Origin IGS: tttctttaacttgaattaagttaataaaataagtaacaatacaagatcaacacccaaggtattaactttgggtgtttttatatataaaaaagattattacaagtttaagtttgtaataatcttcatatttgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acaaatatgaagattattacaaacttaaacttgtaataatcttttttatatataaaaacacccaaagttaataccttgggtgttgatcttgtattgttacttattttattaacttaattcaagttaaagaaa Mask Tandem Repeat Region ================================================ tttctttaacttgaattaagttaataaaataagtaacaatacaagatcaacacccaaggtattaactttgggtgtttttatatataaaaaagattattacaagtttaagtttgtaataatcttcatatttgt Find is-nt database================================================ Query_seq: FN0488:FN0489|FN0488:FN0489:NAD-specific glutamate dehydrogenase:Prolipoprotein diacylglyceryl transferase:-><-:1134517..1134648 132 tttctttaacttgaattaagttaataaaataagtaacaatacaagatcaacacccaaggtattaactttgggtgtttttatatataaaaaagattattacaagtttaagtttgtaataatcttcatatttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0488:FN0489|FN0488:FN0489:NAD-specific glutamate dehydrogenase:Prolipoprotein diacylglyceryl transferase:-><-:1134517..1134648 132 tttctttaacttgaattaagttaataaaataagtaacaatacaagatcaacacccaaggtattaactttgggtgtttttatatataaaaaagattattacaagtttaagtttgtaataatcttcatatttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0488:FN0489|FN0488:FN0489:NAD-specific glutamate dehydrogenase:Prolipoprotein diacylglyceryl transferase:-><-:1134517..1134648 132 tttctttaacttgaattaagttaataaaataagtaacaatacaagatcaacacccaaggtattaactttgggtgtttttatatataaaaaagattattacaagtttaagtttgtaataatcttcatatttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttctttaacttgaattaagttaataaaataagtaacaatacaagatcaacacccaaggtattaactttgggtgtttttatatataaaaaagattattacaagtttaagtttgtaataatcttcatatttgt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 29 End: 130 ............................ M S N N T R S T P K V L T L G V F I Y K K D Y Y K F K F V I I F I F .. tttctttaacttgaattaagttaataaaataagtaacaatacaagatcaacacccaaggtattaactttgggtgtttttatatataaaaaagattattacaagtttaagtttgtaataatcttcatatttgt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttctttaacttgaattaagttaataaaataagtaacaatacaagatcaacacccaaggtattaactttgggtgtttttatatataaaaaagattattacaagtttaagtttgtaataatcttcatatttgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.8 Tail_Score: -5.03994 Start: 51 End: 74 Full_Region: ACAATACAAGATCAA CACCCAAGGT ATTA ACTTTGGGTG TTTTTATATATAAAA ..................................................CACCCAAGGTATTAACTTTGGGTG.......................................................... TransTerm Strand: - Conf: 80 HP_score: -9.6 Tail_Score: -3.47232 Start: 51 End: 74 Full_Region: ttttatatataaaaa cacccaaagt taat accttgggtg ttgatcttgtattgt ..................................................cacccaaagttaataccttgggtg.......................................................... Find igs database================================================ Query_seq: FN0488:FN0489|FN0488:FN0489:NAD-specific glutamate dehydrogenase:Prolipoprotein diacylglyceryl transferase:-><-:1134517..1134648 132 tttctttaacttgaattaagttaataaaataagtaacaatacaagatcaacacccaaggtattaactttgggtgtttttatatataaaaaagattattacaagtttaagtttgtaataatcttcatatttgt Intra-Species Hit: Count: 1 Min: 1 Max: 132 Len: 132 Subject: NC_003454_FN0488_FN0489|NAD-specific glutamate dehydrogenase:Prolipoprotein diacylglyceryl transferase|POSITIVE:NEGATIVE|[1134517,1134648]|132 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 tttctttaacttgaattaagttaataaaataagtaacaatacaagatcaacacccaaggtattaactttgggtgtttttatatataaaaaagattattacaagtttaagtttgtaataatcttcatatttgt tttctttaacttgaattaagttaataaaataagtaacaatacaagatcaacacccaaggtattaactttgggtgtttttatatataaaaaagattattacaagtttaagtttgtaataatcttcatatttgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUUAACUUGAAUUAAGUUAAUAAAAUAAGUAACAAUACAAGAUCAACACCCAAGGUAUUAACUUUGGGUGUUUUUAUAUAUAAAAAAGAUUAUUACAAGUUUAAGUUUGUAAUAAUCUUCAUAUUUGU .....((((((((...))))))))....(((((((.............((((((((((((....)))))))))))).............((((((((((((((......))))))))))))))..))))))) (-35.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAAUAUGAAGAUUAUUACAAACUUAAACUUGUAAUAAUCUUUUUUAUAUAUAAAAACACCCAAAGUUAAUACCUUGGGUGUUGAUCUUGUAUUGUUACUUAUUUUAUUAACUUAAUUCAAGUUAAAGAAA ........((((((((((((((........))))))))))))))...(((((....(((((((((.((....)).))))))))).....))))).........((((.(((((((.....))))))).)))) (-32.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 216 79 37 56 7 NC_003454:FN1130|5end_Tetraacyldisaccharide_4'-kinase_1777840..1778070_POSITIVE 205 98 54 155 117 NC_003454:FN0840|5end_Transposase_1501361..1501591_POSITIVE 203 72 40 62 23 NC_003454:FN0127|5end_Fe-S_oxidoreductase_756312..756542_NEGATIVE 202 79 46 53 11 NC_003454:FN1601|5end_Hypothetical_cytosolic_protein_110908..111138_NEGATIVE 201 72 32 125 84 NC_003454:FN0109|5end_hypothetical_protein_744809..745039_NEGATIVE 198 65 29 67 29 NC_003454:FN0375|5end_Iron(III)-binding_protein_1005293..1005523_POSITIVE 188 95 52 83 24 NC_003454:FN0383|5end_Lipopolysaccharide_N-acetylglucosaminyltransferase_1014148..1014378_POSITIVE 184 62 26 178 131 NC_003454:FN0911|5end_Alpha-ribazole-5'-phosphate_phosphatase_1569318..1569548_NEGATIVE 179 79 48 37 4 NC_003454:FN1497|5end_Multidrug_resistance_protein_2_2138..2368_NEGATIVE 178 110 66 151 110 NC_003454:FN0480|5end_hypothetical_protein_1127454..1127684_POSITIVE 171 80 32 77 17 NC_003454:FN1629|5end_50S_ribosomal_protein_L6_134508..134738_NEGATIVE 170 85 43 207 170 NC_003454:FN0810|5end_Low-specificity_threonine_aldolase_1469038..1469268_POSITIVE 170 46 12 220 180 NC_003454:FN0685|5end_sodium/panthothenate_symporter_1342171..1342401_NEGATIVE 165 85 50 223 185 NC_003454:FN1348|5end_ABC_transporter_ATP-binding_protein_2001141..2001371_NEGATIVE 163 86 51 224 178 NC_003454:FN0806|5end_SpoIID_homolog_1466588..1466818_NEGATIVE 162 90 42 214 172 NC_003454:FN1678|5end_hypothetical_protein_174287..174517_POSITIVE 161 79 48 29 1 NC_003454:FN1616|5end_transcription_antitermination_protein_NusB_126437..126667_NEGATIVE 159 122 83 68 19 NC_003454:FN2068|5end_dGTP_triphosphohydrolase_578986..579216_NEGATIVE 157 95 52 231 195 NC_003454:FN0418|5end_pyrimidine_regulatory_protein_PyrR_1059118..1059348_POSITIVE 157 71 32 72 39 NC_003454:FN0395|5end_Transporter_1033106..1033336_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 76 49 42 15 NC_003454:FN0488|3end_NAD-specific_glutamate_dehydrogenase_1134456..1134606_POSITIVE 249 130 91 83 48 NC_003454:FN1652|3end_Oligopeptide-binding_protein_oppA_146041..146191_NEGATIVE 201 122 86 71 29 NC_003454:FN0225|3end_Gluconate_permease_851715..851865_NEGATIVE 201 72 32 141 100 NC_003454:FN0110|3end_seryl-tRNA_synthetase_744793..744943_NEGATIVE 196 124 84 79 40 NC_003454:FN1800|3end_Peptidyl-prolyl_cis-trans_isomerase_282534..282684_POSITIVE 189 130 83 86 25 NC_003454:FN2055|3end_hypothetical_protein_564002..564152_NEGATIVE 188 95 52 79 20 NC_003454:FN0382|3end_hypothetical_protein_1014224..1014374_POSITIVE 186 89 56 68 34 NC_003454:FN1793|3end_Phosphoenolpyruvate-protein_phosphotransferase_273534..273684_NEGATIVE 178 107 65 64 26 NC_003454:FN1023|3end_5-Nitroimidazole_antibiotic_resistance_protein_1677560..1677710_NEGATIVE 178 110 66 149 108 NC_003454:FN0479|3end_RNA_polymerase_sigma-E_factor_1127532..1127682_POSITIVE 170 130 84 91 40 NC_003454:FN0017|3end_hypothetical_protein_655957..656107_POSITIVE 169 125 88 79 44 NC_003454:FN0749|3end_hypothetical_protein_1407712..1407862_NEGATIVE 167 130 88 89 42 NC_003454:FN0637|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1295636..1295786_NEGATIVE 162 81 43 135 102 NC_003454:FN1423|3end_Flavoprotein_2088853..2089003_NEGATIVE 161 80 40 52 10 NC_003454:FN1630|3end_SSU_ribosomal_protein_S8P_134533..134683_NEGATIVE 160 130 106 73 47 NC_003454:FN1908|3end_Glycerophosphoryl_diester_phosphodiesterase_400596..400746_NEGATIVE 157 99 55 137 92 NC_003454:FN1460|3end_Hypothetical_cytosolic_protein_2141682..2141832_POSITIVE 157 68 40 140 118 NC_003454:FN0390|3end_hypothetical_protein_1028067..1028217_NEGATIVE 157 83 54 69 45 NC_003454:FN1973|3end_Translation_initiation_inhibitor_472230..472380_NEGATIVE 155 82 56 27 3 NC_003454:FN1380|3end_Citrate_lyase_beta_chain_2028878..2029028_POSITIVE