At block level, input clock signals of each channel can be connected either to the external inputs TCLKx, or to the internal I/O signals TIOAx for chaining(1) by programming the Block Mode register (TC_BMR). See Clock Chaining Selection.
Each channel can independently select an internal or external clock source for its counter(2):
This selection is made by the TCCLKS bits in the Channel Mode register (TC_CMRx).
The selected clock can be inverted with TC_CMRx.CLKI. This allows counting on the opposite edges of the clock.
The burst function allows the clock to be validated when an external signal is high. The BURST parameter in the TC_CMRx defines this signal (none, XC0, XC1, XC2). See Clock Selection.