The positioning of the HMA primers on an alignment of multiple subtypes can be seen in an alignment figure.

For those who wish to analyze the data, multiple-sequence alignments of the kit's HIV-1 subtype reference sequences can be obtained here in several file formats:

• FASTA (Pearson)
• Clustal
• MSF (GCG)
• GDE

Note that half the HMA primers were reversed and complemented to match the strand orientation of the alignment.  These primers are indicated within their sequence names.