Figure 1

MLOGD statistics for the alignment of four CPV-1 segment 1 sequences. The four sequences were aligned with code2aln [15]; the alignment is gapless within the VP1 ORF. (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: AF389462]). Note the conserved absence of stop codons in the +0 frame within the VP1 ORF and in the +1 frame in the ORFX region. (4)–(7) MLOGD sliding-window plots. Window size = 20 codons. Step size = 10 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 [6] for further details of the MLOGD software. In (4)–(5) 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 window frame. Positive scores favour the alternative model. There is a strong coding signature in the +0 frame (4) throughout the VP1 ORF, except where it overlaps ORFX. In this region there is a strong coding signature in the +1 frame (5) indicating that ORFX is subject to stronger functional constraints than the overlapping section of VP1. In (6)–(7) the null model, in each window, is that only the VP1 frame is coding, while the alternative model is that both the VP1 frame and the window frame are coding. Only the +1 (6) and +2 (7) frames are shown because the +0 frame is the VP1 frame which is included in the null model. Scores are generally negative with occasional random scatter into low positive scores, except for the ORFX region which has consecutive high-positively scoring windows (6). (8) Map of the reference sequence [GenBank: AF389462].