Origin IGS: taacttaaaaggactgaaaggataaaagcaataaaagaaacagtcaaaagcttatgagcttttcaaagaagattgatacacgaatattcatcaaacaataaataca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgtatttattgtttgatgaatattcgtgtatcaatcttctttgaaaagctcataagcttttgactgtttcttttattgcttttatcctttcagtccttttaagtta Mask Tandem Repeat Region ================================================ taacttaaaaggactgaaaggataaaagcaataaaagaaacagtcaaaagcttatgagcttttcaaagaagattgatacacgaatattcatcaaacaataaataca Find is-nt database================================================ Query_seq: PI0239:PI0240|PI0239:PI0240:conserved hypothetical protein:conserved hypothetical protein:->->:238496..238601 106 taacttaaaaggactgaaaggataaaagcaataaaagaaacagtcaaaagcttatgagcttttcaaagaagattgatacacgaatattcatcaaacaataaataca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0239:PI0240|PI0239:PI0240:conserved hypothetical protein:conserved hypothetical protein:->->:238496..238601 106 taacttaaaaggactgaaaggataaaagcaataaaagaaacagtcaaaagcttatgagcttttcaaagaagattgatacacgaatattcatcaaacaataaataca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0239:PI0240|PI0239:PI0240:conserved hypothetical protein:conserved hypothetical protein:->->:238496..238601 106 taacttaaaaggactgaaaggataaaagcaataaaagaaacagtcaaaagcttatgagcttttcaaagaagattgatacacgaatattcatcaaacaataaataca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacttaaaaggactgaaaggataaaagcaataaaagaaacagtcaaaagcttatgagcttttcaaagaagattgatacacgaatattcatcaaacaataaataca Predict ORF larger than 30AA ================================================ taacttaaaaggactgaaaggataaaagcaataaaagaaacagtcaaaagcttatgagcttttcaaagaagattgatacacgaatattcatcaaacaataaataca 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: 86 Start: 19 End: 48 ..................TTTGACTGTTTCTTTTATTGCTTTTATCCT.......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taacttaaaaggactgaaaggataaaagcaataaaagaaacagtcaaaagcttatgagcttttcaaagaagattgatacacgaatattcatcaaacaataaataca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0239:PI0240|PI0239:PI0240:conserved hypothetical protein:conserved hypothetical protein:->->:238496..238601 106 taacttaaaaggactgaaaggataaaagcaataaaagaaacagtcaaaagcttatgagcttttcaaagaagattgatacacgaatattcatcaaacaataaataca Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: pint_PI0239_PI0240|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[238496,238601]|106 HSP 1 e-value: 6.0E-54 bit: 210.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 106 taacttaaaaggactgaaaggataaaagcaataaaagaaacagtcaaaagcttatgagcttttcaaagaagattgatacacgaatattcatcaaacaataaataca taacttaaaaggactgaaaggataaaagcaataaaagaaacagtcaaaagcttatgagcttttcaaagaagattgatacacgaatattcatcaaacaataaataca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACUUAAAAGGACUGAAAGGAUAAAAGCAAUAAAAGAAACAGUCAAAAGCUUAUGAGCUUUUCAAAGAAGAUUGAUACACGAAUAUUCAUCAAACAAUAAAUACA ...(((.....(((((........................))))).((((((....))))))...)))..(((.((((......)))).))).............. (-10.66) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAUUUAUUGUUUGAUGAAUAUUCGUGUAUCAAUCUUCUUUGAAAAGCUCAUAAGCUUUUGACUGUUUCUUUUAUUGCUUUUAUCCUUUCAGUCCUUUUAAGUUA .(((((((((....)))))))))..((...((((......))))...)).....(((((..(((((........................))))).....))))). (-12.86) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 59 20 96 54 pint:PI0245|5end_possible_mobilization_protein_242946..243176_POSITIVE 233 69 24 223 172 pint:PI0553|5end_recombination_protein_503344..503574_POSITIVE 207 52 11 66 11 pint:PI0608|5end_isochorismate_synthase_555487..555717_POSITIVE 206 60 16 117 80 pint:PI0607|5end_2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxy_lic_acid_synthase/2-oxoglutarate_decarboxylase_553801..554031_POSITIVE 202 90 49 90 50 pint:PI0026|5end_two-component_system_response_regulator_29756..29986_POSITIVE 196 50 2 87 25 pint:PI1579|5end_penicillin-binding_protein_2_1505713..1505943_POSITIVE 195 66 28 218 168 pint:PI0188|5end_phosphomethylpyrimidine_kinase_178433..178663_POSITIVE 194 30 9 200 179 pint:PI0201|5end_hypothetical_protein_195070..195300_POSITIVE 189 57 11 124 59 pint:PI1858|5end_conserved_hypothetical_protein_1804400..1804630_POSITIVE 189 78 35 93 45 pint:PI1529|5end_cytosine/adenosine_deaminase_1449887..1450117_POSITIVE 189 48 14 80 47 pint:PI0598|5end_hypothetical_protein_547061..547291_POSITIVE 187 60 11 127 65 pint:PI1794|5end_conserved_hypothetical_protein_1725609..1725839_POSITIVE 187 60 11 179 128 pint:PI0784|5end_possible_amidase_enhancer_precursor_721892..722122_POSITIVE 186 77 39 196 156 pint:PI0581|5end_conserved_hypothetical_protein_525055..525285_POSITIVE 183 95 56 50 5 pint:PI1086|5end_pyruvate:ferredoxin_oxidoreductase_1006602..1006832_POSITIVE 183 57 11 94 40 pint:PI0386|5end_integrase_354369..354599_POSITIVE 182 60 12 123 77 pint:PI1492|5end_triosephosphate_isomerase_1410155..1410385_POSITIVE 180 59 14 111 75 pint:PI1925|5end_conserved_hypothetical_protein_1866387..1866617_POSITIVE 180 83 48 51 20 pint:PI1134|5end_ABC_transporter,_ATP-binding_protein_1060374..1060604_POSITIVE 180 94 55 159 118 pint:PI0453|5end_conserved_hypothetical_protein_426797..427027_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 242 83 41 98 70 pint:PI1493|3end_conserved_hypothetical_protein_1412818..1412968_POSITIVE 233 69 24 134 83 pint:PI0552|3end_hypothetical_protein_503335..503485_POSITIVE 207 100 55 51 4 pint:PI2052|3end_hypothetical_protein_2009696..2009846_POSITIVE 207 95 54 118 75 pint:PI0576|3end_helicase,_UvrD/Rep_521724..521874_POSITIVE 202 70 27 67 20 pint:PI0058|3end_conserved_hypothetical_protein_57044..57194_POSITIVE 202 90 49 77 37 pint:PI0025|3end_two_component_system_sensor_histidine_kinase_29823..29973_POSITIVE 190 97 59 124 72 pint:PI1882|3end_hypothetical_protein_1826487..1826637_POSITIVE 187 60 11 82 20 pint:PI1793|3end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_1725644..1725794_POSITIVE 187 60 11 147 94 pint:PI1749|3end_conserved_hypothetical_protein_1671637..1671787_POSITIVE 187 60 11 134 83 pint:PI0782|3end_beta-lactamase_induction_signal_transducer,_AmpG_protein_721927..722077_POSITIVE 186 82 41 73 21 pint:PI1222|3end_hypothetical_protein_1143378..1143528_POSITIVE 183 57 11 94 40 pint:PI0385|3end_hypothetical_protein_354449..354599_POSITIVE 182 60 12 76 30 pint:PI1491|3end_conserved_hypothetical_protein_1410188..1410338_POSITIVE 181 40 4 149 117 pint:PI0803|3end_DNA-damage-inducible_protein_F_741171..741321_POSITIVE 180 59 14 139 103 pint:PI1924|3end_cytidine_deaminase_1866495..1866645_POSITIVE 180 94 55 73 32 pint:PI0452|3end_conserved_hypothetical_protein;_possible_surface_antigen_426791..426941_POSITIVE 180 73 36 76 40 pint:PI0192|3end_conserved_hypothetical_protein_184826..184976_POSITIVE 179 80 48 59 31 pint:PI1714|3end_ISPg3-related_transposase_1631352..1631502_POSITIVE 179 63 46 45 28 pint:PI0239|3end_conserved_hypothetical_protein_238435..238585_POSITIVE 177 42 11 42 17 pint:PI1962|3end_conserved_hypothetical_protein_1920706..1920856_POSITIVE