^ in this case is bitwise-OR.

When you bitwise-OR two strings, where the bytes in the two strings are the same, the byte in the resultant string will be chr(0); when they are different, the results will be non-chr(0). This allows you to count the number of differences in two strings very quickly:

$seq1 = 'ACGTACGTACGTACGT';;
$seq2 = 'TCGATCGATCGATCGA';;

print ( $seq1 ^ $seq2 );;
§  §§  §§  §§  §

print length( $seq1) - ( $seq1 ^ $seq2 ) =~ tr[\0][\0];;
8
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