Origin IGS: tctgttaattcgactgattaaaactgattaaatcaggttcggaggaaactaaaaactaaagtgcggtggattttacctgatttttcaggctttctgaaatcaaactgccgaaattgcgaaattttttattttctcgtaaataaattcttgctatcccctaaatttttccgtagaattcacgccctatttatatgaattttatgtgcgaaatgaaacaacattagagcacaattatagcggagtattt .........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 aaatactccgctataattgtgctctaatgttgtttcatttcgcacataaaattcatataaatagggcgtgaattctacggaaaaatttaggggatagcaagaatttatttacgagaaaataaaaaatttcgcaatttcggcagtttgatttcagaaagcctgaaaaatcaggtaaaatccaccgcactttagtttttagtttcctccgaacctgatttaatcagttttaatcagtcgaattaacaga Mask Tandem Repeat Region ================================================ tctgttaattcgactgattaaaactgattaaatcaggttcggaggaaactaaaaactaaagtgcggtggattttacctgatttttcaggctttctgaaatcaaactgccgaaattgcgaaattttttattttctcgtaaataaattcttgctatcccctaaatttttccgtagaattcacgccctatttatatgaattttatgtgcgaaatgaaacaacattagagcacaattatagcggagtattt Find is-nt database================================================ Query_seq: AA02879:AA02880|AA02879:AA02880:octaprenyl-diphosphate synthase:50S ribosomal protein L21:->->:2020650..2020896 247 tctgttaattcgactgattaaaactgattaaatcaggttcggaggaaactaaaaactaaagtgcggtggattttacctgatttttcaggctttctgaaatcaaactgccgaaattgcgaaattttttattttctcgtaaataaattcttgctatcccctaaatttttccgtagaattcacgccctatttatatgaattttatgtgcgaaatgaaacaacattagagcacaattatagcggagtattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02879:AA02880|AA02879:AA02880:octaprenyl-diphosphate synthase:50S ribosomal protein L21:->->:2020650..2020896 247 tctgttaattcgactgattaaaactgattaaatcaggttcggaggaaactaaaaactaaagtgcggtggattttacctgatttttcaggctttctgaaatcaaactgccgaaattgcgaaattttttattttctcgtaaataaattcttgctatcccctaaatttttccgtagaattcacgccctatttatatgaattttatgtgcgaaatgaaacaacattagagcacaattatagcggagtattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02879:AA02880|AA02879:AA02880:octaprenyl-diphosphate synthase:50S ribosomal protein L21:->->:2020650..2020896 247 tctgttaattcgactgattaaaactgattaaatcaggttcggaggaaactaaaaactaaagtgcggtggattttacctgatttttcaggctttctgaaatcaaactgccgaaattgcgaaattttttattttctcgtaaataaattcttgctatcccctaaatttttccgtagaattcacgccctatttatatgaattttatgtgcgaaatgaaacaacattagagcacaattatagcggagtattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctgttaattcgactgattaaaactgattaaatcaggttcggaggaaactaaaaactaaagtgcggtggattttacctgatttttcaggctttctgaaatcaaactgccgaaattgcgaaattttttattttctcgtaaataaattcttgctatcccctaaatttttccgtagaattcacgccctatttatatgaattttatgtgcgaaatgaaacaacattagagcacaattatagcggagtattt Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 61 End: 192 ............................................................ M R W I L P D F S G F L K S N C R N C E I F Y F L V N K F L L S P K F F R R I H A L F I ....................................................... Protein_Len: 36 Strand: + Start: 140 End: 247 ........................................................................................................................................... M N S C Y P L N F S V E F T P Y L Y E F Y V R N E T T L E H N Y S G V F Protein_Len: 32 Strand: - Start: 59 End: 154 .......................................................... L A T S K V Q N K L S E S I L S G F N R F K K N E R L Y I R A M ............................................................................................. tctgttaattcgactgattaaaactgattaaatcaggttcggaggaaactaaaaactaaagtgcggtggattttacctgatttttcaggctttctgaaatcaaactgccgaaattgcgaaattttttattttctcgtaaataaattcttgctatcccctaaatttttccgtagaattcacgccctatttatatgaattttatgtgcgaaatgaaacaacattagagcacaattatagcggagtattt 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: 85 Start: 147 End: 176 ..................................................................................................................................................CTTGCTATCCCCTAAATTTTTCCGTAGAAT....................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 70 End: 99 .....................................................................TTTCAGAAAGCCTGAAAAATCAGGTAAAAT.................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctgttaattcgactgattaaaactgattaaatcaggttcggaggaaactaaaaactaaagtgcggtggattttacctgatttttcaggctttctgaaatcaaactgccgaaattgcgaaattttttattttctcgtaaataaattcttgctatcccctaaatttttccgtagaattcacgccctatttatatgaattttatgtgcgaaatgaaacaacattagagcacaattatagcggagtattt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -6.3 Tail_Score: -4.2828 Start: 24 End: 36 Full_Region: tagtttcctccgaac ctgat tta atcag ttttaatcagtcgaa .......................ctgatttaatcag................................................................................................................................................................................................................... Find igs database================================================ Query_seq: AA02879:AA02880|AA02879:AA02880:octaprenyl-diphosphate synthase:50S ribosomal protein L21:->->:2020650..2020896 247 tctgttaattcgactgattaaaactgattaaatcaggttcggaggaaactaaaaactaaagtgcggtggattttacctgatttttcaggctttctgaaatcaaactgccgaaattgcgaaattttttattttctcgtaaataaattcttgctatcccctaaatttttccgtagaattcacgccctatttatatgaattttatgtgcgaaatgaaacaacattagagcacaattatagcggagtattt Intra-Species Hit: Count: 1 Min: 1 Max: 247 Len: 247 Subject: aact_AA02879_AA02880|octaprenyl-diphosphate synthase:50S ribosomal protein L21|POSITIVE:POSITIVE|[2020650,2020896]|247 HSP 1 e-value: 1.0E-137 bit: 490.0 Len: 247 Query Start:1 Query End:247 Subject Strand: POSITIVE Subject Start: 1 Subject End: 247 tctgttaattcgactgattaaaactgattaaatcaggttcggaggaaactaaaaactaaagtgcggtggattttacctgatttttcaggctttctgaaatcaaactgccgaaattgcgaaattttttattttctcgtaaataaattcttgctatcccctaaatttttccgtagaattcacgccctatttatatgaattttatgtgcgaaatgaaacaacattagagcacaattatagcggagtattt tctgttaattcgactgattaaaactgattaaatcaggttcggaggaaactaaaaactaaagtgcggtggattttacctgatttttcaggctttctgaaatcaaactgccgaaattgcgaaattttttattttctcgtaaataaattcttgctatcccctaaatttttccgtagaattcacgccctatttatatgaattttatgtgcgaaatgaaacaacattagagcacaattatagcggagtattt Inter-species Hit: Count: 1 Min: 58 Max: 200 Len: 143 Subject: NC_000907_HI0880_HI0881|50S ribosomal protein L21:octaprenyl-diphosphate synthase|NEGATIVE:POSITIVE|[932695,932906]|212 HSP 1 e-value: 4.0E-8 bit: 60.0 Len: 46 Query Start:58 Query End:103 Subject Strand: NEGATIVE Subject Start: 147 Subject End: 192 .........................................................aaagtgcggtggattttacctgatttttcaggctttctgaaatcaa................................................................................................................................................ .........................................................aaagtgcggtgcattttacccgaattttcagactttctgaaatcaa................................................................................................................................................ HSP 2 e-value: 2.0E-6 bit: 54.0 Len: 39 Query Start:162 Query End:200 Subject Strand: NEGATIVE Subject Start: 50 Subject End: 88 .................................................................................................................................................................atttttccgtagaattcacgccctatttatatgaatttt............................................... .................................................................................................................................................................atttttccgtagaatttgcgacctatttatatgaatttt............................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUGCGGUGGAUUUUACCUGAUUUUUCAGGCUUUCUGAAAUCAAACUGCCGAAAUUGCGAAAUUUUUUAUUUUCUCGUAAAUAAAUUCUUGCUAUCCCCUAAAUUUUUCCGUAGAAUUCACGCCCUAUUUAUAUGAAUUUU ..((.(((.((((((((((......((((.(((....((....))....)))))))..((((.....(((((((......)))))))...))))..................))))))))))))).))............... (-25.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUCAUAUAAAUAGGGCGUGAAUUCUACGGAAAAAUUUAGGGGAUAGCAAGAAUUUAUUUACGAGAAAAUAAAAAAUUUCGCAAUUUCGGCAGUUUGAUUUCAGAAAGCCUGAAAAAUCAGGUAAAAUCCACCGCACUUU ....................(((..(((....))).......((((((.((.(((.(((((((......)))))))...))).))..(((((((..((((....))))..))).))))...........)))).)).)))... (-25.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 50 1 142 95 aact:AA01673|5end_riboflavin_synthase,_alpha_chain_1131477..1131707_POSITIVE 375 33 2 78 46 aact:AA01188|5end_conserved_hypothetical_protein_813912..814142_POSITIVE 324 33 1 66 32 aact:AA01710|5end_ribosomal_protein_S6_modification_protein_1159348..1159578_POSITIVE 320 42 1 152 113 aact:AA00174|5end_ribosomal_protein_L11_methyltransferase_123072..123302_POSITIVE 320 42 1 48 9 aact:AA00173|5end_hypothetical_protein_122968..123198_POSITIVE 318 45 1 158 109 aact:AA02792|5end_GlpT/UhpT_family_transporter_(hexosphosphate_transport)_1959617..1959847_POSITIVE 314 50 2 54 11 aact:AA00927|5end_ATP-dependent_DNA_helicase_635811..636041_POSITIVE 312 40 1 57 8 aact:AA00087|5end_possible_hydrolase_(alpha/beta_fold_family)_65196..65426_POSITIVE 308 33 1 168 134 aact:AA00557|5end_nitrate/nitrite_sensor_protein_380408..380638_POSITIVE 307 35 1 149 114 aact:AA00148|5end_ATP-dependent_RNA_helicase_105955..106185_POSITIVE 306 50 1 146 96 aact:AA01737|5end_exoribonuclease_II_1172647..1172877_POSITIVE 300 49 1 49 2 aact:AA01759|5end_hydrogenase_isoenzymes_formation_protein_1188675..1188905_POSITIVE 299 46 1 118 71 aact:AA00065|5end_hypothetical_protein_48854..49084_POSITIVE 298 39 1 194 157 aact:AA00919|5end_organic_solvent_tolerance_protein_630168..630398_POSITIVE 298 39 1 70 33 aact:AA00918|5end_hypothetical_protein_630044..630274_POSITIVE 296 127 88 70 26 aact:AA01932|5end_tRNA_pseudouridine_synthase_B_1305098..1305328_POSITIVE 294 61 29 54 23 aact:AA01801|5end_malate_dehydrogenase_1213358..1213588_POSITIVE 292 50 1 163 103 aact:AA01918|5end_anaerobic_C4-dicarboxylate_transporter_1290931..1291161_POSITIVE 288 50 3 144 96 aact:AA01111|5end_conserved_hypothetical_protein_764765..764995_POSITIVE 285 50 1 162 112 aact:AA02597|5end_ribonuclease_D_1807124..1807354_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 50 1 103 56 aact:AA01672|3end_conserved_hypothetical_protein_1131518..1131668_POSITIVE 375 33 2 78 46 aact:AA01187|3end_conserved_hypothetical_protein_813992..814142_POSITIVE 320 42 1 137 98 aact:AA00173|3end_hypothetical_protein_123137..123287_POSITIVE 314 50 2 54 11 aact:AA00926|3end_CyaY_protein_635891..636041_POSITIVE 311 45 1 94 51 aact:AA00166|3end_conserved_hypothetical_protein_(possible_acetyltransferase)_117919..118069_POSITIVE 308 33 1 122 88 aact:AA00555|3end_hypothetical_protein_380442..380592_POSITIVE 307 35 1 58 23 aact:AA00146|3end_UDP-glucose/GDP-mannose_dehydrogenase_105944..106094_POSITIVE 306 50 1 133 83 aact:AA01735|3end_hypothetical_protein_1172714..1172864_POSITIVE 299 40 2 112 68 aact:AA02619|3end_GTP_cyclohydrolase_II_1826193..1826343_POSITIVE 299 46 1 130 83 aact:AA00064|3end_ribosomal_small_subunit_pseudouridine_synthase_48946..49096_POSITIVE 298 39 1 97 60 aact:AA00915|3end_xanthine-guanine_phosphoribosyltransferase_630151..630301_POSITIVE 296 127 88 67 23 aact:AA01930|3end_ribosome-binding_factor_A_1305175..1305325_POSITIVE 294 61 29 74 43 aact:AA01800|3end_hypothetical_protein_1213458..1213608_POSITIVE 292 50 1 148 88 aact:AA01917|3end_hypothetical_protein_1290996..1291146_POSITIVE 285 50 1 68 18 aact:AA02595|3end_cytochrome_c_peroxidase_1807110..1807260_POSITIVE 279 50 1 104 54 aact:AA01145|3end_glycyl-tRNA_synthetase_alpha_subunit_784460..784610_POSITIVE 275 50 1 60 10 aact:AA01663|3end_GTP_cyclohydrolase_I_1128204..1128354_POSITIVE 273 47 1 80 40 aact:AA02883|3end_conserved_hypothetical_protein_2022427..2022577_POSITIVE 272 47 1 111 73 aact:AA01321|3end_DNA_repair_protein_894115..894265_POSITIVE 271 41 1 142 101 aact:AA02824|3end_conserved_hypothetical_protein_1986399..1986549_POSITIVE