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_002946515.2_ASM294651v2	CP026613	Clostridioides difficile strain R1 chromosome, complete genome	1	32260-32345	1	CRISPRCasFinder	no		cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	Orphan	GTTGGCGCTGTGCATTAGCACTTT	24	1	10	32284-32321|32284-32321|32284-32321|32284-32321|32284-32321|32284-32321|32284-32321|32284-32321|32284-32321|32284-32321	CP026613.2_12512-12549|CP026613.2_1048653-1048690|CP026613.2_3066231-3066194|CP026613.2_3819349-3819312|CP026613.2_3949830-3949793|CP026613.2_18052-18089|CP026613.2_134755-134792|CP026613.2_141639-141676|CP026613.2_152200-152237|CP026613.2_157614-157651	NA	1	1	Orphan	cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	NA|74aa|up_1|CP026613.2_28675_28897_+,NA|138aa|down_0|CP026613.2_39570_39984_+	NA|258aa|up_9|CP026613.2_9987_10761_+	TIGR02980, SigBFG, RNA polymerase sigma-70 factor, sigma-B/F/G subfamily	NA|176aa|up_8|CP026613.2_21477_22005_+	COG1827, COG1827, Predicted small molecule binding protein (contains 3H domain) [General function prediction only]	NA|294aa|up_7|CP026613.2_22016_22898_+	PRK10334, PRK10334, small-conductance mechanosensitive channel MscS	NA|424aa|up_6|CP026613.2_23356_24628_+	PRK05431, PRK05431, seryl-tRNA synthetase; Provisional	NA|152aa|up_5|CP026613.2_24949_25405_+	COG0590, CumB, Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]	NA|546aa|up_4|CP026613.2_25875_27513_+	PRK05563, PRK05563, DNA polymerase III subunits gamma and tau; Validated	NA|117aa|up_3|CP026613.2_27571_27922_+	PRK00153, PRK00153, YbaB/EbfC family nucleoid-associated protein	NA|200aa|up_2|CP026613.2_27934_28534_+	PRK00076, recR, recombination protein RecR; Reviewed	NA|74aa|up_1|CP026613.2_28675_28897_+	NA	NA|402aa|up_0|CP026613.2_28967_30173_-	cd17507, GT28_Beta-DGS-like, beta-diglucosyldiacylglycerol synthase and similar proteins	NA|138aa|down_0|CP026613.2_39570_39984_+	NA	NA|1144aa|down_1|CP026613.2_40296_43728_+	PRK12999, PRK12999, pyruvate carboxylase; Reviewed	NA|643aa|down_2|CP026613.2_43969_45898_+	PRK12740, PRK12740, elongation factor G-like protein EF-G2	NA|155aa|down_3|CP026613.2_46354_46819_+	COG4463, CtsR, Transcriptional repressor of class III stress genes [Transcription]	NA|165aa|down_4|CP026613.2_46825_47320_+	COG3880, COG3880, Modulator of heat shock repressor CtsR, McsA [Signal transduction    mechanisms]	NA|342aa|down_5|CP026613.2_47335_48361_+	PRK01059, PRK01059, ATP:guanido phosphotransferase; Provisional	NA|816aa|down_6|CP026613.2_48347_50795_+	COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]	NA|458aa|down_7|CP026613.2_50974_52348_+	PRK11823, PRK11823, DNA repair protein RadA; Provisional	NA|357aa|down_8|CP026613.2_52350_53421_+	PRK13482, PRK13482, DNA integrity scanning protein DisA; Provisional	NA|365aa|down_9|CP026613.2_53509_54604_+	COG4956, COG4956, Integral membrane protein (PIN domain superfamily) [General function prediction only]
GCA_002946515.2_ASM294651v2	CP026613	Clostridioides difficile strain R1 chromosome, complete genome	2	150173-150251	2	CRISPRCasFinder	no		cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	Orphan	TGTTTATAATGTGGATAATATTTAA	25	0	0	NA	NA	NA	1	1	Orphan	cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	NA,NA|40aa|down_2|CP026613.2_164614_164734_+,NA|226aa|down_5|CP026613.2_166914_167592_+	NA|278aa|up_9|CP026613.2_127307_128141_+	TIGR04520, ECF_ATPase_1, energy-coupling factor transporter ATPase	NA|289aa|up_8|CP026613.2_128128_128995_+	PRK13637, cbiO, energy-coupling factor transporter ATPase	NA|268aa|up_7|CP026613.2_128988_129792_+	COG0619, CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]	NA|244aa|up_6|CP026613.2_129824_130556_+	PRK00021, truA, tRNA pseudouridine(38-40) synthase TruA	NA|144aa|up_5|CP026613.2_130675_131107_+	PRK09216, rplM, 50S ribosomal protein L13; Reviewed	NA|131aa|up_4|CP026613.2_131135_131528_+	PRK00132, rpsI, 30S ribosomal protein S9; Reviewed	NA|235aa|up_3|CP026613.2_132036_132741_+	TIGR02883, spore_cwlD, N-acetylmuramoyl-L-alanine amidase CwlD	NA|395aa|up_2|CP026613.2_145223_146408_-	PRK05764, PRK05764, aspartate aminotransferase; Provisional	NA|784aa|up_1|CP026613.2_146780_149132_+	PRK07111, PRK07111, anaerobic ribonucleoside triphosphate reductase; Provisional	NA|180aa|up_0|CP026613.2_149153_149693_+	TIGR02491, Anaerobic_ribonucleoside-triphosphate_reductase, anaerobic ribonucleoside-triphosphate reductase activating protein	NA|280aa|down_0|CP026613.2_162600_163440_+	COG1624, COG1624, Uncharacterized conserved protein [Function unknown]	NA|394aa|down_1|CP026613.2_163436_164618_+	COG4856, COG4856, Uncharacterized protein conserved in bacteria [Function unknown]	NA|40aa|down_2|CP026613.2_164614_164734_+	NA	NA|301aa|down_3|CP026613.2_164921_165824_+	PRK05805, PRK05805, phosphate butyryltransferase; Validated	NA|360aa|down_4|CP026613.2_165845_166925_+	PRK03011, PRK03011, butyrate kinase; Provisional	NA|226aa|down_5|CP026613.2_166914_167592_+	NA	NA|72aa|down_6|CP026613.2_167634_167850_+	COG2221, DsrA, Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]	NA|360aa|down_7|CP026613.2_167878_168958_+	PRK07119, PRK07119, 2-ketoisovalerate ferredoxin reductase; Validated	NA|251aa|down_8|CP026613.2_168957_169710_+	cd03375, TPP_OGFOR, Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor	NA|186aa|down_9|CP026613.2_169710_170268_+	pfam01558, POR, Pyruvate ferredoxin/flavodoxin oxidoreductase
GCA_002946515.2_ASM294651v2	CP026613	Clostridioides difficile strain R1 chromosome, complete genome	3	597150-597257	3	CRISPRCasFinder	no	cas14j	cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	Unclear	TATTAATTGTATTTACTTATTTGATTG	27	0	0	NA	NA	NA	1	1	TypeV	cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	NA|254aa|up_2|CP026613.2_594756_595518_+,NA|78aa|down_6|CP026613.2_606223_606457_-	NA|305aa|up_9|CP026613.2_584330_585245_+	TIGR00276, iron-sulfur_cluster-binding_protein, epoxyqueuosine reductase	NA|746aa|up_8|CP026613.2_585350_587588_+	pfam13654, AAA_32, AAA domain	NA|206aa|up_7|CP026613.2_588025_588643_+	COG0177, Nth, Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]	NA|157aa|up_6|CP026613.2_588836_589307_+	cd18094, SpoU-like_TrmL, SAM-dependent tRNA methylase related to TrmL	NA|283aa|up_5|CP026613.2_589341_590190_+	TIGR00762, DegV, EDD domain protein, DegV family	NA|335aa|up_4|CP026613.2_590477_591482_+	cd06354, PBP1_PrnA-like, periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea	cas14j|373aa|up_3|CP026613.2_592589_593708_+	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|254aa|up_2|CP026613.2_594756_595518_+	NA	NA|273aa|up_1|CP026613.2_595520_596339_+	pfam08812, YtxC, YtxC-like family	NA|201aa|up_0|CP026613.2_596517_597120_+	COG4399, COG4399, Uncharacterized protein conserved in bacteria [Function unknown]	NA|640aa|down_0|CP026613.2_597912_599832_+	PRK00413, thrS, threonyl-tRNA synthetase; Reviewed	NA|364aa|down_1|CP026613.2_600556_601648_+	pfam12784, PDDEXK_2, PD-(D/E)XK nuclease family transposase	NA|66aa|down_2|CP026613.2_601995_602193_-	pfam03551, PadR, Transcriptional regulator PadR-like family	NA|447aa|down_3|CP026613.2_602552_603893_+	cd16935, HATPase_AgrC-ComD-like, Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Staphylococcus aureus AgrC and Streptococcus pneumoniae ComD which are involved in quorum sensing	NA|190aa|down_4|CP026613.2_604234_604804_-	COG2316, COG2316, Predicted hydrolase (HD superfamily) [General function prediction only]	NA|417aa|down_5|CP026613.2_604964_606215_-	cd06173, MFS_MefA_like, Macrolide efflux protein A and similar proteins of the Major Facilitator Superfamily of transporters	NA|78aa|down_6|CP026613.2_606223_606457_-	NA	NA|196aa|down_7|CP026613.2_606507_607095_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|487aa|down_8|CP026613.2_607386_608847_+	cd07082, ALDH_F11_NP-GAPDH, NADP+-dependent non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase and ALDH family 11	NA|202aa|down_9|CP026613.2_609215_609821_+	COG1309, AcrR, Transcriptional regulator [Transcription]
GCA_002946515.2_ASM294651v2	CP026613	Clostridioides difficile strain R1 chromosome, complete genome	6	1244809-1245435	2,6,1	PILER-CR,CRISPRCasFinder,CRT	no		cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	Orphan	GTTTTATATTAACTAAGTGGTATGTAAAG,GTTTTATATTAACTAAGTGGTATGTAAAG,GTTTTATATTAACTAAGTGGTATGTAAAG	29,29,29	1	1	1245039-1245076	CP026613.2_42426-42463	I-A:I-A:I-A	9,9,9	9	Orphan	cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	NA|271aa|up_2|CP026613.2_1241928_1242741_+,NA|53aa|up_0|CP026613.2_1244363_1244522_+,NA|84aa|down_1|CP026613.2_1245825_1246077_+,NA|63aa|down_2|CP026613.2_1246241_1246430_-,NA|220aa|down_3|CP026613.2_1246887_1247547_-,NA|65aa|down_8|CP026613.2_1249681_1249876_-	NA|271aa|up_9|CP026613.2_1232376_1233189_+	cd09009, PNP-EcPNPII_like, purine nucleoside phosphorylases similar to human PNP and Escherichia coli PNP-II (XapA)	NA|447aa|up_8|CP026613.2_1233376_1234717_+	TIGR02644, Thymidine_phosphorylase, pyrimidine-nucleoside phosphorylase	NA|360aa|up_7|CP026613.2_1234929_1236009_+	pfam02618, YceG, YceG-like family	NA|225aa|up_6|CP026613.2_1236180_1236855_+	COG4122, COG4122, Predicted O-methyltransferase [General function prediction only]	NA|416aa|up_5|CP026613.2_1236841_1238089_+	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|555aa|up_4|CP026613.2_1238160_1239825_+	COG0768, FtsI, Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]	NA|505aa|up_3|CP026613.2_1240232_1241747_-	cd00338, Ser_Recombinase, Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain	NA|271aa|up_2|CP026613.2_1241928_1242741_+	NA	NA|482aa|up_1|CP026613.2_1242780_1244226_+	NF033435, S-layer_Clost, S-layer protein SlpA	NA|53aa|up_0|CP026613.2_1244363_1244522_+	NA	NA|45aa|down_0|CP026613.2_1245512_1245647_-	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|84aa|down_1|CP026613.2_1245825_1246077_+	NA	NA|63aa|down_2|CP026613.2_1246241_1246430_-	NA	NA|220aa|down_3|CP026613.2_1246887_1247547_-	NA	NA|146aa|down_4|CP026613.2_1247602_1248040_-	COG1846, MarR, Transcriptional regulators [Transcription]	NA|56aa|down_5|CP026613.2_1248180_1248348_-	pfam12642, TpcC, Conjugative transposon protein TcpC	NA|55aa|down_6|CP026613.2_1248363_1248528_-	pfam00877, NLPC_P60, NlpC/P60 family	NA|170aa|down_7|CP026613.2_1249063_1249573_+	pfam04892, VanZ, VanZ like family	NA|65aa|down_8|CP026613.2_1249681_1249876_-	NA	NA|139aa|down_9|CP026613.2_1250368_1250785_-	PRK05803, PRK05803, RNA polymerase sporulation sigma factor SigK
GCA_002946515.2_ASM294651v2	CP026613	Clostridioides difficile strain R1 chromosome, complete genome	7	1581083-1581180	7	CRISPRCasFinder	no		cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	Orphan	TTATATTAACATAACTATATTTTACTTGATAAA	33	0	0	NA	NA	NA	1	1	Orphan	cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	NA,NA|40aa|down_2|CP026613.2_1584253_1584373_+,NA|51aa|down_6|CP026613.2_1586528_1586681_+,NA|74aa|down_8|CP026613.2_1587951_1588173_+	NA|294aa|up_9|CP026613.2_1570275_1571157_-	cd10944, CE4_SmPgdA_like, Catalytic NodB homology domain of Streptococcus mutans polysaccharide deacetylase PgdA, Bacillus subtilis YheN, and similar proteins	NA|305aa|up_8|CP026613.2_1571572_1572487_+	COG0697, RhaT, Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]	NA|182aa|up_7|CP026613.2_1572709_1573255_+	cd01046, Rubrerythrin_like, rubrerythrin-like, diiron-binding domain	NA|383aa|up_6|CP026613.2_1573345_1574494_+	COG2006, COG2006, Uncharacterized conserved protein [Function unknown]	NA|422aa|up_5|CP026613.2_1574546_1575812_+	PRK09357, pyrC, dihydroorotase; Validated	NA|411aa|up_4|CP026613.2_1576096_1577329_-	COG0577, SalY, ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]	NA|225aa|up_3|CP026613.2_1577331_1578006_-	cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein	NA|411aa|up_2|CP026613.2_1578013_1579246_-	COG0845, AcrA, Membrane-fusion protein [Cell envelope biogenesis, outer membrane]	NA|335aa|up_1|CP026613.2_1579356_1580361_-	cd16948, HATPase_BceS-YxdK-YvcQ-like, Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Bacillus subtilis BceS, YxdK, and Bacillus thuringiensis YvcQ	NA|225aa|up_0|CP026613.2_1580384_1581059_-	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|256aa|down_0|CP026613.2_1581346_1582114_+	COG1136, SalX, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]	NA|646aa|down_1|CP026613.2_1582100_1584038_+	pfam02687, FtsX, FtsX-like permease family	NA|40aa|down_2|CP026613.2_1584253_1584373_+	NA	NA|105aa|down_3|CP026613.2_1584395_1584710_+	pfam06125, DUF961, Bacterial protein of unknown function (DUF961)	NA|129aa|down_4|CP026613.2_1584725_1585112_+	pfam06125, DUF961, Bacterial protein of unknown function (DUF961)	NA|462aa|down_5|CP026613.2_1585140_1586526_+	COG1674, FtsK, DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]	NA|51aa|down_6|CP026613.2_1586528_1586681_+	NA	NA|402aa|down_7|CP026613.2_1586703_1587909_+	pfam02486, Rep_trans, Replication initiation factor	NA|74aa|down_8|CP026613.2_1587951_1588173_+	NA	NA|166aa|down_9|CP026613.2_1588289_1588787_+	pfam07275, ArdA, Antirestriction protein (ArdA)
GCA_002946515.2_ASM294651v2	CP026613	Clostridioides difficile strain R1 chromosome, complete genome	8	1745884-1747032	3,8,2	PILER-CR,CRISPRCasFinder,CRT	no	cas14j	cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	Unclear	GTTTTATATTAACTATGTGGTATGTAAAT,GTTTTATATTAACTATGTGGTATGTAAAT,GTTTTATATTAACTATGTGGTATGTAAAT	29,29,29	0	0	NA	NA	I-A:I-A:I-A	17,17,17	17	TypeV	cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	NA,NA|96aa|down_0|CP026613.2_1747602_1747890_+,NA|59aa|down_4|CP026613.2_1753408_1753585_-,NA|341aa|down_5|CP026613.2_1754633_1755656_+,NA|258aa|down_7|CP026613.2_1756561_1757335_+	NA|200aa|up_9|CP026613.2_1728058_1728658_-	COG4110, COG4110, Uncharacterized protein involved in stress response [General function prediction only]	NA|266aa|up_8|CP026613.2_1728760_1729558_-	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|329aa|up_7|CP026613.2_1729867_1730854_-	TIGR00545, Probable_lipoate-protein_ligase_A, lipoyltransferase and lipoate-protein ligase	NA|577aa|up_6|CP026613.2_1731337_1733068_+	COG1757, NhaC, Na+/H+ antiporter [Energy production and conversion]	NA|825aa|up_5|CP026613.2_1734350_1736825_+	PRK00451, PRK00451, aminomethyl-transferring glycine dehydrogenase subunit GcvPA	NA|486aa|up_4|CP026613.2_1736824_1738282_+	PRK04366, PRK04366, aminomethyl-transferring glycine dehydrogenase subunit GcvPB	NA|786aa|up_3|CP026613.2_1738699_1741057_+	cd02609, P-type_ATPase, uncharacterized subfamily of P-type ATPase transporter, similar to uncharacterized Streptococcus pneumoniae exported protein 7, Exp7	NA|106aa|up_2|CP026613.2_1741141_1741459_-	pfam06865, DUF1255, Protein of unknown function (DUF1255)	cas14j|373aa|up_1|CP026613.2_1742561_1743680_-	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|52aa|up_0|CP026613.2_1745485_1745641_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|96aa|down_0|CP026613.2_1747602_1747890_+	NA	NA|184aa|down_1|CP026613.2_1748424_1748976_-	cd02209, cupin_XRE_C, XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain	NA|321aa|down_2|CP026613.2_1749166_1750129_+	cd01561, CBS_like, CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase	NA|616aa|down_3|CP026613.2_1750409_1752257_+	cd08579, GDPD_memb_like, Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases	NA|59aa|down_4|CP026613.2_1753408_1753585_-	NA	NA|341aa|down_5|CP026613.2_1754633_1755656_+	NA	NA|296aa|down_6|CP026613.2_1755668_1756556_+	cd03264, ABC_drug_resistance_like, ABC-type multidrug transport system, ATPase component	NA|258aa|down_7|CP026613.2_1756561_1757335_+	NA	NA|242aa|down_8|CP026613.2_1757446_1758172_+	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|468aa|down_9|CP026613.2_1758175_1759579_+	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]
GCA_002946515.2_ASM294651v2	CP026613	Clostridioides difficile strain R1 chromosome, complete genome	9	2198296-2201226	9,3,4	CRISPRCasFinder,CRT,PILER-CR	no	csa3	cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	Type I-A	CTTTACATACCACATAGTTAATATAAAAC,CTTTACATACCACATAGTTAATATAAAAC,GTTTTATATTAACTATGTGGTATGTAAAG	29,29,29	0	0	NA	NA	I-A:I-A:I-A	44,44,43	44	Orphan	cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	NA|95aa|up_9|CP026613.2_2192248_2192533_-,NA|86aa|up_8|CP026613.2_2192855_2193113_-,NA|124aa|up_7|CP026613.2_2193251_2193623_-,NA|125aa|up_5|CP026613.2_2194981_2195356_+,NA|41aa|up_4|CP026613.2_2195438_2195561_-,NA|127aa|up_3|CP026613.2_2196354_2196735_-,NA|86aa|up_2|CP026613.2_2196727_2196985_-,NA|78aa|up_1|CP026613.2_2196971_2197205_-,NA|51aa|down_0|CP026613.2_2201504_2201657_-,NA|81aa|down_1|CP026613.2_2202176_2202419_+,NA|55aa|down_4|CP026613.2_2204643_2204808_-,NA|20aa|down_7|CP026613.2_2207239_2207299_+,NA|45aa|down_8|CP026613.2_2207469_2207604_-	NA|95aa|up_9|CP026613.2_2192248_2192533_-	NA	NA|86aa|up_8|CP026613.2_2192855_2193113_-	NA	NA|124aa|up_7|CP026613.2_2193251_2193623_-	NA	NA|191aa|up_6|CP026613.2_2194065_2194638_-	pfam10543, ORF6N, ORF6N domain	NA|125aa|up_5|CP026613.2_2194981_2195356_+	NA	NA|41aa|up_4|CP026613.2_2195438_2195561_-	NA	NA|127aa|up_3|CP026613.2_2196354_2196735_-	NA	NA|86aa|up_2|CP026613.2_2196727_2196985_-	NA	NA|78aa|up_1|CP026613.2_2196971_2197205_-	NA	NA|63aa|up_0|CP026613.2_2197392_2197581_+	smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|51aa|down_0|CP026613.2_2201504_2201657_-	NA	NA|81aa|down_1|CP026613.2_2202176_2202419_+	NA	NA|182aa|down_2|CP026613.2_2202484_2203030_+	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|282aa|down_3|CP026613.2_2203574_2204420_+	pfam13026, DUF3887, Protein of unknown function (DUF3887)	NA|55aa|down_4|CP026613.2_2204643_2204808_-	NA	NA|214aa|down_5|CP026613.2_2205930_2206572_-	COG5658, COG5658, Predicted integral membrane protein [Function unknown]	csa3|99aa|down_6|CP026613.2_2206552_2206849_-	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|20aa|down_7|CP026613.2_2207239_2207299_+	NA	NA|45aa|down_8|CP026613.2_2207469_2207604_-	NA	NA|251aa|down_9|CP026613.2_2207814_2208567_-	PRK10621, PRK10621, hypothetical protein; Provisional
GCA_002946515.2_ASM294651v2	CP026613	Clostridioides difficile strain R1 chromosome, complete genome	10	2248100-2248988	10,4,5	CRISPRCasFinder,CRT,PILER-CR	no		cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	Orphan	ATTTACATACCACTTAGTTAATATAAAAC,ATTTACATACCACTTAGTTAATATAAAAC,GTTTTATATTAACTAAGTGGTATGTAAAT	29,29,29	0	0	NA	NA	I-A:I-A:I-A	13,13,12	13	Orphan	cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	NA|53aa|up_4|CP026613.2_2244915_2245074_+,NA|58aa|up_1|CP026613.2_2246017_2246191_+,NA|98aa|up_0|CP026613.2_2247099_2247393_-,NA|80aa|down_8|CP026613.2_2256995_2257235_-,NA|216aa|down_9|CP026613.2_2257405_2258053_-	NA|345aa|up_9|CP026613.2_2239056_2240091_-	PRK00436, argC, N-acetyl-gamma-glutamyl-phosphate reductase; Validated	NA|256aa|up_8|CP026613.2_2240768_2241536_-	pfam14268, YoaP, YoaP-like	NA|158aa|up_7|CP026613.2_2241828_2242302_+	pfam13673, Acetyltransf_10, Acetyltransferase (GNAT) domain	NA|186aa|up_6|CP026613.2_2242682_2243240_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|233aa|up_5|CP026613.2_2243497_2244196_+	TIGR03502, lipase_Pla1_cef, extracellular lipase, Pla-1/cef family	NA|53aa|up_4|CP026613.2_2244915_2245074_+	NA	NA|156aa|up_3|CP026613.2_2245181_2245649_+	pfam11188, DUF2975, Protein of unknown function (DUF2975)	NA|72aa|up_2|CP026613.2_2245659_2245875_+	COG3655, COG3655, Predicted transcriptional regulator [Transcription]	NA|58aa|up_1|CP026613.2_2246017_2246191_+	NA	NA|98aa|up_0|CP026613.2_2247099_2247393_-	NA	NA|62aa|down_0|CP026613.2_2249285_2249471_+	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|291aa|down_1|CP026613.2_2249623_2250496_-	COG1737, RpiR, Transcriptional regulators [Transcription]	NA|193aa|down_2|CP026613.2_2250889_2251468_-	pfam06962, rRNA_methylase, Putative rRNA methylase	NA|239aa|down_3|CP026613.2_2251524_2252241_-	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|362aa|down_4|CP026613.2_2252431_2253517_+	COG0628, yhhT, Predicted permease, member of the PurR regulon [General function prediction only]	NA|219aa|down_5|CP026613.2_2253670_2254327_-	pfam03154, Atrophin-1, Atrophin-1 family	NA|431aa|down_6|CP026613.2_2254541_2255834_-	cd06828, PLPDE_III_DapDC, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase	NA|398aa|down_7|CP026613.2_2255851_2257045_-	PRK06635, PRK06635, aspartate kinase; Reviewed	NA|80aa|down_8|CP026613.2_2256995_2257235_-	NA	NA|216aa|down_9|CP026613.2_2257405_2258053_-	NA
GCA_002946515.2_ASM294651v2	CP026613	Clostridioides difficile strain R1 chromosome, complete genome	11	2359090-2361688	11,5,6	CRISPRCasFinder,CRT,PILER-CR	no	cas2,cas1,cas4,cas3,cas5,cas7b,cas8b1,cas6	cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	Type I-B	ATTTAAATACATCTCATGTTACTGTTTAAC,ATTTAAATACATCTCATGTTACTGTTTAAC,ATTTAAATACATCTCATGTTACTGTTTAAC	30,30,30	0	0	NA	NA	III-B:III-B:III-B	39,39,38	39	TypeI-B	cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	NA|35aa|up_8|CP026613.2_2350976_2351081_-,NA|275aa|up_7|CP026613.2_2351338_2352163_-,NA|69aa|down_5|CP026613.2_2369173_2369380_+,NA|194aa|down_6|CP026613.2_2369815_2370397_+	NA|375aa|up_9|CP026613.2_2349740_2350865_+	pfam12725, DUF3810, Protein of unknown function (DUF3810)	NA|35aa|up_8|CP026613.2_2350976_2351081_-	NA	NA|275aa|up_7|CP026613.2_2351338_2352163_-	NA	NA|352aa|up_6|CP026613.2_2352510_2353566_-	pfam04551, GcpE, GcpE protein	NA|335aa|up_5|CP026613.2_2353748_2354753_-	pfam02163, Peptidase_M50, Peptidase family M50	NA|385aa|up_4|CP026613.2_2354765_2355920_-	PRK05447, PRK05447, 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional	NA|68aa|up_3|CP026613.2_2356083_2356287_-	COG3655, COG3655, Predicted transcriptional regulator [Transcription]	cas2|97aa|up_2|CP026613.2_2356976_2357267_-	cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2	cas1|333aa|up_1|CP026613.2_2357477_2358476_-	cd09722, Cas1_I-B, CRISPR/Cas system-associated protein Cas1	cas4|165aa|up_0|CP026613.2_2358510_2359005_-	pfam01930, Cas_Cas4, Domain of unknown function DUF83	cas3|853aa|down_0|CP026613.2_2361877_2364436_-	cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3	cas5|247aa|down_1|CP026613.2_2364459_2365200_-	TIGR02592, hypothetical_protein_CTC_01466, CRISPR-associated protein Cas5, subtype I-B/HMARI	cas7b|330aa|down_2|CP026613.2_2365201_2366191_-	pfam05107, Cas_Cas7, CRISPR-associated protein Cas7	cas8b1|587aa|down_3|CP026613.2_2366183_2367944_-	TIGR02591, cas_Csh1, CRISPR-associated protein Cas8b/Csh1, subtype I-B/HMARI	cas6|232aa|down_4|CP026613.2_2367934_2368630_-	TIGR01877, CRISPR-associated_endoribonuclease_Cas6_1, CRISPR-associated endoribonuclease Cas6	NA|69aa|down_5|CP026613.2_2369173_2369380_+	NA	NA|194aa|down_6|CP026613.2_2369815_2370397_+	NA	NA|607aa|down_7|CP026613.2_2370481_2372302_-	cd01948, EAL, EAL domain	NA|33aa|down_8|CP026613.2_2372499_2372598_-	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain	NA|38aa|down_9|CP026613.2_2372687_2372801_-	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain
GCA_002946515.2_ASM294651v2	CP026613	Clostridioides difficile strain R1 chromosome, complete genome	15	3312232-3314353	15,6,7	CRISPRCasFinder,CRT,PILER-CR	no	cas2,cas1,cas4,cas3,cas5,cas7,cas8b2,cas6,WYL	cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	Unclear	CTTTACATACCACTTAGTTAATATAAAAC,CTTTACATACCACTTAGTTAATATAAAAC,TTTTATATTAACTAAGTGGTATGTAAAG	29,29,28	0	0	NA	NA	I-A:I-A:I-A	32,32,32	32	Unclear	cas14j,csa3,WYL,cas3,DEDDh,DinG,RT,cas14k,cas2,cas1,cas4,cas5,cas7b,cas8b1,cas6,cas7,cas8b2	NA|67aa|up_7|CP026613.2_3305137_3305338_+,NA|257aa|up_1|CP026613.2_3310509_3311280_+,NA	NA|740aa|up_9|CP026613.2_3299484_3301704_-	cd01948, EAL, EAL domain	NA|885aa|up_8|CP026613.2_3301979_3304634_-	PRK13805, PRK13805, bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional	NA|67aa|up_7|CP026613.2_3305137_3305338_+	NA	NA|197aa|up_6|CP026613.2_3305544_3306135_-	PRK08305, spoVFB, dipicolinate synthase subunit B; Reviewed	NA|292aa|up_5|CP026613.2_3306137_3307013_-	PRK08306, PRK08306, dipicolinate synthase subunit DpsA	NA|464aa|up_4|CP026613.2_3307088_3308480_-	cd17633, AFD_YhfT-like, fatty acid-CoA ligase VraA	NA|379aa|up_3|CP026613.2_3308483_3309620_-	cd00751, thiolase, Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine	NA|182aa|up_2|CP026613.2_3309640_3310186_-	pfam02632, BioY, BioY family	NA|257aa|up_1|CP026613.2_3310509_3311280_+	NA	NA|143aa|up_0|CP026613.2_3311742_3312171_-	PRK10562, PRK10562, putative acetyltransferase; Provisional	cas2|89aa|down_0|CP026613.2_3314536_3314803_-	cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2	cas1|327aa|down_1|CP026613.2_3314805_3315786_-	TIGR03641, cas1_HMARI, CRISPR-associated endonuclease Cas1, subtype I-B/HMARI/TNEAP	cas4|173aa|down_2|CP026613.2_3315788_3316307_-	pfam01930, Cas_Cas4, Domain of unknown function DUF83	cas3|774aa|down_3|CP026613.2_3316354_3318676_-	TIGR01587, CRISPR-associated_endonuclease/helicase_Cas3, CRISPR-associated helicase Cas3	cas5|234aa|down_4|CP026613.2_3318686_3319388_-	cd09658, Cas5_I-B, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas7|305aa|down_5|CP026613.2_3319389_3320304_-	cd09687, Cas7_I-C, CRISPR/Cas system-associated RAMP superfamily protein Cas7	cas8b2|617aa|down_6|CP026613.2_3320305_3322156_-	pfam09706, Cas_CXXC_CXXC, CRISPR-associated protein (Cas_CXXC_CXXC)	cas6|246aa|down_7|CP026613.2_3322161_3322899_-	cd09652, Cas6-I-III, CRISPR/Cas system-associated RAMP superfamily protein Cas6	WYL|306aa|down_8|CP026613.2_3322976_3323894_-	pfam13280, WYL, WYL domain	NA|639aa|down_9|CP026613.2_3324172_3326089_-	pfam02687, FtsX, FtsX-like permease family
