Origin IGS: gtatctcctccaaaagtatacactgtctacttatctatctttagtatacactgtatactttttattgtcaaataatttgatgctttattctagtctaagatgtggcagaatttgctttcggtaagataaaatgttaaaataatatccaaatgatagcgctttctttttttggggtggattgctcgttgtaaagaaacgctgagaaacggaggacacct .........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 aggtgtcctccgtttctcagcgtttctttacaacgagcaatccaccccaaaaaaagaaagcgctatcatttggatattattttaacattttatcttaccgaaagcaaattctgccacatcttagactagaataaagcatcaaattatttgacaataaaaagtatacagtgtatactaaagatagataagtagacagtgtatacttttggaggagatac Mask Tandem Repeat Region ================================================ gtatctcctccaaaagtatacactgtctacttatctatctttagtatacactgtatactttttattgtcaaataatttgatgctttattctagtctaagatgtggcagaatttgctttcggtaagataaaatgttaaaataatatccaaatgatagcgctttctttttttggggtggattgctcgttgtaaagaaacgctgagaaacggaggacacct Find is-nt database================================================ Query_seq: SSA_0048:SSA_0049|SSA_0048:SSA_0049:Transcriptional regulator, TetR/AcrR family, putative:Dihydroxyacetone kinase (Dak1), putative:<-->:53534..53751 218 gtatctcctccaaaagtatacactgtctacttatctatctttagtatacactgtatactttttattgtcaaataatttgatgctttattctagtctaagatgtggcagaatttgctttcggtaagataaaatgttaaaataatatccaaatgatagcgctttctttttttggggtggattgctcgttgtaaagaaacgctgagaaacggaggacacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0048:SSA_0049|SSA_0048:SSA_0049:Transcriptional regulator, TetR/AcrR family, putative:Dihydroxyacetone kinase (Dak1), putative:<-->:53534..53751 218 gtatctcctccaaaagtatacactgtctacttatctatctttagtatacactgtatactttttattgtcaaataatttgatgctttattctagtctaagatgtggcagaatttgctttcggtaagataaaatgttaaaataatatccaaatgatagcgctttctttttttggggtggattgctcgttgtaaagaaacgctgagaaacggaggacacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0048:SSA_0049|SSA_0048:SSA_0049:Transcriptional regulator, TetR/AcrR family, putative:Dihydroxyacetone kinase (Dak1), putative:<-->:53534..53751 218 gtatctcctccaaaagtatacactgtctacttatctatctttagtatacactgtatactttttattgtcaaataatttgatgctttattctagtctaagatgtggcagaatttgctttcggtaagataaaatgttaaaataatatccaaatgatagcgctttctttttttggggtggattgctcgttgtaaagaaacgctgagaaacggaggacacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtatctcctccaaaagtatacactgtctacttatctatctttagtatacactgtatactttttattgtcaaataatttgatgctttattctagtctaagatgtggcagaatttgctttcggtaagataaaatgttaaaataatatccaaatgatagcgctttctttttttggggtggattgctcgttgtaaagaaacgctgagaaacggaggacacct Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 23 End: 121 ...................... M S T Y L S L V Y T V Y F L L S N N L M L Y S S L R C G R I C F R ................................................................................................. Protein_Len: 43 Strand: - Start: 88 End: 216 ....................................................................................... E L R L H P L I Q K R Y S L I N F Y Y G F S L A K K K Q P P N S T T F F R Q S V S S M .. gtatctcctccaaaagtatacactgtctacttatctatctttagtatacactgtatactttttattgtcaaataatttgatgctttattctagtctaagatgtggcagaatttgctttcggtaagataaaatgttaaaataatatccaaatgatagcgctttctttttttggggtggattgctcgttgtaaagaaacgctgagaaacggaggacacct Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 89 Start: 43 End: 72 ..........................................TTTGACAATAAAAAGTATACAGTGTATACT.................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtatctcctccaaaagtatacactgtctacttatctatctttagtatacactgtatactttttattgtcaaataatttgatgctttattctagtctaagatgtggcagaatttgctttcggtaagataaaatgttaaaataatatccaaatgatagcgctttctttttttggggtggattgctcgttgtaaagaaacgctgagaaacggaggacacct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0048:SSA_0049|SSA_0048:SSA_0049:Transcriptional regulator, TetR/AcrR family, putative:Dihydroxyacetone kinase (Dak1), putative:<-->:53534..53751 218 gtatctcctccaaaagtatacactgtctacttatctatctttagtatacactgtatactttttattgtcaaataatttgatgctttattctagtctaagatgtggcagaatttgctttcggtaagataaaatgttaaaataatatccaaatgatagcgctttctttttttggggtggattgctcgttgtaaagaaacgctgagaaacggaggacacct Intra-Species Hit: Count: 1 Min: 1 Max: 218 Len: 218 Subject: NC_009009_SSA_0048_SSA_0049|Transcriptional regulator, TetR/AcrR family, putative:Dihydroxyacetone kinase (Dak1), putative|NEGATIVE:POSITIVE|[53534,53751]|218 HSP 1 e-value: 1.0E-108 bit: 391.0 Len: 218 Query Start:1 Query End:218 Subject Strand: POSITIVE Subject Start: 1 Subject End: 218 gtatctcctccaaaagtatacactgtctacttatctatctttagtatacactgtatactttttattgtcaaataatttgatgctttattctagtctaagatgtggcagaatttgctttcggtaagataaaatgttaaaataatatccaaatgatagcgctttcnnnnnnnggggtggattgctcgttgtaaagaaacgctgagaaacggaggacacct gtatctcctccaaaagtatacactgtctacttatctatctttagtatacactgtatactttttattgtcaaataatttgatgctttattctagtctaagatgtggcagaatttgctttcggtaagataaaatgttaaaataatatccaaatgatagcgctttctttttttggggtggattgctcgttgtaaagaaacgctgagaaacggaggacacct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUCUCCUCCAAAAGUAUACACUGUCUACUUAUCUAUCUUUAGUAUACACUGUAUACUUUUUAUUGUCAAAUAAUUUGAUGCUUUAUUCUAGUCUAAGAUGUGGCAGAAUUUGCUUUCGGUAAGAUAAAAUGUUAAAAUAAUAUCCAAAUGAUAGCGCUUUCUUUUUUUGGGGUGGAUUGCUCGUUGUAAAGAAACGCUGAGAAACGGAGGACACCU .....((((((.((((((((((.(((.((((...........)))).))).))))))))))...(((((.......((((.((...(((((.(((........))))))))..))..))))...)))))........................(((((.(((((((.....((((.....)))).....))))))))))))......))))))..... (-50.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUGUCCUCCGUUUCUCAGCGUUUCUUUACAACGAGCAAUCCACCCCAAAAAAAGAAAGCGCUAUCAUUUGGAUAUUAUUUUAACAUUUUAUCUUACCGAAAGCAAAUUCUGCCACAUCUUAGACUAGAAUAAAGCAUCAAAUUAUUUGACAAUAAAAAGUAUACAGUGUAUACUAAAGAUAGAUAAGUAGACAGUGUAUACUUUUGGAGGAGAUAC ..((.((((((.......(((((((((((.....((....))..........)))).))))))).....(..((((..........(((((((((........(((.....)))........))).))))))............))))..).....(((((((((((.(((.((((...........)))).))).))))))))))))))))).)).. (-44.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 816 130 81 221 172 NC_009009:SSA_0048|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_53443..53673_NEGATIVE 340 210 161 143 98 NC_009009:SSA_1581|5end_Metal-binding_ABC_transporter_(probably_hemin),_putative_1583662..1583892_POSITIVE 315 193 157 165 125 NC_009009:SSA_2217|5end_Cps9H,_putative_2219045..2219275_NEGATIVE 315 199 156 143 95 NC_009009:SSA_1061|5end_50S_ribosomal_protein_L21,_putative_1077592..1077822_POSITIVE 307 199 151 68 19 NC_009009:SSA_1058|5end_Thiamine_biosynthesis_protein,_putative_1074917..1075147_POSITIVE 285 210 163 72 25 NC_009009:SSA_2356|5end_Replicative_DNA_helicase,_putative_2357958..2358188_NEGATIVE 284 190 145 216 167 NC_009009:SSA_1482|5end_Pullulanase,_putative_1489246..1489476_NEGATIVE 278 125 83 179 132 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 272 116 75 80 34 NC_009009:SSA_0652|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase,_putative_635036..635266_POSITIVE 264 209 163 199 148 NC_009009:SSA_0779|5end_Glycogen_phosphorylase,_putative_762209..762439_POSITIVE 261 208 161 141 100 NC_009009:SSA_0467|5end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_470588..470818_POSITIVE 261 209 169 226 192 NC_009009:SSA_0271|5end_Glycosylhydrolase,_family_35,_putative_264235..264465_POSITIVE 260 177 150 57 30 NC_009009:SSA_0851|5end_Cation_efflux_family_protein,_putative_838900..839130_NEGATIVE 259 187 145 47 2 NC_009009:SSA_1749|5end_Pyruvate_formate-lyase-activating_enzyme,_putative_1735426..1735656_NEGATIVE 259 186 145 230 182 NC_009009:SSA_0032|5end_Phosphoribosylformylglycinamidine_cyclo-ligase,_putative_37938..38168_POSITIVE 257 129 88 171 121 NC_009009:SSA_2281|5end_hypothetical_protein_2282370..2282600_NEGATIVE 256 183 143 140 85 NC_009009:SSA_0159|5end_hypothetical_protein_155000..155230_POSITIVE 255 186 152 219 175 NC_009009:SSA_2047|5end_hypothetical_protein_2049953..2050183_NEGATIVE 255 182 146 207 171 NC_009009:SSA_1955|5end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1952602..1952832_NEGATIVE 253 109 65 217 177 NC_009009:SSA_0643|5end_hypothetical_protein_630194..630424_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 210 161 87 42 NC_009009:SSA_1579|3end_ABC-type_Fe3+-siderophore_transport_system,_ATPase_component,_putative_1583686..1583836_POSITIVE 315 193 157 87 47 NC_009009:SSA_2218|3end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219123..2219273_NEGATIVE 307 199 151 64 15 NC_009009:SSA_1057|3end_Aminotransferase,_class-V,_putative_1074993..1075143_POSITIVE 268 199 159 132 90 NC_009009:SSA_1943|3end_Aspartate_kinase,_putative_1930159..1930309_POSITIVE 261 208 161 141 100 NC_009009:SSA_0466|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_470668..470818_POSITIVE 256 183 143 134 79 NC_009009:SSA_0158|3end_hypothetical_protein_155074..155224_POSITIVE 255 185 141 71 30 NC_009009:SSA_0067|3end_Acyltransferase_(yrhL-like_subfamily_of_SGNH-hydrolases),_putative_69890..70040_POSITIVE 252 130 92 144 107 NC_009009:SSA_2269|3end_hypothetical_protein_2269392..2269542_NEGATIVE 248 210 169 150 115 NC_009009:SSA_1569|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1572630..1572780_POSITIVE 247 114 78 132 95 NC_009009:SSA_0091|3end_V-type_sodium_ATPase,_subunit_A,_putative_92988..93138_POSITIVE 246 210 163 45 1 NC_009009:SSA_2357|3end_50S_ribosomal_protein_L9,_putative_2357985..2358135_NEGATIVE 244 210 165 57 2 NC_009009:SSA_1234|3end_5'-nucleotidase,_putative_1257636..1257786_NEGATIVE 242 197 151 111 63 NC_009009:SSA_0288|3end_hypothetical_protein_280740..280890_NEGATIVE 241 206 163 88 31 NC_009009:SSA_0727|3end_Metal-dependent_membrane_protease,_putative_713639..713789_POSITIVE 240 209 179 41 2 NC_009009:SSA_0490|3end_Cobalamin_5'-phosphate_synthase,_putative_491044..491194_POSITIVE 239 187 153 132 93 NC_009009:SSA_1905|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1899276..1899426_NEGATIVE 239 209 161 85 42 NC_009009:SSA_0351|3end_Signal_peptidase_I,_putative_344278..344428_NEGATIVE 239 189 157 147 118 NC_009009:SSA_0042|3end_Amino_acid_recemase,_putative_48671..48821_POSITIVE 238 130 97 37 3 NC_009009:SSA_2334|3end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2336457..2336607_NEGATIVE 237 199 157 133 95 NC_009009:SSA_1049|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064971..1065121_POSITIVE