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_009913115.1_ASM991311v1	NZ_CP047803	Staphylococcus aureus strain UP_1097 chromosome, complete genome	1	393154-393234	1	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	AATTTCAACAGGCAATGCAAGTTGG	25	1	4	393179-393209|393179-393209|393179-393209|393179-393209	NZ_CP047803.1_1768503-1768473|NZ_CP047803.1_2697078-2697048|NZ_CP047803.1_1768391-1768361|NZ_CP047803.1_1768447-1768417	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|43aa|up_8|NZ_CP047803.1_385854_385983_+,NA|49aa|up_3|NZ_CP047803.1_389019_389166_+,NA	NA|589aa|up_9|NZ_CP047803.1_383756_385523_+	PRK00476, aspS, aspartyl-tRNA synthetase; Validated	NA|43aa|up_8|NZ_CP047803.1_385854_385983_+	NA	NA|258aa|up_7|NZ_CP047803.1_385982_386756_+	COG1179, COG1179, Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]	NA|425aa|up_6|NZ_CP047803.1_386916_388191_-	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|141aa|up_5|NZ_CP047803.1_388275_388698_+	COG1959, COG1959, Predicted transcriptional regulator [Transcription]	NA|61aa|up_4|NZ_CP047803.1_388797_388980_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|49aa|up_3|NZ_CP047803.1_389019_389166_+	NA	NA|338aa|up_2|NZ_CP047803.1_389402_390416_-	TIGR03558, oxido_grp_1, luciferase family oxidoreductase, group 1	NA|381aa|up_1|NZ_CP047803.1_390727_391870_+	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]	NA|373aa|up_0|NZ_CP047803.1_391870_392989_+	PRK00143, mnmA, tRNA-specific 2-thiouridylase MnmA; Reviewed	NA|223aa|down_0|NZ_CP047803.1_393505_394174_+	sd00006, TPR, Tetratricopeptide repeat	NA|826aa|down_1|NZ_CP047803.1_394175_396653_+	TIGR01448, recD_rel, helicase, putative, RecD/TraA family	NA|877aa|down_2|NZ_CP047803.1_396995_399626_+	PRK00252, alaS, alanyl-tRNA synthetase; Reviewed	NA|87aa|down_3|NZ_CP047803.1_399688_399949_+	PRK05473, IreB-like, IreB family regulatory phosphoprotein	NA|143aa|down_4|NZ_CP047803.1_399952_400381_+	COG0816, COG0816, Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B	NA|103aa|down_5|NZ_CP047803.1_400395_400704_+	PRK13678, PRK13678, hypothetical protein; Provisional	NA|213aa|down_6|NZ_CP047803.1_400988_401627_+	COG4122, COG4122, Predicted O-methyltransferase [General function prediction only]	NA|308aa|down_7|NZ_CP047803.1_401629_402553_+	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|423aa|down_8|NZ_CP047803.1_402564_403833_+	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|208aa|down_9|NZ_CP047803.1_403832_404456_+	PRK05480, PRK05480, uridine/cytidine kinase; Provisional
GCF_009913115.1_ASM991311v1	NZ_CP047803	Staphylococcus aureus strain UP_1097 chromosome, complete genome	2	1122602-1122687	2	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	CCAACTTGCACATTATTGTAAGCTGGCTTT	30	1	5	1122632-1122657|1122632-1122657|1122632-1122657|1122632-1122657|1122632-1122657	NZ_CP047803.1_1209971-1209946|NZ_CP047803.1_1805744-1805769|NZ_CP047803.1_2499656-2499681|NZ_CP047803.1_2499712-2499737|NZ_CP047803.1_2499768-2499793	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA	NA|301aa|up_9|NZ_CP047803.1_1106038_1106941_-	COG0179, MhpD, 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]	NA|1218aa|up_8|NZ_CP047803.1_1107106_1110760_-	TIGR02785, ATP-dependent_helicase/nuclease_subunit_A, helicase-exonuclease AddAB, AddA subunit, Firmicutes type	NA|1159aa|up_7|NZ_CP047803.1_1110760_1114237_-	TIGR02773, ATP-dependent_helicase/deoxyribonuclease_subunit_B, helicase-exonuclease AddAB, AddB subunit	NA|192aa|up_6|NZ_CP047803.1_1114396_1114972_-	TIGR02227, Inactive_signal_peptidase_IA	NA|175aa|up_5|NZ_CP047803.1_1114987_1115512_-	TIGR02227, Inactive_signal_peptidase_IA	NA|192aa|up_4|NZ_CP047803.1_1115516_1116092_-	COG0398, COG0398, Uncharacterized conserved protein [Function unknown]	NA|444aa|up_3|NZ_CP047803.1_1117017_1118349_-	PRK14097, pgi, glucose-6-phosphate isomerase; Provisional	NA|402aa|up_2|NZ_CP047803.1_1118699_1119905_+	PRK00509, PRK00509, argininosuccinate synthase; Provisional	NA|460aa|up_1|NZ_CP047803.1_1119894_1121274_+	PRK00855, PRK00855, argininosuccinate lyase; Provisional	NA|310aa|up_0|NZ_CP047803.1_1121515_1122445_+	cd08601, GDPD_SaGlpQ_like, Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins	NA|415aa|down_0|NZ_CP047803.1_1122893_1124138_-	COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]	NA|397aa|down_1|NZ_CP047803.1_1124246_1125437_-	PRK04073, rocD, ornithine--oxo-acid transaminase; Provisional	NA|376aa|down_2|NZ_CP047803.1_1125744_1126872_-	cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4	NA|126aa|down_3|NZ_CP047803.1_1127232_1127610_-	COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]	NA|198aa|down_4|NZ_CP047803.1_1128025_1128619_-	cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain	NA|128aa|down_5|NZ_CP047803.1_1128682_1129066_+	pfam08810, KapB, Kinase associated protein B	NA|802aa|down_6|NZ_CP047803.1_1129196_1131602_+	PRK12645, PRK12645, monovalent cation/H+ antiporter subunit A; Reviewed	NA|143aa|down_7|NZ_CP047803.1_1131594_1132023_+	PRK12573, PRK12573, Na(+)/H(+) antiporter subunit B	NA|110aa|down_8|NZ_CP047803.1_1132034_1132364_+	PRK08600, PRK08600, putative monovalent cation/H+ antiporter subunit C; Reviewed	NA|499aa|down_9|NZ_CP047803.1_1132356_1133853_+	PRK07691, PRK07691, putative monovalent cation/H+ antiporter subunit D; Reviewed
GCF_009913115.1_ASM991311v1	NZ_CP047803	Staphylococcus aureus strain UP_1097 chromosome, complete genome	3	2298142-2298275	1	PILER-CR	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TATTGAAGAAGATACAA	17	1	1	2298222-2298258	NZ_CP047803.1_2294652-2294688	NA	2	2	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA|103aa|down_1|NZ_CP047803.1_2299908_2300217_-,NA|89aa|down_2|NZ_CP047803.1_2300356_2300623_-,NA|109aa|down_9|NZ_CP047803.1_2310404_2310731_+	NA|204aa|up_9|NZ_CP047803.1_2280267_2280879_-	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|426aa|up_8|NZ_CP047803.1_2281425_2282703_+	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|608aa|up_7|NZ_CP047803.1_2283614_2285438_+	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|139aa|up_6|NZ_CP047803.1_2285576_2285993_+	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|231aa|up_5|NZ_CP047803.1_2286223_2286916_+	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|255aa|up_4|NZ_CP047803.1_2287080_2287845_+	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|227aa|up_3|NZ_CP047803.1_2287998_2288679_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|518aa|up_2|NZ_CP047803.1_2288702_2290256_+	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|453aa|up_1|NZ_CP047803.1_2290372_2291731_+	TIGR00791, Gluconate_permease, gluconate transporter	NA|978aa|up_0|NZ_CP047803.1_2292199_2295133_+	pfam10425, SdrG_C_C, C-terminus of bacterial fibrinogen-binding adhesin	NA|289aa|down_0|NZ_CP047803.1_2298915_2299782_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|103aa|down_1|NZ_CP047803.1_2299908_2300217_-	NA	NA|89aa|down_2|NZ_CP047803.1_2300356_2300623_-	NA	NA|603aa|down_3|NZ_CP047803.1_2300906_2302715_-	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|131aa|down_4|NZ_CP047803.1_2302846_2303239_+	cd03425, MutT_pyrophosphohydrolase, The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic pyrophosphate (PPi)	NA|954aa|down_5|NZ_CP047803.1_2303240_2306102_+	COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]	NA|253aa|down_6|NZ_CP047803.1_2306407_2307166_+	pfam04507, DUF576, Csa1 family	NA|258aa|down_7|NZ_CP047803.1_2307277_2308051_+	pfam04507, DUF576, Csa1 family	NA|262aa|down_8|NZ_CP047803.1_2308298_2309084_+	pfam04507, DUF576, Csa1 family	NA|109aa|down_9|NZ_CP047803.1_2310404_2310731_+	NA
GCF_009913115.1_ASM991311v1	NZ_CP047803	Staphylococcus aureus strain UP_1097 chromosome, complete genome	4	2381887-2381980	3	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	CCTTTCTAACAAATAAATTTGAAGAA	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|35aa|up_0|NZ_CP047803.1_2381587_2381692_+,NA|35aa|down_2|NZ_CP047803.1_2384153_2384258_-	NA|453aa|up_9|NZ_CP047803.1_2371520_2372879_+	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase	NA|336aa|up_8|NZ_CP047803.1_2372880_2373888_+	PRK06256, PRK06256, biotin synthase; Validated	NA|372aa|up_7|NZ_CP047803.1_2373865_2374981_+	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|231aa|up_6|NZ_CP047803.1_2374991_2375684_+	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|156aa|up_5|NZ_CP047803.1_2375694_2376162_+	pfam06177, QueT, QueT transporter	NA|326aa|up_4|NZ_CP047803.1_2376220_2377198_-	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|316aa|up_3|NZ_CP047803.1_2377199_2378147_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|310aa|up_2|NZ_CP047803.1_2378714_2379644_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|438aa|up_1|NZ_CP047803.1_2380179_2381493_-	pfam11621, Sbi-IV, C3 binding domain 4 of IgG-bind protein SBI	NA|35aa|up_0|NZ_CP047803.1_2381587_2381692_+	NA	NA|289aa|down_0|NZ_CP047803.1_2382120_2382987_+	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|229aa|down_1|NZ_CP047803.1_2383313_2384000_+	PRK14119, gpmA, phosphoglyceromutase; Provisional	NA|35aa|down_2|NZ_CP047803.1_2384153_2384258_-	NA	NA|260aa|down_3|NZ_CP047803.1_2385981_2386761_+	cd13711, PBP2_Ngo0372_TcyA, Substrate binding domain of ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold	NA|240aa|down_4|NZ_CP047803.1_2386741_2387461_+	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|244aa|down_5|NZ_CP047803.1_2387457_2388189_+	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|417aa|down_6|NZ_CP047803.1_2388285_2389536_-	pfam02388, FemAB, FemAB family	NA|121aa|down_7|NZ_CP047803.1_2389790_2390153_+	pfam14729, DUF4467, Domain of unknown function with cystatin-like fold (DUF4467)	NA|200aa|down_8|NZ_CP047803.1_2390171_2390771_+	COG1651, DsbG, Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]	NA|516aa|down_9|NZ_CP047803.1_2391062_2392610_+	pfam09223, ZinT, ZinT (YodA) periplasmic lipocalin-like zinc-recruitment
GCF_009913115.1_ASM991311v1	NZ_CP047803	Staphylococcus aureus strain UP_1097 chromosome, complete genome	5	2572861-2572993	4	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	GAAACCAATGATATCAAGGGTTTTGTGAGCTTTCGAGTAAAGAG	44	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA|61aa|down_0|NZ_CP047803.1_2573903_2574086_+,NA|67aa|down_1|NZ_CP047803.1_2574067_2574268_-,NA|93aa|down_7|NZ_CP047803.1_2580623_2580902_-	NA|130aa|up_9|NZ_CP047803.1_2564336_2564726_+	PRK05309, PRK05309, 30S ribosomal protein S11; Validated	NA|315aa|up_8|NZ_CP047803.1_2564800_2565745_+	PRK05182, PRK05182, DNA-directed RNA polymerase subunit alpha; Provisional	NA|123aa|up_7|NZ_CP047803.1_2565761_2566130_+	PRK05591, rplQ, 50S ribosomal protein L17; Validated	NA|270aa|up_6|NZ_CP047803.1_2566667_2567477_+	PRK13648, cbiO, cobalt transporter ATP-binding subunit; Provisional	NA|287aa|up_5|NZ_CP047803.1_2567473_2568334_+	PRK13646, cbiO, energy-coupling factor transporter ATPase	NA|269aa|up_4|NZ_CP047803.1_2568323_2569130_+	COG0619, CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]	NA|268aa|up_3|NZ_CP047803.1_2569134_2569938_+	PRK00021, truA, tRNA pseudouridine(38-40) synthase TruA	NA|146aa|up_2|NZ_CP047803.1_2570177_2570615_+	PRK09216, rplM, 50S ribosomal protein L13; Reviewed	NA|133aa|up_1|NZ_CP047803.1_2570628_2571027_+	PRK00132, rpsI, 30S ribosomal protein S9; Reviewed	NA|479aa|up_0|NZ_CP047803.1_2571375_2572812_+	COG2865, COG2865, Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]	NA|61aa|down_0|NZ_CP047803.1_2573903_2574086_+	NA	NA|67aa|down_1|NZ_CP047803.1_2574067_2574268_-	NA	NA|555aa|down_2|NZ_CP047803.1_2574556_2576221_+	PRK08617, PRK08617, acetolactate synthase AlsS	NA|235aa|down_3|NZ_CP047803.1_2576257_2576962_+	COG3527, AlsD, Alpha-acetolactate decarboxylase [Secondary metabolites biosynthesis, transport, and catabolism]	NA|142aa|down_4|NZ_CP047803.1_2577337_2577763_-	pfam03642, MAP, MAP domain	NA|272aa|down_5|NZ_CP047803.1_2578056_2578872_+	cd02605, HAD_SPP, sucrose-phosphatase, similar to Synechocystis sp PCC 6803 SPP	NA|506aa|down_6|NZ_CP047803.1_2579096_2580614_-	cd04949, GT4_GtfA-like, accessory Sec system glycosyltransferase GtfA and similar proteins	NA|93aa|down_7|NZ_CP047803.1_2580623_2580902_-	NA	NA|285aa|down_8|NZ_CP047803.1_2581776_2582631_+	COG0739, NlpD, Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]	NA|807aa|down_9|NZ_CP047803.1_2582829_2585250_-	cd01083, GAG_Lyase, Glycosaminoglycan (GAG) polysaccharide lyase family
GCF_009913115.1_ASM991311v1	NZ_CP047803	Staphylococcus aureus strain UP_1097 chromosome, complete genome	6	2652465-2652553	5	CRISPRCasFinder	no	csa3	DEDDh,csa3,cas3,DinG,WYL	Type I-A	TGCATAAGAGCCCCTAACAACTAAAGTTTAAG	32	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|31aa|up_0|NZ_CP047803.1_2652252_2652345_-,NA|364aa|down_0|NZ_CP047803.1_2652566_2653658_-,NA|77aa|down_5|NZ_CP047803.1_2657444_2657675_+	NA|452aa|up_9|NZ_CP047803.1_2633069_2634425_+	PRK14316, glmM, phosphoglucosamine mutase; Provisional	NA|2460aa|up_8|NZ_CP047803.1_2634708_2642088_+	TIGR04263, cell_wall_surface_anchor_family_protein, SasC/Mrp/FmtB intercellular aggregation domain	NA|369aa|up_7|NZ_CP047803.1_2642410_2643517_-	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional	NA|145aa|up_6|NZ_CP047803.1_2643516_2643951_-	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|711aa|up_5|NZ_CP047803.1_2643962_2646095_-	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|517aa|up_4|NZ_CP047803.1_2646129_2647680_-	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|602aa|up_3|NZ_CP047803.1_2648360_2650166_+	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|261aa|up_2|NZ_CP047803.1_2650398_2651181_+	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|286aa|up_1|NZ_CP047803.1_2651248_2652106_+	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|31aa|up_0|NZ_CP047803.1_2652252_2652345_-	NA	NA|364aa|down_0|NZ_CP047803.1_2652566_2653658_-	NA	NA|326aa|down_1|NZ_CP047803.1_2653923_2654901_-	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	csa3|107aa|down_2|NZ_CP047803.1_2654902_2655223_-	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|222aa|down_3|NZ_CP047803.1_2655374_2656040_+	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	NA|313aa|down_4|NZ_CP047803.1_2656475_2657414_+	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|77aa|down_5|NZ_CP047803.1_2657444_2657675_+	NA	NA|458aa|down_6|NZ_CP047803.1_2658348_2659722_+	pfam01878, EVE, EVE domain	NA|138aa|down_7|NZ_CP047803.1_2660179_2660593_+	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|148aa|down_8|NZ_CP047803.1_2660792_2661236_+	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|237aa|down_9|NZ_CP047803.1_2661356_2662067_-	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase
