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The game was scrappy for much of the opening 45 minutes, with few chances at either end.
Alex Bruce had the first effort of the game for Hull, taking a shot from long range, but his attempt was high of the crossbar.
A strong spell from the visitors resulted in a strike from Ikechi Anya, but the Scot's effort drifted wide.
It looked like the sides would head in level at the break, but Deeney picked up the ball outside the penalty area just before half time to fire Watford in front.