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_009913095.1_ASM991309v1	NZ_CP047859	Staphylococcus aureus strain UP_1405 chromosome, complete genome	1	410980-411064	1	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	TTCTACAGGCAATGCAAGTTGGGGTG	26	1	2	411006-411038|411006-411038	NZ_CP047859.1_726566-726534|NZ_CP047859.1_1288168-1288200	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA	NA|190aa|up_9|NZ_CP047859.1_401609_402179_+	TIGR00482, Probable_nicotinate-nucleotide_adenylyltransferase, nicotinate (nicotinamide) nucleotide adenylyltransferase	NA|195aa|up_8|NZ_CP047859.1_402168_402753_+	COG1713, COG1713, Predicted HD superfamily hydrolase involved in NAD metabolism [Coenzyme metabolism]	NA|118aa|up_7|NZ_CP047859.1_402753_403107_+	COG0799, COG0799, Uncharacterized homolog of plant Iojap protein [Function unknown]	NA|239aa|up_6|NZ_CP047859.1_403109_403826_+	pfam13649, Methyltransf_25, Methyltransferase domain	NA|229aa|up_5|NZ_CP047859.1_403865_404552_+	COG1555, ComEA, DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]	NA|154aa|up_4|NZ_CP047859.1_404643_405105_+	TIGR02571, putative_dCMP_deaminase, ComE operon protein 2	NA|716aa|up_3|NZ_CP047859.1_405163_407311_+	COG2333, ComEC, Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]	NA|325aa|up_2|NZ_CP047859.1_407367_408342_+	PRK05574, holA, DNA polymerase III subunit delta; Reviewed	NA|84aa|up_1|NZ_CP047859.1_408386_408638_-	PRK00239, rpsT, 30S ribosomal protein S20; Reviewed	NA|608aa|up_0|NZ_CP047859.1_408983_410807_+	PRK05433, PRK05433, GTP-binding protein LepA; Provisional	NA|375aa|down_0|NZ_CP047859.1_411372_412497_+	PRK08599, PRK08599, oxygen-independent coproporphyrinogen III oxidase	NA|326aa|down_1|NZ_CP047859.1_412597_413575_+	TIGR00331, Heat-inducible_transcription_repressor_HrcA, heat shock gene repressor HrcA	NA|209aa|down_2|NZ_CP047859.1_413606_414233_+	PRK14140, PRK14140, heat shock protein GrpE; Provisional	NA|611aa|down_3|NZ_CP047859.1_414301_416134_+	PRK00290, dnaK, molecular chaperone DnaK; Provisional	NA|380aa|down_4|NZ_CP047859.1_416269_417409_+	PRK14280, PRK14280, molecular chaperone DnaJ	NA|313aa|down_5|NZ_CP047859.1_417412_418351_+	pfam06325, PrmA, Ribosomal protein L11 methyltransferase (PrmA)	NA|251aa|down_6|NZ_CP047859.1_418352_419105_+	COG1385, COG1385, Uncharacterized protein conserved in bacteria [Function unknown]	NA|449aa|down_7|NZ_CP047859.1_419111_420458_+	COG0621, MiaB, 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]	NA|59aa|down_8|NZ_CP047859.1_420750_420927_+	PRK00270, rpsU, 30S ribosomal protein S21; Reviewed	NA|228aa|down_9|NZ_CP047859.1_421170_421854_+	COG1030, NfeD, Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]
GCF_009913095.1_ASM991309v1	NZ_CP047859	Staphylococcus aureus strain UP_1405 chromosome, complete genome	2	1244995-1245076	2	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	TTCTACAGGCAATGCAAGTTGGGG	24	1	1	1245019-1245052	NZ_CP047859.1_726567-726534	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|38aa|down_1|NZ_CP047859.1_1246059_1246173_-	NA|414aa|up_9|NZ_CP047859.1_1235422_1236664_-	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|436aa|up_8|NZ_CP047859.1_1236778_1238086_-	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|254aa|up_7|NZ_CP047859.1_1238183_1238945_-	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|284aa|up_6|NZ_CP047859.1_1239272_1240124_+	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|65aa|up_5|NZ_CP047859.1_1240357_1240552_-	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|274aa|up_4|NZ_CP047859.1_1240905_1241727_-	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|232aa|up_3|NZ_CP047859.1_1241744_1242440_-	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|342aa|up_2|NZ_CP047859.1_1242432_1243458_-	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|99aa|up_1|NZ_CP047859.1_1243707_1244004_-	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_CP047859.1_1243996_1244383_-	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|293aa|down_0|NZ_CP047859.1_1245179_1246058_-	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|38aa|down_1|NZ_CP047859.1_1246059_1246173_-	NA	NA|127aa|down_2|NZ_CP047859.1_1246236_1246617_-	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|119aa|down_3|NZ_CP047859.1_1246774_1247131_-	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_4|NZ_CP047859.1_1247274_1247595_+	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_5|NZ_CP047859.1_1247745_1248285_-	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|239aa|down_6|NZ_CP047859.1_1248367_1249084_-	PRK13575, PRK13575, type I 3-dehydroquinate dehydratase	NA|141aa|down_7|NZ_CP047859.1_1249231_1249654_+	TIGR03561, organ_hyd_perox, peroxiredoxin, Ohr subfamily	NA|165aa|down_8|NZ_CP047859.1_1250052_1250547_+	pfam13420, Acetyltransf_4, Acetyltransferase (GNAT) domain	NA|206aa|down_9|NZ_CP047859.1_1250701_1251319_+	COG1279, COG1279, Lysine efflux permease [General function prediction only]
GCF_009913095.1_ASM991309v1	NZ_CP047859	Staphylococcus aureus strain UP_1405 chromosome, complete genome	3	1293680-1293758	3	CRISPRCasFinder	no	cas3	DEDDh,csa3,cas3,DinG,WYL,RT	Unclear	AGAATTTCGAAAAGAAATTCTACA	24	1	3	1293704-1293734|1293704-1293734|1293704-1293734	NZ_CP047859.1_1800029-1799999|NZ_CP047859.1_376552-376582|NZ_CP047859.1_1800084-1800054	NA	1	1	Unclear	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|36aa|down_5|NZ_CP047859.1_1301236_1301344_-,NA|35aa|down_7|NZ_CP047859.1_1302776_1302881_-	NA|301aa|up_9|NZ_CP047859.1_1282561_1283464_+	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|196aa|up_8|NZ_CP047859.1_1283706_1284294_-	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|315aa|up_7|NZ_CP047859.1_1284857_1285802_-	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|332aa|up_6|NZ_CP047859.1_1285912_1286908_-	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|304aa|up_5|NZ_CP047859.1_1286904_1287816_-	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|312aa|up_4|NZ_CP047859.1_1288701_1289637_-	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|480aa|up_3|NZ_CP047859.1_1289703_1291143_-	sd00008, TPR_YbbN, C-terminal Tetratricopeptide repeat (TPR) region of YbbN and similar motifs	NA|162aa|up_2|NZ_CP047859.1_1291150_1291636_-	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|280aa|up_1|NZ_CP047859.1_1291643_1292483_-	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|311aa|up_0|NZ_CP047859.1_1292488_1293421_-	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|949aa|down_0|NZ_CP047859.1_1294084_1296931_-	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|662aa|down_1|NZ_CP047859.1_1296938_1298924_-	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|79aa|down_2|NZ_CP047859.1_1299192_1299429_-	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|217aa|down_3|NZ_CP047859.1_1299425_1300076_-	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|280aa|down_4|NZ_CP047859.1_1300249_1301089_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|36aa|down_5|NZ_CP047859.1_1301236_1301344_-	NA	NA|370aa|down_6|NZ_CP047859.1_1301497_1302608_-	PRK00578, prfB, peptide chain release factor 2; Validated	NA|35aa|down_7|NZ_CP047859.1_1302776_1302881_-	NA	NA|844aa|down_8|NZ_CP047859.1_1302922_1305454_-	PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed	NA|191aa|down_9|NZ_CP047859.1_1305867_1306440_-	COG1544, COG1544, Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]
GCF_009913095.1_ASM991309v1	NZ_CP047859	Staphylococcus aureus strain UP_1405 chromosome, complete genome	4	1684855-1684957	4	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	CAAATTTAATACTCAATTCATATA	24	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|179aa|up_7|NZ_CP047859.1_1676473_1677010_+,NA|221aa|up_1|NZ_CP047859.1_1683101_1683764_+,NA|33aa|down_0|NZ_CP047859.1_1685632_1685731_-,NA|128aa|down_6|NZ_CP047859.1_1691978_1692362_+,NA|70aa|down_8|NZ_CP047859.1_1693186_1693396_+	NA|91aa|up_9|NZ_CP047859.1_1674706_1674979_+	COG2963, COG2963, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|235aa|up_8|NZ_CP047859.1_1675377_1676082_+	pfam02452, PemK_toxin, PemK-like, MazF-like toxin of type II toxin-antitoxin system	NA|179aa|up_7|NZ_CP047859.1_1676473_1677010_+	NA	NA|514aa|up_6|NZ_CP047859.1_1677122_1678664_-	PRK00074, guaA, GMP synthase; Reviewed	NA|489aa|up_5|NZ_CP047859.1_1678688_1680155_-	PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase; Reviewed	NA|423aa|up_4|NZ_CP047859.1_1680192_1681461_-	TIGR03173, pbuX, xanthine permease	NA|193aa|up_3|NZ_CP047859.1_1681460_1682039_-	PRK09219, PRK09219, xanthine phosphoribosyltransferase; Validated	NA|136aa|up_2|NZ_CP047859.1_1682551_1682959_+	pfam11181, YflT, Heat induced stress protein YflT	NA|221aa|up_1|NZ_CP047859.1_1683101_1683764_+	NA	NA|319aa|up_0|NZ_CP047859.1_1683881_1684838_+	TIGR02168, Chromosome_partition_protein_Smc, chromosome segregation protein SMC, common bacterial type	NA|33aa|down_0|NZ_CP047859.1_1685632_1685731_-	NA	NA|463aa|down_1|NZ_CP047859.1_1685815_1687204_+	COG1823, COG1823, Predicted Na+/dicarboxylate symporter [General function prediction only]	NA|252aa|down_2|NZ_CP047859.1_1687283_1688039_-	cd02146, NfsA-like, nitroreductase similar to Escherichia coli NfsA	NA|190aa|down_3|NZ_CP047859.1_1688530_1689100_+	TIGR03137, AhpC, peroxiredoxin	NA|508aa|down_4|NZ_CP047859.1_1689115_1690639_+	PRK15317, PRK15317, alkyl hydroperoxide reductase subunit F; Provisional	NA|209aa|down_5|NZ_CP047859.1_1691082_1691709_+	NF033193, lipo_NDxxF, NDxxF motif lipoprotein	NA|128aa|down_6|NZ_CP047859.1_1691978_1692362_+	NA	NA|194aa|down_7|NZ_CP047859.1_1692427_1693009_-	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only]	NA|70aa|down_8|NZ_CP047859.1_1693186_1693396_+	NA	NA|84aa|down_9|NZ_CP047859.1_1693434_1693686_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCF_009913095.1_ASM991309v1	NZ_CP047859	Staphylococcus aureus strain UP_1405 chromosome, complete genome	5	2344315-2344448	1	PILER-CR	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	TATTGAAGAAGATACAA	17	2	2	2344332-2344377|2344395-2344431	NZ_CP047859.1_2340808-2340853|NZ_CP047859.1_2340871-2340907	NA	2	2	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|67aa|up_1|NZ_CP047859.1_2337984_2338185_+,NA|78aa|down_5|NZ_CP047859.1_2352763_2352997_+,NA|103aa|down_6|NZ_CP047859.1_2353104_2353413_-,NA|89aa|down_7|NZ_CP047859.1_2353556_2353823_-	NA|426aa|up_9|NZ_CP047859.1_2327981_2329259_+	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|608aa|up_8|NZ_CP047859.1_2329735_2331559_+	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|139aa|up_7|NZ_CP047859.1_2331697_2332114_+	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|231aa|up_6|NZ_CP047859.1_2332344_2333037_+	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|255aa|up_5|NZ_CP047859.1_2333201_2333966_+	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|227aa|up_4|NZ_CP047859.1_2334118_2334799_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|518aa|up_3|NZ_CP047859.1_2334822_2336376_+	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|453aa|up_2|NZ_CP047859.1_2336492_2337851_+	TIGR00791, Gluconate_permease, gluconate transporter	NA|67aa|up_1|NZ_CP047859.1_2337984_2338185_+	NA	NA|997aa|up_0|NZ_CP047859.1_2338319_2341310_+	pfam10425, SdrG_C_C, C-terminus of bacterial fibrinogen-binding adhesin	NA|289aa|down_0|NZ_CP047859.1_2345056_2345923_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|248aa|down_1|NZ_CP047859.1_2346133_2346877_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|119aa|down_2|NZ_CP047859.1_2347198_2347555_+	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|1116aa|down_3|NZ_CP047859.1_2347859_2351207_+	pfam18483, Bact_lectin, Bacterial lectin	NA|359aa|down_4|NZ_CP047859.1_2351590_2352667_+	cd06173, MFS_MefA_like, Macrolide efflux protein A and similar proteins of the Major Facilitator Superfamily of transporters	NA|78aa|down_5|NZ_CP047859.1_2352763_2352997_+	NA	NA|103aa|down_6|NZ_CP047859.1_2353104_2353413_-	NA	NA|89aa|down_7|NZ_CP047859.1_2353556_2353823_-	NA	NA|603aa|down_8|NZ_CP047859.1_2354106_2355915_-	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|131aa|down_9|NZ_CP047859.1_2356046_2356439_+	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)
GCF_009913095.1_ASM991309v1	NZ_CP047859	Staphylococcus aureus strain UP_1405 chromosome, complete genome	6	2419860-2419938	5	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	TGCAAGTTGGCGGGGCCCCAACA	23	1	4	2419883-2419915|2419883-2419915|2419883-2419915|2419883-2419915	NZ_CP047859.1_1244706-1244738|NZ_CP047859.1_1280925-1280957|NZ_CP047859.1_2812781-2812749|NZ_CP047859.1_1280981-1281013	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|220aa|up_3|NZ_CP047859.1_2416784_2417444_-,NA|36aa|up_0|NZ_CP047859.1_2419433_2419541_+,NA	NA|693aa|up_9|NZ_CP047859.1_2409246_2411325_-	COG0025, NhaP, NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]	NA|470aa|up_8|NZ_CP047859.1_2411462_2412872_-	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|269aa|up_7|NZ_CP047859.1_2413157_2413964_+	TIGR03729, acc_ester, putative phosphoesterase	NA|219aa|up_6|NZ_CP047859.1_2414026_2414683_-	COG4990, COG4990, Uncharacterized protein conserved in bacteria [Function unknown]	NA|158aa|up_5|NZ_CP047859.1_2414795_2415269_+	COG3708, COG3708, Uncharacterized protein conserved in bacteria [Function unknown]	NA|404aa|up_4|NZ_CP047859.1_2415391_2416603_-	cd17320, MFS_MdfA_MDR_like, Multidrug transporter MdfA and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily	NA|220aa|up_3|NZ_CP047859.1_2416784_2417444_-	NA	NA|381aa|up_2|NZ_CP047859.1_2417503_2418646_-	TIGR00045, Glycerate_kinase, glycerate kinase	NA|129aa|up_1|NZ_CP047859.1_2418913_2419300_+	COG2246, COG2246, Predicted membrane protein [Function unknown]	NA|36aa|up_0|NZ_CP047859.1_2419433_2419541_+	NA	NA|588aa|down_0|NZ_CP047859.1_2420243_2422007_+	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|578aa|down_1|NZ_CP047859.1_2422031_2423765_+	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|229aa|down_2|NZ_CP047859.1_2424217_2424904_+	COG0132, BioD, Dethiobiotin synthetase [Coenzyme metabolism]	NA|453aa|down_3|NZ_CP047859.1_2424881_2426240_+	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase	NA|336aa|down_4|NZ_CP047859.1_2426241_2427249_+	PRK06256, PRK06256, biotin synthase; Validated	NA|372aa|down_5|NZ_CP047859.1_2427226_2428342_+	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|231aa|down_6|NZ_CP047859.1_2428352_2429045_+	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|156aa|down_7|NZ_CP047859.1_2429055_2429523_+	pfam06177, QueT, QueT transporter	NA|326aa|down_8|NZ_CP047859.1_2429574_2430552_-	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|316aa|down_9|NZ_CP047859.1_2430553_2431501_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family
GCF_009913095.1_ASM991309v1	NZ_CP047859	Staphylococcus aureus strain UP_1405 chromosome, complete genome	7	2584646-2584726	6	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	CAAGTTGGCGGGGCCCCAACACAGA	25	1	13	2584671-2584701|2584671-2584701|2584671-2584701|2584671-2584701|2584671-2584701|2584671-2584701|2584671-2584701|2584671-2584701|2584671-2584701|2584671-2584701|2584671-2584701|2584671-2584701|2584671-2584701	NZ_CP047859.1_1280985-1281015|NZ_CP047859.1_396400-396370|NZ_CP047859.1_726608-726578|NZ_CP047859.1_932707-932677|NZ_CP047859.1_1461637-1461607|NZ_CP047859.1_1723694-1723664|NZ_CP047859.1_80559-80589|NZ_CP047859.1_638146-638176|NZ_CP047859.1_1035268-1035298|NZ_CP047859.1_1244710-1244740|NZ_CP047859.1_1280929-1280959|NZ_CP047859.1_2021798-2021828|NZ_CP047859.1_2595472-2595502	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|62aa|down_0|NZ_CP047859.1_2584767_2584953_-,NA|84aa|down_5|NZ_CP047859.1_2588092_2588344_-,NA|106aa|down_8|NZ_CP047859.1_2593465_2593783_-,NA|55aa|down_9|NZ_CP047859.1_2594027_2594192_-	NA|202aa|up_9|NZ_CP047859.1_2577538_2578144_+	COG4148, ModC, ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]	NA|335aa|up_8|NZ_CP047859.1_2578313_2579318_+	PRK07688, PRK07688, thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated	NA|169aa|up_7|NZ_CP047859.1_2579348_2579855_+	COG0521, MoaB, Molybdopterin biosynthesis enzymes [Coenzyme metabolism]	NA|165aa|up_6|NZ_CP047859.1_2579856_2580351_-	PRK09364, moaC, cyclic pyranopterin monophosphate synthase MoaC	NA|420aa|up_5|NZ_CP047859.1_2580413_2581673_+	cd00887, MoeA, MoeA family	NA|162aa|up_4|NZ_CP047859.1_2581669_2582155_+	COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]	NA|149aa|up_3|NZ_CP047859.1_2582168_2582615_+	COG0314, MoaE, Molybdopterin converting factor, large subunit [Coenzyme metabolism]	NA|78aa|up_2|NZ_CP047859.1_2582620_2582854_+	cd00754, Ubl_MoaD, ubiquitin-like (Ubl) domain found in molybdenum cofactor biosynthesis protein D (MoaD) and similar proteins	NA|200aa|up_1|NZ_CP047859.1_2582860_2583460_+	PRK00317, mobA, molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed	NA|341aa|up_0|NZ_CP047859.1_2583479_2584502_+	TIGR02666, Cyclic_pyranopterin_monophosphate_synthase, molybdenum cofactor biosynthesis protein A, bacterial	NA|62aa|down_0|NZ_CP047859.1_2584767_2584953_-	NA	NA|117aa|down_1|NZ_CP047859.1_2585078_2585429_+	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|404aa|down_2|NZ_CP047859.1_2585530_2586742_-	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|147aa|down_3|NZ_CP047859.1_2586734_2587175_-	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|255aa|down_4|NZ_CP047859.1_2587336_2588101_+	pfam13468, Glyoxalase_3, Glyoxalase-like domain	NA|84aa|down_5|NZ_CP047859.1_2588092_2588344_-	NA	NA|422aa|down_6|NZ_CP047859.1_2588732_2589998_+	COG2348, COG2348, Peptidoglycan interpeptide bridge formation enzyme [Cell wall/membrane/envelope biogenesis]	NA|1056aa|down_7|NZ_CP047859.1_2590114_2593282_+	COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms]	NA|106aa|down_8|NZ_CP047859.1_2593465_2593783_-	NA	NA|55aa|down_9|NZ_CP047859.1_2594027_2594192_-	NA
GCF_009913095.1_ASM991309v1	NZ_CP047859	Staphylococcus aureus strain UP_1405 chromosome, complete genome	8	2695720-2695805	7	CRISPRCasFinder	no	csa3	DEDDh,csa3,cas3,DinG,WYL,RT	Type I-A	ACTAATGATACGCAAAAATCAGTTGG	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|53aa|down_7|NZ_CP047859.1_2706767_2706926_-,NA|35aa|down_8|NZ_CP047859.1_2707605_2707710_+,NA|364aa|down_9|NZ_CP047859.1_2708142_2709234_-	NA|228aa|up_9|NZ_CP047859.1_2670650_2671334_+	COG1272, COG1272, Predicted membrane protein, hemolysin III homolog [General function prediction only]	NA|448aa|up_8|NZ_CP047859.1_2671510_2672854_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|158aa|up_7|NZ_CP047859.1_2672952_2673426_+	pfam17080, SepA, Multidrug Resistance efflux pump	NA|481aa|up_6|NZ_CP047859.1_2673748_2675191_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|355aa|up_5|NZ_CP047859.1_2675338_2676403_+	pfam10609, ParA, NUBPL iron-transfer P-loop NTPase	NA|440aa|up_4|NZ_CP047859.1_2682693_2684013_+	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|303aa|up_3|NZ_CP047859.1_2684163_2685072_+	cd09989, Arginase, Arginase family	NA|270aa|up_2|NZ_CP047859.1_2685260_2686070_+	COG1624, COG1624, Uncharacterized conserved protein [Function unknown]	NA|311aa|up_1|NZ_CP047859.1_2686071_2687004_+	COG4856, COG4856, Uncharacterized protein conserved in bacteria [Function unknown]	NA|452aa|up_0|NZ_CP047859.1_2687030_2688386_+	PRK14316, glmM, phosphoglucosamine mutase; Provisional	NA|369aa|down_0|NZ_CP047859.1_2696427_2697534_-	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional	NA|145aa|down_1|NZ_CP047859.1_2697533_2697968_-	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|711aa|down_2|NZ_CP047859.1_2697979_2700112_-	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|513aa|down_3|NZ_CP047859.1_2700146_2701685_-	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|602aa|down_4|NZ_CP047859.1_2702365_2704171_+	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|261aa|down_5|NZ_CP047859.1_2704402_2705185_+	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|286aa|down_6|NZ_CP047859.1_2705252_2706110_+	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|53aa|down_7|NZ_CP047859.1_2706767_2706926_-	NA	NA|35aa|down_8|NZ_CP047859.1_2707605_2707710_+	NA	NA|364aa|down_9|NZ_CP047859.1_2708142_2709234_-	NA
GCF_009913095.1_ASM991309v1	NZ_CP047859	Staphylococcus aureus strain UP_1405 chromosome, complete genome	9	2708045-2708126	8	CRISPRCasFinder	no	csa3	DEDDh,csa3,cas3,DinG,WYL,RT	Type I-A	AAGAAGCCCCTAACAACTAAAGTTG	25	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|53aa|up_1|NZ_CP047859.1_2706767_2706926_-,NA|35aa|up_0|NZ_CP047859.1_2707605_2707710_+,NA|364aa|down_0|NZ_CP047859.1_2708142_2709234_-,NA|77aa|down_5|NZ_CP047859.1_2713020_2713251_+	NA|2482aa|up_9|NZ_CP047859.1_2688663_2696109_+	TIGR04263, cell_wall_surface_anchor_family_protein, SasC/Mrp/FmtB intercellular aggregation domain	NA|369aa|up_8|NZ_CP047859.1_2696427_2697534_-	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional	NA|145aa|up_7|NZ_CP047859.1_2697533_2697968_-	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|711aa|up_6|NZ_CP047859.1_2697979_2700112_-	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|513aa|up_5|NZ_CP047859.1_2700146_2701685_-	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|602aa|up_4|NZ_CP047859.1_2702365_2704171_+	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|261aa|up_3|NZ_CP047859.1_2704402_2705185_+	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|286aa|up_2|NZ_CP047859.1_2705252_2706110_+	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|53aa|up_1|NZ_CP047859.1_2706767_2706926_-	NA	NA|35aa|up_0|NZ_CP047859.1_2707605_2707710_+	NA	NA|364aa|down_0|NZ_CP047859.1_2708142_2709234_-	NA	NA|326aa|down_1|NZ_CP047859.1_2709499_2710477_-	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	csa3|107aa|down_2|NZ_CP047859.1_2710478_2710799_-	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|222aa|down_3|NZ_CP047859.1_2710950_2711616_+	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	NA|313aa|down_4|NZ_CP047859.1_2712051_2712990_+	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|77aa|down_5|NZ_CP047859.1_2713020_2713251_+	NA	NA|458aa|down_6|NZ_CP047859.1_2713922_2715296_+	pfam01878, EVE, EVE domain	NA|138aa|down_7|NZ_CP047859.1_2715752_2716166_+	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|148aa|down_8|NZ_CP047859.1_2716365_2716809_+	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|237aa|down_9|NZ_CP047859.1_2716929_2717640_-	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase
GCF_009913095.1_ASM991309v1	NZ_CP047859	Staphylococcus aureus strain UP_1405 chromosome, complete genome	10	2836767-2836848	9	CRISPRCasFinder	no	DEDDh	DEDDh,csa3,cas3,DinG,WYL,RT	Unclear	ACAATGCAAGTTGGGGTGGGGGCC	24	1	5	2836791-2836824|2836791-2836824|2836791-2836824|2836791-2836824|2836791-2836824	NZ_CP047859.1_938308-938275|NZ_CP047859.1_1293726-1293759|NZ_CP047859.1_284329-284296|NZ_CP047859.1_722160-722193|NZ_CP047859.1_2146027-2146060	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|81aa|down_4|NZ_CP047859.1_2843039_2843282_-,NA|61aa|down_6|NZ_CP047859.1_2844375_2844558_-,NA|114aa|down_7|NZ_CP047859.1_2844761_2845103_-	NA|48aa|up_9|NZ_CP047859.1_2826951_2827095_-	smart00794, AgrD, Staphylococcal AgrD protein	NA|188aa|up_8|NZ_CP047859.1_2827097_2827661_-	COG4512, AgrB, Membrane protein putatively involved in post-translational modification of the autoinducing quorum-sensing peptide [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms / Transcription]	NA|45aa|up_7|NZ_CP047859.1_2827896_2828031_+	PRK14752, PRK14752, delta-lysin family phenol-soluble modulin	NA|262aa|up_6|NZ_CP047859.1_2828630_2829416_-	cd07583, nitrilase_5, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases)	NA|209aa|up_5|NZ_CP047859.1_2829776_2830403_-	COG3560, FMR2, Predicted oxidoreductase related to nitroreductase [General function prediction only]	NA|420aa|up_4|NZ_CP047859.1_2830599_2831859_+	PRK10819, PRK10819, transport protein TonB; Provisional	NA|248aa|up_3|NZ_CP047859.1_2831883_2832627_-	pfam02517, Abi, CAAX protease self-immunity	NA|95aa|up_2|NZ_CP047859.1_2832801_2833086_+	PRK00364, groES, co-chaperonin GroES; Reviewed	NA|539aa|up_1|NZ_CP047859.1_2833161_2834778_+	PRK00013, groEL, chaperonin GroEL; Reviewed	NA|436aa|up_0|NZ_CP047859.1_2835317_2836625_-	TIGR00933, Trk_system_potassium_uptake_protein_trkH	NA|408aa|down_0|NZ_CP047859.1_2837068_2838292_-	PRK08588, PRK08588, succinyl-diaminopimelate desuccinylase; Reviewed	NA|352aa|down_1|NZ_CP047859.1_2838727_2839783_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|339aa|down_2|NZ_CP047859.1_2839804_2840821_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|346aa|down_3|NZ_CP047859.1_2841939_2842977_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|81aa|down_4|NZ_CP047859.1_2843039_2843282_-	NA	NA|328aa|down_5|NZ_CP047859.1_2843292_2844276_-	pfam00535, Glycos_transf_2, Glycosyl transferase family 2	NA|61aa|down_6|NZ_CP047859.1_2844375_2844558_-	NA	NA|114aa|down_7|NZ_CP047859.1_2844761_2845103_-	NA	DEDDh|311aa|down_8|NZ_CP047859.1_2845108_2846041_-	PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated	NA|238aa|down_9|NZ_CP047859.1_2846056_2846770_-	COG2932, COG2932, Predicted transcriptional regulator [Transcription]
