Origin IGS: taagcggaaaataatgaatacatagacgaagacggagagccttccgtgagagttgcggatcgtgcgctccgtcttttcttacttacaaaaattaaaccgataaaca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgtttatcggtttaatttttgtaagtaagaaaagacggagcgcacgatccgcaactctcacggaaggctctccgtcttcgtctatgtattcattattttccgctta Mask Tandem Repeat Region ================================================ taagcggaaaataatgaatacatagacgaagacggagagccttccgtgagagttgcggatcgtgcgctccgtcttttcttacttacaaaaattaaaccgataaaca Find is-nt database================================================ Query_seq: TF2803:TF2804|TF2803:TF2804:dehydrogenase, possible NADH-dependent dehydrogenase:conserved hypothetical protein:->->:2993528..2993633 106 taagcggaaaataatgaatacatagacgaagacggagagccttccgtgagagttgcggatcgtgcgctccgtcttttcttacttacaaaaattaaaccgataaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2803:TF2804|TF2803:TF2804:dehydrogenase, possible NADH-dependent dehydrogenase:conserved hypothetical protein:->->:2993528..2993633 106 taagcggaaaataatgaatacatagacgaagacggagagccttccgtgagagttgcggatcgtgcgctccgtcttttcttacttacaaaaattaaaccgataaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2803:TF2804|TF2803:TF2804:dehydrogenase, possible NADH-dependent dehydrogenase:conserved hypothetical protein:->->:2993528..2993633 106 taagcggaaaataatgaatacatagacgaagacggagagccttccgtgagagttgcggatcgtgcgctccgtcttttcttacttacaaaaattaaaccgataaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagcggaaaataatgaatacatagacgaagacggagagccttccgtgagagttgcggatcgtgcgctccgtcttttcttacttacaaaaattaaaccgataaaca Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 3 End: 101 .. A S F L S Y M S S S P S G E T L T A S R A S R R K K S V F I L G M ..... taagcggaaaataatgaatacatagacgaagacggagagccttccgtgagagttgcggatcgtgcgctccgtcttttcttacttacaaaaattaaaccgataaaca 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================================================ taagcggaaaataatgaatacatagacgaagacggagagccttccgtgagagttgcggatcgtgcgctccgtcttttcttacttacaaaaattaaaccgataaaca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 80 HP_score: -6.3 Tail_Score: -4.78572 Start: 31 End: 73 Full_Region: GAATACATAGACGAA GACGGAGAGCCTTCCGTGA GAG TTGCGGATCGTGCGCTCCGTC TTTTCTTACTTACAA ..............................GACGGAGAGCCTTCCGTGAGAGTTGCGGATCGTGCGCTCCGTC................................. Find igs database================================================ Query_seq: TF2803:TF2804|TF2803:TF2804:dehydrogenase, possible NADH-dependent dehydrogenase:conserved hypothetical protein:->->:2993528..2993633 106 taagcggaaaataatgaatacatagacgaagacggagagccttccgtgagagttgcggatcgtgcgctccgtcttttcttacttacaaaaattaaaccgataaaca Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: tfor_TF2803_TF2804|dehydrogenase, possible NADH-dependent dehydrogenase:conserved hypothetical protein|POSITIVE:POSITIVE|[2993528,2993633]|106 HSP 1 e-value: 6.0E-54 bit: 210.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 106 taagcggaaaataatgaatacatagacgaagacggagagccttccgtgagagttgcggatcgtgcgctccgtcttttcttacttacaaaaattaaaccgataaaca taagcggaaaataatgaatacatagacgaagacggagagccttccgtgagagttgcggatcgtgcgctccgtcttttcttacttacaaaaattaaaccgataaaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCGGAAAAUAAUGAAUACAUAGACGAAGACGGAGAGCCUUCCGUGAGAGUUGCGGAUCGUGCGCUCCGUCUUUUCUUACUUACAAAAAUUAAACCGAUAAACA ....(((....((((........(((.((((((((((.(((.((((..(...)..))))..).)).)))))))))))))...........))))..)))....... (-29.01) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUAUCGGUUUAAUUUUUGUAAGUAAGAAAAGACGGAGCGCACGAUCCGCAACUCUCACGGAAGGCUCUCCGUCUUCGUCUAUGUAUUCAUUAUUUUCCGCUUA .......(((...(((....(((.(((.((.(((((((((.((.(..((((.........)))).))).)))))))))..))))).))).....)))..))).... (-26.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 524 80 33 147 99 tfor:TF1327|5end_L-fucose_permease_1405790..1406020_POSITIVE 457 79 32 65 5 tfor:TF2759|5end_xylose_repressor,_ROK_family_2943568..2943798_POSITIVE 456 77 33 197 150 tfor:TF1785|5end_histidine_ammonia-lyase_1924494..1924724_POSITIVE 435 69 21 188 140 tfor:TF2466|5end_pyruvate_kinase_2644385..2644615_POSITIVE 433 78 33 225 166 tfor:TF1179|5end_two-component_sensor_histidine_kinase_1266057..1266287_POSITIVE 432 80 33 113 53 tfor:TF1935|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2082002..2082232_POSITIVE 426 82 41 219 170 tfor:TF0888|5end_transfer_region-related_protein,_TraN_938392..938622_POSITIVE 423 68 21 101 42 tfor:TF1192|5end_alpha-amylase_1274007..1274237_POSITIVE 412 69 27 103 62 tfor:TF0642|5end_exported_transglycosylase,_extracellular_solute-binding_protein,_family_3_682796..683026_POSITIVE 410 82 42 38 1 tfor:TF0585|5end_conserved_hypothetical_protein_614782..615012_POSITIVE 403 66 24 217 173 tfor:TF1669|5end_ATP_synthase,_gamma_subunit_1783566..1783796_POSITIVE 384 66 33 81 37 tfor:TF1908|5end_possible_phosphoglycerate_mutase_2062695..2062925_POSITIVE 379 79 34 166 118 tfor:TF0417|5end_hypothetical_protein_433811..434041_POSITIVE 379 79 34 166 118 tfor:TF0026|5end_hypothetical_protein_21877..22107_POSITIVE 378 70 25 88 23 tfor:TF2333|5end_signal_peptidase_I_2492560..2492790_POSITIVE 378 73 33 220 180 tfor:TF1839|5end_conserved_hypothetical_protein_1989347..1989577_POSITIVE 376 70 28 90 49 tfor:TF2457|5end_ABC_transporter,_permease_component,_zinc-binding_protein_2633147..2633377_POSITIVE 376 70 25 58 16 tfor:TF1215|5end_haloacid_dehalogenase-like_hydrolase_1302510..1302740_POSITIVE 375 80 31 180 126 tfor:TF2047|5end_hypothetical_protein_2210057..2210287_POSITIVE 374 70 22 213 165 tfor:TF0375|5end_thioredoxin_reductase_393323..393553_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 524 80 33 147 99 tfor:TF1325|3end_L-fucose_isomerase_1405870..1406020_POSITIVE 384 70 25 106 53 tfor:TF0242|3end_conserved_hypothetical_protein_274069..274219_POSITIVE 379 79 34 121 73 tfor:TF0416|3end_possible_ATP-binding_protein_433846..433996_POSITIVE 379 79 34 121 73 tfor:TF0025|3end_hypothetical_protein_21912..22062_POSITIVE 376 70 28 71 30 tfor:TF2456|3end_ABC_transporter,_ATP-binding_protein_2633208..2633358_POSITIVE 368 80 33 119 50 tfor:TF2012|3end_conserved_hypothetical_protein_2168720..2168870_POSITIVE 366 69 28 147 103 tfor:TF0727|3end_ABC_transporter,_ATP-binding_protein_780178..780328_POSITIVE 365 79 31 67 18 tfor:TF2803|3end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_2993467..2993617_POSITIVE 360 66 27 46 11 tfor:TF1327|3end_L-fucose_permease_1407195..1407345_POSITIVE 358 75 31 71 21 tfor:TF1618|3end_conserved_hypothetical_protein_1733766..1733916_POSITIVE 348 71 31 127 73 tfor:TF2128|3end_3-oxoacyl-(acyl-carrier_protein)_synthase_2305534..2305684_POSITIVE 344 70 25 142 81 tfor:TF0277|3end_outer_membrane_protein_305647..305797_POSITIVE 343 74 40 54 18 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 340 73 32 46 9 tfor:TF1467|3end_conserved_hypothetical_protein_1557837..1557987_POSITIVE 337 69 22 53 5 tfor:TF1906|3end_conserved_hypothetical_protein_2061646..2061796_POSITIVE 336 77 33 151 105 tfor:TF1205|3end_beta-glucanase/beta-glucan_synthetase;_endoglucanase_related_1288580..1288730_POSITIVE 336 80 33 54 7 tfor:TF0886|3end_conjugative_transposon_protein_fragment_938152..938302_POSITIVE 331 68 29 125 76 tfor:TF0408|3end_possible_gliding_motility-related_lipoprotein_426324..426474_POSITIVE 329 72 31 57 2 tfor:TF2628|3end_conserved_hypothetical_protein_2801376..2801526_POSITIVE 328 70 25 84 24 tfor:TF2044|3end_excinuclease_ABC,_subunit_A_2206163..2206313_POSITIVE