CheckFree ( CKFR) shares dipped Tuesday after an analyst noted that slowing online transactions at Bank of America ( BAC) could pressure the company's growth.

The stock recently shed $1.33, or 3.3%, to $38.69, gaining back some ground after being down as much as 6% earlier in the day.

"We believe the deceleration of online bill pay customers reaffirms Bank of America's maturing online segment, and as the largest single CheckFree client it places greater pressure on growth from other CSP consumer service providers clients," Prudential analyst Bryan Keane wrote in a Tuesday note. He has a hold rating on shares of the company and his firm makes a market in CheckFree.

Bank of America grew its online bill payment clients 2.4% sequentially vs. a 4.1% increase the previous quarter, Keane noted.

In addition, "as bank M&A activity continues, it is possible that CheckFree could lose the business of one of its customers following an acquisition by another bank," he wrote. "Additionally, banks could develop in-house electronic payment systems."

Based on the uncertainty of transaction growth, Keane lowered his EPS growth rate to 15% from 18%. He has a price target of $42 on the shares.

Despite the concerns, CheckFree's second- and third-quarter results should be helped by seasonality.

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