Did you notice how all of the notes used by your flute
are aligned in the same columns right from the top?
This should help to show that the scale your flute plays uses just a portion of
the total notes available in what's known as the "Chromatic Scale". It
should also help show that the distance between the holes in your flute correspond to
the missing notes from the chromatic scale that aren't used by the Pentatonic scale.