Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015333.1 Corchorus capsularis cultivar CVL-1 contig15354, 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: 16268
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:961 original size:28 final size:28
Alignment explanation
Indices: 929--983 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
919 TATTGTCCTT
*
929 ATTTTGTT-GCATATTAGTAACTCAAATA
1 ATTTT-TTGGCATAATAGTAACTCAAATA
*
957 ATTTTTTGGCCTAATAGTAACTCAAAT
1 ATTTTTTGGCATAATAGTAACTCAAAT
984 TCAAATGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (28 bp):
ATTTTTTGGCATAATAGTAACTCAAATA
Found at i:12324 original size:40 final size:40
Alignment explanation
Indices: 12280--12400 Score: 242
Period size: 40 Copynumber: 3.0 Consensus size: 40
12270 GTGAAGGCAG
12280 AATGCTTTTGACTAAGGTTCAACGTTGTCATTGCATGGAC
1 AATGCTTTTGACTAAGGTTCAACGTTGTCATTGCATGGAC
12320 AATGCTTTTGACTAAGGTTCAACGTTGTCATTGCATGGAC
1 AATGCTTTTGACTAAGGTTCAACGTTGTCATTGCATGGAC
12360 AATGCTTTTGACTAAGGTTCAACGTTGTCATTGCATGGAC
1 AATGCTTTTGACTAAGGTTCAACGTTGTCATTGCATGGAC
12400 A
1 A
12401 TTTGTGAATA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (40 bp):
AATGCTTTTGACTAAGGTTCAACGTTGTCATTGCATGGAC
Done.