Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016310.1 Corchorus capsularis cultivar CVL-1 contig16331, 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: 18590
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2029 original size:17 final size:17
Alignment explanation
Indices: 1999--2046 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1989 CTAGGGCCCC
* * *
1999 AGATCACTAATGATATA
1 AGATCACCAGTGATACA
*
2016 AGATCACCAGTGATGCA
1 AGATCACCAGTGATACA
*
2033 AGATCACCGGTGAT
1 AGATCACCAGTGAT
2047 CAAAAATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.23
Consensus pattern (17 bp):
AGATCACCAGTGATACA
Found at i:4066 original size:48 final size:48
Alignment explanation
Indices: 3962--4122 Score: 132
Period size: 48 Copynumber: 3.4 Consensus size: 48
3952 AAGTTAAAGA
* * * ** * * *
3962 CTAACCATCACGACTTT-TGG-GCCAAAATTAACCGAAAATCAAAAGA
1 CTAACCATCAAGACTTTCGGGTGCAAAAATTGTCCGAAAATCCAAGGG
*
4008 CTAAACCATCATGACTTTCGGAG-GCAAAAATTGTCCGAAAA-CGCAAGGG
1 CT-AACCATCAAGACTTTCGG-GTGCAAAAATTGTCCGAAAATC-CAAGGG
* * * *
4057 CTAACCATCAAGACTTTTGGGTGCCAAAATTGTTCGAAAATCCAATGG
1 CTAACCATCAAGACTTTCGGGTGCAAAAATTGTCCGAAAATCCAAGGG
* *
4105 TTAACCATCACGACTTTC
1 CTAACCATCAAGACTTTC
4123 AGGGGTCAAC
Statistics
Matches: 93, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
46 2 0.02
47 15 0.16
48 54 0.58
49 22 0.24
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.23
Consensus pattern (48 bp):
CTAACCATCAAGACTTTCGGGTGCAAAAATTGTCCGAAAATCCAAGGG
Found at i:4299 original size:2 final size:2
Alignment explanation
Indices: 4292--4321 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4282 CGTTTGGCCC
*
4292 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4322 CACAAACTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5287 original size:48 final size:48
Alignment explanation
Indices: 5183--5343 Score: 132
Period size: 48 Copynumber: 3.4 Consensus size: 48
5173 AAGTTAAAGA
* * * ** * * *
5183 CTAACCATCACGACTTT-TGG-GCCAAAATTAACCGAAAATCAAAAGA
1 CTAACCATCAAGACTTTCGGGTGCAAAAATTGTCCGAAAATCCAAGGG
*
5229 CTAAACCATCATGACTTTCGGAG-GCAAAAATTGTCCGAAAA-CGCAAGGG
1 CT-AACCATCAAGACTTTCGG-GTGCAAAAATTGTCCGAAAATC-CAAGGG
* * * *
5278 CTAACCATCAAGACTTTTGGGTGCCAAAATTGTTCGAAAATCCAATGG
1 CTAACCATCAAGACTTTCGGGTGCAAAAATTGTCCGAAAATCCAAGGG
* *
5326 TTAACCATCACGACTTTC
1 CTAACCATCAAGACTTTC
5344 AGGGGTCAAC
Statistics
Matches: 93, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
46 2 0.02
47 15 0.16
48 54 0.58
49 22 0.24
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.23
Consensus pattern (48 bp):
CTAACCATCAAGACTTTCGGGTGCAAAAATTGTCCGAAAATCCAAGGG
Found at i:5522 original size:2 final size:2
Alignment explanation
Indices: 5515--5546 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5505 TTTGGCCCAG
*
5515 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5547 CACAAACTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:7388 original size:96 final size:96
Alignment explanation
Indices: 7214--7427 Score: 222
Period size: 96 Copynumber: 2.2 Consensus size: 96
7204 GACGAAAAGT
*
7214 CAAAGACTAACCATCACA-ACTTTTGGGGACCAAAATTGGCTGAAAATAAAAAAGCTAACAATCA
1 CAAAGGCTAACCATCA-AGACTTTTGGGGACCAAAATTGGCTGAAAATAAAAAAGCTAACAATCA
* * *
7278 TGACTTTCGAAGGCAAAAATTG-TCCAGAAATG
65 CGACTTTCGAAGGCAAAAAATGATCCA-AAATC
* * * ** * *
7310 CAAAGGCTAACTATCAAGACTTTTGGGTG-CCAGAATTGTCTGAAAATCTAAAGGCTAACCATCA
1 CAAAGGCTAACCATCAAGACTTTTGGG-GACCAAAATTGGCTGAAAATAAAAAAGCTAACAATCA
**
7374 CGA-TTATC-AGAGGCAAAAAATGATGTAAAATC
65 CGACTT-TCGA-AGGCAAAAAATGATCCAAAATC
*
7406 CAAAGGCTAACCATCACGACTT
1 CAAAGGCTAACCATCAAGACTT
7428 GGTTTGGATA
Statistics
Matches: 98, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
95 4 0.04
96 91 0.93
97 3 0.03
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (96 bp):
CAAAGGCTAACCATCAAGACTTTTGGGGACCAAAATTGGCTGAAAATAAAAAAGCTAACAATCAC
GACTTTCGAAGGCAAAAAATGATCCAAAATC
Found at i:7992 original size:38 final size:38
Alignment explanation
Indices: 7945--8021 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
7935 AAGGCTAACC
*
7945 ATCACGACTTTCAGGG-GCCAAAATTGTCTGAAAATCCA
1 ATCACGACTTT-AGGGTGCCAAAATTGTCCGAAAATCCA
* *
7983 ATCATGACTTTTGGGTGCCAAAATTGTCCGAAAATCCA
1 ATCACGACTTTAGGGTGCCAAAATTGTCCGAAAATCCA
8021 A
1 A
8022 AGGCTAACCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 3 0.09
38 32 0.91
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (38 bp):
ATCACGACTTTAGGGTGCCAAAATTGTCCGAAAATCCA
Found at i:8039 original size:48 final size:49
Alignment explanation
Indices: 7983--8079 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
7973 TGAAAATCCA
* * * *
7983 ATCATGACTTTT-GGGTGCC-AAAATTGTCCGAAAATCCAAAGGCTAACC
1 ATCATGACTTTTAGAG-GCCAAAAATTGCCCAAAAACCCAAAGGCTAACC
8031 ATCATGACTTTTAGAGGCCAAAAATTGCCCAAAAACCCAAAGGCTAACC
1 ATCATGACTTTTAGAGGCCAAAAATTGCCCAAAAACCCAAAGGCTAACC
8080 GTCACAACAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
48 15 0.35
49 28 0.65
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (49 bp):
ATCATGACTTTTAGAGGCCAAAAATTGCCCAAAAACCCAAAGGCTAACC
Found at i:8487 original size:47 final size:46
Alignment explanation
Indices: 8398--8616 Score: 150
Period size: 47 Copynumber: 4.6 Consensus size: 46
8388 CAAAACTGTC
* ** * * * *
8398 AAAATCTAAAGACTAGTCATCACGACTTTTGGAGGCTAAAAATGGCTC
1 AAAATCCAAAGACTAACCATCACAACTTTCGG-GG-AAAAAATGGCTG
* * *
8446 AATATCCAAAGGCTAACCATCACAATTTTCGGGGCAAAAAATGGCTG
1 AAAATCCAAAGACTAACCATCACAACTTTCGGGG-AAAAAATGGCTG
* * * * *
8493 AAAAGCCAAAGACTCATCATCACGACTTTCGGGGAAAAAATTGCCTG
1 AAAATCCAAAGACTAACCATCACAACTTTCGGGGAAAAAA-TGGCTG
* ** ** * * *
8540 AAAATCCAAAGTCTAACCATCAGGACACTCGTGAGTAAAAAATGACTT
1 AAAATCCAAAGACTAACCATCACAACTTTCG-G-GGAAAAAATGGCTG
** *
8588 AAAATTTAAAGGCTAACCATCACAACTTT
1 AAAATCCAAAGACTAACCATCACAACTTT
8617 TAGGAGTCAA
Statistics
Matches: 133, Mismatches: 35, Indels: 6
0.76 0.20 0.03
Matches are distributed among these distances:
46 6 0.05
47 69 0.52
48 51 0.38
49 7 0.05
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.22
Consensus pattern (46 bp):
AAAATCCAAAGACTAACCATCACAACTTTCGGGGAAAAAATGGCTG
Found at i:8883 original size:46 final size:46
Alignment explanation
Indices: 8755--8921 Score: 148
Period size: 46 Copynumber: 3.6 Consensus size: 46
8745 AAGTTAAAAA
* * *
8755 CTAACCATCACGACTTTCGGAAGTCGAA-ATTGGCC-AAAGATCCAAAGG
1 CTAACCATCACGACTTTCGG-GGCCAAAGATT--CCGAAA-ATCCAAAGG
* *
8803 -TAACCATCACGACTTTCGGGGGCAAAGATTCCGAAAATCTAAAGG
1 CTAACCATCACGACTTTCGGGGCCAAAGATTCCGAAAATCCAAAGG
8848 CTAACCATCACGAC-TT-GGGTGCCAAA-ATTACCCGAAAATCCAAAGG
1 CTAACCATCACGACTTTCGGG-GCCAAAGATT--CCGAAAATCCAAAGG
* **
8894 CTAACCATCAGGACACTCGGGAGCCAAA
1 CTAACCATCACGACTTTCGGG-GCCAAA
8922 AATGACTTAA
Statistics
Matches: 102, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
44 6 0.06
45 17 0.17
46 47 0.46
47 23 0.23
48 9 0.09
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (46 bp):
CTAACCATCACGACTTTCGGGGCCAAAGATTCCGAAAATCCAAAGG
Found at i:10071 original size:46 final size:47
Alignment explanation
Indices: 10010--10132 Score: 149
Period size: 46 Copynumber: 2.6 Consensus size: 47
10000 AGTCAAAGAC
10010 TAACCATCACGACTTTCGGGACCAAAATTGGCCAAAAATCCAAAGG-
1 TAACCATCACGACTTTCGGGACCAAAATTGGCCAAAAATCCAAAGGT
* * * * ** *
10056 TAACTATCACCACTTTCGGGGCCAAAATTGTCTGAAAATCTAAAGGT
1 TAACCATCACGACTTTCGGGACCAAAATTGGCCAAAAATCCAAAGGT
* *
10103 TAACCATCACGACTTTTGGGTTCCAAAATT
1 TAACCATCACGACTTTCGGG-ACCAAAATT
10133 ATCTAAAATT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 39 0.61
47 17 0.27
48 8 0.12
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (47 bp):
TAACCATCACGACTTTCGGGACCAAAATTGGCCAAAAATCCAAAGGT
Found at i:10141 original size:47 final size:45
Alignment explanation
Indices: 10010--10146 Score: 148
Period size: 46 Copynumber: 2.9 Consensus size: 45
10000 AGTCAAAGAC
* * *
10010 TAACCATCACGACTTTCGGGACCAAAATTGGCCAAAAATCCAAAGG
1 TAACCATCACGACTTTCGGGACCAAAATT-GTCTAAAATCTAAAGG
* * *
10056 TAACTATCACCACTTTCGGGGCCAAAATTGTCTGAAAATCTAAAGG
1 TAACCATCACGACTTTCGGGACCAAAATTGTCT-AAAATCTAAAGG
* * *
10102 TTAACCATCACGACTTTTGGGTTCCAAAATTATCTAAAATTCTAA
1 -TAACCATCACGACTTTCGGG-ACCAAAATTGTCTAAAA-TCTAA
10147 CAGTTTGTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
45 2 0.03
46 37 0.49
47 21 0.28
48 16 0.21
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (45 bp):
TAACCATCACGACTTTCGGGACCAAAATTGTCTAAAATCTAAAGG
Found at i:10437 original size:21 final size:21
Alignment explanation
Indices: 10413--10452 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10403 AAACAAGAGG
**
10413 TTTGCTATTTACCGCCCCCCT
1 TTTGCTAAATACCGCCCCCCT
10434 TTTGCTAAATACCGCCCCC
1 TTTGCTAAATACCGCCCCC
10453 ACCCCCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.42, G:0.10, T:0.33
Consensus pattern (21 bp):
TTTGCTAAATACCGCCCCCCT
Found at i:10630 original size:11 final size:11
Alignment explanation
Indices: 10614--10642 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
10604 GCTCGGCCAT
10614 TTTCTTTTTAA
1 TTTCTTTTTAA
10625 TTTCTTTTTAA
1 TTTCTTTTTAA
10636 TTT-TTTT
1 TTTCTTTT
10643 AATATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTAA
Found at i:11774 original size:15 final size:14
Alignment explanation
Indices: 11754--11815 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 14
11744 TACTTAGTTT
11754 ATTAGTTTATGTTTA
1 ATTAGTTTAT-TTTA
*
11769 ATTAG--TA-TCTA
1 ATTAGTTTATTTTA
11780 ATTAGTTTATTATTA
1 ATTAGTTTATT-TTA
11795 ATTAG--TA-TTTA
1 ATTAGTTTATTTTA
11806 ATTAGTTTAT
1 ATTAGTTTAT
11816 GATTAAAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 15
0.69 0.04 0.27
Matches are distributed among these distances:
11 16 0.42
12 1 0.03
13 8 0.21
14 1 0.03
15 12 0.32
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (14 bp):
ATTAGTTTATTTTA
Found at i:11787 original size:26 final size:26
Alignment explanation
Indices: 11754--11821 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
11744 TACTTAGTTT
11754 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
11780 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
11806 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
11822 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:11873 original size:10 final size:10
Alignment explanation
Indices: 11858--11883 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
11848 TGTTAGAAAT
11858 GAAGTTTGAA
1 GAAGTTTGAA
11868 GAAGTTTGAA
1 GAAGTTTGAA
11878 GAAGTT
1 GAAGTT
11884 GTTAGAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (10 bp):
GAAGTTTGAA
Found at i:11996 original size:21 final size:21
Alignment explanation
Indices: 11970--12013 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
11960 CAAAAGTGTA
11970 AAAAGGGGAGCGATATTTAGC
1 AAAAGGGGAGCGATATTTAGC
* * *
11991 AAAAGGGGGGCGGTGTTTAGC
1 AAAAGGGGAGCGATATTTAGC
12012 AA
1 AA
12014 TCCAGTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.39, T:0.18
Consensus pattern (21 bp):
AAAAGGGGAGCGATATTTAGC
Found at i:13531 original size:47 final size:48
Alignment explanation
Indices: 13473--13569 Score: 160
Period size: 47 Copynumber: 2.0 Consensus size: 48
13463 TCTGCCACAT
*
13473 TTGCATTGGTCAATTGAGTTCAGGACCCATCTATTTC-TTTTTTCATG
1 TTGCATTGGTCAATTGAGTTCAGGACCCATCTATGTCTTTTTTTCATG
* *
13520 TTGCTTTGGTCAATTGAGTTCAGGACCTATCTATGTCTTTTTTTCATG
1 TTGCATTGGTCAATTGAGTTCAGGACCCATCTATGTCTTTTTTTCATG
13568 TT
1 TT
13570 TTTATACTCC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 34 0.74
48 12 0.26
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (48 bp):
TTGCATTGGTCAATTGAGTTCAGGACCCATCTATGTCTTTTTTTCATG
Done.