Origin IGS: cgtactaagattgcttggctacatagtagtctaagcaatcttagtacgttactaactgcgtttggcaaataaaatcgatttgccaaacttcgtgtcgtaacgcattttttgcctgatttaggctgattcattgactgaatctgaatcaaaagttgctaatcagttgatggcaatcgctatggtgattgtctagctatcttactaattttgtcgagtaaattgactctatttgtttgaactcatgttgtaattaatagaagaaatataattaatgaagtcaactatatt .........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 aatatagttgacttcattaattatatttcttctattaattacaacatgagttcaaacaaatagagtcaatttactcgacaaaattagtaagatagctagacaatcaccatagcgattgccatcaactgattagcaacttttgattcagattcagtcaatgaatcagcctaaatcaggcaaaaaatgcgttacgacacgaagtttggcaaatcgattttatttgccaaacgcagttagtaacgtactaagattgcttagactactatgtagccaagcaatcttagtacg Mask Tandem Repeat Region ================================================ cgtactaagattgcttggctacatagtagtctaagcaatcttagtacgttactaactgcgtttggcaaataaaatcgatttgccaaacttcgtgtcgtaacgcattttttgcctgatttaggctgattcattgactgaatctgaatcaaaagttgctaatcagttgatggcaatcgctatggtgattgtctagctatcttactaattttgtcgagtaaattgactctatttgtttgaactcatgttgtaattaatagaagaaatataattaatgaagtcaactatatt Find is-nt database================================================ Query_seq: SSA_0698:SSA_0699|SSA_0698:SSA_0699:Peptide chain release factor 3, putative:Methyltransferase, putative:->->:682068..682355 288 cgtactaagattgcttggctacatagtagtctaagcaatcttagtacgttactaactgcgtttggcaaataaaatcgatttgccaaacttcgtgtcgtaacgcattttttgcctgatttaggctgattcattgactgaatctgaatcaaaagttgctaatcagttgatggcaatcgctatggtgattgtctagctatcttactaattttgtcgagtaaattgactctatttgtttgaactcatgttgtaattaatagaagaaatataattaatgaagtcaactatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0698:SSA_0699|SSA_0698:SSA_0699:Peptide chain release factor 3, putative:Methyltransferase, putative:->->:682068..682355 288 cgtactaagattgcttggctacatagtagtctaagcaatcttagtacgttactaactgcgtttggcaaataaaatcgatttgccaaacttcgtgtcgtaacgcattttttgcctgatttaggctgattcattgactgaatctgaatcaaaagttgctaatcagttgatggcaatcgctatggtgattgtctagctatcttactaattttgtcgagtaaattgactctatttgtttgaactcatgttgtaattaatagaagaaatataattaatgaagtcaactatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0698:SSA_0699|SSA_0698:SSA_0699:Peptide chain release factor 3, putative:Methyltransferase, putative:->->:682068..682355 288 cgtactaagattgcttggctacatagtagtctaagcaatcttagtacgttactaactgcgtttggcaaataaaatcgatttgccaaacttcgtgtcgtaacgcattttttgcctgatttaggctgattcattgactgaatctgaatcaaaagttgctaatcagttgatggcaatcgctatggtgattgtctagctatcttactaattttgtcgagtaaattgactctatttgtttgaactcatgttgtaattaatagaagaaatataattaatgaagtcaactatatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtactaagattgcttggctacatagtagtctaagcaatcttagtacgttactaactgcgtttggcaaataaaatcgatttgccaaacttcgtgtcgtaacgcattttttgcctgatttaggctgattcattgactgaatctgaatcaaaagttgctaatcagttgatggcaatcgctatggtgattgtctagctatcttactaattttgtcgagtaaattgactctatttgtttgaactcatgttgtaattaatagaagaaatataattaatgaagtcaactatatt Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: - Start: 3 End: 149 .. V L I A Q S C L L R L L R L V N S V A N P L Y F R N A L S R T T V C K K G S K P Q N M S Q I Q I M ........................................................................................................................................... cgtactaagattgcttggctacatagtagtctaagcaatcttagtacgttactaactgcgtttggcaaataaaatcgatttgccaaacttcgtgtcgtaacgcattttttgcctgatttaggctgattcattgactgaatctgaatcaaaagttgctaatcagttgatggcaatcgctatggtgattgtctagctatcttactaattttgtcgagtaaattgactctatttgtttgaactcatgttgtaattaatagaagaaatataattaatgaagtcaactatatt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgtactaagattgcttggctacatagtagtctaagcaatcttagtacgttactaactgcgtttggcaaataaaatcgatttgccaaacttcgtgtcgtaacgcattttttgcctgatttaggctgattcattgactgaatctgaatcaaaagttgctaatcagttgatggcaatcgctatggtgattgtctagctatcttactaattttgtcgagtaaattgactctatttgtttgaactcatgttgtaattaatagaagaaatataattaatgaagtcaactatatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 48 HP_score: -2.9 Tail_Score: -3.66486 Start: 46 End: 103 Full_Region: CTAAGCAATCTTAGT ACGTTACTAACTGCGTTTGGCAAAT AAAATCG ATTTGCCAAACTTCGTGTCGTAACGC ATTTTTTGCCTGATT .............................................ACGTTACTAACTGCGTTTGGCAAATAAAATCGATTTGCCAAACTTCGTGTCGTAACGC......................................................................................................................................................................................... TransTerm Strand: - Conf: 44 HP_score: -2.3 Tail_Score: -3.17212 Start: 56 End: 92 Full_Region: aaatgcgttacgaca cgaagtttggcaaat cgatttt atttgccaaacgcag ttagtaacgtactaa .......................................................cgaagtttggcaaatcgattttatttgccaaacgcag.................................................................................................................................................................................................... TransTerm Strand: + Conf: 83 HP_score: -10.5 Tail_Score: -3.29471 Start: 60 End: 88 Full_Region: TACGTTACTAACTGC GTTTGGCAAAT AAAATCG ATTTGCCAAAC TTCGTGTCGTAACGC ...........................................................GTTTGGCAAATAAAATCGATTTGCCAAAC........................................................................................................................................................................................................ TransTerm Strand: + Conf: 45 HP_score: -2.1 Tail_Score: -3.48884 Start: 210 End: 224 Full_Region: TATCTTACTAATTTT GTCGA GTAAA TTGAC TCTATTTGTTTGAAC .................................................................................................................................................................................................................GTCGAGTAAATTGAC................................................................ Find igs database================================================ Query_seq: SSA_0698:SSA_0699|SSA_0698:SSA_0699:Peptide chain release factor 3, putative:Methyltransferase, putative:->->:682068..682355 288 cgtactaagattgcttggctacatagtagtctaagcaatcttagtacgttactaactgcgtttggcaaataaaatcgatttgccaaacttcgtgtcgtaacgcattttttgcctgatttaggctgattcattgactgaatctgaatcaaaagttgctaatcagttgatggcaatcgctatggtgattgtctagctatcttactaattttgtcgagtaaattgactctatttgtttgaactcatgttgtaattaatagaagaaatataattaatgaagtcaactatatt Intra-Species Hit: Count: 1 Min: 1 Max: 288 Len: 288 Subject: NC_009009_SSA_0698_SSA_0699|Peptide chain release factor 3, putative:Methyltransferase, putative|POSITIVE:POSITIVE|[682068,682355]|288 HSP 1 e-value: 1.0E-162 bit: 571.0 Len: 288 Query Start:1 Query End:288 Subject Strand: POSITIVE Subject Start: 1 Subject End: 288 cgtactaagattgcttggctacatagtagtctaagcaatcttagtacgttactaactgcgtttggcaaataaaatcgatttgccaaacttcgtgtcgtaacgcattttttgcctgatttaggctgattcattgactgaatctgaatcaaaagttgctaatcagttgatggcaatcgctatggtgattgtctagctatcttactaattttgtcgagtaaattgactctatttgtttgaactcatgttgtaattaatagaagaaatataattaatgaagtcaactatatt cgtactaagattgcttggctacatagtagtctaagcaatcttagtacgttactaactgcgtttggcaaataaaatcgatttgccaaacttcgtgtcgtaacgcattttttgcctgatttaggctgattcattgactgaatctgaatcaaaagttgctaatcagttgatggcaatcgctatggtgattgtctagctatcttactaattttgtcgagtaaattgactctatttgtttgaactcatgttgtaattaatagaagaaatataattaatgaagtcaactatatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUACUAAGAUUGCUUGGCUACAUAGUAGUCUAAGCAAUCUUAGUACGUUACUAACUGCGUUUGGCAAAUAAAAUCGAUUUGCCAAACUUCGUGUCGUAACGCAUUUUUUGCCUGAUUUAGGCUGAUUCAUUGACUGAAUCUGAAUCAAAAGUUGCUAAUCAGUUGAUGGCAAUCGCUAUGGUGAUUGUCUAGCUAUCUUACUAAUUUUGUCGAGUAAAUUGACUCUAUUUGUUUGAACUCAUGUUGUAAUUAAUAGAAGAAAUAUAAUUAAUGAAGUCAACUAUAUU ((((((((((((((((((((((...)))).))))))))))))))))))...........(((((((((((.......)))))))))))........(((((.........(((((...))))).((((((.....))))))..........))))).....((((((((((((((((....)))))))))......((..((.(((...(((((.....)))))...))).))..))..((((((((((.((........)).))))))..)))).)))))))..... (-87.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUAGUUGACUUCAUUAAUUAUAUUUCUUCUAUUAAUUACAACAUGAGUUCAAACAAAUAGAGUCAAUUUACUCGACAAAAUUAGUAAGAUAGCUAGACAAUCACCAUAGCGAUUGCCAUCAACUGAUUAGCAACUUUUGAUUCAGAUUCAGUCAAUGAAUCAGCCUAAAUCAGGCAAAAAAUGCGUUACGACACGAAGUUUGGCAAAUCGAUUUUAUUUGCCAAACGCAGUUAGUAACGUACUAAGAUUGCUUAGACUACUAUGUAGCCAAGCAAUCUUAGUACG (((((((((((.....))))))))))).....((((((((.........(((..(((.....(((((((.(((((..........)))))....((((..(((((........)))))..(((....))))))).....))))))).((((((.....)))))).((((.....)))).........)))..))).....(((((((((((.......)))))))))))..)))))))).((((((((((((((((.(.((((...))))).)))))))))))))))) (-76.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 327 178 131 95 48 NC_009009:SSA_1073|5end_Gamma-glutamyl_phosphate_reductase,_putative_1090886..1091116_POSITIVE 324 197 152 91 33 NC_009009:SSA_0440|5end_30S_ribosomal_protein_S18,_putative_441146..441376_POSITIVE 306 97 52 65 22 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 305 206 167 108 72 NC_009009:SSA_1697|5end_Tagatose-6-phosphate_kinase,_putative_1690120..1690350_NEGATIVE 301 134 92 60 21 NC_009009:SSA_1139|5end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1166823..1167053_POSITIVE 298 130 82 191 141 NC_009009:SSA_2366|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368869..2369099_NEGATIVE 295 198 151 178 137 NC_009009:SSA_2194|5end_Nicotinamide_mononucleotide_transporter,_putative_2195663..2195893_NEGATIVE 293 126 82 164 118 NC_009009:SSA_1769|5end_hypothetical_protein_1757490..1757720_NEGATIVE 287 200 152 101 56 NC_009009:SSA_2329|5end_hypothetical_protein_2332262..2332492_POSITIVE 287 209 169 227 188 NC_009009:SSA_1565|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1569309..1569539_NEGATIVE 286 59 13 95 54 NC_009009:SSA_1037|5end_Cytidine_deaminase,_putative_1052118..1052348_POSITIVE 277 248 208 168 136 NC_009009:SSA_1058|5end_Thiamine_biosynthesis_protein,_putative_1074917..1075147_POSITIVE 274 118 76 77 34 NC_009009:SSA_1174|5end_Dihydrolipoamide_dehydrogenase,_putative_1202854..1203084_NEGATIVE 273 157 111 52 8 NC_009009:SSA_1418|5end_Conserved_uncharacterized_protein_1428927..1429157_NEGATIVE 272 196 153 226 191 NC_009009:SSA_2340|5end_hypothetical_protein_2342843..2343073_NEGATIVE 272 193 153 147 104 NC_009009:SSA_2333|5end_Integral_membrane_protein,_putative_2336460..2336690_NEGATIVE 271 119 76 138 81 NC_009009:SSA_0119|5end_50S_ribosomal_protein_L5,_putative_113692..113922_POSITIVE 268 188 151 53 12 NC_009009:SSA_1506|5end_Lipopolysaccharide_biosynthesis_protein,_putative_1511222..1511452_NEGATIVE 267 190 141 62 12 NC_009009:SSA_0626|5end_hypothetical_protein_616089..616319_POSITIVE 266 122 82 198 153 NC_009009:SSA_1198|5end_ATPase_(PilT_family),_putative_1223314..1223544_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 638 50 1 92 43 NC_009009:SSA_0698|3end_Peptide_chain_release_factor_3,_putative_682007..682157_POSITIVE 327 178 131 73 26 NC_009009:SSA_1072|3end_Glutamate_5-kinase,_putative_1090944..1091094_POSITIVE 306 97 52 72 29 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 305 206 167 95 59 NC_009009:SSA_1698|3end_Galactose-6-phosphate_isomerase,_LacB_subunit,_putative_1690133..1690283_NEGATIVE 301 134 92 41 2 NC_009009:SSA_1138|3end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1166884..1167034_POSITIVE 299 159 111 62 16 NC_009009:SSA_0188|3end_hypothetical_protein_191111..191261_POSITIVE 287 200 152 68 23 NC_009009:SSA_2328|3end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_2332309..2332459_POSITIVE 286 59 13 108 67 NC_009009:SSA_1036|3end_Deoxyribose-phosphate_aldolase,_putative_1052211..1052361_POSITIVE 280 129 81 136 79 NC_009009:SSA_2211|3end_Transmembrane_protein,_putative_2211499..2211649_NEGATIVE 276 129 81 97 44 NC_009009:SSA_0568|3end_Aspartyl-tRNA_synthetase_1,_putative_563490..563640_POSITIVE 273 115 83 41 2 NC_009009:SSA_1279|3end_Oxidoreductase,_putative_1299870..1300020_NEGATIVE 273 197 154 54 3 NC_009009:SSA_0438|3end_Single-strand_binding_protein,_putative_441189..441339_POSITIVE 272 193 153 150 107 NC_009009:SSA_2334|3end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2336457..2336607_NEGATIVE 271 119 76 114 57 NC_009009:SSA_0118|3end_50S_ribosomal_protein_L24,_putative_113748..113898_POSITIVE 269 143 101 149 103 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 267 190 141 75 25 NC_009009:SSA_0625|3end_Phosphopantetheine_adenylyltransferase_616182..616332_POSITIVE 265 100 55 84 35 NC_009009:SSA_1597|3end_hypothetical_protein_1603267..1603417_NEGATIVE 265 125 83 149 102 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 261 190 146 141 87 NC_009009:SSA_2205|3end_Transcription_antitermination_factor_NusG,_putative_2205564..2205714_NEGATIVE 261 194 164 147 121 NC_009009:SSA_0950|3end_hypothetical_protein_957788..957938_POSITIVE