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Missed chances proved costly for the Gills, said boss Steve Evans.
He watched Max Ehmer miss a great chance in the first half and then Alex Jakubiak fail to make the most of an excellent opportunity after the break.
Gillingham lost the game 1-0, a result which took Ipswich Town top of League 1.
Evans said: “There were key moments in the game. Max missed a huge chance, I don’t know how he’s missed it, that should have been a goal.
“It looked like a golden sitter. He missed but he doesn’t mean to. He has given us absolutely everything on the pitch at the other end.
“Within a couple of minutes (of Ehmer’s missed chance) Tommy (O’Connor) hasn’t marked his runner, we get punished (and go 1-0 down).
“We ask the boys for a response second half. We changed the system and personnel and that change caught them out, like it did at Bristol (on Tuesday).
“It worked and they didn’t have a clue what we were doing. Alex goes through and should score, it’s a deflection but he should have put it in, simple.
“You are always going to be subject to the odd counter-attack. They hit the post and Jack (Bonham) has had one saved, I don’t know how many corners and free-kicks we’ve been putting into their box.
“There are numerous emotions. I feel sorry for our players, we asked them to give us absolutely everything, I don’t think there is any one of them that has left anything out on the pitch, not one of our supporters left anything at home.
“In fairness to both clubs, both sets of players and supporters have given everything. Ipswich supporters were very quiet second half until they get into added time and then they sense the opportunity was there because they must have thought, ‘if these score they will beat us?’
“I couldn’t ask my players to give me any more, even the substitutes that came on had an impact, in different areas, and we go home bitterly disappointed, we shouldn’t lose that game but I am sure the wonderful wizard of (Paul) Lambert (the Ipswich manager) will say something different, won’t he?
“You’ve got a team with ten times our budget rolling into town, and that commands good players, so you need to try and find a way to compete with them. I thought our boys did that.”