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for($i=0;$i < length($string)/$len; $i++) {
    $codons[$i] = substr($string,$i*$len,$len);
}

$start=0;
for ($pos=0; $pos < length($string)-1;$pos++) {
...
} # end loop across letters of string

$runs[$i++] = substr($string,$start,$pos-$start+1);