Origin IGS: gatgagtctttagataaatatcaacaattttactttgtaaagataataaagaaaaacaagtaacttttagtttgaaatttagttatatttcagcaagaacaatacagcatatctattttaaatcaattatatagatttatgcataaattttagcatccggttgaaggagggaggc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcctccctccttcaaccggatgctaaaatttatgcataaatctatataattgatttaaaatagatatgctgtattgttcttgctgaaatataactaaatttcaaactaaaagttacttgtttttctttattatctttacaaagtaaaattgttgatatttatctaaagactcatc Mask Tandem Repeat Region ================================================ gatgagtctttagataaatatcaacaattttactttgtaaagataataaagaaaaacaagtaacttttagtttgaaatttagttatatttcagcaagaacaatacagcatatctattttaaatcaattatatagatttatgcataaattttagcatccggttgaaggagggaggc Find is-nt database================================================ Query_seq: TDE0127:TDE0128|TDE0127:TDE0128:DNA-binding protein:HAMP domain/GGDEF domain/EAL domain protein:->->:146205..146379 175 gatgagtctttagataaatatcaacaattttactttgtaaagataataaagaaaaacaagtaacttttagtttgaaatttagttatatttcagcaagaacaatacagcatatctattttaaatcaattatatagatttatgcataaattttagcatccggttgaaggagggaggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0127:TDE0128|TDE0127:TDE0128:DNA-binding protein:HAMP domain/GGDEF domain/EAL domain protein:->->:146205..146379 175 gatgagtctttagataaatatcaacaattttactttgtaaagataataaagaaaaacaagtaacttttagtttgaaatttagttatatttcagcaagaacaatacagcatatctattttaaatcaattatatagatttatgcataaattttagcatccggttgaaggagggaggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0127:TDE0128|TDE0127:TDE0128:DNA-binding protein:HAMP domain/GGDEF domain/EAL domain protein:->->:146205..146379 175 gatgagtctttagataaatatcaacaattttactttgtaaagataataaagaaaaacaagtaacttttagtttgaaatttagttatatttcagcaagaacaatacagcatatctattttaaatcaattatatagatttatgcataaattttagcatccggttgaaggagggaggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgagtctttagataaatatcaacaattttactttgtaaagataataaagaaaaacaagtaacttttagtttgaaatttagttatatttcagcaagaacaatacagcatatctattttaaatcaattatatagatttatgcataaattttagcatccggttgaaggagggaggc Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 18 End: 131 ................. M S T I L L C K D N K E K Q V T F S L K F S Y I S A R T I Q H I Y F K S I I ............................................ gatgagtctttagataaatatcaacaattttactttgtaaagataataaagaaaaacaagtaacttttagtttgaaatttagttatatttcagcaagaacaatacagcatatctattttaaatcaattatatagatttatgcataaattttagcatccggttgaaggagggaggc 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================================================ gatgagtctttagataaatatcaacaattttactttgtaaagataataaagaaaaacaagtaacttttagtttgaaatttagttatatttcagcaagaacaatacagcatatctattttaaatcaattatatagatttatgcataaattttagcatccggttgaaggagggaggc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0127:TDE0128|TDE0127:TDE0128:DNA-binding protein:HAMP domain/GGDEF domain/EAL domain protein:->->:146205..146379 175 gatgagtctttagataaatatcaacaattttactttgtaaagataataaagaaaaacaagtaacttttagtttgaaatttagttatatttcagcaagaacaatacagcatatctattttaaatcaattatatagatttatgcataaattttagcatccggttgaaggagggaggc Intra-Species Hit: Count: 1 Min: 1 Max: 175 Len: 175 Subject: NC_002967_TDE0127_TDE0128|DNA-binding protein:HAMP domain/GGDEF domain/EAL domain protein|POSITIVE:POSITIVE|[146205,146379]|175 HSP 1 e-value: 8.0E-95 bit: 347.0 Len: 175 Query Start:1 Query End:175 Subject Strand: POSITIVE Subject Start: 1 Subject End: 175 gatgagtctttagataaatatcaacaattttactttgtaaagataataaagaaaaacaagtaacttttagtttgaaatttagttatatttcagcaagaacaatacagcatatctattttaaatcaattatatagatttatgcataaattttagcatccggttgaaggagggaggc gatgagtctttagataaatatcaacaattttactttgtaaagataataaagaaaaacaagtaacttttagtttgaaatttagttatatttcagcaagaacaatacagcatatctattttaaatcaattatatagatttatgcataaattttagcatccggttgaaggagggaggc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAGUCUUUAGAUAAAUAUCAACAAUUUUACUUUGUAAAGAUAAUAAAGAAAAACAAGUAACUUUUAGUUUGAAAUUUAGUUAUAUUUCAGCAAGAACAAUACAGCAUAUCUAUUUUAAAUCAAUUAUAUAGAUUUAUGCAUAAAUUUUAGCAUCCGGUUGAAGGAGGGAGGC .....((((((.........(((((..((((.((((((.......))))))))))....(((..((((.(((.(((((........)))))))).))))...))).((((((((((..(((.....))).)))))..))))).................))))).....)))))) (-22.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCUCCCUCCUUCAACCGGAUGCUAAAAUUUAUGCAUAAAUCUAUAUAAUUGAUUUAAAAUAGAUAUGCUGUAUUGUUCUUGCUGAAAUAUAACUAAAUUUCAAACUAAAAGUUACUUGUUUUUCUUUAUUAUCUUUACAAAGUAAAAUUGUUGAUAUUUAUCUAAAGACUCAUC ((.(((...........))).))..........(((((..(((((.(((.....)))..)))))))))).(((..........((((((........))))))..........)))..((((((......((((...((((.......)))).)))).......))))))..... (-18.07) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 240 170 125 201 154 NC_002967:TDE1110|5end_lipoprotein,_putative_1144272..1144502_POSITIVE 223 170 136 152 114 NC_002967:TDE1199|5end_cell_division_protein_FtsL,_putative_1231341..1231571_POSITIVE 211 75 33 214 168 NC_002967:TDE0341|5end_ribonucleotide-diphosphate_reductase_alpha_subunit_382126..382356_NEGATIVE 208 163 129 116 88 NC_002967:TDE2616|5end_cyclic_nucleotide-binding_protein_2658339..2658569_NEGATIVE 208 132 92 93 50 NC_002967:TDE1917|5end_cytidylyltransferase_domain_protein_1937394..1937624_NEGATIVE 206 119 88 99 67 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 199 170 131 159 110 NC_002967:TDE0942|5end_long-chain-fatty-acid--CoA_ligase,_putative_964132..964362_POSITIVE 197 127 92 118 80 NC_002967:TDE0717|5end_hypothetical_protein_751779..752009_POSITIVE 194 111 71 43 2 NC_002967:TDE0252|5end_hypothetical_protein_286263..286493_POSITIVE 192 168 140 201 163 NC_002967:TDE2785|5end_hypothetical_protein_2839182..2839412_NEGATIVE 189 168 140 66 36 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 188 170 130 121 77 NC_002967:TDE0043|5end_TPR_domain_protein_49688..49918_POSITIVE 187 170 131 227 183 NC_002967:TDE1710|5end_ribosomal_protein_S20_1765485..1765715_NEGATIVE 186 170 139 231 204 NC_002967:TDE0144|5end_thiamine_ABC_transporter,_permease_protein_165007..165237_POSITIVE 186 168 140 196 162 NC_002967:TDE0062|5end_PTS_system,_IIA_component_69090..69320_POSITIVE 184 95 59 100 69 NC_002967:TDE2320|5end_RNA_polymerase_sigma-24_factor,_putative_2356951..2357181_NEGATIVE 184 170 148 200 174 NC_002967:TDE1591|5end_inorganic_polyphosphate/ATP-NAD_kinase,_putative_1638582..1638812_POSITIVE 183 87 41 71 10 NC_002967:TDE2201|5end_hypothetical_protein_2238623..2238853_NEGATIVE 182 108 62 136 95 NC_002967:TDE2219|5end_hypothetical_protein_2260646..2260876_NEGATIVE 181 111 91 183 161 NC_002967:TDE1391|5end_NQR2/RnfD/RnfE_family_protein_1430975..1431205_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 223 170 136 150 112 NC_002967:TDE1198|3end_S-adenosyl-methyltransferase_MraW_1231419..1231569_POSITIVE 208 163 129 112 84 NC_002967:TDE2617|3end_cyclic_nucleotide-binding_protein_2658343..2658493_NEGATIVE 208 132 92 96 53 NC_002967:TDE1918|3end_hypothetical_protein_1937391..1937541_NEGATIVE 198 117 79 74 38 NC_002967:TDE1957|3end_hypothetical_protein_1972233..1972383_POSITIVE 192 130 86 94 48 NC_002967:TDE2141|3end_hypothetical_protein_2175583..2175733_NEGATIVE 189 168 140 48 18 NC_002967:TDE0402|3end_hypothetical_protein_454248..454398_NEGATIVE 188 170 130 116 72 NC_002967:TDE0042|3end_phosphate_acetyltransferase_49763..49913_POSITIVE 184 95 59 103 72 NC_002967:TDE2321|3end_hypothetical_protein_2356948..2357098_NEGATIVE 180 170 156 60 45 NC_002967:TDE1894|3end_ferredoxin_1915041..1915191_POSITIVE 177 168 122 74 23 NC_002967:TDE0318|3end_hypothetical_protein_351476..351626_POSITIVE 175 163 125 83 38 NC_002967:TDE1162|3end_ParB-like_nuclease_domain_protein_1196056..1196206_NEGATIVE 174 118 78 64 21 NC_002967:TDE0662|3end_hypothetical_protein_697572..697722_NEGATIVE 174 170 125 88 32 NC_002967:TDE0272|3end_hypothetical_protein_302256..302406_NEGATIVE 172 170 154 119 102 NC_002967:TDE1695|3end_CoA-substrate-specific_enzyme_activase_domain_protein_1749498..1749648_NEGATIVE 171 166 139 69 35 NC_002967:TDE0475|3end_ABC_transporter,_ATP-binding_protein_531153..531303_NEGATIVE 170 162 133 151 129 NC_002967:TDE2716|3end_HAD-superfamily_hydrolase,_subfamily_IA_2773931..2774081_POSITIVE 170 162 140 88 68 NC_002967:TDE2167|3end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2198103..2198253_NEGATIVE 169 167 121 85 20 NC_002967:TDE0343|3end_hydrolase,_alpha/beta_fold_family_384247..384397_NEGATIVE 168 170 156 52 34 NC_002967:TDE2606|3end_urocanate_hydratase_2648551..2648701_POSITIVE 168 92 53 76 37 NC_002967:TDE1449|3end_GTPase_YjeQ_1495379..1495529_POSITIVE