Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2804
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, 507
Length: 846
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Found at i:279 original size:15 final size:16
Alignment explanation
Indices: 261--293 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
251 CGAAGGGAAG
*
261 AAGGAAGAAGA-AGGA
1 AAGGAAAAAGAGAGGA
276 AAGGAAAAAGAGAGGA
1 AAGGAAAAAGAGAGGA
292 AA
1 AA
294 AAAGGAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
AAGGAAAAAGAGAGGA
Found at i:299 original size:24 final size:24
Alignment explanation
Indices: 258--332 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
248 GGTCGAAGGG
258 AAGAAGGAAGAAGAAGGAAAGGAAA
1 AAGAAGGAAGAA-AAGGAAAGGAAA
283 AAGAGAGGAA-AAAAGGAAA-GAAGA
1 AAGA-AGGAAGAAAAGGAAAGGAA-A
* * *
307 AAGAAAGAAGAAAGGGAAAGAAAA
1 AAGAAGGAAGAAAAGGAAAGGAAA
331 AA
1 AA
333 AATAAAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
23 7 0.16
24 23 0.53
25 8 0.19
26 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (24 bp):
AAGAAGGAAGAAAAGGAAAGGAAA
Found at i:312 original size:11 final size:11
Alignment explanation
Indices: 265--320 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
255 GGGAAGAAGG
*
265 AAGAAGAAGGA
1 AAGAAGAAAGA
276 AAGGAA-AAAGA
1 AA-GAAGAAAGA
* *
287 GAGGAAAAAAGGA
1 -AAGAAGAAA-GA
300 AAGAAGAAAGA
1 AAGAAGAAAGA
311 AAGAAGAAAG
1 AAGAAGAAAG
321 GGAAAGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 21 0.57
12 14 0.38
13 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (11 bp):
AAGAAGAAAGA
Found at i:646 original size:11 final size:11
Alignment explanation
Indices: 626--704 Score: 67
Period size: 11 Copynumber: 7.0 Consensus size: 11
616 CAGCAGAGAG
626 GAAAAAAGAAA
1 GAAAAAAGAAA
637 -AAAGAAAGAAA
1 GAAA-AAAGAAA
*
648 GAAGAAAAAAAA
1 GAA-AAAAGAAA
660 GAGAAAAA-AACA
1 GA-AAAAAGAA-A
672 GAAGAAAA-AAA
1 GAA-AAAAGAAA
683 GAAAAAAGAAA
1 GAAAAAAGAAA
694 -AAAACAAGAAA
1 GAAAA-AAGAAA
705 AAAGGGGTTC
Statistics
Matches: 59, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
10 11 0.19
11 23 0.39
12 23 0.39
13 2 0.03
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:684 original size:39 final size:38
Alignment explanation
Indices: 627--707 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 38
617 AGCAGAGAGG
*
627 AAAAAAGAAAAAAGAAAGAAAGAAGAAAAAAA-AGAGAA
1 AAAAAAGAAAAAAGAAAGAAAAAAGAAAAAAACA-AGAA
665 AAAAACAGAAGAAAA-AAAGAAAAAAGAAAAAAACAAGAA
1 AAAAA-AGAA-AAAAGAAAGAAAAAAGAAAAAAACAAGAA
704 AAAA
1 AAAA
708 GGGGTTCAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
38 5 0.13
39 29 0.74
40 5 0.13
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (38 bp):
AAAAAAGAAAAAAGAAAGAAAAAAGAAAAAAACAAGAA
Found at i:705 original size:8 final size:7
Alignment explanation
Indices: 626--696 Score: 74
Period size: 7 Copynumber: 10.0 Consensus size: 7
616 CAGCAGAGAG
626 GAAAAAA
1 GAAAAAA
633 GAAAAAA
1 GAAAAAA
640 GAAAGAAA
1 GAAA-AAA
648 GAAGAAAA
1 GAA-AAAA
*
656 -AAAAGA
1 GAAAAAA
662 GAAAAAA
1 GAAAAAA
* *
669 -ACAGAA
1 GAAAAAA
675 GAAAAAAA
1 G-AAAAAA
683 GAAAAAA
1 GAAAAAA
690 GAAAAAA
1 GAAAAAA
697 ACAAGAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
6 7 0.13
7 31 0.58
8 14 0.26
9 1 0.02
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:705 original size:11 final size:10
Alignment explanation
Indices: 634--707 Score: 73
Period size: 11 Copynumber: 7.3 Consensus size: 10
624 AGGAAAAAAG
634 AAAAAAGAAA
1 AAAAAAGAAA
*
644 GAAAGAAGAAA
1 -AAAAAAGAAA
655 AAAAAGAGAAA
1 AAAAA-AGAAA
*
666 AAAACAGAAGA
1 AAAAAAGAA-A
677 AAAAAAG---
1 AAAAAAGAAA
684 AAAAAAGAAA
1 AAAAAAGAAA
694 AAAACAAGAAA
1 AAAA-AAGAAA
705 AAA
1 AAA
708 GGGGTTCAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
7 7 0.13
10 12 0.23
11 34 0.64
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Done.