Origin IGS: aaattaccctcttatatattatacattcaaaatagcgtactttcaagatagcaattttatctcggcttgtacataagggatttttgttatataattataagtgaggaaataaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttatttcctcacttataattatataacaaaaatcccttatgtacaagccgagataaaattgctatcttgaaagtacgctattttgaatgtataatatataagagggtaattt Mask Tandem Repeat Region ================================================ aaattaccctcttatatattatacattcaaaatagcgtactttcaagatagcaattttatctcggcttgtacataagggatttttgttatataattataagtgaggaaataaaa Find is-nt database================================================ Query_seq: TDE0622:TDE0623|TDE0622:TDE0623:radical SAM domain protein:precorrin-3B C17-methyltransferase:<-->:655809..655922 114 aaattaccctcttatatattatacattcaaaatagcgtactttcaagatagcaattttatctcggcttgtacataagggatttttgttatataattataagtgaggaaataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0622:TDE0623|TDE0622:TDE0623:radical SAM domain protein:precorrin-3B C17-methyltransferase:<-->:655809..655922 114 aaattaccctcttatatattatacattcaaaatagcgtactttcaagatagcaattttatctcggcttgtacataagggatttttgttatataattataagtgaggaaataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0622:TDE0623|TDE0622:TDE0623:radical SAM domain protein:precorrin-3B C17-methyltransferase:<-->:655809..655922 114 aaattaccctcttatatattatacattcaaaatagcgtactttcaagatagcaattttatctcggcttgtacataagggatttttgttatataattataagtgaggaaataaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaattaccctcttatatattatacattcaaaatagcgtactttcaagatagcaattttatctcggcttgtacataagggatttttgttatataattataagtgaggaaataaaa Predict ORF larger than 30AA ================================================ aaattaccctcttatatattatacattcaaaatagcgtactttcaagatagcaattttatctcggcttgtacataagggatttttgttatataattataagtgaggaaataaaa 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: 88 Start: 18 End: 47 .................CTTGAAAGTACGCTATTTTGAATGTATAAT................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 66 End: 95 .................................................................CTTGTACATAAGGGATTTTTGTTATATAAT................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaattaccctcttatatattatacattcaaaatagcgtactttcaagatagcaattttatctcggcttgtacataagggatttttgttatataattataagtgaggaaataaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0622:TDE0623|TDE0622:TDE0623:radical SAM domain protein:precorrin-3B C17-methyltransferase:<-->:655809..655922 114 aaattaccctcttatatattatacattcaaaatagcgtactttcaagatagcaattttatctcggcttgtacataagggatttttgttatataattataagtgaggaaataaaa Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_002967_TDE0622_TDE0623|radical SAM domain protein:precorrin-3B C17-methyltransferase|NEGATIVE:POSITIVE|[655809, 655922]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 aaattaccctcttatatattatacattcaaaatagcgtactttcaagatagcaattttatctcggcttgtacataagggatttttgttatataattataagtgaggaaataaaa aaattaccctcttatatattatacattcaaaatagcgtactttcaagatagcaattttatctcggcttgtacataagggatttttgttatataattataagtgaggaaataaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUACCCUCUUAUAUAUUAUACAUUCAAAAUAGCGUACUUUCAAGAUAGCAAUUUUAUCUCGGCUUGUACAUAAGGGAUUUUUGUUAUAUAAUUAUAAGUGAGGAAAUAAAA ......(((.((((((.((((((....(((((....((((..((.((((((.....)))))).))...)))).........)))))...)))))))))))).).))........ (-16.92) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUUUCCUCACUUAUAAUUAUAUAACAAAAAUCCCUUAUGUACAAGCCGAGAUAAAAUUGCUAUCUUGAAAGUACGCUAUUUUGAAUGUAUAAUAUAUAAGAGGGUAAUUU .......(((((..(((((((((((((...(((((......(((((....(((((((.......)))))))...)))))..)))))...)))))))).))))))))))...... (-20.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 843 80 31 171 122 NC_002967:TDE0622|5end_radical_SAM_domain_protein_655718..655948_NEGATIVE 255 78 32 231 181 NC_002967:TDE2371|5end_iron-sulfur_cluster-binding_protein_2403583..2403813_POSITIVE 243 79 48 39 6 NC_002967:TDE2370|5end_hypothetical_protein_2403390..2403620_POSITIVE 241 66 26 125 87 NC_002967:TDE0293|5end_MATE_efflux_family_protein_323421..323651_NEGATIVE 230 68 35 229 196 NC_002967:TDE2227|5end_hypothetical_protein_2266395..2266625_POSITIVE 228 82 42 176 125 NC_002967:TDE1393|5end_hypothetical_protein_1432494..1432724_POSITIVE 227 72 35 180 132 NC_002967:TDE1033|5end_polyA_polymerase_family_protein_1061069..1061299_POSITIVE 224 77 34 94 48 NC_002967:TDE1035|5end_transcriptional_regulator,_PadR_family_1063454..1063684_POSITIVE 224 73 32 136 90 NC_002967:TDE0701|5end_hypothetical_protein_737247..737477_NEGATIVE 223 86 45 156 111 NC_002967:TDE2310|5end_hypothetical_protein_2348042..2348272_POSITIVE 221 78 34 121 69 NC_002967:TDE0043|5end_TPR_domain_protein_49688..49918_POSITIVE 216 77 35 96 62 NC_002967:TDE1711|5end_RelA/SpoT_domain_protein_1766718..1766948_NEGATIVE 211 88 48 58 27 NC_002967:TDE1865|5end_peptidase,_M16_family_1892194..1892424_NEGATIVE 211 78 32 146 90 NC_002967:TDE0133|5end_transcriptional_regulator,_GntR_family_152373..152603_POSITIVE 210 88 48 231 177 NC_002967:TDE1348|5end_TPR_domain_protein_1388333..1388563_POSITIVE 208 83 64 34 13 NC_002967:TDE2326|5end_cobyric_acid_synthase_CobQ,_putative_2361087..2361317_POSITIVE 208 79 32 147 90 NC_002967:TDE1032|5end_hypothetical_protein_1060154..1060384_POSITIVE 207 99 58 171 123 NC_002967:TDE2304|5end_hypothetical_protein_2343440..2343670_POSITIVE 206 79 50 215 182 NC_002967:TDE2494|5end_hypothetical_protein_2518497..2518727_POSITIVE 206 79 31 175 127 NC_002967:TDE0940|5end_hypothetical_protein_963136..963366_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 79 32 131 79 NC_002967:TDE2717|3end_phosphatidate_cytidylyltransferase,_putative_2773921..2774071_NEGATIVE 243 79 48 38 5 NC_002967:TDE2369|3end_hypothetical_protein_2403469..2403619_POSITIVE 241 66 26 73 35 NC_002967:TDE0294|3end_TrkA_domain_protein_323473..323623_NEGATIVE 233 78 36 149 108 NC_002967:TDE2552|3end_ABC_transporter,_ATP-binding/permease_protein_2577370..2577520_NEGATIVE 227 72 35 128 80 NC_002967:TDE1032|3end_hypothetical_protein_1061097..1061247_POSITIVE 224 73 32 139 93 NC_002967:TDE0702|3end_ABC_transporter,_ATP-binding_protein_737244..737394_NEGATIVE 221 78 34 116 64 NC_002967:TDE0042|3end_phosphate_acetyltransferase_49763..49913_POSITIVE 216 80 34 129 76 NC_002967:TDE1083|3end_RNA_pseudouridylate_synthase_1115031..1115181_POSITIVE 214 83 45 44 10 NC_002967:TDE2325|3end_hypothetical_protein_2361177..2361327_POSITIVE 212 87 47 94 51 NC_002967:TDE2337|3end_aminopeptidase_2374604..2374754_POSITIVE 208 79 32 98 41 NC_002967:TDE1031|3end_hypothetical_protein_1060185..1060335_POSITIVE 206 66 21 87 38 NC_002967:TDE0344|3end_transcriptional_regulator,_AbrB_family_385367..385517_NEGATIVE 204 80 36 78 36 NC_002967:TDE2776|3end_proline_iminopeptidase_2828385..2828535_POSITIVE 204 69 22 131 92 NC_002967:TDE2296|3end_hypothetical_protein_2334283..2334433_NEGATIVE 204 66 26 46 3 NC_002967:TDE0697|3end_hypothetical_protein_734220..734370_NEGATIVE 202 80 40 53 10 NC_002967:TDE1908|3end_hypothetical_protein_1925099..1925249_NEGATIVE 201 66 33 123 80 NC_002967:TDE0860|3end_ribosomal_small_subunit_pseudouridine_synthase_A_881840..881990_POSITIVE 199 87 62 51 24 NC_002967:TDE2176|3end_site-specific_recombinase,_putative_2204401..2204551_NEGATIVE 198 80 34 56 10 NC_002967:TDE2032|3end_hypothetical_protein_2059171..2059321_NEGATIVE 197 80 63 114 94 NC_002967:TDE2495|3end_hypothetical_protein_2518735..2518885_NEGATIVE