Origin IGS: taaaaagaaaaaatcccagactcacgtctcggattcctcgcataaaccatttatataccactaaaaagactttattatgaaatattatgtctgtggatgcaaagataagcacgagacaggtggttctacaagttttcaggccgcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagcggcctgaaaacttgtagaaccacctgtctcgtgcttatctttgcatccacagacataatatttcataataaagtctttttagtggtatataaatggtttatgcgaggaatccgagacgtgagtctgggattttttcttttta Mask Tandem Repeat Region ================================================ taaaaagaaaaaatcccagactcacgtctcggattcctcgcataaaccatttatataccactaaaaagactttattatgaaatattatgtctgtggatgcaaagataagcacgagacaggtggttctacaagttttcaggccgcta Find is-nt database================================================ Query_seq: TF0046:TF0047|TF0046:TF0047:thiamin biosynthesis lipoprotein, ApbE:hypothetical protein:->->:53838..53983 146 taaaaagaaaaaatcccagactcacgtctcggattcctcgcataaaccatttatataccactaaaaagactttattatgaaatattatgtctgtggatgcaaagataagcacgagacaggtggttctacaagttttcaggccgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0046:TF0047|TF0046:TF0047:thiamin biosynthesis lipoprotein, ApbE:hypothetical protein:->->:53838..53983 146 taaaaagaaaaaatcccagactcacgtctcggattcctcgcataaaccatttatataccactaaaaagactttattatgaaatattatgtctgtggatgcaaagataagcacgagacaggtggttctacaagttttcaggccgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0046:TF0047|TF0046:TF0047:thiamin biosynthesis lipoprotein, ApbE:hypothetical protein:->->:53838..53983 146 taaaaagaaaaaatcccagactcacgtctcggattcctcgcataaaccatttatataccactaaaaagactttattatgaaatattatgtctgtggatgcaaagataagcacgagacaggtggttctacaagttttcaggccgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaagaaaaaatcccagactcacgtctcggattcctcgcataaaccatttatataccactaaaaagactttattatgaaatattatgtctgtggatgcaaagataagcacgagacaggtggttctacaagttttcaggccgcta Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: - Start: 2 End: 139 . F L F F G L S V D R I G R M F W K Y V V L F V K N H F I I D T S A F I L V L C T T R C T K M ....... taaaaagaaaaaatcccagactcacgtctcggattcctcgcataaaccatttatataccactaaaaagactttattatgaaatattatgtctgtggatgcaaagataagcacgagacaggtggttctacaagttttcaggccgcta 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: 81 Start: 49 End: 78 ................................................ATTTATATACCACTAAAAAGACTTTATTAT.................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaaagaaaaaatcccagactcacgtctcggattcctcgcataaaccatttatataccactaaaaagactttattatgaaatattatgtctgtggatgcaaagataagcacgagacaggtggttctacaagttttcaggccgcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0046:TF0047|TF0046:TF0047:thiamin biosynthesis lipoprotein, ApbE:hypothetical protein:->->:53838..53983 146 taaaaagaaaaaatcccagactcacgtctcggattcctcgcataaaccatttatataccactaaaaagactttattatgaaatattatgtctgtggatgcaaagataagcacgagacaggtggttctacaagttttcaggccgcta Intra-Species Hit: Count: 1 Min: 14 Max: 146 Len: 133 Subject: tfor_TF0046_TF0047|thiamin biosynthesis lipoprotein, ApbE:hypothetical protein|POSITIVE:POSITIVE|[53838,53983]|146 HSP 1 e-value: 7.0E-70 bit: 264.0 Len: 133 Query Start:14 Query End:146 Subject Strand: POSITIVE Subject Start: 14 Subject End: 146 .............tcccagactcacgtctcggattcctcgcataaaccatttatataccactaaaaagactttattatgaaatattatgtctgtggatgcaaagataagcacgagacaggtggttctacaagttttcaggccgcta .............tcccagactcacgtctcggattcctcgcataaaccatttatataccactaaaaagactttattatgaaatattatgtctgtggatgcaaagataagcacgagacaggtggttctacaagttttcaggccgcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCCAGACUCACGUCUCGGAUUCCUCGCAUAAACCAUUUAUAUACCACUAAAAAGACUUUAUUAUGAAAUAUUAUGUCUGUGGAUGCAAAGAUAAGCACGAGACAGGUGGUUCUACAAGUUUUCAGGCCGCUA (((.((((....)))).)))...((((.................((((.....((((..((((....))))....))))))))..((........)).))))...(((((((.............))))))). (-25.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCGGCCUGAAAACUUGUAGAACCACCUGUCUCGUGCUUAUCUUUGCAUCCACAGACAUAAUAUUUCAUAAUAAAGUCUUUUUAGUGGUAUAUAAAUGGUUUAUGCGAGGAAUCCGAGACGUGAGUCUGGGA ..............((((((((((((..(((((.((((........))))....)))))..((((.((((..(((((...))))))))).))))...)))))).))))))...(((.((((....)))).))) (-33.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 130 81 186 133 tfor:TF2219|5end_two-component_system_sensor_histidine_2390844..2391074_POSITIVE 292 105 66 40 3 tfor:TF1253|5end_hypothetical_protein_1335982..1336212_POSITIVE 290 47 2 227 175 tfor:TF1850|5end_Na+/H+-exchanging_protein_1998542..1998772_POSITIVE 289 130 81 214 159 tfor:TF0824|5end_glucosamine-6-phosphate_isomerase_881600..881830_POSITIVE 284 130 99 220 193 tfor:TF2226|5end_CTn_excision_protein_2395529..2395759_POSITIVE 281 130 84 143 81 tfor:TF1304|5end_conserved_hypothetical_protein_1385008..1385238_POSITIVE 277 130 97 57 14 tfor:TF3087|5end_conserved_hypothetical_protein_3319878..3320108_POSITIVE 272 128 82 192 134 tfor:TF2999|5end_conserved_hypothetical_protein_3215566..3215796_POSITIVE 270 130 85 104 54 tfor:TF1636|5end_hypothetical_protein_1747143..1747373_POSITIVE 270 130 85 67 17 tfor:TF1637|5end_hypothetical_protein_1747106..1747336_POSITIVE 268 130 81 209 149 tfor:TF1228|5end_conserved_hypothetical_protein_1314103..1314333_POSITIVE 266 130 91 45 10 tfor:TF2548|5end_30S_ribosomal_protein_S12_2731238..2731468_POSITIVE 258 105 65 201 155 tfor:TF2943|5end_50S_ribosomal_protein_L7/L12_3143116..3143346_POSITIVE 258 130 90 223 178 tfor:TF1929|5end_conserved_hypothetical_protein_2076049..2076279_POSITIVE 258 129 86 59 12 tfor:TF1000|5end_sec-independent_protein_translocase_1053241..1053471_POSITIVE 256 46 2 76 35 tfor:TF2853|5end_2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_3040172..3040402_POSITIVE 254 130 81 212 157 tfor:TF1824|5end_ABC_transporter,_ATP-binding_protein_1972537..1972767_POSITIVE 254 127 81 229 184 tfor:TF1258|5end_hypothetical_protein_1338321..1338551_POSITIVE 253 38 1 100 54 tfor:TF1842|5end_hypothetical_protein_1992571..1992801_POSITIVE 251 120 75 70 22 tfor:TF2973|5end_transposase_3179214..3179444_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 105 66 62 25 tfor:TF1252|3end_phosphofructokinase;_pyrophosphate-fructose_6-phosphate_1-phosphotransferase_(probable_beta_subunit)_1336084..1336234_POSITIVE 285 127 81 143 92 tfor:TF0434|3end_CTP_synthetase_(UTP_ammonia_ligase)_457027..457177_POSITIVE 280 128 82 55 9 tfor:TF0985|3end_fructose-bisphosphate_aldolase_1042973..1043123_POSITIVE 277 130 97 48 5 tfor:TF3086|3end_conserved_hypothetical_protein_3319949..3320099_POSITIVE 273 119 72 82 35 tfor:TF1247|3end_alanyl-tRNA_synthetase_(alanine--tRNA_ligase)_1330928..1331078_POSITIVE 260 130 82 59 1 tfor:TF2134|3end_conserved_hypothetical_protein_2310187..2310337_POSITIVE 257 130 81 56 12 tfor:TF2515|3end_outer_membrane_protein,_TonB_dependent_receptor_2694865..2695015_POSITIVE 257 111 75 92 60 tfor:TF1374|3end_possible_transposase_1450791..1450941_POSITIVE 256 46 2 45 4 tfor:TF2852|3end_conserved_hypothetical_protein_3040221..3040371_POSITIVE 254 127 81 143 98 tfor:TF1256|3end_hypothetical_protein_1338315..1338465_POSITIVE 251 120 75 130 82 tfor:TF2971|3end_possible_transposase_3179354..3179504_POSITIVE 251 120 75 130 82 tfor:TF1770|3end_hypothetical_protein_1908812..1908962_POSITIVE 251 129 82 83 23 tfor:TF1167|3end_hypothetical_protein_1248932..1249082_POSITIVE 248 130 89 40 5 tfor:TF1874|3end_conserved_hypothetical_protein_2028838..2028988_POSITIVE 248 112 75 65 29 tfor:TF0655|3end_outer_membrane_protein_701907..702057_POSITIVE 248 115 79 57 12 tfor:TF0484|3end_conserved_hypothetical_protein;_possible_O-glycosyl_hydrolase_507386..507536_POSITIVE 245 130 95 43 8 tfor:TF1494|3end_cobinamide_kinase/cobinamide_phosphate_guanylyltransferase_1594602..1594752_POSITIVE 244 120 74 120 56 tfor:TF2409|3end_hypothetical_protein_2584155..2584305_POSITIVE 242 129 81 147 92 tfor:TF3142|3end_conserved_hypothetical_protein_3377510..3377660_POSITIVE 242 129 81 80 13 tfor:TF2943|3end_50S_ribosomal_protein_L7/L12_3143567..3143717_POSITIVE