Origin IGS: taagaacctccttaaattatttctcagtatagtctaaaaaataaaatttatcaagtacaaattactttctattaaaaaatataaaagaaaaaaatcaaatcggtacatatgtagtttgaaatgtttagtttttgg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccaaaaactaaacatttcaaactacatatgtaccgatttgatttttttcttttatattttttaatagaaagtaatttgtacttgataaattttattttttagactatactgagaaataatttaaggaggttctta Mask Tandem Repeat Region ================================================ taagaacctccttaaattatttctcagtatagtctaaaaaataaaatttatcaagtacaaattactttctattaaaaaatataaaagaaaaaaatcaaatcggtacatatgtagtttgaaatgtttagtttttgg Find is-nt database================================================ Query_seq: TDE0031:TDE0032|TDE0031:TDE0032:hypothetical protein:histidine kinase-related ATPase, putative:<-<-:39186..39320 135 taagaacctccttaaattatttctcagtatagtctaaaaaataaaatttatcaagtacaaattactttctattaaaaaatataaaagaaaaaaatcaaatcggtacatatgtagtttgaaatgtttagtttttgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0031:TDE0032|TDE0031:TDE0032:hypothetical protein:histidine kinase-related ATPase, putative:<-<-:39186..39320 135 taagaacctccttaaattatttctcagtatagtctaaaaaataaaatttatcaagtacaaattactttctattaaaaaatataaaagaaaaaaatcaaatcggtacatatgtagtttgaaatgtttagtttttgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0031:TDE0032|TDE0031:TDE0032:hypothetical protein:histidine kinase-related ATPase, putative:<-<-:39186..39320 135 taagaacctccttaaattatttctcagtatagtctaaaaaataaaatttatcaagtacaaattactttctattaaaaaatataaaagaaaaaaatcaaatcggtacatatgtagtttgaaatgtttagtttttgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagaacctccttaaattatttctcagtatagtctaaaaaataaaatttatcaagtacaaattactttctattaaaaaatataaaagaaaaaaatcaaatcggtacatatgtagtttgaaatgtttagtttttgg Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 41 End: 133 ........................................ M K F I K Y K L L S I K K Y K R K K S N R Y I C S L K C L V F .. taagaacctccttaaattatttctcagtatagtctaaaaaataaaatttatcaagtacaaattactttctattaaaaaatataaaagaaaaaaatcaaatcggtacatatgtagtttgaaatgtttagtttttgg 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: 87 Start: 26 End: 55 .........................CTTGATAAATTTTATTTTTTAGACTATACT................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taagaacctccttaaattatttctcagtatagtctaaaaaataaaatttatcaagtacaaattactttctattaaaaaatataaaagaaaaaaatcaaatcggtacatatgtagtttgaaatgtttagtttttgg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 45 HP_score: -2.9 Tail_Score: -3.56366 Start: 17 End: 44 Full_Region: tgtacttgataaatt ttattttttag actata ctgagaaataa tttaaggaggttctt ................ttattttttagactatactgagaaataa........................................................................................... Find igs database================================================ Query_seq: TDE0031:TDE0032|TDE0031:TDE0032:hypothetical protein:histidine kinase-related ATPase, putative:<-<-:39186..39320 135 taagaacctccttaaattatttctcagtatagtctaaaaaataaaatttatcaagtacaaattactttctattaaaaaatataaaagaaaaaaatcaaatcggtacatatgtagtttgaaatgtttagtttttgg Intra-Species Hit: Count: 1 Min: 1 Max: 135 Len: 135 Subject: NC_002967_TDE0031_TDE0032|hypothetical protein:histidine kinase-related ATPase, putative|NEGATIVE:NEGATIVE|[39186,39320]|135 HSP 1 e-value: 2.0E-11 bit: 69.9 Len: 35 Query Start:101 Query End:135 Subject Strand: POSITIVE Subject Start: 101 Subject End: 135 ....................................................................................................cggtacatatgtagtttgaaatgtttagtttttgg ....................................................................................................cggtacatatgtagtttgaaatgtttagtttttgg HSP 2 e-value: 8.0E-11 bit: 67.9 Len: 34 Query Start:1 Query End:34 Subject Strand: POSITIVE Subject Start: 1 Subject End: 34 taagaacctccttaaattatttctcagtatagtc..................................................................................................... taagaacctccttaaattatttctcagtatagtc..................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAACCUCCUUAAAUUAUUUCUCAGUAUAGUCUAAAAAAUAAAAUUUAUCAAGUACAAAUUACUUUCUAUUAAAAAAUAUAAAAGAAAAAAAUCAAAUCGGUACAUAUGUAGUUUGAAAUGUUUAGUUUUUGG ((((......))))...................(((((((.((((.....(((((((((......(((((.(((.......))).)))))...(((.....))).....)))).)))))....)))).))))))) (-11.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCAAAAACUAAACAUUUCAAACUACAUAUGUACCGAUUUGAUUUUUUUCUUUUAUAUUUUUUAAUAGAAAGUAAUUUGUACUUGAUAAAUUUUAUUUUUUAGACUAUACUGAGAAAUAAUUUAAGGAGGUUCUUA ..........(((.((((......((...((((.((((......((((((.(((.......))).)))))).)))).)))).)).......(((((((((((......))))))))))).....))))))).... (-17.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 662 130 81 221 172 NC_002967:TDE0031|5end_hypothetical_protein_39095..39325_NEGATIVE 205 22 1 112 91 NC_002967:TDE0923|5end_ABC_transporter,_ATP-binding/permease_protein_945731..945961_NEGATIVE 204 130 85 195 148 NC_002967:TDE0324|5end_hypothetical_protein_357444..357674_POSITIVE 190 49 7 136 99 NC_002967:TDE2146|5end_hydrolase,_alpha/beta_fold_family_2183060..2183290_POSITIVE 183 128 94 200 160 NC_002967:TDE1657|5end_transcription_antitermination_protein_NusB_1707640..1707870_NEGATIVE 176 46 4 79 36 NC_002967:TDE2350|5end_lipoprotein,_putative_2386661..2386891_NEGATIVE 176 52 23 86 57 NC_002967:TDE1045|5end_hypothetical_protein_1073240..1073470_POSITIVE 167 36 1 155 110 NC_002967:TDE2347|5end_30S_ribosomal_protein_S2_2384378..2384608_NEGATIVE 167 36 3 58 25 NC_002967:TDE2031|5end_hypothetical_protein_2059161..2059391_NEGATIVE 166 129 98 210 171 NC_002967:TDE0987|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1014041..1014271_POSITIVE 161 121 87 45 10 NC_002967:TDE0223|5end_hypothetical_protein_255904..256134_NEGATIVE 160 126 93 147 108 NC_002967:TDE1283|5end_extracellular_solute-binding_lipoprotein,_putative_1317403..1317633_POSITIVE 159 66 22 187 133 NC_002967:TDE1303|5end_hypothetical_protein_1339840..1340070_NEGATIVE 158 126 99 189 162 NC_002967:TDE0728|5end_FAD-binding_protein,_putative_767206..767436_POSITIVE 157 35 3 124 95 NC_002967:TDE1050|5end_hypothetical_protein_1077387..1077617_POSITIVE 157 57 26 130 99 NC_002967:TDE0825|5end_UDP-N-acetylmuramoylalanyl-D-glutamate-2,_6-diaminopimelate_ligase,_putative_845962..846192_POSITIVE 155 47 6 219 172 NC_002967:TDE2320|5end_RNA_polymerase_sigma-24_factor,_putative_2356951..2357181_NEGATIVE 155 126 93 82 50 NC_002967:TDE1826|5end_hypothetical_protein_1859781..1860011_NEGATIVE 154 125 100 52 25 NC_002967:TDE0056|5end_DNA-directed_RNA_polymerase,_omega_subunit,_putative_65706..65936_POSITIVE 153 121 85 215 178 NC_002967:TDE0667|5end_FeS_assembly_protein_SufB_704290..704520_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 205 22 1 92 71 NC_002967:TDE0924|3end_ABC_transporter,_ATP-binding/permease_protein_945751..945901_NEGATIVE 168 128 96 50 15 NC_002967:TDE1968|3end_cell_division_protein_FtsJ_1982493..1982643_NEGATIVE 167 36 3 48 15 NC_002967:TDE2032|3end_hypothetical_protein_2059171..2059321_NEGATIVE 167 36 3 150 117 NC_002967:TDE2031|3end_hypothetical_protein_2059069..2059219_NEGATIVE 165 25 4 33 11 NC_002967:TDE0026|3end_TraB_family_protein_31826..31976_NEGATIVE 161 128 86 66 23 NC_002967:TDE0272|3end_hypothetical_protein_302256..302406_NEGATIVE 160 126 93 135 96 NC_002967:TDE1282|3end_hypothetical_protein_1317471..1317621_POSITIVE 157 130 86 100 52 NC_002967:TDE1113|3end_hypothetical_protein_1147729..1147879_NEGATIVE 157 35 3 111 82 NC_002967:TDE1049|3end_elongation_factor_EF-2_1077454..1077604_POSITIVE 152 119 71 84 31 NC_002967:TDE2229|3end_hypothetical_protein_2268832..2268982_NEGATIVE 151 30 7 42 19 NC_002967:TDE1167|3end_hypothetical_protein_1198714..1198864_NEGATIVE 150 103 62 101 60 NC_002967:TDE1001|3end_orotate_phosphoribosyltransferase_1028437..1028587_POSITIVE 149 35 7 65 37 NC_002967:TDE2748|3end_acetyltransferase,_GNAT_family_2805646..2805796_POSITIVE 148 117 96 77 56 NC_002967:TDE2078|3end_TPR_domain_protein_2106788..2106938_NEGATIVE 148 37 8 132 103 NC_002967:TDE1558|3end_YD_repeat_protein_1610799..1610949_POSITIVE 148 40 1 51 10 NC_002967:TDE1284|3end_methyl-accepting_chemotaxis_protein,_putative_1320923..1321073_POSITIVE 148 130 100 68 41 NC_002967:TDE0573|3end_hypothetical_protein_604910..605060_POSITIVE 147 57 11 54 3 NC_002967:TDE1302|3end_hemerythrin_family_protein_1339213..1339363_NEGATIVE 147 120 96 51 30 NC_002967:TDE1194|3end_hypothetical_protein_1227623..1227773_POSITIVE 146 33 7 126 96 NC_002967:TDE0078|3end_glycine_reductase_complex_selenoprotein_GrdB1_88745..88895_NEGATIVE