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You can use a music tuner to measure your intonation and, over time, become a better musician.
To measure your intonation with a tuner, make sure your microphone is activated. [You can get a little help with that here.] Sustain a tone into your microphone.
The tuner will detect what pitch you're playing and indicate whether it is sharp, flat, or in tune. Adjust your playing so that the tuner indicates that your note is in tune.
Most instruments have a way to alter their intonation over the whole instrument (pulling out a slide on a brass instrument, turning a peg on a string instrument, making a woodwind longer, etc.) "Tuning your instrument" usually refers to this kin of global tuning. However, even doing this expertly does not assure you of always playing in tune. Most instruments have certain notes that are slightly sharp or flat -- try to find these notes and adjust accordingly.
Try leaving myMusicTuner on while practicing. During long tone exercises or slow passages, check your intonation on the tuner. Precise intonation is the mark of a professional musician -- it's a skill that develops over a long time. Keep at it and you'll sound better and better!