Origin IGS: aaagttatctcctatcttatcttacttttaaatattatatcaattttttctttaaactaaaataataaatcttatagtcaaatatataacttaaatcttcatttaaaaaataatattctttattttattaagaaaaattaagaatctaaaaaaatttttaattttttaaaaaaactcttgacatttaattctatatatgatatatatagtctatgattattagcaacctattatatagagtgctaataaatctcccctctatattattttaggtggggcttagctatcaaagattatctttggtagctagctcctcaataataattaaaggataataaaataataaataaaaaaattaatatatagatgatga .........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 tcatcatctatatattaatttttttatttattattttattatcctttaattattattgaggagctagctaccaaagataatctttgatagctaagccccacctaaaataatatagaggggagatttattagcactctatataataggttgctaataatcatagactatatatatcatatatagaattaaatgtcaagagtttttttaaaaaattaaaaatttttttagattcttaatttttcttaataaaataaagaatattattttttaaatgaagatttaagttatatatttgactataagatttattattttagtttaaagaaaaaattgatataatatttaaaagtaagataagataggagataacttt Mask Tandem Repeat Region ================================================ aaagttatctcctatcttatcttacttttaaatattatatcaattttttctttaaactaaaataataaatcttatagtcaaatatataacttaaatcttcatttaaaaaataatattctttattttattaagaaaaattaagaatctaaaaaaatttttaattttttaaaaaaactcttgacatttaattctatatatgatatatatagtctatgattattagcaacctattatatagagtgctaataaatctcccctctatattattttaggtggggcttagctatcaaagattatctttggtagctagctcctcaataataattaaaggataataaaataataaataaaaaaattaatatatagatgatga Find is-nt database================================================ Query_seq: FN1940:FN1941|FN1940:FN1941:Na+ driven multidrug efflux pump:ClpB protein:<-->:441046..441418 373 aaagttatctcctatcttatcttacttttaaatattatatcaattttttctttaaactaaaataataaatcttatagtcaaatatataacttaaatcttcatttaaaaaataatattctttattttattaagaaaaattaagaatctaaaaaaatttttaattttttaaaaaaactcttgacatttaattctatatatgatatatatagtctatgattattagcaacctattatatagagtgctaataaatctcccctctatattattttaggtggggcttagctatcaaagattatctttggtagctagctcctcaataataattaaaggataataaaataataaataaaaaaattaatatatagatgatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1940:FN1941|FN1940:FN1941:Na+ driven multidrug efflux pump:ClpB protein:<-->:441046..441418 373 aaagttatctcctatcttatcttacttttaaatattatatcaattttttctttaaactaaaataataaatcttatagtcaaatatataacttaaatcttcatttaaaaaataatattctttattttattaagaaaaattaagaatctaaaaaaatttttaattttttaaaaaaactcttgacatttaattctatatatgatatatatagtctatgattattagcaacctattatatagagtgctaataaatctcccctctatattattttaggtggggcttagctatcaaagattatctttggtagctagctcctcaataataattaaaggataataaaataataaataaaaaaattaatatatagatgatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1940:FN1941|FN1940:FN1941:Na+ driven multidrug efflux pump:ClpB protein:<-->:441046..441418 373 aaagttatctcctatcttatcttacttttaaatattatatcaattttttctttaaactaaaataataaatcttatagtcaaatatataacttaaatcttcatttaaaaaataatattctttattttattaagaaaaattaagaatctaaaaaaatttttaattttttaaaaaaactcttgacatttaattctatatatgatatatatagtctatgattattagcaacctattatatagagtgctaataaatctcccctctatattattttaggtggggcttagctatcaaagattatctttggtagctagctcctcaataataattaaaggataataaaataataaataaaaaaattaatatatagatgatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagttatctcctatcttatcttacttttaaatattatatcaattttttctttaaactaaaataataaatcttatagtcaaatatataacttaaatcttcatttaaaaaataatattctttattttattaagaaaaattaagaatctaaaaaaatttttaattttttaaaaaaactcttgacatttaattctatatatgatatatatagtctatgattattagcaacctattatatagagtgctaataaatctcccctctatattattttaggtggggcttagctatcaaagattatctttggtagctagctcctcaataataattaaaggataataaaataataaataaaaaaattaatatatagatgatga Predict ORF larger than 30AA ================================================ aaagttatctcctatcttatcttacttttaaatattatatcaattttttctttaaactaaaataataaatcttatagtcaaatatataacttaaatcttcatttaaaaaataatattctttattttattaagaaaaattaagaatctaaaaaaatttttaattttttaaaaaaactcttgacatttaattctatatatgatatatatagtctatgattattagcaacctattatatagagtgctaataaatctcccctctatattattttaggtggggcttagctatcaaagattatctttggtagctagctcctcaataataattaaaggataataaaataataaataaaaaaattaatatatagatgatga 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: 84 Start: 177 End: 206 ................................................................................................................................................................................CTTGACATTTAATTCTATATATGATATATA....................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagttatctcctatcttatcttacttttaaatattatatcaattttttctttaaactaaaataataaatcttatagtcaaatatataacttaaatcttcatttaaaaaataatattctttattttattaagaaaaattaagaatctaaaaaaatttttaattttttaaaaaaactcttgacatttaattctatatatgatatatatagtctatgattattagcaacctattatatagagtgctaataaatctcccctctatattattttaggtggggcttagctatcaaagattatctttggtagctagctcctcaataataattaaaggataataaaataataaataaaaaaattaatatatagatgatga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 75 HP_score: -4.3 Tail_Score: -5.57054 Start: 155 End: 172 Full_Region: taaatgtcaagagtt tttttaa aaaa ttaaaaa tttttttagattctt ..........................................................................................................................................................tttttaaaaaattaaaaa......................................................................................................................................................................................................... Find igs database================================================ Query_seq: FN1940:FN1941|FN1940:FN1941:Na+ driven multidrug efflux pump:ClpB protein:<-->:441046..441418 373 aaagttatctcctatcttatcttacttttaaatattatatcaattttttctttaaactaaaataataaatcttatagtcaaatatataacttaaatcttcatttaaaaaataatattctttattttattaagaaaaattaagaatctaaaaaaatttttaattttttaaaaaaactcttgacatttaattctatatatgatatatatagtctatgattattagcaacctattatatagagtgctaataaatctcccctctatattattttaggtggggcttagctatcaaagattatctttggtagctagctcctcaataataattaaaggataataaaataataaataaaaaaattaatatatagatgatga Intra-Species Hit: Count: 1 Min: 1 Max: 316 Len: 316 Subject: NC_003454_FN1940_FN1941|Na+ driven multidrug efflux pump:ClpB protein|NEGATIVE:POSITIVE|[441046,441418]|373 HSP 1 e-value: 3.0E-37 bit: 157.0 Len: 79 Query Start:238 Query End:316 Subject Strand: POSITIVE Subject Start: 238 Subject End: 316 .............................................................................................................................................................................................................................................gagtgctaataaatctcccctctatattattttaggtggggcttagctatcaaagattatctttggtagctagctcctc......................................................... .............................................................................................................................................................................................................................................gagtgctaataaatctcccctctatattattttaggtggggcttagctatcaaagattatctttggtagctagctcctc......................................................... HSP 2 e-value: 2.0E-20 bit: 101.0 Len: 51 Query Start:1 Query End:51 Subject Strand: POSITIVE Subject Start: 1 Subject End: 51 aaagttatctcctatcttatcttacttttaaatattatatcaattttttct.................................................................................................................................................................................................................................................................................................................................. aaagttatctcctatcttatcttacttttaaatattatatcaattttttct.................................................................................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUUAUCUCCUAUCUUAUCUUACUUUUAAAUAUUAUAUCAAUUUUUUCUUUAAACUAAAAUAAUAAAUCUUAUAGUCAAAUAUAUAACUUAAAUCUUCAUUUAAAAAAUAAUAUUCUUUAUUUUAUUAAGAAAAAUUAAGAAUCUAAAAAAAUUUUUAAUUUUUUAAAAAAACUCUUGACAUUUAAUUCUAUAUAUGAUAUAUAUAGUCUAUGAUUAUUAGCAACCUAUUAUAUAGAGUGCUAAUAAAUCUCCCCUCUAUAUUAUUUUAGGUGGGGCUUAGCUAUCAAAGAUUAUCUUUGGUAGCUAGCUCCUC ........................................................(((((((((((.........(((((.........................(((((((......))))))).....((((((((((((((........))))))))))))))..........)))))........((((((((...)))))))).....(((((((((((..((((...))))..))))))).)))).........)))))))))))..((((((.(((((((((((.....))))))))))))))))).. (-65.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGGAGCUAGCUACCAAAGAUAAUCUUUGAUAGCUAAGCCCCACCUAAAAUAAUAUAGAGGGGAGAUUUAUUAGCACUCUAUAUAAUAGGUUGCUAAUAAUCAUAGACUAUAUAUAUCAUAUAUAGAAUUAAAUGUCAAGAGUUUUUUUAAAAAAUUAAAAAUUUUUUUAGAUUCUUAAUUUUUCUUAAUAAAAUAAAGAAUAUUAUUUUUUAAAUGAAGAUUUAAGUUAUAUAUUUGACUAUAAGAUUUAUUAUUUUAGUUUAAAGAAAAAAUUGAUAUAAUAUUUAAAAGUAAGAUAAGAUAGGAGAUAACUUU ..((.((((((((.(((((.....))))).))))).))).)).((((......(((.(((..(((..(((((((((..((((...))))..))))))))).......((((((((...))))))))...........((((((((....(((((((.....))))))).))))))))..)))..))).))).......((((((((((((((((((.(((((.((((((.((((......)))).))))))..))))).)))))))))..........)))))))))...............)))).......... (-64.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 625 50 1 141 92 NC_003454:FN1940|5end_Na+_driven_multidrug_efflux_pump_440955..441185_NEGATIVE 261 299 251 192 140 NC_003454:FN0129|5end_Urease_accessory_protein_ureG_757595..757825_POSITIVE 251 268 223 229 179 NC_003454:FN2079|5end_ABC_transporter_ATP-binding_protein_591118..591348_NEGATIVE 250 246 217 107 78 NC_003454:FN0113|5end_Heat-inducible_transcription_repressor_hrcA_746557..746787_POSITIVE 250 280 231 47 6 NC_003454:FN1793|5end_Phosphoenolpyruvate-protein_phosphotransferase_275273..275503_NEGATIVE 246 285 252 205 168 NC_003454:FN1628|5end_LSU_ribosomal_protein_L18P_133948..134178_NEGATIVE 241 298 251 150 98 NC_003454:FN1594|5end_Nitrogen_fixation_protein_RNFG_104893..105123_NEGATIVE 239 268 236 85 47 NC_003454:FN1102|5end_tRNA_2'phosphotransferase_1745952..1746182_POSITIVE 226 256 225 116 82 NC_003454:FN1450|5end_Integral_membrane_protein_2131410..2131640_NEGATIVE 224 52 11 72 36 NC_003454:FN0840|5end_Transposase_1501361..1501591_POSITIVE 224 50 3 70 29 NC_003454:FN0485|5end_Transposase_1130267..1130497_POSITIVE 216 289 244 211 156 NC_003454:FN0063|5end_hypothetical_protein_698982..699212_POSITIVE 212 310 266 51 7 NC_003454:FN1498|5end_Integral_membrane_protein_2563..2793_POSITIVE 210 306 276 48 4 NC_003454:FN1815|5end_Transposase_295961..296191_NEGATIVE 206 287 249 149 95 NC_003454:FN0009|5end_L-aspartate_oxidase_648908..649138_POSITIVE 205 288 255 127 95 NC_003454:FN1927|5end_DEGV_protein_427952..428182_NEGATIVE 201 255 213 190 154 NC_003454:FN0605|5end_aspartate_aminotransferase_1259806..1260036_POSITIVE 199 49 3 135 86 NC_003454:FN1298|5end_Adenylate_kinase_1955626..1955856_NEGATIVE 199 281 257 153 125 NC_003454:FN0883|5end_hypothetical_protein_1544357..1544587_POSITIVE 197 280 241 122 83 NC_003454:FN0334|5end_Aspartate/aromatic_aminotransferase_969066..969296_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 246 217 70 41 NC_003454:FN0112|3end_hypothetical_protein_746600..746750_POSITIVE 239 268 236 92 54 NC_003454:FN1101|3end_ATPase_1746039..1746189_POSITIVE 217 290 251 146 108 NC_003454:FN1595|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_B_104883..105033_NEGATIVE 216 289 244 124 69 NC_003454:FN0062|3end_Hypothetical_cytosolic_protein_698975..699125_POSITIVE 207 126 82 59 12 NC_003454:FN0134|3end_hypothetical_protein_770130..770280_POSITIVE 206 287 249 147 93 NC_003454:FN0008|3end_quinolinate_synthetase_648986..649136_POSITIVE 205 288 255 115 83 NC_003454:FN1928|3end_Transcriptional_regulator,_MerR_family_427964..428114_NEGATIVE 199 49 3 66 17 NC_003454:FN1299|3end_dTDP-glucose_4,6-dehydratase_1955695..1955845_NEGATIVE 199 304 269 77 39 NC_003454:FN1525|3end_Dipeptide_transport_ATP-binding_protein_dppF_31631..31781_POSITIVE 198 309 271 85 51 NC_003454:FN1310|3end_TonB_protein_1965148..1965298_NEGATIVE 198 79 42 147 109 NC_003454:FN1133|3end_N-acetylglucosamine-6-phosphate_deacetylase_1780269..1780419_NEGATIVE 198 235 193 141 96 NC_003454:FN0015|3end_hypothetical_protein_652952..653102_NEGATIVE 198 300 258 101 55 NC_003454:FN2085|3end_hypothetical_protein_596560..596710_NEGATIVE 197 280 231 121 59 NC_003454:FN0253|3end_Outer_membrane_protein_875063..875213_POSITIVE 196 275 237 104 58 NC_003454:FN0923|3end_Cardiolipin_synthetase_1577538..1577688_NEGATIVE 191 45 15 115 84 NC_003454:FN2016|3end_ATP-dependent_Clp_protease_proteolytic_subunit_518267..518417_NEGATIVE 191 308 261 79 29 NC_003454:FN1993|3end_SUA5_protein_497650..497800_POSITIVE 191 286 251 116 79 NC_003454:FN1703|3end_ADP-L-glycero-D-manno-heptose-6-epimerase_197994..198144_NEGATIVE 190 285 253 130 95 NC_003454:FN1198|3end_Transporter_1857679..1857829_NEGATIVE 190 35 5 121 95 NC_003454:FN0269|3end_Transposase_896846..896996_POSITIVE