Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012088.1 Corchorus capsularis cultivar CVL-1 contig12109, 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: 16831
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4670 original size:36 final size:36
Alignment explanation
Indices: 4628--4700 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
4618 ATTTTTTAAA
4628 GTGTTAAGTGCTTTATCTCTTTTTTTTACAGGGGAT
1 GTGTTAAGTGCTTTATCTCTTTTTTTTACAGGGGAT
4664 GTGTTAAGTGCTTTATCTCTTTTTTTTACAGGGGAT
1 GTGTTAAGTGCTTTATCTCTTTTTTTTACAGGGGAT
4700 G
1 G
4701 GAAAGGACCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.16, C:0.11, G:0.23, T:0.49
Consensus pattern (36 bp):
GTGTTAAGTGCTTTATCTCTTTTTTTTACAGGGGAT
Found at i:5171 original size:44 final size:44
Alignment explanation
Indices: 5106--5196 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
5096 ATATTTTGAT
*
5106 TTATTTTAGGGAAAAAGTTCATTCTTTTTAATTATGTTCATTAA
1 TTATTTTAGGGAAAAAATTCATTCTTTTTAATTATGTTCATTAA
5150 TTATTTTAGGGAAAAAATTCATTCTTTTTAATTATGTTCATTAA
1 TTATTTTAGGGAAAAAATTCATTCTTTTTAATTATGTTCATTAA
5194 TTA
1 TTA
5197 ATAGAGATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.51
Consensus pattern (44 bp):
TTATTTTAGGGAAAAAATTCATTCTTTTTAATTATGTTCATTAA
Found at i:5776 original size:17 final size:17
Alignment explanation
Indices: 5754--5786 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5744 AGAGAAAACA
5754 TTTTGCGGCAAATATAT
1 TTTTGCGGCAAATATAT
5771 TTTTGCGGCAAATATA
1 TTTTGCGGCAAATATA
5787 CTCCAATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (17 bp):
TTTTGCGGCAAATATAT
Found at i:9849 original size:78 final size:77
Alignment explanation
Indices: 9763--10001 Score: 332
Period size: 78 Copynumber: 3.2 Consensus size: 77
9753 TTTTTTTAAC
*
9763 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
9828 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* *
9841 TAAAATAGTTAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAGAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
9906 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * * *
9919 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTGAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
9977 TTTTTAGTTGAG
66 TTTTTAGTTGAG
9989 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
10002 ACCTAAACAA
Statistics
Matches: 150, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
70 54 0.36
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 85 0.57
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:9974 original size:70 final size:70
Alignment explanation
Indices: 9851--10001 Score: 214
Period size: 70 Copynumber: 2.2 Consensus size: 70
9841 TAAAATAGTT
* * * * * * *
9851 AAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAGAATAGAGTTTTTAGTT
1 AAATAGTAAAATAAAATAATTATAAAGATATTAGATTGAATTAAATAAAAATAGAGTTTTTAGTT
9916 GAGTA
66 GAGTA
*
9921 AAATAGTAAAATAAAATAATTATAAAGATATTATATTGAATTAAATAAAAATAGAGTTTTTAGTT
1 AAATAGTAAAATAAAATAATTATAAAGATATTAGATTGAATTAAATAAAAATAGAGTTTTTAGTT
9986 GAGTA
66 GAGTA
9991 AAACTA-TAAAA
1 AAA-TAGTAAAA
10002 ACCTAAACAA
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
70 70 0.97
71 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.13, T:0.36
Consensus pattern (70 bp):
AAATAGTAAAATAAAATAATTATAAAGATATTAGATTGAATTAAATAAAAATAGAGTTTTTAGTT
GAGTA
Found at i:10222 original size:440 final size:431
Alignment explanation
Indices: 9664--10535 Score: 1620
Period size: 440 Copynumber: 2.0 Consensus size: 431
9654 AATAGTGTTT
9664 TCAGTTGCAAAAGTTTATTTTAAAAAAAATTGTAAAAGTTTAAACAATGTCATTCAGAAATATAT
1 TCAGTTGCAAAAGTTTATTTTAAAAAAAATTGTAAAAGTTTAAACAATGTCATTCAGAAATATAT
9729 TTAAAAAAACTAATATATCAAGTTTTTTTTTAACTAAAATAGTAAAATTGTAAAATATAATAGTT
66 TTAAAAAAACTAATATATCAAGTTTTTTTTTAACTAAAATAGTAAAATTGTAAAATATAATAGTT
*
9794 ATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTTAGTTGAGTAAAATAGTTAAATGGTA
131 ATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTTAGTTGAGTAAAATAGTAAAATGGTA
*
9859 AAATATAATAGTTATAAGGATATTAGATTTAATTATATAAGAATAGAGTTTTTAGTTGAGTAAAA
196 AAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTAGTTGAGTAAAA
9924 TAGTAAAATAAAATAATTATAAAGATATTATATTGAATTAAATAAAAATAGAGTTTTTAGTTGAG
261 TAGTAAAATAAAATAATTATAAAGATATTATATTGAATTAAATAAAAATAGAGTTTTTAGTTGAG
9989 TAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATATATTTAACAAATAAGGGTATAATAGG
326 TAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATATATTTAACAAATAAGGGTATAATAGG
10054 TGATTCAAAAGTTTTACAGCTGAACGTACTTTTTAATATAG
391 TGATTCAAAAGTTTTACAGCTGAACGTACTTTTTAATATAG
10095 TCAGTTGCAAAAGTTTATTTTAAAAAAAAAATTTGTAAAAAGTTTTAAACAAATGTCATTACAAG
1 TCAGTTGCAAAAGTTTATTTT--AAAAAAAA-TTGT-AAAAG-TTTAAAC-AATGTCATT-C-AG
10160 AAATATAATTTTAAAAAAACTAATATATCAAG-TTTTTTTTAACTAAAATAGTAAAATTGTAAAA
58 AAATAT-A-TTTAAAAAAACTAATATATCAAGTTTTTTTTTAACTAAAATAGTAAAATTGTAAAA
10224 TATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTTAGTTGAGTAAAATAG
121 TATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTTAGTTGAGTAAAATAG
10289 TAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTAG
186 TAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTAG
*
10354 TTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTT
251 TTGAGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTGAATTAAATAAAAATAGAGTT
10419 TTTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATATATTTAACAAATAAGG
316 TTTAGTTGAGTAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATATATTTAACAAATAAGG
10484 GTATAATAGGTGATTCAAAAGTTTTACAGCTGAACGTACTTTTTAATATAG
381 GTATAATAGGTGATTCAAAAGTTTTACAGCTGAACGTACTTTTTAATATAG
10535 T
1 T
10536 ATATAGATGT
Statistics
Matches: 428, Mismatches: 3, Indels: 11
0.97 0.01 0.02
Matches are distributed among these distances:
431 21 0.05
433 8 0.02
434 4 0.01
435 5 0.01
436 7 0.02
437 9 0.02
438 1 0.00
439 8 0.02
440 342 0.80
441 23 0.05
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.36
Consensus pattern (431 bp):
TCAGTTGCAAAAGTTTATTTTAAAAAAAATTGTAAAAGTTTAAACAATGTCATTCAGAAATATAT
TTAAAAAAACTAATATATCAAGTTTTTTTTTAACTAAAATAGTAAAATTGTAAAATATAATAGTT
ATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTTAGTTGAGTAAAATAGTAAAATGGTA
AAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTAGTTGAGTAAAA
TAGTAAAATAAAATAATTATAAAGATATTATATTGAATTAAATAAAAATAGAGTTTTTAGTTGAG
TAAAACTATAAAAACCTAAACAATGGCAATTTAGAAATATATTTAACAAATAAGGGTATAATAGG
TGATTCAAAAGTTTTACAGCTGAACGTACTTTTTAATATAG
Found at i:10283 original size:70 final size:70
Alignment explanation
Indices: 10209--10433 Score: 315
Period size: 70 Copynumber: 3.1 Consensus size: 70
10199 TAACTAAAAT
*
10209 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
10274 AGTTG
66 AGTTG
10279 AGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
1 AGT-AAA-A-T----T-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
10344 GAGTTTTTAGTTG
58 GAGTTTTTAGTTG
* * * * * *
10357 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
10422 AGTTG
66 AGTTG
10427 AGTAAAA
1 AGTAAAA
10434 CTATAAAAAC
Statistics
Matches: 140, Mismatches: 7, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
70 66 0.47
71 3 0.02
72 1 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 4 0.03
78 63 0.45
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (70 bp):
AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
AGTTG
Found at i:10287 original size:78 final size:77
Alignment explanation
Indices: 10203--10441 Score: 359
Period size: 78 Copynumber: 3.2 Consensus size: 77
10193 TTTTTTTAAC
*
10203 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
10268 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
10281 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
10346 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * *
10359 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
10417 TTTTTAGTTGAG
66 TTTTTAGTTGAG
10429 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
10442 ACCTAAACAA
Statistics
Matches: 155, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
70 56 0.36
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 88 0.57
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:14777 original size:22 final size:21
Alignment explanation
Indices: 14752--14793 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
14742 GTTTCGACCC
14752 CGAAAAAGGTCGAACTCGAACT
1 CGAAAAAGGTCGAACT-GAACT
14774 CGAAAAAGGTCGAACTGAAC
1 CGAAAAAGGTCGAACTGAAC
14794 CAGATGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (21 bp):
CGAAAAAGGTCGAACTGAACT
Done.