Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010642.1 Corchorus capsularis cultivar CVL-1 contig10663, 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: 30777
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Found at i:263 original size:2 final size:2
Alignment explanation
Indices: 256--293 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
246 TATTGCTTTC
256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
294 AATTCGGACA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3662 original size:16 final size:15
Alignment explanation
Indices: 3614--3682 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 15
3604 TGGGTTACGA
3614 GTCATTCGGGTCTCGG
1 GTCATTCGGGT-TCGG
*
3630 ATCA-TCTGGGTTACGG
1 GTCATTC-GGGTT-CGG
3646 GTCATTCGGGTCTCGG
1 GTCATTCGGGT-TCGG
***
3662 GTCGGACGGGTTCGG
1 GTCATTCGGGTTCGG
3677 GTCATT
1 GTCATT
3683 TACTTTTTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
15 10 0.24
16 28 0.68
17 3 0.07
ACGTcount: A:0.10, C:0.22, G:0.38, T:0.30
Consensus pattern (15 bp):
GTCATTCGGGTTCGG
Found at i:4223 original size:30 final size:30
Alignment explanation
Indices: 4156--4252 Score: 133
Period size: 30 Copynumber: 3.2 Consensus size: 30
4146 AAATTTGGTG
* * *
4156 AGGGACCCAATTGCTCAATTAA-CTCAACTTC
1 AGGGACTCAATTGCTC-ACTAAGTTC-ACTTC
*
4187 AGGGACTCAATTGCTCACTAAGTTCACTTT
1 AGGGACTCAATTGCTCACTAAGTTCACTTC
4217 AGGGACTCAATTGCTCACTAAGTTCACTTC
1 AGGGACTCAATTGCTCACTAAGTTCACTTC
4247 AGGGAC
1 AGGGAC
4253 CCATTTGCAC
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
30 43 0.72
31 17 0.28
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (30 bp):
AGGGACTCAATTGCTCACTAAGTTCACTTC
Found at i:5331 original size:29 final size:30
Alignment explanation
Indices: 5280--5357 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
5270 GCTCAGTTAA
* *
5280 CTCCACTTCAGGGACTAAATTGCATAT-TT-
1 CTCCACTTGAGGGACCAAATTGC-TATGTTC
* * *
5309 TTTCACTTGAGGGACCAAGTTGCTATGTTC
1 CTCCACTTGAGGGACCAAATTGCTATGTTC
5339 GCTCCACTTGAGGGACCAA
1 -CTCCACTTGAGGGACCAA
5358 TTTTGTACTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 3 0.08
29 20 0.51
31 16 0.41
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (30 bp):
CTCCACTTGAGGGACCAAATTGCTATGTTC
Found at i:5439 original size:22 final size:19
Alignment explanation
Indices: 5413--5468 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 19
5403 TTTAAATTTG
5413 CTCTATTTGGTACCCACTTCT
1 CTCTATTTGGTACCCA--TCT
*
5434 CTTCTATTCGGTACCCATCT
1 C-TCTATTTGGTACCCATCT
*
5454 CTCAATTTGGTACCC
1 CTCTATTTGGTACCC
5469 GTTTCCCCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 12 0.39
20 4 0.13
21 1 0.03
22 14 0.45
ACGTcount: A:0.16, C:0.34, G:0.11, T:0.39
Consensus pattern (19 bp):
CTCTATTTGGTACCCATCT
Found at i:5467 original size:19 final size:21
Alignment explanation
Indices: 5417--5468 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
5407 AATTTGCTCT
*
5417 ATTTGGTACCCACTTCTCTTCT
1 ATTTGGTACCCAC-TCTCTTCA
*
5439 ATTCGGTACCCA-TCTC-TCA
1 ATTTGGTACCCACTCTCTTCA
5458 ATTTGGTACCC
1 ATTTGGTACCC
5469 GTTTCCCCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.44
20 4 0.15
22 11 0.41
ACGTcount: A:0.17, C:0.33, G:0.12, T:0.38
Consensus pattern (21 bp):
ATTTGGTACCCACTCTCTTCA
Found at i:5924 original size:47 final size:45
Alignment explanation
Indices: 5855--5946 Score: 139
Period size: 47 Copynumber: 2.0 Consensus size: 45
5845 TTATAGTTGA
5855 TTTAGTTAATTTTTACGGTGGGTATTCAAGGTCTCTGTTGAACAATG
1 TTTAGTTAATTTTTACGGTGGGTATT-AA-GTCTCTGTTGAACAATG
* * *
5902 TTTAGTTTATTTTTACGGTGGGTGTTTAGTCTCTGTTGAACAATG
1 TTTAGTTAATTTTTACGGTGGGTATTAAGTCTCTGTTGAACAATG
5947 ATATTTTTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
45 17 0.40
46 1 0.02
47 24 0.57
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.46
Consensus pattern (45 bp):
TTTAGTTAATTTTTACGGTGGGTATTAAGTCTCTGTTGAACAATG
Found at i:6829 original size:34 final size:34
Alignment explanation
Indices: 6786--6851 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
6776 TTTCATGTTA
*
6786 TGTTTGCTGGAAAAAGGTTTCTGATATCAGGTTG
1 TGTTTGCTGGAAAAAGGTTTCTGAGATCAGGTTG
** *
6820 TGTTTGCTGGGGAGAGGTTTCTGAGATCAGGT
1 TGTTTGCTGGAAAAAGGTTTCTGAGATCAGGT
6852 CTGGTCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.20, C:0.09, G:0.35, T:0.36
Consensus pattern (34 bp):
TGTTTGCTGGAAAAAGGTTTCTGAGATCAGGTTG
Found at i:8007 original size:45 final size:45
Alignment explanation
Indices: 7943--8033 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
7933 CTTCTTTTTG
7943 GTTCTTCGGTGCCGACTGCCTGCTCCCTTTCTTGGGTTGAGCTGA
1 GTTCTTCGGTGCCGACTGCCTGCTCCCTTTCTTGGGTTGAGCTGA
*
7988 GTTCTTTGGTGCCGACTGCCTGCTCCCTTTCTTGGGTTGAGCTGA
1 GTTCTTCGGTGCCGACTGCCTGCTCCCTTTCTTGGGTTGAGCTGA
8033 G
1 G
8034 GCGGTCGATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.07, C:0.27, G:0.30, T:0.36
Consensus pattern (45 bp):
GTTCTTCGGTGCCGACTGCCTGCTCCCTTTCTTGGGTTGAGCTGA
Found at i:14240 original size:24 final size:24
Alignment explanation
Indices: 14208--14256 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
14198 ACCTCTTTTC
14208 ATGCCTTTCATGTCCATATGAAGA
1 ATGCCTTTCATGTCCATATGAAGA
14232 ATGCCTTTCATGTCCATATGAAGA
1 ATGCCTTTCATGTCCATATGAAGA
14256 A
1 A
14257 GAAAGAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (24 bp):
ATGCCTTTCATGTCCATATGAAGA
Found at i:15878 original size:33 final size:33
Alignment explanation
Indices: 15800--15930 Score: 97
Period size: 33 Copynumber: 4.0 Consensus size: 33
15790 GCCAAAATAG
** *
15800 GCGGGTCGCGACCAAACCATGGCCCGGTCGCGC
1 GCGGGTCGCGACCAGGCCATGGCCCGGTCGCAC
* * *
15833 GCAGATCTCGACCAGGCCATGG-CCGAGTCGCAC
1 GCGGGTCGCGACCAGGCCATGGCCCG-GTCGCAC
* * *
15866 GCGGGTCGCGACC-GAGCCATGGTCAGGTTGCAAC
1 GCGGGTCGCGACCAG-GCCATGGCCCGGTCGC-AC
* * * *
15900 CCGCGT-GCGACCCGGCCATGGCCCGATCGCA
1 GCGGGTCGCGACCAGGCCATGGCCCGGTCGCA
15931 GTCCACGCAT
Statistics
Matches: 76, Mismatches: 17, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
32 5 0.07
33 62 0.82
34 9 0.12
ACGTcount: A:0.17, C:0.37, G:0.34, T:0.11
Consensus pattern (33 bp):
GCGGGTCGCGACCAGGCCATGGCCCGGTCGCAC
Found at i:22242 original size:12 final size:12
Alignment explanation
Indices: 22225--22258 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
22215 TTATCTTTTG
22225 TCTCCCTCTTCC
1 TCTCCCTCTTCC
*
22237 TCTCCCTCTCCC
1 TCTCCCTCTTCC
*
22249 TCTTCCTCTT
1 TCTCCCTCTT
22259 GAATGAAGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (12 bp):
TCTCCCTCTTCC
Found at i:28335 original size:437 final size:442
Alignment explanation
Indices: 27463--28335 Score: 1073
Period size: 437 Copynumber: 2.0 Consensus size: 442
27453 CCCGCTTATA
* * *
27463 ATAAACAAATCATTTTTTGTTGGTTTATTTATCAAGTGGTCCCTATACTTTTATGCTTTTTGCTA
1 ATAAACAAATCATTTTTTGTTGGATTATTTATCAAATGGTCCCTATACTTTTATGCTTTATGCTA
* * * *
27528 TTTAGTCCCTCACAATTTTTGGGTTGGACGATTGAACGTTTCAACTTTAATTCTTTTATTTTTTT
66 TTTAATCCCTCACAAATTCTGGGTTAGACGATTGAACGTTTCAACTTTAATTCTTTTATTTTTTT
* * * * *
27593 GTTTTGTTTGTCCAATGAAGGTGATTCAAATGTCTATTAAAAGGTAATTTCATGATCTACAACTT
131 GCTCTATTTGTCCAATCAAGGTGATTCAAATGTCTATTAAAAGGTAATTTAATGATCTACAACTT
* * * *
27658 TCGTGAAGGACTCAAAAGTCAATTTTAATGTTTTAGTTCTAAAAAATAATGCTTATGAAATTTTG
196 TCATGAAAGACTCAAAACTCAATTTTAATGTTTTAGTTCT-AAAAATAATGCTTACGAAATTTTG
* * * * *
27723 TGGTCTCGATTGCCGGTCTATCTAATATTGTATAATTTTCGGTCCACTTGTCCGATTGAGATTGT
260 TGCTCTCGATTACCGGTCTATCTAATATCGTATAATTTTCGGTCCACATGTCCGATTGAGATTCT
* ** *
27788 TTAAGTGTCGGTTAAAAGATTATTGTGTGATCTACGACTTTCGTTAAGGGTCTGAAAGCTGAATT
325 TCAAGTGTCGGTTAAAAGATTATTGTGTGATCTACGACTTTCACTAAGGCTCTGAAAGCTGAATT
* * ** * *** *
27853 TGATTAATGAGTTTCGTGGAGGGTTTGAGAGGGAATTTTTATGTTTGGTCTCC
390 TGATTAATGAGTTTCATGGAGGATTCAAAAACAAATTTGTATGTTTGGTCTCC
*
27906 ATAAACAAAT-ATTTTTT-TTGGATTATTTATTAAATGGT-CCTCATACTTTTATGCTTTATGCT
1 ATAAACAAATCATTTTTTGTTGGATTATTTATCAAATGGTCCCT-ATACTTTTATGCTTTATGCT
* * ***
27968 ATTTAATCCCTCACAAATTCTGGGTTAGACGATTTAATGTTTTGGCTTTAATTCTTTTA-TTTTT
65 ATTTAATCCCTCACAAATTCTGGGTTAGACGATTGAACGTTTCAACTTTAATTCTTTTATTTTTT
** * *
28032 TGCTCTATTTGTCGGATCAAGGTGATTCAAGA-GTCTATTGAAAGGTAATTTAATGATTTACAAC
130 TGCTCTATTTGTCCAATCAAGGTGATTCAA-ATGTCTATTAAAAGGTAATTTAATGATCTACAAC
* * * *
28096 TTTCATTAAAGACTCAAAAACT-AATTTTGATGTTTT-GATTCT-AAAA-AATGTTTCCGAAATT
194 TTTCATGAAAGACTC-AAAACTCAATTTTAATGTTTTAG-TTCTAAAAATAATGCTTACGAAATT
* * ** * * *
28157 TTGTGCTTTCTATTATTGGTCTATTTAATATCGTGTAATTTTCGGTCCACATGTCCGATTGAGGT
257 TTGTGCTCTCGATTACCGGTCTATCTAATATCGTATAATTTTCGGTCCACATGTCCGATTGAGAT
* * * *
28222 TCTTCAAGTGTCGGTTGAAAGGTTATTGTGTGATCTATGACTTTCACTAAGGACT-TGAAAGTTG
322 TCTTCAAGTGTCGGTTAAAAGATTATTGTGTGATCTACGACTTTCACTAAGG-CTCTGAAAGCTG
**
28286 AATTTGATTAATGAGTTTCATGGATTATTCAAAAACAAATTTGTATGTTT
386 AATTTGATTAATGAGTTTCATGGAGGATTCAAAAACAAATTTGTATGTTT
28336 CAAGTTTATG
Statistics
Matches: 364, Mismatches: 61, Indels: 16
0.83 0.14 0.04
Matches are distributed among these distances:
437 158 0.43
438 5 0.01
439 1 0.00
440 90 0.25
441 93 0.26
442 7 0.02
443 10 0.03
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (442 bp):
ATAAACAAATCATTTTTTGTTGGATTATTTATCAAATGGTCCCTATACTTTTATGCTTTATGCTA
TTTAATCCCTCACAAATTCTGGGTTAGACGATTGAACGTTTCAACTTTAATTCTTTTATTTTTTT
GCTCTATTTGTCCAATCAAGGTGATTCAAATGTCTATTAAAAGGTAATTTAATGATCTACAACTT
TCATGAAAGACTCAAAACTCAATTTTAATGTTTTAGTTCTAAAAATAATGCTTACGAAATTTTGT
GCTCTCGATTACCGGTCTATCTAATATCGTATAATTTTCGGTCCACATGTCCGATTGAGATTCTT
CAAGTGTCGGTTAAAAGATTATTGTGTGATCTACGACTTTCACTAAGGCTCTGAAAGCTGAATTT
GATTAATGAGTTTCATGGAGGATTCAAAAACAAATTTGTATGTTTGGTCTCC
Found at i:28561 original size:89 final size:89
Alignment explanation
Indices: 28360--28524 Score: 237
Period size: 89 Copynumber: 1.9 Consensus size: 89
28350 AGTTTATATG
* * *
28360 ATTTGGGTATTGATTTTGTTCTTTAGACATGAAATTTAATTTGTACCAACAAACATTTTCTTATT
1 ATTTGGATATTGATTTGGTT-TTTAGACAGGAAATTTAATTTGTACCAACAAACATTTTCTTATT
* * *
28425 TTGATTATTTATCAAATGATCTATG
65 TTGATTATTGATCAAATCATCTATC
*
28450 ATTTGGATATTGATTTGTTTTTTAGACAGGAAATTTAATTTGTACCAAC-AACATTTTCTTATTT
1 ATTTGGATATTGATTTGGTTTTTAGACAGGAAATTTAATTTGTACCAACAAACATTTTCTTATTT
28514 TG-TT-TTGATCA
66 TGATTATTGATCA
28525 TCAATCATGT
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
86 6 0.09
87 2 0.03
88 17 0.24
89 28 0.40
90 17 0.24
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (89 bp):
ATTTGGATATTGATTTGGTTTTTAGACAGGAAATTTAATTTGTACCAACAAACATTTTCTTATTT
TGATTATTGATCAAATCATCTATC
Found at i:28683 original size:16 final size:18
Alignment explanation
Indices: 28652--28686 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
28642 TGATGAATAT
28652 AATAATTATGATTAATTG
1 AATAATTATGATTAATTG
28670 AATAA-TAT-ATTAATTG
1 AATAATTATGATTAATTG
28686 A
1 A
28687 TTATGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 3 0.18
18 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (18 bp):
AATAATTATGATTAATTG
Found at i:29025 original size:29 final size:27
Alignment explanation
Indices: 28993--29065 Score: 75
Period size: 29 Copynumber: 2.8 Consensus size: 27
28983 ATTTTCTTTC
28993 TCTCCCTTCTCCACGTTTCATGTTCTCCT
1 TCTCCCTTCTCCACGTTTCAT-TTC-CCT
**
29022 TCTCCAGTCTCCACG--TC--TTCCCT
1 TCTCCCTTCTCCACGTTTCATTTCCCT
29045 TCT-CCTTCTCCACGTTTCATT
1 TCTCCCTTCTCCACGTTTCATT
29066 AAGCTTGGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
22 9 0.25
23 6 0.17
24 5 0.14
26 1 0.03
27 2 0.06
29 13 0.36
ACGTcount: A:0.08, C:0.42, G:0.07, T:0.42
Consensus pattern (27 bp):
TCTCCCTTCTCCACGTTTCATTTCCCT
Done.