Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004058.1 Corchorus capsularis cultivar CVL-1 contig04066, 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, 677
Length: 1129
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45
Found at i:1044 original size:109 final size:109
Alignment explanation
Indices: 848--1122 Score: 446
Period size: 109 Copynumber: 2.5 Consensus size: 109
838 ACTATTATAG
* *
848 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
*
913 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAAATTGGATATACTAAAATTTTTTCTAATATACAA
962 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
1027 TTACCAAAAAAATTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAAATTGGATATACTAAAATTTTTTCTAATATACAA
1071 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
1123 TATATTT
Statistics
Matches: 156, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
108 7 0.04
109 123 0.79
110 3 0.02
111 2 0.01
114 21 0.13
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAAATTGGATATACTAAAATTTTTTCTAATATACAA
Done.