Origin IGS: aggaattcttaaaaattaaggattgatattatattcaaattgatttatagtacatacaatgaccgataatcggagggagccggtttaaggtcgggttattgggaggcttata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tataagcctcccaataacccgaccttaaaccggctccctccgattatcggtcattgtatgtactataaatcaatttgaatataatatcaatccttaatttttaagaattcct Mask Tandem Repeat Region ================================================ aggaattcttaaaaattaaggattgatattatattcaaattgatttatagtacatacaatgaccgataatcggagggagccggtttaaggtcgggttattgggaggcttata Find is-nt database================================================ Query_seq: TDE1311:TDE1312|TDE1311:TDE1312:ABC transporter, ATP-binding/permease protein:hypothetical protein:->->:1349116..1349227 112 aggaattcttaaaaattaaggattgatattatattcaaattgatttatagtacatacaatgaccgataatcggagggagccggtttaaggtcgggttattgggaggcttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1311:TDE1312|TDE1311:TDE1312:ABC transporter, ATP-binding/permease protein:hypothetical protein:->->:1349116..1349227 112 aggaattcttaaaaattaaggattgatattatattcaaattgatttatagtacatacaatgaccgataatcggagggagccggtttaaggtcgggttattgggaggcttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1311:TDE1312|TDE1311:TDE1312:ABC transporter, ATP-binding/permease protein:hypothetical protein:->->:1349116..1349227 112 aggaattcttaaaaattaaggattgatattatattcaaattgatttatagtacatacaatgaccgataatcggagggagccggtttaaggtcgggttattgggaggcttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggaattcttaaaaattaaggattgatattatattcaaattgatttatagtacatacaatgaccgataatcggagggagccggtttaaggtcgggttattgggaggcttata Predict ORF larger than 30AA ================================================ aggaattcttaaaaattaaggattgatattatattcaaattgatttatagtacatacaatgaccgataatcggagggagccggtttaaggtcgggttattgggaggcttata 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: 86 Start: 22 End: 51 .....................ATTGATATTATATTCAAATTGATTTATAGT............................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggaattcttaaaaattaaggattgatattatattcaaattgatttatagtacatacaatgaccgataatcggagggagccggtttaaggtcgggttattgggaggcttata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1311:TDE1312|TDE1311:TDE1312:ABC transporter, ATP-binding/permease protein:hypothetical protein:->->:1349116..1349227 112 aggaattcttaaaaattaaggattgatattatattcaaattgatttatagtacatacaatgaccgataatcggagggagccggtttaaggtcgggttattgggaggcttata Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_002967_TDE1311_TDE1312|ABC transporter, ATP-binding/permease protein:hypothetical protein|POSITIVE:POSITIVE|[1349116,1349227]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 aggaattcttaaaaattaaggattgatattatattcaaattgatttatagtacatacaatgaccgataatcggagggagccggtttaaggtcgggttattgggaggcttata aggaattcttaaaaattaaggattgatattatattcaaattgatttatagtacatacaatgaccgataatcggagggagccggtttaaggtcgggttattgggaggcttata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAAUUCUUAAAAAUUAAGGAUUGAUAUUAUAUUCAAAUUGAUUUAUAGUACAUACAAUGACCGAUAAUCGGAGGGAGCCGGUUUAAGGUCGGGUUAUUGGGAGGCUUAUA ...((((((((.....))))))))..(((((((.((.....))..)))))))....(((((((((((((((((......))))))....))).))))))))........... (-24.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAGCCUCCCAAUAACCCGACCUUAAACCGGCUCCCUCCGAUUAUCGGUCAUUGUAUGUACUAUAAAUCAAUUUGAAUAUAAUAUCAAUCCUUAAUUUUUAAGAAUUCCU ..((((..............((((......(((......)))......))))......................((((........))))..))))................ ( -9.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 109 64 54 1 NC_002967:TDE1299|5end_hypothetical_protein_1336613..1336843_NEGATIVE 350 99 55 61 5 NC_002967:TDE0767|5end_ribosomal_protein_L3_806355..806585_POSITIVE 340 106 69 230 197 NC_002967:TDE2106|5end_hypothetical_protein_2131740..2131970_NEGATIVE 338 109 72 58 24 NC_002967:TDE0359|5end_ABC_transporter,_ATP-binding/permease_protein_404100..404330_NEGATIVE 337 105 63 55 12 NC_002967:TDE1664|5end_hypothetical_protein_1717862..1718092_POSITIVE 336 94 53 213 163 NC_002967:TDE0056|5end_DNA-directed_RNA_polymerase,_omega_subunit,_putative_65706..65936_POSITIVE 334 106 64 165 114 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 332 108 71 152 125 NC_002967:TDE2619|5end_RNA_methyltransferase,_TrmA_family,_putative_2660280..2660510_POSITIVE 328 109 71 231 189 NC_002967:TDE1500|5end_hypothetical_protein_1548070..1548300_NEGATIVE 325 94 52 181 147 NC_002967:TDE2751|5end_hypothetical_protein_2807570..2807800_POSITIVE 323 99 61 230 198 NC_002967:TDE2466|5end_hypothetical_protein_2489860..2490090_NEGATIVE 315 109 68 182 149 NC_002967:TDE2094|5end_hypothetical_protein_2121319..2121549_NEGATIVE 314 106 63 229 188 NC_002967:TDE2446|5end_malate_dehydrogenase_2476249..2476479_NEGATIVE 314 108 63 177 134 NC_002967:TDE0915|5end_hypothetical_protein_933320..933550_NEGATIVE 310 109 69 185 124 NC_002967:TDE2152|5end_hypothetical_protein_2189103..2189333_NEGATIVE 308 97 55 205 159 NC_002967:TDE2717|5end_phosphatidate_cytidylyltransferase,_putative_2774547..2774777_NEGATIVE 305 109 73 206 176 NC_002967:TDE1830|5end_hypothetical_protein_1863583..1863813_POSITIVE 295 107 63 193 157 NC_002967:TDE1540|5end_hypothetical_protein_1584422..1584652_POSITIVE 294 100 53 88 40 NC_002967:TDE1486|5end_hypothetical_protein_1530299..1530529_POSITIVE 293 109 72 142 107 NC_002967:TDE2565|5end_hypothetical_protein_2591273..2591503_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 83 63 54 33 NC_002967:TDE2163|3end_hypothetical_protein_2195533..2195683_NEGATIVE 365 109 64 57 4 NC_002967:TDE1300|3end_hypothetical_protein_1336610..1336760_NEGATIVE 338 109 72 56 22 NC_002967:TDE0360|3end_ABC_transporter,_ATP-binding/permease_protein_404102..404252_NEGATIVE 332 108 71 139 112 NC_002967:TDE2618|3end_PHP_domain_protein_2660347..2660497_POSITIVE 318 109 62 82 23 NC_002967:TDE1664|3end_hypothetical_protein_1718982..1719132_POSITIVE 316 85 41 127 87 NC_002967:TDE2265|3end_hypothetical_protein_2302634..2302784_POSITIVE 311 104 71 57 19 NC_002967:TDE2087|3end_translation_initiation_factor_IF-1_2115468..2115618_NEGATIVE 310 107 64 106 50 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE 294 109 72 57 22 NC_002967:TDE2420|3end_DNA-directed_RNA_polymerase_beta'_subunit_2444960..2445110_NEGATIVE 294 110 61 80 37 NC_002967:TDE2317|3end_hemolysin_III_2354118..2354268_NEGATIVE 294 100 53 91 43 NC_002967:TDE1485|3end_hypothetical_protein_1530382..1530532_POSITIVE 293 109 72 83 48 NC_002967:TDE2566|3end_hypothetical_protein_2591332..2591482_NEGATIVE 293 110 64 93 48 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 292 108 65 69 24 NC_002967:TDE2181|3end_PAP2_family_protein_2211995..2212145_NEGATIVE 291 108 64 82 37 NC_002967:TDE2124|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpA_2158763..2158913_POSITIVE 288 106 63 151 106 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 287 107 63 48 10 NC_002967:TDE1451|3end_hypothetical_protein_1497850..1498000_NEGATIVE 284 107 63 76 36 NC_002967:TDE2730|3end_hydrolase,_TatD_family_2787439..2787589_POSITIVE 282 99 63 69 38 NC_002967:TDE0978|3end_hypothetical_protein_1002424..1002574_POSITIVE 281 106 64 79 14 NC_002967:TDE1008|3end_flagellar_protein,_putative_1032806..1032956_POSITIVE