The counting for the civic polls, held yesterday, began this morning.
In Aurangabad, for the 96 of the total 113 seats where trends were available, the alliance was ahead in 55 seats.
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Majlis-e-Ittehadul Muslimeen (MIM) made an impressive debut by leading in 22 seats. The Congress, leading in seven, and NCP, ahead in just three seats, had a poor outing.
Two former women mayors Kala Ojha and Anita Ghodele in Aurangabad tasted defeat while son of Sena MP Chandrakant Khaire won the poll. Khaire's nephew Sachin Khaire, however, lost.
Meanwhile, Khaire said that it would have been better had the Sena contested the polls on its own.
Senior BJP minister Vinod Tawde described Khaire's remarks as his personal opinion.
In Navi Mumbai, for the 82 of the total 111 seats where trends were available, the alliance was ahead in 32 seats, NCP was leading in 36 while Congress was ahead in 10 seats.