'Edit sequence' displays the sequence of the selected contig in detail. It consists of three parts: 'Contig sequence', 'Open reading frames' and 'Selected sequence'
It also contains its own right-click menu.
This part displays the contig sequence. Left-clicking on a base will mark it in red, also a red line appears at the associated position in the 'Open reading frames'-canvas. Right-clicking on a base will open a menu for modifying it.
The blue bars above the bases represent their coverage to a maximum of 30. Then there are green, orange or red squares directly above the bases, these show conformity of the 'read'-bases, which lie at this position. If more than 90% of the 'read'-bases are equal to the 'contig'-base the square is green, it is orange by 60% to 90% and below 60% it is red.
Directly below the bases the amino acids of a selected ORF can be displayed. At last there are six lines, which represent the six frames of the nucleotide sequence. On the lines can appear blue or red regions, these are markers for start (blue) and stop (red) condons in the accordant frame.
The yellow bar in the canvas represents the contig sequence. There is a right-click menu associated with this bar. Then there are six levels, which represent the different frames of the contig. On each level the ORFs are shown in green, start codons in blue and stop codons in red.
Clicking somewhere in the canvas will move the red line to that position, it will also mark the associated base in the 'Contig sequence'. Clicking on a ORF will mark it in a dark green, the sequence of the ORF will appear below the 'Contig sequence' and in the 'Selected sequence'-panel.
Displays the selected nucleotide or protein sequence.
The two right-click menus of 'Edit sequence' contain mainly special function, but also some of the standard right-click menu.
Add to blast
Coverage
Delete
Insert
New sequence
Refresh
Replace with
Search
Show complementary strand
Translate whole frame
See 'Add to blast' in right-click menu.
See 'Coverage' in right-click menu.
Deletes the selected base from the contig sequence. This is no permanent chance to the contig.
Insert a new base at the selected position of the contig sequence. This is no permanent chance to the contig.
See 'New sequence' in right-click menu.
Redraws the 'Open reading frames'-canvas, e. g. to fit a new window size.
Replaces the selected base in the contig sequence. This is no permanent chance to the contig.
Opens a search dialog, which allows to search for patterns in a reference string. The search results will highlighted.
This option is available for the 'Contig sequence'-part and the 'Selected sequence'-panel.
Displays the complementary strand of the contig sequence in the 'Selected sequence'-panel.
Translates the whole frame from nucleotides into amino acids. Stop condons will appear as '*'.