Origin IGS: tgtgttacttcttatgctagttgtggatattctagctttaattattttattttttataagaaataagatttcagataaaaaatttgccaatataaaacaaagaatatttacttggtttattataattatattattctatctaggaagtagagatagaatttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataaattctatctctacttcctagatagaataatataattataataaaccaagtaaatattctttgttttatattggcaaattttttatctgaaatcttatttcttataaaaaataaaataattaaagctagaatatccacaactagcataagaagtaacaca Mask Tandem Repeat Region ================================================ tgtgttacttcttatgctagttgtggatattctagctttaattattttattttttataagaaataagatttcagataaaaaatttgccaatataaaacaaagaatatttacttggtttattataattatattattctatctaggaagtagagatagaatttat Find is-nt database================================================ Query_seq: FN1307:FN1308|FN1307:FN1308:CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase:Phosphatidate cytidylyltransferase:->->:1964117..1964279 163 tgtgttacttcttatgctagttgtggatattctagctttaattattttattttttataagaaataagatttcagataaaaaatttgccaatataaaacaaagaatatttacttggtttattataattatattattctatctaggaagtagagatagaatttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1307:FN1308|FN1307:FN1308:CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase:Phosphatidate cytidylyltransferase:->->:1964117..1964279 163 tgtgttacttcttatgctagttgtggatattctagctttaattattttattttttataagaaataagatttcagataaaaaatttgccaatataaaacaaagaatatttacttggtttattataattatattattctatctaggaagtagagatagaatttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1307:FN1308|FN1307:FN1308:CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase:Phosphatidate cytidylyltransferase:->->:1964117..1964279 163 tgtgttacttcttatgctagttgtggatattctagctttaattattttattttttataagaaataagatttcagataaaaaatttgccaatataaaacaaagaatatttacttggtttattataattatattattctatctaggaagtagagatagaatttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtgttacttcttatgctagttgtggatattctagctttaattattttattttttataagaaataagatttcagataaaaaatttgccaatataaaacaaagaatatttacttggtttattataattatattattctatctaggaagtagagatagaatttat Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 2 End: 163 . M L L L M L V V D I L A L I I L F F I R N K I S D K K F A N I K Q R I F T W F I I I I L F Y L G S R D R I Y Protein_Len: 43 Strand: - Start: 1 End: 129 T N S R I S T T S I R A K I I K N K I L F L I E S L F N A L I F C L I N V Q N I I I M .................................. tgtgttacttcttatgctagttgtggatattctagctttaattattttattttttataagaaataagatttcagataaaaaatttgccaatataaaacaaagaatatttacttggtttattataattatattattctatctaggaagtagagatagaatttat 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================================================ tgtgttacttcttatgctagttgtggatattctagctttaattattttattttttataagaaataagatttcagataaaaaatttgccaatataaaacaaagaatatttacttggtttattataattatattattctatctaggaagtagagatagaatttat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1307:FN1308|FN1307:FN1308:CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase:Phosphatidate cytidylyltransferase:->->:1964117..1964279 163 tgtgttacttcttatgctagttgtggatattctagctttaattattttattttttataagaaataagatttcagataaaaaatttgccaatataaaacaaagaatatttacttggtttattataattatattattctatctaggaagtagagatagaatttat Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: NC_003454_FN1307_FN1308|CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase:Phosphatidate cytidylyltransferase|POSITIVE:POSITIVE|[1964117, 1964279]|163 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 tgtgttacttcttatgctagttgtggatattctagctttaattattttattttttataagaaataagatttcagataaaaaatttgccaatataaaacaaagaatatttacttggtttattataattatattattctatctaggaagtagagatagaatttat tgtgttacttcttatgctagttgtggatattctagctttaattattttattttttataagaaataagatttcagataaaaaatttgccaatataaaacaaagaatatttacttggtttattataattatattattctatctaggaagtagagatagaatttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUGUUACUUCUUAUGCUAGUUGUGGAUAUUCUAGCUUUAAUUAUUUUAUUUUUUAUAAGAAAUAAGAUUUCAGAUAAAAAAUUUGCCAAUAUAAAACAAAGAAUAUUUACUUGGUUUAUUAUAAUUAUAUUAUUCUAUCUAGGAAGUAGAGAUAGAAUUUAU ....((((((((((........(((((((((((...(((((((.....(((((((((..(((((...)))))..))))))))).....))).))))....))))))))))).(((..((.(((....))).))..)))..))))))))))............. (-26.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAUUCUAUCUCUACUUCCUAGAUAGAAUAAUAUAAUUAUAAUAAACCAAGUAAAUAUUCUUUGUUUUAUAUUGGCAAAUUUUUUAUCUGAAAUCUUAUUUCUUAUAAAAAAUAAAAUAAUUAAAGCUAGAAUAUCCACAACUAGCAUAAGAAGUAACACA ....(((((((((.........)))))))))....(((((((......((((..(((((.....)))))....))))...(((((((((..(((((...)))))..)))))))))...)))))))..(((((...........)))))............... (-26.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 57 15 167 129 NC_003454:FN0630|5end_PTS_system,_IIC_component_1289857..1290087_NEGATIVE 225 144 101 74 25 NC_003454:FN0582|5end_Lipoprotein_releasing_system_ATP-binding_protein_lolD_1238246..1238476_POSITIVE 214 152 120 183 149 NC_003454:FN1780|5end_hypothetical_protein_261664..261894_NEGATIVE 208 146 102 121 74 NC_003454:FN1460|5end_Hypothetical_cytosolic_protein_2141429..2141659_POSITIVE 204 37 15 47 23 NC_003454:FN1867|5end_Zn-dependent_alcohol_dehydrogenase_and_related_dehydrogenase_359597..359827_NEGATIVE 200 50 1 96 44 NC_003454:FN1116|5end_Peptidase_E_1759521..1759751_POSITIVE 200 41 8 225 195 NC_003454:FN0002|5end_Ribonuclease_P_protein_component_642548..642778_POSITIVE 195 39 1 163 127 NC_003454:FN0103|5end_Ribonucleoside-diphosphate_reductase_beta_chain_738481..738711_POSITIVE 194 58 16 184 143 NC_003454:FN1376|5end_oxaloacetate_decarboxylase_2023879..2024109_POSITIVE 193 79 31 132 84 NC_003454:FN0649|5end_Exoenzyme_regulatory_protein_aepA_precursor_1307717..1307947_NEGATIVE 191 46 5 77 36 NC_003454:FN0807|5end_3-deoxy-manno-octulosonate_cytidylyltransferase_1467894..1468124_NEGATIVE 190 69 21 60 6 NC_003454:FN1107|5end_Acetyltransferase_1751961..1752191_POSITIVE 190 45 4 132 95 NC_003454:FN0613|5end_hypothetical_protein_1270890..1271120_POSITIVE 188 68 28 147 111 NC_003454:FN0392|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1029624..1029854_POSITIVE 187 42 4 53 9 NC_003454:FN1627|5end_SSU_ribosomal_protein_S5P_133556..133786_NEGATIVE 186 159 114 229 181 NC_003454:FN0315|5end_Transcriptional_regulator,_AraC_family_951934..952164_POSITIVE 186 57 14 40 1 NC_003454:FN0249|5end_hypothetical_protein_872823..873053_POSITIVE 186 57 14 40 1 NC_003454:FN2063|5end_hypothetical_protein_575019..575249_NEGATIVE 186 57 14 40 1 NC_003454:FN2052|5end_hypothetical_protein_560943..561173_NEGATIVE 185 119 78 212 176 NC_003454:FN0742|5end_hypothetical_protein_1400121..1400351_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 225 144 101 105 56 NC_003454:FN0581|3end_Lipoprotein_releasing_system_transmembrane_protein_lolE_1238357..1238507_POSITIVE 220 43 3 145 108 NC_003454:FN0631|3end_PTS_system,_IIB_component_1289868..1290018_NEGATIVE 214 152 120 115 81 NC_003454:FN1781|3end_LytB_protein_261732..261882_NEGATIVE 205 54 16 92 55 NC_003454:FN0047|3end_Exodeoxyribonuclease_III_685268..685418_POSITIVE 204 37 15 29 5 NC_003454:FN1868|3end_Hypothetical_cytosolic_protein_359615..359765_NEGATIVE 200 50 1 94 42 NC_003454:FN1115|3end_Hypothetical_membrane-spanning_protein_1759599..1759749_POSITIVE 195 53 14 97 46 NC_003454:FN1591|3end_RNFB-related_protein_101978..102128_NEGATIVE 194 58 16 85 44 NC_003454:FN1375|3end_Citrate-sodium_symport_2023860..2024010_POSITIVE 193 79 31 132 84 NC_003454:FN0650|3end_NA+/H+_antiporter_NHAC_1307717..1307867_NEGATIVE 188 153 113 118 83 NC_003454:FN0255|3end_Hypothetical_cytosolic_protein_882117..882267_POSITIVE 186 26 1 111 87 NC_003454:FN0536|3end_DNA_polymerase_III,_beta_chain_1190006..1190156_NEGATIVE 186 159 114 146 98 NC_003454:FN0314|3end_Caffeoyl-CoA_O-methyltransferase_951931..952081_POSITIVE 180 145 106 55 18 NC_003454:FN1506|3end_5-amino-6-(5-phosphoribosylamino)uracil_reductase_12060..12210_POSITIVE 177 39 1 108 68 NC_003454:FN0355|3end_S-adenosylmethionine_synthetase_986076..986226_NEGATIVE 173 53 16 61 23 NC_003454:FN1978|3end_Cell_division_protein_ftsH_481703..481853_POSITIVE 172 58 12 106 59 NC_003454:FN1424|3end_ACYL-COA_dehydrogenase,_short-chain_specific_2090095..2090245_NEGATIVE 172 45 3 135 81 NC_003454:FN1218|3end_hypothetical_protein_1877812..1877962_NEGATIVE 172 88 42 129 67 NC_003454:FN0781|3end_Integral_membrane_protein_1437511..1437661_NEGATIVE 170 48 8 101 66 NC_003454:FN1129|3end_Chromosome_partition_protein_smc_1777865..1778015_POSITIVE 169 50 2 99 56 NC_003454:FN0857|3end_Glycogen_phosphorylase_1516553..1516703_NEGATIVE