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_900324295.1_16_LA_309	NZ_LT992467	Staphylococcus aureus isolate 16_LA_309 chromosome I	1	331143-331225	1	CRISPRCasFinder	no		DinG,cas3,csa3,DEDDh,TnsE_C,WYL	Orphan	GAAGCTGACGAAAAAGTCAGCTTAC	25	0	0	NA	NA	NA	1	1	Orphan	DinG,cas3,csa3,DEDDh,TnsE_C,WYL	NA,NA	NA|454aa|up_9|NZ_LT992467.1_315976_317338_+	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|586aa|up_8|NZ_LT992467.1_317681_319439_-	PRK06354, PRK06354, pyruvate kinase; Provisional	NA|323aa|up_7|NZ_LT992467.1_319460_320429_-	PRK03202, PRK03202, ATP-dependent 6-phosphofructokinase	NA|315aa|up_6|NZ_LT992467.1_320697_321642_-	PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated	NA|286aa|up_5|NZ_LT992467.1_321641_322499_-	PRK05654, PRK05654, acetyl-CoA carboxylase carboxyltransferase subunit beta	NA|410aa|up_4|NZ_LT992467.1_322693_323923_-	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|1066aa|up_3|NZ_LT992467.1_324371_327569_-	COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]	NA|314aa|up_2|NZ_LT992467.1_327589_328531_-	COG0618, COG0618, Exopolyphosphatase-related proteins [General function prediction only]	NA|433aa|up_1|NZ_LT992467.1_328900_330199_-	COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]	NA|138aa|up_0|NZ_LT992467.1_330403_330817_+	pfam00582, Usp, Universal stress protein family	NA|230aa|down_0|NZ_LT992467.1_331322_332012_-	PRK00685, PRK00685, metal-dependent hydrolase; Provisional	NA|352aa|down_1|NZ_LT992467.1_332186_333242_+	COG0006, PepP, Xaa-Pro aminopeptidase [Amino acid transport and metabolism]	NA|373aa|down_2|NZ_LT992467.1_333557_334676_-	cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic domains	NA|167aa|down_3|NZ_LT992467.1_334816_335317_+	pfam00582, Usp, Universal stress protein family	NA|401aa|down_4|NZ_LT992467.1_335563_336766_-	PRK00180, PRK00180, acetate kinase A/propionate kinase 2; Reviewed	NA|316aa|down_5|NZ_LT992467.1_336853_337801_-	COG0827, COG0827, Adenine-specific DNA methylase [DNA replication, recombination, and repair]	NA|165aa|down_6|NZ_LT992467.1_337923_338418_-	PRK00522, tpx, thiol peroxidase	NA|257aa|down_7|NZ_LT992467.1_338515_339286_-	PRK10621, PRK10621, hypothetical protein; Provisional	NA|408aa|down_8|NZ_LT992467.1_339329_340553_-	PRK01565, PRK01565, thiamine biosynthesis protein ThiI; Provisional	NA|383aa|down_9|NZ_LT992467.1_340552_341701_-	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]
GCF_900324295.1_16_LA_309	NZ_LT992467	Staphylococcus aureus isolate 16_LA_309 chromosome I	2	420837-420930	2	CRISPRCasFinder	no	csa3	DinG,cas3,csa3,DEDDh,TnsE_C,WYL	Type I-A	GCAATGCGCGTTGGGGTGTGGGGCCCCAACATAG	34	1	1	420871-420896	NZ_LT992467.1_518659-518634	NA	1	1	Orphan	DinG,cas3,csa3,DEDDh,TnsE_C,WYL	NA|75aa|up_6|NZ_LT992467.1_415598_415823_-,NA|148aa|up_3|NZ_LT992467.1_417034_417478_-,NA|101aa|down_1|NZ_LT992467.1_422064_422367_+	csa3|105aa|up_9|NZ_LT992467.1_412775_413090_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|431aa|up_8|NZ_LT992467.1_413089_414382_+	PRK15445, PRK15445, arsenical efflux pump membrane protein ArsB	NA|285aa|up_7|NZ_LT992467.1_414468_415323_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|75aa|up_6|NZ_LT992467.1_415598_415823_-	NA	NA|157aa|up_5|NZ_LT992467.1_416021_416492_+	COG1595, RpoE, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]	NA|148aa|up_4|NZ_LT992467.1_416604_417048_+	pfam06338, ComK, ComK protein	NA|148aa|up_3|NZ_LT992467.1_417034_417478_-	NA	NA|212aa|up_2|NZ_LT992467.1_417775_418411_+	pfam02517, Abi, CAAX protease self-immunity	NA|391aa|up_1|NZ_LT992467.1_418647_419820_+	pfam00872, Transposase_mut, Transposase, Mutator family	NA|207aa|up_0|NZ_LT992467.1_419909_420530_+	pfam02517, Abi, CAAX protease self-immunity	NA|238aa|down_0|NZ_LT992467.1_421092_421806_-	PRK12376, PRK12376, putative translaldolase; Provisional	NA|101aa|down_1|NZ_LT992467.1_422064_422367_+	NA	NA|122aa|down_2|NZ_LT992467.1_422621_422987_+	PRK14201, PRK14201, fluoride efflux transporter CrcB	NA|118aa|down_3|NZ_LT992467.1_422983_423337_+	COG0239, CrcB, Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]	NA|278aa|down_4|NZ_LT992467.1_423586_424420_-	COG0656, ARA1, Aldo/keto reductases, related to diketogulonate reductase [General function prediction only]	NA|303aa|down_5|NZ_LT992467.1_424631_425540_-	pfam08378, NERD, Nuclease-related domain	NA|398aa|down_6|NZ_LT992467.1_425664_426858_-	PRK05250, PRK05250, S-adenosylmethionine synthetase; Validated	NA|531aa|down_7|NZ_LT992467.1_427229_428822_+	cd00484, PEPCK_ATP, Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis	NA|249aa|down_8|NZ_LT992467.1_429118_429865_-	COG1506, DAP2, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]	NA|158aa|down_9|NZ_LT992467.1_429869_430343_-	TIGR02705, conserved_hypothetical_protein, nucleoside triphosphatase YtkD
GCF_900324295.1_16_LA_309	NZ_LT992467	Staphylococcus aureus isolate 16_LA_309 chromosome I	3	709590-709802	3	CRISPRCasFinder	no		DinG,cas3,csa3,DEDDh,TnsE_C,WYL	Orphan	TGATGTGCTGTTGTGGAAGCTTGGTGTCGTGCCATGCTACTTTGATG	47	0	0	NA	NA	NA	2	2	Orphan	DinG,cas3,csa3,DEDDh,TnsE_C,WYL	NA|46aa|up_4|NZ_LT992467.1_706451_706589_-,NA|107aa|down_0|NZ_LT992467.1_709835_710156_+	NA|232aa|up_9|NZ_LT992467.1_699143_699839_+	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|507aa|up_8|NZ_LT992467.1_700191_701712_-	COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]	NA|452aa|up_7|NZ_LT992467.1_702227_703583_-	COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]	NA|357aa|up_6|NZ_LT992467.1_703597_704668_-	PRK01966, ddl, D-alanine--D-alanine ligase	NA|401aa|up_5|NZ_LT992467.1_704985_706188_+	TIGR02210, Rod_shape-determining_protein_RodA, rod shape-determining protein RodA	NA|46aa|up_4|NZ_LT992467.1_706451_706589_-	NA	NA|70aa|up_3|NZ_LT992467.1_706716_706926_-	cd00371, HMA, Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones	NA|98aa|up_2|NZ_LT992467.1_706937_707231_-	cd10152, SaCsoR-like_DUF156, Staphylococcus aureus copper-sensitive operon repressor (CsoR), and related domains; this family was previously known as part of DUF156	NA|495aa|up_1|NZ_LT992467.1_707396_708881_+	TIGR04265, bac_cardiolipin, cardiolipin synthase	NA|216aa|up_0|NZ_LT992467.1_708908_709556_+	COG1418, COG1418, Predicted HD superfamily hydrolase [General function prediction only]	NA|107aa|down_0|NZ_LT992467.1_709835_710156_+	NA	NA|291aa|down_1|NZ_LT992467.1_711797_712670_-	PRK02463, PRK02463, OxaA-like protein precursor; Provisional	NA|214aa|down_2|NZ_LT992467.1_712755_713397_-	PRK00043, thiE, thiamine phosphate synthase	NA|264aa|down_3|NZ_LT992467.1_713398_714190_-	PRK09355, PRK09355, hydroxyethylthiazole kinase; Validated	NA|277aa|down_4|NZ_LT992467.1_714173_715004_-	PRK06427, PRK06427, bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed	NA|230aa|down_5|NZ_LT992467.1_714996_715686_-	TIGR04306, salvage_TenA, thiaminase II	NA|232aa|down_6|NZ_LT992467.1_716072_716768_-	pfam06737, Transglycosylas, Transglycosylase-like domain	NA|132aa|down_7|NZ_LT992467.1_717156_717552_-	pfam00436, SSB, Single-strand binding protein family	NA|391aa|down_8|NZ_LT992467.1_717736_718909_-	pfam00872, Transposase_mut, Transposase, Mutator family	NA|147aa|down_9|NZ_LT992467.1_719077_719518_+	pfam14183, YwpF, YwpF-like protein
GCF_900324295.1_16_LA_309	NZ_LT992467	Staphylococcus aureus isolate 16_LA_309 chromosome I	4	766553-766703	4	CRISPRCasFinder	no	csa3,TnsE_C	DinG,cas3,csa3,DEDDh,TnsE_C,WYL	Type I-A	AACTTTAGTTGTTAGGGGCTCTTATGCA	28	0	0	NA	NA	NA	2	2	Orphan	DinG,cas3,csa3,DEDDh,TnsE_C,WYL	NA|77aa|up_5|NZ_LT992467.1_761425_761656_-,NA|364aa|up_0|NZ_LT992467.1_765443_766535_+,NA|35aa|down_0|NZ_LT992467.1_767032_767137_-,NA|53aa|down_1|NZ_LT992467.1_767816_767975_+,NA|31aa|down_2|NZ_LT992467.1_768410_768503_+	NA|237aa|up_9|NZ_LT992467.1_757035_757746_+	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase	NA|148aa|up_8|NZ_LT992467.1_757866_758310_-	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|138aa|up_7|NZ_LT992467.1_758509_758923_-	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|458aa|up_6|NZ_LT992467.1_759380_760754_-	pfam01878, EVE, EVE domain	NA|77aa|up_5|NZ_LT992467.1_761425_761656_-	NA	NA|313aa|up_4|NZ_LT992467.1_761686_762625_-	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|222aa|up_3|NZ_LT992467.1_763058_763724_-	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	csa3|107aa|up_2|NZ_LT992467.1_763875_764196_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|327aa|up_1|NZ_LT992467.1_764197_765178_+	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	NA|364aa|up_0|NZ_LT992467.1_765443_766535_+	NA	NA|35aa|down_0|NZ_LT992467.1_767032_767137_-	NA	NA|53aa|down_1|NZ_LT992467.1_767816_767975_+	NA	NA|31aa|down_2|NZ_LT992467.1_768410_768503_+	NA	NA|286aa|down_3|NZ_LT992467.1_768632_769490_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|261aa|down_4|NZ_LT992467.1_769557_770340_-	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|203aa|down_5|NZ_LT992467.1_770629_771238_-	pfam08937, DUF1863, MTH538 TIR-like domain (DUF1863)	NA|345aa|down_6|NZ_LT992467.1_771265_772300_-	pfam13676, TIR_2, TIR domain	NA|490aa|down_7|NZ_LT992467.1_772393_773863_-	pfam18185, STALD, Sir2- and TIR-associating SLOG family	NA|97aa|down_8|NZ_LT992467.1_773922_774213_-	pfam11867, DUF3387, Domain of unknown function (DUF3387)	TnsE_C|135aa|down_9|NZ_LT992467.1_774337_774742_-	pfam18623, TnsE_C, TnsE C-terminal domain
GCF_900324295.1_16_LA_309	NZ_LT992467	Staphylococcus aureus isolate 16_LA_309 chromosome I	5	933246-933331	5	CRISPRCasFinder	no	WYL	DinG,cas3,csa3,DEDDh,TnsE_C,WYL	Unclear	AAAGTCAGCTTACAATAATGTGCAAGTTGG	30	1	7	933276-933301|933276-933301|933276-933301|933276-933301|933276-933301|933276-933301|933276-933301	NZ_LT992467.1_208712-208687|NZ_LT992467.1_2267399-2267374|NZ_LT992467.1_722034-722059|NZ_LT992467.1_1066524-1066499|NZ_LT992467.1_2271519-2271544|NZ_LT992467.1_2358343-2358368|NZ_LT992467.1_2796532-2796557	NA	1	1	Orphan	DinG,cas3,csa3,DEDDh,TnsE_C,WYL	NA|65aa|up_6|NZ_LT992467.1_925990_926185_-,NA|78aa|down_1|NZ_LT992467.1_934281_934515_-,NA|110aa|down_8|NZ_LT992467.1_942603_942933_+	NA|248aa|up_9|NZ_LT992467.1_921778_922522_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|652aa|up_8|NZ_LT992467.1_922547_924503_-	COG2207, AraC, AraC-type DNA-binding domain-containing proteins [Transcription]	NA|270aa|up_7|NZ_LT992467.1_925112_925922_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|65aa|up_6|NZ_LT992467.1_925990_926185_-	NA	NA|467aa|up_5|NZ_LT992467.1_926358_927759_-	TIGR00931, Uncharacterized_Na+/H+_antiporter_HI_1107, Na+/H+ antiporter NhaC	NA|361aa|up_4|NZ_LT992467.1_927853_928936_-	pfam02317, Octopine_DH, NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain	NA|141aa|up_3|NZ_LT992467.1_929183_929606_+	COG3296, COG3296, Uncharacterized protein conserved in bacteria [Function unknown]	NA|167aa|up_2|NZ_LT992467.1_929842_930343_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|318aa|up_1|NZ_LT992467.1_930705_931659_+	cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains	NA|375aa|up_0|NZ_LT992467.1_931750_932875_-	PRK06753, PRK06753, hypothetical protein; Provisional	NA|259aa|down_0|NZ_LT992467.1_933483_934260_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|78aa|down_1|NZ_LT992467.1_934281_934515_-	NA	NA|158aa|down_2|NZ_LT992467.1_934809_935283_-	COG2427, COG2427, Uncharacterized conserved protein [Function unknown]	NA|985aa|down_3|NZ_LT992467.1_935282_938237_-	COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General function prediction only]	NA|316aa|down_4|NZ_LT992467.1_938838_939786_-	PRK09379, PRK09379, LytR family transcriptional regulator	NA|266aa|down_5|NZ_LT992467.1_939918_940716_-	COG0483, SuhB, Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]	WYL|231aa|down_6|NZ_LT992467.1_941100_941793_+	COG2378, COG2378, Predicted transcriptional regulator [Transcription]	NA|246aa|down_7|NZ_LT992467.1_941817_942555_-	pfam02517, Abi, CAAX protease self-immunity	NA|110aa|down_8|NZ_LT992467.1_942603_942933_+	NA	NA|291aa|down_9|NZ_LT992467.1_943377_944250_+	COG1737, RpiR, Transcriptional regulators [Transcription]
GCF_900324295.1_16_LA_309	NZ_LT992467	Staphylococcus aureus isolate 16_LA_309 chromosome I	6	1110788-1110882	6	CRISPRCasFinder	no		DinG,cas3,csa3,DEDDh,TnsE_C,WYL	Orphan	AGGCTCTTATGCAGTTGGTGCGAAGCAA	28	0	0	NA	NA	NA	1	1	Orphan	DinG,cas3,csa3,DEDDh,TnsE_C,WYL	NA|249aa|up_9|NZ_LT992467.1_1100373_1101120_+,NA|121aa|down_0|NZ_LT992467.1_1111550_1111913_-,NA|105aa|down_8|NZ_LT992467.1_1118725_1119040_+	NA|249aa|up_9|NZ_LT992467.1_1100373_1101120_+	NA	NA|398aa|up_8|NZ_LT992467.1_1101343_1102537_-	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|250aa|up_7|NZ_LT992467.1_1102548_1103298_-	COG1124, DppF, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|272aa|up_6|NZ_LT992467.1_1103290_1104106_-	COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|290aa|up_5|NZ_LT992467.1_1104102_1104972_-	COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|312aa|up_4|NZ_LT992467.1_1104968_1105904_-	COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|533aa|up_3|NZ_LT992467.1_1105916_1107515_-	TIGR02294, Nickel-binding_periplasmic_protein, nickel ABC transporter, nickel/metallophore periplasmic binding protein	NA|434aa|up_2|NZ_LT992467.1_1107657_1108959_-	COG4408, COG4408, Uncharacterized protein conserved in bacteria [Function unknown]	NA|273aa|up_1|NZ_LT992467.1_1108951_1109770_-	cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family	NA|274aa|up_0|NZ_LT992467.1_1109780_1110602_-	COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and metabolism]	NA|121aa|down_0|NZ_LT992467.1_1111550_1111913_-	NA	NA|273aa|down_1|NZ_LT992467.1_1112175_1112994_-	PRK08589, PRK08589, SDR family oxidoreductase	NA|513aa|down_2|NZ_LT992467.1_1113227_1114766_+	pfam03806, ABG_transport, AbgT putative transporter family	NA|141aa|down_3|NZ_LT992467.1_1114877_1115300_-	COG2128, COG2128, Uncharacterized conserved protein [Function unknown]	NA|133aa|down_4|NZ_LT992467.1_1115771_1116170_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|137aa|down_5|NZ_LT992467.1_1116196_1116607_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|128aa|down_6|NZ_LT992467.1_1117061_1117445_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|403aa|down_7|NZ_LT992467.1_1117511_1118720_+	cd07657, F-BAR_Fes_Fer, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Fes (feline sarcoma) and Fer (Fes related) tyrosine kinases	NA|105aa|down_8|NZ_LT992467.1_1118725_1119040_+	NA	NA|140aa|down_9|NZ_LT992467.1_1120916_1121336_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)
GCF_900324295.1_16_LA_309	NZ_LT992467	Staphylococcus aureus isolate 16_LA_309 chromosome I	7	1138733-1138843	7	CRISPRCasFinder	no		DinG,cas3,csa3,DEDDh,TnsE_C,WYL	Orphan	GGTACTTCTGGTGTCGGTGGCGTTGGT	27	0	0	NA	NA	NA	1	1	Orphan	DinG,cas3,csa3,DEDDh,TnsE_C,WYL	NA|89aa|up_2|NZ_LT992467.1_1133036_1133303_+,NA|103aa|up_1|NZ_LT992467.1_1133446_1133755_+,NA	NA|452aa|up_9|NZ_LT992467.1_1124430_1125786_-	cd00519, Lipase_3, Lipase (class 3)	NA|262aa|up_8|NZ_LT992467.1_1125782_1126568_-	pfam04507, DUF576, Csa1 family	NA|255aa|up_7|NZ_LT992467.1_1126815_1127580_-	pfam04507, DUF576, Csa1 family	NA|258aa|up_6|NZ_LT992467.1_1127691_1128465_-	pfam04507, DUF576, Csa1 family	NA|310aa|up_5|NZ_LT992467.1_1128707_1129637_-	pfam09019, EcoRII-C, EcoRII C terminal	NA|398aa|up_4|NZ_LT992467.1_1129732_1130926_+	TIGR00675, Modification_methylase, DNA-methyltransferase (dcm)	NA|584aa|up_3|NZ_LT992467.1_1131001_1132753_+	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|89aa|up_2|NZ_LT992467.1_1133036_1133303_+	NA	NA|103aa|up_1|NZ_LT992467.1_1133446_1133755_+	NA	NA|289aa|up_0|NZ_LT992467.1_1133880_1134747_-	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|453aa|down_0|NZ_LT992467.1_1141983_1143342_-	TIGR00791, Gluconate_permease, gluconate transporter	NA|518aa|down_1|NZ_LT992467.1_1143458_1145012_-	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|226aa|down_2|NZ_LT992467.1_1145036_1145714_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|255aa|down_3|NZ_LT992467.1_1145870_1146635_-	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|231aa|down_4|NZ_LT992467.1_1146799_1147492_-	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|139aa|down_5|NZ_LT992467.1_1147722_1148139_-	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|608aa|down_6|NZ_LT992467.1_1148277_1150101_-	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|426aa|down_7|NZ_LT992467.1_1151012_1152290_-	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|204aa|down_8|NZ_LT992467.1_1152836_1153448_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|391aa|down_9|NZ_LT992467.1_1153858_1155031_+	pfam00872, Transposase_mut, Transposase, Mutator family
GCF_900324295.1_16_LA_309	NZ_LT992467	Staphylococcus aureus isolate 16_LA_309 chromosome I	8	1687043-1687242	8	CRISPRCasFinder	no		DinG,cas3,csa3,DEDDh,TnsE_C,WYL	Orphan	TGCAAGTTGGCGGGGCCCCAACACAGAAGCT	31	2	2	1687074-1687098|1687130-1687154	NZ_LT992467.1_1687243-1687267|NZ_LT992467.1_721996-722020	NA	3	3	Orphan	DinG,cas3,csa3,DEDDh,TnsE_C,WYL	NA,NA|131aa|down_5|NZ_LT992467.1_1692418_1692811_+	NA|574aa|up_9|NZ_LT992467.1_1674489_1676211_+	pfam18674, TarS_C1, TarS beta-glycosyltransferase C-terminal domain 1	NA|225aa|up_8|NZ_LT992467.1_1676354_1677029_+	PRK13276, PRK13276, iron-sulfur cluster repair di-iron protein ScdA	NA|585aa|up_7|NZ_LT992467.1_1677275_1679030_+	COG3275, LytS, Putative regulator of cell autolysis [Signal transduction mechanisms]	NA|247aa|up_6|NZ_LT992467.1_1679032_1679773_+	PRK14084, PRK14084, DNA-binding response regulator	NA|148aa|up_5|NZ_LT992467.1_1679885_1680329_+	PRK04125, PRK04125, antiholin-like protein LrgA	NA|234aa|up_4|NZ_LT992467.1_1680321_1681023_+	PRK04288, PRK04288, antiholin-like protein LrgB; Provisional	NA|764aa|up_3|NZ_LT992467.1_1681363_1683655_+	COG3256, NorB, Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]	NA|235aa|up_2|NZ_LT992467.1_1683880_1684585_-	COG2188, PhnF, Transcriptional regulators [Transcription]	NA|264aa|up_1|NZ_LT992467.1_1684733_1685525_+	COG2190, NagE, Phosphotransferase system IIA components [Carbohydrate transport and metabolism]	NA|479aa|up_0|NZ_LT992467.1_1685540_1686977_+	PRK09589, celA, 6-phospho-beta-glucosidase; Reviewed	NA|254aa|down_0|NZ_LT992467.1_1687552_1688314_-	pfam13649, Methyltransf_25, Methyltransferase domain	NA|305aa|down_1|NZ_LT992467.1_1688565_1689480_-	TIGR02152, Putative_ribokinase, ribokinase	NA|135aa|down_2|NZ_LT992467.1_1689507_1689912_-	PRK11797, PRK11797, D-ribose pyranase; Provisional	NA|294aa|down_3|NZ_LT992467.1_1689926_1690808_-	pfam06800, Sugar_transport, Sugar transport protein	NA|333aa|down_4|NZ_LT992467.1_1691039_1692038_-	COG1609, PurR, Transcriptional regulators [Transcription]	NA|131aa|down_5|NZ_LT992467.1_1692418_1692811_+	NA	NA|459aa|down_6|NZ_LT992467.1_1692939_1694316_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|331aa|down_7|NZ_LT992467.1_1694549_1695542_+	COG3049, COG3049, Penicillin V acylase and related amidases [Cell envelope biogenesis, outer membrane]	NA|317aa|down_8|NZ_LT992467.1_1695867_1696818_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|220aa|down_9|NZ_LT992467.1_1696869_1697529_-	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]
GCF_900324295.1_16_LA_309	NZ_LT992467	Staphylococcus aureus isolate 16_LA_309 chromosome I	9	2058884-2058992	9	CRISPRCasFinder	no		DinG,cas3,csa3,DEDDh,TnsE_C,WYL	Orphan	AAAGGAACGCAGTTGGATGCTACCGCACAACTGCATAAA	39	0	0	NA	NA	NA	1	1	Orphan	DinG,cas3,csa3,DEDDh,TnsE_C,WYL	NA,NA|169aa|down_4|NZ_LT992467.1_2062725_2063232_+,NA|239aa|down_5|NZ_LT992467.1_2063393_2064110_+	NA|209aa|up_9|NZ_LT992467.1_2048388_2049015_+	pfam04276, DUF443, Protein of unknown function (DUF443)	NA|313aa|up_8|NZ_LT992467.1_2049284_2050223_+	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|179aa|up_7|NZ_LT992467.1_2050668_2051205_+	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|159aa|up_6|NZ_LT992467.1_2051374_2051851_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|432aa|up_5|NZ_LT992467.1_2051890_2053186_+	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|174aa|up_4|NZ_LT992467.1_2053213_2053735_+	pfam08741, YwhD, YwhD family	NA|337aa|up_3|NZ_LT992467.1_2054233_2055244_+	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|139aa|up_2|NZ_LT992467.1_2055519_2055936_+	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|554aa|up_1|NZ_LT992467.1_2055932_2057594_+	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|212aa|up_0|NZ_LT992467.1_2058078_2058714_+	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|296aa|down_0|NZ_LT992467.1_2059043_2059931_+	cd01143, YvrC, Periplasmic binding protein YvrC	NA|317aa|down_1|NZ_LT992467.1_2060081_2061032_+	pfam01032, FecCD, FecCD transport family	NA|240aa|down_2|NZ_LT992467.1_2061086_2061806_+	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|267aa|down_3|NZ_LT992467.1_2061789_2062590_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|169aa|down_4|NZ_LT992467.1_2062725_2063232_+	NA	NA|239aa|down_5|NZ_LT992467.1_2063393_2064110_+	NA	NA|263aa|down_6|NZ_LT992467.1_2064278_2065067_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|125aa|down_7|NZ_LT992467.1_2065318_2065693_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|310aa|down_8|NZ_LT992467.1_2066640_2067570_-	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|75aa|down_9|NZ_LT992467.1_2067762_2067987_-	pfam11148, DUF2922, Protein of unknown function (DUF2922)
GCF_900324295.1_16_LA_309	NZ_LT992467	Staphylococcus aureus isolate 16_LA_309 chromosome I	10	2221033-2221115	10	CRISPRCasFinder	no		DinG,cas3,csa3,DEDDh,TnsE_C,WYL	Orphan	CACCCCAACTCGCATTGCTTGTAGAA	26	1	25	2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089|2221059-2221089	NZ_LT992467.1_518587-518617|NZ_LT992467.1_518697-518727|NZ_LT992467.1_634844-634874|NZ_LT992467.1_2358568-2358538|NZ_LT992467.1_2397369-2397399|NZ_LT992467.1_328710-328680|NZ_LT992467.1_420828-420798|NZ_LT992467.1_886738-886768|NZ_LT992467.1_933194-933164|NZ_LT992467.1_1669113-1669143|NZ_LT992467.1_1669171-1669201|NZ_LT992467.1_1764190-1764160|NZ_LT992467.1_2050381-2050351|NZ_LT992467.1_2174746-2174716|NZ_LT992467.1_2267310-2267340|NZ_LT992467.1_2491668-2491698|NZ_LT992467.1_2591986-2591956|NZ_LT992467.1_2592040-2592010|NZ_LT992467.1_897486-897516|NZ_LT992467.1_897541-897571|NZ_LT992467.1_1336611-1336641|NZ_LT992467.1_2230040-2230070|NZ_LT992467.1_2271448-2271418|NZ_LT992467.1_2800861-2800891|NZ_LT992467.1_2846951-2846981	NA	1	1	Orphan	DinG,cas3,csa3,DEDDh,TnsE_C,WYL	NA,NA	NA|280aa|up_9|NZ_LT992467.1_2208282_2209122_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|217aa|up_8|NZ_LT992467.1_2209295_2209946_+	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|79aa|up_7|NZ_LT992467.1_2209942_2210179_+	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|662aa|up_6|NZ_LT992467.1_2210447_2212433_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|949aa|up_5|NZ_LT992467.1_2212440_2215287_+	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|311aa|up_4|NZ_LT992467.1_2215896_2216829_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|280aa|up_3|NZ_LT992467.1_2216834_2217674_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|162aa|up_2|NZ_LT992467.1_2217681_2218167_+	cd04647, LbH_MAT_like, Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins	NA|480aa|up_1|NZ_LT992467.1_2218174_2219614_+	sd00006, TPR, Tetratricopeptide repeat	NA|312aa|up_0|NZ_LT992467.1_2219680_2220616_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|304aa|down_0|NZ_LT992467.1_2221383_2222295_+	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|332aa|down_1|NZ_LT992467.1_2222291_2223287_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|315aa|down_2|NZ_LT992467.1_2223395_2224340_+	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|196aa|down_3|NZ_LT992467.1_2224909_2225497_+	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|545aa|down_4|NZ_LT992467.1_2225679_2227314_+	PRK13529, PRK13529, oxaloacetate-decarboxylating malate dehydrogenase	NA|301aa|down_5|NZ_LT992467.1_2227520_2228423_-	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|210aa|down_6|NZ_LT992467.1_2229125_2229755_+	PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed	NA|338aa|down_7|NZ_LT992467.1_2230529_2231543_+	COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]	NA|337aa|down_8|NZ_LT992467.1_2231595_2232606_+	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I	NA|397aa|down_9|NZ_LT992467.1_2232744_2233935_+	PRK00073, pgk, phosphoglycerate kinase; Provisional
GCF_900324295.1_16_LA_309	NZ_LT992467	Staphylococcus aureus isolate 16_LA_309 chromosome I	11	2271717-2271797	11	CRISPRCasFinder	no		DinG,cas3,csa3,DEDDh,TnsE_C,WYL	Orphan	TCTTTATCATTTCTGTCCCACTCCC	25	1	1	2271742-2271772	NZ_LT992467.1_2215486-2215456	NA	1	1	Orphan	DinG,cas3,csa3,DEDDh,TnsE_C,WYL	NA,NA|81aa|down_8|NZ_LT992467.1_2280255_2280498_-	NA|180aa|up_9|NZ_LT992467.1_2263847_2264387_+	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|107aa|up_8|NZ_LT992467.1_2264536_2264857_-	cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains	NA|119aa|up_7|NZ_LT992467.1_2265000_2265357_+	cd03036, ArsC_like, Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC	NA|127aa|up_6|NZ_LT992467.1_2265514_2265895_+	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|293aa|up_5|NZ_LT992467.1_2266074_2266953_+	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|129aa|up_4|NZ_LT992467.1_2267654_2268041_+	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|99aa|up_3|NZ_LT992467.1_2268033_2268330_+	cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains	NA|342aa|up_2|NZ_LT992467.1_2268579_2269605_+	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|232aa|up_1|NZ_LT992467.1_2269597_2270293_+	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|274aa|up_0|NZ_LT992467.1_2270310_2271132_+	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|65aa|down_0|NZ_LT992467.1_2271939_2272134_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|284aa|down_1|NZ_LT992467.1_2272367_2273219_-	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|254aa|down_2|NZ_LT992467.1_2273546_2274308_+	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|436aa|down_3|NZ_LT992467.1_2274406_2275714_+	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|417aa|down_4|NZ_LT992467.1_2275819_2277070_+	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|155aa|down_5|NZ_LT992467.1_2277059_2277524_+	TIGR01994, Iron-sulfur_cluster_assembly_scaffold_protein_IscU, SUF system FeS assembly protein, NifU family	NA|466aa|down_6|NZ_LT992467.1_2277674_2279072_+	TIGR01980, UPF0051_protein_slr0074, FeS assembly protein SufB	NA|350aa|down_7|NZ_LT992467.1_2279139_2280189_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|81aa|down_8|NZ_LT992467.1_2280255_2280498_-	NA	NA|328aa|down_9|NZ_LT992467.1_2280508_2281492_-	pfam00535, Glycos_transf_2, Glycosyl transferase family 2
