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_012219925.1_ASM1221992v1	NZ_CP047616	Lactococcus raffinolactis strain Lr_19_5 chromosome, complete genome	1	461328-461476	1	CRISPRCasFinder	no		cas3,DEDDh,csa3,DinG,cas1,cas2,csn2,WYL,cas9,cas6,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10	Orphan	GAAGATCGTGAATGACCCTGCTTGGCAGGAGCGCAAGCGGAAGTCAAGTTTCAAG	55	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,csa3,DinG,cas1,cas2,csn2,WYL,cas9,cas6,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10	NA|77aa|up_3|NZ_CP047616.1_458108_458339_+,NA|81aa|up_2|NZ_CP047616.1_458342_458585_+,NA	NA|133aa|up_9|NZ_CP047616.1_451745_452144_-	COG2501, COG2501, S4-like RNA binding protein [Replication, recombination, and repair]	NA|421aa|up_8|NZ_CP047616.1_452382_453645_+	COG0612, PqqL, Predicted Zn-dependent peptidases [General function prediction only]	NA|428aa|up_7|NZ_CP047616.1_453634_454918_+	COG0612, PqqL, Predicted Zn-dependent peptidases [General function prediction only]	NA|290aa|up_6|NZ_CP047616.1_454991_455861_+	COG1426, COG1426, Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]	NA|186aa|up_5|NZ_CP047616.1_455868_456426_+	TIGR00560, pgsA, CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase	NA|429aa|up_4|NZ_CP047616.1_456825_458112_+	TIGR00442, hisS, histidyl-tRNA synthetase	NA|77aa|up_3|NZ_CP047616.1_458108_458339_+	NA	NA|81aa|up_2|NZ_CP047616.1_458342_458585_+	NA	NA|581aa|up_1|NZ_CP047616.1_458608_460351_+	PRK00476, aspS, aspartyl-tRNA synthetase; Validated	NA|306aa|up_0|NZ_CP047616.1_460317_461235_+	COG1284, COG1284, Uncharacterized conserved protein [Function unknown]	NA|289aa|down_0|NZ_CP047616.1_461515_462382_+	COG1284, COG1284, Uncharacterized conserved protein [Function unknown]	NA|35aa|down_1|NZ_CP047616.1_462527_462632_-	pfam16935, Hol_Tox, Putative Holin-like Toxin (Hol-Tox)	NA|330aa|down_2|NZ_CP047616.1_462871_463861_-	TIGR00737, Probable_tRNA-dihydrouridine_synthase, putative TIM-barrel protein, nifR3 family	NA|287aa|down_3|NZ_CP047616.1_463862_464723_-	PRK00114, hslO, Hsp33 family molecular chaperone HslO	NA|147aa|down_4|NZ_CP047616.1_464911_465352_+	pfam08837, DUF1810, Protein of unknown function (DUF1810)	NA|435aa|down_5|NZ_CP047616.1_465978_467283_+	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|486aa|down_6|NZ_CP047616.1_467287_468745_-	PRK14022, PRK14022, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase	NA|391aa|down_7|NZ_CP047616.1_469799_470972_+	PRK09354, recA, recombinase A; Provisional	NA|133aa|down_8|NZ_CP047616.1_471151_471550_+	PRK01655, spxA, transcriptional regulator Spx; Reviewed	NA|66aa|down_9|NZ_CP047616.1_472050_472248_-	pfam05532, CsbD, CsbD-like
GCF_012219925.1_ASM1221992v1	NZ_CP047616	Lactococcus raffinolactis strain Lr_19_5 chromosome, complete genome	2	1024650-1028317	1,2,1,2,3	PILER-CR,CRISPRCasFinder,CRT,PILER-CR,PILER-CR	no	cas1,cas2,csn2	cas3,DEDDh,csa3,DinG,cas1,cas2,csn2,WYL,cas9,cas6,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10	Type II-A	GTTTTAGAGCTGTGTTGAATTGAATGCCTCCAAAAC,GTTTTAGAGCTGTGTTGAATTGAATGCCTCCAAAAC,GTTTTAGAGCTGTGTTGAATTGAATGCCTCCAAAAC,GTTTTAGAGCTGTGTTGAATTGAATGCCTCCAAAAC,GTTTTAGAGCTGTGTTGAATTGAATGCCTCCAAAAC	36,36,36,36,36	2	3	1025280-1025309|1025479-1025508|1025479-1025508	NZ_CP047617.1_67737-67708|NZ_CP047616.1_2151341-2151370|NZ_CP047617.1_69514-69485	II-A,II-B:II-A,II-B:II-A,II-B:II-A,II-B:II-A,II-B	52,55,55,52,52	55	TypeII-A	cas3,DEDDh,csa3,DinG,cas1,cas2,csn2,WYL,cas9,cas6,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10	NA|98aa|up_3|NZ_CP047616.1_1022122_1022416_+,NA	NA|84aa|up_9|NZ_CP047616.1_1016595_1016847_+	COG0759, COG0759, Uncharacterized conserved protein [Function unknown]	NA|356aa|up_8|NZ_CP047616.1_1017006_1018074_+	COG0577, SalY, ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]	NA|223aa|up_7|NZ_CP047616.1_1018087_1018756_+	COG1136, SalX, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]	NA|90aa|up_6|NZ_CP047616.1_1019102_1019372_+	pfam01757, Acyl_transf_3, Acyltransferase family	NA|317aa|up_5|NZ_CP047616.1_1019331_1020282_-	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]	NA|317aa|up_4|NZ_CP047616.1_1021119_1022070_-	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]	NA|98aa|up_3|NZ_CP047616.1_1022122_1022416_+	NA	cas1|289aa|up_2|NZ_CP047616.1_1022631_1023498_+	TIGR03639, cas1_NMENI, CRISPR-associated endonuclease Cas1, subtype II/NMENI	cas2|115aa|up_1|NZ_CP047616.1_1023494_1023839_+	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms]	csn2|221aa|up_0|NZ_CP047616.1_1023828_1024491_+	cd09758, Csn2, CRISPR/Cas system-associated protein Csn2	NA|110aa|down_0|NZ_CP047616.1_1028517_1028847_-	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|311aa|down_1|NZ_CP047616.1_1029270_1030203_+	PRK10768, PRK10768, ribonucleoside hydrolase RihC; Provisional	NA|458aa|down_2|NZ_CP047616.1_1030195_1031569_+	PRK10654, dcuC, C4-dicarboxylate transporter DcuC; Provisional	NA|166aa|down_3|NZ_CP047616.1_1031592_1032090_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|303aa|down_4|NZ_CP047616.1_1032064_1032973_+	cd01174, ribokinase, Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP	NA|435aa|down_5|NZ_CP047616.1_1034696_1036001_+	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|317aa|down_6|NZ_CP047616.1_1036457_1037408_-	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]	NA|234aa|down_7|NZ_CP047616.1_1037737_1038439_+	cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein	NA|838aa|down_8|NZ_CP047616.1_1038443_1040957_+	COG0577, SalY, ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]	NA|106aa|down_9|NZ_CP047616.1_1041064_1041382_+	TIGR01068, Thioredoxin-like_protein_slr0233, thioredoxin
GCF_012219925.1_ASM1221992v1	NZ_CP047616	Lactococcus raffinolactis strain Lr_19_5 chromosome, complete genome	3	2153796-2154483	4,3,2	PILER-CR,CRISPRCasFinder,CRT	no	cas2,cas1,cas6,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10	cas3,DEDDh,csa3,DinG,cas1,cas2,csn2,WYL,cas9,cas6,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10	Type III-C,Type III-B,Type III-A,Type III-D	GTTCTCGTCCCCTTTTATCGAGGAGCGGTTGTATTT,GTTCTCGTCCCCTTTTATCGAGGAGCGGTTGTATTT,GTTCTCGTCCCCTTTTATCGAGGAGCGGTTGTATTT	36,36,36	0	0	NA	NA	NA:NA:NA	9,9,9	9	TypeIII-C,TypeIII-B,TypeIII-A,TypeIII-D	cas3,DEDDh,csa3,DinG,cas1,cas2,csn2,WYL,cas9,cas6,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10	NA|104aa|up_9|NZ_CP047616.1_2146818_2147130_-,NA|83aa|up_8|NZ_CP047616.1_2147253_2147502_-,NA|113aa|up_7|NZ_CP047616.1_2147922_2148261_-,NA|68aa|down_0|NZ_CP047616.1_2154728_2154932_-,NA|95aa|down_2|NZ_CP047616.1_2156484_2156769_-	NA|104aa|up_9|NZ_CP047616.1_2146818_2147130_-	NA	NA|83aa|up_8|NZ_CP047616.1_2147253_2147502_-	NA	NA|113aa|up_7|NZ_CP047616.1_2147922_2148261_-	NA	NA|97aa|up_6|NZ_CP047616.1_2148261_2148552_-	TIGR02384, Putative_antitoxin_RelB, addiction module antitoxin, RelB/DinJ family	NA|112aa|up_5|NZ_CP047616.1_2149595_2149931_+	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|147aa|up_4|NZ_CP047616.1_2149934_2150375_+	pfam06114, Peptidase_M78, IrrE N-terminal-like domain	NA|196aa|up_3|NZ_CP047616.1_2150682_2151270_-	cd03768, SR_ResInv, Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain	NA|102aa|up_2|NZ_CP047616.1_2151272_2151578_-	pfam08951, EntA_Immun, Enterocin A Immunity	NA|293aa|up_1|NZ_CP047616.1_2151754_2152633_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|96aa|up_0|NZ_CP047616.1_2152635_2152923_-	COG2963, COG2963, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|68aa|down_0|NZ_CP047616.1_2154728_2154932_-	NA	NA|111aa|down_1|NZ_CP047616.1_2156162_2156495_-	TIGR02385, Hypothetical_relE_protein	NA|95aa|down_2|NZ_CP047616.1_2156484_2156769_-	NA	cas2|102aa|down_3|NZ_CP047616.1_2156809_2157115_-	TIGR01573, cas2, CRISPR-associated endonuclease Cas2	cas1|303aa|down_4|NZ_CP047616.1_2157115_2158024_-	TIGR03639, cas1_NMENI, CRISPR-associated endonuclease Cas1, subtype II/NMENI	cas6|221aa|down_5|NZ_CP047616.1_2158001_2158664_-	COG5551, COG5551, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	csm6|413aa|down_6|NZ_CP047616.1_2158744_2159983_-	cd09699, Csm6_III-A, CRISPR/Cas system-associated protein Csm6	csm5gr7|354aa|down_7|NZ_CP047616.1_2159979_2161041_-	cd09662, Csm5_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm5	csm4gr5|298aa|down_8|NZ_CP047616.1_2161037_2161931_-	COG1567, COG1567, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	csm3gr7|215aa|down_9|NZ_CP047616.1_2161932_2162577_-	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3
GCF_012219925.1_ASM1221992v1	NZ_CP047616	Lactococcus raffinolactis strain Lr_19_5 chromosome, complete genome	4	2154960-2156012	5,4,3	PILER-CR,CRISPRCasFinder,CRT	no	cas2,cas1,cas6,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10	cas3,DEDDh,csa3,DinG,cas1,cas2,csn2,WYL,cas9,cas6,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10	Type III-C,Type III-B,Type III-A,Type III-D	GTTCTCGTCCCCTTTTATCGAGGAGCGGTTGTATTT,GTTCTCGTCCCCTTTTATCGAGGAGCGGTTGTATTT,GTTCTCGTCCCCTTTTATCGAGGAGCGGTTGTATTT	36,36,36	0	0	NA	NA	NA:NA:NA	14,14,14	14	TypeIII-C,TypeIII-B,TypeIII-A,TypeIII-D	cas3,DEDDh,csa3,DinG,cas1,cas2,csn2,WYL,cas9,cas6,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10	NA|83aa|up_9|NZ_CP047616.1_2147253_2147502_-,NA|113aa|up_8|NZ_CP047616.1_2147922_2148261_-,NA|68aa|up_0|NZ_CP047616.1_2154728_2154932_-,NA|95aa|down_1|NZ_CP047616.1_2156484_2156769_-	NA|83aa|up_9|NZ_CP047616.1_2147253_2147502_-	NA	NA|113aa|up_8|NZ_CP047616.1_2147922_2148261_-	NA	NA|97aa|up_7|NZ_CP047616.1_2148261_2148552_-	TIGR02384, Putative_antitoxin_RelB, addiction module antitoxin, RelB/DinJ family	NA|112aa|up_6|NZ_CP047616.1_2149595_2149931_+	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|147aa|up_5|NZ_CP047616.1_2149934_2150375_+	pfam06114, Peptidase_M78, IrrE N-terminal-like domain	NA|196aa|up_4|NZ_CP047616.1_2150682_2151270_-	cd03768, SR_ResInv, Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain	NA|102aa|up_3|NZ_CP047616.1_2151272_2151578_-	pfam08951, EntA_Immun, Enterocin A Immunity	NA|293aa|up_2|NZ_CP047616.1_2151754_2152633_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|96aa|up_1|NZ_CP047616.1_2152635_2152923_-	COG2963, COG2963, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|68aa|up_0|NZ_CP047616.1_2154728_2154932_-	NA	NA|111aa|down_0|NZ_CP047616.1_2156162_2156495_-	TIGR02385, Hypothetical_relE_protein	NA|95aa|down_1|NZ_CP047616.1_2156484_2156769_-	NA	cas2|102aa|down_2|NZ_CP047616.1_2156809_2157115_-	TIGR01573, cas2, CRISPR-associated endonuclease Cas2	cas1|303aa|down_3|NZ_CP047616.1_2157115_2158024_-	TIGR03639, cas1_NMENI, CRISPR-associated endonuclease Cas1, subtype II/NMENI	cas6|221aa|down_4|NZ_CP047616.1_2158001_2158664_-	COG5551, COG5551, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	csm6|413aa|down_5|NZ_CP047616.1_2158744_2159983_-	cd09699, Csm6_III-A, CRISPR/Cas system-associated protein Csm6	csm5gr7|354aa|down_6|NZ_CP047616.1_2159979_2161041_-	cd09662, Csm5_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm5	csm4gr5|298aa|down_7|NZ_CP047616.1_2161037_2161931_-	COG1567, COG1567, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	csm3gr7|215aa|down_8|NZ_CP047616.1_2161932_2162577_-	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3	csm2gr11|141aa|down_9|NZ_CP047616.1_2162576_2162999_-	pfam03750, Csm2_III-A, Csm2 Type III-A
GCF_012219925.1_ASM1221992v1	NZ_CP047616	Lactococcus raffinolactis strain Lr_19_5 chromosome, complete genome	5	2201656-2201765	5	CRISPRCasFinder	no		cas3,DEDDh,csa3,DinG,cas1,cas2,csn2,WYL,cas9,cas6,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10	Orphan	TTGTGAGCTGAAATCTAACGAAGTC	25	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,csa3,DinG,cas1,cas2,csn2,WYL,cas9,cas6,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10	NA|159aa|up_9|NZ_CP047616.1_2191458_2191935_-,NA	NA|159aa|up_9|NZ_CP047616.1_2191458_2191935_-	NA	NA|317aa|up_8|NZ_CP047616.1_2191927_2192878_-	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]	NA|56aa|up_7|NZ_CP047616.1_2193529_2193697_+	pfam11240, DUF3042, Protein of unknown function (DUF3042)	NA|198aa|up_6|NZ_CP047616.1_2193815_2194409_-	pfam12732, YtxH, YtxH-like protein	NA|133aa|up_5|NZ_CP047616.1_2194493_2194892_-	COG4768, COG4768, Uncharacterized protein containing a divergent version of the methyl-accepting chemotaxis-like domain [General function prediction only]	NA|266aa|up_4|NZ_CP047616.1_2195009_2195807_-	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|308aa|up_3|NZ_CP047616.1_2195808_2196732_-	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|108aa|up_2|NZ_CP047616.1_2196954_2197278_-	COG1983, PspC, Putative stress-responsive transcriptional regulator [Transcription / Signal transduction mechanisms]	NA|411aa|up_1|NZ_CP047616.1_2197270_2198503_-	COG3595, COG3595, Uncharacterized conserved protein [Function unknown]	NA|933aa|up_0|NZ_CP047616.1_2198673_2201472_-	PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed	NA|238aa|down_0|NZ_CP047616.1_2201987_2202701_-	pfam05103, DivIVA, DivIVA protein	NA|266aa|down_1|NZ_CP047616.1_2202805_2203603_-	COG2302, COG2302, Uncharacterized conserved protein, contains S4-like domain [Function unknown]	NA|82aa|down_2|NZ_CP047616.1_2203602_2203848_-	pfam02325, YGGT, YGGT family	NA|183aa|down_3|NZ_CP047616.1_2203847_2204396_-	COG1799, COG1799, Uncharacterized protein conserved in bacteria [Function unknown]	NA|221aa|down_4|NZ_CP047616.1_2204445_2205108_-	cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins	NA|422aa|down_5|NZ_CP047616.1_2205111_2206377_-	PRK09330, PRK09330, cell division protein FtsZ; Validated	NA|457aa|down_6|NZ_CP047616.1_2206517_2207888_-	COG0849, ftsA, Cell division ATPase FtsA [Cell division and chromosome partitioning]	NA|290aa|down_7|NZ_CP047616.1_2208050_2208920_-	TIGR00762, DegV, EDD domain protein, DegV family	NA|171aa|down_8|NZ_CP047616.1_2208971_2209484_-	pfam05991, NYN_YacP, YacP-like NYN domain	NA|257aa|down_9|NZ_CP047616.1_2209500_2210271_-	TIGR00186, Uncharacterized_tRNA/rRNA_methyltransferase_MG252, rRNA methylase, putative, group 3
