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Is ATMega644A a pin-equivalent substitute for ATMega16A? Answered

Like are the in/out pins the same (On the TQFP)?

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No, they aren't. Perhaps they have the same pinout, but they are from different product ranges:
ATmega164A/164PA/324A/324PA/644A/644PA/1284/1284P and
ATmega16A/32A

What means the registers etc. can be different.

As steveastrouk already sad, look into the datasheets. You'll learn a lot.

JanD

WHat did the datasheet tell you ?