Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015738.1 Corchorus capsularis cultivar CVL-1 contig15759, 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: 67020
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:72 original size:2 final size:2

Alignment explanation

Indices: 65--90 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 55 TATAATGAGG 65 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 91 GAAAGATAGA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:15824 original size:93 final size:93 Alignment explanation

Indices: 15704--15925 Score: 401 Period size: 93 Copynumber: 2.4 Consensus size: 93 15694 GGGTAGAACT * * 15704 TTCT-TATTAGAATTCAAAATGCCATCATCCAAATCAATTTGCGAAACTCTAGCACCAAAACCAT 1 TTCTCTATTTGAATTCAAAATACCATCATCCAAATCAATTTGCGAAACTCTAGCACCAAAACCAT * 15768 AAAAACCATTATCTCCATTGACTAATTC 66 AAAAACCATTATCTCCATTAACTAATTC 15796 TTCTCTATTTGAATTCAAAATACCATCATCCAAATCAATTTGCGAAACTCTAGCACCAAAACCAT 1 TTCTCTATTTGAATTCAAAATACCATCATCCAAATCAATTTGCGAAACTCTAGCACCAAAACCAT 15861 AAAAACCATTATCTCCATTAACTAATTC 66 AAAAACCATTATCTCCATTAACTAATTC * 15889 TTCTCTATTTGAATTCAAAATACCATCATCCATATCA 1 TTCTCTATTTGAATTCAAAATACCATCATCCAAATCA 15926 GTTTCCTTGA Statistics Matches: 125, Mismatches: 4, Indels: 1 0.96 0.03 0.01 Matches are distributed among these distances: 92 4 0.03 93 121 0.97 ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31 Consensus pattern (93 bp): TTCTCTATTTGAATTCAAAATACCATCATCCAAATCAATTTGCGAAACTCTAGCACCAAAACCAT AAAAACCATTATCTCCATTAACTAATTC Found at i:19926 original size:16 final size:16 Alignment explanation

Indices: 19907--19975 Score: 77 Period size: 16 Copynumber: 4.3 Consensus size: 16 19897 ATACGAGTTT 19907 CGGGTCATTCGGGTCC 1 CGGGTCATTCGGGTCC * * 19923 CGGGTCATTCGAGTTC 1 CGGGTCATTCGGGTCC * 19939 CGGGTCATTCGGGTCT 1 CGGGTCATTCGGGTCC * * 19955 CAGGTC-TATCGGGTCT 1 CGGGTCAT-TCGGGTCC 19971 CGGGT 1 CGGGT 19976 TGGGCAGGTT Statistics Matches: 45, Mismatches: 7, Indels: 2 0.83 0.13 0.04 Matches are distributed among these distances: 15 1 0.02 16 44 0.98 ACGTcount: A:0.09, C:0.26, G:0.36, T:0.29 Consensus pattern (16 bp): CGGGTCATTCGGGTCC Found at i:19975 original size:32 final size:32 Alignment explanation

Indices: 19830--19975 Score: 120 Period size: 32 Copynumber: 4.6 Consensus size: 32 19820 AGTTTTTTTG * 19830 GGTTATTCGGGTTTCGGGTCA-TCTGGGT-TCA 1 GGTTATTCGGGTCTCGGGTCATTC-GGGTCTCA * ** * * 19861 GGTTATTTGGGTCTCGGGTTGTTCGGATCTCG 1 GGTTATTCGGGTCTCGGGTCATTCGGGTCTCA * * * * * 19893 GGTTATACGAGTTTCGGGTCATTCGGGTCCCG 1 GGTTATTCGGGTCTCGGGTCATTCGGGTCTCA * * 19925 GGTCATTCGAGT-TCCGGGTCATTCGGGTCTCA 1 GGTTATTCGGGTCT-CGGGTCATTCGGGTCTCA 19957 GGTCTA-TCGGGTCTCGGGT 1 GGT-TATTCGGGTCTCGGGT 19976 TGGGCAGGTT Statistics Matches: 90, Mismatches: 20, Indels: 9 0.76 0.17 0.08 Matches are distributed among these distances: 31 21 0.23 32 67 0.74 33 2 0.02 ACGTcount: A:0.10, C:0.20, G:0.36, T:0.35 Consensus pattern (32 bp): GGTTATTCGGGTCTCGGGTCATTCGGGTCTCA Found at i:20448 original size:21 final size:21 Alignment explanation

Indices: 20423--20470 Score: 78 Period size: 21 Copynumber: 2.3 Consensus size: 21 20413 TAGCCAATTT 20423 ATAATAGGTAAAATCATAACA 1 ATAATAGGTAAAATCATAACA * * 20444 ATAATTGGTAAAATTATAACA 1 ATAATAGGTAAAATCATAACA 20465 ATAATA 1 ATAATA 20471 TAAATTGTAT Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 21 24 1.00 ACGTcount: A:0.56, C:0.06, G:0.08, T:0.29 Consensus pattern (21 bp): ATAATAGGTAAAATCATAACA Found at i:20592 original size:9 final size:9 Alignment explanation

Indices: 20578--20625 Score: 50 Period size: 9 Copynumber: 5.8 Consensus size: 9 20568 GGTTAATGTC 20578 TCGGGTTAT 1 TCGGGTTAT 20587 TCGGG-T-T 1 TCGGGTTAT 20594 TCGGGTTAT 1 TCGGGTTAT * * 20603 ACGGG-TCT 1 TCGGGTTAT 20611 T-GGGTTAT 1 TCGGGTTAT 20619 TCGGGTT 1 TCGGGTT 20626 TCAGGTCATC Statistics Matches: 31, Mismatches: 4, Indels: 8 0.72 0.09 0.19 Matches are distributed among these distances: 7 9 0.29 8 7 0.23 9 15 0.48 ACGTcount: A:0.08, C:0.12, G:0.38, T:0.42 Consensus pattern (9 bp): TCGGGTTAT Found at i:20653 original size:32 final size:32 Alignment explanation

Indices: 20617--20689 Score: 101 Period size: 32 Copynumber: 2.3 Consensus size: 32 20607 GTCTTGGGTT * 20617 ATTCGGGTTTCAGGTCATCTGGATTACAGGTC 1 ATTCGGGTCTCAGGTCATCTGGATTACAGGTC * * * * 20649 ATTCGGGTCTCGGGTCATCTGGGTTGCGGGTC 1 ATTCGGGTCTCAGGTCATCTGGATTACAGGTC 20681 ATTCGGGTC 1 ATTCGGGTC 20690 ACGGGTTCGT Statistics Matches: 36, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 32 36 1.00 ACGTcount: A:0.12, C:0.21, G:0.34, T:0.33 Consensus pattern (32 bp): ATTCGGGTCTCAGGTCATCTGGATTACAGGTC Found at i:20664 original size:16 final size:16 Alignment explanation

Indices: 20575--20695 Score: 79 Period size: 16 Copynumber: 7.6 Consensus size: 16 20565 TCGGGTTAAT * 20575 GTCTCGGGTTATTCGG 1 GTCTCGGGTCATTCGG * * * 20591 GTTTCGGGTTATACGG 1 GTCTCGGGTCATTCGG * * 20607 GTCTTGGGTTATTCGG 1 GTCTCGGGTCATTCGG * * 20623 GTTTCAGGTCA-TCTGG 1 GTCTCGGGTCATTC-GG * * 20639 AT-TACAGGTCATTCGG 1 GTCT-CGGGTCATTCGG 20655 GTCTCGGGTCA-TCTGG 1 GTCTCGGGTCATTC-GG 20671 GT-TGCGGGTCATTCGG 1 GTCT-CGGGTCATTCGG * 20687 GTCACGGGT 1 GTCTCGGGT 20696 TCGTCGGGTC Statistics Matches: 84, Mismatches: 13, Indels: 16 0.74 0.12 0.14 Matches are distributed among these distances: 15 6 0.07 16 73 0.87 17 5 0.06 ACGTcount: A:0.11, C:0.18, G:0.36, T:0.35 Consensus pattern (16 bp): GTCTCGGGTCATTCGG Found at i:20791 original size:26 final size:27 Alignment explanation

Indices: 20749--20801 Score: 81 Period size: 26 Copynumber: 2.0 Consensus size: 27 20739 CTGGTCAAAT * 20749 CGGATTGGACGGGTTAT-GGATTCGGA 1 CGGATTGGACGGATTATCGGATTCGGA * 20775 CGGATTGGATGGATTATCGGATTCGGA 1 CGGATTGGACGGATTATCGGATTCGGA 20802 TCAGATTTTG Statistics Matches: 24, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 26 15 0.62 27 9 0.38 ACGTcount: A:0.21, C:0.11, G:0.40, T:0.28 Consensus pattern (27 bp): CGGATTGGACGGATTATCGGATTCGGA Found at i:31852 original size:24 final size:24 Alignment explanation

Indices: 31820--31875 Score: 112 Period size: 24 Copynumber: 2.3 Consensus size: 24 31810 TAAACCATTG 31820 AAAATTTTCATTTCATTGAAAATT 1 AAAATTTTCATTTCATTGAAAATT 31844 AAAATTTTCATTTCATTGAAAATT 1 AAAATTTTCATTTCATTGAAAATT 31868 AAAATTTT 1 AAAATTTT 31876 TAATGCTTTT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 32 1.00 ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46 Consensus pattern (24 bp): AAAATTTTCATTTCATTGAAAATT Found at i:38384 original size:12 final size:12 Alignment explanation

Indices: 38369--38397 Score: 58 Period size: 12 Copynumber: 2.4 Consensus size: 12 38359 AATACATGTT 38369 TCAATTGAAAAG 1 TCAATTGAAAAG 38381 TCAATTGAAAAG 1 TCAATTGAAAAG 38393 TCAAT 1 TCAAT 38398 AATAATACAA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 17 1.00 ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28 Consensus pattern (12 bp): TCAATTGAAAAG Found at i:38802 original size:26 final size:26 Alignment explanation

Indices: 38766--38828 Score: 74 Period size: 26 Copynumber: 2.4 Consensus size: 26 38756 GAAAGAAGCA * * * 38766 AAAACAGATCTGTCAGGTTTAAT-TGC 1 AAAACAAATCTGT-AGATGTAATCTGC 38792 AAAACAAATCTGTAGATGTAATCTGC 1 AAAACAAATCTGTAGATGTAATCTGC * 38818 GAAACAAATCT 1 AAAACAAATCT 38829 ATATCTTAAT Statistics Matches: 32, Mismatches: 4, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 25 7 0.22 26 25 0.78 ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27 Consensus pattern (26 bp): AAAACAAATCTGTAGATGTAATCTGC Found at i:40552 original size:15 final size:15 Alignment explanation

Indices: 40513--40554 Score: 50 Period size: 15 Copynumber: 2.8 Consensus size: 15 40503 AAATTCAGTA * * 40513 TTAAAATTTCAACAC 1 TTAAATTTTCAGCAC 40528 TT-AATCTTTCAGCAC 1 TTAAAT-TTTCAGCAC 40543 TTAAATTTTCAG 1 TTAAATTTTCAG 40555 TTTATCAAAC Statistics Matches: 23, Mismatches: 2, Indels: 4 0.79 0.07 0.14 Matches are distributed among these distances: 14 2 0.09 15 18 0.78 16 3 0.13 ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40 Consensus pattern (15 bp): TTAAATTTTCAGCAC Found at i:42155 original size:44 final size:44 Alignment explanation

Indices: 42106--42194 Score: 169 Period size: 44 Copynumber: 2.0 Consensus size: 44 42096 CTGATTAAGG * 42106 CTTAGAAATTGTTAAGAACAAAGCATTAAGAACATCAATTCACA 1 CTTAGAAATTGTTAAGAACAAAACATTAAGAACATCAATTCACA 42150 CTTAGAAATTGTTAAGAACAAAACATTAAGAACATCAATTCACA 1 CTTAGAAATTGTTAAGAACAAAACATTAAGAACATCAATTCACA 42194 C 1 C 42195 ATGCATAACA Statistics Matches: 44, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 44 44 1.00 ACGTcount: A:0.48, C:0.17, G:0.10, T:0.25 Consensus pattern (44 bp): CTTAGAAATTGTTAAGAACAAAACATTAAGAACATCAATTCACA Found at i:42698 original size:7 final size:7 Alignment explanation

Indices: 42686--42718 Score: 57 Period size: 7 Copynumber: 4.7 Consensus size: 7 42676 AAGAAGAATA 42686 GAATTGT 1 GAATTGT 42693 GAATTGT 1 GAATTGT 42700 GAATTGT 1 GAATTGT 42707 GAATTGT 1 GAATTGT * 42714 AAATT 1 GAATT 42719 ATGTTCTCTA Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 7 25 1.00 ACGTcount: A:0.33, C:0.00, G:0.24, T:0.42 Consensus pattern (7 bp): GAATTGT Found at i:47446 original size:30 final size:30 Alignment explanation

Indices: 47407--47475 Score: 88 Period size: 30 Copynumber: 2.3 Consensus size: 30 47397 AATTAATAAA * * 47407 TAGGATCAAATGTATATTTCACTAA-TTCAG 1 TAGGGTCAAATGTATAATTCAC-AATTTCAG 47437 TAGGGTCAAATGTATAATTCACAATTTCAG 1 TAGGGTCAAATGTATAATTCACAATTTCAG 47467 T-GAGGTCAA 1 TAG-GGTCAA 47476 TATAAGAAAT Statistics Matches: 35, Mismatches: 2, Indels: 4 0.85 0.05 0.10 Matches are distributed among these distances: 29 3 0.09 30 32 0.91 ACGTcount: A:0.36, C:0.13, G:0.17, T:0.33 Consensus pattern (30 bp): TAGGGTCAAATGTATAATTCACAATTTCAG Found at i:52848 original size:17 final size:16 Alignment explanation

Indices: 52810--52851 Score: 50 Period size: 16 Copynumber: 2.6 Consensus size: 16 52800 ACAAATTTCG * 52810 AATAT-TATAGTATGT 1 AATATATATAGTATAT * 52825 AAGATATATAGTATAT 1 AATATATATAGTATAT 52841 ATATATATATA 1 A-ATATATATA 52852 CTTATATAAG Statistics Matches: 22, Mismatches: 3, Indels: 2 0.81 0.11 0.07 Matches are distributed among these distances: 15 4 0.18 16 10 0.45 17 8 0.36 ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43 Consensus pattern (16 bp): AATATATATAGTATAT Found at i:53038 original size:18 final size:18 Alignment explanation

Indices: 53015--53049 Score: 54 Period size: 18 Copynumber: 1.9 Consensus size: 18 53005 ACAAGCAATC 53015 TTATAAT-ATTTATTTTTA 1 TTATAATAATTT-TTTTTA 53033 TTATAATAATTTTTTTT 1 TTATAATAATTTTTTTT 53050 GAAGAATATT Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 18 12 0.75 19 4 0.25 ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69 Consensus pattern (18 bp): TTATAATAATTTTTTTTA Found at i:57026 original size:27 final size:27 Alignment explanation

Indices: 56985--57049 Score: 112 Period size: 27 Copynumber: 2.4 Consensus size: 27 56975 TGCTAATTAC * 56985 TCCCTTTGTTCCTTTTTAATTGTCCCTT 1 TCCC-TTGTTTCTTTTTAATTGTCCCTT 57013 TCCCTTGTTTCTTTTTAATTGTCCCTT 1 TCCCTTGTTTCTTTTTAATTGTCCCTT 57040 TCCCTTGTTT 1 TCCCTTGTTT 57050 TCCAGAAATA Statistics Matches: 36, Mismatches: 1, Indels: 1 0.95 0.03 0.03 Matches are distributed among these distances: 27 32 0.89 28 4 0.11 ACGTcount: A:0.06, C:0.28, G:0.08, T:0.58 Consensus pattern (27 bp): TCCCTTGTTTCTTTTTAATTGTCCCTT Found at i:57101 original size:24 final size:25 Alignment explanation

Indices: 57069--57115 Score: 87 Period size: 24 Copynumber: 1.9 Consensus size: 25 57059 ACCCTTCTTG 57069 AAACATGCATTTAATTA-AAAGATC 1 AAACATGCATTTAATTAGAAAGATC 57093 AAACATGCATTTAATTAGAAAGA 1 AAACATGCATTTAATTAGAAAGA 57116 AGCAATGACT Statistics Matches: 22, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 24 17 0.77 25 5 0.23 ACGTcount: A:0.51, C:0.11, G:0.11, T:0.28 Consensus pattern (25 bp): AAACATGCATTTAATTAGAAAGATC Found at i:58866 original size:122 final size:122 Alignment explanation

Indices: 58718--58959 Score: 394 Period size: 122 Copynumber: 2.0 Consensus size: 122 58708 ATCCTAATAT * 58718 ATTATTTTGGGTGAATGAAAATATTAATTGGAAAATCAATTTACCCAACCAATCAATTTTGGAAA 1 ATTATTTTGGGTGAATGAAAATATTAATTGGAAAATCAATTTACCCAACCAATAAATTTTGGAAA * 58783 GAGAAAAGCCAAATGCTAAACATACAACAGTTTGGGGATAATTTTAATATATAGGGG 66 GAGAAAAGCCAAATGCTAAACATACAACAGTTTGGGGATAACTTTAATATATAGGGG * * 58840 ATTATTTTGGGTGAATGAAAATATTAATTGTAAAATCAATTTACTCAACCAATAAATTTTGGAAA 1 ATTATTTTGGGTGAATGAAAATATTAATTGGAAAATCAATTTACCCAACCAATAAATTTTGGAAA * * * ** * 58905 TAGAAAAGCCAAATGTTGAGTATACAATAGTTTGGGGATAACTTTAATATATAGG 66 GAGAAAAGCCAAATGCTAAACATACAACAGTTTGGGGATAACTTTAATATATAGG 58960 TAAGATATGC Statistics Matches: 110, Mismatches: 10, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 122 110 1.00 ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32 Consensus pattern (122 bp): ATTATTTTGGGTGAATGAAAATATTAATTGGAAAATCAATTTACCCAACCAATAAATTTTGGAAA GAGAAAAGCCAAATGCTAAACATACAACAGTTTGGGGATAACTTTAATATATAGGGG Found at i:60758 original size:2 final size:2 Alignment explanation

Indices: 60751--60775 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 60741 CAAACTTAAC 60751 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 60776 GGCTTATTGC 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 Found at i:64631 original size:21 final size:21 Alignment explanation

Indices: 64605--64650 Score: 92 Period size: 21 Copynumber: 2.2 Consensus size: 21 64595 CTATGTTATT 64605 TTAGATCACATTGATCATTCA 1 TTAGATCACATTGATCATTCA 64626 TTAGATCACATTGATCATTCA 1 TTAGATCACATTGATCATTCA 64647 TTAG 1 TTAG 64651 TTTGGTAGAA Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 25 1.00 ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39 Consensus pattern (21 bp): TTAGATCACATTGATCATTCA Found at i:64936 original size:3 final size:3 Alignment explanation

Indices: 64928--64973 Score: 74 Period size: 3 Copynumber: 15.3 Consensus size: 3 64918 ATATCAAAAT * * 64928 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AGA ATA ATA AGA ATA A 1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A 64974 AATTTGTTGA Statistics Matches: 39, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 3 39 1.00 ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28 Consensus pattern (3 bp): ATA Found at i:66359 original size:20 final size:20 Alignment explanation

Indices: 66329--66379 Score: 93 Period size: 20 Copynumber: 2.5 Consensus size: 20 66319 GTTACTAAAT 66329 TTTTATTAATAGCATCGTAGG 1 TTTT-TTAATAGCATCGTAGG 66350 TTTTTTAATAGCATCGTAGG 1 TTTTTTAATAGCATCGTAGG 66370 TTTTTTAATA 1 TTTTTTAATA 66380 ACCTCTAAGG Statistics Matches: 30, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 20 26 0.87 21 4 0.13 ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49 Consensus pattern (20 bp): TTTTTTAATAGCATCGTAGG Found at i:66390 original size:20 final size:20 Alignment explanation

Indices: 66329--66395 Score: 82 Period size: 20 Copynumber: 3.3 Consensus size: 20 66319 GTTACTAAAT * 66329 TTTTATTAATAGCATCGTAGG 1 TTTT-TTAATAACATCGTAGG * 66350 TTTTTTAATAGCATCGTAGG 1 TTTTTTAATAACATCGTAGG * 66370 TTTTTTAATAACCTC-TAAGG 1 TTTTTTAATAACATCGT-AGG 66390 TTTTTT 1 TTTTTT 66396 TTTTTACTTA Statistics Matches: 43, Mismatches: 2, Indels: 3 0.90 0.04 0.06 Matches are distributed among these distances: 19 1 0.02 20 38 0.88 21 4 0.09 ACGTcount: A:0.25, C:0.10, G:0.15, T:0.49 Consensus pattern (20 bp): TTTTTTAATAACATCGTAGG Done.