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Kenneth Williams scored on an 80-yard pass from Devontae Payne in the fourth quarter as the Flyers won a Senate Athletic League home game.
South is 8-1, 6-0. JFK led, 6-0, after one quarter.
South moved ahead in the second quarter when Payne connected with Patrick Bennett from 20 yards and Brian Jackson made a two-point conversion.
Jackson capped the scoring in the fourth with a 4-yard run.