This directory contains compressed multiple alignments of the
following assemblies to the human genome (hg17, May 2004):
- chimp (Nov 2003, panTro1)
- macaque (Jan 2006, rheMac2)
- mouse (May 2004, mm7)
- rat (Jun 2003, rn3)
- rabbit (May 2005, oryCun1)
- dog (May 2005, canFam2)
- cow (Mar 2005, bosTau2)
- armadillo (May 2005, dasNov1)
- elephant (May 2005, loxAfr1)
- tenrec (Jul 2005, echTel1)
- opossum (Jun 2005, monDom2)
- chicken (Feb 2004, galGal2)
- frog (Oct 2004, xenTro1)
- zebrafish (May 2005, danRer3)
- Tetraodon (Feb 2004, tetNig1)
- Fugu (Aug 2002, fr1)
The chr*.maf.gz files each contain all the alignments to that
particular human 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
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. 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/hg17/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 -
md5sum.txt 2008-10-16 12:26 2.2K
maf/ 2019-11-06 11:00 -
chrY.maf.gz 2006-04-13 16:07 28M
chrX_random.maf.gz 2006-04-13 16:06 1.9M
chrX.maf.gz 2006-04-13 16:06 264M
chrM.maf.gz 2006-04-13 16:04 95K
chr22_random.maf.gz 2006-04-13 15:37 512K
chr22.maf.gz 2006-04-13 15:37 72M
chr21.maf.gz 2006-04-13 15:36 71M
chr20.maf.gz 2006-04-13 15:36 133M
chr19_random.maf.gz 2006-04-13 15:28 359K
chr19.maf.gz 2006-04-13 15:28 103M
chr18_random.maf.gz 2006-04-13 15:27 23K
chr18.maf.gz 2006-04-13 15:27 166M
chr17_random.maf.gz 2006-04-13 15:26 3.2M
chr17.maf.gz 2006-04-13 15:26 178M
chr16_random.maf.gz 2006-04-13 15:24 145K
chr16.maf.gz 2006-04-13 15:24 177M
chr15_random.maf.gz 2006-04-13 15:22 1.6M
chr15.maf.gz 2006-04-13 15:22 190M
chr14.maf.gz 2006-04-13 15:20 198M
chr13_random.maf.gz 2006-04-13 15:18 457K
chr13.maf.gz 2006-04-13 15:18 207M
chr12_random.maf.gz 2006-04-13 15:16 920K
chr12.maf.gz 2006-04-13 15:16 286M
chr11.maf.gz 2006-04-13 15:13 297M
chr10_random.maf.gz 2006-04-13 15:10 188K
chr10.maf.gz 2006-04-13 15:10 298M
chr9_random.maf.gz 2006-04-13 16:04 1.0M
chr9.maf.gz 2006-04-13 16:04 262M
chr8_random.maf.gz 2006-04-13 16:01 821K
chr8.maf.gz 2006-04-13 16:01 308M
chr7_random.maf.gz 2006-04-13 15:57 958K
chr7.maf.gz 2006-04-13 15:57 334M
chr6_random.maf.gz 2006-04-13 15:54 3.5M
chr6_hla_hap2.maf.gz 2006-04-13 15:54 298K
chr6_hla_hap1.maf.gz 2006-04-13 15:54 285K
chr6.maf.gz 2006-04-13 15:54 376M
chr5_random.maf.gz 2006-04-13 15:50 202K
chr5.maf.gz 2006-04-13 15:50 397M
chr4_random.maf.gz 2006-04-13 15:46 1.3M
chr4.maf.gz 2006-04-13 15:46 401M
chr3_random.maf.gz 2006-04-13 15:42 1.8M
chr3.maf.gz 2006-04-13 15:42 446M
chr2_random.maf.gz 2006-04-13 15:37 482K
chr2.maf.gz 2006-04-13 15:34 540M
chr1_random.maf.gz 2006-04-13 15:28 6.9M
chr1.maf.gz 2006-04-13 15:07 511M
17way.nh 2006-09-18 09:21 588