Origin IGS: taatttcaggataaaatttttgttttcttatgcaggttattttgtaaaataaagaaacttttttcacacaatatagtcaaatagcctgcaaaaagttaaaatccaatcgctaaaaccgattaacttaatacagattatattgcattgaattctttgattcggtgattaacaaagaagaaggaagata .........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 tatcttccttcttctttgttaatcaccgaatcaaagaattcaatgcaatataatctgtattaagttaatcggttttagcgattggattttaactttttgcaggctatttgactatattgtgtgaaaaaagtttctttattttacaaaataacctgcataagaaaacaaaaattttatcctgaaatta Mask Tandem Repeat Region ================================================ taatttcaggataaaatttttgttttcttatgcaggttattttgtaaaataaagaaacttttttcacacaatatagtcaaatagcctgcaaaaagttaaaatccaatcgctaaaaccgattaacttaatacagattatattgcattgaattctttgattcggtgattaacaaagaagaaggaagata Find is-nt database================================================ Query_seq: AA00559:AA00560|AA00559:AA00560:conserved hypothetical protein:RNA polymerase sigma-32 factor:->->:383619..383805 187 taatttcaggataaaatttttgttttcttatgcaggttattttgtaaaataaagaaacttttttcacacaatatagtcaaatagcctgcaaaaagttaaaatccaatcgctaaaaccgattaacttaatacagattatattgcattgaattctttgattcggtgattaacaaagaagaaggaagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00559:AA00560|AA00559:AA00560:conserved hypothetical protein:RNA polymerase sigma-32 factor:->->:383619..383805 187 taatttcaggataaaatttttgttttcttatgcaggttattttgtaaaataaagaaacttttttcacacaatatagtcaaatagcctgcaaaaagttaaaatccaatcgctaaaaccgattaacttaatacagattatattgcattgaattctttgattcggtgattaacaaagaagaaggaagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00559:AA00560|AA00559:AA00560:conserved hypothetical protein:RNA polymerase sigma-32 factor:->->:383619..383805 187 taatttcaggataaaatttttgttttcttatgcaggttattttgtaaaataaagaaacttttttcacacaatatagtcaaatagcctgcaaaaagttaaaatccaatcgctaaaaccgattaacttaatacagattatattgcattgaattctttgattcggtgattaacaaagaagaaggaagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatttcaggataaaatttttgttttcttatgcaggttattttgtaaaataaagaaacttttttcacacaatatagtcaaatagcctgcaaaaagttaaaatccaatcgctaaaaccgattaacttaatacagattatattgcattgaattctttgattcggtgattaacaaagaagaaggaagata Predict ORF larger than 30AA ================================================ taatttcaggataaaatttttgttttcttatgcaggttattttgtaaaataaagaaacttttttcacacaatatagtcaaatagcctgcaaaaagttaaaatccaatcgctaaaaccgattaacttaatacagattatattgcattgaattctttgattcggtgattaacaaagaagaaggaagata 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: 81 Start: 73 End: 102 ........................................................................ATAGTCAAATAGCCTGCAAAAAGTTAAAAT..................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taatttcaggataaaatttttgttttcttatgcaggttattttgtaaaataaagaaacttttttcacacaatatagtcaaatagcctgcaaaaagttaaaatccaatcgctaaaaccgattaacttaatacagattatattgcattgaattctttgattcggtgattaacaaagaagaaggaagata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA00559:AA00560|AA00559:AA00560:conserved hypothetical protein:RNA polymerase sigma-32 factor:->->:383619..383805 187 taatttcaggataaaatttttgttttcttatgcaggttattttgtaaaataaagaaacttttttcacacaatatagtcaaatagcctgcaaaaagttaaaatccaatcgctaaaaccgattaacttaatacagattatattgcattgaattctttgattcggtgattaacaaagaagaaggaagata Intra-Species Hit: Count: 1 Min: 1 Max: 187 Len: 187 Subject: aact_AA00559_AA00560|conserved hypothetical protein:RNA polymerase sigma-32 factor|POSITIVE:POSITIVE|[383619,383805]|187 HSP 1 e-value: 1.0E-102 bit: 371.0 Len: 187 Query Start:1 Query End:187 Subject Strand: POSITIVE Subject Start: 1 Subject End: 187 taatttcaggataaaatttttgttttcttatgcaggttattttgtaaaataaagaaacttttttcacacaatatagtcaaatagcctgcaaaaagttaaaatccaatcgctaaaaccgattaacttaatacagattatattgcattgaattctttgattcggtgattaacaaagaagaaggaagata taatttcaggataaaatttttgttttcttatgcaggttattttgtaaaataaagaaacttttttcacacaatatagtcaaatagcctgcaaaaagttaaaatccaatcgctaaaaccgattaacttaatacagattatattgcattgaattctttgattcggtgattaacaaagaagaaggaagata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUCAGGAUAAAAUUUUUGUUUUCUUAUGCAGGUUAUUUUGUAAAAUAAAGAAACUUUUUUCACACAAUAUAGUCAAAUAGCCUGCAAAAAGUUAAAAUCCAAUCGCUAAAACCGAUUAACUUAAUACAGAUUAUAUUGCAUUGAAUUCUUUGAUUCGGUGAUUAACAAAGAAGAAGGAAGAUA ...............((((((.(((((((.((((((((((((((((.......((((....))))......))))...))))))))))))....(((((.....(((((.......))))).....................(((((((((....))))))))).))))).)))))))..)))))). (-33.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCUUCCUUCUUCUUUGUUAAUCACCGAAUCAAAGAAUUCAAUGCAAUAUAAUCUGUAUUAAGUUAAUCGGUUUUAGCGAUUGGAUUUUAACUUUUUGCAGGCUAUUUGACUAUAUUGUGUGAAAAAAGUUUCUUUAUUUUACAAAAUAACCUGCAUAAGAAAACAAAAAUUUUAUCCUGAAAUUA ...........(((((((.............)))))))...((((((........)))))).........((((((((.(((..((((((...((((((((((.(((((..........(((((((((((...)))).)))))))))))).))))))...))))...))))))..))))))))))). (-32.42) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 231 148 104 229 186 aact:AA02303|5end_ATP-dependent_DNA_helicase_1572696..1572926_POSITIVE 223 176 133 181 134 aact:AA00614|5end_ribonuclease_HII_(RNase_HII)_419890..420120_POSITIVE 220 135 101 170 134 aact:AA01031|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_C_720152..720382_POSITIVE 219 146 101 113 62 aact:AA00705|5end_Inositol-1-monophosphatase_(IMPase);_extragenic_suppressor_483827..484057_POSITIVE 217 118 75 117 73 aact:AA01829|5end_hypothetical_protein_1231403..1231633_POSITIVE 217 125 84 185 142 aact:AA01292|5end_single-stranded_DNA_binding_protein_875827..876057_POSITIVE 216 119 76 160 114 aact:AA02715|5end_paraquat-inducible_protein_pqiB_homolog_1897053..1897283_POSITIVE 216 128 85 39 1 aact:AA02050|5end_1-deoxy-D-xylulose_5-phosphate_synthase_1395625..1395855_POSITIVE 216 92 58 186 153 aact:AA02006|5end_PEP--fructosephosphotransferase_system_repressor,_DeoR_family_1363930..1364160_POSITIVE 213 128 81 168 119 aact:AA01726|5end_conserved_hypothetical_protein_(possible_HipA-like_protein_1168105..1168335_POSITIVE 211 118 82 181 140 aact:AA01630|5end_threonine_efflux_protein_1102381..1102611_POSITIVE 210 89 58 73 37 aact:AA01876|5end_PTS_system,_IIBC_components_1263365..1263595_POSITIVE 210 175 137 219 169 aact:AA00869|5end_tight_adherence_protein_V;_prepilin_peptidase_601255..601485_POSITIVE 208 118 73 197 155 aact:AA00492|5end_conserved_hypothetical_protein_343578..343808_POSITIVE 205 119 75 72 27 aact:AA00037|5end_conserved_hypothetical_protein_29170..29400_POSITIVE 203 47 14 38 6 aact:AA01138|5end_anaerobic_dimethyl_sulfoxide_reductase,_chain_B_780991..781221_POSITIVE 201 110 70 129 80 aact:AA00784|5end_hypothetical_protein_539025..539255_POSITIVE 198 178 136 119 82 aact:AA02757|5end_histidinol-phosphate_aminotransferase_2_1930634..1930864_POSITIVE 197 112 71 145 101 aact:AA02355|5end_nicotinamide_phosphoribosyl_transferase_1612924..1613154_POSITIVE 197 126 87 210 174 aact:AA01457|5end_D-xylose_ABC_transporter,_membrane_spanning_protein_977604..977834_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 231 110 61 125 73 aact:AA01611|3end_anthranilate_synthase_component_II_1089619..1089769_POSITIVE 219 146 101 54 3 aact:AA00702|3end_conserved_hypothetical_protein_483848..483998_POSITIVE 211 118 84 125 95 aact:AA01062|3end_ribonuclease_PH_(RNase_PH)_736499..736649_POSITIVE 210 89 58 134 98 aact:AA01875|3end_PTS_system,_glucose-specific_enzyme_II,_A_component_1263506..1263656_POSITIVE 205 119 75 76 31 aact:AA00036|3end_transposase_29254..29404_POSITIVE 201 110 70 144 95 aact:AA00782|3end_conserved_hypothetical_protein_539120..539270_POSITIVE 200 119 74 145 101 aact:AA00785|3end_conserved_hypothetical_protein_(possible_integrase)_539672..539822_POSITIVE 199 123 86 91 50 aact:AA01115|3end_carboxylesterase_767353..767503_POSITIVE 198 178 136 41 4 aact:AA02756|3end_phosphoserine_aminotransferase_1930636..1930786_POSITIVE 197 112 71 149 105 aact:AA02354|3end_conserved_hypothetical_protein_1613008..1613158_POSITIVE 196 125 100 29 6 aact:AA01753|3end_conserved_hypothetical_protein_1185902..1186052_POSITIVE 195 150 101 52 1 aact:AA02049|3end_hypothetical_protein_1395695..1395845_POSITIVE 194 110 84 28 1 aact:AA02879|3end_octaprenyl-diphosphate_synthase_2020589..2020739_POSITIVE 194 148 106 81 41 aact:AA02118|3end_hypothetical_protein_1445939..1446089_POSITIVE 194 119 77 61 16 aact:AA00652|3end_arginyl-tRNA_synthetase_(arginine--tRNA_ligase)_447486..447636_POSITIVE 192 167 131 68 24 aact:AA00743|3end_conserved_hypothetical_protein_(possible_membrane_protein)_509947..510097_POSITIVE 191 164 127 136 91 aact:AA00934|3end_ribose_ABC_transporter,_ATP_binding_protein_645842..645992_POSITIVE 190 170 140 81 53 aact:AA02245|3end_hypothetical_protein_1527621..1527771_POSITIVE 190 134 93 60 23 aact:AA00156|3end_hypothetical_protein_112102..112252_POSITIVE 189 118 81 118 85 aact:AA02426|3end_uridylyltransferase_1674226..1674376_POSITIVE