Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold689
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: 23831
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2442 original size:10 final size:10
Alignment explanation
Indices: 2404--2464 Score: 52
Period size: 10 Copynumber: 5.7 Consensus size: 10
2394 CAGATCATTT
2404 ATATTTAATAA
1 ATATTTAA-AA
2415 ATATTTAAATGTAA
1 ATATTT-AA---AA
*
2429 ATATATAAAA
1 ATATTTAAAA
*
2439 ATATTTTAAA
1 ATATTTAAAA
2449 AT-TTTAAAA
1 ATATTTAAAA
2458 ATATTTA
1 ATATTTA
2465 TATAAGATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
9 8 0.19
10 16 0.38
11 6 0.14
12 2 0.05
13 2 0.05
14 8 0.19
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (10 bp):
ATATTTAAAA
Found at i:4336 original size:11 final size:11
Alignment explanation
Indices: 4322--4358 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4312 TTATGAAATA
4322 TTTATATTATT
1 TTTATATTATT
4333 TTTATATTATAT
1 TTTATATTAT-T
4345 TTTA-ATT-TT
1 TTTATATTATT
4354 TTTAT
1 TTTAT
4359 TATATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 5 0.21
10 1 0.04
11 13 0.54
12 5 0.21
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTATATTATT
Found at i:5789 original size:21 final size:22
Alignment explanation
Indices: 5760--5804 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
5750 TTAAGATATT
*
5760 ATTTAATTTAT-TGATAATATAA
1 ATTTAATTTATAT-AAAATATAA
5782 ATTT-ATTTATATAAAATATAA
1 ATTTAATTTATATAAAATATAA
5803 AT
1 AT
5805 AATTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTTAATTTATATAAAATATAA
Found at i:10477 original size:12 final size:13
Alignment explanation
Indices: 10456--10484 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
10446 TAAAATTTAA
10456 TTAATCAAAAAAT
1 TTAATCAAAAAAT
10469 TTAAT-AAAAAAT
1 TTAATCAAAAAAT
10481 TTAA
1 TTAA
10485 CTGTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (13 bp):
TTAATCAAAAAAT
Found at i:11296 original size:15 final size:16
Alignment explanation
Indices: 11266--11303 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
11256 TCAAAAATAT
11266 ATATTTTAAAATTTTA
1 ATATTTTAAAATTTTA
11282 AT-TTTTAATAA-TTTA
1 ATATTTTAA-AATTTTA
11297 ATATTTT
1 ATATTTT
11304 CTTTTACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTTTAAAATTTTA
Found at i:11580 original size:19 final size:18
Alignment explanation
Indices: 11556--11593 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
11546 TATTCAAATT
*
11556 TTTTTATATATTAAATAAA
1 TTTTTAAAT-TTAAATAAA
11575 TTTTTAAATTTAAATAAA
1 TTTTTAAATTTAAATAAA
11593 T
1 T
11594 AACTCGACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTTAAATTTAAATAAA
Found at i:19954 original size:6 final size:6
Alignment explanation
Indices: 19945--19978 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
19935 ATACAAGTAC
19945 ATACAT ATACAT ATACAT ATACAT ATACAT ATAC
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATAC
19979 TCCATGGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (6 bp):
ATACAT
Found at i:23504 original size:14 final size:15
Alignment explanation
Indices: 23465--23504 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
23455 ATTTTAAAAA
23465 TAAAATAATAATATT
1 TAAAATAATAATATT
*
23480 TTAAATAAATAAT-TT
1 TAAAAT-AATAATATT
23495 TAAAATAATA
1 TAAAATAATA
23505 TTTGATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 4 0.18
15 12 0.55
16 6 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAAATAATAATATT
Found at i:23594 original size:2 final size:2
Alignment explanation
Indices: 23587--23633 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
23577 GTGATTTCGG
*
23587 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GC GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
23629 GA GA G
1 GA GA G
23634 TCGTAAAACA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.02, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.