Origin IGS: tttcttcgaaagaacacagctctgttttaccggaacagagccttttttattttccttaacttacaaattttttctgtgaacaatacttgatttcaaagggattatgaaaattattataaaacacattggactttgtgaaaaaaatcagggcttggtgttatgtaatagttctatatcatctttgagcatattcttatacaagagcgaaaaaacatgataaattgatagagtaaagtttcttgaagcgttttcattcacaaatggaaatattttcaacaactgaaaatttattttattgaaggagagttatt .........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 aataactctccttcaataaaataaattttcagttgttgaaaatatttccatttgtgaatgaaaacgcttcaagaaactttactctatcaatttatcatgttttttcgctcttgtataagaatatgctcaaagatgatatagaactattacataacaccaagccctgatttttttcacaaagtccaatgtgttttataataattttcataatccctttgaaatcaagtattgttcacagaaaaaatttgtaagttaaggaaaataaaaaaggctctgttccggtaaaacagagctgtgttctttcgaagaaa Mask Tandem Repeat Region ================================================ tttcttcgaaagaacacagctctgttttaccggaacagagccttttttattttccttaacttacaaattttttctgtgaacaatacttgatttcaaagggattatgaaaattattataaaacacattggactttgtgaaaaaaatcagggcttggtgttatgtaatagttctatatcatctttgagcatattcttatacaagagcgaaaaaacatgataaattgatagagtaaagtttcttgaagcgttttcattcacaaatggaaatattttcaacaactgaaaatttattttattgaaggagagttatt Find is-nt database================================================ Query_seq: SSA_0390:SSA_0391|SSA_0390:SSA_0391:hypothetical protein:Pyruvate oxidase, putative:->->:385775..386085 311 tttcttcgaaagaacacagctctgttttaccggaacagagccttttttattttccttaacttacaaattttttctgtgaacaatacttgatttcaaagggattatgaaaattattataaaacacattggactttgtgaaaaaaatcagggcttggtgttatgtaatagttctatatcatctttgagcatattcttatacaagagcgaaaaaacatgataaattgatagagtaaagtttcttgaagcgttttcattcacaaatggaaatattttcaacaactgaaaatttattttattgaaggagagttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0390:SSA_0391|SSA_0390:SSA_0391:hypothetical protein:Pyruvate oxidase, putative:->->:385775..386085 311 tttcttcgaaagaacacagctctgttttaccggaacagagccttttttattttccttaacttacaaattttttctgtgaacaatacttgatttcaaagggattatgaaaattattataaaacacattggactttgtgaaaaaaatcagggcttggtgttatgtaatagttctatatcatctttgagcatattcttatacaagagcgaaaaaacatgataaattgatagagtaaagtttcttgaagcgttttcattcacaaatggaaatattttcaacaactgaaaatttattttattgaaggagagttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0390:SSA_0391|SSA_0390:SSA_0391:hypothetical protein:Pyruvate oxidase, putative:->->:385775..386085 311 tttcttcgaaagaacacagctctgttttaccggaacagagccttttttattttccttaacttacaaattttttctgtgaacaatacttgatttcaaagggattatgaaaattattataaaacacattggactttgtgaaaaaaatcagggcttggtgttatgtaatagttctatatcatctttgagcatattcttatacaagagcgaaaaaacatgataaattgatagagtaaagtttcttgaagcgttttcattcacaaatggaaatattttcaacaactgaaaatttattttattgaaggagagttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttcttcgaaagaacacagctctgttttaccggaacagagccttttttattttccttaacttacaaattttttctgtgaacaatacttgatttcaaagggattatgaaaattattataaaacacattggactttgtgaaaaaaatcagggcttggtgttatgtaatagttctatatcatctttgagcatattcttatacaagagcgaaaaaacatgataaattgatagagtaaagtttcttgaagcgttttcattcacaaatggaaatattttcaacaactgaaaatttattttattgaaggagagttatt Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 83 End: 214 .................................................................................. M L D F K G I M K I I I K H I G L C E K N Q G L V L C N S S I S S L S I F L Y K S E K T ................................................................................................. Protein_Len: 48 Strand: - Start: 148 End: 291 ................................................................................................................................................... P K T N H L L E I D D K L M N K Y L L S F V H Y I S L T F N R S A N E N V F P F I K L L Q F N M .................... Protein_Len: 30 Strand: - Start: 59 End: 148 .......................................................... S V F K K Q S C Y K I E F P N H F N N Y F V N S K T F F I M ................................................................................................................................................................... tttcttcgaaagaacacagctctgttttaccggaacagagccttttttattttccttaacttacaaattttttctgtgaacaatacttgatttcaaagggattatgaaaattattataaaacacattggactttgtgaaaaaaatcagggcttggtgttatgtaatagttctatatcatctttgagcatattcttatacaagagcgaaaaaacatgataaattgatagagtaaagtttcttgaagcgttttcattcacaaatggaaatattttcaacaactgaaaatttattttattgaaggagagttatt 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: 88 Start: 113 End: 142 ................................................................................................................TTTTTCACAAAGTCCAATGTGTTTTATAAT......................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttcttcgaaagaacacagctctgttttaccggaacagagccttttttattttccttaacttacaaattttttctgtgaacaatacttgatttcaaagggattatgaaaattattataaaacacattggactttgtgaaaaaaatcagggcttggtgttatgtaatagttctatatcatctttgagcatattcttatacaagagcgaaaaaacatgataaattgatagagtaaagtttcttgaagcgttttcattcacaaatggaaatattttcaacaactgaaaatttattttattgaaggagagttatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0390:SSA_0391|SSA_0390:SSA_0391:hypothetical protein:Pyruvate oxidase, putative:->->:385775..386085 311 tttcttcgaaagaacacagctctgttttaccggaacagagccttttttattttccttaacttacaaattttttctgtgaacaatacttgatttcaaagggattatgaaaattattataaaacacattggactttgtgaaaaaaatcagggcttggtgttatgtaatagttctatatcatctttgagcatattcttatacaagagcgaaaaaacatgataaattgatagagtaaagtttcttgaagcgttttcattcacaaatggaaatattttcaacaactgaaaatttattttattgaaggagagttatt Intra-Species Hit: Count: 1 Min: 1 Max: 311 Len: 311 Subject: NC_009009_SSA_0390_SSA_0391|hypothetical protein:Pyruvate oxidase, putative|POSITIVE:POSITIVE|[385775,386085]|311 HSP 1 e-value: 1.0E-163 bit: 575.0 Len: 311 Query Start:1 Query End:311 Subject Strand: POSITIVE Subject Start: 1 Subject End: 311 tttcttcgaaagaacacagctctgttttaccggaacagagccttttttattttccttaacttacaaattttttctgtgaacaatacttgatttcaaagggattatgaaaattattataaaacacattggactttgtgnnnnnnntcagggcttggtgttatgtaatagttctatatcatctttgagcatattcttatacaagagcgaaaaaacatgataaattgatagagtaaagtttcttgaagcgttttcattcacaaatggaaatattttcaacaactgaaaatttattttattgaaggagagttatt tttcttcgaaagaacacagctctgttttaccggaacagagccttttttattttccttaacttacaaattttttctgtgaacaatacttgatttcaaagggattatgaaaattattataaaacacattggactttgtgaaaaaaatcagggcttggtgttatgtaatagttctatatcatctttgagcatattcttatacaagagcgaaaaaacatgataaattgatagagtaaagtttcttgaagcgttttcattcacaaatggaaatattttcaacaactgaaaatttattttattgaaggagagttatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUCGAAAGAACACAGCUCUGUUUUACCGGAACAGAGCCUUUUUUAUUUUCCUUAACUUACAAAUUUUUUCUGUGAACAAUACUUGAUUUCAAAGGGAUUAUGAAAAUUAUUAUAAAACACAUUGGACUUUGUGAAAAAAAUCAGGGCUUGGUGUUAUGUAAUAGUUCUAUAUCAUCUUUGAGCAUAUUCUUAUACAAGAGCGAAAAAACAUGAUAAAUUGAUAGAGUAAAGUUUCUUGAAGCGUUUUCAUUCACAAAUGGAAAUAUUUUCAACAACUGAAAAUUUAUUUUAUUGAAGGAGAGUUAUU ....(((....)))....(((((((((.....))))))))).......(((((((((......((..(((((((.(....)....((((...((((((((((...((..(((((((((.(((((...((.(((((..........)))))))..))))).)))))))))))...))).)))))))..(((....))).))))...)))))))..)).......(((((((((((.((((((((((.(((((((((....)))))))))..)))))).....)))).))))))))))).))))))))).... (-71.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAACUCUCCUUCAAUAAAAUAAAUUUUCAGUUGUUGAAAAUAUUUCCAUUUGUGAAUGAAAACGCUUCAAGAAACUUUACUCUAUCAAUUUAUCAUGUUUUUUCGCUCUUGUAUAAGAAUAUGCUCAAAGAUGAUAUAGAACUAUUACAUAACACCAAGCCCUGAUUUUUUUCACAAAGUCCAAUGUGUUUUAUAAUAAUUUUCAUAAUCCCUUUGAAAUCAAGUAUUGUUCACAGAAAAAAUUUGUAAGUUAAGGAAAAUAAAAAAGGCUCUGUUCCGGUAAAACAGAGCUGUGUUCUUUCGAAGAAA ..........((((..........((((((((...)))))))).(((((.((((((((..(....((((..........................(((((((((..((....))..))))))))).((((((..(((((((((.(((((...(((((........((((((......))))))....)))))...))))).)))).)).))).))))))....)))).)..))))))))...((((....))))..)))))........(((((((((.......)))))))))..........))))... (-52.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 268 42 3 220 178 NC_009009:SSA_1611|5end_Era-like_GTP-binding_protein,_putative_1616032..1616262_NEGATIVE 266 273 240 201 169 NC_009009:SSA_1614|5end_Acetyltransferase,_GNAT_family,_putative_1618045..1618275_NEGATIVE 260 57 15 117 72 NC_009009:SSA_2141|5end_Argininosuccinate_lyase,_putative_2142201..2142431_NEGATIVE 259 67 21 123 73 NC_009009:SSA_0687|5end_hypothetical_protein_670467..670697_POSITIVE 255 49 4 217 175 NC_009009:SSA_1470|5end_3-dehydroquinate_dehydratase,_putative_1476984..1477214_NEGATIVE 251 49 1 154 97 NC_009009:SSA_1373|5end_ATPase_components_of_ABC_transporters_with_duplicated_ATPase_domains,_multidrug_transport_system,_putative_1389707..1389937_POSITIVE 242 57 11 113 58 NC_009009:SSA_1610|5end_hypothetical_protein_1614909..1615139_NEGATIVE 242 60 16 88 25 NC_009009:SSA_1014|5end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1017846..1018076_POSITIVE 242 58 17 47 1 NC_009009:SSA_0046|5end_Adenylosuccinate_lyase,_putative_50894..51124_POSITIVE 238 48 1 170 129 NC_009009:SSA_1896|5end_Translation_initiation_factor_IF-2,_putative_1894134..1894364_NEGATIVE 238 246 203 188 135 NC_009009:SSA_0674|5end_Exodeoxyribonuclease_VII_large_subunit,_putative_657071..657301_POSITIVE 238 42 4 65 22 NC_009009:SSA_0591|5end_Conserved_uncharacterized_protein_582769..582999_POSITIVE 237 275 237 204 159 NC_009009:SSA_1644|5end_hypothetical_protein_1645617..1645847_NEGATIVE 236 70 21 53 15 NC_009009:SSA_1303|5end_RimM_protein,_required_for_16S_rRNA_processing,_putative_1322992..1323222_NEGATIVE 235 253 212 152 109 NC_009009:SSA_2099|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2104313..2104543_NEGATIVE 234 55 17 89 44 NC_009009:SSA_1154|5end_hypothetical_protein_1182661..1182891_POSITIVE 233 187 145 63 22 NC_009009:SSA_1879|5end_Glycyl-tRNA_synthetase_beta_chain,_putative_1874262..1874492_NEGATIVE 232 47 4 134 84 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 231 78 38 61 18 NC_009009:SSA_2309|5end_Fimbrial_assembly_protein,_putative_2311886..2312116_NEGATIVE 231 46 4 85 38 NC_009009:SSA_1311|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_1328393..1328623_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 55 11 69 16 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 266 41 19 72 50 NC_009009:SSA_0390|3end_hypothetical_protein_385714..385864_POSITIVE 260 57 15 102 57 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 247 189 146 91 44 NC_009009:SSA_2212|3end_Possible_polysaccharide_transport_protein,_putative_2212627..2212777_NEGATIVE 242 60 16 95 32 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 240 47 7 55 8 NC_009009:SSA_1829|3end_RNA_methyltransferase,_putative_1818959..1819109_NEGATIVE 238 48 1 150 109 NC_009009:SSA_1897|3end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894154..1894304_NEGATIVE 234 158 128 39 5 NC_009009:SSA_1555|3end_Glucose-6-phosphate_1-dehydrogenase,_putative_1558482..1558632_POSITIVE 234 55 17 96 51 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 233 187 145 60 19 NC_009009:SSA_1880|3end_Glycyl-tRNA_synthetase_alpha_chain,_putative_1874265..1874415_NEGATIVE 230 185 145 151 116 NC_009009:SSA_1185|3end_DNA_processing_Smf_protein,_putative_1213690..1213840_NEGATIVE 230 48 18 67 39 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 224 42 14 33 5 NC_009009:SSA_0590|3end_hypothetical_protein_582817..582967_POSITIVE 221 181 141 85 41 NC_009009:SSA_0074|3end_ABC_transporter_substrate-binding_protein-sugar_transport,_putative_78975..79125_POSITIVE 220 56 16 48 2 NC_009009:SSA_1881|3end_hypothetical_protein_1875203..1875353_NEGATIVE 220 182 145 113 78 NC_009009:SSA_0169|3end_hypothetical_protein_168015..168165_POSITIVE 217 52 15 127 89 NC_009009:SSA_0466|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_470668..470818_POSITIVE 216 42 7 44 11 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 216 161 126 83 45 NC_009009:SSA_0216|3end_Histidine_kinase,_putative_213270..213420_POSITIVE 215 50 1 70 3 NC_009009:SSA_2226|3end_Organic_radical_activating_chaperone,_putative_2227151..2227301_NEGATIVE