Background: Replication of chromosomes is one of the central events in the cell cycle.DNA replication begins at a specific site, called an origin of replication, in all three domains of life.In bacteria, replication initiates from a single replication origin, whereas replication initiates from many replication origins activated simultaneously at a specific time in the eukaryotic genome.Methods: Based on the Z-curve theory, with the means of comparative genomics, we have developed a web-based system Ori-Finder for finding oriCs in bacterial genomes with high accuracy and reliability, and the predicted oriC regions in over 1,000 bacterial genomes have been organized into an online database, DoriC.Recently, we have also constructed a Database of Eukaryotic ORIs (DeOri), which contains over ten thousand Eukaryotic ORIs identified by genome-wide analyses currently available.Motif-based sequence analysis tools, the MEME Suite, were used to discover motifs in the replication origins.Results: Analyzing sequence motifs in the replication origins identified by MEME Suite, we found the relationships between the DnaA boxes and taxonomic levels or genomic GC content.In addition, we found the AT-rich motifs are enriched in the replication origins.Conclusions: The discovered motifs in the replication origins will be useful to develop algorithms to predict replication origins, and further analysis of the conserved motifs within the origins will be helpful to reveal the regulatory mechanisms of the initiation step in DNA replication .