The self-excited spanwise homogeneous perturbations arising in shock-wave/boundary-layer interaction (SWBLI) system formed in a hypersonic flow of molecular nitrogen over a double wedge are investigated using the kinetic Direct Simulation Monte Carlo (DSMC) method. The flow has transitional Knudsen and unit Reynolds numbers of 3.4 ×10-3 and 5.2 × 105 m- 1, respectively. Strong thermal nonequilibrium exists downstream of the Mach 7.2 detached (bow) shock generated due to the upper wedge surface. A linear instability mechanism is expected to make the pre-computed 2-D base flow potentially unstable under spanwise perturbations. The specific intent is to assess the growth rates of unstable modes, the wavelength, location, and origin of spanwise periodic flow structures, and the characteristic frequencies present in this interaction.