This directory contains zipped humor (special version of multiz) 
multiple alignments of the mouse (mm3, Feb.2003) assembly and the rat 
(rn3, Jun. 2003) assembly to the human (hg16, Jul. 2003) genome. 

The chr*.maf.gz files each contain all the alignments for a 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.

      Name                    Last modified      Size  Description
Parent Directory - upstream1000.maf.gz 2004-03-01 17:44 13M upstream5000.maf.gz 2004-02-02 15:38 59M upstream2000.maf.gz 2004-02-02 15:29 25M chrY.hmr.maf.gz 2003-10-27 16:07 2.9M chrX_random.hmr.maf.gz 2003-10-27 16:07 701K chrX.hmr.maf.gz 2003-10-27 16:07 49M chrUn_random.hmr.maf.gz 2003-10-27 16:07 908K chrM.hmr.maf.gz 2003-10-27 16:07 18K chr9_random.hmr.maf.gz 2003-10-27 16:07 591K chr9.hmr.maf.gz 2003-10-27 16:07 50M chr8_random.hmr.maf.gz 2003-10-27 16:07 206K chr8.hmr.maf.gz 2003-10-27 16:07 59M chr7_random.hmr.maf.gz 2003-10-27 16:07 95K chr7.hmr.maf.gz 2003-10-27 16:07 63M chr6_random.hmr.maf.gz 2003-10-27 16:07 664K chr6.hmr.maf.gz 2003-10-27 16:07 70M chr5_random.hmr.maf.gz 2003-10-27 16:07 30K chr5.hmr.maf.gz 2003-10-27 16:07 77M chr4_random.hmr.maf.gz 2003-10-27 16:07 122K chr4.hmr.maf.gz 2003-10-27 16:07 74M chr3_random.hmr.maf.gz 2003-10-27 16:07 337K chr3.hmr.maf.gz 2003-10-27 16:07 86M chr22.hmr.maf.gz 2003-10-27 16:07 13M chr2_random.hmr.maf.gz 2003-10-27 16:07 141K chr21.hmr.maf.gz 2003-10-27 16:06 12M chr20.hmr.maf.gz 2003-10-27 16:06 26M chr2.hmr.maf.gz 2003-10-27 16:06 103M chr19.hmr.maf.gz 2003-10-27 16:06 15M chr1_random.hmr.maf.gz 2003-10-27 16:06 1.7M chr18_random.hmr.maf.gz 2003-10-27 16:06 2.7K chr18.hmr.maf.gz 2003-10-27 16:06 31M chr17_random.hmr.maf.gz 2003-10-27 16:06 495K chr17.hmr.maf.gz 2003-10-27 16:06 35M chr16.hmr.maf.gz 2003-10-27 16:06 34M chr15_random.hmr.maf.gz 2003-10-27 16:06 355K chr15.hmr.maf.gz 2003-10-27 16:06 37M chr14.hmr.maf.gz 2003-10-27 16:06 38M chr13_random.hmr.maf.gz 2003-10-27 16:06 78K chr13.hmr.maf.gz 2003-10-27 16:06 37M chr12.hmr.maf.gz 2003-10-27 16:06 53M chr11.hmr.maf.gz 2003-10-27 16:06 57M chr10_random.hmr.maf.gz 2003-10-27 16:06 342K chr10.hmr.maf.gz 2003-10-27 16:06 57M chr1.hmr.maf.gz 2003-10-27 16:06 96M