Origin IGS: ctgattctccttggattggtgtttataaagatagtgtattgcaattgcatttaaaaaccacgatttagatcacattttgaggtttttctgtgtgaaaaaacgccatgatgatcatggcgtttgggttccctttcacttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaagtgaaagggaacccaaacgccatgatcatcatggcgttttttcacacagaaaaacctcaaaatgtgatctaaatcgtggtttttaaatgcaattgcaatacactatctttataaacaccaatccaaggagaatcag Mask Tandem Repeat Region ================================================ ctgattctccttggattggtgtttataaagatagtgtattgcaattgcatttaaaaaccacgatttagatcacattttgaggtttttctgtgtgaaaaaacgccatgatgatcatggcgtttgggttccctttcacttta Find is-nt database================================================ Query_seq: AA01544:AA01546|AA01544:AA01546:conserved hypothetical protein:deoxyribose operon repressor:->->:1035494..1035633 140 ctgattctccttggattggtgtttataaagatagtgtattgcaattgcatttaaaaaccacgatttagatcacattttgaggtttttctgtgtgaaaaaacgccatgatgatcatggcgtttgggttccctttcacttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01544:AA01546|AA01544:AA01546:conserved hypothetical protein:deoxyribose operon repressor:->->:1035494..1035633 140 ctgattctccttggattggtgtttataaagatagtgtattgcaattgcatttaaaaaccacgatttagatcacattttgaggtttttctgtgtgaaaaaacgccatgatgatcatggcgtttgggttccctttcacttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01544:AA01546|AA01544:AA01546:conserved hypothetical protein:deoxyribose operon repressor:->->:1035494..1035633 140 ctgattctccttggattggtgtttataaagatagtgtattgcaattgcatttaaaaaccacgatttagatcacattttgaggtttttctgtgtgaaaaaacgccatgatgatcatggcgtttgggttccctttcacttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgattctccttggattggtgtttataaagatagtgtattgcaattgcatttaaaaaccacgatttagatcacattttgaggtttttctgtgtgaaaaaacgccatgatgatcatggcgtttgggttccctttcacttta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 38 End: 139 ..................................... M A I A F K N H D L D H I L R F F C V K K R H D D H G V W V P F H F . ctgattctccttggattggtgtttataaagatagtgtattgcaattgcatttaaaaaccacgatttagatcacattttgaggtttttctgtgtgaaaaaacgccatgatgatcatggcgtttgggttccctttcacttta 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================================================ ctgattctccttggattggtgtttataaagatagtgtattgcaattgcatttaaaaaccacgatttagatcacattttgaggtttttctgtgtgaaaaaacgccatgatgatcatggcgtttgggttccctttcacttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -13.2 Tail_Score: -3.79481 Start: 101 End: 119 Full_Region: TTCTGTGTGAAAAAA CGCCATGA TGA TCATGGCG TTTGGGTTCCCTTTC ....................................................................................................CGCCATGATGATCATGGCG..................... Find igs database================================================ Query_seq: AA01544:AA01546|AA01544:AA01546:conserved hypothetical protein:deoxyribose operon repressor:->->:1035494..1035633 140 ctgattctccttggattggtgtttataaagatagtgtattgcaattgcatttaaaaaccacgatttagatcacattttgaggtttttctgtgtgaaaaaacgccatgatgatcatggcgtttgggttccctttcacttta Intra-Species Hit: Count: 1 Min: 1 Max: 140 Len: 140 Subject: aact_AA01544_AA01546|conserved hypothetical protein:deoxyribose operon repressor|POSITIVE:POSITIVE|[1035494,1035633]|140 HSP 1 e-value: 5.0E-74 bit: 278.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 ctgattctccttggattggtgtttataaagatagtgtattgcaattgcatttaaaaaccacgatttagatcacattttgaggtttttctgtgtgaaaaaacgccatgatgatcatggcgtttgggttccctttcacttta ctgattctccttggattggtgtttataaagatagtgtattgcaattgcatttaaaaaccacgatttagatcacattttgaggtttttctgtgtgaaaaaacgccatgatgatcatggcgtttgggttccctttcacttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAUUCUCCUUGGAUUGGUGUUUAUAAAGAUAGUGUAUUGCAAUUGCAUUUAAAAACCACGAUUUAGAUCACAUUUUGAGGUUUUUCUGUGUGAAAAAACGCCAUGAUGAUCAUGGCGUUUGGGUUCCCUUUCACUUUA ..((....(((..((...(((....((((....(((...(((....))).........)))..))))...)))..))..)))....))...(((((.((((((((((.....))))))))))((....)).))))).... (-35.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGUGAAAGGGAACCCAAACGCCAUGAUCAUCAUGGCGUUUUUUCACACAGAAAAACCUCAAAAUGUGAUCUAAAUCGUGGUUUUUAAAUGCAAUUGCAAUACACUAUCUUUAUAAACACCAAUCCAAGGAGAAUCAG ...((((...(((((((.((((((((((.....))))))))))..(((((..((......))....)))))..........)))))))...(((....)))...)))).............((.......))........ (-29.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 129 88 59 21 aact:AA01625|5end_riboflavin_synthase,_beta_chain_1099964..1100194_POSITIVE 316 130 81 109 61 aact:AA00531|5end_DNA_polymerase_I_362621..362851_POSITIVE 311 129 82 62 11 aact:AA00675|5end_glutaredoxin_2_462524..462754_POSITIVE 303 130 92 201 160 aact:AA02367|5end_conserved_hypothetical_protein_1623174..1623404_POSITIVE 303 130 92 47 6 aact:AA02366|5end_hypothetical_protein_1623020..1623250_POSITIVE 302 129 82 103 46 aact:AA01618|5end_lipoprotein_releasing_system_transmembrane_protein_1093071..1093301_POSITIVE 293 130 82 204 157 aact:AA02944|5end_30S_ribosomal_protein_S20_2058688..2058918_POSITIVE 293 130 82 51 4 aact:AA02941|5end_hypothetical_protein_2058535..2058765_POSITIVE 289 120 73 141 89 aact:AA02721|5end_spermidine/putrescine_ABC_transporter,_periplasmic-binding_protein_1904121..1904351_POSITIVE 288 137 101 223 178 aact:AA01255|5end_hypothetical_protein_852656..852886_POSITIVE 288 129 90 85 36 aact:AA00212|5end_ribokinase_146056..146286_POSITIVE 287 132 91 229 186 aact:AA01424|5end_threonine_deaminase_(dehydratase)_957740..957970_POSITIVE 283 129 84 141 91 aact:AA02970|5end_tyrosine_phenol-lyase_2076373..2076603_POSITIVE 283 129 82 152 116 aact:AA00237|5end_hypothetical_protein_170934..171164_POSITIVE 275 124 81 213 159 aact:AA02926|5end_hypothetical_protein_2048136..2048366_POSITIVE 273 134 101 227 193 aact:AA00695|5end_uridine_kinase_475033..475263_POSITIVE 272 129 100 161 126 aact:AA02565|5end_transketolase,_N-terminal_subunit_1786366..1786596_POSITIVE 270 119 77 152 100 aact:AA00575|5end_shikimate_5-dehydrogenase_393216..393446_POSITIVE 268 128 99 45 13 aact:AA00062|5end_bicyclomycin_resistance_protein_(Sulfonamide_resistance_protein)_46889..47119_POSITIVE 267 129 88 201 157 aact:AA02939|5end_phosphoserine_phosphatase_2056881..2057111_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 339 129 83 112 62 aact:AA01021|3end_hypothetical_protein_714276..714426_POSITIVE 316 130 81 76 28 aact:AA00530|3end_hypothetical_protein_362668..362818_POSITIVE 306 139 91 95 46 aact:AA01423|3end_cell_division_protein_X,_ABC_system_permease_957680..957830_POSITIVE 302 129 82 100 43 aact:AA01616|3end_lipoprotein_releasing_system_ATP-binding_protein_1093148..1093298_POSITIVE 293 130 82 88 41 aact:AA02940|3end_conserved_hypothetical_protein_2058652..2058802_POSITIVE 288 129 90 112 63 aact:AA00211|3end_hypothetical_protein_146163..146313_POSITIVE 283 129 84 105 55 aact:AA02969|3end_beta_tyrosinase_(tyrosine_phenol-lyase)_2076417..2076567_POSITIVE 275 124 81 148 94 aact:AA02925|3end_conserved_hypothetical_protein_2048151..2048301_POSITIVE 273 120 78 46 2 aact:AA02720|3end_ABC-related_spermidine/putrescine_transport_system_permease_1904106..1904256_POSITIVE 270 119 77 151 99 aact:AA00573|3end_chloramphenicol-sensitive_protein_RarD_393295..393445_POSITIVE 262 136 91 134 90 aact:AA01968|3end_hypothetical_protein_1331949..1332099_POSITIVE 261 139 91 54 5 aact:AA02034|3end_ferredoxin_NADP+_reductase_1386054..1386204_POSITIVE 254 130 81 117 64 aact:AA00424|3end_hypothetical_protein_287403..287553_POSITIVE 252 126 91 92 59 aact:AA00200|3end_thymidylate_synthase_139769..139919_POSITIVE 250 119 78 69 26 aact:AA00469|3end_inorganic_pyrophosphatase,_chain_A_326810..326960_POSITIVE 248 130 91 122 89 aact:AA02821|3end_ribosomal-protein-alanine_acetyltransferase_1982775..1982925_POSITIVE 248 135 92 87 41 aact:AA02714|3end_paraquat-inducible_protein_PqiA_homolog_1897167..1897317_POSITIVE 244 125 91 143 109 aact:AA02717|3end_hypothetical_protein_1901312..1901462_POSITIVE 243 127 91 70 33 aact:AA01299|3end_competence_protein_C_881502..881652_POSITIVE 242 127 97 78 42 aact:AA02351|3end_conserved_hypothetical_protein_1609468..1609618_POSITIVE