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The German rode away from the peloton at the end of a surprisingly hilly stage to take a hard-earned win ahead of Alejandro Valverde (Movistar) and put himself in the blue leader’s jersey.
Former leader and stage one winner Mark Cavendish (Etixx-QuickStep) slips to second place overall, just four seconds behind Degenkolb.
If Cavendish wins Saturday’s flat final stage and Degenkolb is out of the top five, the Manxman could still take the overall win in the race, giving his season – and morale – a big early boost.