Bootscanning of HCV sequences. Query sequence (AY378694) is shown 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 graph of percentage of permutated trees obtained using a sliding window of 200 nucleotides, moving 20 nucleotides at a time. The y-axis gives the percentage of permutated trees. This approach permits to observe levels of phylogenetic relatedness between a query sequence and a reference sequence in different genomic regions. The rest same as Fig. 1A.