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Daryl McMahon admitted Ebbsfleet weren't at their best in a seventh successive National League draw.
Jack Powell fired Fleet in front against Chester with a superb left-footed strike into the top corner on 57 minutes.
But the visitors returned to Kent with just one point after James Akintunde equalised 10 minutes from time.
McMahon admitted: "It wasn’t one of our better performances on Saturday but in the circumstances you take the point and it’s a point gained.
"In the first half was it was quite windy and they were quite direct. Losing their manager, you had a team with a bit more energy than I saw on Tuesday night against Solihull Moors (when Chester lost 2-0).
"They had the home crowd right behind them and they started the game with a lot of energy, which I felt we dealt with mostly, although we weren’t great on the ball ourselves.
"In the second half we started the brighter and got a good goal but still weren’t great with the ball. It was a killer goal conceded late on.
"It’s unusual for us. It’s one of a handful of times I can remember us not being good with the ball. It wasn’t the level we expect on Saturday and it’s probably the first time I’ve said that this season, across the game, which was always going to happen.
"We look to bounce back on Tuesday night against Aldershot."