This directory contains compressed multiple alignments of the 
following assemblies to the rat genome (rn4, Nov. 2004):

  - mouse (Feb 2006, mm8)
  - human (Mar 2006, hg18) 
  - dog (May 2005, canFam2) 
  - cow (Mar 2005, bosTau2) 
  - opossum (Jan 2006, monDom4) 
  - chicken (Feb 2004, galGal2) 
  - frog (Oct 2004, xenTro1) 
  - zebrafish (May 2005, danRer3) 

The "alignments" directory contains compressed FASTA alignments
for the CDS regions of the rat genome (rn4/Baylr 3.4, Nov. 2004)
aligned to the assemblies.

Files included in this directory:
  - chr*.maf.gz files: each contain all the alignments to that 
    particular rat 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 
    rat, 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 rat; 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.

---------------------------------------------------------------
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/rn4/multiz9way. 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.

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt06-Oct-2011 14:20 2.2K 
[DIR]alignments/10-Oct-2011 17:59 -  
[   ]chr1.maf.gz09-Jun-2006 09:46 274M 
[   ]chr1_random.maf.gz09-Jun-2006 09:57 2.7M 
[   ]chr2.maf.gz09-Jun-2006 10:00 257M 
[   ]chr2_random.maf.gz09-Jun-2006 10:01 3.4M 
[   ]chr3.maf.gz09-Jun-2006 10:03 192M 
[   ]chr3_random.maf.gz09-Jun-2006 10:03 1.4M 
[   ]chr4.maf.gz09-Jun-2006 10:05 193M 
[   ]chr4_random.maf.gz09-Jun-2006 10:05 1.4M 
[   ]chr5.maf.gz09-Jun-2006 10:07 179M 
[   ]chr5_random.maf.gz09-Jun-2006 10:07 1.6M 
[   ]chr6.maf.gz09-Jun-2006 10:09 156M 
[   ]chr6_random.maf.gz09-Jun-2006 10:09 1.4M 
[   ]chr7.maf.gz09-Jun-2006 10:10 151M 
[   ]chr7_random.maf.gz09-Jun-2006 10:10 886K 
[   ]chr8.maf.gz09-Jun-2006 10:12 143M 
[   ]chr8_random.maf.gz09-Jun-2006 10:12 708K 
[   ]chr9.maf.gz09-Jun-2006 10:13 122M 
[   ]chr9_random.maf.gz09-Jun-2006 10:13 963K 
[   ]chr10.maf.gz09-Jun-2006 09:48 132M 
[   ]chr10_random.maf.gz09-Jun-2006 09:48 836K 
[   ]chr11.maf.gz09-Jun-2006 09:49 94M 
[   ]chr11_random.maf.gz09-Jun-2006 09:49 1.0M 
[   ]chr12.maf.gz09-Jun-2006 09:49 46M 
[   ]chr12_random.maf.gz09-Jun-2006 09:49 655K 
[   ]chr13.maf.gz09-Jun-2006 09:51 110M 
[   ]chr13_random.maf.gz09-Jun-2006 09:51 307K 
[   ]chr14.maf.gz09-Jun-2006 09:52 112M 
[   ]chr14_random.maf.gz09-Jun-2006 09:52 1.3M 
[   ]chr15.maf.gz09-Jun-2006 09:53 111M 
[   ]chr15_random.maf.gz09-Jun-2006 09:53 1.3M 
[   ]chr16.maf.gz09-Jun-2006 09:54 90M 
[   ]chr16_random.maf.gz09-Jun-2006 09:54 1.1M 
[   ]chr17.maf.gz09-Jun-2006 09:55 98M 
[   ]chr17_random.maf.gz09-Jun-2006 09:55 335K 
[   ]chr18.maf.gz09-Jun-2006 09:56 93M 
[   ]chr18_random.maf.gz09-Jun-2006 09:56 407K 
[   ]chr19.maf.gz09-Jun-2006 09:57 66M 
[   ]chr19_random.maf.gz09-Jun-2006 09:57 855K 
[   ]chr20.maf.gz09-Jun-2006 10:01 56M 
[   ]chr20_random.maf.gz09-Jun-2006 10:01 524K 
[   ]chrM.maf.gz09-Jun-2006 10:13 47K 
[   ]chrUn.maf.gz09-Jun-2006 10:14 41M 
[   ]chrUn_random.maf.gz09-Jun-2006 10:14 4.1M 
[   ]chrX.maf.gz09-Jun-2006 10:15 132M 
[   ]chrX_random.maf.gz09-Jun-2006 10:15 696K 
[TXT]md5sum.txt16-Oct-2008 12:29 2.2K 
[   ]upstream1000.maf.gz07-Jul-2007 11:05 9.5M 
[   ]upstream2000.maf.gz07-Jul-2007 11:05 17M 
[   ]upstream5000.maf.gz07-Jul-2007 11:06 39M 

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