There are two types of sequence editing windows. For primers or probes editing, the default is the Mutagenesis window, and for the entire sequence editing, the default is the Full Screen Edit window. You may edit the entire sequence, as well as single oligos in either window. Each Edit window contains its own menu.
The Full Screen Edit window displays the entire sequence or just a selected oligonucleotide. Either nucleic acid or protein sequences can be edited here.
The Mutagenesis window displays the edited sequence in a single line. You can switch from a nucleic acid sequence to a protein sequence in this edit mode by re-positioning the cursor. This window also displays the most stable hairpin, codon probabilities (of the a.a. at the insertion point), and several other characteristics of the displayed sequence.
The various colors of residues in the amino acid sequence represent the codon frequencies of each residue. The strongest hairpin loop is shown at the bottom part of the window and it is re-calculated in real time as you modify the sequence. Once the sequence is Accepted you may edit its features or perform various searches and analysis.