Origin IGS: aaatcgagcaagccgtttggcttgctgtttttcatttattggcaggaatggtataatagttgatagtcgtgagaagtagattagtgaatttgggagaataatgaaaaagagagttacaaataataaatgatagcgatataatctatcaacttggaaaaaaagaataaaatgtttaattttagatgaagaggtacccc .........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 ggggtacctcttcatctaaaattaaacattttattctttttttccaagttgatagattatatcgctatcatttattatttgtaactctctttttcattattctcccaaattcactaatctacttctcacgactatcaactattataccattcctgccaataaatgaaaaacagcaagccaaacggcttgctcgattt Mask Tandem Repeat Region ================================================ aaatcgagcaagccgtttggcttgctgtttttcatttattggcaggaatggtataatagttgatagtcgtgagaagtagattagtgaatttgggagaataatgaaaaagagagttacaaataataaatgatagcgatataatctatcaacttggaaaaaaagaataaaatgtttaattttagatgaagaggtacccc Find is-nt database================================================ Query_seq: SSA_0931:SSA_0932|SSA_0931:SSA_0932:hypothetical protein:hypothetical protein:->->:941396..941592 197 aaatcgagcaagccgtttggcttgctgtttttcatttattggcaggaatggtataatagttgatagtcgtgagaagtagattagtgaatttgggagaataatgaaaaagagagttacaaataataaatgatagcgatataatctatcaacttggaaaaaaagaataaaatgtttaattttagatgaagaggtacccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0931:SSA_0932|SSA_0931:SSA_0932:hypothetical protein:hypothetical protein:->->:941396..941592 197 aaatcgagcaagccgtttggcttgctgtttttcatttattggcaggaatggtataatagttgatagtcgtgagaagtagattagtgaatttgggagaataatgaaaaagagagttacaaataataaatgatagcgatataatctatcaacttggaaaaaaagaataaaatgtttaattttagatgaagaggtacccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0931:SSA_0932|SSA_0931:SSA_0932:hypothetical protein:hypothetical protein:->->:941396..941592 197 aaatcgagcaagccgtttggcttgctgtttttcatttattggcaggaatggtataatagttgatagtcgtgagaagtagattagtgaatttgggagaataatgaaaaagagagttacaaataataaatgatagcgatataatctatcaacttggaaaaaaagaataaaatgtttaattttagatgaagaggtacccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatcgagcaagccgtttggcttgctgtttttcatttattggcaggaatggtataatagttgatagtcgtgagaagtagattagtgaatttgggagaataatgaaaaagagagttacaaataataaatgatagcgatataatctatcaacttggaaaaaaagaataaaatgtttaattttagatgaagaggtacccc Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 35 End: 142 .................................. K N A P I T Y Y N I T T L L L N T F K P S Y H F L S N C I I F S L S I M ....................................................... Protein_Len: 59 Strand: - Start: 1 End: 177 F R A L R K A Q Q K E N I P L F P I I T S L R S F Y I L S N P L I I F F L T V F L L H Y R Y L R D V Q F F L I F H K M .................... aaatcgagcaagccgtttggcttgctgtttttcatttattggcaggaatggtataatagttgatagtcgtgagaagtagattagtgaatttgggagaataatgaaaaagagagttacaaataataaatgatagcgatataatctatcaacttggaaaaaaagaataaaatgtttaattttagatgaagaggtacccc 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: 86 Start: 28 End: 57 ...........................TTTTTCATTTATTGGCAGGAATGGTATAAT............................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 113 End: 142 ................................................................................................................GTTACAAATAATAAATGATAGCGATATAAT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaatcgagcaagccgtttggcttgctgtttttcatttattggcaggaatggtataatagttgatagtcgtgagaagtagattagtgaatttgggagaataatgaaaaagagagttacaaataataaatgatagcgatataatctatcaacttggaaaaaaagaataaaatgtttaattttagatgaagaggtacccc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0931:SSA_0932|SSA_0931:SSA_0932:hypothetical protein:hypothetical protein:->->:941396..941592 197 aaatcgagcaagccgtttggcttgctgtttttcatttattggcaggaatggtataatagttgatagtcgtgagaagtagattagtgaatttgggagaataatgaaaaagagagttacaaataataaatgatagcgatataatctatcaacttggaaaaaaagaataaaatgtttaattttagatgaagaggtacccc Intra-Species Hit: Count: 1 Min: 1 Max: 197 Len: 197 Subject: NC_009009_SSA_0931_SSA_0932|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[941396,941592]|197 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 197 Query Start:1 Query End:197 Subject Strand: POSITIVE Subject Start: 1 Subject End: 197 aaatcgagcaagccgtttggcttgctgtttttcatttattggcaggaatggtataatagttgatagtcgtgagaagtagattagtgaatttgggagaataatgaaaaagagagttacaaataataaatgatagcgatataatctatcaacttggnnnnnnngaataaaatgtttaattttagatgaagaggtacccc aaatcgagcaagccgtttggcttgctgtttttcatttattggcaggaatggtataatagttgatagtcgtgagaagtagattagtgaatttgggagaataatgaaaaagagagttacaaataataaatgatagcgatataatctatcaacttggaaaaaaagaataaaatgtttaattttagatgaagaggtacccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUCGAGCAAGCCGUUUGGCUUGCUGUUUUUCAUUUAUUGGCAGGAAUGGUAUAAUAGUUGAUAGUCGUGAGAAGUAGAUUAGUGAAUUUGGGAGAAUAAUGAAAAAGAGAGUUACAAAUAAUAAAUGAUAGCGAUAUAAUCUAUCAACUUGGAAAAAAAGAAUAAAAUGUUUAAUUUUAGAUGAAGAGGUACCCC ......((((((((....)))))))).(((((((((((.((.((....)).))....(((((((((((((.........(((.((((.(((................)))...)))).)))...........))))......)))))))))............................)))))))))))....... (-34.04) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGGUACCUCUUCAUCUAAAAUUAAACAUUUUAUUCUUUUUUUCCAAGUUGAUAGAUUAUAUCGCUAUCAUUUAUUAUUUGUAACUCUCUUUUUCAUUAUUCUCCCAAAUUCACUAAUCUACUUCUCACGACUAUCAACUAUUAUACCAUUCCUGCCAAUAAAUGAAAAACAGCAAGCCAAACGGCUUGCUCGAUUU ..((((..........((((((.....)))))).............(((((((((................((((.....)))).......................................((....)))))))))))....)))).......................((((((((....))))))))...... (-25.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 49 4 42 7 NC_009009:SSA_0797|5end_Transcriptional_regulator,_putative_779521..779751_POSITIVE 303 68 24 225 187 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 289 47 4 97 48 NC_009009:SSA_1721|5end_DNA_polymerase_III,_delta'_subunit,_putative_1708028..1708258_NEGATIVE 289 30 7 181 159 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 287 52 15 82 37 NC_009009:SSA_1509|5end_Polysaccharide_biosynthesis_protein/_rhamnosyltransferase,_putative_1514191..1514421_NEGATIVE 284 46 6 99 53 NC_009009:SSA_0335|5end_Phosphomevalonate_kinase,_putative_328792..329022_POSITIVE 278 41 1 228 183 NC_009009:SSA_0962|5end_Lactoylglutathione_lyase,_putative_970965..971195_POSITIVE 278 56 12 217 153 NC_009009:SSA_0511|5end_Propanediol_utilization_kinase,_putative_509610..509840_POSITIVE 276 47 1 173 134 NC_009009:SSA_0981|5end_3-isopropylmalate_dehydratase_small_subunit,_putative_985396..985626_POSITIVE 274 45 4 181 131 NC_009009:SSA_0776|5end_Glucose-1-phosphate_adenylyltransferase,_putative_758298..758528_POSITIVE 273 31 5 163 135 NC_009009:SSA_0634|5end_Anthranilate_phosphoribosyltransferase,_putative_623387..623617_POSITIVE 272 53 11 168 114 NC_009009:SSA_0710|5end_Exopolysaccharide_biosynthesis_protein,_acetyltransferase,_putative_695639..695869_NEGATIVE 268 50 7 206 162 NC_009009:SSA_0884|5end_hypothetical_protein_879063..879293_NEGATIVE 267 70 25 159 117 NC_009009:SSA_2179|5end_Conserved_uncharacterized_protein_2179117..2179347_NEGATIVE 266 50 3 167 109 NC_009009:SSA_2188|5end_Conserved_uncharacterized_protein_2188896..2189126_POSITIVE 266 88 41 163 125 NC_009009:SSA_1830|5end_Aminoglycoside_phosphotransferase,_putative_1820335..1820565_POSITIVE 266 48 2 216 160 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 266 52 12 76 38 NC_009009:SSA_1442|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445941..1446171_NEGATIVE 263 48 1 151 100 NC_009009:SSA_2129|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_2133308..2133538_NEGATIVE 263 37 3 196 152 NC_009009:SSA_1574|5end_Glycosyl_transferase,_family_1,_putative_1577930..1578160_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 53 11 112 68 NC_009009:SSA_0002|3end_DNA_polymerase_III,_beta_chain,_putative_2801..2951_POSITIVE 299 50 3 138 75 NC_009009:SSA_1801|3end_hypothetical_protein_1782652..1782802_NEGATIVE 289 47 4 100 51 NC_009009:SSA_1722|3end_Thymidylate_kinase,_putative_1708025..1708175_NEGATIVE 289 30 7 83 61 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 287 52 15 85 40 NC_009009:SSA_1510|3end_Rhamnosyltransferase,_putative_1514188..1514338_NEGATIVE 284 46 6 109 63 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 278 41 1 114 69 NC_009009:SSA_0961|3end_Possible_ketopantoate_reductase_PanE/ApbA,_putative_970931..971081_POSITIVE 268 34 7 93 65 NC_009009:SSA_0931|3end_hypothetical_protein_941335..941485_POSITIVE 267 70 25 128 86 NC_009009:SSA_2181|3end_Conserved_uncharacterized_protein_2179148..2179298_NEGATIVE 267 25 5 143 124 NC_009009:SSA_0633|3end_Anthranilate_synthase_component_II,_putative_623456..623606_POSITIVE 266 50 3 142 84 NC_009009:SSA_2187|3end_Conserved_hypothetical_membrane_associated_protein_2188951..2189101_POSITIVE 266 52 12 73 35 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 263 70 22 137 80 NC_009009:SSA_2258|3end_hypothetical_protein_2253389..2253539_NEGATIVE 262 50 6 108 66 NC_009009:SSA_0813|3end_Thioredoxin_reductase,_putative_794438..794588_NEGATIVE 260 47 2 148 103 NC_009009:SSA_1200|3end_Formate--tetrahydrofolate_ligase,_putative_1223921..1224071_NEGATIVE 259 43 2 71 32 NC_009009:SSA_0635|3end_Indole-3-glycerol_phosphate_synthase,_putative_625235..625385_POSITIVE 257 32 7 41 12 NC_009009:SSA_0345|3end_hypothetical_protein_339209..339359_POSITIVE 255 43 4 141 110 NC_009009:SSA_1911|3end_Conserved_uncharacterized_protein_1902665..1902815_NEGATIVE 255 52 13 150 106 NC_009009:SSA_0671|3end_Methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase,_putative_655274..655424_POSITIVE 255 44 7 113 63 NC_009009:SSA_0440|3end_30S_ribosomal_protein_S18,_putative_441465..441615_POSITIVE