1.TFcheckpoint
http://www.tfcheckpoint.org/



2.HOMER Motif Database
http://homer.ucsd.edu/homer/motif/HomerMotifDB/homerResults.html
 
3.JASPAR
JASPAR is one of the most accurate and comprehensive resources for transcription factor binding specificity available.  JASPAR is primarily based on published binding site selection experiments (SELEX), and has recently incorporated data from in vitro microarray based factor affinity experiments.  JASPAR is also well organized.
http://jaspar.genereg.net/