Origin IGS: gatgaatacctcctcttagattcttgtattcgtttagccggctagttgtgatcagttactaaacatactttactattctatatgattccggggcttttgtcaatacttacttaaataactttctctttgtaaacgtaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttacgtttacaaagagaaagttatttaagtaagtattgacaaaagccccggaatcatatagaatagtaaagtatgtttagtaactgatcacaactagccggctaaacgaatacaagaatctaagaggaggtattcatc Mask Tandem Repeat Region ================================================ gatgaatacctcctcttagattcttgtattcgtttagccggctagttgtgatcagttactaaacatactttactattctatatgattccggggcttttgtcaatacttacttaaataactttctctttgtaaacgtaa Find is-nt database================================================ Query_seq: SSA_2136:SSA_2137|SSA_2136:SSA_2137:50S ribosomal protein L34, putative:hypothetical protein:<-<-:2137732..2137869 138 gatgaatacctcctcttagattcttgtattcgtttagccggctagttgtgatcagttactaaacatactttactattctatatgattccggggcttttgtcaatacttacttaaataactttctctttgtaaacgtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2136:SSA_2137|SSA_2136:SSA_2137:50S ribosomal protein L34, putative:hypothetical protein:<-<-:2137732..2137869 138 gatgaatacctcctcttagattcttgtattcgtttagccggctagttgtgatcagttactaaacatactttactattctatatgattccggggcttttgtcaatacttacttaaataactttctctttgtaaacgtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2136:SSA_2137|SSA_2136:SSA_2137:50S ribosomal protein L34, putative:hypothetical protein:<-<-:2137732..2137869 138 gatgaatacctcctcttagattcttgtattcgtttagccggctagttgtgatcagttactaaacatactttactattctatatgattccggggcttttgtcaatacttacttaaataactttctctttgtaaacgtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgaatacctcctcttagattcttgtattcgtttagccggctagttgtgatcagttactaaacatactttactattctatatgattccggggcttttgtcaatacttacttaaataactttctctttgtaaacgtaa Predict ORF larger than 30AA ================================================ gatgaatacctcctcttagattcttgtattcgtttagccggctagttgtgatcagttactaaacatactttactattctatatgattccggggcttttgtcaatacttacttaaataactttctctttgtaaacgtaa 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: 88 Start: 75 End: 104 ..........................................................................ATTGACAAAAGCCCCGGAATCATATAGAAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatgaatacctcctcttagattcttgtattcgtttagccggctagttgtgatcagttactaaacatactttactattctatatgattccggggcttttgtcaatacttacttaaataactttctctttgtaaacgtaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2136:SSA_2137|SSA_2136:SSA_2137:50S ribosomal protein L34, putative:hypothetical protein:<-<-:2137732..2137869 138 gatgaatacctcctcttagattcttgtattcgtttagccggctagttgtgatcagttactaaacatactttactattctatatgattccggggcttttgtcaatacttacttaaataactttctctttgtaaacgtaa Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: NC_009009_SSA_2136_SSA_2137|50S ribosomal protein L34, putative:hypothetical protein|NEGATIVE:NEGATIVE|[2137732,2137869]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 gatgaatacctcctcttagattcttgtattcgtttagccggctagttgtgatcagttactaaacatactttactattctatatgattccggggcttttgtcaatacttacttaaataactttctctttgtaaacgtaa gatgaatacctcctcttagattcttgtattcgtttagccggctagttgtgatcagttactaaacatactttactattctatatgattccggggcttttgtcaatacttacttaaataactttctctttgtaaacgtaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAAUACCUCCUCUUAGAUUCUUGUAUUCGUUUAGCCGGCUAGUUGUGAUCAGUUACUAAACAUACUUUACUAUUCUAUAUGAUUCCGGGGCUUUUGUCAAUACUUACUUAAAUAACUUUCUCUUUGUAAACGUAA ((..((..((((.((.((((.....((((..((((((..((((.((....)).)))).))))))))))........))))...))....))))..))..))..(((((((..................))))..))). (-18.19) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACGUUUACAAAGAGAAAGUUAUUUAAGUAAGUAUUGACAAAAGCCCCGGAAUCAUAUAGAAUAGUAAAGUAUGUUUAGUAACUGAUCACAACUAGCCGGCUAAACGAAUACAAGAAUCUAAGAGGAGGUAUUCAUC .(((.(((((.........((((.............)))).............((.....))...)))))))).(((((((..(((........)))...)))))))((((((.....(((....))).))))))... (-16.82) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 897 50 1 141 92 NC_009009:SSA_2136|5end_50S_ribosomal_protein_L34,_putative_2137641..2137871_NEGATIVE 303 50 10 143 98 NC_009009:SSA_0179|5end_hypothetical_protein_183966..184196_POSITIVE 296 47 9 151 102 NC_009009:SSA_0124|5end_30S_ribosomal_protein_S5,_putative_116422..116652_POSITIVE 278 60 17 78 38 NC_009009:SSA_1066|5end_ABC-type_oligopeptide_transport_system,_putative_1084335..1084565_POSITIVE 276 46 12 129 95 NC_009009:SSA_0789|5end_Proton-translocating_ATPase,_F1_sector,_epsilon_subunit,_putative_772451..772681_POSITIVE 273 44 2 209 163 NC_009009:SSA_0938|5end_hypothetical_protein_946587..946817_POSITIVE 272 58 15 137 91 NC_009009:SSA_0729|5end_hypothetical_protein_714397..714627_POSITIVE 270 50 9 226 173 NC_009009:SSA_2317|5end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2319410..2319640_NEGATIVE 269 49 1 62 4 NC_009009:SSA_0536|5end_B12-dependent_diol_dehydratase_small_subunit,_putative_531342..531572_POSITIVE 267 47 1 222 175 NC_009009:SSA_0692|5end_D-Ala-D-Ala_adding_enzyme,_putative_676370..676600_POSITIVE 264 57 11 157 97 NC_009009:SSA_2166|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165642..2165872_NEGATIVE 262 59 13 150 97 NC_009009:SSA_1945|5end_Oligopeptide_transport_ATP-binding_protein,_putative_1937689..1937919_NEGATIVE 262 48 8 225 169 NC_009009:SSA_1509|5end_Polysaccharide_biosynthesis_protein/_rhamnosyltransferase,_putative_1514191..1514421_NEGATIVE 262 66 37 209 173 NC_009009:SSA_1206|5end_A/G-specific_adenine_glycosylase,_putative_1231231..1231461_NEGATIVE 261 45 4 229 188 NC_009009:SSA_1680|5end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1675200..1675430_NEGATIVE 261 45 4 230 189 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 257 53 12 58 16 NC_009009:SSA_0558|5end_Conserved_hypothetical_cytosolic_protein,_putative_552335..552565_POSITIVE 254 80 31 60 3 NC_009009:SSA_1188|5end_Ribonuclease_HII,_putative_1216819..1217049_NEGATIVE 253 42 10 132 98 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 252 57 11 214 172 NC_009009:SSA_0831|5end_Nucleotide_sugar_synthetase-like_protein,_putative_815671..815901_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 50 10 150 105 NC_009009:SSA_0178|3end_UDP-N-acetylglucosamine_2-epimerase,_putative_184053..184203_POSITIVE 296 47 9 133 84 NC_009009:SSA_0123|3end_50S_ribosomal_protein_L18P,_putative_116484..116634_POSITIVE 276 46 12 121 87 NC_009009:SSA_0788|3end_Proton-translocating_ATPase,_F1_sector,_beta_subunit,_putative_772523..772673_POSITIVE 267 47 1 146 99 NC_009009:SSA_0691|3end_D-ala,D-ala_ligase,_putative_676374..676524_POSITIVE 265 79 31 63 9 NC_009009:SSA_0535|3end_Propanediol_utilization:_dehydratase,_medium_subunit,_putative_531391..531541_POSITIVE 262 59 13 141 88 NC_009009:SSA_1946|3end_Oligopeptide_transport_system_permease_protein,_putative_1937698..1937848_NEGATIVE 262 66 37 143 107 NC_009009:SSA_1207|3end_Phosphate_acetyltransferase,_putative_1231297..1231447_NEGATIVE 261 49 7 131 88 NC_009009:SSA_1390|3end_hypothetical_protein_1405633..1405783_NEGATIVE 254 80 31 73 16 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 253 42 10 128 94 NC_009009:SSA_2325|3end_3-methyladenine_DNA_glycosylase,_putative_2330113..2330263_NEGATIVE 251 60 11 144 101 NC_009009:SSA_0041|3end_hypothetical_protein_47969..48119_POSITIVE 250 124 86 91 41 NC_009009:SSA_1662|3end_NADH-dependent_oxidoreductase,_putative_1658235..1658385_NEGATIVE 246 45 3 81 47 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 246 48 8 75 30 NC_009009:SSA_0435|3end_Urocanate_hydratase,_putative_436689..436839_NEGATIVE 245 58 32 143 114 NC_009009:SSA_2268|3end_Type_II_secretory_pathway,_pullulanase_PulA_glycosidase,_putative_2269386..2269536_POSITIVE 244 42 2 120 78 NC_009009:SSA_1439|3end_hypothetical_protein_1443624..1443774_NEGATIVE 244 60 12 86 42 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 241 37 8 94 63 NC_009009:SSA_1440|3end_Phosphoribosyl-ATP_pyrophosphohydrolase,_putative_1444407..1444557_NEGATIVE 239 48 6 144 93 NC_009009:SSA_1497|3end_DCMP_deaminase,_putative_1503068..1503218_NEGATIVE 238 47 9 130 86 NC_009009:SSA_1900|3end_N_utilization_substance_protein_A,_putative_1894750..1894900_NEGATIVE