Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021396.1 Corchorus olitorius cultivar O-4 contig21429, 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: 67745
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33


Found at i:8759 original size:2 final size:2

Alignment explanation

Indices: 8752--8778 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 8742 AGGAAGGGTG 8752 AT 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 AT A 8779 ATTAATCCTA Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:12073 original size:72 final size:73 Alignment explanation

Indices: 11956--12100 Score: 231 Period size: 72 Copynumber: 2.0 Consensus size: 73 11946 TGGTAACTGG * * 11956 GAGAGATGAAGTATGTAGATTAAATGATGGTTGAAACAAAGAGTTGTA-AAAAAAAATAATGATA 1 GAGAGATGAAGTAGGTAGATTAAATGATGGTGGAAACAAAGAGTTGTACAAAAAAAATAATGATA 12020 AGGAAAAA 66 AGGAAAAA * * 12028 GAGAGATGCAGTAGGTAGATTAAATGATGGTGGAAACTAAA-AGTTGTACAAATAAAATAATGAT 1 GAGAGATGAAGTAGGTAGATTAAATGATGGTGGAAAC-AAAGAGTTGTACAAAAAAAATAATGAT 12092 AAGGAAAAA 65 AAGGAAAAA 12101 AAAAGTAGGA Statistics Matches: 67, Mismatches: 4, Indels: 3 0.91 0.05 0.04 Matches are distributed among these distances: 72 41 0.61 73 26 0.39 ACGTcount: A:0.51, C:0.03, G:0.24, T:0.22 Consensus pattern (73 bp): GAGAGATGAAGTAGGTAGATTAAATGATGGTGGAAACAAAGAGTTGTACAAAAAAAATAATGATA AGGAAAAA Found at i:13912 original size:2 final size:2 Alignment explanation

Indices: 13905--13942 Score: 76 Period size: 2 Copynumber: 19.0 Consensus size: 2 13895 GTATGGGAAG 13905 AT AT AT AT AT 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 AT AT AT AT AT 13943 TGTTGACATA Statistics Matches: 36, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 36 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:14535 original size:31 final size:31 Alignment explanation

Indices: 14497--14560 Score: 110 Period size: 31 Copynumber: 2.1 Consensus size: 31 14487 AATCACATGA 14497 TATTTTTCGAAATTTAGAATATAATTTGCGT 1 TATTTTTCGAAATTTAGAATATAATTTGCGT * * 14528 TATTTTTCGAAATTTAGAATATGATTTGTGT 1 TATTTTTCGAAATTTAGAATATAATTTGCGT 14559 TA 1 TA 14561 CAATTGTGGA Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 31 31 1.00 ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50 Consensus pattern (31 bp): TATTTTTCGAAATTTAGAATATAATTTGCGT Found at i:16078 original size:2 final size:2 Alignment explanation

Indices: 16071--16117 Score: 94 Period size: 2 Copynumber: 23.5 Consensus size: 2 16061 GGAGATTTAA 16071 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 16113 AG AG A 1 AG AG A 16118 ATGCGAGGAA Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 45 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:17129 original size:42 final size:43 Alignment explanation

Indices: 17078--17171 Score: 147 Period size: 45 Copynumber: 2.2 Consensus size: 43 17068 AGTACATTAC * 17078 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG 1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG 17119 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG 1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG 17164 CTAATATT 1 CTAATATT 17172 AATTGTTGTT Statistics Matches: 48, Mismatches: 1, Indels: 4 0.91 0.02 0.08 Matches are distributed among these distances: 41 4 0.08 42 6 0.12 45 38 0.79 ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34 Consensus pattern (43 bp): CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG Found at i:24084 original size:16 final size:16 Alignment explanation

Indices: 24038--24084 Score: 58 Period size: 16 Copynumber: 2.9 Consensus size: 16 24028 TCTGAGTTCT * * 24038 AAACCCGAAAAACCCA 1 AAACCCGAATAACCTA * 24054 AAACCCGAATGACCTA 1 AAACCCGAATAACCTA * 24070 AAACCCGAGTAACCT 1 AAACCCGAATAACCT 24085 GAGGATAAAA Statistics Matches: 26, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 16 26 1.00 ACGTcount: A:0.47, C:0.34, G:0.11, T:0.09 Consensus pattern (16 bp): AAACCCGAATAACCTA Found at i:30560 original size:21 final size:21 Alignment explanation

Indices: 30536--30602 Score: 57 Period size: 21 Copynumber: 3.2 Consensus size: 21 30526 AATTCTCTGT 30536 AAATTAAGAAATACTCAACTC 1 AAATTAAGAAATACTCAACTC * * ** * 30557 AAATCATAGAAA-ATTC-TTTGT 1 AAATTA-AGAAATACTCAACT-C 30578 AAATTAAGAAATACTCAACTC 1 AAATTAAGAAATACTCAACTC 30599 AAAT 1 AAAT 30603 CCTAATCCTT Statistics Matches: 32, Mismatches: 10, Indels: 8 0.64 0.20 0.16 Matches are distributed among these distances: 20 6 0.19 21 20 0.62 22 6 0.19 ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28 Consensus pattern (21 bp): AAATTAAGAAATACTCAACTC Found at i:30741 original size:56 final size:57 Alignment explanation

Indices: 30669--30782 Score: 203 Period size: 57 Copynumber: 2.0 Consensus size: 57 30659 TTTATTTTGT * * 30669 AGAATAATTAAGTAGAGATA-GGGGGATATGATTTATTATAACATTTATTGTGTGAA 1 AGAATAATTAAGTAGAGAAAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA 30725 AGAATAATTAAGTAGAGAAAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA 1 AGAATAATTAAGTAGAGAAAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA 30782 A 1 A 30783 TAAAACAGAT Statistics Matches: 55, Mismatches: 2, Indels: 1 0.95 0.03 0.02 Matches are distributed among these distances: 56 19 0.35 57 36 0.65 ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33 Consensus pattern (57 bp): AGAATAATTAAGTAGAGAAAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA Found at i:32235 original size:2 final size:2 Alignment explanation

Indices: 32228--32273 Score: 83 Period size: 2 Copynumber: 23.0 Consensus size: 2 32218 ACTTTGGCCT * 32228 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 32270 TA TA 1 TA TA 32274 CAAGCAAGCC Statistics Matches: 42, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48 Consensus pattern (2 bp): TA Found at i:32939 original size:2 final size:2 Alignment explanation

Indices: 32932--32973 Score: 84 Period size: 2 Copynumber: 21.0 Consensus size: 2 32922 GTCATGATGG 32932 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT 32974 TATGAGCCTT Statistics Matches: 40, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 40 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:33097 original size:43 final size:43 Alignment explanation

Indices: 33050--33294 Score: 340 Period size: 43 Copynumber: 5.8 Consensus size: 43 33040 GTAAGGAGAA 33050 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG 1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG * * * 33093 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG--ATATAG 1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG * 33134 ATGCCTCTATGTTATATATGTGTTTGAGGACTTTGTAATAGAG 1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG * * 33177 ATGCC-CATGTGTTATATATGTGTTTGGGGAC-TTG-AATATAG 1 ATGCCTC-TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG * * 33218 ATGTCTCTGTGTTACATATGTGTTTGAGGACTTTGTAATAGAG 1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG * * 33261 GTGCC-CATGTGTTATATATGTGTTTGGGGACTTT 1 ATGCCTC-TGTGTTATATATGTGTTTGAGGACTTT 33295 TGGTTATTGG Statistics Matches: 177, Mismatches: 18, Indels: 14 0.85 0.09 0.07 Matches are distributed among these distances: 41 69 0.39 42 9 0.05 43 99 0.56 ACGTcount: A:0.22, C:0.10, G:0.26, T:0.42 Consensus pattern (43 bp): ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG Found at i:33162 original size:84 final size:85 Alignment explanation

Indices: 33050--33294 Score: 431 Period size: 84 Copynumber: 2.9 Consensus size: 85 33040 GTAAGGAGAA * 33050 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG 1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCATGTGTTATATATGTG 33115 TTTGGGGACTTTG-ATATAG 66 TTTGGGGACTTTGAATATAG * 33134 ATGCCTCTATGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCATGTGTTATATATGTG 1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCATGTGTTATATATGTG 33199 TTTGGGGAC-TTGAATATAG 66 TTTGGGGACTTTGAATATAG * * * 33218 ATGTCTCTGTGTTACATATGTGTTTGAGGACTTTGTAATAGAGGTGCCCATGTGTTATATATGTG 1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCATGTGTTATATATGTG 33283 TTTGGGGACTTT 66 TTTGGGGACTTT 33295 TGGTTATTGG Statistics Matches: 153, Mismatches: 6, Indels: 3 0.94 0.04 0.02 Matches are distributed among these distances: 83 3 0.02 84 148 0.97 85 2 0.01 ACGTcount: A:0.22, C:0.10, G:0.26, T:0.42 Consensus pattern (85 bp): ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCATGTGTTATATATGTG TTTGGGGACTTTGAATATAG Found at i:34836 original size:45 final size:42 Alignment explanation

Indices: 34772--34865 Score: 127 Period size: 45 Copynumber: 2.2 Consensus size: 42 34762 AACAACAATT * * * 34772 AATATTAGTTTTATTTTGATGAATTATCTAGAGATAAAGGAGTAG 1 AATATTAGATTTATTTTGATAAATTACCTAGAGAT---GGAGTAG 34817 AATATTAGATTTATTTTGATAAATTACCTAGAGATGGAGTAG 1 AATATTAGATTTATTTTGATAAATTACCTAGAGATGGAGTAG 34859 AAT-TTAG 1 AATATTAG 34866 GTAATGCACT Statistics Matches: 46, Mismatches: 3, Indels: 4 0.87 0.06 0.08 Matches are distributed among these distances: 41 4 0.09 42 10 0.22 45 32 0.70 ACGTcount: A:0.38, C:0.03, G:0.19, T:0.39 Consensus pattern (42 bp): AATATTAGATTTATTTTGATAAATTACCTAGAGATGGAGTAG Found at i:35484 original size:29 final size:29 Alignment explanation

Indices: 35451--35549 Score: 78 Period size: 29 Copynumber: 3.3 Consensus size: 29 35441 GAGTATTGCT 35451 CAAATAAGGGATCGATCTTTTAATTTGGC 1 CAAATAAGGGATCGATCTTTTAATTTGGC * * * * ** 35480 CAAATAAGGG-CCTAACATTATCAAAAAT-GC 1 CAAATAAGGGATCGATC-TT-T-TAATTTGGC 35510 TCAAATAAGGGTAT-GATCTTTTAATTTGGC 1 -CAAATAAGGG-ATCGATCTTTTAATTTGGC 35540 CAAATAAGGG 1 CAAATAAGGG 35550 CCTAAAGTTA Statistics Matches: 51, Mismatches: 12, Indels: 14 0.66 0.16 0.18 Matches are distributed among these distances: 28 3 0.06 29 25 0.49 30 6 0.12 31 15 0.29 32 2 0.04 ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29 Consensus pattern (29 bp): CAAATAAGGGATCGATCTTTTAATTTGGC Found at i:35518 original size:31 final size:30 Alignment explanation

Indices: 35480--35583 Score: 81 Period size: 31 Copynumber: 3.4 Consensus size: 30 35470 TTAATTTGGC 35480 CAAATAAGGGCCTAACATTATCAAAAATGCT 1 CAAATAAGGGCCTAA-ATTATCAAAAATGCT * ** ** 35511 CAAATAAGGG--TATGATCT-TTTAATTTGGC- 1 CAAATAAGGGCCTA-AAT-TATCAAAAAT-GCT * 35540 CAAATAAGGGCCTAAAGTTATCGAAAATGCT 1 CAAATAAGGGCCTAAA-TTATCAAAAATGCT 35571 CAAATAAGGGCCT 1 CAAATAAGGGCCT 35584 GGCGTAGAAA Statistics Matches: 55, Mismatches: 10, Indels: 16 0.68 0.12 0.20 Matches are distributed among these distances: 29 18 0.33 30 7 0.13 31 30 0.55 ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26 Consensus pattern (30 bp): CAAATAAGGGCCTAAATTATCAAAAATGCT Found at i:35520 original size:60 final size:60 Alignment explanation

Indices: 35447--35580 Score: 227 Period size: 60 Copynumber: 2.2 Consensus size: 60 35437 CTATGAGTAT 35447 TGCTCAAATAAGGG-ATCGATCTTTTAATTTGGCCAAATAAGGGCCTAACA-TTATCAAAAA 1 TGCTCAAATAAGGGTAT-GATCTTTTAATTTGGCCAAATAAGGGCCTAA-AGTTATCAAAAA * 35507 TGCTCAAATAAGGGTATGATCTTTTAATTTGGCCAAATAAGGGCCTAAAGTTATCGAAAA 1 TGCTCAAATAAGGGTATGATCTTTTAATTTGGCCAAATAAGGGCCTAAAGTTATCAAAAA 35567 TGCTCAAATAAGGG 1 TGCTCAAATAAGGG 35581 CCTGGCGTAG Statistics Matches: 71, Mismatches: 1, Indels: 4 0.93 0.01 0.05 Matches are distributed among these distances: 59 1 0.01 60 68 0.96 61 2 0.03 ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28 Consensus pattern (60 bp): TGCTCAAATAAGGGTATGATCTTTTAATTTGGCCAAATAAGGGCCTAAAGTTATCAAAAA Found at i:35699 original size:60 final size:61 Alignment explanation

Indices: 35624--35784 Score: 229 Period size: 60 Copynumber: 2.7 Consensus size: 61 35614 TGACGCCAGG * 35624 CCCTTATTTGAGCATTTTCGATAACGTTAAG-CCCTTGTTTGGCCAAATTAAAAGATCGGA 1 CCCTTATTTGAGCATTTTCGATAACGTTAAGACCCTTATTTGGCCAAATTAAAAGATCGGA * * * * 35684 TCCTTATTTGAGCATTTACGATAACGTT-AGACCCTTATTTGGCTAAATTAAAAGATCGGG 1 CCCTTATTTGAGCATTTTCGATAACGTTAAGACCCTTATTTGGCCAAATTAAAAGATCGGA ** * 35744 CCCTTATTTGAATATTTTCGATAATGTT-AGACCCTTATTTG 1 CCCTTATTTGAGCATTTTCGATAACGTTAAGACCCTTATTTG 35785 AGCAATTAGC Statistics Matches: 90, Mismatches: 10, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 59 2 0.02 60 88 0.98 ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37 Consensus pattern (61 bp): CCCTTATTTGAGCATTTTCGATAACGTTAAGACCCTTATTTGGCCAAATTAAAAGATCGGA Found at i:39747 original size:7 final size:7 Alignment explanation

Indices: 39735--39775 Score: 82 Period size: 7 Copynumber: 5.9 Consensus size: 7 39725 CATTTTTTAG 39735 GCGATTT 1 GCGATTT 39742 GCGATTT 1 GCGATTT 39749 GCGATTT 1 GCGATTT 39756 GCGATTT 1 GCGATTT 39763 GCGATTT 1 GCGATTT 39770 GCGATT 1 GCGATT 39776 GCGCCCATAC Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 34 1.00 ACGTcount: A:0.15, C:0.15, G:0.29, T:0.41 Consensus pattern (7 bp): GCGATTT Found at i:46298 original size:21 final size:20 Alignment explanation

Indices: 46264--46302 Score: 53 Period size: 21 Copynumber: 1.9 Consensus size: 20 46254 ATTGTATATA 46264 TAATCTATCTATGTTGATAAG 1 TAATCTATCTATG-TGATAAG 46285 TAATCATATC-ATGTGATA 1 TAATC-TATCTATGTGATA 46303 CATATGATCT Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 20 5 0.29 21 8 0.47 22 4 0.24 ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41 Consensus pattern (20 bp): TAATCTATCTATGTGATAAG Found at i:52978 original size:2 final size:2 Alignment explanation

Indices: 52971--53005 Score: 70 Period size: 2 Copynumber: 17.5 Consensus size: 2 52961 CTATTCTTAA 52971 AT AT AT AT AT 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 AT AT AT AT AT A 53006 AATGTAATTG Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 33 1.00 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:56411 original size:53 final size:53 Alignment explanation

Indices: 56346--56533 Score: 277 Period size: 53 Copynumber: 3.5 Consensus size: 53 56336 AGTAATATTC * * 56346 GCAAGTGGCTCTGGCAAGACGGCCCAAGAAAATATCCCATAAATTGGCAGTTT 1 GCAAGTGACTCTGGCAAGACGGCCCAAGAAAATACCCCATAAATTGGCAGTTT * * * 56399 GCAAGTGACTCTGGTAAGACGGTCCAAGAAAATACCCCATAAATTGGCAGCTT 1 GCAAGTGACTCTGGCAAGACGGCCCAAGAAAATACCCCATAAATTGGCAGTTT * * 56452 GCAAGTGATTCTGGCAAGACGGCCCAAGAAAATACCCCATAAATTGGCAGTGT 1 GCAAGTGACTCTGGCAAGACGGCCCAAGAAAATACCCCATAAATTGGCAGTTT * * * * 56505 GTAAGTGGCTCTGACAAGACGGACCAAGA 1 GCAAGTGACTCTGGCAAGACGGCCCAAGA 56534 TGATACCTCG Statistics Matches: 120, Mismatches: 15, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 53 120 1.00 ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19 Consensus pattern (53 bp): GCAAGTGACTCTGGCAAGACGGCCCAAGAAAATACCCCATAAATTGGCAGTTT Found at i:58979 original size:31 final size:31 Alignment explanation

Indices: 58944--59042 Score: 112 Period size: 31 Copynumber: 3.3 Consensus size: 31 58934 GGTTTCACGA 58944 AGGGACTAAATTGATCTCTTTTCAATAGTAG 1 AGGGACTAAATTGATCTCTTTTCAATAGTAG *** * * 58975 AGGGACTAAATTGA-CAGATTTC-ATAATGG 1 AGGGACTAAATTGATCTCTTTTCAATAGTAG * * * 59004 AGGGACTAAAATGATCTTTTTTCAATAGTAC 1 AGGGACTAAATTGATCTCTTTTCAATAGTAG 59035 AGGGACTA 1 AGGGACTA 59043 TTTAGGTTCT Statistics Matches: 54, Mismatches: 12, Indels: 4 0.77 0.17 0.06 Matches are distributed among these distances: 29 18 0.33 30 10 0.19 31 26 0.48 ACGTcount: A:0.35, C:0.12, G:0.21, T:0.31 Consensus pattern (31 bp): AGGGACTAAATTGATCTCTTTTCAATAGTAG Done.