Origin IGS: gatttccctcaattcaagattttacaatccattctattataccactttctagtgtgtttgtataatacaaaaaggacaggtagagccgcggctgaacttgtccttttctttct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agaaagaaaaggacaagttcagccgcggctctacctgtcctttttgtattatacaaacacactagaaagtggtataatagaatggattgtaaaatcttgaattgagggaaatc Mask Tandem Repeat Region ================================================ gatttccctcaattcaagattttacaatccattctattataccactttctagtgtgtttgtataatacaaaaaggacaggtagagccgcggctgaacttgtccttttctttct Find is-nt database================================================ Query_seq: SSA_1510:SSA_1511|SSA_1510:SSA_1511:Rhamnosyltransferase, putative:Glycosyltransferase, putative:<-<-:1515427..1515539 113 gatttccctcaattcaagattttacaatccattctattataccactttctagtgtgtttgtataatacaaaaaggacaggtagagccgcggctgaacttgtccttttctttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1510:SSA_1511|SSA_1510:SSA_1511:Rhamnosyltransferase, putative:Glycosyltransferase, putative:<-<-:1515427..1515539 113 gatttccctcaattcaagattttacaatccattctattataccactttctagtgtgtttgtataatacaaaaaggacaggtagagccgcggctgaacttgtccttttctttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1510:SSA_1511|SSA_1510:SSA_1511:Rhamnosyltransferase, putative:Glycosyltransferase, putative:<-<-:1515427..1515539 113 gatttccctcaattcaagattttacaatccattctattataccactttctagtgtgtttgtataatacaaaaaggacaggtagagccgcggctgaacttgtccttttctttct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatttccctcaattcaagattttacaatccattctattataccactttctagtgtgtttgtataatacaaaaaggacaggtagagccgcggctgaacttgtccttttctttct Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 19 End: 111 .................. M L Q S I L L Y H F L V C L Y N T K R T G R A A A E L V L F F .. gatttccctcaattcaagattttacaatccattctattataccactttctagtgtgtttgtataatacaaaaaggacaggtagagccgcggctgaacttgtccttttctttct 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: 84 Start: 36 End: 65 ...................................TTATACAAACACACTAGAAAGTGGTATAAT................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatttccctcaattcaagattttacaatccattctattataccactttctagtgtgtttgtataatacaaaaaggacaggtagagccgcggctgaacttgtccttttctttct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1510:SSA_1511|SSA_1510:SSA_1511:Rhamnosyltransferase, putative:Glycosyltransferase, putative:<-<-:1515427..1515539 113 gatttccctcaattcaagattttacaatccattctattataccactttctagtgtgtttgtataatacaaaaaggacaggtagagccgcggctgaacttgtccttttctttct Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: NC_009009_SSA_1510_SSA_1511|Rhamnosyltransferase, putative:Glycosyltransferase, putative|NEGATIVE:NEGATIVE|[1515427,1515539]|113 HSP 1 e-value: 5.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 gatttccctcaattcaagattttacaatccattctattataccactttctagtgtgtttgtataatacaaaaaggacaggtagagccgcggctgaacttgtccttttctttct gatttccctcaattcaagattttacaatccattctattataccactttctagtgtgtttgtataatacaaaaaggacaggtagagccgcggctgaacttgtccttttctttct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUCCCUCAAUUCAAGAUUUUACAAUCCAUUCUAUUAUACCACUUUCUAGUGUGUUUGUAUAAUACAAAAAGGACAGGUAGAGCCGCGGCUGAACUUGUCCUUUUCUUUCU ..................................((((((((((((....)))).....))))))))..((((((((((((..(((....)))..))))))))))))...... (-27.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAAGAAAAGGACAAGUUCAGCCGCGGCUCUACCUGUCCUUUUUGUAUUAUACAAACACACUAGAAAGUGGUAUAAUAGAAUGGAUUGUAAAAUCUUGAAUUGAGGGAAAUC .....((((((((((.((..(((....)))..)).)))))))))).((((((((.....((((....))))))))))))....(((((....)))))................ (-27.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 919 100 51 191 142 NC_009009:SSA_1510|5end_Rhamnosyltransferase,_putative_1515336..1515566_NEGATIVE 300 104 66 227 178 NC_009009:SSA_2154|5end_Conserved_uncharacterized_protein_2155259..2155489_NEGATIVE 284 105 72 174 133 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 276 110 79 109 81 NC_009009:SSA_2063|5end_Aminopeptidase_PepS,_putative_2064857..2065087_NEGATIVE 271 60 20 124 80 NC_009009:SSA_2194|5end_Nicotinamide_mononucleotide_transporter,_putative_2195663..2195893_NEGATIVE 271 104 71 179 146 NC_009009:SSA_0878|5end_DNA_gyrase,_putative_871596..871826_POSITIVE 267 110 86 214 186 NC_009009:SSA_2278|5end_Ukp_protein,_putative_2281669..2281899_NEGATIVE 263 107 77 86 52 NC_009009:SSA_1267|5end_crcB-like_protein_2,_putative_1291347..1291577_NEGATIVE 261 100 54 60 12 NC_009009:SSA_2364|5end_Immunodominant_staphylococcal_antigen_A_precursor,_putative_2367032..2367262_NEGATIVE 259 103 72 199 161 NC_009009:SSA_0632|5end_Anthranilate_synthase_component_I,_putative_621458..621688_POSITIVE 257 109 67 194 149 NC_009009:SSA_1771|5end_Conserved_DNA_methyltransferase_protein,_putative_1758799..1759029_NEGATIVE 256 96 51 225 175 NC_009009:SSA_1015|5end_4-hydroxybenzoate_octaprenyltransferase,_putative_1018703..1018933_POSITIVE 255 107 78 148 116 NC_009009:SSA_2202|5end_Elongation_factor_Ts,_putative_2203350..2203580_NEGATIVE 255 110 69 194 161 NC_009009:SSA_0214|5end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210215..210445_POSITIVE 254 104 73 201 175 NC_009009:SSA_1401|5end_Transcriptional_regulator_GntR_family_1413062..1413292_POSITIVE 252 110 73 221 181 NC_009009:SSA_0332|5end_hypothetical_protein_325909..326139_POSITIVE 251 108 79 39 9 NC_009009:SSA_1092|5end_Dihydrofolate_reductase,_putative_1109599..1109829_POSITIVE 251 109 72 108 67 NC_009009:SSA_0160|5end_hypothetical_protein_158735..158965_POSITIVE 250 105 84 46 23 NC_009009:SSA_1077|5end_N-acetyl-glucosamine_matabolism,_putative_1094979..1095209_POSITIVE 250 103 75 35 1 NC_009009:SSA_0942|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_949939..950169_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 104 66 79 30 NC_009009:SSA_2155|3end_hypothetical_protein_2155407..2155557_NEGATIVE 276 110 79 87 59 NC_009009:SSA_2064|3end_hypothetical_protein_2064879..2065029_NEGATIVE 271 60 20 102 58 NC_009009:SSA_2195|3end_ATPase/kinase,_putative_2195685..2195835_NEGATIVE 263 107 77 86 52 NC_009009:SSA_1268|3end_Chorismate_mutase/prephenate_dehydratase,_putative_1291347..1291497_NEGATIVE 259 110 66 92 38 NC_009009:SSA_0170|3end_hypothetical_protein_168130..168280_NEGATIVE 257 109 67 98 53 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 256 96 73 126 97 NC_009009:SSA_2285|3end_hypothetical_protein_2287825..2287975_POSITIVE 255 107 78 75 43 NC_009009:SSA_2203|3end_30S_ribosomal_protein_S2,_putative_2203423..2203573_NEGATIVE 250 105 84 34 11 NC_009009:SSA_1076|3end_hypothetical_protein_1095047..1095197_POSITIVE 249 96 74 40 14 NC_009009:SSA_0411|3end_hypothetical_protein_406480..406630_NEGATIVE 248 109 73 58 30 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 247 97 74 66 35 NC_009009:SSA_1605|3end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1610623..1610773_NEGATIVE 247 103 67 38 1 NC_009009:SSA_0941|3end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_950022..950172_POSITIVE 245 96 51 54 9 NC_009009:SSA_1893|3end_N-acetylglucosamine-6-phosphate_deacetylase,_putative_1889421..1889571_NEGATIVE 241 105 77 67 35 NC_009009:SSA_1720|3end_Initiation-control_protein,_putative_1706796..1706946_NEGATIVE 241 104 63 78 37 NC_009009:SSA_0377|3end_ABC-type_methionine_transporter,_permease_component,_putative_367218..367368_POSITIVE 240 91 54 48 8 NC_009009:SSA_0496|3end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_497009..497159_POSITIVE 238 110 83 36 7 NC_009009:SSA_0671|3end_Methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase,_putative_655274..655424_POSITIVE 237 99 73 125 87 NC_009009:SSA_0416|3end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase,_putative_414222..414372_POSITIVE 235 90 45 135 90 NC_009009:SSA_1943|3end_Aspartate_kinase,_putative_1930159..1930309_POSITIVE