Origin IGS: aattctcccaatttattttcaaaataaagaaataatccagtatatccaaacttgattatactctttatttaaaaaaaagtcaaatataaaaacaaaaaaaatttatttttctgtaacttgtacttttaataaatcaaaaaacactaaacaagaacaaaaaaatccttttacagttacaatatcggctaatatttataggtttgtagcgtatttttgcaaattttaagatttttttttaatttctcttgacataagggctgaatgacggcaatatacaaaa .........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 ttttgtatattgccgtcattcagcccttatgtcaagagaaattaaaaaaaaatcttaaaatttgcaaaaatacgctacaaacctataaatattagccgatattgtaactgtaaaaggatttttttgttcttgtttagtgttttttgatttattaaaagtacaagttacagaaaaataaattttttttgtttttatatttgacttttttttaaataaagagtataatcaagtttggatatactggattatttctttattttgaaaataaattgggagaatt Mask Tandem Repeat Region ================================================ aattctcccaatttattttcaaaataaagaaataatccagtatatccaaacttgattatactctttatttaaaaaaaagtcaaatataaaaacaaaaaaaatttatttttctgtaacttgtacttttaataaatcaaaaaacactaaacaagaacaaaaaaatccttttacagttacaatatcggctaatatttataggtttgtagcgtatttttgcaaattttaagatttttttttaatttctcttgacataagggctgaatgacggcaatatacaaaa Find is-nt database================================================ Query_seq: TDE2083:TDE2084|TDE2083:TDE2084:anti-anti-sigma factor:RNA methyltransferase, TrmH family:<-->:2113254..2113533 280 aattctcccaatttattttcaaaataaagaaataatccagtatatccaaacttgattatactctttatttaaaaaaaagtcaaatataaaaacaaaaaaaatttatttttctgtaacttgtacttttaataaatcaaaaaacactaaacaagaacaaaaaaatccttttacagttacaatatcggctaatatttataggtttgtagcgtatttttgcaaattttaagatttttttttaatttctcttgacataagggctgaatgacggcaatatacaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2083:TDE2084|TDE2083:TDE2084:anti-anti-sigma factor:RNA methyltransferase, TrmH family:<-->:2113254..2113533 280 aattctcccaatttattttcaaaataaagaaataatccagtatatccaaacttgattatactctttatttaaaaaaaagtcaaatataaaaacaaaaaaaatttatttttctgtaacttgtacttttaataaatcaaaaaacactaaacaagaacaaaaaaatccttttacagttacaatatcggctaatatttataggtttgtagcgtatttttgcaaattttaagatttttttttaatttctcttgacataagggctgaatgacggcaatatacaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2083:TDE2084|TDE2083:TDE2084:anti-anti-sigma factor:RNA methyltransferase, TrmH family:<-->:2113254..2113533 280 aattctcccaatttattttcaaaataaagaaataatccagtatatccaaacttgattatactctttatttaaaaaaaagtcaaatataaaaacaaaaaaaatttatttttctgtaacttgtacttttaataaatcaaaaaacactaaacaagaacaaaaaaatccttttacagttacaatatcggctaatatttataggtttgtagcgtatttttgcaaattttaagatttttttttaatttctcttgacataagggctgaatgacggcaatatacaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattctcccaatttattttcaaaataaagaaataatccagtatatccaaacttgattatactctttatttaaaaaaaagtcaaatataaaaacaaaaaaaatttatttttctgtaacttgtacttttaataaatcaaaaaacactaaacaagaacaaaaaaatccttttacagttacaatatcggctaatatttataggtttgtagcgtatttttgcaaattttaagatttttttttaatttctcttgacataagggctgaatgacggcaatatacaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 86 End: 223 ..................................................................................... M K T K K I Y F S V T C T F N K S K N T K Q E Q K N P F T V T I S A N I Y R F V A Y F C K F ......................................................... Protein_Len: 30 Strand: - Start: 189 End: 278 ............................................................................................................................................................................................ Y K Y T Q L T N K C I K L N K K L K E Q C L P Q I V A I Y M .. Protein_Len: 31 Strand: - Start: 137 End: 229 ........................................................................................................................................ F V S F L F L F I R K C N C Y R S I N I P K Y R I K A F K L M ................................................... aattctcccaatttattttcaaaataaagaaataatccagtatatccaaacttgattatactctttatttaaaaaaaagtcaaatataaaaacaaaaaaaatttatttttctgtaacttgtacttttaataaatcaaaaaacactaaacaagaacaaaaaaatccttttacagttacaatatcggctaatatttataggtttgtagcgtatttttgcaaattttaagatttttttttaatttctcttgacataagggctgaatgacggcaatatacaaaa 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: 91 Start: 55 End: 84 ......................................................TTTGACTTTTTTTTAAATAAAGAGTATAAT.................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 245 End: 274 ....................................................................................................................................................................................................................................................CTTGACATAAGGGCTGAATGACGGCAATAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattctcccaatttattttcaaaataaagaaataatccagtatatccaaacttgattatactctttatttaaaaaaaagtcaaatataaaaacaaaaaaaatttatttttctgtaacttgtacttttaataaatcaaaaaacactaaacaagaacaaaaaaatccttttacagttacaatatcggctaatatttataggtttgtagcgtatttttgcaaattttaagatttttttttaatttctcttgacataagggctgaatgacggcaatatacaaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 66 HP_score: -3.4 Tail_Score: -5.20783 Start: 93 End: 113 Full_Region: taaaagtacaagtta cagaaaaa taaat tttttttg tttttatatttgact ............................................................................................cagaaaaataaattttttttg....................................................................................................................................................................... Find igs database================================================ Query_seq: TDE2083:TDE2084|TDE2083:TDE2084:anti-anti-sigma factor:RNA methyltransferase, TrmH family:<-->:2113254..2113533 280 aattctcccaatttattttcaaaataaagaaataatccagtatatccaaacttgattatactctttatttaaaaaaaagtcaaatataaaaacaaaaaaaatttatttttctgtaacttgtacttttaataaatcaaaaaacactaaacaagaacaaaaaaatccttttacagttacaatatcggctaatatttataggtttgtagcgtatttttgcaaattttaagatttttttttaatttctcttgacataagggctgaatgacggcaatatacaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 280 Len: 280 Subject: NC_002967_TDE2083_TDE2084|anti-anti-sigma factor:RNA methyltransferase, TrmH family|NEGATIVE:POSITIVE|[2113254,2113533]|280 HSP 1 e-value: 2.0E-68 bit: 260.0 Len: 179 Query Start:102 Query End:280 Subject Strand: POSITIVE Subject Start: 102 Subject End: 280 .....................................................................................................tttatttttctgtaacttgtacttttaataaatcaaaaaacactaaacaagaacnnnnnnntccttttacagttacaatatcggctaatatttataggtttgtagcgtatttttgcaaattttaagannnnnnnnnaatttctcttgacataagggctgaatgacggcaatatacaaaa .....................................................................................................tttatttttctgtaacttgtacttttaataaatcaaaaaacactaaacaagaacaaaaaaatccttttacagttacaatatcggctaatatttataggtttgtagcgtatttttgcaaattttaagatttttttttaatttctcttgacataagggctgaatgacggcaatatacaaaa HSP 2 e-value: 6.0E-32 bit: 139.0 Len: 70 Query Start:1 Query End:70 Subject Strand: POSITIVE Subject Start: 1 Subject End: 70 aattctcccaatttattttcaaaataaagaaataatccagtatatccaaacttgattatactctttattt.................................................................................................................................................................................................................. aattctcccaatttattttcaaaataaagaaataatccagtatatccaaacttgattatactctttattt.................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUCUCCCAAUUUAUUUUCAAAAUAAAGAAAUAAUCCAGUAUAUCCAAACUUGAUUAUACUCUUUAUUUAAAAAAAAGUCAAAUAUAAAAACAAAAAAAAUUUAUUUUUCUGUAACUUGUACUUUUAAUAAAUCAAAAAACACUAAACAAGAACAAAAAAAUCCUUUUACAGUUACAAUAUCGGCUAAUAUUUAUAGGUUUGUAGCGUAUUUUUGCAAAUUUUAAGAUUUUUUUUUAAUUUCUCUUGACAUAAGGGCUGAAUGACGGCAAUAUACAAAA .((((.(((......((((..(((((((((.((((((.(((........))).))))))..)))))))))..))))..(((((..........(((((((((((.(((((.(((..(((((..........................))))).))).)))))......(((.(((((((.(((..............)))))))))))))...............))))))))))).........)))))....)))..))))................. (-40.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUGUAUAUUGCCGUCAUUCAGCCCUUAUGUCAAGAGAAAUUAAAAAAAAAUCUUAAAAUUUGCAAAAAUACGCUACAAACCUAUAAAUAUUAGCCGAUAUUGUAACUGUAAAAGGAUUUUUUUGUUCUUGUUUAGUGUUUUUUGAUUUAUUAAAAGUACAAGUUACAGAAAAAUAAAUUUUUUUUGUUUUUAUAUUUGACUUUUUUUUAAAUAAAGAGUAUAAUCAAGUUUGGAUAUACUGGAUUAUUUCUUUAUUUUGAAAAUAAAUUGGGAGAAUU ..(((((((..((.(.....).))...)))).)))(((((.....(((((((((((....((((((..(((((((((...............))).)).)))).....))))))))))))))))).)))))........(((((..(((((((((((((.(((((.(((((((((.....)))))))))......)))))))))))....((((((((((.((((((.(((........))).))))))))))))))))....)))))))..)))))... (-48.76) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 668 50 1 141 92 NC_002967:TDE2083|5end_anti-anti-sigma_factor_2113163..2113393_NEGATIVE 271 226 181 190 147 NC_002967:TDE1153|5end_hypothetical_protein_1190858..1191088_NEGATIVE 252 277 254 195 172 NC_002967:TDE1730|5end_glycosyl_hydrolase,_family_2_1785545..1785775_NEGATIVE 234 230 183 130 73 NC_002967:TDE2722|5end_carhohydrate_kinase,_FGGY_family_2780874..2781104_NEGATIVE 229 234 191 50 5 NC_002967:TDE2064|5end_ferrous_iron_transport_protein_A_2091492..2091722_NEGATIVE 228 150 102 97 45 NC_002967:TDE2363|5end_high-affinity_branched_chain_amino_acid_ABC_transporter,_ATP-binding_protein_2398179..2398409_NEGATIVE 226 269 229 224 177 NC_002967:TDE0454|5end_hypothetical_protein_511243..511473_NEGATIVE 223 278 233 131 93 NC_002967:TDE2596|5end_hypothetical_protein_2632039..2632269_NEGATIVE 220 209 166 171 120 NC_002967:TDE1370|5end_YjeF-related_protein_1413284..1413514_NEGATIVE 220 280 251 222 196 NC_002967:TDE0868|5end_oxidoreductase,_FAD/FMN-binding_890385..890615_POSITIVE 219 218 179 55 11 NC_002967:TDE2517|5end_DNA_repair_protein_RadA_2543842..2544072_NEGATIVE 216 269 227 113 80 NC_002967:TDE1591|5end_inorganic_polyphosphate/ATP-NAD_kinase,_putative_1638582..1638812_POSITIVE 215 211 176 42 7 NC_002967:TDE0006|5end_Snf2_family_protein_9694..9924_NEGATIVE 214 220 179 215 169 NC_002967:TDE1673|5end_ATP-dependent_protease_ATP-binding_subunit_1726878..1727108_POSITIVE 213 71 36 90 56 NC_002967:TDE1203|5end_cell_division_protein_FtsA_1235033..1235263_POSITIVE 213 42 4 140 97 NC_002967:TDE0880|5end_nicotinate-nucleotide-dimethylbenzimidazole_phosphoribosyltransferase_899974..900204_POSITIVE 211 251 211 90 52 NC_002967:TDE0771|5end_ribosomal_protein_S19_808795..809025_POSITIVE 210 257 215 156 112 NC_002967:TDE1061|5end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_1086646..1086876_POSITIVE 208 208 164 70 12 NC_002967:TDE0178|5end_methyl-accepting_chemotaxis_protein_212628..212858_NEGATIVE 207 218 186 135 101 NC_002967:TDE1357|5end_aldose_1-epimerase_1396695..1396925_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 206 161 142 96 NC_002967:TDE2336|3end_sodium/dicarboxylate_symporter_family_protein_2371925..2372075_NEGATIVE 234 230 183 133 76 NC_002967:TDE2723|3end_phosphoribosylpyrophosphate_synthetase_2780871..2781021_NEGATIVE 230 229 192 144 110 NC_002967:TDE1495|3end_hypothetical_protein_1539596..1539746_NEGATIVE 228 150 102 97 45 NC_002967:TDE2364|3end_high-affinity_branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein_2398179..2398329_NEGATIVE 223 278 233 134 96 NC_002967:TDE2597|3end_ribulose-phosphate_3-epimerase_2632036..2632186_NEGATIVE 218 219 181 57 13 NC_002967:TDE1810|3end_hypothetical_protein_1845924..1846074_NEGATIVE 217 271 251 150 131 NC_002967:TDE0867|3end_hypothetical_protein_890400..890550_POSITIVE 216 269 227 72 39 NC_002967:TDE1590|3end_aminotransferase,_DegT/DnrJ/EryC1/StrS_family_1638621..1638771_POSITIVE 214 273 241 34 3 NC_002967:TDE1860|3end_hypothetical_protein_1886762..1886912_POSITIVE 213 71 36 97 63 NC_002967:TDE1202|3end_cell_division_protein_FtsQ,_putative_1235120..1235270_POSITIVE 213 42 4 143 100 NC_002967:TDE0879|3end_hypothetical_protein_900057..900207_POSITIVE 212 263 239 49 20 NC_002967:TDE2086|3end_DnaJ_domain_protein_2115475..2115625_POSITIVE 211 251 211 77 39 NC_002967:TDE0770|3end_50S_ribosomal_protein_L2_808862..809012_POSITIVE 210 205 182 146 122 NC_002967:TDE2000|3end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_2019639..2019789_POSITIVE 207 260 218 115 67 NC_002967:TDE0285|3end_translation_elongation_factor_G_315753..315903_POSITIVE 205 209 164 66 25 NC_002967:TDE2609|3end_MiaB-like_tRNA_modifying_enzyme_YliG,_TIGR01125_2651904..2652054_POSITIVE 205 269 232 77 28 NC_002967:TDE0277|3end_hypothetical_protein_308109..308259_NEGATIVE 204 270 224 87 43 NC_002967:TDE2299|3end_apolipoprotein_N-acyltransferase_2339937..2340087_POSITIVE 204 206 162 121 79 NC_002967:TDE1507|3end_L-serine_dehydratase,_iron-sulfur-dependent,_beta_subunit_1555062..1555212_NEGATIVE 203 209 168 129 91 NC_002967:TDE1922|3end_hypothetical_protein_1940913..1941063_NEGATIVE