#! perl -slw
use strict;

$|++;

srand 1;

sub rndStr{ join'', @_[ map{ rand @_ } 1 .. shift ] }

our $N ||= 1000;
our $S ||= 30e6;

my $chrom = chr(0) x $S;
substr( $chrom, $_, 1, ('A', 'C', 'G', 'T' )[ rand 4 ] ) for 0 .. $S-1;

my @probes = map rndStr( 10, 'A', 'C', 'G', 'T' ), 0 .. $N;

warn "Trying $N probes with perl $]";

warn time;
my $re = join '|', @probes[ 0 .. $N ];
$re = qr[$re];

printf "$-[ 0 ] : '$1'\n" while $chrom =~ m[($re)]g;

print "\n";
warn time;

__END__
C:\test>\Perl510\bin\perl5.10.0.exe -s 668954.p10 -S=1e6 -N=13104 | wc -l
Trying 13104 probes with perl 5.010000 at 668954.p10 line 18.
1203549864 at 668954.p10 line 20.
1203549867 at 668954.p10 line 27.
  11282

C:\test>\Perl510\bin\perl5.10.0.exe -s 668954.p10 -S=1e6 -N=13105 | wc -l
Trying 13105 probes with perl 5.010000 at 668954.p10 line 18.
1203549872 at 668954.p10 line 20.
1203550518 at 668954.p10 line 27.
  11282