Origin IGS: cttttcaaattcctctacagaataaattttcggcatattttttttaaacttgaattttaattgcagccttgcaaaatatagtatttttgtttataatgacagaaaaccctaggtcattatggaggggact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtcccctccataatgacctagggttttctgtcattataaacaaaaatactatattttgcaaggctgcaattaaaattcaagtttaaaaaaaatatgccgaaaatttattctgtagaggaatttgaaaag Mask Tandem Repeat Region ================================================ cttttcaaattcctctacagaataaattttcggcatattttttttaaacttgaattttaattgcagccttgcaaaatatagtatttttgtttataatgacagaaaaccctaggtcattatggaggggact Find is-nt database================================================ Query_seq: TDE0051:TDE0052|TDE0051:TDE0052:alcohol dehydrogenase, iron-containing:flagellar biosynthetic protein FliQ:<-->:61315..61444 130 cttttcaaattcctctacagaataaattttcggcatattttttttaaacttgaattttaattgcagccttgcaaaatatagtatttttgtttataatgacagaaaaccctaggtcattatggaggggact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0051:TDE0052|TDE0051:TDE0052:alcohol dehydrogenase, iron-containing:flagellar biosynthetic protein FliQ:<-->:61315..61444 130 cttttcaaattcctctacagaataaattttcggcatattttttttaaacttgaattttaattgcagccttgcaaaatatagtatttttgtttataatgacagaaaaccctaggtcattatggaggggact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0051:TDE0052|TDE0051:TDE0052:alcohol dehydrogenase, iron-containing:flagellar biosynthetic protein FliQ:<-->:61315..61444 130 cttttcaaattcctctacagaataaattttcggcatattttttttaaacttgaattttaattgcagccttgcaaaatatagtatttttgtttataatgacagaaaaccctaggtcattatggaggggact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttttcaaattcctctacagaataaattttcggcatattttttttaaacttgaattttaattgcagccttgcaaaatatagtatttttgtttataatgacagaaaaccctaggtcattatggaggggact Predict ORF larger than 30AA ================================================ cttttcaaattcctctacagaataaattttcggcatattttttttaaacttgaattttaattgcagccttgcaaaatatagtatttttgtttataatgacagaaaaccctaggtcattatggaggggact 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: 91 Start: 68 End: 97 ...................................................................CTTGCAAAATATAGTATTTTTGTTTATAAT................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttttcaaattcctctacagaataaattttcggcatattttttttaaacttgaattttaattgcagccttgcaaaatatagtatttttgtttataatgacagaaaaccctaggtcattatggaggggact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0051:TDE0052|TDE0051:TDE0052:alcohol dehydrogenase, iron-containing:flagellar biosynthetic protein FliQ:<-->:61315..61444 130 cttttcaaattcctctacagaataaattttcggcatattttttttaaacttgaattttaattgcagccttgcaaaatatagtatttttgtttataatgacagaaaaccctaggtcattatggaggggact Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_002967_TDE0051_TDE0052|alcohol dehydrogenase, iron-containing:flagellar biosynthetic protein FliQ|NEGATIVE:POSITIVE|[61315,61444]|130 HSP 1 e-value: 8.0E-54 bit: 210.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 cttttcaaattcctctacagaataaattttcggcatannnnnnnnaaacttgaattttaattgcagccttgcaaaatatagtatttttgtttataatgacagaaaaccctaggtcattatggaggggact cttttcaaattcctctacagaataaattttcggcatattttttttaaacttgaattttaattgcagccttgcaaaatatagtatttttgtttataatgacagaaaaccctaggtcattatggaggggact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUCAAAUUCCUCUACAGAAUAAAUUUUCGGCAUAUUUUUUUUAAACUUGAAUUUUAAUUGCAGCCUUGCAAAAUAUAGUAUUUUUGUUUAUAAUGACAGAAAACCCUAGGUCAUUAUGGAGGGGACU .........((((((((..(((......)))................(((((........((((......)))).........((((((((......))))))))....))))).....))))))))... (-20.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCCCCUCCAUAAUGACCUAGGGUUUUCUGUCAUUAUAAACAAAAAUACUAUAUUUUGCAAGGCUGCAAUUAAAAUUCAAGUUUAAAAAAAAUAUGCCGAAAAUUUAUUCUGUAGAGGAAUUUGAAAAG .((..(((..((((((((..(((....)))))))))))...(((((........)))))..)))..))........(((((((((..........(((.(((......))).)))...)))))))))... (-17.62) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 824 130 81 221 172 NC_002967:TDE0051|5end_alcohol_dehydrogenase,_iron-containing_61224..61454_NEGATIVE 240 46 1 224 186 NC_002967:TDE2524|5end_ABC_transporter,_ATP-binding_protein_2550456..2550686_POSITIVE 219 109 61 227 184 NC_002967:TDE1145|5end_hypothetical_protein_1184811..1185041_NEGATIVE 212 76 35 133 93 NC_002967:TDE0259|5end_transcriptional_regulator,_MarR_family_293257..293487_POSITIVE 210 109 61 183 134 NC_002967:TDE2076|5end_hypothetical_protein_2106008..2106238_NEGATIVE 209 120 80 165 125 NC_002967:TDE1477|5end_flagellar_filament_core_protein_1523333..1523563_NEGATIVE 207 117 74 116 61 NC_002967:TDE2127|5end_vapC_protein,_putative_2159763..2159993_POSITIVE 207 66 30 125 85 NC_002967:TDE1526|5end_hypothetical_protein_1570565..1570795_POSITIVE 206 130 83 141 95 NC_002967:TDE0986|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1013061..1013291_POSITIVE 204 109 61 65 21 NC_002967:TDE1180|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein_1209833..1210063_NEGATIVE 204 70 28 217 166 NC_002967:TDE1067|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1095701..1095931_NEGATIVE 203 100 60 132 92 NC_002967:TDE0220|5end_hypothetical_protein_254005..254235_NEGATIVE 201 58 11 142 100 NC_002967:TDE0873|5end_hypothetical_protein_896143..896373_POSITIVE 200 110 66 66 21 NC_002967:TDE0532|5end_TPR_domain_protein_575570..575800_POSITIVE 198 70 25 58 14 NC_002967:TDE0125|5end_GGDEF_domain_protein_144010..144240_NEGATIVE 196 74 47 161 132 NC_002967:TDE1034|5end_magnesium_and_cobalt_transporter,_putative_1062454..1062684_POSITIVE 196 127 85 117 74 NC_002967:TDE0759|5end_hypothetical_protein_799499..799729_NEGATIVE 195 89 49 171 125 NC_002967:TDE0797|5end_acylphosphatase_820859..821089_POSITIVE 195 43 9 220 190 NC_002967:TDE0459|5end_hypothetical_protein_514382..514612_POSITIVE 193 69 42 231 196 NC_002967:TDE1437|5end_capsular_polysaccharide_biosynthesis_protein_1482232..1482462_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 210 109 61 121 72 NC_002967:TDE2077|3end_hypothetical_protein_2106070..2106220_NEGATIVE 207 117 74 116 61 NC_002967:TDE2126|3end_hypothetical_protein_2159843..2159993_POSITIVE 207 66 30 134 94 NC_002967:TDE1525|3end_hypothetical_protein_1570654..1570804_POSITIVE 206 130 83 54 8 NC_002967:TDE0985|3end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_1013054..1013204_POSITIVE 203 35 3 125 89 NC_002967:TDE2254|3end_hypothetical_protein_2291445..2291595_NEGATIVE 203 100 60 91 51 NC_002967:TDE0221|3end_hypothetical_protein_254046..254196_NEGATIVE 201 73 31 51 10 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 201 58 11 84 42 NC_002967:TDE0872|3end_recA_protein_896165..896315_POSITIVE 198 93 60 55 16 NC_002967:TDE2205|3end_enoate_reductase,_putative_2242575..2242725_NEGATIVE 198 70 25 77 33 NC_002967:TDE0126|3end_hypothetical_protein_143991..144141_NEGATIVE 196 74 47 122 93 NC_002967:TDE1033|3end_polyA_polymerase_family_protein_1062495..1062645_POSITIVE 195 99 63 107 69 NC_002967:TDE1676|3end_ribosomal_protein_S18_1729373..1729523_NEGATIVE 194 110 63 104 49 NC_002967:TDE0997|3end_glutamate_dehydrogenase_1024042..1024192_NEGATIVE 194 78 33 61 11 NC_002967:TDE0875|3end_ribosomal_large_subunit_pseudouridine_synthase_B_898273..898423_POSITIVE 191 73 34 112 65 NC_002967:TDE2779|3end_hypothetical_protein_2829628..2829778_NEGATIVE 191 126 86 106 57 NC_002967:TDE2458|3end_hypothetical_protein_2485849..2485999_POSITIVE 190 90 47 131 99 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE 190 34 9 62 28 NC_002967:TDE0264|3end_ribbon-helix-helix_protein,_CopG_family_297021..297171_NEGATIVE 188 129 83 74 29 NC_002967:TDE1744|3end_chromate_transport_protein_1798503..1798653_NEGATIVE 188 51 12 107 61 NC_002967:TDE1310|3end_modulator_of_DNA_gyrase_family_protein_1347340..1347490_POSITIVE