#! perl -slw
use strict;
use vars qw[$N];
use Benchmark::Timer; my $T= new Benchmark::Timer;
$|++;

$N ||= 10; # The number of random permutations of each string to analyse.

##my $start-seq = <STARTS>;
## No need to count frequencies just to build any array.
##my @bases = split//, $start_seq;

# Simulate the above two lines for testing
my @bases = map{ qw[A C G T N][ rand 5 ] } 1..50_000;


my $perms_count = 0;
for( 1 .. $N ) {
    # Pick our first random 7 char string
    my $sub7= join'', @bases[ map{ rand @bases } 1 .. 7 ];

    my $count = @bases - 7;         # No. of 7 chars string to match against.

    $T->start( 'search' );

    while( $count-- ) {
        printf "\r%d", $count;
    #   print 'Checking: ', $sub7;

        #Unroll the match loop
        $perms_count++ if $sub7 =~ qr '[NT][GCATN][NG][NC][NG][NT][NG]';
        $perms_count++ if $sub7 =~ qr '[NG][NT][NG][NC][NG][GCATN][NT]';
        $perms_count++ if $sub7 =~ qr '[NA][GCATN][NC][NG][NC][NA][NC]';
        $perms_count++ if $sub7 =~ qr '[NC][NA][NC][NG][NC][GCATN][NA]';
        $perms_count++ if $sub7 =~ qr '[NT][GCATN][NG][NC][NG][NT][NG]';
        $perms_count++ if $sub7 =~ qr '[NG][NT][NG][NC][NG][GCATN][NT]';
        $perms_count++ if $sub7 =~ qr '[NA][GCATN][NC][NG][NC][NA][NC]';
        $perms_count++ if $sub7 =~ qr '[NC][NA][NC][NG][NC][GCATN][NA]';
        $perms_count++ if $sub7 =~ qr '[NT][GCATN][NG][NC][NG][NT][NG]';
        $perms_count++ if $sub7 =~ qr '[NG][NT][NG][NC][NG][GCATN][NT]';
        $perms_count++ if $sub7 =~ qr '[NA][GCATN][NC][NG][NC][NA][NC]';
        $perms_count++ if $sub7 =~ qr '[NC][NA][NC][NG][NC][GCATN][NA]';
        $perms_count++ if $sub7 =~ qr '[NT][GCATN][NG][NC][NG][NT][NG]';
        $perms_count++ if $sub7 =~ qr '[NG][NT][NG][NC][NG][GCATN][NT]';
        $perms_count++ if $sub7 =~ qr '[NA][GCATN][NC][NG][NC][NA][NC]';
        $perms_count++ if $sub7 =~ qr '[NC][NA][NC][NG][NC][GCATN][NA]';
        $perms_count++ if $sub7 =~ qr '[NT][GCATN][NG][NC][NG][NT][NG]';
        $perms_count++ if $sub7 =~ qr '[NG][NT][NG][NC][NG][GCATN][NT]';
        $perms_count++ if $sub7 =~ qr '[NA][GCATN][NC][NG][NC][NA][NC]';
        $perms_count++ if $sub7 =~ qr '[NC][NA][NC][NG][NC][GCATN][NA]';
        $perms_count++ if $sub7 =~ qr '[NT][GCATN][NG][NC][NG][NT][NG]';
        $perms_count++ if $sub7 =~ qr '[NG][NT][NG][NC][NG][GCATN][NT]';
        $perms_count++ if $sub7 =~ qr '[NA][GCATN][NC][NG][NC][NA][NC]';
        $perms_count++ if $sub7 =~ qr '[NC][NA][NC][NG][NC][GCATN][NA]';

        # Drop the first char and tack a new one on the end.
        $sub7 = substr( $sub7, 1 ) . $bases[ rand @bases ];
    }
    $T->stop( 'search' );
}

print 'Found: ', $perms_count, ' matches in';

$T->report;