Origin IGS: acactctcctatctcattgcatatattctagtatatcagtaaagctgtcttaaaacaacgtttatatcaatgcaaatcgtatttctgaccgatgaaaatccaagcacagcttttgaatactcctatcctcaaaatttcaatacaagattacaactgataaaaggaaaagccctattcaagacagggctctttca .........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 tgaaagagccctgtcttgaatagggcttttccttttatcagttgtaatcttgtattgaaattttgaggataggagtattcaaaagctgtgcttggattttcatcggtcagaaatacgatttgcattgatataaacgttgttttaagacagctttactgatatactagaatatatgcaatgagataggagagtgt Mask Tandem Repeat Region ================================================ acactctcctatctcattgcatatattctagtatatcagtaaagctgtcttaaaacaacgtttatatcaatgcaaatcgtatttctgaccgatgaaaatccaagcacagcttttgaatactcctatcctcaaaatttcaatacaagattacaactgataaaaggaaaagccctattcaagacagggctctttca Find is-nt database================================================ Query_seq: SSA_2234:SSA_2235|SSA_2234:SSA_2235:Phosphatidylserine/phosphatidylglycerophosphate/ cardiolipin synthase, phospholipase D family, putative:Conserved uncharacterized protein:<-<-:2234867..2235060 194 acactctcctatctcattgcatatattctagtatatcagtaaagctgtcttaaaacaacgtttatatcaatgcaaatcgtatttctgaccgatgaaaatccaagcacagcttttgaatactcctatcctcaaaatttcaatacaagattacaactgataaaaggaaaagccctattcaagacagggctctttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2234:SSA_2235|SSA_2234:SSA_2235:Phosphatidylserine/phosphatidylglycerophosphate/ cardiolipin synthase, phospholipase D family, putative:Conserved uncharacterized protein:<-<-:2234867..2235060 194 acactctcctatctcattgcatatattctagtatatcagtaaagctgtcttaaaacaacgtttatatcaatgcaaatcgtatttctgaccgatgaaaatccaagcacagcttttgaatactcctatcctcaaaatttcaatacaagattacaactgataaaaggaaaagccctattcaagacagggctctttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2234:SSA_2235|SSA_2234:SSA_2235:Phosphatidylserine/phosphatidylglycerophosphate/ cardiolipin synthase, phospholipase D family, putative:Conserved uncharacterized protein:<-<-:2234867..2235060 194 acactctcctatctcattgcatatattctagtatatcagtaaagctgtcttaaaacaacgtttatatcaatgcaaatcgtatttctgaccgatgaaaatccaagcacagcttttgaatactcctatcctcaaaatttcaatacaagattacaactgataaaaggaaaagccctattcaagacagggctctttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acactctcctatctcattgcatatattctagtatatcagtaaagctgtcttaaaacaacgtttatatcaatgcaaatcgtatttctgaccgatgaaaatccaagcacagcttttgaatactcctatcctcaaaatttcaatacaagattacaactgataaaaggaaaagccctattcaagacagggctctttca Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 64 End: 192 ............................................................... M S M Q I V F L T D E N P S T A F E Y S Y P Q N F N T R L Q L I K G K A L F K T G L F .. acactctcctatctcattgcatatattctagtatatcagtaaagctgtcttaaaacaacgtttatatcaatgcaaatcgtatttctgaccgatgaaaatccaagcacagcttttgaatactcctatcctcaaaatttcaatacaagattacaactgataaaaggaaaagccctattcaagacagggctctttca 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================================================ acactctcctatctcattgcatatattctagtatatcagtaaagctgtcttaaaacaacgtttatatcaatgcaaatcgtatttctgaccgatgaaaatccaagcacagcttttgaatactcctatcctcaaaatttcaatacaagattacaactgataaaaggaaaagccctattcaagacagggctctttca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2234:SSA_2235|SSA_2234:SSA_2235:Phosphatidylserine/phosphatidylglycerophosphate/ cardiolipin synthase, phospholipase D family, putative:Conserved uncharacterized protein:<-<-:2234867..2235060 194 acactctcctatctcattgcatatattctagtatatcagtaaagctgtcttaaaacaacgtttatatcaatgcaaatcgtatttctgaccgatgaaaatccaagcacagcttttgaatactcctatcctcaaaatttcaatacaagattacaactgataaaaggaaaagccctattcaagacagggctctttca Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: NC_009009_SSA_2234_SSA_2235|Phosphatidylserine/phosphatidylglycerop hosphate/ cardiolipin synthase, phospholipase D family, putative:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[2234867,2235060]|194 HSP 1 e-value: 1.0E-106 bit: 385.0 Len: 194 Query Start:1 Query End:194 Subject Strand: POSITIVE Subject Start: 1 Subject End: 194 acactctcctatctcattgcatatattctagtatatcagtaaagctgtcttaaaacaacgtttatatcaatgcaaatcgtatttctgaccgatgaaaatccaagcacagcttttgaatactcctatcctcaaaatttcaatacaagattacaactgataaaaggaaaagccctattcaagacagggctctttca acactctcctatctcattgcatatattctagtatatcagtaaagctgtcttaaaacaacgtttatatcaatgcaaatcgtatttctgaccgatgaaaatccaagcacagcttttgaatactcctatcctcaaaatttcaatacaagattacaactgataaaaggaaaagccctattcaagacagggctctttca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACACUCUCCUAUCUCAUUGCAUAUAUUCUAGUAUAUCAGUAAAGCUGUCUUAAAACAACGUUUAUAUCAAUGCAAAUCGUAUUUCUGACCGAUGAAAAUCCAAGCACAGCUUUUGAAUACUCCUAUCCUCAAAAUUUCAAUACAAGAUUACAACUGAUAAAAGGAAAAGCCCUAUUCAAGACAGGGCUCUUUCA .................................(((((((.((((((((((.................(((((.....))))).......(((....))).))).)))))))(((((..................)))))............)))))))...((((.((((((.........)))))).)))). (-32.77) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAGAGCCCUGUCUUGAAUAGGGCUUUUCCUUUUAUCAGUUGUAAUCUUGUAUUGAAAUUUUGAGGAUAGGAGUAUUCAAAAGCUGUGCUUGGAUUUUCAUCGGUCAGAAAUACGAUUUGCAUUGAUAUAAACGUUGUUUUAAGACAGCUUUACUGAUAUACUAGAAUAUAUGCAAUGAGAUAGGAGAGUGU ...(((((((((((.....))))))))))).((((((((.((((((.(((.(((.(((((.((..((.((((.............)))).))..)).)))))...(((((.....((((....))))........((((((....))))))....))))).))).))).....))))))..))))))))..... (-49.92) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 876 130 81 221 172 NC_009009:SSA_2234|5end_Phosphatidylserine/phosphatidylglycerophosphate/_cardiolipin_synthase,_phospholipase_D_family,_putative_2234776..2235006_NEGATIVE 306 188 145 186 135 NC_009009:SSA_1057|5end_Aminotransferase,_class-V,_putative_1073771..1074001_POSITIVE 300 190 144 83 33 NC_009009:SSA_1638|5end_hypothetical_protein_1641325..1641555_NEGATIVE 284 190 142 165 121 NC_009009:SSA_1305|5end_hypothetical_protein_1324079..1324309_NEGATIVE 277 138 99 172 124 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 272 49 3 145 98 NC_009009:SSA_0929|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938438..938668_POSITIVE 264 48 1 146 101 NC_009009:SSA_0019|5end_Secreted_antigen_GbpB/SagA;_peptidoglycan_hydrolase;_PcsB_protein_precursor,_putative_24225..24455_POSITIVE 263 50 5 151 99 NC_009009:SSA_2132|5end_Ure_cluster_protein,_putative_2134170..2134400_POSITIVE 262 138 93 60 20 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 261 116 77 85 39 NC_009009:SSA_0449|5end_Aminopeptidase_P;_XAA-pro_aminopeptidase,_putative_449464..449694_POSITIVE 259 128 86 214 177 NC_009009:SSA_0251|5end_D-tyrosyl-tRNA(Tyr)_deacylase,_putative_244455..244685_POSITIVE 255 49 2 137 89 NC_009009:SSA_1143|5end_Na+-driven_multidrug_efflux_pump,_putative_1173497..1173727_NEGATIVE 254 38 9 127 94 NC_009009:SSA_1110|5end_hypothetical_protein_1135551..1135781_POSITIVE 250 190 154 215 177 NC_009009:SSA_1994|5end_CTP_synthase,_putative_1992474..1992704_NEGATIVE 244 185 146 174 134 NC_009009:SSA_1323|5end_hypothetical_protein_1340450..1340680_NEGATIVE 243 128 83 203 154 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 241 115 78 79 41 NC_009009:SSA_2353|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2355302..2355532_NEGATIVE 241 49 2 136 79 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 240 127 81 83 18 NC_009009:SSA_0172|5end_Transcriptional_regulator,_XRE_family,_putative_169140..169370_POSITIVE 239 130 82 58 12 NC_009009:SSA_0099|5end_hypothetical_protein_100619..100849_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 188 145 85 34 NC_009009:SSA_1056|3end_Firmicute_fructose-1,6-bisphosphatase,_putative_1073750..1073900_POSITIVE 300 190 144 69 19 NC_009009:SSA_1639|3end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase,_putative_1641339..1641489_NEGATIVE 277 138 99 103 55 NC_009009:SSA_1618|3end_hypothetical_protein_1620720..1620870_NEGATIVE 266 187 142 147 108 NC_009009:SSA_1065|3end_Beta-hexosamidase_A,_putative_1084130..1084280_POSITIVE 264 48 1 49 4 NC_009009:SSA_0018|3end_Cell-shape_determining_protein_MreD,_putative_24208..24358_POSITIVE 263 50 5 148 96 NC_009009:SSA_2131|3end_DNA-binding_protein,_putative_2134247..2134397_POSITIVE 259 128 86 145 108 NC_009009:SSA_0250|3end_GTP_pyrophosphokinase,_putative_244466..244616_POSITIVE 254 38 9 72 39 NC_009009:SSA_1109|3end_ABC_transporter_ATP_binding/permease_protein,_putative_1135576..1135726_POSITIVE 245 50 3 149 105 NC_009009:SSA_0928|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938525..938675_POSITIVE 241 49 2 126 69 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 234 46 4 80 39 NC_009009:SSA_1546|3end_Prolipoprotein_diacylglyceryl_transferase,_putative_1549267..1549417_NEGATIVE 230 187 144 50 1 NC_009009:SSA_2369|3end_hypothetical_protein_2370239..2370389_NEGATIVE 230 188 159 32 2 NC_009009:SSA_0611|3end_HtpX_protease,_putative_600515..600665_POSITIVE 229 130 81 147 93 NC_009009:SSA_0582|3end_Methylase,_putative_574583..574733_POSITIVE 227 188 155 44 5 NC_009009:SSA_1829|3end_RNA_methyltransferase,_putative_1818959..1819109_NEGATIVE 226 110 61 138 84 NC_009009:SSA_1722|3end_Thymidylate_kinase,_putative_1708025..1708175_NEGATIVE 226 127 81 148 101 NC_009009:SSA_1121|3end_Cytochrome_C-type_biogenesis_protein,_putative_1147936..1148086_POSITIVE 225 50 5 56 3 NC_009009:SSA_1932|3end_Biotin_carboxylase,_putative_1919507..1919657_NEGATIVE 225 190 148 76 29 NC_009009:SSA_0433|3end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435028..435178_NEGATIVE 223 190 157 69 24 NC_009009:SSA_1453|3end_hypothetical_protein_1459897..1460047_NEGATIVE