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We’ve been hearing for weeks that the Kindle Fire is selling like hash browns at the Waffle House at the end of the universe, but now, one analyst says those sales have put a sizable dent in Apple’s iPad sales for the final quarter of 2011.

Morgan Keegan analyst Tavis McCourt estimates that Apple may have sold as few as 13 million iPads during the recent holiday shopping season — that’s about 2 million less than previously forecast, give or take.

Meanwhile, Amazon claimed to be selling up to one million Kindle units each week throughout the holiday season.

Additionally, the Kindle Fire was Amazon’s top best seller, its most popular gift and the product that appeared on the most wishlists for all of for the holiday season.

“Kindle Fire is the most successful product we’ve ever launched -– it’s the bestselling product across all of Amazon for 11 straight weeks, we’ve already sold millions of units, and we’re building millions more to meet the high demand,” Dave Limp, Amazon’s Kindle-focused vice president, told reporters in mid-December.

Due to the Fire’s popularity, McCourt said in a research note that he thinks Kindle sales (which he pegs at four to five million units) definitely cannibalized iPad sales in the latter months of the year.

“Clearly, a lot of folks who buy Kindle Fires simply are not in the market for a $500 tablet,” McCourt said to AllThingsD‘s John Paczkowski.

“These are customers that either would have purchased a $100 Kindle or no tablet at all,” the analyst continued. “There are some customers who clearly wanted to gift a tablet this year, and it’s cheaper to gift a Fire than and iPad. That’s where the impact comes in.”

The Kindle Fire was announced in late September, and pre-sales for the tablet-ereader hybrid started then. In addition to serving up books and magazines, the Kindle Fire can also surf the web, run apps, deliver and send email, display video content and more.

While its graphics capabilities will leave something to be desires for those with visually intense games and programs to run, the average consumer would find the Fire to be a serviceable iPad substitute.

Some sources in Apple’s supply chain have even been hinting that the company is considering building smaller versions of the iPad to compete with the Fire, the Nook Tablet and others among the iPad’s 7-inch, downmarket cousins.

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