Origin IGS: aataacctcgcttatgacgtataaagtgcggtcatcttagaaagtattttttagaatgtaaaggatgtgctacgtttttgtggggcggatcacaaaattcagatcaattcgtgtagtcacaaaatatccgtgaaaagtttatttttcttgataacaccgctaaaatagcgcatttttgacgaacagagagaacatcacgacttttgcgcctaggattatcctgattgaaaatcgacaactgattttccggcggcataaaacaacattcgcgccgaagaaatcagcaccctgcaagcgtaacgtgagtaggccttatcgctgttacaataggctaggcaattcgattgcctgtgcgtgatcgtcaccaataaggaataaat .........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 atttattccttattggtgacgatcacgcacaggcaatcgaattgcctagcctattgtaacagcgataaggcctactcacgttacgcttgcagggtgctgatttcttcggcgcgaatgttgttttatgccgccggaaaatcagttgtcgattttcaatcaggataatcctaggcgcaaaagtcgtgatgttctctctgttcgtcaaaaatgcgctattttagcggtgttatcaagaaaaataaacttttcacggatattttgtgactacacgaattgatctgaattttgtgatccgccccacaaaaacgtagcacatcctttacattctaaaaaatactttctaagatgaccgcactttatacgtcataagcgaggttatt Mask Tandem Repeat Region ================================================ aataacctcgcttatgacgtataaagtgcggtcatcttagaaagtattttttagaatgtaaaggatgtgctacgtttttgtggggcggatcacaaaattcagatcaattcgtgtagtcacaaaatatccgtgaaaagtttatttttcttgataacaccgctaaaatagcgcatttttgacgaacagagagaacatcacgacttttgcgcctaggattatcctgattgaaaatcgacaactgattttccggcggcataaaacaacattcgcgccgaagaaatcagcaccctgcaagcgtaacgtgagtaggccttatcgctgttacaataggctaggcaattcgattgcctgtgcgtgatcgtcaccaataaggaataaat Find is-nt database================================================ Query_seq: AA00512:AA00513|AA00512:AA00513:conserved hypothetical protein:pseudouridylate synthase (pseudouridine synthase):->->:354710..355089 380 aataacctcgcttatgacgtataaagtgcggtcatcttagaaagtattttttagaatgtaaaggatgtgctacgtttttgtggggcggatcacaaaattcagatcaattcgtgtagtcacaaaatatccgtgaaaagtttatttttcttgataacaccgctaaaatagcgcatttttgacgaacagagagaacatcacgacttttgcgcctaggattatcctgattgaaaatcgacaactgattttccggcggcataaaacaacattcgcgccgaagaaatcagcaccctgcaagcgtaacgtgagtaggccttatcgctgttacaataggctaggcaattcgattgcctgtgcgtgatcgtcaccaataaggaataaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00512:AA00513|AA00512:AA00513:conserved hypothetical protein:pseudouridylate synthase (pseudouridine synthase):->->:354710..355089 380 aataacctcgcttatgacgtataaagtgcggtcatcttagaaagtattttttagaatgtaaaggatgtgctacgtttttgtggggcggatcacaaaattcagatcaattcgtgtagtcacaaaatatccgtgaaaagtttatttttcttgataacaccgctaaaatagcgcatttttgacgaacagagagaacatcacgacttttgcgcctaggattatcctgattgaaaatcgacaactgattttccggcggcataaaacaacattcgcgccgaagaaatcagcaccctgcaagcgtaacgtgagtaggccttatcgctgttacaataggctaggcaattcgattgcctgtgcgtgatcgtcaccaataaggaataaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00512:AA00513|AA00512:AA00513:conserved hypothetical protein:pseudouridylate synthase (pseudouridine synthase):->->:354710..355089 380 aataacctcgcttatgacgtataaagtgcggtcatcttagaaagtattttttagaatgtaaaggatgtgctacgtttttgtggggcggatcacaaaattcagatcaattcgtgtagtcacaaaatatccgtgaaaagtttatttttcttgataacaccgctaaaatagcgcatttttgacgaacagagagaacatcacgacttttgcgcctaggattatcctgattgaaaatcgacaactgattttccggcggcataaaacaacattcgcgccgaagaaatcagcaccctgcaagcgtaacgtgagtaggccttatcgctgttacaataggctaggcaattcgattgcctgtgcgtgatcgtcaccaataaggaataaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aataacctcgcttatgacgtataaagtgcggtcatcttagaaagtattttttagaatgtaaaggatgtgctacgtttttgtggggcggatcacaaaattcagatcaattcgtgtagtcacaaaatatccgtgaaaagtttatttttcttgataacaccgctaaaatagcgcatttttgacgaacagagagaacatcacgacttttgcgcctaggattatcctgattgaaaatcgacaactgattttccggcggcataaaacaacattcgcgccgaagaaatcagcaccctgcaagcgtaacgtgagtaggccttatcgctgttacaataggctaggcaattcgattgcctgtgcgtgatcgtcaccaataaggaataaat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 21 End: 113 .................... M K C G H L R K Y F L E C K G C A T F L W G G S Q N S D Q F V ........................................................................................................................................................................................................................................................................... Protein_Len: 33 Strand: + Start: 67 End: 165 .................................................................. M L R F C G A D H K I Q I N S C S H K I S V K S L F F L I T P L K ....................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 176 End: 355 ............................................................................................................................................................................... M T N R E N I T T F A P R I I L I E N R Q L I F R R H K T T F A P K K S A P C K R N V S R P Y R C Y N R L G N S I A C A ......................... Protein_Len: 54 Strand: - Start: 219 End: 380 .......................................................................................................................................................................................................................... G S Q F D V V S K G A A Y F L M R A S S I L V R C A Y R S Y A K D S N C Y A L C N S Q R H T I T V L L S Y M Protein_Len: 44 Strand: - Start: 163 End: 294 .................................................................................................................................................................. F L A N K V F L S F M V V K A G L I I R I S F R C S I K R R C L V V N A G F F D A G Q M ...................................................................................... Protein_Len: 50 Strand: - Start: 107 End: 256 .......................................................................................................... N T Y D C F I R S F N I K R S L V A L I A C K Q R V S L V D R S K R R P N D Q N F I S L Q N E P P M ............................................................................................................................ aataacctcgcttatgacgtataaagtgcggtcatcttagaaagtattttttagaatgtaaaggatgtgctacgtttttgtggggcggatcacaaaattcagatcaattcgtgtagtcacaaaatatccgtgaaaagtttatttttcttgataacaccgctaaaatagcgcatttttgacgaacagagagaacatcacgacttttgcgcctaggattatcctgattgaaaatcgacaactgattttccggcggcataaaacaacattcgcgccgaagaaatcagcaccctgcaagcgtaacgtgagtaggccttatcgctgttacaataggctaggcaattcgattgcctgtgcgtgatcgtcaccaataaggaataaat 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: 83 Start: 34 End: 63 .................................CTTTACATTCTAAAAAATACTTTCTAAGAT............................................................................................................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 137 End: 166 ........................................................................................................................................GTTTATTTTTCTTGATAACACCGCTAAAAT...................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aataacctcgcttatgacgtataaagtgcggtcatcttagaaagtattttttagaatgtaaaggatgtgctacgtttttgtggggcggatcacaaaattcagatcaattcgtgtagtcacaaaatatccgtgaaaagtttatttttcttgataacaccgctaaaatagcgcatttttgacgaacagagagaacatcacgacttttgcgcctaggattatcctgattgaaaatcgacaactgattttccggcggcataaaacaacattcgcgccgaagaaatcagcaccctgcaagcgtaacgtgagtaggccttatcgctgttacaataggctaggcaattcgattgcctgtgcgtgatcgtcaccaataaggaataaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA00512:AA00513|AA00512:AA00513:conserved hypothetical protein:pseudouridylate synthase (pseudouridine synthase):->->:354710..355089 380 aataacctcgcttatgacgtataaagtgcggtcatcttagaaagtattttttagaatgtaaaggatgtgctacgtttttgtggggcggatcacaaaattcagatcaattcgtgtagtcacaaaatatccgtgaaaagtttatttttcttgataacaccgctaaaatagcgcatttttgacgaacagagagaacatcacgacttttgcgcctaggattatcctgattgaaaatcgacaactgattttccggcggcataaaacaacattcgcgccgaagaaatcagcaccctgcaagcgtaacgtgagtaggccttatcgctgttacaataggctaggcaattcgattgcctgtgcgtgatcgtcaccaataaggaataaat Intra-Species Hit: Count: 1 Min: 1 Max: 380 Len: 380 Subject: aact_AA00512_AA00513|conserved hypothetical protein:pseudouridylate synthase (pseudouridine synthase)|POSITIVE:POSITIVE|[354710,355089]|380 HSP 1 e-value: 0.0 bit: 753.0 Len: 380 Query Start:1 Query End:380 Subject Strand: POSITIVE Subject Start: 1 Subject End: 380 aataacctcgcttatgacgtataaagtgcggtcatcttagaaagtattttttagaatgtaaaggatgtgctacgtttttgtggggcggatcacaaaattcagatcaattcgtgtagtcacaaaatatccgtgaaaagtttatttttcttgataacaccgctaaaatagcgcatttttgacgaacagagagaacatcacgacttttgcgcctaggattatcctgattgaaaatcgacaactgattttccggcggcataaaacaacattcgcgccgaagaaatcagcaccctgcaagcgtaacgtgagtaggccttatcgctgttacaataggctaggcaattcgattgcctgtgcgtgatcgtcaccaataaggaataaat aataacctcgcttatgacgtataaagtgcggtcatcttagaaagtattttttagaatgtaaaggatgtgctacgtttttgtggggcggatcacaaaattcagatcaattcgtgtagtcacaaaatatccgtgaaaagtttatttttcttgataacaccgctaaaatagcgcatttttgacgaacagagagaacatcacgacttttgcgcctaggattatcctgattgaaaatcgacaactgattttccggcggcataaaacaacattcgcgccgaagaaatcagcaccctgcaagcgtaacgtgagtaggccttatcgctgttacaataggctaggcaattcgattgcctgtgcgtgatcgtcaccaataaggaataaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAACCUCGCUUAUGACGUAUAAAGUGCGGUCAUCUUAGAAAGUAUUUUUUAGAAUGUAAAGGAUGUGCUACGUUUUUGUGGGGCGGAUCACAAAAUUCAGAUCAAUUCGUGUAGUCACAAAAUAUCCGUGAAAAGUUUAUUUUUCUUGAUAACACCGCUAAAAUAGCGCAUUUUUGACGAACAGAGAGAACAUCACGACUUUUGCGCCUAGGAUUAUCCUGAUUGAAAAUCGACAACUGAUUUUCCGGCGGCAUAAAACAACAUUCGCGCCGAAGAAAUCAGCACCCUGCAAGCGUAACGUGAGUAGGCCUUAUCGCUGUUACAAUAGGCUAGGCAAUUCGAUUGCCUGUGCGUGAUCGUCACCAAUAAGGAAUAAAU .....(((.(((((((((((..(((((((..((......))..)))))))......(((..(((..(((((..((((((.(((.((((((..(((((.((.(((...(((.(((.((((.(((.((((...((((((....))))))..))))....(((((...)))))..))).))))..)))..)))...)))..)).)))))((((.(((.....)))....((((((((.....)))))))).))))............)))))).))).)))))).))))))))))).))))..))))))))))((((((.(.((......((.((((((((((...)))))))).)).)).....)).).))))))....... (-93.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUAUUCCUUAUUGGUGACGAUCACGCACAGGCAAUCGAAUUGCCUAGCCUAUUGUAACAGCGAUAAGGCCUACUCACGUUACGCUUGCAGGGUGCUGAUUUCUUCGGCGCGAAUGUUGUUUUAUGCCGCCGGAAAAUCAGUUGUCGAUUUUCAAUCAGGAUAAUCCUAGGCGCAAAAGUCGUGAUGUUCUCUCUGUUCGUCAAAAAUGCGCUAUUUUAGCGGUGUUAUCAAGAAAAAUAAACUUUUCACGGAUAUUUUGUGACUACACGAAUUGAUCUGAAUUUUGUGAUCCGCCCCACAAAAACGUAGCACAUCCUUUACAUUCUAAAAAAUACUUUCUAAGAUGACCGCACUUUAUACGUCAUAAGCGAGGUUAUU .......(((..((.((((((...(((.(((((((((...))))))..(((((((((....))))).))))......(((((((((((.....(((((((.....))))))).............(((.(((.(((((((.......)))))))....(((.....))).)))))).))).))))))))......))).)))..(((.((((.((((((((.((((((....((((..............(((((..((((((....))))))...)))))..(((((((........)))))))..((((........)))).))))....))))))..))))))))..)))).)))...)))))).))..)))..... (-98.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 405 305 261 66 5 aact:AA01615|5end_lipoprotein_releasing_system_transmembrane_1091186..1091416_POSITIVE 387 290 243 128 78 aact:AA01947|5end_iron(III)-transport_ATP-binding_protein_1316390..1316620_POSITIVE 370 367 330 49 5 aact:AA01743|5end_lysyl-tRNA_synthetase_1177808..1178038_POSITIVE 354 290 248 215 169 aact:AA02415|5end_hypothetical_protein_1658443..1658673_POSITIVE 354 270 221 192 154 aact:AA01421|5end_phosphoglycolate_phosphatase_955055..955285_POSITIVE 349 366 326 43 4 aact:AA01704|5end_tyrosine-specific_transport_protein_1156170..1156400_POSITIVE 347 275 233 45 1 aact:AA02973|5end_tyrosine-specific_transport_protein_2077707..2077937_POSITIVE 346 319 272 219 162 aact:AA01684|5end_ABC_transporter,_ATP-binding_protein;_possible_ATP-binding_component_of_sulfate_permease_A_protein_1136302..1136532_POSITIVE 343 286 248 61 17 aact:AA01477|5end_type_I_restriction_enzyme_R_protein_992249..992479_POSITIVE 341 318 271 77 19 aact:AA01660|5end_hypothetical_protein_1125035..1125265_POSITIVE 341 366 321 85 39 aact:AA01438|5end_conserved_hypothetical_protein_(possible_ribonuclease_)_965401..965631_POSITIVE 340 348 306 101 56 aact:AA01335|5end_primosomal_protein_N'_901993..902223_POSITIVE 339 319 271 172 113 aact:AA01890|5end_cell-cycle_protein_1274544..1274774_POSITIVE 338 365 327 165 125 aact:AA01780|5end_ABC-related_molybdenum_transport_system_permease_protein_1201084..1201314_POSITIVE 337 337 291 96 40 aact:AA01197|5end_conserved_hypothetical_protein_820863..821093_POSITIVE 337 366 330 64 20 aact:AA00912|5end_short-chain_dehydrogenase_627200..627430_POSITIVE 336 288 241 80 23 aact:AA01019|5end_conserved_hypothetical_protein_712223..712453_POSITIVE 333 326 283 66 15 aact:AA02439|5end_integral_membrane_protein;_possible_ABC_transporter_permease_1683902..1684132_POSITIVE 333 298 252 196 148 aact:AA01441|5end_tRNA/rRNA_methylase_966490..966720_POSITIVE 329 350 302 200 147 aact:AA00550|5end_ferredoxin-type_protein_376444..376674_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 396 306 268 51 9 aact:AA02438|3end_membrane_protein;_possible_ABC_transporter_permease_protein_1683992..1684142_POSITIVE 339 319 271 138 79 aact:AA01889|3end_conserved_hypothetical_protein_(possible_permease)_1274590..1274740_POSITIVE 337 337 291 108 52 aact:AA01196|3end_1-acyl-sn-glycerol-3-phosphate_acetyltransferase_820955..821105_POSITIVE 336 288 241 77 20 aact:AA01018|3end_conserved_hypothetical_protein_(possible_transcriptional_regulator)_712300..712450_POSITIVE 333 298 252 124 76 aact:AA01439|3end_probable_ferredoxin_(fdx-2)_966498..966648_POSITIVE 330 367 331 40 3 aact:AA01965|3end_poly(A)_polymerase_1331021..1331171_POSITIVE 325 276 231 42 5 aact:AA02205|3end_short_chain_dehydrogenase/reductase_1501984..1502134_POSITIVE 324 38 4 106 66 aact:AA02135|3end_hypothetical_protein_1459067..1459217_POSITIVE 324 38 4 122 82 aact:AA02135.1|3end_hypothetical_protein_1459083..1459233_POSITIVE 324 321 286 59 15 aact:AA00257|3end_rod-shape-determining_protein_180904..181054_POSITIVE 318 360 325 133 99 aact:AA02024|3end_acyl_carrier_protein_phosphodiesterase_1378739..1378889_POSITIVE 316 306 261 139 91 aact:AA02196|3end_oxaloacetate_decarboxylase_beta_chain_1497692..1497842_POSITIVE 315 319 272 38 8 aact:AA01158|3end_ribosome_associated_heat_shock_protein_15_homolog_792892..793042_POSITIVE 310 290 248 148 95 aact:AA00254|3end_penicillin-binding_protein_5_178774..178924_POSITIVE 309 68 21 134 86 aact:AA00181|3end_hypothetical_protein_128855..129005_POSITIVE 308 275 233 144 97 aact:AA00863|3end_conserved_hypothetical_protein_598678..598828_POSITIVE 305 280 232 151 101 aact:AA02937|3end_conserved_hypothetical_protein_2056947..2057097_POSITIVE 305 312 271 136 93 aact:AA02456|3end_conserved_hypothetical_protein_1695422..1695572_POSITIVE 305 319 284 69 21 aact:AA00140|3end_hypothetical_protein_100872..101022_POSITIVE 304 277 232 54 1 aact:AA01422|3end_cell_division_protein_E,_ABC_system_ATP-binding_protein_956736..956886_POSITIVE