Origin IGS: tcttttcctctgattgtttatttacggattccggcaaaacacaatatttcgccgttaataaaaaatagcaatgttatttttagtatatataatttctttttgattgtcaagatagcggtgttattttttaatatttaaggaaaatgatgtctctgcaattatagacttacattaatatattttagttactaaaacatattgacaaaaaaagtattttgatgtatatttattttagcaactaaaagaaaaaggaaggcttattttagacaatgcagttggcattgtctaaaaacgctgcgagtttgcttacgcaaacgtcgctttattgattgcactttttcatttcattgcaaaagtgcggcaattcgccaatcctcgccttttgataaaggctgcggttgtcgaattttaagggagatata .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tatatctcccttaaaattcgacaaccgcagcctttatcaaaaggcgaggattggcgaattgccgcacttttgcaatgaaatgaaaaagtgcaatcaataaagcgacgtttgcgtaagcaaactcgcagcgtttttagacaatgccaactgcattgtctaaaataagccttcctttttcttttagttgctaaaataaatatacatcaaaatactttttttgtcaatatgttttagtaactaaaatatattaatgtaagtctataattgcagagacatcattttccttaaatattaaaaaataacaccgctatcttgacaatcaaaaagaaattatatatactaaaaataacattgctattttttattaacggcgaaatattgtgttttgccggaatccgtaaataaacaatcagaggaaaaga Mask Tandem Repeat Region ================================================ tcttttcctctgattgtttatttacggattccggcaaaacacaatatttcgccgttaataaaaaatagcaatgttatttttagtatatataatttctttttgattgtcaagatagcggtgttattttttaatatttaaggaaaatgatgtctctgcaattatagacttacattaatatattttagttactaaaacatattgacaaaaaaagtattttgatgtatatttattttagcaactaaaagaaaaaggaaggcttattttagacaatgcagttggcattgtctaaaaacgctgcgagtttgcttacgcaaacgtcgctttattgattgcactttttcatttcattgcaaaagtgcggcaattcgccaatcctcgccttttgataaaggctgcggttgtcgaattttaagggagatata Find is-nt database================================================ Query_seq: TDE0258:TDE0259|TDE0258:TDE0259:methlytransferase, UbiE/COQ5 family:transcriptional regulator, MarR family:<-->:292975..293396 422 tcttttcctctgattgtttatttacggattccggcaaaacacaatatttcgccgttaataaaaaatagcaatgttatttttagtatatataatttctttttgattgtcaagatagcggtgttattttttaatatttaaggaaaatgatgtctctgcaattatagacttacattaatatattttagttactaaaacatattgacaaaaaaagtattttgatgtatatttattttagcaactaaaagaaaaaggaaggcttattttagacaatgcagttggcattgtctaaaaacgctgcgagtttgcttacgcaaacgtcgctttattgattgcactttttcatttcattgcaaaagtgcggcaattcgccaatcctcgccttttgataaaggctgcggttgtcgaattttaagggagatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0258:TDE0259|TDE0258:TDE0259:methlytransferase, UbiE/COQ5 family:transcriptional regulator, MarR family:<-->:292975..293396 422 tcttttcctctgattgtttatttacggattccggcaaaacacaatatttcgccgttaataaaaaatagcaatgttatttttagtatatataatttctttttgattgtcaagatagcggtgttattttttaatatttaaggaaaatgatgtctctgcaattatagacttacattaatatattttagttactaaaacatattgacaaaaaaagtattttgatgtatatttattttagcaactaaaagaaaaaggaaggcttattttagacaatgcagttggcattgtctaaaaacgctgcgagtttgcttacgcaaacgtcgctttattgattgcactttttcatttcattgcaaaagtgcggcaattcgccaatcctcgccttttgataaaggctgcggttgtcgaattttaagggagatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0258:TDE0259|TDE0258:TDE0259:methlytransferase, UbiE/COQ5 family:transcriptional regulator, MarR family:<-->:292975..293396 422 tcttttcctctgattgtttatttacggattccggcaaaacacaatatttcgccgttaataaaaaatagcaatgttatttttagtatatataatttctttttgattgtcaagatagcggtgttattttttaatatttaaggaaaatgatgtctctgcaattatagacttacattaatatattttagttactaaaacatattgacaaaaaaagtattttgatgtatatttattttagcaactaaaagaaaaaggaaggcttattttagacaatgcagttggcattgtctaaaaacgctgcgagtttgcttacgcaaacgtcgctttattgattgcactttttcatttcattgcaaaagtgcggcaattcgccaatcctcgccttttgataaaggctgcggttgtcgaattttaagggagatata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcttttcctctgattgtttatttacggattccggcaaaacacaatatttcgccgttaataaaaaatagcaatgttatttttagtatatataatttctttttgattgtcaagatagcggtgttattttttaatatttaaggaaaatgatgtctctgcaattatagacttacattaatatattttagttactaaaacatattgacaaaaaaagtattttgatgtatatttattttagcaactaaaagaaaaaggaaggcttattttagacaatgcagttggcattgtctaaaaacgctgcgagtttgcttacgcaaacgtcgctttattgattgcactttttcatttcattgcaaaagtgcggcaattcgccaatcctcgccttttgataaaggctgcggttgtcgaattttaagggagatata Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 10 End: 135 ......... M I V Y L R I P A K H N I S P L I K N S N V I F S I Y N F F L I V K I A V L F F N I ............................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 223 End: 420 .............................................................................................................................................................................................................................. M F I L A T K R K R K A Y F R Q C S W H C L K T L R V C L R K R R F I D C T F S F H C K S A A I R Q S S P F D K G C G C .. Protein_Len: 32 Strand: - Start: 326 End: 421 ..................................................................................................................................................................................................................................................................................................................................... Q N C K K M E N C F H P L E G I R A K Q Y L S R N D F K L P S M . Protein_Len: 38 Strand: - Start: 21 End: 134 .................... K R I G A F C L I E G N I F F L L T I K L I Y L K K K I T L I A T N N K L M ................................................................................................................................................................................................................................................................................................ tcttttcctctgattgtttatttacggattccggcaaaacacaatatttcgccgttaataaaaaatagcaatgttatttttagtatatataatttctttttgattgtcaagatagcggtgttattttttaatatttaaggaaaatgatgtctctgcaattatagacttacattaatatattttagttactaaaacatattgacaaaaaaagtattttgatgtatatttattttagcaactaaaagaaaaaggaaggcttattttagacaatgcagttggcattgtctaaaaacgctgcgagtttgcttacgcaaacgtcgctttattgattgcactttttcatttcattgcaaaagtgcggcaattcgccaatcctcgccttttgataaaggctgcggttgtcgaattttaagggagatata 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: 90 Start: 198 End: 227 .....................................................................................................................................................................................................ATTGACAAAAAAAGTATTTTGATGTATATT................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 82 End: 111 .................................................................................CTTGACAATCAAAAAGAAATTATATATACT....................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 260 End: 289 ...................................................................................................................................................................................................................................................................TTAGACAATGCCAACTGCATTGTCTAAAAT..................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 103 End: 132 ......................................................................................................ATTGTCAAGATAGCGGTGTTATTTTTTAAT.................................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcttttcctctgattgtttatttacggattccggcaaaacacaatatttcgccgttaataaaaaatagcaatgttatttttagtatatataatttctttttgattgtcaagatagcggtgttattttttaatatttaaggaaaatgatgtctctgcaattatagacttacattaatatattttagttactaaaacatattgacaaaaaaagtattttgatgtatatttattttagcaactaaaagaaaaaggaaggcttattttagacaatgcagttggcattgtctaaaaacgctgcgagtttgcttacgcaaacgtcgctttattgattgcactttttcatttcattgcaaaagtgcggcaattcgccaatcctcgccttttgataaaggctgcggttgtcgaattttaagggagatata Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -6.8 Tail_Score: -4.02606 Start: 255 End: 296 Full_Region: cgtaagcaaactcgc agcgtttttagacaatgc caact gcattgtctaaaataagcc ttcctttttctttta ..............................................................................................................................................................................................................................................................agcgtttttagacaatgccaactgcattgtctaaaataagcc.............................................................................................................................. TransTerm Strand: - Conf: 79 HP_score: -10.3 Tail_Score: -2.99123 Start: 256 End: 295 Full_Region: gtaagcaaactcgca gcgtttttagacaatgc caact gcattgtctaaaataagc cttcctttttctttt ...............................................................................................................................................................................................................................................................gcgtttttagacaatgccaactgcattgtctaaaataagc............................................................................................................................... TransTerm Strand: + Conf: 89 HP_score: -9.4 Tail_Score: -4.32951 Start: 297 End: 321 Full_Region: TTGTCTAAAAACGCT GCGAGTTTGC TTAC GCAAACGTCGC TTTATTGATTGCACT ........................................................................................................................................................................................................................................................................................................GCGAGTTTGCTTACGCAAACGTCGC..................................................................................................... TransTerm Strand: + Conf: 75 HP_score: -7.3 Tail_Score: -4.08394 Start: 365 End: 406 Full_Region: GCAAAAGTGCGGCAA TTCGCCAATCCTCGCCTTT TGAT AAAGGCTGCGGTTGTCGAA TTTTAAGGGAGATAT ............................................................................................................................................................................................................................................................................................................................................................................TTCGCCAATCCTCGCCTTTTGATAAAGGCTGCGGTTGTCGAA................ Find igs database================================================ Query_seq: TDE0258:TDE0259|TDE0258:TDE0259:methlytransferase, UbiE/COQ5 family:transcriptional regulator, MarR family:<-->:292975..293396 422 tcttttcctctgattgtttatttacggattccggcaaaacacaatatttcgccgttaataaaaaatagcaatgttatttttagtatatataatttctttttgattgtcaagatagcggtgttattttttaatatttaaggaaaatgatgtctctgcaattatagacttacattaatatattttagttactaaaacatattgacaaaaaaagtattttgatgtatatttattttagcaactaaaagaaaaaggaaggcttattttagacaatgcagttggcattgtctaaaaacgctgcgagtttgcttacgcaaacgtcgctttattgattgcactttttcatttcattgcaaaagtgcggcaattcgccaatcctcgccttttgataaaggctgcggttgtcgaattttaagggagatata Intra-Species Hit: Count: 1 Min: 1 Max: 422 Len: 422 Subject: NC_002967_TDE0258_TDE0259|methlytransferase, UbiE/COQ5 family:transcriptional regulator, MarR family|NEGATIVE:POSITIVE|[292975,293396]|422 HSP 1 e-value: 0.0 bit: 795.0 Len: 422 Query Start:1 Query End:422 Subject Strand: POSITIVE Subject Start: 1 Subject End: 422 tcttttcctctgattgtttatttacggattccggcaaaacacaatatttcgccgttaataaaaaatagcaatgttatttttagtatatataatttctttttgattgtcaagatagcggtgttattttttaatatttaaggaaaatgatgtctctgcaattatagacttacattaatatattttagttactaaaacatattgacnnnnnnngtattttgatgtatatttattttagcaactaaaagaaaaaggaaggcttattttagacaatgcagttggcattgtctaaaaacgctgcgagtttgcttacgcaaacgtcgctttattgattgcactttttcatttcattgcaaaagtgcggcaattcgccaatcctcgccttttgataaaggctgcggttgtcgaattttaagggagatata tcttttcctctgattgtttatttacggattccggcaaaacacaatatttcgccgttaataaaaaatagcaatgttatttttagtatatataatttctttttgattgtcaagatagcggtgttattttttaatatttaaggaaaatgatgtctctgcaattatagacttacattaatatattttagttactaaaacatattgacaaaaaaagtattttgatgtatatttattttagcaactaaaagaaaaaggaaggcttattttagacaatgcagttggcattgtctaaaaacgctgcgagtttgcttacgcaaacgtcgctttattgattgcactttttcatttcattgcaaaagtgcggcaattcgccaatcctcgccttttgataaaggctgcggttgtcgaattttaagggagatata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUUCCUCUGAUUGUUUAUUUACGGAUUCCGGCAAAACACAAUAUUUCGCCGUUAAUAAAAAAUAGCAAUGUUAUUUUUAGUAUAUAUAAUUUCUUUUUGAUUGUCAAGAUAGCGGUGUUAUUUUUUAAUAUUUAAGGAAAAUGAUGUCUCUGCAAUUAUAGACUUACAUUAAUAUAUUUUAGUUACUAAAACAUAUUGACAAAAAAAGUAUUUUGAUGUAUAUUUAUUUUAGCAACUAAAAGAAAAAGGAAGGCUUAUUUUAGACAAUGCAGUUGGCAUUGUCUAAAAACGCUGCGAGUUUGCUUACGCAAACGUCGCUUUAUUGAUUGCACUUUUUCAUUUCAUUGCAAAAGUGCGGCAAUUCGCCAAUCCUCGCCUUUUGAUAAAGGCUGCGGUUGUCGAAUUUUAAGGGAGAUAUA ..(((((((..(((.................((((.(((.......))).))))....((((((((((((.(((((((((........((((((.......)))))).))))))))).))))))))))))..)))..)))))))..((((((((......(((((..((((((((.(((((((.((((.((.....)).))))....))))))).))))))))..)))))((..((((((.........((((.(((...(((((((((((((.....))))))))))))).....((((((((((....)))))).))))...((((.((((((((((.((......)).))))))))))))))..)))..)))).((((((....))))))...))))))..)).......)))))))). (-114.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAUCUCCCUUAAAAUUCGACAACCGCAGCCUUUAUCAAAAGGCGAGGAUUGGCGAAUUGCCGCACUUUUGCAAUGAAAUGAAAAAGUGCAAUCAAUAAAGCGACGUUUGCGUAAGCAAACUCGCAGCGUUUUUAGACAAUGCCAACUGCAUUGUCUAAAAUAAGCCUUCCUUUUUCUUUUAGUUGCUAAAAUAAAUAUACAUCAAAAUACUUUUUUUGUCAAUAUGUUUUAGUAACUAAAAUAUAUUAAUGUAAGUCUAUAAUUGCAGAGACAUCAUUUUCCUUAAAUAUUAAAAAAUAACACCGCUAUCUUGACAAUCAAAAAGAAAUUAUAUAUACUAAAAAUAACAUUGCUAUUUUUUAUUAACGGCGAAAUAUUGUGUUUUGCCGGAAUCCGUAAAUAAACAAUCAGAGGAAAAGA ....((((......((((((.(((((...((((((....))))))..)).))).))))))...((((((((.((......)).))))))))....((((..((((.((((((....)))))))))).((..(((((((((((((.....)))))))))))))...))...........((((((((((((((((..((((....(((((......)))))...))))))))))))))))))))..))))..(((((........))))))))).....((((((((......(((((((((.((........(((.....))).((....))....................)).)))))))))....(((((((((.....))))))))).....................)))))))).. (-108.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 802 60 11 151 102 NC_002967:TDE0258|5end_methlytransferase,_UbiE/COQ5_family_292884..293114_NEGATIVE 691 308 261 165 118 NC_002967:TDE2522|5end_ABC_transporter,_ATP-binding_protein_2548098..2548328_POSITIVE 551 110 61 181 129 NC_002967:TDE0284|5end_hypothetical_protein_313428..313658_NEGATIVE 529 129 81 180 132 NC_002967:TDE0274|5end_ABC_transporter,_ATP-binding/permease_protein_306423..306653_NEGATIVE 485 110 61 164 112 NC_002967:TDE0339|5end_transcriptional_regulator,_TetR_family_377871..378101_POSITIVE 360 400 355 119 78 NC_002967:TDE2515|5end_hypothetical_protein_2542057..2542287_NEGATIVE 355 328 295 105 68 NC_002967:TDE1583|5end_hypothetical_protein_1631808..1632038_POSITIVE 342 320 271 224 174 NC_002967:TDE0609|5end_hypothetical_protein_646166..646396_NEGATIVE 335 320 272 74 24 NC_002967:TDE0389|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase,_beta_subunit,_putative_440008..440238_POSITIVE 332 399 357 166 132 NC_002967:TDE2624|5end_hypothetical_protein_2664905..2665135_NEGATIVE 323 398 354 168 124 NC_002967:TDE0957|5end_glycerophosphoryl_diester_phosphodiesterase_family_protein_980252..980482_POSITIVE 320 320 271 204 163 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 319 417 375 195 152 NC_002967:TDE0770|5end_50S_ribosomal_protein_L2_807952..808182_POSITIVE 316 415 375 51 9 NC_002967:TDE2618|5end_PHP_domain_protein_2659392..2659622_POSITIVE 313 290 249 137 90 NC_002967:TDE2521|5end_hypothetical_protein_2548074..2548304_NEGATIVE 312 398 357 152 113 NC_002967:TDE2197|5end_hypothetical_protein_2232848..2233078_NEGATIVE 310 335 294 226 181 NC_002967:TDE2489|5end_peptide_chain_release_factor_1_2512476..2512706_NEGATIVE 310 370 321 184 135 NC_002967:TDE1368|5end_hypothetical_protein_1409795..1410025_NEGATIVE 308 389 341 49 1 NC_002967:TDE2762|5end_flagellar_motor_switch_protein_FliY_2817744..2817974_NEGATIVE 305 339 293 196 136 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 485 110 61 77 25 NC_002967:TDE0338|3end_methyl-accepting_chemotaxis_protein-like_protein_377864..378014_POSITIVE 438 334 295 102 60 NC_002967:TDE1902|3end_hypothetical_protein_1922377..1922527_NEGATIVE 421 334 294 41 1 NC_002967:TDE2393|3end_hypothetical_protein_2422588..2422738_POSITIVE 361 335 294 66 14 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 349 400 355 135 96 NC_002967:TDE0341|3end_ribonucleotide-diphosphate_reductase_alpha_subunit_379589..379739_NEGATIVE 341 402 361 140 97 NC_002967:TDE1847|3end_hypothetical_protein_1875845..1875995_POSITIVE 334 399 354 100 56 NC_002967:TDE0353|3end_lipase/acylhydrolase,_GDSL_family_396743..396893_NEGATIVE 332 399 357 146 112 NC_002967:TDE2625|3end_ABC_transporter,_ATP-binding/permease_protein_2664925..2665075_NEGATIVE 317 321 297 34 9 NC_002967:TDE0610|3end_3-hydroxyacyl-CoA_dehydrogenase,_putative_646357..646507_NEGATIVE 312 398 357 98 59 NC_002967:TDE2198|3end_pyruvate-ferredoxin_oxidoreductase_2232902..2233052_NEGATIVE 308 389 341 56 8 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 306 333 293 66 26 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 299 379 331 60 13 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 297 400 356 73 28 NC_002967:TDE0340|3end_fructose-bisphosphate_aldolase_379606..379756_POSITIVE 293 404 361 141 102 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 293 332 297 40 1 NC_002967:TDE1277|3end_Fe-hydrogenase_large_subunit_family_protein_1312242..1312392_POSITIVE 293 320 271 85 45 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 292 337 293 99 51 NC_002967:TDE1658|3end_basic_membrane_protein,_putative_1707655..1707805_NEGATIVE 291 400 356 123 73 NC_002967:TDE0792|3end_ribosomal_protein_L17_819006..819156_POSITIVE 289 38 3 147 111 NC_002967:TDE0273|3end_ABC_transporter,_ATP-binding/permease_protein_302867..303017_NEGATIVE