Figure 1.

Synonymous site conservation in alphaviruses. (A) Map of the alphavirus genome. (B) Synonymous site conservation in VEEV-EEEV-WEEV and SINV-AURAV sequence alignments. The plot depicts the probability that the degree of conservation within a 9-codon sliding window could be obtained under a null model of neutral evolution at synonymous sites. Note that the RT stop codon itself has been excluded from the conservation statistics. In order to map the conservation statistic onto the coordinates of a specific sequence in each alignment, all alignment columns with gaps in a chosen reference sequence were removed prior to calculation of conservation. The following reference sequences (GenBank accession numbers) were used: VEEV NC_001449, SINV NC_001547.