A sample of the quantitative analysis of HIV-1 clade B Env protein diversity∧.

∧All percentages are shown to the nearest whole number.
aAmino acid number at the start and end of the nonamer position in the protein alignment. The symbols & and+denote the mixed-variable and highly diverse nonamer positions, respectively (see Figure 3 for definitions).
bTotal number of protein sequences analysed at the respective nonamer position; the differences between nonamer positions was due to the inclusion of both partial and full-length sequences in the alignments.
cShannon nonamer entropy (H(x); see Figure 2 for details).
dThe index nonamer is the most prevalent sequence at the given aligned nonamer position.
eVariants differ by one or more amino acids from the index sequence.
fThe major variant is the most common variant sequence at the position.
gMinor variants are multiple different repeated sequences, each occurring more than once and with an incidence less than or occasionally equal to the major.
hUnique variants are those that occur only once in the alignment.
iNonatypes are the distinct sequences among the variants.
jHXB2 nonamer sequence and its incidence at the given nonamer position; amino acids identical to the index are denoted as “.”.
kC1P nonamer sequence and its incidence at the given nonamer position; amino acids identical to the index are denoted as “.”. HXB2 and C1P nonamers not found at the aligned nonamer position are indicated with 0% incidence.