Higher M parameter improves quality of classification when using the z score method. ROC curves comparing effectiveness of the best control generation method for sequence pairs (i.e. columnwise shuffle of a global sequence alignment) at parameters M = 6 (dark blue) and M = 8 (light blue). Test set is same as for Figure 3. For all other control generation methods, increasing the M parameter value likewise increases the quality of classification (see Additional File 1 in "Additional Files" for supporting figure).