Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1440
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: 36275
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:2337 original size:18 final size:17
Alignment explanation
Indices: 2286--2338 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
2276 AAATCGAGAG
*
2286 AAGAAAAACAGAGATG-A
1 AAGAAAAAGAGA-ATGAA
2303 AAGAAAAAGA-AATTGAA
1 AAGAAAAAGAGAA-TGAA
2320 AAGGAAAAAGAGAATGAA
1 AA-GAAAAAGAGAATGAA
2338 A
1 A
2339 GAGATCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 1 0.03
16 3 0.10
17 12 0.39
18 13 0.42
19 2 0.06
ACGTcount: A:0.68, C:0.02, G:0.23, T:0.08
Consensus pattern (17 bp):
AAGAAAAAGAGAATGAA
Found at i:2339 original size:17 final size:17
Alignment explanation
Indices: 2288--2339 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
2278 ATCGAGAGAA
*
2288 GAAAAACAGAGATGAAA-
1 GAAAAAGAGA-ATGAAAG
2305 GAAAAAGA-AATTGAAAAG
1 GAAAAAGAGAA-TG-AAAG
2323 GAAAAAGAGAATGAAAG
1 GAAAAAGAGAATGAAAG
2340 AGATCAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
15 1 0.03
16 3 0.10
17 14 0.47
18 10 0.33
19 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (17 bp):
GAAAAAGAGAATGAAAG
Found at i:2377 original size:16 final size:16
Alignment explanation
Indices: 2339--2387 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
2329 GAGAATGAAA
* *
2339 GAGATCAAAAAGAGATT
1 GAGAGCAAAAA-AGAAT
2356 GAGAGCAAAAAAGAAT
1 GAGAGCAAAAAAGAAT
*
2372 GTGAGCAAGAAAAGAA
1 GAGAGCAA-AAAAGAA
2388 AGCTGAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.57, C:0.06, G:0.27, T:0.10
Consensus pattern (16 bp):
GAGAGCAAAAAAGAAT
Found at i:9238 original size:31 final size:32
Alignment explanation
Indices: 9200--9268 Score: 122
Period size: 33 Copynumber: 2.2 Consensus size: 32
9190 CATTAATTTA
9200 ACATTTAG-ACACACAATTAATTCGGCCAGAC
1 ACATTTAGAACACACAATTAATTCGGCCAGAC
9231 ACATTTAGACACACACAATTAATTCGGCCAGAC
1 ACATTTAGA-ACACACAATTAATTCGGCCAGAC
9264 ACATT
1 ACATT
9269 AAATAGGCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 8 0.22
33 28 0.78
ACGTcount: A:0.39, C:0.26, G:0.12, T:0.23
Consensus pattern (32 bp):
ACATTTAGAACACACAATTAATTCGGCCAGAC
Found at i:11630 original size:14 final size:14
Alignment explanation
Indices: 11611--11637 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11601 TGCATCTTCC
11611 CATGCATGAATCTA
1 CATGCATGAATCTA
11625 CATGCATGAATCT
1 CATGCATGAATCT
11638 GTCCAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:27861 original size:4 final size:4
Alignment explanation
Indices: 27852--27879 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
27842 TATTTTTATT
27852 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
27880 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Done.