Figure 2.

An example Stockholm alignment for the UPSK pseudoknot from turnip yellow mosaic virus. The Stockholm alignment format is flexible enough to allow generic mark-up of file information with ‘#=GF' lines, sequence information with ‘#=GS' lines and column information with ‘#=GC' lines. Each is followed by at least a two-letter code giving an indication for what follows e.g. ‘ID' implies ‘identifier', ‘AC' implies ‘accession', ‘AU' implies ‘author', etc. All the commonly used tags are documented in the Wikipedia article for Stockholm alignment (25).