Additional file 1:

HIVaINR antisense RNA [14] analyzed by Mfold [31-33].

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Additional file 2:

HIVaINR antisense RNA [14] and predicted HAAmiRNAs at sites 1, 2 and 3 (backward yellow arrows) are shown above the corresponding complementary sequence in the HIV-1 sequence alignments for group M (strains A, B, C, D, F1, G, H, J and K), group N, and group O, as well as chimpanzee (CPZ) strains in the long terminal repeat (LTR), as obtained from the HIV Sequence Compendium 2000[107]. HAAmiRNA 3 overlaps and is partially complementary to the nef microRNA:miR-N367 described by Omoto, S., et al., [29] and HAAmiRNA 1 and precursor (pre-HAAmiRNA 1) overlaps and is complementary sequence to the predicted #4 microRNA precursor described by Bennasser, Y. et al [30]. Predicted seed regions for the microRNAs are shaded, and sequence targeting human mRNA is underlined. The B clade HXB2 is the reference sequence, with identical sequences in the strains below, unless otherwise indicated [107].

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