Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1345
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: 21945
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:6413 original size:15 final size:14
Alignment explanation
Indices: 6388--6416 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6378 CTAGACCGTA
6388 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
6402 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
6416 T
1 T
6417 CTTTTTTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:6423 original size:21 final size:20
Alignment explanation
Indices: 6393--6435 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
6383 CCGTATGCAA
*
6393 TTTTTTTTTTGCA-ATTTTT
1 TTTTTTTTTTTCAGATTTTT
6412 TTTTTCTTTTTTCAGATTTTT
1 TTTTT-TTTTTTCAGATTTTT
6433 TTT
1 TTT
6436 CAAACTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 7 0.33
21 9 0.43
ACGTcount: A:0.09, C:0.07, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTTTTTTTCAGATTTTT
Found at i:6434 original size:13 final size:13
Alignment explanation
Indices: 6418--6460 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
6408 TTTTTTTTTC
*
6418 TTTTTTCAGA-TT
1 TTTTTTCAAACTT
6430 TTTTTTCAAACTT
1 TTTTTTCAAACTT
*
6443 TTTTTT-TAACTT
1 TTTTTTCAAACTT
6455 TTTTTT
1 TTTTTT
6461 GAAGCTACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 20 0.71
13 8 0.29
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.72
Consensus pattern (13 bp):
TTTTTTCAAACTT
Found at i:12426 original size:29 final size:29
Alignment explanation
Indices: 12393--12452 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
12383 ATAACCAAAC
*
12393 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTTATATCCATAAACCCAT
*
12422 CTACATAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTTATATCCATAAACCCAT
12451 CT
1 CT
12453 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.32
Consensus pattern (29 bp):
CTACAAAAACTTTATATCCATAAACCCAT
Found at i:12445 original size:15 final size:15
Alignment explanation
Indices: 12399--12446 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
12389 AAACCTACAA
12399 AAACTTTATATCCAT
1 AAACTTTATATCCAT
** * *
12414 AAA-TCCATCTACAT
1 AAACTTTATATCCAT
12428 AAACTTTATATCCAT
1 AAACTTTATATCCAT
12443 AAAC
1 AAAC
12447 CCATCTTTGA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (15 bp):
AAACTTTATATCCAT
Found at i:12676 original size:10 final size:9
Alignment explanation
Indices: 12661--12686 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12651 AAGTAAGTTT
12661 AAAAAAATG
1 AAAAAAATG
12670 AAAAAAATG
1 AAAAAAATG
12679 AAAAAAAT
1 AAAAAAAT
12687 TTCAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.12
Consensus pattern (9 bp):
AAAAAAATG
Found at i:13791 original size:30 final size:28
Alignment explanation
Indices: 13755--13810 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
13745 AAACGAAAAA
* *
13755 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
13785 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
13811 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:18486 original size:23 final size:25
Alignment explanation
Indices: 18439--18486 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
18429 CAACTTCTAA
18439 AGAAAACTCAAGAGAGAAATCTTGG
1 AGAAAACTCAAGAGAGAAATCTTGG
*
18464 AGAAAACTCAA-AGA-AAATTTTGG
1 AGAAAACTCAAGAGAGAAATCTTGG
18487 TCTCAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.36
24 3 0.14
25 11 0.50
ACGTcount: A:0.50, C:0.10, G:0.21, T:0.19
Consensus pattern (25 bp):
AGAAAACTCAAGAGAGAAATCTTGG
Found at i:21840 original size:23 final size:20
Alignment explanation
Indices: 21790--21841 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
21780 TCCACGTCTT
*
21790 TTTCTTTTTTCTTTTTCTAA
1 TTTCTTTTCTCTTTTTCTAA
21810 -TTCATTTTCTCTTCTTTCTTCAA
1 TTTC-TTTTCTCTT-TTTC-T-AA
21833 TTTCTTTTC
1 TTTCTTTTC
21842 ACTCTCAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 3 0.12
20 8 0.31
21 4 0.15
22 1 0.04
23 7 0.27
24 3 0.12
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTCTTTTCTCTTTTTCTAA
Done.