Valentino Rossi had mixed feelings after finishing a lonely fourth in the Malaysian MotoGP on the Factory Yamaha.

Rossi, who qualified in second place behind Marc Marquez at Sepang, made some progress with the set-up of his M1 but was hampered during the early laps by brake problems, losing the tow of the leading trio of Jorge Lorenzo, Dani Pedrosa and Marquez.

He fought off a challenge by Alvaro Bautista at the beginning of the race to consolidate fourth and was lucky to avoid being rammed by the Gresini Honda rider at the hairpin on lap five, when Bautista ran in too hot on the brakes.

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"I'm happy because this weekend we improved the set-up of the bike and I am fast on new tyres," said Rossi. "I started in second place and after qualifying being a problem at the beginning of the year it's three races in a row that I have been competitive.

"I was less than one tenth from the fastest lap of the race, just like Aragon and Misano, so it means that in the beginning of the race I am strong and I'm happy about this. Now we have to continue to work because in the second half of the race I struggle too much with the tyres.

"I had a problem today that in the beginning of the race I had a problem with the front brake when I was behind other guys. The front brake gets too hot and it becomes difficult to stop the bike. The front three guys are already very fast and with this problem it becomes more difficult.

"I'm happy because I was just three seconds from Jorge and it's a small distance and it means that I rode well for all the race, but at the end, starting front row I had hoped for a podium.

"The Hondas were very strong and could use their tyre in a better way than today and to stay more constant with the rhythm. Me and Jorge had a similar race and when we started to struggle with the tyre we couldn't stay with the Hondas.

"I wasn't strong enough in the first braking and Jorge braked deeper than me. Marquez in the second corner was very aggressive and I had to go wide but it's normal in the first two corners. He risked a bit but he didn't make any problems so it was alright but I lost a bit.

"I knew that even with Lorenzo and Pedrosa not on the front row that they had a better pace so I tried to stay with them. I stayed with them for five or six laps but after that I had to slow down a bit because I started to slide."

Rossi carried a Marco Simoncelli flag on his slowing down lap in a tribute to his fellow countryman, who lost his life at Sepang in 2011.