Beaglebonebalck has 4 on-board LED's you can check shematic page number 6. https://beagleboard.org/static/beaglebone/latest/Docs/Hardware/BONE_SCH.pdf in current software stack this LEDS controled by deriver placed here http://lxr.linux.no/#linux+v4.4/drivers/leds/leds-gpio.c

The task for next loop are: -diactivate current leds-gpio driver. -add to driver ability to define GPIO poperty configuretion such gpios = ; etc.. -add new property in DTS for configure blinking timings in milliseconds, it shuld support two paramiters one for turn on and second for turn off. -led timing should be also configured via sysfs.