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After a first-half low on quality, the Mariners struck first when Charles Vernam put them ahead with a header eight minutes after the break.
And the points were sealed when Luke Waterfall headed home from a corner, to the delight of the 2,000-plus travelling supporters.
From then, Scunthorpe rarely threatened and after substitute Levi Sutton was sent off having played just four minutes, Town closed out a deserved victory over their local rivals.
United: Watson, Butler, van Veen, Perch, Gabriel, Butroid, Gilliead, McArdle, Miller, Bedeau, McAtee
Subs: Lawlor, Songo’o, Sutton, Green, Rowe, Pugh, Liddle.
McKeown (c), Hendrie, Waterfall, Davis, Glennon, Hewitt, Grandin, Whitehouse, Wright, Clarke, Vernam.
Subs: Russell, Davies, Pollock, Tilley, Clifton, Benson, Green.
Referee: Anthony Backhouse