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Alignment of the nucleotide sequences within the LTR region spanning positions -177 to +3 of subclade F1 strains with those of the HXB2_LAI_IIIB_BRU (K03455) HXB2 and consensus sequences of clades a, c, d, g, h and J. Dots indicate nucleotide identity to the HXB2 sequence and dashes (-) represent gaps introduced to achieve the best alignment. Motifs present in the HXB2_LAI_IIIB_BRU (K03455) are underlined. Boxed sequences in subclade F1 isolates indicated 13–15 nucleotides insertion.
