Origin IGS: atttcgtgtttaataataatgattgattctataaatataaaatgcaaaagtagtgggtctgtgatggatggaaaagggataatctgttagaaaattagtcaatatcgaatatttgggaaagcgaatgacggaaaagcggaaaaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attttttccgcttttccgtcattcgctttcccaaatattcgatattgactaattttctaacagattatcccttttccatccatcacagacccactacttttgcattttatatttatagaatcaatcattattattaaacacgaaat Mask Tandem Repeat Region ================================================ atttcgtgtttaataataatgattgattctataaatataaaatgcaaaagtagtgggtctgtgatggatggaaaagggataatctgttagaaaattagtcaatatcgaatatttgggaaagcgaatgacggaaaagcggaaaaaat Find is-nt database================================================ Query_seq: TF0474:TF0475|TF0474:TF0475:outer membrane efflux protein:possible transcriptional regulator, AraC family:->->:493723..493868 146 atttcgtgtttaataataatgattgattctataaatataaaatgcaaaagtagtgggtctgtgatggatggaaaagggataatctgttagaaaattagtcaatatcgaatatttgggaaagcgaatgacggaaaagcggaaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0474:TF0475|TF0474:TF0475:outer membrane efflux protein:possible transcriptional regulator, AraC family:->->:493723..493868 146 atttcgtgtttaataataatgattgattctataaatataaaatgcaaaagtagtgggtctgtgatggatggaaaagggataatctgttagaaaattagtcaatatcgaatatttgggaaagcgaatgacggaaaagcggaaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0474:TF0475|TF0474:TF0475:outer membrane efflux protein:possible transcriptional regulator, AraC family:->->:493723..493868 146 atttcgtgtttaataataatgattgattctataaatataaaatgcaaaagtagtgggtctgtgatggatggaaaagggataatctgttagaaaattagtcaatatcgaatatttgggaaagcgaatgacggaaaagcggaaaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttcgtgtttaataataatgattgattctataaatataaaatgcaaaagtagtgggtctgtgatggatggaaaagggataatctgttagaaaattagtcaatatcgaatatttgggaaagcgaatgacggaaaagcggaaaaaat Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 13 End: 126 ............ Y Y H N I R Y I Y F A F T T P R H H I S F P Y D T L F N T L I S Y K P F R M .................... atttcgtgtttaataataatgattgattctataaatataaaatgcaaaagtagtgggtctgtgatggatggaaaagggataatctgttagaaaattagtcaatatcgaatatttgggaaagcgaatgacggaaaagcggaaaaaat 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: 82 Start: 13 End: 42 ............TTTTATATTTATAGAATCAATCATTATTAT........................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttcgtgtttaataataatgattgattctataaatataaaatgcaaaagtagtgggtctgtgatggatggaaaagggataatctgttagaaaattagtcaatatcgaatatttgggaaagcgaatgacggaaaagcggaaaaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0474:TF0475|TF0474:TF0475:outer membrane efflux protein:possible transcriptional regulator, AraC family:->->:493723..493868 146 atttcgtgtttaataataatgattgattctataaatataaaatgcaaaagtagtgggtctgtgatggatggaaaagggataatctgttagaaaattagtcaatatcgaatatttgggaaagcgaatgacggaaaagcggaaaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 146 Len: 146 Subject: tfor_TF0474_TF0475|outer membrane efflux protein:possible transcriptional regulator, AraC family|POSITIVE:POSITIVE|[493723,493868]|146 HSP 1 e-value: 1.0E-77 bit: 289.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 atttcgtgtttaataataatgattgattctataaatataaaatgcaaaagtagtgggtctgtgatggatggaaaagggataatctgttagaaaattagtcaatatcgaatatttgggaaagcgaatgacggaaaagcggaaaaaat atttcgtgtttaataataatgattgattctataaatataaaatgcaaaagtagtgggtctgtgatggatggaaaagggataatctgttagaaaattagtcaatatcgaatatttgggaaagcgaatgacggaaaagcggaaaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCGUGUUUAAUAAUAAUGAUUGAUUCUAUAAAUAUAAAAUGCAAAAGUAGUGGGUCUGUGAUGGAUGGAAAAGGGAUAAUCUGUUAGAAAAUUAGUCAAUAUCGAAUAUUUGGGAAAGCGAAUGACGGAAAAGCGGAAAAAAU .((((((............(((((((((..............(((....))).......(.((((((((............)))))))).).)))))))))...(((..((((((......)))))).)))....))))))..... (-19.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUUCCGCUUUUCCGUCAUUCGCUUUCCCAAAUAUUCGAUAUUGACUAAUUUUCUAACAGAUUAUCCCUUUUCCAUCCAUCACAGACCCACUACUUUUGCAUUUUAUAUUUAUAGAAUCAAUCAUUAUUAUUAAACACGAAAU ....((((.........((((.(((..(........)..)))...))))..................................................(((.(((((((....)))))))))).................)))). ( -8.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 86 52 99 66 tfor:TF1499|5end_3-oxyacyl-[acyl-carrier_protein]_synthase_1598394..1598624_POSITIVE 309 89 51 218 180 tfor:TF1054|5end_hypothetical_protein_1119583..1119813_POSITIVE 293 138 106 72 43 tfor:TF1401|5end_Holliday_junction_DNA_helicase_1476502..1476732_POSITIVE 291 93 52 46 2 tfor:TF2415|5end_hypothetical_protein_2591424..2591654_POSITIVE 283 91 53 201 155 tfor:TF0229|5end_beta-galactosidase_254857..255087_POSITIVE 275 140 97 48 10 tfor:TF2507|5end_ATP-dependent_DNA_helicase_2683928..2684158_POSITIVE 273 82 44 91 48 tfor:TF1808|5end_DNA_processing_protein_subunit_A_1949356..1949586_POSITIVE 266 88 49 86 54 tfor:TF2391|5end_conserved_hypothetical_protein_2562128..2562358_POSITIVE 266 90 42 218 175 tfor:TF1460|5end_6-phosphogluconate_dehydrogenase_1549262..1549492_POSITIVE 262 139 105 214 172 tfor:TF3036|5end_glucose/galactose_transporter_3261667..3261897_POSITIVE 260 139 93 105 54 tfor:TF0749|5end_protease_II_795562..795792_POSITIVE 251 85 43 163 126 tfor:TF1727|5end_hypothetical_protein_1852311..1852541_POSITIVE 250 81 41 157 111 tfor:TF1293|5end_ATPase,_possible_AAA_superfamily_1374579..1374809_POSITIVE 249 86 54 33 2 tfor:TF1963|5end_hypothetical_protein_2113359..2113589_POSITIVE 249 140 106 58 20 tfor:TF1410|5end_cation_efflux_system_protein,_possible_drug_efflux_protein_1487003..1487233_POSITIVE 246 140 105 57 15 tfor:TF1921|5end_hypothetical_protein_2070322..2070552_POSITIVE 244 140 106 138 106 tfor:TF1425|5end_phospho-N-acetylmuramoyl_pentapeptide_transferase_1508600..1508830_POSITIVE 244 140 96 105 57 tfor:TF0243|5end_conserved_hypothetical_protein_273728..273958_POSITIVE 241 140 94 78 36 tfor:TF3028|5end_1-deoxy-d-xylulose-5-phosphate_reductoisomerase_3251642..3251872_POSITIVE 241 137 106 81 48 tfor:TF1937|5end_conserved_hypothetical_protein_2084476..2084706_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 331 86 52 115 82 tfor:TF1498|3end_GTP-binding_protein_1598490..1598640_POSITIVE 293 138 106 63 34 tfor:TF1400|3end_polysaccharide_biosynthesis_protein;_membrane_protein_1476573..1476723_POSITIVE 283 91 53 73 27 tfor:TF0228|3end_probable_integral_outer_membrane_protein_254809..254959_POSITIVE 273 82 44 80 37 tfor:TF1807|3end_thioesterase_family_protein_1949425..1949575_POSITIVE 260 87 49 151 119 tfor:TF1218|3end_hypothetical_protein_1304383..1304533_POSITIVE 258 83 43 151 120 tfor:TF1867|3end_transposase_2023612..2023762_POSITIVE 253 139 98 146 114 tfor:TF1838|3end_tRNA/rRNA_methyltransferase_1988745..1988895_POSITIVE 251 85 43 53 16 tfor:TF1726|3end_hypothetical_protein_1852281..1852431_POSITIVE 250 81 41 52 6 tfor:TF1292|3end_sensor_histidine_protein_kinase_1374554..1374704_POSITIVE 249 140 106 54 16 tfor:TF1409|3end_outer_membrane_protein_TolC_1487079..1487229_POSITIVE 246 93 57 36 1 tfor:TF2414|3end_hypothetical_protein_2591494..2591644_POSITIVE 244 140 106 132 100 tfor:TF1424|3end_N-acetylymuramoyl-L-alanine-D-glutamate_ligase_1508674..1508824_POSITIVE 241 137 106 74 41 tfor:TF1936|3end_conserved_hypothetical_protein_2084549..2084699_POSITIVE 239 99 52 120 72 tfor:TF1451|3end_conserved_hypothetical_protein_1537587..1537737_POSITIVE 237 140 95 136 88 tfor:TF0746|3end_possible_DNA_polymerase_III_792910..793060_POSITIVE 237 87 42 53 10 tfor:TF0449|3end_transposase_469209..469359_POSITIVE 236 86 42 72 20 tfor:TF1992|3end_hypothetical_protein_2144549..2144699_POSITIVE 236 140 95 145 97 tfor:TF0339|3end_hypothetical_protein_363747..363897_POSITIVE 235 140 100 38 1 tfor:TF1919|3end_hypothetical_protein_2070383..2070533_POSITIVE 234 98 55 60 23 tfor:TF0353|3end_transposase_element_372543..372693_POSITIVE