Another option, that is mostly straightforward...

#!/usr/bin/env perl

use strict;
use warnings;
use List::Util qw(zip);

my $str1='LFGSLSIIVAHHM';
my $str2='LFGSLSIIVSHHM';

my ($s1len, $s2len) = map {length} ($str1, $str2);
die "Length mismatch: $str1 ($s1len) != $str2 ($s2len).\n"
    if $s1len != $s2len;

my $match = grep {$_->[0] eq $_->[1]}
            zip [split //, $str1], [split //, $str2];
my $mismatch = $s1len-$match;

print "Matches: $match\nMismatches: $mismatch\nPercent match: ",
      sprintf("%.01f", ($match / $s1len) * 100),
      "\n";
[download]

The output is:

Matches: 12
Mismatches: 1
Percent match: 92.3
[download]

This uses List::Util, which is a core Perl module, and aside from the slightly mysterious 'zip', reads like how a person would think through the problem; compare the first letter, compare the second, compare the third, and so on. No real magic that would require a #comment