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_011290565.1_ASM1129056v1	NZ_CP049799	Streptococcus pyogenes strain 1040 chromosome, complete genome	1	380084-380215	1	CRISPRCasFinder	no		cas3,DEDDh,csa3,DinG,csm6,cas9,cas1,cas2,csn2,RT,cas4,cas7,cas8c,cas5	Orphan	CCAGGTCCTCCCCAATCATCACGCTTTTCATACCCTGTACCTAAT	45	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,csa3,DinG,csm6,cas9,cas1,cas2,csn2,RT,cas4,cas7,cas8c,cas5	NA,NA|84aa|down_3|NZ_CP049799.1_386219_386471_-	NA|543aa|up_9|NZ_CP049799.1_363513_365142_+	cd08518, PBP2_NikA_DppA_OppA_like_19, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold	NA|326aa|up_8|NZ_CP049799.1_365254_366232_+	COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|274aa|up_7|NZ_CP049799.1_366228_367050_+	COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|268aa|up_6|NZ_CP049799.1_367061_367865_+	COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|209aa|up_5|NZ_CP049799.1_367848_368475_+	COG1124, DppF, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|67aa|up_4|NZ_CP049799.1_368555_368756_-	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|826aa|up_3|NZ_CP049799.1_368925_371403_-	TIGR01363, pneumococcal_histidine_triad_A_protein, streptococcal histidine triad protein	NA|307aa|up_2|NZ_CP049799.1_371415_372336_-	cd01017, AdcA, Metal binding protein AdcA	NA|428aa|up_1|NZ_CP049799.1_372571_373855_-	PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated	NA|1182aa|up_0|NZ_CP049799.1_373951_377497_-	cd07475, Peptidases_S8_C5a_Peptidase, Peptidase S8 family domain in Streptococcal C5a peptidases	NA|422aa|down_0|NZ_CP049799.1_380816_382082_-	TIGR02168, Chromosome_partition_protein_Smc, chromosome segregation protein SMC, common bacterial type	NA|492aa|down_1|NZ_CP049799.1_382291_383767_-	TIGR02168, Chromosome_partition_protein_Smc, chromosome segregation protein SMC, common bacterial type	NA|531aa|down_2|NZ_CP049799.1_383951_385544_-	pfam08270, PRD_Mga, M protein trans-acting positive regulator (MGA) PRD domain	NA|84aa|down_3|NZ_CP049799.1_386219_386471_-	NA	NA|542aa|down_4|NZ_CP049799.1_386549_388175_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|463aa|down_5|NZ_CP049799.1_388276_389665_-	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]	NA|218aa|down_6|NZ_CP049799.1_389661_390315_-	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_7|NZ_CP049799.1_390408_391626_-	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB	NA|225aa|down_8|NZ_CP049799.1_391638_392313_-	COG1136, SalX, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]	NA|423aa|down_9|NZ_CP049799.1_392299_393568_-	COG0845, AcrA, Membrane-fusion protein [Cell envelope biogenesis, outer membrane]
GCF_011290565.1_ASM1129056v1	NZ_CP049799	Streptococcus pyogenes strain 1040 chromosome, complete genome	2	383214-383347	2	CRISPRCasFinder	no		cas3,DEDDh,csa3,DinG,csm6,cas9,cas1,cas2,csn2,RT,cas4,cas7,cas8c,cas5	Orphan	TGGTCTATCGCTAATTCAAGAGCTTTCTTTTTCTCTTCTAACTCTTTTTC	50	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,csa3,DinG,csm6,cas9,cas1,cas2,csn2,RT,cas4,cas7,cas8c,cas5	NA,NA|84aa|down_1|NZ_CP049799.1_386219_386471_-,NA|95aa|down_8|NZ_CP049799.1_393990_394275_-	NA|274aa|up_9|NZ_CP049799.1_366228_367050_+	COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|268aa|up_8|NZ_CP049799.1_367061_367865_+	COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|209aa|up_7|NZ_CP049799.1_367848_368475_+	COG1124, DppF, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|67aa|up_6|NZ_CP049799.1_368555_368756_-	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|826aa|up_5|NZ_CP049799.1_368925_371403_-	TIGR01363, pneumococcal_histidine_triad_A_protein, streptococcal histidine triad protein	NA|307aa|up_4|NZ_CP049799.1_371415_372336_-	cd01017, AdcA, Metal binding protein AdcA	NA|428aa|up_3|NZ_CP049799.1_372571_373855_-	PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated	NA|1182aa|up_2|NZ_CP049799.1_373951_377497_-	cd07475, Peptidases_S8_C5a_Peptidase, Peptidase S8 family domain in Streptococcal C5a peptidases	NA|304aa|up_1|NZ_CP049799.1_379716_380628_-	pfam03482, SIC, sic protein repeat	NA|422aa|up_0|NZ_CP049799.1_380816_382082_-	TIGR02168, Chromosome_partition_protein_Smc, chromosome segregation protein SMC, common bacterial type	NA|531aa|down_0|NZ_CP049799.1_383951_385544_-	pfam08270, PRD_Mga, M protein trans-acting positive regulator (MGA) PRD domain	NA|84aa|down_1|NZ_CP049799.1_386219_386471_-	NA	NA|542aa|down_2|NZ_CP049799.1_386549_388175_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|463aa|down_3|NZ_CP049799.1_388276_389665_-	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]	NA|218aa|down_4|NZ_CP049799.1_389661_390315_-	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_CP049799.1_390408_391626_-	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB	NA|225aa|down_6|NZ_CP049799.1_391638_392313_-	COG1136, SalX, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]	NA|423aa|down_7|NZ_CP049799.1_392299_393568_-	COG0845, AcrA, Membrane-fusion protein [Cell envelope biogenesis, outer membrane]	NA|95aa|down_8|NZ_CP049799.1_393990_394275_-	NA	NA|99aa|down_9|NZ_CP049799.1_394420_394717_-	pfam14131, DUF4298, Domain of unknown function (DUF4298)
GCF_011290565.1_ASM1129056v1	NZ_CP049799	Streptococcus pyogenes strain 1040 chromosome, complete genome	3	1329666-1330097	3	CRISPRCasFinder	no	cas9,cas1,cas2,csn2	cas3,DEDDh,csa3,DinG,csm6,cas9,cas1,cas2,csn2,RT,cas4,cas7,cas8c,cas5	Type II-C,Type II-A,Type II-B	GTTTTAGAGCTATGCTGTTTTGAATGGTCCCAAAAC	36	0	0	NA	NA	II-A	6	6	TypeII-C,TypeII-A,TypeII-B	cas3,DEDDh,csa3,DinG,csm6,cas9,cas1,cas2,csn2,RT,cas4,cas7,cas8c,cas5	NA|214aa|up_8|NZ_CP049799.1_1319125_1319767_+,NA	NA|452aa|up_9|NZ_CP049799.1_1317636_1318992_+	PRK14316, glmM, phosphoglucosamine mutase; Provisional	NA|214aa|up_8|NZ_CP049799.1_1319125_1319767_+	NA	NA|377aa|up_7|NZ_CP049799.1_1319829_1320960_+	PRK08599, PRK08599, oxygen-independent coproporphyrinogen III oxidase	NA|251aa|up_6|NZ_CP049799.1_1320969_1321722_+	COG3884, FatA, Acyl-ACP thioesterase [Lipid metabolism]	NA|255aa|up_5|NZ_CP049799.1_1321721_1322486_+	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_CP049799.1_1322485_1323118_+	COG4478, COG4478, Predicted membrane protein [Function unknown]	cas9|1369aa|up_3|NZ_CP049799.1_1323597_1327704_+	COG3513, COG3513, Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]	cas1|290aa|up_2|NZ_CP049799.1_1327703_1328573_+	cd09720, Cas1_II, CRISPR/Cas system-associated protein Cas1	cas2|114aa|up_1|NZ_CP049799.1_1328569_1328911_+	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms]	csn2|221aa|up_0|NZ_CP049799.1_1328900_1329563_+	cd09758, Csn2, CRISPR/Cas system-associated protein Csn2	NA|611aa|down_0|NZ_CP049799.1_1330740_1332573_+	PRK05433, PRK05433, GTP-binding protein LepA; Provisional	NA|588aa|down_1|NZ_CP049799.1_1332870_1334634_+	PRK12678, PRK12678, transcription termination factor Rho; Provisional	NA|146aa|down_2|NZ_CP049799.1_1334819_1335257_+	PRK00222, PRK00222, peptide-methionine (R)-S-oxide reductase MsrB	NA|340aa|down_3|NZ_CP049799.1_1335386_1336406_+	COG2855, COG2855, Predicted membrane protein [Function unknown]	NA|142aa|down_4|NZ_CP049799.1_1336612_1337038_+	COG2893, ManX, Phosphotransferase system, mannose/fructose-specific component IIA [Carbohydrate transport and metabolism]	NA|164aa|down_5|NZ_CP049799.1_1337056_1337548_+	COG3444, COG3444, Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB [Carbohydrate transport and metabolism]	NA|270aa|down_6|NZ_CP049799.1_1337564_1338374_+	COG3715, ManY, Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIC [Carbohydrate transport and metabolism]	NA|276aa|down_7|NZ_CP049799.1_1338370_1339198_+	COG3716, ManZ, Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IID [Carbohydrate transport and metabolism]	NA|550aa|down_8|NZ_CP049799.1_1339333_1340983_+	COG2972, COG2972, Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]	NA|263aa|down_9|NZ_CP049799.1_1340986_1341775_+	COG4753, COG4753, Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]
GCF_011290565.1_ASM1129056v1	NZ_CP049799	Streptococcus pyogenes strain 1040 chromosome, complete genome	4	1333597-1333928	1	PILER-CR	no	cas9,cas1,cas2,csn2	cas3,DEDDh,csa3,DinG,csm6,cas9,cas1,cas2,csn2,RT,cas4,cas7,cas8c,cas5	Type II-C,Type II-A,Type II-B	GAGCGCGGTGCAACCGGCCCAGTAGGTCCCGCTGGTCCAAAAGGACCTGCAGGTGAAAAAGG	62	3	9	1333659-1333686|1333659-1333686|1333659-1333686|1333659-1333686|1333749-1333776|1333749-1333776|1333749-1333776|1333749-1333776|1333839-1333866	NZ_CP049799.1_1333389-1333416|NZ_CP049799.1_1333479-1333506|NZ_CP049799.1_1333569-1333596|NZ_CP049799.1_1333929-1333956|NZ_CP049799.1_1333389-1333416|NZ_CP049799.1_1333479-1333506|NZ_CP049799.1_1333569-1333596|NZ_CP049799.1_1333929-1333956|NZ_CP049799.1_1334019-1334046	NA	3	3	TypeII-C,TypeII-A,TypeII-B	cas3,DEDDh,csa3,DinG,csm6,cas9,cas1,cas2,csn2,RT,cas4,cas7,cas8c,cas5	NA|214aa|up_9|NZ_CP049799.1_1319125_1319767_+,NA	NA|214aa|up_9|NZ_CP049799.1_1319125_1319767_+	NA	NA|377aa|up_8|NZ_CP049799.1_1319829_1320960_+	PRK08599, PRK08599, oxygen-independent coproporphyrinogen III oxidase	NA|251aa|up_7|NZ_CP049799.1_1320969_1321722_+	COG3884, FatA, Acyl-ACP thioesterase [Lipid metabolism]	NA|255aa|up_6|NZ_CP049799.1_1321721_1322486_+	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_5|NZ_CP049799.1_1322485_1323118_+	COG4478, COG4478, Predicted membrane protein [Function unknown]	cas9|1369aa|up_4|NZ_CP049799.1_1323597_1327704_+	COG3513, COG3513, Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]	cas1|290aa|up_3|NZ_CP049799.1_1327703_1328573_+	cd09720, Cas1_II, CRISPR/Cas system-associated protein Cas1	cas2|114aa|up_2|NZ_CP049799.1_1328569_1328911_+	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms]	csn2|221aa|up_1|NZ_CP049799.1_1328900_1329563_+	cd09758, Csn2, CRISPR/Cas system-associated protein Csn2	NA|611aa|up_0|NZ_CP049799.1_1330740_1332573_+	PRK05433, PRK05433, GTP-binding protein LepA; Provisional	NA|146aa|down_0|NZ_CP049799.1_1334819_1335257_+	PRK00222, PRK00222, peptide-methionine (R)-S-oxide reductase MsrB	NA|340aa|down_1|NZ_CP049799.1_1335386_1336406_+	COG2855, COG2855, Predicted membrane protein [Function unknown]	NA|142aa|down_2|NZ_CP049799.1_1336612_1337038_+	COG2893, ManX, Phosphotransferase system, mannose/fructose-specific component IIA [Carbohydrate transport and metabolism]	NA|164aa|down_3|NZ_CP049799.1_1337056_1337548_+	COG3444, COG3444, Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB [Carbohydrate transport and metabolism]	NA|270aa|down_4|NZ_CP049799.1_1337564_1338374_+	COG3715, ManY, Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIC [Carbohydrate transport and metabolism]	NA|276aa|down_5|NZ_CP049799.1_1338370_1339198_+	COG3716, ManZ, Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IID [Carbohydrate transport and metabolism]	NA|550aa|down_6|NZ_CP049799.1_1339333_1340983_+	COG2972, COG2972, Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]	NA|263aa|down_7|NZ_CP049799.1_1340986_1341775_+	COG4753, COG4753, Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]	NA|349aa|down_8|NZ_CP049799.1_1341768_1342815_+	cd13546, PBP2_BitB, Substrate binding domain of a putative iron transporter BitB, a member of the type 2 periplasmic binding fold superfamily	NA|466aa|down_9|NZ_CP049799.1_1342929_1344327_+	cd07100, ALDH_SSADH1_GabD1, Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like
GCF_011290565.1_ASM1129056v1	NZ_CP049799	Streptococcus pyogenes strain 1040 chromosome, complete genome	5	1780629-1780990	1,2,4	CRT,PILER-CR,CRISPRCasFinder	no	cas2,cas1,cas4,cas7,cas8c,cas5,cas3	cas3,DEDDh,csa3,DinG,csm6,cas9,cas1,cas2,csn2,RT,cas4,cas7,cas8c,cas5	Type I-C,Type I-U, Type I-U?	ATTTCAATCCACTCACCCATGAAGGGTGAGAC,ATTTCAATCCACTCACCCATGAAGGGTGAGAC,TTTCAATCCACTCACCCATGAAGGGTGAGAC	32,32,31	0	0	NA	NA	I-C:I-C:I-C	5,5,5	5	TypeI-C,TypeI-U,TypeI-U?	cas3,DEDDh,csa3,DinG,csm6,cas9,cas1,cas2,csn2,RT,cas4,cas7,cas8c,cas5	NA,NA	NA|412aa|up_9|NZ_CP049799.1_1770563_1771799_-	PRK01388, PRK01388, arginine deiminase; Provisional	NA|227aa|up_8|NZ_CP049799.1_1772072_1772753_-	COG0664, Crp, cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]	NA|158aa|up_7|NZ_CP049799.1_1772894_1773368_+	COG1438, ArgR, Arginine repressor [Transcription]	NA|239aa|up_6|NZ_CP049799.1_1773534_1774251_-	COG3382, COG3382, Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only]	NA|360aa|up_5|NZ_CP049799.1_1774264_1775344_-	COG2315, MmcQ, Uncharacterized protein conserved in bacteria [Function unknown]	NA|578aa|up_4|NZ_CP049799.1_1775416_1777150_-	COG2972, COG2972, Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]	NA|247aa|up_3|NZ_CP049799.1_1777146_1777887_-	COG4753, COG4753, Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]	NA|369aa|up_2|NZ_CP049799.1_1777973_1779080_-	PRK14018, PRK14018, bifunctional peptide-methionine (S)-S-oxide reductase MsrA/peptide-methionine (R)-S-oxide reductase MsrB	NA|208aa|up_1|NZ_CP049799.1_1779122_1779746_-	cd02966, TlpA_like_family, TlpA-like family; composed of  TlpA, ResA, DsbE and similar proteins	NA|237aa|up_0|NZ_CP049799.1_1779758_1780469_-	COG0785, CcdA, Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]	cas2|98aa|down_0|NZ_CP049799.1_1781138_1781432_-	COG1343, COG1343, CRISPR-associated protein Cas2 [Defense mechanisms]	cas1|342aa|down_1|NZ_CP049799.1_1781442_1782468_-	TIGR03640, cas1_DVULG, CRISPR-associated endonuclease Cas1, subtype I-C/DVULG	cas4|225aa|down_2|NZ_CP049799.1_1782464_1783139_-	COG1468, COG1468, CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense    mechanisms]	cas7|283aa|down_3|NZ_CP049799.1_1783140_1783989_-	COG3649, COG3649, CRISPR system related protein [Defense mechanisms]	cas8c|632aa|down_4|NZ_CP049799.1_1783993_1785889_-	cd09642, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c	cas5|243aa|down_5|NZ_CP049799.1_1785888_1786617_-	TIGR01876, cas_Cas5d, CRISPR-associated protein Cas5, subtype I-C/DVULG	cas3|803aa|down_6|NZ_CP049799.1_1786749_1789158_-	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	NA|883aa|down_7|NZ_CP049799.1_1789311_1791960_-	PRK05729, valS, valyl-tRNA synthetase; Reviewed	NA|188aa|down_8|NZ_CP049799.1_1791961_1792525_-	pfam13671, AAA_33, AAA domain	NA|132aa|down_9|NZ_CP049799.1_1793125_1793521_-	PRK07758, PRK07758, hypothetical protein; Provisional
