Supporting Information 2: Stochastic simulations

In this study we have predominantly used a set of ordinary differential equations (ode) to describe the behavior of transposons and host control. However, it is well known that for small numbers of molecules intrinsic noise may play an important role in the dynamics. In order to verify our results with respect to small numbers of transposons, vlp levels and other molecules we also design and study a stochastic version of our model using the stochastic simulation algorithm, or Gillespie algorithm [Gillespie, 1977]. Below we describe the pseudo-reactions of this approach. The reactions, with the corresponding parameters above the reaction arrows, are a straightforward translation from the original models as described in the Methods. Thus parameters are the same as used in the ode model.