Origin IGS: aatatcaccaattagattgtatcataattttttctatttaagaacaaaaaacattattatcaaaactttaaaaataaaagtcaataaaatatttgacattgtcatataaaagtgttatacaatatttattaaaaacatgttctcgtgaacataataatttttttaaggagatgagcttatgatcaaaaaaatctattgcttactactt .........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 aagtagtaagcaatagatttttttgatcataagctcatctccttaaaaaaattattatgttcacgagaacatgtttttaataaatattgtataacacttttatatgacaatgtcaaatattttattgacttttatttttaaagttttgataataatgttttttgttcttaaatagaaaaaattatgatacaatctaattggtgatatt Mask Tandem Repeat Region ================================================ aatatcaccaattagattgtatcataattttttctatttaagaacaaaaaacattattatcaaaactttaaaaataaaagtcaataaaatatttgacattgtcatataaaagtgttatacaatatttattaaaaacatgttctcgtgaacataataatttttttaaggagatgagcttatgatcaaaaaaatctattgcttactactt Find is-nt database================================================ Query_seq: FN1469:FN1470|FN1469:FN1470:Na+ driven multidrug efflux pump:hypothetical protein:<-->:2151800..2152007 208 aatatcaccaattagattgtatcataattttttctatttaagaacaaaaaacattattatcaaaactttaaaaataaaagtcaataaaatatttgacattgtcatataaaagtgttatacaatatttattaaaaacatgttctcgtgaacataataatttttttaaggagatgagcttatgatcaaaaaaatctattgcttactactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1469:FN1470|FN1469:FN1470:Na+ driven multidrug efflux pump:hypothetical protein:<-->:2151800..2152007 208 aatatcaccaattagattgtatcataattttttctatttaagaacaaaaaacattattatcaaaactttaaaaataaaagtcaataaaatatttgacattgtcatataaaagtgttatacaatatttattaaaaacatgttctcgtgaacataataatttttttaaggagatgagcttatgatcaaaaaaatctattgcttactactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1469:FN1470|FN1469:FN1470:Na+ driven multidrug efflux pump:hypothetical protein:<-->:2151800..2152007 208 aatatcaccaattagattgtatcataattttttctatttaagaacaaaaaacattattatcaaaactttaaaaataaaagtcaataaaatatttgacattgtcatataaaagtgttatacaatatttattaaaaacatgttctcgtgaacataataatttttttaaggagatgagcttatgatcaaaaaaatctattgcttactactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatatcaccaattagattgtatcataattttttctatttaagaacaaaaaacattattatcaaaactttaaaaataaaagtcaataaaatatttgacattgtcatataaaagtgttatacaatatttattaaaaacatgttctcgtgaacataataatttttttaaggagatgagcttatgatcaaaaaaatctattgcttactactt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 2 End: 106 . M S P I R L Y H N F F Y L R T K N I I I K T L K I K V N K I F D I V I ...................................................................................................... Protein_Len: 32 Strand: + Start: 84 End: 179 ................................................................................... M K Y L T L S Y K S V I Q Y L L K T C S R E H N N F F K E M S L ............................. Protein_Len: 42 Strand: - Start: 71 End: 196 ...................................................................... F Y F D I F Y K V N D Y L L T I C Y K N F V H E R S C L L K K L S I L K H D F F D M ............ aatatcaccaattagattgtatcataattttttctatttaagaacaaaaaacattattatcaaaactttaaaaataaaagtcaataaaatatttgacattgtcatataaaagtgttatacaatatttattaaaaacatgttctcgtgaacataataatttttttaaggagatgagcttatgatcaaaaaaatctattgcttactactt 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: 56 End: 85 .......................................................ATTGACTTTTATTTTTAAAGTTTTGATAAT........................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 92 End: 121 ...........................................................................................TTTGACATTGTCATATAAAAGTGTTATACA....................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatatcaccaattagattgtatcataattttttctatttaagaacaaaaaacattattatcaaaactttaaaaataaaagtcaataaaatatttgacattgtcatataaaagtgttatacaatatttattaaaaacatgttctcgtgaacataataatttttttaaggagatgagcttatgatcaaaaaaatctattgcttactactt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1469:FN1470|FN1469:FN1470:Na+ driven multidrug efflux pump:hypothetical protein:<-->:2151800..2152007 208 aatatcaccaattagattgtatcataattttttctatttaagaacaaaaaacattattatcaaaactttaaaaataaaagtcaataaaatatttgacattgtcatataaaagtgttatacaatatttattaaaaacatgttctcgtgaacataataatttttttaaggagatgagcttatgatcaaaaaaatctattgcttactactt Intra-Species Hit: Count: 1 Min: 1 Max: 208 Len: 208 Subject: NC_003454_FN1469_FN1470|Na+ driven multidrug efflux pump:hypothetical protein|NEGATIVE:POSITIVE|[2151800,2152007]|208 HSP 1 e-value: 4.0E-23 bit: 109.0 Len: 97 Query Start:112 Query End:208 Subject Strand: POSITIVE Subject Start: 112 Subject End: 208 ...............................................................................................................gtgttatacaatatttattaaaaacatgttctcgtgaacataataannnnnnnaaggagatgagcttatgatcnnnnnnntctattgcttactactt ...............................................................................................................gtgttatacaatatttattaaaaacatgttctcgtgaacataataatttttttaaggagatgagcttatgatcaaaaaaatctattgcttactactt HSP 2 e-value: 3.0E-17 bit: 89.7 Len: 45 Query Start:1 Query End:45 Subject Strand: POSITIVE Subject Start: 1 Subject End: 45 aatatcaccaattagattgtatcataattttttctatttaagaac................................................................................................................................................................... aatatcaccaattagattgtatcataattttttctatttaagaac................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUCACCAAUUAGAUUGUAUCAUAAUUUUUUCUAUUUAAGAACAAAAAACAUUAUUAUCAAAACUUUAAAAAUAAAAGUCAAUAAAAUAUUUGACAUUGUCAUAUAAAAGUGUUAUACAAUAUUUAUUAAAAACAUGUUCUCGUGAACAUAAUAAUUUUUUUAAGGAGAUGAGCUUAUGAUCAAAAAAAUCUAUUGCUUACUACUU ........((((.(((((..(((((((.(((.(((.((((((((.....((((((.((((......((((....)))).(((((........)))))........)))).))))))....................((((((....)))))).......)))))))).))).))).)))))))......))))))))).......... (-29.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAGUAAGCAAUAGAUUUUUUUGAUCAUAAGCUCAUCUCCUUAAAAAAAUUAUUAUGUUCACGAGAACAUGUUUUUAAUAAAUAUUGUAUAACACUUUUAUAUGACAAUGUCAAAUAUUUUAUUGACUUUUAUUUUUAAAGUUUUGAUAAUAAUGUUUUUUGUUCUUAAAUAGAAAAAAUUAUGAUACAAUCUAAUUGGUGAUAUU .((((...(.(((((((((......(((((((.....(((..((((.........(((((((....)))))))....(((.(((((((((.(((.(((((...((((....(((((........)))))..))))....))))).)))...))))))))).)))...))))..))).....)))))))..))))).)))).)..)))) (-30.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 626 140 91 231 182 NC_003454:FN1469|5end_Na+_driven_multidrug_efflux_pump_2151709..2151939_NEGATIVE 198 177 140 53 15 NC_003454:FN2035|5end_DNA-directed_RNA_polymerase_beta'_chain_542781..543011_NEGATIVE 198 200 156 122 74 NC_003454:FN1582|5end_hypothetical_protein_94957..95187_NEGATIVE 192 69 24 211 168 NC_003454:FN0615|5end_Export_ABC_transporter_1273187..1273417_POSITIVE 189 47 2 114 63 NC_003454:FN0391|5end_Hydrolase_(HAD_superfamily)_1028613..1028843_POSITIVE 187 138 99 130 85 NC_003454:FN1905|5end_168_kDa_surface-layer_protein_precursor_398116..398346_NEGATIVE 185 177 155 58 35 NC_003454:FN1725|5end_Potassium_uptake_protein_KtrB_224671..224901_NEGATIVE 180 45 4 99 65 NC_003454:FN1037|5end_flavodoxin_1689447..1689677_POSITIVE 176 39 5 93 56 NC_003454:FN1984|5end_Glutaredoxin-like_protein_485487..485717_POSITIVE 173 32 7 82 56 NC_003454:FN0009|5end_L-aspartate_oxidase_648908..649138_POSITIVE 173 169 122 54 9 NC_003454:FN1721|5end_hypothetical_protein_219945..220175_NEGATIVE 170 142 104 228 193 NC_003454:FN2044|5end_LSU_ribosomal_protein_L33P_550109..550339_NEGATIVE 169 118 90 226 199 NC_003454:FN1202|5end_NAD(+)_synthetase_1862298..1862528_NEGATIVE 166 44 9 112 76 NC_003454:FN0954|5end_Hypothetical_cytosolic_protein_1611616..1611846_NEGATIVE 161 90 48 96 54 NC_003454:FN0773|5end_hypothetical_protein_1429274..1429504_POSITIVE 161 38 5 86 51 NC_003454:FN0191|5end_ATP-dependent_DNA_helicase_recG_815752..815982_POSITIVE 161 43 1 116 71 NC_003454:FN0162|5end_Na+_driven_multidrug_efflux_pump_789924..790154_POSITIVE 160 78 31 120 67 NC_003454:FN0206|5end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_832758..832988_POSITIVE 160 38 7 105 68 NC_003454:FN1724|5end_Potassium_uptake_protein_KtrA_223310..223540_NEGATIVE 159 36 2 160 131 NC_003454:FN1092|5end_hypothetical_protein_1737267..1737497_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 185 177 155 43 20 NC_003454:FN1726|3end_Na+_driven_multidrug_efflux_pump_224686..224836_NEGATIVE 180 45 4 50 16 NC_003454:FN1036|3end_hypothetical_protein_1689478..1689628_POSITIVE 173 32 7 80 54 NC_003454:FN0008|3end_quinolinate_synthetase_648986..649136_POSITIVE 173 46 5 48 2 NC_003454:FN1705|3end_hypothetical_protein_201464..201614_NEGATIVE 170 114 77 76 37 NC_003454:FN0512|3end_Flavoprotein_1161386..1161536_NEGATIVE 160 78 31 90 37 NC_003454:FN0205|3end_Sodium/glutamate_symport_carrier_protein_832808..832958_POSITIVE 160 23 1 136 115 NC_003454:FN1843|3end_Surface_antigen_333468..333618_POSITIVE 160 38 7 90 53 NC_003454:FN1725|3end_Potassium_uptake_protein_KtrB_223325..223475_NEGATIVE 159 36 2 151 122 NC_003454:FN1091|3end_Sigma_factor_sigB_regulation_protein_rsbU_1737338..1737488_POSITIVE 159 49 1 133 68 NC_003454:FN1808|3end_hypothetical_protein_289528..289678_NEGATIVE 158 144 112 87 51 NC_003454:FN0358|3end_ATP_synthase_subunit_B_988286..988436_NEGATIVE 158 36 5 140 104 NC_003454:FN1972|3end_hypothetical_protein_471703..471853_NEGATIVE 155 42 8 97 65 NC_003454:FN1697|3end_hypothetical_protein_192699..192849_NEGATIVE 153 50 9 79 39 NC_003454:FN1372|3end_Ribosomal_large_subunit_pseudouridine_synthase_D_2020022..2020172_NEGATIVE 153 200 158 45 9 NC_003454:FN1641|3end_SSU_ribosomal_protein_S19P_138552..138702_NEGATIVE 152 116 89 63 40 NC_003454:FN1376|3end_oxaloacetate_decarboxylase_2025305..2025455_POSITIVE 152 44 6 143 109 NC_003454:FN0055|3end_Ribosomal-protein-alanine_acetyltransferase_692744..692894_POSITIVE 150 200 166 40 1 NC_003454:FN1583|3end_hypothetical_protein_95039..95189_NEGATIVE 147 183 151 136 104 NC_003454:FN1192|3end_hypothetical_protein_1855031..1855181_POSITIVE 147 146 113 84 52 NC_003454:FN0460|3end_delta-aminolevulinic_acid_dehydratase_1106530..1106680_POSITIVE