Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_338 ID=scaffold_338-JGI_221_v2.0
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: 42479
ACGTcount: A:0.06, C:0.03, G:0.04, T:0.06
Warning! 34410 characters in sequence are not A, C, G, or T
Found at i:4175 original size:7 final size:7
Alignment explanation
Indices: 4155--4188 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
4145 CAAAAAAGAG
4155 ATGAAAA
1 ATGAAAA
**
4162 AACAAAA
1 ATGAAAA
4169 ATGAAAA
1 ATGAAAA
4176 ATGAAAA
1 ATGAAAA
4183 ATGAAA
1 ATGAAA
4189 TAGTAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.74, C:0.03, G:0.12, T:0.12
Consensus pattern (7 bp):
ATGAAAA
Found at i:5535 original size:44 final size:44
Alignment explanation
Indices: 5472--5660 Score: 168
Period size: 44 Copynumber: 4.3 Consensus size: 44
5462 ATATTAGATT
* *
5472 TTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGACGGCGAATC
1 TTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCCAATC
* * ** ** *
5516 TTATCTTCCTAAGCAGTAGTGAAGCAGATTTAA-ACCACCAGTC
1 TTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCCAATC
* * * *
5559 CTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATGG-TAGATC
1 TTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCCA-ATC
* * * * * *
5603 TTATCTCCTTAAGCAGTAGTGGAGCAGGTCAAAGATGG-TAGATT
1 TTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCCA-ATC
5647 TTATCTCCCTAAGC
1 TTATCTCCCTAAGC
5661 NNNNNNNNNN
Statistics
Matches: 118, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
43 34 0.29
44 84 0.71
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (44 bp):
TTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCCAATC
Done.