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I think he's disappointed too. But we don't know how he came into the race, i.e. did he come in tired to time his form right for the Tour.
To be fair, it's been a particularly cold and wet edition of the race. Which affects taller riders like Thomas and Van Garderen more than the smaller riders like Spilak and Lopez, because they're riding with minimal body fat to be competitive in the mountains.
He should move up the GC a bit tomorrow, with a 16 km time trial.
What a disappointing Suisse from Thomas. This felt like a really good opportunity for him to step up and he has been a little lacking.