Origin IGS: gttttaacctctcatacctttatgcattgacaaatagaaacattgcacatttatagtatattttgaaaaagtcgaattgtcaacctacttacctaaaatactttattaattattttcttccgattgtatttttgcaccttttttgatagaataggcaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgcctattctatcaaaaaaggtgcaaaaatacaatcggaagaaaataattaataaagtattttaggtaagtaggttgacaattcgactttttcaaaatatactataaatgtgcaatgtttctatttgtcaatgcataaaggtatgagaggttaaaac Mask Tandem Repeat Region ================================================ gttttaacctctcatacctttatgcattgacaaatagaaacattgcacatttatagtatattttgaaaaagtcgaattgtcaacctacttacctaaaatactttattaattattttcttccgattgtatttttgcaccttttttgatagaataggcaa Find is-nt database================================================ Query_seq: TDE0067:TDE0068|TDE0067:TDE0068:cyclic nucleotide-binding protein:succinyl-diaminopimelate desuccinylase:<-->:75279..75436 158 gttttaacctctcatacctttatgcattgacaaatagaaacattgcacatttatagtatattttgaaaaagtcgaattgtcaacctacttacctaaaatactttattaattattttcttccgattgtatttttgcaccttttttgatagaataggcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0067:TDE0068|TDE0067:TDE0068:cyclic nucleotide-binding protein:succinyl-diaminopimelate desuccinylase:<-->:75279..75436 158 gttttaacctctcatacctttatgcattgacaaatagaaacattgcacatttatagtatattttgaaaaagtcgaattgtcaacctacttacctaaaatactttattaattattttcttccgattgtatttttgcaccttttttgatagaataggcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0067:TDE0068|TDE0067:TDE0068:cyclic nucleotide-binding protein:succinyl-diaminopimelate desuccinylase:<-->:75279..75436 158 gttttaacctctcatacctttatgcattgacaaatagaaacattgcacatttatagtatattttgaaaaagtcgaattgtcaacctacttacctaaaatactttattaattattttcttccgattgtatttttgcaccttttttgatagaataggcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttttaacctctcatacctttatgcattgacaaatagaaacattgcacatttatagtatattttgaaaaagtcgaattgtcaacctacttacctaaaatactttattaattattttcttccgattgtatttttgcaccttttttgatagaataggcaa Predict ORF larger than 30AA ================================================ gttttaacctctcatacctttatgcattgacaaatagaaacattgcacatttatagtatattttgaaaaagtcgaattgtcaacctacttacctaaaatactttattaattattttcttccgattgtatttttgcaccttttttgatagaataggcaa 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: 88 Start: 55 End: 84 ......................................................GTTGACAATTCGACTTTTTCAAAATATACT.......................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 123 End: 152 ..........................................................................................................................ATTGTATTTTTGCACCTTTTTTGATAGAAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gttttaacctctcatacctttatgcattgacaaatagaaacattgcacatttatagtatattttgaaaaagtcgaattgtcaacctacttacctaaaatactttattaattattttcttccgattgtatttttgcaccttttttgatagaataggcaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0067:TDE0068|TDE0067:TDE0068:cyclic nucleotide-binding protein:succinyl-diaminopimelate desuccinylase:<-->:75279..75436 158 gttttaacctctcatacctttatgcattgacaaatagaaacattgcacatttatagtatattttgaaaaagtcgaattgtcaacctacttacctaaaatactttattaattattttcttccgattgtatttttgcaccttttttgatagaataggcaa Intra-Species Hit: Count: 1 Min: 1 Max: 158 Len: 158 Subject: NC_002967_TDE0067_TDE0068|cyclic nucleotide-binding protein:succinyl-diaminopimelate desuccinylase|NEGATIVE:POSITIVE|[75279,75436]|158 HSP 1 e-value: 9.0E-85 bit: 313.0 Len: 158 Query Start:1 Query End:158 Subject Strand: POSITIVE Subject Start: 1 Subject End: 158 gttttaacctctcatacctttatgcattgacaaatagaaacattgcacatttatagtatattttgaaaaagtcgaattgtcaacctacttacctaaaatactttattaattattttcttccgattgtatttttgcaccttttttgatagaataggcaa gttttaacctctcatacctttatgcattgacaaatagaaacattgcacatttatagtatattttgaaaaagtcgaattgtcaacctacttacctaaaatactttattaattattttcttccgattgtatttttgcaccttttttgatagaataggcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUAACCUCUCAUACCUUUAUGCAUUGACAAAUAGAAACAUUGCACAUUUAUAGUAUAUUUUGAAAAAGUCGAAUUGUCAACCUACUUACCUAAAAUACUUUAUUAAUUAUUUUCUUCCGAUUGUAUUUUUGCACCUUUUUUGAUAGAAUAGGCAA ((((....((.(((........(((.(((((((..........(((.........)))...(((((.....))))))))))))...........(((((((........................))))))).))).......))).))...)))).. (-13.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCCUAUUCUAUCAAAAAAGGUGCAAAAAUACAAUCGGAAGAAAAUAAUUAAUAAAGUAUUUUAGGUAAGUAGGUUGACAAUUCGACUUUUUCAAAAUAUACUAUAAAUGUGCAAUGUUUCUAUUUGUCAAUGCAUAAAGGUAUGAGAGGUUAAAAC ..((((.(((((((.......(((((.....((((..(((((......(((.(((..(((((((.((.....(((((((....)))))))..)))))))))..))).)))........)))))..))))...)))))...)))).)))))))...... (-24.64) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 781 50 1 141 92 NC_002967:TDE0067|5end_cyclic_nucleotide-binding_protein_75188..75418_NEGATIVE 239 140 99 114 62 NC_002967:TDE1843|5end_hypothetical_protein_1873005..1873235_NEGATIVE 226 88 41 150 94 NC_002967:TDE0889|5end_hypothetical_protein_905090..905320_POSITIVE 219 139 91 137 101 NC_002967:TDE1721|5end_radical_SAM_domain_protein_1775140..1775370_POSITIVE 215 44 9 135 99 NC_002967:TDE2608|5end_hypothetical_protein_2649275..2649505_POSITIVE 215 34 8 126 100 NC_002967:TDE1108|5end_hypothetical_protein_1142859..1143089_NEGATIVE 215 46 5 201 162 NC_002967:TDE0134|5end_oxidoreductase,_FAD-dependent_153404..153634_POSITIVE 214 138 91 216 170 NC_002967:TDE1442|5end_histidyl-tRNA_synthetase_1487416..1487646_POSITIVE 213 144 105 129 87 NC_002967:TDE2613|5end_hypothetical_protein_2655372..2655602_POSITIVE 212 83 44 167 128 NC_002967:TDE1670|5end_transcriptional_regulator,_MarR_family_1724461..1724691_NEGATIVE 211 30 7 67 47 NC_002967:TDE0052|5end_flagellar_biosynthetic_protein_FliQ_61305..61535_POSITIVE 206 46 10 49 10 NC_002967:TDE1328|5end_hypothetical_protein_1363402..1363632_NEGATIVE 205 47 7 149 103 NC_002967:TDE1209|5end_site-specific_recombinase,_phage_integrase_family_1242345..1242575_POSITIVE 203 150 101 158 101 NC_002967:TDE2624|5end_hypothetical_protein_2664905..2665135_NEGATIVE 202 68 23 84 39 NC_002967:TDE0539|5end_hypothetical_protein_581136..581366_POSITIVE 201 144 112 106 74 NC_002967:TDE0895|5end_transcriptional_regulator,_AraC_family_912174..912404_NEGATIVE 200 132 101 113 83 NC_002967:TDE2345|5end_ribosome_recycling_factor_2382503..2382733_NEGATIVE 198 150 106 146 84 NC_002967:TDE0709|5end_bifunctional_methionine_sulfoxide_reductase_A/B_protein_745434..745664_NEGATIVE 198 120 76 105 62 NC_002967:TDE0492|5end_sensor_histidine_kinase/response_regulator_547468..547698_POSITIVE 195 120 78 132 86 NC_002967:TDE2785|5end_hypothetical_protein_2839182..2839412_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 219 139 91 149 113 NC_002967:TDE1720|3end_radical_SAM_domain_protein_1775232..1775382_POSITIVE 215 44 9 114 78 NC_002967:TDE2607|3end_hypothetical_protein_2649334..2649484_POSITIVE 214 138 91 135 89 NC_002967:TDE1441|3end_dTDP-glucose_4,6-dehydratase_1487415..1487565_POSITIVE 213 144 105 136 94 NC_002967:TDE2612|3end_hypothetical_protein_2655459..2655609_POSITIVE 203 150 101 138 81 NC_002967:TDE2625|3end_ABC_transporter,_ATP-binding/permease_protein_2664925..2665075_NEGATIVE 198 120 76 105 62 NC_002967:TDE0491|3end_hypothetical_protein_547548..547698_POSITIVE 195 120 78 91 45 NC_002967:TDE2786|3end_DNA_polymerase_III_subunit_alpha_2839223..2839373_NEGATIVE 195 150 120 112 82 NC_002967:TDE1873|3end_hypothetical_protein_1894729..1894879_NEGATIVE 192 142 114 44 16 NC_002967:TDE2395|3end_Jag_protein,_putative_2422744..2422894_NEGATIVE 192 148 101 78 32 NC_002967:TDE2213|3end_hypothetical_protein_2253137..2253287_POSITIVE 187 106 71 116 68 NC_002967:TDE0591|3end_acetyl-CoA_carboxylase,_biotin_carboxylase_630033..630183_NEGATIVE 187 138 113 47 23 NC_002967:TDE0355|3end_hypothetical_protein_399657..399807_POSITIVE 187 139 100 50 5 NC_002967:TDE0277|3end_hypothetical_protein_308109..308259_NEGATIVE 182 102 68 61 28 NC_002967:TDE2671|3end_hypothetical_protein_2708143..2708293_NEGATIVE 182 58 11 121 83 NC_002967:TDE0630|3end_sigma_factor_regulatory_protein,_putative_665371..665521_POSITIVE 180 87 55 93 65 NC_002967:TDE1222|3end_iron-dependent_transcriptional_regulator_1256041..1256191_NEGATIVE 179 150 109 111 75 NC_002967:TDE0555|3end_hypothetical_protein_590983..591133_NEGATIVE 177 138 114 37 18 NC_002967:TDE1750|3end_hypothetical_protein_1803439..1803589_NEGATIVE 177 124 81 103 66 NC_002967:TDE1005|3end_hypothetical_protein_1030495..1030645_POSITIVE 175 140 92 150 107 NC_002967:TDE0969|3end_hypothetical_protein_994575..994725_POSITIVE