Options (default settings):¶

-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 score matrix

-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)

-i

match score (BLOSUM62 if -p, else 2 if -f4, else 1)

-j

mismatch cost, 0 means infinite (BLOSUM62 if -p, else 7 if -f4, else 1)

-a

gap existence cost (0)

-b

gap extension cost, 0 means no gaps (7 if -f4, else 0)

-s

minimum repeat probability for masking (0.5)

-n

minimum copy number, affects -f4 only (2)

-f

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

2=repeat counts, 3=BED, 4=tandem repeats (0)

-h, --help

show help message, then exit

--version

show version information, then exit