Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015526.1 Corchorus capsularis cultivar CVL-1 contig15547, 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: 70650
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:5421 original size:91 final size:91
Alignment explanation
Indices: 5266--5444 Score: 322
Period size: 91 Copynumber: 2.0 Consensus size: 91
5256 CAACAGATTG
5266 AAATTCACCAGTTCTAGAGGCATCATTACCATCCTTAAGATCTGCATTGCATCTAACTAGCGCAT
1 AAATTCACCAGTTCTAGAGGCATCATTACCATCCTTAAGATCTGCATTGCATCTAACTAGCGCAT
5331 TAGCAGACGGCTCCGTGACTGCATAT
66 TAGCAGACGGCTCCGTGACTGCATAT
* *
5357 AAATTCACTAGTTCTAGAGGCATCATTGCCATCCTTAAGATCTGCATTGCATCTAACTAGCGCAT
1 AAATTCACCAGTTCTAGAGGCATCATTACCATCCTTAAGATCTGCATTGCATCTAACTAGCGCAT
* *
5422 TAGCAGATGGCTCTGTGACTGCA
66 TAGCAGACGGCTCCGTGACTGCA
5445 CATCAAATGA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (91 bp):
AAATTCACCAGTTCTAGAGGCATCATTACCATCCTTAAGATCTGCATTGCATCTAACTAGCGCAT
TAGCAGACGGCTCCGTGACTGCATAT
Found at i:12499 original size:2 final size:2
Alignment explanation
Indices: 12492--12524 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12482 ACCAAAGAAC
12492 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
12525 CTTGATCATG
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:27159 original size:37 final size:37
Alignment explanation
Indices: 27109--27179 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
27099 TGTCTCATAG
*
27109 GTCAAAGAAACAATCTTCTACCATTGTTATGTAGTAT
1 GTCAAAGAAACAATCTTCCACCATTGTTATGTAGTAT
27146 GTCAAAGAAACAATCTTCCACCATTGTTATGTAG
1 GTCAAAGAAACAATCTTCCACCATTGTTATGTAG
27180 CATGAAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (37 bp):
GTCAAAGAAACAATCTTCCACCATTGTTATGTAGTAT
Found at i:36676 original size:46 final size:46
Alignment explanation
Indices: 36609--36700 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
36599 AAACAAGCTG
* *
36609 CCTCCAAAAAGGAAAATAATACATACATTTAAAAGGTTGCATGCAT
1 CCTCCAAAAAGGAAAATAATACATAAATATAAAAGGTTGCATGCAT
36655 CCTCCAAAAAGGAAAATAATACATAAATATAAAAGGTTGCATGCAT
1 CCTCCAAAAAGGAAAATAATACATAAATATAAAAGGTTGCATGCAT
36701 TTACTTGAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (46 bp):
CCTCCAAAAAGGAAAATAATACATAAATATAAAAGGTTGCATGCAT
Found at i:39505 original size:2 final size:2
Alignment explanation
Indices: 39494--39569 Score: 58
Period size: 2 Copynumber: 41.0 Consensus size: 2
39484 CGACCGACTA
* *
39494 AT AT -T AT AT AT AT AT AT AT AT A- AT -T TT A- AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
39532 AT AT -T AT AT AT ACT A- AT CT AA AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
39570 TTATCAGAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
1 7 0.12
2 50 0.85
3 2 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46566 original size:26 final size:26
Alignment explanation
Indices: 46537--46588 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
46527 GACCTTATAC
46537 ATACAAATGTCATCATGATACACAAA
1 ATACAAATGTCATCATGATACACAAA
46563 ATACAAATGTCATCATGATACACAAA
1 ATACAAATGTCATCATGATACACAAA
46589 CTGTCGACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (26 bp):
ATACAAATGTCATCATGATACACAAA
Found at i:46928 original size:1 final size:1
Alignment explanation
Indices: 46922--46948 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
46912 ACCGATTTAC
46922 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
46949 CTTCTACAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:54942 original size:12 final size:12
Alignment explanation
Indices: 54925--54960 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
54915 ACGCGGTGAA
54925 AAAAAAAAAAAG
1 AAAAAAAAAAAG
*
54937 AAAAAAGAAAAG
1 AAAAAAAAAAAG
54949 AAAAGAAAAAAA
1 AAAA-AAAAAAA
54961 TTAGATAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:54952 original size:17 final size:15
Alignment explanation
Indices: 54923--54960 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 15
54913 TCACGCGGTG
54923 AAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAGA
54938 AAAAAGAAAAGAAAAGA
1 AAAAA-AAAA-AAAAGA
54955 AAAAAA
1 AAAAAA
54961 TTAGATAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.24
16 5 0.24
17 11 0.52
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGA
Found at i:63555 original size:45 final size:46
Alignment explanation
Indices: 63492--63579 Score: 169
Period size: 45 Copynumber: 1.9 Consensus size: 46
63482 TCTTCTCTTT
63492 TTTTTGTTCTTTATCTAAGAAAAATTGTAAAGGACGGATTTAATTC
1 TTTTTGTTCTTTATCTAAGAAAAATTGTAAAGGACGGATTTAATTC
63538 TTTTT-TTCTTTATCTAAGAAAAATTGTAAAGGACGGATTTAA
1 TTTTTGTTCTTTATCTAAGAAAAATTGTAAAGGACGGATTTAA
63580 ATCCTATTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 37 0.88
46 5 0.12
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (46 bp):
TTTTTGTTCTTTATCTAAGAAAAATTGTAAAGGACGGATTTAATTC
Found at i:68917 original size:41 final size:39
Alignment explanation
Indices: 68843--68919 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
68833 TTTTAATTTT
*
68843 TTAATATTAATTAGTTTATGATTAGGTTTAATTAGTTAA
1 TTAAAATTAATTAGTTTATGATTAGGTTTAATTAGTTAA
* * *
68882 TTAAAATTACTTAGTTTATTAGTTTATGTTTAATTAGT
1 TTAAAATTAATTAGTTTA-T-GATTAGGTTTAATTAGT
68920 ATCTAATTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 16 0.50
40 1 0.03
41 15 0.47
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (39 bp):
TTAAAATTAATTAGTTTATGATTAGGTTTAATTAGTTAA
Found at i:68919 original size:15 final size:14
Alignment explanation
Indices: 68869--68960 Score: 56
Period size: 11 Copynumber: 7.0 Consensus size: 14
68859 TATGATTAGG
*
68869 TTTAATTAGTTAAT
1 TTTAATTAGTTTAT
** * *
68883 TAAAATTA-CTTAG
1 TTTAATTAGTTTAT
68896 TTT-ATTAGTTTAT
1 TTTAATTAGTTTAT
68909 GTTTAATTAG--TA-
1 -TTTAATTAGTTTAT
*
68921 TCTAATTAGTTTAT
1 TTTAATTAGTTTAT
68935 TATTAATTAG--TA-
1 T-TTAATTAGTTTAT
68947 TTTAATTAGTTTAT
1 TTTAATTAGTTTAT
68961 GATTAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 20
0.65 0.12 0.23
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.25
14 10 0.18
15 12 0.21
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (14 bp):
TTTAATTAGTTTAT
Found at i:68928 original size:26 final size:26
Alignment explanation
Indices: 68899--68966 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
68889 TACTTAGTTT
68899 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
68925 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
68951 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
68967 AATGAAGAAA
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:69038 original size:15 final size:15
Alignment explanation
Indices: 68992--69039 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
68982 ATTTGAAGAT
68992 TTGTTAGAAATGAAG
1 TTGTTAGAAATGAAG
* *
69007 TTG-AAGAAGTTTGAAG
1 TTGTTAGAA--ATGAAG
69023 TTGTTAGAAATGAAG
1 TTGTTAGAAATGAAG
69038 TT
1 TT
69040 TAGGGTTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 8 0.31
17 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.27, T:0.35
Consensus pattern (15 bp):
TTGTTAGAAATGAAG
Found at i:69340 original size:29 final size:30
Alignment explanation
Indices: 69308--69375 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
69298 ATGCAATTTG
*
69308 GGATATAACGTTAC-AAAACAAGCAATTAA
1 GGATATAACGTTACGAAAACAAGCAAATAA
* *
69337 GGATATAACGTTACGGAAATCGAGCAAATAA
1 GGATATAACGTTAC-GAAAACAAGCAAATAA
69368 GGATATAA
1 GGATATAA
69376 TCCGTTAGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 14 0.41
31 20 0.59
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.21
Consensus pattern (30 bp):
GGATATAACGTTACGAAAACAAGCAAATAA
Found at i:69528 original size:31 final size:30
Alignment explanation
Indices: 69493--69629 Score: 141
Period size: 31 Copynumber: 4.5 Consensus size: 30
69483 CCCTAACTAA
*
69493 TTATATCCTTAATTGCTTGAAATCGAAAACG
1 TTATATCCTTAATTGCTTG-AATCAAAAACG
* *
69524 TTATATCCTTAATTGCTCGAAATAAAAAACG
1 TTATATCCTTAATTGCTTG-AATCAAAAACG
* ****
69555 TTATATCCTTAATTGCTTG-TTTTGTAACG
1 TTATATCCTTAATTGCTTGAATCAAAAACG
* *
69584 TTATATCCTTAATTGCTTGCAGCAACAAACG
1 TTATATCCTTAATTGCTTGAATCAA-AAACG
*
69615 TTATATCCTAAATTG
1 TTATATCCTTAATTG
69630 AGTATTTGAC
Statistics
Matches: 88, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
29 24 0.27
31 64 0.73
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (30 bp):
TTATATCCTTAATTGCTTGAATCAAAAACG
Found at i:69599 original size:60 final size:62
Alignment explanation
Indices: 69493--69629 Score: 170
Period size: 60 Copynumber: 2.2 Consensus size: 62
69483 CCCTAACTAA
*
69493 TTATATCCTTAATTGCTTGAAATCGAAAACGTTATATCCTTAATTGCTCGAAATAAAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACGTTATATCCTTAATTGCTCGAAACAAAAAACG
** * * * * * *
69555 TTATATCCTTAATTGCTTG-TTTTG-TAACGTTATATCCTTAATTGCTTGCAGCAACAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACGTTATATCCTTAATTGCTCGAAACAAAAAACG
*
69615 TTATATCCTAAATTG
1 TTATATCCTTAATTG
69630 AGTATTTGAC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 44 0.68
61 2 0.03
62 19 0.29
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (62 bp):
TTATATCCTTAATTGCTTGAAATCGAAAACGTTATATCCTTAATTGCTCGAAACAAAAAACG
Done.