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

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