Origin IGS: aaaatttcctttctgaaatgaagatacaaatccctcgtaagtgcatttatttctcttgaggcaagtaaaaacctgaagaaagagagggtgttttttaatgggcattatttataaaagcttgagcgatagagttaccgcttagtgtggcagcaaaattatcacttttgaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttcaaaagtgataattttgctgccacactaagcggtaactctatcgctcaagcttttataaataatgcccattaaaaaacaccctctctttcttcaggtttttacttgcctcaagagaaataaatgcacttacgagggatttgtatcttcatttcagaaaggaaatttt Mask Tandem Repeat Region ================================================ aaaatttcctttctgaaatgaagatacaaatccctcgtaagtgcatttatttctcttgaggcaagtaaaaacctgaagaaagagagggtgttttttaatgggcattatttataaaagcttgagcgatagagttaccgcttagtgtggcagcaaaattatcacttttgaaaaa Find is-nt database================================================ Query_seq: SSA_1125:SSA_1126|SSA_1125:SSA_1126:NADPH-dependent FMN reductase, putative:Thiamine biosynthesis lipoprotein, putative:<-<-:1150505..1150676 172 aaaatttcctttctgaaatgaagatacaaatccctcgtaagtgcatttatttctcttgaggcaagtaaaaacctgaagaaagagagggtgttttttaatgggcattatttataaaagcttgagcgatagagttaccgcttagtgtggcagcaaaattatcacttttgaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1125:SSA_1126|SSA_1125:SSA_1126:NADPH-dependent FMN reductase, putative:Thiamine biosynthesis lipoprotein, putative:<-<-:1150505..1150676 172 aaaatttcctttctgaaatgaagatacaaatccctcgtaagtgcatttatttctcttgaggcaagtaaaaacctgaagaaagagagggtgttttttaatgggcattatttataaaagcttgagcgatagagttaccgcttagtgtggcagcaaaattatcacttttgaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1125:SSA_1126|SSA_1125:SSA_1126:NADPH-dependent FMN reductase, putative:Thiamine biosynthesis lipoprotein, putative:<-<-:1150505..1150676 172 aaaatttcctttctgaaatgaagatacaaatccctcgtaagtgcatttatttctcttgaggcaagtaaaaacctgaagaaagagagggtgttttttaatgggcattatttataaaagcttgagcgatagagttaccgcttagtgtggcagcaaaattatcacttttgaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatttcctttctgaaatgaagatacaaatccctcgtaagtgcatttatttctcttgaggcaagtaaaaacctgaagaaagagagggtgttttttaatgggcattatttataaaagcttgagcgatagagttaccgcttagtgtggcagcaaaattatcacttttgaaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 1 End: 108 F N G K Q F S S V F G E Y T C K N R K L C T F V Q L F L P H K K I P M M ................................................................ aaaatttcctttctgaaatgaagatacaaatccctcgtaagtgcatttatttctcttgaggcaagtaaaaacctgaagaaagagagggtgttttttaatgggcattatttataaaagcttgagcgatagagttaccgcttagtgtggcagcaaaattatcacttttgaaaaa 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================================================ aaaatttcctttctgaaatgaagatacaaatccctcgtaagtgcatttatttctcttgaggcaagtaaaaacctgaagaaagagagggtgttttttaatgggcattatttataaaagcttgagcgatagagttaccgcttagtgtggcagcaaaattatcacttttgaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1125:SSA_1126|SSA_1125:SSA_1126:NADPH-dependent FMN reductase, putative:Thiamine biosynthesis lipoprotein, putative:<-<-:1150505..1150676 172 aaaatttcctttctgaaatgaagatacaaatccctcgtaagtgcatttatttctcttgaggcaagtaaaaacctgaagaaagagagggtgttttttaatgggcattatttataaaagcttgagcgatagagttaccgcttagtgtggcagcaaaattatcacttttgaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 172 Len: 172 Subject: NC_009009_SSA_1125_SSA_1126|NADPH-dependent FMN reductase, putative:Thiamine biosynthesis lipoprotein, putative|NEGATIVE:NEGATIVE|[1150505,1150676]|172 HSP 1 e-value: 5.0E-93 bit: 341.0 Len: 172 Query Start:1 Query End:172 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 aaaatttcctttctgaaatgaagatacaaatccctcgtaagtgcatttatttctcttgaggcaagtaaaaacctgaagaaagagagggtgttttttaatgggcattatttataaaagcttgagcgatagagttaccgcttagtgtggcagcaaaattatcacttttgaaaaa aaaatttcctttctgaaatgaagatacaaatccctcgtaagtgcatttatttctcttgaggcaagtaaaaacctgaagaaagagagggtgttttttaatgggcattatttataaaagcttgagcgatagagttaccgcttagtgtggcagcaaaattatcacttttgaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUUCCUUUCUGAAAUGAAGAUACAAAUCCCUCGUAAGUGCAUUUAUUUCUCUUGAGGCAAGUAAAAACCUGAAGAAAGAGAGGGUGUUUUUUAAUGGGCAUUAUUUAUAAAAGCUUGAGCGAUAGAGUUACCGCUUAGUGUGGCAGCAAAAUUAUCACUUUUGAAAAA (((((.((((((((((((((((..(((.............)))..))))))))((((.(((..........))).)))).)))))))).))))).......................(..(((.(((((.(((.((((.....)))).)))....))))).)))..)..... (-33.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCAAAAGUGAUAAUUUUGCUGCCACACUAAGCGGUAACUCUAUCGCUCAAGCUUUUAUAAAUAAUGCCCAUUAAAAAACACCCUCUCUUUCUUCAGGUUUUUACUUGCCUCAAGAGAAAUAAAUGCACUUACGAGGGAUUUGUAUCUUCAUUUCAGAAAGGAAAUUUU ((((((...(((((((...(((((((........)))))))...))))))).................................(((((..((((((.((((........)))).))))))..(((......))).)))))..................))))))....... (-32.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 862 90 41 181 132 NC_009009:SSA_1125|5end_NADPH-dependent_FMN_reductase,_putative_1150414..1150644_NEGATIVE 291 152 116 186 142 NC_009009:SSA_1379|5end_hypothetical_protein_1398528..1398758_NEGATIVE 290 169 121 106 48 NC_009009:SSA_0410|5end_hypothetical_protein_406442..406672_NEGATIVE 281 168 122 82 33 NC_009009:SSA_1066|5end_ABC-type_oligopeptide_transport_system,_putative_1084335..1084565_POSITIVE 281 154 113 50 12 NC_009009:SSA_1015|5end_4-hydroxybenzoate_octaprenyltransferase,_putative_1018703..1018933_POSITIVE 281 138 98 131 90 NC_009009:SSA_0339|5end_hypothetical_protein_333950..334180_NEGATIVE 279 153 116 54 21 NC_009009:SSA_1694|5end_PTS_system,_lactose-specific_IIA_component,_putative_1687128..1687358_NEGATIVE 277 151 114 168 132 NC_009009:SSA_0743|5end_Transcriptional_repressor_(arginine_synthesis),_putative_725759..725989_NEGATIVE 276 151 118 231 199 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 274 151 116 217 177 NC_009009:SSA_1501|5end_Cytidylate_kinase,_putative_1505772..1506002_NEGATIVE 273 147 117 67 31 NC_009009:SSA_0387|5end_Transcriptional_regulator,_GntR_family,_putative_382343..382573_NEGATIVE 271 148 117 212 175 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 269 150 117 227 195 NC_009009:SSA_1241|5end_Orotidine-5'-phosphate_decarboxylase,_putative_1266201..1266431_NEGATIVE 264 140 98 190 152 NC_009009:SSA_2047|5end_hypothetical_protein_2049953..2050183_NEGATIVE 264 153 114 51 6 NC_009009:SSA_1154|5end_hypothetical_protein_1182661..1182891_POSITIVE 264 170 121 189 142 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 263 152 116 156 125 NC_009009:SSA_2316|5end_General_secretory_pathway_protein_F,_putative_2318342..2318572_NEGATIVE 261 87 42 136 86 NC_009009:SSA_0080|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_83785..84015_POSITIVE 260 148 101 229 177 NC_009009:SSA_0331|5end_C3-degrading_proteinase,_putative_325178..325408_POSITIVE 259 76 32 150 96 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 150 117 138 96 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 302 148 101 48 4 NC_009009:SSA_2329|3end_hypothetical_protein_2333169..2333319_POSITIVE 290 169 121 68 10 NC_009009:SSA_0411|3end_hypothetical_protein_406480..406630_NEGATIVE 281 154 113 65 27 NC_009009:SSA_1014|3end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1018798..1018948_POSITIVE 281 138 98 126 85 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 277 80 35 74 22 NC_009009:SSA_0994|3end_Peptidase_E,_putative_995390..995540_POSITIVE 277 151 114 151 115 NC_009009:SSA_0744|3end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_725776..725926_NEGATIVE 270 150 105 53 7 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 264 170 121 79 32 NC_009009:SSA_0500|3end_Peptide_ABC_transporter,_permease_protein,_putative_501524..501674_POSITIVE 262 165 121 83 39 NC_009009:SSA_1212|3end_Ribose-phosphate_pyrophosphokinase_2,_putative_1236437..1236587_POSITIVE 261 87 42 90 40 NC_009009:SSA_0079|3end_ROK_family_protein,_putative_83819..83969_POSITIVE 260 148 101 133 81 NC_009009:SSA_0330|3end_hypothetical_protein_325162..325312_POSITIVE 258 97 51 64 8 NC_009009:SSA_2207|3end_hypothetical_protein_2206868..2207018_NEGATIVE 258 119 72 117 65 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE 257 149 108 127 90 NC_009009:SSA_0601|3end_Phosphorylase,_Pnp/Udp_family,_putative_589988..590138_POSITIVE 254 168 122 61 3 NC_009009:SSA_1229|3end_hypothetical_protein_1252314..1252464_NEGATIVE 253 151 114 144 116 NC_009009:SSA_1943|3end_Aspartate_kinase,_putative_1930159..1930309_POSITIVE 252 151 117 61 34 NC_009009:SSA_2275|3end_hypothetical_protein_2275225..2275375_NEGATIVE 247 150 107 131 89 NC_009009:SSA_2338|3end_Conserved_uncharacterized_protein_2340392..2340542_POSITIVE 247 152 114 151 100 NC_009009:SSA_2018|3end_hypothetical_protein_2017464..2017614_NEGATIVE