Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014997.1 Corchorus capsularis cultivar CVL-1 contig15018, 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: 34267
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--46 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1 TAT
4 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46 T
1 T
47 TACTACTACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:324 original size:31 final size:29
Alignment explanation
Indices: 289--356 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
279 CAAATTAGCT
*
289 CCTTAACTATTCATTTTGGGACAAATTGACC
1 CCTTAACTATT--TTTTGGGACAAATCGACC
* *
320 CCTTAACTCTTTTTTGGGATAAATCGACC
1 CCTTAACTATTTTTTGGGACAAATCGACC
349 CCTTAACT
1 CCTTAACT
357 TTTAAAAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 24 0.71
31 10 0.29
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (29 bp):
CCTTAACTATTTTTTGGGACAAATCGACC
Found at i:1130 original size:31 final size:29
Alignment explanation
Indices: 1051--1130 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
1041 TCTCATTTTT
1051 AAAAGTTAAGGGGCCAATTTATCCCAAAA
1 AAAAGTTAAGGGGCCAATTTATCCCAAAA
*
1080 AAAAGTTAAGAGGCCAATTTAT-CCAAAA
1 AAAAGTTAAGGGGCCAATTTATCCCAAAA
*
1108 ATAGATAGTTAAGGGGCTAATTT
1 A-A-A-AGTTAAGGGGCCAATTT
1131 GGGTATTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 7 0.16
29 22 0.49
30 1 0.02
31 15 0.33
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (29 bp):
AAAAGTTAAGGGGCCAATTTATCCCAAAA
Found at i:5272 original size:31 final size:31
Alignment explanation
Indices: 5236--5334 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 31
5226 TTTTGTGCAC
* * *
5236 GTGGCATGCCACGTGCCATTTTTTGAAACAT
1 GTGGCATGCCACGTGTCACTTTTTGATACAT
* *
5267 GTGGCATGCCACATGTCACTTTTTGATACAC
1 GTGGCATGCCACGTGTCACTTTTTGATACAT
* * * *
5298 GTGGCGTGACATGTGTCACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGATACAT
5329 GTGGCA
1 GTGGCA
5335 CGACTTTTTG
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.33
Consensus pattern (31 bp):
GTGGCATGCCACGTGTCACTTTTTGATACAT
Found at i:5342 original size:53 final size:53
Alignment explanation
Indices: 5284--5386 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
5274 GCCACATGTC
** * * *
5284 ACTTTTTGATACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGATACACGTGGCGTGACACATGTCAATTTTTGATACACGTGGCACG
* * *
5337 ACTTTTTGGTACATGTGGCGTGTCACATGTCAATTTTTGATACACGTGGC
1 ACTTTTTGATACACGTGGCGTGACACATGTCAATTTTTGATACACGTGGC
5387 GTGCCACGTC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.37
Consensus pattern (53 bp):
ACTTTTTGATACACGTGGCGTGACACATGTCAATTTTTGATACACGTGGCACG
Found at i:6444 original size:29 final size:29
Alignment explanation
Indices: 6407--6464 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
6397 TCTCGTTTTT
* **
6407 AAAAGTTAAGGGGTCAATTTGTCCCAAAA
1 AAAAATTAAGGGACCAATTTGTCCCAAAA
*
6436 AAAAATTAAGGGACCAATTTGTCCTAAAA
1 AAAAATTAAGGGACCAATTTGTCCCAAAA
6465 TGAATAGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (29 bp):
AAAAATTAAGGGACCAATTTGTCCCAAAA
Found at i:15402 original size:12 final size:12
Alignment explanation
Indices: 15373--15408 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
15363 CAGAGCATAT
15373 TTCCA-TTTTT-
1 TTCCATTTTTTA
15383 TT-CATTTTTTA
1 TTCCATTTTTTA
15394 TTCCATTTTTTA
1 TTCCATTTTTTA
15406 TTC
1 TTC
15409 TGAAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 7 0.30
11 2 0.09
12 12 0.52
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (12 bp):
TTCCATTTTTTA
Found at i:18921 original size:23 final size:24
Alignment explanation
Indices: 18895--18946 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
18885 CAATGTTTCA
*
18895 GAAATTT-TCTAGTAAGAACAGAG
1 GAAATTTATCTAGTAAAAACAGAG
*
18918 GAAATTTAGTGTAGTAAAAACAGAG
1 GAAATTTA-TCTAGTAAAAACAGAG
18943 GAAA
1 GAAA
18947 ACCAGAATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.28
25 18 0.72
ACGTcount: A:0.48, C:0.06, G:0.23, T:0.23
Consensus pattern (24 bp):
GAAATTTATCTAGTAAAAACAGAG
Found at i:19281 original size:2 final size:2
Alignment explanation
Indices: 19274--19311 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
19264 CATTTTATTG
19274 AT AT AT AT AT AT 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 AT AT AT AT AT AT
19312 TATGTATCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23423 original size:28 final size:28
Alignment explanation
Indices: 23376--23429 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
23366 CTAACGCATC
*
23376 CTCAAATTGCAAGTTCAGGGGACAAAAGT
1 CTCAAATTGAAAGTTCAGGGG-CAAAAGT
*
23405 CTCAAATT-AAAGTTTAGGGGCAAAA
1 CTCAAATTGAAAGTTCAGGGGCAAAA
23430 TTTTAGACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 10 0.43
29 8 0.35
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (28 bp):
CTCAAATTGAAAGTTCAGGGGCAAAAGT
Found at i:32682 original size:30 final size:30
Alignment explanation
Indices: 32646--32705 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
32636 CGGATAGAGT
32646 CTTCCATGGAAGGCACCAGAGTTCACAAGC
1 CTTCCATGGAAGGCACCAGAGTTCACAAGC
*
32676 CTTCCATGGAAGGCACCAGAGTTCAGAAGC
1 CTTCCATGGAAGGCACCAGAGTTCACAAGC
32706 AGACAGAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (30 bp):
CTTCCATGGAAGGCACCAGAGTTCACAAGC
Found at i:33428 original size:31 final size:31
Alignment explanation
Indices: 33390--33483 Score: 188
Period size: 31 Copynumber: 3.0 Consensus size: 31
33380 ACTATACTCC
33390 TCTCAAACTGAATTACTTGGGATTGACACAA
1 TCTCAAACTGAATTACTTGGGATTGACACAA
33421 TCTCAAACTGAATTACTTGGGATTGACACAA
1 TCTCAAACTGAATTACTTGGGATTGACACAA
33452 TCTCAAACTGAATTACTTGGGATTGACACAA
1 TCTCAAACTGAATTACTTGGGATTGACACAA
33483 T
1 T
33484 TAATATTTAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (31 bp):
TCTCAAACTGAATTACTTGGGATTGACACAA
Done.