Origin IGS: actattttagaagaaatactagtgctagaaagaaaaaacatttgacaaacattataaatacgcttataataagtatacatattataaaggagttattgta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tacaataactcctttataatatgtatacttattataagcgtatttataatgtttgtcaaatgttttttctttctagcactagtatttcttctaaaatagt Mask Tandem Repeat Region ================================================ actattttagaagaaatactagtgctagaaagaaaaaacatttgacaaacattataaatacgcttataataagtatacatattataaaggagttattgta Find is-nt database================================================ Query_seq: SSA_0359:SSA_0360|SSA_0359:SSA_0360:Trancriptional regulator, LysR-family, putative:Conserved uncharacterized protein:->->:352744..352843 100 actattttagaagaaatactagtgctagaaagaaaaaacatttgacaaacattataaatacgcttataataagtatacatattataaaggagttattgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0359:SSA_0360|SSA_0359:SSA_0360:Trancriptional regulator, LysR-family, putative:Conserved uncharacterized protein:->->:352744..352843 100 actattttagaagaaatactagtgctagaaagaaaaaacatttgacaaacattataaatacgcttataataagtatacatattataaaggagttattgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0359:SSA_0360|SSA_0359:SSA_0360:Trancriptional regulator, LysR-family, putative:Conserved uncharacterized protein:->->:352744..352843 100 actattttagaagaaatactagtgctagaaagaaaaaacatttgacaaacattataaatacgcttataataagtatacatattataaaggagttattgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actattttagaagaaatactagtgctagaaagaaaaaacatttgacaaacattataaatacgcttataataagtatacatattataaaggagttattgta Predict ORF larger than 30AA ================================================ actattttagaagaaatactagtgctagaaagaaaaaacatttgacaaacattataaatacgcttataataagtatacatattataaaggagttattgta 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: 94 Start: 41 End: 70 ........................................TTTGACAAACATTATAAATACGCTTATAAT.............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actattttagaagaaatactagtgctagaaagaaaaaacatttgacaaacattataaatacgcttataataagtatacatattataaaggagttattgta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0359:SSA_0360|SSA_0359:SSA_0360:Trancriptional regulator, LysR-family, putative:Conserved uncharacterized protein:->->:352744..352843 100 actattttagaagaaatactagtgctagaaagaaaaaacatttgacaaacattataaatacgcttataataagtatacatattataaaggagttattgta Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: NC_009009_SSA_0359_SSA_0360|Trancriptional regulator, LysR-family, putative:Conserved uncharacterized protein|POSITIVE:POSITIVE|[352744,352843]|100 HSP 1 e-value: 2.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 actattttagaagaaatactagtgctagaaagaaaaaacatttgacaaacattataaatacgcttataataagtatacatattataaaggagttattgta actattttagaagaaatactagtgctagaaagaaaaaacatttgacaaacattataaatacgcttataataagtatacatattataaaggagttattgta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAUUUUAGAAGAAAUACUAGUGCUAGAAAGAAAAAACAUUUGACAAACAUUAUAAAUACGCUUAUAAUAAGUAUACAUAUUAUAAAGGAGUUAUUGUA .(((..((((.(....).))))...))).........(((..((((...(.((((((.((..((((...))))..))....)))))).)..)))).))). ( -8.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACAAUAACUCCUUUAUAAUAUGUAUACUUAUUAUAAGCGUAUUUAUAAUGUUUGUCAAAUGUUUUUUCUUUCUAGCACUAGUAUUUCUUCUAAAAUAGU (((..................((.(((..(((((((((....)))))))))..)))))..((((..........))))...)))................ ( -5.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 219 68 24 76 36 NC_009009:SSA_1620|5end_Uridylate_kinase,_putative_1622981..1623211_NEGATIVE 172 60 19 45 2 NC_009009:SSA_1761|5end_Hemolysin_(containing_CBS_domains),_putative_1748777..1749007_NEGATIVE 170 44 13 39 6 NC_009009:SSA_1914|5end_hypothetical_protein_1905195..1905425_NEGATIVE 169 40 3 139 98 NC_009009:SSA_0646|5end_hypothetical_protein_630778..631008_POSITIVE 169 61 22 40 3 NC_009009:SSA_0301|5end_hypothetical_protein_294098..294328_POSITIVE 162 40 1 141 108 NC_009009:SSA_0184|5end_Competence_protein_ComYA,_putative_188156..188386_POSITIVE 161 48 18 78 46 NC_009009:SSA_0458|5end_Formylmethionine_deformylase,_putative_461609..461839_POSITIVE 152 100 60 120 76 NC_009009:SSA_1673|5end_hypothetical_protein_1670353..1670583_POSITIVE 152 36 16 24 3 NC_009009:SSA_0819|5end_hypothetical_protein_800418..800648_POSITIVE 150 27 1 148 123 NC_009009:SSA_2015|5end_Phosphoglycerate_mutase,_putative_2015492..2015722_NEGATIVE 150 47 18 146 117 NC_009009:SSA_1881|5end_hypothetical_protein_1875964..1876194_NEGATIVE 146 98 51 163 116 NC_009009:SSA_0037|5end_Phosphoribosylamine-glycine_ligase;_phosphoribosyl_glycinamide_synthetase_(GARS),_putative_44272..44502_POSITIVE 145 100 62 182 145 NC_009009:SSA_1457|5end_Neopullulanase,_putative_1464239..1464469_NEGATIVE 145 49 1 197 146 NC_009009:SSA_0737|5end_Arginine_deiminase,_putative_718624..718854_POSITIVE 145 82 48 182 151 NC_009009:SSA_0231|5end_Conserved_uncharacterized_protein_225713..225943_POSITIVE 141 40 8 38 3 NC_009009:SSA_2335|5end_D-Ala-teichoic_acid_biosynthesis_protein,_putative_2338158..2338388_NEGATIVE 141 40 8 189 154 NC_009009:SSA_2334|5end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2338007..2338237_NEGATIVE 141 39 19 31 13 NC_009009:SSA_1791|5end_Acylphosphatase,_putative_1773676..1773906_POSITIVE 141 29 3 224 200 NC_009009:SSA_1750|5end_Extracellular_nuclease,_putative_1737922..1738152_NEGATIVE 140 53 21 41 3 NC_009009:SSA_2220|5end_Galactosyltransferase,_putative_2221439..2221669_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 169 40 3 46 5 NC_009009:SSA_0644|3end_DNA_Protection_System,_DNA-binding_ferritin-like_protein_(oxidative_damage_protectant),_putative_630765..630915_POSITIVE 166 40 4 40 1 NC_009009:SSA_0858|3end_DTDP-L-rhamnose_synthase,_putative_846446..846596_POSITIVE 161 48 21 31 1 NC_009009:SSA_0457|3end_Fructokinase,_putative_461642..461792_POSITIVE 157 48 2 47 5 NC_009009:SSA_0336|3end_Isopentenyl-diphosphate_delta-isomerase,_putative_330879..331029_POSITIVE 151 93 64 60 22 NC_009009:SSA_0935|3end_tRNA_pseudouridine_synthase_B,_putative_944973..945123_POSITIVE 150 27 1 48 23 NC_009009:SSA_2016|3end_Phosphoglycerate_mutase,_putative_2015592..2015742_NEGATIVE 145 47 20 139 107 NC_009009:SSA_0587|3end_Metal-dependent_amidase/aminoacylase/carboxypeptidase,_putative_579761..579911_POSITIVE 141 29 3 36 12 NC_009009:SSA_1751|3end_Dextran_glucosidase,_alpha_amylase_family,_putative_1738110..1738260_NEGATIVE 140 34 1 53 18 NC_009009:SSA_1753|3end_Transcriptional_regulator,_GntR_family_(repressor_of_trehalose_operon),_putative_1742740..1742890_POSITIVE 138 63 23 66 23 NC_009009:SSA_1951|3end_Penicillin-binding_protein_3,_putative_1948103..1948253_POSITIVE 138 50 1 139 93 NC_009009:SSA_1596|3end_hypothetical_protein_1602075..1602225_NEGATIVE 136 98 64 110 77 NC_009009:SSA_0180|3end_hypothetical_protein_184989..185139_POSITIVE 134 28 2 88 62 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 133 66 21 93 40 NC_009009:SSA_2263|3end_Ribonucleotide_reductase_(NrdI_family_protein),_putative_2260688..2260838_NEGATIVE 131 28 1 61 36 NC_009009:SSA_1705|3end_hypothetical_protein_1696398..1696548_NEGATIVE 131 26 9 49 31 NC_009009:SSA_1470|3end_3-dehydroquinate_dehydratase,_putative_1476307..1476457_NEGATIVE 131 72 35 46 12 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 130 99 52 105 47 NC_009009:SSA_1700|3end_hypothetical_protein_1691175..1691325_NEGATIVE 130 31 5 122 89 NC_009009:SSA_0874|3end_hypothetical_protein_868995..869145_POSITIVE 129 33 2 63 26 NC_009009:SSA_2286|3end_Dihydroxy-acid_dehydratase,_putative_2287878..2288028_NEGATIVE