Origin IGS: aatttacccctttaactttttattttttattgtccaatatttttaaaaataaatcaagtaatttttaggcttaaatttgacaagtaacaattaatatactatactttataatgataaattttatcttaaaaataaaaatgaggacaaaattggagataattcttaagagcaaaatttagaactaagttacaaagagggtttaatagttgggggagacataaaaatagtacaacaaactattaaaaaaaacttaaacaatactaaaaacaaaatcagattaaacaaaattattaaagtattagttaacttaggaggcagaaaatgaaaaagaaattatttggtgttttattattttca .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaaaataataaaacaccaaataatttctttttcattttctgcctcctaagttaactaatactttaataattttgtttaatctgattttgtttttagtattgtttaagttttttttaatagtttgttgtactatttttatgtctcccccaactattaaaccctctttgtaacttagttctaaattttgctcttaagaattatctccaattttgtcctcatttttatttttaagataaaatttatcattataaagtatagtatattaattgttacttgtcaaatttaagcctaaaaattacttgatttatttttaaaaatattggacaataaaaaataaaaagttaaaggggtaaatt Mask Tandem Repeat Region ================================================ aatttacccctttaactttttattttttattgtccaatatttttaaaaataaatcaagtaatttttaggcttaaatttgacaagtaacaattaatatactatactttataatgataaattttatcttaaaaataaaaatgaggacaaaattggagataattcttaagagcaaaatttagaactaagttacaaagagggtttaatagttgggggagacataaaaatagtacaacaaactattaaaaaaaacttaaacaatactaaaaacaaaatcagattaaacaaaattattaaagtattagttaacttaggaggcagaaaatgaaaaagaaattatttggtgttttattattttca Find is-nt database================================================ Query_seq: FN0048:FN0049|FN0048:FN0049:4-nitrophenylphosphatase:hypothetical protein:<-->:686134..686490 357 aatttacccctttaactttttattttttattgtccaatatttttaaaaataaatcaagtaatttttaggcttaaatttgacaagtaacaattaatatactatactttataatgataaattttatcttaaaaataaaaatgaggacaaaattggagataattcttaagagcaaaatttagaactaagttacaaagagggtttaatagttgggggagacataaaaatagtacaacaaactattaaaaaaaacttaaacaatactaaaaacaaaatcagattaaacaaaattattaaagtattagttaacttaggaggcagaaaatgaaaaagaaattatttggtgttttattattttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0048:FN0049|FN0048:FN0049:4-nitrophenylphosphatase:hypothetical protein:<-->:686134..686490 357 aatttacccctttaactttttattttttattgtccaatatttttaaaaataaatcaagtaatttttaggcttaaatttgacaagtaacaattaatatactatactttataatgataaattttatcttaaaaataaaaatgaggacaaaattggagataattcttaagagcaaaatttagaactaagttacaaagagggtttaatagttgggggagacataaaaatagtacaacaaactattaaaaaaaacttaaacaatactaaaaacaaaatcagattaaacaaaattattaaagtattagttaacttaggaggcagaaaatgaaaaagaaattatttggtgttttattattttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0048:FN0049|FN0048:FN0049:4-nitrophenylphosphatase:hypothetical protein:<-->:686134..686490 357 aatttacccctttaactttttattttttattgtccaatatttttaaaaataaatcaagtaatttttaggcttaaatttgacaagtaacaattaatatactatactttataatgataaattttatcttaaaaataaaaatgaggacaaaattggagataattcttaagagcaaaatttagaactaagttacaaagagggtttaatagttgggggagacataaaaatagtacaacaaactattaaaaaaaacttaaacaatactaaaaacaaaatcagattaaacaaaattattaaagtattagttaacttaggaggcagaaaatgaaaaagaaattatttggtgttttattattttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatttacccctttaactttttattttttattgtccaatatttttaaaaataaatcaagtaatttttaggcttaaatttgacaagtaacaattaatatactatactttataatgataaattttatcttaaaaataaaaatgaggacaaaattggagataattcttaagagcaaaatttagaactaagttacaaagagggtttaatagttgggggagacataaaaatagtacaacaaactattaaaaaaaacttaaacaatactaaaaacaaaatcagattaaacaaaattattaaagtattagttaacttaggaggcagaaaatgaaaaagaaattatttggtgttttattattttca Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 203 End: 322 .......................................................................................................................................................................................................... M V G G D I K I V Q Q T I K K N L N N T K N K I R L N K I I K V L V N L G G R K ................................... Protein_Len: 43 Strand: - Start: 190 End: 318 ............................................................................................................................................................................................. L S P K I T P P S M F I T C C V I L F F K F L V L F L I L N F L I I L T N T L K P P M ....................................... Protein_Len: 34 Strand: - Start: 74 End: 175 ......................................................................... I Q C T V I L I S Y K I I I F K I K F I F I L V F N S I I R L L L M ...................................................................................................................................................................................... aatttacccctttaactttttattttttattgtccaatatttttaaaaataaatcaagtaatttttaggcttaaatttgacaagtaacaattaatatactatactttataatgataaattttatcttaaaaataaaaatgaggacaaaattggagataattcttaagagcaaaatttagaactaagttacaaagagggtttaatagttgggggagacataaaaatagtacaacaaactattaaaaaaaacttaaacaatactaaaaacaaaatcagattaaacaaaattattaaagtattagttaacttaggaggcagaaaatgaaaaagaaattatttggtgttttattattttca 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: 86 Start: 76 End: 105 ...........................................................................TTTGACAAGTAACAATTAATATACTATACT............................................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 83 End: 112 ..................................................................................AGTAACAATTAATATACTATACTTTATAAT..................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatttacccctttaactttttattttttattgtccaatatttttaaaaataaatcaagtaatttttaggcttaaatttgacaagtaacaattaatatactatactttataatgataaattttatcttaaaaataaaaatgaggacaaaattggagataattcttaagagcaaaatttagaactaagttacaaagagggtttaatagttgggggagacataaaaatagtacaacaaactattaaaaaaaacttaaacaatactaaaaacaaaatcagattaaacaaaattattaaagtattagttaacttaggaggcagaaaatgaaaaagaaattatttggtgttttattattttca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0048:FN0049|FN0048:FN0049:4-nitrophenylphosphatase:hypothetical protein:<-->:686134..686490 357 aatttacccctttaactttttattttttattgtccaatatttttaaaaataaatcaagtaatttttaggcttaaatttgacaagtaacaattaatatactatactttataatgataaattttatcttaaaaataaaaatgaggacaaaattggagataattcttaagagcaaaatttagaactaagttacaaagagggtttaatagttgggggagacataaaaatagtacaacaaactattaaaaaaaacttaaacaatactaaaaacaaaatcagattaaacaaaattattaaagtattagttaacttaggaggcagaaaatgaaaaagaaattatttggtgttttattattttca Intra-Species Hit: Count: 1 Min: 79 Max: 357 Len: 279 Subject: NC_003454_FN0048_FN0049|4-nitrophenylphosphatase:hypothetical protein|NEGATIVE:POSITIVE|[686134,686490]|357 HSP 1 e-value: 3.0E-74 bit: 280.0 Len: 141 Query Start:79 Query End:219 Subject Strand: POSITIVE Subject Start: 79 Subject End: 219 ..............................................................................gacaagtaacaattaatatactatactttataatgataaattttatcttaaaaataaaaatgaggacaaaattggagataattcttaagagcaaaatttagaactaagttacaaagagggtttaatagttgggggagacat.......................................................................................................................................... ..............................................................................gacaagtaacaattaatatactatactttataatgataaattttatcttaaaaataaaaatgaggacaaaattggagataattcttaagagcaaaatttagaactaagttacaaagagggtttaatagttgggggagacat.......................................................................................................................................... HSP 2 e-value: 4.0E-27 bit: 123.0 Len: 62 Query Start:296 Query End:357 Subject Strand: POSITIVE Subject Start: 296 Subject End: 357 .......................................................................................................................................................................................................................................................................................................gtattagttaacttaggaggcagaaaatgaaaaagaaattatttggtgttttattattttca .......................................................................................................................................................................................................................................................................................................gtattagttaacttaggaggcagaaaatgaaaaagaaattatttggtgttttattattttca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAAGUAACAAUUAAUAUACUAUACUUUAUAAUGAUAAAUUUUAUCUUAAAAAUAAAAAUGAGGACAAAAUUGGAGAUAAUUCUUAAGAGCAAAAUUUAGAACUAAGUUACAAAGAGGGUUUAAUAGUUGGGGGAGACAUAAAAAUAGUACAACAAACUAUUAAAAAAAACUUAAACAAUACUAAAAACAAAAUCAGAUUAAACAAAAUUAUUAAAGUAUUAGUUAACUUAGGAGGCAGAAAAUGAAAAAGAAAUUAUUUGGUGUUUUAUUAUUUUCA .............(((((....(((((..(((((..((((((((.((((((.(((.....(((........)))......))).))))))..))))))))...((((((((.......(.((((((((((..((....).....((((((.......)))))).........................................)..)))))))))).)......)))))))).....................)))))..)))))..)))))...... (-33.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAAUAAUAAAACACCAAAUAAUUUCUUUUUCAUUUUCUGCCUCCUAAGUUAACUAAUACUUUAAUAAUUUUGUUUAAUCUGAUUUUGUUUUUAGUAUUGUUUAAGUUUUUUUUAAUAGUUUGUUGUACUAUUUUUAUGUCUCCCCCAACUAUUAAACCCUCUUUGUAACUUAGUUCUAAAUUUUGCUCUUAAGAAUUAUCUCCAAUUUUGUCCUCAUUUUUAUUUUUAAGAUAAAAUUUAUCAUUAUAAAGUAUAGUAUAUUAAUUGUUACUUGUC ((((((.......................)))))).............((.((((.(((((((..(((((..((.........))..)))))...))))))).)))).)).....((((((((...(((((((((((((((........(((((....((.......))....))))).(((((((((.((((((((((.........................)))))))))))))))))))....))))))).))))))))..))))))))...... (-34.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 607 50 1 219 170 NC_003454:FN0048|5end_4-nitrophenylphosphatase_686043..686273_NEGATIVE 227 137 96 160 115 NC_003454:FN0664|5end_2-nitropropane_dioxygenase_1319758..1319988_POSITIVE 213 120 71 222 158 NC_003454:FN1256|5end_C4-dicarboxylate_transporter_large_subunit_1913206..1913436_NEGATIVE 208 130 90 39 2 NC_003454:FN1820|5end_Export_ABC_transporter_309245..309475_POSITIVE 207 237 197 143 106 NC_003454:FN1021|5end_Calcium-transporting_ATPase_1674588..1674818_POSITIVE 204 149 104 205 154 NC_003454:FN1790|5end_Cob(I)alamin_adenosyltransferase_271511..271741_POSITIVE 193 153 115 149 106 NC_003454:FN0140|5end_Transposase_772997..773227_NEGATIVE 193 153 115 149 106 NC_003454:FN1676|5end_Transposase_172739..172969_POSITIVE 191 138 94 221 159 NC_003454:FN1060|5end_Molybdate_metabolism_regulator_1707796..1708026_NEGATIVE 191 140 97 204 162 NC_003454:FN1581|5end_DNA_mismatch_repair_protein_mutS_93231..93461_NEGATIVE 189 268 223 71 20 NC_003454:FN0023|5end_Short-chain_fatty_acids_transporter_661201..661431_POSITIVE 185 140 103 68 24 NC_003454:FN0127|5end_Fe-S_oxidoreductase_756312..756542_NEGATIVE 185 138 91 160 113 NC_003454:FN1588|5end_hypothetical_protein_99556..99786_POSITIVE 180 110 82 34 7 NC_003454:FN0190|5end_Two-component_sensor_kinase_yesM_813975..814205_POSITIVE 178 137 111 30 6 NC_003454:FN1340|5end_Glutamyl-tRNA_synthetase_1994903..1995133_NEGATIVE 177 269 238 28 1 NC_003454:FN1363|5end_Dipeptide_transport_ATP-binding_protein_dppF_2014501..2014731_POSITIVE 177 248 217 136 105 NC_003454:FN0073|5end_Dihydropteroate_synthase_712520..712750_POSITIVE 176 125 87 72 32 NC_003454:FN2077|5end_NA+/H+_antiporter_NHAC_587900..588130_POSITIVE 174 137 100 205 166 NC_003454:FN1563|5end_hypothetical_protein_85040..85270_NEGATIVE 172 260 230 229 198 NC_003454:FN1802|5end_hypothetical_protein_283948..284178_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 227 137 96 119 74 NC_003454:FN0663|3end_hypothetical_protein_1319797..1319947_POSITIVE 208 130 90 58 21 NC_003454:FN1819|3end_Export_ABC_transporter_309344..309494_POSITIVE 192 147 112 132 92 NC_003454:FN0171|3end_Hypothetical_cytosolic_protein_796921..797071_POSITIVE 183 148 103 66 25 NC_003454:FN1460|3end_Hypothetical_cytosolic_protein_2141682..2141832_POSITIVE 180 110 82 47 20 NC_003454:FN0189|3end_Two-component_response_regulator_yesN_814068..814218_POSITIVE 167 135 100 112 73 NC_003454:FN1674|3end_hypothetical_protein_172225..172375_POSITIVE 166 150 113 130 81 NC_003454:FN1344|3end_hypothetical_protein_1998034..1998184_POSITIVE 166 138 103 60 26 NC_003454:FN1515|3end_Phophatidylinositol-4-phosphate_5-kinase_20652..20802_POSITIVE 165 144 105 62 22 NC_003454:FN1059|3end_Branched_chain_amino_acid_transport_system_II_carrier_protein_1707020..1707170_POSITIVE 164 269 229 46 10 NC_003454:FN1362|3end_Dipeptide_transport_ATP-binding_protein_dppD_2014599..2014749_POSITIVE 160 80 33 89 30 NC_003454:FN1314|3end_hypothetical_protein_1968500..1968650_NEGATIVE 160 139 106 41 16 NC_003454:FN2085|3end_hypothetical_protein_596560..596710_NEGATIVE 159 99 52 89 45 NC_003454:FN1310|3end_TonB_protein_1965148..1965298_NEGATIVE 159 135 118 98 78 NC_003454:FN0507|3end_hypothetical_protein_1157710..1157860_POSITIVE 157 270 223 63 15 NC_003454:FN0873|3end_Protease_IV_1532703..1532853_NEGATIVE 157 119 73 43 5 NC_003454:FN0702|3end_N-acyl-L-amino_acid_amidohydrolase_1360925..1361075_NEGATIVE 157 119 73 90 46 NC_003454:FN0115|3end_hypothetical_protein_748215..748365_NEGATIVE 157 140 112 51 22 NC_003454:FN0044|3end_Shikimate_5-dehydrogenase_683041..683191_POSITIVE 156 264 228 100 59 NC_003454:FN0798|3end_Fructose-1,6-bisphosphatase_1457852..1458002_POSITIVE 156 120 73 87 26 NC_003454:FN0218|3end_Anthranilate_synthase_component_II_842601..842751_POSITIVE