Origin IGS: tagctttccctctagatattttataagtacacttattgtaatctgacatcttatttttgtcaataaaaacccagtttagactaaaaagtccgaactgggttctgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acagaacccagttcggactttttagtctaaactgggtttttattgacaaaaataagatgtcagattacaataagtgtacttataaaatatctagagggaaagcta Mask Tandem Repeat Region ================================================ tagctttccctctagatattttataagtacacttattgtaatctgacatcttatttttgtcaataaaaacccagtttagactaaaaagtccgaactgggttctgt Find is-nt database================================================ Query_seq: SSA_0255:SSA_0256|SSA_0255:SSA_0256:Multiple antibiotic resistance operon transcription repressor (MarR), putative:Metalloregulator ScaR (Fe/Mn-dependent transcriptional repressor), putative:<-<-:248037..248141 105 tagctttccctctagatattttataagtacacttattgtaatctgacatcttatttttgtcaataaaaacccagtttagactaaaaagtccgaactgggttctgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0255:SSA_0256|SSA_0255:SSA_0256:Multiple antibiotic resistance operon transcription repressor (MarR), putative:Metalloregulator ScaR (Fe/Mn-dependent transcriptional repressor), putative:<-<-:248037..248141 105 tagctttccctctagatattttataagtacacttattgtaatctgacatcttatttttgtcaataaaaacccagtttagactaaaaagtccgaactgggttctgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0255:SSA_0256|SSA_0255:SSA_0256:Multiple antibiotic resistance operon transcription repressor (MarR), putative:Metalloregulator ScaR (Fe/Mn-dependent transcriptional repressor), putative:<-<-:248037..248141 105 tagctttccctctagatattttataagtacacttattgtaatctgacatcttatttttgtcaataaaaacccagtttagactaaaaagtccgaactgggttctgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagctttccctctagatattttataagtacacttattgtaatctgacatcttatttttgtcaataaaaacccagtttagactaaaaagtccgaactgggttctgt Predict ORF larger than 30AA ================================================ tagctttccctctagatattttataagtacacttattgtaatctgacatcttatttttgtcaataaaaacccagtttagactaaaaagtccgaactgggttctgt 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: 89 Start: 35 End: 64 ..................................ATTGACAAAAATAAGATGTCAGATTACAAT......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagctttccctctagatattttataagtacacttattgtaatctgacatcttatttttgtcaataaaaacccagtttagactaaaaagtccgaactgggttctgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 39 HP_score: -2.0 Tail_Score: -2.61239 Start: 28 End: 40 Full_Region: aataagatgtcagat taca ataag tgta cttataaaatatcta ...........................tacaataagtgta................................................................. Find igs database================================================ Query_seq: SSA_0255:SSA_0256|SSA_0255:SSA_0256:Multiple antibiotic resistance operon transcription repressor (MarR), putative:Metalloregulator ScaR (Fe/Mn-dependent transcriptional repressor), putative:<-<-:248037..248141 105 tagctttccctctagatattttataagtacacttattgtaatctgacatcttatttttgtcaataaaaacccagtttagactaaaaagtccgaactgggttctgt Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: NC_009009_SSA_0255_SSA_0256|Multiple antibiotic resistance operon transcription repressor (MarR), putative:Metalloregulator ScaR (Fe/Mn-dependent transcriptional repressor), putative|NEGATIVE:NEGATIVE|[248037,248141]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 tagctttccctctagatattttataagtacacttattgtaatctgacatcttatttttgtcaataaaaacccagtttagactaaaaagtccgaactgggttctgt tagctttccctctagatattttataagtacacttattgtaatctgacatcttatttttgtcaataaaaacccagtttagactaaaaagtccgaactgggttctgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCUUUCCCUCUAGAUAUUUUAUAAGUACACUUAUUGUAAUCUGACAUCUUAUUUUUGUCAAUAAAAACCCAGUUUAGACUAAAAAGUCCGAACUGGGUUCUGU .............((((.....(((((....)))))....))))((((.........))))......(((((((((..((((....))))..))))))))).... (-25.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAGAACCCAGUUCGGACUUUUUAGUCUAAACUGGGUUUUUAUUGACAAAAAUAAGAUGUCAGAUUACAAUAAGUGUACUUAUAAAAUAUCUAGAGGGAAAGCUA ..(((((((((((..((((....))))..)))))))))))..((((((.........))))))......(((((....)))))......(((....)))...... (-28.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 771 50 1 141 92 NC_009009:SSA_0255|5end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_247946..248176_NEGATIVE 211 97 53 136 81 NC_009009:SSA_0231|5end_Conserved_uncharacterized_protein_225713..225943_POSITIVE 209 100 71 74 45 NC_009009:SSA_0591|5end_Conserved_uncharacterized_protein_582769..582999_POSITIVE 208 100 54 57 4 NC_009009:SSA_1592|5end_hypothetical_protein_1596397..1596627_NEGATIVE 208 79 35 51 3 NC_009009:SSA_0077|5end_Oxidoreductase,_putative_80738..80968_POSITIVE 206 97 55 66 28 NC_009009:SSA_1607|5end_Formamidopyrimidine-DNA_glycosylase,_putative_1613255..1613485_NEGATIVE 206 79 40 113 70 NC_009009:SSA_1441|5end_Phosphoribosyl-AMP_cyclohydrolase,_putative_1445183..1445413_NEGATIVE 206 91 57 176 140 NC_009009:SSA_1255|5end_hypothetical_protein_1282244..1282474_NEGATIVE 203 99 51 162 107 NC_009009:SSA_0221|5end_PTS_system,_mannose-specific_IIC_component,_putative_216370..216600_POSITIVE 201 78 32 135 87 NC_009009:SSA_0689|5end_Penicillin-binding_protein_2B,_putative_672262..672492_POSITIVE 200 99 70 39 10 NC_009009:SSA_2088|5end_Carbohydrate_isomerase,_AraD/FucA_family,_putative_2093476..2093706_NEGATIVE 199 74 38 117 81 NC_009009:SSA_0583|5end_Nucleotidyltransferase,_putative_574505..574735_POSITIVE 198 50 2 213 165 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 198 99 78 150 128 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 195 43 2 89 46 NC_009009:SSA_2302|5end_Type_IV_fimbrial_biogenesis_protein,_prepilin_cysteine_protease_(C20)_PilD,_putative_2304044..2304274_NEGATIVE 194 50 2 209 149 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 193 47 2 227 167 NC_009009:SSA_2072|5end_Phosphatidate_cytidylyltransferase,_putative_2075603..2075833_NEGATIVE 193 96 69 212 181 NC_009009:SSA_1087|5end_ABC-type_transporter_(antibiotic_resistance_protein),_ATPase_component,_putative_1104524..1104754_POSITIVE 193 48 4 50 7 NC_009009:SSA_0383|5end_Beta-glucosidase,_putative_374534..374764_POSITIVE 188 99 56 163 118 NC_009009:SSA_1244|5end_hypothetical_protein_1268704..1268934_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 90 44 44 2 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 209 100 71 42 13 NC_009009:SSA_0590|3end_hypothetical_protein_582817..582967_POSITIVE 206 79 40 113 70 NC_009009:SSA_1442|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445183..1445333_NEGATIVE 206 91 57 63 27 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 205 100 51 62 17 NC_009009:SSA_2204|3end_hypothetical_protein_2205507..2205657_POSITIVE 203 99 51 128 80 NC_009009:SSA_2364|3end_Immunodominant_staphylococcal_antigen_A_precursor,_putative_2366442..2366592_NEGATIVE 203 99 51 134 79 NC_009009:SSA_0220|3end_PTS_system,_mannose-specific_IIB_component,_putative_216422..216572_POSITIVE 200 99 70 39 10 NC_009009:SSA_2089|3end_L-xylulose-5-phosphate_3-epimerase,_putative_2093476..2093626_NEGATIVE 199 74 38 115 79 NC_009009:SSA_0582|3end_Methylase,_putative_574583..574733_POSITIVE 198 99 78 150 128 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 197 88 53 60 27 NC_009009:SSA_1130|3end_Iron-dependent_peroxidase,_putative_1157090..1157240_POSITIVE 189 100 65 62 31 NC_009009:SSA_2094|3end_Conserved_uncharacterized_protein_2097990..2098140_NEGATIVE 188 78 31 139 101 NC_009009:SSA_0811|3end_hypothetical_protein_793526..793676_POSITIVE 181 90 48 121 80 NC_009009:SSA_1818|3end_Very_short_patch_repair_endonuclease,_putative_1805655..1805805_NEGATIVE 181 100 53 71 28 NC_009009:SSA_1619|3end_Ribosome_recycling_factor,_putative_1621679..1621829_NEGATIVE 181 98 54 134 85 NC_009009:SSA_0927|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936740..936890_POSITIVE 179 100 54 134 88 NC_009009:SSA_0807|3end_GTP-binding_protein,_putative_790839..790989_POSITIVE 176 50 8 80 40 NC_009009:SSA_0255|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_247485..247635_NEGATIVE 175 96 54 81 38 NC_009009:SSA_0629|3end_hypothetical_protein_619586..619736_POSITIVE 175 100 68 84 60 NC_009009:SSA_0354|3end_Uncharacterized_membrane_protein_346872..347022_POSITIVE