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You need to pick a timer that isn't being used for anything else and configure it as a simple counter with the clock source set to the external clock pin for that timer. At block level, input clock signals of each channel can either be connected to the external inputs TCLK0, TCLK1 or TCLK2, or be connected to the internal I/O signals TIOA0, TIOA1 or TIOA2 ...

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