Displays aligned sequences, with colouring and boxing qualifiers for parameter: sequences Format of the graphical output Format of the graphical output Matrix file This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. Number of residues to be displayed on each line The number of residues to be displayed on each line Residues before a space Residues before a space Colour residues by their consensus value. Colour residues by their consensus value. Colour to display identical residues (RED) Colour to display identical residues (RED) Colour to display similar residues (GREEN) Colour to display similar residues (GREEN) Colour to display other residues (BLACK) Colour to display other residues (BLACK) Colour residues by table oily, amide etc. Colour residues by table oily, amide etc. Do not display the title Do not display the title Shading Set to BPLW for normal shading so for pair = 1.5,1.0,0.5 and shade = BPLW Residues score Colour 1.5 or over....... BLACK (B) 1.0 to 1.5 ....... BROWN (P) 0.5 to 1.0 ....... WHEAT (L) under 0.5 ....... WHITE (W) The only four letters allowed are BPLW, in any order. Values to represent identical similar related Values to represent identical similar related Only match those which are identical in all sequences. Only match those which are identical in all sequences. Display prettyboxes Display prettyboxes Colour the background in the boxes Colour the background in the boxes Colour to be used for background. (GREY) Colour to be used for background. (GREY) Display the sequence names Display the sequence names Margin size for the sequence name. Margin size for the sequence name. Display the residue number Display the residue number Display the date and options used Display the date and options used Plurality check value (totweight/2) Plurality check value (totweight/2) Display the consensus Display the consensus Allow collisions in calculating consensus Allow collisions in calculating consensus Use alternative collisions routine Use alternative collisions routine 0) Normal collision check. (default) 1) checks identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred. 2) If another residue has a greater than or equal to matching score and these do not match then a collision has occurred. 3) Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured. Print residue scores Print residue scores Set page to Portrait Set page to Portrait graphics output data Start the web service and receive the result. Blocks until job is finished. Start the web service and receive a job-id. Returns immediately. Wait until a job (by job-id) has finished. Blocks until job is finished. Get status information about a running job. Returns immediately. Get the results of a job (by job-id) Start the web service and receive the result. Blocks until job is finished. Start the web service and receive a job-id. Returns immediately. Wait until a job (by job-id) has finished. Blocks until job is finished. Get status information about a running job. Returns immediately. Get the results of a job (by job-id)