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.