Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000499.1 Corchorus olitorius cultivar O-4 contig00499, 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: 1820
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Found at i:1239 original size:46 final size:46
Alignment explanation
Indices: 1172--1285 Score: 219
Period size: 46 Copynumber: 2.5 Consensus size: 46
1162 AGGGGTAATC
1172 CATATTCCCTTACAGATCATCTTAGTCAATTCTTATTTGGCTGGTA
1 CATATTCCCTTACAGATCATCTTAGTCAATTCTTATTTGGCTGGTA
*
1218 CATATTCCCTTACAGATCATCTTAGTCAATTCTTATTTGGCTGGTC
1 CATATTCCCTTACAGATCATCTTAGTCAATTCTTATTTGGCTGGTA
1264 CATATTCCCTTACAGATCATCT
1 CATATTCCCTTACAGATCATCT
1286 GGTTTTACAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (46 bp):
CATATTCCCTTACAGATCATCTTAGTCAATTCTTATTTGGCTGGTA
Found at i:1576 original size:20 final size:22
Alignment explanation
Indices: 1553--1592 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1543 TATTTCACAT
*
1553 AAAT-ATTC-CATATCAAATTC
1 AAATAATTCACATATAAAATTC
1573 AAATAATTCACATATAAAAT
1 AAATAATTCACATATAAAAT
1593 ATTGATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATAATTCACATATAAAATTC
Done.