The PatScan pattern searcher is no longer available online.. Have they completely stopped maintaining the software as an online tool?
It used to be available through this address: http://www-unix.mcs.anl.gov/compbio/PatScan/HTML/scanner.html
But all is found at the moment is an installable Unix doppelgänger written in C: http://blog.theseed.org/servers/2010/07/scan-for-matches.html
N.B. I am mainly interested in the web version because my search must encompass the entire GenBank. Furthermore, I currently do not have the required computing resources to run a search using the offline version of the software.
DISCLAIMER: None of the answers here and none of the currently available motif search tools (be it web-based or command line-based) were of any use for my project. I was mainly interested in web-based tools for their efficiency as I had no access to good computing resources. Therefore I ended up buying an AWS Amazon account and scripted everything from scratch and wrote my own motif search programme jointly in R and command line. As a side note, if you are looking for conventional motifs RNABOB and RNAMOT should do just fine, but what I was looking was a very complex motif present on several RNA molecules and thus PatScan, RNABOB, RNAMOT, etc. were incapable of incorporating such requirements.