Origin IGS: aaaaattataaatagctattacattgtggtataatgtaatggctattttaatttataggagtaaataaaatgtatatgaaattcaaaaaaataattttagttatgtcaattttagggatattatttactaatagttattccaatgaagttagagaagttcaattaatagatgatttttcagcagaacttttaggggagacaaaaactcaagatcctgaagttccaaaaccagca .........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 tgctggttttggaacttcaggatcttgagtttttgtctcccctaaaagttctgctgaaaaatcatctattaattgaacttctctaacttcattggaataactattagtaaataatatccctaaaattgacataactaaaattatttttttgaatttcatatacattttatttactcctataaattaaaatagccattacattataccacaatgtaatagctatttataattttt Mask Tandem Repeat Region ================================================ aaaaattataaatagctattacattgtggtataatgtaatggctattttaatttataggagtaaataaaatgtatatgaaattcaaaaaaataattttagttatgtcaattttagggatattatttactaatagttattccaatgaagttagagaagttcaattaatagatgatttttcagcagaacttttaggggagacaaaaactcaagatcctgaagttccaaaaccagca Find is-nt database================================================ Query_seq: FN0059:FN0060|FN0059:FN0060:NifU protein:D-alanyl-D-alanine carboxypeptidase:->->:695680..695913 234 aaaaattataaatagctattacattgtggtataatgtaatggctattttaatttataggagtaaataaaatgtatatgaaattcaaaaaaataattttagttatgtcaattttagggatattatttactaatagttattccaatgaagttagagaagttcaattaatagatgatttttcagcagaacttttaggggagacaaaaactcaagatcctgaagttccaaaaccagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0059:FN0060|FN0059:FN0060:NifU protein:D-alanyl-D-alanine carboxypeptidase:->->:695680..695913 234 aaaaattataaatagctattacattgtggtataatgtaatggctattttaatttataggagtaaataaaatgtatatgaaattcaaaaaaataattttagttatgtcaattttagggatattatttactaatagttattccaatgaagttagagaagttcaattaatagatgatttttcagcagaacttttaggggagacaaaaactcaagatcctgaagttccaaaaccagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0059:FN0060|FN0059:FN0060:NifU protein:D-alanyl-D-alanine carboxypeptidase:->->:695680..695913 234 aaaaattataaatagctattacattgtggtataatgtaatggctattttaatttataggagtaaataaaatgtatatgaaattcaaaaaaataattttagttatgtcaattttagggatattatttactaatagttattccaatgaagttagagaagttcaattaatagatgatttttcagcagaacttttaggggagacaaaaactcaagatcctgaagttccaaaaccagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaattataaatagctattacattgtggtataatgtaatggctattttaatttataggagtaaataaaatgtatatgaaattcaaaaaaataattttagttatgtcaattttagggatattatttactaatagttattccaatgaagttagagaagttcaattaatagatgatttttcagcagaacttttaggggagacaaaaactcaagatcctgaagttccaaaaccagca Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 55 End: 234 ...................................................... M G V N K M Y M K F K K I I L V M S I L G I L F T N S Y S N E V R E V Q L I D D F S A E L L G E T K T Q D P E V P K P A aaaaattataaatagctattacattgtggtataatgtaatggctattttaatttataggagtaaataaaatgtatatgaaattcaaaaaaataattttagttatgtcaattttagggatattatttactaatagttattccaatgaagttagagaagttcaattaatagatgatttttcagcagaacttttaggggagacaaaaactcaagatcctgaagttccaaaaccagca 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: 84 Start: 81 End: 110 ................................................................................ATTGACATAACTAAAATTATTTTTTTGAAT............................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 6 End: 35 .....TTATAAATAGCTATTACATTGTGGTATAAT....................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaattataaatagctattacattgtggtataatgtaatggctattttaatttataggagtaaataaaatgtatatgaaattcaaaaaaataattttagttatgtcaattttagggatattatttactaatagttattccaatgaagttagagaagttcaattaatagatgatttttcagcagaacttttaggggagacaaaaactcaagatcctgaagttccaaaaccagca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0059:FN0060|FN0059:FN0060:NifU protein:D-alanyl-D-alanine carboxypeptidase:->->:695680..695913 234 aaaaattataaatagctattacattgtggtataatgtaatggctattttaatttataggagtaaataaaatgtatatgaaattcaaaaaaataattttagttatgtcaattttagggatattatttactaatagttattccaatgaagttagagaagttcaattaatagatgatttttcagcagaacttttaggggagacaaaaactcaagatcctgaagttccaaaaccagca Intra-Species Hit: Count: 1 Min: 1 Max: 234 Len: 234 Subject: NC_003454_FN0059_FN0060|NifU protein:D-alanyl-D-alanine carboxypeptidase|POSITIVE:POSITIVE|[695680,695913]|234 HSP 1 e-value: 1.0E-117 bit: 422.0 Len: 234 Query Start:1 Query End:234 Subject Strand: POSITIVE Subject Start: 1 Subject End: 234 aaaaattataaatagctattacattgtggtataatgtaatggctattttaatttataggagtaaataaaatgtatatgaaattcnnnnnnntaattttagttatgtcaattttagggatattatttactaatagttattccaatgaagttagagaagttcaattaatagatgatttttcagcagaacttttaggggagacaaaaactcaagatcctgaagttccaaaaccagca aaaaattataaatagctattacattgtggtataatgtaatggctattttaatttataggagtaaataaaatgtatatgaaattcaaaaaaataattttagttatgtcaattttagggatattatttactaatagttattccaatgaagttagagaagttcaattaatagatgatttttcagcagaacttttaggggagacaaaaactcaagatcctgaagttccaaaaccagca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUUAUAAAUAGCUAUUACAUUGUGGUAUAAUGUAAUGGCUAUUUUAAUUUAUAGGAGUAAAUAAAAUGUAUAUGAAAUUCAAAAAAAUAAUUUUAGUUAUGUCAAUUUUAGGGAUAUUAUUUACUAAUAGUUAUUCCAAUGAAGUUAGAGAAGUUCAAUUAAUAGAUGAUUUUUCAGCAGAACUUUUAGGGGAGACAAAAACUCAAGAUCCUGAAGUUCCAAAACCAGCA ..((((((.((((((((((((((((((...))))))))))))))))))))))))...(((((((.......(((.((((.((((..(((((((((....))))).....))))..)))).)))).)))......)))))))......(((.((((((((..(((....)))))))))))))).(((((((.(((((((.......)))....)))))))))))........... (-50.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUGGUUUUGGAACUUCAGGAUCUUGAGUUUUUGUCUCCCCUAAAAGUUCUGCUGAAAAAUCAUCUAUUAAUUGAACUUCUCUAACUUCAUUGGAAUAACUAUUAGUAAAUAAUAUCCCUAAAAUUGACAUAACUAAAAUUAUUUUUUUGAAUUUCAUAUACAUUUUAUUUACUCCUAUAAAUUAAAAUAGCCAUUACAUUAUACCACAAUGUAAUAGCUAUUUAUAAUUUUU .....((..(((((.(((((((.....((((..((((........((((((.......................)))))).............(((.....(((((.....))))))))........)))).))))..........))))))))))))...)).................(((((((((((((.((((((((.......)))))))).))))))).)))))).. (-32.46) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 50 12 215 176 NC_003454:FN1926|5end_Nitrogen_regulatory_IIA_protein_425287..425517_NEGATIVE 225 138 93 219 173 NC_003454:FN0842|5end_hypothetical_protein_1503055..1503285_NEGATIVE 222 54 14 165 129 NC_003454:FN0187|5end_Thiol:disulfide_interchange_protein_tlpA_811590..811820_POSITIVE 217 188 148 70 18 NC_003454:FN1809|5end_Iron/zinc/copper-binding_protein_291031..291261_NEGATIVE 214 220 171 87 38 NC_003454:FN2033|5end_Guanylate_kinase_537904..538134_NEGATIVE 204 53 11 59 11 NC_003454:FN0474|5end_Acriflavin_resistance_protein_B_1118939..1119169_POSITIVE 204 212 176 98 61 NC_003454:FN0300|5end_Iron(III)_dicitrate-binding_protein_934679..934909_POSITIVE 198 197 153 52 9 NC_003454:FN1316|5end_NGG1-interacting_factor_3_1970276..1970506_NEGATIVE 197 217 171 227 180 NC_003454:FN1657|5end_SSU_ribosomal_protein_S6P_153122..153352_NEGATIVE 188 217 174 196 150 NC_003454:FN1333|5end_hypothetical_protein_1987580..1987810_NEGATIVE 187 196 158 46 5 NC_003454:FN1130|5end_Tetraacyldisaccharide_4'-kinase_1777840..1778070_POSITIVE 187 217 171 84 26 NC_003454:FN0798|5end_Fructose-1,6-bisphosphatase_1455835..1456065_POSITIVE 182 198 153 193 150 NC_003454:FN0196|5end_Transcriptional_regulator,_FUR_family_822317..822547_POSITIVE 181 154 118 197 161 NC_003454:FN0885|5end_Hemin-binding_periplasmic_protein_hmuT_precursor_1545615..1545845_NEGATIVE 181 219 179 94 58 NC_003454:FN0094|5end_hypothetical_protein_729740..729970_NEGATIVE 179 195 153 126 71 NC_003454:FN0728|5end_hypothetical_protein_1386120..1386350_NEGATIVE 178 209 164 108 63 NC_003454:FN0696|5end_hypothetical_protein_1353694..1353924_POSITIVE 176 165 128 63 33 NC_003454:FN1125|5end_LemA_protein_1769811..1770041_NEGATIVE 176 150 101 202 156 NC_003454:FN0229|5end_hypothetical_protein_856570..856800_NEGATIVE 175 59 16 94 42 NC_003454:FN0984|5end_Tetracenomycin_polyketide_synthesis_O-methyltransferase_tcmP_1637295..1637525_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 48 3 81 37 NC_003454:FN0059|3end_NifU_protein_695619..695769_POSITIVE 304 50 12 87 48 NC_003454:FN1927|3end_DEGV_protein_425415..425565_NEGATIVE 225 138 93 88 42 NC_003454:FN0843|3end_hypothetical_protein_1503186..1503336_NEGATIVE 222 54 14 81 45 NC_003454:FN0186|3end_Cytochrome_c-type_biogenesis_protein_ccdA_811586..811736_POSITIVE 219 49 7 50 11 NC_003454:FN1391|3end_Acetyltransferase_2049133..2049283_POSITIVE 214 220 171 74 25 NC_003454:FN2034|3end_Protein_yicC_537917..538067_NEGATIVE 198 197 153 55 12 NC_003454:FN1317|3end_RNA_polymerase_sigma_factor_1970273..1970423_NEGATIVE 194 199 156 79 35 NC_003454:FN0587|3end_Hypothetical_membrane-spanning_protein_1241963..1242113_NEGATIVE 192 179 131 145 87 NC_003454:FN0819|3end_Tetratricopeptide_repeat_family_protein_1479325..1479475_POSITIVE 185 223 183 58 18 NC_003454:FN0072|3end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_712619..712769_POSITIVE 180 207 166 57 10 NC_003454:FN1810|3end_Manganese_transport_system_membrane_protein_mntB_291060..291210_NEGATIVE 178 43 7 83 45 NC_003454:FN1266|3end_UTP--glucose-1-phosphate_uridylyltransferase_1922158..1922308_NEGATIVE 176 165 128 54 24 NC_003454:FN1126|3end_Acetyltransferase_1769820..1769970_NEGATIVE 175 48 10 75 40 NC_003454:FN1392|3end_SSU_ribosomal_protein_S16P_2049196..2049346_NEGATIVE 175 59 16 74 22 NC_003454:FN0985|3end_Phosphoribosylglycinamide_formyltransferase_1637315..1637465_NEGATIVE 175 165 121 136 87 NC_003454:FN0469|3end_Copper_homeostasis_protein_cutC_1114614..1114764_POSITIVE 175 67 32 78 31 NC_003454:FN2112|3end_hypothetical_protein_623169..623319_NEGATIVE 173 55 14 93 51 NC_003454:FN0691|3end_hypothetical_protein_1345827..1345977_NEGATIVE 173 144 109 114 76 NC_003454:FN1973|3end_Translation_initiation_inhibitor_472230..472380_NEGATIVE 173 178 131 54 12 NC_003454:FN1696|3end_UDP-4-dehydro-6-deoxy-2-acetamido-D-glucose_4-reductase_190876..191026_NEGATIVE