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_004007475.1_ASM400747v1	CP025342	Bordetella pertussis strain F580 chromosome, complete genome	1	250589-250673	1	CRISPRCasFinder	no		DEDDh,cas3,csa3,DinG	Orphan	GGTGCCTGTCCCCGCGGGGACAG	23	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,csa3,DinG	NA,NA	NA|137aa|up_9|CP025342.1_238114_238525_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|CP025342.1_239546_240290_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|CP025342.1_240333_241377_-	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|CP025342.1_241547_243650_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|CP025342.1_245060_246017_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_4|CP025342.1_246035_246527_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|CP025342.1_246523_247879_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|CP025342.1_247879_248578_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|CP025342.1_248574_249276_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|CP025342.1_249528_250578_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|CP025342.1_250683_251625_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|CP025342.1_251621_253511_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|CP025342.1_253597_254236_+	PRK10847, PRK10847, DedA family protein	NA|415aa|down_3|CP025342.1_254378_255623_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|CP025342.1_255694_256231_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|CP025342.1_256382_257774_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|CP025342.1_257790_258771_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|CP025342.1_258906_259890_+	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|300aa|down_8|CP025342.1_259954_260854_-	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|CP025342.1_260960_262715_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCA_004007475.1_ASM400747v1	CP025342	Bordetella pertussis strain F580 chromosome, complete genome	2	623997-624106	2	CRISPRCasFinder	no		DEDDh,cas3,csa3,DinG	Orphan	GGGGACAGATACCGTCTTGGCCGTCAA	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,csa3,DinG	NA,NA|123aa|down_8|CP025342.1_637437_637806_+	NA|272aa|up_9|CP025342.1_610925_611741_-	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]	NA|293aa|up_8|CP025342.1_611853_612732_-	PRK00030, minC, septum site-determining protein MinC	NA|588aa|up_7|CP025342.1_612843_614607_-	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|447aa|up_6|CP025342.1_614722_616063_+	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|475aa|up_5|CP025342.1_617132_618557_-	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|234aa|up_4|CP025342.1_618556_619258_-	PRK09468, ompR, osmolarity response regulator; Provisional	NA|317aa|up_3|CP025342.1_620762_621713_+	pfam00665, rve, Integrase core domain	NA|333aa|up_2|CP025342.1_621781_622780_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|227aa|up_1|CP025342.1_622784_623465_-	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|131aa|up_0|CP025342.1_623602_623995_+	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|262aa|down_0|CP025342.1_625358_626144_-	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|470aa|down_1|CP025342.1_626238_627648_-	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|267aa|down_2|CP025342.1_627658_628459_-	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|257aa|down_3|CP025342.1_628479_629250_+	pfam08241, Methyltransf_11, Methyltransferase domain	NA|156aa|down_4|CP025342.1_629292_629760_+	PRK00203, rnhA, ribonuclease H; Reviewed	NA|317aa|down_5|CP025342.1_629756_630707_-	pfam00665, rve, Integrase core domain	NA|293aa|down_6|CP025342.1_632655_633534_-	pfam00487, FA_desaturase, Fatty acid desaturase	NA|993aa|down_7|CP025342.1_634460_637439_-	pfam17936, Big_6, Bacterial Ig domain	NA|123aa|down_8|CP025342.1_637437_637806_+	NA	NA|317aa|down_9|CP025342.1_637792_638743_+	pfam00665, rve, Integrase core domain
GCA_004007475.1_ASM400747v1	CP025342	Bordetella pertussis strain F580 chromosome, complete genome	3	2120822-2120949	3	CRISPRCasFinder	no		DEDDh,cas3,csa3,DinG	Orphan	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,csa3,DinG	NA,NA	NA|152aa|up_9|CP025342.1_2109730_2110186_+	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|CP025342.1_2110199_2111003_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|CP025342.1_2110999_2111431_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|CP025342.1_2111427_2112585_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|CP025342.1_2112606_2113383_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|239aa|up_4|CP025342.1_2115547_2116264_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|CP025342.1_2116256_2116898_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|CP025342.1_2116932_2117664_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|71aa|up_1|CP025342.1_2117681_2117894_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|up_0|CP025342.1_2118464_2119415_+	pfam00665, rve, Integrase core domain	NA|243aa|down_0|CP025342.1_2120972_2121701_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|CP025342.1_2121751_2122954_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|CP025342.1_2123031_2125068_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|CP025342.1_2125320_2125812_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|CP025342.1_2126027_2126540_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|CP025342.1_2126557_2127769_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|CP025342.1_2127806_2128217_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|CP025342.1_2128218_2128542_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|CP025342.1_2128544_2129057_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|CP025342.1_2129186_2131049_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCA_004007475.1_ASM400747v1	CP025342	Bordetella pertussis strain F580 chromosome, complete genome	4	2906569-2906685	4	CRISPRCasFinder	no		DEDDh,cas3,csa3,DinG	Orphan	TTTTTTGCCTTGGGGCGGCCCGGCGGCAAAAAAA	34	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,csa3,DinG	NA|59aa|up_0|CP025342.1_2906351_2906528_-,NA|101aa|down_9|CP025342.1_2919368_2919671_+	NA|899aa|up_9|CP025342.1_2888907_2891604_+	PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1; Provisional	NA|761aa|up_8|CP025342.1_2891758_2894041_+	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|211aa|up_7|CP025342.1_2894205_2894838_+	pfam16970, FimA, Type-1 fimbrial protein, A	NA|317aa|up_6|CP025342.1_2894936_2895887_+	pfam00665, rve, Integrase core domain	NA|185aa|up_5|CP025342.1_2895933_2896488_-	PRK01885, greB, transcription elongation factor GreB; Reviewed	NA|282aa|up_4|CP025342.1_2896555_2897401_-	COG0613, COG0613, Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]	NA|323aa|up_3|CP025342.1_2897470_2898439_-	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|599aa|up_2|CP025342.1_2898438_2900235_-	COG2333, ComEC, Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]	NA|1309aa|up_1|CP025342.1_2902134_2906061_-	pfam11924, IAT_beta, Inverse autotransporter, beta-domain	NA|59aa|up_0|CP025342.1_2906351_2906528_-	NA	NA|1077aa|down_0|CP025342.1_2906796_2910027_-	pfam03797, Autotransporter, Autotransporter beta-domain	NA|276aa|down_1|CP025342.1_2910308_2911136_-	cd01310, TatD_DNAse, TatD like proteins;  E	NA|232aa|down_2|CP025342.1_2911169_2911865_-	cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein	NA|427aa|down_3|CP025342.1_2911857_2913138_-	TIGR02212, releasing_system_transmembrane_protein_lolC	NA|326aa|down_4|CP025342.1_2913147_2914125_+	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown]	NA|567aa|down_5|CP025342.1_2914106_2915807_+	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ	NA|368aa|down_6|CP025342.1_2915909_2917014_+	PRK00578, prfB, peptide chain release factor 2; Validated	NA|252aa|down_7|CP025342.1_2917043_2917799_+	PRK07023, PRK07023, SDR family oxidoreductase	NA|507aa|down_8|CP025342.1_2917805_2919326_+	PRK00484, lysS, lysyl-tRNA synthetase; Reviewed	NA|101aa|down_9|CP025342.1_2919368_2919671_+	NA
GCA_004007475.1_ASM400747v1	CP025342	Bordetella pertussis strain F580 chromosome, complete genome	5	3621340-3621433	5	CRISPRCasFinder	no		DEDDh,cas3,csa3,DinG	Orphan	GTGCCTGTCCCGGCGGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,csa3,DinG	NA,NA|132aa|down_8|CP025342.1_3629008_3629404_-	NA|391aa|up_9|CP025342.1_3610146_3611319_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|326aa|up_8|CP025342.1_3611444_3612422_+	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|CP025342.1_3612432_3613404_-	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|CP025342.1_3613470_3614256_-	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|411aa|up_5|CP025342.1_3614248_3615481_-	pfam02515, CoA_transf_3, CoA-transferase family III	NA|252aa|up_4|CP025342.1_3615676_3616432_-	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|173aa|up_3|CP025342.1_3616542_3617061_+	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|467aa|up_2|CP025342.1_3618849_3620250_+	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|CP025342.1_3620349_3620694_+	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|157aa|up_0|CP025342.1_3620782_3621253_+	pfam00582, Usp, Universal stress protein family	NA|133aa|down_0|CP025342.1_3621663_3622062_+	PRK00007, PRK00007, elongation factor G; Reviewed	NA|317aa|down_1|CP025342.1_3622193_3623144_-	pfam00665, rve, Integrase core domain	NA|316aa|down_2|CP025342.1_3623242_3624190_-	cd00408, DHDPS-like, Dihydrodipicolinate synthase family	NA|297aa|down_3|CP025342.1_3624396_3625287_+	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|383aa|down_4|CP025342.1_3625283_3626432_-	pfam02515, CoA_transf_3, CoA-transferase family III	NA|324aa|down_5|CP025342.1_3626439_3627411_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|387aa|down_6|CP025342.1_3627448_3628609_-	cd01160, LCAD, Long chain acyl-CoA dehydrogenase	NA|131aa|down_7|CP025342.1_3628619_3629012_-	cd03441, R_hydratase_like, (R)-hydratase [(R)-specific enoyl-CoA hydratase]	NA|132aa|down_8|CP025342.1_3629008_3629404_-	NA	NA|134aa|down_9|CP025342.1_3629400_3629802_-	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
