Origin IGS: atttgcccccttgggaagattggcggtgtaattggcaatattgacttcggctaaagaggcggtggcgatgccgaggctgagtaataagaatgtttcttgaaaaatatgacgtggtgaaaatttatacatgatccgtgcttgaggttgctattttttgaaagacgaacaataatagtacgcgaatacgcgggagtaaatgcttttctcccgccataaccgattaatttacgctgtggaatccggaggattccacggtttttcttttattcaaatttagggaaaagaaga .........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 tcttcttttccctaaatttgaataaaagaaaaaccgtggaatcctccggattccacagcgtaaattaatcggttatggcgggagaaaagcatttactcccgcgtattcgcgtactattattgttcgtctttcaaaaaatagcaacctcaagcacggatcatgtataaattttcaccacgtcatatttttcaagaaacattcttattactcagcctcggcatcgccaccgcctctttagccgaagtcaatattgccaattacaccgccaatcttcccaagggggcaaat Mask Tandem Repeat Region ================================================ atttgcccccttgggaagattggcggtgtaattggcaatattgacttcggctaaagaggcggtggcgatgccgaggctgagtaataagaatgtttcttgaaaaatatgacgtggtgaaaatttatacatgatccgtgcttgaggttgctattttttgaaagacgaacaataatagtacgcgaatacgcgggagtaaatgcttttctcccgccataaccgattaatttacgctgtggaatccggaggattccacggtttttcttttattcaaatttagggaaaagaaga Find is-nt database================================================ Query_seq: AA01666:AA01668|AA01666:AA01668:penicillin-binding protein 4; D-alanyl-D-alanine carboxypeptidase; D-alanyl-D-alanine-endopeptidase:transcription elongation factor:->->:1129682..1129969 288 atttgcccccttgggaagattggcggtgtaattggcaatattgacttcggctaaagaggcggtggcgatgccgaggctgagtaataagaatgtttcttgaaaaatatgacgtggtgaaaatttatacatgatccgtgcttgaggttgctattttttgaaagacgaacaataatagtacgcgaatacgcgggagtaaatgcttttctcccgccataaccgattaatttacgctgtggaatccggaggattccacggtttttcttttattcaaatttagggaaaagaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01666:AA01668|AA01666:AA01668:penicillin-binding protein 4; D-alanyl-D-alanine carboxypeptidase; D-alanyl-D-alanine-endopeptidase:transcription elongation factor:->->:1129682..1129969 288 atttgcccccttgggaagattggcggtgtaattggcaatattgacttcggctaaagaggcggtggcgatgccgaggctgagtaataagaatgtttcttgaaaaatatgacgtggtgaaaatttatacatgatccgtgcttgaggttgctattttttgaaagacgaacaataatagtacgcgaatacgcgggagtaaatgcttttctcccgccataaccgattaatttacgctgtggaatccggaggattccacggtttttcttttattcaaatttagggaaaagaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01666:AA01668|AA01666:AA01668:penicillin-binding protein 4; D-alanyl-D-alanine carboxypeptidase; D-alanyl-D-alanine-endopeptidase:transcription elongation factor:->->:1129682..1129969 288 atttgcccccttgggaagattggcggtgtaattggcaatattgacttcggctaaagaggcggtggcgatgccgaggctgagtaataagaatgtttcttgaaaaatatgacgtggtgaaaatttatacatgatccgtgcttgaggttgctattttttgaaagacgaacaataatagtacgcgaatacgcgggagtaaatgcttttctcccgccataaccgattaatttacgctgtggaatccggaggattccacggtttttcttttattcaaatttagggaaaagaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttgcccccttgggaagattggcggtgtaattggcaatattgacttcggctaaagaggcggtggcgatgccgaggctgagtaataagaatgtttcttgaaaaatatgacgtggtgaaaatttatacatgatccgtgcttgaggttgctattttttgaaagacgaacaataatagtacgcgaatacgcgggagtaaatgcttttctcccgccataaccgattaatttacgctgtggaatccggaggattccacggtttttcttttattcaaatttagggaaaagaaga Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 124 End: 213 ........................................................................................................................... M H D P C L R L L F F E R R T I I V R E Y A G V N A F L P P ........................................................................... Protein_Len: 30 Strand: - Start: 125 End: 214 ............................................................................................................................ V H D T S S T A I K Q F V F L L L V R I R P L L H K E G A M .......................................................................... Protein_Len: 60 Strand: - Start: 54 End: 248 ..................................................... A S A S Y Y S H K K F F I V H H F N I C S G H K L N S N K S L R V I I T R S Y A P T F A K R G G Y G I L K R Q P I R L M ........................................ Protein_Len: 40 Strand: - Start: 2 End: 121 . K G G Q S S Q R H L Q C Y Q S R S F L R H R H R P Q T I L I N R S F Y S T T F M ....................................................................................................................................................................... Protein_Len: 44 Strand: - Start: 1 End: 132 N A G K P L N A T Y N A I N V E A L S A T A I G L S L L L F T E Q F I H R P S F K Y M M ............................................................................................................................................................ atttgcccccttgggaagattggcggtgtaattggcaatattgacttcggctaaagaggcggtggcgatgccgaggctgagtaataagaatgtttcttgaaaaatatgacgtggtgaaaatttatacatgatccgtgcttgaggttgctattttttgaaagacgaacaataatagtacgcgaatacgcgggagtaaatgcttttctcccgccataaccgattaatttacgctgtggaatccggaggattccacggtttttcttttattcaaatttagggaaaagaaga 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: 144 End: 173 ...............................................................................................................................................GTTGCTATTTTTTGAAAGACGAACAATAAT................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttgcccccttgggaagattggcggtgtaattggcaatattgacttcggctaaagaggcggtggcgatgccgaggctgagtaataagaatgtttcttgaaaaatatgacgtggtgaaaatttatacatgatccgtgcttgaggttgctattttttgaaagacgaacaataatagtacgcgaatacgcgggagtaaatgcttttctcccgccataaccgattaatttacgctgtggaatccggaggattccacggtttttcttttattcaaatttagggaaaagaaga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -9.4 Tail_Score: -3.07787 Start: 186 End: 212 Full_Region: aaattaatcggttat ggcgggagaaaa gca tttactcccgcg tattcgcgtactatt .........................................................................................................................................................................................ggcgggagaaaagcatttactcccgcg............................................................................ TransTerm Strand: + Conf: 100 HP_score: -15.1 Tail_Score: -5.62288 Start: 231 End: 255 Full_Region: ACCGATTAATTTACG CTGTGGAATCC GGA GGATTCCACGG TTTTTCTTTTATTCA ......................................................................................................................................................................................................................................CTGTGGAATCCGGAGGATTCCACGG................................. Find igs database================================================ Query_seq: AA01666:AA01668|AA01666:AA01668:penicillin-binding protein 4; D-alanyl-D-alanine carboxypeptidase; D-alanyl-D-alanine-endopeptidase:transcription elongation factor:->->:1129682..1129969 288 atttgcccccttgggaagattggcggtgtaattggcaatattgacttcggctaaagaggcggtggcgatgccgaggctgagtaataagaatgtttcttgaaaaatatgacgtggtgaaaatttatacatgatccgtgcttgaggttgctattttttgaaagacgaacaataatagtacgcgaatacgcgggagtaaatgcttttctcccgccataaccgattaatttacgctgtggaatccggaggattccacggtttttcttttattcaaatttagggaaaagaaga Intra-Species Hit: Count: 1 Min: 1 Max: 288 Len: 288 Subject: aact_AA01666_AA01668|penicillin-binding protein 4; D-alanyl-D-alanine carboxypeptidase; D-alanyl-D-alanine-endopeptidase:transcription elongation factor|POSITIVE:POSITIVE|[1129682,1129969]|288 HSP 1 e-value: 1.0E-162 bit: 571.0 Len: 288 Query Start:1 Query End:288 Subject Strand: POSITIVE Subject Start: 1 Subject End: 288 atttgcccccttgggaagattggcggtgtaattggcaatattgacttcggctaaagaggcggtggcgatgccgaggctgagtaataagaatgtttcttgaaaaatatgacgtggtgaaaatttatacatgatccgtgcttgaggttgctattttttgaaagacgaacaataatagtacgcgaatacgcgggagtaaatgcttttctcccgccataaccgattaatttacgctgtggaatccggaggattccacggtttttcttttattcaaatttagggaaaagaaga atttgcccccttgggaagattggcggtgtaattggcaatattgacttcggctaaagaggcggtggcgatgccgaggctgagtaataagaatgtttcttgaaaaatatgacgtggtgaaaatttatacatgatccgtgcttgaggttgctattttttgaaagacgaacaataatagtacgcgaatacgcgggagtaaatgcttttctcccgccataaccgattaatttacgctgtggaatccggaggattccacggtttttcttttattcaaatttagggaaaagaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUGCCCCCUUGGGAAGAUUGGCGGUGUAAUUGGCAAUAUUGACUUCGGCUAAAGAGGCGGUGGCGAUGCCGAGGCUGAGUAAUAAGAAUGUUUCUUGAAAAAUAUGACGUGGUGAAAAUUUAUACAUGAUCCGUGCUUGAGGUUGCUAUUUUUUGAAAGACGAACAAUAAUAGUACGCGAAUACGCGGGAGUAAAUGCUUUUCUCCCGCCAUAACCGAUUAAUUUACGCUGUGGAAUCCGGAGGAUUCCACGGUUUUUCUUUUAUUCAAAUUUAGGGAAAAGAAGA .....(((....))).(((((((((((...(((.((..(((((.((.(((((.....((((.......))))..))))))))))))....(((((.(..((((.......((((..(...((((..((((...))))..)))).)..))))))))..).)))))..............)).)))..(((((((.(((....))))))))))....)))).)))))))..((((((((((((...))))))))))))(((((((((.(((.......)))))))))))) (-77.11) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUCUUUUCCCUAAAUUUGAAUAAAAGAAAAACCGUGGAAUCCUCCGGAUUCCACAGCGUAAAUUAAUCGGUUAUGGCGGGAGAAAAGCAUUUACUCCCGCGUAUUCGCGUACUAUUAUUGUUCGUCUUUCAAAAAAUAGCAACCUCAAGCACGGAUCAUGUAUAAAUUUUCACCACGUCAUAUUUUUCAAGAAACAUUCUUAUUACUCAGCCUCGGCAUCGCCACCGCCUCUUUAGCCGAAGUCAAUAUUGCCAAUUACACCGCCAAUCUUCCCAAGGGGGCAAAU .................((((.((((((((.....(((((((((...))))))))).................(((((((((.(((((.....(((...((((....))))..........(((((((((..................))).))))))...)))....))))).)).)))))))..............))))).))).))))....(((...)))...((((((((....((((.....((((.(.........).))))))))..)))))))).... (-58.57) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 440 77 33 75 43 aact:AA02616|5end_transcriptional_regulator_1823684..1823914_POSITIVE 421 76 33 62 12 aact:AA02443|5end_cytochrome_C_related_protein_1686202..1686432_POSITIVE 399 70 21 198 157 aact:AA02899|5end_oligopeptide_ABC_transporter,_ATP-binding_protein_2030063..2030293_POSITIVE 399 86 44 172 134 aact:AA02199|5end_hypothetical_protein_1497627..1497857_POSITIVE 395 70 23 76 42 aact:AA01416|5end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_952780..953010_POSITIVE 382 80 33 190 148 aact:AA02705|5end_hypothetical_protein_1886717..1886947_POSITIVE 379 79 34 218 170 aact:AA00461|5end_heat_shock_protein;_protease_322375..322605_POSITIVE 373 70 22 56 2 aact:AA00460|5end_ATP-dependent_ClpY-related_protease;_heat_shock_protein_321023..321253_POSITIVE 369 77 34 205 159 aact:AA01525|5end_amino_acid_ABC_transporter,_permease_component_1024277..1024507_POSITIVE 364 85 46 64 8 aact:AA01109|5end_oxidoreductase_(possible_short-chain_alcohol_dehydrogenase)_763899..764129_POSITIVE 359 67 21 205 152 aact:AA02560|5end_integral_membrane_protein_1781412..1781642_POSITIVE 358 70 22 212 170 aact:AA00256|5end_rare_lipoprotein_A_precursor_178800..179030_POSITIVE 355 68 21 161 121 aact:AA01654|5end_periplasmic_maltose-binding_protein_precursor_1119896..1120126_POSITIVE 355 68 21 61 21 aact:AA01651|5end_hypothetical_protein_1119796..1120026_POSITIVE 354 70 24 230 188 aact:AA02892|5end_oligopeptide_ABC_transporter,_periplasmic-binding_protein_2026402..2026632_POSITIVE 349 68 22 111 55 aact:AA01424|5end_threonine_deaminase_(dehydratase)_957740..957970_POSITIVE 347 78 31 228 193 aact:AA02440|5end_ABC_transporter,_ATP-binding_protein_1685043..1685273_POSITIVE 345 84 45 44 7 aact:AA02043|5end_tagatose_6-phosphate_kinase_1390218..1390448_POSITIVE 345 80 33 157 107 aact:AA00290|5end_conserved_hypothetical_protein_201272..201502_POSITIVE 341 67 22 59 11 aact:AA01117|5end_signal_recognition_particle_protein_54_(GTP-binding_export_factor)_767919..768149_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 421 76 33 52 2 aact:AA02442|3end_thioredoxin-family_protein_1686272..1686422_POSITIVE 395 70 23 76 42 aact:AA01413|3end_conserved_hypothetical_protein_952860..953010_POSITIVE 378 74 32 123 80 aact:AA02891|3end_oligopeptide-binding_protein_precursor_2026370..2026520_POSITIVE 367 74 44 143 119 aact:AA02196|3end_oxaloacetate_decarboxylase_beta_chain_1497692..1497842_POSITIVE 364 85 46 68 12 aact:AA01108|3end_hypothetical_protein_763983..764133_POSITIVE 359 80 34 139 81 aact:AA02350|3end_possible_lipoprotein_1609179..1609329_POSITIVE 358 70 22 106 64 aact:AA00254|3end_penicillin-binding_protein_5_178774..178924_POSITIVE 339 80 32 80 36 aact:AA01217|3end_hypothetical_protein_832855..833005_POSITIVE 339 98 58 64 21 aact:AA00534|3end_hypothetical_protein_365594..365744_POSITIVE 337 77 32 141 83 aact:AA02777|3end_tRNA-guanine_transglycosylase_1942527..1942677_POSITIVE 336 65 23 61 6 aact:AA00361|3end_50S_ribosomal_protein_L16_244910..245060_POSITIVE 334 69 22 124 70 aact:AA02584|3end_ADP-heptose_synthase_1798729..1798879_POSITIVE 334 77 34 99 58 aact:AA00988|3end_conserved_hypothetical_protein_692264..692414_POSITIVE 333 70 23 105 42 aact:AA01291|3end_excinuclease_ABC_subunit_A_876001..876151_POSITIVE 330 110 61 79 26 aact:AA00855|3end_arginine_ABC_transporter,_permease_protein_590323..590473_POSITIVE 329 80 35 136 93 aact:AA01650|3end_maltose_transport_inner_membrane_protein_1119849..1119999_POSITIVE 329 79 33 151 102 aact:AA00288|3end_conserved_hypothetical_protein_201347..201497_POSITIVE 326 44 5 74 38 aact:AA02560|3end_integral_membrane_protein_1783630..1783780_POSITIVE 326 70 21 129 65 aact:AA02080|3end_ABC_transporter,_ATP-binding/permease_1414794..1414944_POSITIVE 325 79 32 77 17 aact:AA01196|3end_1-acyl-sn-glycerol-3-phosphate_acetyltransferase_820955..821105_POSITIVE