Origin IGS: aattttcctttttggcttttctgaaacgttaaagagcggtattatacccagctatttttatcagcccaacttatttaaaaagtttaaggtttaaccgtgaatattcaatctattttatccgaaaaaatcaaacaggcg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgcctgtttgattttttcggataaaatagattgaatattcacggttaaaccttaaactttttaaataagttgggctgataaaaatagctgggtataataccgctctttaacgtttcagaaaagccaaaaaggaaaatt Mask Tandem Repeat Region ================================================ aattttcctttttggcttttctgaaacgttaaagagcggtattatacccagctatttttatcagcccaacttatttaaaaagtttaaggtttaaccgtgaatattcaatctattttatccgaaaaaatcaaacaggcg Find is-nt database================================================ Query_seq: AA00651:AA00652|AA00651:AA00652:conserved hypothetical protein:arginyl-tRNA synthetase (arginine--tRNA ligase):->->:445720..445857 138 aattttcctttttggcttttctgaaacgttaaagagcggtattatacccagctatttttatcagcccaacttatttaaaaagtttaaggtttaaccgtgaatattcaatctattttatccgaaaaaatcaaacaggcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00651:AA00652|AA00651:AA00652:conserved hypothetical protein:arginyl-tRNA synthetase (arginine--tRNA ligase):->->:445720..445857 138 aattttcctttttggcttttctgaaacgttaaagagcggtattatacccagctatttttatcagcccaacttatttaaaaagtttaaggtttaaccgtgaatattcaatctattttatccgaaaaaatcaaacaggcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00651:AA00652|AA00651:AA00652:conserved hypothetical protein:arginyl-tRNA synthetase (arginine--tRNA ligase):->->:445720..445857 138 aattttcctttttggcttttctgaaacgttaaagagcggtattatacccagctatttttatcagcccaacttatttaaaaagtttaaggtttaaccgtgaatattcaatctattttatccgaaaaaatcaaacaggcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattttcctttttggcttttctgaaacgttaaagagcggtattatacccagctatttttatcagcccaacttatttaaaaagtttaaggtttaaccgtgaatattcaatctattttatccgaaaaaatcaaacaggcg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 2 End: 91 . M F L F G F S E T L K S G I I P S Y F Y Q P N L F K K F K V ............................................... aattttcctttttggcttttctgaaacgttaaagagcggtattatacccagctatttttatcagcccaacttatttaaaaagtttaaggtttaaccgtgaatattcaatctattttatccgaaaaaatcaaacaggcg 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================================================ aattttcctttttggcttttctgaaacgttaaagagcggtattatacccagctatttttatcagcccaacttatttaaaaagtttaaggtttaaccgtgaatattcaatctattttatccgaaaaaatcaaacaggcg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA00651:AA00652|AA00651:AA00652:conserved hypothetical protein:arginyl-tRNA synthetase (arginine--tRNA ligase):->->:445720..445857 138 aattttcctttttggcttttctgaaacgttaaagagcggtattatacccagctatttttatcagcccaacttatttaaaaagtttaaggtttaaccgtgaatattcaatctattttatccgaaaaaatcaaacaggcg Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: aact_AA00651_AA00652|conserved hypothetical protein:arginyl-tRNA synthetase (arginine--tRNA ligase)|POSITIVE:POSITIVE|[445720,445857]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 aattttcctttttggcttttctgaaacgttaaagagcggtattatacccagctatttttatcagcccaacttatttaaaaagtttaaggtttaaccgtgaatattcaatctattttatccgaaaaaatcaaacaggcg aattttcctttttggcttttctgaaacgttaaagagcggtattatacccagctatttttatcagcccaacttatttaaaaagtttaaggtttaaccgtgaatattcaatctattttatccgaaaaaatcaaacaggcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUCCUUUUUGGCUUUUCUGAAACGUUAAAGAGCGGUAUUAUACCCAGCUAUUUUUAUCAGCCCAACUUAUUUAAAAAGUUUAAGGUUUAACCGUGAAUAUUCAAUCUAUUUUAUCCGAAAAAAUCAAACAGGCG ......(((.(((((.(((((.((...(((((..(((((((...))))..)))..........(((.(((((.......)))))...))))))))..(((....)))..........)).)))))..))))).))).. (-17.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCCUGUUUGAUUUUUUCGGAUAAAAUAGAUUGAAUAUUCACGGUUAAACCUUAAACUUUUUAAAUAAGUUGGGCUGAUAAAAAUAGCUGGGUAUAAUACCGCUCUUUAACGUUUCAGAAAAGCCAAAAAGGAAAAUU ..(((.((((..((((..(((......(((..((....)).((((...(((...(((((.......))))).(((((.......))))).))).....)))).))).......)))..))))..)))).)))...... (-20.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 325 60 15 148 93 aact:AA01160|5end_ADP_compounds_hydrolase_793565..793795_POSITIVE 277 66 26 69 15 aact:AA02910|5end_ribonuclease_E_2036137..2036367_POSITIVE 268 55 11 217 174 aact:AA01544|5end_conserved_hypothetical_protein_1034265..1034495_POSITIVE 268 55 11 127 84 aact:AA01543|5end_hypothetical_protein_1034175..1034405_POSITIVE 262 67 25 55 11 aact:AA01863|5end_hypothetical_protein_1252011..1252241_POSITIVE 258 67 25 174 135 aact:AA00292|5end_dihydrofolate_reductase_201800..202030_POSITIVE 258 67 25 89 50 aact:AA00291|5end_hypothetical_protein_201715..201945_POSITIVE 257 63 37 47 19 aact:AA01496|5end_glucose_inhibited_division_protein_A_1005125..1005355_POSITIVE 254 67 21 151 101 aact:AA01371|5end_rod_shape-determining_protein_926579..926809_POSITIVE 251 53 16 216 169 aact:AA02014|5end_probable_hemolysin_1370406..1370636_POSITIVE 247 43 7 91 49 aact:AA00643|5end_hypothetical_protein_440432..440662_POSITIVE 244 97 51 226 186 aact:AA00213|5end_cold_shock_protein_(negative_regulator_of_cspA_transcription)_147071..147301_POSITIVE 242 53 11 132 91 aact:AA01601|5end_PTS_system,_glucose-specific_IIA_componen_1082269..1082499_POSITIVE 242 50 12 149 99 aact:AA01088|5end_rare_lipoprotein_B_precursor_752903..753133_POSITIVE 239 59 26 130 95 aact:AA00260|5end_conserved_hypothetical_protein_183315..183545_POSITIVE 235 67 22 164 94 aact:AA01146|5end_conserved_hypothetical_protein_784433..784663_POSITIVE 232 65 22 151 108 aact:AA01085|5end_mutator_mutT_protein_(7,8-dihydro-8-oxoguanine-triphosphatase)_(8-oxo-dGTPase)_(dGTP_pyrophosphohydrolase)_750970..751200_POSITIVE 231 76 31 176 127 aact:AA02615|5end_conserved_hypothetical_protein_1823040..1823270_POSITIVE 229 65 21 58 14 aact:AA01571|5end_peptide_transport_system_permease_1057919..1058149_POSITIVE 227 70 21 207 164 aact:AA01008|5end_mazG_beta-lactamase_regulatory_protein_homolog_703470..703700_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 57 15 151 99 aact:AA01159|3end_phosphatase_793651..793801_POSITIVE 268 55 11 59 16 aact:AA01539|3end_UDP-N-acetylglucosamine_pyrophosphorylase_(bifunctional_enzyme)_1034187..1034337_POSITIVE 262 67 25 71 27 aact:AA01861|3end_phosphomethylpyrimidine_kinase_1252107..1252257_POSITIVE 258 67 25 107 68 aact:AA00290|3end_conserved_hypothetical_protein_201813..201963_POSITIVE 254 67 21 78 28 aact:AA01370|3end_rod_shape-determining_protein_926586..926736_POSITIVE 251 53 16 104 57 aact:AA02013|3end_carbonic_anhydrase_1370374..1370524_POSITIVE 244 97 51 122 82 aact:AA00212|3end_ribokinase_147047..147197_POSITIVE 242 53 11 68 27 aact:AA01600|3end_phosphotransferase_system_enzyme_I_1082285..1082435_POSITIVE 242 50 12 146 96 aact:AA01087|3end_DNA_polymerase_III,_delta_subunit_752980..753130_POSITIVE 242 70 26 124 71 aact:AA00512|3end_conserved_hypothetical_protein_354649..354799_POSITIVE 239 59 26 67 32 aact:AA00259|3end_conserved_hypothetical_protein_183332..183482_POSITIVE 235 67 22 111 41 aact:AA01145|3end_glycyl-tRNA_synthetase_alpha_subunit_784460..784610_POSITIVE 232 65 22 71 28 aact:AA01083|3end_preprotein_translocase_SecA_subunit_750970..751120_POSITIVE 231 76 31 88 39 aact:AA02614|3end_conserved_hypothetical_protein_1823032..1823182_POSITIVE 230 68 27 103 56 aact:AA00486|3end_nucleoside_transporter_338026..338176_POSITIVE 229 65 21 47 3 aact:AA01569|3end_dipeptide_transport_ATP-binding_protein_1057988..1058138_POSITIVE 227 70 21 103 60 aact:AA01006|3end_conserved_hypothetical_protein_(possible_cytosine_deaminas)_703446..703596_POSITIVE 225 46 8 74 34 aact:AA00618|3end_molybdopterin_biosynthesis_protein_423642..423792_POSITIVE 220 30 1 83 56 aact:AA00249|3end_cysteinyl-tRNA_synthetase_(cysteine--tRNA_ligase)_175422..175572_POSITIVE 217 53 12 74 33 aact:AA02219|3end_LACI-type_transcriptional_regulator_1511207..1511357_POSITIVE