Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_D12

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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33

Warning! 639818 characters in sequence are not A, C, G, or T


File 29 of 196

Found at i:8160695 original size:23 final size:23

Alignment explanation

Indices: 8160665--8160717 Score: 97 Period size: 23 Copynumber: 2.3 Consensus size: 23 8160655 TATCGGATTC 8160665 TTTGGATTTCGGTTGAATTTGCA 1 TTTGGATTTCGGTTGAATTTGCA 8160688 TTTGGATTTCGGTTGAATTTGCA 1 TTTGGATTTCGGTTGAATTTGCA * 8160711 TTCGGAT 1 TTTGGAT 8160718 CGAGCATATC Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 23 29 1.00 ACGTcount: A:0.17, C:0.09, G:0.26, T:0.47 Consensus pattern (23 bp): TTTGGATTTCGGTTGAATTTGCA Found at i:8165358 original size:31 final size:31 Alignment explanation

Indices: 8165316--8165921 Score: 411 Period size: 31 Copynumber: 19.8 Consensus size: 31 8165306 ATCCAATGCT * * ** 8165316 CAAATC-AATTCAACAATATATATTCATATA 1 CAAATCAAATTCAGCAATGTATAACCATATA * * 8165346 CGAATCAAATTCAGCAATGTATAATCATATA 1 CAAATCAAATTCAGCAATGTATAACCATATA ** 8165377 CAAATC-AATTTGGCAATGTATAACCATATA 1 CAAATCAAATTCAGCAATGTATAACCATATA ** * * * * 8165407 TGAATCAAGTTCGGCAATTTTATAATCATATA 1 CAAATCAAATTCAGCAA-TGTATAACCATATA * * * 8165439 CAAAT-TAATTCGGCAACT-TATATCCATATA 1 CAAATCAAATTCAGCAA-TGTATAACCATATA * * * 8165469 CAATTCAATTTCAACAATGTATAACCATATA 1 CAAATCAAATTCAGCAATGTATAACCATATA * * * * 8165500 CAAATTAATTTCAGCAAAGTATAATCATATA 1 CAAATCAAATTCAGCAATGTATAACCATATA ** ** 8165531 TGAATC-AATTC-GTCAACT-TATATTCATATA 1 CAAATCAAATTCAG-CAA-TGTATAACCATATA * * 8165561 CAAATCAATTTC-GATAATGTATAACCATATA 1 CAAATCAAATTCAG-CAATGTATAACCATATA * * 8165592 CAAAT-AAATTTCAGTAATGTACAACCATATA 1 CAAATCAAA-TTCAGCAATGTATAACCATATA * * * 8165623 CGAAT-TAATTCAGCAACT-TATATCCATATA 1 CAAATCAAATTCAGCAA-TGTATAACCATATA * * * 8165653 CAATTCAATTTCAACAATGTATAACCATATA 1 CAAATCAAATTCAGCAATGTATAACCATATA * * ** 8165684 CAAATTAATTTCAGCAATGTATAATTATATA 1 CAAATCAAATTCAGCAATGTATAACCATATA * * * *** 8165715 CGAAT-TAATTCGGCAACT-TATCTTCATATA 1 CAAATCAAATTCAGCAA-TGTATAACCATATA * * 8165745 CAAATCAATTTC-GATAATGTATAACCATATA 1 CAAATCAAATTCAG-CAATGTATAACCATATA * 8165776 CAAAT-AAATTTCAGCAATGTACAACCATATA 1 CAAATCAAA-TTCAGCAATGTATAACCATATA * * * 8165807 CGAAT-TAATTCAGCAACT-TATATCCATATA 1 CAAATCAAATTCAGCAA-TGTATAACCATATA * * * 8165837 CAATTCAATTTCAACAATGTATAACCATATA 1 CAAATCAAATTCAGCAATGTATAACCATATA * * ** 8165868 CAAATTAATTTCAGCAATGTATAATTATATA 1 CAAATCAAATTCAGCAATGTATAACCATATA * * * 8165899 CAAAT-TAATTCGGCAATATATAA 1 CAAATCAAATTCAGCAATGTATAA 8165922 AACAATCAAA Statistics Matches: 454, Mismatches: 99, Indels: 46 0.76 0.17 0.08 Matches are distributed among these distances: 29 1 0.00 30 152 0.33 31 284 0.63 32 17 0.04 ACGTcount: A:0.44, C:0.17, G:0.07, T:0.33 Consensus pattern (31 bp): CAAATCAAATTCAGCAATGTATAACCATATA Found at i:8165911 original size:184 final size:184 Alignment explanation

Indices: 8165332--8165914 Score: 900 Period size: 184 Copynumber: 3.2 Consensus size: 184 8165322 AATTCAACAA * * * ** 8165332 TATATATTCATATACGAATCAAATTCAGCAA-TGTATAATCATATACAAATCAATTT-GGCAATG 1 TATA-ATT-ATATACGAAT-TAATTCGGCAACT-TATATTCATATACAAATCAATTTCGATAATG ** * * * * * * * * 8165395 TATAACCATATATGAATCAAGTTCGGCAATTTTATAATCATATACAAATTAATTCGGCAACTTAT 62 TATAACCATATACAAATAAATTTCAGCAA-TGTACAACCATATACGAATTAATTCAGCAACTTAT * 8165460 ATCCATATACAATTCAATTTCAACAATGTATAACCATATACAAATTAATTTCAGCAAAG 126 ATCCATATACAATTCAATTTCAACAATGTATAACCATATACAAATTAATTTCAGCAATG * * * * 8165519 TATAATCATATATGAATCAATTCGTCAACTTATATTCATATACAAATCAATTTCGATAATGTATA 1 TATAATTATATACGAATTAATTCGGCAACTTATATTCATATACAAATCAATTTCGATAATGTATA * 8165584 ACCATATACAAATAAATTTCAGTAATGTACAACCATATACGAATTAATTCAGCAACTTATATCCA 66 ACCATATACAAATAAATTTCAGCAATGTACAACCATATACGAATTAATTCAGCAACTTATATCCA 8165649 TATACAATTCAATTTCAACAATGTATAACCATATACAAATTAATTTCAGCAATG 131 TATACAATTCAATTTCAACAATGTATAACCATATACAAATTAATTTCAGCAATG * 8165703 TATAATTATATACGAATTAATTCGGCAACTTATCTTCATATACAAATCAATTTCGATAATGTATA 1 TATAATTATATACGAATTAATTCGGCAACTTATATTCATATACAAATCAATTTCGATAATGTATA 8165768 ACCATATACAAATAAATTTCAGCAATGTACAACCATATACGAATTAATTCAGCAACTTATATCCA 66 ACCATATACAAATAAATTTCAGCAATGTACAACCATATACGAATTAATTCAGCAACTTATATCCA 8165833 TATACAATTCAATTTCAACAATGTATAACCATATACAAATTAATTTCAGCAATG 131 TATACAATTCAATTTCAACAATGTATAACCATATACAAATTAATTTCAGCAATG * 8165887 TATAATTATATACAAATTAATTCGGCAA 1 TATAATTATATACGAATTAATTCGGCAA 8165915 TATATAAAAC Statistics Matches: 367, Mismatches: 27, Indels: 7 0.92 0.07 0.02 Matches are distributed among these distances: 184 323 0.88 185 38 0.10 186 2 0.01 187 4 0.01 ACGTcount: A:0.43, C:0.16, G:0.07, T:0.33 Consensus pattern (184 bp): TATAATTATATACGAATTAATTCGGCAACTTATATTCATATACAAATCAATTTCGATAATGTATA ACCATATACAAATAAATTTCAGCAATGTACAACCATATACGAATTAATTCAGCAACTTATATCCA TATACAATTCAATTTCAACAATGTATAACCATATACAAATTAATTTCAGCAATG Found at i:8165934 original size:92 final size:92 Alignment explanation

Indices: 8165316--8165914 Score: 765 Period size: 92 Copynumber: 6.5 Consensus size: 92 8165306 ATCCAATGCT * * * * * * 8165316 CAAATCAA-TTCAACAATATATATTCATATACGAATCAAATTCAGCAA-TGTATAAT-CATATAC 1 CAAATTAATTTCAGCAATGTATAATCATATACGAAT-TAATTCGGCAACT-TAT-ATCCATATAC * ** 8165378 AAATCAATTT-GGCAATGTATAACCATATA 63 AATTCAATTTCAACAATGTATAACCATATA ** * * * * * 8165407 TGAATCAAGTTCGGCAATTTTATAATCATATACAAATTAATTCGGCAACTTATATCCATATACAA 1 CAAATTAATTTCAGCAA-TGTATAATCATATACGAATTAATTCGGCAACTTATATCCATATACAA 8165472 TTCAATTTCAACAATGTATAACCATATA 65 TTCAATTTCAACAATGTATAACCATATA * * * * * * 8165500 CAAATTAATTTCAGCAAAGTATAATCATATATGAATCAATTCGTCAACTTATATTCATATACAAA 1 CAAATTAATTTCAGCAATGTATAATCATATACGAATTAATTCGGCAACTTATATCCATATACAAT * * 8165565 TCAATTTCGATAATGTATAACCATATA 66 TCAATTTCAACAATGTATAACCATATA * * * * * 8165592 CAAATAAATTTCAGTAATGTACAACCATATACGAATTAATTCAGCAACTTATATCCATATACAAT 1 CAAATTAATTTCAGCAATGTATAATCATATACGAATTAATTCGGCAACTTATATCCATATACAAT 8165657 TCAATTTCAACAATGTATAACCATATA 66 TCAATTTCAACAATGTATAACCATATA * * * * 8165684 CAAATTAATTTCAGCAATGTATAATTATATACGAATTAATTCGGCAACTTATCTTCATATACAAA 1 CAAATTAATTTCAGCAATGTATAATCATATACGAATTAATTCGGCAACTTATATCCATATACAAT * * 8165749 TCAATTTCGATAATGTATAACCATATA 66 TCAATTTCAACAATGTATAACCATATA * * * * 8165776 CAAATAAATTTCAGCAATGTACAACCATATACGAATTAATTCAGCAACTTATATCCATATACAAT 1 CAAATTAATTTCAGCAATGTATAATCATATACGAATTAATTCGGCAACTTATATCCATATACAAT 8165841 TCAATTTCAACAATGTATAACCATATA 66 TCAATTTCAACAATGTATAACCATATA * * 8165868 CAAATTAATTTCAGCAATGTATAATTATATACAAATTAATTCGGCAA 1 CAAATTAATTTCAGCAATGTATAATCATATACGAATTAATTCGGCAA 8165915 TATATAAAAC Statistics Matches: 436, Mismatches: 67, Indels: 9 0.85 0.13 0.02 Matches are distributed among these distances: 91 8 0.02 92 382 0.88 93 46 0.11 ACGTcount: A:0.44, C:0.17, G:0.07, T:0.33 Consensus pattern (92 bp): CAAATTAATTTCAGCAATGTATAATCATATACGAATTAATTCGGCAACTTATATCCATATACAAT TCAATTTCAACAATGTATAACCATATA Found at i:8172292 original size:13 final size:12 Alignment explanation

Indices: 8172261--8172294 Score: 52 Period size: 11 Copynumber: 2.8 Consensus size: 12 8172251 AAAGAATTAC 8172261 TATAGAAATTCT 1 TATAGAAATTCT 8172273 T-TAGAAATTCTT 1 TATAGAAATTC-T 8172285 TATAGAAATT 1 TATAGAAATT 8172295 GATATCCTTG Statistics Matches: 20, Mismatches: 0, Indels: 3 0.87 0.00 0.13 Matches are distributed among these distances: 11 9 0.45 12 3 0.15 13 8 0.40 ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44 Consensus pattern (12 bp): TATAGAAATTCT Found at i:8172763 original size:10 final size:10 Alignment explanation

Indices: 8172709--8172763 Score: 56 Period size: 10 Copynumber: 5.2 Consensus size: 10 8172699 CCTTTCAAAT * 8172709 AATTTTAAAA 1 AATTTTTAAA * 8172719 AAGTTTTAAA 1 AATTTTTAAA * 8172729 ATTTTTTAAA 1 AATTTTTAAA 8172739 TATATTTGTTAAA 1 -A-ATTT-TTAAA 8172752 AATTTTTAAA 1 AATTTTTAAA 8172762 AA 1 AA 8172764 ATTCTATATG Statistics Matches: 37, Mismatches: 5, Indels: 6 0.77 0.10 0.12 Matches are distributed among these distances: 10 23 0.62 11 5 0.14 12 4 0.11 13 5 0.14 ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47 Consensus pattern (10 bp): AATTTTTAAA Found at i:8172763 original size:11 final size:11 Alignment explanation

Indices: 8172711--8172766 Score: 53 Period size: 11 Copynumber: 5.1 Consensus size: 11 8172701 TTTCAAATAA * 8172711 TTTTAAAAAAG 1 TTTTAAAAAAT * 8172722 TTTT-AAAATT 1 TTTTAAAAAAT * 8172732 TTTTAAATATAT 1 TTTTAAA-AAAT 8172744 TTGTT-AAAAAT 1 TT-TTAAAAAAT 8172755 TTTTAAAAAAT 1 TTTTAAAAAAT 8172766 T 1 T 8172767 CTATATGAAA Statistics Matches: 36, Mismatches: 5, Indels: 8 0.73 0.10 0.16 Matches are distributed among these distances: 10 10 0.28 11 18 0.50 12 6 0.17 13 2 0.06 ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50 Consensus pattern (11 bp): TTTTAAAAAAT Found at i:8178326 original size:22 final size:24 Alignment explanation

Indices: 8178298--8178341 Score: 65 Period size: 22 Copynumber: 1.9 Consensus size: 24 8178288 ATTTTGTTCA 8178298 ACTTTAACTT-TTAT-TCAAAAAC 1 ACTTTAACTTGTTATATCAAAAAC * 8178320 ACTTTAATTTGTTATATCAAAA 1 ACTTTAACTTGTTATATCAAAA 8178342 CATATTATCA Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 22 9 0.47 23 4 0.21 24 6 0.32 ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43 Consensus pattern (24 bp): ACTTTAACTTGTTATATCAAAAAC Found at i:8181723 original size:25 final size:25 Alignment explanation

Indices: 8181663--8181733 Score: 72 Period size: 25 Copynumber: 2.8 Consensus size: 25 8181653 AATTGGATCG * 8181663 CAAGAGCTTCCCGTTATATGGCTCA 1 CAAGAGCTTCCCGTTACATGGCTCA * * * 8181688 CATGAGGTTCCCGTTACATGGGTCGA 1 CAAGAGCTTCCCGTTACATGGCTC-A * 8181714 -AAGAGCTTCCTGATTACATG 1 CAAGAGCTTCCCG-TTACATG 8181734 CTCGTATGGG Statistics Matches: 37, Mismatches: 7, Indels: 3 0.79 0.15 0.06 Matches are distributed among these distances: 25 29 0.78 26 8 0.22 ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28 Consensus pattern (25 bp): CAAGAGCTTCCCGTTACATGGCTCA Found at i:8191959 original size:31 final size:31 Alignment explanation

Indices: 8191916--8191987 Score: 103 Period size: 31 Copynumber: 2.4 Consensus size: 31 8191906 TCATTGTATG * 8191916 ATTTGTCTTTTTTTTTCTTTTTGACAGTT-A 1 ATTTTTCTTTTTTTTTCTTTTTGACAGTTCA * 8191946 AGTTTTTCTTTTTTTTTCTTTTTGGCAGTTCA 1 A-TTTTTCTTTTTTTTTCTTTTTGACAGTTCA 8191978 ATTTTT-TTTT 1 ATTTTTCTTTT 8191988 ATAAATCAGT Statistics Matches: 38, Mismatches: 2, Indels: 4 0.86 0.05 0.09 Matches are distributed among these distances: 30 5 0.13 31 31 0.82 32 2 0.05 ACGTcount: A:0.11, C:0.10, G:0.10, T:0.69 Consensus pattern (31 bp): ATTTTTCTTTTTTTTTCTTTTTGACAGTTCA Found at i:8192992 original size:16 final size:16 Alignment explanation

Indices: 8192948--8193004 Score: 53 Period size: 16 Copynumber: 3.4 Consensus size: 16 8192938 AAAACATATT 8192948 TAAAAAT-TCAAAAAAA 1 TAAAAATAT-AAAAAAA 8192964 TAATAACAGTATAAAAAAA 1 TAA-AA-A-TATAAAAAAA * * 8192983 TAAAAATATATAAAAC 1 TAAAAATATAAAAAAA 8192999 TAAAAA 1 TAAAAA 8193005 AATCTTTCAA Statistics Matches: 35, Mismatches: 2, Indels: 8 0.78 0.04 0.18 Matches are distributed among these distances: 16 17 0.49 17 3 0.09 18 3 0.09 19 11 0.31 20 1 0.03 ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21 Consensus pattern (16 bp): TAAAAATATAAAAAAA Found at i:8201388 original size:21 final size:21 Alignment explanation

Indices: 8201362--8201402 Score: 73 Period size: 21 Copynumber: 2.0 Consensus size: 21 8201352 TTTAAGAAAA * 8201362 CTGAAAAACTATTCTAATTGC 1 CTGAAAAACTAGTCTAATTGC 8201383 CTGAAAAACTAGTCTAATTG 1 CTGAAAAACTAGTCTAATTG 8201403 TTGATAAGTA Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 19 1.00 ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32 Consensus pattern (21 bp): CTGAAAAACTAGTCTAATTGC Found at i:8203970 original size:83 final size:84 Alignment explanation

Indices: 8203863--8204030 Score: 266 Period size: 84 Copynumber: 2.0 Consensus size: 84 8203853 GAAAAATAAT * * 8203863 TCCTTCAAACTAGGAAAAAACAAACTCATCATCTTTTCCA-CCCAAGGTACCATCAAACATGTCA 1 TCCTTCAAACTAGGAAAAAACAAACTCATCATATTCTCCACCCCAAGGTACCATCAAACATGTCA * * 8203927 TATTTTCTCATACTAAACC 66 TACTGTCTCATACTAAACC * * 8203946 TCCTTCAAACTAGGAAAAAACAAACTCATCATATTCTCCACCCCAAGGTACCGTCAAATATGTCA 1 TCCTTCAAACTAGGAAAAAACAAACTCATCATATTCTCCACCCCAAGGTACCATCAAACATGTCA * 8204011 TACTGTCTCATACTGAACC 66 TACTGTCTCATACTAAACC 8204030 T 1 T 8204031 ATTTCAATCC Statistics Matches: 77, Mismatches: 7, Indels: 1 0.91 0.08 0.01 Matches are distributed among these distances: 83 38 0.49 84 39 0.51 ACGTcount: A:0.36, C:0.29, G:0.08, T:0.27 Consensus pattern (84 bp): TCCTTCAAACTAGGAAAAAACAAACTCATCATATTCTCCACCCCAAGGTACCATCAAACATGTCA TACTGTCTCATACTAAACC Found at i:8205896 original size:2 final size:2 Alignment explanation

Indices: 8205889--8205927 Score: 78 Period size: 2 Copynumber: 19.5 Consensus size: 2 8205879 TCTTAACCAG 8205889 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 8205928 TTACCATCAC Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 37 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:8209119 original size:31 final size:30 Alignment explanation

Indices: 8209084--8209163 Score: 112 Period size: 31 Copynumber: 2.7 Consensus size: 30 8209074 ATAATCCCTG 8209084 AAATTAATTAAATCCTTC-TAAAATAATTAAA 1 AAATTAATTAAATCCTTCATAAAATAA--AAA 8209115 AAATTAATTAAAT-CTTCATAAAATAAAAA 1 AAATTAATTAAATCCTTCATAAAATAAAAA 8209144 ATAA-TAATTAAATCCTTCAT 1 A-AATTAATTAAATCCTTCAT 8209164 TAACATTTTT Statistics Matches: 46, Mismatches: 0, Indels: 7 0.87 0.00 0.13 Matches are distributed among these distances: 29 13 0.28 30 12 0.26 31 21 0.46 ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35 Consensus pattern (30 bp): AAATTAATTAAATCCTTCATAAAATAAAAA Found at i:8213875 original size:112 final size:115 Alignment explanation

Indices: 8213754--8214088 Score: 295 Period size: 114 Copynumber: 2.9 Consensus size: 115 8213744 CGCTTTCTCC * ** 8213754 AAAGCGCCAC-AAAAGTTTT-ATCAAACGACGTCG-TTTCCATGTTGAGGTTTAGACACATTAGT 1 AAAGCGCCACAAAAAGTTTTAAGCAAACGACGTCGTTTTCC-TGTTGAGCATTAGACACATTAGT * * ** 8213816 GGCGCTTTACATAAAACGCTGCGTAAGTCAAA-CATTAGCGGCGATTAAGG 65 GGCGCTTTACAAAAAACGCCGCAAAAGTCAAAGCATTAGCGGCGATTAAGG * * * 8213866 AAAGCGCCACAAAAAGTTTTAAGCAAACGCCGTCGTTTTTCTGTTGAGCATTAGAGACATTAGTG 1 AAAGCGCCACAAAAAGTTTTAAGCAAACGACGTCGTTTTCCTGTTGAGCATTAGACACATTAGTG * * * * *** 8213931 GCGCTTTGCAAAAAATGCCGCAAAAGTCAAAGCATTAGCAGCGCTTTCTCG 66 GCGCTTTACAAAAAACGCCGCAAAAGTCAAAGCATTAGCGGCG-ATTAAGG * * * * ** * * ** * 8213982 AAAGTGCCAC-AATAGTTTTAGGCAAACGACGACGTTTTTTTTTTTAAAATTTAGAGACATTAGT 1 AAAGCGCCACAAAAAGTTTTAAGCAAACGACGTCGTTTTCCTGTTGAGCA-TTAGACACATTAGT * * * ** * 8214046 GGAGCATTCCTCAAAACGCCGCAAAAGTC-AAGAATTAGCGGCG 65 GGCGCTTTACAAAAAACGCCGCAAAAGTCAAAGCATTAGCGGCG 8214089 CTTTCGCAAA Statistics Matches: 182, Mismatches: 35, Indels: 9 0.81 0.15 0.04 Matches are distributed among these distances: 112 10 0.05 113 9 0.05 114 58 0.32 115 56 0.31 116 49 0.27 ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26 Consensus pattern (115 bp): AAAGCGCCACAAAAAGTTTTAAGCAAACGACGTCGTTTTCCTGTTGAGCATTAGACACATTAGTG GCGCTTTACAAAAAACGCCGCAAAAGTCAAAGCATTAGCGGCGATTAAGG Found at i:8213893 original size:114 final size:114 Alignment explanation

Indices: 8213582--8214018 Score: 314 Period size: 114 Copynumber: 3.9 Consensus size: 114 8213572 AGCTTCAAAG * * * * * * * 8213582 ACATTAGTGGCGCTTCA-AACAAAACACCGCAAAAGTCAAA-CATTAGCGGTGCTTTTACAAAAG 1 ACATTAGTGGCGCTTTACAA-AAAACGCCGCAAAAGTCAAAGCATTAGCAGCGCATTAACGAAAG * * * * * * ** * ** * 8213645 CGCCGCAAAACTGTTAAACAGACGATGTCGTTTTAT-TTTAGGTTTAGAG 65 CGCCACAAAAGTTTTAAGCAAACGACGTCGTTTCCTGTTGAGCATTAGAC * * * * * * * ** * 8213694 ACATTAGCGGCG-TTTATAAGGAAACGCCGCAAAAGATCATA-TATTAGCGGCGCTTTCTCCAAA 1 ACATTAGTGGCGCTTTACAA-AAAACGCCGCAAAAG-TCAAAGCATTAGCAGCGCATTAACGAAA * ** 8213757 GCGCCACAAAAGTTTT-ATCAAACGACGTCGTTTCCATGTTGAGGTTTAGAC 64 GCGCCACAAAAGTTTTAAGCAAACGACGTCGTTTCC-TGTTGAGCATTAGAC * * ** * * 8213808 ACATTAGTGGCGCTTTACATAAAACGCTGCGTAAGTCAAA-CATTAGCGGCG-ATTAAGGAAAGC 1 ACATTAGTGGCGCTTTACAAAAAACGCCGCAAAAGTCAAAGCATTAGCAGCGCATTAACGAAAGC * * * 8213871 GCCACAAAAAGTTTTAAGCAAACGCCGTCGTTTTTCTGTTGAGCATTAGAG 66 GCCAC-AAAAGTTTTAAGCAAACGACGTCG-TTTCCTGTTGAGCATTAGAC * * * ** * 8213922 ACATTAGTGGCGCTTTGCAAAAAATGCCGCAAAAGTCAAAGCATTAGCAGCGCTTTCTCGAAAGT 1 ACATTAGTGGCGCTTTACAAAAAACGCCGCAAAAGTCAAAGCATTAGCAGCGCATTAACGAAAGC * * * 8213987 GCCACAATAGTTTTAGGCAAACGACGACGTTT 66 GCCACAAAAGTTTTAAGCAAACGACGTCGTTT 8214019 TTTTTTTTAA Statistics Matches: 258, Mismatches: 57, Indels: 18 0.77 0.17 0.05 Matches are distributed among these distances: 111 3 0.01 112 52 0.20 113 58 0.22 114 94 0.36 115 39 0.15 116 12 0.05 ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25 Consensus pattern (114 bp): ACATTAGTGGCGCTTTACAAAAAACGCCGCAAAAGTCAAAGCATTAGCAGCGCATTAACGAAAGC GCCACAAAAGTTTTAAGCAAACGACGTCGTTTCCTGTTGAGCATTAGAC Found at i:8214037 original size:116 final size:114 Alignment explanation

Indices: 8213580--8214302 Score: 405 Period size: 115 Copynumber: 6.3 Consensus size: 114 8213570 TGAGCTTCAA * * * * 8213580 AGACATTAGTGGCGCTTCA-AACAAAACACCGCAAAAGTCAAACATTAGCGGTGCTTT-TACAAA 1 AGACATTAGTGGCGCTTTACAA-AAAACGCCGCAAAAGTCAAACATTAGCGGCGCTTTCT-CGAA * * * * * * * ** 8213643 AGCGCCGCAAAACTGTTAAACAGACGATGTCG-TTTT-ATTTT-AGGTTTAG 64 AGCGCCACAAAAGT-TTTAGCAAACGACGTCGTTTTTCTTTTTAAAATTTAG * * * * * * 8213692 AGACATTAGCGGCG-TTTATAAGGAAACGCCGCAAAAGATCATATATTAGCGGCGCTTTCTCCAA 1 AGACATTAGTGGCGCTTTACAA-AAAACGCCGCAAAAG-TCAAACATTAGCGGCGCTTTCTCGAA * * * * * ** 8213756 AGCGCCACAAAAGTTTTATCAAACGACGTCG-TTTCCATGTTGAGGTTTAG 64 AGCGCCACAAAAGTTTTAGCAAACGACGTCGTTTTTCTTTTTAAAATTTAG * * * ** * *** 8213806 ACACATTAGTGGCGCTTTACATAAAACGCTGCGTAAGTCAAACATTAGCGGCG-ATTAAGGAAAG 1 AGACATTAGTGGCGCTTTACAAAAAACGCCGCAAAAGTCAAACATTAGCGGCGCTTTCTCGAAAG * * * ** 8213870 CGCCACAAAAAGTTTTAAGCAAACGCCGTCGTTTTTCTGTTGAGCA-TTAG 66 CGCCAC-AAAAGTTTT-AGCAAACGACGTCGTTTTTCTTTTTAAAATTTAG * * * 8213920 AGACATTAGTGGCGCTTTGCAAAAAATGCCGCAAAAGTCAAAGCATTAGCAGCGCTTTCTCGAAA 1 AGACATTAGTGGCGCTTTACAAAAAACGCCGCAAAAGTCAAA-CATTAGCGGCGCTTTCTCGAAA * * * * 8213985 GTGCCACAATAGTTTTAGGCAAACGACGACGTTTTTTTTTTTAAAATTTAG 65 GCGCCACAAAAGTTTTA-GCAAACGACGTCGTTTTTCTTTTTAAAATTTAG * * * ** * * 8214036 AGACATTAGTGGAGCATTCCTCAAAACGCCGCAAAAGTCAAGA-ATTAGCGGCGCTTTCGCAAAA 1 AGACATTAGTGGCGCTTTACAAAAAACGCCGCAAAAGTCAA-ACATTAGCGGCGCTTTCTCGAAA * ** ** * * ** 8214100 GCACCGTAAAAGTTTTTAAGCAAACGACAACG-TTTTGTTGTTAAGGTTTAG 65 GCGCCACAAAAG-TTTT-AGCAAACGACGTCGTTTTTCTTTTTAAAATTTAG ** * * ** * ** * * 8214151 -GCACATTAGCAGCGCAATTA-TAAAAACGCCGCAGGAGTCAAGCAGCAGTGGCGCTTTC-CCAG 1 AG-ACATTAGTGGCGC-TTTACAAAAAACGCCGCAAAAGTCAAACATTAGCGGCGCTTTCTCGA- * * * **** ** ** 8214213 AAGCGCCGCAAAAAGATTTAAGCAAACGGCGTCG-TTTTGGAGTGGATGTTTAG 63 AAGCGCCAC-AAAAG-TTTTAGCAAACGACGTCGTTTTTCTTTTTAAAATTTAG * 8214266 AGACATTAGTGGCGCTTTACAAAAAAATGCCGCAAAA 1 AGACATTAGTGGCGCTTTAC-AAAAAACGCCGCAAAA 8214303 AGTTAAGCAA Statistics Matches: 473, Mismatches: 114, Indels: 44 0.75 0.18 0.07 Matches are distributed among these distances: 111 3 0.01 112 56 0.12 113 59 0.12 114 90 0.19 115 172 0.36 116 91 0.19 117 2 0.00 ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25 Consensus pattern (114 bp): AGACATTAGTGGCGCTTTACAAAAAACGCCGCAAAAGTCAAACATTAGCGGCGCTTTCTCGAAAG CGCCACAAAAGTTTTAGCAAACGACGTCGTTTTTCTTTTTAAAATTTAG Found at i:8214114 original size:115 final size:117 Alignment explanation

Indices: 8213916--8214135 Score: 273 Period size: 116 Copynumber: 1.9 Consensus size: 117 8213906 CTGTTGAGCA * * * * * * 8213916 TTAGAGACATTAGTGGCGCTTTGCAAAAAATGCCGCAAAAGTCAAAGCATTAGCAGCGCTTTCTC 1 TTAGAGACATTAGTGGAGCATTCCAAAAAACGCCGCAAAAGTCAAAGAATTAGCAGCGCTTTCGC * ** * * * 8213981 GAAAGTGCCACAATAG-TTTTAGGCAAACGACGACGTTTTTTTTTTTAAAAT 66 AAAAGCACCACAAAAGTTTTTAAGCAAACGACAACGTTTTTTTTTTTAAAAT ** * 8214032 TTAGAGACATTAGTGGAGCATTCCTCAAAACGCCGCAAAAGTC-AAGAATTAGCGGCGCTTTCGC 1 TTAGAGACATTAGTGGAGCATTCCAAAAAACGCCGCAAAAGTCAAAGAATTAGCAGCGCTTTCGC ** 8214096 AAAAGCACCGTAAAAGTTTTTAAGCAAACGACAACGTTTT 66 AAAAGCACCACAAAAGTTTTTAAGCAAACGACAACGTTTT 8214136 GTTGTTAAGG Statistics Matches: 86, Mismatches: 17, Indels: 2 0.82 0.16 0.02 Matches are distributed among these distances: 115 28 0.33 116 58 0.67 ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26 Consensus pattern (117 bp): TTAGAGACATTAGTGGAGCATTCCAAAAAACGCCGCAAAAGTCAAAGAATTAGCAGCGCTTTCGC AAAAGCACCACAAAAGTTTTTAAGCAAACGACAACGTTTTTTTTTTTAAAAT Found at i:8214412 original size:7 final size:7 Alignment explanation

Indices: 8214393--8214425 Score: 50 Period size: 7 Copynumber: 4.7 Consensus size: 7 8214383 ATTGTTTATT 8214393 GTTTAA- 1 GTTTAAG 8214399 GTGTTAAG 1 GT-TTAAG 8214407 GTTTAAG 1 GTTTAAG 8214414 GTTTAAG 1 GTTTAAG 8214421 GTTTA 1 GTTTA 8214426 TAGTTTATAT Statistics Matches: 25, Mismatches: 0, Indels: 3 0.89 0.00 0.11 Matches are distributed among these distances: 6 2 0.08 7 21 0.84 8 2 0.08 ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45 Consensus pattern (7 bp): GTTTAAG Found at i:8214431 original size:14 final size:13 Alignment explanation

Indices: 8214393--8214432 Score: 53 Period size: 14 Copynumber: 2.8 Consensus size: 13 8214383 ATTGTTTATT 8214393 GTTTAAGTGTTAAG 1 GTTTAAGT-TTAAG 8214407 GTTTAAGGTTTAAG 1 GTTTAA-GTTTAAG 8214421 GTTTATAGTTTA 1 GTTTA-AGTTTA 8214433 TATATGTTTT Statistics Matches: 24, Mismatches: 0, Indels: 4 0.86 0.00 0.14 Matches are distributed among these distances: 14 21 0.88 15 3 0.12 ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47 Consensus pattern (13 bp): GTTTAAGTTTAAG Found at i:8214463 original size:39 final size:39 Alignment explanation

Indices: 8214411--8214498 Score: 140 Period size: 39 Copynumber: 2.3 Consensus size: 39 8214401 GTTAAGGTTT * 8214411 AAGGTTTAAGGTTTATAGTTTATATATGTTTTATGATTC 1 AAGGTTTAAGGTTTATAGTTTATATATGTTCTATGATTC * 8214450 AAGGTTTAGGGTTTATAGTTTATATATGTTCTATGATTC 1 AAGGTTTAAGGTTTATAGTTTATATATGTTCTATGATTC ** 8214489 GGGGTTTAAG 1 AAGGTTTAAG 8214499 AAATATGGGT Statistics Matches: 44, Mismatches: 5, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 39 44 1.00 ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48 Consensus pattern (39 bp): AAGGTTTAAGGTTTATAGTTTATATATGTTCTATGATTC Found at i:8215865 original size:29 final size:29 Alignment explanation

Indices: 8215822--8215896 Score: 114 Period size: 29 Copynumber: 2.6 Consensus size: 29 8215812 CCTTAAATCC * ** 8215822 AGTTATTCAAATCTTCATCTCGTCGGTTT 1 AGTTATTCAATTCTTCATCTCACCGGTTT * 8215851 AGTTATTCATTTCTTCATCTCACCGGTTT 1 AGTTATTCAATTCTTCATCTCACCGGTTT 8215880 AGTTATTCAATTCTTCA 1 AGTTATTCAATTCTTCA 8215897 CAGCATTTAG Statistics Matches: 41, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 29 41 1.00 ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47 Consensus pattern (29 bp): AGTTATTCAATTCTTCATCTCACCGGTTT Found at i:8217311 original size:21 final size:22 Alignment explanation

Indices: 8217282--8217325 Score: 54 Period size: 23 Copynumber: 2.0 Consensus size: 22 8217272 ATAAAGGATT * 8217282 TTAATTGGT-TTTTGCAGCTAA 1 TTAAATGGTATTTTGCAGCTAA * 8217303 TTAAATGGTACTTTTGCTGCTAA 1 TTAAATGGTA-TTTTGCAGCTAA 8217326 GATGGTACAT Statistics Matches: 19, Mismatches: 2, Indels: 2 0.83 0.09 0.09 Matches are distributed among these distances: 21 8 0.42 23 11 0.58 ACGTcount: A:0.25, C:0.11, G:0.18, T:0.45 Consensus pattern (22 bp): TTAAATGGTATTTTGCAGCTAA Found at i:8217699 original size:67 final size:67 Alignment explanation

Indices: 8217557--8217689 Score: 180 Period size: 67 Copynumber: 2.0 Consensus size: 67 8217547 TATATAACAT * * * 8217557 ATATTAATATGGATATATAACCTATATTTCAATTTTATTAATAATAAATTTTATAATTTTAAAAA 1 ATATAAAT-TGGATATATAACCTATATTCCAAATTTATTAATAATAAATTTTATAATTTTAAAAA 8217622 TAA 65 TAA * * 8217625 ATGTAAATTGGATATATAACCTATATTCCAAATTTATTAGTAA-ACAATTTT-TAATTTTTAAAA 1 ATATAAATTGGATATATAACCTATATTCCAAATTTATTAATAATA-AATTTTATAA-TTTTAAAA 8217688 AT 64 AT 8217690 GGTTATAAAT Statistics Matches: 58, Mismatches: 5, Indels: 5 0.85 0.07 0.07 Matches are distributed among these distances: 66 4 0.07 67 48 0.83 68 6 0.10 ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44 Consensus pattern (67 bp): ATATAAATTGGATATATAACCTATATTCCAAATTTATTAATAATAAATTTTATAATTTTAAAAAT AA Found at i:8217710 original size:67 final size:67 Alignment explanation

Indices: 8217568--8217703 Score: 159 Period size: 67 Copynumber: 2.0 Consensus size: 67 8217558 TATTAATATG * * * 8217568 GATATATAACCTATATTTCAATTTTATTAATAATAAATTTTATAATTTTAAAAATAAATGTAAAT 1 GATATATAACCTATATTCCAAATTTATTAATAATAAATTTTATAATTTTAAAAATAAATATAAAT ** 8217633 TG 66 AA * *** 8217635 GATATATAACCTATATTCCAAATTTATTAGTAA-ACAATTTT-TAATTTTTAAAAATGGTTATAA 1 GATATATAACCTATATTCCAAATTTATTAATAATA-AATTTTATAA-TTTTAAAAATAAATATAA 8217698 ATAA 64 ATAA 8217702 GA 1 GA 8217704 AGTATAAAAG Statistics Matches: 58, Mismatches: 9, Indels: 4 0.82 0.13 0.06 Matches are distributed among these distances: 66 4 0.07 67 54 0.93 ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43 Consensus pattern (67 bp): GATATATAACCTATATTCCAAATTTATTAATAATAAATTTTATAATTTTAAAAATAAATATAAAT AA Found at i:8217792 original size:7 final size:7 Alignment explanation

Indices: 8217720--8217744 Score: 50 Period size: 7 Copynumber: 3.6 Consensus size: 7 8217710 AAAGTGATAT 8217720 ATAATAC 1 ATAATAC 8217727 ATAATAC 1 ATAATAC 8217734 ATAATAC 1 ATAATAC 8217741 ATAA 1 ATAA 8217745 ATTTATCAAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 18 1.00 ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28 Consensus pattern (7 bp): ATAATAC Found at i:8217888 original size:9 final size:9 Alignment explanation

Indices: 8217876--8217908 Score: 66 Period size: 9 Copynumber: 3.7 Consensus size: 9 8217866 AAACATAGCC 8217876 TACATAACT 1 TACATAACT 8217885 TACATAACT 1 TACATAACT 8217894 TACATAACT 1 TACATAACT 8217903 TACATA 1 TACATA 8217909 CATAATACAT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 24 1.00 ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33 Consensus pattern (9 bp): TACATAACT Found at i:8217998 original size:25 final size:25 Alignment explanation

Indices: 8217970--8218023 Score: 81 Period size: 25 Copynumber: 2.2 Consensus size: 25 8217960 ATTAATATTA * 8217970 TACACAACTTACATAATACATTACT 1 TACACAACTTACATAATACATAACT ** 8217995 TACAGTACTTACATAATACATAACT 1 TACACAACTTACATAATACATAACT 8218020 TACA 1 TACA 8218024 TAATTTTATT Statistics Matches: 26, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 25 26 1.00 ACGTcount: A:0.44, C:0.22, G:0.02, T:0.31 Consensus pattern (25 bp): TACACAACTTACATAATACATAACT Found at i:8218023 original size:9 final size:9 Alignment explanation

Indices: 8217970--8218026 Score: 52 Period size: 9 Copynumber: 6.8 Consensus size: 9 8217960 ATTAATATTA * 8217970 TACACAACT 1 TACATAACT 8217979 TACATAA-- 1 TACATAACT * 8217986 TACATTACT 1 TACATAACT 8217995 TACAGT-ACT 1 TACA-TAACT 8218004 TACATAA-- 1 TACATAACT 8218011 TACATAACT 1 TACATAACT 8218020 TACATAA 1 TACATAA 8218027 TTTTATTTTA Statistics Matches: 40, Mismatches: 2, Indels: 12 0.74 0.04 0.22 Matches are distributed among these distances: 7 13 0.32 8 1 0.03 9 25 0.62 10 1 0.03 ACGTcount: A:0.46, C:0.21, G:0.02, T:0.32 Consensus pattern (9 bp): TACATAACT Found at i:8218184 original size:43 final size:43 Alignment explanation

Indices: 8218098--8218193 Score: 131 Period size: 43 Copynumber: 2.2 Consensus size: 43 8218088 ACCAAACAAC ** ** 8218098 AGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGGTCATGTTCTTT 1 AGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGAACATGACCTTT 8218141 AGCGGCGTTTGTGG-GAAAAGCGCCGCTAAAGAACATGACCTTT 1 AGCGGCGTTTGTGGAG-AAAGCGCCGCTAAAGAACATGACCTTT * 8218184 AGCAGCGTTT 1 AGCGGCGTTT 8218194 CTGACCCTTG Statistics Matches: 47, Mismatches: 5, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 42 1 0.02 43 46 0.98 ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25 Consensus pattern (43 bp): AGCGGCGTTTGTGGAGAAAGCGCCGCTAAAGAACATGACCTTT Found at i:8230593 original size:21 final size:21 Alignment explanation

Indices: 8230554--8230598 Score: 56 Period size: 23 Copynumber: 2.1 Consensus size: 21 8230544 GGAAACAGCG 8230554 CTCTCTATAATAGTCTCATTTGC 1 CTCTCTATAATAG-CTCA-TTGC * 8230577 CTCTCTATGATAG-TCATTGC 1 CTCTCTATAATAGCTCATTGC 8230597 CT 1 CT 8230599 GTCAAGATTT Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 20 6 0.29 21 3 0.14 23 12 0.57 ACGTcount: A:0.20, C:0.27, G:0.11, T:0.42 Consensus pattern (21 bp): CTCTCTATAATAGCTCATTGC Found at i:8232283 original size:13 final size:13 Alignment explanation

Indices: 8232267--8232297 Score: 53 Period size: 13 Copynumber: 2.4 Consensus size: 13 8232257 TAAACCAAAA 8232267 TTTTCAAAAGCAC 1 TTTTCAAAAGCAC * 8232280 TTTTAAAAAGCAC 1 TTTTCAAAAGCAC 8232293 TTTTC 1 TTTTC 8232298 CACAGTATAT Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 13 16 1.00 ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39 Consensus pattern (13 bp): TTTTCAAAAGCAC Found at i:8234966 original size:24 final size:24 Alignment explanation

Indices: 8234939--8235001 Score: 90 Period size: 25 Copynumber: 2.6 Consensus size: 24 8234929 AATTATATAT 8234939 CAAATATATATTTTTATTTTAAAG 1 CAAATATATATTTTTATTTTAAAG * * 8234963 CAAATATATATATTTTATTTTTAAT 1 CAAATATATAT-TTTTATTTTAAAG * 8234988 AAAATATATATTTT 1 CAAATATATATTTT 8235002 ATATATATTT Statistics Matches: 35, Mismatches: 3, Indels: 2 0.88 0.08 0.05 Matches are distributed among these distances: 24 14 0.40 25 21 0.60 ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52 Consensus pattern (24 bp): CAAATATATATTTTTATTTTAAAG Found at i:8234992 original size:25 final size:24 Alignment explanation

Indices: 8234940--8235015 Score: 89 Period size: 25 Copynumber: 3.0 Consensus size: 24 8234930 ATTATATATC * ** 8234940 AAATATATATTTTTATTTTAAAGC 1 AAATATATATTTTTATTTTTAATA 8234964 AAATATATATATTTTATTTTTAATA 1 AAATATATAT-TTTTATTTTTAATA 8234989 AAATATATATTTTATATATATTTAATA 1 AAATATATATTTT-TAT-T-TTTAATA 8235016 TGGGCCAGGC Statistics Matches: 45, Mismatches: 3, Indels: 5 0.85 0.06 0.09 Matches are distributed among these distances: 24 13 0.29 25 24 0.53 26 1 0.02 27 7 0.16 ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53 Consensus pattern (24 bp): AAATATATATTTTTATTTTTAATA Found at i:8235650 original size:16 final size:16 Alignment explanation

Indices: 8235629--8235660 Score: 64 Period size: 16 Copynumber: 2.0 Consensus size: 16 8235619 ATTTCTAACT 8235629 TAGCATAACTAGACAA 1 TAGCATAACTAGACAA 8235645 TAGCATAACTAGACAA 1 TAGCATAACTAGACAA 8235661 AAACCATTAG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19 Consensus pattern (16 bp): TAGCATAACTAGACAA Found at i:8241165 original size:56 final size:56 Alignment explanation

Indices: 8241079--8241191 Score: 172 Period size: 56 Copynumber: 2.0 Consensus size: 56 8241069 TAATTACGAG * * * 8241079 ATTGAATTATATCTGTCATTGGGTGTGAAATTTTACAGAAGCATTTCAAGTATATT 1 ATTGAATGATATCTGTCATTGGGTATGAAATTGTACAGAAGCATTTCAAGTATATT * ** 8241135 ATTGAATGATATTTGTCATTGGGTATGAAATTGTACAGAAGCATTTTGAGTATATT 1 ATTGAATGATATCTGTCATTGGGTATGAAATTGTACAGAAGCATTTCAAGTATATT 8241191 A 1 A 8241192 GTCGAGATTT Statistics Matches: 51, Mismatches: 6, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 56 51 1.00 ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41 Consensus pattern (56 bp): ATTGAATGATATCTGTCATTGGGTATGAAATTGTACAGAAGCATTTCAAGTATATT Found at i:8246587 original size:44 final size:44 Alignment explanation

Indices: 8246499--8246699 Score: 119 Period size: 44 Copynumber: 4.7 Consensus size: 44 8246489 CTTCGATCCA * * 8246499 CTCCACTACAACTTCAGGGAGATAGGATTATCGAATTCAATCTG 1 CTCCACTATAACTTCAGGGAGATAAGATTATCGAATTCAATCTG * *** * 8246543 CTCCACTATAACCTCAGGGAGATAAGATT-TGCTTTTTCAGTCTG 1 CTCCACTATAACTTCAGGGAGATAAGATTAT-CGAATTCAATCTG * * * * ** * * * 8246587 CCCCACTGTGACTTCAGGGGGATAAGA--CCCG-ATACGATTTG 1 CTCCACTATAACTTCAGGGAGATAAGATTATCGAATTCAATCTG * * * * * 8246628 CTCCTCTACT-GCCT-AGGGAGATAAGATCTATTG-TTTCAATCTG 1 CTCCACTA-TAACTTCAGGGAGATAAGAT-TATCGAATTCAATCTG * * 8246671 CTCCACTACAACTTCAGGGAGATAGGATT 1 CTCCACTATAACTTCAGGGAGATAAGATT 8246700 GATTTCTTCT Statistics Matches: 112, Mismatches: 37, Indels: 17 0.67 0.22 0.10 Matches are distributed among these distances: 40 11 0.10 41 12 0.11 42 2 0.02 43 18 0.16 44 69 0.62 ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29 Consensus pattern (44 bp): CTCCACTATAACTTCAGGGAGATAAGATTATCGAATTCAATCTG Found at i:8247202 original size:86 final size:86 Alignment explanation

Indices: 8246925--8247362 Score: 617 Period size: 86 Copynumber: 5.1 Consensus size: 86 8246915 ACTTGTAATC * * * * * 8246925 TTCGACCTGCTTCACTGTTGACGCA-GAAGGGCAAGATCTGCTATCTTTAACTAGCTCCACTGCC 1 TTCGATCTGCTTCGCTGTTAACGCAGGAA-GGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCA * * 8246989 ACCGATGAAGACAAGGCTTTGTT 64 ACCGATGGAGGCAAGGCTTTGTT * * * 8247012 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTTCTATCTTCAACCAGCTCCATTGCAA 1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCAA 8247077 CCGATGGAGGCAAGGCTTTGTT 65 CCGATGGAGGCAAGGCTTTGTT * * * 8247099 TTCGATCTGCTTTGCTGTTAATGCAGGAAGGTAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC 1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC * * * 8247164 TGATGGAGGCAAGACTTTATT 66 CGATGGAGGCAAGGCTTTGTT * * * * 8247185 TTCGATCTGCTTCGCTGTTAACGTAGGAAGACAAGATCTGCTTTTTTAACTAGCTCCACTGCAAC 1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC * * 8247250 TGATGGAGGCAAGACTTTGTT 66 CGATGGAGGCAAGGCTTTGTT * * 8247271 TTCGATCTGCTTCGTTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC 1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC * 8247336 CGATGGAGGCAAGGCTTTATT 66 CGATGGAGGCAAGGCTTTGTT 8247357 TTCGAT 1 TTCGAT 8247363 TTTCACTGAC Statistics Matches: 314, Mismatches: 36, Indels: 3 0.89 0.10 0.01 Matches are distributed among these distances: 86 200 0.64 87 111 0.35 88 3 0.01 ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31 Consensus pattern (86 bp): TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAAC CGATGGAGGCAAGGCTTTGTT Found at i:8253799 original size:26 final size:23 Alignment explanation

Indices: 8253756--8253806 Score: 66 Period size: 26 Copynumber: 2.1 Consensus size: 23 8253746 ATTAAAATCT * 8253756 AACCTAAAAAAAAGAAAAGAGAA 1 AACCTAAAAAAAAGAAAAGAAAA 8253779 AACCTAAACTAAAAATGAAAAGAAAA 1 AACCTAAA--AAAAA-GAAAAGAAAA 8253805 AA 1 AA 8253807 AAGAAGAAAA Statistics Matches: 24, Mismatches: 1, Indels: 3 0.86 0.04 0.11 Matches are distributed among these distances: 23 8 0.33 25 5 0.21 26 11 0.46 ACGTcount: A:0.73, C:0.10, G:0.10, T:0.08 Consensus pattern (23 bp): AACCTAAAAAAAAGAAAAGAAAA Found at i:8255254 original size:18 final size:17 Alignment explanation

Indices: 8255231--8255278 Score: 69 Period size: 18 Copynumber: 2.7 Consensus size: 17 8255221 ATGGGGCGGG * 8255231 CGGCCCGACCCGACTCGA 1 CGGCCCG-CCCGACCCGA 8255249 CGGCCCGGCCCGACCCGA 1 CGGCCC-GCCCGACCCGA 8255267 CGGCCCGCCCGA 1 CGGCCCGCCCGA 8255279 AATATGGGAG Statistics Matches: 28, Mismatches: 1, Indels: 3 0.88 0.03 0.09 Matches are distributed among these distances: 17 6 0.21 18 21 0.75 19 1 0.04 ACGTcount: A:0.12, C:0.54, G:0.31, T:0.02 Consensus pattern (17 bp): CGGCCCGCCCGACCCGA Found at i:8255343 original size:33 final size:34 Alignment explanation

Indices: 8255273--8255345 Score: 87 Period size: 32 Copynumber: 2.1 Consensus size: 34 8255263 CCGACGGCCC * * * 8255273 GCCCGAAATATGGGAGGGTTTGGGTAAAAATATAG 1 GCCCGAAATAT-GGAGGCTTTGGGTAAAAAAAGAG 8255308 GCCCGAAATAT-G-GGCTTTGGGTAAAAAAACGAG 1 GCCCGAAATATGGAGGCTTTGGGTAAAAAAA-GAG 8255341 GCCCG 1 GCCCG 8255346 TTTAGAAAAC Statistics Matches: 34, Mismatches: 3, Indels: 4 0.83 0.07 0.10 Matches are distributed among these distances: 32 15 0.44 33 8 0.24 35 11 0.32 ACGTcount: A:0.33, C:0.15, G:0.33, T:0.19 Consensus pattern (34 bp): GCCCGAAATATGGAGGCTTTGGGTAAAAAAAGAG Found at i:8255453 original size:17 final size:17 Alignment explanation

Indices: 8255417--8255543 Score: 62 Period size: 17 Copynumber: 7.7 Consensus size: 17 8255407 CTGATATAAT * * 8255417 AAATATATTT-ATTTTT 1 AAATATTTTTAATTTTA * 8255433 AAATTTTTTTAATTTTA 1 AAATATTTTTAATTTTA 8255450 AAATA----T--TTTTA 1 AAATATTTTTAATTTTA 8255461 AAATACTTTTT-ATTTT- 1 AAATA-TTTTTAATTTTA 8255477 --AT-TTTTTAATTTTA 1 AAATATTTTTAATTTTA 8255491 AAATATTTTTAAAATACTTTTTAA 1 AAATATTTTT---A-A--TTTT-A * 8255515 AAATTTTTTTAATTTTA 1 AAATATTTTTAATTTTA 8255532 AAATATTTTTAA 1 AAATATTTTTAA 8255544 AATACTTTTT Statistics Matches: 86, Mismatches: 6, Indels: 37 0.67 0.05 0.29 Matches are distributed among these distances: 11 10 0.12 12 5 0.06 13 6 0.07 14 2 0.02 16 11 0.13 17 30 0.35 18 4 0.05 20 2 0.02 21 2 0.02 23 4 0.05 24 10 0.12 ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60 Consensus pattern (17 bp): AAATATTTTTAATTTTA Found at i:8255459 original size:11 final size:11 Alignment explanation

Indices: 8255445--8255553 Score: 81 Period size: 11 Copynumber: 10.4 Consensus size: 11 8255435 ATTTTTTTAA 8255445 TTTTAAAATAT 1 TTTTAAAATAT 8255456 TTTTAAAATACT 1 TTTTAAAATA-T *** 8255468 TTTTATTTTAT 1 TTTTAAAATAT * 8255479 TTTT----TAA 1 TTTTAAAATAT 8255486 TTTTAAAATAT 1 TTTTAAAATAT 8255497 TTTTAAAATACT 1 TTTTAAAATA-T 8255509 TTTTAAAA-AT 1 TTTTAAAATAT * * 8255519 TTTT---TTAA 1 TTTTAAAATAT 8255527 TTTTAAAATAT 1 TTTTAAAATAT 8255538 TTTTAAAATACT 1 TTTTAAAATA-T 8255550 TTTT 1 TTTT 8255554 TTTAATTTTT Statistics Matches: 78, Mismatches: 9, Indels: 21 0.72 0.08 0.19 Matches are distributed among these distances: 7 6 0.08 8 5 0.06 10 5 0.06 11 40 0.51 12 22 0.28 ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60 Consensus pattern (11 bp): TTTTAAAATAT Found at i:8255487 original size:41 final size:41 Alignment explanation

Indices: 8255437--8255563 Score: 204 Period size: 41 Copynumber: 3.1 Consensus size: 41 8255427 ATTTTTAAAT * 8255437 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTATTTTA 1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTATTTAA ** 8255478 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTA-AAAA 1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTATTTAA 8255518 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTT-TTTAA 1 -TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTATTTAA 8255559 TTTTT 1 TTTTT 8255564 AAAATAAATT Statistics Matches: 79, Mismatches: 5, Indels: 5 0.89 0.06 0.06 Matches are distributed among these distances: 40 6 0.08 41 73 0.92 ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62 Consensus pattern (41 bp): TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTATTTAA Found at i:8255512 original size:30 final size:30 Alignment explanation

Indices: 8255456--8255514 Score: 75 Period size: 29 Copynumber: 2.0 Consensus size: 30 8255446 TTTAAAATAT *** 8255456 TTTTAAAATACTTTTTATTTTATTTTTTAA 1 TTTTAAAATACTTTTTAAAATATTTTTTAA * 8255486 TTTTAAAATA-TTTTTAAAATACTTTTTAA 1 TTTTAAAATACTTTTTAAAATATTTTTTAA 8255515 AAATTTTTTT Statistics Matches: 25, Mismatches: 4, Indels: 1 0.83 0.13 0.03 Matches are distributed among these distances: 29 15 0.60 30 10 0.40 ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61 Consensus pattern (30 bp): TTTTAAAATACTTTTTAAAATATTTTTTAA Found at i:8264044 original size:45 final size:43 Alignment explanation

Indices: 8263978--8264107 Score: 143 Period size: 45 Copynumber: 2.9 Consensus size: 43 8263968 GCTATATGCC ** 8263978 TAAAATGATGAAGACCATAGCTGAAAGATGATATTTCATCATGA 1 TAAAATGAT-AAGACCATAGCTGAAAGATGATATGGCATCATGA * * * 8264022 TATAAATGAGTAAGACCATAGCTGAAAGTTGCTATGGCATCATGG 1 TA-AAATGA-TAAGACCATAGCTGAAAGATGATATGGCATCATGA * * * 8264067 TAAATATGACTACGACCATAGCTAAAAGACGATATGGCATC 1 TAAA-ATGA-TAAGACCATAGCTGAAAGATGATATGGCATC 8264108 CTAATAGTCC Statistics Matches: 72, Mismatches: 11, Indels: 5 0.82 0.12 0.06 Matches are distributed among these distances: 44 4 0.06 45 67 0.93 46 1 0.01 ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25 Consensus pattern (43 bp): TAAAATGATAAGACCATAGCTGAAAGATGATATGGCATCATGA Found at i:8268104 original size:45 final size:45 Alignment explanation

Indices: 8268025--8268110 Score: 118 Period size: 45 Copynumber: 1.9 Consensus size: 45 8268015 TCCTTGACCA * * * * * 8268025 AGTATAAATAATTAATAGTAAATATTATGTAATTTAGTTAAATTT 1 AGTACAAACAATTAATAATAAATACTATGCAATTTAGTTAAATTT * 8268070 AGTACAAACAATTTATAATAAATACTATGCAATTTAGTTAA 1 AGTACAAACAATTAATAATAAATACTATGCAATTTAGTTAA 8268111 TTATTTAGCA Statistics Matches: 35, Mismatches: 6, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 45 35 1.00 ACGTcount: A:0.48, C:0.05, G:0.08, T:0.40 Consensus pattern (45 bp): AGTACAAACAATTAATAATAAATACTATGCAATTTAGTTAAATTT Found at i:8269940 original size:23 final size:23 Alignment explanation

Indices: 8269909--8269961 Score: 88 Period size: 23 Copynumber: 2.3 Consensus size: 23 8269899 AGTGTTGTTG 8269909 ATCAGTGGTAGCTTCAGCTACAT 1 ATCAGTGGTAGCTTCAGCTACAT * * 8269932 TTCAGTGGTAGCTTCGGCTACAT 1 ATCAGTGGTAGCTTCAGCTACAT 8269955 ATCAGTG 1 ATCAGTG 8269962 TGGCACTTAT Statistics Matches: 27, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 23 27 1.00 ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32 Consensus pattern (23 bp): ATCAGTGGTAGCTTCAGCTACAT Found at i:8282704 original size:15 final size:16 Alignment explanation

Indices: 8282674--8282706 Score: 50 Period size: 15 Copynumber: 2.1 Consensus size: 16 8282664 AGAAAAAGGG * 8282674 TAAAATCTGGGCAAGT 1 TAAAATCTGCGCAAGT 8282690 TAAAATCT-CGCAAGT 1 TAAAATCTGCGCAAGT 8282705 TA 1 TA 8282707 GGACTTTTTG Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 15 8 0.50 16 8 0.50 ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27 Consensus pattern (16 bp): TAAAATCTGCGCAAGT Found at i:8284779 original size:38 final size:38 Alignment explanation

Indices: 8284728--8284804 Score: 145 Period size: 38 Copynumber: 2.0 Consensus size: 38 8284718 ACAAGCATGC 8284728 TGCGTGCAAATCCACTCACTCCAATTAAAGTAAAAGAA 1 TGCGTGCAAATCCACTCACTCCAATTAAAGTAAAAGAA * 8284766 TGCGTGCAAATCCATTCACTCCAATTAAAGTAAAAGAA 1 TGCGTGCAAATCCACTCACTCCAATTAAAGTAAAAGAA 8284804 T 1 T 8284805 TTTCACTCTG Statistics Matches: 38, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 38 38 1.00 ACGTcount: A:0.42, C:0.22, G:0.13, T:0.23 Consensus pattern (38 bp): TGCGTGCAAATCCACTCACTCCAATTAAAGTAAAAGAA Found at i:8287219 original size:11 final size:11 Alignment explanation

Indices: 8287203--8287245 Score: 50 Period size: 11 Copynumber: 3.7 Consensus size: 11 8287193 AATCAGTCAT 8287203 ACAAATCACAG 1 ACAAATCACAG * 8287214 ACAAATCAGTCAT 1 ACAAATCA--CAG * 8287227 ACCAATCACAG 1 ACAAATCACAG 8287238 ACAAATCA 1 ACAAATCA 8287246 GTCATTTACA Statistics Matches: 26, Mismatches: 4, Indels: 4 0.76 0.12 0.12 Matches are distributed among these distances: 11 17 0.65 13 9 0.35 ACGTcount: A:0.51, C:0.28, G:0.07, T:0.14 Consensus pattern (11 bp): ACAAATCACAG Found at i:8287220 original size:24 final size:24 Alignment explanation

Indices: 8287193--8287274 Score: 110 Period size: 24 Copynumber: 3.4 Consensus size: 24 8287183 TCATGCTCAG 8287193 AATCAGTCATACAAATCACAGACA 1 AATCAGTCATACAAATCACAGACA * 8287217 AATCAGTCATACCAATCACAGACA 1 AATCAGTCATACAAATCACAGACA ** * * 8287241 AATCAGTCATTTACATCACAGATA 1 AATCAGTCATACAAATCACAGACA * 8287265 AATCAATCAT 1 AATCAGTCAT 8287275 TTACATCACG Statistics Matches: 51, Mismatches: 7, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 24 51 1.00 ACGTcount: A:0.46, C:0.24, G:0.07, T:0.22 Consensus pattern (24 bp): AATCAGTCATACAAATCACAGACA Found at i:8287275 original size:24 final size:24 Alignment explanation

Indices: 8287207--8287303 Score: 117 Period size: 24 Copynumber: 4.0 Consensus size: 24 8287197 AGTCATACAA * 8287207 ATCACAGACAAATCAGTCA--TACC 1 ATCACAGACAAATCAATCATTTA-C * 8287230 AATCACAGACAAATCAGTCATTTAC 1 -ATCACAGACAAATCAATCATTTAC * 8287255 ATCACAGATAAATCAATCATTTAC 1 ATCACAGACAAATCAATCATTTAC * * 8287279 ATCACGGACCAATCAATCATTTAC 1 ATCACAGACAAATCAATCATTTAC 8287303 A 1 A 8287304 CTCGATGGGC Statistics Matches: 66, Mismatches: 5, Indels: 4 0.88 0.07 0.05 Matches are distributed among these distances: 24 63 0.95 25 1 0.02 26 2 0.03 ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24 Consensus pattern (24 bp): ATCACAGACAAATCAATCATTTAC Found at i:8287406 original size:27 final size:27 Alignment explanation

Indices: 8287344--8287499 Score: 127 Period size: 27 Copynumber: 5.7 Consensus size: 27 8287334 AGAGGCTTTA * * * * 8287344 GGGTCATTACGGTCATTTTATCTTACAG 1 GGGT-ATTATGGTCATTTTACCCTATAG * * * 8287372 AGGCATTATGGTCATTTTACCCT-TCG 1 GGGTATTATGGTCATTTTACCCTATAG * 8287398 GCGGTATTATGATCATTTTACCCTATAG 1 G-GGTATTATGGTCATTTTACCCTATAG * * * * 8287426 GGGT-TTTTCGATCATTTTACCCTACAT 1 GGGTATTAT-GGTCATTTTACCCTATAG * * 8287453 GGGTATTACGGTCATTTTACCTTATAG 1 GGGTATTATGGTCATTTTACCCTATAG * * 8287480 GGGTATTACGGTTATTTTAC 1 GGGTATTATGGTCATTTTAC 8287500 AAATATTGGG Statistics Matches: 103, Mismatches: 21, Indels: 9 0.77 0.16 0.07 Matches are distributed among these distances: 26 4 0.04 27 92 0.89 28 7 0.07 ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41 Consensus pattern (27 bp): GGGTATTATGGTCATTTTACCCTATAG Found at i:8287497 original size:54 final size:53 Alignment explanation

Indices: 8287344--8287499 Score: 159 Period size: 54 Copynumber: 2.9 Consensus size: 53 8287334 AGAGGCTTTA * * * * * * 8287344 GGGTCATTACGGTCATTTTATCTTACAGAGGCATTATGGTCATTTTACCCTTCG 1 GGGT-ATTACGGTCATTTTACCTTATAGGGGTATTACGGTCATTTTACCCTACG * * * * * * * 8287398 GCGGTATTATGATCATTTTACCCTATAGGGGTTTTTCGATCATTTTACCCTACAT 1 G-GGTATTACGGTCATTTTACCTTATAGGGGTATTACGGTCATTTTACCCTAC-G * 8287453 GGGTATTACGGTCATTTTACCTTATAGGGGTATTACGGTTATTTTAC 1 GGGTATTACGGTCATTTTACCTTATAGGGGTATTACGGTCATTTTAC 8287500 AAATATTGGG Statistics Matches: 80, Mismatches: 20, Indels: 4 0.77 0.19 0.04 Matches are distributed among these distances: 54 76 0.95 55 4 0.05 ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41 Consensus pattern (53 bp): GGGTATTACGGTCATTTTACCTTATAGGGGTATTACGGTCATTTTACCCTACG Found at i:8294225 original size:21 final size:21 Alignment explanation

Indices: 8294187--8294226 Score: 53 Period size: 21 Copynumber: 1.9 Consensus size: 21 8294177 CTAGAAATTA ** 8294187 ATTTAATTTCTTCAAATTATT 1 ATTTAATTAATTCAAATTATT * 8294208 ATTTAATTAATTCTAATTA 1 ATTTAATTAATTCAAATTA 8294227 AATAATTGAA Statistics Matches: 16, Mismatches: 3, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 21 16 1.00 ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55 Consensus pattern (21 bp): ATTTAATTAATTCAAATTATT Found at i:8294380 original size:17 final size:17 Alignment explanation

Indices: 8294360--8294392 Score: 57 Period size: 17 Copynumber: 1.9 Consensus size: 17 8294350 CAAAATTGGG 8294360 TTGAGAAAATAATTTAA 1 TTGAGAAAATAATTTAA * 8294377 TTGAGAAATTAATTTA 1 TTGAGAAAATAATTTA 8294393 GTTAATTTAA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39 Consensus pattern (17 bp): TTGAGAAAATAATTTAA Found at i:8294399 original size:9 final size:9 Alignment explanation

Indices: 8294383--8294415 Score: 50 Period size: 9 Copynumber: 3.8 Consensus size: 9 8294373 TTAATTGAGA 8294383 AATTAATTT 1 AATTAATTT * 8294392 AGTTAATTT 1 AATTAATTT 8294401 AATTAA-TT 1 AATTAATTT 8294409 AATTAAT 1 AATTAAT 8294416 ATTTTTGGAA Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 8 8 0.38 9 13 0.62 ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52 Consensus pattern (9 bp): AATTAATTT Found at i:8296724 original size:25 final size:25 Alignment explanation

Indices: 8296679--8296726 Score: 62 Period size: 25 Copynumber: 1.9 Consensus size: 25 8296669 ATAAGTTTCC * 8296679 CGTTACATGGCTCACATGAGCTTAT 1 CGTTACATGGCTCACAAGAGCTTAT * 8296704 CGTTATATGGCTCGA-AAGAGCTT 1 CGTTACATGGCTC-ACAAGAGCTT 8296727 CCCATTTATG Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 25 19 0.95 26 1 0.05 ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31 Consensus pattern (25 bp): CGTTACATGGCTCACAAGAGCTTAT Found at i:8300727 original size:25 final size:25 Alignment explanation

Indices: 8300699--8300750 Score: 70 Period size: 25 Copynumber: 2.1 Consensus size: 25 8300689 AGCATCCTGA * 8300699 TATATGGTCCTCT-CGAGCTTTCCGT 1 TATATGGTCCT-TGCGAGCTTCCCGT * 8300724 TATATGGTTCTTGCGAGCTTCCCGT 1 TATATGGTCCTTGCGAGCTTCCCGT 8300749 TA 1 TA 8300751 ATAGCTCTTC Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 24 1 0.04 25 23 0.96 ACGTcount: A:0.13, C:0.25, G:0.21, T:0.40 Consensus pattern (25 bp): TATATGGTCCTTGCGAGCTTCCCGT Found at i:8300759 original size:24 final size:25 Alignment explanation

Indices: 8300712--8300759 Score: 62 Period size: 25 Copynumber: 2.0 Consensus size: 25 8300702 ATGGTCCTCT * * * 8300712 CGAGCTTTCCGTTATATGGTTCTTG 1 CGAGCTTCCCGTTATATAGCTCTTG 8300737 CGAGCTTCCCGTTA-ATAGCTCTT 1 CGAGCTTCCCGTTATATAGCTCTT 8300760 CGGAGCATCT Statistics Matches: 20, Mismatches: 3, Indels: 1 0.83 0.12 0.04 Matches are distributed among these distances: 24 7 0.35 25 13 0.65 ACGTcount: A:0.15, C:0.25, G:0.21, T:0.40 Consensus pattern (25 bp): CGAGCTTCCCGTTATATAGCTCTTG Found at i:8300951 original size:24 final size:24 Alignment explanation

Indices: 8300896--8300953 Score: 71 Period size: 24 Copynumber: 2.4 Consensus size: 24 8300886 TGGCTCTTCG * * 8300896 GAGCTTGCCGATATTGGCTCGCTT 1 GAGCTTCCCAATATTGGCTCGCTT ** * 8300920 GAAATTCCCAATATTGGCTCGTTT 1 GAGCTTCCCAATATTGGCTCGCTT 8300944 GAGCTTCCCA 1 GAGCTTCCCA 8300954 TTATATAGCC Statistics Matches: 27, Mismatches: 7, Indels: 0 0.79 0.21 0.00 Matches are distributed among these distances: 24 27 1.00 ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33 Consensus pattern (24 bp): GAGCTTCCCAATATTGGCTCGCTT Found at i:8306513 original size:17 final size:19 Alignment explanation

Indices: 8306493--8306533 Score: 52 Period size: 18 Copynumber: 2.3 Consensus size: 19 8306483 ATATTATTTT * 8306493 AAAATATA-T-AATACATC 1 AAAATATACTAAAAACATC 8306510 AAAA-ATACTAAAAACATC 1 AAAATATACTAAAAACATC 8306528 AAAATA 1 AAAATA 8306534 AATATTTCCC Statistics Matches: 20, Mismatches: 1, Indels: 4 0.80 0.04 0.16 Matches are distributed among these distances: 16 3 0.15 17 5 0.25 18 11 0.55 19 1 0.05 ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22 Consensus pattern (19 bp): AAAATATACTAAAAACATC Found at i:8306657 original size:29 final size:30 Alignment explanation

Indices: 8306615--8306675 Score: 97 Period size: 29 Copynumber: 2.1 Consensus size: 30 8306605 CTTAACAAGA 8306615 AAATGCCTCTAAAATAATAA-AAAATTAAC 1 AAATGCCTCTAAAATAATAACAAAATTAAC * * 8306644 AAATGTCTTTAAAATAATAACAAAATTAAC 1 AAATGCCTCTAAAATAATAACAAAATTAAC 8306674 AA 1 AA 8306676 TAAAATAAGT Statistics Matches: 29, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 29 18 0.62 30 11 0.38 ACGTcount: A:0.59, C:0.11, G:0.03, T:0.26 Consensus pattern (30 bp): AAATGCCTCTAAAATAATAACAAAATTAAC Found at i:8308193 original size:27 final size:28 Alignment explanation

Indices: 8308142--8308199 Score: 75 Period size: 27 Copynumber: 2.1 Consensus size: 28 8308132 AAGCAGCGGA 8308142 AAACATTATTAAAAATAATAGTTTT-CT 1 AAACATTATTAAAAATAATAGTTTTGCT * * 8308169 AAACATTATTGAAAAA-ATTATTTTTGCT 1 AAACATTATT-AAAAATAATAGTTTTGCT 8308197 AAA 1 AAA 8308200 AGGCACACAA Statistics Matches: 27, Mismatches: 2, Indels: 3 0.84 0.06 0.09 Matches are distributed among these distances: 27 17 0.63 28 10 0.37 ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40 Consensus pattern (28 bp): AAACATTATTAAAAATAATAGTTTTGCT Found at i:8308395 original size:41 final size:41 Alignment explanation

Indices: 8308333--8308481 Score: 151 Period size: 41 Copynumber: 3.7 Consensus size: 41 8308323 AAACTGCAAT * * * 8308333 AGGTAAAGAAGTAGCGACGTTTATGAGAAAAACGCCATAAA 1 AGGTCAAGCAGTAGCGACGTTTATGAGAAAAACGCCACAAA * * * * * 8308374 AGGTCAAGTAGTAGCGGCGTTTATAAGGAAAACACCACAAA 1 AGGTCAAGCAGTAGCGACGTTTATGAGAAAAACGCCACAAA * * * * 8308415 AGGTCAAACAGTAAC-AGCATTTATGAG-AAAACGCCGCAAA 1 AGGTCAAGCAGTAGCGA-CGTTTATGAGAAAAACGCCACAAA * 8308455 AGGT-AAGCAGTAGCTACGTTTATGAGA 1 AGGTCAAGCAGTAGCGACGTTTATGAGA 8308482 TAAATACCGC Statistics Matches: 87, Mismatches: 18, Indels: 7 0.78 0.16 0.06 Matches are distributed among these distances: 39 17 0.20 40 16 0.18 41 54 0.62 ACGTcount: A:0.42, C:0.15, G:0.24, T:0.18 Consensus pattern (41 bp): AGGTCAAGCAGTAGCGACGTTTATGAGAAAAACGCCACAAA Found at i:8313758 original size:99 final size:99 Alignment explanation

Indices: 8313636--8313824 Score: 274 Period size: 99 Copynumber: 1.9 Consensus size: 99 8313626 ATTTGATATT * * * * 8313636 AAGTAAAAACGTTTGTTCAATTATGAA-TT-TTTAAAAAGGTTAATTTAGTTCAATTTATTGAGT 1 AAGTAAAAACGCTTGTTAAATTAT-AAGTTCTTGAAAAA-GTTAATTTAGTTCAATTTATTGAAT * 8313699 TTTGATATTAAGTGGAACCATTTATTCTGTTATACA 64 TTTGATATTAAGTAGAACCATTTATTCTGTTATACA * 8313735 AAGTAAAACCGCTTGTTAAATTATAAGTTCTTGAAAAAGTTAATTTAGTTCAATTTATTGAATTT 1 AAGTAAAAACGCTTGTTAAATTATAAGTTCTTGAAAAAGTTAATTTAGTTCAATTTATTGAATTT * * 8313800 TGATATTAAGTAGAATCGTTTATTC 66 TGATATTAAGTAGAACCATTTATTC 8313825 AATTAGATGT Statistics Matches: 80, Mismatches: 8, Indels: 4 0.87 0.09 0.04 Matches are distributed among these distances: 98 2 0.03 99 71 0.89 100 7 0.09 ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43 Consensus pattern (99 bp): AAGTAAAAACGCTTGTTAAATTATAAGTTCTTGAAAAAGTTAATTTAGTTCAATTTATTGAATTT TGATATTAAGTAGAACCATTTATTCTGTTATACA Found at i:8314198 original size:24 final size:23 Alignment explanation

Indices: 8314171--8314215 Score: 72 Period size: 24 Copynumber: 1.9 Consensus size: 23 8314161 TTTCATAAAT 8314171 ATTATCATAAAAATAATATATTTA 1 ATTATCATAAAAATAAT-TATTTA * 8314195 ATTATCATAAAGATAATTATT 1 ATTATCATAAAAATAATTATT 8314216 GTTTATCTAT Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 23 4 0.20 24 16 0.80 ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42 Consensus pattern (23 bp): ATTATCATAAAAATAATTATTTA Found at i:8320248 original size:66 final size:66 Alignment explanation

Indices: 8320133--8320270 Score: 170 Period size: 66 Copynumber: 2.1 Consensus size: 66 8320123 GCAAATTGCT * * * 8320133 CAACTTAAAGCAGAGGCAGCATCGAGAGAAGCAAAGGCTCAAAGAAAATATGATGAACTCCAGCT 1 CAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCAAAGGCACAAAGAAAATATGACGAACTCCAGCT 8320198 A 66 A * * * ** * * 8320199 CAACTTAAAGCGGAGGTAGCAGCGAGGGAAGCAGGGGCA-ACAAGGAAATATGACGAACTCCTGC 1 CAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCAAAGGCACA-AAGAAAATATGACGAACTCCAGC 8320263 TA 65 TA 8320265 CAACTT 1 CAACTT 8320271 CAAAATATGA Statistics Matches: 61, Mismatches: 10, Indels: 2 0.84 0.14 0.03 Matches are distributed among these distances: 65 1 0.02 66 60 0.98 ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14 Consensus pattern (66 bp): CAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCAAAGGCACAAAGAAAATATGACGAACTCCAGCT A Found at i:8320620 original size:43 final size:43 Alignment explanation

Indices: 8320573--8320672 Score: 119 Period size: 43 Copynumber: 2.3 Consensus size: 43 8320563 AGAACATGCC * * * 8320573 CTTTAGCGGCGTTTGAGGGAAAAGCGCAACTAAAGGTCATGTT 1 CTTTAGCGGCGTTTGAGGAAAAAGCCCAACTAAAGGTCACGTT * * * ** 8320616 CTTTAGCAGCATTTGTGGAAAAAGCCCCGCTAAAGGTCACGTT 1 CTTTAGCGGCGTTTGAGGAAAAAGCCCAACTAAAGGTCACGTT * 8320659 CTATAGCGGCGTTT 1 CTTTAGCGGCGTTT 8320673 TTCCACATAA Statistics Matches: 46, Mismatches: 11, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 43 46 1.00 ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27 Consensus pattern (43 bp): CTTTAGCGGCGTTTGAGGAAAAAGCCCAACTAAAGGTCACGTT Found at i:8325442 original size:23 final size:25 Alignment explanation

Indices: 8325414--8325476 Score: 80 Period size: 23 Copynumber: 2.7 Consensus size: 25 8325404 ATATTTTTCC * 8325414 ATAAAAATATTTAAAAATTAGAA-A 1 ATAAAAATATTTAAAAATCAGAACA * 8325438 A-AAAAATA--TAAAAATCATAACA 1 ATAAAAATATTTAAAAATCAGAACA 8325460 ATAAAAATATTTAAAAA 1 ATAAAAATATTTAAAAA 8325477 ATCTGAAAAA Statistics Matches: 33, Mismatches: 2, Indels: 7 0.79 0.05 0.17 Matches are distributed among these distances: 21 10 0.30 22 2 0.06 23 14 0.42 24 1 0.03 25 6 0.18 ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25 Consensus pattern (25 bp): ATAAAAATATTTAAAAATCAGAACA Found at i:8325450 original size:9 final size:9 Alignment explanation

Indices: 8325438--8325619 Score: 58 Period size: 9 Copynumber: 20.2 Consensus size: 9 8325428 AAATTAGAAA 8325438 AAAAAATAT 1 AAAAAATAT 8325447 -AAAAATCAT 1 AAAAAAT-AT * 8325456 -AACAATA- 1 AAAAAATAT * * 8325463 AAAATATTT 1 AAAAAATAT * 8325472 AAAAAATCT 1 AAAAAATAT 8325481 GAAAAAATCAT 1 -AAAAAAT-AT * 8325492 -ATAAATCAT 1 AAAAAAT-AT * 8325501 AAAAATTAT 1 AAAAAATAT * 8325510 -AAAAATAG 1 AAAAAATAT * 8325518 AAAAAACCAT 1 AAAAAA-TAT * 8325528 CAAAAAT-T 1 AAAAAATAT 8325536 ATAAAAAT-T 1 A-AAAAATAT ** 8325545 ATTAAATAT 1 AAAAAATAT * 8325554 TAAAAATAT 1 AAAAAATAT * * 8325563 GAAAATTGAT 1 AAAAAAT-AT * 8325573 AAAAACT-T 1 AAAAAATAT * 8325581 TAAAAATAT 1 AAAAAATAT 8325590 AAAAAAATTAT 1 -AAAAAA-TAT * * 8325601 ACAAATTAT 1 AAAAAATAT 8325610 -AAAAATAT 1 AAAAAATAT 8325618 AA 1 AA 8325620 TAATTTATAA Statistics Matches: 125, Mismatches: 33, Indels: 30 0.66 0.18 0.16 Matches are distributed among these distances: 8 34 0.27 9 54 0.43 10 33 0.26 11 4 0.03 ACGTcount: A:0.65, C:0.05, G:0.02, T:0.27 Consensus pattern (9 bp): AAAAAATAT Found at i:8325501 original size:45 final size:45 Alignment explanation

Indices: 8325414--8325502 Score: 119 Period size: 47 Copynumber: 2.0 Consensus size: 45 8325404 ATATTTTTCC 8325414 ATAAAAATATTTAAAAATTAGAAAAAAAAATATAAAAATCATAACA 1 ATAAAAATATTTAAAAATTAGAAAAAAAAATAT-AAAATCATAACA ** 8325460 ATAAAAATATTTAAAAAATCT-GAAAAAATCATAT-AAATCATAA 1 ATAAAAATATTT-AAAAAT-TAGAAAAAAAAATATAAAATCATAA 8325503 AAATTATAAA Statistics Matches: 39, Mismatches: 2, Indels: 5 0.85 0.04 0.11 Matches are distributed among these distances: 45 9 0.23 46 12 0.31 47 17 0.44 48 1 0.03 ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26 Consensus pattern (45 bp): ATAAAAATATTTAAAAATTAGAAAAAAAAATATAAAATCATAACA Found at i:8325555 original size:19 final size:18 Alignment explanation

Indices: 8325530--8325755 Score: 94 Period size: 20 Copynumber: 11.7 Consensus size: 18 8325520 AAAACCATCA 8325530 AAAATTATAAAAATTATT 1 AAAATTATAAAAATTATT * 8325548 -AAA-TATTAAAAA-TATG 1 AAAATTA-TAAAAATTATT * 8325564 AAAATTGATAAAAACTT-TA 1 AAAATT-ATAAAAA-TTATT * 8325583 AAAATATAAAAAAATTA-T 1 AAAAT-TATAAAAATTATT 8325601 ACAAATTATAAAAA-TA-T 1 A-AAATTATAAAAATTATT 8325618 AATAATTTATAAAATCAAATT-TAT 1 AA-AA-TTAT--AA--AAATTAT-T * 8325642 AAAATTAATAAAACATTTTT 1 AAAATT-ATAAAA-ATTATT 8325662 AAAATTTTATAAAAGCA-TATT 1 AAAA--TTATAAAA--ATTATT 8325683 AAAATTCTATAAAAATTCA-T 1 AAAA-T-TATAAAAATT-ATT * 8325703 ACACAATTATAAAAAATATT 1 A-A-AATTATAAAAATTATT * * 8325723 AAAATTAATATAAACTTATA 1 AAAATT-ATA-AAAATTATT 8325743 AAAATTATAAAAA 1 AAAATTATAAAAA 8325756 ATCATAAAAA Statistics Matches: 165, Mismatches: 11, Indels: 64 0.69 0.05 0.27 Matches are distributed among these distances: 16 6 0.04 17 18 0.11 18 28 0.17 19 28 0.17 20 40 0.24 21 26 0.16 22 11 0.07 23 5 0.03 24 3 0.02 ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34 Consensus pattern (18 bp): AAAATTATAAAAATTATT Found at i:8325558 original size:54 final size:55 Alignment explanation

Indices: 8325473--8325619 Score: 149 Period size: 54 Copynumber: 2.7 Consensus size: 55 8325463 AAAATATTTA * * * 8325473 AAAAATCTGAAAAAATCATATAAATCATAAAAATTATAAAAATAGA-AAAAACCATC 1 AAAAATATAAAAAAATTATATAAATCATAAAAA-TATAAAAATAGATAAAAA-CATC * * * * * 8325529 AAAAAT-TATAAAAATTAT-TAAAT-ATTAAAAATATGAAAATTGATAAAAACTTT 1 AAAAATATAAAAAAATTATATAAATCA-TAAAAATATAAAAATAGATAAAAACATC * * 8325582 AAAAATATAAAAAAATTATACAAATTATAAAAATATAA 1 AAAAATATAAAAAAATTATATAAATCATAAAAATATAA 8325620 TAATTTATAA Statistics Matches: 76, Mismatches: 10, Indels: 11 0.78 0.10 0.11 Matches are distributed among these distances: 53 19 0.25 54 27 0.36 55 23 0.30 56 7 0.09 ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27 Consensus pattern (55 bp): AAAAATATAAAAAAATTATATAAATCATAAAAATATAAAAATAGATAAAAACATC Found at i:8325675 original size:21 final size:22 Alignment explanation

Indices: 8325636--8325696 Score: 65 Period size: 21 Copynumber: 2.9 Consensus size: 22 8325626 ATAAAATCAA * * 8325636 ATTTATAAAA-TTAATAAAA-C 1 ATTTTTAAAATTTTATAAAAGC 8325656 ATTTTTAAAATTTTATAAAAGC 1 ATTTTTAAAATTTTATAAAAGC * * 8325678 A-TATTAAAATTCTATAAAA 1 ATTTTTAAAATTTTATAAAA 8325697 ATTCATACAC Statistics Matches: 35, Mismatches: 4, Indels: 3 0.83 0.10 0.07 Matches are distributed among these distances: 20 9 0.26 21 24 0.69 22 2 0.06 ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39 Consensus pattern (22 bp): ATTTTTAAAATTTTATAAAAGC Found at i:8325752 original size:9 final size:9 Alignment explanation

Indices: 8325483--8325765 Score: 120 Period size: 9 Copynumber: 30.6 Consensus size: 9 8325473 AAAAATCTGA * 8325483 AAAAATCAT 1 AAAAATTAT * * 8325492 ATAAATCAT 1 AAAAATTAT 8325501 AAAAATTAT 1 AAAAATTAT * 8325510 AAAAA-TAGA 1 AAAAATTA-T ** 8325519 AAAAACCAT 1 AAAAATTAT 8325528 CAAAAATTAT 1 -AAAAATTAT 8325538 AAAAATTAT 1 AAAAATTAT * 8325547 -TAAA-TATT 1 AAAAATTA-T 8325555 AAAAA-TAT 1 AAAAATTAT * 8325563 GAAAATTGAT 1 AAAAATT-AT 8325573 AAAAACTT-T 1 AAAAA-TTAT * 8325582 AAAAATATAA 1 AAAAAT-TAT 8325592 AAAAATTAT 1 AAAAATTAT * 8325601 ACAAATTAT 1 AAAAATTAT 8325610 AAAAA-TAT 1 AAAAATTAT * 8325618 AATAATT-T 1 AAAAATTAT * 8325626 ATAAA--AT 1 AAAAATTAT * * 8325633 CAAATTTAT 1 AAAAATTAT 8325642 -AAAATTAAT 1 AAAAATT-AT * 8325651 AAAACATTTTT 1 AAAA-A-TTAT * 8325662 AAAATTTTAT 1 AAAA-ATTAT 8325672 AAAAGCA-TATT 1 AAAA--ATTA-T * 8325683 AAAATTCTAT 1 AAAAAT-TAT 8325693 AAAAATTCAT 1 AAAAATT-AT * 8325703 ACACAATTAT 1 A-AAAATTAT * 8325713 AAAAAATAT 1 AAAAATTAT * 8325722 TAAAATTAAT 1 AAAAATT-AT * 8325732 ATAAACTTAT 1 A-AAAATTAT 8325742 AAAAATTAT 1 AAAAATTAT * 8325751 AAAAAATCAT 1 -AAAAATTAT 8325761 AAAAA 1 AAAAA 8325766 CTTGAACTGG Statistics Matches: 207, Mismatches: 40, Indels: 54 0.69 0.13 0.18 Matches are distributed among these distances: 7 5 0.02 8 28 0.14 9 90 0.43 10 57 0.28 11 25 0.12 12 2 0.01 ACGTcount: A:0.61, C:0.06, G:0.01, T:0.31 Consensus pattern (9 bp): AAAAATTAT Found at i:8325765 original size:20 final size:19 Alignment explanation

Indices: 8325482--8325765 Score: 97 Period size: 19 Copynumber: 14.8 Consensus size: 19 8325472 AAAAAATCTG * * 8325482 AAAAAATCATATAAATCAT 1 AAAAAATCATAAAAATTAT * * 8325501 -AAAAATTATAAAAA-TAG 1 AAAAAATCATAAAAATTAT * 8325518 AAAAAACCATCAAAAATTAT 1 AAAAAATCAT-AAAAATTAT * * 8325538 -AAAAATTAT-TAAA-TAT 1 AAAAAATCATAAAAATTAT * * 8325554 TAAAAAT-ATGAAAATTGAT 1 AAAAAATCATAAAAATT-AT * * 8325573 AAAAACT-TTAAAAA-TAT 1 AAAAAATCATAAAAATTAT * * 8325590 AAAAAAATTATACAAATTAT 1 -AAAAAATCATAAAAATTAT * 8325610 -AAAAAT-ATAATAATTTAT 1 AAAAAATCATAA-AAATTAT * 8325628 AAAATCAAAT-TTATAAAATTAAT 1 -AAA--AAATCATA-AAAATT-AT * ** * * 8325651 AAAACATTTTTAAAATTTT 1 AAAAAATCATAAAAATTAT * * 8325670 ATAAAAGCATATTAAAATTCTAT 1 AAAAAATCATA--AAAA-T-TAT * * 8325693 AAAAATTCATACACAATTAT 1 AAAAAATCATA-AAAATTAT * 8325713 AAAAAAT-ATTAAAATTAAT 1 AAAAAATCATAAAAATT-AT * * * 8325732 ATAAACTTATAAAAATTAT 1 AAAAAATCATAAAAATTAT 8325751 AAAAAATCATAAAAA 1 AAAAAATCATAAAAA 8325766 CTTGAACTGG Statistics Matches: 195, Mismatches: 46, Indels: 48 0.67 0.16 0.17 Matches are distributed among these distances: 16 5 0.03 17 18 0.09 18 44 0.23 19 58 0.30 20 33 0.17 21 7 0.04 22 17 0.09 23 13 0.07 ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31 Consensus pattern (19 bp): AAAAAATCATAAAAATTAT Found at i:8326277 original size:9 final size:9 Alignment explanation

Indices: 8326265--8326347 Score: 79 Period size: 9 Copynumber: 9.6 Consensus size: 9 8326255 TTTATGTAAA 8326265 TTTTAATAT 1 TTTTAATAT 8326274 TTTT-AT-T 1 TTTTAATAT 8326281 TTTT-AT-T 1 TTTTAATAT 8326288 TTTT-ATAT 1 TTTTAATAT * 8326296 TTTTAAAAT 1 TTTTAATAT * 8326305 TTTTAAAAT 1 TTTTAATAT 8326314 TTTTAATGA- 1 TTTTAAT-AT 8326323 TTTTAATGAT 1 TTTTAAT-AT 8326333 TTTTAATTAT 1 TTTTAA-TAT 8326343 TTTTA 1 TTTTA 8326348 TGAGAAAAAT Statistics Matches: 67, Mismatches: 2, Indels: 9 0.86 0.03 0.12 Matches are distributed among these distances: 7 14 0.21 8 7 0.10 9 31 0.46 10 14 0.21 11 1 0.01 ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67 Consensus pattern (9 bp): TTTTAATAT Found at i:8340709 original size:5 final size:5 Alignment explanation

Indices: 8340694--8340734 Score: 55 Period size: 5 Copynumber: 8.2 Consensus size: 5 8340684 CTCACCCTTA * * * 8340694 ACTTT ATTTT ACTTT ACTTT ACTTT ACTTT AATTT AATTT A 1 ACTTT ACTTT ACTTT ACTTT ACTTT ACTTT ACTTT ACTTT A 8340735 AGGCTATGTC Statistics Matches: 33, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 5 33 1.00 ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61 Consensus pattern (5 bp): ACTTT Found at i:8341187 original size:15 final size:15 Alignment explanation

Indices: 8341163--8341192 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 8341153 CTCCAACTCT 8341163 TTGGTCTTAAGAATG 1 TTGGTCTTAAGAATG * 8341178 TTGGTTTTAAGAATG 1 TTGGTCTTAAGAATG 8341193 ATTGATTGCC Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.27, C:0.03, G:0.27, T:0.43 Consensus pattern (15 bp): TTGGTCTTAAGAATG Found at i:8342813 original size:3 final size:3 Alignment explanation

Indices: 8342795--8342845 Score: 52 Period size: 3 Copynumber: 17.0 Consensus size: 3 8342785 TTAAATACTC * * 8342795 TTA TTA TTT TTA -TA TTA TTAA TT- TTA TTA TTA TTA ATA TTA TTA 1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA 8342839 TGTA TTA 1 T-TA TTA 8342846 GTTTATGTTT Statistics Matches: 40, Mismatches: 4, Indels: 8 0.77 0.08 0.15 Matches are distributed among these distances: 2 4 0.10 3 30 0.75 4 6 0.15 ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65 Consensus pattern (3 bp): TTA Found at i:8342825 original size:15 final size:15 Alignment explanation

Indices: 8342795--8342845 Score: 68 Period size: 15 Copynumber: 3.4 Consensus size: 15 8342785 TTAAATACTC * 8342795 TTATTATTTTTA-TA 1 TTATTAATTTTATTA 8342809 TTATTAATTTTATTA 1 TTATTAATTTTATTA * 8342824 TTATTAATATTATTA 1 TTATTAATTTTATTA 8342839 TGTATTA 1 T-TATTA 8342846 GTTTATGTTT Statistics Matches: 33, Mismatches: 2, Indels: 2 0.89 0.05 0.05 Matches are distributed among these distances: 14 11 0.33 15 17 0.52 16 5 0.15 ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65 Consensus pattern (15 bp): TTATTAATTTTATTA Found at i:8349192 original size:22 final size:22 Alignment explanation

Indices: 8349164--8349213 Score: 100 Period size: 22 Copynumber: 2.3 Consensus size: 22 8349154 TCTGATAGAA 8349164 TTTTTGGAGAAGAAGGTCAAAG 1 TTTTTGGAGAAGAAGGTCAAAG 8349186 TTTTTGGAGAAGAAGGTCAAAG 1 TTTTTGGAGAAGAAGGTCAAAG 8349208 TTTTTG 1 TTTTTG 8349214 CAATTTTCAT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 28 1.00 ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34 Consensus pattern (22 bp): TTTTTGGAGAAGAAGGTCAAAG Found at i:8355730 original size:73 final size:73 Alignment explanation

Indices: 8355611--8356098 Score: 632 Period size: 73 Copynumber: 6.9 Consensus size: 73 8355601 AAGGAAAATT * 8355611 AACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTTTGTTTTC 1 AACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTC 8355676 CAAATTTC 66 CAAATTTC * 8355684 AACTCATATTGCGAGAAATGAGTTGGGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG---T- 1 AACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTC * 8355745 ----TGTC 66 CAAATTTC 8355749 AACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG-----T---TTT-TGTTTTC 1 AACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTC 8355805 CAAATTTC 66 CAAATTTC * 8355813 AACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTTTGTTTTC 1 AACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTC 8355878 CAAATTTC 66 CAAATTTC * * 8355886 AACTCATATTGCGAGAAATGAGCTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTC 1 AACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTC * ** 8355951 AAAAAAATC 66 -CAAATTTC * ** * 8355960 AACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCTGCTTTT 1 AACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG-TTTT * ** 8356025 CAAGAAAATC 65 CCA-AATTTC ** * * * * 8356035 AACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACGCTGAGGTATTTTCCATTTCTGTTTT 1 AACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTT 8356099 TCAATTTTTG Statistics Matches: 372, Mismatches: 23, Indels: 39 0.86 0.05 0.09 Matches are distributed among these distances: 56 2 0.01 57 3 0.01 59 1 0.00 60 1 0.00 64 48 0.13 65 47 0.13 69 1 0.00 70 1 0.00 72 3 0.01 73 135 0.36 74 66 0.18 75 64 0.17 ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32 Consensus pattern (73 bp): AACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTC CAAATTTC Found at i:8356063 original size:75 final size:74 Alignment explanation

Indices: 8355811--8356534 Score: 540 Period size: 74 Copynumber: 9.5 Consensus size: 74 8355801 TTTCCAAATT * 8355811 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTTTGTTT 1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTT * ** 8355876 TC-CAAATT 66 TCAAAAAAA * * 8355884 TCAACTCATATTGCGAGAAATGAGCTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTG 1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTT 8355949 TCAAAAAAA 66 TCAAAAAAA * ** * 8355958 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCTGCTT 1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG-TT * 8356023 TTCAAGAAAA 65 TTCAAAAAAA ** * * * * 8356033 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACGCTGAGGTATTTTCCATTTCTGTTT 1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG-TT * 8356098 TTCAATTTTTGTTTTTCAAAA 65 TTCAA-----------AAAAA * * 8356119 TCAACTCATATTGCGAGAAATGAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTTCTGTTG 1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTT 8356184 TCAAAAAAA 66 TCAAAAAAA ** * * * * * 8356193 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACCGAGGTATTTTCTATTTCTGTTT 1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTT *** 8356258 TC---GTCA 66 TCAAAAAAA * ** * ** * * ** * ** ** 8356264 T-TA-TGTTTTTGAAAGAATCAACTCATATTGCGAGAAATAAGTTGAGC-C-CCAAGACACATTG 1 TCAACTCATATTGCGAG-A--AA-TGA-GTT--GAG-CCTCAG--GA-CACGCTGAGGTA-ATT- * 8356325 AGGT-AATTTCAATTTCTGTTTTC--AAAAT 53 ---TCAA-TT-----TCTGTTTTCAAAAAAA * * * 8356353 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT 1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG-TT * 8356418 TTC--AAAAT 65 TTCAAAAAAA * * 8356426 TCAACTCATATTGCGAGAAATGAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTTCTGTTG 1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTT 8356491 TCAAAAAAA 66 TCAAAAAAA * 8356500 TCAACTCGTATTGCGA-AAAGTGAGTTGAGCCTCAG 1 TCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCAG 8356535 TTCACATGTT Statistics Matches: 515, Mismatches: 91, Indels: 89 0.74 0.13 0.13 Matches are distributed among these distances: 69 7 0.01 70 2 0.00 71 2 0.00 72 8 0.02 73 137 0.27 74 157 0.30 75 73 0.14 76 3 0.01 77 6 0.01 78 7 0.01 79 4 0.01 80 2 0.00 81 5 0.01 82 4 0.01 83 5 0.01 84 3 0.01 85 6 0.01 86 61 0.12 87 2 0.00 88 11 0.02 89 1 0.00 90 2 0.00 91 7 0.01 ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33 Consensus pattern (74 bp): TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTT TCAAAAAAA Found at i:8356105 original size:14 final size:14 Alignment explanation

Indices: 8356082--8356116 Score: 52 Period size: 14 Copynumber: 2.5 Consensus size: 14 8356072 CGCTGAGGTA * 8356082 TTTTCCATTTCTGT 1 TTTTCAATTTCTGT * 8356096 TTTTCAATTTTTGT 1 TTTTCAATTTCTGT 8356110 TTTTCAA 1 TTTTCAA 8356117 AATCAACTCA Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 14 19 1.00 ACGTcount: A:0.14, C:0.14, G:0.06, T:0.66 Consensus pattern (14 bp): TTTTCAATTTCTGT Found at i:8356160 original size:86 final size:84 Alignment explanation

Indices: 8356029--8356489 Score: 351 Period size: 73 Copynumber: 5.8 Consensus size: 84 8356019 GCTTTTCAAG ** * * * * 8356029 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACGCTGAGGTATTTTCCATTTCT 1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCT * 8356094 GTTTTTCAATTTTTGTTTTTC 66 GTTTTTCAA--TTTGTTTTTA * * * 8356115 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTTCT 1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCT * 8356180 G-TTGTCAA---------A 66 GTTTTTCAATTTGTTTTTA ** * * * * * 8356189 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACCGAGGTATTTTCTATTTCT 1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCT 8356254 GTTTTCGTC-ATTATGTTTTTGA 66 GTTTT--TCAATT-TGTTTTT-A * * * 8356276 AAGAATCAACTCATATTGCGAGAAATAAGTTGAGCCCCAAGACACATTGAGGTAATTTCAATTTC 1 AA-AATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTC 8356341 TG-TTTTC-----------A 65 TGTTTTTCAATTTGTTTTTA * ** * 8356349 AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT 1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCT * 8356414 G-----C------TTTTCA 66 GTTTTTCAATTTGTTTTTA * * * * 8356422 AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTTCT 1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCT 8356487 GTT 66 GTT 8356490 GTCAAAAAAA Statistics Matches: 316, Mismatches: 37, Indels: 55 0.77 0.09 0.13 Matches are distributed among these distances: 68 1 0.00 72 59 0.19 73 66 0.21 74 58 0.18 75 2 0.01 76 1 0.00 77 2 0.01 85 8 0.03 86 59 0.19 87 6 0.02 88 54 0.17 ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34 Consensus pattern (84 bp): AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCT GTTTTTCAATTTGTTTTTA Found at i:8356254 original size:160 final size:157 Alignment explanation

Indices: 8355954--8356628 Score: 736 Period size: 160 Copynumber: 4.3 Consensus size: 157 8355944 TGTTGTCAAA * * 8355954 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCT 1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCT * * * * 8356019 GCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGTCACGCTGAGGTATT 66 G-TTGTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGTCACACTGAGGTATT * 8356084 TTCCATTTCTGTTTTTCAATTTTTGTTTTTC 130 TTCTATTTCTGTTTTTC-A--TTTGTTTTTC * * * 8356115 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTTCT 1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCT * * * 8356180 GTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACCGAGGTATTT 66 GTTGTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGTCACACTGAGGTATTT * 8356245 TCTATTTCTGTTTTCGTCATTATGTTTTTGA 131 TCTATTTCTGTTTT--TCATT-TGTTTTT-C * * * 8356276 AAGAATCAACTCATATTGCGAGAAATAAGTTGAGCCCCAAGACACATTGAGGTAATTTCAATTTC 1 AA-AATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTC * * * * ** 8356341 TGTTTTC--AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATT 65 TGTTGTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGTCACACTGAGGTATT * 8356404 TTCAATTTCTG-----C------TTTTC 130 TTCTATTTCTGTTTTTCATTTGTTTTTC * * * 8356421 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTTC 1 AAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTC * * * * 8356486 TGTTGTCAAAAAAATCAACTCGTATTGCGAAAAGTGAGTTGAGCCTC-AGTTCACATGTTGAGAT 65 TGTTGTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAG-TCACA--CTGAGGT * * * 8356550 ATCTT-TAGTTTTTGTTTTTAATGTCTGTTTTT- 127 ATTTTCTA-TTTCTGTTTTTCAT-T-TGTTTTTC * * 8356582 AAAGAGTCAATTCATATTGCGAGAAATGAGTTG-GGCTCAAGATCACA 1 AAA-A-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGA-CACA 8356629 TGACAAGTAA Statistics Matches: 434, Mismatches: 53, Indels: 53 0.80 0.10 0.10 Matches are distributed among these distances: 144 2 0.00 145 62 0.14 146 6 0.01 147 37 0.09 148 1 0.00 149 15 0.03 153 1 0.00 159 2 0.00 160 137 0.32 161 73 0.17 162 98 0.23 ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34 Consensus pattern (157 bp): AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTCT GTTGTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGTCACACTGAGGTATTT TCTATTTCTGTTTTTCATTTGTTTTTC Found at i:8356452 original size:73 final size:72 Alignment explanation

Indices: 8356281--8356533 Score: 373 Period size: 73 Copynumber: 3.5 Consensus size: 72 8356271 TTTGAAAGAA * * * 8356281 TCAACTCATATTGCGAGAAATAAGTTGAGCCCCAAGACACATTGAGGTAATTTCAATTTCTGTTT 1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT 8356346 TCAAAAT 66 TCAAAAT * 8356353 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT 1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTG-TT 8356418 TTCAAAAT 65 TTCAAAAT * * * * 8356426 TCAACTCATATTGCGAGAAATGAGTTGAGCCTTAGGACACGCTGAGGTAATTTCAATTTCTGTTG 1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT * 8356491 TCAAAAAAA 66 TC--AAAAT * 8356500 TCAACTCGTATTGCGA-AAAGTGAGTTGAGCCTCA 1 TCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCA 8356534 GTTCACATGT Statistics Matches: 165, Mismatches: 12, Indels: 6 0.90 0.07 0.03 Matches are distributed among these distances: 72 62 0.38 73 71 0.43 74 32 0.19 ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31 Consensus pattern (72 bp): TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT TCAAAAT Found at i:8358241 original size:3 final size:3 Alignment explanation

Indices: 8358224--8358273 Score: 52 Period size: 3 Copynumber: 17.0 Consensus size: 3 8358214 TTAAATACTC * 8358224 TTA TTA TT- TTA -TA TTA TTAA TT- TTA TTA TTA TTA ATA TTA TTA 1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA 8358267 TGTA TTA 1 T-TA TTA 8358274 GTTTATGTTT Statistics Matches: 40, Mismatches: 2, Indels: 10 0.77 0.04 0.19 Matches are distributed among these distances: 2 6 0.15 3 28 0.70 4 6 0.15 ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64 Consensus pattern (3 bp): TTA Found at i:8358255 original size:15 final size:15 Alignment explanation

Indices: 8358224--8358273 Score: 68 Period size: 15 Copynumber: 3.4 Consensus size: 15 8358214 TTAAATACTC 8358224 TTATT-ATTTTA-TA 1 TTATTAATTTTATTA 8358237 TTATTAATTTTATTA 1 TTATTAATTTTATTA * 8358252 TTATTAATATTATTA 1 TTATTAATTTTATTA 8358267 TGTATTA 1 T-TATTA 8358274 GTTTATGTTT Statistics Matches: 33, Mismatches: 1, Indels: 3 0.89 0.03 0.08 Matches are distributed among these distances: 13 5 0.15 14 6 0.18 15 17 0.52 16 5 0.15 ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64 Consensus pattern (15 bp): TTATTAATTTTATTA Found at i:8362058 original size:60 final size:59 Alignment explanation

Indices: 8361942--8362063 Score: 156 Period size: 60 Copynumber: 2.0 Consensus size: 59 8361932 TTTTTAAATT * * 8361942 TTAAATTTTTAAGAATTAAGACTAAATTGATAGAATGTGTAAAGTTGAGAGCTAAATTTG 1 TTAAATTTTTAAGAATTAAGACTAAATTGATAAAATCTGTAAAGTTGAGA-CTAAATTTG * * * * 8362002 TTAAATTTTTTAGATTTAAGACTAAGTTGATAAAATCTGTAAATATTTGAGA-TAAATTTG 1 TTAAATTTTTAAGAATTAAGACTAAATTGATAAAATCTGT-AA-AGTTGAGACTAAATTTG 8362062 TT 1 TT 8362064 CTTAAGAGTG Statistics Matches: 54, Mismatches: 6, Indels: 4 0.84 0.09 0.06 Matches are distributed among these distances: 60 45 0.83 61 2 0.04 62 7 0.13 ACGTcount: A:0.40, C:0.03, G:0.16, T:0.41 Consensus pattern (59 bp): TTAAATTTTTAAGAATTAAGACTAAATTGATAAAATCTGTAAAGTTGAGACTAAATTTG Found at i:8362814 original size:11 final size:11 Alignment explanation

Indices: 8362800--8362879 Score: 62 Period size: 11 Copynumber: 7.5 Consensus size: 11 8362790 TTTTTTTAAA 8362800 TTTTAAAATAC 1 TTTTAAAATAC 8362811 TTTTAAAATAC 1 TTTTAAAATAC * 8362822 TTTTTTTAAAT-- 1 --TTTTAAAATAC * * 8362833 TTTT---TTAA 1 TTTTAAAATAC * 8362841 TTTTAAAATAT 1 TTTTAAAATAC * 8362852 TTTTAAAATAT 1 TTTTAAAATAC 8362863 TTTTAAAATAC 1 TTTTAAAATAC 8362874 TTTTAA 1 TTTTAA 8362880 TTTTTTTTAA Statistics Matches: 57, Mismatches: 5, Indels: 14 0.75 0.07 0.18 Matches are distributed among these distances: 6 1 0.02 8 4 0.07 9 4 0.07 11 40 0.70 13 8 0.14 ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56 Consensus pattern (11 bp): TTTTAAAATAC Found at i:8362826 original size:41 final size:42 Alignment explanation

Indices: 8362776--8362943 Score: 162 Period size: 49 Copynumber: 3.8 Consensus size: 42 8362766 GCCCGAATAC * 8362776 AATA-ATTTTTTT-ATTTTTTTTAAATTTTAAAATACTTTTAA 1 AATATATTTTTTTAATTTTTTTT-AATTTTAAAATATTTTTAA * * 8362817 AATA-CTTTTTTTAAATTTTTTTAATTTTAAAATATTTTTAA 1 AATATATTTTTTTAATTTTTTTTAATTTTAAAATATTTTTAA * 8362858 AATATTTTTAAAATACTTTTAATTTTTTTTAATTTTAAAATATTTTTAA 1 AATA-TATT----T--TTTTAATTTTTTTTAATTTTAAAATATTTTTAA * * * 8362907 AATAGAATTTTTTATTTTTGTTTTAATTTTTAAAATA 1 AATATATTTTTTTAATTTT-TTTTAA-TTTTAAAATA 8362944 AATTTTTGGT Statistics Matches: 107, Mismatches: 9, Indels: 19 0.79 0.07 0.14 Matches are distributed among these distances: 41 33 0.31 42 17 0.16 43 8 0.07 44 11 0.10 47 1 0.01 48 1 0.01 49 36 0.34 ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60 Consensus pattern (42 bp): AATATATTTTTTTAATTTTTTTTAATTTTAAAATATTTTTAA Found at i:8362845 original size:30 final size:28 Alignment explanation

Indices: 8362811--8362910 Score: 88 Period size: 22 Copynumber: 3.8 Consensus size: 28 8362801 TTTAAAATAC * * 8362811 TTTTAAAATACTTTTTTTAAATTTTTTTAA 1 TTTTAAAATA--TTTTTAAAATATTTTTAA 8362841 TTTTAAAATATTTTTAAAATA----T-- 1 TTTTAAAATATTTTTAAAATATTTTTAA * * * 8362863 TTTTAAAATACTTTT-AATTTTTTTTAA 1 TTTTAAAATATTTTTAAAATATTTTTAA 8362890 TTTTAAAATATTTTTAAAATA 1 TTTTAAAATATTTTTAAAATA 8362911 GAATTTTTTA Statistics Matches: 55, Mismatches: 8, Indels: 16 0.70 0.10 0.20 Matches are distributed among these distances: 21 3 0.05 22 14 0.25 24 1 0.02 25 1 0.02 27 14 0.25 28 12 0.22 30 10 0.18 ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59 Consensus pattern (28 bp): TTTTAAAATATTTTTAAAATATTTTTAA Found at i:8362849 original size:17 final size:17 Alignment explanation

Indices: 8362824--8362857 Score: 50 Period size: 17 Copynumber: 2.0 Consensus size: 17 8362814 TAAAATACTT * * 8362824 TTTTTAAATTTTTTTAA 1 TTTTAAAATATTTTTAA 8362841 TTTTAAAATATTTTTAA 1 TTTTAAAATATTTTTAA 8362858 AATATTTTTA Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65 Consensus pattern (17 bp): TTTTAAAATATTTTTAA Found at i:8362897 original size:49 final size:50 Alignment explanation

Indices: 8362800--8362910 Score: 179 Period size: 49 Copynumber: 2.2 Consensus size: 50 8362790 TTTTTTTAAA 8362800 TTTTAAAATACTTTTAAAATACTTTTTTTAAATTTTTTTAATTTTAAAATAT 1 TTTTAAAATACTTTTAAAATAC--TTTTTAAATTTTTTTAATTTTAAAATAT * * 8362852 TTTTAAAATATTTTTAAAATAC-TTTTAATTTTTTTTAATTTTAAAATAT 1 TTTTAAAATACTTTTAAAATACTTTTTAAATTTTTTTAATTTTAAAATAT 8362901 TTTTAAAATA 1 TTTTAAAATA 8362911 GAATTTTTTA Statistics Matches: 57, Mismatches: 2, Indels: 3 0.92 0.03 0.05 Matches are distributed among these distances: 49 36 0.63 52 21 0.37 ACGTcount: A:0.40, C:0.03, G:0.00, T:0.58 Consensus pattern (50 bp): TTTTAAAATACTTTTAAAATACTTTTTAAATTTTTTTAATTTTAAAATAT Found at i:8362925 original size:38 final size:37 Alignment explanation

Indices: 8362852--8362925 Score: 96 Period size: 38 Copynumber: 1.9 Consensus size: 37 8362842 TTTAAAATAT * * 8362852 TTTTAAAATATTTTTAAAATACTTTTAATTTTTTTTAA 1 TTTTAAAATATTTTTAAAATAATTTT-ATTATTTTTAA 8362890 TTTTAAAATATTTTTAAAATAGAATTTT-TTATTTTT 1 TTTTAAAATATTTTTAAAAT--AATTTTATTATTTTT 8362926 GTTTTAATTT Statistics Matches: 32, Mismatches: 2, Indels: 4 0.84 0.05 0.11 Matches are distributed among these distances: 38 27 0.84 40 5 0.16 ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61 Consensus pattern (37 bp): TTTTAAAATATTTTTAAAATAATTTTATTATTTTTAA Found at i:8364101 original size:8 final size:8 Alignment explanation

Indices: 8364090--8364140 Score: 84 Period size: 8 Copynumber: 6.2 Consensus size: 8 8364080 TTTTTTTATT * 8364090 TTTTAAAG 1 TTTTAAAA 8364098 TTTTAAAA 1 TTTTAAAA 8364106 TTTTAAAA 1 TTTTAAAA 8364114 TTTTAAAA 1 TTTTAAAA 8364122 TTTTAAAA 1 TTTTAAAA 8364130 TTTTAAGAA 1 TTTTAA-AA 8364139 TT 1 TT 8364141 AAGACTAAAG Statistics Matches: 41, Mismatches: 1, Indels: 1 0.95 0.02 0.02 Matches are distributed among these distances: 8 37 0.90 9 4 0.10 ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51 Consensus pattern (8 bp): TTTTAAAA Found at i:8365657 original size:14 final size:14 Alignment explanation

Indices: 8365638--8365665 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 8365628 CTATAAAAAT 8365638 AAAATTAAAAATAA 1 AAAATTAAAAATAA 8365652 AAAATTAAAAATAA 1 AAAATTAAAAATAA 8365666 TTCATTTAAA 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:0.79, C:0.00, G:0.00, T:0.21 Consensus pattern (14 bp): AAAATTAAAAATAA Found at i:8366208 original size:18 final size:19 Alignment explanation

Indices: 8366179--8366223 Score: 56 Period size: 19 Copynumber: 2.4 Consensus size: 19 8366169 AAGGAAAATG * * 8366179 ATTTTTAAAAAATATTTAAT 1 ATTTTTTAAAAA-AGTTAAT 8366199 -TTTTTTAAAAAAGTTAAT 1 ATTTTTTAAAAAAGTTAAT 8366217 ATTTTTT 1 ATTTTTT 8366224 TGTGTTTAGA Statistics Matches: 22, Mismatches: 2, Indels: 3 0.81 0.07 0.11 Matches are distributed among these distances: 18 6 0.27 19 16 0.73 ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56 Consensus pattern (19 bp): ATTTTTTAAAAAAGTTAAT Found at i:8369076 original size:42 final size:42 Alignment explanation

Indices: 8369029--8369227 Score: 251 Period size: 42 Copynumber: 4.7 Consensus size: 42 8369019 AAAAACGTCG * * * * 8369029 CTAAAGATCATATTCTTTAGCGGCGTTTTTCCT-TAAGCGCCA 1 CTAAAGAACATGTTCTTTAGCGGCGTTTTT-TTATAAGCGCCT * 8369071 CTAAAGAACATGTT-TTTCAGCAGCGTTTTTTT-TAAGCGCCT 1 CTAAAGAACATGTTCTTT-AGCGGCGTTTTTTTATAAGCGCCT * * 8369112 CTAAAGAACATGTTCTTTAGCGGCGTTTTTTATATGAGCGCCG 1 CTAAAGAACATGTTCTTTAGCGGCGTTTTTT-TATAAGCGCCT * * * 8369155 CTAAAGAACATGTTCTTTAGCGGCATTTTTTTCTAAGCACCT 1 CTAAAGAACATGTTCTTTAGCGGCGTTTTTTTATAAGCGCCT * 8369197 CTAAAGAACATGTTCTTTAGCGGCGCTTTTT 1 CTAAAGAACATGTTCTTTAGCGGCGTTTTTT 8369228 CTTTGCTTTT Statistics Matches: 138, Mismatches: 15, Indels: 8 0.86 0.09 0.05 Matches are distributed among these distances: 41 38 0.28 42 63 0.46 43 37 0.27 ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37 Consensus pattern (42 bp): CTAAAGAACATGTTCTTTAGCGGCGTTTTTTTATAAGCGCCT Found at i:8369552 original size:5 final size:5 Alignment explanation

Indices: 8369542--8369567 Score: 52 Period size: 5 Copynumber: 5.2 Consensus size: 5 8369532 CGTCGTACTT 8369542 TCTGC TCTGC TCTGC TCTGC TCTGC T 1 TCTGC TCTGC TCTGC TCTGC TCTGC T 8369568 TCTCTTGCTG Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 21 1.00 ACGTcount: A:0.00, C:0.38, G:0.19, T:0.42 Consensus pattern (5 bp): TCTGC Found at i:8369650 original size:21 final size:21 Alignment explanation

Indices: 8369626--8369676 Score: 75 Period size: 21 Copynumber: 2.4 Consensus size: 21 8369616 TTCTTTTGAA * 8369626 CCTCTGCTTCTCTCGTTGCAG 1 CCTCTGCTTCTCTCGCTGCAG * 8369647 CCTCTGCTTCTCTCGCTGCCG 1 CCTCTGCTTCTCTCGCTGCAG * 8369668 CATCTGCTT 1 CCTCTGCTT 8369677 TAAGTTGTAG Statistics Matches: 27, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 21 27 1.00 ACGTcount: A:0.04, C:0.41, G:0.18, T:0.37 Consensus pattern (21 bp): CCTCTGCTTCTCTCGCTGCAG Found at i:8375170 original size:9 final size:9 Alignment explanation

Indices: 8375156--8375315 Score: 125 Period size: 9 Copynumber: 17.8 Consensus size: 9 8375146 TTTTTATGTA 8375156 TTATGTAAG 1 TTATGTAAG 8375165 TTATGTACTAAG 1 TTATG---TAAG * 8375177 TTCTGT-A- 1 TTATGTAAG 8375184 TTATGTAAG 1 TTATGTAAG 8375193 TTATGTAAG 1 TTATGTAAG * 8375202 TTGTGT-A- 1 TTATGTAAG * 8375209 TTATGTGAG 1 TTATGTAAG 8375218 TTATGTAAG 1 TTATGTAAG 8375227 TTATGTAAG 1 TTATGTAAG * * 8375236 TTATTTAAT 1 TTATGTAAG 8375245 TTATGTAAG 1 TTATGTAAG * 8375254 TTTATATATAAG 1 --T-TATGTAAG * 8375266 TTATGTAGG 1 TTATGTAAG * 8375275 CTATGT-A- 1 TTATGTAAG * * 8375282 TTATCTAAA 1 TTATGTAAG * 8375291 TAATGTAAG 1 TTATGTAAG 8375300 TTATGTAAG 1 TTATGTAAG 8375309 TTATGTA 1 TTATGTA 8375316 GGCCATGTAT Statistics Matches: 119, Mismatches: 20, Indels: 24 0.73 0.12 0.15 Matches are distributed among these distances: 7 14 0.12 8 5 0.04 9 83 0.70 10 1 0.01 11 1 0.01 12 15 0.13 ACGTcount: A:0.32, C:0.03, G:0.19, T:0.47 Consensus pattern (9 bp): TTATGTAAG Found at i:8375208 original size:25 final size:25 Alignment explanation

Indices: 8375149--8375382 Score: 160 Period size: 25 Copynumber: 9.3 Consensus size: 25 8375139 TGATATATTT 8375149 TTATGTATTATGTAAGTTATGTACTAAG 1 TTATGTATTATGTAAGTTATG---TAAG * 8375177 TTCTGTATTATGTAAGTTATGTAAG 1 TTATGTATTATGTAAGTTATGTAAG * * 8375202 TTGTGTATTATGTGAGTTATGTAAG 1 TTATGTATTATGTAAGTTATGTAAG * * 8375227 TTATGTAAGTTATTTAATTTATGTAAG 1 TTATGT-A-TTATGTAAGTTATGTAAG * * 8375254 -T-T-TA-TATATAAGTTATGTAGG 1 TTATGTATTATGTAAGTTATGTAAG * * * * 8375275 CTATGTATTATCTAAATAATGTAAG 1 TTATGTATTATGTAAGTTATGTAAG * ** 8375300 TTATGTAAGTTATGTAGGCCATGT-A- 1 TTATGT-A-TTATGTAAGTTATGTAAG * * 8375325 TTATGTTATTATATAAGTTATGCAAG 1 TTATG-TATTATGTAAGTTATGTAAG * * * 8375351 TT-TATA-TATTGTATGTTATTTAAG 1 TTATGTATTA-TGTAAGTTATGTAAG 8375375 TTATGTAT 1 TTATGTAT 8375383 AAGTTATTAT Statistics Matches: 161, Mismatches: 31, Indels: 30 0.73 0.14 0.14 Matches are distributed among these distances: 21 14 0.09 22 1 0.01 23 4 0.02 24 28 0.17 25 62 0.39 26 7 0.04 27 25 0.16 28 20 0.12 ACGTcount: A:0.31, C:0.03, G:0.18, T:0.48 Consensus pattern (25 bp): TTATGTATTATGTAAGTTATGTAAG Found at i:8375227 original size:34 final size:34 Alignment explanation

Indices: 8375184--8375315 Score: 138 Period size: 34 Copynumber: 3.7 Consensus size: 34 8375174 AAGTTCTGTA * * 8375184 TTATGTAAGTTATGTAAGTTGTGTATTATGTGAG 1 TTATGTAAGTTATGTAAGTTATGTATTATGTAAG * 8375218 TTATGTAAGTTATGTAAGTTATTTAATTTATGTAAG 1 TTATGTAAGTTATGTAAGTTATGT-A-TTATGTAAG * * * * * 8375254 TTTATATATAAGTTATGTAGGCTATGTATTATCTAAA 1 --T-TATGTAAGTTATGTAAGTTATGTATTATGTAAG * 8375291 TAATGTAAGTTATGTAAGTTATGTA 1 TTATGTAAGTTATGTAAGTTATGTA 8375316 GGCCATGTAT Statistics Matches: 80, Mismatches: 13, Indels: 10 0.78 0.13 0.10 Matches are distributed among these distances: 34 42 0.52 35 2 0.03 36 8 0.10 37 7 0.09 38 2 0.03 39 19 0.24 ACGTcount: A:0.33, C:0.02, G:0.19, T:0.47 Consensus pattern (34 bp): TTATGTAAGTTATGTAAGTTATGTATTATGTAAG Found at i:8375419 original size:35 final size:35 Alignment explanation

Indices: 8375326--8375431 Score: 105 Period size: 35 Copynumber: 2.9 Consensus size: 35 8375316 GGCCATGTAT 8375326 TATGTTATTATATAAGT-TATGCAAGTTTATATATTG 1 TATGTTATTATATAAGTATAT--AAGTTTATATATTG 8375362 TATGTTA-T-T-TAAGTTATGTATAAG-TTATTATATTG 1 TATGTTATTATATAAG-TA--TATAAGTTTA-TATATTG 8375397 TATGTTATTATATAAGTATATAAGATTCTATATAT 1 TATGTTATTATATAAGTATATAAG-TT-TATATAT 8375432 GTTTATATAT Statistics Matches: 59, Mismatches: 0, Indels: 21 0.74 0.00 0.26 Matches are distributed among these distances: 33 4 0.07 34 5 0.08 35 24 0.41 36 8 0.14 37 12 0.20 38 6 0.10 ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51 Consensus pattern (35 bp): TATGTTATTATATAAGTATATAAGTTTATATATTG Found at i:8375589 original size:17 final size:16 Alignment explanation

Indices: 8375548--8375591 Score: 54 Period size: 15 Copynumber: 2.8 Consensus size: 16 8375538 TAAATTTTGA * * 8375548 AAAAATTATAGATTTT 1 AAAAATTATATATATT 8375564 AAAAA-TATATATATT 1 AAAAATTATATATATT 8375579 AAAAATGTATATA 1 AAAAAT-TATATA 8375592 AATATTTATA Statistics Matches: 24, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 15 13 0.54 16 5 0.21 17 6 0.25 ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39 Consensus pattern (16 bp): AAAAATTATATATATT Found at i:8375838 original size:23 final size:23 Alignment explanation

Indices: 8375794--8375838 Score: 54 Period size: 23 Copynumber: 2.0 Consensus size: 23 8375784 ATAAAATTGG * * 8375794 AATATAGGTTATATGTCCATATT 1 AATATAGGTTATATATCAATATT * * 8375817 AATATATGTTATATATTAATAT 1 AATATAGGTTATATATCAATAT 8375839 ATGTCCCAAA Statistics Matches: 18, Mismatches: 4, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 23 18 1.00 ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47 Consensus pattern (23 bp): AATATAGGTTATATATCAATATT Found at i:8378960 original size:14 final size:15 Alignment explanation

Indices: 8378942--8378980 Score: 55 Period size: 14 Copynumber: 2.7 Consensus size: 15 8378932 TTCTAAACAT 8378942 TAAACCCCAAAAACC 1 TAAACCCCAAAAACC * 8378957 -AAACCCC-AAACCC 1 TAAACCCCAAAAACC 8378970 TAAACCCCAAA 1 TAAACCCCAAA 8378981 TCTCAAACCA Statistics Matches: 21, Mismatches: 1, Indels: 4 0.81 0.04 0.15 Matches are distributed among these distances: 13 5 0.24 14 14 0.67 15 2 0.10 ACGTcount: A:0.51, C:0.44, G:0.00, T:0.05 Consensus pattern (15 bp): TAAACCCCAAAAACC Found at i:8378979 original size:21 final size:21 Alignment explanation

Indices: 8378955--8378994 Score: 53 Period size: 21 Copynumber: 1.9 Consensus size: 21 8378945 ACCCCAAAAA * 8378955 CCAAACCCCAAACCCTAAACC 1 CCAAACCCCAAACCATAAACC * * 8378976 CCAAATCTCAAACCATAAA 1 CCAAACCCCAAACCATAAA 8378995 AGTCAAAACC Statistics Matches: 16, Mismatches: 3, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 21 16 1.00 ACGTcount: A:0.47, C:0.42, G:0.00, T:0.10 Consensus pattern (21 bp): CCAAACCCCAAACCATAAACC Found at i:8379385 original size:35 final size:35 Alignment explanation

Indices: 8379346--8379417 Score: 99 Period size: 35 Copynumber: 2.1 Consensus size: 35 8379336 TGAATCTCTA * * * * * 8379346 AACCCCAAATCACTAACTCTTAACTTCTAATCCTT 1 AACCCCAAACCACTAACCCCTAACTACTAACCCTT 8379381 AACCCCAAACCACTAACCCCTAACTACTAACCCTT 1 AACCCCAAACCACTAACCCCTAACTACTAACCCTT 8379416 AA 1 AA 8379418 ATTACCTTAT Statistics Matches: 32, Mismatches: 5, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 35 32 1.00 ACGTcount: A:0.38, C:0.39, G:0.00, T:0.24 Consensus pattern (35 bp): AACCCCAAACCACTAACCCCTAACTACTAACCCTT Found at i:8379397 original size:14 final size:14 Alignment explanation

Indices: 8379380--8379413 Score: 50 Period size: 14 Copynumber: 2.4 Consensus size: 14 8379370 TTCTAATCCT 8379380 TAACCCCAAACCAC 1 TAACCCCAAACCAC * * 8379394 TAACCCCTAACTAC 1 TAACCCCAAACCAC 8379408 TAACCC 1 TAACCC 8379414 TTAAATTACC Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 14 18 1.00 ACGTcount: A:0.38, C:0.47, G:0.00, T:0.15 Consensus pattern (14 bp): TAACCCCAAACCAC Found at i:8379486 original size:20 final size:20 Alignment explanation

Indices: 8379458--8379512 Score: 56 Period size: 20 Copynumber: 2.7 Consensus size: 20 8379448 ATTAATTAAT * 8379458 CAAAACCCTAAATCCTAACC 1 CAAAACCCTAAACCCTAACC * * 8379478 CAAATCCCTAACCCCTAACC 1 CAAAACCCTAAACCCTAACC ** 8379498 CTTAACCCTTAAACC 1 CAAAACCC-TAAACC 8379513 TTATTTCATA Statistics Matches: 27, Mismatches: 7, Indels: 1 0.77 0.20 0.03 Matches are distributed among these distances: 20 22 0.81 21 5 0.19 ACGTcount: A:0.38, C:0.44, G:0.00, T:0.18 Consensus pattern (20 bp): CAAAACCCTAAACCCTAACC Found at i:8379544 original size:92 final size:93 Alignment explanation

Indices: 8379374--8379563 Score: 218 Period size: 88 Copynumber: 2.1 Consensus size: 93 8379364 CTTAACTTCT 8379374 AATCCTTAACCCCAAACCACTAACCCCTAACTACTAACCCTTAAATTACCTTATTTAATATATAA 1 AATCCTTAACCCCAAACCACTAACCCCTAACTACTAACCCTTAAA-TACCTTATTTAATATATAA 8379439 ATTAAAAATATTAATTAATCAAAACCCTA 65 ATTAAAAATATTAATTAATCAAAACCCTA * * 8379468 AATCC-TAA-CCCAAATCC-CTAACCCCTAAC-CCTTAACCCTT-AA-ACCTTATTTCATA-A-A 1 AATCCTTAACCCCAAA-CCACTAACCCCTAACTAC-TAACCCTTAAATACCTTATTTAATATATA * * * ** 8379525 AATTATAACACACTAATTAATTTAAACCCTA 64 AATTA-AAAATATTAATTAATCAAAACCCTA 8379556 AAT-CTTAA 1 AATCCTTAA 8379564 ATTGACAGTA Statistics Matches: 85, Mismatches: 7, Indels: 14 0.80 0.07 0.13 Matches are distributed among these distances: 87 7 0.08 88 27 0.32 89 12 0.14 91 3 0.04 92 26 0.31 93 5 0.06 94 5 0.06 ACGTcount: A:0.43, C:0.27, G:0.00, T:0.29 Consensus pattern (93 bp): AATCCTTAACCCCAAACCACTAACCCCTAACTACTAACCCTTAAATACCTTATTTAATATATAAA TTAAAAATATTAATTAATCAAAACCCTA Found at i:8379657 original size:14 final size:15 Alignment explanation

Indices: 8379638--8379670 Score: 59 Period size: 14 Copynumber: 2.3 Consensus size: 15 8379628 CTTAAACCAG 8379638 AATCCCTAA-TCCAT 1 AATCCCTAATTCCAT 8379652 AATCCCTAATTCCAT 1 AATCCCTAATTCCAT 8379667 AATC 1 AATC 8379671 TATAAACGTT Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 14 9 0.50 15 9 0.50 ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30 Consensus pattern (15 bp): AATCCCTAATTCCAT Found at i:8380421 original size:114 final size:113 Alignment explanation

Indices: 8380211--8380618 Score: 491 Period size: 114 Copynumber: 3.6 Consensus size: 113 8380201 TTTTTCCTAG * * * * * * 8380211 CGCCACTAATTCTAATCTACCTCAAGACTAAACGCTGCATTTTAGATAAGATATTTTGCAGCGCG 1 CGCCACTAACTCTAATCTACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGC- * * * 8380276 TTC-AG--ACATGCGCAGCTAATACTATGCTTTAGCGGCGTGTTCTCCCAAA 65 TTCTTGTAAAATGC-C-GCTAATACTGTGCTTTAGCGGCGT-TTCTCCCAAA * * * * 8380325 CGCCGCTAACTCTAATCTACCTCAAGACCAAACGGTGCGTTTTGGTTAAGATCTTTTGCGGCACT 1 CGCCACTAACTCTAATCTACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCT * * 8380390 TCTTGTAAAATGCCGCTAATACCGTGCTTTAGCGGCGTATTCTCCCAAG 66 TCTTGTAAAATGCCGCTAATACTGTGCTTTAGCGGCGT-TTCTCCCAAA * * 8380439 CGCCACTAACTCTAATCTACCTCAAGACCAAACGGTGCGTTTTGGTTAAGATCTTTTGCGGCGCT 1 CGCCACTAACTCTAATCTACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCT * * * 8380504 TTTTGTAAAATGTCGCTAATACTGTTCTTTAGCGGCGTTT-TCCCGTAAA 66 TCTTGTAAAATGCCGCTAATACTGTGCTTTAGCGGCGTTTCTCCC--AAA * * * * * * 8380553 TGCCACTAATTCTAATATACCTCAAAACCAAACTCTGCGTTTTGGTTAAGGTATTTTGCGGCGCT 1 CGCCACTAACTCTAATCTACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCT 8380618 T 66 T 8380619 ACAAATAAAC Statistics Matches: 258, Mismatches: 31, Indels: 10 0.86 0.10 0.03 Matches are distributed among these distances: 112 4 0.02 113 5 0.02 114 243 0.94 115 1 0.00 116 5 0.02 ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32 Consensus pattern (113 bp): CGCCACTAACTCTAATCTACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCT TCTTGTAAAATGCCGCTAATACTGTGCTTTAGCGGCGTTTCTCCCAAA Done.