Origin IGS: taaaaatctctaatagctgttatcggcacatttaaagtagccgagagcctttatattgttcagtgcagatagcaatataaacaataggaggtatacaaaaattgcacccgtgttattttgtgtgaaatgtttgccactctcatttcttttttataattttgaagtcgaaaacgtaataagacgtcaagatttgcccaagcaagtgtgagaaggcaaccttgagggaaggataacatttagtttaccgtctgaaaaaacaaattagttacctttccaacccataaaatacaaaaggaaaaaagaacatttttaaataatacaatttacaaaggtaaaatt .........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 aattttacctttgtaaattgtattatttaaaaatgttcttttttccttttgtattttatgggttggaaaggtaactaatttgttttttcagacggtaaactaaatgttatccttccctcaaggttgccttctcacacttgcttgggcaaatcttgacgtcttattacgttttcgacttcaaaattataaaaaagaaatgagagtggcaaacatttcacacaaaataacacgggtgcaatttttgtatacctcctattgtttatattgctatctgcactgaacaatataaaggctctcggctactttaaatgtgccgataacagctattagagattttta Mask Tandem Repeat Region ================================================ taaaaatctctaatagctgttatcggcacatttaaagtagccgagagcctttatattgttcagtgcagatagcaatataaacaataggaggtatacaaaaattgcacccgtgttattttgtgtgaaatgtttgccactctcatttcttttttataattttgaagtcgaaaacgtaataagacgtcaagatttgcccaagcaagtgtgagaaggcaaccttgagggaaggataacatttagtttaccgtctgaaaaaacaaattagttacctttccaacccataaaatacaaaaggaaaaaagaacatttttaaataatacaatttacaaaggtaaaatt Find is-nt database================================================ Query_seq: PI1367:PI1368|PI1367:PI1368:redox-sensitive transcriptional activator, OxyR:enolase (phosphopyruvate hydratase):->->:1287924..1288262 339 taaaaatctctaatagctgttatcggcacatttaaagtagccgagagcctttatattgttcagtgcagatagcaatataaacaataggaggtatacaaaaattgcacccgtgttattttgtgtgaaatgtttgccactctcatttcttttttataattttgaagtcgaaaacgtaataagacgtcaagatttgcccaagcaagtgtgagaaggcaaccttgagggaaggataacatttagtttaccgtctgaaaaaacaaattagttacctttccaacccataaaatacaaaaggaaaaaagaacatttttaaataatacaatttacaaaggtaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1367:PI1368|PI1367:PI1368:redox-sensitive transcriptional activator, OxyR:enolase (phosphopyruvate hydratase):->->:1287924..1288262 339 taaaaatctctaatagctgttatcggcacatttaaagtagccgagagcctttatattgttcagtgcagatagcaatataaacaataggaggtatacaaaaattgcacccgtgttattttgtgtgaaatgtttgccactctcatttcttttttataattttgaagtcgaaaacgtaataagacgtcaagatttgcccaagcaagtgtgagaaggcaaccttgagggaaggataacatttagtttaccgtctgaaaaaacaaattagttacctttccaacccataaaatacaaaaggaaaaaagaacatttttaaataatacaatttacaaaggtaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1367:PI1368|PI1367:PI1368:redox-sensitive transcriptional activator, OxyR:enolase (phosphopyruvate hydratase):->->:1287924..1288262 339 taaaaatctctaatagctgttatcggcacatttaaagtagccgagagcctttatattgttcagtgcagatagcaatataaacaataggaggtatacaaaaattgcacccgtgttattttgtgtgaaatgtttgccactctcatttcttttttataattttgaagtcgaaaacgtaataagacgtcaagatttgcccaagcaagtgtgagaaggcaaccttgagggaaggataacatttagtttaccgtctgaaaaaacaaattagttacctttccaacccataaaatacaaaaggaaaaaagaacatttttaaataatacaatttacaaaggtaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaatctctaatagctgttatcggcacatttaaagtagccgagagcctttatattgttcagtgcagatagcaatataaacaataggaggtatacaaaaattgcacccgtgttattttgtgtgaaatgtttgccactctcatttcttttttataattttgaagtcgaaaacgtaataagacgtcaagatttgcccaagcaagtgtgagaaggcaaccttgagggaaggataacatttagtttaccgtctgaaaaaacaaattagttacctttccaacccataaaatacaaaaggaaaaaagaacatttttaaataatacaatttacaaaggtaaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 53 End: 205 .................................................... M L F S A D S N I N N R R Y T K I A P V L F C V K C L P L S F L F Y N F E V E N V I R R Q D L P K Q V ...................................................................................................................................... Protein_Len: 58 Strand: - Start: 63 End: 236 .............................................................. H L Y C Y L C Y S T Y L F Q V R T I K H S I N A V R M E K K Y N Q L R F R L L V D L N A W A L T L L C G Q P F S L M ....................................................................................................... Protein_Len: 30 Strand: - Start: 13 End: 102 ............ Y S N D A C K F Y G L A K I N N L A S L L I F L L L Y V F M ............................................................................................................................................................................................................................................. taaaaatctctaatagctgttatcggcacatttaaagtagccgagagcctttatattgttcagtgcagatagcaatataaacaataggaggtatacaaaaattgcacccgtgttattttgtgtgaaatgtttgccactctcatttcttttttataattttgaagtcgaaaacgtaataagacgtcaagatttgcccaagcaagtgtgagaaggcaaccttgagggaaggataacatttagtttaccgtctgaaaaaacaaattagttacctttccaacccataaaatacaaaaggaaaaaagaacatttttaaataatacaatttacaaaggtaaaatt 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================================================ taaaaatctctaatagctgttatcggcacatttaaagtagccgagagcctttatattgttcagtgcagatagcaatataaacaataggaggtatacaaaaattgcacccgtgttattttgtgtgaaatgtttgccactctcatttcttttttataattttgaagtcgaaaacgtaataagacgtcaagatttgcccaagcaagtgtgagaaggcaaccttgagggaaggataacatttagtttaccgtctgaaaaaacaaattagttacctttccaacccataaaatacaaaaggaaaaaagaacatttttaaataatacaatttacaaaggtaaaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1367:PI1368|PI1367:PI1368:redox-sensitive transcriptional activator, OxyR:enolase (phosphopyruvate hydratase):->->:1287924..1288262 339 taaaaatctctaatagctgttatcggcacatttaaagtagccgagagcctttatattgttcagtgcagatagcaatataaacaataggaggtatacaaaaattgcacccgtgttattttgtgtgaaatgtttgccactctcatttcttttttataattttgaagtcgaaaacgtaataagacgtcaagatttgcccaagcaagtgtgagaaggcaaccttgagggaaggataacatttagtttaccgtctgaaaaaacaaattagttacctttccaacccataaaatacaaaaggaaaaaagaacatttttaaataatacaatttacaaaggtaaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 280 Len: 280 Subject: pint_PI1367_PI1368|redox-sensitive transcriptional activator, OxyR:enolase (phosphopyruvate hydratase)|POSITIVE:POSITIVE|[1287924,1288262]|339 HSP 1 e-value: 1.0E-157 bit: 555.0 Len: 280 Query Start:1 Query End:280 Subject Strand: POSITIVE Subject Start: 1 Subject End: 280 taaaaatctctaatagctgttatcggcacatttaaagtagccgagagcctttatattgttcagtgcagatagcaatataaacaataggaggtatacaaaaattgcacccgtgttattttgtgtgaaatgtttgccactctcatttcttttttataattttgaagtcgaaaacgtaataagacgtcaagatttgcccaagcaagtgtgagaaggcaaccttgagggaaggataacatttagtttaccgtctgaaaaaacaaattagttacctttccaaccc........................................................... taaaaatctctaatagctgttatcggcacatttaaagtagccgagagcctttatattgttcagtgcagatagcaatataaacaataggaggtatacaaaaattgcacccgtgttattttgtgtgaaatgtttgccactctcatttcttttttataattttgaagtcgaaaacgtaataagacgtcaagatttgcccaagcaagtgtgagaaggcaaccttgagggaaggataacatttagtttaccgtctgaaaaaacaaattagttacctttccaaccc........................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAUCUCUAAUAGCUGUUAUCGGCACAUUUAAAGUAGCCGAGAGCCUUUAUAUUGUUCAGUGCAGAUAGCAAUAUAAACAAUAGGAGGUAUACAAAAAUUGCACCCGUGUUAUUUUGUGUGAAAUGUUUGCCACUCUCAUUUCUUUUUUAUAAUUUUGAAGUCGAAAACGUAAUAAGACGUCAAGAUUUGCCCAAGCAAGUGUGAGAAGGCAACCUUGAGGGAAGGAUAACAUUUAGUUUACCGUCUGAAAAAACAAAUUAGUUACCUUUCCAACCC .....((((((....(((....(((((((.......)).))))).))).((((((((((((......))..)))))))))).....))))))((((((((...(((....)))..)))))))).......(((((.(((.((((((((......((((((((.(((.............))).)))))))).....))).))))).)))..)))))......(((((((.((((((((.((((...........))))))))..)))))))))))..... (-65.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGUUGGAAAGGUAACUAAUUUGUUUUUUCAGACGGUAAACUAAAUGUUAUCCUUCCCUCAAGGUUGCCUUCUCACACUUGCUUGGGCAAAUCUUGACGUCUUAUUACGUUUUCGACUUCAAAAUUAUAAAAAAGAAAUGAGAGUGGCAAACAUUUCACACAAAAUAACACGGGUGCAAUUUUUGUAUACCUCCUAUUGUUUAUAUUGCUAUCUGCACUGAACAAUAUAAAGGCUCUCGGCUACUUUAAAUGUGCCGAUAACAGCUAUUAGAGAUUUUUA (((..((((.((((((......((((..((....)).)))).....)))))).)))))))....(((((((((((...((((....))))...((((.(((.............))).))))................)))))).)))))..(((((..............(((((((.....))))).))...(((((((((...(((.....))).)))))))))....((((.(((((.((.......)))))))....))))....)))))..... (-59.72) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 88 41 82 39 pint:PI0291|5end_hypothetical_protein_274067..274297_POSITIVE 330 232 192 206 171 pint:PI1011|5end_cytochrome_c_biogenesis_protein_CycY_932115..932345_POSITIVE 324 229 181 177 140 pint:PI0921|5end_acyltransferase_852282..852512_POSITIVE 323 97 59 175 134 pint:PI1191|5end_phosphoribosyl_pyrophosphate_synthetase_1109464..1109694_POSITIVE 314 228 182 80 28 pint:PI1890|5end_cell_division_protein_FtsW_1832886..1833116_POSITIVE 314 49 6 66 17 pint:PI0620|5end_hypothetical_protein_569729..569959_POSITIVE 310 230 182 187 128 pint:PI0222|5end_conserved_hypothetical_protein_217808..218038_POSITIVE 309 231 195 69 33 pint:PI1572|5end_hypothetical_protein_1497782..1498012_POSITIVE 304 69 24 169 115 pint:PI0654|5end_K+-dependent_Na+/Ca+_exchanger_related-protein_596283..596513_POSITIVE 304 55 16 188 153 pint:PI0132|5end_hypothetical_protein_123783..124013_POSITIVE 295 230 187 230 188 pint:PI1907|5end_possible_IS1249-related_transposase_1851105..1851335_POSITIVE 294 225 181 91 30 pint:PI0223|5end_topoisomerase_IA_218377..218607_POSITIVE 293 233 192 48 5 pint:PI0211|5end_hypothetical_protein_204067..204297_POSITIVE 292 73 42 85 52 pint:PI0870|5end_branched-chain_amino_acid_aminotransferase_805933..806163_POSITIVE 291 215 178 231 185 pint:PI1642|5end_conserved_hypothetical_protein_1558800..1559030_POSITIVE 290 239 192 94 39 pint:PI0536|5end_hypothetical_protein_492163..492393_POSITIVE 288 234 207 48 23 pint:PI1955|5end_N_utilization_substance_protein_A_1911782..1912012_POSITIVE 288 148 104 71 16 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 286 73 37 84 43 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 286 50 8 54 20 pint:PI0139|5end_pyridoxine_biosynthesis_protein_131835..132065_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 88 41 66 23 pint:PI0290|3end_conserved_hypothetical_protein_274131..274281_POSITIVE 310 230 182 95 36 pint:PI0221|3end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_217796..217946_POSITIVE 294 225 181 76 15 pint:PI0222|3end_conserved_hypothetical_protein_218442..218592_POSITIVE 287 218 172 133 87 pint:PI1973|3end_conserved_hypothetical_protein_1931171..1931321_POSITIVE 285 67 24 104 55 pint:PI0300|3end_transposase_285761..285911_POSITIVE 282 226 181 123 74 pint:PI0037|3end_hypothetical_protein_39616..39766_POSITIVE 280 68 25 70 19 pint:PI0115|3end_hypothetical_protein_108669..108819_POSITIVE 276 69 27 42 6 pint:PI0653|3end_hypothetical_protein_596236..596386_POSITIVE 275 59 22 122 81 pint:PI2142|3end_conserved_hypothetical_protein_2089176..2089326_POSITIVE 273 69 24 87 31 pint:PI0753|3end_hypothetical_protein_683851..684001_POSITIVE 273 229 181 76 17 pint:PI0286|3end_ISPg3-related_transposase_272065..272215_POSITIVE 270 233 191 131 85 pint:PI1314|3end_hypothetical_protein_1231423..1231573_POSITIVE 270 74 36 112 69 pint:PI0056|3end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_55907..56057_POSITIVE 268 230 181 61 8 pint:PI0941|3end_hypothetical_protein_874675..874825_POSITIVE 267 73 34 64 28 pint:PI0607|3end_2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxy_lic_acid_synthase/2-oxoglutarate_decarboxylase_555548..555698_POSITIVE 260 67 23 140 99 pint:PI1380|3end_conserved_hypothetical_protein_1303242..1303392_POSITIVE 258 200 158 119 75 pint:PI1393|3end_aldose_1-epimerase_1313823..1313973_POSITIVE 258 78 37 60 15 pint:PI0157|3end_hypothetical_protein_151387..151537_POSITIVE 253 73 41 110 77 pint:PI0243|3end_hypothetical_protein_240738..240888_POSITIVE 251 69 35 69 45 pint:PI1608|3end_possible_Na+/H+_anti-porter_1536300..1536450_POSITIVE