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.
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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 -
md5sum.txt 2008-10-16 12:29 2.2K
maf/ 2019-11-06 11:14 -
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
chr20_random.maf.gz 2006-06-09 10:01 524K
chr20.maf.gz 2006-06-09 10:01 56M
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
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
chr2.maf.gz 2006-06-09 10:00 257M
chr1_random.maf.gz 2006-06-09 09:57 2.7M
chr1.maf.gz 2006-06-09 09:46 274M
alignments/ 2012-02-21 17:06 -