Origin IGS: cttctcatctcactttcacctcgatatatcgaaccttgatataaaaaaattatatcgcagttcgatatagttgtcaaggatttataaatattttttacaaaaaatgattcatttttatctatcaatgcttcagctaaagctgctttaagtcagaagcataagtgattatagacctacatcctgataaatcagcataaaaaagccaggaacacctgacttactttt .........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 aaaagtaagtcaggtgttcctggcttttttatgctgatttatcaggatgtaggtctataatcacttatgcttctgacttaaagcagctttagctgaagcattgatagataaaaatgaatcattttttgtaaaaaatatttataaatccttgacaactatatcgaactgcgatataatttttttatatcaaggttcgatatatcgaggtgaaagtgagatgagaag Mask Tandem Repeat Region ================================================ cttctcatctcactttcacctcgatatatcgaaccttgatataaaaaaattatatcgcagttcgatatagttgtcaaggatttataaatattttttacaaaaaatgattcatttttatctatcaatgcttcagctaaagctgctttaagtcagaagcataagtgattatagacctacatcctgataaatcagcataaaaaagccaggaacacctgacttactttt Find is-nt database================================================ Query_seq: SSA_2013:SSA_2014|SSA_2013:SSA_2014:hypothetical protein:D-alanyl-D-alanine carboxypeptidase, putative:<-<-:2013884..2014108 225 cttctcatctcactttcacctcgatatatcgaaccttgatataaaaaaattatatcgcagttcgatatagttgtcaaggatttataaatattttttacaaaaaatgattcatttttatctatcaatgcttcagctaaagctgctttaagtcagaagcataagtgattatagacctacatcctgataaatcagcataaaaaagccaggaacacctgacttactttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2013:SSA_2014|SSA_2013:SSA_2014:hypothetical protein:D-alanyl-D-alanine carboxypeptidase, putative:<-<-:2013884..2014108 225 cttctcatctcactttcacctcgatatatcgaaccttgatataaaaaaattatatcgcagttcgatatagttgtcaaggatttataaatattttttacaaaaaatgattcatttttatctatcaatgcttcagctaaagctgctttaagtcagaagcataagtgattatagacctacatcctgataaatcagcataaaaaagccaggaacacctgacttactttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2013:SSA_2014|SSA_2013:SSA_2014:hypothetical protein:D-alanyl-D-alanine carboxypeptidase, putative:<-<-:2013884..2014108 225 cttctcatctcactttcacctcgatatatcgaaccttgatataaaaaaattatatcgcagttcgatatagttgtcaaggatttataaatattttttacaaaaaatgattcatttttatctatcaatgcttcagctaaagctgctttaagtcagaagcataagtgattatagacctacatcctgataaatcagcataaaaaagccaggaacacctgacttactttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttctcatctcactttcacctcgatatatcgaaccttgatataaaaaaattatatcgcagttcgatatagttgtcaaggatttataaatattttttacaaaaaatgattcatttttatctatcaatgcttcagctaaagctgctttaagtcagaagcataagtgattatagacctacatcctgataaatcagcataaaaaagccaggaacacctgacttactttt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: - Start: 3 End: 125 .. R M E S E G R Y I S G Q Y L F I I D C N S I T T L S K Y I N K V F F S E N K D I M .................................................................................................... cttctcatctcactttcacctcgatatatcgaaccttgatataaaaaaattatatcgcagttcgatatagttgtcaaggatttataaatattttttacaaaaaatgattcatttttatctatcaatgcttcagctaaagctgctttaagtcagaagcataagtgattatagacctacatcctgataaatcagcataaaaaagccaggaacacctgacttactttt 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: 92 Start: 49 End: 78 ................................................CTTGACAACTATATCGAACTGCGATATAAT................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttctcatctcactttcacctcgatatatcgaaccttgatataaaaaaattatatcgcagttcgatatagttgtcaaggatttataaatattttttacaaaaaatgattcatttttatctatcaatgcttcagctaaagctgctttaagtcagaagcataagtgattatagacctacatcctgataaatcagcataaaaaagccaggaacacctgacttactttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 61 HP_score: -6.1 Tail_Score: -3.32562 Start: 24 End: 70 Full_Region: CTCACTTTCACCTCG ATATATCGAACCTTGATATAA AAAAA TTATATCGCAGTTCGATATAG TTGTCAAGGATTTAT .......................ATATATCGAACCTTGATATAAAAAAATTATATCGCAGTTCGATATAG........................................................................................................................................................... TransTerm Strand: + Conf: 76 HP_score: -9.6 Tail_Score: -2.59055 Start: 25 End: 69 Full_Region: TCACTTTCACCTCGA TATATCGAACCTTGATATAA AAAAA TTATATCGCAGTTCGATATA GTTGTCAAGGATTTA ........................TATATCGAACCTTGATATAAAAAAATTATATCGCAGTTCGATATA............................................................................................................................................................ TransTerm Strand: + Conf: 66 HP_score: -7.8 Tail_Score: -2.83119 Start: 27 End: 67 Full_Region: ACTTTCACCTCGATA TATCGAACCTTGATATAA AAAAA TTATATCGCAGTTCGATA TAGTTGTCAAGGATT ..........................TATCGAACCTTGATATAAAAAAATTATATCGCAGTTCGATA.............................................................................................................................................................. TransTerm Strand: - Conf: 55 HP_score: -6.0 Tail_Score: -2.88544 Start: 29 End: 65 Full_Region: tccttgacaactata tcgaactgcgatataa ttttt ttatatcaaggttcga tatatcgaggtgaaa ............................tcgaactgcgatataatttttttatatcaaggttcga................................................................................................................................................................ TransTerm Strand: - Conf: 81 HP_score: -2.6 Tail_Score: -5.71712 Start: 50 End: 70 Full_Region: ataaatccttgacaa ctatatcg aactg cgatataa tttttttatatcaag .................................................ctatatcgaactgcgatataa........................................................................................................................................................... TransTerm Strand: - Conf: 68 HP_score: -6.1 Tail_Score: -4.01943 Start: 51 End: 69 Full_Region: taaatccttgacaac tatatcg aactg cgatata atttttttatatcaa ..................................................tatatcgaactgcgatata............................................................................................................................................................ Find igs database================================================ Query_seq: SSA_2013:SSA_2014|SSA_2013:SSA_2014:hypothetical protein:D-alanyl-D-alanine carboxypeptidase, putative:<-<-:2013884..2014108 225 cttctcatctcactttcacctcgatatatcgaaccttgatataaaaaaattatatcgcagttcgatatagttgtcaaggatttataaatattttttacaaaaaatgattcatttttatctatcaatgcttcagctaaagctgctttaagtcagaagcataagtgattatagacctacatcctgataaatcagcataaaaaagccaggaacacctgacttactttt Intra-Species Hit: Count: 1 Min: 1 Max: 225 Len: 225 Subject: NC_009009_SSA_2013_SSA_2014|hypothetical protein:D-alanyl-D-alanine carboxypeptidase, putative|NEGATIVE:NEGATIVE|[2013884,2014108]|225 HSP 1 e-value: 1.0E-112 bit: 404.0 Len: 225 Query Start:1 Query End:225 Subject Strand: POSITIVE Subject Start: 1 Subject End: 225 cttctcatctcactttcacctcgatatatcgaaccttgatatnnnnnnnttatatcgcagttcgatatagttgtcaaggatttataaatattttttacaaaaaatgattcatttttatctatcaatgcttcagctaaagctgctttaagtcagaagcataagtgattatagacctacatcctgataaatcagcataaaaaagccaggaacacctgacttactttt cttctcatctcactttcacctcgatatatcgaaccttgatataaaaaaattatatcgcagttcgatatagttgtcaaggatttataaatattttttacaaaaaatgattcatttttatctatcaatgcttcagctaaagctgctttaagtcagaagcataagtgattatagacctacatcctgataaatcagcataaaaaagccaggaacacctgacttactttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUCAUCUCACUUUCACCUCGAUAUAUCGAACCUUGAUAUAAAAAAAUUAUAUCGCAGUUCGAUAUAGUUGUCAAGGAUUUAUAAAUAUUUUUUACAAAAAAUGAUUCAUUUUUAUCUAUCAAUGCUUCAGCUAAAGCUGCUUUAAGUCAGAAGCAUAAGUGAUUAUAGACCUACAUCCUGAUAAAUCAGCAUAAAAAAGCCAGGAACACCUGACUUACUUUU ........................((((((((((..((((((((.....))))))))..)))))))))).((((((.((((.((....(((...((((.(((((((...)))))))........(((((((.(((((((...)))).)))..)))))))..))))..)))....)).))))))))))............(((.((((....)))).)))...... (-47.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAGUAAGUCAGGUGUUCCUGGCUUUUUUAUGCUGAUUUAUCAGGAUGUAGGUCUAUAAUCACUUAUGCUUCUGACUUAAAGCAGCUUUAGCUGAAGCAUUGAUAGAUAAAAAUGAAUCAUUUUUUGUAAAAAAUAUUUAUAAAUCCUUGACAACUAUAUCGAACUGCGAUAUAAUUUUUUUAUAUCAAGGUUCGAUAUAUCGAGGUGAAAGUGAGAUGAGAAG ......((((((((....))))))))...(((.((((....)))).)))....(((....((((((.((((((....((((((...))))))..)))))).............((((((.((((((....))))))))))))....((((((....(((((((((((..(((((((.....)))))))..)))))))))))))))))...))))))....))).. (-60.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 786 50 1 141 92 NC_009009:SSA_2013|5end_hypothetical_protein_2013793..2014023_NEGATIVE 301 151 112 207 169 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 289 159 127 43 14 NC_009009:SSA_2228|5end_Acetyltransferase_(GNAT)_family,_putative_2228768..2228998_NEGATIVE 283 166 124 80 31 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 279 175 136 183 145 NC_009009:SSA_1923|5end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912698..1912928_NEGATIVE 279 156 111 138 92 NC_009009:SSA_0066|5end_hypothetical_protein_67602..67832_POSITIVE 277 210 161 35 3 NC_009009:SSA_0927|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936049..936279_POSITIVE 274 166 121 174 120 NC_009009:SSA_2214|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_2,_putative_2215835..2216065_NEGATIVE 270 220 179 217 181 NC_009009:SSA_0704|5end_Isocitrate_dehydrogenase_[NADP],_putative_689274..689504_POSITIVE 266 210 162 223 176 NC_009009:SSA_0942|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_949939..950169_POSITIVE 260 167 127 59 17 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 258 152 111 124 74 NC_009009:SSA_1393|5end_hypothetical_protein_1408773..1409003_NEGATIVE 257 179 134 213 169 NC_009009:SSA_2310|5end_hypothetical_protein_2313418..2313648_NEGATIVE 254 168 121 45 5 NC_009009:SSA_0470|5end_Precorrin-4_methylase,_putative_472879..473109_POSITIVE 253 143 121 64 41 NC_009009:SSA_0510|5end_L-threonine-O-3-phosphate_decarboxylase,_putative_508523..508753_POSITIVE 251 157 126 45 3 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 248 153 121 226 196 NC_009009:SSA_1872|5end_Cell_division_protein,_putative_1869186..1869416_NEGATIVE 245 165 122 57 11 NC_009009:SSA_2165|5end_ABC-type_oligopeptide_transporter,_periplasmic_component,_putative_2161734..2161964_POSITIVE 245 156 127 28 1 NC_009009:SSA_0355|5end_DNA_mismatch_repair_protein,_putative_346847..347077_POSITIVE 243 160 116 62 7 NC_009009:SSA_0747|5end_DD-carboxypeptidase,_putative_727936..728166_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 166 124 69 20 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 279 160 112 133 89 NC_009009:SSA_1959|3end_Undecaprenyl-diphosphatase,_putative_1955589..1955739_NEGATIVE 279 156 111 133 87 NC_009009:SSA_0065|3end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67677..67827_POSITIVE 263 75 34 75 26 NC_009009:SSA_1169|3end_Conserved_hypothetical_protein_with_an_alpha/beta_hydrolase_fold,_putative_1196846..1196996_POSITIVE 258 152 111 124 74 NC_009009:SSA_1394|3end_hypothetical_protein_1408773..1408923_NEGATIVE 254 168 121 45 5 NC_009009:SSA_0469|3end_Precorrin-6B_methylase_2,putative_472959..473109_POSITIVE 251 157 126 68 29 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 245 219 171 70 17 NC_009009:SSA_0139|3end_Copper_transport_operon_or_penicillinase_transcriptional_repressor,_putative_134706..134856_POSITIVE 242 34 1 137 102 NC_009009:SSA_1821|3end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810047..1810197_NEGATIVE 241 158 117 113 74 NC_009009:SSA_0609|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_598247..598397_NEGATIVE 240 160 112 115 66 NC_009009:SSA_1462|3end_Prephenate_dehydratase,_putative_1468934..1469084_NEGATIVE 239 162 122 128 82 NC_009009:SSA_1991|3end_Pneumococcal_histidine_triad_protein_A,_putative_1986340..1986490_NEGATIVE 236 173 132 60 19 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 234 220 173 80 36 NC_009009:SSA_0773|3end_PTS_enzyme_I,_putative_754416..754566_POSITIVE 234 167 121 70 22 NC_009009:SSA_0170|3end_hypothetical_protein_168130..168280_NEGATIVE 231 208 169 67 23 NC_009009:SSA_1649|3end_hypothetical_protein_1647906..1648056_NEGATIVE 231 98 55 101 63 NC_009009:SSA_0570|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_565461..565611_POSITIVE 230 219 173 67 28 NC_009009:SSA_2146|3end_Metallo-beta-lactamase,_putative_2146732..2146882_NEGATIVE 230 166 127 138 98 NC_009009:SSA_0539|3end_PduO_protein,_putative_534867..535017_POSITIVE 230 155 124 27 2 NC_009009:SSA_0197|3end_Dihydropteroate_synthase,_putative_196979..197129_POSITIVE