Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008367.1 Corchorus capsularis cultivar CVL-1 contig08388, 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: 19681
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1512 original size:167 final size:169
Alignment explanation
Indices: 1236--1539 Score: 560
Period size: 167 Copynumber: 1.8 Consensus size: 169
1226 AGGGATGTAT
*
1236 ATTGATGGATAGTTAAAAGCATTATTAAAAGTATAGTTATTAGCATAGTTATTGCCTGATAACAC
1 ATTGATGGATAGTTAAAAGCATTATTAAAAGCATAGTTATTAGCATAGTTATTGCCTGATAACAC
1301 CAGATCAATGGTTCAATCGTTCGTTAGATTGATGAATCAATTGCTGGTTTAATA-TTAA-ATTTT
66 CAGATCAATGGTTCAATCGTTCGTTAGATTGATGAATCAATTGCTGGTTTAATATTTAATATTTT
1364 TTATTTTTTATTTTATTTTATCCATCAATCGTTCGTTAG
131 TTATTTTTTATTTTATTTTATCCATCAATCGTTCGTTAG
1403 ATTGATGGATAGTCT-AAAGCATTATTAAAAGCATAGTTATTAGCATAGTTATTGCCTGATAACA
1 ATTGATGGATAGT-TAAAAGCATTATTAAAAGCATAGTTATTAGCATAGTTATTGCCTGATAACA
*
1467 CCAGATCAATGGTTCAATCGTTCGTTAGATTGATGGATCAATTGCTGGTTTAATATTTAATATTT
65 CCAGATCAATGGTTCAATCGTTCGTTAGATTGATGAATCAATTGCTGGTTTAATATTTAATATTT
1532 TTTATTTT
130 TTTATTTT
1540 ATATATATAA
Statistics
Matches: 132, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
167 115 0.87
168 5 0.04
169 12 0.09
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (169 bp):
ATTGATGGATAGTTAAAAGCATTATTAAAAGCATAGTTATTAGCATAGTTATTGCCTGATAACAC
CAGATCAATGGTTCAATCGTTCGTTAGATTGATGAATCAATTGCTGGTTTAATATTTAATATTTT
TTATTTTTTATTTTATTTTATCCATCAATCGTTCGTTAG
Found at i:11307 original size:20 final size:21
Alignment explanation
Indices: 11267--11307 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11257 CATCTCACTC
*
11267 TTAGGGTTTGTCATGTCATGT
1 TTAGGGTTTATCATGTCATGT
*
11288 TTAGGGTTTAT-ATTTCATGT
1 TTAGGGTTTATCATGTCATGT
11308 CATGTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.17, C:0.07, G:0.24, T:0.51
Consensus pattern (21 bp):
TTAGGGTTTATCATGTCATGT
Found at i:11588 original size:25 final size:25
Alignment explanation
Indices: 11560--11615 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
11550 TTTAGGGAAA
*
11560 TGATTTTACATTTTGC-TTAATACAT
1 TGATTTT-CATTTTGCAGTAATACAT
**
11585 TGATTTTTTTTTTGCAGTAATACAT
1 TGATTTTCATTTTGCAGTAATACAT
11610 TGATTT
1 TGATTT
11616 GTTTACGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 6 0.22
25 21 0.78
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.55
Consensus pattern (25 bp):
TGATTTTCATTTTGCAGTAATACAT
Found at i:13686 original size:52 final size:52
Alignment explanation
Indices: 13622--13726 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
13612 TTTTAAGGTG
* *
13622 CAATGATGGATATGAACGATAGTGCTCCAAGTAACTTTTATCTTTTTACCCT
1 CAATGATAGATATGAACAATAGTGCTCCAAGTAACTTTTATCTTTTTACCCT
13674 CAATGATAGATATGAACAATAGTGCTCCAAGTAACTTTTATCTTTTTACCCT
1 CAATGATAGATATGAACAATAGTGCTCCAAGTAACTTTTATCTTTTTACCCT
13726 C
1 C
13727 TTTTCTCTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.36
Consensus pattern (52 bp):
CAATGATAGATATGAACAATAGTGCTCCAAGTAACTTTTATCTTTTTACCCT
Found at i:17052 original size:48 final size:48
Alignment explanation
Indices: 16976--17072 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
16966 GCTCTCAAAT
*
16976 ATCAAGAATGAGGTGCTTTACATTAAACTTAATATTGTGCATGTTAAG
1 ATCAAGAATGAGGTGCTTTACATTAAACTTAATATTGTGCATGCTAAG
* *
17024 ATCAGGAATGAGGTGCTTTACATTAAACTTAATATTGTGTATGCTAAG
1 ATCAAGAATGAGGTGCTTTACATTAAACTTAATATTGTGCATGCTAAG
17072 A
1 A
17073 ATATGCAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (48 bp):
ATCAAGAATGAGGTGCTTTACATTAAACTTAATATTGTGCATGCTAAG
Found at i:18112 original size:45 final size:45
Alignment explanation
Indices: 18061--18146 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
18051 TAATAGAGTA
18061 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGGTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGGTGG
* *
18106 GTGGAATTACTAAAATATTCCTACCCCGGATTAATGATGAG
1 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAG
18147 CTGGAGAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGGTGG
Found at i:19653 original size:2 final size:2
Alignment explanation
Indices: 19646--19678 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19636 GTTACTCCAA
19646 AT AT AT 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 AT AT AT A
19679 GTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.