Allen, who was coming off a course-record 60 Friday, didn't fare as well in Round 2 but managed to hold onto a one-stroke lead at Broken Sound Club.
He finished at 15-under-par 129, one better than Chien Soon Lu (7-under 65) and Scott Dunlap (67).
The low round of the day went to Duffy Waldorf, who jumped into sole possession of fourth place at 13-under with a 9-under 63.
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