Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_A07

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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32

Warning! 2857347 characters in sequence are not A, C, G, or T


File 222 of 290

Found at i:72412925 original size:39 final size:39

Alignment explanation

Indices: 72412688--72412930 Score: 122 Period size: 40 Copynumber: 6.1 Consensus size: 39 72412678 TTGAATGCTG * ** * 72412688 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATA 1 TCCGGGCTAAGTCCCGAAGGCATTGAAC-GAGTGACTATA * * ** * * 72412728 TCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTA-A 1 TCCGGGCTAAG-TCCCGAAGGCA-TTGAACGAGTGACTATA * * ** 72412767 TTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGAT-ACTA-A 1 -TCCGGGCTAAGTCCCGAAGG-CATTGAACGAG-TGACTATA * ** ** * 72412807 TTCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGT-TTTAAAA 1 -TCCGGGCTAAGTCCCGAAGGCATT-GAACGAGTGACT-ATA * * * 72412848 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATA 1 TCCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATA * 72412887 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG-GAGCTATA 1 TCCGGGCTAAGTCCCGAAGGCA-TTGAACGAGTGA-CTATA 72412926 TCCGG 1 TCCGG 72412931 TTAAATTCCG Statistics Matches: 166, Mismatches: 24, Indels: 26 0.77 0.11 0.12 Matches are distributed among these distances: 38 20 0.12 39 27 0.16 40 110 0.66 41 9 0.05 ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27 Consensus pattern (39 bp): TCCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATA Found at i:72416848 original size:46 final size:45 Alignment explanation

Indices: 72416798--72416970 Score: 172 Period size: 46 Copynumber: 3.8 Consensus size: 45 72416788 TGGTTGAGCA 72416798 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G **** * * 72416844 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGGGAAATGTAACTAG-GCA- 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG * * 72416891 TCCAAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G * * 72416937 -CCTGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA 1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA 72416971 GGGGCGGGTT Statistics Matches: 101, Mismatches: 18, Indels: 16 0.75 0.13 0.12 Matches are distributed among these distances: 43 1 0.01 44 3 0.03 45 3 0.03 46 59 0.58 47 30 0.30 48 1 0.01 49 3 0.03 50 1 0.01 ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30 Consensus pattern (45 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG Found at i:72416954 original size:93 final size:93 Alignment explanation

Indices: 72416795--72416965 Score: 281 Period size: 93 Copynumber: 1.8 Consensus size: 93 72416785 GGATGGTTGA * * 72416795 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT 1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT 72416860 TGAGTCCGAGTTCGGGAAATGTAACTAG 66 TGAGTCCGAGTTCGGGAAATGTAACTAG * * 72416888 GCATCCAAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG 1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG * 72416952 TTGAGTCTGAGTTC 65 TTGAGTCCGAGTTC 72416966 ACTTAGGGGC Statistics Matches: 72, Mismatches: 5, Indels: 2 0.91 0.06 0.03 Matches are distributed among these distances: 92 2 0.03 93 70 0.97 ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29 Consensus pattern (93 bp): GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT TGAGTCCGAGTTCGGGAAATGTAACTAG Found at i:72419758 original size:94 final size:92 Alignment explanation

Indices: 72419511--72419775 Score: 283 Period size: 94 Copynumber: 2.8 Consensus size: 92 72419501 GGATAAATTA * * * 72419511 CCGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATATGCGTGCTGATGCATGTCCCA 1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-ATGTG-GCAGATGCATGTCCCA * * 72419576 AACATGTCTTACACTAGCACAACTCTTAG 64 GACATGTCTTACACTAGCACAACTCTGAG * * * * 72419605 CCGATG-CGTGTCCCAGACA-CGTCTTACATTGGCTAC-C-T-CTGTCCAGGCTA-ATGCATGTC 1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-CTCATAATGT---GGC-AGATGCATGTC * * 72419664 CTAGACATGTCTTACACTAGCAC-TCATCTAGATG 61 CCAGACATGTCTTACACTAGCACAAC-TCT-GA-G * 72419698 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCAGAAGCATGTCCCAGA 1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCAGATGCATGTCCCAGA 72419763 CATGTCTTACACT 66 CATGTCTTACACT 72419776 GGCGCACAAA Statistics Matches: 140, Mismatches: 17, Indels: 28 0.76 0.09 0.15 Matches are distributed among these distances: 89 2 0.01 90 1 0.01 91 36 0.26 92 15 0.11 93 21 0.15 94 47 0.34 95 14 0.10 96 1 0.01 97 3 0.02 ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27 Consensus pattern (92 bp): CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCAGATGCATGTCCCAGA CATGTCTTACACTAGCACAACTCTGAG Found at i:72426761 original size:47 final size:46 Alignment explanation

Indices: 72426616--72426782 Score: 151 Period size: 46 Copynumber: 3.6 Consensus size: 46 72426606 CAAGGCTAAT * * * * ** 72426616 GCATGTCCCGAATATGTCTTACTCTGGCACTCATAATATGGTTGAA 1 GCATGTCCCAAACATGTCTTACACTGGCACTCATAATGTGGCCGAA * * * * * 72426662 GCATGT-CCAAGACATGTCTTACACTAGCCCTCGT-CTG-GATGCCGAT 1 GCATGTCCCAA-ACATGTCTTACACTGGCACTCATAATGTG--GCCGAA * * 72426708 GCCATGTCCCATACATGGTCTTACACTGGCTCTCATAATGTGGCCGAA 1 G-CATGTCCCAAACAT-GTCTTACACTGGCACTCATAATGTGGCCGAA 72426756 GCATGTCCCAAACATGTCTTACACTGG 1 GCATGTCCCAAACATGTCTTACACTGG 72426783 TGCACAAATC Statistics Matches: 95, Mismatches: 18, Indels: 16 0.74 0.14 0.12 Matches are distributed among these distances: 44 1 0.01 45 4 0.04 46 40 0.42 47 22 0.23 48 25 0.26 49 2 0.02 50 1 0.01 ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28 Consensus pattern (46 bp): GCATGTCCCAAACATGTCTTACACTGGCACTCATAATGTGGCCGAA Found at i:72443910 original size:90 final size:90 Alignment explanation

Indices: 72443777--72443941 Score: 224 Period size: 90 Copynumber: 1.8 Consensus size: 90 72443767 GTTTGGGTTG * * * * * * 72443777 ATGAGATCCCGTATAAGACCATATCTAGGATATGGCATCGGCATCG-GTATGTGTTATCATGTAA 1 ATGAGATCCCATATAAGACCATACCTAGGACATGGCATCGGCATCGAGT-TGTGATACCAAGTAA 72443841 GACCATATCTGAGATGTGGTGTTGAT 65 GACCATATCTGAGATGTGGTGTTGAT * * * * 72443867 ATGAGATCCCATGTAAGACCATGCCTAGGACATGGCATTGGCATCGAGTTGTGATCCCAAGTAAG 1 ATGAGATCCCATATAAGACCATACCTAGGACATGGCATCGGCATCGAGTTGTGATACCAAGTAAG 72443932 ACCATATCTG 66 ACCATATCTG 72443942 GGATATGGCG Statistics Matches: 64, Mismatches: 10, Indels: 2 0.84 0.13 0.03 Matches are distributed among these distances: 90 62 0.97 91 2 0.03 ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28 Consensus pattern (90 bp): ATGAGATCCCATATAAGACCATACCTAGGACATGGCATCGGCATCGAGTTGTGATACCAAGTAAG ACCATATCTGAGATGTGGTGTTGAT Found at i:72443950 original size:48 final size:48 Alignment explanation

Indices: 72443781--72443959 Score: 140 Period size: 48 Copynumber: 3.9 Consensus size: 48 72443771 GGGTTGATGA * * * 72443781 GATCCCGTATAAGACCATATCTAGGATATGGCATCGGCATCG-GTATGT 1 GATCCCATGTAAGACCATATCTAGGATATGGCATTGGCATCGAGT-TGT * ** * ** * 72443829 GTTATCATGTAAGACCATATCT-GAGATGTGGTGTT-G-AT--A--TGA 1 GATCCCATGTAAGACCATATCTAG-GATATGGCATTGGCATCGAGTTGT ** * 72443871 GATCCCATGTAAGACCATGCCTAGGACATGGCATTGGCATCGAGTTGT 1 GATCCCATGTAAGACCATATCTAGGATATGGCATTGGCATCGAGTTGT * * * 72443919 GATCCCAAGTAAGACCATATCTGGGATATGGCGTTGGCATC 1 GATCCCATGTAAGACCATATCTAGGATATGGCATTGGCATC 72443960 TTACTATGTG Statistics Matches: 96, Mismatches: 26, Indels: 18 0.69 0.19 0.13 Matches are distributed among these distances: 42 26 0.27 43 2 0.02 44 2 0.02 46 3 0.03 47 2 0.02 48 61 0.64 ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28 Consensus pattern (48 bp): GATCCCATGTAAGACCATATCTAGGATATGGCATTGGCATCGAGTTGT Found at i:72445348 original size:66 final size:66 Alignment explanation

Indices: 72445278--72445407 Score: 188 Period size: 66 Copynumber: 2.0 Consensus size: 66 72445268 TAACCCCTTA * * * 72445278 AATCAACAACCCTTTAAACCCCAGACCCTAAATCTCTAATCATAAACCCCTAAAACTATAAACAC 1 AATCAACAACCCTTTAAACACCAGACCCTAAATATCAAATCATAAACCCCTAAAACTATAAACAC 72445343 T 66 T * * * * * 72445344 AATCAATAACTCTTTAAACACCAGACCCTAAATATCAAATCATAAACTCTTAAAACTCTAAACA 1 AATCAACAACCCTTTAAACACCAGACCCTAAATATCAAATCATAAACCCCTAAAACTATAAACA 72445408 ATAAACCTTA Statistics Matches: 56, Mismatches: 8, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 66 56 1.00 ACGTcount: A:0.46, C:0.29, G:0.02, T:0.23 Consensus pattern (66 bp): AATCAACAACCCTTTAAACACCAGACCCTAAATATCAAATCATAAACCCCTAAAACTATAAACAC T Found at i:72445491 original size:22 final size:23 Alignment explanation

Indices: 72445451--72445503 Score: 72 Period size: 22 Copynumber: 2.3 Consensus size: 23 72445441 TCTCAAATCA * * 72445451 TAAACCCTTAAAACTCCAACCCC 1 TAAACCCCTAAAACCCCAACCCC * 72445474 TAAACCCCT-AAACCCCAACCCT 1 TAAACCCCTAAAACCCCAACCCC 72445496 TAAACCCC 1 TAAACCCC 72445504 AAGCCCTAAA Statistics Matches: 27, Mismatches: 3, Indels: 1 0.87 0.10 0.03 Matches are distributed among these distances: 22 19 0.70 23 8 0.30 ACGTcount: A:0.38, C:0.47, G:0.00, T:0.15 Consensus pattern (23 bp): TAAACCCCTAAAACCCCAACCCC Found at i:72445493 original size:14 final size:14 Alignment explanation

Indices: 72445476--72445513 Score: 58 Period size: 14 Copynumber: 2.7 Consensus size: 14 72445466 CCAACCCCTA 72445476 AACCCCTAAACCCC 1 AACCCCTAAACCCC * 72445490 AACCCTTAAACCCC 1 AACCCCTAAACCCC * 72445504 AAGCCCTAAA 1 AACCCCTAAA 72445514 ACAATGTTTA Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 14 21 1.00 ACGTcount: A:0.39, C:0.47, G:0.03, T:0.11 Consensus pattern (14 bp): AACCCCTAAACCCC Found at i:72445495 original size:65 final size:66 Alignment explanation

Indices: 72445371--72445500 Score: 156 Period size: 65 Copynumber: 2.0 Consensus size: 66 72445361 ACACCAGACC * * * * 72445371 CTAAATATCAAATCATAAACTCTTAAAACTCTAAACAATAAACCTTAATCCCAACACCC-TAAAC 1 CTAAATATCAAATCATAAACCCTTAAAACTCCAAACAATAAACCCTAAACCCAACACCCTTAAAC 72445435 T 66 T * * ** * 72445436 CTAAATCTCAAATCATAAACCCTTAAAACTCCAACCCCTAAACCCCTAAACCCCA-ACCCTTAAA 1 CTAAATATCAAATCATAAACCCTTAAAACTCCAAACAATAAA-CCCTAAACCCAACACCCTTAAA 72445500 C 65 C 72445501 CCCAAGCCCT Statistics Matches: 54, Mismatches: 9, Indels: 3 0.82 0.14 0.05 Matches are distributed among these distances: 65 40 0.74 66 14 0.26 ACGTcount: A:0.45, C:0.34, G:0.00, T:0.22 Consensus pattern (66 bp): CTAAATATCAAATCATAAACCCTTAAAACTCCAAACAATAAACCCTAAACCCAACACCCTTAAAC T Found at i:72445816 original size:7 final size:7 Alignment explanation

Indices: 72445806--72445864 Score: 73 Period size: 7 Copynumber: 8.0 Consensus size: 7 72445796 TAAAAAATAA 72445806 AAAATTT 1 AAAATTT 72445813 AAAATTT 1 AAAATTT 72445820 AAAATTT 1 AAAATTT 72445827 AAAAATTT 1 -AAAATTT 72445835 AAAAATTT 1 -AAAATTT 72445843 AAAAATTT 1 -AAAATTT * 72445851 AAAAATT 1 AAAATTT * 72445858 AATATTT 1 AAAATTT 72445865 TAGTCCATAT Statistics Matches: 48, Mismatches: 3, Indels: 2 0.91 0.06 0.04 Matches are distributed among these distances: 7 25 0.52 8 23 0.48 ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41 Consensus pattern (7 bp): AAAATTT Found at i:72445816 original size:8 final size:8 Alignment explanation

Indices: 72445805--72445857 Score: 92 Period size: 8 Copynumber: 6.9 Consensus size: 8 72445795 ATAAAAAATA 72445805 AAAAATTT 1 AAAAATTT 72445813 -AAAATTT 1 AAAAATTT 72445820 -AAAATTT 1 AAAAATTT 72445827 AAAAATTT 1 AAAAATTT 72445835 AAAAATTT 1 AAAAATTT 72445843 AAAAATTT 1 AAAAATTT 72445851 AAAAATT 1 AAAAATT 72445858 AATATTTTAG Statistics Matches: 44, Mismatches: 0, Indels: 2 0.96 0.00 0.04 Matches are distributed among these distances: 7 14 0.32 8 30 0.68 ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38 Consensus pattern (8 bp): AAAAATTT Found at i:72445866 original size:15 final size:15 Alignment explanation

Indices: 72445790--72445859 Score: 86 Period size: 15 Copynumber: 4.6 Consensus size: 15 72445780 AAATAAACTC * * * 72445790 AAAAAATAAAAAATA 1 AAAAATTAAAAATTT * 72445805 AAAAATTTAAAATTT 1 AAAAATTAAAAATTT * 72445820 AAAATTTAAAAATTT 1 AAAAATTAAAAATTT 72445835 AAAAATTTAAAAATTT 1 AAAAA-TTAAAAATTT 72445851 AAAAATTAA 1 AAAAATTAA 72445860 TATTTTAGTC Statistics Matches: 47, Mismatches: 7, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 15 32 0.68 16 15 0.32 ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31 Consensus pattern (15 bp): AAAAATTAAAAATTT Found at i:72445966 original size:9 final size:9 Alignment explanation

Indices: 72445952--72445994 Score: 50 Period size: 9 Copynumber: 4.4 Consensus size: 9 72445942 ATTTTTAAAC 72445952 AAAAAAAAT 1 AAAAAAAAT 72445961 AAAAAAAAT 1 AAAAAAAAT * 72445970 ATATTAAAAAT 1 A-A-AAAAAAT 72445981 AAAAAAAATT 1 AAAAAAAA-T 72445991 AAAA 1 AAAA 72445995 TTAAACAATA Statistics Matches: 29, Mismatches: 2, Indels: 5 0.81 0.06 0.14 Matches are distributed among these distances: 9 15 0.52 10 7 0.24 11 7 0.24 ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19 Consensus pattern (9 bp): AAAAAAAAT Found at i:72447260 original size:7 final size:7 Alignment explanation

Indices: 72447248--72447289 Score: 75 Period size: 7 Copynumber: 6.0 Consensus size: 7 72447238 ATTTGTGCCT 72447248 TAACTCA 1 TAACTCA 72447255 TAACTCA 1 TAACTCA 72447262 TAACTCA 1 TAACTCA 72447269 TAACTCA 1 TAACTCA * 72447276 TAACTTA 1 TAACTCA 72447283 TAACTCA 1 TAACTCA 72447290 CAATAGAATT Statistics Matches: 33, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 7 33 1.00 ACGTcount: A:0.43, C:0.26, G:0.00, T:0.31 Consensus pattern (7 bp): TAACTCA Found at i:72448720 original size:23 final size:23 Alignment explanation

Indices: 72448693--72448989 Score: 192 Period size: 23 Copynumber: 12.9 Consensus size: 23 72448683 TGGCTGCTGT 72448693 TGTTTAAATGCTGCAAATTGAAG 1 TGTTTAAATGCTGCAAATTGAAG * * 72448716 TGTTTGAATGCTGTAAATTGAAG 1 TGTTTAAATGCTGCAAATTGAAG * * 72448739 TGTTTAAATGTTGTAAATTGAAG 1 TGTTTAAATGCTGCAAATTGAAG * * 72448762 TGTTTAAGTACTGCAAATTGAAG 1 TGTTTAAATGCTGCAAATTGAAG * *** 72448785 TGTTGAAGCACTGCAAATTGAAG 1 TGTTTAAATGCTGCAAATTGAAG ** * 72448808 TGTTTAGTTGCTGGAAATTG-AG 1 TGTTTAAATGCTGCAAATTGAAG * * * 72448830 ATGTTT-TATCGTTG-TAATTG-AG 1 -TGTTTAAAT-GCTGCAAATTGAAG ** * ** 72448852 TTGTACAAATGTTGTTAATTG-AG 1 -TGTTTAAATGCTGCAAATTGAAG * 72448875 ATG-TTAAAGTGCTGCAAATTGAAA 1 -TGTTTAAA-TGCTGCAAATTGAAG * * 72448899 TGTTTAAATACTGTAAATTGAAG 1 TGTTTAAATGCTGCAAATTGAAG ** * * 72448922 TACTTAAATGTTGTAAATTGAAG 1 TGTTTAAATGCTGCAAATTGAAG * * * 72448945 TGTTTTAAGTACTACAAATTGAAG 1 TG-TTTAAATGCTGCAAATTGAAG ** * 72448969 TGTTTAGTTGCTGGAAATTGA 1 TGTTTAAATGCTGCAAATTGA 72448990 GATGTTTCAT Statistics Matches: 216, Mismatches: 50, Indels: 16 0.77 0.18 0.06 Matches are distributed among these distances: 22 20 0.09 23 173 0.80 24 23 0.11 ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38 Consensus pattern (23 bp): TGTTTAAATGCTGCAAATTGAAG Found at i:72448940 original size:114 final size:114 Alignment explanation

Indices: 72448696--72448951 Score: 268 Period size: 114 Copynumber: 2.2 Consensus size: 114 72448686 CTGCTGTTGT * * * ** 72448696 TTAAATGCTGCAAATTGAAGTGTTTGAAT-GCTGTAAATTGAAG-TGTTTAAATGTTGTAAATTG 1 TTAAATGCTGGAAATTGAAGTGTTT-TATCGTTGT-AATTG-AGTTGTACAAATGTTGTAAATTG * * * ** 72448759 AAGTGTTTAAGTACTGCAAATTGAAGTGTTGAAGCACTGCAAATTGAAGTGT 63 AAGTGTTAAAGTACTGCAAATTGAAATGTTGAAACACTGCAAATTGAAGTAC ** * 72448811 TTAGTTGCTGGAAATTG-AGATGTTTTATCGTTGTAATTGAGTTGTACAAATGTTGTTAATTG-A 1 TTAAATGCTGGAAATTGAAG-TGTTTTATCGTTGTAATTGAGTTGTACAAATGTTGTAAATTGAA * * * * 72448874 GATGTTAAAGTGCTGCAAATTGAAATGTTTAAATACTGTAAATTGAAGTAC 65 G-TGTTAAAGTACTGCAAATTGAAATGTTGAAACACTGCAAATTGAAGTAC * * 72448925 TTAAATGTTGTAAATTGAAGTGTTTTA 1 TTAAATGCTGGAAATTGAAGTGTTTTA 72448952 AGTACTACAA Statistics Matches: 115, Mismatches: 21, Indels: 11 0.78 0.14 0.07 Matches are distributed among these distances: 113 4 0.03 114 86 0.75 115 25 0.22 ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39 Consensus pattern (114 bp): TTAAATGCTGGAAATTGAAGTGTTTTATCGTTGTAATTGAGTTGTACAAATGTTGTAAATTGAAG TGTTAAAGTACTGCAAATTGAAATGTTGAAACACTGCAAATTGAAGTAC Found at i:72448988 original size:70 final size:69 Alignment explanation

Indices: 72448858--72448989 Score: 158 Period size: 70 Copynumber: 1.9 Consensus size: 69 72448848 TGAGTTGTAC * * * * 72448858 AAATGTTGTTAATTGAGATGTTAAAGTGCTGCAAATTGAAATGTTTAAATACTGTAAATTGAAGT 1 AAATGTTGTAAATTGAGATGTTAAAGTACTACAAATTGAAATGTTTAAATACTGGAAATTGAAGT 72448923 ACTT 66 ACTT * * ** * 72448927 AAATGTTGTAAATTGA-AGTGTTTTAAGTACTACAAATTGAAGTGTTTAGTTGCTGGAAATTGA 1 AAATGTTGTAAATTGAGA-TG-TTAAAGTACTACAAATTGAAATGTTTAAATACTGGAAATTGA 72448990 GATGTTTCAT Statistics Matches: 52, Mismatches: 9, Indels: 3 0.81 0.14 0.05 Matches are distributed among these distances: 68 1 0.02 69 17 0.33 70 34 0.65 ACGTcount: A:0.36, C:0.05, G:0.20, T:0.38 Consensus pattern (69 bp): AAATGTTGTAAATTGAGATGTTAAAGTACTACAAATTGAAATGTTTAAATACTGGAAATTGAAGT ACTT Found at i:72449472 original size:19 final size:19 Alignment explanation

Indices: 72449449--72449495 Score: 51 Period size: 19 Copynumber: 2.5 Consensus size: 19 72449439 ATTTAATCTA * 72449449 ATTTTTATTATTTA-TTTT 1 ATTTTTATTATATATTTTT * * 72449467 AGTTTTGATTCTATATTTTT 1 A-TTTTTATTATATATTTTT 72449487 ATTTTTATT 1 ATTTTTATT 72449496 TTAATAATTA Statistics Matches: 23, Mismatches: 4, Indels: 3 0.77 0.13 0.10 Matches are distributed among these distances: 18 1 0.04 19 17 0.74 20 5 0.22 ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72 Consensus pattern (19 bp): ATTTTTATTATATATTTTT Found at i:72449497 original size:31 final size:30 Alignment explanation

Indices: 72449416--72449507 Score: 91 Period size: 31 Copynumber: 3.0 Consensus size: 30 72449406 AAAATACTTG * 72449416 CTATA-TTTTATTTATATCTTTATATTTAAT 1 CTATATTTTTATTTTTAT-TTTATATTTAAT * 72449446 CTA-ATTTTTATTATTTATTTTAGT-TTTGATT 1 CTATATTTTTATT-TTTATTTTA-TATTT-AAT * 72449477 CTATATTTTTATTTTTATTTTAATAATTAAT 1 CTATATTTTTATTTTTATTTT-ATATTTAAT 72449508 AACTTGAGTT Statistics Matches: 51, Mismatches: 4, Indels: 13 0.75 0.06 0.19 Matches are distributed among these distances: 29 1 0.02 30 17 0.33 31 21 0.41 32 12 0.24 ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65 Consensus pattern (30 bp): CTATATTTTTATTTTTATTTTATATTTAAT Found at i:72454322 original size:93 final size:93 Alignment explanation

Indices: 72454210--72454381 Score: 299 Period size: 93 Copynumber: 1.8 Consensus size: 93 72454200 ACCCATAAGT * * * 72454210 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGAGTCAACTTAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 72454275 CGAGCTCGGATGCCTAGTTACATCTCTC 66 CGAGCTCGGATGCCTAGTTACATCTCTC * 72454303 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA * 72454368 CGAGTTCGGATGCC 66 CGAGCTCGGATGCC 72454382 CAAACATCCT Statistics Matches: 74, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 93 74 1.00 ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGCTCGGATGCCTAGTTACATCTCTC Found at i:72454377 original size:46 final size:46 Alignment explanation

Indices: 72454202--72454377 Score: 205 Period size: 46 Copynumber: 3.8 Consensus size: 46 72454192 TGTGACCCAC * 72454202 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT * * * 72454248 CCATAAGTGAACTCGGAGTCAACTTAACGAGCTCGG--ATGC-CTAGTT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T * *** * 72454294 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT 1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT * 72454341 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA 72454378 TGCCCAAACA Statistics Matches: 108, Mismatches: 15, Indels: 14 0.79 0.11 0.10 Matches are distributed among these distances: 43 1 0.01 44 4 0.04 46 68 0.63 47 30 0.28 49 4 0.04 50 1 0.01 ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT Found at i:72456311 original size:20 final size:20 Alignment explanation

Indices: 72456283--72456334 Score: 50 Period size: 20 Copynumber: 2.6 Consensus size: 20 72456273 AATCAAGTGC * ** 72456283 AAATGATTTTAACCATTTCA 1 AAATCATTTTAACCAAGTCA * * * 72456303 AAATTATTTCAATCAAGTCA 1 AAATCATTTTAACCAAGTCA 72456323 AAATCATTTTAA 1 AAATCATTTTAA 72456335 AATGATTTTT Statistics Matches: 25, Mismatches: 7, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 20 25 1.00 ACGTcount: A:0.44, C:0.13, G:0.04, T:0.38 Consensus pattern (20 bp): AAATCATTTTAACCAAGTCA Found at i:72461075 original size:24 final size:24 Alignment explanation

Indices: 72461024--72461264 Score: 351 Period size: 24 Copynumber: 10.0 Consensus size: 24 72461014 GCTTTATAAT * * 72461024 ATAACTGGAGGCCT-AGCCTCTTTTA 1 ATAACTGG-GGCATAAGCC-CTTTTG * 72461049 ATAACTGGGGCGA-AAGCCCTTTTA 1 ATAACTGGGGC-ATAAGCCCTTTTG 72461073 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG * * 72461097 ATAACTGGGGCGTAAGCCCTTTTA 1 ATAACTGGGGCATAAGCCCTTTTG 72461121 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG * 72461145 ATAGCTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG * 72461169 ATAACTGGGGCATAAGCTCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG * 72461193 ATAGCTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG * * 72461217 ATAACTGGGGCATAAGCTCTTTTA 1 ATAACTGGGGCATAAGCCCTTTTG 72461241 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTG 72461265 CACTTCCTCC Statistics Matches: 197, Mismatches: 16, Indels: 7 0.90 0.07 0.03 Matches are distributed among these distances: 23 1 0.01 24 184 0.93 25 12 0.06 ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30 Consensus pattern (24 bp): ATAACTGGGGCATAAGCCCTTTTG Found at i:72461338 original size:20 final size:21 Alignment explanation

Indices: 72461313--72461369 Score: 77 Period size: 20 Copynumber: 2.9 Consensus size: 21 72461303 TTATGATTAC * 72461313 ATCATGTGCATTTCATA-CAT 1 ATCATGTGCATATCATATCAT 72461333 ATCATGTGCATATCATATCAT 1 ATCATGTGCATATCATATCAT 72461354 -TCATGT--ATATCATATC 1 ATCATGTGCATATCATATC 72461370 CCACTTATCA Statistics Matches: 35, Mismatches: 1, Indels: 4 0.88 0.03 0.10 Matches are distributed among these distances: 18 10 0.29 20 22 0.63 21 3 0.09 ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40 Consensus pattern (21 bp): ATCATGTGCATATCATATCAT Found at i:72461479 original size:24 final size:24 Alignment explanation

Indices: 72461452--72461605 Score: 236 Period size: 24 Copynumber: 6.4 Consensus size: 24 72461442 TCATAGGCGA * 72461452 AAGCCCTTTTAATAACTAGGGCAT 1 AAGCCCTTTTAATAACTGGGGCAT * * 72461476 AAGCCCTTTTGATAACTGGGGCGT 1 AAGCCCTTTTAATAACTGGGGCAT 72461500 AAGCCCTTTTAATAACTGGGGCAT 1 AAGCCCTTTTAATAACTGGGGCAT * * 72461524 AAGCCCTTTTGATAGCTGGGGCAT 1 AAGCCCTTTTAATAACTGGGGCAT * 72461548 AAGCCCTTTTGATAACTGGGGCAT 1 AAGCCCTTTTAATAACTGGGGCAT * * 72461572 AAGCTCTTTTAATAACTAGGGCAT 1 AAGCCCTTTTAATAACTGGGGCAT 72461596 AAGCCCTTTT 1 AAGCCCTTTT 72461606 GCACTTCCTC Statistics Matches: 118, Mismatches: 12, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 24 118 1.00 ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31 Consensus pattern (24 bp): AAGCCCTTTTAATAACTGGGGCAT Found at i:72461680 original size:20 final size:21 Alignment explanation

Indices: 72461655--72461701 Score: 71 Period size: 20 Copynumber: 2.3 Consensus size: 21 72461645 TTATGATTAC * 72461655 ATCATGTGCATTTCATA-CAT 1 ATCATGTGCATATCATATCAT 72461675 ATCATGTGCATATCATATCAT 1 ATCATGTGCATATCATATCAT 72461696 -TCATGT 1 ATCATGT 72461702 ACATCATATC Statistics Matches: 25, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 20 22 0.88 21 3 0.12 ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40 Consensus pattern (21 bp): ATCATGTGCATATCATATCAT Found at i:72461735 original size:342 final size:342 Alignment explanation

Indices: 72461105--72461788 Score: 1296 Period size: 342 Copynumber: 2.0 Consensus size: 342 72461095 TGATAACTGG * * * * 72461105 GGCGTAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTGATAGCTGGGGCATAAGCCCTTTTGA 1 GGCGAAAGCCCTTTTAATAACTAGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTAA * 72461170 TAACTGGGGCATAAGCTCTTTTGATAGCTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCT 66 TAACTGGGGCATAAGCCCTTTTGATAGCTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCT * 72461235 CTTTTAATAACTGGGGCATAAGCCCTTTTGCACTTCCTCCATCCATATAAAAACCCAACCCAATG 131 CTTTTAATAACTAGGGCATAAGCCCTTTTGCACTTCCTCCATCCATATAAAAACCCAACCCAATG * 72461300 CATTTATGATTACATCATGTGCATTTCATACATATCATGTGCATATCATATCATTCATGTATATC 196 CATTTATGATTACATCATGTGCATTTCATACATATCATGTGCATATCATATCATTCATGTACATC 72461365 ATATCCCACTTATCAAATTTATAATTAAACCCTAGGTGTATAATGGTCATTTTTACCTAGGGGCA 261 ATATCCCACTTATCAAATTTATAATTAAACCCTAGGTGTATAATGGTCATTTTTACCTAGGGGCA 72461430 AAGCAGTCATTTTCATA 326 AAGCAGTCATTTTCATA * 72461447 GGCGAAAGCCCTTTTAATAACTAGGGCATAAGCCCTTTTGATAACTGGGGCGTAAGCCCTTTTAA 1 GGCGAAAGCCCTTTTAATAACTAGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTAA 72461512 TAACTGGGGCATAAGCCCTTTTGATAGCTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCT 66 TAACTGGGGCATAAGCCCTTTTGATAGCTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCT 72461577 CTTTTAATAACTAGGGCATAAGCCCTTTTGCACTTCCTCCATCCATATAAAAACCCAACCCAATG 131 CTTTTAATAACTAGGGCATAAGCCCTTTTGCACTTCCTCCATCCATATAAAAACCCAACCCAATG 72461642 CATTTATGATTACATCATGTGCATTTCATACATATCATGTGCATATCATATCATTCATGTACATC 196 CATTTATGATTACATCATGTGCATTTCATACATATCATGTGCATATCATATCATTCATGTACATC 72461707 ATATCCCACTTATCAAATTTATAATTAAACCCTAGGTGTATAATGGTCATTTTTACCTAGGGGCA 261 ATATCCCACTTATCAAATTTATAATTAAACCCTAGGTGTATAATGGTCATTTTTACCTAGGGGCA 72461772 AAGCAGTCATTTTCATA 326 AAGCAGTCATTTTCATA 72461789 TTATAAAGGT Statistics Matches: 334, Mismatches: 8, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 342 334 1.00 ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32 Consensus pattern (342 bp): GGCGAAAGCCCTTTTAATAACTAGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTAA TAACTGGGGCATAAGCCCTTTTGATAGCTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCT CTTTTAATAACTAGGGCATAAGCCCTTTTGCACTTCCTCCATCCATATAAAAACCCAACCCAATG CATTTATGATTACATCATGTGCATTTCATACATATCATGTGCATATCATATCATTCATGTACATC ATATCCCACTTATCAAATTTATAATTAAACCCTAGGTGTATAATGGTCATTTTTACCTAGGGGCA AAGCAGTCATTTTCATA Found at i:72469508 original size:24 final size:24 Alignment explanation

Indices: 72469457--72469648 Score: 269 Period size: 24 Copynumber: 8.0 Consensus size: 24 72469447 GCTTTATCAT * 72469457 ATAACTGGAGGCCT-AGCCTCTTTTA 1 ATAACTGG-GGCATAAGCC-CTTTTA * 72469482 ATAACTGGGGCAAAAGCCCTTTTA 1 ATAACTGGGGCATAAGCCCTTTTA * 72469506 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTA * 72469530 ATAACTGGGGCGTAAGCCCTTTTA 1 ATAACTGGGGCATAAGCCCTTTTA * 72469554 ATAACTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTA * * 72469578 ATAGCTGGGGCATAAGCCCTTTTG 1 ATAACTGGGGCATAAGCCCTTTTA 72469602 ATAACTGGGGCATAAGCCCTTTTA 1 ATAACTGGGGCATAAGCCCTTTTA ** * 72469626 ATAACTAAGGTATAAGCCCTTTT 1 ATAACTGGGGCATAAGCCCTTTT 72469649 GCACTTCTTC Statistics Matches: 152, Mismatches: 14, Indels: 3 0.90 0.08 0.02 Matches are distributed among these distances: 24 140 0.92 25 12 0.08 ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30 Consensus pattern (24 bp): ATAACTGGGGCATAAGCCCTTTTA Found at i:72469723 original size:20 final size:20 Alignment explanation

Indices: 72469698--72469792 Score: 151 Period size: 20 Copynumber: 4.8 Consensus size: 20 72469688 TTATGATTAC * 72469698 ATCATGTGCATTTCATACAT 1 ATCATGTGCATATCATACAT 72469718 ATCATGTGCATATCATACAT 1 ATCATGTGCATATCATACAT 72469738 ATCATGTGCATATCATACAT 1 ATCATGTGCATATCATACAT 72469758 ATCATGTGCATATCATATCAT 1 ATCATGTGCATATCATA-CAT 72469779 -TCATGT--ATATCATA 1 ATCATGTGCATATCATA 72469793 TCCCACTTAT Statistics Matches: 73, Mismatches: 1, Indels: 4 0.94 0.01 0.05 Matches are distributed among these distances: 18 8 0.11 20 62 0.85 21 3 0.04 ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38 Consensus pattern (20 bp): ATCATGTGCATATCATACAT Found at i:72469729 original size:11 final size:11 Alignment explanation

Indices: 72469698--72469773 Score: 74 Period size: 11 Copynumber: 7.5 Consensus size: 11 72469688 TTATGATTAC 72469698 ATCATGTGCAT 1 ATCATGTGCAT * * 72469709 TTCA--TACAT 1 ATCATGTGCAT 72469718 ATCATGTGCAT 1 ATCATGTGCAT * 72469729 ATCA--TACAT 1 ATCATGTGCAT 72469738 ATCATGTGCAT 1 ATCATGTGCAT * 72469749 ATCA--TACAT 1 ATCATGTGCAT 72469758 ATCATGTGCAT 1 ATCATGTGCAT 72469769 ATCAT 1 ATCAT 72469774 ATCATTCATG Statistics Matches: 51, Mismatches: 8, Indels: 12 0.72 0.11 0.17 Matches are distributed among these distances: 9 23 0.45 11 28 0.55 ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37 Consensus pattern (11 bp): ATCATGTGCAT Found at i:72469738 original size:9 final size:9 Alignment explanation

Indices: 72469710--72469762 Score: 52 Period size: 9 Copynumber: 5.4 Consensus size: 9 72469700 CATGTGCATT 72469710 TCATACATA 1 TCATACATA * 72469719 TCATGTGCATA 1 TCA--TACATA 72469730 TCATACATA 1 TCATACATA * 72469739 TCATGTGCATA 1 TCA--TACATA 72469750 TCATACATA 1 TCATACATA 72469759 TCAT 1 TCAT 72469763 GTGCATATCA Statistics Matches: 36, Mismatches: 4, Indels: 8 0.75 0.08 0.17 Matches are distributed among these distances: 9 20 0.56 11 16 0.44 ACGTcount: A:0.36, C:0.21, G:0.08, T:0.36 Consensus pattern (9 bp): TCATACATA Found at i:72479019 original size:28 final size:28 Alignment explanation

Indices: 72478987--72479051 Score: 103 Period size: 28 Copynumber: 2.3 Consensus size: 28 72478977 ATTTACTAGG * 72478987 ATACCCCTATGTATGCAAAATTACCATT 1 ATACCCCTATGTATGCAAAATGACCATT * * 72479015 ATACCCCTATGTATGCTAAATGACCTTT 1 ATACCCCTATGTATGCAAAATGACCATT 72479043 ATACCCCTA 1 ATACCCCTA 72479052 GGGTTAATTT Statistics Matches: 34, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 28 34 1.00 ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32 Consensus pattern (28 bp): ATACCCCTATGTATGCAAAATGACCATT Found at i:72479198 original size:28 final size:28 Alignment explanation

Indices: 72479157--72479245 Score: 121 Period size: 27 Copynumber: 3.2 Consensus size: 28 72479147 AGGAAGCGTC 72479157 CTGGTGGCTA-TGCCACAAATTATCTGTT 1 CTGGTGGC-ACTGCCACAAATTATCTGTT * 72479185 CTGGTGGCCCTGCCAC-AATTATCTG-T 1 CTGGTGGCACTGCCACAAATTATCTGTT * 72479211 CTGGTGGCACTGCCACAAAATATCTGTAT 1 CTGGTGGCACTGCCACAAATTATCTGT-T 72479240 CTGGTG 1 CTGGTG 72479246 ACTCTGTCAC Statistics Matches: 54, Mismatches: 3, Indels: 7 0.84 0.05 0.11 Matches are distributed among these distances: 26 16 0.30 27 17 0.31 28 14 0.26 29 7 0.13 ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31 Consensus pattern (28 bp): CTGGTGGCACTGCCACAAATTATCTGTT Found at i:72479264 original size:54 final size:54 Alignment explanation

Indices: 72479157--72479264 Score: 139 Period size: 54 Copynumber: 2.0 Consensus size: 54 72479147 AGGAAGCGTC * * 72479157 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACAATTATCTGT 1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACAATTATCTGT * * * 72479211 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCAC-ATTTTCTGT 1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACAATTATCTGT 72479265 ATCTGGCAGC Statistics Matches: 47, Mismatches: 5, Indels: 4 0.84 0.09 0.07 Matches are distributed among these distances: 53 1 0.02 54 32 0.68 55 14 0.30 ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34 Consensus pattern (54 bp): CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACAATTATCTGT Found at i:72479734 original size:18 final size:18 Alignment explanation

Indices: 72479695--72479735 Score: 55 Period size: 18 Copynumber: 2.3 Consensus size: 18 72479685 TAATAAGGCC * * 72479695 TTTTAATTATTTTTATGG 1 TTTTAATTACTTTTATGA * 72479713 TTTTAATTACTTTTATTA 1 TTTTAATTACTTTTATGA 72479731 TTTTA 1 TTTTA 72479736 TTTTACTATG Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 18 20 1.00 ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68 Consensus pattern (18 bp): TTTTAATTACTTTTATGA Found at i:72480607 original size:5 final size:5 Alignment explanation

Indices: 72480597--72480623 Score: 54 Period size: 5 Copynumber: 5.4 Consensus size: 5 72480587 CAATTTTTGA 72480597 AAAAT AAAAT AAAAT AAAAT AAAAT AA 1 AAAAT AAAAT AAAAT AAAAT AAAAT AA 72480624 CACACAAATT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 22 1.00 ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19 Consensus pattern (5 bp): AAAAT Found at i:72481123 original size:43 final size:43 Alignment explanation

Indices: 72481013--72481139 Score: 141 Period size: 43 Copynumber: 3.0 Consensus size: 43 72481003 GATCTTACTT * * * ** * * 72481013 GTAATCACATATCGATGCCACTATCCTGGACAGGGTGTTACAC 1 GTAATCACAAATCGATGCCAATGTCCCAGACATGGTCTTACAC * * * 72481056 G-AATCAAAAAT-GATGTCGATGTCCCAGACATGGTCTTACAC 1 GTAATCACAAATCGATGCCAATGTCCCAGACATGGTCTTACAC * 72481097 GTAATCACACATCGATGCCAATGTCCCAGACATGGTCTTACAC 1 GTAATCACAAATCGATGCCAATGTCCCAGACATGGTCTTACAC 72481140 AAGAACACAT Statistics Matches: 68, Mismatches: 14, Indels: 4 0.79 0.16 0.05 Matches are distributed among these distances: 41 23 0.34 42 16 0.24 43 29 0.43 ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24 Consensus pattern (43 bp): GTAATCACAAATCGATGCCAATGTCCCAGACATGGTCTTACAC Found at i:72486605 original size:28 final size:28 Alignment explanation

Indices: 72486569--72486648 Score: 99 Period size: 29 Copynumber: 2.8 Consensus size: 28 72486559 CATACATGCT * * 72486569 TATGGCCCACTAGGCCCATTCTCAT-TCA 1 TATGGCCCACTAGGCCCAATCACATCT-A * * 72486597 TATGACCCATTAGGCCCAAATCACATCTA 1 TATGGCCCACTAGGCCC-AATCACATCTA 72486626 TATGGCCCACTAGGCCCAATCAC 1 TATGGCCCACTAGGCCCAATCAC 72486649 TTTTACAGTC Statistics Matches: 44, Mismatches: 6, Indels: 4 0.81 0.11 0.07 Matches are distributed among these distances: 28 21 0.48 29 22 0.50 30 1 0.02 ACGTcount: A:0.28, C:0.35, G:0.14, T:0.24 Consensus pattern (28 bp): TATGGCCCACTAGGCCCAATCACATCTA Found at i:72486634 original size:29 final size:28 Alignment explanation

Indices: 72486569--72486648 Score: 99 Period size: 28 Copynumber: 2.8 Consensus size: 28 72486559 CATACATGCT * * 72486569 TATGGCCCACTAGGCCCATTCTCATTCA 1 TATGGCCCACTAGGCCCAATCACATTCA * * 72486597 TATGACCCATTAGGCCCAAATCACA-TCTA 1 TATGGCCCACTAGGCCC-AATCACATTC-A 72486626 TATGGCCCACTAGGCCCAATCAC 1 TATGGCCCACTAGGCCCAATCAC 72486649 TTTTACAGTC Statistics Matches: 44, Mismatches: 6, Indels: 4 0.81 0.11 0.07 Matches are distributed among these distances: 28 23 0.52 29 21 0.48 ACGTcount: A:0.28, C:0.35, G:0.14, T:0.24 Consensus pattern (28 bp): TATGGCCCACTAGGCCCAATCACATTCA Found at i:72486892 original size:16 final size:17 Alignment explanation

Indices: 72486873--72486909 Score: 67 Period size: 16 Copynumber: 2.2 Consensus size: 17 72486863 AAATTTTGGC 72486873 TTTTCGACATTTCAG-T 1 TTTTCGACATTTCAGCT 72486889 TTTTCGACATTTCAGCT 1 TTTTCGACATTTCAGCT 72486906 TTTT 1 TTTT 72486910 GGGATTTGTC Statistics Matches: 20, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 16 15 0.75 17 5 0.25 ACGTcount: A:0.16, C:0.19, G:0.11, T:0.54 Consensus pattern (17 bp): TTTTCGACATTTCAGCT Found at i:72495215 original size:45 final size:45 Alignment explanation

Indices: 72495166--72495282 Score: 171 Period size: 45 Copynumber: 2.6 Consensus size: 45 72495156 GTATTTCTGA * * * * 72495166 GTAAGACCACGTCTGGGACGTTGGCATCGATATATGTGTTTTCGT 1 GTAAGACCACGTCTGGGACATTGGCATCGATATATATGGTTACGT * 72495211 GTAAGACCACGTCTAGGACATTGGCATCGATATATATGGTTACGT 1 GTAAGACCACGTCTGGGACATTGGCATCGATATATATGGTTACGT * * 72495256 GTAAGACCATGTCTGGGACATCGGCAT 1 GTAAGACCACGTCTGGGACATTGGCAT 72495283 TGTATTAGAT Statistics Matches: 64, Mismatches: 8, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 45 64 1.00 ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29 Consensus pattern (45 bp): GTAAGACCACGTCTGGGACATTGGCATCGATATATATGGTTACGT Found at i:72495323 original size:41 final size:43 Alignment explanation

Indices: 72495187--72495329 Score: 132 Period size: 45 Copynumber: 3.3 Consensus size: 43 72495177 TCTGGGACGT * * 72495187 TGGCATCGATATATGTGTTTTCGTGTAAGACCAC-GTCTAGGACA 1 TGGCATCGATATATATG-ATTCGTGTAAGACC-CTGTCTAGGACA * * * 72495231 TTGGCATCGATATATATGGTTACGTGTAAGACCATGTCTGGGACA 1 -TGGCATCGATATATATGATT-CGTGTAAGACCCTGTCTAGGACA * * 72495276 TCGGCATTG-TAT-TA-GATTCGAGTAAGACCCTGTCTAGGACA 1 T-GGCATCGATATATATGATTCGTGTAAGACCCTGTCTAGGACA * 72495317 GTGGCATCAATAT 1 -TGGCATCGATAT 72495330 GAGATAGCAT Statistics Matches: 82, Mismatches: 11, Indels: 13 0.77 0.10 0.12 Matches are distributed among these distances: 41 25 0.30 42 7 0.09 43 2 0.02 44 6 0.07 45 42 0.51 ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31 Consensus pattern (43 bp): TGGCATCGATATATATGATTCGTGTAAGACCCTGTCTAGGACA Found at i:72497363 original size:40 final size:40 Alignment explanation

Indices: 72497092--72497356 Score: 333 Period size: 40 Copynumber: 6.7 Consensus size: 40 72497082 TTGAATGATG * * * * 72497092 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA * * * 72497132 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA * ** 72497172 TCCGGGCTAAG-CCCGAAGGCATTTTTATGAGTTACTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA * 72497211 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA * 72497251 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA * 72497291 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA * 72497332 -CCGGGCTATGTCCCGAAGGCATTTG 1 TCCGGGCTAAGTCCCGAAGGCATTTG 72497357 AACGAGTAGC Statistics Matches: 197, Mismatches: 21, Indels: 14 0.85 0.09 0.06 Matches are distributed among these distances: 39 33 0.17 40 154 0.78 41 10 0.05 ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA Found at i:72497363 original size:80 final size:78 Alignment explanation

Indices: 72497093--72497389 Score: 314 Period size: 80 Copynumber: 3.7 Consensus size: 78 72497083 TGAATGATGT * * * * * ** 72497093 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT 1 CCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGTTACTAAATCCGGGTTAAG-TCCGAAGGCATTT * * 72497157 GTGCGAGATACTAATT 64 GTGCGAGTTACTAA-A * * ** 72497173 CCGGGCTAAG-CCCGAAGGCATTTTTATGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTG 1 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAAG-TCCGAAGGCATTTG 72497237 TGCGAGTTACTAAA 65 TGCGAGTTACTAAA * * 72497251 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT 1 -CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAAGT-CCGAAGGCATTT 72497316 GTGCGAGTTACTATAA 64 GTGCGAGTTACTA-AA * * * * 72497332 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG 1 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTA-CTAAATCCGGGTT-AAGTCCGAAGG 72497390 TACGTGATTT Statistics Matches: 189, Mismatches: 21, Indels: 15 0.84 0.09 0.07 Matches are distributed among these distances: 79 77 0.41 80 110 0.58 81 2 0.01 ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26 Consensus pattern (78 bp): CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGT GCGAGTTACTAAA Found at i:72497363 original size:120 final size:118 Alignment explanation

Indices: 72497145--72497389 Score: 307 Period size: 120 Copynumber: 2.1 Consensus size: 118 72497135 GGACTAAGAT * * * 72497145 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTTTATGAGTTACTAA 1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTACGAGTTACTAA ** * 72497210 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTA-CTAAATCCGGGTTAAGTC 66 ATCCGGACTAAGATCCGAAGGCATTTGAACGAG-TAGCTAAATCC-GGTTAAATC * * * 72497264 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA 1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAG-CCCGAAGGCATTTGTACGAGTTACTA * * * * 72497329 TAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAAATT 65 -AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTAGCTAAATCCGGTTAAATC 72497383 CCGAAGG 1 CCGAAGG 72497390 TACGTGATTT Statistics Matches: 109, Mismatches: 13, Indels: 8 0.84 0.10 0.06 Matches are distributed among these distances: 119 52 0.48 120 55 0.50 121 2 0.02 ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27 Consensus pattern (118 bp): CCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTACGAGTTACTAA ATCCGGACTAAGATCCGAAGGCATTTGAACGAGTAGCTAAATCCGGTTAAATC Found at i:72500063 original size:38 final size:38 Alignment explanation

Indices: 72500020--72500130 Score: 168 Period size: 38 Copynumber: 2.9 Consensus size: 38 72500010 TTGCAAATTA * * 72500020 ACATGTATAACCGTGGCATATCCACTTAGCACTACGTT 1 ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT * * 72500058 ACATGTTTAACCGTGGTATATCAACTTAGCACCACGTT 1 ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT * * 72500096 ACACGTATAACTGTGGTATATCCACTTAGCACCAC 1 ACATGTATAACCGTGGTATATCCACTTAGCACCAC 72500131 ATTTTCCCAT Statistics Matches: 65, Mismatches: 8, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 38 65 1.00 ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29 Consensus pattern (38 bp): ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT Found at i:72502756 original size:30 final size:30 Alignment explanation

Indices: 72502721--72502778 Score: 82 Period size: 30 Copynumber: 1.9 Consensus size: 30 72502711 AAAAACTAAG * 72502721 TAAAGAAATTCAAG-ATAGAGAAACCCAAAA 1 TAAAGAAA-TCAAGAATAAAGAAACCCAAAA * 72502751 TAAAGAAATCCAGAATAAAGAAACCCAA 1 TAAAGAAATCAAGAATAAAGAAACCCAA 72502779 GATACGATAC Statistics Matches: 25, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 29 4 0.16 30 21 0.84 ACGTcount: A:0.60, C:0.16, G:0.12, T:0.12 Consensus pattern (30 bp): TAAAGAAATCAAGAATAAAGAAACCCAAAA Found at i:72502757 original size:15 final size:15 Alignment explanation

Indices: 72502739--72502778 Score: 62 Period size: 15 Copynumber: 2.7 Consensus size: 15 72502729 TTCAAGATAG 72502739 AGAAACCCAAAATAA 1 AGAAACCCAAAATAA * * 72502754 AGAAATCCAGAATAA 1 AGAAACCCAAAATAA 72502769 AGAAACCCAA 1 AGAAACCCAA 72502779 GATACGATAC Statistics Matches: 21, Mismatches: 4, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 15 21 1.00 ACGTcount: A:0.62, C:0.20, G:0.10, T:0.07 Consensus pattern (15 bp): AGAAACCCAAAATAA Found at i:72509604 original size:32 final size:32 Alignment explanation

Indices: 72509563--72509623 Score: 122 Period size: 32 Copynumber: 1.9 Consensus size: 32 72509553 AAAAGATTCG 72509563 AAGATGGTTTGAATGAAGACATTAAACTTTCA 1 AAGATGGTTTGAATGAAGACATTAAACTTTCA 72509595 AAGATGGTTTGAATGAAGACATTAAACTT 1 AAGATGGTTTGAATGAAGACATTAAACTT 72509624 ATTGTTGGAA Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 32 29 1.00 ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31 Consensus pattern (32 bp): AAGATGGTTTGAATGAAGACATTAAACTTTCA Found at i:72519881 original size:40 final size:40 Alignment explanation

Indices: 72519804--72519941 Score: 199 Period size: 40 Copynumber: 3.5 Consensus size: 40 72519794 AGACCAAGTA * * * * 72519804 CCTTTGGGATTTAG-CCGGATATAGCT-ACTCACTCAAATG 1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG 72519843 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG * * 72519883 CCTTCGAGACTTAGCCCGAATATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG 72519923 CCTTCGGGACTTAGCCCGG 1 CCTTCGGGACTTAGCCCGG 72519942 TTACCATCTG Statistics Matches: 89, Mismatches: 8, Indels: 3 0.89 0.08 0.03 Matches are distributed among these distances: 39 13 0.15 40 76 0.85 ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25 Consensus pattern (40 bp): CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG Found at i:72523198 original size:28 final size:28 Alignment explanation

Indices: 72523165--72523285 Score: 136 Period size: 28 Copynumber: 4.3 Consensus size: 28 72523155 ATTGCATGAC * * 72523165 TATGAATGTGATTGGGCCTGACGGGCCA 1 TATGAATATGATTGGGCCTGATGGGCCA * 72523193 TATGAA-AGTGATTGGGCTTGATGGGCCA 1 TATGAATA-TGATTGGGCCTGATGGGCCA ** 72523221 TATGAATATGATTGGGCCCAATGGGCCA 1 TATGAATATGATTGGGCCTGATGGGCCA * * * 72523249 TATGAATAAGATTGGGCCTAAAGGGGCCA 1 TATGAATATGATTGGGCCT-GATGGGCCA * 72523278 AATGAATA 1 TATGAATA 72523286 AGTATGGATC Statistics Matches: 80, Mismatches: 10, Indels: 5 0.84 0.11 0.05 Matches are distributed among these distances: 28 64 0.80 29 16 0.20 ACGTcount: A:0.30, C:0.14, G:0.31, T:0.25 Consensus pattern (28 bp): TATGAATATGATTGGGCCTGATGGGCCA Found at i:72525972 original size:36 final size:36 Alignment explanation

Indices: 72525925--72525996 Score: 135 Period size: 36 Copynumber: 2.0 Consensus size: 36 72525915 ATATATCATG 72525925 AATGTTGGTATTCGACAATTAGCATGGAAATTTGAT 1 AATGTTGGTATTCGACAATTAGCATGGAAATTTGAT * 72525961 AATGTTGGTATTCGACAATTAGCATTGAAATTTGAT 1 AATGTTGGTATTCGACAATTAGCATGGAAATTTGAT 72525997 TATTATTTTT Statistics Matches: 35, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 36 35 1.00 ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38 Consensus pattern (36 bp): AATGTTGGTATTCGACAATTAGCATGGAAATTTGAT Found at i:72527395 original size:19 final size:19 Alignment explanation

Indices: 72527371--72527408 Score: 67 Period size: 19 Copynumber: 2.0 Consensus size: 19 72527361 AAAACTTGAA * 72527371 ACAAATAGGAATGATTTTC 1 ACAAATAGAAATGATTTTC 72527390 ACAAATAGAAATGATTTTC 1 ACAAATAGAAATGATTTTC 72527409 TTCTCTAAAA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 19 18 1.00 ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32 Consensus pattern (19 bp): ACAAATAGAAATGATTTTC Found at i:72537573 original size:28 final size:28 Alignment explanation

Indices: 72537499--72537598 Score: 128 Period size: 28 Copynumber: 3.5 Consensus size: 28 72537489 ATTGCATGAC * 72537499 TATGAATGTGATTGGGGCCGATGGGCCA 1 TATGAATGTGATTGGGGCTGATGGGCCA * 72537527 TATGAATGTGATTGGGGCTGATGGGTCA 1 TATGAATGTGATTGGGGCTGATGGGCCA * * * 72537555 TATGAAAGTGATTGGGGCTTAATAGGCCA 1 TATGAATGTGATTGGGGC-TGATGGGCCA * * 72537584 TATGTATGAGATTGG 1 TATGAATGTGATTGG 72537599 ACCTAAAGGG Statistics Matches: 62, Mismatches: 9, Indels: 1 0.86 0.12 0.01 Matches are distributed among these distances: 28 43 0.69 29 19 0.31 ACGTcount: A:0.25, C:0.09, G:0.36, T:0.30 Consensus pattern (28 bp): TATGAATGTGATTGGGGCTGATGGGCCA Found at i:72542153 original size:29 final size:29 Alignment explanation

Indices: 72542098--72542175 Score: 88 Period size: 28 Copynumber: 2.8 Consensus size: 29 72542088 ATTGTATGAT * ** * 72542098 TATGAATGTGATTGGGGCC-GCTGGGCCA 1 TATGAATGTGATTTGGGCCTAATAGGCCA 72542126 TATGAATGTGATTTGGGCCTAATAGGCCA 1 TATGAATGTGATTTGGGCCTAATAGGCCA * * 72542155 CATGAATGAGA-TTGGGCCTAA 1 TATGAATGTGATTTGGGCCTAA 72542176 AGGGGCAAAA Statistics Matches: 43, Mismatches: 6, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 28 28 0.65 29 15 0.35 ACGTcount: A:0.26, C:0.15, G:0.32, T:0.27 Consensus pattern (29 bp): TATGAATGTGATTTGGGCCTAATAGGCCA Found at i:72542169 original size:28 final size:29 Alignment explanation

Indices: 72542121--72542175 Score: 85 Period size: 29 Copynumber: 1.9 Consensus size: 29 72542111 GGGGCCGCTG * * 72542121 GGCCATATGAATGTGATTTGGGCCTAATA 1 GGCCACATGAATGAGATTTGGGCCTAATA 72542150 GGCCACATGAATGAGA-TTGGGCCTAA 1 GGCCACATGAATGAGATTTGGGCCTAA 72542176 AGGGGCAAAA Statistics Matches: 24, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 28 10 0.42 29 14 0.58 ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25 Consensus pattern (29 bp): GGCCACATGAATGAGATTTGGGCCTAATA Found at i:72546165 original size:34 final size:34 Alignment explanation

Indices: 72546119--72546187 Score: 129 Period size: 34 Copynumber: 2.0 Consensus size: 34 72546109 TGATAGATTA * 72546119 TCATCCGGGTAAGGCAAACGTTGTTGCTGATGCT 1 TCATCCGAGTAAGGCAAACGTTGTTGCTGATGCT 72546153 TCATCCGAGTAAGGCAAACGTTGTTGCTGATGCT 1 TCATCCGAGTAAGGCAAACGTTGTTGCTGATGCT 72546187 T 1 T 72546188 TGAGCTGGAA Statistics Matches: 34, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 34 34 1.00 ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30 Consensus pattern (34 bp): TCATCCGAGTAAGGCAAACGTTGTTGCTGATGCT Found at i:72547829 original size:42 final size:42 Alignment explanation

Indices: 72547709--72547830 Score: 101 Period size: 42 Copynumber: 2.9 Consensus size: 42 72547699 CATGACATAG * * 72547709 GATTTCGTGTAAGACCAC-GTCTAGGAT-GTTGGCATCGACTTCT 1 GATTTTGTGTAAGACC-CTGTCTGGGATAG-TGGCATC-ACTTCT * * * 72547752 -ATTTTACGTGTAAGACCATGTTTGGGACA-TCGGCATC-CTATCT 1 GATTTT--GTGTAAGACCCTGTCTGGGATAGT-GGCATCACT-TCT 72547795 GATTTTGTGTAAGACCCTGTCTGGGATAGTGGCATC 1 GATTTTGTGTAAGACCCTGTCTGGGATAGTGGCATC 72547831 GATGTTTGAT Statistics Matches: 63, Mismatches: 8, Indels: 17 0.72 0.09 0.19 Matches are distributed among these distances: 42 31 0.49 43 5 0.08 44 27 0.43 ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34 Consensus pattern (42 bp): GATTTTGTGTAAGACCCTGTCTGGGATAGTGGCATCACTTCT Found at i:72556583 original size:39 final size:40 Alignment explanation

Indices: 72556483--72556667 Score: 200 Period size: 40 Copynumber: 4.7 Consensus size: 40 72556473 TCGAATGATG * * * * 72556483 TCCGGGCTAAGTCTCGAAGGC-TTTGTGCTAAGTGAC-CAT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT * * 72556522 ATCCAGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT 1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT * * 72556563 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT * 72556602 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT * * 72556641 AACCGGGCTATGTCCCGAAGGCATTTG 1 -TCCGGGCTAAGTCCCGAAGGCATTTG 72556668 AACGAGTAGC Statistics Matches: 123, Mismatches: 16, Indels: 12 0.81 0.11 0.08 Matches are distributed among these distances: 39 36 0.29 40 77 0.63 41 10 0.08 ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT Found at i:72556689 original size:79 final size:79 Alignment explanation

Indices: 72556536--72556700 Score: 210 Period size: 79 Copynumber: 2.1 Consensus size: 79 72556526 AGACTAAGAT * ** 72556536 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA 1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA * 72556601 ATCCGGGTTAAGTC 66 ATCCGGGTTAAATC * * 72556615 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC 1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C * * 72556678 TATATCC-GGTTAAATT 63 TAAATCCGGGTTAAATC 72556694 CCGAAGG 1 CCGAAGG 72556701 TACGTGATTC Statistics Matches: 75, Mismatches: 8, Indels: 6 0.84 0.09 0.07 Matches are distributed among these distances: 78 2 0.03 79 49 0.65 80 24 0.32 ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25 Consensus pattern (79 bp): CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA ATCCGGGTTAAATC Found at i:72559673 original size:37 final size:37 Alignment explanation

Indices: 72559623--72559701 Score: 122 Period size: 37 Copynumber: 2.1 Consensus size: 37 72559613 TTATTACGAA * * * 72559623 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG 1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG * 72559660 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG 1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG 72559697 GTCTT 1 GTCTT 72559702 TAGAGCTCGG Statistics Matches: 38, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 37 38 1.00 ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24 Consensus pattern (37 bp): GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG Found at i:72560088 original size:49 final size:47 Alignment explanation

Indices: 72559820--72560376 Score: 902 Period size: 47 Copynumber: 11.7 Consensus size: 47 72559810 CCCTTCGGGA * * * * * * 72559820 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 72559867 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 72559914 CTTACCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 72559961 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 72560008 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 72560055 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGTC 1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC 72560104 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 72560153 CTTATCACATATATACATTTTCACATTCATCACATCGGCCATTGGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 72560200 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC 72560249 CTTATCACATATATACACTTTCA-ATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 72560295 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 72560342 CTTATCACATATATGCA-TGTTCACATCCATCACAT 1 CTTATCACATATATACACT-TTCACATTCATCACAT 72560377 AGAATCCTAA Statistics Matches: 482, Mismatches: 22, Indels: 12 0.93 0.04 0.02 Matches are distributed among these distances: 46 47 0.10 47 298 0.62 49 137 0.28 ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32 Consensus pattern (47 bp): CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC Found at i:72560097 original size:96 final size:94 Alignment explanation

Indices: 72559820--72560376 Score: 902 Period size: 96 Copynumber: 5.9 Consensus size: 94 72559810 CCCTTCGGGA * * * * * * * * 72559820 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC 72559885 TTTCACATTCATCACATCGGCCATTAGGC 66 TTTCACATTCATCACATCGGCCATTAGGC * 72559914 CTTACCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC 72559979 TTTCACATTCATCACATCGGCCATTAGGC 66 TTTCACATTCATCACATCGGCCATTAGGC 72560008 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC * * 72560073 ACTTTCACATTCATCACATTGGCCATTAGTC 64 ACTTTCACATTCATCACATCGGCCATTAGGC 72560104 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC 1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC * * 72560169 ATTTTCACATTCATCACATCGGCCATTGGGC 64 ACTTTCACATTCATCACATCGGCCATTAGGC 72560200 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC 1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC 72560265 ACTTTCA-ATTCATCACATCGGCCATTAGGC 64 ACTTTCACATTCATCACATCGGCCATTAGGC * 72560295 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATGCA- 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC * 72560359 TGTTCACATCCATCACAT 66 T-TTCACATTCATCACAT 72560377 AGAATCCTAA Statistics Matches: 437, Mismatches: 20, Indels: 12 0.93 0.04 0.03 Matches are distributed among these distances: 92 1 0.00 93 59 0.14 94 149 0.34 95 30 0.07 96 151 0.35 98 47 0.11 ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32 Consensus pattern (94 bp): CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC TTTCACATTCATCACATCGGCCATTAGGC Found at i:72564265 original size:40 final size:40 Alignment explanation

Indices: 72564236--72564464 Score: 359 Period size: 40 Copynumber: 5.7 Consensus size: 40 72564226 GCATGATTGT * * * 72564236 TCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGC 1 TCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGC ** * * 72564276 TCTTCGGGGTTTAGCACGGATATATCTCTAGCACGAATGC 1 TCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGC * * * 72564316 TCTTCGGAACTTAGTCCGGATACATCACTAGCACGAATGC 1 TCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGC * 72564356 TCTTCGGGATTTAGCCCGGATATATCACTAGCACGAATGC 1 TCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGC 72564396 TCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGC 1 TCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGC 72564436 TCTTCGGGACTTAGCCCGGATATATCACT 1 TCTTCGGGACTTAGCCCGGATATATCACT 72564465 CTCAATTCTC Statistics Matches: 170, Mismatches: 19, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 40 170 1.00 ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26 Consensus pattern (40 bp): TCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGC Found at i:72565730 original size:37 final size:37 Alignment explanation

Indices: 72565680--72565758 Score: 122 Period size: 37 Copynumber: 2.1 Consensus size: 37 72565670 TTATTACGAA * * * 72565680 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG 1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG * 72565717 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG 1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG 72565754 GTCTT 1 GTCTT 72565759 TAGAGCTCGG Statistics Matches: 38, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 37 38 1.00 ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24 Consensus pattern (37 bp): GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG Found at i:72566051 original size:49 final size:47 Alignment explanation

Indices: 72565877--72566245 Score: 578 Period size: 47 Copynumber: 7.7 Consensus size: 47 72565867 CCCTTCGGGA * * * * * * 72565877 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 72565924 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 72565971 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 72566018 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTGGGC 1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 72566067 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTGGGC 1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC 72566116 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 72566163 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 72566210 CTTATCACATATATGCA-TGTTCACATTCCATCACAT 1 CTTATCACATATATACACT-TTCACATT-CATCACAT 72566246 AGAATCCTAA Statistics Matches: 305, Mismatches: 13, Indels: 7 0.94 0.04 0.02 Matches are distributed among these distances: 46 1 0.00 47 201 0.66 48 8 0.03 49 95 0.31 ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32 Consensus pattern (47 bp): CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC Found at i:72566215 original size:192 final size:190 Alignment explanation

Indices: 72565877--72566223 Score: 613 Period size: 192 Copynumber: 1.8 Consensus size: 190 72565867 CCCTTCGGGA * * * 72565877 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC 1 CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTCGGCCCTATCACATATATACAC 72565942 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC 66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC 72566007 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTGGGC 131 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTGGGC * * * * 72566067 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTGGGCCTTATCACATATATAC 1 CTTATCACAT-T-TATACACTTTCACATCCATCACATCGGCCACTCGGCCCTATCACATATATAC 72566132 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA 64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA 72566197 TCGGCCATTAGGCCTTATCACATATAT 129 TCGGCCATTAGGCCTTATCACATATAT 72566224 GCATGTTCAC Statistics Matches: 148, Mismatches: 7, Indels: 2 0.94 0.04 0.01 Matches are distributed among these distances: 190 10 0.07 191 1 0.01 192 137 0.93 ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32 Consensus pattern (190 bp): CTTATCACATTTATACACTTTCACATCCATCACATCGGCCACTCGGCCCTATCACATATATACAC TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTGGGC Found at i:72580604 original size:55 final size:55 Alignment explanation

Indices: 72580510--72580613 Score: 131 Period size: 55 Copynumber: 1.9 Consensus size: 55 72580500 AGGTCCATGC * * * 72580510 CCGTGTTAATTTGACAGGTTCACCCACGGGTGATGGGCACGGGCGTGTCACACGT 1 CCGTGTTAATTTGACAGGTTCACCCACGGGTCATAGGCACGAGCGTGTCACACGT * * 72580565 CCGTGCTT-ATTTGACAGGTTCGCCCACGGTTTCA-AGGCACGAGCGTGTC 1 CCGTG-TTAATTTGACAGGTTCACCCACGG-GTCATAGGCACGAGCGTGTC 72580614 GCACTCTCAT Statistics Matches: 42, Mismatches: 5, Indels: 4 0.82 0.10 0.08 Matches are distributed among these distances: 55 38 0.90 56 4 0.10 ACGTcount: A:0.17, C:0.27, G:0.31, T:0.25 Consensus pattern (55 bp): CCGTGTTAATTTGACAGGTTCACCCACGGGTCATAGGCACGAGCGTGTCACACGT Found at i:72585198 original size:13 final size:13 Alignment explanation

Indices: 72585189--72585233 Score: 63 Period size: 13 Copynumber: 3.5 Consensus size: 13 72585179 TGGCATGCCT * 72585189 GTGTGACATGCCC 1 GTGTGACACGCCC * 72585202 ATGTGACACGCCC 1 GTGTGACACGCCC * 72585215 GTGTGACACGCCT 1 GTGTGACACGCCC 72585228 GTGTGA 1 GTGTGA 72585234 GGAAGCCCTG Statistics Matches: 28, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 13 28 1.00 ACGTcount: A:0.18, C:0.29, G:0.31, T:0.22 Consensus pattern (13 bp): GTGTGACACGCCC Found at i:72588297 original size:29 final size:29 Alignment explanation

Indices: 72588230--72588422 Score: 200 Period size: 29 Copynumber: 6.8 Consensus size: 29 72588220 TACATACATG * * 72588230 CATATGGCCCACTAGACCCAATCTCA--TT 1 CATATGGCCCATTAGGCCCAAT-TCACGTT * * 72588258 TATATGGCCCATTTGGCCCAATTCACGTT 1 CATATGGCCCATTAGGCCCAATTCACGTT ** * 72588287 CATATAACCCATTAGGCCCAATTCACATT 1 CATATGGCCCATTAGGCCCAATTCACGTT * 72588316 CATATGGCCCATTAGGCCCAATCTTA--TT 1 CATATGGCCCATTAGGCCCAAT-TCACGTT * * 72588344 TATATGGCCCATCCA-GCCCAATTCACGTT 1 CATATGGCCCAT-TAGGCCCAATTCACGTT * 72588373 CATATGGCCCATCAGGCCCAATTCACGTT 1 CATATGGCCCATTAGGCCCAATTCACGTT * * 72588402 TATATGTCCCA-TAGGCCCAAT 1 CATATGGCCCATTAGGCCCAAT 72588423 CTCATTTATG Statistics Matches: 139, Mismatches: 19, Indels: 14 0.81 0.11 0.08 Matches are distributed among these distances: 27 5 0.04 28 49 0.35 29 83 0.60 30 2 0.01 ACGTcount: A:0.26, C:0.32, G:0.13, T:0.28 Consensus pattern (29 bp): CATATGGCCCATTAGGCCCAATTCACGTT Found at i:72588307 original size:57 final size:57 Alignment explanation

Indices: 72588231--72588454 Score: 206 Period size: 57 Copynumber: 3.9 Consensus size: 57 72588221 ACATACATGC * * * * ** * 72588231 ATATGGCCCACTAGACCCAATCTCATTTATATGGCCCATTTGGCCCAATTCACGTTC 1 ATATGACCCATTAGGCCCAATCTCATTCATATGGCCCATCAGGCCCAATTCACGTTT * * * * 72588288 ATATAACCCATTAGGCCCAATTCACATTCATATGGCCCATTAGGCCCAATCTTA--TTT 1 ATATGACCCATTAGGCCCAA-TCTCATTCATATGGCCCATCAGGCCCAAT-TCACGTTT * * 72588345 ATATGGCCCATCCA-GCCCAAT-TCACGTTCATATGGCCCATCAGGCCCAATTCACGTTT 1 ATATGACCCAT-TAGGCCCAATCTCA--TTCATATGGCCCATCAGGCCCAATTCACGTTT * * * * * 72588403 ATATGTCCCA-TAGGCCCAATCTCATTTATGTGGCCCATCCGGCCCAAATCAC 1 ATATGACCCATTAGGCCCAATCTCATTCATATGGCCCATCAGGCCCAATTCAC 72588455 ATTATATTCA Statistics Matches: 137, Mismatches: 21, Indels: 19 0.77 0.12 0.11 Matches are distributed among these distances: 55 2 0.01 56 28 0.20 57 63 0.46 58 42 0.31 59 2 0.01 ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28 Consensus pattern (57 bp): ATATGACCCATTAGGCCCAATCTCATTCATATGGCCCATCAGGCCCAATTCACGTTT Found at i:72588375 original size:86 final size:85 Alignment explanation

Indices: 72588225--72588454 Score: 316 Period size: 86 Copynumber: 2.7 Consensus size: 85 72588215 ACCGCTACAT * * ** 72588225 ACATGCATATGGCCCACTAGACCCAATCTCATTTATATGGCCCATTTGGCCCAATTCACGTTCAT 1 ACATTCATATGGCCCA-TAGGCCCAATCTCATTTATATGGCCCATCCGGCCCAATTCACGTTCAT * 72588290 ATAACCCATTAGGCCCAATTC 65 ATAACCCATCAGGCCCAATTC * * 72588311 ACATTCATATGGCCCATTAGGCCCAATCTTATTTATATGGCCCATCCAGCCCAATTCACGTTCAT 1 ACATTCATATGGCCCA-TAGGCCCAATCTCATTTATATGGCCCATCCGGCCCAATTCACGTTCAT ** 72588376 ATGGCCCATCAGGCCCAATTC 65 ATAACCCATCAGGCCCAATTC * * * * * 72588397 ACGTTTATATGTCCCATAGGCCCAATCTCATTTATGTGGCCCATCCGGCCCAAATCAC 1 ACATTCATATGGCCCATAGGCCCAATCTCATTTATATGGCCCATCCGGCCCAATTCAC 72588455 ATTATATTCA Statistics Matches: 127, Mismatches: 17, Indels: 1 0.88 0.12 0.01 Matches are distributed among these distances: 85 38 0.30 86 89 0.70 ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28 Consensus pattern (85 bp): ACATTCATATGGCCCATAGGCCCAATCTCATTTATATGGCCCATCCGGCCCAATTCACGTTCATA TAACCCATCAGGCCCAATTC Found at i:72588459 original size:28 final size:28 Alignment explanation

Indices: 72588231--72588461 Score: 150 Period size: 29 Copynumber: 8.1 Consensus size: 28 72588221 ACATACATGC * * 72588231 ATATGGCCCA-CTAGACCC-AATCTCATTT 1 ATATGGCCCATC-AGGCCCAAATCACA-TT ** * * 72588259 ATATGGCCCATTTGGCCCAATTCACGTT 1 ATATGGCCCATCAGGCCCAAATCACATT ** * * 72588287 CATATAACCCATTAGGCCCAATTCACATT 1 -ATATGGCCCATCAGGCCCAAATCACATT * ** 72588316 CATATGGCCCATTAGGCCC-AATCTTATTT 1 -ATATGGCCCATCAGGCCCAAATCACA-TT * * 72588345 ATATGGCCCATCCA-GCCCAATTCACGTT 1 ATATGGCCCAT-CAGGCCCAAATCACATT * * 72588373 CATATGGCCCATCAGGCCCAATTCACGTTT 1 -ATATGGCCCATCAGGCCCAAATCAC-ATT * * 72588403 ATATGTCCCAT-AGGCCC-AATCTCATTT 1 ATATGGCCCATCAGGCCCAAATCACA-TT * * 72588430 ATGTGGCCCATCCGGCCCAAATCACATT 1 ATATGGCCCATCAGGCCCAAATCACATT 72588458 ATAT 1 ATAT 72588462 TCATGCTTAT Statistics Matches: 161, Mismatches: 30, Indels: 24 0.75 0.14 0.11 Matches are distributed among these distances: 27 15 0.09 28 55 0.34 29 89 0.55 30 2 0.01 ACGTcount: A:0.26, C:0.31, G:0.13, T:0.29 Consensus pattern (28 bp): ATATGGCCCATCAGGCCCAAATCACATT Found at i:72592899 original size:29 final size:29 Alignment explanation

Indices: 72592828--72593016 Score: 186 Period size: 29 Copynumber: 6.6 Consensus size: 29 72592818 ACCGCTACAT * * 72592828 ACATGCATATGGCCCA-CTAGACCCAA-TC 1 ACATTCATATGGCCCATC-AGGCCCAATTC * * ** 72592856 TCATTTATATGGCCCATTTGGCCCAATTC 1 ACATTCATATGGCCCATCAGGCCCAATTC * 72592885 ACGTTCATATGGCCCATCAGGCCCAATTC 1 ACATTCATATGGCCCATCAGGCCCAATTC * 72592914 ACATTCATATGGCCCATTAGGCCCAA-TC 1 ACATTCATATGGCCCATCAGGCCCAATTC * * * * * * * 72592942 GCATTTATTTGACCCATCCGACACAATTC 1 ACATTCATATGGCCCATCAGGCCCAATTC * 72592971 ACGTTCATATGGCCCATCAGGCCCAATTC 1 ACATTCATATGGCCCATCAGGCCCAATTC * * 72593000 ATATTCATATGACCCAT 1 ACATTCATATGGCCCAT 72593017 TAGCTTAATC Statistics Matches: 126, Mismatches: 32, Indels: 5 0.77 0.20 0.03 Matches are distributed among these distances: 28 39 0.31 29 87 0.69 ACGTcount: A:0.27, C:0.32, G:0.14, T:0.28 Consensus pattern (29 bp): ACATTCATATGGCCCATCAGGCCCAATTC Found at i:72592910 original size:57 final size:57 Alignment explanation

Indices: 72592828--72593040 Score: 191 Period size: 57 Copynumber: 3.7 Consensus size: 57 72592818 ACCGCTACAT * * * * 72592828 ACATGCATATGGCCCA-CTAGACCCAATCTCATTTATATGGCCCATTTGGCCCAATTC 1 ACATTCATATGACCCATC-AGACCCAATCTCATTCATATGGCCCATTAGGCCCAATTC * * * * 72592885 ACGTTCATATGGCCCATCAGGCCCAATTCACATTCATATGGCCCATTAGGCCCAA-TC 1 ACATTCATATGACCCATCAGACCCAA-TCTCATTCATATGGCCCATTAGGCCCAATTC * * * * * * 72592942 GCATTTATTTGACCCATCCGACACAAT-TCACGTTCATATGGCCCATCAGGCCCAATTC 1 ACATTCATATGACCCATCAGACCCAATCTCA--TTCATATGGCCCATTAGGCCCAATTC * * ** * 72593000 ATATTCATATGACCCATTAG-CTTAATCTCATTTATATGGCC 1 ACATTCATATGACCCATCAGACCCAATCTCATTCATATGGCC 72593041 TATCCGGCCC Statistics Matches: 125, Mismatches: 25, Indels: 13 0.77 0.15 0.08 Matches are distributed among these distances: 55 2 0.02 56 11 0.09 57 67 0.54 58 45 0.36 ACGTcount: A:0.27, C:0.31, G:0.14, T:0.29 Consensus pattern (57 bp): ACATTCATATGACCCATCAGACCCAATCTCATTCATATGGCCCATTAGGCCCAATTC Found at i:72592978 original size:86 final size:86 Alignment explanation

Indices: 72592828--72593046 Score: 278 Period size: 86 Copynumber: 2.6 Consensus size: 86 72592818 ACCGCTACAT * * * * ** * * 72592828 ACATGCATATGGCCCACTAGACCCAATCTCATTTATATGGCCCATTTGGCCCAATTCACGTTCAT 1 ACATTCATATGGCCCATTAGACCCAATCGCATTTATATGACCCATCCGACACAATTCACGTTCAT 72592893 ATGGCCCATCAGGCCCAATTC 66 ATGGCCCATCAGGCCCAATTC * * 72592914 ACATTCATATGGCCCATTAGGCCCAATCGCATTTATTTGACCCATCCGACACAATTCACGTTCAT 1 ACATTCATATGGCCCATTAGACCCAATCGCATTTATATGACCCATCCGACACAATTCACGTTCAT 72592979 ATGGCCCATCAGGCCCAATTC 66 ATGGCCCATCAGGCCCAATTC * * ** * * * 72593000 ATATTCATATGACCCATTAG-CTTAATCTCATTTATATGGCCTATCCG 1 ACATTCATATGGCCCATTAGACCCAATCGCATTTATATGACCCATCCG 72593047 GCCCAAATCT Statistics Matches: 115, Mismatches: 18, Indels: 1 0.86 0.13 0.01 Matches are distributed among these distances: 85 21 0.18 86 94 0.82 ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29 Consensus pattern (86 bp): ACATTCATATGGCCCATTAGACCCAATCGCATTTATATGACCCATCCGACACAATTCACGTTCAT ATGGCCCATCAGGCCCAATTC Found at i:72602567 original size:47 final size:47 Alignment explanation

Indices: 72602504--72602608 Score: 165 Period size: 47 Copynumber: 2.2 Consensus size: 47 72602494 CCCTTCGGGA * * 72602504 CTTATCACATTTATACACTTTCACATTCATCACATTGGCCATTCGGC 1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC * * 72602551 TTTATCACATATATACACTTTCACATCCATTACATTGGCCATTCGGC 1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC * 72602598 CTTACCACATA 1 CTTATCACATA 72602609 ATTAATACTA Statistics Matches: 52, Mismatches: 6, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 47 52 1.00 ACGTcount: A:0.28, C:0.30, G:0.08, T:0.35 Consensus pattern (47 bp): CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC Found at i:72606167 original size:21 final size:20 Alignment explanation

Indices: 72606139--72606180 Score: 57 Period size: 21 Copynumber: 2.0 Consensus size: 20 72606129 CAAAATTTGT * 72606139 ATAACTATCATTAAACATTC 1 ATAACTATCATCAAACATTC * 72606159 ATAATCTATCATCAATCATTC 1 ATAA-CTATCATCAAACATTC 72606180 A 1 A 72606181 AATACATGCT Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 20 4 0.21 21 15 0.79 ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36 Consensus pattern (20 bp): ATAACTATCATCAAACATTC Found at i:72616587 original size:19 final size:20 Alignment explanation

Indices: 72616550--72616590 Score: 75 Period size: 20 Copynumber: 2.1 Consensus size: 20 72616540 TATTTTTCTG 72616550 TTGCTTACATCCACGTACCA 1 TTGCTTACATCCACGTACCA 72616570 TTGCTTACATCC-CGTACCA 1 TTGCTTACATCCACGTACCA 72616589 TT 1 TT 72616591 ATCTTTTTCT Statistics Matches: 21, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 19 9 0.43 20 12 0.57 ACGTcount: A:0.22, C:0.34, G:0.10, T:0.34 Consensus pattern (20 bp): TTGCTTACATCCACGTACCA Found at i:72621671 original size:9 final size:9 Alignment explanation

Indices: 72621657--72621687 Score: 53 Period size: 9 Copynumber: 3.4 Consensus size: 9 72621647 ATATTCTTGC 72621657 TTCATGCAT 1 TTCATGCAT 72621666 TTCATGCAT 1 TTCATGCAT * 72621675 TTCATGTAT 1 TTCATGCAT 72621684 TTCA 1 TTCA 72621688 CACACACTAC Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 9 21 1.00 ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48 Consensus pattern (9 bp): TTCATGCAT Found at i:72628445 original size:20 final size:20 Alignment explanation

Indices: 72628417--72628458 Score: 66 Period size: 20 Copynumber: 2.1 Consensus size: 20 72628407 ATGGTAGCCA * * 72628417 TAAATGGTAATTAAATCATT 1 TAAAAGGTAATTAAACCATT 72628437 TAAAAGGTAATTAAACCATT 1 TAAAAGGTAATTAAACCATT 72628457 TA 1 TA 72628459 TATGTTTAGA Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36 Consensus pattern (20 bp): TAAAAGGTAATTAAACCATT Found at i:72631649 original size:6 final size:6 Alignment explanation

Indices: 72631638--72631748 Score: 82 Period size: 6 Copynumber: 17.8 Consensus size: 6 72631628 ATTAGGTGAT * * * 72631638 AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC AGTATC AGAATC 1 AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC AGAATC * * * * 72631687 AGTATC AGGTAA-C AGAATC AAAATC AGAATC AGTATC AGATAAC AGAATC 1 AGAATC A-G-AATC AGAATC AGAATC AGAATC AGAATC AGA-ATC AGAATC * 72631737 AAAAATC AGAAT 1 -AGAATC AGAAT 72631749 GTGAATGCAA Statistics Matches: 81, Mismatches: 16, Indels: 16 0.72 0.14 0.14 Matches are distributed among these distances: 5 3 0.04 6 61 0.75 7 15 0.19 8 2 0.02 ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20 Consensus pattern (6 bp): AGAATC Found at i:72631667 original size:19 final size:18 Alignment explanation

Indices: 72631643--72631713 Score: 81 Period size: 19 Copynumber: 3.8 Consensus size: 18 72631633 GTGATAGAAT * 72631643 CAGAATCAGAATTAGGTGA 1 CAGAATCAGAATCAGGT-A 72631662 CAGAATCAGAATCA-GTA 1 CAGAATCAGAATCAGGTA * 72631679 TCAGAATCAGTATCAGGTAA 1 -CAGAATCAGAATCAGGT-A * 72631699 CAGAATCAAAATCAG 1 CAGAATCAGAATCAG 72631714 AATCAGTATC Statistics Matches: 45, Mismatches: 4, Indels: 6 0.82 0.07 0.11 Matches are distributed among these distances: 17 1 0.02 18 15 0.33 19 28 0.62 20 1 0.02 ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20 Consensus pattern (18 bp): CAGAATCAGAATCAGGTA Found at i:72631673 original size:31 final size:31 Alignment explanation

Indices: 72631640--72631748 Score: 101 Period size: 31 Copynumber: 3.3 Consensus size: 31 72631630 TAGGTGATAG * 72631640 AATCAGAATCAGAATTAGGTGACAGAATCAGAA 1 AATCAGAATCAGAATTAGGTAACAGAATC--AA * * 72631673 TCAGTATCAGAATCAGTATCAGGTAACAGAATCAA 1 --A--ATCAGAATCAGAATTAGGTAACAGAATCAA * * * 72631708 AATCAGAATCAGTATCAGATAACAGAATCAAA 1 AATCAGAATCAGAATTAGGTAACAGAATC-AA 72631740 AATCAGAAT 1 AATCAGAAT 72631749 GTGAATGCAA Statistics Matches: 67, Mismatches: 4, Indels: 9 0.84 0.05 0.11 Matches are distributed among these distances: 31 27 0.40 32 11 0.16 33 1 0.01 35 3 0.04 37 25 0.37 ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20 Consensus pattern (31 bp): AATCAGAATCAGAATTAGGTAACAGAATCAA Found at i:72631676 original size:25 final size:25 Alignment explanation

Indices: 72631619--72631676 Score: 98 Period size: 25 Copynumber: 2.3 Consensus size: 25 72631609 TATCAGAACT * * 72631619 AGAATCAAAATTAGGTGATAGAATC 1 AGAATCAGAATTAGGTGACAGAATC 72631644 AGAATCAGAATTAGGTGACAGAATC 1 AGAATCAGAATTAGGTGACAGAATC 72631669 AGAATCAG 1 AGAATCAG 72631677 TATCAGAATC Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 25 31 1.00 ACGTcount: A:0.47, C:0.10, G:0.22, T:0.21 Consensus pattern (25 bp): AGAATCAGAATTAGGTGACAGAATC Found at i:72631682 original size:37 final size:37 Alignment explanation

Indices: 72631638--72631726 Score: 124 Period size: 37 Copynumber: 2.4 Consensus size: 37 72631628 ATTAGGTGAT * * * 72631638 AGAATCAGAATCAGAATTAGGTGACAGAATCAGAATC 1 AGAATCAGAATCAGAATCAGGTAACAGAATCAAAATC * * 72631675 AGTATCAGAATCAGTATCAGGTAACAGAATCAAAATC 1 AGAATCAGAATCAGAATCAGGTAACAGAATCAAAATC * 72631712 AGAATCAGTATCAGA 1 AGAATCAGAATCAGA 72631727 TAACAGAATC Statistics Matches: 44, Mismatches: 8, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 37 44 1.00 ACGTcount: A:0.46, C:0.15, G:0.19, T:0.20 Consensus pattern (37 bp): AGAATCAGAATCAGAATCAGGTAACAGAATCAAAATC Found at i:72631927 original size:27 final size:26 Alignment explanation

Indices: 72631885--72631986 Score: 132 Period size: 27 Copynumber: 3.8 Consensus size: 26 72631875 GCTCAGTTAT * * 72631885 CAGATATTGTGACAGAGTCACCAGATA 1 CAGATATTGTGGCAGAGCCACCAGA-A 72631912 CAGATATTGTGGCAGAGCCACCAGAA 1 CAGATATTGTGGCAGAGCCACCAGAA * 72631938 CAGATATTTGTGGCATAGCCACCAGAAA 1 CAGATA-TTGTGGCAGAGCCACCAG-AA * * 72631966 CAGATAATGTGGCAAAGCCAC 1 CAGATATTGTGGCAGAGCCAC 72631987 TTAACAGAAT Statistics Matches: 68, Mismatches: 5, Indels: 4 0.88 0.06 0.05 Matches are distributed among these distances: 26 7 0.10 27 53 0.78 28 8 0.12 ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19 Consensus pattern (26 bp): CAGATATTGTGGCAGAGCCACCAGAA Found at i:72632173 original size:22 final size:22 Alignment explanation

Indices: 72632145--72632209 Score: 78 Period size: 22 Copynumber: 3.0 Consensus size: 22 72632135 GTAAATACGT * 72632145 TTGGCACATAGCCATAATCAGG 1 TTGGCACAAAGCCATAATCAGG * * 72632167 TTGGCACAGAGCCAT-ATGTAGG 1 TTGGCACAAAGCCATAAT-CAGG * 72632189 TTGACACAAAGCCATAATCAG 1 TTGGCACAAAGCCATAATCAG 72632210 AAGGCTTTAA Statistics Matches: 36, Mismatches: 5, Indels: 4 0.80 0.11 0.09 Matches are distributed among these distances: 21 2 0.06 22 32 0.89 23 2 0.06 ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22 Consensus pattern (22 bp): TTGGCACAAAGCCATAATCAGG Found at i:72632668 original size:27 final size:27 Alignment explanation

Indices: 72632635--72632876 Score: 265 Period size: 27 Copynumber: 9.0 Consensus size: 27 72632625 AGGGGCAAAA * * 72632635 TGGTAATTTTACCCCACAGGGGTATTT 1 TGGTAATTCTACCCTACAGGGGTATTT ** * 72632662 TAATAATTCTACCCTACAGGGGAATTT 1 TGGTAATTCTACCCTACAGGGGTATTT * * * 72632689 CGATAATTCTACCCTACAGGGGTATTG 1 TGGTAATTCTACCCTACAGGGGTATTT * * * 72632716 CGATAATTCTACCCTACAGGGGCATTT 1 TGGTAATTCTACCCTACAGGGGTATTT * * 72632743 CGGTAATTCTACCCTACAGGGGTATTC 1 TGGTAATTCTACCCTACAGGGGTATTT 72632770 TGGTAATTCTACCCTACAGGGGTATTT 1 TGGTAATTCTACCCTACAGGGGTATTT * ** 72632797 TGGTAATTTTA-CAAACTAGGGGTATTT 1 TGGTAATTCTACCCTAC-AGGGGTATTT * ** 72632824 TGGTAATTTTA-CAAACTAGGGGTATTT 1 TGGTAATTCTACCCTAC-AGGGGTATTT * 72632851 T-GTAATTCTATCCTACAGGGGTATTT 1 TGGTAATTCTACCCTACAGGGGTATTT 72632877 CAGTAATTTC Statistics Matches: 191, Mismatches: 22, Indels: 5 0.88 0.10 0.02 Matches are distributed among these distances: 26 21 0.11 27 170 0.89 ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36 Consensus pattern (27 bp): TGGTAATTCTACCCTACAGGGGTATTT Found at i:72632923 original size:27 final size:27 Alignment explanation

Indices: 72632893--72633032 Score: 165 Period size: 27 Copynumber: 5.2 Consensus size: 27 72632883 TTTCACAATT * * 72632893 GAGGGTAAAACGGTAATTTTGTAAA-C 1 GAGGGTAAAATGGTAATTTTATAAATC 72632919 AGAGGGTAAAATGGTAATTTTATAAATC 1 -GAGGGTAAAATGGTAATTTTATAAATC ** * * 72632947 GAGGGTAAAACAGTAATTTTGTAATTC 1 GAGGGTAAAATGGTAATTTTATAAATC * * 72632974 GAGGGTGAAATGGTAATTTTATAAATT 1 GAGGGTAAAATGGTAATTTTATAAATC * * * 72633001 AAGGGTAAAATGGTAATTCTACAAATC 1 GAGGGTAAAATGGTAATTTTATAAATC 72633028 GAGGG 1 GAGGG 72633033 CATTTCAGTA Statistics Matches: 94, Mismatches: 18, Indels: 2 0.82 0.16 0.02 Matches are distributed among these distances: 27 93 0.99 28 1 0.01 ACGTcount: A:0.39, C:0.06, G:0.25, T:0.30 Consensus pattern (27 bp): GAGGGTAAAATGGTAATTTTATAAATC Found at i:72633006 original size:81 final size:80 Alignment explanation

Indices: 72632889--72633051 Score: 211 Period size: 81 Copynumber: 2.0 Consensus size: 80 72632879 GTAATTTCAC * * * * 72632889 AATTGAGGGTAAAACGGTAATTTTGTAAACAGAGGGTAAAATGGTAATTTTATAAATCGAGGGTA 1 AATTGAGGGTAAAACGGTAATTTTATAAACAGAGGGTAAAATGGTAATTCTACAAATCGAGGGCA 72632954 AAACAGTAATTTTGT 66 AAACAGTAATTTTGT * * * 72632969 AATTCGAGGGTGAAATGGTAATTTTATAAATTA-AGGGTAAAATGGTAATTCTACAAATCGAGGG 1 AATT-GAGGGTAAAACGGTAATTTTATAAA-CAGAGGGTAAAATGGTAATTCTACAAATCGAGGG *** 72633033 CATTTCAGTAATTTTGT 64 CAAAACAGTAATTTTGT 72633050 AA 1 AA 72633052 ACCAATGGTA Statistics Matches: 71, Mismatches: 10, Indels: 3 0.85 0.12 0.04 Matches are distributed among these distances: 80 4 0.06 81 66 0.93 82 1 0.01 ACGTcount: A:0.39, C:0.06, G:0.23, T:0.33 Consensus pattern (80 bp): AATTGAGGGTAAAACGGTAATTTTATAAACAGAGGGTAAAATGGTAATTCTACAAATCGAGGGCA AAACAGTAATTTTGT Found at i:72633030 original size:54 final size:54 Alignment explanation

Indices: 72632889--72633032 Score: 191 Period size: 54 Copynumber: 2.7 Consensus size: 54 72632879 GTAATTTCAC 72632889 AATTGAGGGTAAAACGGTAATTTTGTAAA-CAGAGGGTAAAATGGTAATTTTATA 1 AATTGAGGGTAAAACGGTAATTTTGTAAATC-GAGGGTAAAATGGTAATTTTATA * * * * 72632943 AATCGAGGGTAAAACAGTAATTTTGTAATTCGAGGGTGAAATGGTAATTTTATA 1 AATTGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTATA * * * ** 72632997 AATTAAGGGTAAAATGGTAATTCTACAAATCGAGGG 1 AATTGAGGGTAAAACGGTAATTTTGTAAATCGAGGG 72633033 CATTTCAGTA Statistics Matches: 77, Mismatches: 12, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 54 76 0.99 55 1 0.01 ACGTcount: A:0.40, C:0.06, G:0.24, T:0.31 Consensus pattern (54 bp): AATTGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTATA Found at i:72633133 original size:109 final size:108 Alignment explanation

Indices: 72633014--72633236 Score: 270 Period size: 109 Copynumber: 2.1 Consensus size: 108 72633004 GGTAAAATGG * **** 72633014 TAATTCTACAAATCGAGGGCATTTCAGTAATTTTGTAAACCAATGGTATTTCT-ATAATTTTTAA 1 TAATTTTACAAATCGAGGGCATTTCAGTAATTACACAAACCAATGGTATTT-TGATAA-TTTTAA * * * * 72633078 AAAGTCAAGGGTATTTTTGTAATTTT-TAAATCAGGGGTATTTTGA 64 AAA-CCAAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGA * * * * * 72633123 TAATTTTACAAATTGAGGGTATTTCGGTAATTACACAAACCAGTGGTATTTTGATAATTTTACAA 1 TAATTTTACAAATCGAGGGCATTTCAGTAATTACACAAACCAATGGTATTTTGATAATTTTAAAA * 72633188 ACCAAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGG 66 ACCAAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGA 72633231 TAATTT 1 TAATTT 72633237 GGTAAACTAA Statistics Matches: 97, Mismatches: 15, Indels: 5 0.83 0.13 0.04 Matches are distributed among these distances: 107 20 0.21 108 31 0.32 109 46 0.47 ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40 Consensus pattern (108 bp): TAATTTTACAAATCGAGGGCATTTCAGTAATTACACAAACCAATGGTATTTTGATAATTTTAAAA ACCAAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGA Found at i:72633224 original size:81 final size:80 Alignment explanation

Indices: 72633087--72633235 Score: 194 Period size: 81 Copynumber: 1.9 Consensus size: 80 72633077 AAAAGTCAAG * * * ** 72633087 GGTATTTTTGTAATTTTTAAATCAGGGGTATTTTGATAATTTTACAAATTGAGGGTATTTCGGTA 1 GGTATTTTTGTAATTTTCAAACCAAGGGTATTTTGATAATTTTACAAACAGAGGGTATTTCGGTA 72633152 ATTACACAAACCAGT 66 ATTACACAAACCAGT * * 72633167 GGTA-TTTTGATAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCAG-GGGTATTTTG 1 GGTATTTTTG-TAATTTT-CAAACCAAGGGTATTTTGATAATTTTACAAA-CAGAGGGTATTTCG 72633230 GTAATT 63 GTAATT 72633236 TGGTAAACTA Statistics Matches: 59, Mismatches: 7, Indels: 5 0.83 0.10 0.07 Matches are distributed among these distances: 79 5 0.08 80 11 0.19 81 42 0.71 82 1 0.02 ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41 Consensus pattern (80 bp): GGTATTTTTGTAATTTTCAAACCAAGGGTATTTTGATAATTTTACAAACAGAGGGTATTTCGGTA ATTACACAAACCAGT Found at i:72633243 original size:27 final size:27 Alignment explanation

Indices: 72633086--72633236 Score: 171 Period size: 27 Copynumber: 5.6 Consensus size: 27 72633076 AAAAAGTCAA * * * 72633086 GGGTATTTTTGTAATTTT-TAAATCAG 1 GGGTATTTTGGTAATTTTACAAACCAG * ** 72633112 GGGTATTTTGATAATTTTACAAA-TTG 1 GGGTATTTTGGTAATTTTACAAACCAG * ** 72633138 AGGGTATTTCGGTAATTACACAAACCAG 1 -GGGTATTTTGGTAATTTTACAAACCAG * * * 72633166 TGGTATTTTGATAATTTTACAAACCAA 1 GGGTATTTTGGTAATTTTACAAACCAG 72633193 GGGTATTTTGGTAATTTTACAAACCAG 1 GGGTATTTTGGTAATTTTACAAACCAG 72633220 GGGTATTTTGGTAATTT 1 GGGTATTTTGGTAATTT 72633237 GGTAAACTAA Statistics Matches: 102, Mismatches: 20, Indels: 5 0.80 0.16 0.04 Matches are distributed among these distances: 26 17 0.17 27 84 0.82 28 1 0.01 ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41 Consensus pattern (27 bp): GGGTATTTTGGTAATTTTACAAACCAG Found at i:72636470 original size:40 final size:40 Alignment explanation

Indices: 72636399--72636644 Score: 316 Period size: 40 Copynumber: 6.2 Consensus size: 40 72636389 CAGAATTTAG * * * * 72636399 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC * * * * * 72636439 CCGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC 1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC * * * * 72636479 CCGGAT-ATATCAATTCGCACAAATGCCTTCGGGTCTTAGC 1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC 72636519 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC 1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC 72636559 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC 1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC * * * 72636599 CCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGC 1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC 72636639 CCGGAT 1 CCGGAT 72636645 CTCATTCAAA Statistics Matches: 186, Mismatches: 18, Indels: 4 0.89 0.09 0.02 Matches are distributed among these distances: 39 2 0.01 40 180 0.97 41 4 0.02 ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23 Consensus pattern (40 bp): CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC Found at i:72638869 original size:6 final size:6 Alignment explanation

Indices: 72638845--72638979 Score: 80 Period size: 6 Copynumber: 22.0 Consensus size: 6 72638835 AAGAAACATT * * * * 72638845 ATCAGA A-CTAGA TTCAGA ATCAGA ATCAAA ATTAG- GTGACAGA ATCAGA 1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA * * * * * 72638894 ATCAGA ATTAG- GTGACAAA ATCAGA ATCAGA ATCAGT ATCAGA ATCAGT 1 ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA * * 72638943 ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAGT ATCAGA 1 ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA 72638980 TAACAGAATA Statistics Matches: 96, Mismatches: 22, Indels: 22 0.69 0.16 0.16 Matches are distributed among these distances: 5 5 0.05 6 81 0.84 7 7 0.07 8 3 0.03 ACGTcount: A:0.47, C:0.15, G:0.18, T:0.21 Consensus pattern (6 bp): ATCAGA Found at i:72638929 original size:31 final size:26 Alignment explanation

Indices: 72638858--72638947 Score: 116 Period size: 25 Copynumber: 3.6 Consensus size: 26 72638848 AGAACTAGAT * 72638858 TCAGAATCAGAATCAAAATTAGGTGA 1 TCAGAATCAGAATCAGAATTAGGTGA 72638884 -CAGAATCAGAATCAGAATTAGGTGA 1 TCAGAATCAGAATCAGAATTAGGTGA * * 72638909 -CAAAATCAGAATCAGAATCA-GT-A 1 TCAGAATCAGAATCAGAATTAGGTGA * 72638932 TCAGAATCAGTATCAG 1 TCAGAATCAGAATCAG 72638948 GTAACAGAAT Statistics Matches: 58, Mismatches: 5, Indels: 4 0.87 0.07 0.06 Matches are distributed among these distances: 23 1 0.02 24 15 0.26 25 42 0.72 ACGTcount: A:0.46, C:0.14, G:0.19, T:0.21 Consensus pattern (26 bp): TCAGAATCAGAATCAGAATTAGGTGA Found at i:72638935 original size:43 final size:43 Alignment explanation

Indices: 72638888--72638988 Score: 139 Period size: 43 Copynumber: 2.3 Consensus size: 43 72638878 AGGTGACAGA * * * 72638888 ATCAGAATCAGAATTAGGTGACAAAATCAGAATCAGAATCAGT 1 ATCAGAATCAGAATCAGGTAACAAAATCAAAATCAGAATCAGT * * 72638931 ATCAGAATCAGTATCAGGTAACAGAATCAAAATCAGAATCAGT 1 ATCAGAATCAGAATCAGGTAACAAAATCAAAATCAGAATCAGT * 72638974 ATCAGATAACAGAAT 1 ATCAGA-ATCAGAAT 72638989 AAAAAATCAG Statistics Matches: 50, Mismatches: 7, Indels: 1 0.86 0.12 0.02 Matches are distributed among these distances: 43 44 0.88 44 6 0.12 ACGTcount: A:0.48, C:0.15, G:0.17, T:0.21 Consensus pattern (43 bp): ATCAGAATCAGAATCAGGTAACAAAATCAAAATCAGAATCAGT Found at i:72638956 original size:31 final size:31 Alignment explanation

Indices: 72638913--72639001 Score: 117 Period size: 31 Copynumber: 2.9 Consensus size: 31 72638903 AGGTGACAAA * ** 72638913 ATCAGA-ATCAGAATCAGTATCAGAATCAGT 1 ATCAGATAACAGAATCAAAATCAGAATCAGT * 72638943 ATCAGGTAACAGAATCAAAATCAGAATCAGT 1 ATCAGATAACAGAATCAAAATCAGAATCAGT * 72638974 ATCAGATAACAGAATAAAAAATCAGAAT 1 ATCAGATAACAGAAT-CAAAATCAGAAT 72639002 GTGAATGCAA Statistics Matches: 51, Mismatches: 6, Indels: 2 0.86 0.10 0.03 Matches are distributed among these distances: 30 5 0.10 31 35 0.69 32 11 0.22 ACGTcount: A:0.51, C:0.15, G:0.15, T:0.20 Consensus pattern (31 bp): ATCAGATAACAGAATCAAAATCAGAATCAGT Found at i:72639180 original size:27 final size:26 Alignment explanation

Indices: 72639138--72639239 Score: 114 Period size: 27 Copynumber: 3.8 Consensus size: 26 72639128 GCTCAGTTAT * * * 72639138 CAGATACTGTGACAGAGTCACCAGATA 1 CAGATATTGTGGCAGAGCCACCAGA-A * 72639165 CAGATATTGTGGCAGAGCCACCATAA 1 CAGATATTGTGGCAGAGCCACCAGAA * 72639191 CAGATATTTGTGGCATAGCCACCAGAAA 1 CAGATA-TTGTGGCAGAGCCACCAG-AA * * 72639219 CAGATAATGTGGCAAAGCCAC 1 CAGATATTGTGGCAGAGCCAC 72639240 TTAACAGAAT Statistics Matches: 65, Mismatches: 8, Indels: 4 0.84 0.10 0.05 Matches are distributed among these distances: 26 7 0.11 27 50 0.77 28 8 0.12 ACGTcount: A:0.36, C:0.23, G:0.23, T:0.19 Consensus pattern (26 bp): CAGATATTGTGGCAGAGCCACCAGAA Found at i:72639265 original size:54 final size:54 Alignment explanation

Indices: 72639156--72639257 Score: 127 Period size: 54 Copynumber: 1.9 Consensus size: 54 72639146 GTGACAGAGT * * * ** * 72639156 CACCAGATACAGATATTGTGGCAGAGCCACCATAACAGATATTTGTGGCATAGC 1 CACCAGAAACAGATAATGTGGCAAAGCCACCATAACAGATATACGTGGCAAAGC * 72639210 CACCAGAAACAGATAATGTGGCAAAGCCA-CTTAACAGA-ATACGTGGCA 1 CACCAGAAACAGATAATGTGGCAAAGCCACCATAACAGATATACGTGGCA 72639258 CAAAGCCATC Statistics Matches: 42, Mismatches: 6, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 52 8 0.19 53 8 0.19 54 26 0.62 ACGTcount: A:0.37, C:0.23, G:0.22, T:0.19 Consensus pattern (54 bp): CACCAGAAACAGATAATGTGGCAAAGCCACCATAACAGATATACGTGGCAAAGC Found at i:72639442 original size:22 final size:22 Alignment explanation

Indices: 72639398--72639462 Score: 60 Period size: 22 Copynumber: 3.0 Consensus size: 22 72639388 GCAAATACGT * 72639398 TTGGCACACAGCCATACTCAGG 1 TTGGCACAAAGCCATACTCAGG * * 72639420 TTGGCACAGAGCCATA-TGTAGG 1 TTGGCACAAAGCCATACT-CAGG ** * 72639442 TTAACACAAAGCCATAATCAG 1 TTGGCACAAAGCCATACTCAG 72639463 AAGGCCCATC Statistics Matches: 35, Mismatches: 6, Indels: 4 0.78 0.13 0.09 Matches are distributed among these distances: 21 1 0.03 22 33 0.94 23 1 0.03 ACGTcount: A:0.34, C:0.25, G:0.22, T:0.20 Consensus pattern (22 bp): TTGGCACAAAGCCATACTCAGG Found at i:72639940 original size:27 final size:27 Alignment explanation

Indices: 72639883--72640318 Score: 504 Period size: 27 Copynumber: 16.3 Consensus size: 27 72639873 GGGGTAAAAT * * * * 72639883 GGTAATTTTACCCCACA-AGGTATCTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * 72639909 GGTAATTCCACCCTACAGGGGTATTTT 1 GGTAATTCTACCCTACAGGGGTATTTC * * 72639936 AGTAATTCTACCCTATAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * 72639963 GATAATTCTACCCTATAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * 72639990 GGTAATTCTACCCTACAGGAG--TTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * 72640015 GGTAATTCTACCCTACAGGGGTATTGC 1 GGTAATTCTACCCTACAGGGGTATTTC ** 72640042 AATAATTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * * 72640069 GATAATTCTACCTTACAGGGGTGTTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * 72640096 GGTAATTCTATCCTACAGGGGTATTGC 1 GGTAATTCTACCCTACAGGGGTATTTC * * 72640123 GATAATTCTACCCTACAGTGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * 72640150 GGTAATTCTACCCTACAGGGGTATTTT 1 GGTAATTCTACCCTACAGGGGTATTTC * 72640177 GGTAATTCTACCCTACAGGGGTATTCC 1 GGTAATTCTACCCTACAGGGGTATTTC * 72640204 GGTAATTCTACCCTACAGGGGTATTTT 1 GGTAATTCTACCCTACAGGGGTATTTC * ** * 72640231 GGTAATTTTA-CAAACTAGGGGTATTTT 1 GGTAATTCTACCCTAC-AGGGGTATTTC * ** * 72640258 GGTAATTTTA-CAAACTAGGGGTATTTT 1 GGTAATTCTACCCTAC-AGGGGTATTTC * * 72640285 GGTAATTCTATCCTACGGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * 72640312 AGTAATT 1 GGTAATT 72640319 TCACAATCGA Statistics Matches: 357, Mismatches: 48, Indels: 9 0.86 0.12 0.02 Matches are distributed among these distances: 25 24 0.07 26 17 0.05 27 313 0.88 28 3 0.01 ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35 Consensus pattern (27 bp): GGTAATTCTACCCTACAGGGGTATTTC Found at i:72640369 original size:27 final size:27 Alignment explanation

Indices: 72640323--72640520 Score: 245 Period size: 27 Copynumber: 7.3 Consensus size: 27 72640313 GTAATTTCAC * ** * * 72640323 AATCGACGGTAAAACAGTAATTTTGTA 1 AATCGAGGGTAAAATGGTAATTCTATA * * 72640350 AA-CTGAGGGTAAAATGGTAATTTTGTA 1 AATC-GAGGGTAAAATGGTAATTCTATA * * 72640377 AATCAAGGGTAAAAGGGTAATTCTATA 1 AATCGAGGGTAAAATGGTAATTCTATA 72640404 AATCGAGGGTAAAATGGTAATTCTATA 1 AATCGAGGGTAAAATGGTAATTCTATA * * * * 72640431 AATCAAGGGTAAAATAGTAATTTTGTA 1 AATCGAGGGTAAAATGGTAATTCTATA * 72640458 AATCGAGGGTGAAATGGTAATTCTATA 1 AATCGAGGGTAAAATGGTAATTCTATA * 72640485 AATCGAGGGTAAAATGGTAATTCTACA 1 AATCGAGGGTAAAATGGTAATTCTATA 72640512 AATCGAGGG 1 AATCGAGGG 72640521 CATTTCAGTA Statistics Matches: 149, Mismatches: 20, Indels: 4 0.86 0.12 0.02 Matches are distributed among these distances: 26 1 0.01 27 147 0.99 28 1 0.01 ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29 Consensus pattern (27 bp): AATCGAGGGTAAAATGGTAATTCTATA Found at i:72640540 original size:81 final size:81 Alignment explanation

Indices: 72640355--72640520 Score: 278 Period size: 81 Copynumber: 2.0 Consensus size: 81 72640345 TTGTAAACTG * 72640355 AGGGTAAAATGGTAATTTTGTAAATCAAGGGTAAAAGGGTAATTCTATAAATCGAGGGTAAAATG 1 AGGGTAAAATAGTAATTTTGTAAATCAAGGGTAAAAGGGTAATTCTATAAATCGAGGGTAAAATG * 72640420 GTAATTCTATAAATCA 66 GTAATTCTACAAATCA * * * 72640436 AGGGTAAAATAGTAATTTTGTAAATCGAGGGTGAAATGGTAATTCTATAAATCGAGGGTAAAATG 1 AGGGTAAAATAGTAATTTTGTAAATCAAGGGTAAAAGGGTAATTCTATAAATCGAGGGTAAAATG * 72640501 GTAATTCTACAAATCG 66 GTAATTCTACAAATCA 72640517 AGGG 1 AGGG 72640521 CATTTCAGTA Statistics Matches: 79, Mismatches: 6, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 81 79 1.00 ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29 Consensus pattern (81 bp): AGGGTAAAATAGTAATTTTGTAAATCAAGGGTAAAAGGGTAATTCTATAAATCGAGGGTAAAATG GTAATTCTACAAATCA Found at i:72640560 original size:81 final size:81 Alignment explanation

Indices: 72640355--72640544 Score: 211 Period size: 81 Copynumber: 2.3 Consensus size: 81 72640345 TTGTAAACTG * * * * * * * 72640355 AGGGTAAAATGGTAATTTTGTAAATCAAGGGTAAAAGGGTAATTCTATAAATCGAGGGTAAAATG 1 AGGGTAAAATAGTAATTCTGTAAACCAAGAGTGAAATGATAATTCTATAAATCGAGGGTAAAATG * 72640420 GTAATTCTATAAATCA 66 GTAATTCTACAAATCA * * * * * 72640436 AGGGTAAAATAGTAATTTTGTAAATCGAGGGTGAAATGGTAATTCTATAAATCGAGGGTAAAATG 1 AGGGTAAAATAGTAATTCTGTAAACCAAGAGTGAAATGATAATTCTATAAATCGAGGGTAAAATG * 72640501 GTAATTCTACAAATCG 66 GTAATTCTACAAATCA * ** 72640517 AGGG-CATTTCAGTAATTCTGTAAACCAA 1 AGGGTAAAAT-AGTAATTCTGTAAACCAA 72640545 TAGTATTTCT Statistics Matches: 96, Mismatches: 12, Indels: 2 0.87 0.11 0.02 Matches are distributed among these distances: 80 2 0.02 81 94 0.98 ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29 Consensus pattern (81 bp): AGGGTAAAATAGTAATTCTGTAAACCAAGAGTGAAATGATAATTCTATAAATCGAGGGTAAAATG GTAATTCTACAAATCA Found at i:72640739 original size:54 final size:54 Alignment explanation

Indices: 72640572--72640778 Score: 231 Period size: 54 Copynumber: 3.9 Consensus size: 54 72640562 TTAGAAAGTC ** * *** 72640572 AAGGGTATTTCT-GTAATTTTGA-AAATTAGGGGTATTTTGGTAATTTTACAATTT 1 AAGGGTATTT-TGGTAATTTT-ACAAACCAGGGGTATTTTGATAATTTTACAAACA * * * * * 72640626 GAGGGTATTTCGGTAATTTCAC-AACCAGTGGTATTTTGATAATTTTACAAACC 1 AAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGATAATTTTACAAACA * * * * 72640679 AGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACA 1 AAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGATAATTTTACAAACA * 72640733 AAGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGATAATTT 1 AAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGATAATTT 72640779 GGTAAACTAA Statistics Matches: 127, Mismatches: 23, Indels: 6 0.81 0.15 0.04 Matches are distributed among these distances: 53 43 0.34 54 84 0.66 ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41 Consensus pattern (54 bp): AAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGATAATTTTACAAACA Found at i:72640785 original size:27 final size:27 Alignment explanation

Indices: 72640574--72640778 Score: 195 Period size: 27 Copynumber: 7.6 Consensus size: 27 72640564 AGAAAGTCAA ** 72640574 GGGTATTTCTG-TAATTTTGA-AAATTAG 1 GGGTATTT-TGATAATTTT-ACAAACCAG * *** 72640601 GGGTATTTTGGTAATTTTAC-AATTTG 1 GGGTATTTTGATAATTTTACAAACCAG * * * 72640627 AGGGTATTTCGGTAATTTCAC-AACCAG 1 -GGGTATTTTGATAATTTTACAAACCAG * 72640654 TGGTATTTTGATAATTTTACAAACCAG 1 GGGTATTTTGATAATTTTACAAACCAG * * 72640681 GGGTATTTTGGTAATTTTACAAACTAG 1 GGGTATTTTGATAATTTTACAAACCAG * * * * 72640708 GGGTATTTTGGTAATTTTATAAACAAA 1 GGGTATTTTGATAATTTTACAAACCAG 72640735 GGGTATTTT-AGTAATTTTACAAACCAG 1 GGGTATTTTGA-TAATTTTACAAACCAG 72640762 GGGTATTTTGATAATTT 1 GGGTATTTTGATAATTT 72640779 GGTAAACTAA Statistics Matches: 152, Mismatches: 20, Indels: 12 0.83 0.11 0.07 Matches are distributed among these distances: 26 24 0.16 27 127 0.84 28 1 0.01 ACGTcount: A:0.30, C:0.08, G:0.20, T:0.41 Consensus pattern (27 bp): GGGTATTTTGATAATTTTACAAACCAG Found at i:72641970 original size:27 final size:27 Alignment explanation

Indices: 72641869--72641971 Score: 82 Period size: 27 Copynumber: 3.8 Consensus size: 27 72641859 ATACTTTAGT * * 72641869 TTACCAAATTATTGAAATACCCTCGAC 1 TTACAAAATTACTGAAATACCCTCGAC ** * * 72641896 TTGTAAAATTAC-CAAAGTACCCCCGAC 1 TTACAAAATTACTGAAA-TACCCTCGAC * * *** * 72641923 TTACAGAATTACCGTTTTACCCTCGAT 1 TTACAAAATTACTGAAATACCCTCGAC 72641950 TTACAAAATTACTGAAATACCC 1 TTACAAAATTACTGAAATACCC 72641972 CTATAGGGTA Statistics Matches: 54, Mismatches: 20, Indels: 4 0.69 0.26 0.05 Matches are distributed among these distances: 26 3 0.06 27 51 0.94 ACGTcount: A:0.36, C:0.26, G:0.09, T:0.29 Consensus pattern (27 bp): TTACAAAATTACTGAAATACCCTCGAC Found at i:72641986 original size:27 final size:27 Alignment explanation

Indices: 72641956--72642425 Score: 543 Period size: 27 Copynumber: 17.3 Consensus size: 27 72641946 CGATTTACAA * 72641956 AATTACTGAAATACCCCTATAGGGTAG 1 AATTACTGAAATACCCCTGTAGGGTAG 72641983 AATTACTAATTACTGAAATA-CCCTGTAGGGTAG 1 -A--A-T---TACTGAAATACCCCTGTAGGGTAG * 72642016 AATTACCGAAATACCCCTGTAGGGTAG 1 AATTACTGAAATACCCCTGTAGGGTAG * ** 72642043 AAATACCAAAATACCCCTGTAGGGTAG 1 AATTACTGAAATACCCCTGTAGGGTAG * * 72642070 AATTATTGAAATACCCTTGTAGGGTAG 1 AATTACTGAAATACCCCTGTAGGGTAG * * * 72642097 AA-TACCGAAATACCCTTGTAAGGTAG 1 AATTACTGAAATACCCCTGTAGGGTAG * *** 72642123 AATTACCGAAATACATTTGTAGGGTAG 1 AATTACTGAAATACCCCTGTAGGGTAG * * * * 72642150 AAATACAGAAATACCCCTATAAGGTAG 1 AATTACTGAAATACCCCTGTAGGGTAG * 72642177 AATTACTGAAATACCCTTGTAGGGTAG 1 AATTACTGAAATACCCCTGTAGGGTAG * 72642204 AATTACTGAAATACCCTTGTAGGGTAG 1 AATTACTGAAATACCCCTGTAGGGTAG * 72642231 AATTACTGAAATACCCTTGTAGGGTAG 1 AATTACTGAAATACCCCTGTAGGGTAG * * 72642258 AATTACTGAAATACTCCTGTAAGGTAG 1 AATTACTGAAATACCCCTGTAGGGTAG * * 72642285 AATTACCGAAATACCCTTGTAGGGTAG 1 AATTACTGAAATACCCCTGTAGGGTAG * 72642312 AATTACTGAAACACCCCTGTAGGGTAG 1 AATTACTGAAATACCCCTGTAGGGTAG * * 72642339 AATTACCGAAATACCCTTGTAGGGTAG 1 AATTACTGAAATACCCCTGTAGGGTAG * 72642366 AAATA-TCGAAATACCCCTGTAGGGTAG 1 AATTACT-GAAATACCCCTGTAGGGTAG * * * * 72642393 AATTACTGAGATACCTC-GTGGGGTAA 1 AATTACTGAAATACCCCTGTAGGGTAG 72642419 AATTACT 1 AATTACT 72642426 ATTTTGCCCC Statistics Matches: 384, Mismatches: 48, Indels: 22 0.85 0.11 0.05 Matches are distributed among these distances: 26 46 0.12 27 309 0.80 28 2 0.01 29 1 0.00 30 2 0.01 31 1 0.00 32 1 0.00 33 12 0.03 34 10 0.03 ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26 Consensus pattern (27 bp): AATTACTGAAATACCCCTGTAGGGTAG Found at i:72642017 original size:33 final size:34 Alignment explanation

Indices: 72641956--72642021 Score: 116 Period size: 33 Copynumber: 2.0 Consensus size: 34 72641946 CGATTTACAA 72641956 AATTACTGAAATACCCCTATAGGGTAGAATTACT 1 AATTACTGAAATACCCCTATAGGGTAGAATTACT * 72641990 AATTACTGAAATA-CCCTGTAGGGTAGAATTAC 1 AATTACTGAAATACCCCTATAGGGTAGAATTAC 72642022 CGAAATACCC Statistics Matches: 31, Mismatches: 1, Indels: 1 0.94 0.03 0.03 Matches are distributed among these distances: 33 18 0.58 34 13 0.42 ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29 Consensus pattern (34 bp): AATTACTGAAATACCCCTATAGGGTAGAATTACT Found at i:72642216 original size:81 final size:81 Alignment explanation

Indices: 72641990--72642424 Score: 599 Period size: 81 Copynumber: 5.4 Consensus size: 81 72641980 TAGAATTACT * * * 72641990 AATTACTGAAATA-CCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAATACCAAAA 1 AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCGAAA * 72642054 TACCCCTGTAGGGTAG 66 TACCCTTGTAGGGTAG * * * 72642070 AATTATTGAAATACCCTTGTAGGGTAGAA-TACCGAAATACCCTTGTAAGGTAGAATTACCGAAA 1 AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCGAAA ** 72642134 TACATTTGTAGGGTAG 66 TACCCTTGTAGGGTAG * * * * * * 72642150 AAATACAGAAATACCCCTATAAGGTAGAATTACTGAAATACCCTTGTAGGGTAGAATTACTGAAA 1 AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCGAAA 72642215 TACCCTTGTAGGGTAG 66 TACCCTTGTAGGGTAG * * * 72642231 AATTACTGAAATACCCTTGTAGGGTAGAATTACTGAAATACTCC-TGTAAGGTAGAATTACCGAA 1 AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATAC-CCTTGTAGGGTAGAATTACCGAA 72642295 ATACCCTTGTAGGGTAG 65 ATACCCTTGTAGGGTAG * * * 72642312 AATTACTGAAACACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATATCGAAA 1 AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCGAAA * 72642377 TACCCCTGTAGGGTAG 66 TACCCTTGTAGGGTAG * * * * 72642393 AATTACTGAGATACCTC-GTGGGGTAAAATTAC 1 AATTACTGAAATACCCCTGTAGGGTAGAATTAC 72642425 TATTTTGCCC Statistics Matches: 312, Mismatches: 39, Indels: 8 0.87 0.11 0.02 Matches are distributed among these distances: 80 94 0.30 81 216 0.69 82 2 0.01 ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26 Consensus pattern (81 bp): AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCGAAA TACCCTTGTAGGGTAG Found at i:72645590 original size:48 final size:47 Alignment explanation

Indices: 72645519--72645720 Score: 235 Period size: 47 Copynumber: 4.5 Consensus size: 47 72645509 TGAAAAAACA 72645519 TGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGTAACG 1 TGGTGCTAAGTGGATATACCACGATTACACATATTGATACAT-TAACG * * * * 72645567 TGGTGCTAAGTGGATATGCCACGATTACATATATTGATTCATTAATG 1 TGGTGCTAAGTGGATATACCACGATTACACATATTGATACATTAACG ** 72645614 TGGTGCTAAGTGGATATA-C-C-A-T-GGC-TA---A-ACATGTAACG 1 TGGTGCTAAGTGGATATACCACGATTACACATATTGATACAT-TAACG * * * 72645652 TGGTGCTAAGTGGATATGCCACGATTACATATATTGATTCATTAACG 1 TGGTGCTAAGTGGATATACCACGATTACACATATTGATACATTAACG 72645699 TGGTGCTAAGTGGATATACCAC 1 TGGTGCTAAGTGGATATACCAC 72645721 AGTTAAACAT Statistics Matches: 127, Mismatches: 16, Indels: 23 0.77 0.10 0.14 Matches are distributed among these distances: 37 3 0.02 38 22 0.17 39 1 0.01 40 1 0.01 41 3 0.02 42 1 0.01 43 1 0.01 44 3 0.02 45 1 0.01 46 1 0.01 47 48 0.38 48 42 0.33 ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31 Consensus pattern (47 bp): TGGTGCTAAGTGGATATACCACGATTACACATATTGATACATTAACG Found at i:72645664 original size:38 final size:38 Alignment explanation

Indices: 72645613--72645753 Score: 133 Period size: 38 Copynumber: 3.5 Consensus size: 38 72645603 ATTCATTAAT * 72645613 GTGGTGCTAAGTGGATATACCATGGCTAAACATGTAAC 1 GTGGTGCTAAGTGGATATACCATAGCTAAACATGTAAC * 72645651 GTGGTGCTAAGTGGATATGCCACGATTA-CATATATTGATTCAT-TAAC 1 GTGGTGCTAAGTGGATAT---ACCA-TAGC-TA-A---A--CATGTAAC * * 72645698 GTGGTGCTAAGTGGATATACCACAGTTAAACATGTAAC 1 GTGGTGCTAAGTGGATATACCATAGCTAAACATGTAAC 72645736 GTGGTGCTAAGTGGATAT 1 GTGGTGCTAAGTGGATAT 72645754 GCCACAGTTA Statistics Matches: 85, Mismatches: 5, Indels: 26 0.73 0.04 0.22 Matches are distributed among these distances: 37 3 0.04 38 40 0.47 39 1 0.01 41 4 0.05 42 4 0.05 43 4 0.05 44 3 0.04 46 1 0.01 47 22 0.26 48 3 0.04 ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30 Consensus pattern (38 bp): GTGGTGCTAAGTGGATATACCATAGCTAAACATGTAAC Found at i:72645702 original size:85 final size:85 Alignment explanation

Indices: 72645557--72645758 Score: 368 Period size: 85 Copynumber: 2.4 Consensus size: 85 72645547 ACATATTGAT * 72645557 ACATGTAACGTGGTGCTAAGTGGATATGCCACGATTACATATATTGATTCATTAATGTGGTGCTA 1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGATTACATATATTGATTCATTAACGTGGTGCTA ** 72645622 AGTGGATATACCATGGCTAA 66 AGTGGATATACCACAGCTAA 72645642 ACATGTAACGTGGTGCTAAGTGGATATGCCACGATTACATATATTGATTCATTAACGTGGTGCTA 1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGATTACATATATTGATTCATTAACGTGGTGCTA * 72645707 AGTGGATATACCACAGTTAA 66 AGTGGATATACCACAGCTAA 72645727 ACATGTAACGTGGTGCTAAGTGGATATGCCAC 1 ACATGTAACGTGGTGCTAAGTGGATATGCCAC 72645759 AGTTATACAT Statistics Matches: 113, Mismatches: 4, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 85 113 1.00 ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30 Consensus pattern (85 bp): ACATGTAACGTGGTGCTAAGTGGATATGCCACGATTACATATATTGATTCATTAACGTGGTGCTA AGTGGATATACCACAGCTAA Found at i:72645759 original size:38 final size:38 Alignment explanation

Indices: 72645694--72645770 Score: 136 Period size: 38 Copynumber: 2.0 Consensus size: 38 72645684 ATTGATTCAT 72645694 TAACGTGGTGCTAAGTGGATATACCACAGTTAAACATG 1 TAACGTGGTGCTAAGTGGATATACCACAGTTAAACATG * * 72645732 TAACGTGGTGCTAAGTGGATATGCCACAGTTATACATG 1 TAACGTGGTGCTAAGTGGATATACCACAGTTAAACATG 72645770 T 1 T 72645771 TAATTTGAAA Statistics Matches: 37, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 38 37 1.00 ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29 Consensus pattern (38 bp): TAACGTGGTGCTAAGTGGATATACCACAGTTAAACATG Found at i:72650673 original size:31 final size:31 Alignment explanation

Indices: 72650635--72650718 Score: 116 Period size: 31 Copynumber: 2.7 Consensus size: 31 72650625 TCGTTACAGT 72650635 AAAGGCTTTGGCCCAGTGATATGAATAATGA 1 AAAGGCTTTGGCCCAGTGATATGAATAATGA * * * 72650666 AAAGGCTTTGGCCTAGTGACATGAATAATGT 1 AAAGGCTTTGGCCCAGTGATATGAATAATGA * * 72650697 GAAGGCTTCGGCCCAGT-ATATG 1 AAAGGCTTTGGCCCAGTGATATG 72650719 CTGAGATTGA Statistics Matches: 46, Mismatches: 7, Indels: 1 0.85 0.13 0.02 Matches are distributed among these distances: 30 4 0.09 31 42 0.91 ACGTcount: A:0.31, C:0.15, G:0.27, T:0.26 Consensus pattern (31 bp): AAAGGCTTTGGCCCAGTGATATGAATAATGA Done.