Origin IGS: cttttccctcgaaaaaaagtattttaagatgatacactaaaagctgaaatttgtctacaagagcggaaaaaccagccataaaaaaagcccccttgccttagaggcttgggggctttagtttaaaaagctaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttagctttttaaactaaagcccccaagcctctaaggcaagggggctttttttatggctggtttttccgctcttgtagacaaatttcagcttttagtgtatcatcttaaaatactttttttcgagggaaaag Mask Tandem Repeat Region ================================================ cttttccctcgaaaaaaagtattttaagatgatacactaaaagctgaaatttgtctacaagagcggaaaaaccagccataaaaaaagcccccttgccttagaggcttgggggctttagtttaaaaagctaaa Find is-nt database================================================ Query_seq: TDE2118:TDE2119|TDE2118:TDE2119:DNA topoisomerase IV subunit A:glycine reductase complex selenoprotein GrdB2:<-<-:2151356..2151487 132 cttttccctcgaaaaaaagtattttaagatgatacactaaaagctgaaatttgtctacaagagcggaaaaaccagccataaaaaaagcccccttgccttagaggcttgggggctttagtttaaaaagctaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2118:TDE2119|TDE2118:TDE2119:DNA topoisomerase IV subunit A:glycine reductase complex selenoprotein GrdB2:<-<-:2151356..2151487 132 cttttccctcgaaaaaaagtattttaagatgatacactaaaagctgaaatttgtctacaagagcggaaaaaccagccataaaaaaagcccccttgccttagaggcttgggggctttagtttaaaaagctaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2118:TDE2119|TDE2118:TDE2119:DNA topoisomerase IV subunit A:glycine reductase complex selenoprotein GrdB2:<-<-:2151356..2151487 132 cttttccctcgaaaaaaagtattttaagatgatacactaaaagctgaaatttgtctacaagagcggaaaaaccagccataaaaaaagcccccttgccttagaggcttgggggctttagtttaaaaagctaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttttccctcgaaaaaaagtattttaagatgatacactaaaagctgaaatttgtctacaagagcggaaaaaccagccataaaaaaagcccccttgccttagaggcttgggggctttagtttaaaaagctaaa Predict ORF larger than 30AA ================================================ cttttccctcgaaaaaaagtattttaagatgatacactaaaagctgaaatttgtctacaagagcggaaaaaccagccataaaaaaagcccccttgccttagaggcttgggggctttagtttaaaaagctaaa 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: 29 End: 58 ............................GTAGACAAATTTCAGCTTTTAGTGTATCAT.......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttttccctcgaaaaaaagtattttaagatgatacactaaaagctgaaatttgtctacaagagcggaaaaaccagccataaaaaaagcccccttgccttagaggcttgggggctttagtttaaaaagctaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -13.6 Tail_Score: -4.05788 Start: 87 End: 113 Full_Region: CCAGCCATAAAAAAA GCCCCCTTGCCT TAG AGGCTTGGGGGC TTTAGTTTAAAAAGC ......................................................................................GCCCCCTTGCCTTAGAGGCTTGGGGGC................... Find igs database================================================ Query_seq: TDE2118:TDE2119|TDE2118:TDE2119:DNA topoisomerase IV subunit A:glycine reductase complex selenoprotein GrdB2:<-<-:2151356..2151487 132 cttttccctcgaaaaaaagtattttaagatgatacactaaaagctgaaatttgtctacaagagcggaaaaaccagccataaaaaaagcccccttgccttagaggcttgggggctttagtttaaaaagctaaa Intra-Species Hit: Count: 1 Min: 19 Max: 132 Len: 114 Subject: NC_002967_TDE2118_TDE2119|DNA topoisomerase IV subunit A:glycine reductase complex selenoprotein GrdB2|NEGATIVE:NEGATIVE|[2151356,2151487]|132 HSP 1 e-value: 5.0E-46 bit: 184.0 Len: 114 Query Start:19 Query End:132 Subject Strand: POSITIVE Subject Start: 19 Subject End: 132 ..................gtattttaagatgatacactaaaagctgaaatttgtctacaagagcggaaaaaccagccatnnnnnnngcccccttgccttagaggcttgggggctttagtttaaaaagctaaa ..................gtattttaagatgatacactaaaagctgaaatttgtctacaagagcggaaaaaccagccataaaaaaagcccccttgccttagaggcttgggggctttagtttaaaaagctaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUUUUAAGAUGAUACACUAAAAGCUGAAAUUUGUCUACAAGAGCGGAAAAACCAGCCAUAAAAAAAGCCCCCUUGCCUUAGAGGCUUGGGGGCUUUAGUUUAAAAAGCUAAA (((((.......)))))......((((...............(.((((.....)).)))......(((((((((..(((.....)))..))))))))).........))))... (-32.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAGCUUUUUAAACUAAAGCCCCCAAGCCUCUAAGGCAAGGGGGCUUUUUUUAUGGCUGGUUUUUCCGCUCUUGUAGACAAAUUUCAGCUUUUAGUGUAUCAUCUUAAAAUAC .((((((...((((..(((((((((..(((.....)))..))))))))).)))).))))))......((((...((.((......)).))....))))................ (-31.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 988 100 51 209 160 NC_002967:TDE2118|5end_DNA_topoisomerase_IV_subunit_A_2151265..2151495_NEGATIVE 392 98 59 60 16 NC_002967:TDE2701|5end_hypothetical_protein_2745689..2745919_POSITIVE 336 88 42 110 47 NC_002967:TDE1260|5end_cholinephosphate_cytidylyltransferase/choline_kinase_1294028..1294258_POSITIVE 307 97 54 82 47 NC_002967:TDE2731|5end_TIM-barrel_protein,_putative,_NifR3_family_2787372..2787602_POSITIVE 302 110 64 210 161 NC_002967:TDE0004|5end_hypothetical_protein_4243..4473_POSITIVE 301 109 68 57 8 NC_002967:TDE2499|5end_hypothetical_protein_2523952..2524182_NEGATIVE 300 97 57 136 87 NC_002967:TDE0774|5end_50S_ribosomal_protein_L16_810165..810395_POSITIVE 298 87 41 80 15 NC_002967:TDE0682|5end_preprotein_translocase,_YajC_subunit_721078..721308_NEGATIVE 297 97 54 193 148 NC_002967:TDE0122|5end_dihydrouridine_synthase,_putative_141539..141769_NEGATIVE 293 97 51 152 104 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 290 94 63 225 194 NC_002967:TDE2705|5end_ISTde3,_transposase_2751765..2751995_NEGATIVE 287 63 23 60 27 NC_002967:TDE0955|5end_LemA_family_protein_978842..979072_POSITIVE 284 106 66 138 92 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 282 103 69 72 39 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 275 101 70 37 4 NC_002967:TDE0828|5end_glucose-inhibited_division_protein_A_850169..850399_NEGATIVE 274 103 62 174 134 NC_002967:TDE2593|5end_sigma-54-binding_protein_2627747..2627977_POSITIVE 273 109 61 165 110 NC_002967:TDE1549|5end_recombination_protein_RecR_1592140..1592370_POSITIVE 272 100 54 208 140 NC_002967:TDE0797|5end_acylphosphatase_820859..821089_POSITIVE 269 110 69 158 106 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 269 96 68 180 147 NC_002967:TDE2241|5end_glycosyl_transferase,_group_2_family_protein_2279651..2279881_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 392 98 59 59 15 NC_002967:TDE2700|3end_citrate_carrier_protein,_CCS_family_2745768..2745918_POSITIVE 383 97 59 151 108 NC_002967:TDE2701|3end_hypothetical_protein_2745861..2746011_POSITIVE 351 87 41 64 16 NC_002967:TDE0464|3end_NifU_domain_protein_517948..518098_NEGATIVE 349 103 64 91 54 NC_002967:TDE2204|3end_Na+/H+_antiporter_family_protein_2242550..2242700_POSITIVE 345 107 66 84 28 NC_002967:TDE0823|3end_(3R)-hydroxymyristoyl-(acyl-carrier-protein)_dehydratase,_putative_845252..845402_POSITIVE 333 94 51 62 4 NC_002967:TDE2604|3end_hypothetical_protein_2644224..2644374_NEGATIVE 331 106 71 88 47 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 317 104 66 71 29 NC_002967:TDE2702|3end_hypothetical_protein_2745832..2745982_NEGATIVE 310 110 67 127 82 NC_002967:TDE0616|3end_hypothetical_protein_650079..650229_POSITIVE 307 97 54 69 34 NC_002967:TDE2730|3end_hydrolase,_TatD_family_2787439..2787589_POSITIVE 304 98 56 74 28 NC_002967:TDE2433|3end_treponemal_membrane_protein,_putative_2463265..2463415_POSITIVE 303 79 35 138 96 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 301 109 68 57 8 NC_002967:TDE2500|3end_DJ-1_family_protein_2523952..2524102_NEGATIVE 300 97 57 133 84 NC_002967:TDE0773|3end_30S_ribosomal_protein_S3_810242..810392_POSITIVE 295 80 34 50 10 NC_002967:TDE0239|3end_glycine_reductase_complex_protein_GrdD_271828..271978_NEGATIVE 292 110 70 113 77 NC_002967:TDE2582|3end_GGDEF_domain_protein_2616164..2616314_POSITIVE 290 94 63 74 43 NC_002967:TDE2706|3end_hypothetical_protein_2751916..2752066_NEGATIVE 279 98 55 71 20 NC_002967:TDE2205|3end_enoate_reductase,_putative_2242575..2242725_NEGATIVE 275 110 66 82 40 NC_002967:TDE1052|3end_rubredoxin_1078712..1078862_NEGATIVE 274 103 62 79 39 NC_002967:TDE2592|3end_DbpA_RNA_binding_domain_protein_2627732..2627882_POSITIVE