Origin IGS: agtaacaaaaatgtttcttccgtaaaatcgttgaaaatacaatattacaacggtttacggaagcaaaaagctccttagtgatactgttttgatactaaaaatgagaaaaagtaggtttaaaaggaagttgttgaatttagataaattgtttagaaagccttccatcattttggtgggaggcttttgtggaaatagtagttgataaatttgaatttacctctatttagacatacaaactgttgacaacaaagctcctatatagtatgatttgataaactactatataggagcttttgt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 acaaaagctcctatatagtagtttatcaaatcatactatataggagctttgttgtcaacagtttgtatgtctaaatagaggtaaattcaaatttatcaactactatttccacaaaagcctcccaccaaaatgatggaaggctttctaaacaatttatctaaattcaacaacttccttttaaacctactttttctcatttttagtatcaaaacagtatcactaaggagctttttgcttccgtaaaccgttgtaatattgtattttcaacgattttacggaagaaacatttttgttact Mask Tandem Repeat Region ================================================ agtaacaaaaatgtttcttccgtaaaatcgttgaaaatacaatattacaacggtttacggaagcaaaaagctccttagtgatactgttttgatactaaaaatgagaaaaagtaggtttaaaaggaagttgttgaatttagataaattgtttagaaagccttccatcattttggtgggaggcttttgtggaaatagtagttgataaatttgaatttacctctatttagacatacaaactgttgacaacaaagctcctatatagtatgatttgataaactactatataggagcttttgt Find is-nt database================================================ Query_seq: TDE1718:TDE1719|TDE1718:TDE1719:GMP synthase:transcriptional regulator, MarR family:->->:1773872..1774168 297 agtaacaaaaatgtttcttccgtaaaatcgttgaaaatacaatattacaacggtttacggaagcaaaaagctccttagtgatactgttttgatactaaaaatgagaaaaagtaggtttaaaaggaagttgttgaatttagataaattgtttagaaagccttccatcattttggtgggaggcttttgtggaaatagtagttgataaatttgaatttacctctatttagacatacaaactgttgacaacaaagctcctatatagtatgatttgataaactactatataggagcttttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1718:TDE1719|TDE1718:TDE1719:GMP synthase:transcriptional regulator, MarR family:->->:1773872..1774168 297 agtaacaaaaatgtttcttccgtaaaatcgttgaaaatacaatattacaacggtttacggaagcaaaaagctccttagtgatactgttttgatactaaaaatgagaaaaagtaggtttaaaaggaagttgttgaatttagataaattgtttagaaagccttccatcattttggtgggaggcttttgtggaaatagtagttgataaatttgaatttacctctatttagacatacaaactgttgacaacaaagctcctatatagtatgatttgataaactactatataggagcttttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1718:TDE1719|TDE1718:TDE1719:GMP synthase:transcriptional regulator, MarR family:->->:1773872..1774168 297 agtaacaaaaatgtttcttccgtaaaatcgttgaaaatacaatattacaacggtttacggaagcaaaaagctccttagtgatactgttttgatactaaaaatgagaaaaagtaggtttaaaaggaagttgttgaatttagataaattgtttagaaagccttccatcattttggtgggaggcttttgtggaaatagtagttgataaatttgaatttacctctatttagacatacaaactgttgacaacaaagctcctatatagtatgatttgataaactactatataggagcttttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtaacaaaaatgtttcttccgtaaaatcgttgaaaatacaatattacaacggtttacggaagcaaaaagctccttagtgatactgttttgatactaaaaatgagaaaaagtaggtttaaaaggaagttgttgaatttagataaattgtttagaaagccttccatcattttggtgggaggcttttgtggaaatagtagttgataaatttgaatttacctctatttagacatacaaactgttgacaacaaagctcctatatagtatgatttgataaactactatataggagcttttgt Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 44 End: 199 ........................................... M T T V Y G S K K L L S D T V L I L K M R K S R F K R K L L N L D K L F R K P S I I L V G G F C G N S S .................................................................................................. Protein_Len: 52 Strand: - Start: 58 End: 213 ......................................................... P L L F S R L S V T K I S F I L F L L N L L F N N F K S L N N L F G E M M K T P P K Q P F L L Q Y I Q M .................................................................................... agtaacaaaaatgtttcttccgtaaaatcgttgaaaatacaatattacaacggtttacggaagcaaaaagctccttagtgatactgttttgatactaaaaatgagaaaaagtaggtttaaaaggaagttgttgaatttagataaattgtttagaaagccttccatcattttggtgggaggcttttgtggaaatagtagttgataaatttgaatttacctctatttagacatacaaactgttgacaacaaagctcctatatagtatgatttgataaactactatataggagcttttgt 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: 90 Start: 239 End: 268 ..............................................................................................................................................................................................................................................GTTGACAACAAAGCTCCTATATAGTATGAT............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtaacaaaaatgtttcttccgtaaaatcgttgaaaatacaatattacaacggtttacggaagcaaaaagctccttagtgatactgttttgatactaaaaatgagaaaaagtaggtttaaaaggaagttgttgaatttagataaattgtttagaaagccttccatcattttggtgggaggcttttgtggaaatagtagttgataaatttgaatttacctctatttagacatacaaactgttgacaacaaagctcctatatagtatgatttgataaactactatataggagcttttgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.9 Tail_Score: -4.3898 Start: 157 End: 181 Full_Region: TAAATTGTTTAGAAA GCCTTCCATCA TTT TGGTGGGAGGC TTTTGTGGAAATAGT ............................................................................................................................................................GCCTTCCATCATTTTGGTGGGAGGC.................................................................................................................... TransTerm Strand: - Conf: 79 HP_score: -8.5 Tail_Score: -3.88583 Start: 157 End: 181 Full_Region: actatttccacaaaa gcctcccacca aaa tgatggaaggc tttctaaacaattta ............................................................................................................................................................gcctcccaccaaaatgatggaaggc.................................................................................................................... Find igs database================================================ Query_seq: TDE1718:TDE1719|TDE1718:TDE1719:GMP synthase:transcriptional regulator, MarR family:->->:1773872..1774168 297 agtaacaaaaatgtttcttccgtaaaatcgttgaaaatacaatattacaacggtttacggaagcaaaaagctccttagtgatactgttttgatactaaaaatgagaaaaagtaggtttaaaaggaagttgttgaatttagataaattgtttagaaagccttccatcattttggtgggaggcttttgtggaaatagtagttgataaatttgaatttacctctatttagacatacaaactgttgacaacaaagctcctatatagtatgatttgataaactactatataggagcttttgt Intra-Species Hit: Count: 1 Min: 1 Max: 297 Len: 297 Subject: NC_002967_TDE1718_TDE1719|GMP synthase:transcriptional regulator, MarR family|POSITIVE:POSITIVE|[1773872,1774168]|297 HSP 1 e-value: 1.0E-167 bit: 589.0 Len: 297 Query Start:1 Query End:297 Subject Strand: POSITIVE Subject Start: 1 Subject End: 297 agtaacaaaaatgtttcttccgtaaaatcgttgaaaatacaatattacaacggtttacggaagcaaaaagctccttagtgatactgttttgatactaaaaatgagaaaaagtaggtttaaaaggaagttgttgaatttagataaattgtttagaaagccttccatcattttggtgggaggcttttgtggaaatagtagttgataaatttgaatttacctctatttagacatacaaactgttgacaacaaagctcctatatagtatgatttgataaactactatataggagcttttgt agtaacaaaaatgtttcttccgtaaaatcgttgaaaatacaatattacaacggtttacggaagcaaaaagctccttagtgatactgttttgatactaaaaatgagaaaaagtaggtttaaaaggaagttgttgaatttagataaattgtttagaaagccttccatcattttggtgggaggcttttgtggaaatagtagttgataaatttgaatttacctctatttagacatacaaactgttgacaacaaagctcctatatagtatgatttgataaactactatataggagcttttgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAACAAAAAUGUUUCUUCCGUAAAAUCGUUGAAAAUACAAUAUUACAACGGUUUACGGAAGCAAAAAGCUCCUUAGUGAUACUGUUUUGAUACUAAAAAUGAGAAAAAGUAGGUUUAAAAGGAAGUUGUUGAAUUUAGAUAAAUUGUUUAGAAAGCCUUCCAUCAUUUUGGUGGGAGGCUUUUGUGGAAAUAGUAGUUGAUAAAUUUGAAUUUACCUCUAUUUAGACAUACAAACUGUUGACAACAAAGCUCCUAUAUAGUAUGAUUUGAUAAACUACUAUAUAGGAGCUUUUGU ..(((((......(((((((((((((.((((((.((........)).)))))))))))))))).)))...(((.((((((.((......)).))))))....))).....(((.(((((((.(((.((..(..((((((.....(((((((.((((((((((((((.....))))))))))))))....)))))))......))))))..)....)).))).))))))).)))....)))))...(((((((((((((((((((.............)))))))))))))).))))) (-89.12) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAAAGCUCCUAUAUAGUAGUUUAUCAAAUCAUACUAUAUAGGAGCUUUGUUGUCAACAGUUUGUAUGUCUAAAUAGAGGUAAAUUCAAAUUUAUCAACUACUAUUUCCACAAAAGCCUCCCACCAAAAUGAUGGAAGGCUUUCUAAACAAUUUAUCUAAAUUCAACAACUUCCUUUUAAACCUACUUUUUCUCAUUUUUAGUAUCAAAACAGUAUCACUAAGGAGCUUUUUGCUUCCGUAAACCGUUGUAAUAUUGUAUUUUCAACGAUUUUACGGAAGAAACAUUUUUGUUACU ...(((((((((((((((((.............)))))))))))))))))(((((....((((((..(((..((((((.(((((((....))))))).....))))))..)))(((((((.(((.(.....).))).)))))))..............))))))..)))))..............................((((.(((((..((.((.......(((.....)))((((((((.(((((.((........)).)))))..)))))))).)).))..))))).)))) (-67.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 288 191 152 225 170 NC_002967:TDE1930|5end_hypothetical_protein_1948556..1948786_NEGATIVE 283 189 159 30 1 NC_002967:TDE0828|5end_glucose-inhibited_division_protein_A_850169..850399_NEGATIVE 264 189 163 173 144 NC_002967:TDE2482|5end_hypothetical_protein_2505536..2505766_POSITIVE 264 200 151 51 8 NC_002967:TDE2093|5end_hypothetical_protein_2121003..2121233_NEGATIVE 264 163 122 101 56 NC_002967:TDE0103|5end_aminotransferase,_class-V_123686..123916_NEGATIVE 261 196 156 76 25 NC_002967:TDE1162|5end_ParB-like_nuclease_domain_protein_1197684..1197914_NEGATIVE 258 86 45 222 185 NC_002967:TDE0397|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_446777..447007_POSITIVE 252 175 144 216 182 NC_002967:TDE2359|5end_DAK2_domain_protein_2394782..2395012_NEGATIVE 251 182 157 218 186 NC_002967:TDE1498|5end_hypothetical_protein_1543669..1543899_POSITIVE 250 200 152 194 144 NC_002967:TDE0400|5end_transcriptional_regulator,_LysR_family_451803..452033_NEGATIVE 249 187 156 189 160 NC_002967:TDE1349|5end_rod_shape-determining_protein_MreB_1389286..1389516_POSITIVE 248 187 157 170 134 NC_002967:TDE0407|5end_glutamate_synthase_(NADPH),_homotetrameric_460522..460752_NEGATIVE 247 100 51 155 116 NC_002967:TDE1584|5end_lipoprotein,_putative_1632025..1632255_POSITIVE 246 205 167 77 36 NC_002967:TDE1654|5end_ATP-dependent_helicase_HrpA,_putative_1702219..1702449_POSITIVE 243 220 173 101 57 NC_002967:TDE0570|5end_hypothetical_protein_600169..600399_POSITIVE 243 120 71 173 126 NC_002967:TDE0309|5end_lipoprotein,_putative_340666..340896_POSITIVE 242 91 51 88 55 NC_002967:TDE2435|5end_hypothetical_protein_2466462..2466692_NEGATIVE 242 200 151 197 124 NC_002967:TDE1043|5end_hypothetical_protein_1070945..1071175_POSITIVE 240 197 158 160 117 NC_002967:TDE0433|5end_hypothetical_protein_488717..488947_NEGATIVE 239 165 122 135 99 NC_002967:TDE2524|5end_ABC_transporter,_ATP-binding_protein_2550456..2550686_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 60 17 71 28 NC_002967:TDE1718|3end_GMP_synthase_1773811..1773961_POSITIVE 283 195 156 60 28 NC_002967:TDE2028|3end_OmpA_family_protein_2057019..2057169_POSITIVE 265 194 151 67 16 NC_002967:TDE2604|3end_hypothetical_protein_2644224..2644374_NEGATIVE 264 163 122 104 59 NC_002967:TDE0104|3end_3-dehydroquinate_synthase_123683..123833_NEGATIVE 263 185 145 78 34 NC_002967:TDE2434|3end_polysaccharide_deacetylase_family_protein_2463300..2463450_NEGATIVE 261 196 156 60 9 NC_002967:TDE1163|3end_hypothetical_protein_1197700..1197850_NEGATIVE 250 189 146 143 107 NC_002967:TDE2504|3end_O-sialoglycoprotein_endopeptidase_2530097..2530247_POSITIVE 247 100 51 57 18 NC_002967:TDE1583|3end_hypothetical_protein_1632007..1632157_POSITIVE 245 185 154 25 1 NC_002967:TDE2187|3end_ParB-like_nuclease_domain_protein_2221147..2221297_NEGATIVE 243 120 71 143 96 NC_002967:TDE0308|3end_hypothetical_protein_340716..340866_POSITIVE 239 165 122 114 78 NC_002967:TDE2523|3end_hypothetical_protein_2550515..2550665_POSITIVE 239 198 158 128 95 NC_002967:TDE0078|3end_glycine_reductase_complex_selenoprotein_GrdB1_88745..88895_NEGATIVE 236 189 157 151 121 NC_002967:TDE1278|3end_conserved_hypothetical_protein_TIGR01440_1312228..1312378_NEGATIVE 234 192 156 44 2 NC_002967:TDE2087|3end_translation_initiation_factor_IF-1_2115468..2115618_NEGATIVE 233 198 157 102 46 NC_002967:TDE0688|3end_hypothetical_protein_725757..725907_POSITIVE 230 220 171 108 43 NC_002967:TDE0464|3end_NifU_domain_protein_517948..518098_NEGATIVE 229 189 156 147 104 NC_002967:TDE2603|3end_DNA_mismatch_repair_protein_2644231..2644381_POSITIVE 227 196 152 83 38 NC_002967:TDE2433|3end_treponemal_membrane_protein,_putative_2463265..2463415_POSITIVE 226 189 144 127 89 NC_002967:TDE0773|3end_30S_ribosomal_protein_S3_810242..810392_POSITIVE 224 195 155 57 24 NC_002967:TDE1367|3end_glyoxalase_family_protein_1409440..1409590_POSITIVE