Program SPS scores depending on different motif characteristics. Box plots of the SPS scores obtained by the different alignment programs in subset 1, group V11 (<20% identity) under different conditions. The boxplots indicate the extreme observations (stars), lower quartile, median, upper quartile, and largest observation. Significant differences, according to a Wilcoxon signed ranks test (p < 0.05), are indicated by an asterix on the x-axis. P-values for the Wilcoxon tests are available in additional file 1, table 2. a) SPS scores for motifs found in globular domains versus disordered regions. b) SPS scores for motifs with a conserved residue versus variable motifs.