Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017794.1 Corchorus olitorius cultivar O-4 contig17827, 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: 13188
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Found at i:11135 original size:15 final size:15
Alignment explanation
Indices: 11115--11151 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
11105 TTATTGTTCA
11115 CACCATTGTTATTCG
1 CACCATTGTTATTCG
* *
11130 CACCATTGTTGTTTG
1 CACCATTGTTATTCG
11145 CACCATT
1 CACCATT
11152 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:12040 original size:48 final size:47
Alignment explanation
Indices: 11964--12106 Score: 180
Period size: 49 Copynumber: 3.0 Consensus size: 47
11954 CGAGCGTGCC
* * *
11964 AATCAATTTTGTCAAAAAATTGATAAAAAGTGCAGTGAAAATTAAAA
1 AATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGTGAAAAATAAAA
12011 AATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGT-AAAAATAAAA
1 AATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGC-AGTGAAAAATAAAA
** * *
12060 GTTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 AATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAGTGAAAAATAAA
12107 GGATTGCTTG
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
47 16 0.19
48 26 0.31
49 39 0.46
50 3 0.04
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (47 bp):
AATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGTGAAAAATAAAA
Done.