Origin IGS: aggattacctccttttaaaaaatactgaaatgcatacgtttaggcaaggggattgtacagaagaattcacgaaccttaacaatggcaagaagaacgaaataaggcaaaattatcataaaaagattgttatgcaaggcggagaaagtaacccggcttttacactagacaatttataaaaaaactactaaaataattatgggtgctaaaaaaatagttttttataagtgccctatatttttatataaagggagtgcgcat .........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 atgcgcactccctttatataaaaatatagggcacttataaaaaactatttttttagcacccataattattttagtagtttttttataaattgtctagtgtaaaagccgggttactttctccgccttgcataacaatctttttatgataattttgccttatttcgttcttcttgccattgttaaggttcgtgaattcttctgtacaatccccttgcctaaacgtatgcatttcagtattttttaaaaggaggtaatcct Mask Tandem Repeat Region ================================================ aggattacctccttttaaaaaatactgaaatgcatacgtttaggcaaggggattgtacagaagaattcacgaaccttaacaatggcaagaagaacgaaataaggcaaaattatcataaaaagattgttatgcaaggcggagaaagtaacccggcttttacactagacaatttataaaaaaactactaaaataattatgggtgctaaaaaaatagttttttataagtgccctatatttttatataaagggagtgcgcat Find is-nt database================================================ Query_seq: TDE0351:TDE0352|TDE0351:TDE0352:L-lactate dehydrogenase:ribose 5-phosphate isomerase B:<-->:396089..396346 258 aggattacctccttttaaaaaatactgaaatgcatacgtttaggcaaggggattgtacagaagaattcacgaaccttaacaatggcaagaagaacgaaataaggcaaaattatcataaaaagattgttatgcaaggcggagaaagtaacccggcttttacactagacaatttataaaaaaactactaaaataattatgggtgctaaaaaaatagttttttataagtgccctatatttttatataaagggagtgcgcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0351:TDE0352|TDE0351:TDE0352:L-lactate dehydrogenase:ribose 5-phosphate isomerase B:<-->:396089..396346 258 aggattacctccttttaaaaaatactgaaatgcatacgtttaggcaaggggattgtacagaagaattcacgaaccttaacaatggcaagaagaacgaaataaggcaaaattatcataaaaagattgttatgcaaggcggagaaagtaacccggcttttacactagacaatttataaaaaaactactaaaataattatgggtgctaaaaaaatagttttttataagtgccctatatttttatataaagggagtgcgcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0351:TDE0352|TDE0351:TDE0352:L-lactate dehydrogenase:ribose 5-phosphate isomerase B:<-->:396089..396346 258 aggattacctccttttaaaaaatactgaaatgcatacgtttaggcaaggggattgtacagaagaattcacgaaccttaacaatggcaagaagaacgaaataaggcaaaattatcataaaaagattgttatgcaaggcggagaaagtaacccggcttttacactagacaatttataaaaaaactactaaaataattatgggtgctaaaaaaatagttttttataagtgccctatatttttatataaagggagtgcgcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggattacctccttttaaaaaatactgaaatgcatacgtttaggcaaggggattgtacagaagaattcacgaaccttaacaatggcaagaagaacgaaataaggcaaaattatcataaaaagattgttatgcaaggcggagaaagtaacccggcttttacactagacaatttataaaaaaactactaaaataattatgggtgctaaaaaaatagttttttataagtgccctatatttttatataaagggagtgcgcat Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 30 End: 173 ............................. M H T F R Q G D C T E E F T N L N N G K K N E I R Q N Y H K K I V M Q G G E S N P A F T L D N L ..................................................................................... Protein_Len: 30 Strand: + Start: 169 End: 258 ........................................................................................................................................................................ M Y K K T T K I I M G A K K I V F Y K C P I F L Y K G S A H Protein_Len: 39 Strand: - Start: 18 End: 134 ................. F I S F H M R K P L P I T C F F E R V K V I A L L V F Y P L I I M F L N N H M ............................................................................................................................ Protein_Len: 31 Strand: - Start: 8 End: 100 ....... R R K F F V S I C V N L C P S Q V S S N V F R L L P L F F S M .............................................................................................................................................................. aggattacctccttttaaaaaatactgaaatgcatacgtttaggcaaggggattgtacagaagaattcacgaaccttaacaatggcaagaagaacgaaataaggcaaaattatcataaaaagattgttatgcaaggcggagaaagtaacccggcttttacactagacaatttataaaaaaactactaaaataattatgggtgctaaaaaaatagttttttataagtgccctatatttttatataaagggagtgcgcat 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: 162 End: 191 .................................................................................................................................................................CTAGACAATTTATAAAAAAACTACTAAAAT................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggattacctccttttaaaaaatactgaaatgcatacgtttaggcaaggggattgtacagaagaattcacgaaccttaacaatggcaagaagaacgaaataaggcaaaattatcataaaaagattgttatgcaaggcggagaaagtaacccggcttttacactagacaatttataaaaaaactactaaaataattatgggtgctaaaaaaatagttttttataagtgccctatatttttatataaagggagtgcgcat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0351:TDE0352|TDE0351:TDE0352:L-lactate dehydrogenase:ribose 5-phosphate isomerase B:<-->:396089..396346 258 aggattacctccttttaaaaaatactgaaatgcatacgtttaggcaaggggattgtacagaagaattcacgaaccttaacaatggcaagaagaacgaaataaggcaaaattatcataaaaagattgttatgcaaggcggagaaagtaacccggcttttacactagacaatttataaaaaaactactaaaataattatgggtgctaaaaaaatagttttttataagtgccctatatttttatataaagggagtgcgcat Intra-Species Hit: Count: 1 Min: 1 Max: 258 Len: 258 Subject: NC_002967_TDE0351_TDE0352|L-lactate dehydrogenase:ribose 5-phosphate isomerase B|NEGATIVE:POSITIVE|[396089,396346]|258 HSP 1 e-value: 1.0E-119 bit: 428.0 Len: 258 Query Start:1 Query End:258 Subject Strand: POSITIVE Subject Start: 1 Subject End: 258 aggattacctccttttaaaaaatactgaaatgcatacgtttaggcaaggggattgtacagaagaattcacgaaccttaacaatggcaagaagaacgaaataaggcaaaattatcataaaaagattgttatgcaaggcggagaaagtaacccggcttttacactagacaatttatnnnnnnnctactaaaataattatgggtgctnnnnnnntagttttttataagtgccctatatttttatataaagggagtgcgcat aggattacctccttttaaaaaatactgaaatgcatacgtttaggcaaggggattgtacagaagaattcacgaaccttaacaatggcaagaagaacgaaataaggcaaaattatcataaaaagattgttatgcaaggcggagaaagtaacccggcttttacactagacaatttataaaaaaactactaaaataattatgggtgctaaaaaaatagttttttataagtgccctatatttttatataaagggagtgcgcat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAUUACCUCCUUUUAAAAAAUACUGAAAUGCAUACGUUUAGGCAAGGGGAUUGUACAGAAGAAUUCACGAACCUUAACAAUGGCAAGAAGAACGAAAUAAGGCAAAAUUAUCAUAAAAAGAUUGUUAUGCAAGGCGGAGAAAGUAACCCGGCUUUUACACUAGACAAUUUAUAAAAAAACUACUAAAAUAAUUAUGGGUGCUAAAAAAAUAGUUUUUUAUAAGUGCCCUAUAUUUUUAUAUAAAGGGAGUGCGCAU ........((((((((((((((((......(((....(((.(((...(.(((((.(.....).))))).)...))).)))....)))...............((((...((((....(((((((((((....(((.(((..........))).)))......(((...((((((((.................)))))))).)))....))))))))))))))).))))...)))))))...)))))))))....... (-43.03) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGCGCACUCCCUUUAUAUAAAAAUAUAGGGCACUUAUAAAAAACUAUUUUUUUAGCACCCAUAAUUAUUUUAGUAGUUUUUUUAUAAAUUGUCUAGUGUAAAAGCCGGGUUACUUUCUCCGCCUUGCAUAACAAUCUUUUUAUGAUAAUUUUGCCUUAUUUCGUUCUUCUUGCCAUUGUUAAGGUUCGUGAAUUCUUCUGUACAAUCCCCUUGCCUAAACGUAUGCAUUUCAGUAUUUUUUAAAAGGAGGUAAUCCU .(((((...((((.(((......))).))))...(((((((((((((((.......................))))).))))))))))........)))))......((((((((((((.......(((.((..(((.......)))..)).)))................(((...((((.((((...........................)))).))))...))).................)))))))))))). (-42.73) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 899 90 41 181 132 NC_002967:TDE0351|5end_L-lactate_dehydrogenase_395998..396228_NEGATIVE 302 79 39 202 150 NC_002967:TDE2662|5end_lipoprotein,_putative_2698650..2698880_NEGATIVE 288 177 134 50 5 NC_002967:TDE1889|5end_branched-chain_amino_acid_transport_system_II_carrier_protein_1910888..1911118_NEGATIVE 278 141 114 217 191 NC_002967:TDE1925|5end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_1941980..1942210_POSITIVE 277 166 124 150 93 NC_002967:TDE0978|5end_hypothetical_protein_1001868..1002098_POSITIVE 273 167 123 102 48 NC_002967:TDE2000|5end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_2017859..2018089_POSITIVE 270 97 54 45 1 NC_002967:TDE1698|5end_serine/threonine_protein_phosphatase_family_protein_1757184..1757414_NEGATIVE 265 167 124 204 152 NC_002967:TDE2627|5end_transcriptional_regulator,_TetR_family_2669140..2669370_NEGATIVE 259 170 126 230 182 NC_002967:TDE0043|5end_TPR_domain_protein_49688..49918_POSITIVE 257 73 32 228 182 NC_002967:TDE1830|5end_hypothetical_protein_1863583..1863813_POSITIVE 254 76 43 178 127 NC_002967:TDE1576|5end_tRNA-i(6)A37_modification_enzyme_MiaB_1622778..1623008_POSITIVE 251 89 47 159 113 NC_002967:TDE2483|5end_hypothetical_protein_2506659..2506889_NEGATIVE 251 75 31 101 53 NC_002967:TDE2070|5end_hypothetical_protein_2097035..2097265_POSITIVE 250 171 131 153 111 NC_002967:TDE1505|5end_hypothetical_protein_1553614..1553844_POSITIVE 246 172 135 85 54 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 242 69 28 90 48 NC_002967:TDE0473|5end_heavy_metal_translocating_P-type_ATPase_528621..528851_POSITIVE 239 77 32 108 39 NC_002967:TDE0679|5end_aminotransferase,_class_V_716345..716575_POSITIVE 235 140 95 74 29 NC_002967:TDE2300|5end_trypsin_domain/PDZ_domain_protein_2341434..2341664_NEGATIVE 235 60 12 183 127 NC_002967:TDE2251|5end_uracil_permease_2289440..2289670_POSITIVE 233 159 118 184 135 NC_002967:TDE1352|5end_penicillin-binding_protein_1391700..1391930_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 170 131 116 74 NC_002967:TDE1245|3end_hypothetical_protein_1277905..1278055_NEGATIVE 251 75 31 75 27 NC_002967:TDE2069|3end_endoribonuclease_L-PSP,_putative_2097089..2097239_POSITIVE 250 171 131 92 50 NC_002967:TDE1504|3end_ribosomal_protein_L31_1553633..1553783_POSITIVE 249 154 122 123 86 NC_002967:TDE1997|3end_hypothetical_protein_2015256..2015406_POSITIVE 248 154 120 76 39 NC_002967:TDE2516|3end_hypothetical_protein_2542193..2542343_POSITIVE 242 159 120 134 93 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 242 69 28 63 21 NC_002967:TDE0472|3end_hypothetical_protein_528674..528824_POSITIVE 239 77 32 121 52 NC_002967:TDE0678|3end_hypothetical_protein_716438..716588_POSITIVE 235 60 12 72 16 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 235 106 61 47 4 NC_002967:TDE1699|3end_hypothetical_protein_1757186..1757336_NEGATIVE 232 155 123 43 16 NC_002967:TDE2483|3end_hypothetical_protein_2505880..2506030_NEGATIVE 231 239 197 100 46 NC_002967:TDE0482|3end_hypothetical_protein_538548..538698_NEGATIVE 229 160 134 34 4 NC_002967:TDE2319|3end_hypothetical_protein_2355835..2355985_NEGATIVE 229 89 41 55 13 NC_002967:TDE1709|3end_DNA-binding_protein,_HU_family_1764819..1764969_NEGATIVE 228 160 134 83 56 NC_002967:TDE0569|3end_hypothetical_protein_600162..600312_POSITIVE 228 154 115 35 4 NC_002967:TDE0191|3end_acetyltransferase,_GNAT_family_227378..227528_NEGATIVE 224 71 32 48 5 NC_002967:TDE0960|3end_neuB_family_protein_983595..983745_POSITIVE 224 76 32 77 19 NC_002967:TDE0621|3end_MATE_efflux_family_protein_654776..654926_POSITIVE 223 172 136 37 3 NC_002967:TDE2376|3end_hypothetical_protein_2406661..2406811_NEGATIVE 221 72 37 73 37 NC_002967:TDE2493|3end_hypothetical_protein_2516745..2516895_NEGATIVE