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49ers in crisis mode after loss to Colts

The San Francisco 49ers (1-2) do not look like a Super Bowl contender right now. Not even close.

Sunday’s 27-7 loss to the Indianapolis Colts (2-1) at Candlestick Park was their second straight defeat in which the offense was nonexistent — Andy Lee punted seven times.

The 49ers were penalized six times for 48 yards while the Colts drew just one flag for 10 yards.

Head coach Jim Harbaugh hadn’t lost consecutive games since 2009 while coaching at Stanford with Andrew Luck as his quarterback.

The 49ers are below .500 for the first time since he took the reins in 2011. On today’s loss, Harbaugh said post-game:

“We didn’t make plays. There wasn’t enough opportunities to make plays.”

Colin Kaepernick completed just 13-of-27 passes for 150 yards and carried seven times for 20 yards. He threw an interception and lost a fumble, looking nothing like the NFL’s biggest star and more like a third-year quarterback making his 13th start. He was sacked three times and had six passes batted down.

Kaepernick has been awful protecting the ball with six turnovers in two games; Alex Smith had six turnovers in nine starts in 2012 and just seven in 2011.

Top target Vernon Davis (hamstring) was inactive and starting wide receivers Anquan Boldin and Kyle Williams combined for eight receptions for 79 yards on 14 targets. But the only other catch of note was a 30-yard completion to Garrett Celek.

The backfield chipped in what it could. Frank Gore carried just 11 times, gaining nearly all of his 82 rushing yards on one drive, while Kendall Hunter scored on a 13-yard run. Gore also caught two passes and reportedly had “choice words” for Harbaugh near game’s end.

Meanwhile, the Colts running game torched Vic Fangio’s unit as Trent Richardson, Ahmad Bradshaw, Dee Brown, and Luck combined for 179 yards and three touchdowns. Adam Vinatieri added two field goals.

NaVorro Bowman led the defense with nine tackles and two passes defensed while Justin Smith registered five tackles including his first sack of the season along with four hits on Luck.

Rookie safety Eric Reid already looks like a Pro Bowler with his third solid game. Reid made five tackles and knocked down a pass.

Unfortunately the 49ers finished the game down two All-Pro linebackers as Patrick Willis suffered a groin injury and Aldon Smith is out indefinitely as he enters rehab following his most recent DUI arrest. Smith issued a statement:

“First off I wanted to apologize to the team, the organization, my family and everybody I let down. I also wanted to let it be known that this is a problem and it’s something that I will get fixed, and that I’ll do everything in my power to make sure that this never happens again. I also wanted to let everybody know that once again I’m sorry and, like I said, this won’t happen again.”

Team CEO Jed York supported Smith’s upcoming leave of absence when he spoke to the media today:

“… there’s not a one-day fix. This is a long-term fix. We support Aldon if Aldon is willing to fight for himself and try to make this right.”

Smith will not play in Thursday’s game at St. Louis.

The 49ers have been outscored 56-10 the past two games and are now in the first crisis of the Harbaugh-era. They need to find a solution fast.

Follow @SFBay and @drewmorita on Twitter and at for full coverage of the San Francisco 49ers.

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