The uncle of a missing 5-year-old Utah girl has been charged with murder, police announced Wednesday. Logan police chief Gary Jensen said police have evidence including a broken knife, a PVC pipe and bloody clothing linking 21-year-old Alex Whipple to the disappearance of his niece, Elizabeth "Lizzy" Shelley.

The girl's mother reported her missing after the family woke up Saturday morning to find she had vanished from their Logan home along with Whipple, who had been spending the night.

Alex Whipple, left, is charged in the murder of his niece Elizabeth Shelley, right KUTV

Whipple was found alone Saturday afternoon in a remote area about 10 miles from the family home, several hours after the girl was reported missing. He was combative and refused to identify himself several times when police spotted him walking in a remote area, according to court documents.

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Whipple had already been named the prime suspect in the case and was being held in the Cache County Jail without bail on unrelated charges. Wednesday, he was charged with aggravated murder, child kidnapping, two counts of obstruction of justice and abuse or desecration of a human body by the Cache County District Attorney's office.

An emotional Jensen announced the charges, which indicate investigators believe the child is dead, during a Wednesday press conference. Jensen had previously said police had evidence to indicate she was hurt, but didn't want to dash hopes that she would be found alive.

"Even though we haven't found Lizzy, to hear a charge of aggravated murder brings with it a notion of finality," Jensen said. "This is very difficult for the family, I can't imagine, so our hearts go out to them."

Jensen said the majority of the evidence pointing to Whipple in the disappearance was found within a short distance of the home. It includes a knife that matches the brand of knives found in the family's home, one of which was missing from a knife block. He said the knife had blood on it and was broken, indicative of "traumatic use."

Investigators uncovered a PVC pipe with a red substance on it and a palm print in the substance that matches Whipple, Jensen said. They also found a teal skirt with white lace on it, hastily buried under dirt and bark, that had blood on it and matched the description of Lizzy's clothing. And investigators discovered a hooded sweatshirt and watch that belonged to Whipple which had DNA on it that matched the girl, along with a beer can nearby with Whipple's DNA.

Alex Whipple Cache County Sheriff via KUTV

During a police interview, according to court documents obtained by CBS affiliate KUTV, investigators noticed dark stains on Whipple's pants consistent with blood, that his hands were dirty and had several cuts.

Jensen said investigators haven't determined a possible motive. The documents say Whipple didn't admit involvement in the girl's disappearance, but said alcohol made him "black out" and he sometimes does "criminal things" when he blacks out.

Jensen said the district attorney charged Whipple with desecration of human remains based on investigators' belief that he moved, removed or concealed her body. He said investigators have chased down hundreds of tips and scoured the area in their continuing search for the girl, including searching through mulch piles and a landfill.

When asked by a reporter to describe the emotional impact of the case, Jensen said, "You guys feel it. This is a five-year-old girl, and she's still missing, and that's not easy for anybody."

"We want to find her," Jensen said. "We want the family to have what they deserve and that's closure, and/or Lizzy back in their home. That's what we want, and it is hard."