Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013386.1 Corchorus capsularis cultivar CVL-1 contig13407, 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: 16008
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:2153 original size:278 final size:278
Alignment explanation
Indices: 1654--2184 Score: 981
Period size: 278 Copynumber: 1.9 Consensus size: 278
1644 AAAAAATGAA
* *
1654 ATACAAAGTTATTATTATAAAATTATTAAAAAGCCATCAGACGTTTGACTTGGTGATAGAGTATT
1 ATACAAAATTATTATTATAAAATTATTAAAAAGCCATCAGACGTTTAACTTGGTGATAGAGTATT
*
1719 GAATTCTTAGTTCAGCTTACCTAGATCGTAAGGTCTTGATTTCAAGTCTTACGAAATGTGAATTC
66 GAACTCTTAGTTCAGCTTACCTAGATCGTAAGGTCTTGATTTCAAGTCTTACGAAATGTGAATTC
*
1784 GTTTTAATTTGTTTGTTTGTATATTTGTTAGATAGGTAGTTTATTTAAAACATAATTTCTAGCAA
131 GTTTTAATTTGTTTGTTTGTATATTTGTTAGATAGATAGTTTATTTAAAACATAATTTCTAGCAA
*
1849 GGGCGGAGCTAGTATATAATCAGTGGGGTTGACCCCACTGAACTTTTCAAAATTTATAATTTAGT
196 GGGCGGAGCTAGTATATAACCAGTGGGGTTGACCCCACTGAACTTTTCAAAATTTATAATTTAGT
1914 ACTATACTAGGTTGTATG
261 ACTATACTAGGTTGTATG
1932 ATACAAAATTATTATTATAAAATTATTAAAAAGCCATCAGACGTTTAACTTGGTGATAGAGTATT
1 ATACAAAATTATTATTATAAAATTATTAAAAAGCCATCAGACGTTTAACTTGGTGATAGAGTATT
* *
1997 GAACTCTTAGTTCAGCTTACCTAGATCGTAAGGTCTTGGTTTCAAGTCTTACGAAATGTGAGTTC
66 GAACTCTTAGTTCAGCTTACCTAGATCGTAAGGTCTTGATTTCAAGTCTTACGAAATGTGAATTC
*
2062 GTTTTAATTTGTTTGTTTGTATATTTGTTAGATAGATAGTTTATTTAAAACATAATTTCTAGTAA
131 GTTTTAATTTGTTTGTTTGTATATTTGTTAGATAGATAGTTTATTTAAAACATAATTTCTAGCAA
*
2127 GGGCGGAGCTAGTATATAGCCAGTGGGGTTGACCCCACTGAACTTTTCAAAATTTATA
196 GGGCGGAGCTAGTATATAACCAGTGGGGTTGACCCCACTGAACTTTTCAAAATTTATA
2185 TATATAACCC
Statistics
Matches: 244, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
278 244 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.38
Consensus pattern (278 bp):
ATACAAAATTATTATTATAAAATTATTAAAAAGCCATCAGACGTTTAACTTGGTGATAGAGTATT
GAACTCTTAGTTCAGCTTACCTAGATCGTAAGGTCTTGATTTCAAGTCTTACGAAATGTGAATTC
GTTTTAATTTGTTTGTTTGTATATTTGTTAGATAGATAGTTTATTTAAAACATAATTTCTAGCAA
GGGCGGAGCTAGTATATAACCAGTGGGGTTGACCCCACTGAACTTTTCAAAATTTATAATTTAGT
ACTATACTAGGTTGTATG
Found at i:3166 original size:31 final size:31
Alignment explanation
Indices: 3126--3186 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
3116 CTACCATTGA
3126 TTCTCTTTGTAGCTTTAATTAACAAACCCAG
1 TTCTCTTTGTAGCTTTAATTAACAAACCCAG
*
3157 TTCTTTTTGTAGCTTTAATTAACAAACCCA
1 TTCTCTTTGTAGCTTTAATTAACAAACCCA
3187 ATTGGAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (31 bp):
TTCTCTTTGTAGCTTTAATTAACAAACCCAG
Found at i:3983 original size:28 final size:29
Alignment explanation
Indices: 3943--4008 Score: 98
Period size: 32 Copynumber: 2.2 Consensus size: 29
3933 ATCTCCATGG
3943 TTGTTACGACCG-TATATTAGATGTCAAA
1 TTGTTACGACCGATATATTAGATGTCAAA
3971 TTGTTACGACCGTATATATATTAGATGTCAAA
1 TTGTTACGACCG---ATATATTAGATGTCAAA
4003 TTGTTA
1 TTGTTA
4009 TCAGTTTGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 12 0.35
32 22 0.65
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (29 bp):
TTGTTACGACCGATATATTAGATGTCAAA
Found at i:8363 original size:55 final size:55
Alignment explanation
Indices: 8279--8388 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
8269 CCAATCCCCA
* *
8279 AGCCTTCAATCTACTTCTTCACAAAAGTCAATTAGTATGACACTTTTATTGTCAC
1 AGCCTTCAATCTACTTCTTCACAAAAGTCAATTACTATGACACTTTCATTGTCAC
*
8334 AGCCTTCAATTTACTTCTTCACAAAAGTCAATTACTATGACACTTTCATTGTCAC
1 AGCCTTCAATCTACTTCTTCACAAAAGTCAATTACTATGACACTTTCATTGTCAC
8389 GGTGAGCCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (55 bp):
AGCCTTCAATCTACTTCTTCACAAAAGTCAATTACTATGACACTTTCATTGTCAC
Found at i:8591 original size:54 final size:54
Alignment explanation
Indices: 8509--8611 Score: 188
Period size: 54 Copynumber: 1.9 Consensus size: 54
8499 AACGGAATTG
*
8509 CCTTCACATCCTTTACCTTAAAAAACTCATAGTTGGAGTACTGAAAGGACCCTA
1 CCTTCACATCCTCTACCTTAAAAAACTCATAGTTGGAGTACTGAAAGGACCCTA
*
8563 CCTTCACATCCTCTACCTTCAAAAACTCATAGTTGGAGTACTGAAAGGA
1 CCTTCACATCCTCTACCTTAAAAAACTCATAGTTGGAGTACTGAAAGGA
8612 AAGAAAAGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (54 bp):
CCTTCACATCCTCTACCTTAAAAAACTCATAGTTGGAGTACTGAAAGGACCCTA
Found at i:9637 original size:19 final size:20
Alignment explanation
Indices: 9591--9638 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
9581 TGTGGCACGC
*
9591 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
9613 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
9632 CACATGT
1 CACATGT
9639 CACGTCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:9652 original size:53 final size:53
Alignment explanation
Indices: 9558--9660 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
9548 GACGTGGCAC
* * **
9558 GCCACGTGTACCAAAATGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
* * *
9611 GCCACATGTACCAAAAAGTGACACATGTCACGTCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
9661 GACACGTGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.18
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:9688 original size:31 final size:31
Alignment explanation
Indices: 9610--9707 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
9600 CAAAAAGTCG
* *
9610 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
* * *
9641 CGTCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
**
9672 TGCCACATGTTTCAAAAA-TGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
9702 TGCCAC
1 TGCCAC
9708 GTGCACAAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
30 18 0.32
31 39 0.68
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Found at i:10018 original size:2 final size:2
Alignment explanation
Indices: 10011--10052 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
10001 GACGACAACG
10011 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
10053 GTGTGTCGCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11545 original size:30 final size:30
Alignment explanation
Indices: 11509--11568 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
11499 CTAGGATGAC
11509 TAATATTCTATCAATGATCCCAAATTAATA
1 TAATATTCTATCAATGATCCCAAATTAATA
11539 TAATATTCTATCAATGATCCCAAATTAATA
1 TAATATTCTATCAATGATCCCAAATTAATA
11569 GTCTAGCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.37
Consensus pattern (30 bp):
TAATATTCTATCAATGATCCCAAATTAATA
Found at i:14027 original size:21 final size:21
Alignment explanation
Indices: 14001--14042 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
13991 TTTCGCCTTT
14001 ATGAATGAAAACAAAAGAAAG
1 ATGAATGAAAACAAAAGAAAG
14022 ATGAATGAAAACAAAAGAAAG
1 ATGAATGAAAACAAAAGAAAG
14043 GAGTCTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.67, C:0.05, G:0.19, T:0.10
Consensus pattern (21 bp):
ATGAATGAAAACAAAAGAAAG
Found at i:14235 original size:22 final size:22
Alignment explanation
Indices: 14210--14256 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
14200 ATTTATTCAT
14210 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
14232 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
14254 TAT
1 TAT
14257 AGTATAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:14252 original size:11 final size:11
Alignment explanation
Indices: 14210--14252 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
14200 ATTTATTCAT
*
14210 TATTAATTAAC
1 TATTAATTAGC
*
14221 TATTAATTAGA
1 TATTAATTAGC
14232 TATTAATTAGC
1 TATTAATTAGC
14243 TATTAATTAG
1 TATTAATTAG
14253 ATATAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:14412 original size:14 final size:13
Alignment explanation
Indices: 14393--14422 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
14383 GGGGACAAAA
14393 ATAATATATAGTAT
1 ATAATATATA-TAT
14407 ATAATATATATAT
1 ATAATATATATAT
14420 ATA
1 ATA
14423 TACACACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:15296 original size:38 final size:38
Alignment explanation
Indices: 15240--15467 Score: 350
Period size: 38 Copynumber: 6.0 Consensus size: 38
15230 ATAATCACAA
*
15240 TCTTGCCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
*
15278 TCTTACCAACAGCTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
* * *
15316 TCTTACCATCAGTTTAA-CCCCTGAGGCGCGGGTTCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
*
15353 TCTTACCAACAGTTTAACACCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
* * *
15391 TCTTACCATCAGTTTAACCCCTTGAGGCACGAGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
* *
15429 TCTTACCATCAGTTTAACCCCCTGAGGCGCGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
15467 T
1 T
15468 ATGCACAGCC
Statistics
Matches: 172, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
37 34 0.20
38 138 0.80
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (38 bp):
TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
Found at i:15376 original size:75 final size:75
Alignment explanation
Indices: 15240--15467 Score: 357
Period size: 75 Copynumber: 3.0 Consensus size: 75
15230 ATAATCACAA
* * *
15240 TCTTGCCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGCTTAACCCCCTGAGG
1 TCTTACCATCAGTTTAA-CCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGG
15305 CACGGGTCCAC
65 CACGGGTCCAC
* * *
15316 TCTTACCATCAGTTTAACCCCTGAGGCGCGGGTTCACTCTTACCAACAGTTTAACACCCTGAGGC
1 TCTTACCATCAGTTTAACCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGC
15381 ACGGGTCCAC
66 ACGGGTCCAC
* *
15391 TCTTACCATCAGTTTAACCCCTTGAGGCACGAGTCCACTCTTACCATCAGTTTAACCCCCTGAGG
1 TCTTACCATCAGTTTAACCCC-TGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGG
*
15456 CGCGGGTCCAC
65 CACGGGTCCAC
15467 T
1 T
15468 ATGCACAGCC
Statistics
Matches: 139, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
75 75 0.54
76 64 0.46
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (75 bp):
TCTTACCATCAGTTTAACCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGC
ACGGGTCCAC
Found at i:15443 original size:113 final size:114
Alignment explanation
Indices: 15240--15467 Score: 386
Period size: 113 Copynumber: 2.0 Consensus size: 114
15230 ATAATCACAA
* *
15240 TCTTGCCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGCTTAACCCCCTGAGG
1 TCTTACCAACAGTTTAACACCCTGAGGCACGGGTCCACTCTTACCAACAGCTTAACCCCCTGAGG
* *
15305 CACGGGTCCACTCTTACCATCAGTTTAA-CCCCTGAGGCGCGGGTTCAC
66 CACGAGTCCACTCTTACCATCAGTTTAACCCCCTGAGGCGCGGGTCCAC
* * *
15353 TCTTACCAACAGTTTAACACCCTGAGGCACGGGTCCACTCTTACCATCAGTTTAACCCCTTGAGG
1 TCTTACCAACAGTTTAACACCCTGAGGCACGGGTCCACTCTTACCAACAGCTTAACCCCCTGAGG
15418 CACGAGTCCACTCTTACCATCAGTTTAACCCCCTGAGGCGCGGGTCCAC
66 CACGAGTCCACTCTTACCATCAGTTTAACCCCCTGAGGCGCGGGTCCAC
15467 T
1 T
15468 ATGCACAGCC
Statistics
Matches: 107, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
113 87 0.81
114 20 0.19
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (114 bp):
TCTTACCAACAGTTTAACACCCTGAGGCACGGGTCCACTCTTACCAACAGCTTAACCCCCTGAGG
CACGAGTCCACTCTTACCATCAGTTTAACCCCCTGAGGCGCGGGTCCAC
Done.