The 30-year-old could only manage a disappointing 11th in the 1km time trial before hitting back in the flying lap where he posted the fourth-quickest time.
Cavendish needs a strong showing in the sixth and final discipline later on Saturday, the points race, to have any chance of a place on the podium -- the target he was set by British coach Shane Sutton beforehand.
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The 26-times Tour de France stage winner has never won an Olympic medal of any colour, suffering disappointment in the road race in 2012 when he was one of the favourites.
He is desperate to fill in that glaring omission from his CV this year, but his inclusion in the team was further complicated by youngester Jonathan Dibben's brilliant victory in the points race on Friday.

Britain's Mark Cavendish (L) warms up

Image credit: Reuters

Dibben's surprise gold in his first world championships has given Sutton a possible selection dilemma as the 22-year-old is being tipped as an Olympic medal candidate in the omnium.
What is more Dibben is a better team pursuiter than Cavendish so selecting him would give Britain more options in that discipline in which they are desperate to beat the Australians in Rio.
Italian Elia Viviani, who rides for Team Sky, took the overall lead in the omnium after five events with a superb display in the flying lap.
He leads by 14 points from Colombia's overnight leader Fernando Gaviria Rendon.
The points race is a 40km, 160-lap event featuring sprints every 10 laps which earn riders' points.
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