Origin IGS: tggattctccttatttttactaaaatctgtcctgacatcagaacaggataaacaatggtcgtagaaacgataaaaattgtctcatatctattataagaaaattatccctatatcgcaagatagggataatctcatcggatactttctgaggcttttattcatttgaacttttgcttcatcaagtagaaaaaaacattttataatcaatgaaaatctaagggcaaactagaaagctagctaaggactgaattgaccacagtaaggaagagctgacaagttttgaaagattttcaaagaata .........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 tattctttgaaaatctttcaaaacttgtcagctcttccttactgtggtcaattcagtccttagctagctttctagtttgcccttagattttcattgattataaaatgtttttttctacttgatgaagcaaaagttcaaatgaataaaagcctcagaaagtatccgatgagattatccctatcttgcgatatagggataattttcttataatagatatgagacaatttttatcgtttctacgaccattgtttatcctgttctgatgtcaggacagattttagtaaaaataaggagaatcca Mask Tandem Repeat Region ================================================ tggattctccttatttttactaaaatctgtcctgacatcagaacaggataaacaatggtcgtagaaacgataaaaattgtctcatatctattataagaaaattatccctatatcgcaagatagggataatctcatcggatactttctgaggcttttattcatttgaacttttgcttcatcaagtagaaaaaaacattttataatcaatgaaaatctaagggcaaactagaaagctagctaaggactgaattgaccacagtaaggaagagctgacaagttttgaaagattttcaaagaata Find is-nt database================================================ Query_seq: SSA_2075:SSA_2076|SSA_2075:SSA_2076:Transketolase, putative:Conserved uncharacterized protein:<-<-:2079180..2079479 300 tggattctccttatttttactaaaatctgtcctgacatcagaacaggataaacaatggtcgtagaaacgataaaaattgtctcatatctattataagaaaattatccctatatcgcaagatagggataatctcatcggatactttctgaggcttttattcatttgaacttttgcttcatcaagtagaaaaaaacattttataatcaatgaaaatctaagggcaaactagaaagctagctaaggactgaattgaccacagtaaggaagagctgacaagttttgaaagattttcaaagaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2075:SSA_2076|SSA_2075:SSA_2076:Transketolase, putative:Conserved uncharacterized protein:<-<-:2079180..2079479 300 tggattctccttatttttactaaaatctgtcctgacatcagaacaggataaacaatggtcgtagaaacgataaaaattgtctcatatctattataagaaaattatccctatatcgcaagatagggataatctcatcggatactttctgaggcttttattcatttgaacttttgcttcatcaagtagaaaaaaacattttataatcaatgaaaatctaagggcaaactagaaagctagctaaggactgaattgaccacagtaaggaagagctgacaagttttgaaagattttcaaagaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2075:SSA_2076|SSA_2075:SSA_2076:Transketolase, putative:Conserved uncharacterized protein:<-<-:2079180..2079479 300 tggattctccttatttttactaaaatctgtcctgacatcagaacaggataaacaatggtcgtagaaacgataaaaattgtctcatatctattataagaaaattatccctatatcgcaagatagggataatctcatcggatactttctgaggcttttattcatttgaacttttgcttcatcaagtagaaaaaaacattttataatcaatgaaaatctaagggcaaactagaaagctagctaaggactgaattgaccacagtaaggaagagctgacaagttttgaaagattttcaaagaata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tggattctccttatttttactaaaatctgtcctgacatcagaacaggataaacaatggtcgtagaaacgataaaaattgtctcatatctattataagaaaattatccctatatcgcaagatagggataatctcatcggatactttctgaggcttttattcatttgaacttttgcttcatcaagtagaaaaaaacattttataatcaatgaaaatctaagggcaaactagaaagctagctaaggactgaattgaccacagtaaggaagagctgacaagttttgaaagattttcaaagaata Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 48 End: 146 ............................................... M N N G R R N D K N C L I S I I R K L S L Y R K I G I I S S D T F .......................................................................................................................................................... Protein_Len: 38 Strand: - Start: 94 End: 207 ............................................................................................. L F I I G I D C S L S L R M P Y K R L S K N M Q V K A E D L L F F C K I I M ............................................................................................. Protein_Len: 30 Strand: - Start: 41 End: 130 ........................................ F L I F L P R L F S L F Q R M D I I L F N D R Y R L I P I M .......................................................................................................................................................................... tggattctccttatttttactaaaatctgtcctgacatcagaacaggataaacaatggtcgtagaaacgataaaaattgtctcatatctattataagaaaattatccctatatcgcaagatagggataatctcatcggatactttctgaggcttttattcatttgaacttttgcttcatcaagtagaaaaaaacattttataatcaatgaaaatctaagggcaaactagaaagctagctaaggactgaattgaccacagtaaggaagagctgacaagttttgaaagattttcaaagaata 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: 89 Start: 90 End: 119 .........................................................................................CTTGCGATATAGGGATAATTTTCTTATAAT..................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tggattctccttatttttactaaaatctgtcctgacatcagaacaggataaacaatggtcgtagaaacgataaaaattgtctcatatctattataagaaaattatccctatatcgcaagatagggataatctcatcggatactttctgaggcttttattcatttgaacttttgcttcatcaagtagaaaaaaacattttataatcaatgaaaatctaagggcaaactagaaagctagctaaggactgaattgaccacagtaaggaagagctgacaagttttgaaagattttcaaagaata Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 72 HP_score: -8.6 Tail_Score: -3.15324 Start: 27 End: 46 Full_Region: cgaccattgtttatc ctgttctg atgt caggacag attttagtaaaaata ..........................ctgttctgatgtcaggacag.............................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 71 HP_score: -8.6 Tail_Score: -2.80291 Start: 102 End: 129 Full_Region: TCTATTATAAGAAAA TTATCCCTATAT CGCA AGATAGGGATAA TCTCATCGGATACTT .....................................................................................................TTATCCCTATATCGCAAGATAGGGATAA........................................................................................................................................................................... TransTerm Strand: - Conf: 93 HP_score: -8.6 Tail_Score: -4.81212 Start: 102 End: 129 Full_Region: aagtatccgatgaga ttatccctatct tgcg atatagggataa ttttcttataataga .....................................................................................................ttatccctatcttgcgatatagggataa........................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_2075:SSA_2076|SSA_2075:SSA_2076:Transketolase, putative:Conserved uncharacterized protein:<-<-:2079180..2079479 300 tggattctccttatttttactaaaatctgtcctgacatcagaacaggataaacaatggtcgtagaaacgataaaaattgtctcatatctattataagaaaattatccctatatcgcaagatagggataatctcatcggatactttctgaggcttttattcatttgaacttttgcttcatcaagtagaaaaaaacattttataatcaatgaaaatctaagggcaaactagaaagctagctaaggactgaattgaccacagtaaggaagagctgacaagttttgaaagattttcaaagaata Intra-Species Hit: Count: 1 Min: 1 Max: 300 Len: 300 Subject: NC_009009_SSA_2075_SSA_2076|Transketolase, putative:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[2079180,2079479]|300 HSP 1 e-value: 1.0E-156 bit: 553.0 Len: 300 Query Start:1 Query End:300 Subject Strand: POSITIVE Subject Start: 1 Subject End: 300 tggattctccttatttttactaaaatctgtcctgacatcagaacaggataaacaatggtcgtagaaacgataaaaattgtctcatatctattataagaaaattatccctatatcgcaagatagggataatctcatcggatactttctgaggcttttattcatttgaacttttgcttcatcaagtagnnnnnnncattttataatcaatgaaaatctaagggcaaactagaaagctagctaaggactgaattgaccacagtaaggaagagctgacaagttttgaaagattttcaaagaata tggattctccttatttttactaaaatctgtcctgacatcagaacaggataaacaatggtcgtagaaacgataaaaattgtctcatatctattataagaaaattatccctatatcgcaagatagggataatctcatcggatactttctgaggcttttattcatttgaacttttgcttcatcaagtagaaaaaaacattttataatcaatgaaaatctaagggcaaactagaaagctagctaaggactgaattgaccacagtaaggaagagctgacaagttttgaaagattttcaaagaata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGAUUCUCCUUAUUUUUACUAAAAUCUGUCCUGACAUCAGAACAGGAUAAACAAUGGUCGUAGAAACGAUAAAAAUUGUCUCAUAUCUAUUAUAAGAAAAUUAUCCCUAUAUCGCAAGAUAGGGAUAAUCUCAUCGGAUACUUUCUGAGGCUUUUAUUCAUUUGAACUUUUGCUUCAUCAAGUAGAAAAAAACAUUUUAUAAUCAAUGAAAAUCUAAGGGCAAACUAGAAAGCUAGCUAAGGACUGAAUUGACCACAGUAAGGAAGAGCUGACAAGUUUUGAAAGAUUUUCAAAGAAUA ...(((((.................(((((.(((....))).)))))....(((((.(((((....)))))....))))).........(((((((((..((((((((((..((....)))))))))))).........(((((..((((((.....(((....))).....))))))..)))))..........)))))))))...(((((((((......(((((.(..((((..((....((((.........))))..))...))))..).)))))....))))))))).))))). (-66.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUCUUUGAAAAUCUUUCAAAACUUGUCAGCUCUUCCUUACUGUGGUCAAUUCAGUCCUUAGCUAGCUUUCUAGUUUGCCCUUAGAUUUUCAUUGAUUAUAAAAUGUUUUUUUCUACUUGAUGAAGCAAAAGUUCAAAUGAAUAAAAGCCUCAGAAAGUAUCCGAUGAGAUUAUCCCUAUCUUGCGAUAUAGGGAUAAUUUUCUUAUAAUAGAUAUGAGACAAUUUUUAUCGUUUCUACGACCAUUGUUUAUCCUGUUCUGAUGUCAGGACAGAUUUUAGUAAAAAUAAGGAGAAUCCA ...((..(((((((((....(((((.(..((((((.....((((.........))))....))..))))..).)))))......)))))))))..))........((..(((((((((((..(((.((....((((....))))....)).)))..))))...(((((.((((((((((((........)))))))))))).(((((((.....))))))).........((((....)))).)))))......((((((((....))))))))...............)))))))..)) (-68.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 851 70 21 161 112 NC_009009:SSA_2075|5end_Transketolase,_putative_2079089..2079319_NEGATIVE 301 67 26 78 35 NC_009009:SSA_0947|5end_hypothetical_protein_954203..954433_POSITIVE 294 252 212 228 190 NC_009009:SSA_0409|5end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_405605..405835_NEGATIVE 291 279 233 53 10 NC_009009:SSA_1371|5end_FmtA-like_protein,_putative_1388832..1389062_NEGATIVE 290 277 232 168 120 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 290 259 227 69 34 NC_009009:SSA_1413|5end_GufA-like_protein,_putative_1424919..1425149_NEGATIVE 284 50 1 47 4 NC_009009:SSA_0986|5end_Choline_transporter,_putative_988273..988503_POSITIVE 284 285 241 65 20 NC_009009:SSA_0488|5end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_488364..488594_POSITIVE 280 276 233 54 17 NC_009009:SSA_0092|5end_V-type_sodium_ATPase,_subunit_B,_putative_92895..93125_POSITIVE 278 247 218 103 72 NC_009009:SSA_2039|5end_Aminoacid_specific_permease,_putative_2044455..2044685_NEGATIVE 277 280 233 188 145 NC_009009:SSA_1649|5end_hypothetical_protein_1648886..1649116_NEGATIVE 272 107 66 190 151 NC_009009:SSA_0473|5end_Precorrin-6x_reductase,_putative_475502..475732_POSITIVE 270 265 221 59 21 NC_009009:SSA_1922|5end_hypothetical_protein_1912106..1912336_NEGATIVE 267 62 29 67 31 NC_009009:SSA_1632|5end_Surface_protein,_putative_1634045..1634275_NEGATIVE 267 180 132 100 54 NC_009009:SSA_0973|5end_hypothetical_protein_980296..980526_POSITIVE 267 68 24 85 47 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 266 270 224 199 149 NC_009009:SSA_2281|5end_hypothetical_protein_2282370..2282600_NEGATIVE 266 66 24 60 17 NC_009009:SSA_1051|5end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1065658..1065888_POSITIVE 263 120 71 206 154 NC_009009:SSA_0240|5end_Acetyltransferase,_GNAT_family,_putative_233410..233640_POSITIVE 261 249 211 68 33 NC_009009:SSA_0375|5end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_364257..364487_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 270 221 110 54 NC_009009:SSA_1793|3end_Histidine_kinase_(sensor_protein),_putative_1775126..1775276_NEGATIVE 294 252 212 83 45 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 290 259 227 46 11 NC_009009:SSA_1414|3end_hypothetical_protein_1424942..1425092_NEGATIVE 280 276 233 67 30 NC_009009:SSA_0091|3end_V-type_sodium_ATPase,_subunit_A,_putative_92988..93138_POSITIVE 270 265 221 45 7 NC_009009:SSA_1923|3end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912120..1912270_NEGATIVE 269 274 232 143 107 NC_009009:SSA_1126|3end_Thiamine_biosynthesis_lipoprotein,_putative_1150587..1150737_NEGATIVE 267 180 132 88 42 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 267 68 24 59 21 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 266 66 24 63 20 NC_009009:SSA_1050|3end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1065741..1065891_POSITIVE 259 178 141 133 103 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 256 48 15 140 114 NC_009009:SSA_0331|3end_C3-degrading_proteinase,_putative_325992..326142_POSITIVE 255 48 6 146 96 NC_009009:SSA_2279|3end_hypothetical_protein_2281671..2281821_NEGATIVE 252 176 134 105 68 NC_009009:SSA_0587|3end_Metal-dependent_amidase/aminoacylase/carboxypeptidase,_putative_579761..579911_POSITIVE 251 249 206 73 35 NC_009009:SSA_1854|3end_Conserved_uncharacterized_protein_1849433..1849583_NEGATIVE 250 47 1 138 83 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 250 62 27 77 45 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 249 286 241 49 13 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 247 273 237 54 15 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 247 153 120 51 16 NC_009009:SSA_1462|3end_Prephenate_dehydratase,_putative_1468934..1469084_NEGATIVE 244 179 136 83 40 NC_009009:SSA_0909|3end_Transcriptional_regulator,_AbrB_family_(stationary/sporulation_gene_expression),_putative_921158..921308_POSITIVE