Origin IGS: tttgttcacctctctttttttacttctcttacttaagattttaacatatttttaaaaaaaatgttgacatttatgcaaaaatttattatattaatattaacaagagatgaaagcggttttataactgagggaacatcag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctgatgttccctcagttataaaaccgctttcatctcttgttaatattaatataataaatttttgcataaatgtcaacattttttttaaaaatatgttaaaatcttaagtaagagaagtaaaaaaagagaggtgaacaaa Mask Tandem Repeat Region ================================================ tttgttcacctctctttttttacttctcttacttaagattttaacatatttttaaaaaaaatgttgacatttatgcaaaaatttattatattaatattaacaagagatgaaagcggttttataactgagggaacatcag Find is-nt database================================================ Query_seq: SSA_0052:SSA_0053|SSA_0052:SSA_0053:Transcriptional regulator, GntR family, putative:Beta-galactosidase, putative:<-->:56749..56887 139 tttgttcacctctctttttttacttctcttacttaagattttaacatatttttaaaaaaaatgttgacatttatgcaaaaatttattatattaatattaacaagagatgaaagcggttttataactgagggaacatcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0052:SSA_0053|SSA_0052:SSA_0053:Transcriptional regulator, GntR family, putative:Beta-galactosidase, putative:<-->:56749..56887 139 tttgttcacctctctttttttacttctcttacttaagattttaacatatttttaaaaaaaatgttgacatttatgcaaaaatttattatattaatattaacaagagatgaaagcggttttataactgagggaacatcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0052:SSA_0053|SSA_0052:SSA_0053:Transcriptional regulator, GntR family, putative:Beta-galactosidase, putative:<-->:56749..56887 139 tttgttcacctctctttttttacttctcttacttaagattttaacatatttttaaaaaaaatgttgacatttatgcaaaaatttattatattaatattaacaagagatgaaagcggttttataactgagggaacatcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgttcacctctctttttttacttctcttacttaagattttaacatatttttaaaaaaaatgttgacatttatgcaaaaatttattatattaatattaacaagagatgaaagcggttttataactgagggaacatcag Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 46 End: 138 ............................................. M F L K K M L T F M Q K F I I L I L T R D E S G F I T E G T S . tttgttcacctctctttttttacttctcttacttaagattttaacatatttttaaaaaaaatgttgacatttatgcaaaaatttattatattaatattaacaagagatgaaagcggttttataactgagggaacatcag 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: 89 Start: 63 End: 92 ..............................................................GTTGACATTTATGCAAAAATTTATTATATT............................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttgttcacctctctttttttacttctcttacttaagattttaacatatttttaaaaaaaatgttgacatttatgcaaaaatttattatattaatattaacaagagatgaaagcggttttataactgagggaacatcag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0052:SSA_0053|SSA_0052:SSA_0053:Transcriptional regulator, GntR family, putative:Beta-galactosidase, putative:<-->:56749..56887 139 tttgttcacctctctttttttacttctcttacttaagattttaacatatttttaaaaaaaatgttgacatttatgcaaaaatttattatattaatattaacaagagatgaaagcggttttataactgagggaacatcag Intra-Species Hit: Count: 1 Min: 22 Max: 139 Len: 118 Subject: NC_009009_SSA_0052_SSA_0053|Transcriptional regulator, GntR family, putative:Beta-galactosidase, putative|NEGATIVE:POSITIVE|[56749,56887]|139 HSP 1 e-value: 1.0E-46 bit: 186.0 Len: 118 Query Start:22 Query End:139 Subject Strand: POSITIVE Subject Start: 22 Subject End: 139 .....................acttctcttacttaagattttaacatatttttnnnnnnnntgttgacatttatgcaaaaatttattatattaatattaacaagagatgaaagcggttttataactgagggaacatcag .....................acttctcttacttaagattttaacatatttttaaaaaaaatgttgacatttatgcaaaaatttattatattaatattaacaagagatgaaagcggttttataactgagggaacatcag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUCUCUUACUUAAGAUUUUAACAUAUUUUUAAAAAAAAUGUUGACAUUUAUGCAAAAAUUUAUUAUAUUAAUAUUAACAAGAGAUGAAAGCGGUUUUAUAACUGAGGGAACAUCAG .(.((((((.....((((.(((((((.(((.....))).))))))).))))...........(((((...))))).....)))))).)...............(((((....).)))) (-13.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAUGUUCCCUCAGUUAUAAAACCGCUUUCAUCUCUUGUUAAUAUUAAUAUAAUAAAUUUUUGCAUAAAUGUCAACAUUUUUUUUAAAAAUAUGUUAAAAUCUUAAGUAAGAGAAGU ((((.......)))).................(((((((((((.(((....(((((.(((((((...(((((....)))))....))))))).))))).))).)))).)))))))... (-15.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 718 110 61 222 173 NC_009009:SSA_0052|5end_Transcriptional_regulator,_GntR_family,_putative_56658..56888_NEGATIVE 234 100 53 139 93 NC_009009:SSA_0456|5end_Phosphotransferase_system_IIC_components,_glucose/maltose/N-acetylglucosamine-specific,_putative_458595..458825_POSITIVE 215 110 61 169 113 NC_009009:SSA_2061|5end_Peptide_deformylase,_putative_2062547..2062777_POSITIVE 206 98 69 39 11 NC_009009:SSA_1974|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1970246..1970476_NEGATIVE 193 109 82 163 136 NC_009009:SSA_1033|5end_Pantothenate_kinase,_putative_1049540..1049770_NEGATIVE 191 110 81 48 18 NC_009009:SSA_1877|5end_hypothetical_protein_1871659..1871889_POSITIVE 189 109 61 218 175 NC_009009:SSA_1001|5end_Arabinose_(multiple_sugar_metabolism)_operon_transcriptional_regulator,_putative_1001689..1001919_NEGATIVE 178 59 39 218 197 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 178 110 81 213 189 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 173 106 82 224 202 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 171 105 71 94 59 NC_009009:SSA_1960|5end_hypothetical_protein_1958466..1958696_NEGATIVE 171 105 78 96 68 NC_009009:SSA_1121|5end_Cytochrome_C-type_biogenesis_protein,_putative_1147149..1147379_POSITIVE 170 32 1 106 70 NC_009009:SSA_2230|5end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2231158..2231388_NEGATIVE 169 110 61 167 120 NC_009009:SSA_1552|5end_hypothetical_protein_1554913..1555143_POSITIVE 169 109 61 146 109 NC_009009:SSA_1330|5end_hypothetical_protein_1346368..1346598_NEGATIVE 169 39 2 150 111 NC_009009:SSA_0305|5end_hypothetical_protein_301985..302215_POSITIVE 166 57 21 206 166 NC_009009:SSA_2327|5end_hypothetical_protein_2330925..2331155_POSITIVE 164 47 1 112 53 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 160 99 82 48 34 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 159 107 82 55 29 NC_009009:SSA_1202|5end_Dfp-like_protein,_putative_1226450..1226680_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 202 97 72 43 18 NC_009009:SSA_0080|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_84194..84344_POSITIVE 193 98 79 28 8 NC_009009:SSA_1975|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1970257..1970407_NEGATIVE 191 110 81 51 21 NC_009009:SSA_1876|3end_hypothetical_protein_1871742..1871892_POSITIVE 178 59 39 48 27 NC_009009:SSA_2271|3end_hypothetical_protein_2272238..2272388_NEGATIVE 175 110 83 142 115 NC_009009:SSA_0861|3end_hypothetical_protein_851742..851892_NEGATIVE 169 109 61 41 4 NC_009009:SSA_1331|3end_Conserved_uncharacterized_protein_1346473..1346623_NEGATIVE 167 46 7 50 9 NC_009009:SSA_0808|3end_hypothetical_protein_791012..791162_POSITIVE 164 47 1 108 49 NC_009009:SSA_1009|3end_Galactose-1-phosphate-uridylyltransferase,_putative_1012815..1012965_POSITIVE 164 110 79 151 119 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 160 99 82 48 34 NC_009009:SSA_1660|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1656819..1656969_NEGATIVE 159 107 82 43 17 NC_009009:SSA_1201|3end_hypothetical_protein_1226518..1226668_POSITIVE 154 108 81 77 48 NC_009009:SSA_1525|3end_Lyzozyme_M1_(1,4-beta-N-acetylmuramidase),_putative_1533683..1533833_POSITIVE 152 110 76 74 30 NC_009009:SSA_1135|3end_Na+-driven_multidrug_efflux_pump,_putative_1161775..1161925_POSITIVE 152 109 64 51 1 NC_009009:SSA_0327|3end_Glycosyltransferase,_putative_320436..320586_POSITIVE 152 110 79 150 122 NC_009009:SSA_0116|3end_30S_ribosomal_protein_S17,_putative_112972..113122_POSITIVE 151 31 1 72 44 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 151 34 2 120 82 NC_009009:SSA_1004|3end_ABC_transporter_membrane-spanning_permease-multiple_sugars,_putative_1006094..1006244_POSITIVE 151 109 85 95 65 NC_009009:SSA_0709|3end_hypothetical_protein_695632..695782_NEGATIVE 150 100 82 45 27 NC_009009:SSA_2087|3end_Conserved_uncharacterized_protein_2091674..2091824_NEGATIVE 150 110 83 135 100 NC_009009:SSA_0867|3end_hypothetical_protein_860711..860861_POSITIVE