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_004008915.1_ASM400891v1	CP025366	Bordetella pertussis strain F954 chromosome, complete genome	1	251601-251685	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|CP025366.1_239126_239537_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|CP025366.1_240558_241302_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|CP025366.1_241345_242389_-	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|CP025366.1_242559_244662_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|CP025366.1_246072_247029_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_4|CP025366.1_247047_247539_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|CP025366.1_247535_248891_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|CP025366.1_248891_249590_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|CP025366.1_249586_250288_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|CP025366.1_250540_251590_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|CP025366.1_251695_252637_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|CP025366.1_252633_254523_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|CP025366.1_254609_255248_+	PRK10847, PRK10847, DedA family protein	NA|415aa|down_3|CP025366.1_255390_256635_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|CP025366.1_256706_257243_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|CP025366.1_257394_258786_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|CP025366.1_258802_259783_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|CP025366.1_259918_260902_+	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|300aa|down_8|CP025366.1_260966_261866_-	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|CP025366.1_261972_263727_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCA_004008915.1_ASM400891v1	CP025366	Bordetella pertussis strain F954 chromosome, complete genome	2	435127-435220	2	CRISPRCasFinder	no	DEDDh	DEDDh,csa3,cas3,DinG	Unclear	GTGCCTGTCCCCGCCGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|353aa|up_9|CP025366.1_422466_423525_-	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1	NA|165aa|up_8|CP025366.1_423654_424149_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_7|CP025366.1_424241_425219_+	pfam00665, rve, Integrase core domain	NA|402aa|up_6|CP025366.1_425414_426620_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|504aa|up_5|CP025366.1_426616_428128_+	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|438aa|up_4|CP025366.1_428143_429457_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_3|CP025366.1_429647_429827_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_2|CP025366.1_430236_430971_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|317aa|up_1|CP025366.1_433415_434366_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|CP025366.1_434497_434896_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|CP025366.1_435306_435777_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|CP025366.1_435865_436210_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|467aa|down_2|CP025366.1_436309_437710_-	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|CP025366.1_439498_440017_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_4|CP025366.1_440127_440883_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_5|CP025366.1_441078_442311_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_6|CP025366.1_442303_443089_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_7|CP025366.1_443155_444127_+	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|CP025366.1_444137_445115_-	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|CP025366.1_445240_446413_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26
GCA_004008915.1_ASM400891v1	CP025366	Bordetella pertussis strain F954 chromosome, complete genome	3	1552835-1552962	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|CP025366.1_1541743_1542199_+	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|CP025366.1_1542212_1543016_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|CP025366.1_1543012_1543444_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|CP025366.1_1543440_1544598_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|CP025366.1_1544619_1545396_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|239aa|up_4|CP025366.1_1547560_1548277_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|CP025366.1_1548269_1548911_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|CP025366.1_1548945_1549677_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|71aa|up_1|CP025366.1_1549694_1549907_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|up_0|CP025366.1_1550477_1551428_+	pfam00665, rve, Integrase core domain	NA|243aa|down_0|CP025366.1_1552985_1553714_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|CP025366.1_1553764_1554967_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|CP025366.1_1555044_1557081_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|CP025366.1_1557333_1557825_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|CP025366.1_1558040_1558553_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|CP025366.1_1558570_1559782_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|CP025366.1_1559819_1560230_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|CP025366.1_1560231_1560555_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|CP025366.1_1560557_1561070_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|CP025366.1_1561199_1563062_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCA_004008915.1_ASM400891v1	CP025366	Bordetella pertussis strain F954 chromosome, complete genome	4	2649493-2649609	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|CP025366.1_2649275_2649452_-,NA	NA|899aa|up_9|CP025366.1_2631828_2634525_+	PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1; Provisional	NA|761aa|up_8|CP025366.1_2634679_2636962_+	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|211aa|up_7|CP025366.1_2637129_2637762_+	pfam16970, FimA, Type-1 fimbrial protein, A	NA|317aa|up_6|CP025366.1_2637860_2638811_+	pfam00665, rve, Integrase core domain	NA|185aa|up_5|CP025366.1_2638857_2639412_-	PRK01885, greB, transcription elongation factor GreB; Reviewed	NA|282aa|up_4|CP025366.1_2639479_2640325_-	COG0613, COG0613, Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]	NA|323aa|up_3|CP025366.1_2640394_2641363_-	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|599aa|up_2|CP025366.1_2641362_2643159_-	COG2333, ComEC, Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]	NA|1309aa|up_1|CP025366.1_2645058_2648985_-	pfam11924, IAT_beta, Inverse autotransporter, beta-domain	NA|59aa|up_0|CP025366.1_2649275_2649452_-	NA	NA|1077aa|down_0|CP025366.1_2649720_2652951_-	pfam03797, Autotransporter, Autotransporter beta-domain	NA|276aa|down_1|CP025366.1_2653232_2654060_-	cd01310, TatD_DNAse, TatD like proteins;  E	NA|232aa|down_2|CP025366.1_2654093_2654789_-	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|CP025366.1_2654781_2656062_-	TIGR02212, releasing_system_transmembrane_protein_lolC	NA|326aa|down_4|CP025366.1_2656071_2657049_+	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown]	NA|567aa|down_5|CP025366.1_2657030_2658731_+	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ	NA|368aa|down_6|CP025366.1_2658833_2659938_+	PRK00578, prfB, peptide chain release factor 2; Validated	NA|252aa|down_7|CP025366.1_2659967_2660723_+	PRK07023, PRK07023, SDR family oxidoreductase	NA|507aa|down_8|CP025366.1_2660729_2662250_+	PRK00484, lysS, lysyl-tRNA synthetase; Reviewed	NA|211aa|down_9|CP025366.1_2662577_2663210_-	pfam17932, TetR_C_24, Tetracyclin repressor-like, C-terminal domain
GCA_004008915.1_ASM400891v1	CP025366	Bordetella pertussis strain F954 chromosome, complete genome	5	3436096-3436205	5	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|123aa|up_8|CP025366.1_3422395_3422764_-,NA	NA|317aa|up_9|CP025366.1_3421458_3422409_-	pfam00665, rve, Integrase core domain	NA|123aa|up_8|CP025366.1_3422395_3422764_-	NA	NA|993aa|up_7|CP025366.1_3422762_3425741_+	pfam17936, Big_6, Bacterial Ig domain	NA|293aa|up_6|CP025366.1_3426667_3427546_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|CP025366.1_3429494_3430445_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|CP025366.1_3430441_3430909_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|CP025366.1_3430951_3431722_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|CP025366.1_3431742_3432543_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|CP025366.1_3432553_3433963_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|CP025366.1_3434057_3434843_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|CP025366.1_3436206_3436599_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|CP025366.1_3436736_3437417_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|333aa|down_2|CP025366.1_3437421_3438420_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|down_3|CP025366.1_3438488_3439439_-	pfam00665, rve, Integrase core domain	NA|234aa|down_4|CP025366.1_3440943_3441645_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_5|CP025366.1_3441644_3443069_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|352aa|down_6|CP025366.1_3443085_3444141_-	pfam02322, Cyt_bd_oxida_II, Cytochrome bd terminal oxidase subunit II	NA|447aa|down_7|CP025366.1_3444137_3445478_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_8|CP025366.1_3445593_3447357_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|293aa|down_9|CP025366.1_3447468_3448347_+	PRK00030, minC, septum site-determining protein MinC
