Origin IGS: actcttgctcctaaagtatattgctttattgtatcacaaggatgatatagcttcaagagggaatacggtttttattgattaccaattaattaatcgcttctactcataatatctcataatcattgtagagattatttgaagttaatagtaaaattttaaaaaaaaattaaattttattga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcaataaaatttaatttttttttaaaattttactattaacttcaaataatctctacaatgattatgagatattatgagtagaagcgattaattaattggtaatcaataaaaaccgtattccctcttgaagctatatcatccttgtgatacaataaagcaatatactttaggagcaagagt Mask Tandem Repeat Region ================================================ actcttgctcctaaagtatattgctttattgtatcacaaggatgatatagcttcaagagggaatacggtttttattgattaccaattaattaatcgcttctactcataatatctcataatcattgtagagattatttgaagttaatagtaaaattttaaaaaaaaattaaattttattga Find is-nt database================================================ Query_seq: TDE2236:TDE2237|TDE2236:TDE2237:methylaspartate mutase, E subunit:hypothetical protein:<-<-:2276208..2276387 180 actcttgctcctaaagtatattgctttattgtatcacaaggatgatatagcttcaagagggaatacggtttttattgattaccaattaattaatcgcttctactcataatatctcataatcattgtagagattatttgaagttaatagtaaaattttaaaaaaaaattaaattttattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2236:TDE2237|TDE2236:TDE2237:methylaspartate mutase, E subunit:hypothetical protein:<-<-:2276208..2276387 180 actcttgctcctaaagtatattgctttattgtatcacaaggatgatatagcttcaagagggaatacggtttttattgattaccaattaattaatcgcttctactcataatatctcataatcattgtagagattatttgaagttaatagtaaaattttaaaaaaaaattaaattttattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2236:TDE2237|TDE2236:TDE2237:methylaspartate mutase, E subunit:hypothetical protein:<-<-:2276208..2276387 180 actcttgctcctaaagtatattgctttattgtatcacaaggatgatatagcttcaagagggaatacggtttttattgattaccaattaattaatcgcttctactcataatatctcataatcattgtagagattatttgaagttaatagtaaaattttaaaaaaaaattaaattttattga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actcttgctcctaaagtatattgctttattgtatcacaaggatgatatagcttcaagagggaatacggtttttattgattaccaattaattaatcgcttctactcataatatctcataatcattgtagagattatttgaagttaatagtaaaattttaaaaaaaaattaaattttattga Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 5 End: 106 .... M L L K Y I A L L Y H K D D I A S R G N T V F I D Y Q L I N R F Y S .......................................................................... actcttgctcctaaagtatattgctttattgtatcacaaggatgatatagcttcaagagggaatacggtttttattgattaccaattaattaatcgcttctactcataatatctcataatcattgtagagattatttgaagttaatagtaaaattttaaaaaaaaattaaattttattga 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: 84 Start: 28 End: 57 ...........................CTTGAAGCTATATCATCCTTGTGATACAAT........................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 125 End: 154 ............................................................................................................................GTAGAGATTATTTGAAGTTAATAGTAAAAT.......................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actcttgctcctaaagtatattgctttattgtatcacaaggatgatatagcttcaagagggaatacggtttttattgattaccaattaattaatcgcttctactcataatatctcataatcattgtagagattatttgaagttaatagtaaaattttaaaaaaaaattaaattttattga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2236:TDE2237|TDE2236:TDE2237:methylaspartate mutase, E subunit:hypothetical protein:<-<-:2276208..2276387 180 actcttgctcctaaagtatattgctttattgtatcacaaggatgatatagcttcaagagggaatacggtttttattgattaccaattaattaatcgcttctactcataatatctcataatcattgtagagattatttgaagttaatagtaaaattttaaaaaaaaattaaattttattga Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: NC_002967_TDE2236_TDE2237|methylaspartate mutase, E subunit:hypothetical protein|NEGATIVE:NEGATIVE|[2276208,2276387]|180 HSP 1 e-value: 4.0E-84 bit: 311.0 Len: 157 Query Start:1 Query End:157 Subject Strand: POSITIVE Subject Start: 1 Subject End: 157 actcttgctcctaaagtatattgctttattgtatcacaaggatgatatagcttcaagagggaatacggtttttattgattaccaattaattaatcgcttctactcataatatctcataatcattgtagagattatttgaagttaatagtaaaatttt....................... actcttgctcctaaagtatattgctttattgtatcacaaggatgatatagcttcaagagggaatacggtttttattgattaccaattaattaatcgcttctactcataatatctcataatcattgtagagattatttgaagttaatagtaaaatttt....................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCUUGCUCCUAAAGUAUAUUGCUUUAUUGUAUCACAAGGAUGAUAUAGCUUCAAGAGGGAAUACGGUUUUUAUUGAUUACCAAUUAAUUAAUCGCUUCUACUCAUAAUAUCUCAUAAUCAUUGUAGAGAUUAUUUGAAGUUAAUAGUAAAAUUUU .((((((....((((((.....)))))).(((((((......)))))))....))))))......(((((...((((((.....)))))).)))))....((((..((((.((..((((((........))))))..)).))))..))))....... (-27.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUUUACUAUUAACUUCAAAUAAUCUCUACAAUGAUUAUGAGAUAUUAUGAGUAGAAGCGAUUAAUUAAUUGGUAAUCAAUAAAAACCGUAUUCCCUCUUGAAGCUAUAUCAUCCUUGUGAUACAAUAAAGCAAUAUACUUUAGGAGCAAGAGU ....(((((((..(((..((..((((((........))))))..))..)))..)))))))..(((((.........)))))............((((.(((((((((.(((((...(.((((......)))).)..))))))))))))))...)))) (-25.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 842 70 21 161 112 NC_002967:TDE2236|5end_methylaspartate_mutase,_E_subunit_2276117..2276347_NEGATIVE 377 150 114 177 141 NC_002967:TDE1344|5end_hypothetical_protein_1382392..1382622_POSITIVE 349 150 114 175 139 NC_002967:TDE1691|5end_hypothetical_protein_1748273..1748503_NEGATIVE 249 68 23 221 168 NC_002967:TDE1350|5end_rod_shape-determining_protein_MreC_1390327..1390557_POSITIVE 247 70 22 171 118 NC_002967:TDE1081|5end_hypothetical_protein_1112639..1112869_POSITIVE 242 36 1 38 5 NC_002967:TDE1501|5end_pyruvate_phosphate_dikinase_1548041..1548271_POSITIVE 236 74 42 134 101 NC_002967:TDE1316|5end_hypothetical_protein_1354741..1354971_POSITIVE 235 69 29 171 126 NC_002967:TDE1340|5end_ribosomal_5S_rRNA_E-loop_binding_protein_Ctc/L25/TL5_1376317..1376547_POSITIVE 233 72 37 42 13 NC_002967:TDE2320|5end_RNA_polymerase_sigma-24_factor,_putative_2356951..2357181_NEGATIVE 228 77 42 177 144 NC_002967:TDE0906|5end_ABC_transporter,_ATP-binding_protein_923164..923394_POSITIVE 226 69 23 192 162 NC_002967:TDE1886|5end_MiaB-like_tRNA_modifying_enzyme_1908488..1908718_NEGATIVE 225 105 61 159 107 NC_002967:TDE1163|5end_hypothetical_protein_1197930..1198160_NEGATIVE 222 49 2 173 124 NC_002967:TDE1330|5end_conserved_hypothetical_protein_TIGR00244_1365379..1365609_POSITIVE 220 69 21 86 23 NC_002967:TDE0215|5end_hypothetical_protein_251370..251600_NEGATIVE 218 60 11 197 140 NC_002967:TDE2374|5end_precorrin-8W_decarboxylase,_putative_2405709..2405939_POSITIVE 213 80 35 207 169 NC_002967:TDE0849|5end_hypothetical_protein_871599..871829_POSITIVE 211 67 23 137 100 NC_002967:TDE0144|5end_thiamine_ABC_transporter,_permease_protein_165007..165237_POSITIVE 207 69 23 120 54 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 206 86 44 227 188 NC_002967:TDE2778|5end_PspC_domain_protein_2829604..2829834_NEGATIVE 204 46 2 151 106 NC_002967:TDE2635|5end_acetyltransferase,_GNAT_family_2675453..2675683_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 364 104 67 71 37 NC_002967:TDE1978|3end_hypothetical_protein_1991501..1991651_NEGATIVE 304 104 65 109 80 NC_002967:TDE2097|3end_hypothetical_protein_2124478..2124628_NEGATIVE 251 79 33 132 87 NC_002967:TDE0813|3end_ABC_transporter,_ATP-binding_protein/permease_835707..835857_POSITIVE 247 70 22 151 98 NC_002967:TDE1080|3end_dimethyladenosine_transferase_1112699..1112849_POSITIVE 236 74 42 146 113 NC_002967:TDE1315|3end_hypothetical_protein_1354833..1354983_POSITIVE 235 79 35 69 20 NC_002967:TDE1037|3end_hypothetical_protein_1065461..1065611_POSITIVE 233 72 37 45 16 NC_002967:TDE2321|3end_hypothetical_protein_2356948..2357098_NEGATIVE 231 48 5 133 91 NC_002967:TDE2454|3end_hypothetical_protein_2482351..2482501_NEGATIVE 225 83 45 91 60 NC_002967:TDE0085|3end_ATP-dependent_DNA_helicase,_UvrD/Rep_family_97596..97746_NEGATIVE 222 49 2 60 11 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 213 80 35 86 48 NC_002967:TDE0848|3end_hypothetical_protein_871558..871708_POSITIVE 205 83 43 71 29 NC_002967:TDE2195|3end_RNA_pseudouridylate_synthase_family_protein_2231911..2232061_POSITIVE 205 100 58 151 102 NC_002967:TDE1164|3end_hypothetical_protein_1197933..1198083_NEGATIVE 204 46 2 129 84 NC_002967:TDE2634|3end_hypothetical_protein_2675511..2675661_POSITIVE 203 131 91 55 7 NC_002967:TDE1391|3end_NQR2/RnfD/RnfE_family_protein_1432089..1432239_POSITIVE 203 42 2 70 33 NC_002967:TDE1026|3end_acyl_carrier_protein_1057618..1057768_POSITIVE 201 58 18 96 62 NC_002967:TDE1903|3end_hypothetical_protein_1923135..1923285_POSITIVE 199 91 51 35 1 NC_002967:TDE1260|3end_cholinephosphate_cytidylyltransferase/choline_kinase_1295676..1295826_POSITIVE 198 57 18 70 30 NC_002967:TDE2750|3end_GTP-binding_protein_HflX,_truncation_2807288..2807438_POSITIVE 198 69 23 91 43 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE