Ms Clark said Thomas was placed in a compartment directly behind her.
"Pretty much from the word go he began making sexual comments. He was saying things like calling me a filthy slut ... things similar to that effect. These sort of things carried on for the next 20 or 30 minutes," Ms Clark said.
She said that when they got near Featherston his tone changed and he became frustrated and angry.
"Right after that he said to me, after he gets out, he is going to hunt me down, get a car, and run me over and rape me."
Ms Clark said that once they arrived at the prison she did not deal with Thomas, as she did not feel safe.
Defence lawyer Jock Blathwayt said Ms Clark did not know how many prisoners were in the back and did not know who was talking.
Thomas denied making the comments to Ms Clark.
Judge Bill Hastings said he found Ms Clark's version of the events more credible than Thomas'.