Origin IGS: aaggtttgcgaatgtgttgtgttgaagactaagatgcgggctacaatatcacaaatacggtgagttttctttacctgtatcaagaaaaccaccaaaagaaacgcaataaaaaccgaccgcacttttccaaagaaaaaatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgattttttctttggaaaagtgcggtcggtttttattgcgtttcttttggtggttttcttgatacaggtaaagaaaactcaccgtatttgtgatattgtagcccgcatcttagtcttcaacacaacacattcgcaaacctt Mask Tandem Repeat Region ================================================ aaggtttgcgaatgtgttgtgttgaagactaagatgcgggctacaatatcacaaatacggtgagttttctttacctgtatcaagaaaaccaccaaaagaaacgcaataaaaaccgaccgcacttttccaaagaaaaaatca Find is-nt database================================================ Query_seq: AA01102:AA01104|AA01102:AA01104:pyrimidine operon regulatory protein:conserved hypothetical protein:->->:761154..761294 141 aaggtttgcgaatgtgttgtgttgaagactaagatgcgggctacaatatcacaaatacggtgagttttctttacctgtatcaagaaaaccaccaaaagaaacgcaataaaaaccgaccgcacttttccaaagaaaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01102:AA01104|AA01102:AA01104:pyrimidine operon regulatory protein:conserved hypothetical protein:->->:761154..761294 141 aaggtttgcgaatgtgttgtgttgaagactaagatgcgggctacaatatcacaaatacggtgagttttctttacctgtatcaagaaaaccaccaaaagaaacgcaataaaaaccgaccgcacttttccaaagaaaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01102:AA01104|AA01102:AA01104:pyrimidine operon regulatory protein:conserved hypothetical protein:->->:761154..761294 141 aaggtttgcgaatgtgttgtgttgaagactaagatgcgggctacaatatcacaaatacggtgagttttctttacctgtatcaagaaaaccaccaaaagaaacgcaataaaaaccgaccgcacttttccaaagaaaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaggtttgcgaatgtgttgtgttgaagactaagatgcgggctacaatatcacaaatacggtgagttttctttacctgtatcaagaaaaccaccaaaagaaacgcaataaaaaccgaccgcacttttccaaagaaaaaatca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 48 End: 140 ............................................... M T N T V S F L Y L Y Q E N H Q K K R N K N R P H F S K E K I . Protein_Len: 40 Strand: - Start: 3 End: 122 .. T Q S H T T N F V L I R A V I D C I R H T K K V Q I L F V V L L F A I F V S R M ................... aaggtttgcgaatgtgttgtgttgaagactaagatgcgggctacaatatcacaaatacggtgagttttctttacctgtatcaagaaaaccaccaaaagaaacgcaataaaaaccgaccgcacttttccaaagaaaaaatca 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================================================ aaggtttgcgaatgtgttgtgttgaagactaagatgcgggctacaatatcacaaatacggtgagttttctttacctgtatcaagaaaaccaccaaaagaaacgcaataaaaaccgaccgcacttttccaaagaaaaaatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01102:AA01104|AA01102:AA01104:pyrimidine operon regulatory protein:conserved hypothetical protein:->->:761154..761294 141 aaggtttgcgaatgtgttgtgttgaagactaagatgcgggctacaatatcacaaatacggtgagttttctttacctgtatcaagaaaaccaccaaaagaaacgcaataaaaaccgaccgcacttttccaaagaaaaaatca Intra-Species Hit: Count: 1 Min: 1 Max: 141 Len: 141 Subject: aact_AA01102_AA01104|pyrimidine operon regulatory protein:conserved hypothetical protein|POSITIVE:POSITIVE|[761154,761294]|141 HSP 1 e-value: 1.0E-74 bit: 280.0 Len: 141 Query Start:1 Query End:141 Subject Strand: POSITIVE Subject Start: 1 Subject End: 141 aaggtttgcgaatgtgttgtgttgaagactaagatgcgggctacaatatcacaaatacggtgagttttctttacctgtatcaagaaaaccaccaaaagaaacgcaataaaaaccgaccgcacttttccaaagaaaaaatca aaggtttgcgaatgtgttgtgttgaagactaagatgcgggctacaatatcacaaatacggtgagttttctttacctgtatcaagaaaaccaccaaaagaaacgcaataaaaaccgaccgcacttttccaaagaaaaaatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGUUUGCGAAUGUGUUGUGUUGAAGACUAAGAUGCGGGCUACAAUAUCACAAAUACGGUGAGUUUUCUUUACCUGUAUCAAGAAAACCACCAAAAGAAACGCAAUAAAAACCGACCGCACUUUUCCAAAGAAAAAAUCA ..((((((((..((((..((((((.((.((........)))).)))))))))).....((((.((((((((..........))))))))))))........)))).....))))........(((((....)))))..... (-30.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUUUUUCUUUGGAAAAGUGCGGUCGGUUUUUAUUGCGUUUCUUUUGGUGGUUUUCUUGAUACAGGUAAAGAAAACUCACCGUAUUUGUGAUAUUGUAGCCCGCAUCUUAGUCUUCAACACAACACAUUCGCAAACCUU ..........(((((((..((((((.(...(..(((..((.......(((((((((((((..........)))))))).)))))....))..)))..)..).))))))....((.....))........))).)))).... (-28.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 411 131 95 176 138 aact:AA02706|5end_2-oxoglutarate_dehydrogenase_E1_component_(decarboxylase_component)_1886843..1887073_POSITIVE 411 131 95 50 12 aact:AA02705|5end_hypothetical_protein_1886717..1886947_POSITIVE 390 133 97 176 140 aact:AA01458|5end_aminotransferase_978820..979050_POSITIVE 372 125 89 193 157 aact:AA00268|5end_acyl_carrier_protein_(ACP)_188104..188334_POSITIVE 372 125 89 42 6 aact:AA00267|5end_hypothetical_protein_187953..188183_POSITIVE 370 126 97 127 98 aact:AA01436|5end_fructose-bisphosphate_aldolase_class_II_962981..963211_POSITIVE 368 131 96 218 181 aact:AA00347|5end_50S_ribosomal_protein_L11_232137..232367_POSITIVE 360 126 81 51 3 aact:AA02846|5end_crossover_junction_endodeoxyribonuclease_1998648..1998878_POSITIVE 346 128 96 203 171 aact:AA02944|5end_30S_ribosomal_protein_S20_2058688..2058918_POSITIVE 346 128 96 50 18 aact:AA02941|5end_hypothetical_protein_2058535..2058765_POSITIVE 333 128 96 125 93 aact:AA01603|5end_oligopeptidase_A_1082898..1083128_POSITIVE 328 128 106 209 187 aact:AA02191|5end_hypothetical_protein_1493318..1493548_POSITIVE 328 128 89 155 104 aact:AA00324|5end_tRNA_(Uracil-5-)-methyltransferase_(tRNA(M-5-U54)-methyltransferase)_220147..220377_POSITIVE 327 126 90 165 128 aact:AA02249|5end_thiamine_biosynthesis_protein_1528365..1528595_POSITIVE 314 48 1 183 136 aact:AA01347|5end_conserved_hypothetical_protein_913209..913439_POSITIVE 314 134 97 121 81 aact:AA01008|5end_mazG_beta-lactamase_regulatory_protein_homolog_703470..703700_POSITIVE 314 40 1 72 30 aact:AA00130|5end_mercuric_transport_protein_(periplasmic_mercury_ion_binding_protein)_(mercury_scavenger_protein)_94217..94447_POSITIVE 308 126 97 230 201 aact:AA02966|5end_conserved_hypothetical_protein_2074223..2074453_POSITIVE 308 126 97 76 47 aact:AA02965|5end_hypothetical_protein_2074069..2074299_POSITIVE 304 125 101 40 16 aact:AA00107|5end_histidyl-tRNA_synthetase_76699..76929_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 411 131 95 48 10 aact:AA02704|3end_dihydrolipoamide_succinyltransferase_1886795..1886945_POSITIVE 390 133 97 84 48 aact:AA01457|3end_D-xylose_ABC_transporter,_membrane_spanning_protein_978808..978958_POSITIVE 370 126 97 87 58 aact:AA01434|3end_conserved_hypothetical_protein_(possible_o-antigen_ligase)_963021..963171_POSITIVE 368 131 96 59 22 aact:AA00345|3end_transcription_antitermination_protein_232058..232208_POSITIVE 363 124 89 151 116 aact:AA00267|3end_hypothetical_protein_188143..188293_POSITIVE 357 129 96 87 54 aact:AA02443|3end_cytochrome_C_related_protein_1686590..1686740_POSITIVE 357 129 96 132 99 aact:AA02444|3end_hypothetical_protein_1686635..1686785_POSITIVE 346 128 96 87 55 aact:AA02940|3end_conserved_hypothetical_protein_2058652..2058802_POSITIVE 329 128 95 34 1 aact:AA02540|3end_5-methyltetrahydropteroyltriglutamate-homocystein_e_methyltransferase_1769499..1769649_POSITIVE 329 126 93 121 91 aact:AA02184|3end_anthranilate_isomerase;_indole-3-glycerol_phosphate_synthase;_phosphoribosylanthranilate_isomerase_1492541..1492691_POSITIVE 328 128 106 82 60 aact:AA02190|3end_hydrogenase-2_component_protein_1493271..1493421_POSITIVE 328 128 89 150 99 aact:AA00323|3end_conserved_hypothetical_protein_(possible_SAM-dependent_methyltransferase)_220222..220372_POSITIVE 327 126 90 75 38 aact:AA02246|3end_peptidase_E_1528355..1528505_POSITIVE 313 127 96 77 46 aact:AA01611|3end_anthranilate_synthase_component_II_1089619..1089769_POSITIVE 310 125 98 32 4 aact:AA00592|3end_conserved_hypothetical_protein_(membrane/transport_protein)_407286..407436_POSITIVE 308 126 97 55 26 aact:AA02964|3end_opacity_associated_protein_A_2074128..2074278_POSITIVE 303 130 97 136 101 aact:AA01259|3end_protoporphyrinogen_oxidase_854943..855093_POSITIVE 302 50 8 58 16 aact:AA01450|3end_hypothetical_protein_972032..972182_POSITIVE 299 126 97 41 12 aact:AA01563|3end_transketolase_isozyme_1_1049043..1049193_POSITIVE 298 40 1 106 70 aact:AA01033|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_A_723435..723585_POSITIVE