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TRAP - Tandem Repeats Analysis Program

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Supplementary Material - Table 1
 
Electronic Supplementary Material accompanying the paper entitled "TRAP: automated classification, quantification, and annotation of tandemly repeated sequences" by Sobreira, T.J.P., Durham, A.M. and Gruber A.

Repetitive content percentages of different genomes, according to the repeat unit length. The genome sequences were submitted to TRFa program and the resulting files were processed by TRAP. The repetitive content is presented as percentages of matches between adjacent repeat units overall, and categorized into four satellite DNA classesb, varying on the repeat unit length.

Organism
Genome sizec
(Mbp)
Identity
(%)
Length of the repeat unit (bp)
Microsatellite
(1 to 6)
Unclassified
(7 to 10)
Minisatellite
(11 to 100)
Satelitte
(>100)
E. coli
4.6
70
80
90
100
S. cerevisiae
12.1
70
80
90
100
P. falciparum
23.0
70
80
90
100
C. elegans
100.3
70
80
90
100
D. melanogaster
118.3
70
80
90
100

aTandem Repeats Finder was run using the following parameters: 2 5 7 80 10 25 1000.

bMicrosatellite, minisatellite and satellite repeats are classically defined as presenting repeat units of 1-6, 11-100 and longer than 100 bp, respectively. In order to encompass the size gap (7-10 bp) of the former definition, we analyzed repeats comprised within this range.

cSize determined according to the sum of all contigs of the respective assembly version.




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 © 2005 - Arthur Gruber, Alan M. Durham & Tiago J.P. Sobreira