Origin IGS: ttcaagtatattaggcatatcaaaaacttatatgggtaaattcccataactcctttcattaatgtaatattattttgtaaaatgtaaaataaaaacactttccatattataataagaaatccaaataatttcaataa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttattgaaattatttggatttcttattataatatggaaagtgtttttattttacattttacaaaataatattacattaatgaaaggagttatgggaatttacccatataagtttttgatatgcctaatatacttgaa Mask Tandem Repeat Region ================================================ ttcaagtatattaggcatatcaaaaacttatatgggtaaattcccataactcctttcattaatgtaatattattttgtaaaatgtaaaataaaaacactttccatattataataagaaatccaaataatttcaataa Find is-nt database================================================ Query_seq: FN0215:FN0216|FN0215:FN0216:MGTC/SAPB Family membrane protein:3-oxoacyl-[acyl-carrier protein] reductase:<-<-:840065..840201 137 ttcaagtatattaggcatatcaaaaacttatatgggtaaattcccataactcctttcattaatgtaatattattttgtaaaatgtaaaataaaaacactttccatattataataagaaatccaaataatttcaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0215:FN0216|FN0215:FN0216:MGTC/SAPB Family membrane protein:3-oxoacyl-[acyl-carrier protein] reductase:<-<-:840065..840201 137 ttcaagtatattaggcatatcaaaaacttatatgggtaaattcccataactcctttcattaatgtaatattattttgtaaaatgtaaaataaaaacactttccatattataataagaaatccaaataatttcaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0215:FN0216|FN0215:FN0216:MGTC/SAPB Family membrane protein:3-oxoacyl-[acyl-carrier protein] reductase:<-<-:840065..840201 137 ttcaagtatattaggcatatcaaaaacttatatgggtaaattcccataactcctttcattaatgtaatattattttgtaaaatgtaaaataaaaacactttccatattataataagaaatccaaataatttcaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcaagtatattaggcatatcaaaaacttatatgggtaaattcccataactcctttcattaatgtaatattattttgtaaaatgtaaaataaaaacactttccatattataataagaaatccaaataatttcaataa Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: - Start: 3 End: 134 .. L Y I L C I L F K Y P Y I G M V G K M L T I N N Q L I Y F L F V K W I I I L F G F L K M ... ttcaagtatattaggcatatcaaaaacttatatgggtaaattcccataactcctttcattaatgtaatattattttgtaaaatgtaaaataaaaacactttccatattataataagaaatccaaataatttcaataa 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: 91 Start: 106 End: 135 .........................................................................................................ATTGAAATTATTTGGATTTCTTATTATAAT.. PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 54 End: 83 .....................................................TTTCATTAATGTAATATTATTTTGTAAAAT...................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcaagtatattaggcatatcaaaaacttatatgggtaaattcccataactcctttcattaatgtaatattattttgtaaaatgtaaaataaaaacactttccatattataataagaaatccaaataatttcaataa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0215:FN0216|FN0215:FN0216:MGTC/SAPB Family membrane protein:3-oxoacyl-[acyl-carrier protein] reductase:<-<-:840065..840201 137 ttcaagtatattaggcatatcaaaaacttatatgggtaaattcccataactcctttcattaatgtaatattattttgtaaaatgtaaaataaaaacactttccatattataataagaaatccaaataatttcaataa Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: NC_003454_FN0215_FN0216|MGTC/SAPB Family membrane protein:3-oxoacyl-[acyl-carrier protein] reductase|NEGATIVE:NEGATIVE|[840065,840201]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 ttcaagtatattaggcatatcaaaaacttatatgggtaaattcccataactcctttcattaatgtaatattattttgtaaaatgtaaaataaaaacactttccatattataataagaaatccaaataatttcaataa ttcaagtatattaggcatatcaaaaacttatatgggtaaattcccataactcctttcattaatgtaatattattttgtaaaatgtaaaataaaaacactttccatattataataagaaatccaaataatttcaataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAAGUAUAUUAGGCAUAUCAAAAACUUAUAUGGGUAAAUUCCCAUAACUCCUUUCAUUAAUGUAAUAUUAUUUUGUAAAAUGUAAAAUAAAAACACUUUCCAUAUUAUAAUAAGAAAUCCAAAUAAUUUCAAUAA ........((((.((...............((((((......)))))).....((((.(((.(((((((((((((((.......)))))))............)))))))).))))))).)).)))).......... (-15.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUUGAAAUUAUUUGGAUUUCUUAUUAUAAUAUGGAAAGUGUUUUUAUUUUACAUUUUACAAAAUAAUAUUACAUUAAUGAAAGGAGUUAUGGGAAUUUACCCAUAUAAGUUUUUGAUAUGCCUAAUAUACUUGAA .....((((((.....))))))...........((.(((((((.........))))))).)).....(((((((((..((.(((((...((((((......))))))....))))).)))))..))))))....... (-18.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 767 60 11 151 102 NC_003454:FN0215|5end_MGTC/SAPB_Family_membrane_protein_839974..840204_NEGATIVE 227 76 41 87 55 NC_003454:FN0822|5end_Shikimate_kinase_1481828..1482058_POSITIVE 222 74 33 129 72 NC_003454:FN1790|5end_Cob(I)alamin_adenosyltransferase_271511..271741_POSITIVE 204 47 13 78 45 NC_003454:FN1585|5end_hypothetical_protein_97394..97624_NEGATIVE 203 56 14 229 195 NC_003454:FN1706|5end_Transporter_201433..201663_POSITIVE 196 47 14 35 4 NC_003454:FN1721|5end_hypothetical_protein_219945..220175_NEGATIVE 192 77 44 127 88 NC_003454:FN1635|5end_LSU_ribosomal_protein_L14P_136572..136802_NEGATIVE 189 56 15 145 108 NC_003454:FN0519|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1171669..1171899_NEGATIVE 189 65 25 79 30 NC_003454:FN0163|5end_5-methyltetrahydrofolate--homocysteine_methyltransferase_791318..791548_POSITIVE 188 37 1 104 71 NC_003454:FN0115|5end_hypothetical_protein_748511..748741_NEGATIVE 185 71 41 228 204 NC_003454:FN0284|5end_16S_rRNA_processing_protein_rimM_913923..914153_NEGATIVE 184 57 13 107 55 NC_003454:FN0773|5end_hypothetical_protein_1429274..1429504_POSITIVE 183 78 40 175 129 NC_003454:FN0815|5end_Propionate_permease_1474390..1474620_POSITIVE 182 95 51 176 129 NC_003454:FN1679|5end_LPS_biosynthesis_protein_WbpG_175711..175941_NEGATIVE 181 60 11 108 57 NC_003454:FN1217|5end_Holliday_junction_DNA_helicase_ruvB_1877597..1877827_NEGATIVE 179 73 41 115 85 NC_003454:FN0913|5end_Cobinamide_kinase_1570735..1570965_NEGATIVE 179 63 25 113 73 NC_003454:FN0221|5end_Carbon_starvation_protein_A_845209..845439_POSITIVE 178 61 27 93 57 NC_003454:FN0435|5end_Purine_nucleoside_phosphorylase_1077016..1077246_POSITIVE 175 53 33 221 206 NC_003454:FN0114|5end_GrpE_protein_747623..747853_POSITIVE 174 48 1 76 34 NC_003454:FN0533|5end_Hypothetical_membrane-spanning_protein_1188641..1188871_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 222 74 33 117 60 NC_003454:FN1789|3end_Na+_driven_multidrug_efflux_pump_271579..271729_POSITIVE 205 75 34 137 94 NC_003454:FN2082|3end_Formate--tetrahydrofolate_ligase_593257..593407_NEGATIVE 204 47 13 57 24 NC_003454:FN1586|3end_O-succinylbenzoate-CoA_synthase_97415..97565_NEGATIVE 192 77 44 98 59 NC_003454:FN1636|3end_SSU_ribosomal_protein_S17P_136601..136751_NEGATIVE 189 56 15 136 99 NC_003454:FN0520|3end_hypothetical_protein_1171678..1171828_NEGATIVE 183 78 40 88 42 NC_003454:FN0814|3end_Propionate_CoA-transferase_1474383..1474533_POSITIVE 179 73 41 53 23 NC_003454:FN0914|3end_hypothetical_protein_1570797..1570947_NEGATIVE 173 55 17 92 65 NC_003454:FN0358|3end_ATP_synthase_subunit_B_988286..988436_NEGATIVE 170 105 69 44 3 NC_003454:FN1686|3end_Spore_coat_polysaccharide_biosynthesis_protein_spsF_181027..181177_NEGATIVE 169 58 12 62 12 NC_003454:FN0723|3end_hypothetical_protein_1383464..1383614_POSITIVE 169 60 21 102 51 NC_003454:FN1782|3end_Phosphocarrier_protein_HPr_264221..264371_NEGATIVE 168 78 50 117 85 NC_003454:FN1523|3end_Dipeptide-binding_protein_29867..30017_POSITIVE 167 76 35 97 46 NC_003454:FN0363|3end_ATP_synthase_C_chain,_sodium_ion_specific_993434..993584_NEGATIVE 164 79 39 76 27 NC_003454:FN1735|3end_V-type_ATP_synthase_subunit_A_234251..234401_NEGATIVE 164 58 33 87 63 NC_003454:FN1708|3end_Polyribonucleotide_nucleotidyltransferase_205479..205629_POSITIVE 161 107 66 80 34 NC_003454:FN0376|3end_Iron(III)-transport_ATP-binding_protein_sfuC_1007560..1007710_POSITIVE 161 56 11 89 40 NC_003454:FN0171|3end_Hypothetical_cytosolic_protein_796921..797071_POSITIVE 157 67 26 73 30 NC_003454:FN1326|3end_Undecaprenyl_pyrophosphate_synthetase_1981198..1981348_NEGATIVE 157 43 1 54 6 NC_003454:FN0901|3end_DNA_polymerase,_bacteriophage-type_1560639..1560789_POSITIVE 157 84 43 120 66 NC_003454:FN0319|3end_Citrate_(pro-3S)-lyase_ligase_955818..955968_NEGATIVE