AFC Blackpool and Squires Gate both suffer defeats
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Having trailed by two goals inside half an hour, they had got back on terms before the visitors won it late on.
Maine Walder saw a first-minute effort saved and Liam Birchall hit the post before Runcorn led on eight minutes.
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Hide AdOlly Wright’s through ball found Macauley Clifton, who was able to fire past AFC keeper Dan Hall.
They doubled that advantage on 28 minutes as Liam Kennington played a one-two with Clifton before crossing for Neil Weaver to score.
AFC’s Joe Robinson missed a great chance before they pulled one back with half-time four minutes away.
The visiting defence failed to clear Brendan O’Brien’s pass and Birchall was the beneficiary, netting to make it 2-1 at half-time.
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Hide AdBen Duffield was denied just before the hour, only for Birchall to level matters on 70 minutes; reacting quickest after Duffield’s shot was deflected.
With a draw looming, Runcorn scored the winner on 84 minutes as Lewis Williams slotted home from Charlie Holland’s pass.
AFC have a quick chance to bounce back as they host Steeton in the NWCFL First Division North on Tuesday (8pm).
There was also disappointment for Squires Gate, who exited the Macron Cup with a 2-0 loss at FC St Helens in their quarter-final tie.
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Hide AdThomas Scarborough put the hosts in front just before the half-hour.
Liam Houghton completed the scoring on the hour mark when netting from the spot.
Gate also have a return to league matters on Tuesday with a trip to Ashton Athletic in the NWCFL Premier Division (7.45pm).