Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005705.1 Corchorus capsularis cultivar CVL-1 contig05723, 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: 1989
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.33
Found at i:206 original size:21 final size:21
Alignment explanation
Indices: 180--223 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
170 TTTTTCTGGA
180 TTGCTAAACACCGCCCCAGTT
1 TTGCTAAACACCGCCCCAGTT
** *
201 TTGCTATTCACCGCCCCATTT
1 TTGCTAAACACCGCCCCAGTT
222 TT
1 TT
224 TACGTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.36, G:0.11, T:0.34
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCAGTT
Found at i:287 original size:32 final size:32
Alignment explanation
Indices: 242--365 Score: 137
Period size: 32 Copynumber: 3.8 Consensus size: 32
232 TTTACGCTTT
*
242 TGCCGTGGCGAAGCCGCCCCA-TGAGGGCGGCC
1 TGCCGTGGTGAAGCCGCCCCAGTG-GGGCGGCC
274 TGCCGTGGTGAAGCCGCCCCAGTGGGGCGGCC
1 TGCCGTGGTGAAGCCGCCCCAGTGGGGCGGCC
* *
306 TGCCCATGGTGAAGCCG-CCCAGTGGGGAGGCTC
1 TG-CCGTGGTGAAGCCGCCCCAGTGGGGCGGC-C
* * *
339 CGCCGTGGCTG-AGCCGTCCTAGTGGGG
1 TGCCGTGG-TGAAGCCGCCCCAGTGGGG
366 AGGCTCAGTG
Statistics
Matches: 81, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
32 53 0.65
33 28 0.35
ACGTcount: A:0.11, C:0.33, G:0.42, T:0.14
Consensus pattern (32 bp):
TGCCGTGGTGAAGCCGCCCCAGTGGGGCGGCC
Done.