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_004008975.1_ASM400897v1	CP025371	Bordetella pertussis strain H640 chromosome, complete genome	1	469015-469108	1	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|CP025371.1_461043_461439_+,NA	NA|134aa|up_9|CP025371.1_460645_461047_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|132aa|up_8|CP025371.1_461043_461439_+	NA	NA|131aa|up_7|CP025371.1_461435_461828_+	cd03441, R_hydratase_like, (R)-hydratase [(R)-specific enoyl-CoA hydratase]	NA|387aa|up_6|CP025371.1_461838_462999_+	cd01160, LCAD, Long chain acyl-CoA dehydrogenase	NA|324aa|up_5|CP025371.1_463036_464008_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|383aa|up_4|CP025371.1_464015_465164_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|297aa|up_3|CP025371.1_465160_466051_-	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|CP025371.1_466257_467205_+	cd00408, DHDPS-like, Dihydrodipicolinate synthase family	NA|317aa|up_1|CP025371.1_467303_468254_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|CP025371.1_468385_468784_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|CP025371.1_469194_469665_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|CP025371.1_469753_470098_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|CP025371.1_470197_471598_-	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|CP025371.1_473386_473905_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|CP025371.1_474015_474771_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|CP025371.1_474966_476199_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|CP025371.1_476191_476977_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|CP025371.1_477043_478015_+	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|CP025371.1_478025_479003_-	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|CP025371.1_479128_480301_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCA_004008975.1_ASM400897v1	CP025371	Bordetella pertussis strain H640 chromosome, complete genome	2	1032284-1032378	2	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|CP025371.1_1030270_1030651_+,NA	NA|310aa|up_9|CP025371.1_1017800_1018730_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|609aa|up_8|CP025371.1_1018973_1020800_+	cd01153, ACAD_fadE5, Putative acyl-CoA dehydrogenases similar to fadE5	NA|214aa|up_7|CP025371.1_1020882_1021524_+	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|CP025371.1_1021713_1022748_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|355aa|up_5|CP025371.1_1024584_1025649_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|303aa|up_4|CP025371.1_1026446_1027355_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|425aa|up_3|CP025371.1_1028842_1030117_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|CP025371.1_1030270_1030651_+	NA	NA|291aa|up_1|CP025371.1_1030658_1031531_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|CP025371.1_1031836_1032217_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|242aa|down_0|CP025371.1_1032427_1033153_+	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|CP025371.1_1033248_1034199_-	pfam00665, rve, Integrase core domain	NA|350aa|down_2|CP025371.1_1034303_1035353_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|339aa|down_3|CP025371.1_1035490_1036507_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|191aa|down_4|CP025371.1_1038015_1038588_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|CP025371.1_1038647_1039379_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|306aa|down_6|CP025371.1_1039430_1040348_-	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|CP025371.1_1041155_1044335_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|CP025371.1_1044331_1045714_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|CP025371.1_1045783_1046035_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCA_004008975.1_ASM400897v1	CP025371	Bordetella pertussis strain H640 chromosome, complete genome	3	3451779-3451888	3	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|CP025371.1_3438078_3438447_-,NA	NA|317aa|up_9|CP025371.1_3437141_3438092_-	pfam00665, rve, Integrase core domain	NA|123aa|up_8|CP025371.1_3438078_3438447_-	NA	NA|993aa|up_7|CP025371.1_3438445_3441424_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|CP025371.1_3442350_3443229_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|CP025371.1_3445177_3446128_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|CP025371.1_3446124_3446592_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|CP025371.1_3446634_3447405_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|CP025371.1_3447425_3448226_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|CP025371.1_3448236_3449646_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|CP025371.1_3449740_3450526_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|CP025371.1_3451889_3452282_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|CP025371.1_3452419_3453100_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|333aa|down_2|CP025371.1_3453104_3454103_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|down_3|CP025371.1_3454171_3455122_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|CP025371.1_3456626_3457328_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|CP025371.1_3457327_3458752_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|447aa|down_6|CP025371.1_3459821_3461162_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_7|CP025371.1_3461277_3463041_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_8|CP025371.1_3463152_3464031_+	PRK00030, minC, septum site-determining protein MinC	NA|272aa|down_9|CP025371.1_3464143_3464959_+	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
GCA_004008975.1_ASM400897v1	CP025371	Bordetella pertussis strain H640 chromosome, complete genome	4	3824163-3824247	4	CRISPRCasFinder	no		csa3,cas3,DinG,DEDDh	Orphan	CTGTCCCCGCGGGGACAGGCACC	23	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,DinG,DEDDh	NA,NA	NA|585aa|up_9|CP025371.1_3812120_3813875_-	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]	NA|300aa|up_8|CP025371.1_3813981_3814881_+	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|328aa|up_7|CP025371.1_3814945_3815929_-	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|327aa|up_6|CP025371.1_3816064_3817045_+	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|464aa|up_5|CP025371.1_3817061_3818453_-	PRK00485, fumC, fumarate hydratase; Reviewed	NA|179aa|up_4|CP025371.1_3818604_3819141_+	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|415aa|up_3|CP025371.1_3819212_3820457_+	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|213aa|up_2|CP025371.1_3820599_3821238_-	PRK10847, PRK10847, DedA family protein	NA|630aa|up_1|CP025371.1_3821324_3823214_+	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|314aa|up_0|CP025371.1_3823210_3824152_+	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|350aa|down_0|CP025371.1_3824257_3825307_-	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|234aa|down_1|CP025371.1_3825559_3826261_+	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|233aa|down_2|CP025371.1_3826257_3826956_+	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|452aa|down_3|CP025371.1_3826956_3828312_+	TIGR01942, pcnB, poly(A) polymerase	NA|164aa|down_4|CP025371.1_3828308_3828800_+	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|319aa|down_5|CP025371.1_3828818_3829775_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|701aa|down_6|CP025371.1_3831185_3833288_-	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|348aa|down_7|CP025371.1_3833458_3834502_+	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|248aa|down_8|CP025371.1_3834545_3835289_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|137aa|down_9|CP025371.1_3836310_3836721_-	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase
