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A group of around 10 powered free with 10 kilometres remaining. Thomas, who had been at the front, lost position just before the move went and missed a chance to gain precious time.
Thomas warmed down on his bike and climbed off to explain to reporters waiting by the Sky’s black bus.
"Yeah, it was only 10 seconds in the end, and come the mountains 10 seconds is nothing, but it would've been good for the morale to be there," Thomas said.
"I had the legs to be there, but it was a bit of just missing it going into the roundabout."
Most of team Quick-Step surged free with eventual stage winner and new race leader Fernando Gaviria. Thomas rode at the front in chase with his team, but the situation settled given no-one in the front group posed a major overall threat for the next three weeks.
"It could've been worse, it was only Bob Jungels up there on the GC. Still it's a bit, you always want to be in the front," added Thomas.
"That final was really nervous. There were crosswinds in the last 15K, I was well positioned until the roundabout, I was knocked, braked and then you lose 20 positions.
"Out of the roundabout I was just too far back and made a big effort to get across, and almost made it, but didn't quite get there."
The Belgian Quick-Step team muscled ahead, the same team that Thomas regularly faced when he led Team Sky in the Classics.
"Yeah, for sure, we knew something was going to happen along there, someone was going to try, everyone wanted to be there, and I was there until that little roundabout. I just lost my position there. That's when it all went Pete Tong [wrong]," Thomas said.
"That's their forte. They are always there in the crosswinds, fair play to them. They ride well as a team and have the horsepower to do that, so chapeau to them."
The stage closed the big start, the first three days, in Sardinia. Teams fly to Palermo and enjoy a rest day on Monday. On Tuesday, the Giro re-starts with its first summit finish on Mount Etna.
"We stayed out of trouble and missed any mishaps. We will see on Tuesday, that is going to be interesting. Everyone is going to be testing each other. It could be a bit stop/start if it is windy at the top.
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