Origin IGS: tagtagcggcatctcaggtgcaagagatttccaagacagaatttagggattctattttttaatagtggattagcagctatgtatggaggtggattgttgatttgaaaaagccg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cggctttttcaaatcaacaatccacctccatacatagctgctaatccactattaaaaaatagaatccctaaattctgtcttggaaatctcttgcacctgagatgccgctacta Mask Tandem Repeat Region ================================================ tagtagcggcatctcaggtgcaagagatttccaagacagaatttagggattctattttttaatagtggattagcagctatgtatggaggtggattgttgatttgaaaaagccg Find is-nt database================================================ Query_seq: SSA_0279:SSA_0281|SSA_0279:SSA_0281:Sugar-binding transcriptional repressor (DeoR), putative:hypothetical protein:->->:273431..273543 113 tagtagcggcatctcaggtgcaagagatttccaagacagaatttagggattctattttttaatagtggattagcagctatgtatggaggtggattgttgatttgaaaaagccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0279:SSA_0281|SSA_0279:SSA_0281:Sugar-binding transcriptional repressor (DeoR), putative:hypothetical protein:->->:273431..273543 113 tagtagcggcatctcaggtgcaagagatttccaagacagaatttagggattctattttttaatagtggattagcagctatgtatggaggtggattgttgatttgaaaaagccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0279:SSA_0281|SSA_0279:SSA_0281:Sugar-binding transcriptional repressor (DeoR), putative:hypothetical protein:->->:273431..273543 113 tagtagcggcatctcaggtgcaagagatttccaagacagaatttagggattctattttttaatagtggattagcagctatgtatggaggtggattgttgatttgaaaaagccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagtagcggcatctcaggtgcaagagatttccaagacagaatttagggattctattttttaatagtggattagcagctatgtatggaggtggattgttgatttgaaaaagccg Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 3 End: 101 .. Y R C R L H L L N G L C F K P I R N K L L P N A A I Y P P P N N M ............ tagtagcggcatctcaggtgcaagagatttccaagacagaatttagggattctattttttaatagtggattagcagctatgtatggaggtggattgttgatttgaaaaagccg 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================================================ tagtagcggcatctcaggtgcaagagatttccaagacagaatttagggattctattttttaatagtggattagcagctatgtatggaggtggattgttgatttgaaaaagccg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0279:SSA_0281|SSA_0279:SSA_0281:Sugar-binding transcriptional repressor (DeoR), putative:hypothetical protein:->->:273431..273543 113 tagtagcggcatctcaggtgcaagagatttccaagacagaatttagggattctattttttaatagtggattagcagctatgtatggaggtggattgttgatttgaaaaagccg Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: NC_009009_SSA_0279_SSA_0281|Sugar-binding transcriptional repressor (DeoR), putative:hypothetical protein|POSITIVE:POSITIVE|[273431,273543]|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 tagtagcggcatctcaggtgcaagagatttccaagacagaatttagggattctattttttaatagtggattagcagctatgtatggaggtggattgttgatttgaaaaagccg tagtagcggcatctcaggtgcaagagatttccaagacagaatttagggattctattttttaatagtggattagcagctatgtatggaggtggattgttgatttgaaaaagccg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUAGCGGCAUCUCAGGUGCAAGAGAUUUCCAAGACAGAAUUUAGGGAUUCUAUUUUUUAAUAGUGGAUUAGCAGCUAUGUAUGGAGGUGGAUUGUUGAUUUGAAAAAGCCG ......((((...((((((((((...(((((((....((((((....))))))........(((((.(.....).)))))...)))))))...))))..))))))....)))) (-24.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGCUUUUUCAAAUCAACAAUCCACCUCCAUACAUAGCUGCUAAUCCACUAUUAAAAAAUAGAAUCCCUAAAUUCUGUCUUGGAAAUCUCUUGCACCUGAGAUGCCGCUACUA ((((................((((.........((((.((......))))))......(((((((......)))))))..)))).(((((........)))))))))...... (-17.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 48 3 46 1 NC_009009:SSA_0346|5end_hypothetical_protein_339448..339678_POSITIVE 295 47 2 50 1 NC_009009:SSA_0213|5end_hypothetical_protein_210135..210365_NEGATIVE 293 60 12 222 174 NC_009009:SSA_1979|5end_Alkaline-shock_protein,_putative_1974301..1974531_NEGATIVE 272 48 2 57 5 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 269 46 6 231 179 NC_009009:SSA_0197|5end_Dihydropteroate_synthase,_putative_195946..196176_POSITIVE 257 97 51 69 20 NC_009009:SSA_1628|5end_MutT/nudix_family_protein,_putative_1629864..1630094_POSITIVE 257 48 3 208 161 NC_009009:SSA_1588|5end_Conserved_ABC-type_antimicrobial_permease-like_protein,_putative_1591905..1592135_NEGATIVE 252 39 2 217 180 NC_009009:SSA_1037|5end_Cytidine_deaminase,_putative_1052118..1052348_POSITIVE 250 28 7 228 206 NC_009009:SSA_1974|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1970246..1970476_NEGATIVE 247 105 65 175 140 NC_009009:SSA_0369|5end_NADP-specific_glutamate_dehydrogenase,_putative_359896..360126_NEGATIVE 246 50 1 216 157 NC_009009:SSA_1012|5end_Phosphoenolpyruvate_synthase,_putative_1014739..1014969_POSITIVE 243 47 1 157 108 NC_009009:SSA_1527|5end_hypothetical_protein_1534587..1534817_POSITIVE 242 48 1 207 168 NC_009009:SSA_1657|5end_hypothetical_protein_1653231..1653461_NEGATIVE 242 50 6 59 17 NC_009009:SSA_0917|5end_Cobalamin-independent_methionine_synthase_II,_putative_930250..930480_NEGATIVE 242 38 1 81 40 NC_009009:SSA_0773|5end_PTS_enzyme_I,_putative_752603..752833_POSITIVE 241 49 6 63 10 NC_009009:SSA_2323|5end_Transporter,_putative_2327604..2327834_POSITIVE 239 49 3 197 158 NC_009009:SSA_1777|5end_Ribosomal_large_subunit_pseudouridine_synthase_B,_putative_1765155..1765385_NEGATIVE 239 99 64 156 123 NC_009009:SSA_0744|5end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_726804..727034_NEGATIVE 235 70 21 220 165 NC_009009:SSA_2230|5end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2231158..2231388_NEGATIVE 235 107 63 197 148 NC_009009:SSA_1172|5end_hypothetical_protein_1199926..1200156_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 60 12 79 31 NC_009009:SSA_1980|3end_50S_ribosomal_protein_L28,_putative_1974444..1974594_NEGATIVE 249 47 5 138 103 NC_009009:SSA_1861|3end_Aminopeptidase_C,_putative_1856568..1856718_NEGATIVE 243 68 21 97 56 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE 242 38 1 79 38 NC_009009:SSA_0772|3end_Histidine-containing_phosphocarrier_protein_of_the_PTS,_putative_752681..752831_POSITIVE 239 105 85 148 126 NC_009009:SSA_1769|3end_hypothetical_protein_1756939..1757089_NEGATIVE 239 99 64 146 113 NC_009009:SSA_0745|3end_hypothetical_protein_726814..726964_NEGATIVE 239 50 3 64 1 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 235 49 2 98 31 NC_009009:SSA_0294|3end_hypothetical_protein_287772..287922_NEGATIVE 233 50 5 85 32 NC_009009:SSA_1452|3end_Second_subunit_of_major_exonuclease,_putative_1456415..1456565_NEGATIVE 229 50 3 50 10 NC_009009:SSA_2168|3end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+],_putative_2168563..2168713_POSITIVE 228 22 4 80 63 NC_009009:SSA_2207|3end_hypothetical_protein_2206868..2207018_NEGATIVE 224 38 5 136 94 NC_009009:SSA_1627|3end_hypothetical_protein_1629508..1629658_NEGATIVE 224 50 8 62 8 NC_009009:SSA_0941|3end_ABC-type_phosphate_transport_system,_periplasmic_component,_putative_950022..950172_POSITIVE 222 38 7 81 45 NC_009009:SSA_1130|3end_Iron-dependent_peroxidase,_putative_1157090..1157240_POSITIVE 222 44 1 79 32 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 221 83 48 128 87 NC_009009:SSA_1404|3end_hypothetical_protein_1418052..1418202_NEGATIVE 221 101 65 68 21 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 219 96 64 38 8 NC_009009:SSA_2309|3end_Fimbrial_assembly_protein,_putative_2310474..2310624_NEGATIVE 219 79 31 85 42 NC_009009:SSA_0904|3end_CshA-like_fibrillar_surface_protein_A_902958..903108_POSITIVE 219 48 7 81 34 NC_009009:SSA_0327|3end_Glycosyltransferase,_putative_320436..320586_POSITIVE