Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018701.1 Corchorus olitorius cultivar O-4 contig18734, 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: 4988
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Found at i:3349 original size:15 final size:15
Alignment explanation
Indices: 3329--3365 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3319 TTATTGTTCA
3329 CACCATTGTTATTCG
1 CACCATTGTTATTCG
* *
3344 CACCATTGTTGTTTG
1 CACCATTGTTATTCG
3359 CACCATT
1 CACCATT
3366 CACCCTAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.41
Consensus pattern (15 bp):
CACCATTGTTATTCG
Found at i:4285 original size:49 final size:49
Alignment explanation
Indices: 4184--4313 Score: 149
Period size: 49 Copynumber: 2.7 Consensus size: 49
4174 GAGCGTGCCA
* * * * *
4184 ATCAATTTTG-TCAAAAAATTGATAAAAATTGC-AGTGAAAATTAAAAG
1 ATCAATTTTGCCCTAAAAATTGAGAAAAAGTGCAAGTGAAAAATAAAAG
4231 ATCAATTTTGCCCTAAAAATTGAGAAAAAGATGCAAGT-AAAAATAAAAG
1 ATCAATTTTGCCCTAAAAATTGAGAAAAAG-TGCAAGTGAAAAATAAAAG
* ***
4280 TTCAATTTTGTTGTAAAAATTGAGAAAAAGTGCA
1 ATCAATTTTGCCCTAAAAATTGAGAAAAAGTGCA
4314 GGAAATGTAA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
47 10 0.14
48 19 0.27
49 39 0.55
50 3 0.04
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (49 bp):
ATCAATTTTGCCCTAAAAATTGAGAAAAAGTGCAAGTGAAAAATAAAAG
Done.