Stochastic simulation parameters.

L, Ton, kmax,i, Si, α, and β are parameters associated with CTL response. Values shown in the Dominant (Subdominant) column apply to response at the first (second-sixth) epitopes. U is a uniform random number on [0, 1], meaning that the timing and strength of the subdominant responses is different for each simulation. Values of kmax,i shown are for the strong CTL response simulation. Weak CTL response simulation differ only in kmax,i = .12U for the subdominant responses. ρ, nrec, and μ are parameters associated with recombination and mutation. CTL response parameters are chosen to qualitatively match responses seen in CTL datasets [11, 13] and match estimates given in [44].