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_011403135.1_ASM1140313v1	NZ_AP021848	Staphylococcus lugdunensis strain JICS135	1	119251-120320	1	CRT	no		csa3,WYL,DEDDh,cas3,DinG	Orphan	GANTCAGACGCAGATAGCGA	20	2	2	119505-119550|119943-120012	NZ_AP021848.1_119241-119286|NZ_AP021848.1_119235-119304	NA	14	14	Orphan	csa3,WYL,DEDDh,cas3,DinG	NA|59aa|up_9|NZ_AP021848.1_107700_107877_-,NA|101aa|up_8|NZ_AP021848.1_107882_108185_-,NA|60aa|up_5|NZ_AP021848.1_110307_110487_-,NA|148aa|up_4|NZ_AP021848.1_110616_111060_+,NA|539aa|down_0|NZ_AP021848.1_120639_122256_+,NA|162aa|down_6|NZ_AP021848.1_128666_129152_+	NA|59aa|up_9|NZ_AP021848.1_107700_107877_-	NA	NA|101aa|up_8|NZ_AP021848.1_107882_108185_-	NA	NA|398aa|up_7|NZ_AP021848.1_108337_109531_+	COG0446, HcaD, Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]	NA|232aa|up_6|NZ_AP021848.1_109615_110311_-	smart00939, PepX_C, X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain	NA|60aa|up_5|NZ_AP021848.1_110307_110487_-	NA	NA|148aa|up_4|NZ_AP021848.1_110616_111060_+	NA	NA|443aa|up_3|NZ_AP021848.1_111146_112475_-	cd07724, POD-like_MBL-fold, ETHE1 (PDO type I), persulfide dioxygenase A (PDOA, PDO type II) and related proteins; MBL-fold metallo-hydrolase domain	NA|358aa|up_2|NZ_AP021848.1_112493_113567_-	pfam13686, DrsE_2, DsrE/DsrF/DrsH-like family	NA|87aa|up_1|NZ_AP021848.1_113705_113966_+	cd10155, BsYrkD-like_DUF156, Uncharacterized protein YrkD from Bacillus subtilis and related domains; this domain superfamily was previously known as part of DUF156	NA|253aa|up_0|NZ_AP021848.1_113962_114721_+	pfam01925, TauE, Sulfite exporter TauE/SafE	NA|539aa|down_0|NZ_AP021848.1_120639_122256_+	NA	NA|504aa|down_1|NZ_AP021848.1_122415_123927_-	cd04949, GT4_GtfA-like, accessory Sec system glycosyltransferase GtfA and similar proteins	NA|553aa|down_2|NZ_AP021848.1_123949_125608_-	COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]	NA|133aa|down_3|NZ_AP021848.1_125601_126000_-	PRK11929, PRK11929, bifunctional UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase MurE/UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase MurF	NA|139aa|down_4|NZ_AP021848.1_126949_127366_-	COG2128, COG2128, Uncharacterized conserved protein [Function unknown]	NA|138aa|down_5|NZ_AP021848.1_127468_127882_+	smart00344, HTH_ASNC, helix_turn_helix ASNC type	NA|162aa|down_6|NZ_AP021848.1_128666_129152_+	NA	NA|327aa|down_7|NZ_AP021848.1_129626_130607_+	TIGR03395, Sphingomyelinase_C, sphingomyelin phosphodiesterase	NA|185aa|down_8|NZ_AP021848.1_130714_131269_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|305aa|down_9|NZ_AP021848.1_131444_132359_+	COG1073, COG1073, Hydrolases of the alpha/beta superfamily [General function prediction only]
GCF_011403135.1_ASM1140313v1	NZ_AP021848	Staphylococcus lugdunensis strain JICS135	2	312387-312477	1	CRISPRCasFinder	no		csa3,WYL,DEDDh,cas3,DinG	Orphan	CCCCAACTTGCTTTGCTTGATGAATTTCTTTTT	33	0	0	NA	NA	NA	1	1	Orphan	csa3,WYL,DEDDh,cas3,DinG	NA|107aa|up_9|NZ_AP021848.1_302347_302668_+,NA|90aa|up_8|NZ_AP021848.1_302731_303001_+,NA|193aa|up_5|NZ_AP021848.1_305168_305747_-,NA	NA|107aa|up_9|NZ_AP021848.1_302347_302668_+	NA	NA|90aa|up_8|NZ_AP021848.1_302731_303001_+	NA	NA|266aa|up_7|NZ_AP021848.1_303374_304172_-	pfam00797, Acetyltransf_2, N-acetyltransferase	NA|252aa|up_6|NZ_AP021848.1_304309_305065_-	PRK12826, PRK12826, SDR family oxidoreductase	NA|193aa|up_5|NZ_AP021848.1_305168_305747_-	NA	NA|512aa|up_4|NZ_AP021848.1_305994_307530_+	TIGR02002, PTS_system_glucose-specific_IIABC_component, PTS system, glucose-specific IIBC component	NA|257aa|up_3|NZ_AP021848.1_307735_308506_-	cd05349, BKR_2_SDR_c, putative beta-ketoacyl acyl carrier protein [ACP]reductase (BKR), subgroup 2, classical (c) SDR	NA|478aa|up_2|NZ_AP021848.1_308526_309960_-	cd07080, ALDH_Acyl-CoA-Red_LuxC, Acyl-CoA reductase LuxC	NA|356aa|up_1|NZ_AP021848.1_309972_311040_-	pfam04443, LuxE, Acyl-protein synthetase, LuxE	NA|191aa|up_0|NZ_AP021848.1_311541_312114_+	COG4721, COG4721, ABC-type cobalt transport system, predicted permease component [Inorganic ion transport and metabolism]	NA|459aa|down_0|NZ_AP021848.1_312543_313920_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|1011aa|down_1|NZ_AP021848.1_313932_316965_-	cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4	NA|299aa|down_2|NZ_AP021848.1_317042_317939_-	COG1477, ApbE, Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]	NA|171aa|down_3|NZ_AP021848.1_318258_318771_+	COG3247, HdeD, Uncharacterized conserved protein [Function unknown]	NA|400aa|down_4|NZ_AP021848.1_319283_320483_+	COG1168, MalY, Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]	NA|451aa|down_5|NZ_AP021848.1_321794_323147_+	TIGR01350, Dihydrolipoyl_dehydrogenase, dihydrolipoamide dehydrogenase	NA|316aa|down_6|NZ_AP021848.1_323235_324183_+	cd02000, TPP_E1_PDC_ADC_BCADC, Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain alpha-keto acid dehydrogenase/2-oxoisovalerate dehydrogenase complex (BCADC)	NA|347aa|down_7|NZ_AP021848.1_324198_325239_+	COG0022, AcoB, Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]	NA|431aa|down_8|NZ_AP021848.1_325256_326549_+	PRK11856, PRK11856, branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed	NA|113aa|down_9|NZ_AP021848.1_326694_327033_+	COG1695, COG1695, Predicted transcriptional regulators [Transcription]
GCF_011403135.1_ASM1140313v1	NZ_AP021848	Staphylococcus lugdunensis strain JICS135	3	1124164-1124253	2	CRISPRCasFinder	no		csa3,WYL,DEDDh,cas3,DinG	Orphan	TGATTGAGAAGTCAGTCGAAAAAC	24	0	0	NA	NA	NA	1	1	Orphan	csa3,WYL,DEDDh,cas3,DinG	NA,NA|49aa|down_2|NZ_AP021848.1_1124806_1124953_+,NA|70aa|down_3|NZ_AP021848.1_1124945_1125155_+,NA|115aa|down_9|NZ_AP021848.1_1129792_1130137_+	NA|48aa|up_9|NZ_AP021848.1_1114372_1114516_-	smart00794, AgrD, Staphylococcal AgrD protein	NA|189aa|up_8|NZ_AP021848.1_1114518_1115085_-	smart00793, AgrB, Accessory gene regulator B	NA|262aa|up_7|NZ_AP021848.1_1115712_1116498_-	cd07583, nitrilase_5, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases)	NA|208aa|up_6|NZ_AP021848.1_1116632_1117256_-	COG3560, FMR2, Predicted oxidoreductase related to nitroreductase [General function prediction only]	NA|471aa|up_5|NZ_AP021848.1_1117449_1118862_+	pfam05297, Herpes_LMP1, Herpesvirus latent membrane protein 1 (LMP1)	NA|247aa|up_4|NZ_AP021848.1_1119280_1120021_-	pfam02517, Abi, CAAX protease self-immunity	NA|95aa|up_3|NZ_AP021848.1_1120201_1120486_+	PRK00364, groES, co-chaperonin GroES; Reviewed	NA|541aa|up_2|NZ_AP021848.1_1120545_1122168_+	PRK00013, groEL, chaperonin GroEL; Reviewed	NA|391aa|up_1|NZ_AP021848.1_1122236_1123409_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|225aa|up_0|NZ_AP021848.1_1123422_1124097_-	pfam13443, HTH_26, Cro/C1-type HTH DNA-binding domain	NA|73aa|down_0|NZ_AP021848.1_1124269_1124488_+	smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|106aa|down_1|NZ_AP021848.1_1124492_1124810_+	TIGR01764, Probable_excisionase, DNA binding domain, excisionase family	NA|49aa|down_2|NZ_AP021848.1_1124806_1124953_+	NA	NA|70aa|down_3|NZ_AP021848.1_1124945_1125155_+	NA	NA|108aa|down_4|NZ_AP021848.1_1125157_1125481_+	pfam07342, DUF1474, Protein of unknown function (DUF1474)	NA|290aa|down_5|NZ_AP021848.1_1125544_1126414_+	smart00942, PriCT_1, Primase C terminal 1 (PriCT-1)	NA|570aa|down_6|NZ_AP021848.1_1126427_1128137_+	COG5519, COG5519, Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair]	NA|122aa|down_7|NZ_AP021848.1_1128484_1128850_+	cd03313, enolase, Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways	NA|214aa|down_8|NZ_AP021848.1_1128863_1129505_+	pfam16560, SAPI, Putative mobile pathogenicity island	NA|115aa|down_9|NZ_AP021848.1_1129792_1130137_+	NA
GCF_011403135.1_ASM1140313v1	NZ_AP021848	Staphylococcus lugdunensis strain JICS135	4	1367793-1367883	3	CRISPRCasFinder	no		csa3,WYL,DEDDh,cas3,DinG	Orphan	AAACTCGCCATGCTCGTTAAGTGC	24	0	0	NA	NA	NA	1	1	Orphan	csa3,WYL,DEDDh,cas3,DinG	NA,NA	NA|286aa|up_9|NZ_AP021848.1_1354849_1355707_+	PRK05654, PRK05654, acetyl-CoA carboxylase carboxyltransferase subunit beta	NA|315aa|up_8|NZ_AP021848.1_1355708_1356653_+	PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated	NA|323aa|up_7|NZ_AP021848.1_1356815_1357784_+	PRK03202, PRK03202, ATP-dependent 6-phosphofructokinase	NA|587aa|up_6|NZ_AP021848.1_1357801_1359562_+	PRK06354, PRK06354, pyruvate kinase; Provisional	NA|161aa|up_5|NZ_AP021848.1_1359863_1360346_+	COG1943, COG1943, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|453aa|up_4|NZ_AP021848.1_1360853_1362212_-	PRK11049, PRK11049, D-alanine/D-serine/glycine permease; Provisional	NA|373aa|up_3|NZ_AP021848.1_1362553_1363672_+	PRK14035, PRK14035, citrate synthase; Provisional	NA|423aa|up_2|NZ_AP021848.1_1363719_1364988_+	PRK07006, PRK07006, isocitrate dehydrogenase; Reviewed	NA|237aa|up_1|NZ_AP021848.1_1365191_1365902_+	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|570aa|up_0|NZ_AP021848.1_1365901_1367611_+	TIGR02966, Phosphate_regulon_sensor_protein_PhoR, phosphate regulon sensor kinase PhoR	NA|878aa|down_0|NZ_AP021848.1_1367930_1370564_+	PRK05755, PRK05755, DNA polymerase I; Provisional	NA|291aa|down_1|NZ_AP021848.1_1370580_1371453_+	COG0266, Nei, Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]	NA|202aa|down_2|NZ_AP021848.1_1371468_1372074_+	PRK00081, coaE, dephospho-CoA kinase; Reviewed	NA|334aa|down_3|NZ_AP021848.1_1372220_1373222_+	PRK07729, PRK07729, glyceraldehyde-3-phosphate dehydrogenase; Validated	NA|336aa|down_4|NZ_AP021848.1_1373394_1374402_+	PRK06256, PRK06256, biotin synthase; Validated	NA|157aa|down_5|NZ_AP021848.1_1374718_1375189_+	PRK00464, nrdR, transcriptional repressor NrdR	NA|459aa|down_6|NZ_AP021848.1_1375189_1376566_+	COG3611, DnaB, Replication initiation/membrane attachment protein [DNA replication, recombination, and repair]	NA|307aa|down_7|NZ_AP021848.1_1376565_1377486_+	PRK08939, PRK08939, primosomal protein DnaI; Reviewed	NA|646aa|down_8|NZ_AP021848.1_1377845_1379783_+	PRK00413, thrS, threonyl-tRNA synthetase; Reviewed	NA|498aa|down_9|NZ_AP021848.1_1380246_1381740_+	COG0833, LysP, Amino acid transporters [Amino acid transport and metabolism]
GCF_011403135.1_ASM1140313v1	NZ_AP021848	Staphylococcus lugdunensis strain JICS135	5	1799547-1799633	4	CRISPRCasFinder	no		csa3,WYL,DEDDh,cas3,DinG	Orphan	GAAATTCGACAAACAAAGCAAGTTGGGGTG	30	1	1	1799577-1799603	NZ_AP021848.1_2361026-2361000	NA	1	1	Orphan	csa3,WYL,DEDDh,cas3,DinG	NA,NA	NA|241aa|up_9|NZ_AP021848.1_1787929_1788652_-	PRK00358, pyrH, uridylate kinase; Provisional	NA|293aa|up_8|NZ_AP021848.1_1788788_1789667_-	PRK09377, tsf, elongation factor Ts; Provisional	NA|263aa|up_7|NZ_AP021848.1_1789850_1790639_-	PRK05299, rpsB, 30S ribosomal protein S2; Provisional	NA|258aa|up_6|NZ_AP021848.1_1790857_1791631_-	PRK04158, PRK04158, GTP-sensing pleiotropic transcriptional regulator CodY	NA|468aa|up_5|NZ_AP021848.1_1791652_1793056_-	PRK05201, hslU, ATP-dependent protease ATPase subunit HslU	NA|181aa|up_4|NZ_AP021848.1_1793102_1793645_-	PRK05456, PRK05456, ATP-dependent protease subunit HslV	NA|298aa|up_3|NZ_AP021848.1_1793645_1794539_-	TIGR02224, Tyrosine_recombinase_XerC, tyrosine recombinase XerC	NA|436aa|up_2|NZ_AP021848.1_1794670_1795978_-	PRK05335, PRK05335, tRNA (uracil-5-)-methyltransferase Gid; Reviewed	NA|692aa|up_1|NZ_AP021848.1_1796029_1798105_-	PRK05582, PRK05582, type I DNA topoisomerase	NA|291aa|up_0|NZ_AP021848.1_1798270_1799143_-	pfam02481, DNA_processg_A, DNA recombination-mediator protein A	NA|412aa|down_0|NZ_AP021848.1_1799801_1801037_-	pfam02388, FemAB, FemAB family	NA|303aa|down_1|NZ_AP021848.1_1801199_1802108_-	PRK05678, PRK05678, succinyl-CoA synthetase subunit alpha; Validated	NA|389aa|down_2|NZ_AP021848.1_1802129_1803296_-	PRK00696, sucC, ADP-forming succinate--CoA ligase subunit beta	NA|256aa|down_3|NZ_AP021848.1_1803406_1804174_-	cd07182, RNase_HII_bacteria_HII_like, Bacterial Ribonuclease HII-like	NA|295aa|down_4|NZ_AP021848.1_1804157_1805042_-	PRK09563, rbgA, GTPase YlqF; Reviewed	NA|864aa|down_5|NZ_AP021848.1_1805298_1807890_+	pfam09586, YfhO, Bacterial membrane protein YfhO	NA|869aa|down_6|NZ_AP021848.1_1807894_1810501_+	COG4485, COG4485, Predicted membrane protein [Function unknown]	NA|117aa|down_7|NZ_AP021848.1_1810747_1811098_-	PRK05338, rplS, 50S ribosomal protein L19; Provisional	NA|246aa|down_8|NZ_AP021848.1_1811203_1811941_-	PRK00026, trmD, tRNA (guanine-N(1)-)-methyltransferase; Reviewed	NA|167aa|down_9|NZ_AP021848.1_1811940_1812441_-	PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional
GCF_011403135.1_ASM1140313v1	NZ_AP021848	Staphylococcus lugdunensis strain JICS135	6	2318500-2318580	5	CRISPRCasFinder	no		csa3,WYL,DEDDh,cas3,DinG	Orphan	GGGGCCCCAGCACAAAGAAATGC	23	0	0	NA	NA	NA	1	1	Orphan	csa3,WYL,DEDDh,cas3,DinG	NA|34aa|up_9|NZ_AP021848.1_2310947_2311049_-,NA|227aa|up_5|NZ_AP021848.1_2314324_2315005_+,NA|99aa|up_1|NZ_AP021848.1_2316725_2317022_-,NA|151aa|up_0|NZ_AP021848.1_2317147_2317600_-,NA|56aa|down_3|NZ_AP021848.1_2321846_2322014_-	NA|34aa|up_9|NZ_AP021848.1_2310947_2311049_-	NA	NA|311aa|up_8|NZ_AP021848.1_2311156_2312089_-	COG0523, COG0523, Putative GTPases (G3E family) [General function prediction only]	NA|147aa|up_7|NZ_AP021848.1_2312313_2312754_+	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|291aa|up_6|NZ_AP021848.1_2313135_2314008_+	PRK00281, PRK00281, undecaprenyl-diphosphate phosphatase	NA|227aa|up_5|NZ_AP021848.1_2314324_2315005_+	NA	NA|149aa|up_4|NZ_AP021848.1_2315009_2315456_+	PRK00124, PRK00124, YaiI/YqxD family protein	NA|189aa|up_3|NZ_AP021848.1_2315471_2316038_+	TIGR00730, LOG_family_protein_YJL055W, TIGR00730 family protein	NA|181aa|up_2|NZ_AP021848.1_2316069_2316612_-	pfam13302, Acetyltransf_3, Acetyltransferase (GNAT) domain	NA|99aa|up_1|NZ_AP021848.1_2316725_2317022_-	NA	NA|151aa|up_0|NZ_AP021848.1_2317147_2317600_-	NA	NA|162aa|down_0|NZ_AP021848.1_2318949_2319435_-	COG2839, COG2839, Uncharacterized protein conserved in bacteria [Function unknown]	NA|406aa|down_1|NZ_AP021848.1_2319436_2320654_-	cd17471, MFS_Set, Sugar efflux transporter (Set) family of the Major Facilitator Superfamily of transporters	NA|285aa|down_2|NZ_AP021848.1_2320739_2321594_-	COG0583, LysR, Transcriptional regulator [Transcription]	NA|56aa|down_3|NZ_AP021848.1_2321846_2322014_-	NA	NA|205aa|down_4|NZ_AP021848.1_2322101_2322716_-	COG2306, COG2306, Predicted RNA-binding protein, associated with RNAses E/G family [General function prediction only]	NA|156aa|down_5|NZ_AP021848.1_2323099_2323567_-	cd06121, cupin_YML079wp, Saccharomyces cerevisiae YML079wp and related proteins, cupin domain	NA|239aa|down_6|NZ_AP021848.1_2323566_2324283_-	PRK12378, PRK12378, YebC/PmpR family DNA-binding transcriptional regulator	NA|120aa|down_7|NZ_AP021848.1_2324516_2324876_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|715aa|down_8|NZ_AP021848.1_2325019_2327164_-	COG2207, AraC, AraC-type DNA-binding domain-containing proteins [Transcription]	NA|218aa|down_9|NZ_AP021848.1_2327472_2328126_-	COG0670, COG0670, Integral membrane protein, interacts with FtsH [General function prediction only]
