Origin IGS: tttgatgatcctctattaattagtcatctttaatttaaaacagtatcagccgatacagctgaaaaccaacacaaggacttgtgttacctgtcatcttaaaccgtttaagtaaaaaagtgaaattttttacaattaacgaactaagatattgtttaatacgaagttgaattcaccccatatacttttaacaaatacatatcccttatgaaatgactgtttaaaagttcgaacattatcctactaaaaagccgaaaatcaaacaacttaagtttttttgattattttttaaacaacccaacacctttctagttcactaatcaaccaatcttaagaatttattcagtaaatttaatatttatttgcttttttctactgacaatattctgcatttgtgtgctaagattcggttactttctaccgctctaactaataaagcgtc .........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 gacgctttattagttagagcggtagaaagtaaccgaatcttagcacacaaatgcagaatattgtcagtagaaaaaagcaaataaatattaaatttactgaataaattcttaagattggttgattagtgaactagaaaggtgttgggttgtttaaaaaataatcaaaaaaacttaagttgtttgattttcggctttttagtaggataatgttcgaacttttaaacagtcatttcataagggatatgtatttgttaaaagtatatggggtgaattcaacttcgtattaaacaatatcttagttcgttaattgtaaaaaatttcacttttttacttaaacggtttaagatgacaggtaacacaagtccttgtgttggttttcagctgtatcggctgatactgttttaaattaaagatgactaattaatagaggatcatcaaa Mask Tandem Repeat Region ================================================ tttgatgatcctctattaattagtcatctttaatttaaaacagtatcagccgatacagctgaaaaccaacacaaggacttgtgttacctgtcatcttaaaccgtttaagtaaaaaagtgaaattttttacaattaacgaactaagatattgtttaatacgaagttgaattcaccccatatacttttaacaaatacatatcccttatgaaatgactgtttaaaagttcgaacattatcctactaaaaagccgaaaatcaaacaacttaagtttttttgattattttttaaacaacccaacacctttctagttcactaatcaaccaatcttaagaatttattcagtaaatttaatatttatttgcttttttctactgacaatattctgcatttgtgtgctaagattcggttactttctaccgctctaactaataaagcgtc Find is-nt database================================================ Query_seq: AA02458:AA02459|AA02458:AA02459:outer membrane protein 34:conserved hypothetical protein:->->:1697169..1697607 439 tttgatgatcctctattaattagtcatctttaatttaaaacagtatcagccgatacagctgaaaaccaacacaaggacttgtgttacctgtcatcttaaaccgtttaagtaaaaaagtgaaattttttacaattaacgaactaagatattgtttaatacgaagttgaattcaccccatatacttttaacaaatacatatcccttatgaaatgactgtttaaaagttcgaacattatcctactaaaaagccgaaaatcaaacaacttaagtttttttgattattttttaaacaacccaacacctttctagttcactaatcaaccaatcttaagaatttattcagtaaatttaatatttatttgcttttttctactgacaatattctgcatttgtgtgctaagattcggttactttctaccgctctaactaataaagcgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02458:AA02459|AA02458:AA02459:outer membrane protein 34:conserved hypothetical protein:->->:1697169..1697607 439 tttgatgatcctctattaattagtcatctttaatttaaaacagtatcagccgatacagctgaaaaccaacacaaggacttgtgttacctgtcatcttaaaccgtttaagtaaaaaagtgaaattttttacaattaacgaactaagatattgtttaatacgaagttgaattcaccccatatacttttaacaaatacatatcccttatgaaatgactgtttaaaagttcgaacattatcctactaaaaagccgaaaatcaaacaacttaagtttttttgattattttttaaacaacccaacacctttctagttcactaatcaaccaatcttaagaatttattcagtaaatttaatatttatttgcttttttctactgacaatattctgcatttgtgtgctaagattcggttactttctaccgctctaactaataaagcgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02458:AA02459|AA02458:AA02459:outer membrane protein 34:conserved hypothetical protein:->->:1697169..1697607 439 tttgatgatcctctattaattagtcatctttaatttaaaacagtatcagccgatacagctgaaaaccaacacaaggacttgtgttacctgtcatcttaaaccgtttaagtaaaaaagtgaaattttttacaattaacgaactaagatattgtttaatacgaagttgaattcaccccatatacttttaacaaatacatatcccttatgaaatgactgtttaaaagttcgaacattatcctactaaaaagccgaaaatcaaacaacttaagtttttttgattattttttaaacaacccaacacctttctagttcactaatcaaccaatcttaagaatttattcagtaaatttaatatttatttgcttttttctactgacaatattctgcatttgtgtgctaagattcggttactttctaccgctctaactaataaagcgtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgatgatcctctattaattagtcatctttaatttaaaacagtatcagccgatacagctgaaaaccaacacaaggacttgtgttacctgtcatcttaaaccgtttaagtaaaaaagtgaaattttttacaattaacgaactaagatattgtttaatacgaagttgaattcaccccatatacttttaacaaatacatatcccttatgaaatgactgtttaaaagttcgaacattatcctactaaaaagccgaaaatcaaacaacttaagtttttttgattattttttaaacaacccaacacctttctagttcactaatcaaccaatcttaagaatttattcagtaaatttaatatttatttgcttttttctactgacaatattctgcatttgtgtgctaagattcggttactttctaccgctctaactaataaagcgtc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 214 End: 306 ..................................................................................................................................................................................................................... M F K S S N I I L L K S R K S N N L S F F D Y F L N N P T P F ..................................................................................................................................... Protein_Len: 33 Strand: + Start: 325 End: 423 .................................................................................................................................................................................................................................................................................................................................... M L R I Y S V N L I F I C F F L L T I F C I C V L R F G Y F L P L ................ Protein_Len: 36 Strand: - Start: 156 End: 263 ........................................................................................................................................................... Y S T S N V G Y V K L L Y M D R I F H S N L L E F M I R S F L R F D F M ................................................................................................................................................................................ Protein_Len: 44 Strand: - Start: 38 End: 169 ..................................... F L I L R Y L Q F G V C P S T N G T M K F R K L L F T F N K V I L S S L Y Q K I R L Q M .............................................................................................................................................................................................................................................................................. tttgatgatcctctattaattagtcatctttaatttaaaacagtatcagccgatacagctgaaaaccaacacaaggacttgtgttacctgtcatcttaaaccgtttaagtaaaaaagtgaaattttttacaattaacgaactaagatattgtttaatacgaagttgaattcaccccatatacttttaacaaatacatatcccttatgaaatgactgtttaaaagttcgaacattatcctactaaaaagccgaaaatcaaacaacttaagtttttttgattattttttaaacaacccaacacctttctagttcactaatcaaccaatcttaagaatttattcagtaaatttaatatttatttgcttttttctactgacaatattctgcatttgtgtgctaagattcggttactttctaccgctctaactaataaagcgtc 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: 93 End: 122 ............................................................................................TTTCACTTTTTTACTTAAACGGTTTAAGAT............................................................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttgatgatcctctattaattagtcatctttaatttaaaacagtatcagccgatacagctgaaaaccaacacaaggacttgtgttacctgtcatcttaaaccgtttaagtaaaaaagtgaaattttttacaattaacgaactaagatattgtttaatacgaagttgaattcaccccatatacttttaacaaatacatatcccttatgaaatgactgtttaaaagttcgaacattatcctactaaaaagccgaaaatcaaacaacttaagtttttttgattattttttaaacaacccaacacctttctagttcactaatcaaccaatcttaagaatttattcagtaaatttaatatttatttgcttttttctactgacaatattctgcatttgtgtgctaagattcggttactttctaccgctctaactaataaagcgtc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -8.7 Tail_Score: -2.96152 Start: 46 End: 62 Full_Region: tccttgtgttggttt tcagctg tat cggctga tactgttttaaatta .............................................tcagctgtatcggctga......................................................................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: AA02458:AA02459|AA02458:AA02459:outer membrane protein 34:conserved hypothetical protein:->->:1697169..1697607 439 tttgatgatcctctattaattagtcatctttaatttaaaacagtatcagccgatacagctgaaaaccaacacaaggacttgtgttacctgtcatcttaaaccgtttaagtaaaaaagtgaaattttttacaattaacgaactaagatattgtttaatacgaagttgaattcaccccatatacttttaacaaatacatatcccttatgaaatgactgtttaaaagttcgaacattatcctactaaaaagccgaaaatcaaacaacttaagtttttttgattattttttaaacaacccaacacctttctagttcactaatcaaccaatcttaagaatttattcagtaaatttaatatttatttgcttttttctactgacaatattctgcatttgtgtgctaagattcggttactttctaccgctctaactaataaagcgtc Intra-Species Hit: Count: 1 Min: 1 Max: 439 Len: 439 Subject: aact_AA02458_AA02459|outer membrane protein 34:conserved hypothetical protein|POSITIVE:POSITIVE|[1697169,1697607]|439 HSP 1 e-value: 1.0E-150 bit: 533.0 Len: 269 Query Start:1 Query End:269 Subject Strand: POSITIVE Subject Start: 1 Subject End: 269 tttgatgatcctctattaattagtcatctttaatttaaaacagtatcagccgatacagctgaaaaccaacacaaggacttgtgttacctgtcatcttaaaccgtttaagtaaaaaagtgaaattttttacaattaacgaactaagatattgtttaatacgaagttgaattcaccccatatacttttaacaaatacatatcccttatgaaatgactgtttaaaagttcgaacattatcctactaaaaagccgaaaatcaaacaacttaag.......................................................................................................................................................................... tttgatgatcctctattaattagtcatctttaatttaaaacagtatcagccgatacagctgaaaaccaacacaaggacttgtgttacctgtcatcttaaaccgtttaagtaaaaaagtgaaattttttacaattaacgaactaagatattgtttaatacgaagttgaattcaccccatatacttttaacaaatacatatcccttatgaaatgactgtttaaaagttcgaacattatcctactaaaaagccgaaaatcaaacaacttaag.......................................................................................................................................................................... HSP 2 e-value: 1.0E-80 bit: 301.0 Len: 152 Query Start:288 Query End:439 Subject Strand: POSITIVE Subject Start: 288 Subject End: 439 ...............................................................................................................................................................................................................................................................................................aaacaacccaacacctttctagttcactaatcaaccaatcttaagaatttattcagtaaatttaatatttatttgcttttttctactgacaatattctgcatttgtgtgctaagattcggttactttctaccgctctaactaataaagcgtc ...............................................................................................................................................................................................................................................................................................aaacaacccaacacctttctagttcactaatcaaccaatcttaagaatttattcagtaaatttaatatttatttgcttttttctactgacaatattctgcatttgtgtgctaagattcggttactttctaccgctctaactaataaagcgtc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGAUGAUCCUCUAUUAAUUAGUCAUCUUUAAUUUAAAACAGUAUCAGCCGAUACAGCUGAAAACCAACACAAGGACUUGUGUUACCUGUCAUCUUAAACCGUUUAAGUAAAAAAGUGAAAUUUUUUACAAUUAACGAACUAAGAUAUUGUUUAAUACGAAGUUGAAUUCACCCCAUAUACUUUUAACAAAUACAUAUCCCUUAUGAAAUGACUGUUUAAAAGUUCGAACAUUAUCCUACUAAAAAGCCGAAAAUCAAACAACUUAAGUUUUUUUGAUUAUUUUUUAAACAACCCAACACCUUUCUAGUUCACUAAUCAACCAAUCUUAAGAAUUUAUUCAGUAAAUUUAAUAUUUAUUUGCUUUUUUCUACUGACAAUAUUCUGCAUUUGUGUGCUAAGAUUCGGUUACUUUCUACCGCUCUAACUAAUAAAGCGUC ..(((((.((..((.((((.(((((((.((((((((...((((..(((((.......))))).....(((((((....)))))))..)))).((((((...((((...((((((((......))))))))....))))...)))))).............))))))))..........................((((.....))))..))))))).)))).))...)).)))))...........(((((((..(((.....((((((.....(((((((.................................))))))).....)))))).........(((((((.........))))))).........))).........((((....)))).....))))))).........((((.((.....)).)))).. (-71.01) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACGCUUUAUUAGUUAGAGCGGUAGAAAGUAACCGAAUCUUAGCACACAAAUGCAGAAUAUUGUCAGUAGAAAAAAGCAAAUAAAUAUUAAAUUUACUGAAUAAAUUCUUAAGAUUGGUUGAUUAGUGAACUAGAAAGGUGUUGGGUUGUUUAAAAAAUAAUCAAAAAAACUUAAGUUGUUUGAUUUUCGGCUUUUUAGUAGGAUAAUGUUCGAACUUUUAAACAGUCAUUUCAUAAGGGAUAUGUAUUUGUUAAAAGUAUAUGGGGUGAAUUCAACUUCGUAUUAAACAAUAUCUUAGUUCGUUAAUUGUAAAAAAUUUCACUUUUUUACUUAAACGGUUUAAGAUGACAGGUAACACAAGUCCUUGUGUUGGUUUUCAGCUGUAUCGGCUGAUACUGUUUUAAAUUAAAGAUGACUAAUUAAUAGAGGAUCAUCAAA ((..(((((((((((((..((((........)))).(((((.(((......))).((((((((((..((..(((((((...(((((.....)))))..((((((((.((((((.((..(((((((.(((((.................))))).....)))))))..)).))))))..)))))...))).)))))))..)).))))))))))....(((.(((((((((...((((((((...(((((((((((...(((((((((((.......)))))))))...))....((((((..((((....((((((((......))))))))...))))..)))))))))))))).)))....)))))))).))....(((((((...))))))).))))))).)))...)))))..)))))))))))))..))...... (-106.03) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 71 37 220 182 aact:AA02047|5end_galactitol-1-phosphate_5-dehydrogenase_1393633..1393863_POSITIVE 279 420 371 202 146 aact:AA00895|5end_hypothetical_protein_621285..621515_POSITIVE 276 429 382 192 147 aact:AA01338|5end_hypothetical_protein_904967..905197_POSITIVE 275 409 361 172 130 aact:AA02261|5end_30S_ribosomal_protein_S9_1538013..1538243_POSITIVE 275 428 382 185 134 aact:AA00770|5end_outer_membrane_protein_precursor_530788..531018_POSITIVE 273 419 371 138 85 aact:AA02218|5end_deoxyribose-phosphate_aldolase_(fragment?)_1509758..1509988_POSITIVE 267 420 373 173 133 aact:AA00971|5end_conserved_hypothetical_protein_677208..677438_POSITIVE 265 424 384 231 187 aact:AA02490|5end_hypothetical_protein_1726610..1726840_POSITIVE 265 424 384 75 31 aact:AA02489|5end_hypothetical_protein_1726454..1726684_POSITIVE 260 90 41 113 53 aact:AA00574|5end_regulatory_protein_392113..392343_POSITIVE 257 410 371 138 97 aact:AA02836|5end_colicin_transport_protein_1991777..1992007_POSITIVE 257 410 371 62 21 aact:AA02835|5end_hypothetical_protein_1991701..1991931_POSITIVE 255 85 49 204 170 aact:AA00918|5end_hypothetical_protein_630044..630274_POSITIVE 254 83 41 184 127 aact:AA02199|5end_hypothetical_protein_1497627..1497857_POSITIVE 252 410 362 218 161 aact:AA02493|5end_conserved_hypothetical_protein_1730031..1730261_POSITIVE 252 90 41 64 5 aact:AA01629|5end_phosphatidylglycerophosphatase_A_1101881..1102111_POSITIVE 251 409 378 49 23 aact:AA01579|5end_transcriptional_regulatory_protein_1064247..1064477_POSITIVE 250 409 361 182 122 aact:AA01063|5end_conserved_hypothetical_protein_736537..736767_POSITIVE 249 117 79 163 126 aact:AA02898|5end_oligopeptide_transport_ATP-binding_protein_2029083..2029313_POSITIVE 247 400 362 196 150 aact:AA00637|5end_phosphohistidine_phosphatase_438169..438399_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 413 371 151 111 aact:AA00076|3end_dihydroneopterin_aldolase_56083..56233_POSITIVE 273 419 371 135 82 aact:AA02217|3end_deoxyribose-phosphate_aldolase_1509835..1509985_POSITIVE 265 424 384 59 15 aact:AA02487|3end_hypothetical_protein_1726518..1726668_POSITIVE 257 410 371 49 8 aact:AA02834|3end_colicin_transport_protein_1991768..1991918_POSITIVE 250 409 361 64 4 aact:AA01062|3end_ribonuclease_PH_(RNase_PH)_736499..736649_POSITIVE 249 117 79 150 113 aact:AA02897|3end_oligopeptide_ABC_transporter;_permease_protein_2029150..2029300_POSITIVE 247 400 362 141 95 aact:AA00636|3end_MrsA_protein_(phosphoglucomutase/phosphomannomutase)_438194..438344_POSITIVE 246 88 49 117 75 aact:AA01765|3end_Mu-like_prophage_FluMu_transposase_A_1192636..1192786_POSITIVE 244 90 41 73 2 aact:AA00992|3end_ribonuclease_BN_694568..694718_POSITIVE 241 67 22 120 66 aact:AA01601|3end_PTS_system,_glucose-specific_IIA_componen_1082846..1082996_POSITIVE 241 69 26 118 68 aact:AA01242|3end_DNA-directed_RNA_polymerase_alpha_subunit_847009..847159_POSITIVE 239 427 384 121 81 aact:AA02368|3end_conserved_hypothetical_protein_1624286..1624436_POSITIVE 238 427 391 59 25 aact:AA02546|3end_hypothetical_protein_1774761..1774911_POSITIVE 238 421 385 114 70 aact:AA01948|3end_ABC_transporter_permease,_membrane_spanning_protein_1318196..1318346_POSITIVE 236 83 45 93 51 aact:AA00675|3end_glutaredoxin_2_463248..463398_POSITIVE 235 87 42 103 62 aact:AA01155|3end_hypothetical_protein_791411..791561_POSITIVE 235 419 372 57 21 aact:AA01138|3end_anaerobic_dimethyl_sulfoxide_reductase,_chain_B_781685..781835_POSITIVE 234 89 46 60 7 aact:AA01815|3end_probable_sodium-dependent_transmembrane_transport_protein_1223985..1224135_POSITIVE 233 419 373 151 112 aact:AA00970|3end_uroporphyrinogen_decarboxylase_(uroporphyrinogen_III_decarboxylase)_677267..677417_POSITIVE 232 77 42 140 103 aact:AA00497|3end_hexose_phosphate_transport_system_regulatory_protein;_regulator_of_uhpT_expression_346479..346629_POSITIVE