#/usr/bin/perl
@ARGV = ('test.txt');
open FILE, $ARGV[0] or die "can't open file\n";

$string = '';
@file = <FILE>;
foreach $line(@file){
        if ($line =~ /^>/){next;}
        else {$string .= $line;}
} #the first line is useless so need to skip in

close FILE;
my $search = 'TTGACA';
$string =~ s/\s//g; #getting rid of whitespaces

$n = ($string =~ tr/$search//); 
print "String $search occured $n times\n\n";