Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012095.1 Corchorus capsularis cultivar CVL-1 contig12116, 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: 33883
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:682 original size:101 final size:101
Alignment explanation
Indices: 558--819 Score: 402
Period size: 101 Copynumber: 2.6 Consensus size: 101
548 ATTCAAAGGG
* * *
558 TGACA-TTTTATTTACTAATTACTTAAAAATTCAATCTTTCATTCAAAGATTAAAGCTTTATTTA
1 TGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGATTAAATCTTTATTTA
* *
622 CTAATCATTCTAAAGATTCAATCTTTTACCCGAACA
66 CTAATCACTCTAAAGATTCAATCTTTTACCCAAACA
*
658 TGACATTTTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAA-AGTTAAATCTTTATTT
1 TGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGA-TTAAATCTTTATTT
*
722 ACTAATTACTCTAAAGATTCAATCTTTTACCCAAACA
65 ACTAATCACTCTAAAGATTCAATCTTTTACCCAAACA
* * *
759 TGACATTTTTGTTTACCAATTTACTTAAAAATTCAATATTTTATTCAAAGGTTAAATCTTT
1 TGACATTTTTATTTACCAA-TTACTTAAAAATTCAATCTTTTATTCAAAGATTAAATCTTT
820 TAGCAAAAGG
Statistics
Matches: 147, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
100 6 0.04
101 103 0.70
102 38 0.26
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.43
Consensus pattern (101 bp):
TGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGATTAAATCTTTATTTA
CTAATCACTCTAAAGATTCAATCTTTTACCCAAACA
Found at i:749 original size:51 final size:50
Alignment explanation
Indices: 564--819 Score: 230
Period size: 51 Copynumber: 5.1 Consensus size: 50
554 AGGGTGACAT
* *
564 TTTATTTACTAATTACTTAAAAATTCAATCTTTCATTC-AAAGATTAAAGC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAAG-TTAAATC
* * * ** * * * *
614 TTTATTTACTAATCATTCTAAAGATTCAATCTTTTACCCGAACA-TGACATT
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTC-AAAAGTTAAATC
* *
665 TTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAAGTTAAATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAAGTTAAATC
* ** * * *
715 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTACCCAAACA-TGACATT
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAA-AGTTAAATC
* * * *
766 TTTGTTTACCAATTTACTTAAAAATTCAATATTTTATTCAAAGGTTAAATC
1 TTTATTTACTAA-TTACTTAAAAATTCAATCTTTTATTCAAAAGTTAAATC
817 TTT
1 TTT
820 TAGCAAAAGG
Statistics
Matches: 158, Mismatches: 40, Indels: 15
0.74 0.19 0.07
Matches are distributed among these distances:
49 3 0.02
50 52 0.33
51 95 0.60
52 6 0.04
53 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (50 bp):
TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAAGTTAAATC
Found at i:828 original size:20 final size:20
Alignment explanation
Indices: 805--843 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
795 TATTTTATTC
*
805 AAAGGTTAAATCTTTTAGCA
1 AAAGGTTAAACCTTTTAGCA
*
825 AAAGGTTACACCTTTTAGC
1 AAAGGTTAAACCTTTTAGC
844 CAAATATCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
AAAGGTTAAACCTTTTAGCA
Found at i:3590 original size:27 final size:27
Alignment explanation
Indices: 3541--3646 Score: 133
Period size: 27 Copynumber: 3.9 Consensus size: 27
3531 GTGATCTTAA
* *
3541 AAAAATGA-CTAAATGCCCTCCTGAGTGC
1 AAAAATGACCAAAATG-CC-CCTGGGTGC
*
3569 AAAAATGACCGAAATGCCCCTGGGTGC
1 AAAAATGACCAAAATGCCCCTGGGTGC
*
3596 GAAAATGACCAAAATGCCCCTGGGTGC
1 AAAAATGACCAAAATGCCCCTGGGTGC
* *
3623 AAAAATGACCAAAATACCCTTGGG
1 AAAAATGACCAAAATGCCCCTGGG
3647 CGACTCTAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
27 54 0.77
28 10 0.14
29 6 0.09
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.17
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCCTGGGTGC
Found at i:12855 original size:21 final size:18
Alignment explanation
Indices: 12830--12870 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
12820 GCCTGAAGAC
12830 CATTGAAGATCAATTGGAGAG
1 CATTGAAG-TC-ATTGGA-AG
12851 CATTGAAGTCATTGGAAG
1 CATTGAAGTCATTGGAAG
12869 CA
1 CA
12871 AGAATATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 6 0.30
20 2 0.10
21 8 0.40
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (18 bp):
CATTGAAGTCATTGGAAG
Found at i:14909 original size:30 final size:30
Alignment explanation
Indices: 14869--14927 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
14859 TGTCTTCAAG
14869 TCCATAATAAGTCCTT-GGCGCATAATTCCT
1 TCCATAATAAG-CCTTGGGCGCATAATTCCT
* *
14899 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATAATAAGCCTTGGGCGCATAATTCC
14928 CTCCCCCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATAATTCCT
Found at i:15314 original size:33 final size:33
Alignment explanation
Indices: 15270--15378 Score: 191
Period size: 33 Copynumber: 3.3 Consensus size: 33
15260 TTCTTTTCAC
* *
15270 CCAAAACAGAATTATTTTCAATGTTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
15303 CCAAAATAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
15336 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
15369 CCAAAACAGA
1 CCAAAACAGA
15379 TTTGTTTTCA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:15406 original size:66 final size:66
Alignment explanation
Indices: 15270--15409 Score: 165
Period size: 66 Copynumber: 2.1 Consensus size: 66
15260 TTCTTTTCAC
* * * * * *
15270 CCAAAACAGAATTATTTTCAATGTTATGATCAACCAAAATAGAATTATTTGCAATGCTATGATCA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCA
15335 A
66 A
* * * *
15336 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGATTTGTTTTC-ATCACAATTAGC
1 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAAT-ACAATGAGC
*
15400 AT
65 AA
15402 CCAAAACA
1 CCAAAACA
15410 TATTTAGTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
65 2 0.03
66 60 0.97
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (66 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCA
A
Found at i:15441 original size:33 final size:32
Alignment explanation
Indices: 15404--15508 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 32
15394 ATTAGCATCC
* * *
15404 AAAACATATTTAGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTATCATCGCAAACAACA-CT
* *
15437 AAAACAGATTTAGTGTCATTGCAAACAACACT
1 AAAACAGATTTAGTATCATCGCAAACAACACT
* *
15469 CAAATCAGGTTTAGTATCATCGCAAACAACATCT
1 -AAAACAGATTTAGTATCATCGCAAACAACA-CT
15503 AAAACA
1 AAAACA
15509 CTCTTTACAA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
32 2 0.03
33 57 0.93
34 2 0.03
ACGTcount: A:0.45, C:0.22, G:0.09, T:0.25
Consensus pattern (32 bp):
AAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:17089 original size:8 final size:8
Alignment explanation
Indices: 17061--17094 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
17051 GAATCGGCTA
17061 TGAATTTT
1 TGAATTTT
*
17069 TGAAGTTTC
1 TGAA-TTTT
17078 TGAATTTT
1 TGAATTTT
17086 TGAATTTT
1 TGAATTTT
17094 T
1 T
17095 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:23013 original size:26 final size:25
Alignment explanation
Indices: 22970--23019 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
22960 ATATCAATTT
22970 ATAAAGAAAACAATTAAA-CTAAAA
1 ATAAAGAAAACAATTAAATCTAAAA
22994 ATAAAGCAAAACAAATTAAATCTAAA
1 ATAAAG-AAAAC-AATTAAATCTAAA
23020 TCTAAATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.26
25 5 0.22
26 7 0.30
27 5 0.22
ACGTcount: A:0.68, C:0.10, G:0.04, T:0.18
Consensus pattern (25 bp):
ATAAAGAAAACAATTAAATCTAAAA
Found at i:23021 original size:6 final size:6
Alignment explanation
Indices: 23006--23049 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
22996 AAAGCAAAAC
23006 AAAT-T AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
23050 GCAAATATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.11
6 34 0.89
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATCT
Found at i:25517 original size:10 final size:10
Alignment explanation
Indices: 25502--25526 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25492 TGGTCGAAAC
25502 TTTTTTTATT
1 TTTTTTTATT
25512 TTTTTTTATT
1 TTTTTTTATT
25522 TTTTT
1 TTTTT
25527 GATATTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:26599 original size:30 final size:30
Alignment explanation
Indices: 26532--26600 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
26522 AAAGGGTCAA
*
26532 ATGGCCGATTGTGCCCGGATGGCCCATGCG
1 ATGGCCGGTTGTGCCCGGATGGCCCATGCG
* *
26562 ATGGCCGGTTGTGGCCGG-TTGCACCATGCG
1 ATGGCCGGTTGTGCCCGGATGGC-CCATGCG
26592 ATGGCCGGT
1 ATGGCCGGT
26601 ATGCGAAGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 3 0.09
30 32 0.91
ACGTcount: A:0.12, C:0.28, G:0.39, T:0.22
Consensus pattern (30 bp):
ATGGCCGGTTGTGCCCGGATGGCCCATGCG
Found at i:28196 original size:33 final size:33
Alignment explanation
Indices: 28154--28292 Score: 210
Period size: 33 Copynumber: 4.2 Consensus size: 33
28144 TTTTCACCCT
*
28154 AAACAGAATTAGTTT-TAATGCTATAATCAACCA
1 AAACAGAATTA-TTTGCAATGCTATAATCAACCA
*
28187 AAACAGAATTATTTGCAATGCTATGATCAACCA
1 AAACAGAATTATTTGCAATGCTATAATCAACCA
*
28220 AAACAGAATTATTTGCAATACTA-AGATCAACCA
1 AAACAGAATTATTTGCAATGCTATA-ATCAACCA
*
28253 AAACAGAATTATTTGCAATGCTATGATCAACCA
1 AAACAGAATTATTTGCAATGCTATAATCAACCA
28286 AAACAGA
1 AAACAGA
28293 TTTGTTTTCA
Statistics
Matches: 97, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
32 3 0.03
33 94 0.97
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (33 bp):
AAACAGAATTATTTGCAATGCTATAATCAACCA
Found at i:28355 original size:33 final size:33
Alignment explanation
Indices: 28318--28421 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 33
28308 ATTAGCATCC
**
28318 AAAACAGATTTAGTATCATCATAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* * *
28351 AAAACAGATTTAGTGTCATTGCAAACAACACTC
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
** *
28384 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCGCAAACAACACT-T
28417 AAAAC
1 AAAAC
28422 GCTCTTTTCA
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
32 1 0.02
33 56 0.98
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACTT
Found at i:31205 original size:33 final size:33
Alignment explanation
Indices: 31058--31206 Score: 214
Period size: 33 Copynumber: 4.6 Consensus size: 33
31048 TTCTTTTCAC
*
31058 CCAAAACAGAATTATTTTCAATGC---CATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
* *
31088 CCAAAACAGAATTATTTGCAATGCTGTGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
* *
31121 CCAAAACAAAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
31154 CCAAAACAGAATTATTTTCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
* *
31187 CCAAAACAGATTTGTTTTCA
1 CCAAAACAGAATTATTTTCA
31207 TCACAATTAG
Statistics
Matches: 108, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
30 23 0.21
33 85 0.79
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (33 bp):
CCAAAACAGAATTATTTTCAATGCTATGATCAA
Found at i:31224 original size:66 final size:66
Alignment explanation
Indices: 31085--31229 Score: 175
Period size: 66 Copynumber: 2.2 Consensus size: 66
31075 TCAATGCCAT
* * *
31085 CAACCAAAACAGAATTATTTGCAATGCTGTGATCAACCAAAACAAAATTATTTGCAATGCTATGA
1 CAACCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAAAATTATTTGCAATACAATGA
*
31150 T
66 G
* * * * * *
31151 CAACCAAAACAGAATTATTTTCAATGCTATGATCAACCAAAACAGATTTGTTTTC-ATCACAATT
1 CAACCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAAAATTATTTGCAAT-ACAATG
31215 AG
65 AG
*
31217 CATCCAAAACAGA
1 CAACCAAAACAGA
31230 TTTAGTGTCA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
65 2 0.03
66 65 0.97
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (66 bp):
CAACCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAAAATTATTTGCAATACAATGA
G
Found at i:32707 original size:13 final size:14
Alignment explanation
Indices: 32689--32718 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
32679 CTGGTCAAAA
32689 TTTTTTTTTAT-TT
1 TTTTTTTTTATATT
32702 TTTTTTTTTATATT
1 TTTTTTTTTATATT
32716 TTT
1 TTT
32719 CGATATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTATATT
Found at i:32709 original size:15 final size:15
Alignment explanation
Indices: 32689--32718 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
32679 CTGGTCAAAA
32689 TTTTTTTT-TATTTT
1 TTTTTTTTATATTTT
32703 TTTTTTTTATATTTT
1 TTTTTTTTATATTTT
32718 T
1 T
32719 CGATATAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTTTATATTTT
Done.