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This is a web server that enables the analysis of multiple DNA sequences using sets of Position Weight Matrices from the JASPAR and TRANSFAC databases, using multiple scanning algorithms. (The use of the TRANSFAC matrices for analyses is free for users from non-profit organizations only. Commercial users have to license the TRANSFAC database [Disclaimer].)

Help on using this server can be found by clicking on the linked features within the page and using the FAQ.

Species Matrices
Upload sequence(s) in Fasta format

Limits: 50 sequences or 50K bps.
Clover max. individual sequence length 5K bps.

Stringent MotifLocator Scans 0.1% 0.05% 0.01%
Multi Algorithm Scans
Clover 

P-value Threshold 
Score Threshold 
Pseudocount 
MotifLocator 

Motif Threshold 
 
MotifScanner 

Prior Probability 
 

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