Origin IGS: atggatggatctcaaatgggctcagttcgtnnnnnttaattaattaannnnntaaggatgcagagctatataaggcttattatgaaaagaaaaatcgtaaagta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tactttacgatttttcttttcataataagccttatatagctctgcatccttannnnnttaattaattaannnnnacgaactgagcccatttgagatccatccat Mask Tandem Repeat Region ================================================ atggatggatctcaaatgggctcagttcgtnnnnnttaattaattaannnnntaaggatgcagagctatataaggcttattatgaaaagaaaaatcgtaaagta Find is-nt database================================================ Query_seq: SMT_1894:SMT_1895|SMT_1894:SMT_1895:K02025 multiple sugar transport system permease protein:hypothetical protein predicted by Glimmer/Critica:->->:1847248..1847351 104 atggatggatctcaaatgggctcagttcgtnnnnnttaattaattaannnnntaaggatgcagagctatataaggcttattatgaaaagaaaaatcgtaaagta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1894:SMT_1895|SMT_1894:SMT_1895:K02025 multiple sugar transport system permease protein:hypothetical protein predicted by Glimmer/Critica:->->:1847248..1847351 104 atggatggatctcaaatgggctcagttcgtnnnnnttaattaattaannnnntaaggatgcagagctatataaggcttattatgaaaagaaaaatcgtaaagta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1894:SMT_1895|SMT_1894:SMT_1895:K02025 multiple sugar transport system permease protein:hypothetical protein predicted by Glimmer/Critica:->->:1847248..1847351 104 atggatggatctcaaatgggctcagttcgtnnnnnttaattaattaannnnntaaggatgcagagctatataaggcttattatgaaaagaaaaatcgtaaagta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atggatggatctcaaatgggctcagttcgtnnnnnttaattaattaannnnntaaggatgcagagctatataaggcttattatgaaaagaaaaatcgtaaagta Predict ORF larger than 30AA ================================================ atggatggatctcaaatgggctcagttcgtnnnnnttaattaattaannnnntaaggatgcagagctatataaggcttattatgaaaagaaaaatcgtaaagta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atggatggatctcaaatgggctcagttcgtnnnnnttaattaattaannnnntaaggatgcagagctatataaggcttattatgaaaagaaaaatcgtaaagta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1894:SMT_1895|SMT_1894:SMT_1895:K02025 multiple sugar transport system permease protein:hypothetical protein predicted by Glimmer/Critica:->->:1847248..1847351 104 atggatggatctcaaatgggctcagttcgtnnnnnttaattaattaannnnntaaggatgcagagctatataaggcttattatgaaaagaaaaatcgtaaagta Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: smit_SMT_1894_SMT_1895|K02025 multiple sugar transport system permease protein:hypothetical protein predicted by Glimmer/Critica|POSITIVE:POSITIVE|[1847248,1847351]|104 HSP 1 e-value: 8.0E-35 bit: 147.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 atggatggatctcaaatgggctcagttcgtnnnnnttaattaattaannnnntaaggatgcagagctatataaggcttattatgaaaagaaaaatcgtaaagta atggatggatctcaaatgggctcagttcgtnnnnnttaattaattaannnnntaaggatgcagagctatataaggcttattatgaaaagaaaaatcgtaaagta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGGAUGGAUCUCAAAUGGGCUCAGUUCGUNNNNNUUAAUUAAUUAANNNNNUAAGGAUGCAGAGCUAUAUAAGGCUUAUUAUGAAAAGAAAAAUCGUAAAGUA ((((((.((.(((....))).)).))))))............................(((.(((((......))))).((((((.........)))))).))) (-12.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUUUACGAUUUUUCUUUUCAUAAUAAGCCUUAUAUAGCUCUGCAUCCUUANNNNNUUAAUUAAUUAANNNNNACGAACUGAGCCCAUUUGAGAUCCAUCCAU ..............................((((.((.((((.......................................))))..)).)))).......... ( -4.83) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 444 30 2 212 182 smit:SMT_1912|5end_D-alanyl-D-alanine_carboxypeptidase_1857920..1858150_NEGATIVE 218 28 1 178 146 smit:SMT_992|5end_hypothetical_protein_934882..935112_NEGATIVE 211 97 56 114 55 smit:SMT_535|5end_hypothetical_protein_454215..454445_POSITIVE 196 30 1 174 138 smit:SMT_1989|5end_multimodular_transpeptidase-transglycosylase_1917607..1917837_NEGATIVE 192 25 3 73 45 smit:SMT_598|5end_K07273_lysozyme_514764..514994_NEGATIVE 190 100 53 44 1 smit:SMT_1994|5end_phosphoglycerate_mutase_1920501..1920731_NEGATIVE 189 75 53 124 103 smit:SMT_1937|5end_glycosyl_transferase,_family_2_1874428..1874658_POSITIVE 189 30 11 184 164 smit:SMT_650|5end_pullulanase_559832..560062_NEGATIVE 185 95 55 79 35 smit:SMT_559|5end_D-alanyl-D-alanine_carboxypeptidase_478042..478272_NEGATIVE 184 89 55 228 195 smit:SMT_853|5end_ATP-dependent_endopeptidase_clp_ATP-binding_subunit_ClpX_799285..799515_NEGATIVE 182 93 55 169 130 smit:SMT_546|5end_DNA_topoisomerase_IV_subunit_A_461377..461607_POSITIVE 182 93 55 41 2 smit:SMT_545|5end_hypothetical_protein_predicted_by_Glimmer/Critica_461249..461479_POSITIVE 181 47 1 157 98 smit:SMT_215|5end_leucyl-tRNA_synthetase_147045..147275_POSITIVE 177 25 2 40 15 smit:SMT_1795|5end_DNA_polymerase_III,_delta_subunit_1769847..1770077_NEGATIVE 176 29 1 122 92 smit:SMT_479|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416656..416886_NEGATIVE 176 29 1 122 92 smit:SMT_462|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_401658..401888_NEGATIVE 174 30 3 53 28 smit:SMT_1854|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1818375..1818605_POSITIVE 173 27 2 146 120 smit:SMT_1873|5end_K02006_cobalt_transport_system_ATP-binding_protein_1831936..1832166_POSITIVE 172 30 5 221 193 smit:SMT_1821|5end_Mg2+_and_Co2+_transporter_1793794..1794024_POSITIVE 171 98 55 194 147 smit:SMT_2160|5end_cell_division_protein_FtsA_2033524..2033754_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 30 1 37 2 smit:SMT_2082|3end_ATP-dependent_nuclease_subunit_B_1981408..1981558_NEGATIVE 204 30 1 134 106 smit:SMT_704|3end_Cof_family_protein_614548..614698_POSITIVE 189 30 11 30 10 smit:SMT_651|3end_DNA_ligase_559986..560136_NEGATIVE 184 97 54 58 11 smit:SMT_1866|3end_extramembranal_protein_1827939..1828089_POSITIVE 182 93 55 136 97 smit:SMT_545|3end_hypothetical_protein_predicted_by_Glimmer/Critica_461424..461574_POSITIVE 181 47 1 98 39 smit:SMT_214|3end_leucyl-tRNA_synthetase_147066..147216_POSITIVE 180 26 2 118 83 smit:SMT_2112|3end_transcription-repair_coupling_factor_2000373..2000523_NEGATIVE 169 80 55 117 93 smit:SMT_1898|3end_aminotransferase_(class_V),_putative_1848877..1849027_NEGATIVE 169 70 36 121 83 smit:SMT_607|3end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_520816..520966_POSITIVE 167 29 1 76 41 smit:SMT_1468|3end_pneumococcal_surface_protein,_putative_1448775..1448925_NEGATIVE 166 29 2 138 110 smit:SMT_1798|3end_exonuclease_RexA_1772818..1772968_NEGATIVE 166 29 1 148 118 smit:SMT_482|3end_hypothetical_protein_predicted_by_Glimmer/Critica_418414..418564_NEGATIVE 163 96 62 48 6 smit:SMT_550|3end_K02945_small_subunit_ribosomal_protein_S1_468942..469092_POSITIVE 162 75 36 126 91 smit:SMT_2075|3end_phosphoribosylamine--glycine_ligase_1977769..1977919_NEGATIVE 160 30 4 146 126 smit:SMT_1802|3end_tyrosyl-tRNA_synthetase_1775456..1775606_NEGATIVE 159 29 6 133 105 smit:SMT_866|3end_50S_ribosomal_protein_L11_815809..815959_NEGATIVE 158 85 55 42 16 smit:SMT_1477|3end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1459447..1459597_NEGATIVE 157 30 2 148 122 smit:SMT_1809|3end_MutT/NUDIX_family_protein_1785134..1785284_POSITIVE 157 77 55 106 81 smit:SMT_1169|3end_phosphorylase,_Pnp/UDP_family_1116586..1116736_NEGATIVE 157 79 60 47 26 smit:SMT_480|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416765..416915_NEGATIVE