assembly_id	genome_id	genome_def	crispr_array_locus_merge	crispr_array_location_merge	crispr_locus_id	crispr_pred_method	array_in_prot	prot_within_array_20000	prot_in_genome	crispr_type_by_cas_prot	consensus_repeat	repeat_length	self-targeting_spacer_number	self-targeting_target_number	spacer_location	protospacer_location	repeat_type	spacer_locus_num	spacer_num	correct_crispr_type	genome_cas_prots	unknown_protein_around_crispr	L10	L10_domain	L9	L9_domain	L8	L8_domain	L7	L7_domain	L6	L6_domain	L5	L5_domain	L4	L4_domain	L3	L3_domain	L2	L2_domain	L1	L1_domain	R1	R1_domain	R2	R2_domain	R3	R3_domain	R4	R4_domain	R5	R5_domain	R6	R6_domain	R7	R7_domain	R8	R8_domain	R9	R9_domain	R10	R10_domain
GCF_000055945.1_ASM5594v1	NC_008011	Lawsonia intracellularis PHE/MN1-00, complete genome	1	93380-93478	1	CRISPRCasFinder	no		cas3	Orphan	CCAGATTCAGATCCAATTTATGAT	24	0	0	NA	NA	NA	1	1	Orphan	cas3	NA|107aa|up_9|NC_008011.1_82556_82877_-,NA|227aa|up_7|NC_008011.1_84535_85216_+,NA|96aa|up_1|NC_008011.1_91765_92053_+,NA|68aa|up_0|NC_008011.1_92573_92777_+,NA|142aa|down_0|NC_008011.1_93730_94156_+,NA|183aa|down_1|NC_008011.1_94284_94833_+,NA|153aa|down_2|NC_008011.1_94920_95379_+,NA|159aa|down_3|NC_008011.1_95596_96073_+,NA|57aa|down_4|NC_008011.1_96214_96385_+	NA|107aa|up_9|NC_008011.1_82556_82877_-	NA	NA|231aa|up_8|NC_008011.1_83392_84085_-	cd02165, NMNAT, Nicotinamide/nicotinate mononucleotide adenylyltransferase	NA|227aa|up_7|NC_008011.1_84535_85216_+	NA	NA|133aa|up_6|NC_008011.1_85843_86242_+	pfam05443, ROS_MUCR, ROS/MUCR transcriptional regulator protein	NA|250aa|up_5|NC_008011.1_86419_87169_-	pfam03548, LolA, Outer membrane lipoprotein carrier protein LolA	NA|896aa|up_4|NC_008011.1_87172_89860_-	COG1674, FtsK, DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]	NA|186aa|up_3|NC_008011.1_89936_90494_-	PRK00529, PRK00529, elongation factor P; Validated	NA|203aa|up_2|NC_008011.1_90800_91409_+	PRK00454, engB, GTP-binding protein YsxC; Reviewed	NA|96aa|up_1|NC_008011.1_91765_92053_+	NA	NA|68aa|up_0|NC_008011.1_92573_92777_+	NA	NA|142aa|down_0|NC_008011.1_93730_94156_+	NA	NA|183aa|down_1|NC_008011.1_94284_94833_+	NA	NA|153aa|down_2|NC_008011.1_94920_95379_+	NA	NA|159aa|down_3|NC_008011.1_95596_96073_+	NA	NA|57aa|down_4|NC_008011.1_96214_96385_+	NA	NA|141aa|down_5|NC_008011.1_97538_97961_-	cd00158, RHOD, Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein	NA|268aa|down_6|NC_008011.1_98192_98996_+	cd07402, MPP_GpdQ, Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain	NA|350aa|down_7|NC_008011.1_99013_100063_+	COG3839, MalK, ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]	NA|432aa|down_8|NC_008011.1_100195_101491_+	cd14748, PBP2_UgpB, The periplasmic-binding component of ABC transport system specific for sn-glycerol-3-phosphate; possesses type 2 periplasmic binding fold	NA|296aa|down_9|NC_008011.1_101553_102441_+	COG1175, UgpA, ABC-type sugar transport systems, permease components [Carbohydrate transport and metabolism]
GCF_000055945.1_ASM5594v1	NC_008011	Lawsonia intracellularis PHE/MN1-00, complete genome	2	698545-698685	2	CRISPRCasFinder	no		cas3	Orphan	TGCACCCTGTATTTTATTAAGAGTTTCACTAGCTACGTCTTGTTGTTG	48	0	0	NA	NA	NA	1	1	Orphan	cas3	NA|120aa|up_4|NC_008011.1_693084_693444_-,NA|159aa|up_2|NC_008011.1_694165_694642_+,NA|112aa|down_3|NC_008011.1_703880_704216_+	NA|424aa|up_9|NC_008011.1_687406_688678_-	pfam13023, HD_3, HD domain	NA|145aa|up_8|NC_008011.1_688843_689278_+	PRK09216, rplM, 50S ribosomal protein L13; Reviewed	NA|131aa|up_7|NC_008011.1_689296_689689_+	PRK00132, rpsI, 30S ribosomal protein S9; Reviewed	NA|552aa|up_6|NC_008011.1_689867_691523_+	COG0595, COG0595, mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]	NA|343aa|up_5|NC_008011.1_691764_692793_+	COG5278, COG5278, Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]	NA|120aa|up_4|NC_008011.1_693084_693444_-	NA	NA|164aa|up_3|NC_008011.1_693560_694052_+	pfam04608, PgpA, Phosphatidylglycerophosphatase A	NA|159aa|up_2|NC_008011.1_694165_694642_+	NA	NA|691aa|up_1|NC_008011.1_694774_696847_-	PRK05682, flgE, flagellar hook protein FlgE; Validated	NA|280aa|up_0|NC_008011.1_696930_697770_-	COG1843, FlgD, Flagellar hook capping protein [Cell motility and secretion]	NA|470aa|down_0|NC_008011.1_699819_701229_-	cd03789, GT9_LPS_heptosyltransferase, lipopolysaccharide heptosyltransferase and similar proteins	NA|295aa|down_1|NC_008011.1_701957_702842_+	PRK12802, PRK12802, flagellin; Provisional	NA|234aa|down_2|NC_008011.1_703045_703747_-	PRK00102, rnc, ribonuclease III; Reviewed	NA|112aa|down_3|NC_008011.1_703880_704216_+	NA	NA|174aa|down_4|NC_008011.1_704638_705160_-	PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional	NA|78aa|down_5|NC_008011.1_705169_705403_-	COG1837, COG1837, Predicted RNA-binding protein (contains KH domain) [General function prediction only]	NA|83aa|down_6|NC_008011.1_705478_705727_-	PRK00040, rpsP, 30S ribosomal protein S16; Reviewed	NA|505aa|down_7|NC_008011.1_705859_707374_-	PRK10867, PRK10867, signal recognition particle protein; Provisional	NA|471aa|down_8|NC_008011.1_707510_708923_-	COG2265, TrmA, SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]	NA|293aa|down_9|NC_008011.1_708958_709837_-	TIGR01207, Glucose-1-phosphate_thymidylyltransferase_1, glucose-1-phosphate thymidylyltransferase, short form
GCF_000055945.1_ASM5594v1	NC_008013	Lawsonia intracellularis PHE/MN1-00 plasmid 2, complete sequence	1	6721-6896	1	CRISPRCasFinder	no			Orphan	GTTCCGACATTAAGGTTAGTAATATT	26	0	0	NA	NA	NA	2	2	Orphan	cas3	NA|346aa|up_1|NC_008013.1_2784_3822_+,NA|57aa|up_0|NC_008013.1_4712_4883_+,NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|96aa|up_4|NC_008013.1_403_691_+	COG3905, COG3905, Predicted transcriptional regulator [Transcription]	NA|99aa|up_3|NC_008013.1_678_975_+	pfam05016, ParE_toxin, ParE toxin of type II toxin-antitoxin system, parDE	NA|94aa|up_2|NC_008013.1_2231_2513_-	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|346aa|up_1|NC_008013.1_2784_3822_+	NA	NA|57aa|up_0|NC_008013.1_4712_4883_+	NA	NA|377aa|down_0|NC_008013.1_8333_9464_-	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|724aa|down_1|NC_008013.1_10435_12607_+	smart00869, Autotransporter, Autotransporter beta-domain	NA|627aa|down_2|NC_008013.1_12771_14652_-	TIGR03108, eps_aminotran_1, exosortase A system-associated amidotransferase 1	NA|264aa|down_3|NC_008013.1_14667_15459_-	cd10920, CE4_WbmS, Catalytic domain of a putative polysaccharide deacetylase WbmS from Bordetella bronchiseptica and similar proteins	NA|339aa|down_4|NC_008013.1_15452_16469_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|375aa|down_5|NC_008013.1_16481_17606_-	cd00616, AHBA_syn, 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn)	NA|300aa|down_6|NC_008013.1_17626_18526_-	TIGR04317, W_rSAM_matur, tungsten cofactor oxidoreducase radical SAM maturase	NA|217aa|down_7|NC_008013.1_18587_19238_-	TIGR03570, NeuD_NnaD, sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family	NA|410aa|down_8|NC_008013.1_19367_20597_+	COG4641, COG4641, Uncharacterized protein conserved in bacteria [Function unknown]	NA|277aa|down_9|NC_008013.1_20756_21587_+	pfam13649, Methyltransf_25, Methyltransferase domain
