A series of swashbuckling attacks from Alaphilippe see him leave the
Pyrenees with the yellow jersey and a 1min 35sec lead on second placed
Thomas with 15 eventful stages behind them.
Mastermind of six Tour de France wins from the last seven editions,
Brailsford said Alaphilippe had thrown a spanner in the Ineos works,
taking their attention off who they originally saw as the chief
contenders, and spoiling their plans to control the Tour.
"Alaphilippe has gained time on everyone with great style, his
presence has changed the way all the other teams are riding too, not
just us," said Brailsford.
Alaphilippe, 27, has become a focal point for French fans and will
wear the yellow jersey an 11th time on Tuesday's flat run around Nimes,
where 40 degrees celsius (over 100 fahrenheit) temperatures are
"He is the biggest change to the Tour, he's created a ripple effect," insisted Brailsford.
"Because of him we are forced to react to the situation minute by minute."
Brailsford said that world number one Alaphilippe's presence was an unexpected headache.
"We have the conundrum of trying to get rid of Alaphilippe and dealing with the general classification guys.
"It's both exciting on one level and on another like a game of chess."
"This predicament is making the whole race very different."
When asked if he and Thomas had spoken too soon on the last rest day
when they predicted Alaphilippe would wilt in the individual time trial,
which he won, and suffer in the Pyrenees, where he also extended his
lead over the two days.
"If (Alaphilippe) pulls it off he's on another level to everyone.
"If he was to win this race he'll be one of the greatest riders of all time," said Brailsford.
But former boss of British Olympic cycling insisted he remained
confident his Ineos charges would emerge from high-altitude in the Alps
later this week with the most glittering prize in cycling.
"There are four races that go over the magical 2000m mark and that's
where the real difference will be made," he predicted of the altitude
racing where rarefied oxygen can effect athletes both physically and
"It's going to go down to the wire. But I believe our consistency will pay off," said Brailsford.
The 2018 champion
Thomas complained of overheating in the baking afternoon sun at Pau
during the time-trial, where Alaphilippe wowed the crowds by winning the
race by 14sec from Thomas.
He then admitted feeling 'weak' the following day in the Pyrenees
where he also lost time above the treeline on the climb to the summit of
But after a late surge exposed Alaphilippe for the first time on
Sunday's second Pyrenean jaunt, Thomas was upbeat on the rest day
"I feel I've managed the race well, I have had my bad day and it wasn't that bad either," he explained.
"I'm itching to go now and hoping the Alps will treat me a lot better," said the 33-year-old Welshman.
"I didn't feel that great on the last climb (Sunday)," he admitted
"But I feel motivated going into the Alps, to finish this tour off well.
"This is the biggest race in the world I love it and I relish the
Alps coming up," said Thomas, who suffered a nasty fall in his build up
"I'm second and that's good place to be," he said.
Thomas praised his co-captain Bernal, who is fifth and has worked well alongside the older man.
"We stick together, and I trust him," said Thomas.
Bernal, who has yet to go at what he describes as 'full gas' was also upbeat.
"I love the Alps, I grew up racing at altitude," he said.
"It's been two hard weeks of racing and were very happy with the results so far," he said.