Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012298.1 Corchorus capsularis cultivar CVL-1 contig12319, 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: 18180
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:8396 original size:2 final size:2
Alignment explanation
Indices: 8389--8427 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
8379 AGGGCAGATT
8389 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
8428 TGAAGTCGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:12309 original size:94 final size:94
Alignment explanation
Indices: 12174--12362 Score: 270
Period size: 94 Copynumber: 2.0 Consensus size: 94
12164 GGCTGAGTAG
* * * *
12174 ACTCATGGGTCTGAATAAGAGGCCGAACATAATCGTGAGTCGAAGATTGAGCAATAGACCTAGTA
1 ACTCATGGGTCTGAATAAGAGGCCGAACATAATCATAAGTCGAAGACTGAGCAATAGACATAGTA
*
12239 GAACCGGGAGTCGAAGTAGAAGCCCTAGC
66 GAACCGGGAGTCGAAGTAGAAGCACTAGC
* * ** *
12268 ACTCATGGGTCTGAGTAGGAGGTTGAACATGATCATAAGTCGAAGACTGAGCAATAGACATAGTA
1 ACTCATGGGTCTGAATAAGAGGCCGAACATAATCATAAGTCGAAGACTGAGCAATAGACATAGTA
* *
12333 GAATCGGGATTCGAAGTAGAAGCACTAGC
66 GAACCGGGAGTCGAAGTAGAAGCACTAGC
12362 A
1 A
12363 AGCATAAGAA
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
94 83 1.00
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.20
Consensus pattern (94 bp):
ACTCATGGGTCTGAATAAGAGGCCGAACATAATCATAAGTCGAAGACTGAGCAATAGACATAGTA
GAACCGGGAGTCGAAGTAGAAGCACTAGC
Found at i:13736 original size:19 final size:18
Alignment explanation
Indices: 13691--13738 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
13681 TATCTTGAAT
*
13691 TTTTAATATAAATTAATA
1 TTTTAATATAAAATAATA
**
13709 TATAAAATATAAAATAATTA
1 T-TTTAATATAAAATAA-TA
13729 TTTTAATATA
1 TTTTAATATA
13739 TATTATTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
18 1 0.04
19 19 0.83
20 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTAATATAAAATAATA
Found at i:14981 original size:87 final size:87
Alignment explanation
Indices: 14886--15111 Score: 398
Period size: 87 Copynumber: 2.6 Consensus size: 87
14876 ATAAATTTTG
* *
14886 TAAAGAGAATATTTTTTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAATAAA
1 TAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAA
14951 TAAATTATAAAGATTGAGCTAA
66 TAAATTATAAAGATTGAGCTAA
* *
14973 TAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGATATAAA
1 TAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAA
*
15038 TAAATTATAAAGATTGAGTTAA
66 TAAATTATAAAGATTGAGCTAA
*
15060 TAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATAT
1 TAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATAT
15112 AGAAAAAGAA
Statistics
Matches: 132, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 132 1.00
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.35
Consensus pattern (87 bp):
TAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAA
TAAATTATAAAGATTGAGCTAA
Found at i:15342 original size:26 final size:26
Alignment explanation
Indices: 15306--15362 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
15296 GACTAAATAA
*
15306 TAAAGATATGATTAAAATTCAAAAAC
1 TAAAAATATGATTAAAATTCAAAAAC
15332 TAAAAATATGATTAAAATTCAAAAAC
1 TAAAAATATGATTAAAATTCAAAAAC
15358 TAAAA
1 TAAAA
15363 GAAAGATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.26
Consensus pattern (26 bp):
TAAAAATATGATTAAAATTCAAAAAC
Found at i:15370 original size:26 final size:26
Alignment explanation
Indices: 15306--15370 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
15296 GACTAAATAA
* *
15306 TAAAGATATGATTAAAATTCAAAAAC
1 TAAAAATAAGATTAAAATTCAAAAAC
*
15332 TAAAAATATGATTAAAATTCAAAAAC
1 TAAAAATAAGATTAAAATTCAAAAAC
15358 TAAAAGA-AAGATT
1 TAAAA-ATAAGATT
15371 TGCAATAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 35 0.97
27 1 0.03
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26
Consensus pattern (26 bp):
TAAAAATAAGATTAAAATTCAAAAAC
Found at i:17691 original size:17 final size:17
Alignment explanation
Indices: 17669--17702 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17659 AGTGAAAGGG
* *
17669 TTGTTTTTGGAATAAAA
1 TTGTTTTCGAAATAAAA
17686 TTGTTTTCGAAATAAAA
1 TTGTTTTCGAAATAAAA
17703 GGATGTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (17 bp):
TTGTTTTCGAAATAAAA
Done.