DotKnot (Sperschneider and Datta 2010) secondary structure model for 5′ region 65–126 from segment 2 of genome set 755298. Other predictions by DotKnot for this region are represented by blue shaded nucleotides, which can base-pair with the red shaded nucleotides to form two alternate 5′ helices leaving nucleotides 65–80 unpaired. Base pair counts from an alignment of all unique segment 2 sequences are shown to the right. The nucleotides boxed in orange in the 3′ pseudoknot helix are the start codon for the internal ORF for the PB1-F2 product. This ORF is shifted +1 compared to the PB1 coding region. Figure annotations and base pair counts are as described in Figure 5. Predicted free energies for the pseudoknot were calculated as −14 (DP) or −8 (CC) kcal/mol, depending on the parameters used (Dirks and Pierce 2003; Cao and Chen 2009).
