Origin IGS: tgatttttcaccgaatgtatttccgagaatttgatggtgctcatctgatggcgcgcatttcccaattatcgctgtcgaaacattgtagttatttaataaaaaagaaaaatttgaatcctctcgtttacgggggaaccggacgaaaccctgagagggcaaaatctcgatttttaagcatgagtttgttaaaaaatagagtatattccccgcccttcgggcaccttcccccgtaaacggaagaaggcaagatactttataaaatatcaatgcattacaatttttcgaacacttgtggtttcaacacgtgctttttgttcctattagtactgcgacgtgtacgctatctatcaagtactctaaaaaatggcatagtagacaaagtaccccgacttgtgccggggtattctcttaaaaacacttaaattttttaccgcactttacgaaaaatgattaagcgcgggaaatcatta .........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 taatgatttcccgcgcttaatcatttttcgtaaagtgcggtaaaaaatttaagtgtttttaagagaataccccggcacaagtcggggtactttgtctactatgccattttttagagtacttgatagatagcgtacacgtcgcagtactaataggaacaaaaagcacgtgttgaaaccacaagtgttcgaaaaattgtaatgcattgatattttataaagtatcttgccttcttccgtttacgggggaaggtgcccgaagggcggggaatatactctattttttaacaaactcatgcttaaaaatcgagattttgccctctcagggtttcgtccggttcccccgtaaacgagaggattcaaatttttcttttttattaaataactacaatgtttcgacagcgataattgggaaatgcgcgccatcagatgagcaccatcaaattctcggaaatacattcggtgaaaaatca Mask Tandem Repeat Region ================================================ tgatttttcaccgaatgtatttccgagaatttgatggtgctcatctgatggcgcgcatttcccaattatcgctgtcgaaacattgtagttatttaataaaaaagaaaaatttgaatcctctcgtttacgggggaaccggacgaaaccctgagagggcaaaatctcgatttttaagcatgagtttgttaaaaaatagagtatattccccgcccttcgggcaccttcccccgtaaacggaagaaggcaagatactttataaaatatcaatgcattacaatttttcgaacacttgtggtttcaacacgtgctttttgttcctattagtactgcgacgtgtacgctatctatcaagtactctaaaaaatggcatagtagacaaagtaccccgacttgtgccggggtattctcttaaaaacacttaaattttttaccgcactttacgaaaaatgattaagcgcgggaaatcatta Find is-nt database================================================ Query_seq: AA02954:AA02955|AA02954:AA02955:penicillin tolerance protein; hydroxymethylbutenyl pyrophosphate reductase:trigger factor:->->:2066692..2067161 470 tgatttttcaccgaatgtatttccgagaatttgatggtgctcatctgatggcgcgcatttcccaattatcgctgtcgaaacattgtagttatttaataaaaaagaaaaatttgaatcctctcgtttacgggggaaccggacgaaaccctgagagggcaaaatctcgatttttaagcatgagtttgttaaaaaatagagtatattccccgcccttcgggcaccttcccccgtaaacggaagaaggcaagatactttataaaatatcaatgcattacaatttttcgaacacttgtggtttcaacacgtgctttttgttcctattagtactgcgacgtgtacgctatctatcaagtactctaaaaaatggcatagtagacaaagtaccccgacttgtgccggggtattctcttaaaaacacttaaattttttaccgcactttacgaaaaatgattaagcgcgggaaatcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02954:AA02955|AA02954:AA02955:penicillin tolerance protein; hydroxymethylbutenyl pyrophosphate reductase:trigger factor:->->:2066692..2067161 470 tgatttttcaccgaatgtatttccgagaatttgatggtgctcatctgatggcgcgcatttcccaattatcgctgtcgaaacattgtagttatttaataaaaaagaaaaatttgaatcctctcgtttacgggggaaccggacgaaaccctgagagggcaaaatctcgatttttaagcatgagtttgttaaaaaatagagtatattccccgcccttcgggcaccttcccccgtaaacggaagaaggcaagatactttataaaatatcaatgcattacaatttttcgaacacttgtggtttcaacacgtgctttttgttcctattagtactgcgacgtgtacgctatctatcaagtactctaaaaaatggcatagtagacaaagtaccccgacttgtgccggggtattctcttaaaaacacttaaattttttaccgcactttacgaaaaatgattaagcgcgggaaatcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02954:AA02955|AA02954:AA02955:penicillin tolerance protein; hydroxymethylbutenyl pyrophosphate reductase:trigger factor:->->:2066692..2067161 470 tgatttttcaccgaatgtatttccgagaatttgatggtgctcatctgatggcgcgcatttcccaattatcgctgtcgaaacattgtagttatttaataaaaaagaaaaatttgaatcctctcgtttacgggggaaccggacgaaaccctgagagggcaaaatctcgatttttaagcatgagtttgttaaaaaatagagtatattccccgcccttcgggcaccttcccccgtaaacggaagaaggcaagatactttataaaatatcaatgcattacaatttttcgaacacttgtggtttcaacacgtgctttttgttcctattagtactgcgacgtgtacgctatctatcaagtactctaaaaaatggcatagtagacaaagtaccccgacttgtgccggggtattctcttaaaaacacttaaattttttaccgcactttacgaaaaatgattaagcgcgggaaatcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatttttcaccgaatgtatttccgagaatttgatggtgctcatctgatggcgcgcatttcccaattatcgctgtcgaaacattgtagttatttaataaaaaagaaaaatttgaatcctctcgtttacgggggaaccggacgaaaccctgagagggcaaaatctcgatttttaagcatgagtttgttaaaaaatagagtatattccccgcccttcgggcaccttcccccgtaaacggaagaaggcaagatactttataaaatatcaatgcattacaatttttcgaacacttgtggtttcaacacgtgctttttgttcctattagtactgcgacgtgtacgctatctatcaagtactctaaaaaatggcatagtagacaaagtaccccgacttgtgccggggtattctcttaaaaacacttaaattttttaccgcactttacgaaaaatgattaagcgcgggaaatcatta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 3 End: 230 .. M F H R M Y F R E F D G A H L M A R I S Q L S L S K H C S Y L I K K K N L N P L V Y G G T G R N P E R A K S R F L S M S ................................................................................................................................................................................................................................................ Protein_Len: 43 Strand: + Start: 193 End: 321 ................................................................................................................................................................................................ M E Y I P R P S G T F P R K R K K A R Y F I K Y Q C I T I F R T L V V S T R A F C S Y ..................................................................................................................................................... Protein_Len: 49 Strand: + Start: 263 End: 409 ...................................................................................................................................................................................................................................................................... M N A L Q F F E H L W F Q H V L F V P I S T A T C T L S I K Y S K K W H S R Q S T P T C A G V F S ............................................................. Protein_Len: 57 Strand: + Start: 249 End: 419 ........................................................................................................................................................................................................................................................ M L Y K I S M H Y N F S N T C G F N T C F L F L L V L R R V R Y L S S T L K N G I V D K V P R L V P G Y S L K N T ................................................... Protein_Len: 41 Strand: - Start: 128 End: 250 ............................................................................................................................... P P V P R F G S L A F D R N K L M L K N F F L T Y E G G K P C R G G Y V S S P L M ............................................................................................................................................................................................................................ Protein_Len: 60 Strand: - Start: 1 End: 267 N N L L F S F N S D E R K R P F R V F G Q S P L I E I K L C S N T L F Y L I N G A R R A G E G T F P L L C S V K Y F I M ........................................................................................................................................................................................................... tgatttttcaccgaatgtatttccgagaatttgatggtgctcatctgatggcgcgcatttcccaattatcgctgtcgaaacattgtagttatttaataaaaaagaaaaatttgaatcctctcgtttacgggggaaccggacgaaaccctgagagggcaaaatctcgatttttaagcatgagtttgttaaaaaatagagtatattccccgcccttcgggcaccttcccccgtaaacggaagaaggcaagatactttataaaatatcaatgcattacaatttttcgaacacttgtggtttcaacacgtgctttttgttcctattagtactgcgacgtgtacgctatctatcaagtactctaaaaaatggcatagtagacaaagtaccccgacttgtgccggggtattctcttaaaaacacttaaattttttaccgcactttacgaaaaatgattaagcgcgggaaatcatta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgatttttcaccgaatgtatttccgagaatttgatggtgctcatctgatggcgcgcatttcccaattatcgctgtcgaaacattgtagttatttaataaaaaagaaaaatttgaatcctctcgtttacgggggaaccggacgaaaccctgagagggcaaaatctcgatttttaagcatgagtttgttaaaaaatagagtatattccccgcccttcgggcaccttcccccgtaaacggaagaaggcaagatactttataaaatatcaatgcattacaatttttcgaacacttgtggtttcaacacgtgctttttgttcctattagtactgcgacgtgtacgctatctatcaagtactctaaaaaatggcatagtagacaaagtaccccgacttgtgccggggtattctcttaaaaacacttaaattttttaccgcactttacgaaaaatgattaagcgcgggaaatcatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 44 HP_score: -2.7 Tail_Score: -3.06815 Start: 163 End: 198 Full_Region: CTGAGAGGGCAAAAT CTCGATTTTTAAGCA TGAGTT TGTTAAAAAATAGAG TATATTCCCCGCCCT ..................................................................................................................................................................CTCGATTTTTAAGCATGAGTTTGTTAAAAAATAGAG................................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 79 HP_score: -8.8 Tail_Score: -4.11404 Start: 381 End: 404 Full_Region: agtgtttttaagaga ataccccggc acaa gtcggggtac tttgtctactatgcc ............................................................................................................................................................................................................................................................................................................................................................................................ataccccggcacaagtcggggtac.................................................................. TransTerm Strand: + Conf: 80 HP_score: -10.1 Tail_Score: -3.65812 Start: 382 End: 403 Full_Region: GCATAGTAGACAAAG TACCCCGAC TTGT GCCGGGGTA TTCTCTTAAAAACAC .............................................................................................................................................................................................................................................................................................................................................................................................TACCCCGACTTGTGCCGGGGTA................................................................... TransTerm Strand: - Conf: 87 HP_score: -12.3 Tail_Score: -3.0636 Start: 382 End: 403 Full_Region: gtgtttttaagagaa taccccggc acaa gtcggggta ctttgtctactatgc .............................................................................................................................................................................................................................................................................................................................................................................................taccccggcacaagtcggggta................................................................... TransTerm Strand: - Conf: 78 HP_score: -10.5 Tail_Score: -3.08278 Start: 384 End: 401 Full_Region: gtttttaagagaata ccccggc acaa gtcgggg tactttgtctactat ...............................................................................................................................................................................................................................................................................................................................................................................................ccccggcacaagtcgggg..................................................................... Find igs database================================================ Query_seq: AA02954:AA02955|AA02954:AA02955:penicillin tolerance protein; hydroxymethylbutenyl pyrophosphate reductase:trigger factor:->->:2066692..2067161 470 tgatttttcaccgaatgtatttccgagaatttgatggtgctcatctgatggcgcgcatttcccaattatcgctgtcgaaacattgtagttatttaataaaaaagaaaaatttgaatcctctcgtttacgggggaaccggacgaaaccctgagagggcaaaatctcgatttttaagcatgagtttgttaaaaaatagagtatattccccgcccttcgggcaccttcccccgtaaacggaagaaggcaagatactttataaaatatcaatgcattacaatttttcgaacacttgtggtttcaacacgtgctttttgttcctattagtactgcgacgtgtacgctatctatcaagtactctaaaaaatggcatagtagacaaagtaccccgacttgtgccggggtattctcttaaaaacacttaaattttttaccgcactttacgaaaaatgattaagcgcgggaaatcatta Intra-Species Hit: Count: 2 Min: 1 Max: 470 Len: 470 Subject: aact_AA02954_AA02955|penicillin tolerance protein; hydroxymethylbutenyl pyrophosphate reductase:trigger factor|POSITIVE:POSITIVE|[2066692,2067161]|470 HSP 1 e-value: 0.0 bit: 860.0 Len: 470 Query Start:1 Query End:470 Subject Strand: POSITIVE Subject Start: 1 Subject End: 470 tgatttttcaccgaatgtatttccgagaatttgatggtgctcatctgatggcgcgcatttcccaattatcgctgtcgaaacattgtagttatttaatnnnnnnnnnnnntttgaatcctctcgtttacgggggaaccggacgaaaccctgagagggcaaaatctcgatttttaagcatgagtttgttaaaaaatagagtatattccccgcccttcgggcaccttcccccgtaaacggaagaaggcaagatactttataaaatatcaatgcattacaatttttcgaacacttgtggtttcaacacgtgctttttgttcctattagtactgcgacgtgtacgctatctatcaagtactctaaaaaatggcatagtagacaaagtaccccgacttgtgccggggtattctcttaaaaacacttaaattttttaccgcactttacgaaaaatgattaagcgcgggaaatcatta tgatttttcaccgaatgtatttccgagaatttgatggtgctcatctgatggcgcgcatttcccaattatcgctgtcgaaacattgtagttatttaataaaaaagaaaaatttgaatcctctcgtttacgggggaaccggacgaaaccctgagagggcaaaatctcgatttttaagcatgagtttgttaaaaaatagagtatattccccgcccttcgggcaccttcccccgtaaacggaagaaggcaagatactttataaaatatcaatgcattacaatttttcgaacacttgtggtttcaacacgtgctttttgttcctattagtactgcgacgtgtacgctatctatcaagtactctaaaaaatggcatagtagacaaagtaccccgacttgtgccggggtattctcttaaaaacacttaaattttttaccgcactttacgaaaaatgattaagcgcgggaaatcatta Subject: aact_AA00776_AA00777|conserved hypothetical protein:soluble lytic murein transglycosylase|POSITIVE:POSITIVE|[533930,534458]|529 HSP 1 e-value: 1.0E-9 bit: 65.9 Len: 65 Query Start:224 Query End:288 Subject Strand: POSITIVE Subject Start: 314 Subject End: 376 ...............................................................................................................................................................................................................................tcccccgtaaacggaagaaggcaagatactttataaaatatcaatgcattacaatttttcgaaca...................................................................................................................................................................................... ...............................................................................................................................................................................................................................tcccccgtaaacggaggaaggcaagata-ttta-aaaatatcaatgaattataatgtttcgaaca...................................................................................................................................................................................... HSP 2 e-value: 2.0E-8 bit: 61.9 Len: 51 Query Start:130 Query End:180 Subject Strand: POSITIVE Subject Start: 134 Subject End: 184 .................................................................................................................................ggggaaccggacgaaaccctgagagggcaaaatctcgatttttaagcatga.................................................................................................................................................................................................................................................................................................. .................................................................................................................................ggggagccgggcgaagccctgagggggcaaaatctcaatttttaagcatga.................................................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUUUUCACCGAAUGUAUUUCCGAGAAUUUGAUGGUGCUCAUCUGAUGGCGCGCAUUUCCCAAUUAUCGCUGUCGAAACAUUGUAGUUAUUUAAUAAAAAAGAAAAAUUUGAAUCCUCUCGUUUACGGGGGAACCGGACGAAACCCUGAGAGGGCAAAAUCUCGAUUUUUAAGCAUGAGUUUGUUAAAAAAUAGAGUAUAUUCCCCGCCCUUCGGGCACCUUCCCCCGUAAACGGAAGAAGGCAAGAUACUUUAUAAAAUAUCAAUGCAUUACAAUUUUUCGAACACUUGUGGUUUCAACACGUGCUUUUUGUUCCUAUUAGUACUGCGACGUGUACGCUAUCUAUCAAGUACUCUAAAAAAUGGCAUAGUAGACAAAGUACCCCGACUUGUGCCGGGGUAUUCUCUUAAAAACACUUAAAUUUUUUACCGCACUUUACGAAAAAUGAUUAAGCGCGGGAAAUCAUUA .............((((.(((((.((((((((((.((((((.....(((((((..(((.((.(....(((((((((((((.(((((((.............................((..((((((((((((((..((.......(((((.(((((.....(((.((((((.((((......)))).)))))).)))..........))))))))))..))))))))))))))))..))...(((.((((.((....)).))))..))).))))))).))))).)))...)))))........(((((..(.......)..))))).).)).)))..))))))).....))))))........((.......(((...(((((((((.(....).))))))))).)))......)).))))))))))..((((.(((..............))).))))))))))))). (-122.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGAUUUCCCGCGCUUAAUCAUUUUUCGUAAAGUGCGGUAAAAAAUUUAAGUGUUUUUAAGAGAAUACCCCGGCACAAGUCGGGGUACUUUGUCUACUAUGCCAUUUUUUAGAGUACUUGAUAGAUAGCGUACACGUCGCAGUACUAAUAGGAACAAAAAGCACGUGUUGAAACCACAAGUGUUCGAAAAAUUGUAAUGCAUUGAUAUUUUAUAAAGUAUCUUGCCUUCUUCCGUUUACGGGGGAAGGUGCCCGAAGGGCGGGGAAUAUACUCUAUUUUUUAACAAACUCAUGCUUAAAAAUCGAGAUUUUGCCCUCUCAGGGUUUCGUCCGGUUCCCCCGUAAACGAGAGGAUUCAAAUUUUUCUUUUUUAUUAAAUAACUACAAUGUUUCGACAGCGAUAAUUGGGAAAUGCGCGCCAUCAGAUGAGCACCAUCAAAUUCUCGGAAAUACAUUCGGUGAAAAAUCA ...((((((.((((((((.((........)).))))))))............(((((((..((((..(((((((((....)))))))))............((((((((......((.((((.(((((.(((.......))).)).))).)))).)).....((.((((((....(((....(((((((((.((((((..(((..(((((((....))))))).)))..((((((((((((((((((.((.((((...(((.(((.((.((.(((...(((((((((......)).)))))))..))))).)).))).))).)))).....))...))))))))))))).)))))............................)))))).))))))..))).....)))..)))))).))....))))).)))........))))..)))))))..........)))))) (-139.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 661 249 207 231 189 aact:AA02949|5end_hypothetical_protein_2061944..2062174_POSITIVE 596 170 121 216 167 aact:AA00862|5end_conserved_hypothetical_protein_596465..596695_POSITIVE 491 246 205 231 183 aact:AA01379|5end_glycerophosphoryl_diester_phosphodiesterase_(protein_D)_933029..933259_POSITIVE 479 90 49 193 151 aact:AA00729|5end_possible_hemolysin_(TlyC-like)_500204..500434_POSITIVE 404 156 111 163 119 aact:AA01422|5end_cell_division_protein_E,_ABC_system_ATP-binding_protein_956009..956239_POSITIVE 401 409 364 225 175 aact:AA01859|5end_hypothetical_protein_1251718..1251948_POSITIVE 390 77 31 156 99 aact:AA02692|5end_hydrogenase_4_subunit;_hydrogenase_3_subunit_1876324..1876554_POSITIVE 364 439 391 170 123 aact:AA00451|5end_hypothetical_protein_315068..315298_POSITIVE 362 76 32 226 183 aact:AA01255|5end_hypothetical_protein_852656..852886_POSITIVE 359 67 22 219 153 aact:AA01457|5end_D-xylose_ABC_transporter,_membrane_spanning_protein_977604..977834_POSITIVE 358 249 201 80 19 aact:AA01845|5end_gamma-glutamyltranspeptidase_precursor_1239841..1240071_POSITIVE 353 80 40 143 104 aact:AA02453|5end_conserved_hypothetical_protein_1688947..1689177_POSITIVE 348 249 207 187 131 aact:AA00894|5end_selenium_transferase_(Cysteinyl-tRNA(Sec)_selenium_transferase)_619879..620109_POSITIVE 345 236 209 139 112 aact:AA00895|5end_hypothetical_protein_621285..621515_POSITIVE 343 247 203 59 22 aact:AA02250|5end_possible_cytochrome_c-type_protein_1530125..1530355_POSITIVE 343 439 393 183 129 aact:AA01824|5end_iron(III)_ABC_transporter,_ATP-binding_protein_1227705..1227935_POSITIVE 338 59 12 57 4 aact:AA00229|5end_DNA_polymerase_III,_alpha_subunit_156863..157093_POSITIVE 337 330 281 190 138 aact:AA00482|5end_hydrolase_(haloacid_dehalogenase-like)_(HAD_superfamily)_335232..335462_POSITIVE 335 150 116 177 135 aact:AA01823|5end_hypothetical_protein_1227563..1227793_POSITIVE 335 156 111 197 155 aact:AA01168|5end_6-phosphogluconolactonase_801243..801473_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 661 249 207 81 39 aact:AA02947|3end_riboflavin_biosynthesis_protein_2061874..2062024_POSITIVE 390 77 31 67 10 aact:AA02691|3end_hypothetical_protein_1876315..1876465_POSITIVE 354 249 215 40 1 aact:AA01421|3end_phosphoglycolate_phosphatase_955806..955956_POSITIVE 353 80 40 42 3 aact:AA02451|3end_conserved_hypothetical_protein_1688926..1689076_POSITIVE 348 308 261 130 85 aact:AA01271|3end_hypothetical_protein_863981..864131_POSITIVE 348 308 261 46 1 aact:AA01270|3end_hydrolase_(possible_2-haloalkanoic_acid_dehalogenase_I)_863897..864047_POSITIVE 345 236 209 124 97 aact:AA00894|3end_selenium_transferase_(Cysteinyl-tRNA(Sec)_selenium_transferase)_621350..621500_POSITIVE 343 232 200 149 112 aact:AA02352|3end_glycine_betaine/carnitine/choline_ABC_transporter_1611114..1611264_POSITIVE 343 439 393 145 91 aact:AA01823|3end_hypothetical_protein_1227747..1227897_POSITIVE 343 439 393 69 15 aact:AA01822|3end_lysostaphin_precursor_1227671..1227821_POSITIVE 337 330 281 77 25 aact:AA00480|3end_mannose-specific_phosphotransferase_system_IID_335199..335349_POSITIVE 336 235 202 33 2 aact:AA00166|3end_conserved_hypothetical_protein_(possible_acetyltransferase)_117919..118069_POSITIVE 332 236 204 39 3 aact:AA00105|3end_conserved_hypothetical_protein_75609..75759_POSITIVE 330 75 33 91 55 aact:AA01269|3end_hypothetical_protein_863413..863563_POSITIVE 330 316 272 49 3 aact:AA00776|3end_conserved_hypothetical_protein_533869..534019_POSITIVE 330 439 392 131 67 aact:AA00158|3end_ampD_signalling_protein_(N-acetylmuramyl-L-alanine_amidase)_112935..113085_POSITIVE 327 249 206 78 26 aact:AA01167|3end_glucose-6-phosphate_1-dehydrogenase_801067..801217_POSITIVE 326 80 31 129 74 aact:AA01413|3end_conserved_hypothetical_protein_952860..953010_POSITIVE 322 250 207 86 42 aact:AA01227|3end_hypothetical_protein_838845..838995_POSITIVE 321 79 31 57 8 aact:AA02874|3end_hypothetical_protein_2017899..2018049_POSITIVE