Origin IGS: gaaaaattttaaacatatagcttgcaagaatttcttaattaatatataattaagtgtaagagttttttgaaaggaaatttatgaaatgttaaaagatctttaagcattc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaatgcttaaagatcttttaacatttcataaatttcctttcaaaaaactcttacacttaattatatattaattaagaaattcttgcaagctatatgtttaaaatttttc Mask Tandem Repeat Region ================================================ gaaaaattttaaacatatagcttgcaagaatttcttaattaatatataattaagtgtaagagttttttgaaaggaaatttatgaaatgttaaaagatctttaagcattc Find is-nt database================================================ Query_seq: SMT_2009:SMT_2010|SMT_2009:SMT_2010:GtrA family protein:hypothetical protein predicted by Glimmer/Critica:->->:1929545..1929653 109 gaaaaattttaaacatatagcttgcaagaatttcttaattaatatataattaagtgtaagagttttttgaaaggaaatttatgaaatgttaaaagatctttaagcattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2009:SMT_2010|SMT_2009:SMT_2010:GtrA family protein:hypothetical protein predicted by Glimmer/Critica:->->:1929545..1929653 109 gaaaaattttaaacatatagcttgcaagaatttcttaattaatatataattaagtgtaagagttttttgaaaggaaatttatgaaatgttaaaagatctttaagcattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2009:SMT_2010|SMT_2009:SMT_2010:GtrA family protein:hypothetical protein predicted by Glimmer/Critica:->->:1929545..1929653 109 gaaaaattttaaacatatagcttgcaagaatttcttaattaatatataattaagtgtaagagttttttgaaaggaaatttatgaaatgttaaaagatctttaagcattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaaaattttaaacatatagcttgcaagaatttcttaattaatatataattaagtgtaagagttttttgaaaggaaatttatgaaatgttaaaagatctttaagcattc Predict ORF larger than 30AA ================================================ gaaaaattttaaacatatagcttgcaagaatttcttaattaatatataattaagtgtaagagttttttgaaaggaaatttatgaaatgttaaaagatctttaagcattc 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: 86 Start: 21 End: 50 ....................CTTGCAAGAATTTCTTAATTAATATATAAT........................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaaaaattttaaacatatagcttgcaagaatttcttaattaatatataattaagtgtaagagttttttgaaaggaaatttatgaaatgttaaaagatctttaagcattc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_2009:SMT_2010|SMT_2009:SMT_2010:GtrA family protein:hypothetical protein predicted by Glimmer/Critica:->->:1929545..1929653 109 gaaaaattttaaacatatagcttgcaagaatttcttaattaatatataattaagtgtaagagttttttgaaaggaaatttatgaaatgttaaaagatctttaagcattc Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: smit_SMT_2009_SMT_2010|GtrA family protein:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[1929545,1929653]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 gaaaaattttaaacatatagcttgcaagaatttcttaattaatatataattaagtgtaagagttttttgaaaggaaatttatgaaatgttaaaagatctttaagcattc gaaaaattttaaacatatagcttgcaagaatttcttaattaatatataattaagtgtaagagttttttgaaaggaaatttatgaaatgttaaaagatctttaagcattc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAAUUUUAAACAUAUAGCUUGCAAGAAUUUCUUAAUUAAUAUAUAAUUAAGUGUAAGAGUUUUUUGAAAGGAAAUUUAUGAAAUGUUAAAAGAUCUUUAAGCAUUC .............((((...(((.((((((.((((((.(((((.....)))))...)))))).))))))..))).....)))).((((((.(((....))).)))))). (-15.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUGCUUAAAGAUCUUUUAACAUUUCAUAAAUUUCCUUUCAAAAAACUCUUACACUUAAUUAUAUAUUAAUUAAGAAAUUCUUGCAAGCUAUAUGUUUAAAAUUUUUC ....((((.((((...((((........)))).......................((((((((.....))))))))....))))..))))................... (-10.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 187 99 53 165 110 smit:SMT_1089|5end_hypothetical_protein_1024561..1024791_NEGATIVE 186 78 31 149 99 smit:SMT_416|5end_ribonuclease_Z_359423..359653_POSITIVE 181 75 45 45 10 smit:SMT_773|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase_684365..684595_NEGATIVE 179 69 27 135 93 smit:SMT_1421|5end_K02003_1407342..1407572_NEGATIVE 179 89 46 144 95 smit:SMT_619|5end_riboflavin_kinase_/_FMN_adenylyltransferase_527812..528042_POSITIVE 172 58 19 90 57 smit:SMT_2008|5end_K07485_transposase_1928662..1928892_NEGATIVE 165 99 54 213 160 smit:SMT_645|5end_hypothetical_protein_550816..551046_NEGATIVE 155 91 53 228 187 smit:SMT_826|5end_hypothetical_protein_750022..750252_NEGATIVE 152 100 64 178 141 smit:SMT_105|5end_hypothetical_protein_50919..51149_POSITIVE 150 29 17 131 119 smit:SMT_573|5end_1-phosphofructokinase_490976..491206_POSITIVE 149 68 26 198 154 smit:SMT_402|5end_two-component_response_regulator_YesN_330846..331076_POSITIVE 147 75 31 143 101 smit:SMT_1564|5end_transcriptional_antiterminator,_BglG_family_1555587..1555817_POSITIVE 147 100 52 84 31 smit:SMT_468|5end_ABC-type_oligopeptide_transport_system,_periplasmic_component_404710..404940_POSITIVE 146 77 31 221 182 smit:SMT_1606|5end_glutamate_racemase_1595857..1596087_POSITIVE 144 56 19 182 143 smit:SMT_1228|5end_DNA-binding_protein_1191035..1191265_NEGATIVE 142 37 11 38 14 smit:SMT_1263|5end_hypothetical_protein_1228104..1228334_POSITIVE 140 65 21 79 51 smit:SMT_1208|5end_choline_binding_protein_PcpA_1169690..1169920_NEGATIVE 140 58 14 128 89 smit:SMT_1201|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1163920..1164150_NEGATIVE 139 28 1 122 93 smit:SMT_813|5end_acetyltransferase,_GNAT_family_722322..722552_NEGATIVE 138 100 58 219 185 smit:SMT_499|5end_hypothetical_protein_432572..432802_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 223 99 55 68 24 smit:SMT_495|3end_bacterial_peptide_chain_release_factor_2_(RF-2)_430053..430203_POSITIVE 186 78 31 134 84 smit:SMT_415|3end_hypothetical_protein_359488..359638_POSITIVE 179 69 27 120 78 smit:SMT_1422|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1407357..1407507_NEGATIVE 171 76 49 32 5 smit:SMT_1219|3end_hypothetical_protein_1180398..1180548_POSITIVE 165 99 54 70 17 smit:SMT_646|3end_K07284_sortase_A_550959..551109_NEGATIVE 154 37 1 87 53 smit:SMT_1212|3end_acyl_carrier_protein,_putative_1171424..1171574_NEGATIVE 152 100 64 105 68 smit:SMT_104|3end_DNA_repair_protein_50926..51076_POSITIVE 150 29 17 134 122 smit:SMT_572|3end_fructose_repressor_491059..491209_POSITIVE 149 68 26 127 83 smit:SMT_401|3end_peptide_methionine_sulfoxide_reductase_330855..331005_POSITIVE 147 100 52 74 21 smit:SMT_467|3end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_404780..404930_POSITIVE 142 37 11 36 12 smit:SMT_1262|3end_ribosomal_protein_L11_methyltransferase_1228182..1228332_POSITIVE 141 42 1 146 109 smit:SMT_1470|3end_K06188_aquaporin_Z_1453266..1453416_POSITIVE 140 58 14 103 64 smit:SMT_1202|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1163945..1164095_NEGATIVE 139 28 1 112 83 smit:SMT_814|3end_UDP-N-acetyl_muramate-alanine_ligase_722332..722482_NEGATIVE 136 51 16 113 72 smit:SMT_569|3end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_488553..488703_POSITIVE 134 84 49 139 97 smit:SMT_1158|3end_DNA_gyrase_subunit_B_1102011..1102161_NEGATIVE 134 27 15 57 45 smit:SMT_859|3end_K02086_DNA_replication_protein_803381..803531_NEGATIVE 134 70 21 54 15 smit:SMT_685|3end_LPS_biosynthesis_protein_595237..595387_POSITIVE 134 70 21 111 62 smit:SMT_574|3end_PTS_system,_fructose_specific_IIABC_components_493847..493997_POSITIVE 132 90 45 130 75 smit:SMT_352|3end_hypothetical_protein_290931..291081_POSITIVE