US President Barack Obama sent Afghan President Hamid Karzai a letter of apology over the burning of copies of the Koran at a US military base, Karzai's office said Thursday. Obama said the incident was not intentional and pledged a full investigation, a statement from the president's office said.            At least five people have been killed in violence across Afghanistan after the burning of a Koran at a US base. Crowds shouting "death to Obama" have been throwing stones and setting fire to the US flag. Meanwhile the Taliban has called on Afghans to kill and beat all Westerners in revenge for "insulting" the Koran. In a statement a Taliban spokesman said Afghans should "not stop at protesting" but instead target military bases and personnel to "teach them a lesson that they will never again dare to insult the Holy Koran". On Wednesday seven people were killed and dozens left injured in protests over the burning.  Karzai is meeting tribal leaders and politicians in an effort to find ways to calm tensions. Afghan security officials fear the protests could spread further, with social pressure in other towns and cities to show their outrage at the desecration of the Koran. Obama effigy burnt Emergency talks are being held in the capital Kabul to plan how to protect the city. The BBC reported that many officials sympathise with the outrage the US has provoked across the country.  Police and tribal elders have told the BBC there have been major protests in at least nine areas across the country, each involving many hundreds of people. In northern Baghlan province one civilian was killed and two others were injured, while two police were also hurt. Another person was killed in Laghman province east of Kabul, where local police said several hundred people were chanting "Death to America". In the eastern province of Nangarhar, at least one protester was killed and another injured, a doctor at a hospital there told the BBC. Officials say crowds tried to storm a Nato base in the province and US and Afghan soldiers opened fire. Further south, in Uruzgan province, two people were killed and at least eight others wounded, three of them police, in clashes between protesters and Afghan security forces, local officials told the BBC. In Mehterlam, the capital of Laghman province in the east, more than 3,000 have gathered, with some burning an effigy of Barack Obama. Police say fights broke out as they stopped hundreds of protesters entering the centre of the capital Kabul. And in Asadabad, around 1,500 demonstrators were said to be burning US flags and tyres and shouting anti-American slogans. Earlier President Hamid Karzai called on Afghans "not to resort to violence" in their protests. "Afghan security forces should not use violence... and protect civilian lives and property," Mr Karzai added in a statement. In a statement after an emergency debate, Afghan MPs condemned what had happened. They also called for punishment of those responsible and asked the Afghan government to send its own delegation to Bagram to establish exactly what happened and why. Isaf investigation US Defence Secretary Leon Panetta said he and the top commander of US and Nato forces in Afghanistan, Gen John Allen, had apologised to the Afghan people "and disapprove of such conduct in the strongest possible terms". Muslims consider the Koran the literal word of God and treat each book with deep reverence. The Nato-led Isaf force is now investigating the incident, a spokesman told the BBC. "It was the local workers who discovered the nature of the material and therefore stopped worse things from happening," said Brig Gen Carsten Jacobson. Last year, at least 24 people died in protests across Afghanistan after a hardline US pastor burned a Koran in Florida.