This directory contains compressed multiple alignments of the 
following assemblies to the C. elegans genome (WormBase WS170, ce4, Jan. 2007):

  - C. brenneri (Jan 2007, caePb1)
  - C. remanei (Mar 2006, caeRem2)
  - C. briggsae (Jan 2007, cb3)
  - P. pacificus (Feb 2007, priPac1) 

The chr*.maf.gz files each contain all the alignments to that 
particular C. elegans chromosome.  

The upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription start for Sanger genes with annotated 5' UTRs.
These files differ from the standard MAF format: they display
alignments that extend from start to end of the upstream region in 
C. elegans, whether or not alignments actually exist. In situations where no  
alignments exist or the alignments of one or more species are missing, 
dot (".") is used as a placeholder. Multiple regions of an assembly's
sequence may align to a single region in C. elegans; therefore, only the 
species name is displayed in the alignment data and no position information 
is recorded. The alignment score is always zero in these files.

For a description of multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html.

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If you plan to download a large file or multiple files from this 
directory, we recommend that you use ftp rather than downloading the 
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu, 
then go to the directory goldenPath/ce4/multiz5way. To download 
multiple files, use the "mget" command:

    mget <filename1> <filename2> ...
   - or -
    mget -a (to download all the files in the directory) 

All the files in this directory are freely usable for any 
purpose. For data use restrictions regarding the individual 
genome assemblies, see http://genome.ucsc.edu/goldenPath/credits.html.