Origin IGS: ctttattaacttattttagtaaacaatgttatcattttatcatgttgtatagctaaatacaataaactttatttagctaaacttaatgtttaataatggttttacaaaatcataataaaagttctcacagctgttactagatttgaattgataccttcaattccaacctttgctaaaattgaagttaatgttgcaaaatttctccttattattttcttattttaatatatcttataagttattgtaattaatgtcaatttacaataactttttattttcaaattacttttactatcaattatttatataataaaaaacttatatattaaaataattatattgacaaaagataaaaatggatatattatagcagataagaatagtataaaataaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttattttatactattcttatctgctataatatatccatttttatcttttgtcaatataattattttaatatataagttttttattatataaataattgatagtaaaagtaatttgaaaataaaaagttattgtaaattgacattaattacaataacttataagatatattaaaataagaaaataataaggagaaattttgcaacattaacttcaattttagcaaaggttggaattgaaggtatcaattcaaatctagtaacagctgtgagaacttttattatgattttgtaaaaccattattaaacattaagtttagctaaataaagtttattgtatttagctatacaacatgataaaatgataacattgtttactaaaataagttaataaag Mask Tandem Repeat Region ================================================ ctttattaacttattttagtaaacaatgttatcattttatcatgttgtatagctaaatacaataaactttatttagctaaacttaatgtttaataatggttttacaaaatcataataaaagttctcacagctgttactagatttgaattgataccttcaattccaacctttgctaaaattgaagttaatgttgcaaaatttctccttattattttcttattttaatatatcttataagttattgtaattaatgtcaatttacaataactttttattttcaaattacttttactatcaattatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgacaaaagataaaaatggatatattatagcagataagaatagtataaaataaa Find is-nt database================================================ Query_seq: FN0667:FN0668|FN0667:FN0668:Na+ driven multidrug efflux pump:High-affinity zinc uptake system protein znuA precursor:<-->:1323715..1324108 394 ctttattaacttattttagtaaacaatgttatcattttatcatgttgtatagctaaatacaataaactttatttagctaaacttaatgtttaataatggttttacaaaatcataataaaagttctcacagctgttactagatttgaattgataccttcaattccaacctttgctaaaattgaagttaatgttgcaaaatttctccttattattttcttattttaatatatcttataagttattgtaattaatgtcaatttacaataactttttattttcaaattacttttactatcaattatttatataataaaaaacttatatattaaaataattatattgacaaaagataaaaatggatatattatagcagataagaatagtataaaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0667:FN0668|FN0667:FN0668:Na+ driven multidrug efflux pump:High-affinity zinc uptake system protein znuA precursor:<-->:1323715..1324108 394 ctttattaacttattttagtaaacaatgttatcattttatcatgttgtatagctaaatacaataaactttatttagctaaacttaatgtttaataatggttttacaaaatcataataaaagttctcacagctgttactagatttgaattgataccttcaattccaacctttgctaaaattgaagttaatgttgcaaaatttctccttattattttcttattttaatatatcttataagttattgtaattaatgtcaatttacaataactttttattttcaaattacttttactatcaattatttatataataaaaaacttatatattaaaataattatattgacaaaagataaaaatggatatattatagcagataagaatagtataaaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0667:FN0668|FN0667:FN0668:Na+ driven multidrug efflux pump:High-affinity zinc uptake system protein znuA precursor:<-->:1323715..1324108 394 ctttattaacttattttagtaaacaatgttatcattttatcatgttgtatagctaaatacaataaactttatttagctaaacttaatgtttaataatggttttacaaaatcataataaaagttctcacagctgttactagatttgaattgataccttcaattccaacctttgctaaaattgaagttaatgttgcaaaatttctccttattattttcttattttaatatatcttataagttattgtaattaatgtcaatttacaataactttttattttcaaattacttttactatcaattatttatataataaaaaacttatatattaaaataattatattgacaaaagataaaaatggatatattatagcagataagaatagtataaaataaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttattaacttattttagtaaacaatgttatcattttatcatgttgtatagctaaatacaataaactttatttagctaaacttaatgtttaataatggttttacaaaatcataataaaagttctcacagctgttactagatttgaattgataccttcaattccaacctttgctaaaattgaagttaatgttgcaaaatttctccttattattttcttattttaatatatcttataagttattgtaattaatgtcaatttacaataactttttattttcaaattacttttactatcaattatttatataataaaaaacttatatattaaaataattatattgacaaaagataaaaatggatatattatagcagataagaatagtataaaataaa Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 109 End: 222 ............................................................................................................ M I I K V L T A V T R F E L I P S I P T F A K I E V N V A K F L L I I F L F ............................................................................................................................................................................ Protein_Len: 40 Strand: + Start: 274 End: 390 ................................................................................................................................................................................................................................................................................. M F K L L L L S I I Y I I K N L Y I K I I I L T K D K N G Y I I A D K N S I K * .... Protein_Len: 36 Strand: - Start: 105 End: 212 ........................................................................................................ L I M I F T R V A T V L N S N I G E I G V K A L I S T L T A F N R R I M ...................................................................................................................................................................................... ctttattaacttattttagtaaacaatgttatcattttatcatgttgtatagctaaatacaataaactttatttagctaaacttaatgtttaataatggttttacaaaatcataataaaagttctcacagctgttactagatttgaattgataccttcaattccaacctttgctaaaattgaagttaatgttgcaaaatttctccttattattttcttattttaatatatcttataagttattgtaattaatgtcaatttacaataactttttattttcaaattacttttactatcaattatttatataataaaaaacttatatattaaaataattatattgacaaaagataaaaatggatatattatagcagataagaatagtataaaataaa 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: 87 Start: 229 End: 258 ....................................................................................................................................................................................................................................ATTGACATTAATTACAATAACTTATAAGAT........................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 87 Start: 339 End: 368 ..................................................................................................................................................................................................................................................................................................................................................ATTGACAAAAGATAAAAATGGATATATTAT.......................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 318 End: 347 .............................................................................................................................................................................................................................................................................................................................TTTGTCAATATAATTATTTTAATATATAAG............................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 34 End: 63 .................................ATTGTATTTAGCTATACAACATGATAAAAT........................................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctttattaacttattttagtaaacaatgttatcattttatcatgttgtatagctaaatacaataaactttatttagctaaacttaatgtttaataatggttttacaaaatcataataaaagttctcacagctgttactagatttgaattgataccttcaattccaacctttgctaaaattgaagttaatgttgcaaaatttctccttattattttcttattttaatatatcttataagttattgtaattaatgtcaatttacaataactttttattttcaaattacttttactatcaattatttatataataaaaaacttatatattaaaataattatattgacaaaagataaaaatggatatattatagcagataagaatagtataaaataaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 54 HP_score: -4.9 Tail_Score: -3.48671 Start: 47 End: 82 Full_Region: TCATTTTATCATGTT GTATAGCTAAATACA ATAAAC TTTATTTAGCTAAAC TTAATGTTTAATAAT ..............................................GTATAGCTAAATACAATAAACTTTATTTAGCTAAAC........................................................................................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 48 HP_score: -3.2 Tail_Score: -3.76492 Start: 140 End: 168 Full_Region: TCACAGCTGTTACTA GATTTGAATTGA TACCT TCAATTCCAACC TTTGCTAAAATTGAA ...........................................................................................................................................GATTTGAATTGATACCTTCAATTCCAACC.................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 48 HP_score: -4.4 Tail_Score: -2.78935 Start: 142 End: 166 Full_Region: caattttagcaaagg ttggaattga aggta tcaattcaaa tctagtaacagctgt .............................................................................................................................................ttggaattgaaggtatcaattcaaa.................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 70 HP_score: -4.2 Tail_Score: -5.46706 Start: 238 End: 268 Full_Region: TAATATATCTTATAA GTTATTGTAATT AATGTCA ATTTACAATAAC TTTTTATTTTCAAAT .............................................................................................................................................................................................................................................GTTATTGTAATTAATGTCAATTTACAATAAC.............................................................................................................................. Find igs database================================================ Query_seq: FN0667:FN0668|FN0667:FN0668:Na+ driven multidrug efflux pump:High-affinity zinc uptake system protein znuA precursor:<-->:1323715..1324108 394 ctttattaacttattttagtaaacaatgttatcattttatcatgttgtatagctaaatacaataaactttatttagctaaacttaatgtttaataatggttttacaaaatcataataaaagttctcacagctgttactagatttgaattgataccttcaattccaacctttgctaaaattgaagttaatgttgcaaaatttctccttattattttcttattttaatatatcttataagttattgtaattaatgtcaatttacaataactttttattttcaaattacttttactatcaattatttatataataaaaaacttatatattaaaataattatattgacaaaagataaaaatggatatattatagcagataagaatagtataaaataaa Intra-Species Hit: Count: 1 Min: 1 Max: 262 Len: 262 Subject: NC_003454_FN0667_FN0668|Na+ driven multidrug efflux pump:High-affinity zinc uptake system protein znuA precursor|NEGATIVE:POSITIVE|[1323715,1324108]|394 HSP 1 e-value: 1.0E-146 bit: 519.0 Len: 262 Query Start:1 Query End:262 Subject Strand: POSITIVE Subject Start: 1 Subject End: 262 ctttattaacttattttagtaaacaatgttatcattttatcatgttgtatagctaaatacaataaactttatttagctaaacttaatgtttaataatggttttacaaaatcataataaaagttctcacagctgttactagatttgaattgataccttcaattccaacctttgctaaaattgaagttaatgttgcaaaatttctccttattattttcttattttaatatatcttataagttattgtaattaatgtcaatttac.................................................................................................................................... ctttattaacttattttagtaaacaatgttatcattttatcatgttgtatagctaaatacaataaactttatttagctaaacttaatgtttaataatggttttacaaaatcataataaaagttctcacagctgttactagatttgaattgataccttcaattccaacctttgctaaaattgaagttaatgttgcaaaatttctccttattattttcttattttaatatatcttataagttattgtaattaatgtcaatttac.................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUAUUAACUUAUUUUAGUAAACAAUGUUAUCAUUUUAUCAUGUUGUAUAGCUAAAUACAAUAAACUUUAUUUAGCUAAACUUAAUGUUUAAUAAUGGUUUUACAAAAUCAUAAUAAAAGUUCUCACAGCUGUUACUAGAUUUGAAUUGAUACCUUCAAUUCCAACCUUUGCUAAAAUUGAAGUUAAUGUUGCAAAAUUUCUCCUUAUUAUUUUCUUAUUUUAAUAUAUCUUAUAAGUUAUUGUAAUUAAUGUCAAUUUAC ...((((((((((((((((((((...(((.(((((((((.(((...((.((((((((((..........)))))))))).))...)))..))).))))))...)))(((((.((.(((.((((.....)))).))).)))))))(((((((.....))))))).....)))))))))))..))))))))).....(((((.......(((((...(((((.............))))).....))))).......))))).. (-42.36) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAAUUGACAUUAAUUACAAUAACUUAUAAGAUAUAUUAAAAUAAGAAAAUAAUAAGGAGAAAUUUUGCAACAUUAACUUCAAUUUUAGCAAAGGUUGGAAUUGAAGGUAUCAAUUCAAAUCUAGUAACAGCUGUGAGAACUUUUAUUAUGAUUUUGUAAAACCAUUAUUAAACAUUAAGUUUAGCUAAAUAAAGUUUAUUGUAUUUAGCUAUACAACAUGAUAAAAUGAUAACAUUGUUUACUAAAAUAAGUUAAUAAAG .....................((((((((..(((((....................((((....))))..........(((((((((((((....))))))))))))))))))..........(((((((((.(((......((((((((((.(((.((((.....)))).)))......((.((((((((((..........)))))))))).))..)))))))))).....)))))).))))))..))))))))...... (-47.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 713 140 91 231 182 NC_003454:FN0667|5end_Na+_driven_multidrug_efflux_pump_1323624..1323854_NEGATIVE 245 236 199 134 95 NC_003454:FN1605|5end_Adenylosuccinate_synthetase_115276..115506_NEGATIVE 243 82 45 158 126 NC_003454:FN2044|5end_LSU_ribosomal_protein_L33P_550109..550339_NEGATIVE 235 167 122 73 30 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 233 195 151 141 92 NC_003454:FN0754|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A_1414646..1414876_NEGATIVE 230 163 122 97 50 NC_003454:FN2081|5end_ABC_transporter_substrate-binding_protein_592974..593204_NEGATIVE 224 161 129 223 195 NC_003454:FN0234|5end_hypothetical_protein_859499..859729_NEGATIVE 223 239 193 141 88 NC_003454:FN0928|5end_O-sialoglycoprotein_endopeptidase_1583026..1583256_NEGATIVE 222 206 161 47 10 NC_003454:FN0007|5end_glucose-inhibited_division_protein_A_645938..646168_POSITIVE 220 240 191 120 73 NC_003454:FN0525|5end_Penicillin-binding_protein_1181840..1182070_NEGATIVE 215 160 116 51 7 NC_003454:FN0540|5end_Glutamate-1-semialdehyde_2,1-aminomutase_1193945..1194175_NEGATIVE 213 169 129 226 188 NC_003454:FN0351|5end_hypothetical_protein_982824..983054_POSITIVE 213 194 155 40 8 NC_003454:FN1723|5end_glucose-inhibited_division_protein_A_222645..222875_NEGATIVE 207 84 42 178 125 NC_003454:FN1068|5end_Smf_protein_1713811..1714041_POSITIVE 207 175 142 48 10 NC_003454:FN0476|5end_transcription_termination_factor_Rho_1123450..1123680_POSITIVE 206 42 1 98 58 NC_003454:FN1873|5end_Bis(5'-nucleosyl)-tetraphosphatase_363440..363670_NEGATIVE 204 197 160 46 15 NC_003454:FN0515|5end_Acriflavin_resistance_protein_D_1167006..1167236_NEGATIVE 204 180 131 200 155 NC_003454:FN1929|5end_Competence-damage_protein_cinA_429733..429963_NEGATIVE 202 188 142 54 3 NC_003454:FN0240|5end_Thymidylate_synthase_863894..864124_POSITIVE 201 58 11 60 15 NC_003454:FN0817|5end_ABC_transporter_ATP-binding_protein_1476448..1476678_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 166 129 59 20 NC_003454:FN0235|3end_ABC_transporter_ATP-binding_protein_859674..859824_NEGATIVE 245 236 199 124 85 NC_003454:FN1606|3end_3-deoxy-D-manno-octulosonic-acid_transferase_115286..115436_NEGATIVE 234 184 155 56 26 NC_003454:FN2065|3end_Transcriptional_repressor_576397..576547_POSITIVE 233 195 151 124 75 NC_003454:FN0755|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_C_1414663..1414813_NEGATIVE 220 240 191 59 12 NC_003454:FN0526|3end_Florfenicol_resistance_protein_1181901..1182051_NEGATIVE 206 42 1 85 45 NC_003454:FN1874|3end_Ribose_5-phosphate_isomerase_363453..363603_NEGATIVE 204 197 160 49 18 NC_003454:FN0516|3end_Acriflavin_resistance_protein_E_1167003..1167153_NEGATIVE 200 156 124 44 14 NC_003454:FN0506|3end_Arginyl-tRNA_synthetase_1155802..1155952_NEGATIVE 200 195 154 44 6 NC_003454:FN0260|3end_Transcriptional_repressor_smtB_886261..886411_NEGATIVE 200 232 191 117 74 NC_003454:FN1698|3end_dTDP-4-dehydrorhamnose_reductase_193697..193847_NEGATIVE 199 235 192 146 109 NC_003454:FN1914|3end_Anti-sigma_F_factor_antagonist_411643..411793_NEGATIVE 198 140 98 67 16 NC_003454:FN0272|3end_Acetoacetate:butyrate/acetate_coenzyme_A_transferase_899503..899653_POSITIVE 193 205 163 135 81 NC_003454:FN0703|3end_N-acyl-L-amino_acid_amidohydrolase_1361068..1361218_NEGATIVE 193 240 192 102 49 NC_003454:FN1804|3end_Aminoacyl-histidine_dipeptidase_286465..286615_POSITIVE 192 210 162 95 32 NC_003454:FN0183|3end_Glycerol-3-phosphate_dehydrogenase_807078..807228_NEGATIVE 191 224 182 115 63 NC_003454:FN0782|3end_Methyltransferase_1438281..1438431_NEGATIVE 190 159 112 145 98 NC_003454:FN0783|3end_Acyl-CoA_dehydrogenase_1440391..1440541_POSITIVE 190 170 130 70 36 NC_003454:FN1538|3end_Arsenical_pump-driving_ATPase_51109..51259_NEGATIVE 189 220 171 102 52 NC_003454:FN1084|3end_hypothetical_protein_1728998..1729148_POSITIVE 188 232 193 147 107 NC_003454:FN0929|3end_ATP/GTP_hydrolase_1583007..1583157_NEGATIVE