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Thomas is second in the general classification, 43 seconds behind leader Greg Van Avermaet (BMC), and 59 seconds in front of Sky teammate Froome as cycling’s premier race heads toward the Alpes.
Sky have insisted Froome remains its team leader but also says that Thomas is allowed to race for himself in the early stages of the Tour.
And British cycling great Wiggins, who won the 2012 Tour with Sky, sees trouble ahead.
“This is where it gets difficult, as we hit the first mountain stage,” he said on Eurosport’s “The Bradley Wiggins Show.”
“If Geraint stays where he is and takes the yellow jersey they’ve got a real problem on their hands.”
Wiggins suggested Sky boss Dave Brailsford could be “divisive” as he bids to keep his riders motivated.
“Does Dave B. come in and do his usual and be quite divisive?” Wiggins asked.
“Dave will certainly be in both of their ears and be telling them they can both win it, as a way of motivating them, as a way of playing these cards deep into the race and let the natural selections come in to play.
“He is quite self-serving. For him, it’s about the team winning, it’s not about the individuals.”
Wiggins was twice in the same situation when Froome was his domestique on Sky. There was controversy on the 2011 Vuelta a España, where Wiggins finished third and Froome was second. The next year, in the 2012 Tour, which Wiggins won, Froome was again second overall. However, it appeared that Froome had to ease up to allow Wiggins to win.