Origin IGS: atttttctccttttttgtcaagtatgtacaataaaaaaattgacaaaaaacctgtctttttttaaaattataacatgaaggatgcttactagaaagcggaaactgtcagctgagacaagagggaagaaattgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacaatttcttccctcttgtctcagctgacagtttccgctttctagtaagcatccttcatgttataattttaaaaaaagacaggttttttgtcaatttttttattgtacatacttgacaaaaaaggagaaaaat Mask Tandem Repeat Region ================================================ atttttctccttttttgtcaagtatgtacaataaaaaaattgacaaaaaacctgtctttttttaaaattataacatgaaggatgcttactagaaagcggaaactgtcagctgagacaagagggaagaaattgtt Find is-nt database================================================ Query_seq: SSA_1029:SSA_1030|SSA_1029:SSA_1030:hypothetical protein:Transcriptional regulator, TetR family, putative:<-->:1047100..1047233 134 atttttctccttttttgtcaagtatgtacaataaaaaaattgacaaaaaacctgtctttttttaaaattataacatgaaggatgcttactagaaagcggaaactgtcagctgagacaagagggaagaaattgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1029:SSA_1030|SSA_1029:SSA_1030:hypothetical protein:Transcriptional regulator, TetR family, putative:<-->:1047100..1047233 134 atttttctccttttttgtcaagtatgtacaataaaaaaattgacaaaaaacctgtctttttttaaaattataacatgaaggatgcttactagaaagcggaaactgtcagctgagacaagagggaagaaattgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1029:SSA_1030|SSA_1029:SSA_1030:hypothetical protein:Transcriptional regulator, TetR family, putative:<-->:1047100..1047233 134 atttttctccttttttgtcaagtatgtacaataaaaaaattgacaaaaaacctgtctttttttaaaattataacatgaaggatgcttactagaaagcggaaactgtcagctgagacaagagggaagaaattgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttttctccttttttgtcaagtatgtacaataaaaaaattgacaaaaaacctgtctttttttaaaattataacatgaaggatgcttactagaaagcggaaactgtcagctgagacaagagggaagaaattgtt Predict ORF larger than 30AA ================================================ atttttctccttttttgtcaagtatgtacaataaaaaaattgacaaaaaacctgtctttttttaaaattataacatgaaggatgcttactagaaagcggaaactgtcagctgagacaagagggaagaaattgtt 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: 91 Start: 39 End: 68 ......................................ATTGACAAAAAACCTGTCTTTTTTTAAAAT.................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 67 End: 96 ..................................................................CTTTCTAGTAAGCATCCTTCATGTTATAAT...................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttttctccttttttgtcaagtatgtacaataaaaaaattgacaaaaaacctgtctttttttaaaattataacatgaaggatgcttactagaaagcggaaactgtcagctgagacaagagggaagaaattgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1029:SSA_1030|SSA_1029:SSA_1030:hypothetical protein:Transcriptional regulator, TetR family, putative:<-->:1047100..1047233 134 atttttctccttttttgtcaagtatgtacaataaaaaaattgacaaaaaacctgtctttttttaaaattataacatgaaggatgcttactagaaagcggaaactgtcagctgagacaagagggaagaaattgtt Intra-Species Hit: Count: 1 Min: 1 Max: 134 Len: 134 Subject: NC_009009_SSA_1029_SSA_1030|hypothetical protein:Transcriptional regulator, TetR family, putative|NEGATIVE:POSITIVE|[1047100,1047233]|134 HSP 1 e-value: 2.0E-45 bit: 182.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 134 atttttctccttttttgtcaagtatgtacaatnnnnnnnttgacaaaaaacctgtcnnnnnnnaaaattataacatgaaggatgcttactagaaagcggaaactgtcagctgagacaagagggaagaaattgtt atttttctccttttttgtcaagtatgtacaataaaaaaattgacaaaaaacctgtctttttttaaaattataacatgaaggatgcttactagaaagcggaaactgtcagctgagacaagagggaagaaattgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUUCUCCUUUUUUGUCAAGUAUGUACAAUAAAAAAAUUGACAAAAAACCUGUCUUUUUUUAAAAUUAUAACAUGAAGGAUGCUUACUAGAAAGCGGAAACUGUCAGCUGAGACAAGAGGGAAGAAAUUGUU ...(((((.((((((((((.(((.((.(((....(((((..((((.......))))..)))))...................(((((......))))).....))))))))..)))))))))).)))))..... (-27.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAAUUUCUUCCCUCUUGUCUCAGCUGACAGUUUCCGCUUUCUAGUAAGCAUCCUUCAUGUUAUAAUUUUAAAAAAAGACAGGUUUUUUGUCAAUUUUUUUAUUGUACAUACUUGACAAAAAAGGAGAAAAAU .....(((((((...(((((((..(((((.(((....))).)).))).(((((.....)))))..............))))))).((((((((((..................)))))))))).)))))))... (-24.37) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 924 130 81 221 172 NC_009009:SSA_1029|5end_hypothetical_protein_1047009..1047239_NEGATIVE 291 126 81 88 26 NC_009009:SSA_0506|5end_Iron-sulfur_cluster-binding_protein,_putative_505629..505859_NEGATIVE 287 120 77 84 37 NC_009009:SSA_1553|5end_Permease,_putative_1555047..1555277_POSITIVE 279 124 85 62 20 NC_009009:SSA_0758|5end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_740636..740866_POSITIVE 276 122 83 149 111 NC_009009:SSA_0678|5end_Transcriptional_regulator,_ArgR_family,_putative_660274..660504_POSITIVE 270 115 77 68 20 NC_009009:SSA_1636|5end_ABC-type_antibiotic_exporter,_ATPase_component,_putative_1640905..1641135_NEGATIVE 268 112 82 64 26 NC_009009:SSA_0858|5end_DTDP-L-rhamnose_synthase,_putative_845512..845742_POSITIVE 268 116 74 132 89 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 264 120 73 205 163 NC_009009:SSA_2358|5end_hypothetical_protein_2360497..2360727_NEGATIVE 262 127 91 170 139 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 260 130 81 67 13 NC_009009:SSA_1976|5end_Conserved_uncharacterized_protein_1972158..1972388_NEGATIVE 258 127 88 167 114 NC_009009:SSA_2212|5end_Possible_polysaccharide_transport_protein,_putative_2213928..2214158_NEGATIVE 254 115 75 176 136 NC_009009:SSA_0445|5end_hypothetical_protein_444487..444717_POSITIVE 254 118 74 47 8 NC_009009:SSA_0202|5end_hypothetical_protein_200534..200764_POSITIVE 254 123 81 229 183 NC_009009:SSA_0090|5end_Acetyltransferase,_GNAT_family,_putative_90258..90488_POSITIVE 254 129 93 64 36 NC_009009:SSA_0004|5end_Lipoprotein,_putative_3704..3934_NEGATIVE 252 129 95 223 189 NC_009009:SSA_1927|5end_Exfoliative_toxin,_putative_1915873..1916103_NEGATIVE 252 123 81 211 166 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 251 120 76 59 10 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 251 126 95 50 21 NC_009009:SSA_0898|5end_hypothetical_protein_889863..890093_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 120 77 87 40 NC_009009:SSA_1552|3end_hypothetical_protein_1555130..1555280_POSITIVE 279 124 85 44 2 NC_009009:SSA_0757|3end_N-acetyl-gamma-glutamyl-phosphate_reductase,_putative_740698..740848_POSITIVE 276 123 82 137 93 NC_009009:SSA_0956|3end_surface_protein_D_965418..965568_POSITIVE 268 116 74 123 80 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 264 120 73 89 47 NC_009009:SSA_2359|3end_Glucose_inhibited_division_protein_A,_putative_2360613..2360763_NEGATIVE 264 116 80 42 1 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 262 127 91 70 39 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 254 118 74 45 6 NC_009009:SSA_0201|3end_ABC_multidrug_transporter_(3-component_subtilin_immunity_exporter),_putative_200612..200762_POSITIVE 252 129 95 150 116 NC_009009:SSA_1928|3end_Acyl-CoA_dehydrogenase,_putative_1915946..1916096_NEGATIVE 251 120 76 66 17 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 251 126 95 145 116 NC_009009:SSA_0898|3end_hypothetical_protein_889768..889918_NEGATIVE 245 126 84 141 94 NC_009009:SSA_1162|3end_Possible_fimbrial_assembly_protein_fimC,_putative_1188489..1188639_NEGATIVE 244 117 73 119 56 NC_009009:SSA_1357|3end_hypothetical_protein_1372077..1372227_NEGATIVE 242 123 88 82 42 NC_009009:SSA_1582|3end_Esterase,_alpha/beta_hydrolase_superfamily,_putative_1585443..1585593_POSITIVE 239 110 61 70 27 NC_009009:SSA_1903|3end_hypothetical_protein_1897388..1897538_NEGATIVE 238 114 80 34 5 NC_009009:SSA_1323|3end_hypothetical_protein_1339788..1339938_NEGATIVE 237 123 95 51 20 NC_009009:SSA_1199|3end_Phosphinothricin_acetyltransferase,_putative_1223311..1223461_NEGATIVE 235 115 79 148 116 NC_009009:SSA_1229|3end_hypothetical_protein_1252314..1252464_NEGATIVE 235 122 85 145 107 NC_009009:SSA_0731|3end_Integral_membrane_protein,_putative_715654..715804_POSITIVE 233 119 78 141 97 NC_009009:SSA_1386|3end_NADPH-dependent_FMN_reductase,_putative_1403428..1403578_POSITIVE