-p

interpret the sequences as proteins

-x

letter to use for masking, instead of lowercase

-c

preserve uppercase/lowercase in non-masked regions

-m

file for letter pair scores (+1/-1, but -p selects BLOSUM62)

-r

probability of a repeat starting per position (0.005)

-e

probability of a repeat ending per position (0.05)

-w

maximum tandem repeat period to consider (100, but -p selects 50)

-d

probability decay per period (0.9)

-a

gap existence cost (0)

-b

gap extension cost (infinite: no gaps)

-s

minimum repeat probability for masking (0.5)

-f

output type: 0=masked sequence, 1=repeat probabilities,