Answer to http://nagoyascala.yoshihiro503.cloudbees.net/bbs/thread/114001

gistfile1.aw

<?php
function mkPerms($temp, $alphabet, $depth){
  if($depth==0){ return array($temp); }
  else{
    $ret = array();
    foreach($alphabet as $a){
      $ret = array_merge($ret, mkPerms($temp.$a, $alphabet, $depth-1));
    }
    return $ret;
  }
}
$a = array("A","C","G","T");
$perms = mkPerms("",$a, 5);
foreach( array_filter($perms, function($a){ return strstr($a, "AAG")!==false; })
  as $ans ){
  echo $ans."\n";
}