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_002859645.1_ASM285964v1	CP017923	Bordetella pertussis strain J148 chromosome, complete genome	1	664127-664236	1	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	GGGGACAGATACCGTCTTGGCCGTCAA	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA|81aa|down_7|CP017923.1_671414_671657_+	NA|272aa|up_9|CP017923.1_651055_651871_-	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]	NA|293aa|up_8|CP017923.1_651983_652862_-	PRK00030, minC, septum site-determining protein MinC	NA|588aa|up_7|CP017923.1_652973_654737_-	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|447aa|up_6|CP017923.1_654852_656193_+	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|475aa|up_5|CP017923.1_657262_658687_-	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|234aa|up_4|CP017923.1_658686_659388_-	PRK09468, ompR, osmolarity response regulator; Provisional	NA|301aa|up_3|CP017923.1_660940_661843_+	pfam00665, rve, Integrase core domain	NA|324aa|up_2|CP017923.1_661938_662910_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|227aa|up_1|CP017923.1_662914_663595_-	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|131aa|up_0|CP017923.1_663732_664125_+	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|262aa|down_0|CP017923.1_665488_666274_-	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|470aa|down_1|CP017923.1_666368_667778_-	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|267aa|down_2|CP017923.1_667788_668589_-	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|257aa|down_3|CP017923.1_668609_669380_+	pfam08241, Methyltransf_11, Methyltransferase domain	NA|156aa|down_4|CP017923.1_669422_669890_+	PRK00203, rnhA, ribonuclease H; Reviewed	NA|317aa|down_5|CP017923.1_669886_670837_-	pfam00665, rve, Integrase core domain	NA|107aa|down_6|CP017923.1_670935_671256_-	PRK02106, PRK02106, choline dehydrogenase; Validated	NA|81aa|down_7|CP017923.1_671414_671657_+	NA	NA|317aa|down_8|CP017923.1_671919_672870_+	pfam00665, rve, Integrase core domain	NA|213aa|down_9|CP017923.1_672849_673488_-	PRK06816, PRK06816, StlD/DarB family beta-ketosynthase
GCA_002859645.1_ASM285964v1	CP017923	Bordetella pertussis strain J148 chromosome, complete genome	2	1874160-1874287	2	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|120aa|up_1|CP017923.1_1872749_1873109_-,NA	NA|144aa|up_9|CP017923.1_1864337_1864769_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_8|CP017923.1_1864765_1865923_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_7|CP017923.1_1865944_1866721_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|223aa|up_6|CP017923.1_1868933_1869602_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_5|CP017923.1_1869594_1870236_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_4|CP017923.1_1870270_1871002_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|71aa|up_3|CP017923.1_1871019_1871232_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|301aa|up_2|CP017923.1_1871850_1872753_+	pfam00665, rve, Integrase core domain	NA|120aa|up_1|CP017923.1_1872749_1873109_-	NA	NA|310aa|up_0|CP017923.1_1873154_1874084_+	TIGR01414, Contains:_AIDA-I_translocator, outer membrane autotransporter barrel domain	NA|217aa|down_0|CP017923.1_1874310_1874961_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|CP017923.1_1875089_1876292_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|CP017923.1_1876369_1878406_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|CP017923.1_1878658_1879150_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|CP017923.1_1879365_1879878_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|CP017923.1_1879895_1881107_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|CP017923.1_1881144_1881555_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|CP017923.1_1881556_1881880_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|CP017923.1_1881882_1882395_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|CP017923.1_1882524_1884387_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCA_002859645.1_ASM285964v1	CP017923	Bordetella pertussis strain J148 chromosome, complete genome	3	2941805-2941921	3	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TTTTTTGCCTTGGGGCGGCCCGGCGGCAAAAAAA	34	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|59aa|up_0|CP017923.1_2941587_2941764_-,NA|101aa|down_9|CP017923.1_2954604_2954907_+	NA|163aa|up_9|CP017923.1_2923530_2924019_-	COG1522, Lrp, Transcriptional regulators [Transcription]	NA|899aa|up_8|CP017923.1_2924144_2926841_+	PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1; Provisional	NA|761aa|up_7|CP017923.1_2926995_2929278_+	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|208aa|up_6|CP017923.1_2929450_2930074_+	pfam16970, FimA, Type-1 fimbrial protein, A	NA|301aa|up_5|CP017923.1_2930220_2931123_+	pfam00665, rve, Integrase core domain	NA|185aa|up_4|CP017923.1_2931169_2931724_-	PRK01885, greB, transcription elongation factor GreB; Reviewed	NA|282aa|up_3|CP017923.1_2931791_2932637_-	COG0613, COG0613, Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]	NA|323aa|up_2|CP017923.1_2932706_2933675_-	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|1298aa|up_1|CP017923.1_2937370_2941264_-	pfam11924, IAT_beta, Inverse autotransporter, beta-domain	NA|59aa|up_0|CP017923.1_2941587_2941764_-	NA	NA|1077aa|down_0|CP017923.1_2942032_2945263_-	pfam03797, Autotransporter, Autotransporter beta-domain	NA|276aa|down_1|CP017923.1_2945544_2946372_-	cd01310, TatD_DNAse, TatD like proteins;  E	NA|232aa|down_2|CP017923.1_2946405_2947101_-	cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein	NA|411aa|down_3|CP017923.1_2947093_2948326_-	TIGR02212, releasing_system_transmembrane_protein_lolC	NA|314aa|down_4|CP017923.1_2948419_2949361_+	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown]	NA|567aa|down_5|CP017923.1_2949342_2951043_+	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ	NA|311aa|down_6|CP017923.1_2951317_2952250_+	PRK00578, prfB, peptide chain release factor 2; Validated	NA|252aa|down_7|CP017923.1_2952279_2953035_+	PRK07023, PRK07023, SDR family oxidoreductase	NA|507aa|down_8|CP017923.1_2953041_2954562_+	PRK00484, lysS, lysyl-tRNA synthetase; Reviewed	NA|101aa|down_9|CP017923.1_2954604_2954907_+	NA
GCA_002859645.1_ASM285964v1	CP017923	Bordetella pertussis strain J148 chromosome, complete genome	4	3657633-3657726	4	CRISPRCasFinder	no	DEDDh	DEDDh,csa3,cas3,DinG	Unclear	GTGCCTGTCCCGGCGGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|391aa|up_9|CP017923.1_3646439_3647612_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|326aa|up_8|CP017923.1_3647737_3648715_+	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|324aa|up_7|CP017923.1_3648725_3649697_-	cd07012, PBP2_Bug_TTT, Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold	NA|262aa|up_6|CP017923.1_3649763_3650549_-	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|411aa|up_5|CP017923.1_3650541_3651774_-	pfam02515, CoA_transf_3, CoA-transferase family III	NA|252aa|up_4|CP017923.1_3651969_3652725_-	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|173aa|up_3|CP017923.1_3652835_3653354_+	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|467aa|up_2|CP017923.1_3655142_3656543_+	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|115aa|up_1|CP017923.1_3656642_3656987_+	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|157aa|up_0|CP017923.1_3657075_3657546_+	pfam00582, Usp, Universal stress protein family	NA|133aa|down_0|CP017923.1_3657956_3658355_+	PRK00007, PRK00007, elongation factor G; Reviewed	NA|301aa|down_1|CP017923.1_3658486_3659389_-	pfam00665, rve, Integrase core domain	DEDDh|245aa|down_2|CP017923.1_3661881_3662616_+	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|60aa|down_3|CP017923.1_3663025_3663205_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|438aa|down_4|CP017923.1_3663395_3664709_+	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|504aa|down_5|CP017923.1_3664724_3666236_-	cd13520, PBP2_TAXI_TRAP, Substrate binding domain of TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold	NA|402aa|down_6|CP017923.1_3666232_3667438_-	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|326aa|down_7|CP017923.1_3667633_3668611_-	pfam00665, rve, Integrase core domain	NA|165aa|down_8|CP017923.1_3668703_3669198_-	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|353aa|down_9|CP017923.1_3669327_3670386_+	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1
GCA_002859645.1_ASM285964v1	CP017923	Bordetella pertussis strain J148 chromosome, complete genome	5	3839085-3839169	5	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	CTGTCCCCGCGGGGACAGGCACC	23	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|585aa|up_9|CP017923.1_3827042_3828797_-	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]	NA|300aa|up_8|CP017923.1_3828903_3829803_+	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|CP017923.1_3829867_3830851_-	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|327aa|up_6|CP017923.1_3830986_3831967_+	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|464aa|up_5|CP017923.1_3831983_3833375_-	PRK00485, fumC, fumarate hydratase; Reviewed	NA|179aa|up_4|CP017923.1_3833526_3834063_+	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|462aa|up_3|CP017923.1_3833993_3835379_+	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|207aa|up_2|CP017923.1_3835521_3836142_-	PRK10847, PRK10847, DedA family protein	NA|630aa|up_1|CP017923.1_3836246_3838136_+	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|314aa|up_0|CP017923.1_3838132_3839074_+	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|350aa|down_0|CP017923.1_3839179_3840229_-	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|234aa|down_1|CP017923.1_3840481_3841183_+	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|233aa|down_2|CP017923.1_3841179_3841878_+	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|452aa|down_3|CP017923.1_3841878_3843234_+	TIGR01942, pcnB, poly(A) polymerase	NA|164aa|down_4|CP017923.1_3843230_3843722_+	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|319aa|down_5|CP017923.1_3843740_3844697_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|420aa|down_6|CP017923.1_3846107_3847367_-	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|348aa|down_7|CP017923.1_3848380_3849424_+	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|CP017923.1_3849467_3850211_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|252aa|down_9|CP017923.1_3850227_3850983_-	PRK15461, PRK15461, sulfolactaldehyde 3-reductase
