Phylogenetic profiles of HCV sequences. Results from SimPlot analysis are shown. The query sequence (AY378694) is indicated on the upper part of the figure. Sequences to be compared with the query sequence are indicated on the right side of the figure. When comparisons were done, SimPlot generates a similarity plot using the Kimura-two parameter distance model in a sliding window of 200 nucleotides, moving 20 nucleotides between plots. The y-axis gives the percentage of identity found. Comparison of HCV strain AY378694 with strains AY378615, AY378641 and AY378635 is shown. The red vertical line shows the recombination point at position 286. Red numbers on the bottom part of the figure denote the number of informative sites that support clustering of the query sequence with the respective strains indicated in red on the bottom left side of the figure.