Just guessing, but maybe something like this? 

my $temp_seq = "fooXXXXXXbar";
my $tag_seq  = "foo";

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

print $temp_seq;   # "foobar"

[download]

(removes the six characters following the search pattern "foo", which must occur at the beginning of $temp_seq)

See s/// under Regexp-Quote-Like-Operators.

Another way to achieve the same would be 

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

[download]

where $+[0] is the position after the matched pattern.

In reply to Re: Regex - remove characters (pattern not terminated) by almut
in thread Regex - remove characters (pattern not terminated) by twaddlac

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