Origin IGS: ctcgactccttgtaaatgctacaagtccttaaattatgattacttcgtaatcaccctagaaactcaaaaatctttgaatctttaatttaggattaccttattataatgactgccacttgcagttgtcggagtcgattattacatagataatccaaacaggtggcatattctactattaaacgtaaggataaaaaatagtaaattatgccaagctgatcacatttttagatataaatcaaaaataatcaaacataggtgttttttactattttgctcaagatcaaattataaatttcaataacatctttgcaacacaaagcatagcgcccttgacccggtatgattcagttctaacagttgagattaaaaactagacatcacacataaattctgataacttctcgcccagttttattgatttcttccaacttaacaaacgtaggtctctcag .........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 ctgagagacctacgtttgttaagttggaagaaatcaataaaactgggcgagaagttatcagaatttatgtgtgatgtctagtttttaatctcaactgttagaactgaatcataccgggtcaagggcgctatgctttgtgttgcaaagatgttattgaaatttataatttgatcttgagcaaaatagtaaaaaacacctatgtttgattatttttgatttatatctaaaaatgtgatcagcttggcataatttactattttttatccttacgtttaatagtagaatatgccacctgtttggattatctatgtaataatcgactccgacaactgcaagtggcagtcattataataaggtaatcctaaattaaagattcaaagatttttgagtttctagggtgattacgaagtaatcataatttaaggacttgtagcatttacaaggagtcgag Mask Tandem Repeat Region ================================================ ctcgactccttgtaaatgctacaagtccttaaattatgattacttcgtaatcaccctagaaactcaaaaatctttgaatctttaatttaggattaccttattataatgactgccacttgcagttgtcggagtcgattattacatagataatccaaacaggtggcatattctactattaaacgtaaggataaaaaatagtaaattatgccaagctgatcacatttttagatataaatcaaaaataatcaaacataggtgttttttactattttgctcaagatcaaattataaatttcaataacatctttgcaacacaaagcatagcgcccttgacccggtatgattcagttctaacagttgagattaaaaactagacatcacacataaattctgataacttctcgcccagttttattgatttcttccaacttaacaaacgtaggtctctcag Find is-nt database================================================ Query_seq: AA02841:AA02842|AA02841:AA02842:cytochrome D ubiquinol oxidase, subunit I:conserved hypothetical protein:->->:1996263..1996713 451 ctcgactccttgtaaatgctacaagtccttaaattatgattacttcgtaatcaccctagaaactcaaaaatctttgaatctttaatttaggattaccttattataatgactgccacttgcagttgtcggagtcgattattacatagataatccaaacaggtggcatattctactattaaacgtaaggataaaaaatagtaaattatgccaagctgatcacatttttagatataaatcaaaaataatcaaacataggtgttttttactattttgctcaagatcaaattataaatttcaataacatctttgcaacacaaagcatagcgcccttgacccggtatgattcagttctaacagttgagattaaaaactagacatcacacataaattctgataacttctcgcccagttttattgatttcttccaacttaacaaacgtaggtctctcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02841:AA02842|AA02841:AA02842:cytochrome D ubiquinol oxidase, subunit I:conserved hypothetical protein:->->:1996263..1996713 451 ctcgactccttgtaaatgctacaagtccttaaattatgattacttcgtaatcaccctagaaactcaaaaatctttgaatctttaatttaggattaccttattataatgactgccacttgcagttgtcggagtcgattattacatagataatccaaacaggtggcatattctactattaaacgtaaggataaaaaatagtaaattatgccaagctgatcacatttttagatataaatcaaaaataatcaaacataggtgttttttactattttgctcaagatcaaattataaatttcaataacatctttgcaacacaaagcatagcgcccttgacccggtatgattcagttctaacagttgagattaaaaactagacatcacacataaattctgataacttctcgcccagttttattgatttcttccaacttaacaaacgtaggtctctcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02841:AA02842|AA02841:AA02842:cytochrome D ubiquinol oxidase, subunit I:conserved hypothetical protein:->->:1996263..1996713 451 ctcgactccttgtaaatgctacaagtccttaaattatgattacttcgtaatcaccctagaaactcaaaaatctttgaatctttaatttaggattaccttattataatgactgccacttgcagttgtcggagtcgattattacatagataatccaaacaggtggcatattctactattaaacgtaaggataaaaaatagtaaattatgccaagctgatcacatttttagatataaatcaaaaataatcaaacataggtgttttttactattttgctcaagatcaaattataaatttcaataacatctttgcaacacaaagcatagcgcccttgacccggtatgattcagttctaacagttgagattaaaaactagacatcacacataaattctgataacttctcgcccagttttattgatttcttccaacttaacaaacgtaggtctctcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctcgactccttgtaaatgctacaagtccttaaattatgattacttcgtaatcaccctagaaactcaaaaatctttgaatctttaatttaggattaccttattataatgactgccacttgcagttgtcggagtcgattattacatagataatccaaacaggtggcatattctactattaaacgtaaggataaaaaatagtaaattatgccaagctgatcacatttttagatataaatcaaaaataatcaaacataggtgttttttactattttgctcaagatcaaattataaatttcaataacatctttgcaacacaaagcatagcgcccttgacccggtatgattcagttctaacagttgagattaaaaactagacatcacacataaattctgataacttctcgcccagttttattgatttcttccaacttaacaaacgtaggtctctcag Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 110 End: 298 ............................................................................................................. M P L A V V G V D Y Y I D N P N R W H I L L L N V R I K N S K L C Q A D H I F R Y K S K I I K H R C F L L F C S R S N Y ......................................................................................................................................................... Protein_Len: 40 Strand: + Start: 252 End: 371 ........................................................................................................................................................................................................................................................... M G V F Y Y F A Q D Q I I N F N N I F A T Q S I A P L T R Y D S V L T V E I K N ................................................................................ Protein_Len: 32 Strand: - Start: 249 End: 344 ........................................................................................................................................................................................................................................................ V Y T N K V I K S L I L N Y I E I V D K C C L A Y R G Q G P I M ........................................................................................................... Protein_Len: 37 Strand: - Start: 96 End: 206 ............................................................................................... R I I I V A V Q L Q R L R N N C L Y D L C T A Y E V I L R L S L F Y Y I M ..................................................................................................................................................................................................................................................... ctcgactccttgtaaatgctacaagtccttaaattatgattacttcgtaatcaccctagaaactcaaaaatctttgaatctttaatttaggattaccttattataatgactgccacttgcagttgtcggagtcgattattacatagataatccaaacaggtggcatattctactattaaacgtaaggataaaaaatagtaaattatgccaagctgatcacatttttagatataaatcaaaaataatcaaacataggtgttttttactattttgctcaagatcaaattataaatttcaataacatctttgcaacacaaagcatagcgcccttgacccggtatgattcagttctaacagttgagattaaaaactagacatcacacataaattctgataacttctcgcccagttttattgatttcttccaacttaacaaacgtaggtctctcag 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: 81 Start: 221 End: 250 ............................................................................................................................................................................................................................TTTGATTATTTTTGATTTATATCTAAAAAT......................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctcgactccttgtaaatgctacaagtccttaaattatgattacttcgtaatcaccctagaaactcaaaaatctttgaatctttaatttaggattaccttattataatgactgccacttgcagttgtcggagtcgattattacatagataatccaaacaggtggcatattctactattaaacgtaaggataaaaaatagtaaattatgccaagctgatcacatttttagatataaatcaaaaataatcaaacataggtgttttttactattttgctcaagatcaaattataaatttcaataacatctttgcaacacaaagcatagcgcccttgacccggtatgattcagttctaacagttgagattaaaaactagacatcacacataaattctgataacttctcgcccagttttattgatttcttccaacttaacaaacgtaggtctctcag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA02841:AA02842|AA02841:AA02842:cytochrome D ubiquinol oxidase, subunit I:conserved hypothetical protein:->->:1996263..1996713 451 ctcgactccttgtaaatgctacaagtccttaaattatgattacttcgtaatcaccctagaaactcaaaaatctttgaatctttaatttaggattaccttattataatgactgccacttgcagttgtcggagtcgattattacatagataatccaaacaggtggcatattctactattaaacgtaaggataaaaaatagtaaattatgccaagctgatcacatttttagatataaatcaaaaataatcaaacataggtgttttttactattttgctcaagatcaaattataaatttcaataacatctttgcaacacaaagcatagcgcccttgacccggtatgattcagttctaacagttgagattaaaaactagacatcacacataaattctgataacttctcgcccagttttattgatttcttccaacttaacaaacgtaggtctctcag Intra-Species Hit: Count: 1 Min: 1 Max: 451 Len: 451 Subject: aact_AA02841_AA02842|cytochrome D ubiquinol oxidase, subunit I:conserved hypothetical protein|POSITIVE:POSITIVE|[1996263,1996713]|451 HSP 1 e-value: 0.0 bit: 894.0 Len: 451 Query Start:1 Query End:451 Subject Strand: POSITIVE Subject Start: 1 Subject End: 451 ctcgactccttgtaaatgctacaagtccttaaattatgattacttcgtaatcaccctagaaactcaaaaatctttgaatctttaatttaggattaccttattataatgactgccacttgcagttgtcggagtcgattattacatagataatccaaacaggtggcatattctactattaaacgtaaggataaaaaatagtaaattatgccaagctgatcacatttttagatataaatcaaaaataatcaaacataggtgttttttactattttgctcaagatcaaattataaatttcaataacatctttgcaacacaaagcatagcgcccttgacccggtatgattcagttctaacagttgagattaaaaactagacatcacacataaattctgataacttctcgcccagttttattgatttcttccaacttaacaaacgtaggtctctcag ctcgactccttgtaaatgctacaagtccttaaattatgattacttcgtaatcaccctagaaactcaaaaatctttgaatctttaatttaggattaccttattataatgactgccacttgcagttgtcggagtcgattattacatagataatccaaacaggtggcatattctactattaaacgtaaggataaaaaatagtaaattatgccaagctgatcacatttttagatataaatcaaaaataatcaaacataggtgttttttactattttgctcaagatcaaattataaatttcaataacatctttgcaacacaaagcatagcgcccttgacccggtatgattcagttctaacagttgagattaaaaactagacatcacacataaattctgataacttctcgcccagttttattgatttcttccaacttaacaaacgtaggtctctcag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCGACUCCUUGUAAAUGCUACAAGUCCUUAAAUUAUGAUUACUUCGUAAUCACCCUAGAAACUCAAAAAUCUUUGAAUCUUUAAUUUAGGAUUACCUUAUUAUAAUGACUGCCACUUGCAGUUGUCGGAGUCGAUUAUUACAUAGAUAAUCCAAACAGGUGGCAUAUUCUACUAUUAAACGUAAGGAUAAAAAAUAGUAAAUUAUGCCAAGCUGAUCACAUUUUUAGAUAUAAAUCAAAAAUAAUCAAACAUAGGUGUUUUUUACUAUUUUGCUCAAGAUCAAAUUAUAAAUUUCAAUAACAUCUUUGCAACACAAAGCAUAGCGCCCUUGACCCGGUAUGAUUCAGUUCUAACAGUUGAGAUUAAAAACUAGACAUCACACAUAAAUUCUGAUAACUUCUCGCCCAGUUUUAUUGAUUUCUUCCAACUUAACAAACGUAGGUCUCUCAG .((((((((..............((((((.((((((.((((((...))))))...........(((((....))))).....))))))))))))...........(..(((((.....)))))..).))))))))...((((.....(((((..(((...(((((((...(((((((...(....).......)))))))...))))))).((((((((.((((((.(((....))))))))).......((..((((((..........((((..(((((....((((........)))).))))).))))..........))))))..))........))).))))).......)))..)))))......(((.((((...(((((..(((.............))).))))))))).)))...............))))......... (-84.17) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAGAGACCUACGUUUGUUAAGUUGGAAGAAAUCAAUAAAACUGGGCGAGAAGUUAUCAGAAUUUAUGUGUGAUGUCUAGUUUUUAAUCUCAACUGUUAGAACUGAAUCAUACCGGGUCAAGGGCGCUAUGCUUUGUGUUGCAAAGAUGUUAUUGAAAUUUAUAAUUUGAUCUUGAGCAAAAUAGUAAAAAACACCUAUGUUUGAUUAUUUUUGAUUUAUAUCUAAAAAUGUGAUCAGCUUGGCAUAAUUUACUAUUUUUUAUCCUUACGUUUAAUAGUAGAAUAUGCCACCUGUUUGGAUUAUCUAUGUAAUAAUCGACUCCGACAACUGCAAGUGGCAGUCAUUAUAAUAAGGUAAUCCUAAAUUAAAGAUUCAAAGAUUUUUGAGUUUCUAGGGUGAUUACGAAGUAAUCAUAAUUUAAGGACUUGUAGCAUUUACAAGGAGUCGAG ......(((((...(((((..((((.((.....)).....))))..))))).................(((((((...(((((((....(......)..))))))).))))))).))))).(((((.....))))).(((((((.(((((..(((.((((.......((((((......((((((((...(((((....))))).)))))))).(((....))).........))))))..(((((((.(((((((((................))))))))).)))))))...)))).)))))))).))))))).((((((((....(((((.....))))).......(((((....((((...(((.(((((((((....))))))))).))).((((((((...))))))))......)))))))))...........)))))))). (-101.39) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 135 97 116 71 aact:AA01655|5end_hypothetical_protein_1121187..1121417_POSITIVE 309 148 106 79 30 aact:AA01715|5end_conserved_hypothetical_protein_1160480..1160710_POSITIVE 308 344 301 196 154 aact:AA01335|5end_primosomal_protein_N'_901993..902223_POSITIVE 302 443 401 164 119 aact:AA02164|5end_phenylalanyl-tRNA_synthetase,_beta_chain_1479790..1480020_POSITIVE 296 360 311 99 33 aact:AA02006|5end_PEP--fructosephosphotransferase_system_repressor,_DeoR_family_1363930..1364160_POSITIVE 288 356 311 218 173 aact:AA01255|5end_hypothetical_protein_852656..852886_POSITIVE 282 350 304 189 142 aact:AA00042|5end_hypothetical_protein_33810..34040_POSITIVE 281 338 294 111 71 aact:AA01158|5end_ribosome_associated_heat_shock_protein_15_homolog_792399..792629_POSITIVE 275 129 89 148 109 aact:AA02196|5end_oxaloacetate_decarboxylase_beta_chain_1496308..1496538_POSITIVE 275 343 306 208 171 aact:AA02052|5end_probable_exodeoxyribonuclease_VII_small_subunit_1398461..1398691_POSITIVE 273 349 306 53 1 aact:AA02092|5end_glycogen_synthase_1424674..1424904_POSITIVE 268 360 313 59 5 aact:AA00343|5end_conserved_hypothetical_protein_(possible_cytosolic_protein)_229908..230138_POSITIVE 263 132 96 192 154 aact:AA02111|5end_killing_protein_suppressor_1436877..1437107_POSITIVE 262 129 107 231 207 aact:AA00602|5end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_409077..409307_POSITIVE 261 136 105 180 148 aact:AA00799|5end_iron(III)_dicitrate_transport_ATP-binding_protein_547658..547888_POSITIVE 261 339 306 114 74 aact:AA00240|5end_hypothetical_protein_171390..171620_POSITIVE 258 337 293 152 109 aact:AA02145|5end_iron(III)_ABC_transporter,_ATP-binding_protein_1468602..1468832_POSITIVE 257 349 302 223 183 aact:AA01859|5end_hypothetical_protein_1251718..1251948_POSITIVE 255 134 96 157 117 aact:AA01519|5end_conserved_hypothetical_protein_1021794..1022024_POSITIVE 255 133 105 105 72 aact:AA00989|5end_hypothetical_protein_692319..692549_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 360 311 109 43 aact:AA02005|3end_vancomycin_sensitivity;_SanA_protein_1364020..1364170_POSITIVE 285 130 88 76 31 aact:AA02472|3end_conserved_hypothetical_protein_1708409..1708559_POSITIVE 282 350 304 116 69 aact:AA00041|3end_cytochrome_c-type_biogenesis_protein_33817..33967_POSITIVE 275 129 89 134 95 aact:AA02195|3end_oxaloacetate_decarboxylase_alpha_chain_1496374..1496524_POSITIVE 272 338 295 40 1 aact:AA01156|3end_chaperonin_heat_shock_protein_33_homolog_792408..792558_POSITIVE 267 429 382 139 78 aact:AA01123|3end_possible_hemolysin;_membrane_protein_771657..771807_POSITIVE 261 339 306 62 22 aact:AA00239|3end_hypothetical_protein_171418..171568_POSITIVE 258 337 293 149 106 aact:AA02144|3end_iron_(III)_ABC_transporter,_permease_protein_1468679..1468829_POSITIVE 255 134 96 74 34 aact:AA01517|3end_peptidyl-prolyl_cis-trans_isomerase;_macrophage_infectivity_protein_1021791..1021941_POSITIVE 254 352 318 79 39 aact:AA00734|3end_citrate_lyase,_gamma_chain_(acyl_carrier_protein)_502754..502904_POSITIVE 252 358 311 76 17 aact:AA01064|3end_conserved_hypothetical_protein_(possible_aminomethyltransferase)_738392..738542_POSITIVE 251 340 298 99 52 aact:AA00616|3end_phosphatidate_cytidylyltransferase_422971..423121_POSITIVE 250 360 319 104 72 aact:AA01746|3end_thiol:disulfide_interchange_protein_1181396..1181546_POSITIVE 248 247 206 146 103 aact:AA01531|3end_hypothetical_protein_1028877..1029027_POSITIVE 247 360 311 142 94 aact:AA01547|3end_deoxyribose-phosphate_aldolase_1037019..1037169_POSITIVE 246 344 302 69 31 aact:AA00474|3end_cell_division_protein_Y_(GTP-binding_signal_recognition_particle)_331724..331874_POSITIVE 245 343 301 131 90 aact:AA02684|3end_hydrogenase_4_membrane_subunit_1871612..1871762_POSITIVE 245 130 89 83 42 aact:AA01155|3end_hypothetical_protein_791411..791561_POSITIVE 245 341 303 49 9 aact:AA00080|3end_Na+/H+_antiporter_protein_59844..59994_POSITIVE 244 346 305 137 98 aact:AA00592|3end_conserved_hypothetical_protein_(membrane/transport_protein)_407286..407436_POSITIVE