Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: AWWV01009498.1 Corchorus capsularis cultivar CVL-1 contig09519, 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: 37777 ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32 Found at i:432 original size:24 final size:20 Alignment explanation
Indices: 386--425 Score: 62 Period size: 20 Copynumber: 1.9 Consensus size: 20 376 GTTTAGAAGC * 386 AATTAATTAAAAGCATCAAA 1 AATTAATTAAAAACATCAAA 406 AATTAATTAAAAACAATCAA 1 AATTAATTAAAAAC-ATCAA 426 GAGAAATGTG Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 20 13 0.72 21 5 0.28 ACGTcount: A:0.62, C:0.10, G:0.03, T:0.25 Consensus pattern (20 bp): AATTAATTAAAAACATCAAA Found at i:525 original size:73 final size:74 Alignment explanation
Indices: 428--571 Score: 218 Period size: 73 Copynumber: 2.0 Consensus size: 74 418 ACAATCAAGA * * * * 428 GAAATGTGTAGTTACGAAAAAGGGTAGAAGGAAAAGGAATGGGGGAAACTCATAGAGGGACTTTT 1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAAGAATAGGGGAAACTCATAGAGGGACTTTT 493 TAGTCATTC 66 TAGTCATTC ** * 502 GAAAAGTGTAATTACG-AAAAGGGTAGAAGGAAAAAGAATAGGGGATCCTCATAGAGGGGCTTTT 1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAAGAATAGGGGAAACTCATAGAGGGACTTTT 566 TAGTCA 66 TAGTCA 572 CCCGAAAAAT Statistics Matches: 63, Mismatches: 7, Indels: 1 0.89 0.10 0.01 Matches are distributed among these distances: 73 49 0.78 74 14 0.22 ACGTcount: A:0.39, C:0.08, G:0.31, T:0.22 Consensus pattern (74 bp): GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAAGAATAGGGGAAACTCATAGAGGGACTTTT TAGTCATTC Found at i:5357 original size:3 final size:3 Alignment explanation
Indices: 5349--5375 Score: 54 Period size: 3 Copynumber: 9.0 Consensus size: 3 5339 GACGCGCTTC 5349 CTT CTT CTT CTT CTT CTT CTT CTT CTT 1 CTT CTT CTT CTT CTT CTT CTT CTT CTT 5376 TTTTTTTTAA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 24 1.00 ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67 Consensus pattern (3 bp): CTT Found at i:8609 original size:10 final size:10 Alignment explanation
Indices: 8590--8619 Score: 51 Period size: 10 Copynumber: 3.0 Consensus size: 10 8580 AGATGAGGAC 8590 TCTAGAATTT 1 TCTAGAATTT * 8600 TCTGGAATTT 1 TCTAGAATTT 8610 TCTAGAATTT 1 TCTAGAATTT 8620 ATCAGCAACT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 10 18 1.00 ACGTcount: A:0.27, C:0.10, G:0.13, T:0.50 Consensus pattern (10 bp): TCTAGAATTT Found at i:21116 original size:22 final size:21 Alignment explanation
Indices: 21076--21213 Score: 84 Period size: 22 Copynumber: 6.3 Consensus size: 21 21066 TTTTCACTGG * 21076 AATTTTGATAATCATACTATGA 1 AATTTTG-TAATCACACTATGA * * 21098 AATGTTTGTAAGCACACTATAA 1 AAT-TTTGTAATCACACTATGA * 21120 AATTTTG-AAACATC-CATATGA 1 AATTTTGTAATCA-CAC-TATGA * 21141 AATGTTAGTAATCACACTGA-GA 1 AAT-TTTGTAATCACACT-ATGA * 21163 AATTTTAATAATCACACTATGA 1 AATTTT-GTAATCACACTATGA * * * * * 21185 CATTATGATAACCTCATTATGA 1 AATTTTG-TAATCACACTATGA 21207 AATTTTG 1 AATTTTG 21214 ATAAACCTTC Statistics Matches: 89, Mismatches: 17, Indels: 20 0.71 0.13 0.16 Matches are distributed among these distances: 20 5 0.06 21 15 0.17 22 59 0.66 23 10 0.11 ACGTcount: A:0.41, C:0.13, G:0.11, T:0.36 Consensus pattern (21 bp): AATTTTGTAATCACACTATGA Found at i:21144 original size:43 final size:44 Alignment explanation
Indices: 21076--21184 Score: 125 Period size: 43 Copynumber: 2.5 Consensus size: 44 21066 TTTTCACTGG * 21076 AATTTTGATAATCATACTATGAAATGTTTGTAAGCACACTATAA 1 AATTTTGATAATCATACTATGAAATGTTAGTAAGCACACTATAA * * * 21120 AATTTTGA-AA-CATCCATATGAAATGTTAGTAATCACACTGA-GA 1 AATTTTGATAATCATAC-TATGAAATGTTAGTAAGCACACT-ATAA * * 21163 AATTTTAATAATCACACTATGA 1 AATTTTGATAATCATACTATGA 21185 CATTATGATA Statistics Matches: 54, Mismatches: 7, Indels: 8 0.78 0.10 0.12 Matches are distributed among these distances: 42 4 0.07 43 31 0.57 44 16 0.30 45 3 0.06 ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34 Consensus pattern (44 bp): AATTTTGATAATCATACTATGAAATGTTAGTAAGCACACTATAA Found at i:21215 original size:22 final size:22 Alignment explanation
Indices: 21026--21217 Score: 69 Period size: 22 Copynumber: 8.8 Consensus size: 22 21016 GTATAAATTG * * 21026 TTATGAAATTTTGAAAACCTCG 1 TTATGAAATTTTGATAACCTCA * * 21048 CTATGAAATTTTGATAA-CT-T 1 TTATGAAATTTTGATAACCTCA * 21068 TTCACTGGAATTTTGATAA--TCA 1 TT-A-TGAAATTTTGATAACCTCA * * 21090 TACTATGAAATGTTTG-TAAGCACA 1 T--TATGAAAT-TTTGATAACCTCA * * * 21114 CTATAAAATTTTGA-AACATCCA 1 TTATGAAATTTTGATAACCT-CA * * * 21136 -TATGAAATGTT-AGTAATCACA 1 TTATGAAATTTTGA-TAACCTCA * * * * 21157 CTGA-GAAATTTTAATAATCACA 1 -TTATGAAATTTTGATAACCTCA * * * 21179 CTATGACATTATGATAACCTCA 1 TTATGAAATTTTGATAACCTCA 21201 TTATGAAATTTTGATAA 1 TTATGAAATTTTGATAA 21218 ACCTTCCCAT Statistics Matches: 124, Mismatches: 30, Indels: 32 0.67 0.16 0.17 Matches are distributed among these distances: 20 2 0.02 21 22 0.18 22 90 0.73 23 7 0.06 24 3 0.02 ACGTcount: A:0.39, C:0.13, G:0.11, T:0.36 Consensus pattern (22 bp): TTATGAAATTTTGATAACCTCA Found at i:21266 original size:22 final size:22 Alignment explanation
Indices: 21233--21280 Score: 71 Period size: 22 Copynumber: 2.2 Consensus size: 22 21223 CCCATTGACA 21233 AACCTCGCTATAAAATTTTAAT 1 AACCTCGCTATAAAATTTTAAT * 21255 AACCTC-CTTATAAAATTTTGAT 1 AACCTCGC-TATAAAATTTTAAT 21277 AACC 1 AACC 21281 ATAAACTTTG Statistics Matches: 24, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 21 1 0.04 22 23 0.96 ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35 Consensus pattern (22 bp): AACCTCGCTATAAAATTTTAAT Found at i:21684 original size:22 final size:23 Alignment explanation
Indices: 21637--21827 Score: 87 Period size: 22 Copynumber: 8.5 Consensus size: 23 21627 CCTCGTTATA * * * * 21637 AAATTTTGACAA-CTGCATTATT 1 AAATTTTGATAACCTACACTATG * * 21659 AAATTTTAATAACCT-CCCTATG 1 AAATTTTGATAACCTACACTATG 21681 AAATTTTGATAA-CTACACTATG 1 AAATTTTGATAACCTACACTATG * * * 21703 AAATTTTGATAACTTTC-CTATA 1 AAATTTTGATAACCTACACTATG * * * 21725 AAAATTTGATAATCTTATCTCTATG 1 AAATTTTGATAA-CCTA-CACTATG * * 21750 AAATGTTGATAA--TAACTCTATG 1 AAATTTTGATAACCT-ACACTATG * * 21772 AGATTTTGATTACCT-C-CT-TG 1 AAATTTTGATAACCTACACTATG * * * 21792 TCAAATTTCGATAAAC-ACACTATA 1 --AAATTTTGATAACCTACACTATG * 21816 AAAATTTGATAA 1 AAATTTTGATAA 21828 TCTTCTTATG Statistics Matches: 130, Mismatches: 25, Indels: 28 0.71 0.14 0.15 Matches are distributed among these distances: 20 2 0.02 21 4 0.03 22 97 0.75 23 10 0.08 24 3 0.02 25 14 0.11 ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39 Consensus pattern (23 bp): AAATTTTGATAACCTACACTATG Found at i:21734 original size:44 final size:44 Alignment explanation
Indices: 21624--21761 Score: 132 Period size: 44 Copynumber: 3.1 Consensus size: 44 21614 TTTTGAAATT ** * * * * * 21624 TAACCTCGTTATAAAATTTTGACAACTGCATTATTAAATTTTAA 1 TAACCTCCCTATAAAATTTTGATAACTACACTATGAAATTTTGA * 21668 TAACCTCCCTATGAAATTTTGATAACTACACTATGAAATTTTGA 1 TAACCTCCCTATAAAATTTTGATAACTACACTATGAAATTTTGA * * * * * 21712 TAACTTTCCTATAAAAATTTGATAATCTTATCTCTATGAAATGTTGA 1 TAACCTCCCTATAAAATTTTGATAA-C-TA-CACTATGAAATTTTGA 21759 TAA 1 TAA 21762 TAACTCTATG Statistics Matches: 77, Mismatches: 14, Indels: 3 0.82 0.15 0.03 Matches are distributed among these distances: 44 57 0.74 45 1 0.01 46 2 0.03 47 17 0.22 ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40 Consensus pattern (44 bp): TAACCTCCCTATAAAATTTTGATAACTACACTATGAAATTTTGA Found at i:21923 original size:22 final size:22 Alignment explanation
Indices: 21889--22216 Score: 196 Period size: 22 Copynumber: 14.9 Consensus size: 22 21879 CTAAACTTGG * * 21889 TAACCACATTATGAAATTTTGA 1 TAACTACACTATGAAATTTTGA 21911 TAACTACACTATGAAATTTTGA 1 TAACTACACTATGAAATTTTGA ** * * 21933 TAACCT-TGCTAT-AAAATTTCA 1 TAA-CTACACTATGAAATTTTGA * * * 21954 GTAACCTTC-CCATGAAATTTTGT 1 -TAA-CTACACTATGAAATTTTGA * * 21977 TAACCACACTATGAAATTCTGA 1 TAACTACACTATGAAATTTTGA * * 21999 TAATCT-CGCTATGAAATTCTGA 1 TAA-CTACACTATGAAATTTTGA * * * * 22021 TAACCATACTTTGAAATTTTAA 1 TAACTACACTATGAAATTTTGA * 22043 TAACCTTC-CTAAT-AAATTTT-A 1 TAA-CTACACT-ATGAAATTTTGA * * * 22064 GTAACGTTC-CTATGAATTTTTAA 1 -TAAC-TACACTATGAAATTTTGA 22087 TAAACTGATC-CTATGAAATTTTGA 1 T-AACT-A-CACTATGAAATTTTGA * * 22111 TAACCACTCTATGAAATTTTGA 1 TAACTACACTATGAAATTTTGA * * * 22133 TAACCTTCA-TATGAAATTGTGG 1 TAA-CTACACTATGAAATTTTGA * 22155 TAACCACACTATGAAATTTTGA 1 TAACTACACTATGAAATTTTGA 22177 TAACTACAC--TGAAATTTTGA 1 TAACTACACTATGAAATTTTGA * 22197 TAACCT-CCCTATGAAATTTT 1 TAA-CTACACTATGAAATTTT 22217 TCTAATCAGA Statistics Matches: 240, Mismatches: 44, Indels: 44 0.73 0.13 0.13 Matches are distributed among these distances: 20 16 0.07 21 20 0.08 22 170 0.71 23 20 0.08 24 14 0.06 ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37 Consensus pattern (22 bp): TAACTACACTATGAAATTTTGA Found at i:21950 original size:44 final size:44 Alignment explanation
Indices: 21889--22216 Score: 244 Period size: 44 Copynumber: 7.5 Consensus size: 44 21879 CTAAACTTGG * * 21889 TAACCACATTATGAAATTTTGATAA-CTACACTATGAAATTTTGA 1 TAACCATACTATGAAATTTTGATAACCTAC-CTATGAAATTTTGA * * * * * * * 21933 TAACCTTGCTAT-AAAATTTCAGTAACCTTCCCATGAAATTTTGT 1 TAACCATACTATGAAATTTTGA-TAACCTACCTATGAAATTTTGA * * * * 21977 TAACCACACTATGAAATTCTGATAATCT-CGCTATGAAATTCTGA 1 TAACCATACTATGAAATTTTGATAACCTAC-CTATGAAATTTTGA * * * 22021 TAACCATACTTTGAAATTTTAATAACCTTCCTAAT-AAATTTT-A 1 TAACCATACTATGAAATTTTGATAACCTACCT-ATGAAATTTTGA ** * * * * 22064 GTAACGTTCCTATGAATTTTTAATAAACTGATCCTATGAAATTTTGA 1 -TAACCATACTATGAAATTTTGATAACCT-A-CCTATGAAATTTTGA * * * * 22111 TAACCACT-CTATGAAATTTTGATAACCTTCATATGAAATTGTGG 1 TAACCA-TACTATGAAATTTTGATAACCTACCTATGAAATTTTGA * 22155 TAACCACACTATGAAATTTTGATAA-CTA-C-ACTGAAATTTTGA 1 TAACCATACTATGAAATTTTGATAACCTACCTA-TGAAATTTTGA * 22197 TAACC-TCCCTATGAAATTTT 1 TAACCAT-ACTATGAAATTTT 22217 TCTAATCAGA Statistics Matches: 221, Mismatches: 48, Indels: 32 0.73 0.16 0.11 Matches are distributed among these distances: 41 1 0.00 42 26 0.12 43 11 0.05 44 136 0.62 45 14 0.06 46 31 0.14 47 2 0.01 ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37 Consensus pattern (44 bp): TAACCATACTATGAAATTTTGATAACCTACCTATGAAATTTTGA Found at i:21975 original size:66 final size:66 Alignment explanation
Indices: 21898--22215 Score: 267 Period size: 66 Copynumber: 4.8 Consensus size: 66 21888 GTAACCACAT * 21898 TATGAAATTTTGATAACTACACTATGAAATTTTGATAACCTTGCTATAAAATTTCAGTAACCTTC 1 TATGAAATTTTGATAACTACACTATGAAATTTTGATAACCTTGCTATGAAATTTCAGTAACCTTC 21963 C 66 C * * * * * * * * 21964 CATGAAATTTTGTTAACCACACTATGAAATTCTGATAATCTCGCTATGAAA-TTCTGATAACCAT 1 TATGAAATTTTGATAACTACACTATGAAATTTTGATAACCTTGCTATGAAATTTCAG-TAACCTT * 22028 AC 65 CC * * * * * * * * * 22030 TTTGAAATTTTAATAACCTTC-CTAAT-AAATTTT-AGTAACGTTCCTATGAATTTTTAATAAAC 1 TATGAAATTTTGATAA-CTACACT-ATGAAATTTTGA-TAACCTTGCTATGAAATTTCAGTAACC 22092 TGATCC 63 T--TCC * * * 22098 TATGAAATTTTGATAACCACTCTATGAAATTTTGATAACCTT-CATATGAAATTGT-GGTAACC- 1 TATGAAATTTTGATAACTACACTATGAAATTTTGATAACCTTGC-TATGAAATT-TCAGTAACCT * 22160 ACAC 64 TC-C ** 22164 TATGAAATTTTGATAACTACAC--TGAAATTTTGATAACCTCCCTATGAAATTT 1 TATGAAATTTTGATAACTACACTATGAAATTTTGATAACCTTGCTATGAAATTT 22216 TTCTAATCAG Statistics Matches: 197, Mismatches: 41, Indels: 31 0.73 0.15 0.12 Matches are distributed among these distances: 63 1 0.01 64 26 0.13 65 7 0.04 66 107 0.54 67 11 0.06 68 43 0.22 69 2 0.01 ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37 Consensus pattern (66 bp): TATGAAATTTTGATAACTACACTATGAAATTTTGATAACCTTGCTATGAAATTTCAGTAACCTTC C Found at i:22683 original size:33 final size:34 Alignment explanation
Indices: 22622--22708 Score: 90 Period size: 33 Copynumber: 2.6 Consensus size: 34 22612 CTTTTACACT * ** * 22622 GAGCCTCCCCACTAGAACGG-TTCAGCCACGGCG 1 GAGCCTCCCCACTGGGGCGGCTTCAGCCACGGCA 22655 GAGCCTCCCCACTGGGGCGGCTTC-GCCACGGCA 1 GAGCCTCCCCACTGGGGCGGCTTCAGCCACGGCA * ** 22688 G-GCCGCCCCGGTGGGGCGGCT 1 GAGCCTCCCCACTGGGGCGGCT 22709 AGACCAATTT Statistics Matches: 46, Mismatches: 7, Indels: 3 0.82 0.12 0.05 Matches are distributed among these distances: 32 17 0.37 33 26 0.57 34 3 0.07 ACGTcount: A:0.13, C:0.40, G:0.36, T:0.11 Consensus pattern (34 bp): GAGCCTCCCCACTGGGGCGGCTTCAGCCACGGCA Found at i:24427 original size:2 final size:2 Alignment explanation
Indices: 24415--24450 Score: 58 Period size: 2 Copynumber: 19.0 Consensus size: 2 24405 ATGCTCTTGC 24415 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 24451 ATAATAACAC Statistics Matches: 32, Mismatches: 0, Indels: 4 0.89 0.00 0.11 Matches are distributed among these distances: 1 2 0.06 2 30 0.94 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (2 bp): TA Found at i:26993 original size:2 final size:2 Alignment explanation
Indices: 26988--27015 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 26978 ATCGATCTAC 26988 AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT 27016 GCATATAGAT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:35169 original size:3 final size:3 Alignment explanation
Indices: 35163--35190 Score: 56 Period size: 3 Copynumber: 9.3 Consensus size: 3 35153 AATAATAATA 35163 ATT ATT ATT ATT ATT ATT ATT ATT ATT A 1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A 35191 CTACTAGCAC Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 25 1.00 ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64 Consensus pattern (3 bp): ATT Found at i:35705 original size:2 final size:2 Alignment explanation
Indices: 35698--35730 Score: 50 Period size: 2 Copynumber: 16.5 Consensus size: 2 35688 GTATTATCTT 35698 TA TA TA TA TA TA TA TA TA TA TA T- TA TA CTA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T 35731 CTTATATCTT Statistics Matches: 29, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 1 1 0.03 2 26 0.90 3 2 0.07 ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:35735 original size:12 final size:11 Alignment explanation
Indices: 35697--35737 Score: 55 Period size: 12 Copynumber: 3.5 Consensus size: 11 35687 AGTATTATCT 35697 TTATATATATA 1 TTATATATATA 35708 TATATATATATA 1 T-TATATATATA * 35720 TTATACTATATC 1 TTATA-TATATA 35732 TTATAT 1 TTATAT 35738 CTTATATATC Statistics Matches: 27, Mismatches: 1, Indels: 4 0.84 0.03 0.12 Matches are distributed among these distances: 11 6 0.22 12 21 0.78 ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54 Consensus pattern (11 bp): TTATATATATA Found at i:37433 original size:2 final size:2 Alignment explanation
Indices: 37426--37450 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 37416 AGATTTAGCC 37426 AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT A 37451 AAGTCCTCAA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Done.