Origin IGS: aaaccttattttatcaccttatttaggtgcagacaagaaagtaccctatttcctgtctgatttttagttatttttaagaaaaagggtatattaaatagccttttaaagccctctgcagcaagttttatccgacactgcctatttccaaagtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aactttggaaataggcagtgtcggataaaacttgctgcagagggctttaaaaggctatttaatataccctttttcttaaaaataactaaaaatcagacaggaaatagggtactttcttgtctgcacctaaataaggtgataaaataaggttt Mask Tandem Repeat Region ================================================ aaaccttattttatcaccttatttaggtgcagacaagaaagtaccctatttcctgtctgatttttagttatttttaagaaaaagggtatattaaatagccttttaaagccctctgcagcaagttttatccgacactgcctatttccaaagtt Find is-nt database================================================ Query_seq: SSA_2209:SSA_2210|SSA_2209:SSA_2210:Penicillin-binding protein 2A, putative:Ribosomal large subunit pseudouridine synthase D, putative:<-->:2210463..2210614 152 aaaccttattttatcaccttatttaggtgcagacaagaaagtaccctatttcctgtctgatttttagttatttttaagaaaaagggtatattaaatagccttttaaagccctctgcagcaagttttatccgacactgcctatttccaaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2209:SSA_2210|SSA_2209:SSA_2210:Penicillin-binding protein 2A, putative:Ribosomal large subunit pseudouridine synthase D, putative:<-->:2210463..2210614 152 aaaccttattttatcaccttatttaggtgcagacaagaaagtaccctatttcctgtctgatttttagttatttttaagaaaaagggtatattaaatagccttttaaagccctctgcagcaagttttatccgacactgcctatttccaaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2209:SSA_2210|SSA_2209:SSA_2210:Penicillin-binding protein 2A, putative:Ribosomal large subunit pseudouridine synthase D, putative:<-->:2210463..2210614 152 aaaccttattttatcaccttatttaggtgcagacaagaaagtaccctatttcctgtctgatttttagttatttttaagaaaaagggtatattaaatagccttttaaagccctctgcagcaagttttatccgacactgcctatttccaaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaccttattttatcaccttatttaggtgcagacaagaaagtaccctatttcctgtctgatttttagttatttttaagaaaaagggtatattaaatagccttttaaagccctctgcagcaagttttatccgacactgcctatttccaaagtt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 9 End: 128 ........ K I V K N L H L C S L V R N G T Q N K T I K L F F P I N F L R K F G E A A L K M ........................ aaaccttattttatcaccttatttaggtgcagacaagaaagtaccctatttcctgtctgatttttagttatttttaagaaaaagggtatattaaatagccttttaaagccctctgcagcaagttttatccgacactgcctatttccaaagtt 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: 81 Start: 8 End: 37 .......CTTGTCTGCACCTAAATAAGGTGATAAAAT................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaccttattttatcaccttatttaggtgcagacaagaaagtaccctatttcctgtctgatttttagttatttttaagaaaaagggtatattaaatagccttttaaagccctctgcagcaagttttatccgacactgcctatttccaaagtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2209:SSA_2210|SSA_2209:SSA_2210:Penicillin-binding protein 2A, putative:Ribosomal large subunit pseudouridine synthase D, putative:<-->:2210463..2210614 152 aaaccttattttatcaccttatttaggtgcagacaagaaagtaccctatttcctgtctgatttttagttatttttaagaaaaagggtatattaaatagccttttaaagccctctgcagcaagttttatccgacactgcctatttccaaagtt Intra-Species Hit: Count: 1 Min: 1 Max: 152 Len: 152 Subject: NC_009009_SSA_2209_SSA_2210|Penicillin-binding protein 2A, putative:Ribosomal large subunit pseudouridine synthase D, putative|NEGATIVE:POSITIVE|[2210463,2210614]|152 HSP 1 e-value: 3.0E-81 bit: 301.0 Len: 152 Query Start:1 Query End:152 Subject Strand: POSITIVE Subject Start: 1 Subject End: 152 aaaccttattttatcaccttatttaggtgcagacaagaaagtaccctatttcctgtctgatttttagttatttttaagaaaaagggtatattaaatagccttttaaagccctctgcagcaagttttatccgacactgcctatttccaaagtt aaaccttattttatcaccttatttaggtgcagacaagaaagtaccctatttcctgtctgatttttagttatttttaagaaaaagggtatattaaatagccttttaaagccctctgcagcaagttttatccgacactgcctatttccaaagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACCUUAUUUUAUCACCUUAUUUAGGUGCAGACAAGAAAGUACCCUAUUUCCUGUCUGAUUUUUAGUUAUUUUUAAGAAAAAGGGUAUAUUAAAUAGCCUUUUAAAGCCCUCUGCAGCAAGUUUUAUCCGACACUGCCUAUUUCCAAAGUU ..............(((((.....)))))((((((.((((........)))).)))))).(((((((......)))))))..(((((...(((((......))))).)))))..((((...(((......))).)))).............. (-27.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUUUGGAAAUAGGCAGUGUCGGAUAAAACUUGCUGCAGAGGGCUUUAAAAGGCUAUUUAAUAUACCCUUUUUCUUAAAAAUAACUAAAAAUCAGACAGGAAAUAGGGUACUUUCUUGUCUGCACCUAAAUAAGGUGAUAAAAUAAGGUUU (((((((((((.(((..((((..((((...(((...((.....)).....)))..))))..))))..))).))))..................(((((((((((........)))))))))))(((((.....)))))......))))))). (-33.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 907 140 91 231 182 NC_009009:SSA_2209|5end_Penicillin-binding_protein_2A,_putative_2210372..2210602_NEGATIVE 320 140 96 158 109 NC_009009:SSA_1681|5end_ABC-type_bacitracin_resistance_protein_A,_ATPase_component,_putative_1675960..1676190_NEGATIVE 306 139 95 49 8 NC_009009:SSA_0893|5end_ATP-binding_cassette_transporter-like_protein,_putative_884527..884757_POSITIVE 291 141 107 66 35 NC_009009:SSA_1298|5end_Maltose/maltodextrin_ABC_transporter,_sugar-binding_protein_MalX,_putative_1315291..1315521_POSITIVE 289 138 96 65 24 NC_009009:SSA_0083|5end_hypothetical_protein_85437..85667_POSITIVE 284 140 97 61 24 NC_009009:SSA_1374|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393095..1393325_NEGATIVE 281 128 81 195 136 NC_009009:SSA_0197|5end_Dihydropteroate_synthase,_putative_195946..196176_POSITIVE 279 148 109 64 11 NC_009009:SSA_1417|5end_SAM-dependent_methyltransferase,_putative_1427993..1428223_NEGATIVE 277 138 98 59 22 NC_009009:SSA_0923|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933010..933240_POSITIVE 276 115 95 158 139 NC_009009:SSA_1648|5end_hypothetical_protein_1647909..1648139_NEGATIVE 276 149 103 84 33 NC_009009:SSA_0647|5end_hypothetical_protein_630998..631228_POSITIVE 272 139 96 225 178 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 269 139 101 53 19 NC_009009:SSA_1981|5end_hypothetical_protein_1975421..1975651_NEGATIVE 267 140 95 75 11 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 266 149 101 200 153 NC_009009:SSA_2300|5end_hypothetical_protein_2302508..2302738_NEGATIVE 264 138 97 60 17 NC_009009:SSA_0463|5end_Cobyrinic_acid_A,C-diamide_synthase,_putative_466865..467095_POSITIVE 262 138 95 217 182 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 259 141 107 51 14 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 258 145 106 216 167 NC_009009:SSA_1470|5end_3-dehydroquinate_dehydratase,_putative_1476984..1477214_NEGATIVE 257 139 98 229 182 NC_009009:SSA_0758|5end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_740636..740866_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 140 97 71 34 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 276 149 103 82 31 NC_009009:SSA_0646|3end_hypothetical_protein_631076..631226_POSITIVE 269 129 83 92 52 NC_009009:SSA_2122|3end_hypothetical_protein_2127200..2127350_NEGATIVE 269 139 101 47 13 NC_009009:SSA_1982|3end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975427..1975577_NEGATIVE 263 140 97 145 94 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 254 142 109 72 32 NC_009009:SSA_0388|3end_Mismatch_repair_ATPase_(MutS_family),_putative_384248..384398_POSITIVE 252 150 109 66 28 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 249 139 96 61 6 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 248 150 110 74 35 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 247 139 96 64 22 NC_009009:SSA_0211|3end_hypothetical_protein_208456..208606_POSITIVE 245 138 99 42 9 NC_009009:SSA_2282|3end_Phage_infection_protein,_putative_2282377..2282527_NEGATIVE 241 145 108 64 35 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 240 137 97 131 99 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 240 140 98 97 51 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 239 139 96 126 78 NC_009009:SSA_2287|3end_50S_ribosomal_protein_L32,_putative_2290083..2290233_POSITIVE 239 138 99 69 23 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 239 58 13 106 45 NC_009009:SSA_0367|3end_hypothetical_protein_359291..359441_POSITIVE 236 131 97 58 12 NC_009009:SSA_1923|3end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912120..1912270_NEGATIVE 235 148 107 68 21 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 234 147 102 110 66 NC_009009:SSA_1952|3end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1948212..1948362_NEGATIVE