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Paul Kitagaki Jr. Colin Kaepernick (7) flips the ball to Kendall Hunter. The 49ers had success in the running game Sunday but didn't stick with it.

Colts turned tables on 49ers

Published: Tuesday, Sep. 24, 2013 - 12:00 am | Page 1C
Last Modified: Tuesday, Sep. 24, 2013 - 12:26 am

SANTA CLARA – Conservative, mistake-free offense. A persistent running game. A defense that stonewalls running backs and produces turnovers at key moments.

The formula that has worked so well for coach Jim Harbaugh and the 49ers the past two seasons was run to near perfection Sunday. The catch: It was the visiting Colts, and not the 49ers, who had the right balance.

While Andrew Luck and Indianapolis' low-frills offense were piecing together long drives and gobbling up the clock, Harbaugh and the 49ers continued to drift farther away from the path that got them to the NFC Championship Game during the 2011 season. They had the league's fewest turnovers that year, were a defensive brick wall when it came to opponents' running games and were aided by strong special teams. The three units worked in concert.

The 49ers are discovering this season what happens when they don't mesh.

The offense suffered from terrible field position in Sunday's 27-7 loss.

The 49ers averaged 12 yards on three kickoff returns, and their average offensive possession began at the 19-yard line.

Colin Kaepernick and the offense converted only 25 percent of third downs, and the team had to punt seven times. The defense was solid through three and a half quarters but could not sustain it at the end. For the second game in a row, the 49ers gave up more than 170 rushing yards, and the Colts scored three touchdowns on the ground.

Asked whether the offense is still trying to find the right formula after switching from safe-and-steady Alex Smith to Kaepernick, Harbaugh on Monday said, "It's evolving. Are there changes? Yes."

"Football's not easy. There are struggles," continued Harbaugh, whose team is 1-2 and plays the St. Louis Rams – a team it could not beat last season – on the road Thursday night. "That's one of the things you enjoy about the game, that there are struggles. We've got some adversity, there's no question about it. And we'll also have the rare opportunity of staring adversity in the face and whipping it. That's our goal."

That sort of offensive evolution seemed like a welcome change last season when, partly due to read-option plays, Kaepernick ran for 181 yards in a playoff win against Green Bay and propelled the 49ers to the Super Bowl.

The read option and pistol formation have been lightly used this season, however, and when they have been used, opponents mostly have had answers for them.

That's forced the 49ers into a more traditional offense, and it's had mixed results. Kaepernick threw for a career-high 412 yards in Week 1. But he's struggled to find and hit open receivers in two games since.

San Francisco seemed to rediscover its roots on the second drive of Sunday's game. Frank Gore had runs of 22, 11 and 21 yards – all to the right side – and Kendall Hunter had a 13-yard touchdown run to the right as well.

Coming out of the half, the score was 10-7 Colts, and Gore got three carries on the 49ers' opening possession. But from that point on, he never had another carry despite the 49ers only being six points behind for most of the period. Harbaugh said Gore wasn't hurt, so why didn't the 49ers stick with the ground game?

"It's a discussion we've had in the past," Harbaugh said. "Why throw and not run? Why more runs in the first half than the second? Those were the plays that were called."

In the past two weeks, it's been the 49ers' opponent that's used the running game to ice the clock and wear down the defense. Seattle's offense held the ball for 36 minutes, 43 seconds, Indianapolis' for 36:25. Seventy-four of the Colts' 179 rushing yards came in the fourth quarter.

That's the type of ground game that can grind down a defense, especially when it has a short week to prepare for its next game.

Read Matthew Barrows' blogs at and listen for his reports Tuesdays on ESPN Radio 1320.

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Matt was born in Blacksburg, Va., and attended the University of Virginia. He graduated in 1995, went to Northwestern for a journalism degree a year later, and got his first job at a South Carolina daily in 1997. He joined The Bee as a Metro reporter in 1999 and started covering the 49ers in 2003. His favorite player of all time is Darrell Green.

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