Motivation: The SARS-Cov-2 pandemic has gripped the entire world and a race to find either a cure or a vaccine for this pandemic is on. The public databases have a deluge of information in terms of genomic sequences and protein structures making it possible to study the minute details in terms of conserved motifs and super-motifs in its proteins. In this study we have identified the hidden features of the Spike protein and the Main protease (Mpro) of SARS-Cov2. These domains have been identified using the standard bioinformatics tools and the pfam database. We found four domains reported in the pfam database are present in the spike protein and the Mpro of SARS-Cov2 but have not been reported earlier. These domains are specific to human strains of SARS-Cov2 and are not present in SARS-Cov or the coronaviruses of other animals. Using RIN we also identified the motifs and super-motifs in these two proteins that are important in understanding species wise changes as well as evolution driven variation in amino acids. Our results highlight several interesting features of the spike protein and Mpro of SARS-Cov2 that can be exploited for the development of various drug and vaccine therapies.