Origin IGS: gcttctacctccttcttatgtacccatactactctacatttattgtatgtcttttttcagataaaatcaaggctatttattaattggtatttattaattgagggact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtccctcaattaataaataccaattaataaatagccttgattttatctgaaaaaagacatacaataaatgtagagtagtatgggtacataagaaggaggtagaagc Mask Tandem Repeat Region ================================================ gcttctacctccttcttatgtacccatactactctacatttattgtatgtcttttttcagataaaatcaaggcnnnnnnnnnnnnnnnnnnnnnnnnnnnagggact Find is-nt database================================================ Query_seq: TDE2411:TDE2412|TDE2411:TDE2412:glycogen phosphorylase:acetyltransferase, GNAT family:<-<-:2439778..2439884 107 gcttctacctccttcttatgtacccatactactctacatttattgtatgtcttttttcagataaaatcaaggctatttattaattggtatttattaattgagggact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2411:TDE2412|TDE2411:TDE2412:glycogen phosphorylase:acetyltransferase, GNAT family:<-<-:2439778..2439884 107 gcttctacctccttcttatgtacccatactactctacatttattgtatgtcttttttcagataaaatcaaggctatttattaattggtatttattaattgagggact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2411:TDE2412|TDE2411:TDE2412:glycogen phosphorylase:acetyltransferase, GNAT family:<-<-:2439778..2439884 107 gcttctacctccttcttatgtacccatactactctacatttattgtatgtcttttttcagataaaatcaaggctatttattaattggtatttattaattgagggact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcttctacctccttcttatgtacccatactactctacatttattgtatgtcttttttcagataaaatcaaggctatttattaattggtatttattaattgagggact Predict ORF larger than 30AA ================================================ gcttctacctccttcttatgtacccatactactctacatttattgtatgtcttttttcagataaaatcaaggctatttattaattggtatttattaattgagggact 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: 81 Start: 38 End: 67 .....................................ATTTATTGTATGTCTTTTTTCAGATAAAAT........................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 42 End: 71 .........................................CTTGATTTTATCTGAAAAAAGACATACAAT.................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcttctacctccttcttatgtacccatactactctacatttattgtatgtcttttttcagataaaatcaaggctatttattaattggtatttattaattgagggact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2411:TDE2412|TDE2411:TDE2412:glycogen phosphorylase:acetyltransferase, GNAT family:<-<-:2439778..2439884 107 gcttctacctccttcttatgtacccatactactctacatttattgtatgtcttttttcagataaaatcaaggctatttattaattggtatttattaattgagggact Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_002967_TDE2411_TDE2412|glycogen phosphorylase:acetyltransferase, GNAT family|NEGATIVE:NEGATIVE|[2439778,2439884]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 gcttctacctccttcttatgtacccatactactctacatttattgtatgtcttttttcagataaaatcaaggctatttattaattggtatttattaattgagggact gcttctacctccttcttatgtacccatactactctacatttattgtatgtcttttttcagataaaatcaaggctatttattaattggtatttattaattgagggact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUCUACCUCCUUCUUAUGUACCCAUACUACUCUACAUUUAUUGUAUGUCUUUUUUCAGAUAAAAUCAAGGCUAUUUAUUAAUUGGUAUUUAUUAAUUGAGGGACU .........(((((((((.(((((..........((((.....)))).(((((..((.......))..)))))............)))))....)))..)))))).. (-13.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUCCCUCAAUUAAUAAAUACCAAUUAAUAAAUAGCCUUGAUUUUAUCUGAAAAAAGACAUACAAUAAAUGUAGAGUAGUAUGGGUACAUAAGAAGGAGGUAGAAGC ....((((.((((((........)))))).....((((........(((......)))..((((.....)))).........))))..........))))....... (-11.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 840 50 1 141 92 NC_002967:TDE2411|5end_glycogen_phosphorylase_2439687..2439917_NEGATIVE 247 35 1 101 57 NC_002967:TDE0099|5end_adenine-specific_DNA_modification_methyltransferase_115648..115878_POSITIVE 239 35 1 134 93 NC_002967:TDE1209|5end_site-specific_recombinase,_phage_integrase_family_1242345..1242575_POSITIVE 239 47 2 227 184 NC_002967:TDE0368|5end_type_I_restriction-modification_system,_S_subunit,_putative_418245..418475_NEGATIVE 221 59 19 139 97 NC_002967:TDE1416|5end_ABC_transporter,_permease_protein_1459796..1460026_POSITIVE 216 35 3 129 94 NC_002967:TDE1527|5end_hypothetical_protein_1570804..1571034_POSITIVE 213 45 6 192 158 NC_002967:TDE0565|5end_hypothetical_protein_597031..597261_POSITIVE 208 78 37 107 67 NC_002967:TDE1722|5end_hypothetical_protein_1776085..1776315_POSITIVE 208 42 1 107 63 NC_002967:TDE1612|5end_phosphoribosyl_transferase_domain_protein_1660549..1660779_POSITIVE 205 87 47 117 78 NC_002967:TDE2177|5end_hypothetical_protein_2206524..2206754_NEGATIVE 201 24 3 72 50 NC_002967:TDE2780|5end_hypothetical_protein_2830621..2830851_NEGATIVE 197 60 12 141 94 NC_002967:TDE0425|5end_bacteriocin_ABC_transporter,_ATP-binding/permease,_putative_479700..479930_POSITIVE 196 35 3 188 165 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 196 75 31 140 97 NC_002967:TDE0900|5end_ABC_transporter,_ATP-binding_protein_917188..917418_POSITIVE 194 50 1 179 135 NC_002967:TDE1557|5end_hypothetical_protein_1599986..1600216_POSITIVE 194 87 42 172 143 NC_002967:TDE0196|5end_hypothetical_protein_232571..232801_POSITIVE 194 38 6 230 200 NC_002967:TDE0035|5end_acetyltransferase,_GNAT_family_42020..42250_NEGATIVE 193 30 1 119 98 NC_002967:TDE2424|5end_50S_ribosomal_protein_L1_2454717..2454947_NEGATIVE 192 41 3 174 142 NC_002967:TDE0229|5end_ATPase_family_protein_262746..262976_NEGATIVE 192 51 19 161 126 NC_002967:TDE0108|5end_hypothetical_protein_128399..128629_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 50 2 121 73 NC_002967:TDE0369|3end_type_I_restriction-modification_system,_M_subunit_418356..418506_NEGATIVE 245 36 1 38 12 NC_002967:TDE2196|3end_hypothetical_protein_2231883..2232033_NEGATIVE 239 35 1 141 100 NC_002967:TDE1208|3end_DNA_topoisomerase_I_1242432..1242582_POSITIVE 221 59 19 134 92 NC_002967:TDE1415|3end_nucleotidyl_transferase/aminotransferase,_class_V_1459871..1460021_POSITIVE 219 35 1 151 115 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 218 60 20 124 85 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 216 35 3 132 97 NC_002967:TDE1526|3end_hypothetical_protein_1570887..1571037_POSITIVE 213 45 6 96 62 NC_002967:TDE0564|3end_hypothetical_protein_597015..597165_POSITIVE 208 78 37 70 30 NC_002967:TDE1721|3end_radical_SAM_domain_protein_1776128..1776278_POSITIVE 207 48 1 122 77 NC_002967:TDE0908|3end_ABC_transporter,_ATP-binding/permease_protein_927085..927235_POSITIVE 201 24 3 54 32 NC_002967:TDE2781|3end_ABC_transporter,_ATP-binding/permease_protein_2830639..2830789_NEGATIVE 197 60 12 134 87 NC_002967:TDE0424|3end_bacteriocin-type_signal_domain_protein_479773..479923_POSITIVE 196 75 31 149 106 NC_002967:TDE0899|3end_ABC_transporter,_permease_protein,_putative_917277..917427_POSITIVE 194 38 6 115 85 NC_002967:TDE0036|3end_hypothetical_protein_42135..42285_NEGATIVE 193 30 1 117 96 NC_002967:TDE2425|3end_50S_ribosomal_protein_L11_2454719..2454869_NEGATIVE 192 41 3 121 89 NC_002967:TDE0230|3end_DNA_replication_and_repair_protein_RecF_262799..262949_NEGATIVE 189 50 11 73 33 NC_002967:TDE0288|3end_hypothetical_protein_319124..319274_NEGATIVE 188 34 3 119 89 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE 183 50 1 98 47 NC_002967:TDE2762|3end_flagellar_motor_switch_protein_FliY_2816563..2816713_NEGATIVE 183 37 1 140 88 NC_002967:TDE1660|3end_leucine_Rich_Repeat_domain_protein_1710710..1710860_NEGATIVE