RNA secondary structures in M genome. (A) A stable hairpin at the very 5′ end of the genome important for phage RNA replication. (B) The operator hairpin around the initiation codon of replicase. The analogous hairpins from other Leviviridae phages are shown for comparison. Start codons of the replicase gene are colored green. (C) Structure of the 3′ untranslated region. The termination codon of replicase is colored dark red, the unpaired stretch corresponding to loop V or V2 in other phages in orange and the conserved nucleotide sequence in the loop of hairpin U1 that potentially forms a long-distance pseudoknot in green. On the right, schematic representations of 3′ UTRs from other phages based either on published data [31, 32, 45, 46] or RNA secondary structure predictions are given for comparison. The 3′ UTR of phage Qβ is closely similar to that of phage SP except for a short extra helix which is depicted in gray. The locations of replicase gene termination codons are represented as red boxes. RNA secondary structures were predicted by the RNAfold server .