Origin IGS: gttttagctttttaagaaaaaaaattgagagtgattaatattatgaataaatacgatttcaatatggattttcagtagataaaatattactaaaaaataaaactatagtatttagtaagtataattaataagggatatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatatcccttattaattatacttactaaatactatagttttattttttagtaatattttatctactgaaaatccatattgaaatcgtatttattcataatattaatcactctcaattttttttcttaaaaagctaaaac Mask Tandem Repeat Region ================================================ gttttagctttttaagaaaaaaaattgagagtgattaatattatgaataaatacgatttcaatatggattttcagtagataaaatattactaaaaaataaaactatagtatttagtaagtataattaataagggatatt Find is-nt database================================================ Query_seq: TDE0096:TDE0097|TDE0096:TDE0097:NADH oxidase:hypothetical protein:->->:114198..114336 139 gttttagctttttaagaaaaaaaattgagagtgattaatattatgaataaatacgatttcaatatggattttcagtagataaaatattactaaaaaataaaactatagtatttagtaagtataattaataagggatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0096:TDE0097|TDE0096:TDE0097:NADH oxidase:hypothetical protein:->->:114198..114336 139 gttttagctttttaagaaaaaaaattgagagtgattaatattatgaataaatacgatttcaatatggattttcagtagataaaatattactaaaaaataaaactatagtatttagtaagtataattaataagggatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0096:TDE0097|TDE0096:TDE0097:NADH oxidase:hypothetical protein:->->:114198..114336 139 gttttagctttttaagaaaaaaaattgagagtgattaatattatgaataaatacgatttcaatatggattttcagtagataaaatattactaaaaaataaaactatagtatttagtaagtataattaataagggatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttttagctttttaagaaaaaaaattgagagtgattaatattatgaataaatacgatttcaatatggattttcagtagataaaatattactaaaaaataaaactatagtatttagtaagtataattaataagggatatt Predict ORF larger than 30AA ================================================ gttttagctttttaagaaaaaaaattgagagtgattaatattatgaataaatacgatttcaatatggattttcagtagataaaatattactaaaaaataaaactatagtatttagtaagtataattaataagggatatt 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================================================ gttttagctttttaagaaaaaaaattgagagtgattaatattatgaataaatacgatttcaatatggattttcagtagataaaatattactaaaaaataaaactatagtatttagtaagtataattaataagggatatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0096:TDE0097|TDE0096:TDE0097:NADH oxidase:hypothetical protein:->->:114198..114336 139 gttttagctttttaagaaaaaaaattgagagtgattaatattatgaataaatacgatttcaatatggattttcagtagataaaatattactaaaaaataaaactatagtatttagtaagtataattaataagggatatt Intra-Species Hit: Count: 1 Min: 25 Max: 139 Len: 115 Subject: NC_002967_TDE0096_TDE0097|NADH oxidase:hypothetical protein|POSITIVE:POSITIVE|[114198,114336]|139 HSP 1 e-value: 4.0E-59 bit: 228.0 Len: 115 Query Start:25 Query End:139 Subject Strand: POSITIVE Subject Start: 25 Subject End: 139 ........................ttgagagtgattaatattatgaataaatacgatttcaatatggattttcagtagataaaatattactaaaaaataaaactatagtatttagtaagtataattaataagggatatt ........................ttgagagtgattaatattatgaataaatacgatttcaatatggattttcagtagataaaatattactaaaaaataaaactatagtatttagtaagtataattaataagggatatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAGAGUGAUUAAUAUUAUGAAUAAAUACGAUUUCAAUAUGGAUUUUCAGUAGAUAAAAUAUUACUAAAAAAUAAAACUAUAGUAUUUAGUAAGUAUAAUUAAUAAGGGAUAUU .........((((((..(((...(((((((...(((.....)))((((.(((((........))))).))))...........)))))))....)))..)))))).......... ( -9.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUCCCUUAUUAAUUAUACUUACUAAAUACUAUAGUUUUAUUUUUUAGUAAUAUUUUAUCUACUGAAAAUCCAUAUUGAAAUCGUAUUUAUUCAUAAUAUUAAUCACUCUCAA ..........((((((.........(((((((....((((((.(((((((((..........))))))))).......)))))).)))))))........))))))......... ( -9.33) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 181 56 22 155 111 NC_002967:TDE2649|5end_ABC_transporter,_ATP-binding_protein_2688648..2688878_NEGATIVE 180 45 1 170 134 NC_002967:TDE0478|5end_cyclic_nucleotide_binding_domain_protein_534283..534513_POSITIVE 179 110 66 207 162 NC_002967:TDE1273|5end_oligopeptide/dipeptide_ABC_transporter,_peptide-binding_protein_1308624..1308854_NEGATIVE 174 58 20 193 156 NC_002967:TDE0781|5end_30S_ribosomal_protein_S8_812561..812791_POSITIVE 173 36 3 228 193 NC_002967:TDE2540|5end_lipoprotein,_putative_2567981..2568211_NEGATIVE 157 110 74 187 144 NC_002967:TDE1453|5end_alpha-galactosidase_1499112..1499342_POSITIVE 156 93 53 81 38 NC_002967:TDE1489|5end_hypothetical_protein_1533572..1533802_NEGATIVE 156 35 6 109 78 NC_002967:TDE0290|5end_hypothetical_protein_320794..321024_NEGATIVE 155 44 1 207 151 NC_002967:TDE1386|5end_methyl-accepting_chemotaxis_protein_1424941..1425171_POSITIVE 147 58 16 220 177 NC_002967:TDE0493|5end_hypothetical_protein_549342..549572_NEGATIVE 146 78 32 62 17 NC_002967:TDE0721|5end_hypothetical_protein_756751..756981_POSITIVE 145 52 18 105 72 NC_002967:TDE1816|5end_hypothetical_protein_1851673..1851903_NEGATIVE 143 46 2 205 161 NC_002967:TDE1608|5end_hypothetical_protein_1657570..1657800_POSITIVE 143 83 42 117 80 NC_002967:TDE0360|5end_ABC_transporter,_ATP-binding/permease_protein_405844..406074_NEGATIVE 142 90 50 78 30 NC_002967:TDE2201|5end_hypothetical_protein_2238623..2238853_NEGATIVE 142 109 78 168 129 NC_002967:TDE0799|5end_glycerophosphoryl_diester_phosphodiesterase,_putative_822609..822839_POSITIVE 142 90 49 192 150 NC_002967:TDE0760|5end_hypothetical_protein_799436..799666_POSITIVE 141 70 27 67 18 NC_002967:TDE1773|5end_hypothetical_protein_1817101..1817331_NEGATIVE 139 56 14 109 55 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 139 49 4 55 12 NC_002967:TDE1334|5end_hypothetical_protein_1370144..1370374_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 181 56 22 137 93 NC_002967:TDE2650|3end_transcriptional_regulator,_putative_2688666..2688816_NEGATIVE 157 41 2 147 115 NC_002967:TDE2584|3end_dipeptidase_2617944..2618094_POSITIVE 157 110 74 115 72 NC_002967:TDE1452|3end_hypothetical_protein_1499120..1499270_POSITIVE 156 67 28 43 1 NC_002967:TDE1896|3end_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1915904..1916054_NEGATIVE 156 93 53 81 38 NC_002967:TDE1490|3end_hypothetical_protein_1533572..1533722_NEGATIVE 156 35 6 109 78 NC_002967:TDE0291|3end_hypothetical_protein_320794..320944_NEGATIVE 146 68 23 115 76 NC_002967:TDE2098|3end_hypothetical_protein_2124951..2125101_NEGATIVE 146 78 32 65 20 NC_002967:TDE0720|3end_bacteriocin_ABC_transporter,_bacteriocin-binding_protein,_putative_756834..756984_POSITIVE 146 84 44 103 56 NC_002967:TDE0467|3end_hypothetical_protein_519006..519156_NEGATIVE 139 50 8 93 44 NC_002967:TDE0278|3end_hypothetical_protein_308501..308651_NEGATIVE 133 54 11 59 15 NC_002967:TDE1412|3end_sodium/hydrogen_exchanger_family_protein_1455266..1455416_POSITIVE 130 49 28 146 120 NC_002967:TDE1881|3end_methyltransferase,_putative_1903631..1903781_POSITIVE 128 48 2 92 44 NC_002967:TDE0880|3end_nicotinate-nucleotide-dimethylbenzimidazole_phosphoribosyltransferase_901136..901286_POSITIVE 128 50 29 35 15 NC_002967:TDE0253|3end_hypothetical_protein_288725..288875_POSITIVE 127 100 79 65 40 NC_002967:TDE1576|3end_tRNA-i(6)A37_modification_enzyme_MiaB_1624213..1624363_POSITIVE 125 110 77 83 51 NC_002967:TDE0101|3end_alpha-amylase_family_protein_119017..119167_NEGATIVE 122 50 6 54 1 NC_002967:TDE0292|3end_hypothetical_protein_321175..321325_NEGATIVE 119 56 40 76 56 NC_002967:TDE2409|3end_hypothetical_protein_2435485..2435635_NEGATIVE 119 110 78 38 2 NC_002967:TDE2369|3end_hypothetical_protein_2403469..2403619_POSITIVE 118 49 28 21 2 NC_002967:TDE0416|3end_bacteriocin-type_signal_domain_protein_469522..469672_POSITIVE