Subsequently, you can specify how many structures to include in the output. The algorithm then iterates over all permissible canonical base pairs and computes the minimum free energy and associated secondary structure constrained to contain a specified base pair. These structures are then sorted by their minimum free energy and the most optimal are reported given the specified number of structures. Note that two different sub-optimal structures can have the same minimum free energy. Further information about suboptimal folding can be found in [Zuker, 1989a].