Traces of April Jones' DNA were found "inside the front crotch area" of Mark Bridger's tracksuit bottoms, a court has been told.
Bridger, 47, is accused of murdering the five-year-old after he abducted her as she played outside her home in Machynlleth, mid-Wales, on October 1 last year.
The jury at Mold Crown Court heard Bridger had "tried to explain away potentially damaging evidence" as he gave an excuse to police, shortly after his arrest, if they were to find April's DNA on his penis.
Prosecutor Elwen Evans QC said Bridger told officers that "if there was any of April's DNA on his penis it might be there because he had been for a wee while carrying her".
Miss Evans then told the jury: "This is a man, we say, who is forensically aware. He knew how important it was from his point of view to try and get rid of any forensic scientific evidence linking him to April."
Miss Evans told the court that no DNA evidence was found in a swab taken from the defendant's penis.
She added that traces of April's DNA were in fact found "inside the front crotch area" of Bridger's tracksuit bottoms.
The defendant, who claimed to have served in the SAS but was an abattoir worker, accepts he "probably killed" April in a car accident, but will say he "blanked out" afterwards and cannot remember what he did with her body.
The court heard that three witnesses saw Bridger carrying a black bin bag in a field near his home the morning after April's disappearance.
Miss Evans said: "We ask you, what was Mark Bridger doing at that location? What was in that black bin bag?"
The court heard that the land around that area was excavated but no trace of April was found.
Bridger later claimed that he was in the field because he had to stop to "go for a wee".
But Miss Evans said Bridger made up this story because he "needed to explain away a potentially suspicious sighting".
The jury also heard how Bridger went to his daughter's school at 5.20pm on the day April disappeared for a parents evening and stayed for around 20 minutes.
"Shortly after leaving the school in his vehicle, he approached a couple of girls who were playing in the local area," Miss Evans went on.
She said the girls were aged eight and 10 and were riding their bicycles on the Bryn y Gog estate.
"He wound the window down and there was a discussion during which the defendant invited one of the girls to a sleepover with his daughter," Miss Evans told the jury.
"She declined and he drove off."
The next witness to see Bridger told police she saw the defendant's car pull up next to garages on the estate.
Miss Evans said: "April was seen playing nearby.
"The timing of this sighting of the defendant indicates that the events surrounding the abduction, as we say it was, happened quickly."
Ten minutes later the Land Rover Discovery was seen by another witness driving past Tuffin's petrol station and then on CCTV heading out of the estate.
Miss Evans said: "It is obvious that the defendant had driven out of town before the 999 call was made.
"Where did he go? Where did he take April?
"Of course, he says he doesn't know."
The next time his Land Rover was seen was at 8.30pm when a witness told police she saw it being reversed into his driveway.
Earlier the court was told how Mark Bridger had looked at child porn just hours before April Jones went missing, and had pictures of local young girls stored on his laptop.