Origin IGS: agccgtttcctttctctaccttcctattttaacaaaattaggccaaaaatcctccgtccaaggcatgaaatggggaaatttgtccagcaaaaaagaaaaaccatccgttttaagctaaaaaacttaaaatggacggtttattaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaataaaccgtccattttaagttttttagcttaaaacggatggtttttcttttttgctggacaaatttccccatttcatgccttggacggaggatttttggcctaattttgttaaaataggaaggtagagaaaggaaacggct Mask Tandem Repeat Region ================================================ agccgtttcctttctctaccttcctattttaacaaaattaggccaaaaatcctccgtccaaggcatgaaatggggaaatttgtccagcaaaaaagaaaaaccatccgttttaagctaaaaaacttaaaatggacggtttattaa Find is-nt database================================================ Query_seq: SSA_1844:SSA_1845|SSA_1844:SSA_1845:hypothetical protein:Serine/threonine protein kinase, putative:<-<-:1838274..1838417 144 agccgtttcctttctctaccttcctattttaacaaaattaggccaaaaatcctccgtccaaggcatgaaatggggaaatttgtccagcaaaaaagaaaaaccatccgttttaagctaaaaaacttaaaatggacggtttattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1844:SSA_1845|SSA_1844:SSA_1845:hypothetical protein:Serine/threonine protein kinase, putative:<-<-:1838274..1838417 144 agccgtttcctttctctaccttcctattttaacaaaattaggccaaaaatcctccgtccaaggcatgaaatggggaaatttgtccagcaaaaaagaaaaaccatccgttttaagctaaaaaacttaaaatggacggtttattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1844:SSA_1845|SSA_1844:SSA_1845:hypothetical protein:Serine/threonine protein kinase, putative:<-<-:1838274..1838417 144 agccgtttcctttctctaccttcctattttaacaaaattaggccaaaaatcctccgtccaaggcatgaaatggggaaatttgtccagcaaaaaagaaaaaccatccgttttaagctaaaaaacttaaaatggacggtttattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agccgtttcctttctctaccttcctattttaacaaaattaggccaaaaatcctccgtccaaggcatgaaatggggaaatttgtccagcaaaaaagaaaaaccatccgttttaagctaaaaaacttaaaatggacggtttattaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 26 End: 115 ......................... M L T K L G Q K S S V Q G M K W G N L S S K K E K P S V L S ............................. Protein_Len: 36 Strand: + Start: 37 End: 141 .................................... M R P K I L R P R H E M G K F V Q Q K R K T I R F K L K N L K W T V Y * ... agccgtttcctttctctaccttcctattttaacaaaattaggccaaaaatcctccgtccaaggcatgaaatggggaaatttgtccagcaaaaaagaaaaaccatccgttttaagctaaaaaacttaaaatggacggtttattaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agccgtttcctttctctaccttcctattttaacaaaattaggccaaaaatcctccgtccaaggcatgaaatggggaaatttgtccagcaaaaaagaaaaaccatccgttttaagctaaaaaacttaaaatggacggtttattaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1844:SSA_1845|SSA_1844:SSA_1845:hypothetical protein:Serine/threonine protein kinase, putative:<-<-:1838274..1838417 144 agccgtttcctttctctaccttcctattttaacaaaattaggccaaaaatcctccgtccaaggcatgaaatggggaaatttgtccagcaaaaaagaaaaaccatccgttttaagctaaaaaacttaaaatggacggtttattaa Intra-Species Hit: Count: 1 Min: 1 Max: 144 Len: 144 Subject: NC_009009_SSA_1844_SSA_1845|hypothetical protein:Serine/threonine protein kinase, putative|NEGATIVE:NEGATIVE|[1838274,1838417]|144 HSP 1 e-value: 6.0E-55 bit: 214.0 Len: 144 Query Start:1 Query End:144 Subject Strand: POSITIVE Subject Start: 1 Subject End: 144 agccgtttcctttctctaccttcctattttaacaaaattaggccaaaaatcctccgtccaaggcatgaaatggggaaatttgtccagcnnnnnnnnnnnnccatccgttttaagctaaaaaacttaaaatggacggtttattaa agccgtttcctttctctaccttcctattttaacaaaattaggccaaaaatcctccgtccaaggcatgaaatggggaaatttgtccagcaaaaaagaaaaaccatccgttttaagctaaaaaacttaaaatggacggtttattaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCGUUUCCUUUCUCUACCUUCCUAUUUUAACAAAAUUAGGCCAAAAAUCCUCCGUCCAAGGCAUGAAAUGGGGAAAUUUGUCCAGCAAAAAAGAAAAACCAUCCGUUUUAAGCUAAAAAACUUAAAAUGGACGGUUUAUUAA ..............(((...(((((((((((........(((........)))((......))..)))))))))))..((((.....))))..))).(((((.(((((((((((........))))))))))).)))))..... (-30.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAUAAACCGUCCAUUUUAAGUUUUUUAGCUUAAAACGGAUGGUUUUUCUUUUUUGCUGGACAAAUUUCCCCAUUUCAUGCCUUGGACGGAGGAUUUUUGGCCUAAUUUUGUUAAAAUAGGAAGGUAGAGAAAGGAAACGGCU .....(((((((((.(((((((((....))))))))).)))))))))...(((((((((...((((..(((((..((((.....)))).)).)))..)))).((((.(((....))).))))..))))))))).(....).... (-42.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 955 90 41 181 132 NC_009009:SSA_1844|5end_hypothetical_protein_1838183..1838413_NEGATIVE 320 89 41 90 38 NC_009009:SSA_1442|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445941..1446171_NEGATIVE 314 60 11 145 93 NC_009009:SSA_0561|5end_RNA:NAD_2'-phosphotransferase,_putative_553630..553860_POSITIVE 305 56 11 142 91 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 282 88 44 170 122 NC_009009:SSA_0928|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_936679..936909_POSITIVE 278 110 62 229 179 NC_009009:SSA_2073|5end_Undecaprenyl_pyrophosphate_synthetase,_putative_2076371..2076601_NEGATIVE 277 90 41 168 120 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 275 138 101 41 10 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 272 47 9 160 117 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 271 85 41 49 8 NC_009009:SSA_0329|5end_Glycerol_uptake_facilitator/aquaporin_protein,_putative_322830..323060_POSITIVE 269 90 41 60 17 NC_009009:SSA_0591|5end_Conserved_uncharacterized_protein_582769..582999_POSITIVE 268 75 41 67 16 NC_009009:SSA_2266|5end_4-alpha-glucanotransferase,_putative_2265741..2265971_NEGATIVE 268 113 72 226 178 NC_009009:SSA_1979|5end_Alkaline-shock_protein,_putative_1974301..1974531_NEGATIVE 266 90 41 73 21 NC_009009:SSA_0320|5end_hypothetical_protein_313406..313636_POSITIVE 259 89 43 155 107 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 258 68 42 220 192 NC_009009:SSA_1404|5end_hypothetical_protein_1418723..1418953_NEGATIVE 257 88 41 53 12 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 256 66 37 194 165 NC_009009:SSA_2317|5end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2319410..2319640_NEGATIVE 256 90 48 184 147 NC_009009:SSA_1588|5end_Conserved_ABC-type_antimicrobial_permease-like_protein,_putative_1591905..1592135_NEGATIVE 256 86 41 82 27 NC_009009:SSA_1493|5end_hypothetical_protein_1499480..1499710_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 89 41 87 35 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 305 56 11 145 94 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE 297 59 11 151 100 NC_009009:SSA_0560|3end_hypothetical_protein_553717..553867_POSITIVE 282 88 44 151 103 NC_009009:SSA_0927|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936740..936890_POSITIVE 275 138 101 39 8 NC_009009:SSA_0197|3end_Dihydropteroate_synthase,_putative_196979..197129_POSITIVE 269 90 45 57 21 NC_009009:SSA_0068|3end_Alcohol-acetaldehyde_dehydrogenase,_putative_72848..72998_POSITIVE 268 113 72 83 35 NC_009009:SSA_1980|3end_50S_ribosomal_protein_L28,_putative_1974444..1974594_NEGATIVE 266 90 41 83 31 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 259 89 43 151 103 NC_009009:SSA_2325|3end_3-methyladenine_DNA_glycosylase,_putative_2330113..2330263_NEGATIVE 257 88 41 66 25 NC_009009:SSA_1016|3end_Phosphoenolpyruvate_synthase,_putative_1022165..1022315_POSITIVE 256 85 50 53 23 NC_009009:SSA_0025|3end_DNA_repair_protein_recO,_putative_30547..30697_POSITIVE 255 59 14 54 2 NC_009009:SSA_1642|3end_N-acetylglucosamine-1-phosphate_uridyltransferase,_putative_1643103..1643253_NEGATIVE 255 76 32 148 95 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 254 65 21 64 19 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 251 59 14 124 70 NC_009009:SSA_1834|3end_30S_ribosomal_interface_protein_S30EA,_putative_1829652..1829802_NEGATIVE 250 88 41 63 15 NC_009009:SSA_0039|3end_Phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit,_putative_46401..46551_POSITIVE 247 89 49 134 90 NC_009009:SSA_1608|3end_hypothetical_protein_1613283..1613433_NEGATIVE 245 65 22 148 99 NC_009009:SSA_1612|3end_Diacylglycerol_kinase,_putative_1616099..1616249_NEGATIVE 244 90 54 64 28 NC_009009:SSA_1817|3end_Conserved_uncharacterized_protein_1802878..1803028_NEGATIVE 243 121 86 55 19 NC_009009:SSA_2375|3end_Tryptophanyl-tRNA_synthetase,_putative_2377221..2377371_NEGATIVE