Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4907
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: 12950
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Found at i:2437 original size:17 final size:18
Alignment explanation
Indices: 2401--2439 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2391 TCTTTTTGAA
* *
2401 TTTCTTTTTTTTTTTCAT
1 TTTCTTTTCTTTTGTCAT
2419 TTTCTTTTCTTTTGT-AT
1 TTTCTTTTCTTTTGTCAT
2436 TTTC
1 TTTC
2440 GCTCTTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.05, C:0.13, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTCTTTTCTTTTGTCAT
Found at i:4653 original size:17 final size:17
Alignment explanation
Indices: 4620--4653 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4610 AGACTGTATG
**
4620 CAATTTTTTTTTCTTTT
1 CAATTTTTTTTGATTTT
4637 CAATTTTTTTTGATTTT
1 CAATTTTTTTTGATTTT
4654 TTTTTCGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.09, G:0.03, T:0.74
Consensus pattern (17 bp):
CAATTTTTTTTGATTTT
Found at i:4665 original size:19 final size:18
Alignment explanation
Indices: 4644--4679 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4634 TTTCAATTTT
*
4644 TTTTGATTTTTTTTTCGA
1 TTTTAATTTTTTTTTCGA
4662 TTTTAATTTTTTTTTCGA
1 TTTTAATTTTTTTTTCGA
4680 ACTCCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (18 bp):
TTTTAATTTTTTTTTCGA
Found at i:4669 original size:28 final size:27
Alignment explanation
Indices: 4622--4675 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
4612 ACTGTATGCA
4622 ATTTTTTTTTCTTTTCAATTTTTTTTG
1 ATTTTTTTTTCTTTTCAATTTTTTTTG
4649 ATTTTTTTTTCGATTTT-AATTTTTTTT
1 ATTTTTTTTTC--TTTTCAATTTTTTTT
4676 TCGAACTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 11 0.44
28 10 0.40
29 4 0.16
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.78
Consensus pattern (27 bp):
ATTTTTTTTTCTTTTCAATTTTTTTTG
Found at i:5014 original size:21 final size:21
Alignment explanation
Indices: 4988--5031 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
4978 TTGGTATTTG
4988 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
5009 GGAATTTGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
5030 GG
1 GG
5032 TATGGTCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.02, G:0.34, T:0.32
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:6126 original size:10 final size:10
Alignment explanation
Indices: 6111--6152 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
6101 TTTGCAAGTT
6111 TTGAGCTAAA
1 TTGAGCTAAA
* *
6121 TTGAGCTGAT
1 TTGAGCTAAA
*
6131 TTGAGCT-CA
1 TTGAGCTAAA
6140 TTGAGCTAAA
1 TTGAGCTAAA
6150 TTG
1 TTG
6153 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Done.