Palindromes, homopolymers and simple repeats .

This series contains features that are directly computed from the genome sequence with ad hoc scripts, including short palindromes, homopolymers and simple repeats. Some of these features appear to be enriched or depleted in certains regions. For instance, palindromes are enriched in the regulatory regions of certain species. Simple repeats tend to be depleted in conserved non-coding regions.

• Genome assembly: A. thaliana (Feb 2011 TAIR10/araTha1)
• Source URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.3_TAIR10/
• Input file format: FASTA

From A. thaliana (Feb 2011 TAIR10/araTha1).

Sequence-derived:

	Filename	Description	Feature	GEO-ID
1	wwwwww.sga	W-hexamers	6W	-
2	ssssss.sga	S-hexamers	6S	-
3	rrrrrr.sga	R(+)/Y(-)-hexamers	6R	-
4	mmmmmm.sga	M(+)/K(-)-hexamers	6M	-
5	aaaaaa.sga	hexa-homopolymers (aaaaaa)	aaaaaa	-
6	ababab.sga	3x2-repeats (ababab)	ababab	-
7	abcabc.sga	2x3-repeats (abcabc)	abcabc	-
8	abcxyz.sga	hexa-palindromes (abcxyz)	abcxyz	-
9	abcNxyz.sga	hepta-palindromes (abcNxyz)	abcNxyz	-

For a detailed description of the individual features and how they were produced see the palrep documentation for hg19 at:

https://epd.expasy.org/mga/hg19/palrep/palrep.html