assembly_id	genome_id	genome_def	crispr_array_locus_merge	crispr_array_location_merge	crispr_locus_id	crispr_pred_method	array_in_prot	prot_within_array_20000	prot_in_genome	crispr_type_by_cas_prot	consensus_repeat	repeat_length	self-targeting_spacer_number	self-targeting_target_number	spacer_location	protospacer_location	repeat_type	spacer_locus_num	spacer_num	correct_crispr_type	genome_cas_prots	unknown_protein_around_crispr	L10	L10_domain	L9	L9_domain	L8	L8_domain	L7	L7_domain	L6	L6_domain	L5	L5_domain	L4	L4_domain	L3	L3_domain	L2	L2_domain	L1	L1_domain	R1	R1_domain	R2	R2_domain	R3	R3_domain	R4	R4_domain	R5	R5_domain	R6	R6_domain	R7	R7_domain	R8	R8_domain	R9	R9_domain	R10	R10_domain
GCA_004009355.1_ASM400935v1	CP025364	Bordetella pertussis strain H709 chromosome, complete genome	1	251640-251724	1	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	GGTGCCTGTCCCCGCGGGGACAG	23	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA,NA	NA|137aa|up_9|CP025364.1_239165_239576_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|CP025364.1_240597_241341_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|CP025364.1_241384_242428_-	cd13602, PBP2_TRAP_BpDctp6_7, Substrate-binding domain of a pyroglutamic acid binding DctP subfamily of the tripartite ATP-independent periplasmic transporters; contains the type 2 periplasmic binding protein fold	NA|701aa|up_6|CP025364.1_242598_244701_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|CP025364.1_246111_247068_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_4|CP025364.1_247086_247578_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|CP025364.1_247574_248930_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|CP025364.1_248930_249629_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|CP025364.1_249625_250327_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|CP025364.1_250579_251629_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|CP025364.1_251734_252676_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|CP025364.1_252672_254562_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|CP025364.1_254648_255287_+	PRK10847, PRK10847, DedA family protein	NA|415aa|down_3|CP025364.1_255429_256674_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|CP025364.1_256745_257282_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|CP025364.1_257433_258825_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|CP025364.1_258841_259822_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|CP025364.1_259957_260941_+	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|300aa|down_8|CP025364.1_261005_261905_-	cd08415, PBP2_LysR_opines_like, The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold	NA|585aa|down_9|CP025364.1_262011_263766_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCA_004009355.1_ASM400935v1	CP025364	Bordetella pertussis strain H709 chromosome, complete genome	2	481502-481595	2	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	GTGCCTGTCCCCGCCGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA|132aa|up_8|CP025364.1_473530_473926_+,NA	NA|134aa|up_9|CP025364.1_473132_473534_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|132aa|up_8|CP025364.1_473530_473926_+	NA	NA|131aa|up_7|CP025364.1_473922_474315_+	cd03441, R_hydratase_like, (R)-hydratase [(R)-specific enoyl-CoA hydratase]	NA|387aa|up_6|CP025364.1_474325_475486_+	cd01160, LCAD, Long chain acyl-CoA dehydrogenase	NA|324aa|up_5|CP025364.1_475523_476495_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|383aa|up_4|CP025364.1_476502_477651_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|297aa|up_3|CP025364.1_477647_478538_-	cd08415, PBP2_LysR_opines_like, The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold	NA|316aa|up_2|CP025364.1_478744_479692_+	cd00408, DHDPS-like, Dihydrodipicolinate synthase family	NA|317aa|up_1|CP025364.1_479790_480741_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|CP025364.1_480872_481271_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|CP025364.1_481681_482152_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|CP025364.1_482240_482585_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|CP025364.1_482684_484085_-	COG1167, ARO8, Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]	NA|173aa|down_3|CP025364.1_485873_486392_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|CP025364.1_486502_487258_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|CP025364.1_487453_488686_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|CP025364.1_488678_489464_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|CP025364.1_489530_490502_+	cd07012, PBP2_Bug_TTT, Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold	NA|326aa|down_8|CP025364.1_490512_491490_-	cd08414, PBP2_LTTR_aromatics_like, The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold	NA|391aa|down_9|CP025364.1_491615_492788_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCA_004009355.1_ASM400935v1	CP025364	Bordetella pertussis strain H709 chromosome, complete genome	3	1045820-1045914	3	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	TAAAAGGGCACCCGCAAGGGTGTCCTTTT	29	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA|127aa|up_2|CP025364.1_1043806_1044187_+,NA	NA|310aa|up_9|CP025364.1_1031336_1032266_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|CP025364.1_1032509_1034336_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|CP025364.1_1034418_1035060_+	cd03016, PRX_1cys, Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine	NA|345aa|up_6|CP025364.1_1035249_1036284_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|CP025364.1_1038120_1039185_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|CP025364.1_1039982_1040891_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|CP025364.1_1042378_1043653_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|CP025364.1_1043806_1044187_+	NA	NA|291aa|up_1|CP025364.1_1044194_1045067_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|CP025364.1_1045372_1045753_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|CP025364.1_1045963_1046689_+	cd03426, CoAse, Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes	NA|317aa|down_1|CP025364.1_1046784_1047735_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|CP025364.1_1047839_1048889_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|CP025364.1_1049026_1050043_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|CP025364.1_1051551_1052124_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|CP025364.1_1052183_1052915_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|CP025364.1_1052966_1053884_-	cd08422, PBP2_CrgA_like, The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain	NA|1060aa|down_7|CP025364.1_1054691_1057871_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|CP025364.1_1057867_1059250_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|CP025364.1_1059319_1059571_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCA_004009355.1_ASM400935v1	CP025364	Bordetella pertussis strain H709 chromosome, complete genome	4	1941197-1941324	4	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA,NA	NA|152aa|up_9|CP025364.1_1930105_1930561_+	cd03450, NodN, NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit	NA|268aa|up_8|CP025364.1_1930574_1931378_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|CP025364.1_1931374_1931806_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|CP025364.1_1931802_1932960_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|CP025364.1_1932981_1933758_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|239aa|up_4|CP025364.1_1935922_1936639_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|CP025364.1_1936631_1937273_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|CP025364.1_1937307_1938039_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|71aa|up_1|CP025364.1_1938056_1938269_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|up_0|CP025364.1_1938839_1939790_+	pfam00665, rve, Integrase core domain	NA|243aa|down_0|CP025364.1_1941347_1942076_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|CP025364.1_1942126_1943329_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|CP025364.1_1943406_1945443_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|CP025364.1_1945695_1946187_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|CP025364.1_1946402_1946915_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|CP025364.1_1946932_1948144_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|CP025364.1_1948181_1948592_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|CP025364.1_1948593_1948917_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|CP025364.1_1948919_1949432_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|CP025364.1_1949561_1951424_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCA_004009355.1_ASM400935v1	CP025364	Bordetella pertussis strain H709 chromosome, complete genome	5	3476707-3476816	5	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA|123aa|up_8|CP025364.1_3463006_3463375_-,NA	NA|317aa|up_9|CP025364.1_3462069_3463020_-	pfam00665, rve, Integrase core domain	NA|123aa|up_8|CP025364.1_3463006_3463375_-	NA	NA|993aa|up_7|CP025364.1_3463373_3466352_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|CP025364.1_3467278_3468157_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|CP025364.1_3470105_3471056_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|CP025364.1_3471052_3471520_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|CP025364.1_3471562_3472333_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|CP025364.1_3472353_3473154_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|CP025364.1_3473164_3474574_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|CP025364.1_3474668_3475454_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|CP025364.1_3476817_3477210_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|CP025364.1_3477347_3478028_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|333aa|down_2|CP025364.1_3478032_3479031_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|down_3|CP025364.1_3479099_3480050_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|CP025364.1_3481554_3482256_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|CP025364.1_3482255_3483680_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|CP025364.1_3484749_3486090_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|CP025364.1_3486205_3487969_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|CP025364.1_3488080_3488959_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|CP025364.1_3489071_3489887_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
