The relative specific entropy (SE) function of PCPMer (Bin Zhou et al., in preparation) defines motifs even in alignments where the sequence conservation varies locally. The top of the figure shows a section of the sequence alignment for the NS3 protein. The next section shows the PCPMer output, indicating the motifs in the NS3 protease according to the sequence of DV-2 as a function of the specific entropy level (numbers to the left). PCPMer parameters were: Gap cutoff of 2, length cutoff of 5, relative entropy range between 1 and 2.5 with a step of 0.2. Note the conserved sequences around the active site residues (bold letters) of the protease are followed by variable regions that retain conservation in one of the five physical chemical property vectors. The output is colored to reflect the degree of conservation at each position.