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) 

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.

      Name                    Last modified      Size  Description
Parent Directory - maf/ 2019-11-06 11:14 - alignments/ 2012-02-21 17:06 - md5sum.txt 2008-10-16 12:29 2.2K chrX_random.maf.gz 2006-06-09 10:15 696K chrX.maf.gz 2006-06-09 10:15 132M chrUn_random.maf.gz 2006-06-09 10:14 4.1M chrUn.maf.gz 2006-06-09 10:14 41M chrM.maf.gz 2006-06-09 10:13 47K chr9_random.maf.gz 2006-06-09 10:13 963K chr9.maf.gz 2006-06-09 10:13 122M chr8_random.maf.gz 2006-06-09 10:12 708K chr8.maf.gz 2006-06-09 10:12 143M chr7_random.maf.gz 2006-06-09 10:10 886K chr7.maf.gz 2006-06-09 10:10 151M chr6_random.maf.gz 2006-06-09 10:09 1.4M chr6.maf.gz 2006-06-09 10:09 156M chr5_random.maf.gz 2006-06-09 10:07 1.6M chr5.maf.gz 2006-06-09 10:07 179M chr4_random.maf.gz 2006-06-09 10:05 1.4M chr4.maf.gz 2006-06-09 10:05 193M chr3_random.maf.gz 2006-06-09 10:03 1.4M chr3.maf.gz 2006-06-09 10:03 192M chr2_random.maf.gz 2006-06-09 10:01 3.4M chr20_random.maf.gz 2006-06-09 10:01 524K chr20.maf.gz 2006-06-09 10:01 56M chr2.maf.gz 2006-06-09 10:00 257M chr1_random.maf.gz 2006-06-09 09:57 2.7M chr19_random.maf.gz 2006-06-09 09:57 855K chr19.maf.gz 2006-06-09 09:57 66M chr18_random.maf.gz 2006-06-09 09:56 407K chr18.maf.gz 2006-06-09 09:56 93M chr17_random.maf.gz 2006-06-09 09:55 335K chr17.maf.gz 2006-06-09 09:55 98M chr16_random.maf.gz 2006-06-09 09:54 1.1M chr16.maf.gz 2006-06-09 09:54 90M chr15_random.maf.gz 2006-06-09 09:53 1.3M chr15.maf.gz 2006-06-09 09:53 111M chr14_random.maf.gz 2006-06-09 09:52 1.3M chr14.maf.gz 2006-06-09 09:52 112M chr13_random.maf.gz 2006-06-09 09:51 307K chr13.maf.gz 2006-06-09 09:51 110M chr12_random.maf.gz 2006-06-09 09:49 655K chr12.maf.gz 2006-06-09 09:49 46M chr11_random.maf.gz 2006-06-09 09:49 1.0M chr11.maf.gz 2006-06-09 09:49 94M chr10_random.maf.gz 2006-06-09 09:48 836K chr10.maf.gz 2006-06-09 09:48 132M chr1.maf.gz 2006-06-09 09:46 274M