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Abraham's quickfire double put Chelsea in control early in the FA Cup fourth-round tie on Monday (AEDT), as last season's runner up seemed to be heading for a comfortable success.
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Yet Kepa, brought in as one of seven changes made by Frank Lampard from Tuesday's defeat at Leicester City, enabled Luton to haul themselves into the contest when he failed to keep out Jordan Clark's effort.
Abraham's third goal 16 minutes from time ultimately set up a fifth-round trip to Barnsley, though Werner's woeful run in front of goal continued when his late spot-kick was saved.