This directory contains compressed multiple alignments of the
following assemblies to the human genome (hg18, Mar. 2006):
_ human (Mar. 2006, hg18)
_ chimp (Nov 2003, panTro1)
_ macaque (Jan 2006, rheMac2)
- mouse (Feb 2006, mm8)
- rat (Nov 2004, rn4)
- 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 (Jan 2006, monDom4)
- 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 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
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.
For a description of multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html.
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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 hgdownload.cse.ucsc.edu
user name: anonymous
password: <your email address>
go to the directory goldenPath/hg18/multiz17way
To download multiple files from the UNIX command line, use the "mget" command.
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Use the "prompt" command to toggle the interactive mode if you do not want
to be prompted for each file that you download.
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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 2011-03-21 17:31 2.6K
upstream5000.maf.gz 2008-12-12 11:52 272M
upstream2000.maf.gz 2008-12-12 11:32 124M
upstream1000.maf.gz 2008-12-12 11:18 52M
17way.nh 2006-09-18 09:22 588
chrY.maf.gz 2006-02-22 16:58 28M
chrX_random.maf.gz 2006-02-22 16:57 1.6M
chrX.maf.gz 2006-02-22 16:57 263M
chrM.maf.gz 2006-02-22 16:55 89K
chr9_random.maf.gz 2006-02-22 16:55 726K
chr9.maf.gz 2006-02-22 16:55 263M
chr8_random.maf.gz 2006-02-22 16:52 719K
chr8.maf.gz 2006-02-22 16:52 304M
chr7_random.maf.gz 2006-02-22 16:49 597K
chr7.maf.gz 2006-02-22 16:49 330M
chr6_random.maf.gz 2006-02-22 16:45 3.0M
chr6_qbl_hap2.maf.gz 2006-02-22 16:45 8.7M
chr6_cox_hap1.maf.gz 2006-02-22 16:45 9.5M
chr6.maf.gz 2006-02-22 16:45 372M
chr5_random.maf.gz 2006-02-22 16:41 177K
chr5_h2_hap1.maf.gz 2006-02-22 16:41 3.4M
chr5.maf.gz 2006-02-22 16:41 393M
chr4_random.maf.gz 2006-02-22 16:37 962K
chr4.maf.gz 2006-02-22 16:37 396M
chr3_random.maf.gz 2006-02-22 16:33 1.3M
chr3.maf.gz 2006-02-22 16:33 442M
chr22_random.maf.gz 2006-02-22 16:28 453K
chr22_h2_hap1.maf.gz 2006-02-22 16:28 149K
chr22.maf.gz 2006-02-22 16:28 71M
chr2_random.maf.gz 2006-02-22 16:28 229K
chr21_random.maf.gz 2006-02-22 16:27 1.8M
chr21.maf.gz 2006-02-22 16:27 70M
chr20.maf.gz 2006-02-22 16:26 131M
chr2.maf.gz 2006-02-22 16:24 534M
chr1_random.maf.gz 2006-02-22 16:18 2.3M
chr19_random.maf.gz 2006-02-22 16:18 283K
chr19.maf.gz 2006-02-22 16:18 102M
chr18_random.maf.gz 2006-02-22 16:16 22K
chr18.maf.gz 2006-02-22 16:16 164M
chr17_random.maf.gz 2006-02-22 16:15 2.8M
chr17.maf.gz 2006-02-22 16:14 177M
chr16_random.maf.gz 2006-02-22 16:13 127K
chr16.maf.gz 2006-02-22 16:13 175M
chr15_random.maf.gz 2006-02-22 16:10 1.4M
chr15.maf.gz 2006-02-22 16:10 188M
chr14.maf.gz 2006-02-22 16:08 196M
chr13_random.maf.gz 2006-02-22 16:06 400K
chr13.maf.gz 2006-02-22 16:06 205M
chr12.maf.gz 2006-02-22 16:03 283M
chr11_random.maf.gz 2006-02-22 16:00 150K
chr11.maf.gz 2006-02-22 16:00 295M
chr10_random.maf.gz 2006-02-22 15:57 166K
chr10.maf.gz 2006-02-22 15:57 294M
chr1.maf.gz 2006-02-22 15:54 511M