Origin IGS: tttttttttaaattttactcttaaatgaaataaaatcctacaataataatgataaggcataaaagaattttttgctttatcctaaccattgattaattattattaaggagaaaagtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacttttctccttaataataattaatcaatggttaggataaagcaaaaaattcttttatgccttatcattattattgtaggattttatttcatttaagagtaaaatttaaaaaaaaa Mask Tandem Repeat Region ================================================ tttttttttaaattttactcttaaatgaaataaaatcctacaataataatgataaggcataaaagaattttttgctttatcctaaccattgattaattattattaaggagaaaagtt Find is-nt database================================================ Query_seq: TDE2710:TDE2711|TDE2710:TDE2711:MATE efflux family protein:hypothetical protein:->->:2768035..2768151 117 tttttttttaaattttactcttaaatgaaataaaatcctacaataataatgataaggcataaaagaattttttgctttatcctaaccattgattaattattattaaggagaaaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2710:TDE2711|TDE2710:TDE2711:MATE efflux family protein:hypothetical protein:->->:2768035..2768151 117 tttttttttaaattttactcttaaatgaaataaaatcctacaataataatgataaggcataaaagaattttttgctttatcctaaccattgattaattattattaaggagaaaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2710:TDE2711|TDE2710:TDE2711:MATE efflux family protein:hypothetical protein:->->:2768035..2768151 117 tttttttttaaattttactcttaaatgaaataaaatcctacaataataatgataaggcataaaagaattttttgctttatcctaaccattgattaattattattaaggagaaaagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttttttttaaattttactcttaaatgaaataaaatcctacaataataatgataaggcataaaagaattttttgctttatcctaaccattgattaattattattaaggagaaaagtt Predict ORF larger than 30AA ================================================ tttttttttaaattttactcttaaatgaaataaaatcctacaataataatgataaggcataaaagaattttttgctttatcctaaccattgattaattattattaaggagaaaagtt 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================================================ tttttttttaaattttactcttaaatgaaataaaatcctacaataataatgataaggcataaaagaattttttgctttatcctaaccattgattaattattattaaggagaaaagtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2710:TDE2711|TDE2710:TDE2711:MATE efflux family protein:hypothetical protein:->->:2768035..2768151 117 tttttttttaaattttactcttaaatgaaataaaatcctacaataataatgataaggcataaaagaattttttgctttatcctaaccattgattaattattattaaggagaaaagtt Intra-Species Hit: Count: 1 Min: 10 Max: 117 Len: 108 Subject: NC_002967_TDE2710_TDE2711|MATE efflux family protein:hypothetical protein|POSITIVE:POSITIVE|[2768035,2768151]|117 HSP 1 e-value: 5.0E-55 bit: 214.0 Len: 108 Query Start:10 Query End:117 Subject Strand: POSITIVE Subject Start: 10 Subject End: 117 .........aaattttactcttaaatgaaataaaatcctacaataataatgataaggcataaaagaattttttgctttatcctaaccattgattaattattattaaggagaaaagtt .........aaattttactcttaaatgaaataaaatcctacaataataatgataaggcataaaagaattttttgctttatcctaaccattgattaattattattaaggagaaaagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUUUACUCUUAAAUGAAAUAAAAUCCUACAAUAAUAAUGAUAAGGCAUAAAAGAAUUUUUUGCUUUAUCCUAACCAUUGAUUAAUUAUUAUUAAGGAGAAAAGUU .((((((.(((((.(((((.....((((.............(((((((((.(((.....))).))))))))).........)))).....))))).))))).)))))) (-17.25) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUUUUCUCCUUAAUAAUAAUUAAUCAAUGGUUAGGAUAAAGCAAAAAAUUCUUUUAUGCCUUAUCAUUAUUAUUGUAGGAUUUUAUUUCAUUUAAGAGUAAAAUUU .((((((......(((((.((((...(((((((...(((((.(((.(((.....))).))).)))))...)))))))...)))))))))......))))))....... (-18.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 233 99 59 143 94 NC_002967:TDE0201|5end_hypothetical_protein_235363..235593_POSITIVE 201 74 47 60 29 NC_002967:TDE0070|5end_RNA_polymerase_sigma-70_factor,_region_2_family_77713..77943_POSITIVE 197 86 45 90 52 NC_002967:TDE0252|5end_hypothetical_protein_286263..286493_POSITIVE 196 74 43 184 153 NC_002967:TDE2169|5end_hypothetical_protein_2201037..2201267_POSITIVE 195 76 32 174 124 NC_002967:TDE1883|5end_hypothetical_protein_1905842..1906072_NEGATIVE 193 69 27 135 96 NC_002967:TDE1692|5end_hypothetical_protein_1748293..1748523_POSITIVE 191 95 56 88 43 NC_002967:TDE1203|5end_cell_division_protein_FtsA_1235033..1235263_POSITIVE 188 50 28 172 153 NC_002967:TDE2273|5end_hypothetical_protein_2309980..2310210_POSITIVE 187 81 41 221 177 NC_002967:TDE1007|5end_flagellar_basal-body_rod_protein_FlgG_1031261..1031491_POSITIVE 187 93 60 36 4 NC_002967:TDE0398|5end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein_447773..448003_POSITIVE 186 49 7 72 25 NC_002967:TDE0206|5end_surface_antigen,_putative_241527..241757_NEGATIVE 184 70 28 106 63 NC_002967:TDE2476|5end_carbamate_kinase_2499450..2499680_NEGATIVE 182 79 37 54 12 NC_002967:TDE1505|5end_hypothetical_protein_1553614..1553844_POSITIVE 181 87 41 195 152 NC_002967:TDE0725|5end_exopolysaccharide_biosynthesis_protein_763465..763695_POSITIVE 174 69 45 162 139 NC_002967:TDE1341|5end_hypothetical_protein_1377063..1377293_POSITIVE 173 69 26 157 115 NC_002967:TDE2028|5end_OmpA_family_protein_2052923..2053153_POSITIVE 171 80 31 102 57 NC_002967:TDE2288|5end_hypothetical_protein_2325644..2325874_NEGATIVE 171 76 46 109 79 NC_002967:TDE1372|5end_hypothetical_protein_1416897..1417127_NEGATIVE 170 86 43 208 160 NC_002967:TDE2780|5end_hypothetical_protein_2830621..2830851_NEGATIVE 169 85 50 150 110 NC_002967:TDE1842|5end_hypothetical_protein_1872005..1872235_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 233 99 59 72 23 NC_002967:TDE0200|3end_tetrapyrrole_methylase_family_protein_235372..235522_POSITIVE 203 72 42 40 10 NC_002967:TDE2710|3end_MATE_efflux_family_protein_2767974..2768124_POSITIVE 196 68 41 57 29 NC_002967:TDE2287|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2324309..2324459_NEGATIVE 195 76 32 142 92 NC_002967:TDE1884|3end_hypothetical_protein_1905874..1906024_NEGATIVE 191 95 56 95 50 NC_002967:TDE1202|3end_cell_division_protein_FtsQ,_putative_1235120..1235270_POSITIVE 178 99 59 121 84 NC_002967:TDE1959|3end_hypothetical_protein_1973805..1973955_NEGATIVE 174 78 33 72 20 NC_002967:TDE1642|3end_hypothetical_protein_1692771..1692921_NEGATIVE 174 69 45 51 28 NC_002967:TDE1340|3end_ribosomal_5S_rRNA_E-loop_binding_protein_Ctc/L25/TL5_1377032..1377182_POSITIVE 173 76 46 58 20 NC_002967:TDE2114|3end_ABC_transporter,_ATP-binding_protein_2139390..2139540_NEGATIVE 172 66 28 37 1 NC_002967:TDE0922|3end_ABC_transporter,_ATP-binding/permease_protein_941847..941997_NEGATIVE 167 50 2 147 98 NC_002967:TDE2623|3end_hypothetical_protein_2663584..2663734_NEGATIVE 167 50 3 100 55 NC_002967:TDE2201|3end_hypothetical_protein_2238492..2238642_NEGATIVE 164 68 26 151 110 NC_002967:TDE2027|3end_hypothetical_protein_2052998..2053148_POSITIVE 164 83 45 73 37 NC_002967:TDE1659|3end_alanyl-tRNA_synthetase_1708831..1708981_NEGATIVE 156 76 42 48 13 NC_002967:TDE1560|3end_YD_repeat_protein_1614910..1615060_POSITIVE 154 89 48 96 55 NC_002967:TDE2414|3end_hypothetical_protein_2441021..2441171_NEGATIVE 152 85 47 33 5 NC_002967:TDE2086|3end_DnaJ_domain_protein_2115475..2115625_POSITIVE 152 85 60 36 3 NC_002967:TDE1076|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1108056..1108206_POSITIVE 151 79 48 107 77 NC_002967:TDE1364|3end_valyl-tRNA_synthetase_1407572..1407722_POSITIVE 151 82 48 104 62 NC_002967:TDE1166|3end_hypothetical_protein_1198394..1198544_NEGATIVE