Coding potential statistics for an alignment of four plant fijivirus segment 5 sequences. (1)-(3) The positions of stop codons in each of the four sequences in each of the three forward reading frames (frame defined by alignment to the reference sequence [GenBank: NC_003736]). The FDV sequence has been put into the same frame as the other sequences via the arbitrary insertion of an extra 'U' into the run of five 'U's at NC_007160 nucleotides 2714–2718, as discussed in the text. Note the conserved absence of stop codons in the +0 frame within ORF5-1 and in the +1 frame within ORF5-2. (4)-(6) MLOGD sliding-window plots (window size 75 codons; step size 25 codons). Each window is represented by a small circle (showing the likelihood ratio score for that window), and grey bars showing the width (ends) of the window. See  for further details of the MLOGD software. In (4) the null model, in each window, is that the sequence is non-coding, while the alternative model is that the sequence is coding in the +0 (i.e. ORF5-1) frame. Positive scores favour the alternative model and, as expected, there is a strong coding signature throughout ORF5-1. In (5)-(6) the null model, in each window, is that only ORF5-1 is coding, while the alternative model is that both ORF5-1 and the window frame are coding. Scores are generally negative with some scatter into low positive scores, except for the ORF5-2 region which has consecutive high-positively scoring windows (5). Note that the generally lower MLOGD signal within the overlap region itself (4)-(5), and also at the 5' end of ORF5-1 (4), is due to there being fewer substitutions with which to discrimate the null model from the alternative model in these regions of above-average nucleotide conservation. (7) Map of the reference sequence [GenBank: NC_003736]. (8) Conservation at synonymous sites within ORF5-1 (see text and  for details). Note that the relatively large window size (75 codons) – used here for improved statistical power – explains the broad smoothing of the conservation peak at the edges of the region where ORF5-2 and ORF5-1 overlap.