This directory contains the May 2005 assembly of the elephant genome 
(loxAfr1) obtained from the Broad Institute. More information may be 
found http://www.broad.mit.edu/mammals/.

Files included in this directory:
assembly.agp.gz - Description of how the assembly was generated from
     fragments.  

md5sum.txt - MD5 checksum of these files to verify correct transmission.

rmsk.out.gz - RepeatMasker .out file for scaffolds. These were created 
    by RepeatMasker at the -s sensitive setting. 

scaffold.fa.gz - unmasked scaffolds sequences obtained from the Broad
    Institute.

scaffoldSoftMask.fa.gz - 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 May 3 2005 (open-3-1-0) version with RepBase 
    libraries: RepBase Update 9.11, RM database version 20050112.

trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats 
    with period less than or equal to 12, and translated into one 
    .bed file for all the scaffolds.  


loxAfr1.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/loxAfr1/bigZips. To download multiple files, 
use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory)

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Feb-2015 15:32 1.7K 
[TXT]README.txt.bak05-May-2006 14:21 1.6K 
[   ]assembly.agp.gz20-May-2005 20:08 18M 
[   ]loxAfr1.chrom.sizes23-May-2005 13:06 4.6M 
[TXT]md5sum.txt26-Oct-2007 12:34 247  
[   ]rmsk.out.gz23-May-2005 11:45 103M 
[   ]scaffold.fa.gz22-May-2005 15:18 715M 
[   ]scaffoldSoftMask.fa.gz23-May-2005 12:52 760M 
[   ]trf.bed.gz23-May-2005 12:43 1.2M 

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