Origin IGS: taaccaaaaaaacaaccgcacttttgaaatgtcacgaaagtgcggttaaaatcctttccgtttttctgaattttccgcctttttacaaaccctgtcactggtctactctcttttctatagttttcgctatttagggttaatgaattcaataaccactagatgttgtggttatttttatttttcaccactattcaaagagaataaaaatcctgattttcatcacaattaaatcctgttagcataaacgggattattcttactaatttacaaggttatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataaccttgtaaattagtaagaataatcccgtttatgctaacaggatttaattgtgatgaaaatcaggatttttattctctttgaatagtggtgaaaaataaaaataaccacaacatctagtggttattgaattcattaaccctaaatagcgaaaactatagaaaagagagtagaccagtgacagggtttgtaaaaaggcggaaaattcagaaaaacggaaaggattttaaccgcactttcgtgacatttcaaaagtgcggttgtttttttggtta Mask Tandem Repeat Region ================================================ taaccaaaaaaacaaccgcacttttgaaatgtcacgaaagtgcggttaaaatcctttccgtttttctgaattttccgcctttttacaaaccctgtcactggtctactctcttttctatagttttcgctatttagggttaatgaattcaataaccactagatgttgtggttatttttatttttcaccactattcaaagagaataaaaatcctgattttcatcacaattaaatcctgttagcataaacgggattattcttactaatttacaaggttatt Find is-nt database================================================ Query_seq: AA02208:AA02210|AA02208:AA02210:tryptophan synthase, alpha subunit:ribonucleoside-diphosphate reductase alpha chain:->->:1504057..1504333 277 taaccaaaaaaacaaccgcacttttgaaatgtcacgaaagtgcggttaaaatcctttccgtttttctgaattttccgcctttttacaaaccctgtcactggtctactctcttttctatagttttcgctatttagggttaatgaattcaataaccactagatgttgtggttatttttatttttcaccactattcaaagagaataaaaatcctgattttcatcacaattaaatcctgttagcataaacgggattattcttactaatttacaaggttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02208:AA02210|AA02208:AA02210:tryptophan synthase, alpha subunit:ribonucleoside-diphosphate reductase alpha chain:->->:1504057..1504333 277 taaccaaaaaaacaaccgcacttttgaaatgtcacgaaagtgcggttaaaatcctttccgtttttctgaattttccgcctttttacaaaccctgtcactggtctactctcttttctatagttttcgctatttagggttaatgaattcaataaccactagatgttgtggttatttttatttttcaccactattcaaagagaataaaaatcctgattttcatcacaattaaatcctgttagcataaacgggattattcttactaatttacaaggttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02208:AA02210|AA02208:AA02210:tryptophan synthase, alpha subunit:ribonucleoside-diphosphate reductase alpha chain:->->:1504057..1504333 277 taaccaaaaaaacaaccgcacttttgaaatgtcacgaaagtgcggttaaaatcctttccgtttttctgaattttccgcctttttacaaaccctgtcactggtctactctcttttctatagttttcgctatttagggttaatgaattcaataaccactagatgttgtggttatttttatttttcaccactattcaaagagaataaaaatcctgattttcatcacaattaaatcctgttagcataaacgggattattcttactaatttacaaggttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaccaaaaaaacaaccgcacttttgaaatgtcacgaaagtgcggttaaaatcctttccgtttttctgaattttccgcctttttacaaaccctgtcactggtctactctcttttctatagttttcgctatttagggttaatgaattcaataaccactagatgttgtggttatttttatttttcaccactattcaaagagaataaaaatcctgattttcatcacaattaaatcctgttagcataaacgggattattcttactaatttacaaggttatt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 24 End: 131 ....................... M K C H E S A V K I L S V F L N F P P F Y K P C H W S T L F S I V F A I .................................................................................................................................................. Protein_Len: 45 Strand: + Start: 92 End: 226 ........................................................................................... M S L V Y S L F Y S F R Y L G L M N S I T T R C C G Y F Y F S P L F K E N K N P D F H H N ................................................... Protein_Len: 49 Strand: - Start: 3 End: 149 .. G F F C G C K Q F T V F T R N F D K G N K Q I K R R K V F G T V P R S E K R Y N E S N L T L S N M ................................................................................................................................ taaccaaaaaaacaaccgcacttttgaaatgtcacgaaagtgcggttaaaatcctttccgtttttctgaattttccgcctttttacaaaccctgtcactggtctactctcttttctatagttttcgctatttagggttaatgaattcaataaccactagatgttgtggttatttttatttttcaccactattcaaagagaataaaaatcctgattttcatcacaattaaatcctgttagcataaacgggattattcttactaatttacaaggttatt 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: 88 Start: 23 End: 52 ......................TTTGAAATGTCACGAAAGTGCGGTTAAAAT................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 213 End: 242 ....................................................................................................................................................................................................................ATTTTCATCACAATTAAATCCTGTTAGCAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaccaaaaaaacaaccgcacttttgaaatgtcacgaaagtgcggttaaaatcctttccgtttttctgaattttccgcctttttacaaaccctgtcactggtctactctcttttctatagttttcgctatttagggttaatgaattcaataaccactagatgttgtggttatttttatttttcaccactattcaaagagaataaaaatcctgattttcatcacaattaaatcctgttagcataaacgggattattcttactaatttacaaggttatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 90 HP_score: -5.9 Tail_Score: -5.61881 Start: 150 End: 171 Full_Region: GGTTAATGAATTCAA TAACCACTA GATG TTGTGGTTA TTTTTATTTTTCACC .....................................................................................................................................................TAACCACTAGATGTTGTGGTTA.......................................................................................................... Find igs database================================================ Query_seq: AA02208:AA02210|AA02208:AA02210:tryptophan synthase, alpha subunit:ribonucleoside-diphosphate reductase alpha chain:->->:1504057..1504333 277 taaccaaaaaaacaaccgcacttttgaaatgtcacgaaagtgcggttaaaatcctttccgtttttctgaattttccgcctttttacaaaccctgtcactggtctactctcttttctatagttttcgctatttagggttaatgaattcaataaccactagatgttgtggttatttttatttttcaccactattcaaagagaataaaaatcctgattttcatcacaattaaatcctgttagcataaacgggattattcttactaatttacaaggttatt Intra-Species Hit: Count: 1 Min: 13 Max: 277 Len: 265 Subject: aact_AA02208_AA02210|tryptophan synthase, alpha subunit:ribonucleoside-diphosphate reductase alpha chain|POSITIVE:POSITIVE|[1504057,1504333]|277 HSP 1 e-value: 1.0E-148 bit: 525.0 Len: 265 Query Start:13 Query End:277 Subject Strand: POSITIVE Subject Start: 13 Subject End: 277 ............caaccgcacttttgaaatgtcacgaaagtgcggttaaaatcctttccgtttttctgaattttccgcctttttacaaaccctgtcactggtctactctcttttctatagttttcgctatttagggttaatgaattcaataaccactagatgttgtggttatttttatttttcaccactattcaaagagaataaaaatcctgattttcatcacaattaaatcctgttagcataaacgggattattcttactaatttacaaggttatt ............caaccgcacttttgaaatgtcacgaaagtgcggttaaaatcctttccgtttttctgaattttccgcctttttacaaaccctgtcactggtctactctcttttctatagttttcgctatttagggttaatgaattcaataaccactagatgttgtggttatttttatttttcaccactattcaaagagaataaaaatcctgattttcatcacaattaaatcctgttagcataaacgggattattcttactaatttacaaggttatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAACCGCACUUUUGAAAUGUCACGAAAGUGCGGUUAAAAUCCUUUCCGUUUUUCUGAAUUUUCCGCCUUUUUACAAACCCUGUCACUGGUCUACUCUCUUUUCUAUAGUUUUCGCUAUUUAGGGUUAAUGAAUUCAAUAACCACUAGAUGUUGUGGUUAUUUUUAUUUUUCACCACUAUUCAAAGAGAAUAAAAAUCCUGAUUUUCAUCACAAUUAAAUCCUGUUAGCAUAAACGGGAUUAUUCUUACUAAUUUACAAGGUUAUU .(((((((((((((........))))))))))))).....((((..........((((...((.(..((((((...(((........)))....(((((((...(((((....))))).((((((.((((((...(((((((((........)))))))))))))))....))).)))...))))))).))))))..).))..)))).........(((((((((......)))))))))................))))..... (-59.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAACCUUGUAAAUUAGUAAGAAUAAUCCCGUUUAUGCUAACAGGAUUUAAUUGUGAUGAAAAUCAGGAUUUUUAUUCUCUUUGAAUAGUGGUGAAAAAUAAAAAUAACCACAACAUCUAGUGGUUAUUGAAUUCAUUAACCCUAAAUAGCGAAAACUAUAGAAAAGAGAGUAGACCAGUGACAGGGUUUGUAAAAAGGCGGAAAAUUCAGAAAAACGGAAAGGAUUUUAACCGCACUUUCGUGACAUUUCAAAAGUGCGGUUG ...((((((((...((((((.((((......)))).))))))..((....((((.((((....)))).))))((((((((((((...(((.(((..........(((((((((........)))))))))..........)))))).((((......))))...))))))))))))))....)))))))).............(((((((.............)))))))(((((((((((..(((....)))))))))))))). (-67.47) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 431 48 1 205 159 aact:AA01524|5end_amino_acid_ABC_transporter,_ATP-binding_protein_1023500..1023730_POSITIVE 426 50 4 230 189 aact:AA00505|5end_hypothetical_protein_351561..351791_POSITIVE 386 70 22 149 104 aact:AA02010|5end_peptide_methionine_sulfoxide_reductase;_cytochrome_C-TYPE_biogenesis_protein;_transcriptional_regulator_1367180..1367410_POSITIVE 385 69 21 173 109 aact:AA02993|5end_6-phosphofructokinase_2091766..2091996_POSITIVE 385 36 3 153 117 aact:AA01436|5end_fructose-bisphosphate_aldolase_class_II_962981..963211_POSITIVE 371 66 23 157 119 aact:AA00625|5end_hypothetical_protein_430565..430795_POSITIVE 371 66 23 49 11 aact:AA00623|5end_hypothetical_protein_430457..430687_POSITIVE 364 34 3 141 113 aact:AA00686|5end_hypothetical_protein_468852..469082_POSITIVE 359 70 21 47 3 aact:AA01798|5end_hypothetical_protein_1212070..1212300_POSITIVE 352 50 1 163 112 aact:AA00390|5end_permease_263689..263919_POSITIVE 351 41 3 157 112 aact:AA00552|5end_periplasmic_nitrate_reductase_precursor_377331..377561_POSITIVE 351 41 3 51 6 aact:AA00551|5end_hypothetical_protein_377225..377455_POSITIVE 350 40 3 195 162 aact:AA00185|5end_3-dehydroquinate_dehydratase_II_130792..131022_POSITIVE 350 40 3 85 52 aact:AA00184|5end_hypothetical_protein_130682..130912_POSITIVE 349 70 25 188 146 aact:AA02893|5end_oligopeptide_transport_system_permease_protein,_N-terminal_2027201..2027431_POSITIVE 347 70 24 119 77 aact:AA02362|5end_conserved_hypothetical_protein_1619905..1620135_POSITIVE 346 50 3 214 168 aact:AA02144|5end_iron_(III)_ABC_transporter,_permease_protein_1467583..1467813_POSITIVE 346 50 3 64 18 aact:AA02143|5end_hypothetical_protein_1467433..1467663_POSITIVE 344 70 24 156 111 aact:AA00473|5end_tryptophanyl-tRNA_synthetase_328996..329226_POSITIVE 343 34 3 159 129 aact:AA01519|5end_conserved_hypothetical_protein_1021794..1022024_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 421 70 23 86 43 aact:AA02280|3end_conserved_hypothetical_protein_1552767..1552917_POSITIVE 385 69 21 67 3 aact:AA02992|3end_RNA_methyltransferase_2091740..2091890_POSITIVE 385 36 3 113 77 aact:AA01434|3end_conserved_hypothetical_protein_(possible_o-antigen_ligase)_963021..963171_POSITIVE 371 35 2 77 44 aact:AA02208|3end_tryptophan_synthase,__alpha_subunit_1503996..1504146_POSITIVE 371 66 23 144 106 aact:AA00623|3end_hypothetical_protein_430632..430782_POSITIVE 365 34 3 65 39 aact:AA00223|3end_catalase_(hydroperoxidase;_iron_heme_axial_ligand)_155808..155958_POSITIVE 364 34 3 70 42 aact:AA00684|3end_adenylosuccinate_synthase_468861..469011_POSITIVE 359 70 21 65 21 aact:AA01796|3end_branched-chain_amino_acid_aminotransferase_1212168..1212318_POSITIVE 351 41 3 149 104 aact:AA00551|3end_hypothetical_protein_377403..377553_POSITIVE 350 40 3 68 35 aact:AA00183|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_130745..130895_POSITIVE 349 70 25 84 42 aact:AA02892|3end_oligopeptide_ABC_transporter,_periplasmic-binding_protein_2027177..2027327_POSITIVE 347 70 24 81 39 aact:AA02360|3end_threonine_synthase_1619947..1620097_POSITIVE 346 50 3 83 37 aact:AA02142|3end_outer_membrane_protein_OprM_precursor_1467532..1467682_POSITIVE 344 70 24 63 18 aact:AA00471|3end_3,4-dihydroxy-2-butanone_4-phosphate_synthase;_GTP_cyclohydrase_II_328983..329133_POSITIVE 343 34 3 76 46 aact:AA01517|3end_peptidyl-prolyl_cis-trans_isomerase;_macrophage_infectivity_protein_1021791..1021941_POSITIVE 343 34 3 59 27 aact:AA01019|3end_conserved_hypothetical_protein_712719..712869_POSITIVE 342 70 22 83 34 aact:AA00120|3end_ATP-dependent_Clp_protease_ATP-binding_subunit_90281..90431_POSITIVE 341 67 21 100 50 aact:AA01932|3end_tRNA_pseudouridine_synthase_B_1306092..1306242_POSITIVE 340 40 1 63 28 aact:AA01023|3end_conserved_hypothetical_protein_716435..716585_POSITIVE 333 50 2 141 81 aact:AA01673|3end_riboflavin_synthase,_alpha_chain_1132093..1132243_POSITIVE