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_001611135.1_ASM161113v1	NZ_CP012288	Pediococcus damnosus strain TMW 2.1535 chromosome, complete genome	1	623926-624065	1	CRISPRCasFinder	no		RT,DinG,WYL,cas9,cas1,cas2,csn2,cas3,DEDDh,csa3	Orphan	GATTTTGCGTATGCAACATAGTCATTTAAAAATCGAGGAGG	41	0	0	NA	NA	NA	1	1	Orphan	RT,DinG,WYL,cas9,cas1,cas2,csn2,cas3,DEDDh,csa3	NA|361aa|up_8|NZ_CP012288.1_612464_613547_-,NA|108aa|up_5|NZ_CP012288.1_616147_616471_-,NA|63aa|down_0|NZ_CP012288.1_624072_624261_+,NA|389aa|down_2|NZ_CP012288.1_624993_626160_-,NA|61aa|down_7|NZ_CP012288.1_629963_630146_-,NA|84aa|down_9|NZ_CP012288.1_632101_632353_+	NA|186aa|up_9|NZ_CP012288.1_611453_612011_-	pfam16729, DUF5067, Domain of unknown function (DUF5067)	NA|361aa|up_8|NZ_CP012288.1_612464_613547_-	NA	NA|416aa|up_7|NZ_CP012288.1_613818_615066_+	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|273aa|up_6|NZ_CP012288.1_615312_616131_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|108aa|up_5|NZ_CP012288.1_616147_616471_-	NA	NA|402aa|up_4|NZ_CP012288.1_617007_618213_-	pfam01548, DEDD_Tnp_IS110, Transposase	NA|632aa|up_3|NZ_CP012288.1_618759_620655_-	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|579aa|up_2|NZ_CP012288.1_620641_622378_-	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|151aa|up_1|NZ_CP012288.1_622377_622830_-	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|227aa|up_0|NZ_CP012288.1_623012_623693_-	TIGR02254, hydrolase_haloacid_dehalogenase-like_family, noncanonical pyrimidine nucleotidase, YjjG family	NA|63aa|down_0|NZ_CP012288.1_624072_624261_+	NA	NA|167aa|down_1|NZ_CP012288.1_624480_624981_-	cd02908, Macro_OAADPr_deacetylase, macrodomain, O-acetyl-ADP-ribose (OAADPr) family	NA|389aa|down_2|NZ_CP012288.1_624993_626160_-	NA	NA|398aa|down_3|NZ_CP012288.1_626171_627365_-	cd06173, MFS_MefA_like, Macrolide efflux protein A and similar proteins of the Major Facilitator Superfamily of transporters	NA|127aa|down_4|NZ_CP012288.1_627510_627891_-	pfam01521, Fe-S_biosyn, Iron-sulphur cluster biosynthesis	NA|176aa|down_5|NZ_CP012288.1_628418_628946_+	pfam13302, Acetyltransf_3, Acetyltransferase (GNAT) domain	NA|289aa|down_6|NZ_CP012288.1_628955_629822_-	cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in prokaryotes	NA|61aa|down_7|NZ_CP012288.1_629963_630146_-	NA	NA|456aa|down_8|NZ_CP012288.1_630432_631800_-	pfam06782, UPF0236, Uncharacterized protein family (UPF0236)	NA|84aa|down_9|NZ_CP012288.1_632101_632353_+	NA
GCF_001611135.1_ASM161113v1	NZ_CP012288	Pediococcus damnosus strain TMW 2.1535 chromosome, complete genome	2	1173473-1173698	1	PILER-CR	no		RT,DinG,WYL,cas9,cas1,cas2,csn2,cas3,DEDDh,csa3	Orphan	AGGCAAAGACGGGCGCATGCGGGATCGCAATCCCGCG	37	0	0	NA	NA	NA	2	2	Orphan	RT,DinG,WYL,cas9,cas1,cas2,csn2,cas3,DEDDh,csa3	NA|199aa|up_9|NZ_CP012288.1_1161620_1162217_+,NA|214aa|up_8|NZ_CP012288.1_1162393_1163035_+,NA|53aa|down_0|NZ_CP012288.1_1173858_1174017_+,NA|69aa|down_1|NZ_CP012288.1_1174199_1174406_+,NA|72aa|down_8|NZ_CP012288.1_1180478_1180694_+,NA|112aa|down_9|NZ_CP012288.1_1180803_1181139_+	NA|199aa|up_9|NZ_CP012288.1_1161620_1162217_+	NA	NA|214aa|up_8|NZ_CP012288.1_1162393_1163035_+	NA	NA|402aa|up_7|NZ_CP012288.1_1163546_1164752_+	pfam01548, DEDD_Tnp_IS110, Transposase	NA|551aa|up_6|NZ_CP012288.1_1165267_1166920_-	TIGR02403, Trehalose-6-phosphate_hydrolase, alpha,alpha-phosphotrehalase	NA|239aa|up_5|NZ_CP012288.1_1166932_1167649_-	TIGR02404, Trehalose_operon_transcriptional_repressor, trehalose operon repressor, B	NA|165aa|up_4|NZ_CP012288.1_1167876_1168371_+	pfam00358, PTS_EIIA_1, phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1	NA|506aa|up_3|NZ_CP012288.1_1168389_1169907_+	TIGR01995, beta-glucosides_PTS_EIIBCA, PTS system, beta-glucoside-specific IIABC component	NA|186aa|up_2|NZ_CP012288.1_1170331_1170889_+	PRK13661, PRK13661, ECF-type riboflavin transporter substrate-binding protein	NA|570aa|up_1|NZ_CP012288.1_1170893_1172603_+	cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding cassette component of cobalt transport system	NA|278aa|up_0|NZ_CP012288.1_1172595_1173429_+	COG0619, CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]	NA|53aa|down_0|NZ_CP012288.1_1173858_1174017_+	NA	NA|69aa|down_1|NZ_CP012288.1_1174199_1174406_+	NA	NA|78aa|down_2|NZ_CP012288.1_1174466_1174700_+	pfam11148, DUF2922, Protein of unknown function (DUF2922)	NA|297aa|down_3|NZ_CP012288.1_1174863_1175754_+	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]	NA|256aa|down_4|NZ_CP012288.1_1175755_1176523_+	pfam12730, ABC2_membrane_4, ABC-2 family transporter protein	NA|380aa|down_5|NZ_CP012288.1_1176552_1177692_-	cd06173, MFS_MefA_like, Macrolide efflux protein A and similar proteins of the Major Facilitator Superfamily of transporters	NA|246aa|down_6|NZ_CP012288.1_1177768_1178506_-	PRK06526, PRK06526, transposase; Provisional	NA|408aa|down_7|NZ_CP012288.1_1178515_1179739_-	COG4584, COG4584, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|72aa|down_8|NZ_CP012288.1_1180478_1180694_+	NA	NA|112aa|down_9|NZ_CP012288.1_1180803_1181139_+	NA
GCF_001611135.1_ASM161113v1	NZ_CP012288	Pediococcus damnosus strain TMW 2.1535 chromosome, complete genome	3	1234031-1235322	2,2,1	PILER-CR,CRISPRCasFinder,CRT	no	cas9,cas1,cas2,csn2	RT,DinG,WYL,cas9,cas1,cas2,csn2,cas3,DEDDh,csa3	Type II-C,Type II-B,Type II-A	GTTTTAGAAGAGTGTCGAATCAATATAGTTAAGAGC,GTTTTAGAAGAGTGTCGAATCAATATAGTTAAGAGC,GTTTTAGAAGAGTGTCGAATCAATATAGTTAAGAGC	36,36,36	1	1	1234200-1234230	NZ_CP012288.1_976925-976955	NA:NA:NA	18,19,19	19	TypeII-C,TypeII-B,TypeII-A	RT,DinG,WYL,cas9,cas1,cas2,csn2,cas3,DEDDh,csa3	NA|82aa|up_6|NZ_CP012288.1_1225066_1225312_-,NA	NA|168aa|up_9|NZ_CP012288.1_1222551_1223055_-	PRK00226, greA, transcription elongation factor GreA; Reviewed	NA|334aa|up_8|NZ_CP012288.1_1223407_1224409_-	COG0604, Qor, NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]	NA|161aa|up_7|NZ_CP012288.1_1224526_1225009_+	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|82aa|up_6|NZ_CP012288.1_1225066_1225312_-	NA	NA|171aa|up_5|NZ_CP012288.1_1225527_1226040_-	cd00865, PEBP_bact_arch, PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea	cas9|1379aa|up_4|NZ_CP012288.1_1226234_1230371_+	pfam16592, Cas9_REC, REC lobe of CRISPR-associated endonuclease Cas9	NA|456aa|up_3|NZ_CP012288.1_1230646_1232014_-	pfam06782, UPF0236, Uncharacterized protein family (UPF0236)	cas1|301aa|up_2|NZ_CP012288.1_1232145_1233048_+	cd09720, Cas1_II, CRISPR/Cas system-associated protein Cas1	cas2|86aa|up_1|NZ_CP012288.1_1233025_1233283_+	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms]	csn2|129aa|up_0|NZ_CP012288.1_1233546_1233933_+	cd12218, Csn2, CRISPR/Cas system-associated protein Csn2	NA|154aa|down_0|NZ_CP012288.1_1235451_1235913_+	COG2153, ElaA, Predicted acyltransferase [General function prediction only]	NA|158aa|down_1|NZ_CP012288.1_1236005_1236479_+	pfam02464, CinA, Competence-damaged protein	NA|272aa|down_2|NZ_CP012288.1_1236619_1237435_+	pfam06912, DUF1275, Protein of unknown function (DUF1275)	NA|304aa|down_3|NZ_CP012288.1_1237922_1238834_-	COG0583, LysR, Transcriptional regulator [Transcription]	NA|492aa|down_4|NZ_CP012288.1_1238981_1240457_+	pfam01977, UbiD, 3-octaprenyl-4-hydroxybenzoate carboxy-lyase	NA|187aa|down_5|NZ_CP012288.1_1240479_1241040_+	COG0163, UbiX family flavin prenyltransferase [Coenzyme transport and metabolism]	NA|448aa|down_6|NZ_CP012288.1_1241362_1242706_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|154aa|down_7|NZ_CP012288.1_1242927_1243389_+	cd00293, USP_Like, Usp: Universal stress protein family	NA|457aa|down_8|NZ_CP012288.1_1243432_1244803_+	PRK00701, PRK00701, divalent metal cation transporter MntH	NA|470aa|down_9|NZ_CP012288.1_1245379_1246789_+	TIGR02720, Pyruvate_oxidase, pyruvate oxidase
GCF_001611135.1_ASM161113v1	NZ_CP012288	Pediococcus damnosus strain TMW 2.1535 chromosome, complete genome	4	1406885-1407264	2	CRT	no	RT	RT,DinG,WYL,cas9,cas1,cas2,csn2,cas3,DEDDh,csa3	Unclear	CCAGGTGGCACAANAANNACACCAGGTGG	29	0	0	NA	NA	NA	5	5	Orphan	RT,DinG,WYL,cas9,cas1,cas2,csn2,cas3,DEDDh,csa3	NA|122aa|up_4|NZ_CP012288.1_1401095_1401461_+,NA|595aa|up_0|NZ_CP012288.1_1404977_1406762_+,NA|167aa|down_4|NZ_CP012288.1_1415363_1415864_-	NA|65aa|up_9|NZ_CP012288.1_1394926_1395121_+	COG5547, COG5547, Small integral membrane protein [Function unknown]	NA|182aa|up_8|NZ_CP012288.1_1395197_1395743_+	pfam03780, Asp23, Asp23 family, cell envelope-related function	NA|512aa|up_7|NZ_CP012288.1_1395919_1397455_+	pfam05043, Mga, Mga helix-turn-helix domain	RT|462aa|up_6|NZ_CP012288.1_1397922_1399308_+	TIGR04416, hypothetical_protein, group II intron reverse transcriptase/maturase	NA|502aa|up_5|NZ_CP012288.1_1399574_1401080_+	PRK08581, PRK08581, amidase domain-containing protein	NA|122aa|up_4|NZ_CP012288.1_1401095_1401461_+	NA	NA|243aa|up_3|NZ_CP012288.1_1401848_1402577_+	pfam13731, WxL, WxL domain surface cell wall-binding	NA|358aa|up_2|NZ_CP012288.1_1402603_1403677_+	pfam11797, DUF3324, Protein of unknown function C-terminal (DUF3324)	NA|206aa|up_1|NZ_CP012288.1_1403934_1404552_+	COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|595aa|up_0|NZ_CP012288.1_1404977_1406762_+	NA	NA|519aa|down_0|NZ_CP012288.1_1407859_1409416_+	pfam05109, Herpes_BLLF1, Herpes virus major outer envelope glycoprotein (BLLF1)	NA|337aa|down_1|NZ_CP012288.1_1411866_1412877_+	pfam00535, Glycos_transf_2, Glycosyl transferase family 2	NA|328aa|down_2|NZ_CP012288.1_1412879_1413863_+	cd00761, Glyco_tranf_GTA_type, Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold	NA|398aa|down_3|NZ_CP012288.1_1414127_1415321_-	pfam08757, CotH, CotH kinase protein	NA|167aa|down_4|NZ_CP012288.1_1415363_1415864_-	NA	NA|297aa|down_5|NZ_CP012288.1_1416095_1416986_+	pfam03631, Virul_fac_BrkB, Virulence factor BrkB	NA|121aa|down_6|NZ_CP012288.1_1417020_1417383_+	pfam13038, DUF3899, Domain of unknown function (DUF3899)	NA|269aa|down_7|NZ_CP012288.1_1417435_1418242_-	PRK10513, PRK10513, sugar phosphate phosphatase; Provisional	NA|459aa|down_8|NZ_CP012288.1_1418238_1419615_-	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|147aa|down_9|NZ_CP012288.1_1419842_1420283_+	pfam09148, DUF1934, Domain of unknown function (DUF1934)
GCF_001611135.1_ASM161113v1	NZ_CP012291	Pediococcus damnosus strain TMW 2.1535 plasmid pL21535-3, complete sequence	1	111562-111699	1	CRISPRCasFinder	no			Orphan	ATACAAAGATACAAGGATACAAGGATACA	29	0	0	NA	NA	NA	2	2	Orphan	RT,DinG,WYL,cas9,cas1,cas2,csn2,cas3,DEDDh,csa3	NA|150aa|up_4|NZ_CP012291.1_103831_104281_-,NA|67aa|down_2|NZ_CP012291.1_114284_114485_+,NA|125aa|down_3|NZ_CP012291.1_114497_114872_+,NA|98aa|down_5|NZ_CP012291.1_116997_117291_-	NA|449aa|up_9|NZ_CP012291.1_96319_97666_+	cd17313, MFS_SLC45_SUC, Solute carrier family 45 and similar sugar transporters of the Major Facilitator Superfamily of transporters	NA|589aa|up_8|NZ_CP012291.1_97665_99432_+	cd11338, AmyAc_CMD, Alpha amylase catalytic domain found in cyclomaltodextrinases and related proteins	NA|84aa|up_7|NZ_CP012291.1_99958_100210_+	COG2963, COG2963, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|281aa|up_6|NZ_CP012291.1_100263_101106_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|302aa|up_5|NZ_CP012291.1_101472_102378_+	pfam07859, Abhydrolase_3, alpha/beta hydrolase fold	NA|150aa|up_4|NZ_CP012291.1_103831_104281_-	NA	NA|310aa|up_3|NZ_CP012291.1_104307_105237_+	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]	NA|705aa|up_2|NZ_CP012291.1_105453_107568_+	COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]	NA|117aa|up_1|NZ_CP012291.1_110387_110738_-	pfam17363, DUF5388, Family of unknown function (DUF5388)	NA|267aa|up_0|NZ_CP012291.1_110739_111540_-	pfam13614, AAA_31, AAA domain	NA|416aa|down_0|NZ_CP012291.1_111869_113117_+	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|93aa|down_1|NZ_CP012291.1_113825_114104_+	cd17748, BRCT_DNA_ligase_like, BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins	NA|67aa|down_2|NZ_CP012291.1_114284_114485_+	NA	NA|125aa|down_3|NZ_CP012291.1_114497_114872_+	NA	NA|149aa|down_4|NZ_CP012291.1_116418_116865_+	pfam09851, SHOCT, Short C-terminal domain	NA|98aa|down_5|NZ_CP012291.1_116997_117291_-	NA	NA|247aa|down_6|NZ_CP012291.1_117558_118299_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|72aa|down_7|NZ_CP012291.1_118352_118568_-	pfam13518, HTH_28, Helix-turn-helix domain	NA|344aa|down_8|NZ_CP012291.1_118709_119741_+	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]	NA|318aa|down_9|NZ_CP012291.1_120145_121099_+	cd06294, PBP1_MalR-like, ligand-binding domain of maltose transcription regulator MalR which is a member of the LacI-GalR family repressors
GCF_001611135.1_ASM161113v1	NZ_CP012292	Pediococcus damnosus strain TMW 2.1535 plasmid pL21535-4, complete sequence	1	9329-9483	1	CRISPRCasFinder	no		csa3	Orphan	AATCCCTTGATACAAGCAGACTTCCGAAAAACGGA	35	0	0	NA	NA	NA	1	1	Orphan	RT,DinG,WYL,cas9,cas1,cas2,csn2,cas3,DEDDh,csa3	NA|96aa|up_5|NZ_CP012292.1_4193_4481_+,NA|55aa|up_2|NZ_CP012292.1_6619_6784_-,NA|68aa|up_0|NZ_CP012292.1_7790_7994_+,NA|66aa|down_0|NZ_CP012292.1_10162_10360_+,NA|70aa|down_2|NZ_CP012292.1_11519_11729_-,NA|120aa|down_3|NZ_CP012292.1_11995_12355_-	NA|133aa|up_9|NZ_CP012292.1_2093_2492_+	COG0239, CrcB, Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]	NA|77aa|up_8|NZ_CP012292.1_2485_2716_+	PRK14214, PRK14214, fluoride efflux transporter CrcB	NA|281aa|up_7|NZ_CP012292.1_2876_3719_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|88aa|up_6|NZ_CP012292.1_3759_4023_-	pfam01527, HTH_Tnp_1, Transposase	NA|96aa|up_5|NZ_CP012292.1_4193_4481_+	NA	NA|159aa|up_4|NZ_CP012292.1_4577_5054_+	pfam00582, Usp, Universal stress protein family	NA|308aa|up_3|NZ_CP012292.1_5109_6033_-	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]	NA|55aa|up_2|NZ_CP012292.1_6619_6784_-	NA	NA|262aa|up_1|NZ_CP012292.1_6950_7736_+	COG1192, Soj, ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]	NA|68aa|up_0|NZ_CP012292.1_7790_7994_+	NA	NA|66aa|down_0|NZ_CP012292.1_10162_10360_+	NA	NA|245aa|down_1|NZ_CP012292.1_10410_11145_+	pfam02661, Fic, Fic/DOC family	NA|70aa|down_2|NZ_CP012292.1_11519_11729_-	NA	NA|120aa|down_3|NZ_CP012292.1_11995_12355_-	NA	NA|196aa|down_4|NZ_CP012292.1_12367_12955_-	cd01192, INT_C_like_3, Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain	NA|93aa|down_5|NZ_CP012292.1_13031_13310_+	pfam02604, PhdYeFM_antitox, Antitoxin Phd_YefM, type II toxin-antitoxin system	NA|119aa|down_6|NZ_CP012292.1_13309_13666_+	pfam15738, YafQ_toxin, Bacterial toxin of type II toxin-antitoxin system, YafQ	NA|401aa|down_7|NZ_CP012292.1_13775_14978_-	cd17262, RMtype1_S_Aco12261I-TRD2-CR2, Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Aminobacterium colombiense DSM 12261 S subunit (S	NA|531aa|down_8|NZ_CP012292.1_14970_16563_-	pfam02384, N6_Mtase, N-6 DNA Methylase	NA|991aa|down_9|NZ_CP012292.1_16590_19563_-	COG0610, COG0610, Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
