Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015779.1 Corchorus capsularis cultivar CVL-1 contig15800, 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: 6526
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Found at i:158 original size:92 final size:92
Alignment explanation
Indices: 1--209 Score: 409
Period size: 92 Copynumber: 2.3 Consensus size: 92
1 ATTCTTCATGATAACTTTGCAGACCTTCATAATTTGGCTTTCTCTTCATCCAATGAGTCAGCTTT
1 ATTCTTCATGATAACTTTGCAGACCTTCATAATTTGGCTTTCTCTTCATCCAATGAGTCAGCTTT
*
66 GCATTATTGGAGACAATTTCTGCAGAG
66 GCATTATTGGAGACAATATCTGCAGAG
93 ATTCTTCATGATAACTTTGCAGACCTTCATAATTTGGCTTTCTCTTCATCCAATGAGTCAGCTTT
1 ATTCTTCATGATAACTTTGCAGACCTTCATAATTTGGCTTTCTCTTCATCCAATGAGTCAGCTTT
158 GCATTATTGGAGACAATATCTGCAGAG
66 GCATTATTGGAGACAATATCTGCAGAG
185 ATTCTTCATGATAACTTTGCAGACC
1 ATTCTTCATGATAACTTTGCAGACC
210 ATTATTTTTT
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 116 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (92 bp):
ATTCTTCATGATAACTTTGCAGACCTTCATAATTTGGCTTTCTCTTCATCCAATGAGTCAGCTTT
GCATTATTGGAGACAATATCTGCAGAG
Found at i:225 original size:21 final size:21
Alignment explanation
Indices: 199--240 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
189 TTCATGATAA
199 CTTTGCAGACCATTATTTTTT
1 CTTTGCAGACCATTATTTTTT
220 CTTTGCAGACCATTATTTTTT
1 CTTTGCAGACCATTATTTTTT
241 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (21 bp):
CTTTGCAGACCATTATTTTTT
Done.