Another way is to use map on the original array and set all the entries which you don't want to '', and filter those out lateron..

my @set = qw (AAAAAT ATCGAT TTTTTG GCCCCC GTGGGG);
my $lim = 0.75;
my $len = length $set[0];

print "BEFORE:",scalar(@set),"\n";

map  { ( ((tr/A//)/$len < $lim) &&
          ((tr/T//)/$len < $lim) &&
          ((tr/C//)/$len < $lim) &&
          ((tr/G//)/$len < $lim)    ) or $_ = '' } @set;

print "AFTER:",scalar(@set),"\n";
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Now the @set contains:

$VAR1 = '';
$VAR2 = 'ATCGAT';
$VAR3 = '';
$VAR4 = '';
$VAR5 = '';
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