Origin IGS: agagctacctcctctaaaatggtcggcaaaggacgtcgcatcattcacagaatgattgggctgaccaaaaatcaatcagtccataacgtccgagtgatttgcaactattttcttgtttctattgtaacccttttcagaaaaaaagtaaagataaaatggaaatgctgtcagaaaattgcaagcagaaaaagattcctttactttgaagggttagaaaaggaatagtgatctttatcttataaatcgcttcataatcgcgtgaaaagtgagcttatttttttgttgtcaatcgctttttctggtggtataatgataacattctgatgaatagaggaaaaataaga .........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 tcttatttttcctctattcatcagaatgttatcattataccaccagaaaaagcgattgacaacaaaaaaataagctcacttttcacgcgattatgaagcgatttataagataaagatcactattccttttctaacccttcaaagtaaaggaatctttttctgcttgcaattttctgacagcatttccattttatctttactttttttctgaaaagggttacaatagaaacaagaaaatagttgcaaatcactcggacgttatggactgattgatttttggtcagcccaatcattctgtgaatgatgcgacgtcctttgccgaccattttagaggaggtagctct Mask Tandem Repeat Region ================================================ agagctacctcctctaaaatggtcggcaaaggacgtcgcatcattcacagaatgattgggctgaccaaaaatcaatcagtccataacgtccgagtgatttgcaactattttcttgtttctattgtaacccttttcagaaaaaaagtaaagataaaatggaaatgctgtcagaaaattgcaagcagaaaaagattcctttactttgaagggttagaaaaggaatagtgatctttatcttataaatcgcttcataatcgcgtgaaaagtgagcttatttttttgttgtcaatcgctttttctggtggtataatgataacattctgatgaatagaggaaaaataaga Find is-nt database================================================ Query_seq: SSA_0563:SSA_0564|SSA_0563:SSA_0564:Universal stress protein family, putative:Potential aminotransferase, putative:<-->:555490..555833 344 agagctacctcctctaaaatggtcggcaaaggacgtcgcatcattcacagaatgattgggctgaccaaaaatcaatcagtccataacgtccgagtgatttgcaactattttcttgtttctattgtaacccttttcagaaaaaaagtaaagataaaatggaaatgctgtcagaaaattgcaagcagaaaaagattcctttactttgaagggttagaaaaggaatagtgatctttatcttataaatcgcttcataatcgcgtgaaaagtgagcttatttttttgttgtcaatcgctttttctggtggtataatgataacattctgatgaatagaggaaaaataaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0563:SSA_0564|SSA_0563:SSA_0564:Universal stress protein family, putative:Potential aminotransferase, putative:<-->:555490..555833 344 agagctacctcctctaaaatggtcggcaaaggacgtcgcatcattcacagaatgattgggctgaccaaaaatcaatcagtccataacgtccgagtgatttgcaactattttcttgtttctattgtaacccttttcagaaaaaaagtaaagataaaatggaaatgctgtcagaaaattgcaagcagaaaaagattcctttactttgaagggttagaaaaggaatagtgatctttatcttataaatcgcttcataatcgcgtgaaaagtgagcttatttttttgttgtcaatcgctttttctggtggtataatgataacattctgatgaatagaggaaaaataaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0563:SSA_0564|SSA_0563:SSA_0564:Universal stress protein family, putative:Potential aminotransferase, putative:<-->:555490..555833 344 agagctacctcctctaaaatggtcggcaaaggacgtcgcatcattcacagaatgattgggctgaccaaaaatcaatcagtccataacgtccgagtgatttgcaactattttcttgtttctattgtaacccttttcagaaaaaaagtaaagataaaatggaaatgctgtcagaaaattgcaagcagaaaaagattcctttactttgaagggttagaaaaggaatagtgatctttatcttataaatcgcttcataatcgcgtgaaaagtgagcttatttttttgttgtcaatcgctttttctggtggtataatgataacattctgatgaatagaggaaaaataaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agagctacctcctctaaaatggtcggcaaaggacgtcgcatcattcacagaatgattgggctgaccaaaaatcaatcagtccataacgtccgagtgatttgcaactattttcttgtttctattgtaacccttttcagaaaaaaagtaaagataaaatggaaatgctgtcagaaaattgcaagcagaaaaagattcctttactttgaagggttagaaaaggaatagtgatctttatcttataaatcgcttcataatcgcgtgaaaagtgagcttatttttttgttgtcaatcgctttttctggtggtataatgataacattctgatgaatagaggaaaaataaga Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 99 End: 203 .................................................................................................. M Q L F S C F Y C N P F Q K K S K D K M E M L S E N C K Q K K I P L L ............................................................................................................................................. Protein_Len: 60 Strand: + Start: 19 End: 222 .................. M V G K G R R I I H R M I G L T K N Q S V H N V R V I C N Y F L V S I V T L F R K K V K I K W K C C Q K I A S R K R F L .......................................................................................................................... Protein_Len: 36 Strand: - Start: 137 End: 244 ........................................................................................................................................ F F L L S L I S I S D S F Q L C F F I G K S Q L T L F P I T I K I K Y M .................................................................................................... Protein_Len: 31 Strand: - Start: 79 End: 171 .............................................................................. D M V D S H N A V I K K N R N Y G K E S F F Y L Y F P F A T M ............................................................................................................................................................................. agagctacctcctctaaaatggtcggcaaaggacgtcgcatcattcacagaatgattgggctgaccaaaaatcaatcagtccataacgtccgagtgatttgcaactattttcttgtttctattgtaacccttttcagaaaaaaagtaaagataaaatggaaatgctgtcagaaaattgcaagcagaaaaagattcctttactttgaagggttagaaaaggaatagtgatctttatcttataaatcgcttcataatcgcgtgaaaagtgagcttatttttttgttgtcaatcgctttttctggtggtataatgataacattctgatgaatagaggaaaaataaga 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: 90 Start: 282 End: 311 .........................................................................................................................................................................................................................................................................................GTTGTCAATCGCTTTTTCTGGTGGTATAAT................................. PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 121 End: 150 ........................................................................................................................CTTTACTTTTTTTCTGAAAAGGGTTACAAT.................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agagctacctcctctaaaatggtcggcaaaggacgtcgcatcattcacagaatgattgggctgaccaaaaatcaatcagtccataacgtccgagtgatttgcaactattttcttgtttctattgtaacccttttcagaaaaaaagtaaagataaaatggaaatgctgtcagaaaattgcaagcagaaaaagattcctttactttgaagggttagaaaaggaatagtgatctttatcttataaatcgcttcataatcgcgtgaaaagtgagcttatttttttgttgtcaatcgctttttctggtggtataatgataacattctgatgaatagaggaaaaataaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0563:SSA_0564|SSA_0563:SSA_0564:Universal stress protein family, putative:Potential aminotransferase, putative:<-->:555490..555833 344 agagctacctcctctaaaatggtcggcaaaggacgtcgcatcattcacagaatgattgggctgaccaaaaatcaatcagtccataacgtccgagtgatttgcaactattttcttgtttctattgtaacccttttcagaaaaaaagtaaagataaaatggaaatgctgtcagaaaattgcaagcagaaaaagattcctttactttgaagggttagaaaaggaatagtgatctttatcttataaatcgcttcataatcgcgtgaaaagtgagcttatttttttgttgtcaatcgctttttctggtggtataatgataacattctgatgaatagaggaaaaataaga Intra-Species Hit: Count: 1 Min: 1 Max: 344 Len: 344 Subject: NC_009009_SSA_0563_SSA_0564|Universal stress protein family, putative:Potential aminotransferase, putative|NEGATIVE:POSITIVE|[555490,555833]|344 HSP 1 e-value: 1.0E-170 bit: 599.0 Len: 344 Query Start:1 Query End:344 Subject Strand: POSITIVE Subject Start: 1 Subject End: 344 agagctacctcctctaaaatggtcggcaaaggacgtcgcatcattcacagaatgattgggctgaccaaaaatcaatcagtccataacgtccgagtgatttgcaactattttcttgtttctattgtaacccttttcagnnnnnnngtaaagataaaatggaaatgctgtcagaaaattgcaagcagaaaaagattcctttactttgaagggttagaaaaggaatagtgatctttatcttataaatcgcttcataatcgcgtgaaaagtgagcttannnnnnngttgtcaatcgctttttctggtggtataatgataacattctgatgaatagaggaaaaataaga agagctacctcctctaaaatggtcggcaaaggacgtcgcatcattcacagaatgattgggctgaccaaaaatcaatcagtccataacgtccgagtgatttgcaactattttcttgtttctattgtaacccttttcagaaaaaaagtaaagataaaatggaaatgctgtcagaaaattgcaagcagaaaaagattcctttactttgaagggttagaaaaggaatagtgatctttatcttataaatcgcttcataatcgcgtgaaaagtgagcttatttttttgttgtcaatcgctttttctggtggtataatgataacattctgatgaatagaggaaaaataaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAGCUACCUCCUCUAAAAUGGUCGGCAAAGGACGUCGCAUCAUUCACAGAAUGAUUGGGCUGACCAAAAAUCAAUCAGUCCAUAACGUCCGAGUGAUUUGCAACUAUUUUCUUGUUUCUAUUGUAACCCUUUUCAGAAAAAAAGUAAAGAUAAAAUGGAAAUGCUGUCAGAAAAUUGCAAGCAGAAAAAGAUUCCUUUACUUUGAAGGGUUAGAAAAGGAAUAGUGAUCUUUAUCUUAUAAAUCGCUUCAUAAUCGCGUGAAAAGUGAGCUUAUUUUUUUGUUGUCAAUCGCUUUUUCUGGUGGUAUAAUGAUAACAUUCUGAUGAAUAGAGGAAAAAUAAGA .........(((((((....((((.(((((((((((...(((((((...)))))))((((((((...........))))))))..))))))......)))))..........((((((((.((.(((((((((........(((((((((............((((..(((....)))..))))...........)))))))))))))))))).)).)))))))).)))).(((((..((((.(((((((((......))))..)))))..)))).....((((((((((((((......))))))....))))))))....))))).)))))))......... (-88.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUAUUUUUCCUCUAUUCAUCAGAAUGUUAUCAUUAUACCACCAGAAAAAGCGAUUGACAACAAAAAAAUAAGCUCACUUUUCACGCGAUUAUGAAGCGAUUUAUAAGAUAAAGAUCACUAUUCCUUUUCUAACCCUUCAAAGUAAAGGAAUCUUUUUCUGCUUGCAAUUUUCUGACAGCAUUUCCAUUUUAUCUUUACUUUUUUUCUGAAAAGGGUUACAAUAGAAACAAGAAAAUAGUUGCAAAUCACUCGGACGUUAUGGACUGAUUGAUUUUUGGUCAGCCCAAUCAUUCUGUGAAUGAUGCGACGUCCUUUGCCGACCAUUUUAGAGGAGGUAGCUCU .......((((((((((((....((...(((((.(((((......((((((((....................)))...))))).(((.........)))...))))))))))...)).......((.((.(((((((((((((((((((..........((((..((......))..))))...........)))))))))......)))..))))))).)).))......)))....((((((((......(((((((..((.(((((..(...)..))))).)).(((((((...)))))))..))))))))))).)))).....)))))))))....... (-70.55) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 994 50 1 141 92 NC_009009:SSA_0563|5end_Universal_stress_protein_family,_putative_555399..555629_NEGATIVE 316 67 21 62 8 NC_009009:SSA_0335|5end_Phosphomevalonate_kinase,_putative_328792..329022_POSITIVE 307 45 18 31 2 NC_009009:SSA_2035|5end_Conserved_uncharacterized_protein_2040288..2040518_NEGATIVE 306 69 21 200 152 NC_009009:SSA_0694|5end_Mutator_protein,_putative_677730..677960_POSITIVE 304 329 283 64 18 NC_009009:SSA_0266|5end_ORFB,_transposon_ISSsa1_260134..260364_POSITIVE 302 65 22 52 17 NC_009009:SSA_0092|5end_V-type_sodium_ATPase,_subunit_B,_putative_92895..93125_POSITIVE 299 67 23 215 168 NC_009009:SSA_2074|5end_Preprotein_translocase_subunit_YajC,_putative_2076935..2077165_NEGATIVE 296 48 1 168 121 NC_009009:SSA_1363|5end_FmtA-like_protein,_putative_1380417..1380647_NEGATIVE 294 60 28 48 15 NC_009009:SSA_0314|5end_Nucleoside-diphosphate-sugar_epimerase,_putative_310019..310249_NEGATIVE 293 70 30 201 162 NC_009009:SSA_0310|5end_hypothetical_protein_305306..305536_POSITIVE 292 42 5 142 95 NC_009009:SSA_0973|5end_hypothetical_protein_980296..980526_POSITIVE 287 64 21 69 29 NC_009009:SSA_1530|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1538778..1539008_NEGATIVE 287 63 21 60 22 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 282 66 30 190 152 NC_009009:SSA_1381|5end_hypothetical_protein_1399565..1399795_NEGATIVE 279 119 75 48 10 NC_009009:SSA_0834|5end_Accessory_secretory_protein_Asp2,_putative_819510..819740_POSITIVE 278 79 34 211 159 NC_009009:SSA_1009|5end_Galactose-1-phosphate-uridylyltransferase,_putative_1011254..1011484_POSITIVE 276 46 3 85 38 NC_009009:SSA_0554|5end_hypothetical_protein_549265..549495_POSITIVE 276 49 3 80 20 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 275 262 224 231 189 NC_009009:SSA_1704|5end_Conserved_uncharacterized_protein_1696401..1696631_NEGATIVE 275 108 62 224 175 NC_009009:SSA_0462|5end_ABC-type_multidrug_transport_system_(phospholipid,_LPS,_lipid_A_and_drug_exporter),_ATPase_and_permease_components,_putative_464815..465045_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 45 11 41 1 NC_009009:SSA_2036|3end_Conserved_hypothetical_cytosolic_protein_2040278..2040428_NEGATIVE 316 67 21 72 18 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 302 65 22 65 30 NC_009009:SSA_0091|3end_V-type_sodium_ATPase,_subunit_A,_putative_92988..93138_POSITIVE 296 48 1 103 56 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 292 42 5 130 83 NC_009009:SSA_0972|3end_hypothetical_protein_980364..980514_POSITIVE 287 64 21 69 29 NC_009009:SSA_1531|3end_ABC-type_antimicrobial_peptide_transporter,_ATPase_component,_putative_1538778..1538928_NEGATIVE 287 63 21 49 11 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE 279 119 75 58 20 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 279 59 13 149 104 NC_009009:SSA_0631|3end_Tryptophan_synthase_beta_chain,_putative_621133..621283_POSITIVE 278 308 264 87 48 NC_009009:SSA_0492|3end_NADH-dependent_flavin_oxidoreductase,_putative_492771..492921_POSITIVE 276 46 3 81 34 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 276 49 3 87 27 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 274 97 55 57 12 NC_009009:SSA_1261|3end_Ribose-5-phosphate_isomerase_A,_putative_1286977..1287127_NEGATIVE 272 106 71 54 21 NC_009009:SSA_1252|3end_hypothetical_protein_1276771..1276921_NEGATIVE 271 82 48 48 6 NC_009009:SSA_1747|3end_hypothetical_protein_1732938..1733088_NEGATIVE 266 51 12 43 10 NC_009009:SSA_0337|3end_Hydroxymethylglutaryl-CoA_reductase,_putative_330889..331039_NEGATIVE 264 64 23 90 37 NC_009009:SSA_0636|3end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625809..625959_POSITIVE 263 289 243 85 34 NC_009009:SSA_1196|3end_Acetyltransferase,_GNAT_family,_putative_1221528..1221678_NEGATIVE 263 208 164 101 58 NC_009009:SSA_0127|3end_Multispanning_membrane_protein,_translocator_of_proteins,_putative_119107..119257_POSITIVE 260 90 44 128 87 NC_009009:SSA_2105|3end_hypothetical_protein_2106756..2106906_NEGATIVE