Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012345.1 Corchorus capsularis cultivar CVL-1 contig12366, 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: 47800
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:408 original size:16 final size:16
Alignment explanation
Indices: 389--457 Score: 106
Period size: 16 Copynumber: 4.4 Consensus size: 16
379 CGGGTTCAGG
389 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
405 CGGGTTCGGG-ATTTTT
1 CGGGTTCGGGTA-TTTT
421 CGGGTTCGGGTA-TTT
1 CGGGTTCGGGTATTTT
436 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
452 TGGGTT
1 CGGGTT
458 TGGGCTCGGA
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
15 16 0.33
16 32 0.65
17 1 0.02
ACGTcount: A:0.06, C:0.12, G:0.39, T:0.43
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:430 original size:32 final size:32
Alignment explanation
Indices: 389--457 Score: 115
Period size: 31 Copynumber: 2.2 Consensus size: 32
379 CGGGTTCAGG
389 CGGGTTCGGGTATTTTCGGGTTCGGG-ATTTTT
1 CGGGTTCGGGTA-TTTCGGGTTCGGGTATTTTT
421 CGGGTTCGGGTATTTCGGGTTCGGGTATTTTT
1 CGGGTTCGGGTATTTCGGGTTCGGGTATTTTT
453 -GGGTT
1 CGGGTT
458 TGGGCTCGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
31 18 0.50
32 18 0.50
ACGTcount: A:0.06, C:0.12, G:0.39, T:0.43
Consensus pattern (32 bp):
CGGGTTCGGGTATTTCGGGTTCGGGTATTTTT
Found at i:1263 original size:16 final size:16
Alignment explanation
Indices: 1224--1283 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
1214 TATTTTGATC
* *
1224 TCGGGCTCGGGTCGGGT
1 TCGGGTTCGGG-CGTGT
*
1241 TCAGGTTCGGGCGTGT
1 TCGGGTTCGGGCGTGT
*
1257 TCGGGTTCGGG-TTGT
1 TCGGGTTCGGGCGTGT
1272 CTCGGGTTCGGG
1 -TCGGGTTCGGG
1284 TATTTTGTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
15 3 0.08
16 25 0.68
17 9 0.24
ACGTcount: A:0.02, C:0.20, G:0.48, T:0.30
Consensus pattern (16 bp):
TCGGGTTCGGGCGTGT
Found at i:1363 original size:58 final size:58
Alignment explanation
Indices: 1290--1399 Score: 211
Period size: 58 Copynumber: 1.9 Consensus size: 58
1280 CGGGTATTTT
1290 GTTGACTTTTCTGGTCAATTCGGGTAATTTCGGATTCGGGTTCGGGCGGGTTCAGGAC
1 GTTGACTTTTCTGGTCAATTCGGGTAATTTCGGATTCGGGTTCGGGCGGGTTCAGGAC
*
1348 GTTGACTTTTCTGGTCAATTCGGGTAATTTCGGGTTCGGGTTCGGGCGGGTT
1 GTTGACTTTTCTGGTCAATTCGGGTAATTTCGGATTCGGGTTCGGGCGGGTT
1400 TCGGGTTCAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.12, C:0.16, G:0.35, T:0.36
Consensus pattern (58 bp):
GTTGACTTTTCTGGTCAATTCGGGTAATTTCGGATTCGGGTTCGGGCGGGTTCAGGAC
Found at i:4512 original size:5 final size:5
Alignment explanation
Indices: 4497--4527 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
4487 CCAGTAAGGA
*
4497 ACGGG ATGGG ACGGG ACGGG ACGGG ACGGG A
1 ACGGG ACGGG ACGGG ACGGG ACGGG ACGGG A
4528 TGAGAGGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.16, G:0.58, T:0.03
Consensus pattern (5 bp):
ACGGG
Found at i:4959 original size:22 final size:22
Alignment explanation
Indices: 4931--4972 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
4921 CATCTGTTCC
4931 TCAATAAGCATATTACAATTCT
1 TCAATAAGCATATTACAATTCT
4953 TCAATAAGCATATTACAATT
1 TCAATAAGCATATTACAATT
4973 AAAATTCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TCAATAAGCATATTACAATTCT
Found at i:8047 original size:21 final size:21
Alignment explanation
Indices: 8022--8061 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
8012 CCCTTCATGC
8022 ACTTTTTATTAGCAGTTTTGT
1 ACTTTTTATTAGCAGTTTTGT
8043 ACTTTTTATTAGCAGTTTT
1 ACTTTTTATTAGCAGTTTT
8062 TAATAGGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.10, G:0.12, T:0.57
Consensus pattern (21 bp):
ACTTTTTATTAGCAGTTTTGT
Found at i:8334 original size:61 final size:61
Alignment explanation
Indices: 8259--8563 Score: 578
Period size: 61 Copynumber: 5.0 Consensus size: 61
8249 GAATACTATA
8259 TATGAGCAGAAGAGAGATAAAAATTTATTATACTGACATCAAACATACATGAAACAAGAAT
1 TATGAGCAGAAGAGAGATAAAAATTTATTATACTGACATCAAACATACATGAAACAAGAAT
*
8320 TATGAGCAGAAGAGAGATAAAAATCTATTATACTGACATCAAACATACATGAAACAAGAAT
1 TATGAGCAGAAGAGAGATAAAAATTTATTATACTGACATCAAACATACATGAAACAAGAAT
*
8381 TATGAGCAGAAGAGAGATAAAAATCTATTATACTGACATCAAACATACATGAAACAAGAAT
1 TATGAGCAGAAGAGAGATAAAAATTTATTATACTGACATCAAACATACATGAAACAAGAAT
8442 TATGAGCAGAAGAGAGATAAAAATTTATTATACTGACATCAAACATACATGAAACAAGAAT
1 TATGAGCAGAAGAGAGATAAAAATTTATTATACTGACATCAAACATACATGAAACAAGAAT
8503 TATGAGCAGAAGAGAG--AAAAATTTATTATACTGACATCAAACATACATGAAACAAGAAT
1 TATGAGCAGAAGAGAGATAAAAATTTATTATACTGACATCAAACATACATGAAACAAGAAT
8562 TA
1 TA
8564 CTAGAATATT
Statistics
Matches: 242, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
59 45 0.19
61 197 0.81
ACGTcount: A:0.51, C:0.12, G:0.15, T:0.22
Consensus pattern (61 bp):
TATGAGCAGAAGAGAGATAAAAATTTATTATACTGACATCAAACATACATGAAACAAGAAT
Found at i:10770 original size:30 final size:28
Alignment explanation
Indices: 10699--10776 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
10689 GAACTTACAC
*
10699 AAAACGGCCAAATAAGCCCCTGAACTCT
1 AAAAAGGCCAAATAAGCCCCTGAACTCT
**
10727 -AATTGCAGCCAAATAAGCCCCTGAACTCTTT
1 AAAAAG--GCCAAATAAGCCCCTGAACTC--T
10758 AAAAAGGCCAAATAAGCCC
1 AAAAAGGCCAAATAAGCCC
10777 TTTTCTGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 3 0.07
29 21 0.51
30 13 0.32
31 1 0.02
32 3 0.07
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (28 bp):
AAAAAGGCCAAATAAGCCCCTGAACTCT
Found at i:12213 original size:27 final size:27
Alignment explanation
Indices: 12170--12230 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
12160 TACTAATTAC
12170 TCCCTCTGTTCCATTTTAATTGTCCCTT
1 TCCCT-TGTTCCATTTTAATTGTCCCTT
* *
12198 TCCCTTGTTCCTTTTTAATTGTCTCTT
1 TCCCTTGTTCCATTTTAATTGTCCCTT
12225 TCCCTT
1 TCCCTT
12231 ATTTTCCAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.08, C:0.31, G:0.07, T:0.54
Consensus pattern (27 bp):
TCCCTTGTTCCATTTTAATTGTCCCTT
Found at i:15172 original size:21 final size:21
Alignment explanation
Indices: 15133--15172 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15123 CCTTAGGATG
*
15133 TTGATCACCCATGAGTGGTAT
1 TTGATCACCCAGGAGTGGTAT
15154 TTGATCACCCAAGGA-TGGT
1 TTGATCACCC-AGGAGTGGT
15173 TGTTTAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (21 bp):
TTGATCACCCAGGAGTGGTAT
Found at i:18895 original size:71 final size:70
Alignment explanation
Indices: 18820--18975 Score: 192
Period size: 71 Copynumber: 2.2 Consensus size: 70
18810 TAATTAAAAT
** * ** *
18820 AGTAAAATGGTAAAAT-ATAATAGTTATAAGGATATTAGATTTAATTATATATAAAAA-AGAGTT
1 AGTAAAATAATAAAATAAT-ATAATTATAAACATATTAGATTTAATTA-A-ACAAAAATAGAGTT
18883 TTTAGTTG
63 TTTAGTTG
*
18891 AGTAAAATAATAAAATAATATAATTATAAACATATTATATTTAATTAAACAAAAATAGAGTTTTT
1 AGTAAAATAATAAAATAATATAATTATAAACATATTAGATTTAATTAAACAAAAATAGAGTTTTT
18956 AGTTG
66 AGTTG
18961 AGTAAAACT-ATAAAA
1 AGTAAAA-TAATAAAA
18976 ATCTAAATAA
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
69 6 0.08
70 28 0.37
71 39 0.52
72 2 0.03
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (70 bp):
AGTAAAATAATAAAATAATATAATTATAAACATATTAGATTTAATTAAACAAAAATAGAGTTTTT
AGTTG
Found at i:19123 original size:2 final size:2
Alignment explanation
Indices: 19116--19148 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19106 GGATGAAAGA
19116 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19149 CTTAGAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19256 original size:32 final size:34
Alignment explanation
Indices: 19220--19284 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
19210 TCGTATATTT
19220 GGCTTTATTGATGTT-A-GGGGGCATGAATTGCA
1 GGCTTTATTGATGTTAAGGGGGGCATGAATTGCA
*
19252 GGCTTTATTGATGTTAAGGGGGGCATGAGTTGC
1 GGCTTTATTGATGTTAAGGGGGGCATGAATTGC
19285 TAGTTTTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 15 0.50
33 1 0.03
34 14 0.47
ACGTcount: A:0.20, C:0.09, G:0.37, T:0.34
Consensus pattern (34 bp):
GGCTTTATTGATGTTAAGGGGGGCATGAATTGCA
Found at i:19475 original size:49 final size:49
Alignment explanation
Indices: 19403--19500 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
19393 CAAGTATCTA
19403 AACAATAAATTATTAGAAGAAATAAATCATTATTAGATAGGAAGAGATG
1 AACAATAAATTATTAGAAGAAATAAATCATTATTAGATAGGAAGAGATG
19452 AACAATAAATTATTAGAAGAAATAAATCATTATTAGATAGGAAGAGATG
1 AACAATAAATTATTAGAAGAAATAAATCATTATTAGATAGGAAGAGATG
19501 GTTGTATTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.53, C:0.04, G:0.16, T:0.27
Consensus pattern (49 bp):
AACAATAAATTATTAGAAGAAATAAATCATTATTAGATAGGAAGAGATG
Found at i:28318 original size:30 final size:30
Alignment explanation
Indices: 28245--28320 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
28235 TTGTGTTATA
*
28245 TGTGTTTAGGGACTTTAGTATAAATGCCTC
1 TGTGTTGAGGGACTTTAGTATAAATGCCTC
* *
28275 TGTGTTTAGGGACTTTAGTATAGATGTCCT-
1 TGTGTTGAGGGACTTTAGTATAAATG-CCTC
28305 TGTGCTTGA-GGACTTT
1 TGTG-TTGAGGGACTTT
28321 GAAAAGAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 36 0.86
31 6 0.14
ACGTcount: A:0.20, C:0.12, G:0.26, T:0.42
Consensus pattern (30 bp):
TGTGTTGAGGGACTTTAGTATAAATGCCTC
Found at i:28345 original size:102 final size:98
Alignment explanation
Indices: 28229--28418 Score: 292
Period size: 102 Copynumber: 1.9 Consensus size: 98
28219 GAGAAGAAAA
*
28229 TTGCCCTTGTGTTATATGTGTTTAGGGACTTT-AGTATAAATGCCTCTGTGTTTAGGGACTTTAG
1 TTGCCCCTGTGTTATATGTGTTTAGGGACTTTGA-TATAAATGCCTCTGTGTTTAGGGAC-TTA-
*
28293 TATAGATGTCCTTGTGCTTGAGGACTTTGAAAAGAGAG
63 TA-A-ATGCCCTTGTGCTTGAGGACTTTGAAAAGAGAG
*
28331 TTGCCCCTGTGTTATATGTGTTTAGGGACTTTGATATAGATGCCTCTGTGTTTAGGGACTTATAA
1 TTGCCCCTGTGTTATATGTGTTTAGGGACTTTGATATAAATGCCTCTGTGTTTAGGGACTTATAA
*
28396 ATGCCCTTGTGTTTGAGGACTTT
66 ATGCCCTTGTGCTTGAGGACTTT
28419 TTAGTATAGA
Statistics
Matches: 83, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
98 21 0.25
99 1 0.01
100 2 0.02
101 3 0.04
102 55 0.66
103 1 0.01
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.41
Consensus pattern (98 bp):
TTGCCCCTGTGTTATATGTGTTTAGGGACTTTGATATAAATGCCTCTGTGTTTAGGGACTTATAA
ATGCCCTTGTGCTTGAGGACTTTGAAAAGAGAG
Found at i:28406 original size:26 final size:28
Alignment explanation
Indices: 28347--28451 Score: 101
Period size: 26 Copynumber: 3.6 Consensus size: 28
28337 CTGTGTTATA
28347 TGTGTTTAGGGACTTTGATATAGATGCCTC
1 TGTGTTTAGGGAC-TT-ATATAGATGCCTC
28377 TGTGTTTAGGGACTTATA-A-ATGCC-C
1 TGTGTTTAGGGACTTATATAGATGCCTC
*
28402 TTGTGTTT-GAGGACTTTTTAGTATAGATGTCTC
1 -TGTGTTTAG-GGAC---TTA-TATAGATGCCTC
28435 TGTGTTTAGGGACTTAT
1 TGTGTTTAGGGACTTAT
28452 GAATGTCCTT
Statistics
Matches: 64, Mismatches: 1, Indels: 22
0.74 0.01 0.25
Matches are distributed among these distances:
25 2 0.03
26 16 0.25
27 1 0.02
28 4 0.06
29 8 0.12
30 15 0.23
31 1 0.02
32 15 0.23
33 2 0.03
ACGTcount: A:0.20, C:0.11, G:0.26, T:0.43
Consensus pattern (28 bp):
TGTGTTTAGGGACTTATATAGATGCCTC
Found at i:28437 original size:58 final size:58
Alignment explanation
Indices: 28365--28477 Score: 199
Period size: 58 Copynumber: 1.9 Consensus size: 58
28355 GGGACTTTGA
28365 TATAGATGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAGGACTTTTTAG
1 TATAGATGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAGGACTTTTTAG
* * *
28423 TATAGATGTCTCTGTGTTTAGGGACTTATGAATGTCCTTGTGTTTGAGGACTTTT
1 TATAGATGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAGGACTTTT
28478 ATTGTTGGGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.43
Consensus pattern (58 bp):
TATAGATGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAGGACTTTTTAG
Found at i:28448 original size:32 final size:29
Alignment explanation
Indices: 28347--28449 Score: 99
Period size: 30 Copynumber: 3.5 Consensus size: 29
28337 CTGTGTTATA
*
28347 TGTGTTTAGGGACTTTGATATAGATGCCTC
1 TGTGTTTAGGGACTTTTATATAGATG-CTC
*
28377 TGTGTTTAGGGAC--TTATA-A-ATGCCC
1 TGTGTTTAGGGACTTTTATATAGATGCTC
28402 TTGTGTTT-GAGGACTTTTTAGTATAGATGTCTC
1 -TGTGTTTAG-GGAC-TTTTA-TATAGATG-CTC
28435 TGTGTTTAGGGACTT
1 TGTGTTTAGGGACTT
28450 ATGAATGTCC
Statistics
Matches: 60, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
25 3 0.05
26 14 0.23
27 1 0.02
28 4 0.07
29 3 0.05
30 15 0.25
31 3 0.05
32 14 0.23
33 3 0.05
ACGTcount: A:0.19, C:0.12, G:0.26, T:0.43
Consensus pattern (29 bp):
TGTGTTTAGGGACTTTTATATAGATGCTC
Found at i:28464 original size:26 final size:28
Alignment explanation
Indices: 28347--28475 Score: 76
Period size: 26 Copynumber: 4.5 Consensus size: 28
28337 CTGTGTTATA
*
28347 TGTGTTTAGGGACTT-TGATATAGATGCCTC
1 TGTGTTTAGGGACTTATGAGAT-G-T-CCTC
* *
28377 TGTGTTTAGGGACTTAT-AAATGCCCT-
1 TGTGTTTAGGGACTTATGAGATGTCCTC
*
28403 TGTGTTT-GAGGACTTTTTAGTATAGATGT-CTC
1 TGTGTTTAG-GGAC---TTA-T-GAGATGTCCTC
28435 TGTGTTTAGGGACTTATGA-ATGTCCT-
1 TGTGTTTAGGGACTTATGAGATGTCCTC
28461 TGTGTTT-GAGGACTT
1 TGTGTTTAG-GGACTT
28476 TTATTGTTGG
Statistics
Matches: 82, Mismatches: 5, Indels: 28
0.71 0.04 0.24
Matches are distributed among these distances:
25 2 0.02
26 28 0.34
27 6 0.07
28 1 0.01
29 7 0.09
30 19 0.23
31 3 0.04
32 15 0.18
33 1 0.01
ACGTcount: A:0.19, C:0.12, G:0.26, T:0.43
Consensus pattern (28 bp):
TGTGTTTAGGGACTTATGAGATGTCCTC
Found at i:28760 original size:12 final size:12
Alignment explanation
Indices: 28743--28767 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28733 TTGACCATTG
28743 AAATCCAGTTAT
1 AAATCCAGTTAT
28755 AAATCCAGTTAT
1 AAATCCAGTTAT
28767 A
1 A
28768 CACATGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
AAATCCAGTTAT
Done.