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Gills boss Peter Taylor was left frustrated after seeing his side let the points slip at Priestfield.
Taylor’s men looked on course to pull off a shock against the league leaders but Orient levelled the game in the 70th minute and hit a last-minute winner.
“I am very frustrated after conceding a very late goal and a bad goal on our part,” said Taylor.
“I have spoken to (goalkeeper) Stuart Nelson about it. Stuart had a terrific game and he felt as though he was fouled but to concede so late is very frustrating.
“It’s not the first time it has happened and so we are a bit disappointed with that but overall I felt we created a lot of chances and we could have been nicely up in the first half. We have to make sure we take our chances.
“When you are playing against the top team in the division and you put in a good account of yourselves, I have got to be pleased with that. But of course, the final bit is very disappointing.”
The Gills started the game well, as Adebayo Akinfenwa headed home in the third minute.
“We deserved to score early on and we were very positive,” said the Gills manager.
“It was another good goal from Bayo and it was a good start. We also had a good start to the second half and had another good chance, where Cody went through and if that goes in then I am sure it’s a different situation.”
McDonald put the chance wide, when one on one with the keeper but Taylor was just pleased with the amount of chances his side created.
“I am sure (Cody will be kicking himself) if they keep creating chances for themselves then I am sure in the end they will go in and they will get confidence from that,” said Taylor.
Leyton Orient levelled the game from a corner, which was headed home by Marvin Bartley, unopposed.
Taylor said: “That frustrates us, of course, and there was someone on the edge of the box who should have picked the player up. He is a bit disappointed he didn’t do that. It is all a learning curve for everyone.”
The Gills boss did accept several of his time were tired late on but didn’t feel that contributed to Orient scoring their winner.
“The last goal can’t be put down to tiredness,” he said. “That would be an easy excuse but I did feel there were a couple there that were blowing. We will have to address that.”