Pre-Masked Genomes Download

The following genomes were masked using the computing resources at UCSC. In some cases these datasets will be newer than the version available in the genome tracks at UCSC.

Human

HG19 - Feb 2009 - RepeatMasker open-3.3.0 - Repeat Library 20120124
- hg19.fa.out.gz
- hg19.fa.align.gz

HG19 - Feb 2009 - RepeatMasker open-3.3.0 - Repeat Library 20110920
- hg19.fa.out.gz
- hg19.fa.align.gz

HG19 - Feb 2009 - RepeatMasker open-3.3.0 - Repeat Library 20110419
- hg19.fa.out.gz
- hg19.fa.align.gz

HG19 - Feb 2009 - RepeatMasker open-3.2.8 - Repeat Library 20090604
- hg19.fa.out.gz
- hg19.fa.align.gz

HG18 - Mar 2006 - RepeatMasker open-3.2.7 - Repeat Library 20080120
- hg18.fa.out.gz
- hg18.fa.align.gz

HG18 - Mar 2006 - RepeatMasker open-3.1.9 - Repeat Library 20071204
- hg18.fa.out.gz
- hg18.fa.align.gz

Chimp

panTro2 - Mar 2006 - RepeatMasker open-3.2.4 - Repeat Library 20080521
- panTro2.fa.out.gz
- panTro2.fa.align.gz

Orangutan

ponAbe2 - Jul 2007 - RepeatMasker open-3.2.5 - Repeat Library 20080611
- ponAbe2.fa.out.gz
- ponAbe2.fa.align.gz

Rhesus

rheMac2 - Jan 2006 - RepeatMasker open-3.1.9 - Repeat Library 20071204
- rheMac2.fa.out.gz
- rheMac2.fa.align.gz

Mouse

mm9 - Jul 2007 - RepeatMasker open-3.2.8 - Repeat Library 20090604
- mm9.fa.out.gz
- mm9.fa.align.gz

mm9 - Jul 2007 - RepeatMasker open-3.1.9 - Repeat Library 20071204
- mm9.fa.out.gz
- mm9.fa.align.gz

Rat

rn4 - Nov 2004 - RepeatMasker open-3.3.0 - Repeat Library 20120124
- rn4.fa.out.gz
- rn4.fa.align.gz

rn4 - Nov 2004 - RepeatMasker open-3.2.4 - Repeat Library 20080521
- rn4.fa.out.gz
- rn4.fa.align.gz

Guinea Pig

cavPor3 - Feb 2008 - RepeatMasker open-3.3.0 - Repeat Library 20120124
- cavPor3.fa.out.gz
- cavPor3.fa.align.gz

Cat

felCat3 - Mar 2006 - RepeatMasker open-3.1.9 - Repeat Library 20071204
- felCat3.fa.out.gz
- felCat3.fa.align.gz

Dog

canFam2 - May 2005 - RepeatMasker open-3.3.0 - Repeat Library 20120124
- canFam2.fa.out.gz
- canFam2.fa.align.gz

Cow

bosTau4 - Oct 2007 - RepeatMasker open-3.2.8 - Repeat Library 20090604
- bosTau4.fa.out.gz
- bosTau4.fa.align.gz

bosTau4 - Oct 2007 - RepeatMasker open-3.1.9 - Repeat Library 20071204
- bosTau4.fa.out.gz
- bosTau4.fa.align.gz

Pig

susScr2 - Nov 2009 - RepeatMasker open-3.3.0 - Repeat Library 20120124
- susScr2.fa.out.gz
- susScr2.fa.align.gz

Elephant

loxAfr2 - May 2005 - RepeatMasker open-3.2.7 - Repeat Library 20090120
- loxAfr2.fa.out.gz
- loxAfr2.fa.align.gz

Platypus

ornAna1 - Mar 2007 - RepeatMasker open-3.1.9 - Repeat Library 20071204
- ornAna1.fa.out.gz
- ornAna1.fa.align.gz

Opossum

monDom5 - Oct 2006 - RepeatMasker open-3.2.8 - Repeat Library 20090604
- monDom5.fa.out.gz
- monDom5.fa.align.gz

monDom4 - Jan 2006 - RepeatMasker open-3.1.9 - Repeat Library 20071204
- monDom4.fa.out.gz
- monDom4.fa.align.gz

Rabbit

oryCun2 - Apr 2009 - RepeatMasker open-3.3.0 - Repeat Library 20120124
- oryCun2.fa.out.gz
- oryCun2.fa.align.gz

Bat

myoLuc2 - Jul 2010 - RepeatMasker open-3.3.0 - Repeat Library 20120124
- myoLuc2.fa.out.gz
- myoLuc2.fa.align.gz

Horse

equCab2 - Sep 2007 - RepeatMasker open-3.3.0 - Repeat Library 20110419
- equCab2.fa.out.gz
- equCab2.fa.align.gz

Zebrafinch

taeGut1 - Jul 2008 - RepeatMasker open-3.2.7 - Repeat Library 20090204
- taeGut1.fa.out.gz
- taeGut1.fa.align.gz

Chicken

galGal3 - May 2006 - RepeatMasker open-3.2.7 - Repeat Library 20090204
- galGal3.fa.out.gz
- galGal3.fa.align.gz

galGal3 - May 2006 - RepeatMasker open-3.1.9 - Repeat Library 20071204
- galGal3.fa.out.gz
- galGal3.fa.align.gz

Takifugu

fr2 - Oct 2004 - RepeatMasker open-3.2.5 - Repeat Library 20080611
- fr2.fa.out.gz
- fr2.fa.align.gz

Zebrafish

danRer6 - Jun 2008 - RepeatMasker open-3.2.8 - Repeat Library 20090604
- danRer6.fa.out.gz
- danRer6.fa.align.gz

Lancelet

braFlo1 - Mar 2006 - RepeatMasker open-3.3.0 - Repeat Library 20120124
- braFlo1.fa.out.gz
- braFlo1.fa.align.gz

Ciona

ci2 - Mar 2005 - RepeatMasker open-3.3.0 - Repeat Library 20120124
- ci2.fa.out.gz
- ci2.fa.align.gz

danRer5 - Jul 2007 - RepeatMasker open-3.2.7 - Repeat Library 20090120
- danRer5.fa.out.gz
- danRer5.fa.align.gz

danRer5 - Jul 2007 - RepeatMasker open-3.2.5 - Repeat Library 20080611
- danRer5.fa.out.gz
- danRer5.fa.align.gz

Frog

xenTro2 - Aug 2005 - RepeatMasker open-3.2.7 - Repeat Library 20090202
- xenTro2.fa.out.gz
- xenTro2.fa.align.gz

Stickleback

gasAcu1 - Feb 2006 - RepeatMasker open-3.3.0 - Repeat Library 20120124
- gasAcu1.fa.out.gz
- gasAcu1.fa.align.gz

Sea Urchin

strPur2 - Sep 2006 - RepeatMasker open-3.3.0 - Repeat Library 20120124
- strPur2.fa.out.gz
- strPur2.fa.align.gz

Arabidopsis

araTha5 - Jun 2004 - RepeatMasker open-3.1.9 - Repeat Library 20071204
- araTha5.fa.out.gz
- araTha5.fa.align.gz

Rice

orySat5 - Jan 2007 - RepeatMasker open-3.1.9 - Repeat Library 20071204
- orySat5.fa.out.gz
- orySat5.fa.align.gz

Mosquito

anoGam1 - Feb 2003 - RepeatMasker open-3.2.5 - Repeat Library 20080611
- anoGam1.fa.out.gz
- anoGam1.fa.align.gz

Drosophila

dm3 - Apr 2006 - RepeatMasker open-3.2.5 - Repeat Library 20080611
- dm3.fa.out.gz
- dm3.fa.align.gz

Institute for Systems Biology
This server is made possible by funding from the National Human Genome Research Institute (NIGRI grant # RO1 HG002939).