Aidan O’Brien’s Ballydoyle stable headed away from Newmarket after the Guineas meeting on Sunday with the favourite for next month’s Oaks and two of the top three in the betting for the Derby, but that does not really tell the tale of a difficult weekend here for Ireland’s most powerful yard.

The main positive for O’Brien was the sight of Ylang Ylang running a fine trial for the Oaks as she stayed on into fifth in a blanket finish to the 1,000 Guineas behind the surprise 28-1 winner, Elmalka. There are still no further clues to explain the bitterly disappointing performance of City Of Troy, the odds-on favourite, in Saturday’s 2,000 Guineas, however, or any indication of whether last year’s champion juvenile will head to Epsom for the Derby in four weeks’ time.

Related: Notable Speech wins 2,000 Guineas as favourite City Of Troy slumps

O’Brien was not at Newmarket on Sunday but Paul Smith, from the Coolmore Stud syndicate which supplies Ballydoyle’s firepower, reported that City Of Troy was fit and well on his return home.

“He seems fine this morning,” Smith said. “He got a little bit fractious at the start and Ryan [Moore, his jockey] was never happy. So we’ll let the dust settle, take stock, see if anything comes to light and work back from there.

“We’ve been here before. Aidan knows what to do and we’ll see if anything comes to light. If it doesn’t, he’s a good horse and one bad run and one mishap doesn’t make him a bad one, so we’re all systems go.

“He’d taken his work well, his temperament was fine and he loved his work [before the Guineas], he did everything very easily and there was no sign at all [of any issue]. It was a big disappointment but onwards and upwards, we’ll get to the bottom of it, I’m sure we will, and we’ll see what happens.”

Elmalka’s unexpected success in the 1,000 Guineas on Sunday was a significant triumph for both Roger Varian, who also trained the winner’s dam, Nahrain, and in particular Silvestre de Sousa, her jockey, who has only recently returned to the saddle after picking up a 10-month ban a year ago for “facilitating a bet” for a fellow jockey in Hong Kong.

The Hong Kong stewards accepted that de Sousa had not had a bet himself or failed to ride his horse to achieve the best possible placing, but their penalties for any betting-related activity are famously severe.

For a jockey in his early 40s, a 10-month ban could have been potentially career-ending, but de Sousa’s famous work ethic, which carried him to the British Flat jockeys’ championship in 2015, 2017 and 2018, has ensured that he has swiftly picked up the threads of his British career.

Elmalka’s victory looked highly unlikely as she trailed the field in the early stages of the race, and Ramatuelle, from Christopher Head’s yard in Chantilly, traded at 1-5 in running after she hit the front and opened a useful lead with two furlongs to run. Her stamina was untested at a mile, however, and as her stride started to shorten with the post in sight, de Sousa delivered Elmalka with a perfectly-timed run to beat Porta Fortuna by a neck, with Ramatuelle a short-head away in third.

De Sousa’s championship-winning seasons were based on quantity as much as quality, and this was the first Classic success of his career and only his 12th in all at the highest level.

“I’ve been trying to win a Classic for so long and it’s just an amazing feeling,” he said. “I haven’t had that feeling for a long time. Especially when you’ve had time off and you come back, it was just unbelievable.

“I love British racing so much. To me it’s my base. This is the place where it starts and I hope this is the place where I’m going to finish one day. I’ve been working hard behind the scenes and just want my opportunities back and I’m still capable. I’ll just work hard and see how the season goes.”

Varian expects to keep Elmalka at around a mile and the Falmouth Stakes, at Newmarket’s July meeting, is an option later in the campaign.

Beverley 1.55 Spring Corn 2.30 Willolarupi 3.05 Korroor 3.40 Ardbraccan

4.15 Swatch (nb) 4.50 She’s Got Bottle 5.25 Patronage

Windsor 2.00 Kiss And Run 2.35 Usuario Amigo 3.10 Galyx 3.45 Tipsy Tiger

4.20 Tiriac 4.55 Calm Waters 5.30 Abolish 6.00 High Court Judge

Bath 2.15 Monkey Miss (nap) 2.50 Star Anthem 3.25 Joy Choi 4.00 Bloodhound

4.35 Signcastle City 5.10 Amerigo Vespucci 5.45 Andromedas Kingdom

Warwick 2.40 Midnight Gold 3.15 Get Sky High 3.50 Irish Lullaby 4.25 Fiston De Becon 5.00 Trapista 5.35 Commanding View 6.05 Just Jess

Kempton 2.55 Excelero 3.30 Ideal Des Bordes 4.05 Quick Draw 4.40 Island Run

5.15 Calico 5.50 Playtogetaway

“It’s not a surprise because I wouldn’t have run her if I didn’t think she was going to run well,” Varian said, “but you don’t come into these races thinking you’re going to win.

“She ran a big race at Newbury [in April]. We weren’t set on running in the Guineas that day but the turnaround in the last fortnight has been quite incredible. I was in two minds whether to run her because I didn’t want to do the wrong thing but that’s why we’re here, right, to have a go?”