And Magistrate Judge Lewis Blanton also wrote that he considered information that was presented at last week's detention hearing about Waller's alleged involvement in the disappearance of his wife, Jacque.
"I find that the credible testimony and information submitted at the hearing establishes by clear and convincing evidence that the release of the defendant would constitute a danger to the community," Blanton wrote. "The court further finds by a preponderance of the evidence that the release of the defendant on bond would present a risk of nonappearance."
Waller faces up to five years in prison and up to a $250,000 fine for a charge of transmitting in interstate commerce a threat to injure. Federal prosecutors say that Waller threatened to kill his wife's sister, Cheryl Brenneke, if she hurt his three children. The threat is said to have taken place on an online discussion board.
Pretrial motions are scheduled to be heard in U.S. District Court at 11 a.m. Sept. 29.
Jacque Waller disappeared from a Jackson home June 1, and authorities have investigated her husband in connection with the disappearance. Waller has not been charged in his wife's case.
Federal prosecutor Larry Ferrell declined to comment Thursday, and Waller's federal public defender, Scott Tilsen, was unavailable.
Jacque Waller's family, however, was delighted to hear the news. Her father, Stan Rawson, and her sister, Cheryl Brenneke, in separate interviews each said they were pleased that Clay will be behind bars pending a trial.
"He's done killed one of my daughters," Rawson said. "So I'm thrilled to death for anything that keeps him in jail. There's no doubt in my mind that he's capable of doing what he said."
For her part, Brenneke -- who has temporary custody of Clay and Jacque Waller's 5-year-old triplets -- said she was relieved Clay Waller would remain in the custody of U.S. marshals, who are holding him at the Pemiscot County Jail.
Brenneke alerted law enforcement about a death threat made against her on the online discussion board Topix.
"If my sister hadn't disappeared, I might not have taken him seriously," Brenneke said. "Since I know what he's done -- yeah, I took it very seriously."
The judge's four-page ruling says "the evidence is strong" that Waller committed the federal charge, though he stresses repeatedly that Waller maintains a presumption of innocence.
Blanton also discussed the link prosecutors made between the death threat against Brenneke and the possibility that Waller was involved with his wife's disappearance.
There are many statements of fact presented in the an FBI affidavit that "point to the involvement of James Clay Waller in that disappearance," Blanton wrote.
During the detention hearing Friday and Monday, Blanton heard about removed carpet and padding that was found in a basement crawl space that had Jacque Waller's blood on it. Clay Waller's father also told an FBI special agent that Clay admitted to him that he killed his wife and buried her in a hole that he dug with a shovel.
During the hearing, however, Clay Waller's public defender questioned the mental state of Waller's 71-year-old father. Ferrell did not submit a deposition of Waller's father, but that still could happen at trial.
Meanwhile, Clay Waller still faces state charges for stealing and harassment. A preliminary hearing on those charges is scheduled for Sept. 27, but that may not happen. Typically, when a defendant is taken into federal custody, state charges are put on hold, said Cape Girardeau County assistant prosecuting attorney Angel Woodruff. Woodruff is the prosecutor for Waller's state charges and was the first person to publicly call Waller a suspect in Jacque's disappearance.
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