In my intro to bioinformatics course, we mentioned that TopHat2 and HISAT2 will both try to align as many reads as possible to the reference genome (TopHat2 has been superseded by HISAT2). For the reads that were not mapped, these probably cross exon boundaries. To solve this issue, both TopHat2 and HISAT2 chop up the unmapped reads into around 25bp fragments. Then: "TopHat2 tries to align many fragments from each read using all possible exons as the search space. HISAT2 focuses on one fragment from each read, and once that fragment has been anchored it only searches locally."
My question is about that last part "once that fragment has been anchored, [HISAT2] only searches locally." Isn't it possible that a given fragment will map to many different regions of the genome? So how is it possible that it will be "anchored"? Are we going to anchor it multiple times and see which anchor makes most sense or what exactly?