We study the stability of a zero-pressure gradient boundary layer subjected to free-stream disturbances by means of local stability analysis. The dataset under study corresponds to a direct numerical simulation (DNS) of a flat plate with a sharp leading edge in realistic wind tunnel conditions, with a turbulence level of 3.45 % at the leading edge. We present a method to track the convective evolution of the secondary instabilities of streaks by performing sequential stability calculations following the wave packet, connecting successive unstable eigenfunctions. A scattered nature, in time and space, of secondary instabilities is seen in the stability calculations. These instabilities can be detected before they reach finite amplitude in the DNS, preceding the nucleation of turbulent spots, and whose appearance is well correlated to the transition onset. This represents further evidence regarding the relevance of secondary instabilities of streaks in the bypass transition in realistic flow conditions. Consistent with the spatio-temporal nature of this problem, our approach allows us to integrate directly the local growth rates to obtain the spatial amplification ratio of the individual instabilities, where it is shown that instabilities reaching an -factor in the range [2.5,4] can be directly correlated to more than 65 % of the nucleation events. Interestingly, it is found that high amplification is not only attained by modes with high growth rates, but also by instabilities with sustained low growth rates for a long time.