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.
Name Last modified Size Description
Parent Directory -
md5sum.txt 2005-05-31 15:31 1.4K
chrM.maf.gz 2005-05-31 13:36 27K
upstream1000.maf.gz 2005-05-31 15:21 2.3M
chr25.maf.gz 2005-05-31 13:34 3.9M
chr24.maf.gz 2005-05-31 13:34 4.3M
upstream2000.maf.gz 2005-05-31 15:22 4.7M
chr11.maf.gz 2005-05-31 13:31 5.3M
chr8.maf.gz 2005-05-31 13:36 5.5M
chr12.maf.gz 2005-05-31 13:31 5.6M
chr6.maf.gz 2005-05-31 13:35 5.6M
chr15.maf.gz 2005-05-31 13:32 5.8M
chr21.maf.gz 2005-05-31 13:33 6.0M
chr4.maf.gz 2005-05-31 13:35 6.1M
chr22.maf.gz 2005-05-31 13:34 6.1M
chr13.maf.gz 2005-05-31 13:31 6.4M
chr10.maf.gz 2005-05-31 13:30 6.6M
chr16.maf.gz 2005-05-31 13:32 6.6M
chr3.maf.gz 2005-05-31 13:34 6.9M
chr23.maf.gz 2005-05-31 13:34 7.0M
chr17.maf.gz 2005-05-31 13:32 7.0M
chr19.maf.gz 2005-05-31 13:33 7.6M
chr9.maf.gz 2005-05-31 13:36 7.7M
chr18.maf.gz 2005-05-31 13:32 7.7M
chr2.maf.gz 2005-05-31 13:33 8.2M
chr14.maf.gz 2005-05-31 13:31 9.3M
chr20.maf.gz 2005-05-31 13:33 9.3M
chr7.maf.gz 2005-05-31 13:35 9.8M
chr5.maf.gz 2005-05-31 13:35 11M
upstream5000.maf.gz 2005-05-31 15:23 12M
chrUn.maf.gz 2005-05-31 13:38 27M
chr1.maf.gz 2005-05-31 13:30 27M
chrNA.maf.gz 2005-05-31 13:38 44M