Unrooted and unordered RNA similarities. Nodes of the RNA trees are clustered to motifs marked by letters or numbers (stems, loops, and unpaired nucleotide intervals), where aligned motifs share the same annotation, and unaligned nodes are in gray. Nomenclature is according to . (a) An unrooted alignment between Hammerhead RNAs: PDB_00693 (Type I, top) and RFA_00388 (Type III, bottom), with a computed and corrected, p-value of 2.1250 × 10-7. Arrows mark the roots chosen by our tool. The unrooted mode of FRUUT identifies the high similarity between the molecules, not being restricted to align external loops to each other. (b) An unordered alignment between RNAse P RNAs: ASE_00047 (left) and ASE_00334 (right), with a computed, and corrected, p-value of 1.190 × 10-4. In the unordered mode of FRUUT, the aligned motifs marked by 6 and 8 do not preserve order. In both molecules, pseudoknots occur between intervals annotated by 8 and 2, and between intervals annotated by 13 and 15 (see Figure 12), asserting the validity of the alignment.