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Advanced digital circuits are increasingly sensitive to single event transients (SETs) phenomena. Technology scaling has resulted in a greater sensitivity to single event effects (SEEs) and more in particular to SET propagation, since transients may be generated and propagated through the circuit logic, leading to behavioral errors of the affected circuit. When circuits are implemented on Flash-based FPGAs, SETs generated in the combinational logic resources are the main source of critical behavior. In this paper, we developed a technique based on electrical pulse injection for the analysis of SETs propagation within logic resources of Flash-based FPGAs. We outline logic schematic that allows the injection of different SET pulses. We performed several experimental analyses. We characterized the basic logic gates used by circuits implemented on Flash-based FPGAs evaluating the effect on logic-chains of real lengths. Additionally, we performed an effective analysis evaluating the SET propagation through microprocessor logic paths. Results demonstrated the possibility of mitigating SET-broadening effects by acting on physical place and route constraints.