MANHATTAN — The prime suspect in the brutal rape of a missionary worker at New York University is being held on Rikers Island in connection with several unrelated strong-arm robberies in Manhattan, DNAinfo New York has learned.

DNA evidence taken from a fedora hat that was dropped by the suspect near the Washington Square crime scene matched a homeless ex-con who was arrested more than a week ago in connection with three robberies in Midtown and Chelsea, sources told “On The Inside.”

The suspect, whose name is being withheld, has yet to be charged with the Oct. 31 rape of the 24-year-old Catholic missionary, who recited the “Hail Mary" prayer as she was assaulted and threatened with death.

Authorities want to bring her back to New York from Ohio, where she is recuperating, and give her a chance to identify the suspect in a lineup before formally filing charges against him.

“She is not doing all that well,” a law enforcement source explained.

That lineup could be convened as early as Tuesday by the NYPD and prosecutors from the Manhattan District Attorney’s office, the sources said.

Regardless of its outcome, the ex-con will likely be charged with rape and assault because of the overwhelming evidence already against him — the DNA hit, surveillance footage and other forensic evidence, sources told “On The Inside.”

The rape occurred around 5:30 a.m. as the missionary worker was about to enter the NYU Catholic Center on Washington Square, where she was going to prepare breakfast for the homeless and underprivileged.

"On The Inside” previously reported exclusively that she had been stalked around the park by the suspect, who is in his mid-20s. Police said he then grabbed her and snarled, “I want a piece of you” as he tried to push her to the ground.

She initially tried to fight the man off, but was punched repeatedly in the face and chest until she was overpowered.

Throughout her ordeal, the victim repeated the solemn “Hail Mary” — a cornerstone of Catholic prayer, which is recited over and over again as part of the rosary.

“Hail Mary, full of grace, the Lord is with you. Blessed are you among women," the prayer begins, before ending, "Holy Mary, Mother of God, pray for us sinners, now and at the hour of our death."

When the attack ended, the rapist said, “I should have killed you, too.”

About a week after the assault, investigators obtained a DNA link between the fedora and the ex-con. Detectives launched an intense manhunt in Lower Manhattan of shelters and street corners where homeless people congregate, but came up empty-handed.

Then two men were arrested at the Port Authority roughly two weeks ago for robbery. Police quickly linked the rape suspect to that crime and two other robberies, including a vicious beating in Chelsea where a man was repeatedly punched, kicked and robbed.

As the manhunt continued, the suspect was picked up on an unrelated shoplifting charge. Sex Crimes investigators learned of his arrest and charged him with the three robberies as soon as he was arraigned and freed on bail in the petty shoplifting case.

He is presently being held on Rikers Island in connection with the robbery cases.

The suspect has an extensive record of a dozen arrests, mostly for robbery and assault. None of the previous arrests involved sexual assault. He has served time in state prison.

“He is a bad, bad dude,” a law enforcement sources said. “But this rape could be his first.”