First-half goals from Ben Tozer and Adebayo Akinfenwa put the improving Cobblers on course for victory, but second-placed Cheltenham dominated the second half and rescued a point thanks to a late brace from Darryl Duffy.
"I am gutted because I thought the way we played and the chances we created against a team who are flying high at the top of the division on their own patch was terrific," Boothroyd said.
"We played very well and we could have been out of sight by half-time with some great chances. The second half was always going to be difficult but I still felt comfortable.
"The key moment of the match was the penalty, which hit John Johnson in the face, not the hand. It's disappointing because it gave them momentum, but we still should have dealt with the second goal better.
"It's still a good point and we have to focus on what we do and a couple of good results this week could make it an even better one."
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