|   | seqmatchall | 
The larger the specified word size, the faster the comparison will proceed. Regions whose stretches of identity are shorter than the word size will be missed. You should therefore choose a word size that is small enough to find those regions of similarity you are interested in within a reasonable time-frame.
Here is an example using an increased word size to avoid accidental matches:
| % seqmatchall All-against-all comparison of a set of sequences Input sequence set: @eclac.list Word size [4]: 15 Output alignment [j01636.seqmatchall]: | 
Go to the input files for this example
Go to the output files for this example
| 
   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     Sequence set filename and optional format,
                                  or reference (input USA)
   -wordsize           integer    [4] Word size (Integer 2 or more)
  [-outfile]           align      [*.seqmatchall] Output alignment file name
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:
   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name
   "-outfile" associated qualifiers
   -aformat2           string     Alignment format
   -aextension2        string     File name extension
   -adirectory2        string     Output directory
   -aname2             string     Base file name
   -awidth2            integer    Alignment width
   -aaccshow2          boolean    Show accession number in the header
   -adesshow2          boolean    Show description in the header
   -ausashow2          boolean    Show the full USA in the alignment
   -aglobal2           boolean    Show the full sequence in alignment
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) | Sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required | 
| -wordsize | Word size | Integer 2 or more | 4 | 
| [-outfile] (Parameter 2) | Output alignment file name | Alignment output file | <*>.seqmatchall | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
The sequences must be either all protein or all nucleic acid.
| #Formerly ECLAC tembl:J01636 #Formerly ECLACA tembl:X51872 #Formerly ECLACI tembl:V00294 #Formerly ECLACY tembl:V00295 #Formerly ECLACZ tembl:V00296 | 
| 
########################################
# Program: seqmatchall
# Rundate: Sun 15 Jul 2007 12:00:00
# Commandline: seqmatchall
#    -sequence @../../data/eclac.list
#    -wordsize 15
# Align_format: match
# Report_file: j01636.seqmatchall
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: J01636
# 2: X51872
#=======================================
  1832 J01636          +     5646..7477     X51872          +        1..1832
#=======================================
#
# Aligned_sequences: 2
# 1: J01636
# 2: V00294
#=======================================
  1113 J01636          +       49..1161     V00294          +        1..1113
#=======================================
#
# Aligned_sequences: 2
# 1: J01636
# 2: V00295
#=======================================
  1500 J01636          +     4305..5804     V00295          +        1..1500
#=======================================
#
# Aligned_sequences: 2
# 1: J01636
# 2: V00296
#=======================================
  3078 J01636          +     1287..4364     V00296          +        1..3078
#=======================================
#
# Aligned_sequences: 2
# 1: X51872
# 2: V00295
#=======================================
   159 X51872          +        1..159      V00295          +     1342..1500
#=======================================
#
# Aligned_sequences: 2
# 1: V00295
# 2: V00296
#=======================================
    60 V00295          +        1..60       V00296          +     3019..3078
#---------------------------------------
#---------------------------------------
 | 
ECLAC (the complete E.coli lac operon) matches ECLACI ECLACZ ECLACY and ECLACA (the individual genes), and there is a short overlap between ECLACY and the flanking genes ECLACZ and ECLACA
The output is a list of regions of identity in pairs of sequences, each consisting of one line with 7 columns of data separated by TABs or space characters.
The columns of data consist of:
| Program name | Description | 
|---|---|
| matcher | Finds the best local alignments between two sequences | 
| supermatcher | Match large sequences against one or more other sequences | 
| water | Smith-Waterman local alignment | 
| wordfinder | Match large sequences against one or more other sequences | 
| wordmatch | Finds all exact matches of a given size between 2 sequences | 
polydot will give a graphical view of the same matches.