Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007096.1 Corchorus capsularis cultivar CVL-1 contig07117, 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: 58137
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:9114 original size:22 final size:22
Alignment explanation
Indices: 9089--9131 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
9079 AAACGATTAG
9089 CAAAAACCCTAGTACAACTTGT
1 CAAAAACCCTAGTACAACTTGT
*
9111 CAAAAACCCTAGTACCACTTG
1 CAAAAACCCTAGTACAACTTG
9132 ATCCAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.30, G:0.09, T:0.21
Consensus pattern (22 bp):
CAAAAACCCTAGTACAACTTGT
Found at i:10579 original size:21 final size:22
Alignment explanation
Indices: 10545--10591 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
10535 GCATGTGCAA
10545 GGCCGGGACATGCGATGGTGAT
1 GGCCGGGACATGCGATGGTGAT
10567 GGCCGGG-CATGCGATGGTGAT
1 GGCCGGGACATGCGATGGTGAT
10588 GGCC
1 GGCC
10592 AAGCATGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.17
Consensus pattern (22 bp):
GGCCGGGACATGCGATGGTGAT
Found at i:10597 original size:21 final size:21
Alignment explanation
Indices: 10553--10598 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
10543 AAGGCCGGGA
**
10553 CATGCGATGGTGATGGCCGGG
1 CATGCGATGGTGATGGCCAAG
10574 CATGCGATGGTGATGGCCAAG
1 CATGCGATGGTGATGGCCAAG
10595 CATG
1 CATG
10599 TGGCCGGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.41, T:0.20
Consensus pattern (21 bp):
CATGCGATGGTGATGGCCAAG
Found at i:11800 original size:11 final size:11
Alignment explanation
Indices: 11786--11823 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
11776 ATTCATAACA
11786 AATTTATAATT
1 AATTTATAATT
11797 AATTTATAATT
1 AATTTATAATT
11808 -ATTTGATAATT
1 AATTT-ATAATT
*
11819 TATTT
1 AATTT
11824 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:13121 original size:23 final size:23
Alignment explanation
Indices: 13071--13121 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
13061 TATTAAAAAA
* *
13071 TTTTAATTGAATAAATATATTAT
1 TTTTAATTGAATAAAAATATGAT
*
13094 ATTTAATTGAATAAAAATA-GAGT
1 TTTTAATTGAATAAAAATATGA-T
13117 TTTTA
1 TTTTA
13122 GTAGAGTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (23 bp):
TTTTAATTGAATAAAAATATGAT
Found at i:13941 original size:76 final size:78
Alignment explanation
Indices: 13845--14011 Score: 293
Period size: 78 Copynumber: 2.2 Consensus size: 78
13835 GTTTTTTAAT
*
13845 TAAAATAGTAAAATGGTAAAATAT-A-AGTAATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGATAAAATATAATAGTAATAAGGATATTAGATTTAATTATATAAAAATAGA
13908 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
*
13921 TAAAATAGTAAAATGATAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGATAAAATATAATAGTAATAAGGATATTAGATTTAATTATATAAAAATAGA
*
13986 GTTTTTTGTTGAG
66 GTTTTTAGTTGAG
13999 TAAAATAGTAAAA
1 TAAAATAGTAAAA
14012 AAATAGTTAT
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
76 23 0.27
77 1 0.01
78 62 0.72
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (78 bp):
TAAAATAGTAAAATGATAAAATATAATAGTAATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:14045 original size:65 final size:68
Alignment explanation
Indices: 13927--14077 Score: 195
Period size: 65 Copynumber: 2.2 Consensus size: 68
13917 TGAGTAAAAT
* *
13927 AGTAAAAT-GATAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
1 AGTAAAATAG-TAAAA-ATAATAGTTATAAAGATATTA-ATTTAATTAAATAAAAATAGAGTTTT
* *
13991 TTGTTG
63 TAGTTA
13997 AGTAAAATAGTAAAAA-AATAGTTATAAAGATATT-A-TTAATTAAATAAAAATAGAGTTTTTAG
1 AGTAAAATAGTAAAAATAATAGTTATAAAGATATTAATTTAATTAAATAAAAATAGAGTTTTTAG
14059 TTA
66 TTA
14062 AGTAAAATTA-TAAAAA
1 AGTAAAA-TAGTAAAAA
14078 CCTAAACAAT
Statistics
Matches: 75, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
65 40 0.53
66 3 0.04
68 17 0.23
69 1 0.01
70 13 0.17
71 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (68 bp):
AGTAAAATAGTAAAAATAATAGTTATAAAGATATTAATTTAATTAAATAAAAATAGAGTTTTTAG
TTA
Found at i:15423 original size:24 final size:24
Alignment explanation
Indices: 15396--15445 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
15386 TAATAAATAC
15396 ACAAACAAATAAATTACAAAGAAA
1 ACAAACAAATAAATTACAAAGAAA
15420 ACAAACAAATAAATTACAAAGAAA
1 ACAAACAAATAAATTACAAAGAAA
15444 AC
1 AC
15446 TCACATTCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.70, C:0.14, G:0.04, T:0.12
Consensus pattern (24 bp):
ACAAACAAATAAATTACAAAGAAA
Found at i:16111 original size:27 final size:28
Alignment explanation
Indices: 16056--16111 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 28
16046 CCATTTTCCA
16056 TTCCAATAATAATAGTATATATGGGCTTG
1 TTCCAATAATAATAG-ATATATGGGCTTG
16085 TTCCAATAATAATAG-TATATGGGCTTG
1 TTCCAATAATAATAGATATATGGGCTTG
16112 GGAGCAGCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 12 0.44
29 15 0.56
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (28 bp):
TTCCAATAATAATAGATATATGGGCTTG
Found at i:17520 original size:26 final size:26
Alignment explanation
Indices: 17474--17525 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
17464 ACATTTACTC
* *
17474 AAATAAATAGACTGTACTTATTCTAT
1 AAATAAATAGACTATACTTATGCTAT
* *
17500 AAATAAATAGATTATAGTTATGCTAT
1 AAATAAATAGACTATACTTATGCTAT
17526 GTGTTTGGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (26 bp):
AAATAAATAGACTATACTTATGCTAT
Found at i:21194 original size:1 final size:1
Alignment explanation
Indices: 21188--21227 Score: 80
Period size: 1 Copynumber: 40.0 Consensus size: 1
21178 GATTAAATGG
21188 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21228 GTTCTTCAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:25648 original size:16 final size:16
Alignment explanation
Indices: 25616--25734 Score: 190
Period size: 16 Copynumber: 7.6 Consensus size: 16
25606 GGGCGGGTTT
25616 GGGTTCGGGTA-TTTC
1 GGGTTCGGGTATTTTC
25631 GGGTTCGGGTATTTTC
1 GGGTTCGGGTATTTTC
25647 GGGTTCGGGTATTTTC
1 GGGTTCGGGTATTTTC
25663 GGGTTCGGG-ATTTTTC
1 GGGTTCGGGTA-TTTTC
* *
25679 TGGTTCGGGTTTTTTC
1 GGGTTCGGGTATTTTC
25695 GGGTTCGGGTA-TTTC
1 GGGTTCGGGTATTTTC
25710 GGGTTCGGGTATTTTC
1 GGGTTCGGGTATTTTC
25726 GGGTTCGGG
1 GGGTTCGGG
25735 CTCGGATCGG
Statistics
Matches: 96, Mismatches: 4, Indels: 7
0.90 0.04 0.07
Matches are distributed among these distances:
15 27 0.28
16 69 0.72
ACGTcount: A:0.05, C:0.13, G:0.39, T:0.43
Consensus pattern (16 bp):
GGGTTCGGGTATTTTC
Found at i:25752 original size:48 final size:48
Alignment explanation
Indices: 25616--25734 Score: 190
Period size: 47 Copynumber: 2.5 Consensus size: 48
25606 GGGCGGGTTT
25616 GGGTTCGGGTA-TTTCGGGTTCGGGTATTTTCGGGTTCGGGTATTTTC
1 GGGTTCGGGTATTTTCGGGTTCGGGTATTTTCGGGTTCGGGTATTTTC
* *
25663 GGGTTCGGG-ATTTTTCTGGTTCGGGTTTTTTCGGGTTCGGGTA-TTTC
1 GGGTTCGGGTA-TTTTCGGGTTCGGGTATTTTCGGGTTCGGGTATTTTC
25710 GGGTTCGGGTATTTTCGGGTTCGGG
1 GGGTTCGGGTATTTTCGGGTTCGGG
25735 CTCGGATCGG
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
46 1 0.02
47 35 0.53
48 30 0.45
ACGTcount: A:0.05, C:0.13, G:0.39, T:0.43
Consensus pattern (48 bp):
GGGTTCGGGTATTTTCGGGTTCGGGTATTTTCGGGTTCGGGTATTTTC
Found at i:26635 original size:11 final size:10
Alignment explanation
Indices: 26606--26635 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
26596 TTTCGGGTTT
26606 GGGTTCGGGC
1 GGGTTCGGGC
26616 GGGTTCGGGC
1 GGGTTCGGGC
26626 GGGTTTCGGG
1 GGG-TTCGGG
26636 TTCATTTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.00, C:0.17, G:0.60, T:0.23
Consensus pattern (10 bp):
GGGTTCGGGC
Found at i:43354 original size:39 final size:39
Alignment explanation
Indices: 43307--43390 Score: 168
Period size: 39 Copynumber: 2.2 Consensus size: 39
43297 GAACATAGCT
43307 GAAATTGCCTTCAGCTCGTAGTACTGGTACATGCTGAAA
1 GAAATTGCCTTCAGCTCGTAGTACTGGTACATGCTGAAA
43346 GAAATTGCCTTCAGCTCGTAGTACTGGTACATGCTGAAA
1 GAAATTGCCTTCAGCTCGTAGTACTGGTACATGCTGAAA
43385 GAAATT
1 GAAATT
43391 ACATTTCTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (39 bp):
GAAATTGCCTTCAGCTCGTAGTACTGGTACATGCTGAAA
Found at i:51242 original size:11 final size:11
Alignment explanation
Indices: 51226--51258 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
51216 TATACTATAT
51226 CTAATTAATAG
1 CTAATTAATAG
*
51237 CTAATTAATAT
1 CTAATTAATAG
51248 CTAATTAATAG
1 CTAATTAATAG
51259 TTGTTCTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:51441 original size:31 final size:31
Alignment explanation
Indices: 51403--51467 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
51393 TTGGGTTATC
* * *
51403 AGTCTCCAGATTTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGAATATTTG
51434 AGTCTCCAGATCTTTAGATCTTGAATATTTG
1 AGTCTCCAGATCTTTAGATCTTGAATATTTG
51465 AGT
1 AGT
51468 TAGTTCAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (31 bp):
AGTCTCCAGATCTTTAGATCTTGAATATTTG
Found at i:53625 original size:199 final size:199
Alignment explanation
Indices: 53272--53660 Score: 679
Period size: 199 Copynumber: 2.0 Consensus size: 199
53262 CATCACGTCA
* * *
53272 TCCATGAGATTAACCAATAGAATTTTGATATGTCCAATGAACTCCTAAAATTTTAGGCACGATTT
1 TCCATGAGACTAACCAATAGAATTTCGATACGTCCAATGAACTCCTAAAATTTTAGGCACGATTT
*
53337 TAACCCAAGGTTTAGCACTCTTTTAAAATAAACCCTATATAAAGGGTAAGTCCCAAATTTGAGAT
66 TAACCCAAGGTTTAACACTCTTTTAAAATAAACCCTATATAAAGGGTAAGTCCCAAATTTGAGAT
* * *
53402 ATTATTGACATATTTTAGAAAATTGATGAGTTGTCTTCGTATTATTGGTTGGTGAAGGGTAAGTT
131 ATTATTGACATATTTTAAAAAATTGATGAGTTGTCTTCGTATTATTAGTTAGTGAAGGGTAAGTT
53467 GTCT
196 GTCT
* * * *
53471 TCCATGGGACTAACCAATATAATTTCGATACGTCCAATGAACTCCTAAAATTTTAGGTATGATTT
1 TCCATGAGACTAACCAATAGAATTTCGATACGTCCAATGAACTCCTAAAATTTTAGGCACGATTT
53536 TAACCCAAGGTTTAACACTCTTTTAAAATAAACCCTATATAAAGGGTAAGTCCCAAATTTGAGAT
66 TAACCCAAGGTTTAACACTCTTTTAAAATAAACCCTATATAAAGGGTAAGTCCCAAATTTGAGAT
53601 ATTATTGACATATTTTAAAAAATTGATGAGTTGTCTTCGTATTATTAGTTAGTGAAGGGT
131 ATTATTGACATATTTTAAAAAATTGATGAGTTGTCTTCGTATTATTAGTTAGTGAAGGGT
53661 CTGTCCCACC
Statistics
Matches: 179, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
199 179 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (199 bp):
TCCATGAGACTAACCAATAGAATTTCGATACGTCCAATGAACTCCTAAAATTTTAGGCACGATTT
TAACCCAAGGTTTAACACTCTTTTAAAATAAACCCTATATAAAGGGTAAGTCCCAAATTTGAGAT
ATTATTGACATATTTTAAAAAATTGATGAGTTGTCTTCGTATTATTAGTTAGTGAAGGGTAAGTT
GTCT
Done.