Try using a regex, by replacing your 'X' with '.', you can easily check if they match, something like (untested):

my $t="ABCDABCDXBCDABCXABCDXXCDABXD";
$t =~ s/X/./g;

my $u="ABCDABCDABCDABCDABCDABCDABCDABCDABCDABCD";
if ($u =~/$t/) {
   print "match found\n";
}
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...roboticus

When your only tool is a hammer, all problems look like your thumb.