MOTIVATION: The NCBI database contains mitochondrial DNA (mtDNA) genomes from numerous species. We investigated the presence and locations of inverted repeat sequences (IRs) in these mtDNA sequences, which are known to be important for regulating nuclear genomes. RESULTS: IRs were identified in mtDNA in all species. IR lengths and frequencies correlate with evolutionary age and the greatest variability was detected in subgroups of plants and fungi and the lowest variability in mammals. IR presence is non-random and evolutionary favoured. The frequency of IRs generally decreased with IR length, but not for IRs 24 or 30 bp long, which are 1.5 times more abundant. IRs are enriched in sequences from the replication origin, followed by D-loop, stem-loop and miscellaneous sequences, pointing to the importance of IRs in regulatory regions of mitochondrial DNA. AVAILABILITY AND IMPLEMENTATION: Data were produced using Palindrome analyser, freely available on the web at http://bioinformatics.ibp.cz. CONTACT: vaclav@ibp.cz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Department of Biology and Ecology Institute of Environmental Technologies Faculty of Science University of Ostrava 701 03 Ostrava Czech Republic

Department of Biophysical Chemistry and Molecular Oncology Institute of Biophysics The Czech Academy of Sciences 612 65 Brno Czech Republic

Department of Informatics Mendel University in Brno 613 00 Brno Czech Republic

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