Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003289.1 Corchorus capsularis cultivar CVL-1 contig03297, 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, 906
Length: 1510
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Found at i:1069 original size:31 final size:32
Alignment explanation
Indices: 1028--1102 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 32
1018 ATTTTTGGGT
* ** * *
1028 ACCCAAACCCGAAATTACCCGAATCC-AAACG
1 ACCCGAACCCGAAAGGACCCAAACCCAAAACG
*
1059 ACCCGAACCCGAAAGGACCCAAACCCAAAATG
1 ACCCGAACCCGAAAGGACCCAAACCCAAAACG
1091 ACCCGAACCCGA
1 ACCCGAACCCGA
1103 TCGACCCGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 21 0.57
32 16 0.43
ACGTcount: A:0.41, C:0.40, G:0.13, T:0.05
Consensus pattern (32 bp):
ACCCGAACCCGAAAGGACCCAAACCCAAAACG
Found at i:1083 original size:16 final size:16
Alignment explanation
Indices: 1028--1102 Score: 80
Period size: 16 Copynumber: 4.8 Consensus size: 16
1018 ATTTTTGGGT
* *
1028 ACCCAAACCCGAAATT
1 ACCCGAACCCGAAATG
* *
1044 ACCCGAATCC-AAACG
1 ACCCGAACCCGAAATG
*
1059 ACCCGAACCCGAAAGG
1 ACCCGAACCCGAAATG
* *
1075 ACCCAAACCCAAAATG
1 ACCCGAACCCGAAATG
1091 ACCCGAACCCGA
1 ACCCGAACCCGA
1103 TCGACCCGAC
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
15 12 0.26
16 35 0.74
ACGTcount: A:0.41, C:0.40, G:0.13, T:0.05
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Done.