Origin IGS: actcaacctctctttacagatattttgttctattatatcatttttatcaagtaagggcttacttggattgaaaagaacggtaattttcgatagaataggaagaactattattagataagcaggagaaaccc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gggtttctcctgcttatctaataatagttcttcctattctatcgaaaattaccgttcttttcaatccaagtaagcccttacttgataaaaatgatataatagaacaaaatatctgtaaagagaggttgagt Mask Tandem Repeat Region ================================================ actcaacctctctttacagatattttgttctattatatcatttttatcaagtaagggcttacttggattgaaaagaacggtaattttcgatagaataggaagaactattattagataagcaggagaaaccc Find is-nt database================================================ Query_seq: SSA_1960:SSA_1961|SSA_1960:SSA_1961:hypothetical protein:Amino acid ABC transporter, amino acid-binding protein/permease protein, putative:<-->:1958557..1958687 131 actcaacctctctttacagatattttgttctattatatcatttttatcaagtaagggcttacttggattgaaaagaacggtaattttcgatagaataggaagaactattattagataagcaggagaaaccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1960:SSA_1961|SSA_1960:SSA_1961:hypothetical protein:Amino acid ABC transporter, amino acid-binding protein/permease protein, putative:<-->:1958557..1958687 131 actcaacctctctttacagatattttgttctattatatcatttttatcaagtaagggcttacttggattgaaaagaacggtaattttcgatagaataggaagaactattattagataagcaggagaaaccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1960:SSA_1961|SSA_1960:SSA_1961:hypothetical protein:Amino acid ABC transporter, amino acid-binding protein/permease protein, putative:<-->:1958557..1958687 131 actcaacctctctttacagatattttgttctattatatcatttttatcaagtaagggcttacttggattgaaaagaacggtaattttcgatagaataggaagaactattattagataagcaggagaaaccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actcaacctctctttacagatattttgttctattatatcatttttatcaagtaagggcttacttggattgaaaagaacggtaattttcgatagaataggaagaactattattagataagcaggagaaaccc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 20 End: 115 ................... M F C S I I S F L S S K G L L G L K R T V I F D R I G R T I I R ................ Protein_Len: 37 Strand: - Start: 1 End: 111 S L R E K C I N Q E I I D N K D L L P K S P N F L V T I K S L I P L V I M .................... actcaacctctctttacagatattttgttctattatatcatttttatcaagtaagggcttacttggattgaaaagaacggtaattttcgatagaataggaagaactattattagataagcaggagaaaccc 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: 67 End: 96 ..................................................................ATTGAAAAGAACGGTAATTTTCGATAGAAT................................... PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 12 End: 41 ...........CTTTACAGATATTTTGTTCTATTATATCAT.......................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actcaacctctctttacagatattttgttctattatatcatttttatcaagtaagggcttacttggattgaaaagaacggtaattttcgatagaataggaagaactattattagataagcaggagaaaccc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1960:SSA_1961|SSA_1960:SSA_1961:hypothetical protein:Amino acid ABC transporter, amino acid-binding protein/permease protein, putative:<-->:1958557..1958687 131 actcaacctctctttacagatattttgttctattatatcatttttatcaagtaagggcttacttggattgaaaagaacggtaattttcgatagaataggaagaactattattagataagcaggagaaaccc Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: NC_009009_SSA_1960_SSA_1961|hypothetical protein:Amino acid ABC transporter, amino acid-binding protein/permease protein, putative|NEGATIVE:POSITIVE|[1958557,1958687]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 actcaacctctctttacagatattttgttctattatatcatttttatcaagtaagggcttacttggattgaaaagaacggtaattttcgatagaataggaagaactattattagataagcaggagaaaccc actcaacctctctttacagatattttgttctattatatcatttttatcaagtaagggcttacttggattgaaaagaacggtaattttcgatagaataggaagaactattattagataagcaggagaaaccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCAACCUCUCUUUACAGAUAUUUUGUUCUAUUAUAUCAUUUUUAUCAAGUAAGGGCUUACUUGGAUUGAAAAGAACGGUAAUUUUCGAUAGAAUAGGAAGAACUAUUAUUAGAUAAGCAGGAGAAACCC ........((((((........((((((((((((.((((.(((((.((((.((((......))))..)))).))))).))))......))))))))))))....(((....)))......))))))..... (-23.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGUUUCUCCUGCUUAUCUAAUAAUAGUUCUUCCUAUUCUAUCGAAAAUUACCGUUCUUUUCAAUCCAAGUAAGCCCUUACUUGAUAAAAAUGAUAUAAUAGAACAAAAUAUCUGUAAAGAGAGGUUGAGU ......(((..((((.(((..............(((((.(((((((((.........)))))....(((((((....)))))))........)))).))))).(((.......)))..))).)))).))). (-18.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 823 100 51 191 142 NC_009009:SSA_1960|5end_hypothetical_protein_1958466..1958696_NEGATIVE 244 45 1 138 86 NC_009009:SSA_1701|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_1692054..1692284_NEGATIVE 230 130 85 143 108 NC_009009:SSA_1511|5end_Glycosyltransferase,_putative_1516697..1516927_NEGATIVE 226 70 27 75 30 NC_009009:SSA_1572|5end_hypothetical_protein_1575908..1576138_NEGATIVE 224 58 11 156 101 NC_009009:SSA_2067|5end_hypothetical_protein_2070254..2070484_POSITIVE 221 70 23 176 116 NC_009009:SSA_1421|5end_Adenine_phosphoribosyltransferase,_putative_1431285..1431515_NEGATIVE 216 88 56 140 108 NC_009009:SSA_1862|5end_hypothetical_protein_1858541..1858771_NEGATIVE 216 45 5 135 95 NC_009009:SSA_0574|5end_YdjX_protein,_putative_569427..569657_NEGATIVE 214 98 56 202 149 NC_009009:SSA_2016|5end_Phosphoglycerate_mutase,_putative_2016293..2016523_NEGATIVE 214 40 2 124 92 NC_009009:SSA_1268|5end_Chorismate_mutase/prephenate_dehydratase,_putative_1291610..1291840_NEGATIVE 213 63 21 157 109 NC_009009:SSA_2068|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_2071311..2071541_NEGATIVE 213 66 29 155 116 NC_009009:SSA_0686|5end_Fe2+/Zn2+_uptake_regulation_protein,_putative_669556..669786_POSITIVE 211 45 8 132 98 NC_009009:SSA_1543|5end_hypothetical_protein_1547835..1548065_POSITIVE 211 69 21 170 117 NC_009009:SSA_0891|5end_3-carboxymuconate_cyclase,_putative_884033..884263_NEGATIVE 209 79 35 183 137 NC_009009:SSA_0255|5end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_247946..248176_NEGATIVE 208 40 1 120 86 NC_009009:SSA_1330|5end_hypothetical_protein_1346368..1346598_NEGATIVE 204 104 61 84 40 NC_009009:SSA_2137|5end_hypothetical_protein_2138412..2138642_NEGATIVE 203 65 24 51 4 NC_009009:SSA_1620|5end_Uridylate_kinase,_putative_1622981..1623211_NEGATIVE 203 48 8 140 98 NC_009009:SSA_1547|5end_HPr_kinase/phosphorylase,_putative_1550980..1551210_NEGATIVE 203 126 88 154 123 NC_009009:SSA_1233|5end_Membrane_protein,_YqiH_family,_putative_1256896..1257126_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 46 8 93 56 NC_009009:SSA_2378|3end_Two-component_system_transcriptional_regulator,_LytR/AlgR_family,_putative_2383129..2383279_NEGATIVE 230 130 85 139 104 NC_009009:SSA_1512|3end_hypothetical_protein_1516701..1516851_NEGATIVE 230 98 55 140 100 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE 221 70 23 79 19 NC_009009:SSA_1422|3end_hypothetical_protein_1431382..1431532_NEGATIVE 220 80 39 137 96 NC_009009:SSA_0454|3end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_456050..456200_NEGATIVE 217 120 73 54 4 NC_009009:SSA_0613|3end_Glucosyltransferase,_putative_606633..606783_POSITIVE 216 88 56 92 60 NC_009009:SSA_1863|3end_NH(3)-dependent_NAD(+)_synthetase,_putative_1858589..1858739_NEGATIVE 214 98 56 60 7 NC_009009:SSA_2017|3end_Hypothetical_protein_(possibly_membrane-associated)_2016435..2016585_NEGATIVE 213 63 21 66 18 NC_009009:SSA_2069|3end_Prolyl-tRNA_synthetase,_putative_2071402..2071552_NEGATIVE 212 100 56 68 25 NC_009009:SSA_1217|3end_Conserved_uncharacterized_protein_1239736..1239886_POSITIVE 212 95 55 72 35 NC_009009:SSA_0047|3end_NAD(P)H_dehydrogenase_(Quinone),_putative_52284..52434_NEGATIVE 209 79 35 77 31 NC_009009:SSA_0256|3end_Metalloregulator_ScaR_(Fe/Mn-dependent_transcriptional_repressor),_putative_248052..248202_NEGATIVE 207 59 20 66 24 NC_009009:SSA_1200|3end_Formate--tetrahydrofolate_ligase,_putative_1223921..1224071_NEGATIVE 202 100 53 67 30 NC_009009:SSA_1347|3end_PhnA_protein,_putative_1364791..1364941_NEGATIVE 197 88 43 142 94 NC_009009:SSA_1182|3end_Gid-like_protein,_putative_1209532..1209682_NEGATIVE 195 65 27 103 65 NC_009009:SSA_1453|3end_hypothetical_protein_1459897..1460047_NEGATIVE 195 41 7 61 29 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 194 80 40 104 65 NC_009009:SSA_0330|3end_hypothetical_protein_325162..325312_POSITIVE 193 49 1 64 12 NC_009009:SSA_2245|3end_RecA_protein,_putative_2239961..2240111_NEGATIVE 191 88 51 88 48 NC_009009:SSA_1891|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888146..1888296_NEGATIVE