Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013061.1 Corchorus capsularis cultivar CVL-1 contig13082, 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: 7688
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:1976 original size:440 final size:439
Alignment explanation
Indices: 1071--2000 Score: 1137
Period size: 440 Copynumber: 2.1 Consensus size: 439
1061 CCCTTATAAT
* * * *
1071 AAACAAATCATTTTTTGTTGGTTTATTTATTAGATGATCC-CTATAC-TTTTATGCTTTATGCTA
1 AAACAAA-CATTTTTTTTTGGATTATTTATCAAATGATCCTC-ATACTTTTTATGCTTTATGCTA
* * * *
1134 TTTAGTCCCTTACAATTTTTGGATTGGACGATTGAACGTTTCGCCTTTAATCCTTTTATTTTTTG
64 CTTAATCCCTTACAATTTATGGATTGGACAATTGAACGTTTCGCCTTTAATCCTTTTATTTTTTG
* *
1199 TTTTTCTTGTCTGATCAAGGTGATTCAAGTGTCTATTTAAAAGTAATTTCATGATCTACAACTTC
129 TTTATCTTGTCCGATCAAGGTGATTCAAGTGTCTATTTAAAAGTAATTTCATGATCTACAACTTC
* * ** *
1264 CATGAAGGACTCAAAAGTCAATTTTAATGTTTTGATTCTAAAAAATGCTTCTGAAATTTTGCGGT
194 CATGAAGAACTCAAAAGCCAATTTTAATGTTTAAATTCTAAAAAATGCTTCTGAAATTTTGCGAT
** * *
1329 CTAGATTGCCGGTCTATCTAATATTGTATAATTTTCGGTCTACTTCTCCGATTGAGGTTGTTCAA
259 CTAGATTGCCGGTCTATCTAATATCATAAAATTTTCGGTCCACTTCTCCGATTGAGGTTGTTCAA
* *
1394 GTGTCGATTAAAAGGTTATTATGTGATCTACGACTTTCATCAAGGGCCTGAAAGCTGAATTTGAT
324 GTGTCGATTAAAAGGTTATTATGTGATCTACGACTTTCATCAAGGACCTGAAAACTGAATTTGAT
* * * * * *
1459 TAATGAGTTTCGTGGAGGGTTCGAGAGAGAATTTTTATGTTTGGTCTCTAT
389 TAATGAGTTTCATGGAGAGTTCAAGAGAGAATTTTTATGTTTCGTCTCCAC
*
1510 AAACAAA-TTTTTTTTTTGCCGGATTATTTATCAAATGATCCTCATACTTTTTATGCTTTATAG-
1 AAACAAACATTTTTTTTT---GGATTATTTATCAAATGATCCTCATACTTTTTATGCTTTAT-GC
* * * ** *
1573 TACTTAATCCTTTACAA-TTATGGGTTGGACAATTTAACGTGTT-GGTTTTAAT-TTTTATATTT
62 TACTTAATCCCTTACAATTTATGGATTGGACAATTGAACGT-TTCGCCTTTAATCCTTT-TATTT
1635 TTTGTTCTAT-TTGTCCGATCAAGGTGATTCAAGTGTCTA-TTAAAAGTTAATTTCATGATCTAC
125 TTTGTT-TATCTTGTCCGATCAAGGTGATTCAAGTGTCTATTTAAAAG-TAATTTCATGATCTAC
* * * * * *
1698 AACTTTCATTAATAACTCATAAGCCAATTTTGA-GATTTAAATTCTAAAAGATGCTTCTGAAATT
188 AACTTCCATGAAGAACTCAAAAGCCAATTTTAATG-TTTAAATTCTAAAAAATGCTTCTGAAATT
* * * * *
1762 TTGTGATCTCGATTGCCGGTCTATTTAATATCATAAAATTTTCGGTCCACTTGTCTGATTGAGGT
252 TTGCGATCTAGATTGCCGGTCTATCTAATATCATAAAATTTTCGGTCCACTTCTCCGATTGAGGT
* * * * *
1827 TGTTTAAGTGTCGGTTAAAAGGTTA-TAGTGTGATCTACGACTTTCATTACGGACCTGAAAACTT
317 TGTTCAAGTGTCGATTAAAAGGTTATTA-TGTGATCTACGACTTTCATCAAGGACCTGAAAACTG
* * *
1891 AATTTGATTAGTGAGTTTCATGGAGAGTTTAAGAGGGAATTTTTATGTTTCGTCTCCAC
381 AATTTGATTAATGAGTTTCATGGAGAGTTCAAGAGAGAATTTTTATGTTTCGTCTCCAC
* * *
1950 CAACAAACATTTTCTTATTTGGATTATTTGTCAAAT-AACTCTCATACTTTT
1 AAACAAACATTTT-TT-TTTGGATTATTTATCAAATGATC-CTCATACTTTT
2001 CTAATTTATA
Statistics
Matches: 418, Mismatches: 57, Indels: 31
0.83 0.11 0.06
Matches are distributed among these distances:
437 8 0.02
439 22 0.05
440 346 0.83
441 36 0.09
442 3 0.01
443 3 0.01
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (439 bp):
AAACAAACATTTTTTTTTGGATTATTTATCAAATGATCCTCATACTTTTTATGCTTTATGCTACT
TAATCCCTTACAATTTATGGATTGGACAATTGAACGTTTCGCCTTTAATCCTTTTATTTTTTGTT
TATCTTGTCCGATCAAGGTGATTCAAGTGTCTATTTAAAAGTAATTTCATGATCTACAACTTCCA
TGAAGAACTCAAAAGCCAATTTTAATGTTTAAATTCTAAAAAATGCTTCTGAAATTTTGCGATCT
AGATTGCCGGTCTATCTAATATCATAAAATTTTCGGTCCACTTCTCCGATTGAGGTTGTTCAAGT
GTCGATTAAAAGGTTATTATGTGATCTACGACTTTCATCAAGGACCTGAAAACTGAATTTGATTA
ATGAGTTTCATGGAGAGTTCAAGAGAGAATTTTTATGTTTCGTCTCCAC
Found at i:2334 original size:30 final size:29
Alignment explanation
Indices: 2268--2336 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
2258 TGCCATAAAT
* *
2268 CTCAAATAAGGGCCCGAATTTTAACAAAG
1 CTCAAATAAGGGCCCAAATTTGAACAAAG
*
2297 GTCAAATAAGGGCCCCAACATTTGAA-AAAG
1 CTCAAATAAGGG-CCCAA-ATTTGAACAAAG
2327 CTCAAATAAG
1 CTCAAATAAG
2337 TCCATCCACT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.32
30 17 0.50
31 6 0.18
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.19
Consensus pattern (29 bp):
CTCAAATAAGGGCCCAAATTTGAACAAAG
Found at i:5496 original size:19 final size:20
Alignment explanation
Indices: 5460--5505 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
5450 CTTATGAACT
5460 TTTCAAAAATCCCAAATTTC
1 TTTCAAAAATCCCAAATTTC
5480 TTTC-AAAATACCC-AATTTC
1 TTTCAAAAAT-CCCAAATTTC
5499 TTTCAAA
1 TTTCAAA
5506 CCATAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTCAAAAATCCCAAATTTC
Found at i:6111 original size:31 final size:30
Alignment explanation
Indices: 6076--6145 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
6066 ACGGATTGGA
**
6076 CTTATTTGAGCCTTT-TCAATAAGTTGGGGCC
1 CTTATTTGAGCCTTTGTCAA-AA-TTCAGGCC
*
6107 CTTATTTGA-CCTTTGTTAAAATTCAGGCC
1 CTTATTTGAGCCTTTGTCAAAATTCAGGCC
6136 CTTATTTGAG
1 CTTATTTGAG
6146 ATTTATGGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 15 0.44
30 7 0.21
31 12 0.35
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (30 bp):
CTTATTTGAGCCTTTGTCAAAATTCAGGCC
Found at i:6548 original size:62 final size:62
Alignment explanation
Indices: 6471--6622 Score: 250
Period size: 62 Copynumber: 2.5 Consensus size: 62
6461 ATATCCATAC
* *
6471 GAAATTATGATAACCTTCCTATTAAATTATGATAATTACACTATTTTTAATGACGTCCTTAT
1 GAAATTTTGATAACCTTCCTATAAAATTATGATAATTACACTATTTTTAATGACGTCCTTAT
* *
6533 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATGACGTCCTTAT
1 GAAATTTTGATAACCTTCCTATAAAATTATGATAATTACACTATTTTTAATGACGTCCTTAT
* *
6595 GAAATTTTGATAACATTTCTATAAAATT
1 GAAATTTTGATAACCTTCCTATAAAATT
6623 TCAATAACGA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 84 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (62 bp):
GAAATTTTGATAACCTTCCTATAAAATTATGATAATTACACTATTTTTAATGACGTCCTTAT
Found at i:6555 original size:22 final size:22
Alignment explanation
Indices: 6530--6762 Score: 85
Period size: 22 Copynumber: 10.8 Consensus size: 22
6520 ATGACGTCCT
6530 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
*
6552 TATGAAATTATGATAA--TTACAC
1 TATGAAATTTTGATAACCTT-C-C
* * *
6574 TAT----TTTTTATGA-CGTCC
1 TATGAAATTTTGATAACCTTCC
* *
6591 TTATGAAATTTTGATAACATTTC
1 -TATGAAATTTTGATAACCTTCC
* ** ** *
6614 TATAAAATTTCAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
6636 TATGGAATTTCGATGACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
6658 TAT-AAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
*
6679 TATGAAATTTT-ATTAACCTCCC
1 TATGAAATTTTGA-TAACCTTCC
* * *
6701 AAAGGAATTTTGA-AGACC-TCAC
1 TATGAAATTTTGATA-ACCTTC-C
*
6723 TATGAAGTTTTGATAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
*
6744 GAATGAAATTTTGATAACC
1 -TATGAAATTTTGATAACC
6763 AACAGTACTA
Statistics
Matches: 150, Mismatches: 43, Indels: 35
0.66 0.19 0.15
Matches are distributed among these distances:
17 1 0.01
18 10 0.07
19 1 0.01
20 2 0.01
21 20 0.13
22 111 0.74
23 5 0.03
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:6806 original size:22 final size:21
Alignment explanation
Indices: 6780--6841 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
6770 CTATAAGATG
*
6780 TTGATAACCTCTATATGATATA
1 TTGATAACCTCTATATGA-AAA
*
6802 TTGATAACCACGT-TATGAAAA
1 TTGATAACCTC-TATATGAAAA
* *
6823 TTTAAAACCTCTATATGAA
1 TTGATAACCTCTATATGAA
6842 TTGTCAGTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
20 1 0.03
21 16 0.48
22 15 0.45
23 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (21 bp):
TTGATAACCTCTATATGAAAA
Found at i:6999 original size:22 final size:22
Alignment explanation
Indices: 6876--7111 Score: 151
Period size: 22 Copynumber: 11.1 Consensus size: 22
6866 TTTGATAATC
*
6876 ATAACCTCGCTATGAAATTTTG
1 ATAACCTCACTATGAAATTTTG
*
6898 ATAAACCTTC-CTATAAAATTTTG
1 AT-AACC-TCACTATGAAATTTTG
* *
6921 GTAACCT--C-ATGAAATCTTG
1 ATAACCTCACTATGAAATTTTG
*
6940 ATAA-CT-AC----AAATTTTT
1 ATAACCTCACTATGAAATTTTG
* *
6956 ATAGCCTCCCTATG-AATCTTTG
1 ATAACCTCACTATGAAAT-TTTG
*
6978 ATAACCTCATTATGAAATTTTG
1 ATAACCTCACTATGAAATTTTG
* * *
7000 TTAATCTCCCTATGAAATTTTG
1 ATAACCTCACTATGAAATTTTG
* * *
7022 ATCTACAT-ACTATAAAATTTTG
1 AT-AACCTCACTATGAAATTTTG
*
7044 ATAACCTTC-TTATGAAATTTTG
1 ATAACC-TCACTATGAAATTTTG
* *
7066 A-AAACTAAACTATGAAATTTTG
1 ATAACCT-CACTATGAAATTTTG
7088 ATAACCTTCA-TATGAAATTTTG
1 ATAACC-TCACTATGAAATTTTG
7110 AT
1 AT
7112 TACTCCATAG
Statistics
Matches: 164, Mismatches: 32, Indels: 36
0.71 0.14 0.16
Matches are distributed among these distances:
16 9 0.05
17 2 0.01
18 3 0.02
19 13 0.08
20 2 0.01
21 9 0.05
22 97 0.59
23 26 0.16
24 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
ATAACCTCACTATGAAATTTTG
Found at i:7245 original size:22 final size:22
Alignment explanation
Indices: 7220--7268 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
7210 AATCATATTT
*
7220 TGAAAAATTGATAACCTCTTTA
1 TGAAAAATTGATAACCTCTCTA
**
7242 TGAAATTTTGATAACCTCTCTA
1 TGAAAAATTGATAACCTCTCTA
7264 T-AAAA
1 TGAAAA
7269 TTTTGTTGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (22 bp):
TGAAAAATTGATAACCTCTCTA
Found at i:7269 original size:22 final size:22
Alignment explanation
Indices: 7227--7340 Score: 88
Period size: 22 Copynumber: 5.2 Consensus size: 22
7217 TTTTGAAAAA
*
7227 TTGATAACCTCTTTATGAAATT
1 TTGATAACCTCTCTATGAAATT
*
7249 TTGATAACCTCTCTATAAAATT
1 TTGATAACCTCTCTATGAAATT
* **
7271 TTGTTGGCC-CTTCTATGAAATT
1 TTGATAACCTC-TCTATGAAATT
* * *
7293 TTGATAATCACAT-TATGCAATT
1 TTGATAACCTC-TCTATGAAATT
* * * *
7315 TTAATAACCGCGCTTTGAAATT
1 TTGATAACCTCTCTATGAAATT
7337 TTGA
1 TTGA
7341 AATTGGATCA
Statistics
Matches: 70, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
21 1 0.01
22 67 0.96
23 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (22 bp):
TTGATAACCTCTCTATGAAATT
Found at i:7639 original size:31 final size:30
Alignment explanation
Indices: 7574--7646 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
7564 TTTAGTAATG
* * *
7574 ACAATTCGGAAATATGTCTTTAAAAAAGGGT
1 ACAATT-GGAAATATATCTTTAAAAAAAGAT
7605 ACAATTGGAAATATAT-TTTAAAAATAAAGAT
1 ACAATTGGAAATATATCTTT-AAAA-AAAGAT
*
7636 ACAATCGGAAA
1 ACAATTGGAAA
7647 ACATAAAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 3 0.08
30 13 0.36
31 20 0.56
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.27
Consensus pattern (30 bp):
ACAATTGGAAATATATCTTTAAAAAAAGAT
Done.