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Winning the tournament offers Arsenal hope of playing in next season’s Champions League – but Arteta knows a fifth successive season without qualifying for Europe’s elite competition from their league position is far from ideal for the club.
“It is not what we want but there are a lot of things that have happened in that period for many reasons,” he said.
“But obviously no one accepts that situation and we want to change it straight away and this season we still have the opportunity to do that.”
Defender Kieran Tierney could make a return to the side for the first time since suffering a knee injury in the defeat to Liverpool in early April.
Alexandre Lacazette is also in contention after overcoming a hamstring issue, but centre-back David Luiz (hamstring) is unlikely to feature.
Aubameyang came off the bench during the first leg in Spain after recovering from contracting malaria while on international duty in March.
The 31-year-old then netted Arsenal’s second goal – and assisted Mohamed Elneny’s opener – during the 2-0 win over Newcastle in the Premier League on Sunday.