Gardai searching Patrick Quirke's home found a hand written note relating to Mary Lowry and the disappearance of Bobby Ryan, the Central Criminal Court has heard.
Detective John Walsh said he discovered the notes on an A-4 sheet of paper in an office area in Mr Quirke's house during a search in May 2013.
He read from the document: "Mary last one to see him", "body naked, either murdered and clothes taken off or never left the house".
The words "never left the house" were underlined, the witness told Michael Bowman SC for the prosecution.
It also contained questions including: "Why did she find the van so quickly? Why did she look for him in a place where she knew he wouldn't have needed to go? Why didn't she act on leads? Why did she give varying accounts of how long he was in the yard before he left for work? Two minutes? Ten minutes?
Why was she so adamant no activity took place in the yard? How would she hear? It wasn't always possible. Why did she rip down photos of Bobby Ryan after his family put them up? Why was she relieved after Crime Call was a rubbish programme and got no help to jog anyone's memory?"
The note also contained the comment: "V strange."Mr Quirke (50) of Breanshamore, Co Tipperary has pleaded not guilty to the murder of part-time DJ Bobby Ryan. Mr Ryan went missing on June 3, 2011 after leaving his girlfriend Mary Lowry's home at about 6.30am.
His body was found in an underground run-off tank on the farm owned by Ms Lowry and leased by the accused at Fawnagown, Tipperary 22 months later in April 2013.
The prosecution claims Mr Quirke murdered Mr Ryan so he could rekindle an affair with Ms Lowry (52).
Det Walsh further told Mr Bowman that he seized a brown envelope inside which was a document relating to Mr Quirke's lease of Ms Lowry's land at Fawnagowan.
Detective Garda Kieran Keane told Mr Bowman that he is the exhibits officer assigned to the investigation into Mr Ryan's death. Following the search he took possession of a computer, two memory keys, two mobile phones, an iPad, a hard drive from one of the farm houses and a phone bill seized from the kitchen.
Swabs were taken for analysis from a pair of overalls hanging in the boiler house, a cow trailer and a crew cab door.
Det Gda Keane agreed with Lorcan Staines SC for the defence that analyses of the overalls, cow trailer and door provided nothing of evidential value.
Plumber Stephen O'Sullivan said gardai asked him in 2013 to test whether Patrick Quirke was telling the truth when he described how water leaking from a mains pipe flowed from an old dairy farm into the tank where Mr Ryan's body was found.
Mr Quirke told gardai that he opened the tank because he needed water to agitate slurry and believed there would be water in it because of the leak some weeks earlier.
Mr O'Sullivan told David Humphries BL for the prosecution how water running from a leak in the area identified by Mr Quirke would have made its way to that tank and told defence counsel Lorcan Staines SC that what the accused told gardai was the truth.
He further stated that there was evidence that pipes in that area had leaked and were repaired by a handyman rather than a professional plumber, something he said would be common on farms.
While the witness carried out the test in 2013, he told Mr Condon he was called as a witness earlier this year.
Siobhan Phillips is a manager at the Cliff House Hotel in Ardmore, Co Waterford. She told Mr Humphries that a booking was made over the phone for a twin room for September 6, 2011.
She said the booking was taken up and included dinner in the Michelin star restaurant. She said she can't say who stayed there or who had the dinner but the bill, which came to €416.20, was paid by Laser on September 7.
The trial has previously heard that Ms Lowry, who said she couldn't remember staying at the Cliff House Hotel, had a bank record detailing a payment to the Cliff House for more than €400.
Ms Phillips agreed with defence counsel Bernard Condon SC that the booking was for a "top end package", famed for its food, in a stunning location with beautiful views.
Mr Condon added: "I'm not trying to sell it for you but it's pretty well known."
The witness agreed.
She said the booking was made under the name Patrick Quirke with an address at Fawnagowan, Tipperary.
The payment was made using a Laser card which was used in the hotel and would have required a PIN. The witness said she was first approached by gardai to make a statement in January.
Under reexamination Ms Phillips told Mr Humphries she doesn't know who made the phone call to make the reservation but the name given was Patrick Quirke.
She also said that whoever made the booking requested a twin room and although the room in question contained a double and single bed, the guest would not have known that.
Sergeant Debbie Marsh told Mr Bowman she and a team of searchers spent three days emptying the tank where Mr Ryan's body was found and searching through its contents.
It consisted of silt, water and debris and gardai used a soil sieve to examine the contents. Any items gathered were brought to the attention of the scenes of crime officers, she said.
Due to health and safety concerns on the first day her team was ordered out of the tank and the Garda subaqua unit went in.
The trial continues in front of Justice Eileen Creedon and a jury of six men and six women.