Origin IGS: atgttttttttgcaaagataatgatcaatcaggataaaagatgaagaatttgctgatttttacccgtactgataatataaagataaaacaaagagggagatagaaccactaagcaacaatctccctcttttgttcatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatgaacaaaagagggagattgttgcttagtggttctatctccctctttgttttatctttatattatcagtacgggtaaaaatcagcaaattcttcatcttttatcctgattgatcattatctttgcaaaaaaaacat Mask Tandem Repeat Region ================================================ atgttttttttgcaaagataatgatcaatcaggataaaagatgaagaatttgctgatttttacccgtactgataatataaagataaaacaaagagggagatagaaccactaagcaacaatctccctcttttgttcatta Find is-nt database================================================ Query_seq: TF1140:TF1141|TF1140:TF1141:transcriptional regulator, AraC family:conserved hypothetical protein:->->:1217973..1218111 139 atgttttttttgcaaagataatgatcaatcaggataaaagatgaagaatttgctgatttttacccgtactgataatataaagataaaacaaagagggagatagaaccactaagcaacaatctccctcttttgttcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1140:TF1141|TF1140:TF1141:transcriptional regulator, AraC family:conserved hypothetical protein:->->:1217973..1218111 139 atgttttttttgcaaagataatgatcaatcaggataaaagatgaagaatttgctgatttttacccgtactgataatataaagataaaacaaagagggagatagaaccactaagcaacaatctccctcttttgttcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1140:TF1141|TF1140:TF1141:transcriptional regulator, AraC family:conserved hypothetical protein:->->:1217973..1218111 139 atgttttttttgcaaagataatgatcaatcaggataaaagatgaagaatttgctgatttttacccgtactgataatataaagataaaacaaagagggagatagaaccactaagcaacaatctccctcttttgttcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgttttttttgcaaagataatgatcaatcaggataaaagatgaagaatttgctgatttttacccgtactgataatataaagataaaacaaagagggagatagaaccactaagcaacaatctccctcttttgttcatta Predict ORF larger than 30AA ================================================ atgttttttttgcaaagataatgatcaatcaggataaaagatgaagaatttgctgatttttacccgtactgataatataaagataaaacaaagagggagatagaaccactaagcaacaatctccctcttttgttcatta 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================================================ atgttttttttgcaaagataatgatcaatcaggataaaagatgaagaatttgctgatttttacccgtactgataatataaagataaaacaaagagggagatagaaccactaagcaacaatctccctcttttgttcatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1140:TF1141|TF1140:TF1141:transcriptional regulator, AraC family:conserved hypothetical protein:->->:1217973..1218111 139 atgttttttttgcaaagataatgatcaatcaggataaaagatgaagaatttgctgatttttacccgtactgataatataaagataaaacaaagagggagatagaaccactaagcaacaatctccctcttttgttcatta Intra-Species Hit: Count: 1 Min: 12 Max: 139 Len: 128 Subject: tfor_TF1140_TF1141|transcriptional regulator, AraC family:conserved hypothetical protein|POSITIVE:POSITIVE|[1217973,1218111]|139 HSP 1 e-value: 7.0E-67 bit: 254.0 Len: 128 Query Start:12 Query End:139 Subject Strand: POSITIVE Subject Start: 12 Subject End: 139 ...........gcaaagataatgatcaatcaggataaaagatgaagaatttgctgatttttacccgtactgataatataaagataaaacaaagagggagatagaaccactaagcaacaatctccctcttttgttcatta ...........gcaaagataatgatcaatcaggataaaagatgaagaatttgctgatttttacccgtactgataatataaagataaaacaaagagggagatagaaccactaagcaacaatctccctcttttgttcatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAAGAUAAUGAUCAAUCAGGAUAAAAGAUGAAGAAUUUGCUGAUUUUUACCCGUACUGAUAAUAUAAAGAUAAAACAAAGAGGGAGAUAGAACCACUAAGCAACAAUCUCCCUCUUUUGUUCAUUA .......((((((...(((((...........(((((((....))))))).......)))))..............((((((((((((((.................))))))))).))))))))))) (-25.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGAACAAAAGAGGGAGAUUGUUGCUUAGUGGUUCUAUCUCCCUCUUUGUUUUAUCUUUAUAUUAUCAGUACGGGUAAAAAUCAGCAAAUUCUUCAUCUUUUAUCCUGAUUGAUCAUUAUCUUUGC ((((((...((((((((((((....(((....)))...)))))))))))).................(((((..((((((((..................))))))))..)))))))))))....... (-32.07) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 89 41 186 121 tfor:TF2658|5end_transposase_2831155..2831385_POSITIVE 258 60 12 135 80 tfor:TF0602|5end_aminotripeptidase;_peptidase_T_632169..632399_POSITIVE 252 120 74 184 137 tfor:TF1303|5end_conserved_hypothetical_protein_1383869..1384099_POSITIVE 247 116 73 99 48 tfor:TF0750|5end_conserved_hypothetical_protein_797776..798006_POSITIVE 243 60 17 148 101 tfor:TF1973|5end_propionyl-CoA_carboxylase,_beta_subunit_2119360..2119590_POSITIVE 241 118 84 219 188 tfor:TF0763|5end_chromate_transport_protein_809675..809905_POSITIVE 238 120 75 165 108 tfor:TF0187|5end_ferredoxin_202151..202381_POSITIVE 233 60 14 56 14 tfor:TF1207|5end_outer_membrane_receptor,_TonB-dependent_1290062..1290292_POSITIVE 232 46 12 190 167 tfor:TF1926|5end_hypothetical_protein_2074415..2074645_POSITIVE 230 70 21 129 72 tfor:TF2378|5end_peptide_chain_release_factor_1_2542682..2542912_POSITIVE 230 89 41 179 132 tfor:TF0421|5end_alpha-L-fucosidase_436021..436251_POSITIVE 227 57 13 179 121 tfor:TF1621|5end_DNA_replication_and_repair_protein_RecF_1735293..1735523_POSITIVE 226 104 63 206 169 tfor:TF3102|5end_hypothetical_protein_3332686..3332916_POSITIVE 223 68 35 154 117 tfor:TF2541|5end_transposase_2723914..2724144_POSITIVE 218 69 21 98 51 tfor:TF0489|5end_D-xylose-proton_symporter_511493..511723_POSITIVE 217 88 41 131 76 tfor:TF3160|5end_conserved_hypothetical_protein_3395531..3395761_POSITIVE 217 96 54 117 74 tfor:TF0039|5end_conserved_hypothetical_protein_41407..41637_POSITIVE 216 120 80 63 6 tfor:TF0766|5end_hypothetical_protein_811934..812164_POSITIVE 216 120 81 156 123 tfor:TF0543|5end_glycine_cleavage_system_p-protein_572251..572481_POSITIVE 212 118 80 143 116 tfor:TF2000|5end_conserved_hypothetical_protein_2153931..2154161_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 60 12 129 74 tfor:TF0601|3end_aminomethyltransferase_(glycine_cleavage_system_T_protein)_632243..632393_POSITIVE 252 120 74 71 24 tfor:TF1302|3end_conserved_hypothetical_protein;_possible_tetracycline_resistance_element_1383836..1383986_POSITIVE 247 116 73 74 23 tfor:TF0749|3end_protease_II_797831..797981_POSITIVE 243 60 17 123 76 tfor:TF1972|3end_conserved_hypothetical_protein_2119415..2119565_POSITIVE 233 60 14 50 8 tfor:TF1206|3end_conserved_hypothetical_protein_1290136..1290286_POSITIVE 230 70 21 73 16 tfor:TF2377|3end_orotidine_5'_phosphate_decarboxylase_2542706..2542856_POSITIVE 226 104 63 99 62 tfor:TF3101|3end_hypothetical_protein_3332659..3332809_POSITIVE 218 69 21 55 8 tfor:TF0488|3end_xylose_isomerase_511530..511680_POSITIVE 217 88 41 131 76 tfor:TF3159|3end_conserved_hypothetical_protein;_possible_transcriptional_regulator_3395611..3395761_POSITIVE 217 78 36 112 65 tfor:TF2530|3end_conserved_hypothetical_protein_2712926..2713076_POSITIVE 216 120 80 63 6 tfor:TF0765|3end_conserved_hypothetical_protein_812014..812164_POSITIVE 216 120 81 149 116 tfor:TF0542|3end_hypothetical_protein_572324..572474_POSITIVE 212 57 20 147 104 tfor:TF2450|3end_outer_membrane_protein_2629256..2629406_POSITIVE 212 118 80 66 39 tfor:TF1999|3end_ArgK_protein_with_ATPase_and_kinase_domains_2153934..2154084_POSITIVE 212 118 74 57 16 tfor:TF0408|3end_possible_gliding_motility-related_lipoprotein_426324..426474_POSITIVE 205 119 84 53 9 tfor:TF2418|3end_GTP-binding_protein_2598384..2598534_POSITIVE 204 120 82 64 21 tfor:TF0132|3end_conserved_hypothetical_protein_144999..145149_POSITIVE 203 60 20 135 88 tfor:TF1909|3end_cobalamin_(5`-phosphate)_synthase_2064075..2064225_POSITIVE 203 96 53 151 111 tfor:TF1440|3end_hypothetical_protein_1525659..1525809_POSITIVE 200 60 20 135 86 tfor:TF1580|3end_conserved_hypothetical_protein;_possible_fibronectin_domain_containing_protein_1689258..1689408_POSITIVE