Sequence and structure motifs for five CLIP-seq sets showing significant improvement of GraphProt structure over sequence models. In the visualized logos, the character size determines its importance and structure elements are labeled as follows: stems (S), external regions (E), hairpins (H), internal loops (I), multiloops (M) and bulges (B). All motifs show preferences to both stems and unpaired regions simultaneously. Sequence and structure motifs for Ago1-4 and ZC3H7B are very similar. This can be attributed to the large overlap between ZC3H7B and Ago1-4 PAR-CLIP sites (5,752 of the 28,238 ZC3H7B sites overlap AGO1-4 sites). CLIP, cross-linking and immunoprecipitation; PAR-CLIP, photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation.