Origin IGS: aatgtttccttatatacagagaattattttctcccgggatctacatcacaaaaaattcggatttaaaaatctgtaaacttgagcacagataaaaatcaagagaatgaatttaaggtgagaattttataaagaaaattgatttgataaaatgcggtttataaagaacttccgggagtaaggtctttgccgcttgttaaaaataatactgtaatcatagagcacctcccataagttttaaaatttagtaaaaagacattaagctaaaataaagattttgtcaagcaggtattcttgcaaatagcaataccgat .........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 atcggtattgctatttgcaagaatacctgcttgacaaaatctttattttagcttaatgtctttttactaaattttaaaacttatgggaggtgctctatgattacagtattatttttaacaagcggcaaagaccttactcccggaagttctttataaaccgcattttatcaaatcaattttctttataaaattctcaccttaaattcattctcttgatttttatctgtgctcaagtttacagatttttaaatccgaattttttgtgatgtagatcccgggagaaaataattctctgtatataaggaaacatt Mask Tandem Repeat Region ================================================ aatgtttccttatatacagagaattattttctcccgggatctacatcacaaaaaattcggatttaaaaatctgtaaacttgagcacagataaaaatcaagagaatgaatttaaggtgagaattttataaagaaaattgatttgataaaatgcggtttataaagaacttccgggagtaaggtctttgccgcttgttaaaaataatactgtaatcatagagcacctcccataagttttaaaatttagtaaaaagacattaagctaaaataaagattttgtcaagcaggtattcttgcaaatagcaataccgat Find is-nt database================================================ Query_seq: TDE2727:TDE2728|TDE2727:TDE2728:GTPase YjeQ, putative:hypothetical protein:<-->:2785436..2785746 311 aatgtttccttatatacagagaattattttctcccgggatctacatcacaaaaaattcggatttaaaaatctgtaaacttgagcacagataaaaatcaagagaatgaatttaaggtgagaattttataaagaaaattgatttgataaaatgcggtttataaagaacttccgggagtaaggtctttgccgcttgttaaaaataatactgtaatcatagagcacctcccataagttttaaaatttagtaaaaagacattaagctaaaataaagattttgtcaagcaggtattcttgcaaatagcaataccgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2727:TDE2728|TDE2727:TDE2728:GTPase YjeQ, putative:hypothetical protein:<-->:2785436..2785746 311 aatgtttccttatatacagagaattattttctcccgggatctacatcacaaaaaattcggatttaaaaatctgtaaacttgagcacagataaaaatcaagagaatgaatttaaggtgagaattttataaagaaaattgatttgataaaatgcggtttataaagaacttccgggagtaaggtctttgccgcttgttaaaaataatactgtaatcatagagcacctcccataagttttaaaatttagtaaaaagacattaagctaaaataaagattttgtcaagcaggtattcttgcaaatagcaataccgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2727:TDE2728|TDE2727:TDE2728:GTPase YjeQ, putative:hypothetical protein:<-->:2785436..2785746 311 aatgtttccttatatacagagaattattttctcccgggatctacatcacaaaaaattcggatttaaaaatctgtaaacttgagcacagataaaaatcaagagaatgaatttaaggtgagaattttataaagaaaattgatttgataaaatgcggtttataaagaacttccgggagtaaggtctttgccgcttgttaaaaataatactgtaatcatagagcacctcccataagttttaaaatttagtaaaaagacattaagctaaaataaagattttgtcaagcaggtattcttgcaaatagcaataccgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatgtttccttatatacagagaattattttctcccgggatctacatcacaaaaaattcggatttaaaaatctgtaaacttgagcacagataaaaatcaagagaatgaatttaaggtgagaattttataaagaaaattgatttgataaaatgcggtttataaagaacttccgggagtaaggtctttgccgcttgttaaaaataatactgtaatcatagagcacctcccataagttttaaaatttagtaaaaagacattaagctaaaataaagattttgtcaagcaggtattcttgcaaatagcaataccgat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 127 End: 222 .............................................................................................................................. L S F Q N S L I R N I F F K R S Y P R Q R K N F I I S Y D Y L M ......................................................................................... aatgtttccttatatacagagaattattttctcccgggatctacatcacaaaaaattcggatttaaaaatctgtaaacttgagcacagataaaaatcaagagaatgaatttaaggtgagaattttataaagaaaattgatttgataaaatgcggtttataaagaacttccgggagtaaggtctttgccgcttgttaaaaataatactgtaatcatagagcacctcccataagttttaaaatttagtaaaaagacattaagctaaaataaagattttgtcaagcaggtattcttgcaaatagcaataccgat 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: 253 End: 282 ............................................................................................................................................................................................................................................................CTTGACAAAATCTTTATTTTAGCTTAATGT............................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 211 End: 240 ..................................................................................................................................................................................................................TTTTAAAACTTATGGGAGGTGCTCTATGAT....................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatgtttccttatatacagagaattattttctcccgggatctacatcacaaaaaattcggatttaaaaatctgtaaacttgagcacagataaaaatcaagagaatgaatttaaggtgagaattttataaagaaaattgatttgataaaatgcggtttataaagaacttccgggagtaaggtctttgccgcttgttaaaaataatactgtaatcatagagcacctcccataagttttaaaatttagtaaaaagacattaagctaaaataaagattttgtcaagcaggtattcttgcaaatagcaataccgat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 48 HP_score: -4.3 Tail_Score: -2.98823 Start: 19 End: 33 Full_Region: tgatgtagatcccgg gagaa aataa ttctc tgtatataaggaaac ..................gagaaaataattctc...................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TDE2727:TDE2728|TDE2727:TDE2728:GTPase YjeQ, putative:hypothetical protein:<-->:2785436..2785746 311 aatgtttccttatatacagagaattattttctcccgggatctacatcacaaaaaattcggatttaaaaatctgtaaacttgagcacagataaaaatcaagagaatgaatttaaggtgagaattttataaagaaaattgatttgataaaatgcggtttataaagaacttccgggagtaaggtctttgccgcttgttaaaaataatactgtaatcatagagcacctcccataagttttaaaatttagtaaaaagacattaagctaaaataaagattttgtcaagcaggtattcttgcaaatagcaataccgat Intra-Species Hit: Count: 1 Min: 1 Max: 311 Len: 311 Subject: NC_002967_TDE2727_TDE2728|GTPase YjeQ, putative:hypothetical protein|NEGATIVE:POSITIVE|[2785436,2785746]|311 HSP 1 e-value: 1.0E-175 bit: 617.0 Len: 311 Query Start:1 Query End:311 Subject Strand: POSITIVE Subject Start: 1 Subject End: 311 aatgtttccttatatacagagaattattttctcccgggatctacatcacaaaaaattcggatttaaaaatctgtaaacttgagcacagataaaaatcaagagaatgaatttaaggtgagaattttataaagaaaattgatttgataaaatgcggtttataaagaacttccgggagtaaggtctttgccgcttgttaaaaataatactgtaatcatagagcacctcccataagttttaaaatttagtaaaaagacattaagctaaaataaagattttgtcaagcaggtattcttgcaaatagcaataccgat aatgtttccttatatacagagaattattttctcccgggatctacatcacaaaaaattcggatttaaaaatctgtaaacttgagcacagataaaaatcaagagaatgaatttaaggtgagaattttataaagaaaattgatttgataaaatgcggtttataaagaacttccgggagtaaggtctttgccgcttgttaaaaataatactgtaatcatagagcacctcccataagttttaaaatttagtaaaaagacattaagctaaaataaagattttgtcaagcaggtattcttgcaaatagcaataccgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGUUUCCUUAUAUACAGAGAAUUAUUUUCUCCCGGGAUCUACAUCACAAAAAAUUCGGAUUUAAAAAUCUGUAAACUUGAGCACAGAUAAAAAUCAAGAGAAUGAAUUUAAGGUGAGAAUUUUAUAAAGAAAAUUGAUUUGAUAAAAUGCGGUUUAUAAAGAACUUCCGGGAGUAAGGUCUUUGCCGCUUGUUAAAAAUAAUACUGUAAUCAUAGAGCACCUCCCAUAAGUUUUAAAAUUUAGUAAAAAGACAUUAAGCUAAAAUAAAGAUUUUGUCAAGCAGGUAUUCUUGCAAAUAGCAAUACCGAU (((((((..((((.(((((...((((((((((((((((((((...((((...((((((((((((....((((((..........))))))..))))).......)))))))...))))..............((((((((((....)))).))))))....)))..)))))))))...(((....)))........)))))))).)))))....((((((...........)))))).......))))..)))))))..((((.......(((...)))..(((((....)))))...))))......... (-59.21) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGGUAUUGCUAUUUGCAAGAAUACCUGCUUGACAAAAUCUUUAUUUUAGCUUAAUGUCUUUUUACUAAAUUUUAAAACUUAUGGGAGGUGCUCUAUGAUUACAGUAUUAUUUUUAACAAGCGGCAAAGACCUUACUCCCGGAAGUUCUUUAUAAACCGCAUUUUAUCAAAUCAAUUUUCUUUAUAAAAUUCUCACCUUAAAUUCAUUCUCUUGAUUUUUAUCUGUGCUCAAGUUUACAGAUUUUUAAAUCCGAAUUUUUUGUGAUGUAGAUCCCGGGAGAAAAUAAUUCUCUGUAUAUAAGGAAACAUU ...((((.(((..((((((((........)))).)))).......................................(((((.((((((.((((.((....)).))))...............((......))...)))))).)))))...........)))...))))........((((((((((......((((...((((((........(((((..(((((((........)))))))....))))).))))))...))))...........((((((.....))))))...)))))))))).... (-52.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 816 50 1 141 92 NC_002967:TDE2727|5end_GTPase_YjeQ,_putative_2785345..2785575_NEGATIVE 299 189 146 77 30 NC_002967:TDE1384|5end_cadmium-translocating_P-type_ATPase_1422765..1422995_POSITIVE 296 194 152 58 8 NC_002967:TDE1265|5end_1-hydroxy-2-methyl-2-(E)-butenyl_4-diphosphate_synthase_1300436..1300666_NEGATIVE 294 189 149 218 168 NC_002967:TDE1096|5end_hydroxymethylbutenyl_pyrophosphate_reductase_1130989..1131219_POSITIVE 284 234 205 114 83 NC_002967:TDE1029|5end_Hsp20/alpha_crystallin_family_protein_1058574..1058804_POSITIVE 283 213 177 68 30 NC_002967:TDE0594|5end_cysteine_protease_domain,_YopT-type_634805..635035_NEGATIVE 282 189 144 59 12 NC_002967:TDE2554|5end_chaperonin,_33_kDa_family_2580745..2580975_POSITIVE 281 206 168 84 38 NC_002967:TDE1974|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1988910..1989140_NEGATIVE 280 50 8 90 50 NC_002967:TDE2740|5end_type_I_restriction-modification_system,_S_subunit,_truncation_2795202..2795432_POSITIVE 275 189 142 163 110 NC_002967:TDE0945|5end_hypothetical_protein_967128..967358_POSITIVE 274 190 150 214 180 NC_002967:TDE1143|5end_hypothetical_protein_1181834..1182064_NEGATIVE 272 195 152 202 165 NC_002967:TDE1485|5end_hypothetical_protein_1529697..1529927_POSITIVE 266 192 158 225 186 NC_002967:TDE0133|5end_transcriptional_regulator,_GntR_family_152373..152603_POSITIVE 264 187 152 118 82 NC_002967:TDE1084|5end_folylpolyglutamate_synthetase,_putative_1116286..1116516_NEGATIVE 264 189 148 70 35 NC_002967:TDE0408|5end_oxidoreductase,_NAD-binding_461372..461602_NEGATIVE 259 310 265 187 150 NC_002967:TDE2697|5end_3-oxo-5-alpha-steroid_4-dehydrogenase_family_protein_2740260..2740490_POSITIVE 258 206 162 81 33 NC_002967:TDE2460|5end_aminotransferase,_class_V_2485983..2486213_POSITIVE 257 189 155 126 87 NC_002967:TDE1308|5end_transketolase_1342463..1342693_POSITIVE 257 189 166 123 101 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 256 196 151 90 49 NC_002967:TDE2197|5end_hypothetical_protein_2232848..2233078_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 189 146 83 36 NC_002967:TDE1383|3end_hypothetical_protein_1422851..1423001_POSITIVE 286 191 151 51 12 NC_002967:TDE1980|3end_hypothetical_protein_1991960..1992110_NEGATIVE 284 234 205 121 90 NC_002967:TDE1028|3end_hypothetical_protein_1058661..1058811_POSITIVE 266 192 158 68 29 NC_002967:TDE0132|3end_hypothetical_protein_152296..152446_POSITIVE 265 200 151 47 4 NC_002967:TDE2248|3end_HesA/MoeB/ThiF_family_protein_2286756..2286906_NEGATIVE 259 189 143 70 25 NC_002967:TDE0933|3end_acetate_kinase_959336..959486_POSITIVE 257 189 155 104 65 NC_002967:TDE1307|3end_hypothetical_protein_1342521..1342671_POSITIVE 257 189 166 121 99 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 253 195 153 151 101 NC_002967:TDE2129|3end_hypothetical_protein_2161635..2161785_POSITIVE 253 195 153 74 24 NC_002967:TDE2128|3end_hypothetical_protein_2161558..2161708_POSITIVE 251 189 141 69 19 NC_002967:TDE0886|3end_hypothetical_protein_904374..904524_POSITIVE 249 189 150 87 45 NC_002967:TDE1905|3end_hypothetical_protein_1923722..1923872_NEGATIVE 248 195 152 55 14 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 247 225 186 60 11 NC_002967:TDE2200|3end_methionine_gamma-lyase_2237250..2237400_NEGATIVE 244 195 152 48 5 NC_002967:TDE2135|3end_hypothetical_protein_2165418..2165568_POSITIVE 243 213 183 35 3 NC_002967:TDE0595|3end_hypothetical_protein_634838..634988_NEGATIVE 242 227 184 104 70 NC_002967:TDE0104|3end_3-dehydroquinate_synthase_123683..123833_NEGATIVE 240 199 151 113 67 NC_002967:TDE0016|3end_ATPase,_AAA_family_21862..22012_POSITIVE 236 200 151 112 68 NC_002967:TDE2678|3end_alpha-amylase_family_protein_2715785..2715935_NEGATIVE 235 188 141 80 24 NC_002967:TDE1925|3end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1942605..1942755_POSITIVE