Dispute over DNA, alleged weapon

The knife: The prosecution in 2009 said that a knife found in Raffaele Sollecito's house has the DNA of Amanda Knox on the handle and the DNA of victim Meredith Kercher on the blade, suggesting it's the murder weapon. The defense said the knife doesn't match the shape and size of wounds on Kercher's body or an outline of the knife left on her bed. The defense also presented experts who said DNA on the blade was too small to be definitive.

DNA on Kercher's bra clasp: The prosecution said that a bra clasp that was ripped from Kercher's bra and found on the floor of her room has Sollecito's DNA on it, proving he was in the room when she was killed. The defense said the bra clasp is contaminated and essentially tainted evidence because it was moved around the crime scene and left there for more than six weeks before it was picked up as evidence.

Knox's confession: The prosecution said that during her interrogation, Knox said she could hear Kercher screaming. She also pointed the finger early on at Patrick Lumumba, who was eventually released. The prosecution said Knox's false statement proves she is lying and was at the home when Kercher was killed. The defense said that Knox's statements were made when she was asked to imagine what would have happened that night in her apartment. The defense said Knox pointed the finger at Lumumba because she was confused and pressured. Eventually, the confession was thrown out because Knox was not questioned with a lawyer present.

Bloody footprint on bathroom rug: The prosecution attributed a bloody footprint on a rug in the bathroom to Sollecito, which they said proves he was there at the time of the murder. The defense, in this instance Sollecito's lawyers, presented forensic experts who said the print was in no way a match to Sollecito, but instead a match to Rudy Guede, a man from the Ivory Coast who was convicted in a separate trial for murdering Kercher. The defense focused on Sollecito's hammer toe, which they said wouldn't leave an imprint like the print found on the mat.

The window: The prosecution said a broken window in the home Knox shared with Kercher was an attempt by the American to stage a break-in as a cover for the murder. The prosecution said it would be impossible for someone to break the window and climb through the window as proposed by the defense. The defense said the window was broken by Guede, a known drifter who had broken into homes before. Defense expert Francesco Pasquali simulated how glass would break if a rock were thrown from the outside. His testimony included that he believes a burglar could have thrown a rock that way.

Allegations of crime scene contamination: The defense argued that several pieces of key DNA were contaminated at the scene. Crime scene video shows investigators sometimes not wearing gloves or hair coverings, prodding their fingers in Kercher's wounds, leaving key pieces of evidence at the scene for weeks and moving them around, and at one point breaking a window for no reason. The prosecution argued that all the evidence was indeed properly handled and that it isn't their job to prove the crime scene work was good enough. Instead, they said, that's the job of the defense.

Bloody shoe print in Kercher's room: The prosecution said the bloody shoe print found next to Kercher's body belonged to Sollecito and placed him in Kercher's room when she was murdered. The defense said that after Guede was found to have a shoe box for shoes matching the print, they argued for a re-examination of the print. Francesco Vinci, a coroner and forensic specialist for Sollecito, testified he believes it was wrongly attributed to Sollecito and belongs to Guede.

• Italian court convicted Amanda Knox and Raffaele Sollecito of murder -- again


• The two were convicted in 2009 and acquitted on appeal in 2011


• Opposing sides argues over what is revealed by alleged murder weapon, DNA evidence

Editor's note: This is an edited version of a story first published in November 2009 during the first murder trial of Amanda Knox and Rafaelle Sollecito looking at the disputed evidence in the case, which has largely remained the same.

(CNN) -- Within weeks of British student Meredith Kercher's death in the vibrant college town of Perugia, Italy, in 2007, prosecutors and police declared the case closed.

They'd seized two knives in their search for the murder weapon. They took DNA from the room where Kercher was killed. And at least one suspect had confessed to being at the murder scene. Or so they said.

Kercher had been stabbed in a sexual misadventure, officials said. And they knew the killers.

American Amanda Knox, Kercher's roommate; Italian Raffaele Sollecito, Knox's former boyfriend; and Ivory Coast native Rudy Guede, a drifter known in the area, had their pictures splattered across the world's media.

Knox's photo was even hung in the police plaza alongside Italy's most infamous mobsters and criminals.

The prosecution case seemed a sensational slam-dunk, almost too good to be true.

Knox's supporters say that's because it is.

"In the beginning, all of this supposed evidence was being leaked, showing what sounded like a pretty convincing case," Anne Bremner, a lawyer and former prosecutor working with the group Friends of Amanda, told CNN.

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The case couldn't look more different depending on where you stand.

That is as true now, following Knox and Sollecito's second conviction Thursday, as it was during the first trial that ended in two convictions in 2009 and the appeal in 2011 that acquitted them based on "lack of evidence."

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Italy's Supreme Court decided in 2013 to retry the case, saying the jury that acquitted Knox and Sollecito didn't consider all the evidence, and that discrepancies in testimony needed to be answered.

On Thursday the acquittals were overturned, and Knox, who remains at her home in Seattle, was sentenced in absentia to 28½ years in prison. Sollecito was sentenced to 25 years.

Knox vowed Friday to fight her conviction "until the very end" and said she "will never go willingly" back to Italy. Her lawyers say they will appeal the ruling.

Speaking on ABC's "Good Morning America," Knox said news of the guilty verdict Thursday "really has hit me like a train."

Amanda Knox: I'm going to fight this

Guilty...once again

Knox conviction raises new questions

"I did not expect this to happen. I really expected so much better from the Italian justice system," she said. "They found me innocent before. How can they say that it's guilt beyond a reasonable doubt?

Italian authorities on Friday stopped Sollecito near the border with Austria and Slovenia, Italian police told CNN.

Sollecito, who is not allowed to leave Italy while the legal process continues, was halted in the northern Italian town of Udine, police said. Sollecito's lawyer told CNN his client never intended to flee the country, but he was driving with his girlfriend to her house in Udine, when they were forced to stop due to snow.

Same evidence, two very different conclusions

The case has always been about the evidence. But how you view the evidence, simply depends on what side you believe. It all comes down to disputed DNA.

In Knox's corner: her friends and family from Seattle, Washington.

For them, she is the victim -- railroaded by an overzealous Italian prosecutor, whose credibility was marred by allegations of prosecutorial misconduct in another case.

Knox's supporters say he's tried to force the evidence to fit his theory of what happened. And with negative and often false details about the case appearing in the press -- all for the world to read -- Knox supporters feared she would be convicted regardless of the facts.

On the other side: Perugia's prosecutor Giuliano Mignini. For him and his colleagues, the answer is simple -- Guede, Knox and Sollecito are all responsible for leaving Kercher partially clothed, strangled and with her throat cut on November 2, 2007.

Timeline: Murder to now

And the two sides still couldn't be further apart on how they view the very evidence that has over the course of nearly seven years both been used to find her guilty and to overturn that ruling.

Independent experts testified during the in 2011 appeal that they believed some of the evidence had been contaminated.

The testimony fueled the fire that started during the first trial about the effectiveness of Italy's justice system given widespread doubts over the handling of the investigation and key pieces of evidence.

But Italian prosecutors, police and those who collected the evidence maintain those arguments are nothing more than last-ditch efforts by a pair guilty of murdering Kercher in cold blood.

And the second conviction shows the Italian court, this time, believes the prosecution. But questions about the specific pieces evidence that led to two convictions and one acquittal still continue.

The murder weapon: The knife

The crime scene was gruesome. The 21-year old British student was found under a duvet on the floor by her bed, covered in blood. A bloody handprint was streaked on the wall above her.

A source close to the prosecution says Kercher was held down while she was strangled and stabbed. The source says Sollecito's 6 ½-inch kitchen knife was used to slit her throat and then taken back to his apartment.

Knox's DNA is on the handle and that of Kercher is on the blade, said a source close to the prosecution who did not wish to be identified discussing an ongoing case.

Kercher had never been to Sollecito's apartment and wouldn't have come in contact with the knife, he said, yet there was her DNA. Those "unmistakable facts" show the knife played a role in the murder, the source said.

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Bremner and experts testifying for the defense say there is no way that specific knife could be the murder weapon.

Dr. Carlo Torre, a leading forensics expert in Italy, testified that the knife taken from Sollecito's apartment wouldn't have made the wounds on Kercher's body.

"It doesn't match the size or shape [of the wounds,]" Bremner told CNN. "And Sollecito's knife also doesn't match a bloody outline of a knife left on the bedding."

Bremner, who offered her legal advice pro bono to the Knox family, questioned the validity of the DNA evidence, saying the knife had been "improperly transported in a shoe box."

Furthermore, Bremner said the jury heard from defense expert Sarah Gino, a geneticist and private coroner in Italy, who said that the DNA sample was too small to be definitive. Bremner said the presence of Knox's DNA on the knife handle was no surprise, as the couple had dinner at his house occasionally.

Prosecutors have maintained just because the knife doesn't match everything doesn't mean it wasn't used. The source close to the prosecution said it was possible, based on the wounds, that several different items made them.

Damning DNA or 'Fellini Forensics'

On the night Kercher was killed, Knox and her boyfriend say they were at his house watching a movie and smoking hashish.

Their recollection of events, they admitted, was hazy from the drugs, but both swore they went back to the house the next morning. Knox says she was unable to gain entry - and called police.

For their case, prosecutors had to prove that Knox and Sollecito - who had recently started dating - were lying and place them at the home when Kercher was killed.

Some reports spoke of a scurry of people - more than one - on the night of the murder around the house. It was a positive lead for prosecutor Mignini - but came to nothing in court.

But the prosecution had more evidence in the form of a bra clasp, one that fell to the floor after the murderer cut Kercher's bra in half before she was killed.

And on it was Sollecito's DNA.

Bremner says that evidence on the clasp is fundamentally flawed, like much from the crime scene collection, calling the work "Fellini forensics."

"In the [crime scene] video, you can see it went from being white in color to nearly black because it got so dirty being moved around," Bremner said of the clasp, noting that tainted the only evidence that placed Sollecito at the scene.

Bremner described other errors she saw on the crime scene video.

"They were putting their fingers in Kercher's wound, they were shaking out evidence, picking up hairs and dropping them," she said. "Some people didn't wear gloves or had their hair draping on the floor, they crashed into a window at one point and threw aside evidence. It was just wrong on all levels."

The prosecution source maintains the crime scene was handled properly, and the evidence shows what it shows.

A big win for Italy or the 'greatest travesty' ever?

Knox's introduction to the world came in a whirlwind of tabloid headlines.

The prosecution touted hard evidence early that they said unquestionably showed they had their killers.

There was a footprint in Knox and Kercher's bathroom that was attributed to Sollecito - though later analysts admitted it belonged to Guede, who was convicted of Kercher's murder in 2008.

The prosecution also presented what they called a confession by Knox, but Knox later said any apparent admission she was at the scene was made when investigators told her to imagine what she might have seen if she had been there.

The argument became moot when a higher court ruled the alleged confession could not be used because the statement was made without an attorney or translator present.

The tabloid headlines continue as Knox's third ruling was handed down and she was convicted for a second time.

Media around the world focused early on Knox's sexual history, what clothes she wears to court and whether a bump on her lip means the girl they dubbed "Foxy Knoxy" has herpes.

From then on it has all been distraction from the lack of evidence, Bremner said.

"It's the greatest travesty of a prosecution ever," Bremner said. "It's so ludicrous. You've got to have a theory, or a motive, but the theory has to fit the facts somehow. And in this case, there's no solid evidence, no motive and no match whatsoever."

Knox's supporters maintain that the prosecution did get one thing right - putting Guede behind bars. He chose a fast-track trial, separate from Sollecito and Knox, and was convicted of murder and attempted sexual assault and sentenced to 30 years. They believe he was Kercher's sole killer. He appealed the verdict, which was upheld, but his sentence was reduced to 16 years.

Supporters of Knox and Sollecito say they are only being prosecuted because the pair was flaunted so publicly as the killers for so long that it would look bad for officials to admit they got it wrong.

The prosecution source rejects that, and portrays Knox, Sollecito and Guede as three people who together ended the life of the young British woman. And they say the way Knox originally pointed the finger at another man - who was cleared with an alibi - shows she had something to hide.

Both sides agree the truth is in the evidence; the question is which truth reveals what really happened the night Kercher died. And the truth may be, we'll never know.