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_009912035.1_ASM991203v1	NZ_CP047778	Staphylococcus aureus strain UP_1572 chromosome, complete genome	1	71308-71499	1	CRT	no	DEDDh	DEDDh,csa3,cas3,DinG,WYL	Unclear	GGTGGGGCCCNCAACANAGANN	22	2	9	71387-71420|71387-71420|71387-71420|71387-71420|71387-71420|71387-71420|71387-71420|71387-71420|71442-71478	NZ_CP047778.1_338725-338692|NZ_CP047778.1_1031669-1031702|NZ_CP047778.1_1290779-1290812|NZ_CP047778.1_1325090-1325057|NZ_CP047778.1_1762554-1762521|NZ_CP047778.1_1835674-1835641|NZ_CP047778.1_2427700-2427667|NZ_CP047778.1_2569702-2569735|NZ_CP047778.1_1277549-1277585	NA	3	3	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|49aa|up_0|NZ_CP047778.1_70856_71003_+,NA|31aa|down_5|NZ_CP047778.1_76884_76977_+,NA|37aa|down_9|NZ_CP047778.1_79982_80093_+	NA|101aa|up_9|NZ_CP047778.1_59037_59340_+	COG4496, COG4496, Uncharacterized protein conserved in bacteria [Function unknown]	NA|231aa|up_8|NZ_CP047778.1_59522_60215_+	COG1646, COG1646, Predicted phosphate-binding enzymes, TIM-barrel fold [General function prediction only]	NA|731aa|up_7|NZ_CP047778.1_60211_62404_+	TIGR01073, ATP-dependent_DNA_helicase_PcrA, ATP-dependent DNA helicase PcrA	NA|668aa|up_6|NZ_CP047778.1_62407_64411_+	PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated	NA|400aa|up_5|NZ_CP047778.1_64423_65623_+	COG4851, CamS, Protein involved in sex pheromone biosynthesis [General function prediction only]	NA|513aa|up_4|NZ_CP047778.1_65711_67250_-	TIGR02121, Osmoregulated_proline_transporter, sodium/proline symporter	NA|101aa|up_3|NZ_CP047778.1_67616_67919_+	PRK00034, gatC, Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC	NA|486aa|up_2|NZ_CP047778.1_67920_69378_+	PRK00012, gatA, Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA	NA|476aa|up_1|NZ_CP047778.1_69390_70818_+	PRK05477, gatB, Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB	NA|49aa|up_0|NZ_CP047778.1_70856_71003_+	NA	NA|316aa|down_0|NZ_CP047778.1_71640_72588_+	PRK13337, PRK13337, putative lipid kinase; Reviewed	NA|454aa|down_1|NZ_CP047778.1_72668_74030_+	COG2265, TrmA, SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]	NA|177aa|down_2|NZ_CP047778.1_74199_74730_+	pfam11667, DUF3267, Putative zincin peptidase	NA|357aa|down_3|NZ_CP047778.1_74976_76047_+	PRK02406, PRK02406, DNA polymerase IV; Validated	DEDDh|185aa|down_4|NZ_CP047778.1_76113_76668_-	cd06130, DNA_pol_III_epsilon_like, an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III	NA|31aa|down_5|NZ_CP047778.1_76884_76977_+	NA	NA|167aa|down_6|NZ_CP047778.1_77058_77559_-	COG1528, Ftn, Ferritin-like protein [Inorganic ion transport and metabolism]	NA|438aa|down_7|NZ_CP047778.1_77850_79164_+	COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]	NA|244aa|down_8|NZ_CP047778.1_79165_79897_+	COG3442, COG3442, Predicted glutamine amidotransferase [General function prediction only]	NA|37aa|down_9|NZ_CP047778.1_79982_80093_+	NA
GCF_009912035.1_ASM991203v1	NZ_CP047778	Staphylococcus aureus strain UP_1572 chromosome, complete genome	2	424500-424579	1	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	CCCAACATAGAGAATTTCGTAAAGAA	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|43aa|up_8|NZ_CP047778.1_417058_417187_+,NA|49aa|up_3|NZ_CP047778.1_420223_420370_+,NA	NA|589aa|up_9|NZ_CP047778.1_414959_416726_+	PRK00476, aspS, aspartyl-tRNA synthetase; Validated	NA|43aa|up_8|NZ_CP047778.1_417058_417187_+	NA	NA|258aa|up_7|NZ_CP047778.1_417186_417960_+	COG1179, COG1179, Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]	NA|425aa|up_6|NZ_CP047778.1_418120_419395_-	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|141aa|up_5|NZ_CP047778.1_419479_419902_+	COG1959, COG1959, Predicted transcriptional regulator [Transcription]	NA|61aa|up_4|NZ_CP047778.1_420001_420184_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|49aa|up_3|NZ_CP047778.1_420223_420370_+	NA	NA|338aa|up_2|NZ_CP047778.1_420606_421620_-	TIGR03558, oxido_grp_1, luciferase family oxidoreductase, group 1	NA|381aa|up_1|NZ_CP047778.1_421929_423072_+	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]	NA|373aa|up_0|NZ_CP047778.1_423072_424191_+	PRK00143, mnmA, tRNA-specific 2-thiouridylase MnmA; Reviewed	NA|223aa|down_0|NZ_CP047778.1_424872_425541_+	sd00006, TPR, Tetratricopeptide repeat	NA|826aa|down_1|NZ_CP047778.1_425542_428020_+	TIGR01448, recD_rel, helicase, putative, RecD/TraA family	NA|877aa|down_2|NZ_CP047778.1_428362_430993_+	PRK00252, alaS, alanyl-tRNA synthetase; Reviewed	NA|87aa|down_3|NZ_CP047778.1_431055_431316_+	PRK05473, IreB-like, IreB family regulatory phosphoprotein	NA|143aa|down_4|NZ_CP047778.1_431319_431748_+	COG0816, COG0816, Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B	NA|103aa|down_5|NZ_CP047778.1_431762_432071_+	PRK13678, PRK13678, hypothetical protein; Provisional	NA|213aa|down_6|NZ_CP047778.1_432355_432994_+	COG4122, COG4122, Predicted O-methyltransferase [General function prediction only]	NA|308aa|down_7|NZ_CP047778.1_432996_433920_+	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|423aa|down_8|NZ_CP047778.1_433931_435200_+	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|208aa|down_9|NZ_CP047778.1_435199_435823_+	PRK05480, PRK05480, uridine/cytidine kinase; Provisional
GCF_009912035.1_ASM991203v1	NZ_CP047778	Staphylococcus aureus strain UP_1572 chromosome, complete genome	3	882410-882502	2	CRISPRCasFinder	no	cas3	DEDDh,csa3,cas3,DinG,WYL	Unclear	AGTTATCAATTTATTGATTACTGTTTCTTA	30	0	0	NA	NA	NA	1	1	Unclear	DEDDh,csa3,cas3,DinG,WYL	NA,NA	NA|117aa|up_9|NZ_CP047778.1_871973_872324_-	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|246aa|up_8|NZ_CP047778.1_872426_873164_-	PRK00026, trmD, tRNA (guanine-N(1)-)-methyltransferase; Reviewed	NA|168aa|up_7|NZ_CP047778.1_873163_873667_-	PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional	NA|92aa|up_6|NZ_CP047778.1_873854_874130_-	COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]	NA|456aa|up_5|NZ_CP047778.1_874564_875932_-	PRK10867, PRK10867, signal recognition particle protein; Provisional	NA|111aa|up_4|NZ_CP047778.1_875957_876290_-	PRK00118, PRK00118, putative DNA-binding protein; Validated	NA|417aa|up_3|NZ_CP047778.1_876276_877527_-	PRK10416, PRK10416, signal recognition particle-docking protein FtsY; Provisional	NA|1189aa|up_2|NZ_CP047778.1_877526_881093_-	COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	NA|244aa|up_1|NZ_CP047778.1_881239_881971_-	PRK00102, rnc, ribonuclease III; Reviewed	NA|78aa|up_0|NZ_CP047778.1_882086_882320_-	PRK00982, acpP, acyl carrier protein; Provisional	NA|245aa|down_0|NZ_CP047778.1_882625_883360_-	PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Validated	NA|309aa|down_1|NZ_CP047778.1_883352_884279_-	COG0331, FabD, (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]	NA|329aa|down_2|NZ_CP047778.1_884271_885258_-	PRK05331, PRK05331, phosphate acyltransferase PlsX	NA|191aa|down_3|NZ_CP047778.1_885262_885835_-	PRK04424, PRK04424, transcription factor FapR	cas3|687aa|down_4|NZ_CP047778.1_886037_888098_-	PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional	NA|549aa|down_5|NZ_CP047778.1_888287_889934_-	COG1461, COG1461, Predicted kinase related to dihydroxyacetone kinase [General function prediction only]	NA|125aa|down_6|NZ_CP047778.1_889948_890323_-	COG1302, COG1302, Uncharacterized protein conserved in bacteria [Function unknown]	NA|63aa|down_7|NZ_CP047778.1_890765_890954_+	PRK00359, rpmB, 50S ribosomal protein L28; Reviewed	NA|214aa|down_8|NZ_CP047778.1_891334_891976_-	COG1564, THI80, Thiamine pyrophosphokinase [Coenzyme metabolism]	NA|215aa|down_9|NZ_CP047778.1_891982_892627_-	COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]
GCF_009912035.1_ASM991203v1	NZ_CP047778	Staphylococcus aureus strain UP_1572 chromosome, complete genome	4	1183610-1183695	3	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	CCAACTTGCACATTATTGTAAGCTGGCTTT	30	1	2	1183640-1183665|1183640-1183665	NZ_CP047778.1_2735539-2735564|NZ_CP047778.1_2795623-2795648	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA	NA|301aa|up_9|NZ_CP047778.1_1167644_1168547_-	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_CP047778.1_1168712_1172366_-	TIGR02785, ATP-dependent_helicase/nuclease_subunit_A, helicase-exonuclease AddAB, AddA subunit, Firmicutes type	NA|1159aa|up_7|NZ_CP047778.1_1172366_1175843_-	TIGR02773, ATP-dependent_helicase/deoxyribonuclease_subunit_B, helicase-exonuclease AddAB, AddB subunit	NA|192aa|up_6|NZ_CP047778.1_1176002_1176578_-	TIGR02227, Inactive_signal_peptidase_IA	NA|175aa|up_5|NZ_CP047778.1_1176593_1177118_-	TIGR02227, Inactive_signal_peptidase_IA	NA|192aa|up_4|NZ_CP047778.1_1177122_1177698_-	COG0398, COG0398, Uncharacterized conserved protein [Function unknown]	NA|444aa|up_3|NZ_CP047778.1_1178023_1179355_-	PRK14097, pgi, glucose-6-phosphate isomerase; Provisional	NA|402aa|up_2|NZ_CP047778.1_1179705_1180911_+	PRK00509, PRK00509, argininosuccinate synthase; Provisional	NA|460aa|up_1|NZ_CP047778.1_1180900_1182280_+	PRK00855, PRK00855, argininosuccinate lyase; Provisional	NA|310aa|up_0|NZ_CP047778.1_1182521_1183451_+	cd08601, GDPD_SaGlpQ_like, Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins	NA|415aa|down_0|NZ_CP047778.1_1183845_1185090_-	COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]	NA|397aa|down_1|NZ_CP047778.1_1185198_1186389_-	PRK04073, rocD, ornithine--oxo-acid transaminase; Provisional	NA|376aa|down_2|NZ_CP047778.1_1186696_1187824_-	cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4	NA|126aa|down_3|NZ_CP047778.1_1188185_1188563_-	COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]	NA|198aa|down_4|NZ_CP047778.1_1188977_1189571_-	cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain	NA|128aa|down_5|NZ_CP047778.1_1189634_1190018_+	pfam08810, KapB, Kinase associated protein B	NA|802aa|down_6|NZ_CP047778.1_1190148_1192554_+	PRK12645, PRK12645, monovalent cation/H+ antiporter subunit A; Reviewed	NA|143aa|down_7|NZ_CP047778.1_1192546_1192975_+	PRK12573, PRK12573, Na(+)/H(+) antiporter subunit B	NA|110aa|down_8|NZ_CP047778.1_1192986_1193316_+	PRK08600, PRK08600, putative monovalent cation/H+ antiporter subunit C; Reviewed	NA|499aa|down_9|NZ_CP047778.1_1193308_1194805_+	PRK07691, PRK07691, putative monovalent cation/H+ antiporter subunit D; Reviewed
GCF_009912035.1_ASM991203v1	NZ_CP047778	Staphylococcus aureus strain UP_1572 chromosome, complete genome	5	1232736-1232815	4	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	GGGCCCCAACATAGAAGCTGACGG	24	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA	NA|414aa|up_9|NZ_CP047778.1_1223055_1224297_-	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|436aa|up_8|NZ_CP047778.1_1224411_1225719_-	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|254aa|up_7|NZ_CP047778.1_1225816_1226578_-	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|284aa|up_6|NZ_CP047778.1_1226905_1227757_+	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|65aa|up_5|NZ_CP047778.1_1227990_1228185_-	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|274aa|up_4|NZ_CP047778.1_1229000_1229822_-	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|232aa|up_3|NZ_CP047778.1_1229839_1230535_-	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|342aa|up_2|NZ_CP047778.1_1230527_1231553_-	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|99aa|up_1|NZ_CP047778.1_1231802_1232099_-	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|up_0|NZ_CP047778.1_1232091_1232478_-	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|293aa|down_0|NZ_CP047778.1_1233068_1233947_-	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|127aa|down_1|NZ_CP047778.1_1234124_1234505_-	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|119aa|down_2|NZ_CP047778.1_1234662_1235019_-	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_3|NZ_CP047778.1_1235162_1235483_+	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_4|NZ_CP047778.1_1235632_1236172_-	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|239aa|down_5|NZ_CP047778.1_1236254_1236971_-	PRK13575, PRK13575, type I 3-dehydroquinate dehydratase	NA|141aa|down_6|NZ_CP047778.1_1237118_1237541_+	TIGR03561, organ_hyd_perox, peroxiredoxin, Ohr subfamily	NA|165aa|down_7|NZ_CP047778.1_1237939_1238434_+	pfam13420, Acetyltransf_4, Acetyltransferase (GNAT) domain	NA|206aa|down_8|NZ_CP047778.1_1238589_1239207_+	COG1279, COG1279, Lysine efflux permease [General function prediction only]	NA|187aa|down_9|NZ_CP047778.1_1239279_1239840_-	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only]
GCF_009912035.1_ASM991203v1	NZ_CP047778	Staphylococcus aureus strain UP_1572 chromosome, complete genome	6	1290793-1290877	5	CRISPRCasFinder	no	cas3	DEDDh,csa3,cas3,DinG,WYL	Unclear	TTCTACAGGCAATGCAAGTTGGGGTG	26	1	2	1290819-1290851|1290819-1290851	NZ_CP047778.1_2535448-2535416|NZ_CP047778.1_1057827-1057859	NA	1	1	Unclear	DEDDh,csa3,cas3,DinG,WYL	NA,NA|33aa|down_1|NZ_CP047778.1_1292337_1292436_-	NA|312aa|up_9|NZ_CP047778.1_1277946_1278882_-	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|480aa|up_8|NZ_CP047778.1_1278948_1280388_-	sd00008, TPR_YbbN, C-terminal Tetratricopeptide repeat (TPR) region of YbbN and similar motifs	NA|162aa|up_7|NZ_CP047778.1_1280395_1280881_-	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|281aa|up_6|NZ_CP047778.1_1280888_1281731_-	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|311aa|up_5|NZ_CP047778.1_1281736_1282669_-	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|949aa|up_4|NZ_CP047778.1_1283279_1286126_-	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|662aa|up_3|NZ_CP047778.1_1286133_1288119_-	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|79aa|up_2|NZ_CP047778.1_1288387_1288624_-	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|217aa|up_1|NZ_CP047778.1_1288620_1289271_-	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|280aa|up_0|NZ_CP047778.1_1289444_1290284_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|370aa|down_0|NZ_CP047778.1_1291052_1292163_-	PRK00578, prfB, peptide chain release factor 2; Validated	NA|33aa|down_1|NZ_CP047778.1_1292337_1292436_-	NA	NA|844aa|down_2|NZ_CP047778.1_1292477_1295009_-	PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed	NA|316aa|down_3|NZ_CP047778.1_1295389_1296337_-	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]	NA|191aa|down_4|NZ_CP047778.1_1296496_1297069_-	COG1544, COG1544, Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]	NA|225aa|down_5|NZ_CP047778.1_1297129_1297804_-	COG1040, ComFC, Predicted amidophosphoribosyltransferases [General function prediction only]	cas3|361aa|down_6|NZ_CP047778.1_1297796_1298879_-	COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]	NA|289aa|down_7|NZ_CP047778.1_1299242_1300109_-	TIGR00762, DegV, EDD domain protein, DegV family	NA|214aa|down_8|NZ_CP047778.1_1300252_1300894_+	COG1739, COG1739, Uncharacterized conserved protein [Function unknown]	NA|352aa|down_9|NZ_CP047778.1_1301057_1302113_-	cd06853, GT_WecA_like, This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins
GCF_009912035.1_ASM991203v1	NZ_CP047778	Staphylococcus aureus strain UP_1572 chromosome, complete genome	7	1690455-1690610	1	PILER-CR	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TTGGTGTTGGTTGTGGCGATTGCGGTTGTACATTTGGTGAAGGCGG	46	0	0	NA	NA	NA	2	2	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|103aa|up_9|NZ_CP047778.1_1679506_1679815_+,NA|496aa|up_8|NZ_CP047778.1_1679920_1681408_-,NA|40aa|up_4|NZ_CP047778.1_1685348_1685468_+,NA|51aa|down_5|NZ_CP047778.1_1696366_1696519_+,NA|179aa|down_7|NZ_CP047778.1_1699344_1699881_+	NA|103aa|up_9|NZ_CP047778.1_1679506_1679815_+	NA	NA|496aa|up_8|NZ_CP047778.1_1679920_1681408_-	NA	NA|233aa|up_7|NZ_CP047778.1_1681426_1682125_-	PRK13036, PRK13036, superantigen-like protein; Reviewed	NA|411aa|up_6|NZ_CP047778.1_1682507_1683740_-	cd17258, RMtype1_S_Sau13435ORF2165P-TRD1-CR1_like, Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S	NA|519aa|up_5|NZ_CP047778.1_1683732_1685289_-	COG0286, HsdM, Type I restriction-modification system methyltransferase subunit [Defense mechanisms]	NA|40aa|up_4|NZ_CP047778.1_1685348_1685468_+	NA	NA|228aa|up_3|NZ_CP047778.1_1685550_1686234_-	PRK13038, PRK13038, superantigen-like protein; Reviewed	NA|233aa|up_2|NZ_CP047778.1_1686596_1687295_-	PRK13345, PRK13345, superantigen-like protein; Reviewed	NA|232aa|up_1|NZ_CP047778.1_1687635_1688331_-	PRK13346, PRK13346, superantigen-like protein 7; Reviewed	NA|235aa|up_0|NZ_CP047778.1_1688777_1689482_-	PRK13035, PRK13035, superantigen-like protein 5; Reviewed	NA|344aa|down_0|NZ_CP047778.1_1691166_1692198_-	PRK13335, PRK13335, superantigen-like protein; Reviewed	NA|234aa|down_1|NZ_CP047778.1_1692485_1693187_-	PRK13041, PRK13041, superantigen-like protein; Reviewed	NA|227aa|down_2|NZ_CP047778.1_1693469_1694150_-	PRK13037, PRK13037, superantigen-like protein; Reviewed	NA|282aa|down_3|NZ_CP047778.1_1694621_1695467_+	cd05269, TMR_SDR_a, triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs	NA|120aa|down_4|NZ_CP047778.1_1695485_1695845_+	COG3759, COG3759, Predicted membrane protein [Function unknown]	NA|51aa|down_5|NZ_CP047778.1_1696366_1696519_+	NA	NA|109aa|down_6|NZ_CP047778.1_1696776_1697103_+	COG2963, COG2963, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|179aa|down_7|NZ_CP047778.1_1699344_1699881_+	NA	NA|514aa|down_8|NZ_CP047778.1_1700410_1701952_-	PRK00074, guaA, GMP synthase; Reviewed	NA|489aa|down_9|NZ_CP047778.1_1701976_1703443_-	PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase; Reviewed
GCF_009912035.1_ASM991203v1	NZ_CP047778	Staphylococcus aureus strain UP_1572 chromosome, complete genome	8	2333675-2333933	2,6	PILER-CR,CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TATTGAAGAAGATACAA,GCCAACACCACCGACACCAGAGGTACCA	17,28	0	0	NA	NA	NA:NA	2,2	2	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|67aa|up_0|NZ_CP047778.1_2330970_2331171_+,NA|103aa|down_1|NZ_CP047778.1_2335366_2335675_-,NA|89aa|down_2|NZ_CP047778.1_2335818_2336085_-,NA|41aa|down_8|NZ_CP047778.1_2344406_2344529_-,NA|64aa|down_9|NZ_CP047778.1_2344963_2345155_+	NA|204aa|up_9|NZ_CP047778.1_2319804_2320416_-	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|426aa|up_8|NZ_CP047778.1_2320966_2322244_+	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|608aa|up_7|NZ_CP047778.1_2322720_2324544_+	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|139aa|up_6|NZ_CP047778.1_2324682_2325099_+	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|231aa|up_5|NZ_CP047778.1_2325329_2326022_+	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|244aa|up_4|NZ_CP047778.1_2326186_2326918_+	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|227aa|up_3|NZ_CP047778.1_2327104_2327785_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|518aa|up_2|NZ_CP047778.1_2327809_2329363_+	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|453aa|up_1|NZ_CP047778.1_2329479_2330838_+	TIGR00791, Gluconate_permease, gluconate transporter	NA|67aa|up_0|NZ_CP047778.1_2330970_2331171_+	NA	NA|289aa|down_0|NZ_CP047778.1_2334373_2335240_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|103aa|down_1|NZ_CP047778.1_2335366_2335675_-	NA	NA|89aa|down_2|NZ_CP047778.1_2335818_2336085_-	NA	NA|603aa|down_3|NZ_CP047778.1_2336368_2338177_-	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|131aa|down_4|NZ_CP047778.1_2338293_2338686_+	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_CP047778.1_2338687_2341549_+	COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]	NA|258aa|down_6|NZ_CP047778.1_2341855_2342629_+	pfam04507, DUF576, Csa1 family	NA|265aa|down_7|NZ_CP047778.1_2343608_2344403_+	pfam04507, DUF576, Csa1 family	NA|41aa|down_8|NZ_CP047778.1_2344406_2344529_-	NA	NA|64aa|down_9|NZ_CP047778.1_2344963_2345155_+	NA
GCF_009912035.1_ASM991203v1	NZ_CP047778	Staphylococcus aureus strain UP_1572 chromosome, complete genome	9	2414059-2414163	7	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TGCATAAGCCTTTCTAGCTCATAAAATCCGCAGAAA	36	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|35aa|up_0|NZ_CP047778.1_2413699_2413804_+,NA|35aa|down_2|NZ_CP047778.1_2416335_2416440_-	NA|453aa|up_9|NZ_CP047778.1_2403657_2405016_+	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase	NA|336aa|up_8|NZ_CP047778.1_2405017_2406025_+	PRK06256, PRK06256, biotin synthase; Validated	NA|372aa|up_7|NZ_CP047778.1_2406002_2407118_+	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|231aa|up_6|NZ_CP047778.1_2407128_2407821_+	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|156aa|up_5|NZ_CP047778.1_2407831_2408299_+	pfam06177, QueT, QueT transporter	NA|326aa|up_4|NZ_CP047778.1_2408350_2409328_-	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|316aa|up_3|NZ_CP047778.1_2409329_2410277_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|310aa|up_2|NZ_CP047778.1_2410826_2411756_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|438aa|up_1|NZ_CP047778.1_2412291_2413605_-	pfam11621, Sbi-IV, C3 binding domain 4 of IgG-bind protein SBI	NA|35aa|up_0|NZ_CP047778.1_2413699_2413804_+	NA	NA|289aa|down_0|NZ_CP047778.1_2414303_2415170_+	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|229aa|down_1|NZ_CP047778.1_2415496_2416183_+	PRK14119, gpmA, phosphoglyceromutase; Provisional	NA|35aa|down_2|NZ_CP047778.1_2416335_2416440_-	NA	NA|480aa|down_3|NZ_CP047778.1_2416613_2418053_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|260aa|down_4|NZ_CP047778.1_2418173_2418953_+	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_CP047778.1_2418933_2419653_+	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|244aa|down_6|NZ_CP047778.1_2419649_2420381_+	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|417aa|down_7|NZ_CP047778.1_2420477_2421728_-	pfam02388, FemAB, FemAB family	NA|121aa|down_8|NZ_CP047778.1_2421982_2422345_+	pfam14729, DUF4467, Domain of unknown function with cystatin-like fold (DUF4467)	NA|200aa|down_9|NZ_CP047778.1_2422363_2422963_+	COG1651, DsbG, Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]
GCF_009912035.1_ASM991203v1	NZ_CP047778	Staphylococcus aureus strain UP_1572 chromosome, complete genome	10	2569619-2569699	8	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	CAAATTGGCGGGGCCCCAACATAGA	25	1	6	2569644-2569674|2569644-2569674|2569644-2569674|2569644-2569674|2569644-2569674|2569644-2569674	NZ_CP047778.1_458607-458637|NZ_CP047778.1_1031609-1031639|NZ_CP047778.1_1183704-1183674|NZ_CP047778.1_1228533-1228503|NZ_CP047778.1_82006-82036|NZ_CP047778.1_1277431-1277461	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA|57aa|down_0|NZ_CP047778.1_2569755_2569926_-,NA|84aa|down_5|NZ_CP047778.1_2573066_2573318_-,NA|106aa|down_8|NZ_CP047778.1_2578442_2578760_-,NA|55aa|down_9|NZ_CP047778.1_2579004_2579169_-	NA|202aa|up_9|NZ_CP047778.1_2562515_2563121_+	COG4148, ModC, ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]	NA|335aa|up_8|NZ_CP047778.1_2563288_2564293_+	PRK07688, PRK07688, thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated	NA|169aa|up_7|NZ_CP047778.1_2564321_2564828_+	COG0521, MoaB, Molybdopterin biosynthesis enzymes [Coenzyme metabolism]	NA|165aa|up_6|NZ_CP047778.1_2564829_2565324_-	PRK09364, moaC, cyclic pyranopterin monophosphate synthase MoaC	NA|420aa|up_5|NZ_CP047778.1_2565386_2566646_+	cd00887, MoeA, MoeA family	NA|162aa|up_4|NZ_CP047778.1_2566642_2567128_+	COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]	NA|149aa|up_3|NZ_CP047778.1_2567141_2567588_+	COG0314, MoaE, Molybdopterin converting factor, large subunit [Coenzyme metabolism]	NA|78aa|up_2|NZ_CP047778.1_2567593_2567827_+	cd00754, Ubl_MoaD, ubiquitin-like (Ubl) domain found in molybdenum cofactor biosynthesis protein D (MoaD) and similar proteins	NA|200aa|up_1|NZ_CP047778.1_2567833_2568433_+	PRK00317, mobA, molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed	NA|341aa|up_0|NZ_CP047778.1_2568452_2569475_+	TIGR02666, Cyclic_pyranopterin_monophosphate_synthase, molybdenum cofactor biosynthesis protein A, bacterial	NA|57aa|down_0|NZ_CP047778.1_2569755_2569926_-	NA	NA|117aa|down_1|NZ_CP047778.1_2570051_2570402_+	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|404aa|down_2|NZ_CP047778.1_2570503_2571715_-	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|147aa|down_3|NZ_CP047778.1_2571707_2572148_-	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|255aa|down_4|NZ_CP047778.1_2572310_2573075_+	pfam13468, Glyoxalase_3, Glyoxalase-like domain	NA|84aa|down_5|NZ_CP047778.1_2573066_2573318_-	NA	NA|422aa|down_6|NZ_CP047778.1_2573706_2574972_+	COG2348, COG2348, Peptidoglycan interpeptide bridge formation enzyme [Cell wall/membrane/envelope biogenesis]	NA|1056aa|down_7|NZ_CP047778.1_2575088_2578256_+	COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms]	NA|106aa|down_8|NZ_CP047778.1_2578442_2578760_-	NA	NA|55aa|down_9|NZ_CP047778.1_2579004_2579169_-	NA
GCF_009912035.1_ASM991203v1	NZ_CP047778	Staphylococcus aureus strain UP_1572 chromosome, complete genome	11	2609581-2609706	9	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TGATATCAAGGGTTTTGTGAGCTTTCGAGTAAAGAGG	37	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA|61aa|down_1|NZ_CP047778.1_2610600_2610783_+,NA|56aa|down_8|NZ_CP047778.1_2619131_2619299_-	NA|315aa|up_9|NZ_CP047778.1_2599853_2600798_+	PRK05182, PRK05182, DNA-directed RNA polymerase subunit alpha; Provisional	NA|123aa|up_8|NZ_CP047778.1_2600814_2601183_+	PRK05591, rplQ, 50S ribosomal protein L17; Validated	NA|523aa|up_7|NZ_CP047778.1_2601435_2603003_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|270aa|up_6|NZ_CP047778.1_2603378_2604188_+	PRK13648, cbiO, cobalt transporter ATP-binding subunit; Provisional	NA|287aa|up_5|NZ_CP047778.1_2604184_2605045_+	PRK13646, cbiO, energy-coupling factor transporter ATPase	NA|269aa|up_4|NZ_CP047778.1_2605034_2605841_+	COG0619, CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]	NA|265aa|up_3|NZ_CP047778.1_2605845_2606640_+	PRK00021, truA, tRNA pseudouridine(38-40) synthase TruA	NA|146aa|up_2|NZ_CP047778.1_2606888_2607326_+	PRK09216, rplM, 50S ribosomal protein L13; Reviewed	NA|133aa|up_1|NZ_CP047778.1_2607339_2607738_+	PRK00132, rpsI, 30S ribosomal protein S9; Reviewed	NA|479aa|up_0|NZ_CP047778.1_2608086_2609523_+	COG2865, COG2865, Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]	NA|60aa|down_0|NZ_CP047778.1_2609771_2609951_+	PRK09775, PRK09775, type II toxin-antitoxin system HipA family toxin YjjJ	NA|61aa|down_1|NZ_CP047778.1_2610600_2610783_+	NA	NA|555aa|down_2|NZ_CP047778.1_2611252_2612917_+	PRK08617, PRK08617, acetolactate synthase AlsS	NA|235aa|down_3|NZ_CP047778.1_2612953_2613658_+	COG3527, AlsD, Alpha-acetolactate decarboxylase [Secondary metabolites biosynthesis, transport, and catabolism]	NA|142aa|down_4|NZ_CP047778.1_2614048_2614474_-	pfam03642, MAP, MAP domain	NA|272aa|down_5|NZ_CP047778.1_2614768_2615584_+	cd02605, HAD_SPP, sucrose-phosphatase, similar to Synechocystis sp PCC 6803 SPP	NA|285aa|down_6|NZ_CP047778.1_2615794_2616649_+	pfam01551, Peptidase_M23, Peptidase family M23	NA|809aa|down_7|NZ_CP047778.1_2616708_2619135_-	cd01083, GAG_Lyase, Glycosaminoglycan (GAG) polysaccharide lyase family	NA|56aa|down_8|NZ_CP047778.1_2619131_2619299_-	NA	NA|139aa|down_9|NZ_CP047778.1_2619541_2619958_+	cd01109, HTH_YyaN, Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB
GCF_009912035.1_ASM991203v1	NZ_CP047778	Staphylococcus aureus strain UP_1572 chromosome, complete genome	12	2819599-2819688	10	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TGATTGAGAAGTCAGTCGAAAAAC	24	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA|52aa|down_2|NZ_CP047778.1_2820241_2820397_+,NA|68aa|down_3|NZ_CP047778.1_2820381_2820585_+,NA|128aa|down_4|NZ_CP047778.1_2820586_2820970_+,NA|127aa|down_8|NZ_CP047778.1_2824255_2824636_+	NA|188aa|up_9|NZ_CP047778.1_2809967_2810531_-	smart00793, AgrB, Accessory gene regulator B	NA|45aa|up_8|NZ_CP047778.1_2810766_2810901_+	PRK14752, PRK14752, delta-lysin family phenol-soluble modulin	NA|262aa|up_7|NZ_CP047778.1_2811503_2812289_-	cd07583, nitrilase_5, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases)	NA|209aa|up_6|NZ_CP047778.1_2812649_2813276_-	COG3560, FMR2, Predicted oxidoreductase related to nitroreductase [General function prediction only]	NA|404aa|up_5|NZ_CP047778.1_2813472_2814684_+	PRK10819, PRK10819, transport protein TonB; Provisional	NA|248aa|up_4|NZ_CP047778.1_2814708_2815452_-	pfam02517, Abi, CAAX protease self-immunity	NA|95aa|up_3|NZ_CP047778.1_2815626_2815911_+	PRK00364, groES, co-chaperonin GroES; Reviewed	NA|539aa|up_2|NZ_CP047778.1_2815986_2817603_+	PRK00013, groEL, chaperonin GroEL; Reviewed	NA|391aa|up_1|NZ_CP047778.1_2817671_2818844_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|225aa|up_0|NZ_CP047778.1_2818857_2819532_-	pfam13443, HTH_26, Cro/C1-type HTH DNA-binding domain	NA|73aa|down_0|NZ_CP047778.1_2819704_2819923_+	smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|106aa|down_1|NZ_CP047778.1_2819927_2820245_+	TIGR01764, Probable_excisionase, DNA binding domain, excisionase family	NA|52aa|down_2|NZ_CP047778.1_2820241_2820397_+	NA	NA|68aa|down_3|NZ_CP047778.1_2820381_2820585_+	NA	NA|128aa|down_4|NZ_CP047778.1_2820586_2820970_+	NA	NA|106aa|down_5|NZ_CP047778.1_2820970_2821288_+	pfam07342, DUF1474, Protein of unknown function (DUF1474)	NA|290aa|down_6|NZ_CP047778.1_2821351_2822221_+	smart00942, PriCT_1, Primase C terminal 1 (PriCT-1)	NA|570aa|down_7|NZ_CP047778.1_2822234_2823944_+	COG5519, COG5519, Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair]	NA|127aa|down_8|NZ_CP047778.1_2824255_2824636_+	NA	NA|214aa|down_9|NZ_CP047778.1_2824632_2825274_+	pfam16560, SAPI, Putative mobile pathogenicity island
