Origin IGS: attccctccgtctaccaattaaaataattatctccataattgaagatgatgtcaaatatttaggggctcattcggtgctagggaatttgtcactaatgatgtttgaagcgaaaaaatatgcttatcacattaaatgtgtttttacggcgttgtaggattttgaaccaccaccttcaaataaatctagattttagagtataaaacttgtttcatattcacatataaatcatactagccaacaaaaatttaatggcctcataaggataacccc .........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 ggggttatccttatgaggccattaaatttttgttggctagtatgatttatatgtgaatatgaaacaagttttatactctaaaatctagatttatttgaaggtggtggttcaaaatcctacaacgccgtaaaaacacatttaatgtgataagcatattttttcgcttcaaacatcattagtgacaaattccctagcaccgaatgagcccctaaatatttgacatcatcttcaattatggagataattattttaattggtagacggagggaat Mask Tandem Repeat Region ================================================ attccctccgtctaccaattaaaataattatctccataattgaagatgatgtcaaatatttaggggctcattcggtgctagggaatttgtcactaatgatgtttgaagcgaaaaaatatgcttatcacattaaatgtgtttttacggcgttgtaggattttgaaccaccaccttcaaataaatctagattttagagtataaaacttgtttcatattcacatataaatcatactagccaacaaaaatttaatggcctcataaggataacccc Find is-nt database================================================ Query_seq: AA00432:AA00434|AA00432:AA00434:conserved hypothetical protein; possible methyltransferase:VgrG-like protein (Rhs accessory genetic element):->->:294694..294964 271 attccctccgtctaccaattaaaataattatctccataattgaagatgatgtcaaatatttaggggctcattcggtgctagggaatttgtcactaatgatgtttgaagcgaaaaaatatgcttatcacattaaatgtgtttttacggcgttgtaggattttgaaccaccaccttcaaataaatctagattttagagtataaaacttgtttcatattcacatataaatcatactagccaacaaaaatttaatggcctcataaggataacccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00432:AA00434|AA00432:AA00434:conserved hypothetical protein; possible methyltransferase:VgrG-like protein (Rhs accessory genetic element):->->:294694..294964 271 attccctccgtctaccaattaaaataattatctccataattgaagatgatgtcaaatatttaggggctcattcggtgctagggaatttgtcactaatgatgtttgaagcgaaaaaatatgcttatcacattaaatgtgtttttacggcgttgtaggattttgaaccaccaccttcaaataaatctagattttagagtataaaacttgtttcatattcacatataaatcatactagccaacaaaaatttaatggcctcataaggataacccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00432:AA00434|AA00432:AA00434:conserved hypothetical protein; possible methyltransferase:VgrG-like protein (Rhs accessory genetic element):->->:294694..294964 271 attccctccgtctaccaattaaaataattatctccataattgaagatgatgtcaaatatttaggggctcattcggtgctagggaatttgtcactaatgatgtttgaagcgaaaaaatatgcttatcacattaaatgtgtttttacggcgttgtaggattttgaaccaccaccttcaaataaatctagattttagagtataaaacttgtttcatattcacatataaatcatactagccaacaaaaatttaatggcctcataaggataacccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attccctccgtctaccaattaaaataattatctccataattgaagatgatgtcaaatatttaggggctcattcggtgctagggaatttgtcactaatgatgtttgaagcgaaaaaatatgcttatcacattaaatgtgtttttacggcgttgtaggattttgaaccaccaccttcaaataaatctagattttagagtataaaacttgtttcatattcacatataaatcatactagccaacaaaaatttaatggcctcataaggataacccc Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 18 End: 152 ................. M K I I I S I I E D D V K Y L G A H S V L G N L S L M M F E A K K Y A Y H I K C V F T A L ....................................................................................................................... Protein_Len: 32 Strand: + Start: 103 End: 198 ...................................................................................................... M K R K N M L I T L N V F L R R C R I L N H H L Q I N L D F R V ......................................................................... attccctccgtctaccaattaaaataattatctccataattgaagatgatgtcaaatatttaggggctcattcggtgctagggaatttgtcactaatgatgtttgaagcgaaaaaatatgcttatcacattaaatgtgtttttacggcgttgtaggattttgaaccaccaccttcaaataaatctagattttagagtataaaacttgtttcatattcacatataaatcatactagccaacaaaaatttaatggcctcataaggataacccc 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: 89 Start: 27 End: 56 ..........................TTTGACATCATCTTCAATTATGGAGATAAT....................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attccctccgtctaccaattaaaataattatctccataattgaagatgatgtcaaatatttaggggctcattcggtgctagggaatttgtcactaatgatgtttgaagcgaaaaaatatgcttatcacattaaatgtgtttttacggcgttgtaggattttgaaccaccaccttcaaataaatctagattttagagtataaaacttgtttcatattcacatataaatcatactagccaacaaaaatttaatggcctcataaggataacccc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -6.3 Tail_Score: -4.60255 Start: 126 End: 138 Full_Region: AAAAAATATGCTTAT CACAT TAA ATGTG TTTTTACGGCGTTGT .............................................................................................................................CACATTAAATGTG..................................................................................................................................... Find igs database================================================ Query_seq: AA00432:AA00434|AA00432:AA00434:conserved hypothetical protein; possible methyltransferase:VgrG-like protein (Rhs accessory genetic element):->->:294694..294964 271 attccctccgtctaccaattaaaataattatctccataattgaagatgatgtcaaatatttaggggctcattcggtgctagggaatttgtcactaatgatgtttgaagcgaaaaaatatgcttatcacattaaatgtgtttttacggcgttgtaggattttgaaccaccaccttcaaataaatctagattttagagtataaaacttgtttcatattcacatataaatcatactagccaacaaaaatttaatggcctcataaggataacccc Intra-Species Hit: Count: 1 Min: 1 Max: 271 Len: 271 Subject: aact_AA00432_AA00434|conserved hypothetical protein; possible methyltransferase:VgrG-like protein (Rhs accessory genetic element)|POSITIVE:POSITIVE|[294694,294964]|271 HSP 1 e-value: 1.0E-152 bit: 537.0 Len: 271 Query Start:1 Query End:271 Subject Strand: POSITIVE Subject Start: 1 Subject End: 271 attccctccgtctaccaattaaaataattatctccataattgaagatgatgtcaaatatttaggggctcattcggtgctagggaatttgtcactaatgatgtttgaagcgaaaaaatatgcttatcacattaaatgtgtttttacggcgttgtaggattttgaaccaccaccttcaaataaatctagattttagagtataaaacttgtttcatattcacatataaatcatactagccaacaaaaatttaatggcctcataaggataacccc attccctccgtctaccaattaaaataattatctccataattgaagatgatgtcaaatatttaggggctcattcggtgctagggaatttgtcactaatgatgtttgaagcgaaaaaatatgcttatcacattaaatgtgtttttacggcgttgtaggattttgaaccaccaccttcaaataaatctagattttagagtataaaacttgtttcatattcacatataaatcatactagccaacaaaaatttaatggcctcataaggataacccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCCCUCCGUCUACCAAUUAAAAUAAUUAUCUCCAUAAUUGAAGAUGAUGUCAAAUAUUUAGGGGCUCAUUCGGUGCUAGGGAAUUUGUCACUAAUGAUGUUUGAAGCGAAAAAAUAUGCUUAUCACAUUAAAUGUGUUUUUACGGCGUUGUAGGAUUUUGAACCACCACCUUCAAAUAAAUCUAGAUUUUAGAGUAUAAAACUUGUUUCAUAUUCACAUAUAAAUCAUACUAGCCAACAAAAAUUUAAUGGCCUCAUAAGGAUAACCCC ((((((((((....((..........(((((((.((....)).))))))).............)).......)))....)))))))(((((.((.((((......(((((........)))))....((((((((.((((.....(((...(((.(((((((((........)))))................((((((.(((....))).)))))).......)))).)))..)))))))...))))))))...)))).))))))).... (-49.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGGUUAUCCUUAUGAGGCCAUUAAAUUUUUGUUGGCUAGUAUGAUUUAUAUGUGAAUAUGAAACAAGUUUUAUACUCUAAAAUCUAGAUUUAUUUGAAGGUGGUGGUUCAAAAUCCUACAACGCCGUAAAAACACAUUUAAUGUGAUAAGCAUAUUUUUUCGCUUCAAACAUCAUUAGUGACAAAUUCCCUAGCACCGAAUGAGCCCCUAAAUAUUUGACAUCAUCUUCAAUUAUGGAGAUAAUUAUUUUAAUUGGUAGACGGAGGGAAU .......(((((.....((((((((((.((((..((((.(((((((((((((....))))))).......))))))........((((....(((((..((((..((........)).....)))).......(((.....((((...((((..........))))...)))).....))).)))))...)))).........))))..)))).))))))....(((((((....)))))))............)))).....)))))... (-48.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 110 61 58 1 aact:AA00105|5end_conserved_hypothetical_protein_74477..74707_POSITIVE 308 110 62 69 17 aact:AA00301|5end_conserved_hypothetical_protein_(possible_deoxyribonuclease)_204341..204571_POSITIVE 300 111 73 32 1 aact:AA01615|5end_lipoprotein_releasing_system_transmembrane_1091186..1091416_POSITIVE 284 109 62 89 36 aact:AA02263|5end_conserved_hypothetical_protein_1539092..1539322_POSITIVE 280 110 65 181 140 aact:AA02132|5end_dihydroorotate_dehydrogenase_1455089..1455319_POSITIVE 280 110 63 214 165 aact:AA01556|5end_ABC_transporter_ATP-binding_protein_1044218..1044448_POSITIVE 279 269 229 212 161 aact:AA00493|5end_hypothetical_protein_344663..344893_POSITIVE 262 110 64 194 147 aact:AA00459|5end_hypothetical_protein_320851..321081_POSITIVE 259 90 45 181 129 aact:AA00982|5end_aldo-keto_reductase_686526..686756_POSITIVE 257 110 63 202 159 aact:AA00303|5end_thymidylate_kinase_(DTMP)_206107..206337_POSITIVE 256 170 127 74 24 aact:AA02881|5end_50S_ribosomal_protein_L27_2021089..2021319_POSITIVE 254 107 61 106 58 aact:AA02487|5end_hypothetical_protein_1726277..1726507_POSITIVE 254 167 126 55 19 aact:AA01854|5end_conserved_hypothetical_protein_1246662..1246892_POSITIVE 253 82 43 200 152 aact:AA00256|5end_rare_lipoprotein_A_precursor_178800..179030_POSITIVE 251 171 133 43 3 aact:AA00340|5end_NADP(H)_oxidoreductase_(NAD(P)H_dehydrogenase_(quinone))_228797..229027_POSITIVE 250 171 131 210 171 aact:AA01522|5end_conserved_hypothetical_protein_1022840..1023070_POSITIVE 250 114 74 76 34 aact:AA00041|5end_cytochrome_c-type_biogenesis_protein_31881..32111_POSITIVE 249 110 65 216 171 aact:AA01780|5end_ABC-related_molybdenum_transport_system_permease_protein_1201084..1201314_POSITIVE 249 87 45 220 175 aact:AA00266|5end_conserved_hypothetical_protein_(probable_metabolite_transport_protein)_186634..186864_POSITIVE 248 98 59 94 51 aact:AA02135|5end_hypothetical_protein_1458886..1459116_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 308 110 62 82 30 aact:AA00299|3end_hypothetical_protein_204434..204584_POSITIVE 288 110 63 103 63 aact:AA02350|3end_possible_lipoprotein_1609179..1609329_POSITIVE 284 110 67 88 45 aact:AA01331|3end_50S_ribosomal_protein_L31_898721..898871_POSITIVE 273 168 121 145 101 aact:AA02504|3end_lipid_A_biosynthesis_(kdo)2-(lauroyl)-lipid_IVA_acyltransferase_1739248..1739398_POSITIVE 270 109 62 137 95 aact:AA01467|3end_mannose-specific_phosphotransferase_system_IID_987214..987364_POSITIVE 262 110 64 147 100 aact:AA00458|3end_nickel-binding_periplasmic_protein_320884..321034_POSITIVE 254 107 61 61 13 aact:AA02486|3end_topoisomerase_IV,_subunit_B_1726312..1726462_POSITIVE 254 98 65 150 123 aact:AA02131|3end_conserved_hypothetical_protein_(possible_TrpH_protein)_1455152..1455302_POSITIVE 253 82 43 94 46 aact:AA00254|3end_penicillin-binding_protein_5_178774..178924_POSITIVE 250 114 74 80 38 aact:AA00040|3end_thiol:disulfide_interchange_protein_31965..32115_POSITIVE 249 87 45 89 44 aact:AA00265|3end_transcription_termination_factor_186583..186733_POSITIVE 247 84 41 31 1 aact:AA00519|3end_O-acetyltransferase_357821..357971_POSITIVE 244 109 65 111 52 aact:AA01767|3end_conserved_hypothetical_protein_1192961..1193111_POSITIVE 241 115 72 149 104 aact:AA02897|3end_oligopeptide_ABC_transporter;_permease_protein_2029150..2029300_POSITIVE 240 170 128 50 1 aact:AA02880|3end_50S_ribosomal_protein_L21_2021145..2021295_POSITIVE 240 106 62 102 65 aact:AA00371|3end_transcriptional_regulator_250154..250304_POSITIVE 238 174 136 73 26 aact:AA02595|3end_cytochrome_c_peroxidase_1807110..1807260_POSITIVE 237 179 135 106 49 aact:AA01657|3end_maltose_high-affinity_receptor_1124095..1124245_POSITIVE 235 110 66 82 31 aact:AA01780|3end_ABC-related_molybdenum_transport_system_permease_protein_1201934..1202084_POSITIVE 233 149 106 121 74 aact:AA00674|3end_nicotinate-nucleotide-dimethylbenzimidazole_phosphoribosyltransferase_462585..462735_POSITIVE