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The district disaster management authority has issued an orange alert on May 17 and 19 in Dakshina Kannada and Udupi districts.
A red alert has been sounded on May 18.
Fishermen have been warned against venturing into the sea or the river.
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Monday morning was cloudy, with some showers. But by midday, almost everywhere on the coast, heavy showers were seen.
Heavy rains were reported from areas adjoining the Western Ghats Including Sullia, Belthangady, Karkala, and Kundapur, of the twin districts.