Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007523.1 Corchorus capsularis cultivar CVL-1 contig07544, 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: 3899
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:237 original size:15 final size:15
Alignment explanation
Indices: 190--238 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 15
180 TTTATAATTG
190 TTATAAA-TATATA-
1 TTATAAATTATATAT
* *
203 TTAAAAAAT-TATAT
1 TTATAAATTATATAT
217 TT-TAAATTATATAT
1 TTATAAATTATATAT
231 TTATAAAT
1 TTATAAAT
239 ATTTCAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 14 0.48
14 10 0.34
15 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATAAATTATATAT
Found at i:263 original size:25 final size:24
Alignment explanation
Indices: 213--264 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
203 TTAAAAAATT
* *
213 ATATTTTAAATTATATATTTATAA
1 ATATTTCAAATTATATATTTAAAA
237 ATATTTCAAA-TATATTAATTTAAAA
1 ATATTTCAAATTATA-T-ATTTAAAA
262 ATA
1 ATA
265 ATAAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 10 0.42
25 10 0.42
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATTTCAAATTATATATTTAAAA
Found at i:582 original size:16 final size:16
Alignment explanation
Indices: 561--636 Score: 82
Period size: 16 Copynumber: 4.8 Consensus size: 16
551 GGTTCGGGTT
* *
561 ATTCGGGTTTTGAGTC
1 ATTCGGGTCTCGAGTC
*
577 ATTCGGGTCTCGGGTC
1 ATTCGGGTCTCGAGTC
*
593 ATTTGGGTCTCGAGTC
1 ATTCGGGTCTCGAGTC
* *
609 AATCGGGTTTCTG-GTC
1 ATTCGGGTCTC-GAGTC
625 ATTCGGGTCTCG
1 ATTCGGGTCTCG
637 GGTTGGGCGG
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
15 1 0.02
16 47 0.96
17 1 0.02
ACGTcount: A:0.11, C:0.20, G:0.33, T:0.37
Consensus pattern (16 bp):
ATTCGGGTCTCGAGTC
Found at i:590 original size:32 final size:31
Alignment explanation
Indices: 523--636 Score: 106
Period size: 32 Copynumber: 3.6 Consensus size: 31
513 GACAGTTTTC
* *
523 TCGGGTCATTCAGGTTTCG-GTTC-ATCTGGGT
1 TCGGGTCATTCGGGTCTCGAG-TCAATC-GGGT
* * * *
554 TCGGGTTATTCGGGTTTTGAGTCATTCGGGT
1 TCGGGTCATTCGGGTCTCGAGTCAATCGGGT
*
585 CTCGGGTCATTTGGGTCTCGAGTCAATCGGGTT
1 -TCGGGTCATTCGGGTCTCGAGTCAATCGGG-T
*
618 TCTGGTCATTCGGGTCTCG
1 TCGGGTCATTCGGGTCTCG
637 GGTTGGGCGG
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
31 22 0.32
32 45 0.66
33 1 0.01
ACGTcount: A:0.10, C:0.19, G:0.33, T:0.38
Consensus pattern (31 bp):
TCGGGTCATTCGGGTCTCGAGTCAATCGGGT
Found at i:626 original size:48 final size:46
Alignment explanation
Indices: 526--639 Score: 138
Period size: 48 Copynumber: 2.4 Consensus size: 46
516 AGTTTTCTCG
* * * * * *
526 GGTCATTCAGGTTTCGGTTCATCTGGGTTCGGGTTATTCGGGTTTT
1 GGTCATTCGGGTCTCGGGTCATCTGGGTTCGAGTCAATCGGGTTTT
*
572 GAGTCATTCGGGTCTCGGGTCATTTGGGTCTCGAGTCAATCGGGTTTCT
1 G-GTCATTCGGGTCTCGGGTCATCTGGGT-TCGAGTCAATCGGGTTT-T
621 GGTCATTCGGGTCTCGGGT
1 GGTCATTCGGGTCTCGGGT
640 TGGGCGGGTT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
46 1 0.02
47 23 0.40
48 32 0.55
49 2 0.03
ACGTcount: A:0.10, C:0.18, G:0.34, T:0.38
Consensus pattern (46 bp):
GGTCATTCGGGTCTCGGGTCATCTGGGTTCGAGTCAATCGGGTTTT
Found at i:909 original size:42 final size:42
Alignment explanation
Indices: 863--944 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
853 TAGATATTAA
* *
863 TTTTGAATATTAAATACATAATTGATTATCAGGTGTGGTAGG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTAGG
905 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
945 TGTGTCAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTAGG
Found at i:1457 original size:45 final size:45
Alignment explanation
Indices: 1406--1495 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
1396 TAATAGAGTA
1406 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
* *
1451 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
1496 AGAAGTAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
Done.