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Pentagon clears general of misconduct over e-mails

WASHINGTON — A Pentagon investigation has cleared General John Allen, the top US commander in Afghanistan, of professional misconduct in exchanging e-mails with a civilian woman linked to the sex scandal that led retired General David Petraeus to resign as CIA director.

Pentagon press secretary George Little said Tuesday that Defense Secretary Leon Panetta was informed of the conclusion by the Pentagon’s inspector general.

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‘‘The secretary was pleased to learn that allegations of professional misconduct were not substantiated by the investigation,’’ Little said, adding that Panetta has ‘‘complete confidence in the continued leadership’’ of Allen.

The matter had been referred to the Pentagon in November by the FBI during the course of its investigation of e-mails between Petraeus and his biographer-turned-paramour, Paula Broadwell. The FBI turned up thousands of e-mails between Allen and Jill Kelley, who was said to have received threatening e-mails from Broadwell.

At the time, officials said 20,000 to 30,000 pages of e-mails and other documents from Allen’s communications with Kelley between 2010 and 2012 were in question.

Shortly after being contacted by the FBI, Panetta referred the matter to the Pentagon’s inspector general, while expressing confidence in Allen and deciding that he would remain in Kabul as commander of all allied forces in Afghanistan.

At the same time, Allen’s nomination to be the next US commander of NATO forces in Europe was put on hold. The officials said Tuesday that the White House had not decided whether to go forward with the nomination.

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