I have some sequences that I know they come from repeats, but don't know the coordinates on the reference genome. I'm using bowtie2 (they are longer sequences) and wish to set the parameters such that a lot of hits are reported (-k 10000) but they should be of high quality (--score-min L,0,-0.3). I'm not completely sure I understand this well, does setting --score-min to this value (default is L, -0.6, -0.6) actually sets the threshold to a higher quality? Do I also need to set different --mp parameters (MX,MN are 6,2 by default)? I'm quite new to this, so any help is welcomed, thanks.