Origin IGS: cgtatcttcctctatcgcagtcaatcgttcgatctctttcggcatacttttcttttgctaatgtattgttacattgcaaacttacgaataattcgtaagaatacaagccttttctacgaaaatttcgcagatctat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atagatctgcgaaattttcgtagaaaaggcttgtattcttacgaattattcgtaagtttgcaatgtaacaatacattagcaaaagaaaagtatgccgaaagagatcgaacgattgactgcgatagaggaagatacg Mask Tandem Repeat Region ================================================ cgtatcttcctctatcgcagtcaatcgttcgatctctttcggcatacttttcttttgctaatgtattgttacattgcaaacttacgaataattcgtaagaatacaagccttttctacgaaaatttcgcagatctat Find is-nt database================================================ Query_seq: PG2186:PG2187|PG2186:PG2187:transcriptional regulator, putative:1,4-dihydroxy-2-naphthoate octaprenyltransferase:<-<-:2293710..2293845 136 cgtatcttcctctatcgcagtcaatcgttcgatctctttcggcatacttttcttttgctaatgtattgttacattgcaaacttacgaataattcgtaagaatacaagccttttctacgaaaatttcgcagatctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2186:PG2187|PG2186:PG2187:transcriptional regulator, putative:1,4-dihydroxy-2-naphthoate octaprenyltransferase:<-<-:2293710..2293845 136 cgtatcttcctctatcgcagtcaatcgttcgatctctttcggcatacttttcttttgctaatgtattgttacattgcaaacttacgaataattcgtaagaatacaagccttttctacgaaaatttcgcagatctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2186:PG2187|PG2186:PG2187:transcriptional regulator, putative:1,4-dihydroxy-2-naphthoate octaprenyltransferase:<-<-:2293710..2293845 136 cgtatcttcctctatcgcagtcaatcgttcgatctctttcggcatacttttcttttgctaatgtattgttacattgcaaacttacgaataattcgtaagaatacaagccttttctacgaaaatttcgcagatctat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtatcttcctctatcgcagtcaatcgttcgatctctttcggcatacttttcttttgctaatgtattgttacattgcaaacttacgaataattcgtaagaatacaagccttttctacgaaaatttcgcagatctat Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 4 End: 135 ... M F L Y R S Q S F D L F R H T F L L L M Y C Y I A N L R I I R K N T S L F Y E N F A D L . Protein_Len: 45 Strand: - Start: 2 End: 136 . Y R G R D C D I T R D R E A Y K E K A L T N N C Q L S V F L E Y S Y L G K R R F N R L D M cgtatcttcctctatcgcagtcaatcgttcgatctctttcggcatacttttcttttgctaatgtattgttacattgcaaacttacgaataattcgtaagaatacaagccttttctacgaaaatttcgcagatctat 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================================================ cgtatcttcctctatcgcagtcaatcgttcgatctctttcggcatacttttcttttgctaatgtattgttacattgcaaacttacgaataattcgtaagaatacaagccttttctacgaaaatttcgcagatctat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG2186:PG2187|PG2186:PG2187:transcriptional regulator, putative:1,4-dihydroxy-2-naphthoate octaprenyltransferase:<-<-:2293710..2293845 136 cgtatcttcctctatcgcagtcaatcgttcgatctctttcggcatacttttcttttgctaatgtattgttacattgcaaacttacgaataattcgtaagaatacaagccttttctacgaaaatttcgcagatctat Intra-Species Hit: Count: 1 Min: 1 Max: 136 Len: 136 Subject: NC_002950_PG2186_PG2187|transcriptional regulator, putative:1,4-dihydroxy-2-naphthoate octaprenyltransferase|NEGATIVE:NEGATIVE|[2293710, 2293845]|136 HSP 1 e-value: 1.0E-71 bit: 270.0 Len: 136 Query Start:1 Query End:136 Subject Strand: POSITIVE Subject Start: 1 Subject End: 136 cgtatcttcctctatcgcagtcaatcgttcgatctctttcggcatacttttcttttgctaatgtattgttacattgcaaacttacgaataattcgtaagaatacaagccttttctacgaaaatttcgcagatctat cgtatcttcctctatcgcagtcaatcgttcgatctctttcggcatacttttcttttgctaatgtattgttacattgcaaacttacgaataattcgtaagaatacaagccttttctacgaaaatttcgcagatctat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUAUCUUCCUCUAUCGCAGUCAAUCGUUCGAUCUCUUUCGGCAUACUUUUCUUUUGCUAAUGUAUUGUUACAUUGCAAACUUACGAAUAAUUCGUAAGAAUACAAGCCUUUUCUACGAAAAUUUCGCAGAUCUAU ..............................(((((.....(((..........(((((.((((((....)))))))))))(((((((.....))))))).......))).......(((.....))).)))))... (-25.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGAUCUGCGAAAUUUUCGUAGAAAAGGCUUGUAUUCUUACGAAUUAUUCGUAAGUUUGCAAUGUAACAAUACAUUAGCAAAAGAAAAGUAUGCCGAAAGAGAUCGAACGAUUGACUGCGAUAGAGGAAGAUACG ....((((.........((((((....(((.......(((((((.....)))))))(((((((((((....)))))).)))))..........)))......((((....))))..)))))).......))))... (-31.19) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 927 50 1 141 92 NC_002950:PG2186|5end_transcriptional_regulator,_putative_2293619..2293849_NEGATIVE 328 49 2 55 6 NC_002950:PG1017|5end_pyruvate_phosphate_dikinase_1076138..1076368_POSITIVE 319 59 11 223 166 NC_002950:PG2179|5end_NADH-ubiquinone_oxidoreductase_2287806..2288036_NEGATIVE 312 59 11 129 87 NC_002950:PG1053|5end_transcriptional_regulator,_putative_1120065..1120295_POSITIVE 304 57 12 69 19 NC_002950:PG1318|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1397768..1397998_NEGATIVE 303 43 1 192 141 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 303 43 9 223 192 NC_002950:PG0215|5end_hypothetical_protein_251460..251690_POSITIVE 301 43 5 180 149 NC_002950:PG1104|5end_hypothetical_protein_1174935..1175165_POSITIVE 295 47 1 165 119 NC_002950:PG1542|5end_collagenase_1620788..1621018_POSITIVE 293 42 7 63 26 NC_002950:PG0294|5end_glycosyl_transferase,_group_2_family_protein_330161..330391_NEGATIVE 291 49 4 177 120 NC_002950:PG1903|5end_hypothetical_protein_2004221..2004451_NEGATIVE 288 50 1 108 53 NC_002950:PG1814|5end_DNA_primase_1910627..1910857_NEGATIVE 286 43 1 212 166 NC_002950:PG0132|5end_hypothetical_protein_152879..153109_POSITIVE 281 50 6 105 59 NC_002950:PG0955|5end_hypothetical_protein_1014832..1015062_POSITIVE 281 45 6 116 76 NC_002950:PG0065|5end_efflux_transporter,_RND_family,_MFP_subunit_81187..81417_NEGATIVE 280 47 6 230 180 NC_002950:PG1937|5end_50S_ribosomal_protein_L4_2024136..2024366_NEGATIVE 279 78 31 57 2 NC_002950:PG0059|5end_hypothetical_protein_71526..71756_POSITIVE 278 41 1 85 37 NC_002950:PG1391|5end_hypothetical_protein_1471670..1471900_POSITIVE 276 59 15 199 153 NC_002950:PG1133|5end_hypothetical_protein_1213571..1213801_POSITIVE 274 44 1 62 15 NC_002950:PG0481|5end_2-amino-3-ketobutyrate_coenzyme_A_ligase_522622..522852_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 56 11 144 102 NC_002950:PG1459|3end_hypothetical_protein_1539632..1539782_NEGATIVE 312 59 11 110 68 NC_002950:PG1052|3end_transcriptional_regulator,_putative_1120126..1120276_POSITIVE 293 42 7 48 11 NC_002950:PG0295|3end_DNA_processing_protein_DprA,_putative_330176..330326_NEGATIVE 291 42 1 121 81 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 288 50 1 66 11 NC_002950:PG1815|3end_3-deoxy-manno-octulosonate_cytidylyltransferase_1910669..1910819_NEGATIVE 275 59 16 121 72 NC_002950:PG0344|3end_purple_acid_phosphatase_378543..378693_NEGATIVE 272 59 19 49 15 NC_002950:PG0431|3end_hypothetical_protein_469174..469324_POSITIVE 269 46 1 151 106 NC_002950:PG1541|3end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_1620855..1621005_POSITIVE 267 60 12 71 1 NC_002950:PG1733|3end_hypothetical_protein_1821186..1821336_NEGATIVE 265 48 1 84 29 NC_002950:PG1895|3end_hypothetical_protein_1994240..1994390_POSITIVE 262 58 13 107 59 NC_002950:PG0333|3end_hypothetical_protein_368811..368961_POSITIVE 261 44 5 66 33 NC_002950:PG1091|3end_DHH_subfamily_1_protein_1158092..1158242_POSITIVE 258 46 8 147 101 NC_002950:PG1778|3end_hypothetical_protein_1867922..1868072_POSITIVE 256 43 4 44 6 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE 256 56 14 79 42 NC_002950:PG0618|3end_alkyl_hydroperoxide_reductase,_C_subunit_671018..671168_POSITIVE 256 44 1 56 6 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 255 42 8 98 68 NC_002950:PG0261|3end_ISPg3,_transposase_293862..294012_NEGATIVE 254 59 11 65 8 NC_002950:PG0436|3end_capsular_polysaccharide_transport_protein,_putative_473461..473611_NEGATIVE 253 43 1 130 79 NC_002950:PG1002|3end_hypothetical_protein_1059237..1059387_POSITIVE 253 58 16 147 86 NC_002950:PG0628|3end_ABC_transporter,_ATP-binding_protein_681684..681834_NEGATIVE