Origin IGS: aatgcctccaaaaaatttatataaaatttaaaatgctttgccaattaataatgatggcatttttattctatattaaattcatttattattcaagggtctatatattatagaatttaaacgcaaagcattcagaagtttaatttataattacccattgccaatttccc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gggaaattggcaatgggtaattataaattaaacttctgaatgctttgcgtttaaattctataatatatagacccttgaataataaatgaatttaatatagaataaaaatgccatcattattaattggcaaagcattttaaattttatataaattttttggaggcatt Mask Tandem Repeat Region ================================================ aatgcctccaaaaaatttatataaaatttaaaatgctttgccaattaataatgatggcatttttattctatattaaattcatttattattcaagggtctatatattatagaatttaaacgcaaagcattcagaagtttaatttataattacccattgccaatttccc Find is-nt database================================================ Query_seq: TDE0240:TDE0241|TDE0240:TDE0241:glycine reductase complex protein GrdC:hypothetical protein:<-<-:274624..274790 167 aatgcctccaaaaaatttatataaaatttaaaatgctttgccaattaataatgatggcatttttattctatattaaattcatttattattcaagggtctatatattatagaatttaaacgcaaagcattcagaagtttaatttataattacccattgccaatttccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0240:TDE0241|TDE0240:TDE0241:glycine reductase complex protein GrdC:hypothetical protein:<-<-:274624..274790 167 aatgcctccaaaaaatttatataaaatttaaaatgctttgccaattaataatgatggcatttttattctatattaaattcatttattattcaagggtctatatattatagaatttaaacgcaaagcattcagaagtttaatttataattacccattgccaatttccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0240:TDE0241|TDE0240:TDE0241:glycine reductase complex protein GrdC:hypothetical protein:<-<-:274624..274790 167 aatgcctccaaaaaatttatataaaatttaaaatgctttgccaattaataatgatggcatttttattctatattaaattcatttattattcaagggtctatatattatagaatttaaacgcaaagcattcagaagtttaatttataattacccattgccaatttccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatgcctccaaaaaatttatataaaatttaaaatgctttgccaattaataatgatggcatttttattctatattaaattcatttattattcaagggtctatatattatagaatttaaacgcaaagcattcagaagtttaatttataattacccattgccaatttccc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 15 End: 107 .............. M Y I K F K M L C Q L I M M A F L F Y I K F I Y Y S R V Y I L ............................................................ Protein_Len: 30 Strand: + Start: 77 End: 166 ............................................................................ M H L L F K G L Y I I E F K R K A F R S L I Y N Y P L P I S . aatgcctccaaaaaatttatataaaatttaaaatgctttgccaattaataatgatggcatttttattctatattaaattcatttattattcaagggtctatatattatagaatttaaacgcaaagcattcagaagtttaatttataattacccattgccaatttccc 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: 85 Start: 65 End: 94 ................................................................CTTGAATAATAAATGAATTTAATATAGAAT......................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 37 End: 66 ....................................TTTGCCAATTAATAATGATGGCATTTTTAT..................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 16 End: 45 ...............ATTGGCAAAGCATTTTAAATTTTATATAAA.......................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 104 End: 133 .......................................................................................................TCTGAATGCTTTGCGTTTAAATTCTATAAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatgcctccaaaaaatttatataaaatttaaaatgctttgccaattaataatgatggcatttttattctatattaaattcatttattattcaagggtctatatattatagaatttaaacgcaaagcattcagaagtttaatttataattacccattgccaatttccc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0240:TDE0241|TDE0240:TDE0241:glycine reductase complex protein GrdC:hypothetical protein:<-<-:274624..274790 167 aatgcctccaaaaaatttatataaaatttaaaatgctttgccaattaataatgatggcatttttattctatattaaattcatttattattcaagggtctatatattatagaatttaaacgcaaagcattcagaagtttaatttataattacccattgccaatttccc Intra-Species Hit: Count: 1 Min: 1 Max: 167 Len: 167 Subject: NC_002967_TDE0240_TDE0241|glycine reductase complex protein GrdC:hypothetical protein|NEGATIVE:NEGATIVE|[274624,274790]|167 HSP 1 e-value: 4.0E-90 bit: 331.0 Len: 167 Query Start:1 Query End:167 Subject Strand: POSITIVE Subject Start: 1 Subject End: 167 aatgcctccaaaaaatttatataaaatttaaaatgctttgccaattaataatgatggcatttttattctatattaaattcatttattattcaagggtctatatattatagaatttaaacgcaaagcattcagaagtttaatttataattacccattgccaatttccc aatgcctccaaaaaatttatataaaatttaaaatgctttgccaattaataatgatggcatttttattctatattaaattcatttattattcaagggtctatatattatagaatttaaacgcaaagcattcagaagtttaatttataattacccattgccaatttccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGCCUCCAAAAAAUUUAUAUAAAAUUUAAAAUGCUUUGCCAAUUAAUAAUGAUGGCAUUUUUAUUCUAUAUUAAAUUCAUUUAUUAUUCAAGGGUCUAUAUAUUAUAGAAUUUAAACGCAAAGCAUUCAGAAGUUUAAUUUAUAAUUACCCAUUGCCAAUUUCCC ................(((((..((((((..((((((((((.....(((((((((((....((((........)))).))).))))))))......((((((...))))))........))))))))))...))))))....))))).................... (-22.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGAAAUUGGCAAUGGGUAAUUAUAAAUUAAACUUCUGAAUGCUUUGCGUUUAAAUUCUAUAAUAUAUAGACCCUUGAAUAAUAAAUGAAUUUAAUAUAGAAUAAAAAUGCCAUCAUUAUUAAUUGGCAAAGCAUUUUAAAUUUUAUAUAAAUUUUUUGGAGGCAUU .........((...((((...((((.((((......(((((((...))))))).......)))).)))).))))........((((.(((((((.((((((((.(((((((..(((........)))....)))))))..)))))))))))))))))))...))... (-25.82) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 741 140 91 231 182 NC_002967:TDE0240|5end_glycine_reductase_complex_protein_GrdC_274533..274763_NEGATIVE 230 68 35 203 162 NC_002967:TDE2541|5end_hypothetical_protein_2568165..2568395_POSITIVE 209 65 21 217 164 NC_002967:TDE2631|5end_peptide_ABC_transporter,_permease_protein,_putative_2671829..2672059_POSITIVE 207 57 26 229 200 NC_002967:TDE1512|5end_hypothetical_protein_1559203..1559433_POSITIVE 206 70 23 148 106 NC_002967:TDE0839|5end_rhodanese-like_domain_protein_859341..859571_NEGATIVE 202 65 23 180 143 NC_002967:TDE1073|5end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_1103515..1103745_POSITIVE 201 96 56 223 190 NC_002967:TDE2476|5end_carbamate_kinase_2499450..2499680_NEGATIVE 198 43 3 90 52 NC_002967:TDE1501|5end_pyruvate_phosphate_dikinase_1548041..1548271_POSITIVE 197 29 5 173 148 NC_002967:TDE1290|5end_hypothetical_protein_1327399..1327629_POSITIVE 197 29 5 88 63 NC_002967:TDE1289|5end_hypothetical_protein_1327314..1327544_POSITIVE 195 72 34 180 142 NC_002967:TDE1413|5end_cytidylyltransferase/phosphoenolpyruvate_phosphomutase,_putative_1455510..1455740_POSITIVE 191 41 3 129 94 NC_002967:TDE2723|5end_phosphoribosylpyrophosphate_synthetase_2782127..2782357_NEGATIVE 189 59 35 176 148 NC_002967:TDE2130|5end_hypothetical_protein_2162059..2162289_NEGATIVE 189 30 5 111 85 NC_002967:TDE1288|5end_CAAX_amino_terminal_protease_family_protein_1326317..1326547_POSITIVE 187 58 33 159 137 NC_002967:TDE1037|5end_hypothetical_protein_1064470..1064700_POSITIVE 181 71 34 80 38 NC_002967:TDE0662|5end_hypothetical_protein_697835..698065_NEGATIVE 180 130 89 167 128 NC_002967:TDE2281|5end_LysM_domain_protein_2318493..2318723_NEGATIVE 180 59 39 71 50 NC_002967:TDE2204|5end_Na+/H+_antiporter_family_protein_2241169..2241399_POSITIVE 180 131 91 90 50 NC_002967:TDE1989|5end_acyltransferase_family_protein_2006343..2006573_NEGATIVE 179 24 2 119 94 NC_002967:TDE2729|5end_hypothetical_protein_2786457..2786687_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 207 57 26 140 111 NC_002967:TDE1511|3end_pathogen-specific_surface_antigen,_putative_1559194..1559344_POSITIVE 206 70 23 70 28 NC_002967:TDE0840|3end_hypothetical_protein_859419..859569_NEGATIVE 198 159 119 52 13 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 192 159 118 132 93 NC_002967:TDE1753|3end_UDP-glucose_4-epimerase_1805521..1805671_NEGATIVE 189 59 35 145 117 NC_002967:TDE2131|3end_cobalamin_biosynthesis_protein_CbiM,_putative_2162090..2162240_NEGATIVE 184 159 119 47 9 NC_002967:TDE1839|3end_hypothetical_protein_1870391..1870541_NEGATIVE 181 71 34 75 33 NC_002967:TDE0663|3end_hypothetical_protein_697840..697990_NEGATIVE 180 131 91 66 26 NC_002967:TDE1990|3end_ATP-dependent_helicase,_DinG_family_2006367..2006517_NEGATIVE 180 115 87 68 36 NC_002967:TDE0439|3end_hypothetical_protein_495104..495254_NEGATIVE 179 43 11 115 79 NC_002967:TDE2108|3end_hypothetical_protein_2132902..2133052_NEGATIVE 176 97 52 133 86 NC_002967:TDE0672|3end_hypothetical_protein_712011..712161_POSITIVE 175 61 33 48 22 NC_002967:TDE1323|3end_hypothetical_protein_1360968..1361118_POSITIVE 175 91 52 83 46 NC_002967:TDE0398|3end_oligopeptide/dipeptide_ABC_transporter,_periplasmic_peptide-binding_protein_449436..449586_POSITIVE 174 159 119 105 69 NC_002967:TDE2346|3end_elongation_factor_Ts_2382587..2382737_NEGATIVE 174 59 36 79 51 NC_002967:TDE1659|3end_alanyl-tRNA_synthetase_1708831..1708981_NEGATIVE 174 155 125 60 24 NC_002967:TDE0509|3end_hypothetical_protein_559804..559954_NEGATIVE 174 60 36 66 46 NC_002967:TDE0134|3end_oxidoreductase,_FAD-dependent_155010..155160_POSITIVE 172 145 116 87 58 NC_002967:TDE1941|3end_hypothetical_protein_1956505..1956655_NEGATIVE 171 65 24 88 48 NC_002967:TDE0327|3end_CRISPR-associated_SAG0894_family_protein_365148..365298_POSITIVE 169 43 3 44 7 NC_002967:TDE2772|3end_ABC_transporter,_ATP-binding_protein,_truncation_2825884..2826034_POSITIVE