This directory contains zipped multiple alignments of the Human genome
(hg17, May 2004) to the following assemblies:

 - Chimp Nov. 2003 (panTro1)
 - Mouse May 2004 (mm5)
 - Rat Jun. 2003 (rn3)
 - Dog Jul. 2004 (canFam1)
 - Chicken Feb. 2004 (galGal2) 
 - Fugu Aug. 2002 (fr1)
 - Zebrafish Nov. 2003 (danRer1)

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

The upstream*.maf.gz files contain alignments in regions upstream of
annotated transcription start 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.

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 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/hg17/multiz8way/. 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 available for public use.

For data restrictions regarding the chimp, dog, chicken, fugu, and
zebrafish genomes, see http://genome.ucsc.edu/goldenPath/credits.html.