Origin IGS: atacaaaataggcaatctagtttttctagactagattttttaatccagagtatttagaaacaaatcgaaatacctaagaaggattagattgcttcgtttcgtactctttatttagaaaatcttctaaatagatagataaaggagaaaagatgaaaagaggattacttttattgcttataggcttgctcacggttttatccgtctgctgggcaatcccgtcttggatcgttttcaaaaatagacgaaaattggaaggaaaaattaa .........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 ttaatttttccttccaattttcgtctatttttgaaaacgatccaagacgggattgcccagcagacggataaaaccgtgagcaagcctataagcaataaaagtaatcctcttttcatcttttctcctttatctatctatttagaagattttctaaataaagagtacgaaacgaagcaatctaatccttcttaggtatttcgatttgtttctaaatactctggattaaaaaatctagtctagaaaaactagattgcctattttgtat Mask Tandem Repeat Region ================================================ atacaaaataggcaatctagtttttctagactagattttttaatccagagtatttagaaacaaatcgaaatacctaagaaggattagattgcttcgtttcgtactctttatttagaaaatcttctaaatagatagataaaggagaaaagatgaaaagaggattacttttattgcttataggcttgctcacggttttatccgtctgctgggcaatcccgtcttggatcgttttcaaaaatagacgaaaattggaaggaaaaattaa Find is-nt database================================================ Query_seq: SSA_0723:SSA_0724|SSA_0723:SSA_0724:hypothetical protein:ABC-type multidrug/protein/lipid transport system (pediocin PA-1 exporter), ATPase and permease components, putative:->->:708527..708791 265 atacaaaataggcaatctagtttttctagactagattttttaatccagagtatttagaaacaaatcgaaatacctaagaaggattagattgcttcgtttcgtactctttatttagaaaatcttctaaatagatagataaaggagaaaagatgaaaagaggattacttttattgcttataggcttgctcacggttttatccgtctgctgggcaatcccgtcttggatcgttttcaaaaatagacgaaaattggaaggaaaaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0723:SSA_0724|SSA_0723:SSA_0724:hypothetical protein:ABC-type multidrug/protein/lipid transport system (pediocin PA-1 exporter), ATPase and permease components, putative:->->:708527..708791 265 atacaaaataggcaatctagtttttctagactagattttttaatccagagtatttagaaacaaatcgaaatacctaagaaggattagattgcttcgtttcgtactctttatttagaaaatcttctaaatagatagataaaggagaaaagatgaaaagaggattacttttattgcttataggcttgctcacggttttatccgtctgctgggcaatcccgtcttggatcgttttcaaaaatagacgaaaattggaaggaaaaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0723:SSA_0724|SSA_0723:SSA_0724:hypothetical protein:ABC-type multidrug/protein/lipid transport system (pediocin PA-1 exporter), ATPase and permease components, putative:->->:708527..708791 265 atacaaaataggcaatctagtttttctagactagattttttaatccagagtatttagaaacaaatcgaaatacctaagaaggattagattgcttcgtttcgtactctttatttagaaaatcttctaaatagatagataaaggagaaaagatgaaaagaggattacttttattgcttataggcttgctcacggttttatccgtctgctgggcaatcccgtcttggatcgttttcaaaaatagacgaaaattggaaggaaaaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atacaaaataggcaatctagtttttctagactagattttttaatccagagtatttagaaacaaatcgaaatacctaagaaggattagattgcttcgtttcgtactctttatttagaaaatcttctaaatagatagataaaggagaaaagatgaaaagaggattacttttattgcttataggcttgctcacggttttatccgtctgctgggcaatcccgtcttggatcgttttcaaaaatagacgaaaattggaaggaaaaattaa Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 132 End: 263 ................................................................................................................................... M D K G E K M K R G L L L L L I G L L T V L S V C W A I P S W I V F K N R R K L E G K I .. Protein_Len: 60 Strand: - Start: 77 End: 262 ............................................................................ N S Q K T E Y E K N L F D E L Y I S L P S F I F L P N S K N S I P K S V T K D T Q Q A I G D Q I T K L F L R F N S P F M ... atacaaaataggcaatctagtttttctagactagattttttaatccagagtatttagaaacaaatcgaaatacctaagaaggattagattgcttcgtttcgtactctttatttagaaaatcttctaaatagatagataaaggagaaaagatgaaaagaggattacttttattgcttataggcttgctcacggttttatccgtctgctgggcaatcccgtcttggatcgttttcaaaaatagacgaaaattggaaggaaaaattaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atacaaaataggcaatctagtttttctagactagattttttaatccagagtatttagaaacaaatcgaaatacctaagaaggattagattgcttcgtttcgtactctttatttagaaaatcttctaaatagatagataaaggagaaaagatgaaaagaggattacttttattgcttataggcttgctcacggttttatccgtctgctgggcaatcccgtcttggatcgttttcaaaaatagacgaaaattggaaggaaaaattaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0723:SSA_0724|SSA_0723:SSA_0724:hypothetical protein:ABC-type multidrug/protein/lipid transport system (pediocin PA-1 exporter), ATPase and permease components, putative:->->:708527..708791 265 atacaaaataggcaatctagtttttctagactagattttttaatccagagtatttagaaacaaatcgaaatacctaagaaggattagattgcttcgtttcgtactctttatttagaaaatcttctaaatagatagataaaggagaaaagatgaaaagaggattacttttattgcttataggcttgctcacggttttatccgtctgctgggcaatcccgtcttggatcgttttcaaaaatagacgaaaattggaaggaaaaattaa Intra-Species Hit: Count: 1 Min: 1 Max: 265 Len: 265 Subject: NC_009009_SSA_0723_SSA_0724|hypothetical protein:ABC-type multidrug/protein/lipid transport system (pediocin PA-1 exporter), ATPase and permease components, putative|POSITIVE:POSITIVE|[708527,708791]|265 HSP 1 e-value: 1.0E-148 bit: 525.0 Len: 265 Query Start:1 Query End:265 Subject Strand: POSITIVE Subject Start: 1 Subject End: 265 atacaaaataggcaatctagtttttctagactagattttttaatccagagtatttagaaacaaatcgaaatacctaagaaggattagattgcttcgtttcgtactctttatttagaaaatcttctaaatagatagataaaggagaaaagatgaaaagaggattacttttattgcttataggcttgctcacggttttatccgtctgctgggcaatcccgtcttggatcgttttcaaaaatagacgaaaattggaaggaaaaattaa atacaaaataggcaatctagtttttctagactagattttttaatccagagtatttagaaacaaatcgaaatacctaagaaggattagattgcttcgtttcgtactctttatttagaaaatcttctaaatagatagataaaggagaaaagatgaaaagaggattacttttattgcttataggcttgctcacggttttatccgtctgctgggcaatcccgtcttggatcgttttcaaaaatagacgaaaattggaaggaaaaattaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUACAAAAUAGGCAAUCUAGUUUUUCUAGACUAGAUUUUUUAAUCCAGAGUAUUUAGAAACAAAUCGAAAUACCUAAGAAGGAUUAGAUUGCUUCGUUUCGUACUCUUUAUUUAGAAAAUCUUCUAAAUAGAUAGAUAAAGGAGAAAAGAUGAAAAGAGGAUUACUUUUAUUGCUUAUAGGCUUGCUCACGGUUUUAUCCGUCUGCUGGGCAAUCCCGUCUUGGAUCGUUUUCAAAAAUAGACGAAAAUUGGAAGGAAAAAUUAA ...(((...((((((((((((((((((...((.((((....)))).)).((((((.((......)).))))))...))))))))))))))))))..((((((....(((((((((((....)))))))))))..((.(((.((...((((((..(((((.....)))))..........((.((((((((((......)))).....)))))).))))))))...)).)))))........)))))).))).............. (-65.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAUUUUUCCUUCCAAUUUUCGUCUAUUUUUGAAAACGAUCCAAGACGGGAUUGCCCAGCAGACGGAUAAAACCGUGAGCAAGCCUAUAAGCAAUAAAAGUAAUCCUCUUUUCAUCUUUUCUCCUUUAUCUAUCUAUUUAGAAGAUUUUCUAAAUAAAGAGUACGAAACGAAGCAAUCUAAUCCUUCUUAGGUAUUUCGAUUUGUUUCUAAAUACUCUGGAUUAAAAAAUCUAGUCUAGAAAAACUAGAUUGCCUAUUUUGUAU ..................((((((((......(((((.(((..((((.((((((((...((..((((......))))..))..((......)).......)))))))).)))).)))))))).............(((((((((....)))))))))...)).))))))....((((((((..........(((((((.((......)).)))))))((((((((.......))))))))......))))))))........... (-56.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 392 230 181 209 148 NC_009009:SSA_2229|5end_hypothetical_protein_2228994..2229224_NEGATIVE 391 228 181 191 144 NC_009009:SSA_1667|5end_hypothetical_protein_1667704..1667934_NEGATIVE 381 213 173 227 184 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 370 229 182 230 168 NC_009009:SSA_0490|5end_Cobalamin_5'-phosphate_synthase,_putative_490236..490466_POSITIVE 362 47 4 222 183 NC_009009:SSA_1565|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1569309..1569539_NEGATIVE 345 220 171 206 134 NC_009009:SSA_1694|5end_PTS_system,_lactose-specific_IIA_component,_putative_1687128..1687358_NEGATIVE 341 230 181 57 6 NC_009009:SSA_1070|5end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_1088742..1088972_POSITIVE 340 218 171 177 112 NC_009009:SSA_0825|5end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_803864..804094_POSITIVE 339 229 181 226 168 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 336 237 191 217 156 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 335 222 181 159 110 NC_009009:SSA_1867|5end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1863096..1863326_NEGATIVE 335 237 191 207 156 NC_009009:SSA_1584|5end_Ring-cleavage_extradiol_dioxygenase,_putative_1587030..1587260_NEGATIVE 334 224 181 160 118 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 332 229 181 229 168 NC_009009:SSA_0883|5end_Glycerate_kinase,_putative_877560..877790_POSITIVE 328 220 171 171 124 NC_009009:SSA_1940|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_1927129..1927359_NEGATIVE 325 228 184 47 7 NC_009009:SSA_2296|5end_Transcriptional_regulator,_XRE_family,_putative_2298773..2299003_NEGATIVE 324 217 172 171 116 NC_009009:SSA_0064|5end_hypothetical_protein_66330..66560_POSITIVE 322 225 199 45 15 NC_009009:SSA_1938|5end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1925738..1925968_NEGATIVE 322 219 173 46 1 NC_009009:SSA_0831|5end_Nucleotide_sugar_synthetase-like_protein,_putative_815671..815901_POSITIVE 321 234 199 198 169 NC_009009:SSA_0893|5end_ATP-binding_cassette_transporter-like_protein,_putative_884527..884757_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 224 181 148 110 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 341 230 181 73 22 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 325 228 184 44 4 NC_009009:SSA_2297|3end_hypothetical_protein_2298776..2298926_NEGATIVE 319 245 205 150 111 NC_009009:SSA_1916|3end_hypothetical_protein_1906379..1906529_POSITIVE 317 228 187 146 91 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 314 224 181 150 98 NC_009009:SSA_0892|3end_ATP-binding_cassette_lipoprotein,_putative_884578..884728_POSITIVE 313 225 182 57 5 NC_009009:SSA_1575|3end_Glycosyl_transferase,_putative_1577932..1578082_NEGATIVE 311 228 181 68 7 NC_009009:SSA_1444|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1446644..1446794_NEGATIVE 311 226 185 78 33 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 311 217 171 52 3 NC_009009:SSA_0089|3end_V-type_sodium_ATPase,_subunit_F,_putative_90330..90480_POSITIVE 308 188 147 116 75 NC_009009:SSA_1985|3end_hypothetical_protein_1979623..1979773_NEGATIVE 308 220 174 125 79 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 307 225 185 40 1 NC_009009:SSA_0590|3end_hypothetical_protein_582817..582967_POSITIVE 307 226 181 146 94 NC_009009:SSA_0164|3end_hypothetical_protein_163997..164147_POSITIVE 306 213 173 55 11 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 298 229 181 128 69 NC_009009:SSA_1446|3end_Histidinol_dehydrogenase,_putative_1447898..1448048_NEGATIVE 298 220 173 48 5 NC_009009:SSA_0836|3end_SecA-like_protein,_putative_823969..824119_POSITIVE 296 218 180 150 106 NC_009009:SSA_0789|3end_Proton-translocating_ATPase,_F1_sector,_epsilon_subunit,_putative_772953..773103_POSITIVE 295 223 182 150 103 NC_009009:SSA_2052|3end_Thioredoxin,_putative_2057193..2057343_NEGATIVE 293 219 173 146 88 NC_009009:SSA_0429|3end_Histidine_ammonia-lyase,_putative_429701..429851_NEGATIVE