Partial representation (most proximal region) of the aligned 1 kb upstream regions of the S. cerevisiae STE12 gene and its orthologs. (a) The highest scoring 7-mers found by FastCompare in a comparison between S. cerevisiae and S. bayanus are highlighted. FastCompare correctly predicts the conserved and experimentally verified binding sites for Mcm1, Matalpha2 and Ste12 (proximal) (see  for review). A more distal non-verified binding site for Ste12, and a RRPE site close to the distal Matalpha2 are conserved between the four species, and also predicted by FastCompare. FastCompare predicts several nonconserved sites in each species. For example, in S. cerevisiae, it identifies a Rox1-binding site overlapping with the second Ste12 site, and a putative Upc2-binding site. (b) Aligned 1 kb upstream region of the S. cerevisiae STE2 gene and its S. paradoxus ortholog only, with the same highlighted 7-mers as in (a). Since the two yeast species diverged very recently, the two upstream regions appear highly conserved. However, using the FastCompare output allows efficient selection of verified and putative binding sites. CER, S. cerevisiae; Bay, S. bayanus; Par, S. paradoxus; Mik, S. mikatae.