Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014427.1 Corchorus olitorius cultivar O-4 contig14460, 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: 3509
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:3509 original size:40 final size:40
Alignment explanation
Indices: 3226--3508 Score: 480
Period size: 40 Copynumber: 7.1 Consensus size: 40
3216 TTATCTAGTC
3226 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT
1 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT
*
3266 TAAATACCCAGTTTGCCCTTCCCCATCGG-AGGTGTTGTT
1 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT
3305 TAAATACCCAGTTTG-CCTTCCCCACCGGAAGGTGTTGTT
1 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT
* *
3344 TAAATACCCAGTTTGCCCTTCCCCTCCAGAAGGTGTTGTT
1 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT
* * *
3384 TAAATTCCCAATTTGCCCTTCCCCACCGGAAGGTATTGTT
1 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT
3424 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT
1 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT
* *
3464 TAAATTCCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTT
1 TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT
3504 TAAAT
1 TAAAT
3509 T
Statistics
Matches: 227, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
38 12 0.05
39 50 0.22
40 165 0.73
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (40 bp):
TAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT
Done.