Diagrammatic representation of how simulated recombinants were generated.

For a particular recombination event specifying a major parent, a minor parent, and a pair of recombination breakpoint locations delineating a fragment of sequence derived from the minor parent (containing in this particular case two nucleotides that vary between the major and minor parents), an in silico mimic of the real recombinant sequence is created using the minor and the major parent sequences. Following that, a set of N simulated recombinants is generated in a similar way to the mimic recombinant, but using random starting and ending positions, whilst maintaining the same number of either variable nucleotides (for the RNA folding tests) or non-synonymous codon sites (for the protein folding tests) between the randomized breakpoint sites as occur in the mimic recombinant. In this example the mimic and simulated recombinants all have two such “informative” sites between the 3′ and 5′ breakpoints that are not identical between the parental sequences.