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. 2014 Apr 10;15(8):767–779. doi: 10.1111/mpp.12130

Figure 3.

figure

The most stable structures for both polarities of Chrysanthemum chlorotic mottle viroid (CChMVd). The final structural models of both CChMVd (+) (A) and CChMVd (–) (B) obtained by selective 2′‐hydroxyl acylation analysed by primer extension (SHAPE) and folded by RNAstructure. The nucleotides in black denote low SHAPE reactivities (0–0.40), those in orange intermediate reactivities (0.40–0.85) and those in red highly reactive nucleotides (>0.85). The nucleotides forming the hammerhead are underlined, the cleavage site is indicated by an arrow and the mutated nucleotides are identified by stars. The numbering of the stems is in accordance with the first full stem encountered clockwise of the first nucleotide of the (+) polarity strand. The numbering of the stems of the (–) polarity structure is in accordance with that used for the (+) polarity structure.