Origin IGS: gtgaaatgaagaatcagttctaagagctggttctttttattgaagaaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaataaaagaaataggtttttagaataaggagtggaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attccactccttattctaaaaacctatttcttttattctacactatttttctaaaatagcaagtatattttgtaattttcagaaaatttcttcaataaaaagaaccagctcttagaactgattcttcatttcac Mask Tandem Repeat Region ================================================ gtgaaatgaagaatcagttctaagagctggttctttttattgaagaaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaataaaagaaataggtttttagaataaggagtggaat Find is-nt database================================================ Query_seq: SMT_546:SMT_547|SMT_546:SMT_547:DNA topoisomerase IV subunit A:branched-chain amino acid aminotransferase:->->:463953..464086 134 gtgaaatgaagaatcagttctaagagctggttctttttattgaagaaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaataaaagaaataggtttttagaataaggagtggaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_546:SMT_547|SMT_546:SMT_547:DNA topoisomerase IV subunit A:branched-chain amino acid aminotransferase:->->:463953..464086 134 gtgaaatgaagaatcagttctaagagctggttctttttattgaagaaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaataaaagaaataggtttttagaataaggagtggaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_546:SMT_547|SMT_546:SMT_547:DNA topoisomerase IV subunit A:branched-chain amino acid aminotransferase:->->:463953..464086 134 gtgaaatgaagaatcagttctaagagctggttctttttattgaagaaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaataaaagaaataggtttttagaataaggagtggaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgaaatgaagaatcagttctaagagctggttctttttattgaagaaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaataaaagaaataggtttttagaataaggagtggaat Predict ORF larger than 30AA ================================================ gtgaaatgaagaatcagttctaagagctggttctttttattgaagaaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaataaaagaaataggtttttagaataaggagtggaat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtgaaatgaagaatcagttctaagagctggttctttttattgaagaaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaataaaagaaataggtttttagaataaggagtggaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_546:SMT_547|SMT_546:SMT_547:DNA topoisomerase IV subunit A:branched-chain amino acid aminotransferase:->->:463953..464086 134 gtgaaatgaagaatcagttctaagagctggttctttttattgaagaaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaataaaagaaataggtttttagaataaggagtggaat Intra-Species Hit: Count: 1 Min: 1 Max: 134 Len: 134 Subject: smit_SMT_546_SMT_547|DNA topoisomerase IV subunit A:branched-chain amino acid aminotransferase|POSITIVE:POSITIVE|[463953,464086]|134 HSP 1 e-value: 2.0E-70 bit: 266.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 134 gtgaaatgaagaatcagttctaagagctggttctttttattgaagaaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaataaaagaaataggtttttagaataaggagtggaat gtgaaatgaagaatcagttctaagagctggttctttttattgaagaaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaataaaagaaataggtttttagaataaggagtggaat Inter-species Hit: Count: 3 Min: 1 Max: 134 Len: 134 Subject: NC_003028_SP_0855_SP_0856|DNA topoisomerase IV subunit A:branched-chain amino acid aminotransferase|POSITIVE:POSITIVE|[803172,803302]|131 HSP 1 e-value: 5.0E-55 bit: 214.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 gtgaaatgaagaatcagttctaagagctggttctttttattgaagaaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaataaaagaaataggtttttagaataaggagtggaat gtgaaatgaagaatcagttctaagagttggtt---tttattggagaaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaatataagaaataggtttttagaataaggagtggaat Subject: NC_008533_SPD_0748_SPD_0749|DNA topoisomerase IV, A subunit:branched-chain amino acid aminotransferase|POSITIVE:POSITIVE|[762253,762381]|129 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 gtgaaatgaagaatcagttctaagagctggttctttttattgaagaaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaataaaagaaataggtttttagaataaggagtggaat gtgaaatgaagaatcagttctaaga--tgg---tttttattggaggaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaatataagaaataggtttttagaataaggagtggaat Subject: NC_003098_spr0757_spr0758|DNA topoisomerase IV subunit A:branched-chain amino acid aminotransferase|POSITIVE:POSITIVE|[754722,754850]|129 HSP 1 e-value: 2.0E-48 bit: 192.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 gtgaaatgaagaatcagttctaagagctggttctttttattgaagaaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaataaaagaaataggtttttagaataaggagtggaat gtgaaatgaagaatcagttctaaga--tgg---tttttattggaggaattttctgaaaattacaaaatatacttgctattttagaaaaatagtgtagaatataagaaataggtttttagaataaggagtggaat Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGAAAUGAAGAAUCAGUUCUAAGAGCUGGUUCUUUUUAUUGAAGAAAUUUUCUGAAAAUUACAAAAUAUACUUGCUAUUUUAGAAAAAUAGUGUAGAAUAAAAGAAAUAGGUUUUUAGAAUAAGGAGUGGAAU ((((...(((((((((((((...)))))))))))))(((..(((....)))..)))...))))......(((((..(((((((((((..((.................))..)))))))))))..))))).... (-27.53) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCCACUCCUUAUUCUAAAAACCUAUUUCUUUUAUUCUACACUAUUUUUCUAAAAUAGCAAGUAUAUUUUGUAAUUUUCAGAAAAUUUCUUCAAUAAAAAGAACCAGCUCUUAGAACUGAUUCUUCAUUUCAC .............((((((....((..(((((((............(((((((((((.(((((.....))))).))))).))))))...........)))))))..))...)))))).(((....)))...... (-16.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 228 56 16 43 3 smit:SMT_1787|5end_phosphoribosylformylglycinamidine_synthase_1764915..1765145_NEGATIVE 228 56 16 43 3 smit:SMT_1196|5end_phosphoribosylformylglycinamidine_synthase_1158637..1158867_NEGATIVE 224 59 13 171 123 smit:SMT_2082|5end_ATP-dependent_nuclease_subunit_B_1982286..1982516_NEGATIVE 218 59 11 215 164 smit:SMT_742|5end_hypothetical_protein_646818..647048_NEGATIVE 215 40 8 137 107 smit:SMT_1076|5end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_/_dihydroneopterin_aldolase_1014813..1015043_NEGATIVE 210 39 6 76 42 smit:SMT_1955|5end_carbamoyl-phosphate_synthase_small_chain_1889408..1889638_NEGATIVE 205 54 17 74 31 smit:SMT_2066|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1973105..1973335_POSITIVE 205 54 17 74 31 smit:SMT_1321|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1290674..1290904_POSITIVE 204 49 3 86 39 smit:SMT_1216|5end_hypothetical_protein_1174879..1175109_POSITIVE 204 43 2 88 37 smit:SMT_773|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase_684365..684595_NEGATIVE 202 78 31 177 122 smit:SMT_1594|5end_oligopeptide_transport_system_permease_protein_OppB_1583472..1583702_POSITIVE 201 45 11 207 181 smit:SMT_940|5end_tRNA_pseudouridine_synthase_A_892764..892994_NEGATIVE 198 61 23 128 83 smit:SMT_131|5end_phosphatase,_putative_83663..83893_NEGATIVE 196 48 1 130 64 smit:SMT_250|5end_site-specific_recombinase,_phage_integrase_family_185256..185486_NEGATIVE 195 128 81 221 178 smit:SMT_831|5end_transcriptional_activator,_putative_772791..773021_POSITIVE 195 33 6 111 83 smit:SMT_577|5end_transcriptional_regulator,_LysR_family_495324..495554_POSITIVE 194 35 6 210 173 smit:SMT_1085|5end_sensor_histidine_kinase_(homolog_to_HK11_Spn)_1022267..1022497_NEGATIVE 193 36 9 191 162 smit:SMT_1845|5end_K01191_alpha-mannosidase_1809663..1809893_POSITIVE 193 66 21 177 128 smit:SMT_1350|5end_multidrug_resistance_efflux_pump_1329225..1329455_NEGATIVE 193 36 9 191 162 smit:SMT_114|5end_alpha-mannosidase_62804..63034_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 41 5 91 50 smit:SMT_546|3end_DNA_topoisomerase_IV_subunit_A_463892..464042_POSITIVE 307 38 2 85 43 smit:SMT_271|3end_autoinducer-2_production_protein_211254..211404_NEGATIVE 253 39 9 86 59 smit:SMT_1147|3end_hypothetical_protein_1091203..1091353_NEGATIVE 239 41 1 95 60 smit:SMT_1146|3end_maltose_operon_transcriptional_repressor_1091202..1091352_POSITIVE 230 38 5 70 34 smit:SMT_270|3end_ATP-binding_subunit_of_Clp_protease_and_DnaK/DnaJ_chaperones_211225..211375_POSITIVE 215 40 8 94 64 smit:SMT_1077|3end_GTP_cyclohydrolase_I_1014856..1015006_NEGATIVE 213 54 13 151 112 smit:SMT_330|3end_membrane-associated_phospholipid_phosphatase_266187..266337_POSITIVE 210 129 89 66 18 smit:SMT_1290|3end_autolysin_1253753..1253903_POSITIVE 205 54 17 74 31 smit:SMT_2065|3end_transcriptional_regulator,_MarR_family_1973185..1973335_POSITIVE 205 54 17 74 31 smit:SMT_1320|3end_transcriptional_regulator,_MarR_family_1290754..1290904_POSITIVE 202 78 31 110 55 smit:SMT_1593|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1583485..1583635_POSITIVE 201 45 11 108 82 smit:SMT_941|3end_hypothetical_protein_892863..893013_NEGATIVE 200 52 14 56 10 smit:SMT_2108|3end_adenylosuccinate_lyase_1998744..1998894_NEGATIVE 199 55 16 56 18 smit:SMT_1950|3end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_1885069..1885219_POSITIVE 198 61 23 106 61 smit:SMT_132|3end_L-serine_dehydratase_alpha_subunit_83685..83835_NEGATIVE 195 33 6 114 86 smit:SMT_576|3end_transcriptional_regulator,_LysR_family_495407..495557_POSITIVE 193 36 9 92 63 smit:SMT_1844|3end_hypothetical_protein_1809644..1809794_POSITIVE 193 36 9 92 63 smit:SMT_113|3end_hypothetical_protein_62785..62935_POSITIVE 190 78 32 63 4 smit:SMT_1913|3end_RBL02035_1858765..1858915_POSITIVE 187 49 2 83 43 smit:SMT_631|3end_glycerate_kinase_537307..537457_POSITIVE