Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020922.1 Corchorus olitorius cultivar O-4 contig20955, 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, 822
Length: 1370
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Found at i:434 original size:27 final size:27
Alignment explanation
Indices: 404--461 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
394 TTTCCCTTTC
*
404 TTTTTCTCTTCCT-TTTT-TTTTTTATT
1 TTTTTC-CTTCCTATTTTATTATTTATT
*
430 TTTTTCCTTTCTATTTTATTATTTATT
1 TTTTTCCTTCCTATTTTATTATTTATT
457 TTTTT
1 TTTTT
462 TTTTAAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 5 0.18
26 10 0.36
27 13 0.46
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (27 bp):
TTTTTCCTTCCTATTTTATTATTTATT
Found at i:1252 original size:2 final size:2
Alignment explanation
Indices: 1245--1370 Score: 252
Period size: 2 Copynumber: 63.0 Consensus size: 2
1235 GTTTCTTTGT
1245 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1287 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1329 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 124 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.