Although subject to sequence context effects, duplexes containing a single base bulge are predicted to be more stable than those containing single nucleotide mismatches (34, (39) (40) (41) . This is reflected in the lower average hybridization specificity of single base deletion and insertion probes relative to that of substitution probes (Table 1 and Figure 4) . Conversely, duplexes containing two base bulges are predicted to be generally less stable than those containing a single base mismatch (40, 41) . In part, this is due to the assumption that helical stacking is interrupted by bulges of two or greater bases in length while it is preserved for one base bulges (40, 41) . The higher average hybridization specificity ratios of two base (38) was used to predict the intramolecular structures with the lowest Gibbs free energy (DG) for either the 25-30 base stretches that encompass each listed sequence tract in the target or for the PM probes complementary to each sequence tract. We use these DG values to predict the stability of these structures. DG > (À1 kcal/mmol) = weak (W); (À1 kcal/mmol) > DG > (À3 kcal/mmol) = medium (M); and DG < (À3 kcal/mmol) = strong (S). c Type of mismatch probe that provided poor hybridization specificity ratios. d Low hybridization specificity found on both sense and antisense strands. e Immediately following the 3 0 end of this segment is a (T) 5 sequence tract.