Systems, methods and tools for identifying potential errors or inconsistencies occurring during the runtime of multi-threaded applications and reporting the errors to a user, administrator or developer for correction and adjustments to the program code or thread timings. Embodiments of the disclosure capture thread sequences during a runtime or simulation environment and store the thread sequences as a matrix or tabular representation in a file. Multi-threaded application runs having an error free thread sequence, may be used as benchmarks for identifying potential errors and mis-runs of variations to the multi-threaded application as changes occur to the application code or new threads are added to the application code. This comparison may be performed by comparing the captured thread sequences of both the passing run and the mis-run of the multi-threaded application for differences in the thread sequences that may have caused the mis-run to occur.