Origin IGS: tttaatatcggcttgacacgctatatatagtgtgttatcctgtagtgtataattagatacgctatttttgggagggagggatgccggcttttaggcatcctgtaagtaaaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attttacttacaggatgcctaaaagccggcatccctccctcccaaaaatagcgtatctaattatacactacaggataacacactatatatagcgtgtcaagccgatattaaa Mask Tandem Repeat Region ================================================ tttaatatcggcttgacacgctatatatagtgtgttatcctgtagtgtataattagatacgctatttttgggagggagggatgccggcttttaggcatcctgtaagtaaaat Find is-nt database================================================ Query_seq: TDE1329:TDE1330|TDE1329:TDE1330:ATPase, AAA family:conserved hypothetical protein TIGR00244:->->:1365407..1365518 112 tttaatatcggcttgacacgctatatatagtgtgttatcctgtagtgtataattagatacgctatttttgggagggagggatgccggcttttaggcatcctgtaagtaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1329:TDE1330|TDE1329:TDE1330:ATPase, AAA family:conserved hypothetical protein TIGR00244:->->:1365407..1365518 112 tttaatatcggcttgacacgctatatatagtgtgttatcctgtagtgtataattagatacgctatttttgggagggagggatgccggcttttaggcatcctgtaagtaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1329:TDE1330|TDE1329:TDE1330:ATPase, AAA family:conserved hypothetical protein TIGR00244:->->:1365407..1365518 112 tttaatatcggcttgacacgctatatatagtgtgttatcctgtagtgtataattagatacgctatttttgggagggagggatgccggcttttaggcatcctgtaagtaaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttaatatcggcttgacacgctatatatagtgtgttatcctgtagtgtataattagatacgctatttttgggagggagggatgccggcttttaggcatcctgtaagtaaaat Predict ORF larger than 30AA ================================================ tttaatatcggcttgacacgctatatatagtgtgttatcctgtagtgtataattagatacgctatttttgggagggagggatgccggcttttaggcatcctgtaagtaaaat 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: 12 End: 41 ...........CTTGACACGCTATATATAGTGTGTTATCCT....................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttaatatcggcttgacacgctatatatagtgtgttatcctgtagtgtataattagatacgctatttttgggagggagggatgccggcttttaggcatcctgtaagtaaaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 66 HP_score: -3.8 Tail_Score: -4.56597 Start: 43 End: 64 Full_Region: TAGTGTGTTATCCTG TAGTGTAT AATTAG ATACGCTA TTTTTGGGAGGGAGG ..........................................TAGTGTATAATTAGATACGCTA................................................ Find igs database================================================ Query_seq: TDE1329:TDE1330|TDE1329:TDE1330:ATPase, AAA family:conserved hypothetical protein TIGR00244:->->:1365407..1365518 112 tttaatatcggcttgacacgctatatatagtgtgttatcctgtagtgtataattagatacgctatttttgggagggagggatgccggcttttaggcatcctgtaagtaaaat Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_002967_TDE1329_TDE1330|ATPase, AAA family:conserved hypothetical protein TIGR00244|POSITIVE:POSITIVE|[1365407,1365518]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 tttaatatcggcttgacacgctatatatagtgtgttatcctgtagtgtataattagatacgctatttttgggagggagggatgccggcttttaggcatcctgtaagtaaaat tttaatatcggcttgacacgctatatatagtgtgttatcctgtagtgtataattagatacgctatttttgggagggagggatgccggcttttaggcatcctgtaagtaaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAUAUCGGCUUGACACGCUAUAUAUAGUGUGUUAUCCUGUAGUGUAUAAUUAGAUACGCUAUUUUUGGGAGGGAGGGAUGCCGGCUUUUAGGCAUCCUGUAAGUAAAAU ..........(((((((((((((....))))))))).(((((((((((((......)))))))))....))))....((((((((........))))))))..))))..... (-37.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUACUUACAGGAUGCCUAAAAGCCGGCAUCCCUCCCUCCCAAAAAUAGCGUAUCUAAUUAUACACUACAGGAUAACACACUAUAUAUAGCGUGUCAAGCCGAUAUUAAA ............(((((((........)))))))..............(((.((((......)))).)))..((...((((.(((....))).))))....))......... (-23.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 104 61 194 150 NC_002967:TDE1743|5end_chromate_transport_protein_1798503..1798733_NEGATIVE 362 105 71 229 197 NC_002967:TDE0043|5end_TPR_domain_protein_49688..49918_POSITIVE 331 104 62 74 34 NC_002967:TDE1858|5end_transcriptional_regulator,_PadR_family_1884632..1884862_POSITIVE 316 96 66 186 161 NC_002967:TDE1182|5end_hypothetical_protein_1210458..1210688_POSITIVE 313 106 71 78 41 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 311 98 55 151 108 NC_002967:TDE1675|5end_ribosomal_protein_L9_1729242..1729472_NEGATIVE 310 107 66 179 136 NC_002967:TDE1098|5end_hypothetical_protein_1133678..1133908_NEGATIVE 310 107 68 53 14 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 308 99 51 170 121 NC_002967:TDE0084|5end_phosphoenolpyruvate-protein_phosphotransferase_97455..97685_NEGATIVE 305 37 5 178 142 NC_002967:TDE1855|5end_hypothetical_protein_1882846..1883076_POSITIVE 303 97 54 215 158 NC_002967:TDE2618|5end_PHP_domain_protein_2659392..2659622_POSITIVE 303 110 63 229 164 NC_002967:TDE0584|5end_permease,_putative_623134..623364_NEGATIVE 298 109 62 171 118 NC_002967:TDE2536|5end_hypothetical_protein_2562320..2562550_POSITIVE 297 96 53 140 85 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 291 107 66 217 172 NC_002967:TDE1193|5end_hypothetical_protein_1219657..1219887_NEGATIVE 291 107 66 217 172 NC_002967:TDE0579|5end_hypothetical_protein_610029..610259_NEGATIVE 288 87 55 213 175 NC_002967:TDE0978|5end_hypothetical_protein_1001868..1002098_POSITIVE 285 80 32 150 96 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 285 100 59 96 45 NC_002967:TDE2141|5end_hypothetical_protein_2175768..2175998_NEGATIVE 285 106 68 197 151 NC_002967:TDE2094|5end_hypothetical_protein_2121319..2121549_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 106 62 55 4 NC_002967:TDE2210|3end_hypothetical_protein_2249394..2249544_NEGATIVE 323 42 9 82 49 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 320 103 68 45 12 NC_002967:TDE1131|3end_hypothetical_protein_1163531..1163681_POSITIVE 316 102 69 58 16 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 312 91 51 48 9 NC_002967:TDE2728|3end_hypothetical_protein_2785815..2785965_POSITIVE 310 103 73 110 79 NC_002967:TDE1977|3end_hypothetical_protein_1991348..1991498_POSITIVE 310 107 66 121 78 NC_002967:TDE1099|3end_acetyltransferase,_GNAT_family_1133736..1133886_NEGATIVE 310 107 68 40 1 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 285 102 62 151 105 NC_002967:TDE2535|3end_pyruvate_kinase_2562387..2562537_POSITIVE 283 110 70 75 29 NC_002967:TDE2489|3end_peptide_chain_release_factor_1_2511391..2511541_NEGATIVE 281 107 65 41 2 NC_002967:TDE2450|3end_ankyrin_repeat_protein_2479887..2480037_POSITIVE 281 102 64 51 5 NC_002967:TDE0293|3end_MATE_efflux_family_protein_322018..322168_NEGATIVE 279 105 61 116 66 NC_002967:TDE2179|3end_voltage-gated_chloride_channel_2210614..2210764_POSITIVE 277 102 61 146 101 NC_002967:TDE1149|3end_hypothetical_protein_1186426..1186576_NEGATIVE 276 88 66 76 47 NC_002967:TDE0481|3end_hypothetical_protein_538197..538347_NEGATIVE 274 87 56 54 18 NC_002967:TDE2163|3end_hypothetical_protein_2195533..2195683_NEGATIVE 273 92 55 58 13 NC_002967:TDE2326|3end_cobyric_acid_synthase_CobQ,_putative_2362027..2362177_POSITIVE 273 100 60 137 107 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 273 96 69 88 57 NC_002967:TDE0194|3end_hypothetical_protein_230739..230889_NEGATIVE 272 99 61 64 13 NC_002967:TDE1072|3end_lipoprotein,_putative_1103436..1103586_POSITIVE