Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3752
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: 30441
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Found at i:4393 original size:15 final size:15
Alignment explanation
Indices: 4373--4427 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
4363 ACTCTCCTCA
*
4373 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
4388 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
4403 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
4417 TTCTTTT-TCTC
1 TTCTTTTCTCTC
4428 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:9432 original size:15 final size:15
Alignment explanation
Indices: 9412--9465 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 15
9402 CTTCTTCTTC
9412 TTTTTTTCACGAAAA
1 TTTTTTTCACGAAAA
**
9427 TTTTTTTTTTCACGAATT
1 ---TTTTTTTCACGAAAA
9445 TTTTTTTCACG-AAA
1 TTTTTTTCACGAAAA
9459 TTTTTTT
1 TTTTTTT
9466 TTCAACTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.25
15 11 0.34
18 13 0.41
ACGTcount: A:0.22, C:0.11, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTTTTCACGAAAA
Found at i:9433 original size:16 final size:16
Alignment explanation
Indices: 9412--9469 Score: 91
Period size: 16 Copynumber: 3.6 Consensus size: 16
9402 CTTCTTCTTC
9412 TTTTTTTCACGAAAATTT
1 TTTTTTTCACG-AAA-TT
9430 TTTTTTTCACG-AATT
1 TTTTTTTCACGAAATT
9445 TTTTTTTCACGAAATT
1 TTTTTTTCACGAAATT
9461 TTTTTTTCA
1 TTTTTTTCA
9470 ACTTGATATC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
15 13 0.33
16 15 0.38
18 11 0.28
ACGTcount: A:0.22, C:0.12, G:0.05, T:0.60
Consensus pattern (16 bp):
TTTTTTTCACGAAATT
Found at i:9466 original size:15 final size:15
Alignment explanation
Indices: 9412--9466 Score: 74
Period size: 15 Copynumber: 3.5 Consensus size: 15
9402 CTTCTTCTTC
9412 TTTTTTTCACGAAAATTT
1 TTTTTTTCACG-AAA--T
*
9430 TTTTTTTCACGAATT
1 TTTTTTTCACGAAAT
9445 TTTTTTTCACGAAAT
1 TTTTTTTCACGAAAT
9460 TTTTTTT
1 TTTTTTT
9467 TCAACTTGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
15 22 0.63
17 2 0.06
18 11 0.31
ACGTcount: A:0.22, C:0.11, G:0.05, T:0.62
Consensus pattern (15 bp):
TTTTTTTCACGAAAT
Found at i:9527 original size:12 final size:12
Alignment explanation
Indices: 9510--9552 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
9500 GAAACCAAAT
9510 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
9522 TTTTTTTTCGAA
1 TTTTTTTTTGAA
*
9534 ATTTTTTTTGAA
1 TTTTTTTTTGAA
9546 TTTTTTT
1 TTTTTTT
9553 CGAGAAACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.74
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:23558 original size:15 final size:15
Alignment explanation
Indices: 23538--23592 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
23528 ACTCTCCTCA
*
23538 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
23553 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
23568 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
23582 TTCTTTT-TCTC
1 TTCTTTTCTCTC
23593 GCTCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Done.