This directory contains zipped multiple alignments of the zebrafish genome
(danRer2, Jun. 2004) to the following assemblies:


 - Human (hg17, May 2004)
 - Mouse (mm6, Mar. 2005)
 - Opossum (monDom1, Oct. 2004)
 - Fugu (fr1, Aug. 2002)
 - Tetraodon (tetNig1, Feb. 2004)

The chr*.maf.gz files each contain all the alignments to that 
particular zebrafish 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 
zebrafish, 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 zebrafish; 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/danRer2/multiz6way/. 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 aligned genomes, see http://genome.ucsc.edu/goldenPath/credits.html.

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