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The weather agency on Saturday sounded an orange alert for Thiruvananthapuram, Kollam, Pathanamthitta, and Idukki.
A yellow alert indicates rainfall ranging from 64.5 mm to 115.5 mm within 24 hours.
The rainfall deficiency in Idukki district is 54%.
Chennai and nearby Chengalpet, Kancheepuram and Tiruvallur districts among others received widespread rains since late Sunday.
Thunderstorms with lightning accompanied by gusty winds speed reaching 30-40 kmph is very likely to occur till Thursday.
Pathanamthitta, Ernakulam and Idukki districts have been placed under yellow alert for five days.
Adverse weather in the United Arab Emirates has caused some disruption to flights at Dubai's main airport.
The improvement is expected to be reflected in the air quality index as the day progresses -- the AQI at any given time is the average of readings taken in the last 24 hours.
It also said that heavy rains were likely at isolated places in the state between November 6 and 9.
The Met Department predicted isolated heavy rainfall in Kerala for the next few days due to the prevailing weather conditions over the southern part of the country.
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