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_000968535.2_ASM96853v1	NC_016112	Methylomicrobium alcaliphilum 20Z, complete genome	1	1109992-1110086	1	CRISPRCasFinder	no		cas3,csa3,WYL,DEDDh,cas5,cas8c,cas7,cas4,cas1,cas2,cas6,RT,DinG,cas6e,cse2gr11,cas8e	Orphan	TTCCTCGTTCCCAAGCTCCGGCTTG	25	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,WYL,DEDDh,cas5,cas8c,cas7,cas4,cas1,cas2,cas6,RT,DinG,cas6e,cse2gr11,cas8e	NA|80aa|up_3|NC_016112.1_1100021_1100261_-,NA|2182aa|up_1|NC_016112.1_1102327_1108873_+,NA|124aa|down_3|NC_016112.1_1116027_1116399_+,NA|344aa|down_7|NC_016112.1_1120863_1121895_+	NA|1306aa|up_9|NC_016112.1_1082755_1086673_+	pfam12447, DUF3683, Protein of unknown function (DUF3683)	NA|664aa|up_8|NC_016112.1_1088297_1090289_-	pfam13688, Reprolysin_5, Metallo-peptidase family M12	NA|568aa|up_7|NC_016112.1_1091339_1093043_+	COG4618, ArpD, ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]	NA|442aa|up_6|NC_016112.1_1093058_1094384_+	TIGR01843, Hemolysin_secretion_protein_D_plasmid, type I secretion membrane fusion protein, HlyD family	NA|521aa|up_5|NC_016112.1_1094352_1095915_+	PRK09465, tolC, outer membrane channel protein; Reviewed	NA|896aa|up_4|NC_016112.1_1096362_1099050_-	COG2931, COG2931, RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]	NA|80aa|up_3|NC_016112.1_1100021_1100261_-	NA	NA|274aa|up_2|NC_016112.1_1100486_1101308_-	pfam07277, SapC, SapC	NA|2182aa|up_1|NC_016112.1_1102327_1108873_+	NA	NA|291aa|up_0|NC_016112.1_1109020_1109893_+	PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional	NA|520aa|down_0|NC_016112.1_1110453_1112013_+	COG4584, COG4584, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|249aa|down_1|NC_016112.1_1111999_1112746_+	PRK09183, PRK09183, transposase/IS protein; Provisional	NA|166aa|down_2|NC_016112.1_1115243_1115741_+	PRK12704, PRK12704, phosphodiesterase; Provisional	NA|124aa|down_3|NC_016112.1_1116027_1116399_+	NA	NA|409aa|down_4|NC_016112.1_1116578_1117805_-	pfam01610, DDE_Tnp_ISL3, Transposase	NA|146aa|down_5|NC_016112.1_1117885_1118323_-	COG3666, COG3666, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|221aa|down_6|NC_016112.1_1118408_1119071_-	PRK05467, PRK05467, Fe(II)-dependent oxygenase superfamily protein; Provisional	NA|344aa|down_7|NC_016112.1_1120863_1121895_+	NA	NA|167aa|down_8|NC_016112.1_1123469_1123970_-	pfam05130, FlgN, FlgN protein	NA|103aa|down_9|NC_016112.1_1123966_1124275_-	TIGR03824, FlgM_jcvi, flagellar biosynthesis anti-sigma factor FlgM
GCF_000968535.2_ASM96853v1	NC_016112	Methylomicrobium alcaliphilum 20Z, complete genome	2	1516465-1519654	1,2,1	PILER-CR,CRISPRCasFinder,CRT	no	WYL,cas3,cas5,cas8c,cas7,cas4,cas1,cas2	cas3,csa3,WYL,DEDDh,cas5,cas8c,cas7,cas4,cas1,cas2,cas6,RT,DinG,cas6e,cse2gr11,cas8e	 Type I-U?,Type I-C,Type I-U	GTATCTCCCGGCCAAACAGCCGGGAGCGGATTGAAAC,GTATCTCCCGGCCAAACAGCCGGGAGCGGATTGAAAC,GTATCTCCCGGCCAAACAGCCGGGAGCGGATTGAAAC	37,37,37	0	0	NA	NA	I-C:I-C:I-C	43,44,44	44	TypeI-U,TypeI-U?,TypeI-C	cas3,csa3,WYL,DEDDh,cas5,cas8c,cas7,cas4,cas1,cas2,cas6,RT,DinG,cas6e,cse2gr11,cas8e	NA,NA|68aa|down_1|NC_016112.1_1521169_1521373_-	NA|289aa|up_9|NC_016112.1_1505473_1506340_+	PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed	NA|191aa|up_8|NC_016112.1_1506784_1507357_-	pfam03352, Adenine_glyco, Methyladenine glycosylase	WYL|289aa|up_7|NC_016112.1_1507402_1508269_-	COG2378, COG2378, Predicted transcriptional regulator [Transcription]	cas3|768aa|up_6|NC_016112.1_1508367_1510671_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas5|223aa|up_5|NC_016112.1_1510822_1511491_+	cd09752, Cas5_I-C, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas8c|589aa|up_4|NC_016112.1_1511480_1513247_+	pfam09709, Cas_Csd1, CRISPR-associated protein (Cas_Csd1)	cas7|316aa|up_3|NC_016112.1_1513246_1514194_+	pfam05107, Cas_Cas7, CRISPR-associated protein Cas7	cas4|219aa|up_2|NC_016112.1_1514293_1514950_+	TIGR00372, conserved_hypothetical_protein, CRISPR-associated protein Cas4	cas1|345aa|up_1|NC_016112.1_1514946_1515981_+	TIGR03640, cas1_DVULG, CRISPR-associated endonuclease Cas1, subtype I-C/DVULG	cas2|97aa|up_0|NC_016112.1_1515993_1516284_+	cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2	NA|338aa|down_0|NC_016112.1_1519919_1520933_+	PRK10260, PRK10260, L,D-transpeptidase; Provisional	NA|68aa|down_1|NC_016112.1_1521169_1521373_-	NA	NA|195aa|down_2|NC_016112.1_1521716_1522301_-	cd08645, FMT_core_GART, Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART)	NA|480aa|down_3|NC_016112.1_1522485_1523925_-	PRK06467, PRK06467, dihydrolipoamide dehydrogenase; Reviewed	NA|438aa|down_4|NC_016112.1_1524025_1525339_-	PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed	NA|893aa|down_5|NC_016112.1_1525355_1528034_-	PRK09405, aceE, pyruvate dehydrogenase subunit E1; Reviewed	NA|433aa|down_6|NC_016112.1_1528449_1529748_-	PRK05614, gltA, citrate synthase	NA|217aa|down_7|NC_016112.1_1530582_1531233_-	PRK05718, PRK05718, keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional	NA|607aa|down_8|NC_016112.1_1531288_1533109_-	PRK09054, PRK09054, phosphogluconate dehydratase; Validated	NA|165aa|down_9|NC_016112.1_1533656_1534151_+	COG0041, PurE, Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]
GCF_000968535.2_ASM96853v1	NC_016112	Methylomicrobium alcaliphilum 20Z, complete genome	3	2435093-2437273	2,3,2,3	PILER-CR,CRISPRCasFinder,CRT,PILER-CR	no	cas2,cas1,cas4,cas7,cas8c,cas5,cas3,RT	cas3,csa3,WYL,DEDDh,cas5,cas8c,cas7,cas4,cas1,cas2,cas6,RT,DinG,cas6e,cse2gr11,cas8e	 Type I-U?,Type I-C,Type I-U	GTTTCAATCCACGCGCCCGCACGGGGCGCGAC,GTTTCAATCCACGCGCCCGCACGGGGCGCGAC,GTTTCAATCCACGCGCCCGCACGGGGCGCGAC,GTTTCAATCCACGCGCCCGCACGGGGCGCGAC	32,32,32,32	0	0	NA	NA	I-C:I-C:I-C:I-C	31,33,33,31	33	TypeI-U,TypeI-U?,TypeI-C	cas3,csa3,WYL,DEDDh,cas5,cas8c,cas7,cas4,cas1,cas2,cas6,RT,DinG,cas6e,cse2gr11,cas8e	NA|203aa|up_4|NC_016112.1_2432062_2432671_-,NA|90aa|down_8|NC_016112.1_2448015_2448285_-	NA|151aa|up_9|NC_016112.1_2424038_2424491_-	cd01285, nucleoside_deaminase, Nucleoside deaminases include adenosine, guanine and cytosine deaminases	NA|205aa|up_8|NC_016112.1_2425227_2425842_-	pfam14246, TetR_C_7, AefR-like transcriptional repressor, C-terminal region	NA|405aa|up_7|NC_016112.1_2425946_2427161_+	TIGR01730, COG0845:_Membrane-fusion_protein, RND family efflux transporter, MFP subunit	NA|1062aa|up_6|NC_016112.1_2427167_2430353_+	TIGR00915, Probable_aminoglycoside_efflux_pump, The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family	NA|490aa|up_5|NC_016112.1_2430349_2431819_+	TIGR01845, Outer_membrane_protein_OprM, efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family	NA|203aa|up_4|NC_016112.1_2432062_2432671_-	NA	NA|57aa|up_3|NC_016112.1_2432923_2433094_-	COG0610, COG0610, Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]	NA|336aa|up_2|NC_016112.1_2433086_2434094_-	pfam13310, Virulence_RhuM, Virulence protein RhuM family	NA|123aa|up_1|NC_016112.1_2434104_2434473_-	COG1487, VapC, Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]	NA|65aa|up_0|NC_016112.1_2434475_2434670_-	pfam09957, VapB_antitoxin, Bacterial antitoxin of type II TA system, VapB	cas2|97aa|down_0|NC_016112.1_2437451_2437742_-	cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2	cas1|345aa|down_1|NC_016112.1_2437756_2438791_-	TIGR03640, cas1_DVULG, CRISPR-associated endonuclease Cas1, subtype I-C/DVULG	cas4|209aa|down_2|NC_016112.1_2438793_2439420_-	TIGR00372, conserved_hypothetical_protein, CRISPR-associated protein Cas4	cas7|288aa|down_3|NC_016112.1_2439480_2440344_-	cd09689, Cas7_I-C, CRISPR/Cas system-associated RAMP superfamily protein Cas7	cas8c|677aa|down_4|NC_016112.1_2440340_2442371_-	cd09757, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c	cas5|235aa|down_5|NC_016112.1_2442367_2443072_-	cd09651, Cas5_I-C, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas3|819aa|down_6|NC_016112.1_2443081_2445538_-	cd17930, DEXHc_cas3, DEXH/Q-box helicase domain of Cas3	RT|417aa|down_7|NC_016112.1_2445981_2447232_-	TIGR04416, hypothetical_protein, group II intron reverse transcriptase/maturase	NA|90aa|down_8|NC_016112.1_2448015_2448285_-	NA	NA|442aa|down_9|NC_016112.1_2449108_2450434_-	COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]
GCF_000968535.2_ASM96853v1	NC_016112	Methylomicrobium alcaliphilum 20Z, complete genome	4	3711360-3711431	4	CRISPRCasFinder	no	DinG	cas3,csa3,WYL,DEDDh,cas5,cas8c,cas7,cas4,cas1,cas2,cas6,RT,DinG,cas6e,cse2gr11,cas8e	Type IV-A	CTGCATTCACGCCATCCATGGCG	23	1	6	3711383-3711408|3711383-3711408|3711383-3711408|3711383-3711408|3711383-3711408|3711383-3711408	NC_016112.1_429910-429885|NC_016112.1_2837175-2837200|NC_016112.1_2837224-2837249|NC_016112.1_3393894-3393919|NC_016112.1_75064-75039|NC_016112.1_3895993-3896018	NA	1	1	Orphan	cas3,csa3,WYL,DEDDh,cas5,cas8c,cas7,cas4,cas1,cas2,cas6,RT,DinG,cas6e,cse2gr11,cas8e	NA,NA|253aa|down_9|NC_016112.1_3724388_3725147_-	NA|280aa|up_9|NC_016112.1_3698911_3699751_-	PRK10700, PRK10700, 23S rRNA pseudouridine(2605) synthase RluB	NA|220aa|up_8|NC_016112.1_3699770_3700430_-	pfam04079, SMC_ScpB, Segregation and condensation complex subunit ScpB	NA|272aa|up_7|NC_016112.1_3700896_3701712_-	COG1354, scpA, Rec8/ScpA/Scc1-like protein (kleisin family) [Replication,    recombination, and repair]	NA|219aa|up_6|NC_016112.1_3701751_3702408_-	cd06158, S2P-M50_like_1, Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms	NA|207aa|up_5|NC_016112.1_3702423_3703044_-	PRK11630, PRK11630, threonylcarbamoyl-AMP synthase	NA|228aa|up_4|NC_016112.1_3703083_3703767_-	TIGR03725, T6A_YeaZ, tRNA threonylcarbamoyl adenosine modification protein YeaZ	DinG|640aa|up_3|NC_016112.1_3703763_3705683_-	COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]	NA|345aa|up_2|NC_016112.1_3705692_3706727_-	PRK00892, lpxD, UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional	NA|695aa|up_1|NC_016112.1_3707082_3709167_+	PRK00007, PRK00007, elongation factor G; Reviewed	NA|444aa|up_0|NC_016112.1_3709900_3711232_+	pfam08014, DUF1704, Domain of unknown function (DUF1704)	NA|206aa|down_0|NC_016112.1_3711896_3712514_+	pfam05494, MlaC, MlaC protein	NA|175aa|down_1|NC_016112.1_3712609_3713134_+	COG2716, GcvR, Glycine cleavage system regulatory protein [Amino acid transport and metabolism]	NA|158aa|down_2|NC_016112.1_3713143_3713617_+	COG1225, Bcp, Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]	NA|471aa|down_3|NC_016112.1_3713716_3715129_+	COG1875, COG1875, NYN ribonuclease and ATPase of PhoH family domains [General    function prediction only]	NA|367aa|down_4|NC_016112.1_3715720_3716821_-	COG0628, yhhT, Predicted permease, member of the PurR regulon [General function prediction only]	NA|704aa|down_5|NC_016112.1_3717049_3719161_-	cd11326, AmyAc_Glg_debranch, Alpha amylase catalytic domain found in glycogen debranching enzymes	NA|485aa|down_6|NC_016112.1_3719755_3721210_+	COG4783, COG4783, Putative Zn-dependent protease, contains TPR repeats [General function prediction only]	NA|385aa|down_7|NC_016112.1_3721986_3723141_-	pfam07995, GSDH, Glucose / Sorbosone dehydrogenase	NA|173aa|down_8|NC_016112.1_3723180_3723699_-	COG4067, COG4067, Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]	NA|253aa|down_9|NC_016112.1_3724388_3725147_-	NA
GCF_000968535.2_ASM96853v1	NC_016112	Methylomicrobium alcaliphilum 20Z, complete genome	5	4283753-4285859	5,3,4,5	CRISPRCasFinder,CRT,PILER-CR,PILER-CR	no	cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,cas3,WYL	cas3,csa3,WYL,DEDDh,cas5,cas8c,cas7,cas4,cas1,cas2,cas6,RT,DinG,cas6e,cse2gr11,cas8e	Type I-E	CGGTTCATCCCCACGGGCGTGGGGAACGC,CGGTTCATCCCCACGGGCGTGGGGAACGC,CGGTTCATCCCCACGGGCGTGGGGAACGC,CGGTTCATCCCCACGGGCGTGGGGAACGC	29,29,29,29	0	0	NA	NA	I-E:I-E:I-E:I-E	34,34,29,29	34	TypeI-E	cas3,csa3,WYL,DEDDh,cas5,cas8c,cas7,cas4,cas1,cas2,cas6,RT,DinG,cas6e,cse2gr11,cas8e	NA|49aa|up_6|NC_016112.1_4274176_4274323_-,NA|189aa|up_4|NC_016112.1_4277657_4278224_+,NA	NA|573aa|up_9|NC_016112.1_4270020_4271739_+	NF012181, MSCRAMM_SdrD, MSCRAMM family adhesin SdrD	NA|249aa|up_8|NC_016112.1_4271759_4272506_-	PRK09183, PRK09183, transposase/IS protein; Provisional	NA|520aa|up_7|NC_016112.1_4272492_4274052_-	COG4584, COG4584, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|49aa|up_6|NC_016112.1_4274176_4274323_-	NA	NA|984aa|up_5|NC_016112.1_4274471_4277423_+	NF012181, MSCRAMM_SdrD, MSCRAMM family adhesin SdrD	NA|189aa|up_4|NC_016112.1_4277657_4278224_+	NA	NA|614aa|up_3|NC_016112.1_4278410_4280252_+	cd04791, LanC_SerThrkinase, Lanthionine synthetase C-like domain associated with serine/threonine kinases	NA|173aa|up_2|NC_016112.1_4280416_4280935_+	COG4627, COG4627, Uncharacterized protein conserved in bacteria [Function unknown]	NA|489aa|up_1|NC_016112.1_4281299_4282766_+	COG3914, Spy, Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]	NA|261aa|up_0|NC_016112.1_4282859_4283642_-	pfam12811, BaxI_1, Bax inhibitor 1 like	cas2|101aa|down_0|NC_016112.1_4285974_4286277_-	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	cas1|304aa|down_1|NC_016112.1_4286409_4287321_-	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	NA|101aa|down_2|NC_016112.1_4287324_4287627_-	pfam05016, ParE_toxin, ParE toxin of type II toxin-antitoxin system, parDE	NA|90aa|down_3|NC_016112.1_4287627_4287897_-	pfam02604, PhdYeFM_antitox, Antitoxin Phd_YefM, type II toxin-antitoxin system	NA|92aa|down_4|NC_016112.1_4288016_4288292_-	pfam02604, PhdYeFM_antitox, Antitoxin Phd_YefM, type II toxin-antitoxin system	NA|144aa|down_5|NC_016112.1_4288541_4288973_-	cd18696, PIN_MtVapC26-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC26 and related proteins	NA|86aa|down_6|NC_016112.1_4288950_4289208_-	pfam12651, RHH_3, Ribbon-helix-helix domain	cas6e|207aa|down_7|NC_016112.1_4289689_4290310_-	pfam08798, CRISPR_assoc, CRISPR associated protein	cas5|231aa|down_8|NC_016112.1_4290296_4290989_-	TIGR01868, hypothetical_protein, CRISPR-associated protein Cas5/CasD, subtype I-E/ECOLI	cas7|417aa|down_9|NC_016112.1_4290992_4292243_-	pfam09344, Cas_CT1975, CT1975-like protein
