Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015154.1 Corchorus capsularis cultivar CVL-1 contig15175, 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: 26641
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Found at i:10291 original size:15 final size:15
Alignment explanation
Indices: 10271--10300 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10261 GACCGACAGA
*
10271 TTTAATATTTATAAT
1 TTTAATATATATAAT
10286 TTTAATATATATAAT
1 TTTAATATATATAAT
10301 ATAAAACCCT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAATATATATAAT
Found at i:12360 original size:2 final size:2
Alignment explanation
Indices: 12353--12379 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12343 CTTTCAGAAA
12353 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12380 AGGTGTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12692 original size:18 final size:18
Alignment explanation
Indices: 12669--12703 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12659 CGTGGATTTA
*
12669 TGTAAAATTGATCACTTT
1 TGTAAAATTGAACACTTT
*
12687 TGTAAATTTGAACACTT
1 TGTAAAATTGAACACTT
12704 ATACTATCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (18 bp):
TGTAAAATTGAACACTTT
Found at i:13089 original size:29 final size:29
Alignment explanation
Indices: 13056--13129 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
13046 ACTTGTAGCG
*
13056 TTTGGATGTTTTGCCCCATGAACTTCAAT
1 TTTGGACGTTTTGCCCCATGAACTTCAAT
* * * *
13085 TTTGGACATTTTACCCCCTGAATTTCAAT
1 TTTGGACGTTTTGCCCCATGAACTTCAAT
13114 TTTGGGACGTTTTGCC
1 TTT-GGACGTTTTGCC
13130 ACCTTAATCT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 27 0.73
30 10 0.27
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.42
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCATGAACTTCAAT
Found at i:16234 original size:10 final size:10
Alignment explanation
Indices: 16215--16248 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
16205 TTTTATTATC
16215 TAAA-AAAAA
1 TAAATAAAAA
16224 TAAATAAAAA
1 TAAATAAAAA
16234 TAAAATAAAAA
1 T-AAATAAAAA
16245 TAAA
1 TAAA
16249 AGCTTTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.17
10 9 0.39
11 10 0.43
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
TAAATAAAAA
Found at i:16239 original size:11 final size:11
Alignment explanation
Indices: 16219--16249 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
16209 ATTATCTAAA
16219 AAAAAT-AAAT
1 AAAAATAAAAT
16229 AAAAATAAAAT
1 AAAAATAAAAT
16240 AAAAATAAAA
1 AAAAATAAAA
16250 GCTTTACTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:21673 original size:34 final size:34
Alignment explanation
Indices: 21630--21697 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
21620 AAGGATGTAG
21630 TTCCTTTTACTAATATCAGTATTTCGTAATGCAA
1 TTCCTTTTACTAATATCAGTATTTCGTAATGCAA
21664 TTCCTTTTACTAATATCAGTATTTCGTAATGCAA
1 TTCCTTTTACTAATATCAGTATTTCGTAATGCAA
21698 GTGGTTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (34 bp):
TTCCTTTTACTAATATCAGTATTTCGTAATGCAA
Done.