The Ulsterman is 7 under after a 66 while Shane Lowry is 2 under.
Hideki Matsuyama leads by 3 shots on 13 under after a 65.
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McIlroy says he putted better today than yesterday.
Meanwhile, Seamus Power is among the leaders heading into the second round of the Sanderson Farms Championship.
The Waterford man is 7 under which is just 2 behind leader Kevin Streelman.
