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The reason is that the earth's rotation sets up an apparent force (called the Coriolis force) that pulls the winds to the right in the Northern Hemisphere (and to the left in the Southern Hemisphere). So when a low pressure starts to form north of the equator, the surface winds will flow inward trying to fill in the low and will be deflected to the right and a counter-clockwise rotation will be initiated. The opposite (a deflection to the left and a clockwise rotation) will occur south of the equator.

NOTE: This force is too tiny to effect rotation in, for example, water that is going down the drains of sinks and toilets. The rotation in those will be determined by the geometry of the container and the original motion of the water. Thus one can find both clockwise and counter- clockwise flowing drains no matter what hemisphere you are located. If you don't believe this, test it out for yourself.