Origin IGS: gcaatatttgttgacaaacttaaatttttatgataacataaataggattaacgcataataaaggtgttcagcaaccttatattagcgaattacatatggaggtgttaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attaacacctccatatgtaattcgctaatataaggttgctgaacacctttattatgcgttaatcctatttatgttatcataaaaatttaagtttgtcaacaaatattgc Mask Tandem Repeat Region ================================================ gcaatatttgttgacaaacttaaatttttatgataacataaataggattaacgcataataaaggtgttcagcaaccttatattagcgaattacatatggaggtgttaat Find is-nt database================================================ Query_seq: FN1116:FN1117|FN1116:FN1117:Peptidase E:LSU ribosomal protein L21P:->->:1760273..1760381 109 gcaatatttgttgacaaacttaaatttttatgataacataaataggattaacgcataataaaggtgttcagcaaccttatattagcgaattacatatggaggtgttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1116:FN1117|FN1116:FN1117:Peptidase E:LSU ribosomal protein L21P:->->:1760273..1760381 109 gcaatatttgttgacaaacttaaatttttatgataacataaataggattaacgcataataaaggtgttcagcaaccttatattagcgaattacatatggaggtgttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1116:FN1117|FN1116:FN1117:Peptidase E:LSU ribosomal protein L21P:->->:1760273..1760381 109 gcaatatttgttgacaaacttaaatttttatgataacataaataggattaacgcataataaaggtgttcagcaaccttatattagcgaattacatatggaggtgttaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaatatttgttgacaaacttaaatttttatgataacataaataggattaacgcataataaaggtgttcagcaaccttatattagcgaattacatatggaggtgttaat Predict ORF larger than 30AA ================================================ gcaatatttgttgacaaacttaaatttttatgataacataaataggattaacgcataataaaggtgttcagcaaccttatattagcgaattacatatggaggtgttaat 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: 10 End: 39 .........GTTGACAAACTTAAATTTTTATGATAACAT...................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcaatatttgttgacaaacttaaatttttatgataacataaataggattaacgcataataaaggtgttcagcaaccttatattagcgaattacatatggaggtgttaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1116:FN1117|FN1116:FN1117:Peptidase E:LSU ribosomal protein L21P:->->:1760273..1760381 109 gcaatatttgttgacaaacttaaatttttatgataacataaataggattaacgcataataaaggtgttcagcaaccttatattagcgaattacatatggaggtgttaat Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_003454_FN1116_FN1117|Peptidase E:LSU ribosomal protein L21P|POSITIVE:POSITIVE|[1760273,1760381]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 gcaatatttgttgacaaacttaaatttttatgataacataaataggattaacgcataataaaggtgttcagcaaccttatattagcgaattacatatggaggtgttaat gcaatatttgttgacaaacttaaatttttatgataacataaataggattaacgcataataaaggtgttcagcaaccttatattagcgaattacatatggaggtgttaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAUAUUUGUUGACAAACUUAAAUUUUUAUGAUAACAUAAAUAGGAUUAACGCAUAAUAAAGGUGUUCAGCAACCUUAUAUUAGCGAAUUACAUAUGGAGGUGUUAAU .........(((((((..(((.....((((((....)))))).........(((.((((((((((........))))).))))))))...........))).))))))) (-19.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAACACCUCCAUAUGUAAUUCGCUAAUAUAAGGUUGCUGAACACCUUUAUUAUGCGUUAAUCCUAUUUAUGUUAUCAUAAAAAUUUAAGUUUGUCAACAAAUAUUGC ......................((((((((.(((((........)))))))))).))).........((((((....)))))).......(((((....)))))..... (-14.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 208 98 59 36 2 NC_003454:FN0519|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1171669..1171899_NEGATIVE 207 87 51 80 44 NC_003454:FN2101|5end_Transporter_610246..610476_POSITIVE 196 90 62 32 2 NC_003454:FN1592|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_D_103746..103976_NEGATIVE 190 86 43 88 37 NC_003454:FN0208|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase_beta-subunit_834968..835198_POSITIVE 189 49 1 228 185 NC_003454:FN0013|5end_Transporter_652218..652448_POSITIVE 188 98 51 183 139 NC_003454:FN1085|5end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_enzyme_1728934..1729164_POSITIVE 180 74 36 217 177 NC_003454:FN1175|5end_hypothetical_protein_1836748..1836978_NEGATIVE 178 44 1 82 42 NC_003454:FN1724|5end_Potassium_uptake_protein_KtrA_223310..223540_NEGATIVE 176 76 31 55 17 NC_003454:FN1169|5end_L-lactate_dehydrogenase_1828536..1828766_NEGATIVE 174 81 53 159 136 NC_003454:FN0852|5end_Hydrolase_1510224..1510454_POSITIVE 174 84 54 74 40 NC_003454:FN0487|5end_D-lactate_dehydrogenase_1132772..1133002_NEGATIVE 170 86 63 213 184 NC_003454:FN1073|5end_hypothetical_protein_1720403..1720633_POSITIVE 169 46 6 184 145 NC_003454:FN0327|5end_Bacterial_Protein_Translation_Initiation_Factor_3_(IF-3)_962149..962379_NEGATIVE 162 88 53 81 54 NC_003454:FN1923|5end_Adenine-specific_methyltransferase_421097..421327_NEGATIVE 161 86 41 100 54 NC_003454:FN1082|5end_hypothetical_protein_1727691..1727921_POSITIVE 160 49 17 80 50 NC_003454:FN0932|5end_hypothetical_protein_1584678..1584908_POSITIVE 159 93 57 162 132 NC_003454:FN0789|5end_Transporter_1445278..1445508_NEGATIVE 159 95 53 210 166 NC_003454:FN1595|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_B_105827..106057_NEGATIVE 157 95 61 91 57 NC_003454:FN1214|5end_Fe-S_oxidoreductase_1875473..1875703_NEGATIVE 156 47 7 193 158 NC_003454:FN0547|5end_recombinase_A_1199643..1199873_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 207 87 51 70 34 NC_003454:FN2100|3end_hypothetical_protein_610316..610466_POSITIVE 201 87 52 39 4 NC_003454:FN1116|3end_Peptidase_E_1760212..1760362_POSITIVE 196 90 62 35 5 NC_003454:FN1593|3end_NADH-ubiquinone_oxidoreductase_103743..103893_NEGATIVE 190 86 43 66 15 NC_003454:FN0207|3end_(R)-2-hydroxyglutaryl-CoA_dehydratase_alpha-subunit_835026..835176_POSITIVE 178 44 1 67 27 NC_003454:FN1725|3end_Potassium_uptake_protein_KtrB_223325..223475_NEGATIVE 174 81 53 123 100 NC_003454:FN0851|3end_Biotin_synthesis_protein_bioC_1510268..1510418_POSITIVE 168 70 25 134 79 NC_003454:FN1423|3end_Flavoprotein_2088853..2089003_NEGATIVE 159 93 57 146 116 NC_003454:FN0790|3end_Xylose_repressor_1445294..1445444_NEGATIVE 157 95 61 104 70 NC_003454:FN1215|3end_Hypothetical_cytosolic_protein_1875460..1875610_NEGATIVE 157 76 47 151 119 NC_003454:FN1084|3end_hypothetical_protein_1728998..1729148_POSITIVE 156 89 44 71 31 NC_003454:FN1943|3end_Tryptophanase_446568..446718_POSITIVE 154 80 44 67 28 NC_003454:FN1899|3end_Hypothetical_lipoprotein_386714..386864_NEGATIVE 151 88 45 41 2 NC_003454:FN1333|3end_hypothetical_protein_1987164..1987314_NEGATIVE 151 94 61 53 13 NC_003454:FN0516|3end_Acriflavin_resistance_protein_E_1167003..1167153_NEGATIVE 150 78 60 80 58 NC_003454:FN0624|3end_NA+/H+_antiporter_NHAC_1282995..1283145_NEGATIVE 149 89 61 72 39 NC_003454:FN1154|3end_Ribonuclease_BN_1809502..1809652_POSITIVE 149 94 65 124 92 NC_003454:FN0520|3end_hypothetical_protein_1171678..1171828_NEGATIVE 149 97 66 68 31 NC_003454:FN0183|3end_Glycerol-3-phosphate_dehydrogenase_807078..807228_NEGATIVE 148 85 41 60 16 NC_003454:FN1258|3end_C4-dicarboxylate-binding_protein_1913792..1913942_NEGATIVE 148 79 38 85 53 NC_003454:FN0590|3end_N-acyl-L-amino_acid_amidohydrolase_1242856..1243006_NEGATIVE