Origin IGS: tggcaaatccttattttgtcgttatagtttttccatgaggctgttatattttaaacaagctctattttatagttgcaacattattgtaacaataaaaaaatacataattcggcatattagaatttaattttatgatctaagtcataaaatttcatacttcaatctcttgttgccaaaataaaaaatcctccgatgcaatgcatcatcggaggataattgagcgcaaggctcaaagttacacacaaaaacagaaactctctttta .........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 taaaagagagtttctgtttttgtgtgtaactttgagccttgcgctcaattatcctccgatgatgcattgcatcggaggattttttattttggcaacaagagattgaagtatgaaattttatgacttagatcataaaattaaattctaatatgccgaattatgtatttttttattgttacaataatgttgcaactataaaatagagcttgtttaaaatataacagcctcatggaaaaactataacgacaaaataaggatttgcca Mask Tandem Repeat Region ================================================ tggcaaatccttattttgtcgttatagtttttccatgaggctgttatattttaaacaagctctattttatagttgcaacattattgtaacaataaaaaaatacataattcggcatattagaatttaattttatgatctaagtcataaaatttcatacttcaatctcttgttgccaaaataaaaaatcctccgatgcaatgcatcatcggaggataattgagcgcaaggctcaaagttacacacaaaaacagaaactctctttta Find is-nt database================================================ Query_seq: AA02902:AA02903|AA02902:AA02903:aerobic respiration control protein:conserved hypothetical protein (ribosomal protein L36):->->:2032016..2032279 264 tggcaaatccttattttgtcgttatagtttttccatgaggctgttatattttaaacaagctctattttatagttgcaacattattgtaacaataaaaaaatacataattcggcatattagaatttaattttatgatctaagtcataaaatttcatacttcaatctcttgttgccaaaataaaaaatcctccgatgcaatgcatcatcggaggataattgagcgcaaggctcaaagttacacacaaaaacagaaactctctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02902:AA02903|AA02902:AA02903:aerobic respiration control protein:conserved hypothetical protein (ribosomal protein L36):->->:2032016..2032279 264 tggcaaatccttattttgtcgttatagtttttccatgaggctgttatattttaaacaagctctattttatagttgcaacattattgtaacaataaaaaaatacataattcggcatattagaatttaattttatgatctaagtcataaaatttcatacttcaatctcttgttgccaaaataaaaaatcctccgatgcaatgcatcatcggaggataattgagcgcaaggctcaaagttacacacaaaaacagaaactctctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02902:AA02903|AA02902:AA02903:aerobic respiration control protein:conserved hypothetical protein (ribosomal protein L36):->->:2032016..2032279 264 tggcaaatccttattttgtcgttatagtttttccatgaggctgttatattttaaacaagctctattttatagttgcaacattattgtaacaataaaaaaatacataattcggcatattagaatttaattttatgatctaagtcataaaatttcatacttcaatctcttgttgccaaaataaaaaatcctccgatgcaatgcatcatcggaggataattgagcgcaaggctcaaagttacacacaaaaacagaaactctctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tggcaaatccttattttgtcgttatagtttttccatgaggctgttatattttaaacaagctctattttatagttgcaacattattgtaacaataaaaaaatacataattcggcatattagaatttaattttatgatctaagtcataaaatttcatacttcaatctcttgttgccaaaataaaaaatcctccgatgcaatgcatcatcggaggataattgagcgcaaggctcaaagttacacacaaaaacagaaactctctttta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 35 End: 124 .................................. M R L L Y F K Q A L F Y S C N I I V T I K K Y I I R H I R I ............................................................................................................................................ Protein_Len: 40 Strand: + Start: 144 End: 263 ............................................................................................................................................... M K F H T S I S C C Q N K K S S D A M H H R R I I E R K A Q S Y T Q K Q K L S F . Protein_Len: 30 Strand: - Start: 162 End: 251 ................................................................................................................................................................. D R T A L I F F G G I C H M M P P Y N L A L S L T V C L F M ............. Protein_Len: 33 Strand: - Start: 145 End: 243 ................................................................................................................................................ L I E Y K L R K N G F Y F I R R H L A D D S S L Q A C P E F N C M ..................... tggcaaatccttattttgtcgttatagtttttccatgaggctgttatattttaaacaagctctattttatagttgcaacattattgtaacaataaaaaaatacataattcggcatattagaatttaattttatgatctaagtcataaaatttcatacttcaatctcttgttgccaaaataaaaaatcctccgatgcaatgcatcatcggaggataattgagcgcaaggctcaaagttacacacaaaaacagaaactctctttta 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: 64 End: 93 ...............................................................ATTGTTACAATAATGTTGCAACTATAAAAT........................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: -1 End: 28 ttTGGCAAATCCTTATTTTGTCGTTATAGT............................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tggcaaatccttattttgtcgttatagtttttccatgaggctgttatattttaaacaagctctattttatagttgcaacattattgtaacaataaaaaaatacataattcggcatattagaatttaattttatgatctaagtcataaaatttcatacttcaatctcttgttgccaaaataaaaaatcctccgatgcaatgcatcatcggaggataattgagcgcaaggctcaaagttacacacaaaaacagaaactctctttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 53 HP_score: -4.6 Tail_Score: -3.25786 Start: 128 End: 149 Full_Region: gattgaagtatgaaa ttttatga cttaga tcataaaa ttaaattctaatatg ...............................................................................................................................ttttatgacttagatcataaaa................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -11.4 Tail_Score: -5.79595 Start: 186 End: 213 Full_Region: ccttgcgctcaatta tcctccgatg atgcattg catcggagga ttttttattttggca .........................................................................................................................................................................................tcctccgatgatgcattgcatcggagga................................................... Find igs database================================================ Query_seq: AA02902:AA02903|AA02902:AA02903:aerobic respiration control protein:conserved hypothetical protein (ribosomal protein L36):->->:2032016..2032279 264 tggcaaatccttattttgtcgttatagtttttccatgaggctgttatattttaaacaagctctattttatagttgcaacattattgtaacaataaaaaaatacataattcggcatattagaatttaattttatgatctaagtcataaaatttcatacttcaatctcttgttgccaaaataaaaaatcctccgatgcaatgcatcatcggaggataattgagcgcaaggctcaaagttacacacaaaaacagaaactctctttta Intra-Species Hit: Count: 1 Min: 1 Max: 264 Len: 264 Subject: aact_AA02902_AA02903|aerobic respiration control protein:conserved hypothetical protein (ribosomal protein L36)|POSITIVE:POSITIVE|[2032016,2032279]|264 HSP 1 e-value: 1.0E-135 bit: 482.0 Len: 264 Query Start:1 Query End:264 Subject Strand: POSITIVE Subject Start: 1 Subject End: 264 tggcaaatccttattttgtcgttatagtttttccatgaggctgttatattttaaacaagctctattttatagttgcaacattattgtaacaatnnnnnnntacataattcggcatattagaatttaattttatgatctaagtcataaaatttcatacttcaatctcttgttgccaaaataaaaaatcctccgatgcaatgcatcatcggaggataattgagcgcaaggctcaaagttacacacaaaaacagaaactctctttta tggcaaatccttattttgtcgttatagtttttccatgaggctgttatattttaaacaagctctattttatagttgcaacattattgtaacaataaaaaaatacataattcggcatattagaatttaattttatgatctaagtcataaaatttcatacttcaatctcttgttgccaaaataaaaaatcctccgatgcaatgcatcatcggaggataattgagcgcaaggctcaaagttacacacaaaaacagaaactctctttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGCAAAUCCUUAUUUUGUCGUUAUAGUUUUUCCAUGAGGCUGUUAUAUUUUAAACAAGCUCUAUUUUAUAGUUGCAACAUUAUUGUAACAAUAAAAAAAUACAUAAUUCGGCAUAUUAGAAUUUAAUUUUAUGAUCUAAGUCAUAAAAUUUCAUACUUCAAUCUCUUGUUGCCAAAAUAAAAAAUCCUCCGAUGCAAUGCAUCAUCGGAGGAUAAUUGAGCGCAAGGCUCAAAGUUACACACAAAAACAGAAACUCUCUUUUA .((((((.......))))))................(((.(((((.((((((.((((((.....((((((.(((((((.....))))))).))))))......................(((...(((((((((((....)))))))))))......))).....))))))...))))))....(((((((((((........)))))))))))..((((((.....)))))).............)))))...)))....... (-61.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGAGAGUUUCUGUUUUUGUGUGUAACUUUGAGCCUUGCGCUCAAUUAUCCUCCGAUGAUGCAUUGCAUCGGAGGAUUUUUUAUUUUGGCAACAAGAGAUUGAAGUAUGAAAUUUUAUGACUUAGAUCAUAAAAUUAAAUUCUAAUAUGCCGAAUUAUGUAUUUUUUUAUUGUUACAAUAAUGUUGCAACUAUAAAAUAGAGCUUGUUUAAAAUAUAACAGCCUCAUGGAAAAACUAUAACGACAAAAUAAGGAUUUGCCA ......((..(((((..(((((((((((((.((((((.....))))))..(((((((((((........)))))))))))....((.(((((((.(((....))).((.((..((((((((((......))))))))))..)).))....))))))).)).........((((((...)))))).))))))..)))))))..(((.(((((........))))).)))..)))))..))...............((.....)). (-58.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 230 181 146 92 aact:AA00992|5end_ribonuclease_BN_693661..693891_POSITIVE 320 230 187 225 182 aact:AA00537|5end_conserved_hypothetical_protein_367992..368222_POSITIVE 314 230 189 211 169 aact:AA02125|5end_conserved_hypothetical_protein;_possible_universal_stress_protein_1449412..1449642_POSITIVE 309 223 186 85 42 aact:AA01173|5end_VapD-homolog_803850..804080_POSITIVE 301 223 191 43 7 aact:AA00208|5end_D-ribose_ABC_transporter,_permease_protein_/_Galactoside_transport_system_permease_protein_144097..144327_POSITIVE 300 229 185 171 122 aact:AA00957|5end_porphobilinogen_deaminase_(hydroxymethylbilane_synthase)_661006..661236_POSITIVE 300 230 183 224 169 aact:AA00165|5end_conserved_hypothetical_protein_117358..117588_POSITIVE 299 229 188 50 2 aact:AA02947|5end_riboflavin_biosynthesis_protein_2060871..2061101_POSITIVE 297 229 187 171 131 aact:AA02910|5end_ribonuclease_E_2036137..2036367_POSITIVE 297 209 161 195 147 aact:AA01568|5end_dipeptide_transport_system_ATP-binding_protein_1056037..1056267_POSITIVE 284 229 184 125 69 aact:AA01066|5end_conserved_hypothetical_protein_738380..738610_POSITIVE 283 229 182 222 178 aact:AA00605|5end_CDP-diglyceride_pyrophosphorylase_410930..411160_POSITIVE 282 214 171 65 19 aact:AA02060|5end_cardiolipin_synthase_1401956..1402186_POSITIVE 281 236 194 195 141 aact:AA01039|5end_transcriptional_regulator_(possible_murein_gene_regulator)_723864..724094_POSITIVE 279 229 189 184 144 aact:AA02132|5end_dihydroorotate_dehydrogenase_1455089..1455319_POSITIVE 279 229 187 76 27 aact:AA00269|5end_3-oxoacyl-(acyl-carrier-protein)_reductase/short-chain_alcohol_dehydrogenase_188608..188838_POSITIVE 278 229 186 49 4 aact:AA01830|5end_2,3-cyclic-nucleotide_2-phosphodiesterase_1231556..1231786_POSITIVE 278 229 185 215 178 aact:AA00971|5end_conserved_hypothetical_protein_677208..677438_POSITIVE 277 232 194 60 27 aact:AA02371|5end_oxygen-independent_coproporphyrinogen_III_oxidase_1624580..1624810_POSITIVE 277 230 188 74 30 aact:AA00343|5end_conserved_hypothetical_protein_(possible_cytosolic_protein)_229908..230138_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 230 181 146 92 aact:AA00991|3end_conserved_hypothetical_protein_693741..693891_POSITIVE 314 230 189 89 47 aact:AA02124|3end_anaerobic_regulatory_protein;_transcription_regulator_Fnr_1449370..1449520_POSITIVE 301 223 191 43 7 aact:AA00207|3end_D-ribose_ABC_transporter,_ATP-binding_protein_/_galactoside_ABC_transporter,_ATP-binding_protein_144177..144327_POSITIVE 296 229 187 75 24 aact:AA01829|3end_hypothetical_protein_1231662..1231812_POSITIVE 284 229 184 57 1 aact:AA01064|3end_conserved_hypothetical_protein_(possible_aminomethyltransferase)_738392..738542_POSITIVE 277 232 194 48 15 aact:AA02369|3end_conserved_hypothetical_protein_1624648..1624798_POSITIVE 271 238 191 146 89 aact:AA00988|3end_conserved_hypothetical_protein_692264..692414_POSITIVE 267 251 214 43 7 aact:AA01805|3end_electron_transport_complex_protein_1216773..1216923_POSITIVE 266 250 202 78 37 aact:AA01136|3end_hypothetical_protein_778502..778652_POSITIVE 265 229 182 43 2 aact:AA01158|3end_ribosome_associated_heat_shock_protein_15_homolog_792892..793042_POSITIVE 261 229 183 106 52 aact:AA02048|3end_galactitol_utilization_operon_repressor_1395579..1395729_POSITIVE 259 228 183 83 35 aact:AA02575|3end_transmembrane_protein_1794518..1794668_POSITIVE 259 230 185 122 71 aact:AA01679|3end_aspartate-semialdehyde_dehydrogenase;_PTS_system_enzyme_II_A_component_1135236..1135386_POSITIVE 253 229 192 48 12 aact:AA00686|3end_hypothetical_protein_469219..469369_POSITIVE 250 223 185 150 106 aact:AA00954|3end_uroporphyrinogen_III_synthase_661070..661220_POSITIVE 250 242 204 140 111 aact:AA00616|3end_phosphatidate_cytidylyltransferase_422971..423121_POSITIVE 250 229 187 130 82 aact:AA00205|3end_ribose_ABC_transporter_protein_/_high_affinity_D-ribose_transport_protein_142658..142808_POSITIVE 249 230 183 74 14 aact:AA01842|3end_conserved_hypothetical_protein_1238467..1238617_POSITIVE 246 230 186 56 11 aact:AA01709|3end_glutathione-S-transferase-nitroreductase_A_fusion_protein;_modulator_of_drug_activity_A_1159334..1159484_POSITIVE 245 46 16 151 115 aact:AA02714|3end_paraquat-inducible_protein_PqiA_homolog_1897167..1897317_POSITIVE