Many of the EMBOSS programs produce reports as output. These can have various formats (and are user selectable). So if, instead of the somewhat pictorial display of motifs seen in the previous exercise, one wanted a 'listfile' so that the individual sequence matches could be retrieved for some later purpose, the report format can be specified using the -rformat qualifier. Illustrating this with the previous example:

% patmatmotifs L07770.pep -rformat listfile
Search a PROSITE motif database with a protein sequence
Output report [L07770_1.patmatmotifs]: L07770_1.patmatmotifs
% more L07770_1.patmatmotifs

########################################
# Program: patmatmotifs
# Rundate: Wed 18 Feb 2009 15:03:36
# Commandline: patmatmotifs
#    [-sequence] L07770.pep
#    -rformat listfile
#    -outfile L07770_1.patmatmotifs
# Report_format: listfile
# Report_file: L07770_1.patmatmotifs
########################################

#=======================================
#
# Sequence: fasta::L07770.pep:L07770_1     from: 1   to: 354
# HitCount: 2
#
# Full: No
# Prune: Yes
# Data_file: /m2/emboss/emboss/emboss/data/PROSITE/prosite.lines
#
#=======================================

fasta::L07770.pep:L07770_1[123:139]
fasta::L07770.pep:L07770_1[290:306]

#---------------------------------------
#---------------------------------------

You can now retrieve these sequences using e.g. seqret with L07770_1.patmatmotifs as a 'listfile'.

There are other report formats (including feature table style formats). The EMBOSS web site has up to date documentation on the formats that are available.