Origin IGS: gatgtttctcctttaattactttgtttatacttttagtatacaaactaaatttcaaatatttctcaagaaattctaaaatatttctaaagaaatttaaaattgaaaagattaaaatgagccagtcaagaaccagctcattgttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaacaatgagctggttcttgactggctcattttaatcttttcaattttaaatttctttagaaatattttagaatttcttgagaaatatttgaaatttagtttgtatactaaaagtataaacaaagtaattaaaggagaaacatc Mask Tandem Repeat Region ================================================ gatgtttctcctttaattactttgtttatacttttagtatacaaactnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgaaaagattaaaatgagccagtcaagaaccagctcattgttta Find is-nt database================================================ Query_seq: SSA_0407:SSA_0408|SSA_0407:SSA_0408:ABC-type multidrug transport system (3-component subtilin immunity exporter), ATPase component, putative:hypothetical protein:<-<-:403934..404078 145 gatgtttctcctttaattactttgtttatacttttagtatacaaactaaatttcaaatatttctcaagaaattctaaaatatttctaaagaaatttaaaattgaaaagattaaaatgagccagtcaagaaccagctcattgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0407:SSA_0408|SSA_0407:SSA_0408:ABC-type multidrug transport system (3-component subtilin immunity exporter), ATPase component, putative:hypothetical protein:<-<-:403934..404078 145 gatgtttctcctttaattactttgtttatacttttagtatacaaactaaatttcaaatatttctcaagaaattctaaaatatttctaaagaaatttaaaattgaaaagattaaaatgagccagtcaagaaccagctcattgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0407:SSA_0408|SSA_0407:SSA_0408:ABC-type multidrug transport system (3-component subtilin immunity exporter), ATPase component, putative:hypothetical protein:<-<-:403934..404078 145 gatgtttctcctttaattactttgtttatacttttagtatacaaactaaatttcaaatatttctcaagaaattctaaaatatttctaaagaaatttaaaattgaaaagattaaaatgagccagtcaagaaccagctcattgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgtttctcctttaattactttgtttatacttttagtatacaaactaaatttcaaatatttctcaagaaattctaaaatatttctaaagaaatttaaaattgaaaagattaaaatgagccagtcaagaaccagctcattgttta Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 16 End: 144 ............... M T L F I L L V Y K L N F K Y F S R N S K I F L K K F K I E K I K M S Q S R T S S L F . Protein_Len: 44 Strand: - Start: 3 End: 134 .. T E G K I V K N I S K T Y L S F K L Y K E L F E L I N R F F N L I S F I L I L W D L V M ........... gatgtttctcctttaattactttgtttatacttttagtatacaaactaaatttcaaatatttctcaagaaattctaaaatatttctaaagaaatttaaaattgaaaagattaaaatgagccagtcaagaaccagctcattgttta 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: 51 End: 80 ..................................................TTTCAAATATTTCTCAAGAAATTCTAAAAT................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 71 End: 100 ......................................................................TTTTAAATTTCTTTAGAAATATTTTAGAAT............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatgtttctcctttaattactttgtttatacttttagtatacaaactaaatttcaaatatttctcaagaaattctaaaatatttctaaagaaatttaaaattgaaaagattaaaatgagccagtcaagaaccagctcattgttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0407:SSA_0408|SSA_0407:SSA_0408:ABC-type multidrug transport system (3-component subtilin immunity exporter), ATPase component, putative:hypothetical protein:<-<-:403934..404078 145 gatgtttctcctttaattactttgtttatacttttagtatacaaactaaatttcaaatatttctcaagaaattctaaaatatttctaaagaaatttaaaattgaaaagattaaaatgagccagtcaagaaccagctcattgttta Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: NC_009009_SSA_0407_SSA_0408|ABC-type multidrug transport system (3-component subtilin immunity exporter), ATPase component, putative:hypothetical protein|NEGATIVE:NEGATIVE|[403934,404078]|145 HSP 1 e-value: 2.0E-18 bit: 93.7 Len: 47 Query Start:1 Query End:47 Subject Strand: POSITIVE Subject Start: 1 Subject End: 47 gatgtttctcctttaattactttgtttatacttttagtatacaaact.................................................................................................. gatgtttctcctttaattactttgtttatacttttagtatacaaact.................................................................................................. HSP 2 e-value: 8.0E-8 bit: 58.0 Len: 29 Query Start:117 Query End:145 Subject Strand: POSITIVE Subject Start: 117 Subject End: 145 ....................................................................................................................gagccagtcaagaaccagctcattgttta ....................................................................................................................gagccagtcaagaaccagctcattgttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGUUUCUCCUUUAAUUACUUUGUUUAUACUUUUAGUAUACAAACUAAAUUUCAAAUAUUUCUCAAGAAAUUCUAAAAUAUUUCUAAAGAAAUUUAAAAUUGAAAAGAUUAAAAUGAGCCAGUCAAGAACCAGCUCAUUGUUUA ................(((.(((((..((((.....))))))))).))).((((((..((((((..((((((........))))))..))))))......)))))).......(((((((..((.....))..)))))))..... (-22.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACAAUGAGCUGGUUCUUGACUGGCUCAUUUUAAUCUUUUCAAUUUUAAAUUUCUUUAGAAAUAUUUUAGAAUUUCUUGAGAAAUAUUUGAAAUUUAGUUUGUAUACUAAAAGUAUAAACAAAGUAAUUAAAGGAGAAACAUC .....(((((((..(((...)))..)))))))....((((((.(((((((((((((((.((((((........)))))).)))))..))))))))))..((((((((.......))))))))...........))))))...... (-34.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 735 140 91 231 182 NC_009009:SSA_0407|5end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_403843..404073_NEGATIVE 515 90 41 177 128 NC_009009:SSA_0409|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_405605..405835_NEGATIVE 275 90 42 200 156 NC_009009:SSA_0412|5end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_408163..408393_NEGATIVE 275 90 41 177 128 NC_009009:SSA_0253|5end_CAAX_amino_terminal_protease_family_protein,_putative_246289..246519_POSITIVE 241 140 107 221 187 NC_009009:SSA_1387|5end_hypothetical_protein_1403796..1404026_NEGATIVE 236 140 118 50 25 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 228 37 3 193 153 NC_009009:SSA_1294|5end_hypothetical_protein_1312581..1312811_NEGATIVE 227 138 109 71 38 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 223 137 118 226 209 NC_009009:SSA_2060|5end_Arabinose_efflux_permease,_putative_2062403..2062633_NEGATIVE 219 138 102 151 117 NC_009009:SSA_0841|5end_hypothetical_protein_826935..827165_POSITIVE 217 138 106 43 15 NC_009009:SSA_0793|5end_DNA-entry_nuclease,_putative_774859..775089_POSITIVE 215 137 118 224 201 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 213 139 116 148 125 NC_009009:SSA_0066|5end_hypothetical_protein_67602..67832_POSITIVE 212 43 2 141 90 NC_009009:SSA_0048|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_53443..53673_NEGATIVE 206 138 104 59 21 NC_009009:SSA_1927|5end_Exfoliative_toxin,_putative_1915873..1916103_NEGATIVE 205 140 119 76 56 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 201 137 116 69 48 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 201 135 100 46 8 NC_009009:SSA_0175|5end_Penicillin-binding_protein_1B,_putative_172152..172382_POSITIVE 196 42 2 132 90 NC_009009:SSA_0315|5end_Transcriptional_regulator,_MarR_family,_putative_310102..310332_POSITIVE 196 135 105 35 5 NC_009009:SSA_0189|5end_Competence_protein_ComGF,_putative_191015..191245_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 409 94 59 36 1 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 275 90 42 48 4 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 242 140 102 48 12 NC_009009:SSA_0921|3end_Zn-dependeant_threonine_dehydrogenase,_putative_932164..932314_POSITIVE 236 140 118 50 25 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 219 138 102 149 115 NC_009009:SSA_0839|3end_hypothetical_protein_827013..827163_POSITIVE 213 139 116 143 120 NC_009009:SSA_0065|3end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67677..67827_POSITIVE 204 136 106 98 65 NC_009009:SSA_2256|3end_hypothetical_protein_2251235..2251385_POSITIVE 201 137 116 72 51 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 196 135 105 51 21 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE 195 136 117 27 7 NC_009009:SSA_0671|3end_Methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase,_putative_655274..655424_POSITIVE 195 138 114 149 121 NC_009009:SSA_0546|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_541963..542113_POSITIVE 193 67 25 65 29 NC_009009:SSA_0616|3end_YlbN-like_protein,_putative_609855..610005_POSITIVE 190 140 100 48 6 NC_009009:SSA_1051|3end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1066808..1066958_POSITIVE 188 139 111 80 42 NC_009009:SSA_0020|3end_Ribose-phosphate_pyrophosphokinase_1,_putative_26609..26759_POSITIVE 186 137 102 75 37 NC_009009:SSA_2144|3end_Glutamyl-tRNA_synthetase,_putative_2144315..2144465_NEGATIVE 186 137 104 147 119 NC_009009:SSA_0759|3end_Acetylglutamate_kinase,_putative_742658..742808_POSITIVE 185 135 102 42 2 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 185 138 116 142 119 NC_009009:SSA_0572|3end_Dehydrogenase,_putative_568552..568702_POSITIVE 183 139 119 131 109 NC_009009:SSA_0647|3end_hypothetical_protein_631458..631608_POSITIVE 182 134 101 101 67 NC_009009:SSA_0122|3end_50S_ribosomal_protein_L6,_putative_116043..116193_POSITIVE