Calculation of HPV31, 33 and 35 variations by genome region and open reading frame (ORF).

aThe number of nucleotides within each ORF and region of the genome based on one genome size for each HPV type calculated from the global sequence alignments. Range of values and location in the papillomavirus genome are shown in Figure S4;
bTotal number and percentage of positions based on one genome size for each HPV type calculated from the global sequence alignments. Nucleotide variations include SNPs and indels;
cMaximum number of encoded amino acids for each ORF;
dTotal number and percentage of variable amino acids based on the maximum number of amino acids derived from the established genome size for each HPV type;
eCG, complete genome. Each nucleotide position is counted once. A single genome size is inferred from the nucleotide alignment (indel was treated as one event).
NCR1, non-coding region 1 (between E2 and E5 ORFs); NCR2, non-coding region 2 (between E5 and L2 ORFs); URR, up stream regulatory region (between stop codon of L1 and start codon of E6).