Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: AWUE01020334.1 Corchorus olitorius cultivar O-4 contig20367, 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: 52619 ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33 Found at i:3516 original size:15 final size:15 Alignment explanation
Indices: 3488--3532 Score: 60 Period size: 15 Copynumber: 3.1 Consensus size: 15 3478 ACCACTCTCA 3488 TTTTCTTTT-T-CTT 1 TTTTCTTTTCTCCTT 3501 TCTTT-TTTTCTCCTT 1 T-TTTCTTTTCTCCTT 3516 TTTTCTTTTCTCCTT 1 TTTTCTTTTCTCCTT 3531 TT 1 TT 3533 ACTCCTCTCT Statistics Matches: 28, Mismatches: 0, Indels: 6 0.82 0.00 0.18 Matches are distributed among these distances: 13 5 0.18 14 7 0.25 15 16 0.57 ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78 Consensus pattern (15 bp): TTTTCTTTTCTCCTT Found at i:7377 original size:42 final size:42 Alignment explanation
Indices: 7318--7418 Score: 193 Period size: 42 Copynumber: 2.4 Consensus size: 42 7308 ATAGGCAAAA 7318 TTGATATATTGTAAATTATTATCTAAGGATCTTATTAGTTGT 1 TTGATATATTGTAAATTATTATCTAAGGATCTTATTAGTTGT * 7360 TTGATATATTGTAAATTATTATCTAAGGATTTTATTAGTTGT 1 TTGATATATTGTAAATTATTATCTAAGGATCTTATTAGTTGT 7402 TTGATATATTGTAAATT 1 TTGATATATTGTAAATT 7419 GATATATTGA Statistics Matches: 58, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 42 58 1.00 ACGTcount: A:0.32, C:0.03, G:0.14, T:0.51 Consensus pattern (42 bp): TTGATATATTGTAAATTATTATCTAAGGATCTTATTAGTTGT Found at i:10309 original size:13 final size:13 Alignment explanation
Indices: 10291--10315 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 10281 TTTAGTTAAG 10291 AAAATAAAAAATA 1 AAAATAAAAAATA 10304 AAAATAAAAAAT 1 AAAATAAAAAAT 10316 CTTTCTTCCC Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16 Consensus pattern (13 bp): AAAATAAAAAATA Found at i:16191 original size:84 final size:85 Alignment explanation
Indices: 16065--16224 Score: 270 Period size: 84 Copynumber: 1.9 Consensus size: 85 16055 CACCACACTG 16065 AACACACCTGAATTTATTGCAAAGGTTTTGGAATTTAATGGAAG-TTCTTATTCACAAAATCCAA 1 AACACACCTGAATTTATTGCAAAGGTTTTGGAATTTAATGGAAGCTT-TTATTCACAAAATCCAA 16129 ACTAGATTTGCATCACACTAA 65 ACTAGATTTGCATCACACTAA * * * 16150 AACACACCTGTATTTATTGCTAA-GTTTTGGAGTTTAATGGAAGCTTTTATTCACAAAATCCAAA 1 AACACACCTGAATTTATTGCAAAGGTTTTGGAATTTAATGGAAGCTTTTATTCACAAAATCCAAA 16214 CTAGATTTGCA 66 CTAGATTTGCA 16225 ATAATACCTT Statistics Matches: 71, Mismatches: 3, Indels: 3 0.92 0.04 0.04 Matches are distributed among these distances: 84 48 0.68 85 23 0.32 ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34 Consensus pattern (85 bp): AACACACCTGAATTTATTGCAAAGGTTTTGGAATTTAATGGAAGCTTTTATTCACAAAATCCAAA CTAGATTTGCATCACACTAA Found at i:18892 original size:24 final size:22 Alignment explanation
Indices: 18849--18902 Score: 56 Period size: 23 Copynumber: 2.4 Consensus size: 22 18839 TTTTAAAAAT ** 18849 TTTATAT-GTTTTCATTTTAATA 1 TTTATATAGTTTAAATTTTAA-A 18871 TTTATATAGTTTAAATTATTAAA 1 TTTATATAGTTTAAATT-TTAAA 18894 TTTAATATA 1 TTT-ATATA 18903 AAATAATATT Statistics Matches: 27, Mismatches: 2, Indels: 4 0.82 0.06 0.12 Matches are distributed among these distances: 22 7 0.26 23 11 0.41 24 9 0.33 ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57 Consensus pattern (22 bp): TTTATATAGTTTAAATTTTAAA Found at i:24209 original size:33 final size:33 Alignment explanation
Indices: 24146--24212 Score: 82 Period size: 33 Copynumber: 2.0 Consensus size: 33 24136 GGGAAGTTAA * * 24146 AGAATATTGCCGTTAATAGTGATATTGAGTCTG 1 AGAATATTGCCGTCAATAGTGATATCGAGTCTG * * 24179 AGAATATTGGCGTCAATGGTGATGA-CGAGTCTG 1 AGAATATTGCCGTCAATAGTGAT-ATCGAGTCTG 24212 A 1 A 24213 CATTGTTAAG Statistics Matches: 29, Mismatches: 4, Indels: 2 0.83 0.11 0.06 Matches are distributed among these distances: 33 28 0.97 34 1 0.03 ACGTcount: A:0.30, C:0.10, G:0.28, T:0.31 Consensus pattern (33 bp): AGAATATTGCCGTCAATAGTGATATCGAGTCTG Found at i:27524 original size:76 final size:77 Alignment explanation
Indices: 27389--27539 Score: 234 Period size: 76 Copynumber: 2.0 Consensus size: 77 27379 TTATAGGTTA * * 27389 AAATAGTTTCATTTTGTCAATGGTCACGTGGTTTATTTTACTAATATTTCTATTAATCGATCTCA 1 AAATAGTTTCATTTTGTCAATGGTCACGTGATTTATTATACTAATATTTCTATTAATCGATCTCA 27454 TAAAAATAAAGT 66 TAAAAATAAAGT * * * 27466 AAATAGTTTCATTTTGTCAA-GGTCACGTGATTTATTATAGTACTATTT-TCATTGATCGATCTC 1 AAATAGTTTCATTTTGTCAATGGTCACGTGATTTATTATACTAATATTTCT-ATTAATCGATCTC 27529 ATAAAAATAAA 65 ATAAAAATAAA 27540 ATAATCCTTA Statistics Matches: 68, Mismatches: 5, Indels: 3 0.89 0.07 0.04 Matches are distributed among these distances: 75 1 0.01 76 47 0.69 77 20 0.29 ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42 Consensus pattern (77 bp): AAATAGTTTCATTTTGTCAATGGTCACGTGATTTATTATACTAATATTTCTATTAATCGATCTCA TAAAAATAAAGT Found at i:27959 original size:4 final size:4 Alignment explanation
Indices: 27950--27998 Score: 98 Period size: 4 Copynumber: 12.2 Consensus size: 4 27940 TGTTGAATGG 27950 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA 1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA 27998 A 1 A 27999 AACTCATTTT Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 45 1.00 ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24 Consensus pattern (4 bp): ATAA Found at i:34328 original size:19 final size:18 Alignment explanation
Indices: 34283--34334 Score: 50 Period size: 19 Copynumber: 2.7 Consensus size: 18 34273 CATAGGTCTT * 34283 TTAATAATAATTATTCAA 1 TTAATAATTATTATTCAA * * 34301 TAAAATAATTATTATTTAA 1 T-TAATAATTATTATTCAA 34320 TTAATTAATTTATTA 1 TTAA-TAA-TTATTA 34335 ATTTCAGCCC Statistics Matches: 27, Mismatches: 4, Indels: 4 0.77 0.11 0.11 Matches are distributed among these distances: 18 3 0.11 19 18 0.67 20 6 0.22 ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50 Consensus pattern (18 bp): TTAATAATTATTATTCAA Found at i:34703 original size:13 final size:13 Alignment explanation
Indices: 34685--34710 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 34675 AAGGTAACAA 34685 CAAAAATCATCAC 1 CAAAAATCATCAC 34698 CAAAAATCATCAC 1 CAAAAATCATCAC 34711 TCATGCCAAG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15 Consensus pattern (13 bp): CAAAAATCATCAC Found at i:35738 original size:10 final size:10 Alignment explanation
Indices: 35721--35753 Score: 50 Period size: 10 Copynumber: 3.3 Consensus size: 10 35711 ATGGATCTGA 35721 TATATATAA- 1 TATATATAAC 35730 TATTATATAAC 1 TA-TATATAAC 35741 TATATATAAC 1 TATATATAAC 35751 TAT 1 TAT 35754 CACCTTTCTT Statistics Matches: 22, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 9 2 0.09 10 18 0.82 11 2 0.09 ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45 Consensus pattern (10 bp): TATATATAAC Found at i:45245 original size:179 final size:178 Alignment explanation
Indices: 44933--45271 Score: 495 Period size: 179 Copynumber: 1.9 Consensus size: 178 44923 TTCCACCATA * * * ** 44933 AGCAGAAATTATGTAATATTAAGTAAACCGTCTATTTCCGTTAATCGAAACAACTAATTCTTTGG 1 AGCAGAAATTATATAATATTAAGTAAACCGTCTATTTCCGTTAAGCGAAACAACAAATTCTTCAG * * * 44998 AAGCATTTTTTATATCTTGAACATTAAATTTAGTTTTCGAGTGCTTCATGAAAGTTGTAGATCAT 66 AAGCATTTTTGATATCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTACATCAT * 45063 GGAACAACCTTTTAAGAGACACTTGAATCATCTCAATCAGACATCTGG 131 GGAACAACCTTTTAAGAGACACTTAAATCATCTCAATCAGACATCTGG ** 45111 AGCA-AAAGTTATATAATATTAAGTGGACCGTCTATTTCCCGTTAAGCGAAACAACAAACTT-TT 1 AGCAGAAA-TTATATAATATTAAGTAAACCGTCTATTT-CCGTTAAGCGAAACAACAAA-TTCTT 45174 CAGAAGCATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTACA 63 CAGAAGCATTTTTGATATCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTACA * * * 45238 TCATGGAACAATCTTTTAATAGAGACTTAAATCA 127 TCATGGAACAACCTTTTAAGAGACACTTAAATCA 45272 CCTTAATTGG Statistics Matches: 143, Mismatches: 14, Indels: 7 0.87 0.09 0.04 Matches are distributed among these distances: 177 3 0.02 178 34 0.24 179 104 0.73 180 2 0.01 ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34 Consensus pattern (178 bp): AGCAGAAATTATATAATATTAAGTAAACCGTCTATTTCCGTTAAGCGAAACAACAAATTCTTCAG AAGCATTTTTGATATCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTACATCAT GGAACAACCTTTTAAGAGACACTTAAATCATCTCAATCAGACATCTGG Found at i:45304 original size:179 final size:179 Alignment explanation
Indices: 44932--45320 Score: 491 Period size: 179 Copynumber: 2.2 Consensus size: 179 44922 ATTCCACCAT * * * * 44932 AAGC-AGAAATTATGTAATATTAAGTAAACCGTCTATTTCCGTTAATCGAAACAACTAATTCTTT 1 AAGCAAGAAATTATATAATATTAAGTAAACCGTCTATTTCCGTTAAGCGAAACAACAAATTCTTC * * * * 44996 GGAAGCATTTTTTATATCTTGAACATTAAATTTAGTTTTCGAGTGCTTCATGAAAGTTGTAGATC 66 AGAAGCATTTTTGATATCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTACATC * * * * 45061 ATGGAACAACCTTTTAAGAGACACTTGAATCATCTCAATCAGACATCTG 131 ATGGAACAACCTTTTAAGAGACACTTAAATCACCTCAATCAGACAACCG * * ** 45110 GAGCAA-AAGTTATATAATATTAAGTGGACCGTCTATTTCCCGTTAAGCGAAACAACAAACTT-T 1 AAGCAAGAAATTATATAATATTAAGTAAACCGTCTATTT-CCGTTAAGCGAAACAACAAA-TTCT 45173 TCAGAAGCATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAC 64 TCAGAAGCATTTTTGATATCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAC * * * * ** * 45237 ATCATGGAACAATCTTTTAATAGAGACTTAAATCACCTTAATTGGATAACCG 128 ATCATGGAACAACCTTTTAAGAGACACTTAAATCACCTCAATCAGACAACCG * * 45289 AAG-AAGAAATTATATAATGTTAAATAAACCGT 1 AAGCAAGAAATTATATAATATTAAGTAAACCGT 45321 TTAACTAAAC Statistics Matches: 177, Mismatches: 29, Indels: 9 0.82 0.13 0.04 Matches are distributed among these distances: 178 37 0.21 179 138 0.78 180 2 0.01 ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33 Consensus pattern (179 bp): AAGCAAGAAATTATATAATATTAAGTAAACCGTCTATTTCCGTTAAGCGAAACAACAAATTCTTC AGAAGCATTTTTGATATCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTACATC ATGGAACAACCTTTTAAGAGACACTTAAATCACCTCAATCAGACAACCG Found at i:46531 original size:10 final size:10 Alignment explanation
Indices: 46516--46543 Score: 56 Period size: 10 Copynumber: 2.8 Consensus size: 10 46506 CAAGAGTCCT 46516 TCCTTTCCCA 1 TCCTTTCCCA 46526 TCCTTTCCCA 1 TCCTTTCCCA 46536 TCCTTTCC 1 TCCTTTCC 46544 TGACCTTTAC Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 18 1.00 ACGTcount: A:0.07, C:0.50, G:0.00, T:0.43 Consensus pattern (10 bp): TCCTTTCCCA Found at i:48388 original size:149 final size:152 Alignment explanation
Indices: 48235--48514 Score: 368 Period size: 155 Copynumber: 1.8 Consensus size: 152 48225 TATTGGAATC * * * * 48235 GGAATTTGACACAAAAATTATATTTTCATTTCTAAGAATGTTGCTAGTTAA-T-T-TGAACATTA 1 GGAATTTCACACAAAAATTATATTTCCATTTCTAAGAACGTTGCTAGCTAATTATATGAACATTA * * * * 48297 GTTTTATTTGGATTATTATAAAGACAAGGAGTGGAAATATTTAAAGAAATAATATCATTTATAGA 66 GTTTTACTTAGACTATTATAAAGACAAGGAGTGGAAATATTTAAAGAAATAATATCATCTATAGA 48362 TTTTTTTTTTTCAATTTGAAAT 131 TTTTTTTTTTTCAATTTGAAAT *** * * 48384 GGAATTTCACATGGAAATTATATTTCCGTTTCTGAGAACGTTGCTAGCTAATTATAAAATGAACA 1 GGAATTTCACACAAAAATTATATTTCCATTTCTAAGAACGTTGCTAGCTAATTAT---ATGAACA ** * 48449 TTAGTTTTACTTAGACTATTATAAAGACAAGGAGTGGAAATATTTACGGAAATAATTTCATCTAT 63 TTAGTTTTACTTAGACTATTATAAAGACAAGGAGTGGAAATATTTAAAGAAATAATATCATCTAT 48514 A 128 A 48515 AATGTTTCAC Statistics Matches: 109, Mismatches: 16, Indels: 6 0.83 0.12 0.05 Matches are distributed among these distances: 149 42 0.39 150 1 0.01 151 1 0.01 155 65 0.60 ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39 Consensus pattern (152 bp): GGAATTTCACACAAAAATTATATTTCCATTTCTAAGAACGTTGCTAGCTAATTATATGAACATTA GTTTTACTTAGACTATTATAAAGACAAGGAGTGGAAATATTTAAAGAAATAATATCATCTATAGA TTTTTTTTTTTCAATTTGAAAT Found at i:48529 original size:15 final size:15 Alignment explanation
Indices: 48511--48542 Score: 64 Period size: 15 Copynumber: 2.1 Consensus size: 15 48501 TAATTTCATC 48511 TATAAATGTTTCACT 1 TATAAATGTTTCACT 48526 TATAAATGTTTCACT 1 TATAAATGTTTCACT 48541 TA 1 TA 48543 GAAACGAAAT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 17 1.00 ACGTcount: A:0.34, C:0.12, G:0.06, T:0.47 Consensus pattern (15 bp): TATAAATGTTTCACT Found at i:48612 original size:164 final size:155 Alignment explanation
Indices: 48288--48616 Score: 388 Period size: 164 Copynumber: 2.1 Consensus size: 155 48278 CTAGTTAATT * * * 48288 TGAACATTAGTTTTATTTGGATTATTATAAAGACAAGGAGTGGAAATATTTAAAGAAATAATATC 1 TGAACATTAGTTTTACTTAGACTATTATAAAGACAAGGAGTGGAAATATTTAAAGAAATAATATC * * * * * * * * * 48353 ATTTATAGATTTTTTTTTTTCAATTTGAAATGGAATTTCACATGGAAATTATATTTCCGTTTCTG 66 ATCTATAAATTTTTTTTTTTCAATTAGAAACGAAATTTCAAACGGAAATTATATTTCCGCTTCTA * * * 48418 AGAACGTTGCTAGCTAATTATAAAA 131 AAAACGTTGCTAACTAATCATAAAA ** * 48443 TGAACATTAGTTTTACTTAGACTATTATAAAGACAAGGAGTGGAAATATTTACGGAAATAATTTC 1 TGAACATTAGTTTTACTTAGACTATTATAAAGACAAGGAGTGGAAATATTTAAAGAAATAATATC * 48508 ATCTATAAATGTTTCACTTATAAATGTTTCACTTAGAAACGAAATTTCAAACGGAAATTATATTT 66 ATCTATAAAT-TTT---TT-T---T-TTTCAATTAGAAACGAAATTTCAAACGGAAATTATATTT * * 48573 TCGCTTCTAAAAACGTTGTTAACTAATCATAAAA 122 CCGCTTCTAAAAACGTTGCTAACTAATCATAAAA 48607 TGAACATTAG 1 TGAACATTAG 48617 AATTTTATTC Statistics Matches: 144, Mismatches: 21, Indels: 9 0.83 0.12 0.05 Matches are distributed among these distances: 155 67 0.47 156 3 0.02 159 2 0.01 160 1 0.01 163 1 0.01 164 70 0.49 ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38 Consensus pattern (155 bp): TGAACATTAGTTTTACTTAGACTATTATAAAGACAAGGAGTGGAAATATTTAAAGAAATAATATC ATCTATAAATTTTTTTTTTTCAATTAGAAACGAAATTTCAAACGGAAATTATATTTCCGCTTCTA AAAACGTTGCTAACTAATCATAAAA Found at i:50107 original size:15 final size:15 Alignment explanation
Indices: 50089--50124 Score: 54 Period size: 15 Copynumber: 2.4 Consensus size: 15 50079 GAGAATTTAG 50089 AAATGAAACATTTCA 1 AAATGAAACATTTCA * * 50104 AAATGCATCATTTCA 1 AAATGAAACATTTCA 50119 AAATGA 1 AAATGA 50125 TAGCATTTAT Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28 Consensus pattern (15 bp): AAATGAAACATTTCA Found at i:51403 original size:76 final size:76 Alignment explanation
Indices: 51263--51406 Score: 216 Period size: 76 Copynumber: 1.9 Consensus size: 76 51253 GTTGTCCTTA * * * * 51263 CTTAACAAATTGGTTTTAGGTTGGACAGTTAACACTCTGGTTTTTATTTATCTTACTATGTTGTG 1 CTTAACAAATTGGTTTTAGGTTGGACACTTAACACTCTGATTTTTATTTATCTTAATATATTGTG 51328 TATAGTGTCCT 66 TATAGTGTCCT * * * * 51339 CTTAACTAATTGGTTTTATGTTGGACACTTAACACTCTGATTTTTATTTGTTTTAATATATTGTG 1 CTTAACAAATTGGTTTTAGGTTGGACACTTAACACTCTGATTTTTATTTATCTTAATATATTGTG 51404 TAT 66 TAT 51407 GGTAAAACCA Statistics Matches: 60, Mismatches: 8, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 76 60 1.00 ACGTcount: A:0.24, C:0.12, G:0.16, T:0.49 Consensus pattern (76 bp): CTTAACAAATTGGTTTTAGGTTGGACACTTAACACTCTGATTTTTATTTATCTTAATATATTGTG TATAGTGTCCT Found at i:51494 original size:33 final size:34 Alignment explanation
Indices: 51422--51494 Score: 114 Period size: 33 Copynumber: 2.2 Consensus size: 34 51412 AACCATAGGT * * 51422 ATACATGTAGAAACTTGGGAACTAAATATAGTTT 1 ATACATGTAGAAACTTGGGAAATAAATATAGTTA 51456 A-ACATGTAGAAACTTGGGAAATAAATATA-TTA 1 ATACATGTAGAAACTTGGGAAATAAATATAGTTA 51488 ATACATG 1 ATACATG 51495 ATTAGCCAAA Statistics Matches: 36, Mismatches: 2, Indels: 3 0.88 0.05 0.07 Matches are distributed among these distances: 32 3 0.08 33 32 0.89 34 1 0.03 ACGTcount: A:0.45, C:0.08, G:0.16, T:0.30 Consensus pattern (34 bp): ATACATGTAGAAACTTGGGAAATAAATATAGTTA Done.