In bacteria and archaea, RNA-Seq deep sequencing methodology allows for the detection of abundance and processing sites of the small RNAs that comprise a CRISPR (clustered regularly interspaced short palindromic repeats) RNome. Comparative analyses of these CRISPR RNome sets highlight conserved patterns that include the gradual decline of CRISPR RNA abundance from the leader-proximal to the leader-distal end. In the present review, we discuss exceptions to these patterns that indicate the extensive impact of individual spacer sequences on CRISPR array transcription and RNA maturation. Spacer sequences can contain promoter and terminator elements and can promote the formation of CRISPR RNA-anti-CRISPR RNA duplexes. In addition, potential RNA duplex formation with host tRNA was observed. These factors can influence the functionality of CRISPR-Cas (CRISPR-associated) systems and need to be considered in the design of synthetic CRISPR arrays.