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_000349925.2_ASM34992v2	NC_020540	Streptococcus pyogenes M1 476 chromosome 1, complete sequence	1	798183-798416	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-B,Type II-C	GTTTTAGAGCTATGCTGTTTTGAATGGTCCCAAAAC,GTTTTAGAGCTATGCTGTTTTGAATGGTCCCAAAAC,GTTTTAGAGCTATGCTGTTTTGAATGGTCCCAAAAC	36,36,36	0	0	NA	NA	II-A:II-A:II-A	2,3,3	3	TypeII-A,TypeII-B,TypeII-C	cas3,DEDDh,DinG,csm6,cas9,cas1,cas2,csn2,cas4,cas7,cas8c,cas5,csa3	NA|214aa|up_8|NC_020540.2_787642_788284_+,NA	NA|452aa|up_9|NC_020540.2_786153_787509_+	PRK14316, glmM, phosphoglucosamine mutase; Provisional	NA|214aa|up_8|NC_020540.2_787642_788284_+	NA	NA|377aa|up_7|NC_020540.2_788346_789477_+	PRK08599, PRK08599, oxygen-independent coproporphyrinogen III oxidase	NA|251aa|up_6|NC_020540.2_789486_790239_+	COG3884, FatA, Acyl-ACP thioesterase [Lipid metabolism]	NA|255aa|up_5|NC_020540.2_790238_791003_+	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|NC_020540.2_791002_791635_+	COG4478, COG4478, Predicted membrane protein [Function unknown]	cas9|1369aa|up_3|NC_020540.2_792114_796221_+	COG3513, COG3513, Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]	cas1|290aa|up_2|NC_020540.2_796220_797090_+	cd09720, Cas1_II, CRISPR/Cas system-associated protein Cas1	cas2|114aa|up_1|NC_020540.2_797086_797428_+	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms]	csn2|221aa|up_0|NC_020540.2_797417_798080_+	cd09758, Csn2, CRISPR/Cas system-associated protein Csn2	NA|611aa|down_0|NC_020540.2_799059_800892_+	PRK05433, PRK05433, GTP-binding protein LepA; Provisional	NA|294aa|down_1|NC_020540.2_801149_802031_+	pfam00746, Gram_pos_anchor, LPXTG cell wall anchor motif	NA|146aa|down_2|NC_020540.2_802216_802654_+	PRK00222, PRK00222, peptide-methionine (R)-S-oxide reductase MsrB	NA|340aa|down_3|NC_020540.2_802768_803788_+	COG2855, COG2855, Predicted membrane protein [Function unknown]	NA|142aa|down_4|NC_020540.2_803994_804420_+	COG2893, ManX, Phosphotransferase system, mannose/fructose-specific component IIA [Carbohydrate transport and metabolism]	NA|164aa|down_5|NC_020540.2_804438_804930_+	COG3444, COG3444, Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB [Carbohydrate transport and metabolism]	NA|270aa|down_6|NC_020540.2_804946_805756_+	COG3715, ManY, Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIC [Carbohydrate transport and metabolism]	NA|276aa|down_7|NC_020540.2_805752_806580_+	COG3716, ManZ, Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IID [Carbohydrate transport and metabolism]	NA|550aa|down_8|NC_020540.2_806715_808365_+	COG2972, COG2972, Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]	NA|263aa|down_9|NC_020540.2_808368_809157_+	COG4753, COG4753, Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]
GCF_000349925.2_ASM34992v2	NC_020540	Streptococcus pyogenes M1 476 chromosome 1, complete sequence	2	992652-992753	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|NC_020540.2_1000583_1001369_+,NA|63aa|down_8|NC_020540.2_1002700_1002889_-	NA|83aa|up_9|NC_020540.2_980369_980618_-	COG2261, COG2261, Predicted membrane protein [Function unknown]	NA|773aa|up_8|NC_020540.2_980981_983300_-	TIGR01073, ATP-dependent_DNA_helicase_PcrA, ATP-dependent DNA helicase PcrA	NA|441aa|up_7|NC_020540.2_983828_985151_+	COG1115, AlsT, Na+/alanine symporter [Amino acid transport and metabolism]	NA|412aa|up_6|NC_020540.2_985270_986506_+	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|258aa|up_5|NC_020540.2_986874_987648_-	pfam07373, CAMP_factor, CAMP factor (Cfa)	NA|279aa|up_4|NC_020540.2_988017_988854_-	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|NC_020540.2_988869_989499_-	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|214aa|up_2|NC_020540.2_989508_990150_-	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|112aa|up_1|NC_020540.2_990255_990591_-	COG2824, PhnA, Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]	NA|605aa|up_0|NC_020540.2_990786_992601_-	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|186aa|down_0|NC_020540.2_992776_993334_-	TIGR02227, Inactive_signal_peptidase_IA	NA|501aa|down_1|NC_020540.2_993551_995054_-	PRK05826, PRK05826, pyruvate kinase; Provisional	NA|338aa|down_2|NC_020540.2_995116_996130_-	PRK03202, PRK03202, ATP-dependent 6-phosphofructokinase	NA|1037aa|down_3|NC_020540.2_996209_999320_-	PRK07279, dnaE, DNA polymerase III DnaE; Reviewed	NA|124aa|down_4|NC_020540.2_999504_999876_+	COG1725, COG1725, Predicted transcriptional regulators [Transcription]	NA|233aa|down_5|NC_020540.2_999875_1000574_+	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]	NA|262aa|down_6|NC_020540.2_1000583_1001369_+	NA	NA|205aa|down_7|NC_020540.2_1001495_1002110_-	COG0398, COG0398, Uncharacterized conserved protein [Function unknown]	NA|63aa|down_8|NC_020540.2_1002700_1002889_-	NA	NA|252aa|down_9|NC_020540.2_1003108_1003864_+	pfam02876, Stap_Strp_tox_C, Staphylococcal/Streptococcal toxin, beta-grasp domain
GCF_000349925.2_ASM34992v2	NC_020540	Streptococcus pyogenes M1 476 chromosome 1, complete sequence	3	1098252-1098387	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,NA	NA|495aa|up_9|NC_020540.2_1086229_1087714_+	PRK13663, PRK13663, hypothetical protein; Provisional	NA|134aa|up_8|NC_020540.2_1087820_1088222_-	COG2050, PaaI, HGG motif-containing thioesterase, possibly involved in aromatic compounds catabolism [Secondary metabolites biosynthesis,    transport, and catabolism]	NA|463aa|up_7|NC_020540.2_1089123_1090512_-	COG2265, TrmA, SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]	NA|484aa|up_6|NC_020540.2_1090560_1092012_-	COG1316, LytR, Transcriptional regulator [Transcription]	NA|164aa|up_5|NC_020540.2_1092219_1092711_-	PRK00131, aroK, shikimate kinase; Reviewed	NA|428aa|up_4|NC_020540.2_1092703_1093987_-	PRK02427, PRK02427, 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional	NA|322aa|up_3|NC_020540.2_1094097_1095063_-	COG1295, Rbn, Ribonuclease BN family enzyme [Replication, recombination, and repair]	NA|287aa|up_2|NC_020540.2_1095064_1095925_-	PRK07281, PRK07281, methionyl aminopeptidase	NA|428aa|up_1|NC_020540.2_1095940_1097224_-	COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]	NA|181aa|up_0|NC_020540.2_1097232_1097775_-	COG1670, RimL, Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]	NA|420aa|down_0|NC_020540.2_1099023_1100283_-	PRK12830, PRK12830, UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Reviewed	NA|399aa|down_1|NC_020540.2_1100456_1101653_-	PRK05250, PRK05250, S-adenosylmethionine synthetase; Validated	NA|793aa|down_2|NC_020540.2_1102189_1104568_-	COG4886, COG4886, Leucine-rich repeat (LRR) protein [Function unknown]	NA|314aa|down_3|NC_020540.2_1104771_1105713_+	PRK11886, PRK11886, bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA	NA|68aa|down_4|NC_020540.2_1105687_1105891_-	pfam11676, DUF3272, Protein of unknown function (DUF3272)	NA|557aa|down_5|NC_020540.2_1105985_1107656_-	PRK05563, PRK05563, DNA polymerase III subunits gamma and tau; Validated	NA|166aa|down_6|NC_020540.2_1107655_1108153_-	COG1956, COG1956, GAF domain-containing protein [Signal transduction mechanisms]	NA|270aa|down_7|NC_020540.2_1108297_1109107_+	COG2339, prsW, Membrane proteinase, regulator of anti-sigma factor [Posttranslational modification, protein turnover, chaperones]	NA|88aa|down_8|NC_020540.2_1109159_1109423_-	COG3326, COG3326, Predicted membrane protein [Function unknown]	NA|209aa|down_9|NC_020540.2_1109502_1110129_-	PRK05480, PRK05480, uridine/cytidine kinase; Provisional
GCF_000349925.2_ASM34992v2	NC_020540	Streptococcus pyogenes M1 476 chromosome 1, complete sequence	4	1258507-1258801	4,2,2	CRISPRCasFinder,CRT,PILER-CR	no	cas2,cas1,cas4,cas7,cas8c,cas5,cas3	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|NC_020540.2_1248441_1249677_-	PRK01388, PRK01388, arginine deiminase; Provisional	NA|227aa|up_8|NC_020540.2_1249950_1250631_-	COG0664, Crp, cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]	NA|158aa|up_7|NC_020540.2_1250772_1251246_+	COG1438, ArgR, Arginine repressor [Transcription]	NA|239aa|up_6|NC_020540.2_1251411_1252128_-	COG3382, COG3382, Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only]	NA|360aa|up_5|NC_020540.2_1252141_1253221_-	COG2315, MmcQ, Uncharacterized protein conserved in bacteria [Function unknown]	NA|578aa|up_4|NC_020540.2_1253293_1255027_-	COG2972, COG2972, Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]	NA|247aa|up_3|NC_020540.2_1255023_1255764_-	COG4753, COG4753, Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]	NA|369aa|up_2|NC_020540.2_1255851_1256958_-	PRK14018, PRK14018, bifunctional peptide-methionine (S)-S-oxide reductase MsrA/peptide-methionine (R)-S-oxide reductase MsrB	NA|208aa|up_1|NC_020540.2_1257000_1257624_-	cd02966, TlpA_like_family, TlpA-like family; composed of  TlpA, ResA, DsbE and similar proteins	NA|237aa|up_0|NC_020540.2_1257636_1258347_-	COG0785, CcdA, Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]	cas2|98aa|down_0|NC_020540.2_1258949_1259243_-	COG1343, COG1343, CRISPR-associated protein Cas2 [Defense mechanisms]	cas1|342aa|down_1|NC_020540.2_1259253_1260279_-	TIGR03640, cas1_DVULG, CRISPR-associated endonuclease Cas1, subtype I-C/DVULG	cas4|225aa|down_2|NC_020540.2_1260275_1260950_-	COG1468, COG1468, CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense    mechanisms]	cas7|283aa|down_3|NC_020540.2_1260951_1261800_-	COG3649, COG3649, CRISPR system related protein [Defense mechanisms]	cas8c|632aa|down_4|NC_020540.2_1261804_1263700_-	cd09642, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c	cas5|243aa|down_5|NC_020540.2_1263699_1264428_-	TIGR01876, cas_Cas5d, CRISPR-associated protein Cas5, subtype I-C/DVULG	cas3|803aa|down_6|NC_020540.2_1264560_1266969_-	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	NA|883aa|down_7|NC_020540.2_1267122_1269771_-	PRK05729, valS, valyl-tRNA synthetase; Reviewed	NA|188aa|down_8|NC_020540.2_1269772_1270336_-	pfam13238, AAA_18, AAA domain	NA|132aa|down_9|NC_020540.2_1270936_1271332_-	PRK07758, PRK07758, hypothetical protein; Provisional
GCF_000349925.2_ASM34992v2	NC_020540	Streptococcus pyogenes M1 476 chromosome 1, complete sequence	5	1676949-1677082	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,NA|84aa|down_1|NC_020540.2_1679930_1680182_-,NA|95aa|down_8|NC_020540.2_1687677_1687962_-	NA|256aa|up_9|NC_020540.2_1658609_1659377_-	COG1636, COG1636, Uncharacterized protein conserved in bacteria [Function unknown]	NA|595aa|up_8|NC_020540.2_1659494_1661279_-	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|569aa|up_7|NC_020540.2_1661281_1662988_-	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|150aa|up_6|NC_020540.2_1662980_1663430_-	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|339aa|up_5|NC_020540.2_1663727_1664744_+	PRK00094, gpsA, NAD(P)H-dependent glycerol-3-phosphate dehydrogenase	NA|300aa|up_4|NC_020540.2_1664776_1665676_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|224aa|up_3|NC_020540.2_1665774_1666446_-	COG0705, COG0705, Membrane associated serine protease [Amino acid transport and metabolism]	NA|356aa|up_2|NC_020540.2_1668143_1669211_-	TIGR01168, M_protein_serotype, Gram-positive signal peptide, YSIRK family	NA|1165aa|up_1|NC_020540.2_1669307_1672802_-	cd07475, Peptidases_S8_C5a_Peptidase, Peptidase S8 family domain in Streptococcal C5a peptidases	NA|273aa|up_0|NC_020540.2_1675019_1675838_-	pfam03482, SIC, sic protein repeat	NA|530aa|down_0|NC_020540.2_1677665_1679255_-	pfam08270, PRD_Mga, M protein trans-acting positive regulator (MGA) PRD domain	NA|84aa|down_1|NC_020540.2_1679930_1680182_-	NA	NA|534aa|down_2|NC_020540.2_1680260_1681862_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|463aa|down_3|NC_020540.2_1681963_1683352_-	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]	NA|218aa|down_4|NC_020540.2_1683348_1684002_-	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|NC_020540.2_1684095_1685313_-	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB	NA|225aa|down_6|NC_020540.2_1685325_1686000_-	COG1136, SalX, ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]	NA|423aa|down_7|NC_020540.2_1685986_1687255_-	COG0845, AcrA, Membrane-fusion protein [Cell envelope biogenesis, outer membrane]	NA|95aa|down_8|NC_020540.2_1687677_1687962_-	NA	NA|99aa|down_9|NC_020540.2_1688108_1688405_-	pfam14131, DUF4298, Domain of unknown function (DUF4298)
