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for (0..$#line2) {
   my $i = $line2[$_];
...
      print $i if if $i eq $j;
   }
}

my %lookup;
++$lookup{$_} for @line2;
...
for (@line1) {
   print if $lookup{$_};
}

my %lookup;
$lookup{$_} = -1 for @line2;
...
for (@line1) {
   print if !++$lookup{$_};
}