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:		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:
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).

Score: >=		Filter out all repeats which score below this threshold.
Divergence: <	%	Filter out all repeats with a higher divergence.
Repeat Classes:		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.