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Abdul Quader, the headmaster of Sirajul Ulum Maria Nesa Madrasa, was arrested on Monday night in a case filed by the father of the victim, local police station chief Abul Kalam said.
Qader, 42, is the son of Sirajul Islam.
Citing eyewitnesses, OC Kalam said, Quader called up the girl into his room during Fazr on Saturday and raped her. He then committed the act for a second time around 8pm.
The girl shared the incident with a classmate on Monday and it spread among the people of the area. This angered the locals who vandalised the madrasa, according to the police official.
The girl has been admitted to Kushtia General Hospital.