Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: AWUE01018504.1 Corchorus olitorius cultivar O-4 contig18537, 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: 65663 ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31 Found at i:7099 original size:34 final size:34 Alignment explanation
Indices: 7056--7136 Score: 162 Period size: 34 Copynumber: 2.4 Consensus size: 34 7046 CCCAGTGGGA 7056 ATGTCATTCCCAGGAATGTGATATTGTTGGATAT 1 ATGTCATTCCCAGGAATGTGATATTGTTGGATAT 7090 ATGTCATTCCCAGGAATGTGATATTGTTGGATAT 1 ATGTCATTCCCAGGAATGTGATATTGTTGGATAT 7124 ATGTCATTCCCAG 1 ATGTCATTCCCAG 7137 TAATCTCACA Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 34 47 1.00 ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37 Consensus pattern (34 bp): ATGTCATTCCCAGGAATGTGATATTGTTGGATAT Found at i:8249 original size:15 final size:15 Alignment explanation
Indices: 8229--8257 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 8219 GGACCAGTAA 8229 GGGACGGGATGAGAC 1 GGGACGGGATGAGAC 8244 GGGACGGGATGAGA 1 GGGACGGGATGAGA 8258 GGTCCTTTTA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.28, C:0.10, G:0.55, T:0.07 Consensus pattern (15 bp): GGGACGGGATGAGAC Found at i:9269 original size:7 final size:7 Alignment explanation
Indices: 9257--9282 Score: 52 Period size: 7 Copynumber: 3.7 Consensus size: 7 9247 GAGGAGGAAT 9257 TAATGAA 1 TAATGAA 9264 TAATGAA 1 TAATGAA 9271 TAATGAA 1 TAATGAA 9278 TAATG 1 TAATG 9283 GGTTAAATAC Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 19 1.00 ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31 Consensus pattern (7 bp): TAATGAA Found at i:11457 original size:6 final size:6 Alignment explanation
Indices: 11446--11472 Score: 54 Period size: 6 Copynumber: 4.5 Consensus size: 6 11436 GCATGGGAAT 11446 TGGAGA TGGAGA TGGAGA TGGAGA TGG 1 TGGAGA TGGAGA TGGAGA TGGAGA TGG 11473 GGGGAATGGT Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 21 1.00 ACGTcount: A:0.30, C:0.00, G:0.52, T:0.19 Consensus pattern (6 bp): TGGAGA Found at i:18943 original size:17 final size:16 Alignment explanation
Indices: 18919--18959 Score: 73 Period size: 17 Copynumber: 2.5 Consensus size: 16 18909 ATTTGCCATA 18919 TATATATATATATAAT 1 TATATATATATATAAT 18935 TATTATATATATATAAT 1 TA-TATATATATATAAT 18952 TATATATA 1 TATATATA 18960 GAAAAAATAG Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 16 8 0.33 17 16 0.67 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (16 bp): TATATATATATATAAT Found at i:18975 original size:2 final size:2 Alignment explanation
Indices: 18916--18959 Score: 53 Period size: 2 Copynumber: 24.5 Consensus size: 2 18906 ATAATTTGCC 18916 AT AT AT AT AT AT AT AT A- AT -T AT -T AT AT AT AT AT A- AT -T 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 18953 AT AT AT A 1 AT AT AT A 18960 GAAAAAATAG Statistics Matches: 37, Mismatches: 0, Indels: 10 0.79 0.00 0.21 Matches are distributed among these distances: 1 5 0.14 2 32 0.86 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:24562 original size:32 final size:32 Alignment explanation
Indices: 24523--24614 Score: 121 Period size: 32 Copynumber: 2.8 Consensus size: 32 24513 ATAGAATAGC * 24523 GGCGTTTATTACCAAAAACGCCACTATATAAT 1 GGCGTTTATTACCAAAAACGCCACTATATAAG * * * 24555 GGTGTTTATTACCAAAAACGCCTCTATATAGG 1 GGCGTTTATTACCAAAAACGCCACTATATAAG * * 24587 GGCGTTTATTACAGAAAAACGCCGCTAT 1 GGCGTTTATTAC-CAAAAACGCCACTAT 24615 TGTATGGGTT Statistics Matches: 52, Mismatches: 7, Indels: 1 0.87 0.12 0.02 Matches are distributed among these distances: 32 39 0.75 33 13 0.25 ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28 Consensus pattern (32 bp): GGCGTTTATTACCAAAAACGCCACTATATAAG Found at i:30472 original size:19 final size:19 Alignment explanation
Indices: 30450--30508 Score: 75 Period size: 19 Copynumber: 3.2 Consensus size: 19 30440 CAAAAAGAAG 30450 CAGTTCATACCAAAAAACA 1 CAGTTCATACCAAAAAACA ** 30469 CAGTAGATACCAAAAAA-A 1 CAGTTCATACCAAAAAACA * * 30487 TAATTCATACCAAAAAACA 1 CAGTTCATACCAAAAAACA 30506 CAG 1 CAG 30509 GTCCCAAACA Statistics Matches: 31, Mismatches: 8, Indels: 2 0.76 0.20 0.05 Matches are distributed among these distances: 18 14 0.45 19 17 0.55 ACGTcount: A:0.56, C:0.22, G:0.07, T:0.15 Consensus pattern (19 bp): CAGTTCATACCAAAAAACA Found at i:30478 original size:38 final size:37 Alignment explanation
Indices: 30425--30508 Score: 109 Period size: 37 Copynumber: 2.3 Consensus size: 37 30415 GGGAGATTCC * * 30425 AAAAA-ACAGTGGATA-CAAAAAGAAGCAGTTCATACCA 1 AAAAACACAGTAGATACCAAAAA-AA-CAATTCATACCA * 30462 AAAAACACAGTAGATACCAAAAAAATAATTCATACCA 1 AAAAACACAGTAGATACCAAAAAAACAATTCATACCA 30499 AAAAACACAG 1 AAAAACACAG 30509 GTCCCAAACA Statistics Matches: 42, Mismatches: 3, Indels: 4 0.86 0.06 0.08 Matches are distributed among these distances: 37 25 0.60 38 11 0.26 39 6 0.14 ACGTcount: A:0.58, C:0.18, G:0.11, T:0.13 Consensus pattern (37 bp): AAAAACACAGTAGATACCAAAAAAACAATTCATACCA Found at i:46015 original size:29 final size:27 Alignment explanation
Indices: 45982--46049 Score: 82 Period size: 32 Copynumber: 2.3 Consensus size: 27 45972 TCGTTTTGAA * 45982 AAAAAAAAATTGTTTTGTGTTTTTGCGTCG 1 AAAAAAAAATAGTTTTGTG---TTGCGTCG 46012 AAAAAAAAAAATAGTTTTGTGTTGCGTCG 1 --AAAAAAAAATAGTTTTGTGTTGCGTCG 46041 AAAAAAAAA 1 AAAAAAAAA 46050 AAAAGGTTTT Statistics Matches: 35, Mismatches: 1, Indels: 5 0.85 0.02 0.12 Matches are distributed among these distances: 27 9 0.26 29 8 0.23 32 18 0.51 ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32 Consensus pattern (27 bp): AAAAAAAAATAGTTTTGTGTTGCGTCG Found at i:46050 original size:29 final size:29 Alignment explanation
Indices: 45979--46081 Score: 111 Period size: 29 Copynumber: 3.4 Consensus size: 29 45969 GCGTCGTTTT * 45979 GAAAAAAAAAAATTGTTTTGTGTTTTTGCGTC 1 GAAAAAAAAAAATAGTTTTGTG---TTGCGTC 46011 GAAAAAAAAAAATAGTTTTGTGTTGCGTC 1 GAAAAAAAAAAATAGTTTTGTGTTGCGTC * * * 46040 GAAAAAAAAAAAAAGGTTT-TGCTGCGTC 1 GAAAAAAAAAAATAGTTTTGTGTTGCGTC 46068 -ATAAATAAAAAAAT 1 GA-AAA-AAAAAAAT 46082 TCTTGTTCCT Statistics Matches: 64, Mismatches: 5, Indels: 7 0.84 0.07 0.09 Matches are distributed among these distances: 27 1 0.02 28 11 0.17 29 31 0.48 32 21 0.33 ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30 Consensus pattern (29 bp): GAAAAAAAAAAATAGTTTTGTGTTGCGTC Found at i:53061 original size:76 final size:76 Alignment explanation
Indices: 52964--53159 Score: 311 Period size: 76 Copynumber: 2.6 Consensus size: 76 52954 GAATCTCATT * * 52964 AGAATTTTTGTTTAAGAAAACCTGCTTAGGTCCCTGCTTAGAATCTTGTTTGTTTAACCTGCTTA 1 AGAATTTTCGTTTAAGCAAACCTGCTTAGGTCCCTGCTTAGAATCTTGTTTGTTTAACCTGCTTA * * 53029 GGTCCTTGTTC 66 GATCCATGTTC * 53040 AGAATTTTCGTTTAAGCAAACCTGCTTAGGTCCCTGCTTAGGATCTTGTTTGTTTAACCTGCTTA 1 AGAATTTTCGTTTAAGCAAACCTGCTTAGGTCCCTGCTTAGAATCTTGTTTGTTTAACCTGCTTA * 53105 GATCCATGTTT 66 GATCCATGTTC * * * 53116 AGAATTTTCGTTTATGCAAACCTGCTTAGGTCCTTGTTTAGAAT 1 AGAATTTTCGTTTAAGCAAACCTGCTTAGGTCCCTGCTTAGAAT 53160 TTCCGTTTAA Statistics Matches: 110, Mismatches: 10, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 76 110 1.00 ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41 Consensus pattern (76 bp): AGAATTTTCGTTTAAGCAAACCTGCTTAGGTCCCTGCTTAGAATCTTGTTTGTTTAACCTGCTTA GATCCATGTTC Found at i:53070 original size:39 final size:38 Alignment explanation
Indices: 52962--53186 Score: 210 Period size: 39 Copynumber: 5.9 Consensus size: 38 52952 TAGAATCTCA * * 52962 TTAGAATTTTTGTTTAAGAAAACCTGCTTAGGTCCCTG 1 TTAGAATTTTCGTTTAAGCAAACCTGCTTAGGTCCCTG * ** * 53000 CTTAGAATCTT-GTTT--GTTTAACCTGCTTAGGTCCTTG 1 -TTAGAATTTTCGTTTAAG-CAAACCTGCTTAGGTCCCTG 53037 TTCAGAATTTTCGTTTAAGCAAACCTGCTTAGGTCCCTG 1 TT-AGAATTTTCGTTTAAGCAAACCTGCTTAGGTCCCTG * * ** * * 53076 CTTAGGATCTT-GTTT--GTTTAACCTGCTTAGATCCATG 1 -TTAGAATTTTCGTTTAAG-CAAACCTGCTTAGGTCCCTG * * 53113 TTTAGAATTTTCGTTTATGCAAACCTGCTTAGGTCCTTG 1 -TTAGAATTTTCGTTTAAGCAAACCTGCTTAGGTCCCTG * 53152 TTTAGAATTTCCGTTTAAGCAAACCTGCTTAGGTC 1 -TTAGAATTTTCGTTTAAGCAAACCTGCTTAGGTC 53187 TCCGTTCCGT Statistics Matches: 153, Mismatches: 23, Indels: 20 0.78 0.12 0.10 Matches are distributed among these distances: 36 4 0.03 37 48 0.31 38 16 0.10 39 81 0.53 40 4 0.03 ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41 Consensus pattern (38 bp): TTAGAATTTTCGTTTAAGCAAACCTGCTTAGGTCCCTG Found at i:53371 original size:147 final size:146 Alignment explanation
Indices: 53095--53373 Score: 323 Period size: 147 Copynumber: 1.9 Consensus size: 146 53085 TTGTTTGTTT * * 53095 AACCTGCTTAGATCCATGTTTAGAATTTTCGTTTATGCAAACCTGCTTAGGTCCTTGTTTAGAAT 1 AACCTGCTTAGATCCATGTTTAGAAGTTTCGTTTATGCAAACCCGCTTAGGTCCTTGTTTAGAAT * * * * * 53160 TTCCGTTTAAGCAAACCTGCTTAGGTCTCCGTTCCGTCTAAGTAAACCTGTTTAGGACTTCTTCT 66 TCCCGCTTAAGCAAACCTGCTTAGGTCTCAGTTCCGTCTAAGTAAACCTGCTTAGGA-TCCTTCT 53225 TTGAGTTCAGTCAAGTA 130 TTGAGTTCAGTCAAGTA * * * * 53242 AACCTGCTTAGGT-CTTCGTTTAGAAGTTTCGTTTAAT-CAAACCCGCTTAGGTTCTTGTTTAGT 1 AACCTGCTTAGATCCAT-GTTTAGAAGTTTCGTTT-ATGCAAACCCGCTTAGGTCCTTGTTTAGA ** * * * * 53305 ATTCCCGCTTAAGTGAACCTGTTTAGGTCTATGAGTTTCGT-TCAATTAAACCTGCTTAGG-TCC 64 ATTCCCGCTTAAGCAAACCTGCTTAGGTC--TCAGTTCCGTCT-AAGTAAACCTGCTTAGGATCC 53368 TTCTTT 126 TTCTTT 53374 AGAATCTCAT Statistics Matches: 110, Mismatches: 17, Indels: 10 0.80 0.12 0.07 Matches are distributed among these distances: 146 2 0.02 147 83 0.75 148 3 0.03 149 22 0.20 ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39 Consensus pattern (146 bp): AACCTGCTTAGATCCATGTTTAGAAGTTTCGTTTATGCAAACCCGCTTAGGTCCTTGTTTAGAAT TCCCGCTTAAGCAAACCTGCTTAGGTCTCAGTTCCGTCTAAGTAAACCTGCTTAGGATCCTTCTT TGAGTTCAGTCAAGTA Found at i:55479 original size:19 final size:18 Alignment explanation
Indices: 55435--55524 Score: 67 Period size: 19 Copynumber: 4.8 Consensus size: 18 55425 GGGGGGGGAG ** 55435 ATACC-AAAAAACAGTGG 1 ATACCAAAAAAACAGTTC * 55452 ATA-AAAAAAGAAGCAGTTC 1 ATACCAAAAA-AA-CAGTTC ** 55471 ATACCAAAAAACACAGTAG 1 ATACCAAAAAA-ACAGTTC * 55490 ATACCAAAAAAAACAATTC 1 ATACC-AAAAAAACAGTTC 55509 ATACCAAAAAACACAG 1 ATACCAAAAAA-ACAG 55525 ATTCCAAACA Statistics Matches: 56, Mismatches: 10, Indels: 12 0.72 0.13 0.15 Matches are distributed among these distances: 17 7 0.12 18 8 0.14 19 29 0.52 20 12 0.21 ACGTcount: A:0.59, C:0.19, G:0.10, T:0.12 Consensus pattern (18 bp): ATACCAAAAAAACAGTTC Found at i:55510 original size:38 final size:38 Alignment explanation
Indices: 55435--55524 Score: 116 Period size: 38 Copynumber: 2.4 Consensus size: 38 55425 GGGGGGGGAG * * 55435 ATACC-AAAAA-ACAGTGGATAAAAAAAGAAGCAGTTC 1 ATACCAAAAAACACAGTAGATAAAAAAAGAAGCAATTC 55471 ATACCAAAAAACACAGTAGATACCAAAAAA-AA-CAATTC 1 ATACCAAAAAACACAGTAGATA--AAAAAAGAAGCAATTC 55509 ATACCAAAAAACACAG 1 ATACCAAAAAACACAG 55525 ATTCCAAACA Statistics Matches: 48, Mismatches: 2, Indels: 6 0.86 0.04 0.11 Matches are distributed among these distances: 36 5 0.10 37 5 0.10 38 30 0.62 39 2 0.04 40 6 0.12 ACGTcount: A:0.59, C:0.19, G:0.10, T:0.12 Consensus pattern (38 bp): ATACCAAAAAACACAGTAGATAAAAAAAGAAGCAATTC Found at i:59270 original size:35 final size:35 Alignment explanation
Indices: 59182--59320 Score: 131 Period size: 36 Copynumber: 3.8 Consensus size: 35 59172 AAAATGCTTT * * 59182 TGATGGAAACTTTCCCACTTTGAAAACTAA-AA-C 1 TGATGGGAACTTTCCCAATTTGAAAACTAAGAACC ** 59215 TGAAAATGACGAGAACTTTCCCTAAACTGAAAACTAA-AACC 1 TG---ATG--G-GAACTTTCCC-AATTTGAAAACTAAGAACC * * 59256 TGATGGGAACTTTCCCAATTTGAAAATTTAAGAACT 1 TGATGGGAACTTTCCCAATTTGAAAA-CTAAGAACC 59292 TGATGGGAACTTTCCCAATTTGAAAACTA 1 TGATGGGAACTTTCCCAATTTGAAAACTA 59321 TGAAGGAAAT Statistics Matches: 87, Mismatches: 9, Indels: 18 0.76 0.08 0.16 Matches are distributed among these distances: 33 2 0.02 34 8 0.09 35 15 0.17 36 33 0.38 38 4 0.05 39 9 0.10 40 13 0.15 41 3 0.03 ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27 Consensus pattern (35 bp): TGATGGGAACTTTCCCAATTTGAAAACTAAGAACC Found at i:60365 original size:22 final size:22 Alignment explanation
Indices: 60323--60365 Score: 52 Period size: 22 Copynumber: 2.0 Consensus size: 22 60313 TTTAATCTAA * 60323 TCTTAATTCCTTAAATTTTATC 1 TCTTAATTCCTTAAATATTATC * 60345 TCTTATTTCC-TAAATAATTAT 1 TCTTAATTCCTTAAAT-ATTAT 60366 TTAACAAAAG Statistics Matches: 18, Mismatches: 2, Indels: 2 0.82 0.09 0.09 Matches are distributed among these distances: 21 5 0.28 22 13 0.72 ACGTcount: A:0.30, C:0.16, G:0.00, T:0.53 Consensus pattern (22 bp): TCTTAATTCCTTAAATATTATC Found at i:60634 original size:20 final size:21 Alignment explanation
Indices: 60611--60657 Score: 55 Period size: 20 Copynumber: 2.3 Consensus size: 21 60601 TAATAATGCT 60611 AAATTAACCCAAA-T-AAATC 1 AAATTAACCCAAATTGAAATC * 60630 GAAATT-ACCTAAATTGAAATC 1 -AAATTAACCCAAATTGAAATC 60651 AAATTAA 1 AAATTAA 60658 AAGCTAACAT Statistics Matches: 23, Mismatches: 1, Indels: 5 0.79 0.03 0.17 Matches are distributed among these distances: 19 6 0.26 20 11 0.48 21 6 0.26 ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26 Consensus pattern (21 bp): AAATTAACCCAAATTGAAATC Found at i:61882 original size:30 final size:30 Alignment explanation
Indices: 61848--61908 Score: 86 Period size: 30 Copynumber: 2.0 Consensus size: 30 61838 CTGTCTGTTA * 61848 TTGCTTATGAGGCTCTCTGATGACATGTAT 1 TTGCTTATGAGGATCTCTGATGACATGTAT * * * 61878 TTGCTTATGTGGATCTTTGATGGCATGTAT 1 TTGCTTATGAGGATCTCTGATGACATGTAT 61908 T 1 T 61909 CCCGATGTGG Statistics Matches: 27, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 30 27 1.00 ACGTcount: A:0.18, C:0.13, G:0.25, T:0.44 Consensus pattern (30 bp): TTGCTTATGAGGATCTCTGATGACATGTAT Found at i:63141 original size:28 final size:28 Alignment explanation
Indices: 63101--63158 Score: 116 Period size: 28 Copynumber: 2.1 Consensus size: 28 63091 AAGCGCGAAT 63101 AACAAATTTTAAAAGGATATGTAACCAA 1 AACAAATTTTAAAAGGATATGTAACCAA 63129 AACAAATTTTAAAAGGATATGTAACCAA 1 AACAAATTTTAAAAGGATATGTAACCAA 63157 AA 1 AA 63159 ATGGATGTCT Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 30 1.00 ACGTcount: A:0.55, C:0.10, G:0.10, T:0.24 Consensus pattern (28 bp): AACAAATTTTAAAAGGATATGTAACCAA Found at i:64111 original size:64 final size:61 Alignment explanation
Indices: 64053--64171 Score: 175 Period size: 64 Copynumber: 1.9 Consensus size: 61 64043 TGAATGTTTT * * * 64053 GAAAACTTGATGAGAACTTTTCCTAGATTGAAAACCTTTGAAAAAAACTTGAATTGAATACTTC 1 GAAAACTGGATGAGAACTTTCCCAAGATTGAAAA-CTTT--AAAAAACTTGAATTGAATACTTC * 64117 GAAAACTGGATGAGATCTTTCCCAAGATTGAAAACTTTAAAAAACTTGAATTGAA 1 GAAAACTGGATGAGAACTTTCCCAAGATTGAAAACTTTAAAAAACTTGAATTGAA 64172 ATTCTTTTTG Statistics Matches: 51, Mismatches: 4, Indels: 3 0.88 0.07 0.05 Matches are distributed among these distances: 61 17 0.33 63 4 0.08 64 30 0.59 ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29 Consensus pattern (61 bp): GAAAACTGGATGAGAACTTTCCCAAGATTGAAAACTTTAAAAAACTTGAATTGAATACTTC Found at i:65012 original size:24 final size:24 Alignment explanation
Indices: 64993--65040 Score: 87 Period size: 24 Copynumber: 2.0 Consensus size: 24 64983 TAATTAAATT * 64993 TTGAAAGCCCAAACAGATTAAGAA 1 TTGAAAGCCCAAACAAATTAAGAA 65017 TTGAAAGCCCAAACAAATTAAGAA 1 TTGAAAGCCCAAACAAATTAAGAA 65041 ATCCAAATAA Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 24 23 1.00 ACGTcount: A:0.52, C:0.17, G:0.15, T:0.17 Consensus pattern (24 bp): TTGAAAGCCCAAACAAATTAAGAA Done.