#! perl -slw
use strict;
use Time::HiRes qw[ time ];

my $start = time();

local $/;
my $DNA = <>;
$DNA =~ tr[\n][]d;

my $seek = 'AGAGAGAA';

my $p = 0;
printf "%s found at position %d\n",
    $seek, $p while $p = 1+index $DNA, $seek, $p;

printf STDERR "Took %.3f seconds\n", time() - $start;

__END__
C:\test>DNAsearch1 randDNA.txt | wc -l
Took 11.281 seconds
  15313