Origin IGS: attcctaatcttcaatttataatcgttaacttatcccctgcttgaaaaaaaactttagtttgaatataatccaaaaataacttacaagttgctttggagtgcttaaaggt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acctttaagcactccaaagcaacttgtaagttatttttggattatattcaaactaaagttttttttcaagcaggggataagttaacgattataaattgaagattaggaat Mask Tandem Repeat Region ================================================ attcctaatcttcaatttataatcgttaacttatcccctgcttgaaaaaaaactttagtttgaatataatccaaaaataacttacaagttgctttggagtgcttaaaggt Find is-nt database================================================ Query_seq: TDE2324:TDE2325|TDE2324:TDE2325:DNA-binding response regulator:hypothetical protein:->->:2359982..2360091 110 attcctaatcttcaatttataatcgttaacttatcccctgcttgaaaaaaaactttagtttgaatataatccaaaaataacttacaagttgctttggagtgcttaaaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2324:TDE2325|TDE2324:TDE2325:DNA-binding response regulator:hypothetical protein:->->:2359982..2360091 110 attcctaatcttcaatttataatcgttaacttatcccctgcttgaaaaaaaactttagtttgaatataatccaaaaataacttacaagttgctttggagtgcttaaaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2324:TDE2325|TDE2324:TDE2325:DNA-binding response regulator:hypothetical protein:->->:2359982..2360091 110 attcctaatcttcaatttataatcgttaacttatcccctgcttgaaaaaaaactttagtttgaatataatccaaaaataacttacaagttgctttggagtgcttaaaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attcctaatcttcaatttataatcgttaacttatcccctgcttgaaaaaaaactttagtttgaatataatccaaaaataacttacaagttgctttggagtgcttaaaggt Predict ORF larger than 30AA ================================================ attcctaatcttcaatttataatcgttaacttatcccctgcttgaaaaaaaactttagtttgaatataatccaaaaataacttacaagttgctttggagtgcttaaaggt 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: 89 Start: 41 End: 70 ........................................CTTGAAAAAAAACTTTAGTTTGAATATAAT........................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attcctaatcttcaatttataatcgttaacttatcccctgcttgaaaaaaaactttagtttgaatataatccaaaaataacttacaagttgctttggagtgcttaaaggt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2324:TDE2325|TDE2324:TDE2325:DNA-binding response regulator:hypothetical protein:->->:2359982..2360091 110 attcctaatcttcaatttataatcgttaacttatcccctgcttgaaaaaaaactttagtttgaatataatccaaaaataacttacaagttgctttggagtgcttaaaggt Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_002967_TDE2324_TDE2325|DNA-binding response regulator:hypothetical protein|POSITIVE:POSITIVE|[2359982,2360091]|110 HSP 1 e-value: 6.0E-42 bit: 170.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 attcctaatcttcaatttataatcgttaacttatcccctgcttgnnnnnnnnctttagtttgaatataatccaaaaataacttacaagttgctttggagtgcttaaaggt attcctaatcttcaatttataatcgttaacttatcccctgcttgaaaaaaaactttagtttgaatataatccaaaaataacttacaagttgctttggagtgcttaaaggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCCUAAUCUUCAAUUUAUAAUCGUUAACUUAUCCCCUGCUUGAAAAAAAACUUUAGUUUGAAUAUAAUCCAAAAAUAACUUACAAGUUGCUUUGGAGUGCUUAAAGGU ...(((..........(((((.(((..((((.........................))))))).)))))((((((..(((((....))))).))))))........))). (-10.11) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUUUAAGCACUCCAAAGCAACUUGUAAGUUAUUUUUGGAUUAUAUUCAAACUAAAGUUUUUUUUCAAGCAGGGGAUAAGUUAACGAUUAUAAAUUGAAGAUUAGGAAU ..((((((....(((((((.((((....))))..)))))))(((((.((.(((....)))..((..(.....)..)).........)).))))).))))))......... (-12.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 224 44 1 115 73 NC_002967:TDE2662|5end_lipoprotein,_putative_2698650..2698880_NEGATIVE 220 45 6 123 81 NC_002967:TDE1094|5end_hypothetical_protein_1128065..1128295_POSITIVE 212 104 65 156 111 NC_002967:TDE2062|5end_hypothetical_protein_2088344..2088574_NEGATIVE 208 59 11 136 77 NC_002967:TDE0777|5end_50S_ribosomal_protein_L14_811109..811339_POSITIVE 200 108 85 40 11 NC_002967:TDE0985|5end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein,_putative_1011037..1011267_POSITIVE 196 42 4 80 25 NC_002967:TDE1158|5end_phage_terminase,_small_subunit,_putative_1194024..1194254_NEGATIVE 191 110 70 54 6 NC_002967:TDE0355|5end_hypothetical_protein_399005..399235_POSITIVE 189 44 17 187 165 NC_002967:TDE0953|5end_branched-chain_amino_acid_ABC_transporter,_permease_protein_976863..977093_POSITIVE 189 44 2 116 66 NC_002967:TDE0597|5end_hypothetical_protein_637212..637442_NEGATIVE 187 105 71 50 17 NC_002967:TDE2358|5end_hypothetical_protein_2394136..2394366_NEGATIVE 187 56 23 116 88 NC_002967:TDE2208|5end_conserved_hypothetical_protein_TIGR00486_2246733..2246963_POSITIVE 185 39 3 105 73 NC_002967:TDE1007|5end_flagellar_basal-body_rod_protein_FlgG_1031261..1031491_POSITIVE 185 49 9 217 173 NC_002967:TDE0388|5end_hypothetical_protein_439173..439403_POSITIVE 184 44 2 191 141 NC_002967:TDE1997|5end_hypothetical_protein_2014796..2015026_POSITIVE 184 45 2 177 130 NC_002967:TDE0822|5end_hypothetical_protein_844467..844697_POSITIVE 184 45 2 88 41 NC_002967:TDE0821|5end_hypothetical_protein_844378..844608_POSITIVE 183 44 8 149 111 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 183 49 1 113 67 NC_002967:TDE1927|5end_phenylalanyl-tRNA_synthetase_beta_subunit_1943984..1944214_POSITIVE 182 47 1 168 110 NC_002967:TDE1207|5end_DNA_processing_protein_DprA,_putative_1239236..1239466_POSITIVE 182 42 1 220 188 NC_002967:TDE1144|5end_hypothetical_protein_1182855..1183085_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 42 3 138 83 NC_002967:TDE1958|3end_surface_protein,_putative_1972309..1972459_NEGATIVE 224 44 1 149 107 NC_002967:TDE2663|3end_isoleucyl-tRNA_synthetase_2698616..2698766_NEGATIVE 220 45 6 136 94 NC_002967:TDE1093|3end_hypothetical_protein_1128158..1128308_POSITIVE 212 104 65 70 25 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 208 59 11 117 58 NC_002967:TDE0776|3end_ribosomal_protein_S17_811170..811320_POSITIVE 196 42 4 76 21 NC_002967:TDE1159|3end_hypothetical_protein_1194028..1194178_NEGATIVE 194 66 21 151 101 NC_002967:TDE1774|3end_hypothetical_protein_1817500..1817650_NEGATIVE 191 43 1 130 94 NC_002967:TDE1862|3end_hypothetical_protein_1887979..1888129_POSITIVE 185 39 3 83 51 NC_002967:TDE1006|3end_flagellar_basal-body_rod_protein_FlgG_1031319..1031469_POSITIVE 180 107 73 84 53 NC_002967:TDE2169|3end_hypothetical_protein_2201509..2201659_POSITIVE 180 108 81 130 104 NC_002967:TDE1352|3end_penicillin-binding_protein_1393633..1393783_POSITIVE 176 42 24 57 38 NC_002967:TDE2621|3end_hypothetical_protein_2662197..2662347_POSITIVE 176 110 88 28 11 NC_002967:TDE1204|3end_cell_division_protein_FtsZ_1237666..1237816_POSITIVE 174 50 5 87 34 NC_002967:TDE1157|3end_phage_terminase,_large_subunit,_putative_1192040..1192190_NEGATIVE 173 58 23 48 17 NC_002967:TDE2451|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2480955..2481105_POSITIVE 172 73 33 52 3 NC_002967:TDE0218|3end_hypothetical_protein_253367..253517_POSITIVE 171 45 24 30 9 NC_002967:TDE1840|3end_hypothetical_protein_1871324..1871474_NEGATIVE 171 103 78 116 87 NC_002967:TDE1491|3end_chemotaxis_protein_CheA_1537294..1537444_POSITIVE 168 42 1 111 81 NC_002967:TDE2007|3end_ABC_transporter,_ATP-binding/permease_protein_2028641..2028791_POSITIVE 167 102 70 50 21 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE