Initial graph model. (a) Initial graph model representing two annotated sequences sA= GCAGCAU and sB= AGAUUCC. Solid lines represent lines, dashed lines represent interaction edges. Please note that in this toy example minimum loop lengths constraints on the interaction edges are violated for sake of compactness of the illustration. Interactions () and () are in conflict with each other, () and () form a pseudoknot. Sequence sAcontains only nested interactions. (b) A subset of all possible lines is shown representing the alignment (c).