Origin IGS: acactaacctcctctcattcactgaatttaagctattctaactcacttatcttattatataattttgagttgactccaagtcaagcattttgcgtctaatcgaaaaattttttatcattatcagttctcttattagcataccttttcatcaatcaaagaaagagg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cctctttctttgattgatgaaaaggtatgctaataagagaactgataatgataaaaaatttttcgattagacgcaaaatgcttgacttggagtcaactcaaaattatataataagataagtgagttagaatagcttaaattcagtgaatgagaggaggttagtgt Mask Tandem Repeat Region ================================================ acactaacctcctctcattcactgaatttaagctattctaactcacttatcttattatataattttgagttgactccaagtcaagcattttgcgtctaatcgaaaaattttttatcattatcagttctcttattagcataccttttcatcaatcaaagaaagagg Find is-nt database================================================ Query_seq: SMT_1017:SMT_1018|SMT_1017:SMT_1018:transcriptional regulator, MerR family:hypothetical protein predicted by Glimmer/Critica:<-->:954539..954703 165 acactaacctcctctcattcactgaatttaagctattctaactcacttatcttattatataattttgagttgactccaagtcaagcattttgcgtctaatcgaaaaattttttatcattatcagttctcttattagcataccttttcatcaatcaaagaaagagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1017:SMT_1018|SMT_1017:SMT_1018:transcriptional regulator, MerR family:hypothetical protein predicted by Glimmer/Critica:<-->:954539..954703 165 acactaacctcctctcattcactgaatttaagctattctaactcacttatcttattatataattttgagttgactccaagtcaagcattttgcgtctaatcgaaaaattttttatcattatcagttctcttattagcataccttttcatcaatcaaagaaagagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1017:SMT_1018|SMT_1017:SMT_1018:transcriptional regulator, MerR family:hypothetical protein predicted by Glimmer/Critica:<-->:954539..954703 165 acactaacctcctctcattcactgaatttaagctattctaactcacttatcttattatataattttgagttgactccaagtcaagcattttgcgtctaatcgaaaaattttttatcattatcagttctcttattagcataccttttcatcaatcaaagaaagagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acactaacctcctctcattcactgaatttaagctattctaactcacttatcttattatataattttgagttgactccaagtcaagcattttgcgtctaatcgaaaaattttttatcattatcagttctcttattagcataccttttcatcaatcaaagaaagagg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 50 End: 139 ................................................. R I I Y N Q T S E L D L M K R R I S F N K I M I L E R I L M .......................... acactaacctcctctcattcactgaatttaagctattctaactcacttatcttattatataattttgagttgactccaagtcaagcattttgcgtctaatcgaaaaattttttatcattatcagttctcttattagcataccttttcatcaatcaaagaaagagg 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: 81 Start: 89 End: 118 ........................................................................................TTTGCGTCTAATCGAAAAATTTTTTATCAT............................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acactaacctcctctcattcactgaatttaagctattctaactcacttatcttattatataattttgagttgactccaagtcaagcattttgcgtctaatcgaaaaattttttatcattatcagttctcttattagcataccttttcatcaatcaaagaaagagg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1017:SMT_1018|SMT_1017:SMT_1018:transcriptional regulator, MerR family:hypothetical protein predicted by Glimmer/Critica:<-->:954539..954703 165 acactaacctcctctcattcactgaatttaagctattctaactcacttatcttattatataattttgagttgactccaagtcaagcattttgcgtctaatcgaaaaattttttatcattatcagttctcttattagcataccttttcatcaatcaaagaaagagg Intra-Species Hit: Count: 1 Min: 1 Max: 165 Len: 165 Subject: smit_SMT_1017_SMT_1018|transcriptional regulator, MerR family:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:POSITIVE|[954539,954703]|165 HSP 1 e-value: 7.0E-89 bit: 327.0 Len: 165 Query Start:1 Query End:165 Subject Strand: POSITIVE Subject Start: 1 Subject End: 165 acactaacctcctctcattcactgaatttaagctattctaactcacttatcttattatataattttgagttgactccaagtcaagcattttgcgtctaatcgaaaaattttttatcattatcagttctcttattagcataccttttcatcaatcaaagaaagagg acactaacctcctctcattcactgaatttaagctattctaactcacttatcttattatataattttgagttgactccaagtcaagcattttgcgtctaatcgaaaaattttttatcattatcagttctcttattagcataccttttcatcaatcaaagaaagagg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACACUAACCUCCUCUCAUUCACUGAAUUUAAGCUAUUCUAACUCACUUAUCUUAUUAUAUAAUUUUGAGUUGACUCCAAGUCAAGCAUUUUGCGUCUAAUCGAAAAAUUUUUUAUCAUUAUCAGUUCUCUUAUUAGCAUACCUUUUCAUCAAUCAAAGAAAGAGG ..........(((((.....(((((......(((.....((((((.((((........))))...))))))(((.....))).))).((((.((......)).)))).............)))))................((((.........))))..))))) (-17.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUCUUUCUUUGAUUGAUGAAAAGGUAUGCUAAUAAGAGAACUGAUAAUGAUAAAAAAUUUUUCGAUUAGACGCAAAAUGCUUGACUUGGAGUCAACUCAAAAUUAUAUAAUAAGAUAAGUGAGUUAGAAUAGCUUAAAUUCAGUGAAUGAGAGGAGGUUAGUGU ((((((((.((.(((((....(((.(((.(((((..(((..(((((...((...........)).)))))..((.....)).((((.....)))).)))....((((........))))....))))).))).)))....))))).)).)))).))))....... (-28.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 819 50 1 141 92 smit:SMT_1017|5end_transcriptional_regulator,_MerR_family_954448..954678_NEGATIVE 304 109 74 97 59 smit:SMT_1259|5end_hypothetical_protein_1225139..1225369_POSITIVE 248 92 64 183 152 smit:SMT_1573|5end_MutT/NUDIX_family_protein_1566413..1566643_POSITIVE 242 101 67 116 82 smit:SMT_194|5end_hypothetical_protein_predicted_by_Glimmer/Critica_126952..127182_NEGATIVE 241 130 87 115 83 smit:SMT_702|5end_hypothetical_protein_612311..612541_NEGATIVE 239 86 41 209 163 smit:SMT_643|5end_hypothetical_protein_548495..548725_NEGATIVE 237 98 51 229 175 smit:SMT_1096|5end_glyceraldehyde-3-phosphate_dehydrogenase_1038376..1038606_NEGATIVE 229 102 64 180 139 smit:SMT_198|5end_50S_ribosomal_protein_L17_128632..128862_POSITIVE 225 104 64 92 39 smit:SMT_532|5end_30S_ribosomal_protein_S16_453076..453306_POSITIVE 223 46 2 123 87 smit:SMT_2027|5end_competence-specific_global_transcription_modulator_1943204..1943434_NEGATIVE 223 138 93 113 66 smit:SMT_1806|5end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781229..1781459_POSITIVE 223 138 93 113 66 smit:SMT_1635|5end_putative_N-acetyldiaminopimelate_deacetylase_1621426..1621656_POSITIVE 221 105 63 101 50 smit:SMT_307|5end_K02078_acyl_carrier_protein_249187..249417_POSITIVE 218 120 74 114 65 smit:SMT_1537|5end_hypothetical_protein_1522668..1522898_NEGATIVE 218 60 11 142 96 smit:SMT_1070|5end_hypothetical_protein_1009946..1010176_NEGATIVE 218 150 122 58 23 smit:SMT_855|5end_dihydrofolate_reductase_799998..800228_NEGATIVE 218 119 78 186 145 smit:SMT_572|5end_fructose_repressor_490239..490469_POSITIVE 218 97 64 225 181 smit:SMT_533|5end_RNA_binding_protein_453218..453448_POSITIVE 218 97 64 225 181 smit:SMT_526|5end_RNA_binding_protein_451149..451379_POSITIVE 218 97 64 225 181 smit:SMT_510|5end_hypothetical_protein_439038..439268_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 245 55 11 134 79 smit:SMT_766|3end_hypothetical_protein_673385..673535_NEGATIVE 239 86 41 113 67 smit:SMT_644|3end_O-acetylhomoserine_(thiol)-lyase_548591..548741_NEGATIVE 218 120 74 113 64 smit:SMT_1538|3end_two-component_response_regulator_YvqC_1522669..1522819_NEGATIVE 209 148 113 128 79 smit:SMT_407|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_353166..353316_POSITIVE 206 48 4 137 73 smit:SMT_1779|3end_hypothetical_protein_1755093..1755243_NEGATIVE 206 99 66 71 29 smit:SMT_812|3end_acetyltransferase,_GNAT_family_721664..721814_NEGATIVE 204 101 71 90 59 smit:SMT_1509|3end_phosphopentomutase_1491570..1491720_NEGATIVE 201 131 92 122 81 smit:SMT_1636|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1623187..1623337_POSITIVE 200 47 3 118 71 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE 199 160 115 109 59 smit:SMT_1870|3end_K07566_putative_translation_factor_1829217..1829367_NEGATIVE 199 138 94 45 4 smit:SMT_1805|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1781241..1781391_POSITIVE 199 138 94 45 4 smit:SMT_1634|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621438..1621588_POSITIVE 197 46 11 140 99 smit:SMT_379|3end_acetyltransferase,_GNAT_family_316456..316606_POSITIVE 197 46 11 140 99 smit:SMT_370|3end_acetyltransferase,_GNAT_family_305328..305478_POSITIVE 196 138 92 116 63 smit:SMT_2088|3end_glucose-1-phosphate_thymidylyltransferase_1985066..1985216_POSITIVE 196 102 62 148 96 smit:SMT_1818|3end_tryptophan_synthase,_alpha_subunit_1793037..1793187_POSITIVE 196 98 63 34 4 smit:SMT_304|3end_hypothetical_protein_247583..247733_POSITIVE 196 138 92 116 63 smit:SMT_290|3end_glucose-1-phosphate_thymidylyltransferase_234276..234426_POSITIVE 195 103 70 97 61 smit:SMT_918|3end_hypothetical_protein_871290..871440_NEGATIVE 195 95 58 140 92 smit:SMT_554|3end_K09013_Fe-S_cluster_assembly_ATP-binding_protein_472323..472473_POSITIVE