Figure 3.
Example of separation of conserved blocks from the background. The alignment for the promoter of ORF YCL030 (HIS4), where * indicates a base conserved across all four species. The gray highlights mark the high conservation regions identified by the hidden Markov model. Low conservation regions are comprised of the remaining sites with sequence data in all four species. Gapped regions (dashes and lowercase letters) were classified separately. Known transcription-factor-binding sites from SCPD (Zhu and Zhang 1999) are labeled.
