A forensic sample that has a 100 per cent match to Madeleine McCann has been discovered in the car hired by her parents five weeks after she disappeared, it was reported last night.

Portuguese detectives are said to believe the findings, reported on Sky News, are evidence that Kate and Gerry McCann had carried the child’s body in the car.

Samples sent to the Birmingham-based Forensic Science Service have been analysed and the results sent to the investigating officers. While the exact nature of the material remains unclear, it is believed to be either blood or biological fluid from Madeleine. A source linked to the investigation said: “It shows that the parents have a lot of explaining to do.”

Another sample is believed to show an 80 per cent match to the genetic profile of Madeleine, who vanished from the Algarve resort just a few days before her fourth birthday. Both samples were found under upholstery in the boot of the Renault Scenic after police seized the vehicle last month.

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It was claimed that the sample could not simply have been transferred from clothing or a cuddly toy. But it remained unclear exactly what material the DNA had been retrieved from. If it was a hair or flakes of skin - the most easily transferrable form of material that yields DNA - it would not have a dramatic impact on the investigation.

However, if it was blood, one of the most easily degradable forms of DNA, or internal fluids associated with a body, it would be a breakthrough.

Technicians from the Portuguese forensic science laboratory who reportedly obtained the material from the car had expected to find a large quantity of samples linked to Madeleine because the vehicle had been used to carry all of the child’s belongings, including toys and clothing, when the family moved from the Ocean Club where she disappeared to a rented villa on the outskirts of Praia da Luz.

The two important samples were accompanied with one partial match found on the windowsill of the apartment where the McCanns had initially stayed. Traces of Madeleine’s blood were found on the floor of the apartment but another sample found on the wall was thought to have come from a male, but was too degraded to secure an exact match.

The Portuguese prosecutor, who will decide whether to charge the McCanns with killing their daughter, will today be handed a mass of police files about the case. Joao Cunha de Magalhães e Menezes, the district attorney in the Algarve, was handed accounts of the DNA and forensic evidence. The bundle also contained transcripts of the couple’s lengthy police interviews, said to include some 40 questions that they refused to answer.

The files are also believed to include details from intercepted e-mails and tapped phone calls between the McCanns and friends. The public prosecutor is also expected to approve new searches of key locations in an attempt to try to find the girl’s body.

Leicestershire police are now expected to play a more active role in the inquiry and senior officers may be called upon by their Portuguese counterparts to questions the parents.

Mrs McCann was said to have said that claims that minute bloodstains in the apartment where Madeleine stayed could have got there if she had a graze or cut or even a nosebleed.

She dismissed the suggestion that there was the scent of death on some of her clothes and the child’s soft toy by saying that any such smell found by sniffer dogs was a result of her job as a local GP where she encountered corpses, it was reported.

Police are still trying to establish whether the child died after being hit or pushed by a parent. Another theory is that she overdosed on adult medicine which had been left within her reach or that she died from oversedation. They have not ruled out the possibility that someone helped the couple to dispose of the body. Newspaper reports in Portugal claimed the public prosecutor in Portimao had considered charging the couple, both 39, before they flew back to Britain on Sunday.

But the Attorney-General, Pinto Monteiro, travelled from Lisbon to Portimao for a private meeting with the McCanns’ lawyer, Carlos Pinto de Abreu. Portuguese newspapers said some form of “deal” was struck.

Detectives were said to be livid that the meeting had meant the move towards arrests and a court hearing to establish bail conditions was abandoned. They also felt that the McCanns’ decision to leave frustrated the investigation.

New searches were due to be carried out on “specific locations” south of the Ocean Club where Madeleine disappeared from her apartment. The police would focus on an area of wasteland and a street where roadworks were being carried out. Officers are also expected to search the villa they left on Sunday.

The couple were allowed to return because they gave police their home address in Rothley, Leicestershire. They must inform police if they plan to leave home for more than five days. They can remain formal suspects without charge for eight months before investigating officers have to approach a judge to apply for an extension.

Reliability of evidence rests on size of sample

What is the DNA evidence that has supposedly been found by the Portuguese investigators?
Newspapers in Portugal have been reporting that “biological fluids” with an 80 per cent match to Madeleine’s DNA have been found underneath upholstery in the boot of the McCanns’ rented Renault Scenic. Sky News claimed last night that another DNA sample with a 100 per cent match to that of Madeleine’s profile had been found in the car.

What would this tell us?
Perhaps nothing. If it was sourced from something such as a hair follicle or skin cells then that could have been one of Madeleine’s hairs that had stuck to the clothes of a family member or her “cuddle cat” toy that her mother carries. If it was from Madeleine’s blood or corpse, that could be more significant. The most important issue is the size of the sample found. If there was a substantial amount of material it is unlikely to be from accidental contamination and would indicate that Madeleine had been in the car.

Can investigators establish if the DNA sample comes from someone who was alive or dead?
Unlikely, according to British experts. A DNA profile does not change just because someone dies. You can tell if DNA has degraded but that can happen if, for example, it had been exposed to sunshine.

Does an 80 per cent match with biological fluids indicate that Madeleine was definitely in the car?
No. The sample will have been tested against a definite sample of Madeleine’s. A 80 per cent match indicates that profilers could find only 16 of the 20 markers usually used for such analysis and suggests that the biological traces are tiny and degraded. Additionally, the twins Sean and Amelie could share a high percentage of DNA characteristics as most siblings do.

What complicates the matter further is that all three of the McCanns’ children were born through IVF and it is unknown whether the couple’s sperm and eggs were used for conception.

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