The easiest way to set your intonation is to tune the 12th fret harmonic to be exactly in tune, using an electronic tuner. Then push down precisely on where the 12th fret would be and if it's flat, move the bridge saddle forwards, then use the same method again and it should be closer. Keep doing this until it is in tune.
If it's sharp do the same, but move the bridge saddle backwards (ie. away from the neck). It can help slackening the string off when moving the saddle backwards.
There are more in depth guides and probably better ways, but in a nutshell that's how you do it. You'll certainly get a better result if your intonation is way out, though on this occasion it appears to have been your tuner. I recommend a Boss TU-2 or better for picking up the low B.
If it's sharp do the same, but move the bridge saddle backwards (ie. away from the neck). It can help slackening the string off when moving the saddle backwards.
There are more in depth guides and probably better ways, but in a nutshell that's how you do it. You'll certainly get a better result if your intonation is way out, though on this occasion it appears to have been your tuner. I recommend a Boss TU-2 or better for picking up the low B.