Origin IGS: agctagtgctaacattgcaaattttttcattattgatccctccttgagtttcttcgcttataatacatcattttttaataaaaatcaagactttttttcaaaatcaattatattggtatacatatttcatttttcgttcttttgtgtactttgtaaagttagtgtctaattttaaaacctttgtcgcttttcaaacagataaattagcttttaaggtatttaaaatttgaatgttttttatataaaacatatatcaaaaatattattat .........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 ataataatatttttgatatatgttttatataaaaaacattcaaattttaaataccttaaaagctaatttatctgtttgaaaagcgacaaaggttttaaaattagacactaactttacaaagtacacaaaagaacgaaaaatgaaatatgtataccaatataattgattttgaaaaaaagtcttgatttttattaaaaaatgatgtattataagcgaagaaactcaaggagggatcaataatgaaaaaatttgcaatgttagcactagct Mask Tandem Repeat Region ================================================ agctagtgctaacattgcaaattttttcattattgatccctccttgagtttcttcgcttataatacatcattttttaataaaaatcaagactttttttcaaaatcaattatattggtatacatatttcatttttcgttcttttgtgtactttgtaaagttagtgtctaattttaaaacctttgtcgcttttcaaacagataaattagcttttaaggtatttaaaatttgaatgttttttatataaaacatatatcaaaaatattattat Find is-nt database================================================ Query_seq: FN1792:FN1793|FN1792:FN1793:hypothetical protein:Phosphoenolpyruvate-protein phosphotransferase:<-<-:273355..273623 269 agctagtgctaacattgcaaattttttcattattgatccctccttgagtttcttcgcttataatacatcattttttaataaaaatcaagactttttttcaaaatcaattatattggtatacatatttcatttttcgttcttttgtgtactttgtaaagttagtgtctaattttaaaacctttgtcgcttttcaaacagataaattagcttttaaggtatttaaaatttgaatgttttttatataaaacatatatcaaaaatattattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1792:FN1793|FN1792:FN1793:hypothetical protein:Phosphoenolpyruvate-protein phosphotransferase:<-<-:273355..273623 269 agctagtgctaacattgcaaattttttcattattgatccctccttgagtttcttcgcttataatacatcattttttaataaaaatcaagactttttttcaaaatcaattatattggtatacatatttcatttttcgttcttttgtgtactttgtaaagttagtgtctaattttaaaacctttgtcgcttttcaaacagataaattagcttttaaggtatttaaaatttgaatgttttttatataaaacatatatcaaaaatattattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1792:FN1793|FN1792:FN1793:hypothetical protein:Phosphoenolpyruvate-protein phosphotransferase:<-<-:273355..273623 269 agctagtgctaacattgcaaattttttcattattgatccctccttgagtttcttcgcttataatacatcattttttaataaaaatcaagactttttttcaaaatcaattatattggtatacatatttcatttttcgttcttttgtgtactttgtaaagttagtgtctaattttaaaacctttgtcgcttttcaaacagataaattagcttttaaggtatttaaaatttgaatgttttttatataaaacatatatcaaaaatattattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agctagtgctaacattgcaaattttttcattattgatccctccttgagtttcttcgcttataatacatcattttttaataaaaatcaagactttttttcaaaatcaattatattggtatacatatttcatttttcgttcttttgtgtactttgtaaagttagtgtctaattttaaaacctttgtcgcttttcaaacagataaattagcttttaaggtatttaaaatttgaatgttttttatataaaacatatatcaaaaatattattat Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 14 End: 166 ............. M A N F F I I D P S L S F F A Y N T S F F N K N Q D F F S K S I I L V Y I F H F S F F C V L C K V S V ....................................................................................................... Protein_Len: 56 Strand: + Start: 60 End: 227 ........................................................... M I H H F L I K I K T F F Q N Q L Y W Y T Y F I F R S F V Y F V K L V S N F K T F V A F Q T D K L A F K V F K I .......................................... agctagtgctaacattgcaaattttttcattattgatccctccttgagtttcttcgcttataatacatcattttttaataaaaatcaagactttttttcaaaatcaattatattggtatacatatttcatttttcgttcttttgtgtactttgtaaagttagtgtctaattttaaaacctttgtcgcttttcaaacagataaattagcttttaaggtatttaaaatttgaatgttttttatataaaacatatatcaaaaatattattat 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: 83 Start: 60 End: 89 ...........................................................CTTGATTTTTATTAAAAAATGATGTATTAT.................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agctagtgctaacattgcaaattttttcattattgatccctccttgagtttcttcgcttataatacatcattttttaataaaaatcaagactttttttcaaaatcaattatattggtatacatatttcatttttcgttcttttgtgtactttgtaaagttagtgtctaattttaaaacctttgtcgcttttcaaacagataaattagcttttaaggtatttaaaatttgaatgttttttatataaaacatatatcaaaaatattattat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1792:FN1793|FN1792:FN1793:hypothetical protein:Phosphoenolpyruvate-protein phosphotransferase:<-<-:273355..273623 269 agctagtgctaacattgcaaattttttcattattgatccctccttgagtttcttcgcttataatacatcattttttaataaaaatcaagactttttttcaaaatcaattatattggtatacatatttcatttttcgttcttttgtgtactttgtaaagttagtgtctaattttaaaacctttgtcgcttttcaaacagataaattagcttttaaggtatttaaaatttgaatgttttttatataaaacatatatcaaaaatattattat Intra-Species Hit: Count: 1 Min: 1 Max: 269 Len: 269 Subject: NC_003454_FN1792_FN1793|hypothetical protein:Phosphoenolpyruvate-protein phosphotransferase|NEGATIVE:NEGATIVE|[273355,273623]|269 HSP 1 e-value: 1.0E-138 bit: 492.0 Len: 269 Query Start:1 Query End:269 Subject Strand: POSITIVE Subject Start: 1 Subject End: 269 agctagtgctaacattgcaaattttttcattattgatccctccttgagtttcttcgcttataatacatcattttttaataaaaatcaagacnnnnnnncaaaatcaattatattggtatacatatttcatttttcgttcttttgtgtactttgtaaagttagtgtctaattttaaaacctttgtcgcttttcaaacagataaattagcttttaaggtatttaaaatttgaatgttttttatataaaacatatatcaaaaatattattat agctagtgctaacattgcaaattttttcattattgatccctccttgagtttcttcgcttataatacatcattttttaataaaaatcaagactttttttcaaaatcaattatattggtatacatatttcatttttcgttcttttgtgtactttgtaaagttagtgtctaattttaaaacctttgtcgcttttcaaacagataaattagcttttaaggtatttaaaatttgaatgttttttatataaaacatatatcaaaaatattattat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUAGUGCUAACAUUGCAAAUUUUUUCAUUAUUGAUCCCUCCUUGAGUUUCUUCGCUUAUAAUACAUCAUUUUUUAAUAAAAAUCAAGACUUUUUUUCAAAAUCAAUUAUAUUGGUAUACAUAUUUCAUUUUUCGUUCUUUUGUGUACUUUGUAAAGUUAGUGUCUAAUUUUAAAACCUUUGUCGCUUUUCAAACAGAUAAAUUAGCUUUUAAGGUAUUUAAAAUUUGAAUGUUUUUUAUAUAAAACAUAUAUCAAAAAUAUUAUUAU .....(..(((((.((((((...........((((((.......(((((......))))).........((((((....)))))).................))))))......((((((((....................)))))))))))))).)))))..)..((((((((((((((....(((..((.....))......)))....))))).)))))))))..(((((((((.(((((.....))))).)))))))))..... (-38.95) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUAAUAUUUUUGAUAUAUGUUUUAUAUAAAAAACAUUCAAAUUUUAAAUACCUUAAAAGCUAAUUUAUCUGUUUGAAAAGCGACAAAGGUUUUAAAAUUAGACACUAACUUUACAAAGUACACAAAAGAACGAAAAAUGAAAUAUGUAUACCAAUAUAAUUGAUUUUGAAAAAAAGUCUUGAUUUUUAUUAAAAAAUGAUGUAUUAUAAGCGAAGAAACUCAAGGAGGGAUCAAUAAUGAAAAAAUUUGCAAUGUUAGCACUAGCU ((((((.(((((((.(((((((((((((...........((.(((((((((.(((((....(((..((((......)))).)))....)))))))))))))).)).....((((....)))).................)))))))))))))............((((((.....)))))).............)))))))...))))))..(((((....(((.....))).(((....))).....)))))...((((....)))). (-37.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 814 50 1 141 92 NC_003454:FN1792|5end_hypothetical_protein_273264..273494_NEGATIVE 296 47 1 132 78 NC_003454:FN2061|5end_Hypothetical_membrane-spanning_protein_574046..574276_NEGATIVE 296 47 1 132 78 NC_003454:FN2050|5end_Hypothetical_membrane-spanning_protein_559970..560200_NEGATIVE 292 49 1 133 78 NC_003454:FN0251|5end_Hypothetical_membrane-spanning_Protein_873796..874026_POSITIVE 290 45 3 106 64 NC_003454:FN0252|5end_hypothetical_protein_874193..874423_POSITIVE 290 45 3 106 64 NC_003454:FN2060|5end_hypothetical_protein_573649..573879_NEGATIVE 290 45 3 106 64 NC_003454:FN2049|5end_hypothetical_protein_559573..559803_NEGATIVE 288 50 3 111 67 NC_003454:FN1859|5end_Major_outer_membrane_protein_349655..349885_NEGATIVE 273 50 1 115 59 NC_003454:FN0264|5end_hypothetical_protein_890862..891092_POSITIVE 263 68 21 98 49 NC_003454:FN1657|5end_SSU_ribosomal_protein_S6P_153122..153352_NEGATIVE 249 62 24 192 160 NC_003454:FN1367|5end_Methyl-accepting_chemotaxis_protein_2018143..2018373_NEGATIVE 248 43 7 103 67 NC_003454:FN0162|5end_Na+_driven_multidrug_efflux_pump_789924..790154_POSITIVE 245 57 19 113 65 NC_003454:FN1950|5end_Serine_protease_457855..458085_NEGATIVE 242 53 11 119 69 NC_003454:FN1740|5end_ATP_synthase_subunit_K_238400..238630_NEGATIVE 241 70 21 175 97 NC_003454:FN0428|5end_hypothetical_protein_1070037..1070267_POSITIVE 235 58 20 128 81 NC_003454:FN0273|5end_Butyrate-acetoacetate_CoA-transferase_subunit_B_899423..899653_POSITIVE 231 57 25 125 86 NC_003454:FN0129|5end_Urease_accessory_protein_ureG_757595..757825_POSITIVE 230 47 1 213 167 NC_003454:FN1867|5end_Zn-dependent_alcohol_dehydrogenase_and_related_dehydrogenase_359597..359827_NEGATIVE 229 77 37 174 134 NC_003454:FN0514|5end_hypothetical_protein_1163431..1163661_POSITIVE 229 49 1 111 50 NC_003454:FN2065|5end_Transcriptional_repressor_575850..576080_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 47 1 71 17 NC_003454:FN2062|3end_hypothetical_protein_574107..574257_NEGATIVE 296 47 1 71 17 NC_003454:FN2051|3end_hypothetical_protein_560031..560181_NEGATIVE 292 49 1 72 17 NC_003454:FN0250|3end_hypothetical_protein_873815..873965_POSITIVE 290 45 3 89 47 NC_003454:FN0251|3end_Hypothetical_membrane-spanning_Protein_874256..874406_POSITIVE 290 45 3 89 47 NC_003454:FN2061|3end_Hypothetical_membrane-spanning_protein_573666..573816_NEGATIVE 290 45 3 89 47 NC_003454:FN2050|3end_Hypothetical_membrane-spanning_protein_559590..559740_NEGATIVE 235 58 20 128 81 NC_003454:FN0272|3end_Acetoacetate:butyrate/acetate_coenzyme_A_transferase_899503..899653_POSITIVE 231 57 25 125 86 NC_003454:FN0128|3end_Spermidine/putrescine-binding_protein_757675..757825_POSITIVE 226 58 14 68 26 NC_003454:FN0336|3end_hypothetical_protein_969748..969898_NEGATIVE 224 45 1 66 13 NC_003454:FN1479|3end_hypothetical_protein_2160703..2160853_NEGATIVE 222 44 22 92 71 NC_003454:FN1178|3end_Hypothetical_cytosolic_protein_1838793..1838943_NEGATIVE 220 45 7 73 23 NC_003454:FN0856|3end_glycogen_branching_enzyme_1514689..1514839_NEGATIVE 216 51 19 98 62 NC_003454:FN0480|3end_hypothetical_protein_1127839..1127989_POSITIVE 216 45 18 111 82 NC_003454:FN0044|3end_Shikimate_5-dehydrogenase_683041..683191_POSITIVE 215 50 1 88 33 NC_003454:FN1162|3end_Hydroxyacylglutathione_hydrolase_1820864..1821014_POSITIVE 211 64 23 103 52 NC_003454:FN0438|3end_Branched_chain_amino_acid_transport_system_II_carrier_protein_1079635..1079785_NEGATIVE 210 65 22 120 65 NC_003454:FN0695|3end_ABC_transporter_ATP-binding_protein_1353691..1353841_POSITIVE 210 55 12 59 6 NC_003454:FN0113|3end_Heat-inducible_transcription_repressor_hrcA_747692..747842_POSITIVE 208 46 1 76 27 NC_003454:FN1319|3end_DNA_primase_1972386..1972536_NEGATIVE 208 50 3 145 99 NC_003454:FN0941|3end_Gamma-glutamyltranspeptidase_1593527..1593677_NEGATIVE