Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012934.1 Corchorus olitorius cultivar O-4 contig12967, 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: 4994
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Found at i:1279 original size:24 final size:21
Alignment explanation
Indices: 1224--1278 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1214 CGGCCATTCA
*
1224 CCGTGACACCACCGGTTAAGC
1 CCGTGCCACCACCGGTTAAGC
*
1245 CCGTGCCACCACCGGTTATGC
1 CCGTGCCACCACCGGTTAAGC
*
1266 CCGTGCCATCACC
1 CCGTGCCACCACC
1279 ATTCCAAGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.18, C:0.44, G:0.22, T:0.16
Consensus pattern (21 bp):
CCGTGCCACCACCGGTTAAGC
Found at i:2414 original size:268 final size:269
Alignment explanation
Indices: 1911--2447 Score: 846
Period size: 268 Copynumber: 2.0 Consensus size: 269
1901 CTGAAAATTT
* *
1911 TGAAAATTTTGCATGTATTGAGTGATTTGATTTAATGATGATTGAAGAATACTTAGAATTTTTAA
1 TGAAAATTTTGCATATATTAAGTGATTTGATTTAATGATGATTGAAGAATACTTAGAATTTTTAA
*
1976 GAAAATTTTATTTGATTGATTGATTTATAGCATGATATCTGATTTCTTAGATTAGGTATAATTAG
66 GAAAATTTTATTTAATTGATTGATTTATAGCATGATATCTGATTTCTTAGATTAGGTATAATTAG
** * * * **
2041 AGTTTTGTGATATGATCTTATTGTTTATTATTTCTATGAATACCTATTTCTAGAACTTATGTTTA
131 AGTTTTGTGATAAAAGCATATTGTTCATTATTTCTATGAATACCTATTTCTAGAACTTATGTCCA
* *
2106 ATTTTTATTGAAATTACAATTATGAAAGTATGTTATGGATATGTCAAGAACAAGTGTGGGGGACT
196 ATCTTGATTGAAATTACAATTATGAAAGTATGTTATGGATATGTCAAGAACAAGTGTGGGGGACT
2171 ACTTATATA
261 ACTTATATA
* * *
2180 TGAAAATTTTGCATATATTAATTGA-TTGATTTGATTATGATTGAAGAATACTTAGAATTTTTAA
1 TGAAAATTTTGCATATATTAAGTGATTTGATTTAATGATGATTGAAGAATACTTAGAATTTTTAA
*
2244 GAATATTTTATTTAATTGATTGATTTATAGCATGATATCTGATTTCTTAGATTAGGTATAATT-G
66 GAAAATTTTATTTAATTGATTGATTTATAGCATGATATCTGATTTCTTAGATTAGGTATAATTAG
* * *
2308 AAG-TTTGTGATAAAAGCATATTGTTCATTAATTTCTATGATTATCTATTTCTAGAACTTGTGTC
131 -AGTTTTGTGATAAAAGCATATTGTTCATT-ATTTCTATGAATACCTATTTCTAGAACTTATGTC
* *
2372 CAATCTTGATTGAAATTACAATTTTGATAGTATGTTATGGATATGTCAAGAACAAGTGTGGGGGA
194 CAATCTTGATTGAAATTACAATTATGAAAGTATGTTATGGATATGTCAAGAACAAGTGTGGGGGA
2437 CTACTTATATA
259 CTACTTATATA
2448 AAAGGGTAGT
Statistics
Matches: 245, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
267 22 0.09
268 201 0.82
269 22 0.09
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.44
Consensus pattern (269 bp):
TGAAAATTTTGCATATATTAAGTGATTTGATTTAATGATGATTGAAGAATACTTAGAATTTTTAA
GAAAATTTTATTTAATTGATTGATTTATAGCATGATATCTGATTTCTTAGATTAGGTATAATTAG
AGTTTTGTGATAAAAGCATATTGTTCATTATTTCTATGAATACCTATTTCTAGAACTTATGTCCA
ATCTTGATTGAAATTACAATTATGAAAGTATGTTATGGATATGTCAAGAACAAGTGTGGGGGACT
ACTTATATA
Found at i:4055 original size:11 final size:11
Alignment explanation
Indices: 4039--4064 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4029 AGATAATTTC
4039 TTTTCTTCTAG
1 TTTTCTTCTAG
4050 TTTTCTTCTAG
1 TTTTCTTCTAG
4061 TTTT
1 TTTT
4065 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:4834 original size:15 final size:15
Alignment explanation
Indices: 4802--4843 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
4792 TTACTTTGCT
*
4802 TTGTTTTCTAGCTTAA
1 TTGTTTTCT-GTTTAA
4818 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
4833 TTGCTTTCTGT
1 TTGTTTTCTGT
4844 CAATCTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.12, C:0.12, G:0.14, T:0.62
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Done.