Mark Johnston was on the mark for the second time at Royal Ascot this week when Hartnell took the Queen's Vase.
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The 7/2 second-favourite took advantage when a gap opened on the inside rail two furlongs out and burst into a clear advantage.
But towards the winning post, Hartnell suddenly started to get lonely on his own and drifted markedly left towards the centre of the track and the staying-on Century, trained by Aidan O'Brien.
The pair collided in the final strides of the contest and a stewards' inquiry was called into the interference, however the placings were left unchanged despite O'Brien doing his best to persuade the stewards that he was certain that the collision had "cost him the race".
At the line Hartnell had the verdict by a neck, while favourite Marzocco finished third despite also being hampered in the closing stages.
"Joe was adamant that he hadn't broken the rules when he came back in and if that was the case, there was no way he should lose the race," said the trainer, winning the race for the seventh time.
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"He told me the horse started to drift left when he gave him a couple of taps with the whip. As soon as he came off a true line, Joe put his stick down and just used his hands and heels to guide him home.
"We've got a good record in this race and usually target our mile and a half horses in it. We were actually quite keen on running Hartnell in the King Edward VII Stakes but decided to come here instead.
"He always impressed us as a two-year-old and I thought over the winter that this could be the best chance we had of winning the Derby for a long time. He's always been the type to improve between two and three and I don't think we've seen the best of him yet.
"In the end, we decided to miss Epsom and I think that was the right decision. I don't see him as a two miler this year and we've had the St Leger in mind for him ever since he ran at Lingfield.
"That will be his long term target - where he goes next I'm not too sure. Hopefully this will be a good stepping stone towards Doncaster."
Fanning added: "I don't know why he did it. Maybe he just saw the gate. But he definitely deserved that."
Sky Bet installed the winner at 14/1 to win the Ladbrokes St Leger on the back of this result.
Adelaide's trainer Aidan O'Brien commented: "I was delighted with the run and Joseph (O'Brien) was coming there at the end."
John Gosden, trainer of third-placed Marzocco, said: "That was a solid run and the interference didn't affect our placing - we would have been third in any case. This is still an immature horse."