Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008757.1 Corchorus olitorius cultivar O-4 contig08784, 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, 813
Length: 1355
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Found at i:435 original size:3 final size:3
Alignment explanation
Indices: 427--461 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
417 TGGGAGCTAG
*
427 GAA GAA GAA GAA GAA GAA GAA GAA GAG GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
462 GGGGAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:462 original size:9 final size:9
Alignment explanation
Indices: 425--463 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
415 GCTGGGAGCT
425 AGGAAGAAG
1 AGGAAGAAG
*
434 AAGAAGAAG
1 AGGAAGAAG
*
443 AAGAAGAAG
1 AGGAAGAAG
452 AGGAAGAAG
1 AGGAAGAAG
461 AGG
1 AGG
464 GGAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (9 bp):
AGGAAGAAG
Found at i:594 original size:20 final size:20
Alignment explanation
Indices: 556--651 Score: 68
Period size: 25 Copynumber: 4.3 Consensus size: 20
546 GCCCAAGCCG
556 AAAAAAAAATAGAAAAGAAAAGAA
1 AAAAAAAAATAGAAAAG----GAA
580 AAGAAAAAAATAGAAAAGGAA
1 AA-AAAAAAATAGAAAAGGAA
* **
601 TAAAAAAAATA-AAATAATAA
1 AAAAAAAAATAGAAA-AGGAA
621 TAAAAAAAATATAGAAAAGGGAA
1 -AAAAAAAA-ATAGAAAA-GGAA
644 AAGAAAAA
1 AA-AAAAA
652 GTAAGAGGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
19 3 0.05
20 12 0.20
21 11 0.19
22 6 0.10
23 10 0.17
24 2 0.03
25 15 0.25
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (20 bp):
AAAAAAAAATAGAAAAGGAA
Found at i:605 original size:16 final size:15
Alignment explanation
Indices: 566--639 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
556 AAAAAAAAAT
566 AGAAAAGAAA-AGAAA
1 AGAAAA-AAATAGAAA
581 AGAAAAAAATAGAAA
1 AGAAAAAAATAGAAA
* *
596 AGGAATAAA-A-AAA
1 AGAAAAAAATAGAAA
* *
609 ATAAAATAATA-ATAA
1 AGAAAAAAATAGA-AA
*
624 A-AAAAATATAGAAA
1 AGAAAAAAATAGAAA
638 AG
1 AG
640 GGAAAAGAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
13 8 0.17
14 16 0.35
15 22 0.48
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (15 bp):
AGAAAAAAATAGAAA
Found at i:606 original size:25 final size:24
Alignment explanation
Indices: 556--616 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
546 GCCCAAGCCG
556 AAAAAAAAATAGAAAAGAAAAGAA
1 AAAAAAAAATAGAAAAGAAAAGAA
580 AAGAAAAAAATAGAAAAGGAATAA-AA
1 AA-AAAAAAATAGAAAA-GAA-AAGAA
*
606 AAAATAAAATA
1 AAAAAAAAATA
617 ATAATAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 2 0.06
25 22 0.67
26 7 0.21
27 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.08
Consensus pattern (24 bp):
AAAAAAAAATAGAAAAGAAAAGAA
Found at i:607 original size:11 final size:9
Alignment explanation
Indices: 557--631 Score: 55
Period size: 9 Copynumber: 8.1 Consensus size: 9
547 CCCAAGCCGA
557 AAAAAAAAT
1 AAAAAAAAT
* *
566 AGAAAAGA-
1 AAAAAAAAT
*
574 AAAGAAAA-
1 AAAAAAAAT
*
582 GAAAAAAAT
1 AAAAAAAAT
*
591 AGAAAAGGAAT
1 A-AAAA-AAAT
602 AAAAAAAAT
1 AAAAAAAAT
611 AAAATAATAAT
1 AAAA-AA-AAT
622 AAAAAAAAT
1 AAAAAAAAT
631 A
1 A
632 TAGAAAAGGG
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
8 11 0.22
9 17 0.33
10 12 0.24
11 11 0.22
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:638 original size:11 final size:10
Alignment explanation
Indices: 571--638 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 10
561 AAAATAGAAA
571 AGAAAAGAAA-
1 AGAAAA-AAAT
581 AGAAAAAAAT
1 AGAAAAAAAT
*
591 AGAAAAGGAAT
1 AGAAAA-AAAT
602 A-AAAAAAAT
1 AGAAAAAAAT
611 A-AAATAATAAT
1 AGAAA-AA-AAT
*
622 AAAAAAAATAT
1 AGAAAAAA-AT
633 AGAAAA
1 AGAAAA
639 GGGAAAAGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
9 10 0.20
10 19 0.39
11 17 0.35
12 3 0.06
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (10 bp):
AGAAAAAAAT
Done.