Origin IGS: accaaaattccaacacatttcttaatgaaatggaattataaagaacctcgggtaaaattcatagtaagcgacgcagtttatttgttataaaattgtgataaaaacagccttattctgttaaaaacacctcaaaaatgccaaatatttttgacgtgcatcaaatattaaaaattaattaaaaaaagactttggttccaggtcaaattaatttgaaaacttcaaaatttttgataaaatccgcaccgttcaattaatatacaaacgcgccaaatttaggaggcattt .........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 aaatgcctcctaaatttggcgcgtttgtatattaattgaacggtgcggattttatcaaaaattttgaagttttcaaattaatttgacctggaaccaaagtctttttttaattaatttttaatatttgatgcacgtcaaaaatatttggcatttttgaggtgtttttaacagaataaggctgtttttatcacaattttataacaaataaactgcgtcgcttactatgaattttacccgaggttctttataattccatttcattaagaaatgtgttggaattttggt Mask Tandem Repeat Region ================================================ accaaaattccaacacatttcttaatgaaatggaattataaagaacctcgggtaaaattcatagtaagcgacgcagtttatttgttataaaattgtgataaaaacagccttattctgttaaaaacacctcaaaaatgccaaatatttttgacgtgcatcaaatattaaaaattaattaaaaaaagactttggttccaggtcaaattaatttgaaaacttcaaaatttttgataaaatccgcaccgttcaattaatatacaaacgcgccaaatttaggaggcattt Find is-nt database================================================ Query_seq: AA03000:AA03001|AA03000:AA03001:uracil-DNA glycosylase (UDG):probable glycyl radical protein/pyruvate-formate lyase:->->:2095882..2096166 285 accaaaattccaacacatttcttaatgaaatggaattataaagaacctcgggtaaaattcatagtaagcgacgcagtttatttgttataaaattgtgataaaaacagccttattctgttaaaaacacctcaaaaatgccaaatatttttgacgtgcatcaaatattaaaaattaattaaaaaaagactttggttccaggtcaaattaatttgaaaacttcaaaatttttgataaaatccgcaccgttcaattaatatacaaacgcgccaaatttaggaggcattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA03000:AA03001|AA03000:AA03001:uracil-DNA glycosylase (UDG):probable glycyl radical protein/pyruvate-formate lyase:->->:2095882..2096166 285 accaaaattccaacacatttcttaatgaaatggaattataaagaacctcgggtaaaattcatagtaagcgacgcagtttatttgttataaaattgtgataaaaacagccttattctgttaaaaacacctcaaaaatgccaaatatttttgacgtgcatcaaatattaaaaattaattaaaaaaagactttggttccaggtcaaattaatttgaaaacttcaaaatttttgataaaatccgcaccgttcaattaatatacaaacgcgccaaatttaggaggcattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA03000:AA03001|AA03000:AA03001:uracil-DNA glycosylase (UDG):probable glycyl radical protein/pyruvate-formate lyase:->->:2095882..2096166 285 accaaaattccaacacatttcttaatgaaatggaattataaagaacctcgggtaaaattcatagtaagcgacgcagtttatttgttataaaattgtgataaaaacagccttattctgttaaaaacacctcaaaaatgccaaatatttttgacgtgcatcaaatattaaaaattaattaaaaaaagactttggttccaggtcaaattaatttgaaaacttcaaaatttttgataaaatccgcaccgttcaattaatatacaaacgcgccaaatttaggaggcattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accaaaattccaacacatttcttaatgaaatggaattataaagaacctcgggtaaaattcatagtaagcgacgcagtttatttgttataaaattgtgataaaaacagccttattctgttaaaaacacctcaaaaatgccaaatatttttgacgtgcatcaaatattaaaaattaattaaaaaaagactttggttccaggtcaaattaatttgaaaacttcaaaatttttgataaaatccgcaccgttcaattaatatacaaacgcgccaaatttaggaggcattt Predict ORF larger than 30AA ================================================ accaaaattccaacacatttcttaatgaaatggaattataaagaacctcgggtaaaattcatagtaagcgacgcagtttatttgttataaaattgtgataaaaacagccttattctgttaaaaacacctcaaaaatgccaaatatttttgacgtgcatcaaatattaaaaattaattaaaaaaagactttggttccaggtcaaattaatttgaaaacttcaaaatttttgataaaatccgcaccgttcaattaatatacaaacgcgccaaatttaggaggcattt 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: 175 End: 204 ..............................................................................................................................................................................TTTGACCTGGAACCAAAGTCTTTTTTTAAT................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 208 End: 237 ...............................................................................................................................................................................................................ATTTGAAAACTTCAAAATTTTTGATAAAAT................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ accaaaattccaacacatttcttaatgaaatggaattataaagaacctcgggtaaaattcatagtaagcgacgcagtttatttgttataaaattgtgataaaaacagccttattctgttaaaaacacctcaaaaatgccaaatatttttgacgtgcatcaaatattaaaaattaattaaaaaaagactttggttccaggtcaaattaatttgaaaacttcaaaatttttgataaaatccgcaccgttcaattaatatacaaacgcgccaaatttaggaggcattt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -5.6 Tail_Score: -4.57569 Start: 125 End: 155 Full_Region: ttttaatatttgatg cacgtcaaaaat atttggc atttttgaggtg tttttaacagaataa ............................................................................................................................cacgtcaaaaatatttggcatttttgaggtg.................................................................................................................................. Find igs database================================================ Query_seq: AA03000:AA03001|AA03000:AA03001:uracil-DNA glycosylase (UDG):probable glycyl radical protein/pyruvate-formate lyase:->->:2095882..2096166 285 accaaaattccaacacatttcttaatgaaatggaattataaagaacctcgggtaaaattcatagtaagcgacgcagtttatttgttataaaattgtgataaaaacagccttattctgttaaaaacacctcaaaaatgccaaatatttttgacgtgcatcaaatattaaaaattaattaaaaaaagactttggttccaggtcaaattaatttgaaaacttcaaaatttttgataaaatccgcaccgttcaattaatatacaaacgcgccaaatttaggaggcattt Intra-Species Hit: Count: 1 Min: 1 Max: 285 Len: 285 Subject: aact_AA03000_AA03001|uracil-DNA glycosylase (UDG):probable glycyl radical protein/pyruvate-formate lyase|POSITIVE:POSITIVE|[2095882,2096166]|285 HSP 1 e-value: 1.0E-60 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 accaaaattccaacacatttcttaatgaaatggaattataaagaacctcgggtaaaattcatagtaagcgacgcagtttatttgttataaaattgtgataaaaacagccttattctgt....................................................................................................................................................................... accaaaattccaacacatttcttaatgaaatggaattataaagaacctcgggtaaaattcatagtaagcgacgcagtttatttgttataaaattgtgataaaaacagccttattctgt....................................................................................................................................................................... HSP 2 e-value: 2.0E-50 bit: 200.0 Len: 101 Query Start:185 Query End:285 Subject Strand: POSITIVE Subject Start: 185 Subject End: 285 ........................................................................................................................................................................................gactttggttccaggtcaaattaatttgaaaacttcaaaatttttgataaaatccgcaccgttcaattaatatacaaacgcgccaaatttaggaggcattt ........................................................................................................................................................................................gactttggttccaggtcaaattaatttgaaaacttcaaaatttttgataaaatccgcaccgttcaattaatatacaaacgcgccaaatttaggaggcattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCAAAAUUCCAACACAUUUCUUAAUGAAAUGGAAUUAUAAAGAACCUCGGGUAAAAUUCAUAGUAAGCGACGCAGUUUAUUUGUUAUAAAAUUGUGAUAAAAACAGCCUUAUUCUGUUAAAAACACCUCAAAAAUGCCAAAUAUUUUUGACGUGCAUCAAAUAUUAAAAAUUAAUUAAAAAAAGACUUUGGUUCCAGGUCAAAUUAAUUUGAAAACUUCAAAAUUUUUGAUAAAAUCCGCACCGUUCAAUUAAUAUACAAACGCGCCAAAUUUAGGAGGCAUUU .....(((((((...((((....))))...))))))).....((((..(((((......((.((((((....((.((((..((((((((....)))))))))))).)))))))).)).......(((.(((((((((.....))))))))).))).......(((((((((((...........(((((.(....))))))........((((.....)))))))))))))))..)))))....)))).................(((..........))).... (-48.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUGCCUCCUAAAUUUGGCGCGUUUGUAUAUUAAUUGAACGGUGCGGAUUUUAUCAAAAAUUUUGAAGUUUUCAAAUUAAUUUGACCUGGAACCAAAGUCUUUUUUUAAUUAAUUUUUAAUAUUUGAUGCACGUCAAAAAUAUUUGGCAUUUUUGAGGUGUUUUUAACAGAAUAAGGCUGUUUUUAUCACAAUUUUAUAACAAAUAAACUGCGUCGCUUACUAUGAAUUUUACCCGAGGUUCUUUAUAAUUCCAUUUCAUUAAGAAAUGUGUUGGAAUUUUGGU .................((((((((((((((..(((((...(((.(((......(((((...(((((.....)))))....))))).)))..)))..((((((.((((.((((.....))))..((((.((((.((((((((.......)))))))).))))..)))).)))).))))))..........))))).))).)))))).....)))))..................((((((((((..(((....((((((.....))))))))).)))))))))). (-52.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 280 238 227 179 aact:AA00803|5end_hypothetical_protein_549526..549756_POSITIVE 253 243 204 117 75 aact:AA01141|5end_conserved_hypothetical_protein_(possible_component_of_anaerobic_dehydrogenase/oxidoreductase)_782497..782727_POSITIVE 251 74 31 201 156 aact:AA01547|5end_deoxyribose-phosphate_aldolase_1036271..1036501_POSITIVE 249 280 236 87 44 aact:AA01411|5end_stationary-phase_survival_protein_951000..951230_POSITIVE 247 280 234 83 30 aact:AA00816|5end_lacZ_expression_regulator_560900..561130_POSITIVE 245 270 233 158 117 aact:AA02230|5end_sugar_kinase_1515984..1516214_POSITIVE 238 269 223 221 173 aact:AA01496|5end_glucose_inhibited_division_protein_A_1005125..1005355_POSITIVE 237 140 94 63 14 aact:AA02088|5end_glycogen_operon_protein_1421282..1421512_POSITIVE 237 270 238 63 32 aact:AA00429|5end_conserved_hypothetical_protein_290567..290797_POSITIVE 237 268 237 101 78 aact:AA00329|5end_molybdopterin-guanine_dinucleotide_biosynthesis_protein_222737..222967_POSITIVE 236 96 64 215 176 aact:AA01718|5end_DNA_polymerase_III,_chi_subunit_1162790..1163020_POSITIVE 235 280 234 67 18 aact:AA01423|5end_cell_division_protein_X,_ABC_system_permease_956668..956898_POSITIVE 234 86 45 75 23 aact:AA01852|5end_peptide_chain_release_factor_3_1244891..1245121_POSITIVE 234 279 238 113 64 aact:AA01745|5end_conserved_hypothetical_protein_(possible_peptide_chain_release_factor_2)_1180394..1180624_POSITIVE 234 105 66 61 22 aact:AA00179|5end_conserved_hypothetical_protein_(possible_outer_membrane_protein)_126260..126490_POSITIVE 232 200 151 70 15 aact:AA02091|5end_hypothetical_protein_1424441..1424671_POSITIVE 231 109 67 166 132 aact:AA00259|5end_conserved_hypothetical_protein_182788..183018_POSITIVE 230 268 236 211 173 aact:AA00961|5end_conserved_hypothetical_protein_667179..667409_POSITIVE 229 120 75 206 162 aact:AA01984|5end_tellurite_resistance_protein;_hemagglutinin_homolog_1344817..1345047_POSITIVE 225 268 228 101 61 aact:AA01066|5end_conserved_hypothetical_protein_738380..738610_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 243 204 66 24 aact:AA01140|3end_anaerobic_dimethyl_sulfoxide_reductase,_chain_C_782526..782676_POSITIVE 249 280 236 56 13 aact:AA01409|3end_lipoprotein_B_951049..951199_POSITIVE 245 270 233 105 64 aact:AA02228|3end_regulatory_protein,_sorC_family_1516011..1516161_POSITIVE 235 280 234 55 6 aact:AA01422|3end_cell_division_protein_E,_ABC_system_ATP-binding_protein_956736..956886_POSITIVE 234 86 45 53 1 aact:AA01851|3end_hypothetical_protein_1244949..1245099_POSITIVE 232 200 151 98 43 aact:AA02090|3end_glucose-1-phosphate_adenylyltransferase_1424549..1424699_POSITIVE 231 109 67 150 116 aact:AA00258|3end_penicillin_binding_protein_2_182852..183002_POSITIVE 229 120 75 47 3 aact:AA01983|3end_maltose_regulon_positive_regulatory_protein_1344738..1344888_POSITIVE 229 160 113 94 46 aact:AA00618|3end_molybdopterin_biosynthesis_protein_423642..423792_POSITIVE 220 267 238 125 81 aact:AA02368|3end_conserved_hypothetical_protein_1624286..1624436_POSITIVE 220 75 38 71 28 aact:AA02082|3end_glutaminyl-tRNA_synthetase_1417848..1417998_POSITIVE 220 280 237 128 78 aact:AA01252|3end_conserved_hypothetical_protein_(probable_SirA_homolog)_852282..852432_POSITIVE 220 90 41 58 10 aact:AA01012|3end_probable_carbon_storage_regulator_homolog_708074..708224_POSITIVE 218 250 202 70 16 aact:AA00488|3end_purine_nucleoside_phosphorylase_338871..339021_POSITIVE 215 75 47 144 109 aact:AA01890|3end_cell-cycle_protein_1275967..1276117_POSITIVE 213 277 233 76 25 aact:AA01006|3end_conserved_hypothetical_protein_(possible_cytosine_deaminas)_703446..703596_POSITIVE 213 280 235 116 49 aact:AA00585|3end_glycerol-3-phosphate_regulon_repressor_399778..399928_POSITIVE 212 280 241 54 5 aact:AA00332|3end_PTS_system,_fructose-specific_IIA/FPr_component_(diphosphoryl_transfer_protein)_225617..225767_POSITIVE 211 270 238 150 117 aact:AA02140|3end_ABC_transporter_ATP-binding_protein_1464965..1465115_POSITIVE 211 76 48 109 78 aact:AA00443|3end_hypothetical_protein_308796..308946_POSITIVE