Origin IGS: atgggtttctccatcttttagatttttagatttaattaagattatagcatagatagtactaaaagtaaaataaattttcagaatattaagttagctcactggcaccctcagatgtttatgtaatcaggtttcccgcatgtctgtcatctaggattagacaaccttagtctcgcccattccgcctctaaaatcatcaaaaatcccactgttgctacaatgggattttcttgat .........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 atcaagaaaatcccattgtagcaacagtgggatttttgatgattttagaggcggaatgggcgagactaaggttgtctaatcctagatgacagacatgcgggaaacctgattacataaacatctgagggtgccagtgagctaacttaatattctgaaaatttattttacttttagtactatctatgctataatcttaattaaatctaaaaatctaaaagatggagaaacccat Mask Tandem Repeat Region ================================================ atgggtttctccatcttttagatttttagatttaattaagattatagcatagatagtactaaaagtaaaataaattttcagaatattaagttagctcactggcaccctcagatgtttatgtaatcaggtttcccgcatgtctgtcatctaggattagacaaccttagtctcgcccattccgcctctaaaatcatcaaaaatcccactgttgctacaatgggattttcttgat Find is-nt database================================================ Query_seq: SSA_1948:SSA_1949|SSA_1948:SSA_1949:Oligopeptide-binding lipoprotein precursor, putative:AliA protein, putative:<-<-:1942261..1942492 232 atgggtttctccatcttttagatttttagatttaattaagattatagcatagatagtactaaaagtaaaataaattttcagaatattaagttagctcactggcaccctcagatgtttatgtaatcaggtttcccgcatgtctgtcatctaggattagacaaccttagtctcgcccattccgcctctaaaatcatcaaaaatcccactgttgctacaatgggattttcttgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1948:SSA_1949|SSA_1948:SSA_1949:Oligopeptide-binding lipoprotein precursor, putative:AliA protein, putative:<-<-:1942261..1942492 232 atgggtttctccatcttttagatttttagatttaattaagattatagcatagatagtactaaaagtaaaataaattttcagaatattaagttagctcactggcaccctcagatgtttatgtaatcaggtttcccgcatgtctgtcatctaggattagacaaccttagtctcgcccattccgcctctaaaatcatcaaaaatcccactgttgctacaatgggattttcttgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1948:SSA_1949|SSA_1948:SSA_1949:Oligopeptide-binding lipoprotein precursor, putative:AliA protein, putative:<-<-:1942261..1942492 232 atgggtttctccatcttttagatttttagatttaattaagattatagcatagatagtactaaaagtaaaataaattttcagaatattaagttagctcactggcaccctcagatgtttatgtaatcaggtttcccgcatgtctgtcatctaggattagacaaccttagtctcgcccattccgcctctaaaatcatcaaaaatcccactgttgctacaatgggattttcttgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgggtttctccatcttttagatttttagatttaattaagattatagcatagatagtactaaaagtaaaataaattttcagaatattaagttagctcactggcaccctcagatgtttatgtaatcaggtttcccgcatgtctgtcatctaggattagacaaccttagtctcgcccattccgcctctaaaatcatcaaaaatcccactgttgctacaatgggattttcttgat Predict ORF larger than 30AA ================================================ atgggtttctccatcttttagatttttagatttaattaagattatagcatagatagtactaaaagtaaaataaattttcagaatattaagttagctcactggcaccctcagatgtttatgtaatcaggtttcccgcatgtctgtcatctaggattagacaaccttagtctcgcccattccgcctctaaaatcatcaaaaatcccactgttgctacaatgggattttcttgat 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: 88 Start: 41 End: 70 ........................................TTTTACTTTTAGTACTATCTATGCTATAAT.................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atgggtttctccatcttttagatttttagatttaattaagattatagcatagatagtactaaaagtaaaataaattttcagaatattaagttagctcactggcaccctcagatgtttatgtaatcaggtttcccgcatgtctgtcatctaggattagacaaccttagtctcgcccattccgcctctaaaatcatcaaaaatcccactgttgctacaatgggattttcttgat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1948:SSA_1949|SSA_1948:SSA_1949:Oligopeptide-binding lipoprotein precursor, putative:AliA protein, putative:<-<-:1942261..1942492 232 atgggtttctccatcttttagatttttagatttaattaagattatagcatagatagtactaaaagtaaaataaattttcagaatattaagttagctcactggcaccctcagatgtttatgtaatcaggtttcccgcatgtctgtcatctaggattagacaaccttagtctcgcccattccgcctctaaaatcatcaaaaatcccactgttgctacaatgggattttcttgat Intra-Species Hit: Count: 1 Min: 1 Max: 232 Len: 232 Subject: NC_009009_SSA_1948_SSA_1949|Oligopeptide-binding lipoprotein precursor, putative:AliA protein, putative|NEGATIVE:NEGATIVE|[1942261,1942492]|232 HSP 1 e-value: 1.0E-128 bit: 460.0 Len: 232 Query Start:1 Query End:232 Subject Strand: POSITIVE Subject Start: 1 Subject End: 232 atgggtttctccatcttttagatttttagatttaattaagattatagcatagatagtactaaaagtaaaataaattttcagaatattaagttagctcactggcaccctcagatgtttatgtaatcaggtttcccgcatgtctgtcatctaggattagacaaccttagtctcgcccattccgcctctaaaatcatcaaaaatcccactgttgctacaatgggattttcttgat atgggtttctccatcttttagatttttagatttaattaagattatagcatagatagtactaaaagtaaaataaattttcagaatattaagttagctcactggcaccctcagatgtttatgtaatcaggtttcccgcatgtctgtcatctaggattagacaaccttagtctcgcccattccgcctctaaaatcatcaaaaatcccactgttgctacaatgggattttcttgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGGGUUUCUCCAUCUUUUAGAUUUUUAGAUUUAAUUAAGAUUAUAGCAUAGAUAGUACUAAAAGUAAAAUAAAUUUUCAGAAUAUUAAGUUAGCUCACUGGCACCCUCAGAUGUUUAUGUAAUCAGGUUUCCCGCAUGUCUGUCAUCUAGGAUUAGACAACCUUAGUCUCGCCCAUUCCGCCUCUAAAAUCAUCAAAAAUCCCACUGUUGCUACAAUGGGAUUUUCUUGAU ((((((.........((((((((...(((((........((((...(((((((((...((.(((((.......))))).))........(((((....))))).........))))))))))))).((....))....)))))..))))))))..((((.......)))).))))))............((((...(((((((((.(((....))).)))))))))..)))) (-46.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAGAAAAUCCCAUUGUAGCAACAGUGGGAUUUUUGAUGAUUUUAGAGGCGGAAUGGGCGAGACUAAGGUUGUCUAAUCCUAGAUGACAGACAUGCGGGAAACCUGAUUACAUAAACAUCUGAGGGUGCCAGUGAGCUAACUUAAUAUUCUGAAAAUUUAUUUUACUUUUAGUACUAUCUAUGCUAUAAUCUUAAUUAAAUCUAAAAAUCUAAAAGAUGGAGAAACCCAU ((((.((((((((((((((....))))))))))))))..))))((((((..((((((((((.((((.......)))).((((((((((.((....)).((....))............))))).))))))))..((((....)))).)))))))...(((((.((......(((((.......))))).......)).))))).......))))))..((((......)))) (-54.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 954 140 91 231 182 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 343 179 132 49 3 NC_009009:SSA_0263|5end_Zinc_metalloproteinase_in_scaA_5'region,_putative_256274..256504_POSITIVE 315 173 135 142 95 NC_009009:SSA_0570|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_563915..564145_POSITIVE 313 180 133 58 20 NC_009009:SSA_1784|5end_Glutamate_racemase,_putative_1769897..1770127_NEGATIVE 311 137 93 163 118 NC_009009:SSA_0089|5end_V-type_sodium_ATPase,_subunit_F,_putative_89930..90160_POSITIVE 305 136 95 46 1 NC_009009:SSA_0021|5end_hypothetical_protein_26842..27072_POSITIVE 297 208 162 132 61 NC_009009:SSA_0240|5end_Acetyltransferase,_GNAT_family,_putative_233410..233640_POSITIVE 295 170 126 205 158 NC_009009:SSA_0406|5end_hypothetical_protein_402918..403148_NEGATIVE 294 136 99 107 66 NC_009009:SSA_0961|5end_Possible_ketopantoate_reductase_PanE/ApbA,_putative_969913..970143_POSITIVE 293 176 133 67 17 NC_009009:SSA_1092|5end_Dihydrofolate_reductase,_putative_1109599..1109829_POSITIVE 288 136 94 134 87 NC_009009:SSA_2089|5end_L-xylulose-5-phosphate_3-epimerase,_putative_2094339..2094569_NEGATIVE 288 187 141 72 32 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 287 187 142 222 157 NC_009009:SSA_1540|5end_hypothetical_protein_1545268..1545498_NEGATIVE 286 139 91 137 70 NC_009009:SSA_1370|5end_CAAX_amino_terminal_protease_family,_putative_1386968..1387198_NEGATIVE 285 210 162 75 26 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 284 206 162 107 46 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 284 137 95 41 5 NC_009009:SSA_0264|5end_PEP_phosphonomutase-like_protein,_putative_258400..258630_POSITIVE 283 147 101 91 47 NC_009009:SSA_0773|5end_PTS_enzyme_I,_putative_752603..752833_POSITIVE 283 146 102 145 94 NC_009009:SSA_0497|5end_Nickel_ABC_transporter,_putative_496922..497152_POSITIVE 278 180 131 132 78 NC_009009:SSA_1209|5end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1234030..1234260_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 173 135 142 95 NC_009009:SSA_0569|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563995..564145_POSITIVE 308 207 164 62 7 NC_009009:SSA_1889|3end_Conserved_uncharacterized_protein_1886283..1886433_NEGATIVE 297 208 162 135 64 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 294 136 99 91 50 NC_009009:SSA_0960|3end_Sensor_protein_ciaH,_putative_969977..970127_POSITIVE 288 136 94 130 83 NC_009009:SSA_2090|3end_Hexulose-6-phosphate_synthase,_putative_2094343..2094493_NEGATIVE 284 206 162 135 74 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 283 147 101 89 45 NC_009009:SSA_0772|3end_Histidine-containing_phosphocarrier_protein_of_the_PTS,_putative_752681..752831_POSITIVE 275 220 171 124 69 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 273 190 141 131 73 NC_009009:SSA_2044|3end_Cysteinyl-tRNA_synthetase,_putative_2047066..2047216_NEGATIVE 273 196 153 139 90 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 273 139 93 47 16 NC_009009:SSA_0624|3end_hypothetical_protein_615698..615848_POSITIVE 269 139 96 142 95 NC_009009:SSA_0496|3end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_497009..497159_POSITIVE 269 149 101 77 17 NC_009009:SSA_0388|3end_Mismatch_repair_ATPase_(MutS_family),_putative_384248..384398_POSITIVE 267 188 141 65 16 NC_009009:SSA_0392|3end_hypothetical_protein_388303..388453_POSITIVE 266 136 98 70 29 NC_009009:SSA_1050|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1065741..1065891_POSITIVE 264 150 101 58 5 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 264 180 131 148 89 NC_009009:SSA_1003|3end_ABC_transporter_substrate-binding_protein-multiple_sugars,_putative_1005214..1005364_POSITIVE 263 179 133 71 29 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 261 139 93 135 94 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 260 174 133 47 1 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE