use strict;
use warnings FATAL => 'all';

my $count1 = 0;

my $line = do {local $/; <DATA>;};

$line =~ s/\n//g;

while (($line =~ m/(?:aaggt){2}([atgcn]{100,})/ig)) {
    $count1++;
    print " $1\tcount1 \t $count1\n";
}

__DATA__
aatgatgataaggtaaggtatgatgatgatgatgatagtagannnnnnnnnatgcatgaatgcaatgactagcaatgac
tagcaaggtaaggtaaggtaaggtaaggtatgatgatgannnnatgatgactagactgacaaggtaaggtaaggtatga
tgatgatcgatgacgat

##</code><code>##

open my $inFile, '<', $fileName or die "cannot open $fileName: $!\n";