## Average values for the run time and the entropy values for 100 random RNA sequences of length *n*, each having expected compositional frequency of 0:25 for A,C,G,U, where *n* ranges from 20 to 500 with increments of 5 for conformational entropy.

*(A)* Average run times as a function of sequence length, where error bars represent ±1 standard deviation. Methods used: DP, FTD, FTD*, ViennaRNA, ViennaRNA*. For random RNAs of length 500 nt, Vienna RNA Package is about three times faster than our code. *(B)* Standard deviation of the entropy values computed for 100 random RNA, displayed as a function of sequence length. From top to bottom, the first three curves represent uncentered ViennaRNA with Δ*T* = 10^{−4}, centered ViennaRNA* with Δ*T* = 10^{−4}, and DP. The bottom curve represents centered FTD with Δ*T* = 10^{−4}, centered FTD* with Δ*T* = 10^{−2}, uncentered ViennaRNA with Δ*T* = 10^{−2}, centered ViennaRNA* with Δ*T* = 10^{−2}. The average entropy values computed by FTD, FTD*, ViennaRNA, and ViennaRNA* are indistinguishable and since FTD values are shown in the right panel of Fig 1, they are not shown here.