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_001051095.1_ASM105109v1	NZ_CP012045	Streptococcus pyogenes strain HKU488, complete genome	1	802761-802994	1,1,1	PILER-CR,CRISPRCasFinder,CRT	no	cas9,cas1,cas2,csn2	cas3,DEDDh,DinG,csm6,cas9,cas1,cas2,csn2,cas4,cas7,cas8c,cas5,csa3	Type II-A,Type II-C,Type II-B	GTTTTAGAGCTATGCTGTTTTGAATGGTCCCAAAAC,GTTTTAGAGCTATGCTGTTTTGAATGGTCCCAAAAC,GTTTTAGAGCTATGCTGTTTTGAATGGTCCCAAAAC	36,36,36	0	0	NA	NA	II-A:II-A:II-A	2,3,3	3	TypeII-A,TypeII-C,TypeII-B	cas3,DEDDh,DinG,csm6,cas9,cas1,cas2,csn2,cas4,cas7,cas8c,cas5,csa3	NA|214aa|up_8|NZ_CP012045.1_792220_792862_+,NA	NA|452aa|up_9|NZ_CP012045.1_790731_792087_+	PRK14316, glmM, phosphoglucosamine mutase; Provisional	NA|214aa|up_8|NZ_CP012045.1_792220_792862_+	NA	NA|377aa|up_7|NZ_CP012045.1_792924_794055_+	PRK08599, PRK08599, oxygen-independent coproporphyrinogen III oxidase	NA|251aa|up_6|NZ_CP012045.1_794064_794817_+	COG3884, FatA, Acyl-ACP thioesterase [Lipid metabolism]	NA|255aa|up_5|NZ_CP012045.1_794816_795581_+	cd07530, HAD_Pase_UmpH-like, UmpH/NagD family phosphatase, similar to Escherichia coli UmpH UMP phosphatase/NagD nucleotide phosphatase and Mycobacterium tuberculosis Rv1692 glycerol 3-phosphate phosphatase	NA|211aa|up_4|NZ_CP012045.1_795580_796213_+	COG4478, COG4478, Predicted membrane protein [Function unknown]	cas9|1369aa|up_3|NZ_CP012045.1_796692_800799_+	COG3513, COG3513, Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]	cas1|290aa|up_2|NZ_CP012045.1_800798_801668_+	cd09720, Cas1_II, CRISPR/Cas system-associated protein Cas1	cas2|114aa|up_1|NZ_CP012045.1_801664_802006_+	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms]	csn2|221aa|up_0|NZ_CP012045.1_801995_802658_+	cd09758, Csn2, CRISPR/Cas system-associated protein Csn2	NA|60aa|down_0|NZ_CP012045.1_803124_803304_+	cd04413, NDPk_I, Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside triphosphate (NTP) donor onto a nucleoside diphosphate (NDP) acceptor through a phosphohistidine intermediate	NA|49aa|down_1|NZ_CP012045.1_803367_803514_+	PRK00668, ndk, mulitfunctional nucleoside diphosphate kinase/apyrimidinic endonuclease/3'-; Validated	NA|611aa|down_2|NZ_CP012045.1_803637_805470_+	PRK05433, PRK05433, GTP-binding protein LepA; Provisional	NA|294aa|down_3|NZ_CP012045.1_805737_806619_+	pfam00746, Gram_pos_anchor, LPXTG cell wall anchor motif	NA|146aa|down_4|NZ_CP012045.1_806804_807242_+	PRK00222, PRK00222, peptide-methionine (R)-S-oxide reductase MsrB	NA|340aa|down_5|NZ_CP012045.1_807356_808376_+	COG2855, COG2855, Predicted membrane protein [Function unknown]	NA|142aa|down_6|NZ_CP012045.1_808582_809008_+	COG2893, ManX, Phosphotransferase system, mannose/fructose-specific component IIA [Carbohydrate transport and metabolism]	NA|164aa|down_7|NZ_CP012045.1_809026_809518_+	COG3444, COG3444, Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB [Carbohydrate transport and metabolism]	NA|270aa|down_8|NZ_CP012045.1_809534_810344_+	COG3715, ManY, Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIC [Carbohydrate transport and metabolism]	NA|276aa|down_9|NZ_CP012045.1_810340_811168_+	COG3716, ManZ, Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IID [Carbohydrate transport and metabolism]
GCF_001051095.1_ASM105109v1	NZ_CP012045	Streptococcus pyogenes strain HKU488, complete genome	2	997239-997340	2	CRISPRCasFinder	no		cas3,DEDDh,DinG,csm6,cas9,cas1,cas2,csn2,cas4,cas7,cas8c,cas5,csa3	Orphan	AATAATTGGTATAGTCTAATTATA	24	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csm6,cas9,cas1,cas2,csn2,cas4,cas7,cas8c,cas5,csa3	NA,NA|262aa|down_6|NZ_CP012045.1_1005170_1005956_+,NA|63aa|down_8|NZ_CP012045.1_1007288_1007477_-	NA|83aa|up_9|NZ_CP012045.1_984956_985205_-	COG2261, COG2261, Predicted membrane protein [Function unknown]	NA|773aa|up_8|NZ_CP012045.1_985568_987887_-	TIGR01073, ATP-dependent_DNA_helicase_PcrA, ATP-dependent DNA helicase PcrA	NA|441aa|up_7|NZ_CP012045.1_988415_989738_+	COG1115, AlsT, Na+/alanine symporter [Amino acid transport and metabolism]	NA|412aa|up_6|NZ_CP012045.1_989857_991093_+	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|258aa|up_5|NZ_CP012045.1_991461_992235_-	pfam07373, CAMP_factor, CAMP factor (Cfa)	NA|279aa|up_4|NZ_CP012045.1_992604_993441_-	cd00996, PBP2_AatB_like, Polar amino acids-binding domain of ATP-binding cassette transporter-like systems that belong to the type 2 periplasmic binding fold protein superfamily	NA|210aa|up_3|NZ_CP012045.1_993456_994086_-	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|214aa|up_2|NZ_CP012045.1_994095_994737_-	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|112aa|up_1|NZ_CP012045.1_994842_995178_-	COG2824, PhnA, Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]	NA|605aa|up_0|NZ_CP012045.1_995373_997188_-	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|186aa|down_0|NZ_CP012045.1_997363_997921_-	TIGR02227, Inactive_signal_peptidase_IA	NA|501aa|down_1|NZ_CP012045.1_998138_999641_-	PRK05826, PRK05826, pyruvate kinase; Provisional	NA|338aa|down_2|NZ_CP012045.1_999703_1000717_-	PRK03202, PRK03202, ATP-dependent 6-phosphofructokinase	NA|1037aa|down_3|NZ_CP012045.1_1000796_1003907_-	PRK07279, dnaE, DNA polymerase III DnaE; Reviewed	NA|124aa|down_4|NZ_CP012045.1_1004091_1004463_+	COG1725, COG1725, Predicted transcriptional regulators [Transcription]	NA|233aa|down_5|NZ_CP012045.1_1004462_1005161_+	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]	NA|262aa|down_6|NZ_CP012045.1_1005170_1005956_+	NA	NA|205aa|down_7|NZ_CP012045.1_1006082_1006697_-	COG0398, COG0398, Uncharacterized conserved protein [Function unknown]	NA|63aa|down_8|NZ_CP012045.1_1007288_1007477_-	NA	NA|252aa|down_9|NZ_CP012045.1_1007696_1008452_+	pfam02876, Stap_Strp_tox_C, Staphylococcal/Streptococcal toxin, beta-grasp domain
GCF_001051095.1_ASM105109v1	NZ_CP012045	Streptococcus pyogenes strain HKU488, complete genome	3	1163841-1163976	3	CRISPRCasFinder	no		cas3,DEDDh,DinG,csm6,cas9,cas1,cas2,csn2,cas4,cas7,cas8c,cas5,csa3	Orphan	CAGCTTCTTCTGATTGTAAAGCGTCTGTTTGATCCGCCAATGCTTCTAAGGC	52	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csm6,cas9,cas1,cas2,csn2,cas4,cas7,cas8c,cas5,csa3	NA|94aa|up_9|NZ_CP012045.1_1154263_1154545_-,NA|53aa|up_8|NZ_CP012045.1_1154551_1154710_-,NA	NA|94aa|up_9|NZ_CP012045.1_1154263_1154545_-	NA	NA|53aa|up_8|NZ_CP012045.1_1154551_1154710_-	NA	NA|464aa|up_7|NZ_CP012045.1_1154709_1156101_-	COG2265, TrmA, SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]	NA|484aa|up_6|NZ_CP012045.1_1156149_1157601_-	COG1316, LytR, Transcriptional regulator [Transcription]	NA|164aa|up_5|NZ_CP012045.1_1157808_1158300_-	PRK00131, aroK, shikimate kinase; Reviewed	NA|431aa|up_4|NZ_CP012045.1_1158292_1159585_-	PRK02427, PRK02427, 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional	NA|322aa|up_3|NZ_CP012045.1_1159686_1160652_-	COG1295, Rbn, Ribonuclease BN family enzyme [Replication, recombination, and repair]	NA|287aa|up_2|NZ_CP012045.1_1160653_1161514_-	PRK07281, PRK07281, methionyl aminopeptidase	NA|428aa|up_1|NZ_CP012045.1_1161529_1162813_-	COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]	NA|181aa|up_0|NZ_CP012045.1_1162821_1163364_-	COG1670, RimL, Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]	NA|420aa|down_0|NZ_CP012045.1_1164612_1165872_-	PRK12830, PRK12830, UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Reviewed	NA|399aa|down_1|NZ_CP012045.1_1166045_1167242_-	PRK05250, PRK05250, S-adenosylmethionine synthetase; Validated	NA|793aa|down_2|NZ_CP012045.1_1167778_1170157_-	COG4886, COG4886, Leucine-rich repeat (LRR) protein [Function unknown]	NA|314aa|down_3|NZ_CP012045.1_1170360_1171302_+	PRK11886, PRK11886, bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA	NA|91aa|down_4|NZ_CP012045.1_1171276_1171549_-	pfam11676, DUF3272, Protein of unknown function (DUF3272)	NA|557aa|down_5|NZ_CP012045.1_1171574_1173245_-	PRK05563, PRK05563, DNA polymerase III subunits gamma and tau; Validated	NA|166aa|down_6|NZ_CP012045.1_1173244_1173742_-	COG1956, COG1956, GAF domain-containing protein [Signal transduction mechanisms]	NA|270aa|down_7|NZ_CP012045.1_1173886_1174696_+	COG2339, prsW, Membrane proteinase, regulator of anti-sigma factor [Posttranslational modification, protein turnover, chaperones]	NA|88aa|down_8|NZ_CP012045.1_1174748_1175012_-	COG3326, COG3326, Predicted membrane protein [Function unknown]	NA|209aa|down_9|NZ_CP012045.1_1175091_1175718_-	PRK05480, PRK05480, uridine/cytidine kinase; Provisional
GCF_001051095.1_ASM105109v1	NZ_CP012045	Streptococcus pyogenes strain HKU488, complete genome	4	1324095-1324389	4,2,2	CRISPRCasFinder,CRT,PILER-CR	no	cas2,cas1,cas4,cas7,cas8c,cas5	cas3,DEDDh,DinG,csm6,cas9,cas1,cas2,csn2,cas4,cas7,cas8c,cas5,csa3	Type I-U,Type I-C, Type I-U?	ATTTCAATCCACTCACCCATGAAGGGTGAGAC,ATTTCAATCCACTCACCCATGAAGGGTGAGAC,TTTCAATCCACTCACCCATGAAGGGTGAGAC	32,32,31	0	0	NA	NA	I-C:I-C:I-C	4,4,4	4	TypeI-U,TypeI-C,TypeI-U?	cas3,DEDDh,DinG,csm6,cas9,cas1,cas2,csn2,cas4,cas7,cas8c,cas5,csa3	NA,NA	NA|412aa|up_9|NZ_CP012045.1_1314029_1315265_-	PRK01388, PRK01388, arginine deiminase; Provisional	NA|227aa|up_8|NZ_CP012045.1_1315538_1316219_-	COG0664, Crp, cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]	NA|158aa|up_7|NZ_CP012045.1_1316360_1316834_+	COG1438, ArgR, Arginine repressor [Transcription]	NA|239aa|up_6|NZ_CP012045.1_1316999_1317716_-	COG3382, COG3382, Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only]	NA|360aa|up_5|NZ_CP012045.1_1317729_1318809_-	COG2315, MmcQ, Uncharacterized protein conserved in bacteria [Function unknown]	NA|578aa|up_4|NZ_CP012045.1_1318881_1320615_-	COG2972, COG2972, Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]	NA|247aa|up_3|NZ_CP012045.1_1320611_1321352_-	COG4753, COG4753, Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]	NA|369aa|up_2|NZ_CP012045.1_1321439_1322546_-	PRK14018, PRK14018, bifunctional peptide-methionine (S)-S-oxide reductase MsrA/peptide-methionine (R)-S-oxide reductase MsrB	NA|208aa|up_1|NZ_CP012045.1_1322588_1323212_-	cd02966, TlpA_like_family, TlpA-like family; composed of  TlpA, ResA, DsbE and similar proteins	NA|237aa|up_0|NZ_CP012045.1_1323224_1323935_-	COG0785, CcdA, Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]	cas2|98aa|down_0|NZ_CP012045.1_1324537_1324831_-	COG1343, COG1343, CRISPR-associated protein Cas2 [Defense mechanisms]	cas1|342aa|down_1|NZ_CP012045.1_1324841_1325867_-	TIGR03640, cas1_DVULG, CRISPR-associated endonuclease Cas1, subtype I-C/DVULG	cas4|225aa|down_2|NZ_CP012045.1_1325863_1326538_-	COG1468, COG1468, CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense    mechanisms]	cas7|283aa|down_3|NZ_CP012045.1_1326539_1327388_-	COG3649, COG3649, CRISPR system related protein [Defense mechanisms]	cas8c|632aa|down_4|NZ_CP012045.1_1327392_1329288_-	cd09642, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c	cas5|243aa|down_5|NZ_CP012045.1_1329287_1330016_-	TIGR01876, cas_Cas5d, CRISPR-associated protein Cas5, subtype I-C/DVULG	NA|883aa|down_6|NZ_CP012045.1_1332709_1335358_-	PRK05729, valS, valyl-tRNA synthetase; Reviewed	NA|188aa|down_7|NZ_CP012045.1_1335359_1335923_-	pfam13238, AAA_18, AAA domain	NA|67aa|down_8|NZ_CP012045.1_1335919_1336120_-	COG1670, RimL, Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]	NA|132aa|down_9|NZ_CP012045.1_1336523_1336919_-	PRK07758, PRK07758, hypothetical protein; Provisional
GCF_001051095.1_ASM105109v1	NZ_CP012045	Streptococcus pyogenes strain HKU488, complete genome	5	1789207-1789340	5	CRISPRCasFinder	no		cas3,DEDDh,DinG,csm6,cas9,cas1,cas2,csn2,cas4,cas7,cas8c,cas5,csa3	Orphan	TGGTCTATCGCTAATTCAAGAGCTTTCTTTTTCTCTTCTAACTCTTTTTC	50	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csm6,cas9,cas1,cas2,csn2,cas4,cas7,cas8c,cas5,csa3	NA|35aa|up_4|NZ_CP012045.1_1778689_1778794_-,NA|84aa|down_1|NZ_CP012045.1_1792188_1792440_-,NA|135aa|down_8|NZ_CP012045.1_1799935_1800340_-	NA|569aa|up_9|NZ_CP012045.1_1773309_1775016_-	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|150aa|up_8|NZ_CP012045.1_1775008_1775458_-	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|339aa|up_7|NZ_CP012045.1_1775755_1776772_+	PRK00094, gpsA, NAD(P)H-dependent glycerol-3-phosphate dehydrogenase	NA|300aa|up_6|NZ_CP012045.1_1776804_1777704_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|224aa|up_5|NZ_CP012045.1_1777802_1778474_-	COG0705, COG0705, Membrane associated serine protease [Amino acid transport and metabolism]	NA|35aa|up_4|NZ_CP012045.1_1778689_1778794_-	NA	NA|378aa|up_3|NZ_CP012045.1_1778798_1779932_-	COG5433, COG5433, Transposase [DNA replication, recombination, and repair]	NA|356aa|up_2|NZ_CP012045.1_1780182_1781250_-	TIGR01168, M_protein_serotype, Gram-positive signal peptide, YSIRK family	NA|1165aa|up_1|NZ_CP012045.1_1781346_1784841_-	cd07475, Peptidases_S8_C5a_Peptidase, Peptidase S8 family domain in Streptococcal C5a peptidases	NA|346aa|up_0|NZ_CP012045.1_1787058_1788096_-	pfam03482, SIC, sic protein repeat	NA|530aa|down_0|NZ_CP012045.1_1789923_1791513_-	pfam08270, PRD_Mga, M protein trans-acting positive regulator (MGA) PRD domain	NA|84aa|down_1|NZ_CP012045.1_1792188_1792440_-	NA	NA|534aa|down_2|NZ_CP012045.1_1792518_1794120_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|463aa|down_3|NZ_CP012045.1_1794221_1795610_-	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]	NA|218aa|down_4|NZ_CP012045.1_1795606_1796260_-	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|406aa|down_5|NZ_CP012045.1_1796353_1797571_-	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB	NA|225aa|down_6|NZ_CP012045.1_1797583_1798258_-	COG1136, SalX, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]	NA|423aa|down_7|NZ_CP012045.1_1798244_1799513_-	COG0845, AcrA, Membrane-fusion protein [Cell envelope biogenesis, outer membrane]	NA|135aa|down_8|NZ_CP012045.1_1799935_1800340_-	NA	NA|99aa|down_9|NZ_CP012045.1_1800366_1800663_-	pfam14131, DUF4298, Domain of unknown function (DUF4298)
