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Gills boss Justin Edinburgh admitted his team got away with it on Monday.
A solitary strike from Dominic Samuel settled the League 1 clash in Gillingham’s favour.
Edinburgh made just one change to the team which had won back to back games on the road but the tough Christmas schedule caught up with some, he admitted.
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He said: “We were tempted to rest one or two. They are a young group and they put a lot of effort into those two away games, we toyed with it and we didn’t and I think we got away with it.”
Edinburgh made a double change at the break, admitting his side struggled to get out of first gear.
“The last two games took a hell of a lot out of us, more than I probably realised,” the manager said.
“I did toy with the idea of resting but you have to draw on what you know as a player and I know that had I been left out, from what I had done from the previous two games, I would have probably been disappointed. Maybe, looking at it now, I should have freshened it up a little.
“We got through to half time and the two boys we brought on did give us a lift and an impact.”
Colchester had more chances than the Gills and left feeling they deserved something from the match.
“It was a tough encounter and probably our biggest and best win of the season,” Edinburgh said.
“Everyone was coming here expecting us to win comfortably but I said it was going to be tough and it certainly was.
“In our last game here we lost our unbeaten record and we were conscious of getting back on track. We had two fantastic away performances and results and I think that would have been wasted had we not collected all three points.
“We started slow and over the last 24 hours I had contemplated making changes but on the back of those two fantastic performances you tend to want to stick with the same group.
“I have to say, one or two of them did look a little leggy and we didn’t get out of first gear. We got better second half once we made the two subs. Luke Norris came on and was a presence, he got us further up the pitch and Doug Loft had a real good influence on the game.”