Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1234
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: 2310
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.16
Warning! 1258 characters in sequence are not A, C, G, or T
Found at i:302 original size:108 final size:110
Alignment explanation
Indices: 94--311 Score: 395
Period size: 108 Copynumber: 2.0 Consensus size: 110
84 ATCACTTTCG
94 GCTTCATTCGGATCATATAGGTCGTCTTGATTGATTTCCAATTGGTCTCGCCTTCTTTGCGTGAT
1 GCTTCATTCGGATCATATAGGTCGTCTTGATTGATTTCCAATTGGTCTCGCCTTCTTTGCGTGAT
***
159 GTGCACACGCTCACACCAACAAAGCAAACTGATCCGGAGGTCTTA
66 GTGCACACGCTCACACCAACAAAGCAAAAACATCCGGAGGTCTTA
204 GCTTCATTC-G-TCATATAGGTCGTCTTGATTGATTTCCAATTGGTCTCGCCTTCTTTGCGTGAT
1 GCTTCATTCGGATCATATAGGTCGTCTTGATTGATTTCCAATTGGTCTCGCCTTCTTTGCGTGAT
267 GTGCACACGCTCACACCAACAAAGCAAAAACATCCGGAGGTCTTA
66 GTGCACACGCTCACACCAACAAAGCAAAAACATCCGGAGGTCTTA
312 CCATTAGGAC
Statistics
Matches: 105, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
108 95 0.90
109 1 0.01
110 9 0.09
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (110 bp):
GCTTCATTCGGATCATATAGGTCGTCTTGATTGATTTCCAATTGGTCTCGCCTTCTTTGCGTGAT
GTGCACACGCTCACACCAACAAAGCAAAAACATCCGGAGGTCTTA
Found at i:2204 original size:52 final size:52
Alignment explanation
Indices: 2121--2221 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
2111 TAAGGAAACG
* * *
2121 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAACTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
*
2173 TAATAGACAGCAACTTAAGACCTCTTTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAACTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
2222 TATGTGCATG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (52 bp):
TAATAGACAGCAACTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Done.