Origin IGS: accagtattcatatcttgatctaggacttctgtactattagaataagaaagaaatgacaagcataaaaaaataactgctagtaagtatttcttcatatatcctcctatctattttatattttactcatttataaaatactgatgtattataccatagaatattaaaatttacaaatctatgtataccaatgtaaaaatg .........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 catttttacattggtatacatagatttgtaaattttaatattctatggtataatacatcagtattttataaatgagtaaaatataaaatagataggaggatatatgaagaaatacttactagcagttatttttttatgcttgtcatttctttcttattctaatagtacagaagtcctagatcaagatatgaatactggt Mask Tandem Repeat Region ================================================ accagtattcatatcttgatctaggacttctgtactattagaataagaaagaaatgacaagcataaaaaaataactgctagtaagtatttcttcatatatcctcctatctattttatattttactcatttataaaatactgatgtattataccatagaatattaaaatttacaaatctatgtataccaatgtaaaaatg Find is-nt database================================================ Query_seq: FN1894:FN1895|FN1894:FN1895:BAX protein:hypothetical protein:<-<-:382433..382631 199 accagtattcatatcttgatctaggacttctgtactattagaataagaaagaaatgacaagcataaaaaaataactgctagtaagtatttcttcatatatcctcctatctattttatattttactcatttataaaatactgatgtattataccatagaatattaaaatttacaaatctatgtataccaatgtaaaaatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1894:FN1895|FN1894:FN1895:BAX protein:hypothetical protein:<-<-:382433..382631 199 accagtattcatatcttgatctaggacttctgtactattagaataagaaagaaatgacaagcataaaaaaataactgctagtaagtatttcttcatatatcctcctatctattttatattttactcatttataaaatactgatgtattataccatagaatattaaaatttacaaatctatgtataccaatgtaaaaatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1894:FN1895|FN1894:FN1895:BAX protein:hypothetical protein:<-<-:382433..382631 199 accagtattcatatcttgatctaggacttctgtactattagaataagaaagaaatgacaagcataaaaaaataactgctagtaagtatttcttcatatatcctcctatctattttatattttactcatttataaaatactgatgtattataccatagaatattaaaatttacaaatctatgtataccaatgtaaaaatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accagtattcatatcttgatctaggacttctgtactattagaataagaaagaaatgacaagcataaaaaaataactgctagtaagtatttcttcatatatcctcctatctattttatattttactcatttataaaatactgatgtattataccatagaatattaaaatttacaaatctatgtataccaatgtaaaaatg Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: - Start: 1 End: 108 G T N M D Q D L V E T S N S Y S L F S L C L F I V A L L Y K K M Y G G M ........................................................................................... accagtattcatatcttgatctaggacttctgtactattagaataagaaagaaatgacaagcataaaaaaataactgctagtaagtatttcttcatatatcctcctatctattttatattttactcatttataaaatactgatgtattataccatagaatattaaaatttacaaatctatgtataccaatgtaaaaatg 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: 90 Start: 146 End: 175 .................................................................................................................................................TTTGTAAATTTTAATATTCTATGGTATAAT........................ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 91 End: 120 ..........................................................................................CTTCATATATCCTCCTATCTATTTTATATT............................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 15 End: 44 ..............CTTGATCTAGGACTTCTGTACTATTAGAAT........................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ accagtattcatatcttgatctaggacttctgtactattagaataagaaagaaatgacaagcataaaaaaataactgctagtaagtatttcttcatatatcctcctatctattttatattttactcatttataaaatactgatgtattataccatagaatattaaaatttacaaatctatgtataccaatgtaaaaatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1894:FN1895|FN1894:FN1895:BAX protein:hypothetical protein:<-<-:382433..382631 199 accagtattcatatcttgatctaggacttctgtactattagaataagaaagaaatgacaagcataaaaaaataactgctagtaagtatttcttcatatatcctcctatctattttatattttactcatttataaaatactgatgtattataccatagaatattaaaatttacaaatctatgtataccaatgtaaaaatg Intra-Species Hit: Count: 1 Min: 1 Max: 199 Len: 199 Subject: NC_003454_FN1894_FN1895|BAX protein:hypothetical protein|NEGATIVE:NEGATIVE|[382433,382631]|199 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 199 Query Start:1 Query End:199 Subject Strand: POSITIVE Subject Start: 1 Subject End: 199 accagtattcatatcttgatctaggacttctgtactattagaataagaaagaaatgacaagcatnnnnnnntaactgctagtaagtatttcttcatatatcctcctatctattttatattttactcatttataaaatactgatgtattataccatagaatattaaaatttacaaatctatgtataccaatgtaaaaatg accagtattcatatcttgatctaggacttctgtactattagaataagaaagaaatgacaagcataaaaaaataactgctagtaagtatttcttcatatatcctcctatctattttatattttactcatttataaaatactgatgtattataccatagaatattaaaatttacaaatctatgtataccaatgtaaaaatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCAGUAUUCAUAUCUUGAUCUAGGACUUCUGUACUAUUAGAAUAAGAAAGAAAUGACAAGCAUAAAAAAAUAACUGCUAGUAAGUAUUUCUUCAUAUAUCCUCCUAUCUAUUUUAUAUUUUACUCAUUUAUAAAAUACUGAUGUAUUAUACCAUAGAAUAUUAAAAUUUACAAAUCUAUGUAUACCAAUGUAAAAAUG ..........(((((......(((((.(((((......)))))...(((.((((((((.((((............)))).))...)))))))))........)))))..(((((((((...........)))))))))..)))))..(((((.(((((.................)))))))))).............. (-25.83) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUUUUACAUUGGUAUACAUAGAUUUGUAAAUUUUAAUAUUCUAUGGUAUAAUACAUCAGUAUUUUAUAAAUGAGUAAAAUAUAAAAUAGAUAGGAGGAUAUAUGAAGAAAUACUUACUAGCAGUUAUUUUUUUAUGCUUGUCAUUUCUUUCUUAUUCUAAUAGUACAGAAGUCCUAGAUCAAGAUAUGAAUACUGGU .........((..((((.((((..((((...((((.....((((.((.(((.........(((((((((......))))))))).....(((.(((((((((((((((((((((((.......)).))))))))))))..)))).))))).))).......))).)).)))).....)))))))).)))).))))..)) (-32.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 778 50 1 141 92 NC_003454:FN1894|5end_BAX_protein_382342..382572_NEGATIVE 293 130 83 128 78 NC_003454:FN0466|5end_Lysyl-tRNA_synthetase_1111301..1111531_POSITIVE 271 106 62 101 58 NC_003454:FN0968|5end_hypothetical_protein_1621809..1622039_NEGATIVE 266 113 75 109 70 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 257 108 76 103 68 NC_003454:FN0426|5end_Orotidine_5'-phosphate_decarboxylase_1068720..1068950_POSITIVE 246 116 75 114 67 NC_003454:FN0941|5end_Gamma-glutamyltranspeptidase_1595266..1595496_NEGATIVE 246 110 74 136 99 NC_003454:FN0335|5end_Outer_membrane_porin_F_969675..969905_NEGATIVE 240 159 114 126 81 NC_003454:FN0607|5end_metal_dependent_phosphohydrolase_1261564..1261794_POSITIVE 239 107 67 143 102 NC_003454:FN2121|5end_Hypothetical_exported_24-amino_acid_repeat_protein_629728..629958_NEGATIVE 234 124 81 121 65 NC_003454:FN1448|5end_Hypothetical_cytosolic_protein_2118428..2118658_NEGATIVE 233 111 76 85 47 NC_003454:FN1321|5end_Acetoacetate_metabolism_regulatory_protein_atoC_1977390..1977620_NEGATIVE 233 138 91 136 86 NC_003454:FN1029|5end_Zinc_protease_1683611..1683841_NEGATIVE 232 117 71 114 72 NC_003454:FN1724|5end_Potassium_uptake_protein_KtrA_223310..223540_NEGATIVE 230 116 87 115 78 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 230 120 74 128 80 NC_003454:FN1580|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_90919..91149_NEGATIVE 229 110 65 170 117 NC_003454:FN0767|5end_Hemin-binding_periplasmic_protein_hmuT_precursor_1422630..1422860_POSITIVE 222 105 61 103 66 NC_003454:FN0724|5end_flavodoxin_1384167..1384397_NEGATIVE 222 106 76 107 65 NC_003454:FN0061|5end_Thermostable_carboxypeptidase_1_697019..697249_POSITIVE 222 110 79 126 91 NC_003454:FN2089|5end_hypothetical_protein_601549..601779_NEGATIVE 222 116 74 112 63 NC_003454:FN1943|5end_Tryptophanase_444851..445081_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 130 83 105 55 NC_003454:FN0465|3end_hypothetical_protein_1111358..1111508_POSITIVE 271 106 62 104 61 NC_003454:FN0969|3end_hypothetical_protein_1621806..1621956_NEGATIVE 257 108 76 78 43 NC_003454:FN0425|3end_Hypothetical_cytosolic_protein_1068775..1068925_POSITIVE 246 110 74 63 26 NC_003454:FN0336|3end_hypothetical_protein_969748..969898_NEGATIVE 239 107 67 73 32 NC_003454:FN2122|3end_Phenylalanyl-tRNA_synthetase_beta_chain_629798..629948_NEGATIVE 233 138 91 117 67 NC_003454:FN1030|3end_Hypothetical_membrane-spanning_protein_1683630..1683780_NEGATIVE 232 117 71 99 57 NC_003454:FN1725|3end_Potassium_uptake_protein_KtrB_223325..223475_NEGATIVE 222 105 61 89 52 NC_003454:FN0725|3end_Molybdopterin_biosynthesis_MoeB_protein_1384181..1384331_NEGATIVE 222 110 79 139 104 NC_003454:FN2090|3end_hypothetical_protein_601536..601686_NEGATIVE 219 125 88 95 50 NC_003454:FN0856|3end_glycogen_branching_enzyme_1514689..1514839_NEGATIVE 216 115 71 97 43 NC_003454:FN0874|3end_Phosphohydrolase_(MUTT/NUDIX_family_protein)_1534372..1534522_NEGATIVE 213 104 73 78 47 NC_003454:FN1862|3end_L-beta-lysine_5,6-aminomutase_beta_subunit_352331..352481_NEGATIVE 211 120 72 104 50 NC_003454:FN0710|3end_hypothetical_protein_1369632..1369782_POSITIVE 209 106 61 64 19 NC_003454:FN1112|3end_Dipeptide_transport_system_permease_protein_dppC_1756165..1756315_NEGATIVE 207 121 84 71 30 NC_003454:FN1172|3end_Phosphate_acetyltransferase_1833612..1833762_NEGATIVE 207 118 74 150 104 NC_003454:FN1581|3end_DNA_mismatch_repair_protein_mutS_90895..91045_NEGATIVE 206 125 82 102 51 NC_003454:FN0628|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing]_1287199..1287349_NEGATIVE 206 130 89 103 60 NC_003454:FN0227|3end_hypothetical_protein_854114..854264_NEGATIVE 206 128 85 111 71 NC_003454:FN1949|3end_Xaa-Pro_dipeptidase_453534..453684_NEGATIVE 206 120 74 78 38 NC_003454:FN1620|3end_30S_ribosomal_protein_S2_128719..128869_POSITIVE