Table 6.

Comparison of nucleotide substitution frequencies in PSTVd quasispecies

			G/U
	A/U or G/C	Loop	Total G/U	Case 0	Case 1	Case 2
Theoretical	0.607	0.298	0.095	0.050	0.022	0.022
Observed	0.349	0.600	0.052	0.034	0.009	0.008
Observed/theoretical	0.574	2.012	0.546	0.688	0.417	0.358

The proportion of nucleotides involved in A/U or G/C base pairs, G/U pairs, and loops in the PSTVd secondary structure (Theoretical) are compared with the proportion of substitutions detected at these nucleotides (Observed) in the sequenced population derived from a cloned Master sequence. Substitution frequencies for G/U nucleotides in different contexts (Case 0, Case 1 and Case 2) are also indicated.