Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001897.1 Corchorus capsularis cultivar CVL-1 contig01899, 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, 745
Length: 1243
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Found at i:80 original size:21 final size:20
Alignment explanation
Indices: 56--118 Score: 87
Period size: 21 Copynumber: 3.2 Consensus size: 20
46 CATGGATTCC
56 TTTTATAGATAATGTCTAATT
1 TTTTATAGATAATGTCTAA-T
77 TTTTATAGATAATGTCTAA-
1 TTTTATAGATAATGTCTAAT
96 --TTATAGATAATGTCTAAT
1 TTTTATAGATAATGTCTAAT
114 GTTTT
1 -TTTT
119 GTTATAATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
17 17 0.45
21 21 0.55
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (20 bp):
TTTTATAGATAATGTCTAAT
Found at i:101 original size:17 final size:17
Alignment explanation
Indices: 58--113 Score: 76
Period size: 17 Copynumber: 3.1 Consensus size: 17
48 TGGATTCCTT
58 TTATAGATAATGTCTAA
1 TTATAGATAATGTCTAA
75 TTTTTTATAGATAATGTCTAA
1 ----TTATAGATAATGTCTAA
96 TTATAGATAATGTCTAA
1 TTATAGATAATGTCTAA
113 T
1 T
114 GTTTTGTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
17 18 0.51
21 17 0.49
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (17 bp):
TTATAGATAATGTCTAA
Done.