 Alignment explanation

Indices: 276019--276081 Score: 108 Period size: 4 Copynumber: 15.8 Consensus size: 4 276009 CGAACAGACA * * 276019 GACG GACA GACG GACG GACG GACG GACG GACG GACG GACG GACG GACA 1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG 276067 GACG GACG GACG GAC 1 GACG GACG GACG GAC 276082 AAGGTGATTC Statistics Matches: 55, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 4 55 1.00 ACGTcount: A:0.29, C:0.25, G:0.46, T:0.00 Consensus pattern (4 bp): GACG Found at i:283879 original size:24 final size:24 Alignment explanation

Indices: 283847--283896 Score: 91 Period size: 24 Copynumber: 2.1 Consensus size: 24 283837 GCGTAACGCC 283847 CATCCCAATCAATACTGGGATCAA 1 CATCCCAATCAATACTGGGATCAA * 283871 CATCCCAATCTATACTGGGATCAA 1 CATCCCAATCAATACTGGGATCAA 283895 CA 1 CA 283897 ACCCTCACTT Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 24 25 1.00 ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22 Consensus pattern (24 bp): CATCCCAATCAATACTGGGATCAA Found at i:284333 original size:51 final size:51 Alignment explanation

Indices: 284290--284403 Score: 158 Period size: 51 Copynumber: 2.2 Consensus size: 51 284280 TTCATCTACT * * 284290 TCGGTCTCCTCCCGTCTGAAGCTCTCTCGAGGGGTAGTCGCTTCCTCGTCC 1 TCGGACTCCTCCCGTCTGAAGCTCTCTCGAGGGGTAGTCGCTTCATCGTCC * * * * 284341 TCGGACTCCTCCTGTCTGAAGCTCTCTGGAGGGGTAG-CGGCGTCCTCGTCC 1 TCGGACTCCTCCCGTCTGAAGCTCTCTCGAGGGGTAGTC-GCTTCATCGTCC 284392 TCGGACTCCTCC 1 TCGGACTCCTCC 284404 AGGCAGATGC Statistics Matches: 58, Mismatches: 4, Indels: 2 0.91 0.06 0.03 Matches are distributed among these distances: 50 1 0.02 51 57 0.98 ACGTcount: A:0.09, C:0.37, G:0.27, T:0.27 Consensus pattern (51 bp): TCGGACTCCTCCCGTCTGAAGCTCTCTCGAGGGGTAGTCGCTTCATCGTCC Found at i:284895 original size:5 final size:5 Alignment explanation

Indices: 284885--284925 Score: 82 Period size: 5 Copynumber: 8.2 Consensus size: 5 284875 GAATGCACGT 284885 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC A 1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC A 284926 ATGTCCCTTT Statistics Matches: 36, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 36 1.00 ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39 Consensus pattern (5 bp): ATATC Found at i:290259 original size:1 final size:1 Alignment explanation

Indices: 290253--290307 Score: 56 Period size: 1 Copynumber: 55.0 Consensus size: 1 290243 ACCTTCACAT * * * * * * 290253 AAAAAAAAAACAAAAAAAAAAAACAAAACAAAAACAAACAAAAAACAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 290308 CCCGACATTC Statistics Matches: 42, Mismatches: 12, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 1 42 1.00 ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:290269 original size:11 final size:11 Alignment explanation

Indices: 290253--290307 Score: 74 Period size: 11 Copynumber: 4.8 Consensus size: 11 290243 ACCTTCACAT 290253 AAAAAAAAAAC 1 AAAAAAAAAAC 290264 AAAAAAAAAAAAC 1 --AAAAAAAAAAC * 290277 AAAACAAAAAC 1 AAAAAAAAAAC * 290288 AAACAAAAAAC 1 AAAAAAAAAAC 290299 AAAAAAAAA 1 AAAAAAAAA 290308 CCCGACATTC Statistics Matches: 38, Mismatches: 4, Indels: 2 0.86 0.09 0.05 Matches are distributed among these distances: 11 27 0.71 13 11 0.29 ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00 Consensus pattern (11 bp): AAAAAAAAAAC Found at i:291424 original size:2 final size:2 Alignment explanation

Indices: 291417--291475 Score: 118 Period size: 2 Copynumber: 29.5 Consensus size: 2 291407 GGAATCTGAA 291417 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 291459 TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC T 291476 TCCAGAAGCA 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:299299 original size:9 final size:9 Alignment explanation

Indices: 299285--299322 Score: 76 Period size: 9 Copynumber: 4.2 Consensus size: 9 299275 AATATTATTG 299285 CAAATATGT 1 CAAATATGT 299294 CAAATATGT 1 CAAATATGT 299303 CAAATATGT 1 CAAATATGT 299312 CAAATATGT 1 CAAATATGT 299321 CA 1 CA 299323 GTTTGTACTT Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 29 1.00 ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32 Consensus pattern (9 bp): CAAATATGT Found at i:300019 original size:10 final size:10 Alignment explanation

Indices: 300002--300048 Score: 69 Period size: 10 Copynumber: 4.8 Consensus size: 10 299992 TCCCACTGGG 300002 TTTTTTTGTT 1 TTTTTTTGTT * 300012 TGTTTTTG-T 1 TTTTTTTGTT * 300021 TTTGTTTGTT 1 TTTTTTTGTT 300031 TTTTTTTGTT 1 TTTTTTTGTT 300041 TTTTTTTG 1 TTTTTTTG 300049 CAATTTTTAC Statistics Matches: 32, Mismatches: 4, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 9 7 0.22 10 25 0.78 ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85 Consensus pattern (10 bp): TTTTTTTGTT Found at i:300025 original size:15 final size:15 Alignment explanation

Indices: 300005--300048 Score: 72 Period size: 15 Copynumber: 3.0 Consensus size: 15 299995 CACTGGGTTT 300005 TTTTGTTTGTTTTTG 1 TTTTGTTTGTTTTTG 300020 TTTTGTTTGTTTTT- 1 TTTTGTTTGTTTTTG * 300034 TTTTGTTTTTTTTTG 1 TTTTGTTTGTTTTTG 300049 CAATTTTTAC Statistics Matches: 27, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 14 13 0.48 15 14 0.52 ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84 Consensus pattern (15 bp): TTTTGTTTGTTTTTG Found at i:300030 original size:19 final size:18 Alignment explanation

Indices: 300001--300045 Score: 72 Period size: 19 Copynumber: 2.4 Consensus size: 18 299991 ATCCCACTGG 300001 GTTTTTTTGTTTGTTTTT 1 GTTTTTTTGTTTGTTTTT * 300019 GTTTTGTTTGTTTTTTTTT 1 GTTTT-TTTGTTTGTTTTT 300038 GTTTTTTT 1 GTTTTTTT 300046 TTGCAATTTT Statistics Matches: 25, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 18 8 0.32 19 17 0.68 ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84 Consensus pattern (18 bp): GTTTTTTTGTTTGTTTTT Found at i:301943 original size:330 final size:329 Alignment explanation

Indices: 301342--302000 Score: 1309 Period size: 330 Copynumber: 2.0 Consensus size: 329 301332 TTTGATTATC 301342 TTTTATTTTCTTTGATGTAATTGTGGATATCACTTGAGGATGCAATAGTTATAAGCAATGCTTTT 1 TTTTATTTTCTTTGATGTAATTGTGGATATCACTTGAGGATGCAATAGTTATAAGCAATGCTTTT 301407 TTTCTTTTCTTTGTCCTGTTATAAAATCTGCTTATGATGTGTTTCTATTTATTCCAGTGTATTTG 66 TTTCTTTTCTTTGTCCTGTTATAAAATCTGCTTATGATGTGTTTCTATTTATTCCAGTGTATTTG 301472 TGAAAAGTGACACAGACGACAGAAAGGGGTTCTCTAGCGATCATTTCTAGCCAAGGATTATGCTC 131 TGAAAAGTGACACAGACGACAGAAAGGGGTTCTCTAGCGATCATTTCTAGCCAAGGATTATGCTC 301537 GTGAATTGTAGAAACGTGAACTGTTGATCATAAACTCTATAACTGTGTCCTTAACCATATATTTA 196 GTGAATTGTAGAAACGTGAACTGTTGATCATAAACTCTATAACTGTGTCCTTAACCATATATTTA 301602 TTTTATTTGTATATCAATGCTCAGTATTCATGTACATAAAAAGAATTATAATAAATAGGTGATCT 261 TTTTATTTGTATATCAATGCTCAGTATTCATGTACATAAAAAGAATTATAATAAATAGGTGATCT 301667 ACCA 326 ACCA 301671 NTTTTATTTTCTTTGATGTAATTGTGGATATCACTTGAGGATGCAATAGTTATAAGCAATGCTTT 1 -TTTTATTTTCTTTGATGTAATTGTGGATATCACTTGAGGATGCAATAGTTATAAGCAATGCTTT 301736 TTTTCTTTTCTTTGTCCTGTTATAAAATCTGCTTATGATGTGTTTCTATTTATTCCAGTGTATTT 65 TTTTCTTTTCTTTGTCCTGTTATAAAATCTGCTTATGATGTGTTTCTATTTATTCCAGTGTATTT 301801 GTGAAAAGTGACACAGACGACAGAAAGGGGTTCTCTAGCGATCATTTCTAGCCAAGGATTATGCT 130 GTGAAAAGTGACACAGACGACAGAAAGGGGTTCTCTAGCGATCATTTCTAGCCAAGGATTATGCT 301866 CGTGAATTGTAGAAACGTGAACTGTTGATCATAAACTCTATAACTGTGTCCTTAACCATATATTT 195 CGTGAATTGTAGAAACGTGAACTGTTGATCATAAACTCTATAACTGTGTCCTTAACCATATATTT 301931 ATTTTATTTGTATATCAATGCTCAGTATTCATGTACATAAAAAGAATTATAATAAATAGGTGATC 260 ATTTTATTTGTATATCAATGCTCAGTATTCATGTACATAAAAAGAATTATAATAAATAGGTGATC 301996 TACCA 325 TACCA 302001 GTATTAGTTA Statistics Matches: 329, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 330 329 1.00 ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39 Consensus pattern (329 bp): TTTTATTTTCTTTGATGTAATTGTGGATATCACTTGAGGATGCAATAGTTATAAGCAATGCTTTT TTTCTTTTCTTTGTCCTGTTATAAAATCTGCTTATGATGTGTTTCTATTTATTCCAGTGTATTTG TGAAAAGTGACACAGACGACAGAAAGGGGTTCTCTAGCGATCATTTCTAGCCAAGGATTATGCTC GTGAATTGTAGAAACGTGAACTGTTGATCATAAACTCTATAACTGTGTCCTTAACCATATATTTA TTTTATTTGTATATCAATGCTCAGTATTCATGTACATAAAAAGAATTATAATAAATAGGTGATCT ACCA Found at i:309458 original size:27 final size:26 Alignment explanation

Indices: 309429--309483 Score: 83 Period size: 27 Copynumber: 2.1 Consensus size: 26 309419 GGGGGGGTGT * * 309429 TTGTTTTTGTTTTTTTGTTTTTTGTTT 1 TTGTTTTTGTTTTTGT-TTTTTTGGTT 309456 TTGTTTTTGTTTTTGTTTTTTTGGTT 1 TTGTTTTTGTTTTTGTTTTTTTGGTT 309482 TT 1 TT 309484 CAGTTTTGTG Statistics Matches: 26, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 26 11 0.42 27 15 0.58 ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84 Consensus pattern (26 bp): TTGTTTTTGTTTTTGTTTTTTTGGTT Found at i:309483 original size:6 final size:6 Alignment explanation

Indices: 309428--309475 Score: 69 Period size: 6 Copynumber: 7.5 Consensus size: 6 309418 GGGGGGGGTG 309428 TTTGTT TTTGTTTT TTTGTTT TTTGTT TTTGTT TTTGTT TTTGTT TTT 1 TTTGTT TTTG--TT TTTG-TT TTTGTT TTTGTT TTTGTT TTTGTT TTT 309476 TTGGTTTTCA Statistics Matches: 40, Mismatches: 0, Indels: 4 0.91 0.00 0.09 Matches are distributed among these distances: 6 27 0.68 7 7 0.17 8 6 0.15 ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85 Consensus pattern (6 bp): TTTGTT Found at i:309490 original size:27 final size:27 Alignment explanation

Indices: 309431--309495 Score: 78 Period size: 27 Copynumber: 2.3 Consensus size: 27 309421 GGGGGTGTTT * * 309431 GTTTTTGTTTTTTTGTTTTTTGTTTTT 1 GTTTTTGTTTTTTTGTTTTTGGTTTTA 309458 GTTTTTGTTTTTGTT-TTTTTGGTTTTCA 1 GTTTTTGTTTTT-TTGTTTTTGGTTTT-A 309486 GTTTTGTGTT 1 GTTTT-TGTT 309496 GCATGTTGAT Statistics Matches: 33, Mismatches: 2, Indels: 4 0.85 0.05 0.10 Matches are distributed among these distances: 27 22 0.67 28 7 0.21 29 4 0.12 ACGTcount: A:0.02, C:0.02, G:0.18, T:0.78 Consensus pattern (27 bp): GTTTTTGTTTTTTTGTTTTTGGTTTTA Found at i:309491 original size:33 final size:33 Alignment explanation

Indices: 309428--309495 Score: 100 Period size: 33 Copynumber: 2.0 Consensus size: 33 309418 GGGGGGGGTG ** 309428 TTTGTTTTTGTTTTTTTGTTTTTTGTTTTTGTT 1 TTTGTTTTTGTTTTTTTGTTTTCAGTTTTTGTT 309461 TTTGTTTTTGTTTTTTTGGTTTTCAGTTTTGTGTT 1 TTTGTTTTTGTTTTTTT-GTTTTCAGTTTT-TGTT 309496 GCATGTTGAT Statistics Matches: 31, Mismatches: 2, Indels: 2 0.89 0.06 0.06 Matches are distributed among these distances: 33 17 0.55 34 10 0.32 35 4 0.13 ACGTcount: A:0.01, C:0.01, G:0.18, T:0.79 Consensus pattern (33 bp): TTTGTTTTTGTTTTTTTGTTTTCAGTTTTTGTT Found at i:310632 original size:21 final size:21 Alignment explanation

Indices: 310526--310621 Score: 183 Period size: 21 Copynumber: 4.6 Consensus size: 21 310516 TCAATCACCC 310526 CAAGGCTATGCCGCACCCCAA 1 CAAGGCTATGCCGCACCCCAA * 310547 CAAGGCTATGCTGCACCCCAA 1 CAAGGCTATGCCGCACCCCAA 310568 CAAGGCTATGCCGCACCCCAA 1 CAAGGCTATGCCGCACCCCAA 310589 CAAGGCTATGCCGCACCCCAA 1 CAAGGCTATGCCGCACCCCAA 310610 CAAGGCTATGCC 1 CAAGGCTATGCC 310622 CCATCTCAAC Statistics Matches: 73, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 21 73 1.00 ACGTcount: A:0.28, C:0.41, G:0.20, T:0.11 Consensus pattern (21 bp): CAAGGCTATGCCGCACCCCAA Found at i:311924 original size:21 final size:21 Alignment explanation

Indices: 311900--311939 Score: 55 Period size: 21 Copynumber: 1.9 Consensus size: 21 311890 CATCATTACG 311900 AAATTTGTTATCATT-TTTATC 1 AAATTT-TTATCATTCTTTATC * 311921 AAATTTTTTTCATTCTTTA 1 AAATTTTTATCATTCTTTA 311940 ATGTCGTTTG Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 20 7 0.41 21 10 0.59 ACGTcount: A:0.28, C:0.10, G:0.03, T:0.60 Consensus pattern (21 bp): AAATTTTTATCATTCTTTATC Found at i:315127 original size:21 final size:21 Alignment explanation

Indices: 315103--315212 Score: 143 Period size: 21 Copynumber: 5.2 Consensus size: 21 315093 AGGGTACCCC * 315103 CCGCCCCAACAGGGCTATGGT 1 CCGCCCCAACAGGGGTATGGT * 315124 CCGCCCCAACAGGGTTATGGT 1 CCGCCCCAACAGGGGTATGGT * 315145 CCGCCCCAACAGGGTTATGGT 1 CCGCCCCAACAGGGGTATGGT * 315166 CCGCCACC-ACAGGGGTACGGT 1 CCGCC-CCAACAGGGGTATGGT * 315187 CCGCCACC-ACAGGGGTACGGT 1 CCGCC-CCAACAGGGGTATGGT 315208 CCGCC 1 CCGCC 315213 GCCACAAGGC Statistics Matches: 85, Mismatches: 3, Indels: 2 0.94 0.03 0.02 Matches are distributed among these distances: 21 83 0.98 22 2 0.02 ACGTcount: A:0.18, C:0.38, G:0.30, T:0.14 Consensus pattern (21 bp): CCGCCCCAACAGGGGTATGGT Found at i:320928 original size:11 final size:11 Alignment explanation

Indices: 320909--320940 Score: 55 Period size: 11 Copynumber: 2.9 Consensus size: 11 320899 TTTTAAAAAA 320909 TGGCTTAAAGG 1 TGGCTTAAAGG * 320920 TGTCTTAAAGG 1 TGGCTTAAAGG 320931 TGGCTTAAAG 1 TGGCTTAAAG 320941 AAGTTTGGAC Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 11 19 1.00 ACGTcount: A:0.28, C:0.09, G:0.31, T:0.31 Consensus pattern (11 bp): TGGCTTAAAGG Found at i:320988 original size:11 final size:11 Alignment explanation

Indices: 320972--321000 Score: 58 Period size: 11 Copynumber: 2.6 Consensus size: 11 320962 ATAAGTCCTC 320972 CTTAAAGGTGG 1 CTTAAAGGTGG 320983 CTTAAAGGTGG 1 CTTAAAGGTGG 320994 CTTAAAG 1 CTTAAAG 321001 ACAGTCTTTA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28 Consensus pattern (11 bp): CTTAAAGGTGG Found at i:321022 original size:11 final size:11 Alignment explanation

Indices: 321006--321081 Score: 109 Period size: 11 Copynumber: 7.0 Consensus size: 11 320996 TAAAGACAGT * 321006 CTTTAAGCCGC 1 CTTTAAGCCAC * 321017 CTTTAAG-GAC 1 CTTTAAGCCAC * 321027 CTTTAAGCCAT 1 CTTTAAGCCAC * 321038 CTTTAAGTCAC 1 CTTTAAGCCAC 321049 CTTTAAGCCAC 1 CTTTAAGCCAC 321060 CTTTAAGCCAC 1 CTTTAAGCCAC 321071 CTTTAAGCCAC 1 CTTTAAGCCAC 321082 ATTGAAACTT Statistics Matches: 57, Mismatches: 7, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 10 8 0.14 11 49 0.86 ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:321147 original size:10 final size:10 Alignment explanation

Indices: 321123--321161 Score: 60 Period size: 11 Copynumber: 3.7 Consensus size: 10 321113 TAAAGACCGT 321123 CTTTAAGCTAC 1 CTTTAAGC-AC 321134 CTTTAAGCAC 1 CTTTAAGCAC 321144 CTTTAAGCCAC 1 CTTTAAG-CAC 321155 CTTTAAG 1 CTTTAAG 321162 GAGAACTTAA Statistics Matches: 27, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 10 9 0.33 11 18 0.67 ACGTcount: A:0.28, C:0.28, G:0.10, T:0.33 Consensus pattern (10 bp): CTTTAAGCAC Found at i:326972 original size:19 final size:19 Alignment explanation

Indices: 326950--326986 Score: 58 Period size: 19 Copynumber: 1.9 Consensus size: 19 326940 CTTTTTTTTT 326950 TCTTTTTGA-ATTTTATTAG 1 TCTTTTT-ATATTTTATTAG 326969 TCTTTTTATATTTTATTA 1 TCTTTTTATATTTTATTA 326987 TTTTTATTTT Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 18 1 0.06 19 16 0.94 ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68 Consensus pattern (19 bp): TCTTTTTATATTTTATTAG Found at i:329223 original size:2 final size:2 Alignment explanation

Indices: 329216--329254 Score: 78 Period size: 2 Copynumber: 19.5 Consensus size: 2 329206 CTGATTTCAA 329216 CT CT CT 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 CT CT CT C 329255 GCAGTTCTTA Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 37 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:333068 original size:1 final size:1 Alignment explanation

Indices: 333064--333093 Score: 51 Period size: 1 Copynumber: 30.0 Consensus size: 1 333054 CCCCCCCCCC * 333064 AAAAAAAAAAAAAATAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 333094 CAAACCAAAC Statistics Matches: 27, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 1 27 1.00 ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03 Consensus pattern (1 bp): A Found at i:333084 original size:15 final size:15 Alignment explanation

Indices: 333064--333092 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 333054 CCCCCCCCCC 333064 AAAAAAAAAAAAAAT 1 AAAAAAAAAAAAAAT 333079 AAAAAAAAAAAAAA 1 AAAAAAAAAAAAAA 333093 ACAAACCAAA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03 Consensus pattern (15 bp): AAAAAAAAAAAAAAT Found at i:343394 original size:1 final size:1 Alignment explanation

Indices: 343390--343423 Score: 68 Period size: 1 Copynumber: 34.0 Consensus size: 1 343380 TTGGTTGTTG 343390 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 343424 GTAGTTGGGG Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 33 1.00 ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00 Consensus pattern (1 bp): T Done.