RNAalifold output from alignments of constrained regions in H1N1pdm09 viruses originating from human hosts, as predicted by RNAdescent.

Filename convention within the zip file is as follows: HA/NA type, then host type, then whether the region was identified through analysis of raw (unranked) data, ranked data, or both, then the gene name, then the nucleotide location within the analysed alignment of the gene name, then the nucleotide location within the reference sequences (corresponding to locations listed in S2 Table and S10 Table), then a note if the analysis was performed using only one example of each distinct sequence, then a note if the fold uses the reverse complement of the cRNA (i.e. the vRNA), rather than the cRNA. All folds have been generated using alignments with loci where the consensus nucleotide is a gap removed. Base pairs are highlighted in deep/mid/light red when all/all but one/all but two sequences are capable of forming the pairs shown. Base pairs are highlighted in deep/mid/light yellow when all/all but one/all but two sequences are capable of forming the pair shown or one other pair (including GU pairs). Base pairs are highlighted in deep/mid/light green when all/all but one/all but two sequences are capable of forming the pair shown or one of two other pairs (including GU pairs). RNAalifold was used with input options disallowing lonely pairs, allowing G-quadruplexes, and with the ribosum scoring matrix enabled. (ZIP)