Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002548.1 Corchorus capsularis cultivar CVL-1 contig02556, 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, 686
Length: 1144
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Found at i:103 original size:21 final size:20
Alignment explanation
Indices: 79--141 Score: 87
Period size: 21 Copynumber: 3.2 Consensus size: 20
69 CATGGATTCC
79 TTTTATAGATAATGTCTAATT
1 TTTTATAGATAATGTCTAA-T
100 TTTTATAGATAATGTCTAA-
1 TTTTATAGATAATGTCTAAT
119 --TTATAGATAATGTCTAAT
1 TTTTATAGATAATGTCTAAT
137 GTTTT
1 -TTTT
142 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:124 original size:17 final size:17
Alignment explanation
Indices: 81--136 Score: 76
Period size: 17 Copynumber: 3.1 Consensus size: 17
71 TGGATTCCTT
81 TTATAGATAATGTCTAA
1 TTATAGATAATGTCTAA
98 TTTTTTATAGATAATGTCTAA
1 ----TTATAGATAATGTCTAA
119 TTATAGATAATGTCTAA
1 TTATAGATAATGTCTAA
136 T
1 T
137 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.