Unfortunately, clarinets do not play perfectly in tune without help. However, even if an instrument were made which naturally played every note exactly in tune with its ideal, there would still be a need to manipulate the pitch. This has to do with the concept of the tempered scale. A complete explanation of tempered scale is quite mathematical, complex, and well beyond the scope of this article. In fact, the intervals of major third, minor third, major sixth, and minor sixth are severely out of tune.
Tuners use the same tempered tuning standard as pianos.
In general clarinetists do strive to play an even-tempered scale, like pianos do. The meter on a tuner uses a measuring standard called cents. When a pitch is perfectly in tune, the meter indicates 0 cents. To tune a pure interval with a tuner, you should compensate for the difference between the tempered and pure version of the interval. In order to do this you must first understand the context of the pitch you are trying to tune.