Origin IGS: aataatcctccttgatatgaataatatcaatttatataagccattagcttataataacataatattttataaacttcaagctcattgcaaaataaaatgatagctaataacatatattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatatatgttattagctatcattttattttgcaatgagcttgaagtttataaaatattatgttattataagctaatggcttatataaattgatattattcatatcaaggaggattatt Mask Tandem Repeat Region ================================================ aataatcctccttgatatgaataatatcaatttatataagccattagcttataataacataatattttataaacttcaagctcattgcaaaataaaatgatagctaataacatatattt Find is-nt database================================================ Query_seq: TDE2444:TDE2445|TDE2444:TDE2445:hypothetical protein:DNA-binding protein:<-->:2474303..2474421 119 aataatcctccttgatatgaataatatcaatttatataagccattagcttataataacataatattttataaacttcaagctcattgcaaaataaaatgatagctaataacatatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2444:TDE2445|TDE2444:TDE2445:hypothetical protein:DNA-binding protein:<-->:2474303..2474421 119 aataatcctccttgatatgaataatatcaatttatataagccattagcttataataacataatattttataaacttcaagctcattgcaaaataaaatgatagctaataacatatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2444:TDE2445|TDE2444:TDE2445:hypothetical protein:DNA-binding protein:<-->:2474303..2474421 119 aataatcctccttgatatgaataatatcaatttatataagccattagcttataataacataatattttataaacttcaagctcattgcaaaataaaatgatagctaataacatatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aataatcctccttgatatgaataatatcaatttatataagccattagcttataataacataatattttataaacttcaagctcattgcaaaataaaatgatagctaataacatatattt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 2 End: 97 . M I L L D M N N I N L Y K P L A Y N N I I F Y K L Q A H C K I K ...................... aataatcctccttgatatgaataatatcaatttatataagccattagcttataataacataatattttataaacttcaagctcattgcaaaataaaatgatagctaataacatatattt 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: 85 Start: 51 End: 80 ..................................................CTTGAAGTTTATAAAATATTATGTTATTAT....................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 84 End: 113 ...................................................................................ATTGCAAAATAAAATGATAGCTAATAACAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aataatcctccttgatatgaataatatcaatttatataagccattagcttataataacataatattttataaacttcaagctcattgcaaaataaaatgatagctaataacatatattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2444:TDE2445|TDE2444:TDE2445:hypothetical protein:DNA-binding protein:<-->:2474303..2474421 119 aataatcctccttgatatgaataatatcaatttatataagccattagcttataataacataatattttataaacttcaagctcattgcaaaataaaatgatagctaataacatatattt Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: NC_002967_TDE2444_TDE2445|hypothetical protein:DNA-binding protein|NEGATIVE:POSITIVE|[2474303,2474421]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 aataatcctccttgatatgaataatatcaatttatataagccattagcttataataacataatattttataaacttcaagctcattgcaaaataaaatgatagctaataacatatattt aataatcctccttgatatgaataatatcaatttatataagccattagcttataataacataatattttataaacttcaagctcattgcaaaataaaatgatagctaataacatatattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAUCCUCCUUGAUAUGAAUAAUAUCAAUUUAUAUAAGCCAUUAGCUUAUAAUAACAUAAUAUUUUAUAAACUUCAAGCUCAUUGCAAAAUAAAAUGAUAGCUAAUAACAUAUAUUU ...........(((((((.....)))))))....(((((((.....))))))).........................((((((((.........)))))..))).............. (-15.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAUAUGUUAUUAGCUAUCAUUUUAUUUUGCAAUGAGCUUGAAGUUUAUAAAAUAUUAUGUUAUUAUAAGCUAAUGGCUUAUAUAAAUUGAUAUUAUUCAUAUCAAGGAGGAUUAUU ..(((((.((((((((((..(((..((((((...((((((.....))))))))))))..)))........)))))))))).)))))...(((((((.....)))))))........... (-23.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 718 50 1 141 92 NC_002967:TDE2444|5end_hypothetical_protein_2474212..2474442_NEGATIVE 215 45 1 211 175 NC_002967:TDE0157|5end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_183859..184089_POSITIVE 214 60 14 132 87 NC_002967:TDE2219|5end_hypothetical_protein_2260646..2260876_NEGATIVE 194 50 6 137 99 NC_002967:TDE1477|5end_flagellar_filament_core_protein_1523333..1523563_NEGATIVE 193 38 6 140 99 NC_002967:TDE1501|5end_pyruvate_phosphate_dikinase_1548041..1548271_POSITIVE 191 42 7 137 101 NC_002967:TDE2625|5end_ABC_transporter,_ATP-binding/permease_protein_2666664..2666894_NEGATIVE 183 106 78 57 27 NC_002967:TDE0955|5end_LemA_family_protein_978842..979072_POSITIVE 180 50 2 137 75 NC_002967:TDE0076|5end_aldolase,_DeoC/FbaB_family_87386..87616_NEGATIVE 179 48 6 142 95 NC_002967:TDE2479|5end_hypothetical_protein_2503290..2503520_NEGATIVE 178 106 72 63 26 NC_002967:TDE0705|5end_SPFH_domain/Band_7_family_protein_740268..740498_NEGATIVE 178 50 1 135 82 NC_002967:TDE0428|5end_TPR_domain_protein_485193..485423_NEGATIVE 177 95 58 212 180 NC_002967:TDE1649|5end_hypothetical_protein_1697437..1697667_NEGATIVE 172 61 35 59 32 NC_002967:TDE1505|5end_hypothetical_protein_1553614..1553844_POSITIVE 169 49 7 99 51 NC_002967:TDE0243|5end_ABC_transporter,_ATP-binding_protein_277501..277731_NEGATIVE 168 106 73 118 85 NC_002967:TDE1919|5end_hypothetical_protein_1939890..1940120_NEGATIVE 168 46 6 133 99 NC_002967:TDE1114|5end_transcriptional_regulator,_TetR_family_1148905..1149135_NEGATIVE 166 41 4 149 101 NC_002967:TDE2418|5end_hypothetical_protein_2443833..2444063_NEGATIVE 165 98 63 228 197 NC_002967:TDE2476|5end_carbamate_kinase_2499450..2499680_NEGATIVE 162 106 66 230 194 NC_002967:TDE2605|5end_phosphoglycerate_mutase_family_protein_2645818..2646048_POSITIVE 162 48 6 227 181 NC_002967:TDE2345|5end_ribosome_recycling_factor_2382503..2382733_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 191 42 7 144 108 NC_002967:TDE2626|3end_ABC_transporter,_ATP-binding/permease_protein_2666657..2666807_NEGATIVE 180 50 2 101 39 NC_002967:TDE0077|3end_glycine_reductase_complex_proprotein_GrdE1_87422..87572_NEGATIVE 179 48 6 66 19 NC_002967:TDE2480|3end_heat_shock_protein_90_2503366..2503516_NEGATIVE 178 50 1 123 70 NC_002967:TDE0429|3end_hypothetical_protein_485205..485355_NEGATIVE 169 49 7 111 63 NC_002967:TDE0244|3end_ABC_transporter,_ATP-binding/permease_protein_277489..277639_NEGATIVE 168 106 73 90 57 NC_002967:TDE1920|3end_lipoprotein,_putative_1939918..1940068_NEGATIVE 162 48 6 143 97 NC_002967:TDE2346|3end_elongation_factor_Ts_2382587..2382737_NEGATIVE 162 42 7 51 15 NC_002967:TDE0251|3end_tryptophanase_284717..284867_NEGATIVE 159 79 39 126 79 NC_002967:TDE0444|3end_glutamine_amidotransferase_class-I_domain_protein_499771..499921_POSITIVE 158 105 70 113 80 NC_002967:TDE1942|3end_hypothetical_protein_1959438..1959588_POSITIVE 156 85 41 99 52 NC_002967:TDE2141|3end_hypothetical_protein_2175583..2175733_NEGATIVE 156 93 65 65 30 NC_002967:TDE0563|3end_hypothetical_protein_596309..596459_POSITIVE 155 88 69 37 15 NC_002967:TDE2604|3end_hypothetical_protein_2644224..2644374_NEGATIVE 155 27 7 138 120 NC_002967:TDE1648|3end_hypothetical_protein_1696486..1696636_NEGATIVE 155 33 6 129 99 NC_002967:TDE0681|3end_protein_export_protein_SecD_718856..719006_NEGATIVE 154 49 18 33 10 NC_002967:TDE1378|3end_hypothetical_protein_1419810..1419960_NEGATIVE 153 78 42 107 76 NC_002967:TDE0708|3end_nitroreductase_family_protein_744495..744645_POSITIVE 152 29 3 33 8 NC_002967:TDE0662|3end_hypothetical_protein_697572..697722_NEGATIVE 149 54 11 58 15 NC_002967:TDE2598|3end_hypothetical_protein_2632719..2632869_NEGATIVE 148 105 65 128 89 NC_002967:TDE0170|3end_nuclease_SbcCD,_D_subunit,_putative_200020..200170_POSITIVE