Figure 1.

Loops with cuts have to be scored differently. Top row: hairpins and interior loops containing the cut between n1 (black ball) and n1 + 1 (white ball). Below: multi loops containing the cut. Neither M1 nor M components must start at n1 + 1 or stop at n1. Note that the construction of ZM out of ZM and ZM1 ensures that the cut is not inside the loop part of ZM either.

Bernhart et al. Algorithms for Molecular Biology 2006 1:3   doi:10.1186/1748-7188-1-3
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