Origin IGS: gtaaaaacctctaagttagtttatattttctaacttagaggtggtttgtggctcattgcctatatattattaaaaagttattacctacaattaatttaaaaacaatttacttagttatattattttttaatttattagttattaagggattttataaagtgaaattttttagtaaattgtttttaaaaaattaattgcatcttcaagggtaagtttataaacaaattctctttcttcctcatttaacaaactaaactttcttttaaattctaaaaaatgcataagtaacaactcctttttt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaaaggagttgttacttatgcattttttagaatttaaaagaaagtttagtttgttaaatgaggaagaaagagaatttgtttataaacttacccttgaagatgcaattaattttttaaaaacaatttactaaaaaatttcactttataaaatcccttaataactaataaattaaaaaataatataactaagtaaattgtttttaaattaattgtaggtaataactttttaataatatataggcaatgagccacaaaccacctctaagttagaaaatataaactaacttagaggtttttac Mask Tandem Repeat Region ================================================ gtaaaaacctctaagttagtttatattttctaacttagaggtggtttgtggctcattgcctatatattattaaaaagttattacctacaattaatttaaaaacaatttacttagttatattattttttaatttattagttattaagggattttataaagtgaaattttttagtaaattgtttttaaaaaattaattgcatcttcaagggtaagtttataaacaaattctctttcttcctcatttaacaaactaaactttcttttaaattctaaaaaatgcataagtaacaactcctttttt Find is-nt database================================================ Query_seq: FN1587:FN1588|FN1587:FN1588:Acetyltransferase:hypothetical protein:->->:99395..99695 301 gtaaaaacctctaagttagtttatattttctaacttagaggtggtttgtggctcattgcctatatattattaaaaagttattacctacaattaatttaaaaacaatttacttagttatattattttttaatttattagttattaagggattttataaagtgaaattttttagtaaattgtttttaaaaaattaattgcatcttcaagggtaagtttataaacaaattctctttcttcctcatttaacaaactaaactttcttttaaattctaaaaaatgcataagtaacaactcctttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1587:FN1588|FN1587:FN1588:Acetyltransferase:hypothetical protein:->->:99395..99695 301 gtaaaaacctctaagttagtttatattttctaacttagaggtggtttgtggctcattgcctatatattattaaaaagttattacctacaattaatttaaaaacaatttacttagttatattattttttaatttattagttattaagggattttataaagtgaaattttttagtaaattgtttttaaaaaattaattgcatcttcaagggtaagtttataaacaaattctctttcttcctcatttaacaaactaaactttcttttaaattctaaaaaatgcataagtaacaactcctttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1587:FN1588|FN1587:FN1588:Acetyltransferase:hypothetical protein:->->:99395..99695 301 gtaaaaacctctaagttagtttatattttctaacttagaggtggtttgtggctcattgcctatatattattaaaaagttattacctacaattaatttaaaaacaatttacttagttatattattttttaatttattagttattaagggattttataaagtgaaattttttagtaaattgtttttaaaaaattaattgcatcttcaagggtaagtttataaacaaattctctttcttcctcatttaacaaactaaactttcttttaaattctaaaaaatgcataagtaacaactcctttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtaaaaacctctaagttagtttatattttctaacttagaggtggtttgtggctcattgcctatatattattaaaaagttattacctacaattaatttaaaaacaatttacttagttatattattttttaatttattagttattaagggattttataaagtgaaattttttagtaaattgtttttaaaaaattaattgcatcttcaagggtaagtttataaacaaattctctttcttcctcatttaacaaactaaactttcttttaaattctaaaaaatgcataagtaacaactcctttttt Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 48 End: 191 ............................................... M A H C L Y I I K K L L P T I N L K T I Y L V I L F F N L L V I K G F Y K V K F F S K L F L K N .............................................................................................................. Protein_Len: 40 Strand: - Start: 172 End: 291 ........................................................................................................................................................................... Y I T K L F N I A D E L T L K Y V F E R E E E N L L S F K R K F E L F H M L L M .......... gtaaaaacctctaagttagtttatattttctaacttagaggtggtttgtggctcattgcctatatattattaaaaagttattacctacaattaatttaaaaacaatttacttagttatattattttttaatttattagttattaagggattttataaagtgaaattttttagtaaattgtttttaaaaaattaattgcatcttcaagggtaagtttataaacaaattctctttcttcctcatttaacaaactaaactttcttttaaattctaaaaaatgcataagtaacaactcctttttt 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: 94 End: 123 .............................................................................................ATTTAAAAACAATTTACTTAGTTATATTAT.................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtaaaaacctctaagttagtttatattttctaacttagaggtggtttgtggctcattgcctatatattattaaaaagttattacctacaattaatttaaaaacaatttacttagttatattattttttaatttattagttattaagggattttataaagtgaaattttttagtaaattgtttttaaaaaattaattgcatcttcaagggtaagtttataaacaaattctctttcttcctcatttaacaaactaaactttcttttaaattctaaaaaatgcataagtaacaactcctttttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1587:FN1588|FN1587:FN1588:Acetyltransferase:hypothetical protein:->->:99395..99695 301 gtaaaaacctctaagttagtttatattttctaacttagaggtggtttgtggctcattgcctatatattattaaaaagttattacctacaattaatttaaaaacaatttacttagttatattattttttaatttattagttattaagggattttataaagtgaaattttttagtaaattgtttttaaaaaattaattgcatcttcaagggtaagtttataaacaaattctctttcttcctcatttaacaaactaaactttcttttaaattctaaaaaatgcataagtaacaactcctttttt Intra-Species Hit: Count: 1 Min: 1 Max: 301 Len: 301 Subject: NC_003454_FN1587_FN1588|Acetyltransferase:hypothetical protein|POSITIVE:POSITIVE|[99395,99695]|301 HSP 1 e-value: 8.0E-53 bit: 208.0 Len: 105 Query Start:197 Query End:301 Subject Strand: POSITIVE Subject Start: 197 Subject End: 301 ....................................................................................................................................................................................................gcatcttcaagggtaagtttataaacaaattctctttcttcctcatttaacaaactaaactttcttttaaattctaaaaaatgcataagtaacaactcctttttt ....................................................................................................................................................................................................gcatcttcaagggtaagtttataaacaaattctctttcttcctcatttaacaaactaaactttcttttaaattctaaaaaatgcataagtaacaactcctttttt HSP 2 e-value: 6.0E-26 bit: 119.0 Len: 60 Query Start:1 Query End:60 Subject Strand: POSITIVE Subject Start: 1 Subject End: 60 gtaaaaacctctaagttagtttatattttctaacttagaggtggtttgtggctcattgcc................................................................................................................................................................................................................................................. gtaaaaacctctaagttagtttatattttctaacttagaggtggtttgtggctcattgcc................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAAAACCUCUAAGUUAGUUUAUAUUUUCUAACUUAGAGGUGGUUUGUGGCUCAUUGCCUAUAUAUUAUUAAAAAGUUAUUACCUACAAUUAAUUUAAAAACAAUUUACUUAGUUAUAUUAUUUUUUAAUUUAUUAGUUAUUAAGGGAUUUUAUAAAGUGAAAUUUUUUAGUAAAUUGUUUUUAAAAAAUUAAUUGCAUCUUCAAGGGUAAGUUUAUAAACAAAUUCUCUUUCUUCCUCAUUUAACAAACUAAACUUUCUUUUAAAUUCUAAAAAAUGCAUAAGUAACAACUCCUUUUUU (((...(((((((((((((..........)))))))))))))((((((((((.....)))....................((((((.((((((((((((((((((((((((...(((((..((((((((((.........))))))))))..))))).............)))))))))))))))...))))))))).........)))))).................................))))))).........................)))..................... (-57.59) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAAGGAGUUGUUACUUAUGCAUUUUUUAGAAUUUAAAAGAAAGUUUAGUUUGUUAAAUGAGGAAGAAAGAGAAUUUGUUUAUAAACUUACCCUUGAAGAUGCAAUUAAUUUUUUAAAAACAAUUUACUAAAAAAUUUCACUUUAUAAAAUCCCUUAAUAACUAAUAAAUUAAAAAAUAAUAUAACUAAGUAAAUUGUUUUUAAAUUAAUUGUAGGUAAUAACUUUUUAAUAAUAUAUAGGCAAUGAGCCACAAACCACCUCUAAGUUAGAAAAUAUAAACUAACUUAGAGGUUUUUAC ....(((((((((((((((((((((((((..((((((......)))))).((((((.(((..((............))..)))))))))........)))))))).........(((((((((((((((((................(((......)))...........((((.....)))).......)))))))))))))))))......)))))))))))))))))...........(((.....))).......(((((((((((((..........)))))))))))))...... (-63.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 235 86 49 164 134 NC_003454:FN1186|5end_Amidohydrolase_1848756..1848986_POSITIVE 232 59 12 174 113 NC_003454:FN1593|5end_NADH-ubiquinone_oxidoreductase_104360..104590_NEGATIVE 218 239 194 161 115 NC_003454:FN1482|5end_Guanosine-3',5'-bis(Diphosphate)_3'-pyrophosphohydrolase_2165992..2166222_NEGATIVE 212 50 7 65 14 NC_003454:FN1640|5end_LSU_ribosomal_protein_L22P_138517..138747_NEGATIVE 207 262 224 108 66 NC_003454:FN0464|5end_hypothetical_protein_1109675..1109905_POSITIVE 206 67 25 132 95 NC_003454:FN0437|5end_Allophanate_hydrolase_1079642..1079872_NEGATIVE 206 42 3 105 70 NC_003454:FN0419|5end_aspartate_carbamoyltransferase_catalytic_subunit_1059713..1059943_POSITIVE 204 66 22 194 152 NC_003454:FN0953|5end_hypothetical_protein_1610246..1610476_NEGATIVE 202 47 6 141 90 NC_003454:FN1431|5end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2100252..2100482_NEGATIVE 202 265 221 69 12 NC_003454:FN0494|5end_Short_chain_dehydrogenase_1138777..1139007_POSITIVE 202 64 21 131 88 NC_003454:FN1927|5end_DEGV_protein_427952..428182_NEGATIVE 201 271 231 78 30 NC_003454:FN0470|5end_Putative_efflux_pump_component_MtrF_1114741..1114971_POSITIVE 200 59 11 61 10 NC_003454:FN1903|5end_Coenzyme_A_disulfide_reductase/_disulfide_bond_regulator_domain_393104..393334_NEGATIVE 197 239 195 109 58 NC_003454:FN0754|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A_1414646..1414876_NEGATIVE 195 73 33 101 53 NC_003454:FN0176|5end_Cell_division_inhibitor_MinD_801157..801387_POSITIVE 195 60 12 171 130 NC_003454:FN0036|5end_Hypothetical_membrane-spanning_Protein_677609..677839_NEGATIVE 194 37 9 59 28 NC_003454:FN0870|5end_Rhodanese-related_sulfurtransferase_1529635..1529865_NEGATIVE 194 237 200 189 154 NC_003454:FN0073|5end_Dihydropteroate_synthase_712520..712750_POSITIVE 190 60 11 181 135 NC_003454:FN1314|5end_hypothetical_protein_1968682..1968912_NEGATIVE 190 63 28 106 62 NC_003454:FN1305|5end_Hypothetical_cytosolic_protein_1961205..1961435_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 42 7 84 49 NC_003454:FN1587|3end_Acetyltransferase_99334..99484_POSITIVE 218 239 194 142 96 NC_003454:FN1483|3end_adenine_phosphoribosyltransferase_2166011..2166161_NEGATIVE 214 206 171 48 8 NC_003454:FN1547|3end_PTS_permease_for_N-acetylglucosamine_and_glucose_61801..61951_NEGATIVE 207 73 49 149 125 NC_003454:FN1855|3end_Methylaspartate_mutase_345486..345636_POSITIVE 206 67 25 139 102 NC_003454:FN0438|3end_Branched_chain_amino_acid_transport_system_II_carrier_protein_1079635..1079785_NEGATIVE 206 42 3 43 8 NC_003454:FN0418|3end_pyrimidine_regulatory_protein_PyrR_1059731..1059881_POSITIVE 204 66 22 71 29 NC_003454:FN0954|3end_Hypothetical_cytosolic_protein_1610369..1610519_NEGATIVE 202 64 21 119 76 NC_003454:FN1928|3end_Transcriptional_regulator,_MerR_family_427964..428114_NEGATIVE 197 239 195 92 41 NC_003454:FN0755|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_C_1414663..1414813_NEGATIVE 195 73 33 99 51 NC_003454:FN0175|3end_Cell_division_inhibitor_MinC_801235..801385_POSITIVE 190 262 221 144 93 NC_003454:FN1348|3end_ABC_transporter_ATP-binding_protein_2000470..2000620_NEGATIVE 189 166 121 133 89 NC_003454:FN0363|3end_ATP_synthase_C_chain,_sodium_ion_specific_993434..993584_NEGATIVE 189 68 21 67 17 NC_003454:FN1505|3end_6,7-dimethyl-8-ribityllumazine_synthase_10949..11099_POSITIVE 188 239 195 135 85 NC_003454:FN1458|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_2138977..2139127_NEGATIVE 188 300 253 92 59 NC_003454:FN1415|3end_NADH-dependent_butanol_dehydrogenase_A_2075608..2075758_NEGATIVE 188 146 104 124 73 NC_003454:FN0922|3end_Homoserine_kinase_1576588..1576738_NEGATIVE 187 62 23 50 5 NC_003454:FN1182|3end_hypothetical_protein_1843885..1844035_NEGATIVE 187 299 253 88 40 NC_003454:FN0319|3end_Citrate_(pro-3S)-lyase_ligase_955818..955968_NEGATIVE 185 240 192 111 50 NC_003454:FN0715|3end_hypothetical_protein_1374056..1374206_POSITIVE 185 239 193 74 14 NC_003454:FN1533|3end_Electron_transfer_flavoprotein_alpha-subunit_45350..45500_NEGATIVE