RepeatMasker: screens DNA sequences for low complexity DNA sequences and interspersed repeats (Smit. A, Green. P)

Sequence File : please enter either :

1. the name of a file:
2. or the actual data here:

(sequence format)


Species options


Masking options


Running options


Output options

1. the name of a file:
2. or the actual data here:

only clips E coli insertion elements (-is_only)
clips IS elements before analysis (-is_clip)
skips bacterial insertion element check (-no_is)
only checks for rodent specific repeats (-rodspec)
only checks for primate specific repeats (-primspec)

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Running options

Output options

Shows the alignments in a .align output file (-a)
Alignments are presented in the orientation of the repeat (with option -a) (-inv)
Saves a sequence (in file.cut) from which full-length repeats are excised (-cut)
Returns complete masked sequence in lower case (-small)
Returns repetitive regions in lowercase (rest capitals) rather than masked (-xsmall)
Returns repetitive regions masked with Xs rather than Ns (-x)
Reports simple repeats that may be polymorphic (in file.poly) (-poly)
Creates an additional output file in ACeDB format (-ace)
Creates a General Feature Finding format output (-gff)
Creates an untouched annotation file besides the manipulated file (-u)
Creates an additional output file in cross_match format (for parsing) (-xm)
Creates an (old style) annotation file with fixed width column (-fixed)
leaves out final column with unique ID for each element (-no_id)
calculates repeat densities excluding runs of >25 Ns in query (-e)

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Some explanations about the options