Figure 2

Motif candidate compilation. We employ three different strategies to extract motif candidates from genome sequences. A: Local alignments of 4 species are translated into IUPAC symbols. Only ungapped motifs (in capital letters) are collected with a sliding window approach. B: All subsequences that are covered by local alignments are collected and GEMODA is run on this file. C: FootPrinter is run on upstream regions where the gene start (first exon) is conserved in all four species.