Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010147.1 Corchorus capsularis cultivar CVL-1 contig10168, 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: 25589
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:513 original size:27 final size:26
Alignment explanation
Indices: 444--516 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 26
434 AAGTGAACTT
*
444 AAAATGACCAAAATACCCCCTAAATGCA
1 AAAATGACCAAAAT-GCCCCTAAATG-A
472 AAAATGACCAAAATGCCCCTGAACATG-
1 AAAATGACCAAAATGCCCCT-AA-ATGA
499 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
517 TTATGTGACC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
27 23 0.55
28 16 0.38
29 3 0.07
ACGTcount: A:0.48, C:0.27, G:0.11, T:0.14
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCCTAAATGA
Found at i:4292 original size:13 final size:14
Alignment explanation
Indices: 4274--4303 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4264 TTCACTCCAC
4274 TAAAATAAT-ATAA
1 TAAAATAATAATAA
4287 TAAAATAATAATAA
1 TAAAATAATAATAA
4301 TAA
1 TAA
4304 TTAAATTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAATAATAATAA
Found at i:12408 original size:37 final size:37
Alignment explanation
Indices: 12358--12433 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
12348 TAAAGCAGAG
12358 TGTCCAAAGTTTTACATCTAAATTGGTAATCCAAAAA
1 TGTCCAAAGTTTTACATCTAAATTGGTAATCCAAAAA
12395 TGTCCAAAGTTTTACATCTAAATTGGTAATCCAAAAA
1 TGTCCAAAGTTTTACATCTAAATTGGTAATCCAAAAA
12432 TG
1 TG
12434 ATAGTAGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (37 bp):
TGTCCAAAGTTTTACATCTAAATTGGTAATCCAAAAA
Found at i:17764 original size:53 final size:53
Alignment explanation
Indices: 17684--17789 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
17674 TAAACTCTTC
17684 TAGCAACAACCCTTCCCAACAAGTCAGATTGGAGGAGAGGATTGAGGGTGGAT
1 TAGCAACAACCCTTCCCAACAAGTCAGATTGGAGGAGAGGATTGAGGGTGGAT
17737 TAGCAACAACCCTTCCCAACAAGTCAGATTGGAGGAGAGGATTGAGGGTGGAT
1 TAGCAACAACCCTTCCCAACAAGTCAGATTGGAGGAGAGGATTGAGGGTGGAT
17790 AAAATTGAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.32, C:0.19, G:0.30, T:0.19
Consensus pattern (53 bp):
TAGCAACAACCCTTCCCAACAAGTCAGATTGGAGGAGAGGATTGAGGGTGGAT
Found at i:18038 original size:34 final size:34
Alignment explanation
Indices: 17995--18063 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
17985 GTTGCAGAAG
17995 TATGATGCCAAGTGAAGTATATCATCCCTGAGAT
1 TATGATGCCAAGTGAAGTATATCATCCCTGAGAT
18029 TATGATGCCAAGTGAAGTATATCATCCCTGAGAT
1 TATGATGCCAAGTGAAGTATATCATCCCTGAGAT
18063 T
1 T
18064 CTCCAGATGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (34 bp):
TATGATGCCAAGTGAAGTATATCATCCCTGAGAT
Done.