The CPU on BBB is powered by 3V3. This means all digital output (GPIO, PWM, 
...) will be at 3V3 as well.

In order to get a 5V pulse train, you'll need an external driver. I use 
darlington arrays for that purpose, like ULN2804 
<http://html.alldatasheet.com/html-pdf/55062/ALLEGRO/ULN2804/246/1/ULN2804.html>
.

BR

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