Finds all exact matches of a given size between 2 sequences emboss wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto Sequence 1 Sequence 2 Word size Output Alignment File Format Match (m) Simple (m) FASTA (m) MSF (m) SRS (m) Pair (p) Markx0 (p) Markx1 (p) Markx2 (p) Markx3 (p) Markx10 (p) SRS pair (p) Score (p) Output Feature 1 File Format GFF EMBL SwissProt Output Feature 2 File Format GFF EMBL SwissProt .. class:: warningmark The input datasets need to be sequences. ----- You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html