bioinformatics - TFBS predictions for yeast and pombe?

This question is quite old, but I think it might be useful to mention this:

You can also look at RSAT (Regulatory Sequence Analysis Tools):

go in the Fungi portail, in "motif discovery" choose "oligo-analysis"; there you can predict putative TFBS from upstream sequences for example. It detects repeated motifs. To be more specific of Saccharomyces cerevisiae or S. pombe, select these species in the "Background model" section.