Origin IGS: actgtctttattatagtagaaaacgagggaattgacaactattaggggaagaaagcccttgccattctctcaaggcatcatccttttttagaaaaattaaaagaaaaacacatagctccggaacggcaatattgcattac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtaatgcaatattgccgttccggagctatgtgtttttcttttaatttttctaaaaaaggatgatgccttgagagaatggcaagggctttcttcccctaatagttgtcaattccctcgttttctactataataaagacagt Mask Tandem Repeat Region ================================================ actgtctttattatagtagaaaacgagggaattgacaactattaggggaagaaagcccttgccattctctcaaggcatcatccttttttagaaaaattaaaagaaaaacacatagctccggaacggcaatattgcattac Find is-nt database================================================ Query_seq: TDE0084:TDE0085|TDE0084:TDE0085:phosphoenolpyruvate-protein phosphotransferase:ATP-dependent DNA helicase, UvrD/Rep family:<-<-:97546..97685 140 actgtctttattatagtagaaaacgagggaattgacaactattaggggaagaaagcccttgccattctctcaaggcatcatccttttttagaaaaattaaaagaaaaacacatagctccggaacggcaatattgcattac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0084:TDE0085|TDE0084:TDE0085:phosphoenolpyruvate-protein phosphotransferase:ATP-dependent DNA helicase, UvrD/Rep family:<-<-:97546..97685 140 actgtctttattatagtagaaaacgagggaattgacaactattaggggaagaaagcccttgccattctctcaaggcatcatccttttttagaaaaattaaaagaaaaacacatagctccggaacggcaatattgcattac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0084:TDE0085|TDE0084:TDE0085:phosphoenolpyruvate-protein phosphotransferase:ATP-dependent DNA helicase, UvrD/Rep family:<-<-:97546..97685 140 actgtctttattatagtagaaaacgagggaattgacaactattaggggaagaaagcccttgccattctctcaaggcatcatccttttttagaaaaattaaaagaaaaacacatagctccggaacggcaatattgcattac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actgtctttattatagtagaaaacgagggaattgacaactattaggggaagaaagcccttgccattctctcaaggcatcatccttttttagaaaaattaaaagaaaaacacatagctccggaacggcaatattgcattac Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 14 End: 130 ............. L L F R P F Q C S N P S S L G Q W E R L A D D K K L F I L L F V C L E P V A M .......... actgtctttattatagtagaaaacgagggaattgacaactattaggggaagaaagcccttgccattctctcaaggcatcatccttttttagaaaaattaaaagaaaaacacatagctccggaacggcaatattgcattac 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: 91 Start: 10 End: 39 .........GTTGTCAATTCCCTCGTTTTCTACTATAAT..................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actgtctttattatagtagaaaacgagggaattgacaactattaggggaagaaagcccttgccattctctcaaggcatcatccttttttagaaaaattaaaagaaaaacacatagctccggaacggcaatattgcattac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0084:TDE0085|TDE0084:TDE0085:phosphoenolpyruvate-protein phosphotransferase:ATP-dependent DNA helicase, UvrD/Rep family:<-<-:97546..97685 140 actgtctttattatagtagaaaacgagggaattgacaactattaggggaagaaagcccttgccattctctcaaggcatcatccttttttagaaaaattaaaagaaaaacacatagctccggaacggcaatattgcattac Intra-Species Hit: Count: 1 Min: 1 Max: 140 Len: 140 Subject: NC_002967_TDE0084_TDE0085|phosphoenolpyruvate-protein phosphotransferase:ATP-dependent DNA helicase, UvrD/Rep family|NEGATIVE:NEGATIVE|[97546,97685]|140 HSP 1 e-value: 5.0E-74 bit: 278.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 actgtctttattatagtagaaaacgagggaattgacaactattaggggaagaaagcccttgccattctctcaaggcatcatccttttttagaaaaattaaaagaaaaacacatagctccggaacggcaatattgcattac actgtctttattatagtagaaaacgagggaattgacaactattaggggaagaaagcccttgccattctctcaaggcatcatccttttttagaaaaattaaaagaaaaacacatagctccggaacggcaatattgcattac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGUCUUUAUUAUAGUAGAAAACGAGGGAAUUGACAACUAUUAGGGGAAGAAAGCCCUUGCCAUUCUCUCAAGGCAUCAUCCUUUUUUAGAAAAAUUAAAAGAAAAACACAUAGCUCCGGAACGGCAAUAUUGCAUUAC (((((.......))))).......((((((((.(.((......((((........))))))).))))))))...(((......((((((((.....))))))))..........(((.......))).....)))..... (-20.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAUGCAAUAUUGCCGUUCCGGAGCUAUGUGUUUUUCUUUUAAUUUUUCUAAAAAAGGAUGAUGCCUUGAGAGAAUGGCAAGGGCUUUCUUCCCCUAAUAGUUGUCAAUUCCCUCGUUUUCUACUAUAAUAAAGACAGU .....(((((..(((((((((.(((....(((((.(((((((...........))))))).))))))))..).))))))))((((........))))....)))))..........(((((...........)))))... (-24.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 931 80 31 171 122 NC_002967:TDE0084|5end_phosphoenolpyruvate-protein_phosphotransferase_97455..97685_NEGATIVE 325 76 31 78 30 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 294 98 55 110 66 NC_002967:TDE1514|5end_permease_domain_protein_1560652..1560882_POSITIVE 292 58 22 45 8 NC_002967:TDE2403|5end_metallo-beta-lactamase_family_protein_2429282..2429512_NEGATIVE 291 60 18 47 14 NC_002967:TDE1057|5end_hypothetical_protein_1086245..1086475_NEGATIVE 288 76 41 174 140 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 285 90 54 195 158 NC_002967:TDE0028|5end_ABC_transporter,_ATP-binding_protein,_HlyB_family_35930..36160_NEGATIVE 284 118 73 133 86 NC_002967:TDE1880|5end_hypothetical_protein_1902535..1902765_POSITIVE 282 70 22 165 111 NC_002967:TDE1241|5end_HD_domain_protein_1272269..1272499_POSITIVE 281 76 42 140 105 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 273 86 50 230 191 NC_002967:TDE2359|5end_DAK2_domain_protein_2394782..2395012_NEGATIVE 272 78 43 63 25 NC_002967:TDE2782|5end_ABC_transporter,_ATP-binding/permease_protein_2834276..2834506_NEGATIVE 268 90 55 53 17 NC_002967:TDE0452|5end_hypothetical_protein_510143..510373_NEGATIVE 266 69 21 224 175 NC_002967:TDE2614|5end_ApbE_family_protein_2657133..2657363_NEGATIVE 264 64 22 173 133 NC_002967:TDE1576|5end_tRNA-i(6)A37_modification_enzyme_MiaB_1622778..1623008_POSITIVE 257 85 44 52 18 NC_002967:TDE1062|5end_ABC_transporter,_ATP-binding_protein,_HlyB_family_1088430..1088660_POSITIVE 256 97 55 125 77 NC_002967:TDE1183|5end_ABC_transporter,_ATP-binding_protein_1210612..1210842_POSITIVE 249 82 42 145 107 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 249 90 44 187 144 NC_002967:TDE1497|5end_hypothetical_protein_1543208..1543438_POSITIVE 247 136 110 59 27 NC_002967:TDE2406|5end_TldD/PmbA_family_protein_2433513..2433743_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 60 14 85 40 NC_002967:TDE1083|3end_RNA_pseudouridylate_synthase_1115031..1115181_POSITIVE 306 136 92 65 24 NC_002967:TDE1003|3end_hypothetical_protein_1029325..1029475_POSITIVE 294 98 55 76 32 NC_002967:TDE1513|3end_hypothetical_protein_1560698..1560848_POSITIVE 291 60 18 60 27 NC_002967:TDE1058|3end_hypothetical_protein_1086232..1086382_NEGATIVE 288 76 41 87 53 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 282 83 41 119 90 NC_002967:TDE1913|3end_hypothetical_protein_1930897..1931047_POSITIVE 273 76 31 123 75 NC_002967:TDE2136|3end_hypothetical_protein_2165390..2165540_NEGATIVE 272 61 25 63 18 NC_002967:TDE2337|3end_aminopeptidase_2374604..2374754_POSITIVE 268 86 47 43 7 NC_002967:TDE1857|3end_hypothetical_protein_1883929..1884079_NEGATIVE 268 90 55 53 17 NC_002967:TDE0453|3end_hypothetical_protein_510143..510293_NEGATIVE 266 84 43 57 16 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 264 69 23 111 69 NC_002967:TDE2460|3end_aminotransferase,_class_V_2487229..2487379_POSITIVE 263 48 4 65 24 NC_002967:TDE2461|3end_selenide,_water_dikinase_(selenocysteine-containing)_2487196..2487346_NEGATIVE 257 85 44 52 18 NC_002967:TDE1061|3end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_1088510..1088660_POSITIVE 256 97 55 111 63 NC_002967:TDE1182|3end_hypothetical_protein_1210678..1210828_POSITIVE 254 77 31 123 82 NC_002967:TDE1665|3end_hypothetical_protein_1718908..1719058_NEGATIVE 252 63 44 49 23 NC_002967:TDE0239|3end_glycine_reductase_complex_protein_GrdD_271828..271978_NEGATIVE 252 98 56 139 88 NC_002967:TDE0157|3end_KHG/KDPG_family_aldolase/carbohydrate_kinase,_PfkB_family_185711..185861_POSITIVE 251 136 105 105 67 NC_002967:TDE0745|3end_glycine_reductase_complex_selenoprotein_GrdA_780840..780990_POSITIVE 251 71 32 80 29 NC_002967:TDE0479|3end_hydroxylamine_reductase_535029..535179_NEGATIVE