Origin IGS: ccattaccccccaagtctatatttaatcacaaaaagacttcctgagaattcatacaggaagtcttagagaaaattcattgtctatgctgttgtgcttctttttggaagaagcacaacaaggtccggcataaagccggtattttgctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagcaaaataccggctttatgccggaccttgttgtgcttcttccaaaaagaagcacaacagcatagacaatgaattttctctaagacttcctgtatgaattctcaggaagtctttttgtgattaaatatagacttggggggtaatgg Mask Tandem Repeat Region ================================================ ccattaccccccaagtctatatttaatcacaaaaagacttcctgagaattcatacaggaagtcttagagaaaattcattgtctatgctgttgtgcttctttttggaagaagcacaacaaggtccggcataaagccggtattttgctta Find is-nt database================================================ Query_seq: TDE2421:TDE2422|TDE2421:TDE2422:DNA-directed RNA polymerase beta subunit:ribosomal protein L7/L12:<-<-:2452853..2453000 148 ccattaccccccaagtctatatttaatcacaaaaagacttcctgagaattcatacaggaagtcttagagaaaattcattgtctatgctgttgtgcttctttttggaagaagcacaacaaggtccggcataaagccggtattttgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2421:TDE2422|TDE2421:TDE2422:DNA-directed RNA polymerase beta subunit:ribosomal protein L7/L12:<-<-:2452853..2453000 148 ccattaccccccaagtctatatttaatcacaaaaagacttcctgagaattcatacaggaagtcttagagaaaattcattgtctatgctgttgtgcttctttttggaagaagcacaacaaggtccggcataaagccggtattttgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2421:TDE2422|TDE2421:TDE2422:DNA-directed RNA polymerase beta subunit:ribosomal protein L7/L12:<-<-:2452853..2453000 148 ccattaccccccaagtctatatttaatcacaaaaagacttcctgagaattcatacaggaagtcttagagaaaattcattgtctatgctgttgtgcttctttttggaagaagcacaacaaggtccggcataaagccggtattttgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccattaccccccaagtctatatttaatcacaaaaagacttcctgagaattcatacaggaagtcttagagaaaattcattgtctatgctgttgtgcttctttttggaagaagcacaacaaggtccggcataaagccggtattttgctta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 52 End: 147 ................................................... M Q E V L E K I H C L C C C A S F W K K H N K V R H K A G I L L . ccattaccccccaagtctatatttaatcacaaaaagacttcctgagaattcatacaggaagtcttagagaaaattcattgtctatgctgttgtgcttctttttggaagaagcacaacaaggtccggcataaagccggtattttgctta 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================================================ ccattaccccccaagtctatatttaatcacaaaaagacttcctgagaattcatacaggaagtcttagagaaaattcattgtctatgctgttgtgcttctttttggaagaagcacaacaaggtccggcataaagccggtattttgctta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 83 HP_score: -7.1 Tail_Score: -4.98857 Start: 36 End: 63 Full_Region: atgaattttctctaa gacttcctg tatgaattct caggaagtc tttttgtgattaaat ...................................gacttcctgtatgaattctcaggaagtc..................................................................................... Find igs database================================================ Query_seq: TDE2421:TDE2422|TDE2421:TDE2422:DNA-directed RNA polymerase beta subunit:ribosomal protein L7/L12:<-<-:2452853..2453000 148 ccattaccccccaagtctatatttaatcacaaaaagacttcctgagaattcatacaggaagtcttagagaaaattcattgtctatgctgttgtgcttctttttggaagaagcacaacaaggtccggcataaagccggtattttgctta Intra-Species Hit: Count: 1 Min: 1 Max: 148 Len: 148 Subject: NC_002967_TDE2421_TDE2422|DNA-directed RNA polymerase beta subunit:ribosomal protein L7/L12|NEGATIVE:NEGATIVE|[2452853,2453000]|148 HSP 1 e-value: 8.0E-79 bit: 293.0 Len: 148 Query Start:1 Query End:148 Subject Strand: POSITIVE Subject Start: 1 Subject End: 148 ccattaccccccaagtctatatttaatcacaaaaagacttcctgagaattcatacaggaagtcttagagaaaattcattgtctatgctgttgtgcttctttttggaagaagcacaacaaggtccggcataaagccggtattttgctta ccattaccccccaagtctatatttaatcacaaaaagacttcctgagaattcatacaggaagtcttagagaaaattcattgtctatgctgttgtgcttctttttggaagaagcacaacaaggtccggcataaagccggtattttgctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCAUUACCCCCCAAGUCUAUAUUUAAUCACAAAAAGACUUCCUGAGAAUUCAUACAGGAAGUCUUAGAGAAAAUUCAUUGUCUAUGCUGUUGUGCUUCUUUUUGGAAGAAGCACAACAAGGUCCGGCAUAAAGCCGGUAUUUUGCUUA .....(((..........................((((((((((..........))))))))))((((.((......)).))))...((((((((((((((...)))))))))))))).)))(((((.....)))))........... (-44.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCAAAAUACCGGCUUUAUGCCGGACCUUGUUGUGCUUCUUCCAAAAAGAAGCACAACAGCAUAGACAAUGAAUUUUCUCUAAGACUUCCUGUAUGAAUUCUCAGGAAGUCUUUUUGUGAUUAAAUAUAGACUUGGGGGGUAAUGG ...((......(((((.....)))))....(((((((((((((.....))))))))))))))).............(..(((.(((((((((((...(....).)))))))))))((((((......))))))...)))..)...... (-49.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 944 140 91 231 182 NC_002967:TDE2421|5end_DNA-directed_RNA_polymerase_beta_subunit_2452762..2452992_NEGATIVE 334 137 92 52 1 NC_002967:TDE1225|5end_zinc_ABC_transporter,_ATP-binding_protein_1259518..1259748_NEGATIVE 327 137 91 80 28 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 306 128 82 71 28 NC_002967:TDE1048|5end_30S_ribosomal_protein_S7_1074482..1074712_POSITIVE 297 100 53 222 171 NC_002967:TDE1996|5end_hypothetical_protein_2014243..2014473_POSITIVE 293 137 92 84 37 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 291 139 93 63 14 NC_002967:TDE2234|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2273245..2273475_NEGATIVE 291 133 93 65 29 NC_002967:TDE0066|5end_hypothetical_protein_73926..74156_NEGATIVE 289 127 81 171 111 NC_002967:TDE1332|5end_hflK_protein,_putative_1368042..1368272_POSITIVE 288 139 92 57 1 NC_002967:TDE0108|5end_hypothetical_protein_128399..128629_POSITIVE 281 128 81 71 36 NC_002967:TDE0693|5end_phosphomethylpyrimidine_kinase_729942..730172_POSITIVE 277 138 102 181 130 NC_002967:TDE2571|5end_hypothetical_protein_2598152..2598382_NEGATIVE 270 127 86 181 138 NC_002967:TDE2576|5end_RNA_pseudouridylate_synthase_family_protein_2601672..2601902_POSITIVE 269 139 91 120 65 NC_002967:TDE2326|5end_cobyric_acid_synthase_CobQ,_putative_2361087..2361317_POSITIVE 269 49 6 149 97 NC_002967:TDE1753|5end_UDP-glucose_4-epimerase_1806540..1806770_NEGATIVE 269 140 100 158 115 NC_002967:TDE0960|5end_neuB_family_protein_982376..982606_POSITIVE 268 134 95 140 99 NC_002967:TDE1200|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,_6-diaminopimelate--D-alanyl-D-alanyl_ligase_1231618..1231848_POSITIVE 266 136 92 215 168 NC_002967:TDE1148|5end_hypothetical_protein_1186357..1186587_NEGATIVE 260 135 94 49 9 NC_002967:TDE1062|5end_ABC_transporter,_ATP-binding_protein,_HlyB_family_1088430..1088660_POSITIVE 259 43 5 208 159 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 137 91 108 56 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 306 128 82 60 17 NC_002967:TDE1047|3end_30S_ribosomal_protein_S12_1074551..1074701_POSITIVE 297 100 53 143 92 NC_002967:TDE1995|3end_magnesium_chelatase_family_protein_2014244..2014394_POSITIVE 293 137 92 112 65 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 293 137 92 112 65 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 292 138 91 72 25 NC_002967:TDE2547|3end_hypothetical_protein_2573184..2573334_POSITIVE 291 133 93 50 14 NC_002967:TDE0067|3end_cyclic_nucleotide-binding_protein_73941..74091_NEGATIVE 289 127 81 123 63 NC_002967:TDE1331|3end_anaerobic_ribonucleoside_triphosphate_reductase_1368074..1368224_POSITIVE 286 127 85 143 92 NC_002967:TDE1103|3end_hypothetical_protein_1136670..1136820_POSITIVE 278 136 95 99 65 NC_002967:TDE2299|3end_apolipoprotein_N-acyltransferase_2339937..2340087_POSITIVE 271 137 108 89 57 NC_002967:TDE1848|3end_hypothetical_protein_1875897..1876047_NEGATIVE 270 127 86 141 98 NC_002967:TDE2575|3end_hypothetical_protein_2601712..2601862_POSITIVE 269 98 56 144 105 NC_002967:TDE2326|3end_cobyric_acid_synthase_CobQ,_putative_2362027..2362177_POSITIVE 269 139 91 130 75 NC_002967:TDE2325|3end_hypothetical_protein_2361177..2361327_POSITIVE 269 139 104 58 10 NC_002967:TDE1988|3end_hypothetical_protein_2005590..2005740_POSITIVE 269 140 100 67 24 NC_002967:TDE0959|3end_hypothetical_protein_982365..982515_POSITIVE 269 128 86 84 35 NC_002967:TDE0113|3end_Tpl_protein_133609..133759_POSITIVE 268 134 95 147 106 NC_002967:TDE1199|3end_cell_division_protein_FtsL,_putative_1231705..1231855_POSITIVE 266 136 92 146 99 NC_002967:TDE1149|3end_hypothetical_protein_1186426..1186576_NEGATIVE 265 138 119 91 70 NC_002967:TDE0845|3end_conserved_hypothetical_protein_TIGR00266_868549..868699_POSITIVE