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_004009635.1_ASM400963v1	CP025528	Bordetella pertussis strain D869 chromosome, complete genome	1	250582-250666	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|CP025528.1_238107_238518_+	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase	NA|248aa|up_8|CP025528.1_239539_240283_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_7|CP025528.1_240326_241370_-	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|CP025528.1_241540_243643_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|319aa|up_5|CP025528.1_245053_246010_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_4|CP025528.1_246028_246520_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|CP025528.1_246516_247872_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|CP025528.1_247872_248571_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|CP025528.1_248567_249269_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|CP025528.1_249521_250571_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|CP025528.1_250676_251618_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|CP025528.1_251614_253504_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|CP025528.1_253590_254229_+	PRK10847, PRK10847, DedA family protein	NA|415aa|down_3|CP025528.1_254371_255616_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|CP025528.1_255687_256224_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|CP025528.1_256375_257767_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|327aa|down_6|CP025528.1_257783_258764_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|CP025528.1_258899_259883_+	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|300aa|down_8|CP025528.1_259947_260847_-	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|CP025528.1_260953_262708_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCA_004009635.1_ASM400963v1	CP025528	Bordetella pertussis strain D869 chromosome, complete genome	2	622939-623048	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|CP025528.1_636378_636747_+	NA|272aa|up_9|CP025528.1_609867_610683_-	COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]	NA|293aa|up_8|CP025528.1_610795_611674_-	PRK00030, minC, septum site-determining protein MinC	NA|588aa|up_7|CP025528.1_611785_613549_-	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|447aa|up_6|CP025528.1_613664_615005_+	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|475aa|up_5|CP025528.1_616074_617499_-	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|234aa|up_4|CP025528.1_617498_618200_-	PRK09468, ompR, osmolarity response regulator; Provisional	NA|317aa|up_3|CP025528.1_619704_620655_+	pfam00665, rve, Integrase core domain	NA|333aa|up_2|CP025528.1_620723_621722_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|227aa|up_1|CP025528.1_621726_622407_-	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|131aa|up_0|CP025528.1_622544_622937_+	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|262aa|down_0|CP025528.1_624300_625086_-	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|470aa|down_1|CP025528.1_625180_626590_-	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|267aa|down_2|CP025528.1_626600_627401_-	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|257aa|down_3|CP025528.1_627421_628192_+	pfam08241, Methyltransf_11, Methyltransferase domain	NA|156aa|down_4|CP025528.1_628234_628702_+	PRK00203, rnhA, ribonuclease H; Reviewed	NA|317aa|down_5|CP025528.1_628698_629649_-	pfam00665, rve, Integrase core domain	NA|293aa|down_6|CP025528.1_631596_632475_-	pfam00487, FA_desaturase, Fatty acid desaturase	NA|993aa|down_7|CP025528.1_633401_636380_-	pfam17936, Big_6, Bacterial Ig domain	NA|123aa|down_8|CP025528.1_636378_636747_+	NA	NA|317aa|down_9|CP025528.1_636733_637684_+	pfam00665, rve, Integrase core domain
GCA_004009635.1_ASM400963v1	CP025528	Bordetella pertussis strain D869 chromosome, complete genome	3	2122812-2122939	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|CP025528.1_2111720_2112176_+	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|CP025528.1_2112189_2112993_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|CP025528.1_2112989_2113421_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|CP025528.1_2113417_2114575_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|CP025528.1_2114596_2115373_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|239aa|up_4|CP025528.1_2117537_2118254_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|CP025528.1_2118246_2118888_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|CP025528.1_2118922_2119654_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|71aa|up_1|CP025528.1_2119671_2119884_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|up_0|CP025528.1_2120454_2121405_+	pfam00665, rve, Integrase core domain	NA|243aa|down_0|CP025528.1_2122962_2123691_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|CP025528.1_2123741_2124944_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|CP025528.1_2125021_2127058_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|CP025528.1_2127310_2127802_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|CP025528.1_2128017_2128530_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|CP025528.1_2128547_2129759_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|CP025528.1_2129796_2130207_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|CP025528.1_2130208_2130532_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|CP025528.1_2130534_2131047_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|CP025528.1_2131176_2133039_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCA_004009635.1_ASM400963v1	CP025528	Bordetella pertussis strain D869 chromosome, complete genome	4	2908437-2908553	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|CP025528.1_2908219_2908396_-,NA|101aa|down_9|CP025528.1_2921236_2921539_+	NA|899aa|up_9|CP025528.1_2890775_2893472_+	PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1; Provisional	NA|761aa|up_8|CP025528.1_2893626_2895909_+	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|211aa|up_7|CP025528.1_2896073_2896706_+	pfam16970, FimA, Type-1 fimbrial protein, A	NA|317aa|up_6|CP025528.1_2896804_2897755_+	pfam00665, rve, Integrase core domain	NA|185aa|up_5|CP025528.1_2897801_2898356_-	PRK01885, greB, transcription elongation factor GreB; Reviewed	NA|282aa|up_4|CP025528.1_2898423_2899269_-	COG0613, COG0613, Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]	NA|323aa|up_3|CP025528.1_2899338_2900307_-	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|599aa|up_2|CP025528.1_2900306_2902103_-	COG2333, ComEC, Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]	NA|1309aa|up_1|CP025528.1_2904002_2907929_-	pfam11924, IAT_beta, Inverse autotransporter, beta-domain	NA|59aa|up_0|CP025528.1_2908219_2908396_-	NA	NA|1077aa|down_0|CP025528.1_2908664_2911895_-	pfam03797, Autotransporter, Autotransporter beta-domain	NA|276aa|down_1|CP025528.1_2912176_2913004_-	cd01310, TatD_DNAse, TatD like proteins;  E	NA|232aa|down_2|CP025528.1_2913037_2913733_-	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|CP025528.1_2913725_2915006_-	TIGR02212, releasing_system_transmembrane_protein_lolC	NA|326aa|down_4|CP025528.1_2915015_2915993_+	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown]	NA|567aa|down_5|CP025528.1_2915974_2917675_+	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ	NA|368aa|down_6|CP025528.1_2917777_2918882_+	PRK00578, prfB, peptide chain release factor 2; Validated	NA|252aa|down_7|CP025528.1_2918911_2919667_+	PRK07023, PRK07023, SDR family oxidoreductase	NA|507aa|down_8|CP025528.1_2919673_2921194_+	PRK00484, lysS, lysyl-tRNA synthetase; Reviewed	NA|101aa|down_9|CP025528.1_2921236_2921539_+	NA
GCA_004009635.1_ASM400963v1	CP025528	Bordetella pertussis strain D869 chromosome, complete genome	5	3621082-3621175	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|CP025528.1_3628749_3629145_-	NA|391aa|up_9|CP025528.1_3609888_3611061_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|326aa|up_8|CP025528.1_3611186_3612164_+	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|CP025528.1_3612174_3613146_-	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|CP025528.1_3613212_3613998_-	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|411aa|up_5|CP025528.1_3613990_3615223_-	pfam02515, CoA_transf_3, CoA-transferase family III	NA|252aa|up_4|CP025528.1_3615418_3616174_-	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|173aa|up_3|CP025528.1_3616284_3616803_+	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|467aa|up_2|CP025528.1_3618591_3619992_+	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|CP025528.1_3620091_3620436_+	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|157aa|up_0|CP025528.1_3620524_3620995_+	pfam00582, Usp, Universal stress protein family	NA|133aa|down_0|CP025528.1_3621405_3621804_+	PRK00007, PRK00007, elongation factor G; Reviewed	NA|317aa|down_1|CP025528.1_3621935_3622886_-	pfam00665, rve, Integrase core domain	NA|316aa|down_2|CP025528.1_3622983_3623931_-	cd00408, DHDPS-like, Dihydrodipicolinate synthase family	NA|297aa|down_3|CP025528.1_3624137_3625028_+	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|CP025528.1_3625024_3626173_-	pfam02515, CoA_transf_3, CoA-transferase family III	NA|324aa|down_5|CP025528.1_3626180_3627152_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|387aa|down_6|CP025528.1_3627189_3628350_-	cd01160, LCAD, Long chain acyl-CoA dehydrogenase	NA|131aa|down_7|CP025528.1_3628360_3628753_-	cd03441, R_hydratase_like, (R)-hydratase [(R)-specific enoyl-CoA hydratase]	NA|132aa|down_8|CP025528.1_3628749_3629145_-	NA	NA|134aa|down_9|CP025528.1_3629141_3629543_-	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
