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Forensic scientist Stuart Bailey said DNA found on Alesha MacPhail’s neck, private parts, shorts and vest is more than one billion times more likely to be from the accused than someone unrelated to him.
Giving evidence at the High Court in Glasgow, he said DNA traces which could be from the accused were also found on Alesha’s thighs, wrists, right hand, ankles, face, underarms and areas of bruising, as well as her pants.
This could be explained by the 16-year-old coming into contact with these areas of her body and clothes.
Mr Bailey said semen from the accused was found inside Alesha.
He said an explanation for this was intercourse but the defence suggestion that the accused’s semen was “planted” there was scientifically possible.
Questioned if the accused’s DNA could have been found on Alesha though secondary transfer from a third party, Mr Bailey said: “I can’t rule it out but I find it highly unlikely given the amount of DNA attributed to [the accused].”
The schoolgirl had been staying in the house her father shared with her grandparents on the Isle of Bute when she was reported missing shortly after 6am on July 2 last year.
Her body was found hours later in a wooded area on the island.
The 16-year-old, who cannot be named for legal reasons, denies abducting, raping and murdering Alesha, and attempting to hide evidence.
He has lodged a special defence of incrimination, blaming Toni McLachlan - the girlfriend of Alesha’s father Robert MacPhail - for the killing.
The trial, before judge Lord Matthews, continues.