Origin IGS: atcatatcctccttaatttttttatttgattgaatatatattcaactgaacatttgtatagtatcactaaacaaaaaaaatgtcaactattttttattaattttataaacttttatttttttcttgattttttcactaattaagactaaacttaattatgactattcacattattttttagtctaattgtaataaatgaattttattagaaaaggaagtaatatat .........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 atatattacttccttttctaataaaattcatttattacaattagactaaaaaataatgtgaatagtcataattaagtttagtcttaattagtgaaaaaatcaagaaaaaaataaaagtttataaaattaataaaaaatagttgacattttttttgtttagtgatactatacaaatgttcagttgaatatatattcaatcaaataaaaaaattaaggaggatatgat Mask Tandem Repeat Region ================================================ atcatatcctccttaatttttttatttgattgaatatatattcaactgaacatttgtatagtatcactaaacaaaaaaaatgtcaactattttttattaattttataaacttttatttttttcttgattttttcactaattaagactaaacttaattatgactattcacattattttttagtctaattgtaataaatgaattttattagaaaaggaagtaatatat Find is-nt database================================================ Query_seq: FN1884:FN1885|FN1884:FN1885:hypothetical protein:Hemolysin III:<-->:370598..370823 226 atcatatcctccttaatttttttatttgattgaatatatattcaactgaacatttgtatagtatcactaaacaaaaaaaatgtcaactattttttattaattttataaacttttatttttttcttgattttttcactaattaagactaaacttaattatgactattcacattattttttagtctaattgtaataaatgaattttattagaaaaggaagtaatatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1884:FN1885|FN1884:FN1885:hypothetical protein:Hemolysin III:<-->:370598..370823 226 atcatatcctccttaatttttttatttgattgaatatatattcaactgaacatttgtatagtatcactaaacaaaaaaaatgtcaactattttttattaattttataaacttttatttttttcttgattttttcactaattaagactaaacttaattatgactattcacattattttttagtctaattgtaataaatgaattttattagaaaaggaagtaatatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1884:FN1885|FN1884:FN1885:hypothetical protein:Hemolysin III:<-->:370598..370823 226 atcatatcctccttaatttttttatttgattgaatatatattcaactgaacatttgtatagtatcactaaacaaaaaaaatgtcaactattttttattaattttataaacttttatttttttcttgattttttcactaattaagactaaacttaattatgactattcacattattttttagtctaattgtaataaatgaattttattagaaaaggaagtaatatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcatatcctccttaatttttttatttgattgaatatatattcaactgaacatttgtatagtatcactaaacaaaaaaaatgtcaactattttttattaattttataaacttttatttttttcttgattttttcactaattaagactaaacttaattatgactattcacattattttttagtctaattgtaataaatgaattttattagaaaaggaagtaatatat Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 30 End: 140 ............................. M N I Y S T E H L Y S I T K Q K K C Q L F F I N F I N F Y F F L D F F T N ...................................................................................... atcatatcctccttaatttttttatttgattgaatatatattcaactgaacatttgtatagtatcactaaacaaaaaaaatgtcaactattttttattaattttataaacttttatttttttcttgattttttcactaattaagactaaacttaattatgactattcacattattttttagtctaattgtaataaatgaattttattagaaaaggaagtaatatat 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: 58 End: 87 .........................................................GTTGACATTTTTTTTGTTTAGTGATACTAT........................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 123 End: 152 ..........................................................................................................................CTTGATTTTTTCACTAATTAAGACTAAACT.......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcatatcctccttaatttttttatttgattgaatatatattcaactgaacatttgtatagtatcactaaacaaaaaaaatgtcaactattttttattaattttataaacttttatttttttcttgattttttcactaattaagactaaacttaattatgactattcacattattttttagtctaattgtaataaatgaattttattagaaaaggaagtaatatat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1884:FN1885|FN1884:FN1885:hypothetical protein:Hemolysin III:<-->:370598..370823 226 atcatatcctccttaatttttttatttgattgaatatatattcaactgaacatttgtatagtatcactaaacaaaaaaaatgtcaactattttttattaattttataaacttttatttttttcttgattttttcactaattaagactaaacttaattatgactattcacattattttttagtctaattgtaataaatgaattttattagaaaaggaagtaatatat Intra-Species Hit: Count: 1 Min: 1 Max: 226 Len: 226 Subject: NC_003454_FN1884_FN1885|hypothetical protein:Hemolysin III|NEGATIVE:POSITIVE|[370598,370823]|226 HSP 1 e-value: 9.0E-46 bit: 184.0 Len: 93 Query Start:134 Query End:226 Subject Strand: POSITIVE Subject Start: 134 Subject End: 226 .....................................................................................................................................cactaattaagactaaacttaattatgactattcacattattttttagtctaattgtaataaatgaattttattagaaaaggaagtaatatat .....................................................................................................................................cactaattaagactaaacttaattatgactattcacattattttttagtctaattgtaataaatgaattttattagaaaaggaagtaatatat HSP 2 e-value: 1.0E-20 bit: 101.0 Len: 72 Query Start:1 Query End:72 Subject Strand: POSITIVE Subject Start: 1 Subject End: 72 atcatatcctccttaannnnnnnatttgattgaatatatattcaactgaacatttgtatagtatcactaaac.......................................................................................................................................................... atcatatcctccttaatttttttatttgattgaatatatattcaactgaacatttgtatagtatcactaaac.......................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUAUCCUCCUUAAUUUUUUUAUUUGAUUGAAUAUAUAUUCAACUGAACAUUUGUAUAGUAUCACUAAACAAAAAAAAUGUCAACUAUUUUUUAUUAAUUUUAUAAACUUUUAUUUUUUUCUUGAUUUUUUCACUAAUUAAGACUAAACUUAAUUAUGACUAUUCACAUUAUUUUUUAGUCUAAUUGUAAUAAAUGAAUUUUAUUAGAAAAGGAAGUAAUAUAU .(((((..............(((((..((((((.......(((....)))..(((((.(((.....))).))))).....................))))))..))))).......(((..((((((((........))))))))..)))......)))))........((((((((((..((((((...(((......)))..))))))..)))))))))).... (-27.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUAUUACUUCCUUUUCUAAUAAAAUUCAUUUAUUACAAUUAGACUAAAAAAUAAUGUGAAUAGUCAUAAUUAAGUUUAGUCUUAAUUAGUGAAAAAAUCAAGAAAAAAAUAAAAGUUUAUAAAAUUAAUAAAAAAUAGUUGACAUUUUUUUUGUUUAGUGAUACUAUACAAAUGUUCAGUUGAAUAUAUAUUCAAUCAAAUAAAAAAAUUAAGGAGGAUAUGAU .(((((..(((((((...........((((((.((((.....((((((((......(((((....)))))......)))))))))))).))))))...((((......(((((((((.......(((((........))))).......)))))))))..))))..........((((..(((((((....)))))))..))))........)))))))))))).. (-34.14) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 687 90 41 181 132 NC_003454:FN1884|5end_hypothetical_protein_370507..370737_NEGATIVE 253 124 81 99 49 NC_003454:FN0240|5end_Thymidylate_synthase_863894..864124_POSITIVE 237 44 5 137 96 NC_003454:FN1423|5end_Flavoprotein_2090070..2090300_NEGATIVE 220 41 8 131 100 NC_003454:FN1522|5end_Dipeptide_transport_system_permease_protein_dppC_27327..27557_POSITIVE 215 137 91 197 148 NC_003454:FN0575|5end_hypothetical_protein_1225331..1225561_POSITIVE 207 185 145 191 152 NC_003454:FN0385|5end_hypothetical_protein_1017920..1018150_POSITIVE 204 50 9 144 99 NC_003454:FN0640|5end_Transporter_1298320..1298550_NEGATIVE 201 126 81 106 64 NC_003454:FN1380|5end_Citrate_lyase_beta_chain_2027248..2027478_POSITIVE 196 154 123 84 52 NC_003454:FN0508|5end_Serine_protease_1158652..1158882_NEGATIVE 196 45 2 166 112 NC_003454:FN0471|5end_Cell_surface_protein_1116525..1116755_POSITIVE 195 142 110 57 22 NC_003454:FN2032|5end_DNA-directed_RNA_polymerase_omega_chain_537315..537545_NEGATIVE 193 49 1 141 95 NC_003454:FN0636|5end_hypothetical_protein_1295170..1295400_POSITIVE 193 191 151 187 143 NC_003454:FN0515|5end_Acriflavin_resistance_protein_D_1167006..1167236_NEGATIVE 192 33 2 111 82 NC_003454:FN1092|5end_hypothetical_protein_1737267..1737497_POSITIVE 191 177 140 191 152 NC_003454:FN1468|5end_Flavoredoxin_2150385..2150615_NEGATIVE 189 120 81 225 187 NC_003454:FN0244|5end_COP_associated_protein_868115..868345_POSITIVE 188 68 21 92 44 NC_003454:FN0966|5end_Precorrin-6Y_C5,15-methyltransferase_[decarboxylating]_1619969..1620199_NEGATIVE 188 42 1 134 87 NC_003454:FN0065|5end_Transcription_accessory_protein_(S1_RNA_binding_domain)_699933..700163_POSITIVE 185 66 21 169 117 NC_003454:FN1463|5end_pyridoxine_biosynthesis_protein_2145002..2145232_POSITIVE 185 136 92 188 147 NC_003454:FN0526|5end_Florfenicol_resistance_protein_1182977..1183207_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 237 44 5 112 71 NC_003454:FN1424|3end_ACYL-COA_dehydrogenase,_short-chain_specific_2090095..2090245_NEGATIVE 220 41 8 130 99 NC_003454:FN1521|3end_Dipeptide_transport_system_permease_protein_dppB_27406..27556_POSITIVE 215 137 91 69 20 NC_003454:FN0574|3end_Hypothetical_cytosolic_protein_1225283..1225433_POSITIVE 204 50 9 121 76 NC_003454:FN0641|3end_Methyltransferase_1298343..1298493_NEGATIVE 201 126 81 103 61 NC_003454:FN1379|3end_Citrate_lyase_beta_chain_2027325..2027475_POSITIVE 194 124 84 48 1 NC_003454:FN0239|3end_hypothetical_protein_863923..864073_POSITIVE 192 33 2 102 73 NC_003454:FN1091|3end_Sigma_factor_sigB_regulation_protein_rsbU_1737338..1737488_POSITIVE 189 120 81 64 26 NC_003454:FN0243|3end_Poly(A)_polymerase_868034..868184_POSITIVE 188 68 21 138 90 NC_003454:FN0967|3end_CbiD_protein_1619923..1620073_NEGATIVE 181 136 91 52 10 NC_003454:FN1209|3end_Hypothetical_RNA_binding_protein_1868615..1868765_NEGATIVE 181 128 83 106 68 NC_003454:FN1012|3end_HPr_kinase/phosphorylase_1665680..1665830_NEGATIVE 181 45 1 125 66 NC_003454:FN1543|3end_Ubiquinone/menaquinone_biosynthesis_methyltransferase_UBIE_57889..58039_POSITIVE 180 145 102 132 84 NC_003454:FN1422|3end_NA+/H+_antiporter_NHAC_2087005..2087155_NEGATIVE 179 44 7 145 101 NC_003454:FN1538|3end_Arsenical_pump-driving_ATPase_51109..51259_NEGATIVE 178 68 34 73 36 NC_003454:FN1458|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_2138977..2139127_NEGATIVE 177 27 4 92 63 NC_003454:FN2036|3end_DNA-directed_RNA_polymerase_beta_chain_542817..542967_NEGATIVE 176 25 1 42 12 NC_003454:FN1308|3end_Phosphatidate_cytidylyltransferase_1964861..1965011_POSITIVE 173 47 5 115 76 NC_003454:FN0985|3end_Phosphoribosylglycinamide_formyltransferase_1637315..1637465_NEGATIVE 172 66 21 61 18 NC_003454:FN0848|3end_hypothetical_protein_1507763..1507913_POSITIVE 172 210 171 64 27 NC_003454:FN0106|3end_hypothetical_protein_741462..741612_POSITIVE