Finds MAR/SAR sites in nucleic sequences emboss marscan -sequence $input1 -outfile $out_file1 -rformat2 $out_format1 -auto Sequence Output Report File Format GFF EMBL GENBANK PIR SwissProt DbMotif Diffseq Excel (tab delimited) FeatTable Motif Regions SeqTable SRS Simple SRS Table TagSeq

You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/marscan.html