Looking at just $length and $len, the code shown has the following content:

...
my $len;
my $sequenza;
...
my $j;
...
my $length = length($sequenza);
...
print "Insert query:\n";
$query = <STDIN>;
chomp $query;

$len = length($query);
...
for($j = $length; $j < $length - $len; $j--)
{
    ...
}
...
[download]

As you can see, when $length is initialized, $sequenza is undefined, so $length still has a numerical value of zero (as I pointed out above).

However, even if $length were to be initialized correctly before the for loop, the loop condition still looks wrong to me. $j is initially assigned the value in $length, and is then decremented on each iteration. The stopping condition is $j < $length - $len, and neither $length nor $len is changed in the loop body. So if the condition is initially true, i.e., if $j is initially less than some fixed value, decrementing $j will never make the condition false (well, not until an integer underflow occurs, anyway), which means you effectively have an infinite loop.

Hope that helps,