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And Emir Strati punished Well when he struck the winner after 66 minutes.
BBC: Flamurtari 1-0 Motherwell
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Ermir Strati put the Albanians in front in the 66th minute when his 20-yard strike beat Michael Fraser and went in off the post.
BBC: Gannon unhappy over Well penalty
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Having escaped the penalty scare, Flamurtari set about gaining an advantage to take into the second leg and were rewarded when Strati's half-volley from 20 yards found the bottom-left corner of the net.
BBC: Flamurtari 1-0 Motherwell