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San Francisco 49ers quarterback Colin Kaepernick (7) avoids the tackle attempt from Buffalo Bills safety Bryan Scott (43) in the fourth quarter of their game at Candlestick Park in San Francisco, Calif., on Sunday, Oct. 7, 2012. (Anda Chu/Staff)

SANTA CLARA -- Colin Kaepernick's exciting cameos might be giving way to concern for the 49ers offense.

After early success against the New York Jets and Buffalo Bills, the WildKap scheme has lately interrupted the 49ers' rhythm instead of enhancing it.

Coincidence or not, in each of the past two games, Alex Smith had a pass intercepted on the ensuing play after a Kaepernick snap. The 49ers' production the past two games: one touchdown in 21 offensive series, not counting their kneel-down drive that capped Thursday night's 13-6 win over the Seattle Seahawks.

That begs the question: Is Smith hindered by this unorthodox and sporadic rotation?

"I'll say this: It's fun to come in when it's first down. It's not fun to come back in when it's third-and-long," Smith told Yahoo! Sports after Thursday's win. "In hindsight, it's easy to say (it's a mistake). But it's also been very effective for us at times."

Kaepernick, the 49ers' second-round draft pick last year, had a breakout performance Sept. 30 against the Jets (five carries, 50 yards). He ran for a touchdown in that game, as well as in the following week's 45-3 rout of the Buffalo Bills.

The 49ers' newfound asset didn't fare as well Oct. 14 in a 26-3 loss to the Giants, perhaps resulting in Kaepernick being used on only one snap against the Seahawks.


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Offensive coordinator Greg Roman conceded after the Giants defeat that Kaepernick's insertion indeed could disrupt the offense's flow.

"Yeah, I think that's something that we've got to be mindful of," Roman said. "Got to really take a look at and try to make the best decision for the team."

Coach Jim Harbaugh said last week that Kaepernick is merely "an added weapon" and that the 49ers are happy to get "plenty of everything" from Smith.

Running back Frank Gore insisted the offense's rhythm, or at least confidence, doesn't change when Kaepernick replaces Smith.

"When Coach brings in Kaepernick, everyone feels we can make the play work," Gore said. "It doesn't bother us."

The 49ers (5-2) are prone to use as many options as possible in their strive for unpredictability. Overall, that strategy has complemented their still-dominant defense, and they're sitting atop the NFC West heading into Monday night's visit to the Arizona Cardinals (4-3).

But the 49ers have the 29th-ranked pass offense, averaging 199.9 yards per game. Smith has slid to seventh place with a 93.9 passer rating after leading the league in passing efficiency two games ago.

When Smith said "it's not fun" inheriting an ugly down-and-distance situation, a couple recent instances proved that point.

In their loss to the Giants, a wild sequence ensued with the WildKap: Smith completed a 55-yard pass to Randy Moss, Kaepernick came in to get sacked for an 11-yard loss and Smith took over a second-and-21 situation. That drive ultimately ended with the 49ers turning the ball over on downs and trailing 23-3.

Last game, the 49ers found themselves deep in Seahawks territory thanks to a 37-yard run by Gore. Two snaps later, Kaepernick came in and was stopped for a 1-yard loss on second-and-goal from the 6. Smith returned, scrambled and spotted Randy Moss in the end zone but had his pass intercepted.

Harbaugh and Roman have consistently referred to Kaepernick as Smith's "understudy," and there hasn't been a hint of quarterback controversy inside the locker room.

"His first year was somewhat of a redshirt year. But he's doing a nice job," Roman said. "He brings in a different dynamic when we bring him in there. We can run some quarterback runs, some play-actions off those types of plays."

Having an arsenal of options stands to help the 49ers' cause as they navigate the defense-rich NFC West. The Cardinals, their next foe, offer the league's seventh-ranked defense in terms of yards allowed.

Arizona's run defense, however, ranks only 20th -- a matchup that might entice the 49ers to once again break out the WildKap, for better or worse.

For more on the 49ers, see Cam Inman's Hot Read blog at blogs.mercurynews.com/49ers. Follow him on Twitter at twitter.com/CamInman.