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_009720125.1_ASM972012v1	NZ_CP046246	Tetragenococcus halophilus strain YJ1 chromosome, complete genome	1	51209-51317	1	CRISPRCasFinder	no		cas3,DinG,RT,DEDDh,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,csa3,cas14j,cas2,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	TAGTTTTCTTAAAATTTAGAGCTAGTC	27	0	0	NA	NA	NA	1	1	Orphan	cas3,DinG,RT,DEDDh,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,csa3,cas14j,cas2,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA,NA	NA|656aa|up_9|NZ_CP046246.1_36250_38218_+	TIGR01995, beta-glucosides_PTS_EIIBCA, PTS system, beta-glucoside-specific IIABC component	NA|76aa|up_8|NZ_CP046246.1_38878_39106_+	PRK00373, PRK00373, V-type ATP synthase subunit D; Reviewed	NA|109aa|up_7|NZ_CP046246.1_40737_41064_-	pfam07883, Cupin_2, Cupin domain	NA|261aa|up_6|NZ_CP046246.1_41368_42151_-	COG1737, RpiR, Transcriptional regulators [Transcription]	NA|459aa|up_5|NZ_CP046246.1_42304_43681_+	COG2723, BglB, Beta-glucosidase/6-phospho-beta-glucosidase/beta-galactosidase [Carbohydrate transport and metabolism]	NA|431aa|up_4|NZ_CP046246.1_43692_44985_+	COG1455, CelB, Phosphotransferase system cellobiose-specific component IIC [Carbohydrate transport and metabolism]	NA|88aa|up_3|NZ_CP046246.1_45133_45397_+	PRK08588, PRK08588, succinyl-diaminopimelate desuccinylase; Reviewed	NA|364aa|up_2|NZ_CP046246.1_45634_46726_+	PRK08588, PRK08588, succinyl-diaminopimelate desuccinylase; Reviewed	NA|444aa|up_1|NZ_CP046246.1_48614_49946_+	cd05298, GH4_GlvA_pagL_like, Glycoside Hydrolases Family 4; GlvA- and pagL-like glycosidases	NA|254aa|up_0|NZ_CP046246.1_50087_50849_+	COG1737, RpiR, Transcriptional regulators [Transcription]	NA|459aa|down_0|NZ_CP046246.1_51328_52705_-	PRK00855, PRK00855, argininosuccinate lyase; Provisional	NA|404aa|down_1|NZ_CP046246.1_52701_53913_-	PRK00509, PRK00509, argininosuccinate synthase; Provisional	NA|230aa|down_2|NZ_CP046246.1_54220_54910_+	PRK12656, PRK12656, fructose-6-phosphate aldolase; Reviewed	NA|210aa|down_3|NZ_CP046246.1_55203_55833_-	pfam01923, Cob_adeno_trans, Cobalamin adenosyltransferase	NA|863aa|down_4|NZ_CP046246.1_55849_58438_-	PRK08115, PRK08115, vitamin B12-dependent ribonucleotide reductase	NA|487aa|down_5|NZ_CP046246.1_58620_60081_+	PRK06529, PRK06529, amidase; Provisional	NA|273aa|down_6|NZ_CP046246.1_60144_60963_+	COG2819, COG2819, Predicted hydrolase of the alpha/beta superfamily [General function prediction only]	NA|251aa|down_7|NZ_CP046246.1_61026_61779_-	COG4947, COG4947, Uncharacterized protein conserved in bacteria [Function unknown]	NA|399aa|down_8|NZ_CP046246.1_61796_62993_-	PRK01372, ddl, D-alanine--D-alanine ligase; Reviewed	NA|108aa|down_9|NZ_CP046246.1_63227_63551_+	COG1695, COG1695, Predicted transcriptional regulators [Transcription]
GCF_009720125.1_ASM972012v1	NZ_CP046246	Tetragenococcus halophilus strain YJ1 chromosome, complete genome	2	513280-517286	2,1,1,2	CRISPRCasFinder,CRT,PILER-CR,PILER-CR	no	DEDDh,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,cas3	cas3,DinG,RT,DEDDh,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,csa3,cas14j,cas2,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Type I-E	GGATCACCCCCGCTTATGCGGGAAAGAC,GGATCACCCCCGCTTATGCGGGAAAGAC,GGATCACCCCCGCTTATGCGGGAAAGAC,GGATCACCCCCGCTTATGCGGGAAAGAC	28,28,28,28	0	0	NA	NA	NA:NA:NA:NA	65,65,65,65	65	TypeI-E	cas3,DinG,RT,DEDDh,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,csa3,cas14j,cas2,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|86aa|up_9|NZ_CP046246.1_500430_500688_-,NA|287aa|up_6|NZ_CP046246.1_502710_503571_+,NA	NA|86aa|up_9|NZ_CP046246.1_500430_500688_-	NA	NA|147aa|up_8|NZ_CP046246.1_500775_501216_-	pfam02566, OsmC, OsmC-like protein	NA|255aa|up_7|NZ_CP046246.1_501456_502221_-	cd07025, Peptidase_S66, LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein	NA|287aa|up_6|NZ_CP046246.1_502710_503571_+	NA	NA|248aa|up_5|NZ_CP046246.1_503656_504400_-	pfam06912, DUF1275, Protein of unknown function (DUF1275)	NA|369aa|up_4|NZ_CP046246.1_504968_506075_+	pfam01609, DDE_Tnp_1, Transposase DDE domain	NA|473aa|up_3|NZ_CP046246.1_506725_508144_-	pfam06782, UPF0236, Uncharacterized protein family (UPF0236)	NA|441aa|up_2|NZ_CP046246.1_508684_510007_+	pfam13701, DDE_Tnp_1_4, Transposase DDE domain group 1	NA|454aa|up_1|NZ_CP046246.1_511326_512688_+	pfam13546, DDE_5, DDE superfamily endonuclease	NA|94aa|up_0|NZ_CP046246.1_512957_513239_-	TIGR02384, Putative_antitoxin_RelB, addiction module antitoxin, RelB/DinJ family	DEDDh|300aa|down_0|NZ_CP046246.1_517315_518215_-	cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family	cas1|315aa|down_1|NZ_CP046246.1_518214_519159_-	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas6e|212aa|down_2|NZ_CP046246.1_519162_519798_-	pfam08798, CRISPR_assoc, CRISPR associated protein	cas5|234aa|down_3|NZ_CP046246.1_519799_520501_-	cd09756, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas7|362aa|down_4|NZ_CP046246.1_520502_521588_-	pfam09344, Cas_CT1975, CT1975-like protein	cse2gr11|197aa|down_5|NZ_CP046246.1_521590_522181_-	pfam09485, CRISPR_Cse2, CRISPR-associated protein Cse2 (CRISPR_cse2)	cas8e|567aa|down_6|NZ_CP046246.1_522194_523895_-	pfam09481, CRISPR_Cse1, CRISPR-associated protein Cse1 (CRISPR_cse1)	cas3|922aa|down_7|NZ_CP046246.1_523881_526647_-	PRK09694, PRK09694, CRISPR-associated helicase/endonuclease Cas3	NA|392aa|down_8|NZ_CP046246.1_527764_528940_-	COG4552, Eis, Predicted acetyltransferase involved in intracellular survival and related acetyltransferases [General function prediction only]	NA|418aa|down_9|NZ_CP046246.1_529034_530288_-	COG1455, CelB, Phosphotransferase system cellobiose-specific component IIC [Carbohydrate transport and metabolism]
GCF_009720125.1_ASM972012v1	NZ_CP046246	Tetragenococcus halophilus strain YJ1 chromosome, complete genome	3	745214-745302	3	CRISPRCasFinder	no	csa3	cas3,DinG,RT,DEDDh,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,csa3,cas14j,cas2,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Type I-A	AGCCATTCATGTTGGGCGAGGGCACGAT	28	0	0	NA	NA	NA	1	1	Orphan	cas3,DinG,RT,DEDDh,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,csa3,cas14j,cas2,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA,NA|41aa|down_0|NZ_CP046246.1_745612_745735_-,NA|204aa|down_3|NZ_CP046246.1_747326_747938_-	NA|156aa|up_9|NZ_CP046246.1_733900_734368_-	cd15904, TSPO_MBR, Translocator protein (TSPO)/peripheral-type benzodiazepine receptor (MBR) family	NA|278aa|up_8|NZ_CP046246.1_734393_735227_-	pfam13649, Methyltransf_25, Methyltransferase domain	NA|209aa|up_7|NZ_CP046246.1_735256_735883_-	pfam13508, Acetyltransf_7, Acetyltransferase (GNAT) domain	NA|748aa|up_6|NZ_CP046246.1_735896_738140_-	COG0178, UvrA, Excinuclease ATPase subunit [DNA replication, recombination, and repair]	NA|168aa|up_5|NZ_CP046246.1_738337_738841_-	PLN02316, PLN02316, synthase/transferase	NA|541aa|up_4|NZ_CP046246.1_738921_740544_-	cd11333, AmyAc_SI_OligoGlu_DGase, Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins	NA|161aa|up_3|NZ_CP046246.1_740715_741198_-	pfam06983, 3-dmu-9_3-mt, 3-demethylubiquinone-9 3-methyltransferase	NA|194aa|up_2|NZ_CP046246.1_741550_742132_-	cd04647, LbH_MAT_like, Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins	NA|295aa|up_1|NZ_CP046246.1_742270_743155_+	COG0583, LysR, Transcriptional regulator [Transcription]	NA|174aa|up_0|NZ_CP046246.1_743262_743784_-	pfam03780, Asp23, Asp23 family, cell envelope-related function	NA|41aa|down_0|NZ_CP046246.1_745612_745735_-	NA	NA|185aa|down_1|NZ_CP046246.1_745748_746303_-	NF033218, anchor_AmaP, alkaline shock response membrane anchor protein AmaP	NA|165aa|down_2|NZ_CP046246.1_746399_746894_-	pfam03780, Asp23, Asp23 family, cell envelope-related function	NA|204aa|down_3|NZ_CP046246.1_747326_747938_-	NA	NA|280aa|down_4|NZ_CP046246.1_748058_748898_-	pfam01116, F_bP_aldolase, Fructose-bisphosphate aldolase class-II	NA|173aa|down_5|NZ_CP046246.1_748944_749463_-	pfam01894, UPF0047, Uncharacterized protein family UPF0047	NA|233aa|down_6|NZ_CP046246.1_749465_750164_-	PRK04302, PRK04302, triosephosphate isomerase; Provisional	NA|309aa|down_7|NZ_CP046246.1_750338_751265_+	COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]	NA|147aa|down_8|NZ_CP046246.1_751323_751764_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|144aa|down_9|NZ_CP046246.1_751916_752348_+	smart00850, LytTR, LytTr DNA-binding domain
GCF_009720125.1_ASM972012v1	NZ_CP046246	Tetragenococcus halophilus strain YJ1 chromosome, complete genome	4	1032915-1034309	4,2,3	CRISPRCasFinder,CRT,PILER-CR	no	cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	cas3,DinG,RT,DEDDh,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,csa3,cas14j,cas2,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Type III-D,Type III-C,Type III-A,Type III-B	GTTCTCGTCCCCTAATGATGGGGTTAGGTATCTATT,GTTCTCGTCCCCTAATGATGGGGTTAGGTATCTATT,GTTCTCGTCCCCTAATGATGGGGTTAGGTATCTATT	36,36,36	0	0	NA	NA	NA:NA:NA	19,19,16	19	TypeIII-D,TypeIII-C,TypeIII-A,TypeIII-B	cas3,DinG,RT,DEDDh,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,csa3,cas14j,cas2,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|162aa|up_6|NZ_CP046246.1_1025874_1026360_+,NA	NA|453aa|up_9|NZ_CP046246.1_1018881_1020240_-	pfam13546, DDE_5, DDE superfamily endonuclease	NA|726aa|up_8|NZ_CP046246.1_1020477_1022655_-	pfam13166, AAA_13, AAA domain	NA|477aa|up_7|NZ_CP046246.1_1022897_1024328_-	pfam13586, DDE_Tnp_1_2, Transposase DDE domain	NA|162aa|up_6|NZ_CP046246.1_1025874_1026360_+	NA	NA|369aa|up_5|NZ_CP046246.1_1026484_1027591_+	pfam01609, DDE_Tnp_1, Transposase DDE domain	NA|153aa|up_4|NZ_CP046246.1_1027805_1028264_-	cd00211, PTS_IIA_fru, PTS_IIA, PTS system, fructose/mannitol specific IIA subunit	NA|441aa|up_3|NZ_CP046246.1_1028467_1029790_+	pfam13701, DDE_Tnp_1_4, Transposase DDE domain group 1	NA|109aa|up_2|NZ_CP046246.1_1030415_1030742_+	smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins	cas2|102aa|up_1|NZ_CP046246.1_1031658_1031964_-	TIGR01573, cas2, CRISPR-associated endonuclease Cas2	cas1|303aa|up_0|NZ_CP046246.1_1031964_1032873_-	TIGR03639, cas1_NMENI, CRISPR-associated endonuclease Cas1, subtype II/NMENI	csm6|416aa|down_0|NZ_CP046246.1_1034455_1035703_-	cd09699, Csm6_III-A, CRISPR/Cas system-associated protein Csm6	csm5gr7|338aa|down_1|NZ_CP046246.1_1035704_1036718_-	cd09662, Csm5_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm5	csm4gr5|299aa|down_2|NZ_CP046246.1_1036735_1037632_-	pfam17953, Csm4_C, CRISPR Csm4 C-terminal domain	csm3gr7|225aa|down_3|NZ_CP046246.1_1037628_1038303_-	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3	csm2gr11|143aa|down_4|NZ_CP046246.1_1038314_1038743_-	pfam03750, Csm2_III-A, Csm2 Type III-A	cas10|763aa|down_5|NZ_CP046246.1_1038751_1041040_-	cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10	cas6|249aa|down_6|NZ_CP046246.1_1041032_1041779_-	TIGR01877, CRISPR-associated_endoribonuclease_Cas6_1, CRISPR-associated endoribonuclease Cas6	NA|441aa|down_7|NZ_CP046246.1_1043238_1044561_-	pfam13701, DDE_Tnp_1_4, Transposase DDE domain group 1	NA|315aa|down_8|NZ_CP046246.1_1045129_1046074_-	COG2421, COG2421, Predicted acetamidase/formamidase [Energy production and conversion]	NA|454aa|down_9|NZ_CP046246.1_1046353_1047715_+	pfam13546, DDE_5, DDE superfamily endonuclease
