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_003482305.1_ASM348230v1	CP016104	Clostridioides difficile strain DSM 29629 chromosome, complete genome	1	634935-635059	1	CRISPRCasFinder	no	WYL	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	Unclear	TGATGGTTGATAAGAATAGTAAGAAAAAAATAGATAATTAAAG	43	0	0	NA	NA	NA	1	1	Orphan	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	NA|204aa|up_4|CP016104.1_629636_630248_+,NA|219aa|down_0|CP016104.1_635270_635927_+	NA|147aa|up_9|CP016104.1_625605_626046_+	cd00732, CheW, CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea	NA|268aa|up_8|CP016104.1_626081_626885_+	COG1352, CheR, Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]	NA|199aa|up_7|CP016104.1_626924_627521_+	cd16432, CheB_Rec, Chemotaxis response regulator protein-glutamate methylesterase, CheB, with N-terminal REC domain	NA|288aa|up_6|CP016104.1_627626_628490_+	pfam13739, DUF4163, Domain of unknown function (DUF4163)	NA|330aa|up_5|CP016104.1_628556_629546_+	PRK08618, PRK08618, ornithine cyclodeaminase family protein	NA|204aa|up_4|CP016104.1_629636_630248_+	NA	NA|260aa|up_3|CP016104.1_630695_631475_+	pfam06161, DUF975, Protein of unknown function (DUF975)	NA|120aa|up_2|CP016104.1_631679_632039_+	pfam03965, Penicillinase_R, Penicillinase repressor	NA|461aa|up_1|CP016104.1_632049_633432_+	cd07341, M56_BlaR1_MecR1_like, Peptidase M56-like including those in BlaR1 and MecR1, integral membrane metallopeptidase	NA|137aa|up_0|CP016104.1_633647_634058_+	pfam02181, FH2, Formin Homology 2 Domain	NA|219aa|down_0|CP016104.1_635270_635927_+	NA	NA|424aa|down_1|CP016104.1_636397_637669_-	pfam01471, PG_binding_1, Putative peptidoglycan binding domain	NA|239aa|down_2|CP016104.1_637913_638630_+	pfam13367, PrsW-protease, Protease prsW family	NA|437aa|down_3|CP016104.1_638708_640019_+	PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed	NA|179aa|down_4|CP016104.1_640118_640655_+	TIGR02227, Inactive_signal_peptidase_IA	NA|179aa|down_5|CP016104.1_640820_641357_+	TIGR02227, Inactive_signal_peptidase_IA	NA|252aa|down_6|CP016104.1_641366_642122_+	pfam01261, AP_endonuc_2, Xylose isomerase-like TIM barrel	NA|556aa|down_7|CP016104.1_642195_643863_+	cd02028, UMPK_like, Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2	NA|310aa|down_8|CP016104.1_644634_645564_+	TIGR03814, Glutaminase_1, glutaminase A	NA|188aa|down_9|CP016104.1_645661_646225_+	pfam12840, HTH_20, Helix-turn-helix domain
GCA_003482305.1_ASM348230v1	CP016104	Clostridioides difficile strain DSM 29629 chromosome, complete genome	2	1347267-1347822	1,2,1	PILER-CR,CRISPRCasFinder,CRT	no		csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	Orphan	GTTTTATATTAACTAAGTGGTATGTAAAG,GTTTTATATTAACTAAGTGGTATGTAAAG,GTTTTATATTAACTAAGTGGTATGTAAAG	29,29,29	0	0	NA	NA	I-A:I-A:I-A	8,8,8	8	Orphan	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	NA,NA|84aa|down_1|CP016104.1_1349434_1349686_+,NA|38aa|down_2|CP016104.1_1350002_1350116_+,NA|127aa|down_3|CP016104.1_1350339_1350720_+,NA|128aa|down_4|CP016104.1_1350903_1351287_-,NA|106aa|down_5|CP016104.1_1353131_1353449_-,NA|65aa|down_8|CP016104.1_1355804_1355999_-	NA|271aa|up_9|CP016104.1_1334361_1335174_+	cd09009, PNP-EcPNPII_like, purine nucleoside phosphorylases similar to human PNP and Escherichia coli PNP-II (XapA)	NA|442aa|up_8|CP016104.1_1335377_1336703_+	TIGR02644, Thymidine_phosphorylase, pyrimidine-nucleoside phosphorylase	NA|360aa|up_7|CP016104.1_1336915_1337995_+	pfam02618, YceG, YceG-like family	NA|225aa|up_6|CP016104.1_1338166_1338841_+	COG4122, COG4122, Predicted O-methyltransferase [General function prediction only]	NA|416aa|up_5|CP016104.1_1338827_1340075_+	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|555aa|up_4|CP016104.1_1340146_1341811_+	COG0768, FtsI, Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]	NA|95aa|up_3|CP016104.1_1341907_1342192_-	PRK05803, PRK05803, RNA polymerase sporulation sigma factor SigK	NA|506aa|up_2|CP016104.1_1342214_1343732_-	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_1|CP016104.1_1343856_1344678_-	sd00006, TPR, Tetratricopeptide repeat	NA|476aa|up_0|CP016104.1_1344868_1346296_+	NF033435, S-layer_Clost, S-layer protein SlpA	NA|47aa|down_0|CP016104.1_1348191_1348332_-	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|84aa|down_1|CP016104.1_1349434_1349686_+	NA	NA|38aa|down_2|CP016104.1_1350002_1350116_+	NA	NA|127aa|down_3|CP016104.1_1350339_1350720_+	NA	NA|128aa|down_4|CP016104.1_1350903_1351287_-	NA	NA|106aa|down_5|CP016104.1_1353131_1353449_-	NA	NA|130aa|down_6|CP016104.1_1354480_1354870_+	pfam03965, Penicillinase_R, Penicillinase repressor	NA|170aa|down_7|CP016104.1_1355193_1355703_+	pfam04892, VanZ, VanZ like family	NA|65aa|down_8|CP016104.1_1355804_1355999_-	NA	NA|131aa|down_9|CP016104.1_1356515_1356908_-	PRK05803, PRK05803, RNA polymerase sporulation sigma factor SigK
GCA_003482305.1_ASM348230v1	CP016104	Clostridioides difficile strain DSM 29629 chromosome, complete genome	3	1557411-1558098	2,3,2	PILER-CR,CRISPRCasFinder,CRT	no	DinG	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	Type IV-A	GTTTTATATTAACTAAGTGGTATGTAAAT,GTTTTATATTAACTAAGTGGTATGTAAAT,GTTTTATATTAACTAAGTGGTATGTAAAT	29,29,29	0	0	NA	NA	I-A:I-A:I-A	9,10,10	10	Orphan	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	NA|183aa|up_5|CP016104.1_1552098_1552647_-,NA|80aa|down_4|CP016104.1_1565248_1565488_+,NA|59aa|down_5|CP016104.1_1565674_1565851_-	NA|195aa|up_9|CP016104.1_1547288_1547873_-	pfam00882, Zn_dep_PLPC, Zinc dependent phospholipase C	NA|481aa|up_8|CP016104.1_1548072_1549515_-	COG3829, RocR, Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]	NA|315aa|up_7|CP016104.1_1549829_1550774_+	TIGR00950, Uncharacterized_inner_membrane_transporter_YicL, Carboxylate/Amino Acid/Amine Transporter	NA|329aa|up_6|CP016104.1_1551044_1552031_-	COG1242, COG1242, Predicted Fe-S oxidoreductase [General function prediction only]	NA|183aa|up_5|CP016104.1_1552098_1552647_-	NA	NA|143aa|up_4|CP016104.1_1552798_1553227_+	pfam04657, DMT_YdcZ, Putative inner membrane exporter, YdcZ	NA|217aa|up_3|CP016104.1_1553311_1553962_+	cd01994, Alpha_ANH_like_IV, This is a subfamily of Adenine nucleotide alpha hydrolases superfamily	NA|452aa|up_2|CP016104.1_1554079_1555435_-	cd13143, MATE_MepA_like, Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA	NA|187aa|up_1|CP016104.1_1555937_1556498_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|119aa|up_0|CP016104.1_1556527_1556884_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|578aa|down_0|CP016104.1_1558423_1560157_-	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain	NA|282aa|down_1|CP016104.1_1560393_1561239_-	cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain	NA|745aa|down_2|CP016104.1_1561269_1563504_-	cd01948, EAL, EAL domain	NA|270aa|down_3|CP016104.1_1564286_1565096_+	cd00592, HTH_MerR-like, Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators	NA|80aa|down_4|CP016104.1_1565248_1565488_+	NA	NA|59aa|down_5|CP016104.1_1565674_1565851_-	NA	NA|225aa|down_6|CP016104.1_1566342_1567017_-	COG1285, SapB, Uncharacterized membrane protein [Function unknown]	NA|185aa|down_7|CP016104.1_1567236_1567791_-	cd01014, nicotinamidase_related, Nicotinamidase_ related amidohydrolases	NA|122aa|down_8|CP016104.1_1567868_1568234_-	COG1733, COG1733, Predicted transcriptional regulators [Transcription]	NA|45aa|down_9|CP016104.1_1568464_1568599_+	TIGR00232, Transketolase_2, transketolase, bacterial and yeast
GCA_003482305.1_ASM348230v1	CP016104	Clostridioides difficile strain DSM 29629 chromosome, complete genome	4	1667351-1667773	3,4,3	PILER-CR,CRISPRCasFinder,CRT	no		csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	Orphan	GTTTTATATTAACTATATGGAATGTAAAT,GTTTTATATTAACTATATGGAATGTAAAT,GTTTTATATTAACTATATGGAATGTAAAT	29,29,29	0	0	NA	NA	I-A:I-A:I-A	5,6,6	6	Orphan	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	NA|190aa|up_7|CP016104.1_1657447_1658017_+,NA|61aa|up_4|CP016104.1_1660701_1660884_-,NA|323aa|down_4|CP016104.1_1672685_1673654_+	NA|195aa|up_9|CP016104.1_1655806_1656391_+	cd02966, TlpA_like_family, TlpA-like family; composed of  TlpA, ResA, DsbE and similar proteins	NA|300aa|up_8|CP016104.1_1656543_1657443_+	TIGR02163, Ferredoxin-type_protein_NapH_homolog, ferredoxin-type protein, NapH/MauN family	NA|190aa|up_7|CP016104.1_1657447_1658017_+	NA	NA|216aa|up_6|CP016104.1_1658183_1658831_-	pfam02589, LUD_dom, LUD domain	NA|305aa|up_5|CP016104.1_1659221_1660136_-	pfam11155, DUF2935, Domain of unknown function (DUF2935)	NA|61aa|up_4|CP016104.1_1660701_1660884_-	NA	NA|283aa|up_3|CP016104.1_1661351_1662200_-	PRK00380, panC, pantoate--beta-alanine ligase; Reviewed	NA|276aa|up_2|CP016104.1_1662218_1663046_-	PRK00311, panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase; Reviewed	NA|299aa|up_1|CP016104.1_1663020_1663917_-	pfam10728, DUF2520, Domain of unknown function (DUF2520)	NA|698aa|up_0|CP016104.1_1664596_1666690_+	cd01948, EAL, EAL domain	NA|273aa|down_0|CP016104.1_1668421_1669240_+	cd04782, HTH_BltR, Helix-Turn-Helix DNA binding domain of the BltR transcription regulator	NA|707aa|down_1|CP016104.1_1669372_1671493_-	COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion transport and metabolism]	NA|76aa|down_2|CP016104.1_1671518_1671746_-	pfam04023, FeoA, FeoA domain	NA|147aa|down_3|CP016104.1_1672072_1672513_-	COG2153, ElaA, Predicted acyltransferase [General function prediction only]	NA|323aa|down_4|CP016104.1_1672685_1673654_+	NA	NA|403aa|down_5|CP016104.1_1674130_1675339_+	PRK13354, PRK13354, tyrosyl-tRNA synthetase; Provisional	NA|294aa|down_6|CP016104.1_1675420_1676302_-	cd10944, CE4_SmPgdA_like, Catalytic NodB homology domain of Streptococcus mutans polysaccharide deacetylase PgdA, Bacillus subtilis YheN, and similar proteins	NA|305aa|down_7|CP016104.1_1676717_1677632_+	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_8|CP016104.1_1677854_1678400_+	cd01046, Rubrerythrin_like, rubrerythrin-like, diiron-binding domain	NA|383aa|down_9|CP016104.1_1678490_1679639_+	COG2006, COG2006, Uncharacterized conserved protein [Function unknown]
GCA_003482305.1_ASM348230v1	CP016104	Clostridioides difficile strain DSM 29629 chromosome, complete genome	5	1757541-1758096	4,5,4	PILER-CR,CRISPRCasFinder,CRT	no		csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	Orphan	GTTTTAGATTAACTATATGGAATGTAAAT,GTTTTAGATTAACTATATGGAATGTAAAT,GTTTTAGATTAACTATATGGAATGTAAAT	29,29,29	0	0	NA	NA	I-A:I-A:I-A	7,8,8	8	Orphan	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	NA|134aa|up_8|CP016104.1_1752226_1752628_+,NA|116aa|up_7|CP016104.1_1752621_1752969_+,NA|146aa|up_5|CP016104.1_1753386_1753824_+,NA|62aa|up_4|CP016104.1_1753807_1753993_+,NA|35aa|up_0|CP016104.1_1757145_1757250_+,NA|53aa|down_2|CP016104.1_1760871_1761030_+	NA|78aa|up_9|CP016104.1_1751983_1752217_+	TIGR03752, conj_TIGR03752, integrating conjugative element protein, PFL_4705 family	NA|134aa|up_8|CP016104.1_1752226_1752628_+	NA	NA|116aa|up_7|CP016104.1_1752621_1752969_+	NA	NA|142aa|up_6|CP016104.1_1752968_1753394_+	pfam04883, HK97-gp10_like, Bacteriophage HK97-gp10, putative tail-component	NA|146aa|up_5|CP016104.1_1753386_1753824_+	NA	NA|62aa|up_4|CP016104.1_1753807_1753993_+	NA	NA|437aa|up_3|CP016104.1_1753993_1755304_+	pfam04984, Phage_sheath_1, Phage tail sheath protein subtilisin-like domain	NA|157aa|up_2|CP016104.1_1755320_1755791_+	pfam09393, DUF2001, Phage tail tube protein	NA|147aa|up_1|CP016104.1_1755862_1756303_+	pfam08890, Phage_TAC_5, Phage XkdN-like tail assembly chaperone protein, TAC	NA|35aa|up_0|CP016104.1_1757145_1757250_+	NA	NA|57aa|down_0|CP016104.1_1759678_1759849_+	pfam01402, RHH_1, Ribbon-helix-helix protein, copG family	NA|281aa|down_1|CP016104.1_1759976_1760819_+	smart01040, Bro-N, BRO family, N-terminal domain	NA|53aa|down_2|CP016104.1_1760871_1761030_+	NA	NA|261aa|down_3|CP016104.1_1761587_1762370_+	pfam09851, SHOCT, Short C-terminal domain	NA|784aa|down_4|CP016104.1_1762433_1764785_+	TIGR02675, Mu-like_prophage_FluMu_protein_gp42, tape measure domain	NA|230aa|down_5|CP016104.1_1764800_1765490_+	PRK11198, PRK11198, LysM domain/BON superfamily protein; Provisional	NA|655aa|down_6|CP016104.1_1765482_1767447_+	pfam00877, NLPC_P60, NlpC/P60 family	NA|87aa|down_7|CP016104.1_1767460_1767721_+	pfam10844, DUF2577, Protein of unknown function (DUF2577)	NA|140aa|down_8|CP016104.1_1767725_1768145_+	pfam10934, DUF2634, Protein of unknown function (DUF2634)	NA|350aa|down_9|CP016104.1_1768145_1769195_+	pfam04865, Baseplate_J, Baseplate J-like protein
GCA_003482305.1_ASM348230v1	CP016104	Clostridioides difficile strain DSM 29629 chromosome, complete genome	6	1758698-1759519	5,6,5	PILER-CR,CRISPRCasFinder,CRT	no		csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	Orphan	GTTTTAGATTAACTAAGTGGAATGTAAAT,GTTTTAGATTAACTATATGGAATGTAAAT,GTTTTAGATTAACTAAGTGGAATGTAAAT	29,29,29	0	0	NA	NA	I-A:I-A:I-A	10,12,12	12	Orphan	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	NA|134aa|up_8|CP016104.1_1752226_1752628_+,NA|116aa|up_7|CP016104.1_1752621_1752969_+,NA|146aa|up_5|CP016104.1_1753386_1753824_+,NA|62aa|up_4|CP016104.1_1753807_1753993_+,NA|35aa|up_0|CP016104.1_1757145_1757250_+,NA|53aa|down_2|CP016104.1_1760871_1761030_+	NA|78aa|up_9|CP016104.1_1751983_1752217_+	TIGR03752, conj_TIGR03752, integrating conjugative element protein, PFL_4705 family	NA|134aa|up_8|CP016104.1_1752226_1752628_+	NA	NA|116aa|up_7|CP016104.1_1752621_1752969_+	NA	NA|142aa|up_6|CP016104.1_1752968_1753394_+	pfam04883, HK97-gp10_like, Bacteriophage HK97-gp10, putative tail-component	NA|146aa|up_5|CP016104.1_1753386_1753824_+	NA	NA|62aa|up_4|CP016104.1_1753807_1753993_+	NA	NA|437aa|up_3|CP016104.1_1753993_1755304_+	pfam04984, Phage_sheath_1, Phage tail sheath protein subtilisin-like domain	NA|157aa|up_2|CP016104.1_1755320_1755791_+	pfam09393, DUF2001, Phage tail tube protein	NA|147aa|up_1|CP016104.1_1755862_1756303_+	pfam08890, Phage_TAC_5, Phage XkdN-like tail assembly chaperone protein, TAC	NA|35aa|up_0|CP016104.1_1757145_1757250_+	NA	NA|57aa|down_0|CP016104.1_1759678_1759849_+	pfam01402, RHH_1, Ribbon-helix-helix protein, copG family	NA|281aa|down_1|CP016104.1_1759976_1760819_+	smart01040, Bro-N, BRO family, N-terminal domain	NA|53aa|down_2|CP016104.1_1760871_1761030_+	NA	NA|261aa|down_3|CP016104.1_1761587_1762370_+	pfam09851, SHOCT, Short C-terminal domain	NA|784aa|down_4|CP016104.1_1762433_1764785_+	TIGR02675, Mu-like_prophage_FluMu_protein_gp42, tape measure domain	NA|230aa|down_5|CP016104.1_1764800_1765490_+	PRK11198, PRK11198, LysM domain/BON superfamily protein; Provisional	NA|655aa|down_6|CP016104.1_1765482_1767447_+	pfam00877, NLPC_P60, NlpC/P60 family	NA|87aa|down_7|CP016104.1_1767460_1767721_+	pfam10844, DUF2577, Protein of unknown function (DUF2577)	NA|140aa|down_8|CP016104.1_1767725_1768145_+	pfam10934, DUF2634, Protein of unknown function (DUF2634)	NA|350aa|down_9|CP016104.1_1768145_1769195_+	pfam04865, Baseplate_J, Baseplate J-like protein
GCA_003482305.1_ASM348230v1	CP016104	Clostridioides difficile strain DSM 29629 chromosome, complete genome	7	1761107-1761463	6,6,7	CRT,PILER-CR,CRISPRCasFinder	no		csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	Orphan	GTTTTATATTAACTATGTGGTATGTAAA,TTTATATTAACTATGTGGTATGTAAA,TTATATTAACTATGTGGTATGTAAAG	28,26,26	0	0	NA	NA	I-A:I-A:I-A	5,4,5	5	Orphan	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	NA|146aa|up_8|CP016104.1_1753386_1753824_+,NA|62aa|up_7|CP016104.1_1753807_1753993_+,NA|35aa|up_3|CP016104.1_1757145_1757250_+,NA|53aa|up_0|CP016104.1_1760871_1761030_+,NA	NA|142aa|up_9|CP016104.1_1752968_1753394_+	pfam04883, HK97-gp10_like, Bacteriophage HK97-gp10, putative tail-component	NA|146aa|up_8|CP016104.1_1753386_1753824_+	NA	NA|62aa|up_7|CP016104.1_1753807_1753993_+	NA	NA|437aa|up_6|CP016104.1_1753993_1755304_+	pfam04984, Phage_sheath_1, Phage tail sheath protein subtilisin-like domain	NA|157aa|up_5|CP016104.1_1755320_1755791_+	pfam09393, DUF2001, Phage tail tube protein	NA|147aa|up_4|CP016104.1_1755862_1756303_+	pfam08890, Phage_TAC_5, Phage XkdN-like tail assembly chaperone protein, TAC	NA|35aa|up_3|CP016104.1_1757145_1757250_+	NA	NA|57aa|up_2|CP016104.1_1759678_1759849_+	pfam01402, RHH_1, Ribbon-helix-helix protein, copG family	NA|281aa|up_1|CP016104.1_1759976_1760819_+	smart01040, Bro-N, BRO family, N-terminal domain	NA|53aa|up_0|CP016104.1_1760871_1761030_+	NA	NA|261aa|down_0|CP016104.1_1761587_1762370_+	pfam09851, SHOCT, Short C-terminal domain	NA|784aa|down_1|CP016104.1_1762433_1764785_+	TIGR02675, Mu-like_prophage_FluMu_protein_gp42, tape measure domain	NA|230aa|down_2|CP016104.1_1764800_1765490_+	PRK11198, PRK11198, LysM domain/BON superfamily protein; Provisional	NA|655aa|down_3|CP016104.1_1765482_1767447_+	pfam00877, NLPC_P60, NlpC/P60 family	NA|87aa|down_4|CP016104.1_1767460_1767721_+	pfam10844, DUF2577, Protein of unknown function (DUF2577)	NA|140aa|down_5|CP016104.1_1767725_1768145_+	pfam10934, DUF2634, Protein of unknown function (DUF2634)	NA|350aa|down_6|CP016104.1_1768145_1769195_+	pfam04865, Baseplate_J, Baseplate J-like protein	NA|206aa|down_7|CP016104.1_1769187_1769805_+	pfam10076, DUF2313, Uncharacterized protein conserved in bacteria (DUF2313)	NA|331aa|down_8|CP016104.1_1769816_1770809_+	pfam12571, DUF3751, Phage tail-collar fibre protein	NA|551aa|down_9|CP016104.1_1770823_1772476_+	pfam12810, Gly_rich, Glycine rich protein
GCA_003482305.1_ASM348230v1	CP016104	Clostridioides difficile strain DSM 29629 chromosome, complete genome	8	1893798-1894091	7,8,7	PILER-CR,CRISPRCasFinder,CRT	no		csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	Orphan	GTTTTATATTAACTATGTGGTATGTAAAT,GTTTTATATTAACTATGTGGTATGTAAAT,GTTTTATATTAACTATGTGGTATGTAAAT	29,29,29	0	0	NA	NA	I-A:I-A:I-A	4,4,4	4	Orphan	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	NA,NA|96aa|down_0|CP016104.1_1894497_1894785_+,NA|33aa|down_1|CP016104.1_1894809_1894908_+,NA|59aa|down_6|CP016104.1_1901171_1901348_-,NA|341aa|down_7|CP016104.1_1901916_1902939_+,NA|258aa|down_9|CP016104.1_1903845_1904619_+	NA|266aa|up_9|CP016104.1_1876895_1877693_-	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|329aa|up_8|CP016104.1_1878002_1878989_-	TIGR00545, Probable_lipoate-protein_ligase_A, lipoyltransferase and lipoate-protein ligase	NA|577aa|up_7|CP016104.1_1879471_1881202_+	COG1757, NhaC, Na+/H+ antiporter [Energy production and conversion]	NA|172aa|up_6|CP016104.1_1881726_1882242_+	pfam13787, HXXEE, Protein of unknown function with HXXEE motif	NA|825aa|up_5|CP016104.1_1883031_1885506_+	PRK00451, PRK00451, aminomethyl-transferring glycine dehydrogenase subunit GcvPA	NA|486aa|up_4|CP016104.1_1885505_1886963_+	PRK04366, PRK04366, aminomethyl-transferring glycine dehydrogenase subunit GcvPB	NA|786aa|up_3|CP016104.1_1887385_1889743_+	cd02609, P-type_ATPase, uncharacterized subfamily of P-type ATPase transporter, similar to uncharacterized Streptococcus pneumoniae exported protein 7, Exp7	NA|106aa|up_2|CP016104.1_1889828_1890146_-	pfam06865, DUF1255, Protein of unknown function (DUF1255)	NA|252aa|up_1|CP016104.1_1890482_1891238_+	pfam12395, DUF3658, Protein of unknown function	NA|424aa|up_0|CP016104.1_1891878_1893150_-	cd01303, GDEase, Guanine deaminase (GDEase)	NA|96aa|down_0|CP016104.1_1894497_1894785_+	NA	NA|33aa|down_1|CP016104.1_1894809_1894908_+	NA	NA|184aa|down_2|CP016104.1_1895323_1895875_-	cd02209, cupin_XRE_C, XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain	NA|321aa|down_3|CP016104.1_1896065_1897028_+	cd01561, CBS_like, CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase	NA|615aa|down_4|CP016104.1_1897319_1899164_+	cd08579, GDPD_memb_like, Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases	NA|195aa|down_5|CP016104.1_1899484_1900069_+	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|CP016104.1_1901171_1901348_-	NA	NA|341aa|down_7|CP016104.1_1901916_1902939_+	NA	NA|296aa|down_8|CP016104.1_1902952_1903840_+	cd03264, ABC_drug_resistance_like, ABC-type multidrug transport system, ATPase component	NA|258aa|down_9|CP016104.1_1903845_1904619_+	NA
GCA_003482305.1_ASM348230v1	CP016104	Clostridioides difficile strain DSM 29629 chromosome, complete genome	9	2690171-2690331	9,8	CRISPRCasFinder,PILER-CR	no	cas3,cas5,cas7,cas6,c2c9_V-U4	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	Unclear	TGAAATCCACTTAGTTAATCTTAAAC,TAGGTTTAAGATTAACTAAGTGGATTTCA	26,29	0	0	NA	NA	NA:NA	2,2	2	Unclear	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	NA,NA|492aa|down_3|CP016104.1_2694752_2696228_-	NA|448aa|up_9|CP016104.1_2682627_2683971_-	pfam06898, YqfD, Putative stage IV sporulation protein YqfD	NA|79aa|up_8|CP016104.1_2683983_2684220_-	pfam07873, YabP, YabP family	NA|188aa|up_7|CP016104.1_2684434_2684998_-	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|CP016104.1_2685190_2685688_-	cd15904, TSPO_MBR, Translocator protein (TSPO)/peripheral-type benzodiazepine receptor (MBR) family	NA|148aa|up_5|CP016104.1_2685798_2686242_-	pfam09424, YqeY, Yqey-like protein	NA|60aa|up_4|CP016104.1_2686271_2686451_-	PRK00270, rpsU, 30S ribosomal protein S21; Reviewed	NA|117aa|up_3|CP016104.1_2686613_2686964_-	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|CP016104.1_2687006_2688305_-	COG0621, MiaB, 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]	NA|253aa|up_1|CP016104.1_2688306_2689065_-	PRK11713, PRK11713, 16S ribosomal RNA methyltransferase RsmE; Provisional	NA|316aa|up_0|CP016104.1_2689083_2690031_-	pfam06325, PrmA, Ribosomal protein L11 methyltransferase (PrmA)	cas3|803aa|down_0|CP016104.1_2690471_2692880_-	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas5|266aa|down_1|CP016104.1_2692906_2693704_-	cd09658, Cas5_I-B, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas7|338aa|down_2|CP016104.1_2693719_2694733_-	cd09687, Cas7_I-C, CRISPR/Cas system-associated RAMP superfamily protein Cas7	NA|492aa|down_3|CP016104.1_2694752_2696228_-	NA	cas6|246aa|down_4|CP016104.1_2696232_2696970_-	TIGR01877, CRISPR-associated_endoribonuclease_Cas6_1, CRISPR-associated endoribonuclease Cas6	NA|153aa|down_5|CP016104.1_2697283_2697742_+	COG2452, COG2452, Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]	c2c9_V-U4|388aa|down_6|CP016104.1_2697778_2698942_+	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|370aa|down_7|CP016104.1_2699094_2700204_+	PRK11650, ugpC, sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC	NA|256aa|down_8|CP016104.1_2700233_2701001_+	COG2508, COG2508, Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]	NA|458aa|down_9|CP016104.1_2701188_2702562_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily
GCA_003482305.1_ASM348230v1	CP016104	Clostridioides difficile strain DSM 29629 chromosome, complete genome	10	2777500-2778381	9,10,8	PILER-CR,CRISPRCasFinder,CRT	no	cas14j	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	Unclear	GTTTTATATTAACTATATGGAATGTAAAT,ATTTACATTCCATATAGTTAATATAAAAC,ATTTACATTCCATATAGTTAATATAAAAC	29,29,29	0	0	NA	NA	I-A:I-A:I-A	13,13,13	13	TypeV	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	NA,NA|53aa|down_0|CP016104.1_2778666_2778825_-	cas14j|370aa|up_9|CP016104.1_2766096_2767206_-	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|39aa|up_8|CP016104.1_2767952_2768069_-	cd05298, GH4_GlvA_pagL_like, Glycoside Hydrolases Family 4; GlvA- and pagL-like glycosidases	NA|517aa|up_7|CP016104.1_2768167_2769718_-	TIGR02005, PTS-IIBC-alpha, PTS system, alpha-glucoside-specific IIBC component	NA|272aa|up_6|CP016104.1_2769770_2770586_-	PRK09772, PRK09772, transcriptional antiterminator BglG; Provisional	NA|161aa|up_5|CP016104.1_2770606_2771089_-	pfam00358, PTS_EIIA_1, phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1	NA|127aa|up_4|CP016104.1_2771372_2771753_-	TIGR00004, RutC_family_protein, reactive intermediate/imine deaminase	NA|406aa|up_3|CP016104.1_2771847_2773065_-	PRK08198, PRK08198, threonine dehydratase; Provisional	NA|543aa|up_2|CP016104.1_2773722_2775351_+	TIGR03801, For_A_Pyridoxal-5-_Phosphate, aspartate 4-decarboxylase	NA|332aa|up_1|CP016104.1_2775471_2776467_+	cd08964, L-asparaginase_II, Type II (periplasmic) bacterial L-asparaginase	NA|128aa|up_0|CP016104.1_2776651_2777035_-	pfam03965, Penicillinase_R, Penicillinase repressor	NA|53aa|down_0|CP016104.1_2778666_2778825_-	NA	NA|457aa|down_1|CP016104.1_2779182_2780553_-	NF033435, S-layer_Clost, S-layer protein SlpA	NA|141aa|down_2|CP016104.1_2780951_2781374_+	pfam14659, Phage_int_SAM_3, Phage integrase, N-terminal SAM-like domain	NA|223aa|down_3|CP016104.1_2782359_2783028_-	pfam04892, VanZ, VanZ like family	NA|807aa|down_4|CP016104.1_2783909_2786330_-	PRK00390, leuS, leucyl-tRNA synthetase; Validated	NA|117aa|down_5|CP016104.1_2786683_2787034_-	pfam02410, RsfS, Ribosomal silencing factor during starvation	NA|191aa|down_6|CP016104.1_2787150_2787723_-	COG1713, COG1713, Predicted HD superfamily hydrolase involved in NAD metabolism [Coenzyme metabolism]	NA|230aa|down_7|CP016104.1_2787723_2788413_-	PRK00071, nadD, nicotinate-nucleotide adenylyltransferase	NA|213aa|down_8|CP016104.1_2788688_2789327_+	PRK00117, recX, recombination regulator RecX; Reviewed	NA|668aa|down_9|CP016104.1_2789479_2791483_+	PLN02447, PLN02447, 1,4-alpha-glucan-branching enzyme
GCA_003482305.1_ASM348230v1	CP016104	Clostridioides difficile strain DSM 29629 chromosome, complete genome	16	3642123-3642326	16	CRISPRCasFinder	no		csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	Orphan	TCATCATATAAACCTATTAAATATTATCTTATTTATTGGTATATGGAAT	49	0	0	NA	NA	NA	1	1	Orphan	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	NA,NA|46aa|down_3|CP016104.1_3648645_3648783_-	NA|82aa|up_9|CP016104.1_3631078_3631324_-	pfam00269, SASP, Small, acid-soluble spore proteins, alpha/beta type	NA|373aa|up_8|CP016104.1_3631454_3632573_-	cd05670, M20_Acy1_YkuR-like, M20 Peptidase aminoacyclase-1 YkuR-like proteins, including YkuR and Ama/HipO/HyuC proteins	NA|398aa|up_7|CP016104.1_3632778_3633972_-	TIGR00720, hypothetical_protein_NEICINOT_00681, L-serine dehydratase, iron-sulfur-dependent, single chain form	NA|294aa|up_6|CP016104.1_3634294_3635176_+	PRK03170, PRK03170, dihydrodipicolinate synthase; Provisional	NA|334aa|up_5|CP016104.1_3635605_3636607_+	PRK14874, PRK14874, aspartate-semialdehyde dehydrogenase; Provisional	NA|296aa|up_4|CP016104.1_3636723_3637611_+	PRK03170, PRK03170, dihydrodipicolinate synthase; Provisional	NA|250aa|up_3|CP016104.1_3637677_3638427_+	PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional	NA|239aa|up_2|CP016104.1_3638645_3639362_+	TIGR03532, DapD_Ac, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase	NA|330aa|up_1|CP016104.1_3639824_3640814_-	cd03402, SPFH_like_u2, Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily	NA|252aa|up_0|CP016104.1_3641253_3642009_+	PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional	NA|180aa|down_0|CP016104.1_3644287_3644827_-	COG0634, Hpt, Hypoxanthine-guanine phosphoribosyltransferase [Nucleotide transport and metabolism]	NA|436aa|down_1|CP016104.1_3645154_3646462_-	COG3681, COG3681, L-cysteine desulfidase [Amino acid transport and metabolism]	NA|589aa|down_2|CP016104.1_3646873_3648640_-	COG3829, RocR, Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]	NA|46aa|down_3|CP016104.1_3648645_3648783_-	NA	NA|190aa|down_4|CP016104.1_3648860_3649430_-	COG2226, UbiE, Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]	NA|212aa|down_5|CP016104.1_3649613_3650249_-	PRK05813, PRK05813, single-stranded DNA-binding protein; Provisional	NA|294aa|down_6|CP016104.1_3650916_3651798_-	pfam01925, TauE, Sulfite exporter TauE/SafE	NA|336aa|down_7|CP016104.1_3651917_3652925_-	PRK13969, PRK13969, proline racemase; Provisional	NA|158aa|down_8|CP016104.1_3652944_3653418_-	TIGR04480, D-proline_reductase_PrdA_proprotein, D-proline reductase (dithiol), PrdA proprotein	NA|156aa|down_9|CP016104.1_3653444_3653912_-	TIGR04480, D-proline_reductase_PrdA_proprotein, D-proline reductase (dithiol), PrdA proprotein
GCA_003482305.1_ASM348230v1	CP016104	Clostridioides difficile strain DSM 29629 chromosome, complete genome	17	3642858-3644034	9	CRT	no		csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	Orphan	TTGCTCCNGTTGNNCCNGTNNNTCC	25	4	7	3643693-3643712|3643693-3643712|3643792-3643811|3643792-3643811|3643837-3643856|3643936-3643955|3643936-3643955	CP016104.1_3757505-3757524|CP016104.1_3756983-3757002|CP016104.1_3757505-3757524|CP016104.1_3756983-3757002|CP016104.1_3757505-3757524|CP016104.1_3757505-3757524|CP016104.1_3756983-3757002	NA	20	20	Orphan	csa3,cas14j,PD-DExK,WYL,c2c9_V-U4,cas3,DEDDh,DinG,cas14k,cas5,cas7,cas6	NA,NA|46aa|down_3|CP016104.1_3648645_3648783_-	NA|82aa|up_9|CP016104.1_3631078_3631324_-	pfam00269, SASP, Small, acid-soluble spore proteins, alpha/beta type	NA|373aa|up_8|CP016104.1_3631454_3632573_-	cd05670, M20_Acy1_YkuR-like, M20 Peptidase aminoacyclase-1 YkuR-like proteins, including YkuR and Ama/HipO/HyuC proteins	NA|398aa|up_7|CP016104.1_3632778_3633972_-	TIGR00720, hypothetical_protein_NEICINOT_00681, L-serine dehydratase, iron-sulfur-dependent, single chain form	NA|294aa|up_6|CP016104.1_3634294_3635176_+	PRK03170, PRK03170, dihydrodipicolinate synthase; Provisional	NA|334aa|up_5|CP016104.1_3635605_3636607_+	PRK14874, PRK14874, aspartate-semialdehyde dehydrogenase; Provisional	NA|296aa|up_4|CP016104.1_3636723_3637611_+	PRK03170, PRK03170, dihydrodipicolinate synthase; Provisional	NA|250aa|up_3|CP016104.1_3637677_3638427_+	PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional	NA|239aa|up_2|CP016104.1_3638645_3639362_+	TIGR03532, DapD_Ac, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase	NA|330aa|up_1|CP016104.1_3639824_3640814_-	cd03402, SPFH_like_u2, Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily	NA|252aa|up_0|CP016104.1_3641253_3642009_+	PRK00048, PRK00048, dihydrodipicolinate reductase; Provisional	NA|180aa|down_0|CP016104.1_3644287_3644827_-	COG0634, Hpt, Hypoxanthine-guanine phosphoribosyltransferase [Nucleotide transport and metabolism]	NA|436aa|down_1|CP016104.1_3645154_3646462_-	COG3681, COG3681, L-cysteine desulfidase [Amino acid transport and metabolism]	NA|589aa|down_2|CP016104.1_3646873_3648640_-	COG3829, RocR, Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]	NA|46aa|down_3|CP016104.1_3648645_3648783_-	NA	NA|190aa|down_4|CP016104.1_3648860_3649430_-	COG2226, UbiE, Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]	NA|212aa|down_5|CP016104.1_3649613_3650249_-	PRK05813, PRK05813, single-stranded DNA-binding protein; Provisional	NA|294aa|down_6|CP016104.1_3650916_3651798_-	pfam01925, TauE, Sulfite exporter TauE/SafE	NA|336aa|down_7|CP016104.1_3651917_3652925_-	PRK13969, PRK13969, proline racemase; Provisional	NA|158aa|down_8|CP016104.1_3652944_3653418_-	TIGR04480, D-proline_reductase_PrdA_proprotein, D-proline reductase (dithiol), PrdA proprotein	NA|156aa|down_9|CP016104.1_3653444_3653912_-	TIGR04480, D-proline_reductase_PrdA_proprotein, D-proline reductase (dithiol), PrdA proprotein
