Impact of constrained bases on the difficulty of secondary structure design using RNA-SSD. Correlation between the fraction of bases constrained in a particular structure (x-axis) and the median expected run time for designing the structure with RNA-SSD (y-axis). We report the fraction of constrained bases after propagation for constraints on randomly chosen base positions. This fraction, for both randomly chosen bases and stems, corresponds to the median fraction of bases constrained in a set of 50 constraints that were generated by fixing a given percentage of bases or stems. There are two curves in each graph, one for designing structures with base constraints located in random positions and the other for constraints located in stems. (a) VS ribozyme from Neurospora mitochondria; (b) Group II intron ribozyme D135 from Saccharomyces.