Multiple Align Show

Multiple Align Show accepts a group of aligned sequences (in FASTA or GDE format) and formats the alignment to your specifications. You can specify the number of residues per line, and the font size and font style. You can also set a consensus level, which specifies the fraction of residues that need to be identical or similar in a column of the alignment for highlighting to be added. Use Multiple Align Show to enhance the output of sequence alignment programs.

Paste the aligned sequences in FASTA or GDE format into the text area below.

  • Show residues per line.
  • Font style:
  • Font size:
  • Use colored to highlight residues.

Choose the colors you wish to use for highlighting. Identical amino acids have the highest priority for coloring, followed by similar amino acids.

  • Color identical amino acids and similar amino acids
  • Percentage of sequences that must agree for identity or similarity coloring to be added:
  • The default color (the color used if no identity or similarity coloring is added):
  • The color of all gaps:

Enter the groups of similar amino acids separated by commas to be used for the similarity calculation.

Enter the colors to be used for the by amino acid color scheme if it is selected from any of the above lists. Each amino acid is described by two colors separated by a blank space. Each color pair is followed by a comma, except for the last pair. The first color in each pair is used for the text if colored text is used, or the background if colored backgrounds are used. The second color in each pair is used for the text when colored backgrounds are used. The colors are entered as hexadecimal color codes.

Enter the starting positions of the sequences separated by commas (to alter residue numbering). An example entry is: 3,200,5,1. If no numbers are given, the default starting position of 0 is used for each sequence.