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2014 MotoGP champion elect Marc Marquez led the way from Valentino Rossi during Saturday morning practice for the Japanese MotoGP at Motegi.

Reigning champion Marquez, who has his first chance to wrap-up the 2014 title on Sunday, continued a complicated weekend. After a fall early on Friday morning, then sixth in the afternoon, the young Spaniard again struck trouble early in FP3.

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Marquez pulled off track after hearing strange noises from a new engine on his Repsol Honda - but returned to set the fastest ever two-wheel Motegi lap, a 1m 44.940s, by the halfway stage of the 45-minutes.

That lap (the 7th of 18) remained Marquez's best, while by contrast Rossi popped into second place by +0.227s on his very final lap. The Movistar Yamaha rider, who broke a finger and was briefly knocked out last time at Aragon, had been fifth fastest in both Friday sessions.

Day one pace setter Andrea Dovizioso was only ninth this morning (+0.625s) but the Ducati rider's Friday time was enough for second on combined times.

Third in the Saturday session was Monster Yamaha Tech 3s Pol Espargaro, who then ran wide and tipped over in the gravel. Rossi's team-mate Jorge Lorenzo, the best in terms of race pace on Friday, slipped from second to fourth (+0.423s).

Medium front and soft rear was the favoured tyre combination for the Factory riders this morning. That looks to be the likely race choice, although the Ducati and Open class riders are sure to play their joker card in the form of the extra-soft rear in qualifying.

Pramac's Andrea Iannone used the rubber to set fifth (+0.460s) in FP3, with factory team rider Cal Crutchlow (+0.598s) likewise moving into seventh on his GP14.

But the extra soft tyre wasn't enough to help Aragon runner-up Aleix Espargaro break into the combined top ten and he will thus join the likes of Gresini Factory class rider Alvaro Bautista and Pramac's GP13 rider Yonny Hernandez in Qualifying 1.

Just scrapping into the combined top ten were Marquez's team-mate Dani Pedrosa and LCR's Stefan Bradl. Bradl had been the best Honda rider, in third on Friday, but could only manage twelfth in FP3, while Pedrosa dropped from fourth to eighth.

Due to Dovizioso's Friday pace, that put them ninth (Pedrosa) and tenth (Bradl) on combined times. Pedrosa is currently Marquez's closest title rival.

Free Practice 3:
1. Marc Marquez
2. Valentino Rossi
3. Pol Espargaro
4. Jorge Lorenzo
5. Andrea Iannone
6. Bradley Smith
7. Cal Crutchlow
8. Dani Pedrosa
9. Andrea Dovizioso
10. Alvaro Bautista
11. Aleix Espargaro
12. Yonny Hernandez
13. Stefan Bradl
14. Hector Barbera
15. Katsuyuki Nakasuga
16. Hiroshi Aoyama
17. Nicky Hayden
18. Alex De Angelis
19. Danilo Petrucci
20. Karel Abraham
21. Scott Redding
22. Broc Parkes
23. Mike Di Meglio
24. Michael Laverty