Origin IGS: agctaatccctccttacaaaataatttaatttatacaaaaaactgcaaagccgaataaattcaaccctgcggtttttagattgagaaaaataagtattaacagctttaattagagatattttacttaatagagaaaatgggggggggtaaacctaggctaacatttttcaagtcatttttattccgtaaatatcgggaaagagaaaattgtaaatcgacaaaaaatttcgttaccatggcttaattatagcataaaatatagaaaaactcacgtatcaattatcaaatttacaataggaaacctctaaaaacttcaatttttagaggtttcatttgattttaattcgagatgcttcctt .........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 aaggaagcatctcgaattaaaatcaaatgaaacctctaaaaattgaagtttttagaggtttcctattgtaaatttgataattgatacgtgagtttttctatattttatgctataattaagccatggtaacgaaattttttgtcgatttacaattttctctttcccgatatttacggaataaaaatgacttgaaaaatgttagcctaggtttacccccccccattttctctattaagtaaaatatctctaattaaagctgttaatacttatttttctcaatctaaaaaccgcagggttgaatttattcggctttgcagttttttgtataaattaaattattttgtaaggagggattagct Mask Tandem Repeat Region ================================================ agctaatccctccttacaaaataatttaatttatacaaaaaactgcaaagccgaataaattcaaccctgcggtttttagattgagaaaaataagtattaacagctttaattagagatattttacttaatagagaaaatgggggggggtaaacctaggctaacatttttcaagtcatttttattccgtaaatatcgggaaagagaaaattgtaaatcgacaaaaaatttcgttaccatggcttaattatagcataaaatatagaaaaactcacgtatcaattatcaaatttacaataggaaacctctaaaaacttcaatttttagaggtttcatttgattttaattcgagatgcttcctt Find is-nt database================================================ Query_seq: TDE2269:TDE2270|TDE2269:TDE2270:hypothetical protein:methyl-accepting chemotaxis protein:<-<-:2306011..2306369 359 agctaatccctccttacaaaataatttaatttatacaaaaaactgcaaagccgaataaattcaaccctgcggtttttagattgagaaaaataagtattaacagctttaattagagatattttacttaatagagaaaatgggggggggtaaacctaggctaacatttttcaagtcatttttattccgtaaatatcgggaaagagaaaattgtaaatcgacaaaaaatttcgttaccatggcttaattatagcataaaatatagaaaaactcacgtatcaattatcaaatttacaataggaaacctctaaaaacttcaatttttagaggtttcatttgattttaattcgagatgcttcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2269:TDE2270|TDE2269:TDE2270:hypothetical protein:methyl-accepting chemotaxis protein:<-<-:2306011..2306369 359 agctaatccctccttacaaaataatttaatttatacaaaaaactgcaaagccgaataaattcaaccctgcggtttttagattgagaaaaataagtattaacagctttaattagagatattttacttaatagagaaaatgggggggggtaaacctaggctaacatttttcaagtcatttttattccgtaaatatcgggaaagagaaaattgtaaatcgacaaaaaatttcgttaccatggcttaattatagcataaaatatagaaaaactcacgtatcaattatcaaatttacaataggaaacctctaaaaacttcaatttttagaggtttcatttgattttaattcgagatgcttcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2269:TDE2270|TDE2269:TDE2270:hypothetical protein:methyl-accepting chemotaxis protein:<-<-:2306011..2306369 359 agctaatccctccttacaaaataatttaatttatacaaaaaactgcaaagccgaataaattcaaccctgcggtttttagattgagaaaaataagtattaacagctttaattagagatattttacttaatagagaaaatgggggggggtaaacctaggctaacatttttcaagtcatttttattccgtaaatatcgggaaagagaaaattgtaaatcgacaaaaaatttcgttaccatggcttaattatagcataaaatatagaaaaactcacgtatcaattatcaaatttacaataggaaacctctaaaaacttcaatttttagaggtttcatttgattttaattcgagatgcttcctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agctaatccctccttacaaaataatttaatttatacaaaaaactgcaaagccgaataaattcaaccctgcggtttttagattgagaaaaataagtattaacagctttaattagagatattttacttaatagagaaaatgggggggggtaaacctaggctaacatttttcaagtcatttttattccgtaaatatcgggaaagagaaaattgtaaatcgacaaaaaatttcgttaccatggcttaattatagcataaaatatagaaaaactcacgtatcaattatcaaatttacaataggaaacctctaaaaacttcaatttttagaggtttcatttgattttaattcgagatgcttcctt Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 116 End: 241 ................................................................................................................... M F Y L I E K M G G G K P R L T F F K S F L F R K Y R E R E N C K S T K N F V T M A ...................................................................................................................... Protein_Len: 38 Strand: + Start: 192 End: 305 ............................................................................................................................................................................................... M G K E K I V N R Q K I S L P W L N Y S I K Y R K T H V S I I K F T I G N L ...................................................... Protein_Len: 38 Strand: - Start: 124 End: 237 ........................................................................................................................... K I S F I P P P L G L S V N K L D N K N R L Y R S L S F Q L D V F F K T V M .......................................................................................................................... Protein_Len: 39 Strand: - Start: 6 End: 119 ..... * D R R V F Y N L K Y L F S C L R I F E V R R N K S Q S F Y T N V A K I L S M ................................................................................................................................................................................................................................................ agctaatccctccttacaaaataatttaatttatacaaaaaactgcaaagccgaataaattcaaccctgcggtttttagattgagaaaaataagtattaacagctttaattagagatattttacttaatagagaaaatgggggggggtaaacctaggctaacatttttcaagtcatttttattccgtaaatatcgggaaagagaaaattgtaaatcgacaaaaaatttcgttaccatggcttaattatagcataaaatatagaaaaactcacgtatcaattatcaaatttacaataggaaacctctaaaaacttcaatttttagaggtttcatttgattttaattcgagatgcttcctt 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: 83 Start: 244 End: 273 ...................................................................................................................................................................................................................................................CGTGAGTTTTTCTATATTTTATGCTATAAT...................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agctaatccctccttacaaaataatttaatttatacaaaaaactgcaaagccgaataaattcaaccctgcggtttttagattgagaaaaataagtattaacagctttaattagagatattttacttaatagagaaaatgggggggggtaaacctaggctaacatttttcaagtcatttttattccgtaaatatcgggaaagagaaaattgtaaatcgacaaaaaatttcgttaccatggcttaattatagcataaaatatagaaaaactcacgtatcaattatcaaatttacaataggaaacctctaaaaacttcaatttttagaggtttcatttgattttaattcgagatgcttcctt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 75 HP_score: -3.5 Tail_Score: -5.38951 Start: 43 End: 72 Full_Region: ttctcaatctaaaaa ccgcagggttgaa ttta ttcggctttgcag ttttttgtataaatt ..........................................ccgcagggttgaatttattcggctttgcag............................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 72 HP_score: -6.2 Tail_Score: -4.41494 Start: 291 End: 337 Full_Region: TCAATTATCAAATTT ACAATAGGAAACCTCTAAAAA CTTCAA TTTTTAGAGGTTTCATTTGA TTTTAATTCGAGATG ..................................................................................................................................................................................................................................................................................................ACAATAGGAAACCTCTAAAAACTTCAATTTTTAGAGGTTTCATTTGA...................... TransTerm Strand: + Conf: 95 HP_score: -10.7 Tail_Score: -4.27062 Start: 297 End: 332 Full_Region: ATCAAATTTACAATA GGAAACCTCTAAAAA CTTCAA TTTTTAGAGGTTTCA TTTGATTTTAATTCG ........................................................................................................................................................................................................................................................................................................GGAAACCTCTAAAAACTTCAATTTTTAGAGGTTTCA........................... TransTerm Strand: - Conf: 93 HP_score: -11.4 Tail_Score: -3.31199 Start: 297 End: 332 Full_Region: cgaattaaaatcaaa tgaaacctctaaaaat tgaa gtttttagaggtttcc tattgtaaatttgat ........................................................................................................................................................................................................................................................................................................tgaaacctctaaaaattgaagtttttagaggtttcc........................... TransTerm Strand: + Conf: 100 HP_score: -14.2 Tail_Score: -3.15152 Start: 298 End: 331 Full_Region: TCAAATTTACAATAG GAAACCTCTAAAAA CTTCAA TTTTTAGAGGTTTC ATTTGATTTTAATTC .........................................................................................................................................................................................................................................................................................................GAAACCTCTAAAAACTTCAATTTTTAGAGGTTTC............................ TransTerm Strand: - Conf: 100 HP_score: -14.9 Tail_Score: -2.57996 Start: 298 End: 331 Full_Region: gaattaaaatcaaat gaaacctctaaaaat tgaa gtttttagaggtttc ctattgtaaatttga .........................................................................................................................................................................................................................................................................................................gaaacctctaaaaattgaagtttttagaggtttc............................ Find igs database================================================ Query_seq: TDE2269:TDE2270|TDE2269:TDE2270:hypothetical protein:methyl-accepting chemotaxis protein:<-<-:2306011..2306369 359 agctaatccctccttacaaaataatttaatttatacaaaaaactgcaaagccgaataaattcaaccctgcggtttttagattgagaaaaataagtattaacagctttaattagagatattttacttaatagagaaaatgggggggggtaaacctaggctaacatttttcaagtcatttttattccgtaaatatcgggaaagagaaaattgtaaatcgacaaaaaatttcgttaccatggcttaattatagcataaaatatagaaaaactcacgtatcaattatcaaatttacaataggaaacctctaaaaacttcaatttttagaggtttcatttgattttaattcgagatgcttcctt Intra-Species Hit: Count: 1 Min: 1 Max: 359 Len: 359 Subject: NC_002967_TDE2269_TDE2270|hypothetical protein:methyl-accepting chemotaxis protein|NEGATIVE:NEGATIVE|[2306011,2306369]|359 HSP 1 e-value: 0.0 bit: 658.0 Len: 359 Query Start:1 Query End:359 Subject Strand: POSITIVE Subject Start: 1 Subject End: 359 agctaatccctccttacaaaataatttaatttatacaaaaaactgcaaagccgaataaattcaaccctgcggtttttagattgagaaaaataagtattaacagctttaattagagatattttacttaatagagaaaatnnnnnnnnntaaacctaggctaacatttttcaagtcatttttattccgtaaatatcgggaaagagaaaattgtaaatcgacaaaaaatttcgttaccatggcttaattatagcataaaatatagaaaaactcacgtatcaattatcaaatttacaataggaaacctctaaaaacttcaatttttagaggtttcatttgattttaattcgagatgcttcctt agctaatccctccttacaaaataatttaatttatacaaaaaactgcaaagccgaataaattcaaccctgcggtttttagattgagaaaaataagtattaacagctttaattagagatattttacttaatagagaaaatgggggggggtaaacctaggctaacatttttcaagtcatttttattccgtaaatatcgggaaagagaaaattgtaaatcgacaaaaaatttcgttaccatggcttaattatagcataaaatatagaaaaactcacgtatcaattatcaaatttacaataggaaacctctaaaaacttcaatttttagaggtttcatttgattttaattcgagatgcttcctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUAAUCCCUCCUUACAAAAUAAUUUAAUUUAUACAAAAAACUGCAAAGCCGAAUAAAUUCAACCCUGCGGUUUUUAGAUUGAGAAAAAUAAGUAUUAACAGCUUUAAUUAGAGAUAUUUUACUUAAUAGAGAAAAUGGGGGGGGGUAAACCUAGGCUAACAUUUUUCAAGUCAUUUUUAUUCCGUAAAUAUCGGGAAAGAGAAAAUUGUAAAUCGACAAAAAAUUUCGUUACCAUGGCUUAAUUAUAGCAUAAAAUAUAGAAAAACUCACGUAUCAAUUAUCAAAUUUACAAUAGGAAACCUCUAAAAACUUCAAUUUUUAGAGGUUUCAUUUGAUUUUAAUUCGAGAUGCUUCCUU .(((((((((((((((........(((((((((.....(((((((((.....(((....))).....)))))))))))))))))).....((((((.......((((....))))......))))))..........))))))))))).....(((((((...............(((((.(((((.......))))).)))))...((((......))))...............)))))))....)))).....................(((((....................((((((((((((((......))))))))))))))..((((.......)))))))))...... (-75.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGAAGCAUCUCGAAUUAAAAUCAAAUGAAACCUCUAAAAAUUGAAGUUUUUAGAGGUUUCCUAUUGUAAAUUUGAUAAUUGAUACGUGAGUUUUUCUAUAUUUUAUGCUAUAAUUAAGCCAUGGUAACGAAAUUUUUUGUCGAUUUACAAUUUUCUCUUUCCCGAUAUUUACGGAAUAAAAAUGACUUGAAAAAUGUUAGCCUAGGUUUACCCCCCCCCAUUUUCUCUAUUAAGUAAAAUAUCUCUAAUUAAAGCUGUUAAUACUUAUUUUUCUCAAUCUAAAAACCGCAGGGUUGAAUUUAUUCGGCUUUGCAGUUUUUUGUAUAAAUUAAAUUAUUUUGUAAGGAGGGAUUAGCU .....(((.....(((............(((((((((((((((....)))))))))))))))..((((((((((.(((((..(((.((((.((((...((((........))))...))))))))........)))..))))))))))))))).)))....((((....((((((((((((...(((...(((((((((((((..((.((((.........(((((((......)).))))).........)))).))))))))....))))))))))....((((((.(((((((((((....))))))))))).)))))).............))))))))))))..))))...))) (-77.77) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 822 90 41 181 132 NC_002967:TDE2269|5end_hypothetical_protein_2305920..2306150_NEGATIVE 362 169 131 168 122 NC_002967:TDE0617|5end_hypothetical_protein_650227..650457_NEGATIVE 337 332 297 109 75 NC_002967:TDE0629|5end_chaperone_protein_DnaJ_662587..662817_POSITIVE 335 338 295 157 115 NC_002967:TDE2256|5end_hypothetical_protein_2293387..2293617_NEGATIVE 294 340 295 155 110 NC_002967:TDE2461|5end_selenide,_water_dikinase_(selenocysteine-containing)_2488260..2488490_NEGATIVE 270 331 294 146 108 NC_002967:TDE0346|5end_protease_PrtB_387897..388127_NEGATIVE 269 331 297 201 167 NC_002967:TDE0943|5end_hypothetical_protein_965983..966213_POSITIVE 263 158 114 197 151 NC_002967:TDE1980|5end_hypothetical_protein_1992061..1992291_NEGATIVE 262 169 131 49 13 NC_002967:TDE1057|5end_hypothetical_protein_1086245..1086475_NEGATIVE 260 174 133 44 7 NC_002967:TDE1931|5end_cytidine_deaminase_1948530..1948760_POSITIVE 260 334 292 212 171 NC_002967:TDE0332|5end_transcriptional_regulator,_TetR_family_370940..371170_POSITIVE 256 180 138 176 134 NC_002967:TDE0084|5end_phosphoenolpyruvate-protein_phosphotransferase_97455..97685_NEGATIVE 252 238 192 92 45 NC_002967:TDE1725|5end_hypothetical_protein_1779277..1779507_NEGATIVE 252 83 43 230 191 NC_002967:TDE1063|5end_methionyl-tRNA_synthetase_1090507..1090737_POSITIVE 251 328 286 153 110 NC_002967:TDE1269|5end_hypothetical_protein_1304522..1304752_NEGATIVE 248 174 134 214 159 NC_002967:TDE1540|5end_hypothetical_protein_1584422..1584652_POSITIVE 246 198 151 53 11 NC_002967:TDE2535|5end_pyruvate_kinase_2560892..2561122_POSITIVE 246 187 141 77 28 NC_002967:TDE0994|5end_hypothetical_protein_1020538..1020768_POSITIVE 245 218 171 79 38 NC_002967:TDE0459|5end_hypothetical_protein_514382..514612_POSITIVE 244 187 141 69 17 NC_002967:TDE2605|5end_phosphoglycerate_mutase_family_protein_2645818..2646048_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 404 340 296 92 47 NC_002967:TDE0185|3end_ABC_transporter,_ATP-binding_protein,_HlyB_family_222335..222485_POSITIVE 376 331 295 88 51 NC_002967:TDE1264|3end_hypothetical_protein_1298152..1298302_NEGATIVE 360 340 296 78 29 NC_002967:TDE0186|3end_hypothetical_protein_222373..222523_NEGATIVE 337 332 297 71 37 NC_002967:TDE0628|3end_molecular_chaperone_DnaK_662629..662779_POSITIVE 333 350 302 55 5 NC_002967:TDE2257|3end_5'-nucleotidase_family_protein_2293503..2293653_NEGATIVE 332 330 294 87 52 NC_002967:TDE1992|3end_OmpA_family_protein_2010902..2011052_POSITIVE 327 167 131 151 107 NC_002967:TDE0618|3end_hypothetical_protein_650242..650392_NEGATIVE 297 340 291 92 44 NC_002967:TDE0525|3end_hypothetical_protein_571163..571313_POSITIVE 294 340 295 110 65 NC_002967:TDE2462|3end_hypothetical_protein_2488305..2488455_NEGATIVE 285 331 297 85 49 NC_002967:TDE2029|3end_hydrolase,_TatD_family_2057148..2057298_NEGATIVE 283 330 296 82 46 NC_002967:TDE1993|3end_aspartate_ammonia-lyase,_putative_2010917..2011067_NEGATIVE 276 180 138 74 30 NC_002967:TDE1356|3end_lipoprotein,_putative_1395674..1395824_NEGATIVE 269 331 297 77 43 NC_002967:TDE0942|3end_long-chain-fatty-acid--CoA_ligase,_putative_965939..966089_POSITIVE 262 169 131 62 26 NC_002967:TDE1058|3end_hypothetical_protein_1086232..1086382_NEGATIVE 260 350 301 87 31 NC_002967:TDE0860|3end_ribosomal_small_subunit_pseudouridine_synthase_A_881840..881990_POSITIVE 251 328 286 98 55 NC_002967:TDE1270|3end_hypothetical_protein_1304577..1304727_NEGATIVE 246 188 142 145 99 NC_002967:TDE2778|3end_PspC_domain_protein_2829371..2829521_NEGATIVE 244 159 130 66 29 NC_002967:TDE2337|3end_aminopeptidase_2374604..2374754_POSITIVE 243 158 127 72 39 NC_002967:TDE1351|3end_rod_shape-determining_protein_MreD_1391793..1391943_POSITIVE 243 217 184 151 116 NC_002967:TDE1313|3end_signal_peptidase_I_1351266..1351416_POSITIVE