Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2896
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: 34716
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:2339 original size:20 final size:21
Alignment explanation
Indices: 2303--2350 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
2293 ATTTTGATAT
*
2303 ACATGATTTGATATGATATGC
1 ACATGATATGATATGATATGC
2324 ACATGATATG-TATGATATGC
1 ACATGATATGATATGATATGC
2344 ACATGAT
1 ACATGAT
2351 GTATTCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (21 bp):
ACATGATATGATATGATATGC
Found at i:8754 original size:20 final size:20
Alignment explanation
Indices: 8729--8766 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
8719 TGTTAAAAAC
8729 ACTTATTTTACTAATATTCT
1 ACTTATTTTACTAATATTCT
8749 ACTTATTTTACTAATATT
1 ACTTATTTTACTAATATT
8767 TATCATAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (20 bp):
ACTTATTTTACTAATATTCT
Found at i:9669 original size:19 final size:20
Alignment explanation
Indices: 9645--9683 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
9635 TCCCATTATT
9645 TATTTATTTTT-TGTTTTAA
1 TATTTATTTTTATGTTTTAA
9664 TATTTATTTTTATGTTTTAA
1 TATTTATTTTTATGTTTTAA
9684 ATGTATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATGTTTTAA
Found at i:9701 original size:25 final size:23
Alignment explanation
Indices: 9645--9709 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 23
9635 TCCCATTATT
*
9645 TATTTATTTTT-TGTTTT-AA--
1 TATTTATTTTTATATTTTAAATG
*
9664 TATTTATTTTTATGTTTTAAATG
1 TATTTATTTTTATATTTTAAATG
9687 TATTTGATTTATTATATTTTAAA
1 TATTT-ATTT-TTATATTTTAAA
9710 GTTTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 11 0.28
20 6 0.15
21 2 0.05
23 5 0.13
24 4 0.10
25 11 0.28
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (23 bp):
TATTTATTTTTATATTTTAAATG
Found at i:10082 original size:7 final size:7
Alignment explanation
Indices: 10039--10066 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
10029 AACTTGCAAT
10039 TAAAAAC
1 TAAAAAC
10046 TAAAAAC
1 TAAAAAC
10053 TAAAAAC
1 TAAAAAC
10060 TAAAAAC
1 TAAAAAC
10067 GAAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (7 bp):
TAAAAAC
Found at i:13121 original size:21 final size:21
Alignment explanation
Indices: 13077--13121 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
13067 TTTGCAAACT
**
13077 TAATTCATTGCTCGTCCCGTG
1 TAATTCATTGCTCGTCCCAAG
13098 TAATTCATTGCTCGTCCCAAG
1 TAATTCATTGCTCGTCCCAAG
13119 TAA
1 TAA
13122 AAAGGCCCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.36
Consensus pattern (21 bp):
TAATTCATTGCTCGTCCCAAG
Found at i:15915 original size:25 final size:24
Alignment explanation
Indices: 15870--15917 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
15860 AAGAAAATGA
*
15870 AGAAAAATGGAAGGGAATGAAGAC
1 AGAAAAATGGAAGAGAATGAAGAC
15894 AGAAAAAT-GAGAGAGAAGTGAAGA
1 AGAAAAATGGA-AGAGAA-TGAAGA
15918 GATGAGAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 13 0.62
25 6 0.29
ACGTcount: A:0.56, C:0.02, G:0.33, T:0.08
Consensus pattern (24 bp):
AGAAAAATGGAAGAGAATGAAGAC
Done.