Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009834.1 Corchorus capsularis cultivar CVL-1 contig09855, 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: 55148
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:289 original size:1 final size:1
Alignment explanation
Indices: 283--310 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
273 ACACTACAAT
283 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
311 CAACACACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:318 original size:2 final size:2
Alignment explanation
Indices: 313--343 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
303 AAAAAAAACA
313 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
344 AGTTCAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:9145 original size:16 final size:16
Alignment explanation
Indices: 9124--9156 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
9114 GCTGTTCAAC
9124 ATATTTGCTTGCCATG
1 ATATTTGCTTGCCATG
9140 ATATTTGCTTGCCATG
1 ATATTTGCTTGCCATG
9156 A
1 A
9157 ATATCATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (16 bp):
ATATTTGCTTGCCATG
Found at i:21050 original size:14 final size:14
Alignment explanation
Indices: 21031--21060 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
21021 TAAACTTGGT
21031 AGTAAATTTAAGAA
1 AGTAAATTTAAGAA
21045 AGTAAATTTAAGAA
1 AGTAAATTTAAGAA
21059 AG
1 AG
21061 AGAATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.27
Consensus pattern (14 bp):
AGTAAATTTAAGAA
Found at i:21753 original size:69 final size:69
Alignment explanation
Indices: 21649--21779 Score: 219
Period size: 69 Copynumber: 1.9 Consensus size: 69
21639 AAGTGAAGAG
*
21649 GATGGAAAGCAGCAGATTGCTAGAGTGGTGCCAAAGAAGAATATTGCTGAAAGTGCACAGGAAAG
1 GATGGAAAGCAGCAGATTGCGAGAGTGGTGCCAAAGAAGAATATTGCTGAAAGTGCACAGGAAAG
21714 TGGA
66 TGGA
* *
21718 GATGGAAAGCAGCAGATTGGCGA-AGTGGTGCCAAAGAAGAATGTTGCTGAAAGTGCAGAGGA
1 GATGGAAAGCAGCAGATT-GCGAGAGTGGTGCCAAAGAAGAATATTGCTGAAAGTGCACAGGA
21780 GGCAGAGACG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
69 55 0.95
70 3 0.05
ACGTcount: A:0.37, C:0.11, G:0.35, T:0.17
Consensus pattern (69 bp):
GATGGAAAGCAGCAGATTGCGAGAGTGGTGCCAAAGAAGAATATTGCTGAAAGTGCACAGGAAAG
TGGA
Found at i:23868 original size:53 final size:53
Alignment explanation
Indices: 23810--23916 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
23800 TTATTTGGCT
23810 ATTTTATGTAAATTTAGGTGTCTTTTTGAGCAATAAACCTACTAAGAAAATAG
1 ATTTTATGTAAATTTAGGTGTCTTTTTGAGCAATAAACCTACTAAGAAAATAG
*
23863 ATTTTATGTAAATTTAGGTGTCTTTTTGAGCAATAAGCCTACTAAGAAAATAG
1 ATTTTATGTAAATTTAGGTGTCTTTTTGAGCAATAAACCTACTAAGAAAATAG
23916 A
1 A
23917 GAGGAGCTGA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (53 bp):
ATTTTATGTAAATTTAGGTGTCTTTTTGAGCAATAAACCTACTAAGAAAATAG
Found at i:24030 original size:46 final size:46
Alignment explanation
Indices: 23962--24050 Score: 169
Period size: 46 Copynumber: 1.9 Consensus size: 46
23952 TAGTGTTGGA
*
23962 CATTCTGCAACTTTTGAGAGGAGTGTCTTGCTATGAATTCAGTGGC
1 CATTCTGCAACTTTTGAAAGGAGTGTCTTGCTATGAATTCAGTGGC
24008 CATTCTGCAACTTTTGAAAGGAGTGTCTTGCTATGAATTCAGT
1 CATTCTGCAACTTTTGAAAGGAGTGTCTTGCTATGAATTCAGT
24051 TAGTGAAGAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (46 bp):
CATTCTGCAACTTTTGAAAGGAGTGTCTTGCTATGAATTCAGTGGC
Found at i:53223 original size:16 final size:16
Alignment explanation
Indices: 53198--53228 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53188 CTTTTGATTT
*
53198 AGAGAGAGAAAGAGAA
1 AGAGAAAGAAAGAGAA
53214 AGAGAAAGAAAGAGA
1 AGAGAAAGAAAGAGA
53229 GAGGATGAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (16 bp):
AGAGAAAGAAAGAGAA
Found at i:54697 original size:33 final size:33
Alignment explanation
Indices: 54660--54734 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
54650 CACCCTTCTA
* * *
54660 GGGCGGCACTACCATGGCCAGGCCGCCTCCCTG
1 GGGCGGCACTACCATGGACAGACCGCCCCCCTG
* * *
54693 GGGCGGCTCTGCCATGGATAGACCGCCCCCCTG
1 GGGCGGCACTACCATGGACAGACCGCCCCCCTG
*
54726 AGGCGGCAC
1 GGGCGGCAC
54735 CAGTACTAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.13, C:0.40, G:0.35, T:0.12
Consensus pattern (33 bp):
GGGCGGCACTACCATGGACAGACCGCCCCCCTG
Found at i:54943 original size:33 final size:33
Alignment explanation
Indices: 54790--54949 Score: 207
Period size: 33 Copynumber: 4.9 Consensus size: 33
54780 AAATAGCCTT
* * *
54790 GCCGCCCTAGTTGGGCGGCT-AGCCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* * * *
54822 GCCGTCTTAGTGGGGTGGCTCCACCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
*
54855 GCCGCCCTAGTGGGGAGGCTCCACCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
54888 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* * *
54921 ACCGTCTTAGTGGGGAGGCTCCG-CGTGGC
1 GCCGCCCTAGTGGGGAGGCTCCGCCGTGGC
54950 TAAGGGCAAA
Statistics
Matches: 114, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
32 22 0.19
33 92 0.81
ACGTcount: A:0.12, C:0.31, G:0.41, T:0.16
Consensus pattern (33 bp):
GCCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
Found at i:55121 original size:2 final size:2
Alignment explanation
Indices: 55114--55148 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
55104 ATATACTGTG
55114 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.