Origin IGS: aaagttaaattaatatgatacaaactgcctcaaacgtataaactttgtaaaaacatgtatatagaatacagtttgctcaaaattttacgctatcggattgttgtatttaatattctttaacta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagttaaagaatattaaatacaacaatccgatagcgtaaaattttgagcaaactgtattctatatacatgtttttacaaagtttatacgtttgaggcagtttgtatcatattaatttaacttt Mask Tandem Repeat Region ================================================ aaagttaaattaatatgatacaaactgcctcaaacgtataaactttgtaaaaacatgtatatagaatacagtttgctcaaaattttacgctatcggattgttgtatttaatattctttaacta Find is-nt database================================================ Query_seq: TF1207:TF1208|TF1207:TF1208:outer membrane receptor, TonB-dependent:anti-sigma factor:->->:1293613..1293735 123 aaagttaaattaatatgatacaaactgcctcaaacgtataaactttgtaaaaacatgtatatagaatacagtttgctcaaaattttacgctatcggattgttgtatttaatattctttaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1207:TF1208|TF1207:TF1208:outer membrane receptor, TonB-dependent:anti-sigma factor:->->:1293613..1293735 123 aaagttaaattaatatgatacaaactgcctcaaacgtataaactttgtaaaaacatgtatatagaatacagtttgctcaaaattttacgctatcggattgttgtatttaatattctttaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1207:TF1208|TF1207:TF1208:outer membrane receptor, TonB-dependent:anti-sigma factor:->->:1293613..1293735 123 aaagttaaattaatatgatacaaactgcctcaaacgtataaactttgtaaaaacatgtatatagaatacagtttgctcaaaattttacgctatcggattgttgtatttaatattctttaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagttaaattaatatgatacaaactgcctcaaacgtataaactttgtaaaaacatgtatatagaatacagtttgctcaaaattttacgctatcggattgttgtatttaatattctttaacta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 25 End: 117 ........................ M P Q T Y K L C K N M Y I E Y S L L K I L R Y R I V V F N I L ...... aaagttaaattaatatgatacaaactgcctcaaacgtataaactttgtaaaaacatgtatatagaatacagtttgctcaaaattttacgctatcggattgttgtatttaatattctttaacta 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================================================ aaagttaaattaatatgatacaaactgcctcaaacgtataaactttgtaaaaacatgtatatagaatacagtttgctcaaaattttacgctatcggattgttgtatttaatattctttaacta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1207:TF1208|TF1207:TF1208:outer membrane receptor, TonB-dependent:anti-sigma factor:->->:1293613..1293735 123 aaagttaaattaatatgatacaaactgcctcaaacgtataaactttgtaaaaacatgtatatagaatacagtttgctcaaaattttacgctatcggattgttgtatttaatattctttaacta Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: tfor_TF1207_TF1208|outer membrane receptor, TonB-dependent:anti-sigma factor|POSITIVE:POSITIVE|[1293613,1293735]|123 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 aaagttaaattaatatgatacaaactgcctcaaacgtataaactttgtaaaaacatgtatatagaatacagtttgctcaaaattttacgctatcggattgttgtatttaatattctttaacta aaagttaaattaatatgatacaaactgcctcaaacgtataaactttgtaaaaacatgtatatagaatacagtttgctcaaaattttacgctatcggattgttgtatttaatattctttaacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUUAAAUUAAUAUGAUACAAACUGCCUCAAACGUAUAAACUUUGUAAAAACAUGUAUAUAGAAUACAGUUUGCUCAAAAUUUUACGCUAUCGGAUUGUUGUAUUUAAUAUUCUUUAACUA ..(((((((..((((((((((((....((.....((((.(((.((((...((((.(((((.....)))))))))...)))).))))))).....))....)))))))..))))).))))))). (-24.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUAAAGAAUAUUAAAUACAACAAUCCGAUAGCGUAAAAUUUUGAGCAAACUGUAUUCUAUAUACAUGUUUUUACAAAGUUUAUACGUUUGAGGCAGUUUGUAUCAUAUUAAUUUAACUUU .(((((((.(((((...((((((....((...((((((((((((((...(((((((((.....))))).))))...)))))))).))))))...))....)))))).)))))..))))))).. (-27.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 108 69 210 182 tfor:TF0529|5end_transposase_554776..555006_POSITIVE 241 100 54 218 177 tfor:TF0046|5end_thiamin_biosynthesis_lipoprotein,_ApbE_52522..52752_POSITIVE 214 66 24 228 187 tfor:TF2300|5end_conserved_hypothetical_protein_2450621..2450851_POSITIVE 214 96 69 192 163 tfor:TF0810|5end_possible_outer_membrane_efflux_protein_868438..868668_POSITIVE 211 109 68 65 25 tfor:TF0908|5end_integrase_fragment_950729..950959_POSITIVE 208 76 35 217 166 tfor:TF3067|5end_conserved_hypothetical_protein_3292432..3292662_POSITIVE 208 119 74 90 43 tfor:TF3035|5end_aldose_1-epimerase_3260538..3260768_POSITIVE 208 103 64 140 103 tfor:TF2371|5end_conserved_hypothetical_protein_2536974..2537204_POSITIVE 204 55 24 83 44 tfor:TF3072|5end_conserved_hypothetical_protein_3295302..3295532_POSITIVE 202 100 69 149 120 tfor:TF2219|5end_two-component_system_sensor_histidine_2390844..2391074_POSITIVE 202 115 73 89 41 tfor:TF1888|5end_RNA_polymerase_ECF-type_sigma_factor_2040940..2041170_POSITIVE 201 103 66 217 178 tfor:TF2829|5end_conserved_hypothetical_protein_3019562..3019792_POSITIVE 200 50 12 66 31 tfor:TF2979|5end_possible_outer_membrane__protein_3190778..3191008_POSITIVE 199 68 25 119 76 tfor:TF2508|5end_ATP-dependent_Clp_protease,_ATP-binding_subunit_clpX_2686315..2686545_POSITIVE 199 106 64 92 35 tfor:TF1986|5end_hypothetical_protein_2137021..2137251_POSITIVE 199 108 68 115 80 tfor:TF0267|5end_conserved_hypothetical_protein_295803..296033_POSITIVE 196 78 35 145 107 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 194 95 62 175 144 tfor:TF1224|5end_hypothetical_protein_1311203..1311433_POSITIVE 193 110 73 139 103 tfor:TF0633|5end_hypothetical_protein_668922..669152_POSITIVE 190 97 63 142 109 tfor:TF1507|5end_outer_membrane_receptor,_TonB-dependent_1614536..1614766_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 98 54 151 90 tfor:TF1275|3end_transcription-repair_coupling_factor_1361290..1361440_POSITIVE 265 108 69 133 105 tfor:TF0528|3end_two-component_system_sensor_histidine_kinase_554779..554929_POSITIVE 208 76 35 117 66 tfor:TF3065|3end_enolase_3292412..3292562_POSITIVE 208 103 64 130 93 tfor:TF2370|3end_tRNA_delta-2_isopentenylpyrophosphate_transferase_2537044..2537194_POSITIVE 204 55 24 83 44 tfor:TF3071|3end_integral_membrane_protein,_possible_MotA/TolQ/ExbB_proton_channel_family_3295382..3295532_POSITIVE 200 50 12 70 35 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 199 68 25 89 46 tfor:TF2507|3end_ATP-dependent_DNA_helicase_2686365..2686515_POSITIVE 199 97 52 134 94 tfor:TF1824|3end_ABC_transporter,_ATP-binding_protein_1973510..1973660_POSITIVE 192 104 71 36 6 tfor:TF1165|3end_conserved_hypothetical_protein_1245921..1246071_POSITIVE 189 115 73 106 70 tfor:TF1319|3end_outer_membrane_protein_1398460..1398610_POSITIVE 186 57 15 96 40 tfor:TF2657|3end_conserved_hypothetical_protein_2830873..2831023_POSITIVE 182 112 71 143 97 tfor:TF1832|3end_3-isopropylmalate_dehydratase,_small_subunit_1981502..1981652_POSITIVE 181 93 54 54 16 tfor:TF2501|3end_DNA_mismatch_repair_protein_2678183..2678333_POSITIVE 180 105 61 84 37 tfor:TF2850|3end_endoribonuclease_L-PSP_3038871..3039021_POSITIVE 180 108 64 73 29 tfor:TF1575|3end_DNA-binding_response_regulator_1685895..1686045_POSITIVE 179 104 70 142 112 tfor:TF2048|3end_conserved_hypothetical_protein_2213182..2213332_POSITIVE 178 102 70 117 79 tfor:TF2843|3end_conserved_hypothetical_protein;_possible_lipoprotein_3033760..3033910_POSITIVE 177 105 69 47 11 tfor:TF2832|3end_possible_proton/sodium:glutamate_symporter_protein_3023939..3024089_POSITIVE 177 114 81 64 29 tfor:TF2525|3end_conserved_hypothetical_protein_2705612..2705762_POSITIVE 177 111 88 146 123 tfor:TF1725|3end_hypothetical_protein_1852094..1852244_POSITIVE