From owner-celegans@net.bio.net Tue Aug 06 23:00:00 1996 Path: biosci!agate!newsxfer2.itd.umich.edu!howland.erols.net!cs.utexas.edu!news.sprintlink.net!news-stk-200.sprintlink.net!EU.net!usenet2.news.uk.psi.net!uknet!usenet1.news.uk.psi.net!uknet!uknet!lyra.csx.cam.ac.uk!news From: Steve Jones Newsgroups: bionet.celegans Subject: Re: Repeats Date: Wed, 07 Aug 1996 14:36:31 +0100 Organization: The Sanger Centre Lines: 22 Message-ID: <32089BDF.41C6@sanger.ac.uk> References: <4u71ru$elk@mserv1.dl.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.2 IP22) There are two basic types of repeats that are found in the worm. Firstly there are the local repetitive regions. This category includes tandemly repeated sequences and inverted repeats. In C. elegans about 4% of the current genomic sequence is occupied by the arms of inverted repeats whilst around 9% is between such arms. A further 2.2% of the current genomic sequence is made up of tandem repeats. These figures are depend strongly however on the stringency of the search criteria e.g. how identical do the arms of an inverted repeat have to be and how far apart can they be. In the same way, how divergeant can the individual units of a tandem repeat be and still be determined as part of a tandem array. The above figures are calculated using relatively stringent criteria. Secondly, there are the repeat families or long range repeats i.e. similar sequences found numerous times throughout the genome. Currently we have defined 17 of these families which in total occupy about 1.7% of the current genomic sequence. Many more such families are currently being characterised. Steven Jones The Sanger Centre http://www.sanger.ac.uk/ .