Even when the Patriots found themselves down 28 points against the 49ers Sunday, quarterback Tom Brady was confident his team could rally.

“I thought we were going to come back and win the game,” Brady said Monday on WEEI’s Dennis and Callahan show. “A lot of our problems on offense were self-inflicted, and I have a lot of respect for that defense. They rush, they cover, they’re physical, they force turnovers. It was just a sloppy game by us; it was a sloppy game by both teams in some respect. They just weren’t quite as sloppy as we were. You can’t play 25 minutes of good football against a good team. You just can’t do it.

“When you dig yourself a hole, you’ve got to dig yourself out of it,” he said. “We almost did. We just didn’t do quite enough.”

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Brady was unhappy with a fourth-quarter sequence in which the 49ers were granted a timeout as Brady attempted to run a hurry-up offense. He had the ball in his hands after it was snapped and the play blown dead, and he reacted with disgust, spiking the ball into the ground.

“They were trying to call a timeout and the ball got snapped and then they blew the whistle to stop the play ... You can’t call time out in the middle of the play and we had an uncovered receiever out there so ... we had a few out there that I couldn’t understand.”

The Patriots have already clinched the AFC East title, but Brady said that they still have regular season games to concentrate on before they start thinking about the playoffs.

“We don’t get too far beyond the next week’s opponent ... It was about playing a really good team during Sunday Night Football and the things we needed to do to get that done. Now it’s Jacksonville. Our season is not over by any means. We lost to a good team playing very average football. We’re 10-4, it’s certainly not a great record but it’s where we deserve to be. We’ve got to be able to move on with mental toughness this week.”

After the game, Brady exchanged friendly words with 49ers’ QB Colin Kaepernick.

“I wished him luck,” said Brady. “He’s obviously got them winning and that’s the most important thing in football games.”

Tight end Rob Gronkowski started practicing with the team again this week after a broken forearm kept him off the field for four weeks, and Brady said the timing of Gronk’s return to games is uncertain.

“He is a big help to our offense with what he is able to do both in the run game and the pass game,” Brady said. “He’s really a dynamic player for us, so whenever he’s ready to go, I’m sure he’ll be out there ... I know he doesn’t want to be sitting there, I’ll tell you that.”

Brady has three children, and his his oldest, son Jack is a five-year-old kindergartener. He spoke briefly on the shootings at an elementary school in Newtown, Conn., on Friday.

“It certainly puts a lot of things in perspective,” Brady said. “Who knows why these things happen bu t... you realize that what we did last night just pales in comparison to what the families of the victims are feeling this week, so our thoughts are with them.”