#!/usr/bin/perl
use strict;
use warnings;

my $FILE;

open (my $out, ">output.txt");
if (open $FILE, "<", 'chr.fa')
{
}
else
{
	print "Enter file name:\t";
	$FILE=<STDIN>;
}

local $/ = ">";
my $count = 0;


while (<$FILE>) 
{
    chomp;
	if ( $_ =~ /^(.*?)$(.*)$/ms) 
	{
		my $header = $1;
 		my $seq = $2;
 		$seq =~ s/\s//g; 
		while ( $seq  =~ /([AAGC)/g) 
		{
		 	print $out $1, "\n";
		 	$count = $count +1;
		}
	}
}
print $out "$count sequences were found\n";