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A parked police motorbike on the left side of the road caused Wilco Kelderman (Sunweb) to crash and a wave of carnage afterwards. Team Sky's Thomas crashed with co-captain Mikel Landa and at least two other team-mates.
Thomas lost 5-08 minutes to stage winner and new pink jersey leader Nairo Quintana (Movistar).
"Yeah," Thomas said when asked if he thought his race was over at that point.
"I got back on, I got to the finish, but I knew deep down there was no coming back from that. I was on the floor for quite a while and then waiting to get a bike and everything. It was just a shame because that shouldn't happen."
Thomas warmed down on his bike before speaking to the press. He pedalled as normal, but scrapes and blood marked his legs.
The crash occurred at 14.3km to race as Movistar were speeding to the base of Blockhaus for captain Quintana.
"The next I know, the guys in front of me went down and clipped a motorbike, that was it and I was down on the floor," Thomas said.
"My shoulder was... I thought I'd done something bad, but as the doc lifted me up it kind of popped back in. It was okay, but obviously I had to get a bike and it was game over then."
Thomas in theory should have been racing for the pink jersey on Tuesday, after Monday's rest day near Perugia. However, he is now lucky to keep racing and will be fighting to claw back minutes.
"At the moment it's hard to think of that but I doubt the boys are going to just let me gain back that time easily," Thomas added.
"I don't know, I'll just go back to the hotel tonight and rest tomorrow and plan how we are going to ride the rest of the race."
Kelderman broke his finger in the crash. Landa struggled further behind and finished at 26-56 minutes.
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