Origin IGS: taagtcagggtattgacccctattgagcccaagtgcggtcgatgttaaaaacgttttgaaaaacgaccgcacttgaataagtttaactccgacaggagcaaatct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agatttgctcctgtcggagttaaacttattcaagtgcggtcgtttttcaaaacgtttttaacatcgaccgcacttgggctcaataggggtcaataccctgactta Mask Tandem Repeat Region ================================================ taagtcagggtattgacccctattgagcccaagtgcggtcgatgttaaaaacgttttgaaaaacgaccgcacttgaataagtttaactccgacaggagcaaatct Find is-nt database================================================ Query_seq: AA00355:AA00356|AA00355:AA00356:DNA-directed RNA polymerase beta chain (transcriptase beta chain):DNA-directed RNA polymerase, beta' chain:->->:238972..239076 105 taagtcagggtattgacccctattgagcccaagtgcggtcgatgttaaaaacgttttgaaaaacgaccgcacttgaataagtttaactccgacaggagcaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00355:AA00356|AA00355:AA00356:DNA-directed RNA polymerase beta chain (transcriptase beta chain):DNA-directed RNA polymerase, beta' chain:->->:238972..239076 105 taagtcagggtattgacccctattgagcccaagtgcggtcgatgttaaaaacgttttgaaaaacgaccgcacttgaataagtttaactccgacaggagcaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00355:AA00356|AA00355:AA00356:DNA-directed RNA polymerase beta chain (transcriptase beta chain):DNA-directed RNA polymerase, beta' chain:->->:238972..239076 105 taagtcagggtattgacccctattgagcccaagtgcggtcgatgttaaaaacgttttgaaaaacgaccgcacttgaataagtttaactccgacaggagcaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagtcagggtattgacccctattgagcccaagtgcggtcgatgttaaaaacgttttgaaaaacgaccgcacttgaataagtttaactccgacaggagcaaatct Predict ORF larger than 30AA ================================================ taagtcagggtattgacccctattgagcccaagtgcggtcgatgttaaaaacgttttgaaaaacgaccgcacttgaataagtttaactccgacaggagcaaatct 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================================================ taagtcagggtattgacccctattgagcccaagtgcggtcgatgttaaaaacgttttgaaaaacgaccgcacttgaataagtttaactccgacaggagcaaatct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 79 HP_score: -10.8 Tail_Score: -3.11732 Start: 33 End: 72 Full_Region: CCCTATTGAGCCCAA GTGCGGTCGATGTTAAAA ACGT TTTGAAAAACGACCGCAC TTGAATAAGTTTAAC ................................GTGCGGTCGATGTTAAAAACGTTTTGAAAAACGACCGCAC................................. Find igs database================================================ Query_seq: AA00355:AA00356|AA00355:AA00356:DNA-directed RNA polymerase beta chain (transcriptase beta chain):DNA-directed RNA polymerase, beta' chain:->->:238972..239076 105 taagtcagggtattgacccctattgagcccaagtgcggtcgatgttaaaaacgttttgaaaaacgaccgcacttgaataagtttaactccgacaggagcaaatct Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: aact_AA00355_AA00356|DNA-directed RNA polymerase beta chain (transcriptase beta chain):DNA-directed RNA polymerase, beta' chain|POSITIVE:POSITIVE|[238972,239076]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 taagtcagggtattgacccctattgagcccaagtgcggtcgatgttaaaaacgttttgaaaaacgaccgcacttgaataagtttaactccgacaggagcaaatct taagtcagggtattgacccctattgagcccaagtgcggtcgatgttaaaaacgttttgaaaaacgaccgcacttgaataagtttaactccgacaggagcaaatct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGUCAGGGUAUUGACCCCUAUUGAGCCCAAGUGCGGUCGAUGUUAAAAACGUUUUGAAAAACGACCGCACUUGAAUAAGUUUAACUCCGACAGGAGCAAAUCU .......((((....))))...((((((.((((((((((((...(((((.....)))))....)))))))))))).....))))))((((....))))....... (-33.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUUUGCUCCUGUCGGAGUUAAACUUAUUCAAGUGCGGUCGUUUUUCAAAACGUUUUUAACAUCGACCGCACUUGGGCUCAAUAGGGGUCAAUACCCUGACUUA ..(((.((((((((..((((.........(((((((((((((......................))))))))))))))))).)))))))).)))........... (-34.75) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 526 74 31 158 115 aact:AA00766|5end_heat_shock_protein_B25.3_(HSP-70_cofactor)_527384..527614_POSITIVE 494 74 31 157 114 aact:AA02700|5end_succinyl-CoA_synthase,_alpha_subunit_1883256..1883486_POSITIVE 486 74 31 219 176 aact:AA02778|5end_hypothetical_protein_1942585..1942815_POSITIVE 483 74 31 150 107 aact:AA00386|5end_aspartate--ammonia_ligase_(asparagine_synthetase_A)_261150..261380_POSITIVE 467 74 31 168 125 aact:AA00721|5end_probable_beta-N-acetylhexosaminidase_(lacto-N-biosidase);_dispersin_B_494739..494969_POSITIVE 467 74 31 56 13 aact:AA00719|5end_hypothetical_protein_494627..494857_POSITIVE 446 74 31 149 111 aact:AA02084|5end_conserved_hypothetical_protein_1417843..1418073_POSITIVE 442 74 31 163 112 aact:AA02249|5end_thiamine_biosynthesis_protein_1528365..1528595_POSITIVE 436 74 31 150 107 aact:AA01648|5end_alpha-amylase_protein;_1,4-alpha-D-glucan_glucanohydrolase_1115170..1115400_POSITIVE 436 74 31 49 6 aact:AA01646|5end_hypothetical_protein_1115069..1115299_POSITIVE 432 74 31 121 81 aact:AA00792|5end_conserved_hypothetical_protein_543142..543372_POSITIVE 414 74 33 152 116 aact:AA00300|5end_conserved_hypothetical_protein_203785..204015_POSITIVE 414 74 32 175 136 aact:AA00212|5end_ribokinase_146056..146286_POSITIVE 414 74 32 74 35 aact:AA00211|5end_hypothetical_protein_145955..146185_POSITIVE 407 74 31 61 7 aact:AA00313|5end_hypothetical_protein_212822..213052_POSITIVE 404 74 32 136 93 aact:AA02410|5end_cell_division_protein_1655429..1655659_POSITIVE 403 74 31 123 83 aact:AA02716|5end_peptidase_T_1899789..1900019_POSITIVE 398 76 34 188 140 aact:AA00113|5end_uracil_phosphoribosyltransferase_81286..81516_POSITIVE 391 74 31 149 106 aact:AA02888|5end_ssrA-binding_protein,_small_protein_B_2024628..2024858_POSITIVE 390 76 32 152 96 aact:AA01111|5end_conserved_hypothetical_protein_764765..764995_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 486 74 31 81 38 aact:AA02777|3end_tRNA-guanine_transglycosylase_1942527..1942677_POSITIVE 483 74 31 88 45 aact:AA00384|3end_conserved_hypothetical_protein_(possible_nitrogen_fixation_protein)_261168..261318_POSITIVE 479 75 31 61 17 aact:AA00355|3end_DNA-directed_RNA_polymerase_beta_chain_(transcriptase_beta_chain)_238911..239061_POSITIVE 472 74 34 41 1 aact:AA00764|3end_hemoglobin_binding_protein_A_527347..527497_POSITIVE 467 74 31 72 29 aact:AA00718|3end_ABC-related_ATP-binding_protein;_MRP_protein_494723..494873_POSITIVE 446 74 31 74 36 aact:AA02082|3end_glutaminyl-tRNA_synthetase_1417848..1417998_POSITIVE 442 74 31 73 22 aact:AA02246|3end_peptidase_E_1528355..1528505_POSITIVE 436 74 31 84 41 aact:AA01645|3end_ferric_transport_ABC-related_ATP-binding_protein_1115184..1115334_POSITIVE 414 74 32 71 32 aact:AA00209|3end_D-ribose_ABC_transporter,_periplasmic-binding_protein_146032..146182_POSITIVE 413 76 31 59 18 aact:AA00010|3end_transposase_orfB_fragment_6297..6447_POSITIVE 407 74 31 81 27 aact:AA00312|3end_conserved_hypothetical_protein_(possible_hydroxypyruvate_isomerase)_212922..213072_POSITIVE 403 74 31 41 1 aact:AA02715|3end_paraquat-inducible_protein_pqiB_homolog_1899787..1899937_POSITIVE 398 76 34 61 13 aact:AA00112|3end_uracil_permease_81239..81389_POSITIVE 394 82 43 90 47 aact:AA00578|3end_DNA_topoisomerase_395201..395351_POSITIVE 391 74 31 75 32 aact:AA02886|3end_OBG-related_GTP-binding_protein_2024634..2024784_POSITIVE 387 79 31 145 96 aact:AA01978|3end_hypothetical_protein_1337257..1337407_POSITIVE 384 74 31 73 19 aact:AA02595|3end_cytochrome_c_peroxidase_1807110..1807260_POSITIVE 382 74 31 85 42 aact:AA01966|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_1331514..1331664_POSITIVE 375 74 31 79 24 aact:AA00709|3end_metallocluster_assembly_(NifU_protein)_487838..487988_POSITIVE 374 74 47 33 6 aact:AA00790|3end_recombination_DNA_repair_protein_543134..543284_POSITIVE