Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: AWUE01017021.1 Corchorus olitorius cultivar O-4 contig17054, whole genome shotgun sequence 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: 19287 ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33 Found at i:1971 original size:14 final size:15 Alignment explanation
Indices: 1952--1981 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 1942 CAATCAAAGC 1952 AATAAT-CAAGGAAA 1 AATAATGCAAGGAAA 1966 AATAATGCAAGGAAA 1 AATAATGCAAGGAAA 1981 A 1 A 1982 TTAAAAAGAT Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 6 0.40 15 9 0.60 ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13 Consensus pattern (15 bp): AATAATGCAAGGAAA Found at i:2360 original size:21 final size:21 Alignment explanation
Indices: 2336--2390 Score: 74 Period size: 21 Copynumber: 2.6 Consensus size: 21 2326 GGCACTGAAT * * 2336 GGTGATGGCACGGACATAGCC 1 GGTGGTGGCACGGACATAACC * * 2357 GGTGGTGGCACGGGCTTAACC 1 GGTGGTGGCACGGACATAACC 2378 GGTGGTGGCACGG 1 GGTGGTGGCACGG 2391 TGAATGGTCG Statistics Matches: 30, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 21 30 1.00 ACGTcount: A:0.16, C:0.22, G:0.45, T:0.16 Consensus pattern (21 bp): GGTGGTGGCACGGACATAACC Found at i:5592 original size:29 final size:29 Alignment explanation
Indices: 5524--5613 Score: 110 Period size: 29 Copynumber: 3.0 Consensus size: 29 5514 GAAAATAAAG * 5524 AAATTTTTTTTTTTCTAAAAACGCAGGAACA 1 AAATTTTTTTTTTT-TAAAAACGCA-AAACA * 5555 AGAAATTTTTTTTTTTAGAAAACGCAAAAC- 1 A-AATTTTTTTTTTTTA-AAAACGCAAAACA 5585 AAATTTTTTTTTTTTCAAAAACGCAAAAC 1 AAATTTTTTTTTTTT-AAAAACGCAAAAC 5614 TAATAAATTA Statistics Matches: 53, Mismatches: 3, Indels: 8 0.83 0.05 0.12 Matches are distributed among these distances: 29 25 0.47 30 2 0.04 31 6 0.11 32 20 0.38 ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39 Consensus pattern (29 bp): AAATTTTTTTTTTTTAAAAACGCAAAACA Found at i:5717 original size:21 final size:21 Alignment explanation
Indices: 5656--5717 Score: 70 Period size: 23 Copynumber: 2.9 Consensus size: 21 5646 TTTATGAAAA ** 5656 ACGCAAAAACCTTTTTTTATG 1 ACGCAAAAAAATTTTTTTATG * 5677 ACGCAGAAACAAAATTTTTTATG 1 ACGCA-AAA-AAATTTTTTTATG * 5700 ACGCAAAAATATTTTTTT 1 ACGCAAAAAAATTTTTTT 5718 TTCCGATGCA Statistics Matches: 34, Mismatches: 5, Indels: 4 0.79 0.12 0.09 Matches are distributed among these distances: 21 13 0.38 22 6 0.18 23 15 0.44 ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37 Consensus pattern (21 bp): ACGCAAAAAAATTTTTTTATG Found at i:5908 original size:29 final size:29 Alignment explanation
Indices: 5867--5934 Score: 109 Period size: 29 Copynumber: 2.3 Consensus size: 29 5857 GTCTATTTTT 5867 CCTTCCCCTGGCAAAAACCAAAAAAAGTTC 1 CCTTCCCC-GGCAAAAACCAAAAAAAGTTC * * 5897 CCTTCCCCGGCAAATACCAGAAAAAGTTC 1 CCTTCCCCGGCAAAAACCAAAAAAAGTTC 5926 CCTTCCCCG 1 CCTTCCCCG 5935 TCAACGGCGC Statistics Matches: 36, Mismatches: 2, Indels: 1 0.92 0.05 0.03 Matches are distributed among these distances: 29 28 0.78 30 8 0.22 ACGTcount: A:0.32, C:0.38, G:0.12, T:0.18 Consensus pattern (29 bp): CCTTCCCCGGCAAAAACCAAAAAAAGTTC Found at i:6138 original size:15 final size:16 Alignment explanation
Indices: 6114--6153 Score: 64 Period size: 15 Copynumber: 2.6 Consensus size: 16 6104 AGAGATTGAC * 6114 AGAAAGCAATTAAA-T 1 AGAAAACAATTAAACT 6129 AGAAAACAATTAAACT 1 AGAAAACAATTAAACT 6145 AGAAAACAA 1 AGAAAACAA 6154 AGCAGAGTAA Statistics Matches: 23, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 15 13 0.57 16 10 0.43 ACGTcount: A:0.65, C:0.10, G:0.10, T:0.15 Consensus pattern (16 bp): AGAAAACAATTAAACT Found at i:11165 original size:47 final size:49 Alignment explanation
Indices: 11016--12440 Score: 954 Period size: 47 Copynumber: 28.5 Consensus size: 49 11006 TATTACTGCT * * * * * 11016 TTTTACTTTTTTAGTTTAATTACTCTGAACTAAACTAATTACTCTTACTCTTTC 1 TTTTAC-TATTTAGTTTAATTACCCAGAATTAAACTAATTCCTC-T--TC-TTC * ** * * * 11070 TTTTACTCTTTAACTTAATTACTCAGAATTAAACTAATTACTGTTTACTCTTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATT-C-CTCT--TC-TTC * * * 11124 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTGTTTACTCTTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATT-C-CTCT--TC-TTC * 11178 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTGCTTTACTTCTTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATT-C--C--T-CTTC-TTC * * * ** * * 11234 TTTTACTCTTTAGTTTAATTACTCATAATTAAACTAATTATTGTT-TAC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC * * 11282 TCTTT-CT-TTTACTCTTTTAATTACCCAGAATTAAACTAATTACTGTTTTACTTCTTTC 1 T-TTTACTATTTA---GTTTAATTACCCAGAATTAAACTAATT-C----CT-CTTC-TTC * * 11340 TTTTACTCTTTAGTTTAATTACCCATAATTAAACTAATTACTGCTTTACTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATT-C--C--T-CTTCTTC * * * 11395 TTTTACTCTTTAGTTTAATTGCCCAGAATTAAACTAACTTATGCTTTACTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA--T-T-C-CT-CTTCTTC * * * * 11450 CTTTACTCTTTAGTTTAATTGCCCATAATTAAACTAACTTCTGCTTTGCTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-TTC--C--T-CTTCTTC * * * * * 11505 TTTTACTCTTTAGTTTAATTGCCCAGAATTAAACTGA--CTTCTGCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC * * * 11552 TTTTACTATTTAGTTTAATTGCCCAGAATTAAACTGA--CTTCTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC * * * 11599 TTTTACTATTTAGTTTAATTAACCTGAATTAAACTGACTTCTGCTTTACTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACT-AATTC--C--T-CTTCTTC * * * 11654 TTTTACTCTTTAGTTTAATTGCCCAGAATTAAACTGACTTCTGCTTTACTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACT-AATTC--C--T-CTTCTTC * * * 11709 TTTTACTCTTTAGTTTAATTACCCAAAATTAAACCAA--CCTCTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC * * * * ** *** * * * ** 11756 TTTTACTCTTTAGTTAAACTAACC--TCTTCTTCT-TTTACTATT-TAA 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC * * * *** * 11801 TTTAAACTAACCTCTT-CTTCT-TTTACTCTTTAGTTAAACTAA--CCTCTTCTTC 1 TTT-TACT-A--T-TTAGTT-TAATTAC-CCAGAATTAAACTAATTCCTCTTCTTC * * * * 11853 -TTTACTATTTAGTTTAATTACCTAGAATTATACCAA--CCTCTT-TTT 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC * 11898 TCTTTACTATTTATTTTAATTACCCAGAATTAAACTAA--CCTCTTCTTC 1 T-TTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC * * * * 11946 TTTTACTATTTAATTTGATTACCTAGAATTAAACCAA--CCTCTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC ** 11993 -TTTACTATTTAGTTTAATTACCTGGAATTAAACTAA--CCTCTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC * * * 12039 TTTTACTATTTAGTTTAATCACCTAGAATTAAACTAA--CCTCTCCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC * * * 12086 TTTTACTATTTAGTTTAATTACCTAGAATTAAAGT-A-GCCTCTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC * * 12133 TTTTACTATTTAGTTTAATCACCTAGAATTAAACTAA--CCTCTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC * * * 12180 TTTTACTATTTAGTTTAATTACCTATAATTAAACT-A-CCCTCTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC * * * 12227 TTATACTATTTAGTTTAATTACCTAGAATTAAACTAA--CTTCTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC * * * 12274 TTTTACTATTTAGTTTAATTACCTAGAATTAAACT-A-GCATCTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC * * * 12321 TTTTACTATTTAGTTTAATTACCTAGAATTAAACTAACCTCTTCTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAA-TTCCTCTTCTTC * ** 12371 TTTTACTATTTAGTTTAATTACCTAGAATTAAACT-A-GGCTCTTCTTC 1 TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC * 12418 TTTTACTATTTAGTTCAATTACC 1 TTTTACTATTTAGTTTAATTACC 12441 TGATTTAAAC Statistics Matches: 1171, Mismatches: 137, Indels: 133 0.81 0.10 0.09 Matches are distributed among these distances: 45 9 0.01 46 71 0.06 47 523 0.45 48 13 0.01 49 10 0.01 50 78 0.07 51 7 0.01 52 8 0.01 53 29 0.02 54 111 0.09 55 217 0.19 56 78 0.07 57 5 0.00 58 8 0.01 59 4 0.00 ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48 Consensus pattern (49 bp): TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTCCTCTTCTTC Found at i:11425 original size:55 final size:55 Alignment explanation
Indices: 11016--11742 Score: 854 Period size: 55 Copynumber: 13.6 Consensus size: 55 11006 TATTACTGCT * * * * 11016 TTTTACTTTTTTAGTTTAATTACTCTGAACTAAACTAATTACT-C-TTAC-TCTTTC 1 TTTTAC-TCTTTAGTTTAATTACCCAGAATTAAACTAATTACTGCTTTACTTC-TTC ** * 11070 TTTTACTCTTTAACTTAATTACTCAGAATTAAACTAATTACTG-TTTAC-TCTTTC 1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTGCTTTACTTC-TTC 11124 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTG-TTTAC-TCTTTC 1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTGCTTTACTTC-TTC 11178 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTGCTTTACTTCTTTC 1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTGCTTTACTTC-TTC * * * 11234 TTTTACTCTTTAGTTTAATTACTCATAATTAAACTAATTATTG-TTTAC-TCTTTC 1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTGCTTTACTTC-TTC * 11288 TTTTACTC--T--TTTAATTACCCAGAATTAAACTAATTACTGTTTTACTTCTTTC 1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTGCTTTACTTC-TTC * 11340 TTTTACTCTTTAGTTTAATTACCCATAATTAAACTAATTACTGCTTTACTTCTTC 1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTGCTTTACTTCTTC * 11395 TTTTACTCTTTAGTTTAATTGCCCAGAATTAAACTAACTTA-TGCTTTACTTCTTC 1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAA-TTACTGCTTTACTTCTTC * * * * 11450 CTTTACTCTTTAGTTTAATTGCCCATAATTAAACTAACTT-CTGCTTTGCTTCTTC 1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAA-TTACTGCTTTACTTCTTC * * * 11505 TTTTACTCTTTAGTTTAATTGCCCAGAATTAAAC---TGA---C-TT-CTGCTTC 1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTGCTTTACTTCTTC * * * 11552 TTTTACTATTTAGTTTAATTGCCCAGAATTAAAC---TGA---C-TT-CTTCTTC 1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTGCTTTACTTCTTC * * * * 11599 TTTTACTATTTAGTTTAATTAACCTGAATTAAACTGACTT-CTGCTTTACTTCTTC 1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACT-AATTACTGCTTTACTTCTTC * * 11654 TTTTACTCTTTAGTTTAATTGCCCAGAATTAAACTGACTT-CTGCTTTACTTCTTC 1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACT-AATTACTGCTTTACTTCTTC * 11709 TTTTACTCTTTAGTTTAATTACCCAAAATTAAAC 1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAAC 11743 CAACCTCTTC Statistics Matches: 614, Mismatches: 37, Indels: 43 0.88 0.05 0.06 Matches are distributed among these distances: 47 82 0.13 48 2 0.00 49 1 0.00 50 27 0.04 51 7 0.01 52 15 0.02 53 32 0.05 54 127 0.21 55 235 0.38 56 86 0.14 ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48 Consensus pattern (55 bp): TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTGCTTTACTTCTTC Found at i:11811 original size:33 final size:32 Alignment explanation
Indices: 11737--11866 Score: 208 Period size: 32 Copynumber: 4.1 Consensus size: 32 11727 TTACCCAAAA * * 11737 TTAAACCAACCTCTTCTTCTTTTACTCTTTAG 1 TTAAACTAACCTCTTCTTCTTTTACTATTTAG * 11769 TTAAACTAACCTCTTCTTCTTTTACTATTTAAT 1 TTAAACTAACCTCTTCTTCTTTTACTATTT-AG * 11802 TTAAACTAACCTCTTCTTCTTTTACTCTTTAG 1 TTAAACTAACCTCTTCTTCTTTTACTATTTAG 11834 TTAAACTAACCTCTTCTTC-TTTACTATTTAG 1 TTAAACTAACCTCTTCTTCTTTTACTATTTAG 11865 TT 1 TT 11867 TAATTACCTA Statistics Matches: 91, Mismatches: 6, Indels: 3 0.91 0.06 0.03 Matches are distributed among these distances: 31 13 0.14 32 48 0.53 33 30 0.33 ACGTcount: A:0.24, C:0.24, G:0.02, T:0.50 Consensus pattern (32 bp): TTAAACTAACCTCTTCTTCTTTTACTATTTAG Found at i:11813 original size:65 final size:64 Alignment explanation
Indices: 11737--11869 Score: 239 Period size: 65 Copynumber: 2.1 Consensus size: 64 11727 TTACCCAAAA 11737 TTAAACCAACCTCTTCTTCTTTTACTCTTTAGTTAAACTAACCTCTTCTTCTTTTACTATTTAAT 1 TTAAACCAACCTCTTCTTCTTTTACTCTTTAGTTAAACTAACCTCTTCTTC-TTTACTATTTAAT * * 11802 TTAAACTAACCTCTTCTTCTTTTACTCTTTAGTTAAACTAACCTCTTCTTCTTTACTATTTAGT 1 TTAAACCAACCTCTTCTTCTTTTACTCTTTAGTTAAACTAACCTCTTCTTCTTTACTATTTAAT 11866 TTAA 1 TTAA 11870 TTACCTAGAA Statistics Matches: 66, Mismatches: 2, Indels: 1 0.96 0.03 0.01 Matches are distributed among these distances: 64 16 0.24 65 50 0.76 ACGTcount: A:0.25, C:0.23, G:0.02, T:0.50 Consensus pattern (64 bp): TTAAACCAACCTCTTCTTCTTTTACTCTTTAGTTAAACTAACCTCTTCTTCTTTACTATTTAAT Found at i:12858 original size:24 final size:23 Alignment explanation
Indices: 12831--12886 Score: 58 Period size: 24 Copynumber: 2.3 Consensus size: 23 12821 AAACTAAATT * * 12831 AAGCCCAAATGCAAGGGAAAATCA 1 AAGCCCAAATG-AAAGGAAAATAA * * 12855 AAGCCCCGAATGAAAGGAAATTAA 1 AAG-CCCAAATGAAAGGAAAATAA 12879 AAGCCCAA 1 AAGCCCAA 12887 CTATGCAAAT Statistics Matches: 26, Mismatches: 5, Indels: 3 0.76 0.15 0.09 Matches are distributed among these distances: 23 4 0.15 24 15 0.58 25 7 0.27 ACGTcount: A:0.50, C:0.21, G:0.20, T:0.09 Consensus pattern (23 bp): AAGCCCAAATGAAAGGAAAATAA Found at i:15519 original size:27 final size:27 Alignment explanation
Indices: 15462--15519 Score: 64 Period size: 27 Copynumber: 2.1 Consensus size: 27 15452 ATTCAAGGCT * * * 15462 AAAAGGTCCAAATGCAAGTCAAAAGCT 1 AAAACGTCCAAATGCAAGCCAAAAGCC * 15489 AAAACGTCCAAGTGCAAGACCAAAA-CC 1 AAAACGTCCAAATGCAAG-CCAAAAGCC 15516 AAAA 1 AAAA 15520 TGGTAACAAC Statistics Matches: 26, Mismatches: 4, Indels: 2 0.81 0.12 0.06 Matches are distributed among these distances: 27 21 0.81 28 5 0.19 ACGTcount: A:0.52, C:0.22, G:0.16, T:0.10 Consensus pattern (27 bp): AAAACGTCCAAATGCAAGCCAAAAGCC Found at i:17825 original size:27 final size:27 Alignment explanation
Indices: 17790--17841 Score: 77 Period size: 27 Copynumber: 1.9 Consensus size: 27 17780 ATCCTAGTCA 17790 AAGGCTACTGCCATATCAGATAAATGC 1 AAGGCTACTGCCATATCAGATAAATGC * * * 17817 AAGGCTACTGCTATTTTAGATAAAT 1 AAGGCTACTGCCATATCAGATAAAT 17842 ATTGTCGTTG Statistics Matches: 22, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 27 22 1.00 ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29 Consensus pattern (27 bp): AAGGCTACTGCCATATCAGATAAATGC Found at i:18373 original size:32 final size:33 Alignment explanation
Indices: 18337--18417 Score: 89 Period size: 31 Copynumber: 2.6 Consensus size: 33 18327 TAATTTGGTT * 18337 AATTAAGTCCCTAACGTTAG-AAAATCGGTTCA 1 AATTAAGTCCCTAACGTTAGCAAAATCGGCTCA ** 18369 AATT-AGTCCCTAACAAT-GCAAAATCGGCTCA 1 AATTAAGTCCCTAACGTTAGCAAAATCGGCTCA * * 18400 AA-TAAGTTCCTAAAGTTA 1 AATTAAGTCCCTAACGTTA 18418 ACATTTTGAG Statistics Matches: 39, Mismatches: 7, Indels: 6 0.75 0.13 0.12 Matches are distributed among these distances: 30 2 0.05 31 33 0.85 32 4 0.10 ACGTcount: A:0.40, C:0.20, G:0.14, T:0.27 Consensus pattern (33 bp): AATTAAGTCCCTAACGTTAGCAAAATCGGCTCA Found at i:19271 original size:15 final size:16 Alignment explanation
Indices: 19237--19275 Score: 53 Period size: 15 Copynumber: 2.5 Consensus size: 16 19227 AAAAATTAAA * 19237 TATTTTTATTTTAATG 1 TATTTTTATTTAAATG * 19253 TATTTTTA-TTAAATT 1 TATTTTTATTTAAATG 19268 TATTTTTA 1 TATTTTTA 19276 ATAATTAAAA Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 15 13 0.62 16 8 0.38 ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69 Consensus pattern (16 bp): TATTTTTATTTAAATG Done.