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Turkish media has shown footage of the house where the man accused of carrying out the Reina nightclub attack was arrested.
Images from inside the house, which is reported as being in the city's Esenyurt district, show a broken door and dirty kitchen.
Police sources say that since the attack in the early hours of New Year's Day the suspect, named as Abdulkadir Masharipov, never left Istanbul.
But he is thought to have changed locations within the city several times ahead of his arrest.
Istanbul's governor has said that 50 people were detained in the operation to apprehend the man suspected of carrying out the Reina nightclub attack.
Vasip Sahin said that three women and an Iraqi man had been arrested alongside Abdulkadir Masharipov.
He said the attack, which killed 39 people, had been carried out on behalf of the so-called Islamic State group.
The man arrested over the Reina nightclub attack has admitted he carried out the attack, Istanbul's governor has said.
Vasip Sahin told assembled journalists that the man had been identified as Abdulkadir Masharipov and that his fingerprints matched those of the attacker.
He said that Maharipov, an Uzbekistan national, had received training in Afghanistan and entered Turkey illegally.
Mr Sahin said it was clear that Maharipov had carried out the attack on behalf of the so-called Islamic State group.
Turkey's prime minister has confirmed the arrest of the man accused of carrying out the New Year attack on the Istanbul nightclub in which 39 people were killed.
Binali Yildirim on Tuesday said he hopes the interrogation of the arrested Reina nightclub gunman will reveal the "forces" behind the attack.
He did not provide further details on the arrest or the investigation, saying authorities would provide details "in time."
Turkey's Deputy Prime Minister has congratulated police for detaining the suspected gunman accused of killing 39 people at an Istanbul nightclub on New Year's Day.
Numan Kurtulmus, who is also the government spokesman, wrote on Twitter: "I congratulate our police who caught the perpetrator of the Ortakoy massacre.
"Our war with terror and the powers behind it will continue to the end."
Police searched two houses and arrested five people during the operation to detain the suspect behind the Istanbul nightclub attack, ITV News understands.
It is believed three women and two men have been detained.
According to police sources, the man entered Turkey from Iran, but since the attack in the early hours of New Year's Day has never left Istanbul.
The suspect was pictured wearing a bloodied grey t-shirt and was taken to a city hospital under a large police escort on Monday evening.
Some police sources suggest he has changed location up to four times.
The suspected gunman behind the Istanbul nightclub attack was found at a house belonging to a Kyrgyz friend in a special police operation in Istanbul's Esenyurt district, according to private NTV television.
Hurriyet newspaper and other media identified the suspect as Abdulkadir Masharipov, an Uzbek national.
ITV News understands he is currently being treated in hospital for unknown injuries.
Media reports said he would 'undergo medical checks' before being taken to a police headquarters for questioning.
Dogan news agency published an image showing a bruised, black-haired man in a grey, bloodied shirt being held by his neck. NTV television said he had resisted arrest.
The suspected gunman had been on the run since the attack.
The suspected gunman who killed 39 people in an Istanbul nightclub on New Year's Day has been caught in the city's Esenyurt district, according to various Turkish media.
Islamic State claimed responsibility for the attack, which it said was revenge for Turkish military involvement in Syria.
Soon after the attack, Turkish authorities identified the main suspect who they said was a member of the Uighur community - a Muslim group who lived in western China.
Authorities in Turkey have established the possible links and location of the main suspect behind the New Year's Day attack at an Istanbul nightclub.
In an interview with broadcaster A Haber, the country's Deputy Prime Minster Veysi Kaynak said he could not rule out the possibility of the gunman fleeing abroad.
It is believed the suspect is a member of the Uighur community - a Muslim group who live in western China.
He also said it was clear the attacker acted alone, but could have been helped by others.