Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01003620.1 Corchorus olitorius cultivar O-4 contig03628, 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, 818
Length: 1364
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Found at i:564 original size:7 final size:7
Alignment explanation
Indices: 552--592 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
542 GGGATTAGTA
552 GTCAGGG
1 GTCAGGG
559 GTCAGGG
1 GTCAGGG
566 GTCAGGG
1 GTCAGGG
* **
573 ATCAGTA
1 GTCAGGG
580 GTCAGGG
1 GTCAGGG
587 GTCAGG
1 GTCAGG
593 TATTAGGGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.20, C:0.15, G:0.49, T:0.17
Consensus pattern (7 bp):
GTCAGGG
Found at i:600 original size:28 final size:28
Alignment explanation
Indices: 542--602 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
532 TGTCTGAAAG
* *
542 GGGATTAGTAGTCAGGGGTCAGGGGTCA
1 GGGATCAGTAGTCAGGGGTCAGGGATCA
* *
570 GGGATCAGTAGTCAGGGGTCAGGTATTA
1 GGGATCAGTAGTCAGGGGTCAGGGATCA
598 GGGAT
1 GGGAT
603 TAGGTATTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.10, G:0.44, T:0.23
Consensus pattern (28 bp):
GGGATCAGTAGTCAGGGGTCAGGGATCA
Found at i:652 original size:7 final size:7
Alignment explanation
Indices: 642--701 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 7
632 GGTTAACTGG
*
642 TAACTTA
1 TAACTCA
649 TAACTCA
1 TAACTCA
*
656 CAACTCA
1 TAACTCA
*
663 TAACTCG
1 TAACTCA
*
670 TAACCCA
1 TAACTCA
677 TAACTC-
1 TAACTCA
683 TCAACTCA
1 T-AACTCA
*
691 TAACCCA
1 TAACTCA
698 TAAC
1 TAAC
702 CCGCAACTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
6 1 0.02
7 41 0.95
8 1 0.02
ACGTcount: A:0.40, C:0.33, G:0.02, T:0.25
Consensus pattern (7 bp):
TAACTCA
Found at i:667 original size:28 final size:28
Alignment explanation
Indices: 648--715 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
638 CTGGTAACTT
648 ATAACTCACAACTCATAACTCGTAACCC
1 ATAACTCACAACTCATAACTCGTAACCC
* * *
676 ATAACTCTCAACTCATAACCCATAACCC
1 ATAACTCACAACTCATAACTCGTAACCC
**
704 GCAACTCACAAC
1 ATAACTCACAAC
716 CCGCAACTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.40, C:0.38, G:0.03, T:0.19
Consensus pattern (28 bp):
ATAACTCACAACTCATAACTCGTAACCC
Found at i:688 original size:21 final size:21
Alignment explanation
Indices: 664--757 Score: 98
Period size: 21 Copynumber: 4.5 Consensus size: 21
654 CACAACTCAT
*
664 AACTCGTAACCCATAACTCTC
1 AACTCATAACCCATAACTCTC
* *
685 AACTCATAACCCATAACCCGC
1 AACTCATAACCCATAACTCTC
* ** *
706 AACTCACAACCCGCAACTCAC
1 AACTCATAACCCATAACTCTC
* *
727 AACCCATAACCAATAACTCTC
1 AACTCATAACCCATAACTCTC
*
748 AACTCGTAAC
1 AACTCATAAC
758 AACTGACCCC
Statistics
Matches: 57, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.38, C:0.40, G:0.04, T:0.17
Consensus pattern (21 bp):
AACTCATAACCCATAACTCTC
Found at i:718 original size:14 final size:14
Alignment explanation
Indices: 699--731 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
689 CATAACCCAT
699 AACCCGCAACTCAC
1 AACCCGCAACTCAC
713 AACCCGCAACTCAC
1 AACCCGCAACTCAC
727 AACCC
1 AACCC
732 ATAACCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.52, G:0.06, T:0.06
Consensus pattern (14 bp):
AACCCGCAACTCAC
Done.