Figure 6.

Two examples to the algorithm for prediction of suboptimal structures. The nucleotides are numbered from 1 to N. Sequence parts I and E belong to the ‘included fragment’ with nucleotide indices from i to j and to the ‘excluded fragment’ with j ≤ N < 1 ≤ i, respectively. Doubling of memory space (84) in comparison to that used in (83) permitted the algorithm to find for any given basepair i, j the optimal structures in direction of I and E. (A) If the basepair i, j belongs to a structure with minimum free energy, the optimal structure is found. (B) If the basepair i, j is not part of a structure with minimum free energy, a suboptimal structure is found.