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_900327865.1_VS401	LS398605	Bordetella pertussis strain VS401 genome assembly, chromosome: I	1	254787-254871	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|238aa|up_9|LS398605.1_243744_244458_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|348aa|up_8|LS398605.1_244531_245575_-	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_7|LS398605.1_245745_247848_+	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|277aa|up_6|LS398605.1_248401_249232_+	pfam03972, MmgE_PrpD, MmgE/PrpD family	NA|319aa|up_5|LS398605.1_249258_250215_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|164aa|up_4|LS398605.1_250233_250725_-	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|452aa|up_3|LS398605.1_250721_252077_-	TIGR01942, pcnB, poly(A) polymerase	NA|233aa|up_2|LS398605.1_252077_252776_-	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|234aa|up_1|LS398605.1_252772_253474_-	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|350aa|up_0|LS398605.1_253726_254776_+	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|314aa|down_0|LS398605.1_254881_255823_-	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|630aa|down_1|LS398605.1_255819_257709_-	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|213aa|down_2|LS398605.1_257795_258434_+	PRK10847, PRK10847, DedA family protein	NA|415aa|down_3|LS398605.1_258576_259821_-	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|179aa|down_4|LS398605.1_259892_260429_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|464aa|down_5|LS398605.1_260580_261972_+	PRK00485, fumC, fumarate hydratase; Reviewed	NA|304aa|down_6|LS398605.1_261988_262900_-	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|328aa|down_7|LS398605.1_263104_264088_+	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|300aa|down_8|LS398605.1_264152_265052_-	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|LS398605.1_265158_266913_+	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]
GCA_900327865.1_VS401	LS398605	Bordetella pertussis strain VS401 genome assembly, chromosome: I	2	438329-438422	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|156aa|up_9|LS398605.1_426883_427351_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|326aa|up_8|LS398605.1_427443_428421_+	pfam00665, rve, Integrase core domain	NA|402aa|up_7|LS398605.1_428616_429822_+	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|502aa|up_6|LS398605.1_429824_431330_+	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_5|LS398605.1_431345_432659_-	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|60aa|up_4|LS398605.1_432849_433029_-	pfam04391, DUF533, Protein of unknown function (DUF533)	DEDDh|245aa|up_3|LS398605.1_433438_434173_-	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|791aa|up_2|LS398605.1_434181_436554_-	COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms]	NA|317aa|up_1|LS398605.1_436617_437568_+	pfam00665, rve, Integrase core domain	NA|133aa|up_0|LS398605.1_437699_438098_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|LS398605.1_438508_438979_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|LS398605.1_439067_439412_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|459aa|down_2|LS398605.1_439511_440888_-	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|604aa|down_3|LS398605.1_440892_442704_+	PRK00007, PRK00007, elongation factor G; Reviewed	NA|173aa|down_4|LS398605.1_442700_443219_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|252aa|down_5|LS398605.1_443329_444085_+	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|411aa|down_6|LS398605.1_444280_445513_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|262aa|down_7|LS398605.1_445505_446291_+	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|324aa|down_8|LS398605.1_446357_447329_+	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_9|LS398605.1_447339_448317_-	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
GCA_900327865.1_VS401	LS398605	Bordetella pertussis strain VS401 genome assembly, chromosome: I	3	1032939-1033033	3	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TAAAAGGGCACCCGCAAGGGTGTCCTTTT	29	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|127aa|up_2|LS398605.1_1030925_1031306_+,NA	NA|345aa|up_9|LS398605.1_1022368_1023403_+	COG1613, Sbp, ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]	NA|224aa|up_8|LS398605.1_1023646_1024318_+	TIGR02139, permease_CysT, sulfate ABC transporter, permease protein CysT	NA|261aa|up_7|LS398605.1_1024432_1025215_+	COG4208, CysW, ABC-type sulfate transport system, permease component [Inorganic ion transport and metabolism]	NA|355aa|up_6|LS398605.1_1025239_1026304_+	cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain of the sulfate transporter	NA|570aa|up_5|LS398605.1_1026300_1028010_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|259aa|up_4|LS398605.1_1028532_1029309_+	COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]	NA|425aa|up_3|LS398605.1_1029497_1030772_+	TIGR04470, hypothetical_protein_ALIPUT_00462, radical SAM mobile pair protein B	NA|127aa|up_2|LS398605.1_1030925_1031306_+	NA	NA|278aa|up_1|LS398605.1_1031313_1032147_-	TIGR03340, phn_DUF6, phosphonate utilization associated putative membrane protein	NA|127aa|up_0|LS398605.1_1032491_1032872_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|222aa|down_0|LS398605.1_1033142_1033808_+	cd03426, CoAse, Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes	NA|350aa|down_1|LS398605.1_1033909_1034959_+	cd19094, AKR_Tas-like, Escherichia coli Tas protein and similar proteins	NA|310aa|down_2|LS398605.1_1035096_1036026_-	pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family	NA|428aa|down_3|LS398605.1_1036265_1037549_-	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|191aa|down_4|LS398605.1_1037621_1038194_-	COG3161, UbiC, 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]	NA|244aa|down_5|LS398605.1_1038253_1038985_+	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|312aa|down_6|LS398605.1_1039036_1039972_-	cd08422, PBP2_CrgA_like, The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain	NA|1060aa|down_7|LS398605.1_1040761_1043941_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|461aa|down_8|LS398605.1_1043937_1045320_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|84aa|down_9|LS398605.1_1045389_1045641_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCA_900327865.1_VS401	LS398605	Bordetella pertussis strain VS401 genome assembly, chromosome: I	4	1900045-1900172	4	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	AAAAAGCCCCCTCGGGGGGCAGCAAGCCCGCATAGCGGGCGCAGCG	46	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA|191aa|up_5|LS398605.1_1893779_1894352_+,NA	NA|144aa|up_9|LS398605.1_1890222_1890654_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_8|LS398605.1_1890650_1891808_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_7|LS398605.1_1891829_1892606_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|393aa|up_6|LS398605.1_1892608_1893787_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|191aa|up_5|LS398605.1_1893779_1894352_+	NA	NA|239aa|up_4|LS398605.1_1894770_1895487_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|LS398605.1_1895479_1896121_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|LS398605.1_1896155_1896887_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|up_1|LS398605.1_1897687_1898638_+	pfam00665, rve, Integrase core domain	NA|359aa|up_0|LS398605.1_1898892_1899969_+	TIGR01414, Contains:_AIDA-I_translocator, outer membrane autotransporter barrel domain	NA|217aa|down_0|LS398605.1_1900195_1900846_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|LS398605.1_1900974_1902177_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|LS398605.1_1902254_1904291_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|LS398605.1_1904543_1905035_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|LS398605.1_1905250_1905763_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|LS398605.1_1905780_1906992_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|LS398605.1_1907029_1907440_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|LS398605.1_1907441_1907765_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|LS398605.1_1907767_1908280_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|LS398605.1_1908409_1910272_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCA_900327865.1_VS401	LS398605	Bordetella pertussis strain VS401 genome assembly, chromosome: I	5	3486733-3486842	5	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG	Orphan	TTGACTGCCAAGACGGTATCTGTCCCC	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG	NA,NA	NA|317aa|up_9|LS398605.1_3472095_3473046_-	pfam00665, rve, Integrase core domain	NA|993aa|up_8|LS398605.1_3473399_3476378_+	pfam17936, Big_6, Bacterial Ig domain	NA|172aa|up_7|LS398605.1_3476544_3477060_+	pfam04116, FA_hydroxylase, Fatty acid hydroxylase superfamily	NA|293aa|up_6|LS398605.1_3477304_3478183_+	pfam00487, FA_desaturase, Fatty acid desaturase	NA|317aa|up_5|LS398605.1_3480131_3481082_+	pfam00665, rve, Integrase core domain	NA|156aa|up_4|LS398605.1_3481078_3481546_-	PRK00203, rnhA, ribonuclease H; Reviewed	NA|257aa|up_3|LS398605.1_3481588_3482359_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|267aa|up_2|LS398605.1_3482379_3483180_+	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|470aa|up_1|LS398605.1_3483190_3484600_+	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|262aa|up_0|LS398605.1_3484694_3485480_+	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|131aa|down_0|LS398605.1_3486843_3487236_-	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|227aa|down_1|LS398605.1_3487373_3488054_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|327aa|down_2|LS398605.1_3488058_3489039_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|down_3|LS398605.1_3489125_3490076_-	pfam00665, rve, Integrase core domain	NA|410aa|down_4|LS398605.1_3490157_3491387_-	COG3188, FimD, P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]	NA|234aa|down_5|LS398605.1_3491580_3492282_+	PRK09468, ompR, osmolarity response regulator; Provisional	NA|475aa|down_6|LS398605.1_3492281_3493706_+	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|352aa|down_7|LS398605.1_3493722_3494778_-	pfam02322, Cyt_bd_oxida_II, Cytochrome bd terminal oxidase subunit II	NA|447aa|down_8|LS398605.1_3494774_3496115_-	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|588aa|down_9|LS398605.1_3496230_3497994_+	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional
