Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3413
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, 450
Length: 751
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Found at i:531 original size:28 final size:28
Alignment explanation
Indices: 458--531 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 28
448 CAATCACTCT
* * *
458 TTTTTTTCTT-TTTTTTTCAATTTTGAT
1 TTTTTTTCTTCTTTTTTTTAATTCTGAA
485 TTTTTTTCTTCTTTTTTTTAATTCTGAA
1 TTTTTTTCTTCTTTTTTTTAATTCTGAA
513 TTTTTTTCTTCTTTTTTTT
1 TTTTTTTCTTCTTTTTTTT
532 TCTTCAATAC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
27 10 0.23
28 33 0.77
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.78
Consensus pattern (28 bp):
TTTTTTTCTTCTTTTTTTTAATTCTGAA
Found at i:595 original size:13 final size:13
Alignment explanation
Indices: 577--622 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
567 GAATACAAAC
*
577 TTTTTTTTTGAAT
1 TTTTTTTTTAAAT
*
590 TTTTTTTTCAAAT
1 TTTTTTTTTAAAT
603 TTTTTTTTTCAAAT
1 TTTTTTTTT-AAAT
617 TTTTTT
1 TTTTTT
623 ATATTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTAAAT
Found at i:596 original size:14 final size:14
Alignment explanation
Indices: 572--622 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
562 AAATTGAATA
*
572 CAAACTTTTTTTTT
1 CAAATTTTTTTTTT
*
586 -GAA-TTTTTTTTT
1 CAAATTTTTTTTTT
598 CAAATTTTTTTTTT
1 CAAATTTTTTTTTT
612 CAAATTTTTTT
1 CAAATTTTTTT
623 ATATTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 9 0.27
13 4 0.12
14 20 0.61
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.69
Consensus pattern (14 bp):
CAAATTTTTTTTTT
Done.