Origin IGS: aggcgtgctttttgcagaatatattttttatgttactttgcatatcccaacctttaaatttgcttaaatcatttgtttttaatacttaactaaagaacgtatttaaacattgcacaatagtccgggttcttagggcagagccctaagcagcgcgaggaaaaggaagtaggggttttaggggaggaaggaaaacctgttctgtcgggttgtccttcctcccctaaattgt .........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 acaatttaggggaggaaggacaacccgacagaacaggttttccttcctcccctaaaacccctacttccttttcctcgcgctgcttagggctctgccctaagaacccggactattgtgcaatgtttaaatacgttctttagttaagtattaaaaacaaatgatttaagcaaatttaaaggttgggatatgcaaagtaacataaaaaatatattctgcaaaaagcacgcct Mask Tandem Repeat Region ================================================ aggcgtgctttttgcagaatatattttttatgttactttgcatatcccaacctttaaatttgcttaaatcatttgtttttaatacttaactaaagaacgtatttaaacattgcacaatagtccgggttcttagggcagagccctaagcagcgcgaggaaaaggaagtaggggttttaggggaggaaggaaaacctgttctgtcgggttgtccttcctcccctaaattgt Find is-nt database================================================ Query_seq: TDE0827:TDE0828|TDE0827:TDE0828:hypothetical protein:glucose-inhibited division protein A:<-<-:848144..848372 229 aggcgtgctttttgcagaatatattttttatgttactttgcatatcccaacctttaaatttgcttaaatcatttgtttttaatacttaactaaagaacgtatttaaacattgcacaatagtccgggttcttagggcagagccctaagcagcgcgaggaaaaggaagtaggggttttaggggaggaaggaaaacctgttctgtcgggttgtccttcctcccctaaattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0827:TDE0828|TDE0827:TDE0828:hypothetical protein:glucose-inhibited division protein A:<-<-:848144..848372 229 aggcgtgctttttgcagaatatattttttatgttactttgcatatcccaacctttaaatttgcttaaatcatttgtttttaatacttaactaaagaacgtatttaaacattgcacaatagtccgggttcttagggcagagccctaagcagcgcgaggaaaaggaagtaggggttttaggggaggaaggaaaacctgttctgtcgggttgtccttcctcccctaaattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0827:TDE0828|TDE0827:TDE0828:hypothetical protein:glucose-inhibited division protein A:<-<-:848144..848372 229 aggcgtgctttttgcagaatatattttttatgttactttgcatatcccaacctttaaatttgcttaaatcatttgtttttaatacttaactaaagaacgtatttaaacattgcacaatagtccgggttcttagggcagagccctaagcagcgcgaggaaaaggaagtaggggttttaggggaggaaggaaaacctgttctgtcgggttgtccttcctcccctaaattgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggcgtgctttttgcagaatatattttttatgttactttgcatatcccaacctttaaatttgcttaaatcatttgtttttaatacttaactaaagaacgtatttaaacattgcacaatagtccgggttcttagggcagagccctaagcagcgcgaggaaaaggaagtaggggttttaggggaggaaggaaaacctgttctgtcgggttgtccttcctcccctaaattgt Predict ORF larger than 30AA ================================================ aggcgtgctttttgcagaatatattttttatgttactttgcatatcccaacctttaaatttgcttaaatcatttgtttttaatacttaactaaagaacgtatttaaacattgcacaatagtccgggttcttagggcagagccctaagcagcgcgaggaaaaggaagtaggggttttaggggaggaaggaaaacctgttctgtcgggttgtccttcctcccctaaattgt 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================================================ aggcgtgctttttgcagaatatattttttatgttactttgcatatcccaacctttaaatttgcttaaatcatttgtttttaatacttaactaaagaacgtatttaaacattgcacaatagtccgggttcttagggcagagccctaagcagcgcgaggaaaaggaagtaggggttttaggggaggaaggaaaacctgttctgtcgggttgtccttcctcccctaaattgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 54 HP_score: -5.4 Tail_Score: -3.1706 Start: 187 End: 212 Full_Region: GTTTTAGGGGAGGAA GGAAAACCTG TTCTGT CGGGTTGTCC TTCCTCCCCTAAATT ..........................................................................................................................................................................................GGAAAACCTGTTCTGTCGGGTTGTCC................. Find igs database================================================ Query_seq: TDE0827:TDE0828|TDE0827:TDE0828:hypothetical protein:glucose-inhibited division protein A:<-<-:848144..848372 229 aggcgtgctttttgcagaatatattttttatgttactttgcatatcccaacctttaaatttgcttaaatcatttgtttttaatacttaactaaagaacgtatttaaacattgcacaatagtccgggttcttagggcagagccctaagcagcgcgaggaaaaggaagtaggggttttaggggaggaaggaaaacctgttctgtcgggttgtccttcctcccctaaattgt Intra-Species Hit: Count: 1 Min: 1 Max: 229 Len: 229 Subject: NC_002967_TDE0827_TDE0828|hypothetical protein:glucose-inhibited division protein A|NEGATIVE:NEGATIVE|[848144,848372]|229 HSP 1 e-value: 1.0E-127 bit: 454.0 Len: 229 Query Start:1 Query End:229 Subject Strand: POSITIVE Subject Start: 1 Subject End: 229 aggcgtgctttttgcagaatatattttttatgttactttgcatatcccaacctttaaatttgcttaaatcatttgtttttaatacttaactaaagaacgtatttaaacattgcacaatagtccgggttcttagggcagagccctaagcagcgcgaggaaaaggaagtaggggttttaggggaggaaggaaaacctgttctgtcgggttgtccttcctcccctaaattgt aggcgtgctttttgcagaatatattttttatgttactttgcatatcccaacctttaaatttgcttaaatcatttgtttttaatacttaactaaagaacgtatttaaacattgcacaatagtccgggttcttagggcagagccctaagcagcgcgaggaaaaggaagtaggggttttaggggaggaaggaaaacctgttctgtcgggttgtccttcctcccctaaattgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGCGUGCUUUUUGCAGAAUAUAUUUUUUAUGUUACUUUGCAUAUCCCAACCUUUAAAUUUGCUUAAAUCAUUUGUUUUUAAUACUUAACUAAAGAACGUAUUUAAACAUUGCACAAUAGUCCGGGUUCUUAGGGCAGAGCCCUAAGCAGCGCGAGGAAAAGGAAGUAGGGGUUUUAGGGGAGGAAGGAAAACCUGUUCUGUCGGGUUGUCCUUCCUCCCCUAAAUUGU ...(.((((((((((((((((((.....)))))...)))))...(((..............(((.........(((((..(((((.............))))).))))).........))).((.(((((((((((...)))))))).))).)).)))..)))))))).)...((((((((((((((((.((((((......)))))).)))))))))))))))).... (-75.49) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAUUUAGGGGAGGAAGGACAACCCGACAGAACAGGUUUUCCUUCCUCCCCUAAAACCCCUACUUCCUUUUCCUCGCGCUGCUUAGGGCUCUGCCCUAAGAACCCGGACUAUUGUGCAAUGUUUAAAUACGUUCUUUAGUUAAGUAUUAAAAACAAAUGAUUUAAGCAAAUUUAAAGGUUGGGAUAUGCAAAGUAACAUAAAAAAUAUAUUCUGCAAAAAGCACGCCU ....((((((((((((((((.((((.(......).)))).))))))))))))))))..(((.....(((((.....((((..((((((((...)))))))).............))))..(((((((((.((((.((((((.....))))))....))))))))))))).....)))))..)))...((((.((((............)))).))))............ (-70.76) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 871 140 91 231 182 NC_002967:TDE0827|5end_hypothetical_protein_848053..848283_NEGATIVE 814 170 124 66 18 NC_002967:TDE2141|5end_hypothetical_protein_2175768..2175998_NEGATIVE 581 220 174 151 105 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 527 180 132 221 177 NC_002967:TDE1060|5end_hypothetical_protein_1086519..1086749_POSITIVE 434 153 122 71 40 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 412 170 123 223 178 NC_002967:TDE2419|5end_hypothetical_protein_2444769..2444999_NEGATIVE 400 220 173 173 103 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 399 200 153 182 135 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 384 208 161 64 14 NC_002967:TDE1057|5end_hypothetical_protein_1086245..1086475_NEGATIVE 371 220 171 191 143 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 364 153 124 35 3 NC_002967:TDE0618|5end_hypothetical_protein_650355..650585_NEGATIVE 364 153 124 163 131 NC_002967:TDE0617|5end_hypothetical_protein_650227..650457_NEGATIVE 364 218 177 59 12 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 364 218 177 181 134 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 362 179 137 77 27 NC_002967:TDE0450|5end_hypothetical_protein_508529..508759_NEGATIVE 360 220 171 221 155 NC_002967:TDE0469|5end_hypothetical_protein_523987..524217_NEGATIVE 357 210 161 116 62 NC_002967:TDE0760|5end_hypothetical_protein_799436..799666_POSITIVE 356 220 171 182 130 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 351 172 135 50 17 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 350 218 177 80 33 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 589 170 123 74 19 NC_002967:TDE1008|3end_flagellar_protein,_putative_1032806..1032956_POSITIVE 503 190 141 53 7 NC_002967:TDE2420|3end_DNA-directed_RNA_polymerase_beta'_subunit_2444960..2445110_NEGATIVE 440 220 171 90 39 NC_002967:TDE0969|3end_hypothetical_protein_994575..994725_POSITIVE 440 220 171 90 39 NC_002967:TDE0724|3end_hypothetical_protein_763237..763387_POSITIVE 440 220 171 90 39 NC_002967:TDE0722|3end_lipoprotein,_putative_759864..760014_POSITIVE 433 186 141 52 9 NC_002967:TDE1058|3end_hypothetical_protein_1086232..1086382_NEGATIVE 413 180 132 75 26 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE 411 148 116 143 109 NC_002967:TDE1057|3end_hypothetical_protein_1086105..1086255_NEGATIVE 390 199 152 88 40 NC_002967:TDE0723|3end_hypothetical_protein_761661..761811_POSITIVE 390 199 152 68 20 NC_002967:TDE0715|3end_hypothetical_protein_750550..750700_POSITIVE 382 219 177 83 37 NC_002967:TDE0665|3end_pyruvate_ferredoxin/flavodoxin_oxidoreductase_family_protein_699792..699942_NEGATIVE 371 220 171 137 89 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 364 220 175 49 1 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 364 153 124 148 116 NC_002967:TDE0618|3end_hypothetical_protein_650242..650392_NEGATIVE 341 186 149 102 59 NC_002967:TDE0492|3end_sensor_histidine_kinase/response_regulator_548657..548807_POSITIVE 340 219 171 83 11 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 337 207 161 79 34 NC_002967:TDE0158|3end_hypothetical_protein_185724..185874_NEGATIVE 335 177 131 85 31 NC_002967:TDE1443|3end_RNA_methyltransferase,_TrmH_family,_group_3_1488809..1488959_NEGATIVE 332 174 133 71 19 NC_002967:TDE2582|3end_GGDEF_domain_protein_2616164..2616314_POSITIVE 330 180 135 69 17 NC_002967:TDE1451|3end_hypothetical_protein_1497850..1498000_NEGATIVE