Transcription factor binding sites: several sites are available but I have not been particular impressed with the results when analyzing prokaryotic sequences

Tfsitescan (Institute for Transcriptional Informatics, Pittsburgh, U.S.A.)

PLACE (National Institute of Agrobiological Sciences, Japan) - Plant cis-acting regulatory DNA elements 

TRANSFAC (Gesellschaft für Biotechnologische Forschung mbH (GBF), Braunschweig, Germany) - The Transcription Factor Database.

rVista 2.0 (Comparative Genomics Center, Lawrence Livermore National Laboratory, U.S.A.) - High-throughput discovery of functional regulatory elements in sequence alignments. Excluding up to 95% false positive transcription factor binding sites predictions while maintaining high sensitivity of the search.

 TESS (Transcription Element Search System) is a web tool for predicting transcription factor binding sites in DNA sequences. It can identify binding sites using site or consensus strings and positional weight matrices from the TRANSFAC, JASPAR, IMD, and our CBIL-GibbsMat database.  This resource is best for scanning short DNA sequences.