bookmark ConBind A method to enhance alignment of short motifs, even if their mutual sequence similarity is only partial. ConBind improves the identification of conserved transcription factor binding sites (TFBSs) by improving the alignment accuracy of TFBS families within orthologous DNA sequences. In addition to the analysis of known regulatory regions, our web tool is useful for the analysis of TFBSs on so far unknown DNA regions identified through ChIP-sequencing. Our pipeline is based on three steps: (i) identification of suitable orthologous regions, (ii) motif-aware alignment of the orthologous sequences and finally (iii) visualization of conserved TFBSs. ConBind exposes a RESTful API interface, which allows to programmatically access (i.e. without using the web user interface) and integrate ConBind in other analysis workflows and tools.