The clustered regularly interspaced short palindromic repeats (CRISPR) are genetic sequences that conventionally confer immunity to prokaryotes against invading genetic elements. The objective of this work was to perform an analysis of these sequences at the thermodynamic level, determining the minimum free formation energy (MFE) of the direct repeats (DR) and of the complete CRISPR structures that include the spacer sequences (DRSP), and to analyze the possible relationship between the energetics of formation and the associated non-canonical mechanism in 30 prokaryotic reported genomes, to understand their biological significance. We found that all non-conventional CRISPR was thermodynamically more stable and spontaneous in their formation than the rest of the adjacent CRISPRs. The bioinformatics strategy applied allowed us to conclude that all non-conventional CRISPR were those with MFE values of higher magnitude and negative sign, that is, the structures most favored thermodynamically for their formation. These findings could only be established reliably with DRSP, in contrast to results obtained with their respective DR. Moreover, spontaneity was seen as not only associated with a particular function but with aspects related to transcription. We propose to consider the analysis of the DRSP as a strategy to discriminating that CRISPR with determinant roles in microorganisms.are not presented and substantiated in the main text and should not exaggerate the main conclusions.