Origin IGS: tcgtgatttcctccttatgaaaatcaaaaaatttttatgtgaaaagagtaacttgagttgctacaaatcacctttcaacatttctattatatacttaattgaggtaaaatgcaactgatttcattgttattaacaagtattatgaattctttcactaactttcatttcggctttcattgatttgaaaaagcaaagcagtaacttttgaaaatgcaggaatacaacttacaagataaatcatttactctttttattgaggaatcgatcctctaaaaaatagaaaaagcacccgcgaatgcgagtgccaaggtttgctcaaggc .........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 gccttgagcaaaccttggcactcgcattcgcgggtgctttttctattttttagaggatcgattcctcaataaaaagagtaaatgatttatcttgtaagttgtattcctgcattttcaaaagttactgctttgctttttcaaatcaatgaaagccgaaatgaaagttagtgaaagaattcataatacttgttaataacaatgaaatcagttgcattttacctcaattaagtatataatagaaatgttgaaaggtgatttgtagcaactcaagttactcttttcacataaaaattttttgattttcataaggaggaaatcacga Mask Tandem Repeat Region ================================================ tcgtgatttcctccttatgaaaatcaaaaaatttttatgtgaaaagagtaacttgagttgctacaaatcacctttcaacatttctattatatacttaattgaggtaaaatgcaactgatttcattgttattaacaagtattatgaattctttcactaactttcatttcggctttcattgatttgaaaaagcaaagcagtaacttttgaaaatgcaggaatacaacttacaagataaatcatttactctttttattgaggaatcgatcctctaaaaaatagaaaaagcacccgcgaatgcgagtgccaaggtttgctcaaggc Find is-nt database================================================ Query_seq: SSA_2108:SSA_2109|SSA_2108:SSA_2109:Glyceraldehyde 3-phosphate dehydrogenase, putative:Elongation factor G, putative:<-<-:2112555..2112876 322 tcgtgatttcctccttatgaaaatcaaaaaatttttatgtgaaaagagtaacttgagttgctacaaatcacctttcaacatttctattatatacttaattgaggtaaaatgcaactgatttcattgttattaacaagtattatgaattctttcactaactttcatttcggctttcattgatttgaaaaagcaaagcagtaacttttgaaaatgcaggaatacaacttacaagataaatcatttactctttttattgaggaatcgatcctctaaaaaatagaaaaagcacccgcgaatgcgagtgccaaggtttgctcaaggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2108:SSA_2109|SSA_2108:SSA_2109:Glyceraldehyde 3-phosphate dehydrogenase, putative:Elongation factor G, putative:<-<-:2112555..2112876 322 tcgtgatttcctccttatgaaaatcaaaaaatttttatgtgaaaagagtaacttgagttgctacaaatcacctttcaacatttctattatatacttaattgaggtaaaatgcaactgatttcattgttattaacaagtattatgaattctttcactaactttcatttcggctttcattgatttgaaaaagcaaagcagtaacttttgaaaatgcaggaatacaacttacaagataaatcatttactctttttattgaggaatcgatcctctaaaaaatagaaaaagcacccgcgaatgcgagtgccaaggtttgctcaaggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2108:SSA_2109|SSA_2108:SSA_2109:Glyceraldehyde 3-phosphate dehydrogenase, putative:Elongation factor G, putative:<-<-:2112555..2112876 322 tcgtgatttcctccttatgaaaatcaaaaaatttttatgtgaaaagagtaacttgagttgctacaaatcacctttcaacatttctattatatacttaattgaggtaaaatgcaactgatttcattgttattaacaagtattatgaattctttcactaactttcatttcggctttcattgatttgaaaaagcaaagcagtaacttttgaaaatgcaggaatacaacttacaagataaatcatttactctttttattgaggaatcgatcctctaaaaaatagaaaaagcacccgcgaatgcgagtgccaaggtttgctcaaggc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcgtgatttcctccttatgaaaatcaaaaaatttttatgtgaaaagagtaacttgagttgctacaaatcacctttcaacatttctattatatacttaattgaggtaaaatgcaactgatttcattgttattaacaagtattatgaattctttcactaactttcatttcggctttcattgatttgaaaaagcaaagcagtaacttttgaaaatgcaggaatacaacttacaagataaatcatttactctttttattgaggaatcgatcctctaaaaaatagaaaaagcacccgcgaatgcgagtgccaaggtttgctcaaggc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 17 End: 115 ................ M K I K K F L C E K S N L S C Y K S P F N I S I I Y L I E V K C N ............................................................................................................................................................................................................... Protein_Len: 30 Strand: - Start: 177 End: 266 ................................................................................................................................................................................ Q N S F A F C Y S K F I C S Y L K C S L D N V R K I S S D M ........................................................ tcgtgatttcctccttatgaaaatcaaaaaatttttatgtgaaaagagtaacttgagttgctacaaatcacctttcaacatttctattatatacttaattgaggtaaaatgcaactgatttcattgttattaacaagtattatgaattctttcactaactttcatttcggctttcattgatttgaaaaagcaaagcagtaacttttgaaaatgcaggaatacaacttacaagataaatcatttactctttttattgaggaatcgatcctctaaaaaatagaaaaagcacccgcgaatgcgagtgccaaggtttgctcaaggc 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: 87 Start: 86 End: 115 .....................................................................................GTTGCATTTTACCTCAATTAAGTATATAAT............................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcgtgatttcctccttatgaaaatcaaaaaatttttatgtgaaaagagtaacttgagttgctacaaatcacctttcaacatttctattatatacttaattgaggtaaaatgcaactgatttcattgttattaacaagtattatgaattctttcactaactttcatttcggctttcattgatttgaaaaagcaaagcagtaacttttgaaaatgcaggaatacaacttacaagataaatcatttactctttttattgaggaatcgatcctctaaaaaatagaaaaagcacccgcgaatgcgagtgccaaggtttgctcaaggc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2108:SSA_2109|SSA_2108:SSA_2109:Glyceraldehyde 3-phosphate dehydrogenase, putative:Elongation factor G, putative:<-<-:2112555..2112876 322 tcgtgatttcctccttatgaaaatcaaaaaatttttatgtgaaaagagtaacttgagttgctacaaatcacctttcaacatttctattatatacttaattgaggtaaaatgcaactgatttcattgttattaacaagtattatgaattctttcactaactttcatttcggctttcattgatttgaaaaagcaaagcagtaacttttgaaaatgcaggaatacaacttacaagataaatcatttactctttttattgaggaatcgatcctctaaaaaatagaaaaagcacccgcgaatgcgagtgccaaggtttgctcaaggc Intra-Species Hit: Count: 1 Min: 1 Max: 322 Len: 322 Subject: NC_009009_SSA_2108_SSA_2109|Glyceraldehyde 3-phosphate dehydrogenase, putative:Elongation factor G, putative|NEGATIVE:NEGATIVE|[2112555,2112876]|322 HSP 1 e-value: 0.0 bit: 638.0 Len: 322 Query Start:1 Query End:322 Subject Strand: POSITIVE Subject Start: 1 Subject End: 322 tcgtgatttcctccttatgaaaatcaaaaaatttttatgtgaaaagagtaacttgagttgctacaaatcacctttcaacatttctattatatacttaattgaggtaaaatgcaactgatttcattgttattaacaagtattatgaattctttcactaactttcatttcggctttcattgatttgaaaaagcaaagcagtaacttttgaaaatgcaggaatacaacttacaagataaatcatttactctttttattgaggaatcgatcctctaaaaaatagaaaaagcacccgcgaatgcgagtgccaaggtttgctcaaggc tcgtgatttcctccttatgaaaatcaaaaaatttttatgtgaaaagagtaacttgagttgctacaaatcacctttcaacatttctattatatacttaattgaggtaaaatgcaactgatttcattgttattaacaagtattatgaattctttcactaactttcatttcggctttcattgatttgaaaaagcaaagcagtaacttttgaaaatgcaggaatacaacttacaagataaatcatttactctttttattgaggaatcgatcctctaaaaaatagaaaaagcacccgcgaatgcgagtgccaaggtttgctcaaggc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGUGAUUUCCUCCUUAUGAAAAUCAAAAAAUUUUUAUGUGAAAAGAGUAACUUGAGUUGCUACAAAUCACCUUUCAACAUUUCUAUUAUAUACUUAAUUGAGGUAAAAUGCAACUGAUUUCAUUGUUAUUAACAAGUAUUAUGAAUUCUUUCACUAACUUUCAUUUCGGCUUUCAUUGAUUUGAAAAAGCAAAGCAGUAACUUUUGAAAAUGCAGGAAUACAACUUACAAGAUAAAUCAUUUACUCUUUUUAUUGAGGAAUCGAUCCUCUAAAAAAUAGAAAAAGCACCCGCGAAUGCGAGUGCCAAGGUUUGCUCAAGGC ............((((..(.(((((......((((((((((((((((((((..(((((((...................(((((.((((......)))).))))).........(((.(((((..((((((...((((....((((....))))...))))........(((((((......)))..)))).....))))))...)))))...))).....)))))))...((....))..))))))))))))).(((((.....)))))......)))))))..((((.(((....))).))))...))))).)..)))). (-62.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCUUGAGCAAACCUUGGCACUCGCAUUCGCGGGUGCUUUUUCUAUUUUUUAGAGGAUCGAUUCCUCAAUAAAAAGAGUAAAUGAUUUAUCUUGUAAGUUGUAUUCCUGCAUUUUCAAAAGUUACUGCUUUGCUUUUUCAAAUCAAUGAAAGCCGAAAUGAAAGUUAGUGAAAGAAUUCAUAAUACUUGUUAAUAACAAUGAAAUCAGUUGCAUUUUACCUCAAUUAAGUAUAUAAUAGAAAUGUUGAAAGGUGAUUUGUAGCAACUCAAGUUACUCUUUUCACAUAAAAAUUUUUUGAUUUUCAUAAGGAGGAAAUCACGA ((.....)).......(((((((((....)))))))))(((((((.....)))))))..((((((((....((((((((((..(((((...((((..............((((((..(((((....)))))((((((..........)))))).)))))).((((..(((((....)))))...)))).......))))..))))).((((((..((((((((((..................)))))..)))))..))))))........))))))))))......((((((....))))))......)))).)))).... (-70.57) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 754 80 31 171 122 NC_009009:SSA_2108|5end_Glyceraldehyde_3-phosphate_dehydrogenase,_putative_2112464..2112694_NEGATIVE 327 308 266 121 80 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 320 318 285 138 107 NC_009009:SSA_1564|5end_Histidine_kinase,_putative_1568615..1568845_NEGATIVE 303 317 287 75 40 NC_009009:SSA_0335|5end_Phosphomevalonate_kinase,_putative_328792..329022_POSITIVE 300 319 285 48 3 NC_009009:SSA_0547|5end_Acyl_carrier_protein_synthase,_putative_541991..542221_POSITIVE 275 179 149 229 202 NC_009009:SSA_1698|5end_Galactose-6-phosphate_isomerase,_LacB_subunit,_putative_1690648..1690878_NEGATIVE 273 97 52 106 52 NC_009009:SSA_0064|5end_hypothetical_protein_66330..66560_POSITIVE 269 300 255 223 185 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 258 316 283 192 156 NC_009009:SSA_0875|5end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_868928..869158_POSITIVE 256 316 284 65 25 NC_009009:SSA_0375|5end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_364257..364487_POSITIVE 255 315 275 230 188 NC_009009:SSA_2268|5end_Type_II_secretory_pathway,_pullulanase_PulA_glycosidase,_putative_2267228..2267458_POSITIVE 254 85 45 217 178 NC_009009:SSA_0336|5end_Isopentenyl-diphosphate_delta-isomerase,_putative_329792..330022_POSITIVE 248 318 286 163 127 NC_009009:SSA_1485|5end_Citrulline_cluster-linked_gene,_putative_1492809..1493039_NEGATIVE 247 200 151 171 104 NC_009009:SSA_0604|5end_hypothetical_protein_592451..592681_POSITIVE 247 317 286 171 144 NC_009009:SSA_0522|5end_Ethanolamine_utilization_protein,_putative_521067..521297_POSITIVE 245 198 154 155 97 NC_009009:SSA_1990|5end_Zn-porter_lipoprotein,_putative_1986319..1986549_NEGATIVE 245 80 33 94 46 NC_009009:SSA_0895|5end_ATP-binding_cassette_transporter-like_protein,_putative_886466..886696_POSITIVE 243 88 46 77 32 NC_009009:SSA_0746|5end_Glucosamine-6-phosphate_deaminase,_putative_727078..727308_POSITIVE 242 318 282 188 140 NC_009009:SSA_1879|5end_Glycyl-tRNA_synthetase_beta_chain,_putative_1874262..1874492_NEGATIVE 240 317 283 192 163 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 318 285 145 114 NC_009009:SSA_1565|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1568608..1568758_NEGATIVE 309 42 2 57 19 NC_009009:SSA_1857|3end_Conserved_DivIVA-like_protein,_putative_1852725..1852875_NEGATIVE 303 317 287 85 50 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 273 97 52 109 55 NC_009009:SSA_0063|3end_Holliday_junction_DNA_helicase_ruvB,_putative_66413..66563_POSITIVE 271 310 265 148 97 NC_009009:SSA_2106|3end_Flavin_monoxygenase,_putative_2108015..2108165_NEGATIVE 270 316 273 75 33 NC_009009:SSA_1245|3end_Transcriptional_regulator,_LysR_family,_putative_1269710..1269860_POSITIVE 266 320 288 45 1 NC_009009:SSA_1323|3end_hypothetical_protein_1339788..1339938_NEGATIVE 264 300 255 146 108 NC_009009:SSA_1134|3end_Xanthine_phosphoribosyltransferase,_putative_1160316..1160466_POSITIVE 257 318 275 119 70 NC_009009:SSA_2267|3end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_2267190..2267340_POSITIVE 255 305 262 72 28 NC_009009:SSA_0867|3end_hypothetical_protein_860711..860861_POSITIVE 254 316 285 49 2 NC_009009:SSA_1250|3end_Conserved_uncharacterized_protein,_putative_1273982..1274132_NEGATIVE 246 315 274 82 47 NC_009009:SSA_1951|3end_Penicillin-binding_protein_3,_putative_1948103..1948253_POSITIVE 245 198 154 134 76 NC_009009:SSA_1991|3end_Pneumococcal_histidine_triad_protein_A,_putative_1986340..1986490_NEGATIVE 245 80 33 81 33 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE 239 316 287 53 14 NC_009009:SSA_1315|3end_hypothetical_protein_1331408..1331558_NEGATIVE 236 199 151 151 85 NC_009009:SSA_0603|3end_Cobalt_transporter,_putative_592512..592662_POSITIVE 235 295 251 76 38 NC_009009:SSA_0743|3end_Transcriptional_repressor_(arginine_synthesis),_putative_725289..725439_NEGATIVE 232 318 278 54 27 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 231 204 165 92 62 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 230 316 286 81 47 NC_009009:SSA_0216|3end_Histidine_kinase,_putative_213270..213420_POSITIVE