Technology Review: Neanderthal Genome Unraveled

Technology Review: Neanderthal Genome Unraveled:

"Using previously sequenced genomes from other species was also crucial, says John Hawks, a biological anthropologist at the University of Wisconsin. 'Bootstrapping computer information about genomes really made all of this possible,' he says. 'To be able to take snippets of DNA of 50 base pairs or less and have the computer say that it's the same as a bacterial sequence has enabled the reconstruction of genuine Neanderthal sequence.'"

I wonder how this relates to recent findings about horizontal gene transfer? Are all of those 50-base-pair sequences unique to bacteria, or are they just "most likely to occur" in bacteria?