Origin IGS: gtttggcaaacctactataccacattttaatgccatattctaaataaacgtttattttcttttggtgcaaaaatactgttttattttgatattaatcatcaatagaacattattttgcacttcggttctaaatcttgagcgtattttacgtgagctttattcgcctctgtcttgcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagcaagacagaggcgaataaagctcacgtaaaatacgctcaagatttagaaccgaagtgcaaaataatgttctattgatgattaatatcaaaataaaacagtatttttgcaccaaaagaaaataaacgtttatttagaatatggcattaaaatgtggtatagtaggtttgccaaac Mask Tandem Repeat Region ================================================ gtttggcaaacctactataccacattttaatgccatattctaaataaacgtttattttcttttggtgcaaaaatactgttttattttgatattaatcatcaatagaacattattttgcacttcggttctaaatcttgagcgtattttacgtgagctttattcgcctctgtcttgcta Find is-nt database================================================ Query_seq: PI2147:PI2148|PI2147:PI2148:GTP-binding protein:ribonuclease III:->->:2094468..2094644 177 gtttggcaaacctactataccacattttaatgccatattctaaataaacgtttattttcttttggtgcaaaaatactgttttattttgatattaatcatcaatagaacattattttgcacttcggttctaaatcttgagcgtattttacgtgagctttattcgcctctgtcttgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI2147:PI2148|PI2147:PI2148:GTP-binding protein:ribonuclease III:->->:2094468..2094644 177 gtttggcaaacctactataccacattttaatgccatattctaaataaacgtttattttcttttggtgcaaaaatactgttttattttgatattaatcatcaatagaacattattttgcacttcggttctaaatcttgagcgtattttacgtgagctttattcgcctctgtcttgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI2147:PI2148|PI2147:PI2148:GTP-binding protein:ribonuclease III:->->:2094468..2094644 177 gtttggcaaacctactataccacattttaatgccatattctaaataaacgtttattttcttttggtgcaaaaatactgttttattttgatattaatcatcaatagaacattattttgcacttcggttctaaatcttgagcgtattttacgtgagctttattcgcctctgtcttgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttggcaaacctactataccacattttaatgccatattctaaataaacgtttattttcttttggtgcaaaaatactgttttattttgatattaatcatcaatagaacattattttgcacttcggttctaaatcttgagcgtattttacgtgagctttattcgcctctgtcttgcta Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 44 End: 175 ........................................... M N V Y F L L V Q K Y C F I L I L I I N R T L F C T S V L N L E R I L R E L Y S P L S C .. Protein_Len: 30 Strand: - Start: 55 End: 144 ...................................................... K R K T C F Y Q K I K I N I M L L V N N Q V E T R F R S R M ................................. gtttggcaaacctactataccacattttaatgccatattctaaataaacgtttattttcttttggtgcaaaaatactgttttattttgatattaatcatcaatagaacattattttgcacttcggttctaaatcttgagcgtattttacgtgagctttattcgcctctgtcttgcta 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: 82 Start: 2 End: 31 .TTTGGCAAACCTACTATACCACATTTTAAT.................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtttggcaaacctactataccacattttaatgccatattctaaataaacgtttattttcttttggtgcaaaaatactgttttattttgatattaatcatcaatagaacattattttgcacttcggttctaaatcttgagcgtattttacgtgagctttattcgcctctgtcttgcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI2147:PI2148|PI2147:PI2148:GTP-binding protein:ribonuclease III:->->:2094468..2094644 177 gtttggcaaacctactataccacattttaatgccatattctaaataaacgtttattttcttttggtgcaaaaatactgttttattttgatattaatcatcaatagaacattattttgcacttcggttctaaatcttgagcgtattttacgtgagctttattcgcctctgtcttgcta Intra-Species Hit: Count: 1 Min: 1 Max: 177 Len: 177 Subject: pint_PI2147_PI2148|GTP-binding protein:ribonuclease III|POSITIVE:POSITIVE|[2094468,2094644]|177 HSP 1 e-value: 5.0E-96 bit: 351.0 Len: 177 Query Start:1 Query End:177 Subject Strand: POSITIVE Subject Start: 1 Subject End: 177 gtttggcaaacctactataccacattttaatgccatattctaaataaacgtttattttcttttggtgcaaaaatactgttttattttgatattaatcatcaatagaacattattttgcacttcggttctaaatcttgagcgtattttacgtgagctttattcgcctctgtcttgcta gtttggcaaacctactataccacattttaatgccatattctaaataaacgtttattttcttttggtgcaaaaatactgttttattttgatattaatcatcaatagaacattattttgcacttcggttctaaatcttgagcgtattttacgtgagctttattcgcctctgtcttgcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUGGCAAACCUACUAUACCACAUUUUAAUGCCAUAUUCUAAAUAAACGUUUAUUUUCUUUUGGUGCAAAAAUACUGUUUUAUUUUGAUAUUAAUCAUCAAUAGAACAUUAUUUUGCACUUCGGUUCUAAAUCUUGAGCGUAUUUUACGUGAGCUUUAUUCGCCUCUGUCUUGCUA ((..((((........(((((.((.((((..(((.......((((((....))))))......(((((((((.((.(((((((((.((((....))))..))))))))).)))))))))))..)))..))))...)).).)))).....(((((.....)))))...))))..)).. (-33.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCAAGACAGAGGCGAAUAAAGCUCACGUAAAAUACGCUCAAGAUUUAGAACCGAAGUGCAAAAUAAUGUUCUAUUGAUGAUUAAUAUCAAAAUAAAACAGUAUUUUUGCACCAAAAGAAAAUAAACGUUUAUUUAGAAUAUGGCAUUAAAAUGUGGUAUAGUAGGUUUGCCAAAC ............(((((((...((..((((......((.((........))..))..((((((((...((((.((((..((((....)))).)))).))))....)))))))).............)))).........((((.((((....)))).)))).))..))))))).... (-33.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 166 122 184 143 pint:PI0583|5end_hypothetical_protein_525948..526178_POSITIVE 289 159 112 117 54 pint:PI1619|5end_two-component_system_response_regulator_1543210..1543440_POSITIVE 272 166 121 97 28 pint:PI2137|5end_RNA_methylase_SpoU_family_2083173..2083403_POSITIVE 265 155 116 145 110 pint:PI0584|5end_hypothetical_protein_527352..527582_POSITIVE 263 168 135 42 8 pint:PI0355|5end_probable__N-acetylmuramoyl-L-alanine_amidase_326157..326387_POSITIVE 262 167 123 131 91 pint:PI1650|5end_N-acetylmuramoyl-L-alanine_amidase_1563195..1563425_POSITIVE 257 169 121 199 143 pint:PI0197|5end_acetate_kinase_188602..188832_POSITIVE 252 170 137 48 10 pint:PI0364|5end_hypothetical_protein_334002..334232_POSITIVE 246 170 124 121 64 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 241 156 119 37 2 pint:PI1923|5end_conserved_hypothetical_protein_1865560..1865790_POSITIVE 240 157 117 173 141 pint:PI2063|5end_conserved_hypothetical_protein_2023946..2024176_POSITIVE 238 155 115 62 27 pint:PI2020|5end_glycosyl_transferase,_group_2_family_protein_1976866..1977096_POSITIVE 238 168 121 74 15 pint:PI0146|5end_transcription_elongation_factor_140338..140568_POSITIVE 232 168 122 190 143 pint:PI0361|5end_hypothetical_protein_333062..333292_POSITIVE 231 170 122 90 33 pint:PI1605|5end_conserved_hypothetical_protein_1534244..1534474_POSITIVE 229 168 122 74 40 pint:PI0248|5end_protein_associated_with_conjugate_transformation/chromosome_partioning_246139..246369_POSITIVE 228 160 114 120 66 pint:PI0414|5end_hypothetical_protein_384327..384557_POSITIVE 225 169 133 50 10 pint:PI1634|5end_conserved_hypothetical_protein_1553179..1553409_POSITIVE 225 169 133 50 10 pint:PI0340|5end_conserved_hypothetical_protein_316095..316325_POSITIVE 224 140 96 181 135 pint:PI0740|5end_hypothetical_protein_672112..672342_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 165 131 60 23 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 272 166 121 97 28 pint:PI2135|3end_conserved_hypothetical_protein_2083253..2083403_POSITIVE 266 168 124 46 3 pint:PI0354|3end_hypothetical_protein_326241..326391_POSITIVE 252 156 116 146 92 pint:PI1171|3end_hypothetical_protein_1091836..1091986_POSITIVE 246 170 121 149 92 pint:PI0444|3end_50S_ribosomal_protein_L7/L12_413390..413540_POSITIVE 246 170 121 118 61 pint:PI0445|3end_conserved_hypothetical_protein_413359..413509_POSITIVE 235 169 122 49 1 pint:PI1649|3end_hypothetical_protein_1563441..1563591_POSITIVE 232 170 123 117 53 pint:PI0583|3end_hypothetical_protein_526276..526426_POSITIVE 231 155 115 151 110 pint:PI0563|3end_possible_integral_membrane_protein_511179..511329_POSITIVE 229 168 122 87 53 pint:PI0247|3end_conjugative_transposon_protein,_TraA_246232..246382_POSITIVE 225 170 123 65 1 pint:PI0849|3end_hypothetical_protein_783542..783692_POSITIVE 224 155 118 77 28 pint:PI1621|3end_hypothetical_protein_1545740..1545890_POSITIVE 224 140 96 150 104 pint:PI0739|3end_conserved_hypothetical_protein_672161..672311_POSITIVE 222 155 118 77 28 pint:PI0327|3end_hypothetical_protein_309107..309257_POSITIVE 222 155 117 133 102 pint:PI0027|3end_aminopeptidase_C_31756..31906_POSITIVE 219 158 118 139 94 pint:PI0639|3end_small_heat_shock_protein_583165..583315_POSITIVE 216 159 118 101 37 pint:PI2068|3end_hypothetical_protein_2028800..2028950_POSITIVE 216 170 121 140 91 pint:PI0252|3end_conserved_hypothetical_protein_248383..248533_POSITIVE 213 165 124 151 112 pint:PI0630|3end_peptidyl-tRNA_hydrolase_(aminoacyl-tRNA_hydrolase)_577694..577844_POSITIVE 212 168 124 87 41 pint:PI1223|3end_conserved_hypothetical_protein_1144459..1144609_POSITIVE