Model development and curve-fitting^a.

a<p>Concluding (optimal) models are indicated in bold and their details are presented in other tables and figures.</p>b<p>SM, single (non-bulge) mismatch; BM, bulge mismatch; TM, tandem mismatch; sln, for in solution hybridization; ma, for microarray hybridization.</p>c<p>Parameters in italics are used in best-fitting. The use of additional parameters <i>α</i> and <i>β</i>, when applicable, is shown in the free energy column under model description (see text for best-fitting values). Other parameters derived using M3, M5, and M9 are the free energy rules in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043862#pone.0043862.s005" target="_blank">Tables S1A, S1B</a>, and S1D, with 10, 104, and 8 additions, respectively.</p>d<p>N_F, number of probes used in fitting; N_T, total number of probes; <i>ε</i>²_val and <i>ε</i>²_ov, average squares of prediction errors in validation set (i.e., not used in fitting) and overall set, respectively. See Materials and Methods for other parameters.</p>e<p>Absolute value of the deviation of predicted half-denaturation point (% formamide) from the apparent experimental value, as described by its average/standard deviation (<i>µ/σ</i>) and percentage of values below 5% formamide.</p>f<p>ΔG° for perfect matches and ΔΔG° for mismatches (see Materials and Methods).