Origin IGS: agctgacagtatagcataaattagtccaaaattaaactaggcaacacattcaattttctattagaacttacttgaaaaaaaatatattttcttttagtatttttgatattcttttacaaaaaaacatacaacaatagtagaggtgatagtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aactatcacctctactattgttgtatgtttttttgtaaaagaatatcaaaaatactaaaagaaaatatattttttttcaagtaagttctaatagaaaattgaatgtgttgcctagtttaattttggactaatttatgctatactgtcagct Mask Tandem Repeat Region ================================================ agctgacagtatagcataaattagtccaaaattaaactaggcaacacattcaattttctattagaacttacttgaaaaaaaatatattttcttttagtatttttgatattcttttacaaaaaaacatacaacaatagtagaggtgatagtt Find is-nt database================================================ Query_seq: TDE2586:TDE2587|TDE2586:TDE2587:DNA polymerase III subunits gamma and tau:endonuclease/exonuclease/phosphatase family protein:<-->:2622180..2622330 151 agctgacagtatagcataaattagtccaaaattaaactaggcaacacattcaattttctattagaacttacttgaaaaaaaatatattttcttttagtatttttgatattcttttacaaaaaaacatacaacaatagtagaggtgatagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2586:TDE2587|TDE2586:TDE2587:DNA polymerase III subunits gamma and tau:endonuclease/exonuclease/phosphatase family protein:<-->:2622180..2622330 151 agctgacagtatagcataaattagtccaaaattaaactaggcaacacattcaattttctattagaacttacttgaaaaaaaatatattttcttttagtatttttgatattcttttacaaaaaaacatacaacaatagtagaggtgatagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2586:TDE2587|TDE2586:TDE2587:DNA polymerase III subunits gamma and tau:endonuclease/exonuclease/phosphatase family protein:<-->:2622180..2622330 151 agctgacagtatagcataaattagtccaaaattaaactaggcaacacattcaattttctattagaacttacttgaaaaaaaatatattttcttttagtatttttgatattcttttacaaaaaaacatacaacaatagtagaggtgatagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agctgacagtatagcataaattagtccaaaattaaactaggcaacacattcaattttctattagaacttacttgaaaaaaaatatattttcttttagtatttttgatattcttttacaaaaaaacatacaacaatagtagaggtgatagtt Predict ORF larger than 30AA ================================================ agctgacagtatagcataaattagtccaaaattaaactaggcaacacattcaattttctattagaacttacttgaaaaaaaatatattttcttttagtatttttgatattcttttacaaaaaaacatacaacaatagtagaggtgatagtt 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: 86 Start: 71 End: 100 ......................................................................CTTGAAAAAAAATATATTTTCTTTTAGTAT................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 8 End: 37 .......GTTTAATTTTGGACTAATTTATGCTATACT.................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agctgacagtatagcataaattagtccaaaattaaactaggcaacacattcaattttctattagaacttacttgaaaaaaaatatattttcttttagtatttttgatattcttttacaaaaaaacatacaacaatagtagaggtgatagtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2586:TDE2587|TDE2586:TDE2587:DNA polymerase III subunits gamma and tau:endonuclease/exonuclease/phosphatase family protein:<-->:2622180..2622330 151 agctgacagtatagcataaattagtccaaaattaaactaggcaacacattcaattttctattagaacttacttgaaaaaaaatatattttcttttagtatttttgatattcttttacaaaaaaacatacaacaatagtagaggtgatagtt Intra-Species Hit: Count: 1 Min: 1 Max: 151 Len: 151 Subject: NC_002967_TDE2586_TDE2587|DNA polymerase III subunits gamma and tau:endonuclease/exonuclease/phosphatase family protein|NEGATIVE:POSITIVE|[2622180,2622330]|151 HSP 1 e-value: 1.0E-53 bit: 210.0 Len: 151 Query Start:1 Query End:151 Subject Strand: POSITIVE Subject Start: 1 Subject End: 151 agctgacagtatagcataaattagtccaaaattaaactaggcaacacattcaattttctattagaacttacttgnnnnnnnntatattttcttttagtatttttgatattcttttacnnnnnnncatacaacaatagtagaggtgatagtt agctgacagtatagcataaattagtccaaaattaaactaggcaacacattcaattttctattagaacttacttgaaaaaaaatatattttcttttagtatttttgatattcttttacaaaaaaacatacaacaatagtagaggtgatagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUGACAGUAUAGCAUAAAUUAGUCCAAAAUUAAACUAGGCAACACAUUCAAUUUUCUAUUAGAACUUACUUGAAAAAAAAUAUAUUUUCUUUUAGUAUUUUUGAUAUUCUUUUACAAAAAAACAUACAACAAUAGUAGAGGUGAUAGUU .((((......))))...(((((..((............(....)...........(((((((..........(((((........))))).....((.((((((.((......)))))))).)).........)))))))))...))))) (-16.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUAUCACCUCUACUAUUGUUGUAUGUUUUUUUGUAAAAGAAUAUCAAAAAUACUAAAAGAAAAUAUAUUUUUUUUCAAGUAAGUUCUAAUAGAAAAUUGAAUGUGUUGCCUAGUUUAAUUUUGGACUAAUUUAUGCUAUACUGUCAGCU ..............(((((((((.(((((((((....))))))))))))...((((..(((((((.....)))))))..)))).....))))))....((((..((((.((.(((((((....)))))))......)).))))..)))).. (-20.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 796 50 1 141 92 NC_002967:TDE2586|5end_DNA_polymerase_III_subunits_gamma_and_tau_2622089..2622319_NEGATIVE 207 53 18 125 91 NC_002967:TDE1753|5end_UDP-glucose_4-epimerase_1806540..1806770_NEGATIVE 202 64 23 60 18 NC_002967:TDE0073|5end_riboflavin_biosynthesis_protein_RibF,_putative_84082..84312_NEGATIVE 198 46 2 207 156 NC_002967:TDE0566|5end_hypothetical_protein_597185..597415_POSITIVE 198 46 2 53 2 NC_002967:TDE0565|5end_hypothetical_protein_597031..597261_POSITIVE 195 16 2 98 84 NC_002967:TDE0951|5end_lipoprotein,_putative_974252..974482_POSITIVE 190 150 111 73 33 NC_002967:TDE2448|5end_hypothetical_protein_2477417..2477647_NEGATIVE 187 145 112 53 22 NC_002967:TDE1190|5end_hypothetical_protein_1218223..1218453_POSITIVE 181 45 2 83 41 NC_002967:TDE0940|5end_hypothetical_protein_963136..963366_POSITIVE 180 41 1 61 22 NC_002967:TDE0256|5end_hypothetical_protein_291440..291670_NEGATIVE 177 66 40 106 75 NC_002967:TDE1564|5end_hypothetical_protein_1616502..1616732_POSITIVE 176 52 11 90 42 NC_002967:TDE0139|5end_hypothetical_protein_162583..162813_NEGATIVE 173 147 113 157 123 NC_002967:TDE2498|5end_metallo-beta-lactamase_family_protein_2522961..2523191_NEGATIVE 173 31 2 57 35 NC_002967:TDE1862|5end_hypothetical_protein_1886928..1887158_POSITIVE 173 60 11 103 47 NC_002967:TDE1598|5end_ABC_transporter,_ATP-binding_protein_1648910..1649140_NEGATIVE 172 148 116 75 43 NC_002967:TDE1663|5end_OmpA_family_protein_1717319..1717549_POSITIVE 170 28 2 136 102 NC_002967:TDE2756|5end_bacterial_extracellular_solute-binding_protein,_family_5_2813517..2813747_NEGATIVE 170 43 2 32 3 NC_002967:TDE2557|5end_hypothetical_protein_2583383..2583613_NEGATIVE 170 42 1 67 34 NC_002967:TDE2091|5end_amino_acid_ABC_transporter,_amino_acid-binding_protein,_putative_2118713..2118943_POSITIVE 170 44 13 54 23 NC_002967:TDE2012|5end_hypothetical_protein_2034351..2034581_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 185 43 1 149 109 NC_002967:TDE1434|3end_hypothetical_protein_1478238..1478388_NEGATIVE 181 45 2 81 39 NC_002967:TDE0939|3end_lipoprotein,_putative_963214..963364_POSITIVE 177 66 40 37 6 NC_002967:TDE1563|3end_hypothetical_protein_1616513..1616663_POSITIVE 173 60 11 93 37 NC_002967:TDE1599|3end_ABC_transporter,_ATP-binding/permease_protein_1648920..1649070_NEGATIVE 170 44 13 46 15 NC_002967:TDE2013|3end_hypothetical_protein_2034359..2034509_NEGATIVE 166 70 40 113 77 NC_002967:TDE0635|3end_hypothetical_protein_670578..670728_POSITIVE 165 43 2 68 34 NC_002967:TDE0759|3end_hypothetical_protein_799128..799278_NEGATIVE 164 148 115 61 22 NC_002967:TDE2298|3end_galactokinase,_putative_2337113..2337263_NEGATIVE 161 16 1 56 40 NC_002967:TDE2062|3end_hypothetical_protein_2087802..2087952_NEGATIVE 160 44 1 56 23 NC_002967:TDE1284|3end_methyl-accepting_chemotaxis_protein,_putative_1320923..1321073_POSITIVE 158 145 111 46 6 NC_002967:TDE1316|3end_hypothetical_protein_1355024..1355174_POSITIVE 157 51 15 104 66 NC_002967:TDE2352|3end_flagellar_hook-associated_protein_2389186..2389336_POSITIVE 154 129 84 124 86 NC_002967:TDE1341|3end_hypothetical_protein_1378525..1378675_POSITIVE 154 66 34 121 88 NC_002967:TDE1117|3end_hypothetical_protein_1149871..1150021_POSITIVE 152 114 89 85 60 NC_002967:TDE2356|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2392098..2392248_POSITIVE 152 63 21 128 91 NC_002967:TDE1412|3end_sodium/hydrogen_exchanger_family_protein_1455266..1455416_POSITIVE 152 117 87 35 3 NC_002967:TDE0221|3end_hypothetical_protein_254046..254196_NEGATIVE 151 44 1 64 21 NC_002967:TDE2487|3end_acetyltransferase,_GNAT_family_2510393..2510543_POSITIVE 150 70 40 40 6 NC_002967:TDE2249|3end_phospho-N-acetylmuramoyl-pentapeptide-_transferase_2287498..2287648_NEGATIVE 149 103 62 137 99 NC_002967:TDE0893|3end_ABC_transporter,_ATP-binding_protein_910451..910601_POSITIVE