Origin IGS: cgtatttattttatgattcgttttacaagcgcaaagatagctcgatccttaccctgaaaatgtaatctatgtgacagttgggcggatttttaggaaaaattcaggttaaaaagaaaaaaacagatacctttccggcaaggtcaggcatctgtttttggggtaagcatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgatgcttaccccaaaaacagatgcctgaccttgccggaaaggtatctgtttttttctttttaacctgaatttttcctaaaaatccgcccaactgtcacatagattacattttcagggtaaggatcgagctatctttgcgcttgtaaaacgaatcataaaataaatacg Mask Tandem Repeat Region ================================================ cgtatttattttatgattcgttttacaagcgcaaagatagctcgatccttaccctgaaaatgtaatctatgtgacagttgggcggatttttaggaaaaattcaggttaaaaagaaaaaaacagatacctttccggcaaggtcaggcatctgtttttggggtaagcatca Find is-nt database================================================ Query_seq: TF0311:TF0312|TF0311:TF0312:conserved hypothetical protein:outer membrane protein:->->:336444..336612 169 cgtatttattttatgattcgttttacaagcgcaaagatagctcgatccttaccctgaaaatgtaatctatgtgacagttgggcggatttttaggaaaaattcaggttaaaaagaaaaaaacagatacctttccggcaaggtcaggcatctgtttttggggtaagcatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0311:TF0312|TF0311:TF0312:conserved hypothetical protein:outer membrane protein:->->:336444..336612 169 cgtatttattttatgattcgttttacaagcgcaaagatagctcgatccttaccctgaaaatgtaatctatgtgacagttgggcggatttttaggaaaaattcaggttaaaaagaaaaaaacagatacctttccggcaaggtcaggcatctgtttttggggtaagcatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0311:TF0312|TF0311:TF0312:conserved hypothetical protein:outer membrane protein:->->:336444..336612 169 cgtatttattttatgattcgttttacaagcgcaaagatagctcgatccttaccctgaaaatgtaatctatgtgacagttgggcggatttttaggaaaaattcaggttaaaaagaaaaaaacagatacctttccggcaaggtcaggcatctgtttttggggtaagcatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtatttattttatgattcgttttacaagcgcaaagatagctcgatccttaccctgaaaatgtaatctatgtgacagttgggcggatttttaggaaaaattcaggttaaaaagaaaaaaacagatacctttccggcaaggtcaggcatctgtttttggggtaagcatca Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 78 End: 167 ............................................................................. M G G F L G K I Q V K K K K T D T F P A R S G I C F W G K H .. cgtatttattttatgattcgttttacaagcgcaaagatagctcgatccttaccctgaaaatgtaatctatgtgacagttgggcggatttttaggaaaaattcaggttaaaaagaaaaaaacagatacctttccggcaaggtcaggcatctgtttttggggtaagcatca 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================================================ cgtatttattttatgattcgttttacaagcgcaaagatagctcgatccttaccctgaaaatgtaatctatgtgacagttgggcggatttttaggaaaaattcaggttaaaaagaaaaaaacagatacctttccggcaaggtcaggcatctgtttttggggtaagcatca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 66 HP_score: -3.9 Tail_Score: -4.62069 Start: 121 End: 151 Full_Region: TTAAAAAGAAAAAAA CAGATACCTTTCC GGCAA GGTCAGGCATCTG TTTTTGGGGTAAGCA ........................................................................................................................CAGATACCTTTCCGGCAAGGTCAGGCATCTG.................. Find igs database================================================ Query_seq: TF0311:TF0312|TF0311:TF0312:conserved hypothetical protein:outer membrane protein:->->:336444..336612 169 cgtatttattttatgattcgttttacaagcgcaaagatagctcgatccttaccctgaaaatgtaatctatgtgacagttgggcggatttttaggaaaaattcaggttaaaaagaaaaaaacagatacctttccggcaaggtcaggcatctgtttttggggtaagcatca Intra-Species Hit: Count: 1 Min: 1 Max: 169 Len: 169 Subject: tfor_TF0311_TF0312|conserved hypothetical protein:outer membrane protein|POSITIVE:POSITIVE|[336444,336612]|169 HSP 1 e-value: 3.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 cgtatttattttatgattcgttttacaagcgcaaagatagctcgatccttaccctgaaaatgtaatctatgtgacagttgggcggatttttaggaaaaattcaggtt.............................................................. cgtatttattttatgattcgttttacaagcgcaaagatagctcgatccttaccctgaaaatgtaatctatgtgacagttgggcggatttttaggaaaaattcaggtt.............................................................. HSP 2 e-value: 1.0E-19 bit: 97.6 Len: 49 Query Start:121 Query End:169 Subject Strand: POSITIVE Subject Start: 121 Subject End: 169 ........................................................................................................................cagatacctttccggcaaggtcaggcatctgtttttggggtaagcatca ........................................................................................................................cagatacctttccggcaaggtcaggcatctgtttttggggtaagcatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUAUUUAUUUUAUGAUUCGUUUUACAAGCGCAAAGAUAGCUCGAUCCUUACCCUGAAAAUGUAAUCUAUGUGACAGUUGGGCGGAUUUUUAGGAAAAAUUCAGGUUAAAAAGAAAAAAACAGAUACCUUUCCGGCAAGGUCAGGCAUCUGUUUUUGGGGUAAGCAUCA .(.((((.(((((.((((((((..((...((((.((((.((....((........))....)).)))).))))...))..))))))))..))))).)))).).(.(((.......((((((((((.(((..((.....))..))).))))))))))....))).).... (-38.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUGCUUACCCCAAAAACAGAUGCCUGACCUUGCCGGAAAGGUAUCUGUUUUUUUCUUUUUAACCUGAAUUUUUCCUAAAAAUCCGCCCAACUGUCACAUAGAUUACAUUUUCAGGGUAAGGAUCGAGCUAUCUUUGCGCUUGUAAAACGAAUCAUAAAAUAAAUACG .(((.(((((((.((((((((((((((..((.....))..))))))))))))))......................................((((...))))............))))))).)))..((.......)).............................. (-37.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 160 121 153 112 tfor:TF2391|5end_conserved_hypothetical_protein_2562128..2562358_POSITIVE 336 158 120 48 1 tfor:TF0339|5end_hypothetical_protein_363470..363700_POSITIVE 319 160 127 71 33 tfor:TF1417|5end_conserved_hypothetical_protein_1499544..1499774_POSITIVE 299 160 121 64 23 tfor:TF2809|5end_conserved_hypothetical_protein;_possible_translation_factor_(SUA5)_2999832..3000062_POSITIVE 299 160 119 159 117 tfor:TF0775|5end_ABC_transporter,_permease_component_823664..823894_POSITIVE 297 158 133 166 135 tfor:TF2282|5end_hypothetical_protein_2439401..2439631_POSITIVE 291 62 30 155 126 tfor:TF2123|5end_conserved_hypothetical_protein;_TPR-repeat_protein_2297268..2297498_POSITIVE 288 160 127 84 39 tfor:TF1710|5end_possible_cell_filamentation_protein_1829679..1829909_POSITIVE 287 159 121 62 23 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 283 147 103 164 120 tfor:TF0426|5end_conserved_hypothetical_protein_444728..444958_POSITIVE 281 157 127 179 140 tfor:TF2430|5end_hypothetical_protein_2612660..2612890_POSITIVE 280 158 128 218 180 tfor:TF3135|5end_hypothetical_protein_3369821..3370051_POSITIVE 279 160 127 209 174 tfor:TF1319|5end_outer_membrane_protein_1396872..1397102_POSITIVE 278 147 102 193 142 tfor:TF1286|5end_hypothetical_protein_1369199..1369429_POSITIVE 274 160 123 211 166 tfor:TF0687|5end_hypothetical_protein_732226..732456_POSITIVE 274 160 123 184 139 tfor:TF0686|5end_hypothetical_protein_732199..732429_POSITIVE 272 95 60 54 19 tfor:TF0472|5end_multidrug_resistance_protein,_AcrB/AcrD/AcrF_family_(cation_efflux_pump)_487813..488043_POSITIVE 271 79 31 155 110 tfor:TF1574|5end_two-component_system_response_regulator_1681807..1682037_POSITIVE 269 156 121 64 28 tfor:TF2349|5end_conserved_hypothetical_protein_2513192..2513422_POSITIVE 269 58 13 204 157 tfor:TF0754|5end_GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-redu_ctase_(GDP-L-fucose_synthetase)_801631..801861_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 372 158 116 54 3 tfor:TF0338|3end_alkaline_phosphatase_363556..363706_POSITIVE 342 160 121 78 37 tfor:TF2390|3end_conserved_hypothetical_protein_2562133..2562283_POSITIVE 299 160 121 61 20 tfor:TF2808|3end_bacterial_sugar_transferase_2999909..3000059_POSITIVE 299 160 119 145 103 tfor:TF0774|3end_membrane-fusion_protein;_36_kDa_antigen_823730..823880_POSITIVE 293 158 121 83 37 tfor:TF2515|3end_outer_membrane_protein,_TonB_dependent_receptor_2694865..2695015_POSITIVE 291 62 30 32 3 tfor:TF2121|3end_phosphoenolpyruvate_synthase_2297225..2297375_POSITIVE 287 159 121 57 18 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 283 147 103 61 17 tfor:TF0425|3end_outer_membrane_protein_444705..444855_POSITIVE 282 149 126 65 35 tfor:TF2340|3end_hypothetical_protein_2500915..2501065_POSITIVE 276 95 53 133 94 tfor:TF2143|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2319704..2319854_POSITIVE 272 95 60 47 12 tfor:TF0471|3end_conserved_hypothetical_protein_487886..488036_POSITIVE 269 156 121 44 8 tfor:TF2348|3end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2513252..2513402_POSITIVE 266 159 122 41 3 tfor:TF0864|3end_O-succinylbenzoate--CoA_ligase_915708..915858_POSITIVE 263 57 14 54 1 tfor:TF0462|3end_possible_cobalamin_biosynthesis_precorrin-3_methylase_479095..479245_POSITIVE 260 159 121 95 55 tfor:TF1740|3end_hypothetical_protein_1869192..1869342_POSITIVE 257 57 12 151 107 tfor:TF1824|3end_ABC_transporter,_ATP-binding_protein_1973510..1973660_POSITIVE 256 60 16 105 59 tfor:TF2659|3end_conserved_hypothetical_protein_2833055..2833205_POSITIVE 255 158 121 146 118 tfor:TF2607|3end_conserved_hypothetical_protein_2784645..2784795_POSITIVE 254 152 112 150 98 tfor:TF0192|3end_hypothetical_protein_207984..208134_POSITIVE 253 157 116 135 94 tfor:TF2526|3end_outer_membrane_protein,_TonB_dependent_receptor_2709007..2709157_POSITIVE