Origin IGS: aacaaagaagaaagaatacaaattgttacaaatttaactattgatttgtagcaaacatattctttctttttaattttagacaatatatctgtataatttatttcacaaattcgtgaaataaaaaaaagctagaaaaatctataaaaaaattgtattattaattaaataaatatttctataaactatatgcatatttttttaaatgtttgatatacaacttttaatgtaaaattttagaacagtgaaattttaaagaactattggaggtaaaaatgctaaaaaagcagcattttgaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttcaaaatgctgcttttttagcatttttacctccaatagttctttaaaatttcactgttctaaaattttacattaaaagttgtatatcaaacatttaaaaaaatatgcatatagtttatagaaatatttatttaattaataatacaatttttttatagatttttctagcttttttttatttcacgaatttgtgaaataaattatacagatatattgtctaaaattaaaaagaaagaatatgtttgctacaaatcaatagttaaatttgtaacaatttgtattctttcttctttgtt Mask Tandem Repeat Region ================================================ aacaaagaagaaagaatacaaattgttacaaatttaactattgatttgtagcaaacatattctttctttttaattttagacaatatatctgtataatttatttcacaaattcgtgaaataaaaaaaagctagaaaaatctataaaaaaattgtattattaattaaataaatatttctataaactatatgcatatttttttaaatgtttgatatacaacttttaatgtaaaattttagaacagtgaaattttaaagaactattggaggtaaaaatgctaaaaaagcagcattttgaa Find is-nt database================================================ Query_seq: FN0197:FN0198|FN0197:FN0198:Methyltransferase:Transcriptional regulatory protein:->->:823605..823900 296 aacaaagaagaaagaatacaaattgttacaaatttaactattgatttgtagcaaacatattctttctttttaattttagacaatatatctgtataatttatttcacaaattcgtgaaataaaaaaaagctagaaaaatctataaaaaaattgtattattaattaaataaatatttctataaactatatgcatatttttttaaatgtttgatatacaacttttaatgtaaaattttagaacagtgaaattttaaagaactattggaggtaaaaatgctaaaaaagcagcattttgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0197:FN0198|FN0197:FN0198:Methyltransferase:Transcriptional regulatory protein:->->:823605..823900 296 aacaaagaagaaagaatacaaattgttacaaatttaactattgatttgtagcaaacatattctttctttttaattttagacaatatatctgtataatttatttcacaaattcgtgaaataaaaaaaagctagaaaaatctataaaaaaattgtattattaattaaataaatatttctataaactatatgcatatttttttaaatgtttgatatacaacttttaatgtaaaattttagaacagtgaaattttaaagaactattggaggtaaaaatgctaaaaaagcagcattttgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0197:FN0198|FN0197:FN0198:Methyltransferase:Transcriptional regulatory protein:->->:823605..823900 296 aacaaagaagaaagaatacaaattgttacaaatttaactattgatttgtagcaaacatattctttctttttaattttagacaatatatctgtataatttatttcacaaattcgtgaaataaaaaaaagctagaaaaatctataaaaaaattgtattattaattaaataaatatttctataaactatatgcatatttttttaaatgtttgatatacaacttttaatgtaaaattttagaacagtgaaattttaaagaactattggaggtaaaaatgctaaaaaagcagcattttgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacaaagaagaaagaatacaaattgttacaaatttaactattgatttgtagcaaacatattctttctttttaattttagacaatatatctgtataatttatttcacaaattcgtgaaataaaaaaaagctagaaaaatctataaaaaaattgtattattaattaaataaatatttctataaactatatgcatatttttttaaatgtttgatatacaacttttaatgtaaaattttagaacagtgaaattttaaagaactattggaggtaaaaatgctaaaaaagcagcattttgaa Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 3 End: 119 .. L S S L I C I T V F K V I S K Y C V Y E K K K I K S L I D T Y N I E C I R S M ................................................................................................................................................................................. aacaaagaagaaagaatacaaattgttacaaatttaactattgatttgtagcaaacatattctttctttttaattttagacaatatatctgtataatttatttcacaaattcgtgaaataaaaaaaagctagaaaaatctataaaaaaattgtattattaattaaataaatatttctataaactatatgcatatttttttaaatgtttgatatacaacttttaatgtaaaattttagaacagtgaaattttaaagaactattggaggtaaaaatgctaaaaaagcagcattttgaa 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: 83 Start: 68 End: 97 ...................................................................TTTTAATTTTAGACAATATATCTGTATAAT....................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacaaagaagaaagaatacaaattgttacaaatttaactattgatttgtagcaaacatattctttctttttaattttagacaatatatctgtataatttatttcacaaattcgtgaaataaaaaaaagctagaaaaatctataaaaaaattgtattattaattaaataaatatttctataaactatatgcatatttttttaaatgtttgatatacaacttttaatgtaaaattttagaacagtgaaattttaaagaactattggaggtaaaaatgctaaaaaagcagcattttgaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -8.5 Tail_Score: -3.33087 Start: 97 End: 122 Full_Region: tttttctagcttttt tttatttcacg aatt tgtgaaataaa ttatacagatatatt ................................................................................................tttatttcacgaatttgtgaaataaa.............................................................................................................................................................................. Find igs database================================================ Query_seq: FN0197:FN0198|FN0197:FN0198:Methyltransferase:Transcriptional regulatory protein:->->:823605..823900 296 aacaaagaagaaagaatacaaattgttacaaatttaactattgatttgtagcaaacatattctttctttttaattttagacaatatatctgtataatttatttcacaaattcgtgaaataaaaaaaagctagaaaaatctataaaaaaattgtattattaattaaataaatatttctataaactatatgcatatttttttaaatgtttgatatacaacttttaatgtaaaattttagaacagtgaaattttaaagaactattggaggtaaaaatgctaaaaaagcagcattttgaa Intra-Species Hit: Count: 1 Min: 1 Max: 296 Len: 296 Subject: NC_003454_FN0197_FN0198|Methyltransferase:Transcriptional regulatory protein|POSITIVE:POSITIVE|[823605,823900]|296 HSP 1 e-value: 9.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 aacaaagaagaaagaatacaaattgttacaaatttaactattgatttgtagcaaacatattctttctttttaattttagacaatatatctgtataatttatttcacaaattcgtg..................................................................................................................................................................................... aacaaagaagaaagaatacaaattgttacaaatttaactattgatttgtagcaaacatattctttctttttaattttagacaatatatctgtataatttatttcacaaattcgtg..................................................................................................................................................................................... HSP 2 e-value: 2.0E-47 bit: 190.0 Len: 96 Query Start:201 Query End:296 Subject Strand: POSITIVE Subject Start: 201 Subject End: 296 ........................................................................................................................................................................................................aaatgtttgatatacaacttttaatgtaaaattttagaacagtgaaattttaaagaactattggaggtaaaaatgctaaaaaagcagcattttgaa ........................................................................................................................................................................................................aaatgtttgatatacaacttttaatgtaaaattttagaacagtgaaattttaaagaactattggaggtaaaaatgctaaaaaagcagcattttgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAAAGAAGAAAGAAUACAAAUUGUUACAAAUUUAACUAUUGAUUUGUAGCAAACAUAUUCUUUCUUUUUAAUUUUAGACAAUAUAUCUGUAUAAUUUAUUUCACAAAUUCGUGAAAUAAAAAAAAGCUAGAAAAAUCUAUAAAAAAAUUGUAUUAUUAAUUAAAUAAAUAUUUCUAUAAACUAUAUGCAUAUUUUUUUAAAUGUUUGAUAUACAACUUUUAAUGUAAAAUUUUAGAACAGUGAAAUUUUAAAGAACUAUUGGAGGUAAAAAUGCUAAAAAAGCAGCAUUUUGAA ....((((((((((((((....((((((((((((........))))))))))))...))))))))))))))....(((((((.....(((((....((((((((((......)))))))))).....)).)))........((((((((((((((...............................))))).)))))))))..)))))))......((((((((((((((((((((......))))))))))......)))))))))).((((((((........))))))))... (-61.88) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAAAAUGCUGCUUUUUUAGCAUUUUUACCUCCAAUAGUUCUUUAAAAUUUCACUGUUCUAAAAUUUUACAUUAAAAGUUGUAUAUCAAACAUUUAAAAAAAUAUGCAUAUAGUUUAUAGAAAUAUUUAUUUAAUUAAUAAUACAAUUUUUUUAUAGAUUUUUCUAGCUUUUUUUUAUUUCACGAAUUUGUGAAAUAAAUUAUACAGAUAUAUUGUCUAAAAUUAAAAAGAAAGAAUAUGUUUGCUACAAAUCAAUAGUUAAAUUUGUAACAAUUUGUAUUCUUUCUUCUUUGUU ...(((((((((......)))))))))......(((((..(((.((..........(((..(((((((......(((((((((((.........(((((.((((((...((((...))))...)))))).)))))......)))))))))))....)))))))...))).....(((((((((((....)))))))))))...)).)))..)))))........(((((((((((((((((.(((.(((((((..........))))))).)))..))))))))))))).)))).. (-52.66) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 230 53 11 164 120 NC_003454:FN2104|5end_hypothetical_protein_614237..614467_POSITIVE 227 130 84 110 59 NC_003454:FN0846|5end_hypothetical_protein_1504242..1504472_POSITIVE 202 99 61 154 111 NC_003454:FN1104|5end_Holliday_junction_DNA_helicase_ruvA_1749453..1749683_POSITIVE 202 80 49 150 119 NC_003454:FN0444|5end_Phosphoadenosine_phosphosulfate_reductase_1083074..1083304_POSITIVE 199 290 256 48 17 NC_003454:FN1494|5end_Rod_shape-determining_protein_mreC_2174386..2174616_NEGATIVE 196 286 262 103 74 NC_003454:FN1470|5end_hypothetical_protein_2151868..2152098_POSITIVE 195 86 43 111 76 NC_003454:FN0838|5end_hypothetical_protein_1500747..1500977_POSITIVE 192 190 168 46 23 NC_003454:FN0340|5end_Hypothetical_membrane-spanning_Protein_973948..974178_NEGATIVE 185 104 62 209 161 NC_003454:FN0785|5end_Electron_transfer_flavoprotein_alpha-subunit_1441146..1441376_POSITIVE 183 89 41 126 75 NC_003454:FN2038|5end_LSU_ribosomal_protein_L10P_547696..547926_NEGATIVE 181 149 103 46 3 NC_003454:FN1080|5end_Export_ABC_transporter_1725534..1725764_POSITIVE 181 279 241 88 57 NC_003454:FN0251|5end_Hypothetical_membrane-spanning_Protein_873796..874026_POSITIVE 181 279 241 88 57 NC_003454:FN2061|5end_Hypothetical_membrane-spanning_protein_574046..574276_NEGATIVE 181 279 241 88 57 NC_003454:FN2050|5end_Hypothetical_membrane-spanning_protein_559970..560200_NEGATIVE 178 228 195 219 184 NC_003454:FN1366|5end_Triosephosphate_isomerase_2017518..2017748_NEGATIVE 178 73 47 223 196 NC_003454:FN1544|5end_Probable_electron_transfer_flavoprotein-quinone_oxidoreductase_ydiS_57835..58065_POSITIVE 173 81 44 199 159 NC_003454:FN0332|5end_Magnesium_and_cobalt_transport_protein_corA_967230..967460_NEGATIVE 172 234 192 215 174 NC_003454:FN1243|5end_Glycosyl_transferase_1900484..1900714_NEGATIVE 172 108 63 146 96 NC_003454:FN1170|5end_Pyruvate-flavodoxin_oxidoreductase_1832273..1832503_NEGATIVE 171 59 24 158 123 NC_003454:FN0082|5end_Ethanolamine_utilization_protein_eutM_720699..720929_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 249 70 23 85 37 NC_003454:FN0197|3end_Methyltransferase_823544..823694_POSITIVE 230 53 11 56 12 NC_003454:FN2103|3end_RecA_protein_614209..614359_POSITIVE 229 50 8 64 25 NC_003454:FN0225|3end_Gluconate_permease_851715..851865_NEGATIVE 228 70 21 76 37 NC_003454:FN0739|3end_Formiminotetrahydrofolate_cyclodeaminase_1397017..1397167_NEGATIVE 228 70 23 68 34 NC_003454:FN1881|3end_Esterase_368250..368400_NEGATIVE 210 53 12 81 44 NC_003454:FN0853|3end_Glycogen_synthase_1510922..1511072_NEGATIVE 208 53 11 63 17 NC_003454:FN1807|3end_hypothetical_protein_288685..288835_NEGATIVE 202 99 61 142 99 NC_003454:FN1103|3end_Excinuclease_ABC_subunit_A_1749521..1749671_POSITIVE 198 53 20 78 48 NC_003454:FN0852|3end_Hydrolase_1510903..1511053_POSITIVE 185 64 23 86 49 NC_003454:FN0589|3end_Transcriptional_regulator,_MarR_family_1242833..1242983_POSITIVE 181 92 57 41 4 NC_003454:FN1937|3end_hypothetical_protein_437705..437855_NEGATIVE 179 50 5 72 28 NC_003454:FN0636|3end_hypothetical_protein_1295609..1295759_POSITIVE 178 53 11 103 63 NC_003454:FN1806|3end_Integral_membrane_protein_288667..288817_POSITIVE 174 95 58 125 92 NC_003454:FN1942|3end_Hypothetical_cytosolic_protein_444000..444150_NEGATIVE 172 108 63 54 4 NC_003454:FN1171|3end_Acetate_kinase_1832365..1832515_NEGATIVE 172 53 11 77 33 NC_003454:FN1141|3end_Formate_transporter_1790493..1790643_NEGATIVE 171 285 247 143 118 NC_003454:FN0133|3end_hypothetical_protein_769653..769803_POSITIVE 171 59 24 147 112 NC_003454:FN0081|3end_Ethanolamine_utilization_protein_eutL_720768..720918_POSITIVE 171 65 23 85 56 NC_003454:FN1880|3end_Dihydropteridine_reductase_368211..368361_POSITIVE 170 90 45 67 16 NC_003454:FN0058|3end_Cysteine_desulfhydrase_695180..695330_POSITIVE