Origin IGS: ttaataatgattttaaattctaaaaaagaatatagcacaggagatttaaaaaaacaagtaatccttttaatggttttattttagggcaaaataaattaaaggcgagtactttattcgtgcggaggctttaataccccgacgcttgcgtctgggtaagttgattcaatgaaggttttatgatataattgtttgtgt .........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 acacaaacaattatatcataaaaccttcattgaatcaacttacccagacgcaagcgtcggggtattaaagcctccgcacgaataaagtactcgcctttaatttattttgccctaaaataaaaccattaaaaggattacttgtttttttaaatctcctgtgctatattcttttttagaatttaaaatcattattaa Mask Tandem Repeat Region ================================================ ttaataatgattttaaattctaaaaaagaatatagcacaggagatttaaaaaaacaagtaatccttttaatggttttattttagggcaaaataaattaaaggcgagtactttattcgtgcggaggctttaataccccgacgcttgcgtctgggtaagttgattcaatgaaggttttatgatataattgtttgtgt Find is-nt database================================================ Query_seq: TDE0712:TDE0713|TDE0712:TDE0713:hypothetical protein:transcription antitermination protein, NusG family:<-->:747054..747248 195 ttaataatgattttaaattctaaaaaagaatatagcacaggagatttaaaaaaacaagtaatccttttaatggttttattttagggcaaaataaattaaaggcgagtactttattcgtgcggaggctttaataccccgacgcttgcgtctgggtaagttgattcaatgaaggttttatgatataattgtttgtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0712:TDE0713|TDE0712:TDE0713:hypothetical protein:transcription antitermination protein, NusG family:<-->:747054..747248 195 ttaataatgattttaaattctaaaaaagaatatagcacaggagatttaaaaaaacaagtaatccttttaatggttttattttagggcaaaataaattaaaggcgagtactttattcgtgcggaggctttaataccccgacgcttgcgtctgggtaagttgattcaatgaaggttttatgatataattgtttgtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0712:TDE0713|TDE0712:TDE0713:hypothetical protein:transcription antitermination protein, NusG family:<-->:747054..747248 195 ttaataatgattttaaattctaaaaaagaatatagcacaggagatttaaaaaaacaagtaatccttttaatggttttattttagggcaaaataaattaaaggcgagtactttattcgtgcggaggctttaataccccgacgcttgcgtctgggtaagttgattcaatgaaggttttatgatataattgtttgtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaataatgattttaaattctaaaaaagaatatagcacaggagatttaaaaaaacaagtaatccttttaatggttttattttagggcaaaataaattaaaggcgagtactttattcgtgcggaggctttaataccccgacgcttgcgtctgggtaagttgattcaatgaaggttttatgatataattgtttgtgt Predict ORF larger than 30AA ================================================ ttaataatgattttaaattctaaaaaagaatatagcacaggagatttaaaaaaacaagtaatccttttaatggttttattttagggcaaaataaattaaaggcgagtactttattcgtgcggaggctttaataccccgacgcttgcgtctgggtaagttgattcaatgaaggttttatgatataattgtttgtgt 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: 87 Start: 157 End: 186 ............................................................................................................................................................GTTGATTCAATGAAGGTTTTATGATATAAT......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttaataatgattttaaattctaaaaaagaatatagcacaggagatttaaaaaaacaagtaatccttttaatggttttattttagggcaaaataaattaaaggcgagtactttattcgtgcggaggctttaataccccgacgcttgcgtctgggtaagttgattcaatgaaggttttatgatataattgtttgtgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 74 HP_score: -9.2 Tail_Score: -3.03124 Start: 134 End: 153 Full_Region: cattgaatcaactta cccagacg caag cgtcgggg tattaaagcctccgc .....................................................................................................................................cccagacgcaagcgtcgggg.......................................... Find igs database================================================ Query_seq: TDE0712:TDE0713|TDE0712:TDE0713:hypothetical protein:transcription antitermination protein, NusG family:<-->:747054..747248 195 ttaataatgattttaaattctaaaaaagaatatagcacaggagatttaaaaaaacaagtaatccttttaatggttttattttagggcaaaataaattaaaggcgagtactttattcgtgcggaggctttaataccccgacgcttgcgtctgggtaagttgattcaatgaaggttttatgatataattgtttgtgt Intra-Species Hit: Count: 1 Min: 1 Max: 195 Len: 195 Subject: NC_002967_TDE0712_TDE0713|hypothetical protein:transcription antitermination protein, NusG family|NEGATIVE:POSITIVE|[747054,747248]|195 HSP 1 e-value: 3.0E-94 bit: 345.0 Len: 195 Query Start:1 Query End:195 Subject Strand: POSITIVE Subject Start: 1 Subject End: 195 ttaataatgattttaaattctaaaaaagaatatagcacaggagatttnnnnnnncaagtaatccttttaatggttttattttagggcaaaataaattaaaggcgagtactttattcgtgcggaggctttaataccccgacgcttgcgtctgggtaagttgattcaatgaaggttttatgatataattgtttgtgt ttaataatgattttaaattctaaaaaagaatatagcacaggagatttaaaaaaacaagtaatccttttaatggttttattttagggcaaaataaattaaaggcgagtactttattcgtgcggaggctttaataccccgacgcttgcgtctgggtaagttgattcaatgaaggttttatgatataattgtttgtgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAUAAUGAUUUUAAAUUCUAAAAAAGAAUAUAGCACAGGAGAUUUAAAAAAACAAGUAAUCCUUUUAAUGGUUUUAUUUUAGGGCAAAAUAAAUUAAAGGCGAGUACUUUAUUCGUGCGGAGGCUUUAAUACCCCGACGCUUGCGUCUGGGUAAGUUGAUUCAAUGAAGGUUUUAUGAUAUAAUUGUUUGUGU ................(((((.....)))))...(((((((.((((...........((((..((((((.(((.((((((((.....)))))))).(((((.(..((((.......))))...).))))).(((((.((((....)))).))))).......))).))))))..)))).....)))).))))))) (-38.79) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACACAAACAAUUAUAUCAUAAAACCUUCAUUGAAUCAACUUACCCAGACGCAAGCGUCGGGGUAUUAAAGCCUCCGCACGAAUAAAGUACUCGCCUUUAAUUUAUUUUGCCCUAAAAUAAAACCAUUAAAAGGAUUACUUGUUUUUUUAAAUCUCCUGUGCUAUAUUCUUUUUUAGAAUUUAAAAUCAUUAUUAA .............................(((((((....(((((.((((....)))).))))).....((....))..(((((.(((((..........(((((((((...)))))))))....((((((((((.....)))))))))).......))))).))))).......).))))))............ (-32.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 897 140 91 231 182 NC_002967:TDE0712|5end_hypothetical_protein_746963..747193_NEGATIVE 798 160 111 171 110 NC_002967:TDE0167|5end_ABC_transporter,_ATP-binding_protein_196574..196804_NEGATIVE 766 160 111 156 107 NC_002967:TDE0538|5end_hypothetical_protein_580066..580296_POSITIVE 757 160 111 175 115 NC_002967:TDE0371|5end_hypothetical_protein_422687..422917_POSITIVE 719 160 111 173 112 NC_002967:TDE1470|5end_hypothetical_protein_1518026..1518256_NEGATIVE 483 163 124 178 144 NC_002967:TDE0509|5end_hypothetical_protein_560373..560603_NEGATIVE 419 155 118 164 126 NC_002967:TDE0017|5end_hypothetical_protein_22936..23166_NEGATIVE 391 160 117 121 81 NC_002967:TDE0830|5end_hypothetical_protein_852025..852255_NEGATIVE 382 149 118 230 191 NC_002967:TDE1051|5end_hypothetical_protein_1078496..1078726_NEGATIVE 381 173 133 205 165 NC_002967:TDE1194|5end_hypothetical_protein_1224973..1225203_POSITIVE 381 173 133 174 134 NC_002967:TDE0580|5end_hypothetical_protein_615338..615568_POSITIVE 380 147 101 227 164 NC_002967:TDE0238|5end_thioredoxin,_selenocysteine-containing_271380..271610_POSITIVE 358 160 113 225 169 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 347 156 116 71 34 NC_002967:TDE2505|5end_hypothetical_protein_2530125..2530355_POSITIVE 343 160 117 121 81 NC_002967:TDE2691|5end_hypothetical_protein_2728838..2729068_POSITIVE 341 163 133 86 56 NC_002967:TDE2690|5end_hypothetical_protein_2728898..2729128_NEGATIVE 340 159 114 80 29 NC_002967:TDE0353|5end_lipase/acylhydrolase,_GDSL_family_398338..398568_NEGATIVE 331 154 113 51 7 NC_002967:TDE0745|5end_glycine_reductase_complex_selenoprotein_GrdA_780287..780517_POSITIVE 323 153 116 62 21 NC_002967:TDE0793|5end_hypothetical_protein_818910..819140_POSITIVE 322 156 114 54 5 NC_002967:TDE0120|5end_hypothetical_protein_137648..137878_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 798 160 111 78 17 NC_002967:TDE0168|3end_transcriptional_regulator,_GntR_family_196667..196817_NEGATIVE 766 160 111 88 39 NC_002967:TDE0537|3end_hypothetical_protein_580078..580228_POSITIVE 757 160 111 78 18 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 719 160 111 99 39 NC_002967:TDE0133|3end_transcriptional_regulator,_GntR_family_153202..153352_POSITIVE 701 149 101 129 69 NC_002967:TDE2458|3end_hypothetical_protein_2485849..2485999_POSITIVE 661 160 111 79 30 NC_002967:TDE0202|3end_hypothetical_protein_235870..236020_NEGATIVE 584 160 119 54 1 NC_002967:TDE1471|3end_hypothetical_protein_1518145..1518295_NEGATIVE 483 163 124 138 104 NC_002967:TDE0510|3end_hypothetical_protein_560413..560563_NEGATIVE 462 155 118 90 45 NC_002967:TDE0710|3end_hypothetical_protein_745667..745817_POSITIVE 452 139 110 151 122 NC_002967:TDE2690|3end_hypothetical_protein_2728743..2728893_NEGATIVE 413 155 118 67 22 NC_002967:TDE2499|3end_hypothetical_protein_2523191..2523341_NEGATIVE 406 170 124 61 5 NC_002967:TDE0333|3end_MATE_efflux_family_protein_373083..373233_POSITIVE 397 154 118 42 1 NC_002967:TDE2139|3end_hypothetical_protein_2172897..2173047_POSITIVE 391 160 117 51 11 NC_002967:TDE0831|3end_hypothetical_protein_852095..852245_NEGATIVE 389 175 133 64 14 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 355 170 131 45 2 NC_002967:TDE0018|3end_LysM_domain_protein_23073..23223_NEGATIVE 347 163 136 61 33 NC_002967:TDE0370|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_422594..422744_POSITIVE 344 155 118 125 80 NC_002967:TDE2459|3end_hypothetical_protein_2485764..2485914_NEGATIVE 343 160 117 51 11 NC_002967:TDE2689|3end_hypothetical_protein_2728848..2728998_POSITIVE 323 153 116 78 37 NC_002967:TDE0792|3end_ribosomal_protein_L17_819006..819156_POSITIVE