Origin IGS: ctgaacgtacttttcctttttcttatatgaattatctttcctcattctgccgcaaaggtacaatgtttcctgttttaaacaatgaatagtagctatcgaaggcgttaatgattattaatataatgtataaaagcaatcgtaaataacgtttaatcttacggtggttttctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagaaaaccaccgtaagattaaacgttatttacgattgcttttatacattatattaataatcattaacgccttcgatagctactattcattgtttaaaacaggaaacattgtacctttgcggcagaatgaggaaagataattcatataagaaaaaggaaaagtacgttcag Mask Tandem Repeat Region ================================================ ctgaacgtacttttcctttttcttatatgaattatctttcctcattctgccgcaaaggtacaatgtttcctgttttaaacaatgaatagtagctatcgaaggcgttaatgattattaatataatgtataaaagcaatcgtaaataacgtttaatcttacggtggttttctta Find is-nt database================================================ Query_seq: PI1197:PI1198|PI1197:PI1198:pseudouridylate synthetase:acetyltransferase:->->:1114550..1114721 172 ctgaacgtacttttcctttttcttatatgaattatctttcctcattctgccgcaaaggtacaatgtttcctgttttaaacaatgaatagtagctatcgaaggcgttaatgattattaatataatgtataaaagcaatcgtaaataacgtttaatcttacggtggttttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1197:PI1198|PI1197:PI1198:pseudouridylate synthetase:acetyltransferase:->->:1114550..1114721 172 ctgaacgtacttttcctttttcttatatgaattatctttcctcattctgccgcaaaggtacaatgtttcctgttttaaacaatgaatagtagctatcgaaggcgttaatgattattaatataatgtataaaagcaatcgtaaataacgtttaatcttacggtggttttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1197:PI1198|PI1197:PI1198:pseudouridylate synthetase:acetyltransferase:->->:1114550..1114721 172 ctgaacgtacttttcctttttcttatatgaattatctttcctcattctgccgcaaaggtacaatgtttcctgttttaaacaatgaatagtagctatcgaaggcgttaatgattattaatataatgtataaaagcaatcgtaaataacgtttaatcttacggtggttttctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgaacgtacttttcctttttcttatatgaattatctttcctcattctgccgcaaaggtacaatgtttcctgttttaaacaatgaatagtagctatcgaaggcgttaatgattattaatataatgtataaaagcaatcgtaaataacgtttaatcttacggtggttttctta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 35 End: 154 .................................. R E E N Q R L P V I N G T K F L S Y Y S D F A N I I I L I I Y L L L R L Y R K M .................. Protein_Len: 32 Strand: - Start: 1 End: 96 Q V Y K E K K K Y S N D K R M R G C L Y L T E Q K L C H I T A M ............................................................................ ctgaacgtacttttcctttttcttatatgaattatctttcctcattctgccgcaaaggtacaatgtttcctgttttaaacaatgaatagtagctatcgaaggcgttaatgattattaatataatgtataaaagcaatcgtaaataacgtttaatcttacggtggttttctta 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================================================ ctgaacgtacttttcctttttcttatatgaattatctttcctcattctgccgcaaaggtacaatgtttcctgttttaaacaatgaatagtagctatcgaaggcgttaatgattattaatataatgtataaaagcaatcgtaaataacgtttaatcttacggtggttttctta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 53 HP_score: -2.7 Tail_Score: -4.07678 Start: 43 End: 65 Full_Region: TGAATTATCTTTCCT CATTCTGCC GCAAA GGTACAATG TTTCCTGTTTTAAAC ..........................................CATTCTGCCGCAAAGGTACAATG........................................................................................................... Find igs database================================================ Query_seq: PI1197:PI1198|PI1197:PI1198:pseudouridylate synthetase:acetyltransferase:->->:1114550..1114721 172 ctgaacgtacttttcctttttcttatatgaattatctttcctcattctgccgcaaaggtacaatgtttcctgttttaaacaatgaatagtagctatcgaaggcgttaatgattattaatataatgtataaaagcaatcgtaaataacgtttaatcttacggtggttttctta Intra-Species Hit: Count: 1 Min: 1 Max: 172 Len: 172 Subject: pint_PI1197_PI1198|pseudouridylate synthetase:acetyltransferase|POSITIVE:POSITIVE|[1114550, 1114721]|172 HSP 1 e-value: 5.0E-93 bit: 341.0 Len: 172 Query Start:1 Query End:172 Subject Strand: POSITIVE Subject Start: 1 Subject End: 172 ctgaacgtacttttcctttttcttatatgaattatctttcctcattctgccgcaaaggtacaatgtttcctgttttaaacaatgaatagtagctatcgaaggcgttaatgattattaatataatgtataaaagcaatcgtaaataacgtttaatcttacggtggttttctta ctgaacgtacttttcctttttcttatatgaattatctttcctcattctgccgcaaaggtacaatgtttcctgttttaaacaatgaatagtagctatcgaaggcgttaatgattattaatataatgtataaaagcaatcgtaaataacgtttaatcttacggtggttttctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAACGUACUUUUCCUUUUUCUUAUAUGAAUUAUCUUUCCUCAUUCUGCCGCAAAGGUACAAUGUUUCCUGUUUUAAACAAUGAAUAGUAGCUAUCGAAGGCGUUAAUGAUUAUUAAUAUAAUGUAUAAAAGCAAUCGUAAAUAACGUUUAAUCUUACGGUGGUUUUCUUA ...................(((......)))...........((((.((((.....)))).))))....((((((........)))))).(((((((((((((((((((((((.((..((((...))))..)).))))))...)))))).....))).))))))))...... (-23.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAAAACCACCGUAAGAUUAAACGUUAUUUACGAUUGCUUUUAUACAUUAUAUUAAUAAUCAUUAACGCCUUCGAUAGCUACUAUUCAUUGUUUAAAACAGGAAACAUUGUACCUUUGCGGCAGAAUGAGGAAAGAUAAUUCAUAUAAGAAAAAGGAAAAGUACGUUCAG ...(((......((((((...........))))))..(((((((.....((((((.(((.(((.((..(.(.(((....((.......((.(((((........))))).)).......))....))).).)..))))).))).))))))........)))))))..))).. (-21.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 170 125 167 127 pint:PI1495|5end_conserved_hypothetical_protein_1414432..1414662_POSITIVE 293 76 47 228 200 pint:PI0939|5end_TonB-dependent_outer_membrane_protein_869869..870099_POSITIVE 260 60 13 178 116 pint:PI1438|5end_penicillin_tolerance_protein/steroid_biosynthesis_1356263..1356493_POSITIVE 252 162 123 222 189 pint:PI1796|5end_2-hydroxyhepta-2,4-diene-1,7-dioate_isomerase,_fumarylacetoacetate_hydrolase_family_protein_1730452..1730682_POSITIVE 244 74 36 214 175 pint:PI1818|5end_hypothetical_protein_1756891..1757121_POSITIVE 243 66 25 176 137 pint:PI1189|5end_conserved_hypothetical_protein_1107114..1107344_POSITIVE 243 71 44 173 152 pint:PI1048|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_966277..966507_POSITIVE 242 72 40 223 200 pint:PI0266|5end_DNA_primase_(bacterial_type)_257931..258161_POSITIVE 241 72 31 85 34 pint:PI1390|5end_hypothetical_protein_1311154..1311384_POSITIVE 239 89 45 201 148 pint:PI1549|5end_conserved_hypothetical_protein_1467021..1467251_POSITIVE 239 72 33 102 56 pint:PI0098|5end_conserved_hypothetical_protein_(possible_glycosyl/glycerophosphate_transferase)_94622..94852_POSITIVE 237 76 38 137 101 pint:PI0612|5end_lysyl-tRNA_synthetase_560461..560691_POSITIVE 235 129 83 111 57 pint:PI0903|5end_conserved_hypothetical_protein_832674..832904_POSITIVE 233 59 14 221 162 pint:PI0336|5end_hypothetical_protein_314499..314729_POSITIVE 232 58 11 195 144 pint:PI0396|5end_possible_tetracycline_resistance_element_mobilization_regulatory_protein,_C-terminal_fragment_361993..362223_POSITIVE 231 72 35 109 69 pint:PI1558|5end_conserved_hypothetical_protein_1473957..1474187_POSITIVE 230 111 82 105 76 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 229 89 41 62 7 pint:PI0242|5end_hypothetical_protein_240007..240237_POSITIVE 228 47 1 208 154 pint:PI0359|5end_hypothetical_protein_328339..328569_POSITIVE 227 105 71 68 39 pint:PI0792|5end_conserved_hypothetical_protein_729068..729298_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 60 13 67 5 pint:PI1436|3end_hypothetical_protein_1356232..1356382_POSITIVE 239 117 71 133 82 pint:PI1130|3end_probable_glucose/galactose_transporter_1057056..1057206_POSITIVE 239 72 33 82 36 pint:PI0097|3end_aspartate_aminotransferase_94682..94832_POSITIVE 233 59 14 62 3 pint:PI0335|3end_hypothetical_protein_314420..314570_POSITIVE 231 72 35 58 18 pint:PI1557|3end_conserved_hypothetical_protein_1473986..1474136_POSITIVE 227 72 45 140 114 pint:PI1554|3end_hypothetical_protein_1470483..1470633_POSITIVE 227 105 71 126 97 pint:PI0790|3end_hypothetical_protein_729206..729356_POSITIVE 225 106 69 120 82 pint:PI1916|3end_conserved_hypothetical_protein_1860740..1860890_POSITIVE 225 71 37 139 107 pint:PI0632|3end_NusB_family_protein_(N_utilization_substance_protein_B)_579731..579881_POSITIVE 225 65 27 112 70 pint:PI0251|3end_hypothetical_protein_247810..247960_POSITIVE 224 62 44 41 23 pint:PI0394|3end_transcriptional_regulator,_AraC_family_360329..360479_POSITIVE 223 75 41 49 11 pint:PI0333|3end_hypothetical_protein_313788..313938_POSITIVE 222 110 61 82 27 pint:PI1686|3end_hypothetical_protein_1601898..1602048_POSITIVE 222 50 6 147 96 pint:PI0418|3end_hypothetical_protein_386856..387006_POSITIVE 222 50 6 119 68 pint:PI0420|3end_hypothetical_protein_386828..386978_POSITIVE 221 60 15 135 77 pint:PI0190|3end_3-dehydroquinate_dehydratase_II_181126..181276_POSITIVE 221 110 67 93 50 pint:PI0031|3end_peptidylprolyl_isomerase_36131..36281_POSITIVE 220 71 36 146 104 pint:PI0301|3end_probable_transposase_285982..286132_POSITIVE 218 98 52 148 108 pint:PI2001|3end_hypothetical_protein_1960478..1960628_POSITIVE 217 76 37 135 77 pint:PI1923|3end_conserved_hypothetical_protein_1865912..1866062_POSITIVE