Additional file 1:

Previously published sequences tabulated and identified by Naito et. al. (2007) [33], were scored for conservation using our tool and compared against original conservation estimates.

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Additional file 2:

An additional data file containing (i) a table of the the number of sequences in the HIV-1 partial gene fragments data set, (ii) a table summarizing the number of 19 nt. sequences analyzed, (iii) a summary table of the numbers of most highly conserved targets, (iv) a list of the 96 selected targets and surrounding sequence, (v) a table of the 22 overlapping regions containing the 96 targets, (vi) a list of the 20 and 21 bp matched targets, (vii) a list of the overlapping hairpins with adjacent start sites 1 nt. apart, (viii) a detailed list of the % conservation for each position in the 5 sequence profile for all 96 selected targets, (ix) a table summarizing the differences in the fluorescent reporters used, (x) a list of the hairpins in scored and ranked order, (xi) additional method information such as oligonucleotide sequences, and (xii) the NL4-3 gene sequences used to generate the targets and make the reporters.

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