Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: Scaffold1697 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: 44940 ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31 Found at i:2624 original size:17 final size:18 Alignment explanation
Indices: 2599--2636 Score: 51 Period size: 17 Copynumber: 2.2 Consensus size: 18 2589 TTTCTTCAAC * * 2599 TTCTTTTTCA-ATTTCTT 1 TTCTGTTTCACATTCCTT 2616 TTCTGTTTCACATTCCTT 1 TTCTGTTTCACATTCCTT 2634 TTC 1 TTC 2637 ACTCTCAATC Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 17 9 0.50 18 9 0.50 ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63 Consensus pattern (18 bp): TTCTGTTTCACATTCCTT Found at i:6792 original size:23 final size:22 Alignment explanation
Indices: 6741--6792 Score: 54 Period size: 23 Copynumber: 2.3 Consensus size: 22 6731 CCTCGTCTTT * 6741 TTCTTTTGTTTCTTTTTCTAAC 1 TTCTTTTCTTTCTTTTTCTAAC 6763 -TCATTTTCTCTTCTTTCTTC-AAC 1 TTC-TTTTCT-TTCTTT-TTCTAAC 6786 TTCTTTT 1 TTCTTTT 6793 TCAATTTCTT Statistics Matches: 25, Mismatches: 1, Indels: 7 0.76 0.03 0.21 Matches are distributed among these distances: 21 2 0.08 22 5 0.20 23 13 0.52 24 5 0.20 ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65 Consensus pattern (22 bp): TTCTTTTCTTTCTTTTTCTAAC Found at i:6801 original size:12 final size:13 Alignment explanation
Indices: 6772--6805 Score: 52 Period size: 12 Copynumber: 2.7 Consensus size: 13 6762 CTCATTTTCT 6772 CTTCTTTCTTCAA 1 CTTCTTTCTTCAA 6785 CTTCTTT-TTCAA 1 CTTCTTTCTTCAA * 6797 TTTCTTTCT 1 CTTCTTTCT 6806 GTTTCACATT Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 12 11 0.58 13 8 0.42 ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62 Consensus pattern (13 bp): CTTCTTTCTTCAA Found at i:12947 original size:20 final size:20 Alignment explanation
Indices: 12924--12970 Score: 67 Period size: 20 Copynumber: 2.4 Consensus size: 20 12914 GGGTTAAGAT * 12924 TGAGCTGAATTGAGCTTGAG 1 TGAGCTGAATTGAGCTCGAG * * 12944 TGAGTTGACTTGAGCTCGAG 1 TGAGCTGAATTGAGCTCGAG 12964 TGAGCTG 1 TGAGCTG 12971 GAAACGAGCT Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 20 23 1.00 ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30 Consensus pattern (20 bp): TGAGCTGAATTGAGCTCGAG Found at i:14695 original size:48 final size:48 Alignment explanation
Indices: 14640--14745 Score: 137 Period size: 48 Copynumber: 2.2 Consensus size: 48 14630 TTGTCTTTTC * 14640 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA 1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA * * 14688 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA 1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA 14736 TTTCTTTTTC 1 TTTCTTTTTC 14746 CATGACACTC Statistics Matches: 52, Mismatches: 3, Indels: 6 0.85 0.05 0.10 Matches are distributed among these distances: 48 40 0.77 49 8 0.15 50 4 0.08 ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59 Consensus pattern (48 bp): TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA Found at i:14742 original size:18 final size:18 Alignment explanation
Indices: 14721--14804 Score: 62 Period size: 18 Copynumber: 4.6 Consensus size: 18 14711 TTTTCACATC * 14721 CTTTTTCAATCTCAATTT 1 CTTTTTCAATCTCACTTT * * * 14739 CTTTTTCCATGACACTCTTT 1 CTTTTTCAAT--CTCACTTT * * * 14759 CTTTTACACTCTC-GTTT 1 CTTTTTCAATCTCACTTT * 14776 CTTTCTTCAATCTCACTCT 1 CTTT-TTCAATCTCACTTT 14795 CTTTTTCAAT 1 CTTTTTCAAT 14805 TTCTTGTTCC Statistics Matches: 49, Mismatches: 13, Indels: 8 0.70 0.19 0.11 Matches are distributed among these distances: 17 7 0.14 18 24 0.49 19 6 0.12 20 12 0.24 ACGTcount: A:0.17, C:0.29, G:0.02, T:0.52 Consensus pattern (18 bp): CTTTTTCAATCTCACTTT Found at i:17396 original size:20 final size:20 Alignment explanation
Indices: 17373--17419 Score: 67 Period size: 20 Copynumber: 2.4 Consensus size: 20 17363 GGGTTAAGAT * 17373 TGAGCTGAATTGAGCTTGAG 1 TGAGCTGAATTGAGCTCGAG * * 17393 TGAGTTGACTTGAGCTCGAG 1 TGAGCTGAATTGAGCTCGAG 17413 TGAGCTG 1 TGAGCTG 17420 GAAACGAGCT Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 20 23 1.00 ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30 Consensus pattern (20 bp): TGAGCTGAATTGAGCTCGAG Found at i:18402 original size:18 final size:17 Alignment explanation
Indices: 18381--18425 Score: 54 Period size: 18 Copynumber: 2.5 Consensus size: 17 18371 GAATGACGAG 18381 AGAAAAAGAAACTGAAAA 1 AGAAAAA-AAACTGAAAA * 18399 AGAAACAAAAATTGAAAA 1 AGAAA-AAAAACTGAAAA 18417 AGAGAAAAA 1 AGA-AAAAA 18426 GATTGGAGAA Statistics Matches: 24, Mismatches: 1, Indels: 4 0.83 0.03 0.14 Matches are distributed among these distances: 18 20 0.83 19 4 0.17 ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07 Consensus pattern (17 bp): AGAAAAAAAACTGAAAA Found at i:18430 original size:18 final size:18 Alignment explanation
Indices: 18379--18430 Score: 52 Period size: 18 Copynumber: 2.8 Consensus size: 18 18369 AAGAATGACG * 18379 AGAGAAAAAGAAACTGAAAA 1 AGAGAAAAAG--ATTGAAAA * 18399 AGA-AACAAAAATTGAAAA 1 AGAGAA-AAAGATTGAAAA 18417 AGAGAAAAAGATTG 1 AGAGAAAAAGATTG 18431 GAGAAAGAAA Statistics Matches: 27, Mismatches: 3, Indels: 6 0.75 0.08 0.17 Matches are distributed among these distances: 18 17 0.63 19 4 0.15 20 6 0.22 ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10 Consensus pattern (18 bp): AGAGAAAAAGATTGAAAA Found at i:19940 original size:23 final size:21 Alignment explanation
Indices: 19909--19952 Score: 61 Period size: 23 Copynumber: 2.0 Consensus size: 21 19899 AAGGGCATAA * 19909 AATGCTCTTTAAAGACTCCTTTT 1 AATGATCTTT-AAG-CTCCTTTT 19932 AATGATCTTTAAGCTCCTTTT 1 AATGATCTTTAAGCTCCTTTT 19953 TTTTAACAGC Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 21 8 0.40 22 3 0.15 23 9 0.45 ACGTcount: A:0.25, C:0.20, G:0.09, T:0.45 Consensus pattern (21 bp): AATGATCTTTAAGCTCCTTTT Found at i:20104 original size:21 final size:23 Alignment explanation
Indices: 20059--20105 Score: 62 Period size: 23 Copynumber: 2.1 Consensus size: 23 20049 TCACCTGCAA * * 20059 TAAACACATTAAAATGAGTTTAT 1 TAAACACATTAAAATCAGCTTAT 20082 TAAACACATTAAAA-CA-CTTAT 1 TAAACACATTAAAATCAGCTTAT 20103 TAA 1 TAA 20106 TCATAACACA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 21 7 0.32 22 1 0.05 23 14 0.64 ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32 Consensus pattern (23 bp): TAAACACATTAAAATCAGCTTAT Found at i:22862 original size:11 final size:10 Alignment explanation
Indices: 22841--22897 Score: 53 Period size: 10 Copynumber: 5.6 Consensus size: 10 22831 ATAAAAAAAA * 22841 TGAGCTGAAT 1 TGAGCTAAAT 22851 TGTAGCTAAAT 1 TG-AGCTAAAT ** 22862 TGAGCTTGAT 1 TGAGCTAAAT 22872 TGAGCTGAAA- 1 TGAGCT-AAAT * 22882 TGAGCTCAAT 1 TGAGCTAAAT 22892 TGAGCT 1 TGAGCT 22898 GGTCGGAGTT Statistics Matches: 38, Mismatches: 6, Indels: 6 0.76 0.12 0.12 Matches are distributed among these distances: 9 2 0.05 10 26 0.68 11 10 0.26 ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32 Consensus pattern (10 bp): TGAGCTAAAT Found at i:22877 original size:20 final size:20 Alignment explanation
Indices: 22838--22898 Score: 70 Period size: 20 Copynumber: 3.0 Consensus size: 20 22828 CCAATAAAAA * 22838 AAATGAGCTGAATTGTAGCT- 1 AAATGAGCTCAATTG-AGCTG ** 22858 AAATTGAGCTTGATTGAGCTG 1 AAA-TGAGCTCAATTGAGCTG 22879 AAATGAGCTCAATTGAGCTG 1 AAATGAGCTCAATTGAGCTG 22899 GTCGGAGTTG Statistics Matches: 35, Mismatches: 4, Indels: 4 0.81 0.09 0.09 Matches are distributed among these distances: 20 22 0.63 21 13 0.37 ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30 Consensus pattern (20 bp): AAATGAGCTCAATTGAGCTG Found at i:29138 original size:23 final size:22 Alignment explanation
Indices: 29087--29138 Score: 54 Period size: 23 Copynumber: 2.3 Consensus size: 22 29077 CCTCGTCTTT * 29087 TTCTTTTGTTTCTTTTTCTAAC 1 TTCTTTTCTTTCTTTTTCTAAC 29109 -TCATTTTCTCTTCTTTCTTC-AAC 1 TTC-TTTTCT-TTCTTT-TTCTAAC 29132 TTCTTTT 1 TTCTTTT 29139 TCAATTTTTT Statistics Matches: 25, Mismatches: 1, Indels: 7 0.76 0.03 0.21 Matches are distributed among these distances: 21 2 0.08 22 5 0.20 23 13 0.52 24 5 0.20 ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65 Consensus pattern (22 bp): TTCTTTTCTTTCTTTTTCTAAC Found at i:32613 original size:17 final size:16 Alignment explanation
Indices: 32591--32647 Score: 98 Period size: 16 Copynumber: 3.6 Consensus size: 16 32581 CTTCTTCTTC 32591 TTTTTTT-ACGAAATTT 1 TTTTTTTCACG-AATTT 32607 TTTTTTTCACGAATTT 1 TTTTTTTCACGAATTT 32623 TTTTTTTCACGAATTT 1 TTTTTTTCACGAATTT 32639 TTTTTTTCA 1 TTTTTTTCA 32648 ACTTGATATC Statistics Matches: 40, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 16 37 0.93 17 3 0.08 ACGTcount: A:0.19, C:0.11, G:0.05, T:0.65 Consensus pattern (16 bp): TTTTTTTCACGAATTT Found at i:32704 original size:11 final size:11 Alignment explanation
Indices: 32688--32739 Score: 70 Period size: 11 Copynumber: 4.7 Consensus size: 11 32678 GAAACCAAAT 32688 TTTTTTTTGAA 1 TTTTTTTTGAA 32699 TTTTTTTTGAA 1 TTTTTTTTGAA ** 32710 TTTTTTTTTTA 1 TTTTTTTTGAA 32721 -TTTTTTTGAAA 1 TTTTTTTTG-AA 32732 TTTTTTTT 1 TTTTTTTT 32740 TGAAGAAACT Statistics Matches: 35, Mismatches: 4, Indels: 3 0.83 0.10 0.07 Matches are distributed among these distances: 10 7 0.20 11 21 0.60 12 7 0.20 ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79 Consensus pattern (11 bp): TTTTTTTTGAA Found at i:32715 original size:21 final size:22 Alignment explanation
Indices: 32689--32738 Score: 59 Period size: 21 Copynumber: 2.3 Consensus size: 22 32679 AAACCAAATT 32689 TTTTTTTGAAT-TTTTTTTG-AA 1 TTTTTTT-AATATTTTTTTGAAA ** 32710 TTTTTTTTTTATTTTTTTGAAA 1 TTTTTTTAATATTTTTTTGAAA 32732 TTTTTTT 1 TTTTTTT 32739 TTGAAGAAAC Statistics Matches: 25, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 20 1 0.04 21 15 0.60 22 9 0.36 ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78 Consensus pattern (22 bp): TTTTTTTAATATTTTTTTGAAA Found at i:32740 original size:22 final size:24 Alignment explanation
Indices: 32684--32743 Score: 90 Period size: 22 Copynumber: 2.6 Consensus size: 24 32674 AATGGAAACC 32684 AAATTTTTTTTTGAATTTTTTTTG 1 AAATTTTTTTTTGAATTTTTTTTG * 32708 -AATTTTTTTTT-TA-TTTTTTTG 1 AAATTTTTTTTTGAATTTTTTTTG 32729 AAATTTTTTTTTGAA 1 AAATTTTTTTTTGAA 32744 GAAACTACTA Statistics Matches: 32, Mismatches: 2, Indels: 5 0.82 0.05 0.13 Matches are distributed among these distances: 21 8 0.25 22 12 0.38 23 12 0.38 ACGTcount: A:0.22, C:0.00, G:0.07, T:0.72 Consensus pattern (24 bp): AAATTTTTTTTTGAATTTTTTTTG Found at i:33778 original size:21 final size:23 Alignment explanation
Indices: 33733--33779 Score: 62 Period size: 23 Copynumber: 2.1 Consensus size: 23 33723 TCACCTGCAA * * 33733 TAAACACATTAAAATGAGTTTAT 1 TAAACACATTAAAATCAGCTTAT 33756 TAAACACATTAAAA-CA-CTTAT 1 TAAACACATTAAAATCAGCTTAT 33777 TAA 1 TAA 33780 TCATAACACA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 21 7 0.32 22 1 0.05 23 14 0.64 ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32 Consensus pattern (23 bp): TAAACACATTAAAATCAGCTTAT Found at i:39193 original size:12 final size:12 Alignment explanation
Indices: 39176--39219 Score: 81 Period size: 12 Copynumber: 3.8 Consensus size: 12 39166 AATGGAAACC 39176 AATTTTTTTTTG 1 AATTTTTTTTTG 39188 AATTTTTTTTTG 1 AATTTTTTTTTG 39200 AA-TTTTTTTTG 1 AATTTTTTTTTG 39211 AATTTTTTT 1 AATTTTTTT 39220 GAAGAAACTA Statistics Matches: 31, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 11 11 0.35 12 20 0.65 ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75 Consensus pattern (12 bp): AATTTTTTTTTG Found at i:39195 original size:11 final size:11 Alignment explanation
Indices: 39179--39219 Score: 73 Period size: 11 Copynumber: 3.6 Consensus size: 11 39169 GGAAACCAAT 39179 TTTTTTTTGAA 1 TTTTTTTTGAA 39190 TTTTTTTTTGAA 1 -TTTTTTTTGAA 39202 TTTTTTTTGAA 1 TTTTTTTTGAA 39213 TTTTTTT 1 TTTTTTT 39220 GAAGAAACTA Statistics Matches: 29, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 11 18 0.62 12 11 0.38 ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78 Consensus pattern (11 bp): TTTTTTTTGAA Found at i:40256 original size:21 final size:23 Alignment explanation
Indices: 40211--40257 Score: 62 Period size: 23 Copynumber: 2.1 Consensus size: 23 40201 TCACCTGCAA * * 40211 TAAACACATTAAAATGAGTTTAT 1 TAAACACATTAAAATCAGCTTAT 40234 TAAACACATTAAAA-CA-CTTAT 1 TAAACACATTAAAATCAGCTTAT 40255 TAA 1 TAA 40258 TCATAACACA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 21 7 0.32 22 1 0.05 23 14 0.64 ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32 Consensus pattern (23 bp): TAAACACATTAAAATCAGCTTAT Done.