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Steve Lovell felt the teams were well matched on Saturday but the Gills lacked the firepower.
Peterborough went ahead from the penalty spot and doubled the lead as the game opened up.
It was Gills’ first defeat in four.
“We could have been out there until 12 o’clock (at night) and we wouldn’t have scored,” said the manager.
Report: Peterborough 2 Gillingham 0
“It was one of those games. I don’t think there was much between the teams whatsoever and we performed well without really causing too many problems.
“I thought we had a lot of opportunities where we could have done something.
“I am just disappointed with the result, we had been in the game up until the penalty and it looked as thought it might have even been a 0-0.
“I know before the game I said it could be open and it could be 6-6 but it never looked like that as the game went on.
“The boys did well and gave everything but the penalty turned the game and then you try forcing it.”
The Gills were penalised for a foul on Siriki Dembele as he looked to dance his way through to goal.
While the penalty proved crucial, Lovell wasn’t moaning about the decision.
He said: “The referee has given it, so it’s a penalty. Thats the end of it.
“I go by what the referee does. He is not going to change his mind if you disagree with it but I didn’t see much.
“The boys said there wasn’t much in it but the referee has seen it and given it and that goal then gave them the impetus to go on.
“But I didn’t think there was much between the two sides. You wouldn’t have thought that we were on the points we have got and they are in the position they are.
“We tried to get an equaliser and it opened up for them, that is when their best spell came, in the last 10 minutes when we were pushing to try and get a goal.
“It wasn’t a bad performance and I thought we played well, especially first half, we had a lot of balls into certain areas where we could have done better but on another day we could have had a couple, but this wasn’t to be.”
It wasn’t Tom Eaves’ day, the leading scorer heading at the keeper in the first half and missing another chance in the second.
Fellow striker Brandon Hanlan didn’t get much joy either.
“Sometimes you have to give the opposition a bit of credit for the way that they defend,” Lovell said.
“They handled Tom and Brandon very well and they didn’t get to many opportunities although Tom had two chances where he could have done better but it was one of those days for Tom. He had opportunities and he tried but it didn’t come off.
“Sometimes they go in and sometimes they go over the stand and unfortunately they went over the stand.”