I'm slightly confused by the way Bowtie reports reads that align to multiple locations. If I understand correctly from the manual, http://bowtie-bio.sourceforge.net/manual.shtml#reporting , by default only 1 alignment is returned (-k 1). But this may not necessarily be the best alignment, because then --best must be specified aswell. So is this a random or just a 'good' alignment? And what is the difference with -M 1? According to the manual this gives 1 random alignment from the best alignments, but is this not the same as -k 1?