NIOS II Timer Interval Core Question!

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You might find it best to write your own timer/counter - then you'll know exactly what is happening.

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will writing my own timer/counter keep all three clock in sync? All three clocks being in sync is very important. Also these three clocks are just the first phase of the program. Eventually, i will need to generate 9 clocks ( 3 sets of 3 clocks) and all these three clocks will be interdependent of each other and all three clocks must be reconfigurable!