Origin IGS: taataaataaaaatcctattagtttaggattttttttatttataaattttaaataaattcataatatttataattactatatataatatatatcatatatagtttgaataaaaattatcctaaaatagattaaaattttatcgttttttaaataatttaagttgctttttaattaaaactagactattatgtatttaagataaagttttattagccaacaaaacctaaaaatttaacgatttctatttatggaggtagattttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaatctacctccataaatagaaatcgttaaatttttaggttttgttggctaataaaactttatcttaaatacataatagtctagttttaattaaaaagcaacttaaattatttaaaaaacgataaaattttaatctattttaggataatttttattcaaactatatatgatatatattatatatagtaattataaatattatgaatttatttaaaatttataaataaaaaaaatcctaaactaataggatttttatttatta Mask Tandem Repeat Region ================================================ taataaataaaaatcctattagtttaggattttttttatttataaattttaaataaattcataatatttataattactatatataatatatatcatatatagtttgaataaaaattatcctaaaatagattaaaattttatcgttttttaaataatttaagttgctttttaattaaaactagactattatgtatttaagataaagttttattagccaacaaaacctaaaaatttaacgatttctatttatggaggtagattttt Find is-nt database================================================ Query_seq: FN1119:FN1120|FN1119:FN1120:50S ribosomal protein L27:phosphoenolpyruvate carboxykinase:->->:1761314..1761577 264 taataaataaaaatcctattagtttaggattttttttatttataaattttaaataaattcataatatttataattactatatataatatatatcatatatagtttgaataaaaattatcctaaaatagattaaaattttatcgttttttaaataatttaagttgctttttaattaaaactagactattatgtatttaagataaagttttattagccaacaaaacctaaaaatttaacgatttctatttatggaggtagattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1119:FN1120|FN1119:FN1120:50S ribosomal protein L27:phosphoenolpyruvate carboxykinase:->->:1761314..1761577 264 taataaataaaaatcctattagtttaggattttttttatttataaattttaaataaattcataatatttataattactatatataatatatatcatatatagtttgaataaaaattatcctaaaatagattaaaattttatcgttttttaaataatttaagttgctttttaattaaaactagactattatgtatttaagataaagttttattagccaacaaaacctaaaaatttaacgatttctatttatggaggtagattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1119:FN1120|FN1119:FN1120:50S ribosomal protein L27:phosphoenolpyruvate carboxykinase:->->:1761314..1761577 264 taataaataaaaatcctattagtttaggattttttttatttataaattttaaataaattcataatatttataattactatatataatatatatcatatatagtttgaataaaaattatcctaaaatagattaaaattttatcgttttttaaataatttaagttgctttttaattaaaactagactattatgtatttaagataaagttttattagccaacaaaacctaaaaatttaacgatttctatttatggaggtagattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taataaataaaaatcctattagtttaggattttttttatttataaattttaaataaattcataatatttataattactatatataatatatatcatatatagtttgaataaaaattatcctaaaatagattaaaattttatcgttttttaaataatttaagttgctttttaattaaaactagactattatgtatttaagataaagttttattagccaacaaaacctaaaaatttaacgatttctatttatggaggtagattttt Predict ORF larger than 30AA ================================================ taataaataaaaatcctattagtttaggattttttttatttataaattttaaataaattcataatatttataattactatatataatatatatcatatatagtttgaataaaaattatcctaaaatagattaaaattttatcgttttttaaataatttaagttgctttttaattaaaactagactattatgtatttaagataaagttttattagccaacaaaacctaaaaatttaacgatttctatttatggaggtagattttt 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: 82 Start: 161 End: 190 ................................................................................................................................................................GTTGCTTTTTAATTAAAACTAGACTATTAT.......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taataaataaaaatcctattagtttaggattttttttatttataaattttaaataaattcataatatttataattactatatataatatatatcatatatagtttgaataaaaattatcctaaaatagattaaaattttatcgttttttaaataatttaagttgctttttaattaaaactagactattatgtatttaagataaagttttattagccaacaaaacctaaaaatttaacgatttctatttatggaggtagattttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1119:FN1120|FN1119:FN1120:50S ribosomal protein L27:phosphoenolpyruvate carboxykinase:->->:1761314..1761577 264 taataaataaaaatcctattagtttaggattttttttatttataaattttaaataaattcataatatttataattactatatataatatatatcatatatagtttgaataaaaattatcctaaaatagattaaaattttatcgttttttaaataatttaagttgctttttaattaaaactagactattatgtatttaagataaagttttattagccaacaaaacctaaaaatttaacgatttctatttatggaggtagattttt Intra-Species Hit: Count: 1 Min: 1 Max: 264 Len: 264 Subject: NC_003454_FN1119_FN1120|50S ribosomal protein L27:phosphoenolpyruvate carboxykinase|POSITIVE:POSITIVE|[1761314,1761577]|264 HSP 1 e-value: 2.0E-41 bit: 170.0 Len: 86 Query Start:179 Query End:264 Subject Strand: POSITIVE Subject Start: 179 Subject End: 264 ..................................................................................................................................................................................ctagactattatgtatttaagataaagttttattagccaacaaaacctaaaaatttaacgatttctatttatggaggtagattttt ..................................................................................................................................................................................ctagactattatgtatttaagataaagttttattagccaacaaaacctaaaaatttaacgatttctatttatggaggtagattttt HSP 2 e-value: 6.0E-7 bit: 56.0 Len: 28 Query Start:1 Query End:28 Subject Strand: POSITIVE Subject Start: 1 Subject End: 28 taataaataaaaatcctattagtttagg............................................................................................................................................................................................................................................ taataaataaaaatcctattagtttagg............................................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUAAAUAAAAAUCCUAUUAGUUUAGGAUUUUUUUUAUUUAUAAAUUUUAAAUAAAUUCAUAAUAUUUAUAAUUACUAUAUAUAAUAUAUAUCAUAUAUAGUUUGAAUAAAAAUUAUCCUAAAAUAGAUUAAAAUUUUAUCGUUUUUUAAAUAAUUUAAGUUGCUUUUUAAUUAAAACUAGACUAUUAUGUAUUUAAGAUAAAGUUUUAUUAGCCAACAAAACCUAAAAAUUUAACGAUUUCUAUUUAUGGAGGUAGAUUUUU ..(((((((.(((((...(((.((((((((..((((((((((..........((((((.......))))))....(((((((((.((....)).))))))))).))))))))))..)))))))).)))..((((((((((((.....(((((((.....((((..((((.....))))...))))......)))))))))))))))))))...........................))))).))))))).............. (-42.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUCUACCUCCAUAAAUAGAAAUCGUUAAAUUUUUAGGUUUUGUUGGCUAAUAAAACUUUAUCUUAAAUACAUAAUAGUCUAGUUUUAAUUAAAAAGCAACUUAAAUUAUUUAAAAAACGAUAAAAUUUUAAUCUAUUUUAGGAUAAUUUUUAUUCAAACUAUAUAUGAUAUAUAUUAUAUAUAGUAAUUAUAAAUAUUAUGAAUUUAUUUAAAAUUUAUAAAUAAAAAAAAUCCUAAACUAAUAGGAUUUUUAUUUAUUA ..............(((((((((((((.((((((.(((((((..((((...((((((((((....((............))...)))))).))))...)))))))))))..))))))...................((((((((((((..((((((.....((((((((((((....))))))))))))...........((((((((((.....)))))))))).))))))..)))))))...)))))))))))))))))).. (-47.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 209 187 141 58 12 NC_003454:FN1913|5end_hydrolase_(HD_superfamily)_411580..411810_NEGATIVE 205 127 82 223 181 NC_003454:FN0821|5end_hypothetical_protein_1480859..1481089_POSITIVE 194 248 207 129 98 NC_003454:FN1755|5end_thiamine_biosynthesis_protein_ThiF_251737..251967_NEGATIVE 184 105 64 168 120 NC_003454:FN0818|5end_DNA-binding_protein_HU_1477034..1477264_NEGATIVE 184 51 13 135 95 NC_003454:FN0040|5end_asparaginyl-tRNA_synthetase_680609..680839_NEGATIVE 180 227 181 128 81 NC_003454:FN1789|5end_Na+_driven_multidrug_efflux_pump_270120..270350_POSITIVE 179 210 163 57 4 NC_003454:FN0190|5end_Two-component_sensor_kinase_yesM_813975..814205_POSITIVE 177 159 111 130 93 NC_003454:FN1664|5end_hypothetical_protein_162115..162345_POSITIVE 175 39 16 63 40 NC_003454:FN0319|5end_Citrate_(pro-3S)-lyase_ligase_956855..957085_NEGATIVE 175 150 107 105 60 NC_003454:FN2120|5end_Hypothetical_exported_24-amino_acid_repeat_protein_628930..629160_NEGATIVE 171 49 12 231 188 NC_003454:FN0815|5end_Propionate_permease_1474390..1474620_POSITIVE 171 250 209 219 186 NC_003454:FN0639|5end_hypothetical_protein_1297427..1297657_NEGATIVE 169 226 181 164 112 NC_003454:FN1293|5end_hypothetical_protein_1952147..1952377_NEGATIVE 168 229 181 215 156 NC_003454:FN0590|5end_N-acyl-L-amino_acid_amidohydrolase_1244037..1244267_NEGATIVE 168 245 202 208 179 NC_003454:FN1733|5end_ATP_synthase_subunit_D_232871..233101_NEGATIVE 165 195 160 136 90 NC_003454:FN0858|5end_4-alpha-glucanotransferase_1520507..1520737_NEGATIVE 163 210 164 68 36 NC_003454:FN0873|5end_Protease_IV_1534187..1534417_NEGATIVE 163 44 9 167 132 NC_003454:FN0833|5end_hypothetical_protein_1494853..1495083_POSITIVE 163 151 114 148 116 NC_003454:FN2071|5end_hypothetical_protein_582375..582605_NEGATIVE 161 51 11 150 107 NC_003454:FN0933|5end_3-phosphoshikimate_1-carboxyvinyltransferase_1585182..1585412_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 205 127 82 103 61 NC_003454:FN0820|3end_Mercuric_reductase_1480819..1480969_POSITIVE 195 40 2 89 51 NC_003454:FN1119|3end_50S_ribosomal_protein_L27_1761253..1761403_POSITIVE 194 248 207 125 94 NC_003454:FN1756|3end_ThiS_protein_251741..251891_NEGATIVE 191 51 12 146 101 NC_003454:FN0814|3end_Propionate_CoA-transferase_1474383..1474533_POSITIVE 184 51 13 125 85 NC_003454:FN0041|3end_hypothetical_protein_680619..680769_NEGATIVE 179 210 163 70 17 NC_003454:FN0189|3end_Two-component_response_regulator_yesN_814068..814218_POSITIVE 177 259 215 80 36 NC_003454:FN1680|3end_Transposase_175971..176121_NEGATIVE 175 76 31 122 68 NC_003454:FN1624|3end_preprotein_translocase_SecY_131080..131230_NEGATIVE 163 44 9 83 48 NC_003454:FN0832|3end_hypothetical_protein_1494849..1494999_POSITIVE 163 42 7 113 78 NC_003454:FN0164|3end_Anhydro-N-acetylmuramyl-tripeptide_amidase_793291..793441_POSITIVE 161 51 11 149 106 NC_003454:FN0932|3end_hypothetical_protein_1585261..1585411_POSITIVE 160 259 216 138 102 NC_003454:FN0400|3end_Dipeptide_transport_ATP-binding_protein_dppF_1039700..1039850_POSITIVE 159 96 57 52 17 NC_003454:FN0111|3end_hypothetical_protein_746155..746305_NEGATIVE 158 50 3 115 60 NC_003454:FN0347|3end_phosphatidylserine_decarboxylase_979254..979404_NEGATIVE 158 42 5 73 36 NC_003454:FN0191|3end_ATP-dependent_DNA_helicase_recG_817265..817415_POSITIVE 156 260 214 69 24 NC_003454:FN0681|3end_Transcriptional_regulator,_MarR_family_1336872..1337022_POSITIVE 156 257 223 142 97 NC_003454:FN0287|3end_Dimethyladenosine_transferase_914434..914584_NEGATIVE 156 50 5 92 47 NC_003454:FN0190|3end_Two-component_sensor_kinase_yesM_815713..815863_POSITIVE 156 243 206 81 39 NC_003454:FN2029|3end_O-antigen_acetylase_532049..532199_NEGATIVE 156 259 215 57 18 NC_003454:FN1747|3end_Cysteine_permease_247262..247412_POSITIVE