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Arroyo comes in fifth, with Soler driving the next group across the line for spot number six.
Basso (7th), Leipheimer (8th), Rodriguez (9th) and Rogers (10th) made the stage top ten complete.
Danilo Di Luca extended his overall lead on Denis Menchov to a minute and 20 seconds.
SHOOT: Seems like Armstrong come in just after the top 10 riders. Armstrong in Twitter this morning said: "I hear Ironman legend Dave Scott had a nasty crash yesterday. Wishing him well. He was one of my idols growing up."
SHOOT: The time trial stage later this week should change the standings a lot:
In preparing for the Giro, Basso spent an almost unheard of 100 miles on his time-trial bike one day.
"Time trialing is the area I lost the most in when I was (banned)," he said. "You need to race to keep up your time-trialing form."
Leipheimer and Menchov are expected to gain significant time on the likes of Di Luca and Basso in the race against the clock. The stage is highly technical, with several steep downhill sections, and Basso struggles going downhill.