Origin IGS: atttcctccatattaaaaattttataaatctttagacttagtataacatttttattaaaaaagacaaaataattaatatgctaaactttttttataaagcaattttttcac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtgaaaaaattgctttataaaaaaagtttagcatattaattattttgtcttttttaataaaaatgttatactaagtctaaagatttataaaatttttaatatggaggaaat Mask Tandem Repeat Region ================================================ atttcctccatattaaaaattttataaatctttagacttagtataacatttttattaaaaaagacaaaataattaatatgctaaactttttttataaagcaattttttcac Find is-nt database================================================ Query_seq: FN1652:FN1653|FN1652:FN1653:Oligopeptide-binding protein oppA:Na+ driven multidrug efflux pump:<-<-:147631..147741 111 atttcctccatattaaaaattttataaatctttagacttagtataacatttttattaaaaaagacaaaataattaatatgctaaactttttttataaagcaattttttcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1652:FN1653|FN1652:FN1653:Oligopeptide-binding protein oppA:Na+ driven multidrug efflux pump:<-<-:147631..147741 111 atttcctccatattaaaaattttataaatctttagacttagtataacatttttattaaaaaagacaaaataattaatatgctaaactttttttataaagcaattttttcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1652:FN1653|FN1652:FN1653:Oligopeptide-binding protein oppA:Na+ driven multidrug efflux pump:<-<-:147631..147741 111 atttcctccatattaaaaattttataaatctttagacttagtataacatttttattaaaaaagacaaaataattaatatgctaaactttttttataaagcaattttttcac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttcctccatattaaaaattttataaatctttagacttagtataacatttttattaaaaaagacaaaataattaatatgctaaactttttttataaagcaattttttcac Predict ORF larger than 30AA ================================================ atttcctccatattaaaaattttataaatctttagacttagtataacatttttattaaaaaagacaaaataattaatatgctaaactttttttataaagcaattttttcac 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================================================ atttcctccatattaaaaattttataaatctttagacttagtataacatttttattaaaaaagacaaaataattaatatgctaaactttttttataaagcaattttttcac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1652:FN1653|FN1652:FN1653:Oligopeptide-binding protein oppA:Na+ driven multidrug efflux pump:<-<-:147631..147741 111 atttcctccatattaaaaattttataaatctttagacttagtataacatttttattaaaaaagacaaaataattaatatgctaaactttttttataaagcaattttttcac Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_003454_FN1652_FN1653|Oligopeptide-binding protein oppA:Na+ driven multidrug efflux pump|NEGATIVE:NEGATIVE|[147631,147741]|111 HSP 1 e-value: 2.0E-44 bit: 178.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 atttcctccatattaaaaattttataaatctttagacttagtataacatttttattaaaaaagacaaaataattaatatgctaaacnnnnnnnataaagcaattttttcac atttcctccatattaaaaattttataaatctttagacttagtataacatttttattaaaaaagacaaaataattaatatgctaaactttttttataaagcaattttttcac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCCUCCAUAUUAAAAAUUUUAUAAAUCUUUAGACUUAGUAUAACAUUUUUAUUAAAAAAGACAAAAUAAUUAAUAUGCUAAACUUUUUUUAUAAAGCAAUUUUUUCAC ...................(((((((((.....((..((((((((......(((((...........)))))....)))))))).))...)))))))))............ ( -8.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGAAAAAAUUGCUUUAUAAAAAAAGUUUAGCAUAUUAAUUAUUUUGUCUUUUUUAAUAAAAAUGUUAUACUAAGUCUAAAGAUUUAUAAAAUUUUUAAUAUGGAGGAAAU ..........((((..((.......))..))))..............(((((..((.(((((((.(((((...((((....))))))))).))))))).))..)))))... (-13.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 630 50 1 141 92 NC_003454:FN1652|5end_Oligopeptide-binding_protein_oppA_147540..147770_NEGATIVE 196 43 1 227 167 NC_003454:FN0835|5end_hypothetical_protein_1498189..1498419_POSITIVE 193 89 48 198 152 NC_003454:FN0048|5end_4-nitrophenylphosphatase_686043..686273_NEGATIVE 188 41 1 130 95 NC_003454:FN0897|5end_Hypothetical_cytosolic_protein_1555833..1556063_POSITIVE 186 39 5 138 98 NC_003454:FN0120|5end_hypothetical_protein_752891..753121_NEGATIVE 185 36 1 103 68 NC_003454:FN0973|5end_Histidinol-phosphate_aminotransferase_1626699..1626929_NEGATIVE 183 106 79 65 38 NC_003454:FN1745|5end_Cystathionine_gamma-synthase_244143..244373_NEGATIVE 178 50 1 149 93 NC_003454:FN0937|5end_Gamma-polyglutamic_acid_synthetase_1590245..1590475_NEGATIVE 178 46 4 147 101 NC_003454:FN0600|5end_hypothetical_protein_1256019..1256249_NEGATIVE 177 50 5 117 79 NC_003454:FN0462|5end_DNA_mismatch_repair_protein_mutL_1107184..1107414_POSITIVE 176 27 4 119 96 NC_003454:FN0467|5end_murein_hydrolase_exporter_1112864..1113094_POSITIVE 176 50 5 150 100 NC_003454:FN0339|5end_hypothetical_protein_972035..972265_POSITIVE 176 50 3 170 123 NC_003454:FN1550|5end_hypothetical_protein_65630..65860_NEGATIVE 175 49 2 136 93 NC_003454:FN1335|5end_Protein_translocase_subunit_YajC_1989011..1989241_NEGATIVE 175 35 1 85 39 NC_003454:FN1111|5end_Dipeptide-binding_protein_1756181..1756411_NEGATIVE 173 44 3 118 76 NC_003454:FN1456|5end_UDP-N-acetylmuramate--alanine_ligase_2137922..2138152_NEGATIVE 173 49 2 152 94 NC_003454:FN0475|5end_MIAB_protein_1122120..1122350_POSITIVE 171 110 68 140 95 NC_003454:FN0247|5end_Hypothetical_cytosolic_protein_870707..870937_POSITIVE 171 50 1 136 95 NC_003454:FN1732|5end_hypothetical_protein_232078..232308_NEGATIVE 169 47 7 68 23 NC_003454:FN1877|5end_Guanine-hypoxanthine_permease_366537..366767_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 186 39 5 121 81 NC_003454:FN0121|3end_hypothetical_protein_752908..753058_NEGATIVE 185 36 1 86 51 NC_003454:FN0974|3end_Lactoylglutathione_lyase_1626716..1626866_NEGATIVE 179 45 2 115 74 NC_003454:FN1147|3end_hypothetical_protein_1796594..1796744_NEGATIVE 178 50 1 57 1 NC_003454:FN0938|3end_hypothetical_protein_1590337..1590487_NEGATIVE 178 46 4 64 18 NC_003454:FN0601|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1256102..1256252_NEGATIVE 176 27 4 37 14 NC_003454:FN0466|3end_Lysyl-tRNA_synthetase_1112862..1113012_POSITIVE 176 50 5 132 82 NC_003454:FN0338|3end_hypothetical_protein_972097..972247_POSITIVE 176 50 3 146 99 NC_003454:FN1551|3end_hypothetical_protein_65654..65804_NEGATIVE 175 35 1 101 55 NC_003454:FN1112|3end_Dipeptide_transport_system_permease_protein_dppC_1756165..1756315_NEGATIVE 173 44 3 137 95 NC_003454:FN1457|3end_UDP-N-acetylglucosamine-N-acetylmuramyl-_Pentapeptide_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_2137903..2138053_NEGATIVE 168 44 2 132 102 NC_003454:FN1532|3end_murein_hydrolase_exporter_44936..45086_NEGATIVE 167 39 1 109 75 NC_003454:FN0873|3end_Protease_IV_1532703..1532853_NEGATIVE 167 45 3 76 32 NC_003454:FN1940|3end_Na+_driven_multidrug_efflux_pump_439585..439735_NEGATIVE 165 34 1 112 79 NC_003454:FN1318|3end_RNA_polymerase_sigma_factor_rpoD_1971101..1971251_NEGATIVE 162 43 3 118 85 NC_003454:FN1378|3end_Citrate_lyase_acyl_carrier_protein_2026426..2026576_POSITIVE 161 50 1 58 10 NC_003454:FN1713|3end_tRNA_(Uracil-5-)_-methyltransferase_208968..209118_POSITIVE 157 33 2 134 98 NC_003454:FN1611|3end_Competence_protein_120597..120747_NEGATIVE 154 23 4 82 62 NC_003454:FN0639|3end_hypothetical_protein_1297131..1297281_NEGATIVE 154 110 71 133 96 NC_003454:FN0420|3end_dihydroorotase_1061998..1062148_POSITIVE 153 28 3 126 101 NC_003454:FN1082|3end_hypothetical_protein_1728046..1728196_POSITIVE