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This loss could pay off for Patriots

The 49ers offense appeared to turn Rob Ninkovich and the Patriots defense upside down at times on Sunday night.

Jim Davis/Globe Staff

The 49ers offense appeared to turn Rob Ninkovich and the Patriots defense upside down at times on Sunday night.

FOXBOROUGH — You didn’t think it was going to be that easy, did you?

That the Patriots were just going to keep beating their opponents like a drum, the young defense was just going to keep getting better and roll to a long-awaited (around here) fourth Super Bowl title to put a bowtie on the greatness of Bill Belichick and Tom Brady?

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In the National Football League, no matter how comfy things are in the AFC Least, things are never that easy.

The Patriots put on a wake-your-kids-up-so-they-can-see-it comeback — trailing, 31-3, with 10:26 left in the third quarter to tie it at 31 with 6:43 left in the fourth quarter — but eventually lost to the 49ers, 41-34, Sunday night at Gillette Stadium.

What happened in the final flurry clouded it a bit, but what the Patriots will take out of this game is a much-needed dose of reality, especially for the defense.

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And they’ll be much better for it in the long run.

That’s the type of loss that teaches the lessons that will be heeded and applied in January and, hopefully, February.

“[The performance was] not good enough to win against a quality team like the 49ers,” linebacker Jerod Mayo said.

Since surviving the Jets in overtime Oct. 21, the defense has been able to rely on a 12th player — the scoreboard — in rolling to their last six victories prior to Sunday night.

The Patriots had leads of 28-7 (Rams), 31-17 (Bills), 38-17 (Colts), 35-0 (Jets), and 23-10 (Dolphins). The Patriots’ defense certainly played their part in building those leads, but while it gets harder to play offense with a lead — look at the 49ers after getting up, 31-3 — it gets much easier to play defense.

In the secondary, you just worry about not getting beat deep to avoid quick chunk plays. Up front, you can rush the passer with reckless abandon because if the opponent runs the ball, all the better because the clock will keep moving toward zero.

And in the process, some of your minor flaws get masked.

But against a quality opponent like the 49ers, they come to light.

In the past few weeks, the Patriots’ defense has blown some coverages, not filled against the run properly, and exhibited some shoddy tackling.

It was certainly good enough to win and the type of performance of which 85 percent of the league would be envious.

And considering the average age of the defense is just 25.6 years and includes three rookies, it was play that was admirable and showed improvement.

But while the Patriots were playing good enough to roll to regular-season victories, and even against an AFC contender like the Texans, that type of play would not be good enough against the elite competition that will stand in the way of another Lombardi Trophy: the Broncos in the AFC, and the 49ers, Packers, Falcons, and Giants in the NFC.

The 49ers came out and did what opponents should do against the Patriots: go wide open with a passing attack. There were completions of 11, 13, and 12 yards on the first three plays as second-year quarterback Colin Kaepernick was hardly rushed and saw his reads clearly.

On third and 7, a down that favors the defense, not only did the 49ers score on a 24-yard pass to Randy Moss, but Moss did it rather easily. Rookie cornerback Alfonzo Dennard didn’t reroute Moss, and safety Devin McCourty, despite having two vertical routes on that side of the field, was way too late to clean up a play that he should break up.

There was a 35-yard pass interference penalty on Aqib Talib on which the ghost of the problematic early-season secondary — failure to turn around and locate the ball — made another appearance.

In the second quarter, Kaepernick didn’t have much trouble finding tight end Delanie Walker on a 34-yard touchdown pass that made it 14-3. With three defensive tackles — Vince Wilfork, Brandon Deaderick, and Kyle Love — rushing with Rob Ninkovich, Kaepernick looked comfortable in the pocket, throwing after 3.27 seconds.

But there was also the issue of no one rerouting tight end Vernon Davis, which meant Dennard was in the impossible position of having to choose between Davis and Walker as he attempted to cover a third of the field in Cover 3.

To close the half, the 49ers toyed with the Patriots on a monster 15-play, 76-yard drive that used up all of the 6:04 left on the clock. On the drive, rookie linebacker Dont’a Hightower lost containment against Kaepernick — one of the key game plan points was to keep the athletic quarterback in the pocket — or failed to stay in his gap rushing the passer three times. Brandon Spikes ran into the wrong gap on a 15-yard run and didn’t offer much defense on a 10-yard pass to Davis.

To start the second half, the 49ers easily converted on third and 15 — on a 26-yard screen pass to Frank Gore, no less — on which rookies Chandler Jones and Justin Francis just missed Gore, and the safeties were nowhere to be seen until well after the first-down marker. The Patriots were bailed out by a terrible decision by Kaepernick that resulted in a McCourty interception.

The 49ers went up, 24-3, on a touchdown run by Gore where the ball was fumbled 5 yards backward yet still run in basically untouched.

The score was 31-3 when Kaepernick, again under no rush, split McCourty and Steve Gregory on a 27-yard pass.

“It was frustrating,” Mayo said. “It was very disappointing.”

But after that, the Patriots’ defense got after it. They hit hard. They covered. They rushed Kaepernick well and even sacked him on a huge 13-yard loss by Ninkovich.

They made the plays the Patriots desperately needed to get back into the game.

They’ll be able to remember that when they get into another dogfight in the playoffs.

But only if they heed the warning signs that were covered during the win streak, then illuminated in the loss to the 49ers.

The players, especially the less-experienced ones, won’t be able to gloss over their mistakes because of the scoreboard and a bunch of victories.

They now know again, for the first time in two months, that less than fundamentally sound play against a tough opponent can lead to a loss.

Better they learn that now than in January.

It was a tough, emotionally draining loss for the Patriots and their defense. But it could be one that leads to a more important victory down the line.

Greg A. Bedard can be reached at gbedard@globe.com. Follow him on Twitter @gregabedard.
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