Thanks everyoene for your help. This is the finished code in case you're interested. 
#!/usr/bin/perl
use strict;
use warnings;

my $infile = $ARGV[0];
unless (open (INFILE, "$infile")){
        print STDERR "Can't open $infile $!\n";
        die;
}

my ($header, $count , $match) = ('',0,0);
print "\n\n";
#This algorithm will work only when the sequence is on one line
while (<INFILE>) {
                chomp;
                if ($_ =~ />(.*)/) { #a header line
                                $header = $1;
                                $count++; #keep running total of seque
+nce number
                }
                else { #not a header
                                my $i = 0;
                                while ( $_ =~ /([VILMFWCA]{8,})/g) {
                                                my $domain = $1;
                                                my $len = length $doma
+in;
                                                $len--;
                                                if ($i == 0){
                                                        print "Hydroph
+obic strecth found in: $header\n";
                                                        $match++;
                                                        $i++;
                                                }
                                                print "$domain\n";
                                                print "The match was a
+t potistion: ", pos() - $len, "\n";;
                                }
                                if ($i > 0){
                                        print "\n\n";
                                }
                }
}
close INFILE;
print "Hydrophobic region(s) found in $match sequences out of $count s
+equences\n";

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In reply to need help with a regex by aquinom

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