Origin IGS: gataattcctaaatggtttatttataaatgcggttaatcagattatttttttttataaatccaataaaaaaatctcttttgcccaatatttccattttgcatacaatacaacaatacttagtgtttggtactttcttactggttaaagagtttccaattaagtatgatgttgtgtttgcatattgtttggttgttccaaacgaagtaacaaaagttactattttatttcctgtatattaggcttattcgccggacaccgctccctaaaaagagcggtgttttttatggctgaattctaacatagttatctgccgatttcctgctcccgctcacaaatccgagtgcgcttcgcttcttcgcccaaaatttcatttgtttttgtgattaaaatattttaaatccttatggaataaggtagattaaaaataacctaaataacaatatacacataaggaaaaact .........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.........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 agtttttccttatgtgtatattgttatttaggttatttttaatctaccttattccataaggatttaaaatattttaatcacaaaaacaaatgaaattttgggcgaagaagcgaagcgcactcggatttgtgagcgggagcaggaaatcggcagataactatgttagaattcagccataaaaaacaccgctctttttagggagcggtgtccggcgaataagcctaatatacaggaaataaaatagtaacttttgttacttcgtttggaacaaccaaacaatatgcaaacacaacatcatacttaattggaaactctttaaccagtaagaaagtaccaaacactaagtattgttgtattgtatgcaaaatggaaatattgggcaaaagagatttttttattggatttataaaaaaaaataatctgattaaccgcatttataaataaaccatttaggaattatc Mask Tandem Repeat Region ================================================ gataattcctaaatggtttatttataaatgcggttaatcagattatttttttttataaatccaataaaaaaatctcttttgcccaatatttccattttgcatacaatacaacaatacttagtgtttggtactttcttactggttaaagagtttccaattaagtatgatgttgtgtttgcatattgtttggttgttccaaacgaagtaacaaaagttactattttatttcctgtatattaggcttattcgccggacaccgctccctaaaaagagcggtgttttttatggctgaattctaacatagttatctgccgatttcctgctcccgctcacaaatccgagtgcgcttcgcttcttcgcccaaaatttcatttgtttttgtgattaaaatattttaaatccttatggaataaggtagattaaaaataacctaaataacaatatacacataaggaaaaact Find is-nt database================================================ Query_seq: AA01794:AA01796|AA01794:AA01796:glycine cleavage system transcription activator:branched-chain amino acid aminotransferase:->->:1210751..1211211 461 gataattcctaaatggtttatttataaatgcggttaatcagattatttttttttataaatccaataaaaaaatctcttttgcccaatatttccattttgcatacaatacaacaatacttagtgtttggtactttcttactggttaaagagtttccaattaagtatgatgttgtgtttgcatattgtttggttgttccaaacgaagtaacaaaagttactattttatttcctgtatattaggcttattcgccggacaccgctccctaaaaagagcggtgttttttatggctgaattctaacatagttatctgccgatttcctgctcccgctcacaaatccgagtgcgcttcgcttcttcgcccaaaatttcatttgtttttgtgattaaaatattttaaatccttatggaataaggtagattaaaaataacctaaataacaatatacacataaggaaaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01794:AA01796|AA01794:AA01796:glycine cleavage system transcription activator:branched-chain amino acid aminotransferase:->->:1210751..1211211 461 gataattcctaaatggtttatttataaatgcggttaatcagattatttttttttataaatccaataaaaaaatctcttttgcccaatatttccattttgcatacaatacaacaatacttagtgtttggtactttcttactggttaaagagtttccaattaagtatgatgttgtgtttgcatattgtttggttgttccaaacgaagtaacaaaagttactattttatttcctgtatattaggcttattcgccggacaccgctccctaaaaagagcggtgttttttatggctgaattctaacatagttatctgccgatttcctgctcccgctcacaaatccgagtgcgcttcgcttcttcgcccaaaatttcatttgtttttgtgattaaaatattttaaatccttatggaataaggtagattaaaaataacctaaataacaatatacacataaggaaaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01794:AA01796|AA01794:AA01796:glycine cleavage system transcription activator:branched-chain amino acid aminotransferase:->->:1210751..1211211 461 gataattcctaaatggtttatttataaatgcggttaatcagattatttttttttataaatccaataaaaaaatctcttttgcccaatatttccattttgcatacaatacaacaatacttagtgtttggtactttcttactggttaaagagtttccaattaagtatgatgttgtgtttgcatattgtttggttgttccaaacgaagtaacaaaagttactattttatttcctgtatattaggcttattcgccggacaccgctccctaaaaagagcggtgttttttatggctgaattctaacatagttatctgccgatttcctgctcccgctcacaaatccgagtgcgcttcgcttcttcgcccaaaatttcatttgtttttgtgattaaaatattttaaatccttatggaataaggtagattaaaaataacctaaataacaatatacacataaggaaaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gataattcctaaatggtttatttataaatgcggttaatcagattatttttttttataaatccaataaaaaaatctcttttgcccaatatttccattttgcatacaatacaacaatacttagtgtttggtactttcttactggttaaagagtttccaattaagtatgatgttgtgtttgcatattgtttggttgttccaaacgaagtaacaaaagttactattttatttcctgtatattaggcttattcgccggacaccgctccctaaaaagagcggtgttttttatggctgaattctaacatagttatctgccgatttcctgctcccgctcacaaatccgagtgcgcttcgcttcttcgcccaaaatttcatttgtttttgtgattaaaatattttaaatccttatggaataaggtagattaaaaataacctaaataacaatatacacataaggaaaaact Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 24 End: 143 ....................... M N A V N Q I I F F Y K S N K K I S F A Q Y F H F A Y N T T I L S V W Y F L T G .............................................................................................................................................................................................................................................................................................................................. Protein_Len: 60 Strand: + Start: 28 End: 237 ........................... M R L I R L F F F I N P I K K S L L P N I S I L H T I Q Q Y L V F G T F L L V K E F P I K Y D V V F A Y C L V V P N E V ................................................................................................................................................................................................................................ Protein_Len: 39 Strand: + Start: 180 End: 296 ................................................................................................................................................................................... M L F G C S K R S N K S Y Y F I S C I L G L F A G H R S L K R A V F F M A E F ..................................................................................................................................................................... Protein_Len: 31 Strand: + Start: 289 End: 381 ................................................................................................................................................................................................................................................................................................ M N S N I V I C R F P A P A H K S E C A S L L R P K F H L F L ................................................................................ Protein_Len: 60 Strand: - Start: 21 End: 221 .................... N N K K I F G I F F D R K G L I E M K C V I C C Y K T N P V K K S T L S N G I L Y S T T N A Y Q K T T G F S T V F T V M ................................................................................................................................................................................................................................................ gataattcctaaatggtttatttataaatgcggttaatcagattatttttttttataaatccaataaaaaaatctcttttgcccaatatttccattttgcatacaatacaacaatacttagtgtttggtactttcttactggttaaagagtttccaattaagtatgatgttgtgtttgcatattgtttggttgttccaaacgaagtaacaaaagttactattttatttcctgtatattaggcttattcgccggacaccgctccctaaaaagagcggtgttttttatggctgaattctaacatagttatctgccgatttcctgctcccgctcacaaatccgagtgcgcttcgcttcttcgcccaaaatttcatttgtttttgtgattaaaatattttaaatccttatggaataaggtagattaaaaataacctaaataacaatatacacataaggaaaaact 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: 86 Start: 78 End: 107 .............................................................................TTTGCCCAATATTTCCATTTTGCATACAAT.................................................................................................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gataattcctaaatggtttatttataaatgcggttaatcagattatttttttttataaatccaataaaaaaatctcttttgcccaatatttccattttgcatacaatacaacaatacttagtgtttggtactttcttactggttaaagagtttccaattaagtatgatgttgtgtttgcatattgtttggttgttccaaacgaagtaacaaaagttactattttatttcctgtatattaggcttattcgccggacaccgctccctaaaaagagcggtgttttttatggctgaattctaacatagttatctgccgatttcctgctcccgctcacaaatccgagtgcgcttcgcttcttcgcccaaaatttcatttgtttttgtgattaaaatattttaaatccttatggaataaggtagattaaaaataacctaaataacaatatacacataaggaaaaact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -9.6 Tail_Score: -5.28176 Start: 255 End: 278 Full_Region: GGCTTATTCGCCGGA CACCGCTC CCTAAAAA GAGCGGTG TTTTTTATGGCTGAA ..............................................................................................................................................................................................................................................................CACCGCTCCCTAAAAAGAGCGGTG....................................................................................................................................................................................... Find igs database================================================ Query_seq: AA01794:AA01796|AA01794:AA01796:glycine cleavage system transcription activator:branched-chain amino acid aminotransferase:->->:1210751..1211211 461 gataattcctaaatggtttatttataaatgcggttaatcagattatttttttttataaatccaataaaaaaatctcttttgcccaatatttccattttgcatacaatacaacaatacttagtgtttggtactttcttactggttaaagagtttccaattaagtatgatgttgtgtttgcatattgtttggttgttccaaacgaagtaacaaaagttactattttatttcctgtatattaggcttattcgccggacaccgctccctaaaaagagcggtgttttttatggctgaattctaacatagttatctgccgatttcctgctcccgctcacaaatccgagtgcgcttcgcttcttcgcccaaaatttcatttgtttttgtgattaaaatattttaaatccttatggaataaggtagattaaaaataacctaaataacaatatacacataaggaaaaact Intra-Species Hit: Count: 1 Min: 1 Max: 461 Len: 461 Subject: aact_AA01794_AA01796|glycine cleavage system transcription activator:branched-chain amino acid aminotransferase|POSITIVE:POSITIVE|[1210751,1211211]|461 HSP 1 e-value: 0.0 bit: 819.0 Len: 461 Query Start:1 Query End:461 Subject Strand: POSITIVE Subject Start: 1 Subject End: 461 gataattcctaaatggtttatttataaatgcggttaatcagattannnnnnnnnataaatccaatnnnnnnntctcttttgcccaatatttccattttgcatacaatacaacaatacttagtgtttggtactttcttactggttaaagagtttccaattaagtatgatgttgtgtttgcatattgtttggttgttccaaacgaagtaacaaaagttactattttatttcctgtatattaggcttattcgccggacaccgctccctaaaaagagcggtgttttttatggctgaattctaacatagttatctgccgatttcctgctcccgctcacaaatccgagtgcgcttcgcttcttcgcccaaaatttcatttgtttttgtgattaaaatattttaaatccttatggaataaggtagattaaaaataacctaaataacaatatacacataaggaaaaact gataattcctaaatggtttatttataaatgcggttaatcagattatttttttttataaatccaataaaaaaatctcttttgcccaatatttccattttgcatacaatacaacaatacttagtgtttggtactttcttactggttaaagagtttccaattaagtatgatgttgtgtttgcatattgtttggttgttccaaacgaagtaacaaaagttactattttatttcctgtatattaggcttattcgccggacaccgctccctaaaaagagcggtgttttttatggctgaattctaacatagttatctgccgatttcctgctcccgctcacaaatccgagtgcgcttcgcttcttcgcccaaaatttcatttgtttttgtgattaaaatattttaaatccttatggaataaggtagattaaaaataacctaaataacaatatacacataaggaaaaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAAUUCCUAAAUGGUUUAUUUAUAAAUGCGGUUAAUCAGAUUAUUUUUUUUUAUAAAUCCAAUAAAAAAAUCUCUUUUGCCCAAUAUUUCCAUUUUGCAUACAAUACAACAAUACUUAGUGUUUGGUACUUUCUUACUGGUUAAAGAGUUUCCAAUUAAGUAUGAUGUUGUGUUUGCAUAUUGUUUGGUUGUUCCAAACGAAGUAACAAAAGUUACUAUUUUAUUUCCUGUAUAUUAGGCUUAUUCGCCGGACACCGCUCCCUAAAAAGAGCGGUGUUUUUUAUGGCUGAAUUCUAACAUAGUUAUCUGCCGAUUUCCUGCUCCCGCUCACAAAUCCGAGUGCGCUUCGCUUCUUCGCCCAAAAUUUCAUUUGUUUUUGUGAUUAAAAUAUUUUAAAUCCUUAUGGAAUAAGGUAGAUUAAAAAUAACCUAAAUAACAAUAUACACAUAAGGAAAAACU .....(((((..(((((.((((.....((((((..(((.((((....(((((((((.......)))))))))...((((((................((((...((((((((((((((((((...(((....(((((........)))))...))))))))))))..)))))))))))))..((((((((.....)))))))).....)))))).....)))).)))..)))))).(((((.(((((.((((((((((((((........)))))))))).....)))).................(((((((...((((.((....))(((((((..((((((......((......)).........))))))..)))))))......................))))...)))))))....)))))))))).....)))).)).))).)))))..... (-106.86) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUUUCCUUAUGUGUAUAUUGUUAUUUAGGUUAUUUUUAAUCUACCUUAUUCCAUAAGGAUUUAAAAUAUUUUAAUCACAAAAACAAAUGAAAUUUUGGGCGAAGAAGCGAAGCGCACUCGGAUUUGUGAGCGGGAGCAGGAAAUCGGCAGAUAACUAUGUUAGAAUUCAGCCAUAAAAAACACCGCUCUUUUUAGGGAGCGGUGUCCGGCGAAUAAGCCUAAUAUACAGGAAAUAAAAUAGUAACUUUUGUUACUUCGUUUGGAACAACCAAACAAUAUGCAAACACAACAUCAUACUUAAUUGGAAACUCUUUAACCAGUAAGAAAGUACCAAACACUAAGUAUUGUUGUAUUGUAUGCAAAAUGGAAAUAUUGGGCAAAAGAGAUUUUUUUAUUGGAUUUAUAAAAAAAAAUAAUCUGAUUAACCGCAUUUAUAAAUAAACCAUUUAGGAAUUAUC .((..(((((.(((.((.((((((((.(((((((((((((.((((.((...((((......................(((((((..((((......))))..(((....(((...)))..)))..)))))))((....)).))))...)).))))..........((((((((((.......(((((((((((....)))))))))))..)))......(((((((((..............((((((....))))))..((((((.....))))))..(((((((..((((((..(((((((.((((....((((........)))).....))))....))))))))))))).)))))))..........))))))))).................)))))))......))))))))))))).))))..........)))).)))))..)))))..)). (-109.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 412 289 248 164 110 aact:AA00454|5end_conserved_hypothetical_protein_318020..318250_POSITIVE 398 360 311 227 182 aact:AA01688|5end_conserved_hypothetical_protein;_possible_membrane_protein_1139635..1139865_POSITIVE 392 370 324 228 188 aact:AA00208|5end_D-ribose_ABC_transporter,_permease_protein_/_Galactoside_transport_system_permease_protein_144097..144327_POSITIVE 383 359 311 63 7 aact:AA00475|5end_conserved_hypothetical_protein_(possible_N6-adenine-specific_methylase)_331621..331851_POSITIVE 376 290 245 95 52 aact:AA02023|5end_NADH_dehydrogenase_1376701..1376931_POSITIVE 369 345 310 177 140 aact:AA00887|5end_hypothetical_protein_616739..616969_POSITIVE 364 358 311 112 60 aact:AA01335|5end_primosomal_protein_N'_901993..902223_POSITIVE 357 299 258 223 179 aact:AA01575|5end_conserved_hypothetical_protein_1061664..1061894_POSITIVE 357 284 250 171 137 aact:AA00501|5end_hypothetical_protein_347293..347523_POSITIVE 353 360 319 217 169 aact:AA02017|5end_conserved_hypothetical_protein_1371656..1371886_POSITIVE 351 359 320 197 152 aact:AA00535|5end_hypothetical_protein_365695..365925_POSITIVE 349 363 321 219 178 aact:AA00930|5end_pantothenate_kinase_640275..640505_POSITIVE 349 328 288 169 129 aact:AA00918|5end_hypothetical_protein_630044..630274_POSITIVE 348 288 241 191 134 aact:AA02179|5end_anthanilate_phosphoribosyltransferase_1489367..1489597_POSITIVE 348 360 311 207 140 aact:AA00796|5end_iron(III)_dicitrate_transport_system_permease_protein_545686..545916_POSITIVE 347 360 314 185 140 aact:AA02731|5end_outer_membrane_lipoprotein_carrier_precursor_1911498..1911728_POSITIVE 340 346 309 156 108 aact:AA01996|5end_prephenate_dehydrogenase_1355314..1355544_POSITIVE 337 346 307 53 7 aact:AA00383|5end_chloride_channel_protein_258894..259124_POSITIVE 336 285 245 81 38 aact:AA01908|5end_conserved_hypothetical_protein_1287068..1287298_POSITIVE 334 354 311 63 20 aact:AA00993|5end_possible_D-tyrosyl-tRNA(Tyr)_deacylase_694488..694718_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 412 289 248 73 19 aact:AA00453|3end_phosphoglyceromutase_318009..318159_POSITIVE 383 359 311 86 30 aact:AA00474|3end_cell_division_protein_Y_(GTP-binding_signal_recognition_particle)_331724..331874_POSITIVE 376 290 245 68 25 aact:AA02022|3end_hypothetical_protein_1376754..1376904_POSITIVE 357 284 250 77 43 aact:AA00499|3end_pyridoxamine-5'-phosphate_oxidase_347279..347429_POSITIVE 334 354 311 63 20 aact:AA00992|3end_ribonuclease_BN_694568..694718_POSITIVE 330 281 250 151 120 aact:AA00500|3end_hypothetical_protein_347356..347506_POSITIVE 329 360 313 144 94 aact:AA01168|3end_6-phosphogluconolactonase_802018..802168_POSITIVE 327 287 248 79 30 aact:AA00345|3end_transcription_antitermination_protein_232058..232208_POSITIVE 318 278 240 61 24 aact:AA02366|3end_hypothetical_protein_1623252..1623402_POSITIVE 316 278 239 33 6 aact:AA02977|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase_2081888..2082038_POSITIVE 316 352 311 148 101 aact:AA02046|3end_PTS_system_galactitol-specific_enzyme_IIC_1393687..1393837_POSITIVE 314 360 311 61 8 aact:AA02075|3end_conserved_hypothetical_protein_1409979..1410129_POSITIVE 313 289 246 137 95 aact:AA00985|3end_transcriptional_regulator_(LysR_family)_689741..689891_POSITIVE 311 289 241 131 71 aact:AA02545|3end_conserved_hypothetical_protein_1774221..1774371_POSITIVE 311 290 243 144 92 aact:AA00682|3end_S-adenosylmethionine-dependent_methyltransferase_467475..467625_POSITIVE 311 359 312 151 103 aact:AA00531|3end_DNA_polymerase_I_365385..365535_POSITIVE 308 289 245 64 13 aact:AA01881|3end_adenylate_kinase_1269765..1269915_POSITIVE 306 369 322 79 29 aact:AA01289|3end_hypothetical_protein_872848..872998_POSITIVE 306 349 303 98 32 aact:AA01053|3end_conserved_hypothetical_protein_733747..733897_POSITIVE 305 347 301 134 90 aact:AA01284|3end_heat_shock_protein_(hsp60)_870294..870444_POSITIVE