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
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
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80