Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008064.1 Corchorus capsularis cultivar CVL-1 contig08085, 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: 80349
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:105 original size:33 final size:33
Alignment explanation
Indices: 63--125 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
53 GGAGCATTTC
63 TTTATCTCACTTAGGGTTTACATATCATGTATT
1 TTTATCTCACTTAGGGTTTACATATCATGTATT
* *
96 TTTATCTCACTTAGGGTTTAGATTTCATGT
1 TTTATCTCACTTAGGGTTTACATATCATGT
126 CATGTCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.49
Consensus pattern (33 bp):
TTTATCTCACTTAGGGTTTACATATCATGTATT
Found at i:300 original size:32 final size:32
Alignment explanation
Indices: 259--320 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
249 GGGGCATATC
*
259 TTTATCTCACTTAGGGTTTATATATCATGTAT
1 TTTATCTCACTTAGGGTTTAGATATCATGTAT
*
291 TTTATCTCACTTAGGGTTTAGATTTCATGT
1 TTTATCTCACTTAGGGTTTAGATATCATGT
321 CATGTCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.50
Consensus pattern (32 bp):
TTTATCTCACTTAGGGTTTAGATATCATGTAT
Found at i:343 original size:197 final size:196
Alignment explanation
Indices: 1--358 Score: 621
Period size: 196 Copynumber: 1.8 Consensus size: 196
* * *
1 ACATTGAATGTTGACATTTAGACTATCTCACTTAGGGTTTAATATAGTTTTTGGAGCATTTCTTT
1 ACATAGAATGTTGAAATTTAGACTATCTCACTTAGGGTTTAATATAGTTTTTGGAGCATATCTTT
66 ATCTCACTTAGGGTTTACATATCATGTATTTTTATCTCACTTAGGGTTTAGATTTCATGTCATGT
66 ATCTCACTTAGGGTTTACATATCATGTATTTTTATCTCACTTAGGGTTTAGATTTCATGTCATGT
*
131 CATTTTTTTGTCTCTCATATCCATTTTTTTTTTGTTTCAAATTTTGACTCTTCAACCACTTTTTA
131 CATTTTTTTGTCTCTCATAGCC-TTTTTTTTTTGTTTCAAATTTTGACTCTTCAACCACTTTTTA
196 TG
195 TG
*
198 ACATAGAATGTTGAAATTTAGACTATCTCACTTAGGGTTTAATATAG-TTTTGGGGCATATCTTT
1 ACATAGAATGTTGAAATTTAGACTATCTCACTTAGGGTTTAATATAGTTTTTGGAGCATATCTTT
*
262 ATCTCACTTAGGGTTTATATATCATGTA-TTTTATCTCACTTAGGGTTTAGATTTCATGTCATGT
66 ATCTCACTTAGGGTTTACATATCATGTATTTTTATCTCACTTAGGGTTTAGATTTCATGTCATGT
326 CATTTTTTTTGGTCTCTCATAGCCTTTTTTTTT
131 CA-TTTTTTT-GTCTCTCATAGCCTTTTTTTTT
359 AAAAAAATTC
Statistics
Matches: 153, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
195 38 0.25
196 58 0.38
197 57 0.37
ACGTcount: A:0.23, C:0.15, G:0.14, T:0.49
Consensus pattern (196 bp):
ACATAGAATGTTGAAATTTAGACTATCTCACTTAGGGTTTAATATAGTTTTTGGAGCATATCTTT
ATCTCACTTAGGGTTTACATATCATGTATTTTTATCTCACTTAGGGTTTAGATTTCATGTCATGT
CATTTTTTTGTCTCTCATAGCCTTTTTTTTTTGTTTCAAATTTTGACTCTTCAACCACTTTTTAT
G
Found at i:2225 original size:78 final size:78
Alignment explanation
Indices: 2142--2304 Score: 299
Period size: 78 Copynumber: 2.1 Consensus size: 78
2132 TTTTTTTAAC
* * *
2142 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAATGGGAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
2207 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
2220 TAAAATAGTAAAATGGGAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGGAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
2285 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
2298 TAAAATA
1 TAAAATA
2305 AAATAATTAT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 82 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (78 bp):
TAAAATAGTAAAATGGGAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:2334 original size:62 final size:62
Alignment explanation
Indices: 2237--2364 Score: 184
Period size: 62 Copynumber: 2.1 Consensus size: 62
2227 GTAAAATGGG
* * * * *
2237 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTAGTTGAGT
1 AAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACT
* * *
2299 AAAATAAAATAATTATAAAGATGTTATATTTAATTAAATAAAAATAGAGTTTTTTGTTGACT
1 AAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACT
2361 AAAA
1 AAAA
2365 CTATAAAAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.48, C:0.01, G:0.12, T:0.39
Consensus pattern (62 bp):
AAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACT
Found at i:4447 original size:1 final size:1
Alignment explanation
Indices: 4441--4479 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
4431 AAAATCACAC
4441 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4480 GAAAGAAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9906 original size:2 final size:2
Alignment explanation
Indices: 9899--9923 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9889 GGATATAGTG
9899 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 A
9924 AAACTTAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10059 original size:26 final size:26
Alignment explanation
Indices: 10030--10082 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
10020 TAAAAAGGTA
*
10030 GAGCAAGAACCCTAATTCCAATTTAC
1 GAGCAAGAACCCTAACTCCAATTTAC
*
10056 GAGCAAGAACCCTAACTCCGATTTAC
1 GAGCAAGAACCCTAACTCCAATTTAC
10082 G
1 G
10083 TTTGAAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (26 bp):
GAGCAAGAACCCTAACTCCAATTTAC
Found at i:12256 original size:26 final size:26
Alignment explanation
Indices: 12216--12280 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
12206 AAATTTTAAA
*
12216 TATAAATATATAAA-TTATTATAAAACAT
1 TATAAAT-TAAAAATTTA-TATAAAA-AT
*
12244 TA-AAATTAAAAATTTATATATAAAT
1 TATAAATTAAAAATTTATATAAAAAT
12269 TATAAATTAAAA
1 TATAAATTAAAA
12281 CTAAATAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 4 0.12
26 20 0.61
27 7 0.21
28 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
TATAAATTAAAAATTTATATAAAAAT
Found at i:24770 original size:156 final size:156
Alignment explanation
Indices: 24486--24797 Score: 459
Period size: 156 Copynumber: 2.0 Consensus size: 156
24476 TGGAGACTTC
*
24486 TTGTTCCTTAAACTTACAATATGAGGATATGTTAATCCCTCTCAAAAGGTATTACTAATATGACA
1 TTGTTCCTTAAACTTACAATATGAGGACATGTTAATCCCTCTCAAAAGGTATTACTAATATGACA
* * *
24551 ATGCCACGTCGAATCAAAAAGATCACATGGTAAGACCACGTCAGACCAAGACGCTAATGTGGCAA
66 ATGCCACATCGAACCAAAAAGACCACATGGTAAGACCACGTCAGACCAAGACGCTAATGTGGCAA
*
24616 TGGTGACGTCAGCAATATTGTTTGAG
131 TGGTGACATCAGCAATATTGTTTGAG
* * *
24642 TTGTTCCTTAAACTT-CTAATATGAGGACATGTTAGTCCCTCTCAAACGGTATTACTCAA-ATGG
1 TTGTTCCTTAAACTTAC-AATATGAGGACATGTTAATCCCTCTCAAAAGGTATTACT-AATATGA
* * * *
24705 CAATGCCACATCGAACCAAAAA-AGCCACGTGGTAAGACTACGTTAGACCAAGGCGCTAATGTGG
64 CAATGCCACATCGAACCAAAAAGA-CCACATGGTAAGACCACGTCAGACCAAGACGCTAATGTGG
*
24769 CAATGGTGATATCAGCAATATTGTTTGAG
128 CAATGGTGACATCAGCAATATTGTTTGAG
24798 AGGGACTAAA
Statistics
Matches: 140, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
155 2 0.01
156 136 0.97
157 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (156 bp):
TTGTTCCTTAAACTTACAATATGAGGACATGTTAATCCCTCTCAAAAGGTATTACTAATATGACA
ATGCCACATCGAACCAAAAAGACCACATGGTAAGACCACGTCAGACCAAGACGCTAATGTGGCAA
TGGTGACATCAGCAATATTGTTTGAG
Found at i:36767 original size:17 final size:17
Alignment explanation
Indices: 36740--36794 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
36730 AACCCATGTA
* *
36740 ATCTTTGATCACCGGTG
1 ATCTTAGATCACTGGTG
36757 ATCTT-GCATCACTGGTG
1 ATCTTAG-ATCACTGGTG
36774 ATCTTAGATCACTGGTG
1 ATCTTAGATCACTGGTG
36791 ATCT
1 ATCT
36795 GGAGGGTGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
16 1 0.03
17 33 0.94
18 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (17 bp):
ATCTTAGATCACTGGTG
Found at i:39225 original size:3 final size:3
Alignment explanation
Indices: 39217--39246 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
39207 TGAACTCACG
39217 GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC
1 GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC
39247 AGCTTCCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.67, T:0.00
Consensus pattern (3 bp):
GGC
Found at i:46657 original size:177 final size:177
Alignment explanation
Indices: 46361--46715 Score: 710
Period size: 177 Copynumber: 2.0 Consensus size: 177
46351 CAATTCCTAG
46361 TGCTTGCAAGACAAGAACAGTTTCTTCGGGAGTTAAAGGGCAAGACCCATCTTGTCTTCTCCTTT
1 TGCTTGCAAGACAAGAACAGTTTCTTCGGGAGTTAAAGGGCAAGACCCATCTTGTCTTCTCCTTT
46426 TCGAATTTATCCCTTTATGCTTCCAATCATCGTAAGAATATCTCATTTCTGTGACTTCTTTAATC
66 TCGAATTTATCCCTTTATGCTTCCAATCATCGTAAGAATATCTCATTTCTGTGACTTCTTTAATC
46491 TCTTGTGGAGTTAAGCCTTCGACACAACCGGTAAATGCCACCATGTC
131 TCTTGTGGAGTTAAGCCTTCGACACAACCGGTAAATGCCACCATGTC
46538 TGCTTGCAAGACAAGAACAGTTTCTTCGGGAGTTAAAGGGCAAGACCCATCTTGTCTTCTCCTTT
1 TGCTTGCAAGACAAGAACAGTTTCTTCGGGAGTTAAAGGGCAAGACCCATCTTGTCTTCTCCTTT
46603 TCGAATTTATCCCTTTATGCTTCCAATCATCGTAAGAATATCTCATTTCTGTGACTTCTTTAATC
66 TCGAATTTATCCCTTTATGCTTCCAATCATCGTAAGAATATCTCATTTCTGTGACTTCTTTAATC
46668 TCTTGTGGAGTTAAGCCTTCGACACAACCGGTAAATGCCACCATGTC
131 TCTTGTGGAGTTAAGCCTTCGACACAACCGGTAAATGCCACCATGTC
46715 T
1 T
46716 TTTTCGTATC
Statistics
Matches: 178, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 178 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (177 bp):
TGCTTGCAAGACAAGAACAGTTTCTTCGGGAGTTAAAGGGCAAGACCCATCTTGTCTTCTCCTTT
TCGAATTTATCCCTTTATGCTTCCAATCATCGTAAGAATATCTCATTTCTGTGACTTCTTTAATC
TCTTGTGGAGTTAAGCCTTCGACACAACCGGTAAATGCCACCATGTC
Found at i:47658 original size:166 final size:166
Alignment explanation
Indices: 47335--47664 Score: 446
Period size: 166 Copynumber: 2.0 Consensus size: 166
47325 TCATTTGTCA
* *
47335 ATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATAAAAAATTAGGACATTTAA
1 ATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATAAAAAATTAGGACATTTAA
* * * * * ** * ** *
47400 GTAATCTGCCAAGTAGGTAAAGACGAAAAATGTTAGTTCTCTAGCTCATCATCAATTCTTGATGG
66 GCAATCTGCCAAGTAGGAAAAGACGAAAAATATAAGTTCTCTAACTCAAAAGCAAGCCTTGATAG
* * * *
47465 GGATCATTTATTAACTCCACTACTCTATTCAAGTCC
131 GAATCATTTAGTAACTCCACCACTCTATTAAAGTCC
* *
47501 ATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTAA
1 ATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATAAAAAATTAGGACATTTAA
*
47566 GCAATCTGCCAAGTAGGAAAAGACGAAAAA-ATAAGTTCTCTAACTCCAAAAGCAAGCCTTGGTA
66 GCAATCTGCCAAGTAGGAAAAGACGAAAAATATAAGTTCTCTAACT-CAAAAGCAAGCCTTGATA
* *
47630 GGAATCTTTTAGTAATTCCACCACTCTATTAAAGT
130 GGAATCATTTAGTAACTCCACCACTCTATTAAAGT
47665 TTAGGACATT
Statistics
Matches: 141, Mismatches: 22, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
165 12 0.09
166 129 0.91
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.29
Consensus pattern (166 bp):
ATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATAAAAAATTAGGACATTTAA
GCAATCTGCCAAGTAGGAAAAGACGAAAAATATAAGTTCTCTAACTCAAAAGCAAGCCTTGATAG
GAATCATTTAGTAACTCCACCACTCTATTAAAGTCC
Found at i:47774 original size:45 final size:45
Alignment explanation
Indices: 47718--47807 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
47708 GATTACTTCT
*
47718 CCAGCTCATCATTAATTCGGGGTAAGG-ATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATTCAGGGT-AGGAATCTTTTAGTAATTCCAC
*
47763 CCAGCTTATCATTAATTCAGGGTAGGAATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATTCAGGGTAGGAATCTTTTAGTAATTCCAC
47808 TACTCTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 3 0.07
45 39 0.93
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (45 bp):
CCAGCTCATCATTAATTCAGGGTAGGAATCTTTTAGTAATTCCAC
Found at i:51274 original size:2 final size:2
Alignment explanation
Indices: 51229--51258 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
51219 TTTTCAGCTC
51229 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51259 GCTTTTCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53742 original size:33 final size:33
Alignment explanation
Indices: 53698--53794 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 33
53688 AAATAGCCTT
* *
53698 GCCGTCATAGTGGGGCGGCTGCGCCGTGGCTGA
1 GCCGTCCTAGTGGGGCGGCTACGCCGTGGCTGA
*
53731 GCCGTCCTAGTGGGGCGGCTACGCCGTGGCAGA
1 GCCGTCCTAGTGGGGCGGCTACGCCGTGGCTGA
* * *
53764 GCCGTCCTAGTGGGGAGGCTCCGCCATGGCT
1 GCCGTCCTAGTGGGGCGGCTACGCCGTGGCT
53795 AAGGGCAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.10, C:0.30, G:0.42, T:0.18
Consensus pattern (33 bp):
GCCGTCCTAGTGGGGCGGCTACGCCGTGGCTGA
Found at i:71567 original size:12 final size:12
Alignment explanation
Indices: 71550--71574 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
71540 AGAAGACGAA
71550 GAAATTGCAAAT
1 GAAATTGCAAAT
71562 GAAATTGCAAAT
1 GAAATTGCAAAT
71574 G
1 G
71575 TTGAAGCTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (12 bp):
GAAATTGCAAAT
Found at i:76427 original size:2 final size:2
Alignment explanation
Indices: 76422--76449 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
76412 TGTGTGTGTG
76422 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
76450 CACACACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.