Additional statistical tests^a,b.

a<p>See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043862#pone-0043862-t002" target="_blank">Table 2</a> for the definition of models and parameters and the reference values. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043862#pone.0043862.s007" target="_blank">Text S1</a> for the details of the statistical tests.</p>b<p>Randomization and permutation tests are based on at least 100 runs until convergence. Significant figures in these results reflect the uncertainty in the converged values.</p>c<p>Probes were permuted while maintaining the original sequence of each probe. This test corresponds to permuting the probe length in addition to the nearest neighbor free energies.</p>d<p>Show improvement over original models although statistical parameters indicate otherwise. The discrepancy reflects the fact that half-denaturation point is not a perfect representation of the melting point for experimental profiles without a plateau (e.g., see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043862#pone.0043862.s003" target="_blank">Figure S3C</a>). This adversely affects the results with <i>γ</i>-factors more than without, as the models without <i>γ</i>-factors tend to compensate for the lack of good fitting in the vertical by moving closer to experimental values in the horizontal, although this movement does not mean a better match. Since the original models in the main text always use <i>γ</i>-factors, the evaluation of model predictions are conservative and more accurate with respect to half-denaturation points. This analysis provides just another way of seeing how <i>γ</i>-factors buffer experimental artifacts as discussed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043862#pone.0043862.s007" target="_blank">Text S1</a>.</p>e<p>Best-fitted <i>γ</i> replaced by a model-derived factor (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043862#pone.0043862.s007" target="_blank">Text S1</a>).