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SANTA CLARA — Chip Kelly is facing the unenviable task of getting his team ready for its next game to stop the worst losing streak in franchise history.

Kelly’s 49ers have lost 12 consecutive game, with the past two coming against teams with 18 losses combined while starting backup quarterbacks. Falling to the Matt Barkley-led Bears and Bryce Petty-led Jets has Kelly trying to pick up the pieces before traveling to Atlanta to play the Falcons (8-5) and MVP candidate Matt Ryan.

“I think you just have to stand up and fight again,” Kelly said Monday.

Despite the losing streak that’s given San Francisco the second-worst record in the NFL, Kelly said his players are still playing hard.

“When you look at the tape, these guys play with great effort. They give you everything that they have,” Kelly said.

The effort wasn’t enough Sunday against the Jets. The 49ers surrendered a 17-3 lead before losing 23-17 in overtime. The offense managed just two first downs and no points in the third and fourth quarters, allowing the Jets to wear down Kelly’s last-ranked defense.

New York backup running back Bilal Powell, who scored the game-winning touchdown in overtime, ran for 145 yards on 29 carries, becoming the 10th 100-yard rusher San Francisco has allowed this season.

The Jets had the time of possession edge, 41:55 to 24:30, while the 49ers’ defense struggled to make tackles in the second half.

Kelly attributed the issues on defense to his offense being unable to move the chains.

“We didn’t stay on the field offensively,” Kelly said. “That’s the biggest thing, we need to convert, keep drives alive, and keep our defense off the field.”

The 49ers for the day converted two of 12 third downs, where they rank 27th in the NFL. Colin Kaepernick threw for 17 yards on just four-of-11 completions after halftime, continuing an ongoing trend of second-half struggles for Kelly’s offense.

It was a particularly dispiriting offensive effort after San Francisco jumped out a 14-0 lead, making Sunday the third time Kelly’s team blew a two-touchdown advantage at home this season.

Kelly faced questions when the 49ers hired him last winter about his up-tempo offense and the effects it had on his defenses at his previous stops in Philadelphia and in college at Oregon. He said Monday the no-huddle offense is moving slower than it did previously.

“If you look at us, most of the time we’re into single digits on the play clock,” said Kelly. “There’s a lot of times where we’re working it down, making sure we’re in the right play and the right protection. So, it’s not like we’re playing fast football right now. It’s just we’re not converting when we need to convert and that’s the biggest thing.”

San Francisco also dealt with injuries to key players.

The 49ers placed tight end Vance McDonald on injured reserve Monday after he sustained a shoulder injury in the first half. McDonald led the team with four touchdown receptions and was third with 24 catches for 391 yards.

McDonald signed a five-year extension with San Francisco two days before playing the Jets. The 49ers’ remaining tight ends are Garrett Celek, Blake Bell and Je’Ron Hamm.

Receiver Torrey Smith was lost in the second half with a concussion after jumping for a pass and slamming his head on the turf.

Smith needed to be carted off to the locker room after lying motionless on the field. Kelly said Smith will begin the week in the concussion protocol. Smith Tweeted after the game, “Thanks for all the prayers!”

Center Daniel Kilgore went down in the first half with a knee injury.