This work develops an integrated system which, after a set of genes are inputted, is able to predict transcriptional regulatory sites and to detect the co-occurrence of these regulatory sites. The system integrates several site detection methods such as known site matching, over-presented oligonucleotide detection and DNA motif discovery programs. User profiles and history pages enable users to trace the sequence analyses of these transcriptional regulatory sites. Two groups of co-regulated genes were used to test the proposed system. The results predicted by the proposed system consist of known site homologs and putative regulatory sites. By comparing these sites with previously published results, the proposed system is able to help biologists identify possible candidates for the regulatory sites from groups of co-regulated genes. The integrated system is now available at http://rgsminer. csie.ncu.edu.tw/.