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The Department expects more than 20-centimetre rains at many places in the three districts.
Monsoon is raging in the State, with widespread rains being received across the coastal areas on Monday while only a few areas in northern and interior parts of the State received rainfall.
At Panambur, Kota and Agumbe 9 centimetres of rains were received while in Mangaluru its was 8 centimetre.
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Accordingly, Orange Alert has been issued in all three districts on June 16 and 17 and a Red Alert on June 18.
Additionally, the wind speeds are expected to reach 45 to 55 kilometres per hour in coastal areas.
Orange Alerts has also been issued for Shivamogga, Chikkamagaluru, Hassan, Kodagu, Belagavi, Dharwad and Haveri districts till June 17.
The Met Department has also issued an advisory to fishermen to not go out to sea on June 17.