Origin IGS: tctttcctcctcaaacaacagaaaaagtctccttattacaaggagacttcagaaaaatctagtcaggcaagctaaaacaagacgcacttgcttacactccacccatctttttacttgctccttgtctatctctctggatagaattaaaggattatttaattttttatactatatcacaaattcaaaactatttcaagaaaaaaattgtattttttctgtttgactaaataaggattagtgaaatctgtttttcatctacaagtacaagtct .........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 agacttgtacttgtagatgaaaaacagatttcactaatccttatttagtcaaacagaaaaaatacaatttttttcttgaaatagttttgaatttgtgatatagtataaaaaattaaataatcctttaattctatccagagagatagacaaggagcaagtaaaaagatgggtggagtgtaagcaagtgcgtcttgttttagcttgcctgactagatttttctgaagtctccttgtaataaggagactttttctgttgtttgaggaggaaaga Mask Tandem Repeat Region ================================================ tctttcctcctcaaacaacagaaaaagtctccttattacaaggagacttcagaaaaatctagtcaggcaagctaaaacaagacgcacttgcttacactccacccatctttttacttgctccttgtctatctctctggatagaattaaaggattatttaattttttatactatatcacaaattcaaaactatttcaagaaaaaaattgtattttttctgtttgactaaataaggattagtgaaatctgtttttcatctacaagtacaagtct Find is-nt database================================================ Query_seq: SSA_1345:SSA_1346|SSA_1345:SSA_1346:Bifunctional pyrimidine operon transcriptional attenuation protein/uracil phosphoribosyltransferase, putative:hypothetical protein:<-<-:1363970..1364240 271 tctttcctcctcaaacaacagaaaaagtctccttattacaaggagacttcagaaaaatctagtcaggcaagctaaaacaagacgcacttgcttacactccacccatctttttacttgctccttgtctatctctctggatagaattaaaggattatttaattttttatactatatcacaaattcaaaactatttcaagaaaaaaattgtattttttctgtttgactaaataaggattagtgaaatctgtttttcatctacaagtacaagtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1345:SSA_1346|SSA_1345:SSA_1346:Bifunctional pyrimidine operon transcriptional attenuation protein/uracil phosphoribosyltransferase, putative:hypothetical protein:<-<-:1363970..1364240 271 tctttcctcctcaaacaacagaaaaagtctccttattacaaggagacttcagaaaaatctagtcaggcaagctaaaacaagacgcacttgcttacactccacccatctttttacttgctccttgtctatctctctggatagaattaaaggattatttaattttttatactatatcacaaattcaaaactatttcaagaaaaaaattgtattttttctgtttgactaaataaggattagtgaaatctgtttttcatctacaagtacaagtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1345:SSA_1346|SSA_1345:SSA_1346:Bifunctional pyrimidine operon transcriptional attenuation protein/uracil phosphoribosyltransferase, putative:hypothetical protein:<-<-:1363970..1364240 271 tctttcctcctcaaacaacagaaaaagtctccttattacaaggagacttcagaaaaatctagtcaggcaagctaaaacaagacgcacttgcttacactccacccatctttttacttgctccttgtctatctctctggatagaattaaaggattatttaattttttatactatatcacaaattcaaaactatttcaagaaaaaaattgtattttttctgtttgactaaataaggattagtgaaatctgtttttcatctacaagtacaagtct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctttcctcctcaaacaacagaaaaagtctccttattacaaggagacttcagaaaaatctagtcaggcaagctaaaacaagacgcacttgcttacactccacccatctttttacttgctccttgtctatctctctggatagaattaaaggattatttaattttttatactatatcacaaattcaaaactatttcaagaaaaaaattgtattttttctgtttgactaaataaggattagtgaaatctgtttttcatctacaagtacaagtct Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 35 End: 220 .................................. M T R R L Q K N L V R Q A K T R R T C L H S T H L F T C S L S I S L D R I K G L F N F L Y Y I T N S K L F Q E K N C I F ................................................... Protein_Len: 40 Strand: + Start: 105 End: 224 ........................................................................................................ M F L L A P C L S L W I E L K D Y L I F Y T I S Q I Q N Y F K K K I V F F L F D ............................................... Protein_Len: 31 Strand: - Start: 52 End: 144 ................................................... F F R T L C A L V L R V Q K C E V W R K V Q E K D I E R S L M ............................................................................................................................... tctttcctcctcaaacaacagaaaaagtctccttattacaaggagacttcagaaaaatctagtcaggcaagctaaaacaagacgcacttgcttacactccacccatctttttacttgctccttgtctatctctctggatagaattaaaggattatttaattttttatactatatcacaaattcaaaactatttcaagaaaaaaattgtattttttctgtttgactaaataaggattagtgaaatctgtttttcatctacaagtacaagtct 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: 168 End: 197 .......................................................................................................................................................................CTTGAAATAGTTTTGAATTTGTGATATAGT.......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctttcctcctcaaacaacagaaaaagtctccttattacaaggagacttcagaaaaatctagtcaggcaagctaaaacaagacgcacttgcttacactccacccatctttttacttgctccttgtctatctctctggatagaattaaaggattatttaattttttatactatatcacaaattcaaaactatttcaagaaaaaaattgtattttttctgtttgactaaataaggattagtgaaatctgtttttcatctacaagtacaagtct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.5 Tail_Score: -5.23765 Start: 27 End: 47 Full_Region: ctagatttttctgaa gtctccttg taa taaggagac tttttctgttgtttg ..........................gtctccttgtaataaggagac................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 57 HP_score: -3.4 Tail_Score: -4.28774 Start: 78 End: 90 Full_Region: tgggtggagtgtaag caag tgcgt cttg ttttagcttgcctga .............................................................................caagtgcgtcttg..................................................................................................................................................................................... TransTerm Strand: + Conf: 50 HP_score: -3.7 Tail_Score: -3.41569 Start: 197 End: 216 Full_Region: TCAAAACTATTTCAA GAAAAAA ATTGTA TTTTTTC TGTTTGACTAAATAA ....................................................................................................................................................................................................GAAAAAAATTGTATTTTTTC....................................................... Find igs database================================================ Query_seq: SSA_1345:SSA_1346|SSA_1345:SSA_1346:Bifunctional pyrimidine operon transcriptional attenuation protein/uracil phosphoribosyltransferase, putative:hypothetical protein:<-<-:1363970..1364240 271 tctttcctcctcaaacaacagaaaaagtctccttattacaaggagacttcagaaaaatctagtcaggcaagctaaaacaagacgcacttgcttacactccacccatctttttacttgctccttgtctatctctctggatagaattaaaggattatttaattttttatactatatcacaaattcaaaactatttcaagaaaaaaattgtattttttctgtttgactaaataaggattagtgaaatctgtttttcatctacaagtacaagtct Intra-Species Hit: Count: 1 Min: 1 Max: 271 Len: 271 Subject: NC_009009_SSA_1345_SSA_1346|Bifunctional pyrimidine operon transcriptional attenuation protein/uracil phosphoribosyltransferase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1363970,1364240]|271 HSP 1 e-value: 1.0E-139 bit: 496.0 Len: 271 Query Start:1 Query End:271 Subject Strand: POSITIVE Subject Start: 1 Subject End: 271 tctttcctcctcaaacaacagaaaaagtctccttattacaaggagacttcagaaaaatctagtcaggcaagctaaaacaagacgcacttgcttacactccacccatctttttacttgctccttgtctatctctctggatagaattaaaggattatttaattttttatactatatcacaaattcaaaactatttcaagnnnnnnnttgtattttttctgtttgactaaataaggattagtgaaatctgtttttcatctacaagtacaagtct tctttcctcctcaaacaacagaaaaagtctccttattacaaggagacttcagaaaaatctagtcaggcaagctaaaacaagacgcacttgcttacactccacccatctttttacttgctccttgtctatctctctggatagaattaaaggattatttaattttttatactatatcacaaattcaaaactatttcaagaaaaaaattgtattttttctgtttgactaaataaggattagtgaaatctgtttttcatctacaagtacaagtct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUCCUCCUCAAACAACAGAAAAAGUCUCCUUAUUACAAGGAGACUUCAGAAAAAUCUAGUCAGGCAAGCUAAAACAAGACGCACUUGCUUACACUCCACCCAUCUUUUUACUUGCUCCUUGUCUAUCUCUCUGGAUAGAAUUAAAGGAUUAUUUAAUUUUUUAUACUAUAUCACAAAUUCAAAACUAUUUCAAGAAAAAAAUUGUAUUUUUUCUGUUUGACUAAAUAAGGAUUAGUGAAAUCUGUUUUUCAUCUACAAGUACAAGUCU ................((((((..((((((((((.....))))))))))..(((((((...((.(((((((...............))))))))).......................(((((.(((((((....)))))))....))))).......)))))))........((((.(((((.........(((((((((((......))))))))...)))........))))).))))..))))))...................... (-50.09) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGACUUGUACUUGUAGAUGAAAAACAGAUUUCACUAAUCCUUAUUUAGUCAAACAGAAAAAAUACAAUUUUUUUCUUGAAAUAGUUUUGAAUUUGUGAUAUAGUAUAAAAAAUUAAAUAAUCCUUUAAUUCUAUCCAGAGAGAUAGACAAGGAGCAAGUAAAAAGAUGGGUGGAGUGUAAGCAAGUGCGUCUUGUUUUAGCUUGCCUGACUAGAUUUUUCUGAAGUCUCCUUGUAAUAAGGAGACUUUUUCUGUUGUUUGAGGAGGAAAGA ....(((((((..(((((..(((((..(((((.((((.......))))......((((((((......)))))))).))))).)))))..)))))..)....))))))............((((((...((((((......))))))((((.((((.......((.((((..(.((..(((((((.....)))))))..)))..)))).))..........((((((((((((...))))))))))))...)))).)))).)))))).... (-62.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 949 110 61 201 152 NC_009009:SSA_1345|5end_Bifunctional_pyrimidine_operon_transcriptional_attenuation_protein/uracil_phosphoribosyltransferase,_putative_1363879..1364109_NEGATIVE 358 104 65 82 52 NC_009009:SSA_0298|5end_Malate_permease,_putative_291336..291566_POSITIVE 297 120 71 127 82 NC_009009:SSA_0894|5end_ATP-binding_cassette_protein,_putative_885779..886009_POSITIVE 288 108 64 202 158 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 287 127 81 99 61 NC_009009:SSA_2176|5end_hypothetical_protein_2175159..2175389_NEGATIVE 285 100 59 88 36 NC_009009:SSA_1392|5end_hypothetical_protein_1408423..1408653_NEGATIVE 281 86 41 138 97 NC_009009:SSA_1014|5end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1017846..1018076_POSITIVE 281 137 91 121 75 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 280 116 71 101 45 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 279 118 71 59 14 NC_009009:SSA_0781|5end_Mannose-6-phosphate_isomerase,_putative_765373..765603_POSITIVE 276 127 85 101 53 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 276 74 31 130 82 NC_009009:SSA_0511|5end_Propanediol_utilization_kinase,_putative_509610..509840_POSITIVE 275 129 81 110 49 NC_009009:SSA_0594|5end_Transcriptional_regulator,_AraC_family,_putative_585630..585860_POSITIVE 274 130 84 67 19 NC_009009:SSA_0827|5end_Conserved_uncharacterized_cytosolic_protein,_putative_806033..806263_POSITIVE 273 105 65 64 7 NC_009009:SSA_1914|5end_hypothetical_protein_1905195..1905425_NEGATIVE 269 126 82 128 86 NC_009009:SSA_1969|5end_Acetolactate_synthase_small_subunit,_putative_1965222..1965452_NEGATIVE 268 92 51 68 34 NC_009009:SSA_2056|5end_Cinnamoyl_ester_hydrolase,_putative_2058587..2058817_POSITIVE 268 108 65 152 111 NC_009009:SSA_1668|5end_NrdI_protein,_putative_1668091..1668321_NEGATIVE 267 106 62 66 14 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 266 130 82 213 156 NC_009009:SSA_1788|5end_Integral_membrane_protein,_possible_receptor,_putative_1772339..1772569_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 104 65 77 47 NC_009009:SSA_0297|3end_Malolactic_enzyme,_putative_291411..291561_POSITIVE 297 120 71 140 95 NC_009009:SSA_0893|3end_ATP-binding_cassette_transporter-like_protein,_putative_885872..886022_POSITIVE 288 108 64 104 60 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 285 100 59 97 45 NC_009009:SSA_1393|3end_hypothetical_protein_1408414..1408564_NEGATIVE 281 86 41 145 104 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 281 137 91 124 78 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 280 127 83 57 5 NC_009009:SSA_1532|3end_Membrane-fusion_protein_/_periplasmic_component_of_efflux_system,_putative_1539460..1539610_NEGATIVE 280 116 71 91 35 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 278 120 80 151 101 NC_009009:SSA_2207|3end_hypothetical_protein_2206868..2207018_NEGATIVE 276 127 85 85 37 NC_009009:SSA_2102|3end_Conserved_uncharacterized_protein_2105409..2105559_NEGATIVE 276 74 31 137 89 NC_009009:SSA_0510|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_509697..509847_POSITIVE 271 130 85 147 97 NC_009009:SSA_2321|3end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326050..2326200_NEGATIVE 269 126 82 135 93 NC_009009:SSA_1970|3end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1965215..1965365_NEGATIVE 268 108 65 148 107 NC_009009:SSA_1669|3end_hypothetical_protein_1668095..1668245_NEGATIVE 262 140 91 145 104 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 261 157 116 139 97 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 259 150 106 138 86 NC_009009:SSA_1395|3end_hypothetical_protein_1409045..1409195_NEGATIVE 258 141 114 54 29 NC_009009:SSA_0575|3end_Hydrolase,_HAD_superfamily,_putative_570116..570266_POSITIVE 256 128 89 109 70 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 255 127 81 106 59 NC_009009:SSA_0345|3end_hypothetical_protein_339209..339359_POSITIVE