Origin IGS: gcaattaaaaatctgtaagaaggacaatttatagaaaaatcataaaacaaaaaagctgcccaagcatttgaacttggacagctttttaattatcggtttaaagtaaaagac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtcttttactttaaaccgataattaaaaagctgtccaagttcaaatgcttgggcagcttttttgttttatgatttttctataaattgtccttcttacagatttttaattgc Mask Tandem Repeat Region ================================================ gcaattaaaaatctgtaagaaggacaatttatagaaaaatcataaaacaaaaaagctgcccaagcatttgaacttggacagctttttaattatcggtttaaagtaaaagac Find is-nt database================================================ Query_seq: TDE0406:TDE0407|TDE0406:TDE0407:hypothetical protein:glutamate synthase (NADPH), homotetrameric:-><-:458990..459100 111 gcaattaaaaatctgtaagaaggacaatttatagaaaaatcataaaacaaaaaagctgcccaagcatttgaacttggacagctttttaattatcggtttaaagtaaaagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0406:TDE0407|TDE0406:TDE0407:hypothetical protein:glutamate synthase (NADPH), homotetrameric:-><-:458990..459100 111 gcaattaaaaatctgtaagaaggacaatttatagaaaaatcataaaacaaaaaagctgcccaagcatttgaacttggacagctttttaattatcggtttaaagtaaaagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0406:TDE0407|TDE0406:TDE0407:hypothetical protein:glutamate synthase (NADPH), homotetrameric:-><-:458990..459100 111 gcaattaaaaatctgtaagaaggacaatttatagaaaaatcataaaacaaaaaagctgcccaagcatttgaacttggacagctttttaattatcggtttaaagtaaaagac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaattaaaaatctgtaagaaggacaatttatagaaaaatcataaaacaaaaaagctgcccaagcatttgaacttggacagctttttaattatcggtttaaagtaaaagac Predict ORF larger than 30AA ================================================ gcaattaaaaatctgtaagaaggacaatttatagaaaaatcataaaacaaaaaagctgcccaagcatttgaacttggacagctttttaattatcggtttaaagtaaaagac Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcaattaaaaatctgtaagaaggacaatttatagaaaaatcataaaacaaaaaagctgcccaagcatttgaacttggacagctttttaattatcggtttaaagtaaaagac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 82 HP_score: -7.0 Tail_Score: -4.93968 Start: 55 End: 82 Full_Region: TCATAAAACAAAAAA GCTGCCCAAG CATTTGAA CTTGGACAGC TTTTTAATTATCGGT ......................................................GCTGCCCAAGCATTTGAACTTGGACAGC............................. Find igs database================================================ Query_seq: TDE0406:TDE0407|TDE0406:TDE0407:hypothetical protein:glutamate synthase (NADPH), homotetrameric:-><-:458990..459100 111 gcaattaaaaatctgtaagaaggacaatttatagaaaaatcataaaacaaaaaagctgcccaagcatttgaacttggacagctttttaattatcggtttaaagtaaaagac Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_002967_TDE0406_TDE0407|hypothetical protein:glutamate synthase (NADPH), homotetrameric|POSITIVE:NEGATIVE|[458990,459100]|111 HSP 1 e-value: 1.0E-24 bit: 113.0 Len: 57 Query Start:55 Query End:111 Subject Strand: POSITIVE Subject Start: 55 Subject End: 111 ......................................................gctgcccaagcatttgaacttggacagctttttaattatcggtttaaagtaaaagac ......................................................gctgcccaagcatttgaacttggacagctttttaattatcggtttaaagtaaaagac HSP 2 e-value: 6.0E-11 bit: 67.9 Len: 34 Query Start:1 Query End:34 Subject Strand: POSITIVE Subject Start: 1 Subject End: 34 gcaattaaaaatctgtaagaaggacaatttatag............................................................................. gcaattaaaaatctgtaagaaggacaatttatag............................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAUUAAAAAUCUGUAAGAAGGACAAUUUAUAGAAAAAUCAUAAAACAAAAAAGCUGCCCAAGCAUUUGAACUUGGACAGCUUUUUAAUUAUCGGUUUAAAGUAAAAGAC ...........((((((((........)))))))).(((((((((....(((((((((.(((((........))))).)))))))))..)))).)))))............ (-23.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUUUUACUUUAAACCGAUAAUUAAAAAGCUGUCCAAGUUCAAAUGCUUGGGCAGCUUUUUUGUUUUAUGAUUUUUCUAUAAAUUGUCCUUCUUACAGAUUUUUAAUUGC .................(((((((((((((((((((((((......))))))))))))))))........((....))....)))))))...................... (-26.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 97 53 142 95 NC_002967:TDE1312|5end_hypothetical_protein_1349088..1349318_POSITIVE 274 100 52 210 166 NC_002967:TDE1919|5end_hypothetical_protein_1939890..1940120_NEGATIVE 263 98 51 178 130 NC_002967:TDE2428|5end_ribosomal_protein_L33_2456292..2456522_NEGATIVE 260 85 46 212 174 NC_002967:TDE1421|5end_hypothetical_protein_1465632..1465862_POSITIVE 256 77 39 121 79 NC_002967:TDE1512|5end_hypothetical_protein_1559203..1559433_POSITIVE 246 99 53 95 57 NC_002967:TDE1415|5end_nucleotidyl_transferase/aminotransferase,_class_V_1457941..1458171_POSITIVE 245 109 64 178 131 NC_002967:TDE0143|5end_thiamine_ABC_transporter,_thiamine-binding_protein_164013..164243_POSITIVE 241 85 50 186 149 NC_002967:TDE0655|5end_response_regulator_690921..691151_POSITIVE 240 43 8 70 32 NC_002967:TDE0189|5end_hypothetical_protein_226460..226690_NEGATIVE 236 84 50 206 177 NC_002967:TDE1830|5end_hypothetical_protein_1863583..1863813_POSITIVE 235 96 54 216 178 NC_002967:TDE1592|5end_ABC_transporter,_ATP-binding_protein_1639491..1639721_POSITIVE 235 96 56 67 31 NC_002967:TDE1507|5end_L-serine_dehydratase,_iron-sulfur-dependent,_beta_subunit_1555724..1555954_NEGATIVE 235 60 14 229 182 NC_002967:TDE0834|5end_Na(+)-translocating_NADH-quinone_reductase,_E_subunit_854863..855093_NEGATIVE 232 99 56 175 139 NC_002967:TDE2714|5end_hypothetical_protein_2772618..2772848_NEGATIVE 229 96 51 209 161 NC_002967:TDE1093|5end_hypothetical_protein_1127374..1127604_POSITIVE 227 99 51 83 39 NC_002967:TDE0306|5end_signal_peptide_peptidase_SppA_338619..338849_NEGATIVE 226 99 55 174 121 NC_002967:TDE1291|5end_HD_domain_protein_1329213..1329443_NEGATIVE 225 99 53 75 27 NC_002967:TDE0955|5end_LemA_family_protein_978842..979072_POSITIVE 224 98 51 114 59 NC_002967:TDE1335|5end_alginate_O-acetylation_protein,_putative_1370816..1371046_POSITIVE 224 96 52 218 179 NC_002967:TDE1314|5end_penicillin-binding_protein_1351174..1351404_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 87 50 41 4 NC_002967:TDE0406|3end_hypothetical_protein_458929..459079_POSITIVE 285 87 49 87 49 NC_002967:TDE1012|3end_tex_protein,_putative_1043926..1044076_POSITIVE 275 85 48 75 41 NC_002967:TDE0948|3end_hypothetical_protein_970959..971109_NEGATIVE 257 95 51 61 15 NC_002967:TDE1013|3end_hemerythrin-related_protein_1043977..1044127_NEGATIVE 254 96 55 97 63 NC_002967:TDE0658|3end_ABC_transporter,_permease_protein_695679..695829_POSITIVE 247 97 51 85 36 NC_002967:TDE1673|3end_ATP-dependent_protease_ATP-binding_subunit_1728205..1728355_POSITIVE 246 99 53 102 64 NC_002967:TDE1414|3end_phosphonopyruvate_decarboxylase,_putative_1458028..1458178_POSITIVE 245 109 64 150 103 NC_002967:TDE0141|3end_hypothetical_protein_164065..164215_POSITIVE 244 77 48 32 3 NC_002967:TDE1511|3end_pathogen-specific_surface_antigen,_putative_1559194..1559344_POSITIVE 241 99 51 82 41 NC_002967:TDE2584|3end_dipeptidase_2617944..2618094_POSITIVE 241 85 50 43 6 NC_002967:TDE0654|3end_peptidase,_M20/M25/M40_family_690858..691008_POSITIVE 240 43 8 51 13 NC_002967:TDE0190|3end_hypothetical_protein_226479..226629_NEGATIVE 237 87 43 68 34 NC_002967:TDE2778|3end_PspC_domain_protein_2829371..2829521_NEGATIVE 230 100 54 115 69 NC_002967:TDE1942|3end_hypothetical_protein_1959438..1959588_POSITIVE 226 99 55 73 20 NC_002967:TDE1292|3end_TldD/PmbA_family_protein_1329314..1329464_NEGATIVE 224 98 51 92 37 NC_002967:TDE1334|3end_hypothetical_protein_1370874..1371024_POSITIVE 223 82 46 151 116 NC_002967:TDE1420|3end_hypothetical_protein_1465654..1465804_POSITIVE 222 99 54 72 30 NC_002967:TDE1767|3end_hypothetical_protein_1812926..1813076_NEGATIVE 221 99 55 104 65 NC_002967:TDE1106|3end_translation_initiation_factor_IF-2_1138192..1138342_NEGATIVE 219 85 55 33 5 NC_002967:TDE2162|3end_NOL1/NOP2/sun_family_protein_2195560..2195710_POSITIVE