Origin IGS: taaatgcaatatttggcccataagccacacccctcgagtgtgatcaaagaaaaagcactaaaggacatacttggatatttaataaataacaaactgatataaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttatatcagtttgttatttattaaatatccaagtatgtcctttagtgctttttctttgatcacactcgaggggtgtggcttatgggccaaatattgcattta Mask Tandem Repeat Region ================================================ taaatgcaatatttggcccataagccacacccctcgagtgtgatcaaagaaaaagcactaaaggacatacttggatatttaataaataacaaactgatataaaaa Find is-nt database================================================ Query_seq: TF0500:TF0501|TF0500:TF0501:hypothetical protein:conserved hypothetical protein, HicB-related:->->:526984..527088 105 taaatgcaatatttggcccataagccacacccctcgagtgtgatcaaagaaaaagcactaaaggacatacttggatatttaataaataacaaactgatataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0500:TF0501|TF0500:TF0501:hypothetical protein:conserved hypothetical protein, HicB-related:->->:526984..527088 105 taaatgcaatatttggcccataagccacacccctcgagtgtgatcaaagaaaaagcactaaaggacatacttggatatttaataaataacaaactgatataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0500:TF0501|TF0500:TF0501:hypothetical protein:conserved hypothetical protein, HicB-related:->->:526984..527088 105 taaatgcaatatttggcccataagccacacccctcgagtgtgatcaaagaaaaagcactaaaggacatacttggatatttaataaataacaaactgatataaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaatgcaatatttggcccataagccacacccctcgagtgtgatcaaagaaaaagcactaaaggacatacttggatatttaataaataacaaactgatataaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 4 End: 99 ... M Q Y L A H K P H P S S V I K E K A L K D I L G Y L I N N K L I ...... Protein_Len: 32 Strand: - Start: 3 End: 98 .. I C Y K A W L G C G E L T I L S F A S F S M S P Y K I F L L S M ....... taaatgcaatatttggcccataagccacacccctcgagtgtgatcaaagaaaaagcactaaaggacatacttggatatttaataaataacaaactgatataaaaa 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================================================ taaatgcaatatttggcccataagccacacccctcgagtgtgatcaaagaaaaagcactaaaggacatacttggatatttaataaataacaaactgatataaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0500:TF0501|TF0500:TF0501:hypothetical protein:conserved hypothetical protein, HicB-related:->->:526984..527088 105 taaatgcaatatttggcccataagccacacccctcgagtgtgatcaaagaaaaagcactaaaggacatacttggatatttaataaataacaaactgatataaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: tfor_TF0500_TF0501|hypothetical protein:conserved hypothetical protein, HicB-related|POSITIVE:POSITIVE|[526984,527088]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 taaatgcaatatttggcccataagccacacccctcgagtgtgatcaaagaaaaagcactaaaggacatacttggatatttaataaataacaaactgatataaaaa taaatgcaatatttggcccataagccacacccctcgagtgtgatcaaagaaaaagcactaaaggacatacttggatatttaataaataacaaactgatataaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUGCAAUAUUUGGCCCAUAAGCCACACCCCUCGAGUGUGAUCAAAGAAAAAGCACUAAAGGACAUACUUGGAUAUUUAAUAAAUAACAAACUGAUAUAAAAA ((((((.......((((......))))......(((((((((.((..((........))....))))))))))).))))))........................ (-14.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUAUAUCAGUUUGUUAUUUAUUAAAUAUCCAAGUAUGUCCUUUAGUGCUUUUUCUUUGAUCACACUCGAGGGGUGUGGCUUAUGGGCCAAAUAUUGCAUUUA ....(((((..(..((((........))))..)..)))))......(((((...((((((((......))))))))..(((((....)))))......))))).. (-17.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 44 4 185 125 tfor:TF0446|5end_hypothetical_protein_466473..466703_POSITIVE 311 45 5 168 120 tfor:TF0285|5end_conserved_hypothetical_protein_314465..314695_POSITIVE 310 77 32 133 79 tfor:TF2368|5end_uridine_phosphorylase_2533666..2533896_POSITIVE 290 40 4 197 160 tfor:TF2931|5end_3-deoxy-D-manno-2-octulosonic_acid_(Kdo_transferase)_3134275..3134505_POSITIVE 279 42 14 47 23 tfor:TF0808|5end_cation_efflux_system_protein_864106..864336_POSITIVE 274 52 11 201 155 tfor:TF0344|5end_hypothetical_protein_366722..366952_POSITIVE 269 50 6 82 19 tfor:TF2615|5end_conserved_hypothetical_protein_2790569..2790799_POSITIVE 263 73 31 48 4 tfor:TF2482|5end_hypothetical_protein_2658503..2658733_POSITIVE 259 45 4 56 14 tfor:TF1538|5end_conserved_hypothetical_protein_1643531..1643761_POSITIVE 259 60 19 203 159 tfor:TF0495|5end_conserved_hypothetical_protein;_possible_S-layer_related_protein_precursor_520862..521092_POSITIVE 250 44 5 150 118 tfor:TF1899|5end_anti-sigma_factor_2052767..2052997_POSITIVE 249 45 11 35 3 tfor:TF2477|5end_phosphatase_2654229..2654459_POSITIVE 248 52 16 44 7 tfor:TF0349|5end_hypothetical_protein_370367..370597_POSITIVE 245 76 33 188 142 tfor:TF2829|5end_conserved_hypothetical_protein_3019562..3019792_POSITIVE 243 43 11 53 18 tfor:TF1873|5end_possible_hemolysin_secretion_protein_2026745..2026975_POSITIVE 243 42 12 190 144 tfor:TF1599|5end_ribonuclease_P_protein_component_1713564..1713794_POSITIVE 243 43 11 53 18 tfor:TF1131|5end_membrane-fusion_protein;_possible_hemolysin_secretion_protein_1207611..1207841_POSITIVE 241 58 14 170 113 tfor:TF3080|5end_conserved_hypothetical_protein_3310480..3310710_POSITIVE 238 49 4 229 172 tfor:TF1619|5end_riboflavin_synthase,_beta_subunit_1733948..1734178_POSITIVE 238 53 11 46 1 tfor:TF0243|5end_conserved_hypothetical_protein_273728..273958_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 44 4 150 90 tfor:TF0444|3end_Na+-translocating_NADH-quinone_oxidoreductase,_subunit_5_466518..466668_POSITIVE 310 77 32 97 43 tfor:TF2367|3end_delta-1-pyrroline-5-carboxylate_dehydrogenase_2533710..2533860_POSITIVE 298 47 4 149 97 tfor:TF0207|3end_conserved_hypothetical_protein_233505..233655_POSITIVE 269 50 6 69 6 tfor:TF2614|3end_conserved_hypothetical_protein_2790636..2790786_POSITIVE 263 73 31 48 4 tfor:TF2481|3end_possible_thiol_protease/hemagglutinin_PrtT_2658583..2658733_POSITIVE 261 75 36 92 51 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 258 52 14 42 2 tfor:TF0342|3end_hypothetical_protein_366643..366793_POSITIVE 250 44 5 73 41 tfor:TF1898|3end_RNA_polymerase_ECF-type_sigma_factor_2052770..2052920_POSITIVE 248 45 3 80 39 tfor:TF0877|3end_ISPg2-related_(PGIS2-related)_transposase_931817..931967_POSITIVE 248 52 16 44 7 tfor:TF0348|3end_hypothetical_protein_370447..370597_POSITIVE 244 35 11 129 96 tfor:TF2486|3end_hypothetical_protein_2662731..2662881_POSITIVE 243 43 11 39 4 tfor:TF1872|3end_ABC_transporter,_ATP-binding/permease_component_2026811..2026961_POSITIVE 243 43 11 39 4 tfor:TF1130|3end_ABC_transporter_ATP-binding_protein/permease_component_1207677..1207827_POSITIVE 235 43 3 68 29 tfor:TF1585|3end_hypothetical_protein_1690610..1690760_POSITIVE 235 43 3 61 22 tfor:TF1584|3end_hypothetical_protein_1690603..1690753_POSITIVE 233 60 14 82 20 tfor:TF2951|3end_O-succinylbenzoic_acid--CoA_ligase_3159622..3159772_POSITIVE 232 59 14 142 107 tfor:TF1519|3end_hypothetical_protein_1628022..1628172_POSITIVE 231 57 16 136 92 tfor:TF0105|3end_DNA-binding_stress_protein,_Dps_family_113907..114057_POSITIVE 228 57 15 64 22 tfor:TF2379|3end_phosphoribosylformylglycinamidine_cyclo-ligase_(AIR_synthase)_2545092..2545242_POSITIVE 227 47 14 91 45 tfor:TF2650|3end_succinate_dehydrogenase,_iron-sulfur_subunit_2821806..2821956_POSITIVE