Origin IGS: ttttcaataaatctccttttgagtaaaatttctaatatctagttcaaaaacaaagaaaaacagatttaaatctgtttatttgcgaacgatattttaaattataataaaaaacattcactttttcaagatgaatgtctcgctattc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaatagcgagacattcatcttgaaaaagtgaatgttttttattataatttaaaatatcgttcgcaaataaacagatttaaatctgtttttctttgtttttgaactagatattagaaattttactcaaaaggagatttattgaaaa Mask Tandem Repeat Region ================================================ ttttcaataaatctccttttgagtaaaatttctaatatctagttcaaaaacaaagaaaaacagatttaaatctgtttatttgcgaacgatattttaaattataataaaaaacattcactttttcaagatgaatgtctcgctattc Find is-nt database================================================ Query_seq: SSA_1913:SSA_1914|SSA_1913:SSA_1914:Xanthine/uracil permease family protein, putative:hypothetical protein:<-<-:1904757..1904901 145 ttttcaataaatctccttttgagtaaaatttctaatatctagttcaaaaacaaagaaaaacagatttaaatctgtttatttgcgaacgatattttaaattataataaaaaacattcactttttcaagatgaatgtctcgctattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1913:SSA_1914|SSA_1913:SSA_1914:Xanthine/uracil permease family protein, putative:hypothetical protein:<-<-:1904757..1904901 145 ttttcaataaatctccttttgagtaaaatttctaatatctagttcaaaaacaaagaaaaacagatttaaatctgtttatttgcgaacgatattttaaattataataaaaaacattcactttttcaagatgaatgtctcgctattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1913:SSA_1914|SSA_1913:SSA_1914:Xanthine/uracil permease family protein, putative:hypothetical protein:<-<-:1904757..1904901 145 ttttcaataaatctccttttgagtaaaatttctaatatctagttcaaaaacaaagaaaaacagatttaaatctgtttatttgcgaacgatattttaaattataataaaaaacattcactttttcaagatgaatgtctcgctattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttcaataaatctccttttgagtaaaatttctaatatctagttcaaaaacaaagaaaaacagatttaaatctgtttatttgcgaacgatattttaaattataataaaaaacattcactttttcaagatgaatgtctcgctattc Predict ORF larger than 30AA ================================================ ttttcaataaatctccttttgagtaaaatttctaatatctagttcaaaaacaaagaaaaacagatttaaatctgtttatttgcgaacgatattttaaattataataaaaaacattcactttttcaagatgaatgtctcgctattc 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: 98 End: 127 .................................................................................................CTTGAAAAAGTGAATGTTTTTTATTATAAT.................. PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 0 End: 29 tTTTTCAATAAATCTCCTTTTGAGTAAAAT.................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttcaataaatctccttttgagtaaaatttctaatatctagttcaaaaacaaagaaaaacagatttaaatctgtttatttgcgaacgatattttaaattataataaaaaacattcactttttcaagatgaatgtctcgctattc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 81 HP_score: -5.3 Tail_Score: -5.63012 Start: 61 End: 74 Full_Region: tcgttcgcaaataaa cagat ttaa atctg tttttctttgttttt ............................................................cagatttaaatctg....................................................................... Find igs database================================================ Query_seq: SSA_1913:SSA_1914|SSA_1913:SSA_1914:Xanthine/uracil permease family protein, putative:hypothetical protein:<-<-:1904757..1904901 145 ttttcaataaatctccttttgagtaaaatttctaatatctagttcaaaaacaaagaaaaacagatttaaatctgtttatttgcgaacgatattttaaattataataaaaaacattcactttttcaagatgaatgtctcgctattc Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_009009_SSA_1913_SSA_1914|Xanthine/uracil permease family protein, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1904757,1904901]|145 HSP 1 e-value: 5.0E-77 bit: 287.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 ttttcaataaatctccttttgagtaaaatttctaatatctagttcaaaaacaaagaaaaacagatttaaatctgtttatttgcgaacgatattttaaattataataaaaaacattcactttttcaagatgaatgtctcgctattc ttttcaataaatctccttttgagtaaaatttctaatatctagttcaaaaacaaagaaaaacagatttaaatctgtttatttgcgaacgatattttaaattataataaaaaacattcactttttcaagatgaatgtctcgctattc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCAAUAAAUCUCCUUUUGAGUAAAAUUUCUAAUAUCUAGUUCAAAAACAAAGAAAAACAGAUUUAAAUCUGUUUAUUUGCGAACGAUAUUUUAAAUUAUAAUAAAAAACAUUCACUUUUUCAAGAUGAAUGUCUCGCUAUUC ....................(((...(((((..((((((..((((.....((((...((((((((....)))))))).)))).))))))))))..)))))..........((((((((((....))).))))))))))....... (-24.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUAGCGAGACAUUCAUCUUGAAAAAGUGAAUGUUUUUUAUUAUAAUUUAAAAUAUCGUUCGCAAAUAAACAGAUUUAAAUCUGUUUUUCUUUGUUUUUGAACUAGAUAUUAGAAAUUUUACUCAAAAGGAGAUUUAUUGAAAA .(((((.((((((((((.(((....))))))))))))))))))..(((((..(((((((((((((((.((((((((....))))))))...)))))....))))..))))))..)))))...(((.....)))............ (-32.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 701 90 41 181 132 NC_009009:SSA_1913|5end_Xanthine/uracil_permease_family_protein,_putative_1904666..1904896_NEGATIVE 298 46 10 184 150 NC_009009:SSA_0434|5end_Glutamate_formiminotransferase,_putative_436568..436798_NEGATIVE 272 140 111 60 27 NC_009009:SSA_0572|5end_Dehydrogenase,_putative_567426..567656_POSITIVE 208 139 114 194 163 NC_009009:SSA_2023|5end_Fructan_beta-fructosidase_precursor,_putative_2028826..2029056_NEGATIVE 191 57 12 153 97 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 191 140 91 161 105 NC_009009:SSA_0661|5end_Isoleucyl-tRNA_synthetase,_putative_644876..645106_POSITIVE 188 90 69 31 8 NC_009009:SSA_2320|5end_hypothetical_protein_2325796..2326026_NEGATIVE 182 140 103 177 127 NC_009009:SSA_0975|5end_2-isopropylmalate_synthase,_putative_980971..981201_POSITIVE 180 58 15 157 116 NC_009009:SSA_1626|5end_DNA_translocase_ftsK,_putative_1629377..1629607_NEGATIVE 178 140 119 200 180 NC_009009:SSA_0731|5end_Integral_membrane_protein,_putative_715065..715295_POSITIVE 177 140 96 161 119 NC_009009:SSA_0907|5end_Fibronectin-binding_protein_A,_putative_919217..919447_NEGATIVE 175 140 114 59 29 NC_009009:SSA_1289|5end_hypothetical_protein_1308385..1308615_NEGATIVE 174 55 13 143 98 NC_009009:SSA_0587|5end_Metal-dependent_amidase/aminoacylase/carboxypeptidase,_putative_578539..578769_POSITIVE 173 48 12 127 95 NC_009009:SSA_1822|5end_hypothetical_protein_1811125..1811355_NEGATIVE 173 24 1 108 82 NC_009009:SSA_0613|5end_Glucosyltransferase,_putative_601847..602077_POSITIVE 172 48 1 137 91 NC_009009:SSA_1128|5end_Voltage_gated_chloride_channel_EriC,_putative_1153250..1153480_POSITIVE 170 39 1 126 85 NC_009009:SSA_0991|5end_Deoxyribonuclease,_putative_993342..993572_NEGATIVE 169 124 86 164 123 NC_009009:SSA_1183|5end_hypothetical_protein_1211453..1211683_NEGATIVE 167 136 112 195 171 NC_009009:SSA_0888|5end_Magnesium/cobalt_transporter,_putative_881329..881559_POSITIVE 166 95 72 27 5 NC_009009:SSA_0183|5end_hypothetical_protein_187646..187876_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 46 10 63 29 NC_009009:SSA_0435|3end_Urocanate_hydratase,_putative_436689..436839_NEGATIVE 181 89 41 144 88 NC_009009:SSA_1169|3end_Conserved_hypothetical_protein_with_an_alpha/beta_hydrolase_fold,_putative_1196846..1196996_POSITIVE 173 48 12 100 68 NC_009009:SSA_1823|3end_hypothetical_protein_1811152..1811302_NEGATIVE 173 24 1 38 12 NC_009009:SSA_0612|3end_Rgg_protein,_putative_601857..602007_POSITIVE 171 49 1 58 14 NC_009009:SSA_0827|3end_Conserved_uncharacterized_cytosolic_protein,_putative_806952..807102_POSITIVE 170 43 4 51 13 NC_009009:SSA_0817|3end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_799375..799525_POSITIVE 169 124 86 105 64 NC_009009:SSA_1184|3end_DNA_topoisomerase_I,_putative_1211512..1211662_NEGATIVE 168 87 61 136 106 NC_009009:SSA_0698|3end_Peptide_chain_release_factor_3,_putative_682007..682157_POSITIVE 164 83 41 56 14 NC_009009:SSA_0683|3end_DNA-binding_protein_HU,_putative_664739..664889_POSITIVE 162 140 114 133 107 NC_009009:SSA_1653|3end_hypothetical_protein_1650409..1650559_NEGATIVE 162 43 13 139 94 NC_009009:SSA_1312|3end_RADC-like_protein,_putative_1328737..1328887_NEGATIVE 159 139 103 86 43 NC_009009:SSA_2116|3end_Cmp-binding-factor_1,_putative_2117622..2117772_NEGATIVE 156 86 49 58 25 NC_009009:SSA_0857|3end_hypothetical_protein_845482..845632_POSITIVE 155 95 52 124 75 NC_009009:SSA_2382|3end_Chromosome_partitioning_protein_ParB_or_transcriptional_regulator_Spo0J,_putative_2388375..2388525_POSITIVE 155 33 4 57 30 NC_009009:SSA_2311|3end_Nitric_oxide_reductase_NorD_/_Von_Willebrand_factor_type_A_(vWA)_domain_protein,_putative_2313431..2313581_NEGATIVE 155 43 11 133 97 NC_009009:SSA_1947|3end_Oligopeptide_transport_system_permease_protein,_putative_1938624..1938774_NEGATIVE 155 30 3 106 72 NC_009009:SSA_1816|3end_hypothetical_protein_1800927..1801077_NEGATIVE 155 48 9 100 53 NC_009009:SSA_0869|3end_Peptide_chain_release_factor_2,_putative_862971..863121_POSITIVE 153 99 61 61 23 NC_009009:SSA_0310|3end_hypothetical_protein_305973..306123_POSITIVE 152 80 51 83 58 NC_009009:SSA_2271|3end_hypothetical_protein_2272238..2272388_NEGATIVE