Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014875.1 Corchorus capsularis cultivar CVL-1 contig14896, 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: 78223
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:5362 original size:2 final size:2
Alignment explanation
Indices: 5351--5380 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5341 AATAAAGGTT
5351 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5381 CTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6560 original size:20 final size:20
Alignment explanation
Indices: 6535--6573 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6525 AATTAGTGAA
6535 TTACTAAATACCGCCCCCTT
1 TTACTAAATACCGCCCCCTT
**
6555 TTACTAGCTACCGCCCCCT
1 TTACTAAATACCGCCCCCT
6574 CTTGGACTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.44, G:0.08, T:0.28
Consensus pattern (20 bp):
TTACTAAATACCGCCCCCTT
Found at i:8389 original size:33 final size:33
Alignment explanation
Indices: 8347--8415 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
8337 CCGCCCTCCT
* *
8347 AGGGCGGCTTACCATGGCACAGGCCGCCCCAGG
1 AGGGAGGCTTACCAGGGCACAGGCCGCCCCAGG
* *
8380 AGGGAGGCTTACCAGGGCTCATGCCGCCCCAGG
1 AGGGAGGCTTACCAGGGCACAGGCCGCCCCAGG
8413 AGG
1 AGG
8416 ACGGCACGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.19, C:0.33, G:0.38, T:0.10
Consensus pattern (33 bp):
AGGGAGGCTTACCAGGGCACAGGCCGCCCCAGG
Found at i:9691 original size:6 final size:6
Alignment explanation
Indices: 9680--9706 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
9670 AATGTATATA
9680 TATCTT TATCTT TATCTT TATCTT TAT
1 TATCTT TATCTT TATCTT TATCTT TAT
9707 ATTATATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.67
Consensus pattern (6 bp):
TATCTT
Found at i:11456 original size:15 final size:15
Alignment explanation
Indices: 11433--11462 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11423 ATCCCCATGA
*
11433 TCCATCCATGTCTCC
1 TCCACCCATGTCTCC
11448 TCCACCCATGTCTCC
1 TCCACCCATGTCTCC
11463 AAGTGAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.50, G:0.07, T:0.30
Consensus pattern (15 bp):
TCCACCCATGTCTCC
Found at i:12536 original size:15 final size:15
Alignment explanation
Indices: 12525--12555 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12515 CCCCCTCCTT
12525 ACCCCACCCCTCCCC
1 ACCCCACCCCTCCCC
*
12540 GCCCCACCCCTCCCC
1 ACCCCACCCCTCCCC
12555 A
1 A
12556 TTTGAACCAA
Statistics
Matches: 14, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.77, G:0.03, T:0.06
Consensus pattern (15 bp):
ACCCCACCCCTCCCC
Found at i:20762 original size:3 final size:3
Alignment explanation
Indices: 20705--20744 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
20695 AGTCATTTAA
20705 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20745 CTCCATAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28432 original size:15 final size:16
Alignment explanation
Indices: 28407--28436 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28397 AATAATTATT
28407 TTTAGATTATAATATA
1 TTTAGATTATAATATA
28423 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
28437 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:32831 original size:301 final size:301
Alignment explanation
Indices: 32254--32850 Score: 901
Period size: 301 Copynumber: 2.0 Consensus size: 301
32244 GCGCCGAGAC
** * *
32254 TCCTTGAAATATCTATATTCATCTAATTAATCTCAGCCACATTGAATTTACGGATTTGTTTTTAC
1 TCCTTGAAATATCTATATTCATCTAACAAATCTCAGCCACATTGAATTTAAGGATTTGCTTTTAC
*
32319 GAGTATCTGAATCTTGTTTCGATTTAATTAGAAAATAATTCAGAAAAATATGAAAAGCAATATTA
66 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAAATAATTCAGAAAAATATGAAAAGCAATATTA
* * * *
32384 AAAGTGTGAAAAAGGCTTTCGATTCGATTTTTATGGCGTTGAAATATATGTTTTTTGTCAATATT
131 AAAGCGTGAAAAAGGCTTTCGATTCGATTTTTATGGCGTCGAAATATATATTTTTTATCAATATT
* *
32449 TTCGCTAGAAATCAAGGAAAAATATTTCGAATCAATTTTTGCAAAACTTTAGCCGAAATCGTGTA
196 TTAGCTAGAAATCAAGGAAAAATATTTCGAATCAATTTTTGCAAAACTTTAGCCGAAATCGTCTA
* *
32514 CTAATCATCACGG-TTTTCGGCTAAAAACGCGTTCCGGCAA
261 CTAAACATCACGGTTTTTCGGCTAAAAACGCATTCCGGCAA
* * * **
32554 TCCTTGAAATATTTATATTTATCTAACCAAATCTCTGCCACATTTTATTTAAGGATTTGCTTTTA
1 TCCTTGAAATATCTATATTCATCTAA-CAAATCTCAGCCACATTGAATTTAAGGATTTGCTTTTA
*
32619 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAGCAATATT
65 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAATAATTCAGAAAAATATGAAAAGCAATATT
* * *
32684 AGAAA-CGTGAAAAAGGCTTTCGATTCGATTTTTATGGCGTCGAATTATATATTTTTTATGAGTA
130 A-AAAGCGTGAAAAAGGCTTTCGATTCGATTTTTATGGCGTCGAAATATATATTTTTTATCAATA
* * * ** *
32748 TTTTAGCTAGAAATCGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTC
194 TTTTAGCTAGAAATCAAGGAAAAATATTTCGAATCAATTTTTGCAAAACTTTAGCCGAAATCGTC
*
32813 TACTAAACATCACGGTTTTTTGGCTAAAAACGCATTCC
259 TACTAAACATCACGGTTTTTCGGCTAAAAACGCATTCC
32851 AGAACCACAG
Statistics
Matches: 265, Mismatches: 29, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
300 24 0.09
301 218 0.82
302 23 0.09
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (301 bp):
TCCTTGAAATATCTATATTCATCTAACAAATCTCAGCCACATTGAATTTAAGGATTTGCTTTTAC
GAGCATCTGAATCTTGTTTCGATTTAATTAGAAAATAATTCAGAAAAATATGAAAAGCAATATTA
AAAGCGTGAAAAAGGCTTTCGATTCGATTTTTATGGCGTCGAAATATATATTTTTTATCAATATT
TTAGCTAGAAATCAAGGAAAAATATTTCGAATCAATTTTTGCAAAACTTTAGCCGAAATCGTCTA
CTAAACATCACGGTTTTTCGGCTAAAAACGCATTCCGGCAA
Found at i:38385 original size:11 final size:11
Alignment explanation
Indices: 38342--38379 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
38332 TTCCTATATA
*
38342 AAATAAATTAT
1 AAATTAATTAT
38353 CAAA-TAATTAT
1 -AAATTAATTAT
38364 AAATTAATTAT
1 AAATTAATTAT
38375 AAATT
1 AAATT
38380 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:39312 original size:20 final size:20
Alignment explanation
Indices: 39287--39326 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
39277 CAAATAAATC
39287 CCTTCTATATATGAAAGTGA
1 CCTTCTATATATGAAAGTGA
39307 CCTTCTATATATGAAAGTGA
1 CCTTCTATATATGAAAGTGA
39327 TATTGTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (20 bp):
CCTTCTATATATGAAAGTGA
Found at i:40125 original size:114 final size:114
Alignment explanation
Indices: 39925--40263 Score: 561
Period size: 114 Copynumber: 3.0 Consensus size: 114
39915 TATTTAATTT
* *
39925 TTCTGCTTGAAGCAGAAATGAAGAATCAACATTCTTTCTTATTCAAGCAACCAATTCAATTGCTT
1 TTCTGCTTGAAGCAGAAATGAAGAATCAACCTTCTTTCTTATTCAAGCAACCAATCCAATTGCTT
* *
39990 TGAAATGTGCATACTTTAAACTCTCCTATGGAGATTGGCAAATTTTTAA
66 TGAAATCTGCATACTTTAAACTCTCCTAAGGAGATTGGCAAATTTTTAA
* * *
40039 TTCTGTTTAAAGCAGAAATGAAGAATCAACCTTCTTTCTTATTCAAGTAACCAATCCAATTGCTT
1 TTCTGCTTGAAGCAGAAATGAAGAATCAACCTTCTTTCTTATTCAAGCAACCAATCCAATTGCTT
* * *
40104 TGAAATCTGCATACTTTAAACTCTCCTAAAGAGATTGGTAAAATTTTAA
66 TGAAATCTGCATACTTTAAACTCTCCTAAGGAGATTGGCAAATTTTTAA
* *
40153 TTCTGCTTGAAGCAGAGATGAAGAATCAACCTTCTTTCTTATTCAAGCAATCAATCCAATTGCTT
1 TTCTGCTTGAAGCAGAAATGAAGAATCAACCTTCTTTCTTATTCAAGCAACCAATCCAATTGCTT
*
40218 TGAAATCTGCATACTTTAAACTCTTCTAAGGAGATTGGCAAATTTT
66 TGAAATCTGCATACTTTAAACTCTCCTAAGGAGATTGGCAAATTTT
40264 AAATAATAGG
Statistics
Matches: 206, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 206 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (114 bp):
TTCTGCTTGAAGCAGAAATGAAGAATCAACCTTCTTTCTTATTCAAGCAACCAATCCAATTGCTT
TGAAATCTGCATACTTTAAACTCTCCTAAGGAGATTGGCAAATTTTTAA
Found at i:46502 original size:30 final size:30
Alignment explanation
Indices: 46466--46527 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
46456 AGATCCCTTG
*
46466 GAGGAGGAGATGAGGAGAAAGAAGAGAGAA
1 GAGGAGGAGATGAGGAGAAAGAAGAGAAAA
* * * *
46496 GAGGAGGAGTTGTGGTGGAAGAAGAGAAAA
1 GAGGAGGAGATGAGGAGAAAGAAGAGAAAA
46526 GA
1 GA
46528 AGAATGGGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.47, T:0.08
Consensus pattern (30 bp):
GAGGAGGAGATGAGGAGAAAGAAGAGAAAA
Found at i:49148 original size:1 final size:1
Alignment explanation
Indices: 49142--49168 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
49132 ATTAAAACTG
49142 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
49169 CCCTCACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:56574 original size:46 final size:46
Alignment explanation
Indices: 56521--56612 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
56511 ACTCATGGCG
56521 ACATGTCTCTAAATATCCACTCTTTGCTTCATAGCTTGAGATGTGA
1 ACATGTCTCTAAATATCCACTCTTTGCTTCATAGCTTGAGATGTGA
56567 ACATGTCTCTAAATATCCACTCTTTGCTTCATAGCTTGAGATGTGA
1 ACATGTCTCTAAATATCCACTCTTTGCTTCATAGCTTGAGATGTGA
56613 TAGTGATGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (46 bp):
ACATGTCTCTAAATATCCACTCTTTGCTTCATAGCTTGAGATGTGA
Found at i:67262 original size:16 final size:16
Alignment explanation
Indices: 67237--67270 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
67227 CCCGCTGTTC
*
67237 TTCTTCTTTTTTTTCT
1 TTCTTCTTTTTCTTCT
*
67253 TTCTTTTTTTTCTTCT
1 TTCTTCTTTTTCTTCT
67269 TT
1 TT
67271 AAAGACTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTCTTCTTTTTCTTCT
Found at i:67268 original size:12 final size:12
Alignment explanation
Indices: 67237--67270 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 12
67227 CCCGCTGTTC
67237 TTCTTCTTTTTT
1 TTCTTCTTTTTT
67249 TTCTTTCTTTTTT
1 TTC-TTCTTTTTT
67262 TTCTTCTTT
1 TTCTTCTTT
67271 AAAGACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTCTTCTTTTTT
Found at i:67282 original size:14 final size:14
Alignment explanation
Indices: 67265--67300 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
67255 CTTTTTTTTC
67265 TTCTTTAAAGACTT
1 TTCTTTAAAGACTT
* *
67279 TTCTTTTAAGATTT
1 TTCTTTAAAGACTT
67293 TTCTTTAA
1 TTCTTTAA
67301 TTTCCTTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.25, C:0.11, G:0.06, T:0.58
Consensus pattern (14 bp):
TTCTTTAAAGACTT
Found at i:71539 original size:23 final size:21
Alignment explanation
Indices: 71513--71569 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 21
71503 ATATTTCTTG
*
71513 TTTTTCTAATTTGGCCTTTTTCT
1 TTTTTTTAATTTGGCC-TTTT-T
71536 TTTTTTTAATTT-G-CTTTTT
1 TTTTTTTAATTTGGCCTTTTT
71555 TTTTTTTAATTTGGC
1 TTTTTTTAATTTGGC
71570 TCCTTGATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 13 0.42
20 5 0.16
21 1 0.03
22 1 0.03
23 11 0.35
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.70
Consensus pattern (21 bp):
TTTTTTTAATTTGGCCTTTTT
Found at i:71559 original size:19 final size:20
Alignment explanation
Indices: 71506--71567 Score: 72
Period size: 19 Copynumber: 2.9 Consensus size: 20
71496 GCCCCCCATA
71506 TTTCTTGTTTTTCTAATTTGGCCTT
1 TTTCTT-TTTTT-TAATTT-G-C-T
71531 TTTCTTTTTTTTAATTTGCT
1 TTTCTTTTTTTTAATTTGCT
71551 TTT-TTTTTTTTAATTTG
1 TTTCTTTTTTTTAATTTG
71568 GCTCCTTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.38
20 4 0.11
21 1 0.03
22 1 0.03
23 6 0.16
24 5 0.14
25 6 0.16
ACGTcount: A:0.10, C:0.10, G:0.08, T:0.73
Consensus pattern (20 bp):
TTTCTTTTTTTTAATTTGCT
Found at i:77439 original size:7 final size:7
Alignment explanation
Indices: 77424--77455 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
77414 GATGGAGACG
*
77424 AAGAAGA
1 AAGAGGA
77431 AAGAGGA
1 AAGAGGA
77438 AAGAGGA
1 AAGAGGA
77445 AAGAGGA
1 AAGAGGA
77452 AAGA
1 AAGA
77456 TATATGAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (7 bp):
AAGAGGA
Found at i:77859 original size:2 final size:2
Alignment explanation
Indices: 77843--77886 Score: 61
Period size: 2 Copynumber: 20.5 Consensus size: 2
77833 GTTAAAAATA
77843 AT AT AT ACT ACT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT A-T A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
77886 A
1 A
77887 AAAGTACGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 33 0.82
3 7 0.17
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:77950 original size:31 final size:31
Alignment explanation
Indices: 77922--77980 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
77912 TGTTTTCCGG
77922 TTGTACCCTTATT-TTTAAAACATATTTCCAA
1 TTGTACCCTT-TTCTTTAAAACATATTTCCAA
77953 TTGTACCCTTTTCTTTAAAACATATTTC
1 TTGTACCCTTTTCTTTAAAACATATTTC
77981 GAAATTGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.47
Consensus pattern (31 bp):
TTGTACCCTTTTCTTTAAAACATATTTCCAA
Done.