Origin IGS: ttgctttatccttttaatgtgaaaagtgcggtggattataacatagtttcttgaattcagcggtttattgtaccggcggattgtggtattttagacgccatttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaatggcgtctaaaataccacaatccgccggtacaataaaccgctgaattcaagaaactatgttataatccaccgcacttttcacattaaaaggataaagcaa Mask Tandem Repeat Region ================================================ ttgctttatccttttaatgtgaaaagtgcggtggattataacatagtttcttgaattcagcggtttattgtaccggcggattgtggtattttagacgccatttta Find is-nt database================================================ Query_seq: AA01991:AA01992|AA01991:AA01992:conserved hypothetical protein (possible nitroreductase):protease IV; signal peptide peptidase; Endopeptidase IV:->->:1353064..1353168 105 ttgctttatccttttaatgtgaaaagtgcggtggattataacatagtttcttgaattcagcggtttattgtaccggcggattgtggtattttagacgccatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01991:AA01992|AA01991:AA01992:conserved hypothetical protein (possible nitroreductase):protease IV; signal peptide peptidase; Endopeptidase IV:->->:1353064..1353168 105 ttgctttatccttttaatgtgaaaagtgcggtggattataacatagtttcttgaattcagcggtttattgtaccggcggattgtggtattttagacgccatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01991:AA01992|AA01991:AA01992:conserved hypothetical protein (possible nitroreductase):protease IV; signal peptide peptidase; Endopeptidase IV:->->:1353064..1353168 105 ttgctttatccttttaatgtgaaaagtgcggtggattataacatagtttcttgaattcagcggtttattgtaccggcggattgtggtattttagacgccatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgctttatccttttaatgtgaaaagtgcggtggattataacatagtttcttgaattcagcggtttattgtaccggcggattgtggtattttagacgccatttta Predict ORF larger than 30AA ================================================ ttgctttatccttttaatgtgaaaagtgcggtggattataacatagtttcttgaattcagcggtttattgtaccggcggattgtggtattttagacgccatttta 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================================================ ttgctttatccttttaatgtgaaaagtgcggtggattataacatagtttcttgaattcagcggtttattgtaccggcggattgtggtattttagacgccatttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01991:AA01992|AA01991:AA01992:conserved hypothetical protein (possible nitroreductase):protease IV; signal peptide peptidase; Endopeptidase IV:->->:1353064..1353168 105 ttgctttatccttttaatgtgaaaagtgcggtggattataacatagtttcttgaattcagcggtttattgtaccggcggattgtggtattttagacgccatttta Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: aact_AA01991_AA01992|conserved hypothetical protein (possible nitroreductase):protease IV; signal peptide peptidase; Endopeptidase IV|POSITIVE:POSITIVE|[1353064,1353168]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 ttgctttatccttttaatgtgaaaagtgcggtggattataacatagtttcttgaattcagcggtttattgtaccggcggattgtggtattttagacgccatttta ttgctttatccttttaatgtgaaaagtgcggtggattataacatagtttcttgaattcagcggtttattgtaccggcggattgtggtattttagacgccatttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCUUUAUCCUUUUAAUGUGAAAAGUGCGGUGGAUUAUAACAUAGUUUCUUGAAUUCAGCGGUUUAUUGUACCGGCGGAUUGUGGUAUUUUAGACGCCAUUUUA ..(((((.(((.......).)))))))..((((..(.(((.((((((((..((....)).((((.......))))..)))))))).)))...)..))))...... (-17.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUGGCGUCUAAAAUACCACAAUCCGCCGGUACAAUAAACCGCUGAAUUCAAGAAACUAUGUUAUAAUCCACCGCACUUUUCACAUUAAAAGGAUAAAGCAA .....(((..(.....)..)))..((((..((((.......))))..........((((...(((...........)))..)))).........))))....... ( -9.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 70 24 43 2 aact:AA00637|5end_phosphohistidine_phosphatase_438169..438399_POSITIVE 335 100 51 170 108 aact:AA00380|5end_carbamate_kinase_256528..256758_POSITIVE 329 98 62 111 73 aact:AA02758|5end_3-phosphoshikimate_1-carboxyvinyltransferase_1931802..1932032_POSITIVE 328 54 17 147 109 aact:AA00635|5end_dihydropteroate_synthase_435897..436127_POSITIVE 325 49 2 153 102 aact:AA01464|5end_hypothetical_protein_984210..984440_POSITIVE 320 49 5 73 27 aact:AA01041|5end_hypothetical_protein_724853..725083_POSITIVE 319 100 55 68 25 aact:AA01538|5end_conserved_hypothetical_protein_1031527..1031757_POSITIVE 318 100 55 74 38 aact:AA02524|5end_orotidine_5'-phosphate_decarboxylase_1753313..1753543_POSITIVE 313 70 23 75 15 aact:AA00143|5end_gluconate_permease_(GntP_family)_102445..102675_POSITIVE 310 88 47 68 28 aact:AA01424|5end_threonine_deaminase_(dehydratase)_957740..957970_POSITIVE 297 100 58 198 167 aact:AA01810|5end_electron_transport_complex_protein_1219250..1219480_POSITIVE 297 99 56 37 1 aact:AA01471|5end_type_I_restriction_enzyme_M_(modification_chain)_987321..987551_POSITIVE 296 64 23 185 143 aact:AA00292|5end_dihydrofolate_reductase_201800..202030_POSITIVE 296 64 23 100 58 aact:AA00291|5end_hypothetical_protein_201715..201945_POSITIVE 295 99 60 41 5 aact:AA02472|5end_conserved_hypothetical_protein_1707631..1707861_POSITIVE 291 88 46 221 182 aact:AA00312|5end_conserved_hypothetical_protein_(possible_hydroxypyruvate_isomerase)_212069..212299_POSITIVE 290 96 62 106 75 aact:AA00473|5end_tryptophanyl-tRNA_synthetase_328996..329226_POSITIVE 290 55 15 138 92 aact:AA00250|5end_lipoate_biosynthesis_protein_A_175496..175726_POSITIVE 289 86 48 226 188 aact:AA01476|5end_hypothetical_protein_991402..991632_POSITIVE 288 70 21 162 110 aact:AA02597|5end_ribonuclease_D_1807124..1807354_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 49 2 63 12 aact:AA01463|3end_probable_transport_protein_984200..984350_POSITIVE 320 49 5 86 40 aact:AA01040|3end_possible_lipoprotein_724946..725096_POSITIVE 319 100 55 68 25 aact:AA01537|3end_possible_glucokinase_regulatory_protein_1031607..1031757_POSITIVE 318 100 55 65 29 aact:AA02523|3end_conserved_hypothetical_protein_1753384..1753534_POSITIVE 316 79 33 133 84 aact:AA00143|3end_gluconate_permease_(GntP_family)_103796..103946_POSITIVE 313 70 23 75 15 aact:AA00142|3end_glycerate_kinase_102525..102675_POSITIVE 297 87 50 133 96 aact:AA01778|3end_aminopeptidase_A/I;_cytosol_aminopeptidase;_leucyl_aminopeptidase_1199965..1200115_POSITIVE 296 64 23 118 76 aact:AA00290|3end_conserved_hypothetical_protein_201813..201963_POSITIVE 288 70 21 68 16 aact:AA02595|3end_cytochrome_c_peroxidase_1807110..1807260_POSITIVE 286 98 73 37 11 aact:AA02757|3end_histidinol-phosphate_aminotransferase_2_1931808..1931958_POSITIVE 284 68 21 104 56 aact:AA02743|3end_outer_membrane_lipoprotein_precursor/glutamyl-tRNA_reductase_subunit_1923356..1923506_POSITIVE 281 45 14 54 25 aact:AA00231|3end_long-chain-fatty-acid--CoA_ligase_162399..162549_POSITIVE 278 61 23 92 51 aact:AA00166|3end_conserved_hypothetical_protein_(possible_acetyltransferase)_117919..118069_POSITIVE 275 99 61 87 51 aact:AA01923|3end_type_III_restriction-modification_system_methylation_subunit_1299936..1300086_POSITIVE 275 32 3 67 38 aact:AA01280|3end_groES_chaperonin_868530..868680_POSITIVE 275 64 21 138 99 aact:AA00083|3end_hypothetical_protein_60851..61001_POSITIVE 275 64 21 54 15 aact:AA00081|3end_fatty_acid_metabolism_regulator_protein_60767..60917_POSITIVE 274 36 5 96 62 aact:AA01515|3end_SlyX_family_protein_1021034..1021184_POSITIVE 274 70 23 131 73 aact:AA00265|3end_transcription_termination_factor_186583..186733_POSITIVE 269 88 46 149 107 aact:AA00761|3end_conserved_hypothetical_protein_(possible_peptidase)_524086..524236_POSITIVE