The younger girl, now 21-year-old, told a jury neither she nor her 24-year-old sister had told anyone what they allegedly suffered at William Russell’s hands 15 years ago.
It was only when they had a long talk about the “nightmares” each of them was experiencing last year that they realised both had had similar experiences, she said.
Russell (35), from Brightons, is charged with raping the older sister between April 2003 and April 2005 at the family home in a Stirlingshire village.
He is also charged with using lewd, indecent and libidinous practices towards her and her younger sister, who was aged between 11 and 12 when she was allegedly abused.
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Russell denies the charges and is standing trial by jury at the High Court in Livingston.
Giving evidence in his own defence he claimed he had only babysat for the girls on one occasion – when he had sex with their mum’s niece on a bouncy castle in their living room.
The older sister gave evidence on Friday that Russell raped her when she was nine-years-old.
The younger sister, giving evidence from behind a screen yesterday (Monday), said Russell had moved in with her family briefly around 2004.
She said she was “confused” about the way the accused had treated her as a child.
She said: “I vaguely remember, I was in the junk room. We were meant to be playing hide and seek with William, my sister and me.
“I was in the toy room counting, and once I finished counting he was standing in front of me with his penis in his hand. I was scared.
“He was touching it... just stroking it while he was looking at me. He was about a metre or so in front. He was wearing his clothes.
“When I was younger I didn’t think anything of it but as I got older I realised it wasn’t right, exposing himself to a young child.”
She agreed with the prosecution’s suggestion that the accused had been masturbating but said she didn’t understand at the time what that was.
She added: “I remember he tried to get me to touch it. He tried to force my hand.
“He grabbed my hand and put it on his penis. I started crying. I wanted to run away.”
Through tears she went on: “I stroked his penis, not (for) very long. I ran out of the room screaming.
“I remember I went to my sister who gave me a cuddle and told me everything would be all right because mum would be home soon.”
On a second occasion, she said she was asleep on the living room couch when she was wakened by Russell pulling her off the couch and onto a mattress on the floor.
She recalled: “He was touching me over my clothes mainly on my arms and my legs, on the top of my thigh on the outside. I was frightened.
“I fell back asleep. I was in my pyjamas. I think they were owls because they were my favourite.
“I woke up wearing just my vest and my pants. I couldn’t find my pyjamas anywhere.”
She said she didn’t tell her mum at the time because she didn’t want to upset her.
She admitted she and her sister didn’t see a lot of their mother and had a “distant” relationship with her.
She told the jury: “She was working a lot of hours to make up for the money my dad took when he left. She had a crazy lifestyle, smoking weed.”
She continued to keep the alleged incidents to herself until last year when she confided in her sister during a lengthy phone call while she was travelling back to Glasgow on the bus.
She told the jury: “She was talking to me about the nightmares and I told her that I thought it was a nightmare what happened with William.
“She opened up and told me it had happened to her too. I told her about the night in the toy room and the night in the living room.
She said her sister had told her about a Facebook Messenger exchange she had had with the accused during the same phone call.
She said: “She sent me a screenshot of messages that she sent back to William.
“I told my husband the same night. I never went into detail.”
She said she and her sister agreed we wanted to go and report the allegations to the police together, but her husband jumped in and did it when she was at work.
She said: “He did it without my knowledge. I was very annoyed. He said he’d gone to the police and they’d be contacting me when I was at work.”
She finally gave police a statement on March 24, 2017 accusing Russell of sexually abusing her.
Under cross-examination by defence counsel Drew McKenzie she admitted that she might have put the two incidents in the wrong order.
She said she might have thought it was just a dream if Russell had put her pyjamas back on.
She said she did not remember if the accused had called it their “little secret”, as he allegedly did with her sister, or if he had bribed her with sweets to keep quiet.
The girls’ 48-year-old mum said her family had been friends with Russell’s family. She said her ex husband had taken the accused “under his wing”.
She said Russell had acted as a babysitter for all four of her children and slept in her living room “on and off” from the age of around 16 upwards.
She said the accused was in his early 20s when her older daughter turned nine years old. She denied smoking cannabis but admitted taking anti-depressants on prescription for several years.
Russell claimed in his own defence, that the two complainers and their mum were “lying” that he had acted as their babysitter and lying about being sexually abused by him.
Mr McKenzie said to him: “You’re in the High Court facing serious allegations. Is there any truth in these allegations?”
Russell replied: “No. None whatsoever.”
He told the jury: “They’re lying. How many times did they trip themselves up?”
He even claimed that as a teenager she had sent him photographs of herself standing in her bra and underwear.
He added: “I knew that she must have obviously fancied me if she sent me the photos.”
The trial, before Lord Burns, continues.