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The home side had the first chance of the match when Sean Morrison rose highest to meet a corner and headed against the frame of the goal.
The Royals were soon ahead when they broke quickly and Jason Roberts sidefooted a volley into the roof of the net.
Just a minute later and Reading were three up when young Gunners keeper Damian Martinez palmed a Mikele Leigertwood shot behind him into the net.
Arsenal struggled to muster any kind of attack and Reading nearly made it four in the 33rd minute when Noel Hunt let fly from distance, but Martinez this time held on to the ball low to his right.
The Gunners were remarkably four goals down when McClearly clipped a cross to the back post that was met by Hunt and went in off the upright.
Theo Walcott gave Arsenal a glimpse of hope by sprinting clear of the Royals backline and dinking over the advancing Adam Federici to pull a goal back right at the end of the 45.