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. Author manuscript; available in PMC: 2017 Nov 18.
Published in final edited form as: Curr Protoc Microbiol. 2016 Nov 18;43:14B.9.1–14B.9.20. doi: 10.1002/cpmc.16

Figure 2. Location of degenerate primers and amplicons within the L1 ORF.

Figure 2

Sequences corresponding to the L1 ORF for all known human Alphapapillomaviruses were downloaded from PaVE (accessed on 7/11/2016)(Van Doorslaer et al., 2013). The sequences were aligned, and a neighbor-joining phylogenetic tree was constructed. The sub-alignment is numbered according to HPV16 (excluding gaps; top) or the alignment (including gaps; bottom). Red lines below the alignment indicate the SPF10 primers, while the green lines show the positions of the GP5+/6+. The alignment highlights the differences between each sequence and HPV34, which was chosen as reference. A dot (“.”) indicates an identical nucleotide, a colored box indicates a single nucleotide polymorphism, while a dash “-” represents an indel.