Figure 3.

Localization of PLMVd-associated siRNAs. The number of occurrences of each nucleotide, when all of the aligned siRNAs are considered, is plotted over the nucleotide's position on the linear representation of the PLMVd genome. The upper graph corresponds to the PLMVd-associated siRNAs of (+) polarity, and the lower one to those of (-) polarity. Paired regions of the secondary structures (P) are shown in grey, while the single-stranded regions (bulges and loops) are shown in white. The letters "hh" indicate the position of the hammerhead self-cleavage sites. The regions of the secondary structures that have more than 25 000 occurrences are shown in bold on the proposed secondary structures for both the (+) and the (-) polarities. The secondary structures used are according to [18] and [25] respectively.