Fig. 2

The variability analysis of aligned sequences and prediction of secondary structure of the N primers and probe annealing sites. After “Positional nucleotide numerical summary calculation” the entropy values were calculated for the entire of the N gene. The entropy plot was obtained by plotting the entropy values against the N gene positions. The variation per position is expressed by the column height. The conserved region as amplicon is shown with red line (a). The primers and probe designed to hybridized with cyclic structure (no stem structure) (b)