Table 1.

Accessibility Parameters

Region	Pa,DomSub	ssLoop	LFE	SFold	Convolution
250	0.7682	0.8462	1.0	0.6547	0.4256
350 †	0.1950	0.0513	0.0016	0.0397	6.35 × 10−7
485 †	0.133	0.1026	0.4315	0.1167	6.87 × 10−4
780	0.9933	0.2051	0.5436	0.9954	0.1102
1190-1	0.3864	1.0	0.6902	0.4219	0.1125
1190-2	0.2163	0.3077	0.6902	0.0907	0.0042
1410	0.5955	0.3590	0.7050	0.8604	0.1297

Rank Order of Convolution: 250 > 1410 > 1190-1 > 780 > 1190-2 > 485 > 350

P_a,DomSub (MFold frequency of dominant substate) mean values were calculated from the ensembles containing the region of interest. ssLoop was obtained for the maximum single stranded platform of the dominant substate conformation and then normalized to the largest ss loop found in the entire dataset (Site 1190-1, 39 nt). LFE (target break energy) was calculated with a 15 nt window operated over all of the substates in a given ensemble. The value of the area under the peak of LFE around a region of interest was obtained after subtracting a linear regression line fit to the LFE map in that region. These values (positive and negative) were additively scaled so that all entries were positive and then normalized to the maximum value. SFold is the true probability of accessibility taken as an average over the primary sequence bounding the largest region of accessibility in the dominant substate as determined by MFold.

^†Sites 350 and 485: P_a was assigned on the basis of the local Mfold frequency value determined by sstrand output. The largest ssLoop identified in the most dominant substate of 350 was 2 nt and 4 nt for region 485.