Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold8552.1
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: 5032
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Found at i:309 original size:75 final size:75
Alignment explanation
Indices: 186--334 Score: 280
Period size: 75 Copynumber: 2.0 Consensus size: 75
176 AAACTTCGCA
186 TCTCGGTCGGACACAATCGTCCTAGGCATGCCATGCAACCTGACCACTTCTTTGAAAAATAAATT
1 TCTCGGTCGGACACAATCGTCCTAGGCATGCCATGCAACCTGACCACTTCTTTGAAAAATAAATT
251 AGCAATATTG
66 AGCAATATTG
* *
261 TCTCGGTCGGACACAATTGTCCTAGGCATGCCATGCAACTTGACCACTTCTTTGAAAAATAAATT
1 TCTCGGTCGGACACAATCGTCCTAGGCATGCCATGCAACCTGACCACTTCTTTGAAAAATAAATT
326 AGCAATATT
66 AGCAATATT
335 CACGGCATCA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (75 bp):
TCTCGGTCGGACACAATCGTCCTAGGCATGCCATGCAACCTGACCACTTCTTTGAAAAATAAATT
AGCAATATTG
Found at i:2393 original size:24 final size:25
Alignment explanation
Indices: 2340--2393 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
2330 AACAAATTCT
* *
2340 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
2365 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
2388 TTTTTT
1 TTTTTT
2394 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Done.