This directory contains compressed multiple alignments of the
following assemblies to the chicken genome (galGal3, May 2006):
- human (Mar 2006, hg18)
- mouse (Feb 2006, mm8)
- rat (Nov. 2004, rn4)
- opossum (Jan 2006, monDom4)
- frog (Aug 2005, xenTro2)
- zebrafish (Mar 2006, danRer4)
Files included in this directory:
- chr*.maf.gz files: each contain all the alignments to that
particular chicken 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
chicken, 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 chicken; 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/galGal3/multiz7way. 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 12:21 2.8K
maf/ 2019-11-06 10:55 -
chrZ_random.maf.gz 2006-07-28 11:35 118K
chrZ.maf.gz 2006-07-28 11:35 29M
chrW_random.maf.gz 2006-07-28 11:35 247K
chrW.maf.gz 2006-07-28 11:35 88K
chrUn_random.maf.gz 2006-07-28 11:35 19M
chrM.maf.gz 2006-07-28 11:34 36K
chrE64_random.maf.gz 2006-07-28 11:34 193K
chrE64.maf.gz 2006-07-28 11:34 49K
chrE22C19W28_E50C23_random.maf.gz 2006-07-28 11:34 139K
chrE22C19W28_E50C23.maf.gz 2006-07-28 11:34 771K
chr32.maf.gz 2006-07-28 11:33 64
chr28_random.maf.gz 2006-07-28 11:32 91K
chr28.maf.gz 2006-07-28 11:32 2.7M
chr27.maf.gz 2006-07-28 11:32 2.5M
chr26.maf.gz 2006-07-28 11:32 3.4M
chr25_random.maf.gz 2006-07-28 11:32 11K
chr25.maf.gz 2006-07-28 11:32 1.0M
chr24.maf.gz 2006-07-28 11:32 3.9M
chr23.maf.gz 2006-07-28 11:32 3.1M
chr22_random.maf.gz 2006-07-28 11:32 78K
chr22.maf.gz 2006-07-28 11:32 2.2M
chr21.maf.gz 2006-07-28 11:32 4.5M
chr20_random.maf.gz 2006-07-28 11:31 34K
chr20.maf.gz 2006-07-28 11:31 7.3M
chr19.maf.gz 2006-07-28 11:30 6.2M
chr18_random.maf.gz 2006-07-28 11:30 22K
chr18.maf.gz 2006-07-28 11:30 6.3M
chr17_random.maf.gz 2006-07-28 11:30 71
chr17.maf.gz 2006-07-28 11:30 6.3M
chr16_random.maf.gz 2006-07-28 11:30 129K
chr16.maf.gz 2006-07-28 11:30 334K
chr15.maf.gz 2006-07-28 11:30 7.3M
chr14.maf.gz 2006-07-28 11:30 8.3M
chr13_random.maf.gz 2006-07-28 11:30 14K
chr13.maf.gz 2006-07-28 11:30 8.6M
chr12_random.maf.gz 2006-07-28 11:30 71
chr12.maf.gz 2006-07-28 11:30 9.8M
chr11_random.maf.gz 2006-07-28 11:30 7.7K
chr11.maf.gz 2006-07-28 11:30 11M
chr10_random.maf.gz 2006-07-28 11:30 2.5K
chr10.maf.gz 2006-07-28 11:30 12M
chr9.maf.gz 2006-07-28 11:34 12M
chr8_random.maf.gz 2006-07-28 11:34 289K
chr8.maf.gz 2006-07-28 11:34 16M
chr7_random.maf.gz 2006-07-28 11:34 53K
chr7.maf.gz 2006-07-28 11:34 19M
chr6_random.maf.gz 2006-07-28 11:34 2.8K
chr6.maf.gz 2006-07-28 11:34 16M
chr5_random.maf.gz 2006-07-28 11:34 19K
chr5.maf.gz 2006-07-28 11:34 28M
chr4_random.maf.gz 2006-07-28 11:33 83K
chr4.maf.gz 2006-07-28 11:33 39M
chr3.maf.gz 2006-07-28 11:33 47M
chr2_random.maf.gz 2006-07-28 11:32 31K
chr2.maf.gz 2006-07-28 11:31 59M
chr1_random.maf.gz 2006-07-28 11:30 98K
chr1.maf.gz 2006-07-28 11:29 76M