**.** The

-axis represents the number of base pairs per structure, taken over the ensemble of all secondary structures for the given RNA sequence; the

-axis represents Boltzmann probability

, where

is the partition function for all secondary structures having exactly

base pairs.

*(Left)* For the selenocysteine (SECIS) element AB030643.1/4176-4241 from Rfam family RF00031, the standard deviation

of the number of base pairs, taken over the ensemble of all secondary structures, is

, while the logarithm base 10 of the mean first passage time (logMFPT) is

.

*(Center)* For the selenocysteine (SECIS) element AL645723.11/192421-192359 from Rfam family RF00031, the standard deviation

of the number of base pairs, taken over the ensemble of all secondary structures, is

, while logMFPT is

. Among the 61 sequences in the seed alignment of RF00031, AB030643.1/4176-4241 was the fastest folder, while AL645723.11/192421-192359 was the slowest folder.

*(Right)* Superimposition of output of FFTbor for two TPP riboswitch aptamers: the 97 nt sequence BX842649.1/277414-277318 and the 99 nt sequence AACY022101973.1/389-487, both obtained when taking the empty structure for the initial structure

. The mean

for the FFTbor structural profile near the empty structure is

[resp.

], the standard deviation

for the FFTbor structural profile is

[resp.

], and the Kinfold MFPT is

[resp.

] for the TPP riboswitch aptamer AB030643.1/4176-4241 [resp. AL645723.11/192421-192359]. The right panel of this figure should be compared with . These anecdotal results bear up the correlation between standard deviation

and logMFPT described in .

## PubMed Commons