Origin IGS: gggagaggattcaacatcataaaaagctcagaaatgggcggggtatcctaataacatccgaaatataaaatagggcgaaacgatttgtgtagtcgtttcgctctttttttatagtaataaatttagcgttataaatctatctcatgctaatgctagagaaaataaatgattaacagatgaaaaatcaatctaacacaatgatgagtataatgaatttgcttcttactcatttttctgtcatagaaaaaacttactgagatcaaaattaaaagtatggatattaaagttttcagtaaaaaattgaagaaaaataaattcagaagggttaggaaaaataaaaataaacttacgattaatgagattttggagctgccaatcttctttttataagcaaaataggttgaaaataataagagaatggagtaaacaaaagctatatagttcattagatatcctccgtaatctaaagtgatttgtcttaacaatcacaacactgtc .........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.........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 gacagtgttgtgattgttaagacaaatcactttagattacggaggatatctaatgaactatatagcttttgtttactccattctcttattattttcaacctattttgcttataaaaagaagattggcagctccaaaatctcattaatcgtaagtttatttttatttttcctaacccttctgaatttatttttcttcaattttttactgaaaactttaatatccatacttttaattttgatctcagtaagttttttctatgacagaaaaatgagtaagaagcaaattcattatactcatcattgtgttagattgatttttcatctgttaatcatttattttctctagcattagcatgagatagatttataacgctaaatttattactataaaaaaagagcgaaacgactacacaaatcgtttcgccctattttatatttcggatgttattaggataccccgcccatttctgagctttttatgatgttgaatcctctccc Mask Tandem Repeat Region ================================================ gggagaggattcaacatcataaaaagctcagaaatgggcggggtatcctaataacatccgaaatataaaatagggcgaaacgatttgtgtagtcgtttcgctctttttttatagtaataaatttagcgttataaatctatctcatgctaatgctagagaaaataaatgattaacagatgaaaaatcaatctaacacaatgatgagtataatgaatttgcttcttactcatttttctgtcatagaaaaaacttactgagatcaaaattaaaagtatggatattaaagttttcagtaaaaaattgaagaaaaataaattcagaagggttaggaaaaataaaaataaacttacgattaatgagattttggagctgccaatcttctttttataagcaaaataggttgaaaataataagagaatggagtaaacaaaagctatatagttcattagatatcctccgtaatctaaagtgatttgtcttaacaatcacaacactgtc Find is-nt database================================================ Query_seq: SSA_0212:SSA_0213|SSA_0212:SSA_0213:Phenylalanyl-tRNA synthetase, beta subunit, putative:hypothetical protein:-><-:209140..209637 498 gggagaggattcaacatcataaaaagctcagaaatgggcggggtatcctaataacatccgaaatataaaatagggcgaaacgatttgtgtagtcgtttcgctctttttttatagtaataaatttagcgttataaatctatctcatgctaatgctagagaaaataaatgattaacagatgaaaaatcaatctaacacaatgatgagtataatgaatttgcttcttactcatttttctgtcatagaaaaaacttactgagatcaaaattaaaagtatggatattaaagttttcagtaaaaaattgaagaaaaataaattcagaagggttaggaaaaataaaaataaacttacgattaatgagattttggagctgccaatcttctttttataagcaaaataggttgaaaataataagagaatggagtaaacaaaagctatatagttcattagatatcctccgtaatctaaagtgatttgtcttaacaatcacaacactgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0212:SSA_0213|SSA_0212:SSA_0213:Phenylalanyl-tRNA synthetase, beta subunit, putative:hypothetical protein:-><-:209140..209637 498 gggagaggattcaacatcataaaaagctcagaaatgggcggggtatcctaataacatccgaaatataaaatagggcgaaacgatttgtgtagtcgtttcgctctttttttatagtaataaatttagcgttataaatctatctcatgctaatgctagagaaaataaatgattaacagatgaaaaatcaatctaacacaatgatgagtataatgaatttgcttcttactcatttttctgtcatagaaaaaacttactgagatcaaaattaaaagtatggatattaaagttttcagtaaaaaattgaagaaaaataaattcagaagggttaggaaaaataaaaataaacttacgattaatgagattttggagctgccaatcttctttttataagcaaaataggttgaaaataataagagaatggagtaaacaaaagctatatagttcattagatatcctccgtaatctaaagtgatttgtcttaacaatcacaacactgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0212:SSA_0213|SSA_0212:SSA_0213:Phenylalanyl-tRNA synthetase, beta subunit, putative:hypothetical protein:-><-:209140..209637 498 gggagaggattcaacatcataaaaagctcagaaatgggcggggtatcctaataacatccgaaatataaaatagggcgaaacgatttgtgtagtcgtttcgctctttttttatagtaataaatttagcgttataaatctatctcatgctaatgctagagaaaataaatgattaacagatgaaaaatcaatctaacacaatgatgagtataatgaatttgcttcttactcatttttctgtcatagaaaaaacttactgagatcaaaattaaaagtatggatattaaagttttcagtaaaaaattgaagaaaaataaattcagaagggttaggaaaaataaaaataaacttacgattaatgagattttggagctgccaatcttctttttataagcaaaataggttgaaaataataagagaatggagtaaacaaaagctatatagttcattagatatcctccgtaatctaaagtgatttgtcttaacaatcacaacactgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gggagaggattcaacatcataaaaagctcagaaatgggcggggtatcctaataacatccgaaatataaaatagggcgaaacgatttgtgtagtcgtttcgctctttttttatagtaataaatttagcgttataaatctatctcatgctaatgctagagaaaataaatgattaacagatgaaaaatcaatctaacacaatgatgagtataatgaatttgcttcttactcatttttctgtcatagaaaaaacttactgagatcaaaattaaaagtatggatattaaagttttcagtaaaaaattgaagaaaaataaattcagaagggttaggaaaaataaaaataaacttacgattaatgagattttggagctgccaatcttctttttataagcaaaataggttgaaaataataagagaatggagtaaacaaaagctatatagttcattagatatcctccgtaatctaaagtgatttgtcttaacaatcacaacactgtc Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 259 End: 387 .................................................................................................................................................................................................................................................................. M K I K S M D I K V F S K K L K K N K F R R V R K N K N K L T I N E I L E L P I F F L ............................................................................................................... Protein_Len: 53 Strand: + Start: 311 End: 469 ...................................................................................................................................................................................................................................................................................................................... M N S E G L G K I K I N L R L M R F W S C Q S S F Y K Q N R L K I I R E W S K Q K L Y S S L D I L R N L K ............................. Protein_Len: 34 Strand: - Start: 388 End: 489 ................................................................................................................................................................................................................................................................................................................................................................................................... L C F L N F I I L S H L L C F S Y L E N S I R R L R F H N T K V I M ......... Protein_Len: 39 Strand: - Start: 241 End: 357 ................................................................................................................................................................................................................................................ L F F K S L D F N F T H I N F N E T F F Q L F I F E S P N P F I F I F K R N M ............................................................................................................................................. Protein_Len: 60 Strand: - Start: 156 End: 485 ........................................................................................................................................................... F F L N L L T L F F L F L S V I L S I K S S G I K K K Y A F Y T S F L L L I S Y V F A I Y N M L Y G G Y D L T I Q R L M ............. Protein_Len: 39 Strand: - Start: 20 End: 136 ................... L F S L F P R P I R I V D S I Y F L A F R N T Y D N R E K K I T I F K A N Y M .......................................................................................................................................................................................................................................................................................................................................................................... gggagaggattcaacatcataaaaagctcagaaatgggcggggtatcctaataacatccgaaatataaaatagggcgaaacgatttgtgtagtcgtttcgctctttttttatagtaataaatttagcgttataaatctatctcatgctaatgctagagaaaataaatgattaacagatgaaaaatcaatctaacacaatgatgagtataatgaatttgcttcttactcatttttctgtcatagaaaaaacttactgagatcaaaattaaaagtatggatattaaagttttcagtaaaaaattgaagaaaaataaattcagaagggttaggaaaaataaaaataaacttacgattaatgagattttggagctgccaatcttctttttataagcaaaataggttgaaaataataagagaatggagtaaacaaaagctatatagttcattagatatcctccgtaatctaaagtgatttgtcttaacaatcacaacactgtc 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================================================ gggagaggattcaacatcataaaaagctcagaaatgggcggggtatcctaataacatccgaaatataaaatagggcgaaacgatttgtgtagtcgtttcgctctttttttatagtaataaatttagcgttataaatctatctcatgctaatgctagagaaaataaatgattaacagatgaaaaatcaatctaacacaatgatgagtataatgaatttgcttcttactcatttttctgtcatagaaaaaacttactgagatcaaaattaaaagtatggatattaaagttttcagtaaaaaattgaagaaaaataaattcagaagggttaggaaaaataaaaataaacttacgattaatgagattttggagctgccaatcttctttttataagcaaaataggttgaaaataataagagaatggagtaaacaaaagctatatagttcattagatatcctccgtaatctaaagtgatttgtcttaacaatcacaacactgtc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 75 HP_score: -5.7 Tail_Score: -4.79451 Start: 71 End: 105 Full_Region: ttattactataaaaa aagagcgaaacgact acaca aatcgtttcgcccta ttttatatttcggat ......................................................................aagagcgaaacgactacacaaatcgtttcgcccta......................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -12.7 Tail_Score: -5.67967 Start: 73 End: 103 Full_Region: CCGAAATATAAAATA GGGCGAAACGATT TGTGT AGTCGTTTCGCTC TTTTTTTATAGTAAT ........................................................................GGGCGAAACGATTTGTGTAGTCGTTTCGCTC........................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 78 HP_score: -8.3 Tail_Score: -4.00843 Start: 73 End: 103 Full_Region: attactataaaaaaa gagcgaaacgact acaca aatcgtttcgccc tattttatatttcgg ........................................................................gagcgaaacgactacacaaatcgtttcgccc........................................................................................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0212:SSA_0213|SSA_0212:SSA_0213:Phenylalanyl-tRNA synthetase, beta subunit, putative:hypothetical protein:-><-:209140..209637 498 gggagaggattcaacatcataaaaagctcagaaatgggcggggtatcctaataacatccgaaatataaaatagggcgaaacgatttgtgtagtcgtttcgctctttttttatagtaataaatttagcgttataaatctatctcatgctaatgctagagaaaataaatgattaacagatgaaaaatcaatctaacacaatgatgagtataatgaatttgcttcttactcatttttctgtcatagaaaaaacttactgagatcaaaattaaaagtatggatattaaagttttcagtaaaaaattgaagaaaaataaattcagaagggttaggaaaaataaaaataaacttacgattaatgagattttggagctgccaatcttctttttataagcaaaataggttgaaaataataagagaatggagtaaacaaaagctatatagttcattagatatcctccgtaatctaaagtgatttgtcttaacaatcacaacactgtc Intra-Species Hit: Count: 1 Min: 1 Max: 498 Len: 498 Subject: NC_009009_SSA_0212_SSA_0213|Phenylalanyl-tRNA synthetase, beta subunit, putative:hypothetical protein|POSITIVE:NEGATIVE|[209140,209637]|498 HSP 1 e-value: 1.0E-133 bit: 476.0 Len: 261 Query Start:1 Query End:261 Subject Strand: POSITIVE Subject Start: 1 Subject End: 261 gggagaggattcaacatcataaaaagctcagaaatgggcggggtatcctaataacatccgaaatataaaatagggcgaaacgatttgtgtagtcgtttcgctcnnnnnnnatagtaataaatttagcgttataaatctatctcatgctaatgctagagaaaataaatgattaacagatgaaaaatcaatctaacacaatgatgagtataatgaatttgcttcttactcatttttctgtcatagaaaaaacttactgagatc............................................................................................................................................................................................................................................. gggagaggattcaacatcataaaaagctcagaaatgggcggggtatcctaataacatccgaaatataaaatagggcgaaacgatttgtgtagtcgtttcgctctttttttatagtaataaatttagcgttataaatctatctcatgctaatgctagagaaaataaatgattaacagatgaaaaatcaatctaacacaatgatgagtataatgaatttgcttcttactcatttttctgtcatagaaaaaacttactgagatc............................................................................................................................................................................................................................................. HSP 2 e-value: 3.0E-81 bit: 303.0 Len: 153 Query Start:346 Query End:498 Subject Strand: POSITIVE Subject Start: 346 Subject End: 498 .........................................................................................................................................................................................................................................................................................................................................................cttacgattaatgagattttggagctgccaatcttctttttataagcaaaataggttgaaaataataagagaatggagtaaacaaaagctatatagttcattagatatcctccgtaatctaaagtgatttgtcttaacaatcacaacactgtc .........................................................................................................................................................................................................................................................................................................................................................cttacgattaatgagattttggagctgccaatcttctttttataagcaaaataggttgaaaataataagagaatggagtaaacaaaagctatatagttcattagatatcctccgtaatctaaagtgatttgtcttaacaatcacaacactgtc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAGAGGAUUCAACAUCAUAAAAAGCUCAGAAAUGGGCGGGGUAUCCUAAUAACAUCCGAAAUAUAAAAUAGGGCGAAACGAUUUGUGUAGUCGUUUCGCUCUUUUUUUAUAGUAAUAAAUUUAGCGUUAUAAAUCUAUCUCAUGCUAAUGCUAGAGAAAAUAAAUGAUUAACAGAUGAAAAAUCAAUCUAACACAAUGAUGAGUAUAAUGAAUUUGCUUCUUACUCAUUUUUCUGUCAUAGAAAAAACUUACUGAGAUCAAAAUUAAAAGUAUGGAUAUUAAAGUUUUCAGUAAAAAAUUGAAGAAAAAUAAAUUCAGAAGGGUUAGGAAAAAUAAAAAUAAACUUACGAUUAAUGAGAUUUUGGAGCUGCCAAUCUUCUUUUUAUAAGCAAAAUAGGUUGAAAAUAAUAAGAGAAUGGAGUAAACAAAAGCUAUAUAGUUCAUUAGAUAUCCUCCGUAAUCUAAAGUGAUUUGUCUUAACAAUCACAACACUGUC ..(.((((((((..((((((.....(((((....)))))...............((((.(...(((((((.((((((((((((((.....))))))))))))))..)))))))........((((((((((................))))))))))................).))))..................))))))....(((((((((.((((.((((((..((((((...........(((((((..(((((...(((((..(((.(..((((....((((((((.....))))))))......(((((....)))))............))))..).)))..)))))..)))))..).(((..................)))....))))))..........))))))..))))))....)))).....))))))))))).)))))))..........((((((.((....))))))))......... (-107.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAGUGUUGUGAUUGUUAAGACAAAUCACUUUAGAUUACGGAGGAUAUCUAAUGAACUAUAUAGCUUUUGUUUACUCCAUUCUCUUAUUAUUUUCAACCUAUUUUGCUUAUAAAAAGAAGAUUGGCAGCUCCAAAAUCUCAUUAAUCGUAAGUUUAUUUUUAUUUUUCCUAACCCUUCUGAAUUUAUUUUUCUUCAAUUUUUUACUGAAAACUUUAAUAUCCAUACUUUUAAUUUUGAUCUCAGUAAGUUUUUUCUAUGACAGAAAAAUGAGUAAGAAGCAAAUUCAUUAUACUCAUCAUUGUGUUAGAUUGAUUUUUCAUCUGUUAAUCAUUUAUUUUCUCUAGCAUUAGCAUGAGAUAGAUUUAUAACGCUAAAUUUAUUACUAUAAAAAAAGAGCGAAACGACUACACAAAUCGUUUCGCCCUAUUUUAUAUUUCGGAUGUUAUUAGGAUACCCCGCCCAUUUCUGAGCUUUUUAUGAUGUUGAAUCCUCUCCC .....((..((((((((....)).))))))..))......(((((((...................(((((....(((((.((((((.((((...(((......)))...)))).))).))).))).))...)))))..(((...((((((((..............((((((..(((((..(((((((((((((((....((((((((.((..((((...........))))..))....)))))))).........))).)))))))))))).)))))...((((......(((((....((((((((.(((((...(....)..))))).........))))))))....))))).((((((((......))))))))....(((((((..((.(((((((((.........))))))))).)).)))))))....))))....))))))......((.((....)).))..))))))))..))))))))))... (-92.02) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 48 4 196 149 NC_009009:SSA_0250|5end_GTP_pyrophosphokinase,_putative_242167..242397_POSITIVE 277 76 35 210 175 NC_009009:SSA_0320|5end_hypothetical_protein_313406..313636_POSITIVE 270 49 8 230 193 NC_009009:SSA_0459|5end_hypothetical_protein_462098..462328_POSITIVE 263 43 1 202 169 NC_009009:SSA_2211|5end_Transmembrane_protein,_putative_2212473..2212703_NEGATIVE 262 257 215 217 182 NC_009009:SSA_2067|5end_hypothetical_protein_2070254..2070484_POSITIVE 262 49 26 58 36 NC_009009:SSA_0346|5end_hypothetical_protein_339448..339678_POSITIVE 260 112 73 108 64 NC_009009:SSA_0173|5end_23S_rRNA_m1G745_methyltransferase,_putative_170535..170765_NEGATIVE 258 458 413 188 141 NC_009009:SSA_1106|5end_IgA-specific_metalloendopeptidase_1125974..1126204_POSITIVE 251 388 341 113 53 NC_009009:SSA_1724|5end_CBS_domain_protein,_putative_1710553..1710783_NEGATIVE 251 49 2 174 118 NC_009009:SSA_0207|5end_hypothetical_protein_204430..204660_POSITIVE 248 47 1 53 6 NC_009009:SSA_1597|5end_hypothetical_protein_1604235..1604465_NEGATIVE 248 45 25 137 110 NC_009009:SSA_1364|5end_hypothetical_protein_1381297..1381527_NEGATIVE 243 119 73 186 151 NC_009009:SSA_1410|5end_DTDP-4-keto-6-deoxyglucose-3,5-epimerase,_putative_1423086..1423316_NEGATIVE 243 54 11 57 10 NC_009009:SSA_0679|5end_DNA_repair_and_genetic_recombination,_putative_660714..660944_POSITIVE 241 50 1 186 139 NC_009009:SSA_2045|5end_Reductase,_putative_2048948..2049178_NEGATIVE 239 105 70 70 24 NC_009009:SSA_1719|5end_Conserved_uncharacterized_protein_1706793..1707023_NEGATIVE 239 108 63 148 93 NC_009009:SSA_1162|5end_Possible_fimbrial_assembly_protein_fimC,_putative_1189250..1189480_NEGATIVE 239 49 1 77 34 NC_009009:SSA_0233|5end_Permease,_putative_227203..227433_POSITIVE 238 127 81 82 43 NC_009009:SSA_1104|5end_50S_ribosomal_protein_L10,_putative_1124743..1124973_POSITIVE 237 65 23 84 51 NC_009009:SSA_1488|5end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_1494657..1494887_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 110 65 91 49 NC_009009:SSA_1172|3end_hypothetical_protein_1199288..1199438_NEGATIVE 319 48 4 64 17 NC_009009:SSA_0249|3end_hypothetical_protein_242115..242265_POSITIVE 286 48 3 151 102 NC_009009:SSA_1065|3end_Beta-hexosamidase_A,_putative_1084130..1084280_POSITIVE 282 108 63 81 32 NC_009009:SSA_1278|3end_Rhodanese-like_domain_protein,_putative_1299563..1299713_NEGATIVE 279 224 181 82 41 NC_009009:SSA_1616|3end_PhoH-like_protein,_putative_1619356..1619506_NEGATIVE 270 49 8 151 114 NC_009009:SSA_0458|3end_Formylmethionine_deformylase,_putative_462099..462249_POSITIVE 265 42 1 70 20 NC_009009:SSA_0144|3end_Transcriptional_regulator,_TetR_family,_putative_137993..138143_NEGATIVE 263 43 1 48 15 NC_009009:SSA_2212|3end_Possible_polysaccharide_transport_protein,_putative_2212627..2212777_NEGATIVE 262 230 184 126 82 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 260 47 1 66 7 NC_009009:SSA_1533|3end_Glutathione_reductase,_putative_1542212..1542362_POSITIVE 257 43 1 82 29 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE 248 45 25 82 55 NC_009009:SSA_1365|3end_FmtA-like_protein,_putative_1381352..1381502_NEGATIVE 245 44 18 88 57 NC_009009:SSA_1357|3end_hypothetical_protein_1372077..1372227_NEGATIVE 243 54 11 48 1 NC_009009:SSA_0678|3end_Transcriptional_regulator,_ArgR_family,_putative_660785..660935_POSITIVE 239 105 70 67 21 NC_009009:SSA_1720|3end_Initiation-control_protein,_putative_1706796..1706946_NEGATIVE 239 108 63 62 7 NC_009009:SSA_1163|3end_GMP_synthase_[glutamine-hydrolyzing],_putative_1189336..1189486_NEGATIVE 239 49 1 71 28 NC_009009:SSA_0232|3end_hypothetical_protein_227277..227427_POSITIVE 236 489 453 86 46 NC_009009:SSA_1313|3end_hypothetical_protein_1329715..1329865_NEGATIVE 235 110 73 148 114 NC_009009:SSA_1009|3end_Galactose-1-phosphate-uridylyltransferase,_putative_1012815..1012965_POSITIVE 234 61 23 49 6 NC_009009:SSA_0874|3end_hypothetical_protein_868995..869145_POSITIVE