Origin IGS: gaggacctccaatattacgacaggaatatagctatgattataatataaaattggaggattgaaaagtgccctttgtaaaatcgaccgtcttatccacctcttcttgcttttctttttacttttttaagtagtataatatgtctaaaagtcagaggttttctggaaggggtgaggacattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatgtcctcaccccttccagaaaacctctgacttttagacatattatactacttaaaaaagtaaaaagaaaagcaagaagaggtggataagacggtcgattttacaaagggcacttttcaatcctccaattttatattataatcatagctatattcctgtcgtaatattggaggtcctc Mask Tandem Repeat Region ================================================ gaggacctccaatattacgacaggaatatagctatgattataatataaaattggaggattgaaaagtgccctttgtaaaatcgaccgtcttatccacctcttcttgcttttctttttacttttttaagtagtataatatgtctaaaagtcagaggttttctggaaggggtgaggacattt Find is-nt database================================================ Query_seq: SSA_0387:SSA_0388|SSA_0387:SSA_0388:Transcriptional regulator, GntR family, putative:Mismatch repair ATPase (MutS family), putative:<-->:382434..382613 180 gaggacctccaatattacgacaggaatatagctatgattataatataaaattggaggattgaaaagtgccctttgtaaaatcgaccgtcttatccacctcttcttgcttttctttttacttttttaagtagtataatatgtctaaaagtcagaggttttctggaaggggtgaggacattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0387:SSA_0388|SSA_0387:SSA_0388:Transcriptional regulator, GntR family, putative:Mismatch repair ATPase (MutS family), putative:<-->:382434..382613 180 gaggacctccaatattacgacaggaatatagctatgattataatataaaattggaggattgaaaagtgccctttgtaaaatcgaccgtcttatccacctcttcttgcttttctttttacttttttaagtagtataatatgtctaaaagtcagaggttttctggaaggggtgaggacattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0387:SSA_0388|SSA_0387:SSA_0388:Transcriptional regulator, GntR family, putative:Mismatch repair ATPase (MutS family), putative:<-->:382434..382613 180 gaggacctccaatattacgacaggaatatagctatgattataatataaaattggaggattgaaaagtgccctttgtaaaatcgaccgtcttatccacctcttcttgcttttctttttacttttttaagtagtataatatgtctaaaagtcagaggttttctggaaggggtgaggacattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaggacctccaatattacgacaggaatatagctatgattataatataaaattggaggattgaaaagtgccctttgtaaaatcgaccgtcttatccacctcttcttgcttttctttttacttttttaagtagtataatatgtctaaaagtcagaggttttctggaaggggtgaggacattt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 1 End: 93 L V E L I V V P I Y S H N Y Y L I P P N F L A R Q L I S R R M ....................................................................................... gaggacctccaatattacgacaggaatatagctatgattataatataaaattggaggattgaaaagtgccctttgtaaaatcgaccgtcttatccacctcttcttgcttttctttttacttttttaagtagtataatatgtctaaaagtcagaggttttctggaaggggtgaggacattt 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: 87 Start: 37 End: 66 ....................................CTTTTCAATCCTCCAATTTTATATTATAAT.................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 108 End: 137 ...........................................................................................................TTTTCTTTTTACTTTTTTAAGTAGTATAAT........................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaggacctccaatattacgacaggaatatagctatgattataatataaaattggaggattgaaaagtgccctttgtaaaatcgaccgtcttatccacctcttcttgcttttctttttacttttttaagtagtataatatgtctaaaagtcagaggttttctggaaggggtgaggacattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0387:SSA_0388|SSA_0387:SSA_0388:Transcriptional regulator, GntR family, putative:Mismatch repair ATPase (MutS family), putative:<-->:382434..382613 180 gaggacctccaatattacgacaggaatatagctatgattataatataaaattggaggattgaaaagtgccctttgtaaaatcgaccgtcttatccacctcttcttgcttttctttttacttttttaagtagtataatatgtctaaaagtcagaggttttctggaaggggtgaggacattt Intra-Species Hit: Count: 1 Min: 1 Max: 180 Len: 180 Subject: NC_009009_SSA_0387_SSA_0388|Transcriptional regulator, GntR family, putative:Mismatch repair ATPase (MutS family), putative|NEGATIVE:POSITIVE|[382434,382613]|180 HSP 1 e-value: 3.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 gaggacctccaatattacgacaggaatatagctatgattataatataaaattggaggattgaaaagtgccctttgtaaaatcgaccgtcttatccacctcttcttgc......................................................................... gaggacctccaatattacgacaggaatatagctatgattataatataaaattggaggattgaaaagtgccctttgtaaaatcgaccgtcttatccacctcttcttgc......................................................................... HSP 2 e-value: 3.0E-23 bit: 109.0 Len: 55 Query Start:126 Query End:180 Subject Strand: POSITIVE Subject Start: 126 Subject End: 180 .............................................................................................................................aagtagtataatatgtctaaaagtcagaggttttctggaaggggtgaggacattt .............................................................................................................................aagtagtataatatgtctaaaagtcagaggttttctggaaggggtgaggacattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGGACCUCCAAUAUUACGACAGGAAUAUAGCUAUGAUUAUAAUAUAAAAUUGGAGGAUUGAAAAGUGCCCUUUGUAAAAUCGACCGUCUUAUCCACCUCUUCUUGCUUUUCUUUUUACUUUUUUAAGUAGUAUAAUAUGUCUAAAAGUCAGAGGUUUUCUGGAAGGGGUGAGGACAUUU ((((.((((((((.(((......((.(((....))).))......))).))))))))(((....)))..)))).............(((((...((((((((((.......(((((.((((((....(((......)))....)))))).)))))......))))))))))))))).... (-40.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUGUCCUCACCCCUUCCAGAAAACCUCUGACUUUUAGACAUAUUAUACUACUUAAAAAAGUAAAAAGAAAAGCAAGAAGAGGUGGAUAAGACGGUCGAUUUUACAAAGGGCACUUUUCAAUCCUCCAAUUUUAUAUUAUAAUCAUAGCUAUAUUCCUGUCGUAAUAUUGGAGGUCCUC ...((((((((((.((((((((.....))))...................(((((....))))).............)))).))))(((......)))..........)))))).........((((((.....(((((((....((((........)))).)))))))))))))..... (-31.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 909 100 51 191 142 NC_009009:SSA_0387|5end_Transcriptional_regulator,_GntR_family,_putative_382343..382573_NEGATIVE 314 118 71 104 53 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 294 118 78 118 72 NC_009009:SSA_0703|5end_Citrate_synthase,_putative_688154..688384_POSITIVE 292 118 79 106 51 NC_009009:SSA_1842|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_HTH_DNA-binding_domains),_putative_1836494..1836724_NEGATIVE 287 106 73 114 75 NC_009009:SSA_0752|5end_hypothetical_protein_734171..734401_POSITIVE 283 110 65 61 20 NC_009009:SSA_1103|5end_hypothetical_protein_1123833..1124063_POSITIVE 276 100 52 102 54 NC_009009:SSA_1449|5end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1451931..1452161_NEGATIVE 274 126 83 201 151 NC_009009:SSA_1574|5end_Glycosyl_transferase,_family_1,_putative_1577930..1578160_NEGATIVE 273 109 66 156 116 NC_009009:SSA_1242|5end_Dihydroorotate_dehydrogenase_B,_putative_1267386..1267616_NEGATIVE 264 100 51 207 154 NC_009009:SSA_1048|5end_ABC_transporter_ATP-binding_protein-spermidine/putrescine_transport,_putative_1062947..1063177_POSITIVE 264 108 67 229 181 NC_009009:SSA_0189|5end_Competence_protein_ComGF,_putative_191015..191245_POSITIVE 262 109 64 108 57 NC_009009:SSA_0498|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_systems,_permease_components,_putative_497910..498140_POSITIVE 261 113 72 164 126 NC_009009:SSA_1231|5end_hypothetical_protein_1254758..1254988_NEGATIVE 260 105 68 103 54 NC_009009:SSA_2182|5end_hypothetical_protein_2181020..2181250_NEGATIVE 255 110 62 165 94 NC_009009:SSA_1294|5end_hypothetical_protein_1312581..1312811_NEGATIVE 254 175 139 75 30 NC_009009:SSA_2117|5end_DNA_recombination_protein_RmuC,_putative_2119812..2120042_NEGATIVE 254 107 68 47 1 NC_009009:SSA_1303|5end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322992..1323222_NEGATIVE 254 93 51 61 15 NC_009009:SSA_0909|5end_Transcriptional_regulator,_AbrB_family_(stationary/sporulation_gene_expression),_putative_920887..921117_POSITIVE 252 124 85 108 60 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 250 127 83 167 118 NC_009009:SSA_2228|5end_Acetyltransferase_(GNAT)_family,_putative_2228768..2228998_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 120 74 118 67 NC_009009:SSA_2023|3end_Fructan_beta-fructosidase_precursor,_putative_2024609..2024759_NEGATIVE 294 118 78 115 69 NC_009009:SSA_0702|3end_Aconitase_A,_putative_688231..688381_POSITIVE 292 118 79 128 73 NC_009009:SSA_1843|3end_Histidine_kinase,_putative_1836472..1836622_NEGATIVE 287 106 73 112 73 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE 273 109 66 144 104 NC_009009:SSA_1243|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1267398..1267548_NEGATIVE 270 128 88 130 89 NC_009009:SSA_0904|3end_CshA-like_fibrillar_surface_protein_A_902958..903108_POSITIVE 269 109 64 148 93 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 262 172 151 28 2 NC_009009:SSA_1398|3end_Membrane_protein,_hemolysin_III-like,_putative_1411626..1411776_POSITIVE 262 109 64 115 64 NC_009009:SSA_0497|3end_Nickel_ABC_transporter,_putative_497997..498147_POSITIVE 261 113 72 116 78 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 254 175 139 73 28 NC_009009:SSA_2118|3end_Thiamine_pyrophosphokinase,_putative_2119814..2119964_NEGATIVE 250 127 83 114 65 NC_009009:SSA_2229|3end_hypothetical_protein_2228821..2228971_NEGATIVE 249 174 138 62 23 NC_009009:SSA_0461|3end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_464905..465055_POSITIVE 249 100 53 101 47 NC_009009:SSA_0262|3end_ABC-type_Mn/Zn_transporter,_ATP-ase_component,_putative_255455..255605_NEGATIVE 248 96 55 60 8 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 247 104 69 136 98 NC_009009:SSA_0421|3end_Phosphoglycerate_mutase_family_protein,_putative_420240..420390_POSITIVE 241 120 83 92 50 NC_009009:SSA_0704|3end_Isocitrate_dehydrogenase_[NADP],_putative_690550..690700_POSITIVE 240 110 69 108 60 NC_009009:SSA_0808|3end_hypothetical_protein_791012..791162_POSITIVE 239 126 81 89 36 NC_009009:SSA_0895|3end_ATP-binding_cassette_transporter-like_protein,_putative_887763..887913_POSITIVE 238 102 67 107 66 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE