Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020082.1 Corchorus olitorius cultivar O-4 contig20115, 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: 53783
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:1396 original size:15 final size:15

Alignment explanation

Indices: 1376--1409 Score: 59 Period size: 15 Copynumber: 2.3 Consensus size: 15 1366 CATGGTAAAT * 1376 TTTTTTCTAATTATA 1 TTTTTTCTAACTATA 1391 TTTTTTCTAACTATA 1 TTTTTTCTAACTATA 1406 TTTT 1 TTTT 1410 ATATAGTATA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68 Consensus pattern (15 bp): TTTTTTCTAACTATA Found at i:8246 original size:6 final size:6 Alignment explanation

Indices: 8235--8268 Score: 52 Period size: 6 Copynumber: 5.8 Consensus size: 6 8225 TCGGATATTT * 8235 TCGGGC TCGGGC TCGGG- TCGGGT TCGGGC TCGGG 1 TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGG 8269 TTTGATTTCG Statistics Matches: 26, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 5 5 0.19 6 21 0.81 ACGTcount: A:0.00, C:0.26, G:0.53, T:0.21 Consensus pattern (6 bp): TCGGGC Found at i:8261 original size:17 final size:17 Alignment explanation

Indices: 8235--8269 Score: 61 Period size: 17 Copynumber: 2.1 Consensus size: 17 8225 TCGGATATTT 8235 TCGGGCTCGGGCTCGGG 1 TCGGGCTCGGGCTCGGG * 8252 TCGGGTTCGGGCTCGGG 1 TCGGGCTCGGGCTCGGG 8269 T 1 T 8270 TTGATTTCGA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 17 1.00 ACGTcount: A:0.00, C:0.26, G:0.51, T:0.23 Consensus pattern (17 bp): TCGGGCTCGGGCTCGGG Found at i:8746 original size:31 final size:31 Alignment explanation

Indices: 8711--8782 Score: 76 Period size: 31 Copynumber: 2.3 Consensus size: 31 8701 TAAATTATTG * 8711 CAAATTAAAACAAATTAAA-CATTAAATTAAA 1 CAAATTAAAA-AAATGAAAGCATTAAATTAAA * * * 8742 CAAA-TAATTAAAATGAAAGCCTTAAATTTAA 1 CAAATTAA-AAAAATGAAAGCATTAAATTAAA 8773 CAAATTAAAA 1 CAAATTAAAA 8783 GATGATAGTG Statistics Matches: 33, Mismatches: 5, Indels: 6 0.75 0.11 0.14 Matches are distributed among these distances: 30 10 0.30 31 20 0.61 32 3 0.09 ACGTcount: A:0.61, C:0.10, G:0.03, T:0.26 Consensus pattern (31 bp): CAAATTAAAAAAATGAAAGCATTAAATTAAA Found at i:8878 original size:26 final size:27 Alignment explanation

Indices: 8848--8914 Score: 82 Period size: 26 Copynumber: 2.5 Consensus size: 27 8838 TTTCTTAATT ** 8848 GGCATTTTGGTCATTTTTATACT-AGG 1 GGCATTTTGGTCATTTGCATACTCAGG * * 8874 GGCATTCTGGTCATTTGCATATTCAGG 1 GGCATTTTGGTCATTTGCATACTCAGG * 8901 CGCATTTTGGTCAT 1 GGCATTTTGGTCAT 8915 ATTAAGTCCA Statistics Matches: 34, Mismatches: 6, Indels: 1 0.83 0.15 0.02 Matches are distributed among these distances: 26 19 0.56 27 15 0.44 ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42 Consensus pattern (27 bp): GGCATTTTGGTCATTTGCATACTCAGG Found at i:10943 original size:22 final size:22 Alignment explanation

Indices: 10915--10983 Score: 138 Period size: 22 Copynumber: 3.1 Consensus size: 22 10905 GGACTGAAGA 10915 CTCAGGAGACAGGCAATTCAAG 1 CTCAGGAGACAGGCAATTCAAG 10937 CTCAGGAGACAGGCAATTCAAG 1 CTCAGGAGACAGGCAATTCAAG 10959 CTCAGGAGACAGGCAATTCAAG 1 CTCAGGAGACAGGCAATTCAAG 10981 CTC 1 CTC 10984 TCTGGCTCTC Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 47 1.00 ACGTcount: A:0.35, C:0.25, G:0.26, T:0.14 Consensus pattern (22 bp): CTCAGGAGACAGGCAATTCAAG Found at i:11659 original size:21 final size:21 Alignment explanation

Indices: 11610--11651 Score: 57 Period size: 21 Copynumber: 2.0 Consensus size: 21 11600 TAAGATGTTT * * 11610 TCAATTTTTTTTTTTAATTTCA 1 TCAA-TTTCTTTTTTAATTGCA 11632 TCAATTTCTTTTTTAATTGC 1 TCAATTTCTTTTTTAATTGC 11652 TTCGATTTGG Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 21 14 0.78 22 4 0.22 ACGTcount: A:0.21, C:0.12, G:0.02, T:0.64 Consensus pattern (21 bp): TCAATTTCTTTTTTAATTGCA Found at i:18463 original size:18 final size:19 Alignment explanation

Indices: 18417--18465 Score: 98 Period size: 19 Copynumber: 2.6 Consensus size: 19 18407 AACAAAATGA 18417 TTTTCAAAAAGAGTCATGG 1 TTTTCAAAAAGAGTCATGG 18436 TTTTCAAAAAGAGTCATGG 1 TTTTCAAAAAGAGTCATGG 18455 TTTTCAAAAAG 1 TTTTCAAAAAG 18466 TTTTTGATAA Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 30 1.00 ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33 Consensus pattern (19 bp): TTTTCAAAAAGAGTCATGG Found at i:18777 original size:7 final size:7 Alignment explanation

Indices: 18765--18796 Score: 55 Period size: 7 Copynumber: 4.4 Consensus size: 7 18755 CTCCATCAAG 18765 AAATTCA 1 AAATTCA 18772 AAATTCA 1 AAATTCA 18779 AAATTACA 1 AAATT-CA 18787 AAATTCA 1 AAATTCA 18794 AAA 1 AAA 18797 AAAAAAAAAC Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 7 17 0.71 8 7 0.29 ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25 Consensus pattern (7 bp): AAATTCA Found at i:18790 original size:15 final size:14 Alignment explanation

Indices: 18765--18796 Score: 55 Period size: 15 Copynumber: 2.2 Consensus size: 14 18755 CTCCATCAAG 18765 AAATTCAAAATTCA 1 AAATTCAAAATTCA 18779 AAATTACAAAATTCA 1 AAATT-CAAAATTCA 18794 AAA 1 AAA 18797 AAAAAAAAAC Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 5 0.29 15 12 0.71 ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25 Consensus pattern (14 bp): AAATTCAAAATTCA Found at i:19527 original size:49 final size:50 Alignment explanation

Indices: 19468--19589 Score: 138 Period size: 51 Copynumber: 2.4 Consensus size: 50 19458 GGATTGCATT * * * * 19468 CCAAGGTCAAAATTTGCTTTT-ATAATAAGATTGCATTCTATTTGTGAGT 1 CCAAGATCAAAATTTGCTTTTCAAAATAAGATTGCATTCCATTTGTGAGA * * * * 19517 GCAAGATCAAAACTCGCTTTTTCAAAATAAGATTGCATTCCGTTTGTGAGA 1 CCAAGATCAAAATTTGC-TTTTCAAAATAAGATTGCATTCCATTTGTGAGA * * 19568 CCAAGACCAAAGTTTGCTTTTC 1 CCAAGATCAAAATTTGCTTTTC 19590 GAAGGGCATT Statistics Matches: 58, Mismatches: 13, Indels: 3 0.78 0.18 0.04 Matches are distributed among these distances: 49 13 0.22 50 9 0.16 51 36 0.62 ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35 Consensus pattern (50 bp): CCAAGATCAAAATTTGCTTTTCAAAATAAGATTGCATTCCATTTGTGAGA Found at i:20600 original size:69 final size:69 Alignment explanation

Indices: 20517--21245 Score: 1109 Period size: 69 Copynumber: 10.6 Consensus size: 69 20507 CGAGTCAATT * * * 20517 AGCAACATAGGCTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA 1 AGCAGCATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA 20582 TCCA 66 TCCA * * * 20586 AGCAGCAGGGGCTTTTCCAAAAGCCAAACTCGTTTCCATATGAGTCAGTTCAAGCCTTGGTTCCA 1 AGCAGCATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA 20651 TCCA 66 TCCA * * * 20655 AGCAGCATGTGCTTTTCCATAAGCCAAACTCGTTTCCATACGATTCAGTTCAAGCCTTGGTTCCA 1 AGCAGCATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA 20720 TCCA 66 TCCA * * 20724 AGCAGCAGGGGCTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA 1 AGCAGCATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA 20789 TCCA 66 TCCA * * * * * * 20793 AACAGCATAGGCATTTCCATAAGCCACACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCA 1 AGCAGCATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA 20858 TCCA 66 TCCA * * * * 20862 AGCAGCAGGGGCTTTTCCACAAGTCAAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTACA 1 AGCAGCATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA 20927 TCCA 66 TCCA * * * 20931 AGCAGCAGGGGCTTTTCCAAAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA 1 AGCAGCATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA 20996 TCCA 66 TCCA * * * * * * 21000 AGCAGCATAGGCTTTTCTACAAGCCACATTCATTTCCATACGAGCCAGTTCAAGCCTTGGTTCCA 1 AGCAGCATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA 21065 TCCA 66 TCCA * * 21069 AGCAGCATGTGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA 1 AGCAGCATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA 21134 TCCA 66 TCCA * * 21138 AGCAGCATGGGCTTTTCCACAAGCCTAACTCGTTGCCATACGAGTCAGTTCAAGCCTTGGTTCCA 1 AGCAGCATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA 21203 TCCA 66 TCCA * * * 21207 AGCCA-CATAGGCTTTTCCACAAGCCACATTCGTTTCCAT 1 AG-CAGCATGGGCTTTTCCACAAGCCAAACTCGTTTCCAT 21246 TCGGTGCATT Statistics Matches: 596, Mismatches: 63, Indels: 2 0.90 0.10 0.00 Matches are distributed among these distances: 69 594 1.00 70 2 0.00 ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27 Consensus pattern (69 bp): AGCAGCATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCA TCCA Found at i:21678 original size:26 final size:27 Alignment explanation

Indices: 21648--21714 Score: 82 Period size: 26 Copynumber: 2.5 Consensus size: 27 21638 TTTCATAATT ** 21648 GGCATTTTGGTCATTTTTATACT-AGG 1 GGCATTTTGGTCATTTGCATACTCAGG * * 21674 GGCATTCTGGTCATTTGCATATTCAGG 1 GGCATTTTGGTCATTTGCATACTCAGG * 21701 GGCATTTGGGTCAT 1 GGCATTTTGGTCAT 21715 ATTAAGTCCA Statistics Matches: 34, Mismatches: 6, Indels: 1 0.83 0.15 0.02 Matches are distributed among these distances: 26 19 0.56 27 15 0.44 ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40 Consensus pattern (27 bp): GGCATTTTGGTCATTTGCATACTCAGG Found at i:22779 original size:44 final size:43 Alignment explanation

Indices: 22671--22840 Score: 265 Period size: 42 Copynumber: 4.0 Consensus size: 43 22661 ACTTTATTTT * 22671 AAAAACTTTGATGGGATCTTTCCTCTAAATTGAAAAGTTTG--AA 1 AAAAAC-TTGATGGGATCTTTCC-CTAAATTGAAAACTTTGAAAA * * 22714 ATAAACTTGATGGGATATTTCCCTAAATTGAAAACTTTGAAAAA 1 AAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTG-AAAA 22758 AAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAA 1 AAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAA 22801 AAAAA-TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAA 1 AAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTGAA 22841 GGAAATTCTT Statistics Matches: 119, Mismatches: 5, Indels: 7 0.91 0.04 0.05 Matches are distributed among these distances: 41 16 0.13 42 50 0.42 43 14 0.12 44 39 0.33 ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32 Consensus pattern (43 bp): AAAAACTTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAA Found at i:22810 original size:86 final size:87 Alignment explanation

Indices: 22671--22840 Score: 281 Period size: 86 Copynumber: 2.0 Consensus size: 87 22661 ACTTTATTTT * * * 22671 AAAAACTTTGATGGGATCTTTCCTCTAAATTGAAAAGTTTGAAATAAACTTGATGGGATATTTCC 1 AAAAACTTTGATGGGATCTTTCCTCTAAATTGAAAACTTTGAAAAAAAATTGATGGGATATTTCC 22736 CTAAATTGAAAACTTTGAAAAA 66 CTAAATTGAAAACTTTGAAAAA * 22758 AAAAAC-TTGATGGGATCTTTCC-CTAAATTGAAAACTTTGAAAAAAAAATTGATGGGATCTTTC 1 AAAAACTTTGATGGGATCTTTCCTCTAAATTGAAAACTTTG-AAAAAAAATTGATGGGATATTTC 22821 CCTAAATTGAAAACTTTGAA 65 CCTAAATTGAAAACTTTGAA 22841 GGAAATTCTT Statistics Matches: 78, Mismatches: 4, Indels: 3 0.92 0.05 0.04 Matches are distributed among these distances: 85 16 0.21 86 56 0.72 87 6 0.08 ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32 Consensus pattern (87 bp): AAAAACTTTGATGGGATCTTTCCTCTAAATTGAAAACTTTGAAAAAAAATTGATGGGATATTTCC CTAAATTGAAAACTTTGAAAAA Found at i:29379 original size:13 final size:13 Alignment explanation

Indices: 29361--29387 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 29351 GTACCAAAGC 29361 ACATGGCATCAAG 1 ACATGGCATCAAG 29374 ACATGGCATCAAG 1 ACATGGCATCAAG 29387 A 1 A 29388 GCAATGGTTA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15 Consensus pattern (13 bp): ACATGGCATCAAG Found at i:32298 original size:18 final size:20 Alignment explanation

Indices: 32267--32303 Score: 51 Period size: 18 Copynumber: 1.9 Consensus size: 20 32257 TAGAGATAGA 32267 AAAAGATCAAAAAA-AAAAG 1 AAAAGATCAAAAAATAAAAG * 32286 AAAA-ATCAGAAAATAAAA 1 AAAAGATCAAAAAATAAAA 32304 AGAGGCAATA Statistics Matches: 16, Mismatches: 1, Indels: 2 0.84 0.05 0.11 Matches are distributed among these distances: 18 8 0.50 19 8 0.50 ACGTcount: A:0.78, C:0.05, G:0.08, T:0.08 Consensus pattern (20 bp): AAAAGATCAAAAAATAAAAG Found at i:33242 original size:2 final size:2 Alignment explanation

Indices: 33229--33260 Score: 55 Period size: 2 Copynumber: 16.0 Consensus size: 2 33219 TGCTTTAAGT * 33229 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 33261 GTTAGTAGTT Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50 Consensus pattern (2 bp): TA Found at i:36877 original size:12 final size:12 Alignment explanation

Indices: 36860--36885 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 36850 TTTAGATCTA 36860 TTCTTCTAGTTT 1 TTCTTCTAGTTT 36872 TTCTTCTAGTTT 1 TTCTTCTAGTTT 36884 TT 1 TT 36886 AGGCAAGGGT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69 Consensus pattern (12 bp): TTCTTCTAGTTT Found at i:43138 original size:22 final size:21 Alignment explanation

Indices: 43113--43158 Score: 56 Period size: 22 Copynumber: 2.1 Consensus size: 21 43103 CACCACCAAA 43113 CCACAACCGGCCATTCAACGAG 1 CCACAACCGGCCA-TCAACGAG * * * 43135 CCACCACTGGCCATCAACGTG 1 CCACAACCGGCCATCAACGAG 43156 CCA 1 CCA 43159 TTTCCGGCCA Statistics Matches: 21, Mismatches: 3, Indels: 1 0.84 0.12 0.04 Matches are distributed among these distances: 21 10 0.48 22 11 0.52 ACGTcount: A:0.28, C:0.43, G:0.17, T:0.11 Consensus pattern (21 bp): CCACAACCGGCCATCAACGAG Found at i:44143 original size:18 final size:18 Alignment explanation

Indices: 44120--44156 Score: 56 Period size: 18 Copynumber: 2.1 Consensus size: 18 44110 AAAGGGTAGT * 44120 TAAAAAAAATTGTTTTCA 1 TAAAAAAAAGTGTTTTCA * 44138 TAAAAAGAAGTGTTTTCA 1 TAAAAAAAAGTGTTTTCA 44156 T 1 T 44157 GCAAGAGGAG Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38 Consensus pattern (18 bp): TAAAAAAAAGTGTTTTCA Found at i:45719 original size:12 final size:12 Alignment explanation

Indices: 45702--45727 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 45692 TTTAGATCTA 45702 TTCTTCTAGTTT 1 TTCTTCTAGTTT 45714 TTCTTCTAGTTT 1 TTCTTCTAGTTT 45726 TT 1 TT 45728 AGGCAAGGGT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69 Consensus pattern (12 bp): TTCTTCTAGTTT Found at i:47071 original size:16 final size:17 Alignment explanation

Indices: 47043--47074 Score: 57 Period size: 16 Copynumber: 1.9 Consensus size: 17 47033 GTTTCTGGGT 47043 TAACACGGTTACACGAA 1 TAACACGGTTACACGAA 47060 TAACAC-GTTACACGA 1 TAACACGGTTACACGA 47075 CACGTTAGAC Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 9 0.60 17 6 0.40 ACGTcount: A:0.41, C:0.25, G:0.16, T:0.19 Consensus pattern (17 bp): TAACACGGTTACACGAA Found at i:47857 original size:4 final size:4 Alignment explanation

Indices: 47829--47887 Score: 77 Period size: 4 Copynumber: 15.2 Consensus size: 4 47819 CACGTTTTCG * * * 47829 TGTA TGTA --TA TGCA TGCA TGCA TGTA TGTA TGTA TGTA TGTA TGTA 1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA 47875 TGTA TGTA TGTA T 1 TGTA TGTA TGTA T 47888 TAAAGACATT Statistics Matches: 51, Mismatches: 2, Indels: 4 0.89 0.04 0.07 Matches are distributed among these distances: 2 2 0.04 4 49 0.96 ACGTcount: A:0.25, C:0.05, G:0.24, T:0.46 Consensus pattern (4 bp): TGTA Done.