BOSTON — Boston Mayor Thomas Menino says he won’t try to stop Chick-fil-A from applying for permits to open a restaurant near Faneuil Hall.

Menino is acknowledging that there is little he can do to prevent the fast food chain from coming to Boston, though he stands by his position that the company isn’t welcome in the city because of its strong opposition to gay marriage.

The mayor clarified his position on Thursday.

In a sharply-worded letter last week to Chick-fil-A president Dan Cathy, Menino wrote: “There is no place for discrimination on Boston’s Freedom Trail and no place for your company alongside it.”

Menino now says he was just expressing his own opinion.

Gay rights groups have called for a boycott of the chain and some Chicago politicians hope to stop a restaurant from opening there.