Investigators are looking at a pop-up storm-related lightning strike as the cause of a fire that destroyed a home under construction in Peconic on Wednesday, police said.

The same intense thunderstorm also spawned a weak tornado that briefly touched down in nearby Mattituck.

Southold Town Police Chief Martin Flatley said the fire at the home on Wells Road in Peconic was reported at 4:29 p.m. and that Southold Fire Department volunteers responded to find the home engulfed. The house, under renovation, was unoccupied, and the contractor told police that no workers were at the site when the fire began.

Police said in addition to the home being destroyed, a shed was damaged, as were trees and a neighboring house.

The Suffolk County police Arson Squad is investigating, looking at the possibility that a lightning strike caused the fire, Flatley said.

As the powerful storm moved quickly over the east end, Flatley said officials recorded 5 1/4 inches of rain at police headquarters Wednesday — a downpour that caused flooding from Cutchogue to Greenport.

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A “weak” tornado also was reported in Mattituck, meteorologists said. It was considered an EF0, the National Weather service said, or the lowest on the scale.

But resident Frank Ficner, 89, said he was in his home on Village Lane when he heard a “roaring like a freight train.”

As the tornado touched down between Main Road and New Suffolk Avenue about 4:25 p.m., Ficner, who lives a few blocks away, said the strong winds that battered the region nearly uprooted a tree in his backyard.

“It only lasted about two or three minutes,” Ficner said. “If it would have gone on any longer, I would have lost the roof off my house.”

The Southold Fire Department puts down hot spots Wednesday, Aug. 10, 2016, after a fire gutted a house under construction on Wells Road in Peconic. A lightning strike is being investigated as a possible cause for the fire, police said. Photo Credit: Randee Daddona

Ficner, who was born in Cutchogue, said he’s seen a lot of weird weather on the North Fork, including a twister that touched down 17 years ago on Marratooka Road and Park Avenue in Mattituck and moved east over the water to Kimogener Point in New Suffolk and later to Nassau Point. That twister reached an EF2 rating with winds of up to 113 to 155 miles per hour and damaged several homes throughout the area.

Wednesday’s tornado was much tamer in comparison, with estimated wind speeds of about 70 miles per hour.

“As a severe thunderstorm moved southeast across eastern Suffolk County, it produced a small, weak, short-lived tornado in Mattituck. Most wind damage was concentrated between Main Road and New Suffolk Avenue close to the corridor from Cardinal Drive southeast to Blossom Bend, where the tornado lifted before reaching New Suffolk Avenue. Wind damage was confined mainly to trees, where several trees were snapped in half,” the National Weather Service said Wednesday.

Harry Hubbard, 21, said he was driving down Main Road to deliver a pizza about 4:25 p.m. when he saw what he believed was the tornado.

“I saw a bolt of lightning and then looked in my rearview mirror and saw debris scattered on the ground and a tree that had broken into pieces,” he said.

Published reports said the last time a twister touched down on Long Island was exactly five years before the one that struck Wednesday. On Aug. 10, 2011, a tornado blew through Great River, Oakdale, Bohemia and Lake Ronkonkoma.