Origin IGS: gacacctccaatttatttccatatcgaaacgaataaaacaattgtaacactcatcgttccaactgtcaactatttcgatttagaaataatttttcccagtaaaaaaatctcctacccaaggtagaagatttcaatcttataaaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gttttataagattgaaatcttctaccttgggtaggagatttttttactgggaaaaattatttctaaatcgaaatagttgacagttggaacgatgagtgttacaattgttttattcgtttcgatatggaaataaattggaggtgtc Mask Tandem Repeat Region ================================================ gacacctccaatttatttccatatcgaaacgaataaaacaattgtaacactcatcgttccaactgtcaactatttcgatttagaaataatttttcccagtaaaaaaatctcctacccaaggtagaagatttcaatcttataaaac Find is-nt database================================================ Query_seq: SMT_1024:SMT_1025|SMT_1024:SMT_1025:transcriptional regulator, MarR family:hypothetical protein:<-<-:959495..959639 145 gacacctccaatttatttccatatcgaaacgaataaaacaattgtaacactcatcgttccaactgtcaactatttcgatttagaaataatttttcccagtaaaaaaatctcctacccaaggtagaagatttcaatcttataaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1024:SMT_1025|SMT_1024:SMT_1025:transcriptional regulator, MarR family:hypothetical protein:<-<-:959495..959639 145 gacacctccaatttatttccatatcgaaacgaataaaacaattgtaacactcatcgttccaactgtcaactatttcgatttagaaataatttttcccagtaaaaaaatctcctacccaaggtagaagatttcaatcttataaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1024:SMT_1025|SMT_1024:SMT_1025:transcriptional regulator, MarR family:hypothetical protein:<-<-:959495..959639 145 gacacctccaatttatttccatatcgaaacgaataaaacaattgtaacactcatcgttccaactgtcaactatttcgatttagaaataatttttcccagtaaaaaaatctcctacccaaggtagaagatttcaatcttataaaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacacctccaatttatttccatatcgaaacgaataaaacaattgtaacactcatcgttccaactgtcaactatttcgatttagaaataatttttcccagtaaaaaaatctcctacccaaggtagaagatttcaatcttataaaac Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 11 End: 121 .......... M Y F H I E T N K T I V T L I V P T V N Y F D L E I I F P S K K I S Y P R ........................ gacacctccaatttatttccatatcgaaacgaataaaacaattgtaacactcatcgttccaactgtcaactatttcgatttagaaataatttttcccagtaaaaaaatctcctacccaaggtagaagatttcaatcttataaaac 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: 90 Start: 41 End: 70 ........................................GTTGACAGTTGGAACGATGAGTGTTACAAT........................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gacacctccaatttatttccatatcgaaacgaataaaacaattgtaacactcatcgttccaactgtcaactatttcgatttagaaataatttttcccagtaaaaaaatctcctacccaaggtagaagatttcaatcttataaaac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 62 HP_score: -2.3 Tail_Score: -4.84642 Start: 39 End: 65 Full_Region: aatcgaaatagttga cagttggaacg atgag tgttacaattg ttttattcgtttcga ......................................cagttggaacgatgagtgttacaattg................................................................................ TransTerm Strand: + Conf: 77 HP_score: -8.3 Tail_Score: -3.79071 Start: 108 End: 128 Full_Region: TTCCCAGTAAAAAAA TCTCCTACC CAA GGTAGAAGA TTTCAATCTTATAAA ...........................................................................................................TCTCCTACCCAAGGTAGAAGA................. Find igs database================================================ Query_seq: SMT_1024:SMT_1025|SMT_1024:SMT_1025:transcriptional regulator, MarR family:hypothetical protein:<-<-:959495..959639 145 gacacctccaatttatttccatatcgaaacgaataaaacaattgtaacactcatcgttccaactgtcaactatttcgatttagaaataatttttcccagtaaaaaaatctcctacccaaggtagaagatttcaatcttataaaac Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: smit_SMT_1024_SMT_1025|transcriptional regulator, MarR family:hypothetical protein|NEGATIVE:NEGATIVE|[959495,959639]|145 HSP 1 e-value: 2.0E-64 bit: 246.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 gacacctccaatttatttccatatcgaaacgaataaaacaattgtaacactcatcgttccaactgtcaactatttcgatttagaaataatttttcccagtnnnnnnntctcctacccaaggtagaagatttcaatcttataaaac gacacctccaatttatttccatatcgaaacgaataaaacaattgtaacactcatcgttccaactgtcaactatttcgatttagaaataatttttcccagtaaaaaaatctcctacccaaggtagaagatttcaatcttataaaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACACCUCCAAUUUAUUUCCAUAUCGAAACGAAUAAAACAAUUGUAACACUCAUCGUUCCAACUGUCAACUAUUUCGAUUUAGAAAUAAUUUUUCCCAGUAAAAAAAUCUCCUACCCAAGGUAGAAGAUUUCAAUCUUAUAAAAC ............(((((((...(((((((........(((.(((.(((.......))).))).)))......)))))))...)))))))...............((((((.(((((...))))).)))))).............. (-23.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUAUAAGAUUGAAAUCUUCUACCUUGGGUAGGAGAUUUUUUUACUGGGAAAAAUUAUUUCUAAAUCGAAAUAGUUGACAGUUGGAACGAUGAGUGUUACAAUUGUUUUAUUCGUUUCGAUAUGGAAAUAAAUUGGAGGUGUC .((((...(((..(((((((((((((...)))))))))))))..).))..))))..(((((((((.(((((((((((.((((((((.((((.....)))).))))))))..))).)))))))).)))))))))............ (-42.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 792 70 21 161 112 smit:SMT_1024|5end_transcriptional_regulator,_MarR_family_959404..959634_NEGATIVE 285 130 90 214 172 smit:SMT_1341|5end_putative_cell_division_protein_1319115..1319345_NEGATIVE 257 99 51 209 158 smit:SMT_132|5end_L-serine_dehydratase_alpha_subunit_84557..84787_NEGATIVE 249 67 21 224 172 smit:SMT_1866|5end_extramembranal_protein_1827290..1827520_POSITIVE 249 67 21 224 172 smit:SMT_1313|5end_extramembranal_protein_1277274..1277504_POSITIVE 237 137 91 185 124 smit:SMT_905|5end_hypothetical_protein_predicted_by_Glimmer/Critica_853467..853697_NEGATIVE 229 100 53 137 94 smit:SMT_152|5end_sensor_histidine_kinase,_putative_100759..100989_POSITIVE 218 127 96 131 88 smit:SMT_387|5end_hypothetical_protein_predicted_by_Glimmer/Critica_320937..321167_POSITIVE 217 136 109 148 123 smit:SMT_806|5end_hypothetical_protein_716166..716396_NEGATIVE 217 100 53 102 50 smit:SMT_230|5end_hypothetical_protein_predicted_by_Glimmer/Critica_165830..166060_NEGATIVE 216 132 97 213 184 smit:SMT_1192|5end_phosphoribosylaminoimidazolecarboxamide_formyltransferase_/_IMP_cyclohydrolase_1151406..1151636_NEGATIVE 215 80 38 119 77 smit:SMT_338|5end_heat-inducible_transcription_repressor_HrcA_276825..277055_POSITIVE 212 79 55 217 183 smit:SMT_774|5end_hypothetical_protein_685231..685461_NEGATIVE 209 98 55 104 65 smit:SMT_1276|5end_rod_shape-determining_protein_MreD_1239412..1239642_POSITIVE 206 78 45 199 169 smit:SMT_1853|5end_1,4-alpha-glucan_branching_enzyme_1818064..1818294_NEGATIVE 204 68 24 60 12 smit:SMT_850|5end_hypothetical_protein_797014..797244_NEGATIVE 204 94 51 86 46 smit:SMT_432|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_373553..373783_POSITIVE 202 118 73 230 180 smit:SMT_871|5end_K03311_branched-chain_amino_acid:cation_transporter,_LIVCS_family_820160..820390_NEGATIVE 202 118 73 230 180 smit:SMT_386|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_320353..320583_POSITIVE 200 129 110 45 21 smit:SMT_2041|5end_transcription-repair_coupling_factor_1952518..1952748_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 130 90 53 11 smit:SMT_1342|3end_protease_maturation_protein,_putative_1319276..1319426_NEGATIVE 230 99 53 80 37 smit:SMT_1069|3end_acetyl_xylan_esterase,_putative_1009595..1009745_POSITIVE 218 127 96 116 73 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 211 122 83 50 4 smit:SMT_1862|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1825460..1825610_POSITIVE 209 98 55 104 65 smit:SMT_1275|3end_rod_shape-determining_protein_MreC_1239492..1239642_POSITIVE 204 94 51 84 44 smit:SMT_431|3end_UDP-N-acetylmuramoyl-L-alanyl-D-glutamate_synthetase_373631..373781_POSITIVE 202 118 73 59 9 smit:SMT_872|3end_hypothetical_protein_820331..820481_NEGATIVE 202 118 73 59 9 smit:SMT_385|3end_hypothetical_protein_320262..320412_POSITIVE 200 75 38 85 37 smit:SMT_532|3end_30S_ribosomal_protein_S16_453278..453428_POSITIVE 200 75 38 85 37 smit:SMT_529|3end_30S_ribosomal_protein_S16_452379..452529_POSITIVE 200 75 38 85 37 smit:SMT_525|3end_30S_ribosomal_protein_S16_451209..451359_POSITIVE 200 75 38 85 37 smit:SMT_509|3end_30S_ribosomal_protein_S16_439098..439248_POSITIVE 198 83 42 56 9 smit:SMT_1348|3end_exoribonuclease_II_1325148..1325298_NEGATIVE 197 96 56 44 12 smit:SMT_1948|3end_IS1381_transposase_protein_A_1883581..1883731_POSITIVE 194 80 47 107 70 smit:SMT_1513|3end_hypothetical_protein_1494761..1494911_NEGATIVE 184 68 29 133 103 smit:SMT_270|3end_ATP-binding_subunit_of_Clp_protease_and_DnaK/DnaJ_chaperones_211225..211375_POSITIVE 182 139 108 84 45 smit:SMT_1780|3end_PTS_system,_glucose-specific_IIABC_component_1755960..1756110_NEGATIVE 180 76 37 61 6 smit:SMT_1888|3end_K02026_multiple_sugar_transport_system_permease_protein_1842842..1842992_POSITIVE 180 78 49 94 66 smit:SMT_1826|3end_ATP_synthase_beta_chain_1797622..1797772_POSITIVE 178 140 91 94 42 smit:SMT_663|3end_phosphate_acetyltransferase_574016..574166_NEGATIVE