Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2099
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, 661
Length: 1103
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:457 original size:19 final size:19
Alignment explanation
Indices: 435--476 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
425 GGCTTCTTTC
435 TTTTGCCTATTATTTATTT
1 TTTTGCCTATTATTTATTT
* * *
454 TTTTTCGTGTTATTTATTT
1 TTTTGCCTATTATTTATTT
473 TTTT
1 TTTT
477 CATATTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.74
Consensus pattern (19 bp):
TTTTGCCTATTATTTATTT
Found at i:482 original size:15 final size:14
Alignment explanation
Indices: 464--510 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
454 TTTTTCGTGT
464 TATTTATTTTTTTCA
1 TATTT-TTTTTTTCA
*
479 TATTTTTTTTGTC-
1 TATTTTTTTTTTCA
492 TGATTTTTTTTTTCGA
1 T-ATTTTTTTTTTC-A
508 TAT
1 TAT
511 CACGTAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 1 0.04
14 18 0.67
15 7 0.26
16 1 0.04
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.72
Consensus pattern (14 bp):
TATTTTTTTTTTCA
Found at i:497 original size:29 final size:30
Alignment explanation
Indices: 449--510 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
439 GCCTATTATT
* *
449 TATTTTTTTTCGTGTTATTTATTTTTTTC-A
1 TATTTTTTTTCGTCTGATTT-TTTTTTTCGA
479 TATTTTTTTT-GTCTGATTTTTTTTTTCGA
1 TATTTTTTTTCGTCTGATTTTTTTTTTCGA
508 TAT
1 TAT
511 CACGTAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 8 0.28
29 11 0.38
30 10 0.34
ACGTcount: A:0.13, C:0.06, G:0.08, T:0.73
Consensus pattern (30 bp):
TATTTTTTTTCGTCTGATTTTTTTTTTCGA
Found at i:596 original size:13 final size:13
Alignment explanation
Indices: 578--617 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
568 TTGAGAACTT
578 AAAAATATTTTCA
1 AAAAATATTTTCA
591 AAAAATATTTT--
1 AAAAATATTTTCA
*
602 TAAAATATTTTCA
1 AAAAATATTTTCA
615 AAA
1 AAA
618 CTTTCTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 10 0.43
13 13 0.57
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAATATTTTCA
Found at i:606 original size:11 final size:11
Alignment explanation
Indices: 592--742 Score: 61
Period size: 11 Copynumber: 12.6 Consensus size: 11
582 ATATTTTCAA
592 AAAATATTTTT
1 AAAATATTTTT
*
603 AAAATATTTTC
1 AAAATATTTTT
*
614 AAAACT-TTCTT
1 AAAA-TATTTTT
625 AAGGAATATTTTT
1 AA--AATATTTTT
* *
638 AACATGCATGTTT
1 AAAAT--ATTTTT
651 ACAGGCAATATTTTT
1 A-A---AATATTTTT
* * *
666 GAATTATTTTA
1 AAAATATTTTT
677 AAAATATTTTTT
1 AAAATA-TTTTT
* * *
689 GTAAACATTTTC
1 -AAAATATTTTT
701 AAAATATTCCTTT
1 AAAATATT--TTT
* *
714 AAAATGTTTTA
1 AAAATATTTTT
*
725 AAAATATTTTG
1 AAAATATTTTT
736 AAAATAT
1 AAAATAT
743 CTTAATTACA
Statistics
Matches: 102, Mismatches: 24, Indels: 28
0.66 0.16 0.18
Matches are distributed among these distances:
11 56 0.55
12 10 0.10
13 27 0.26
14 2 0.02
15 5 0.05
17 2 0.02
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:698 original size:24 final size:22
Alignment explanation
Indices: 671--734 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 22
661 TTTTTGAATT
671 ATTTTAAAAATATTTTTTGTAAA
1 ATTTTAAAAATATTTTTT-TAAA
* **
694 CATTTTCAAAATATTCCTTTAAA
1 -ATTTTAAAAATATTTTTTTAAA
717 ATGTTTTAAAAATATTTT
1 A--TTTTAAAAATATTTT
735 GAAAATATCT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
22 1 0.03
23 4 0.12
24 27 0.84
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (22 bp):
ATTTTAAAAATATTTTTTTAAA
Done.