Origin IGS: ataaggtcagtagctgtgcgcctgcccagctgctaggattcttcttgtaaaaagcgataaaataatctataatgttactaatcacatgatttatcttaccgtgagaaagaggagaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttctcctctttctcacggtaagataaatcatgtgattagtaacattatagattattttatcgctttttacaagaagaatcctagcagctgggcaggcgcacagctactgaccttat Mask Tandem Repeat Region ================================================ ataaggtcagtagctgtgcgcctgcccagctgctaggattcttcttgtaaaaagcgataaaataatctataatgttactaatcacatgatttatcttaccgtgagaaagaggagaaaa Find is-nt database================================================ Query_seq: SSA_0141:SSA_0142|SSA_0141:SSA_0142:Copper chaperone, putative:hypothetical protein:->->:137252..137369 118 ataaggtcagtagctgtgcgcctgcccagctgctaggattcttcttgtaaaaagcgataaaataatctataatgttactaatcacatgatttatcttaccgtgagaaagaggagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0141:SSA_0142|SSA_0141:SSA_0142:Copper chaperone, putative:hypothetical protein:->->:137252..137369 118 ataaggtcagtagctgtgcgcctgcccagctgctaggattcttcttgtaaaaagcgataaaataatctataatgttactaatcacatgatttatcttaccgtgagaaagaggagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0141:SSA_0142|SSA_0141:SSA_0142:Copper chaperone, putative:hypothetical protein:->->:137252..137369 118 ataaggtcagtagctgtgcgcctgcccagctgctaggattcttcttgtaaaaagcgataaaataatctataatgttactaatcacatgatttatcttaccgtgagaaagaggagaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataaggtcagtagctgtgcgcctgcccagctgctaggattcttcttgtaaaaagcgataaaataatctataatgttactaatcacatgatttatcttaccgtgagaaagaggagaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 14 End: 118 ............. M C A C P A A R I L L V K S D K I I Y N V T N H M I Y L T V R K R R K Protein_Len: 31 Strand: - Start: 2 End: 94 . L T L L Q A G A W S S P N K K Y F A I F Y D I I N S I V H N M ........................ ataaggtcagtagctgtgcgcctgcccagctgctaggattcttcttgtaaaaagcgataaaataatctataatgttactaatcacatgatttatcttaccgtgagaaagaggagaaaa 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: 86 Start: 44 End: 73 ...........................................CTTGTAAAAAGCGATAAAATAATCTATAAT............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ataaggtcagtagctgtgcgcctgcccagctgctaggattcttcttgtaaaaagcgataaaataatctataatgttactaatcacatgatttatcttaccgtgagaaagaggagaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0141:SSA_0142|SSA_0141:SSA_0142:Copper chaperone, putative:hypothetical protein:->->:137252..137369 118 ataaggtcagtagctgtgcgcctgcccagctgctaggattcttcttgtaaaaagcgataaaataatctataatgttactaatcacatgatttatcttaccgtgagaaagaggagaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: NC_009009_SSA_0141_SSA_0142|Copper chaperone, putative:hypothetical protein|POSITIVE:POSITIVE|[137252,137369]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 ataaggtcagtagctgtgcgcctgcccagctgctaggattcttcttgtaaaaagcgataaaataatctataatgttactaatcacatgatttatcttaccgtgagaaagaggagaaaa ataaggtcagtagctgtgcgcctgcccagctgctaggattcttcttgtaaaaagcgataaaataatctataatgttactaatcacatgatttatcttaccgtgagaaagaggagaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAGGUCAGUAGCUGUGCGCCUGCCCAGCUGCUAGGAUUCUUCUUGUAAAAAGCGAUAAAAUAAUCUAUAAUGUUACUAAUCACAUGAUUUAUCUUACCGUGAGAAAGAGGAGAAAA ........((((((((.((....)).))))))))....((((((((.......(((.(((.((((......((((........))))...)))).))).)))......)))))))).. (-27.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUCCUCUUUCUCACGGUAAGAUAAAUCAUGUGAUUAGUAACAUUAUAGAUUAUUUUAUCGCUUUUUACAAGAAGAAUCCUAGCAGCUGGGCAGGCGCACAGCUACUGACCUUAU ((((((...........(((((((((((.((.((((((.......))))))))))))))))))).........))))))....(((.(((((.((....)).))))).)))....... (-24.35) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 391 42 4 52 6 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 384 46 4 229 177 NC_009009:SSA_1309|5end_RNA-binding_protein_(KH_domain),_putative_1327318..1327548_NEGATIVE 362 50 3 72 27 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 349 50 1 229 163 NC_009009:SSA_0337|5end_Hydroxymethylglutaryl-CoA_reductase,_putative_332163..332393_NEGATIVE 346 56 17 68 23 NC_009009:SSA_1434|5end_Conserved_uncharacterized_Firmicutes_protein_1440850..1441080_POSITIVE 339 49 1 76 23 NC_009009:SSA_0514|5end_PduQ_protein,_putative_512877..513107_POSITIVE 333 46 5 228 166 NC_009009:SSA_1803|5end_GTP-binding_protein,_putative_1787909..1788139_NEGATIVE 329 37 1 165 131 NC_009009:SSA_0650|5end_GTP-binding_protein_TypA/BipA,_putative_632548..632778_POSITIVE 328 47 6 150 113 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 327 47 4 194 148 NC_009009:SSA_0710|5end_Exopolysaccharide_biosynthesis_protein,_acetyltransferase,_putative_695639..695869_NEGATIVE 326 46 5 225 182 NC_009009:SSA_1501|5end_Cytidylate_kinase,_putative_1505772..1506002_NEGATIVE 319 38 4 54 16 NC_009009:SSA_0667|5end_Transcriptional_regulator,_putative_649778..650008_POSITIVE 315 60 11 176 118 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 314 43 5 81 34 NC_009009:SSA_0605|5end_Methyltransferase_gidB,_putative_593707..593937_NEGATIVE 312 44 1 120 69 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 311 44 6 61 21 NC_009009:SSA_0272|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_266023..266253_POSITIVE 310 57 14 144 102 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 308 50 7 125 78 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 308 41 3 79 35 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 307 38 3 60 20 NC_009009:SSA_0458|5end_Formylmethionine_deformylase,_putative_461609..461839_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 391 42 4 52 6 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 362 50 3 79 34 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 351 44 2 144 96 NC_009009:SSA_1105|3end_50S_ribosomal_protein_L7/_L12,_putative_1125765..1125915_POSITIVE 348 56 11 137 92 NC_009009:SSA_2121|3end_Cell_wall_surface_anchor_family_protein,_putative_2122222..2122372_NEGATIVE 320 47 3 150 95 NC_009009:SSA_1869|3end_ATP-dependent_RNA_helicase,_putative_1864152..1864302_NEGATIVE 315 33 7 147 110 NC_009009:SSA_1418|3end_Conserved_uncharacterized_protein_1428139..1428289_NEGATIVE 312 47 6 59 9 NC_009009:SSA_0345|3end_hypothetical_protein_339209..339359_POSITIVE 312 44 1 120 69 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 311 44 6 51 11 NC_009009:SSA_0271|3end_Glycosylhydrolase,_family_35,_putative_266093..266243_POSITIVE 308 41 3 69 25 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 307 42 6 151 116 NC_009009:SSA_0977|3end_3-isopropylmalate_dehydrogenase,_putative_983819..983969_POSITIVE 307 60 17 48 4 NC_009009:SSA_0211|3end_hypothetical_protein_208456..208606_POSITIVE 301 49 6 90 34 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 300 46 5 91 47 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 295 56 12 68 34 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 294 47 6 142 104 NC_009009:SSA_2082|3end_Carbohydrate_kinase,_FGGY_family,_putative_2085351..2085501_NEGATIVE 293 47 5 99 44 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 293 48 4 61 24 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 292 46 1 147 103 NC_009009:SSA_0064|3end_hypothetical_protein_66979..67129_POSITIVE 290 41 12 141 105 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE