The output file is list of intergenic sequences, one contig for each. Also, the line numbers of the original masterfile are maintained. Each non-coding region in the masterfile will be in a separate contig. Pepper will assign appropriate name to those contigs. It will be used only to determine the genetic code to use during translation, to define deviations to the current code or to redefine the start codons.
Pepper produces on output a file which contains the genetic elements found.
Note that invalid qualifiers will be ignored by pepper. The switch -x should not be considered to infer anything as to the type of genetic element to extract. To extract all orfs, specify the string 'orf'. Pepper does not support any kind of wild-card character for the gene string specification. So every character is treated as is, except the comma.