Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014743.1 Corchorus capsularis cultivar CVL-1 contig14764, 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: 14117
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Found at i:1712 original size:2 final size:2
Alignment explanation
Indices: 1678--1703 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1668 TCCCTCTTTC
1678 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
1704 GCTATATATT
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:3368 original size:2 final size:2
Alignment explanation
Indices: 3361--3397 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3351 ATGTTGAATT
3361 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3398 TATATATACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3402 original size:2 final size:2
Alignment explanation
Indices: 3397--3426 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3387 ACACACACAC
*
3397 AT AT AT AT AC 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
3427 CTTCTATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4475 original size:29 final size:28
Alignment explanation
Indices: 4438--4492 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
4428 CGACTTTCAC
**
4438 AAAAAGATCAATTGTGTCCCTCTACTAA
1 AAAAAGATCAATTCAGTCCCTCTACTAA
4466 AAAAACGATCAATTCAGTCCCTCTACT
1 AAAAA-GATCAATTCAGTCCCTCTACT
4493 TGACACTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.27
Consensus pattern (28 bp):
AAAAAGATCAATTCAGTCCCTCTACTAA
Found at i:5182 original size:80 final size:80
Alignment explanation
Indices: 5049--5207 Score: 291
Period size: 80 Copynumber: 2.0 Consensus size: 80
5039 CTCTAGATAA
*
5049 TTCATCAAAATAAAACTAATAGTAATTGTTTTGTTTGAAATGTATGTTGATTATCTAAAAAAGCA
1 TTCATCAAAATAAAACTAATAGTAATTGTTTTGTTTGAAATGTATGTTGATTATCTAAAAAAACA
5114 TAGTATGATGCGGTT
66 TAGTATGATGCGGTT
* *
5129 TTCATCAAAATAAAGCTAATATTAATTGTTTTGTTTGAAATGTATGTTGATTATCTAAAAAAACA
1 TTCATCAAAATAAAACTAATAGTAATTGTTTTGTTTGAAATGTATGTTGATTATCTAAAAAAACA
5194 TAGTATGATGCGGT
66 TAGTATGATGCGGT
5208 CATTTTTTAA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.39
Consensus pattern (80 bp):
TTCATCAAAATAAAACTAATAGTAATTGTTTTGTTTGAAATGTATGTTGATTATCTAAAAAAACA
TAGTATGATGCGGTT
Found at i:5603 original size:21 final size:21
Alignment explanation
Indices: 5565--5604 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5555 GCCCAAAAAA
*
5565 GAAAAAACAGATCGTGCAAAG
1 GAAAAAAAAGATCGTGCAAAG
* *
5586 GAAAAAAAAGTTCTTGCAA
1 GAAAAAAAAGATCGTGCAA
5605 GAATAGAAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.12, G:0.20, T:0.15
Consensus pattern (21 bp):
GAAAAAAAAGATCGTGCAAAG
Found at i:7150 original size:442 final size:436
Alignment explanation
Indices: 6317--7626 Score: 1530
Period size: 442 Copynumber: 3.0 Consensus size: 436
6307 CCGCTTATAG
* * *
6317 TAAACAAATCA-TTTTTTTGCTGG-TCTATTTATCAAATGATCCCTATATTTTTATGCTTTATGC
1 TAAACAAATAATTTTTTTTGCTGGAT-TA-TTATCAAATGAT-CCTATACTTTTATGATTTATGC
* * * * *
6380 TATTTAGTCCTTCACAATTTTTGGGTTGGACGATTAACGTTTCGACTTTAATTATTTTATTTTTT
63 TATTTAGTCCATCATAAATTATGGGTTGGACGATTAACGTTTCGATTTTAATT-TTTTATTTTTT
* * *
6445 GTTTTGTTTGTCAGATGAAGGTGATTCAACTGTCTATTAAAAGGTAATTTCATGATCTACAACTT
127 GTTTT-TTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTT
* * * * *
6510 TCATGAAGGACTCAAAAGTCAATTTTAGTGTTTTGATTCAAAAAAAAT-CTTCTGAAATTCTGTG
191 TCATGAAGGACTCAAAAGCCAATTTTAATGTTTTGATTCTAAAAAAATGCTTTTGAAATTTTGTG
* * * *
6574 GTCTCGATTGTCGGTGTATTTGATATTTTATAAATTTCGGTCCACTTGTCCGATTGAGGTTGTTC
256 GTCTCGATTG-CGGTCTATTTAATATTGTATAATTTTCGGTCCACTTGTCCGATTGAGGTTGTTC
* * *
6639 AAGTGTCGGTTAAAAGGTTATTGTGTGATCTACGACTTTCGTTAAGGGCCT-AAAAGCTGAATTT
320 AAGTGTCGGTTAAAAGTTTATTGTATGATCTACGACTTTCGTTAAGGGCTTGAAAA-CTGAATTT
6703 GATTAATGAGTTTCGTGGAGGGTTCAAGAGGGAATTTTTATGTTTGGTCTCCA
384 GATTAATGAGTTTCGTGGAGGGTTCAAGAGGGAATTTTTATGTTTGGTCTCCA
*
6756 TAAACAAATAATTTTTTTTGCTGGATTAGTTATCAAATGATCGCTATACTTTTATAATTTATGCT
1 TAAACAAATAATTTTTTTTGCTGGATTA-TTATCAAATGATC-CTATACTTTTATGATTTATGCT
* * *
6821 ATTTAGTCCCTCATAAATTCTGGGTTGGACGATTGAACGTTTCGGTTTTAATTCTTTTATTTTTT
64 ATTTAGTCCATCATAAATTATGGGTTGGACGATT-AACGTTTCGATTTTAATT-TTTTATTTTTT
* * *
6886 GTTTTTCTTGTCCGATCAAGATGATTTAAGTGTCTACTAAAAGGTAATTTCATGATCTACAACTT
127 GTTTTT-TTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTT
* * *
6951 TCATGAAGGACTCAAAAGGCAATTTTAATGTTTTGATTTTAAAAAAATGCTTTTGAAATTTTATG
191 TCATGAAGGACTCAAAAGCCAATTTTAATGTTTTGATTCTAAAAAAATGCTTTTGAAATTTTGTG
* * *
7016 GTCTCCATTGCAGGTCTATTTAATATTGTATAATTTTCGGTCCACTTATCCGATTGAGGTTGTTT
256 GTCTCGATTGC-GGTCTATTTAATATTGTATAATTTTCGGTCCACTTGTCCGATTGAGGTTGTTC
*
7081 AAGTGTCGATTAAAAGTTTATTGTATGATCTACGACTTTCGTTAAGGGCTTGAAAACTGAATTTG
320 AAGTGTCGGTTAAAAGTTTATTGTATGATCTACGACTTTCGTTAAGGGCTTGAAAACTGAATTTG
* * * * * *
7146 ATTAATGAGTTTTGTGGAAGATTCGAGAGAGAATTTTTATGTTTGGTCTTCA
385 ATTAATGAGTTTCGTGGAGGGTTCAAGAGGGAATTTTTATGTTTGGTCTCCA
* * * * *
7198 TAAACAAATATTTTTTTTTTGCTAGATTATCTATCAAATAATCATCATACTTTTATGTTTTATGC
1 TAAACAAATA-ATTTTTTTTGCTGGATTAT-TATCAAATGATCCT-ATACTTTTATGATTTATGC
* *
7263 TATTTAAT-CAT-TTACAATTATGGGTTGGACGATTTAACGCTTT-GAATTTT-ATTTTTGTATT
63 TATTTAGTCCATCATA-AATTATGGGTTGGACGA-TTAACG-TTTCG-ATTTTAATTTTT-TATT
* * * * ** *
7324 TTCTGTTCTATTTGTCCGATCAAGGTGACTCAAGTGTATATTATGAGGTAATTTCATGATTTACA
123 TTTTGTT-TTTTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACA
* * * * ** * *
7389 ACTTTCATGAAGGATTCAGAAGCCAA--ATAATATTTCAATTCT-AAAAAATGATTTTTAAATTT
187 ACTTTCATGAAGGACTCAAAAGCCAATTTTAATGTTTTGATTCTAAAAAAATGCTTTTGAAATTT
* * * * * * *
7451 CGTGGTTTTGATTGCCGATCTATTTAATATATTGTATAATTTTTGCTCCACTTGTCCAATTGTA-
252 TGTGGTCTCGATTG-CGGTCTATTT-A-ATATTGTATAATTTTCGGTCCACTTGTCCGATTG-AG
* * * ** ***
7515 GTTGTTCAAGTGTCGGTTAAAA-TGTTATTGTCTAATCTACGATTTTCACTAAGGGCTTGAATGT
313 GTTGTTCAAGTGTCGGTTAAAAGT-TTATTGTATGATCTACGACTTTCGTTAAGGGCTTGAAAAC
* * * *
7579 TGAATTTGATTCATGAGTTTCATGAAGGGTTCAAGAGGTAATTTTTAT
377 TGAATTTGATTAATGAGTTTCGTGGAGGGTTCAAGAGGGAATTTTTAT
7627 TTTTCATCTC
Statistics
Matches: 747, Mismatches: 102, Indels: 42
0.84 0.11 0.05
Matches are distributed among these distances:
439 46 0.06
440 90 0.12
441 256 0.34
442 289 0.39
443 66 0.09
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (436 bp):
TAAACAAATAATTTTTTTTGCTGGATTATTATCAAATGATCCTATACTTTTATGATTTATGCTAT
TTAGTCCATCATAAATTATGGGTTGGACGATTAACGTTTCGATTTTAATTTTTTATTTTTTGTTT
TTTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATG
AAGGACTCAAAAGCCAATTTTAATGTTTTGATTCTAAAAAAATGCTTTTGAAATTTTGTGGTCTC
GATTGCGGTCTATTTAATATTGTATAATTTTCGGTCCACTTGTCCGATTGAGGTTGTTCAAGTGT
CGGTTAAAAGTTTATTGTATGATCTACGACTTTCGTTAAGGGCTTGAAAACTGAATTTGATTAAT
GAGTTTCGTGGAGGGTTCAAGAGGGAATTTTTATGTTTGGTCTCCA
Found at i:8260 original size:14 final size:16
Alignment explanation
Indices: 8241--8278 Score: 62
Period size: 14 Copynumber: 2.5 Consensus size: 16
8231 GTTAATCATG
8241 TATATTATATA-TAT-
1 TATATTATATACTATA
8255 TATATTATATACTATA
1 TATATTATATACTATA
8271 TATATTAT
1 TATATTAT
8279 TTTTGTAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 11 0.50
15 3 0.14
16 8 0.36
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATTATATACTATA
Done.