Origin IGS: ctcccagtcaattctgggagttttatgcgtaattgggcaagctttctaggttgtctatcttgctaaaacgtagaaaaaacgatatgatagataatgacaaaagaggtatcaagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acttgatacctcttttgtcattatctatcatatcgttttttctacgttttagcaagatagacaacctagaaagcttgcccaattacgcataaaactcccagaattgactgggag Mask Tandem Repeat Region ================================================ ctcccagtcaattctgggagttttatgcgtaattgggcaagctttctaggttgtctatcttgctaaaacgtagaaaaaacgatatgatagataatgacaaaagaggtatcaagt Find is-nt database================================================ Query_seq: SMT_403:SMT_404|SMT_403:SMT_404:two-component sensor kinase YesM:hypothetical protein:->->:333412..333525 114 ctcccagtcaattctgggagttttatgcgtaattgggcaagctttctaggttgtctatcttgctaaaacgtagaaaaaacgatatgatagataatgacaaaagaggtatcaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_403:SMT_404|SMT_403:SMT_404:two-component sensor kinase YesM:hypothetical protein:->->:333412..333525 114 ctcccagtcaattctgggagttttatgcgtaattgggcaagctttctaggttgtctatcttgctaaaacgtagaaaaaacgatatgatagataatgacaaaagaggtatcaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_403:SMT_404|SMT_403:SMT_404:two-component sensor kinase YesM:hypothetical protein:->->:333412..333525 114 ctcccagtcaattctgggagttttatgcgtaattgggcaagctttctaggttgtctatcttgctaaaacgtagaaaaaacgatatgatagataatgacaaaagaggtatcaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctcccagtcaattctgggagttttatgcgtaattgggcaagctttctaggttgtctatcttgctaaaacgtagaaaaaacgatatgatagataatgacaaaagaggtatcaagt Predict ORF larger than 30AA ================================================ ctcccagtcaattctgggagttttatgcgtaattgggcaagctttctaggttgtctatcttgctaaaacgtagaaaaaacgatatgatagataatgacaaaagaggtatcaagt 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: 59 End: 88 ..........................................................CTTGCTAAAACGTAGAAAAAACGATATGAT.......................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 84 End: 113 ...................................................................................CTTGATACCTCTTTTGTCATTATCTATCAT. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctcccagtcaattctgggagttttatgcgtaattgggcaagctttctaggttgtctatcttgctaaaacgtagaaaaaacgatatgatagataatgacaaaagaggtatcaagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_403:SMT_404|SMT_403:SMT_404:two-component sensor kinase YesM:hypothetical protein:->->:333412..333525 114 ctcccagtcaattctgggagttttatgcgtaattgggcaagctttctaggttgtctatcttgctaaaacgtagaaaaaacgatatgatagataatgacaaaagaggtatcaagt Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: smit_SMT_403_SMT_404|two-component sensor kinase YesM:hypothetical protein|POSITIVE:POSITIVE|[333412,333525]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 ctcccagtcaattctgggagttttatgcgtaattgggcaagctttctaggttgtctatcttgctaaaacgtagaaaaaacgatatgatagataatgacaaaagaggtatcaagt ctcccagtcaattctgggagttttatgcgtaattgggcaagctttctaggttgtctatcttgctaaaacgtagaaaaaacgatatgatagataatgacaaaagaggtatcaagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCCCAGUCAAUUCUGGGAGUUUUAUGCGUAAUUGGGCAAGCUUUCUAGGUUGUCUAUCUUGCUAAAACGUAGAAAAAACGAUAUGAUAGAUAAUGACAAAAGAGGUAUCAAGU .((((((......))))))((((((.(((....(((((((.((....)).)))))))...)))))))))...........(((((....................))))).... (-26.85) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUGAUACCUCUUUUGUCAUUAUCUAUCAUAUCGUUUUUUCUACGUUUUAGCAAGAUAGACAACCUAGAAAGCUUGCCCAAUUACGCAUAAAACUCCCAGAAUUGACUGGGAG ..........(((.(((((..(((((.......(((.......)))........))))))))))...))).....(((........))).....(((((((......))))))) (-21.36) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 64 21 229 181 smit:SMT_448|5end_K03707_transcriptional_activator_TenA_386789..387019_POSITIVE 323 50 1 167 118 smit:SMT_1059|5end_NAD(P)H-flavin_oxidoreductase_997379..997609_POSITIVE 302 49 12 147 103 smit:SMT_1212|5end_acyl_carrier_protein,_putative_1171657..1171887_NEGATIVE 299 47 1 142 99 smit:SMT_452|5end_phosphomethylpyrimidine_kinase_390568..390798_NEGATIVE 293 59 12 224 173 smit:SMT_293|5end_dTDP-4-dehydrorhamnose_reductase_235919..236149_POSITIVE 288 50 1 50 2 smit:SMT_392|5end_acetyltransferase,_GNAT_family_323616..323846_POSITIVE 285 50 2 202 144 smit:SMT_1930|5end_peptide_chain_release_factor_1_1870765..1870995_NEGATIVE 282 70 23 212 153 smit:SMT_1872|5end_K03217_preprotein_translocase_YidC_subunit_1831764..1831994_NEGATIVE 282 70 23 189 130 smit:SMT_389|5end_PTS_system,_galactitol-specific_IIA_component,_putative_321779..322009_POSITIVE 269 69 27 200 160 smit:SMT_2143|5end_threonyl-tRNA_synthetase_2020255..2020485_POSITIVE 269 46 1 89 43 smit:SMT_1067|5end_alanine_racemase_1005769..1005999_POSITIVE 266 60 15 107 49 smit:SMT_791|5end_thiamine_biosynthesis_protein_ThiI_702377..702607_NEGATIVE 264 59 14 118 62 smit:SMT_1967|5end_dicarboxylate/amino_acid:cation_(Na+_or_H+)_symporter_(DAACS)_family_protein_1899683..1899913_NEGATIVE 263 37 1 177 130 smit:SMT_865|5end_50S_ribosomal_protein_L1_815711..815941_NEGATIVE 262 47 1 183 135 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 261 64 26 141 111 smit:SMT_2005|5end_pullulanase,_type_I_1926289..1926519_NEGATIVE 261 64 26 209 179 smit:SMT_304|5end_hypothetical_protein_246580..246810_POSITIVE 260 56 25 164 124 smit:SMT_219|5end_phosphatidate_cytidylyltransferase_150922..151152_POSITIVE 258 49 4 226 178 smit:SMT_126|5end_hypothetical_membrane_associated_protein_78250..78480_NEGATIVE 257 65 22 189 133 smit:SMT_1857|5end_hypothetical_protein_1820931..1821161_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 49 12 141 97 smit:SMT_1213|3end_fatty_acid/phospholipid_synthesis_protein_PlsX_1171663..1171813_NEGATIVE 282 70 23 107 48 smit:SMT_2044|3end_transcriptional_activator_TipA,_putative_1955274..1955424_NEGATIVE 282 70 23 107 48 smit:SMT_2026|3end_K03466_DNA_segregation_ATPase_FtsK/SpoIIIE,_S-DNA-T_family_1941905..1942055_NEGATIVE 282 70 23 107 48 smit:SMT_2016|3end_tyrosine_recombinase_1933021..1933171_NEGATIVE 282 70 23 107 48 smit:SMT_2006|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1926803..1926953_POSITIVE 282 70 23 117 58 smit:SMT_2001|3end_membrane_protease_protein_family_1923889..1924039_POSITIVE 282 70 23 117 58 smit:SMT_1985|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1914407..1914557_NEGATIVE 282 70 23 107 48 smit:SMT_1957|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1890829..1890979_POSITIVE 282 70 23 65 6 smit:SMT_1955|3end_carbamoyl-phosphate_synthase_small_chain_1888992..1889142_NEGATIVE 282 70 23 107 48 smit:SMT_1886|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1841198..1841348_POSITIVE 282 70 23 107 48 smit:SMT_1658|3end_hypothetical_protein_1648937..1649087_POSITIVE 282 70 23 107 48 smit:SMT_1558|3end_hypothetical_protein_1543855..1544005_NEGATIVE 282 70 23 117 58 smit:SMT_1464|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1445361..1445511_POSITIVE 282 70 23 107 48 smit:SMT_1155|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1099183..1099333_NEGATIVE 269 69 27 117 77 smit:SMT_2142|3end_hypothetical_protein_predicted_by_Glimmer/Critica_2020252..2020402_POSITIVE 269 46 1 99 53 smit:SMT_1066|3end_holo-(acyl_carrier_protein)_synthase_1005859..1006009_POSITIVE 265 59 11 133 82 smit:SMT_1892|3end_hypothetical_protein_1846193..1846343_POSITIVE 264 56 14 133 101 smit:SMT_221|3end_prolyl-tRNA_synthetase_154952..155102_POSITIVE 263 50 7 116 68 smit:SMT_1153|3end_alpha-mannosidase_1097383..1097533_NEGATIVE 263 37 1 79 32 smit:SMT_866|3end_50S_ribosomal_protein_L11_815809..815959_NEGATIVE