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CNN) -- A former Massachusetts chemist accused of mishandling evidence affecting numerous state criminal cases pleaded guilty in a Boston court Friday afternoon to 27 counts.Annie Dookhan, 36, pleaded guilty to tampering with evidence, perjury, obstruction of justice, and falsely claiming to holding a master's degree.The judge also ordered that she serve two years of probation after serving the prison time.In August, Massachusetts Gov. Deval Patrick's administration said the cases of more than 40,000 defendants could be affected by the alleged drug tampering, dating back to 2003.Dookhan worked as a state chemist testing drug evidence submitted by law enforcement agencies from 2003 until March 2012, when she resigned, according to the Massachusetts attorney general's office.The attorney general's office began a criminal investigation in July 2012, after Massachusetts State Police were tipped off by Dookhan's co-workers, who alleged her work might be unreliable.