Origin IGS: ttttatctccttaaataataagtaatttcattatagaataaaactaatgagctgtcaaaaatctaactgttttttaaagaaatcaaaaattcctatttttcctccttgaattaatttgaaaactttatagtattaaaaacaagcaactacttttatgataaaagggtatatatttttatcgtttttcgatatgtttttcttgaaatacaataaaaaatagattataataagaataaaaggaaaagaaaatctactgccggctgattttcgatagaggtaagcatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatgcttacctctatcgaaaatcagccggcagtagattttcttttccttttattcttattataatctattttttattgtatttcaagaaaaacatatcgaaaaacgataaaaatatatacccttttatcataaaagtagttgcttgtttttaatactataaagttttcaaattaattcaaggaggaaaaataggaatttttgatttctttaaaaaacagttagatttttgacagctcattagttttattctataatgaaattacttattatttaaggagataaaa Mask Tandem Repeat Region ================================================ ttttatctccttaaataataagtaatttcattatagaataaaactaatgagctgtcaaaaatctaactgttttttaaagaaatcaaaaattcctatttttcctccttgaattaatttgaaaactttatagtattaaaaacaagcaactacttttatgataaaagggtatatatttttatcgtttttcgatatgtttttcttgaaatacaataaaaaatagattataataagaataaaaggaaaagaaaatctactgccggctgattttcgatagaggtaagcatc Find is-nt database================================================ Query_seq: SSA_1689:SSA_1690|SSA_1689:SSA_1690:hypothetical protein:hypothetical protein:<-->:1682596..1682880 285 ttttatctccttaaataataagtaatttcattatagaataaaactaatgagctgtcaaaaatctaactgttttttaaagaaatcaaaaattcctatttttcctccttgaattaatttgaaaactttatagtattaaaaacaagcaactacttttatgataaaagggtatatatttttatcgtttttcgatatgtttttcttgaaatacaataaaaaatagattataataagaataaaaggaaaagaaaatctactgccggctgattttcgatagaggtaagcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1689:SSA_1690|SSA_1689:SSA_1690:hypothetical protein:hypothetical protein:<-->:1682596..1682880 285 ttttatctccttaaataataagtaatttcattatagaataaaactaatgagctgtcaaaaatctaactgttttttaaagaaatcaaaaattcctatttttcctccttgaattaatttgaaaactttatagtattaaaaacaagcaactacttttatgataaaagggtatatatttttatcgtttttcgatatgtttttcttgaaatacaataaaaaatagattataataagaataaaaggaaaagaaaatctactgccggctgattttcgatagaggtaagcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1689:SSA_1690|SSA_1689:SSA_1690:hypothetical protein:hypothetical protein:<-->:1682596..1682880 285 ttttatctccttaaataataagtaatttcattatagaataaaactaatgagctgtcaaaaatctaactgttttttaaagaaatcaaaaattcctatttttcctccttgaattaatttgaaaactttatagtattaaaaacaagcaactacttttatgataaaagggtatatatttttatcgtttttcgatatgtttttcttgaaatacaataaaaaatagattataataagaataaaaggaaaagaaaatctactgccggctgattttcgatagaggtaagcatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttatctccttaaataataagtaatttcattatagaataaaactaatgagctgtcaaaaatctaactgttttttaaagaaatcaaaaattcctatttttcctccttgaattaatttgaaaactttatagtattaaaaacaagcaactacttttatgataaaagggtatatatttttatcgtttttcgatatgtttttcttgaaatacaataaaaaatagattataataagaataaaaggaaaagaaaatctactgccggctgattttcgatagaggtaagcatc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 136 End: 234 ....................................................................................................................................... F C A V V K I I F P Y I N K D N K S I N K K F Y L L F Y I I I L M ................................................... ttttatctccttaaataataagtaatttcattatagaataaaactaatgagctgtcaaaaatctaactgttttttaaagaaatcaaaaattcctatttttcctccttgaattaatttgaaaactttatagtattaaaaacaagcaactacttttatgataaaagggtatatatttttatcgtttttcgatatgtttttcttgaaatacaataaaaaatagattataataagaataaaaggaaaagaaaatctactgccggctgattttcgatagaggtaagcatc 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: 93 Start: 30 End: 59 .............................TTTGACAGCTCATTAGTTTTATTCTATAAT.................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 89 Start: 199 End: 228 ......................................................................................................................................................................................................CTTGAAATACAATAAAAAATAGATTATAAT......................................................... PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 221 End: 250 ............................................................................................................................................................................................................................ATTTTCTTTTCCTTTTATTCTTATTATAAT................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 10 End: 39 .........CTTAAATAATAAGTAATTTCATTATAGAAT...................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttatctccttaaataataagtaatttcattatagaataaaactaatgagctgtcaaaaatctaactgttttttaaagaaatcaaaaattcctatttttcctccttgaattaatttgaaaactttatagtattaaaaacaagcaactacttttatgataaaagggtatatatttttatcgtttttcgatatgtttttcttgaaatacaataaaaaatagattataataagaataaaaggaaaagaaaatctactgccggctgattttcgatagaggtaagcatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1689:SSA_1690|SSA_1689:SSA_1690:hypothetical protein:hypothetical protein:<-->:1682596..1682880 285 ttttatctccttaaataataagtaatttcattatagaataaaactaatgagctgtcaaaaatctaactgttttttaaagaaatcaaaaattcctatttttcctccttgaattaatttgaaaactttatagtattaaaaacaagcaactacttttatgataaaagggtatatatttttatcgtttttcgatatgtttttcttgaaatacaataaaaaatagattataataagaataaaaggaaaagaaaatctactgccggctgattttcgatagaggtaagcatc Intra-Species Hit: Count: 1 Min: 1 Max: 285 Len: 285 Subject: NC_009009_SSA_1689_SSA_1690|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1682596,1682880]|285 HSP 1 e-value: 1.0E-110 bit: 398.0 Len: 201 Query Start:1 Query End:201 Subject Strand: POSITIVE Subject Start: 1 Subject End: 201 ttttatctccttaaataataagtaatttcattatagaataaaactaatgagctgtcaaaaatctaactgttttttaaagaaatcaaaaattcctatttttcctccttgaattaatttgaaaactttatagtattaaaaacaagcaactacttttatgataaaagggtatatatttttatcgtttttcgatatgtttttctt.................................................................................... ttttatctccttaaataataagtaatttcattatagaataaaactaatgagctgtcaaaaatctaactgttttttaaagaaatcaaaaattcctatttttcctccttgaattaatttgaaaactttatagtattaaaaacaagcaactacttttatgataaaagggtatatatttttatcgtttttcgatatgtttttctt.................................................................................... HSP 2 e-value: 5.0E-11 bit: 69.9 Len: 35 Query Start:251 Query End:285 Subject Strand: POSITIVE Subject Start: 251 Subject End: 285 ..........................................................................................................................................................................................................................................................ctactgccggctgattttcgatagaggtaagcatc ..........................................................................................................................................................................................................................................................ctactgccggctgattttcgatagaggtaagcatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUCUCCUUAAAUAAUAAGUAAUUUCAUUAUAGAAUAAAACUAAUGAGCUGUCAAAAAUCUAACUGUUUUUUAAAGAAAUCAAAAAUUCCUAUUUUUCCUCCUUGAAUUAAUUUGAAAACUUUAUAGUAUUAAAAACAAGCAACUACUUUUAUGAUAAAAGGGUAUAUAUUUUUAUCGUUUUUCGAUAUGUUUUUCUUGAAAUACAAUAAAAAAUAGAUUAUAAUAAGAAUAAAAGGAAAAGAAAAUCUACUGCCGGCUGAUUUUCGAUAGAGGUAAGCAUC .((((((((.................(((((((...........))))))).((((.((((((...((((((((((......((((((((((...............)))))..)))))..........(((((..((..(((((.........((((((((((........)))))))))).........)))))...))..)))))..))))))))))..................((...((........)).))....)))))).)))))))))))).... (-38.03) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGCUUACCUCUAUCGAAAAUCAGCCGGCAGUAGAUUUUCUUUUCCUUUUAUUCUUAUUAUAAUCUAUUUUUUAUUGUAUUUCAAGAAAAACAUAUCGAAAAACGAUAAAAAUAUAUACCCUUUUAUCAUAAAAGUAGUUGCUUGUUUUUAAUACUAUAAAGUUUUCAAAUUAAUUCAAGGAGGAAAAAUAGGAAUUUUUGAUUUCUUUAAAAAACAGUUAGAUUUUUGACAGCUCAUUAGUUUUAUUCUAUAAUGAAAUUACUUAUUAUUUAAGGAGAUAAAA ........(((.....(((((((.((.....)).))))))).(((((((((......((((.........((((((.(((((.((((...(((.(((((.....)))))............((((((...))))))..))).)))).....))))).)))))).........))))...)))))))))...)))........(((((((((((.....(((((....))))).......((((((((((....)))))))))).......))))))))))).... (-45.37) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 700 70 21 161 112 NC_009009:SSA_1689|5end_hypothetical_protein_1682505..1682735_NEGATIVE 284 204 165 125 85 NC_009009:SSA_0867|5end_hypothetical_protein_859840..860070_POSITIVE 250 131 97 128 93 NC_009009:SSA_2381|5end_DegP_protein,_putative_2386298..2386528_POSITIVE 243 264 244 144 127 NC_009009:SSA_1625|5end_Lactoylglutathione_lyase,_putative_1626963..1627193_NEGATIVE 241 277 236 44 3 NC_009009:SSA_0608|5end_Macrolide-efflux_protein,_putative_598184..598414_NEGATIVE 241 275 236 227 167 NC_009009:SSA_0238|5end_hypothetical_protein_232481..232711_POSITIVE 236 279 250 223 186 NC_009009:SSA_2323|5end_Transporter,_putative_2327604..2327834_POSITIVE 236 109 62 122 69 NC_009009:SSA_1327|5end_hypothetical_protein_1344301..1344531_NEGATIVE 231 277 239 52 11 NC_009009:SSA_2284|5end_Histidyl-tRNA_synthetase,_putative_2287272..2287502_NEGATIVE 229 130 89 130 86 NC_009009:SSA_2103|5end_hypothetical_protein_2106700..2106930_NEGATIVE 228 278 256 217 197 NC_009009:SSA_0933|5end_Acetyltransferase,_GNAT_family,_putative_942734..942964_POSITIVE 228 185 143 178 133 NC_009009:SSA_0131|5end_30S_ribosomal_protein_S11,_putative_120717..120947_POSITIVE 227 277 244 191 150 NC_009009:SSA_1700|5end_hypothetical_protein_1691288..1691518_NEGATIVE 224 277 248 155 123 NC_009009:SSA_2092|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095975..2096205_NEGATIVE 224 279 251 147 116 NC_009009:SSA_1037|5end_Cytidine_deaminase,_putative_1052118..1052348_POSITIVE 221 189 142 52 11 NC_009009:SSA_2098|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2103617..2103847_NEGATIVE 218 279 242 210 179 NC_009009:SSA_0287|5end_Glycerol_dehydrogenase,_NAD+_dependent,_putative_279528..279758_POSITIVE 217 272 231 207 159 NC_009009:SSA_1636|5end_ABC-type_antibiotic_exporter,_ATPase_component,_putative_1640905..1641135_NEGATIVE 215 264 252 51 39 NC_009009:SSA_0412|5end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_408163..408393_NEGATIVE 214 264 235 47 17 NC_009009:SSA_1275|5end_hypothetical_protein_1297606..1297836_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 278 241 62 27 NC_009009:SSA_1753|3end_Transcriptional_regulator,_GntR_family_(repressor_of_trehalose_operon),_putative_1742740..1742890_POSITIVE 259 279 231 148 108 NC_009009:SSA_2018|3end_hypothetical_protein_2017464..2017614_NEGATIVE 244 279 233 147 93 NC_009009:SSA_0731|3end_Integral_membrane_protein,_putative_715654..715804_POSITIVE 243 264 244 30 13 NC_009009:SSA_1626|3end_DNA_translocase_ftsK,_putative_1627077..1627227_NEGATIVE 236 109 62 81 28 NC_009009:SSA_1328|3end_hypothetical_protein_1344342..1344492_NEGATIVE 229 130 89 74 30 NC_009009:SSA_2105|3end_hypothetical_protein_2106756..2106906_NEGATIVE 224 277 248 125 93 NC_009009:SSA_2093|3end_PTS_system,_membrane_component,_putative_2096005..2096155_NEGATIVE 221 189 142 48 7 NC_009009:SSA_2099|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2103621..2103771_NEGATIVE 219 277 233 65 24 NC_009009:SSA_1453|3end_hypothetical_protein_1459897..1460047_NEGATIVE 217 272 231 95 47 NC_009009:SSA_1638|3end_hypothetical_protein_1641017..1641167_NEGATIVE 216 100 51 48 2 NC_009009:SSA_0172|3end_Transcriptional_regulator,_XRE_family,_putative_169672..169822_POSITIVE 214 264 235 145 115 NC_009009:SSA_1275|3end_hypothetical_protein_1297508..1297658_NEGATIVE 213 204 170 36 1 NC_009009:SSA_0866|3end_Cation-transporting_ATPase,_E1-E_2_family,_putative_859831..859981_POSITIVE 211 178 140 151 108 NC_009009:SSA_0130|3end_30S_ribosomal_protein_S13,_putative_120777..120927_POSITIVE 207 110 68 109 67 NC_009009:SSA_1872|3end_Cell_division_protein,_putative_1868863..1869013_NEGATIVE 206 145 115 83 52 NC_009009:SSA_0623|3end_hypothetical_protein_615080..615230_POSITIVE 205 279 238 118 76 NC_009009:SSA_1993|3end_Conserved_uncharacterized_protein_1990380..1990530_NEGATIVE 204 280 256 69 30 NC_009009:SSA_1201|3end_hypothetical_protein_1226518..1226668_POSITIVE 203 278 237 70 24 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE 202 149 103 53 7 NC_009009:SSA_2041|3end_Leucine-rich_protein,_putative_2045807..2045957_NEGATIVE