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_003029645.1_ASM302964v1	NZ_CP028163	Staphylococcus aureus strain CFSAN064038 chromosome, complete genome	1	739845-739978	1	PILER-CR	no		csa3,WYL,TnsE_C,DEDDh,cas3,DinG	Orphan	TATTGAAGAAGATACAA	17	0	0	NA	NA	NA	2	2	Orphan	csa3,WYL,TnsE_C,DEDDh,cas3,DinG	NA,NA|103aa|down_1|NZ_CP028163.1_745112_745421_-,NA|89aa|down_2|NZ_CP028163.1_745564_745831_-	NA|388aa|up_9|NZ_CP028163.1_724158_725322_+	cd17474, MFS_YfmO_like, Bacillus subtilis multidrug efflux protein YfmO and similar transporters of the Major Facilitator Superfamily	NA|204aa|up_8|NZ_CP028163.1_725419_726031_-	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|426aa|up_7|NZ_CP028163.1_726577_727855_+	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|608aa|up_6|NZ_CP028163.1_728766_730590_+	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|139aa|up_5|NZ_CP028163.1_730728_731145_+	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|231aa|up_4|NZ_CP028163.1_731375_732068_+	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|255aa|up_3|NZ_CP028163.1_732232_732997_+	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|226aa|up_2|NZ_CP028163.1_733153_733831_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|518aa|up_1|NZ_CP028163.1_733855_735409_+	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|453aa|up_0|NZ_CP028163.1_735525_736884_+	TIGR00791, Gluconate_permease, gluconate transporter	NA|289aa|down_0|NZ_CP028163.1_744120_744987_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|103aa|down_1|NZ_CP028163.1_745112_745421_-	NA	NA|89aa|down_2|NZ_CP028163.1_745564_745831_-	NA	NA|584aa|down_3|NZ_CP028163.1_746114_747866_-	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|398aa|down_4|NZ_CP028163.1_747941_749135_-	TIGR00675, Modification_methylase, DNA-methyltransferase (dcm)	NA|310aa|down_5|NZ_CP028163.1_749230_750160_+	pfam09019, EcoRII-C, EcoRII C terminal	NA|258aa|down_6|NZ_CP028163.1_750402_751176_+	pfam04507, DUF576, Csa1 family	NA|255aa|down_7|NZ_CP028163.1_751287_752052_+	pfam04507, DUF576, Csa1 family	NA|262aa|down_8|NZ_CP028163.1_752299_753085_+	pfam04507, DUF576, Csa1 family	NA|452aa|down_9|NZ_CP028163.1_753081_754437_+	cd00519, Lipase_3, Lipase (class 3)
GCF_003029645.1_ASM302964v1	NZ_CP028163	Staphylococcus aureus strain CFSAN064038 chromosome, complete genome	2	743389-743522	2	PILER-CR	no		csa3,WYL,TnsE_C,DEDDh,cas3,DinG	Orphan	TATTGAAGAAGATACAA	17	0	0	NA	NA	NA	2	2	Orphan	csa3,WYL,TnsE_C,DEDDh,cas3,DinG	NA,NA|103aa|down_1|NZ_CP028163.1_745112_745421_-,NA|89aa|down_2|NZ_CP028163.1_745564_745831_-	NA|204aa|up_9|NZ_CP028163.1_725419_726031_-	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|426aa|up_8|NZ_CP028163.1_726577_727855_+	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|608aa|up_7|NZ_CP028163.1_728766_730590_+	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|139aa|up_6|NZ_CP028163.1_730728_731145_+	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|231aa|up_5|NZ_CP028163.1_731375_732068_+	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|255aa|up_4|NZ_CP028163.1_732232_732997_+	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|226aa|up_3|NZ_CP028163.1_733153_733831_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|518aa|up_2|NZ_CP028163.1_733855_735409_+	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|453aa|up_1|NZ_CP028163.1_735525_736884_+	TIGR00791, Gluconate_permease, gluconate transporter	NA|1018aa|up_0|NZ_CP028163.1_737352_740406_+	pfam10425, SdrG_C_C, C-terminus of bacterial fibrinogen-binding adhesin	NA|289aa|down_0|NZ_CP028163.1_744120_744987_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|103aa|down_1|NZ_CP028163.1_745112_745421_-	NA	NA|89aa|down_2|NZ_CP028163.1_745564_745831_-	NA	NA|584aa|down_3|NZ_CP028163.1_746114_747866_-	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|398aa|down_4|NZ_CP028163.1_747941_749135_-	TIGR00675, Modification_methylase, DNA-methyltransferase (dcm)	NA|310aa|down_5|NZ_CP028163.1_749230_750160_+	pfam09019, EcoRII-C, EcoRII C terminal	NA|258aa|down_6|NZ_CP028163.1_750402_751176_+	pfam04507, DUF576, Csa1 family	NA|255aa|down_7|NZ_CP028163.1_751287_752052_+	pfam04507, DUF576, Csa1 family	NA|262aa|down_8|NZ_CP028163.1_752299_753085_+	pfam04507, DUF576, Csa1 family	NA|452aa|down_9|NZ_CP028163.1_753081_754437_+	cd00519, Lipase_3, Lipase (class 3)
GCF_003029645.1_ASM302964v1	NZ_CP028163	Staphylococcus aureus strain CFSAN064038 chromosome, complete genome	3	767986-768080	1	CRISPRCasFinder	no		csa3,WYL,TnsE_C,DEDDh,cas3,DinG	Orphan	TTGCTTCGCAACAACTGCATAAGAGCCT	28	0	0	NA	NA	NA	1	1	Orphan	csa3,WYL,TnsE_C,DEDDh,cas3,DinG	NA|105aa|up_8|NZ_CP028163.1_759827_760142_-,NA|121aa|up_0|NZ_CP028163.1_766954_767317_+,NA|249aa|down_9|NZ_CP028163.1_777747_778494_-	NA|140aa|up_9|NZ_CP028163.1_757531_757951_+	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|105aa|up_8|NZ_CP028163.1_759827_760142_-	NA	NA|403aa|up_7|NZ_CP028163.1_760147_761356_-	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|128aa|up_6|NZ_CP028163.1_761422_761806_+	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|137aa|up_5|NZ_CP028163.1_762260_762671_+	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|133aa|up_4|NZ_CP028163.1_762697_763096_+	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|141aa|up_3|NZ_CP028163.1_763567_763990_+	COG2128, COG2128, Uncharacterized conserved protein [Function unknown]	NA|513aa|up_2|NZ_CP028163.1_764101_765640_-	pfam03806, ABG_transport, AbgT putative transporter family	NA|273aa|up_1|NZ_CP028163.1_765873_766692_+	PRK08589, PRK08589, SDR family oxidoreductase	NA|121aa|up_0|NZ_CP028163.1_766954_767317_+	NA	NA|274aa|down_0|NZ_CP028163.1_768265_769087_+	COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and metabolism]	NA|273aa|down_1|NZ_CP028163.1_769097_769916_+	cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family	NA|434aa|down_2|NZ_CP028163.1_769908_771210_+	COG4408, COG4408, Uncharacterized protein conserved in bacteria [Function unknown]	NA|533aa|down_3|NZ_CP028163.1_771352_772951_+	TIGR02294, Nickel-binding_periplasmic_protein, nickel ABC transporter, nickel/metallophore periplasmic binding protein	NA|312aa|down_4|NZ_CP028163.1_772963_773899_+	COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|290aa|down_5|NZ_CP028163.1_773895_774765_+	COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|272aa|down_6|NZ_CP028163.1_774761_775577_+	COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|250aa|down_7|NZ_CP028163.1_775569_776319_+	COG1124, DppF, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|398aa|down_8|NZ_CP028163.1_776330_777524_+	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|249aa|down_9|NZ_CP028163.1_777747_778494_-	NA
GCF_003029645.1_ASM302964v1	NZ_CP028163	Staphylococcus aureus strain CFSAN064038 chromosome, complete genome	4	812333-812411	2	CRISPRCasFinder	no		csa3,WYL,TnsE_C,DEDDh,cas3,DinG	Orphan	TGCAAGTTGGCGGGGCCCCAACA	23	1	1	812356-812388	NZ_CP028163.1_195159-195127	NA	1	1	Orphan	csa3,WYL,TnsE_C,DEDDh,cas3,DinG	NA|220aa|up_3|NZ_CP028163.1_809257_809917_-,NA|36aa|up_0|NZ_CP028163.1_811905_812013_+,NA|56aa|down_2|NZ_CP028163.1_816468_816636_+	NA|693aa|up_9|NZ_CP028163.1_801713_803792_-	COG0025, NhaP, NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]	NA|470aa|up_8|NZ_CP028163.1_803929_805339_-	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|269aa|up_7|NZ_CP028163.1_805624_806431_+	TIGR03729, acc_ester, putative phosphoesterase	NA|219aa|up_6|NZ_CP028163.1_806493_807150_-	COG4990, COG4990, Uncharacterized protein conserved in bacteria [Function unknown]	NA|158aa|up_5|NZ_CP028163.1_807262_807736_+	COG3708, COG3708, Uncharacterized protein conserved in bacteria [Function unknown]	NA|404aa|up_4|NZ_CP028163.1_807858_809070_-	cd17320, MFS_MdfA_MDR_like, Multidrug transporter MdfA and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily	NA|220aa|up_3|NZ_CP028163.1_809257_809917_-	NA	NA|381aa|up_2|NZ_CP028163.1_809976_811119_-	TIGR00045, Glycerate_kinase, glycerate kinase	NA|129aa|up_1|NZ_CP028163.1_811385_811772_+	COG2246, COG2246, Predicted membrane protein [Function unknown]	NA|36aa|up_0|NZ_CP028163.1_811905_812013_+	NA	NA|588aa|down_0|NZ_CP028163.1_812716_814480_+	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|578aa|down_1|NZ_CP028163.1_814504_816238_+	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|56aa|down_2|NZ_CP028163.1_816468_816636_+	NA	NA|229aa|down_3|NZ_CP028163.1_816690_817377_+	COG0132, BioD, Dethiobiotin synthetase [Coenzyme metabolism]	NA|453aa|down_4|NZ_CP028163.1_817354_818713_+	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase	NA|336aa|down_5|NZ_CP028163.1_818714_819722_+	PRK06256, PRK06256, biotin synthase; Validated	NA|372aa|down_6|NZ_CP028163.1_819699_820815_+	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|231aa|down_7|NZ_CP028163.1_820825_821518_+	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|156aa|down_8|NZ_CP028163.1_821528_821996_+	pfam06177, QueT, QueT transporter	NA|326aa|down_9|NZ_CP028163.1_822047_823025_-	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin
GCF_003029645.1_ASM302964v1	NZ_CP028163	Staphylococcus aureus strain CFSAN064038 chromosome, complete genome	5	827710-827804	3	CRISPRCasFinder	no		csa3,WYL,TnsE_C,DEDDh,cas3,DinG	Orphan	GCCTTTCTAACAAATAAATTTGAAGAA	27	0	0	NA	NA	NA	1	1	Orphan	csa3,WYL,TnsE_C,DEDDh,cas3,DinG	NA|40aa|up_0|NZ_CP028163.1_827411_827531_+,NA|35aa|down_2|NZ_CP028163.1_829978_830083_-	NA|453aa|up_9|NZ_CP028163.1_817354_818713_+	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase	NA|336aa|up_8|NZ_CP028163.1_818714_819722_+	PRK06256, PRK06256, biotin synthase; Validated	NA|372aa|up_7|NZ_CP028163.1_819699_820815_+	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|231aa|up_6|NZ_CP028163.1_820825_821518_+	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|156aa|up_5|NZ_CP028163.1_821528_821996_+	pfam06177, QueT, QueT transporter	NA|326aa|up_4|NZ_CP028163.1_822047_823025_-	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|316aa|up_3|NZ_CP028163.1_823026_823974_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|310aa|up_2|NZ_CP028163.1_824541_825471_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|437aa|up_1|NZ_CP028163.1_826006_827317_-	pfam11621, Sbi-IV, C3 binding domain 4 of IgG-bind protein SBI	NA|40aa|up_0|NZ_CP028163.1_827411_827531_+	NA	NA|289aa|down_0|NZ_CP028163.1_827945_828812_+	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|229aa|down_1|NZ_CP028163.1_829138_829825_+	PRK14119, gpmA, phosphoglyceromutase; Provisional	NA|35aa|down_2|NZ_CP028163.1_829978_830083_-	NA	NA|480aa|down_3|NZ_CP028163.1_830256_831696_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|260aa|down_4|NZ_CP028163.1_831816_832596_+	cd13711, PBP2_Ngo0372_TcyA, Substrate binding domain of ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold	NA|240aa|down_5|NZ_CP028163.1_832576_833296_+	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|244aa|down_6|NZ_CP028163.1_833292_834024_+	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|417aa|down_7|NZ_CP028163.1_834120_835371_-	pfam02388, FemAB, FemAB family	NA|121aa|down_8|NZ_CP028163.1_835625_835988_+	pfam14729, DUF4467, Domain of unknown function with cystatin-like fold (DUF4467)	NA|200aa|down_9|NZ_CP028163.1_836006_836606_+	COG1651, DsbG, Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]
GCF_003029645.1_ASM302964v1	NZ_CP028163	Staphylococcus aureus strain CFSAN064038 chromosome, complete genome	6	944136-944221	4	CRISPRCasFinder	no	WYL	csa3,WYL,TnsE_C,DEDDh,cas3,DinG	Unclear	CCAACTTGCACATTATTGTAAGCTGACTTT	30	1	5	944166-944191|944166-944191|944166-944191|944166-944191|944166-944191	NZ_CP028163.1_2469668-2469643|NZ_CP028163.1_1153770-1153795|NZ_CP028163.1_1930849-1930874|NZ_CP028163.1_2377397-2377422|NZ_CP028163.1_2465498-2465523	NA	1	1	Orphan	csa3,WYL,TnsE_C,DEDDh,cas3,DinG	NA|110aa|up_8|NZ_CP028163.1_934533_934863_-,NA|78aa|up_1|NZ_CP028163.1_942951_943185_+,NA|65aa|down_6|NZ_CP028163.1_951281_951476_+	NA|291aa|up_9|NZ_CP028163.1_933216_934089_-	COG1737, RpiR, Transcriptional regulators [Transcription]	NA|110aa|up_8|NZ_CP028163.1_934533_934863_-	NA	NA|246aa|up_7|NZ_CP028163.1_934911_935649_+	pfam02517, Abi, CAAX protease self-immunity	WYL|231aa|up_6|NZ_CP028163.1_935673_936366_-	COG2378, COG2378, Predicted transcriptional regulator [Transcription]	NA|266aa|up_5|NZ_CP028163.1_936750_937548_+	COG0483, SuhB, Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]	NA|316aa|up_4|NZ_CP028163.1_937680_938628_+	PRK09379, PRK09379, LytR family transcriptional regulator	NA|985aa|up_3|NZ_CP028163.1_939229_942184_+	COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General function prediction only]	NA|158aa|up_2|NZ_CP028163.1_942183_942657_+	COG2427, COG2427, Uncharacterized conserved protein [Function unknown]	NA|78aa|up_1|NZ_CP028163.1_942951_943185_+	NA	NA|259aa|up_0|NZ_CP028163.1_943206_943983_+	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|375aa|down_0|NZ_CP028163.1_944591_945716_+	PRK06753, PRK06753, hypothetical protein; Provisional	NA|318aa|down_1|NZ_CP028163.1_945807_946761_-	cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains	NA|167aa|down_2|NZ_CP028163.1_947123_947624_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|141aa|down_3|NZ_CP028163.1_947860_948283_-	COG3296, COG3296, Uncharacterized protein conserved in bacteria [Function unknown]	NA|361aa|down_4|NZ_CP028163.1_948530_949613_+	pfam02317, Octopine_DH, NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain	NA|467aa|down_5|NZ_CP028163.1_949707_951108_+	TIGR00931, Uncharacterized_Na+/H+_antiporter_HI_1107, Na+/H+ antiporter NhaC	NA|65aa|down_6|NZ_CP028163.1_951281_951476_+	NA	NA|270aa|down_7|NZ_CP028163.1_951544_952354_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|248aa|down_8|NZ_CP028163.1_954936_955680_+	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|109aa|down_9|NZ_CP028163.1_955743_956070_+	pfam14470, bPH_3, Bacterial PH domain
GCF_003029645.1_ASM302964v1	NZ_CP028163	Staphylococcus aureus strain CFSAN064038 chromosome, complete genome	7	1109126-1109276	5	CRISPRCasFinder	no	TnsE_C,csa3	csa3,WYL,TnsE_C,DEDDh,cas3,DinG	Type I-A	TGCATAAGAGCCCCTTACAACTAAAGTT	28	0	0	NA	NA	NA	2	2	Orphan	csa3,WYL,TnsE_C,DEDDh,cas3,DinG	NA|31aa|up_2|NZ_CP028163.1_1107325_1107418_-,NA|53aa|up_1|NZ_CP028163.1_1107853_1108012_-,NA|35aa|up_0|NZ_CP028163.1_1108691_1108796_+,NA|364aa|down_0|NZ_CP028163.1_1109293_1110385_-,NA|77aa|down_5|NZ_CP028163.1_1114172_1114403_+	TnsE_C|135aa|up_9|NZ_CP028163.1_1101086_1101491_+	pfam18623, TnsE_C, TnsE C-terminal domain	NA|97aa|up_8|NZ_CP028163.1_1101615_1101906_+	pfam11867, DUF3387, Domain of unknown function (DUF3387)	NA|490aa|up_7|NZ_CP028163.1_1101965_1103435_+	pfam18185, STALD, Sir2- and TIR-associating SLOG family	NA|345aa|up_6|NZ_CP028163.1_1103528_1104563_+	pfam13676, TIR_2, TIR domain	NA|203aa|up_5|NZ_CP028163.1_1104590_1105199_+	pfam08937, DUF1863, MTH538 TIR-like domain (DUF1863)	NA|261aa|up_4|NZ_CP028163.1_1105488_1106271_+	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|286aa|up_3|NZ_CP028163.1_1106338_1107196_+	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|31aa|up_2|NZ_CP028163.1_1107325_1107418_-	NA	NA|53aa|up_1|NZ_CP028163.1_1107853_1108012_-	NA	NA|35aa|up_0|NZ_CP028163.1_1108691_1108796_+	NA	NA|364aa|down_0|NZ_CP028163.1_1109293_1110385_-	NA	NA|327aa|down_1|NZ_CP028163.1_1110650_1111631_-	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	csa3|107aa|down_2|NZ_CP028163.1_1111632_1111953_-	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|222aa|down_3|NZ_CP028163.1_1112104_1112770_+	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	NA|313aa|down_4|NZ_CP028163.1_1113203_1114142_+	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|77aa|down_5|NZ_CP028163.1_1114172_1114403_+	NA	NA|458aa|down_6|NZ_CP028163.1_1115074_1116448_+	pfam01878, EVE, EVE domain	NA|138aa|down_7|NZ_CP028163.1_1116905_1117319_+	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|148aa|down_8|NZ_CP028163.1_1117518_1117962_+	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|237aa|down_9|NZ_CP028163.1_1118082_1118793_-	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase
GCF_003029645.1_ASM302964v1	NZ_CP028163	Staphylococcus aureus strain CFSAN064038 chromosome, complete genome	8	1164695-1164907	6	CRISPRCasFinder	no		csa3,WYL,TnsE_C,DEDDh,cas3,DinG	Orphan	CATCAAAGTAGCATGGCATGACACCAAGCTTCCACAACAGCACATCA	47	0	0	NA	NA	NA	2	2	Orphan	csa3,WYL,TnsE_C,DEDDh,cas3,DinG	NA|107aa|up_0|NZ_CP028163.1_1164340_1164661_-,NA|46aa|down_4|NZ_CP028163.1_1167907_1168045_+	NA|147aa|up_9|NZ_CP028163.1_1155813_1156254_+	PRK00006, fabZ, 3-hydroxyacyl-ACP dehydratase FabZ	NA|147aa|up_8|NZ_CP028163.1_1156310_1156751_-	pfam14183, YwpF, YwpF-like protein	NA|132aa|up_7|NZ_CP028163.1_1156944_1157340_+	pfam00436, SSB, Single-strand binding protein family	NA|232aa|up_6|NZ_CP028163.1_1157728_1158424_+	pfam06737, Transglycosylas, Transglycosylase-like domain	NA|230aa|up_5|NZ_CP028163.1_1158810_1159500_+	TIGR04306, salvage_TenA, thiaminase II	NA|277aa|up_4|NZ_CP028163.1_1159492_1160323_+	PRK06427, PRK06427, bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed	NA|264aa|up_3|NZ_CP028163.1_1160306_1161098_+	PRK09355, PRK09355, hydroxyethylthiazole kinase; Validated	NA|214aa|up_2|NZ_CP028163.1_1161099_1161741_+	PRK00043, thiE, thiamine phosphate synthase	NA|291aa|up_1|NZ_CP028163.1_1161826_1162699_+	PRK02463, PRK02463, OxaA-like protein precursor; Provisional	NA|107aa|up_0|NZ_CP028163.1_1164340_1164661_-	NA	NA|216aa|down_0|NZ_CP028163.1_1164940_1165588_-	COG1418, COG1418, Predicted HD superfamily hydrolase [General function prediction only]	NA|495aa|down_1|NZ_CP028163.1_1165615_1167100_-	TIGR04265, bac_cardiolipin, cardiolipin synthase	NA|98aa|down_2|NZ_CP028163.1_1167265_1167559_+	cd10152, SaCsoR-like_DUF156, Staphylococcus aureus copper-sensitive operon repressor (CsoR), and related domains; this family was previously known as part of DUF156	NA|70aa|down_3|NZ_CP028163.1_1167570_1167780_+	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|46aa|down_4|NZ_CP028163.1_1167907_1168045_+	NA	NA|401aa|down_5|NZ_CP028163.1_1168308_1169511_-	TIGR02210, Rod_shape-determining_protein_RodA, rod shape-determining protein RodA	NA|357aa|down_6|NZ_CP028163.1_1169828_1170899_+	PRK01966, ddl, D-alanine--D-alanine ligase	NA|452aa|down_7|NZ_CP028163.1_1170913_1172269_+	COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]	NA|507aa|down_8|NZ_CP028163.1_1172784_1174305_+	COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]	NA|232aa|down_9|NZ_CP028163.1_1174657_1175353_-	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]
GCF_003029645.1_ASM302964v1	NZ_CP028163	Staphylococcus aureus strain CFSAN064038 chromosome, complete genome	9	1527174-1527256	7	CRISPRCasFinder	no		csa3,WYL,TnsE_C,DEDDh,cas3,DinG	Orphan	GTAAGCTGACTTTTTCGTCAGCTTC	25	0	0	NA	NA	NA	1	1	Orphan	csa3,WYL,TnsE_C,DEDDh,cas3,DinG	NA,NA	NA|383aa|up_9|NZ_CP028163.1_1516697_1517846_+	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]	NA|408aa|up_8|NZ_CP028163.1_1517845_1519069_+	PRK01565, PRK01565, thiamine biosynthesis protein ThiI; Provisional	NA|257aa|up_7|NZ_CP028163.1_1519112_1519883_+	PRK10621, PRK10621, hypothetical protein; Provisional	NA|165aa|up_6|NZ_CP028163.1_1519980_1520475_+	PRK00522, tpx, thiol peroxidase	NA|316aa|up_5|NZ_CP028163.1_1520597_1521545_+	COG0827, COG0827, Adenine-specific DNA methylase [DNA replication, recombination, and repair]	NA|401aa|up_4|NZ_CP028163.1_1521632_1522835_+	PRK00180, PRK00180, acetate kinase A/propionate kinase 2; Reviewed	NA|167aa|up_3|NZ_CP028163.1_1523081_1523582_-	pfam00582, Usp, Universal stress protein family	NA|373aa|up_2|NZ_CP028163.1_1523722_1524841_+	cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic domains	NA|352aa|up_1|NZ_CP028163.1_1525156_1526212_-	COG0006, PepP, Xaa-Pro aminopeptidase [Amino acid transport and metabolism]	NA|230aa|up_0|NZ_CP028163.1_1526386_1527076_+	PRK00685, PRK00685, metal-dependent hydrolase; Provisional	NA|138aa|down_0|NZ_CP028163.1_1527581_1527995_-	pfam00582, Usp, Universal stress protein family	NA|433aa|down_1|NZ_CP028163.1_1528199_1529498_+	COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]	NA|314aa|down_2|NZ_CP028163.1_1529866_1530808_+	COG0618, COG0618, Exopolyphosphatase-related proteins [General function prediction only]	NA|1066aa|down_3|NZ_CP028163.1_1530828_1534026_+	COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]	NA|410aa|down_4|NZ_CP028163.1_1534474_1535704_+	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|286aa|down_5|NZ_CP028163.1_1535898_1536756_+	PRK05654, PRK05654, acetyl-CoA carboxylase carboxyltransferase subunit beta	NA|315aa|down_6|NZ_CP028163.1_1536755_1537700_+	PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated	NA|323aa|down_7|NZ_CP028163.1_1537968_1538937_+	PRK03202, PRK03202, ATP-dependent 6-phosphofructokinase	NA|586aa|down_8|NZ_CP028163.1_1538958_1540716_+	PRK06354, PRK06354, pyruvate kinase; Provisional	NA|454aa|down_9|NZ_CP028163.1_1541059_1542421_-	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]
GCF_003029645.1_ASM302964v1	NZ_CP028163	Staphylococcus aureus strain CFSAN064038 chromosome, complete genome	10	2062860-2062952	8	CRISPRCasFinder	no	cas3	csa3,WYL,TnsE_C,DEDDh,cas3,DinG	Unclear	AGTTATCAATTTATTGATTACTGTTTCTTA	30	0	0	NA	NA	NA	1	1	Unclear	csa3,WYL,TnsE_C,DEDDh,cas3,DinG	NA,NA	NA|117aa|up_9|NZ_CP028163.1_2052423_2052774_-	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|246aa|up_8|NZ_CP028163.1_2052876_2053614_-	PRK00026, trmD, tRNA (guanine-N(1)-)-methyltransferase; Reviewed	NA|168aa|up_7|NZ_CP028163.1_2053613_2054117_-	PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional	NA|92aa|up_6|NZ_CP028163.1_2054304_2054580_-	COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]	NA|456aa|up_5|NZ_CP028163.1_2055014_2056382_-	PRK10867, PRK10867, signal recognition particle protein; Provisional	NA|111aa|up_4|NZ_CP028163.1_2056407_2056740_-	PRK00118, PRK00118, putative DNA-binding protein; Validated	NA|417aa|up_3|NZ_CP028163.1_2056726_2057977_-	PRK10416, PRK10416, signal recognition particle-docking protein FtsY; Provisional	NA|1189aa|up_2|NZ_CP028163.1_2057976_2061543_-	COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	NA|244aa|up_1|NZ_CP028163.1_2061689_2062421_-	PRK00102, rnc, ribonuclease III; Reviewed	NA|78aa|up_0|NZ_CP028163.1_2062536_2062770_-	PRK00982, acpP, acyl carrier protein; Provisional	NA|245aa|down_0|NZ_CP028163.1_2063075_2063810_-	PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Validated	NA|309aa|down_1|NZ_CP028163.1_2063802_2064729_-	COG0331, FabD, (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]	NA|329aa|down_2|NZ_CP028163.1_2064721_2065708_-	PRK05331, PRK05331, phosphate acyltransferase PlsX	NA|191aa|down_3|NZ_CP028163.1_2065712_2066285_-	PRK04424, PRK04424, transcription factor FapR	cas3|687aa|down_4|NZ_CP028163.1_2066487_2068548_-	PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional	NA|549aa|down_5|NZ_CP028163.1_2068737_2070384_-	COG1461, COG1461, Predicted kinase related to dihydroxyacetone kinase [General function prediction only]	NA|125aa|down_6|NZ_CP028163.1_2070398_2070773_-	COG1302, COG1302, Uncharacterized protein conserved in bacteria [Function unknown]	NA|63aa|down_7|NZ_CP028163.1_2071215_2071404_+	PRK00359, rpmB, 50S ribosomal protein L28; Reviewed	NA|214aa|down_8|NZ_CP028163.1_2071784_2072426_-	COG1564, THI80, Thiamine pyrophosphokinase [Coenzyme metabolism]	NA|215aa|down_9|NZ_CP028163.1_2072432_2073077_-	COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]
GCF_003029645.1_ASM302964v1	NZ_CP028163	Staphylococcus aureus strain CFSAN064038 chromosome, complete genome	11	2465245-2465325	9	CRISPRCasFinder	no		csa3,WYL,TnsE_C,DEDDh,cas3,DinG	Orphan	GGGAGTGGGAGAGAAATGATAAAGA	25	1	1	2465270-2465300	NZ_CP028163.1_2520254-2520224	NA	1	1	Orphan	csa3,WYL,TnsE_C,DEDDh,cas3,DinG	NA|311aa|up_9|NZ_CP028163.1_2455648_2456581_+,NA	NA|311aa|up_9|NZ_CP028163.1_2455648_2456581_+	NA	NA|60aa|up_8|NZ_CP028163.1_2456560_2456740_-	PLN02296, PLN02296, carbonate dehydratase	NA|350aa|up_7|NZ_CP028163.1_2456852_2457902_+	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|466aa|up_6|NZ_CP028163.1_2457969_2459367_-	TIGR01980, UPF0051_protein_slr0074, FeS assembly protein SufB	NA|155aa|up_5|NZ_CP028163.1_2459517_2459982_-	TIGR01994, Iron-sulfur_cluster_assembly_scaffold_protein_IscU, SUF system FeS assembly protein, NifU family	NA|417aa|up_4|NZ_CP028163.1_2459971_2461222_-	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|436aa|up_3|NZ_CP028163.1_2461327_2462635_-	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|254aa|up_2|NZ_CP028163.1_2462733_2463495_-	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|284aa|up_1|NZ_CP028163.1_2463822_2464674_+	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|65aa|up_0|NZ_CP028163.1_2464907_2465102_-	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|274aa|down_0|NZ_CP028163.1_2465909_2466731_-	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|232aa|down_1|NZ_CP028163.1_2466748_2467444_-	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|342aa|down_2|NZ_CP028163.1_2467436_2468462_-	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|99aa|down_3|NZ_CP028163.1_2468711_2469008_-	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|129aa|down_4|NZ_CP028163.1_2469000_2469387_-	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|293aa|down_5|NZ_CP028163.1_2470088_2470967_-	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|127aa|down_6|NZ_CP028163.1_2471146_2471527_-	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|119aa|down_7|NZ_CP028163.1_2471684_2472041_-	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|107aa|down_8|NZ_CP028163.1_2472184_2472505_+	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|180aa|down_9|NZ_CP028163.1_2472654_2473194_-	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA
GCF_003029645.1_ASM302964v1	NZ_CP028163	Staphylococcus aureus strain CFSAN064038 chromosome, complete genome	12	2676855-2676963	10	CRISPRCasFinder	no		csa3,WYL,TnsE_C,DEDDh,cas3,DinG	Orphan	TTTATGCAGTTGTGCGGTAGCATCCAACTGCGTTCCTTT	39	0	0	NA	NA	NA	1	1	Orphan	csa3,WYL,TnsE_C,DEDDh,cas3,DinG	NA|239aa|up_5|NZ_CP028163.1_2671736_2672453_-,NA|169aa|up_4|NZ_CP028163.1_2672614_2673121_-,NA	NA|75aa|up_9|NZ_CP028163.1_2667859_2668084_+	pfam11148, DUF2922, Protein of unknown function (DUF2922)	NA|310aa|up_8|NZ_CP028163.1_2668276_2669206_+	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|125aa|up_7|NZ_CP028163.1_2670153_2670528_+	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|263aa|up_6|NZ_CP028163.1_2670779_2671568_-	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|239aa|up_5|NZ_CP028163.1_2671736_2672453_-	NA	NA|169aa|up_4|NZ_CP028163.1_2672614_2673121_-	NA	NA|267aa|up_3|NZ_CP028163.1_2673256_2674057_-	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|240aa|up_2|NZ_CP028163.1_2674040_2674760_-	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|317aa|up_1|NZ_CP028163.1_2674814_2675765_-	pfam01032, FecCD, FecCD transport family	NA|296aa|up_0|NZ_CP028163.1_2675915_2676803_-	cd01143, YvrC, Periplasmic binding protein YvrC	NA|212aa|down_0|NZ_CP028163.1_2677132_2677768_-	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|554aa|down_1|NZ_CP028163.1_2678252_2679914_-	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|139aa|down_2|NZ_CP028163.1_2679910_2680327_-	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|337aa|down_3|NZ_CP028163.1_2680602_2681613_-	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|174aa|down_4|NZ_CP028163.1_2682111_2682633_-	pfam08741, YwhD, YwhD family	NA|432aa|down_5|NZ_CP028163.1_2682660_2683956_-	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|159aa|down_6|NZ_CP028163.1_2683995_2684472_-	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|179aa|down_7|NZ_CP028163.1_2684641_2685178_-	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|313aa|down_8|NZ_CP028163.1_2685623_2686562_-	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|209aa|down_9|NZ_CP028163.1_2686831_2687458_-	pfam04276, DUF443, Protein of unknown function (DUF443)
