Origin IGS: ggaatttacccaaatataattaaagcggcagaaagatcttgcggtctctgccgcttttttatttttctaagatttggcaaataaaacttgacaaatttcagcctctatgttaatatgttggtggtaagaccacagctcaagtatcgggagtatgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacatactcccgatacttgagctgtggtcttaccaccaacatattaacatagaggctgaaatttgtcaagttttatttgccaaatcttagaaaaataaaaaagcggcagagaccgcaagatctttctgccgctttaattatatttgggtaaattcc Mask Tandem Repeat Region ================================================ ggaatttacccaaatataattaaagcggcagaaagatcttgcggtctctgccgcttttttatttttctaagatttggcaaataaaacttgacaaatttcagcctctatgttaatatgttggtggtaagaccacagctcaagtatcgggagtatgtt Find is-nt database================================================ Query_seq: TDE0132:TDE0133|TDE0132:TDE0133:hypothetical protein:transcriptional regulator, GntR family:->->:152357..152512 156 ggaatttacccaaatataattaaagcggcagaaagatcttgcggtctctgccgcttttttatttttctaagatttggcaaataaaacttgacaaatttcagcctctatgttaatatgttggtggtaagaccacagctcaagtatcgggagtatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0132:TDE0133|TDE0132:TDE0133:hypothetical protein:transcriptional regulator, GntR family:->->:152357..152512 156 ggaatttacccaaatataattaaagcggcagaaagatcttgcggtctctgccgcttttttatttttctaagatttggcaaataaaacttgacaaatttcagcctctatgttaatatgttggtggtaagaccacagctcaagtatcgggagtatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0132:TDE0133|TDE0132:TDE0133:hypothetical protein:transcriptional regulator, GntR family:->->:152357..152512 156 ggaatttacccaaatataattaaagcggcagaaagatcttgcggtctctgccgcttttttatttttctaagatttggcaaataaaacttgacaaatttcagcctctatgttaatatgttggtggtaagaccacagctcaagtatcgggagtatgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggaatttacccaaatataattaaagcggcagaaagatcttgcggtctctgccgcttttttatttttctaagatttggcaaataaaacttgacaaatttcagcctctatgttaatatgttggtggtaagaccacagctcaagtatcgggagtatgtt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 9 End: 101 ........ G F I I L A A S L D Q P R Q R K K I K R L N P L Y F K V F K M ....................................................... ggaatttacccaaatataattaaagcggcagaaagatcttgcggtctctgccgcttttttatttttctaagatttggcaaataaaacttgacaaatttcagcctctatgttaatatgttggtggtaagaccacagctcaagtatcgggagtatgtt 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: 89 Start: 87 End: 116 ......................................................................................CTTGACAAATTTCAGCCTCTATGTTAATAT........................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggaatttacccaaatataattaaagcggcagaaagatcttgcggtctctgccgcttttttatttttctaagatttggcaaataaaacttgacaaatttcagcctctatgttaatatgttggtggtaagaccacagctcaagtatcgggagtatgtt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -7.2 Tail_Score: -4.11501 Start: 25 End: 54 Full_Region: tagaaaaataaaaaa gcggcagaga ccgcaagatc tttctgccgc tttaattatatttgg ........................gcggcagagaccgcaagatctttctgccgc...................................................................................................... Find igs database================================================ Query_seq: TDE0132:TDE0133|TDE0132:TDE0133:hypothetical protein:transcriptional regulator, GntR family:->->:152357..152512 156 ggaatttacccaaatataattaaagcggcagaaagatcttgcggtctctgccgcttttttatttttctaagatttggcaaataaaacttgacaaatttcagcctctatgttaatatgttggtggtaagaccacagctcaagtatcgggagtatgtt Intra-Species Hit: Count: 1 Min: 1 Max: 156 Len: 156 Subject: NC_002967_TDE0132_TDE0133|hypothetical protein:transcriptional regulator, GntR family|POSITIVE:POSITIVE|[152357,152512]|156 HSP 1 e-value: 4.0E-62 bit: 238.0 Len: 156 Query Start:1 Query End:156 Subject Strand: POSITIVE Subject Start: 1 Subject End: 156 ggaatttacccaaatataattaaagcggcagaaagatcttgcggtctctgccgcnnnnnnnnnnnnctaagatttggcaaataaaacttgacaaatttcagcctctatgttaatatgttggtggtaagaccacagctcaagtatcgggagtatgtt ggaatttacccaaatataattaaagcggcagaaagatcttgcggtctctgccgcttttttatttttctaagatttggcaaataaaacttgacaaatttcagcctctatgttaatatgttggtggtaagaccacagctcaagtatcgggagtatgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAAUUUACCCAAAUAUAAUUAAAGCGGCAGAAAGAUCUUGCGGUCUCUGCCGCUUUUUUAUUUUUCUAAGAUUUGGCAAAUAAAACUUGACAAAUUUCAGCCUCUAUGUUAAUAUGUUGGUGGUAAGACCACAGCUCAAGUAUCGGGAGUAUGUU ........(((....((((..(((((((((((..((((....))))))))))))))).)))).........(((((((...........((((.(((.((.......))..))).)))).((((.....)))).)).)))))...)))........ (-39.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAUACUCCCGAUACUUGAGCUGUGGUCUUACCACCAACAUAUUAACAUAGAGGCUGAAAUUUGUCAAGUUUUAUUUGCCAAAUCUUAGAAAAAUAAAAAAGCGGCAGAGACCGCAAGAUCUUUCUGCCGCUUUAAUUAUAUUUGGGUAAAUUCC ........(((((..........((((.....))))...................((((.(((((.(((((...))))).))))).)))).........(((((((((((((.(....)...)))))))))))))........)))))........ (-39.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 65 22 231 196 NC_002967:TDE1711|5end_RelA/SpoT_domain_protein_1766718..1766948_NEGATIVE 328 68 26 168 115 NC_002967:TDE1004|5end_flagellar_filament_core_protein_1030136..1030366_NEGATIVE 301 66 23 58 16 NC_002967:TDE2728|5end_hypothetical_protein_2785607..2785837_POSITIVE 299 68 24 78 33 NC_002967:TDE0362|5end_bacterial_Ig-like_domain_protein_409444..409674_NEGATIVE 299 52 24 49 20 NC_002967:TDE0135|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_154927..155157_POSITIVE 296 78 32 212 156 NC_002967:TDE2113|5end_hypothetical_protein_2139412..2139642_NEGATIVE 291 66 25 194 156 NC_002967:TDE1126|5end_TPR_domain_protein_1157545..1157775_POSITIVE 285 69 27 104 42 NC_002967:TDE1459|5end_hypothetical_protein_1508707..1508937_NEGATIVE 282 80 39 58 13 NC_002967:TDE1132|5end_chorismate_synthase_1163415..1163645_POSITIVE 281 68 22 169 125 NC_002967:TDE0617|5end_hypothetical_protein_650227..650457_NEGATIVE 281 54 24 55 20 NC_002967:TDE0472|5end_hypothetical_protein_528376..528606_POSITIVE 274 63 26 88 46 NC_002967:TDE0496|5end_DNA-binding_protein,_putative_551189..551419_NEGATIVE 273 55 25 56 20 NC_002967:TDE1246|5end_lipoprotein,_putative_1279039..1279269_POSITIVE 270 62 28 207 173 NC_002967:TDE1485|5end_hypothetical_protein_1529697..1529927_POSITIVE 267 53 24 50 16 NC_002967:TDE0743|5end_thioredoxin_reductase_778718..778948_POSITIVE 265 57 26 156 123 NC_002967:TDE2399|5end_ribonuclease_P_protein_component_2426160..2426390_NEGATIVE 264 59 22 198 154 NC_002967:TDE2436|5end_hypothetical_protein_2466602..2466832_POSITIVE 261 55 26 227 186 NC_002967:TDE1906|5end_hypothetical_protein_1923883..1924113_POSITIVE 260 79 36 178 130 NC_002967:TDE0628|5end_molecular_chaperone_DnaK_660609..660839_POSITIVE 259 79 39 202 153 NC_002967:TDE0174|5end_nicotinate_phosphoribosyltransferase_206534..206764_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 452 57 22 69 34 NC_002967:TDE0132|3end_hypothetical_protein_152296..152446_POSITIVE 349 56 26 150 120 NC_002967:TDE0860|3end_ribosomal_small_subunit_pseudouridine_synthase_A_881840..881990_POSITIVE 343 66 22 84 48 NC_002967:TDE1712|3end_flagellar_filament_outer_layer_protein_1766866..1767016_NEGATIVE 342 70 26 84 31 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 299 52 24 52 23 NC_002967:TDE0134|3end_oxidoreductase,_FAD-dependent_155010..155160_POSITIVE 285 69 27 104 42 NC_002967:TDE1460|3end_hypothetical_protein_1508707..1508857_NEGATIVE 274 89 42 105 58 NC_002967:TDE0973|3end_DNA_repair_protein_RadC_997940..998090_NEGATIVE 274 60 21 142 99 NC_002967:TDE0199|3end_hypothetical_protein_234199..234349_NEGATIVE 272 56 23 67 31 NC_002967:TDE2729|3end_hypothetical_protein_2785756..2785906_NEGATIVE 271 138 91 73 25 NC_002967:TDE2516|3end_hypothetical_protein_2542193..2542343_POSITIVE 269 54 23 70 32 NC_002967:TDE2712|3end_hypothetical_protein_2769615..2769765_POSITIVE 265 57 26 144 111 NC_002967:TDE2400|3end_50S_ribosomal_protein_L34_2426172..2426322_NEGATIVE 264 61 25 33 2 NC_002967:TDE2268|3end_hypothetical_protein_2304822..2304972_NEGATIVE 263 66 24 150 109 NC_002967:TDE0793|3end_hypothetical_protein_819205..819355_POSITIVE 259 60 32 131 106 NC_002967:TDE2725|3end_cyclic_nucleotide_binding_domain/GGDEF_domain_protein_2782240..2782390_NEGATIVE 259 61 24 81 44 NC_002967:TDE0162|3end_hypothetical_protein_192882..193032_POSITIVE 258 59 25 45 13 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 258 89 41 76 22 NC_002967:TDE1235|3end_hypothetical_protein_1269557..1269707_POSITIVE 258 87 41 143 85 NC_002967:TDE0899|3end_ABC_transporter,_permease_protein,_putative_917277..917427_POSITIVE 256 58 25 147 110 NC_002967:TDE2057|3end_hypothetical_protein_2085158..2085308_NEGATIVE