This directory contains compressed multiple alignments of the
following assemblies to the mouse genome (mm8, Feb. 2006):
- mouse (Feb 2006, mm8)
- rat (Nov 2004, rn4)
- rabbit (May 2005, oryCun1)
- human (Mar. 2006, hg18)
- chimp (Mar. 2006, panTro2)
- macaque (Jan 2006, rheMac2)
- dog (May 2005, canFam2)
- cow (Mar 2005, bosTau2)
- armadillo (May 2005, dasNov1)
- elephant (May 2005, loxAfr1)
- tenrec (Jul 2005, echTel1)
- opossum (Jan 2006, monDom4)
- chicken (Feb 2004, galGal2)
- frog (Aug 2005, xenTro2)
- zebrafish (Mar 2006, danRer4)
- Tetraodon (Feb 2004, tetNig1)
- Fugu (Aug 2002, fr1)
The chr*.maf.gz files each contain all the alignments to that
particular mouse 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
mouse, 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 mouse; 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 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/mm8/multiz17way. 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 usable for any
purpose. For data use restrictions regarding the individual
genome assemblies, see http://genome.ucsc.edu/goldenPath/credits.html.
Name Last modified Size Description
Parent Directory -
maf/ 2019-11-06 11:05 -
md5sum.txt 2008-10-16 12:27 1.6K
chr10_random.maf.gz 2007-03-27 14:13 35K
chr9_random.maf.gz 2007-03-27 14:11 37K
chr15_random.maf.gz 2007-03-27 14:15 57K
chr17_random.maf.gz 2007-03-27 14:17 67K
chrX_random.maf.gz 2007-03-27 14:19 82K
chrM.maf.gz 2007-03-27 14:20 86K
chr7_random.maf.gz 2007-03-27 14:22 166K
chr1_random.maf.gz 2007-03-27 14:24 178K
chr8_random.maf.gz 2007-03-27 14:26 289K
chr13_random.maf.gz 2007-03-27 14:28 545K
chrUn_random.maf.gz 2007-03-27 14:30 1.0M
chr5_random.maf.gz 2007-03-27 14:32 1.8M
chrY.maf.gz 2007-03-27 14:33 2.2M
chrY_random.maf.gz 2007-03-27 14:35 7.7M
chr19.maf.gz 2007-03-27 14:39 120M
chr17.maf.gz 2007-03-27 14:44 159M
chr18.maf.gz 2007-03-27 14:49 162M
chr16.maf.gz 2007-03-27 14:55 172M
chr15.maf.gz 2007-03-27 15:00 177M
chr13.maf.gz 2007-03-27 15:07 205M
chr12.maf.gz 2007-03-27 15:30 213M
chr14.maf.gz 2007-03-27 15:23 214M
chrX.maf.gz 2007-03-27 15:16 215M
chr8.maf.gz 2007-03-27 15:37 226M
chr10.maf.gz 2007-03-27 15:45 232M
chr9.maf.gz 2007-03-27 16:02 235M
chr7.maf.gz 2007-03-27 15:54 236M
chr11.maf.gz 2007-03-27 16:17 240M
chr5.maf.gz 2007-03-27 16:38 257M
chr6.maf.gz 2007-03-27 16:55 263M
chr3.maf.gz 2007-03-27 17:08 276M
chr4.maf.gz 2007-03-27 17:20 277M
chr1.maf.gz 2007-03-27 17:34 342M
chr2.maf.gz 2007-03-27 17:48 351M