Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009581.1 Corchorus capsularis cultivar CVL-1 contig09602, 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: 27679
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1361 original size:24 final size:25
Alignment explanation
Indices: 1329--1378 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
1319 TAAGCTACAT
1329 GATTATTAGAGCAGT-GATTGAAAC
1 GATTATTAGAGCAGTAGATTGAAAC
1353 GATTATTAGAGCAGTAGATTGAAAC
1 GATTATTAGAGCAGTAGATTGAAAC
1378 G
1 G
1379 GAGTTTATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (25 bp):
GATTATTAGAGCAGTAGATTGAAAC
Found at i:8810 original size:4 final size:4
Alignment explanation
Indices: 8801--8831 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
8791 TTTCTCCCCT
*
8801 TTTA TTTA TTTA TTTG TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
8832 TTTGCACCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:8820 original size:16 final size:16
Alignment explanation
Indices: 8801--8831 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
8791 TTTCTCCCCT
8801 TTTATTTATTTATTTG
1 TTTATTTATTTATTTG
8817 TTTATTTATTTATTT
1 TTTATTTATTTATTT
8832 TTTGCACCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTATTTATTTATTTG
Found at i:20379 original size:15 final size:15
Alignment explanation
Indices: 20356--20385 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20346 AAGGACCGTT
20356 GGGTATTGGATTTGG
1 GGGTATTGGATTTGG
*
20371 GGGTCTTGGATTTGG
1 GGGTATTGGATTTGG
20386 AAGGGCAGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.03, G:0.47, T:0.40
Consensus pattern (15 bp):
GGGTATTGGATTTGG
Found at i:23405 original size:1 final size:1
Alignment explanation
Indices: 23399--23427 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
23389 ACATTTTCGC
23399 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23428 GCTAATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:24158 original size:9 final size:9
Alignment explanation
Indices: 24146--24194 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
24136 CGGTGGTGGC
24146 GGTGCTGGT
1 GGTGCTGGT
*
24155 GGTGCTGGA
1 GGTGCTGGT
24164 GGTGCTGGT
1 GGTGCTGGT
*
24173 GGCGCTGGT
1 GGTGCTGGT
*
24182 GGCGCTGGT
1 GGTGCTGGT
24191 GGTG
1 GGTG
24195 GTGGCGGTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.02, C:0.14, G:0.57, T:0.27
Consensus pattern (9 bp):
GGTGCTGGT
Found at i:25441 original size:17 final size:16
Alignment explanation
Indices: 25421--25466 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
25411 AAGAGATCCC
25421 AAATATTCAATTAAAAT
1 AAATATT-AATTAAAAT
* *
25438 AAATATTTAAATAATAT
1 AAATA-TTAATTAAAAT
25455 AAATATTAATTA
1 AAATATTAATTA
25467 GAACGGATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 6 0.24
17 17 0.68
18 2 0.08
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATATTAATTAAAAT
Done.