Origin IGS: tgagccccagcaatagtaaacgttctgttttataagaggattcaggaaatgcatatagggaaaatgatataaaaaacagagaggaaaaagacgataaacttaaataaatcttatatgat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcatataagatttatttaagtttatcgtctttttcctctctgttttttatatcattttccctatatgcatttcctgaatcctcttataaaacagaacgtttactattgctggggctca Mask Tandem Repeat Region ================================================ tgagccccagcaatagtaaacgttctgttttataagaggattcaggaaatgcatatagggaaaatgatataaaaaacagagaggaaaaagacgataaacttaaataaatcttatatgat Find is-nt database================================================ Query_seq: TF2700:TF2701|TF2700:TF2701:possible nifS-like aminotransferase:conserved hypothetical protein:->->:2874195..2874313 119 tgagccccagcaatagtaaacgttctgttttataagaggattcaggaaatgcatatagggaaaatgatataaaaaacagagaggaaaaagacgataaacttaaataaatcttatatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2700:TF2701|TF2700:TF2701:possible nifS-like aminotransferase:conserved hypothetical protein:->->:2874195..2874313 119 tgagccccagcaatagtaaacgttctgttttataagaggattcaggaaatgcatatagggaaaatgatataaaaaacagagaggaaaaagacgataaacttaaataaatcttatatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2700:TF2701|TF2700:TF2701:possible nifS-like aminotransferase:conserved hypothetical protein:->->:2874195..2874313 119 tgagccccagcaatagtaaacgttctgttttataagaggattcaggaaatgcatatagggaaaatgatataaaaaacagagaggaaaaagacgataaacttaaataaatcttatatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagccccagcaatagtaaacgttctgttttataagaggattcaggaaatgcatatagggaaaatgatataaaaaacagagaggaaaaagacgataaacttaaataaatcttatatgat Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 2 End: 109 . L G L L L L R E T K Y S S E P F A Y L S F S I F F L S S F S S L S L Y M .......... tgagccccagcaatagtaaacgttctgttttataagaggattcaggaaatgcatatagggaaaatgatataaaaaacagagaggaaaaagacgataaacttaaataaatcttatatgat 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================================================ tgagccccagcaatagtaaacgttctgttttataagaggattcaggaaatgcatatagggaaaatgatataaaaaacagagaggaaaaagacgataaacttaaataaatcttatatgat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2700:TF2701|TF2700:TF2701:possible nifS-like aminotransferase:conserved hypothetical protein:->->:2874195..2874313 119 tgagccccagcaatagtaaacgttctgttttataagaggattcaggaaatgcatatagggaaaatgatataaaaaacagagaggaaaaagacgataaacttaaataaatcttatatgat Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: tfor_TF2700_TF2701|possible nifS-like aminotransferase:conserved hypothetical protein|POSITIVE:POSITIVE|[2874195,2874313]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 tgagccccagcaatagtaaacgttctgttttataagaggattcaggaaatgcatatagggaaaatgatataaaaaacagagaggaaaaagacgataaacttaaataaatcttatatgat tgagccccagcaatagtaaacgttctgttttataagaggattcaggaaatgcatatagggaaaatgatataaaaaacagagaggaaaaagacgataaacttaaataaatcttatatgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGCCCCAGCAAUAGUAAACGUUCUGUUUUAUAAGAGGAUUCAGGAAAUGCAUAUAGGGAAAAUGAUAUAAAAAACAGAGAGGAAAAAGACGAUAAACUUAAAUAAAUCUUAUAUGAU ...((....))...........(((((..((.......))..)))))....(((((((((................(.....)....(((........))).......))))))))).. ( -9.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUAUAAGAUUUAUUUAAGUUUAUCGUCUUUUUCCUCUCUGUUUUUUAUAUCAUUUUCCCUAUAUGCAUUUCCUGAAUCCUCUUAUAAAACAGAACGUUUACUAUUGCUGGGGCUCA ...((((((((..................................))))))))......(((((...(((.....(((((..(((........)))..)))))....)))))))).... (-10.18) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 261 46 4 184 142 tfor:TF3062|5end_conserved_hypothetical_protein_3286140..3286370_POSITIVE 249 44 7 71 24 tfor:TF2970|5end_hypothetical_protein_3178410..3178640_POSITIVE 246 85 41 121 82 tfor:TF0381|5end_cell_cycle_protein_401632..401862_POSITIVE 240 47 1 129 78 tfor:TF2282|5end_hypothetical_protein_2439401..2439631_POSITIVE 238 66 22 113 66 tfor:TF0870|5end_conserved_hypothetical_protein_922126..922356_POSITIVE 234 46 1 193 135 tfor:TF3097|5end_conserved_hypothetical_protein_3328661..3328891_POSITIVE 233 47 4 54 19 tfor:TF1645|5end_conserved_hypothetical_protein_1755427..1755657_POSITIVE 230 45 3 215 181 tfor:TF2755|5end_hypothetical_protein_2940785..2941015_POSITIVE 227 47 10 223 188 tfor:TF2771|5end_undecaprenol_kinase,_bacitracin_resistance_protein_2956559..2956789_POSITIVE 221 80 33 141 92 tfor:TF2108|5end_hypothetical_protein_2277385..2277615_POSITIVE 221 80 33 74 25 tfor:TF2106|5end_hypothetical_protein_2277318..2277548_POSITIVE 221 60 21 223 188 tfor:TF1888|5end_RNA_polymerase_ECF-type_sigma_factor_2040940..2041170_POSITIVE 221 35 2 93 62 tfor:TF0292|5end_conserved_hypothetical_protein_320087..320317_POSITIVE 220 70 22 127 80 tfor:TF1312|5end_hypothetical_protein_1388465..1388695_POSITIVE 220 70 22 127 80 tfor:TF1311|5end_hypothetical_protein_1388242..1388472_POSITIVE 220 70 22 127 80 tfor:TF1310|5end_hypothetical_protein_1388019..1388249_POSITIVE 219 60 12 184 136 tfor:TF1971|5end_biotin_carboxyl_carrier_protein_2117976..2118206_POSITIVE 219 69 21 203 159 tfor:TF1590|5end_hypothetical_protein_1705811..1706041_POSITIVE 217 47 3 69 26 tfor:TF3067|5end_conserved_hypothetical_protein_3292432..3292662_POSITIVE 216 39 1 159 116 tfor:TF2947|5end_isochorismate_synthase_3153633..3153863_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 249 44 7 58 11 tfor:TF2968|3end_hypothetical_protein_3178477..3178627_POSITIVE 249 44 7 49 2 tfor:TF2969|3end_hypothetical_protein_3178468..3178618_POSITIVE 246 85 41 42 3 tfor:TF0380|3end_conserved_hypothetical_protein_401633..401783_POSITIVE 240 47 1 122 71 tfor:TF2280|3end_hypothetical_protein_2439474..2439624_POSITIVE 237 94 58 99 62 tfor:TF0566|3end_hypothetical_protein_598858..599008_POSITIVE 233 47 4 50 15 tfor:TF1644|3end_conserved_hypothetical_protein_1755503..1755653_POSITIVE 233 60 21 103 55 tfor:TF0021|3end_outer_membrane_phospholipase_A_16919..17069_POSITIVE 221 80 33 112 63 tfor:TF2107|3end_hypothetical_protein_2277436..2277586_POSITIVE 221 35 2 57 26 tfor:TF0291|3end_triose-phosphate_isomerase_320131..320281_POSITIVE 220 70 22 140 93 tfor:TF1312|3end_hypothetical_protein_1388781..1388931_POSITIVE 220 70 22 140 93 tfor:TF1311|3end_hypothetical_protein_1388558..1388708_POSITIVE 220 70 22 140 93 tfor:TF1310|3end_hypothetical_protein_1388335..1388485_POSITIVE 219 69 21 58 14 tfor:TF1589|3end_surface_antigen_BspA_1705746..1705896_POSITIVE 215 47 2 101 47 tfor:TF2883|3end_peptidyl-prolyl_cis-trans_isomerase_3075129..3075279_POSITIVE 215 49 2 76 28 tfor:TF2290|3end_ABC_transporter,_ATP-binding/permease_component_2446178..2446328_POSITIVE 215 69 21 99 54 tfor:TF0413|3end_succinyl-diaminopimelate_desuccinylase_431869..432019_POSITIVE 212 47 3 93 47 tfor:TF2021|3end_hypothetical_protein_2178588..2178738_POSITIVE 209 91 55 100 62 tfor:TF1580|3end_conserved_hypothetical_protein;_possible_fibronectin_domain_containing_protein_1689258..1689408_POSITIVE 209 45 3 76 35 tfor:TF0881|3end_conserved_hypothetical_protein_935993..936143_POSITIVE 204 68 35 44 11 tfor:TF2526|3end_outer_membrane_protein,_TonB_dependent_receptor_2709007..2709157_POSITIVE