NAME

       simpal -- proof of concept

SYNOPSIS

       simpal.pl [options] <ref seq> <target seq> [target2 target3 ...]

OPTIONS

        Set options by something like --tolerance=5 or -t 5 or whatever.
       maxLoop -- specifies max separation for the ends of the palindromes
       maxDistance -- specifies the maximum difference in palindrome length
                      when comparing palindromes
       tolerance -- max permissable misses in palindromes between sequences

       Setting either to -1 means no limit

       seedlength -- length of seeds to use for finding palindromes