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Arabidopsis thaliana Repeat Maps

Last modified
07-Mar-2016 05:19
07-Mar-2016 05:19
07-Mar-2016 05:19
07-Mar-2016 05:19
07-Mar-2016 05:19

DNA sequences of the A. thaliana chromosomes I-V were downloaded 
from NCBI in November 2001) 

name    length   GenBank's gi and acc. num.
AT_I   29640317   gi:15217430  NC_003070.1
AT_II  19643621   gi:15224037  NC_003071.1
AT_III 23333883   gi:15228160  NC_003074.1
AT_IV  17549528   gi:15233324  NC_003075.1
AT_V   26269328   gi:15237134  NC_003076.1

The "December 2001" version of the Arabidopsis thaliana 
section (athrep.ref) of Repbase Update was used for 
annotation of the chromosomes. The annotation 
shows localization of transposable elements in the 
chromosomes. These elements have been identified
by using the BLAST and CENSOR searches.

Each line in the annotation represents a chromosomal
fragment that can be classified as a transposable or
noncoding repetitive element. Every line is composed
of 8 columns that, in order, represent the following
1. Chromosome
2. Fragment start position in the chromosome
3. Fragment end position in the chromosome
4. Name of a transposable or repetitive element in Repbase Update
   most similar to the fragment
5. Fragment start position in the Repbase update element
6. Fragment end position in the Repbase update element
7. Orientation of the element, 'd' for direct, 'c' for complement
8. Percent identity between the chromosomal fragment and transposable 
   element from Repbase Update.

DNA sequences of all annotated elements are available in
the A. thaliana section of The Transposon Pub.

Reference: Kapitonov,V.V. and Jurka,J. (2002) Distribution of transposable and repetitive elements in the A. thaliana chromosomes, www.girinst.org/server/TransPub/ATinfo.html

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