Origin IGS: attttctagtgttacgatttaaatttgatactgtggtattaaaatccccacgtaatttagcccgatctttaacaaatccattatgtatatcggaatactctgttggattttgcaatacacgagagacaatacttaaatcaactaaacgtttcagtgtagccatcatatataacctccaagtctttagtacaaccgttgagatacatcatattacattgaacaaaaagtacagtcaaaattatagaacagttttttattaatatatttttatgtaattaggaaatttcccatagccccccctgctgacgcaagcgtttttcacttgtacttttttatttctacaaatatatattttcagcacaagtgtggacgcttgtgcgctatcgtttaaaattcatcgtaaaaaaccaccgcactttccacgcccagccgtaccatcggcgtaaattatgatctcaatcacggttttgatggagtgaatccgctagaatgaaactcccatttcaaaaatatgaggaaacgactg .........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 cagtcgtttcctcatatttttgaaatgggagtttcattctagcggattcactccatcaaaaccgtgattgagatcataatttacgccgatggtacggctgggcgtggaaagtgcggtggttttttacgatgaattttaaacgatagcgcacaagcgtccacacttgtgctgaaaatatatatttgtagaaataaaaaagtacaagtgaaaaacgcttgcgtcagcagggggggctatgggaaatttcctaattacataaaaatatattaataaaaaactgttctataattttgactgtactttttgttcaatgtaatatgatgtatctcaacggttgtactaaagacttggaggttatatatgatggctacactgaaacgtttagttgatttaagtattgtctctcgtgtattgcaaaatccaacagagtattccgatatacataatggatttgttaaagatcgggctaaattacgtggggattttaataccacagtatcaaatttaaatcgtaacactagaaaat Mask Tandem Repeat Region ================================================ attttctagtgttacgatttaaatttgatactgtggtattaaaatccccacgtaatttagcccgatctttaacaaatccattatgtatatcggaatactctgttggattttgcaatacacgagagacaatacttaaatcaactaaacgtttcagtgtagccatcatatataacctccaagtctttagtacaaccgttgagatacatcatattacattgaacaaaaagtacagtcaaaattatagaacagttttttattaatatatttttatgtaattaggaaatttcccatagccccccctgctgacgcaagcgtttttcacttgtacttttttatttctacaaatatatattttcagcacaagtgtggacgcttgtgcgctatcgtttaaaattcatcgtaaaaaaccaccgcactttccacgcccagccgtaccatcggcgtaaattatgatctcaatcacggttttgatggagtgaatccgctagaatgaaactcccatttcaaaaatatgaggaaacgactg Find is-nt database================================================ Query_seq: AA02191:AA02193|AA02191:AA02193:hypothetical protein:oxaloacetate decarboxylase gamma chain:->->:1493833..1494358 526 attttctagtgttacgatttaaatttgatactgtggtattaaaatccccacgtaatttagcccgatctttaacaaatccattatgtatatcggaatactctgttggattttgcaatacacgagagacaatacttaaatcaactaaacgtttcagtgtagccatcatatataacctccaagtctttagtacaaccgttgagatacatcatattacattgaacaaaaagtacagtcaaaattatagaacagttttttattaatatatttttatgtaattaggaaatttcccatagccccccctgctgacgcaagcgtttttcacttgtacttttttatttctacaaatatatattttcagcacaagtgtggacgcttgtgcgctatcgtttaaaattcatcgtaaaaaaccaccgcactttccacgcccagccgtaccatcggcgtaaattatgatctcaatcacggttttgatggagtgaatccgctagaatgaaactcccatttcaaaaatatgaggaaacgactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02191:AA02193|AA02191:AA02193:hypothetical protein:oxaloacetate decarboxylase gamma chain:->->:1493833..1494358 526 attttctagtgttacgatttaaatttgatactgtggtattaaaatccccacgtaatttagcccgatctttaacaaatccattatgtatatcggaatactctgttggattttgcaatacacgagagacaatacttaaatcaactaaacgtttcagtgtagccatcatatataacctccaagtctttagtacaaccgttgagatacatcatattacattgaacaaaaagtacagtcaaaattatagaacagttttttattaatatatttttatgtaattaggaaatttcccatagccccccctgctgacgcaagcgtttttcacttgtacttttttatttctacaaatatatattttcagcacaagtgtggacgcttgtgcgctatcgtttaaaattcatcgtaaaaaaccaccgcactttccacgcccagccgtaccatcggcgtaaattatgatctcaatcacggttttgatggagtgaatccgctagaatgaaactcccatttcaaaaatatgaggaaacgactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02191:AA02193|AA02191:AA02193:hypothetical protein:oxaloacetate decarboxylase gamma chain:->->:1493833..1494358 526 attttctagtgttacgatttaaatttgatactgtggtattaaaatccccacgtaatttagcccgatctttaacaaatccattatgtatatcggaatactctgttggattttgcaatacacgagagacaatacttaaatcaactaaacgtttcagtgtagccatcatatataacctccaagtctttagtacaaccgttgagatacatcatattacattgaacaaaaagtacagtcaaaattatagaacagttttttattaatatatttttatgtaattaggaaatttcccatagccccccctgctgacgcaagcgtttttcacttgtacttttttatttctacaaatatatattttcagcacaagtgtggacgcttgtgcgctatcgtttaaaattcatcgtaaaaaaccaccgcactttccacgcccagccgtaccatcggcgtaaattatgatctcaatcacggttttgatggagtgaatccgctagaatgaaactcccatttcaaaaatatgaggaaacgactg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttctagtgttacgatttaaatttgatactgtggtattaaaatccccacgtaatttagcccgatctttaacaaatccattatgtatatcggaatactctgttggattttgcaatacacgagagacaatacttaaatcaactaaacgtttcagtgtagccatcatatataacctccaagtctttagtacaaccgttgagatacatcatattacattgaacaaaaagtacagtcaaaattatagaacagttttttattaatatatttttatgtaattaggaaatttcccatagccccccctgctgacgcaagcgtttttcacttgtacttttttatttctacaaatatatattttcagcacaagtgtggacgcttgtgcgctatcgtttaaaattcatcgtaaaaaaccaccgcactttccacgcccagccgtaccatcggcgtaaattatgatctcaatcacggttttgatggagtgaatccgctagaatgaaactcccatttcaaaaatatgaggaaacgactg Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 9 End: 257 ........ M L R F K F D T V V L K S P R N L A R S L T N P L C I S E Y S V G F C N T R E T I L K S T K R F S V A I I Y N L Q V F S ............................................................................................................................................................................................................................................................................. Protein_Len: 43 Strand: + Start: 260 End: 388 ................................................................................................................................................................................................................................................................... M Y F Y V I R K F P I A P P A D A S V F H L Y F F I S T N I Y F Q H K C G R L C A I V .......................................................................................................................................... Protein_Len: 48 Strand: + Start: 300 End: 443 ........................................................................................................................................................................................................................................................................................................... M L T Q A F F T C T F L F L Q I Y I F S T S V D A C A L S F K I H R K K P P H F P R P A V P S A ................................................................................... Protein_Len: 34 Strand: + Start: 349 End: 450 ............................................................................................................................................................................................................................................................................................................................................................ M F S A Q V W T L V R Y R L K F I V K N H R T F H A Q P Y H R R K L ............................................................................ Protein_Len: 45 Strand: - Start: 260 End: 394 ................................................................................................................................................................................................................................................................... Y I K I Y N P F K G Y G G R S V C A N K V Q V K K N R C I Y I K L V L T S A Q A S D N L M .................................................................................................................................... Protein_Len: 41 Strand: - Start: 141 End: 263 ............................................................................................................................................ S F T E T Y G D Y I V E L D K T C G N L Y M M N C Q V F L V T L I I S C N K I L M ....................................................................................................................................................................................................................................................................... Protein_Len: 36 Strand: - Start: 22 End: 129 ..................... I Q Y Q P I L I G V Y N L G I K L L D M I Y I P I S Q Q I K C Y V L S M ............................................................................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 60 Strand: - Start: 2 End: 202 . N S V T T N F D G R L K A R D K V F G N H I D S Y E T P N Q L V R S V I S L D V L R K L T A M M Y L R W T K L V V T S M .................................................................................................................................................................................................................................................................................................................................... attttctagtgttacgatttaaatttgatactgtggtattaaaatccccacgtaatttagcccgatctttaacaaatccattatgtatatcggaatactctgttggattttgcaatacacgagagacaatacttaaatcaactaaacgtttcagtgtagccatcatatataacctccaagtctttagtacaaccgttgagatacatcatattacattgaacaaaaagtacagtcaaaattatagaacagttttttattaatatatttttatgtaattaggaaatttcccatagccccccctgctgacgcaagcgtttttcacttgtacttttttatttctacaaatatatattttcagcacaagtgtggacgcttgtgcgctatcgtttaaaattcatcgtaaaaaaccaccgcactttccacgcccagccgtaccatcggcgtaaattatgatctcaatcacggttttgatggagtgaatccgctagaatgaaactcccatttcaaaaatatgaggaaacgactg 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: 85 Start: 208 End: 237 ...............................................................................................................................................................................................................TTTGACTGTACTTTTTGTTCAATGTAATAT................................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attttctagtgttacgatttaaatttgatactgtggtattaaaatccccacgtaatttagcccgatctttaacaaatccattatgtatatcggaatactctgttggattttgcaatacacgagagacaatacttaaatcaactaaacgtttcagtgtagccatcatatataacctccaagtctttagtacaaccgttgagatacatcatattacattgaacaaaaagtacagtcaaaattatagaacagttttttattaatatatttttatgtaattaggaaatttcccatagccccccctgctgacgcaagcgtttttcacttgtacttttttatttctacaaatatatattttcagcacaagtgtggacgcttgtgcgctatcgtttaaaattcatcgtaaaaaaccaccgcactttccacgcccagccgtaccatcggcgtaaattatgatctcaatcacggttttgatggagtgaatccgctagaatgaaactcccatttcaaaaatatgaggaaacgactg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 47 HP_score: -2.2 Tail_Score: -3.57147 Start: 309 End: 325 Full_Region: CCCCCCCTGCTGACG CAAGCG TTTTT CACTTG TACTTTTTTATTTCT ....................................................................................................................................................................................................................................................................................................................CAAGCGTTTTTCACTTG......................................................................................................................................................................................................... Find igs database================================================ Query_seq: AA02191:AA02193|AA02191:AA02193:hypothetical protein:oxaloacetate decarboxylase gamma chain:->->:1493833..1494358 526 attttctagtgttacgatttaaatttgatactgtggtattaaaatccccacgtaatttagcccgatctttaacaaatccattatgtatatcggaatactctgttggattttgcaatacacgagagacaatacttaaatcaactaaacgtttcagtgtagccatcatatataacctccaagtctttagtacaaccgttgagatacatcatattacattgaacaaaaagtacagtcaaaattatagaacagttttttattaatatatttttatgtaattaggaaatttcccatagccccccctgctgacgcaagcgtttttcacttgtacttttttatttctacaaatatatattttcagcacaagtgtggacgcttgtgcgctatcgtttaaaattcatcgtaaaaaaccaccgcactttccacgcccagccgtaccatcggcgtaaattatgatctcaatcacggttttgatggagtgaatccgctagaatgaaactcccatttcaaaaatatgaggaaacgactg Intra-Species Hit: Count: 1 Min: 1 Max: 526 Len: 526 Subject: aact_AA02191_AA02193|hypothetical protein:oxaloacetate decarboxylase gamma chain|POSITIVE:POSITIVE|[1493833,1494358]|526 HSP 1 e-value: 0.0 bit: 1001.0 Len: 526 Query Start:1 Query End:526 Subject Strand: POSITIVE Subject Start: 1 Subject End: 526 attttctagtgttacgatttaaatttgatactgtggtattaaaatccccacgtaatttagcccgatctttaacaaatccattatgtatatcggaatactctgttggattttgcaatacacgagagacaatacttaaatcaactaaacgtttcagtgtagccatcatatataacctccaagtctttagtacaaccgttgagatacatcatattacattgaacaaaaagtacagtcaaaattatagaacagttttttattaatatatttttatgtaattaggaaatttcccatagnnnnnnntgctgacgcaagcgtttttcacttgtacttttttatttctacaaatatatattttcagcacaagtgtggacgcttgtgcgctatcgtttaaaattcatcgtaaaaaaccaccgcactttccacgcccagccgtaccatcggcgtaaattatgatctcaatcacggttttgatggagtgaatccgctagaatgaaactcccatttcaaaaatatgaggaaacgactg attttctagtgttacgatttaaatttgatactgtggtattaaaatccccacgtaatttagcccgatctttaacaaatccattatgtatatcggaatactctgttggattttgcaatacacgagagacaatacttaaatcaactaaacgtttcagtgtagccatcatatataacctccaagtctttagtacaaccgttgagatacatcatattacattgaacaaaaagtacagtcaaaattatagaacagttttttattaatatatttttatgtaattaggaaatttcccatagccccccctgctgacgcaagcgtttttcacttgtacttttttatttctacaaatatatattttcagcacaagtgtggacgcttgtgcgctatcgtttaaaattcatcgtaaaaaaccaccgcactttccacgcccagccgtaccatcggcgtaaattatgatctcaatcacggttttgatggagtgaatccgctagaatgaaactcccatttcaaaaatatgaggaaacgactg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUCUAGUGUUACGAUUUAAAUUUGAUACUGUGGUAUUAAAAUCCCCACGUAAUUUAGCCCGAUCUUUAACAAAUCCAUUAUGUAUAUCGGAAUACUCUGUUGGAUUUUGCAAUACACGAGAGACAAUACUUAAAUCAACUAAACGUUUCAGUGUAGCCAUCAUAUAUAACCUCCAAGUCUUUAGUACAACCGUUGAGAUACAUCAUAUUACAUUGAACAAAAAGUACAGUCAAAAUUAUAGAACAGUUUUUUAUUAAUAUAUUUUUAUGUAAUUAGGAAAUUUCCCAUAGCCCCCCCUGCUGACGCAAGCGUUUUUCACUUGUACUUUUUUAUUUCUACAAAUAUAUAUUUUCAGCACAAGUGUGGACGCUUGUGCGCUAUCGUUUAAAAUUCAUCGUAAAAAACCACCGCACUUUCCACGCCCAGCCGUACCAUCGGCGUAAAUUAUGAUCUCAAUCACGGUUUUGAUGGAGUGAAUCCGCUAGAAUGAAACUCCCAUUUCAAAAAUAUGAGGAAACGACUG .....((((.((((((.......((((((((....)))))))).......))))))))))................(((.((((((............((((.(((((.(..(..(((((..(((((....................))))).))))).((((((.....((((.....(((....).))....((((((((.(((....((((..((((.((((((((((((.((((.........(((((((((...(((((....)))))...)))))))))................(((......)))..)))).)).))))))))))........................(((((((((....)))))))))..............))))..)))).........................((((......)))).......)))))))))))...)))).)))))).)..)))))).)))).(((((......)))))...)))))))))........ (-101.79) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUCGUUUCCUCAUAUUUUUGAAAUGGGAGUUUCAUUCUAGCGGAUUCACUCCAUCAAAACCGUGAUUGAGAUCAUAAUUUACGCCGAUGGUACGGCUGGGCGUGGAAAGUGCGGUGGUUUUUUACGAUGAAUUUUAAACGAUAGCGCACAAGCGUCCACACUUGUGCUGAAAAUAUAUAUUUGUAGAAAUAAAAAAGUACAAGUGAAAAACGCUUGCGUCAGCAGGGGGGGCUAUGGGAAAUUUCCUAAUUACAUAAAAAUAUAUUAAUAAAAAACUGUUCUAUAAUUUUGACUGUACUUUUUGUUCAAUGUAAUAUGAUGUAUCUCAACGGUUGUACUAAAGACUUGGAGGUUAUAUAUGAUGGCUACACUGAAACGUUUAGUUGAUUUAAGUAUUGUCUCUCGUGUAUUGCAAAAUCCAACAGAGUAUUCCGAUAUACAUAAUGGAUUUGUUAAAGAUCGGGCUAAAUUACGUGGGGAUUUUAAUACCACAGUAUCAAAUUUAAAUCGUAACACUAGAAAAU ((((.((..((((((((.((((...(((((......))))).))))....(((((....((((((...(((((((((...((((((((......)))).(((((..((((((((((((((((((((.((((.(((((...............(((.(((.((((((((((.....((((....))))..........)))))))))).......(((((....)))))))).))).(((((....)))))........))))).))))..)))))))))..............))))))))))))))))...))))....))).))))))))))))............))))).....)))))).))..)))))).....((((((((((((((((.(((...((.((((((((..((((((.((....((..(((((..(((.........))).....)))))..))......))..))))))))))).)))))...)))))))))))))....)))))).... (-126.18) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 475 425 391 127 93 aact:AA01181|5end_conserved_hypothetical_protein_808774..809004_POSITIVE 453 443 405 156 125 aact:AA00409|5end_methionyl-tRNA_formyltransferase_273611..273841_POSITIVE 445 419 376 180 134 aact:AA02668|5end_gluconate_permease_1856758..1856988_POSITIVE 403 434 396 134 98 aact:AA01936|5end_tyrosyl-tRNA_synthetase_1307043..1307273_POSITIVE 398 447 408 60 26 aact:AA02250|5end_possible_cytochrome_c-type_protein_1530125..1530355_POSITIVE 388 443 401 150 105 aact:AA01553|5end_conserved_hypothetical_protein_1039220..1039450_POSITIVE 386 449 409 228 181 aact:AA01635|5end_ribonucleoside_diphosphate_reductase,_beta_chain_1104615..1104845_POSITIVE 385 419 376 150 113 aact:AA02084|5end_conserved_hypothetical_protein_1417843..1418073_POSITIVE 384 443 402 151 104 aact:AA01187|5end_conserved_hypothetical_protein_813331..813561_POSITIVE 382 443 408 56 3 aact:AA01419|5end_D-ribulose-phosphate-3_epimerase_954378..954608_POSITIVE 378 440 394 66 18 aact:AA00323|5end_conserved_hypothetical_protein_(possible_SAM-dependent_methyltransferase)_219387..219617_POSITIVE 375 445 403 183 133 aact:AA00324|5end_tRNA_(Uracil-5-)-methyltransferase_(tRNA(M-5-U54)-methyltransferase)_220147..220377_POSITIVE 372 426 390 40 2 aact:AA02667|5end_hypothetical_protein_1856609..1856839_POSITIVE 366 440 391 158 103 aact:AA02369|5end_conserved_hypothetical_protein_1624248..1624478_POSITIVE 366 440 396 77 15 aact:AA01660|5end_hypothetical_protein_1125035..1125265_POSITIVE 366 419 371 133 70 aact:AA00464|5end_conserved_hypothetical_protein_323912..324142_POSITIVE 365 445 402 199 137 aact:AA02409|5end_DNA_ligase_1653315..1653545_POSITIVE 365 443 406 66 25 aact:AA01140|5end_anaerobic_dimethyl_sulfoxide_reductase,_chain_C_781610..781840_POSITIVE 363 446 404 180 132 aact:AA00974|5end_glucosamine-fructose-6-phosphate_679215..679445_POSITIVE 362 419 371 136 95 aact:AA01027|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_717676..717906_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 475 425 391 74 40 aact:AA01179|3end_beta-ketoacyl-ACP_reductase;_short-chain_alcohol_dehydrogenase_808801..808951_POSITIVE 425 444 408 128 77 aact:AA02564|3end_transketolase_N-terminal_section_1786783..1786933_POSITIVE 417 442 405 149 122 aact:AA00408|3end_SUN_protein_(FMU_protein)_273688..273838_POSITIVE 412 447 403 115 59 aact:AA01611|3end_anthranilate_synthase_component_II_1089619..1089769_POSITIVE 388 443 401 150 105 aact:AA01552|3end_hypothetical_protein_1039300..1039450_POSITIVE 385 419 376 75 38 aact:AA02082|3end_glutaminyl-tRNA_synthetase_1417848..1417998_POSITIVE 384 443 402 141 94 aact:AA01185|3end_conserved_hypothetical_protein_(possible_membrane_protein)_813401..813551_POSITIVE 366 440 391 116 61 aact:AA02368|3end_conserved_hypothetical_protein_1624286..1624436_POSITIVE 365 414 376 151 110 aact:AA02667|3end_hypothetical_protein_1856814..1856964_POSITIVE 365 443 406 61 20 aact:AA01138|3end_anaerobic_dimethyl_sulfoxide_reductase,_chain_B_781685..781835_POSITIVE 363 446 404 122 74 aact:AA00973|3end_transcriptional_regulator,_DeoR_family_679237..679387_POSITIVE 362 419 371 149 108 aact:AA01025|3end_hypothetical_protein_717769..717919_POSITIVE 357 443 404 136 74 aact:AA00384|3end_conserved_hypothetical_protein_(possible_nitrogen_fixation_protein)_261168..261318_POSITIVE 355 422 381 95 50 aact:AA02090|3end_glucose-1-phosphate_adenylyltransferase_1424549..1424699_POSITIVE 354 419 376 58 21 aact:AA01619|3end_phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthase)_1095578..1095728_POSITIVE 348 447 409 147 108 aact:AA01151|3end_porphobilinogen_synthase_(delta-aminolevulinic_acid_dehydratase)_789422..789572_POSITIVE 347 470 423 93 44 aact:AA00474|3end_cell_division_protein_Y_(GTP-binding_signal_recognition_particle)_331724..331874_POSITIVE 345 428 388 51 2 aact:AA00420|3end_tRNA/rRNA_methyltransferase_285506..285656_POSITIVE 344 433 396 48 6 aact:AA01530|3end_conserved_hypothetical_protein_1028749..1028899_POSITIVE 344 419 371 131 81 aact:AA00158|3end_ampD_signalling_protein_(N-acetylmuramyl-L-alanine_amidase)_112935..113085_POSITIVE