Origin IGS: ccgtttttcctccttttgcaaatagatgatatatcatctatttaagattttatattttttaactaaaattgtcaacaatttacctaatctagtgtaaaatagtatagaagtgatttttgaaaggagagcagc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gctgctctcctttcaaaaatcacttctatactattttacactagattaggtaaattgttgacaattttagttaaaaaatataaaatcttaaatagatgatatatcatctatttgcaaaaggaggaaaaacgg Mask Tandem Repeat Region ================================================ ccgtttttcctccttttgcaaatagatgatatatcatctatttaagattttatattttttaactaaaattgtcaacaatttacctaatctagtgtaaaatagtatagaagtgatttttgaaaggagagcagc Find is-nt database================================================ Query_seq: SSA_0314:SSA_0315|SSA_0314:SSA_0315:Nucleoside-diphosphate-sugar epimerase, putative:Transcriptional regulator, MarR family, putative:<-->:310110..310241 132 ccgtttttcctccttttgcaaatagatgatatatcatctatttaagattttatattttttaactaaaattgtcaacaatttacctaatctagtgtaaaatagtatagaagtgatttttgaaaggagagcagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0314:SSA_0315|SSA_0314:SSA_0315:Nucleoside-diphosphate-sugar epimerase, putative:Transcriptional regulator, MarR family, putative:<-->:310110..310241 132 ccgtttttcctccttttgcaaatagatgatatatcatctatttaagattttatattttttaactaaaattgtcaacaatttacctaatctagtgtaaaatagtatagaagtgatttttgaaaggagagcagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0314:SSA_0315|SSA_0314:SSA_0315:Nucleoside-diphosphate-sugar epimerase, putative:Transcriptional regulator, MarR family, putative:<-->:310110..310241 132 ccgtttttcctccttttgcaaatagatgatatatcatctatttaagattttatattttttaactaaaattgtcaacaatttacctaatctagtgtaaaatagtatagaagtgatttttgaaaggagagcagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccgtttttcctccttttgcaaatagatgatatatcatctatttaagattttatattttttaactaaaattgtcaacaatttacctaatctagtgtaaaatagtatagaagtgatttttgaaaggagagcagc Predict ORF larger than 30AA ================================================ ccgtttttcctccttttgcaaatagatgatatatcatctatttaagattttatattttttaactaaaattgtcaacaatttacctaatctagtgtaaaatagtatagaagtgatttttgaaaggagagcagc 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: 88 Start: 47 End: 76 ..............................................GTTGACAATTTTAGTTAAAAAATATAAAAT........................................................ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 71 End: 100 ......................................................................GTCAACAATTTACCTAATCTAGTGTAAAAT................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ccgtttttcctccttttgcaaatagatgatatatcatctatttaagattttatattttttaactaaaattgtcaacaatttacctaatctagtgtaaaatagtatagaagtgatttttgaaaggagagcagc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0314:SSA_0315|SSA_0314:SSA_0315:Nucleoside-diphosphate-sugar epimerase, putative:Transcriptional regulator, MarR family, putative:<-->:310110..310241 132 ccgtttttcctccttttgcaaatagatgatatatcatctatttaagattttatattttttaactaaaattgtcaacaatttacctaatctagtgtaaaatagtatagaagtgatttttgaaaggagagcagc Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: NC_009009_SSA_0314_SSA_0315|Nucleoside-diphosphate-sugar epimerase, putative:Transcriptional regulator, MarR family, putative|NEGATIVE:POSITIVE|[310110,310241]|132 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 ccgtttttcctccttttgcaaatagatgatatatcatctatttaagattttatattttttaactaaaattgtcaacaatttacctaatctagtgtaaaatagtatagaagtgatttttgaaaggagagcagc ccgtttttcctccttttgcaaatagatgatatatcatctatttaagattttatattttttaactaaaattgtcaacaatttacctaatctagtgtaaaatagtatagaagtgatttttgaaaggagagcagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGUUUUUCCUCCUUUUGCAAAUAGAUGAUAUAUCAUCUAUUUAAGAUUUUAUAUUUUUUAACUAAAAUUGUCAACAAUUUACCUAAUCUAGUGUAAAAUAGUAUAGAAGUGAUUUUUGAAAGGAGAGCAGC .........((((((((..((((((((((....))))))))))....((((((((((((((((((((((((....))))))........)))).))))).))))))))).........))))))))...... (-29.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUGCUCUCCUUUCAAAAAUCACUUCUAUACUAUUUUACACUAGAUUAGGUAAAUUGUUGACAAUUUUAGUUAAAAAAUAUAAAAUCUUAAAUAGAUGAUAUAUCAUCUAUUUGCAAAAGGAGGAAAAACGG .....((((((((.............................(((((..(((.....(((((.......)))))....)))..)))))(((((((((((....)))))))))))..))))))))........ (-23.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 771 130 81 221 172 NC_009009:SSA_0314|5end_Nucleoside-diphosphate-sugar_epimerase,_putative_310019..310249_NEGATIVE 223 130 91 69 30 NC_009009:SSA_0234|5end_hypothetical_protein_228938..229168_NEGATIVE 218 40 2 139 89 NC_009009:SSA_1143|5end_Na+-driven_multidrug_efflux_pump,_putative_1173497..1173727_NEGATIVE 213 129 86 129 82 NC_009009:SSA_1206|5end_A/G-specific_adenine_glycosylase,_putative_1231231..1231461_NEGATIVE 209 43 1 198 147 NC_009009:SSA_1231|5end_hypothetical_protein_1254758..1254988_NEGATIVE 205 46 1 138 88 NC_009009:SSA_1381|5end_hypothetical_protein_1399565..1399795_NEGATIVE 204 41 1 91 49 NC_009009:SSA_2105|5end_hypothetical_protein_2107802..2108032_NEGATIVE 203 122 83 74 44 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 195 38 2 124 89 NC_009009:SSA_0990|5end_hypothetical_protein_991733..991963_POSITIVE 193 42 1 133 93 NC_009009:SSA_2164|5end_Glutamine_amidotransferase,_putative_2161555..2161785_NEGATIVE 190 44 2 139 89 NC_009009:SSA_1158|5end_hypothetical_protein_1186253..1186483_POSITIVE 190 49 1 141 88 NC_009009:SSA_1139|5end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1166823..1167053_POSITIVE 189 49 1 132 88 NC_009009:SSA_0888|5end_Magnesium/cobalt_transporter,_putative_881329..881559_POSITIVE 189 25 2 42 20 NC_009009:SSA_0245|5end_hypothetical_protein_239136..239366_POSITIVE 186 29 1 180 137 NC_009009:SSA_1091|5end_Thymidylate_synthase,_putative_1108635..1108865_POSITIVE 186 39 1 220 176 NC_009009:SSA_0504|5end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_503009..503239_POSITIVE 185 30 2 119 89 NC_009009:SSA_1532|5end_Membrane-fusion_protein_/_periplasmic_component_of_efflux_system,_putative_1540623..1540853_NEGATIVE 185 129 83 151 101 NC_009009:SSA_1305|5end_hypothetical_protein_1324079..1324309_NEGATIVE 185 130 84 190 133 NC_009009:SSA_1201|5end_hypothetical_protein_1225755..1225985_POSITIVE 184 129 81 177 131 NC_009009:SSA_1510|5end_Rhamnosyltransferase,_putative_1515336..1515566_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 213 129 86 63 16 NC_009009:SSA_1207|3end_Phosphate_acetyltransferase,_putative_1231297..1231447_NEGATIVE 211 46 1 50 5 NC_009009:SSA_0685|3end_hypothetical_protein_669432..669582_POSITIVE 209 43 1 150 99 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 195 38 2 127 92 NC_009009:SSA_0989|3end_Conserved_protein,_possible_transcriptional_regulator_(sigma-70,_region_4),_putative_991816..991966_POSITIVE 192 129 90 48 8 NC_009009:SSA_1105|3end_50S_ribosomal_protein_L7/_L12,_putative_1125765..1125915_POSITIVE 190 49 1 122 69 NC_009009:SSA_1138|3end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1166884..1167034_POSITIVE 189 129 92 151 115 NC_009009:SSA_2010|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_2011296..2011446_NEGATIVE 189 130 83 148 103 NC_009009:SSA_0911|3end_hypothetical_protein_922898..923048_POSITIVE 186 29 1 75 32 NC_009009:SSA_1090|3end_Glucokinase,_putative_1108610..1108760_POSITIVE 184 129 81 63 17 NC_009009:SSA_1511|3end_Glycosyltransferase,_putative_1515450..1515600_NEGATIVE 184 47 8 65 18 NC_009009:SSA_0817|3end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_799375..799525_POSITIVE 183 38 4 132 100 NC_009009:SSA_1652|3end_Acetyltransferases,_putative_1649955..1650105_NEGATIVE 183 49 2 146 92 NC_009009:SSA_0421|3end_Phosphoglycerate_mutase_family_protein,_putative_420240..420390_POSITIVE 181 30 4 86 63 NC_009009:SSA_1277|3end_D-alanyl-D-alanine_carboxypeptidase_1298476..1298626_NEGATIVE 180 122 83 38 8 NC_009009:SSA_1366|3end_Alkaline_D-stereospecific_endopeptidase_precursor,_putative_1382296..1382446_NEGATIVE 179 54 11 50 3 NC_009009:SSA_1648|3end_hypothetical_protein_1647166..1647316_NEGATIVE 177 129 81 86 27 NC_009009:SSA_1681|3end_ABC-type_bacitracin_resistance_protein_A,_ATPase_component,_putative_1675181..1675331_NEGATIVE 176 127 83 69 22 NC_009009:SSA_2253|3end_3-Methyladenine_DNA_glycosylase_I,_constitutive,_putative_2248870..2249020_NEGATIVE 176 41 1 104 64 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 172 39 1 49 15 NC_009009:SSA_2177|3end_hypothetical_protein_2175232..2175382_NEGATIVE