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Open Access Highly Accessed Research article

Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach

Christoph Mayer*, Florian Leese and Ralph Tollrian

Author Affiliations

Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Universitaetsstrasse 150, 44801 Bochum, Germany

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BMC Genomics 2010, 11:277  doi:10.1186/1471-2164-11-277

Published: 30 April 2010

Additional files

Additional file 1:

Comparison of Phobos search parameters used in this analysis and default parameters of the Tandem Repeats Finder (TRF) program.

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Additional file 2:

Density and mean length of STRs versus genome size, divided into perfect and imperfect repeats.

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Additional file 3:

Genomic densities, mean lengths, number of satellites and mean perfection for tandem repeat classes in all twelve genomes.

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Additional file 4:

Genomic density (grey columns) and mean length (black line) of TRs with a unit size of 1- 50 bp in Daphnia pulex. The mean length of short tandem repeats is comparatively small. Repeat units with a unit size of 17 bp and 34 bp have much longer mean lengths than other repeats of similar unit size.

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Additional file 5:

Genomic density, mean lengths, number of satellites, and mean perfection of TR classes in different genomic regions of Daphnia pulex, the euchromatic genome of Drosophila melanogaster, and Apis mellifera.

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Additional file 6:

Table of tandem repeats found in coding regions of Daphnia pulex.

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Additional file 7:

Genomic density, mean lengths, number of satellites and mean perfection of individual TR motifs in different genomic regions of Daphnia pulex, the euchromatic genome of Drosophila melanogaster and Apis mellifera. Only repeats in the unit size range 1-50 bp are shown that have a minimum density of 50 bp/Mbp in one genomic region of the three genomes. The second column in the table assists detecting motif pairs that differ only by the reverse complement. An A stands for the normal form and B for the reverse complement of motif A. "-" indicates palindromic motifs for which the unit is identical to its reverse complement (e.g. AT). If only one of the two motifs is present, the letters a and b are used. Thus "a" indicates that only the normal form is present, whereas "b" indicates that only the reverse complement of the normal form was found.

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Open Data