Origin IGS: ttgtttcttcctatgtttaagttttcgctcattgcgataagttaagtagtgtatgtacttaccgaaaatttacaacgtttttggcaagaggtcaaacctcaaaaaacattgaattttcacaaagacatacagtgaaaaaaaatagttacgtctttcacgaacccttgaacgacctaaccaagttacattgcggaggcgattttaacactaagccgaacgtttggctattgcttttatcctatttaccgcacgtaacctttcgccaaataccgccta .........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 taggcggtatttggcgaaaggttacgtgcggtaaataggataaaagcaatagccaaacgttcggcttagtgttaaaatcgcctccgcaatgtaacttggttaggtcgttcaagggttcgtgaaagacgtaactattttttttcactgtatgtctttgtgaaaattcaatgttttttgaggtttgacctcttgccaaaaacgttgtaaattttcggtaagtacatacactacttaacttatcgcaatgagcgaaaacttaaacataggaagaaacaa Mask Tandem Repeat Region ================================================ ttgtttcttcctatgtttaagttttcgctcattgcgataagttaagtagtgtatgtacttaccgaaaatttacaacgtttttggcaagaggtcaaacctcaaaaaacattgaattttcacaaagacatacagtgaaaaaaaatagttacgtctttcacgaacccttgaacgacctaaccaagttacattgcggaggcgattttaacactaagccgaacgtttggctattgcttttatcctatttaccgcacgtaacctttcgccaaataccgccta Find is-nt database================================================ Query_seq: AA00268:AA00269|AA00268:AA00269:acyl carrier protein (ACP):3-oxoacyl-(acyl-carrier-protein) reductase/short-chain alcohol dehydrogenase:->->:188472..188747 276 ttgtttcttcctatgtttaagttttcgctcattgcgataagttaagtagtgtatgtacttaccgaaaatttacaacgtttttggcaagaggtcaaacctcaaaaaacattgaattttcacaaagacatacagtgaaaaaaaatagttacgtctttcacgaacccttgaacgacctaaccaagttacattgcggaggcgattttaacactaagccgaacgtttggctattgcttttatcctatttaccgcacgtaacctttcgccaaataccgccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00268:AA00269|AA00268:AA00269:acyl carrier protein (ACP):3-oxoacyl-(acyl-carrier-protein) reductase/short-chain alcohol dehydrogenase:->->:188472..188747 276 ttgtttcttcctatgtttaagttttcgctcattgcgataagttaagtagtgtatgtacttaccgaaaatttacaacgtttttggcaagaggtcaaacctcaaaaaacattgaattttcacaaagacatacagtgaaaaaaaatagttacgtctttcacgaacccttgaacgacctaaccaagttacattgcggaggcgattttaacactaagccgaacgtttggctattgcttttatcctatttaccgcacgtaacctttcgccaaataccgccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00268:AA00269|AA00268:AA00269:acyl carrier protein (ACP):3-oxoacyl-(acyl-carrier-protein) reductase/short-chain alcohol dehydrogenase:->->:188472..188747 276 ttgtttcttcctatgtttaagttttcgctcattgcgataagttaagtagtgtatgtacttaccgaaaatttacaacgtttttggcaagaggtcaaacctcaaaaaacattgaattttcacaaagacatacagtgaaaaaaaatagttacgtctttcacgaacccttgaacgacctaaccaagttacattgcggaggcgattttaacactaagccgaacgtttggctattgcttttatcctatttaccgcacgtaacctttcgccaaataccgccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgtttcttcctatgtttaagttttcgctcattgcgataagttaagtagtgtatgtacttaccgaaaatttacaacgtttttggcaagaggtcaaacctcaaaaaacattgaattttcacaaagacatacagtgaaaaaaaatagttacgtctttcacgaacccttgaacgacctaaccaagttacattgcggaggcgattttaacactaagccgaacgtttggctattgcttttatcctatttaccgcacgtaacctttcgccaaataccgccta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 81 End: 275 ................................................................................ M A R G Q T S K N I E F S Q R H T V K K N S Y V F H E P L N D L T K L H C G G D F N T K P N V W L L L L S Y L P H V T F . ttgtttcttcctatgtttaagttttcgctcattgcgataagttaagtagtgtatgtacttaccgaaaatttacaacgtttttggcaagaggtcaaacctcaaaaaacattgaattttcacaaagacatacagtgaaaaaaaatagttacgtctttcacgaacccttgaacgacctaaccaagttacattgcggaggcgattttaacactaagccgaacgtttggctattgcttttatcctatttaccgcacgtaacctttcgccaaataccgccta 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: 199 End: 228 ......................................................................................................................................................................................................ATAGCCAAACGTTCGGCTTAGTGTTAAAAT................................................ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 67 End: 96 ..................................................................TTTGACCTCTTGCCAAAAACGTTGTAAATT.................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgtttcttcctatgtttaagttttcgctcattgcgataagttaagtagtgtatgtacttaccgaaaatttacaacgtttttggcaagaggtcaaacctcaaaaaacattgaattttcacaaagacatacagtgaaaaaaaatagttacgtctttcacgaacccttgaacgacctaaccaagttacattgcggaggcgattttaacactaagccgaacgtttggctattgcttttatcctatttaccgcacgtaacctttcgccaaataccgccta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 91 HP_score: -4.9 Tail_Score: -5.83822 Start: 143 End: 180 Full_Region: ctccgcaatgtaact tggttaggtcgttcaag ggtt cgtgaaagacgtaacta ttttttttcactgta ..............................................................................................................................................tggttaggtcgttcaagggttcgtgaaagacgtaacta................................................................................................ TransTerm Strand: - Conf: 73 HP_score: -5.3 Tail_Score: -4.5536 Start: 145 End: 178 Full_Region: ccgcaatgtaacttg gttaggtcgttcaag ggtt cgtgaaagacgtaac tattttttttcactg ................................................................................................................................................gttaggtcgttcaagggttcgtgaaagacgtaac.................................................................................................. Find igs database================================================ Query_seq: AA00268:AA00269|AA00268:AA00269:acyl carrier protein (ACP):3-oxoacyl-(acyl-carrier-protein) reductase/short-chain alcohol dehydrogenase:->->:188472..188747 276 ttgtttcttcctatgtttaagttttcgctcattgcgataagttaagtagtgtatgtacttaccgaaaatttacaacgtttttggcaagaggtcaaacctcaaaaaacattgaattttcacaaagacatacagtgaaaaaaaatagttacgtctttcacgaacccttgaacgacctaaccaagttacattgcggaggcgattttaacactaagccgaacgtttggctattgcttttatcctatttaccgcacgtaacctttcgccaaataccgccta Intra-Species Hit: Count: 1 Min: 1 Max: 276 Len: 276 Subject: aact_AA00268_AA00269|acyl carrier protein (ACP):3-oxoacyl-(acyl-carrier-protein) reductase/short-chain alcohol dehydrogenase|POSITIVE:POSITIVE|[188472,188747]|276 HSP 1 e-value: 1.0E-140 bit: 500.0 Len: 276 Query Start:1 Query End:276 Subject Strand: POSITIVE Subject Start: 1 Subject End: 276 ttgtttcttcctatgtttaagttttcgctcattgcgataagttaagtagtgtatgtacttaccgaaaatttacaacgtttttggcaagaggtcaaacctcaaaaaacattgaattttcacaaagacatacagtgnnnnnnnntagttacgtctttcacgaacccttgaacgacctaaccaagttacattgcggaggcgattttaacactaagccgaacgtttggctattgcttttatcctatttaccgcacgtaacctttcgccaaataccgccta ttgtttcttcctatgtttaagttttcgctcattgcgataagttaagtagtgtatgtacttaccgaaaatttacaacgtttttggcaagaggtcaaacctcaaaaaacattgaattttcacaaagacatacagtgaaaaaaaatagttacgtctttcacgaacccttgaacgacctaaccaagttacattgcggaggcgattttaacactaagccgaacgtttggctattgcttttatcctatttaccgcacgtaacctttcgccaaataccgccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUUUCUUCCUAUGUUUAAGUUUUCGCUCAUUGCGAUAAGUUAAGUAGUGUAUGUACUUACCGAAAAUUUACAACGUUUUUGGCAAGAGGUCAAACCUCAAAAAACAUUGAAUUUUCACAAAGACAUACAGUGAAAAAAAAUAGUUACGUCUUUCACGAACCCUUGAACGACCUAACCAAGUUACAUUGCGGAGGCGAUUUUAACACUAAGCCGAACGUUUGGCUAUUGCUUUUAUCCUAUUUACCGCACGUAACCUUUCGCCAAAUACCGCCUA ..........((((..((((.((.((((.....)))).)).)))))))).((((((.(((...(((((((((....((((((.....((((.....)))).))))))..)))))))))...))))))))).((((((.......((((.(((.((((.(....).)))).))).))))...(((((..((((((((((((..........((((((....)))))))))))))............))))).))))).))))))............. (-63.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGCGGUAUUUGGCGAAAGGUUACGUGCGGUAAAUAGGAUAAAAGCAAUAGCCAAACGUUCGGCUUAGUGUUAAAAUCGCCUCCGCAAUGUAACUUGGUUAGGUCGUUCAAGGGUUCGUGAAAGACGUAACUAUUUUUUUUCACUGUAUGUCUUUGUGAAAAUUCAAUGUUUUUUGAGGUUUGACCUCUUGCCAAAAACGUUGUAAAUUUUCGGUAAGUACAUACACUACUUAACUUAUCGCAAUGAGCGAAAACUUAAACAUAGGAAGAAACAA ...((.(....).))....((((((((((((.....(((.....((((..((((........))))...)))).......))))))).))))))))((((((.(((.((((........)))).))).)))))).((((((((..((((((((((..((((((((((((((((((.((((.....)))).....))))))))))..))))))))..))).)))))))....((((.((.((((.....)))).)).)))).....))))))))... (-75.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 370 230 181 115 74 aact:AA02996|5end_probable_cation_transport_protein_2093369..2093599_POSITIVE 321 199 154 68 3 aact:AA02466|5end_N-acetylneuraminate_lyase_1704963..1705193_POSITIVE 313 224 191 186 154 aact:AA00822|5end_conserved_hypothetical_protein_(possible_arsenate_reductase)_564596..564826_POSITIVE 312 255 212 202 151 aact:AA01434|5end_conserved_hypothetical_protein_(possible_o-antigen_ligase)_961631..961861_POSITIVE 308 226 186 41 7 aact:AA02881|5end_50S_ribosomal_protein_L27_2021089..2021319_POSITIVE 301 230 190 89 39 aact:AA01708|5end_glutaredoxin_1158136..1158366_POSITIVE 297 230 187 124 76 aact:AA02153|5end_iron(III)_ABC_transporter,_permease_protein_1472530..1472760_POSITIVE 296 197 152 219 175 aact:AA01232|5end_30S_ribosomal_protein_S8_840445..840675_POSITIVE 295 220 176 44 4 aact:AA00962|5end_exopolyphosphatase_(metaphosphatase)_671060..671290_POSITIVE 292 230 182 226 186 aact:AA02511|5end_transmembrane_protein_1742047..1742277_POSITIVE 290 228 190 183 149 aact:AA02199|5end_hypothetical_protein_1497627..1497857_POSITIVE 288 230 186 164 120 aact:AA01839|5end_conserved_hypothetical_protein_(possible_transcriptional_regulator)_1236870..1237100_POSITIVE 287 230 188 62 23 aact:AA02777|5end_tRNA-guanine_transglycosylase_1941299..1941529_POSITIVE 282 185 145 181 143 aact:AA02047|5end_galactitol-1-phosphate_5-dehydrogenase_1393633..1393863_POSITIVE 281 234 193 202 150 aact:AA01181|5end_conserved_hypothetical_protein_808774..809004_POSITIVE 280 257 214 125 73 aact:AA01628|5end_thiamin-monophosphate_kinase_1100888..1101118_POSITIVE 277 219 178 50 12 aact:AA01301|5end_competence_protein_B_881467..881697_POSITIVE 275 248 201 59 4 aact:AA01790|5end_riboflavin_bifunctional_biosynthesis_protein_1206934..1207164_POSITIVE 275 225 186 71 28 aact:AA00390|5end_permease_263689..263919_POSITIVE 275 199 163 130 100 aact:AA00167|5end_possible_amino-acid_transporter_(sodium-alanine_symporters)_118239..118469_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 224 191 46 14 aact:AA00820|3end_succinyl-diaminopimelate_desuccinylase_564536..564686_POSITIVE 304 199 153 74 22 aact:AA02480|3end_excinuclease_ABC_subunit_B_1718442..1718592_POSITIVE 297 230 187 124 76 aact:AA02152|3end_ferric_enterobactin_transport;_ABC_transporter_ATP-binding_protein_1472610..1472760_POSITIVE 290 225 181 43 4 aact:AA00961|3end_conserved_hypothetical_protein_671134..671284_POSITIVE 289 225 185 147 108 aact:AA00221|3end_NADP-specific_glutamate_dehydrogenase_153865..154015_POSITIVE 281 234 193 149 97 aact:AA01179|3end_beta-ketoacyl-ACP_reductase;_short-chain_alcohol_dehydrogenase_808801..808951_POSITIVE 280 257 214 103 51 aact:AA01626|3end_N_utilization_substance_protein_B_1100946..1101096_POSITIVE 274 198 151 130 93 aact:AA01145|3end_glycyl-tRNA_synthetase_alpha_subunit_784460..784610_POSITIVE 273 230 181 73 19 aact:AA00549|3end_ferredoxin-type_protein_376521..376671_POSITIVE 272 240 196 112 61 aact:AA01401|3end_3-deoxy-D-manno-octulosonic-acid_transferase_947525..947675_POSITIVE 269 225 182 145 110 aact:AA02205|3end_short_chain_dehydrogenase/reductase_1501984..1502134_POSITIVE 269 198 156 48 6 aact:AA01301|3end_competence_protein_B_882095..882245_POSITIVE 266 226 186 44 10 aact:AA00973|3end_transcriptional_regulator,_DeoR_family_679237..679387_POSITIVE 265 253 211 126 82 aact:AA01649|3end_maltose_ABC_transporter,_permease_protein_1118283..1118433_POSITIVE 265 228 187 82 38 aact:AA00980|3end_hypothetical_protein_685409..685559_POSITIVE 265 219 175 143 99 aact:AA00015|3end_malate_dehydrogenase_8333..8483_POSITIVE 264 65 26 69 30 aact:AA02324|3end_ABC_transporter_ATP_binding_protein_1587392..1587542_POSITIVE 263 198 156 130 94 aact:AA01475|3end_conserved_hypothetical_protein_(possible_cytoplasmic_protein;_DNA_binding_protein)_991430..991580_POSITIVE 262 225 188 78 44 aact:AA00989|3end_hypothetical_protein_692644..692794_POSITIVE 260 239 191 149 89 aact:AA01565|3end_conserved_hypothetical_protein_1050967..1051117_POSITIVE