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_004008655.1_ASM400865v1	CP025357	Bordetella pertussis strain F578 chromosome, complete genome	1	251640-251724	1	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	GGTGCCTGTCCCCGCGGGGACAG	23	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|137aa|up_9|CP025357.1_239165_239576_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|CP025357.1_240597_241341_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|CP025357.1_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|CP025357.1_242598_244701_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|CP025357.1_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|CP025357.1_247086_247578_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|CP025357.1_247574_248930_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|CP025357.1_248930_249629_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|CP025357.1_249625_250327_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|CP025357.1_250579_251629_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|CP025357.1_251734_252676_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|CP025357.1_252672_254562_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|CP025357.1_254648_255287_+	PRK10847, PRK10847, DedA family protein	NA|415aa|down_3|CP025357.1_255429_256674_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|CP025357.1_256745_257282_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|CP025357.1_257433_258825_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|CP025357.1_258841_259822_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|CP025357.1_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|CP025357.1_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|CP025357.1_262011_263766_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCA_004008655.1_ASM400865v1	CP025357	Bordetella pertussis strain F578 chromosome, complete genome	2	625048-625157	2	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	GGGGACAGATACCGTCTTGGCCGTCAA	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA|123aa|down_8|CP025357.1_638488_638857_+	NA|272aa|up_9|CP025357.1_611976_612792_-	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]	NA|293aa|up_8|CP025357.1_612904_613783_-	PRK00030, minC, septum site-determining protein MinC	NA|588aa|up_7|CP025357.1_613894_615658_-	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|447aa|up_6|CP025357.1_615773_617114_+	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|475aa|up_5|CP025357.1_618183_619608_-	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|234aa|up_4|CP025357.1_619607_620309_-	PRK09468, ompR, osmolarity response regulator; Provisional	NA|317aa|up_3|CP025357.1_621813_622764_+	pfam00665, rve, Integrase core domain	NA|333aa|up_2|CP025357.1_622832_623831_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|227aa|up_1|CP025357.1_623835_624516_-	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|131aa|up_0|CP025357.1_624653_625046_+	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|262aa|down_0|CP025357.1_626409_627195_-	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|470aa|down_1|CP025357.1_627289_628699_-	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|267aa|down_2|CP025357.1_628709_629510_-	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|257aa|down_3|CP025357.1_629530_630301_+	pfam08241, Methyltransf_11, Methyltransferase domain	NA|156aa|down_4|CP025357.1_630343_630811_+	PRK00203, rnhA, ribonuclease H; Reviewed	NA|317aa|down_5|CP025357.1_630807_631758_-	pfam00665, rve, Integrase core domain	NA|293aa|down_6|CP025357.1_633706_634585_-	pfam00487, FA_desaturase, Fatty acid desaturase	NA|993aa|down_7|CP025357.1_635511_638490_-	pfam17936, Big_6, Bacterial Ig domain	NA|123aa|down_8|CP025357.1_638488_638857_+	NA	NA|317aa|down_9|CP025357.1_638843_639794_+	pfam00665, rve, Integrase core domain
GCA_004008655.1_ASM400865v1	CP025357	Bordetella pertussis strain F578 chromosome, complete genome	3	1829523-1829650	3	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|152aa|up_9|CP025357.1_1818431_1818887_+	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|CP025357.1_1818900_1819704_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|CP025357.1_1819700_1820132_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|CP025357.1_1820128_1821286_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|CP025357.1_1821307_1822084_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|239aa|up_4|CP025357.1_1824248_1824965_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|CP025357.1_1824957_1825599_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|CP025357.1_1825633_1826365_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|71aa|up_1|CP025357.1_1826382_1826595_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|up_0|CP025357.1_1827165_1828116_+	pfam00665, rve, Integrase core domain	NA|243aa|down_0|CP025357.1_1829673_1830402_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|CP025357.1_1830452_1831655_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|CP025357.1_1831732_1833769_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|CP025357.1_1834021_1834513_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|CP025357.1_1834728_1835241_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|CP025357.1_1835258_1836470_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|CP025357.1_1836507_1836918_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|CP025357.1_1836919_1837243_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|CP025357.1_1837245_1837758_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|CP025357.1_1837887_1839750_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCA_004008655.1_ASM400865v1	CP025357	Bordetella pertussis strain F578 chromosome, complete genome	4	2899272-2899388	4	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|CP025357.1_2899054_2899231_-,NA|101aa|down_9|CP025357.1_2912071_2912374_+	NA|899aa|up_9|CP025357.1_2881612_2884309_+	PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1; Provisional	NA|761aa|up_8|CP025357.1_2884463_2886746_+	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|211aa|up_7|CP025357.1_2886908_2887541_+	pfam16970, FimA, Type-1 fimbrial protein, A	NA|317aa|up_6|CP025357.1_2887639_2888590_+	pfam00665, rve, Integrase core domain	NA|185aa|up_5|CP025357.1_2888636_2889191_-	PRK01885, greB, transcription elongation factor GreB; Reviewed	NA|282aa|up_4|CP025357.1_2889258_2890104_-	COG0613, COG0613, Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]	NA|323aa|up_3|CP025357.1_2890173_2891142_-	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|599aa|up_2|CP025357.1_2891141_2892938_-	COG2333, ComEC, Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]	NA|1309aa|up_1|CP025357.1_2894837_2898764_-	pfam11924, IAT_beta, Inverse autotransporter, beta-domain	NA|59aa|up_0|CP025357.1_2899054_2899231_-	NA	NA|1077aa|down_0|CP025357.1_2899499_2902730_-	pfam03797, Autotransporter, Autotransporter beta-domain	NA|276aa|down_1|CP025357.1_2903011_2903839_-	cd01310, TatD_DNAse, TatD like proteins;  E	NA|232aa|down_2|CP025357.1_2903872_2904568_-	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|CP025357.1_2904560_2905841_-	TIGR02212, releasing_system_transmembrane_protein_lolC	NA|326aa|down_4|CP025357.1_2905850_2906828_+	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown]	NA|567aa|down_5|CP025357.1_2906809_2908510_+	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ	NA|368aa|down_6|CP025357.1_2908612_2909717_+	PRK00578, prfB, peptide chain release factor 2; Validated	NA|252aa|down_7|CP025357.1_2909746_2910502_+	PRK07023, PRK07023, SDR family oxidoreductase	NA|507aa|down_8|CP025357.1_2910508_2912029_+	PRK00484, lysS, lysyl-tRNA synthetase; Reviewed	NA|101aa|down_9|CP025357.1_2912071_2912374_+	NA
GCA_004008655.1_ASM400865v1	CP025357	Bordetella pertussis strain F578 chromosome, complete genome	5	3612994-3613087	5	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	GTGCCTGTCCCGGCGGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA|132aa|down_8|CP025357.1_3620662_3621058_-	NA|391aa|up_9|CP025357.1_3601800_3602973_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|326aa|up_8|CP025357.1_3603098_3604076_+	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|CP025357.1_3604086_3605058_-	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|CP025357.1_3605124_3605910_-	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|411aa|up_5|CP025357.1_3605902_3607135_-	pfam02515, CoA_transf_3, CoA-transferase family III	NA|252aa|up_4|CP025357.1_3607330_3608086_-	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|173aa|up_3|CP025357.1_3608196_3608715_+	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|467aa|up_2|CP025357.1_3610503_3611904_+	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|CP025357.1_3612003_3612348_+	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|157aa|up_0|CP025357.1_3612436_3612907_+	pfam00582, Usp, Universal stress protein family	NA|133aa|down_0|CP025357.1_3613317_3613716_+	PRK00007, PRK00007, elongation factor G; Reviewed	NA|317aa|down_1|CP025357.1_3613847_3614798_-	pfam00665, rve, Integrase core domain	NA|316aa|down_2|CP025357.1_3614896_3615844_-	cd00408, DHDPS-like, Dihydrodipicolinate synthase family	NA|297aa|down_3|CP025357.1_3616050_3616941_+	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|CP025357.1_3616937_3618086_-	pfam02515, CoA_transf_3, CoA-transferase family III	NA|324aa|down_5|CP025357.1_3618093_3619065_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|387aa|down_6|CP025357.1_3619102_3620263_-	cd01160, LCAD, Long chain acyl-CoA dehydrogenase	NA|131aa|down_7|CP025357.1_3620273_3620666_-	cd03441, R_hydratase_like, (R)-hydratase [(R)-specific enoyl-CoA hydratase]	NA|132aa|down_8|CP025357.1_3620662_3621058_-	NA	NA|134aa|down_9|CP025357.1_3621054_3621456_-	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
