This directory contains zipped multiple alignments of the Human genome
(hg17, May 2004) to the following assemblies:

 - Chimp Nov. 2003 (panTro1)
 - Mouse May 2004 (mm5)
 - Rat Jun. 2003 (rn3)
 - Dog Jul. 2004 (canFam1)
 - Chicken Feb. 2004 (galGal2) 
 - Fugu Aug. 2002 (fr1)
 - Zebrafish Nov. 2003 (danRer1)

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 the 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 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/multiz8way/. 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 available for public use.

For data restrictions regarding the chimp, dog, chicken, fugu, and
zebrafish genomes, see http://genome.ucsc.edu/goldenPath/credits.html.
      Name                    Last modified      Size  Description
Parent Directory - chr1.maf.gz 2004-07-20 14:51 233M chr1_random.maf.gz 2004-07-20 14:56 3.1M chr2.maf.gz 2004-07-20 14:57 246M chr2_random.maf.gz 2004-07-20 14:57 266K chr3.maf.gz 2004-07-20 14:58 203M chr3_random.maf.gz 2004-07-20 14:58 889K chr4.maf.gz 2004-07-20 14:59 186M chr4_random.maf.gz 2004-07-20 14:59 699K chr5.maf.gz 2004-07-20 15:00 182M chr5_random.maf.gz 2004-07-20 15:00 104K chr6.maf.gz 2004-07-20 15:01 172M chr6_hla_hap1.maf.gz 2004-07-20 15:01 183 chr6_hla_hap2.maf.gz 2004-07-20 15:01 116K chr6_random.maf.gz 2004-07-20 15:01 1.7M chr7.maf.gz 2004-07-20 15:02 156M chr7_random.maf.gz 2004-07-20 15:02 517K chr8.maf.gz 2004-07-20 15:02 144M chr8_random.maf.gz 2004-07-20 15:02 397K chr9.maf.gz 2004-07-20 15:03 121M chr9_random.maf.gz 2004-07-20 15:03 540K chr10.maf.gz 2004-07-20 14:51 138M chr10_random.maf.gz 2004-07-20 14:51 98K chr11.maf.gz 2004-07-20 14:52 137M chr12.maf.gz 2004-07-20 14:53 133M chr12_random.maf.gz 2004-07-20 14:53 402K chr13.maf.gz 2004-07-20 14:53 95M chr13_random.maf.gz 2004-07-20 14:53 221K chr14.maf.gz 2004-07-20 14:54 92M chr15.maf.gz 2004-07-20 14:54 88M chr15_random.maf.gz 2004-07-20 14:54 756K chr16.maf.gz 2004-07-20 14:55 84M chr16_random.maf.gz 2004-07-20 14:55 75K chr17.maf.gz 2004-07-20 14:55 86M chr17_random.maf.gz 2004-07-20 14:55 1.7M chr18.maf.gz 2004-07-20 14:55 76M chr18_random.maf.gz 2004-07-20 14:55 188 chr19.maf.gz 2004-07-20 14:56 52M chr19_random.maf.gz 2004-07-20 14:56 168K chr20.maf.gz 2004-07-20 14:57 63M chr21.maf.gz 2004-07-20 14:57 33M chr22.maf.gz 2004-07-20 14:57 36M chr22_random.maf.gz 2004-07-20 14:57 243K chrM.maf.gz 2004-07-20 15:03 46K chrX.maf.gz 2004-07-20 15:03 121M chrX_random.maf.gz 2004-07-20 15:03 946K chrY.maf.gz 2004-07-20 15:04 15M md5sum.txt 2006-04-21 15:40 2.2K multiz8way.sql 2006-04-25 10:46 631 multiz8way.txt.gz 2006-04-25 10:51 175M