Here is the pinout for the serial ports running by default on the SAMA5D3 XPLAINED board (same for Yocto/Poky and Debian):
/dev/ttyS0 pins 20(tx)/21(rx) - used by Console
/dev/ttyS1 pins 18(tx)/19(rx) - available
/dev/ttyS2 pins 16(tx)/17(rx) - available
/dev/ttyS5 pins 0(rx)/1(tx) - available
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