Origin IGS: actttacttatcggctaaatatatatataaattagtttataaagtataatcttctatactcagagcaaaatattattttttcattaaattctatctgctgatttgattaattttcattaaatcatcatgttttttacggcttttttgcatagattaatcatatatgacatcctgttaaaattattttttaagattatctaaataaataatgagtatctttcattttaaaatatattaacctacagtgaaaagtaaaatcata .........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 tatgattttacttttcactgtaggttaatatattttaaaatgaaagatactcattatttatttagataatcttaaaaaataattttaacaggatgtcatatatgattaatctatgcaaaaaagccgtaaaaaacatgatgatttaatgaaaattaatcaaatcagcagatagaatttaatgaaaaaataatattttgctctgagtatagaagattatactttataaactaatttatatatatatttagccgataagtaaagt Mask Tandem Repeat Region ================================================ actttacttatcggctaaatatatatataaattagtttataaagtataatcttctatactcagagcaaaatattattttttcattaaattctatctgctgatttgattaattttcattaaatcatcatgttttttacggcttttttgcatagattaatcatatatgacatcctgttaaaattattttttaagattatctaaataaataatgagtatctttcattttaaaatatattaacctacagtgaaaagtaaaatcata Find is-nt database================================================ Query_seq: TDE0228:TDE0229|TDE0228:TDE0229:hypothetical protein:ATPase family protein:<-<-:260694..260955 262 actttacttatcggctaaatatatatataaattagtttataaagtataatcttctatactcagagcaaaatattattttttcattaaattctatctgctgatttgattaattttcattaaatcatcatgttttttacggcttttttgcatagattaatcatatatgacatcctgttaaaattattttttaagattatctaaataaataatgagtatctttcattttaaaatatattaacctacagtgaaaagtaaaatcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0228:TDE0229|TDE0228:TDE0229:hypothetical protein:ATPase family protein:<-<-:260694..260955 262 actttacttatcggctaaatatatatataaattagtttataaagtataatcttctatactcagagcaaaatattattttttcattaaattctatctgctgatttgattaattttcattaaatcatcatgttttttacggcttttttgcatagattaatcatatatgacatcctgttaaaattattttttaagattatctaaataaataatgagtatctttcattttaaaatatattaacctacagtgaaaagtaaaatcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0228:TDE0229|TDE0228:TDE0229:hypothetical protein:ATPase family protein:<-<-:260694..260955 262 actttacttatcggctaaatatatatataaattagtttataaagtataatcttctatactcagagcaaaatattattttttcattaaattctatctgctgatttgattaattttcattaaatcatcatgttttttacggcttttttgcatagattaatcatatatgacatcctgttaaaattattttttaagattatctaaataaataatgagtatctttcattttaaaatatattaacctacagtgaaaagtaaaatcata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actttacttatcggctaaatatatatataaattagtttataaagtataatcttctatactcagagcaaaatattattttttcattaaattctatctgctgatttgattaattttcattaaatcatcatgttttttacggcttttttgcatagattaatcatatatgacatcctgttaaaattattttttaagattatctaaataaataatgagtatctttcattttaaaatatattaacctacagtgaaaagtaaaatcata Predict ORF larger than 30AA ================================================ actttacttatcggctaaatatatatataaattagtttataaagtataatcttctatactcagagcaaaatattattttttcattaaattctatctgctgatttgattaattttcattaaatcatcatgttttttacggcttttttgcatagattaatcatatatgacatcctgttaaaattattttttaagattatctaaataaataatgagtatctttcattttaaaatatattaacctacagtgaaaagtaaaatcata 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================================================ actttacttatcggctaaatatatatataaattagtttataaagtataatcttctatactcagagcaaaatattattttttcattaaattctatctgctgatttgattaattttcattaaatcatcatgttttttacggcttttttgcatagattaatcatatatgacatcctgttaaaattattttttaagattatctaaataaataatgagtatctttcattttaaaatatattaacctacagtgaaaagtaaaatcata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0228:TDE0229|TDE0228:TDE0229:hypothetical protein:ATPase family protein:<-<-:260694..260955 262 actttacttatcggctaaatatatatataaattagtttataaagtataatcttctatactcagagcaaaatattattttttcattaaattctatctgctgatttgattaattttcattaaatcatcatgttttttacggcttttttgcatagattaatcatatatgacatcctgttaaaattattttttaagattatctaaataaataatgagtatctttcattttaaaatatattaacctacagtgaaaagtaaaatcata Intra-Species Hit: Count: 1 Min: 1 Max: 262 Len: 262 Subject: NC_002967_TDE0228_TDE0229|hypothetical protein:ATPase family protein|NEGATIVE:NEGATIVE|[260694,260955]|262 HSP 1 e-value: 1.0E-146 bit: 519.0 Len: 262 Query Start:1 Query End:262 Subject Strand: POSITIVE Subject Start: 1 Subject End: 262 actttacttatcggctaaatatatatataaattagtttataaagtataatcttctatactcagagcaaaatattattttttcattaaattctatctgctgatttgattaattttcattaaatcatcatgttttttacggcttttttgcatagattaatcatatatgacatcctgttaaaattattttttaagattatctaaataaataatgagtatctttcattttaaaatatattaacctacagtgaaaagtaaaatcata actttacttatcggctaaatatatatataaattagtttataaagtataatcttctatactcagagcaaaatattattttttcattaaattctatctgctgatttgattaattttcattaaatcatcatgttttttacggcttttttgcatagattaatcatatatgacatcctgttaaaattattttttaagattatctaaataaataatgagtatctttcattttaaaatatattaacctacagtgaaaagtaaaatcata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUUACUUAUCGGCUAAAUAUAUAUAUAAAUUAGUUUAUAAAGUAUAAUCUUCUAUACUCAGAGCAAAAUAUUAUUUUUUCAUUAAAUUCUAUCUGCUGAUUUGAUUAAUUUUCAUUAAAUCAUCAUGUUUUUUACGGCUUUUUUGCAUAGAUUAAUCAUAUAUGACAUCCUGUUAAAAUUAUUUUUUAAGAUUAUCUAAAUAAAUAAUGAGUAUCUUUCAUUUUAAAAUAUAUUAACCUACAGUGAAAAGUAAAAUCAUA ..(((((((.((.........(((((((..((((((((((..((((((......)))))).(((((.............................((.(((((((((........))))))))).)).((.....)).))))).....)))))))))).))))))).....((((......(((.((((((..((((....))))..((((((.....)))))))))))).))).......)))).)).)))))))...... (-34.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGAUUUUACUUUUCACUGUAGGUUAAUAUAUUUUAAAAUGAAAGAUACUCAUUAUUUAUUUAGAUAAUCUUAAAAAAUAAUUUUAACAGGAUGUCAUAUAUGAUUAAUCUAUGCAAAAAAGCCGUAAAAAACAUGAUGAUUUAAUGAAAAUUAAUCAAAUCAGCAGAUAGAAUUUAAUGAAAAAAUAAUAUUUUGCUCUGAGUAUAGAAGAUUAUACUUUAUAAACUAAUUUAUAUAUAUAUUUAGCCGAUAAGUAAAGU ....(((((((((.((......(((((((((((..((((......((((..(.((((((....))))))..((((((.....))))))..)..))))...(((((((..(((((((...................((((...(((((....)))))....)))).((((((((((...((......))...)))))).)))).))))))).))))))).............))))...))))).)))))))).))))))))) (-40.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 730 140 91 231 182 NC_002967:TDE0228|5end_hypothetical_protein_260603..260833_NEGATIVE 248 163 122 93 48 NC_002967:TDE0494|5end_hypothetical_protein_550515..550745_NEGATIVE 244 103 62 194 154 NC_002967:TDE2239|5end_hypothetical_protein_2277546..2277776_NEGATIVE 244 103 62 112 72 NC_002967:TDE2101|5end_hypothetical_protein_2126619..2126849_NEGATIVE 236 176 134 107 61 NC_002967:TDE1917|5end_cytidylyltransferase_domain_protein_1937394..1937624_NEGATIVE 232 174 137 57 28 NC_002967:TDE1885|5end_hypothetical_protein_1906857..1907087_POSITIVE 232 99 58 104 65 NC_002967:TDE0394|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_443981..444211_POSITIVE 229 169 127 106 69 NC_002967:TDE0370|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_421084..421314_POSITIVE 229 114 72 47 9 NC_002967:TDE0226|5end_hypothetical_protein_256693..256923_NEGATIVE 228 123 82 115 76 NC_002967:TDE1973|5end_CvpA_family_protein_1987706..1987936_NEGATIVE 219 175 137 62 23 NC_002967:TDE1891|5end_hypothetical_protein_1911206..1911436_POSITIVE 216 167 124 68 17 NC_002967:TDE2465|5end_hypothetical_protein_2489651..2489881_NEGATIVE 215 140 92 61 4 NC_002967:TDE0038|5end_3-oxoacyl-(acyl-carrier-protein)_synthase_II_44271..44501_NEGATIVE 213 148 109 219 174 NC_002967:TDE1863|5end_Holliday_junction_DNA_helicase_RuvA_1888579..1888809_NEGATIVE 212 172 137 101 55 NC_002967:TDE2495|5end_hypothetical_protein_2521053..2521283_NEGATIVE 210 140 91 89 39 NC_002967:TDE0083|5end_GTP-binding_protein_EngA_95684..95914_NEGATIVE 208 160 114 171 136 NC_002967:TDE0629|5end_chaperone_protein_DnaJ_662587..662817_POSITIVE 203 148 102 122 75 NC_002967:TDE0775|5end_ribosomal_protein_L29_810597..810827_POSITIVE 198 152 120 221 183 NC_002967:TDE2327|5end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpB_2364627..2364857_NEGATIVE 198 179 132 131 76 NC_002967:TDE1594|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_1644822..1645052_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 248 163 122 96 51 NC_002967:TDE0495|3end_hypothetical_protein_550512..550662_NEGATIVE 244 103 62 115 75 NC_002967:TDE2240|3end_hypothetical_protein_2277625..2277775_NEGATIVE 244 103 62 115 75 NC_002967:TDE2102|3end_hypothetical_protein_2126616..2126766_NEGATIVE 238 246 206 91 49 NC_002967:TDE2023|3end_TPR_domain_protein_2049505..2049655_NEGATIVE 236 176 134 110 64 NC_002967:TDE1918|3end_hypothetical_protein_1937391..1937541_NEGATIVE 228 123 82 86 47 NC_002967:TDE1974|3end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1987735..1987885_NEGATIVE 223 158 127 133 96 NC_002967:TDE1278|3end_conserved_hypothetical_protein_TIGR01440_1312228..1312378_NEGATIVE 216 167 124 68 17 NC_002967:TDE2466|3end_hypothetical_protein_2489651..2489801_NEGATIVE 210 140 91 102 52 NC_002967:TDE0084|3end_phosphoenolpyruvate-protein_phosphotransferase_95671..95821_NEGATIVE 208 160 114 133 98 NC_002967:TDE0628|3end_molecular_chaperone_DnaK_662629..662779_POSITIVE 203 148 102 109 62 NC_002967:TDE0774|3end_50S_ribosomal_protein_L16_810664..810814_POSITIVE 198 176 135 117 64 NC_002967:TDE1563|3end_hypothetical_protein_1616513..1616663_POSITIVE 196 98 52 134 86 NC_002967:TDE0370|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_422594..422744_POSITIVE 194 133 96 73 37 NC_002967:TDE2352|3end_flagellar_hook-associated_protein_2389186..2389336_POSITIVE 193 175 132 54 12 NC_002967:TDE1038|3end_hypothetical_protein_1065405..1065555_NEGATIVE 192 140 91 76 29 NC_002967:TDE2428|3end_ribosomal_protein_L33_2456122..2456272_NEGATIVE 187 100 52 124 78 NC_002967:TDE1272|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1305990..1306140_NEGATIVE 185 173 138 75 37 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 184 126 90 145 109 NC_002967:TDE0264|3end_ribbon-helix-helix_protein,_CopG_family_297021..297171_NEGATIVE 183 150 127 136 107 NC_002967:TDE1625|3end_glycine_cleavage_system_P_protein,_subunit_1_1673519..1673669_NEGATIVE