Alberto Hernandez is facing 13 charges, including rape, criminal sex act, and predatory sexual assault.
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Police say the alleged rapes occurred over a period of four years, when the girl was 6 to 10 years old.
It happened at the Maria Cortez Family Daycare, located on Heath Avenue in the Melrose section, which Hernandez operated with his wife for the past 25 years, investigators said.
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Police say the child, who is now 13, came forward on Monday. Hernandez was arrested Wednesday.
He had no comment as he was being walked out by police.
Authorities are now investigating if there could be more victims. Anyone with information is urged to come forward.
The New York State Office of Children and Family Care announced it is immediately suspending and moving to revoke the child care provider's license pending the outcome of an investigation into the matter.
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