Origin IGS: atccagtatatcggcataaaaaaatatgtttttaggctaaattaaataagaaaaggcctaaaacttataaaagttttaagcctttcgttaaaaactataatggggtaaaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctttaccccattatagtttttaacgaaaggcttaaaacttttataagttttaggccttttcttatttaatttagcctaaaaacatatttttttatgccgatatactggat Mask Tandem Repeat Region ================================================ atccagtatatcggcataaaaaaatatgtttttaggctaaattaaataagaaaaggcctaaaacttataaaagttttaagcctttcgttaaaaactataatggggtaaaga Find is-nt database================================================ Query_seq: TDE2753:TDE2754|TDE2753:TDE2754:LysM domain/M23/M37 peptidase domain protein:ornithine cyclodeaminase:<-<-:2810740..2810850 111 atccagtatatcggcataaaaaaatatgtttttaggctaaattaaataagaaaaggcctaaaacttataaaagttttaagcctttcgttaaaaactataatggggtaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2753:TDE2754|TDE2753:TDE2754:LysM domain/M23/M37 peptidase domain protein:ornithine cyclodeaminase:<-<-:2810740..2810850 111 atccagtatatcggcataaaaaaatatgtttttaggctaaattaaataagaaaaggcctaaaacttataaaagttttaagcctttcgttaaaaactataatggggtaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2753:TDE2754|TDE2753:TDE2754:LysM domain/M23/M37 peptidase domain protein:ornithine cyclodeaminase:<-<-:2810740..2810850 111 atccagtatatcggcataaaaaaatatgtttttaggctaaattaaataagaaaaggcctaaaacttataaaagttttaagcctttcgttaaaaactataatggggtaaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atccagtatatcggcataaaaaaatatgtttttaggctaaattaaataagaaaaggcctaaaacttataaaagttttaagcctttcgttaaaaactataatggggtaaaga Predict ORF larger than 30AA ================================================ atccagtatatcggcataaaaaaatatgtttttaggctaaattaaataagaaaaggcctaaaacttataaaagttttaagcctttcgttaaaaactataatggggtaaaga 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================================================ atccagtatatcggcataaaaaaatatgtttttaggctaaattaaataagaaaaggcctaaaacttataaaagttttaagcctttcgttaaaaactataatggggtaaaga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -12.8 Tail_Score: -4.07246 Start: 47 End: 90 Full_Region: ccccattatagtttt taacgaaaggcttaaaactt ttat aagttttaggccttttctta tttaatttagcctaa ..............................................taacgaaaggcttaaaacttttataagttttaggccttttctta..................... TransTerm Strand: - Conf: 95 HP_score: -11.2 Tail_Score: -4.15396 Start: 50 End: 86 Full_Region: attatagtttttaac gaaaggcttaaaactt ttat aagttttaggccttttc ttatttaatttagcc .................................................gaaaggcttaaaacttttataagttttaggccttttc......................... Find igs database================================================ Query_seq: TDE2753:TDE2754|TDE2753:TDE2754:LysM domain/M23/M37 peptidase domain protein:ornithine cyclodeaminase:<-<-:2810740..2810850 111 atccagtatatcggcataaaaaaatatgtttttaggctaaattaaataagaaaaggcctaaaacttataaaagttttaagcctttcgttaaaaactataatggggtaaaga Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_002967_TDE2753_TDE2754|LysM domain/M23/M37 peptidase domain protein:ornithine cyclodeaminase|NEGATIVE:NEGATIVE|[2810740,2810850]|111 HSP 1 e-value: 2.0E-44 bit: 178.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 atccagtatatcggcatnnnnnnntatgtttttaggctaaattaaataagaaaaggcctaaaacttataaaagttttaagcctttcgttaaaaactataatggggtaaaga atccagtatatcggcataaaaaaatatgtttttaggctaaattaaataagaaaaggcctaaaacttataaaagttttaagcctttcgttaaaaactataatggggtaaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCAGUAUAUCGGCAUAAAAAAAUAUGUUUUUAGGCUAAAUUAAAUAAGAAAAGGCCUAAAACUUAUAAAAGUUUUAAGCCUUUCGUUAAAAACUAUAAUGGGGUAAAGA .((((.((((..(((.((((((......)))))).)))........(((..((((((.((((((((....)))))))).))))))..))).....)))).))))....... (-24.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUACCCCAUUAUAGUUUUUAACGAAAGGCUUAAAACUUUUAUAAGUUUUAGGCCUUUUCUUAUUUAAUUUAGCCUAAAAACAUAUUUUUUUAUGCCGAUAUACUGGAU ........(((.((((.....(((.((((((((((((((((....)))))))))))))))).))).........((.((((((......)))))).))...)))).))).. (-27.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 716 60 11 151 102 NC_002967:TDE2753|5end_LysM_domain/M23/M37_peptidase_domain_protein_2810649..2810879_NEGATIVE 219 96 56 57 11 NC_002967:TDE0629|5end_chaperone_protein_DnaJ_662587..662817_POSITIVE 218 105 61 175 131 NC_002967:TDE2384|5end_phosphoglycerate_mutase_family_protein_2413626..2413856_POSITIVE 214 88 54 216 173 NC_002967:TDE0199|5end_hypothetical_protein_234708..234938_NEGATIVE 211 60 11 180 132 NC_002967:TDE2219|5end_hypothetical_protein_2260646..2260876_NEGATIVE 205 90 53 93 53 NC_002967:TDE1000|5end_3-hydroxyacid_dehydrogenase_family_protein_1026763..1026993_POSITIVE 204 44 4 136 99 NC_002967:TDE1445|5end_hypothetical_protein_1491927..1492157_NEGATIVE 203 110 71 213 171 NC_002967:TDE1448|5end_glutamate_racemase,_putative_1493535..1493765_POSITIVE 201 39 2 212 174 NC_002967:TDE0004|5end_hypothetical_protein_4243..4473_POSITIVE 200 83 53 47 20 NC_002967:TDE1505|5end_hypothetical_protein_1553614..1553844_POSITIVE 199 106 79 115 82 NC_002967:TDE2708|5end_hypothetical_protein_2761498..2761728_NEGATIVE 196 90 54 106 58 NC_002967:TDE2398|5end_conserved_hypothetical_protein_TIGR00278_2425807..2426037_NEGATIVE 195 98 55 76 29 NC_002967:TDE0685|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_722620..722850_NEGATIVE 195 88 51 91 48 NC_002967:TDE0485|5end_hypothetical_protein_542791..543021_NEGATIVE 194 71 34 49 12 NC_002967:TDE2567|5end_hypothetical_protein_2595076..2595306_NEGATIVE 190 92 53 65 23 NC_002967:TDE1908|5end_hypothetical_protein_1926058..1926288_NEGATIVE 188 40 1 190 153 NC_002967:TDE1767|5end_hypothetical_protein_1813567..1813797_NEGATIVE 188 92 57 132 104 NC_002967:TDE1552|5end_hypothetical_protein_1595759..1595989_POSITIVE 185 97 54 195 146 NC_002967:TDE0845|5end_conserved_hypothetical_protein_TIGR00266_867795..868025_POSITIVE 183 85 48 160 121 NC_002967:TDE0163|5end_flavodoxin_193383..193613_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 207 59 12 80 21 NC_002967:TDE2327|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpB_2362048..2362198_NEGATIVE 199 90 45 82 35 NC_002967:TDE1904|3end_hypothetical_protein_1923197..1923347_NEGATIVE 196 90 54 109 61 NC_002967:TDE2399|3end_ribonuclease_P_protein_component_2425804..2425954_NEGATIVE 195 88 51 70 27 NC_002967:TDE0486|3end_hypothetical_protein_542812..542962_NEGATIVE 191 85 47 134 106 NC_002967:TDE1500|3end_hypothetical_protein_1546763..1546913_NEGATIVE 190 92 53 75 33 NC_002967:TDE1909|3end_conserved_hypothetical_protein_TIGR00159_1926048..1926198_NEGATIVE 188 85 51 72 40 NC_002967:TDE2089|3end_signal_recognition_particle_protein_2116232..2116382_NEGATIVE 188 40 1 88 51 NC_002967:TDE1768|3end_hypothetical_protein_1813669..1813819_NEGATIVE 185 108 68 143 103 NC_002967:TDE2693|3end_ankyrin_repeat_protein_2734014..2734164_POSITIVE 185 97 54 93 44 NC_002967:TDE0844|3end_pyruvate_phosphate_dikinase,_putative_867773..867923_POSITIVE 183 85 48 126 87 NC_002967:TDE0164|3end_hypothetical_protein_193417..193567_NEGATIVE 181 83 47 46 20 NC_002967:TDE2433|3end_treponemal_membrane_protein,_putative_2463265..2463415_POSITIVE 180 36 2 61 25 NC_002967:TDE2604|3end_hypothetical_protein_2644224..2644374_NEGATIVE 180 94 54 104 72 NC_002967:TDE0941|3end_NLP/P60_family_protein_963623..963773_NEGATIVE 180 106 64 114 79 NC_002967:TDE0590|3end_acetyl-CoA_carboxylase,_carboxyl_transferase,_beta_subunit_629065..629215_NEGATIVE 179 87 55 39 6 NC_002967:TDE0445|3end_amino_acid_permease_501104..501254_POSITIVE 178 107 72 41 2 NC_002967:TDE2500|3end_DJ-1_family_protein_2523952..2524102_NEGATIVE 176 87 71 43 27 NC_002967:TDE0790|3end_30S_ribosomal_protein_S11_817411..817561_POSITIVE 174 85 48 52 17 NC_002967:TDE0239|3end_glycine_reductase_complex_protein_GrdD_271828..271978_NEGATIVE 173 90 49 89 39 NC_002967:TDE2313|3end_hypothetical_protein_2349506..2349656_NEGATIVE