Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003051.1 Corchorus capsularis cultivar CVL-1 contig03059, 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, 817
Length: 1362
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Found at i:201 original size:29 final size:28
Alignment explanation
Indices: 175--237 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
165 GTAAAAAGTG
175 GTAATAAATAAAAGAGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
***
203 GTAATTGGTAAAA-AGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
230 GTAA-AAAT
1 GTAATAAAT
238 GATAAAAGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
26 1 0.03
27 18 0.62
28 10 0.34
ACGTcount: A:0.60, C:0.00, G:0.22, T:0.17
Consensus pattern (28 bp):
GTAATAAATAAAAGAGAGTAAGAAAAGA
Found at i:243 original size:29 final size:28
Alignment explanation
Indices: 182--245 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 28
172 GTGGTAATAA
*
182 ATAAAAGAGAGTAAGAAAAGAGTAATTG
1 ATAAAAGAGAGTAAGAAAAGAGTAAATG
*
210 GTAAAA-AGAGTAAGAAAAGAGTAAAAATG
1 ATAAAAGAGAGTAAGAAAAGAGT--AAATG
239 ATAAAAG
1 ATAAAAG
246 CAGCAACAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 16 0.53
28 5 0.17
29 9 0.30
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (28 bp):
ATAAAAGAGAGTAAGAAAAGAGTAAATG
Done.