1. To run a single query across a genome place both sequences in FASTA format into a single file that we will call "input". 2. Then make sure the Probalign 1.4 local alignment version available from http://cs.njit.edu/usman/RNAgenome/probalign1.4_local.tgz is compiled and in the current directory as the scripts. The executable should be called just "probalign". 3. Finally run "perl cover.pl input 26 1 6 > output". The last three numbers are default and recommended gap open, gap extension, and temperature values.