Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023693.1 Corchorus olitorius cultivar O-4 contig23726, 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: 61937
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:209 original size:15 final size:14

Alignment explanation

Indices: 189--218 Score: 51 Period size: 15 Copynumber: 2.1 Consensus size: 14 179 TCTAAATCCA 189 AATAAATAAGTATAT 1 AATAAATAA-TATAT 204 AATAAATAATATAT 1 AATAAATAATATAT 218 A 1 A 219 CTTAATTAGT Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 6 0.40 15 9 0.60 ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33 Consensus pattern (14 bp): AATAAATAATATAT Found at i:4618 original size:82 final size:82 Alignment explanation

Indices: 4517--4682 Score: 323 Period size: 82 Copynumber: 2.0 Consensus size: 82 4507 CTCATTAGAT * 4517 CAACATGGACCTAACCAAATCAAATTTTGTTTCCTGCGATAAATCCATATTAACACAAATGATCA 1 CAACATGGACCTAACCAAATCAAATTTTGTTTCCTGCAATAAATCCATATTAACACAAATGATCA 4582 AAGAGCTAATGCCAAAC 66 AAGAGCTAATGCCAAAC 4599 CAACATGGACCTAACCAAATCAAATTTTGTTTCCTGCAATAAATCCATATTAACACAAATGATCA 1 CAACATGGACCTAACCAAATCAAATTTTGTTTCCTGCAATAAATCCATATTAACACAAATGATCA 4664 AAGAGCTAATGCCAAAC 66 AAGAGCTAATGCCAAAC 4681 CA 1 CA 4683 CCAAATATTG Statistics Matches: 83, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 82 83 1.00 ACGTcount: A:0.42, C:0.23, G:0.10, T:0.24 Consensus pattern (82 bp): CAACATGGACCTAACCAAATCAAATTTTGTTTCCTGCAATAAATCCATATTAACACAAATGATCA AAGAGCTAATGCCAAAC Found at i:5877 original size:12 final size:12 Alignment explanation

Indices: 5860--5884 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 5850 TGAGATTAAG 5860 AGAAAAGAAAAA 1 AGAAAAGAAAAA 5872 AGAAAAGAAAAA 1 AGAAAAGAAAAA 5884 A 1 A 5885 TATAGTATTA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00 Consensus pattern (12 bp): AGAAAAGAAAAA Found at i:6680 original size:25 final size:27 Alignment explanation

Indices: 6646--6699 Score: 85 Period size: 25 Copynumber: 2.1 Consensus size: 27 6636 AATATTCTTA * 6646 TTCAATGTTACT-AAAAA-TGCAGTTG 1 TTCAAGGTTACTAAAAAAGTGCAGTTG 6671 TTCAAGGTTACTAAAAAAGTGCAGTTG 1 TTCAAGGTTACTAAAAAAGTGCAGTTG 6698 TT 1 TT 6700 ATTAAGGCTG Statistics Matches: 26, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 25 11 0.42 26 5 0.19 27 10 0.38 ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35 Consensus pattern (27 bp): TTCAAGGTTACTAAAAAAGTGCAGTTG Found at i:23885 original size:20 final size:20 Alignment explanation

Indices: 23860--23897 Score: 60 Period size: 20 Copynumber: 1.9 Consensus size: 20 23850 CTCATAAGAT 23860 AATAAT-ATAATAATTTAACC 1 AATAATAATAAT-ATTTAACC 23880 AATAATAATAATATTTAA 1 AATAATAATAATATTTAA 23898 ATTGACATCA Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 20 12 0.71 21 5 0.29 ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37 Consensus pattern (20 bp): AATAATAATAATATTTAACC Found at i:30859 original size:434 final size:432 Alignment explanation

Indices: 30325--31398 Score: 1256 Period size: 434 Copynumber: 2.5 Consensus size: 432 30315 ACGCGTTACC * * * * 30325 TTTTATTTTTTTATTTTTTATCCTATTTGTCCGATTAAGCTGATTTAAGTGTCTATTAAAAGGTA 1 TTTTATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGCTGATTCAA-TGTCTATTAAAAGGTA * * * * * 30390 ATTTAATGATCTACAATTTTCATTAAGAACTCAAAAGTC-AATTGTAAAG-TTCTGATTCTAAAA 65 ATTTAATGATCTACAACTTTCATGAAGGACTCAAAAG-CAAATTGTAAAGTTTC-AATTCAAAAA * * * * 30453 AATGCTTCCGAAATTT-TGT-GATTTTGATTGCCGGT-TAATTTAATATCGTATCATTTTTTG-T 128 AATGCTTCCGAAATTTGT-TCG-TTTCGATTGCCGGTCT-ATTTAATACCATAT-AATTTTTGAT * * * * * * 30514 CCACATGTCCGATTGAAGTTATTGAAGTGTCGGTTAAAAGATTATTGCATGATTTACGACTTTCA 189 CCACATGTCCAATTAAAGTTATTCAAGTGTCGGTCAAAAGATTATTGCATAATCTACGACTTTCA * * 30579 TGAAGGACCCAAAAGCTAAATTTGATCTACGAGTTTCGTGAAGGGTTCAAAAGGGAATTTTTATG 254 TGAAGAACCCAAAAG-TAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATG * * * 30644 TTTCAAGATCTCCATTAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCATAC-TT 318 TTTCAAGATCTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTT * * 30708 TCTACTTTA-TACTTAGTCCTTTACAAATTCTATCTTAATCTAACG-TTTAA-G 383 TCTACTTTACTACATAGTCCTTTACAAATTCTATCTT-A-CT--CGATTTAACA * * 30759 TTTTATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGTTGATTCATATGTCCATTAAAAGGTA 1 TTTTATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGCTGATTCA-ATGTCTATTAAAAGGTA * * * * 30824 ATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTTATGTTTCAATTCAAAAAAA 65 ATTTAATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTGTAAAGTTTCAATTCAAAAAAA * ** 30889 TGCTTCCTAAATTTGTTCGTTTCGATTGTTGGTCTATTTAATACCATATAATTTTTGATCCACAT 130 TGCTTCCGAAATTTGTTCGTTTCGATTGCCGGTCTATTTAATACCATATAATTTTTGATCCACAT * * 30954 GTCCAATTAAAGTTATTCAAGTGTCGGTCAAAAGGTTATTGTATAATCTACGACTTTCATGAAGA 195 GTCCAATTAAAGTTATTCAAGTGTCGGTCAAAAGATTATTGCATAATCTACGACTTTCATGAAGA * * * 31019 ACTCGAAAGTTAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAG 260 ACCCAAAAGTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAG * * 31084 ATCTCCATTAACAAATATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTATTT 325 ATCTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACTT * 31149 TATGCTACATAGTCCTTTCCAAATTCTATCTTACTCGATTTAACA 390 TA--CTACATAGTCCTTTACAAATTCTATCTTACTCGATTTAACA * * * * * * * 31194 CTTCA-TTTTTT-TTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTGTCTATTAAAAGATA 1 TTTTATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGCTGATTCA-ATGTCTATTAAAAGGTA * * * * * * * 31257 ATTTTATAATCTACAACTTTCATGAAAGACTCAAAAGCTAATTTTTATA-TTTCAATTCTAAAAA 65 ATTTAATGATCTACAACTTTCATGAAGGACTCAAAAGC-AAATTGTAAAGTTTCAATTCAAAAAA * ** * * * ** * * * 31321 ATGATTTTGAAATTTTTTGTGATTTCGATTGACAATCTATTTAATATCATATTATTTTTGATCTA 129 ATGCTTCCGAAATTTGTT-CG-TTTCGATTGCCGGTCTATTTAATACCATATAATTTTTGATCCA * * 31386 GATGTCCGATTAA 192 CATGTCCAATTAA 31399 CAAAGATTCA Statistics Matches: 549, Mismatches: 75, Indels: 31 0.84 0.11 0.05 Matches are distributed among these distances: 433 222 0.40 434 242 0.44 435 59 0.11 436 1 0.00 437 25 0.05 ACGTcount: A:0.31, C:0.14, G:0.12, T:0.42 Consensus pattern (432 bp): TTTTATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGCTGATTCAATGTCTATTAAAAGGTAA TTTAATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTGTAAAGTTTCAATTCAAAAAAAT GCTTCCGAAATTTGTTCGTTTCGATTGCCGGTCTATTTAATACCATATAATTTTTGATCCACATG TCCAATTAAAGTTATTCAAGTGTCGGTCAAAAGATTATTGCATAATCTACGACTTTCATGAAGAA CCCAAAAGTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGA TCTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACTTT ACTACATAGTCCTTTACAAATTCTATCTTACTCGATTTAACA Found at i:31219 original size:433 final size:431 Alignment explanation

Indices: 30329--31351 Score: 1276 Period size: 433 Copynumber: 2.4 Consensus size: 431 30319 GTTACCTTTT * * * * 30329 ATTTTTTTATTTTTTATCCTATTTGTCCGATTAAGCTGATTTAAGTGTCTATTAAAAGGTAATTT 1 ATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGCTGATTCAA-TGTCTATTAAAAGGTAATTT * * * * * * * 30394 AATGATCTACAATTTTCATTAAGAACTCAAAAGTCAATTGTAAAG-TTCTGATTCTAAAAAATGC 65 AATGATCTACAACTTTCATGAAGGACTCAAAAG-CAATTTTTATGTTTC-AATTCTAAAAAATGC * * * * 30458 TTCCGAAATTTTGTGATTTTGATTGCCGGTTAATTTAATATCGTATCATTTTTTGTCCACATGTC 128 TTCCGAAATTTTGTGATTTCGATTGCCGGTTAATTTAATACCATATCAATTTTTGTCCACATGTC * * * * * * * 30523 CGATTGAAGTTATTGAAGTGTCGGTTAAAAGATTATTGCATGATTTACGACTTTCATGAAGGACC 193 CAATTAAAGTTATTCAAGTGTCGGTCAAAAGATTATTGCATAATCTACGACTTTCATGAAGAACC * 30588 CAAAAGCTAAATTTGATCTACGAGTTTCGTGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGAT 258 CAAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGAT * * * 30653 CTCCATTAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCATACTTTCTACTTTAT 323 CTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTCTACTTTAT * ** * 30718 ACTTAGTCCTTTACAAATTCTATCTTAATCTAACGTTTAAGTTTT 388 ACATAGTCCTTTACAAATTCTATCTTAATCT-ACGTTTAAACTTC * * 30763 ATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGTTGATTCATATGTCCATTAAAAGGTAATTT 1 ATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGCTGATTCA-ATGTCTATTAAAAGGTAATTT * * 30828 CATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTTATGTTTCAATTCAAAAAAATGCT 65 AATGATCTACAACTTTCATGAAGGACTCAAAAGC-AATTTTTATGTTTCAATTCTAAAAAATGCT * ** 30893 TCCTAAA-TTTGTTCG-TTTCGATTGTTGGTCT-ATTTAATACCATAT-AATTTTTGATCCACAT 129 TCCGAAATTTTG-T-GATTTCGATTGCCGGT-TAATTTAATACCATATCAATTTTTG-TCCACAT * * 30954 GTCCAATTAAAGTTATTCAAGTGTCGGTCAAAAGGTTATTGTATAATCTACGACTTTCATGAAGA 190 GTCCAATTAAAGTTATTCAAGTGTCGGTCAAAAGATTATTGCATAATCTACGACTTTCATGAAGA * * * 31019 ACTCGAAAG-TTAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAA 255 ACCCAAAAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAA * * 31083 GATCTCCATTAACAAATATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTATT 320 GATCTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATAC-TTTCTACT * 31148 TTATGCTACATAGTCCTTTCCAAATTCTATCTT-A-CT-CGATTTAACACTTC 384 TTA---TACATAGTCCTTTACAAATTCTATCTTAATCTACG-TTTAA-ACTTC * * * * * 31198 A-TTTTTT-TTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTGTCTATTAAAAGATAATTT 1 ATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGCTGATTCA-ATGTCTATTAAAAGGTAATTT * * * * * 31261 TATAATCTACAACTTTCATGAAAGACTCAAAAGCTAATTTTTATATTTCAATTCTAAAAAATGAT 65 AATGATCTACAACTTTCATGAAGGACTCAAAAGC-AATTTTTATGTTTCAATTCTAAAAAATGCT ** 31326 TTTGAAATTTTTTGTGATTTCGATTG 129 TCCGAAA--TTTTGTGATTTCGATTG 31352 ACAATCTATT Statistics Matches: 510, Mismatches: 62, Indels: 33 0.84 0.10 0.05 Matches are distributed among these distances: 433 230 0.45 434 229 0.45 435 21 0.04 436 5 0.01 437 25 0.05 ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42 Consensus pattern (431 bp): ATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGCTGATTCAATGTCTATTAAAAGGTAATTTA ATGATCTACAACTTTCATGAAGGACTCAAAAGCAATTTTTATGTTTCAATTCTAAAAAATGCTTC CGAAATTTTGTGATTTCGATTGCCGGTTAATTTAATACCATATCAATTTTTGTCCACATGTCCAA TTAAAGTTATTCAAGTGTCGGTCAAAAGATTATTGCATAATCTACGACTTTCATGAAGAACCCAA AAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTC CATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTCTACTTTATACA TAGTCCTTTACAAATTCTATCTTAATCTACGTTTAAACTTC Found at i:32208 original size:77 final size:77 Alignment explanation

Indices: 32077--32230 Score: 256 Period size: 77 Copynumber: 2.0 Consensus size: 77 32067 CACTCCATCG * * * 32077 TTAGGCAAGACCCATTTGACATGAAAACAATATTAACCGCCAGCATAGAATTAGCTAGAGCCTGC 1 TTAGGCAAGACCCATTTGACATGAAAACAACACTAACCGCCAGCATAGAATTAGCTAGAGCCCGC 32142 ATGACTTCCTCA 66 ATGACTTCCTCA * 32154 TTAGGCAAGACCCATTTGACATGAAAACAACACTAACCGCC-GTCATAGAGTTAGCTAGAGCCCG 1 TTAGGCAAGACCCATTTGACATGAAAACAACACTAACCGCCAG-CATAGAATTAGCTAGAGCCCG 32218 CATGACTTCCTCA 65 CATGACTTCCTCA 32231 GTGATGCCCA Statistics Matches: 72, Mismatches: 4, Indels: 2 0.92 0.05 0.03 Matches are distributed among these distances: 76 1 0.01 77 71 0.99 ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22 Consensus pattern (77 bp): TTAGGCAAGACCCATTTGACATGAAAACAACACTAACCGCCAGCATAGAATTAGCTAGAGCCCGC ATGACTTCCTCA Found at i:39622 original size:15 final size:16 Alignment explanation

Indices: 39598--39637 Score: 55 Period size: 15 Copynumber: 2.6 Consensus size: 16 39588 AAAGGTTGAA * 39598 AGAAAGCAATTAAAC- 1 AGAAAACAATTAAACT * 39613 AGAAAACAATTATACT 1 AGAAAACAATTAAACT 39629 AGAAAACAA 1 AGAAAACAA 39638 AGCAAAATAA 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:0.10, T:0.15 Consensus pattern (16 bp): AGAAAACAATTAAACT Found at i:46314 original size:15 final size:16 Alignment explanation

Indices: 46281--46320 Score: 55 Period size: 15 Copynumber: 2.6 Consensus size: 16 46271 TTACTTTGCT 46281 TTGTTTTCTAGTATAA 1 TTGTTTTCTAGTATAA * 46297 TTGTTTTCT-GTTTAA 1 TTGTTTTCTAGTATAA * 46312 TTGCTTTCT 1 TTGTTTTCT 46321 TTCAACCTCT 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:0.15, C:0.10, G:0.12, T:0.62 Consensus pattern (16 bp): TTGTTTTCTAGTATAA Found at i:50305 original size:15 final size:14 Alignment explanation

Indices: 50285--50314 Score: 51 Period size: 15 Copynumber: 2.1 Consensus size: 14 50275 ATCTTTTTAA 50285 TTTTCCTTACATTAT 1 TTTTCCTTA-ATTAT 50300 TTTTCCTTAATTAT 1 TTTTCCTTAATTAT 50314 T 1 T 50315 GCTTTGATTG Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 6 0.40 15 9 0.60 ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63 Consensus pattern (14 bp): TTTTCCTTAATTAT Found at i:55371 original size:15 final size:15 Alignment explanation

Indices: 55338--55396 Score: 57 Period size: 15 Copynumber: 3.7 Consensus size: 15 55328 TTACTTTGCT * 55338 TTGTTTTCTAGTATAA 1 TTGTTTTCT-GTTTAA 55354 TTGTTTTCTGTTTAA 1 TTGTTTTCTGTTTAA * 55369 TTGCTTTCT-TTTAA 1 TTGTTTTCTGTTTAA 55383 CCTCTGTTTTCTGT 1 --T-TGTTTTCTGT 55397 GTTTTGTTTT Statistics Matches: 36, Mismatches: 3, Indels: 6 0.80 0.07 0.13 Matches are distributed among these distances: 14 5 0.14 15 13 0.36 16 10 0.28 17 7 0.19 18 1 0.03 ACGTcount: A:0.14, C:0.14, G:0.12, T:0.61 Consensus pattern (15 bp): TTGTTTTCTGTTTAA Found at i:56395 original size:7 final size:7 Alignment explanation

Indices: 56383--56412 Score: 60 Period size: 7 Copynumber: 4.3 Consensus size: 7 56373 GATTGAGGCG 56383 AGGAAGA 1 AGGAAGA 56390 AGGAAGA 1 AGGAAGA 56397 AGGAAGA 1 AGGAAGA 56404 AGGAAGA 1 AGGAAGA 56411 AG 1 AG 56413 AAGTTTGATT Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 23 1.00 ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00 Consensus pattern (7 bp): AGGAAGA Found at i:56938 original size:92 final size:91 Alignment explanation

Indices: 56758--56975 Score: 226 Period size: 92 Copynumber: 2.4 Consensus size: 91 56748 TGATCTCTTC * ** * * 56758 TTGAGTTAATTTTAATTAGGAAAATTAAGTCTTTGATTTAAAGTTTGAATTTTTGAATTAAAATT 1 TTGAGTTAATTTTAATT-TGAAAATTAAAACTTTGAATTAAAGTTTGAATTTTTGAATTAAAACT ** * 56823 AACTTGGAAATTGAGTATTGAATCATT 65 AACTTGGAAAGGGAGTATCGAATCATT ** 56850 TTGAGTTAATTTTAATTTGAAAACCAAAACTTTGAATTAAAGGTTT-AATTTTCT-AGATTAAAA 1 TTGAGTTAATTTTAATTTGAAAATTAAAACTTTGAATTAAA-GTTTGAATTTT-TGA-ATTAAAA * * 56913 CTAACTTGGAAAGGGATTGA-CGAATCTTT 63 CTAACTTGGAAAGGGAGT-ATCGAATCATT * ** * 56942 TTGAGTTGATCCTAATTTAAAAATTAAAACTTTG 1 TTGAGTTAATTTTAATTTGAAAATTAAAACTTTG 56976 GTTTAAAGAT Statistics Matches: 104, Mismatches: 18, Indels: 8 0.80 0.14 0.06 Matches are distributed among these distances: 91 25 0.24 92 78 0.75 93 1 0.01 ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41 Consensus pattern (91 bp): TTGAGTTAATTTTAATTTGAAAATTAAAACTTTGAATTAAAGTTTGAATTTTTGAATTAAAACTA ACTTGGAAAGGGAGTATCGAATCATT Done.