Origin IGS: caggttttctagagacttaataaacgacttcatttgaaaaataaggaacattttatatcaaaaagctgagattcaatcccagcttttttgctttatcactgtaccaatttcaggggaacagccagtatttcttatttctttcttctttaaattgattaaaaataggacaaatttatagtctgtgtttaatttttgacacaattcattttttaatgaacaaaaattactagaatggattgcaaattggtatagatagacttataatagatataagtacacaagatgaaagaaaaaacgacagccgattagaagccatcgtttttaatc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 gattaaaaacgatggcttctaatcggctgtcgttttttctttcatcttgtgtacttatatctattataagtctatctataccaatttgcaatccattctagtaatttttgttcattaaaaaatgaattgtgtcaaaaattaaacacagactataaatttgtcctatttttaatcaatttaaagaagaaagaaataagaaatactggctgttcccctgaaattggtacagtgataaagcaaaaaagctgggattgaatctcagctttttgatataaaatgttccttatttttcaaatgaagtcgtttattaagtctctagaaaacctg Mask Tandem Repeat Region ================================================ caggttttctagagacttaataaacgacttcatttgaaaaataaggaacattttatatcaaaaagctgagattcaatcccagcttttttgctttatcactgtaccaatttcaggggaacagccagtatttcttatttctttcttctttaaattgattaaaaataggacaaatttatagtctgtgtttaatttttgacacaattcattttttaatgaacaaaaattactagaatggattgcaaattggtatagatagacttataatagatataagtacacaagatgaaagaaaaaacgacagccgattagaagccatcgtttttaatc Find is-nt database================================================ Query_seq: SSA_0051:SSA_0052|SSA_0051:SSA_0052:Dihydroxyacetone kinase phosphotransfer protein, putative:Transcriptional regulator, GntR family, putative:-><-:55705..56031 327 caggttttctagagacttaataaacgacttcatttgaaaaataaggaacattttatatcaaaaagctgagattcaatcccagcttttttgctttatcactgtaccaatttcaggggaacagccagtatttcttatttctttcttctttaaattgattaaaaataggacaaatttatagtctgtgtttaatttttgacacaattcattttttaatgaacaaaaattactagaatggattgcaaattggtatagatagacttataatagatataagtacacaagatgaaagaaaaaacgacagccgattagaagccatcgtttttaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0051:SSA_0052|SSA_0051:SSA_0052:Dihydroxyacetone kinase phosphotransfer protein, putative:Transcriptional regulator, GntR family, putative:-><-:55705..56031 327 caggttttctagagacttaataaacgacttcatttgaaaaataaggaacattttatatcaaaaagctgagattcaatcccagcttttttgctttatcactgtaccaatttcaggggaacagccagtatttcttatttctttcttctttaaattgattaaaaataggacaaatttatagtctgtgtttaatttttgacacaattcattttttaatgaacaaaaattactagaatggattgcaaattggtatagatagacttataatagatataagtacacaagatgaaagaaaaaacgacagccgattagaagccatcgtttttaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0051:SSA_0052|SSA_0051:SSA_0052:Dihydroxyacetone kinase phosphotransfer protein, putative:Transcriptional regulator, GntR family, putative:-><-:55705..56031 327 caggttttctagagacttaataaacgacttcatttgaaaaataaggaacattttatatcaaaaagctgagattcaatcccagcttttttgctttatcactgtaccaatttcaggggaacagccagtatttcttatttctttcttctttaaattgattaaaaataggacaaatttatagtctgtgtttaatttttgacacaattcattttttaatgaacaaaaattactagaatggattgcaaattggtatagatagacttataatagatataagtacacaagatgaaagaaaaaacgacagccgattagaagccatcgtttttaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caggttttctagagacttaataaacgacttcatttgaaaaataaggaacattttatatcaaaaagctgagattcaatcccagcttttttgctttatcactgtaccaatttcaggggaacagccagtatttcttatttctttcttctttaaattgattaaaaataggacaaatttatagtctgtgtttaatttttgacacaattcattttttaatgaacaaaaattactagaatggattgcaaattggtatagatagacttataatagatataagtacacaagatgaaagaaaaaacgacagccgattagaagccatcgtttttaatc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 57 End: 152 ........................................................ M K K L R F N P S F F A L S L Y Q F Q G N S Q Y F L F L S S L N ............................................................................................................................................................................... Protein_Len: 45 Strand: + Start: 41 End: 175 ........................................ M R N I L Y Q K A E I Q S Q L F C F I T V P I S G E Q P V F L I S F F F K L I K N R T N L ........................................................................................................................................................ Protein_Len: 30 Strand: + Start: 237 End: 326 ............................................................................................................................................................................................................................................ M Q I G I D R L I I D I S T Q D E R K N D S R L E A I V F N . Protein_Len: 54 Strand: - Start: 76 End: 237 ........................................................................... D W S K Q K I V T G I E P S C G T N R I E K K K L N I L F L V F K Y D T N L K Q C L E N K L S C F N S S H M .......................................................................................... caggttttctagagacttaataaacgacttcatttgaaaaataaggaacattttatatcaaaaagctgagattcaatcccagcttttttgctttatcactgtaccaatttcaggggaacagccagtatttcttatttctttcttctttaaattgattaaaaataggacaaatttatagtctgtgtttaatttttgacacaattcattttttaatgaacaaaaattactagaatggattgcaaattggtatagatagacttataatagatataagtacacaagatgaaagaaaaaacgacagccgattagaagccatcgtttttaatc 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: 236 End: 265 ...........................................................................................................................................................................................................................................ATTGCAAATTGGTATAGATAGACTTATAAT.............................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caggttttctagagacttaataaacgacttcatttgaaaaataaggaacattttatatcaaaaagctgagattcaatcccagcttttttgctttatcactgtaccaatttcaggggaacagccagtatttcttatttctttcttctttaaattgattaaaaataggacaaatttatagtctgtgtttaatttttgacacaattcattttttaatgaacaaaaattactagaatggattgcaaattggtatagatagacttataatagatataagtacacaagatgaaagaaaaaacgacagccgattagaagccatcgtttttaatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -7.4 Tail_Score: -5.42514 Start: 65 End: 83 Full_Region: ATTTTATATCAAAAA GCTGAGAT TCA ATCCCAGC TTTTTTGCTTTATCA ................................................................GCTGAGATTCAATCCCAGC.................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -9.6 Tail_Score: -4.80882 Start: 65 End: 83 Full_Region: tgataaagcaaaaaa gctgggat tga atctcagc tttttgatataaaat ................................................................gctgggattgaatctcagc.................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 48 HP_score: -3.8 Tail_Score: -3.052 Start: 258 End: 274 Full_Region: ctttcatcttgtgta cttata tctat tataag tctatctataccaat .................................................................................................................................................................................................................................................................cttatatctattataag..................................................... Find igs database================================================ Query_seq: SSA_0051:SSA_0052|SSA_0051:SSA_0052:Dihydroxyacetone kinase phosphotransfer protein, putative:Transcriptional regulator, GntR family, putative:-><-:55705..56031 327 caggttttctagagacttaataaacgacttcatttgaaaaataaggaacattttatatcaaaaagctgagattcaatcccagcttttttgctttatcactgtaccaatttcaggggaacagccagtatttcttatttctttcttctttaaattgattaaaaataggacaaatttatagtctgtgtttaatttttgacacaattcattttttaatgaacaaaaattactagaatggattgcaaattggtatagatagacttataatagatataagtacacaagatgaaagaaaaaacgacagccgattagaagccatcgtttttaatc Intra-Species Hit: Count: 1 Min: 1 Max: 327 Len: 327 Subject: NC_009009_SSA_0051_SSA_0052|Dihydroxyacetone kinase phosphotransfer protein, putative:Transcriptional regulator, GntR family, putative|POSITIVE:NEGATIVE|[55705,56031]|327 HSP 1 e-value: 0.0 bit: 648.0 Len: 327 Query Start:1 Query End:327 Subject Strand: POSITIVE Subject Start: 1 Subject End: 327 caggttttctagagacttaataaacgacttcatttgaaaaataaggaacattttatatcaaaaagctgagattcaatcccagcttttttgctttatcactgtaccaatttcaggggaacagccagtatttcttatttctttcttctttaaattgattaaaaataggacaaatttatagtctgtgtttaatttttgacacaattcattttttaatgaacaaaaattactagaatggattgcaaattggtatagatagacttataatagatataagtacacaagatgaaagaaaaaacgacagccgattagaagccatcgtttttaatc caggttttctagagacttaataaacgacttcatttgaaaaataaggaacattttatatcaaaaagctgagattcaatcccagcttttttgctttatcactgtaccaatttcaggggaacagccagtatttcttatttctttcttctttaaattgattaaaaataggacaaatttatagtctgtgtttaatttttgacacaattcattttttaatgaacaaaaattactagaatggattgcaaattggtatagatagacttataatagatataagtacacaagatgaaagaaaaaacgacagccgattagaagccatcgtttttaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGGUUUUCUAGAGACUUAAUAAACGACUUCAUUUGAAAAAUAAGGAACAUUUUAUAUCAAAAAGCUGAGAUUCAAUCCCAGCUUUUUUGCUUUAUCACUGUACCAAUUUCAGGGGAACAGCCAGUAUUUCUUAUUUCUUUCUUCUUUAAAUUGAUUAAAAAUAGGACAAAUUUAUAGUCUGUGUUUAAUUUUUGACACAAUUCAUUUUUUAAUGAACAAAAAUUACUAGAAUGGAUUGCAAAUUGGUAUAGAUAGACUUAUAAUAGAUAUAAGUACACAAGAUGAAAGAAAAAACGACAGCCGAUUAGAAGCCAUCGUUUUUAAUC ..((((.((......((((.....(((......))).....))))..............(((((((((.(((...))).)))))))))...((((((.((((((((((((.(((((((.((..((((.....)))).)))))))))(((((..(((((((....((((.........))))...))))))))))))..(((((((((((.((((........))))..))))))))))).))))))))))))....(((((((.....)))))))......)))))).........)).))))((((((((((....)))))))))) (-63.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUAAAAACGAUGGCUUCUAAUCGGCUGUCGUUUUUUCUUUCAUCUUGUGUACUUAUAUCUAUUAUAAGUCUAUCUAUACCAAUUUGCAAUCCAUUCUAGUAAUUUUUGUUCAUUAAAAAAUGAAUUGUGUCAAAAAUUAAACACAGACUAUAAAUUUGUCCUAUUUUUAAUCAAUUUAAAGAAGAAAGAAAUAAGAAAUACUGGCUGUUCCCCUGAAAUUGGUACAGUGAUAAAGCAAAAAAGCUGGGAUUGAAUCUCAGCUUUUUGAUAUAAAAUGUUCCUUAUUUUUCAAAUGAAGUCGUUUAUUAAGUCUCUAGAAAACCUG ((..(((((((((((((.......)))))))))))))....)).....(((.(((((((.....))))))).)))....................((((((..((((..(((((((....))))))).((((..........)))).((((....(((((.....(((((((.....)))))))....(((((((((.((((...(((((...((.......)).))))).........(((((((((((((...))))))))))))).........)))).))))))))))))))..)))).......))))..))))))...... (-67.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 106 62 210 171 NC_009009:SSA_0336|5end_Isopentenyl-diphosphate_delta-isomerase,_putative_329792..330022_POSITIVE 303 87 60 133 107 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 293 95 53 139 100 NC_009009:SSA_0996|5end_cGMP-specific_phosphodiesterase,_putative_996282..996512_POSITIVE 291 319 282 166 131 NC_009009:SSA_0154|5end_hypothetical_protein_149836..150066_POSITIVE 282 111 71 138 96 NC_009009:SSA_1985|5end_hypothetical_protein_1981773..1982003_NEGATIVE 281 122 82 71 33 NC_009009:SSA_1903|5end_hypothetical_protein_1898182..1898412_NEGATIVE 278 105 71 35 2 NC_009009:SSA_1896|5end_Translation_initiation_factor_IF-2,_putative_1894134..1894364_NEGATIVE 276 146 104 68 18 NC_009009:SSA_2228|5end_Acetyltransferase_(GNAT)_family,_putative_2228768..2228998_NEGATIVE 275 124 81 145 95 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 274 129 81 146 96 NC_009009:SSA_0834|5end_Accessory_secretory_protein_Asp2,_putative_819510..819740_POSITIVE 273 105 64 183 135 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 270 99 63 55 17 NC_009009:SSA_2359|5end_Glucose_inhibited_division_protein_A,_putative_2362520..2362750_NEGATIVE 270 157 120 229 188 NC_009009:SSA_0400|5end_hypothetical_protein_398251..398481_NEGATIVE 268 125 81 129 66 NC_009009:SSA_1016|5end_Phosphoenolpyruvate_synthase,_putative_1019602..1019832_POSITIVE 268 105 65 199 156 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 263 110 64 220 170 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 259 117 80 230 193 NC_009009:SSA_2242|5end_hypothetical_protein_2238663..2238893_NEGATIVE 259 125 83 142 98 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 259 138 91 214 162 NC_009009:SSA_0033|5end_Phosphoribosylglycinamide_(GAR)_formyltransferase,_putative_38957..39187_POSITIVE 258 125 81 130 93 NC_009009:SSA_1783|5end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1769106..1769336_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 89 42 66 20 NC_009009:SSA_0234|3end_hypothetical_protein_228423..228573_NEGATIVE 303 87 60 85 59 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 293 95 53 109 70 NC_009009:SSA_0995|3end_Antibiotic-resistance_protein,_alpha/beta_superfamily_hydrolase,_putative_996332..996482_POSITIVE 289 99 54 99 46 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 279 127 81 139 98 NC_009009:SSA_1774|3end_RRNA_methylase,_putative_1760489..1760639_NEGATIVE 275 124 81 134 84 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 273 89 43 92 39 NC_009009:SSA_2301|3end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2302669..2302819_NEGATIVE 273 105 64 50 2 NC_009009:SSA_2018|3end_hypothetical_protein_2017464..2017614_NEGATIVE 268 125 81 129 66 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 264 106 64 148 102 NC_009009:SSA_2209|3end_Penicillin-binding_protein_2A,_putative_2208144..2208294_NEGATIVE 259 117 80 124 87 NC_009009:SSA_2243|3end_Conserved_uncharacterized_protein_2238769..2238919_NEGATIVE 259 125 83 57 13 NC_009009:SSA_1460|3end_Transcriptional_attenuator_LytR,_putative_1467566..1467716_NEGATIVE 258 125 81 133 96 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE 254 155 112 110 59 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 253 130 82 125 67 NC_009009:SSA_2186|3end_Glutathione_biosynthesis_bifunctional_protein_gshAB_(Gamma-GCS-GS)_(GCS-GS),_putative_2187870..2188020_POSITIVE 251 106 66 134 104 NC_009009:SSA_0870|3end_Cell_division_protein_FtsE,_putative_863708..863858_POSITIVE 251 130 82 87 29 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 249 116 78 57 24 NC_009009:SSA_0575|3end_Hydrolase,_HAD_superfamily,_putative_570116..570266_POSITIVE 248 314 273 42 1 NC_009009:SSA_0597|3end_hypothetical_protein_588563..588713_POSITIVE 247 127 81 136 88 NC_009009:SSA_1861|3end_Aminopeptidase_C,_putative_1856568..1856718_NEGATIVE