Fig. 4.

Puf2p peak locations are related to the position of highest motif density. (A) Δpoly(N) Puf2p peaks are often near the position of highest UAAU motif density (black line). The position of highest UAAU density is rarely near the position of highest UAAG motif density (red line), indicating that an alternative specificity Puf2p would frequently change binding site location. Negative numbers represent peaks upstream of the predicted peak location. (B) Genome-wide, the position of highest UAAU density is just after the stop codon (black line). The position of highest UAAG density is more often in the CDS (red line). Positive numbers depict positions downstream of the stop codon.