Origin IGS: taaaaaagtgcggtcacaaaaaacaatgttttttgaacataggttctgacaatgatgccgaagagtgaatcaatcacttctgtgatttatgaataactgcccaagcgttttaaaaacgccggaaaaactaaccgcacttttaatgcggtggaacaaaaaacgccgagcacaatatactcggcgtttttattctgactaaaatca .........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 tgattttagtcagaataaaaacgccgagtatattgtgctcggcgttttttgttccaccgcattaaaagtgcggttagtttttccggcgtttttaaaacgcttgggcagttattcataaatcacagaagtgattgattcactcttcggcatcattgtcagaacctatgttcaaaaaacattgttttttgtgaccgcactttttta Mask Tandem Repeat Region ================================================ taaaaaagtgcggtcacaaaaaacaatgttttttgaacataggttctgacaatgatgccgaagagtgaatcaatcacttctgtgatttatgaataactgcccaagcgttttaaaaacgccggaaaaactaaccgcacttttaatgcggtggaacaaaaaacgccgagcacaatatactcggcgtttttattctgactaaaatca Find is-nt database================================================ Query_seq: AA02913:AA02915|AA02913:AA02915:ribosomal large subunit pseudouridine synthase:thioredoxin m:->->:2040588..2040791 204 taaaaaagtgcggtcacaaaaaacaatgttttttgaacataggttctgacaatgatgccgaagagtgaatcaatcacttctgtgatttatgaataactgcccaagcgttttaaaaacgccggaaaaactaaccgcacttttaatgcggtggaacaaaaaacgccgagcacaatatactcggcgtttttattctgactaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02913:AA02915|AA02913:AA02915:ribosomal large subunit pseudouridine synthase:thioredoxin m:->->:2040588..2040791 204 taaaaaagtgcggtcacaaaaaacaatgttttttgaacataggttctgacaatgatgccgaagagtgaatcaatcacttctgtgatttatgaataactgcccaagcgttttaaaaacgccggaaaaactaaccgcacttttaatgcggtggaacaaaaaacgccgagcacaatatactcggcgtttttattctgactaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02913:AA02915|AA02913:AA02915:ribosomal large subunit pseudouridine synthase:thioredoxin m:->->:2040588..2040791 204 taaaaaagtgcggtcacaaaaaacaatgttttttgaacataggttctgacaatgatgccgaagagtgaatcaatcacttctgtgatttatgaataactgcccaagcgttttaaaaacgccggaaaaactaaccgcacttttaatgcggtggaacaaaaaacgccgagcacaatatactcggcgtttttattctgactaaaatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaaagtgcggtcacaaaaaacaatgttttttgaacataggttctgacaatgatgccgaagagtgaatcaatcacttctgtgatttatgaataactgcccaagcgttttaaaaacgccggaaaaactaaccgcacttttaatgcggtggaacaaaaaacgccgagcacaatatactcggcgtttttattctgactaaaatca Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 97 End: 192 ................................................................................................ M P K R F K N A G K T N R T F N A V E Q K T P S T I Y S A F L F ............ Protein_Len: 36 Strand: + Start: 89 End: 196 ........................................................................................ M N N C P S V L K T P E K L T A L L M R W N K K R R A Q Y T R R F Y S D ........ taaaaaagtgcggtcacaaaaaacaatgttttttgaacataggttctgacaatgatgccgaagagtgaatcaatcacttctgtgatttatgaataactgcccaagcgttttaaaaacgccggaaaaactaaccgcacttttaatgcggtggaacaaaaaacgccgagcacaatatactcggcgtttttattctgactaaaatca 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================================================ taaaaaagtgcggtcacaaaaaacaatgttttttgaacataggttctgacaatgatgccgaagagtgaatcaatcacttctgtgatttatgaataactgcccaagcgttttaaaaacgccggaaaaactaaccgcacttttaatgcggtggaacaaaaaacgccgagcacaatatactcggcgtttttattctgactaaaatca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 76 HP_score: -8.7 Tail_Score: -3.80855 Start: 132 End: 148 Full_Region: gcgttttttgttcca ccgcatt aaa agtgcgg ttagtttttccggcg ...................................................................................................................................ccgcattaaaagtgcgg........................................................ TransTerm Strand: + Conf: 100 HP_score: -9.1 Tail_Score: -5.20333 Start: 161 End: 183 Full_Region: CGGTGGAACAAAAAA CGCCGAGCA CAATA TACTCGGCG TTTTTATTCTGACTA ................................................................................................................................................................CGCCGAGCACAATATACTCGGCG..................... Find igs database================================================ Query_seq: AA02913:AA02915|AA02913:AA02915:ribosomal large subunit pseudouridine synthase:thioredoxin m:->->:2040588..2040791 204 taaaaaagtgcggtcacaaaaaacaatgttttttgaacataggttctgacaatgatgccgaagagtgaatcaatcacttctgtgatttatgaataactgcccaagcgttttaaaaacgccggaaaaactaaccgcacttttaatgcggtggaacaaaaaacgccgagcacaatatactcggcgtttttattctgactaaaatca Intra-Species Hit: Count: 1 Min: 1 Max: 204 Len: 204 Subject: aact_AA02913_AA02915|ribosomal large subunit pseudouridine synthase:thioredoxin m|POSITIVE:POSITIVE|[2040588,2040791]|204 HSP 1 e-value: 1.0E-112 bit: 404.0 Len: 204 Query Start:1 Query End:204 Subject Strand: POSITIVE Subject Start: 1 Subject End: 204 taaaaaagtgcggtcacaaaaaacaatgttttttgaacataggttctgacaatgatgccgaagagtgaatcaatcacttctgtgatttatgaataactgcccaagcgttttaaaaacgccggaaaaactaaccgcacttttaatgcggtggaacaaaaaacgccgagcacaatatactcggcgtttttattctgactaaaatca taaaaaagtgcggtcacaaaaaacaatgttttttgaacataggttctgacaatgatgccgaagagtgaatcaatcacttctgtgatttatgaataactgcccaagcgttttaaaaacgccggaaaaactaaccgcacttttaatgcggtggaacaaaaaacgccgagcacaatatactcggcgtttttattctgactaaaatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAAGUGCGGUCACAAAAAACAAUGUUUUUUGAACAUAGGUUCUGACAAUGAUGCCGAAGAGUGAAUCAAUCACUUCUGUGAUUUAUGAAUAACUGCCCAAGCGUUUUAAAAACGCCGGAAAAACUAACCGCACUUUUAAUGCGGUGGAACAAAAAACGCCGAGCACAAUAUACUCGGCGUUUUUAUUCUGACUAAAAUCA ...(((((((((((.........((.((((....((((....)))).)))).))...(((...(((...((((((((....)))))...)))...)))......(((((.....))))))))........))))))))))).....(((((((..((((((((((((.........)))))))))))).)))).)))....... (-57.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUUUAGUCAGAAUAAAAACGCCGAGUAUAUUGUGCUCGGCGUUUUUUGUUCCACCGCAUUAAAAGUGCGGUUAGUUUUUCCGGCGUUUUUAAAACGCUUGGGCAGUUAUUCAUAAAUCACAGAAGUGAUUGAUUCACUCUUCGGCAUCAUUGUCAGAACCUAUGUUCAAAAAACAUUGUUUUUUGUGACCGCACUUUUUUA .(((....))).(((((((((((((((((((...)))))))))).))))))))).........(((((((((((((........((((((.....))))))((((((....(((...((((((....))))))............((((....)))).)))....)))))).................)))))))))))))... (-63.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 495 38 3 231 196 aact:AA02168|5end_possible_protease;_heat_shock_protein_1483529..1483759_POSITIVE 494 152 112 59 11 aact:AA01041|5end_hypothetical_protein_724853..725083_POSITIVE 479 149 101 164 104 aact:AA00324|5end_tRNA_(Uracil-5-)-methyltransferase_(tRNA(M-5-U54)-methyltransferase)_220147..220377_POSITIVE 457 153 113 230 185 aact:AA00347|5end_50S_ribosomal_protein_L11_232137..232367_POSITIVE 424 152 112 161 114 aact:AA01416|5end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_952780..953010_POSITIVE 417 47 5 169 126 aact:AA01090|5end_leucyl-tRNA_synthetase,_leucyl-tRNA_ligase_753548..753778_POSITIVE 405 144 101 107 56 aact:AA01437|5end_phosphoglycerate_kinase_964125..964355_POSITIVE 404 150 102 189 135 aact:AA01666|5end_penicillin-binding_protein_4;_D-alanyl-D-alanine_carboxypeptidase;_D-alanyl-D-alanine-endopeptidase_1128231..1128461_POSITIVE 404 140 97 122 70 aact:AA01603|5end_oligopeptidase_A_1082898..1083128_POSITIVE 404 152 112 173 137 aact:AA00250|5end_lipoate_biosynthesis_protein_A_175496..175726_POSITIVE 401 47 4 184 146 aact:AA02050|5end_1-deoxy-D-xylulose_5-phosphate_synthase_1395625..1395855_POSITIVE 401 47 4 85 47 aact:AA02049|5end_hypothetical_protein_1395526..1395756_POSITIVE 398 50 2 164 117 aact:AA02666|5end_DNA_helicase_II_1854410..1854640_POSITIVE 398 45 4 200 159 aact:AA00988|5end_conserved_hypothetical_protein_690898..691128_POSITIVE 393 146 103 55 19 aact:AA02846|5end_crossover_junction_endodeoxyribonuclease_1998648..1998878_POSITIVE 391 156 112 83 19 aact:AA02941|5end_hypothetical_protein_2058535..2058765_POSITIVE 390 148 104 179 132 aact:AA02597|5end_ribonuclease_D_1807124..1807354_POSITIVE 383 49 3 225 180 aact:AA03011|5end_inner_membrane_protein,_60_kDa_2102585..2102815_POSITIVE 383 149 104 139 85 aact:AA01024|5end_thiamine_biosynthesis_lipoprotein_precursor_716437..716667_POSITIVE 381 144 106 203 162 aact:AA01109|5end_oxidoreductase_(possible_short-chain_alcohol_dehydrogenase)_763899..764129_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 533 50 3 111 61 aact:AA02167|3end_hypothetical_protein_1483474..1483624_POSITIVE 494 152 112 72 24 aact:AA01040|3end_possible_lipoprotein_724946..725096_POSITIVE 457 153 113 71 26 aact:AA00345|3end_transcription_antitermination_protein_232058..232208_POSITIVE 448 140 91 145 93 aact:AA00323|3end_conserved_hypothetical_protein_(possible_SAM-dependent_methyltransferase)_220222..220372_POSITIVE 417 47 5 138 95 aact:AA01089|3end_hypothetical_protein_753597..753747_POSITIVE 407 148 112 151 114 aact:AA01413|3end_conserved_hypothetical_protein_952860..953010_POSITIVE 404 150 102 82 28 aact:AA01663|3end_GTP_cyclohydrolase_I_1128204..1128354_POSITIVE 401 47 4 58 20 aact:AA02048|3end_galactitol_utilization_operon_repressor_1395579..1395729_POSITIVE 392 155 112 57 7 aact:AA01436|3end_fructose-bisphosphate_aldolase_class_II_964137..964287_POSITIVE 391 156 112 120 56 aact:AA02940|3end_conserved_hypothetical_protein_2058652..2058802_POSITIVE 390 148 104 85 38 aact:AA02595|3end_cytochrome_c_peroxidase_1807110..1807260_POSITIVE 383 49 3 94 49 aact:AA03010|3end_thiophene_and_furan_oxidation_protein_2102534..2102684_POSITIVE 383 149 104 57 3 aact:AA01023|3end_conserved_hypothetical_protein_716435..716585_POSITIVE 371 148 102 92 36 aact:AA02671|3end_gluconokinase_1858917..1859067_POSITIVE 369 149 107 60 9 aact:AA00453|3end_phosphoglyceromutase_318009..318159_POSITIVE 367 153 112 106 60 aact:AA00081|3end_fatty_acid_metabolism_regulator_protein_60767..60917_POSITIVE 364 150 105 44 1 aact:AA02936|3end_lipoprotein_E_precursor;_outer_membrane_protein_P4_precursor;_acid_phosphatase_2056373..2056523_POSITIVE 364 149 104 69 10 aact:AA02251|3end_biotin_sulfoxide_reductase;_Trimethylamine-N-oxide_reductase_precursor_1533843..1533993_POSITIVE 358 158 112 50 5 aact:AA01703|3end_L-ribulose-phosphate_4-epimerase_1156161..1156311_POSITIVE 358 140 94 149 105 aact:AA01025|3end_hypothetical_protein_717769..717919_POSITIVE