Repeat Annotation Request Form
The following form facilitates extraction of short lengths of repeat sequence annotation from commonly available genomes.
If you would like to download the raw annotations for the entire genome, *.out and *.align files can be found
African savannah elephant - May 2005 - loxAfr2
Anopheles gambiae - Apr 2006 - anoGam1
Arabidopsis - Jun 2004 - araTha5
Cat - Mar 2006 - felCat3
Chicken - Feb 2004 - galGal2
Chicken - May 2006 - galGal3
Chimpanzee - Mar 2006 - panTro2
Chimpanzee - Nov 2003 - panTro1
Ciona - Mar 2005 - ci2
Cow - Oct 2007 - bosTau4
Dog - May 2005 - canFam2
Duckbill platypus - Jan 2006 - ornAna1
Florida lancelet - Mar 2006 - braFlo1
Fruit fly - Apr 2006 - dm3
Gray short-tailed opossum - Jan 2006 - monDom4
Gray short-tailed opossum - Oct 2006 - monDom5
Guinea Pig - Feb 2008 - cavPor3
Horse - Sep 2007 - equCab2
Human - Feb 2009 - hg19
Human - Mar 2006 - hg18
Human - May 2004 - hg17
Little brown bat - Jul 2010 - myoLuc2
Mouse - Dec 2011 - mm10
Mouse - July 2007 - mm9
Mouse - May 2004 - mm5
Norway rat - Jun 2003 - rn3
Norway rat - Nov 2004 - rn4
Pig - Nov 2009 - susScr2
Pongo abelii - Jul 2007 - ponAbe2
Purple urchin - Sep 2006 - strPur2
Rabbit - Apr 2009 - oryCun2
Rhesus macaque - Jan 2006 - rheMac2
Rice - Jan 2007 - orySat5
Takifugu - Aug 2002 - fr1
Takifugu - Oct 2004 - fr2
Three spined stickleback - Feb 2006 - gasAcu1
Xenopus tropicalis - Aug 2005 - xenTro2
Zebra finch - May 2005 - taeGut1
Zebrafish - Jul 2007 - danRer5
Zebrafish - Jun 2008 - danRer6
Zebrafish - May 2005 - danDer3
Select the genome and assembly from one of the options in the drop down box.
Ranges consist of three identifiers. A valid dna chromosome for the genome specified followed by a start and end position (inclusive). For example human chromosome 1 from position 10-1000 would be chr1:10-1000. Multiple ranges can be entered separated by a ";".
masked genomic sequence
Select the result type for the range. "annotations" returns RepeatMasker style table of repeat annotations. "raw alignments" returns the alignment file used to create the RepeatMasker annotations. "masked genomic sequence" returns fasta formatted data from the assembly with interspersed repeats masked. "fasta" returns each interspersed repeat instance sequence in fasta format.
Specify the character to use for masking or use lower case to designate repetitive sequences.
Filter out all repeats which score below this threshold.
Filter out all repeats with a higher divergence.
Repeat classes you would like included in your results.
Search for a particular repeat name ie. "AluSx". Do not include the type information in your name ie. "AluSx#SINE/Alu". The classes filter should be set to "All" if you are using a name filter.
Institute for Systems Biology
This server is made possible by funding from the National Human Genome Research Institute (NHGRI grant # RO1 HG002939-01) 2003.