Origin IGS: tatatattgactttcaaaatatatagtgtataataatagtataaaataaagtagctaaaagattggggtgaaaattatggatgcttataaaaactataatagagaagaatttaatagaattttaaatggaaaaataacaagaaaattaataatcacagctactatattggctggattaggaatattgaataaaacactttaaaatttttaaattaaacaatagcaaaaaggaactatctaatagttcct .........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 aggaactattagatagttcctttttgctattgtttaatttaaaaattttaaagtgttttattcaatattcctaatccagccaatatagtagctgtgattattaattttcttgttatttttccatttaaaattctattaaattcttctctattatagtttttataagcatccataattttcaccccaatcttttagctactttattttatactattattatacactatatattttgaaagtcaatatata Mask Tandem Repeat Region ================================================ tatatattgactttcaaaatatatagtgtataataatagtataaaataaagtagctaaaagattggggtgaaaattatggatgcttataaaaactataatagagaagaatttaatagaattttaaatggaaaaataacaagaaaattaataatcacagctactatattggctggattaggaatattgaataaaacactttaaaatttttaaattaaacaatagcaaaaaggaactatctaatagttcct Find is-nt database================================================ Query_seq: FN1615:FN1616|FN1615:FN1616:Integral membrane protein:transcription antitermination protein NusB:-><-:125817..126065 249 tatatattgactttcaaaatatatagtgtataataatagtataaaataaagtagctaaaagattggggtgaaaattatggatgcttataaaaactataatagagaagaatttaatagaattttaaatggaaaaataacaagaaaattaataatcacagctactatattggctggattaggaatattgaataaaacactttaaaatttttaaattaaacaatagcaaaaaggaactatctaatagttcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1615:FN1616|FN1615:FN1616:Integral membrane protein:transcription antitermination protein NusB:-><-:125817..126065 249 tatatattgactttcaaaatatatagtgtataataatagtataaaataaagtagctaaaagattggggtgaaaattatggatgcttataaaaactataatagagaagaatttaatagaattttaaatggaaaaataacaagaaaattaataatcacagctactatattggctggattaggaatattgaataaaacactttaaaatttttaaattaaacaatagcaaaaaggaactatctaatagttcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1615:FN1616|FN1615:FN1616:Integral membrane protein:transcription antitermination protein NusB:-><-:125817..126065 249 tatatattgactttcaaaatatatagtgtataataatagtataaaataaagtagctaaaagattggggtgaaaattatggatgcttataaaaactataatagagaagaatttaatagaattttaaatggaaaaataacaagaaaattaataatcacagctactatattggctggattaggaatattgaataaaacactttaaaatttttaaattaaacaatagcaaaaaggaactatctaatagttcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatatattgactttcaaaatatatagtgtataataatagtataaaataaagtagctaaaagattggggtgaaaattatggatgcttataaaaactataatagagaagaatttaatagaattttaaatggaaaaataacaagaaaattaataatcacagctactatattggctggattaggaatattgaataaaacactttaaaatttttaaattaaacaatagcaaaaaggaactatctaatagttcct Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 62 End: 199 ............................................................. M G V K I M D A Y K N Y N R E E F N R I L N G K I T R K L I I T A T I L A G L G I L N K T L .................................................. Protein_Len: 33 Strand: - Start: 17 End: 115 ................ F I Y H I I I T Y F L T A L L N P H F N H I S I F V I I S F F K M ...................................................................................................................................... tatatattgactttcaaaatatatagtgtataataatagtataaaataaagtagctaaaagattggggtgaaaattatggatgcttataaaaactataatagagaagaatttaatagaattttaaatggaaaaataacaagaaaattaataatcacagctactatattggctggattaggaatattgaataaaacactttaaaatttttaaattaaacaatagcaaaaaggaactatctaatagttcct 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================================================ tatatattgactttcaaaatatatagtgtataataatagtataaaataaagtagctaaaagattggggtgaaaattatggatgcttataaaaactataatagagaagaatttaatagaattttaaatggaaaaataacaagaaaattaataatcacagctactatattggctggattaggaatattgaataaaacactttaaaatttttaaattaaacaatagcaaaaaggaactatctaatagttcct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1615:FN1616|FN1615:FN1616:Integral membrane protein:transcription antitermination protein NusB:-><-:125817..126065 249 tatatattgactttcaaaatatatagtgtataataatagtataaaataaagtagctaaaagattggggtgaaaattatggatgcttataaaaactataatagagaagaatttaatagaattttaaatggaaaaataacaagaaaattaataatcacagctactatattggctggattaggaatattgaataaaacactttaaaatttttaaattaaacaatagcaaaaaggaactatctaatagttcct Intra-Species Hit: Count: 1 Min: 1 Max: 249 Len: 249 Subject: NC_003454_FN1615_FN1616|Integral membrane protein:transcription antitermination protein NusB|POSITIVE:NEGATIVE|[125817,126065]|249 HSP 1 e-value: 1.0E-139 bit: 494.0 Len: 249 Query Start:1 Query End:249 Subject Strand: POSITIVE Subject Start: 1 Subject End: 249 tatatattgactttcaaaatatatagtgtataataatagtataaaataaagtagctaaaagattggggtgaaaattatggatgcttataaaaactataatagagaagaatttaatagaattttaaatggaaaaataacaagaaaattaataatcacagctactatattggctggattaggaatattgaataaaacactttaaaatttttaaattaaacaatagcaaaaaggaactatctaatagttcct tatatattgactttcaaaatatatagtgtataataatagtataaaataaagtagctaaaagattggggtgaaaattatggatgcttataaaaactataatagagaagaatttaatagaattttaaatggaaaaataacaagaaaattaataatcacagctactatattggctggattaggaatattgaataaaacactttaaaatttttaaattaaacaatagcaaaaaggaactatctaatagttcct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAUAUUGACUUUCAAAAUAUAUAGUGUAUAAUAAUAGUAUAAAAUAAAGUAGCUAAAAGAUUGGGGUGAAAAUUAUGGAUGCUUAUAAAAACUAUAAUAGAGAAGAAUUUAAUAGAAUUUUAAAUGGAAAAAUAACAAGAAAAUUAAUAAUCACAGCUACUAUAUUGGCUGGAUUAGGAAUAUUGAAUAAAACACUUUAAAAUUUUUAAAUUAAACAAUAGCAAAAAGGAACUAUCUAAUAGUUCCU ....(((((............((((((.((((.....(((((...((((....(((..........))).....))))..)))))))))...)))))).........(((((((..((((((((((((.........(((....(((..(((((.((((((......)))))))))))..))).))).......)).)))))))))))))))))...)))))......(((((((((...))))))))) (-41.39) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAACUAUUAGAUAGUUCCUUUUUGCUAUUGUUUAAUUUAAAAAUUUUAAAGUGUUUUAUUCAAUAUUCCUAAUCCAGCCAAUAUAGUAGCUGUGAUUAUUAAUUUUCUUGUUAUUUUUCCAUUUAAAAUUCUAUUAAAUUCUUCUCUAUUAUAGUUUUUAUAAGCAUCCAUAAUUUUCACCCCAAUCUUUUAGCUACUUUAUUUUAUACUAUUAUUAUACACUAUAUAUUUUGAAAGUCAAUAUAUA (((((((((...)))))))))......(((((.....(((((((....((.(((((..............((.....))..((((.(((((((((((..((((...................((((((.......))))))..............((((....)))).....))))..))))...........))))))).))))...............))))).))..)))))))...))))).... (-29.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 247 69 21 184 123 NC_003454:FN1199|5end_DNA_polymerase_IV_1859061..1859291_POSITIVE 235 95 54 128 78 NC_003454:FN1805|5end_hypothetical_protein_286453..286683_POSITIVE 223 52 12 229 190 NC_003454:FN0113|5end_Heat-inducible_transcription_repressor_hrcA_746557..746787_POSITIVE 201 180 139 59 16 NC_003454:FN0716|5end_Phophatidylinositol-4-phosphate_5-kinase_1373969..1374199_POSITIVE 195 108 64 64 25 NC_003454:FN0112|5end_hypothetical_protein_746353..746583_POSITIVE 194 55 11 142 98 NC_003454:FN0789|5end_Transporter_1445278..1445508_NEGATIVE 190 80 36 200 145 NC_003454:FN1280|5end_Endonuclease_1938442..1938672_POSITIVE 190 81 53 206 175 NC_003454:FN0808|5end_Phosphoglycerate_mutase_1467955..1468185_POSITIVE 183 80 32 189 134 NC_003454:FN1835|5end_hypothetical_protein_323680..323910_NEGATIVE 182 160 114 175 125 NC_003454:FN0317|5end_tryptophan_synthase_subunit_beta_955006..955236_NEGATIVE 181 138 95 110 68 NC_003454:FN1970|5end_Hemin-binding_periplasmic_protein_hmuT_precursor_469056..469286_NEGATIVE 180 193 159 53 24 NC_003454:FN1705|5end_hypothetical_protein_201673..201903_NEGATIVE 177 181 156 53 28 NC_003454:FN1640|5end_LSU_ribosomal_protein_L22P_138517..138747_NEGATIVE 172 114 77 42 8 NC_003454:FN1477|5end_Hypothetical_membrane-spanning_protein_2159504..2159734_POSITIVE 170 240 216 108 80 NC_003454:FN1155|5end_Cell_division_protein_ftsI_1809442..1809672_POSITIVE 169 69 23 56 10 NC_003454:FN1356|5end_hypothetical_protein_2007922..2008152_POSITIVE 169 69 23 56 10 NC_003454:FN0510|5end_hypothetical_protein_1160326..1160556_NEGATIVE 169 185 158 214 184 NC_003454:FN1868|5end_Hypothetical_cytosolic_protein_360433..360663_NEGATIVE 168 192 155 73 29 NC_003454:FN1800|5end_Peptidyl-prolyl_cis-trans_isomerase_281630..281860_POSITIVE 166 190 157 54 23 NC_003454:FN1138|5end_Hypothetical_cytosolic_protein_1785469..1785699_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 235 95 54 60 10 NC_003454:FN1804|3end_Aminoacyl-histidine_dipeptidase_286465..286615_POSITIVE 211 72 53 150 131 NC_003454:FN0388|3end_Tetracenomycin_polyketide_synthesis_O-methyltransferase_tcmP_1026600..1026750_NEGATIVE 206 87 58 103 67 NC_003454:FN1263|3end_Cobalt_chelatase_1919725..1919875_NEGATIVE 201 180 139 66 23 NC_003454:FN0715|3end_hypothetical_protein_1374056..1374206_POSITIVE 194 55 11 126 82 NC_003454:FN0790|3end_Xylose_repressor_1445294..1445444_NEGATIVE 185 73 34 59 12 NC_003454:FN0007|3end_glucose-inhibited_division_protein_A_647904..648054_POSITIVE 182 69 36 148 107 NC_003454:FN1615|3end_Integral_membrane_protein_125756..125906_POSITIVE 175 235 203 47 13 NC_003454:FN0702|3end_N-acyl-L-amino_acid_amidohydrolase_1360925..1361075_NEGATIVE 170 240 216 88 60 NC_003454:FN1154|3end_Ribonuclease_BN_1809502..1809652_POSITIVE 168 110 61 54 1 NC_003454:FN1509|3end_hypothetical_protein_14099..14249_NEGATIVE 163 197 161 59 22 NC_003454:FN0493|3end_hypothetical_protein_1137623..1137773_NEGATIVE 162 81 50 82 55 NC_003454:FN0027|3end_hypothetical_protein_664763..664913_NEGATIVE 159 198 159 150 108 NC_003454:FN1646|3end_SSU_ribosomal_protein_S10P_141449..141599_NEGATIVE 158 49 3 54 1 NC_003454:FN0349|3end_D-tyrosyl-tRNA_deacylase_982336..982486_POSITIVE 157 182 145 97 64 NC_003454:FN1859|3end_Major_outer_membrane_protein_348549..348699_NEGATIVE 154 185 153 128 95 NC_003454:FN1398|3end_Amino_acid_carrier_protein_alsT_2054300..2054450_POSITIVE 154 69 23 48 5 NC_003454:FN1704|3end_Serine_protease_201497..201647_POSITIVE 153 186 155 59 25 NC_003454:FN1897|3end_ABC_transporter_integral_membrane_protein_383965..384115_NEGATIVE 153 180 150 68 36 NC_003454:FN1595|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_B_104883..105033_NEGATIVE 151 78 50 87 62 NC_003454:FN1039|3end_Branched-chain_amino_acid_transport_protein_azlC_1691829..1691979_POSITIVE