On the day Annie Le disappeared, Raymond Clark III reported seeing the Yale University graduate student leave the Yale Animal Research Center carrying a notebook and two bags of mouse food.

But police said she never left the building.

In the days after Le was reported missing on Sept. 8 and before the Sept. 13 discovery of her body, found stuffed into a wall of the research center, police looked closely at Clark. An arrest warrant affidavit released Friday charging Clark with killing Le accuses Clark of trying to cover his tracks by cleaning up the crime scene and hiding potential evidence.

Superior Court Judge Roland D. Fasano last week ordered the arrest warrant affidavit released. The 13-page document reveals what led police to Clark: security key cards that showed the movements of both Clark and Le on Sept. 8, scratches on Clark's body, Clark's apparent attempts to clean up the crime scene and ultimately the discovery of both his and Le's DNA on a green-ink pen and socks found at the scene.

The affidavit does not offer a motive for the strangulation, but sources familiar with the investigation have told The Courant that the crime stemmed from a work dispute between Clark and Le.

Only a small portion of the affidavit - about six lines - is redacted. That information appears to be about the discovery of Le's body.

The affidavit details the movements of Le and Clark on the day police believe Le was killed.

Le, 24, a third-year doctoral student in pharmacology from Placerville, Calif., swiped her key card at 10:11 a.m. in a lab room, G13, at the Yale Animal Research Center on Sept. 8. Clark, a 24-year-old lab technician from Middletown who tended the animals at the research center, wasn't far behind Le, reporting for work at the center 29 minutes later that day, according to the affidavit.

At 11:04 a.m., Clark, wearing blue jeans, white shoes and a dark-colored jacket with white stripes, entered the lab where Le was working and remained there for 46 minutes. He signed in as "RC," using a green-ink pen, the document states.

Clark was busy at the lab that day, according to key-card activity that shows a person's movement in, out and throughout the center, a state-of-the-art secure building that is part of the Yale School of Medicine complex.

From 10:40 a.m. that morning until 3:45 p.m., Clark went in and out of the lab room where Le was working and another room, G22, down the hall 55 times, according to the documents.

When he left the building that day, Clark was seen wearing different clothes from the ones he entered wearing.

Le, however, was never heard from again.

By 11 p.m. Sept. 8, police were already wondering what happened to Le, who was looking forward to marrying her college sweetheart that Sunday in a lavish Long Island wedding.

Le's roommate, Natalie Powers, who shared an apartment with Le in the city's East Rock neighborhood, called police when Le failed to return home the evening of Sept. 8.

During an interview with Powers at her Lawrence Street apartment, Yale University police learned Le never called Powers that day, which was "very unusual" for her roommate and friend.

By all accounts from Le's family and friends, the friendly and smart 24-year-old was excited about her upcoming wedding. Rumors about her being a runaway bride soon turned into concern about Le's safety.

New Haven police, state police, and the FBI joined the search for Le. Immediately, they turned to the research center and the building's electronic video surveillance. It showed Le entering the research center at 10 Amistad St. at 10:09 a.m. Le's electronic key card log for that day showed her card was used to get into the lab at 10:11 a.m.

When both Le's key card and video surveillance cameras - which are posted in all of the building's exits, according to the FBI - showed that Le never left the building, investigators began an all-out search inside the research center, interviewing Le's co-workers and other employees who may have seen Le.