Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1217
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: 22377
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:5481 original size:12 final size:12
Alignment explanation
Indices: 5460--5506 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
5450 ATAGTAGTTT
5460 CTCG-AAAAAAA
1 CTCGAAAAAAAA
5471 CTCGAAAAAAAA
1 CTCGAAAAAAAA
* *
5483 TTCAAAAAAAAA
1 CTCGAAAAAAAA
*
5495 TTCGAAAAAAAA
1 CTCGAAAAAAAA
5507 ACTAGTTTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
11 4 0.12
12 28 0.88
ACGTcount: A:0.68, C:0.13, G:0.06, T:0.13
Consensus pattern (12 bp):
CTCGAAAAAAAA
Found at i:5567 original size:14 final size:14
Alignment explanation
Indices: 5548--5597 Score: 70
Period size: 13 Copynumber: 3.8 Consensus size: 14
5538 TATCAAGTTG
5548 TGAAAAAAAAATTT
1 TGAAAAAAAAATTT
*
5562 TG-AAAAAAAATTG
1 TGAAAAAAAAATTT
5575 TGAAAAAAAAA--T
1 TGAAAAAAAAATTT
5587 TGAAAAAAAAA
1 TGAAAAAAAAA
5598 GAGAGCTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 11 0.33
13 12 0.36
14 10 0.30
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (14 bp):
TGAAAAAAAAATTT
Found at i:5569 original size:12 final size:12
Alignment explanation
Indices: 5552--5595 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
5542 AAGTTGTGAA
5552 AAAAAAATTTTG
1 AAAAAAATTTTG
*
5564 AAAAAAAATTGTG
1 -AAAAAAATTTTG
**
5577 AAAAAAAAATTG
1 AAAAAAATTTTG
5589 AAAAAAA
1 AAAAAAA
5596 AAGAGAGCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (12 bp):
AAAAAAATTTTG
Found at i:5575 original size:27 final size:25
Alignment explanation
Indices: 5545--5596 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 25
5535 GGATATCAAG
5545 TTGTGAAAAAAAAATTTTGAAAAAAAA
1 TTGTGAAAAAAAAA--TTGAAAAAAAA
5572 TTGTGAAAAAAAAATTGAAAAAAAA
1 TTGTGAAAAAAAAATTGAAAAAAAA
5597 AGAGAGCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 11 0.44
27 14 0.56
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (25 bp):
TTGTGAAAAAAAAATTGAAAAAAAA
Found at i:13046 original size:19 final size:18
Alignment explanation
Indices: 13010--13049 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
13000 TTTCCACTCG
*
13010 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
13028 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
13047 TTT
1 TTT
13050 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:20649 original size:20 final size:20
Alignment explanation
Indices: 20626--20668 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
20616 CAAATCTTGG
20626 AAATCTTG-GTCCAAAAACGC
1 AAATCTTGAG-CCAAAAACGC
20646 AAATCTTGCAGCCAAAAACGC
1 AAATCTTG-AGCCAAAAACGC
20667 AA
1 AA
20669 TGGATCTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.38
21 12 0.57
22 1 0.05
ACGTcount: A:0.44, C:0.26, G:0.14, T:0.16
Consensus pattern (20 bp):
AAATCTTGAGCCAAAAACGC
Done.