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_900637995.1_54466_G01	LR134480	Bordetella bronchiseptica strain NCTC8344 genome assembly, chromosome: 1	1	149184-149268	1	CRISPRCasFinder	no	csa3	csa3,DEDDh,cas3,DinG	Type I-A	GGTGCCTGTCCCCGCGGGGACAG	23	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,cas3,DinG	NA|255aa|up_9|LR134480.1_138478_139243_+,NA	NA|255aa|up_9|LR134480.1_138478_139243_+	NA	NA|169aa|up_8|LR134480.1_139304_139811_-	cd08896, SRPBCC_CalC_Aha1-like_3, Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins	csa3|113aa|up_7|LR134480.1_139807_140146_-	COG0640, ArsR, Predicted transcriptional regulators [Transcription]	NA|840aa|up_6|LR134480.1_140574_143094_+	PRK10833, PRK10833, putative assembly protein; Provisional	NA|129aa|up_5|LR134480.1_143090_143477_+	pfam03476, MOSC_N, MOSC N-terminal beta barrel domain	NA|406aa|up_4|LR134480.1_143484_144702_-	pfam03594, BenE, Benzoate membrane transport protein	NA|84aa|up_3|LR134480.1_144698_144950_-	cd10549, MtMvhB_like, Uncharacterized polyferredoxin-like protein	NA|170aa|up_2|LR134480.1_145004_145514_-	PRK00168, coaD, phosphopantetheine adenylyltransferase; Provisional	NA|207aa|up_1|LR134480.1_145534_146155_-	COG0742, COG0742, N6-adenine-specific methylase [DNA replication, recombination, and repair]	NA|356aa|up_0|LR134480.1_146362_147430_+	PRK10416, PRK10416, signal recognition particle-docking protein FtsY; Provisional	NA|274aa|down_0|LR134480.1_149314_150136_-	TIGR01097, PhnE, phosphonate ABC transporter, permease protein PhnE	NA|300aa|down_1|LR134480.1_150132_151032_-	TIGR01097, PhnE, phosphonate ABC transporter, permease protein PhnE	NA|257aa|down_2|LR134480.1_151019_151790_-	cd03256, ABC_PhnC_transporter, ATP-binding cassette domain of the binding protein-dependent phosphonate transport system	NA|336aa|down_3|LR134480.1_151792_152800_-	cd13573, PBP2_PnhD_3, Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold	NA|276aa|down_4|LR134480.1_152948_153776_-	COG1414, IclR, Transcriptional regulator [Transcription]	NA|266aa|down_5|LR134480.1_153781_154579_-	TIGR01484, Putative_mannosyl-3-phosphoglycerate_phosphatase, HAD-superfamily hydrolase, subfamily IIB	NA|392aa|down_6|LR134480.1_154724_155900_+	PRK14019, PRK14019, bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II	NA|176aa|down_7|LR134480.1_155913_156441_+	PRK00061, ribH, 6,7-dimethyl-8-ribityllumazine synthase; Provisional	NA|167aa|down_8|LR134480.1_156412_156913_+	PRK00202, nusB, transcription antitermination factor NusB	NA|333aa|down_9|LR134480.1_156970_157969_+	PRK05731, PRK05731, thiamine monophosphate kinase; Provisional
GCA_900637995.1_54466_G01	LR134480	Bordetella bronchiseptica strain NCTC8344 genome assembly, chromosome: 1	2	553080-553169	2	CRISPRCasFinder	no		csa3,DEDDh,cas3,DinG	Orphan	GGATCGGTGCCTGTCCCTGCGGGGACAGGCAC	32	1	1	553112-553137	LR134480.1_567870-567895	NA	1	1	Orphan	csa3,DEDDh,cas3,DinG	NA|144aa|up_7|LR134480.1_546514_546946_-,NA|292aa|up_4|LR134480.1_549281_550157_-,NA	NA|1146aa|up_9|LR134480.1_542165_545603_+	pfam05359, DUF748, Domain of Unknown Function (DUF748)	NA|295aa|up_8|LR134480.1_545620_546505_+	COG0412, COG0412, Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]	NA|144aa|up_7|LR134480.1_546514_546946_-	NA	NA|168aa|up_6|LR134480.1_547184_547688_+	cd03013, PRX5_like, Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol	NA|467aa|up_5|LR134480.1_547765_549166_+	cd17477, MFS_YcaD_like, YcaD and similar transporters of the Major Facilitator Superfamily	NA|292aa|up_4|LR134480.1_549281_550157_-	NA	NA|336aa|up_3|LR134480.1_550153_551161_-	TIGR00433, biotin_synthase, biotin synthase	NA|102aa|up_2|LR134480.1_551629_551935_+	pfam13663, DUF4148, Domain of unknown function (DUF4148)	NA|102aa|up_1|LR134480.1_551998_552304_+	pfam13663, DUF4148, Domain of unknown function (DUF4148)	NA|197aa|up_0|LR134480.1_552428_553019_+	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|298aa|down_0|LR134480.1_553671_554565_-	cd00377, ICL_PEPM, Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage	NA|885aa|down_1|LR134480.1_554794_557449_+	PRK09277, PRK09277, aconitate hydratase AcnA	NA|458aa|down_2|LR134480.1_557473_558847_+	cd01302, Cyclic_amidohydrolases, Cyclic amidohydrolases, including hydantoinase, dihydropyrimidinase, allantoinase, and dihydroorotase, are involved in the metabolism of pyrimidines and purines, sharing the property of hydrolyzing the cyclic amide bond of each substrate to the corresponding N-carbamyl amino acids	NA|240aa|down_3|LR134480.1_558880_559600_+	cd01015, CSHase, N-carbamoylsarcosine amidohydrolase (CSHase) hydrolyzes N-carbamoylsarcosine to sarcosine, carbon dioxide and ammonia	NA|334aa|down_4|LR134480.1_559610_560612_+	COG0523, COG0523, Putative GTPases (G3E family) [General function prediction only]	NA|340aa|down_5|LR134480.1_560749_561769_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|462aa|down_6|LR134480.1_561787_563173_+	TIGR01813, Fumarate_reductase_flavoprotein_subunit, flavocytochrome c	NA|459aa|down_7|LR134480.1_563169_564546_+	pfam03972, MmgE_PrpD, MmgE/PrpD family	NA|332aa|down_8|LR134480.1_564614_565610_+	cd13578, PBP2_Bug27, Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family;  contains the type 2 periplasmic binding fold	NA|462aa|down_9|LR134480.1_565640_567026_-	pfam03972, MmgE_PrpD, MmgE/PrpD family
GCA_900637995.1_54466_G01	LR134480	Bordetella bronchiseptica strain NCTC8344 genome assembly, chromosome: 1	3	672115-672201	3	CRISPRCasFinder	no		csa3,DEDDh,cas3,DinG	Orphan	AGTGTGCCTGTCCCCGCAGGGACAG	25	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,cas3,DinG	NA,NA|106aa|down_5|LR134480.1_678125_678443_-	NA|109aa|up_9|LR134480.1_660443_660770_+	PRK00153, PRK00153, YbaB/EbfC family nucleoid-associated protein	NA|203aa|up_8|LR134480.1_660819_661428_+	PRK00076, recR, recombination protein RecR; Reviewed	NA|417aa|up_7|LR134480.1_661502_662753_+	pfam02515, CoA_transf_3, CoA-transferase family III	NA|347aa|up_6|LR134480.1_662858_663899_+	cd13649, PBP2_Cae31940, Substrate binding domain of an uncharacterized protein similar to ABC-type transporter for thiamin biosynthetic pathway intermediates; a member of the type 2 periplasmic binding fold superfamily	NA|270aa|up_5|LR134480.1_663891_664701_+	COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]	NA|265aa|up_4|LR134480.1_664704_665499_+	COG0600, TauC, ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]	NA|321aa|up_3|LR134480.1_665540_666503_-	PRK05269, PRK05269, transaldolase B; Provisional	NA|348aa|up_2|LR134480.1_666840_667884_+	PRK12564, PRK12564, carbamoyl-phosphate synthase small subunit	NA|1081aa|up_1|LR134480.1_667894_671137_+	PRK05294, carB, carbamoyl-phosphate synthase large subunit	NA|255aa|up_0|LR134480.1_671287_672052_+	PRK07024, PRK07024, SDR family oxidoreductase	NA|215aa|down_0|LR134480.1_672232_672877_-	pfam00300, His_Phos_1, Histidine phosphatase superfamily (branch 1)	NA|300aa|down_1|LR134480.1_672887_673787_-	COG0583, LysR, Transcriptional regulator [Transcription]	NA|362aa|down_2|LR134480.1_673834_674920_-	COG3842, PotA, ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]	NA|570aa|down_3|LR134480.1_674916_676626_-	COG1178, ThiP, ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]	NA|441aa|down_4|LR134480.1_676702_678025_-	cd13518, PBP2_Fe3_thiamine_like, Substrate binding domain of iron and thiamine transporters-like, a member of the type 2 periplasmic binding fold superfamily	NA|106aa|down_5|LR134480.1_678125_678443_-	NA	NA|438aa|down_6|LR134480.1_678576_679890_+	TIGR03616, Putative_pyrimidine_permease_RutG, pyrimidine utilization transport protein G	NA|544aa|down_7|LR134480.1_679920_681552_-	PRK15041, PRK15041, methyl-accepting chemotaxis protein	NA|159aa|down_8|LR134480.1_682181_682658_+	PRK00226, greA, transcription elongation factor GreA; Reviewed	NA|201aa|down_9|LR134480.1_683012_683615_-	smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly
GCA_900637995.1_54466_G01	LR134480	Bordetella bronchiseptica strain NCTC8344 genome assembly, chromosome: 1	4	1150691-1150820	4	CRISPRCasFinder	no		csa3,DEDDh,cas3,DinG	Orphan	TTTGCCGCCGGGCCGCCCCAAGGCAAAAAAGCCCCCTCGGGGGGCA	46	1	2	1150737-1150774|1150737-1150774	LR134480.1_584561-584598|LR134480.1_584645-584682	NA	1	1	Orphan	csa3,DEDDh,cas3,DinG	NA,NA|237aa|down_0|LR134480.1_1151010_1151721_+	NA|1077aa|up_9|LR134480.1_1137196_1140427_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|500aa|up_8|LR134480.1_1140423_1141923_+	PRK09837, PRK09837, Cu(I)/Ag(I) efflux RND transporter outer membrane protein	NA|249aa|up_7|LR134480.1_1141919_1142666_+	PRK05265, PRK05265, pyridoxine 5'-phosphate synthase; Provisional	NA|154aa|up_6|LR134480.1_1142750_1143212_+	PRK00070, acpS, 4'-phosphopantetheinyl transferase; Provisional	NA|354aa|up_5|LR134480.1_1143250_1144312_+	PRK05337, PRK05337, beta-hexosaminidase; Provisional	NA|610aa|up_4|LR134480.1_1144274_1146104_+	PRK00558, uvrC, excinuclease ABC subunit UvrC	NA|191aa|up_3|LR134480.1_1146143_1146716_+	PRK10832, PRK10832, CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase	NA|416aa|up_2|LR134480.1_1146885_1148133_+	cd17325, MFS_MdtG_SLC18_like, bacterial MdtG-like and eukaryotic solute carrier 18 (SLC18) family of the Major Facilitator Superfamily of transporters	NA|274aa|up_1|LR134480.1_1148139_1148961_-	PRK11792, queF, 7-cyano-7-deazaguanine reductase; Provisional	NA|441aa|up_0|LR134480.1_1149279_1150602_+	PRK15063, PRK15063, isocitrate lyase; Provisional	NA|237aa|down_0|LR134480.1_1151010_1151721_+	NA	NA|248aa|down_1|LR134480.1_1151731_1152475_-	pfam04172, LrgB, LrgB-like family	NA|120aa|down_2|LR134480.1_1152467_1152827_-	pfam03788, LrgA, LrgA family	NA|479aa|down_3|LR134480.1_1152814_1154251_-	pfam13500, AAA_26, AAA domain	NA|218aa|down_4|LR134480.1_1154247_1154901_-	TIGR01738, Pimeloyl-_methyl_ester_esterase, pimelyl-[acyl-carrier protein] methyl ester esterase	NA|398aa|down_5|LR134480.1_1154897_1156091_-	TIGR00858, Putative_8-amino-7-oxononanoate_synthase, 8-amino-7-oxononanoate synthase	NA|425aa|down_6|LR134480.1_1156194_1157469_+	PRK05964, PRK05964, adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional	NA|325aa|down_7|LR134480.1_1157533_1158508_+	cd02079, P-type_ATPase_HM, P-type heavy metal-transporting ATPase	NA|48aa|down_8|LR134480.1_1158504_1158648_+	pfam03597, FixS, Cytochrome oxidase maturation protein cbb3-type	NA|496aa|down_9|LR134480.1_1158772_1160260_+	PRK14488, PRK14488, cbb3-type cytochrome c oxidase subunit I; Provisional
GCA_900637995.1_54466_G01	LR134480	Bordetella bronchiseptica strain NCTC8344 genome assembly, chromosome: 1	6	3555502-3555595	6	CRISPRCasFinder	no	DEDDh	csa3,DEDDh,cas3,DinG	Unclear	GTGCCTGTCCCCGCCGGGACAGGCAC	26	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,cas3,DinG	NA,NA	NA|398aa|up_9|LR134480.1_3543922_3545116_-	PRK06954, PRK06954, acetyl-CoA C-acetyltransferase	NA|343aa|up_8|LR134480.1_3545181_3546210_-	pfam00441, Acyl-CoA_dh_1, Acyl-CoA dehydrogenase, C-terminal domain	NA|391aa|up_7|LR134480.1_3546236_3547409_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|326aa|up_6|LR134480.1_3547534_3548512_+	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_5|LR134480.1_3548522_3549494_-	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_4|LR134480.1_3549560_3550346_-	PRK09245, PRK09245, crotonase/enoyl-CoA hydratase family protein	NA|411aa|up_3|LR134480.1_3550338_3551571_-	pfam02515, CoA_transf_3, CoA-transferase family III	NA|252aa|up_2|LR134480.1_3551766_3552522_-	COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]	NA|173aa|up_1|LR134480.1_3552632_3553151_+	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|708aa|up_0|LR134480.1_3553147_3555271_-	PRK00007, PRK00007, elongation factor G; Reviewed	NA|157aa|down_0|LR134480.1_3555681_3556152_-	pfam00582, Usp, Universal stress protein family	NA|115aa|down_1|LR134480.1_3556240_3556585_-	COG3453, COG3453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|482aa|down_2|LR134480.1_3556684_3558130_-	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|325aa|down_3|LR134480.1_3558213_3559188_+	COG0697, RhaT, Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]	NA|220aa|down_4|LR134480.1_3559184_3559844_+	COG1280, RhtB, Putative threonine efflux protein [Amino acid transport and metabolism]	NA|308aa|down_5|LR134480.1_3559933_3560857_+	pfam12146, Hydrolase_4, Serine aminopeptidase, S33	NA|152aa|down_6|LR134480.1_3560862_3561318_-	COG4125, COG4125, Predicted membrane protein [Function unknown]	NA|306aa|down_7|LR134480.1_3561314_3562232_-	cd10807, YdjC_like_3, uncharacterized YdjC-like family proteins from bacteria	NA|132aa|down_8|LR134480.1_3562250_3562646_+	pfam04138, GtrA, GtrA-like protein	NA|533aa|down_9|LR134480.1_3562605_3564204_-	COG1807, ArnT, 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]
GCA_900637995.1_54466_G01	LR134480	Bordetella bronchiseptica strain NCTC8344 genome assembly, chromosome: 1	7	3910147-3910227	7	CRISPRCasFinder	no		csa3,DEDDh,cas3,DinG	Orphan	GTGCCTGTCCCCGCGGGGACAGGCACCT	28	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,cas3,DinG	NA|79aa|up_8|LR134480.1_3900823_3901060_+,NA	NA|287aa|up_9|LR134480.1_3899835_3900696_+	cd01171, YXKO-related, B	NA|79aa|up_8|LR134480.1_3900823_3901060_+	NA	NA|543aa|up_7|LR134480.1_3901358_3902987_+	cd08498, PBP2_NikA_DppA_OppA_like_2, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold	NA|323aa|up_6|LR134480.1_3903110_3904079_+	cd06910, M14_ASTE_ASPA-like, Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup	NA|326aa|up_5|LR134480.1_3904137_3905115_+	COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|307aa|up_4|LR134480.1_3905122_3906043_+	COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|328aa|up_3|LR134480.1_3906039_3907023_+	COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|337aa|up_2|LR134480.1_3907019_3908030_+	COG4608, AppF, ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]	NA|302aa|up_1|LR134480.1_3908032_3908938_+	COG3509, LpqC, Poly(3-hydroxybutyrate) depolymerase [Secondary metabolites biosynthesis, transport, and catabolism]	NA|378aa|up_0|LR134480.1_3908981_3910115_+	cd03885, M20_CPDG2, M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme	NA|690aa|down_0|LR134480.1_3910245_3912315_-	TIGR01074, ATP-dependent_DNA_helicase_Rep, ATP-dependent DNA helicase Rep	NA|701aa|down_1|LR134480.1_3912357_3914460_-	PRK05580, PRK05580, primosome assembly protein PriA; Validated	NA|359aa|down_2|LR134480.1_3914766_3915843_-	PRK00115, hemE, uroporphyrinogen decarboxylase; Validated	NA|294aa|down_3|LR134480.1_3915918_3916800_-	PRK15115, PRK15115, response regulator GlrR; Provisional	NA|141aa|down_4|LR134480.1_3916982_3917405_-	PRK00571, atpC, F0F1 ATP synthase subunit epsilon; Validated	NA|467aa|down_5|LR134480.1_3917414_3918815_-	PRK09280, PRK09280, F0F1 ATP synthase subunit beta; Validated	NA|302aa|down_6|LR134480.1_3918857_3919763_-	PRK05621, PRK05621, F0F1 ATP synthase subunit gamma; Validated	NA|514aa|down_7|LR134480.1_3919861_3921403_-	PRK09281, PRK09281, F0F1 ATP synthase subunit alpha; Validated	NA|180aa|down_8|LR134480.1_3921437_3921977_-	PRK05758, PRK05758, F0F1 ATP synthase subunit delta; Validated	NA|157aa|down_9|LR134480.1_3921989_3922460_-	PRK05759, PRK05759, F0F1 ATP synthase subunit B; Validated
