Origin IGS: atttgacttagtttccttactatatcacagataaaaacaatgtcaagcaagaaatttcttatattatatggtaaaatgagatatagaactctaaaactgatttaaattcagactcggaatttcatcataaggagaagat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcttctccttatgatgaaattccgagtctgaatttaaatcagttttagagttctatatctcattttaccatataatataagaaatttcttgcttgacattgtttttatctgtgatatagtaaggaaactaagtcaaat Mask Tandem Repeat Region ================================================ atttgacttagtttccttactatatcacagataaaaacaatgtcaagcaagaaatttcttatattatatggtaaaatgagatatagaactctaaaactgatttaaattcagactcggaatttcatcataaggagaagat Find is-nt database================================================ Query_seq: SSA_2167:SSA_2168|SSA_2167:SSA_2168:ABC-type multidrug transporter, ATPase and permease components, putative:Glycerol-3-phosphate dehydrogenase [NAD(P)+], putative:<-->:2167462..2167600 139 atttgacttagtttccttactatatcacagataaaaacaatgtcaagcaagaaatttcttatattatatggtaaaatgagatatagaactctaaaactgatttaaattcagactcggaatttcatcataaggagaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2167:SSA_2168|SSA_2167:SSA_2168:ABC-type multidrug transporter, ATPase and permease components, putative:Glycerol-3-phosphate dehydrogenase [NAD(P)+], putative:<-->:2167462..2167600 139 atttgacttagtttccttactatatcacagataaaaacaatgtcaagcaagaaatttcttatattatatggtaaaatgagatatagaactctaaaactgatttaaattcagactcggaatttcatcataaggagaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2167:SSA_2168|SSA_2167:SSA_2168:ABC-type multidrug transporter, ATPase and permease components, putative:Glycerol-3-phosphate dehydrogenase [NAD(P)+], putative:<-->:2167462..2167600 139 atttgacttagtttccttactatatcacagataaaaacaatgtcaagcaagaaatttcttatattatatggtaaaatgagatatagaactctaaaactgatttaaattcagactcggaatttcatcataaggagaagat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttgacttagtttccttactatatcacagataaaaacaatgtcaagcaagaaatttcttatattatatggtaaaatgagatatagaactctaaaactgatttaaattcagactcggaatttcatcataaggagaagat Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 3 End: 101 .. Q S L K R V I D C I F V I D L L F N R I N Y P L I L Y L V R F S M ...................................... atttgacttagtttccttactatatcacagataaaaacaatgtcaagcaagaaatttcttatattatatggtaaaatgagatatagaactctaaaactgatttaaattcagactcggaatttcatcataaggagaagat 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================================================ atttgacttagtttccttactatatcacagataaaaacaatgtcaagcaagaaatttcttatattatatggtaaaatgagatatagaactctaaaactgatttaaattcagactcggaatttcatcataaggagaagat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2167:SSA_2168|SSA_2167:SSA_2168:ABC-type multidrug transporter, ATPase and permease components, putative:Glycerol-3-phosphate dehydrogenase [NAD(P)+], putative:<-->:2167462..2167600 139 atttgacttagtttccttactatatcacagataaaaacaatgtcaagcaagaaatttcttatattatatggtaaaatgagatatagaactctaaaactgatttaaattcagactcggaatttcatcataaggagaagat Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: NC_009009_SSA_2167_SSA_2168|ABC-type multidrug transporter, ATPase and permease components, putative:Glycerol-3-phosphate dehydrogenase [NAD(P)+], putative|NEGATIVE:POSITIVE|[2167462,2167600]|139 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 atttgacttagtttccttactatatcacagataaaaacaatgtcaagcaagaaatttcttatattatatggtaaaatgagatatagaactctaaaactgatttaaattcagactcggaatttcatcataaggagaagat atttgacttagtttccttactatatcacagataaaaacaatgtcaagcaagaaatttcttatattatatggtaaaatgagatatagaactctaaaactgatttaaattcagactcggaatttcatcataaggagaagat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUGACUUAGUUUCCUUACUAUAUCACAGAUAAAAACAAUGUCAAGCAAGAAAUUUCUUAUAUUAUAUGGUAAAAUGAGAUAUAGAACUCUAAAACUGAUUUAAAUUCAGACUCGGAAUUUCAUCAUAAGGAGAAGAU ...........((((((((..........((((.......))))......((((((((.((((((.(((......))).))))))...........((((.......))))....))))))))....)))))))).... (-23.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUUCUCCUUAUGAUGAAAUUCCGAGUCUGAAUUUAAAUCAGUUUUAGAGUUCUAUAUCUCAUUUUACCAUAUAAUAUAAGAAAUUUCUUGCUUGACAUUGUUUUUAUCUGUGAUAUAGUAAGGAAACUAAGUCAAAU .((((.....((((.((((((...(((...((((((.((......)).)))))).....))))))))).))))......))))..........(((((...((((((..((((...))))...))))))...))))).. (-19.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 741 50 1 141 92 NC_009009:SSA_2167|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2167371..2167601_NEGATIVE 216 60 12 170 115 NC_009009:SSA_1798|5end_hypothetical_protein_1780513..1780743_NEGATIVE 210 49 1 135 90 NC_009009:SSA_1139|5end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1166823..1167053_POSITIVE 207 52 11 148 96 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 203 126 96 40 7 NC_009009:SSA_0594|5end_Transcriptional_regulator,_AraC_family,_putative_585630..585860_POSITIVE 193 95 68 62 33 NC_009009:SSA_1877|5end_hypothetical_protein_1871659..1871889_POSITIVE 192 58 20 75 34 NC_009009:SSA_0457|5end_Fructokinase,_putative_460663..460893_POSITIVE 185 115 71 220 180 NC_009009:SSA_2073|5end_Undecaprenyl_pyrophosphate_synthetase,_putative_2076371..2076601_NEGATIVE 184 30 5 172 148 NC_009009:SSA_0514|5end_PduQ_protein,_putative_512877..513107_POSITIVE 182 52 16 160 126 NC_009009:SSA_0714|5end_hypothetical_protein_700042..700272_POSITIVE 181 83 41 176 131 NC_009009:SSA_1494|5end_Conserved_uncharacterized_protein_1500773..1501003_NEGATIVE 180 112 73 164 117 NC_009009:SSA_2282|5end_Phage_infection_protein,_putative_2285337..2285567_NEGATIVE 180 90 41 59 8 NC_009009:SSA_1773|5end_hypothetical_protein_1760092..1760322_NEGATIVE 179 47 4 141 84 NC_009009:SSA_2363|5end_Phosphoglycolate_phosphatase,_putative_2365632..2365862_POSITIVE 178 118 77 174 141 NC_009009:SSA_0173|5end_23S_rRNA_m1G745_methyltransferase,_putative_170535..170765_NEGATIVE 177 51 15 133 97 NC_009009:SSA_1243|5end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1268204..1268434_NEGATIVE 176 48 1 138 90 NC_009009:SSA_1040|5end_Sugar_ABC_transporter,_permease_protein,_putative_1055302..1055532_POSITIVE 174 99 52 189 149 NC_009009:SSA_0017|5end_Cell_shape_determining_protein_MreC,_putative_22811..23041_POSITIVE 172 28 7 186 163 NC_009009:SSA_1989|5end_ABC-type_transport_system_(uncharacterized),_ATPase_component,_putative_1985182..1985412_NEGATIVE 172 33 4 66 34 NC_009009:SSA_0969|5end_hypothetical_protein_977212..977442_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 99 54 119 79 NC_009009:SSA_1535|3end_hypothetical_protein_1542457..1542607_NEGATIVE 218 84 42 113 76 NC_009009:SSA_2143|3end_Conserved_uncharacterized_protein_2143590..2143740_NEGATIVE 210 49 1 116 71 NC_009009:SSA_1138|3end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1166884..1167034_POSITIVE 207 52 11 137 85 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 193 95 68 65 36 NC_009009:SSA_1876|3end_hypothetical_protein_1871742..1871892_POSITIVE 183 80 40 40 4 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 182 52 16 66 32 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 180 119 73 67 30 NC_009009:SSA_1300|3end_Maltose_ABC_transporter,_permease_protein,_putative_1318903..1319053_POSITIVE 179 47 4 89 32 NC_009009:SSA_2362|3end_L-serine_dehydratase_alpha_subunit_2365660..2365810_POSITIVE 179 126 107 145 125 NC_009009:SSA_1976|3end_Conserved_uncharacterized_protein_1971550..1971700_NEGATIVE 178 118 77 80 47 NC_009009:SSA_0174|3end_Tyrosyl-tRNA_synthetase_1,_putative_170629..170779_NEGATIVE 176 48 1 145 97 NC_009009:SSA_1039|3end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_1055389..1055539_POSITIVE 175 117 75 106 71 NC_009009:SSA_0851|3end_Cation_efflux_family_protein,_putative_837644..837794_NEGATIVE 171 115 76 97 50 NC_009009:SSA_2379|3end_Signal_transduction_protein_with_a_C-terminal_ATPase/histidine_kinase_domain,_putative_2383899..2384049_NEGATIVE 169 48 5 148 103 NC_009009:SSA_1235|3end_Dihydroorotase,_putative_1259959..1260109_NEGATIVE 168 59 23 75 40 NC_009009:SSA_0748|3end_Sugar:H+_symporter,_permease_of_the_major_facilitator_superfamily,_putative_730635..730785_POSITIVE 167 60 11 62 10 NC_009009:SSA_1889|3end_Conserved_uncharacterized_protein_1886283..1886433_NEGATIVE 166 50 2 129 81 NC_009009:SSA_1181|3end_Hydrolase,_alpha/beta_superfamily,_putative_1208592..1208742_NEGATIVE 166 118 91 149 125 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 163 31 5 142 107 NC_009009:SSA_2107|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing],_putative_2109295..2109445_NEGATIVE