Origin IGS: aaatatcattttggattattttcaattaaaatagagtagaaaaatttatcataattcagtatagttagctaatactaactttataaaacgaaagtggagataaacaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattgtttatctccactttcgttttataaagttagtattagctaactatactgaattatgataaatttttctactctattttaattgaaaataatccaaaatgatattt Mask Tandem Repeat Region ================================================ aaatatcattttggattattttcaattaaaatagagtagaaaaatttatcataattcagtatagttagctaatactaactttataaaacgaaagtggagataaacaatt Find is-nt database================================================ Query_seq: TDE2509:TDE2510|TDE2509:TDE2510:transcriptional regulator, AraC family:ABC transporter, ATP-binding/permease protein:->->:2534213..2534321 109 aaatatcattttggattattttcaattaaaatagagtagaaaaatttatcataattcagtatagttagctaatactaactttataaaacgaaagtggagataaacaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2509:TDE2510|TDE2509:TDE2510:transcriptional regulator, AraC family:ABC transporter, ATP-binding/permease protein:->->:2534213..2534321 109 aaatatcattttggattattttcaattaaaatagagtagaaaaatttatcataattcagtatagttagctaatactaactttataaaacgaaagtggagataaacaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2509:TDE2510|TDE2509:TDE2510:transcriptional regulator, AraC family:ABC transporter, ATP-binding/permease protein:->->:2534213..2534321 109 aaatatcattttggattattttcaattaaaatagagtagaaaaatttatcataattcagtatagttagctaatactaactttataaaacgaaagtggagataaacaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatatcattttggattattttcaattaaaatagagtagaaaaatttatcataattcagtatagttagctaatactaactttataaaacgaaagtggagataaacaatt Predict ORF larger than 30AA ================================================ aaatatcattttggattattttcaattaaaatagagtagaaaaatttatcataattcagtatagttagctaatactaactttataaaacgaaagtggagataaacaatt 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================================================ aaatatcattttggattattttcaattaaaatagagtagaaaaatttatcataattcagtatagttagctaatactaactttataaaacgaaagtggagataaacaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2509:TDE2510|TDE2509:TDE2510:transcriptional regulator, AraC family:ABC transporter, ATP-binding/permease protein:->->:2534213..2534321 109 aaatatcattttggattattttcaattaaaatagagtagaaaaatttatcataattcagtatagttagctaatactaactttataaaacgaaagtggagataaacaatt Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_002967_TDE2509_TDE2510|transcriptional regulator, AraC family:ABC transporter, ATP-binding/permease protein|POSITIVE:POSITIVE|[2534213,2534321]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 aaatatcattttggattattttcaattaaaatagagtagaaaaatttatcataattcagtatagttagctaatactaactttataaaacgaaagtggagataaacaatt aaatatcattttggattattttcaattaaaatagagtagaaaaatttatcataattcagtatagttagctaatactaactttataaaacgaaagtggagataaacaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAUCAUUUUGGAUUAUUUUCAAUUAAAAUAGAGUAGAAAAAUUUAUCAUAAUUCAGUAUAGUUAGCUAAUACUAACUUUAUAAAACGAAAGUGGAGAUAAACAAUU ..........(((..((((((((.......(((((((.((........)).......(((((((....)).))))).)))))))...((....)))))))))).))).. (-15.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUGUUUAUCUCCACUUUCGUUUUAUAAAGUUAGUAUUAGCUAACUAUACUGAAUUAUGAUAAAUUUUUCUACUCUAUUUUAAUUGAAAAUAAUCCAAAAUGAUAUUU ..................(((((((....(((((((....)))))))....(.(((((.((((.............)))).))))).).........)))))))..... (-11.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 153 75 32 103 65 NC_002967:TDE0127|5end_DNA-binding_protein_145750..145980_POSITIVE 150 92 58 211 177 NC_002967:TDE2025|5end_hypothetical_protein_2051440..2051670_NEGATIVE 150 70 24 72 23 NC_002967:TDE1134|5end_hypothetical_protein_1165187..1165417_NEGATIVE 150 70 24 201 152 NC_002967:TDE1133|5end_hypothetical_protein_1165058..1165288_NEGATIVE 148 70 32 104 62 NC_002967:TDE1708|5end_apolipoprotein_N-acyltransferase_1764822..1765052_NEGATIVE 147 77 43 148 113 NC_002967:TDE2204|5end_Na+/H+_antiporter_family_protein_2241169..2241399_POSITIVE 147 98 65 115 85 NC_002967:TDE0156|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_183571..183801_NEGATIVE 146 62 34 101 68 NC_002967:TDE2320|5end_RNA_polymerase_sigma-24_factor,_putative_2356951..2357181_NEGATIVE 146 100 62 211 173 NC_002967:TDE1938|5end_hypothetical_protein_1953640..1953870_POSITIVE 146 45 1 229 183 NC_002967:TDE0338|5end_methyl-accepting_chemotaxis_protein-like_protein_377317..377547_POSITIVE 145 67 24 78 41 NC_002967:TDE0529|5end_hypothetical_protein_573801..574031_POSITIVE 143 95 51 171 123 NC_002967:TDE2083|5end_anti-anti-sigma_factor_2113163..2113393_NEGATIVE 143 99 74 64 39 NC_002967:TDE0766|5end_30S_ribosomal_protein_S10_805984..806214_POSITIVE 142 99 63 204 163 NC_002967:TDE1492|5end_chemotaxis_protein_CheW_1537231..1537461_POSITIVE 141 70 34 165 125 NC_002967:TDE2606|5end_urocanate_hydratase_2646447..2646677_POSITIVE 141 98 72 40 18 NC_002967:TDE1773|5end_hypothetical_protein_1817101..1817331_NEGATIVE 140 76 32 205 178 NC_002967:TDE2321|5end_hypothetical_protein_2357301..2357531_NEGATIVE 140 100 64 122 84 NC_002967:TDE1530|5end_hypothetical_protein_1575872..1576102_NEGATIVE 139 77 31 170 127 NC_002967:TDE2546|5end_hypothetical_protein_2572761..2572991_NEGATIVE 139 24 6 23 4 NC_002967:TDE1806|5end_hypothetical_protein_1843462..1843692_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 157 77 31 78 22 NC_002967:TDE1804|3end_hypothetical_protein_1839476..1839626_NEGATIVE 157 99 63 111 71 NC_002967:TDE0621|3end_MATE_efflux_family_protein_654776..654926_POSITIVE 155 70 23 116 61 NC_002967:TDE2680|3end_hypothetical_protein_2720449..2720599_NEGATIVE 151 40 2 125 87 NC_002967:TDE2111|3end_hypothetical_protein_2136271..2136421_NEGATIVE 150 70 24 67 18 NC_002967:TDE1135|3end_hypothetical_protein_1165192..1165342_NEGATIVE 150 50 4 120 72 NC_002967:TDE0201|3end_hypothetical_protein_235724..235874_POSITIVE 148 70 32 107 65 NC_002967:TDE1709|3end_DNA-binding_protein,_HU_family_1764819..1764969_NEGATIVE 146 62 34 104 71 NC_002967:TDE2321|3end_hypothetical_protein_2356948..2357098_NEGATIVE 145 67 24 76 39 NC_002967:TDE0528|3end_hypothetical_protein_573879..574029_POSITIVE 141 70 34 78 38 NC_002967:TDE2605|3end_phosphoglycerate_mutase_family_protein_2646440..2646590_POSITIVE 141 66 21 117 69 NC_002967:TDE2358|3end_hypothetical_protein_2393129..2393279_NEGATIVE 139 59 27 35 2 NC_002967:TDE2773|3end_hypothetical_protein_2825823..2825973_NEGATIVE 139 24 6 51 32 NC_002967:TDE1807|3end_hypothetical_protein_1843434..1843584_NEGATIVE 139 47 5 91 53 NC_002967:TDE1740|3end_hypothetical_protein_1792630..1792780_NEGATIVE 134 95 55 56 20 NC_002967:TDE0329|3end_CRISPR-associated_protein_Cas2_366327..366477_POSITIVE 133 94 60 63 30 NC_002967:TDE0362|3end_bacterial_Ig-like_domain_protein_407501..407651_NEGATIVE 132 69 36 117 81 NC_002967:TDE1987|3end_hypothetical_protein_2002802..2002952_POSITIVE 130 84 45 144 115 NC_002967:TDE1831|3end_hypothetical_protein_1864415..1864565_NEGATIVE 130 84 45 144 115 NC_002967:TDE1797|3end_hypothetical_protein_1835655..1835805_NEGATIVE 130 99 54 57 16 NC_002967:TDE0953|3end_branched-chain_amino_acid_ABC_transporter,_permease_protein_978007..978157_POSITIVE