Origin IGS: taaagatctgtataaaaagacagtaattctacctagggcaaggcattgcctcgggtattacagttgttcgaaacattataattcattgatatttttttaaatatcttgccttcctccgtttacggggggacaaaacgcattgcgttttgagcgttggctctgccaacgcccccaaaggggtgagcaagtaagtttacgaacttgcgaataacgtgcccgaagggcggaaggggggatttatcttgatgttttcacaagatcatgcttaaaaattgagatttccccccctcagggcttcgcccagctcccccgtgaacgaggggaaccaagttttttctttttatataaatagttacaatgtttcgaacagttgtgccccgggtatccccgctta .........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 taagcggggatacccggggcacaactgttcgaaacattgtaactatttatataaaaagaaaaaacttggttcccctcgttcacgggggagctgggcgaagccctgagggggggaaatctcaatttttaagcatgatcttgtgaaaacatcaagataaatccccccttccgcccttcgggcacgttattcgcaagttcgtaaacttacttgctcacccctttgggggcgttggcagagccaacgctcaaaacgcaatgcgttttgtccccccgtaaacggaggaaggcaagatatttaaaaaaatatcaatgaattataatgtttcgaacaactgtaatacccgaggcaatgccttgccctaggtagaattactgtctttttatacagatcttta Mask Tandem Repeat Region ================================================ taaagatctgtataaaaagacagtaattctacctagggcaaggcattgcctcgggtattacagttgttcgaaacattataattcattgatatttttttaaatatcttgccttcctccgtttacggggggacaaaacgcattgcgttttgagcgttggctctgccaacgcccccaaaggggtgagcaagtaagtttacgaacttgcgaataacgtgcccgaagggcggaaggggggatttatcttgatgttttcacaagatcatgcttaaaaattgagatttccccccctcagggcttcgcccagctcccccgtgaacgaggggaaccaagttttttctttttatataaatagttacaatgtttcgaacagttgtgccccgggtatccccgctta Find is-nt database================================================ Query_seq: AA00861:AA00862|AA00861:AA00862:transcription repair coupling factor:conserved hypothetical protein:->->:596211..596604 394 taaagatctgtataaaaagacagtaattctacctagggcaaggcattgcctcgggtattacagttgttcgaaacattataattcattgatatttttttaaatatcttgccttcctccgtttacggggggacaaaacgcattgcgttttgagcgttggctctgccaacgcccccaaaggggtgagcaagtaagtttacgaacttgcgaataacgtgcccgaagggcggaaggggggatttatcttgatgttttcacaagatcatgcttaaaaattgagatttccccccctcagggcttcgcccagctcccccgtgaacgaggggaaccaagttttttctttttatataaatagttacaatgtttcgaacagttgtgccccgggtatccccgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00861:AA00862|AA00861:AA00862:transcription repair coupling factor:conserved hypothetical protein:->->:596211..596604 394 taaagatctgtataaaaagacagtaattctacctagggcaaggcattgcctcgggtattacagttgttcgaaacattataattcattgatatttttttaaatatcttgccttcctccgtttacggggggacaaaacgcattgcgttttgagcgttggctctgccaacgcccccaaaggggtgagcaagtaagtttacgaacttgcgaataacgtgcccgaagggcggaaggggggatttatcttgatgttttcacaagatcatgcttaaaaattgagatttccccccctcagggcttcgcccagctcccccgtgaacgaggggaaccaagttttttctttttatataaatagttacaatgtttcgaacagttgtgccccgggtatccccgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00861:AA00862|AA00861:AA00862:transcription repair coupling factor:conserved hypothetical protein:->->:596211..596604 394 taaagatctgtataaaaagacagtaattctacctagggcaaggcattgcctcgggtattacagttgttcgaaacattataattcattgatatttttttaaatatcttgccttcctccgtttacggggggacaaaacgcattgcgttttgagcgttggctctgccaacgcccccaaaggggtgagcaagtaagtttacgaacttgcgaataacgtgcccgaagggcggaaggggggatttatcttgatgttttcacaagatcatgcttaaaaattgagatttccccccctcagggcttcgcccagctcccccgtgaacgaggggaaccaagttttttctttttatataaatagttacaatgtttcgaacagttgtgccccgggtatccccgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaagatctgtataaaaagacagtaattctacctagggcaaggcattgcctcgggtattacagttgttcgaaacattataattcattgatatttttttaaatatcttgccttcctccgtttacggggggacaaaacgcattgcgttttgagcgttggctctgccaacgcccccaaaggggtgagcaagtaagtttacgaacttgcgaataacgtgcccgaagggcggaaggggggatttatcttgatgttttcacaagatcatgcttaaaaattgagatttccccccctcagggcttcgcccagctcccccgtgaacgaggggaaccaagttttttctttttatataaatagttacaatgtttcgaacagttgtgccccgggtatccccgctta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 8 End: 97 ....... M Y K K T V I L P R A R H C L G Y Y S C S K H Y N S L I F F ......................................................................................................................................................................................................................................................................................................... Protein_Len: 36 Strand: + Start: 101 End: 208 .................................................................................................... M S C L P P F T G G Q N A L R F E R W L C Q R P Q R G E Q V S L R T C E .......................................................................................................................................................................................... Protein_Len: 38 Strand: + Start: 236 End: 349 ........................................................................................................................................................................................................................................... M Y L D V F T R S C L K I E I S P P Q G F A Q L P R E R G E P S F F F L Y K ............................................. Protein_Len: 40 Strand: + Start: 273 End: 392 ................................................................................................................................................................................................................................................................................ M R F P P L R A S P S S P V N E G N Q V F S F Y I N S Y N V S N S C A P G I P A .. Protein_Len: 35 Strand: - Start: 255 End: 359 .............................................................................................................................................................................................................................................................. L I M S L F Q S K G G E P S R G A G G H V L P V L N K R K I Y I T V M ................................... Protein_Len: 46 Strand: - Start: 100 End: 237 ................................................................................................... I D Q R G G N V P P C F A N R K S R Q S Q W R G W L P S C T L K R V Q S Y R A R L A S P P M ............................................................................................................................................................. Protein_Len: 34 Strand: - Start: 86 End: 187 ..................................................................................... Q Y K K L Y R A K R R K R P S L V C Q T K L T P E A L A G L P T L M ............................................................................................................................................................................................................... taaagatctgtataaaaagacagtaattctacctagggcaaggcattgcctcgggtattacagttgttcgaaacattataattcattgatatttttttaaatatcttgccttcctccgtttacggggggacaaaacgcattgcgttttgagcgttggctctgccaacgcccccaaaggggtgagcaagtaagtttacgaacttgcgaataacgtgcccgaagggcggaaggggggatttatcttgatgttttcacaagatcatgcttaaaaattgagatttccccccctcagggcttcgcccagctcccccgtgaacgaggggaaccaagttttttctttttatataaatagttacaatgtttcgaacagttgtgccccgggtatccccgctta 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================================================ taaagatctgtataaaaagacagtaattctacctagggcaaggcattgcctcgggtattacagttgttcgaaacattataattcattgatatttttttaaatatcttgccttcctccgtttacggggggacaaaacgcattgcgttttgagcgttggctctgccaacgcccccaaaggggtgagcaagtaagtttacgaacttgcgaataacgtgcccgaagggcggaaggggggatttatcttgatgttttcacaagatcatgcttaaaaattgagatttccccccctcagggcttcgcccagctcccccgtgaacgaggggaaccaagttttttctttttatataaatagttacaatgtttcgaacagttgtgccccgggtatccccgctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA00861:AA00862|AA00861:AA00862:transcription repair coupling factor:conserved hypothetical protein:->->:596211..596604 394 taaagatctgtataaaaagacagtaattctacctagggcaaggcattgcctcgggtattacagttgttcgaaacattataattcattgatatttttttaaatatcttgccttcctccgtttacggggggacaaaacgcattgcgttttgagcgttggctctgccaacgcccccaaaggggtgagcaagtaagtttacgaacttgcgaataacgtgcccgaagggcggaaggggggatttatcttgatgttttcacaagatcatgcttaaaaattgagatttccccccctcagggcttcgcccagctcccccgtgaacgaggggaaccaagttttttctttttatataaatagttacaatgtttcgaacagttgtgccccgggtatccccgctta Intra-Species Hit: Count: 5 Min: 1 Max: 394 Len: 394 Subject: aact_AA00861_AA00862|transcription repair coupling factor:conserved hypothetical protein|POSITIVE:POSITIVE|[596211,596604]|394 HSP 1 e-value: 1.0E-178 bit: 626.0 Len: 394 Query Start:1 Query End:394 Subject Strand: POSITIVE Subject Start: 1 Subject End: 394 taaagatctgtataaaaagacagtaattctacctagggcaaggcattgcctcgggtattacagttgttcgaaacattataattcattgatannnnnnnaaatatcttgccttcctccgtttacggggggacaaaacgcattgcgttttgagcgttggctctgccaacgcccccaaaggggtgagcaagtaagtttacgaacttgcgaataacgtgcccgaagggcggaaggggggatttatcttgatgttttcacaagatcatgcttaaaaattgagatttnnnnnnntcagggcttcgcccagctcccccgtgaacgaggggaaccaagnnnnnnnnnnnnatataaatagttacaatgtttcgaacagttgtgccccgggtatccccgctta taaagatctgtataaaaagacagtaattctacctagggcaaggcattgcctcgggtattacagttgttcgaaacattataattcattgatatttttttaaatatcttgccttcctccgtttacggggggacaaaacgcattgcgttttgagcgttggctctgccaacgcccccaaaggggtgagcaagtaagtttacgaacttgcgaataacgtgcccgaagggcggaaggggggatttatcttgatgttttcacaagatcatgcttaaaaattgagatttccccccctcagggcttcgcccagctcccccgtgaacgaggggaaccaagttttttctttttatataaatagttacaatgtttcgaacagttgtgccccgggtatccccgctta Subject: aact_AA00776_AA00777|conserved hypothetical protein:soluble lytic murein transglycosylase|POSITIVE:POSITIVE|[533930,534458]|529 HSP 1 e-value: 2.0E-97 bit: 357.0 Len: 258 Query Start:65 Query End:322 Subject Strand: NEGATIVE Subject Start: 121 Subject End: 376 ................................................................tgttcgaaacattataattcattgatannnnnnnaaatatcttgccttcctccgtttacggggggacaaaacgcattgcgttttgagcgttggctctgccaacgcccccaaaggggtgagcaagtaagtttacgaacttgcgaataacgtgcccgaagggcggaaggggggatttatcttgatgttttcacaagatcatgcttaaaaattgagatttnnnnnnntcagggcttcgcccagctcccc-cgtgaacgaggg........................................................................ ................................................................tgttcgaaacattataattcattgatattttt--aaatatcttgccttcctccgtttacggggg-acaaaacgcattgcgttttgagcgttggctctgccaacgaccccaaaggggtgagcaagtaagttttcgaacttgcgaataacgtgcccgaagggcggaaggggggatttatcttgatgtttccacaagatcatgcttaaaaattgagattttgccccctcagggcttcgcccggctcccctcgtgaacgaggg........................................................................ Subject: aact_AA01173_AA01174|VapD-homolog:hypothetical protein|POSITIVE:POSITIVE|[804446,804839]|394 HSP 1 e-value: 9.0E-75 bit: 281.0 Len: 271 Query Start:60 Query End:330 Subject Strand: NEGATIVE Subject Start: 89 Subject End: 358 ...........................................................acagttgttcgaaacattataattcattgatannnnnnnaaatatcttgccttcctccgtttacggggggacaaaacgcattgcgttttgagcgttggctctgccaacgcccccaaaggggtgagcaagtaagtttacgaacttgcgaataacgtgcccgaagggcggaaggggggatttatcttgatgttttcacaagatcatgcttaaaaattgaga-tttnnnnnnntcagggcttcgcccagct-cccccgtgaacgaggggaaccaag................................................................ ...........................................................acagctgttcgaaacattataatttattgatatctta--aaatatcttgccttcctccgtttacggggg-acaaaacgcaatgcgttttgagcgttggttctgccaacgaccccaaaggggtaagcaagtgagtttccgagcttgcgaataacgtacccgaagggcggaagggggaatttatctcgatgtattcacaagatcatgcttaaaaattgagattttgcccccctcagggcttcgcccagctccccccgcgaacgaggggagccaag................................................................ Subject: aact_AA01167_AA01168|glucose-6-phosphate 1-dehydrogenase:6- phosphogluconolactonase|POSITIVE:POSITIVE|[801128, 801382]|255 HSP 1 e-value: 1.0E-39 bit: 165.0 Len: 107 Query Start:125 Query End:231 Subject Strand: POSITIVE Subject Start: 33 Subject End: 139 ............................................................................................................................gggggacaaaacgcattgcgttttgagcgttggctctgccaacgcccccaaaggggtgagcaagtaagtttacgaacttgcgaataacgtgcccgaagggcggaagg................................................................................................................................................................... ............................................................................................................................gggggacaaaacgcaatgcgttttgagcgttggctctgccaacgaccccaaaggggtgagtaagtgagtttccgagcttgcgaataacgtgcccgaagggcggaagg................................................................................................................................................................... Subject: aact_AA00726_AA00729|apolipoprotein N-acyltransferase, copper:possible hemolysin (TlyC-like)|POSITIVE:POSITIVE|[499947,500343]|397 HSP 1 e-value: 8.0E-29 bit: 129.0 Len: 69 Query Start:213 Query End:281 Subject Strand: NEGATIVE Subject Start: 182 Subject End: 250 ....................................................................................................................................................................................................................gtgcccgaagggcggaaggggggatttatcttgatgttttcacaagatcatgcttaaaaattgagattt................................................................................................................. ....................................................................................................................................................................................................................gtgcccgaagggcggaaggggggatttatcttgattttttcacaagatcatgcttaaaaattgagattt................................................................................................................. HSP 2 e-value: 6.0E-11 bit: 69.9 Len: 61 Query Start:66 Query End:126 Subject Strand: NEGATIVE Subject Start: 255 Subject End: 313 .................................................................gttcgaaacattataattcattgatannnnnnnaaatatcttgccttcctccgtttacggg............................................................................................................................................................................................................................................................................ .................................................................gttcgaaacattataattcattgatattttt--aaatatcttgccttcctccgtttacggg............................................................................................................................................................................................................................................................................ HSP 3 e-value: 4.0E-6 bit: 54.0 Len: 42 Query Start:289 Query End:330 Subject Strand: NEGATIVE Subject Start: 127 Subject End: 169 ................................................................................................................................................................................................................................................................................................tcagggcttcgcccagctccccc-gtgaacgaggggaaccaag................................................................ ................................................................................................................................................................................................................................................................................................tcagggctgcgcccagctccccctgtgaacgaggggagccaag................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGAUCUGUAUAAAAAGACAGUAAUUCUACCUAGGGCAAGGCAUUGCCUCGGGUAUUACAGUUGUUCGAAACAUUAUAAUUCAUUGAUAUUUUUUUAAAUAUCUUGCCUUCCUCCGUUUACGGGGGGACAAAACGCAUUGCGUUUUGAGCGUUGGCUCUGCCAACGCCCCCAAAGGGGUGAGCAAGUAAGUUUACGAACUUGCGAAUAACGUGCCCGAAGGGCGGAAGGGGGGAUUUAUCUUGAUGUUUUCACAAGAUCAUGCUUAAAAAUUGAGAUUUCCCCCCCUCAGGGCUUCGCCCAGCUCCCCCGUGAACGAGGGGAACCAAGUUUUUUCUUUUUAUAUAAAUAGUUACAAUGUUUCGAACAGUUGUGCCCCGGGUAUCCCCGCUUA .......((((........))))......((((..((((((....))))))..)))).((((..(((((((((((((.(((((.(((.((((............((((..(((((((((((((((((((.((((((((...)))))))).((((((((...))))))))........((((((((..(((((((....))))))).........((((...)))).((.(((((((...((((..((.(((...((......))...))).))..)))).))))))).))...)).))))))...))))))))))))).)))))).))))............)))).)))))))).)))))))))))))..))))...((((....)))).... (-153.85) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCGGGGAUACCCGGGGCACAACUGUUCGAAACAUUGUAACUAUUUAUAUAAAAAGAAAAAACUUGGUUCCCCUCGUUCACGGGGGAGCUGGGCGAAGCCCUGAGGGGGGGAAAUCUCAAUUUUUAAGCAUGAUCUUGUGAAAACAUCAAGAUAAAUCCCCCCUUCCGCCCUUCGGGCACGUUAUUCGCAAGUUCGUAAACUUACUUGCUCACCCCUUUGGGGGCGUUGGCAGAGCCAACGCUCAAAACGCAAUGCGUUUUGUCCCCCCGUAAACGGAGGAAGGCAAGAUAUUUAAAAAAAUAUCAAUGAAUUAUAAUGUUUCGAACAACUGUAAUACCCGAGGCAAUGCCUUGCCCUAGGUAGAAUUACUGUCUUUUUAUACAGAUCUUUA .....(((((((((..((((.....((((((((((((((((...((((((..............((..(((((((.((....)))))))))..))....(((..((((((((((.((((..((.(((..(((......)))..))).))..))))...))))))))))...((((((...(((......((((((..(....)..))))))..........((((((((((((...)))))))).((((((((...)))))))).)))).)))...))))))..)))..(((((((....))))))).))))))))))))))))))))))............(((((...)))))))))..))))......((((........)))).))))). (-143.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 836 150 101 215 167 aact:AA01174|5end_hypothetical_protein_804700..804930_POSITIVE 765 188 141 231 184 aact:AA00200|5end_thymidylate_synthase_138892..139122_POSITIVE 633 120 71 228 181 aact:AA00729|5end_possible_hemolysin_(TlyC-like)_500204..500434_POSITIVE 603 185 141 134 85 aact:AA01098|5end_bis(5'-nucleosyl)-tetraphosphatase_757699..757929_POSITIVE 600 188 142 196 147 aact:AA02108|5end_2-acylglycerophosphoethanolamine_acyltransferase;_acyl-acyl_carrier_protein_synthetase_1433393..1433623_POSITIVE 544 188 146 44 1 aact:AA02106|5end_hypothetical_protein_1433241..1433471_POSITIVE 497 183 143 224 182 aact:AA00988|5end_conserved_hypothetical_protein_690898..691128_POSITIVE 484 325 284 227 183 aact:AA01379|5end_glycerophosphoryl_diester_phosphodiesterase_(protein_D)_933029..933259_POSITIVE 469 189 145 163 119 aact:AA01633|5end_probable_ferredoxin-like_protein_1104008..1104238_POSITIVE 450 185 145 197 153 aact:AA01090|5end_leucyl-tRNA_synthetase,_leucyl-tRNA_ligase_753548..753778_POSITIVE 438 143 106 158 130 aact:AA02949|5end_hypothetical_protein_2061944..2062174_POSITIVE 415 185 141 229 176 aact:AA00404|5end_conserved_hypothetical_protein_269822..270052_POSITIVE 408 170 123 95 41 aact:AA00652|5end_arginyl-tRNA_synthetase_(arginine--tRNA_ligase)_445718..445948_POSITIVE 406 190 143 91 35 aact:AA01195|5end_acyl_carrier_protein_819849..820079_POSITIVE 406 185 149 41 1 aact:AA01089|5end_hypothetical_protein_753392..753622_POSITIVE 404 318 272 179 129 aact:AA02271|5end_hypothetical_protein_1548623..1548853_POSITIVE 400 183 144 183 143 aact:AA02666|5end_DNA_helicase_II_1854410..1854640_POSITIVE 393 188 142 217 139 aact:AA00991|5end_conserved_hypothetical_protein_693191..693421_POSITIVE 391 170 126 203 157 aact:AA01146|5end_conserved_hypothetical_protein_784433..784663_POSITIVE 383 169 123 47 4 aact:AA02296|5end_conserved_hypothetical_protein_(possible_cell_wall-associated_hydrolase)_1566070..1566300_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 503 382 341 48 8 aact:AA01173|3end_VapD-homolog_804385..804535_POSITIVE 496 187 145 58 18 aact:AA01342|3end_conserved_hypotheticl_protein_(possible_ribosomal_RNA_adenine_dimethylase)_911085..911235_POSITIVE 474 183 145 127 89 aact:AA02167|3end_hypothetical_protein_1483474..1483624_POSITIVE 473 185 150 40 1 aact:AA01097|3end_conserved_hypothetical_protein_757685..757835_POSITIVE 450 185 145 52 8 aact:AA01088|3end_rare_lipoprotein_B_precursor_753483..753633_POSITIVE 406 190 143 85 29 aact:AA01194|3end_acyl_carrier_protein_819923..820073_POSITIVE 404 318 272 144 94 aact:AA02270|3end_endopeptidase_La;_lon_protease;_protease_La_homolog;_ATP-dependent_protease_LA_(lon-1)_1548668..1548818_POSITIVE 400 183 144 44 4 aact:AA02663|3end_DNA_ligase_1854351..1854501_POSITIVE 391 170 126 150 104 aact:AA01145|3end_glycyl-tRNA_synthetase_alpha_subunit_784460..784610_POSITIVE 390 325 282 74 32 aact:AA02947|3end_riboflavin_biosynthesis_protein_2061874..2062024_POSITIVE 387 180 131 69 34 aact:AA01167|3end_glucose-6-phosphate_1-dehydrogenase_801067..801217_POSITIVE 373 177 135 59 8 aact:AA02932|3end_lytic_murein_transglycosylase_A_2053544..2053694_POSITIVE 371 189 143 88 27 aact:AA01986|3end_pyruvate_dehydrogenase_complex_E2_1350500..1350650_POSITIVE 371 189 141 104 48 aact:AA01044|3end_A/G-specific_adenine_glycosylase_727978..728128_POSITIVE 367 150 103 113 59 aact:AA01890|3end_cell-cycle_protein_1275967..1276117_POSITIVE 367 178 132 81 33 aact:AA01289|3end_hypothetical_protein_872848..872998_POSITIVE 356 236 204 70 28 aact:AA01522|3end_conserved_hypothetical_protein_1023279..1023429_POSITIVE 354 186 142 110 69 aact:AA01751|3end_conserved_hypothetical_protein_1185392..1185542_POSITIVE 349 240 196 90 31 aact:AA00908|3end_probable_sigma-E_factor_regulatory_protein_626590..626740_POSITIVE 348 382 351 31 1 aact:AA00776|3end_conserved_hypothetical_protein_533869..534019_POSITIVE