Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1317
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: 19622
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.30
Found at i:4271 original size:14 final size:15
Alignment explanation
Indices: 4244--4280 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
4234 AAATTGTGAC
4244 ATATT-TATCTATTA
1 ATATTATATCTATTA
*
4258 TTATTATATC-ATTA
1 ATATTATATCTATTA
4272 ATATTATAT
1 ATATTATAT
4281 TATAATACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATTATATCTATTA
Found at i:4719 original size:18 final size:20
Alignment explanation
Indices: 4686--4725 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
4676 TGACACATCT
4686 TAAATAATATAAAAGTTTTC
1 TAAATAATATAAAAGTTTTC
4706 TAAA-AATA-AAAAGTTTTC
1 TAAATAATATAAAAGTTTTC
4724 TA
1 TA
4726 TTCTTACACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.60
19 4 0.20
20 4 0.20
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAATAATATAAAAGTTTTC
Found at i:18019 original size:2 final size:2
Alignment explanation
Indices: 18012--18044 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18002 AGCAGTACGT
18012 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
18045 ATCTGAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18256 original size:24 final size:25
Alignment explanation
Indices: 18224--18285 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
18214 CATTTTATTC
* **
18224 AAATATATTTTTAT-ATTTAAAAAA
1 AAATTTATTTTTATAATAAAAAAAA
*
18248 AAATTTATTTAAATATAATAAAAAAAA
1 AAATTTATTT--TTATAATAAAAAAAA
18275 AAATTTATTTT
1 AAATTTATTTT
18286 GATAGAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
24 9 0.30
26 3 0.10
27 18 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATTTATTTTTATAATAAAAAAAA
Found at i:18646 original size:17 final size:18
Alignment explanation
Indices: 18626--18674 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 18
18616 ACTATGATTT
18626 ATTTTATATTAT-TAATA
1 ATTTTATATTATATAATA
*
18643 ATTTTATATATTTCATAATA
1 ATTTTATAT-TAT-ATAATA
18663 ATATTTATATTA
1 AT-TTTATATTA
18675 CATAGTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 9 0.35
18 2 0.08
20 8 0.31
21 7 0.27
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTATATTATATAATA
Found at i:18673 original size:19 final size:20
Alignment explanation
Indices: 18625--18678 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
18615 AACTATGATT
* *
18625 TATTTTATATTA-TTAATAA
1 TATTATATATTACATAATAA
* *
18644 TTTTATATATTTCATAATAA
1 TATTATATATTACATAATAA
18664 TATT-TATATTACATA
1 TATTATATATTACATA
18679 GTTTTAATAC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTATATATTACATAATAA
Found at i:18708 original size:25 final size:23
Alignment explanation
Indices: 18680--18740 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 23
18670 TATTACATAG
*
18680 TTTTAATACATATACGTATTTTTTA
1 TTTTAATACATATAC-T-TCTTTTA
*
18705 TTTTAATATTATATACTTCTTTTA
1 TTTTAATA-CATATACTTCTTTTA
18729 TTTTAATACATA
1 TTTTAATACATA
18741 ATTATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 3 0.09
24 14 0.44
25 9 0.28
26 6 0.19
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTAATACATATACTTCTTTTA
Done.