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Gills boss Peter Taylor admitted his side made hard work of winning Friday night’s match.
Adebayo Akinfenwa scored twice and Tranmere played most of the second half with 10 men but the Gills had to hang on at the end, after conceding with 13 minutes left.
“It is lovely to have got three points but we made awfully hard work of it,” said Taylor, whose side ended a run of three matches without a win in League 1.
The Gills were cruising before a long ball over the top put the defence in trouble and home striker Ryan Lowe pounced, to set up a tense finish.
“The effort was fantastic but we conceded a really bad goal, which made for a nervy finish and we need to get better than that,” said the Gills boss.
“The players said the wind changed where the ball was going, which was why they didn’t clear it, but overall I have to be pleased with three points and we just have to take our chances a bit more.
“Last Saturday there was a good feeling around Priestfield and I think the supporters played a massive part and they helped us to have the confidence to go to Tranmere and put on a confident performance. It rewarded the supporters who travelled.
“I am pleased for the young players as well. Bradley Dack and Jake Hessenthaler again played ever so well and I thought it was Steven Gregory’s best game since I’ve been here.
“He broke up a lot of their play. They still had some good footballers in midfield and so you had to do that. He was terrific and I am sure he is good for Jake in there as that will be helping him in certain areas.”
One player who didn’t see any action was Craig Fagan but Taylor insists he is now ready for a return.
Taylor said: “He was absolutely fine and we could have put him on. I really thought about putting him on but in the end because it was getting so tight and because of the poor goal we gave away, I didn’t want to take that chance. I also thought the referee might then add a few more minutes if we made the substitution, so you have to be careful when you do that.”