Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013791.1 Corchorus capsularis cultivar CVL-1 contig13812, 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: 32222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:347 original size:18 final size:18
Alignment explanation
Indices: 324--373 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
314 ATTAATCATG
324 AATAAACTAATTAAAACT
1 AATAAACTAATTAAAACT
* **
342 AATAAAATAATTAATCCT
1 AATAAACTAATTAAAACT
*
360 AATAAACTATTTAA
1 AATAAACTAATTAA
374 CAATAATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAACTAATTAAAACT
Found at i:362 original size:28 final size:30
Alignment explanation
Indices: 330--393 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 30
320 CATGAATAAA
330 CTAATTAAAACTA-ATAA-AATAATTAATC
1 CTAATTAAAACTATATAACAATAATTAATC
* *
358 CTAA-T-AAACTATTTAACAATAATTAATG
1 CTAATTAAAACTATATAACAATAATTAATC
*
386 TTAATTAA
1 CTAATTAA
394 TTTCAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 6 0.21
27 4 0.14
28 17 0.59
29 1 0.03
30 1 0.03
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (30 bp):
CTAATTAAAACTATATAACAATAATTAATC
Found at i:380 original size:18 final size:18
Alignment explanation
Indices: 324--380 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
314 ATTAATCATG
324 AATAAACTAATTAA-AACT
1 AATAAACTAATTAACAA-T
* *
342 AATAAAATAATTAATC-CT
1 AATAAACTAATTAA-CAAT
*
360 AATAAACTATTTAACAAT
1 AATAAACTAATTAACAAT
378 AAT
1 AAT
381 TAATGTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 1 0.03
18 30 0.97
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAACTAATTAACAAT
Found at i:497 original size:21 final size:22
Alignment explanation
Indices: 455--502 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
445 CCTGATTAAC
455 AATAATTAATCTAAATTAAATT
1 AATAATTAATCTAAATTAAATT
*
477 AATAA-TAAT-TAATATTCAATT
1 AATAATTAATCTAA-ATTAAATT
498 AATAA
1 AATAA
503 ATTTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 3 0.12
21 16 0.67
22 5 0.21
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAATTAATCTAAATTAAATT
Found at i:4401 original size:7 final size:7
Alignment explanation
Indices: 4389--4422 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
4379 AATGAAATAA
4389 TAAAAAT
1 TAAAAAT
4396 TAAAAAT
1 TAAAAAT
4403 TAAAAAT
1 TAAAAAT
4410 TAAAAAT
1 TAAAAAT
4417 TAAAAA
1 TAAAAA
4423 ATCATTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
TAAAAAT
Found at i:8235 original size:16 final size:16
Alignment explanation
Indices: 8214--8244 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
8204 CCGCAAGGTA
8214 TTTTTTAGCTTAATTT
1 TTTTTTAGCTTAATTT
8230 TTTTTTAGCTTAATT
1 TTTTTTAGCTTAATT
8245 AAGAATAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.68
Consensus pattern (16 bp):
TTTTTTAGCTTAATTT
Found at i:8307 original size:16 final size:16
Alignment explanation
Indices: 8286--8334 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
8276 GTTCGGGTGC
8286 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
8302 TTCGGGTTCGGGT-TCT
1 TTCGGGTTCGGGTAT-T
*
8318 ATCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
8334 T
1 T
8335 CGAGTTCGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.06, C:0.14, G:0.37, T:0.43
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:8312 original size:31 final size:31
Alignment explanation
Indices: 8274--8342 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
8264 GGGCGAGTTT
8274 GGGTTCGGGTGCT-TCGGGTTCGGGTATTTTC
1 GGGTTCGGGTGCTATCGGGTTCGGGTA-TTTC
*
8305 GGGTTCGGGTTCTATCGGGTTCGGGTATTTC
1 GGGTTCGGGTGCTATCGGGTTCGGGTATTTC
*
8336 GAGTTCG
1 GGGTTCG
8343 AGTTCGGGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 22 0.63
32 13 0.37
ACGTcount: A:0.06, C:0.16, G:0.41, T:0.38
Consensus pattern (31 bp):
GGGTTCGGGTGCTATCGGGTTCGGGTATTTC
Found at i:9686 original size:2 final size:2
Alignment explanation
Indices: 9676--9717 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
9666 GAAGTTTTTT
9676 TA TA T- TA TA TA TA T- TCA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
9717 T
1 T
9718 TGTTTAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 34 0.92
3 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12124 original size:18 final size:18
Alignment explanation
Indices: 12103--12139 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12093 TGATTTTAAT
*
12103 TTTCCTTACAATTTTTCC
1 TTTCCCTACAATTTTTCC
*
12121 TTTCCCTACCATTTTTCC
1 TTTCCCTACAATTTTTCC
12139 T
1 T
12140 ACTTCCAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.32, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTCCCTACAATTTTTCC
Found at i:18969 original size:15 final size:14
Alignment explanation
Indices: 18918--19010 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 14
18908 TTATGATTAG
*
18918 TTTTAATTAGTTAA
1 TTTTAATTAGTTTA
** *
18932 TTAAAATTA-CTTA
1 TTTTAATTAGTTTA
*
18945 GTTT-ATTAGTTTA
1 TTTTAATTAGTTTA
18958 TGTTTAATTAG--TA
1 T-TTTAATTAGTTTA
*
18971 -TCTAATTAGTTTA
1 TTTTAATTAGTTTA
18984 TTATTAATTAG--TA
1 TT-TTAATTAGTTTA
18997 -TTTAATTAGTTTA
1 TTTTAATTAGTTTA
19010 T
1 T
19011 GATTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 20
0.65 0.12 0.22
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.24
14 11 0.19
15 12 0.21
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (14 bp):
TTTTAATTAGTTTA
Found at i:18978 original size:26 final size:26
Alignment explanation
Indices: 18949--19016 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
18939 TACTTAGTTT
18949 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
18975 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
19001 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
19017 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:19064 original size:24 final size:25
Alignment explanation
Indices: 19025--19084 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
19015 AAAATGAAGG
*
19025 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
19048 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
*
19073 GAAATGAAGTTT
1 AAAATGAAGTTT
19085 ATGGTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 8 0.24
24 7 0.21
25 18 0.55
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:23324 original size:34 final size:33
Alignment explanation
Indices: 23286--23367 Score: 103
Period size: 34 Copynumber: 2.5 Consensus size: 33
23276 TGATGTCCAT
* * *
23286 AAAAAAA-AATCTTTTCTTCATTAATAATTTGC
1 AAAAAAACAATCTTTTCTCCAATAATAATCTGC
*
23318 AGAAAAATCAATCTTTTCTCCAATAATAATCTGC
1 A-AAAAAACAATCTTTTCTCCAATAATAATCTGC
23352 AAAAATAACAATCTTT
1 AAAAA-AACAATCTTT
23368 GCTACAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 1 0.02
33 9 0.21
34 32 0.76
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (33 bp):
AAAAAAACAATCTTTTCTCCAATAATAATCTGC
Done.