The base-interaction patterns (left panel) and 3D structures (right panel) of (A) a true sarcin–ricin motif instance and (B) an unrelated motif instance. RNAMotifScan ranks A below B and does not identify A in its top list. However, RNAMotifScanX is capable of identifying A and ranking it in the very top of its prediction list by aligning one additional base-stacking interaction (highlighted using cyan box in left panel). The right panel shows that lack of such stacking interaction in the second instance leads to significant changes in the dihedral angle between the corresponding nucleotides (U1972, A1973 in A and A1778, A1779 in B). Such change further leads to different orientations of the bulged guanine residues (magenta).
