Sequence variability and CD8+ CTL epitope density in HIV proteins. Sequence variability and CD8+ CTL epitope density in HIV proteins. Multiple sequence analysis of all HIV-1 and −2 isolates sequences available at the National Centre for Biotechnology Information (NCBI) Taxonomy database (January 2006) were carried out using CLUSTALW. The upper black line represents the % aminoacid conservation along the sequence of selected HIV proteins. The dotted black line represents the minimum conservation threshold (70%) required for the aminoacids within any given region to be considered as conserved. The location of potential CD8+ CTL epitopes was identified in silico using a proprietary algorithm. The lower red line represents the number of identified 9-mer epitopes, in the context of HLA A-02, *A-24, *B-27 and *B35, whose first aminoacid falls at the indicated position within the analysed protein.