Origin IGS: tttcctcagtcaaaaagaggtcaatttttccttgcgccgcctttttatgttatacttagagaagaaaatttttaggaaataagacaaggaagtaacttttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaagttacttccttgtcttatttcctaaaaattttcttctctaagtataacataaaaaggcggcgcaaggaaaaattgacctctttttgactgaggaaa Mask Tandem Repeat Region ================================================ tttcctcagtcaaaaagaggtcaatttttccttgcgccgcctttttatgttatacttagagaagaaaatttttaggaaataagacaaggaagtaacttttt Find is-nt database================================================ Query_seq: SSA_1475:SSA_1476|SSA_1475:SSA_1476:hypothetical protein:Phosphoglycerol transferase, alkaline phosphatase superfamily, putative:<-->:1480212..1480312 101 tttcctcagtcaaaaagaggtcaatttttccttgcgccgcctttttatgttatacttagagaagaaaatttttaggaaataagacaaggaagtaacttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1475:SSA_1476|SSA_1475:SSA_1476:hypothetical protein:Phosphoglycerol transferase, alkaline phosphatase superfamily, putative:<-->:1480212..1480312 101 tttcctcagtcaaaaagaggtcaatttttccttgcgccgcctttttatgttatacttagagaagaaaatttttaggaaataagacaaggaagtaacttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1475:SSA_1476|SSA_1475:SSA_1476:hypothetical protein:Phosphoglycerol transferase, alkaline phosphatase superfamily, putative:<-->:1480212..1480312 101 tttcctcagtcaaaaagaggtcaatttttccttgcgccgcctttttatgttatacttagagaagaaaatttttaggaaataagacaaggaagtaacttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttcctcagtcaaaaagaggtcaatttttccttgcgccgcctttttatgttatacttagagaagaaaatttttaggaaataagacaaggaagtaacttttt Predict ORF larger than 30AA ================================================ tttcctcagtcaaaaagaggtcaatttttccttgcgccgcctttttatgttatacttagagaagaaaatttttaggaaataagacaaggaagtaacttttt 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================================================ tttcctcagtcaaaaagaggtcaatttttccttgcgccgcctttttatgttatacttagagaagaaaatttttaggaaataagacaaggaagtaacttttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1475:SSA_1476|SSA_1475:SSA_1476:hypothetical protein:Phosphoglycerol transferase, alkaline phosphatase superfamily, putative:<-->:1480212..1480312 101 tttcctcagtcaaaaagaggtcaatttttccttgcgccgcctttttatgttatacttagagaagaaaatttttaggaaataagacaaggaagtaacttttt Intra-Species Hit: Count: 1 Min: 1 Max: 101 Len: 101 Subject: NC_009009_SSA_1475_SSA_1476|hypothetical protein:Phosphoglycerol transferase, alkaline phosphatase superfamily, putative|NEGATIVE:POSITIVE|[1480212,1480312]|101 HSP 1 e-value: 6.0E-51 bit: 200.0 Len: 101 Query Start:1 Query End:101 Subject Strand: POSITIVE Subject Start: 1 Subject End: 101 tttcctcagtcaaaaagaggtcaatttttccttgcgccgcctttttatgttatacttagagaagaaaatttttaggaaataagacaaggaagtaacttttt tttcctcagtcaaaaagaggtcaatttttccttgcgccgcctttttatgttatacttagagaagaaaatttttaggaaataagacaaggaagtaacttttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCCUCAGUCAAAAAGAGGUCAAUUUUUCCUUGCGCCGCCUUUUUAUGUUAUACUUAGAGAAGAAAAUUUUUAGGAAAUAAGACAAGGAAGUAACUUUUU ((((((..(((..(((((((((((.......)))....))))))))........((((((((......))))))))......))).))))))......... (-18.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAGUUACUUCCUUGUCUUAUUUCCUAAAAAUUUUCUUCUCUAAGUAUAACAUAAAAAGGCGGCGCAAGGAAAAAUUGACCUCUUUUUGACUGAGGAAA ..........((((((((.(..(((............(((....)))............)))..).)))))))).......((((.........))))... (-13.25) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 867 50 1 141 92 NC_009009:SSA_1475|5end_hypothetical_protein_1480121..1480351_NEGATIVE 304 50 1 146 98 NC_009009:SSA_0163|5end_hypothetical_protein_162127..162357_POSITIVE 275 49 15 43 1 NC_009009:SSA_1529|5end_Lysyl-tRNA_synthetase,_putative_1535871..1536101_POSITIVE 274 60 19 118 74 NC_009009:SSA_1904|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1899279..1899509_NEGATIVE 272 42 1 134 96 NC_009009:SSA_1438|5end_Acetyltransferase,_putative_1443612..1443842_NEGATIVE 269 43 1 213 177 NC_009009:SSA_0216|5end_Histidine_kinase,_putative_211877..212107_POSITIVE 266 41 5 195 153 NC_009009:SSA_0603|5end_Cobalt_transporter,_putative_591596..591826_POSITIVE 263 41 3 58 12 NC_009009:SSA_2146|5end_Metallo-beta-lactamase,_putative_2148399..2148629_NEGATIVE 263 39 3 161 126 NC_009009:SSA_1076|5end_hypothetical_protein_1094227..1094457_POSITIVE 254 44 4 200 163 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 251 65 21 185 136 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 249 40 3 51 5 NC_009009:SSA_0117|5end_50S_ribosomal_protein_L14,_putative_112918..113148_POSITIVE 247 44 5 175 132 NC_009009:SSA_1012|5end_Phosphoenolpyruvate_synthase,_putative_1014739..1014969_POSITIVE 244 43 8 175 139 NC_009009:SSA_1664|5end_Phosphatidylethanolamine_N-methyltransferase,_putative_1665189..1665419_NEGATIVE 243 45 1 157 93 NC_009009:SSA_0202|5end_hypothetical_protein_200534..200764_POSITIVE 242 58 16 56 7 NC_009009:SSA_0629|5end_hypothetical_protein_618967..619197_POSITIVE 242 42 2 102 65 NC_009009:SSA_0618|5end_hypothetical_protein_611973..612203_NEGATIVE 240 65 36 176 146 NC_009009:SSA_0692|5end_D-Ala-D-Ala_adding_enzyme,_putative_676370..676600_POSITIVE 238 49 15 32 3 NC_009009:SSA_1302|5end_tRNA_(Guanine-N(1)-)-methyltransferase,_putative_1322484..1322714_NEGATIVE 237 41 5 69 19 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 50 1 78 30 NC_009009:SSA_0162|3end_hypothetical_protein_162139..162289_POSITIVE 292 46 5 87 43 NC_009009:SSA_0983|3end_Conserved_uncharacterized_protein_986945..987095_POSITIVE 289 42 1 149 102 NC_009009:SSA_1822|3end_hypothetical_protein_1810871..1811021_NEGATIVE 274 60 19 121 77 NC_009009:SSA_1905|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1899276..1899426_NEGATIVE 272 42 1 122 84 NC_009009:SSA_1439|3end_hypothetical_protein_1443624..1443774_NEGATIVE 271 40 1 56 5 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 248 42 6 134 91 NC_009009:SSA_1746|3end_hypothetical_protein_1732292..1732442_NEGATIVE 246 45 5 104 62 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 244 43 8 142 106 NC_009009:SSA_1665|3end_hypothetical_protein_1665222..1665372_NEGATIVE 242 58 16 69 20 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 242 42 2 124 87 NC_009009:SSA_0620|3end_hypothetical_protein_611951..612101_NEGATIVE 240 65 36 100 70 NC_009009:SSA_0691|3end_D-ala,D-ala_ligase,_putative_676374..676524_POSITIVE 238 49 15 42 13 NC_009009:SSA_1303|3end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322474..1322624_NEGATIVE 237 46 1 116 71 NC_009009:SSA_1230|3end_Conserved_uncharacterized_protein_1252612..1252762_NEGATIVE 235 65 22 49 1 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 231 46 4 48 1 NC_009009:SSA_0421|3end_Phosphoglycerate_mutase_family_protein,_putative_420240..420390_POSITIVE 230 48 18 34 1 NC_009009:SSA_0158|3end_hypothetical_protein_155074..155224_POSITIVE 229 46 1 58 4 NC_009009:SSA_2086|3end_hypothetical_protein_2090397..2090547_NEGATIVE 227 49 5 67 22 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 227 40 2 132 94 NC_009009:SSA_1107|3end_Lipid/multidrug/protein-type_ABC_exporter,_ATP_binding/membrane-spanning_protein,_putative_1133784..1133934_POSITIVE