Origin IGS: aattatcaaataaagaacttagttttaaactgggttctttattttttataagaaaatgaaaatattgattaaacactaaaaataagatacaataaaatatattgtaggagggtaaata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatttaccctcctacaatatattttattgtatcttatttttagtgtttaatcaatattttcattttcttataaaaaataaagaacccagtttaaaactaagttctttatttgataatt Mask Tandem Repeat Region ================================================ aattatcaaataaagaacttagttttaaactgggttctttattttttataagaaaatgaaaatattgattaaacactaaaaataagatacaataaaatatattgtaggagggtaaata Find is-nt database================================================ Query_seq: FN0190:FN0191|FN0190:FN0191:Two-component sensor kinase yesM:ATP-dependent DNA helicase recG:->->:815774..815891 118 aattatcaaataaagaacttagttttaaactgggttctttattttttataagaaaatgaaaatattgattaaacactaaaaataagatacaataaaatatattgtaggagggtaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0190:FN0191|FN0190:FN0191:Two-component sensor kinase yesM:ATP-dependent DNA helicase recG:->->:815774..815891 118 aattatcaaataaagaacttagttttaaactgggttctttattttttataagaaaatgaaaatattgattaaacactaaaaataagatacaataaaatatattgtaggagggtaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0190:FN0191|FN0190:FN0191:Two-component sensor kinase yesM:ATP-dependent DNA helicase recG:->->:815774..815891 118 aattatcaaataaagaacttagttttaaactgggttctttattttttataagaaaatgaaaatattgattaaacactaaaaataagatacaataaaatatattgtaggagggtaaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattatcaaataaagaacttagttttaaactgggttctttattttttataagaaaatgaaaatattgattaaacactaaaaataagatacaataaaatatattgtaggagggtaaata Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 2 End: 100 . N D F L S S L K L S P E K N K I L F H F Y Q N F V L F L I C Y F M .................. aattatcaaataaagaacttagttttaaactgggttctttattttttataagaaaatgaaaatattgattaaacactaaaaataagatacaataaaatatattgtaggagggtaaata 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: 82 Start: 64 End: 93 ...............................................................ATTGATTAAACACTAAAAATAAGATACAAT......................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 2 End: 31 .ATTATCAAATAAAGAACTTAGTTTTAAACT....................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattatcaaataaagaacttagttttaaactgggttctttattttttataagaaaatgaaaatattgattaaacactaaaaataagatacaataaaatatattgtaggagggtaaata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0190:FN0191|FN0190:FN0191:Two-component sensor kinase yesM:ATP-dependent DNA helicase recG:->->:815774..815891 118 aattatcaaataaagaacttagttttaaactgggttctttattttttataagaaaatgaaaatattgattaaacactaaaaataagatacaataaaatatattgtaggagggtaaata Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_003454_FN0190_FN0191|Two-component sensor kinase yesM:ATP-dependent DNA helicase recG|POSITIVE:POSITIVE|[815774,815891]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 aattatcaaataaagaacttagttttaaactgggttctttattttttataagaaaatgaaaatattgattaaacactaaaaataagatacaataaaatatattgtaggagggtaaata aattatcaaataaagaacttagttttaaactgggttctttattttttataagaaaatgaaaatattgattaaacactaaaaataagatacaataaaatatattgtaggagggtaaata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAUCAAAUAAAGAACUUAGUUUUAAACUGGGUUCUUUAUUUUUUAUAAGAAAAUGAAAAUAUUGAUUAAACACUAAAAAUAAGAUACAAUAAAAUAUAUUGUAGGAGGGUAAAUA ..(((((..((((((((((((((.....))))))))))))))(((((((......))))))).........................(((((((.....)))))))....)))))... (-22.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUACCCUCCUACAAUAUAUUUUAUUGUAUCUUAUUUUUAGUGUUUAAUCAAUAUUUUCAUUUUCUUAUAAAAAAUAAAGAACCCAGUUUAAAACUAAGUUCUUUAUUUGAUAAUU ............(((((((.....)))))))....................................((((...(((((((((((..(((.....)))..))))))))))).)))).. (-16.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 335 43 8 228 193 NC_003454:FN0192|5end_Dipeptide-binding_protein_817342..817572_POSITIVE 225 63 21 198 147 NC_003454:FN0972|5end_Cobyrinic_acid_a,c-diamide_synthase_1625607..1625837_NEGATIVE 206 48 24 33 9 NC_003454:FN1328|5end_Exodeoxyribonuclease_VII_small_subunit_1983129..1983359_NEGATIVE 182 109 64 217 176 NC_003454:FN0635|5end_tRNA_pseudouridine_synthase_B_1294993..1295223_NEGATIVE 176 47 5 153 111 NC_003454:FN1258|5end_C4-dicarboxylate-binding_protein_1914793..1915023_NEGATIVE 176 42 13 146 117 NC_003454:FN0002|5end_Ribonuclease_P_protein_component_642548..642778_POSITIVE 166 48 3 102 48 NC_003454:FN1084|5end_hypothetical_protein_1728661..1728891_POSITIVE 163 98 51 83 35 NC_003454:FN0481|5end_hypothetical_protein_1127777..1128007_POSITIVE 160 108 64 170 132 NC_003454:FN0535|5end_hypothetical_protein_1189351..1189581_POSITIVE 158 67 23 51 4 NC_003454:FN0370|5end_Signal_peptidase_I_999832..1000062_NEGATIVE 158 51 20 218 192 NC_003454:FN0283|5end_tRNA_(Guanine-N1)_-methyltransferase_913405..913635_NEGATIVE 155 55 23 45 14 NC_003454:FN1454|5end_D-alanine--D-alanine_ligase_2135659..2135889_NEGATIVE 155 110 85 201 179 NC_003454:FN1352|5end_ABC_transporter_ATP-binding_protein_2004180..2004410_NEGATIVE 151 100 51 183 132 NC_003454:FN1469|5end_Na+_driven_multidrug_efflux_pump_2151709..2151939_NEGATIVE 151 72 31 207 166 NC_003454:FN0679|5end_GTPase_1334596..1334826_POSITIVE 148 108 67 189 148 NC_003454:FN1522|5end_Dipeptide_transport_system_permease_protein_dppC_27327..27557_POSITIVE 147 53 18 185 148 NC_003454:FN1551|5end_hypothetical_protein_66187..66417_NEGATIVE 145 108 61 224 176 NC_003454:FN1650|5end_Oligopeptide_transport_system_permease_protein_oppC_144834..145064_NEGATIVE 143 90 41 213 166 NC_003454:FN0671|5end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1326616..1326846_POSITIVE 143 43 19 216 189 NC_003454:FN1534|5end_Electron_transfer_flavoprotein_beta-subunit_47112..47342_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 44 8 83 47 NC_003454:FN0190|3end_Two-component_sensor_kinase_yesM_815713..815863_POSITIVE 177 42 8 71 35 NC_003454:FN0575|3end_hypothetical_protein_1225584..1225734_POSITIVE 171 53 14 143 87 NC_003454:FN1792|3end_hypothetical_protein_272899..273049_NEGATIVE 163 98 51 65 17 NC_003454:FN0480|3end_hypothetical_protein_1127839..1127989_POSITIVE 160 108 64 105 67 NC_003454:FN0534|3end_hypothetical_protein_1189366..1189516_POSITIVE 154 49 3 91 46 NC_003454:FN1119|3end_50S_ribosomal_protein_L27_1761253..1761403_POSITIVE 149 50 17 135 93 NC_003454:FN1364|3end_LSU_ribosomal_protein_L32P_2015382..2015532_NEGATIVE 147 71 31 53 15 NC_003454:FN1250|3end_Guanine-hypoxanthine_permease_1906486..1906636_NEGATIVE 147 40 1 149 105 NC_003454:FN0103|3end_Ribonucleoside-diphosphate_reductase_beta_chain_739607..739757_POSITIVE 142 47 22 80 51 NC_003454:FN0151|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_780092..780242_POSITIVE 139 48 15 88 49 NC_003454:FN0545|3end_Lipopolysaccharide_core_biosynthesis_protein_rfaY_1198717..1198867_POSITIVE 139 59 20 127 85 NC_003454:FN1624|3end_preprotein_translocase_SecY_131080..131230_NEGATIVE 138 68 28 144 112 NC_003454:FN2104|3end_hypothetical_protein_614760..614910_POSITIVE 137 56 31 149 121 NC_003454:FN1210|3end_Metal_dependent_hydrolase_1868940..1869090_NEGATIVE 137 47 13 59 19 NC_003454:FN0733|3end_peptidase_T_1390882..1391032_POSITIVE 136 55 29 30 6 NC_003454:FN1455|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_2135674..2135824_NEGATIVE 136 40 14 36 11 NC_003454:FN0877|3end_Sodium/proline_symporter_1537503..1537653_NEGATIVE 135 64 35 53 25 NC_003454:FN0034|3end_hypothetical_protein_675439..675589_NEGATIVE 135 47 13 65 37 NC_003454:FN1640|3end_LSU_ribosomal_protein_L22P_138182..138332_NEGATIVE 133 48 13 38 1 NC_003454:FN1427|3end_Phenazine_biosynthesis_protein_phzF_2096763..2096913_POSITIVE