Origin IGS: aaaaactcctttttatataaagcctaaaagcttaaatttgatcacagaataagtttgatcacagaataaggatacactatatttttaaaaattgcaaggttaagaatgcaaaattgcaaaaaatgcccacagcatttgaacctcatactttgacatttgcactttg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caaagtgcaaatgtcaaagtatgaggttcaaatgctgtgggcattttttgcaattttgcattcttaaccttgcaatttttaaaaatatagtgtatccttattctgtgatcaaacttattctgtgatcaaatttaagcttttaggctttatataaaaaggagttttt Mask Tandem Repeat Region ================================================ aaaaactcctttttatataaagcctaaaagcttaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngatacactatatttttaaaaattgcaaggttaagaatgcaaaattgcaaaaaatgcccacagcatttgaacctcatactttgacatttgcactttg Find is-nt database================================================ Query_seq: TDE0947:TDE0948|TDE0947:TDE0948:translation elongation factor G, putative:hypothetical protein:<-<-:970883..971048 166 aaaaactcctttttatataaagcctaaaagcttaaatttgatcacagaataagtttgatcacagaataaggatacactatatttttaaaaattgcaaggttaagaatgcaaaattgcaaaaaatgcccacagcatttgaacctcatactttgacatttgcactttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0947:TDE0948|TDE0947:TDE0948:translation elongation factor G, putative:hypothetical protein:<-<-:970883..971048 166 aaaaactcctttttatataaagcctaaaagcttaaatttgatcacagaataagtttgatcacagaataaggatacactatatttttaaaaattgcaaggttaagaatgcaaaattgcaaaaaatgcccacagcatttgaacctcatactttgacatttgcactttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0947:TDE0948|TDE0947:TDE0948:translation elongation factor G, putative:hypothetical protein:<-<-:970883..971048 166 aaaaactcctttttatataaagcctaaaagcttaaatttgatcacagaataagtttgatcacagaataaggatacactatatttttaaaaattgcaaggttaagaatgcaaaattgcaaaaaatgcccacagcatttgaacctcatactttgacatttgcactttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaactcctttttatataaagcctaaaagcttaaatttgatcacagaataagtttgatcacagaataaggatacactatatttttaaaaattgcaaggttaagaatgcaaaattgcaaaaaatgcccacagcatttgaacctcatactttgacatttgcactttg Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 66 End: 164 ................................................................. M R I H Y I F K N C K V K N A K L Q K M P T A F E P H T L T F A L .. Protein_Len: 34 Strand: - Start: 45 End: 146 ............................................ L I L K I V S Y P Y V I N K F I A L N L I C F Q L F H G C C K F R M .................... aaaaactcctttttatataaagcctaaaagcttaaatttgatcacagaataagtttgatcacagaataaggatacactatatttttaaaaattgcaaggttaagaatgcaaaattgcaaaaaatgcccacagcatttgaacctcatactttgacatttgcactttg 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: 82 Start: 69 End: 98 ....................................................................CTTGCAATTTTTAAAAATATAGTGTATCCT.................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 54 End: 83 .....................................................TTTGATCACAGAATAAGGATACACTATATT................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaactcctttttatataaagcctaaaagcttaaatttgatcacagaataagtttgatcacagaataaggatacactatatttttaaaaattgcaaggttaagaatgcaaaattgcaaaaaatgcccacagcatttgaacctcatactttgacatttgcactttg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0947:TDE0948|TDE0947:TDE0948:translation elongation factor G, putative:hypothetical protein:<-<-:970883..971048 166 aaaaactcctttttatataaagcctaaaagcttaaatttgatcacagaataagtttgatcacagaataaggatacactatatttttaaaaattgcaaggttaagaatgcaaaattgcaaaaaatgcccacagcatttgaacctcatactttgacatttgcactttg Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: NC_002967_TDE0947_TDE0948|translation elongation factor G, putative:hypothetical protein|NEGATIVE:NEGATIVE|[970883,971048]|166 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 aaaaactcctttttatataaagcctaaaagcttaaatttgatcacagaataagtttgatcacagaataaggatacactatatttttaaaaattgcaaggttaagaatgcaaaattgcaaaaaatgcccacagcatttgaacctcatactttgacatttgcactttg aaaaactcctttttatataaagcctaaaagcttaaatttgatcacagaataagtttgatcacagaataaggatacactatatttttaaaaattgcaaggttaagaatgcaaaattgcaaaaaatgcccacagcatttgaacctcatactttgacatttgcactttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACUCCUUUUUAUAUAAAGCCUAAAAGCUUAAAUUUGAUCACAGAAUAAGUUUGAUCACAGAAUAAGGAUACACUAUAUUUUUAAAAAUUGCAAGGUUAAGAAUGCAAAAUUGCAAAAAAUGCCCACAGCAUUUGAACCUCAUACUUUGACAUUUGCACUUUG ......(((((.((.....((((......)))).....((((((...........))))))...)).)))))................(((.((((((((((((..((((....))))..((((((.....))))))...........)))))).)))))).))). (-27.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAGUGCAAAUGUCAAAGUAUGAGGUUCAAAUGCUGUGGGCAUUUUUUGCAAUUUUGCAUUCUUAACCUUGCAAUUUUUAAAAAUAUAGUGUAUCCUUAUUCUGUGAUCAAACUUAUUCUGUGAUCAAAUUUAAGCUUUUAGGCUUUAUAUAAAAAGGAGUUUUU .....((((((((((..(((((.........)))))...)))))...)))))...(((((..........)))))...................(((((......((((((...........)))))).....(((((....)))))........)))))...... (-29.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 804 140 91 231 182 NC_002967:TDE0947|5end_translation_elongation_factor_G,_putative_970792..971022_NEGATIVE 251 134 92 57 17 NC_002967:TDE0405|5end_major_outer_sheath_protein_455470..455700_POSITIVE 242 134 91 65 18 NC_002967:TDE1679|5end_ATP_synthase_subunit_K_1731049..1731279_NEGATIVE 229 154 125 55 29 NC_002967:TDE0797|5end_acylphosphatase_820859..821089_POSITIVE 228 160 113 220 173 NC_002967:TDE2640|5end_hypothetical_protein_2680034..2680264_POSITIVE 221 147 109 92 46 NC_002967:TDE1132|5end_chorismate_synthase_1163415..1163645_POSITIVE 220 110 63 90 38 NC_002967:TDE2145|5end_hypothetical_protein_2182925..2183155_NEGATIVE 219 160 117 40 4 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 218 136 106 34 8 NC_002967:TDE1865|5end_peptidase,_M16_family_1892194..1892424_NEGATIVE 218 41 6 147 98 NC_002967:TDE0198|5end_hypothetical_protein_233155..233385_POSITIVE 216 139 91 198 129 NC_002967:TDE2242|5end_antigen,_putative_2282034..2282264_NEGATIVE 214 158 111 59 7 NC_002967:TDE0077|5end_glycine_reductase_complex_proprotein_GrdE1_88732..88962_NEGATIVE 212 129 89 54 13 NC_002967:TDE2673|5end_hypothetical_protein_2712377..2712607_NEGATIVE 209 58 20 108 60 NC_002967:TDE2565|5end_hypothetical_protein_2591273..2591503_NEGATIVE 209 147 104 59 17 NC_002967:TDE2418|5end_hypothetical_protein_2443833..2444063_NEGATIVE 204 158 120 85 35 NC_002967:TDE0847|5end_hypothetical_protein_870894..871124_POSITIVE 202 129 85 75 30 NC_002967:TDE2674|5end_hypothetical_protein_2713277..2713507_NEGATIVE 202 160 123 151 109 NC_002967:TDE1926|5end_hypothetical_protein_1942495..1942725_POSITIVE 201 146 102 119 67 NC_002967:TDE0545|5end_hypothetical_protein_584774..585004_POSITIVE 201 159 112 83 40 NC_002967:TDE0058|5end_hypothetical_protein_66986..67216_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 154 126 130 96 NC_002967:TDE1636|3end_surface_antigen,_putative_1683517..1683667_NEGATIVE 249 141 102 52 14 NC_002967:TDE0407|3end_glutamate_synthase_(NADPH),_homotetrameric_459011..459161_NEGATIVE 229 154 125 62 36 NC_002967:TDE0796|3end_histidinol_phosphate_phosphatase_HisJ_family_protein_820946..821096_POSITIVE 228 141 106 37 8 NC_002967:TDE0947|3end_translation_elongation_factor_G,_putative_968714..968864_NEGATIVE 222 150 105 73 13 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 221 147 109 128 82 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 219 160 117 150 114 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 218 41 6 137 88 NC_002967:TDE0197|3end_PIN_domain_protein_233225..233375_POSITIVE 211 146 106 42 1 NC_002967:TDE2604|3end_hypothetical_protein_2644224..2644374_NEGATIVE 209 58 20 49 1 NC_002967:TDE2566|3end_hypothetical_protein_2591332..2591482_NEGATIVE 205 108 66 124 77 NC_002967:TDE2720|3end_conserved_hypothetical_protein_TIGR00046_2776996..2777146_NEGATIVE 202 160 113 53 11 NC_002967:TDE1806|3end_hypothetical_protein_1843190..1843340_NEGATIVE 201 146 102 131 79 NC_002967:TDE0544|3end_hypothetical_protein_584866..585016_POSITIVE 198 123 91 82 51 NC_002967:TDE2095|3end_hypothetical_protein_2123283..2123433_POSITIVE 196 140 92 69 23 NC_002967:TDE0597|3end_hypothetical_protein_636019..636169_NEGATIVE 192 140 93 69 25 NC_002967:TDE1795|3end_funZ_protein,_putative_1833063..1833213_NEGATIVE 191 140 95 79 32 NC_002967:TDE2234|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2272310..2272460_NEGATIVE 191 60 19 81 47 NC_002967:TDE2146|3end_hydrolase,_alpha/beta_fold_family_2184054..2184204_POSITIVE 190 139 110 145 119 NC_002967:TDE2260|3end_hypothetical_protein_2297573..2297723_POSITIVE 189 133 91 69 30 NC_002967:TDE1396|3end_hypothetical_protein_1436127..1436277_POSITIVE