Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006269.1 Corchorus olitorius cultivar O-4 contig06294, 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, 632
Length: 1054
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Found at i:621 original size:17 final size:17
Alignment explanation
Indices: 561--623 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
551 TTTAAAAAAA
* * *
561 AAAAAAAAAAAAAAAAG
1 AAAAGAAAAAGAAGAAG
*
578 AAAAGAAGAAGAAGAAG
1 AAAAGAAAAAGAAGAAG
595 AGAAAG-AAAAGAAGAAG
1 A-AAAGAAAAAGAAGAAG
*
612 AAAGGAAAAAGA
1 AAAAGAAAAAGA
624 GTGGGCCTGG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
16 3 0.08
17 31 0.82
18 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAGAAGAAG
Found at i:623 original size:11 final size:11
Alignment explanation
Indices: 554--623 Score: 67
Period size: 11 Copynumber: 6.6 Consensus size: 11
544 CCCAAAATTT
554 AAAAA-AAAA-
1 AAAAAGAAAAG
563 AAAAA-AAAA-
1 AAAAAGAAAAG
572 AAAAAGAAAAG
1 AAAAAGAAAAG
*
583 AAGAAGAAGAAG
1 AAAAAGAA-AAG
*
595 AGAAAGAAAAG
1 AAAAAGAAAAG
* *
606 AAGAAGAAAGG
1 AAAAAGAAAAG
617 AAAAAGA
1 AAAAAGA
624 GTGGGCCTGG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
9 14 0.27
10 4 0.08
11 24 0.47
12 9 0.18
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Done.