Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009814.1 Corchorus olitorius cultivar O-4 contig09846, 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: 2029
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Found at i:638 original size:27 final size:27
Alignment explanation
Indices: 608--692 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
598 ATACCATGAT
608 TTAATTAGAAAATTAGGAGTATTAAAA
1 TTAATTAGAAAATTAGGAGTATTAAAA
* *** * * ** * *
635 TTAATAATTTAATT-GTAATACCATGAT
1 TTAATTAGAAAATTAGGAGTATTA-AAA
662 TTAATTAGAAAATTAGGAGTATTAAAA
1 TTAATTAGAAAATTAGGAGTATTAAAA
689 TTAA
1 TTAA
693 GAATTTAAGT
Statistics
Matches: 36, Mismatches: 20, Indels: 4
0.60 0.33 0.07
Matches are distributed among these distances:
26 5 0.14
27 26 0.72
28 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (27 bp):
TTAATTAGAAAATTAGGAGTATTAAAA
Found at i:655 original size:54 final size:54
Alignment explanation
Indices: 591--700 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
581 AGGAGGGGAG
*
591 AATTGTAATACCATGATTTAATTAGAAAATTAGGAGTATTAAAATTAATAATTT
1 AATTGTAATACCATGATTTAATTAGAAAATTAGGAGTATTAAAATTAAGAATTT
645 AATTGTAATACCATGATTTAATTAGAAAATTAGGAGTATTAAAATTAAGAATTT
1 AATTGTAATACCATGATTTAATTAGAAAATTAGGAGTATTAAAATTAAGAATTT
699 AA
1 AA
701 GTGGGAATTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.37
Consensus pattern (54 bp):
AATTGTAATACCATGATTTAATTAGAAAATTAGGAGTATTAAAATTAAGAATTT
Done.