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The correct sentences with prepositions of direction are 'The kite is flying through the clouds.' and 'The kite is flying over the clouds.' The prepositions of direction 'through' and 'over' tell us about the movement of 'the kite'. ‘Over’ tells us that the kite is moving across the sky without touching the clouds below it. ‘Through’ tells us that the kite is moving from the opening to the clouds on one end till the exit from the clouds on the other end.