If your ignore set are too complicated for character classes, you can OR them together into a regex. I doubt it would be necessary here, more likely for sets fo words.
my $ignoreStrings = join "|", @ignore;
my $deleteThese = qr/$ignoreStrings/g;
$strting =~ s/$deleteThese//;
By the way, you're using $_ to represent the various elements of @ignore, but also to denote the default object of s///. That's why I tend to avoid defaults .... better to be explicit, self-documenting, and avoid irritating errors.
--
TTTATCGGTCGTTATATAGATGTTTGCA