Figure 3

Coding potential statistics for the seadornavirus VP7 CDS and the overlapping ORFX. (1) Map of the VP7 CDS of Banna virus [GenBank: AF052018], showing the proposed new coding sequence, ORFX, overlapping the VP7 CDS in the +1 reading frame. (2-7) Coding potential statistics based on an alignment of six Banna virus sequences with complete coverage of the VP7 CDS (see Figure 4 for accession numbers). (2-4) Positions of stop codons in each of the three forward reading frames. Note the conserved absence of stop codons in the +1 frame within the ORFX region. (5-6) Conservation at synonymous sites within the VP7 CDS (see Figure 1 caption for details). Note the unusually high conservation within the ORFX region. (7) MLOGD statistics for ORFX (see [2] for details). The null model is that the sequence in the ORFX region is only coding in the +0 (VP7 CDS) frame, while the alternative model is that the ORFX region is coding in both the +0 and the +1 (ORFX) reading frames. Positive scores favour the alternative model. MLOGD coding potential scores are produced for each alignment column and averaged over a 21 nt sliding window for clarity. The predominantly positive scores indicate that ORFX is likely to be a coding sequence.