The example below shows how the Pro-Coffee mode can be used to align the 2000 base pairs (bp) upstream region of the human gene C18orf19 to its orthologous regions in mouse, dog, cow, and chicken (as defined in Ensembl):

The procoffee mode produces by default three different types of output files:

• c18orf19.dnd: guide tree used to assemble the progressive alignment.
• c18orf19.aln: final alignment given in ClustalW format.
• c18orf19.html: final alignment colored in function of the CORE index from red (very consistent) to blue (poorly consistent).
  

Figure 9 shows side by side the Pro-Coffee MSA and its T-Coffee counterpart. Highlighted are factor binding regions determined by ChIP-seq experiments, in green, predicted TFBS falling in these regions, and in red, predicted TFBS outside of the regions. Interestingly, Pro-Coffee manages to match the predicted CEBPA binding sites that fall within the ChIP-seq regions corresponding to this transcription factor. By contrast the default version of T-Coffee fails to align these sites.