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_009664475.1_ASM966447v1	NZ_CP045931	Streptococcus pneumoniae strain AUSMDU00010538 chromosome, complete genome	1	110777-110872	1	CRISPRCasFinder	no		cas3,DEDDh,PrimPol,DinG,RT	Orphan	AATGTGTAAGATTTTTATATATAA	24	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,PrimPol,DinG,RT	NA|47aa|up_9|NZ_CP045931.1_101349_101490_-,NA|260aa|up_5|NZ_CP045931.1_106059_106839_+,NA|107aa|down_7|NZ_CP045931.1_118591_118912_-,NA|118aa|down_8|NZ_CP045931.1_119675_120029_+,NA|253aa|down_9|NZ_CP045931.1_119995_120754_+	NA|47aa|up_9|NZ_CP045931.1_101349_101490_-	NA	NA|492aa|up_8|NZ_CP045931.1_101533_103009_+	pfam12010, DUF3502, Domain of unknown function (DUF3502)	NA|329aa|up_7|NZ_CP045931.1_103280_104267_+	PRK00142, PRK00142, rhodanese-related sulfurtransferase	NA|287aa|up_6|NZ_CP045931.1_104541_105402_+	pfam14132, DUF4299, Domain of unknown function (DUF4299)	NA|260aa|up_5|NZ_CP045931.1_106059_106839_+	NA	NA|66aa|up_4|NZ_CP045931.1_107387_107585_+	cd00267, ABC_ATPase, ATP-binding cassette transporter nucleotide-binding domain	NA|355aa|up_3|NZ_CP045931.1_107821_108886_-	pfam10310, DUF5427, Family of unknown function (DUF5427)	NA|304aa|up_2|NZ_CP045931.1_108948_109860_-	pfam13349, DUF4097, Putative adhesin	NA|198aa|up_1|NZ_CP045931.1_109852_110446_-	COG4709, COG4709, Predicted membrane protein [Function unknown]	NA|109aa|up_0|NZ_CP045931.1_110432_110759_-	COG1695, COG1695, Predicted transcriptional regulators [Transcription]	NA|389aa|down_0|NZ_CP045931.1_110897_112064_-	cd17339, MFS_NIMT_CynX_like, 2-nitroimidazole and cyanate transporters and similar proteins of the Major Facilitator Superfamily of transporters	NA|386aa|down_1|NZ_CP045931.1_112121_113279_+	cd02525, Succinoglycan_BP_ExoA, ExoA is involved in the biosynthesis of succinoglycan	NA|617aa|down_2|NZ_CP045931.1_113320_115171_+	COG1086, COG1086, Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]	NA|211aa|down_3|NZ_CP045931.1_115518_116151_-	cd04302, HAD_5NT, haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to the Pseudomonas aeruginosa PA0065	NA|291aa|down_4|NZ_CP045931.1_116172_117045_-	TIGR00718, Probable_L-serine_dehydratase_alpha_chain, L-serine dehydratase, iron-sulfur-dependent, alpha subunit	NA|224aa|down_5|NZ_CP045931.1_117053_117725_-	COG1760, SdaA, L-serine deaminase [Amino acid transport and metabolism]	NA|191aa|down_6|NZ_CP045931.1_117966_118539_+	cd00118, LysM, Lysin Motif is a small domain involved in binding peptidoglycan	NA|107aa|down_7|NZ_CP045931.1_118591_118912_-	NA	NA|118aa|down_8|NZ_CP045931.1_119675_120029_+	NA	NA|253aa|down_9|NZ_CP045931.1_119995_120754_+	NA
GCF_009664475.1_ASM966447v1	NZ_CP045931	Streptococcus pneumoniae strain AUSMDU00010538 chromosome, complete genome	2	1048023-1048134	2	CRISPRCasFinder	no		cas3,DEDDh,PrimPol,DinG,RT	Orphan	GATGAAAATGGAAACTTGATTGAACCACCTGTTA	34	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,PrimPol,DinG,RT	NA|393aa|up_1|NZ_CP045931.1_1039500_1040679_+,NA	NA|380aa|up_9|NZ_CP045931.1_1024524_1025664_+	TIGR02092, Glycogen_biosynthesis_protein_GlgD, glucose-1-phosphate adenylyltransferase, GlgD subunit	NA|478aa|up_8|NZ_CP045931.1_1025660_1027094_+	PRK00654, glgA, glycogen synthase GlgA	NA|272aa|up_7|NZ_CP045931.1_1027794_1028610_+	COG1929, COG1929, Glycerate kinase [Carbohydrate transport and metabolism]	NA|149aa|up_6|NZ_CP045931.1_1028606_1029053_-	COG5506, COG5506, Uncharacterized conserved protein [Function unknown]	NA|435aa|up_5|NZ_CP045931.1_1029216_1030521_+	PRK00077, eno, enolase; Provisional	NA|149aa|up_4|NZ_CP045931.1_1030658_1031105_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|1092aa|up_3|NZ_CP045931.1_1032363_1035639_+	TIGR02774, putative_ATP-dependent_exonuclease_subunit_B, ATP-dependent nuclease subunit B	NA|1217aa|up_2|NZ_CP045931.1_1035635_1039286_+	TIGR02785, ATP-dependent_helicase/nuclease_subunit_A, helicase-exonuclease AddAB, AddA subunit, Firmicutes type	NA|393aa|up_1|NZ_CP045931.1_1039500_1040679_+	NA	NA|2142aa|up_0|NZ_CP045931.1_1040887_1047313_+	pfam07580, Peptidase_M26_C, M26 IgA1-specific Metallo-endopeptidase C-terminal region	NA|284aa|down_0|NZ_CP045931.1_1052823_1053675_+	PRK09563, rbgA, GTPase YlqF; Reviewed	NA|260aa|down_1|NZ_CP045931.1_1053661_1054441_+	PRK00015, rnhB, ribonuclease HII; Validated	NA|517aa|down_2|NZ_CP045931.1_1054456_1056007_+	cd01031, EriC, ClC chloride channel EriC	NA|357aa|down_3|NZ_CP045931.1_1056590_1057661_+	PRK05084, xerS, site-specific tyrosine recombinase XerS; Reviewed	NA|330aa|down_4|NZ_CP045931.1_1057733_1058723_-	TIGR00545, Probable_lipoate-protein_ligase_A, lipoyltransferase and lipoate-protein ligase	NA|568aa|down_5|NZ_CP045931.1_1058786_1060490_-	TIGR01350, Dihydrolipoyl_dehydrogenase, dihydrolipoamide dehydrogenase	NA|348aa|down_6|NZ_CP045931.1_1060535_1061579_-	PRK14843, PRK14843, dihydrolipoamide acetyltransferase; Provisional	NA|331aa|down_7|NZ_CP045931.1_1061796_1062789_-	COG0022, AcoB, Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]	NA|323aa|down_8|NZ_CP045931.1_1062804_1063773_-	COG1071, AcoA, Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]	NA|454aa|down_9|NZ_CP045931.1_1063926_1065288_-	cd13131, MATE_NorM_like, Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM
GCF_009664475.1_ASM966447v1	NZ_CP045931	Streptococcus pneumoniae strain AUSMDU00010538 chromosome, complete genome	3	1393627-1393763	3	CRISPRCasFinder	no		cas3,DEDDh,PrimPol,DinG,RT	Orphan	ACTTCTGGTGTCGGTACATTTGGTGTTGG	29	0	0	NA	NA	NA	2	2	Orphan	cas3,DEDDh,PrimPol,DinG,RT	NA,NA|532aa|down_3|NZ_CP045931.1_1403062_1404658_-	NA|120aa|up_9|NZ_CP045931.1_1385671_1386031_-	PRK07252, PRK07252, S1 RNA-binding domain-containing protein	NA|467aa|up_8|NZ_CP045931.1_1386032_1387433_-	COG0652, PpiB, Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family [Posttranslational modification, protein turnover, chaperones]	NA|80aa|up_7|NZ_CP045931.1_1387727_1387967_-	PRK00391, rpsR, 30S ribosomal protein S18; Reviewed	NA|157aa|up_6|NZ_CP045931.1_1387998_1388469_-	PRK07275, PRK07275, single-stranded DNA-binding protein; Provisional	NA|97aa|up_5|NZ_CP045931.1_1388480_1388771_-	PRK00453, rpsF, 30S ribosomal protein S6; Reviewed	NA|448aa|up_4|NZ_CP045931.1_1388923_1390267_-	PRK03932, asnC, asparaginyl-tRNA synthetase; Validated	NA|75aa|up_3|NZ_CP045931.1_1390426_1390651_-	cd07262, VOC_like, uncharacterized subfamily of vicinal oxygen chelate (VOC) family	NA|396aa|up_2|NZ_CP045931.1_1390643_1391831_-	PRK05764, PRK05764, aspartate aminotransferase; Provisional	NA|144aa|up_1|NZ_CP045931.1_1391827_1392259_-	COG5353, COG5353, Uncharacterized protein conserved in bacteria [Function unknown]	NA|183aa|up_0|NZ_CP045931.1_1392636_1393185_+	COG0431, COG0431, Predicted flavoprotein [General function prediction only]	NA|503aa|down_0|NZ_CP045931.1_1400365_1401874_+	pfam08270, PRD_Mga, M protein trans-acting positive regulator (MGA) PRD domain	NA|243aa|down_1|NZ_CP045931.1_1401924_1402653_-	PRK02101, PRK02101, peroxide stress protein YaaA	NA|60aa|down_2|NZ_CP045931.1_1402731_1402911_-	pfam13129, DUF3953, Protein of unknown function (DUF3953)	NA|532aa|down_3|NZ_CP045931.1_1403062_1404658_-	NA	NA|137aa|down_4|NZ_CP045931.1_1404669_1405080_-	PRK09218, PRK09218, peptide deformylase; Validated	NA|264aa|down_5|NZ_CP045931.1_1405195_1405987_-	PRK11752, PRK11752, putative S-transferase; Provisional	NA|899aa|down_6|NZ_CP045931.1_1405999_1408696_-	cd02089, P-type_ATPase_Ca_prok, prokaryotic P-type Ca(2+)-ATPase similar to Synechococcus elongatus sp	NA|395aa|down_7|NZ_CP045931.1_1408999_1410184_+	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|624aa|down_8|NZ_CP045931.1_1410326_1412198_-	COG0488, Uup, ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]	NA|400aa|down_9|NZ_CP045931.1_1412194_1413394_-	PRK13299, PRK13299, tRNA CCA-pyrophosphorylase; Provisional
GCF_009664475.1_ASM966447v1	NZ_CP045931	Streptococcus pneumoniae strain AUSMDU00010538 chromosome, complete genome	4	1527733-1527821	4	CRISPRCasFinder	no	cas3	cas3,DEDDh,PrimPol,DinG,RT	Unclear	GCTGGCTCTTCACCGGATGTCCCTAATGG	29	0	0	NA	NA	NA	1	1	Unclear	cas3,DEDDh,PrimPol,DinG,RT	NA,NA|76aa|down_0|NZ_CP045931.1_1530769_1530997_-,NA|76aa|down_8|NZ_CP045931.1_1541436_1541664_-	NA|299aa|up_9|NZ_CP045931.1_1514656_1515553_-	COG1175, UgpA, ABC-type sugar transport systems, permease components [Carbohydrate transport and metabolism]	NA|443aa|up_8|NZ_CP045931.1_1515774_1517103_-	COG1653, UgpB, ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]	NA|511aa|up_7|NZ_CP045931.1_1517227_1518760_-	TIGR02002, PTS_system_glucose-specific_IIABC_component, PTS system, glucose-specific IIBC component	NA|233aa|up_6|NZ_CP045931.1_1518763_1519462_-	PRK01130, PRK01130, putative N-acetylmannosamine-6-phosphate 2-epimerase	NA|368aa|up_5|NZ_CP045931.1_1519635_1520739_-	COG0673, MviM, Predicted dehydrogenases and related proteins [General function prediction only]	NA|698aa|up_4|NZ_CP045931.1_1520751_1522845_-	COG4409, NanH, Neuraminidase (sialidase) [Carbohydrate transport and metabolism]	NA|278aa|up_3|NZ_CP045931.1_1522862_1523696_-	COG0395, UgpE, ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]	NA|295aa|up_2|NZ_CP045931.1_1523695_1524580_-	COG1175, UgpA, ABC-type sugar transport systems, permease components [Carbohydrate transport and metabolism]	NA|446aa|up_1|NZ_CP045931.1_1524658_1525996_-	cd13585, PBP2_TMBP_like, The periplasmic-binding component of ABC transport systems specific for trehalose/maltose and similar oligosaccharides; possess type 2 periplasmic binding fold	NA|151aa|up_0|NZ_CP045931.1_1526014_1526467_-	TIGR00022, Uncharacterized_protein_HI_0227, YhcH/YjgK/YiaL family protein	NA|76aa|down_0|NZ_CP045931.1_1530769_1530997_-	NA	NA|327aa|down_1|NZ_CP045931.1_1531801_1532782_-	COG3458, COG3458, Acetyl esterase (deacetylase) [Secondary metabolites biosynthesis, transport, and catabolism]	cas3|672aa|down_2|NZ_CP045931.1_1533098_1535114_-	PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional	NA|368aa|down_3|NZ_CP045931.1_1535132_1536236_-	PRK00053, alr, alanine racemase; Reviewed	NA|123aa|down_4|NZ_CP045931.1_1536225_1536594_-	PRK00070, acpS, 4'-phosphopantetheinyl transferase; Provisional	NA|344aa|down_5|NZ_CP045931.1_1536632_1537664_-	COG0722, AroG, 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]	NA|344aa|down_6|NZ_CP045931.1_1537665_1538697_-	COG0722, AroG, 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]	NA|838aa|down_7|NZ_CP045931.1_1538777_1541291_-	PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed	NA|76aa|down_8|NZ_CP045931.1_1541436_1541664_-	NA	NA|217aa|down_9|NZ_CP045931.1_1541734_1542385_-	cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A
GCF_009664475.1_ASM966447v1	NZ_CP045931	Streptococcus pneumoniae strain AUSMDU00010538 chromosome, complete genome	5	1642673-1642757	5	CRISPRCasFinder	no		cas3,DEDDh,PrimPol,DinG,RT	Orphan	CTTTTTTTGAAACGTTTCATTTTT	24	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,PrimPol,DinG,RT	NA|60aa|up_5|NZ_CP045931.1_1635201_1635381_-,NA	NA|361aa|up_9|NZ_CP045931.1_1632549_1633632_-	pfam02163, Peptidase_M50, Peptidase family M50	NA|157aa|up_8|NZ_CP045931.1_1633635_1634106_-	pfam11217, DUF3013, Protein of unknown function (DUF3013)	NA|151aa|up_7|NZ_CP045931.1_1634396_1634849_-	COG1598, COG1598, Predicted nuclease of the RNAse H fold, HicB family [General    function prediction only]	NA|69aa|up_6|NZ_CP045931.1_1634885_1635092_-	pfam07927, HicA_toxin, HicA toxin of bacterial toxin-antitoxin,	NA|60aa|up_5|NZ_CP045931.1_1635201_1635381_-	NA	NA|424aa|up_4|NZ_CP045931.1_1636053_1637325_+	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|440aa|up_3|NZ_CP045931.1_1637870_1639190_-	COG1621, SacC, Beta-fructosidases (levanase/invertase) [Carbohydrate transport and metabolism]	NA|539aa|up_2|NZ_CP045931.1_1639199_1640816_-	cd13581, PBP2_AlgQ_like_2, Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold	NA|297aa|up_1|NZ_CP045931.1_1640844_1641735_-	COG0395, UgpE, ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]	NA|306aa|up_0|NZ_CP045931.1_1641745_1642663_-	COG4209, LplB, ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]	NA|334aa|down_0|NZ_CP045931.1_1642813_1643815_-	COG1609, PurR, Transcriptional regulators [Transcription]	NA|494aa|down_1|NZ_CP045931.1_1644176_1645658_-	pfam08270, PRD_Mga, M protein trans-acting positive regulator (MGA) PRD domain	NA|55aa|down_2|NZ_CP045931.1_1646100_1646265_+	COG2261, COG2261, Predicted membrane protein [Function unknown]	NA|189aa|down_3|NZ_CP045931.1_1646348_1646915_+	NF033218, anchor_AmaP, alkaline shock response membrane anchor protein AmaP	NA|57aa|down_4|NZ_CP045931.1_1646926_1647097_+	COG5547, COG5547, Small integral membrane protein [Function unknown]	NA|203aa|down_5|NZ_CP045931.1_1647135_1647744_+	COG1302, COG1302, Uncharacterized protein conserved in bacteria [Function unknown]	NA|68aa|down_6|NZ_CP045931.1_1647774_1647978_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|96aa|down_7|NZ_CP045931.1_1648669_1648957_+	COG2826, Tra8, Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]	NA|257aa|down_8|NZ_CP045931.1_1649234_1650005_-	pfam01925, TauE, Sulfite exporter TauE/SafE	NA|106aa|down_9|NZ_CP045931.1_1651163_1651481_-	pfam02255, PTS_IIA, PTS system, Lactose/Cellobiose specific IIA subunit
