Fig. 1.

Example alignment $\mathcal{A}$ of two RNA sequences A and B together with (non-crossing) structures $S=\{a_1,a_2,a_3,a_4,a_5\}$ and $T=\{b_1,b_2,b_3,b_4,b_5\}$. We highlight the positions in the loop closed by a₁ and in the loop closed by b₂. The base pair a₁ is the parent of the highlighted positions in A and of a₂. The base pair a₁ closes a 2-loop; a₂, a 1-loop and a₃, a multiloop. The latter is a 3-loop, since a₃ has two inner base pairs (a₄ and a₅.) Note that the structure alignment triple $(\mathcal{A},S,T)$ covers the external base pairs $a_1,a_3,b_1$ and $b_2;$ as well as the inner base pairs of the two multiloops. Finally, $(\mathcal{A},S,T)$ deletes the entire 2-loop of a₁ and inserts the entire 2-loop of b₂