Table 3.

Homology analysis of Shigella spacers (partial results)

Location	Query	Gi	Species	Genes	Identities (%)	Alignment length (bp)	Seed
Chromosome	SH_CRb_sp1	344915202	Shigella flexneri 2a str. 301	folK	100	15	N
	SH_CRb_sp2	74310614	Shigella sonnei Ss046	ybbX	100	14	Y
	SH_CRd_sp1	74310614	Shigella sonnei Ss046	glgP	94.44	18	Y
	SH_CRd_sp9	82775382	Shigella dysenteriae Sd197	pyrG	100	14	N
	SH_CRe_sp1	74310614	Shigella sonnei Ss046	yfcU	100	14	Y/N
	SH_CRe_sp3	82542618	Shigella boydii Sb227	yfeA	100	14	N
	SH_CRe_sp4	82775382	Shigella dysenteriae Sd197	nrdI	100	14	Y
	SH_CRe_sp6	82775382	Shigella dysenteriae Sd197	metR	100	14	N
	SH_CRc_sp1	110804074	Shigella flexneri 5 str. 8401	nrdB	95.24	42	—
	SH_CRf_sp1	384541581	Shigella flexneri 2002017	zntA	94.44	18	—
Plasmid	SH_CRd_sp5	459466044	Shigella sonnei plasmid pDPT3	mobA	94.74	19	N
	SH_CRd_sp5	204309817	Escherichia coli plasmid pO26-S4	mobA	94.74	19	N
	SH_CRd_sp5	190410160	Escherichia coli plasmid pIGMS5	mobA	94.74	19	N
Phage	SH_CRb_sp3	20065797	Stx2 converting phage I	non_coding_region	100	13	Y/N
	SH_CRe_sp5	20065797	Stx2 converting phage I	non_coding_region	100	13	Y/N
	SH_CRe_sp8	116221992	Stx2-converting phage 86	Stx2-86_gp30	100	13	N
	SH_CRd_sp11	20065797	Stx2 converting phage I	non_coding_region	100	13	N
	SH_CRd_sp10	45686283	Enterobacteria phage T1	T1p48	100	14	N
	SH_CRe_sp11	17570786	Enterobacteria phage T3	gene 1	100	14	Y/N
	SH_CRe_sp7	29366675	Enterobacteria phage T4	gene 10	100	13	Y/N
	SH_CRe_sp2	29366675	Enterobacteria phage T4	gene sp	100	13	N

Complete and detailed homology analysis results are listed in Supplementary Table S1.

GI: serial number of species genome; gene: genes potentially targeted by the spacers. Whether the homologous sequence contains the seed sequence is also indicated: Y, located completely within the seed region; Y/N, located across both seed region and non-seed region; N, outside of the seed region.

The seed sequences of the CRa, CRc, and CRf loci have not been reported.