Origin IGS: tttttccctccaattaattttaattaaaatttacctaataattctaacataaatcatatacttttccaactaaaatatttaattatatcatattctatatcccaatcttcttgtaattattttttaacagaaaacctttatattatttaaaaaagatgataaaattgaagtataaataaaatacattaaaggag .........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 ctcctttaatgtattttatttatacttcaattttatcatcttttttaaataatataaaggttttctgttaaaaaataattacaagaagattgggatatagaatatgatataattaaatattttagttggaaaagtatatgatttatgttagaattattaggtaaattttaattaaaattaattggagggaaaaa Mask Tandem Repeat Region ================================================ tttttccctccaattaattttaattaaaatttacctaataattctaacataaatcatatacttttccaactaaaatatttaattatatcatattctatatcccaatcttcttgtaattattttttaacagaaaacctttatattatttaaaaaagatgataaaattgaagtataaataaaatacattaaaggag Find is-nt database================================================ Query_seq: FN1658:FN1659|FN1658:FN1659:prolyl-tRNA synthetase:hypothetical protein:<-->:154982..155175 194 tttttccctccaattaattttaattaaaatttacctaataattctaacataaatcatatacttttccaactaaaatatttaattatatcatattctatatcccaatcttcttgtaattattttttaacagaaaacctttatattatttaaaaaagatgataaaattgaagtataaataaaatacattaaaggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1658:FN1659|FN1658:FN1659:prolyl-tRNA synthetase:hypothetical protein:<-->:154982..155175 194 tttttccctccaattaattttaattaaaatttacctaataattctaacataaatcatatacttttccaactaaaatatttaattatatcatattctatatcccaatcttcttgtaattattttttaacagaaaacctttatattatttaaaaaagatgataaaattgaagtataaataaaatacattaaaggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1658:FN1659|FN1658:FN1659:prolyl-tRNA synthetase:hypothetical protein:<-->:154982..155175 194 tttttccctccaattaattttaattaaaatttacctaataattctaacataaatcatatacttttccaactaaaatatttaattatatcatattctatatcccaatcttcttgtaattattttttaacagaaaacctttatattatttaaaaaagatgataaaattgaagtataaataaaatacattaaaggag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttccctccaattaattttaattaaaatttacctaataattctaacataaatcatatacttttccaactaaaatatttaattatatcatattctatatcccaatcttcttgtaattattttttaacagaaaacctttatattatttaaaaaagatgataaaattgaagtataaataaaatacattaaaggag Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 49 End: 147 ................................................ M N H I L F Q L K Y L I I S Y S I S Q S S C N Y F L T E N L Y I I ............................................... tttttccctccaattaattttaattaaaatttacctaataattctaacataaatcatatacttttccaactaaaatatttaattatatcatattctatatcccaatcttcttgtaattattttttaacagaaaacctttatattatttaaaaaagatgataaaattgaagtataaataaaatacattaaaggag 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: 85 Start: 41 End: 70 ........................................GTTGGAAAAGTATATGATTTATGTTAGAAT............................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 62 End: 91 .............................................................TTTTCCAACTAAAATATTTAATTATATCAT....................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttttccctccaattaattttaattaaaatttacctaataattctaacataaatcatatacttttccaactaaaatatttaattatatcatattctatatcccaatcttcttgtaattattttttaacagaaaacctttatattatttaaaaaagatgataaaattgaagtataaataaaatacattaaaggag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1658:FN1659|FN1658:FN1659:prolyl-tRNA synthetase:hypothetical protein:<-->:154982..155175 194 tttttccctccaattaattttaattaaaatttacctaataattctaacataaatcatatacttttccaactaaaatatttaattatatcatattctatatcccaatcttcttgtaattattttttaacagaaaacctttatattatttaaaaaagatgataaaattgaagtataaataaaatacattaaaggag Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: NC_003454_FN1658_FN1659|prolyl-tRNA synthetase:hypothetical protein|NEGATIVE:POSITIVE|[154982,155175]|194 HSP 1 e-value: 1.0E-106 bit: 385.0 Len: 194 Query Start:1 Query End:194 Subject Strand: POSITIVE Subject Start: 1 Subject End: 194 tttttccctccaattaattttaattaaaatttacctaataattctaacataaatcatatacttttccaactaaaatatttaattatatcatattctatatcccaatcttcttgtaattattttttaacagaaaacctttatattatttaaaaaagatgataaaattgaagtataaataaaatacattaaaggag tttttccctccaattaattttaattaaaatttacctaataattctaacataaatcatatacttttccaactaaaatatttaattatatcatattctatatcccaatcttcttgtaattattttttaacagaaaacctttatattatttaaaaaagatgataaaattgaagtataaataaaatacattaaaggag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCCCUCCAAUUAAUUUUAAUUAAAAUUUACCUAAUAAUUCUAACAUAAAUCAUAUACUUUUCCAACUAAAAUAUUUAAUUAUAUCAUAUUCUAUAUCCCAAUCUUCUUGUAAUUAUUUUUUAACAGAAAACCUUUAUAUUAUUUAAAAAAGAUGAUAAAAUUGAAGUAUAAAUAAAAUACAUUAAAGGAG .......((((..(((((((((.(((.((((........)))).)))..(((((.(((((.(((((....(((((....((((((((........................))))))))..)))))...)))))....))))).)))))..........))))))))).((((.......))))......)))) (-17.26) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCUUUAAUGUAUUUUAUUUAUACUUCAAUUUUAUCAUCUUUUUUAAAUAAUAUAAAGGUUUUCUGUUAAAAAAUAAUUACAAGAAGAUUGGGAUAUAGAAUAUGAUAUAAUUAAAUAUUUUAGUUGGAAAAGUAUAUGAUUUAUGUUAGAAUUAUUAGGUAAAUUUUAAUUAAAAUUAAUUGGAGGGAAAAA .(((((((((....((((.(((((..((((((((((.(((((................((((((((((............)).)))))))))))))))))))).)))))))).)))).(((((((((((((...((((((((((......)))))))...)))..)))))))))))))..)))))))))..... (-28.89) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 670 110 61 201 152 NC_003454:FN1658|5end_prolyl-tRNA_synthetase_154891..155121_NEGATIVE 248 122 81 117 68 NC_003454:FN1010|5end_Hypothetical_cytosolic_protein_1664608..1664838_NEGATIVE 239 110 65 171 112 NC_003454:FN0675|5end_60_kDa_chaperonin_GROEL_1332090..1332320_NEGATIVE 223 132 91 210 177 NC_003454:FN1831|5end_Nitrogen_assimilation_regulatory_protein_321423..321653_NEGATIVE 216 189 147 196 152 NC_003454:FN0508|5end_Serine_protease_1158652..1158882_NEGATIVE 212 144 105 148 100 NC_003454:FN1190|5end_Probable_cadmium-transporting_ATPase_1851677..1851907_POSITIVE 202 114 87 99 72 NC_003454:FN1100|5end_Plasmid_addiction_system_poison_protein_1744177..1744407_POSITIVE 195 140 96 106 47 NC_003454:FN2078|5end_Transcriptional_regulator,_DeoR_family_590266..590496_NEGATIVE 192 98 53 133 87 NC_003454:FN0155|5end_hypothetical_protein_783141..783371_POSITIVE 192 118 90 44 14 NC_003454:FN0071|5end_GTP_cyclohydrolase_I_710962..711192_POSITIVE 191 138 93 126 86 NC_003454:FN1367|5end_Methyl-accepting_chemotaxis_protein_2018143..2018373_NEGATIVE 191 111 75 170 126 NC_003454:FN1750|5end_Pyruvate-flavodoxin_oxidoreductase_247811..248041_POSITIVE 190 50 1 133 79 NC_003454:FN0263|5end_Peptidyl-prolyl_cis-trans_isomerase_890064..890294_POSITIVE 189 71 34 201 159 NC_003454:FN2122|5end_Phenylalanyl-tRNA_synthetase_beta_chain_632194..632424_NEGATIVE 188 103 61 99 55 NC_003454:FN0040|5end_asparaginyl-tRNA_synthetase_680609..680839_NEGATIVE 187 45 1 172 128 NC_003454:FN1205|5end_Protease_1865162..1865392_NEGATIVE 187 126 93 114 77 NC_003454:FN0623|5end_Malonate_transporter_1281952..1282182_POSITIVE 185 32 4 125 96 NC_003454:FN1317|5end_RNA_polymerase_sigma_factor_1971085..1971315_NEGATIVE 182 130 83 192 156 NC_003454:FN1840|5end_Dihydroxyacetone_kinase_329835..330065_POSITIVE 181 110 63 184 138 NC_003454:FN1762|5end_Protein_yaaA_256004..256234_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 212 144 105 141 93 NC_003454:FN1189|3end_hypothetical_protein_1851750..1851900_POSITIVE 204 108 65 151 94 NC_003454:FN0676|3end_10_kDa_chaperonin_GROES_1332108..1332258_NEGATIVE 202 114 87 114 87 NC_003454:FN1099|3end_hypothetical_protein_1744272..1744422_POSITIVE 192 98 53 108 62 NC_003454:FN0154|3end_Ribonuclease_G_783196..783346_POSITIVE 192 118 90 44 14 NC_003454:FN0070|3end_Glycyl-tRNA_synthetase_beta_chain_711042..711192_POSITIVE 191 138 93 112 72 NC_003454:FN1368|3end_COMF_operon_protein_3_2018157..2018307_NEGATIVE 188 103 61 89 45 NC_003454:FN0041|3end_hypothetical_protein_680619..680769_NEGATIVE 187 45 1 121 77 NC_003454:FN1206|3end_Hemolysin_1865213..1865363_NEGATIVE 187 126 93 93 56 NC_003454:FN0622|3end_N-glycosylase/DNA_lyase_1282011..1282161_POSITIVE 185 32 4 109 80 NC_003454:FN1318|3end_RNA_polymerase_sigma_factor_rpoD_1971101..1971251_NEGATIVE 182 130 83 122 86 NC_003454:FN1839|3end_glycerol_kinase_329845..329995_POSITIVE 180 111 78 107 68 NC_003454:FN1644|3end_50S_ribosomal_protein_L4_140017..140167_NEGATIVE 177 125 88 116 81 NC_003454:FN1993|3end_SUA5_protein_497650..497800_POSITIVE 176 140 109 69 28 NC_003454:FN1650|3end_Oligopeptide_transport_system_permease_protein_oppC_144118..144268_NEGATIVE 175 43 6 113 82 NC_003454:FN0249|3end_hypothetical_protein_873262..873412_POSITIVE 175 43 6 113 82 NC_003454:FN2063|3end_hypothetical_protein_574660..574810_NEGATIVE 175 43 6 113 82 NC_003454:FN2052|3end_hypothetical_protein_560584..560734_NEGATIVE 173 121 92 139 104 NC_003454:FN0461|3end_Probable_sigma(54)_modulation_protein_1107147..1107297_POSITIVE 173 126 101 52 30 NC_003454:FN0201|3end_Glutaconyl-COA_decarboxylase_beta_subunit_827749..827899_POSITIVE 170 115 71 151 108 NC_003454:FN0019|3end_Transcription-repair_coupling_factor_659574..659724_POSITIVE