Origin IGS: gagaaactcctccttattaaaaccattataccaaatttgccttaaaaaaaactcaactctctacattttacatgagatagctgagttttctttttattttaggcttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataagcctaaaataaaaagaaaactcagctatctcatgtaaaatgtagagagttgagttttttttaaggcaaatttggtataatggttttaataaggaggagtttctc Mask Tandem Repeat Region ================================================ gagaaactcctccttattaaaaccattataccaaatttgccttaaaaaaaactcaactctctacattttacatgagatagctgagttttctttttattttaggcttat Find is-nt database================================================ Query_seq: SMT_1166:SMT_1167|SMT_1166:SMT_1167:DNA-binding response regulator CiaR:aminopeptidase N:<-<-:1112575..1112682 108 gagaaactcctccttattaaaaccattataccaaatttgccttaaaaaaaactcaactctctacattttacatgagatagctgagttttctttttattttaggcttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1166:SMT_1167|SMT_1166:SMT_1167:DNA-binding response regulator CiaR:aminopeptidase N:<-<-:1112575..1112682 108 gagaaactcctccttattaaaaccattataccaaatttgccttaaaaaaaactcaactctctacattttacatgagatagctgagttttctttttattttaggcttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1166:SMT_1167|SMT_1166:SMT_1167:DNA-binding response regulator CiaR:aminopeptidase N:<-<-:1112575..1112682 108 gagaaactcctccttattaaaaccattataccaaatttgccttaaaaaaaactcaactctctacattttacatgagatagctgagttttctttttattttaggcttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagaaactcctccttattaaaaccattataccaaatttgccttaaaaaaaactcaactctctacattttacatgagatagctgagttttctttttattttaggcttat Predict ORF larger than 30AA ================================================ gagaaactcctccttattaaaaccattataccaaatttgccttaaaaaaaactcaactctctacattttacatgagatagctgagttttctttttattttaggcttat 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================================================ gagaaactcctccttattaaaaccattataccaaatttgccttaaaaaaaactcaactctctacattttacatgagatagctgagttttctttttattttaggcttat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1166:SMT_1167|SMT_1166:SMT_1167:DNA-binding response regulator CiaR:aminopeptidase N:<-<-:1112575..1112682 108 gagaaactcctccttattaaaaccattataccaaatttgccttaaaaaaaactcaactctctacattttacatgagatagctgagttttctttttattttaggcttat Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: smit_SMT_1166_SMT_1167|DNA-binding response regulator CiaR:aminopeptidase N|NEGATIVE:NEGATIVE|[1112575,1112682]|108 HSP 1 e-value: 9.0E-41 bit: 167.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 gagaaactcctccttattaaaaccattataccaaatttgccttnnnnnnnnctcaactctctacattttacatgagatagctgagttttctttttattttaggcttat gagaaactcctccttattaaaaccattataccaaatttgccttaaaaaaaactcaactctctacattttacatgagatagctgagttttctttttattttaggcttat Inter-species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_003028_SP_0797_SP_0798|aminopeptidase N:DNA-binding response regulator CiaR|POSITIVE:POSITIVE|[751854,751961]|108 HSP 1 e-value: 5.0E-36 bit: 151.0 Len: 108 Query Start:1 Query End:108 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 108 gagaaactcctccttattaaaaccattataccaaatttgccttnnnnnnnnctcaactctctacattttacatgagatagctgagttttctttttattttaggcttat gagaaactcctccttattaaaactattataccaaatttgccttaaaaaaaactcaactctctgcattttacatgagatagctgagttttctttttattttaggcttat Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAAACUCCUCCUUAUUAAAACCAUUAUACCAAAUUUGCCUUAAAAAAAACUCAACUCUCUACAUUUUACAUGAGAUAGCUGAGUUUUCUUUUUAUUUUAGGCUUAU (((......)))..........................(((((((((((((((((.((.(((.(((.....)))))).)).)))))))..))))))....)))).... (-18.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAGCCUAAAAUAAAAAGAAAACUCAGCUAUCUCAUGUAAAAUGUAGAGAGUUGAGUUUUUUUUAAGGCAAAUUUGGUAUAAUGGUUUUAAUAAGGAGGAGUUUCUC ....((((.......(((((((((((((((.((((((.....))).))).))))))))))))))).))))..........................((((....)))) (-25.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 748 90 41 181 132 smit:SMT_1166|5end_DNA-binding_response_regulator_CiaR_1112484..1112714_NEGATIVE 252 77 37 79 46 smit:SMT_1106|5end_ribonuclease_P_protein_component_1047972..1048202_NEGATIVE 243 75 31 214 168 smit:SMT_1645|5end_hypothetical_protein_1631738..1631968_POSITIVE 235 93 56 219 180 smit:SMT_1727|5end_uridine_kinase_1712483..1712713_POSITIVE 216 96 51 62 13 smit:SMT_376|5end_DNA_(cytosine-5-)-methyltransferase_312900..313130_POSITIVE 213 50 6 160 95 smit:SMT_773|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase_684365..684595_NEGATIVE 206 81 52 43 12 smit:SMT_302|5end_K07444_putative_N6-adenine-specific_DNA_methylase_244808..245038_POSITIVE 205 44 1 120 77 smit:SMT_393|5end_hypothetical_protein_predicted_by_Glimmer/Critica_323973..324203_POSITIVE 204 96 53 69 21 smit:SMT_2042|5end_K04077_chaperonin_GroEL_(Hsp60)_1953889..1954119_NEGATIVE 203 45 8 130 79 smit:SMT_1870|5end_K07566_putative_translation_factor_1829819..1830049_NEGATIVE 203 96 55 156 112 smit:SMT_1737|5end_peptidyl-prolyl_cis-trans_isomerase_1719862..1720092_POSITIVE 203 100 51 112 70 smit:SMT_1266|5end_predicted_transcriptional_regulator_1231362..1231592_POSITIVE 202 93 57 70 30 smit:SMT_1957|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1890645..1890875_POSITIVE 200 97 59 154 114 smit:SMT_1095|5end_ribosomal_large_subunit_pseudouridine_synthase,_RluD_subfamily_1036373..1036603_POSITIVE 200 99 58 167 117 smit:SMT_736|5end_hypothetical_protein_642270..642500_NEGATIVE 199 92 53 85 43 smit:SMT_855|5end_dihydrofolate_reductase_799998..800228_NEGATIVE 196 96 58 72 37 smit:SMT_2014|5end_tryptophan_synthase_beta_chain_1932471..1932701_POSITIVE 196 41 8 31 3 smit:SMT_1473|5end_hypothetical_protein_1454320..1454550_POSITIVE 192 85 52 34 2 smit:SMT_1692|5end_hypothetical_protein_1675169..1675399_POSITIVE 192 99 53 154 108 smit:SMT_767|5end_hypothetical_protein_676454..676684_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 252 77 37 62 29 smit:SMT_1107|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1047989..1048139_NEGATIVE 235 93 56 109 70 smit:SMT_1726|3end_tRNA_pseudouridine_synthase_B_1712453..1712603_POSITIVE 205 44 1 74 31 smit:SMT_392|3end_acetyltransferase,_GNAT_family_324007..324157_POSITIVE 203 45 8 146 95 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 203 96 55 76 32 smit:SMT_1736|3end_acetyltransferase,_GNAT_family_1719862..1720012_POSITIVE 199 99 73 145 118 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 196 96 58 42 7 smit:SMT_2013|3end_alpha-glycerophosphate_oxidase_1932521..1932671_POSITIVE 193 48 18 69 39 smit:SMT_568|3end_hypothetical_protein_486389..486539_POSITIVE 192 85 52 34 2 smit:SMT_1691|3end_putative_deoxyribonuclease_1675249..1675399_POSITIVE 192 63 22 45 3 smit:SMT_348|3end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_287282..287432_POSITIVE 191 96 66 134 106 smit:SMT_1112|3end_K02248_competence_protein_ComGF_1051387..1051537_NEGATIVE 191 42 7 73 33 smit:SMT_830|3end_hypothetical_protein_765064..765214_NEGATIVE 189 91 53 71 31 smit:SMT_1097|3end_alcohol_dehydrogenase_/_acetaldehyde_dehydrogenase_1038697..1038847_NEGATIVE 189 50 8 58 7 smit:SMT_920|3end_serine/threonine_protein_kinase_872588..872738_NEGATIVE 188 92 53 60 25 smit:SMT_1157|3end_septation_ring_formation_regulator_EzrA_1100202..1100352_NEGATIVE 188 100 52 97 43 smit:SMT_430|3end_hypothetical_protein_372164..372314_POSITIVE 179 97 53 128 85 smit:SMT_1341|3end_putative_cell_division_protein_1317892..1318042_NEGATIVE 175 93 65 151 119 smit:SMT_101|3end_cell_division_protein_34067..34217_POSITIVE 174 100 57 139 98 smit:SMT_1544|3end_mevalonate_kinase_1528006..1528156_NEGATIVE 173 100 53 50 10 smit:SMT_1060|3end_K03977_GTP-binding_protein_999496..999646_POSITIVE