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The IMD issued the red alert in Pathanamthitta, Kottayam and Idukki districts of the state for May 19 and 20.
Additionally, an orange alert was issued for Thiruvananthapuram, Kollam, Alappuzha, and Ernakulam for those two days.
The weather department further issued an orange alert in nine districts for May 21 and said some of them were likely to receive rains similar to that of a red alert.
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For Saturday, it issued an orange alert in Pathanamthitta, Idukki and Malappuram districts.
A red alert indicates heavy to extremely heavy rain of over 20 cm in 24 hours, while an orange alert means very heavy rain (6 cm to 20 cm). A yellow alert means heavy rainfall between 6 to 11 cm.
The IMD on Thursday had predicted very heavy rainfall in the state between May 18 and 20 due to the likely prevalence of strong westerly and south westerly winds in the region.