Fig. 2

PAM determination of repeat clusters. A Sequence logos of upstream flank of hits to spacers from type I repeat clusters. Sequence logos of protospacer flanking regions per repeat cluster. Y-axes show the information content per nucleotide position. The label includes the subtype of the repeat cluster and a representative genus in which this repeat cluster is found. The PAM of the I-E and I-F repeat clusters depicted here has been determined previously in model systems containing the same repeat [49, 50]. B The same as A but for downstream flanks of spacers from type II repeat clusters. The PAM of the type II-A (Streptococcus) and type II-C (Listeria) systems has been previously described in model systems that are closely related to the strains studied here [51, 52]. C The same as A but for upstream flanks from type III repeat clusters. D Frequency of PAM-determined repeat clusters with more than 25 hits. Nucleotide positions were considered part of PAM with a bitscore of at least 0.4 and 10 times above the median bitscore of the 23 nucleotides surrounding the hits. PAM size was at least 2 nucleotides. E Frequency of PAM-determined repeat clusters for type III systems that contain Cas1-2 vs type III systems that lack Cas1-2. Additional file 5 contains the PAM for each strain-subtype combination (Additional file 2)