A jury has begun deliberating in the trial of two men accused of raping and sexually assaulting a drunk, teenage schoolgirl at a Stuart Flats unit last year.

Jason Dodd, 40, and Kevin O'Rafferty, 42, are facing the ACT Supreme Court for allegedly sexually assaulting the 16-year-old while she slept on the couch of Dodd's unit in May last year.

But the men say the alleged incident never happened.

The girl, who had known Dodd for about two months, had been drinking when she went to his unit with a friend on May 17.

She continued to drink and fell asleep on the couch.

The alleged victim told police she awoke to discover she had been stripped semi-naked and was being sexually assaulted by Dodd, O'Rafferty and a third man, who was never found by police.

She reported the incident the following day.

But Dodd, from the witness box, denied the alleged assault and told the court he believed the allegations were revenge for kicking the two girls out.

He said he had slept on the couch after a night of drinking and was awoken early the next day by the girl's friend who was chatting loudly on her phone.

He became upset and he told her the two girls were no longer welcome in his unit as he had had enough of the way they treated him.

Dodd said he went back to sleep and last saw the alleged victim as she left to pick up ''bumpers'', or cigarettes.

During the trial, jurors also heard from a forensic expert who said samples taken from Dodd's underwear had strongly matched the DNA of the girl.

The witness said that a sample tested was 140 billion times more likely to have come from the alleged victim than from a random person.

But the court heard no DNA evidence was recovered from the girl or her clothing and there was no genetic material to link O'Rafferty to the alleged crime.

The court also heard a medical expert's opinion that the girl's injuries - abrasions and trauma - were consistent with her allegations of a sexual assault.

In final submissions, Crown prosecutor Sara Gul told jurors the evidence added up to one a conclusion, a guilty verdict.

But defence lawyers for the men said the lack of DNA evidence had raised reasonable doubt.

Justice John Nield gave the jurors final directions on Friday before sending them to deliberate.