besides basic DNA alphabet, IUPAC code contains other letters. DNA_ALPHABET [1] "A" "C" "G" "T" "M" "R" "W" "S" "Y" "K" "V" "H" "D" "B" "N" "-" "+" "." I can get the meanings of letter but the three ones "-", "+", "." can someone kindly explains?

You could just look at the help page for DNA_ALPHABET to find out for yourself:

The DNA alphabet:

     This alphabet contains all letters from the IUPAC Extended Genetic
     Alphabet (see '?IUPAC_CODE_MAP') plus '"-"' (the _gap_ letter),
     '"+"' (the _hard masking_ letter), and '"."' (the _not a letter_
     or _not available_ letter).  It is stored in the 'DNA_ALPHABET'
     predefined constant (character vector).