Might be worth you doing some research on this as your question raises a few questions about your understanding of intonation as you said your strings were intonated perfectly when open.
The general idea is that once you have your strings in tune (open) you want it to play as close as possible on the fretted notes. When you fret at the 12th and measure the tone it may be slightly sharp or flat, the primary cause is the bend in the string adding tension. You would then have to look at the bridge and change the saddle location forwards if its flat or backwards if its sharp. (Easy if Electric)
If its intoned correctly at the 12th then the 5th frets should be pretty good too.
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