Origin IGS: aattatcctcctcctctttccggattgtgtgatactatatttagactgatttttcaagttaaaaacagaatttattataagagcaatccgcaaaactgataatttcacaagattgctcttgtaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttacaagagcaatcttgtgaaattatcagttttgcggattgctcttataataaattctgtttttaacttgaaaaatcagtctaaatatagtatcacacaatccggaaagaggaggaggataatt Mask Tandem Repeat Region ================================================ aattatcctcctcctctttccggattgtgtgatactatatttagactgatttttcaagttaaaaacagaatttattataagagcaatccgcaaaactgataatttcacaagattgctcttgtaa Find is-nt database================================================ Query_seq: TDE2456:TDE2457|TDE2456:TDE2457:hypothetical protein:hypothetical protein:<-<-:2484664..2484787 124 aattatcctcctcctctttccggattgtgtgatactatatttagactgatttttcaagttaaaaacagaatttattataagagcaatccgcaaaactgataatttcacaagattgctcttgtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2456:TDE2457|TDE2456:TDE2457:hypothetical protein:hypothetical protein:<-<-:2484664..2484787 124 aattatcctcctcctctttccggattgtgtgatactatatttagactgatttttcaagttaaaaacagaatttattataagagcaatccgcaaaactgataatttcacaagattgctcttgtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2456:TDE2457|TDE2456:TDE2457:hypothetical protein:hypothetical protein:<-<-:2484664..2484787 124 aattatcctcctcctctttccggattgtgtgatactatatttagactgatttttcaagttaaaaacagaatttattataagagcaatccgcaaaactgataatttcacaagattgctcttgtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattatcctcctcctctttccggattgtgtgatactatatttagactgatttttcaagttaaaaacagaatttattataagagcaatccgcaaaactgataatttcacaagattgctcttgtaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 1 End: 108 I I R R R K G S Q T I S Y K S Q N K L N F V S N I I L A I R L V S L K M ................ aattatcctcctcctctttccggattgtgtgatactatatttagactgatttttcaagttaaaaacagaatttattataagagcaatccgcaaaactgataatttcacaagattgctcttgtaa 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: 86 Start: 74 End: 103 .........................................................................ATTATCAGTTTTGCGGATTGCTCTTATAAT..................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 29 End: 58 ............................CTTGAAAAATCAGTCTAAATATAGTATCAC.................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattatcctcctcctctttccggattgtgtgatactatatttagactgatttttcaagttaaaaacagaatttattataagagcaatccgcaaaactgataatttcacaagattgctcttgtaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2456:TDE2457|TDE2456:TDE2457:hypothetical protein:hypothetical protein:<-<-:2484664..2484787 124 aattatcctcctcctctttccggattgtgtgatactatatttagactgatttttcaagttaaaaacagaatttattataagagcaatccgcaaaactgataatttcacaagattgctcttgtaa Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: NC_002967_TDE2456_TDE2457|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2484664,2484787]|124 HSP 1 e-value: 1.0E-64 bit: 246.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 aattatcctcctcctctttccggattgtgtgatactatatttagactgatttttcaagttaaaaacagaatttattataagagcaatccgcaaaactgataatttcacaagattgctcttgtaa aattatcctcctcctctttccggattgtgtgatactatatttagactgatttttcaagttaaaaacagaatttattataagagcaatccgcaaaactgataatttcacaagattgctcttgtaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAUCCUCCUCCUCUUUCCGGAUUGUGUGAUACUAUAUUUAGACUGAUUUUUCAAGUUAAAAACAGAAUUUAUUAUAAGAGCAAUCCGCAAAACUGAUAAUUUCACAAGAUUGCUCUUGUAA .((((..(...(((.......)))..)..))))......(((((..(((....)))..)))))...........((((((((((((((........(((.....)))...)))))))))))))) (-22.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACAAGAGCAAUCUUGUGAAAUUAUCAGUUUUGCGGAUUGCUCUUAUAAUAAAUUCUGUUUUUAACUUGAAAAAUCAGUCUAAAUAUAGUAUCACACAAUCCGGAAAGAGGAGGAGGAUAAUU (((.(((((((((((.(..((((.....))))..)))))))))))).)))......((((.((((..((((....))))..)))).))))((((......(((.......)))....))))... (-28.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 845 50 1 141 92 NC_002967:TDE2456|5end_hypothetical_protein_2484573..2484803_NEGATIVE 273 59 12 170 125 NC_002967:TDE1217|5end_flagellar_assembly_protein_1249511..1249741_POSITIVE 258 41 1 94 43 NC_002967:TDE1339|5end_stage_V_sporulation_protein_G_1375807..1376037_POSITIVE 258 32 6 173 135 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 247 27 6 29 4 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 236 21 7 185 171 NC_002967:TDE1621|5end_hypothetical_protein_1670743..1670973_NEGATIVE 227 39 7 158 114 NC_002967:TDE1312|5end_hypothetical_protein_1349088..1349318_POSITIVE 225 35 4 136 91 NC_002967:TDE0773|5end_30S_ribosomal_protein_S3_809443..809673_POSITIVE 223 34 5 217 181 NC_002967:TDE2239|5end_hypothetical_protein_2277546..2277776_NEGATIVE 223 34 5 135 99 NC_002967:TDE2101|5end_hypothetical_protein_2126619..2126849_NEGATIVE 223 49 4 146 96 NC_002967:TDE1916|5end_glycerol_kinase_1934767..1934997_NEGATIVE 222 44 1 137 86 NC_002967:TDE1858|5end_transcriptional_regulator,_PadR_family_1884632..1884862_POSITIVE 222 119 80 43 6 NC_002967:TDE0142|5end_hypothetical_protein_164074..164304_NEGATIVE 219 48 10 129 94 NC_002967:TDE1938|5end_hypothetical_protein_1953640..1953870_POSITIVE 219 117 74 80 39 NC_002967:TDE0207|5end_permease,_GntP_family_241602..241832_POSITIVE 218 50 6 53 11 NC_002967:TDE1185|5end_lipoprotein,_putative_1212973..1213203_NEGATIVE 217 50 10 52 4 NC_002967:TDE2355|5end_carbon_storage_regulator_2390838..2391068_POSITIVE 216 31 8 132 98 NC_002967:TDE0834|5end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854863..855093_NEGATIVE 215 116 79 61 15 NC_002967:TDE2131|5end_cobalamin_biosynthesis_protein_CbiM,_putative_2162683..2162913_NEGATIVE 213 45 6 187 147 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 273 59 12 149 104 NC_002967:TDE1216|3end_flagellar_motor_protein_1249570..1249720_POSITIVE 263 45 6 42 3 NC_002967:TDE2169|3end_hypothetical_protein_2201509..2201659_POSITIVE 260 117 79 151 118 NC_002967:TDE1132|3end_chorismate_synthase_1164580..1164730_POSITIVE 247 27 6 130 105 NC_002967:TDE1847|3end_hypothetical_protein_1875845..1875995_POSITIVE 242 43 2 93 35 NC_002967:TDE2548|3end_hypothetical_protein_2573064..2573214_NEGATIVE 237 118 74 42 3 NC_002967:TDE0100|3end_hypothetical_protein_116974..117124_NEGATIVE 236 21 7 108 94 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE 235 32 11 26 1 NC_002967:TDE0678|3end_hypothetical_protein_716438..716588_POSITIVE 227 39 7 45 1 NC_002967:TDE1311|3end_ABC_transporter,_ATP-binding/permease_protein_1349055..1349205_POSITIVE 226 34 7 27 5 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 225 35 4 133 88 NC_002967:TDE0772|3end_50S_ribosomal_protein_L22_809520..809670_POSITIVE 223 34 5 138 102 NC_002967:TDE2240|3end_hypothetical_protein_2277625..2277775_NEGATIVE 223 34 5 138 102 NC_002967:TDE2102|3end_hypothetical_protein_2126616..2126766_NEGATIVE 223 49 4 149 99 NC_002967:TDE1917|3end_cytidylyltransferase_domain_protein_1934764..1934914_NEGATIVE 222 119 80 138 101 NC_002967:TDE0142|3end_hypothetical_protein_163979..164129_NEGATIVE 217 50 10 52 4 NC_002967:TDE2354|3end_hypothetical_protein_2390918..2391068_POSITIVE 216 31 8 128 94 NC_002967:TDE0835|3end_NADH-ubiquinone_oxidoreductase_854867..855017_NEGATIVE 209 21 6 55 38 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 208 48 6 143 98 NC_002967:TDE1210|3end_ATP-dependent_protease_peptidase_subunit_1243945..1244095_POSITIVE 207 34 8 56 25 NC_002967:TDE2120|3end_glycine_reductase_complex_proprotein_GrdE2_2152705..2152855_NEGATIVE