EMBOSS explorer


Display a multiple sequence alignment in pretty format (read the manual)

Unshaded fields are optional and can safely be ignored. (hide optional fields)

Input section

Select an input sequence. Use one of the following three fields:

  1. To access a sequence from a database, enter the USA here:
  2. To upload a sequence from your local computer, select it here:
  3. To enter the sequence data manually, type here:

Similarity scoring Matrix file. Use one of the following two fields:

  1. To access a standard EMBOSS data file, enter the name here: (default is EBLOSUM62 for protein, EDNAFULL for nucleic)
  2. To upload a data file from your local computer, select it here:
Additional section
The number or the name of the reference sequence
Display the reference sequence at the bottom?
What to show
Output order of the sequences
Show similar residues in lower-case?
Display the consensus line?
Advanced section
Regions to put in uppercase (eg: 4-57,78-94) (If this is left blank, then the sequence case is left alone.)
Number the sequences?
Display ruler?
Width of sequence to display
Length of margin for sequence names
Use HTML formatting?
Regions to colour in HTML (eg: 4-57 red 78-94 green)
Plurality check % for consensus
Threshold above which the consensus is given in uppercase
Required % of identities at a position for consensus
Use gap characters in consensus?
Output section
Run section
Email address: If you are submitting a long job and would like to be informed by email when it finishes, enter your email address here.