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_900088425.1_A12	NZ_LT599053	Lactococcus lactis subsp. lactis strain A12 plasmid pA12-4, complete sequence	1	11933-12087	1	PILER-CR	no			Orphan	AATACAACATTTTTACGTCATA	22	0	0	NA	NA	NA	2	2	Orphan	cas3,DEDDh,csa3,DinG	NA|64aa|up_9|NZ_LT599053.1_2987_3179_+,NA|227aa|up_8|NZ_LT599053.1_3598_4279_+,NA|56aa|up_4|NZ_LT599053.1_7850_8018_+,NA|78aa|up_1|NZ_LT599053.1_9729_9963_-,NA|64aa|down_4|NZ_LT599053.1_17690_17882_+,NA|59aa|down_5|NZ_LT599053.1_17933_18110_+	NA|64aa|up_9|NZ_LT599053.1_2987_3179_+	NA	NA|227aa|up_8|NZ_LT599053.1_3598_4279_+	NA	NA|198aa|up_7|NZ_LT599053.1_4284_4878_+	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]	NA|342aa|up_6|NZ_LT599053.1_5223_6249_+	pfam18734, HEPN_AbiU2, AbiU2	NA|489aa|up_5|NZ_LT599053.1_6394_7861_+	cd01700, PolY_Pol_V_umuC, umuC subunit of DNA Polymerase V	NA|56aa|up_4|NZ_LT599053.1_7850_8018_+	NA	NA|243aa|up_3|NZ_LT599053.1_8229_8958_-	cd16406, ParB_N_like, ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning systems	NA|253aa|up_2|NZ_LT599053.1_8961_9720_-	pfam13614, AAA_31, AAA domain	NA|78aa|up_1|NZ_LT599053.1_9729_9963_-	NA	NA|451aa|up_0|NZ_LT599053.1_10474_11827_-	pfam01051, Rep_3, Initiator Replication protein	NA|621aa|down_0|NZ_LT599053.1_13168_15031_+	cd02079, P-type_ATPase_HM, P-type heavy metal-transporting ATPase	NA|76aa|down_1|NZ_LT599053.1_15732_15960_+	COG2608, CopZ, Copper chaperone [Inorganic ion transport and metabolism]	NA|182aa|down_2|NZ_LT599053.1_16008_16554_+	cd01043, DPS, DPS protein, ferritin-like diiron-binding domain	NA|230aa|down_3|NZ_LT599053.1_16639_17329_+	COG0664, Crp, cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]	NA|64aa|down_4|NZ_LT599053.1_17690_17882_+	NA	NA|59aa|down_5|NZ_LT599053.1_17933_18110_+	NA	NA|38aa|down_6|NZ_LT599053.1_20070_20184_-	pfam04369, Lactococcin, Lactococcin-like family	NA|235aa|down_7|NZ_LT599053.1_20932_21637_-	pfam02517, Abi, CAAX protease self-immunity	NA|50aa|down_8|NZ_LT599053.1_21747_21897_-	pfam04369, Lactococcin, Lactococcin-like family	NA|227aa|down_9|NZ_LT599053.1_22073_22754_+	COG3316, COG3316, Transposase and inactivated derivatives [DNA replication, recombination, and repair]
GCF_900088425.1_A12	NZ_LT599049	Lactococcus lactis subsp. lactis strain A12 chromosome 1	1	1211892-1211988	1	CRISPRCasFinder	no		cas3,DEDDh,csa3,DinG	Orphan	CTTCCTCTGGTCGCATTGAACTGAT	25	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,csa3,DinG	NA|200aa|up_1|NZ_LT599049.1_1210116_1210716_+,NA|188aa|down_8|NZ_LT599049.1_1221820_1222384_+	NA|117aa|up_9|NZ_LT599049.1_1202384_1202735_+	COG1539, FolB, Dihydroneopterin aldolase [Coenzyme metabolism]	NA|350aa|up_8|NZ_LT599049.1_1202814_1203864_+	COG0302, FolE, GTP cyclohydrolase I [Coenzyme metabolism]	NA|358aa|up_7|NZ_LT599049.1_1203860_1204934_+	TIGR01496, Dihydropteroate_synthase, dihydropteroate synthase	NA|166aa|up_6|NZ_LT599049.1_1204936_1205434_+	cd03674, Nudix_Hydrolase_1, Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X	NA|428aa|up_5|NZ_LT599049.1_1205452_1206736_+	COG0285, FolC, Folylpolyglutamate synthase [Coenzyme metabolism]	NA|214aa|up_4|NZ_LT599049.1_1206862_1207504_+	COG1428, COG1428, Deoxynucleoside kinases [Nucleotide transport and metabolism]	NA|429aa|up_3|NZ_LT599049.1_1207680_1208967_+	PRK06349, PRK06349, homoserine dehydrogenase; Provisional	NA|297aa|up_2|NZ_LT599049.1_1208971_1209862_+	PRK01212, PRK01212, homoserine kinase; Provisional	NA|200aa|up_1|NZ_LT599049.1_1210116_1210716_+	NA	NA|300aa|up_0|NZ_LT599049.1_1210758_1211658_+	PRK13905, murB, UDP-N-acetylmuramate dehydrogenase	NA|429aa|down_0|NZ_LT599049.1_1212381_1213668_+	COG3842, PotA, ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]	NA|263aa|down_1|NZ_LT599049.1_1213664_1214453_+	COG1176, PotB, ABC-type spermidine/putrescine transport system, permease component I [Amino acid transport and metabolism]	NA|267aa|down_2|NZ_LT599049.1_1214454_1215255_+	COG1177, PotC, ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]	NA|356aa|down_3|NZ_LT599049.1_1215302_1216370_+	cd13663, PBP2_PotD_PotF_like_2, The periplasmic substrate-binding component of an uncharacterized active transport system closely related to spermidine and putrescine transporters; contains the type 2 periplasmic binding fold	NA|287aa|down_4|NZ_LT599049.1_1216744_1217605_+	TIGR01716, HTH-type_transcriptional_regulator_rgg, transcriptional activator, Rgg/GadR/MutR family, C-terminal domain	NA|753aa|down_5|NZ_LT599049.1_1217703_1219962_+	TIGR04479, bcpD_PhpK_rSAM, radical SAM P-methyltransferase, PhpK family	NA|409aa|down_6|NZ_LT599049.1_1220219_1221446_+	cd06173, MFS_MefA_like, Macrolide efflux protein A and similar proteins of the Major Facilitator Superfamily of transporters	NA|130aa|down_7|NZ_LT599049.1_1221468_1221858_+	pfam14478, DUF4430, Domain of unknown function (DUF4430)	NA|188aa|down_8|NZ_LT599049.1_1221820_1222384_+	NA	NA|116aa|down_9|NZ_LT599049.1_1223022_1223370_+	pfam18860, AbiJ_NTD3, AbiJ N-terminal domain 3
GCF_900088425.1_A12	NZ_LT599049	Lactococcus lactis subsp. lactis strain A12 chromosome 1	2	1481471-1481569	2	CRISPRCasFinder	no		cas3,DEDDh,csa3,DinG	Orphan	CTATCCATAAAATGCTCGCTTTGGTCGC	28	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,csa3,DinG	NA,NA|185aa|down_5|NZ_LT599049.1_1487554_1488109_-	NA|393aa|up_9|NZ_LT599049.1_1473390_1474569_-	pfam05816, TelA, Toxic anion resistance protein (TelA)	NA|209aa|up_8|NZ_LT599049.1_1474713_1475340_-	COG4915, XpaC, 5-bromo-4-chloroindolyl phosphate hydrolysis protein [General function prediction only]	NA|342aa|up_7|NZ_LT599049.1_1475531_1476557_+	PRK00094, gpsA, NAD(P)H-dependent glycerol-3-phosphate dehydrogenase	NA|314aa|up_6|NZ_LT599049.1_1476599_1477541_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|136aa|up_5|NZ_LT599049.1_1477611_1478019_+	COG5341, COG5341, Uncharacterized protein conserved in bacteria [Function unknown]	NA|177aa|up_4|NZ_LT599049.1_1478015_1478546_+	COG4769, COG4769, Predicted membrane protein [Function unknown]	NA|320aa|up_3|NZ_LT599049.1_1478536_1479496_+	COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]	NA|239aa|up_2|NZ_LT599049.1_1479492_1480209_+	COG0357, GidB, Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]	NA|155aa|up_1|NZ_LT599049.1_1480224_1480689_-	COG3071, HemY, Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]	NA|238aa|up_0|NZ_LT599049.1_1480690_1481404_-	PRK00230, PRK00230, orotidine-5'-phosphate decarboxylase	NA|312aa|down_0|NZ_LT599049.1_1481624_1482560_-	PRK07259, PRK07259, dihydroorotate dehydrogenase	NA|263aa|down_1|NZ_LT599049.1_1482632_1483421_-	cd06218, DHOD_e_trans, FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase	NA|455aa|down_2|NZ_LT599049.1_1483819_1485184_-	cd17503, MFS_LmrB_MDR_like, Bacillus subtilis lincomycin resistance protein (LmrB) and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily	NA|239aa|down_3|NZ_LT599049.1_1485346_1486063_-	COG2188, PhnF, Transcriptional regulators [Transcription]	NA|476aa|down_4|NZ_LT599049.1_1486134_1487562_-	COG2723, BglB, Beta-glucosidase/6-phospho-beta-glucosidase/beta-galactosidase [Carbohydrate transport and metabolism]	NA|185aa|down_5|NZ_LT599049.1_1487554_1488109_-	NA	NA|279aa|down_6|NZ_LT599049.1_1488105_1488942_-	COG0395, UgpE, ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]	NA|304aa|down_7|NZ_LT599049.1_1488941_1489853_-	COG1175, UgpA, ABC-type sugar transport systems, permease components [Carbohydrate transport and metabolism]	NA|440aa|down_8|NZ_LT599049.1_1489926_1491246_-	COG1653, UgpB, ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]	NA|309aa|down_9|NZ_LT599049.1_1491359_1492286_-	cd19606, GH113-like, Glycoside hydrolase family 113 beta-mannosidase and similar proteins
GCF_900088425.1_A12	NZ_LT599049	Lactococcus lactis subsp. lactis strain A12 chromosome 1	3	1483491-1483592	3	CRISPRCasFinder	no		cas3,DEDDh,csa3,DinG	Orphan	CTCATGTTAATCGCATTACTGACAGAAAGTTCAG	34	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,csa3,DinG	NA,NA|185aa|down_3|NZ_LT599049.1_1487554_1488109_-	NA|342aa|up_9|NZ_LT599049.1_1475531_1476557_+	PRK00094, gpsA, NAD(P)H-dependent glycerol-3-phosphate dehydrogenase	NA|314aa|up_8|NZ_LT599049.1_1476599_1477541_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|136aa|up_7|NZ_LT599049.1_1477611_1478019_+	COG5341, COG5341, Uncharacterized protein conserved in bacteria [Function unknown]	NA|177aa|up_6|NZ_LT599049.1_1478015_1478546_+	COG4769, COG4769, Predicted membrane protein [Function unknown]	NA|320aa|up_5|NZ_LT599049.1_1478536_1479496_+	COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]	NA|239aa|up_4|NZ_LT599049.1_1479492_1480209_+	COG0357, GidB, Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]	NA|155aa|up_3|NZ_LT599049.1_1480224_1480689_-	COG3071, HemY, Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]	NA|238aa|up_2|NZ_LT599049.1_1480690_1481404_-	PRK00230, PRK00230, orotidine-5'-phosphate decarboxylase	NA|312aa|up_1|NZ_LT599049.1_1481624_1482560_-	PRK07259, PRK07259, dihydroorotate dehydrogenase	NA|263aa|up_0|NZ_LT599049.1_1482632_1483421_-	cd06218, DHOD_e_trans, FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase	NA|455aa|down_0|NZ_LT599049.1_1483819_1485184_-	cd17503, MFS_LmrB_MDR_like, Bacillus subtilis lincomycin resistance protein (LmrB) and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily	NA|239aa|down_1|NZ_LT599049.1_1485346_1486063_-	COG2188, PhnF, Transcriptional regulators [Transcription]	NA|476aa|down_2|NZ_LT599049.1_1486134_1487562_-	COG2723, BglB, Beta-glucosidase/6-phospho-beta-glucosidase/beta-galactosidase [Carbohydrate transport and metabolism]	NA|185aa|down_3|NZ_LT599049.1_1487554_1488109_-	NA	NA|279aa|down_4|NZ_LT599049.1_1488105_1488942_-	COG0395, UgpE, ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]	NA|304aa|down_5|NZ_LT599049.1_1488941_1489853_-	COG1175, UgpA, ABC-type sugar transport systems, permease components [Carbohydrate transport and metabolism]	NA|440aa|down_6|NZ_LT599049.1_1489926_1491246_-	COG1653, UgpB, ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]	NA|309aa|down_7|NZ_LT599049.1_1491359_1492286_-	cd19606, GH113-like, Glycoside hydrolase family 113 beta-mannosidase and similar proteins	NA|313aa|down_8|NZ_LT599049.1_1492385_1493324_+	pfam05448, AXE1, Acetyl xylan esterase (AXE1)	NA|404aa|down_9|NZ_LT599049.1_1493490_1494702_+	COG4260, COG4260, Membrane protease subunit, stomatin/prohibitin family [Amino acid    transport and metabolism]
GCF_900088425.1_A12	NZ_LT599049	Lactococcus lactis subsp. lactis strain A12 chromosome 1	4	1997467-1997561	4	CRISPRCasFinder	no		cas3,DEDDh,csa3,DinG	Orphan	TTTATTACTGACAGACTTGTCAGC	24	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,csa3,DinG	NA|145aa|up_9|NZ_LT599049.1_1990788_1991223_+,NA|51aa|up_8|NZ_LT599049.1_1991212_1991365_-,NA|87aa|up_7|NZ_LT599049.1_1991522_1991783_-,NA	NA|145aa|up_9|NZ_LT599049.1_1990788_1991223_+	NA	NA|51aa|up_8|NZ_LT599049.1_1991212_1991365_-	NA	NA|87aa|up_7|NZ_LT599049.1_1991522_1991783_-	NA	NA|246aa|up_6|NZ_LT599049.1_1991796_1992534_-	pfam10552, ORF6C, ORF6C domain	NA|73aa|up_5|NZ_LT599049.1_1992564_1992783_-	pfam05339, DUF739, Protein of unknown function (DUF739)	NA|181aa|up_4|NZ_LT599049.1_1992951_1993494_+	PRK13355, PRK13355, bifunctional HTH-domain containing protein/aminotransferase; Provisional	NA|146aa|up_3|NZ_LT599049.1_1993490_1993928_+	cd07325, M48_Ste24p_like, M48 Ste24 endopeptidase-like, integral membrane metallopeptidase	NA|194aa|up_2|NZ_LT599049.1_1993990_1994572_+	pfam14387, DUF4418, Domain of unknown function (DUF4418)	NA|380aa|up_1|NZ_LT599049.1_1994691_1995831_+	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|471aa|up_0|NZ_LT599049.1_1996033_1997446_-	TIGR01980, UPF0051_protein_slr0074, FeS assembly protein SufB	NA|148aa|down_0|NZ_LT599049.1_1997693_1998137_-	TIGR01994, Iron-sulfur_cluster_assembly_scaffold_protein_IscU, SUF system FeS assembly protein, NifU family	NA|161aa|down_1|NZ_LT599049.1_1998252_1998735_-	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|406aa|down_2|NZ_LT599049.1_1998736_1999954_-	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|419aa|down_3|NZ_LT599049.1_1999953_2001210_-	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|257aa|down_4|NZ_LT599049.1_2001347_2002118_-	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|444aa|down_5|NZ_LT599049.1_2002292_2003624_-	cd06853, GT_WecA_like, This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins	NA|234aa|down_6|NZ_LT599049.1_2003626_2004328_-	COG4862, MecA, Negative regulator of genetic competence, sporulation and motility [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms / Cell motility and secretion]	NA|245aa|down_7|NZ_LT599049.1_2004457_2005192_-	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|229aa|down_8|NZ_LT599049.1_2005191_2005878_-	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|303aa|down_9|NZ_LT599049.1_2006024_2006933_-	COG1597, LCB5, Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]
GCF_900088425.1_A12	NZ_LT599049	Lactococcus lactis subsp. lactis strain A12 chromosome 1	5	2047940-2048129	5	CRISPRCasFinder	no	DinG	cas3,DEDDh,csa3,DinG	Type IV-A	GAGGAAGCATTTTATCGGTGAATAAAGGAACTGGCAGTGAAGCTGA	46	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,csa3,DinG	NA|69aa|up_9|NZ_LT599049.1_2040091_2040298_-,NA|566aa|up_8|NZ_LT599049.1_2040858_2042556_-,NA|90aa|up_7|NZ_LT599049.1_2042565_2042835_-,NA|85aa|up_6|NZ_LT599049.1_2042980_2043235_-,NA|65aa|up_3|NZ_LT599049.1_2044258_2044453_-,NA|213aa|down_1|NZ_LT599049.1_2051194_2051833_-,NA|152aa|down_8|NZ_LT599049.1_2056535_2056991_-,NA|180aa|down_9|NZ_LT599049.1_2057180_2057720_+	NA|69aa|up_9|NZ_LT599049.1_2040091_2040298_-	NA	NA|566aa|up_8|NZ_LT599049.1_2040858_2042556_-	NA	NA|90aa|up_7|NZ_LT599049.1_2042565_2042835_-	NA	NA|85aa|up_6|NZ_LT599049.1_2042980_2043235_-	NA	NA|57aa|up_5|NZ_LT599049.1_2043236_2043407_-	pfam07868, DUF1655, Protein of unknown function (DUF1655)	NA|231aa|up_4|NZ_LT599049.1_2043471_2044164_-	COG3646, COG3646, Uncharacterized phage-encoded protein [Function unknown]	NA|65aa|up_3|NZ_LT599049.1_2044258_2044453_-	NA	NA|229aa|up_2|NZ_LT599049.1_2044610_2045297_+	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|148aa|up_1|NZ_LT599049.1_2046717_2047161_+	COG2153, ElaA, Predicted acyltransferase [General function prediction only]	NA|191aa|up_0|NZ_LT599049.1_2047246_2047819_-	cd10033, UDG_like, uncharacterized family of the uracil-DNA glycosylase superfamily	NA|941aa|down_0|NZ_LT599049.1_2048293_2051116_-	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|213aa|down_1|NZ_LT599049.1_2051194_2051833_-	NA	NA|175aa|down_2|NZ_LT599049.1_2051901_2052426_+	pfam00300, His_Phos_1, Histidine phosphatase superfamily (branch 1)	NA|105aa|down_3|NZ_LT599049.1_2052422_2052737_+	COG2827, COG2827, Predicted endonuclease containing a URI domain [DNA replication, recombination, and repair]	NA|450aa|down_4|NZ_LT599049.1_2052750_2054100_-	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|306aa|down_5|NZ_LT599049.1_2054582_2055500_-	COG0673, MviM, Predicted dehydrogenases and related proteins [General function prediction only]	NA|212aa|down_6|NZ_LT599049.1_2055531_2056167_-	COG1564, THI80, Thiamine pyrophosphokinase [Coenzyme metabolism]	NA|116aa|down_7|NZ_LT599049.1_2056163_2056511_-	cd11541, NTP-PPase_u4, Nucleoside Triphosphate Pyrophosphohydrolase (EC 3	NA|152aa|down_8|NZ_LT599049.1_2056535_2056991_-	NA	NA|180aa|down_9|NZ_LT599049.1_2057180_2057720_+	NA
