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Ribbon multiple alignment and trace file edition
 Edit button
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 More button
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 Align sequences and optimize directions
- Align the selected sequence only.
- Align all sequences.
- Reverse the direction of the selected sequence.
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 Find conflicts
Go from the selected position to the previous or next conflict.
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 Find primers
Saved primers can be selected and used to find the position of the primer in the sequence(s).
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 RC primer
Activate this button to search for the reverse compliment primer sequence.
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 Find sequence
Search for a given part of the sequence.
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 Base caller
This value is used to calculate the threshold level, depending on the selected algorithm in the Options dialog.
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 Zoom in/out horizontally
Adapt the width of the peaks.
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 Zoom in/out vertically
Adapt the height of the peaks.
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 Higher/Smaller
Enlarge the height of the sequence section.
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 Collapse/Expand
Collapse or expand the sequence section (expand to see the waves).
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 Show or hide chromatogram
Show or hide chromatogram for each of the nucleotides.
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 Confidence level
Show or hide the level of confidence of the consensus base pare at any given point of the alignment.
A confidence value can be computed for each nucleotide. The trace wave is giving the intensity of the signal for each of the four nucleotides.
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 Majority rule display
When checked this option will display the most frequent letter at any given point of the alignment.
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 Ambiguity letters
Letters displayed in the consensus sequence are ambiguity letters instead of majority rule letters.
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 Colored background
Letters will be displayed in black with colored background.
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 Show colored letters
Letters will be displayed in colors with a white background.
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 Regular interval
When checked, this option makes the interval between base pairs regular or standardized. Otherwise the original trace file file is displayed.
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 Show conflicts
Check this button to see the conflicts between the basepairs. When unchecked, the protein letters are displayed (based on selected the Protein translation option).
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 Protein translation options
Frames: 1, 2 or 3. Position of the 3 nucleotides being translated to protein. Shifting 1 position each frame.
Genetic code: DNA is translated to proteins using these genetic codes:
Choose from: Standard, Mitochondrial, Yeast Mitochondrial, Invertebrate, Ciliate Nuclear, Echinoderm Mitochondrial, Mycoplasma, Bacterial.
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 Redraw tree
Select one of the nine provided algorithms to (re)draw a tree based on the sequences.
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 Toggle tree display
Removes the drawn tree in front of the multiple alignment.
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