What does the engine light mean when it is flashing and the car is running rough on a Mazda millenia 2000?

the check engine light comes on when one or more of about (500 to 1000) computer regulated components either begins to fail, is getting abnormal readings for its purpose thus the check engine light comes on to symbolize that their is a problem. you have to find out what type of problem it is by getting an engine diagnostic, in which they hook up a scan tool pull the trouble code/s and then test components related to the set code to see which are malfunctioning. make no mistake this will cost you about $90 unless you know a diagnostic tech. autozones free check engine light package will not tell you whats wrong it will only pull the code as stated in the above sentences, this does you no good as it does not tell you which part requires replacement. and they will guess do to their inexpertise which if you listen will cost you alot more money than just handling it with a diagnostic. Cylinder misfire(s),the spark plug is firing at the wrong time and that will cause the engine to run rough.