if # you forgot some parens here, like someone said
        {    $line1=~ /^$pattern/;
                        $line2=~ /^$pattern/;
                         $line1==$line2;
                        {  print $line1;    }
}

##</code><code>##

my $pattern='/^LOC_Os0[1-7]g[0-9]*.[0-9]\s';
...
$line1=~ /^$pattern/;
# $line1 (and 2) will expand to smth like /^^LOC_0s.../, which is probably not what you want. Try
my $pat = qr/^LOC_0s.../
$line1 =~ $pat;