Okay so here`s the deal regarding intonation. Intonation problems are created when the length of the guitar string is not precisely matched to the length of your guitar. Why does this matter? Well, when you play a guitar you are dividing the string into different lengths in the process of fretting notes, this causes the strings frequency to increase or decrease in an inverse relationship with the strings length.
Simply put if you play your E string at the twelfth fret – an octave above open string tuning – you are dividing the string in half. Now, if the division of the string isn`t exact then the pitch of the note will be out. That is why your electric guitar has moveable saddles in the bridge – so you can check and resolve intonation problems because nothing sounds more out of whack than skipping to the twelfth fret for a burn up and finding that all your notes are just a little bit flat or sharp.
SO, if you want to Test your Intonation plug in your tuner and for each string perform the following actions:
1. play the open string and make sure it is exactly in tune.
2. play the same string at the twelfth threat and adjust your bridge saddles until the string is exactly in tune.
3. play a harmonic at the twelfth fret and double check the tuning.
4. Repeat across all strings.
5. Start playing.