Origin IGS: taaaagcacctgtcaaatatagcttagttatattataagggtttttagttttttgtcaataagggattccggatattttttttaacgagtgaggttggttgtgagtatgagagaacttctttaattataagttgggtattcagttttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaactgaatacccaacttataattaaagaagttctctcatactcacaaccaacctcactcgttaaaaaaaatatccggaatcccttattgacaaaaaactaaaaacccttataatataactaagctatatttgacaggtgctttta Mask Tandem Repeat Region ================================================ taaaagcacctgtcaaatatagcttagttatattataagggtttttagttttttgtcaataagggattccggatattttttttaacgagtgaggttggttgtgagtatgagagaacttctttaattataagttgggtattcagttttt Find is-nt database================================================ Query_seq: TDE1606:TDE1607|TDE1606:TDE1607:transcriptional regulator, TetR family:MutT/nudix family protein:<-<-:1656949..1657096 148 taaaagcacctgtcaaatatagcttagttatattataagggtttttagttttttgtcaataagggattccggatattttttttaacgagtgaggttggttgtgagtatgagagaacttctttaattataagttgggtattcagttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1606:TDE1607|TDE1606:TDE1607:transcriptional regulator, TetR family:MutT/nudix family protein:<-<-:1656949..1657096 148 taaaagcacctgtcaaatatagcttagttatattataagggtttttagttttttgtcaataagggattccggatattttttttaacgagtgaggttggttgtgagtatgagagaacttctttaattataagttgggtattcagttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1606:TDE1607|TDE1606:TDE1607:transcriptional regulator, TetR family:MutT/nudix family protein:<-<-:1656949..1657096 148 taaaagcacctgtcaaatatagcttagttatattataagggtttttagttttttgtcaataagggattccggatattttttttaacgagtgaggttggttgtgagtatgagagaacttctttaattataagttgggtattcagttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaagcacctgtcaaatatagcttagttatattataagggtttttagttttttgtcaataagggattccggatattttttttaacgagtgaggttggttgtgagtatgagagaacttctttaattataagttgggtattcagttttt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 48 End: 143 ............................................... N K T L L P N R I N K K V L S T P Q S Y S L V E K I I L Q T N M ..... taaaagcacctgtcaaatatagcttagttatattataagggtttttagttttttgtcaataagggattccggatattttttttaacgagtgaggttggttgtgagtatgagagaacttctttaattataagttgggtattcagttttt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaagcacctgtcaaatatagcttagttatattataagggtttttagttttttgtcaataagggattccggatattttttttaacgagtgaggttggttgtgagtatgagagaacttctttaattataagttgggtattcagttttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1606:TDE1607|TDE1606:TDE1607:transcriptional regulator, TetR family:MutT/nudix family protein:<-<-:1656949..1657096 148 taaaagcacctgtcaaatatagcttagttatattataagggtttttagttttttgtcaataagggattccggatattttttttaacgagtgaggttggttgtgagtatgagagaacttctttaattataagttgggtattcagttttt Intra-Species Hit: Count: 1 Min: 1 Max: 148 Len: 148 Subject: NC_002967_TDE1606_TDE1607|transcriptional regulator, TetR family:MutT/nudix family protein|NEGATIVE:NEGATIVE|[1656949,1657096]|148 HSP 1 e-value: 2.0E-64 bit: 246.0 Len: 148 Query Start:1 Query End:148 Subject Strand: POSITIVE Subject Start: 1 Subject End: 148 taaaagcacctgtcaaatatagcttagttatattataagggtttttagttttttgtcaataagggattccggatannnnnnnnaacgagtgaggttggttgtgagtatgagagaacttctttaattataagttgggtattcagttttt taaaagcacctgtcaaatatagcttagttatattataagggtttttagttttttgtcaataagggattccggatattttttttaacgagtgaggttggttgtgagtatgagagaacttctttaattataagttgggtattcagttttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGCACCUGUCAAAUAUAGCUUAGUUAUAUUAUAAGGGUUUUUAGUUUUUUGUCAAUAAGGGAUUCCGGAUAUUUUUUUUAACGAGUGAGGUUGGUUGUGAGUAUGAGAGAACUUCUUUAAUUAUAAGUUGGGUAUUCAGUUUUU (((((((.(((....((((((((...))))))))...))))))))))....(((((.(.(((((((((((..((((((...(((((.......)))))....))))))..).))).))))))).).)))))................. (-23.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACUGAAUACCCAACUUAUAAUUAAAGAAGUUCUCUCAUACUCACAACCAACCUCACUCGUUAAAAAAAAUAUCCGGAAUCCCUUAUUGACAAAAAACUAAAAACCCUUAUAAUAUAACUAAGCUAUAUUUGACAGGUGCUUUUA ...............(((((..........)))))......................(((..((((((..........((....)).......................((((.........)))).....))))))..)))...... ( -7.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 846 110 61 201 152 NC_002967:TDE1606|5end_transcriptional_regulator,_TetR_family_1656858..1657088_NEGATIVE 288 108 61 177 121 NC_002967:TDE1472|5end_flagellar_hook-associated_protein_1520715..1520945_NEGATIVE 284 120 80 226 174 NC_002967:TDE1972|5end_hypothetical_protein_1987224..1987454_NEGATIVE 271 137 93 83 20 NC_002967:TDE2721|5end_helicase_domain_protein_2779605..2779835_NEGATIVE 247 105 63 137 99 NC_002967:TDE2552|5end_ABC_transporter,_ATP-binding/permease_protein_2578944..2579174_NEGATIVE 244 106 66 70 30 NC_002967:TDE0669|5end_hypothetical_protein_707827..708057_NEGATIVE 243 84 47 117 81 NC_002967:TDE1227|5end_hypothetical_protein_1260513..1260743_POSITIVE 237 77 31 169 127 NC_002967:TDE0839|5end_rhodanese-like_domain_protein_859341..859571_NEGATIVE 236 72 38 165 128 NC_002967:TDE2536|5end_hypothetical_protein_2562320..2562550_POSITIVE 235 107 61 70 19 NC_002967:TDE2025|5end_hypothetical_protein_2051440..2051670_NEGATIVE 234 109 62 79 42 NC_002967:TDE1198|5end_S-adenosyl-methyltransferase_MraW_1230392..1230622_POSITIVE 234 97 54 218 169 NC_002967:TDE1096|5end_hydroxymethylbutenyl_pyrophosphate_reductase_1130989..1131219_POSITIVE 233 110 62 227 180 NC_002967:TDE2600|5end_hypothetical_protein_2633958..2634188_POSITIVE 230 56 23 131 102 NC_002967:TDE2139|5end_hypothetical_protein_2172032..2172262_POSITIVE 230 129 81 116 59 NC_002967:TDE1097|5end_acetyltransferase,_GNAT_family_1132766..1132996_NEGATIVE 227 100 51 130 64 NC_002967:TDE1316|5end_hypothetical_protein_1354741..1354971_POSITIVE 227 69 37 123 94 NC_002967:TDE0912|5end_hypothetical_protein_931350..931580_POSITIVE 226 99 51 183 133 NC_002967:TDE0848|5end_hypothetical_protein_871269..871499_POSITIVE 223 80 37 40 1 NC_002967:TDE1474|5end_hypothetical_protein_1521353..1521583_NEGATIVE 223 97 63 206 172 NC_002967:TDE0322|5end_regulatory_protein,_P-II_family_355405..355635_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 96 64 77 46 NC_002967:TDE0940|3end_hypothetical_protein_963635..963785_POSITIVE 288 108 61 132 76 NC_002967:TDE1473|3end_flagellin_FlaG,_putative_1520760..1520910_NEGATIVE 240 139 93 54 7 NC_002967:TDE1767|3end_hypothetical_protein_1812926..1813076_NEGATIVE 239 113 86 133 98 NC_002967:TDE0742|3end_hypothetical_protein_778450..778600_NEGATIVE 237 77 31 91 49 NC_002967:TDE0840|3end_hypothetical_protein_859419..859569_NEGATIVE 234 80 36 59 19 NC_002967:TDE1475|3end_flagellar_filament_core_protein_1521334..1521484_NEGATIVE 234 80 36 132 92 NC_002967:TDE1474|3end_hypothetical_protein_1521261..1521411_NEGATIVE 234 109 62 73 36 NC_002967:TDE1197|3end_conserved_hypothetical_protein_TIGR00242_1230466..1230616_POSITIVE 232 99 59 46 9 NC_002967:TDE2446|3end_malate_dehydrogenase_2474774..2474924_NEGATIVE 230 56 23 113 84 NC_002967:TDE2138|3end_ankyrin_repeat_protein_2172094..2172244_POSITIVE 230 129 81 112 55 NC_002967:TDE1098|3end_hypothetical_protein_1132770..1132920_NEGATIVE 228 110 61 111 50 NC_002967:TDE1066|3end_hypothetical_protein_1094335..1094485_NEGATIVE 227 100 51 142 76 NC_002967:TDE1315|3end_hypothetical_protein_1354833..1354983_POSITIVE 220 76 39 81 47 NC_002967:TDE0091|3end_RNA_polymerase_sigma-24_factor,_putative_109190..109340_NEGATIVE 218 80 39 54 13 NC_002967:TDE1106|3end_translation_initiation_factor_IF-2_1138192..1138342_NEGATIVE 217 112 71 109 59 NC_002967:TDE1666|3end_hypothetical_protein_1720021..1720171_POSITIVE 216 136 91 72 25 NC_002967:TDE2338|3end_hypothetical_protein_2374624..2374774_NEGATIVE 215 108 66 51 4 NC_002967:TDE2224|3end_hypothetical_protein_2264951..2265101_POSITIVE 215 60 11 109 58 NC_002967:TDE1951|3end_ribonuclease_Z_1967403..1967553_NEGATIVE 211 119 84 84 46 NC_002967:TDE1443|3end_RNA_methyltransferase,_TrmH_family,_group_3_1488809..1488959_NEGATIVE