This directory contains zipped multiple alignments of the following
genomes to the Human genome (hg16, Jul. 2003):
- Chimp (panTro1, Nov. 2003) 
- Mouse (mm3, Feb. 2003) 
- Rat (rn3, Jun. 2003)
- Chicken (galGal2, Feb. 2004) 

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

The pt1, mm3, rn3, and gg2 directories contained gzipped mafs
for the pairwise (blastz) alignments used in the multiple alignment.

The maf/upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription starts for RefSeq 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 
human, 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 human; 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. These files
are updated weekly.

For a description of the 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/hg16/mzPt1Mm3Rn3Gg2. To download multiple 
files, use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
 
All files in this directory are freely available for public use.
For data use restrictions regarding the genome assemblies used in this
annotation, see http://genome.ucsc.edu/goldenPath/credits.html.