Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: AWUE01019316.1 Corchorus olitorius cultivar O-4 contig19349, 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: 59160 ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31 Found at i:749 original size:21 final size:21 Alignment explanation
Indices: 716--764 Score: 55 Period size: 21 Copynumber: 2.3 Consensus size: 21 706 GAGAATTGTA ** 716 GCTT-CTTGGAAATGGCTCTT 1 GCTTCCTTGGAAATCCCTCTT * 736 GCTTCCTTTGAAATCCCTCTT 1 GCTTCCTTGGAAATCCCTCTT 757 GCATTCCT 1 GC-TTCCT 765 AAAGCATTGA Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 20 4 0.17 21 15 0.62 22 5 0.21 ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41 Consensus pattern (21 bp): GCTTCCTTGGAAATCCCTCTT Found at i:3625 original size:76 final size:76 Alignment explanation
Indices: 3488--3638 Score: 173 Period size: 76 Copynumber: 2.0 Consensus size: 76 3478 ACAAGGACCC * * * 3488 CGACTCCACCTGGGCGGCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT 1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT 3553 GGGCAGTGTCA 66 GGGCAGTGTCA * * * ** 3564 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA 1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA * 3626 GATGGGCTGTGTC 63 GATGGGCAGTGTC 3639 TTAGCTCATC Statistics Matches: 63, Mismatches: 9, Indels: 6 0.81 0.12 0.08 Matches are distributed among these distances: 75 4 0.06 76 53 0.84 77 6 0.10 ACGTcount: A:0.17, C:0.29, G:0.30, T:0.25 Consensus pattern (76 bp): CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT GGGCAGTGTCA Found at i:17465 original size:21 final size:21 Alignment explanation
Indices: 17441--17489 Score: 55 Period size: 21 Copynumber: 2.3 Consensus size: 21 17431 ATAGTTTAGA * 17441 TTTAATTTAGTTTGC-TTTATT 1 TTTAATTTA-ATTGCTTTTATT * * 17462 TTTAGTTTAATTGCTTTTCTT 1 TTTAATTTAATTGCTTTTATT 17483 TTTAATT 1 TTTAATT 17490 GTTCTATTTA Statistics Matches: 23, Mismatches: 4, Indels: 2 0.79 0.14 0.07 Matches are distributed among these distances: 20 4 0.17 21 19 0.83 ACGTcount: A:0.18, C:0.06, G:0.08, T:0.67 Consensus pattern (21 bp): TTTAATTTAATTGCTTTTATT Found at i:18324 original size:13 final size:13 Alignment explanation
Indices: 18308--18337 Score: 51 Period size: 13 Copynumber: 2.3 Consensus size: 13 18298 CACCAAAAAA 18308 AGAATTAGAAATC 1 AGAATTAGAAATC * 18321 AGAATTAGAAATT 1 AGAATTAGAAATC 18334 AGAA 1 AGAA 18338 GATAAAGTGG Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 13 16 1.00 ACGTcount: A:0.57, C:0.03, G:0.17, T:0.23 Consensus pattern (13 bp): AGAATTAGAAATC Found at i:21916 original size:38 final size:39 Alignment explanation
Indices: 21874--21979 Score: 164 Period size: 39 Copynumber: 2.8 Consensus size: 39 21864 TTTAATTAAC 21874 TAATTCCAAAAGAAGATTTTGGAAAATTAAAGTTT-AGA 1 TAATTCCAAAAGAAGATTTTGGAAAATTAAAGTTTAAGA * 21912 TAATTCCAAAAGAAGATTTTGGAAAAATAAAAGTTTAAGA 1 TAATTCCAAAAGAAGATTTTGG-AAAATTAAAGTTTAAGA * 21952 T-ATTCTAAAAGAAGATTTTGG-AAATTAA 1 TAATTCCAAAAGAAGATTTTGGAAAATTAA 21980 TTGATTAAAC Statistics Matches: 63, Mismatches: 3, Indels: 5 0.89 0.04 0.07 Matches are distributed among these distances: 37 6 0.10 38 22 0.35 39 31 0.49 40 4 0.06 ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31 Consensus pattern (39 bp): TAATTCCAAAAGAAGATTTTGGAAAATTAAAGTTTAAGA Found at i:23208 original size:25 final size:25 Alignment explanation
Indices: 23174--23229 Score: 78 Period size: 25 Copynumber: 2.2 Consensus size: 25 23164 GTTCGCGTTC * 23174 TTTGGGCTTGCAT-TTTGGACTTTAA 1 TTTGGACTTGCATCTTTGG-CTTTAA 23199 TTTGGACTTGCATCTTTGGCTTTAA 1 TTTGGACTTGCATCTTTGGCTTTAA * 23224 TCTGGA 1 TTTGGA 23230 TGGTTTGCAT Statistics Matches: 28, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 25 23 0.82 26 5 0.18 ACGTcount: A:0.16, C:0.14, G:0.23, T:0.46 Consensus pattern (25 bp): TTTGGACTTGCATCTTTGGCTTTAA Found at i:26630 original size:28 final size:28 Alignment explanation
Indices: 26598--26686 Score: 83 Period size: 28 Copynumber: 3.2 Consensus size: 28 26588 AGTTTAATTT * 26598 AGAGTAATTAAACTAAAGAGTAAAAGAA 1 AGAGTAATTAAACTAAAGAGTAAAACAA * ** ** *** 26626 AGAGTAA--AAAGTAATTAGTTTAATTT 1 AGAGTAATTAAACTAAAGAGTAAAACAA 26652 AGAGTAATTAAACTAAAGAGTAAAACAA 1 AGAGTAATTAAACTAAAGAGTAAAACAA 26680 AGAGTAA 1 AGAGTAA 26687 GCAGTAATTA Statistics Matches: 43, Mismatches: 16, Indels: 4 0.68 0.25 0.06 Matches are distributed among these distances: 26 18 0.42 28 25 0.58 ACGTcount: A:0.56, C:0.03, G:0.17, T:0.24 Consensus pattern (28 bp): AGAGTAATTAAACTAAAGAGTAAAACAA Found at i:26645 original size:54 final size:54 Alignment explanation
Indices: 26559--27331 Score: 1041 Period size: 54 Copynumber: 14.7 Consensus size: 54 26549 TTAAACTAAA * * * 26559 AAAGAGTAAAAG-AAGAGTAAACAGTAAGTAGTTTAATT-TAGAGTAATTAAACT 1 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTCT-GGGTAATTAAACT ** * 26612 AAAGAGTAAAAGAAAGAGTAAAAAGTAATTAGTTTAATT-TAGAGTAATTAAACT 1 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTCT-GGGTAATTAAACT * * * 26666 AAAGAGTAAAACAAAGAGTAAGCAGTAATTACTTTAATTATGGGTAATTAAACT 1 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTCTGGGTAATTAAACT * * * 26720 AAAGAGTAAAAGAAAGAGTAAACAGTAATTAGTTTAATTCAGAGTAATTAAACT 1 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTCTGGGTAATTAAACT * * 26774 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTTTGGGTAGTTAAAC- 1 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTCTGGGTAATTAAACT * 26827 ------T-----AAAGAGTAAGCAGTAATTAGTTTAATTATGGGTAATTAAACT 1 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTCTGGGTAATTAAACT * * * * 26870 AAGGAATAAAAGAAAGAGTAAGCAATAATCAGTTTAATTCTGGGTAATTAAACT 1 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTCTGGGTAATTAAACT * * 26924 AACGAGTAAAAGAAAGAGTAAGCAGTAATTCGTTTAATTCTGGGTAATTAAACT 1 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTCTGGGTAATTAAACT * * * * 26978 AAATAGTAAAAGAATGA-TAAGCAATAATTAGTTTAGTTCTGGGTAATTAAACT 1 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTCTGGGTAATTAAACT * * 27031 AAAGAGTAAAAGAAAGAGTAAGTAGTAATTAGTTTAATTCTGGGTAGTTAAACT 1 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTCTGGGTAATTAAACT * 27085 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTCG--T--TT-TGGGTAATTAAACT 1 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTCTGGGTAATTAAACT * * * 27134 AAAGAGTAAAAGAATGA-TAAGCAGTAATTAGTTTAGTTATGGGTAATTAAACT 1 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTCTGGGTAATTAAACT * * 27187 AAAGAGTAAAAGAAAGAGTAAGTAGTAATTAGTTTAATTCTGGGTAGTTAAACT 1 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTCTGGGTAATTAAACT * * * 27241 AAAGAGTAAAAGAAAAAGTAAACAGTAATTAGTTTAATTCTGAGTAATTAAACT 1 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTCTGGGTAATTAAACT * 27295 AAAGAGTAAAAGAAAGAGTAAGCAGCAATTAGTTTAA 1 AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAA 27332 CTCAAAATAA Statistics Matches: 641, Mismatches: 58, Indels: 41 0.87 0.08 0.06 Matches are distributed among these distances: 42 39 0.06 47 1 0.00 48 13 0.02 49 30 0.05 50 3 0.00 52 3 0.00 53 90 0.14 54 461 0.72 55 1 0.00 ACGTcount: A:0.47, C:0.05, G:0.19, T:0.28 Consensus pattern (54 bp): AAAGAGTAAAAGAAAGAGTAAGCAGTAATTAGTTTAATTCTGGGTAATTAAACT Found at i:26658 original size:26 final size:26 Alignment explanation
Indices: 26572--26658 Score: 66 Period size: 26 Copynumber: 3.3 Consensus size: 26 26562 GAGTAAAAGA * * 26572 AGAGTAAACAGTAAGTAGTTTAATTT 1 AGAGTAAAAAGTAAATAGTTTAATTT * * ** *** 26598 AGAGTAATTAAACTAAAGAGTAAAAGAA 1 AGAGTAA--AAAGTAAATAGTTTAATTT * 26626 AGAGTAAAAAGTAATTAGTTTAATTT 1 AGAGTAAAAAGTAAATAGTTTAATTT 26652 AGAGTAA 1 AGAGTAA 26659 TTAAACTAAA Statistics Matches: 42, Mismatches: 17, Indels: 4 0.67 0.27 0.06 Matches are distributed among these distances: 26 25 0.60 28 17 0.40 ACGTcount: A:0.51, C:0.02, G:0.18, T:0.29 Consensus pattern (26 bp): AGAGTAAAAAGTAAATAGTTTAATTT Found at i:26792 original size:28 final size:28 Alignment explanation
Indices: 26709--26794 Score: 77 Period size: 28 Copynumber: 3.1 Consensus size: 28 26699 TTAATTATGG 26709 GTAATTAAACTAAAGAGTAAAAGAAAGA 1 GTAATTAAACTAAAGAGTAAAAGAAAGA * * ** ** *** 26737 GTAA--ACAGTAATTAGTTTAATTCAGA 1 GTAATTAAACTAAAGAGTAAAAGAAAGA 26763 GTAATTAAACTAAAGAGTAAAAGAAAGA 1 GTAATTAAACTAAAGAGTAAAAGAAAGA 26791 GTAA 1 GTAA 26795 GCAGTAATTA Statistics Matches: 38, Mismatches: 18, Indels: 4 0.63 0.30 0.07 Matches are distributed among these distances: 26 17 0.45 28 21 0.55 ACGTcount: A:0.55, C:0.05, G:0.17, T:0.23 Consensus pattern (28 bp): GTAATTAAACTAAAGAGTAAAAGAAAGA Found at i:26833 original size:42 final size:42 Alignment explanation
Indices: 26786--26871 Score: 154 Period size: 42 Copynumber: 2.0 Consensus size: 42 26776 AGAGTAAAAG * * 26786 AAAGAGTAAGCAGTAATTAGTTTAATTTTGGGTAGTTAAACT 1 AAAGAGTAAGCAGTAATTAGTTTAATTATGGGTAATTAAACT 26828 AAAGAGTAAGCAGTAATTAGTTTAATTATGGGTAATTAAACT 1 AAAGAGTAAGCAGTAATTAGTTTAATTATGGGTAATTAAACT 26870 AA 1 AA 26872 GGAATAAAAG Statistics Matches: 42, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 42 42 1.00 ACGTcount: A:0.42, C:0.05, G:0.20, T:0.34 Consensus pattern (42 bp): AAAGAGTAAGCAGTAATTAGTTTAATTATGGGTAATTAAACT Found at i:27026 original size:161 final size:161 Alignment explanation
Indices: 26834--27330 Score: 797 Period size: 156 Copynumber: 3.1 Consensus size: 161 26824 AACTAAAGAG * * * * * 26834 TAAGCAGTAATTAGTTTAATTATGGGTAATTAAACTAAGGAATAAAAGAAAGAGTAAGCAATAAT 1 TAAGCAGTAATTAGTTTAGTTATGGGTAATTAAACTAAAGAGTAAAAGAAAGAGTAAGTAGTAAT * * * 26899 CAGTTTAATTCTGGGTAATTAAACTAACGAGTAAAAGAAAGAGTAAGCAGTAATTCGTTTAATTC 66 TAGTTTAATTCTGGGTAGTTAAACTAAAGAGTAAAAGAAAGAGTAAGCAGTAATTCGTTTAATTC * 26964 TGGGTAATTAAACTAAATAGTAAAAGAATGA 131 TGGGTAATTAAACTAAAGAGTAAAAGAATGA * * 26995 TAAGCAATAATTAGTTTAGTTCTGGGTAATTAAACTAAAGAGTAAAAGAAAGAGTAAGTAGTAAT 1 TAAGCAGTAATTAGTTTAGTTATGGGTAATTAAACTAAAGAGTAAAAGAAAGAGTAAGTAGTAAT 27060 TAGTTTAATTCTGGGTAGTTAAACTAAAGAGTAAAAGAAAGAGTAAGCAGTAATTCG--T--TT- 66 TAGTTTAATTCTGGGTAGTTAAACTAAAGAGTAAAAGAAAGAGTAAGCAGTAATTCGTTTAATTC 27120 TGGGTAATTAAACTAAAGAGTAAAAGAATGA 131 TGGGTAATTAAACTAAAGAGTAAAAGAATGA 27151 TAAGCAGTAATTAGTTTAGTTATGGGTAATTAAACTAAAGAGTAAAAGAAAGAGTAAGTAGTAAT 1 TAAGCAGTAATTAGTTTAGTTATGGGTAATTAAACTAAAGAGTAAAAGAAAGAGTAAGTAGTAAT * * * 27216 TAGTTTAATTCTGGGTAGTTAAACTAAAGAGTAAAAGAAAAAGTAAACAGTAATTAGTTTAATTC 66 TAGTTTAATTCTGGGTAGTTAAACTAAAGAGTAAAAGAAAGAGTAAGCAGTAATTCGTTTAATTC * * 27281 TGAGTAATTAAACTAAAGAGTAAAAGAAAGA 131 TGGGTAATTAAACTAAAGAGTAAAAGAATGA * 27312 GTAAGCAGCAATTAGTTTA 1 -TAAGCAGTAATTAGTTTA 27331 ACTCAAAATA Statistics Matches: 311, Mismatches: 19, Indels: 11 0.91 0.06 0.03 Matches are distributed among these distances: 156 147 0.47 157 2 0.01 158 1 0.00 159 1 0.00 160 2 0.01 161 141 0.45 162 17 0.05 ACGTcount: A:0.46, C:0.06, G:0.20, T:0.29 Consensus pattern (161 bp): TAAGCAGTAATTAGTTTAGTTATGGGTAATTAAACTAAAGAGTAAAAGAAAGAGTAAGTAGTAAT TAGTTTAATTCTGGGTAGTTAAACTAAAGAGTAAAAGAAAGAGTAAGCAGTAATTCGTTTAATTC TGGGTAATTAAACTAAAGAGTAAAAGAATGA Found at i:31649 original size:30 final size:29 Alignment explanation
Indices: 31606--31662 Score: 89 Period size: 30 Copynumber: 1.9 Consensus size: 29 31596 TTAGGATTAG 31606 TTATTTATGCTTTAATTTTCAA-TTTCCT 1 TTATTTATGCTTTAATTTTCAAGTTTCCT 31634 TTATCTTATGTCTTTAATTTTCAAGTTTC 1 TTAT-TTATG-CTTTAATTTTCAAGTTTC 31663 ACTAATAAAC Statistics Matches: 26, Mismatches: 0, Indels: 3 0.90 0.00 0.10 Matches are distributed among these distances: 28 4 0.15 29 5 0.19 30 13 0.50 31 4 0.15 ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60 Consensus pattern (29 bp): TTATTTATGCTTTAATTTTCAAGTTTCCT Found at i:42283 original size:19 final size:18 Alignment explanation
Indices: 42259--42294 Score: 54 Period size: 19 Copynumber: 1.9 Consensus size: 18 42249 TGAAGATTTA 42259 TTGAAGACAATTTGAAGAT 1 TTGAAGACAA-TTGAAGAT * 42278 TTGAAGACCATTGAAGA 1 TTGAAGACAATTGAAGA 42295 ATAATTTCAA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 7 0.44 19 9 0.56 ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28 Consensus pattern (18 bp): TTGAAGACAATTGAAGAT Found at i:44592 original size:15 final size:16 Alignment explanation
Indices: 44568--44604 Score: 58 Period size: 15 Copynumber: 2.4 Consensus size: 16 44558 AGAGGTTGAA * 44568 AGAAAGCAATTAAAC- 1 AGAAAACAATTAAACT 44583 AGAAAACAATTAAACT 1 AGAAAACAATTAAACT 44599 AGAAAA 1 AGAAAA 44605 AAAAAACAAA Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 15 14 0.70 16 6 0.30 ACGTcount: A:0.65, C:0.11, G:0.11, T:0.14 Consensus pattern (16 bp): AGAAAACAATTAAACT Found at i:50733 original size:22 final size:21 Alignment explanation
Indices: 50705--50745 Score: 64 Period size: 22 Copynumber: 1.9 Consensus size: 21 50695 AAGAAAATAG 50705 TTTTTTTATGACGCATAAACGA 1 TTTTTTTATGACGCA-AAACGA * 50727 TTTTTTTTTGACGCAAAAC 1 TTTTTTTATGACGCAAAAC 50746 TCAAAACTTT Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 21 4 0.22 22 14 0.78 ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44 Consensus pattern (21 bp): TTTTTTTATGACGCAAAACGA Found at i:50838 original size:51 final size:51 Alignment explanation
Indices: 50748--50854 Score: 128 Period size: 51 Copynumber: 2.1 Consensus size: 51 50738 CGCAAAACTC 50748 AAAACTTTTTTTTTTTCAAAAACGCAAACAAAA-AATTTTT-TATGACGCA 1 AAAACTTTTTTTTTTTCAAAAACGCAAACAAAATAATTTTTATATGACGCA ** * ** 50797 AAAACTTTATTTTTTTTTCAAAAACGCAAGACTCATTTTTTTTTATATGACGCA 1 AAAAC-TT-TTTTTTTTTCAAAAACGCAA-ACAAAATAATTTTTATATGACGCA 50851 AAAA 1 AAAA 50855 AACAAAACAA Statistics Matches: 48, Mismatches: 5, Indels: 5 0.83 0.09 0.09 Matches are distributed among these distances: 49 5 0.10 50 2 0.04 51 20 0.42 52 3 0.06 53 5 0.10 54 13 0.27 ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39 Consensus pattern (51 bp): AAAACTTTTTTTTTTTCAAAAACGCAAACAAAATAATTTTTATATGACGCA Found at i:51240 original size:15 final size:16 Alignment explanation
Indices: 51216--51255 Score: 55 Period size: 15 Copynumber: 2.6 Consensus size: 16 51206 AGAGGTTGAA * 51216 AGAAAGCAATTAAAC- 1 AGAAAACAATTAAACT * 51231 AGAAAACAATTAAGCT 1 AGAAAACAATTAAACT 51247 AGAAAACAA 1 AGAAAACAA 51256 AACAAAGCAA Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 15 13 0.59 16 9 0.41 ACGTcount: A:0.62, C:0.12, G:0.12, T:0.12 Consensus pattern (16 bp): AGAAAACAATTAAACT Found at i:55725 original size:11 final size:11 Alignment explanation
Indices: 55691--55738 Score: 52 Period size: 11 Copynumber: 4.7 Consensus size: 11 55681 TTGAACTAAT 55691 TCTTC-AATAG 1 TCTTCAAATAG 55701 TCTTC--A-AG 1 TCTTCAAATAG 55709 TCTTCAAATTA- 1 TCTTCAAA-TAG 55720 TCTTCAAATAG 1 TCTTCAAATAG 55731 TCTTCAAA 1 TCTTCAAA 55739 CACGAACTTC Statistics Matches: 33, Mismatches: 0, Indels: 9 0.79 0.00 0.21 Matches are distributed among these distances: 8 7 0.21 9 1 0.03 10 8 0.24 11 16 0.48 12 1 0.03 ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40 Consensus pattern (11 bp): TCTTCAAATAG Done.