Pairwise comparison of D1/D2 sequences cloned from strains with intra-genomically variable D1/D2 sequences.

Intra-genomic D1/D2 variants cloned from individual strains are indicated as D1/D2 copies. The number of transitional (si) and transversional (sv) mutations, as well as number of indels and the involved nucleotides, were computed with MEGA6. The number of nucleotides in pairwise-aligned sequences is indicated as nt (tot), whereas the number of nucleotides in indels (N° nt) is reported in brackets. Identity (%) indicates the percentage of identical nucleotides between D1/D2 variants within individual genomes.