Quote:
Originally Posted by Bluesyzep
First. Is the scale in standard tuning different from 1st, 4th, and 5th in major scale? This may be why I'm confused.
Example: In E major It's open low E, open A, and 5th string 2nd fret is B.
The way I read it is by standard tuning. That gives me open low E, 5th string fourth fret (C#/D flat), and 5th string 5th fret (D).
What am I missing? 
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The example you gave (E,A & B) is the 1st, 4th, & 5th of the scale of E major as they appear in STANDARD tuning.
I've no idea what you mean about the E, C# and D, though.