- Conserved Matches, precalculated: There are some websites where you can see Precalculated alignments and Matrix hits. I don't like them too much and they are not applicable for my model organism.
- corg shows alignments of upstream regions of many model species and can display conserved binding sites. Unfortunately, I have only seen pairwise alignments. Look at UCSC for multiple alignments with an easy to use interface.
- [Consite] Any 2 sequences and hits on Transfac
- famous [UCSC] Genome Browser has a TFBS-track for the human genome, where all hits against Transfac Pro 8.3 are documented and can be downloaded as GFF (hint: What can you do with many hits?)
- Conserved Matches, configurable:
- synor searches a pair of human/chicken/mouse/frog for a combination of conserved binding sites
- oPOSSUM Looks better than the other conserved genomic searchers as you can configure the parameters. Only human/mouse? (Thanks to Malcolm Cook!)
- TFBSCluster Searches human-mouse for matches to a subset of matrices from Transfac4 or your IUPAC-strings.