Origin IGS: tactttaaagcatgccagtcccaacatttaccaagctcttggaaacttatgatagacagacttgatactatttagaaacttttgccattaatagagggagactaaagacattagatgcgattttttgtctttggtcctcctctttcttttttgaaaaataaacactttctcaaacacgattcttttctttcatttcaaaagtctctttcatattatttcacactttttcatatattaatctgttgtattttctgttttcctaatttattaaaacatttctatagctatggtttgcttatacctatatttatcaggcattcagtgaatactgacatttttgaaagaaaaagtcgtttttaggaacaaacgcttgcatttttcatgaaaacgttttataataaacttgccttaaagttttcttaaaacttaagtcaaacattttataaggagga .........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.........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 tcctccttataaaatgtttgacttaagttttaagaaaactttaaggcaagtttattataaaacgttttcatgaaaaatgcaagcgtttgttcctaaaaacgactttttctttcaaaaatgtcagtattcactgaatgcctgataaatataggtataagcaaaccatagctatagaaatgttttaataaattaggaaaacagaaaatacaacagattaatatatgaaaaagtgtgaaataatatgaaagagacttttgaaatgaaagaaaagaatcgtgtttgagaaagtgtttatttttcaaaaaagaaagaggaggaccaaagacaaaaaatcgcatctaatgtctttagtctccctctattaatggcaaaagtttctaaatagtatcaagtctgtctatcataagtttccaagagcttggtaaatgttgggactggcatgctttaaagta Mask Tandem Repeat Region ================================================ tactttaaagcatgccagtcccaacatttaccaagctcttggaaacttatgatagacagacttgatactatttagaaacttttgccattaatagagggagactaaagacattagatgcgattttttgtctttggtcctcctctttcttttttgaaaaataaacactttctcaaacacgattcttttctttcatttcaaaagtctctttcatattatttcacactttttcatatattaatctgttgtattttctgttttcctaatttattaaaacatttctatagctatggtttgcttatacctatatttatcaggcattcagtgaatactgacatttttgaaagaaaaagtcgtttttaggaacaaacgcttgcatttttcatgaaaacgttttataataaacttgccttaaagttttcttaaaacttaagtcaaacattttataaggagga Find is-nt database================================================ Query_seq: SSA_1917:SSA_1918|SSA_1917:SSA_1918:Alcohol dehydrogenase, propanol-preferring, putative:Phosphotransferase system, mannose-specific EIIAB, putative:->->:1907677..1908128 452 tactttaaagcatgccagtcccaacatttaccaagctcttggaaacttatgatagacagacttgatactatttagaaacttttgccattaatagagggagactaaagacattagatgcgattttttgtctttggtcctcctctttcttttttgaaaaataaacactttctcaaacacgattcttttctttcatttcaaaagtctctttcatattatttcacactttttcatatattaatctgttgtattttctgttttcctaatttattaaaacatttctatagctatggtttgcttatacctatatttatcaggcattcagtgaatactgacatttttgaaagaaaaagtcgtttttaggaacaaacgcttgcatttttcatgaaaacgttttataataaacttgccttaaagttttcttaaaacttaagtcaaacattttataaggagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1917:SSA_1918|SSA_1917:SSA_1918:Alcohol dehydrogenase, propanol-preferring, putative:Phosphotransferase system, mannose-specific EIIAB, putative:->->:1907677..1908128 452 tactttaaagcatgccagtcccaacatttaccaagctcttggaaacttatgatagacagacttgatactatttagaaacttttgccattaatagagggagactaaagacattagatgcgattttttgtctttggtcctcctctttcttttttgaaaaataaacactttctcaaacacgattcttttctttcatttcaaaagtctctttcatattatttcacactttttcatatattaatctgttgtattttctgttttcctaatttattaaaacatttctatagctatggtttgcttatacctatatttatcaggcattcagtgaatactgacatttttgaaagaaaaagtcgtttttaggaacaaacgcttgcatttttcatgaaaacgttttataataaacttgccttaaagttttcttaaaacttaagtcaaacattttataaggagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1917:SSA_1918|SSA_1917:SSA_1918:Alcohol dehydrogenase, propanol-preferring, putative:Phosphotransferase system, mannose-specific EIIAB, putative:->->:1907677..1908128 452 tactttaaagcatgccagtcccaacatttaccaagctcttggaaacttatgatagacagacttgatactatttagaaacttttgccattaatagagggagactaaagacattagatgcgattttttgtctttggtcctcctctttcttttttgaaaaataaacactttctcaaacacgattcttttctttcatttcaaaagtctctttcatattatttcacactttttcatatattaatctgttgtattttctgttttcctaatttattaaaacatttctatagctatggtttgcttatacctatatttatcaggcattcagtgaatactgacatttttgaaagaaaaagtcgtttttaggaacaaacgcttgcatttttcatgaaaacgttttataataaacttgccttaaagttttcttaaaacttaagtcaaacattttataaggagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tactttaaagcatgccagtcccaacatttaccaagctcttggaaacttatgatagacagacttgatactatttagaaacttttgccattaatagagggagactaaagacattagatgcgattttttgtctttggtcctcctctttcttttttgaaaaataaacactttctcaaacacgattcttttctttcatttcaaaagtctctttcatattatttcacactttttcatatattaatctgttgtattttctgttttcctaatttattaaaacatttctatagctatggtttgcttatacctatatttatcaggcattcagtgaatactgacatttttgaaagaaaaagtcgtttttaggaacaaacgcttgcatttttcatgaaaacgttttataataaacttgccttaaagttttcttaaaacttaagtcaaacattttataaggagga Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 115 End: 357 .................................................................................................................. M R F F V F G P P L S F L K N K H F L K H D S F L S F Q K S L S Y Y F T L F H I L I C C I F C F P N L L K H F Y S Y G L ............................................................................................... Protein_Len: 30 Strand: - Start: 91 End: 180 .......................................................................................... Y L S V L S M L H S K K D K T R R K R K Q F I F V K E F V M ................................................................................................................................................................................................................................................................................ tactttaaagcatgccagtcccaacatttaccaagctcttggaaacttatgatagacagacttgatactatttagaaacttttgccattaatagagggagactaaagacattagatgcgattttttgtctttggtcctcctctttcttttttgaaaaataaacactttctcaaacacgattcttttctttcatttcaaaagtctctttcatattatttcacactttttcatatattaatctgttgtattttctgttttcctaatttattaaaacatttctatagctatggtttgcttatacctatatttatcaggcattcagtgaatactgacatttttgaaagaaaaagtcgtttttaggaacaaacgcttgcatttttcatgaaaacgttttataataaacttgccttaaagttttcttaaaacttaagtcaaacattttataaggagga 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: 87 Start: 370 End: 399 .................................................................................................................................................................................................................................................................................................................................................................................CTTGCATTTTTCATGAAAACGTTTTATAAT..................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 395 End: 424 ..........................................................................................................................................................................................................................................................................................................................................................................................................TTTAAGAAAACTTTAAGGCAAGTTTATTAT............................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tactttaaagcatgccagtcccaacatttaccaagctcttggaaacttatgatagacagacttgatactatttagaaacttttgccattaatagagggagactaaagacattagatgcgattttttgtctttggtcctcctctttcttttttgaaaaataaacactttctcaaacacgattcttttctttcatttcaaaagtctctttcatattatttcacactttttcatatattaatctgttgtattttctgttttcctaatttattaaaacatttctatagctatggtttgcttatacctatatttatcaggcattcagtgaatactgacatttttgaaagaaaaagtcgtttttaggaacaaacgcttgcatttttcatgaaaacgttttataataaacttgccttaaagttttcttaaaacttaagtcaaacattttataaggagga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.7 Tail_Score: -5.04249 Start: 94 End: 142 Full_Region: CTTTTGCCATTAATA GAGGGAGACTAAAGACATTAGAT GCG ATTTTTTGTCTTTGGTCCTCCTC TTTCTTTTTTGAAAA .............................................................................................GAGGGAGACTAAAGACATTAGATGCGATTTTTTGTCTTTGGTCCTCCTC...................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1917:SSA_1918|SSA_1917:SSA_1918:Alcohol dehydrogenase, propanol-preferring, putative:Phosphotransferase system, mannose-specific EIIAB, putative:->->:1907677..1908128 452 tactttaaagcatgccagtcccaacatttaccaagctcttggaaacttatgatagacagacttgatactatttagaaacttttgccattaatagagggagactaaagacattagatgcgattttttgtctttggtcctcctctttcttttttgaaaaataaacactttctcaaacacgattcttttctttcatttcaaaagtctctttcatattatttcacactttttcatatattaatctgttgtattttctgttttcctaatttattaaaacatttctatagctatggtttgcttatacctatatttatcaggcattcagtgaatactgacatttttgaaagaaaaagtcgtttttaggaacaaacgcttgcatttttcatgaaaacgttttataataaacttgccttaaagttttcttaaaacttaagtcaaacattttataaggagga Intra-Species Hit: Count: 1 Min: 1 Max: 452 Len: 452 Subject: NC_009009_SSA_1917_SSA_1918|Alcohol dehydrogenase, propanol-preferring, putative:Phosphotransferase system, mannose-specific EIIAB, putative|POSITIVE:POSITIVE|[1907677,1908128]|452 HSP 1 e-value: 0.0 bit: 896.0 Len: 452 Query Start:1 Query End:452 Subject Strand: POSITIVE Subject Start: 1 Subject End: 452 tactttaaagcatgccagtcccaacatttaccaagctcttggaaacttatgatagacagacttgatactatttagaaacttttgccattaatagagggagactaaagacattagatgcgattttttgtctttggtcctcctctttcttttttgaaaaataaacactttctcaaacacgattcttttctttcatttcaaaagtctctttcatattatttcacactttttcatatattaatctgttgtattttctgttttcctaatttattaaaacatttctatagctatggtttgcttatacctatatttatcaggcattcagtgaatactgacatttttgaaagaaaaagtcgtttttaggaacaaacgcttgcatttttcatgaaaacgttttataataaacttgccttaaagttttcttaaaacttaagtcaaacattttataaggagga tactttaaagcatgccagtcccaacatttaccaagctcttggaaacttatgatagacagacttgatactatttagaaacttttgccattaatagagggagactaaagacattagatgcgattttttgtctttggtcctcctctttcttttttgaaaaataaacactttctcaaacacgattcttttctttcatttcaaaagtctctttcatattatttcacactttttcatatattaatctgttgtattttctgttttcctaatttattaaaacatttctatagctatggtttgcttatacctatatttatcaggcattcagtgaatactgacatttttgaaagaaaaagtcgtttttaggaacaaacgcttgcatttttcatgaaaacgttttataataaacttgccttaaagttttcttaaaacttaagtcaaacattttataaggagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUUUAAAGCAUGCCAGUCCCAACAUUUACCAAGCUCUUGGAAACUUAUGAUAGACAGACUUGAUACUAUUUAGAAACUUUUGCCAUUAAUAGAGGGAGACUAAAGACAUUAGAUGCGAUUUUUUGUCUUUGGUCCUCCUCUUUCUUUUUUGAAAAAUAAACACUUUCUCAAACACGAUUCUUUUCUUUCAUUUCAAAAGUCUCUUUCAUAUUAUUUCACACUUUUUCAUAUAUUAAUCUGUUGUAUUUUCUGUUUUCCUAAUUUAUUAAAACAUUUCUAUAGCUAUGGUUUGCUUAUACCUAUAUUUAUCAGGCAUUCAGUGAAUACUGACAUUUUUGAAAGAAAAAGUCGUUUUUAGGAACAAACGCUUGCAUUUUUCAUGAAAACGUUUUAUAAUAAACUUGCCUUAAAGUUUUCUUAAAACUUAAGUCAAACAUUUUAUAAGGAGGA ....................((........((((....))))...(((((((......((((((......((((((((....(((.......(((((..(((((((((((..((((...))))..)))))))))))..))))).......................(((..(((.((((((.((((((((((....(((.(((...(((((..............................((((((.....((((((...........))))))....))))))....(..((((((((........))).)))))..).)))))....))).))).)))))))))))))))).)))..))).........)))..)))).))))...((((((....((((((......))))))...)))))).)))))).......)))))))..)). (-87.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUCCUUAUAAAAUGUUUGACUUAAGUUUUAAGAAAACUUUAAGGCAAGUUUAUUAUAAAACGUUUUCAUGAAAAAUGCAAGCGUUUGUUCCUAAAAACGACUUUUUCUUUCAAAAAUGUCAGUAUUCACUGAAUGCCUGAUAAAUAUAGGUAUAAGCAAACCAUAGCUAUAGAAAUGUUUUAAUAAAUUAGGAAAACAGAAAAUACAACAGAUUAAUAUAUGAAAAAGUGUGAAAUAAUAUGAAAGAGACUUUUGAAAUGAAAGAAAAGAAUCGUGUUUGAGAAAGUGUUUAUUUUUCAAAAAAGAAAGAGGAGGACCAAAGACAAAAAAUCGCAUCUAAUGUCUUUAGUCUCCCUCUAUUAAUGGCAAAAGUUUCUAAAUAGUAUCAAGUCUGUCUAUCAUAAGUUUCCAAGAGCUUGGUAAAUGUUGGGACUGGCAUGCUUUAAAGUA .....................((((.....))))...(((((((((((.(((.......((((((((.(((.....))).))))))))..((((((..((.((((((((.........(((..(((((..(((....((((((.......(((........)))......(((....)))........))))))....)))..))))).)))...........)))))))))).......(((((.(((((((((((..((............((...(((((((((.......)))))))))...)).(((((..(((.(((((((...............))))))).)))..)))))....))..)))))))))))..((((........))))...))))).((((((((....)))).)))).))))))..))).))))))))))). (-99.31) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 154 113 114 74 NC_009009:SSA_2166|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165642..2165872_NEGATIVE 331 43 12 128 95 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 302 42 10 177 145 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 291 48 5 220 173 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 277 42 10 158 123 NC_009009:SSA_1783|5end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1769106..1769336_NEGATIVE 272 38 8 231 199 NC_009009:SSA_0995|5end_Antibiotic-resistance_protein,_alpha/beta_superfamily_hydrolase,_putative_995716..995946_POSITIVE 269 150 106 185 137 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 269 59 13 128 75 NC_009009:SSA_0241|5end_Ribosomal_protein_L11_methyltransferase,_putative_234021..234251_POSITIVE 268 105 61 75 27 NC_009009:SSA_0053|5end_Beta-galactosidase,_putative_56748..56978_POSITIVE 265 60 14 65 17 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 261 140 91 104 39 NC_009009:SSA_0092|5end_V-type_sodium_ATPase,_subunit_B,_putative_92895..93125_POSITIVE 258 149 116 112 82 NC_009009:SSA_2110|5end_30S_ribosomal_protein_S7,_putative_2115579..2115809_NEGATIVE 258 108 61 147 99 NC_009009:SSA_1511|5end_Glycosyltransferase,_putative_1516697..1516927_NEGATIVE 255 140 109 64 31 NC_009009:SSA_2082|5end_Carbohydrate_kinase,_FGGY_family,_putative_2086874..2087104_NEGATIVE 255 55 11 151 116 NC_009009:SSA_1040|5end_Sugar_ABC_transporter,_permease_protein,_putative_1055302..1055532_POSITIVE 253 44 3 70 32 NC_009009:SSA_0987|5end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_988994..989224_POSITIVE 253 384 352 67 26 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 252 140 91 195 146 NC_009009:SSA_2155|5end_hypothetical_protein_2156102..2156332_NEGATIVE 252 150 114 109 64 NC_009009:SSA_0135|5end_Multiple_antibiotic_resistance_operon_transcriptional_repressor_(MarR),_putative_130574..130804_POSITIVE 251 85 41 70 22 NC_009009:SSA_1708|5end_hypothetical_protein_1698319..1698549_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 154 113 112 72 NC_009009:SSA_2167|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165644..2165794_NEGATIVE 331 43 12 126 93 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE 295 60 11 132 86 NC_009009:SSA_1435|3end_hypothetical_protein_1441751..1441901_NEGATIVE 280 150 103 92 33 NC_009009:SSA_0080|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_84194..84344_POSITIVE 265 60 14 68 20 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 262 60 14 60 6 NC_009009:SSA_0186|3end_Competence_protein_ComYC,_putative_190458..190608_POSITIVE 261 140 91 117 52 NC_009009:SSA_0091|3end_V-type_sodium_ATPase,_subunit_A,_putative_92988..93138_POSITIVE 258 149 116 92 62 NC_009009:SSA_2111|3end_30S_ribosomal_protein_S12,_putative_2115599..2115749_NEGATIVE 258 108 61 143 95 NC_009009:SSA_1512|3end_hypothetical_protein_1516701..1516851_NEGATIVE 257 139 91 147 99 NC_009009:SSA_1856|3end_hypothetical_protein_1852077..1852227_NEGATIVE 253 44 3 77 39 NC_009009:SSA_0986|3end_Choline_transporter,_putative_989081..989231_POSITIVE 252 140 91 81 32 NC_009009:SSA_2156|3end_Conserved_uncharacterized_protein_2156216..2156366_NEGATIVE 251 85 41 76 28 NC_009009:SSA_1709|3end_hypothetical_protein_1698313..1698463_NEGATIVE 250 220 177 146 102 NC_009009:SSA_2378|3end_Two-component_system_transcriptional_regulator,_LytR/AlgR_family,_putative_2383129..2383279_NEGATIVE 248 170 122 149 95 NC_009009:SSA_0776|3end_Glucose-1-phosphate_adenylyltransferase,_putative_759520..759670_POSITIVE 245 115 81 119 80 NC_009009:SSA_1665|3end_hypothetical_protein_1665222..1665372_NEGATIVE 244 144 111 92 63 NC_009009:SSA_0123|3end_50S_ribosomal_protein_L18P,_putative_116484..116634_POSITIVE 240 59 13 42 4 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 239 138 94 146 100 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 238 317 276 142 95 NC_009009:SSA_2222|3end_Tyrosine-protein_kinase_Wze,_putative_2223299..2223449_NEGATIVE