Origin IGS: gatgctgtaattttttcagtttgacctgacaaaattaccttatttctctgagacggcaaaaaaacatccgaaaaattcctgtacgtagagagcaggagagccccaagacggattta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaatccgtcttggggctctcctgctctctacgtacaggaatttttcggatgtttttttgccgtctcagagaaataaggtaattttgtcaggtcaaactgaaaaaattacagcatc Mask Tandem Repeat Region ================================================ gatgctgtaattttttcagtttgacctgacaaaattaccttatttctctgagacggcaaaaaaacatccgaaaaattcctgtacgtagagagcaggagagccccaagacggattta Find is-nt database================================================ Query_seq: TF0693:TF0694|TF0693:TF0694:sigma-54 dependent transcriptional regulator:possible hemolysin, acyltransferase family:->->:738221..738336 116 gatgctgtaattttttcagtttgacctgacaaaattaccttatttctctgagacggcaaaaaaacatccgaaaaattcctgtacgtagagagcaggagagccccaagacggattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0693:TF0694|TF0693:TF0694:sigma-54 dependent transcriptional regulator:possible hemolysin, acyltransferase family:->->:738221..738336 116 gatgctgtaattttttcagtttgacctgacaaaattaccttatttctctgagacggcaaaaaaacatccgaaaaattcctgtacgtagagagcaggagagccccaagacggattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0693:TF0694|TF0693:TF0694:sigma-54 dependent transcriptional regulator:possible hemolysin, acyltransferase family:->->:738221..738336 116 gatgctgtaattttttcagtttgacctgacaaaattaccttatttctctgagacggcaaaaaaacatccgaaaaattcctgtacgtagagagcaggagagccccaagacggattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgctgtaattttttcagtttgacctgacaaaattaccttatttctctgagacggcaaaaaaacatccgaaaaattcctgtacgtagagagcaggagagccccaagacggattta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 3 End: 113 .. A T I K E T Q G S L I V K N R Q S P L F V D S F N R Y T S L L L A G L R M ... gatgctgtaattttttcagtttgacctgacaaaattaccttatttctctgagacggcaaaaaaacatccgaaaaattcctgtacgtagagagcaggagagccccaagacggattta 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================================================ gatgctgtaattttttcagtttgacctgacaaaattaccttatttctctgagacggcaaaaaaacatccgaaaaattcctgtacgtagagagcaggagagccccaagacggattta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0693:TF0694|TF0693:TF0694:sigma-54 dependent transcriptional regulator:possible hemolysin, acyltransferase family:->->:738221..738336 116 gatgctgtaattttttcagtttgacctgacaaaattaccttatttctctgagacggcaaaaaaacatccgaaaaattcctgtacgtagagagcaggagagccccaagacggattta Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: tfor_TF0693_TF0694|sigma-54 dependent transcriptional regulator:possible hemolysin, acyltransferase family|POSITIVE:POSITIVE|[738221,738336]|116 HSP 1 e-value: 3.0E-47 bit: 188.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 gatgctgtaattttttcagtttgacctgacaaaattaccttatttctctgagacggcnnnnnnncatccgaaaaattcctgtacgtagagagcaggagagccccaagacggattta gatgctgtaattttttcagtttgacctgacaaaattaccttatttctctgagacggcaaaaaaacatccgaaaaattcctgtacgtagagagcaggagagccccaagacggattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGCUGUAAUUUUUUCAGUUUGACCUGACAAAAUUACCUUAUUUCUCUGAGACGGCAAAAAAACAUCCGAAAAAUUCCUGUACGUAGAGAGCAGGAGAGCCCCAAGACGGAUUUA ..((((((((((((.((((......)))).))))))))((((......))))..)))).......(((((.....(((((((.(.....).)))))))...(....).)))))... (-24.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUCCGUCUUGGGGCUCUCCUGCUCUCUACGUACAGGAAUUUUUCGGAUGUUUUUUUGCCGUCUCAGAGAAAUAAGGUAAUUUUGUCAGGUCAAACUGAAAAAAUUACAGCAUC ...((((((((((((((......))))........)))))......)))))(((((((((......)))))))))...((((((((.((((......)))).))))))))...... (-26.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 102 75 67 39 tfor:TF0778|5end_outer_membrane_protein,_TonB_dependent_receptor_827284..827514_POSITIVE 296 105 67 51 12 tfor:TF2250|5end_transfer_region-related_protein,_TraD_2423380..2423610_POSITIVE 291 103 74 76 38 tfor:TF2671|5end_dipeptidyl_peptidase_IV_(DPP_IV)_N-terminal_region_2843918..2844148_POSITIVE 286 100 54 213 169 tfor:TF2886|5end_RNA_methylase_SpoU_family_3075651..3075881_POSITIVE 286 110 65 217 166 tfor:TF0250|5end_glycosyltransferase_Family_2_protein_279176..279406_POSITIVE 277 97 52 91 38 tfor:TF0408|5end_possible_gliding_motility-related_lipoprotein_425777..426007_POSITIVE 273 108 68 123 73 tfor:TF2952|5end_transposase_3159572..3159802_POSITIVE 272 105 67 200 150 tfor:TF1857|5end_conserved_hypothetical_protein_2014366..2014596_POSITIVE 271 110 78 92 66 tfor:TF0122|5end_hypothetical_protein_133162..133392_POSITIVE 269 110 79 121 83 tfor:TF2218|5end_two-component_system_response_regulator_2390162..2390392_POSITIVE 268 99 53 103 64 tfor:TF0690|5end_preprotein_translocase_subunit_735243..735473_POSITIVE 266 101 65 70 30 tfor:TF1342|5end_possible_lipoprotein_1423125..1423355_POSITIVE 263 97 55 53 5 tfor:TF2618|5end_integral_membrane_protein,_possible_zinc_transporter_2795215..2795445_POSITIVE 259 100 51 58 16 tfor:TF1803|5end_conserved_hypothetical_protein_1946327..1946557_POSITIVE 258 85 43 151 114 tfor:TF2979|5end_possible_outer_membrane__protein_3190778..3191008_POSITIVE 258 110 78 60 26 tfor:TF2503|5end_conserved_hypothetical_protein_2678430..2678660_POSITIVE 256 107 78 184 146 tfor:TF0776|5end_ABC_transporter,_permease_component_824855..825085_POSITIVE 255 108 61 110 54 tfor:TF2182|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_2354874..2355104_POSITIVE 253 108 69 120 78 tfor:TF2731|5end_Fe2+/Zn2+_uptake_regulation_protein_2911196..2911426_POSITIVE 253 110 65 103 38 tfor:TF2246|5end_hypothetical_protein_2421288..2421518_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 277 97 52 78 25 tfor:TF0407|3end_lipoate-protein_ligase_B_(lipoyltransferase)_425844..425994_POSITIVE 273 108 68 93 43 tfor:TF2951|3end_O-succinylbenzoic_acid--CoA_ligase_3159622..3159772_POSITIVE 271 110 78 67 41 tfor:TF0121|3end_hypothetical_protein_133217..133367_POSITIVE 269 110 79 44 6 tfor:TF2217|3end_hypothetical_protein_2390165..2390315_POSITIVE 266 101 65 65 25 tfor:TF1341|3end_glycogen_synthase_1423200..1423350_POSITIVE 259 100 51 58 16 tfor:TF1802|3end_conserved_hypothetical_protein_1946407..1946557_POSITIVE 259 110 65 84 39 tfor:TF1689|3end_conserved_hypothetical_protein_1806614..1806764_POSITIVE 258 110 78 41 7 tfor:TF2502|3end_conserved_hypothetical_protein_2678491..2678641_POSITIVE 255 108 61 119 63 tfor:TF2181|3end_conserved_hypothetical_protein_2354963..2355113_POSITIVE 252 108 78 50 11 tfor:TF0124|3end_ABC_transporter,_permease_component_136333..136483_POSITIVE 251 109 67 95 58 tfor:TF1623|3end_5-formyltetrahydrofolate_cyclo-ligase_1737332..1737482_POSITIVE 248 109 63 139 94 tfor:TF1744|3end_phenylacetate-CoA_ligase_1879218..1879368_POSITIVE 248 107 64 51 4 tfor:TF1679|3end_conserved_hypothetical_protein_1793319..1793469_POSITIVE 246 110 61 83 24 tfor:TF1932|3end_pigmentation_and_extracellular_proteinase_regulator_2079755..2079905_POSITIVE 245 108 61 51 2 tfor:TF1821|3end_cation_efflux_system_protein_1967645..1967795_POSITIVE 244 110 63 79 23 tfor:TF2900|3end_conserved_hypothetical_protein_3090029..3090179_POSITIVE 244 110 68 150 104 tfor:TF0865|3end_chloromuconate_cycloisomerase_916805..916955_POSITIVE 241 110 68 55 9 tfor:TF0213|3end_conserved_hypothetical_protein_239903..240053_POSITIVE 240 86 43 50 5 tfor:TF2759|3end_xylose_repressor,_ROK_family_2944853..2945003_POSITIVE 239 109 67 31 1 tfor:TF2878|3end_conserved_hypothetical_protein;_possible_CAAX_amino_terminal_protease_family_3068283..3068433_POSITIVE