I'm hoping somebody help.

I'm trying to get the intonation on my guitar set up and having problems.

I'm plugging my guitar into the microphone connection on my PC and using AP Tuner software for tuning. Here's what happens -

I tune the open string up, then set the intonation so the 12th fret is tuned up to the same note. This seems to work pretty well. The problem is that this leaves the notes at the other frets way off. Is there something more drastic that needs to be done ? Isn't making a lot of sense to me.

Here's the figures in AP Tuner for the D string as it is at the moment for example -

Open string +0.1
1st fret +17.5
2nd fret +9.0
3rd fret +12.5
4th fret +8.0
5th fret +11.0
6th fret +11.0
7th fret +6.0
8th fret +4.5
9th fret +1.0
10th fret +1.5
11th fret +0.5
12th fret -1.5
it doesnt make sense for the 12th fret to be out when the string is tuned correctly and you set it up at the 12th. you must be doing it wrong.

adjust the saddle so that the harmonic is in tune AND the 12th fret is in tune
You could be getting bad quality sound from your microphone interface.

Just use your ear at the 12th fret with the harmonic and open string.
Thanks for the replies.
I hadn't heard of the harmonics method so I've looked on YouTube and there's a video that explains it. Just got to learn how to play harmonics now.
It's fairly simple, just very easy to be told the Wrong way to do it.

What you need to compare is the tuning of an open note Of Some Sort, and a fretted note Of Some Sort.

We use the 12th fret as it's in the middle of the fretboard (lengthwise) and also the same note, one octave up, as the open note, to make things as easy as possible.

For your open note, you could use a 12th fret harmonic, Or just the open note. All that matters is that the string is correctly tuned to open, Before you start fretting any notes. People use harmonics to tune sometimes as it's considered a more accurate way of tuning, as it's easier for the tuner to pick out the note we're trying to tune.

If your open note is tuned correctly, and the note at the 12th fret is flat, move the saddle towards the headstock. Reverse applies for if it's sharp.

Hope that helps
Those figures for the first few frets make me suspect that your nut might be too high...meaning you have to press the string a long way....making it go sharp
Thanks again for the replies. Really helpful.

I've got it as good as I can get it anyway using a youtube video explaining harmonics. I've come to the conclusion that some of the problem is due to having to set the action fairly high otherwise I get string buzz when fretting up the neck. It's a pretty cheap guitar..

Cheers for the help