Origin IGS: aaattatattataccaaagattgtgaaaattctcaaagtatattttacatttgaattaataaaagatttcacaaacaagtgcaaaacgaccataaacctctccatagagaggataaggcttttatagaaatattacaatttcgccgatttaaaatatctcaaatgcggctcaaattttccttaactggagaaattatgttagacttagaggagaaaatttttaggaaataagacaagcaaggcagagaggtatattaccacaaaaaacctctcagaactatcttcaagatttctgagaggttgttcattcattcagaaatattccaaatagtatctgaaa .........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 tttcagatactatttggaatatttctgaatgaatgaacaacctctcagaaatcttgaagatagttctgagaggttttttgtggtaatatacctctctgccttgcttgtcttatttcctaaaaattttctcctctaagtctaacataatttctccagttaaggaaaatttgagccgcatttgagatattttaaatcggcgaaattgtaatatttctataaaagccttatcctctctatggagaggtttatggtcgttttgcacttgtttgtgaaatcttttattaattcaaatgtaaaatatactttgagaattttcacaatctttggtataatataattt Mask Tandem Repeat Region ================================================ aaattatattataccaaagattgtgaaaattctcaaagtatattttacatttgaattaataaaagatttcacaaacaagtgcaaaacgaccataaacctctccatagagaggataaggcttttatagaaatattacaatttcgccgatttaaaatatctcaaatgcggctcaaattttccttaactggagaaattatgttagacttagaggagaaaatttttaggaaataagacaagcaaggcagagaggtatattaccacaaaaaacctctcagaactatcttcaagatttctgagaggttgttcattcattcagaaatattccaaatagtatctgaaa Find is-nt database================================================ Query_seq: SSA_1471:SSA_1472|SSA_1471:SSA_1472:hypothetical protein:hypothetical protein:<-<-:1478235..1478574 340 aaattatattataccaaagattgtgaaaattctcaaagtatattttacatttgaattaataaaagatttcacaaacaagtgcaaaacgaccataaacctctccatagagaggataaggcttttatagaaatattacaatttcgccgatttaaaatatctcaaatgcggctcaaattttccttaactggagaaattatgttagacttagaggagaaaatttttaggaaataagacaagcaaggcagagaggtatattaccacaaaaaacctctcagaactatcttcaagatttctgagaggttgttcattcattcagaaatattccaaatagtatctgaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1471:SSA_1472|SSA_1471:SSA_1472:hypothetical protein:hypothetical protein:<-<-:1478235..1478574 340 aaattatattataccaaagattgtgaaaattctcaaagtatattttacatttgaattaataaaagatttcacaaacaagtgcaaaacgaccataaacctctccatagagaggataaggcttttatagaaatattacaatttcgccgatttaaaatatctcaaatgcggctcaaattttccttaactggagaaattatgttagacttagaggagaaaatttttaggaaataagacaagcaaggcagagaggtatattaccacaaaaaacctctcagaactatcttcaagatttctgagaggttgttcattcattcagaaatattccaaatagtatctgaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1471:SSA_1472|SSA_1471:SSA_1472:hypothetical protein:hypothetical protein:<-<-:1478235..1478574 340 aaattatattataccaaagattgtgaaaattctcaaagtatattttacatttgaattaataaaagatttcacaaacaagtgcaaaacgaccataaacctctccatagagaggataaggcttttatagaaatattacaatttcgccgatttaaaatatctcaaatgcggctcaaattttccttaactggagaaattatgttagacttagaggagaaaatttttaggaaataagacaagcaaggcagagaggtatattaccacaaaaaacctctcagaactatcttcaagatttctgagaggttgttcattcattcagaaatattccaaatagtatctgaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaattatattataccaaagattgtgaaaattctcaaagtatattttacatttgaattaataaaagatttcacaaacaagtgcaaaacgaccataaacctctccatagagaggataaggcttttatagaaatattacaatttcgccgatttaaaatatctcaaatgcggctcaaattttccttaactggagaaattatgttagacttagaggagaaaatttttaggaaataagacaagcaaggcagagaggtatattaccacaaaaaacctctcagaactatcttcaagatttctgagaggttgttcattcattcagaaatattccaaatagtatctgaaa Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 8 End: 124 ....... M I P K I V K I L K V Y F T F E L I K D F T N K C K T T I N L S I E R I R L L ........................................................................................................................................................................................................................ Protein_Len: 58 Strand: + Start: 55 End: 228 ...................................................... M N K R F H K Q V Q N D H K P L H R E D K A F I E I L Q F R R F K I S Q M R L K F S L T G E I M L D L E E K I F R K ................................................................................................................ Protein_Len: 35 Strand: - Start: 208 End: 312 ............................................................................................................................................................................................................... L L F N K P F L V L L A S L Y I V V F F R E S S D E L N R L P Q E N M ............................ Protein_Len: 36 Strand: - Start: 7 End: 114 ...... I I G F I T F I R L T Y K V N S N I F S K V F L H L V V M F R E M S L M .................................................................................................................................................................................................................................. aaattatattataccaaagattgtgaaaattctcaaagtatattttacatttgaattaataaaagatttcacaaacaagtgcaaaacgaccataaacctctccatagagaggataaggcttttatagaaatattacaatttcgccgatttaaaatatctcaaatgcggctcaaattttccttaactggagaaattatgttagacttagaggagaaaatttttaggaaataagacaagcaaggcagagaggtatattaccacaaaaaacctctcagaactatcttcaagatttctgagaggttgttcattcattcagaaatattccaaatagtatctgaaa 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: 92 Start: 8 End: 37 .......TTTGAGAATTTTCACAATCTTTGGTATAAT............................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaattatattataccaaagattgtgaaaattctcaaagtatattttacatttgaattaataaaagatttcacaaacaagtgcaaaacgaccataaacctctccatagagaggataaggcttttatagaaatattacaatttcgccgatttaaaatatctcaaatgcggctcaaattttccttaactggagaaattatgttagacttagaggagaaaatttttaggaaataagacaagcaaggcagagaggtatattaccacaaaaaacctctcagaactatcttcaagatttctgagaggttgttcattcattcagaaatattccaaatagtatctgaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 83 HP_score: -9.0 Tail_Score: -4.05816 Start: 97 End: 112 Full_Region: ctataaaagccttat cctctc tatg gagagg tttatggtcgttttg ................................................................................................cctctctatggagagg.................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 93 HP_score: -8.5 Tail_Score: -5.32882 Start: 268 End: 300 Full_Region: tgaatgaatgaacaa cctctcagaaatctt gaa gatagttctgagagg ttttttgtggtaata ...........................................................................................................................................................................................................................................................................cctctcagaaatcttgaagatagttctgagagg........................................ Find igs database================================================ Query_seq: SSA_1471:SSA_1472|SSA_1471:SSA_1472:hypothetical protein:hypothetical protein:<-<-:1478235..1478574 340 aaattatattataccaaagattgtgaaaattctcaaagtatattttacatttgaattaataaaagatttcacaaacaagtgcaaaacgaccataaacctctccatagagaggataaggcttttatagaaatattacaatttcgccgatttaaaatatctcaaatgcggctcaaattttccttaactggagaaattatgttagacttagaggagaaaatttttaggaaataagacaagcaaggcagagaggtatattaccacaaaaaacctctcagaactatcttcaagatttctgagaggttgttcattcattcagaaatattccaaatagtatctgaaa Intra-Species Hit: Count: 1 Min: 1 Max: 340 Len: 340 Subject: NC_009009_SSA_1471_SSA_1472|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1478235,1478574]|340 HSP 1 e-value: 0.0 bit: 674.0 Len: 340 Query Start:1 Query End:340 Subject Strand: POSITIVE Subject Start: 1 Subject End: 340 aaattatattataccaaagattgtgaaaattctcaaagtatattttacatttgaattaataaaagatttcacaaacaagtgcaaaacgaccataaacctctccatagagaggataaggcttttatagaaatattacaatttcgccgatttaaaatatctcaaatgcggctcaaattttccttaactggagaaattatgttagacttagaggagaaaatttttaggaaataagacaagcaaggcagagaggtatattaccacaaaaaacctctcagaactatcttcaagatttctgagaggttgttcattcattcagaaatattccaaatagtatctgaaa aaattatattataccaaagattgtgaaaattctcaaagtatattttacatttgaattaataaaagatttcacaaacaagtgcaaaacgaccataaacctctccatagagaggataaggcttttatagaaatattacaatttcgccgatttaaaatatctcaaatgcggctcaaattttccttaactggagaaattatgttagacttagaggagaaaatttttaggaaataagacaagcaaggcagagaggtatattaccacaaaaaacctctcagaactatcttcaagatttctgagaggttgttcattcattcagaaatattccaaatagtatctgaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUAUAUUAUACCAAAGAUUGUGAAAAUUCUCAAAGUAUAUUUUACAUUUGAAUUAAUAAAAGAUUUCACAAACAAGUGCAAAACGACCAUAAACCUCUCCAUAGAGAGGAUAAGGCUUUUAUAGAAAUAUUACAAUUUCGCCGAUUUAAAAUAUCUCAAAUGCGGCUCAAAUUUUCCUUAACUGGAGAAAUUAUGUUAGACUUAGAGGAGAAAAUUUUUAGGAAAUAAGACAAGCAAGGCAGAGAGGUAUAUUACCACAAAAAACCUCUCAGAACUAUCUUCAAGAUUUCUGAGAGGUUGUUCAUUCAUUCAGAAAUAUUCCAAAUAGUAUCUGAAA ......((.((((((..(((((((((......((((((((.....))).)))))....(((((((.((((((......))).)))...........((((((....))))))......))))))).......))))))))).((((((.......))).....(((...((...((((((......))))))...........((((((((......))))))))......))...))).))).....)))))).))........((((((((((((..(((.....))))))))))))))).........((((((..(((.....)))...)))))). (-72.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCAGAUACUAUUUGGAAUAUUUCUGAAUGAAUGAACAACCUCUCAGAAAUCUUGAAGAUAGUUCUGAGAGGUUUUUUGUGGUAAUAUACCUCUCUGCCUUGCUUGUCUUAUUUCCUAAAAAUUUUCUCCUCUAAGUCUAACAUAAUUUCUCCAGUUAAGGAAAAUUUGAGCCGCAUUUGAGAUAUUUUAAAUCGGCGAAAUUGUAAUAUUUCUAUAAAAGCCUUAUCCUCUCUAUGGAGAGGUUUAUGGUCGUUUUGCACUUGUUUGUGAAAUCUUUUAUUAAUUCAAAUGUAAAAUAUACUUUGAGAAUUUUCACAAUCUUUGGUAUAAUAUAAUUU .((((((...(((.....)))..))))))...(..((.(((((((((((((((.....)))..)))))))))))).))..).(((.((((((.....((...))...............(((((((((..............(((((((((((((....((((........((((.(((((((....)))))))))))(((((......))))).............)))).....)))))))).)))))...((((((((.(((...(((((....))))).....))).)))))))).......)))))))))..........)))))).)))..... (-73.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 904 120 71 211 162 NC_009009:SSA_1471|5end_hypothetical_protein_1478144..1478374_NEGATIVE 523 237 194 179 136 NC_009009:SSA_1475|5end_hypothetical_protein_1480121..1480351_NEGATIVE 273 250 222 49 15 NC_009009:SSA_0843|5end_hypothetical_protein_827682..827912_POSITIVE 270 220 171 190 144 NC_009009:SSA_0765|5end_hypothetical_protein_745519..745749_POSITIVE 267 275 231 215 158 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 265 246 201 151 113 NC_009009:SSA_0804|5end_Phosphoglucomutase/phosphomannomutase_family_protein,_putative_785995..786225_POSITIVE 261 325 281 100 62 NC_009009:SSA_0512|5end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_510439..510669_POSITIVE 259 145 106 55 20 NC_009009:SSA_1514|5end_Cell-wall_biogenesis_glycosyltransferase,_putative_1521780..1522010_NEGATIVE 259 144 102 187 144 NC_009009:SSA_0338|5end_Hydroxymethylglutaryl-CoA_synthase,_putative_333338..333568_NEGATIVE 254 275 234 206 151 NC_009009:SSA_0701|5end_Cation_transporter_CorA_family,_putative_684368..684598_POSITIVE 253 252 223 35 9 NC_009009:SSA_2335|5end_D-Ala-teichoic_acid_biosynthesis_protein,_putative_2338158..2338388_NEGATIVE 253 252 223 186 160 NC_009009:SSA_2334|5end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2338007..2338237_NEGATIVE 252 119 72 89 40 NC_009009:SSA_1789|5end_Metal-dependent_phosphohydrolase,_HD_superfamily,_putative_1772856..1773086_NEGATIVE 252 319 271 211 168 NC_009009:SSA_0461|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_463059..463289_POSITIVE 250 276 232 225 162 NC_009009:SSA_1679|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1673049..1673279_NEGATIVE 250 190 141 112 66 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 247 179 136 158 110 NC_009009:SSA_1564|5end_Histidine_kinase,_putative_1568615..1568845_NEGATIVE 242 317 272 68 21 NC_009009:SSA_1558|5end_Hydrolase,_HAD_superfamily_1560862..1561092_NEGATIVE 240 203 164 71 32 NC_009009:SSA_1400|5end_Pyridoxal_kinase,_putative_1413072..1413302_NEGATIVE 239 208 163 45 8 NC_009009:SSA_2137|5end_hypothetical_protein_2138412..2138642_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 273 250 222 77 43 NC_009009:SSA_0842|3end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827790..827940_POSITIVE 266 250 210 57 9 NC_009009:SSA_1048|3end_ABC_transporter_ATP-binding_protein-spermidine/putrescine_transport,_putative_1064184..1064334_POSITIVE 265 246 201 56 18 NC_009009:SSA_0803|3end_hypothetical_protein_785980..786130_POSITIVE 263 318 271 146 94 NC_009009:SSA_1327|3end_hypothetical_protein_1343750..1343900_NEGATIVE 262 127 86 139 93 NC_009009:SSA_1314|3end_Fe-S-cluster_oxidoreductase,_putative_1330746..1330896_NEGATIVE 261 325 281 137 99 NC_009009:SSA_0511|3end_Propanediol_utilization_kinase,_putative_510556..510706_POSITIVE 259 145 106 65 30 NC_009009:SSA_1515|3end_hypothetical_protein_1521770..1521920_NEGATIVE 250 276 232 74 11 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE 250 190 141 59 13 NC_009009:SSA_0679|3end_DNA_repair_and_genetic_recombination,_putative_662452..662602_POSITIVE 243 249 205 56 18 NC_009009:SSA_0739|3end_Carbamate_kinase,_putative_722114..722264_POSITIVE 242 317 272 68 21 NC_009009:SSA_1559|3end_Conserved_uncharacterized_protein_1560862..1561012_NEGATIVE 241 247 207 71 33 NC_009009:SSA_1916|3end_hypothetical_protein_1906379..1906529_POSITIVE 241 313 272 68 23 NC_009009:SSA_0913|3end_Acetyltransferase,_putative_924784..924934_POSITIVE 240 147 106 140 94 NC_009009:SSA_0725|3end_hypothetical_protein_710812..710962_POSITIVE 238 308 269 123 75 NC_009009:SSA_1550|3end_hypothetical_protein_1552228..1552378_NEGATIVE 238 179 139 53 13 NC_009009:SSA_0009|3end_Ribosome-associated_heat_shock_protein_(S4),_putative_9511..9661_POSITIVE 237 120 78 69 31 NC_009009:SSA_0674|3end_Exodeoxyribonuclease_VII_large_subunit,_putative_658491..658641_POSITIVE 231 305 268 123 79 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 230 160 114 78 39 NC_009009:SSA_1790|3end_SpoU_rRNA_Methylase_family_protein,_putative_1772901..1773051_NEGATIVE 226 123 88 130 87 NC_009009:SSA_1318|3end_GTP-binding_protein_lepA,_putative_1333989..1334139_NEGATIVE