This directory contains the Build 33 assembly of the mouse genome 
(mm5, May 2004) from the Mouse Genome Sequencing Consortium. This 
assembly was produced at NCBI.  

Files included in this directory:

chromAgp.zip - Description of how the assembly was generated from
     fragments, unpacking to one file per chromosome.  

chromFa.zip - The assembly sequence in one file per chromosome.
    Repeats from RepeatMasker and Tandem Repeats Finder (with period
    of 12 or less) are shown in lower case; non-repeating sequence is
    shown in upper case.  RepeatMasker June 2003 version with RepBase
    libraries: RepBase Update 8.4, RM database version 20030619

chromFaMasked.zip - The assembly sequence in one file per 
    chromosome. Repeats are masked by capital Ns; non-repeating 
    sequence is shown in upper case.  

chromOut.zip - RepeatMasker .out file for chromosomes. These were 
    created by RepeatMasker at the -s sensitive setting.

chromTrf.zip - Tandem Repeats Finder locations, filtered to keep 
    repeats with period of less than or equal to 12, and translated 
    into one .bed file per chromosome.  

contigAgp.zip - Description of how the assembly was generated from
    fragments at a contig layout level. 

contigFa.zip - The assembly sequence contig, in one file per contig.
    Repeats from RepeatMasker and Tandem Repeats Finder (with period
    of 12 or less) are shown in lower case; non-repeating sequence is
    shown in upper case.

contigFaMasked.zip - The assembly sequence contigs, in one file
    per contig. Repeats are masked by capital Ns; non-repeating sequence 
    is shown in upper case.  

contigOut.zip - RepeatMasker .out file for contigs.  These were 
    created by RepeatMasker at the -s sensitive setting.

contigTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12, and translated into one .bed 
    file per contig.  

est.fa.gz - Mouse ESTs from GenBank, updated once a week via automatic 
    GenBank updates.

mrna.fa.gz - Mouse mRNA from GenBank, updated once a week via automatic 
    GenBank updates.

refMrna.fa.gz - RefSeq mRNA from the same species as the genome, updated 
    once a week via automatic GenBank updates.

upstream1000.zip - Sequences 1000 bases upstream of annotated
    transcription start of RefSeq genes.  This includes only the
    cases where the transcription start is annotated separately
    from the coding region start.  Note that upstream files are 
    generated only when an assembly is released. Therefore, the
    data may be slightly out of synch with the RefSeq data in
    assemblies that are updated nightly.

upstream2000.zip - Same as upstream1000, but 2000 bases.

upstream5000.zip - Same as upstream1000, but 5000 bases.

xenoMrna.fa.gz - GenBank mRNA from species other than that of the genome,
    updated once a week via automatic GenBank updates.


mm5.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

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If you plan to download a large file or multiple files from this 
directory, we recommend 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/mm5/bigZips/. To download multiple 
files, use the "mget" command:
mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 

All the tables in this directory are freely usable for any purpose. 
      Name                    Last modified      Size  Description
Parent Directory - refMrna.fa.gz 2008-07-25 02:12 21M est.fa.gz 2008-07-25 02:12 784M xenoMrna.fa.gz 2008-07-25 01:52 564M mrna.fa.gz 2008-07-25 01:48 127M upstream5000.zip 2004-07-14 21:09 22M upstream2000.zip 2004-07-14 21:06 9.0M upstream1000.zip 2004-07-14 21:04 4.7M contigTrf.zip 2004-07-14 16:36 17M chromTrf.zip 2004-07-14 16:35 16M contigFaMasked.zip 2004-07-14 16:35 488M contigFa.zip 2004-07-14 16:16 824M contigOut.zip 2004-07-14 15:46 145M contigAgp.zip 2004-07-14 15:44 3.4M chromFaMasked.zip 2004-07-14 15:43 488M chromFa.zip 2004-07-14 15:27 823M chromOut.zip 2004-07-14 14:56 146M chromAgp.zip 2004-07-14 14:53 3.2M mm5.chrom.sizes 2004-06-27 20:25 777