Sequence Layout
These preferences determine the overall layout of the sequence:
- Spacing. Inserts a space at a specified interval:
- No spacing. The sequence is shown with no spaces.
- Every 10 residues. There is a space every 10 residues, starting from the beginning of the sequence.
- Every 3 residues, frame 1. There is a space every 3 residues, corresponding to the reading frame starting at the first residue.
- Every 3 residues, frame 2. There is a space every 3 residues, corresponding to the reading frame starting at the second residue.
- Every 3 residues, frame 3. There is a space every 3 residues, corresponding to the reading frame starting at the third residue.
- Wrap sequences. Shows the sequence on more than one line.
- No wrap. The sequence is displayed on one line.
- Auto wrap. Wraps the sequence to fit the width of the view, not matter if it is zoomed in our out (displays minimum 10 nucleotides on each line).
- Fixed wrap. Makes it possible to specify when the sequence should be wrapped. In the text field below, you can choose the number of residues to display on each line.
- Double stranded. Shows both strands of a sequence (only applies to DNA sequences).
- Numbers on sequences. Shows residue positions along the sequence. The starting point can be changed by setting the number in the field below. If you set it to e.g. 101, the first residue will have the position of -100. This can also be done by right-clicking an annotation and choosing Set Numbers Relative to This Annotation.
- Numbers on plus strand. Whether to set the numbers relative to the positive or the negative strand in a nucleotide sequence (only applies to DNA sequences).
- Lock numbers. When you scroll vertically, the position numbers remain visible. (Only possible when the sequence is not wrapped.)
- Lock labels. When you scroll horizontally, the label of the sequence remains visible.
- Sequence label. Defines the label to the left of the sequence.
- Name (this is the default information to be shown).
- Accession (sequences downloaded from databases like GenBank have an accession number).
- Latin name.
- Latin name (accession).
- Common name.
- Common name (accession).
- Matching residues as dots Residues in aligned sequences identical to residues in the first (reference) sequence will be presented as dots. An option that is only available for "Alignments" and "Read mappings".