Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g02476.F2
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: 3900
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Found at i:558 original size:69 final size:69
Alignment explanation
Indices: 447--583 Score: 256
Period size: 69 Copynumber: 2.0 Consensus size: 69
437 GCACATCAAG
447 AAGTTAGTTTATTTTTCAGAAAAGAAAAACAATTTAATCTGTAAATAGAGTTTAATTTCCAATTT
1 AAGTTAGTTTATTTTTCAGAAAAGAAAAACAATTTAATCTGTAAATAGAGTTTAATTTCCAATTT
512 ATAC
66 ATAC
* *
516 AAGTTAGTTTATTTTTCAGAAAAGGAGAACAATTTAATCTGTAAATAGAGTTTAATTTCCAATTT
1 AAGTTAGTTTATTTTTCAGAAAAGAAAAACAATTTAATCTGTAAATAGAGTTTAATTTCCAATTT
581 ATA
66 ATA
584 TAAATTGGTC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (69 bp):
AAGTTAGTTTATTTTTCAGAAAAGAAAAACAATTTAATCTGTAAATAGAGTTTAATTTCCAATTT
ATAC
Found at i:2687 original size:33 final size:32
Alignment explanation
Indices: 2582--2699 Score: 114
Period size: 33 Copynumber: 3.7 Consensus size: 32
2572 CGGTTAGTAC
* *
2582 GGATGATGCTCCTTTAAGCAGGACAAGTAGCAG
1 GGATGATGC-CCCTTAAGCAGGCCAAGTAGCAG
* * * * * *
2615 GGATG-TG-TCCATAAGCCGGCTAATTAGTAG
1 GGATGATGCCCCTTAAGCAGGCCAAGTAGCAG
2645 GGATGATGCCCCTTCAAGCAGGCCAAGTAGCAG
1 GGATGATGCCCCTT-AAGCAGGCCAAGTAGCAG
*
2678 GGATGATGCCCCTATAATCAGG
1 GGATGATGCCCCT-TAAGCAGG
2700 TTGGGTACTG
Statistics
Matches: 66, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
30 20 0.30
31 2 0.03
32 5 0.08
33 38 0.58
34 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (32 bp):
GGATGATGCCCCTTAAGCAGGCCAAGTAGCAG
Done.