Table 3. Subtype B and C HIV-1 prediction and analysis of RNA secondary structure.

RNA Sequence	NucleotideHomology* †	Amino AcidHomology* †	ΔG 1‡	ΔG 2‡	ΔΔG 1*	ΔΔG 2*	K65 location
Subtype BHIV-1	100%	100%	-65.7	-	0.0	0.0	In the unpaired loop of a stem-loop structure
Subtype CHIV-1	90%	93%	-64.6	-63.4	1.1	2.3	In the unpaired loop of a stem-loop structure or in an unpaired bulge
SIV cpz	78%	88%	-66.6	-65.7	0.9	0.0	Between an unpaired loop and a paired stem structure or in a paired stem structure

*Nt homology, amino acid homology and differences in Gibbs free energy values of subtype C are compared to those of subtype B.

‡Gibbs free energy values are expressed in kcal/mole.

†Nt and amino acid homology was evaluated only for the RT portion of the pol gene.