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.

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