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_003313585.1_ASM331358v1	CP011848	Clostridioides difficile strain DSM 27640 chromosome, complete genome	1	150328-150406	1	CRISPRCasFinder	no		csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	Orphan	TGTTTATAATGTGGATAATATTTAA	25	0	0	NA	NA	NA	1	1	Orphan	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	NA,NA|226aa|down_4|CP011848.1_167242_167920_+	NA|278aa|up_9|CP011848.1_127578_128412_+	TIGR04520, ECF_ATPase_1, energy-coupling factor transporter ATPase	NA|289aa|up_8|CP011848.1_128399_129266_+	PRK13637, cbiO, energy-coupling factor transporter ATPase	NA|268aa|up_7|CP011848.1_129259_130063_+	COG0619, CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]	NA|244aa|up_6|CP011848.1_130094_130826_+	PRK00021, truA, tRNA pseudouridine(38-40) synthase TruA	NA|144aa|up_5|CP011848.1_130945_131377_+	PRK09216, rplM, 50S ribosomal protein L13; Reviewed	NA|131aa|up_4|CP011848.1_131405_131798_+	PRK00132, rpsI, 30S ribosomal protein S9; Reviewed	NA|251aa|up_3|CP011848.1_132256_133009_+	TIGR02883, spore_cwlD, N-acetylmuramoyl-L-alanine amidase CwlD	NA|395aa|up_2|CP011848.1_145377_146562_-	PRK05764, PRK05764, aspartate aminotransferase; Provisional	NA|784aa|up_1|CP011848.1_146934_149286_+	PRK07111, PRK07111, anaerobic ribonucleoside triphosphate reductase; Provisional	NA|180aa|up_0|CP011848.1_149307_149847_+	TIGR02491, Anaerobic_ribonucleoside-triphosphate_reductase, anaerobic ribonucleoside-triphosphate reductase activating protein	NA|280aa|down_0|CP011848.1_162928_163768_+	COG1624, COG1624, Uncharacterized conserved protein [Function unknown]	NA|394aa|down_1|CP011848.1_163764_164946_+	COG4856, COG4856, Uncharacterized protein conserved in bacteria [Function unknown]	NA|301aa|down_2|CP011848.1_165249_166152_+	PRK05805, PRK05805, phosphate butyryltransferase; Validated	NA|360aa|down_3|CP011848.1_166173_167253_+	PRK03011, PRK03011, butyrate kinase; Provisional	NA|226aa|down_4|CP011848.1_167242_167920_+	NA	NA|72aa|down_5|CP011848.1_167962_168178_+	COG2221, DsrA, Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]	NA|360aa|down_6|CP011848.1_168206_169286_+	PRK07119, PRK07119, 2-ketoisovalerate ferredoxin reductase; Validated	NA|251aa|down_7|CP011848.1_169285_170038_+	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_8|CP011848.1_170038_170596_+	pfam01558, POR, Pyruvate ferredoxin/flavodoxin oxidoreductase	NA|449aa|down_9|CP011848.1_170765_172112_+	PRK14316, glmM, phosphoglucosamine mutase; Provisional
GCA_003313585.1_ASM331358v1	CP011848	Clostridioides difficile strain DSM 27640 chromosome, complete genome	3	1007152-1007229	3	CRISPRCasFinder	no	cas14j	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	Unclear	AAAAAATAAGAAAGTTTATAAATA	24	0	0	NA	NA	NA	1	1	TypeV	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	NA,NA	NA|527aa|up_9|CP011848.1_991791_993372_+	COG0063, COG0063, Predicted sugar kinase [Carbohydrate transport and metabolism]	cas14j|370aa|up_8|CP011848.1_994126_995236_+	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|149aa|up_7|CP011848.1_995519_995966_+	COG1585, COG1585, Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]	NA|348aa|up_6|CP011848.1_995986_997030_+	COG0330, HflC, Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]	NA|387aa|up_5|CP011848.1_997800_998961_+	PRK05293, glgC, glucose-1-phosphate adenylyltransferase; Provisional	NA|377aa|up_4|CP011848.1_998962_1000093_+	TIGR02092, Glycogen_biosynthesis_protein_GlgD, glucose-1-phosphate adenylyltransferase, GlgD subunit	NA|481aa|up_3|CP011848.1_1000121_1001564_+	cd03791, GT5_Glycogen_synthase_DULL1-like, Glycogen synthase GlgA and similar proteins	NA|807aa|up_2|CP011848.1_1001577_1003998_+	cd04300, GT35_Glycogen_Phosphorylase, glycogen phosphorylase and similar proteins	NA|622aa|up_1|CP011848.1_1004002_1005868_+	cd11338, AmyAc_CMD, Alpha amylase catalytic domain found in cyclomaltodextrinases and related proteins	NA|218aa|up_0|CP011848.1_1006112_1006766_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|492aa|down_0|CP011848.1_1007403_1008879_+	COG1982, LdcC, Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]	NA|138aa|down_1|CP011848.1_1008965_1009379_+	TIGR03330, SAM_DCase_Bsu, S-adenosylmethionine decarboxylase proenzyme, Bacillus form	NA|284aa|down_2|CP011848.1_1009408_1010260_+	PRK00811, PRK00811, polyamine aminopropyltransferase	NA|293aa|down_3|CP011848.1_1010249_1011128_+	cd11593, Agmatinase-like_2, Agmatinase and related proteins	NA|67aa|down_4|CP011848.1_1011307_1011508_-	COG1278, CspC, Cold shock proteins [Transcription]	NA|497aa|down_5|CP011848.1_1011974_1013465_+	TIGR04105, hypothetical_protein, [FeFe] hydrogenase, group B1/B3	NA|499aa|down_6|CP011848.1_1013722_1015219_+	TIGR04105, hypothetical_protein, [FeFe] hydrogenase, group B1/B3	NA|117aa|down_7|CP011848.1_1015352_1015703_+	cd07731, ComA-like_MBL-fold, Competence protein ComA, ComEC and related proteins; MBL-fold metallo hydrolase domain	cas14j|370aa|down_8|CP011848.1_1016350_1017460_+	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|177aa|down_9|CP011848.1_1017620_1018151_+	COG2333, ComEC, Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]
GCA_003313585.1_ASM331358v1	CP011848	Clostridioides difficile strain DSM 27640 chromosome, complete genome	4	1302343-1303300	1,4,1	PILER-CR,CRISPRCasFinder,CRT	no		csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	Orphan	GTTTTATATTAACTAAGTGGTATGTAAAG,GTTTTATATTAACTAAGTGGTATGTAAAG,GTTTTATATTAACTAAGTGGTATGTAAAG	29,29,29	0	0	NA	NA	I-A:I-A:I-A	14,14,14	14	Orphan	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	NA,NA|52aa|down_0|CP011848.1_1304516_1304672_+,NA|84aa|down_1|CP011848.1_1304917_1305169_+,NA|38aa|down_2|CP011848.1_1305478_1305592_+,NA|70aa|down_3|CP011848.1_1305799_1306009_+,NA|128aa|down_4|CP011848.1_1306377_1306761_-,NA|115aa|down_5|CP011848.1_1306887_1307232_+,NA|106aa|down_6|CP011848.1_1308615_1308933_-,NA|190aa|down_7|CP011848.1_1309224_1309794_-	NA|360aa|up_9|CP011848.1_1290180_1291260_+	pfam02618, YceG, YceG-like family	NA|225aa|up_8|CP011848.1_1291431_1292106_+	COG4122, COG4122, Predicted O-methyltransferase [General function prediction only]	NA|416aa|up_7|CP011848.1_1292092_1293340_+	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|555aa|up_6|CP011848.1_1293411_1295076_+	COG0768, FtsI, Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]	NA|95aa|up_5|CP011848.1_1295172_1295457_-	PRK05803, PRK05803, RNA polymerase sporulation sigma factor SigK	NA|506aa|up_4|CP011848.1_1295479_1296997_-	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|274aa|up_3|CP011848.1_1297121_1297943_-	sd00006, TPR, Tetratricopeptide repeat	NA|476aa|up_2|CP011848.1_1298133_1299561_+	NF033435, S-layer_Clost, S-layer protein SlpA	NA|224aa|up_1|CP011848.1_1299870_1300542_+	pfam13518, HTH_28, Helix-turn-helix domain	NA|300aa|up_0|CP011848.1_1300535_1301435_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|52aa|down_0|CP011848.1_1304516_1304672_+	NA	NA|84aa|down_1|CP011848.1_1304917_1305169_+	NA	NA|38aa|down_2|CP011848.1_1305478_1305592_+	NA	NA|70aa|down_3|CP011848.1_1305799_1306009_+	NA	NA|128aa|down_4|CP011848.1_1306377_1306761_-	NA	NA|115aa|down_5|CP011848.1_1306887_1307232_+	NA	NA|106aa|down_6|CP011848.1_1308615_1308933_-	NA	NA|190aa|down_7|CP011848.1_1309224_1309794_-	NA	NA|61aa|down_8|CP011848.1_1310237_1310420_+	pfam03965, Penicillinase_R, Penicillinase repressor	NA|170aa|down_9|CP011848.1_1310947_1311457_+	pfam04892, VanZ, VanZ like family
GCA_003313585.1_ASM331358v1	CP011848	Clostridioides difficile strain DSM 27640 chromosome, complete genome	5	1511689-1512441	2,5,2	PILER-CR,CRISPRCasFinder,CRT	no	DinG	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	Type IV-A	GTTTTATATTAACTAAGTGGTATGTAAAT,GTTTTATATTAACTAAGTGGTATGTAAAT,GTTTTATATTAACTAAGTGGTATGTAAAT	29,29,29	0	0	NA	NA	I-A:I-A:I-A	10,11,10	11	Orphan	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	NA|183aa|up_5|CP011848.1_1506334_1506883_-,NA|80aa|down_4|CP011848.1_1519573_1519813_+,NA|59aa|down_5|CP011848.1_1520000_1520177_-,NA|45aa|down_9|CP011848.1_1522803_1522938_+	NA|195aa|up_9|CP011848.1_1501534_1502119_-	pfam00882, Zn_dep_PLPC, Zinc dependent phospholipase C	NA|477aa|up_8|CP011848.1_1502318_1503749_-	COG3829, RocR, Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]	NA|315aa|up_7|CP011848.1_1504064_1505009_+	TIGR00950, Uncharacterized_inner_membrane_transporter_YicL, Carboxylate/Amino Acid/Amine Transporter	NA|312aa|up_6|CP011848.1_1505279_1506215_-	COG1242, COG1242, Predicted Fe-S oxidoreductase [General function prediction only]	NA|183aa|up_5|CP011848.1_1506334_1506883_-	NA	NA|143aa|up_4|CP011848.1_1507034_1507463_+	pfam04657, DMT_YdcZ, Putative inner membrane exporter, YdcZ	NA|217aa|up_3|CP011848.1_1507547_1508198_+	cd01994, Alpha_ANH_like_IV, This is a subfamily of Adenine nucleotide alpha hydrolases superfamily	NA|452aa|up_2|CP011848.1_1508315_1509671_-	cd13143, MATE_MepA_like, Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA	NA|120aa|up_1|CP011848.1_1510412_1510772_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|119aa|up_0|CP011848.1_1510801_1511158_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|578aa|down_0|CP011848.1_1512766_1514500_-	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain	NA|282aa|down_1|CP011848.1_1514739_1515585_-	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain	NA|745aa|down_2|CP011848.1_1515615_1517850_-	cd01948, EAL, EAL domain	NA|270aa|down_3|CP011848.1_1518619_1519429_+	cd00592, HTH_MerR-like, Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators	NA|80aa|down_4|CP011848.1_1519573_1519813_+	NA	NA|59aa|down_5|CP011848.1_1520000_1520177_-	NA	NA|225aa|down_6|CP011848.1_1520681_1521356_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|185aa|down_7|CP011848.1_1521575_1522130_-	cd01014, nicotinamidase_related, Nicotinamidase_ related amidohydrolases	NA|122aa|down_8|CP011848.1_1522207_1522573_-	COG1733, COG1733, Predicted transcriptional regulators [Transcription]	NA|45aa|down_9|CP011848.1_1522803_1522938_+	NA
GCA_003313585.1_ASM331358v1	CP011848	Clostridioides difficile strain DSM 27640 chromosome, complete genome	6	1623060-1623353	3,6,3	PILER-CR,CRISPRCasFinder,CRT	no		csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	Orphan	GTTTTATATTAACTATATGGAATGTAAAT,GTTTTATATTAACTATATGGAATGTAAAT,GTTTTATATTAACTATATGGAATGTAAAT	29,29,29	0	0	NA	NA	I-A:I-A:I-A	3,4,4	4	Orphan	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	NA|190aa|up_7|CP011848.1_1612948_1613518_+,NA|61aa|up_4|CP011848.1_1616467_1616650_-,NA|95aa|down_0|CP011848.1_1623520_1623805_-,NA|323aa|down_5|CP011848.1_1628275_1629244_+	NA|195aa|up_9|CP011848.1_1611307_1611892_+	cd02966, TlpA_like_family, TlpA-like family; composed of  TlpA, ResA, DsbE and similar proteins	NA|300aa|up_8|CP011848.1_1612044_1612944_+	TIGR02163, Ferredoxin-type_protein_NapH_homolog, ferredoxin-type protein, NapH/MauN family	NA|190aa|up_7|CP011848.1_1612948_1613518_+	NA	NA|216aa|up_6|CP011848.1_1613684_1614332_-	pfam02589, LUD_dom, LUD domain	NA|305aa|up_5|CP011848.1_1614721_1615636_-	pfam11155, DUF2935, Domain of unknown function (DUF2935)	NA|61aa|up_4|CP011848.1_1616467_1616650_-	NA	NA|283aa|up_3|CP011848.1_1617060_1617909_-	PRK00380, panC, pantoate--beta-alanine ligase; Reviewed	NA|276aa|up_2|CP011848.1_1617927_1618755_-	PRK00311, panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase; Reviewed	NA|299aa|up_1|CP011848.1_1618729_1619626_-	pfam10728, DUF2520, Domain of unknown function (DUF2520)	NA|698aa|up_0|CP011848.1_1620305_1622399_+	cd01948, EAL, EAL domain	NA|95aa|down_0|CP011848.1_1623520_1623805_-	NA	NA|273aa|down_1|CP011848.1_1624011_1624830_+	cd04782, HTH_BltR, Helix-Turn-Helix DNA binding domain of the BltR transcription regulator	NA|707aa|down_2|CP011848.1_1624962_1627083_-	COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion transport and metabolism]	NA|76aa|down_3|CP011848.1_1627108_1627336_-	pfam04023, FeoA, FeoA domain	NA|147aa|down_4|CP011848.1_1627662_1628103_-	COG2153, ElaA, Predicted acyltransferase [General function prediction only]	NA|323aa|down_5|CP011848.1_1628275_1629244_+	NA	NA|403aa|down_6|CP011848.1_1629719_1630928_+	PRK13354, PRK13354, tyrosyl-tRNA synthetase; Provisional	NA|294aa|down_7|CP011848.1_1630988_1631870_-	cd10944, CE4_SmPgdA_like, Catalytic NodB homology domain of Streptococcus mutans polysaccharide deacetylase PgdA, Bacillus subtilis YheN, and similar proteins	NA|305aa|down_8|CP011848.1_1632285_1633200_+	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|down_9|CP011848.1_1633422_1633968_+	cd01046, Rubrerythrin_like, rubrerythrin-like, diiron-binding domain
GCA_003313585.1_ASM331358v1	CP011848	Clostridioides difficile strain DSM 27640 chromosome, complete genome	7	1715737-1716093	4,7,4	PILER-CR,CRISPRCasFinder,CRT	no		csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	Orphan	GTTTTAGATTAACTATATGGAATGTAAAT,GTTTTAGATTAACTATATGGAATGTAAAT,GTTTTAGATTAACTATATGGAATGTAAAT	29,29,29	0	0	NA	NA	I-A:I-A:I-A	4,5,5	5	Orphan	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	NA|116aa|up_9|CP011848.1_1708788_1709136_+,NA|269aa|up_7|CP011848.1_1709535_1710342_+,NA|146aa|up_6|CP011848.1_1710690_1711128_+,NA|59aa|up_5|CP011848.1_1711120_1711297_+,NA|276aa|up_2|CP011848.1_1713153_1713981_+,NA|35aa|up_0|CP011848.1_1715341_1715446_+,NA|45aa|down_1|CP011848.1_1717557_1717692_+	NA|116aa|up_9|CP011848.1_1708788_1709136_+	NA	NA|97aa|up_8|CP011848.1_1709135_1709426_+	pfam04883, HK97-gp10_like, Bacteriophage HK97-gp10, putative tail-component	NA|269aa|up_7|CP011848.1_1709535_1710342_+	NA	NA|146aa|up_6|CP011848.1_1710690_1711128_+	NA	NA|59aa|up_5|CP011848.1_1711120_1711297_+	NA	NA|437aa|up_4|CP011848.1_1711297_1712608_+	pfam04984, Phage_sheath_1, Phage tail sheath protein subtilisin-like domain	NA|157aa|up_3|CP011848.1_1712624_1713095_+	pfam09393, DUF2001, Phage tail tube protein	NA|276aa|up_2|CP011848.1_1713153_1713981_+	NA	NA|147aa|up_1|CP011848.1_1714052_1714493_+	pfam08890, Phage_TAC_5, Phage XkdN-like tail assembly chaperone protein, TAC	NA|35aa|up_0|CP011848.1_1715341_1715446_+	NA	NA|289aa|down_0|CP011848.1_1716638_1717505_+	smart01040, Bro-N, BRO family, N-terminal domain	NA|45aa|down_1|CP011848.1_1717557_1717692_+	NA	NA|176aa|down_2|CP011848.1_1718369_1718897_+	pfam11611, DUF4352, Domain of unknown function (DUF4352)	NA|256aa|down_3|CP011848.1_1719034_1719802_+	pfam14471, DUF4428, Domain of unknown function (DUF4428)	NA|791aa|down_4|CP011848.1_1719867_1722240_+	TIGR02675, Mu-like_prophage_FluMu_protein_gp42, tape measure domain	NA|230aa|down_5|CP011848.1_1722256_1722946_+	PRK11198, PRK11198, LysM domain/BON superfamily protein; Provisional	NA|631aa|down_6|CP011848.1_1722938_1724831_+	pfam00877, NLPC_P60, NlpC/P60 family	NA|87aa|down_7|CP011848.1_1724844_1725105_+	pfam10844, DUF2577, Protein of unknown function (DUF2577)	NA|140aa|down_8|CP011848.1_1725109_1725529_+	pfam10934, DUF2634, Protein of unknown function (DUF2634)	NA|350aa|down_9|CP011848.1_1725529_1726579_+	pfam04865, Baseplate_J, Baseplate J-like protein
GCA_003313585.1_ASM331358v1	CP011848	Clostridioides difficile strain DSM 27640 chromosome, complete genome	8	1717958-1718248	8	CRISPRCasFinder	no		csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	Orphan	GTTTTATATTAACTATATGGAATGTAAATC	30	0	0	NA	NA	I-A	4	4	Orphan	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	NA|269aa|up_9|CP011848.1_1709535_1710342_+,NA|146aa|up_8|CP011848.1_1710690_1711128_+,NA|59aa|up_7|CP011848.1_1711120_1711297_+,NA|276aa|up_4|CP011848.1_1713153_1713981_+,NA|35aa|up_2|CP011848.1_1715341_1715446_+,NA|45aa|up_0|CP011848.1_1717557_1717692_+,NA	NA|269aa|up_9|CP011848.1_1709535_1710342_+	NA	NA|146aa|up_8|CP011848.1_1710690_1711128_+	NA	NA|59aa|up_7|CP011848.1_1711120_1711297_+	NA	NA|437aa|up_6|CP011848.1_1711297_1712608_+	pfam04984, Phage_sheath_1, Phage tail sheath protein subtilisin-like domain	NA|157aa|up_5|CP011848.1_1712624_1713095_+	pfam09393, DUF2001, Phage tail tube protein	NA|276aa|up_4|CP011848.1_1713153_1713981_+	NA	NA|147aa|up_3|CP011848.1_1714052_1714493_+	pfam08890, Phage_TAC_5, Phage XkdN-like tail assembly chaperone protein, TAC	NA|35aa|up_2|CP011848.1_1715341_1715446_+	NA	NA|289aa|up_1|CP011848.1_1716638_1717505_+	smart01040, Bro-N, BRO family, N-terminal domain	NA|45aa|up_0|CP011848.1_1717557_1717692_+	NA	NA|176aa|down_0|CP011848.1_1718369_1718897_+	pfam11611, DUF4352, Domain of unknown function (DUF4352)	NA|256aa|down_1|CP011848.1_1719034_1719802_+	pfam14471, DUF4428, Domain of unknown function (DUF4428)	NA|791aa|down_2|CP011848.1_1719867_1722240_+	TIGR02675, Mu-like_prophage_FluMu_protein_gp42, tape measure domain	NA|230aa|down_3|CP011848.1_1722256_1722946_+	PRK11198, PRK11198, LysM domain/BON superfamily protein; Provisional	NA|631aa|down_4|CP011848.1_1722938_1724831_+	pfam00877, NLPC_P60, NlpC/P60 family	NA|87aa|down_5|CP011848.1_1724844_1725105_+	pfam10844, DUF2577, Protein of unknown function (DUF2577)	NA|140aa|down_6|CP011848.1_1725109_1725529_+	pfam10934, DUF2634, Protein of unknown function (DUF2634)	NA|350aa|down_7|CP011848.1_1725529_1726579_+	pfam04865, Baseplate_J, Baseplate J-like protein	NA|206aa|down_8|CP011848.1_1726571_1727189_+	pfam10076, DUF2313, Uncharacterized protein conserved in bacteria (DUF2313)	NA|342aa|down_9|CP011848.1_1727200_1728226_+	pfam12571, DUF3751, Phage tail-collar fibre protein
GCA_003313585.1_ASM331358v1	CP011848	Clostridioides difficile strain DSM 27640 chromosome, complete genome	9	1855522-1856476	5,9,5	PILER-CR,CRISPRCasFinder,CRT	no		csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	Orphan	GTTTTATATTAACTATGTGGTATGTAAAT,GTTTTATATTAACTATGTGGTATGTAAAT,GTTTTATATTAACTATGTGGTATGTAAAT	29,29,29	0	0	NA	NA	I-A:I-A:I-A	14,14,14	14	Orphan	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	NA,NA|96aa|down_0|CP011848.1_1856884_1857172_+,NA|31aa|down_1|CP011848.1_1857196_1857289_+,NA|59aa|down_6|CP011848.1_1863559_1863736_-,NA|341aa|down_7|CP011848.1_1864310_1865333_+,NA|258aa|down_9|CP011848.1_1866239_1867013_+	NA|200aa|up_9|CP011848.1_1838346_1838946_-	COG4110, COG4110, Uncharacterized protein involved in stress response [General function prediction only]	NA|266aa|up_8|CP011848.1_1839048_1839846_-	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|329aa|up_7|CP011848.1_1840155_1841142_-	TIGR00545, Probable_lipoate-protein_ligase_A, lipoyltransferase and lipoate-protein ligase	NA|577aa|up_6|CP011848.1_1841625_1843356_+	COG1757, NhaC, Na+/H+ antiporter [Energy production and conversion]	NA|825aa|up_5|CP011848.1_1844756_1847231_+	PRK00451, PRK00451, aminomethyl-transferring glycine dehydrogenase subunit GcvPA	NA|486aa|up_4|CP011848.1_1847230_1848688_+	PRK04366, PRK04366, aminomethyl-transferring glycine dehydrogenase subunit GcvPB	NA|786aa|up_3|CP011848.1_1849110_1851468_+	cd02609, P-type_ATPase, uncharacterized subfamily of P-type ATPase transporter, similar to uncharacterized Streptococcus pneumoniae exported protein 7, Exp7	NA|106aa|up_2|CP011848.1_1851553_1851871_-	pfam06865, DUF1255, Protein of unknown function (DUF1255)	NA|252aa|up_1|CP011848.1_1852209_1852965_+	pfam12395, DUF3658, Protein of unknown function	NA|424aa|up_0|CP011848.1_1853603_1854875_-	cd01303, GDEase, Guanine deaminase (GDEase)	NA|96aa|down_0|CP011848.1_1856884_1857172_+	NA	NA|31aa|down_1|CP011848.1_1857196_1857289_+	NA	NA|184aa|down_2|CP011848.1_1857709_1858261_-	cd02209, cupin_XRE_C, XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain	NA|321aa|down_3|CP011848.1_1858451_1859414_+	cd01561, CBS_like, CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase	NA|615aa|down_4|CP011848.1_1859708_1861553_+	cd08579, GDPD_memb_like, Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases	NA|195aa|down_5|CP011848.1_1861874_1862459_+	cd03357, LbH_MAT_GAT, Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates	NA|59aa|down_6|CP011848.1_1863559_1863736_-	NA	NA|341aa|down_7|CP011848.1_1864310_1865333_+	NA	NA|296aa|down_8|CP011848.1_1865346_1866234_+	cd03264, ABC_drug_resistance_like, ABC-type multidrug transport system, ATPase component	NA|258aa|down_9|CP011848.1_1866239_1867013_+	NA
GCA_003313585.1_ASM331358v1	CP011848	Clostridioides difficile strain DSM 27640 chromosome, complete genome	10	2205780-2206463	6,10,6	CRT,CRISPRCasFinder,PILER-CR	no		csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	Orphan	TTTACATTCCATATAGTTAATATAAAAC,CTTTACATTCCATATAGTTAATATAAAAC,GTTTTATATTAACTATATGGAATGTAAAG	28,29,29	0	0	NA	NA	I-A:I-A:I-A	10,9,8	10	Orphan	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	NA|95aa|up_0|CP011848.1_2205384_2205669_-,NA|206aa|down_7|CP011848.1_2215082_2215700_-,NA|567aa|down_8|CP011848.1_2215869_2217570_-,NA|188aa|down_9|CP011848.1_2217966_2218530_-	NA|287aa|up_9|CP011848.1_2195619_2196480_-	cd04250, AAK_NAGK-C, AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the non-acetylated, cyclic route of ornithine biosynthesis	NA|406aa|up_8|CP011848.1_2196494_2197712_-	cd02152, OAT, Ornithine acetyltransferase (OAT) family; also referred to as ArgJ	NA|345aa|up_7|CP011848.1_2197753_2198788_-	PRK00436, argC, N-acetyl-gamma-glutamyl-phosphate reductase; Validated	NA|255aa|up_6|CP011848.1_2199477_2200242_-	pfam14268, YoaP, YoaP-like	NA|158aa|up_5|CP011848.1_2200544_2201018_+	pfam13673, Acetyltransf_10, Acetyltransferase (GNAT) domain	NA|186aa|up_4|CP011848.1_2201386_2201944_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|233aa|up_3|CP011848.1_2202201_2202900_+	TIGR03502, lipase_Pla1_cef, extracellular lipase, Pla-1/cef family	NA|156aa|up_2|CP011848.1_2203921_2204389_+	pfam11188, DUF2975, Protein of unknown function (DUF2975)	NA|72aa|up_1|CP011848.1_2204399_2204615_+	COG3655, COG3655, Predicted transcriptional regulator [Transcription]	NA|95aa|up_0|CP011848.1_2205384_2205669_-	NA	NA|291aa|down_0|CP011848.1_2207293_2208166_-	COG1737, RpiR, Transcriptional regulators [Transcription]	NA|193aa|down_1|CP011848.1_2208559_2209138_-	pfam06962, rRNA_methylase, Putative rRNA methylase	NA|239aa|down_2|CP011848.1_2209195_2209912_-	COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]	NA|362aa|down_3|CP011848.1_2210102_2211188_+	COG0628, yhhT, Predicted permease, member of the PurR regulon [General function prediction only]	NA|220aa|down_4|CP011848.1_2211342_2212002_-	pfam03154, Atrophin-1, Atrophin-1 family	NA|431aa|down_5|CP011848.1_2212218_2213511_-	cd06828, PLPDE_III_DapDC, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase	NA|398aa|down_6|CP011848.1_2213528_2214722_-	PRK06635, PRK06635, aspartate kinase; Reviewed	NA|206aa|down_7|CP011848.1_2215082_2215700_-	NA	NA|567aa|down_8|CP011848.1_2215869_2217570_-	NA	NA|188aa|down_9|CP011848.1_2217966_2218530_-	NA
GCA_003313585.1_ASM331358v1	CP011848	Clostridioides difficile strain DSM 27640 chromosome, complete genome	11	2666414-2666571	7	PILER-CR	no	cas3,cas5,cas7,cas6	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	Unclear	AGGTTTAAGATTAACTAAGTGGATTTCA	28	0	0	NA	NA	NA	2	2	Unclear	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	NA,NA|492aa|down_3|CP011848.1_2671002_2672478_-	NA|448aa|up_9|CP011848.1_2658870_2660214_-	pfam06898, YqfD, Putative stage IV sporulation protein YqfD	NA|79aa|up_8|CP011848.1_2660226_2660463_-	pfam07873, YabP, YabP family	NA|188aa|up_7|CP011848.1_2660675_2661239_-	cd00552, RaiA, RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY,  is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site	NA|166aa|up_6|CP011848.1_2661431_2661929_-	cd15904, TSPO_MBR, Translocator protein (TSPO)/peripheral-type benzodiazepine receptor (MBR) family	NA|148aa|up_5|CP011848.1_2662039_2662483_-	pfam09424, YqeY, Yqey-like protein	NA|60aa|up_4|CP011848.1_2662512_2662692_-	PRK00270, rpsU, 30S ribosomal protein S21; Reviewed	NA|117aa|up_3|CP011848.1_2662854_2663205_-	cd01276, PKCI_related, Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides	NA|433aa|up_2|CP011848.1_2663247_2664546_-	COG0621, MiaB, 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]	NA|253aa|up_1|CP011848.1_2664547_2665306_-	PRK11713, PRK11713, 16S ribosomal RNA methyltransferase RsmE; Provisional	NA|316aa|up_0|CP011848.1_2665324_2666272_-	pfam06325, PrmA, Ribosomal protein L11 methyltransferase (PrmA)	cas3|803aa|down_0|CP011848.1_2666712_2669121_-	TIGR01587, CRISPR-associated_endonuclease/helicase_Cas3, CRISPR-associated helicase Cas3	cas5|269aa|down_1|CP011848.1_2669147_2669954_-	cd09658, Cas5_I-B, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas7|338aa|down_2|CP011848.1_2669969_2670983_-	cd09687, Cas7_I-C, CRISPR/Cas system-associated RAMP superfamily protein Cas7	NA|492aa|down_3|CP011848.1_2671002_2672478_-	NA	cas6|246aa|down_4|CP011848.1_2672482_2673220_-	cd09652, Cas6-I-III, CRISPR/Cas system-associated RAMP superfamily protein Cas6	NA|370aa|down_5|CP011848.1_2673478_2674588_+	PRK11650, ugpC, sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC	NA|256aa|down_6|CP011848.1_2674617_2675385_+	COG2508, COG2508, Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]	NA|458aa|down_7|CP011848.1_2675572_2676946_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|312aa|down_8|CP011848.1_2676981_2677917_-	COG1940, NagC, Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]	NA|385aa|down_9|CP011848.1_2678882_2680037_-	PRK10767, PRK10767, chaperone protein DnaJ; Provisional
GCA_003313585.1_ASM331358v1	CP011848	Clostridioides difficile strain DSM 27640 chromosome, complete genome	14	3249998-3251744	13,7,8	CRISPRCasFinder,CRT,PILER-CR	no	cas2,cas1,cas4,cas3,cas5,cas7,cas8b2,cas6,WYL	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	Unclear	ATTTACATACCACTTAGTTAATATAAAAC,ATTTACATACCACTTAGTTAATATAAAAC,GTTTTATATTAACTAAGTGGTATGTAAAT	29,29,29	0	0	NA	NA	I-A:I-A:I-A	26,24,23	26	Unclear	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	NA|67aa|up_7|CP011848.1_3242889_3243090_+,NA|260aa|up_1|CP011848.1_3248273_3249053_+,NA	NA|740aa|up_9|CP011848.1_3237236_3239456_-	cd01948, EAL, EAL domain	NA|885aa|up_8|CP011848.1_3239731_3242386_-	PRK13805, PRK13805, bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional	NA|67aa|up_7|CP011848.1_3242889_3243090_+	NA	NA|197aa|up_6|CP011848.1_3243297_3243888_-	PRK08305, spoVFB, dipicolinate synthase subunit B; Reviewed	NA|292aa|up_5|CP011848.1_3243890_3244766_-	PRK08306, PRK08306, dipicolinate synthase subunit DpsA	NA|464aa|up_4|CP011848.1_3244841_3246233_-	cd17633, AFD_YhfT-like, fatty acid-CoA ligase VraA	NA|379aa|up_3|CP011848.1_3246236_3247373_-	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|CP011848.1_3247404_3247950_-	pfam02632, BioY, BioY family	NA|260aa|up_1|CP011848.1_3248273_3249053_+	NA	NA|143aa|up_0|CP011848.1_3249508_3249937_-	PRK10562, PRK10562, putative acetyltransferase; Provisional	cas2|89aa|down_0|CP011848.1_3251927_3252194_-	cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2	cas1|327aa|down_1|CP011848.1_3252196_3253177_-	TIGR03641, cas1_HMARI, CRISPR-associated endonuclease Cas1, subtype I-B/HMARI/TNEAP	cas4|190aa|down_2|CP011848.1_3253179_3253749_-	pfam01930, Cas_Cas4, Domain of unknown function DUF83	cas3|774aa|down_3|CP011848.1_3253745_3256067_-	TIGR01587, CRISPR-associated_endonuclease/helicase_Cas3, CRISPR-associated helicase Cas3	cas5|234aa|down_4|CP011848.1_3256077_3256779_-	cd09658, Cas5_I-B, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas7|305aa|down_5|CP011848.1_3256780_3257695_-	cd09687, Cas7_I-C, CRISPR/Cas system-associated RAMP superfamily protein Cas7	cas8b2|626aa|down_6|CP011848.1_3257696_3259574_-	cd09665, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1	cas6|246aa|down_7|CP011848.1_3259579_3260317_-	cd09652, Cas6-I-III, CRISPR/Cas system-associated RAMP superfamily protein Cas6	WYL|296aa|down_8|CP011848.1_3260394_3261282_-	pfam13280, WYL, WYL domain	NA|639aa|down_9|CP011848.1_3261590_3263507_-	pfam02687, FtsX, FtsX-like permease family
GCA_003313585.1_ASM331358v1	CP011848	Clostridioides difficile strain DSM 27640 chromosome, complete genome	15	3497132-3497754	14,8,9	CRISPRCasFinder,CRT,PILER-CR	no	WYL,cas3,cas7,cas6,cas5	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	Unclear	ATTTATAACTAACTTAGTGTAATTTAAAC,ATTTATAACTAACTTAGTGTAATTTAAAC,ATTTATAACTAACTTAGTGTAATTTAAAC	29,29,29	0	0	NA	NA	NA:NA:NA	9,9,8	9	Unclear	csa3,cas14j,c2c9_V-U4,WYL,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6,cas2,cas1,cas4,cas8b2	NA|243aa|up_9|CP011848.1_3486339_3487068_-,NA|540aa|up_8|CP011848.1_3487085_3488705_-,NA|110aa|up_2|CP011848.1_3494890_3495220_-,NA|389aa|down_2|CP011848.1_3501093_3502260_-,NA|91aa|down_6|CP011848.1_3505543_3505816_-,NA|248aa|down_8|CP011848.1_3507412_3508156_-,NA|105aa|down_9|CP011848.1_3508177_3508492_-	NA|243aa|up_9|CP011848.1_3486339_3487068_-	NA	NA|540aa|up_8|CP011848.1_3487085_3488705_-	NA	NA|337aa|up_7|CP011848.1_3488704_3489715_-	pfam09983, DUF2220, Uncharacterized protein conserved in bacteria C-term(DUF2220)	NA|67aa|up_6|CP011848.1_3490313_3490514_+	COG2963, COG2963, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|130aa|up_5|CP011848.1_3490615_3491005_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|431aa|up_4|CP011848.1_3491446_3492739_-	pfam03235, DUF262, Protein of unknown function DUF262	NA|401aa|up_3|CP011848.1_3492738_3493941_-	pfam08867, FRG, FRG domain	NA|110aa|up_2|CP011848.1_3494890_3495220_-	NA	NA|112aa|up_1|CP011848.1_3495283_3495619_-	pfam13751, DDE_Tnp_1_6, Transposase DDE domain	NA|149aa|up_0|CP011848.1_3495865_3496312_-	COG3666, COG3666, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	cas3|662aa|down_0|CP011848.1_3498006_3499992_-	TIGR01587, CRISPR-associated_endonuclease/helicase_Cas3, CRISPR-associated helicase Cas3	cas7|357aa|down_1|CP011848.1_3500002_3501073_-	TIGR02585, conserved_protein, CRISPR-associated protein Cas7/Cst2/DevR, subtype I-B/TNEAP	NA|389aa|down_2|CP011848.1_3501093_3502260_-	NA	cas6|255aa|down_3|CP011848.1_3502261_3503026_-	COG1583, COG1583, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	cas5|216aa|down_4|CP011848.1_3503016_3503664_-	TIGR01895, conserved_hypothetical_protein, CRISPR-associated protein Cas5, subtype I-B/TNEAP	NA|376aa|down_5|CP011848.1_3504143_3505271_-	COG3183, COG3183, Predicted restriction endonuclease [Defense mechanisms]	NA|91aa|down_6|CP011848.1_3505543_3505816_-	NA	NA|412aa|down_7|CP011848.1_3506065_3507301_-	TIGR00665, DnaB, replicative DNA helicase	NA|248aa|down_8|CP011848.1_3507412_3508156_-	NA	NA|105aa|down_9|CP011848.1_3508177_3508492_-	NA
