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my $temp_seq = "fooXXXXXXbar";
my $tag_seq  = "foo";
...
$temp_seq =~ s/^($tag_seq)\w{6}(.*)/$1$2/;

print $temp_seq;   # "foobar"

if ($temp_seq =~ /^$tag_seq/) {
    substr($temp_seq, $+[0], 6) = '';
}