25.2.2.2 Timer/Counter Clock and Prescaler
TCC is clocked asynchronously to the system clock by a GCLK (Generic Clock) channel. The GCLK channel can be connected to any of the GCLK generators. The GCLK generators are configured to use one of the available clock sources in the system such as internal oscillator, external crystals, etc. - see the Generic Clock driver for more information.
Each TCC module in the SAM has its own individual clock prescaler, which can be used to divide the input clock frequency used by the counter. This prescaler only scales the clock used to provide clock pulses for the counter to count, and does not affect the digital register interface portion of the module, thus the timer registers will synchronized to the raw GCLK frequency input to the module.
As a result of this, when selecting a GCLK frequency and timer prescaler value the user application should consider both the timer resolution required and the synchronization frequency, to avoid lengthy synchronization times of the module if a very slow GCLK frequency is fed into the TCC module. It is preferable to use a higher module GCLK frequency as the input to the timer and prescale this down as much as possible to obtain a suitable counter frequency in latency-sensitive applications.