Origin IGS: aggtgacctcgtactttcctttgttgtttcttattttatcataaaaagaccagaaattcttaaaatttctggaatcctagctaaagcaaaaagaatccgggtattcagcccagattcttctttttattagc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gctaataaaaagaagaatctgggctgaatacccggattctttttgctttagctaggattccagaaattttaagaatttctggtctttttatgataaaataagaaacaacaaaggaaagtacgaggtcacct Mask Tandem Repeat Region ================================================ aggtgacctcgtactttcctttgttgtttcttattttatcataaaaagaccagaaattcttaaaatttctggaatcctagctaaagcaaaaagaatccgggtattcagcccagattcttctttttattagc Find is-nt database================================================ Query_seq: SSA_1464:SSA_1465|SSA_1464:SSA_1465:3-phosphoshikimate 1-carboxyvinyltransferase, putative:Conserved uncharacterized protein:<-<-:1471607..1471737 131 aggtgacctcgtactttcctttgttgtttcttattttatcataaaaagaccagaaattcttaaaatttctggaatcctagctaaagcaaaaagaatccgggtattcagcccagattcttctttttattagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1464:SSA_1465|SSA_1464:SSA_1465:3-phosphoshikimate 1-carboxyvinyltransferase, putative:Conserved uncharacterized protein:<-<-:1471607..1471737 131 aggtgacctcgtactttcctttgttgtttcttattttatcataaaaagaccagaaattcttaaaatttctggaatcctagctaaagcaaaaagaatccgggtattcagcccagattcttctttttattagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1464:SSA_1465|SSA_1464:SSA_1465:3-phosphoshikimate 1-carboxyvinyltransferase, putative:Conserved uncharacterized protein:<-<-:1471607..1471737 131 aggtgacctcgtactttcctttgttgtttcttattttatcataaaaagaccagaaattcttaaaatttctggaatcctagctaaagcaaaaagaatccgggtattcagcccagattcttctttttattagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggtgacctcgtactttcctttgttgtttcttattttatcataaaaagaccagaaattcttaaaatttctggaatcctagctaaagcaaaaagaatccgggtattcagcccagattcttctttttattagc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 38 End: 127 ..................................... M I K R P E I L K I S G I L A K A K R I R V F S P D S S F Y * .... aggtgacctcgtactttcctttgttgtttcttattttatcataaaaagaccagaaattcttaaaatttctggaatcctagctaaagcaaaaagaatccgggtattcagcccagattcttctttttattagc 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================================================ aggtgacctcgtactttcctttgttgtttcttattttatcataaaaagaccagaaattcttaaaatttctggaatcctagctaaagcaaaaagaatccgggtattcagcccagattcttctttttattagc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 87 HP_score: -10.0 Tail_Score: -4.08042 Start: 50 End: 72 Full_Region: gctttagctaggatt ccagaaattt taa gaatttctgg tctttttatgataaa .................................................ccagaaattttaagaatttctgg........................................................... Find igs database================================================ Query_seq: SSA_1464:SSA_1465|SSA_1464:SSA_1465:3-phosphoshikimate 1-carboxyvinyltransferase, putative:Conserved uncharacterized protein:<-<-:1471607..1471737 131 aggtgacctcgtactttcctttgttgtttcttattttatcataaaaagaccagaaattcttaaaatttctggaatcctagctaaagcaaaaagaatccgggtattcagcccagattcttctttttattagc Intra-Species Hit: Count: 1 Min: 1 Max: 131 Len: 131 Subject: NC_009009_SSA_1464_SSA_1465|3-phosphoshikimate 1-carboxyvinyltransferase, putative:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[1471607,1471737]|131 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 131 Query Start:1 Query End:131 Subject Strand: POSITIVE Subject Start: 1 Subject End: 131 aggtgacctcgtactttcctttgttgtttcttattttatcataaaaagaccagaaattcttaaaatttctggaatcctagctaaagcaaaaagaatccgggtattcagcccagattcttctttttattagc aggtgacctcgtactttcctttgttgtttcttattttatcataaaaagaccagaaattcttaaaatttctggaatcctagctaaagcaaaaagaatccgggtattcagcccagattcttctttttattagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUGACCUCGUACUUUCCUUUGUUGUUUCUUAUUUUAUCAUAAAAAGACCAGAAAUUCUUAAAAUUUCUGGAAUCCUAGCUAAAGCAAAAAGAAUCCGGGUAUUCAGCCCAGAUUCUUCUUUUUAUUAGC (((.(((..((..........))..))).)))........((((((((.(((((((((.....))))))))).......((....))...(((((((.((((.....)))).))))))))))))))).... (-29.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUAAUAAAAAGAAGAAUCUGGGCUGAAUACCCGGAUUCUUUUUGCUUUAGCUAGGAUUCCAGAAAUUUUAAGAAUUUCUGGUCUUUUUAUGAUAAAAUAAGAAACAACAAAGGAAAGUACGAGGUCACCU (((((....((((((((((((((.......))))))))))))))...))))).(((...((((((((((...))))))))))..(((((((......)))))))........................))) (-38.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 916 120 71 211 162 NC_009009:SSA_1464|5end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1471516..1471746_NEGATIVE 310 124 85 159 127 NC_009009:SSA_1772|5end_hypothetical_protein_1759545..1759775_NEGATIVE 282 109 66 174 133 NC_009009:SSA_0097|5end_Multi_antimicrobial_extrusion_(MATE)_family_transporter,_putative_98148..98378_POSITIVE 281 44 6 132 97 NC_009009:SSA_1296|5end_hypothetical_protein_1313013..1313243_NEGATIVE 279 118 79 76 29 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 268 119 76 209 169 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 268 118 71 162 117 NC_009009:SSA_1644|5end_hypothetical_protein_1645617..1645847_NEGATIVE 268 113 77 39 3 NC_009009:SSA_0793|5end_DNA-entry_nuclease,_putative_774859..775089_POSITIVE 265 120 71 56 3 NC_009009:SSA_0781|5end_Mannose-6-phosphate_isomerase,_putative_765373..765603_POSITIVE 264 117 74 171 121 NC_009009:SSA_1116|5end_hypothetical_protein_1142352..1142582_POSITIVE 263 115 78 62 28 NC_009009:SSA_1927|5end_Exfoliative_toxin,_putative_1915873..1916103_NEGATIVE 259 30 1 213 182 NC_009009:SSA_0064|5end_hypothetical_protein_66330..66560_POSITIVE 258 109 71 68 27 NC_009009:SSA_0253|5end_CAAX_amino_terminal_protease_family_protein,_putative_246289..246519_POSITIVE 257 120 75 193 139 NC_009009:SSA_1122|5end_Thioredoxin_family_protein,_putative_1147871..1148101_POSITIVE 257 129 85 59 15 NC_009009:SSA_0763|5end_Transcription_repressor,_putative_744980..745210_POSITIVE 255 111 74 136 92 NC_009009:SSA_2090|5end_Hexulose-6-phosphate_synthase,_putative_2095038..2095268_NEGATIVE 255 114 79 82 38 NC_009009:SSA_0221|5end_PTS_system,_mannose-specific_IIC_component,_putative_216370..216600_POSITIVE 253 110 63 188 133 NC_009009:SSA_1229|5end_hypothetical_protein_1252421..1252651_NEGATIVE 250 118 71 207 171 NC_009009:SSA_0736|5end_Catabolite_gene_activator_and_regulatory_subunit_of_cAMP-dependent_protein_kinases,_putative_717648..717878_POSITIVE 249 129 84 206 145 NC_009009:SSA_2160|5end_Deoxyuridinetriphosphatase,_putative_2160066..2160296_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 109 66 65 24 NC_009009:SSA_0095|3end_Threonine_synthase,_putative_98119..98269_POSITIVE 279 118 79 79 32 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 268 119 76 73 33 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 267 125 83 52 12 NC_009009:SSA_1964|3end_conserved_uncharacterized_protein_1960996..1961146_NEGATIVE 264 114 80 61 29 NC_009009:SSA_1927|3end_Exfoliative_toxin,_putative_1914956..1915106_NEGATIVE 264 117 74 143 93 NC_009009:SSA_1115|3end_Cytochrome_C-type_biogenesis_protein,_putative_1142404..1142554_POSITIVE 255 111 74 112 68 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 255 119 72 132 96 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 255 114 79 54 10 NC_009009:SSA_0220|3end_PTS_system,_mannose-specific_IIB_component,_putative_216422..216572_POSITIVE 254 119 71 82 39 NC_009009:SSA_1751|3end_Dextran_glucosidase,_alpha_amylase_family,_putative_1738110..1738260_NEGATIVE 249 129 84 121 60 NC_009009:SSA_2161|3end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160151..2160301_NEGATIVE 247 108 68 71 26 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 245 126 96 82 45 NC_009009:SSA_1259|3end_Purine_nucleoside_phosphorylase,_putative_1284910..1285060_NEGATIVE 243 113 71 141 94 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 243 113 73 46 8 NC_009009:SSA_1230|3end_Conserved_uncharacterized_protein_1252612..1252762_NEGATIVE 243 127 81 105 64 NC_009009:SSA_0583|3end_Nucleotidyltransferase,_putative_575679..575829_POSITIVE 234 125 82 69 27 NC_009009:SSA_1962|3end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1960930..1961080_POSITIVE 232 119 77 52 5 NC_009009:SSA_1575|3end_Glycosyl_transferase,_putative_1577932..1578082_NEGATIVE 232 124 81 61 13 NC_009009:SSA_1067|3end_hypothetical_protein_1087345..1087495_POSITIVE 231 123 97 133 106 NC_009009:SSA_0401|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_399222..399372_POSITIVE