Paul Lee Dwyer, 52, is facing several charges of statutory rape as well as indecent liberties with a child.
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According to the arrest warrants, the offenses started in February of 2011 and ended in December of 2015.
The child was 13 years old when the offenses began.
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Dwyer is being held on $5 million bond. If released, he is ordered to stay away from the victim.
In court Monday, the judge told him he faces a maximum sentence of life in prison if convicted.
Dwyer was a graduate of the Air Force Academy and doesn't have much on his criminal record, other than a charge in 2000 for misuse of a government computer.