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.

---------------------------------------------------------------
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.

---------------------------------------------------------------
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 - 17way.nh 2006-09-18 09:22 588 chr1.maf.gz 2006-02-22 15:54 511M chr1_random.maf.gz 2006-02-22 16:18 2.3M chr2.maf.gz 2006-02-22 16:24 534M chr2_random.maf.gz 2006-02-22 16:28 229K chr3.maf.gz 2006-02-22 16:33 442M chr3_random.maf.gz 2006-02-22 16:33 1.3M chr4.maf.gz 2006-02-22 16:37 396M chr4_random.maf.gz 2006-02-22 16:37 962K chr5.maf.gz 2006-02-22 16:41 393M chr5_h2_hap1.maf.gz 2006-02-22 16:41 3.4M chr5_random.maf.gz 2006-02-22 16:41 177K chr6.maf.gz 2006-02-22 16:45 372M chr6_cox_hap1.maf.gz 2006-02-22 16:45 9.5M chr6_qbl_hap2.maf.gz 2006-02-22 16:45 8.7M chr6_random.maf.gz 2006-02-22 16:45 3.0M chr7.maf.gz 2006-02-22 16:49 330M chr7_random.maf.gz 2006-02-22 16:49 597K chr8.maf.gz 2006-02-22 16:52 304M chr8_random.maf.gz 2006-02-22 16:52 719K chr9.maf.gz 2006-02-22 16:55 263M chr9_random.maf.gz 2006-02-22 16:55 726K chr10.maf.gz 2006-02-22 15:57 294M chr10_random.maf.gz 2006-02-22 15:57 166K chr11.maf.gz 2006-02-22 16:00 295M chr11_random.maf.gz 2006-02-22 16:00 150K chr12.maf.gz 2006-02-22 16:03 283M chr13.maf.gz 2006-02-22 16:06 205M chr13_random.maf.gz 2006-02-22 16:06 400K chr14.maf.gz 2006-02-22 16:08 196M chr15.maf.gz 2006-02-22 16:10 188M chr15_random.maf.gz 2006-02-22 16:10 1.4M chr16.maf.gz 2006-02-22 16:13 175M chr16_random.maf.gz 2006-02-22 16:13 127K chr17.maf.gz 2006-02-22 16:14 177M chr17_random.maf.gz 2006-02-22 16:15 2.8M chr18.maf.gz 2006-02-22 16:16 164M chr18_random.maf.gz 2006-02-22 16:16 22K chr19.maf.gz 2006-02-22 16:18 102M chr19_random.maf.gz 2006-02-22 16:18 283K chr20.maf.gz 2006-02-22 16:26 131M chr21.maf.gz 2006-02-22 16:27 70M chr21_random.maf.gz 2006-02-22 16:27 1.8M chr22.maf.gz 2006-02-22 16:28 71M chr22_h2_hap1.maf.gz 2006-02-22 16:28 149K chr22_random.maf.gz 2006-02-22 16:28 453K chrM.maf.gz 2006-02-22 16:55 89K chrX.maf.gz 2006-02-22 16:57 263M chrX_random.maf.gz 2006-02-22 16:57 1.6M chrY.maf.gz 2006-02-22 16:58 28M md5sum.txt 2011-03-21 17:31 2.6K upstream1000.maf.gz 2008-12-12 11:18 52M upstream2000.maf.gz 2008-12-12 11:32 124M upstream5000.maf.gz 2008-12-12 11:52 272M