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
here
.
Sequence Selection
Genome/Assembly:
A. mellifera - May 2005 - apiMel3
African savannah elephant - May 2005 - loxAfr2
Alligator - Aug 2012 - allMis1
Alligator - Nov 2012 - allMis2
Alpaca - Mar 2013 - vicPac2
Anopheles gambiae - Apr 2006 - anoGam1
Arabidopsis - Jun 2004 - araTha5
Armadillo - Dec 2011 - dasNov3
Bushbaby - Mar 2011 - otoGar3
C. briggsae - Jan 2007 - cb3
Cat - Mar 2006 - felCat3
Cat - Sep 2011 - felCat5
Chicken - Feb 2004 - galGal2
Chicken - May 2006 - galGal3
Chicken - Nov 2011 - galGal4
Chimp - Feb 2011 - panTro4
Chimpanzee - Mar 2006 - panTro2
Chimpanzee - Nov 2003 - panTro1
Ciona - Mar 2005 - ci2
Coelacanth - Aug 2011 - latCha1
Cow - Oct 2007 - bosTau4
Cow - Oct 2011 - bosTau7
Crab-eating macaque - Jun 2013 - macFas5
Crocodile - Aug 2012 - croPor2
D. melanogaster - Aug 2014 - dm6
Dog - May 2005 - canFam2
Dog - Sep 2011 - canFam3
Dolphin - Oct 2011 - turTru2
Duckbill platypus - Jan 2006 - ornAna1
Elephant - Jul 2009 - loxAfr3
Florida lancelet - Mar 2006 - braFlo1
Fruit fly - Apr 2006 - dm3
Fugu - Oct 2011 - fr3
Gharial - Sep 2012 - gavGan1
Gibbon - Oct 2012 - nomLeu3
Gorilla - May 2011 - gorGor3
Gray short-tailed opossum - Jan 2006 - monDom4
Gray short-tailed opossum - Oct 2006 - monDom5
Guinea Pig - Feb 2008 - cavPor3
Hedgehog - May 2012 - eriEur2
Horse - Sep 2007 - equCab2
Human - Dec 2013 - hg38
Human - Feb 2009 - hg19
Human - Mar 2006 - hg18
Human - May 2004 - hg17
Killer whale - Jan 2013 - orcOrc1
Lamprey - Sep 2010 - petMar2
Lancelet - Apr 2008 - braFlo2
Little brown bat - Jul 2010 - myoLuc2
Lizard - May 2010 - anoCar2
Mallard duck - Apr 2013 - anaPla1
Manatee - Oct 2011 - triMan1
Marmoset - Mar 2009 - calJac3
Megabat - Jul 2008 - pteVam1
Mouse - Dec 2011 - mm10
Mouse - July 2007 - mm9
Mouse - May 2004 - mm5
Mouse lemur - Jul 2007 - micMur1
Norway rat - Jun 2003 - rn3
Norway rat - Nov 2004 - rn4
Panda - Dec 2009 - ailMel1
Pig - Aug 2011 - susScr3
Pig - Nov 2009 - susScr2
Pika - May 2012 - ochPri3
Pongo abelii - Jul 2007 - ponAbe2
Prairie vole - Oct 2012 - micOch1
Purple urchin - Sep 2006 - strPur2
Rabbit - Apr 2009 - oryCun2
Rat - Mar 2012 - rn5
Rhesus - Oct 2010 - rheMac3
Rhesus macaque - Jan 2006 - rheMac2
Rice - Jan 2007 - orySat5
Rock hyrax - Jul 2008 - proCap1
Sea hare - Sep 2008 - aplCal1
Shrew - Aug 2008 - sorAra2
Sloth - Jul 2008 - choHof1
Spotted gar - Dec 2011 - lepOcu1
Squirrel - Nov 2011 - speTri2
Starlet sea anemone - Jun. 2007 - nemVec1
Takifugu - Aug 2002 - fr1
Takifugu - Oct 2004 - fr2
Tarsier - Aug 2008 - tarSyr1
Tenrec - Nov 2012 - echTel2
Three spined stickleback - Feb 2006 - gasAcu1
Tree shrew - Dec 2006 - tupBel1
Wallaby - Sep 2009 - macEug2
Weddell seal - Mar 2013 - lepWed1
Worm - Oct 2010 - ce10
X. tropicalis - Sep 2012 - xenTro7
Xenopus tropicalis - Aug 2005 - xenTro2
Zebra finch - May 2005 - taeGut1
Zebrafish - Jul 2007 - danRer5
Zebrafish - Jul 2010 - danRer7
Zebrafish - Jun 2008 - danRer6
Zebrafish - May 2005 - danDer3
Zebrafish - Sep 2014 - danRer10
Select the genome and assembly from one of the options in the drop down box.
Range:
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 ";".
Result Type:
annotations
raw alignments
masked genomic sequence
fasta
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.
Masking Format:
x
n
lower case
Specify the character to use for masking or use lower case to designate repetitive sequences.
Filtering
Score:
>=
Filter out all repeats which score below this threshold.
Divergence: <
%
Filter out all repeats with a higher divergence.
Repeat Classes:
snRNA
rRNA
DNA
LINE
scRNA
Other
RNA
tRNA
All
Interspersed Only
Low_complexity
LTR
SINE
Satellite
Simple_repeat
ARTEFACT
RC
Repeat classes you would like included in your results.
Repeat Name:
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).