Origin IGS: ttttgctccttatacgccatagcatatagattttattttatacgctatgaagtatagaattgtgtttatatcttgtaaagtataaattatggtttatatcttatgcgatataaaataaaatgattaaaattcctaccgcactttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaagtgcggtaggaattttaatcattttattttatatcgcataagatataaaccataatttatactttacaagatataaacacaattctatacttcatagcgtataaaataaaatctatatgctatggcgtataaggagcaaaa Mask Tandem Repeat Region ================================================ ttttgctccttatacgccatagcatatagattttattttatacgctatgaagtatagaattgtgtttatatcttgtaaagtataaattatggtttatatcttatgcgatataaaataaaatgattaaaattcctaccgcactttta Find is-nt database================================================ Query_seq: AA01730:AA01731|AA01730:AA01731:conserved hypothetical protein (possible transcriptional regulator):multidrug resistance protein B:->->:1169144..1169289 146 ttttgctccttatacgccatagcatatagattttattttatacgctatgaagtatagaattgtgtttatatcttgtaaagtataaattatggtttatatcttatgcgatataaaataaaatgattaaaattcctaccgcactttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01730:AA01731|AA01730:AA01731:conserved hypothetical protein (possible transcriptional regulator):multidrug resistance protein B:->->:1169144..1169289 146 ttttgctccttatacgccatagcatatagattttattttatacgctatgaagtatagaattgtgtttatatcttgtaaagtataaattatggtttatatcttatgcgatataaaataaaatgattaaaattcctaccgcactttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01730:AA01731|AA01730:AA01731:conserved hypothetical protein (possible transcriptional regulator):multidrug resistance protein B:->->:1169144..1169289 146 ttttgctccttatacgccatagcatatagattttattttatacgctatgaagtatagaattgtgtttatatcttgtaaagtataaattatggtttatatcttatgcgatataaaataaaatgattaaaattcctaccgcactttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttgctccttatacgccatagcatatagattttattttatacgctatgaagtatagaattgtgtttatatcttgtaaagtataaattatggtttatatcttatgcgatataaaataaaatgattaaaattcctaccgcactttta Predict ORF larger than 30AA ================================================ ttttgctccttatacgccatagcatatagattttattttatacgctatgaagtatagaattgtgtttatatcttgtaaagtataaattatggtttatatcttatgcgatataaaataaaatgattaaaattcctaccgcactttta 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: 82 Start: 51 End: 80 ..................................................CTTTACAAGATATAAACACAATTCTATACT.................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 92 End: 121 ...........................................................................................GTTTATATCTTATGCGATATAAAATAAAAT......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttgctccttatacgccatagcatatagattttattttatacgctatgaagtatagaattgtgtttatatcttgtaaagtataaattatggtttatatcttatgcgatataaaataaaatgattaaaattcctaccgcactttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01730:AA01731|AA01730:AA01731:conserved hypothetical protein (possible transcriptional regulator):multidrug resistance protein B:->->:1169144..1169289 146 ttttgctccttatacgccatagcatatagattttattttatacgctatgaagtatagaattgtgtttatatcttgtaaagtataaattatggtttatatcttatgcgatataaaataaaatgattaaaattcctaccgcactttta Intra-Species Hit: Count: 1 Min: 1 Max: 146 Len: 146 Subject: aact_AA01730_AA01731|conserved hypothetical protein (possible transcriptional regulator):multidrug resistance protein B|POSITIVE:POSITIVE|[1169144,1169289]|146 HSP 1 e-value: 1.0E-77 bit: 289.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 ttttgctccttatacgccatagcatatagattttattttatacgctatgaagtatagaattgtgtttatatcttgtaaagtataaattatggtttatatcttatgcgatataaaataaaatgattaaaattcctaccgcactttta ttttgctccttatacgccatagcatatagattttattttatacgctatgaagtatagaattgtgtttatatcttgtaaagtataaattatggtttatatcttatgcgatataaaataaaatgattaaaattcctaccgcactttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGCUCCUUAUACGCCAUAGCAUAUAGAUUUUAUUUUAUACGCUAUGAAGUAUAGAAUUGUGUUUAUAUCUUGUAAAGUAUAAAUUAUGGUUUAUAUCUUAUGCGAUAUAAAAUAAAAUGAUUAAAAUUCCUACCGCACUUUUA ...(((....(((((..((((((.((((((......)))))).))))))..))))).(((..(.((((((((.(((((..(((((((....)))))))..))))).)))))))).....)..)))............)))...... (-32.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGUGCGGUAGGAAUUUUAAUCAUUUUAUUUUAUAUCGCAUAAGAUAUAAACCAUAAUUUAUACUUUACAAGAUAUAAACACAAUUCUAUACUUCAUAGCGUAUAAAAUAAAAUCUAUAUGCUAUGGCGUAUAAGGAGCAAAA ......(((.......................((((((((....(((.((((((......))))))))).....)))))))).....((((((((.((((((((((((..........)))))))))))).)))).)))))))... (-29.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 58 13 190 143 aact:AA01609|5end_p-aminobenzoate_synthase_component_I_homolog_1087903..1088133_POSITIVE 215 50 5 121 75 aact:AA01324|5end_50S_ribosomal_protein_L33_894495..894725_POSITIVE 211 50 3 128 72 aact:AA01566|5end_conserved_hypothetical_protein_1051811..1052041_POSITIVE 211 50 3 128 72 aact:AA01261|5end_conserved_hypothetical_protein_856443..856673_POSITIVE 201 54 15 97 57 aact:AA02439|5end_integral_membrane_protein;_possible_ABC_transporter_permease_1683902..1684132_POSITIVE 201 48 13 200 166 aact:AA00317|5end_DNA_mismatch_repair_protein_215472..215702_POSITIVE 198 60 11 210 161 aact:AA01717|5end_fumarate_hydratase,_class_II_1161189..1161419_POSITIVE 198 47 1 209 177 aact:AA00896|5end_prolyl-tRNA_synthetase_(proline-tRNA_ligase)_621414..621644_POSITIVE 198 47 1 80 48 aact:AA00895|5end_hypothetical_protein_621285..621515_POSITIVE 196 75 43 210 178 aact:AA02278|5end_conserved_hypothetical_protein_1550642..1550872_POSITIVE 196 140 91 106 63 aact:AA01837|5end_transcriptional_regulatory_protein_1235450..1235680_POSITIVE 193 70 21 206 170 aact:AA01734|5end_DNA-binding_protein;_DPS_family_protein_1172043..1172273_POSITIVE 193 46 3 69 18 aact:AA00106|5end_1-hydroxy-2-methyl-2-(E)-butenyl_4-diphosphate_synthase_75544..75774_POSITIVE 190 23 1 115 91 aact:AA00900|5end_conserved_hypothetical_protein_623442..623672_POSITIVE 190 81 41 218 179 aact:AA00057|5end_cytochrome_c-type_biogenesis_protein_44440..44670_POSITIVE 186 140 98 158 115 aact:AA01883|5end_recycling_protein;_permease_1269821..1270051_POSITIVE 185 140 91 134 88 aact:AA01020|5end_enonolase;_2-phosphoglycerate_dehydratase_712741..712971_POSITIVE 184 47 3 68 28 aact:AA00871|5end_rough_colony_protein_A_602561..602791_POSITIVE 183 44 15 187 160 aact:AA02589|5end_NAD(P)H_oxidoreductase_1800493..1800723_POSITIVE 183 77 43 52 7 aact:AA01238|5end_50S_ribosomal_protein_L36_844248..844478_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 222 107 68 146 111 aact:AA00113|3end_uracil_phosphoribosyltransferase_81989..82139_POSITIVE 215 50 5 106 60 aact:AA01323|3end_50S_ribosomal_protein_L28_894560..894710_POSITIVE 206 48 4 73 22 aact:AA01441|3end_tRNA/rRNA_methylase_967643..967793_POSITIVE 204 56 11 80 35 aact:AA01730|3end_conserved_hypothetical_protein_(possible_transcriptional_regulator)_1169083..1169233_POSITIVE 203 50 1 71 13 aact:AA00882|3end_hypothetical_protein_613645..613795_POSITIVE 201 54 15 107 67 aact:AA02438|3end_membrane_protein;_possible_ABC_transporter_permease_protein_1683992..1684142_POSITIVE 198 60 11 103 54 aact:AA01715|3end_conserved_hypothetical_protein_1161162..1161312_POSITIVE 198 47 1 65 33 aact:AA00894|3end_selenium_transferase_(Cysteinyl-tRNA(Sec)_selenium_transferase)_621350..621500_POSITIVE 193 70 21 74 38 aact:AA01733|3end_hypothetical_protein_1171991..1172141_POSITIVE 193 46 3 54 3 aact:AA00105|3end_conserved_hypothetical_protein_75609..75759_POSITIVE 190 23 1 72 48 aact:AA00899|3end_possible_quaternary_ammonium_compound_resistance_protein_623479..623629_POSITIVE 188 53 15 110 65 aact:AA01614|3end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_1090719..1090869_POSITIVE 184 47 3 63 23 aact:AA00870|3end_rough_colony_protein_C_602636..602786_POSITIVE 182 66 24 143 103 aact:AA01045|3end_S-adenosylmethionine-dependent_methyltransferase_728908..729058_POSITIVE 180 31 4 137 111 aact:AA02978|3end_sufI_protein_precursor_homolog_2083308..2083458_POSITIVE 180 140 117 142 119 aact:AA01092|3end_hypothetical_protein_756361..756511_POSITIVE 180 140 106 128 93 aact:AA00500|3end_hypothetical_protein_347356..347506_POSITIVE 180 140 106 51 16 aact:AA00499|3end_pyridoxamine-5'-phosphate_oxidase_347279..347429_POSITIVE 177 109 71 131 104 aact:AA00684|3end_adenylosuccinate_synthase_468861..469011_POSITIVE 175 30 1 48 18 aact:AA02407|3end_thymidine_kinase_1653240..1653390_POSITIVE