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Nucleotide sequence alignments of HIV-1 subtypes and CRFs. The name of the subtype or CRF labeled with “CON_X” means consensus of subtype X or CRF X, e.g., “CON_B” stands for consensus of subtype B strains. Some subtypes or CRFs are only represented by one sequence, e.g., 05.VI1310, meaning CRF05-VI1310. The sequences are not continuous, numbered according to the HXB2. The positions for subtype-specific primers are underlined.
