Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold362

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: 59669
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:4936 original size:79 final size:81

Alignment explanation

Indices: 4823--5005 Score: 232 Period size: 79 Copynumber: 2.3 Consensus size: 81 4813 TACTCGTTCA * * 4823 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG 1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG * * 4886 ATTTAGTAAC-TCGCACC 65 ATATAGTAACTTAGCA-C ** 4903 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA 1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA * * 4966 TATGGTCACTTAGCAC 66 TATAGTAACTTAGCAC * 4982 AAAGCCTTCGGGACTTAGCCCGGA 1 AATGCCTTCGGGACTTAGCCCGGA 5006 CATCATTCGA Statistics Matches: 90, Mismatches: 9, Indels: 8 0.84 0.08 0.07 Matches are distributed among these distances: 78 3 0.03 79 59 0.66 80 28 0.31 ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24 Consensus pattern (81 bp): AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA TATAGTAACTTAGCAC Found at i:5005 original size:40 final size:40 Alignment explanation

Indices: 4821--5005 Score: 234 Period size: 40 Copynumber: 4.7 Consensus size: 40 4811 GCTACTCGTT * * 4821 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA * * 4861 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA * 4901 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA * * * * 4940 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA 1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA 4981 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 5006 CATCATTCGA Statistics Matches: 126, Mismatches: 13, Indels: 12 0.83 0.09 0.08 Matches are distributed among these distances: 38 2 0.02 39 32 0.25 40 80 0.63 41 12 0.10 ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA Found at i:13114 original size:79 final size:81 Alignment explanation

Indices: 12972--13154 Score: 223 Period size: 79 Copynumber: 2.3 Consensus size: 81 12962 TACTTGTTCA * * * 12972 AATGCCTTCGGGACATAGCCCAG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA 1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA * * 13036 TTTAGTAAC-TCGCACC 66 TATAGTAACTTAGCA-C ** 13052 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG 1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG * * 13114 ATATGGTCACTTAGCAC 65 ATATAGTAACTTAGCAC * 13131 AAAGCCTTCGGGACTTAGCCCGGA 1 AATGCCTTCGGGACTTAGCCCGGA 13155 CATCATTCGA Statistics Matches: 89, Mismatches: 10, Indels: 8 0.83 0.09 0.07 Matches are distributed among these distances: 78 3 0.03 79 58 0.65 80 28 0.31 ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24 Consensus pattern (81 bp): AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA TATAGTAACTTAGCAC Found at i:13154 original size:40 final size:40 Alignment explanation

Indices: 12970--13154 Score: 225 Period size: 40 Copynumber: 4.7 Consensus size: 40 12960 GCTACTTGTT * * * 12970 CAAATGCCTTCGGGACATAGCCCAGTTATAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA * * 13010 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA * 13050 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA * * * * 13089 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA 1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA 13130 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 13155 CATCATTCGA Statistics Matches: 125, Mismatches: 14, Indels: 12 0.83 0.09 0.08 Matches are distributed among these distances: 38 2 0.02 39 32 0.26 40 79 0.63 41 12 0.10 ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA Found at i:15223 original size:3 final size:3 Alignment explanation

Indices: 15215--15285 Score: 142 Period size: 3 Copynumber: 23.7 Consensus size: 3 15205 CAACCATCCA 15215 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT 1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT 15263 ATT ATT ATT ATT ATT ATT ATT AT 1 ATT ATT ATT ATT ATT ATT ATT AT 15286 GTGTCAAAAA Statistics Matches: 68, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 68 1.00 ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66 Consensus pattern (3 bp): ATT Found at i:25788 original size:24 final size:24 Alignment explanation

Indices: 25758--25806 Score: 98 Period size: 24 Copynumber: 2.0 Consensus size: 24 25748 GAAAAAAAGT 25758 AGTGAAAATTTATTTTAAGAATAA 1 AGTGAAAATTTATTTTAAGAATAA 25782 AGTGAAAATTTATTTTAAGAATAA 1 AGTGAAAATTTATTTTAAGAATAA 25806 A 1 A 25807 TTCTATCTTC Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 25 1.00 ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37 Consensus pattern (24 bp): AGTGAAAATTTATTTTAAGAATAA Found at i:28467 original size:14 final size:14 Alignment explanation

Indices: 28448--28476 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 28438 GCACACGCCT 28448 GTGTGTGACATACG 1 GTGTGTGACATACG 28462 GTGTGTGACATACG 1 GTGTGTGACATACG 28476 G 1 G 28477 CCATGTGGCA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.21, C:0.14, G:0.38, T:0.28 Consensus pattern (14 bp): GTGTGTGACATACG Found at i:29706 original size:18 final size:18 Alignment explanation

Indices: 29683--29721 Score: 69 Period size: 18 Copynumber: 2.2 Consensus size: 18 29673 GCCGTGTAGG * 29683 CCACATGGGCGTGTGAGC 1 CCACATGGGCATGTGAGC 29701 CCACATGGGCATGTGAGC 1 CCACATGGGCATGTGAGC 29719 CCA 1 CCA 29722 ATTTTCTGTA Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 20 1.00 ACGTcount: A:0.21, C:0.31, G:0.33, T:0.15 Consensus pattern (18 bp): CCACATGGGCATGTGAGC Found at i:31626 original size:101 final size:101 Alignment explanation

Indices: 31498--31710 Score: 309 Period size: 101 Copynumber: 2.1 Consensus size: 101 31488 TCATGCCCTG * * * * 31498 CCATGGTCTTACGTTCATAGTGCCATAACCAAGTTATGGTCTTATCATCAGAATGTCTTAACCGA 1 CCATGGTCTTACGTCCATAGTGCCATAACCAAGTTATGGTCTTATCATCAGAATGCCATAACCCA * * 31563 GGTATGGTCTTACATATAAACACTTCCATGGTCCAA 66 GGTACGGTCTTACATATAAACACTACCATGGTCCAA * * * * 31599 CCATGGTCTTACGTCCATAGTGTCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAGCCCA 1 CCATGGTCTTACGTCCATAGTGCCATAACCAAGTTATGGTCTTATCATCAGAATGCCATAACCCA * * 31664 GGTACGGTCTTACATATATACACTACCATGTTCCAA 66 GGTACGGTCTTACATATAAACACTACCATGGTCCAA * 31700 TCATGGTCTTA 1 CCATGGTCTTA 31711 TGTTTGAATA Statistics Matches: 99, Mismatches: 13, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 101 99 1.00 ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32 Consensus pattern (101 bp): CCATGGTCTTACGTCCATAGTGCCATAACCAAGTTATGGTCTTATCATCAGAATGCCATAACCCA GGTACGGTCTTACATATAAACACTACCATGGTCCAA Found at i:33673 original size:5 final size:5 Alignment explanation

Indices: 33645--33686 Score: 52 Period size: 5 Copynumber: 8.4 Consensus size: 5 33635 ATGTTTTAAA 33645 TATAT TAT-T TA-AT TATAAAT TATAT TATAT TATAT TATAT TA 1 TATAT TATAT TATAT TAT--AT TATAT TATAT TATAT TATAT TA 33687 GTATGTAATA Statistics Matches: 33, Mismatches: 0, Indels: 8 0.80 0.00 0.20 Matches are distributed among these distances: 4 6 0.18 5 22 0.67 7 5 0.15 ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57 Consensus pattern (5 bp): TATAT Found at i:33681 original size:15 final size:14 Alignment explanation

Indices: 33640--33686 Score: 51 Period size: 15 Copynumber: 3.2 Consensus size: 14 33630 TTTTTATGTT * 33640 TTAAATATATTAT- 1 TTAATTATATTATA 33653 TTAATTATAAATTATA 1 TTAATTAT--ATTATA 33669 TTATATTATATTATA 1 TTA-ATTATATTATA 33684 TTA 1 TTA 33687 GTATGTAATA Statistics Matches: 29, Mismatches: 1, Indels: 6 0.81 0.03 0.17 Matches are distributed among these distances: 13 7 0.24 15 14 0.48 16 3 0.10 17 5 0.17 ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55 Consensus pattern (14 bp): TTAATTATATTATA Found at i:33848 original size:18 final size:19 Alignment explanation

Indices: 33816--33862 Score: 69 Period size: 19 Copynumber: 2.5 Consensus size: 19 33806 TAAAACAAAT 33816 GAAACAAATGAAATA-AAAA 1 GAAACAAA-GAAATAGAAAA * 33835 GAAATAAAGAAATAGAAAA 1 GAAACAAAGAAATAGAAAA 33854 GAAACAAAG 1 GAAACAAAG 33863 TAACAGAATA Statistics Matches: 25, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 18 6 0.24 19 19 0.76 ACGTcount: A:0.72, C:0.04, G:0.15, T:0.09 Consensus pattern (19 bp): GAAACAAAGAAATAGAAAA Found at i:33870 original size:19 final size:19 Alignment explanation

Indices: 33816--33870 Score: 58 Period size: 19 Copynumber: 2.9 Consensus size: 19 33806 TAAAACAAAT * 33816 GAAACAAATGAAATA-AAAA 1 GAAACAAA-GAAACAGAAAA * * 33835 GAAATAAAGAAATAGAAAA 1 GAAACAAAGAAACAGAAAA * 33854 GAAACAAAGTAACAGAA 1 GAAACAAAGAAACAGAA 33871 TATGAAACGA Statistics Matches: 31, Mismatches: 4, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 18 6 0.19 19 25 0.81 ACGTcount: A:0.71, C:0.05, G:0.15, T:0.09 Consensus pattern (19 bp): GAAACAAAGAAACAGAAAA Found at i:35657 original size:27 final size:27 Alignment explanation

Indices: 35633--35828 Score: 250 Period size: 27 Copynumber: 7.3 Consensus size: 27 35623 CTCAATTTGT * * 35633 AAAATTACCATTTTACCCTCGATTTAT 1 AAAATTACCGTTTTACCCTCGATTTAC * * * * 35660 AGAA-TGCCATTTTACCCTCGATTTAT 1 AAAATTACCGTTTTACCCTCGATTTAC * * 35686 AGAATTACCGTTTTATCCTCGATTTAC 1 AAAATTACCGTTTTACCCTCGATTTAC * 35713 AAAATTACCGTTTTACCCTCGATTTAT 1 AAAATTACCGTTTTACCCTCGATTTAC * * * 35740 AGAATTACCATTTTACCCTTGATTTAC 1 AAAATTACCGTTTTACCCTCGATTTAC * 35767 AAAATTATCGTTTTACCCTCGATTTAC 1 AAAATTACCGTTTTACCCTCGATTTAC * * 35794 AGAATTACCGTTTTACCCTCAATTTAC 1 AAAATTACCGTTTTACCCTCGATTTAC 35821 AAAATTAC 1 AAAATTAC 35829 TAAAATACCC Statistics Matches: 147, Mismatches: 21, Indels: 2 0.86 0.12 0.01 Matches are distributed among these distances: 26 25 0.17 27 122 0.83 ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39 Consensus pattern (27 bp): AAAATTACCGTTTTACCCTCGATTTAC Found at i:35744 original size:54 final size:54 Alignment explanation

Indices: 35635--35828 Score: 282 Period size: 54 Copynumber: 3.6 Consensus size: 54 35625 CAATTTGTAA * * * * 35635 AATTACCATTTTACCCTCGATTTATAGAA-TGCCATTTTACCCTCGATTTATAG 1 AATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAG * * 35688 AATTACCGTTTTATCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAG 1 AATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAG * * * 35742 AATTACCATTTTACCCTTGATTTACAAAATTATCGTTTTACCCTCGATTTACAG 1 AATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAG * * 35796 AATTACCGTTTTACCCTCAATTTACAAAATTAC 1 AATTACCATTTTACCCTCGATTTACAAAATTAC 35829 TAAAATACCC Statistics Matches: 125, Mismatches: 15, Indels: 1 0.89 0.11 0.01 Matches are distributed among these distances: 53 25 0.20 54 100 0.80 ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40 Consensus pattern (54 bp): AATTACCATTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAG Found at i:35787 original size:81 final size:81 Alignment explanation

Indices: 35633--35828 Score: 286 Period size: 81 Copynumber: 2.4 Consensus size: 81 35623 CTCAATTTGT * * * * 35633 AAAATTACCATTTTACCCTCGATTTATAGAA-TGCCATTTTACCCTCGATTTATAGAATTACCGT 1 AAAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGT * 35697 TTTATCCTCGATTTAC 66 TTTACCCTCGATTTAC * * 35713 AAAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTTGATTTACAAAATTATCGT 1 AAAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGT 35778 TTTACCCTCGATTTAC 66 TTTACCCTCGATTTAC * * * * 35794 AGAATTACCGTTTTACCCTCAATTTACAAAATTAC 1 AAAATTACCGTTTTACCCTCGATTTATAGAATTAC 35829 TAAAATACCC Statistics Matches: 104, Mismatches: 11, Indels: 1 0.90 0.09 0.01 Matches are distributed among these distances: 80 30 0.29 81 74 0.71 ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39 Consensus pattern (81 bp): AAAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTACCGT TTTACCCTCGATTTAC Found at i:35837 original size:27 final size:27 Alignment explanation

Indices: 35627--35946 Score: 142 Period size: 27 Copynumber: 11.9 Consensus size: 27 35617 AATGTTCTCA * *** 35627 ATTTGTAAAATTACCATTTTACCCTCG 1 ATTTATAAAATTACCAAAATACCCTCG * * *** 35654 ATTTATAGAA-TGCCATTTTACCCTCG 1 ATTTATAAAATTACCAAAATACCCTCG * **** * 35680 ATTTATAGAATTACCGTTTTATCCTCG 1 ATTTATAAAATTACCAAAATACCCTCG * **** 35707 ATTTACAAAATTACCGTTTTACCCTCG 1 ATTTATAAAATTACCAAAATACCCTCG * *** * 35734 ATTTATAGAATTACCATTTTACCCTTG 1 ATTTATAAAATTACCAAAATACCCTCG * * **** 35761 ATTTACAAAATTATCGTTTTACCCTCG 1 ATTTATAAAATTACCAAAATACCCTCG * * **** * 35788 ATTTACAGAATTACCGTTTTACCCTCA 1 ATTTATAAAATTACCAAAATACCCTCG * * * 35815 ATTTACAAAATTACTAAAATACCCTTG 1 ATTTATAAAATTACCAAAATACCCTCG * * 35842 GTTTAGAAAATTACCAAAATACCCTCG 1 ATTTATAAAATTACCAAAATACCCTCG * * 35869 A-TCAGTAAAATTACCAAAATACCCTTG 1 ATTTA-TAAAATTACCAAAATACCCTCG * * * 35896 GTTTTTAAAATTACTAAAATA-CCTCTG 1 ATTTATAAAATTACCAAAATACCCTC-G * * * 35923 GTTTGTAAAATTACCGAAATACCC 1 ATTTATAAAATTACCAAAATACCC 35947 CTGTAGGGTA Statistics Matches: 243, Mismatches: 45, Indels: 9 0.82 0.15 0.03 Matches are distributed among these distances: 26 30 0.12 27 210 0.86 28 3 0.01 ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37 Consensus pattern (27 bp): ATTTATAAAATTACCAAAATACCCTCG Found at i:35838 original size:81 final size:81 Alignment explanation

Indices: 35672--35856 Score: 235 Period size: 81 Copynumber: 2.3 Consensus size: 81 35662 AATGCCATTT * * * * * 35672 TACCCTCGATTTATAGAATTACCGTTTTATCCTCGATTTACAAAATTACCGTTTTACCCTCGATT 1 TACCCTTGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCAATT * * *** 35737 TATAGAATTACCATTT 66 TACAAAATTACCAAAA * * 35753 TACCCTTGATTTACAAAATTATCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCAATT 1 TACCCTTGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCAATT * 35818 TACAAAATTACTAAAA 66 TACAAAATTACCAAAA * * 35834 TACCCTTGGTTTAGAAAATTACC 1 TACCCTTGATTTACAAAATTACC 35857 AAAATACCCT Statistics Matches: 88, Mismatches: 16, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 81 88 1.00 ACGTcount: A:0.31, C:0.22, G:0.08, T:0.38 Consensus pattern (81 bp): TACCCTTGATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCAATT TACAAAATTACCAAAA Found at i:35854 original size:54 final size:54 Alignment explanation

Indices: 35627--35909 Score: 210 Period size: 54 Copynumber: 5.3 Consensus size: 54 35617 AATGTTCTCA * * * * *** 35627 ATTTGTAAAATTACCATTTTACCCTCGATTTATAGAA-TGCCATTTTACCCTCG 1 ATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAATACCCTCG * * * **** 35680 ATTTATAGAATTACCGTTTTATCCTCGATTTACAAAATTACCGTTTTACCCTCG 1 ATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAATACCCTCG * * * **** 35734 ATTTATAGAATTACCATTTTACCCTTGATTTACAAAATTATCGTTTTACCCTCG 1 ATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAATACCCTCG * * * * * * 35788 ATTTACAGAATTACCGTTTTACCCTCAATTTACAAAATTACTAAAATACCCTTG 1 ATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAATACCCTCG * * *** * * * 35842 GTTTAGAAAATTACCAAAATACCCTCGA-TCAGTAAAATTACCAAAATACCCTTG 1 ATTTATAAAATTACCATTTTACCCTCGATTTA-CAAAATTACCAAAATACCCTCG * * 35896 GTTTTTAAAATTAC 1 ATTTATAAAATTAC 35910 TAAAATACCT Statistics Matches: 192, Mismatches: 36, Indels: 3 0.83 0.16 0.01 Matches are distributed among these distances: 53 33 0.17 54 159 0.83 ACGTcount: A:0.33, C:0.21, G:0.08, T:0.37 Consensus pattern (54 bp): ATTTATAAAATTACCATTTTACCCTCGATTTACAAAATTACCAAAATACCCTCG Found at i:35915 original size:54 final size:54 Alignment explanation

Indices: 35821--35946 Score: 164 Period size: 54 Copynumber: 2.3 Consensus size: 54 35811 CTCAATTTAC * 35821 AAAATTACTAAAATACCCTTGGTTTAGAAAATTACCAAAATACC-CTCGATCAGT 1 AAAATTACCAAAATACCCTTGGTTTAGAAAATTACCAAAATACCTCT-GATCAGT ** * * ** 35875 AAAATTACCAAAATACCCTTGGTTTTTAAAATTACTAAAATACCTCTGGTTTGT 1 AAAATTACCAAAATACCCTTGGTTTAGAAAATTACCAAAATACCTCTGATCAGT * 35929 AAAATTACCGAAATACCC 1 AAAATTACCAAAATACCC 35947 CTGTAGGGTA Statistics Matches: 63, Mismatches: 8, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 54 61 0.97 55 2 0.03 ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30 Consensus pattern (54 bp): AAAATTACCAAAATACCCTTGGTTTAGAAAATTACCAAAATACCTCTGATCAGT Found at i:35961 original size:27 final size:27 Alignment explanation

Indices: 35931--36072 Score: 169 Period size: 27 Copynumber: 5.3 Consensus size: 27 35921 TGGTTTGTAA * 35931 AATTACCGAAATACCCCTGTAGGGTAG 1 AATTACCGAAATACCCTTGTAGGGTAG * 35958 AATTACCAAAATACCCTTGTAGGGTAG 1 AATTACCGAAATACCCTTGTAGGGTAG * * * 35985 AATTACCAAAATACCCTTATAGGATAG 1 AATTACCGAAATACCCTTGTAGGGTAG * 36012 AAATACCGAAATATCCCTT-TAGGGTAG 1 AATTACCGAAATA-CCCTTGTAGGGTAG * * * * * 36039 AATTATCGAGATACCATTGTGGGGTAA 1 AATTACCGAAATACCCTTGTAGGGTAG 36066 AATTACC 1 AATTACC 36073 ATTTTGCCCC Statistics Matches: 99, Mismatches: 14, Indels: 4 0.85 0.12 0.03 Matches are distributed among these distances: 26 4 0.04 27 90 0.91 28 5 0.05 ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26 Consensus pattern (27 bp): AATTACCGAAATACCCTTGTAGGGTAG Found at i:35962 original size:81 final size:81 Alignment explanation

Indices: 35821--35976 Score: 214 Period size: 81 Copynumber: 1.9 Consensus size: 81 35811 CTCAATTTAC 35821 AAAATTACTAAAATACCCTTGGTTTAGAAAATTACCAAAATACCCTCGATCAGTAAAATTACCAA 1 AAAATTACTAAAATACCCTTGGTTTAGAAAATTACCAAAATACCCTCGATCAGTAAAATTACCAA 35886 AATACCCTTGGTTTTT 66 AATACCCTTGGTTTTT * * 35902 AAAATTACTAAAATA-CCTCTGGTTT-GTAAAATTACCGAAATACCC-CTG-T-AGGGTAGAATT 1 AAAATTACTAAAATACCCT-TGGTTTAG-AAAATTACCAAAATACCCTC-GATCA--GTAAAATT 35962 ACCAAAATACCCTTG 61 ACCAAAATACCCTTG 35977 TAGGGTAGAA Statistics Matches: 68, Mismatches: 2, Indels: 10 0.85 0.03 0.12 Matches are distributed among these distances: 79 1 0.01 80 6 0.09 81 61 0.90 ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29 Consensus pattern (81 bp): AAAATTACTAAAATACCCTTGGTTTAGAAAATTACCAAAATACCCTCGATCAGTAAAATTACCAA AATACCCTTGGTTTTT Found at i:35989 original size:81 final size:78 Alignment explanation

Indices: 35821--36071 Score: 213 Period size: 81 Copynumber: 3.1 Consensus size: 78 35811 CTCAATTTAC * * 35821 AAAATTACTAAAATACCCTTGGTTTAG-AAAATTACCAAAATACCCTCGATCA--GTAAAATTAC 1 AAAATTACTAAAATACCC-TGGTTT-GTAAAATTACCGAAATACCCT-G-T-AGGGTAGAATTAC *** 35883 CAAAATACCCTTGGTTTTT 61 CAAAATACCCTT-GTGGGT 35902 AAAATTACTAAAATACCTCTGGTTTGTAAAATTACCGAAATACCCCTGTAGGGTAGAATTACCAA 1 AAAATTACTAAAATACC-CTGGTTTGTAAAATTACCGAAATA-CCCTGTAGGGTAGAATTACCAA 35967 AATACCCTTGTAGGGT 64 AATACCCTTGT-GGGT * * ** ** * * * 35983 AGAATTACCAAAATACCCTTATAGGATAGAAA-TACCGAAATATCCCTTTAGGGTAGAATTATCG 1 AAAATTACTAAAATACCCTGGTTTG-TA-AAATTACCGAAATA-CCCTGTAGGGTAGAATTACCA * * 36047 AGATACCATTGTGGGGT 63 AAATACCCTTGT-GGGT 36064 AAAATTAC 1 AAAATTAC 36072 CATTTTGCCC Statistics Matches: 143, Mismatches: 19, Indels: 16 0.80 0.11 0.09 Matches are distributed among these distances: 79 1 0.01 80 8 0.06 81 126 0.88 82 8 0.06 ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29 Consensus pattern (78 bp): AAAATTACTAAAATACCCTGGTTTGTAAAATTACCGAAATACCCTGTAGGGTAGAATTACCAAAA TACCCTTGTGGGT Found at i:36314 original size:25 final size:25 Alignment explanation

Indices: 36277--36371 Score: 163 Period size: 25 Copynumber: 3.8 Consensus size: 25 36267 AGGAAGTGCT * 36277 AAAAGGGCCTTGCCCCAGTTTACCG 1 AAAAGGGCTTTGCCCCAGTTTACCG 36302 AAAAGGGCTTTGCCCCAGTTTACCG 1 AAAAGGGCTTTGCCCCAGTTTACCG * * 36327 AAAAGGGCTTTGCCCCAGTTTATCA 1 AAAAGGGCTTTGCCCCAGTTTACCG 36352 AAAAGGGCTTTGCCCCAGTT 1 AAAAGGGCTTTGCCCCAGTT 36372 ATTAAAAGAG Statistics Matches: 67, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 25 67 1.00 ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24 Consensus pattern (25 bp): AAAAGGGCTTTGCCCCAGTTTACCG Found at i:36384 original size:24 final size:24 Alignment explanation

Indices: 36277--36407 Score: 129 Period size: 25 Copynumber: 5.2 Consensus size: 24 36267 AGGAAGTGCT * * 36277 AAAAGGGCCTTGCCCCAGTTTACCG 1 AAAAGGGCTTTGCCCCAGTTTA-TG * 36302 AAAAGGGCTTTGCCCCAGTTTACCG 1 AAAAGGGCTTTGCCCCAGTTTA-TG * 36327 AAAAGGGCTTTGCCCCAGTTTATCA 1 AAAAGGGCTTTGCCCCAGTTTAT-G * 36352 AAAAGGGCTTTGCCCCAG-TTATT 1 AAAAGGGCTTTGCCCCAGTTTATG ** 36375 AAAAGAGGCTAGGCCTCCAGTTATATG 1 AAAAG-GGCTTTGCC-CCAGTT-TATG 36402 ATAAAG 1 A-AAAG 36408 CAGCTATGCT Statistics Matches: 93, Mismatches: 7, Indels: 9 0.85 0.06 0.08 Matches are distributed among these distances: 23 5 0.05 24 11 0.12 25 68 0.73 26 1 0.01 27 4 0.04 28 4 0.04 ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24 Consensus pattern (24 bp): AAAAGGGCTTTGCCCCAGTTTATG Found at i:41290 original size:27 final size:27 Alignment explanation

Indices: 41252--41381 Score: 183 Period size: 27 Copynumber: 4.8 Consensus size: 27 41242 AAGACCTCAG 41252 TTTGTAAAATTACCAAAATACCCCTGA 1 TTTGTAAAATTACCAAAATACCCCTGA * * 41279 TTTGTAATATTA-CAGAAATACCCTTGA 1 TTTGTAAAATTACCA-AAATACCCCTGA 41306 TTTGTAAAATTACCAAAATACCCCATG- 1 TTTGTAAAATTACCAAAATACCCC-TGA * * 41333 TTTGTAAAATTACCGAAATACCCTTGA 1 TTTGTAAAATTACCAAAATACCCCTGA * 41360 TTTGTAAAATTACCGAAATACC 1 TTTGTAAAATTACCAAAATACC 41382 TTGTAGTGTA Statistics Matches: 93, Mismatches: 6, Indels: 8 0.87 0.06 0.07 Matches are distributed among these distances: 26 4 0.04 27 85 0.91 28 4 0.04 ACGTcount: A:0.39, C:0.19, G:0.09, T:0.32 Consensus pattern (27 bp): TTTGTAAAATTACCAAAATACCCCTGA Found at i:41337 original size:54 final size:54 Alignment explanation

Indices: 41252--41381 Score: 217 Period size: 54 Copynumber: 2.4 Consensus size: 54 41242 AAGACCTCAG * 41252 TTTGTAAAATTACCAAAATACCCCTGATTTGTAATATTACAGAAATACCCTTGA 1 TTTGTAAAATTACCAAAATACCCCTGATTTGTAAAATTACAGAAATACCCTTGA * 41306 TTTGTAAAATTACCAAAATACCCCATG-TTTGTAAAATTACCGAAATACCCTTGA 1 TTTGTAAAATTACCAAAATACCCC-TGATTTGTAAAATTACAGAAATACCCTTGA * 41360 TTTGTAAAATTACCGAAATACC 1 TTTGTAAAATTACCAAAATACC 41382 TTGTAGTGTA Statistics Matches: 72, Mismatches: 3, Indels: 2 0.94 0.04 0.03 Matches are distributed among these distances: 54 70 0.97 55 2 0.03 ACGTcount: A:0.39, C:0.19, G:0.09, T:0.32 Consensus pattern (54 bp): TTTGTAAAATTACCAAAATACCCCTGATTTGTAAAATTACAGAAATACCCTTGA Found at i:41421 original size:27 final size:26 Alignment explanation

Indices: 41255--41420 Score: 127 Period size: 27 Copynumber: 6.2 Consensus size: 26 41245 ACCTCAGTTT * * ** 41255 GTAAAATTACCAAAATACCCCTGATTT 1 GTAAAATTACCGAAATACCCATG-TAG * * * ** 41282 GTAATATTACAGAAATACCCTTGATTT 1 GTAAAATTACCGAAATACCCATG-TAG * ** 41309 GTAAAATTACCAAAATACCCCATGTTT 1 GTAAAATTACCGAAATA-CCCATGTAG * ** 41336 GTAAAATTACCGAAATACCCTTGATTT 1 GTAAAATTACCGAAATACCCATG-TAG * 41363 GTAAAATTACCGAAATA-CCTTGTAG 1 GTAAAATTACCGAAATACCCATGTAG * 41388 TGTAAAATTATCGAAATACCCATGTAG 1 -GTAAAATTACCGAAATACCCATGTAG 41415 GTAAAA 1 GTAAAA 41421 AGACTATTTT Statistics Matches: 121, Mismatches: 14, Indels: 9 0.84 0.10 0.06 Matches are distributed among these distances: 25 1 0.01 26 32 0.26 27 83 0.69 28 5 0.04 ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31 Consensus pattern (26 bp): GTAAAATTACCGAAATACCCATGTAG Found at i:42116 original size:22 final size:21 Alignment explanation

Indices: 42086--42126 Score: 73 Period size: 22 Copynumber: 1.9 Consensus size: 21 42076 TATTCCCCAC 42086 AGGTAGTGCAGGGTTGGATAG 1 AGGTAGTGCAGGGTTGGATAG 42107 AGGTAAGTGCAGGGTTGGAT 1 AGGT-AGTGCAGGGTTGGAT 42127 TGGATAGCAT Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 21 4 0.21 22 15 0.79 ACGTcount: A:0.24, C:0.05, G:0.46, T:0.24 Consensus pattern (21 bp): AGGTAGTGCAGGGTTGGATAG Found at i:45905 original size:29 final size:27 Alignment explanation

Indices: 45887--45956 Score: 113 Period size: 27 Copynumber: 2.6 Consensus size: 27 45877 ATATTAAGTC 45887 CGCACACTCAGTGCTATATAATCAACT 1 CGCACACTCAGTGCTATATAATCAACT * 45914 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTCAGTGCTATATAATC-AACT * 45942 CGCACACTTAGTGCT 1 CGCACACTCAGTGCT 45957 GTACAATTTA Statistics Matches: 41, Mismatches: 1, Indels: 1 0.95 0.02 0.02 Matches are distributed among these distances: 27 22 0.54 28 19 0.46 ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27 Consensus pattern (27 bp): CGCACACTCAGTGCTATATAATCAACT Found at i:45950 original size:28 final size:28 Alignment explanation

Indices: 45887--45984 Score: 135 Period size: 28 Copynumber: 3.5 Consensus size: 28 45877 ATATTAAGTC * 45887 CGCACACTCAGTGCTATATAATC-AACT 1 CGCACACTTAGTGCTATATAATCAAACT 45914 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTATATAATCAAACT * * * * 45942 CGCACACTTAGTGCTGTACAATTTAAACC 1 CGCACACTTAGTGCTATATAA-TCAAACT 45971 CGCACACTTAGTGC 1 CGCACACTTAGTGC 45985 CAATCTCATG Statistics Matches: 64, Mismatches: 5, Indels: 2 0.90 0.07 0.03 Matches are distributed among these distances: 27 22 0.34 28 23 0.36 29 19 0.30 ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27 Consensus pattern (28 bp): CGCACACTTAGTGCTATATAATCAAACT Found at i:53944 original size:29 final size:27 Alignment explanation

Indices: 53926--53995 Score: 113 Period size: 27 Copynumber: 2.6 Consensus size: 27 53916 ATATTAAGTC 53926 CGCACACTCAGTGCTATATAATCAACT 1 CGCACACTCAGTGCTATATAATCAACT * 53953 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTCAGTGCTATATAATC-AACT * 53981 CGCACACTTAGTGCT 1 CGCACACTCAGTGCT 53996 GTACAATTTA Statistics Matches: 41, Mismatches: 1, Indels: 1 0.95 0.02 0.02 Matches are distributed among these distances: 27 22 0.54 28 19 0.46 ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27 Consensus pattern (27 bp): CGCACACTCAGTGCTATATAATCAACT Found at i:53989 original size:28 final size:28 Alignment explanation

Indices: 53926--54023 Score: 135 Period size: 28 Copynumber: 3.5 Consensus size: 28 53916 ATATTAAGTC * 53926 CGCACACTCAGTGCTATATAATC-AACT 1 CGCACACTTAGTGCTATATAATCAAACT 53953 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTATATAATCAAACT * * * * 53981 CGCACACTTAGTGCTGTACAATTTAAACC 1 CGCACACTTAGTGCTATATAA-TCAAACT 54010 CGCACACTTAGTGC 1 CGCACACTTAGTGC 54024 CAATCTCATG Statistics Matches: 64, Mismatches: 5, Indels: 2 0.90 0.07 0.03 Matches are distributed among these distances: 27 22 0.34 28 23 0.36 29 19 0.30 ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27 Consensus pattern (28 bp): CGCACACTTAGTGCTATATAATCAAACT Found at i:57923 original size:12 final size:12 Alignment explanation

Indices: 57878--57920 Score: 52 Period size: 12 Copynumber: 3.5 Consensus size: 12 57868 TATGTTTACT * 57878 TATTATATAAGTA 1 TATTAT-TAAATA 57891 T-TTATTAAATA 1 TATTATTAAATA 57902 TATTATTAAATA 1 TATTATTAAATA 57914 TTATTAT 1 -TATTAT 57921 AAAACAAATG Statistics Matches: 27, Mismatches: 1, Indels: 4 0.84 0.03 0.12 Matches are distributed among these distances: 11 6 0.22 12 14 0.52 13 7 0.26 ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53 Consensus pattern (12 bp): TATTATTAAATA Found at i:57954 original size:19 final size:19 Alignment explanation

Indices: 57930--57976 Score: 69 Period size: 19 Copynumber: 2.5 Consensus size: 19 57920 TAAAACAAAT 57930 GAAATAAATGAAATA-AAAA 1 GAAATAAA-GAAATAGAAAA 57949 GAAATAAAGAAATAGAAAA 1 GAAATAAAGAAATAGAAAA * 57968 GAAACAAAG 1 GAAATAAAG 57977 TAACAGAATA Statistics Matches: 26, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 18 6 0.23 19 20 0.77 ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11 Consensus pattern (19 bp): GAAATAAAGAAATAGAAAA Found at i:57984 original size:19 final size:19 Alignment explanation

Indices: 57945--57984 Score: 53 Period size: 19 Copynumber: 2.1 Consensus size: 19 57935 AAATGAAATA * * 57945 AAAAGAAATAAAGAAATAG 1 AAAAGAAACAAAGAAACAG * 57964 AAAAGAAACAAAGTAACAG 1 AAAAGAAACAAAGAAACAG 57983 AA 1 AA 57985 TATGAAACGA Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 19 18 1.00 ACGTcount: A:0.72, C:0.05, G:0.15, T:0.07 Consensus pattern (19 bp): AAAAGAAACAAAGAAACAG Found at i:58023 original size:17 final size:17 Alignment explanation

Indices: 58003--58039 Score: 56 Period size: 17 Copynumber: 2.2 Consensus size: 17 57993 GAAAATAGAG * 58003 AAGAAAAGAAGGAAAAA 1 AAGAAAAGAAAGAAAAA * 58020 AAGAAAAGAAAGAAAGA 1 AAGAAAAGAAAGAAAAA 58037 AAG 1 AAG 58040 GGAAATTAGG Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 17 18 1.00 ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00 Consensus pattern (17 bp): AAGAAAAGAAAGAAAAA Found at i:58025 original size:8 final size:9 Alignment explanation

Indices: 58003--58039 Score: 51 Period size: 8 Copynumber: 4.3 Consensus size: 9 57993 GAAAATAGAG 58003 AAGAAAAGA 1 AAGAAAAGA * 58012 AGGAAAA-A 1 AAGAAAAGA 58020 AAGAAAAGA 1 AAGAAAAGA 58029 AAG-AAAGA 1 AAGAAAAGA 58037 AAG 1 AAG 58040 GGAAATTAGG Statistics Matches: 25, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 8 15 0.60 9 10 0.40 ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00 Consensus pattern (9 bp): AAGAAAAGA Found at i:59282 original size:18 final size:18 Alignment explanation

Indices: 59246--59359 Score: 95 Period size: 18 Copynumber: 6.2 Consensus size: 18 59236 TAAATAAAAG * * 59246 TACTGAATGACTGACTGT 1 TACTGAATAACTGATTGT * * 59264 TATTGAATAATTGATTGT 1 TACTGAATAACTGATTGT * 59282 TACTGAATAACTGATTGC 1 TACTGAATAACTGATTGT * 59300 TACTGTGAGA-AAATGATTGT 1 TAC--TGA-ATAACTGATTGT * * 59320 TACTAAATAACTAATTGT 1 TACTGAATAACTGATTGT * * * 59338 TACTGAATGATTGAATGT 1 TACTGAATAACTGATTGT 59356 TACT 1 TACT 59360 AAATGAAACT Statistics Matches: 75, Mismatches: 17, Indels: 8 0.75 0.17 0.08 Matches are distributed among these distances: 17 1 0.01 18 59 0.79 20 14 0.19 21 1 0.01 ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39 Consensus pattern (18 bp): TACTGAATAACTGATTGT Found at i:59364 original size:18 final size:18 Alignment explanation

Indices: 59315--59365 Score: 59 Period size: 18 Copynumber: 2.8 Consensus size: 18 59305 TGAGAAAATG * 59315 ATTGTTACTAAATAACTA 1 ATTGTTACTAAATGACTA * * 59333 ATTGTTACTGAATGATTGA 1 ATTGTTACTAAATGACT-A 59352 A-TGTTACTAAATGA 1 ATTGTTACTAAATGA 59366 AACTGATAAA Statistics Matches: 28, Mismatches: 4, Indels: 2 0.82 0.12 0.06 Matches are distributed among these distances: 18 26 0.93 19 2 0.07 ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39 Consensus pattern (18 bp): ATTGTTACTAAATGACTA Done.