Multiple sequence alignments of the avian FOXE1 and HOX protein sequences, which share similarity. (A) The sequences of the avian FOXE1 proteins, which share similarity to the N-terminal sequence of the HOXA13 proteins. (B) The sequence of the avian FOXE1 showing the similarity to HOXB3 proteins. The positively selected sites are shown in box. NN- represents the sequence which has an undetermined 5'- end. (C) Consensus sequences of the identified motifs, shared between avian FOXE1 and HOX proteins were generated with the program Logo. The data for these logo sequences were generated based on six protein sequences. Gaps in the consensus sequence indicate alignment gaps. The logo sequences were generated with the WebLogo program .