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Margate's FA Cup run ended against Southern League Division One Central side Barton Rovers at Hartsdown Park.
Gate fell behind to a Kev Kilroy penalty on 36 minutes to go in at the break a goal down.
However, they hit back straight after half-time, Charlie Allen netting a minute into the second half to give the home support renewed hope.
But it wasn't to be as the away side struck what turned out to be the winner seven minutes later through Louis Lee to send Rovers into the third qualifying round.