Origin IGS: tgagagtataaaactctcaacttattctatacaaaggtagtacttttttgcgagatatacaaatatttgtcataaaaaaacgcctcaaaataaaagatttttgaggcgtttttatgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acataaaaacgcctcaaaaatcttttattttgaggcgtttttttatgacaaatatttgtatatctcgcaaaaaagtactacctttgtatagaataagttgagagttttatactctca Mask Tandem Repeat Region ================================================ tgagagtataaaactctcaacttattctatacaaaggtagtacttttttgcgagatatacaaatatttgtcataaaaaaacgcctcaaaataaaagatttttgaggcgtttttatgt Find is-nt database================================================ Query_seq: PI0371:PI0372|PI0371:PI0372:thymidylate synthase:conserved hypothetical protein; possible ATPase:->->:342034..342150 117 tgagagtataaaactctcaacttattctatacaaaggtagtacttttttgcgagatatacaaatatttgtcataaaaaaacgcctcaaaataaaagatttttgaggcgtttttatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0371:PI0372|PI0371:PI0372:thymidylate synthase:conserved hypothetical protein; possible ATPase:->->:342034..342150 117 tgagagtataaaactctcaacttattctatacaaaggtagtacttttttgcgagatatacaaatatttgtcataaaaaaacgcctcaaaataaaagatttttgaggcgtttttatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0371:PI0372|PI0371:PI0372:thymidylate synthase:conserved hypothetical protein; possible ATPase:->->:342034..342150 117 tgagagtataaaactctcaacttattctatacaaaggtagtacttttttgcgagatatacaaatatttgtcataaaaaaacgcctcaaaataaaagatttttgaggcgtttttatgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagagtataaaactctcaacttattctatacaaaggtagtacttttttgcgagatatacaaatatttgtcataaaaaaacgcctcaaaataaaagatttttgaggcgtttttatgt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 20 End: 115 ................... S I R Y L P L V K K R S I C I N T M F F R R L I F S K Q P T K M .. tgagagtataaaactctcaacttattctatacaaaggtagtacttttttgcgagatatacaaatatttgtcataaaaaaacgcctcaaaataaaagatttttgaggcgtttttatgt 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================================================ tgagagtataaaactctcaacttattctatacaaaggtagtacttttttgcgagatatacaaatatttgtcataaaaaaacgcctcaaaataaaagatttttgaggcgtttttatgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0371:PI0372|PI0371:PI0372:thymidylate synthase:conserved hypothetical protein; possible ATPase:->->:342034..342150 117 tgagagtataaaactctcaacttattctatacaaaggtagtacttttttgcgagatatacaaatatttgtcataaaaaaacgcctcaaaataaaagatttttgaggcgtttttatgt Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: pint_PI0371_PI0372|thymidylate synthase:conserved hypothetical protein; possible ATPase|POSITIVE:POSITIVE|[342034,342150]|117 HSP 1 e-value: 7.0E-48 bit: 190.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 tgagagtataaaactctcaacttattctatacaaaggtagtacttttttgcgagatatacaaatatttgtcatnnnnnnncgcctcaaaataaaagatttttgaggcgtttttatgt tgagagtataaaactctcaacttattctatacaaaggtagtacttttttgcgagatatacaaatatttgtcataaaaaaacgcctcaaaataaaagatttttgaggcgtttttatgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGAGUAUAAAACUCUCAACUUAUUCUAUACAAAGGUAGUACUUUUUUGCGAGAUAUACAAAUAUUUGUCAUAAAAAAACGCCUCAAAAUAAAAGAUUUUUGAGGCGUUUUUAUGU (((((((.....)))))))........((((((((.(((...(((......)))...))).....))))).))).(((((((((((((((........))))))))))))))).... (-32.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUAAAAACGCCUCAAAAAUCUUUUAUUUUGAGGCGUUUUUUUAUGACAAAUAUUUGUAUAUCUCGCAAAAAAGUACUACCUUUGUAUAGAAUAAGUUGAGAGUUUUAUACUCUCA .((((((((((((((((((........)))))))))))..))))))).......(((((.......)))))...((((.......)))).........(((((((.....))))))) (-31.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 87 44 168 125 pint:PI0492|5end_hypothetical_protein_451701..451931_POSITIVE 242 52 14 201 159 pint:PI1328|5end_conserved_hypothetical_protein_1246197..1246427_POSITIVE 237 54 13 219 174 pint:PI1818|5end_hypothetical_protein_1756891..1757121_POSITIVE 237 55 14 57 1 pint:PI0950|5end_50S_ribosomal_protein_L31_883327..883557_POSITIVE 236 110 79 213 182 pint:PI1339|5end_hypothetical_protein_1256671..1256901_POSITIVE 236 110 79 110 79 pint:PI1340|5end_hypothetical_protein_1256568..1256798_POSITIVE 213 63 32 211 181 pint:PI1622|5end_hypothetical_protein_1546782..1547012_POSITIVE 206 55 13 178 143 pint:PI0382|5end_conserved_hypothetical_protein_351510..351740_POSITIVE 200 72 32 45 1 pint:PI1545|5end_conserved_hypothetical_protein_1463587..1463817_POSITIVE 199 53 12 216 174 pint:PI0363|5end_hypothetical_protein_332832..333062_POSITIVE 196 60 42 229 211 pint:PI0855|5end_hypothetical_protein_789094..789324_POSITIVE 193 37 4 86 55 pint:PI1488|5end_hypothetical_protein_1406994..1407224_POSITIVE 193 50 17 40 3 pint:PI0373|5end_hypothetical_protein_344293..344523_POSITIVE 191 85 43 154 118 pint:PI0407|5end_tryptophanyl-tRNA_synthetase_(tryptophan--tRNA_ligase)_372973..373203_POSITIVE 188 71 36 179 146 pint:PI2172|5end_hypothetical_protein_2113819..2114049_POSITIVE 188 71 36 155 122 pint:PI2173|5end_hypothetical_protein_2113795..2114025_POSITIVE 186 46 1 216 173 pint:PI0438|5end_elongation_factor_Tu_409037..409267_POSITIVE 184 51 14 89 58 pint:PI1846|5end_hypothetical_protein_1791705..1791935_POSITIVE 183 50 1 145 97 pint:PI0527|5end_outer_membrane_efflux_protein_482375..482605_POSITIVE 183 51 12 146 103 pint:PI0026|5end_two-component_system_response_regulator_29756..29986_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 69 21 85 37 pint:PI0976|3end_dihydrolipoamide_dehydrogenase_(dihydrolipoyl_dehydrogenanse)_903732..903882_POSITIVE 236 110 79 56 25 pint:PI1338|3end_phosphoserine_phosphatase_1256594..1256744_POSITIVE 216 72 31 57 12 pint:PI1544|3end_hypothetical_protein_1463679..1463829_POSITIVE 206 55 13 142 107 pint:PI0381|3end_probable_transcriptional_regulator,_AraC_family_351554..351704_POSITIVE 196 108 80 111 82 pint:PI1638|3end_conserved_hypothetical_protein_1556613..1556763_POSITIVE 193 37 4 74 43 pint:PI1486|3end_alginate_O-acetylation_protein_1407062..1407212_POSITIVE 188 71 36 111 78 pint:PI2171|3end_conserved_hypothetical_protein_2113831..2113981_POSITIVE 188 65 25 141 106 pint:PI0984|3end_hypothetical_protein_910144..910294_POSITIVE 184 51 14 56 25 pint:PI1845|3end_hypothetical_protein_1791752..1791902_POSITIVE 183 50 1 129 81 pint:PI0526|3end_hypothetical_protein_482439..482589_POSITIVE 183 51 12 133 90 pint:PI0025|3end_two_component_system_sensor_histidine_kinase_29823..29973_POSITIVE 180 51 14 56 25 pint:PI1839|3end_hypothetical_protein_1782500..1782650_POSITIVE 179 83 45 86 53 pint:PI0597|3end_hypothetical_protein_547062..547212_POSITIVE 177 54 32 35 2 pint:PI1332|3end_aminotransferase,_possible_pyridoxal-phosphate-dependent_aminotransferase_1250566..1250716_POSITIVE 176 107 73 133 104 pint:PI1806|3end_integral_membrane_transport_protein;_possible_sugar_transport_proteins_1742191..1742341_POSITIVE 176 109 77 78 38 pint:PI0268|3end_lysozyme-related_protein_259790..259940_POSITIVE 174 68 22 53 1 pint:PI0491|3end_hypothetical_protein_451227..451377_POSITIVE 173 107 77 119 93 pint:PI1912|3end_possible_DNA_repair_protein_1857166..1857316_POSITIVE 172 55 29 149 124 pint:PI0684|3end_coproporphyrinogen_III_oxidase_620507..620657_POSITIVE 170 43 2 82 41 pint:PI0081|3end_hypothetical_protein_80700..80850_POSITIVE