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Fig. 1. Computational search for the X-box motif. (A) Schematic of the X-box search algorithm. The algorithm finds all matches for a defined motif consensus and cross-matches them against a list of predicted genes or available ESTs. The search space upstream of predicted genes was set to 1000 bp. (B) The number of matches obtained with different consensus sequences (top to bottom: relaxed, average, refined) searching the C. elegans genome. (C) The `relaxed' X-box consensus (RYYNYY WW RRNRAC), used for initial searches, generates the largest number of matches that spread equally within promoter regions. (D) The `refined' X-box consensus (GTHNYY AT RRNAAC), obtained on the basis of in vivo expression analysis of xbx genes, shows a significant concentration of matches in the region of around 100 bp upstream of the ATG.





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