Figure 1.

Output of RNAboron the 27 nt bistable switch with nucleotide sequence CUUAUGAGGG UACUCAUAAG AGUAUCC and initial structure S₀, the minimum free energy (MFE) structure....... ((((((((....)))))))) with free energy -10.3 kcal/mol. The 16-neighbor of S₀ is the metastable structure ((((((((....))))))))....... with free energy -9.9 kcal/mol. The MFE structure appears above the leftmost peak, while the MFE(16) structure appears above the rightmost peak. The output of RNAbor includes a graph of the Boltzmann probabilities $p_k=\frac{Z_k}{Z}$, and MFE(k) structures, for all 0 ≤ k ≤ 2n. The existence of distinct 'peaks' suggests the presence of a conformational switch.