$x ||= something; is commonly used to give $x a value if it hasn't one already (more correctly, if the current value is false). In the case cited it is to pick up the first non-zero length of a dna string. There is an implicit assumption that all dna strings are the same length.

Note that Perl returns the value of which ever true value it finds when evaluating || (not simply a true or false value) so $x gets the value 'something' regardless of what the nature of 'something' is if $x is false to start with. In particular, this trick can be used to set a scalar to a default string if the scalar hasn't been set already:

my $error;

...

$error ||= 'No error found';
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