I think getting one scalar out of a pair of arrays is going to give you one list (rather than the pair you want to compare). You can try this by adding a print $base line right inside the loop and seeing how many times it loops. Also, unless lines1 is an array of arrays, you want to get your character from it through a scalar like $lines1[0].

Depending on how good you are with perl you might find the following alternate too simple (or too c-like) but the foreach loop can replace the for loop (I think). And I never liked shifting.

# e.g @lines1 contains CACTATGAGTGATCGC and @lines2 contains
# ACTGACTAATGCGTTG.

@lines1= split(//,"CACTATGAGTGATCGC");
@lines2= split(//,"ACTGACTAATGCGTTG");

$line1length=@lines1;
$line2length=@lines2;

print ("1 :",@lines1,"\n");
print ("2 :",@lines2,"\n");


if ($line1length!=$line2length) {
    
    print "Length Mismatch\n";

} else {
    print "M :";
    for ($x=0;$x<$line1length;$x++) {
        if ($lines1[$x] eq $lines2[$x]) {
            print $lines1[$x];
        } else {
            print "*";
        }
    }
    print "\n";

}
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-- termix