Origin IGS: tttgtacctcctttatttaatcgcttaatgattaaacgtcttaactatatgctactatcataatgctctgttgtcaaggccaaaatagaaaaaaaatagaactttttgtaataaatttatacgcttttcatttgtgatgagctttaccggtatttttcagatgattgatattatcaaagtccaaaaaaaatactttattttataaaaatattgataaaagcgctcttttatctttacatttattagaaaatggtttatatttactattaagatgggatatagagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actctatatcccatcttaatagtaaatataaaccattttctaataaatgtaaagataaaagagcgcttttatcaatatttttataaaataaagtattttttttggactttgataatatcaatcatctgaaaaataccggtaaagctcatcacaaatgaaaagcgtataaatttattacaaaaagttctattttttttctattttggccttgacaacagagcattatgatagtagcatatagttaagacgtttaatcattaagcgattaaataaaggaggtacaaa Mask Tandem Repeat Region ================================================ tttgtacctcctttatttaatcgcttaatgattaaacgtcttaactatatgctactatcataatgctctgttgtcaaggccaaaatagaaaaaaaatagaactttttgtaataaatttatacgcttttcatttgtgatgagctttaccggtatttttcagatgattgatattatcaaagtccaaaaaaaatactttattttataaaaatattgataaaagcgctcttttatctttacatttattagaaaatggtttatatttactattaagatgggatatagagt Find is-nt database================================================ Query_seq: TDE0816:TDE0817|TDE0816:TDE0817:peptidase, M20/M25/M40 family:histidine kinase-related ATPase, putative:<-->:838655..838939 285 tttgtacctcctttatttaatcgcttaatgattaaacgtcttaactatatgctactatcataatgctctgttgtcaaggccaaaatagaaaaaaaatagaactttttgtaataaatttatacgcttttcatttgtgatgagctttaccggtatttttcagatgattgatattatcaaagtccaaaaaaaatactttattttataaaaatattgataaaagcgctcttttatctttacatttattagaaaatggtttatatttactattaagatgggatatagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0816:TDE0817|TDE0816:TDE0817:peptidase, M20/M25/M40 family:histidine kinase-related ATPase, putative:<-->:838655..838939 285 tttgtacctcctttatttaatcgcttaatgattaaacgtcttaactatatgctactatcataatgctctgttgtcaaggccaaaatagaaaaaaaatagaactttttgtaataaatttatacgcttttcatttgtgatgagctttaccggtatttttcagatgattgatattatcaaagtccaaaaaaaatactttattttataaaaatattgataaaagcgctcttttatctttacatttattagaaaatggtttatatttactattaagatgggatatagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0816:TDE0817|TDE0816:TDE0817:peptidase, M20/M25/M40 family:histidine kinase-related ATPase, putative:<-->:838655..838939 285 tttgtacctcctttatttaatcgcttaatgattaaacgtcttaactatatgctactatcataatgctctgttgtcaaggccaaaatagaaaaaaaatagaactttttgtaataaatttatacgcttttcatttgtgatgagctttaccggtatttttcagatgattgatattatcaaagtccaaaaaaaatactttattttataaaaatattgataaaagcgctcttttatctttacatttattagaaaatggtttatatttactattaagatgggatatagagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgtacctcctttatttaatcgcttaatgattaaacgtcttaactatatgctactatcataatgctctgttgtcaaggccaaaatagaaaaaaaatagaactttttgtaataaatttatacgcttttcatttgtgatgagctttaccggtatttttcagatgattgatattatcaaagtccaaaaaaaatactttattttataaaaatattgataaaagcgctcttttatctttacatttattagaaaatggtttatatttactattaagatgggatatagagt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 165 End: 284 .................................................................................................................................................................... M I L S K S K K N T L F Y K N I D K S A L L S L H L L E N G L Y L L L R W D I E . Protein_Len: 38 Strand: - Start: 160 End: 273 ............................................................................................................................................................... I I S I I L T W F F Y K I K Y F Y Q Y F R E K I K V N I L F H N I N V I L M ............ Protein_Len: 31 Strand: - Start: 61 End: 153 ............................................................ L A R N D L G F Y F F F L V K Q L L N I R K E N T I L K V P M .................................................................................................................................... tttgtacctcctttatttaatcgcttaatgattaaacgtcttaactatatgctactatcataatgctctgttgtcaaggccaaaatagaaaaaaaatagaactttttgtaataaatttatacgcttttcatttgtgatgagctttaccggtatttttcagatgattgatattatcaaagtccaaaaaaaatactttattttataaaaatattgataaaagcgctcttttatctttacatttattagaaaatggtttatatttactattaagatgggatatagagt 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: 85 Start: 49 End: 78 ................................................CTTGACAACAGAGCATTATGATAGTAGCAT............................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 232 End: 261 .......................................................................................................................................................................................................................................CTTTACATTTATTAGAAAATGGTTTATATT........................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 210 End: 239 .................................................................................................................................................................................................................ATTGATAAAAGCGCTCTTTTATCTTTACAT.............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttgtacctcctttatttaatcgcttaatgattaaacgtcttaactatatgctactatcataatgctctgttgtcaaggccaaaatagaaaaaaaatagaactttttgtaataaatttatacgcttttcatttgtgatgagctttaccggtatttttcagatgattgatattatcaaagtccaaaaaaaatactttattttataaaaatattgataaaagcgctcttttatctttacatttattagaaaatggtttatatttactattaagatgggatatagagt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 75 HP_score: -8.0 Tail_Score: -3.93262 Start: 213 End: 232 Full_Region: TTTTATAAAAATATT GATAAAAG CGCT CTTTTATC TTTACATTTATTAGA ....................................................................................................................................................................................................................GATAAAAGCGCTCTTTTATC..................................................... Find igs database================================================ Query_seq: TDE0816:TDE0817|TDE0816:TDE0817:peptidase, M20/M25/M40 family:histidine kinase-related ATPase, putative:<-->:838655..838939 285 tttgtacctcctttatttaatcgcttaatgattaaacgtcttaactatatgctactatcataatgctctgttgtcaaggccaaaatagaaaaaaaatagaactttttgtaataaatttatacgcttttcatttgtgatgagctttaccggtatttttcagatgattgatattatcaaagtccaaaaaaaatactttattttataaaaatattgataaaagcgctcttttatctttacatttattagaaaatggtttatatttactattaagatgggatatagagt Intra-Species Hit: Count: 1 Min: 1 Max: 285 Len: 285 Subject: NC_002967_TDE0816_TDE0817|peptidase, M20/M25/M40 family:histidine kinase-related ATPase, putative|NEGATIVE:POSITIVE|[838655,838939]|285 HSP 1 e-value: 1.0E-131 bit: 470.0 Len: 285 Query Start:1 Query End:285 Subject Strand: POSITIVE Subject Start: 1 Subject End: 285 tttgtacctcctttatttaatcgcttaatgattaaacgtcttaactatatgctactatcataatgctctgttgtcaaggccaaaatagnnnnnnnntagaactttttgtaataaatttatacgcttttcatttgtgatgagctttaccggtatttttcagatgattgatattatcaaagtccnnnnnnnntactttattttataaaaatattgataaaagcgctcttttatctttacatttattagaaaatggtttatatttactattaagatgggatatagagt tttgtacctcctttatttaatcgcttaatgattaaacgtcttaactatatgctactatcataatgctctgttgtcaaggccaaaatagaaaaaaaatagaactttttgtaataaatttatacgcttttcatttgtgatgagctttaccggtatttttcagatgattgatattatcaaagtccaaaaaaaatactttattttataaaaatattgataaaagcgctcttttatctttacatttattagaaaatggtttatatttactattaagatgggatatagagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUACCUCCUUUAUUUAAUCGCUUAAUGAUUAAACGUCUUAACUAUAUGCUACUAUCAUAAUGCUCUGUUGUCAAGGCCAAAAUAGAAAAAAAAUAGAACUUUUUGUAAUAAAUUUAUACGCUUUUCAUUUGUGAUGAGCUUUACCGGUAUUUUUCAGAUGAUUGAUAUUAUCAAAGUCCAAAAAAAAUACUUUAUUUUAUAAAAAUAUUGAUAAAAGCGCUCUUUUAUCUUUACAUUUAUUAGAAAAUGGUUUAUAUUUACUAUUAAGAUGGGAUAUAGAGU ((((((..(((....((((((((.....))))))))((((((((..........((((......((..((....))..))....)))).....((((((((((((((.(((((((((((((.((((.(((....))).))))......(((((((((..(((..(((((...))))).)))....)))))))))......))))))..((..((((((((....))))))))..))..))))))).)))).))))).)))))....))))))))))))))))).. (-48.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCUAUAUCCCAUCUUAAUAGUAAAUAUAAACCAUUUUCUAAUAAAUGUAAAGAUAAAAGAGCGCUUUUAUCAAUAUUUUUAUAAAAUAAAGUAUUUUUUUUGGACUUUGAUAAUAUCAAUCAUCUGAAAAAUACCGGUAAAGCUCAUCACAAAUGAAAAGCGUAUAAAUUUAUUACAAAAAGUUCUAUUUUUUUUCUAUUUUGGCCUUGACAACAGAGCAUUAUGAUAGUAGCAUAUAGUUAAGACGUUUAAUCAUUAAGCGAUUAAAUAAAGGAGGUACAAA .((((........(((((((.((((......(((........(((((.(((..((((((((....))))))))..))).)))))........(((((((((..(((..(((((...)))))...)))))))))))).)))...(((..(((....)))..)))...........)))).....((((((((......((...(((.......)))...))......))))).))).....))))))).((((((((.......))))))))...))))....... (-47.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 819 80 31 171 122 NC_002967:TDE0816|5end_peptidase,_M20/M25/M40_family_838564..838794_NEGATIVE 282 80 34 53 1 NC_002967:TDE1139|5end_hypothetical_protein_1168615..1168845_NEGATIVE 266 170 121 230 180 NC_002967:TDE1149|5end_hypothetical_protein_1187388..1187618_NEGATIVE 266 156 117 94 54 NC_002967:TDE0689|5end_5-methylthioribose_kinase_725690..725920_POSITIVE 259 163 122 121 82 NC_002967:TDE1895|5end_GTP-binding_protein_Era_1914963..1915193_POSITIVE 251 86 55 117 85 NC_002967:TDE2622|5end_ABC_transporter,_ATP-binding_protein_2663590..2663820_NEGATIVE 237 167 122 201 152 NC_002967:TDE2130|5end_hypothetical_protein_2162059..2162289_NEGATIVE 228 158 122 200 149 NC_002967:TDE2537|5end_hypothetical_protein_2563266..2563496_POSITIVE 227 163 136 156 135 NC_002967:TDE0908|5end_ABC_transporter,_ATP-binding/permease_protein_925254..925484_POSITIVE 224 110 67 58 17 NC_002967:TDE2497|5end_hypothetical_protein_2522083..2522313_NEGATIVE 220 152 121 162 132 NC_002967:TDE0057|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_65935..66165_POSITIVE 217 80 37 130 89 NC_002967:TDE2545|5end_hypothetical_protein_2571814..2572044_NEGATIVE 217 158 118 107 64 NC_002967:TDE1878|5end_hydrolase,_haloacid_dehalogenase-like_family_1900745..1900975_NEGATIVE 216 163 121 195 152 NC_002967:TDE2397|5end_hypothetical_protein_2425564..2425794_NEGATIVE 216 80 31 94 47 NC_002967:TDE1962|5end_hypothetical_protein_1975204..1975434_NEGATIVE 215 158 121 196 159 NC_002967:TDE1978|5end_hypothetical_protein_1991758..1991988_NEGATIVE 214 168 122 197 139 NC_002967:TDE1020|5end_dicarboxylate_transporter,_periplasmic_dicarboxylate-binding_protein,_putative_1052593..1052823_NEGATIVE 213 89 47 47 9 NC_002967:TDE0803|5end_hypothetical_protein_825317..825547_POSITIVE 212 180 133 94 40 NC_002967:TDE1753|5end_UDP-glucose_4-epimerase_1806540..1806770_NEGATIVE 212 82 43 90 43 NC_002967:TDE1507|5end_L-serine_dehydratase,_iron-sulfur-dependent,_beta_subunit_1555724..1555954_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 156 117 81 41 NC_002967:TDE0688|3end_hypothetical_protein_725757..725907_POSITIVE 259 163 122 119 80 NC_002967:TDE1894|3end_ferredoxin_1915041..1915191_POSITIVE 251 86 55 123 91 NC_002967:TDE2623|3end_hypothetical_protein_2663584..2663734_NEGATIVE 227 163 136 142 121 NC_002967:TDE0907|3end_hypothetical_protein_925320..925470_POSITIVE 220 152 121 139 109 NC_002967:TDE0056|3end_DNA-directed_RNA_polymerase,_omega_subunit,_putative_65992..66142_POSITIVE 219 160 112 144 92 NC_002967:TDE1684|3end_adenine_phosphoribosyltransferase_1736755..1736905_NEGATIVE 217 80 37 67 26 NC_002967:TDE2546|3end_hypothetical_protein_2571877..2572027_NEGATIVE 213 161 127 138 106 NC_002967:TDE0920|3end_transcriptional_regulator,_AraC_family_939100..939250_NEGATIVE 212 152 113 102 60 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 212 80 38 117 82 NC_002967:TDE0772|3end_50S_ribosomal_protein_L22_809520..809670_POSITIVE 212 70 21 139 78 NC_002967:TDE0697|3end_hypothetical_protein_734220..734370_NEGATIVE 210 187 141 147 95 NC_002967:TDE1689|3end_ABC_transporter,_ATP-binding_protein_1745807..1745957_NEGATIVE 209 90 56 137 106 NC_002967:TDE2497|3end_hypothetical_protein_2521982..2522132_NEGATIVE 209 166 125 73 30 NC_002967:TDE0253|3end_hypothetical_protein_288725..288875_POSITIVE 206 165 123 129 85 NC_002967:TDE1733|3end_methionine_aminopeptidase,_type_I_1788679..1788829_POSITIVE 205 168 125 132 84 NC_002967:TDE0055|3end_flagellar_biosynthesis_protein_65741..65891_POSITIVE 204 41 6 36 1 NC_002967:TDE2711|3end_hypothetical_protein_2768991..2769141_POSITIVE 204 167 122 57 17 NC_002967:TDE2631|3end_peptide_ABC_transporter,_permease_protein,_putative_2672733..2672883_POSITIVE 203 159 123 151 125 NC_002967:TDE2637|3end_hypothetical_protein_2676792..2676942_NEGATIVE 203 243 219 114 93 NC_002967:TDE2425|3end_50S_ribosomal_protein_L11_2454719..2454869_NEGATIVE