image University of W
ashington Department of Computer Science & Engineering


News: CMfinder software download is available now.

You need help adjusting the parameters of CMfinder? Please read the manual. Questions?send mail
You can run CMfinder using 2 sets of parameters at one time
First configuration:
Number of stem-loops
Number of motifs <10
Minimum length of motif >15
Maximum length of motif <150
Number of Candidates <100
Second configuration:
Number of stem-loops
Number of motifs < 10
Minimum length of motif > 15
Maximum length of motif < 150
Number of Candidates < 100


Paste Sequences (*) in FastA Format
Please limit your dataset to
4~60 sequences with length < 500bp

Or Upload a FastA file (*):

Post process options: Remove Redundant motifs

Output compression Options: zip archive gzipped tar ball

Your email address where results will be sent to

Press to submit information, or to default parameters.