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