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ATLANTA — Attrition struck the already undermanned 49ers hard Sunday as they lost their 13th consecutive game, extending that franchise record with a 41-13 defeat to the Atlanta Falcons.

Safeties became middle linebackers. Offensive linemen debuted in new spots. Colin Kaepernick stayed put, but he lost another center, wide receiver and tight end in the process, for a second straight game.

“I hadn’t been in a game like this,” 49ers coach Chip Kelly said. “I had to do a lot of mixing and matching. Give our players credit. Some had to play a little bit out of position at times.”

The shuffling began even before kickoff, when the 49ers (1-13) did not dress starting linebacker Gerald Hodges, and although general manager Trent Baalke attributed that disciple to a rules violation, Kelly repeatedly claimed it was a “coach’s decision.”

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Hodges’ absence, compounded by the fact NaVorro Bowman and Ray-Ray Armstrong are on injured reserve, resulted in the 49ers promptly running out of linebackers.

Nick Bellore exited with an elbow injury on the third snap, and the 49ers scrambled. That meant converted safeties Antoine Bethea and Vinnie Sunseri, and even outside linebacker Ahmad Brooks, had to fill in next to Michael Wilhoite, their only healthy inside linebacker on the roster.

“Just the nature of the game. That’s the league,” Kelly said. “Everybody has the same rules. We all dress 46. We kept trying to make the 46 work.”

It didn’t work, as the Falcons (9-5) raced to a 21-0 lead and let the 49ers only get as close as 28-13, the halftime score.

Now having lost all nine of his starts this season, Kaepernick said the 49ers must make beyond “pieces here and there” to return to contention, four years after clinching a Super Bowl berth here.

“It can also be the culture of this team changing, which it needs to,” Kaepernick said. “We have to be able to create our opportunities and go out and create wins for our team.

“We have to create a culture of winning, and winning by any means,” added Kaepernick, who can opt for free agency in March. “Right now our culture isn’t that.”

The 49ers have lost 16 of 17 road games dating back to December 2014, and all but three defeats were by at least 10 points. An 0-8 road record this season — and the potential No. 2 overall draft pick — is at stake if they fall Saturday to the Rams, their first meeting in Los Angeles since 1994.

The Falcons’ Matt Ryan (286 passing yards, two touchdowns) and Davonta Freeman (139 rushing yards, three touchdown runs) preyed on the 49ers’ jumbled defense.

Amid the carnage, the 49ers set a single-season record for most rushing yards allowed in a season, yielding 248 on Sunday and raising their season total to 2,468 yards; the previous record was 2,365 yards in 1978.

The league’s highest-scoring team pumped out touchdowns on 4 of 5 possessions before halftime, and the only time they were denied, Wilhoite forced and recovered a fumble at the 49ers’ 1-yard line. The Falcons set a single-season franchise record for most points in the process of Sunday’s first-half scoring spree.

Kaepernick and Brooks were the only 49ers starters also in the lineup their last visit to Atlanta, when they rallied to win the NFC Championship four long seasons ago.

“With Patrick Willis retiring, Justin Smith retiring and some other big-name guys leaving the team, we just have to rebuild,” Brooks said. “I guess we’re in the rebuilding stage right now.

“This season may be over but we still have two games left. Then we’ll see what’s going to happen next season,” Brooks, an 11-year veteran, added. “I’m not in the rebuilding stage of my career. … I really have no time to be rebuilding. I want to win.”

Brooks, their starter at left outside linebacker since 2011, made a cameo at inside linebacker after Sunseri and Bethea gave it a shot.

“I haven’t played inside linebacker in 10 years, and I felt the wrath of it,” Brooks said. “It’s a different beast out there. You have to do a lot of running.”

Bethea volunteered to switch spats and eventually settled in at linebacker during the 49ers’ second-most lopsided loss of the season; they fell 45-16 at Buffalo on Oct. 16.

“I played safety in this defense, I sit in the meeting rooms, and as a pro, you have to know what other players do around you as well,” Bethea said. “That’s what kind of helped me out, being able to plug in.”

Other adjustments had to be made as wide receiver Quinton Patton (foot), tight end Blake Bell (shoulder) and cornerback Jimmie Ward (shoulder) did not return from first-half injuries. In the third quarter, an ankle injury forced out Marcus Martin, who made his first start this season at center in place of an injured Daniel Kilgore.

With left tackle Joe Staley (hamstring) out a second straight game, the offensive line took on more of a makeshift look in the fourth quarter, as rookie John Theus made his debut at Staley’s spot. Zane Beadles had started his second straight game at left tackle but moved to center upon Martin’s exit.

The 49ers got shut out after halftime for a third straight game, the first time that’s happened in franchise history since 1999.

“At halftime, our mentality was if we get a stop out of the gate and go down and score, it’s a one-score game,” Kaepernick said. “We had an opportunity to close that gap. We weren’t able to do that.”