As well as viewing the sequence in the main view of the window, this editor has multiple tabs in the same way that the Single Sequence editor and the The MSA Editor have. These are accessible using the various tabs below the toolbar. The Map tab will show a graphical representation of the Features table. It will also show aligned and unaligned reads. This view is connected to the sequence view and with two Replica windows open, clicking a feature will move to and show that selected sequence in the sequence window.
- Use the horizontal scroll bar at the bottom of the window to scroll through the assembly. The lower trace files will also scroll (if that panel is visible) - only those traces that overlap the center base in the currently visible consensus sequence will be displayed.
- The vertical scroll bars let you scroll through the sample sequences in both the upper and lower panes. Note that each sample sequence gets its own line in the upper pane if you are in "Tiled Mode". Click on the preferences toolbar button to change the display mode.
- Use the vertical and horizontal splitter controls (next to the scrollbars) to resize the upper pane and the left margin.
-The main Editor tab, the Map tab and the Features table tab are all connected. If you have multiple Replica windows open, then clicking a feature in the Map tab and/or the Features Tab will move to and show that selected sequence in the sequence window. To select a single feature of a multi segmented feature hold down the OPTION key whilst clicking on that feature.
- If you click on the title "button" in the upper left margin, that will select the sample sequence and also automatically scroll the alignment to ensure that sequence is visible.
- Double-clicking on any sequence (including the reference) selects that entire sequence. If you have aligned a cDNA/mRNA sequence then this only selects either the exon sequence or the intron (represented by gaps). Also in this mode you can move between exons and introns by use of the [OPTION] + left/right cursor keys. This is very useful for annotating either introns or exons to your sequence.
- You can drag select in the consensus sequence to select the corresponding region in all overlapping trace files.
- Visual cues in the left hand margin indicate the direction of assembly of each sample sequence.
- If you click or drag-select on a sample sequence, the display does not automatically become realigned. However, the selection is replicated in both the upper and lower panes so that you can easily see the trace region corresponding to the residues in the upper pane.
- Similarly, you can select the residues in the trace panes to highlight residues there and in the corresponsing sample sequence in the upper pane.
- You can select the residues in the trace panes to highlight residues there and in the corresponsing sample sequence in the upper pane.
- If you click on the consensus sequence, the display is refreshed so that the traces are centered at the selected residue. The consensus and all sample sequences become highlighted at that position. Use this to quickly align traces so that you can examine the source of mismatches in the chromatograms. The consensus is highlighted in the primary highlight color - the others get highlighted in gray to indicate they are selected, but are not the primary focus.
- If you click on the reference sequence, the display is refreshed so that the traces are centered at the selected residue. The reference, consensus and all sample sequences become highlighted at that position. Use this to quickly align traces so that you can examine the source of mismatches in the chromatograms. The reference is highlighted in the primary highlight color - the others get highlighted in gray to indicate they are selected, but are not the primary focus.
- Clicking in the consensus sequence is very similar to clicking in the reference, except that the reference sequence is not highlighted and the consensus gets the primary highlight color.
- If you click or drag-select on a sample sequence, the display does not automatically become realigned. However, the selection is replicated in both the upper and lower panes so that you can easily see the trace region corresponding to the residues in the upper pane.
- Double-clicking on any sequence (including the reference) selects that entire sequence.
- Click on the "Show Dots" toolbar button (has two small rows of "AGCT") to toggle the display mode so that all matches between sample sequences or the consensus and the reference squence are shown as dots. This makes it extremely easy to visually identify important mismatches.
- Click on the "Find Mismatches" toolbar button (the small binoculars) to find the first Mismatch. Click the next Mismatch button to move between mismatches. The assembly is automatically scrolled and the reference residue highlighted so that you can immediately see the trace files aligned at that position.