Origin IGS: ttgattttcctctttattctagcaacataaactgttacatttataagtaaagtatatcatacggtaatcggtttcacaaaccattttcggcagaaagaaagactttcttttataatacagaaagtaaaaagtcgcggatgtgtactatagatttgaaaaacataactcttttcaaatattttggaaaaatgggtaaaaaagttataataaaagtaattaaaatgtcatacaaaaattgctgacgaagaatcttacgtttaaaatactttttacaagaacgaaaaactgtttcagatttatttgagtaaaagggctgactttgtgaaagcttgtaagctgagattgatggcaggagaaaggaggaggac .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtcctcctcctttctcctgccatcaatctcagcttacaagctttcacaaagtcagcccttttactcaaataaatctgaaacagtttttcgttcttgtaaaaagtattttaaacgtaagattcttcgtcagcaatttttgtatgacattttaattacttttattataacttttttacccatttttccaaaatatttgaaaagagttatgtttttcaaatctatagtacacatccgcgactttttactttctgtattataaaagaaagtctttctttctgccgaaaatggtttgtgaaaccgattaccgtatgatatactttacttataaatgtaacagtttatgttgctagaataaagaggaaaatcaa Mask Tandem Repeat Region ================================================ ttgattttcctctttattctagcaacataaactgttacatttataagtaaagtatatcatacggtaatcggtttcacaaaccattttcggcagaaagaaagactttcttttataatacagaaagtaaaaagtcgcggatgtgtactatagatttgaaaaacataactcttttcaaatattttggaaaaatgggtaaaaaagttataataaaagtaattaaaatgtcatacaaaaattgctgacgaagaatcttacgtttaaaatactttttacaagaacgaaaaactgtttcagatttatttgagtaaaagggctgactttgtgaaagcttgtaagctgagattgatggcaggagaaaggaggaggac Find is-nt database================================================ Query_seq: SSA_0342:SSA_0343|SSA_0342:SSA_0343:Pyruvate formate-lyase, putative:DNA-damage-inducible protein P, putative:<-->:337297..337664 368 ttgattttcctctttattctagcaacataaactgttacatttataagtaaagtatatcatacggtaatcggtttcacaaaccattttcggcagaaagaaagactttcttttataatacagaaagtaaaaagtcgcggatgtgtactatagatttgaaaaacataactcttttcaaatattttggaaaaatgggtaaaaaagttataataaaagtaattaaaatgtcatacaaaaattgctgacgaagaatcttacgtttaaaatactttttacaagaacgaaaaactgtttcagatttatttgagtaaaagggctgactttgtgaaagcttgtaagctgagattgatggcaggagaaaggaggaggac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0342:SSA_0343|SSA_0342:SSA_0343:Pyruvate formate-lyase, putative:DNA-damage-inducible protein P, putative:<-->:337297..337664 368 ttgattttcctctttattctagcaacataaactgttacatttataagtaaagtatatcatacggtaatcggtttcacaaaccattttcggcagaaagaaagactttcttttataatacagaaagtaaaaagtcgcggatgtgtactatagatttgaaaaacataactcttttcaaatattttggaaaaatgggtaaaaaagttataataaaagtaattaaaatgtcatacaaaaattgctgacgaagaatcttacgtttaaaatactttttacaagaacgaaaaactgtttcagatttatttgagtaaaagggctgactttgtgaaagcttgtaagctgagattgatggcaggagaaaggaggaggac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0342:SSA_0343|SSA_0342:SSA_0343:Pyruvate formate-lyase, putative:DNA-damage-inducible protein P, putative:<-->:337297..337664 368 ttgattttcctctttattctagcaacataaactgttacatttataagtaaagtatatcatacggtaatcggtttcacaaaccattttcggcagaaagaaagactttcttttataatacagaaagtaaaaagtcgcggatgtgtactatagatttgaaaaacataactcttttcaaatattttggaaaaatgggtaaaaaagttataataaaagtaattaaaatgtcatacaaaaattgctgacgaagaatcttacgtttaaaatactttttacaagaacgaaaaactgtttcagatttatttgagtaaaagggctgactttgtgaaagcttgtaagctgagattgatggcaggagaaaggaggaggac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttgattttcctctttattctagcaacataaactgttacatttataagtaaagtatatcatacggtaatcggtttcacaaaccattttcggcagaaagaaagactttcttttataatacagaaagtaaaaagtcgcggatgtgtactatagatttgaaaaacataactcttttcaaatattttggaaaaatgggtaaaaaagttataataaaagtaattaaaatgtcatacaaaaattgctgacgaagaatcttacgtttaaaatactttttacaagaacgaaaaactgtttcagatttatttgagtaaaagggctgactttgtgaaagcttgtaagctgagattgatggcaggagaaaggaggaggac Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 43 End: 147 .......................................... M S K V Y H T V I G F T N H F R Q K E R L S F I I Q K V K S R G C V L ............................................................................................................................................................................................................................. Protein_Len: 60 Strand: + Start: 54 End: 239 ..................................................... M S Y G N R F H K P F S A E R K T F F Y N T E S K K S R M C T I D L K N I T L F K Y F G K M G K K V I I K V I K M S Y K ................................................................................................................................. Protein_Len: 60 Strand: - Start: 113 End: 352 ................................................................................................................ L Y K P F I P L F T I I F T I L I D Y L F Q Q R L I K R K F Y K K C S R F V T E S K N S Y F P Q S Q S L K Y A S I S P M ................ Protein_Len: 40 Strand: - Start: 60 End: 179 ........................................................... V T I P K V F W K R C F S L S E K I I C F T F L R P H T S Y I Q F V Y S K E F M ............................................................................................................................................................................................. Protein_Len: 33 Strand: - Start: 22 End: 120 ..................... C C L S N C K Y T F Y I M R Y D T E C V M K P L F F S K R K Y Y M ........................................................................................................................................................................................................................................................ ttgattttcctctttattctagcaacataaactgttacatttataagtaaagtatatcatacggtaatcggtttcacaaaccattttcggcagaaagaaagactttcttttataatacagaaagtaaaaagtcgcggatgtgtactatagatttgaaaaacataactcttttcaaatattttggaaaaatgggtaaaaaagttataataaaagtaattaaaatgtcatacaaaaattgctgacgaagaatcttacgtttaaaatactttttacaagaacgaaaaactgtttcagatttatttgagtaaaagggctgactttgtgaaagcttgtaagctgagattgatggcaggagaaaggaggaggac 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: 83 Start: 204 End: 233 ...........................................................................................................................................................................................................TTTGTATGACATTTTAATTACTTTTATTAT....................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 235 End: 264 ..........................................................................................................................................................................................................................................ATTGCTGACGAAGAATCTTACGTTTAAAAT........................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 51 End: 80 ..................................................TTTGTGAAACCGATTACCGTATGATATACT................................................................................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 179 End: 208 ..................................................................................................................................................................................TTTTGGAAAAATGGGTAAAAAAGTTATAAT................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttgattttcctctttattctagcaacataaactgttacatttataagtaaagtatatcatacggtaatcggtttcacaaaccattttcggcagaaagaaagactttcttttataatacagaaagtaaaaagtcgcggatgtgtactatagatttgaaaaacataactcttttcaaatattttggaaaaatgggtaaaaaagttataataaaagtaattaaaatgtcatacaaaaattgctgacgaagaatcttacgtttaaaatactttttacaagaacgaaaaactgtttcagatttatttgagtaaaagggctgactttgtgaaagcttgtaagctgagattgatggcaggagaaaggaggaggac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 66 HP_score: -4.3 Tail_Score: -4.46212 Start: 93 End: 107 Full_Region: AAACCATTTTCGGCA GAAAG AAAGA CTTTC TTTTATAATACAGAA ............................................................................................GAAAGAAAGACTTTC..................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 40 HP_score: -2.3 Tail_Score: -2.94416 Start: 152 End: 176 Full_Region: catttttccaaaata tttgaaaag agttatg tttttcaaa tctatagtacacatc .......................................................................................................................................................tttgaaaagagttatgtttttcaaa................................................................................................................................................................................................ Find igs database================================================ Query_seq: SSA_0342:SSA_0343|SSA_0342:SSA_0343:Pyruvate formate-lyase, putative:DNA-damage-inducible protein P, putative:<-->:337297..337664 368 ttgattttcctctttattctagcaacataaactgttacatttataagtaaagtatatcatacggtaatcggtttcacaaaccattttcggcagaaagaaagactttcttttataatacagaaagtaaaaagtcgcggatgtgtactatagatttgaaaaacataactcttttcaaatattttggaaaaatgggtaaaaaagttataataaaagtaattaaaatgtcatacaaaaattgctgacgaagaatcttacgtttaaaatactttttacaagaacgaaaaactgtttcagatttatttgagtaaaagggctgactttgtgaaagcttgtaagctgagattgatggcaggagaaaggaggaggac Intra-Species Hit: Count: 1 Min: 1 Max: 368 Len: 368 Subject: NC_009009_SSA_0342_SSA_0343|Pyruvate formate-lyase, putative:DNA-damage-inducible protein P, putative|NEGATIVE:POSITIVE|[337297,337664]|368 HSP 1 e-value: 3.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 ttgattttcctctttattctagcaacataaactgttacatttataagtaaagtatatcatacggtaatcggtttcacaaaccattttcggcagaaagaaagactttcttttataatacagaaagtaaaaagtcgcggatgtgtactatagatttgaaaaacataactcttttc................................................................................................................................................................................................... ttgattttcctctttattctagcaacataaactgttacatttataagtaaagtatatcatacggtaatcggtttcacaaaccattttcggcagaaagaaagactttcttttataatacagaaagtaaaaagtcgcggatgtgtactatagatttgaaaaacataactcttttc................................................................................................................................................................................................... HSP 2 e-value: 8.0E-69 bit: 262.0 Len: 132 Query Start:237 Query End:368 Subject Strand: POSITIVE Subject Start: 237 Subject End: 368 ............................................................................................................................................................................................................................................tgctgacgaagaatcttacgtttaaaatactttttacaagaacgaaaaactgtttcagatttatttgagtaaaagggctgactttgtgaaagcttgtaagctgagattgatggcaggagaaaggaggaggac ............................................................................................................................................................................................................................................tgctgacgaagaatcttacgtttaaaatactttttacaagaacgaaaaactgtttcagatttatttgagtaaaagggctgactttgtgaaagcttgtaagctgagattgatggcaggagaaaggaggaggac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAUUUUCCUCUUUAUUCUAGCAACAUAAACUGUUACAUUUAUAAGUAAAGUAUAUCAUACGGUAAUCGGUUUCACAAACCAUUUUCGGCAGAAAGAAAGACUUUCUUUUAUAAUACAGAAAGUAAAAAGUCGCGGAUGUGUACUAUAGAUUUGAAAAACAUAACUCUUUUCAAAUAUUUUGGAAAAAUGGGUAAAAAAGUUAUAAUAAAAGUAAUUAAAAUGUCAUACAAAAAUUGCUGACGAAGAAUCUUACGUUUAAAAUACUUUUUACAAGAACGAAAAACUGUUUCAGAUUUAUUUGAGUAAAAGGGCUGACUUUGUGAAAGCUUGUAAGCUGAGAUUGAUGGCAGGAGAAAGGAGGAGGAC ....(((((((((((.((((.((.......(((((......((((.......))))....))))).(((((((((......((((..((((.(((((((.....)))))))....(((.....)))....))))..))))..((((((((((((((((......(((((((((((.....)))))))...)))).(((((((.....((((.((((......(((((............))))).......)))).))))....))))))).................))))))))))))...))))....((((.((...((....))..)).))))))))))))).)).)))).))))))))))). (-73.72) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCCUCCUCCUUUCUCCUGCCAUCAAUCUCAGCUUACAAGCUUUCACAAAGUCAGCCCUUUUACUCAAAUAAAUCUGAAACAGUUUUUCGUUCUUGUAAAAAGUAUUUUAAACGUAAGAUUCUUCGUCAGCAAUUUUUGUAUGACAUUUUAAUUACUUUUAUUAUAACUUUUUUACCCAUUUUUCCAAAAUAUUUGAAAAGAGUUAUGUUUUUCAAAUCUAUAGUACACAUCCGCGACUUUUUACUUUCUGUAUUAUAAAAGAAAGUCUUUCUUUCUGCCGAAAAUGGUUUGUGAAACCGAUUACCGUAUGAUAUACUUUACUUAUAAAUGUAACAGUUUAUGUUGCUAGAAUAAAGAGGAAAAUCAA .(((((.....((((.........((((..((((....))))((((((((.((((....((((......)))).))))......((((((.....(((((((((.........((((((((....(((((((.....))).)))).................((((((((((((....((((.....)))).....)))))))))))).......)))))....))).........)))))))))...............((((((.....))))))..))))))...))))))))...))))...(((..(((.(((((((........)))).))).)))..))).))))....)))))....... (-59.47) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 838 110 61 201 152 NC_009009:SSA_0342|5end_Pyruvate_formate-lyase,_putative_337206..337436_NEGATIVE 341 360 312 211 162 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 308 355 316 231 199 NC_009009:SSA_0543|5end_SecA,_putative_537279..537509_POSITIVE 298 339 293 186 144 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 294 358 311 166 119 NC_009009:SSA_2338|5end_Conserved_uncharacterized_protein_2339272..2339502_POSITIVE 282 355 311 172 127 NC_009009:SSA_0896|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_887705..887935_POSITIVE 280 360 314 62 17 NC_009009:SSA_2204|5end_hypothetical_protein_2204663..2204893_POSITIVE 280 360 313 74 31 NC_009009:SSA_0190|5end_hypothetical_protein_191481..191711_POSITIVE 277 354 312 189 145 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 274 37 4 128 90 NC_009009:SSA_1964|5end_conserved_uncharacterized_protein_1961211..1961441_NEGATIVE 274 360 318 58 4 NC_009009:SSA_1748|5end_Inorganic_pyrophosphatase/exopolyphosphatase,_putative_1734478..1734708_NEGATIVE 273 356 311 146 94 NC_009009:SSA_1027|5end_hypothetical_protein_1043527..1043757_POSITIVE 270 353 311 199 156 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 267 355 313 223 190 NC_009009:SSA_1379|5end_hypothetical_protein_1398528..1398758_NEGATIVE 267 350 302 184 136 NC_009009:SSA_0465|5end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_469185..469415_POSITIVE 265 359 323 47 12 NC_009009:SSA_1570|5end_hypothetical_protein_1572659..1572889_POSITIVE 262 355 311 148 106 NC_009009:SSA_2024|5end_hypothetical_protein_2029272..2029502_NEGATIVE 258 336 300 198 152 NC_009009:SSA_1268|5end_Chorismate_mutase/prephenate_dehydratase,_putative_1291610..1291840_NEGATIVE 257 354 318 144 108 NC_009009:SSA_0159|5end_hypothetical_protein_155000..155230_POSITIVE 254 338 292 202 155 NC_009009:SSA_1743|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1730170..1730400_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 350 302 98 43 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 314 149 104 75 34 NC_009009:SSA_0563|3end_Universal_stress_protein_family,_putative_554947..555097_NEGATIVE 298 339 293 61 19 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 296 360 311 151 101 NC_009009:SSA_0105|3end_Uridine_kinase,_putative_107479..107629_POSITIVE 295 360 311 54 9 NC_009009:SSA_2076|3end_Conserved_uncharacterized_protein_2079390..2079540_NEGATIVE 290 357 311 73 18 NC_009009:SSA_1126|3end_Thiamine_biosynthesis_lipoprotein,_putative_1150587..1150737_NEGATIVE 289 356 311 133 74 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 282 355 311 150 105 NC_009009:SSA_0895|3end_ATP-binding_cassette_transporter-like_protein,_putative_887763..887913_POSITIVE 278 360 311 115 59 NC_009009:SSA_0288|3end_hypothetical_protein_280740..280890_NEGATIVE 274 353 311 141 99 NC_009009:SSA_1386|3end_NADPH-dependent_FMN_reductase,_putative_1403428..1403578_POSITIVE 271 353 316 81 39 NC_009009:SSA_1432|3end_HflX_GTPase,_putative_1438663..1438813_NEGATIVE 265 360 314 62 11 NC_009009:SSA_0254|3end_hypothetical_protein_247067..247217_NEGATIVE 259 328 286 130 100 NC_009009:SSA_0418|3end_AraC-type_DNA-binding_domain-containing_protein,_putative_416184..416334_POSITIVE 258 330 281 118 67 NC_009009:SSA_2018|3end_hypothetical_protein_2017464..2017614_NEGATIVE 257 350 303 149 105 NC_009009:SSA_2155|3end_hypothetical_protein_2155407..2155557_NEGATIVE 257 354 318 138 102 NC_009009:SSA_0158|3end_hypothetical_protein_155074..155224_POSITIVE 255 352 313 82 43 NC_009009:SSA_0813|3end_Thioredoxin_reductase,_putative_794438..794588_NEGATIVE 252 346 312 143 116 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 252 357 311 66 17 NC_009009:SSA_0898|3end_hypothetical_protein_889768..889918_NEGATIVE 251 355 311 60 18 NC_009009:SSA_2275|3end_hypothetical_protein_2275225..2275375_NEGATIVE