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. 2015 Oct 17;43(21):10168–10179. doi: 10.1093/nar/gkv1039

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© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 3. — The PPfold 3.1 structure coloured by comparison with the Watts09 structure. The predictions were made with identical SHAPE data. Common structural elements are indicated in red (base pairs) and blue (unpaired nucleotides). Elements paired in both structures (but with different partners) are indicated by yellow. Nucleotides paired in one but unpaired in the other are indicated in brown. 72% of all unpaired nucleotides and 31% of base paired nucleotides were found in both predictions. Over half of the genome is unpaired in both predictions (blue). A higher resolution version of the figure with nucleotide identities is available in Supplementary Figure S3.