Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024260.1 Corchorus olitorius cultivar O-4 contig24293, 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: 5365
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Found at i:187 original size:50 final size:52
Alignment explanation
Indices: 89--188 Score: 127
Period size: 50 Copynumber: 2.0 Consensus size: 52
79 TTTTTTCTAA
* * *
89 AAAAAAAAATATTTTTGCGTCATAAAAAAAAATTGTTTTGTGTTTTGCGTCG
1 AAAAAAAAATATTTCTGCGTCATAAAAAAAAATTGTCTTGTGTCTTGCGTCG
141 AAAAAAAAA-A-TTCTGCGTCATAAATAAAAATATT-TCTTGT-TCTTGCGT
1 AAAAAAAAATATTTCTGCGTCATAAA-AAAAA-ATTGTCTTGTGTCTTGCGT
189 TTTTAGATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
50 20 0.47
51 11 0.26
52 12 0.28
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (52 bp):
AAAAAAAAATATTTCTGCGTCATAAAAAAAAATTGTCTTGTGTCTTGCGTCG
Found at i:2701 original size:21 final size:21
Alignment explanation
Indices: 2675--2723 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2665 CCGATTGCCA
**
2675 CACCACCGGTTAAGCCCGTGC
1 CACCACCGGCCAAGCCCGTGC
*
2696 CACCACCGGCCATGCCCGTGC
1 CACCACCGGCCAAGCCCGTGC
*
2717 CATCACC
1 CACCACC
2724 ATTCCAAGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.49, G:0.20, T:0.12
Consensus pattern (21 bp):
CACCACCGGCCAAGCCCGTGC
Done.