RSA tools:
http://www.ucmb.ulb.ac.be/bioinformatics/rsa-tools/

TRANSFAC:
http://transfac.gbf.de/TRANSFAC/

MatInspector:
http://transfac.gbf.de/cgi-bin/matSearch/matsearch.pl

Available matrices (TRANSFAC):
http://transfac.gbf.de/programs/matinspector/matrix_list.html

PROMO:
http://www.lsi.upc.es/~alggen/recerca/promo/intro-promo.html

AlignACE (Gibbs sampling):
http://atlas.med.harvard.edu/

AlignACE Server:
http://atlas.med.harvard.edu/cgi-bin/alignace.pl

CompareACE Server:
http://atlas.med.harvard.edu/cgi-bin/compareace.pl

Sequence logos:
http://www-lmmb.ncifcrf.gov/~toms/sequencelogo.html

makelogo program:
http://www.lecb.ncifcrf.gov/~toms/delila/makelogo.html

weblogo server:
http://www.bio.cam.ac.uk/cgi-bin/seqlogo/logo.cgi

Saccaromyces Cerevisiae Promoter Database (SCPD):
http://cgsigma.cshl.org/jian/

Transcription Regulatory Regions Database (TRRD):
http://www.bionet.nsc.ru/trrd/

Object oriented Transcription Factors Database (ooTFD):
http://www.ifti.org/