Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013265.1 Corchorus capsularis cultivar CVL-1 contig13286, 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: 116718
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:8725 original size:2 final size:2
Alignment explanation
Indices: 8718--8743 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8708 AATGACCTTA
8718 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
8744 CATAAATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8878 original size:2 final size:2
Alignment explanation
Indices: 8873--8916 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
8863 TCCATGCATG
* *
8873 TA TA TA TA CCA TA TA TA TA AA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8915 TA
1 TA
8917 ATAATTCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.94
3 1 0.03
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:9362 original size:22 final size:22
Alignment explanation
Indices: 9334--9385 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
9324 TGAATTTGCT
9334 AAGTAATTAAAATTACTTGATA
1 AAGTAATTAAAATTACTTGATA
9356 AAGTAATTAAAATTACTTGATA
1 AAGTAATTAAAATTACTTGATA
9378 AAGTAATT
1 AAGTAATT
9386 GCCAATGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.37
Consensus pattern (22 bp):
AAGTAATTAAAATTACTTGATA
Found at i:9689 original size:19 final size:20
Alignment explanation
Indices: 9651--9690 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
9641 TTAAGGAAAA
*
9651 TAAAATATAAAATCTGACTT
1 TAAAATATAAAAACTGACTT
*
9671 TAAAAT-TAAAAACTTACTT
1 TAAAATATAAAAACTGACTT
9690 T
1 T
9691 TTTGTCGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (20 bp):
TAAAATATAAAAACTGACTT
Found at i:12531 original size:3 final size:3
Alignment explanation
Indices: 12523--12567 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
12513 CACCCATGCT
* *
12523 ATC ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC TTC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
12568 TCCTTCCTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:15947 original size:24 final size:24
Alignment explanation
Indices: 15900--15950 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
15890 TGACACGTAT
* * *
15900 CACTTTTTGGTACATGTGATGTGC
1 CACTTTTTGGCACACGTGACGTGC
*
15924 CACTTTTTGGCACACGTGGCGTGC
1 CACTTTTTGGCACACGTGACGTGC
15948 CAC
1 CAC
15951 GTGTCACTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.33
Consensus pattern (24 bp):
CACTTTTTGGCACACGTGACGTGC
Found at i:15962 original size:31 final size:31
Alignment explanation
Indices: 15924--16013 Score: 96
Period size: 30 Copynumber: 2.9 Consensus size: 31
15914 TGTGATGTGC
*
15924 CACTTTTTGGCA-CACGTGGCGTGCCACGTGT
1 CACTTTTTGG-ATCACGTGGCCTGCCACGTGT
*
15955 CACTTTTT-GATCACGTGGCCTGCCATGTGT
1 CACTTTTTGGATCACGTGGCCTGCCACGTGT
* * *
15985 TACTTTTT-GATCCACATGGCATGCCACGT
1 CACTTTTTGGAT-CACGTGGCCTGCCACGT
16014 CGGACACCGT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
29 1 0.02
30 28 0.55
31 22 0.43
ACGTcount: A:0.16, C:0.28, G:0.23, T:0.33
Consensus pattern (31 bp):
CACTTTTTGGATCACGTGGCCTGCCACGTGT
Found at i:18364 original size:16 final size:16
Alignment explanation
Indices: 18321--18365 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
18311 TTTTTTCCCT
18321 ATAATAATAT-ACAAA
1 ATAATAATATAACAAA
* * *
18336 CTAATAGTGTAACAAA
1 ATAATAATATAACAAA
18352 ATAATAATATAACA
1 ATAATAATATAACA
18366 CTACAAAATT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.27
Consensus pattern (16 bp):
ATAATAATATAACAAA
Found at i:25387 original size:2 final size:2
Alignment explanation
Indices: 25376--25457 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
25366 GGGACACTTA
25376 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25417 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
25458 AGAAGTGTAA
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 78 0.99
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42244 original size:13 final size:13
Alignment explanation
Indices: 42226--42258 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
42216 CTACTGCTTA
42226 CTGTTCCTGTGAT
1 CTGTTCCTGTGAT
42239 CTGTTCCTGTGAT
1 CTGTTCCTGTGAT
42252 CTGTTCC
1 CTGTTCC
42259 ATATTCTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.06, C:0.27, G:0.21, T:0.45
Consensus pattern (13 bp):
CTGTTCCTGTGAT
Found at i:42268 original size:12 final size:12
Alignment explanation
Indices: 42251--42277 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42241 GTTCCTGTGA
42251 TCTGTTCCATAT
1 TCTGTTCCATAT
42263 TCTGTTCCATAT
1 TCTGTTCCATAT
42275 TCT
1 TCT
42278 AGTCATCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.26, G:0.07, T:0.52
Consensus pattern (12 bp):
TCTGTTCCATAT
Found at i:42707 original size:6 final size:6
Alignment explanation
Indices: 42696--42729 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
42686 AACGAAGTCC
42696 CCCAGG CCCAGG CCCAGG CCCAGG CCCAGG CCCA
1 CCCAGG CCCAGG CCCAGG CCCAGG CCCAGG CCCA
42730 TCCAGTGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.53, G:0.29, T:0.00
Consensus pattern (6 bp):
CCCAGG
Found at i:47087 original size:32 final size:31
Alignment explanation
Indices: 47034--47097 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 31
47024 ACAAAACTTG
47034 TTTTCTTTTTCTAATTAATAGGGTAATTAGC
1 TTTTCTTTTTCTAATTAATAGGGTAATTAGC
*
47065 TTTTTTTTTTGCTACATT-ATAGGGTAATTAGC
1 TTTTCTTTTT-CTA-ATTAATAGGGTAATTAGC
47097 T
1 T
47098 ACTTGCCTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 9 0.30
32 18 0.60
33 3 0.10
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.53
Consensus pattern (31 bp):
TTTTCTTTTTCTAATTAATAGGGTAATTAGC
Found at i:47182 original size:25 final size:25
Alignment explanation
Indices: 47152--47201 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
47142 TATGCCCTAA
47152 CTCCTACAATAGAAGGAAGAATAAT
1 CTCCTACAATAGAAGGAAGAATAAT
*
47177 CTCCTACAATATAAGGAAGAATAAT
1 CTCCTACAATAGAAGGAAGAATAAT
47202 GCAGTTTGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (25 bp):
CTCCTACAATAGAAGGAAGAATAAT
Found at i:49015 original size:28 final size:28
Alignment explanation
Indices: 48978--49031 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
48968 TTCTTGAAGC
*
48978 AATATCATTTTAGTTT-GAAAGATTGGCA
1 AATATAATTTTAGTTTAG-AAGATTGGCA
49006 AATATAATTTTAGTTTAGAAGATTGG
1 AATATAATTTTAGTTTAGAAGATTGG
49032 TAAACTAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.41
Consensus pattern (28 bp):
AATATAATTTTAGTTTAGAAGATTGGCA
Found at i:55442 original size:2 final size:2
Alignment explanation
Indices: 55437--55481 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
55427 ACTTATGTGT
55437 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
55479 AC A
1 AC A
55482 TATATATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:57471 original size:57 final size:57
Alignment explanation
Indices: 57383--57498 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
57373 ACGTGTTTTT
57383 ACGAGGTTGGTCCAGTAGACTGGTCCCACCACTATTAAAGTGGAGTTTTGCTACAAA
1 ACGAGGTTGGTCCAGTAGACTGGTCCCACCACTATTAAAGTGGAGTTTTGCTACAAA
*
57440 ACGAGGTTGGTCCAGTAGACTGGTCCCACCACTATTTAAGTGGAGTTTTGCTACAAA
1 ACGAGGTTGGTCCAGTAGACTGGTCCCACCACTATTAAAGTGGAGTTTTGCTACAAA
57497 AC
1 AC
57499 ATAGGATGAC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.27
Consensus pattern (57 bp):
ACGAGGTTGGTCCAGTAGACTGGTCCCACCACTATTAAAGTGGAGTTTTGCTACAAA
Found at i:62022 original size:28 final size:28
Alignment explanation
Indices: 61990--62047 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
61980 TTTATGAAGC
*
61990 AATATCATTCTAGTTTGAAAGATTGGTA
1 AATATAATTCTAGTTTGAAAGATTGGTA
* *
62018 AATATAATTTTAGTTTGGAAGATTGGTA
1 AATATAATTCTAGTTTGAAAGATTGGTA
62046 AA
1 AA
62048 CTAAGAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.40
Consensus pattern (28 bp):
AATATAATTCTAGTTTGAAAGATTGGTA
Found at i:77071 original size:31 final size:30
Alignment explanation
Indices: 77016--77073 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
77006 AAGGGGACGT
77016 TAAAATTTCTTCTAATCAAATATTAAAAAA
1 TAAAATTTCTTCTAATCAAATATTAAAAAA
*
77046 TAAAATTTCTT-TAAAATTAAATATTAAA
1 TAAAATTTCTTCT--AATCAAATATTAAA
77074 TTGTTTCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 1 0.04
30 11 0.44
31 13 0.52
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (30 bp):
TAAAATTTCTTCTAATCAAATATTAAAAAA
Found at i:79400 original size:13 final size:13
Alignment explanation
Indices: 79384--79413 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
79374 TTATGTATTC
79384 ATCTTTAGGTTCT
1 ATCTTTAGGTTCT
79397 ATCTTTAGGTTCT
1 ATCTTTAGGTTCT
79410 ATCT
1 ATCT
79414 CCTCAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.53
Consensus pattern (13 bp):
ATCTTTAGGTTCT
Found at i:81333 original size:1 final size:1
Alignment explanation
Indices: 81327--81379 Score: 106
Period size: 1 Copynumber: 53.0 Consensus size: 1
81317 CACCATATAG
81327 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
81380 GAATAATTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:83676 original size:31 final size:31
Alignment explanation
Indices: 83594--83692 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 31
83584 TTAAGTCAGG
*
83594 TCGGGTTGAATTTGAGTAAGGTTAATTCGGAT
1 TCGGGTTGAATTTGAGTCAGGTTAATTCGG-T
* * * *
83626 TTGAGTTGAATTTGTGTCAGGTTAATTTGGT
1 TCGGGTTGAATTTGAGTCAGGTTAATTCGGT
* * * *
83657 TCGGGTTGAACTTGGGTCAGATTAATTCGGG
1 TCGGGTTGAATTTGAGTCAGGTTAATTCGGT
83688 TCGGG
1 TCGGG
83693 GTTCATTTTG
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
31 30 0.55
32 25 0.45
ACGTcount: A:0.20, C:0.08, G:0.33, T:0.38
Consensus pattern (31 bp):
TCGGGTTGAATTTGAGTCAGGTTAATTCGGT
Found at i:85773 original size:17 final size:17
Alignment explanation
Indices: 85751--85796 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
85741 GTTCCTACCC
*
85751 TACTCACTTGGTACAAA
1 TACTCACCTGGTACAAA
*
85768 TACTCACCTGGTACCAA
1 TACTCACCTGGTACAAA
85785 TACTCACCTGGT
1 TACTCACCTGGT
85797 GAGGTCACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.28
Consensus pattern (17 bp):
TACTCACCTGGTACAAA
Found at i:90613 original size:20 final size:20
Alignment explanation
Indices: 90584--90638 Score: 56
Period size: 25 Copynumber: 2.5 Consensus size: 20
90574 GACTAGTCTG
*
90584 GCATGATTTTAACAATTATA
1 GCATGCTTTTAACAATTATA
90604 GCATGCTTTTTATCTAACAATTATA
1 GCATGC---TT-T-TAACAATTATA
90629 GCATGCTTTT
1 GCATGCTTTT
90639 TATCTTGTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
20 6 0.21
21 1 0.03
22 2 0.07
23 2 0.07
24 1 0.03
25 17 0.59
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (20 bp):
GCATGCTTTTAACAATTATA
Found at i:90627 original size:25 final size:25
Alignment explanation
Indices: 90593--90643 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
90583 GGCATGATTT
90593 TAACAATTATAGCATGCTTTTTATC
1 TAACAATTATAGCATGCTTTTTATC
90618 TAACAATTATAGCATGCTTTTTATC
1 TAACAATTATAGCATGCTTTTTATC
90643 T
1 T
90644 TGTCTTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.45
Consensus pattern (25 bp):
TAACAATTATAGCATGCTTTTTATC
Found at i:94112 original size:15 final size:15
Alignment explanation
Indices: 94092--94121 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
94082 CATGCATATT
94092 CAATGAAATTAAGAA
1 CAATGAAATTAAGAA
94107 CAATGAAATTAAGAA
1 CAATGAAATTAAGAA
94122 AAGCATTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (15 bp):
CAATGAAATTAAGAA
Found at i:109520 original size:14 final size:16
Alignment explanation
Indices: 109491--109522 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
109481 TTTAATTTTT
109491 TTCATGTTTTTCTATG
1 TTCATGTTTTTCTATG
109507 TTCAT-TTTTT-TATG
1 TTCATGTTTTTCTATG
109521 TT
1 TT
109523 TCGGATTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 5 0.31
16 5 0.31
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.69
Consensus pattern (16 bp):
TTCATGTTTTTCTATG
Found at i:116667 original size:3 final size:3
Alignment explanation
Indices: 116661--116708 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
116651 GGTAGCCCCA
*
116661 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT TTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
116709 TTTTTTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Done.