$ cat abc.pl 
#!/usr/bin/perl
use strict;
use warnings;

my $string = "AATCGGGTATGAAAAATTTTGCCGGCGTTTGCG";

if ($string =~ /ATGAA(.*?)TGCCG/) {
    my $sequence = $1;
    print "Found it: '$1'\n";
}
else {
    print "I don't see it!\n";
}

$ perl abc.pl
Found it: 'AAATTT'