Origin IGS: tgattagtaatccaataaccttgttatagcaaaatttcttattttaatttgaagttgtaacgcttatattatataatagattataagagtaacaaggggtgtctcatgaaaaaaaaacataaaattatactaattatcgtcagtttgtttgtagctatttgtctgggaggggga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tccccctcccagacaaatagctacaaacaaactgacgataattagtataattttatgtttttttttcatgagacaccccttgttactcttataatctattatataatataagcgttacaacttcaaattaaaataagaaattttgctataacaaggttattggattactaatca Mask Tandem Repeat Region ================================================ tgattagtaatccaataaccttgttatagcaaaatttcttattttaatttgaagttgtaacgcttatattatataatagattataagagtaacaaggggtgtctcatgaaaaaaaaacataaaattatactaattatcgtcagtttgtttgtagctatttgtctgggaggggga Find is-nt database================================================ Query_seq: SSA_0245:SSA_0246|SSA_0245:SSA_0246:hypothetical protein:Conserved uncharacterized protein:->->:239669..239842 174 tgattagtaatccaataaccttgttatagcaaaatttcttattttaatttgaagttgtaacgcttatattatataatagattataagagtaacaaggggtgtctcatgaaaaaaaaacataaaattatactaattatcgtcagtttgtttgtagctatttgtctgggaggggga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0245:SSA_0246|SSA_0245:SSA_0246:hypothetical protein:Conserved uncharacterized protein:->->:239669..239842 174 tgattagtaatccaataaccttgttatagcaaaatttcttattttaatttgaagttgtaacgcttatattatataatagattataagagtaacaaggggtgtctcatgaaaaaaaaacataaaattatactaattatcgtcagtttgtttgtagctatttgtctgggaggggga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0245:SSA_0246|SSA_0245:SSA_0246:hypothetical protein:Conserved uncharacterized protein:->->:239669..239842 174 tgattagtaatccaataaccttgttatagcaaaatttcttattttaatttgaagttgtaacgcttatattatataatagattataagagtaacaaggggtgtctcatgaaaaaaaaacataaaattatactaattatcgtcagtttgtttgtagctatttgtctgggaggggga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgattagtaatccaataaccttgttatagcaaaatttcttattttaatttgaagttgtaacgcttatattatataatagattataagagtaacaaggggtgtctcatgaaaaaaaaacataaaattatactaattatcgtcagtttgtttgtagctatttgtctgggaggggga Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 73 End: 174 ........................................................................ M I D Y K S N K G C L M K K K H K I I L I I V S L F V A I C L G G G tgattagtaatccaataaccttgttatagcaaaatttcttattttaatttgaagttgtaacgcttatattatataatagattataagagtaacaaggggtgtctcatgaaaaaaaaacataaaattatactaattatcgtcagtttgtttgtagctatttgtctgggaggggga 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: 48 End: 77 ...............................................TTTGAAGTTGTAACGCTTATATTATATAAT................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 41 End: 70 ........................................ATTTTAATTTGAAGTTGTAACGCTTATATT........................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgattagtaatccaataaccttgttatagcaaaatttcttattttaatttgaagttgtaacgcttatattatataatagattataagagtaacaaggggtgtctcatgaaaaaaaaacataaaattatactaattatcgtcagtttgtttgtagctatttgtctgggaggggga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0245:SSA_0246|SSA_0245:SSA_0246:hypothetical protein:Conserved uncharacterized protein:->->:239669..239842 174 tgattagtaatccaataaccttgttatagcaaaatttcttattttaatttgaagttgtaacgcttatattatataatagattataagagtaacaaggggtgtctcatgaaaaaaaaacataaaattatactaattatcgtcagtttgtttgtagctatttgtctgggaggggga Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: NC_009009_SSA_0245_SSA_0246|hypothetical protein:Conserved uncharacterized protein|POSITIVE:POSITIVE|[239669,239842]|174 HSP 1 e-value: 4.0E-78 bit: 291.0 Len: 174 Query Start:1 Query End:174 Subject Strand: POSITIVE Subject Start: 1 Subject End: 174 tgattagtaatccaataaccttgttatagcaaaatttcttattttaatttgaagttgtaacgcttatattatataatagattataagagtaacaaggggtgtctcatgnnnnnnnnncataaaattatactaattatcgtcagtttgtttgtagctatttgtctgggaggggga tgattagtaatccaataaccttgttatagcaaaatttcttattttaatttgaagttgtaacgcttatattatataatagattataagagtaacaaggggtgtctcatgaaaaaaaaacataaaattatactaattatcgtcagtttgtttgtagctatttgtctgggaggggga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUAGUAAUCCAAUAACCUUGUUAUAGCAAAAUUUCUUAUUUUAAUUUGAAGUUGUAACGCUUAUAUUAUAUAAUAGAUUAUAAGAGUAACAAGGGGUGUCUCAUGAAAAAAAAACAUAAAAUUAUACUAAUUAUCGUCAGUUUGUUUGUAGCUAUUUGUCUGGGAGGGGGA (((((((((.........(((((((((.....((((((..((....))..))))))......((((((.............)))))).))))))))).((((....(....)....)))).......))))))))).......(((.(((.((((.....).))).))).))). (-26.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCCCCUCCCAGACAAAUAGCUACAAACAAACUGACGAUAAUUAGUAUAAUUUUAUGUUUUUUUUUCAUGAGACACCCCUUGUUACUCUUAUAAUCUAUUAUAUAAUAUAAGCGUUACAACUUCAAAUUAAAAUAAGAAAUUUUGCUAUAACAAGGUUAUUGGAUUACUAAUCA (((.....((......(((((.........(((((......))))).((((((..((((((........))))))....((((.((.((((((.............)))))).)).))))....))))))..............))))).....)).....))).......... (-18.72) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 119 72 145 104 NC_009009:SSA_1401|5end_Transcriptional_regulator_GntR_family_1413062..1413292_POSITIVE 255 169 134 67 27 NC_009009:SSA_2081|5end_hypothetical_protein_2085309..2085539_POSITIVE 239 168 128 223 180 NC_009009:SSA_0562|5end_hypothetical_protein_554468..554698_POSITIVE 229 167 138 120 89 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 228 170 132 160 120 NC_009009:SSA_0371|5end_NADP-specific_glutamate_dehydrogenase,_putative_361759..361989_NEGATIVE 225 169 139 43 15 NC_009009:SSA_0761|5end_Transcriptional_regulator,_XRE_family,_putative_743877..744107_POSITIVE 221 170 124 170 120 NC_009009:SSA_1685|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1679076..1679306_NEGATIVE 218 169 142 164 135 NC_009009:SSA_0323|5end_Flavoprotein,_putative_316799..317029_NEGATIVE 216 107 61 202 136 NC_009009:SSA_0736|5end_Catabolite_gene_activator_and_regulatory_subunit_of_cAMP-dependent_protein_kinases,_putative_717648..717878_POSITIVE 211 170 139 158 128 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 210 169 129 73 33 NC_009009:SSA_2257|5end_DNA_mismatch_repair_protein,_putative_2253184..2253414_NEGATIVE 210 170 134 62 15 NC_009009:SSA_1803|5end_GTP-binding_protein,_putative_1787909..1788139_NEGATIVE 208 170 130 204 166 NC_009009:SSA_1821|5end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810610..1810840_NEGATIVE 202 108 61 196 146 NC_009009:SSA_1995|5end_hypothetical_protein_1993358..1993588_NEGATIVE 201 167 122 144 99 NC_009009:SSA_1443|5end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1446672..1446902_NEGATIVE 200 170 126 51 7 NC_009009:SSA_0747|5end_DD-carboxypeptidase,_putative_727936..728166_POSITIVE 199 170 136 44 6 NC_009009:SSA_0321|5end_Methylase,_putative_313867..314097_POSITIVE 197 109 61 209 163 NC_009009:SSA_2201|5end_hypothetical_protein_2201807..2202037_POSITIVE 193 75 35 148 108 NC_009009:SSA_2259|5end_hypothetical_protein_2255422..2255652_NEGATIVE 193 99 62 192 148 NC_009009:SSA_0923|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933010..933240_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 214 170 130 143 102 NC_009009:SSA_0571|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_B,_putative_566894..567044_POSITIVE 205 170 134 149 107 NC_009009:SSA_0817|3end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_799375..799525_POSITIVE 202 108 61 75 25 NC_009009:SSA_1996|3end_DNA-directed_RNA_polymerase_delta_subunit,_putative_1993479..1993629_NEGATIVE 198 170 137 136 101 NC_009009:SSA_1143|3end_Na+-driven_multidrug_efflux_pump,_putative_1172148..1172298_NEGATIVE 194 158 134 151 128 NC_009009:SSA_2081|3end_hypothetical_protein_2085490..2085640_POSITIVE 189 168 139 127 85 NC_009009:SSA_1010|3end_UDP-glucose_4-epimerase,_putative_1013862..1014012_POSITIVE 188 164 127 71 29 NC_009009:SSA_2245|3end_RecA_protein,_putative_2239961..2240111_NEGATIVE 187 169 135 55 20 NC_009009:SSA_0537|3end_Propanediol_utilization:dioldehydratase_reactivation,_putative_533893..534043_POSITIVE 186 170 134 133 101 NC_009009:SSA_2226|3end_Organic_radical_activating_chaperone,_putative_2227151..2227301_NEGATIVE 186 126 82 88 41 NC_009009:SSA_0989|3end_Conserved_protein,_possible_transcriptional_regulator_(sigma-70,_region_4),_putative_991816..991966_POSITIVE 185 167 126 97 49 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE 183 167 138 39 11 NC_009009:SSA_1912|3end_hypothetical_protein_1903113..1903263_NEGATIVE 182 170 130 78 29 NC_009009:SSA_2002|3end_tRNA_pseudouridine_synthase_A,_putative_1998210..1998360_NEGATIVE 182 169 136 148 108 NC_009009:SSA_1442|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445183..1445333_NEGATIVE 182 170 137 121 85 NC_009009:SSA_0509|3end_Propanediol_utilization_protein,_putative_508538..508688_POSITIVE 181 104 61 44 1 NC_009009:SSA_2092|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095697..2095847_NEGATIVE 180 165 130 150 115 NC_009009:SSA_2216|3end_LPS_biosynthesis_protein,_putative_2217157..2217307_NEGATIVE 180 170 132 85 45 NC_009009:SSA_1971|3end_hypothetical_protein_1967597..1967747_POSITIVE 180 167 124 136 95 NC_009009:SSA_0226|3end_60_kDa_chaperonin_220649..220799_POSITIVE 178 168 136 148 124 NC_009009:SSA_1532|3end_Membrane-fusion_protein_/_periplasmic_component_of_efflux_system,_putative_1539460..1539610_NEGATIVE