The SAM processor has 3 programmable clock pins but the function is not supported by Arduino.
From the data sheet
The PMC controls 3 signals to be output on external pins, PCKx. Each signal can be independently
programmed via the Programmable Clock Registers (PMC_PCKx).
PCKx can be independently selected between the Slow Clock (SLCK), the Main Clock
(MAINCK), the PLLA Clock (PLLACK), UTMI PLL Clock (UPLLCK/2) and the Master Clock
(MCK) by writing the CSS field in PMC_PCKx. Each output signal can also be divided by a
power of 2 between 1 and 64 by writing the PRES (Prescaler) field in PMC_PCKx.
I've not used them though so can't advise on that. They may not even be broken out on the Due.