Pairwise Alignment section

To access options affecting the display of pairwise alignments in the Pairwise view, click on the Style panel expand bar entitled Pairwise Alignment, or choose View > Style > Pairwise Alignment.

Task	How To
Specify the wrapping style for rows	Use the Layout drop-down menu. Choose between: Linear – All information for a sequence appears on a single row with no line breaks. A horizontal scrollbar is provided. Automatic wrapping – The alignment is wrapped to fit within the view. Wrapping adjusts automatically if the view’s width changes. Fixed wrapping – The alignment is wrapped at the specified number of residues. Enter a number in the Size box to wrap after a different number of residues. Vertical splits are not available in either type of wrapped view. However, any existing splits are restored if wrapping is turned off.
Visualize flanking segments of sequences that are not within the aligned segment	Check the Show context box. A local alignment reports the highest scoring contiguous segment of alignment between two sequences, even if the full extent of one or both of the sequences is not included in the final alignment. Local alignments are ideal for finding short sequences within a larger sequence. When you check Show context, the flanking segments appear in a dimmer color scheme than the alignment. As an example, consider a local alignment of a long sequence to a short one. Any positions that aren’t part of the alignment are considered to be context and are not displayed in the Pairwise view unless Show context is selected. In the case below, the segment “GGGC” in on the left of Seq1 is context, as is the trailing “TTAAAA”. The internal part of Seq2 that spans a gap in Seq1 might be considered unaligned, but is actual context, because it’s not internal to the alignment. Seq1 GGGC CCC -- TTA TTAAAA Seq2 ---- CCC C C TTA ------
Specify how to color the sequences and the consensus to facilitate visual comparisons	Use the Alignment coloring drop-down menu to s. Sequence comparisons can only be performed with aligned sequences. Choose between: Color all residues – All residues appear in the color schemes chosen in Foreground color (dark ‘T’ icon) and Background color (white ‘T’ icon; see row below). Color only differences from reference – Only residues that differ from the consensus are colored. If you chose this option, you should select the reference sequence from the Reference drop-down menu. The reference can be the consensus or any of the aligned sequences. Color only matches to reference – Only residues that are identical to the consensus are colored. If you chose this option, you should select the reference sequence from the Reference drop-down menu. The reference can be the consensus or any of the aligned sequences. Show only differences from reference – Only residues that differ from the consensus are displayed and colored. All other residues are shown as uncolored dashes. If you chose this option, you should select the reference sequence from the Reference drop-down menu. The reference can be the consensus or any of the aligned sequences. Choose either Color only conserved residues or Color only non-conserved residues to color according to whether or not residues are conserved. A residue is “conserved” if all sequences have the same residue in that column. Otherwise, it is “non-conserved.” If you prefer to ignore gaps when determining whether or not a residue is “conserved,” check the box next to Ignore gaps. The Ignore gaps checkbox is only enabled if you selected Color only conserved/non-conserved residues above.
Reference	Choose which sequence to use as the “Reference” in the pairwise comparison. Choices are Target (top sequence) or Query (bottom sequence).
Specify the color of sequence characters	Use the Foreground color tools to the right of . To display the letters in a single solid color of your choice, check the upper box. Then click on the ‘A’ tool to the right of the checkbox and choose a color from the color picker. To instead choose a preset color scheme, check the lower box and make a selection from the drop-down menu. Color scheme choices are described in Available color schemes.
Specify the background color (boxes around each letter)	Use the Background color tools to the right of . To use a single solid color of your choice, check the upper box. Then click on the ‘highlighter pen’ tool to the right of the checkbox and choose a color from the color picker. To instead choose a preset color scheme, check the lower box and make a selection from the drop-down menu (see image in row above). Color scheme choices are described in Available color schemes.
Specify the background color for gaps	Use the Background color for gaps tools to the right of . To use a single solid color of your choice, check the box next to Solid. Then click on the ‘highlighter pen’ tool to the right of the checkbox and choose a color from the color picker. If you do not wish to use a background color for gaps, check the Default box.
Specify the appearance of the match bar track	Use the Match bar section to customize display of the optional Match bar track. This track is used to show similarities and differences between the query and target sequences. These options are mirrored in the Match Bar track options section. Choices made in either location are instantly reflected in the other location. To choose how to show the connection between the query and the target, use the Show identity as drop-down menu. Vertical bars causes the connection to appear as a symbol, depending on the match status. See the small table below for a description of symbols used to show identity. Vertical bars only causes only matches (vertical lines) to be shown. Favorable and neutral mismatches (colons and periods, respectively) are not displayed. Residues in target case or Residues in query case cause the connection to appear as a copy of the residue from the target or query sequence. To add a background color behind each residue, check the Color background check box and use the adjacent drop-down menu to choose between Same as query and Same as target.

*Note: Once you set up styles, you can save them and apply them to future projects, either by default or when you specify.