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
GCF_001686625.1_ASM168662v1	NZ_CP015771	Bordetella pertussis strain UT25Sm1 chromosome, complete genome	1	628084-628211	1	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|NZ_CP015771.1_616992_617448_+	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|266aa|up_8|NZ_CP015771.1_617467_618265_+	COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]	NA|144aa|up_7|NZ_CP015771.1_618261_618693_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|386aa|up_6|NZ_CP015771.1_618689_619847_+	PRK06158, PRK06158, thiolase; Provisional	NA|259aa|up_5|NZ_CP015771.1_619868_620645_+	PRK05653, fabG, 3-oxoacyl-ACP reductase FabG	NA|223aa|up_4|NZ_CP015771.1_622857_623526_+	TIGR02429, 3-oxoadipate_CoA-transferase_subunit_A, 3-oxoacid CoA-transferase, A subunit	NA|214aa|up_3|NZ_CP015771.1_623518_624160_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|244aa|up_2|NZ_CP015771.1_624194_624926_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|71aa|up_1|NZ_CP015771.1_624943_625156_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|317aa|up_0|NZ_CP015771.1_625726_626677_+	pfam00665, rve, Integrase core domain	NA|217aa|down_0|NZ_CP015771.1_628234_628885_-	PRK00215, PRK00215, transcriptional repressor LexA	NA|401aa|down_1|NZ_CP015771.1_629013_630216_-	PRK09257, PRK09257, aromatic amino acid transaminase	NA|679aa|down_2|NZ_CP015771.1_630293_632330_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|164aa|down_3|NZ_CP015771.1_632582_633074_+	cd16343, LMWPTP, Low molecular weight protein tyrosine phosphatase	NA|171aa|down_4|NZ_CP015771.1_633289_633802_+	TIGR02010, Putative_HTH-type_transcriptional_regulator, iron-sulfur cluster assembly transcription factor IscR	NA|404aa|down_5|NZ_CP015771.1_633819_635031_+	PRK14012, PRK14012, IscS subfamily cysteine desulfurase	NA|137aa|down_6|NZ_CP015771.1_635068_635479_+	PRK11325, PRK11325, scaffold protein; Provisional	NA|108aa|down_7|NZ_CP015771.1_635480_635804_+	TIGR02011, Protein_yfhF	NA|171aa|down_8|NZ_CP015771.1_635806_636319_+	PRK03578, hscB, Fe-S protein assembly co-chaperone HscB	NA|621aa|down_9|NZ_CP015771.1_636448_638311_+	PRK05183, hscA, chaperone protein HscA; Provisional
GCF_001686625.1_ASM168662v1	NZ_CP015771	Bordetella pertussis strain UT25Sm1 chromosome, complete genome	2	1724752-1724868	2	CRISPRCasFinder	no		DEDDh,cas3,csa3,DinG	Orphan	TTTTTTGCCTTGGGGCGGCCCGGCGGCAAAAAAA	34	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,csa3,DinG	NA,NA	NA|163aa|up_9|NZ_CP015771.1_1706473_1706962_-	COG1522, Lrp, Transcriptional regulators [Transcription]	NA|899aa|up_8|NZ_CP015771.1_1707087_1709784_+	PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1; Provisional	NA|761aa|up_7|NZ_CP015771.1_1709938_1712221_+	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|211aa|up_6|NZ_CP015771.1_1712388_1713021_+	pfam16970, FimA, Type-1 fimbrial protein, A	NA|317aa|up_5|NZ_CP015771.1_1713119_1714070_+	pfam00665, rve, Integrase core domain	NA|185aa|up_4|NZ_CP015771.1_1714116_1714671_-	PRK01885, greB, transcription elongation factor GreB; Reviewed	NA|282aa|up_3|NZ_CP015771.1_1714738_1715584_-	COG0613, COG0613, Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]	NA|323aa|up_2|NZ_CP015771.1_1715653_1716622_-	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|599aa|up_1|NZ_CP015771.1_1716621_1718418_-	COG2333, ComEC, Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]	NA|1309aa|up_0|NZ_CP015771.1_1720317_1724244_-	pfam11924, IAT_beta, Inverse autotransporter, beta-domain	NA|1077aa|down_0|NZ_CP015771.1_1724979_1728210_-	pfam03797, Autotransporter, Autotransporter beta-domain	NA|276aa|down_1|NZ_CP015771.1_1728491_1729319_-	cd01310, TatD_DNAse, TatD like proteins;  E	NA|232aa|down_2|NZ_CP015771.1_1729352_1730048_-	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|NZ_CP015771.1_1730040_1731321_-	TIGR02212, releasing_system_transmembrane_protein_lolC	NA|314aa|down_4|NZ_CP015771.1_1731366_1732308_+	COG4255, COG4255, Uncharacterized protein conserved in bacteria [Function unknown]	NA|567aa|down_5|NZ_CP015771.1_1732289_1733990_+	PRK11070, PRK11070, single-stranded-DNA-specific exonuclease RecJ	NA|368aa|down_6|NZ_CP015771.1_1734092_1735197_+	PRK00578, prfB, peptide chain release factor 2; Validated	NA|252aa|down_7|NZ_CP015771.1_1735226_1735982_+	PRK07023, PRK07023, SDR family oxidoreductase	NA|507aa|down_8|NZ_CP015771.1_1735988_1737509_+	PRK00484, lysS, lysyl-tRNA synthetase; Reviewed	NA|211aa|down_9|NZ_CP015771.1_1737836_1738469_-	pfam17932, TetR_C_24, Tetracyclin repressor-like, C-terminal domain
GCF_001686625.1_ASM168662v1	NZ_CP015771	Bordetella pertussis strain UT25Sm1 chromosome, complete genome	3	2441590-2441683	3	CRISPRCasFinder	no	DEDDh	DEDDh,cas3,csa3,DinG	Unclear	GTGCCTGTCCCGGCGGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,csa3,DinG	NA,NA	NA|391aa|up_9|NZ_CP015771.1_2430396_2431569_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|326aa|up_8|NZ_CP015771.1_2431694_2432672_+	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|NZ_CP015771.1_2432682_2433654_-	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|NZ_CP015771.1_2433720_2434506_-	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|411aa|up_5|NZ_CP015771.1_2434498_2435731_-	pfam02515, CoA_transf_3, CoA-transferase family III	NA|252aa|up_4|NZ_CP015771.1_2435926_2436682_-	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|173aa|up_3|NZ_CP015771.1_2436792_2437311_+	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|467aa|up_2|NZ_CP015771.1_2439099_2440500_+	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|NZ_CP015771.1_2440599_2440944_+	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|157aa|up_0|NZ_CP015771.1_2441032_2441503_+	pfam00582, Usp, Universal stress protein family	NA|133aa|down_0|NZ_CP015771.1_2441913_2442312_+	PRK00007, PRK00007, elongation factor G; Reviewed	NA|317aa|down_1|NZ_CP015771.1_2442443_2443394_-	pfam00665, rve, Integrase core domain	DEDDh|245aa|down_2|NZ_CP015771.1_2445838_2446573_+	PRK05711, PRK05711, DNA polymerase III subunit epsilon; Provisional	NA|60aa|down_3|NZ_CP015771.1_2446982_2447162_+	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|438aa|down_4|NZ_CP015771.1_2447352_2448666_+	COG2031, AtoE, Short chain fatty acids transporter [Lipid metabolism]	NA|504aa|down_5|NZ_CP015771.1_2448681_2450193_-	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|402aa|down_6|NZ_CP015771.1_2450189_2451395_-	TIGR00210, Sodium/glutamate_symport_carrier_protein, sodium--glutamate symport carrier (gltS)	NA|326aa|down_7|NZ_CP015771.1_2451590_2452568_-	pfam00665, rve, Integrase core domain	NA|165aa|down_8|NZ_CP015771.1_2452660_2453155_-	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|353aa|down_9|NZ_CP015771.1_2453284_2454343_+	cd04187, DPM1_like_bac, Bacterial DPM1_like enzymes are related to eukaryotic DPM1
GCF_001686625.1_ASM168662v1	NZ_CP015771	Bordetella pertussis strain UT25Sm1 chromosome, complete genome	4	2625140-2625224	4	CRISPRCasFinder	no		DEDDh,cas3,csa3,DinG	Orphan	CTGTCCCCGCGGGGACAGGCACC	23	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,csa3,DinG	NA,NA	NA|585aa|up_9|NZ_CP015771.1_2613097_2614852_-	COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and metabolism]	NA|300aa|up_8|NZ_CP015771.1_2614958_2615858_+	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|328aa|up_7|NZ_CP015771.1_2615922_2616906_-	cd13577, PBP2_BugE_Glu, Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold	NA|327aa|up_6|NZ_CP015771.1_2617041_2618022_+	COG0679, COG0679, Predicted permeases [General function prediction only]	NA|464aa|up_5|NZ_CP015771.1_2618038_2619430_-	PRK00485, fumC, fumarate hydratase; Reviewed	NA|179aa|up_4|NZ_CP015771.1_2619581_2620118_+	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|462aa|up_3|NZ_CP015771.1_2620048_2621434_+	PRK10319, PRK10319, N-acetylmuramoyl-L-alanine amidase AmiA	NA|207aa|up_2|NZ_CP015771.1_2621576_2622197_-	PRK10847, PRK10847, DedA family protein	NA|630aa|up_1|NZ_CP015771.1_2622301_2624191_+	PRK00095, mutL, DNA mismatch repair endonuclease MutL	NA|314aa|up_0|NZ_CP015771.1_2624187_2625129_+	PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed	NA|350aa|down_0|NZ_CP015771.1_2625234_2626284_-	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|234aa|down_1|NZ_CP015771.1_2626536_2627238_+	PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated	NA|233aa|down_2|NZ_CP015771.1_2627234_2627933_+	cd02612, HAD_PGPPase, phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C	NA|452aa|down_3|NZ_CP015771.1_2627933_2629289_+	TIGR01942, pcnB, poly(A) polymerase	NA|164aa|down_4|NZ_CP015771.1_2629285_2629777_+	PRK14092, PRK14092, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase	NA|319aa|down_5|NZ_CP015771.1_2629795_2630752_-	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|701aa|down_6|NZ_CP015771.1_2632162_2634265_-	TIGR00786, TRAP_transporter_permease_protein_SiaT, TRAP transporter, DctM subunit	NA|348aa|down_7|NZ_CP015771.1_2634435_2635479_+	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|248aa|down_8|NZ_CP015771.1_2635522_2636266_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|137aa|down_9|NZ_CP015771.1_2637287_2637698_-	TIGR02425, putative_gamma-carboxymuconolactone_decarboxylase, 4-carboxymuconolactone decarboxylase
GCF_001686625.1_ASM168662v1	NZ_CP015771	Bordetella pertussis strain UT25Sm1 chromosome, complete genome	5	3550642-3550751	5	CRISPRCasFinder	no		DEDDh,cas3,csa3,DinG	Orphan	GGGGACAGATACCGTCTTGGCCGTCAA	27	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,csa3,DinG	NA,NA	NA|293aa|up_9|NZ_CP015771.1_3538499_3539378_-	PRK00030, minC, septum site-determining protein MinC	NA|588aa|up_8|NZ_CP015771.1_3539489_3541253_-	PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional	NA|447aa|up_7|NZ_CP015771.1_3541368_3542709_+	pfam01654, Cyt_bd_oxida_I, Cytochrome bd terminal oxidase subunit I	NA|352aa|up_6|NZ_CP015771.1_3542705_3543761_+	pfam02322, Cyt_bd_oxida_II, Cytochrome bd terminal oxidase subunit II	NA|475aa|up_5|NZ_CP015771.1_3543777_3545202_-	PRK09467, envZ, osmolarity sensor protein; Provisional	NA|234aa|up_4|NZ_CP015771.1_3545201_3545903_-	PRK09468, ompR, osmolarity response regulator; Provisional	NA|317aa|up_3|NZ_CP015771.1_3547407_3548358_+	pfam00665, rve, Integrase core domain	NA|324aa|up_2|NZ_CP015771.1_3548453_3549425_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|227aa|up_1|NZ_CP015771.1_3549429_3550110_-	pfam04391, DUF533, Protein of unknown function (DUF533)	NA|131aa|up_0|NZ_CP015771.1_3550247_3550640_+	COG1765, COG1765, Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]	NA|262aa|down_0|NZ_CP015771.1_3552003_3552789_-	PRK06997, PRK06997, enoyl-[acyl-carrier-protein] reductase FabI	NA|470aa|down_1|NZ_CP015771.1_3552883_3554293_-	PRK10783, mltD, membrane-bound lytic murein transglycosylase D; Provisional	NA|267aa|down_2|NZ_CP015771.1_3554303_3555104_-	TIGR03413, GSH_gloB, hydroxyacylglutathione hydrolase	NA|257aa|down_3|NZ_CP015771.1_3555124_3555895_+	pfam08241, Methyltransf_11, Methyltransferase domain	NA|156aa|down_4|NZ_CP015771.1_3555937_3556405_+	PRK00203, rnhA, ribonuclease H; Reviewed	NA|317aa|down_5|NZ_CP015771.1_3556401_3557352_-	pfam00665, rve, Integrase core domain	NA|293aa|down_6|NZ_CP015771.1_3559300_3560179_-	pfam00487, FA_desaturase, Fatty acid desaturase	NA|993aa|down_7|NZ_CP015771.1_3561105_3564084_-	pfam17936, Big_6, Bacterial Ig domain	NA|317aa|down_8|NZ_CP015771.1_3564437_3565388_+	pfam00665, rve, Integrase core domain	NA|363aa|down_9|NZ_CP015771.1_3565384_3566473_-	cd08948, 5beta-POR_like_SDR_a, progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs
