Fig 3. A snapshot of the output of the VfoldCPX server. Based on the total length of the input effective one-RNA system, the server provides up to three sets of predicted structures, corresponding to the three structural ensembles shown in Fig 2(B).

In this example, the predicted most probable 2D structure (plotted using VARNA [35]) has the free energy of -50.24 kcal/mol. The predicted base pairing distributions shown by the density plot and the alternative stable structures provide important information about the structures and stabilities.