Rank and N scores of 17 conserved sites in potyvirus genomes along with their locations and sequence and the method used to identify each one.

1Sites with equal N scores (see Materials and Methods) were ranked as equal (e.g. 7th for sites at position 4458 and 7899)
2Nucleotide positions refer to the 5′ residue of the site in the sequence of the Tobacco etch virus genome [Accession code M11458].
3CI (cylindrical inclusion), a multifunctional protein that acts as an RNA helicase and is involved in genome replication and cell-to-cell movement; NIb (large nuclear inclusion protein), RdRp (RNA-dependent RNA polymerase); CP (coat protein), RNA encapsidation.
4Only the most abundant variants, those present in 8 or more potyvirus genomes are shown. Italicised amino acids have other variants present at the same site in fewer than 8 potyvirus genomes.
5Regions were identified by using conservation measures implemented in the program NCSF are coded C1 to C5, E1 to E5, R1 to R5, or V1 to V5 where the codes represent the ranking according to the dominant base count(C), Shannon entropy score (E), redundancy score (R) or sub-sequence variants count (V).
6R4 and C5 both start from 9237 whereas V1 starts from 9240
7Nicholas and Laliberte (1991) identified part of this motif and designed primers that targeted NIIENG. This is part of a conserved region 69 nucleotides long (with one nucleotide gap) that encodes: KKH/FKG/VNNSGQPSTVVDNTLMVV/II. Langeveld et al. (1991) identified part of the region and designed primers that targeted TVVDNTLMV. Gibbs and Mackenzie (1997) designed primers that targeted G/VNNSGQ in this region.
8One sequence (Accession code AJ310102) was removed from analysis of this site as there was 1 codon (3 nucleotides) insertion at position 9165.
9Langeveld et al. (1991) identified part of this motif and designed primers that targeted AHFQMKTA. Pappu et al. (1993) modified Langeveld's primer and designed primer that targeted QMKAAA.
10Langeveld et al. (1991) identified this motif and designed primers to target MVCIENG. Pappu et al. (1993) designed primers to target WCIEN.