The goal of this research is to understand the shock-boundary layer interaction (SBLI) in hypersonic flows over angular sections of vehicle in near continuum, transitional flow regimes (Re1=105 m−1 ) with the use of particle based Direct Simulation Monte Carlo (DSMC) method, which solves the Boltzmann equation of transport. This is achieved by the rigorous development of our scalable, in-house DSMC code, SUGAR, that have been demonstrated to simulate billions of particles on adaptive mesh refinement (AMR)/Octree grids. The specific intent of the ongoing work is to understand the stability of previously studied 2-D hypersonic SBLI system over a double wedge to spanwise perturbations. Spanwise structures have been observed in an exploratory spanwise periodic simulation started from a steady state 2-D base flow. Based on those results an approximate estimate of the spanwise wavelength has been made and a more refined simulation is performed to verify the existance of spanwise periodicity. Analysis of the observed structures in terms of their origin, governing mechanisms, coupling of shock activity with spanwise periodicity, and inherent self-excited eigenmodes are discussed in detail.