Maybe this?

use Data::Dumper;

my $lines;

while( <DATA> ){
  /^\s*$/ and next;s/\n//;
  $lines->{$_}{count}++;
  push @{$lines->{$_}{linenum}}, $.
}

print Dumper($lines);

__DATA__

one
one
aaa
bbb
ccc
aaa

__END__

          'one' => {
                     'count' => 2,
                     'linenum' => [
                                    '2',
                                    '3'
                                  ]
                   },
          'bbb' => {
                     'count' => 1,
                     'linenum' => [
                                    '5'
                                  ]
                   }
...
[download]