A graphical representation of where the open reading frames are in all 6 reading frames is shown. The ORFs are displayed as blue boxes.
ORFs in this program are defined as being regions between START and STOP codons.
Note that this definition of an ORF would miss those exons in eukaryotic genomic sequences which do not contain a START codon. plotorf is only really useful when dealing with prokaryotic or mRNA eukaryotic sequences.
The default START codon is: "ATG".
The default STOP codons are: "TAA,TAG,TGA".
You can specify your own set of start and stop codons using the -start and -stop qualifiers.
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Note that this definition of an ORF would miss those exons in eukaryotic genomic sequences which do not contain a START codon. plotorf is only really useful when dealing with prokaryotic or mRNA eukaryotic sequences.