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.

  • Use the Layout drop-down menu to specify the wrapping style for rows in the Sequences view. 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.

  • A local alignment reports the highest scoring contigous 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 a short sequences within a larger sequence. Flanking segments of sequences that are not within the aligned segment can be visualized by checking the Show context box. The flanking segments appear in a dimmer color scheme than the alignment.

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 ------

  • Use the Comparison drop-down menu to specify how to color the sequences and the consensus to facilitate visual comparisons. Sequence comparisons can only be performed with aligned sequences. Choose between:

    • None – All residues appear in the color schemes chosen in Color foreground and Color background (see row above).

    • 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 one of the two comparison options described in this bullet point.
  • The Match bar section affects display of the optional Match bar track. This track is used to show similarities and differences between the query and target sequences:

    • Use the Show identity as drop-down menu to choose how to show the connection between the query and the target. Choosing 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. Choosing Vertical bars causes the connection to appear as a symbol, depending on the match status.
Symbol Interpretation Weight table value
Vertical line Match 1
Colon Favorable mismatch (0,1)
Period Neutral mismatch 0
Space Unfavorable mismatch < 0
    • 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.

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