Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013262.1 Corchorus olitorius cultivar O-4 contig13295, 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: 2875
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:688 original size:30 final size:31
Alignment explanation
Indices: 646--726 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
636 TTGAGAAGTT
646 TGGTAAGG-TTGTGAAAGTTGA-GAAAAAGAA
1 TGGTAAGGTTTGTGAAAGTTGAGGAAAAAG-A
* *
676 TGGT-AGGTTTGTGAGAA-TTGAGGAAGATGA
1 TGGTAAGGTTTGTGA-AAGTTGAGGAAAAAGA
706 TGGTAAGGTTTG-GAAAGTTGA
1 TGGTAAGGTTTGTGAAAGTTGA
727 AAAGAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
29 5 0.11
30 25 0.57
31 14 0.32
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (31 bp):
TGGTAAGGTTTGTGAAAGTTGAGGAAAAAGA
Found at i:2363 original size:26 final size:28
Alignment explanation
Indices: 2325--2377 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 28
2315 AAAAATTGCG
*
2325 TTTTTGCATTTTTGTTTATATTTGCATA
1 TTTTTGCATTTTTCTTTATATTTGCATA
* *
2353 TTTTT-CA-TTTTCTTTTTGTTTGCAT
1 TTTTTGCATTTTTCTTTATATTTGCAT
2378 GCATTGCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 15 0.68
27 2 0.09
28 5 0.23
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.68
Consensus pattern (28 bp):
TTTTTGCATTTTTCTTTATATTTGCATA
Done.