In and other fungi, the protein frequency (FRQ) is an integral part and a negative element in the fungal circadian oscillator. In and many other higher organisms, the protein period (PER) is an integral part and a negative element of their circadian oscillator. Employing bioinformatic techniques, such as BLAST, CLUSTAL, and MEME (Multiple Em for Motif Elicitation), 11 regions (sequences) of potential similarity were found between the fungal FRQ and the PER. Many of these FRQ regions are conserved in many fungal FRQ(s). Many of these PER regions are conserved in many insects. In addition, these regions are also of biological significance since mutations in these regions lead to changes in the circadian clock of and . Many of these regions of similarity between FRQ and PER are also conserved between the PER and the mouse PER (mPER2). This suggests conserved and important regions for all 3 proteins and a common ancestor, possibly in those amoeba, such as , that sits at the base of the phylogenetic tree where fungi and animals diverged. Two additional examples of a possible common ancestor between and were found. One, the white collar (WC-1) protein of and the PER, shows significant similarity in its Per/Arnt/Sim (PAS) motifs to the PAS motif of an ARNT-like protein found in the amoeba, . Two, both of the positive elements in each system (i.e., WC-1 in and cycle [CYC] in ), show significant similarity to this ARNT protein. A discussion of these findings centers on the long-time debate about the origins of the many different clock systems (i.e., independent evolution or common ancestor as well as to the question of how new genes are formed).