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The saffron party settled for eight seats in Thrissur, while the UDF swept to power with 33 seats.
Congress has also alleged bogus votes in Thrissur.
The EVMs are currently in the custody of the District Election Officer, Thrissur.
Muraleedharan said his disappointment would have been less if the Left candidate had won.
The case pertains to the actor-politician registering two cars in the UT evaded taxes.
In a video that went viral on Saturday, Gopi was seen losing his cool with the BJP's booth-level workers while visiting the Shasthampoovam tribal colony.
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