Origin IGS: gagaattcctcctttaatctaggtgctagttttgattctagcaactgtgttttgatactgttagtctatcacttttatctcctttttcaccataaaatctttaattgcccttgaaatttcctgaatgatactgttaagattttatgataaaatagttgtaagattatcatgcttatttgaggaacaagatacccttcaggagcgttaaaggcctgtttaggatttggtgggcttgtatcaaagtatttttgctattctctttttaggaagaaatcgaaacaaggagagtaagaag .........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 cttcttactctccttgtttcgatttcttcctaaaaagagaatagcaaaaatactttgatacaagcccaccaaatcctaaacaggcctttaacgctcctgaagggtatcttgttcctcaaataagcatgataatcttacaactattttatcataaaatcttaacagtatcattcaggaaatttcaagggcaattaaagattttatggtgaaaaaggagataaaagtgatagactaacagtatcaaaacacagttgctagaatcaaaactagcacctagattaaaggaggaattctc Mask Tandem Repeat Region ================================================ gagaattcctcctttaatctaggtgctagttttgattctagcaactgtgttttgatactgttagtctatcacttttatctcctttttcaccataaaatctttaattgcccttgaaatttcctgaatgatactgttaagattttatgataaaatagttgtaagattatcatgcttatttgaggaacaagatacccttcaggagcgttaaaggcctgtttaggatttggtgggcttgtatcaaagtatttttgctattctctttttaggaagaaatcgaaacaaggagagtaagaag Find is-nt database================================================ Query_seq: SMT_347:SMT_348|SMT_347:SMT_348:hypothetical protein:K07707 two-component system, AgrA family, response regulator AgrA:<-->:286301..286595 295 gagaattcctcctttaatctaggtgctagttttgattctagcaactgtgttttgatactgttagtctatcacttttatctcctttttcaccataaaatctttaattgcccttgaaatttcctgaatgatactgttaagattttatgataaaatagttgtaagattatcatgcttatttgaggaacaagatacccttcaggagcgttaaaggcctgtttaggatttggtgggcttgtatcaaagtatttttgctattctctttttaggaagaaatcgaaacaaggagagtaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_347:SMT_348|SMT_347:SMT_348:hypothetical protein:K07707 two-component system, AgrA family, response regulator AgrA:<-->:286301..286595 295 gagaattcctcctttaatctaggtgctagttttgattctagcaactgtgttttgatactgttagtctatcacttttatctcctttttcaccataaaatctttaattgcccttgaaatttcctgaatgatactgttaagattttatgataaaatagttgtaagattatcatgcttatttgaggaacaagatacccttcaggagcgttaaaggcctgtttaggatttggtgggcttgtatcaaagtatttttgctattctctttttaggaagaaatcgaaacaaggagagtaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_347:SMT_348|SMT_347:SMT_348:hypothetical protein:K07707 two-component system, AgrA family, response regulator AgrA:<-->:286301..286595 295 gagaattcctcctttaatctaggtgctagttttgattctagcaactgtgttttgatactgttagtctatcacttttatctcctttttcaccataaaatctttaattgcccttgaaatttcctgaatgatactgttaagattttatgataaaatagttgtaagattatcatgcttatttgaggaacaagatacccttcaggagcgttaaaggcctgtttaggatttggtgggcttgtatcaaagtatttttgctattctctttttaggaagaaatcgaaacaaggagagtaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gagaattcctcctttaatctaggtgctagttttgattctagcaactgtgttttgatactgttagtctatcacttttatctcctttttcaccataaaatctttaattgcccttgaaatttcctgaatgatactgttaagattttatgataaaatagttgtaagattatcatgcttatttgaggaacaagatacccttcaggagcgttaaaggcctgtttaggatttggtgggcttgtatcaaagtatttttgctattctctttttaggaagaaatcgaaacaaggagagtaagaag Predict ORF larger than 30AA ================================================ gagaattcctcctttaatctaggtgctagttttgattctagcaactgtgttttgatactgttagtctatcacttttatctcctttttcaccataaaatctttaattgcccttgaaatttcctgaatgatactgttaagattttatgataaaatagttgtaagattatcatgcttatttgaggaacaagatacccttcaggagcgttaaaggcctgtttaggatttggtgggcttgtatcaaagtatttttgctattctctttttaggaagaaatcgaaacaaggagagtaagaag 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: 124 End: 153 ...........................................................................................................................AATGATACTGTTAAGATTTTATGATAAAAT.............................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gagaattcctcctttaatctaggtgctagttttgattctagcaactgtgttttgatactgttagtctatcacttttatctcctttttcaccataaaatctttaattgcccttgaaatttcctgaatgatactgttaagattttatgataaaatagttgtaagattatcatgcttatttgaggaacaagatacccttcaggagcgttaaaggcctgtttaggatttggtgggcttgtatcaaagtatttttgctattctctttttaggaagaaatcgaaacaaggagagtaagaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_347:SMT_348|SMT_347:SMT_348:hypothetical protein:K07707 two-component system, AgrA family, response regulator AgrA:<-->:286301..286595 295 gagaattcctcctttaatctaggtgctagttttgattctagcaactgtgttttgatactgttagtctatcacttttatctcctttttcaccataaaatctttaattgcccttgaaatttcctgaatgatactgttaagattttatgataaaatagttgtaagattatcatgcttatttgaggaacaagatacccttcaggagcgttaaaggcctgtttaggatttggtgggcttgtatcaaagtatttttgctattctctttttaggaagaaatcgaaacaaggagagtaagaag Intra-Species Hit: Count: 1 Min: 1 Max: 295 Len: 295 Subject: smit_SMT_347_SMT_348|hypothetical protein:K07707 two-component system, AgrA family, response regulator AgrA|NEGATIVE:POSITIVE|[286301,286595]|295 HSP 1 e-value: 1.0E-166 bit: 585.0 Len: 295 Query Start:1 Query End:295 Subject Strand: POSITIVE Subject Start: 1 Subject End: 295 gagaattcctcctttaatctaggtgctagttttgattctagcaactgtgttttgatactgttagtctatcacttttatctcctttttcaccataaaatctttaattgcccttgaaatttcctgaatgatactgttaagattttatgataaaatagttgtaagattatcatgcttatttgaggaacaagatacccttcaggagcgttaaaggcctgtttaggatttggtgggcttgtatcaaagtatttttgctattctctttttaggaagaaatcgaaacaaggagagtaagaag gagaattcctcctttaatctaggtgctagttttgattctagcaactgtgttttgatactgttagtctatcacttttatctcctttttcaccataaaatctttaattgcccttgaaatttcctgaatgatactgttaagattttatgataaaatagttgtaagattatcatgcttatttgaggaacaagatacccttcaggagcgttaaaggcctgtttaggatttggtgggcttgtatcaaagtatttttgctattctctttttaggaagaaatcgaaacaaggagagtaagaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGAAUUCCUCCUUUAAUCUAGGUGCUAGUUUUGAUUCUAGCAACUGUGUUUUGAUACUGUUAGUCUAUCACUUUUAUCUCCUUUUUCACCAUAAAAUCUUUAAUUGCCCUUGAAAUUUCCUGAAUGAUACUGUUAAGAUUUUAUGAUAAAAUAGUUGUAAGAUUAUCAUGCUUAUUUGAGGAACAAGAUACCCUUCAGGAGCGUUAAAGGCCUGUUUAGGAUUUGGUGGGCUUGUAUCAAAGUAUUUUUGCUAUUCUCUUUUUAGGAAGAAAUCGAAACAAGGAGAGUAAGAAG .....((((((((.......))).....(((((((((.((((((..((((((((((((....(((((((((........................((((((.(((.(((.((((...((((((((..((..((((..(((((((..((......))..))))))).(((........)))..))))..))....))))))))..)))).)))..))).))))))))))))))).))))))))))))..))))))...(((((....)))))))))))))).)))))......... (-68.95) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUUACUCUCCUUGUUUCGAUUUCUUCCUAAAAAGAGAAUAGCAAAAAUACUUUGAUACAAGCCCACCAAAUCCUAAACAGGCCUUUAACGCUCCUGAAGGGUAUCUUGUUCCUCAAAUAAGCAUGAUAAUCUUACAACUAUUUUAUCAUAAAAUCUUAACAGUAUCAUUCAGGAAAUUUCAAGGGCAAUUAAAGAUUUUAUGGUGAAAAAGGAGAUAAAAGUGAUAGACUAACAGUAUCAAAACACAGUUGCUAGAAUCAAAACUAGCACCUAGAUUAAAGGAGGAAUUCUC ....................((.((((((((.....((...((((((......((((((((.....(((((((((........((((((.....(((((((.(((((((((((.....)))))).(((((((.............)))))))............))))).)))))))......)))))).......))))...)))))..............(((.....)))....))))))))......))))))...))....((((...)))).....)))))))).)).. (-64.18) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 855 50 1 141 92 smit:SMT_347|5end_hypothetical_protein_286210..286440_NEGATIVE 339 230 187 136 93 smit:SMT_768|5end_hypothetical_protein_679243..679473_NEGATIVE 312 230 181 202 160 smit:SMT_1887|5end_LicC_protein_1841445..1841675_POSITIVE 311 221 185 69 26 smit:SMT_2083|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1982411..1982641_POSITIVE 285 235 191 103 53 smit:SMT_541|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457842..458072_NEGATIVE 280 212 171 163 128 smit:SMT_898|5end_polyribonucleotide_nucleotidyltransferase_846861..847091_NEGATIVE 279 67 25 162 118 smit:SMT_1009|5end_hypothetical_protein_predicted_by_Glimmer/Critica_948206..948436_POSITIVE 279 240 196 189 136 smit:SMT_880|5end_beta-lactam_resistance_factor_828300..828530_NEGATIVE 278 257 211 151 96 smit:SMT_2123|5end_hypothetical_protein_2008201..2008431_POSITIVE 277 240 194 90 32 smit:SMT_1008|5end_hypothetical_protein_948021..948251_NEGATIVE 276 54 19 45 9 smit:SMT_141|5end_K03495_glucose_inhibited_division_protein_A_91408..91638_POSITIVE 274 236 198 149 116 smit:SMT_997|5end_integral_membrane_protein_938243..938473_POSITIVE 271 66 22 193 154 smit:SMT_1158|5end_DNA_gyrase_subunit_B_1103957..1104187_NEGATIVE 271 48 2 148 95 smit:SMT_142|5end_hypothetical_protein_95088..95318_NEGATIVE 270 231 197 54 16 smit:SMT_1472|5end_hypothetical_protein,_coenzyme_PQQ_synthesis_homologue_1454262..1454492_NEGATIVE 270 239 194 193 138 smit:SMT_346|5end_K01992_ABC-2_type_transport_system_permease_protein_284720..284950_POSITIVE 269 253 214 185 144 smit:SMT_538|5end_DNA-binding_response_regulator_CiaR_455337..455567_POSITIVE 269 122 81 103 61 smit:SMT_494|5end_K04767_acetoin_utilization_protein_AcuB_428155..428385_POSITIVE 268 47 3 76 26 smit:SMT_1806|5end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781229..1781459_POSITIVE 268 47 3 76 26 smit:SMT_1635|5end_putative_N-acetyldiaminopimelate_deacetylase_1621426..1621656_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 233 193 87 45 smit:SMT_225|3end_pullulanase_159666..159816_NEGATIVE 290 240 193 148 76 smit:SMT_1656|3end_glutamine_ABC_transporter_ATP-binding_protein_1645172..1645322_NEGATIVE 276 54 11 55 2 smit:SMT_140|3end_NUDIX_family_hydrolase_91498..91648_POSITIVE 274 236 198 81 48 smit:SMT_1967|3end_dicarboxylate/amino_acid:cation_(Na+_or_H+)_symporter_(DAACS)_family_protein_1899498..1899648_NEGATIVE 274 236 198 81 48 smit:SMT_996|3end_K03309_dicarboxylate/amino_acid:cation_(Na+_or_H+)_symporter,_DAACS_family_938255..938405_POSITIVE 271 48 2 146 93 smit:SMT_143|3end_hypothetical_protein_95090..95240_NEGATIVE 269 253 214 136 95 smit:SMT_537|3end_oxidoreductase,_aldo/keto_reductase_family_455368..455518_POSITIVE 264 270 221 56 12 smit:SMT_1651|3end_chromosome_segregation_SMC_protein_1640617..1640767_POSITIVE 264 46 1 133 73 smit:SMT_774|3end_hypothetical_protein_684479..684629_NEGATIVE 262 50 2 115 73 smit:SMT_1688|3end_putative_N-acylglucosamine-6-phosphate_2-epimerase_1671603..1671753_POSITIVE 258 234 193 65 25 smit:SMT_1722|3end_x-prolyl-dipeptidyl_aminopeptidase_1709012..1709162_POSITIVE 258 99 51 104 52 smit:SMT_923|3end_methionyl-tRNA_formyltransferase_876559..876709_NEGATIVE 255 238 192 44 1 smit:SMT_1852|3end_1,4-alpha-glucan_branching_enzyme_1816467..1816617_NEGATIVE 255 238 192 44 1 smit:SMT_326|3end_K02029_polar_amino_acid_transport_system_permease_protein_263217..263367_NEGATIVE 254 259 212 134 86 smit:SMT_1480|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1462266..1462416_POSITIVE 253 127 82 140 87 smit:SMT_909|3end_type_I_restriction_enzyme_M_protein_857223..857373_NEGATIVE 252 232 197 45 9 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 248 228 182 75 30 smit:SMT_869|3end_hypothetical_protein_817228..817378_NEGATIVE 248 65 21 85 51 smit:SMT_463|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_402839..402989_POSITIVE 246 58 12 145 96 smit:SMT_950|3end_UDP-glucose_4-epimerase_897677..897827_NEGATIVE