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
GCA_003402855.1_ASM340285v1	CP031545	Streptococcus thermophilus strain ST109 chromosome, complete genome	2	634280-637481	2,1,1	CRISPRCasFinder,CRT,PILER-CR	no	cas9,cas1,cas2,csn2	DEDDh,cas3,cas9,cas1,cas2,csn2,DinG,cas6,cas10,csm2gr11,csm3gr7,csm4gr5,csm5gr7,csm6	Type II-A,Type II-B,Type II-C	GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC,GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC,GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC	36,36,36	0	0	NA	NA	NA:NA:NA	48,48,46	48	TypeII-A,TypeII-B,TypeII-C	DEDDh,cas3,cas9,cas1,cas2,csn2,DinG,cas6,cas10,csm2gr11,csm3gr7,csm4gr5,csm5gr7,csm6	NA,NA	NA|305aa|up_9|CP031545.1_620000_620915_-	cd09325, TDT_C4-dicarb_trans, C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family	NA|355aa|up_8|CP031545.1_620931_621996_-	COG1960, CaiA, Acyl-CoA dehydrogenases [Lipid metabolism]	NA|183aa|up_7|CP031545.1_622035_622584_-	COG2128, COG2128, Uncharacterized conserved protein [Function unknown]	NA|454aa|up_6|CP031545.1_622799_624161_+	COG2265, TrmA, SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]	NA|205aa|up_5|CP031545.1_626091_626706_+	pfam09911, DUF2140, Uncharacterized protein conserved in bacteria (DUF2140)	NA|435aa|up_4|CP031545.1_626765_628070_-	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	cas9|1124aa|up_3|CP031545.1_628383_631755_+	cd09643, Csn1, CRISPR/Cas system-associated protein Cas9	cas1|304aa|up_2|CP031545.1_631931_632843_+	cd09720, Cas1_II, CRISPR/Cas system-associated protein Cas1	cas2|108aa|up_1|CP031545.1_632844_633168_+	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms]	csn2|351aa|up_0|CP031545.1_633164_634217_+	pfam16813, Cas_St_Csn2, CRISPR-associated protein Csn2 subfamily St	NA|272aa|down_0|CP031545.1_637522_638338_-	COG3689, COG3689, Predicted membrane protein [Function unknown]	NA|301aa|down_1|CP031545.1_638337_639240_-	COG0701, COG0701, Predicted permeases [General function prediction only]	NA|711aa|down_2|CP031545.1_639603_641736_+	COG2183, Tex, Transcriptional accessory protein [Transcription]	NA|147aa|down_3|CP031545.1_641722_642163_+	PRK04351, PRK04351, SprT family protein	NA|88aa|down_4|CP031545.1_642228_642492_+	COG1983, PspC, Putative stress-responsive transcriptional regulator [Transcription / Signal transduction mechanisms]	NA|310aa|down_5|CP031545.1_642624_643554_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|264aa|down_6|CP031545.1_643553_644345_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|133aa|down_7|CP031545.1_644467_644866_+	COG4768, COG4768, Uncharacterized protein containing a divergent version of the methyl-accepting chemotaxis-like domain [General function prediction only]	NA|147aa|down_8|CP031545.1_644878_645319_+	pfam12732, YtxH, YtxH-like protein	NA|99aa|down_9|CP031545.1_645339_645636_-	pfam11674, DUF3270, Protein of unknown function (DUF3270)
GCA_003402855.1_ASM340285v1	CP031545	Streptococcus thermophilus strain ST109 chromosome, complete genome	3	862938-863039	3	CRISPRCasFinder	no	cas2,cas6,cas10,csm2gr11,csm3gr7,csm4gr5,csm5gr7,csm6	DEDDh,cas3,cas9,cas1,cas2,csn2,DinG,cas6,cas10,csm2gr11,csm3gr7,csm4gr5,csm5gr7,csm6	Type III-B,Type III-A,Type III-C,Type III-D	GATATAAACCTAATTACCTCGAGAGGGGAC	30	0	0	NA	NA	NA	1	1	TypeIII-B,TypeIII-A,TypeIII-C,TypeIII-D	DEDDh,cas3,cas9,cas1,cas2,csn2,DinG,cas6,cas10,csm2gr11,csm3gr7,csm4gr5,csm5gr7,csm6	NA|73aa|up_7|CP031545.1_857450_857669_+,NA|72aa|up_3|CP031545.1_859410_859626_-,NA	NA|162aa|up_9|CP031545.1_856333_856819_+	cd04684, Nudix_Hydrolase_25, Contains a crystal structure of the Nudix hydrolase from Enterococcus faecalis, which has an unknown function	NA|64aa|up_8|CP031545.1_856822_857014_+	COG4405, COG4405, Uncharacterized protein conserved in bacteria [Function unknown]	NA|73aa|up_7|CP031545.1_857450_857669_+	NA	NA|223aa|up_6|CP031545.1_857870_858539_+	pfam05857, TraX, TraX protein	NA|75aa|up_5|CP031545.1_858539_858764_+	pfam05857, TraX, TraX protein	NA|183aa|up_4|CP031545.1_858805_859354_+	cd03135, GATase1_DJ-1, Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1	NA|72aa|up_3|CP031545.1_859410_859626_-	NA	NA|268aa|up_2|CP031545.1_859594_860398_+	PRK00054, PRK00054, dihydroorotate dehydrogenase electron transfer subunit; Reviewed	NA|316aa|up_1|CP031545.1_860416_861364_+	PRK07259, PRK07259, dihydroorotate dehydrogenase	cas2|110aa|up_0|CP031545.1_862507_862837_+	cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2	cas6|244aa|down_0|CP031545.1_863175_863907_+	TIGR01877, CRISPR-associated_endoribonuclease_Cas6_1, CRISPR-associated endoribonuclease Cas6	cas10|759aa|down_1|CP031545.1_863887_866164_+	cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10	csm2gr11|127aa|down_2|CP031545.1_866167_866548_+	pfam03750, Csm2_III-A, Csm2 Type III-A	csm3gr7|221aa|down_3|CP031545.1_866547_867210_+	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3	csm4gr5|300aa|down_4|CP031545.1_867211_868111_+	pfam17953, Csm4_C, CRISPR Csm4 C-terminal domain	csm5gr7|358aa|down_5|CP031545.1_868113_869187_+	COG1332, COG1332, CRISPR system related protein, RAMP superfamily [Defense mechanisms]	csm6|392aa|down_6|CP031545.1_869340_870516_+	cd09699, Csm6_III-A, CRISPR/Cas system-associated protein Csm6	NA|232aa|down_7|CP031545.1_870715_871411_+	PRK00230, PRK00230, orotidine-5'-phosphate decarboxylase	NA|210aa|down_8|CP031545.1_871499_872129_+	PRK00455, pyrE, orotate phosphoribosyltransferase; Validated	NA|484aa|down_9|CP031545.1_872825_874277_-	COG3104, PTR2, Dipeptide/tripeptide permease [Amino acid transport and metabolism]
GCA_003402855.1_ASM340285v1	CP031545	Streptococcus thermophilus strain ST109 chromosome, complete genome	4	948237-948332	4	CRISPRCasFinder	no		DEDDh,cas3,cas9,cas1,cas2,csn2,DinG,cas6,cas10,csm2gr11,csm3gr7,csm4gr5,csm5gr7,csm6	Orphan	ACCCACTACAGTTGACAAAGAGC	23	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,cas9,cas1,cas2,csn2,DinG,cas6,cas10,csm2gr11,csm3gr7,csm4gr5,csm5gr7,csm6	NA|64aa|up_7|CP031545.1_939541_939733_-,NA	NA|284aa|up_9|CP031545.1_938262_939114_-	cd07208, Pat_hypo_Ecoli_yjju_like, Hypothetical patatin similar to yjju protein of Escherichia coli	NA|153aa|up_8|CP031545.1_939110_939569_-	cd01841, NnaC_like, NnaC (CMP-NeuNAc synthetase) _like subfamily of SGNH_hydrolases, a diverse family of lipases and esterases	NA|64aa|up_7|CP031545.1_939541_939733_-	NA	NA|526aa|up_6|CP031545.1_939736_941314_-	COG0661, AarF, Predicted unusual protein kinase [General function prediction only]	NA|93aa|up_5|CP031545.1_941331_941610_-	COG3937, COG3937, Uncharacterized conserved protein [Function unknown]	NA|77aa|up_4|CP031545.1_941864_942095_-	PRK09852, PRK09852, cryptic 6-phospho-beta-glucosidase; Provisional	NA|50aa|up_3|CP031545.1_943100_943250_-	COG2723, BglB, Beta-glucosidase/6-phospho-beta-glucosidase/beta-galactosidase [Carbohydrate transport and metabolism]	NA|379aa|up_2|CP031545.1_943371_944508_-	COG0628, yhhT, Predicted permease, member of the PurR regulon [General function prediction only]	NA|211aa|up_1|CP031545.1_944563_945196_-	pfam00300, His_Phos_1, Histidine phosphatase superfamily (branch 1)	NA|192aa|up_0|CP031545.1_946232_946808_+	pfam04892, VanZ, VanZ like family	NA|472aa|down_0|CP031545.1_948615_950031_-	cd13128, MATE_Wzx_like, Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins	NA|328aa|down_1|CP031545.1_951105_952089_-	cd00761, Glyco_tranf_GTA_type, Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold	NA|346aa|down_2|CP031545.1_952849_953887_-	pfam00535, Glycos_transf_2, Glycosyl transferase family 2	NA|365aa|down_3|CP031545.1_953883_954978_-	pfam14897, EpsG, EpsG family	NA|368aa|down_4|CP031545.1_954991_956095_-	cd03820, GT4_AmsD-like, amylovoran biosynthesis glycosyltransferase AmsD and similar proteins	NA|392aa|down_5|CP031545.1_956091_957267_-	cd04955, GT4-like, glycosyltransferase family 4 proteins	NA|265aa|down_6|CP031545.1_957320_958115_-	pfam02397, Bac_transf, Bacterial sugar transferase	NA|456aa|down_7|CP031545.1_958147_959515_-	TIGR03025, EPS_sugtrans, exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase	NA|247aa|down_8|CP031545.1_959571_960312_-	TIGR01007, Tyrosine-protein_kinase_CpsD, capsular exopolysaccharide family	NA|231aa|down_9|CP031545.1_960321_961014_-	TIGR01006, Capsular_polysaccharide_biosynthesis_protein_CapA, polysaccharide export protein, MPA1 family, Gram-positive type
GCA_003402855.1_ASM340285v1	CP031545	Streptococcus thermophilus strain ST109 chromosome, complete genome	5	1321671-1322102	2,5,2	PILER-CR,CRISPRCasFinder,CRT	no	csn2,cas2,cas1,cas9	DEDDh,cas3,cas9,cas1,cas2,csn2,DinG,cas6,cas10,csm2gr11,csm3gr7,csm4gr5,csm5gr7,csm6	Type II-A,Type II-B,Type II-C	GTTTTGGAACCATTCGAAACAACACAGCTCTAAAAC,GTTTTGGAACCATTCGAAACAACACAGCTCTAAAAC,GTTTTGGAACCATTCGAAACAACACAGCTCTAAAAC	36,36,36	0	0	NA	NA	II-A,II-B:II-A,II-B:II-A,II-B	6,6,6	6	TypeII-A,TypeII-B,TypeII-C	DEDDh,cas3,cas9,cas1,cas2,csn2,DinG,cas6,cas10,csm2gr11,csm3gr7,csm4gr5,csm5gr7,csm6	NA|66aa|up_7|CP031545.1_1315381_1315579_-,NA|148aa|up_4|CP031545.1_1318463_1318907_-,NA|80aa|up_0|CP031545.1_1321347_1321587_-,NA	NA|737aa|up_9|CP031545.1_1312358_1314569_+	cd13619, PBP2_GlnP, Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold protein superfamily	NA|247aa|up_8|CP031545.1_1314568_1315309_+	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|66aa|up_7|CP031545.1_1315381_1315579_-	NA	NA|438aa|up_6|CP031545.1_1315745_1317059_-	PRK12297, obgE, GTPase CgtA; Reviewed	NA|43aa|up_5|CP031545.1_1317152_1317281_-	pfam13253, DUF4044, Protein of unknown function (DUF4044)	NA|148aa|up_4|CP031545.1_1318463_1318907_-	NA	NA|128aa|up_3|CP031545.1_1318937_1319321_-	COG2050, PaaI, HGG motif-containing thioesterase, possibly involved in aromatic compounds catabolism [Secondary metabolites biosynthesis,    transport, and catabolism]	NA|81aa|up_2|CP031545.1_1320009_1320252_+	COG2182, MalE, Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism]	NA|297aa|up_1|CP031545.1_1320419_1321310_+	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|CP031545.1_1321347_1321587_-	NA	csn2|220aa|down_0|CP031545.1_1322423_1323083_-	cd09758, Csn2, CRISPR/Cas system-associated protein Csn2	cas2|115aa|down_1|CP031545.1_1323072_1323417_-	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms]	cas1|290aa|down_2|CP031545.1_1323413_1324283_-	cd09720, Cas1_II, CRISPR/Cas system-associated protein Cas1	cas9|1389aa|down_3|CP031545.1_1324282_1328449_-	TIGR01865, conserved_hypothetical_protein, CRISPR subtype II/NMENI RNA-guided endonuclease Cas9/Csn1	NA|216aa|down_4|CP031545.1_1328781_1329429_-	cd07500, HAD_PSP, phosphoserine phosphatase (PSP), similar to Methanococcus Jannaschii PSP and Saccharomyces cerevisiae SER2p	NA|575aa|down_5|CP031545.1_1329540_1331265_-	PRK04778, PRK04778, septation ring formation regulator EzrA; Provisional	NA|651aa|down_6|CP031545.1_1331361_1333314_-	PRK05644, gyrB, DNA gyrase subunit B; Validated	NA|202aa|down_7|CP031545.1_1333314_1333920_-	cd07523, HAD_YsbA-like, uncharacterized family of the haloacid dehalogenase-like superfamily, similar to the uncharacterized Lactococcus lactis YsbA	NA|232aa|down_8|CP031545.1_1333960_1334656_-	pfam04172, LrgB, LrgB-like family	NA|125aa|down_9|CP031545.1_1334648_1335023_-	pfam03788, LrgA, LrgA family
GCA_003402855.1_ASM340285v1	CP031545	Streptococcus thermophilus strain ST109 chromosome, complete genome	6	1540204-1540295	6	CRISPRCasFinder	no	cas3	DEDDh,cas3,cas9,cas1,cas2,csn2,DinG,cas6,cas10,csm2gr11,csm3gr7,csm4gr5,csm5gr7,csm6	Unclear	CTTTTCTTTACGATATCAATTTTAACATCTTT	32	0	0	NA	NA	NA	1	1	Unclear	DEDDh,cas3,cas9,cas1,cas2,csn2,DinG,cas6,cas10,csm2gr11,csm3gr7,csm4gr5,csm5gr7,csm6	NA|86aa|up_3|CP031545.1_1535822_1536080_-,NA|143aa|down_6|CP031545.1_1546196_1546625_-,NA|64aa|down_9|CP031545.1_1547808_1548000_-	cas3|673aa|up_9|CP031545.1_1527272_1529291_-	PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional	NA|368aa|up_8|CP031545.1_1529419_1530523_-	PRK00053, alr, alanine racemase; Reviewed	NA|120aa|up_7|CP031545.1_1530543_1530903_-	PRK00070, acpS, 4'-phosphopantetheinyl transferase; Provisional	NA|344aa|up_6|CP031545.1_1530906_1531938_-	PRK09261, PRK09261, phospho-2-dehydro-3-deoxyheptonate aldolase; Validated	NA|344aa|up_5|CP031545.1_1532035_1533067_-	COG0722, AroG, 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]	NA|850aa|up_4|CP031545.1_1533090_1535640_-	PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed	NA|86aa|up_3|CP031545.1_1535822_1536080_-	NA	NA|316aa|up_2|CP031545.1_1536166_1537114_-	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|298aa|up_1|CP031545.1_1537179_1538073_-	pfam00480, ROK, ROK family	NA|634aa|up_0|CP031545.1_1538257_1540159_-	TIGR01996, Includes:_Phosphotransferase_enzyme_IIB_component, PTS system, sucrose-specific IIBC component	NA|481aa|down_0|CP031545.1_1540407_1541850_+	TIGR01322, Sucrose-6-phosphate_hydrolase, sucrose-6-phosphate hydrolase	NA|322aa|down_1|CP031545.1_1541858_1542824_+	cd06291, PBP1_Qymf-like, ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs	NA|145aa|down_2|CP031545.1_1542913_1543348_-	PRK00202, nusB, transcription antitermination factor NusB	NA|130aa|down_3|CP031545.1_1543340_1543730_-	pfam03780, Asp23, Asp23 family, cell envelope-related function	NA|187aa|down_4|CP031545.1_1543800_1544361_-	PRK00529, PRK00529, elongation factor P; Validated	NA|152aa|down_5|CP031545.1_1544473_1544929_-	TIGR02571, putative_dCMP_deaminase, ComE operon protein 2	NA|143aa|down_6|CP031545.1_1546196_1546625_-	NA	NA|198aa|down_7|CP031545.1_1546669_1547263_-	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]	NA|130aa|down_8|CP031545.1_1547231_1547621_-	cd03268, ABC_BcrA_bacitracin_resist, ATP-binding cassette domain of the bacitracin-resistance transporter	NA|64aa|down_9|CP031545.1_1547808_1548000_-	NA
