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Justin Edinburgh admitted the difference in class shone through on Wednesday night.
His League 1 side failed to contain a Tottenham team who bossed the EFL Cup third round match from start to finish, winning 5-0.
Tottenham were 1-0 up at the break and added four more goals in the second half.
Edinburgh said: “Without really being a threat I always felt that at 1-0 there might be a chance but once they put on the burners and pulled away at 3-0 it was damage limitation.
“We will feel a slight tinge of disappointment that in possession of the ball we didn’t do ourselves justice and show what we are capable of.
“That is not what I wanted the scoreline to be and it’s not what envisaged but the gulf in class came through in the end.”
Read the match report from Gills' 5-0 defeat by clicking here
Christian Eriksen opened the scoring as the Gills gave him just a bit too much room and he took full advantage, firing home from 25 yards.
Edinburgh said: “Sometimes as defenders you feel as if people are shooting from outside the box then you are doing your job but there just wasn’t enough pressure.
“He has pulled the trigger and it’s flown into the back of the net. We had defended well and we put in some really good blocks from shots and the balls have fizzed past the post and you think that maybe we’ve rode our luck and we can get to half time but it wasn’t to be.”
The Gills had beaten Watford in the previous round but were unable to replicate that performance.
Edinburgh said: “We probably didn’t do ourselves justice in possession like we did against Watford, where we really excelled in possession of the ball but we didn’t give ourselves the chance with the quick goals after the break.
“It didn’t allow us to put an impression on them.
“We will reflect and analyse but be realistic in that we are probably not going to come up against a team as good as we have. It was a gap too far.”