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_900474985.1_41965_C01	NZ_LS483339	Streptococcus thermophilus strain NCTC12958 chromosome 1	1	571739-571848	1	CRISPRCasFinder	no		cas3,DEDDh,RT,cas9,cas1,cas2,csn2,DinG,csa3	Orphan	TAACATCTAGAGAGGACCGGATAGGTCCTTTTTTTATG	38	1	21	571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810|571777-571810	NZ_LS483339.1_348664-348697|NZ_LS483339.1_559291-559324|NZ_LS483339.1_821640-821607|NZ_LS483339.1_825694-825661|NZ_LS483339.1_855837-855870|NZ_LS483339.1_1121081-1121048|NZ_LS483339.1_1154358-1154325|NZ_LS483339.1_1237987-1237954|NZ_LS483339.1_1415660-1415627|NZ_LS483339.1_1444899-1444932|NZ_LS483339.1_1627462-1627495|NZ_LS483339.1_1730699-1730666|NZ_LS483339.1_1740262-1740229|NZ_LS483339.1_1899362-1899329|NZ_LS483339.1_1997995-1997962|NZ_LS483339.1_2022147-2022114|NZ_LS483339.1_28119-28152|NZ_LS483339.1_139324-139357|NZ_LS483339.1_420868-420901|NZ_LS483339.1_919461-919428|NZ_LS483339.1_1615619-1615586	NA	1	1	Orphan	cas3,DEDDh,RT,cas9,cas1,cas2,csn2,DinG,csa3	NA|71aa|up_5|NZ_LS483339.1_564530_564743_+,NA|212aa|down_2|NZ_LS483339.1_574814_575450_-,NA|88aa|down_6|NZ_LS483339.1_578813_579077_+,NA|159aa|down_8|NZ_LS483339.1_579544_580021_+,NA|75aa|down_9|NZ_LS483339.1_580164_580389_+	NA|412aa|up_9|NZ_LS483339.1_560840_562076_+	COG0004, AmtB, Ammonia permease [Inorganic ion transport and metabolism]	NA|114aa|up_8|NZ_LS483339.1_562086_562428_+	COG0347, GlnK, Nitrogen regulatory protein PII [Amino acid transport and metabolism]	NA|219aa|up_7|NZ_LS483339.1_562525_563182_+	COG1705, FlgJ, Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]	NA|274aa|up_6|NZ_LS483339.1_563204_564026_+	cd07516, HAD_Pase, phosphatase, similar to Escherichia coli Cof and Thermotoga maritima TM0651; belongs to the haloacid dehalogenase-like superfamily	NA|71aa|up_5|NZ_LS483339.1_564530_564743_+	NA	NA|197aa|up_4|NZ_LS483339.1_564730_565321_+	COG1283, NptA, Na+/phosphate symporter [Inorganic ion transport and metabolism]	NA|383aa|up_3|NZ_LS483339.1_565405_566554_+	cd00854, NagA, N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate	NA|306aa|up_2|NZ_LS483339.1_568183_569101_+	PRK09348, glyQ, glycyl-tRNA synthetase subunit alpha; Validated	NA|679aa|up_1|NZ_LS483339.1_569386_571423_+	PRK01233, glyS, glycyl-tRNA synthetase subunit beta; Validated	NA|86aa|up_0|NZ_LS483339.1_571435_571693_+	PRK02539, PRK02539, DUF896 family protein	NA|54aa|down_0|NZ_LS483339.1_572277_572439_-	pfam01610, DDE_Tnp_ISL3, Transposase	NA|464aa|down_1|NZ_LS483339.1_573353_574745_+	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|212aa|down_2|NZ_LS483339.1_574814_575450_-	NA	NA|59aa|down_3|NZ_LS483339.1_575751_575928_+	TIGR01995, beta-glucosides_PTS_EIIBCA, PTS system, beta-glucoside-specific IIABC component	NA|412aa|down_4|NZ_LS483339.1_576423_577659_+	TIGR01995, beta-glucosides_PTS_EIIBCA, PTS system, beta-glucoside-specific IIABC component	NA|253aa|down_5|NZ_LS483339.1_577694_578453_-	COG0652, PpiB, Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family [Posttranslational modification, protein turnover, chaperones]	NA|88aa|down_6|NZ_LS483339.1_578813_579077_+	NA	NA|136aa|down_7|NZ_LS483339.1_579140_579548_+	pfam02322, Cyt_bd_oxida_II, Cytochrome bd terminal oxidase subunit II	NA|159aa|down_8|NZ_LS483339.1_579544_580021_+	NA	NA|75aa|down_9|NZ_LS483339.1_580164_580389_+	NA
GCF_900474985.1_41965_C01	NZ_LS483339	Streptococcus thermophilus strain NCTC12958 chromosome 1	2	803250-805592	2,1,1	CRISPRCasFinder,CRT,PILER-CR	no	cas9,cas1,cas2,csn2	cas3,DEDDh,RT,cas9,cas1,cas2,csn2,DinG,csa3	Type II-C,Type II-A,Type II-B	GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC,GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC,GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC	36,36,36	1	1	804011-804040	NZ_LS483339.1_742007-742036	NA:NA:NA	35,35,20	35	TypeII-C,TypeII-A,TypeII-B	cas3,DEDDh,RT,cas9,cas1,cas2,csn2,DinG,csa3	NA|121aa|up_5|NZ_LS483339.1_794926_795289_+,NA	NA|76aa|up_9|NZ_LS483339.1_789809_790037_-	TIGR01716, HTH-type_transcriptional_regulator_rgg, transcriptional activator, Rgg/GadR/MutR family, C-terminal domain	NA|66aa|up_8|NZ_LS483339.1_792887_793085_-	pfam03029, ATP_bind_1, Conserved hypothetical ATP binding protein	NA|131aa|up_7|NZ_LS483339.1_793780_794173_+	pfam08349, DUF1722, Protein of unknown function (DUF1722)	NA|121aa|up_6|NZ_LS483339.1_794169_794532_+	TIGR02328, TIGR02328, conserved hypothetical protein	NA|121aa|up_5|NZ_LS483339.1_794926_795289_+	NA	NA|204aa|up_4|NZ_LS483339.1_796494_797106_+	pfam09911, DUF2140, Uncharacterized protein conserved in bacteria (DUF2140)	cas9|1121aa|up_3|NZ_LS483339.1_797361_800724_+	cd09643, Csn1, CRISPR/Cas system-associated protein Cas9	cas1|304aa|up_2|NZ_LS483339.1_800901_801813_+	cd09720, Cas1_II, CRISPR/Cas system-associated protein Cas1	cas2|108aa|up_1|NZ_LS483339.1_801814_802138_+	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms]	csn2|351aa|up_0|NZ_LS483339.1_802134_803187_+	pfam16813, Cas_St_Csn2, CRISPR-associated protein Csn2 subfamily St	NA|272aa|down_0|NZ_LS483339.1_805633_806449_-	COG3689, COG3689, Predicted membrane protein [Function unknown]	NA|301aa|down_1|NZ_LS483339.1_806448_807351_-	COG0701, COG0701, Predicted permeases [General function prediction only]	NA|711aa|down_2|NZ_LS483339.1_807714_809847_+	COG2183, Tex, Transcriptional accessory protein [Transcription]	NA|147aa|down_3|NZ_LS483339.1_809833_810274_+	PRK04351, PRK04351, SprT family protein	NA|88aa|down_4|NZ_LS483339.1_810338_810602_+	COG1983, PspC, Putative stress-responsive transcriptional regulator [Transcription / Signal transduction mechanisms]	NA|310aa|down_5|NZ_LS483339.1_810729_811659_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|264aa|down_6|NZ_LS483339.1_811658_812450_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|133aa|down_7|NZ_LS483339.1_812571_812970_+	COG4768, COG4768, Uncharacterized protein containing a divergent version of the methyl-accepting chemotaxis-like domain [General function prediction only]	NA|147aa|down_8|NZ_LS483339.1_812982_813423_+	pfam12732, YtxH, YtxH-like protein	NA|99aa|down_9|NZ_LS483339.1_813443_813740_-	pfam11674, DUF3270, Protein of unknown function (DUF3270)
GCF_900474985.1_41965_C01	NZ_LS483339	Streptococcus thermophilus strain NCTC12958 chromosome 1	3	1568082-1569571	3,2,2	CRISPRCasFinder,CRT,PILER-CR	no	csn2,cas2,cas1,cas9	cas3,DEDDh,RT,cas9,cas1,cas2,csn2,DinG,csa3	Type II-C,Type II-A,Type II-B	GTTTTGGAACCATTCGAAACAACACAGCTCTAAAAC,GTTTTGGAACCATTCGAAACAACACAGCTCTAAAAC,GTTTTGGAACCATTCGAAACAACACAGCTCTAAAAC	36,36,36	0	0	NA	NA	II-A,II-B:II-A,II-B:II-A,II-B	22,22,18	22	TypeII-C,TypeII-A,TypeII-B	cas3,DEDDh,RT,cas9,cas1,cas2,csn2,DinG,csa3	NA|148aa|up_5|NZ_LS483339.1_1564874_1565318_-,NA|80aa|up_0|NZ_LS483339.1_1567758_1567998_-,NA	NA|438aa|up_9|NZ_LS483339.1_1562023_1563337_-	PRK12297, obgE, GTPase CgtA; Reviewed	NA|43aa|up_8|NZ_LS483339.1_1563430_1563559_-	pfam13253, DUF4044, Protein of unknown function (DUF4044)	NA|244aa|up_7|NZ_LS483339.1_1563640_1564372_-	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|69aa|up_6|NZ_LS483339.1_1564372_1564579_-	COG3708, COG3708, Uncharacterized protein conserved in bacteria [Function unknown]	NA|148aa|up_5|NZ_LS483339.1_1564874_1565318_-	NA	NA|128aa|up_4|NZ_LS483339.1_1565348_1565732_-	COG2050, PaaI, HGG motif-containing thioesterase, possibly involved in aromatic compounds catabolism [Secondary metabolites biosynthesis,    transport, and catabolism]	NA|102aa|up_3|NZ_LS483339.1_1565825_1566131_-	pfam02566, OsmC, OsmC-like protein	NA|81aa|up_2|NZ_LS483339.1_1566420_1566663_+	COG2182, MalE, Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism]	NA|297aa|up_1|NZ_LS483339.1_1566830_1567721_+	COG0697, RhaT, Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]	NA|80aa|up_0|NZ_LS483339.1_1567758_1567998_-	NA	csn2|220aa|down_0|NZ_LS483339.1_1569892_1570552_-	cd09758, Csn2, CRISPR/Cas system-associated protein Csn2	cas2|115aa|down_1|NZ_LS483339.1_1570541_1570886_-	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms]	cas1|290aa|down_2|NZ_LS483339.1_1570882_1571752_-	cd09720, Cas1_II, CRISPR/Cas system-associated protein Cas1	cas9|1389aa|down_3|NZ_LS483339.1_1571751_1575918_-	TIGR01865, conserved_hypothetical_protein, CRISPR subtype II/NMENI RNA-guided endonuclease Cas9/Csn1	NA|216aa|down_4|NZ_LS483339.1_1576250_1576898_-	cd07500, HAD_PSP, phosphoserine phosphatase (PSP), similar to Methanococcus Jannaschii PSP and Saccharomyces cerevisiae SER2p	NA|575aa|down_5|NZ_LS483339.1_1577009_1578734_-	PRK04778, PRK04778, septation ring formation regulator EzrA; Provisional	NA|651aa|down_6|NZ_LS483339.1_1578830_1580783_-	PRK05644, gyrB, DNA gyrase subunit B; Validated	NA|232aa|down_7|NZ_LS483339.1_1581431_1582127_-	pfam04172, LrgB, LrgB-like family	NA|125aa|down_8|NZ_LS483339.1_1582119_1582494_-	pfam03788, LrgA, LrgA family	NA|118aa|down_9|NZ_LS483339.1_1582773_1583127_-	cd03036, ArsC_like, Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC
GCF_900474985.1_41965_C01	NZ_LS483339	Streptococcus thermophilus strain NCTC12958 chromosome 1	4	1988592-1988673	4	CRISPRCasFinder	no	csa3	cas3,DEDDh,RT,cas9,cas1,cas2,csn2,DinG,csa3	Type I-A	AATAACATTCAAGTGTTTGTTTGAATA	27	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,RT,cas9,cas1,cas2,csn2,DinG,csa3	NA|113aa|up_5|NZ_LS483339.1_1981143_1981482_-,NA|119aa|up_4|NZ_LS483339.1_1981514_1981871_-,NA|100aa|down_6|NZ_LS483339.1_1994758_1995058_-,NA|122aa|down_7|NZ_LS483339.1_1995050_1995416_-	NA|49aa|up_9|NZ_LS483339.1_1979643_1979790_-	TIGR01992, phosphotransferase_system_trehalose_permease, PTS system, trehalose-specific IIBC component	NA|53aa|up_8|NZ_LS483339.1_1979804_1979963_+	COG2188, PhnF, Transcriptional regulators [Transcription]	NA|183aa|up_7|NZ_LS483339.1_1979966_1980515_+	TIGR02404, Trehalose_operon_transcriptional_repressor, trehalose operon repressor, B	NA|187aa|up_6|NZ_LS483339.1_1980570_1981131_-	PRK13690, PRK13690, hypothetical protein; Provisional	NA|113aa|up_5|NZ_LS483339.1_1981143_1981482_-	NA	NA|119aa|up_4|NZ_LS483339.1_1981514_1981871_-	NA	NA|399aa|up_3|NZ_LS483339.1_1983573_1984770_-	pfam00589, Phage_integrase, Phage integrase family	NA|68aa|up_2|NZ_LS483339.1_1984849_1985053_-	pfam09035, Tn916-Xis, Excisionase from transposon Tn916	NA|77aa|up_1|NZ_LS483339.1_1985442_1985673_-	pfam12645, HTH_16, Helix-turn-helix domain	NA|708aa|up_0|NZ_LS483339.1_1986450_1988574_-	cd07545, P-type_ATPase_Cd-like, P-type heavy metal-transporting ATPase, similar to Staphylococcus aureus plasmid pI258 CadA, a cadmium-efflux ATPase	NA|168aa|down_0|NZ_LS483339.1_1988800_1989304_+	pfam01252, Peptidase_A8, Signal peptidase (SPase) II	csa3|112aa|down_1|NZ_LS483339.1_1989474_1989810_-	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|382aa|down_2|NZ_LS483339.1_1989981_1991126_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|419aa|down_3|NZ_LS483339.1_1991188_1992445_-	cd06173, MFS_MefA_like, Macrolide efflux protein A and similar proteins of the Major Facilitator Superfamily of transporters	NA|91aa|down_4|NZ_LS483339.1_1992474_1992747_-	cd04793, LanC, Cyclases involved in the biosynthesis of lantibiotics	NA|335aa|down_5|NZ_LS483339.1_1993045_1994050_+	pfam05598, DUF772, Transposase domain (DUF772)	NA|100aa|down_6|NZ_LS483339.1_1994758_1995058_-	NA	NA|122aa|down_7|NZ_LS483339.1_1995050_1995416_-	NA	NA|157aa|down_8|NZ_LS483339.1_1997660_1998131_+	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|294aa|down_9|NZ_LS483339.1_1998153_1999035_-	PRK07315, PRK07315, fructose-bisphosphate aldolase; Provisional
