dcode website, home site for a suite of tools for comparative sequence alignments and regulatory element discovery:
http://www.dcode.org/
zpicture, BlastZ alignments and interactive analysis of conserved sequence blocks in user-supplied sequences up to 1 Mb:
http://zpicture.dcode.org/
ECR browser, precomputed alignments of vertebrate sequenced genomes with interactive conserved sequence analysis and links to conserved binding site data:
http://ecrbrowser.dcode.org/
Transfac and Jaspar, two websites with information regarding transcription factors and their binding sites :
http://jaspar.genereg.net/
http://www.gene-regulation.com/pub/databases.html
Meme, sequence analysis tool that predicts over-represented sequence motifs in DNA sequences:
http://meme.sdsc.edu/meme4_5_0/intro.html
(The Meme suite also contains direct links to other useful tools)
Patser, program to find specified motifs or strings in user supplied sequence (also available as a web program through RSAT):
http://rsat.ulb.ac.be/rsat/patser_form.cgi
RSAT, a set of programs for the analysis of functional non-coding elements, e.g. retrieval of upstream sequences, pattern matching, motif discovery*:
http://rsat.ulb.ac.be/rsat/
the Mexican mirror: http://embnet.ccg.unam.mx/rsa-tools/
*publications describing these tools are included in the package. Other references are listed on/provided by the various websites.