Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005469.1 Corchorus capsularis cultivar CVL-1 contig05487, 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: 10029
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:864 original size:37 final size:38
Alignment explanation
Indices: 809--887 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 38
799 CTTATATACT
* *
809 TGATCAACATACATGTCTTTTCATATAGACATAACTTTA
1 TGATCAACA-ACATGTCTTTCCAAATAGACATAACTTTA
848 TGATCAAC-ACATGTCTTTCCAAATAGACATAACTTTA
1 TGATCAACAACATGTCTTTCCAAATAGACATAACTTTA
885 TGA
1 TGA
888 ATAATTATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 30 0.79
39 8 0.21
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (38 bp):
TGATCAACAACATGTCTTTCCAAATAGACATAACTTTA
Found at i:952 original size:31 final size:31
Alignment explanation
Indices: 916--975 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
906 TACCTTTTAT
916 AGACAAATAAGTCTCTTCATAATTGTTCATA
1 AGACAAATAAGTCTCTTCATAATTGTTCATA
*
947 AGACAAATAAGTCTCTTCATAGTTGTTCA
1 AGACAAATAAGTCTCTTCATAATTGTTCA
976 CTTATGAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (31 bp):
AGACAAATAAGTCTCTTCATAATTGTTCATA
Done.