Origin IGS: gtaaggataaaatctagaaagttaatgcaaacctttgcataaatgagtgaattttgttatactagtactgtaagcattttcaattaattcataattaaaaaggagaatatg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 catattctcctttttaattatgaattaattgaaaatgcttacagtactagtataacaaaattcactcatttatgcaaaggtttgcattaactttctagattttatccttac Mask Tandem Repeat Region ================================================ gtaaggataaaatctagaaagttaatgcaaacctttgcataaatgagtgaattttgttatactagtactgtaagcattttcaattaattcataattaaaaaggagaatatg Find is-nt database================================================ Query_seq: SMT_409:SMT_410|SMT_409:SMT_410:pneumococcal surface protein, putative:glucokinase:->->:354467..354577 111 gtaaggataaaatctagaaagttaatgcaaacctttgcataaatgagtgaattttgttatactagtactgtaagcattttcaattaattcataattaaaaaggagaatatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_409:SMT_410|SMT_409:SMT_410:pneumococcal surface protein, putative:glucokinase:->->:354467..354577 111 gtaaggataaaatctagaaagttaatgcaaacctttgcataaatgagtgaattttgttatactagtactgtaagcattttcaattaattcataattaaaaaggagaatatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_409:SMT_410|SMT_409:SMT_410:pneumococcal surface protein, putative:glucokinase:->->:354467..354577 111 gtaaggataaaatctagaaagttaatgcaaacctttgcataaatgagtgaattttgttatactagtactgtaagcattttcaattaattcataattaaaaaggagaatatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtaaggataaaatctagaaagttaatgcaaacctttgcataaatgagtgaattttgttatactagtactgtaagcattttcaattaattcataattaaaaaggagaatatg Predict ORF larger than 30AA ================================================ gtaaggataaaatctagaaagttaatgcaaacctttgcataaatgagtgaattttgttatactagtactgtaagcattttcaattaattcataattaaaaaggagaatatg Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 34 End: 63 .................................TTTGCATAAATGAGTGAATTTTGTTATACT................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtaaggataaaatctagaaagttaatgcaaacctttgcataaatgagtgaattttgttatactagtactgtaagcattttcaattaattcataattaaaaaggagaatatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_409:SMT_410|SMT_409:SMT_410:pneumococcal surface protein, putative:glucokinase:->->:354467..354577 111 gtaaggataaaatctagaaagttaatgcaaacctttgcataaatgagtgaattttgttatactagtactgtaagcattttcaattaattcataattaaaaaggagaatatg Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: smit_SMT_409_SMT_410|pneumococcal surface protein, putative:glucokinase|POSITIVE:POSITIVE|[354467, 354577]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 gtaaggataaaatctagaaagttaatgcaaacctttgcataaatgagtgaattttgttatactagtactgtaagcattttcaattaattcataattaaaaaggagaatatg gtaaggataaaatctagaaagttaatgcaaacctttgcataaatgagtgaattttgttatactagtactgtaagcattttcaattaattcataattaaaaaggagaatatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAGGAUAAAAUCUAGAAAGUUAAUGCAAACCUUUGCAUAAAUGAGUGAAUUUUGUUAUACUAGUACUGUAAGCAUUUUCAAUUAAUUCAUAAUUAAAAAGGAGAAUAUG (((..((((((((.......(((.((((((....)))))).)))......)))))))).))).............((((((..(((((.....)))))....))))))... (-13.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUAUUCUCCUUUUUAAUUAUGAAUUAAUUGAAAAUGCUUACAGUACUAGUAUAACAAAAUUCACUCAUUUAUGCAAAGGUUUGCAUUAACUUUCUAGAUUUUAUCCUUAC ..........((((((((((.....)))))))))).....................((((((.........((((((....))))))..........))))))........ (-10.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 224 43 1 184 143 smit:SMT_404|5end_hypothetical_protein_333386..333616_POSITIVE 211 79 36 60 17 smit:SMT_1099|5end_protein_tyrosine_phosphatase_1042241..1042471_NEGATIVE 206 49 3 202 154 smit:SMT_272|5end_hypothetical_protein_213315..213545_NEGATIVE 204 68 26 119 59 smit:SMT_629|5end_glycogen_synthase_533967..534197_POSITIVE 203 76 48 65 31 smit:SMT_2121|5end_putative_mucus_binding_protein_2007145..2007375_NEGATIVE 202 75 33 145 100 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 196 76 32 66 4 smit:SMT_1221|5end_choline_binding_protein_A_1185539..1185769_NEGATIVE 195 66 21 88 45 smit:SMT_1824|5end_hypothetical_protein_1796126..1796356_POSITIVE 194 76 37 148 104 smit:SMT_2009|5end_GtrA_family_protein_1928973..1929203_POSITIVE 192 89 44 149 105 smit:SMT_405|5end_zinc_metalloprotease_ZmpB,_truncated_333952..334182_POSITIVE 185 78 31 73 17 smit:SMT_1375|5end_putative_glucose-inhibited_division_protein_1354438..1354668_NEGATIVE 184 48 5 215 167 smit:SMT_2008|5end_K07485_transposase_1928662..1928892_NEGATIVE 184 48 5 84 36 smit:SMT_2005|5end_pullulanase,_type_I_1926289..1926519_NEGATIVE 184 48 5 178 130 smit:SMT_1967|5end_dicarboxylate/amino_acid:cation_(Na+_or_H+)_symporter_(DAACS)_family_protein_1899683..1899913_NEGATIVE 184 48 5 178 130 smit:SMT_1955|5end_carbamoyl-phosphate_synthase_small_chain_1889408..1889638_NEGATIVE 184 48 5 222 174 smit:SMT_1954|5end_6-phospho-beta-glucosidase_1888548..1888778_POSITIVE 184 48 5 213 165 smit:SMT_1944|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1879494..1879724_NEGATIVE 184 48 5 178 130 smit:SMT_1690|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1674779..1675009_NEGATIVE 184 48 5 227 179 smit:SMT_1155|5end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1099665..1099895_NEGATIVE 184 48 5 178 130 smit:SMT_779|5end_ribonuclease_BN,_putative_688530..688760_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 224 43 1 69 28 smit:SMT_403|3end_two-component_sensor_kinase_YesM_333351..333501_POSITIVE 204 68 26 122 62 smit:SMT_628|3end_glucose-1-phosphate_adenylyltransferase,_GlgD_subunit_534050..534200_POSITIVE 202 75 33 143 98 smit:SMT_1693|3end_dimethyladenosine_transferase_1676752..1676902_POSITIVE 192 89 44 146 102 smit:SMT_404|3end_hypothetical_protein_334029..334179_POSITIVE 188 76 32 48 16 smit:SMT_2049|3end_3-oxoacyl-_1958736..1958886_NEGATIVE 187 76 31 73 13 smit:SMT_1210|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1170959..1171109_NEGATIVE 184 48 5 49 1 smit:SMT_1956|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1889537..1889687_NEGATIVE 176 91 55 85 49 smit:SMT_85|3end_hypothetical_protein_predicted_by_Glimmer/Critica_16630..16780_NEGATIVE 171 50 17 53 23 smit:SMT_846|3end_hypothetical_protein_791855..792005_NEGATIVE 171 69 38 30 5 smit:SMT_828|3end_surface_protein_Rib_751186..751336_NEGATIVE 170 48 25 44 22 smit:SMT_387|3end_hypothetical_protein_predicted_by_Glimmer/Critica_321118..321268_POSITIVE 169 76 32 74 30 smit:SMT_1538|3end_two-component_response_regulator_YvqC_1522669..1522819_NEGATIVE 167 107 80 35 8 smit:SMT_405|3end_zinc_metalloprotease_ZmpB,_truncated_339938..340088_POSITIVE 166 105 61 62 17 smit:SMT_1473|3end_hypothetical_protein_1455119..1455269_POSITIVE 165 69 27 62 12 smit:SMT_1428|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1414269..1414419_NEGATIVE 162 75 45 33 7 smit:SMT_915|3end_sucrose_operon_repressor_868619..868769_POSITIVE 160 82 42 140 109 smit:SMT_208|3end_leucyl-tRNA_synthetase_142558..142708_POSITIVE 159 95 62 79 46 smit:SMT_1733|3end_DNA_repair_protein_RecN_1718636..1718786_POSITIVE 159 54 11 147 93 smit:SMT_640|3end_PTS_system,_lactose-specific_IIBC_component_545099..545249_NEGATIVE 157 106 66 68 20 smit:SMT_1081|3end_K06901_putative_MFS_transporter,_AGZA_family,_xanthine/uracil_permease_1018595..1018745_NEGATIVE