This directory contains zipped multiple alignments of the zebrafish genome
(danRer3, May 2005) to the following assemblies:

 - Tetraodon (tetNig1, Feb. 2004)
 - Fugu (fr1, Aug. 2002)
 - Human (hg18, Feb. 2006)
 - Mouse (mm7, Aug. 2005)

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

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 
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. These files
are updated weekly.

For a description of the multiple alignment format (MAF), 

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, then go to 
the directory goldenPath/danRer3/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 available for public use.

For data restrictions regarding the aligned genomes, see

      Name                    Last modified      Size  Description
Parent Directory - chr1.maf.gz 2006-02-06 08:15 7.7M chr2.maf.gz 2006-02-06 08:17 7.0M chr3.maf.gz 2006-02-06 08:17 7.1M chr4.maf.gz 2006-02-06 08:17 5.0M chr5.maf.gz 2006-02-06 08:18 11M chr6.maf.gz 2006-02-06 08:17 4.8M chr7.maf.gz 2006-02-06 08:18 8.5M chr8.maf.gz 2006-02-06 08:17 5.8M chr9.maf.gz 2006-02-06 08:17 6.2M chr10.maf.gz 2006-02-06 08:14 6.0M chr11.maf.gz 2006-02-06 08:14 5.4M chr12.maf.gz 2006-02-06 08:14 4.9M chr13.maf.gz 2006-02-06 08:15 6.8M chr14.maf.gz 2006-02-06 08:15 9.4M chr15.maf.gz 2006-02-06 08:14 6.5M chr16.maf.gz 2006-02-06 08:15 7.3M chr17.maf.gz 2006-02-06 08:15 6.9M chr18.maf.gz 2006-02-06 08:15 7.0M chr19.maf.gz 2006-02-06 08:18 9.3M chr20.maf.gz 2006-02-06 08:17 7.5M chr21.maf.gz 2006-02-06 08:17 5.5M chr22.maf.gz 2006-02-06 08:17 6.4M chr23.maf.gz 2006-02-06 08:17 7.5M chr24.maf.gz 2006-02-06 08:17 4.8M chr25.maf.gz 2006-02-06 08:16 3.8M chrM.maf.gz 2006-02-06 08:15 21K chrNA.maf.gz 2006-02-06 08:24 31M chrUn.maf.gz 2006-02-06 08:22 24M maf/ 2019-11-06 10:46 - md5sum.txt 2006-02-22 10:03 1.3K