This directory contains compressed multiple alignments of the 
following assemblies to the D. melanogaster genome
(dm2, Apr. 2004, BDGP Release 4 + DHGP Release 3.2).

- D. simulans (droSim1, Apr. 2005)
- D. sechellia (droSec1, Oct. 2005)
- D. yakuba (droYak2, Nov. 2005)
- D. erecta (droEre2, Feb. 2006)
- D. ananassae (droAna3, Feb. 2006)
- D. pseudoobscura (dp4, Feb. 2006) 
- D. persimilis (droPer1, Oct. 2005)
- D. willistoni (droWil1, Feb. 2006)
- D. virilis (droVir3, Feb. 2006) 
- D. mojavensis (droMoj3, Feb. 2006) 
- D. grimshawi (droGri2, Feb. 2006)
- A. gambiae (anoGam1, Feb. 2003) 
- A. mellifera (apiMel2, Jan. 2005) 
- T. castaneum (triCas2, Sep. 2005)

Files included in this directory:
  - chr*.maf.gz files: each contain all the alignments to that 
    particular D. melanogaster 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 
    D. melanogaster, 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 D. melanogaster; 
    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.

---------------------------------------------------------------
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/dm2/multiz15way. 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.

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt24-Feb-2011 12:22 2.3K 
[   ]chr2L.maf.gz28-Sep-2006 21:26 98M 
[   ]chr2R.maf.gz28-Sep-2006 21:27 86M 
[   ]chr2h.maf.gz28-Sep-2006 21:27 3.8M 
[   ]chr3L.maf.gz28-Sep-2006 21:28 102M 
[   ]chr3R.maf.gz28-Sep-2006 21:29 120M 
[   ]chr3h.maf.gz28-Sep-2006 21:29 6.0M 
[   ]chr4.maf.gz28-Sep-2006 21:29 5.6M 
[   ]chr4h.maf.gz28-Sep-2006 21:29 220K 
[   ]chrM.maf.gz28-Sep-2006 21:29 85K 
[   ]chrU.maf.gz28-Sep-2006 21:29 11M 
[   ]chrX.maf.gz28-Sep-2006 21:30 92M 
[   ]chrXh.maf.gz28-Sep-2006 21:30 1.3M 
[   ]chrYh.maf.gz28-Sep-2006 21:30 796K 
[TXT]md5sum.txt28-Sep-2006 21:46 769  
[   ]upstream1000.maf.gz28-Sep-2006 17:39 39M 
[   ]upstream2000.maf.gz28-Sep-2006 17:41 100M 
[   ]upstream5000.maf.gz28-Sep-2006 17:44 252M 

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