Origin IGS: actccaaaaatagtttagattgagacactctatatttattataatatattaatatttattaaaaaaaattacaagtagttgaggtaaatatataaaattttattgttatgtttgagcagtttcgtttaaaaactcattacggtagtttgagatattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatatctcaaactaccgtaatgagtttttaaacgaaactgctcaaacataacaataaaattttatatatttacctcaactacttgtaattttttttaataaatattaatatattataataaatatagagtgtctcaatctaaactatttttggagt Mask Tandem Repeat Region ================================================ actccaaaaatagtttagattgagacactctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncaagtagttgaggtaaatatataaaattttattgttatgtttgagcagtttcgtttaaaaactcattacggtagtttgagatattt Find is-nt database================================================ Query_seq: TDE0392:TDE0393|TDE0392:TDE0393:(R)-2-hydroxyglutaryl-CoA dehydratase, beta subunit, putative:transcriptional regulator, TetR family:<-<-:443115..443271 157 actccaaaaatagtttagattgagacactctatatttattataatatattaatatttattaaaaaaaattacaagtagttgaggtaaatatataaaattttattgttatgtttgagcagtttcgtttaaaaactcattacggtagtttgagatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0392:TDE0393|TDE0392:TDE0393:(R)-2-hydroxyglutaryl-CoA dehydratase, beta subunit, putative:transcriptional regulator, TetR family:<-<-:443115..443271 157 actccaaaaatagtttagattgagacactctatatttattataatatattaatatttattaaaaaaaattacaagtagttgaggtaaatatataaaattttattgttatgtttgagcagtttcgtttaaaaactcattacggtagtttgagatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0392:TDE0393|TDE0392:TDE0393:(R)-2-hydroxyglutaryl-CoA dehydratase, beta subunit, putative:transcriptional regulator, TetR family:<-<-:443115..443271 157 actccaaaaatagtttagattgagacactctatatttattataatatattaatatttattaaaaaaaattacaagtagttgaggtaaatatataaaattttattgttatgtttgagcagtttcgtttaaaaactcattacggtagtttgagatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actccaaaaatagtttagattgagacactctatatttattataatatattaatatttattaaaaaaaattacaagtagttgaggtaaatatataaaattttattgttatgtttgagcagtttcgtttaaaaactcattacggtagtttgagatattt Predict ORF larger than 30AA ================================================ actccaaaaatagtttagattgagacactctatatttattataatatattaatatttattaaaaaaaattacaagtagttgaggtaaatatataaaattttattgttatgtttgagcagtttcgtttaaaaactcattacggtagtttgagatattt 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: 46 End: 75 .............................................CTTGTAATTTTTTTTAATAAATATTAATAT.................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actccaaaaatagtttagattgagacactctatatttattataatatattaatatttattaaaaaaaattacaagtagttgaggtaaatatataaaattttattgttatgtttgagcagtttcgtttaaaaactcattacggtagtttgagatattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0392:TDE0393|TDE0392:TDE0393:(R)-2-hydroxyglutaryl-CoA dehydratase, beta subunit, putative:transcriptional regulator, TetR family:<-<-:443115..443271 157 actccaaaaatagtttagattgagacactctatatttattataatatattaatatttattaaaaaaaattacaagtagttgaggtaaatatataaaattttattgttatgtttgagcagtttcgtttaaaaactcattacggtagtttgagatattt Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: NC_002967_TDE0392_TDE0393|(R)-2-hydroxyglutaryl-CoA dehydratase, beta subunit, putative:transcriptional regulator, TetR family|NEGATIVE:NEGATIVE|[443115,443271]|157 HSP 1 e-value: 8.0E-70 bit: 264.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 actccaaaaatagtttagattgagacactctatatttattataatatattaatatttattnnnnnnnnttacaagtagttgaggtaaatatataaaattttattgttatgtttgagcagtttcgtttaaaaactcattacggtagtttgagatattt actccaaaaatagtttagattgagacactctatatttattataatatattaatatttattaaaaaaaattacaagtagttgaggtaaatatataaaattttattgttatgtttgagcagtttcgtttaaaaactcattacggtagtttgagatattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCCAAAAAUAGUUUAGAUUGAGACACUCUAUAUUUAUUAUAAUAUAUUAAUAUUUAUUAAAAAAAAUUACAAGUAGUUGAGGUAAAUAUAUAAAAUUUUAUUGUUAUGUUUGAGCAGUUUCGUUUAAAAACUCAUUACGGUAGUUUGAGAUAUUU .............(((((((.(((((.(((.((((.....((((.((.((((((((((((......(((((....)))))..))))))))).))).)).))))....))))..)))..))))))))))))..((((..((....)).))))...... (-20.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAUCUCAAACUACCGUAAUGAGUUUUUAAACGAAACUGCUCAAACAUAACAAUAAAAUUUUAUAUAUUUACCUCAACUACUUGUAAUUUUUUUUAAUAAAUAUUAAUAUAUUAUAAUAAAUAUAGAGUGUCUCAAUCUAAACUAUUUUUGGAGU ...........(((.(((.....(((((......((.((.((((..........((((....)))).................(((((((.....(((((....)))))...)))))))........)))))).)).....))))).....)))))) (-14.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 697 120 71 211 162 NC_002967:TDE0392|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase,_beta_subunit,_putative_443024..443254_NEGATIVE 232 129 93 46 8 NC_002967:TDE0971|5end_arginyl-tRNA_synthetase_995179..995409_POSITIVE 226 148 112 116 75 NC_002967:TDE1526|5end_hypothetical_protein_1570565..1570795_POSITIVE 212 149 105 218 181 NC_002967:TDE1474|5end_hypothetical_protein_1521353..1521583_NEGATIVE 204 45 2 135 100 NC_002967:TDE0839|5end_rhodanese-like_domain_protein_859341..859571_NEGATIVE 202 50 1 142 97 NC_002967:TDE1052|5end_rubredoxin_1078870..1079100_NEGATIVE 202 146 111 180 146 NC_002967:TDE0064|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_72651..72881_NEGATIVE 199 146 109 196 160 NC_002967:TDE1207|5end_DNA_processing_protein_DprA,_putative_1239236..1239466_POSITIVE 197 143 112 173 139 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 196 150 113 180 145 NC_002967:TDE1340|5end_ribosomal_5S_rRNA_E-loop_binding_protein_Ctc/L25/TL5_1376317..1376547_POSITIVE 194 150 103 137 70 NC_002967:TDE0736|5end_hypothetical_protein_775230..775460_NEGATIVE 193 150 101 162 112 NC_002967:TDE2453|5end_hypothetical_protein_2481437..2481667_POSITIVE 193 113 73 163 124 NC_002967:TDE0539|5end_hypothetical_protein_581136..581366_POSITIVE 190 93 64 218 183 NC_002967:TDE1307|5end_hypothetical_protein_1340954..1341184_POSITIVE 185 117 72 231 184 NC_002967:TDE2531|5end_hypothetical_protein_2558241..2558471_POSITIVE 185 141 101 94 52 NC_002967:TDE0906|5end_ABC_transporter,_ATP-binding_protein_923164..923394_POSITIVE 185 144 109 216 177 NC_002967:TDE0564|5end_hypothetical_protein_596285..596515_POSITIVE 182 145 103 212 173 NC_002967:TDE1498|5end_hypothetical_protein_1543669..1543899_POSITIVE 181 135 111 230 206 NC_002967:TDE0668|5end_FeS_assembly_protein_SufD_705759..705989_POSITIVE 179 142 103 33 6 NC_002967:TDE0622|5end_radical_SAM_domain_protein_655718..655948_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 227 148 104 115 71 NC_002967:TDE1706|3end_competence/damage-inducible_protein_CinA_1762175..1762325_NEGATIVE 226 148 112 125 84 NC_002967:TDE1525|3end_hypothetical_protein_1570654..1570804_POSITIVE 204 125 83 116 75 NC_002967:TDE1818|3end_hypothetical_protein_1852832..1852982_NEGATIVE 204 45 2 57 22 NC_002967:TDE0840|3end_hypothetical_protein_859419..859569_NEGATIVE 202 50 1 82 37 NC_002967:TDE1053|3end_lipoprotein,_putative_1078930..1079080_NEGATIVE 194 150 114 114 66 NC_002967:TDE0199|3end_hypothetical_protein_234199..234349_NEGATIVE 193 118 93 42 17 NC_002967:TDE0646|3end_hypothetical_protein_681242..681392_NEGATIVE 193 113 73 76 37 NC_002967:TDE0538|3end_hypothetical_protein_581129..581279_POSITIVE 192 144 110 151 115 NC_002967:TDE2217|3end_galactose/glucose-binding_lipoprotein_2256764..2256914_NEGATIVE 191 150 108 40 1 NC_002967:TDE1117|3end_hypothetical_protein_1149871..1150021_POSITIVE 185 141 101 78 36 NC_002967:TDE0905|3end_hypothetical_protein_923228..923378_POSITIVE 178 149 107 68 28 NC_002967:TDE1793|3end_hydrolase,_carbon-nitrogen_family_1829957..1830107_NEGATIVE 177 149 109 106 64 NC_002967:TDE1106|3end_translation_initiation_factor_IF-2_1138192..1138342_NEGATIVE 177 149 106 132 91 NC_002967:TDE0679|3end_aminotransferase,_class_V_717573..717723_POSITIVE 175 147 106 127 86 NC_002967:TDE2425|3end_50S_ribosomal_protein_L11_2454719..2454869_NEGATIVE 175 146 116 124 95 NC_002967:TDE2223|3end_hypothetical_protein_2264826..2264976_POSITIVE 175 148 101 125 83 NC_002967:TDE1497|3end_hypothetical_protein_1543704..1543854_POSITIVE 174 149 111 109 78 NC_002967:TDE2264|3end_ABC_transporter,_ATP-binding/permease_protein_2300243..2300393_NEGATIVE 174 139 108 49 20 NC_002967:TDE1492|3end_chemotaxis_protein_CheW_1538645..1538795_POSITIVE 174 149 108 113 59 NC_002967:TDE0272|3end_hypothetical_protein_302256..302406_NEGATIVE